Percentage of TAR10 and ATR49 triplets in various taxa independently of the V-R size.
\r\n\tThe aim of this book will be to describe the most common forms of dermatitis putting emphasis on the pathophysiology, clinical appearance and diagnostic of each disease. We also will aim to describe the therapeutic management and new therapeutic approaches of each condition that are currently being studied and are supposed to be used in the near future.
",isbn:null,printIsbn:"979-953-307-X-X",pdfIsbn:null,doi:null,price:0,priceEur:0,priceUsd:0,slug:null,numberOfPages:0,isOpenForSubmission:!1,hash:"278931ae110500350d8b64805c70f193",bookSignature:"Dr. Eleni Papakonstantinou",publishedDate:null,coverURL:"https://cdn.intechopen.com/books/images_new/7934.jpg",keywords:"Atopic eczema, Interleukin, Topical corticosteroids, Hand eczema, Blisters, Pruritus, Irritant contact dermatitis, Allergic contact dermatitis, Discoid eczema, Sebaceous glands, Inflammatory dermatitis, Facial rash",numberOfDownloads:null,numberOfWosCitations:0,numberOfCrossrefCitations:0,numberOfDimensionsCitations:0,numberOfTotalCitations:0,isAvailableForWebshopOrdering:!0,dateEndFirstStepPublish:"February 5th 2019",dateEndSecondStepPublish:"March 19th 2019",dateEndThirdStepPublish:"May 18th 2019",dateEndFourthStepPublish:"August 6th 2019",dateEndFifthStepPublish:"October 5th 2019",remainingDaysToSecondStep:"2 years",secondStepPassed:!0,currentStepOfPublishingProcess:5,editedByType:null,kuFlag:!1,biosketch:null,coeditorOneBiosketch:null,coeditorTwoBiosketch:null,coeditorThreeBiosketch:null,coeditorFourBiosketch:null,coeditorFiveBiosketch:null,editors:[{id:"203520",title:"Dr.",name:"Eleni",middleName:null,surname:"Papakonstantinou",slug:"eleni-papakonstantinou",fullName:"Eleni Papakonstantinou",profilePictureURL:"https://mts.intechopen.com/storage/users/203520/images/system/203520.jpg",biography:"Dr. med. Eleni Papakonstantinou is a Doctor of Medicine graduate and board certified Dermatologist-Venereologist. She studied medicine at the Aristotle University of Thessaloniki, in Greece and she continued with her dermatology specialty in Germany (2012-2017) at the University of Magdeburg and Hannover Medical School, where she completed her dissertation in 2016 with research work on atopic dermatitis in children. During this time she gained wide experience in the whole dermatological field with special focus on the diagnosis and treatment of chronic inflammatory skin diseases and also the prevention and treatment of melanocytic and non-melanocytic skin tumors. Her research interests were beside atopic dermatitis and pruritus also the pathophysiology of blistering dermatoses. In addition to lectures at german and international congresses, she has published several articles in german and international journals and her work has been awarded with various prizes (poster prize of the German Dermatological Society for the project: 'Bullous pemphigoid and comorbidities' (DDG Leipzig 2016), 'Michael Hornstein Memorial Scholarship' (EADV Athens 2016), travel grant (EAACI Vienna 2016). Since 2017, she works as a specialist dermatologist in private practice in Dortmund, in Germany. Parallel she co-administrates an international dermatologic network, Wikiderm International and she writes a dermatology public guide for patients, as she is convinced that evidence-based knowledge has to be shared not only with colleagues but also with patients.",institutionString:"Private Practice, Dermatology and Venereology",position:null,outsideEditionCount:0,totalCites:0,totalAuthoredChapters:"1",totalChapterViews:"0",totalEditedBooks:"0",institution:null}],coeditorOne:null,coeditorTwo:null,coeditorThree:null,coeditorFour:null,coeditorFive:null,topics:[{id:"16",title:"Medicine",slug:"medicine"}],chapters:null,productType:{id:"1",title:"Edited Volume",chapterContentType:"chapter",authoredCaption:"Edited by"},personalPublishingAssistant:{id:"270941",firstName:"Sandra",lastName:"Maljavac",middleName:null,title:"Ms.",imageUrl:"https://mts.intechopen.com/storage/users/270941/images/7824_n.jpg",email:"sandra.m@intechopen.com",biography:"As an Author Service Manager my responsibilities include monitoring and facilitating all publishing activities for authors and editors. From chapter submission and review, to approval and revision, copyediting and design, until final publication, I work closely with authors and editors to ensure a simple and easy publishing process. I maintain constant and effective communication with authors, editors and reviewers, which allows for a level of personal support that enables contributors to fully commit and concentrate on the chapters they are writing, editing, or reviewing. I assist authors in the preparation of their full chapter submissions and track important deadlines and ensure they are met. I help to coordinate internal processes such as linguistic review, and monitor the technical aspects of the process. As an ASM I am also involved in the acquisition of editors. Whether that be identifying an exceptional author and proposing an editorship collaboration, or contacting researchers who would like the opportunity to work with IntechOpen, I establish and help manage author and editor acquisition and contact."}},relatedBooks:[{type:"book",id:"6550",title:"Cohort Studies in Health Sciences",subtitle:null,isOpenForSubmission:!1,hash:"01df5aba4fff1a84b37a2fdafa809660",slug:"cohort-studies-in-health-sciences",bookSignature:"R. Mauricio Barría",coverURL:"https://cdn.intechopen.com/books/images_new/6550.jpg",editedByType:"Edited by",editors:[{id:"88861",title:"Dr.",name:"R. Mauricio",surname:"Barría",slug:"r.-mauricio-barria",fullName:"R. 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Venkateswarlu",coverURL:"https://cdn.intechopen.com/books/images_new/371.jpg",editedByType:"Edited by",editors:[{id:"58592",title:"Dr.",name:"Arun",surname:"Shanker",slug:"arun-shanker",fullName:"Arun Shanker"}],productType:{id:"1",chapterContentType:"chapter",authoredCaption:"Edited by"}},{type:"book",id:"878",title:"Phytochemicals",subtitle:"A Global Perspective of Their Role in Nutrition and Health",isOpenForSubmission:!1,hash:"ec77671f63975ef2d16192897deb6835",slug:"phytochemicals-a-global-perspective-of-their-role-in-nutrition-and-health",bookSignature:"Venketeshwer Rao",coverURL:"https://cdn.intechopen.com/books/images_new/878.jpg",editedByType:"Edited by",editors:[{id:"82663",title:"Dr.",name:"Venketeshwer",surname:"Rao",slug:"venketeshwer-rao",fullName:"Venketeshwer Rao"}],productType:{id:"1",chapterContentType:"chapter",authoredCaption:"Edited by"}},{type:"book",id:"4816",title:"Face Recognition",subtitle:null,isOpenForSubmission:!1,hash:"146063b5359146b7718ea86bad47c8eb",slug:"face_recognition",bookSignature:"Kresimir Delac and Mislav Grgic",coverURL:"https://cdn.intechopen.com/books/images_new/4816.jpg",editedByType:"Edited by",editors:[{id:"528",title:"Dr.",name:"Kresimir",surname:"Delac",slug:"kresimir-delac",fullName:"Kresimir Delac"}],productType:{id:"1",chapterContentType:"chapter",authoredCaption:"Edited by"}}]},chapter:{item:{type:"chapter",id:"60263",title:"True Mitochondrial tRNA Punctuation and Initiation Using Overlapping Stop and Start Codons at Specific and Conserved Positions",doi:"10.5772/intechopen.75555",slug:"true-mitochondrial-trna-punctuation-and-initiation-using-overlapping-stop-and-start-codons-at-specif",body:'\nTransfer RNAs are key partners in the ribosome-translation machinery. Generally, they are composed of c.70–90 nucleotides (nts). Moreover, they are the most abundant nucleic acid species, constituting up to 10% of all cellular RNAs [1]. Therewith, the number of tRNA molecules is, e.g., about 2 × 105 in Escherichia coli and 3 × 106 in yeast cell [2]. Due to their anticodon, they read genetic information on mRNAs and deliver codon specified amino acids attached to their distal 3′-extremity for peptide bond synthesis on the ribosome. In this sense, tRNA is a key molecule which makes it possible to pass from a covalent bond between a RNA and an amino acid (fossil trace of the RNA world to the RNA/protein world transition) to peptide bonds (RNA/protein world). Genes specifying tRNAs (noted trn) are present in prokaryotic and nuclear genomes and in most of the DNAs of organelles (chloroplasts and mitochondria). Usually, tRNAs have a characteristic canonical cloverleaf secondary structure made up of the aminoacyl acceptor-stem and the D-arms (as it contains dihydrouridine), anticodon-arms, and T-arms (for the sequence TΨC where Ψ is pseudouridine), the hairpins, or “arms” consisting of a stem (helicoidal region in 3D) ending in a loop (Figure 1). The lengths of each arm, as well as the loop “diameter,” vary from the tRNA type and from species to species. Furthermore, deduced trn sequences and even sequenced mature tRNAs exhibit reduced D-arms or T-arms or even lacking at least one of them, and in the extreme situation such as in Enoplea (nematodes) mitochondrial (mt)-trn genes are totally armless [3]. However, around 90% of the mt-tRNAs fold into the canonical cloverleaf structure [4]. In all the genetic systems, the tRNAs can carry a myriad of idiosyncratic posttranscriptional chemical modifications (e.g.,
Typical cloverleaf secondary structure of a metazoan mt-ss-tRNA (left) with 3D image of an L-shaped tRNA (right). In 2D structure, the standard numbering was applied [5]. The first two nucleotides of the variable region and those of the D-loops and T-loops were represented by circles. The diagonal dashed line indicates the approximate separation between the “top half” and the “cherry-bob”/“bottom half”. Nucleotide types were given for UAG10 and AUG49 triplets, the discriminator base (which is preferentially an A), and the CCA tail at the 3′-end. Short lines connect nucleotides forming Watson-Crick pairing within stems. Coloring: acceptor-stem in purple, D-arm in red, anticodon-arm in blue with the anticodon in black, T-arm in green, and CCA tail in orange. The yellow segments represented respectively in descending order of size, the variable region (connector 2), the connector 1 and the nt 26. 3D structure reproduced with the kind permission of Prof. N.R. Voss (Roosevelt University, Ill.) https://commons.wikimedia.org/wiki/File:3d_tRNA.png.
The ribosome allows the best possible spatial arrangement of the various partners and ensures catalysis, but the adaptor molecule which acts as a link between codes of mRNA and amino acids of polypeptides is the tRNA. In order to fill this major role, tRNAs have two distinct characteristics corresponding to two different genetic codes, the anticodon and the operational codes. The latter which is mainly embodied in the acceptor-stem allows to bind covalently and with high specificity an amino acid to a tRNA, a reaction catalyzed by a specific aminoacyl-tRNA synthetase (aaRS) [6]. The operational code might have actually predated the “classic” code associated with anticodons [7]. Moreover, the tRNAs exhibit diversity in uniqueness, all of them must be similar for entering the ribosome machinery; therefore, they generally look structurally homogeneous, especially in their secondary and tertiary structures even if “non-classical” tRNAs are known [3]. Moreover, cloverleaf structure and especially the tertiary interaction network governing the L-shaped tRNA architecture imply conserved and semiconserved bps and nts. On the other side, each type of tRNA structures must interact specifically with aaRSs and posttranscriptional modification enzymes, which implies that parts of their sequences and of their structures (as the V-R size) allow to distinguish them.
\nReduced bacterial and most organelle genomes do not encode the full set of 32 tRNA species required to read all triplets of the standard genetic code according to the conventional wobble rules. Superwobbling where a single tRNA species contains modifications of the anticodon-loop, such as an hypermodified uridine at the wobble position 34 of the anticodon, reads all 4 nts at third codon position and has been suggested as a possible mechanism for how reduced tRNA sets may be functional [8]. Indeed, many metazoan mtDNAs have only a total of 22 tRNAs, apparently sufficient to recognize all codons (two tRNAs each for serine and leucine and one tRNA for each of the other 18 amino acids). However, superwobbling induces a reduced translational efficiency, which could explain why most organisms have adopted pairs of isoaccepting tRNAs over the superwobbling mechanism [9]. Moreover, e.g., in Cnidaria (sea anemones, corals, etc.) or Chaetognatha (marine invertebrates), current mtDNAs have lost several of their trn genes, and the absence of an apparently full set of mt-trn genes has also been mentioned [10]. Studies have investigated the fate of missing tRNAs and their corresponding aaRSs [11], and in many cases, the lost tRNAs are functionally replaced by imported nucleus-encoded tRNAs [10]. However, recent search strategies suggest that efficient reanalyzes detect several tRNA-like structures (TLS), which can be efficient tRNAs [12].
\nCompared to mitochondria found in other eukaryotic kingdoms, those of metazoa are massively reduced in their genetic structure [4]. Their mtDNA is a short, circular molecule that generally contains about 13 intronless, protein-coding genes, all of which are involved in aerobic respiration (also called oxidative phosphorylation) [13]. Moreover, the coding sequences of genes are usually separated by at most a few nts and long polycistronic precursor transcripts may be processed into mature mRNA and rRNA by precise cleavage of the 5′ and 3′-termini of the flanking tRNAs. This processing, which is known as the tRNA punctuation model [14], is mediated by RNase P and Z endonucleases, respectively [15]. However, this model is not always applicable, genes are not bound by trn genes or these latter may not be involved in the processing of precursor RNAs. Besides, in several taxa mt-mRNAs, rRNAs and even tRNAs may be oligoadenylated or polyadenylated [16]. This has numerous consequences with potentially dual and opposite roles: this promotes transcript stability or offers a target for initiating degradation. Overlapping genes on the same DNA strand occur throughout metazoa [17]. Therefore, the termination points of the protein-encoding genes could be difficult to infer as stop codons (generally UAA or UAG) may be absent. It is accepted that abbreviated stop codons (U or UA) are converted to UAA codons by polyadenylation after transcript cleavage, and this has been confirmed by analyzes of transcripts in some cases [18]. Sometimes, the initiation codon may also not have been detected. For several protein-encoding genes, the question of a possible overlapping with adjacent downstream or upstream trn genes is often raised [19]. Moreover, overlaps between adjacent mt-trn genes are frequent, but it is out of our topic [19, 20].
