Open access peer-reviewed chapter
Abstract
When a Dunaliella salina cell is stressed, a series of adaptive changes occur, including gene expression regulation, acclimating to new conditions, and maintaining survival. Due to the natural habitat and the high adaptability of this extraordinary organism to the intolerable environment for other photosynthetic organisms, the plasticity of metabolic pathways has been proven. In this regard, it seems that manipulating the amount and activity of enzymes involved in these pathways is inevitable. Therefore, both nuclear and organelles genomes must sense environmental fluctuation quickly and accurately to respond appropriately to those changes during transcription or post-transcriptional stages. In addition to the nuclear genome, D. salina has an autonomous chloroplast genome, consisting of 66, and a mitochondria genome consisting of seven genes encoding proteins. The mystery of D. salina survival in harsh environments, from 5 M salinity salt lakes to the Atacama Desert Caves, lies in this flexibility and adaptability from molecular levels to the metabolic pathway of D. salina cells. Therefore, who can say prudently that the prosperity of D. salina depends on flexibility in the regulation of plastid gene expression?
Keywords
- acclimation
- transcription
- Dunaliella salina
- chloroplast genome
- survival
1. Introduction
Microalgae are worldwide microscopic organisms capable of producing valuable bioactive components from biomass to molecules with drug properties. The rapid growth, utilization of a wide variety of water sources, and photosynthetic activity are the reason for microalgae’s success in producing such compounds. High photosynthesis efficiency in microalgae and acclimation power in various ecosystems make microalgae attractive model organisms for the investigation of tolerance mechanisms.
Though the genus and its species have been studied for over a century and a half, there are still a lot of unanswered questions about its magic tools for such behavior.
The interest in
So, in this chapter, an attempt has been made to be paid a slight aspect of the flexibility of
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2. Endosymbiotic theory and the origin of the organelle genome
Endosymbiosis proposes that the origin of today’s eukaryotic organelles evolved through a symbiosis process between two primitive free-living cells. One prokaryote cell was swallowed by the precursor of modern eukaryotes. According to Martin et al. [1], the primary nucleus probably consists of pressing a piece of the cytoplasmic membrane around chromosomes. The nucleated primary cell, which moved like an amoeba by creating false feet, then swallowed the primary prokaryotic cells during phagocytosis, and, for some unknown reason, a number of the ingested prokaryotes survived inside the amoebic cell and became the basis for the symbiosis of above-mentioned cells [1].
According to endosymbiont theory, ingested early prokaryotes retained their specific traits while surviving. They benefited their nucleated host from the advantages of their specific metabolic abilities. It is believed that a bacterium capable of oxidative metabolism is the ancestor of primary mitochondria and a photosynthetic bacterium is the ancestor of primary chloroplast [2].
They eventually lost their cell wall and much of their DNA because they were useless inside the host cell. Thus, both mitochondria and chloroplasts have their DNA, but both also depend on nuclear genes for some functions [2]. Some organellar protein genes (as whole or partial) are present in the nucleus.
Three issues mentioned by Mereschkowsky [3] about plastid insertion into eucaryotic cells are as follows:
plastids are indubitably diminished cyanobacteria that entered into a symbiosis with a heterotrophic nucleated host cell in early evolution,
heterotrophic nucleated host cell was itself the product of an earlier symbiosis between a larger, heterotrophic, amoeboid host cell and a smaller “micrococcal” endosymbiont that make the nucleus, which gained plastids,
the plant’s autotrophy and self-sufficiency are completely beholden to cyanobacteria [1].
The following provides further evidence for the Endosymbiotic Theory:
Chloroplast’s size, division method (fission), and the existence of Fts proteins at their dividing surface is similar to prokaryotic cells.
Mitochondria size, division method (dual fission), and the existence of Fts homologs at their dividing surface are similar to prokaryotic cells.
Mitochondria and chloroplasts have their DNA, which is circular, not linear.
Mitochondria and chloroplasts have their organellar ribosomes (the 30S and 50S subunits), not 40S and 60S [1].
The possibility of the presence of some genes outside the nucleus – which were originally known as extra-chromosomal genes –was first proposed in the 1950s to justify the unusual inherited pattern of some genes in the fungus
Simultaneous biochemical and electron microscopy studies have increased the possibility of the presence of DNA in mitochondria and chloroplasts. As a result, in the early 1960s, different sets of data were put together and the existence of chloroplasts and mitochondria genomes was accepted independently of the eukaryotic nucleus genome.
The theory of endosymbiotic is corroborated by observations in which the processes of gene expression in organelles are similar to those processes in bacteria. In addition, when the nucleotide sequences were compared, the genes of the organelles were very similar to their counterparts in the bacteria rather than to the genes in the eukaryotic nucleus.
