The Adaptor hypothesis revisited

Ibba, Michael; Becker, Hubert Dominique; Stathopoulos, Constantinos; Tumbula, Debra L.; Söll, Dieter

doi:10.1016/s0968-0004(00)01600-5

Cited by 118 publications

(110 citation statements)

References 42 publications

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“…6,[26][27][28][29] Given GatCAB is present in both Archaea and Bacteria while GatDE is archaeal specific, it was speculated the AdT in LUCA was GatCAB with GatDE evolving later in early archaea. 30 To address this hypothesis and to gain a better understanding of the evolution of the two AdTs, we examined the phylogenetic relationship between the kinase subunits of the two AdTs (GatB and GatE). We constructed phylogenetic trees for four additional components of tRNAdependent Gln and Asn synthesis: GatA, AnsA and the GatD family, tRNA Gln , and tRNA Asn .…”

Section: Introductionmentioning

confidence: 99%

On the Evolution of the tRNA-Dependent Amidotransferases, GatCAB and GatDE

Sheppard

Söll

2008

Journal of Molecular Biology

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SummaryGlutaminyl-tRNA synthetase and asparaginyl-tRNA synthetase evolved from glutamyl-tRNA synthetase and aspartyl-tRNA synthetase, respectively, after the split in the last universal communal ancestor (LUCA). Glutaminyl-tRNA Gln and asparaginyl-tRNA Asn were likely formed in LUCA by amidation of the mischarged species, glutamyl-tRNA Gln and aspartyl-tRNA Asn , by tRNA-dependent amidotransferases as is still the case in most bacteria and all known archaea. The amidotransferase GatCAB is found in both domains of life while the heterodimeric amidotransferase, GatDE, is found only in Archaea. The GatB and GatE subunits belong to a unique protein family with Pet112 that is encoded in the nuclear genomes of numerous eukaryotes. GatE was thought to have evolved from GatB after the emergence of the modern lines of decent. Our phylogenetic analysis though places the split between GatE and GatB prior to the phylogenetic divide between Bacteria and Archaea and Pet112 to be of mitochondrial origin. In addition, GatD appears to have emerged prior to the bacterialarchaeal phylogenetic divide. Thus, while GatDE is an archaeal signature protein it likely was present in LUCA together with GatCAB. Archaea retained both amidotransferases while Bacteria emerged with only GatCAB. The presence of GatDE has favored a unique archaeal tRNA Gln that may be preventing acquisition of glutaminyl-tRNA synthetase in Archaea. Archaeal GatCAB on the other hand has not favored a distinct tRNA Asn suggesting tRNA Asn recognition is not a major barrier to the retention of asparaginyl-tRNA synthetase in more Archaea.

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Section: Introductionmentioning

confidence: 99%

On the Evolution of the tRNA-Dependent Amidotransferases, GatCAB and GatDE

Sheppard

Söll

2008

Journal of Molecular Biology

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“…Both aspartyl-tRNA synthetase (AspRS) 1 and glutamyl-tRNA synthetase (GluRS) occur in mischarging forms, often in organisms that lack asparaginyl-tRNA synthetase (AsnRS) or glutaminyl-tRNA synthetase (GlnRS) (reviewed in Ref. 4). These organisms generate Asn-tRNA or Gln-tRNA by pre-translational amino acid modification.…”

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confidence: 99%

“…1B). The heterotrimeric bacterial GatCAB enzyme can also form Gln-tRNA from Glu-tRNA Gln (4). The absence of the genes encoding AsnRS (asnS) or GlnRS (glnS) in most completed microbial genome sequences (4 -6) emphasizes that the transamidation pathways are widespread in nature.…”

mentioning

confidence: 99%

Evolutionary Divergence of the Archaeal Aspartyl-tRNA Synthetases into Discriminating and Nondiscriminating Forms

Hansen¹,

Feng²,

Toogood³

et al. 2002

Journal of Biological Chemistry

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Asparaginyl-tRNA (Asn-tRNA) is generated in nature via two alternate routes, either direct acylation of tRNA with asparagine by asparaginyl-tRNA synthetase (AsnRS) or in a two-step pathway that requires misacylated Asp-tRNA Asn as an intermediate. This misacylated aminoacyl-tRNA is formed by a nondiscriminating aspartyltRNA synthetase (AspRS), an enzyme that in addition to forming Asp-tRNA Asp also misacylates tRNA Asn . In contrast, a discriminating AspRS cannot acylate tRNA Asn . It has been suggested that the archaeal AspRS enzymes are nondiscriminating, whereas the bacterial ones discriminate. The archaeal and bacterial AspRS proteins are indeed distinct in sequence and structure. However, we show that both discriminating and nondiscriminating forms of AspRS exist among the archaea. Using unfractionated methanobacterial and pyrococcal tRNA, the Methanothermobacter thermautotrophicus AspRS acylated approximately twice as much tRNA as did AspRS from Pyrococcus kodakaraensis or Ferroplasma acidarmanus. Proof that Asp-tRNA Asn was generated by the methanogen synthetase was the conversion of AsptRNA formed by M. thermautotrophicus AspRS to AsntRNA by M. thermautotrophicus Asp-tRNA Asn amidotransferase. In contrast, Asp-tRNA formed by the Pyrococcus or Ferroplasma enzymes was not a substrate for the amidotransferase. Also, although all three AspRS enzymes charged tRNA Asp transcripts, only M. thermautotrophicus AspRS aspartylated the tRNA Asn transcript. Genomic analysis provides a rationale for the nature of these enzymes. The mischarging AspRS correlates with the absence in the genome of AsnRS and the presence of Asp-tRNA Asn amidotransferase, employed by the transamidation pathway. In contrast, the discriminating AspRS correlates with the absence of the amidotransferase and the presence of AsnRS, forming Asn-tRNA by direct aminoacylation. The high sequence identity, up to 60% between discriminating and nondiscriminating archaeal AspRSs, suggests that few mutational steps may be necessary to convert the tRNA-discriminating ability of a tRNA synthetase.

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“…Each class attaches the aa to a different side of the tRNA molecule. Different major branches of life have different subsets of these systems: we and other mammals basically use a simple, direct system, 6,8 and sequence phylogenies of the aaRS genes do not completely fit the standard phylogenetic tree of archaeae, bacteria and eukaryotes (including us). This suggests that these enzymes or even the translation mechanism, arose twice in evolution, either because of dual origins of translation itself or a deep evolutionary history of horizontal transfer of these vital genes, that is, between taxa.…”

Section: A Tale Within or Upon A Talementioning

confidence: 99%