PMID- 10447505
OWN - NLM
STAT- MEDLINE
DCOM- 19991206
LR  - 20051117
IS  - 1088-9051 (Print)
IS  - 1088-9051 (Linking)
VI  - 9
IP  - 8
DP  - 1999 Aug
TI  - Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures 
      and phylogenetic trees reveals a complex history of horizontal gene transfer
      events.
PG  - 689-710
AB  - Phylogenetic analysis of aminoacyl-tRNA synthetases (aaRSs) of all 20
      specificities from completely sequenced bacterial, archaeal, and eukaryotic
      genomes reveals a complex evolutionary picture. Detailed examination of the
      domain architecture of aaRSs using sequence profile searches delineated a network
      of partially conserved domains that is even more elaborate than previously
      suspected. Several unexpected evolutionary connections were identified, including
      the apparent origin of the beta-subunit of bacterial GlyRS from the HD
      superfamily of hydrolases, a domain shared by bacterial AspRS and the B subunit
      of archaeal glutamyl-tRNA amidotransferases, and another previously undetected
      domain that is conserved in a subset of ThrRS, guanosine polyphosphate hydrolases
      and synthetases, and a family of GTPases. Comparison of domain architectures and 
      multiple alignments resulted in the delineation of synapomorphies-shared derived 
      characters, such as extra domains or inserts-for most of the aaRSs specificities.
      These synapomorphies partition sets of aaRSs with the same specificity into two
      or more distinct and apparently monophyletic groups. In conjunction with cluster 
      analysis and a modification of the midpoint-rooting procedure, this partitioning 
      was used to infer the likely root position in phylogenetic trees. The topologies 
      of the resulting rooted trees for most of the aaRSs specificities are compatible 
      with the evolutionary "standard model" whereby the earliest radiation event
      separated bacteria from the common ancestor of archaea and eukaryotes as opposed 
      to the two other possible evolutionary scenarios for the three major divisions of
      life. For almost all aaRSs specificities, however, this simple scheme is
      confounded by displacement of some of the bacterial aaRSs by their eukaryotic or,
      less frequently, archaeal counterparts. Displacement of ancestral eukaryotic aaRS
      genes by bacterial ones, presumably of mitochondrial origin, was observed for
      three aaRSs. In contrast, there was no convincing evidence of displacement of
      archaeal aaRSs by bacterial ones. Displacement of aaRS genes by eukaryotic
      counterparts is most common among parasitic and symbiotic bacteria, particularly 
      the spirochaetes, in which 10 of the 19 aaRSs seem to have been displaced by the 
      respective eukaryotic genes and two by the archaeal counterpart. Unlike the
      primary radiation events between the three main divisions of life, that were
      readily traceable through the phylogenetic analysis of aaRSs, no consistent
      large-scale bacterial phylogeny could be established. In part, this may be due to
      additional gene displacement events among bacterial lineages. Argument is
      presented that, although lineage-specific gene loss might have contributed to the
      evolution of some of the aaRSs, this is not a viable alternative to horizontal
      gene transfer as the principal evolutionary phenomenon in this gene class.
FAU - Wolf, Y I
AU  - Wolf YI
AD  - National Center for Biotechnology Information (NCBI), National Library of
      Medicine, National Institutes of Health (NIH), Bethesda Maryland 20894, USA.
FAU - Aravind, L
AU  - Aravind L
FAU - Grishin, N V
AU  - Grishin NV
FAU - Koonin, E V
AU  - Koonin EV
LA  - eng
PT  - Journal Article
PL  - United States
TA  - Genome Res
JT  - Genome research
JID - 9518021
RN  - 0 (Genetic Markers)
RN  - 0 (Peptides)
RN  - EC 6.1.1.- (Amino Acyl-tRNA Synthetases)
SB  - IM
MH  - Amino Acid Sequence
MH  - Amino Acyl-tRNA Synthetases/*chemistry/*genetics
MH  - Animals
MH  - *Evolution, Molecular
MH  - Genes, Bacterial
MH  - Genetic Markers
MH  - Humans
MH  - Molecular Sequence Data
MH  - Peptides/*chemistry/genetics
MH  - *Phylogeny
MH  - Protein Structure, Tertiary/genetics
MH  - Sequence Alignment
EDAT- 1999/08/14 00:00
MHDA- 1999/08/14 00:01
CRDT- 1999/08/14 00:00
PHST- 1999/08/14 00:00 [pubmed]
PHST- 1999/08/14 00:01 [medline]
PHST- 1999/08/14 00:00 [entrez]
PST - ppublish
SO  - Genome Res. 1999 Aug;9(8):689-710.