The theory of endosymbiotic was confirmed by the discovery of organisms that show more primitive stages of endosymbiosis than mitochondria and chloroplasts. For example, the early stages of endosymbiosis have been observed in the single-called
According to the theory of endosymbiotic, after the primary cyanobacteria eaten by the primary eukaryotic cell are not digested for unknown reasons, the newcomer’s behavior must be controlled by the host and transform from a self-sufficient organism to a semi-self-sufficient employee. They exchanged genetic material and somehow divided tasks. Regarding the information required for the biosynthesis of the important photosynthetic enzyme Rubisco, this division of tasks has been done in such a way that the genes related to the large subunit remain in the genome of the old cyanobacterium and the new organ that had been the feature of oxygen photosynthesis. However, small subunit genes that were responsible for regulating enzyme function and activity were transferred to the host cell nucleus. It seems that the original genome thus wanted and was able to control and initiate the function and status and activity of the enzyme within the primary chloroplast. Another group of genes in the chloroplast organelle genome is related to the proteins and nucleic acids of the organellar ribosomes.
2.1 Physical properties of the organelle genome
Almost all eukaryotes have a mitochondrial genome and all photosynthetic eukaryotes have a chloroplast genome in addition to the mitochondrial ones. All organelle genomes were initially thought to be circular DNA molecules. Electron microscopy showed that in some organelles, DNA was present in both circular and linear shapes. But linear molecules were assumed to be simple fragments of circular genomes created by breaking circular genomes during sample preparation for electron microscopy.
The genomes of most mitochondria and chloroplasts are now believed to be circular, but it has recently been discovered that there are many different forms of genomes in different organisms. In many eukaryotes, circular genomes are present along with linear types in the organelles, and in chloroplasts, there are small circular fragments that make up the entire subset of the genome. A recent pattern culminates in seaweed Dinoflagellate, whose chloroplast genome is divided into many small rings, each carrying only one gene. We now find that the mitochondrial genomes of some microbial eukaryotes, such as Paramecium, Chlamydomonas, and the types of yeasts, are always linear.
The number of organelles genome copies is not well defined. Each mitochondrion of a human cell has approximately 10 identical molecules, reaching about 8000 copies per cell, but in
The size of the mitochondrial genome varies and does not depend on the complexity of the organism. Most multicellular organisms have small mitochondrial genomes with a compact genetic organization in which the genes are close together and slightly apart. Most lower eukaryotes, such as
2.2 Genetic content of an organelle genome
The genome of organelles is much smaller than the genome of the cell nucleus, so their gene content is expected to be very limited. In terms of genetic content, the mitochondrial genome shows more diversity. Their gene content varies from five genes in the malaria parasite Plasmodium falciparum to 92 genes in the
In genomes with higher gene content, there are genes for tRNA, ribosomal proteins, and proteins involved in the transcription, translation, and transfer of other proteins from the cell cytoplasm into the mitochondria. Most chloroplast genomes have a similar set of 200 genes or more than encode rRNA, tRNA, ribosomal proteins, and photosynthetic proteins.
An important principle of the endosymbiotic theory is the preservation of organelles genomes. Why have organelles preserved their DNA? John F. Allen’s CoRR hypothesis (co-location for redox regulation) described the best answer to that question: It proposes that organelles have protected genomes to be independent in the expression of the respiratory and photosynthetic electron transport chains elements. This independence is essential to maintain
For the explanation of the redox balance phrase, can be said it refers to the smooth flow of electrons through the electron transport chain in mitochondria and chloroplasts. These two organelles have electron transport chains that generate proton gradients and produce ATP. Quinols and quinones are essential components in both electron transport chains [5].
If the flow of electrons through the inner mitochondrial membrane or the thylakoid as a bioenergetic membrane is disrupted, the steady-state quinol (reduced form of the quinones) concentration increases and the quinols can transfer electrons non-enzymatically to O2 and generate the superoxide radical (O2−), the start point of ROS dissemination. Electron flow disturbance occurs when, downstream components are in insufficient amounts, or upstream components are too active. Without retaining the genome, the electron transport chain and the redox state of the organelle will be abandoned, leading to the destruction of the organelle [6].