\nIncidentally, in 2004, searching for chaetognath mt-trn genes [21], it was observed that tRNAs bear nt triplets corresponding to stop or start codons at precise conserved positions, and this constitutes the original topic of this chapter.
\nMost of the research was done in two databases which include primary sequences and graphical representations of tRNA 2D structures, tRNAdb (
Visual observations of tRNA deduced 2D structures suggested that nt triplets which could correspond to stop or start codons seemed to be particularly represented at specific positions. The UAR (R for purine) triplets at position 8–10 in the standard numbering and therefore will be named UAR10, whereas the potential initiation codons whose last nt is at the position 49 will be called AUR49 (Figure 1). We chose to number the codons only according to their last nt because the nt 47 is frequently missing in the metazoan mt-tRNAs. Analyzes focus on DNA; hence, these are usually annotated TAR or ATR instead of UAR or AUR. All the tRNAs which bear one or both of these codons are named ss-tRNAs (ss for stop and start) or ss-trn for the corresponding genes. Using tRNAdb and mitotRNAdb databases, these triplets’ frequencies were investigated in different taxa including nuclear and organelle genomes for eukaryotes (Table 1). Excluding taxa for which the number of trn genes is too low for statistical analysis, TAR10 always occurs at high frequencies, whether in prokaryotic, nuclear, or organelle genomes. Values range from 41.1% for fungi to 81.6% for pseudocoelomates. In all the taxa and all tRNA species combined, the percentage of TAG10 triplets is always significantly higher than those of TAA10. The differences are very important in prokaryotic and nuclear genomes, since the percentage of TAA10 is always less than 1, while that of TAG10 is at least 40%. Within the organelle genomes, the difference is smaller but can vary by a factor of 2.5–22.
\nPercentage of TAR10 and ATR49 triplets in various taxa independently of the V-R size.
Metazoan taxa are in italics. Abbreviation: Nb, number of trn genes. TAR + ATR for % of trn genes bearing the two types of triplet. * Mitochondria.
As the TAR10 triplet (principally TAG) is present in at least 40% of the trn genes for all taxa and genomic systems combined, it could have been present in trn genes of the Last Unicellular Common Ancestor (LUCA), which presumably lived some 3.5–3.8 billion years ago [24]. It is probably an ancestral character which was present in proto-trn sequences. As the percentage of TAA10 strongly increases in trn genes of organelles, one can ask whether this character was not already present in their bacterial ancestor. It is now assumed that despite their diversity, all mitochondria derive from an endosymbiotic α-proteobacterium which has been integrated into a host cell related to Asgard Archaea approximately 1.5–2 billion years ago [25]. However, the earliest fossils possessing features typical of fungi date to 2.4 billion years ago [26]. Moreover, the eukaryotic cells would be chimeras constituted of an archaebacterium and one or more Eubacteria [27]. In addition, all current models for the origin of eukaryotes suggest that the eukaryotic common ancestor had mitochondria. Therefore, as the level of TAA10 is very low in trn genes of α-proteobacteria, it could therefore be a derived trait that may be related to the increase in AT% in mtDNA and/or recognition constraints by mt-aaRSs and modification enzymes. Similarly, it is generally accepted that all chloroplasts and their derivatives are derived from a single cyanobacterial ancestor [28], and in current cyanobacteria, the respective percentage of TAG10 and TAA10 triplets are 62.5 and 3.6, respectively. The increase in the percentage of TAA10 characterizes organelles.
\nIn all the taxa for all tRNA species combined, the ATR49 triplets are always present in smaller numbers than TAR10. Moreover, their numbers are negligible except in organelle genomes, mainly mitochondria. The low level of ATR49 triplets in Pseudocoelomata is due to the frequent absence of T-arm in their mt-tRNAs. In mitochondria, in some taxa, the frequency of ATG49 is higher than of ATA49, while in others, the opposite occurs. The variability is not surprising, given approximately 2 billion years of mtDNA evolution [29]. It must be noted that the nt G is overrepresented at the 5′-end of the 5′-acceptor- and D-stems, quite often at the 5′-end of the T-stem but rarely at the equivalent position of the anticodon-stem. In taxa where the percentage of ATA49 is higher than those of ATG49, G is most often not the nt majority at the 5′-end of the T-stem. Moreover, differences between the relative percentages of ATG49 and ATA49 could be due, at least in part, to variations in the AT% in organelle DNAs. The percentage of ATR49 is very low in α-proteobacteria and weaker in this last taxon compared to all Proteobacteria or Eubacteria, and it is also very weak in cyanobacteria, and so the significant rate of ATR49 triplets would seem to be a derived condition of organelle DNAs rather than a conserved primitive state lost in current prokaryotes. This trait probably appeared during the transition from endosymbiotic bacterium to permanent organelle that implied massive evolutionary changes including genome reduction, endosymbiotic and lateral gene transfers, and emergence of new genes and the retargeting of proteins [25]. The timing of the mt-endosymbiosis and of the proto-mitochondria to mitochondria transition is uncertain, but one might trace the origin of the ATR49 triplets between at least the first eukaryotic common ancestor (FECA) and the last eukaryotic common ancestor (LECA). A second event occurred, at least, in the mitochondria of the ancestors of Opisthokonta (i.e., Metazoa and Fungi), which would have led to a net increase in numbers of ATR49. ATR49 means that the last two nts of the V-R are AT. It turns out that this mainly concerns the mt-trn genes, whose V-R has only 4 nts, which are almost exclusively present in the Fungi/Metazoa clade.
\nThere are large differences in the frequencies of the TAR10 and ATR49 triplets depending on the species of trn genes (Table 2) and taxa (data not shown), and the selective variations in some taxa suggest that the increase in frequency for some types of triplets would be much more recent than mentioned above; in addition, decreases are also observed. There are, however, very conservative trends such as the presence of ATR49 triplets in genes specifying tRNA-Ala. Analyzes on mt-trn genes of Deuterostomia for which a great number of sequences for each type are available (from 1085 to 1382) show that only the tRNA-Cys and tRNA-Glu species have intermediate TAR10 percentages (Table 2). In all other tRNA species, the values are extreme, 9 and 10 tRNA species with values ranging from 0.4 to 9.8% or greater than 82.4%, respectively (Table 2). In contrast, half of the tRNA species have low ATR49 percentages (≤ to 10.8), and for only four types percentages are ≥77.8. There would also be a tendency suggesting that tRNA species with very high or very low percentages of TAR10 most often have low ATR49 (the tRNA species with the 7 highest and the 8 lowest TAR10 percentages exhibit 10 out of 11 of the lower percentages for ATR49).
\nPercentages of TAR10 and ATR49 by mt-trn gene species in Deuterostomia.
The trn genes are represented by three-letter codes of amino acids. The tRNAs are ordered by decreasing TAR10 percentages. The percentage values ≥ to 77.8, between 17.0 to 56.5 and ≤ to 10.8 are underlined in yellow, blue, and green, respectively.
In order to investigate possible implications of TAR10 and ATR49 triplets in translation, analyzes were performed in GenBank using as keywords: “TAA stop codon is completed by the addition of 3\' A residues to the mRNA”, “alternative start codon” or “start codon not determined” and mitochondrion (or mitochondrial DNA) complete genome. Then, it was researched whether upstream (for start codon) or downstream (for stop codon) of the protein-encoding gene was a trn gene. When a trn gene was found, TAR10 or ATR49 triplets were searched, and the same investigation was then made in conspecific mt-genomes. Using this strategy, these triplets have been only found in metazoan mtDNAs, in which overlapping mt-trn genes have long been known.
\nAn example of putative uses of TAR10 triplets as stop codons is presented in Table 3 for a subclass of parasitic flatworms (Platyhelminthes : Eucestoda). Their mt-genetic code has only UAG and UAA as stop codons, avoiding possible bias due to use of other types of termination codons. In 51 among 66 complete mt-genomes, the first in-frame potential stop codon of the cox1 gene is in the downstream trnT gene (24 cases with TAG10 suggesting a 10 nt overlap between cox1 and trnT genes). Authors considering that this long overlap would be impossible have proposed a number of alternative options favoring overlap avoidance (e.g., [30]). (1) cox1 might use an earlier atypical stop codon. (2) The 3′-end of the cox1 mRNA could have an abbreviated stop codon (U or UA instead of UAG10) upstream the trnT gene which is completed by polyadenylation. (3) If in the potential long transcript, the cleavage would occur just after G10, the cox1 mRNA would end with the complete UAG10 as stop codon and the first 10 nts of the trnT gene would be added by an unknown editing process. (4) The trnT gene would be shorter in its 5′-end lacking the nts from 1 to 8 or 9, e.g., this has been proposed for the mt-trnT of Cyclophyllidea (Echinococcus granulosus, Hymenolepis diminuta, and Taenia crassiceps). If the full stop codon is used, then there is only a single nt (G10) overlap between cox1 and trnT. Moreover, if the end of the cox1 gene is at the level of T9, the stop codon would complete by polyadenylation; whereas if the protein gene has a complete stop codon, the nt G10 would be added by edition. In the alternative structures, the D-arm is absent, whereas it is typical for this tRNA in digeneans (a class of Platyhelminthes) and in other phyla. However, mt-trnT genes issuing from Cyclophyllidea for which the first potential stop codon is at different positions (upstream or downstream the trnT gene, or in this last gene but upstream or downstream TAG10 or at this last position) exhibit similar secondary structures, including a D-arm. In addition, the high level of nt conservation in the 5′-end of the trnT genes of cestoda (i.e., G1, G2, T7, T8, A9, G10, T11, T12 and A14) suggests strongly that the 5′-acceptor-stem and the D-stem are under positive selection. All this implies that the hypothesis of D-armless tRNAs is, according to us, improbable.
\nPosition of the first complete in-frame stop codon of the cox1 gene versus the following trnT gene in Cestoda (Platyhelminthes).
Species names are followed by their accession number(s). *: sequences for which the authors of these latter considered that there was an abbreviated stop codon and this latter was upstream the trn sequence. Symbols: X TAR10 was the first in-frame putative stop codon; §, $, & and μ, the putative stop codon was upstream the trn gene (tg), in the tg but upstream or downstream TAR10 or nts 8–10, downstream the tg, respectively. Abbreviations: P. c., Pseudanoplocephala crawfordi; Proteoce., Proteocephalidea; stop cod., putative stop codon according to the authors of the sequences.
Concerning the putative ATR49 start codon, in GenBank, the number of complete mt-genomes found using the keywords previously mentioned was relatively low; moreover, in some cases, the upstream gene encoded a protein, specified a rRNA and/or there was only one mention for a given taxon. A significant example within Deuterostomia (frogs) is presented in Table 4. In the superfamily Hyloidea, the ATA49 triplet is frequently the first potential complete start codon at the level of the gene pair encoding and specifying NAD1 and tRNA-Leu2, respectively. In two families (Bufonidae, Hylidae), for all the sequences (16 belonging to 14 different species), the first ATR triplet found in frame in the ORF of the nd1 gene is ATA49. For four sequences belonging to three other frog families, the ATR49 triplet is missing from the trnL2gene; moreover, an ATA triplet is integrally present in the V-R of the trnL2 gene of Heleophryne regis, but it is not in frame with the following gene. For these last four cases, the authors of the sequences proposed alternative start codons. This seems obligatory, but this has not been experimentally verified. For several authors who have sequenced parts of mtDNAs of Hylidae, the nd1 gene would start at ATA49 for about 140 sequences (e.g., Roelants and Bossuyt [31]).
\nPosition of the first putative start codon of the nad1 gene versus the upstream gene specifying tRNA-Leu2 in Hyloidea, a superfamily of frogs.
X: ATA49 as the first putative in-frame start codon. *: “start codon not determined” according to the authors of the sequences. Alternative start codons are given by the authors of the sequences. §: alternative start codon in the trn gene. Abbreviations: Dendro, Dendrobatidae; Cerato., Ceratophryidae; Heleo., Heleophrynidae.
In the two studied taxa, Blast analyzes of the NCBI ESTs and SRA (SequenceRead Archive) databases have been performed, but no result supports the proposed hypotheses: transcripts starting at an ATR49 or terminating at a TAR10 were not found. However, for each taxon, few mt-transcripts occur, and fully matured transcripts are even rarer.
\nForemost, biases in the search strategy cannot be excluded, but the important point to note is that mt-genomes of animals, fungi, protists, and plants differ drastically in all major characteristics including gene content and large size variation. Generally, metazoans have ultra-compact mtDNAs (from c.10,000 to c.50,000 bp); usually, nonfunctional sequences are rapidly eliminated, and there are short intergenic regions and frequent overlaps [13]. However, nonbilaterian mt-genomes have higher variation in size, gene content, shape, and genetic code [32]. The mtDNA size range is from 30,000 to 90,000 bp in fungi, and generally, intergenic regions are relatively long. A broader range of mtDNA size is found in higher plants (from 0.2 × 106 to about 11.3 × 106 bp [33]), and the largest known mt-genome in this lineage exceeds sizes of reduced bacterial and nuclear genomes [34]. The increased sizes of plant mtDNAs are mostly due to noncoding DNA sequences, large inserted nuclear regions, and many introns and not to a large increase in gene numbers. The nuclear-derived sequences amount to up nearly half of their size as in melon [35], and so presence of mt-trn genes with nuclear origin cannot be excluded. Although not directly correlated, intergenic distances are generally much higher in larger genomes, reducing the number of overlaps. In addition, the situation of plant mt-tRNAs is very complex. Indeed, they contain few “native” tRNAs expressed from true mt-trn genes. They possess “chloroplast-like” trn genes inserted into the mtDNA. They compensate the loss of mt-trn genes by importing several nucleus-encoded tRNAs [36]. In addition, most often in plants, the standard code applies to the reading of organelle genomes, even if ATA is frequently used as start codon. Metazoan mt-genomes are generally small, very constrained and exhibit several gene overlaps between trn and protein-encoding genes or between trn genes. Their tRNAs have sequence and structural peculiarities and tend to shortening [19]. Our exploration is not exhaustive, but this might explain the presence of putative stop or start codons specifically within mt-ss-trn genes of this taxon.
