Abstract:Glycyl tRNA synthetase (GlyRS) provides a unique case among class II aminoacyl tRNA synthetases, with two clearly widespread types of enzymes: a dimeric (α2) species present in some bacteria, archaea, and eukaryotes; and a heterotetrameric form (α2β2) present in most bacteria. Although the differences between both types of GlyRS at the anticodon binding domain level are evident, the extent and implications of the variations in the catalytic domain have not been described, and it is unclear whether the mechanis… Show more
“…Pfu was selected as an example of an ancient archaea with a similar translation system to LUCA [9]. Separate structural comparisons (structural dendograms) of class I and class II aaRS enzymes have been published [24–26], and our analysis is consistent with these. Surprisingly, however, we identify similarities in protein sequences comparing class I and class II Pfu aaRS enzymes, which, to our knowledge, have not previously been reported (however, see Figure 13 of reference [26]).…”
Section: Resultssupporting
confidence: 53%
“…AaRS enzyme classes are structurally related enzymes for archaea, bacteria and eukaryotes, except for LysRS, which is typically structural class IE in archaea and class IIB in bacteria and eukarya [1,2]. GlyRS is class IIA in archaea and eukaryotes but class IID (or historically classified IIC) in many bacteria [24]. 10.1080/21541264.2018.1467718-f0011Figure 11.An approximate sequence of events for the requirement of different mechanisms for discrimination of tRNA identities by aaRS enzymes and the evolution of ribosome fidelity.…”
The genetic code sectored via tRNA charging errors, and the code progressed toward closure and universality because of evolution of aminoacyl-tRNA synthetase (aaRS) fidelity and translational fidelity mechanisms. Class I and class II aaRS folds are identified as homologs. From sequence alignments, a structurally conserved Zn-binding domain common to class I and class II aaRS was identified. A model for the class I and class II aaRS alternate folding pathways is posited. Five mechanisms toward code closure are highlighted: 1) aaRS proofreading to remove mischarged amino acids from tRNA; 2) accurate aaRS active site specification of amino acid substrates; 3) aaRS-tRNA anticodon recognition; 4) conformational coupling proofreading of the anticodon-codon interaction; and 5) deamination of tRNA wobble adenine to inosine. In tRNA anticodons there is strong wobble sequence preference that results in a broader spectrum of contacts to synonymous mRNA codon wobble bases. Adenine is excluded from the anticodon wobble position of tRNA unless it is modified to inosine. Uracil is generally preferred to cytosine in the tRNA anticodon wobble position. Because of wobble ambiguity when tRNA reads mRNA, the maximal coding capacity of the three nucleotide code read by tRNA is 31 amino acids + stops.
“…Pfu was selected as an example of an ancient archaea with a similar translation system to LUCA [9]. Separate structural comparisons (structural dendograms) of class I and class II aaRS enzymes have been published [24–26], and our analysis is consistent with these. Surprisingly, however, we identify similarities in protein sequences comparing class I and class II Pfu aaRS enzymes, which, to our knowledge, have not previously been reported (however, see Figure 13 of reference [26]).…”
Section: Resultssupporting
confidence: 53%
“…AaRS enzyme classes are structurally related enzymes for archaea, bacteria and eukaryotes, except for LysRS, which is typically structural class IE in archaea and class IIB in bacteria and eukarya [1,2]. GlyRS is class IIA in archaea and eukaryotes but class IID (or historically classified IIC) in many bacteria [24]. 10.1080/21541264.2018.1467718-f0011Figure 11.An approximate sequence of events for the requirement of different mechanisms for discrimination of tRNA identities by aaRS enzymes and the evolution of ribosome fidelity.…”
The genetic code sectored via tRNA charging errors, and the code progressed toward closure and universality because of evolution of aminoacyl-tRNA synthetase (aaRS) fidelity and translational fidelity mechanisms. Class I and class II aaRS folds are identified as homologs. From sequence alignments, a structurally conserved Zn-binding domain common to class I and class II aaRS was identified. A model for the class I and class II aaRS alternate folding pathways is posited. Five mechanisms toward code closure are highlighted: 1) aaRS proofreading to remove mischarged amino acids from tRNA; 2) accurate aaRS active site specification of amino acid substrates; 3) aaRS-tRNA anticodon recognition; 4) conformational coupling proofreading of the anticodon-codon interaction; and 5) deamination of tRNA wobble adenine to inosine. In tRNA anticodons there is strong wobble sequence preference that results in a broader spectrum of contacts to synonymous mRNA codon wobble bases. Adenine is excluded from the anticodon wobble position of tRNA unless it is modified to inosine. Uracil is generally preferred to cytosine in the tRNA anticodon wobble position. Because of wobble ambiguity when tRNA reads mRNA, the maximal coding capacity of the three nucleotide code read by tRNA is 31 amino acids + stops.
