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![An unusual 5S rRNA insertion. A schematic diagram showing (A) a possible secondary structure of the insert as predicted by mfold [50] and RNAstructure [51] and (B) the usual 5S rRNA secondary structure model (available at RNAcentral (https://rnacentral.org/) and the Comparative RNA Web (CRW) Site( http://www.rna.ccbb.utexas.edu)) [52,53] and modified; the insert is between positions U104 and G105 as per Halococcus morrhuae 5S rRNA numbering. The equivalent positions in Haloarcula marismortui are C108 and G109. What would be the 5′ and 3′ ends of the insert if it were an independent RNA are indicated in (A).](publication/344000520/figure/fig1/AS:11431281180260015@1691545479851/An-unusual-5S-rRNA-insertion-A-schematic-diagram-showing-A-a-possible-secondary.png)
An unusual 5S rRNA insertion. A schematic diagram showing (A) a possible secondary structure of the insert as predicted by mfold [50] and RNAstructure [51] and (B) the usual 5S rRNA secondary structure model (available at RNAcentral (https://rnacentral.org/) and the Comparative RNA Web (CRW) Site( http://www.rna.ccbb.utexas.edu)) [52,53] and modified; the insert is between positions U104 and G105 as per Halococcus morrhuae 5S rRNA numbering. The equivalent positions in Haloarcula marismortui are C108 and G109. What would be the 5′ and 3′ ends of the insert if it were an independent RNA are indicated in (A).
Source publication
The extreme halophile Halococcus morrhuae (ATCC® 17082) contains a 108‐nucleotide insertion in its 5S rRNA. Large rRNA expansions in Archaea are rare. This one almost doubles the length of the 5S rRNA. In order to understand how such an insertion is accommodated in the ribosome, we obtained a cryo‐electron microscopy reconstruction of the native la...
Citations
... In eukaryotes, rRNAs size expansion occurs by virtue of incorporation of additional rRNA sequences, the expansion segments, within the universally conserved prokaryotic-like rRNA core [23,24,61]. These expansion segments are varying in size and composition across eukaryotes [23,24,61,62] and may have originated early on during rRNA evolution, since some progenitors of these expansion segments have been traced within modern archaeal but also in some case in bacterial rRNAs [23][24][25][63][64][65][66]. ...
Ribosomes are universally conserved ribonucleoprotein complexes involved in the decoding of the genetic information contained in messenger RNAs into proteins. Accordingly, ribosome biogenesis is a fundamental cellular process required for functional ribosome homeostasis and to preserve satisfactory gene expression capability. Although the ribosome is universally conserved, its biogenesis shows an intriguing degree of variability across the tree of lifeTree of life. These differences also raise yet unresolved questions. Among them are (a) what are, if existing, the remaining ancestral common principles of ribosome biogenesisRibosome biogenesis; (b) what are the molecular impacts of the evolutionEvolution history and how did they contribute to (re)shape the ribosome biogenesisRibosome biogenesis pathway across the tree of lifeTree of life; (c) what is the extent of functional divergence and/or convergence (functional mimicry), and in the latter case (if existing) what is the molecular basis; (d) considering the universal ribosome conservation, what is the capability of functional plasticityPlasticity and cellular adaptation of the ribosome biogenesisRibosome biogenesis pathway? In this review, we provide a brief overview of ribosome biogenesisRibosome biogenesis across the tree of lifeTree of life and try to illustrate some potential and/or emerging answers to these unresolved questions.
... Ribosomes are universally conserved macromolecules and some of their structural components-the ribosomal RNA (rRNA) and ribosomal proteins (r-proteins)-are commonly used as phylogenetic markers (see below) (Melnikov et al. 2012;Petrov et al. 2014aPetrov et al. , 2014bPetrov et al. , 2015Bowman et al. 2020). Although the ribosome, as a functional entity conducting the translation process, is universally present in any living cell, there are significant structural and compositional variations across and within the main taxonomic lineages: bacteria, archaea, and eukaryotes (Melnikov et al. 2012;Shasmal and Sengupta 2012;Hashem et al. 2013;Ban et al. 2014;Bowman et al. 2020;Penev et al. 2020;Tirumalai et al. 2020;Waltz et al. 2020;Stepanov and Fox 2021;Vicens et al. 2021). Likewise, ribosome biogenesis, the process by which ribosomal subunits are generated, shows substantial differences across, but also within, the main taxonomic groups (Thomson et al. 2013;Henras et al. 2015; Davis and Williamson 2017;Ferreira-Cerca 2017;Baßler and Hurt 2019;Klinge and Woolford 2019;Londei and Ferreira-Cerca 2021). ...