\nOne may wonder why the hypotheses concerning the TAR10 and ATR49 triplets were not proposed before? At least, the presence of these characteristic triplets could have been observed by some authors but considered as having no connection with the translation of neighboring protein genes. Among the first sequenced and the most studied were mt-genomes of Homo sapiens (J01415) and Mus musculus (J01420). In these latter, no putative start or stop codon occurs at these positions within trn sequences adjacent to protein genes (data not shown).
\nIn the living world, many nucleic sequences with secondary structures playing a physiological role involving stop and/or start codons have been discovered. Some representative examples are briefly presented here. (1) The tropism switching of the bacteriophage BPP-1 is mediated by a phage-encoded diversity-generating retroelement, which introduces nt substitutions in a gene that specifies a host cell-binding protein (Mtd) [37]. The nt substitutions are introduced in a variable repeat located at the 3′-end of this gene. Two nts after this region, the UAG stop codon is present, and its last nt is situated at the 5′ beginning of the 5′-stem of a hairpin. Both the UAG codon and hairpin are required for phage tropism switching. (2) Programmed translational bypassing is a process, whereby ribosomes “ignore” a substantial interval of mRNA sequence. In a bacteriophage T4 gene, bypassing requires translational blockage at a “takeoff codon” immediately upstream of the UAG stop codon, and both codons are in the 5′-stem of a hairpin; moreover, this region is mobile [38]. (3) The operon flgFG of the bacterium Campylobacter jejuni can encode two genes (flgF and flgG). Its expression in E. coli produces a fusion protein probably due to ribosomal frameshifting (translational hopping) [39]. The putative hop region contains, among others, a hairpin beginning by the last nt of the UAA stop codon of the first mRNA. The AUG start codon of the second gene is in the loop of the following hairpin. (4) In Eubacteria, riboswitches are regulatory segments of DNA or mRNA that can bind a small molecule (the effector), which repress or activate their cognate genes at transcriptional and/or translational levels. In the riboflavin and cob operons, conformational changes can form a stem loop which sequesters the translational start site, consisting of the Shine-Dalgarno (SD) sequence plus start codon thus preventing gene translation [40]. (5) Bacterial transfer-messenger RNAs (tmRNAs) have dual TLS and mRNA-like properties. They rescue stalled ribosomes on mRNAs lacking proper translational stop signal; the tRNA-like structure acts first as an alanine-tRNA, and then the short mRNA reading frame is translated and the product is released [41]. This trans-translation terminates at the stop codon terminating the tmRNA reading frame. This stop can be in a little loop or totally or partially integrated in the stem of a hairpin-like structure. In eukaryotes, structurally reduced tmRNAs (no mRNA-like domain) rarely occur in chloroplasts [42] and in mt-genomes (in Jakobids, presumably close to the most ancient living eukaryotes with bacterial-like mt-genome) [41]. Moreover, tmRNA TLSs function even without any canonical initiation factors. These examples show that start or stop codons located in hairpin may have various functions, as we suggest for TAR10 and ATR49.
\nAncient tRNAs probably had diverse functions in replication and proto-metabolism before protein translation [43] and modern tRNAs have also various functions in all the living organisms [1]. These functions include cell wall synthesis, protein N-terminal modification, nutritional stress management, porphyrin biosynthesis (heme and chlorophyll), lipid remodeling, and initiation of retrovirus reverse transcription. Accumulating experimental evidence suggests also that they have important regulatory roles in translation, viral infections, and tumor development (reviewed in [44]). Mt-tRNAs interfere with a cytochrome c-mediated apoptotic pathway and promote cell survival [45] and function as replication origins [46]. Moreover, nuclear-tRNA abundance and modifications are dynamically regulated, and tRNAs and their tRNA-derived RNA fragments (tRFs) are centrally involved in stress signaling and adaptive translation [47, 48]. This suggests that the choice of cleavage sites of mRNA transcripts with or not part of the neighboring ss-tRNA could be dynamic and also respond to environmental changes. Some of the noncanonical translation functions of tRNAs can also be driven or enhanced by their ability to adopt different complex three-dimensional structures, and these conformational changes can be linked to functional states [49]. Moreover, the tRNA multifunctionality has also been considered to be, at least in part, random due to the high amount of tRNA species within the cell [1]. In addition, the mt-trn genes represent natural pause sites for replication forks and could also prone double-strand breaks [50], and their role, as “punctuation signals,” for processing of mtDNA polycistronic transcripts has already been mentioned.
\nEnormous numbers of tRFs in all domains of life were found in the last decade [44]. In the plant Arabidopsis thaliana, nucleus-, plastid-, and mt-encoded tRNAs can produce tRFs [36]. The tRFs are not randomly degraded tRNAs. Experiments showed several functions including regulation of tumor development and viral infections [44]. Degradations resulting from cleavages at TAR10 and ATR49 triplets could produce a conformation exhibiting two loops linked by a forked-stem structure, roughly resembling a pair of cherries, so called “cherry-bob” (Figure 2). Our hypothesis predicts this structure which however has never been observed [51].
\n2D “cherry-bob”/“bottom half” structure. AUG/UAG triplets are discussed in text. Colors as Figure 1.
Metazoan mt-genomes are believed optimized for rapid replication and transcription. Potentially, TAG10 and ATR49 make transcription/translation more complex but perhaps more efficient. Examples in the Section 3.2 (i.e., Eucestoda) suggest mt-overlaps appeared 100s millions of years (MY) ago, enabling co-evolution between protein-encoding genes and those specifying tRNA.
\nOverlaps involve numerous constraints for genes including sequence bias. Constraints are probably less stringent for trn genes, which can evolve rapidly because relatively standard secondary structure coupled with a specific anticodon might suffice for tRNA function [52]. Incomplete cloverleaf structures may also be repaired post-transcriptionally [53].
\nAlternative processing might be possible for the production of either a supposed complete mRNA or a complete tRNA. In the first case, the synthesis of new complete mRNAs could be promoted by high mitosolic tRNA numbers. Moreover, amino acid starvation can regulate mt-tRNA levels [54]. However, if mt-tRNAs already present are not destroyed, translation would not immediately stop because mt-tRNA half-life which is lower than that of their cytosolic counterparts can nevertheless exceed 10 h [54]. Moreover, aberrant mt-tRNAs can be corrected by RNA editing during or after transcription, and this process appeared independently several times in a wide variety of eukaryotes [5]. As an extreme example, due to large overlaps between trn genes, up to 34 nts are added post-transcriptionally during the editing process to the mt-tRNA sequences encoded in an onychophora species, rebuilding the acceptor-stem, the T-arm, and in some extreme cases, the V-R and even a part of the anticodon-stem [55]. In that species, several edition types must be combined, including template-dependent editing [55]. This last example suggests that complete tRNA could be restored after a cleavage just upstream of ATR49. However, edition of parts of the 5′-end of tRNAs seems more problematic. Besides, mRNAs with upstream or downstream ss-tRNA can form a partially double strand region with a homologous ss-tRNA at the level of the acceptor-stem. This might induce mRNA degradation via antisense mechanisms. In bacteria, uncharged tRNAs cause antisense RNA inhibition [56], and small interfering cytosolic tRNA-derived RNAs exist [57]. Modifications (methylation, edition, etc.) of incomplete tRNAs generated after cleavages of polycistronic transcripts at TAR10 or ATR49 triplets would indicate regulatory functions.
\nPutative use of TAR10 or ATR49 triplets affects protein length. When in frame, this could generate a protein at least 3 or 9 amino acids longer, respectively. Extension length depends on positions of upstream stop codons completed by polyadenylation and/or on downstream (alternative) initiator codons. Not only complete proteins may be functional. Depending on cleavage positions in polycistronic transcripts, consequences may be neutral, disadvantageous, or favorable in specific contexts. In yeast, extended proteins can increase fitness under stress conditions [58]. In addition, in bacteria and in organelles, alternative initiation codons decrease efficiency [5], and it must be noted that ATR49 triplets are “canonical” start codons.
\nIn other conditions, incomplete mRNAs could be favored. Mitosolic mRNA accumulations can be due to lack of translation because of tRNA paucity. Thus, high mRNA levels might indirectly promote cleavage of entire tRNA transcripts while reducing the synthesis of new functional mRNAs and favoring translation of those which are already present into proteins. Presence/absence of hairpins involving stop or start codons might regulate translation. This regulation could involve proteins that stabilize the hairpins or posttranscriptional modifications. Moreover, translational products of “incomplete” mRNAs might have housekeeping functions.
\nRegulation of alternative processing producing either complete tRNAs or complete mRNAs requires elucidation. Factors, probably proteins, need characterization. Note that metazoan mt-atp8 and atp6 genes overlap (mainly by 10 bp in vertebrates) and are transcribed as joint bicistronic transcript [59]. This proven overlap is inherent to mt-metabolism. Hence, similar overlaps assumed for TAR10 triplets are plausible.
\nOverlap conservation might reflect the need to produce bicistronic transcripts (5′-tRNA-mRNA-3′ or 5′-mRNA-tRNA-3′) or functional constraints at protein level (i.e., preserving specific amino acid patterns upstream or downstream the ORF). When overlap regions have conserved, amino acid sequences at the protein N- or C-terminal functional constraints at protein level for overlaps are probable [19]. In viruses, mutation rates are low in DNA regions coding for multiple protein products in separate reading frames (called overprinted genes) because point mutations compatible with functional products from all frames are rare. In these regions, the frame is said “close off.” Partial overlap between protein-encoding genes and ss-trn genes would present similar situations explaining greater conservation of extremities of protein and tRNA sequences when the corresponding genes overlap. This lock almost only concerns the ss-tRNA’s “top half,” limiting changes in the region interacting with many processing enzymes. The ss-trn genes could also regulate translation upstream, bicistronic mRNA/ss-tRNA transcripts could be more stable, and likewise, ss-trn genes could also play roles in replication and transcription.
\nMethylation is much rarer in mt- than nuclear-DNA [60]. However, these might occur at trn genes (particularly around TAR10 and ATR49) and might have deleterious consequences especially because differential mtDNA methylations are linked to aging and diseases (including diabetes and cancers) [60]. Methylation of nts of UAR10 and AUR49 is known as those of A9 and G10 which can be important for correct tRNA foldings [61]. We are unaware whether posttranscriptional modifications occur on bicistronic mt-transcripts containing complete or partial tRNAs. This would be worth investigating including possible consequences on maturation and translation.
\nSeveral codon-amino acid reassignments are known, mainly from mitochondria [62, 63]. In 11 different mt-genetic codes, UGA stops code for tryptophan and AUA codes for methionine instead of isoleucine in 8 and 5 mt-genetic codes, respectively [63]. Both reassignments avoid potential errors along traditional wobble rules. Reassigning UGA-stop to UGA-Trp fits the “capture” hypothesis, and UGA codons mutate first to synonymous UAA codon in AT-rich mt-genomes. Then, UGA reappears occasionally by mutations, free for “capture” by an amino acid, like Trp [64]. AUA is frequently used as alternative initiation codon. Its reassignment to internal sense Met codon could also have evolved in AT-rich genomes. Moreover, the standard genetic code assigns six codons to arginine, whereas two would fit arginine’s relatively low frequency in current proteins [65]. In 8 out of 11 mt-codes, different strategies reduce Arg codons to four, AGR reassignments to other amino acids (in six genetic codes), lack of two Arg codons (CGA and CGC yeast mt-code), and AGR as terminators in vertebrates. These AGR codons were believed mt-stop codons since early vertebrate evolution [66]. However, at least in humans, AGRs are not recognized terminators [67], suggesting that AGRs have no assignment. Hence, the vertebrate mt-genetic code could be the most optimized known genetic code (that of yeast was not retained because four Leu codons were reassigned to Thr). Characteristics of the nt triplets at the position 8–10 and ending at position 49 should be analyzed for each mt-genetic code.
\nVarious models could explain tRNA origins (see reviews [68, 69, 70]). The modern tRNA cloverleaf structure might result from direct duplication of primordial RNA hairpins (e.g., [68]). However, studies lend strong support to the “two halves” hypothesis [43], in which tRNAs consist of two coaxially stacked helices with presumed independent structural and functional domains. These correspond to the “top half” containing the acceptor-stem and the T-arm and the “bottom half” with the D-arm and anticodon-arm (Figure 1). The 2D representation of the latter corresponds to the “cherry-bob” structure (Figure 2). The “top half” of modern tRNA embeds the “operational code” in the identity elements of the acceptor-stem that interacts with the catalytic domain of specific aaRSs and is recognized by RNases P and Z and the CCA-adding enzyme (therefore mainly RNA end processing reactions) [70, 71]. This domain also interacts with translation elongation factor Tu and one rRNA subunit [71]. The importance of this domain in most macromolecular interactions involving tRNAs (including in vitro even when it is detached from the “bottom half”) suggests that these half’s specificities were established before the tRNA’s “bottom half,” presumably incorporated later [72]. Growing evidence for tRNA elements involved in both RNA and DNA replication with the 3′-end playing a determinant role has led to the idea that the “top half” initially evolved for replication in the RNA world before the advent of protein synthesis [73]. The supposed evolutionarily recent tRNA “bottom half” provides genetic code specificity. This suggests late implementation of the standard genetic code and late appearance of interactions between the tRNA “bottom half” and ribosomes [74]. Whether the “bottom half” derived from a loop or extra loop belonging to the “top half” or was an independent structural and functional domain that was subsequently incorporated into the “top half” remains unresolved [71]. Some authors suggest independent evolutionary origins [71, 72].
