Stationary‐phase expression and aminoacylation of a transfer‐RNA‐like small RNA

Ataide, Sandro F.; Jester, Brian C.; Devine, Kevin M.; Ibba, Michael

doi:10.1038/sj.embor.7400474

Cited by 19 publications

(34 citation statements)

References 27 publications

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“…Class II LysRS (LysRS2), however, is found in eukaryotes and most bacteria. Most organisms contain one class of LysRS or the other, with the exception of the archaeal group, Methanosarcinaceae , and a few isolated species in other genera, such as Nitrosococcus oceani [185] and Bacillus cereus [186, 187] where both LysRS genes are present [188]. The existence of the same aaRS in two distinct structural classes provides an example of convergent evolution in which divergent mechanisms achieve the same functional goal.…”

Section: Non-canonical Aminoacyl-trna Synthetasesmentioning

confidence: 99%

Emergence and Evolution

Bullwinkle

Ibba

2013

Topics in Current Chemistry

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The aminoacyl-tRNA synthetases (aaRSs) are essential components of the protein synthesis machinery responsible for defining the genetic code by pairing the correct amino acids to their cognate tRNAs. The aaRSs are an ancient enzyme family believed to have origins that may predate the last common ancestor and as such they provide insights into the evolution and development of the extant genetic code. Although the aaRSs have long been viewed as a highly conserved group of enzymes, findings within the last couple of decades have started to demonstrate how diverse and versatile these enzymes really are. Beyond their central role in translation, aaRSs and their numerous homologs have evolved a wide array of alternative functions both inside and outside translation. Current understanding of the emergence of the aaRSs, and their subsequent evolution into a functionally diverse enzyme family, are discussed in this chapter.

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Section: Non-canonical Aminoacyl-trna Synthetasesmentioning

confidence: 99%

Emergence and Evolution

Bullwinkle

Ibba

2013

Topics in Current Chemistry

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“…For this purpose, in vitro-transcribed tRNA Ala and AlaRS from E. coli and in vitro-transcribed tRNA Lys and LysRS from either human or Borrelia burgdorferi were used in an in vitro aminoacyl transferase assay (18). tRNA Lys transcripts from other systems such as E. coli (20) and B. subtilis (21) show minimal activity in vitro and are not suitable for assays of MprF activity. To continuously monitor activity, an excess of AlaRS or LysRS was used to maintain a steady level of aminoacyl-tRNA in the reaction media, allowing the determination of the aminoacylation level of tRNA and PG simultaneously during the time course of the reaction.…”

Section: The Aminoacyl Moiety Is the Primary Determinant For Aminoacymentioning

confidence: 99%

RNA-dependent lipid remodeling by bacterial multiple peptide resistance factors

Roy

Ibba

2008

Proc. Natl. Acad. Sci. U.S.A.

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Multiple peptide resistance (MprF) virulence factors control cellular permeability to cationic antibiotics by aminoacylating inner membrane lipids. It has been shown previously that one class of MprF can use Lys-tRNA Lys to modify phosphatidylglycerol (PG), but the mechanism of recognition and possible role of other MprFs are unknown. Here, we used an in vitro reconstituted lipid aminoacylation system to investigate the two phylogenetically distinct MprF paralogs (MprF1 and MprF2) found in the bacterial pathogen Clostridium perfringens. Although both forms of MprF aminoacylate PG, they do so with different amino acids; MprF1 is specific for Ala-tRNA Ala , and MprF2 utilizes Lys-tRNA Lys . This provides a mechanism by which the cell can fine tune the charge of the inner membrane by using the neutral amino acid alanine, potentially providing resistance to a broader range of antibiotics than offered by lysine modification alone. Mutation of tRNA Ala and tRNA Lys had little effect on either MprF activity, indicating that the aminoacyl moiety is the primary determinant for aminoacyl-tRNA recognition. The lack of discrimination of the tRNA is consistent with the role of MprF as a virulence factor, because species-specific differences in tRNA sequence would not present a barrier to horizontal gene transfer. Taken together, our findings reveal how the MprF proteins provide a potent virulence mechanism by which pathogens can readily acquire resistance to chemically diverse antibiotics.alanine ͉ lysine ͉ tRNA