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3.1
3.2 Transfer of genetic material between the
3. Why Dunaliella
Given the title of this book, the author intends to clarify the importance and role of adaptation and flexibility of transcription regulation of all proteins encoding proteins in organelles genomes, especially chloroplasts, by focusing on popular microalgae
Easiness of cultivation, diversity of known strains (such as CCAP19/18, CCAP 19/20, and CCAP 19/30) and geographical isolates, lack of disturbing rigid cell wall for DNA extraction, being unicellular and having only one cup shape chloroplast (that means only a plastid genome that facilitates the develop homoplasmic lines of plastid transformants versus multicellular species) and relativity with
Such a large area and habitation in a diverse environment in terms of physical and chemical conditions can only indicate and confirm the fact that “
Environmental changes can include light intensity, temperature, acidity (pH), the amount and concentration of nutrients, the amount of water, salinity, heavy metals, and even the presence of other organisms for which they may appear as pathogens or pests.
Understanding such a variety of physicochemical and biological factors requires highly sensitive and efficient sensors and receivers that can transmit environmental messages to the cell control room scilicet NUCLEUS.
In the next step, the nucleus genome modulates the biosynthesis of some metabolites and overproduces some other metabolites, including glycerol and beta-carotene, by regulating the transcription of specific genes, especially those involved in specific metabolic pathways.
The presence of some protein-coding genes in organelle genomes inevitably regulates their transcription and coordination with the transcription process of nuclear genes. Therefore, the nucleus sends representatives, including transcription factors, to the organelles to control transcription. Each TF is affected by one or more environmental factors. It carries the message to genes that have the corresponding transcription elements and the TF binding site above the initial codon.
One or more TF may be located in the regulatory and promoter region of a gene or gene clusters (some organelles genes, especially in chloroplasts, are operated under the control of a promoter), the result of which can accelerate gene recognition by RNA polymerase and start transcription, or vice versa, prevent the establishment of RNA polymerase in its area and do not allow transcription.
3.1 Dunaliella organellar genome
The
The GC content of the
Coding DNA: 33%(mtDNA) and 34%(ptDNA);
Introns and intronic open reading frames (ORFs): 34%(mtDNA) and 32%(ptDNA);
Intergenic regions: 37%(mtDNA) and 31%(ptDNA).
It is better to know the GC content for the different codon-site positions of the mtDNA and ptDNA protein-coding regions, is approximately.
1st position: 38%(mtDNA) and 42%(ptDNA);
2nd position: 38% (mtDNA) and 52% (ptDNA);
3rd position: 19% (mtDNA) and 13% (ptDNA).
The
3.2 Transfer of genetic material between the Dunaliella chloroplast and nucleus
The CoRR theory seems to explain well the presence of independent genomes of organelles comes from the Endosymbiotic theory. But the grade of independence of organelle genomes has changed over time.
In this way, several genes have been transferred to the nucleus genome, and some have been intelligently conserved in the organelle’s genome. But the same genes located in the organelle’s genome can be controlled and regulated by the nucleus genome.
Numerous regulatory regions and sites can be identified above the origin codon organelle’s genome. Cis-regulatory elements are known to be controllable by organ-specific transcription factors. These transcription factors originate from the nuclear genome and enter the organelle to regulate the transcription of the organelle’s genome.
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4. The importance of collaboration and coordination between
4. The importance of collaboration and coordination between Dunaliella genomes
Nuclear monitoring of chloroplast transcription is essential for harmony. The expression of genes encoded by the chloroplast genome is highly dependent on a wide range of factors of nuclear origin. In turn, these factors regulate the expression of plastid genes in response to various environmental and developmental signals. Regulatory factors are widely present at various stages of plastid gene expression, including transcription, RNA editing, post-transcriptional RNA modification, RNA binding, and translation [15].
The transcription system of prokaryotes is different and simplest than that of eukaryotes. It is believed that the prokaryotic gene transcription features have been hired for genome transcription in chloroplasts. Although, at the plastome whole-genome level, the polycistronic operon transcription model cannot account for all the chloroplast transcription products, especially regarding various RNA isoforms. Analysis of algal and higher plants plastids and cyanobacteria transcriptomes revealed that the entire plastome is transcribed and that this attribute is inherited from prokaryotic cyanobacteria, the ancestor of the chloroplast genomes that separated about 1 billion years ago. A multiple arrangement transcription model was proposed by Shi and Wang that multiple transcription initiations and terminations combine randomly to execute the genome transcription followed by subsequent RNA processing events, which elucidates the full chloroplast genome transcription phenomenon and numerous functional and/or aberrant pre-RNAs [16].