“…Among the missing CSCGs (Table S1), the presence of a specific Ile-tRNA with rare UAU anticodon accounts for the loss of the tilS gene responsible for the anticodon U34 modification (55). The glycine-tRNA ligase is probably encoded by glyR, which is a streamlined convergent version of widespread glyS and glyQ (56). Several elements (ftsY, ffh, and secE) for the preprotein translocation were missing and could be replaced by proteins involved in division (57).…”
Protective symbiosis has been reported in many organisms, but the molecular mechanisms of the mutualistic interactions between the symbionts and their hosts are unclear. Here, we sequenced the 424-kbp genome of " Spiroplasma holothuricola," which dominated the hindgut microbiome of a sea cucumber, a major scavenger captured in the Mariana Trench (6,140 m depth). Phylogenetic relationships indicated that the dominant bacterium in the hindgut was derived from a basal group of species. In this organism, the genes responsible for the biosynthesis of amino acids, glycolysis, and sugar transporters were lost, strongly suggesting endosymbiosis. The highly decayed genome consists of two chromosomes and harbors genes coding for proteolysis, microbial toxin, restriction-methylation systems, and clustered regularly interspaced short palindromic repeats (CRISPRs), composed of three genes and 76 CRISPR spacers. The holothurian host is probably protected against invading viruses from sediments by the CRISPRs/Cas and restriction systems of the endosymbiotic spiroplasma. The protective endosymbiosis indicates the important ecological role of the ancient symbiont in the maintenance of hadal ecosystems. Sea cucumbers are major inhabitants in hadal trenches. They collect microbes in surface sediment and remain tolerant against potential pathogenic bacteria and viruses. This study presents the genome of endosymbiotic spiroplasmas in the gut of a sea cucumber captured in the Mariana Trench. The extreme reduction of the genome and loss of essential metabolic pathways strongly support its endosymbiotic lifestyle. Moreover, a considerable part of the genome was occupied by a CRISPR/Cas system to provide immunity against viruses and antimicrobial toxin-encoding genes for the degradation of microbes. This novel species of is probably an important protective symbiont for the sea cucumbers in the hadal zone.
“…Although there is consensus in the division of class II synthetases into 3 subgroups (a, b and c), the classification of class I is more complex, with some authors classifying them into 3 subgroups (Cusack 1995;Ribas de Pouplana and Schimmel 2001b;First 2005) while others propose up to 5 subclasses (Perona and Hadd 2012;Valencia-Sánchez et al 2016). Interesting relations between the aaRSs and their amino acid substrates emerge when considering the grouping into subclasses.…”
Section: 1-classification Of Aminoacyl-trna Synthetasesmentioning
confidence: 99%
“…Another well studied example is recognition of glycine, the smallest amino acid which also lacks a side chain. The GlyRS active site is a highly negatively charged pocket, while one serine residue (eukaryotic) or two threonine residues (bacterial) prevent activation of any other amino acids larger than glycine (Valencia-Sánchez et al 2016). Some aaRSs employ coordinated metal ions in the active site to discriminate the cognate amino acid.…”
Section: Translation Fidelity and Quality Controlmentioning
The aminoacyl-tRNA synthetases are an essential and universally distributed family of enzymes that plays a critical role in protein synthesis, pairing tRNAs with their cognate amino acids for decoding mRNAs according to the genetic code. Synthetases help to ensure accurate translation of the genetic code by using both highly accurate cognate substrate recognition and stringent proofreading of noncognate products. While alterations in the quality control mechanisms of synthetases are generally detrimental to cellular viability, recent studies suggest that in some instances such changes facilitate adaption to stress conditions. Beyond their central role in translation, synthetases are also emerging as key players in an increasing number of other cellular processes, with far-reaching consequences in health and disease. The biochemical versatility of the synthetases has also proven pivotal in efforts to expand the genetic code, further emphasizing the wide-ranging roles of the aminoacyl-tRNA synthetase family in synthetic and natural biology.
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