\nThe study of ss-tRNAs suggests a model partially explaining canonical tRNA origins (Figure 3). The DNA region specifying the “bottom half” would be integrated in a sequence that can specify the “top half” but at the junction between the parts corresponding to the 3′-end of the 5′-acceptor stem and the 5′-end of the 5′-T-stem.
\nProposed model for the origin of genes specifying tRNAs with canonical cloverleaf structure. It can be summarized by insertion (follow the arrow) of the region specifying the “bottom half” into those specifying the “top half”. Here, the entire TAG10 triplet presumably belonged to the “bottom half” region as well as the first 2 nts of ATG49. Colors as Figure 1.
On the other hand, the “bottom half”/“cherry bob” structure could also be integrated at RNA level, either in the RNA world by intermolecular RNA-RNA recombination or template switches or later with retrotranscription events. Fujishima and Kanai [70] also proposed an equivalent model where a long hairpin corresponding to about the “top half” region merged with a viral RNA element corresponding to the “bottom half” to give the TLS found in modern viral genomes (who however possessed a pseudoknotted acceptor-stem). Besides, rare pre-tRNA molecules from the three domains of life exhibit an intron. The intron’s origin is debated. The “introns-early” scenario assumes most of them were lost during evolution, and the opposite scenario theorizes that introns were inserted into some trn genes after their emergence [75]. To date, our hypothesis would rather favor the second scenario, even though it could be considered that the “cherry bob” structure could be an ancestral intron becoming unspliceable.
\nIn tRNAs, the two first nts of both UAR10 and AUR49 belong to connector 1 and 2, respectively. They are thus at the junction between the top and bottom halves and are very close physically in the 3D structure (Figure 1). The belonging of some of the nts of the TAR10 and ATR49 triplets to either of the two parts is not discussed here because the theoretical model of Figure 3 is applicable independently of “bottom half” extremities. However, as the V-R is important for aminoacylation [76], ATR49 triplets could rather integrally belong to the “top half.” The tRNA L-shape is stabilized by various tertiary interactions of the V-R with the D-arm and between the D- and T-loops. Nucleotides of the connectors form contacts with the D-arm, and in some tRNAs, the G10 can establish potential tertiary interactions with a nt of the V-R upstream the putative start codon [77]. At least in cytosolic tRNAs, frequently U8 and sometimes U48 form noncanonical pairs. Moreover, generally, base pair 15–48 is more conserved in mt-tRNAs than 8–14, and this is probably due to the fundamental role played by the first in maintaining the tRNA L-shape [5]. UAR10 and AUR49 had to play first only a role in the L-shaped tertiary structure of tRNAs, and their implication as codons, if it exists, would be only a derived character. It was hypothesized that DNA punctuation evolved from 2D structures signaling polymerization initiation, termination, and/or processing to linear sequence motifs, which further evolved to translational signals [78]. In ss-tRNA, UAR10 triplet probably already plays a structural role in proto-tRNAs, whereas AUR49 would have appeared only during the evolution of organelle tRNAs and was related to L-shaped tertiary structures of organelle tRNAs and due to severe genome reduction and extreme base compositions. The opposite hypothesis would imply that the AUR49 triplet would have been a plesiomorphic character counter-selected in large genomes but kept in certain bacterial genomes up to mt-ancestors.
\nSome authors have hypothesized that tRNAs may be the precursors of mRNAs, rRNAs (and therefore proto-ribosomes), and also of the first genomes. Several suggested similar origins for tRNA and rRNA [79]. Analyzes of sequences and secondary structures of ribosome suggested that the ribosomal peptidyl transferase center (PTC) which forms peptide bonds between adjacent amino acids originates from fused proto-tRNAs [80]. Strikingly, the ribosome is a ribozyme, since only RNA catalyzes peptide bond formation [81]. Otherwise, current eubacterial rRNAs themselves could encode several tRNAs [82] and chaetognath 16S rRNA genes appear as tRNA nurseries [12] (or the opposite). Eubacterial 5S rRNAs contain TLSs similar to alanine and arginine tRNAs [82], exhibiting tRNA-like 2D structures [83]. Some suggest that rRNAs are fused tRNA molecules [80].
\nMolecular biology dogmatically assumes that “tRNA genes are of course entirely noncoding” [84]. But in 1981, Eigen and Winkler-Oswatitsch suggested that in the RNA world to the RNA/protein world transition, ancestral tRNAs were mRNAs [85]. Assuming that the first mRNAs had been recruited from proto-tRNAs, it follows that TLSs were inside viral and cellular mRNAs [86]. Self-recognition between tRNA-like mRNAs and canonical cloverleaf tRNAs could stabilize these molecules and produce proto-proteins [87]. The first proteins potentially emerged from junctions of ancestral tRNAs, and among the modern proteins, the only polymerase which matched with tRNAs translated like a mRNA was the RNA-dependent RNA polymerase [87]. Otherwise, eubacterial rRNAs could also encode several active sites of key proteins involved in the translation machinery [82]. Then, analyzes of sequences and secondary structures of ribosomes suggested that these derived from tRNAs also functioned as a protogenome [82]. The very parsimonious syncretic model “tRNA core hypothesis” assumes that some proto-tRNAs were classical tRNAs and also functioned as rRNAs and mRNAs, a self-recognition between these molecules allowed to obtain proto-proteins [88].
\nAssuming that the ATR49 triplets are a primitive character lost during the first genome expansions and that they could already act as an initiation codon seems too speculative, but RNA structures having characteristics of ss-tRNAs could have accumulated many advantages in the RNA/protein world. Structures with both start and stop codons partially in a stem-loop (as ss-tRNA), constituting basic signals for translation, could be a missing link of the RNA world hypothesis. Furthermore, in these proto-tRNAs, 3D structures could act as initiation and termination signals before the emergence of standard codons. Moreover, mRNAs in the form of ss-tRNA or a combination of several of these molecules would have been relatively stable. The cloverleaf structure could facilitate its entry into the PTC, and then interactions with other factors could allow a short region to be in linear form and thus could be read. Upstream and downstream of the linear region, the arrangement in hairpins protected the proto-mRNA from degradation during its reading, and as soon as a long enough region was read, it could take again its original 3D structure. Otherwise, circular proto-mRNAs derived from ss-tRNA-like molecules could not be excluded, although the hypothesis of circular tRNA-like ancestor (“proto-tRNA”) was first proposed by Ohnishi in 1990 [89]. Furthermore, nuclear-encoded mt-tRNAs of Kinetoplastid protists are imported into the mitochondrion, and circularized mature tRNA molecules are produced probably by mt-endogenous RNA ligase activity (in vivo or during mt-isolation) [90]. Moreover, in red and green algae and possibly in one Archaea, the maturation of permuted trn genes, in which the sequences encoding the 5′-half and 3′-half of the specific tRNA are separated and inverted on the genome, needs the formation of a characteristic circular RNA intermediate which after cleavage at the acceptor-stem generates the typical cloverleaf structure with functional termini [91]. If in a ss-tRNA with a T-loop of 7 nts, the nt72 is ligated to the nt1; this creates a small ORF starting with a start codon (AUR49), which potentially codes for a peptide of 12 amino acids if UAR10 is used as stop codon. However, the circularization could be done elsewhere than at levels of nts 72 and 1. Thus, UAR10 would not be in frame, and therefore, this could allow the synthesis of smaller or longer peptides. To date, the formation of this type of structure and its translation remains hypothetical; however, experimental data shown that circular RNAs can be translated in prokaryotic and eukaryotic systems in the absence of any particular element for internal ribosome entry as SD sequence, poly-A tail, or cap structure [92]. Therefore, the evolutionary advantage of a circular proto-mRNA is also posited to be the simplicity of its replication mechanism and not be able to be degraded by the extremities that do not have one.
\nBesides, the fusion of tRNA-like mRNA and a classical tRNA could be at the origin of the ancestors of tmRNAs, and it can be mentioned just for guidance that the size of the tag peptide encoded by bacteria is of the same order of magnitude as those corresponding to putative translation of a ss-tRNA from the ATR49 triplet. Moreover, evolution of self-charging proto-tRNAs may also be selected [93], it has even been proposed that the activity of the juxtaposed 2′/3′-OHs of the tRNA A76 ribose qualifies tRNA as a ribozyme [94] and some RNAs (the early tRNA adaptor) must have had the ability to undergo 3′-aminoacylation. It has also been previously shown that many hairpin-structured RNAs bear ribozyme activity. These catalyze self-cleavage and ligation reactions [95]. In addition, it remains possible that circular ss-tRNAs with amino acid-anchored structure could be at the origins of tmRNAs. Indeed, two-piece bacterial tmRNAs (e.g., in α-proteobacteria) are encoded by a circularly permuted gene sequence implying that pre-tmRNA is processed, and that the two pieces are held together by noncovalent interactions. Moreover, in line with an α-proteobacterial origin of mitochondria, probable mt-encoded circular permuted tmRNA genes have been found in the oomycete (water mold) Phytophthora sojae and in the jakobid Reclinomonas americana [96]. A proto-trnA gene could be at the origin of modern tmRNAs [41]. Metazoan mt-trnA genes combine the highest levels of TAR10 and ATR49 triplets (>95% for each), but in the prokaryotic world, if the rate of TAG10 is always higher than 91%, only one ATR49 occurs in Eubacteria and none in Archaea.
\nStudies strongly suggest that the tRNA cloverleaf structure unfolded prior to the appearance of a fully functional ribosomal core, making it one of the most ancient RNAs of the RNA world [70, 97] or even the oldest [98]. Though the “RNA-world” hypothesis is well accepted, the successive events leading to the emergence of different partners playing a role in translation and the involvement of tRNAs in this evolution are highly controversial coveted field [99]. However, some hypotheses as the “tRNA core” [88] strongly suggest that tRNAs would be at the origin of the primitive genetic material and gave rise to mRNA and rRNA, as well as the conformational structure of the first proto-ribozymes. The base module being a pleiofunctional RNA that can adopt the cloverleaf structure is found today in various sequences without direct link with translation. One may conclude that “one should not change a winning secondary structure.” In a precellular context, a molecule with ss-tRNA characteristics (small ORF associated with cloverleaf structure) would be advantageous. Putatively, ss-tRNA-like molecules cumulating both tRNA and mRNA functions would have been the first molecules on Earth to support nonrandom protein synthesis.
\nThe antiquity of ss-tRNAs can be discussed, and it is very likely that the TAR10 (and especially TAG) triplets played very early a critical role in the tertiary folding of some tRNAs. Their implication in translation termination would be an exaptation where firstly, they were part of a structural signal. Origin of ATR49 triplets is less clear perhaps tracing to the first endosymbiosis. Hence it would be apomorphic (derived character). Analyzes by taxa and tRNA species suggest a nonhomogeneous evolution. At the beginning of the RNA/protein world, it has quickly become essential to start peptide synthesis at particular codons and one cannot exclude that ATR49 was an ancestral state which would have not been retained as intergenic spaces increased. Analyzes of known tRNAs of α-proteobacteria and cyanobacteria could suggest that in organelles, ATR49 triplets would have been selected with genome reduction. Organelle genomes may be under increased pressure for size reduction with resulting overlaps (see, [100]). However, several features strongly suggest that overlapping genes are not a direct mechanism to substantially reduce genome size. Gene overlaps allow mtDNA genome compaction while avoiding the loss of tRNA genes [53]. Nevertheless, overlaps may allow a more efficient control in the regulation of gene expression, the regulatory pathways are simplified, and the number of proteins (and genes) required decreases [100]. Among others, short antiparallel overlaps may be involved in antisense regulatory mechanisms. Consequently, genomes with compact sizes enable putatively less flexible but more efficient physiologies.
\nThe selection of tRNAs had to be done mainly on two seemingly opposite criteria, stability and plasticity, making it a kind of Swiss army knife of the RNA world. This explains that beyond their central role in protein synthesis, tRNAs have many other crucial functions. To date, it can be hypothesized that ss-tRNAs might regulate gene expression, stress responses, and metabolic processes. Indeed, in silico analyzes allowed to speculate that several overlapping sequences may code simultaneously for mRNAs and tRNAs in most of the metazoan mt-genomes. These overlaps can have a variable (sometimes large) number of nts; however, when annotating their genomes, several authors voluntarily underestimated the number and the size of overlaps, speculating that there would be upstream abbreviated stop codons or downstream alternative start codons but most often without any direct demonstration so far. However, the high number of possible overlaps on the same strand in which the first in-frame complete stop codon or standard start codon are located at specific positions in the sequences of trn genes (TAR10 and ATR49, respectively) strongly suggest an exclusive relationship between obtaining tRNAs and translation of mRNAs and/or the development of repair system to keep the two genes functional due in some cases to co-evolution during several hundred MY. We can therefore speculate that ss-trn genes could allow true tRNA punctuation and initiation. Noted that ss-tRNAs seem to be hybrid molecules which would contain three essential coding or decoding informations in the form of nt triplets (i.e., anticodon and stop/start codons) which are all at least in part integrated into stem or loop; moreover, after the ATR49, nt triplets play the role of internal sense codons. To date, it is unclear what biochemical mechanism would allow to choose between different alternate cleavage sites, leading to the complete tRNA rather than to the mRNA or vice versa, but reduced/expanded proteins can be functional, and various processes including editing suggest this also for incomplete tRNAs. Hence, despite lacking experimental evidence, TAR10 and ATR49 triplets have probable roles, including regulation. Future analyzes of the processed bicistronic transcripts (tRNA/protein-encoding or the contrary) are required. Moreover, even if mt-trn genes are most often expressed at very low levels [53], only direct sequencing of tRNAs can validate transcription, epitranscriptomic maturation and can pinpoint nt modifications including post-transcriptionally edited positions. Purified native, or even synthetic, tRNAs should also be tested for their in vitro activity to confirm the functionality of aberrant transcripts. Similar experiments must be made on the flanking mRNAs and their products. If as we think, ss-tRNAs could play regulatory roles, initially experiments should compare stress and nonstress conditions.