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“…Immunoblotting was performed as described previously (31) using rabbit polyclonal antibodies raised against yeast cytosolic PheRS (AnimalPharm, Healdsburg, CA). tRNA Trp and tryptophanyl-tRNA synthetase were prepared as described previously (31).…”

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confidence: 99%

Loss of Editing Activity during the Evolution of Mitochondrial Phenylalanyl-tRNA Synthetase

Roy

Ling

Alfonzo

et al. 2005

Journal of Biological Chemistry

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100

104

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Accurate selection of amino acids is essential for faithful translation of the genetic code. Errors during amino acid selection are usually corrected by the editing activity of aminoacyl-tRNA synthetases such as phenylalanyl-tRNA synthetases (PheRS), which edit misactivated tyrosine. Comparison of cytosolic and mitochondrial PheRS from the yeast Saccharomyces cerevisiae suggested that the organellar protein might lack the editing activity. Yeast cytosolic PheRS was found to contain an editing site, which upon disruption abolished both cis and trans editing of Tyr-tRNA Phe . Wild-type mitochondrial PheRS lacked cis and trans editing and could synthesize Tyr-tRNA Phe , an activity enhanced in active site variants with improved tyrosine recognition. Possible trans editing was investigated in isolated mitochondrial extracts, but no such activity was detected. These data indicate that the mitochondrial protein synthesis machinery lacks the tyrosine proofreading activity characteristic of cytosolic translation. This difference between the mitochondria and the cytosol suggests that either organellar protein synthesis quality control is focused on another step or that translation in this compartment is inherently less accurate than in the cytosol.The aminoacyl-tRNA synthetases (aaRS) 2 are a ubiquitous and essential protein family required for protein synthesis (1-3). Structurally and functionally the aaRSs are divided into two unrelated but biochemically analogous groups, class I and class II (4 -6). The aaRSs attach amino acids to the 3Ј-ends of tRNA containing the corresponding anticodon sequence, and the resulting aminoacyl-tRNAs (aa-tRNAs) are used as substrates for ribosomal translation of mRNA. The accuracy of aa-tRNA synthesis is generally assured by the existence of aaRSs specific for each particular amino acid-tRNA pair. Cognate tRNA recognition and discrimination of non-cognate RNAs are achieved by sequencespecific direct and indirect readout of the numerous combinations of bases present in tRNAs (7-10). The relative structural simplicity and inherent similarity between the amino acid substrates makes their accurate recognition and discrimination more challenging. Although some amino acids such as cysteine and tyrosine are different enough to allow their specific recognition by a particular aaRS (11, 12), others such as valine and isoleucine are less easily distinguished. For example the class I aaRS isoleucyl-tRNA synthetase (IleRS) is only able to poorly discriminate against valine, which has a misactivation rate of about 1:200 compared with the cognate substrate isoleucine. Despite this significant rate of misactivation and misaminoacylation, the accuracy of translation is not compromised because of the existence of an intrinsic proofreading and editing mechanism in IleRS that specifically hydrolyzes both misactivated Val-AMP and misaminoacylated Val-tRNA Ile (13,14). In addition to IleRS, many other class I and class II aaRSs also employ editing to prevent release of non-cognate aa-tRNA and subsequent l...

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Stationary‐phase expression and aminoacylation of a transfer‐RNA‐like small RNA

Cited by 19 publications

References 27 publications

Emergence and Evolution

Emergence and Evolution

RNA-dependent lipid remodeling by bacterial multiple peptide resistance factors

Loss of Editing Activity during the Evolution of Mitochondrial Phenylalanyl-tRNA Synthetase

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