Aminoacyl-tRNA Synthesis: A Postgenomic Perspective

Stathopoulos, Constantinos; Ahel, Ivan; Ali, K.; Ambrogelly, Alex; Becker, Hubert Dominique; Bunjun, Shipra; Feng, Liang; Herring, Stephanie C.; Jacquin-Becker, Clarisse; Kobayashi, Hiroyuki; Korenčić, Dragana; Krett, Bethany; Mejlhede, Nina; Min, Bokkee; Nakano, Hiroaki; Namgoong, Suk; Polycarpo, Carla; Raczniak, Gregory; Rinehart, Jesse; Rosas-Sandoval, Guillermina; Ruan, Benfang; Sabina, Jeffrey; Sauerwald, Anselm; Toogood, Helen S.; Hansen, Debra T.; Ibba, Michael; Söll, Dieter

doi:10.1101/sqb.2001.66.175

Cited by 5 publications

(6 citation statements)

References 17 publications

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“…The accuracy of the AARS enzymes is essential for correct translation of the genetic code. Most bacteria differ from the E. coli model of tRNA aminoacylation for asparagine, glutamine, cysteine, proline, and lysine (26,27). The sequencing of numerous genomes verified the absence of the regular glutaminyl and asparginyl AARSs (Table 4 and supporting information in Table 10).…”

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confidence: 99%

“…Subsequently, the correct charging of both asn-tRNA asn and gln-tRNA gln occurs by comparable transamidation reactions compensating for the lack of AsnRS and GlnRS function, respectively (26,27). Strikingly, the five ␦-proteobacterial genomes include asnS and glnS as well as the genes for the GatCAB amidotransferase complex ( Table 4).…”

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confidence: 99%

“…AARS representations in ␥-proteobacterial genomes are variable, with most in possession of the cognate AARS for every amino acid but not in Pseudomonas genomes (ref. 26 and Table 4). The five ␦ genomes possess the regular AARS for each amino acid (Table 10), including two gene copies for GluRS in MYXXA and DESVU; two gene copies for LysRS in MYXXA, BDEBA, GEOSU, and DESPS; two gene copies for ThrRS in MYXXA and BDEBA; and two gene copies for LeuRS in MYXXA.…”

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Distinguishing features of δ-proteobacterial genomes

Karlin¹,

Brocchieri²,

Mrázek

et al. 2006

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

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We analyzed several features of five currently available ␦-proteobacterial genomes, including two aerobic bacteria exhibiting predatory behavior and three anaerobic sulfate-reducing bacteria. The ␦ genomes are distinguished from other bacteria by several properties: (i) The ␦ genomes contain two ''giant'' S1 ribosomal protein genes in contrast to all other bacterial types, which encode a single or no S1; (ii) in most ␦-proteobacterial genomes the major ribosomal protein (RP) gene cluster is near the replication terminus whereas most bacterial genomes place the major RP cluster near the origin of replication; (iii) the ␦ genomes possess the rare combination of discriminating asparaginyl and glutaminyl tRNA synthetase (AARS) together with the amidotransferase complex (Gat CAB) genes that modify Asp-tRNA Asn into Asn-tRNA Asn and Glu-tRNA Gln into Gln-tRNA Gln ; (iv) the TonB receptors and ferric siderophore receptors that facilitate uptake and removal of complex metals are common among ␦ genomes; (v) the anaerobic ␦ genomes encode multiple copies of the anaerobic detoxification protein rubrerythrin that can neutralize hydrogen peroxide; and (vi) 54

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confidence: 99%

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Distinguishing features of δ-proteobacterial genomes

Karlin¹,

Brocchieri²,

Mrázek

et al. 2006

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

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“…Deviations from the adaptor hypothesis arise because some organisms possess fewer than the requisite 20 aaRSs for the 20 standard amino acids, whereas others possess apparent duplications (8,9). The ability of many taxa in the archaea and the bacteria to survive on as few as 16 of the 20 canonical enzymes is the result of their ability to synthesize amino acids by using ''indirect'' pathways.…”