\nHere, the bias for metazoan mtDNA does not allow for a complete picture of variation in the entire eukaryotic world, and protist mt-genomes should also be considered. Special attention should also be paid to noncanonical base pairings potentially formed by UAR10 and AUR49 nts, in perspective with tRNA structure and V-R length. Accounting for TAR10 and ATR49 triplet presences in the algorithms predicting tRNAs could improve mt-genome annotations, reducing numbers of false positives and negatives, and more accurately determine tRNA termini while accounting tRNA species, taxa, and genomic systems.
\nMtDNA plays a central role in apoptosis, aging, and cancer [13]. Moreover, mt-diseases are among the most common inherited metabolic and neurological disorders [101]. In addition, as new functions and new mechanisms of action of tRNAs are continuously discovered [1] and as ss-trn genes could affect the cellular dynamic during normal and stress conditions leading to pathologies, potential subtleties of action and regulation of these genes and products should be more thoroughly investigated.
\nThe authors declare no potential commercial or financial conflicts of interest.
In the past, Japanese houses were ridiculed as being “rabbit hutches” as they were smaller in scale, lower in quality, and shorter in average service life than those of Western countries, and examples were often given illustrating Japan as having the worst residential environment among major advanced countries. However, after the period of high economic growth since the chaotic postwar period, this environment has already greatly improved. In recent years high-performance housing stock has accumulated, and housing with functions not found in other countries have become common.
\nNeedless to say, when attempting an analysis of a housing market, it is necessary to fully understand the characteristics of the country. Below, we set out the reasons that have led to the false perception of Japanese housing still belonging to the era when they were ridiculed as rabbit hutches.
\nAlthough commonalities can be found in many parts of the Japanese housing market in comparison with the European and US housing markets, the following heterogeneity is conceivable as the postwar historical origin is different. It is possible that these are the cause of many misunderstandings.
\nIn Japan, many houses were destroyed due to the large-scale air raids during the Second World War, not only in metropolitan areas but also in regional cities. In particular, a large number of houses were destroyed in the Tokyo metropolitan area,1 and very-low-quality houses were built in a disorganized manner to satisfy the urgent housing demand in the chaotic postwar period. In the so-called high economic growth period that began in the mid-1950s, such houses were rapidly upgraded as large numbers of apartment buildings came up throughout Japan.2 In addition, the drastic change in Japanese lifestyle through the rapid economic growth triggered the renewal of old housing stock by Westernizing the traditional housing style of Japan.
\nThe private sector led construction to realize such a large-scale housing supply because the public sector was saddled with the large financial burden of postwar reconstruction. In particular, the government established a personal loan system to promote housing investment by households, and as a result, the ownership rate in postwar Japan significantly increased in comparison to before the war. Furthermore, as the supply of public housing was limited, a dedicated housing market for single-person renters formed in the rental housing market, which was rarely seen in Europe and the United States.
\nAs a result of these short-term housing renewals, Japanese housing was brought into a state where their style, quality, and housing equipment were greatly different depending on the period of construction. In addition, due to natural disasters such as the Great Hanshin earthquake3 and the Great East Japan earthquake,4 housing earthquake resistance and other legal regulations have been successively strengthened, thereby rapidly increasing the performance requirements of housing.5\n
\nThis history is also closely related to the shortness of service life, which is a characteristic of the previously ridiculed Japanese houses. Several reasons can be envisaged to explain the short service life of Japanese houses, but the two most influential factors are considered to be the urgent task of promoting the renovation of low-quality housing stock that was built to temporarily compensate for the housing shortage after the war and the fact that the stock renewal was promoted by strengthening public regulations due to large-scale earthquakes and other disasters.
\nIn addition, the high urban renewal rate can also be cited as a reason. In the rapid economic growth of postwar Japan, the main industrial structure shifted from primary to secondary industry in a single stroke, and urbanization was promoted throughout the country in the 1970s by developing highway and railway networks across the country, known as “Japanese archipelago remodeling.” In the 1980s, a policy was developed to transform the industrial structure, which was centered on secondary industry to tertiary industry. The transformation of Tokyo into an international financial center was a symbolic policy, and against this background, redevelopment rapidly advanced in major cities. Under such circumstances, the conversion of building use of even physically usable housing into offices, commercial facilities, and so on was promoted through rebuilding, and the advancement of land use was promoted [1].
\nAs a result, it can be said that the average service life of housing seen throughout the stock as a whole has been shortened over a long period.
\nIn addition to these features, it should be noted that the speed of technological innovation in Japanese housing is fast. “Technological innovation” here refers not only to the improvement of productivity on the manufacturing side but also the significant improvement of household welfare levels through the release of new products developed by R&D. In recent years, smart houses utilizing IOT and so on have become symbolic of advancing technology, but functions such as TV intercoms, bathroom dryers, system kitchens, and toilets with washlets, which are not often seen in European and American houses, have become common functions in Japanese houses and have greatly improved household living standards.
\nHowever, in a market where products with such new features arrive so quickly, the speed of obsolescence also increases. In these markets, when a new product appears, the old product is ordered to be withdrawn from the market, or its commodity value is greatly depreciated, that is, the service life of products is shortened.
\nThis study aims to measure the economic value of the functions of housing with new quality in the rental housing market in Tokyo, where technological advancement has been the greatest, and to clarify how much economic depreciation is occurring due to obsolescence. In Section 2, we present the model and the framework for empirical analysis together with the data, and in Section 3, we present the estimated results. According to the obtained results, new functions are being added sequentially to Japanese rental housing according to the age of the building, and these functions are non-negligible in the determination of housing rent, even when compared with location (LC) and the building structure (ST). The effect of obsolescence due to the addition of new functions was roughly—5%. In Section 4, we summarize the results by way of a conclusion.
\nA technique known as the hedonic approach is effective to decompose prices of commodities corresponding to different qualities. Since the hedonic approach theoretically depicts the behavior of suppliers and consumers in a market with diverse quality and presents a framework for empirical analysis, it is possible to approximately measure the household limit shadow price for new functions and to identify economic deterioration accompanying obsolescence [2, 3].
\nGenerally, the construction of household selection models in the residential market faces many difficulties compared to regular commodities and service markets. Not only is consumption expenditure high for housing, but consumers are also troubled by its highly nonuniform nature. Even when located in the same place, prices vary depending on the quality of housing, and even if the buildings are of the same quality, prices vary depending on the location. Furthermore, since housing has durability, depreciation has to be taken into consideration.
\nIn such a market, the law of one price assumed by traditional pricing theory cannot be applied. Furthermore, the application of a model that deals with differentiated products as analyzed by Lancaster [4] is not effective both theoretically and in empirical analysis. Accordingly, Rosen [5] theoretically clarified the type of market mechanism that is generated when commodity price data are a bundle of such attributes. Specifically, the relationship between the offer function of the commodity supplier, the bid function of the commodity consumer, and the market price function established by the equilibrium of these is closely examined, and the market price is characterized from the behavior of consumers and producers [6].
\nHowever, when attempting to estimate the hedonic function, we face various difficulties. The first is the existence of unobservable variables, the so-called omitted variable bias problem [7]. In general, in the estimation of a hedonic function for the housing market, only the location and building attributes, which are easy to obtain, are taken into consideration. However, it is also easy to envisage that the actual market price of housing will change depending on the environment surrounding the house and the various kinds of performance of the building.
\nAs for variable selection in the estimation of hedonic functions in Tokyo’s rental housing market, Nishi et al. [8] have conducted an exhaustive survey of the previous research. Nishi et al. [8] pointed that the housing amenities used in hedonic analyses are categorized as “location or accessibility,” “housing features,” and “site advantages.” This paper is focused on housing features, because they can be reflected in the rent due to the technological progress in the information systems and supply management.
\nAccessibility is defined as the “main accessibility related to commuting.” Housing features are defined as “amenities that can be changed by landlords.” Accessibility and housing features are the basic characteristics used as explanatory variables in hedonic models and are widely used in previous studies [2, 6, 9, 10].
\nSite advantages have also been researched recently using variables calculated using geographical information system or GIS [11, 12]. Shimizu [11] demonstrates that the environment surrounding housing is important in the case where house prices are determined by building use conditions and the characteristics of neighboring residents and suggests that in the case such variables are not taken into consideration and the estimated statistics of the hedonic function lack robustness. Nishi et al. [8] also show that there is a similar problem with estimated statistics when housing equipment is not taken into consideration. Fuerst and Shimizu [13] show that in the new condominium market in Tokyo, the offered value for highly novel functionality such as environmental performance differs greatly when taking the household’s annual income into account.
\nAs can be understood from these facts, attention must be given to the kind of variables that are used in estimating the hedonic function. According to Nelson [14], housing characteristics to be considered in function estimation are classified as follows.
\nExcluding characteristics related to traffic convenience, Nelson [14] considers it possible to categorize the positional characteristics of housing into housing equipment and location. Of these, “housing equipment” is variable and depends on the owner of the house, and “location” is an element that cannot be changed. Meanwhile, Chau and Chin [15] and Shimizu [11] add neighborhood characteristics.
\nIn addition to location and building structure, this study classifies housing equipment into equipment ancillary to the room (room equipment (RE)) and to the building (building equipment (BE)) and also takes the conditions of the contract into account to estimate their marginal price effect by estimating the hedonic function and to estimate the extent of obsolescence caused by the appearance of products with new performance.
\nSince the latter half of the 1990s, the use of the Internet for real estate advertising has expanded rapidly in Japan, and websites dealing with a large amount of rental advert data have been developed. This study uses the data on homes managed by LIFULL Co., Ltd. which is a major real estate portal site.6\n
\nMultiple real estate companies post concurrent advertisements for the same property on the real estate website, so we eliminated the duplicates from the data by grouping them by the criteria of address, property name, and room number.7 Furthermore, we independently assigned daytime railway travel time from Tokyo station to the nearest station to the property (minutes), which was not included in the data posted on the portal.
\nSince the aim of this study is to identify the effect due to the addition of new functions over time, we hypothesize that the price structure will change according to the period of construction.8 Data were segmented into the following three stocks:
Old stock: built between 1968 and 1981
Main stock: built between 1982 and 1999
New stock: built between 2000 and 2018
Earthquake resistance standards were greatly revised in 1981 according to the Building Standards Act, which stipulates building quality in Japan, and the earthquake resistance of buildings differs greatly according to whether they were built in or before 1981 or in or after 1982; buildings were therefore categorized using 1981 as a basis. There was also a major change in earthquake resistance standards in 2000, so this was also used as the standard for a category. In addition, the data used are for the 23 wards of Tokyo where a large volume of housing stocks was supplied due to a large population inflow.
\nAs a result of this process, 53,550 data points were acquired as data for analysis.9\n
\nA general hedonic model can be expressed as
\nwhere y is the explanatory variable, p is the housing rent, xi\n is the explanatory variable (housing characteristic), and βi\n and α are the estimation parameters.
\nIn this study, in addition to the commonly used location and building structure, housing equipment was added to the estimation of the hedonic function for the housing market. Specifically, we classified housing equipment into equipment ancillary to the room (room equipment) and equipment ancillary to the building (building equipment) and took the conditions of contract (CC) into account to construct a hedonic function.
\n\nEq. (1) can be rewritten as follows:
\nHere, the actual estimation formula can be expressed as follows:
\nIn Eq. (1), ln pit\n represents the log rent for i property at time t (October 2018). \n
Before analysis, we calculated the descriptive statistics of the data to be analyzed (\nTable 1\n). From the descriptive statistics, there are several features as follows, depending on the period of construction:
There is little difference between old and main stocks in average rent, but it is about 20% higher for new stock than the old stock.
There is no significant difference in the average floor area, the number of minutes by foot from the nearest station, and the number of minutes by train from Tokyo station.
Concerning the years since construction, the average of the total is 18.5 years and the standard deviation is 12.7 years, and the average value and standard deviation by construction date are consistent with the classification.
Variable | \nType | \nMean | \nStd. dev. | \nMin. | \nMax. | \n
---|---|---|---|---|---|
Monthly rent | \nAll | \n94,779 | \n34,873 | \n30,000 | \n249,000 | \n
(JYE) | \nOld stock | \n84,968 | \n30,631 | \n30,000 | \n240,000 | \n
\n | Main stock | \n85,305 | \n32,566 | \n30,000 | \n249,000 | \n
\n | New stock | \n103,040 | \n34,994 | \n45,000 | \n249,000 | \n
\n | New/old | \n121.3% | \n114.2% | \n150.0% | \n103.8% | \n
Floor space | \nAll | \n31.3 | \n13.4 | \n15.0 | \n100.0 | \n
(m2) | \nOld stock | \n32.5 | \n12.4 | \n15.0 | \n91.4 | \n
\n | Main stock | \n32.0 | \n15.3 | \n15.0 | \n100.0 | \n
\n | New stock | \n30.6 | \n12.1 | \n15.0 | \n99.5 | \n
\n | New/old | \n94.3% | \n97.7% | \n100.0% | \n108.9% | \n
Monthly rent/m3\n | \nAll | \n3192 | \n806 | \n988 | \n8134 | \n
(JYE) | \nOld stock | \n2717 | \n668 | \n1076 | \n6528 | \n
\n | Main stock | \n2864 | \n701 | \n988 | \n7535 | \n
\n | New stock | \n3501 | \n766 | \n1165 | \n8134 | \n
\n | New/old | \n128.9% | \n114.8% | \n108.3% | \n124.6% | \n
Age of unit | \nAll | \n18.5 | \n12.7 | \n0.0 | \n50.0 | \n
(year) | \nOld stock | \n42.3 | \n3.8 | \n37.0 | \n50.0 | \n
\n | Main stock | \n27.4 | \n4.4 | \n19.0 | \n36.0 | \n
\n | New stock | \n8.3 | \n5.5 | \n0.0 | \n18.0 | \n
\n | New/old | \n19.7% | \n144.0% | \n0.0% | \n36.0% | \n
Time to the nearest station | \nAll | \n7.7 | \n4.6 | \n0.6 | \n41.0 | \n
(minutes) | \nOld stock | \n7.4 | \n4.4 | \n1.0 | \n41.0 | \n
\n | Main stock | \n8.1 | \n4.8 | \n1.0 | \n40.0 | \n
\n | New stock | \n7.4 | \n4.4 | \n0.6 | \n38.0 | \n
\n | New/old | \n99.4% | \n98.8% | \n62.5% | \n92.7% | \n
Time to Tokyo station | \nAll | \n27.2 | \n8.6 | \n1.0 | \n48.0 | \n
(minutes) | \nOld stock | \n26.5 | \n8.3 | \n4.0 | \n48.0 | \n
\n | Main stock | \n28.8 | \n8.1 | \n4.0 | \n48.0 | \n
\n | New stock | \n26.2 | \n8.8 | \n1.0 | \n48.0 | \n
\n | New/old | \n99.1% | \n105.4% | \n25.0% | \n100.0% | \n
Number of observations (all) = 53,550 | \n
Descriptive statistics.