Our understanding of microbial diversity and their evolutionary relationships has increased substantially over the last decade. Such an understanding has been greatly fuelled by culture-independent metagenomics analyses. However, the outcome of some of these studies and their biological and evolutionary implications, like the origin of the eukaryotic lineage from the recently discovered archaeal Asgard phylum, are debated.
The sequences of the ribosomal constituents are amongst the most used phylogenetic markers. However, the functional consequences underlying the analysed sequence diversity and their putative evolutionary implications are essentially not taken into consideration. Here, we propose to exploit additional functional hallmarks of ribosome biogenesis to help disentangle competing evolutionary hypotheses.
Using, selected examples, like the multiple origins of halophily in archaea or the evolutionary relationship between the Asgard Archaea and Eukaryotes, we illustrate and discuss how function-aware phylogenetic framework can contribute to refining our understanding of archaeal phylogeny and the origin of eukaryotic cells.
... Furthermore, in studies on halophilic archaea, ribosome stability is known to be severely affected in low-salt concentration buffers (112,113). However, despite the salt requirement for its stability, the overall basic structure of the ribosome in extreme halophilic archaea, such as H. morrhuae (113) or H. marismortui (114,115), is similar to that found in bacteria. ...
... Furthermore, in studies on halophilic archaea, ribosome stability is known to be severely affected in low-salt concentration buffers (112,113). However, despite the salt requirement for its stability, the overall basic structure of the ribosome in extreme halophilic archaea, such as H. morrhuae (113) or H. marismortui (114,115), is similar to that found in bacteria. The amino acid residues are reported to undergo significant intermolecular segregation along the ribosomal proteins based on their charges. ...
Net positive charge(s) on ribosomal proteins (r-proteins) have been reported to influence the assembly and folding of ribosomes. A high percentage of r-proteins from extremely halophilic archaea are known to be acidic or even negatively charged. Those proteins that remain positively charged are typically far less positively charged. Here, the analysis is extended to non-archaeal halophilic bacteria, eukaryotes, and halotolerant archaea. The net charges (pH 7.4) of the r-proteins that comprise the S10-spc operon/cluster from individual microbial and eukaryotic genomes were estimated and intercompared. It was observed that, as a general rule, the net charges of individual proteins remained mostly basic as the salt tolerance of the bacterial strains increased from 5 to 15%. The most striking exceptions were the extremely halophilic bacterial strains, Salinibacter ruber SD01, Acetohalobium arabaticum DSM 5501 and Selenihalanaerobacter shriftii ATCC BAA-73, which are reported to require a minimum of 18% to 21% salt for their growth. All three strains have higher numbers of acidic S10-spc cluster r-proteins than what is seen in the moderate halophiles or the halotolerant strains. Of the individual proteins, only uL2 never became acidic. uS14 and uL16 also seldom became acidic. The net negative charges on several of the S10-spc cluster r-proteins are a feature generally shared by all extremely halophilic archaea and bacteria. The S10-spc cluster r-proteins of halophilic fungi and algae (eukaryotes) were exceptions: These were positively charged despite the halophilicity of the organisms.
... are characterized by the presence of so-called expansion segments (ES), which are additional RNA elements of various sizes incorporated into the universal prokaryotic rRNA core (Gerbi, 1996;Bowman et al., 2020; Figure 1). These ES increase the size and complexity of the respective rRNAs; however, recent analyses have provided evidence for the presence of such ES in both bacteria and archaea (Armache et al., 2013;Penev et al., 2020;Tirumalai et al., 2020;Stepanov and Fox, 2021). Although most of these sequence additions are limited in size and number (Armache et al., 2013;Penev et al., 2020;Tirumalai et al., 2020;Stepanov and Fox, 2021), larger ES, similar in size to those commonly observed in eukaryotes, have been recently described in the Asgard archaeal phylum , which is proposed to be the cradle of the eukaryotic lineage (Spang et al., 2015;Zaremba-Niedzwiedzka et al., 2017;. ...