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tRNA synthetase paralogs: Evolutionary links in the transition from tRNA-dependent amino acid biosynthesis to de novo biosynthesis

Francklyn

2003

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

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“…This difference had been previously proposed to be due to the loss of non-essential regions of the sequence (Ibba and Soll 2001). The distinction between the two gene types was also illustrated by the mean of K values.…”

Section: Red Model Vii: Ancient Divergence-tyrosyl-trna Synthetasementioning

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Biochemistry and genetics of autotrophy in Methanococcus

Whitman¹

2009

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An acetate-requiring mutant of Methanococcus maripaludis allowed efficient labeling of riboses following growth in minimal medium supplemented with [2-13 C]acetate. Nuclear magnetic resonance and mass spectroscopic analysis of purified cytidine and uridine demonstrated that the C-1 of the ribose was about 67% enriched for 13 C. This value was inconsistent with the formation of erythrose 4-phosphate (E4P) exclusively by the carboxylation of a triose. Instead, these results suggest that either (i) E4P is formed by both the nonoxidative pentose phosphate and triose carboxylation pathways or (ii) E4P is formed exclusively by the nonoxidative pentose phosphate pathway and is not a precursor of aromatic amino acids.The pentose phosphate pathway provides pentoses for nucleosides and erythrose 4-phosphate (E4P) for aromatic amino acids (AroAAs) (8, 21). In most methanogens, pentoses are formed by the oxidative pentose phosphate pathway by oxidative decarboxylation of hexoses (2,(4)(5)(6). Because extracts of Methanococcus maripaludis contained high activities for transketolase and transaldolase and lacked detectable glucose-6-phosphate and 6-phosphogluconate dehydrogenase activities, Yu et al. proposed that this organism formed pentoses by a nonoxidative pentose phosphate (NOPP) pathway (Fig. 1a) (22). Subsequent labeling studies with Methanococcus voltae and Methanococcus jannaschii confirmed some aspects of this proposed pathway (2). However, in the methanococci as well as in Methanobacterium thermoautotrophicum, Methanosphaera stadtmaniae, Methanobrevibacter smithii, and Methanospirillum hungatei, phenylalanine and tyrosine were preferentially enriched at the C-7 atom (and not at both the C-7 and C-8 atoms) following labeling with [1-13 C]pyruvate (2, 5). This pattern was not consistent with the formation of these amino acids by E4P formed by the NOPP. Thus, it was proposed that E4P was formed by carboxylation of a 3-carbon sugar and not by the NOPP pathway (Fig. 1b) (2, 5). However, there is an alternative explanation for these results. E4P may not be a precursor of AroAA biosynthesis in methanogens. This alternative can be examined in methanococci, where the enrichment of ribose is expected to be affected by the removal of E4P for AroAA biosynthesis. Thus, the labeling patterns of ribose were determined in cells of M. maripaludis grown on [2-13 C]acetate. MATERIALS AND METHODSStrain and growth conditions. For the labeling experiment, all glassware was washed overnight in 10% H 2 SO 4 and rinsed in deionized and distilled water. M. maripaludis JJ12, an acetate-requiring mutant of strain JJ1 (12), was grown in mineral medium supplemented with 1.36 g of CH 3 COONa ⅐ 3H 2 O per liter. Cultures (5 ml) were inoculated with fewer than 2.5 ϫ 10 7 cells to avoid selection for revertants and were grown under 276-kPa H 2 :CO 2 (80:20, vol/vol) at 37°C as described previously (19), except that the vitamin solution was omitted. Following overnight growth, these cultures were inoculated into 100 ml of medium containing 0.73 g o...

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Aminoacyl-tRNA Synthesis: A Postgenomic Perspective

Cited by 5 publications

References 17 publications

Distinguishing features of δ-proteobacterial genomes

Distinguishing features of δ-proteobacterial genomes

tRNA synthetase paralogs: Evolutionary links in the transition from tRNA-dependent amino acid biosynthesis to de novo biosynthesis

Biochemistry and genetics of autotrophy in Methanococcus

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