Based on these features, there is found to be little difference between the physical space distribution due to the period of construction and only the building quality changes.
\nNext, we examined the distribution of old/main/new stock for each of the 23 wards (\nTable 2\n). The ratio of new stock ratio exceeds 70% in Chiyoda, Chuo, and Minato wards, which make up the center of Tokyo. As previously mentioned, the probability of large-scale redevelopment and so on being carried out increases for more urban areas, which may have caused this result due to active stock renewal.10\n
\n\n | Number of observations | \nRatio | \n|||||||
---|---|---|---|---|---|---|---|---|---|
Item | \nTotal | \nOld stock | \nMain stock | \nNew stock | \nTotal | \nOld stock | \nMain stock | \nNew stock | \nNew-old | \n
\nRoom equipment\n | \n|||||||||
Air conditioning | \n49.088 | \n4029 | \n17.883 | \n27.176 | \n91.7% | \n82.8% | \n89.5% | \n94.7% | \n11.9% | \n
Hot water supply | \n44.841 | \n3879 | \n16.961 | \n24.001 | \n83.7% | \n79.7% | \n84.9% | \n83.6% | \n3.9% | \n
Indoor WM area | \n43.954 | \n2663 | \n14.696 | \n26.595 | \n82.1% | \n54.7% | \n73.5% | \n92.7% | \n38.0% | \n
Separate bath and toilet | \n43.943 | \n3447 | \n12.851 | \n27.645 | \n82.1% | \n70.8% | \n64.3% | \n96.3% | \n25.5% | \n
Flooring | \n43.269 | \n3364 | \n14.915 | \n24.990 | \n80.8% | \n69.1% | \n74.6% | \n87.1% | \n18.0% | \n
Balcony | \n40.851 | \n3204 | \n15.276 | \n22.371 | \n76.3% | \n65.8% | \n76.4% | \n77.9% | \n12.1% | \n
System kitchen | \n27.758 | \n1093 | \n5666 | \n20.999 | \n51.8% | \n22.5% | \n28.4% | \n73.2% | \n50.7% | \n
Separate washroom | \n26.292 | \n1412 | \n6221 | \n18.659 | \n49.1% | \n29.0% | \n31.1% | \n65.0% | \n36.0% | \n
1 gas stove | \n25.300 | \n1416 | \n6396 | \n17.488 | \n47.2% | \n29.1% | \n32.0% | \n60.9% | \n31.8% | \n
Washlet | \n23.221 | \n1089 | \n3265 | \n18.867 | \n43.4% | \n22.4% | \n16.3% | \n65.7% | \n43.4% | \n
Bathroom dryer | \n20.322 | \n186 | \n1077 | \n19.059 | \n37.9% | \n3.8% | \n5.4% | \n66.4% | \n62.6% | \n
2 gas stoves | \n18.632 | \n1081 | \n3304 | \n14.247 | \n34.8% | \n22.2% | \n16.5% | \n49.6% | \n27.4% | \n
Reheating bath | \n15.127 | \n1268 | \n3459 | \n10.400 | \n28.2% | \n26.0% | \n17.3% | \n36.2% | \n10.2% | \n
Washroom with shower | \n12.678 | \n364 | \n1764 | \n10.550 | \n23.7% | \n7.5% | \n8.8% | \n36.8% | \n29.3% | \n
Own house rental | \n7187 | \n497 | \n1588 | \n5102 | \n13.4% | \n10.2% | \n7.9% | \n17.8% | \n7.6% | \n
IH stovetop | \n6623 | \n215 | \n2653 | \n3755 | \n12.4% | \n4.4% | \n13.3% | \n13.1% | \n8.7% | \n
Walk-in closet | \n3694 | \n88 | \n235 | \n3371 | \n6.9% | \n1.8% | \n1.2% | \n11.7% | \n9.9% | \n
Counter kitchen | \n3409 | \n70 | \n516 | \n2823 | \n6.4% | \n1.4% | \n2.6% | \n9.8% | \n8.4% | \n
With loft | \n2110 | \n19 | \n754 | \n1337 | \n3.9% | \n0.4% | \n3.8% | \n4.7% | \n4.3% | \n
Underfloor heating | \n1147 | \n8 | \n87 | \n1052 | \n2.1% | \n0.2% | \n0.4% | \n3.7% | \n3.5% | \n
\nBuilding equipment\n | \n\n | \n | \n | \n | \n | \n | \n | \n | \n |
Bicycle parking lot | \n33.795 | \n2096 | \n11.385 | \n20.314 | \n63.1% | \n43.1% | \n57.0% | \n70.8% | \n27.7% | \n
Fiber optic Internet | \n27.307 | \n2085 | \n10.056 | \n15.166 | \n51.0% | \n42.8% | \n50.3% | \n52.8% | \n10.0% | \n
TV intercom | \n26.689 | \n953 | \n4232 | \n21.504 | \n49.8% | \n19.6% | \n21.2% | \n74.9% | \n55.4% | \n
Automatic entrance door | \n26.042 | \n337 | \n5062 | \n20.643 | \n48.6% | \n6.9% | \n25.3% | \n71.9% | \n65.0% | \n
Cable TV | \n23.211 | \n1316 | \n8314 | \n13.581 | \n43.3% | \n27.0% | \n41.6% | \n47.3% | \n20.3% | \n
BS antenna | \n20.013 | \n472 | \n4430 | \n15.111 | \n37.4% | \n9.7% | \n22.2% | \n52.7% | \n43.0% | \n
Elevator | \n19.587 | \n1189 | \n5387 | \n13.011 | \n36.6% | \n24.4% | \n27.0% | \n45.3% | \n20.9% | \n
Tiling wall | \n15.751 | \n561 | \n5265 | \n9925 | \n29.4% | \n11.5% | \n26.3% | \n34.6% | \n23.1% | \n
Delivery locker | \n15.163 | \n119 | \n1550 | \n13.494 | \n28.3% | \n2.4% | \n7.8% | \n47.0% | \n44.6% | \n
Security camera | \n12.694 | \n302 | \n1849 | \n10.543 | \n23.7% | \n6.2% | \n9.3% | \n36.7% | \n30.5% | \n
CS antenna | \n11.888 | \n304 | \n1837 | \n9747 | \n22.2% | \n6.2% | \n9.2% | \n34.0% | \n27.7% | \n
Garbage 24H available | \n6670 | \n130 | \n728 | \n5812 | \n12.5% | \n2.7% | \n3.6% | \n20.3% | \n17.6% | \n
Bike parking lot | \n6335 | \n354 | \n1875 | \n4106 | \n11.8% | \n7.3% | \n9.4% | \n14.3% | \n7.0% | \n
Design by artist | \n4068 | \n29 | \n286 | \n3753 | \n7.6% | \n0.6% | \n1.4% | \n13.1% | \n12.5% | \n
Seismic structure | \n3827 | \n37 | \n702 | \n3088 | \n7.1% | \n0.8% | \n3.5% | \n10.8% | \n10.0% | \n
\nContract conditions\n | \n\n | \n | \n | \n | \n | \n | \n | \n | \n |
with NO guarantor | \n20.257 | \n1214 | \n6274 | \n12.769 | \n37.8% | \n24.9% | \n31.4% | \n44.5% | \n19.6% | \n
No pets | \n8417 | \n733 | \n3540 | \n4144 | \n15.7% | \n15.1% | \n17.7% | \n14.4% | \n-0.6% | \n
NO musical instrument | \n6704 | \n605 | \n2702 | \n3397 | \n12.5% | \n12.4% | \n13.5% | \n11.8% | \n-0.6% | \n
NO office use | \n5253 | \n297 | \n1731 | \n3225 | \n9.8% | \n6.1% | \n8.7% | \n11.2% | \n5.1% | \n
FREE Internet | \n4682 | \n100 | \n616 | \n3966 | \n8.7% | \n2.1% | \n3.1% | \n13.8% | \n11.8% | \n
Pet consultation | \n3906 | \n210 | \n801 | \n2895 | \n7.3% | \n4.3% | \n4.0% | \n10.1% | \n5.8% | \n
Pets allowed | \n2189 | \n150 | \n437 | \n1602 | \n4.1% | \n3.1% | \n2.2% | \n5.6% | \n2.5% | \n
Contract with limited term | \n1673 | \n311 | \n511 | \n851 | \n3.1% | \n6.4% | \n2.6% | \n3.0% | \n-3.4% | \n
Office use allowed | \n1319 | \n362 | \n508 | \n449 | \n2.5% | \n7.4% | \n2.5% | \n1.6% | \n-5.9% | \n
\nBuilding structure\n | \n\n | \n | \n | \n | \n | \n | \n | \n | \n |
Wooden | \n10.851 | \n1285 | \n4273 | \n5293 | \n20.3% | \n26.4% | \n21.4% | \n18.4% | \n-8.0% | \n
Steel frame | \n13.796 | \n891 | \n6044 | \n6861 | \n25.8% | \n18.3% | \n30.2% | \n23.9% | \n5.6% | \n
RC | \n23.654 | \n2074 | \n7635 | \n13.945 | \n44.2% | \n42.6% | \n38.2% | \n48.6% | \n6.0% | \n
SRC | \n3644 | \n599 | \n1626 | \n1419 | \n6.8% | \n12.3% | \n8.1% | \n4.9% | \n-7.4% | \n
Others | \n1605 | \n19 | \n404 | \n1182 | \n3.0% | \n0.4% | \n2.0% | \n4.1% | \n3.7% | \n
\nOthers\n | \n\n | \n | \n | \n | \n | \n | \n | \n | \n |
High-rise block (16F over) | \n387 | \n3 | \n54 | \n330 | \n0.7% | \n0.1% | \n0.3% | \n1.1% | \n1.1% | \n
Room on the first floor | \n13.265 | \n894 | \n5217 | \n7154 | \n24.8% | \n18.4% | \n26.1% | \n24.9% | \n6.6% | \n
Distribution of equipment in old stock, main stock, and new stock.
Outside the three wards of the city center, the ratio of new stock is over 70% in Taito and Sumida wards and over 60% in Koto and Shinagawa wards, but this may be due to the supply of large-scale high-rise condominiums due to the relaxation of regulations in the 1990s. The ratio of new stock in other wards is around 50% (\nTable 3\n).
\nWard | \nOld stock | \nMain stock | \nNew stock | \nTotal | \nOld stock | \nMain stock | \nNew stock | \n
---|---|---|---|---|---|---|---|
Chiyoda | \n39 | \n65 | \n342 | \n446 | \n8.7% | \n14.6% | \n76.7% | \n
Chuo | \n57 | \n117 | \n740 | \n914 | \n6.2% | \n12.8% | \n81.0% | \n
Minato | \n137 | \n182 | \n927 | \n1246 | \n11.0% | \n14.6% | \n74.4% | \n
Shinjuku | \n284 | \n574 | \n1264 | \n2122 | \n13.4% | \n27.0% | \n59.6% | \n
Bunkyo | \n144 | \n379 | \n706 | \n1229 | \n11.7% | \n30.8% | \n57.4% | \n
Taito | \n86 | \n210 | \n796 | \n1092 | \n7.9% | \n19.2% | \n72.9% | \n
Sumida | \n103 | \n348 | \n1077 | \n1528 | \n6.7% | \n22.8% | \n70.5% | \n
Kouto | \n134 | \n454 | \n1056 | \n1644 | \n8.2% | \n27.6% | \n64.2% | \n
Shinagawa | \n190 | \n650 | \n1463 | \n2303 | \n8.3% | \n28.2% | \n63.5% | \n
Meguro | \n134 | \n537 | \n789 | \n1460 | \n9.2% | \n36.8% | \n54.0% | \n
Ota | \n458 | \n2022 | \n3054 | \n5534 | \n8.3% | \n36.5% | \n55.2% | \n
Setagaya | \n494 | \n2605 | \n2450 | \n5549 | \n8.9% | \n46.9% | \n44.2% | \n
Shibuya | \n188 | \n425 | \n908 | \n1521 | \n12.4% | \n27.9% | \n59.7% | \n
Nakano | \n292 | \n996 | \n1367 | \n2655 | \n11.0% | \n37.5% | \n51.5% | \n
Suginami | \n421 | \n1915 | \n1778 | \n4114 | \n10.2% | \n46.5% | \n43.2% | \n
Toshima | \n189 | \n687 | \n1019 | \n1895 | \n10.0% | \n36.3% | \n53.8% | \n
Kita | \n300 | \n797 | \n1061 | \n2158 | \n13.9% | \n36.9% | \n49.2% | \n
Arakawa | \n100 | \n339 | \n582 | \n1021 | \n9.8% | \n33.2% | \n57.0% | \n
Itabashi | \n291 | \n1254 | \n1441 | \n2986 | \n9.7% | \n42.0% | \n48.3% | \n
Nerima | \n243 | \n1639 | \n1796 | \n3678 | \n6.6% | \n44.6% | \n48.8% | \n
Adachi | \n182 | \n1020 | \n1518 | \n2720 | \n6.7% | \n37.5% | \n55.8% | \n
Katsushika | \n177 | \n926 | \n1074 | \n2177 | \n8.1% | \n42.5% | \n49.3% | \n
Edogawa | \n225 | \n1841 | \n1492 | \n3558 | \n6.3% | \n51.7% | \n41.9% | \n
Total | \n4868 | \n19,982 | \n28,700 | \n53,550 | \n9.1% | \n37.3% | \n53.6% | \n
Spatial distribution of rental housing.
