Cryo‐electron microscopy visualization of a large insertion in the 5S ribosomal RNA of the extremely halophilic archaeon <i>Halococcus morrhuae</i>

Tirumalai, Madhan R.; Kaelber, Jason T.; Park, Donghyun R; Tran, Quyen; Fox, George E.

doi:10.1002/2211-5463.12962

Cited by 9 publications

(6 citation statements)

References 70 publications

(103 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…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 (Penev et al, 2020), which is proposed to be the cradle of the eukaryotic lineage (Spang et al, 2015;Zaremba-Niedzwiedzka et al, 2017;.…”

Section: Ribosomal Subunit Composition: Archaeal Specificity and Common Featuresmentioning

confidence: 99%

“…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 (Penev et al, 2020), 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 (Penev et al, 2020).…”

Section: Ribosomal Subunit Composition: Archaeal Specificity and Common Featuresmentioning

confidence: 99%

See 1 more Smart Citation

Ribosome Biogenesis in Archaea

Londei

Ferreira-Cerca

2021

Front. Microbiol.

View full text Add to dashboard Cite

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.

show abstract

Section: Ribosomal Subunit Composition: Archaeal Specificity and Common Featuresmentioning

confidence: 99%

Section: Ribosomal Subunit Composition: Archaeal Specificity and Common Featuresmentioning

confidence: 99%

Ribosome Biogenesis in Archaea

Londei

Ferreira-Cerca

2021

Front. Microbiol.

View full text Add to dashboard Cite

show abstract

“…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.…”

Section: Discussionmentioning

confidence: 99%

Net Charges of the Ribosomal Proteins of the S10 and spc Clusters of Halophiles Are Inversely Related to the Degree of Halotolerance

Tirumalai

Anane-Bediakoh

Rajesh³

et al. 2021

Microbiol Spectr

Self Cite

View full text Add to dashboard Cite

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.

show abstract

“…Furthermore, in studies on halophilic archaea, the stability of ribosomes is known to be severely affected at low-salt concentration buffers (115,116). However, despite the salt requirement for its stability, the overall basic structure of the ribosome from extreme halophilic archaea such as H. morrhuae (116) or H. marismortui (117,118), is similar to those found in bacteria. The amino acid residues are reported to undergo significant intermolecular segregation along the ribosomal proteins, based on their charges.…”

Section: Implications Of Net Charges On Translational Rate(s) and Ribosome Stabilitymentioning

confidence: 96%

Net charges of the ribosomal proteins of theS10andspcclusters of halophiles are inversely related to the degree of halotolerance

Tirumalai

Anane-Bediakoh

Rajesh³

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

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.ImportanceThe 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.

show abstract

Cryo‐electron microscopy visualization of a large insertion in the 5S ribosomal RNA of the extremely halophilic archaeon Halococcus morrhuae

Cited by 9 publications

References 70 publications

Ribosome Biogenesis in Archaea

Ribosome Biogenesis in Archaea

Net Charges of the Ribosomal Proteins of the S10 and spc Clusters of Halophiles Are Inversely Related to the Degree of Halotolerance

Net charges of the ribosomal proteins of theS10andspcclusters of halophiles are inversely related to the degree of halotolerance

Contact Info

Product

Resources

About