1. Introduction
Telomeres are essential nucleoprotein structures at the ends of eukaryotic chromosomes. They play several essential roles preserving genome stability and function, including distinguishing chromosome ends from DNA double stranded breaks (DSBs) and maintenance of chromosome length. Due to the inability of conventional DNA polymerases to replicate the very end of a chromosome, sometimes known as the end replication problem, chromosome ends shorten with every round of DNA replication. In the absence of special telomere maintenance mechanisms this telomere shortening leads to replicative senescence and apoptosis. Several telomere maintenance mechanisms have been identified; these are reflected in several known types of telomeres. In most eukaryotes telomeres comprise a tandem array of a short, 5-8 bp, well conserved repeat unit, and telomere length is maintained by telomerase, a specialized reverse transcriptase that carries its own RNA template and adds telomeric sequences onto chromosome ends [1]. Nevertheless, in some organisms the array of short telomeric sequence motifs has been replaced with less conventional sequences, such as satellite sequences or transposable elements. The telomeres of such organisms are maintained through homologous recombination or through transposition of the mobile elements [2,3]. These different telomere types present distinct difficulties for chromosome end protection. Telomeres maintained by telomerase are protected by a proteinaceous telomere cap, termed shelterin, that recognizes chromosome ends in a DNA sequence specific manner, while telomeres with long terminal repeat units are protected by a cap, termed terminin, that binds to chromosome ends independently of DNA sequence.
2. The structure of telomeric DNA: “usual” and “unusual” telomeres
The most common telomere structure found across the whole eukaryotic tree is a simple telomeric repeat of the form (TxAyGz)n generated by telomerase. For example, the sequence in unikonts generally, including animals, fungi and amoebozoa, is T2AG3, while in most plants and green algae it is T3AG3. Within these broad generalizations, however, there are exceptions. Some species seem to have lost the canonical telomeric motif altogether. We will mention a few examples here, then describe one of these examples in more detail.
2.1. Chromalveolata
The terminal sequence motif seems to be quite variable among the Chromalveolates, while still adhering to the consensus telomeric motif (Figure 1). Apicomplexa species use three different motifs [4-6], and ciliates use two [4,7]. Dinoflagellates use T3AG3 [8], similar to plants and green algae, while diatoms use T2AG3 [9], similar to unikonts. Photosynthetic species in the Chromalveolates are derived from the engulfment of a red alga. The resulting nucleomorphs retain the algal linear chromosomes and telomeres that are very different. The cryptomonad,
It seems likely that the telomere binding proteins in these organisms are either different in the two intracellular bodies, or do not bind in a DNA sequence specific manner.
2.2. Plantae
Among the Plantae, land plants and green algae mostly use T3AG3 as a telomeric motif, while the red algae have a very different sequence at their chromosome ends. The red alga
Similarly, while most land plants retain the canonical T3AG3 telomeric motif, telomeres in a few orders differ from this structure. Within the monocot order Asparagales some species of Alliaceae have switched to the sequence T2AG3, and others appear to have lost the canonical telomeric sequence completely. It has been proposed that the telomeres of these latter Alliaceae species are maintained through transposition of mobile elements or through homologous recombination between the satellite sequences [15,16]. In the eudicot order Solanales the canonical telomeric motif as well as telomerase are absent from several genera of the family Solanaceae [17-20]. The actual telomeric sequence and compensation mechanism in this group of plants, however, remain unknown.
2.3. Unikonta
The T2AG3 telomeric sequence is found widely among the unikonts (Figure 1). While this is generally true within the fungi, representatives of two classes, Schizosaccharomycetes and Saccharomycetes, use variable, degenerate telomeric sequences that may result from replication infidelity or slippage [12]. In
Similarly, T2AG3 is found widely at chromosome ends among metazoans. The animal phylum Arthropoda, however, uses the sequence T2AG2 at telomeres, and its sister phylum Tardigrada lacks both of these telomeric motifs [21]. Insects are the largest class of arthropods, and even here individual insect taxa may have different forms of the canonical sequence or even unrelated telomeric sequences. Insects seem to have lost the canonical arthropod telomeric motif several times [22,23]. In some cases, such as the coleopteran superfamily Tenebrionoidea, the arthropod repeat has been replaced by a similar motif, in this case TCAG2 [24], while in many other instances the new telomeric DNA sequence has not been identified.
Insects of the orders Diptera, Mecoptera and Siphonaptera (superorder Antliophora) do not carry a canonical telomeric DNA sequence at their chromosome ends [23,25]; nor do they have a telomerase gene [26], indicating that telomerase was lost some 260-280 Mya. Even so, Diptera is one of the most successful insect orders, with some 152,000 species [27]. This suggests that telomerase and the canonical telomeric DNA sequences generated by telomerase,
Long satellite sequences have been reported in nematoceran species. Chromosome tips of several
Telomere structures have only been examined in a single brachyceran genus,
Human telomeres have been shown to form a large terminal loop dependent on the presence of a 3' G strand overhang at the telomeric end. This 3' end is tucked back into the double-stranded DNA as a loop, termed a t-loop [42]. Similar t-loops may also be formed in yeast [43].