\n\nTable 4\n shows the ancillary equipment rate by period of construction. Equipment was classified into that ancillary to the room, ancillary to the building, and conditions of contract.11\n
\nDependent variable | \nln (monthly rent) JPY | \n\n | \n | \n | \n | \n | \n | ||||
---|---|---|---|---|---|---|---|---|---|---|---|
Estimation method | \n\n | OLS | \n|||||||||
Number of observations | \n\n | 53,520 | \n4867 | \n19,975 | \n28,678 | \n\n | |||||
Adj R-squared | \n\n | 0.894 | \n0.853 | \n0.897 | \n0.892 | \n\n | |||||
\nIndependent variables\n | \n\nMark\n | \n\nAll\n | \n\nOld stock\n | \n\nMain stock\n | \n\nNew stock\n | \nNew-old | \n|||||
\nCoef.\n | \n\nP>t\n | \n\nCoef.\n | \n\nP>t\n | \n\nCoef.\n | \n\nP>t\n | \n\nCoef.\n | \n\nP>t\n | \nCoef. | \n|||
Age of unit (year) | \n\n | −0.53% | \n0.00 | \n−0.13% | \n0.01 | \n−0.43% | \n0.00 | \n−0.63% | \n0.00 | \n−0.50% | \n|
Old stock dummy | \n\n | 1.53% | \n0.00 | \n(Omitted) | \n(Omitted) | \n(Omitted) | \n− | \n||||
Main stock dummy | \n−0.54% | \n0.01 | \n(Omitted) | \n(Omitted) | \n(Omitted) | \n− | \n|||||
New stock dummy | \nBaseline | \n(Omitted) | \n(Omitted) | \n(Omitted) | \n− | \n||||||
Floor space (m2) | \n\n | 1.69% | \n0.00 | \n1.60% | \n0.00 | \n1.61% | \n0.00 | \n1.73% | \n0.00 | \n0.13% | \n|
Time to Tokyo station (minutes) | \n−0.70% | \n0.00 | \n−0.67% | \n0.00 | \n−0.77% | \n0.00 | \n−0.64% | \n0.00 | \n0.03% | \n||
Time to the nearest station (minutes) | \n−0.62% | \n0.00 | \n−0.53% | \n0.00 | \n−0.61% | \n0.00 | \n−0.64% | \n0.00 | \n−0.11% | \n||
Building | \nWooden | \n\n | Baseline | \nBaseline | \nBaseline | \nBaseline | \n− | \n||||
Structure | \nSteel frame | \n4.28% | \n0.00 | \n7.22% | \n0.00 | \n3.67% | \n0.00 | \n3.51% | \n0.00 | \n−3.71% | \n|
\n | RC | \n\n | 9.26% | \n0.00 | \n13.04% | \n0.00 | \n8.41% | \n0.00 | \n8.17% | \n0.00 | \n−4.87% | \n
\n | SRC | \n\n | 10.75% | \n0.00 | \n13.10% | \n0.00 | \n9.72% | \n0.00 | \n8.99% | \n0.00 | \n−4.11% | \n
\n | Others | \n\n | 4.01% | \n0.00 | \n6.83% | \n0.11 | \n4.20% | \n0.00 | \n3.25% | \n0.00 | \n−3.58% | \n
Wards | \nChiyoda | \n\n | −1.44% | \n0.01 | \n8.72% | \n0.00 | \n3.21% | \n0.03 | \n−3.03% | \n0.00 | \n−11.75% | \n
\n | Chuo | \n\n | −3.77% | \n0.00 | \n0.14% | \n0.94 | \n−2.84% | \n0.01 | \n−4.29% | \n0.00 | \n−4.43% | \n
\n | Minato | \n\n | 12.01% | \n0.00 | \n17.08% | \n0.00 | \n11.20% | \n0.00 | \n10.75% | \n0.00 | \n−6.34% | \n
\n | Shinjuku | \n\n | 0.54% | \n0.07 | \n3.46% | \n0.00 | \n0.15% | \n0.77 | \n−0.54% | \n0.14 | \n−4.00% | \n
\n | Bunkyo | \n\n | −5.38% | \n0.00 | \n−4.39% | \n0.00 | \n−5.82% | \n0.00 | \n−5.52% | \n0.00 | \n−1.13% | \n
\n | Taito | \n\n | −14.43% | \n0.00 | \n−12.95% | \n0.00 | \n−14.68% | \n0.00 | \n−14.73% | \n0.00 | \n−1.78% | \n
\n | Sumida | \n\n | −15.60% | \n0.00 | \n−15.02% | \n0.00 | \n−14.04% | \n0.00 | \n−16.21% | \n0.00 | \n−1.19% | \n
\n | Koto | \n\n | −13.38% | \n0.00 | \n−12.53% | \n0.00 | \n−12.56% | \n0.00 | \n−13.80% | \n0.00 | \n−1.27% | \n
\n | Shinagawa | \n\n | −6.09% | \n0.00 | \n−2.83% | \n0.02 | \n−6.83% | \n0.00 | \n−6.62% | \n0.00 | \n−3.79% | \n
\n | Meguro | \n\n | 8.18% | \n0.00 | \n10.71% | \n0.00 | \n6.95% | \n0.00 | \n7.76% | \n0.00 | \n−2.95% | \n
\n | Ota | \n\n | −11.59% | \n0.00 | \n−9.71% | \n0.00 | \n−10.11% | \n0.00 | \n−13.14% | \n0.00 | \n−3.42% | \n
\n | Setagaya | \n\n | Baseline | \nBaseline | \nBaseline | \nBaseline | \n− | \n||||
\n | Shibuya | \n\n | 10.74% | \n0.00 | \n12.23% | \n0.00 | \n7.93% | \n0.00 | \n11.20% | \n0.00 | \n−1.03% | \n
\n | Nakano | \n\n | −4.79% | \n0.00 | \n−3.33% | \n0.00 | \n−3.76% | \n0.00 | \n−6.01% | \n0.00 | \n−2.68% | \n
\n | Suginami | \n\n | −5.20% | \n0.00 | \n−4.42% | \n0.00 | \n−4.99% | \n0.00 | \n−5.64% | \n0.00 | \n−1.22% | \n
\n | Toshima | \n\n | −7.34% | \n0.00 | \n−4.23% | \n0.00 | \n−6.35% | \n0.00 | \n−9.01% | \n0.00 | \n−4.79% | \n
\n | Kita | \n\n | −16.82% | \n0.00 | \n−14.43% | \n0.00 | \n−16.10% | \n0.00 | \n−17.69% | \n0.00 | \n−3.25% | \n
\n | Arakawa | \n\n | −19.82% | \n0.00 | \n−17.14% | \n0.00 | \n−18.83% | \n0.00 | \n−20.71% | \n0.00 | \n−3.57% | \n
\n | Itabashi | \n\n | −15.50% | \n0.00 | \n−15.73% | \n0.00 | \n−15.13% | \n0.00 | \n−15.86% | \n0.00 | \n−0.12% | \n
\n | Nerima | \n\n | −12.61% | \n0.00 | \n−10.86% | \n0.00 | \n−12.29% | \n0.00 | \n−12.95% | \n0.00 | \n−2.09% | \n
\n | Adachi | \n\n | −27.31% | \n0.00 | \n−24.71% | \n0.00 | \n−27.17% | \n0.00 | \n−27.90% | \n0.00 | \n−3.19% | \n
\n | Katsushika | \n\n | −26.27% | \n0.00 | \n−24.68% | \n0.00 | \n−26.83% | \n0.00 | \n−25.97% | \n0.00 | \n−1.29% | \n
\n | Edogawa | \n\n | −21.84% | \n0.00 | \n−19.56% | \n0.00 | \n−21.90% | \n0.00 | \n−21.92% | \n0.00 | \n−2.35% | \n
Difference between max. and min. | \n39.32% | \n\n | 41.79% | \n\n | 38.37% | \n\n | 39.10% | \n\n | −2.69% | \n
Results of hedonic equations: main estimated results.
Housing equipment items are arranged in descending order of ancillary rate in all samples, and a comparison is made between old, main, and new stocks.
\nIn terms of room equipment, the five items (i) air conditioning, (ii) hot water supply, (iii) indoor washing machine area, (iv) separate bath and toilet, and (v) flooring have a high ancillary rate of over 80%. The equipments for which there is a large difference in ancillary rate between old and new stocks (ancillary rate increased) are bathroom dryer (+62.6%), system kitchen (+50.7%), toilet with washlet (+43.4%), indoor washing machine area (+38.0%), and separate washroom (+36.0%).
\nIn terms of building equipment, the ancillary rate is over 50% for the bicycle parking lot and fiber optic Internet. The equipment for which there is a large difference in ancillary rate between old and new stocks (ancillary rate increased) is automatic entrance door (+65.0%), TV intercom (+55.4%), delivery locker (+44.6%), BS antenna (+43.0%), and security camera (+30.5%). In the conditions of contract, there are no items of note except for guarantor unnecessary, which is high at 37.8%, and only guarantor unnecessary (+19.6%) has a large difference in ancillary rate between old and new stocks (ancillary rate increased), but free Internet is also +11.8%.12\n
\nOverall, the rise in security equipment is significant in building equipment, and the rise in the equipment that improves the living convenience is significant in room equipment. In addition, the ratio of building structures also shows changes, such as wooden buildings decreasing by 8.0% and SRC by 7.4%, while steel frames increase by 5.6% and RC by 6.0%.13\n
\n\n\nTable 5\n shows the estimated results of the model. In addition, \nFigure 1\n illustrates the dummy partial regression coefficients for the equipment.