Despite living in eukaryotic host cells for almost one billion years since their coexistence event, plastids still retain their prokaryotic properties. Previous studies have shown that plastids preserved some prokaryotic properties, such as prokaryotic gene promoters and terminators, and clustered transcripts of the gene. At first, it was thought that some chloroplast functional genes are transcribed as polystyrene transcripts and then processed into small, mature RNAs. There are almost 20 large transcription units and most of these areas are not transcribed, such as areas between two transcription units. Under such a polystyrene operon transcription model, plastome genes can be transcribed from intrinsic true promoters and later constituted constant-size transcripts. However, this model cannot consider all transcription products across the genome, including massive plastid-encoded RNA output, gene-like transcription, multiple or multiple alternative promoters and terminators, overlapping isoforms, and gene transcription binding in the same polystyrene. This transcriptional and heterogeneous dynamics suggest that an additional overall transcriptional mechanism causes transcription of the entire plastom.
Transcription of chloroplast genome genes is controlled by various factors of nuclear origin. Primary factors affecting the transcription of genes in the chloroplast genome are NEP and additional and non-nuclear PEP subunits. In a group of additional PEP subunits, additional nuclear-encoded protein factors (PAPs) and transcription initiation factors (sigma factors) can be detected. It is well known that PAPs are essential in transcription regulation, however, some of their exact functions have not been proven.
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5.3.2 Stresses affecting transcription factors of
5. Transcription machine and transcription regulation methods in chloroplasts
Chloroplasts are believed to have emerged as a result of the coexistence of photosynthetic cyanobacteria and the ancestors of modern eukaryotic plant cells following various genomic rearrangements. Compared to the genome of cyanobacteria, which is 3Mpz, the genome of terrestrial chloroplasts is 20 times smaller. Despite such a size difference between the two genomes, the expression of chloroplast genes is regulated by more complex systems than cyanobacterial genes. Most importantly, the expression of chloroplast genes strongly depends on post-transcriptional regulation, which includes polystyrene mRNA processing, intron binding, and RNA editing. Chloroplast genes are transcribed in flowering plants by two types of RNA polymerase. Multi-subunit bacterial species (PEP) RNA is encoded by the chloroplast genome and Phage Polymerase T3/T7 RNA (NEP) is encoded by the nuclear genome. In adult chloroplasts, PEP represents the primary transcription machine, which transcribes more than 80% of the original chloroplast transcripts. NEP, on the other hand, transcribes chloroplast housekeeping genes. NEP is a phage-type RNA polymerase enzyme with a single subunit [15].
Both PEP and NEP are essential for the transcription of chloroplast proteins. Even though NEP and PEP identify different promoters, many chloroplast genes have promoters that are detected by both PEP and NEP. Promoters detected by NEP can be divided into three groups—2,1a, 1b. All promoters belonging to species 1a are identified by a protected nuclear motif called YRTa. Promoters of this type are several nucleotides higher than the transcription initiation sequence. Type 1b promoters, in addition to the protected motif in their structure called the GAAbox, are located between the 18th and 20th nucleotides above the YRTa motif.
Experiments on mutant tobacco have shown an essential role of the GAA motif for proper recognition of the promoter performed by NEP.
In contrast, type 2 promoters all consist of NEP promoters without the YRTa motif. Many promoters have been identified by PEP similar to bacterial G70 promoters and are identified by two motifs of normal sequences spaced from the transcription start site by −10 and −35 nucleotides. The first motif of 10 nucleotides that is farther from the transcription site is the TATAAT sequence. Whereas, the second motif of 35 nucleotides that is farther away from the transcription site is the TTG ACT sequence. Due to the great diversity among plants, the position of conventional sequences of specific PEE promoters may be different. For example, in the barley chloroplast genome, the TATAAT 3–9 nucleotide sequence is located above the transcription start site, while the TTG ACT 15–21 nucleotide sequence is located upstream of the transcription start site.
PEP is mainly responsible for the transcription of chloroplast genes, which are protein products that are related to photosynthesis in various ways. However, some genes encoding proteins involved in photosynthesis are encoded by NEP. There is a small group of chloroplast genes that are not related to photosynthesis and are specifically transcribed by NEP. It includes the ACCD gene encoding acetyl-CoA carboxylase subunit in dicotyledonous plants, RPL23 gene encoding ribosomal protein L23, CLPP gene encoding ATP-dependent proteolytic subunit in monocotyledonous plants, and RPOB gene encoding all major subunits in PE. Therefore, chloroplast genes with their promoters can be divided into three categories, which are as follows:
Transcribed genes only with the participation of NEP.
Genes transcribed only with the participation of PEP.
Genes transcribed with both NEP and PEP.
In the case of dicotyledonous plants where two different NEPs have been detected, an extended portion of the promoters can be suggested. The activity of RPOTp and RPOTmp in tissues is different at different stages of plant development. In
Regulation of transcription of chloroplast genes is essential for the proper functioning of chloroplasts and overall plant growth under normal and adverse conditions.