3. Proteins associated with telomeres
The telomere cap, a multiprotein structure at chromosome end ensuring stability and integrity of the genome, was revealed by early cytological observations of chromosomal rearrangements after exposure to ionizing radiation [44]. The telomere cap allows cells to distinguish their natural chromosome ends from DSBs, thus protecting the chromosome termini from inadvertent DNA damage response (DDR) activities. Defects in the cap, or DSBs elsewhere in the genome, lead to activation of cell cycle checkpoints followed by DDR mechanisms. A consequence of inappropriate DSB repair are end-to-end fusions of chromosomes, i.e. formation of ring chromosomes or dicentric linear chromosomes, followed by chromosome breakage, which results in genomic instability and loss of cellular viability [45,46]. Although, in this context, telomeres perform the same essential function across phyla, cap proteins of diverse organisms are less conserved that one might expect. Even within a single taxonomic class, such as mammals, telomeric proteins display less conservation than other chromosomal proteins [47]. In mammals the telomere-specific cap complex has been termed ‘shelterin’ (Figure 2). The six-protein complex is formed by double-stranded TTAGG repeat-binding proteins TRF1 and TRF2, which recruit TIN2 and TPP1. The latter proteins make a bridge between the TRF proteins and G-overhang-binding protein, POT1. The sixth protein is the TRF2-interacting protein RAP1 [46,48,49]. A characteristic of shelterin proteins is specific and exclusive association with telomeric DNA, where they are permanently present throughout the cell cycle and serve as platform for a transient and dynamic recruitment of a number of telomere-associated factors, referred to as non-shelterin telomeric proteins. These non-shelterin proteins are required for telomere protection and replication but also have numerous nontelomeric functions. Examples include DDR proteins that are commonly involved in DSB repair through nonhomologous end joining (NHEJ) or homologous recombination (HR), such as ATM, ATR and Ku70/80, which associate with TRF1 and TRF2, and the MRN complex, composed of the MRE11, RAD50 and NBS1 (MRN) proteins, which associates with TRF2 [50-55]. Another protein associated with TRF2 is Apollo, an exonuclease important for recreating the 3' overhang [51,56]. The binding of shelterin proteins and formation of a functional cap require a terminal DNA array of specific sequence and of satisfactory length.
Analysis of deleterious events at shelterin-free telomeres revealed six pathways for end protection [57]. The primery protection by shelterin is against classical NHEJ and unwanted activation of ATM and ATR signaling. Additionally, shelterin provides a defense against alternate NHEJ, HR and 5' end resection. Another protective layer is achieved through the Ku70/80 heterodimer or 53BP1. 53BP1 minimizes resection but only at telomeres eliciting a DNA damage signal. Ku70/80 blocks alternate NHEJ and HR at telomeres independent of a DNA damage signal [57].
Telomeres in
A multiprotein capping complex in
As there is no specific telomeric DNA sequence in Drosophila, terminin binding to telomeric DNA is sequence-independent, which makes a substantial difference between mammalian and Drosophila telomeres. In contrast to mammals, the complete loss of a Drosophila telomere does not definitely mean inescapable damage to genome stability and cell death, because under the right circumstances the telomere cap can be formed
Similar to shelterin, terminin presents a docking site for binding of additional proteins, called non-terminin capping proteins. Although not exclusively located at telomeres and having some telomere-unrelated functions, these proteins are required for the capping function and, in many cases, facilitate terminin assembly. There are several known non-terminin proteins; most of them were identified because their mutants display frequent telomeric fusions [61]. The best characterized is HP1a that is encoded by
A highly condensed chromatin structure is a common characteristic of telomeres from yeast to man. Usually telomeres are heterochromatic, and the heterochromatic properties are thought to play an important role in telomeric function [75-77]. Telomeric chromatin is the source of telomeric position effect (TPE), a silencing of transgenes inserted into telomeres or their vicinity [78]. Besides the cap region,
4. Telomeric replication and its difficulties
Based on DNA and protein composition, telomeres are typical heterochromatin, so their replication should correspond with a common paradigm of late heterochromatin replication. Based on early microscopic studies, it is generally accepted that DNA replication at early stages of S phase is associated with expressed genes, whereas repressed tissue-specific genes or heterochromatic regions are replicated during the late stages of replication [82-84]. The late replication seems to be common, but definitely is not universal [85]. Replication of human telomeres takes place throughout S phase, and specific telomeres tend to replicate at defined stages, some replicating early and others late [86]. The pattern of replication timing seems to be conserved between homologous chromosomes and does not vary between cells of different individuals. Although no correlation was found with telomere length or telomerase activity, a strong association was observed with nuclear localization. Late-replicating telomeres show a preferential association with the nuclear periphery, while early-replicating telomeres are preferentially located near the nuclear center [86]. A different situation was found in budding yeast,
Because of the repetitive nature of telomeric DNA, telomeres present a significant problem for their replication. Spontaneous replication fork regression in telomeric DNA
In yeast, the replication of telomeres is initiated in subtelomeric regions, and the replication fork moves towards the chromosome termini [96]. In mammalian cells, the origin of telomeric replication and direction is ambiguous.
