Residue conservation elucidates the evolution of r-proteins in ribosomal assembly and function

Pilla, Smita P.; Bahadur, Ranjit Prasad

doi:10.1016/j.ijbiomac.2019.08.127

Cited by 9 publications

(8 citation statements)

References 47 publications

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“…This suggests that unlike protein‐protein contacts, protein‐RNA contacts can be more permissible to the change in the protein component that will allow the adjustment of the N‐terminus for protease cleavage. Our observation agrees with the study of sequence conservation of ribosomal proteins that revealed that amino acids on the protein‐RNA interfaces are indeed less conserved than amino acids on the protein‐protein interfaces (Pilla & Bahadur, 2019 ). Supposedly, RNA‐protein interfaces are the most ancient and important for ribosome assembly, so their smaller conservation compared with protein‐protein interfaces might seem counterintuitive (Fox, 2010 ).…”

Section: Discussionsupporting

confidence: 92%

Widespread use of unconventional targeting signals in mitochondrial ribosome proteins

et al. 2021

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Mitochondrial ribosomes are complex molecular machines indispensable for respiration. Their assembly involves the import of several dozens of mitochondrial ribosomal proteins (MRPs), encoded in the nuclear genome, into the mitochondrial matrix. Proteomic and structural data as well as computational predictions indicate that up to 25% of yeast MRPs do not have a conventional N-terminal mitochondrial targeting signal (MTS). We experimentally characterized a set of 15 yeast MRPs in vivo and found that five use internal MTSs. Further analysis of a conserved model MRP, Mrp17/bS6m, revealed the identity of the internal targeting signal. Similar to conventional MTS-containing proteins, the internal sequence mediates binding to TOM complexes. The entire sequence of Mrp17 contains positive charges mediating translocation. The fact that these sequence properties could not be reliably predicted by standard methods shows that mitochondrial protein targeting is more versatile than expected. We hypothesize that structural constraints imposed by ribosome assembly interfaces may have disfavored N-terminal presequences and driven the evolution of internal targeting signals in MRPs.

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Section: Discussionsupporting

confidence: 92%

Widespread use of unconventional targeting signals in mitochondrial ribosome proteins

et al. 2021

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“…This suggests that unlike protein-protein contacts, protein-RNA contacts can be more permissible to the change in the protein component that will allow the adjustment of the Nterminus for protease cleavage. Our observation agrees with the study of sequence conservation of ribosomal proteins that revealed that amino acids on the protein-RNA interfaces are indeed less conserved than the amino acids on the protein-protein interfaces (Pilla and Bahadur, 2019). Supposedly, RNA-protein interfaces are the most ancient and important for ribosome assembly, so their smaller conservation compared to protein-protein interfaces might seem counterintuitive (Fox, 2010).…”

Section: Discussionsupporting

confidence: 89%

Mitochondrial ribosomal proteins developed unconventional mitochondrial targeting signals due to structural constraints

Bykov

Flohr

Boos

et al. 2021

Preprint

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Mitochondrial ribosomes are complex molecular machines indispensable for respiration. Their assembly involves the import of several dozens of mitochondrial ribosomal proteins (MRPs), encoded in the nuclear genome, into the mitochondrial matrix. Available proteomic and structural data as well as computational predictions indicate that up to 25% of MRPs do not have a conventional N-terminal mitochondrial targeting signal (MTS). We characterized a set of 15 yeast MRPs in vivo and showed that 30% of them use internal mitochondrial targeting signals. We isolated a novel internal targeting signal from the conserved MRP Mrp17 (bS6). The Mrp17 targeting signal shares some properties as well as import components with conventional MTS-containing proteins but is not reliably predicted indicating that mitochondrial protein targeting is more versatile than expected. We hypothesize that internal targeting signals arose in MRPs when the N-terminus extension was constrained by ribosome assembly interfaces.

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“…The discovery of specific signatures of the evolution of bacterial ribosomes may provide a new insight at the emergence and evolution of not only the protein component of ribosomes, but also the evolution of bacteria 1‐5 . The family of ribosomal S1 proteins is a unique family of proteins characterized by a different number of S1 structural domains, each of which has a number of specific characteristics 6,7 .…”

Section: Introductionmentioning

confidence: 99%

Sequence and evolutionary analysis of bacterial ribosomal S1 proteins

et al. 2021

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The multi‐domain bacterial S1 protein is the largest and most functionally important ribosomal protein of the 30S subunit, which interacts with both mRNA and proteins. The family of ribosomal S1 proteins differs in the classical sense from a protein with tandem repeats and has a “bead‐on‐string” organization, where each repeat is folded into a globular domain. Based on our recent data, the study of evolutionary relationships for the bacterial phyla will provide evidence for one of the proposed theories of the evolutionary development of proteins with structural repeats: from multiple repeats of assembles to single repeats, or vice versa. In this comparative analysis of 1333 S1 sequences that were identified in 24 different phyla, we demonstrate how such phyla can form independently/dependently during evolution. To the best of our knowledge, this work is the first study of the evolutionary history of bacterial ribosomal S1 proteins. The collected and structured data can be useful to computer biologists as a resource for determining percent identity, amino acid composition and logo motifs, as well as dN/dS ratio in bacterial S1 protein. The obtained research data indicate that the evolutionary development of bacterial ribosomal S1 proteins evolved from multiple assemblies to single repeat. The presented data are integrated into the server, which can be accessed at http://oka.protres.ru:4200.

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Residue conservation elucidates the evolution of r-proteins in ribosomal assembly and function

Cited by 9 publications

References 47 publications

Widespread use of unconventional targeting signals in mitochondrial ribosome proteins

Widespread use of unconventional targeting signals in mitochondrial ribosome proteins

Mitochondrial ribosomal proteins developed unconventional mitochondrial targeting signals due to structural constraints

Sequence and evolutionary analysis of bacterial ribosomal S1 proteins

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