5.1 RNA polymerase types
It is an enzyme that consists of several subunits. Although most of the genes in the PEP subunit have been transferred to the nuclear genome, the genes encoding the primary and nuclear PEP subunits (α, β, β′, and β′′) have been preserved in the chloroplast genome. One of the main differences between the central subunits of PEP is their molecular weight. The alpha subunit has a molecular weight of 38 kDa, the beta subunit has a molecular weight of 120 kDa, the beta subunit has a molecular weight of 85 kDa, and the beta subunit has a molecular weight of 185 kDa. Similarly, in bacteria and most land plants, the RPOA gene encodes the alpha major subunit and with the ribosomal protein genes, organizes into an operon under the control of the same promoter. In contrast, the RPOC2, RPOC1, and RPOB genes encode the major and central subunits of β, β′, and β′′, respectively, and form a separate operon designated as RPOBC. In addition to the major subunits, PEP is composed of additional protein factors encoded by the nucleus genome, including sigma factors (SIGs) and PAPs, polymerase-related proteins. Sigma chloroplast factors, which are stations for the bacterial transcription initiation factor, play an essential role in the transcription of the chloroplast encoded gene. Sigma factors regulate transcription at different developmental stages by identifying different promoters and allowing a complete set of PEP to begin to polymerize. The highlighted secondary PEP factor appears to be PAPs that are involved in almost every stage of transcription [17].
PEP has a promoter-identifier subunit called the sigma factor. The major PEP enzyme subunits are encoded by a set of genes located in the plastid genome: rpoA, rpoB, rpoC1, and rpoC2. Conversely, during evolution, the sigma factor genes, which specifically provide the promoter needed for PEP, have been transferred to the nucleus genome to possibly allow the nucleus to regulate the expression of the chloroplast gene in response to environmental and developmental signals. PEP and a set of proteins associated with polymerase PAPs constitute a massive protein complex required for transcription. All PAPs are encoded by genes in the nucleus, and most are components of the active pTAC transcription chromosome. These proteins are predicted to be involved in DNA and RNA metabolism, regulate redox from photosynthesis, and protect the PEP complex from reactive oxygen species (ROS).
5.2 Sigma factors
Chloroplasts are the cytoplasmic organs in which photosynthesis takes place in plants and algae. Due to their cyanobacterial strain, chloroplasts contain a small transcriptional active genome and a bacterial gene expression machine.
Sigma factors are separable subunits of bacterial RNA polymerases that ensure effective transcription initiation of gene promoters. Chloroplasts together have a type of bacterial RNA polymerase with a sigma factor subunit due to their prokaryotic origin. The excellent plant
Sigma factors are bacterial RNA polymerase subunits. They are capable of effective transcription of bacterial genes with their three distinct activities—transferring the promoter recognition property to RNA polymerase, melting two strands of the promoter region into single single-stranded open complexes capable of transcription, and interacting with other DNA-binding transcription factors that are regulated for gene expression.
The genome of chloroplasts usually contains 100–300 genes that are mostly organized in polystyrene operons, such as bacteria. Most chloroplast genes contain promoter elements of bacterial types 10 and 35 that are identified and transcribed by a multi-subunit bacterial RNA polymerase. The major subunits of the bacterial RNA polymerase are encoded in the plastid genome and are called PEP. Like bacterial polymerase, the original PEP enzyme requires reversible binding to the sigma factor subunit encoded in the nucleus for effective transcription [18].
Is a single subunit enzyme that performs a single transcription protein; from the identification of the promoter to the end of the process, regardless of the structural pattern of DNA. This enzyme evolved through replication of the mitochondrial RNA polymerase encoding nuclear gene and bears a strong resemblance to phage species RNA polymerase and is also made of a subunit. Three types of NEP are detectable, and all three are encoded by RPOT genes. RPOTp occurs in monocotyledonous plants, while RPOTp and RPOTmp have been identified in dicotyledonous plants. In addition, the third form of the NEP family enzyme, RPOTm, has occurred in mitochondria [17]. In
In flowering plants and mosses, one or more single subunits of phage RNA polymerase, known as NEP, transcribe a small subset of chloroplast genes from distinct promoter elements. Genes transcribed by NEP include rpoB, the PEP beta subunit encoder, and several tRNA genes. Some chloroplast genes include NEP and PEP promoters, which are transcribed by two RNA polymerases at all stages of plastid development and in all plant tissues [18].