After the replication fork reaches the chromosome terminus, the lagging strand gains a 3' overhang due to the removal of the primer for the terminal Okazaki fragment. At the same time C-strand specific resection occurs by nucleases Exo1 and/or Dna2 to produce a G-overhang on the leading strand [89]. If active, telomerase elongates the G-overhangs by addition of new telomeric repeats. Telomerase action is followed by complementary C-strand synthesis by DNA pol α. The process is terminated by additional processing to remove the RNA primer and to leave a 40-400 nucleotide G-overhang. The timing of the events differs between species. In human cells, telomere replication occurs at the same time as telomerase-mediated extension, and fill-in synthesis of C- strand is delayed until S/G2. Budding yeast shows tight coupling between G-strand extension and C-strand synthesis [89,91].
5. The mechanisms of telomeric elongation and their regulation
Telomerase is a ribonucleoprotein reverse transcriptase that utilizes its protein subunit (TERT in mammals, Est2p in
Telomerase is regulated through genetic, epigenetic and environmental factors: TERT and TR transcription, posttranscriptional and posttranslational modifications of TERT, and telomerase recruitment and processivity [104]. TERT promoter activity has been studied extensively, and numerous transcription factors have been found to interact with TERT. TERT transcription is, for instance, activated by the oncogene c-Myc and suppressed by the tumor-suppressor WT1 (Wilm’s tumor suppresor). Misregulation of TERT through the c-Myc or WT1 pathways is associated with telomerase reactivation in cancer cells [107,108]. Although transcription of TERT is the major determinant of telomerase activity, TERT transcript levels do not always correlate with enzyme activity. Posttranslational phosphorylation may regulate telomerase activity, as may telomerase degradation through ubiquitination, as the half-life of telomerase activity was approximately 24 hours [109]. In human cells the POT1-TPP1 complex was found to be a key regulator of telomerase processivity [110-113].
Little is known about the regulation of telomere length in
Telomere length is maintained through an interplay between telomere maintenance mechanisms and telomere shortening events. Based on human research it has been proposed that telomerase activity and telomere length are modulated by different endogenous and exogenous factors, such as emotional or physical stress, health conditions and aging [102]. However, the prime factor in telomeric shortening may well be oxidative stress. Due to a high content of guanines, telomeres are particularly vulnerable to oxidative damage, and the impact of oxidative stress on telomeric length has been proposed to be much larger than the end-replication problem [122]. Endogenous oxidative stress is associated with several cellular processes, such as the mitochondrial OXPHOS system and inflammation. Mitochondrial dysfunction-induced reactive oxygen species and hyperoxia
6. Conclusion
The ends of all linear chromosomes face the same difficulties regardless of their structures. Chromosome ends are not replicated completely by the standard replication machinery, resulting in loss of sequence and a 3' overhang on half of the replication products. Early eukaryotes may have solved the end replication problem by co-opting a reverse transcriptase that had arisen in a retrotransposable element [124] and using it to generate arrays of a simple repeat unit. They then solved the end protection problem by engineering long 3' overhangs on all termini, which could then loop around and tuck into the double stranded telomeric region and coating the terminal arrays with proteins that recognize the product of the reverse transcriptase. This combination of telomere maintenance by telomerase and protection by CST/shelterin served eukaryotes well and has been amazingly stable for more than a billion years.
Depending on how strictly shelterin recognizes the telomeric motif, the sequence may be conserved over long expanses of time, as in unikonts. If shelterin is less strict in recognizing the telomerase-generated motif, this sequence may have more latitude to vary, as in chromalveolates. If the protective telomere cap completely loses its ability to recognize the telomeric sequence, telomerase and the canonical telomeric motif may be lost. Many eukaryotes, including yeast and humans use unequal homologous recombination/gene conversion as a backup telomere maintenance system. It appears that in some species of plants and animals telomerase has been lost, and gene conversion has taken over as the primary mechanism to maintain chromosome length, with the eventual loss of telomeric motif. Chromosome length maintenance and end protection must be maintained through all of this. The evolution of new telomere structures, therefore, requires a delicate interplay between these two functions, as well as other telomeric functions that may be less well understood, such as heterochromatin formation and meiotic chromosome pairing.
Acknowledgments
The authors were supported in part by the Intramural Research Program, NIEHS, U. S. National Institutes of Health and by grant no. GAČR P501/10/1215 (Grant Agency of the Czech Republic, Prague).
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