... These ES increase the size and complexity of the respective rRNAs; however, recent analyses have provided evidence for the presence of such ES in both bacteria and archaea (Armache et al., 2013;Penev et al., 2020;Tirumalai et al., 2020;Stepanov and Fox, 2021). Although most of these sequence additions are limited in size and number (Armache et al., 2013;Penev et al., 2020;Tirumalai et al., 2020;Stepanov and Fox, 2021), larger ES, similar in size to those commonly observed in eukaryotes, have been recently described in the Asgard archaeal phylum , which is proposed to be the cradle of the eukaryotic lineage (Spang et al., 2015;Zaremba-Niedzwiedzka et al., 2017;. However, a common evolutionary relationshipbased on sequence and/or structure homology-of the larger archaeal and eukaryotic ES could not be established . ...
Making ribosomes is a major cellular process essential for the maintenance of functional ribosome homeostasis and to ensure appropriate gene expression. Strikingly, although ribosomes are universally conserved ribonucleoprotein complexes decoding the genetic information contained in messenger RNAs into proteins, their biogenesis shows an intriguing degree of variability across the tree of life. In this review, we summarize our knowledge on the least understood ribosome biogenesis pathway: the archaeal one. Furthermore, we highlight some evolutionary conserved and divergent molecular features of making ribosomes across the tree of life.
... It does not seem improbable because 5S rRNA is located at the periphery of the ribosome and only partially buried in it. The expansion segments may therefore be rooted in the exposed parts of the 5S rRNA core, and either occupy the nearby cavities or protrude outwards into the surrounding environment (Tirumalai et al. 2020 In order to assess the abundance of the expanded 5S rRNAs in prokaryotes, we have performed a broad screen of 5S rRNA sequence databases and publicly available genome sequences of bacteria and archaea. A number of novel oversized 5S rRNAs have been identified, some of them harboring not just one but two or even three expansion segments. ...
... This insertion was reproducibly observed as an integral part of the only 5S rRNA type present in total RNA pools of several H. morrhuae strains (Nicholson 1982, Luehrsen et al. 1981. It is also visible in a 6.4Å cryo-EM reconstruction of the H. morrhuae ribosome as a density bulge protruding out from the 5S rRNA core (Tirumalai et al. 2020). Another case of valid 5S rRNA expansion is represented by the oversized 5S rRNA species isolated from the large subunit of Th. thermosaccharolyticum ribosome (Sutton and Woese, 1975). ...
The large ribosomal RNAs of eukaryotes frequently contain expansion sequences that add to the size of the rRNAs but do not affect their overall structural layout and are compatible with major ribosomal function as an mRNA translation machine. The expansion of prokaryotic ribosomal RNAs is much less explored. In order to obtain more insight into the structural variability of these conserved molecules, we herein report the results of a comprehensive search for the expansion sequences in prokaryotic 5S rRNAs. Overall, 89 expanded 5S rRNAs of 15 structural types were identified in 15 archaeal and 36 bacterial genomes. Expansion segments ranging in length from 13 to 109 residues were found to be distributed among 17 insertion sites. The strains harboring the expanded 5S rRNAs belong to the bacterial orders Clostridiales, Halanaerobiales, Thermoanaerobacterales, and Alteromonadales as well as the archael order Halobacterales. When several copies of 5S rRNA gene are present in a genome, the expanded versions may co-exist with normal 5S rRNA genes. The insertion sequences are typically capable of forming extended helices, which do not seemingly interfere with folding of the conserved core. The expanded 5S rRNAs have largely been overlooked in 5S rRNA databases.
... Some archaea exhibit short ESs (m-ESs) protruding from the same regions as eukaryotic ESs (Armache et al. 2013). Halococcus morrhuae, a halophilic archaeon, contains a large rRNA insertion in an LSU region that lacks ESs in eukaryotes (Tirumalai et al. 2020). ESs are larger and more numerous on the LSU than on the SSU; across phylogeny, size variation of SSU rRNA is around 10% of that of LSU rRNA (Gutell 1992;Gerbi 1996;Bernier et al. 2018). ...