Conversely, SIGs (sigma factors) are important for PEP binding to promoters of relevant genes. Six different SIGs are involved in the transcription of
Large-scale prediction and analysis of primary operons in plastids reveal unique genetic features in the evolution of chloroplasts. While bacterial operons have been thoroughly studied, therefore, there is little analysis of chloroplast operons (limited ability to study the basic elements of these structures and apply them to synthetic biology).
Plastids are cellular organelles found mainly in a diverse group of photosynthetic organisms. The endosymbiotic theory explains the origin of plastids (Section 2). Since the beginning of this common evolutionary interaction, most cyanobacterial genes have been lost or transferred horizontally to the host nucleus genome, while the plastid genome has largely retained photosynthesis-related genes and conservative genes. As a result, the plastid is heavily dependent on encoded nuclear proteins for basic operations, making it a non-autonomous organelle. Nevertheless, it retains many of its ancestral characteristics and genomic traits, such as the cyclic structure of the genome, bacterial 70S ribosomes, and PEP or the organization of genes in operon transcription units such as bacteria. Operons are DNA units made up of several genes controlled by a single promoter that often share a common function.
Unlike bacteria, plastid operons are not available in databases and are only examined by a small number of studies focused on higher plant model organisms, in which the entire operon map was revealed in the atmosphere by a differential RNA sequence. In tobacco, part of the polystyrene transcripts was detected using the northern stain. In spinach, psbB and rpoBC operons were detected using Northern blot, while ATP synthase operons were proposed in Escherichia coli by comparing their gene content and ordering their homology to gene clusters.
In algae, part of the operons of
The expression of the plastid gene differs from the bacterial model in terms of different characteristics. Chloroplast transcripts are often edited and bound by RNA. The role of transcription termination is significantly reduced, many noncoding RNAs are replicated repeatedly, and the plastid genome is suggested to be completely transcribed. In addition, gene expression often relies on RNA-binding proteins (Pentatricopeptide repeat family) that bind Cis elements upstream of the starting codon. Thus, it inhibits the activity of exoribonucleases and stimulates translation by suppressing the stem-loop, which inhibits ribosome binding. In addition, polystyrenes are regulated by several promoters and are widely processed, thus contributing to the formation of various transcript isoforms derived from a single primary transcription unit. Thus, the structure of plastid operons has evolved significantly compared to classical bacterial operons. This difference likely affected the composition and properties of chloroplast operons and gave rise to unique properties. Consequently, the ability to convert synthetic and synthetic genes into plastids has had a major impact on plant biotechnology, when it points to significant advantages over nuclear deformation. These benefits include uniform composition based on specific coalition location, no gene silencing, relatively high expression of dissimilar genes, and long-term deformation in most crops due to maternal inheritance.
One obvious advantage specifically for this study is the use of the ability of natural plastids to express polystyrenes and to design vectors with multiple genes under the control of a single promoter, thus minimizing plasmid sizes and allowing the introduction of multiple metabolites to the cells. Associated with transgenes in a single deformation. Because both basic scientific questions and biological ideas are hampered by the lack of extensive information on plastid operons.
5.3 Transcription factors
Transcription factors are proteins that bind to DNA regulatory sequences (amplifiers, suppressors, or extinguishers), which are usually located in the 5′ region of target genes, to adjust the speed of transcription and the number of transcripts. This may lead to enhancing or reducing gene transcription and protein synthesis, consequently altering cell function. There are several families of transcription factors, and members of each family may have common structural characteristics. These families include:
Helix-turn-helix
Helix–loop–helix
Zinc finger
Basic protein-leucine zipper
β-sheet motifs.
Many transcription factors are common to several cell types (ubiquitous), while others are cell-specific and may specify the phenotypic characteristics of a cell. Transcription factors may be activated directly by ligands, such as glucocorticoids and vitamins A and D. Also, stimulation of cell surface receptors launches multiple intracellular signal transduction pathways, including MAPK, PKA, JAK, and PKC that lead to indirect activation of transcription factors. Transcription factors may act as the nucleus messenger and translate transient peripheral signals at the cell surface into long-term changes in gene transcription. Transcription factors may be activated within the nucleus, often with a transcription factor already attached to DNA, or within the cytoplasm, leading to exposure to nuclear localization signals and targeting the nucleus. Phosphorylation, acetylation, and nitration in transcription factors as post-translational changes can affect the DNA binding quality or transcriptional activity [20].