\nIndependent variables | \nAll | \nOld stock | \nMain stock | \nNew stock | \nNew-old | \n||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Coef. | \nP>t | \nCoef. | \nP>t | \nCoef. | \nP>t | \nCoef. | \nP>t | \nCoef. | \n|||
High-rise block (16F over) | \n8.74% | \n0.00 | \n14.12% | \n0.08 | \n4.35% | \n0.01 | \n9.22% | \n0.00 | \n−4.89% | \n||
Room on the first floor | \n−2.76% | \n0.00 | \n−0.55% | \n0.28 | \n−2.94% | \n0.00 | \n−3.00% | \n0.00 | \n−2.44% | \n||
RE | \nAir conditioning | \n\n | 0.82% | \n0.00 | \n1.87% | \n0.00 | \n0.18% | \n0.48 | \n0.02% | \n0.96 | \n−1.86% | \n
\n | Hot water supply | \n\n | −1.77% | \n0.00 | \n0.58% | \n0.24 | \n−1.03% | \n0.00 | \n−2.42% | \n0.00 | \n−3.01% | \n
\n | Indoor WM area | \n\n | 1.27% | \n0.00 | \n2.73% | \n0.00 | \n1.73% | \n0.00 | \n−0.77% | \n0.00 | \n−3.50% | \n
\n | Flooring | \n\nA\n | \n0.16% | \n0.22 | \n3.35% | \n0.00 | \n0.50% | \n0.01 | \n−1.81% | \n0.00 | \n−5.17% | \n
\n | Separate bath and toilet | \n\nA\n | \n5.07% | \n0.00 | \n5.58% | \n0.00 | \n6.46% | \n0.00 | \n1.55% | \n0.00 | \n−4.03% | \n
\n | balcony | \n\nA\n | \n0.84% | \n0.00 | \n3.28% | \n0.00 | \n1.82% | \n0.00 | \n0.01% | \n0.95 | \n−3.27% | \n
\n | System kitchen | \n\n | 1.85% | \n0.00 | \n4.62% | \n0.00 | \n2.40% | \n0.00 | \n0.79% | \n0.00 | \n−3.83% | \n
\n | Separate washroom | \n\n | 2.11% | \n0.00 | \n2.18% | \n0.00 | \n2.35% | \n0.00 | \n2.16% | \n0.00 | \n−0.03% | \n
\n | 1 gas stove | \n\n | −0.52% | \n0.00 | \n−1.09% | \n0.04 | \n0.13% | \n0.52 | \n−1.13% | \n0.00 | \n−0.05% | \n
\n | Washlet | \n\nA\n | \n2.20% | \n0.00 | \n3.17% | \n0.00 | \n2.75% | \n0.00 | \n1.16% | \n0.00 | \n−2.01% | \n
\n | Bathroom dryer | \n\nA\n | \n1.35% | \n0.00 | \n4.90% | \n0.00 | \n3.07% | \n0.00 | \n1.29% | \n0.00 | \n−3.61% | \n
\n | 2 gas stoves | \n\n | −0.34% | \n0.01 | \n−0.03% | \n0.95 | \n1.17% | \n0.00 | \n−0.09% | \n0.55 | \n−0.05% | \n
\n | Reheating bath | \n\nC\n | \n2.22% | \n0.00 | \n0.26% | \n0.56 | \n0.06% | \n0.82 | \n3.45% | \n0.00 | \n3.18% | \n
\n | Washroom with shower | \n\n | −1.16% | \n0.00 | \n0.64% | \n0.41 | \n−0.18% | \n0.55 | \n−1.33% | \n0.00 | \n−1.97% | \n
\n | Own house rental | \n\nD\n | \n−2.92% | \n0.00 | \n−0.54% | \n0.45 | \n−1.87% | \n0.00 | \n−3.42% | \n0.00 | \n−2.88% | \n
\n | IH stovetop | \n\nD\n | \n−1.03% | \n0.00 | \n−0.65% | \n0.49 | \n−1.68% | \n0.00 | \n−1.62% | \n0.00 | \n−0.97% | \n
\n | Walk-in closet | \n\nB\n | \n1.22% | \n0.00 | \n4.33% | \n0.00 | \n0.77% | \n0.29 | \n0.88% | \n0.00 | \n−3.45% | \n
\n | Counter kitchen | \n\n | 1.10% | \n0.00 | \n2.83% | \n0.08 | \n0.03% | \n0.95 | \n0.72% | \n0.00 | \n−2.11% | \n
\n | With loft | \n\n | 4.72% | \n0.00 | \n5.59% | \n0.07 | \n4.08% | \n0.00 | \n4.19% | \n0.00 | \n−1.40% | \n
\n | Underfloor heating | \n\nC\n | \n5.19% | \n0.00 | \n−1.55% | \n0.73 | \n−1.09% | \n0.36 | \n4.97% | \n0.00 | \n6.52% | \n
BE | \nBicycle parking lot | \n\n | −0.94% | \n0.00 | \n−0.71% | \n0.09 | \n−0.70% | \n0.00 | \n−0.96% | \n0.00 | \n−0.25% | \n
\n | Fiber optic Internet | \n\n | −1.04% | \n0.00 | \n−1.83% | \n0.00 | \n−0.93% | \n0.00 | \n−0.91% | \n0.00 | \n0.92% | \n
\n | TV intercom | \n\nA\n | \n1.08% | \n0.00 | \n3.99% | \n0.00 | \n1.71% | \n0.00 | \n−0.15% | \n0.34 | \n−4.14% | \n
\n | Automatic entrance door | \n\nA\n | \n1.74% | \n0.00 | \n4.47% | \n0.00 | \n2.72% | \n0.00 | \n1.63% | \n0.00 | \n−2.84% | \n
\n | Cable TV | \n\n | −0.63% | \n0.00 | \n−1.61% | \n0.00 | \n−0.26% | \n0.13 | \n−0.51% | \n0.00 | \n1.10% | \n
\n | BS antenna | \n\n | −1.25% | \n0.00 | \n−2.58% | \n0.01 | \n−0.05% | \n0.83 | \n−1.45% | \n0.00 | \n1.13% | \n
\n | Elevator | \n\n | 2.52% | \n0.00 | \n2.89% | \n0.00 | \n2.10% | \n0.00 | \n2.63% | \n0.00 | \n−0.26% | \n
\n | Tiling wall | \n\n | −1.44% | \n0.00 | \n−1.91% | \n0.00 | \n−1.21% | \n0.00 | \n−0.97% | \n0.00 | \n0.93% | \n
\n | Delivery locker | \n\nA\n | \n2.03% | \n0.00 | \n4.55% | \n0.00 | \n1.42% | \n0.00 | \n2.68% | \n0.00 | \n−1.87% | \n
\n | Security camera | \n\nC\n | \n1.33% | \n0.00 | \n0.62% | \n0.45 | \n1.06% | \n0.00 | \n1.61% | \n0.00 | \n0.99% | \n
\n | CS antenna | \n\n | 0.60% | \n0.00 | \n1.76% | \n0.15 | \n−0.69% | \n0.04 | \n1.25% | \n0.00 | \n−0.51% | \n
\n | Garbage 24H available | \n\nC\n | \n−0.13% | \n0.49 | \n−1.58% | \n0.18 | \n−0.84% | \n0.06 | \n0.98% | \n0.00 | \n2.56% | \n
\n | Bike parking lot | \n\nC\n | \n0.75% | \n0.00 | \n−0.38% | \n0.61 | \n0.29% | \n0.28 | \n0.94% | \n0.00 | \n1.32% | \n
\n | Design by artist | \n\n | 0.45% | \n0.02 | \n0.62% | \n0.80 | \n1.78% | \n0.01 | \n0.52% | \n0.01 | \n−0.09% | \n
\n | Seismic structure | \n\n | −2.25% | \n0.00 | \n−4.11% | \n0.05 | \n−1.95% | \n0.00 | \n−1.82% | \n0.00 | \n2.29% | \n
CC | \nwith NO guarantor | \n\nD\n | \n−0.82% | \n0.00 | \n−1.47% | \n0.00 | \n−1.07% | \n0.00 | \n−0.23% | \n0.08 | \n1.24% | \n
\n | No pets | \n\n | 0.06% | \n0.77 | \n−1.46% | \n0.12 | \n0.37% | \n0.25 | \n0.47% | \n0.07 | \n1.93% | \n
\n | Pet consultation | \n\n | 3.24% | \n0.00 | \n2.85% | \n0.00 | \n4.13% | \n0.00 | \n3.10% | \n0.00 | \n0.25% | \n
\n | Pets allowed | \n\n | 2.57% | \n0.00 | \n2.17% | \n0.05 | \n3.40% | \n0.00 | \n2.35% | \n0.00 | \n0.18% | \n
\n | No musical instrument | \n\n | −0.32% | \n0.15 | \n1.61% | \n0.11 | \n0.22% | \n0.54 | \n−0.83% | \n0.00 | \n−2.44% | \n
\n | No office use | \n\n | 0.81% | \n0.00 | \n−1.18% | \n0.18 | \n0.01% | \n0.97 | \n1.13% | \n0.00 | \n2.31% | \n
\n | Office use allowed | \n\nC\n | \n5.04% | \n0.00 | \n2.34% | \n0.00 | \n4.01% | \n0.00 | \n6.11% | \n0.00 | \n3.77% | \n
\n | Free Internet | \n\nB\n | \n0.82% | \n0.00 | \n3.01% | \n0.02 | \n0.58% | \n0.19 | \n0.68% | \n0.00 | \n−2.33% | \n
\n | Contract with limited term | \n\nB\n | \n−0.82% | \n0.00 | \n−2.80% | \n0.00 | \n−0.86% | \n0.08 | \n−0.30% | \n0.39 | \n2.50% | \n
_cons | \n\n | \n | 0.00% | \n0.00 | \n0.00% | \n0.00 | \n0.00% | \n0.00 | \n0.00% | \n0.00 | \n– | \n
Estimated results of room equipment (RE), building equipment (BE), and contract conditions (CC).
Marginal price effect on RE, BE, and CC.
Looking at the estimated results, as floor area increases, rent goes up, and as the number of minutes on foot from the station increases or the railway travel time from Tokyo station increases, the rent goes down. When taking a wooden structure as the baseline of the building structure, the rent will increase in the order of steel frame, RC, and SRC. The rent varies greatly depending on the ward in which the property is located; a high-rise condominium is a positive driver, and a 1F apartment positions a negative driver for rent. These results are consistent with previous studies and the intuition of market participants.
\nThe effect of the number of years since construction differs depending on the period of construction, and as a whole, there is a −0.53% reduction in rent per year after construction. However, looking at the old/main/new period of construction dummy, the speed of reduction is high for new stock and low for old stock. This shows that the effect of years since construction is nonlinear, indicating that the decline in rent will be considerably smaller after a certain number of years. Such nonlinearity is also consistent with a series of previous studies.
\nThe influence of the ancillary equipment situation on the rent changes according to the period of construction (\nFigure 1\n). The change can be classified into the following four patterns.14\n
Pattern A: Items considered to have lost value because of commonness
In Pattern A, it is assumed that the equipment premium that was once a differentiating factor for price was lost because of the advancing commonness of equipment. This corresponds to room equipment (RE) such as flooring, separate bath and toilet, balcony, toilet with washlet, and bathroom dryer and building equipment (BE) such as TV intercom, automatic entrance door, delivery locker, and so on. In all cases, the ancillary rate has increased, so the superiority of the ancillary equipment falls, the influence on rent differs between old and new stocks, and such influence is generally small in new stock. Flooring and TV intercoms have a negative impact on new stock. This indicates that flooring and TV intercoms are no longer special equipment and do not offer price advantages.
Pattern B: Items considered to have lost value because they satisfied limited needs
In Pattern B, it is assumed that the price premium of the equipment was lost because the needs the equipment satisfied were limited in the first place and have been satisfied. The walk-in closet corresponds to this in room equipment (RE), nothing corresponds to this in building equipment (BE), and free Internet and contract with limited term correspond to this in contract conditions (CC). Contract with limited term has a negative impact on rent in new stock.
Pattern C: Items for which demand is considered to be increasing but the ancillary rate is low, and value is increasing
Pattern C is such that although consumer demand is increasing over time, a price premium exists because of the low ancillary rate in the housing stock. Equipment such as a reheating bath and underfloor heating corresponds to this in room equipment (RE), and security cameras, garbage disposal available 24-hours a day, and bike parking correspond to this in building equipment (BE). Items such as use as an office correspond to this in contract conditions (CC). In particular, the reheating bath and use as an office have a significant influence of +3.45 and +3.77%, respectively.
Pattern D: Items considered to be due to other individual factors
Items for which a price premium exists due to other factors correspond to owner-owned condominium for lease in room equipment (RE) and guarantor unnecessary in contract conditions (CC). Regarding condominium for lease, the effect of the increase in supply is considered to be caused by the change in the social situation, where the tendency for relatives to avoid guaranteeing rent obligations has strengthened.
\n\nFigure 2\n shows the depreciation rate of all rents (All) and for the case where the ancillary equipment situation is poor (Poor). The equipment being poor indicates there is no (i) washlet, (ii) bathroom dryer, (iii) reheating bath, (iv) TV intercom, (iv) automatic entrance door, (iv) delivery locker, or (vii) security camera. These types of equipment have become more common in recent years and can be installed in existing buildings.
\nDepreciation in rental housing.
There were 13,033 properties with poor equipment; a regression analysis similar to the previous one was carried out with the logarithm of the rent as a target variable, and the regression coefficient of the years since construction was obtained. That is, as of October 2018, data points without the aforementioned equipment exist regardless of whether they are new, main, or old stock. This means that low-quality rental housing that does not have equipment that has become popular in recent years is still supplied. By extracting such data and comparing the depreciation of rental housing with new functions that benefited from technological progress and the depreciation of low-quality rental housing with no new functions, it is possible to extract the depreciation that accompanies obsolescence.
\nIn \nFigure 2\n, the depreciation rate for each period is calculated with the rent at the time of construction as 100 to demonstrate the theoretical effect of the increasing number of years since construction on rent. When comparing the depreciation rate of all rents with that of rents of properties with a poor ancillary equipment situation, the depreciation rate increases in all cases (new, main, and old stocks). Roughly 60 years after construction, the difference was found to be 5.5%.
\nIn addition to the measurement of the magnitude of the age effect accompanying obsolescence, this result means that rent depreciation can be mitigated if appropriate ancillary equipment investment is made with respect to the demands for housing equipment that have increased with economic growth and changes in lifestyle. We believe that this will provide pointers for high-level policy with respect to Japan’s rental housing market, where the aging of stock will advance in the future.
\nChanges in prices over time are broken down into changes due to supply-demand relationships and those caused by quality changes. In particular, this means that in markets with rapid technological progress, the price rise accompanying quality change increases as new products are introduced successively, but at the same time, in markets where such new products are introduced, the speed of obsolescence is fast.
\nCompared with Western countries, new products are easy to create in the Japanese housing market. The background to this is there are many housing providers and a comparatively large number of companies that do business throughout Japan and overseas. Such companies possess, for example, think tanks to develop new products, and are developing integrated business from large-scale procurement of raw materials to design, construction, sales, and management.
\nIn this study, we focused on the period in which the housing was supplied and clarified the types of functions and equipment supplied to the market in each period and the extent of the marginal price effect in 2018. In addition, we measured the magnitude of obsolescence that accompanies the addition of a new function.
\nThe conclusion can be summarized as follows.
Rent is strongly influenced by the floor area, years since construction, building structure, number of minutes on foot from the nearest station, railway travel time from Tokyo station, location, and so on. This confirms conclusions provided by previous studies.
The ancillary conditions of housing equipment vary greatly depending on the construction year. This suggests that the Japanese rental housing market is strongly influenced by regulations such as the Building Standards Act and the improvement of living standards by economic growth.
Some ancillary conditions have a large influence on rent, but if the ancillary rate increases, the influence becomes smaller due to commonness, and housing equipment responding to new needs have a positive influence on rent.
Even if the number of years since construction is large, depreciation of the rent can be reduced if additional investment in appropriate housing equipment is carried out.
These evaluations are for the present time, and they are expected to change in the future as housing equipment ancillary rates change and social conditions, lifestyles, and resident demands evolve. The conclusion of this study shows the possibility of increasing profitability by responding to resident demands and raising rent through adding ancillary equipment, even in countries in Europe and in the United States, where housing building restrictions are strict.
\nHowever, several tasks remain. First, it is possible to add new functionality even to housing classified as old stock through large-scale renovation investment. In this sense, this study has not been able to measure the effect of investment in renovation. Moreover, in order to generalize the study result, it is necessary to identify appropriate housing equipment according to changes in lifestyle and social conditions, in addition to the influence of housing equipment on rent. Even if the scope is restricted to Japan, it is also necessary to consider points such as the type of differences that arise depending on the scale of the city and the standard of living and climate in different regions, as well as whether the necessary housing equipment differs according to the age, gender, family composition, income, and so on of the residents.
\nWe would like to clarify these questions as future research tasks.
\nThe second author gratefully acknowledges the financial support of the Nomura Foundation.
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