... The difference in directionality of Ha in Asgard and Eukarya combined with the high evolutionary rates in ESs, and the lack of structural or sequence similarity, implies parallel evolution of ES39 with differential functions. Previous research has shown that archaeal ribosomes can contain m-ESs (Armache et al. 2013;Petrov et al. 2014b) and large ES in a novel LSU region (Tirumalai et al. 2020). It is possible that Last Archaeal and Eukaryotic Common Ancestor (LAECA) had a larger ES39 ( fig. ...
The ribosome's common core, comprised of ribosomal RNA (rRNA) and universal ribosomal proteins, connects all life back to a common ancestor and serves as a window to relationships among organisms. The rRNA of the common core is most similar to rRNA of extant bacteria. In eukaryotes, the rRNA of the common core is decorated by expansion segments (ESs) that vastly increase its size. Supersized ESs have not been observed previously in Archaea, and the origin of eukaryotic ESs remains enigmatic. We discovered that the large subunit (LSU) rRNA of two Asgard phyla, Lokiarchaeota and Heimdallarchaeota, considered to be the closest modern archaeal cell lineages to Eukarya, bridge the gap in size between prokaryotic and eukaryotic LSU rRNA. The elongated LSU rRNAs in Lokiarchaeota and Heimdallarchaeota stem from the presence of two supersized ESs, ES9 and ES39. We applied chemical footprinting experiments to study the structure of Lokiarchaeota ES39. Furthermore, we used covariation and sequence analysis to study the evolution of Asgard ES39s and ES9s. By defining the common eukaryotic ES39 signature fold, we found that Asgard ES39s have more and longer helices than eukaryotic ES39s. While Asgard ES39s have sequences and structures distinct from eukaryotic ES39s, we found overall conservation of a three-way junction across the Asgard species that matches eukaryotic ES39 topology, a result consistent with the accretion model of ribosomal evolution.
... In Eukarya, the rRNA of the common core is elaborated by expansion segments (ES's, Fig. 39 1) (Veldman, et al. 1981;Clark, et al. 1984;Hassouna, et al. 1984;Gonzalez, et al. 1985;Michot 40 and Bachellerie 1987; Bachellerie and Michot 1989;Gutell 1992;Lapeyre, et al. 1993;Gerbi 1996 in eukaryotes (Tirumalai, et al. 2020). Expansion segments are larger and more numerous on the 47 LSU than on the SSU; across phylogeny, size variation of the SSU rRNA is around 10% of that of 48 LSU rRNA (Gutell 1992;Gerbi 1996;Bernier, et al. 2018). ...
The ribosome’s common core, comprised of ribosomal RNA (rRNA) and universal ribosomal proteins, connects all life back to a common ancestor and serves as a window to relationships among organisms. The rRNA of the common core is most similar to rRNA of extant bacteria. In eukaryotes, the rRNA of the common core is decorated by expansion segments (ES’s) that vastly increase its size. Supersized ES’s have not been observed previously in Archaea, and the origin of eukaryotic ES’s remains enigmatic. We discovered that the large subunit (LSU) rRNA of two Asgard phyla, Lokiarchaeota and Heimdallarchaeota, considered to be the closest modern archaeal cell lineages to Eukarya, bridge the gap in size between prokaryotic and eukaryotic LSU rRNA. The elongated LSU rRNAs in Lokiarchaeota and Heimdallarchaeota stem from the presence of two supersized ES’s, ES9 and ES39. We applied chemical footprinting experiments to study the structure of Lokiarchaeota ES39. Furthermore, we used covariation and sequence analysis to study the evolution of Asgard ES39’s and ES9’s. By defining the common eukaryotic ES39 signature fold, we found that Asgard ES39’s have more and longer helices than eukaryotic ES39’s. While Asgard ES39’s have sequences and structures distinct from eukaryotic ES39’s, we found overall conservation of a three-way junction across the Asgard species that matches eukaryotic ES39 topology, a result consistent with the accretion model of ribosomal evolution.