Membrane-transcription factors are transcription factors that are anchored in the membranes in a passive state and are activated by external or internal stimuli. These transcription factors are released from the maternal membranes and transported to the nucleus. Research shows that some proteins attached to the cytoplasmic membrane (PM) and some proteins attached to the endoplasmic reticulum can enter the nucleus. Based on specific signal recognition signals, some transcription factors attached to membrane-bound proteins undergo proteolytic cleavage to release intracellular fragments that enter the nucleus to control gene transcription. In addition, some transcription factors bind to membrane proteins as integral proteins in the cell nucleus through smuggling into the Golgi and endoplasmic reticulum, where membrane-releasing mechanisms rely on endocytosis. In contrast, transcription factors attached to the membrane of the endoplasmic reticulum are transmitted directly to the nucleus or by transfer to the Golgi. In both pathways, only fragments of transcription factors attached to the membrane of the endoplasmic reticulum are transported to the nucleus. Most transcription factors are located in the cytoplasm. After receiving a signal from the transmembrane signal transduction, the transcription factors are activated and transported to the nucleus after the cytoplasm, where they interact with the corresponding DNA framework (cis active elements) [21]. But keep in mind that transcription factors originate from the nucleus and target the promoter of nuclear and chloroplast genes.
Transcription factors are proteins involved in the process of converting DNA to RNA. They contain a large number of proteins, except RNA polymerase, which initiates and regulates gene transcription. One of the hallmarks of transcription factors is that they have DNA-binding domains that give them the ability to bind to specific DNA sequences called amplifier sequences or promoter sequences. Other transcription factors bind to regulatory sequences, such as activating and suppressing sequences, which can stimulate or suppress transcription of the relevant gene [22].
The task of transcription factors is to regulate and turn off genes to ensure that they are expressed in the cell at the right time and in the right amount throughout the life of the cell. The transcription factor group acts in concert to guide cell division, cell growth, and cell death throughout life. Transcription factors are members of the proteome as well as the regulome. Transcription factors alone or with other proteins in a complex act as activators or inhibitors of RNA polymerase affinity to specific genes [23]. They are classified into different classes based on their DNA-binding domains [24].
5.3.1 Family classification of transcription factors belonging to D. salina species
| TF involve in nuclear gene transcription (10 No) | TF involve in chloroplast gene transcription (21 No) |
|---|---|
| RWP-RK, C2C2-CO-like, C2C2-LSD, DDT, TUB, NF-X1, C3H, Whirly, PLATZ, Nin-like. | AP2, ERF, HSF, CSD, B3, WRKY, CPP, MADS box, ARR-B, MYB, MYB-related, C2C2-YABBY, C2C2-GATA, SBP, GARP-G2-like, C2H2, NF-YB, NF-YC, bZIP, Homeodomain, bHLH. |
Table 1.
Out of a total of 31 types of transcription factors related to
In this way can be arranged
| No | TF families | |
|---|---|---|
| 1 | 1. AP2 (APETALA2) 2. ERF (ETHYLENE-RESPONSIVE FACTOR) | AP2/ERF Domain |
| 2 | 3. B3 | B3 DNA-binding Domain |
| 3 | 4. bHLH (Basic Helix–Loop–Helix) | HLH DNA-binding domain |
| 4 | 5. bZIP (Basic Region/Leucine Zipper Motif) | bZIP Domain |
| 5 | 6. C2C2-LSD 7. C2C2-CO-like (CONSTANS LIKE) 8. C2C2-YABBY 9. C2C2-GATA | C2C2 Zinc Finger |
| 6 | 10. C2H2 (Cysteine2Histidine2) | C2H2 Zinc Finger |
| 7 | 11. C3H | CCCH Zinc Finger |
| 8 | 12. CPP (Cysteine-rich Polycomb-Like Protein) | CxC Domain |
| 9 | 13. CSD (Cold Shock Domain) | Cold Shock Domain, β-Sheet |
| 10 | 14. DDT | DDT Zinc Finger (NEW)* |
| 11 | 15. GARP-G2-like (Golden 2-Like) GLKP 16. ARR-B ( | MYB-like DNA Binding Domain |
| 12 | 17. MYB (myeloblastosis Oncogene) 18. MYB-related | MYB-like DNA-binding Domain |
| 13. | 19. HB-other (Homeobox) | Homeodomain (helix-turn-helix) |
| 14 | 20. MADS box (M-type, …) (Maintenance of minichromosome1 Agamous deficiency Serum) | MADS Domain |
| 15 | 21. HSF (Heat Shock Factor) | Heat Shock Domain |
| 16 | 22. NF-X1 | NF-X1 type zinc finger |
| 17 | 23. NF-YB (Nuclear Factor Y Subunit β) 24. NF-YC (Nuclear Factor Y Subunit γ or Gamma) | CCAAT motif, CBF (NF-Y, CP1), HisFold Domain |
| 18 | 25. PLATZ (Plant AT-rich sequence and zinc binding Protein 1) | PLAT zinc binding Domain |
| 19 | 26. RWP-RK 27. Nin-like (Nodule inception) NLP | RWP-RK Domain or RKD |
| 20 | 28. SBP (Squamosa Promoter Binding Protein-like) SPL | SBP Domain |
| 21 | 29. TUB (TUBBY-like) or TUB Bipartite TF | -tubulin, TUB Familyβ |
| 22 | 30. Whirly (Why) ssDNA-binding transcriptional regulator or Protein (TF) | single-stranded DNA-binding Domain |
| 23 | 31. WRKY (WRKY DNA-binding Protein) | WRKY Domain or β-Sheet DBD (ZF-Like) |
Table 2.
Classification of
The GARP transcription factor family (made up of G2-like and ARR-B) (family number 11 in Table 2) has a structural but distant relationship with the MYB transcription factor (family number 12 in Table 2).
The SBP transcription factor family (family number 20 in Table 2) interacts with the C3H transcription factor (family number 7 in Table 2).
Homeobox encodes a DNA helix-turn-helix binding motif called the homeodomain. The second DNA binding is a second independent folded protein that contains at least one structural motif that recognizes dual or single-stranded DNA. A second DNA binding can identify a specific DNA sequence (a recognition sequence) or have a general tendency for DNA [7].
Transcription-activating domains are regions of transcription factors that, in conjunction with a DNA-binding domain, can activate transcription from the promoter by direct contact with the transcription machine (general transcription factor and RNA polymerase) or via other proteins that are known as co-activators. Transcription suppressor domains are regions of transcription factors that, in conjunction with a DNA binding domain, can suppress transcription from the promoter by contact with transcription machines or through other proteins known as Co. repressors.
5.3.2 Stresses affecting transcription factors of D. salina
Plant stress is a condition in which the plant grows in non-ideal conditions, which increases the demand for it. The effects of stress can lead to stunted growth, crop yield, permanent damage, or death if the stress is too much for the plant. Plant stress factors are mainly classified into two main groups: Biotic and abiotic factors. Abiotic factors include various environmental factors that affect plant growth (such as light, water, and temperature), while biotic factors are other organisms that share the environment with plants (such as pathogens, pests, and weeds). Stress response usually involves complex molecular mechanisms, including changes in gene expression and regulatory networks [19].
Stress-responsive transcription factors play a key role in responding to abiotic stresses and stress tolerance [25]. Therefore, these stress-responsive transcription factors may be important targets for product development by increasing abiotic stress tolerance. Plant stress hormones, such as abscisic acid and jasmonic acid, regulate plant abiotic stress responses. The abscisic acid signaling pathways activate target transcription factors. For example, bZIP, ABF, and Jasmonic acid signaling pathways activate MIC bHLH transcription factors. This abscisic acid and jasmonic acid-dependent transcription factors control the expression of stress-responsive genes, as demonstrated by overexpression and deletion systems. In addition, computational and experimental approaches have identified other transcription factors belonging to the WRKY, MYB, AP2/ERF, and NAC families that are not direct components of the abscisic acid and jasmonic acid signaling pathways but are essential to responding plants to Abiotic stress [26].
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6. Conclusion
Plants are constantly exposed to environmental fluctuations, including biotic and abiotic stresses that cause metabolic, morphological, physiological, and molecular changes in plants/algae and all photosynthetic organisms that affect the growth, development, and final production of the plant. In response to these stresses, algae-like plants have evolved various defense systems and have mechanisms to deal with abiotic and biotic stresses. As a result, the stress response in cells begins with perception. Stress clues to living or nonliving factors in cell walls or membranes that are perceived by secondary messengers (such as calcium ions, reactive oxygen species, and hormones) and as intracellular signals. They are transmitted to signal transduction or transduction pathways of downstream signals, such as kinases or phosphatases. Transduction pathways regulate the expression of transcription factors, which in turn modulate the expression of stress-responsive genes in photosynthetic cells.
When a plant is stressed, several adaptive changes occur in plant cells to maintain growth, including over-regulation or under-regulation of various genes. Regulatory proteins act in stress signal transduction by influencing the expression of downstream target genes (functional genes). These regulatory proteins include protein kinases, protein phosphatases, and transcription factors. Transcription factors bind to specific sequences (Cis elements) in the promoter of target genes (stress-related genes), thereby regulating gene expression and affecting biological phenotypes. Transcription factors are key regulatory components of the biotic and abiotic stress signaling pathway.
The chloroplast genome like the nuclear genome is a potential binding site for transcription factors. It can be concluded that environmental stresses affect the regulation of expression and transcription of
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