Ribosomes, the molecular machines that are central to protein synthesis, have gradually been gaining prominence for their potential regulatory role in translation. Eukaryotic cytosolic ribosomes are typically larger than the bacterial ones, partly due to multi-nucleotide insertions at specific conserved positions in the ribosomal RNAs (rRNAs). Such insertions called expansion segments (ESs) are present primarily on the ribosomal surface, with their role in translation and its regulation remaining under-explored. One such ES in the ribosomal large subunit (LSU) is ES30L, which is observed mostly in mammals and birds among eukaryotes. In this study, we show that ES30L possesses complementarity to many protein-coding transcripts in humans and that the complementarity is enriched around the start codon, indicating a possible role in translation regulation. Further, our in silico analysis analyses and in vitro pull-down assays show that ES30L may bind to secondary structures in the 5′ UTR of several transcripts and RNA binding proteins (RBPs) that are essential for translation. Thus, we have identified a potential regulatory role for ES30L in translation.
Expansion segments (ESs) are multinucleotide insertions present across phyla at specific conserved positions in eukaryotic rRNAs. ESs are generally absent in bacterial rRNAs with some exceptions, while the archaeal rRNAs have microexpansions at regions that coincide with those of eukaryotic ESs. Although there is an increasing prominence of ribosomes, especially the ribosomal proteins, in fine‐tuning gene expression through translation regulation, the role of rRNA ESs is relatively underexplored. While rRNAs have been established as the major catalytic hub in ribosome function, the presence of ESs widens their scope as a species‐specific regulatory hub of protein synthesis. In this comprehensive review, we have elaborately discussed the current understanding of the functional aspects of rRNA ESs of cytoplasmic eukaryotic ribosomes and discuss their past, present, and future.
This article is categorized under: RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems
Translation > Ribosome Structure/Function
Translation > Regulation
Net positive charge(s) on ribosomal proteins (r-proteins) have been reported to influence the assembly and folding of ribosomes. A high percentage of r-proteins from extremely halophilic archaea are known to be acidic or even negatively charged. Those proteins that remain positively charged are typically far less so. Herein the analysis is extended to the non-archaeal halophilic bacteria, eukaryotes and halotolerant archaea. The net charges (pH 7.4) of r-proteins that comprise the S10-spc operon/cluster from individual microbial and eukaryotic genomes were estimated and intercompared. It was observed that as a general rule, as the salt tolerance of the bacterial strains increased from 5 to 15%, the net charges of the individual proteins remained mostly basic. The most striking exceptions were the extremely halophilic bacterial strains, Salinibacter ruber SD01, Acetohalobium arabaticum DSM 5501 and Selenihalanaerobacter shriftii ATCC BAA-73, which are reported to require a minimum of 18%-21% of salt for their growth. All three strains have a higher number of acidic S10-spc cluster r-proteins than what is seen in the moderate halophiles or the halotolerant strains. Of the individual proteins, only uL2 never became acidic. uS14 and uL16 also seldom became acidic. The net negative charges on several of the S10-spc cluster r-proteins is a feature generally shared by all extremely halophilic archaea and bacteria. The S10-spc cluster r-proteins of halophilic fungi and algae (eukaryotes) were exceptions. They were positively charged despite the halophilicity of the organisms.
Importance
The net charges (at pH 7.4) of the ribosomal proteins (r-proteins) that comprise the S10-spc cluster show an inverse relationship with the halophilicity/halotolerance levels in both bacteria and archaea. In non-halophilic bacteria, the S10-spc cluster r-proteins are generally basic (positively charged), while the rest of the proteomes in these strains are generally acidic. On the other hand, the whole proteomes of the extremely halophilic strains are overall negatively charged including the S10-spc cluster r-proteins. Given that the distribution of charged residues in the ribosome exit tunnel influences co-translational folding, the contrasting charges observed in the S10-spc cluster r-proteins has potential implications for the rate of passage of these proteins through the ribosomal exit tunnel. Furthermore, the universal protein uL2 which lies in the oldest part of the ribosome is always positively charged irrespective of the strain/organism it belongs to. This has implications for its role in the prebiotic context.
