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Volume 147, Issue 9

The use of signature sequences in different proteins to determine the relative branching order of bacterial divisions: evidence that diverged at a similar time to and the division

The GenBank accession numbers for the sequences reported in this paper are AY017380, AY017381, AY017382 and AY017383.

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Abstract

The phylogenetic placement of the rumen bacterium was determined using a signature sequence approach that allows determination of the relative branching order of the major divisions among [Gupta, R. S. (2000) 24, 367–402]. For this purpose, segments of the Hsp60 (), Hsp70 (), CTP synthase and alanyl-tRNA synthetase genes, which are known to contain signature sequences that are useful for phylogenetic deterministic purposes, were cloned. Using degenerate oligonucleotide primers for highly conserved regions in these proteins, 14 kb, 075 kb, 401 bp and 171 bp fragments of the Hsp70, Hsp60, CTP synthase and alanyl-tRNA synthetase genes respectively were amplified by PCR, and these fragments were cloned and sequenced. These primers, because of their high degree of conservation, could also be used for cloning these genes from other bacterial species. The Hsp70 homologues from different Gram-negative bacteria contain a 21–23 aa insert that is not found in any Gram-positive bacteria. The presence of this insert in the Hsp70 supports its placement within the Gram-negative group of bacteria. A conserved insert in Hsp60 that is commonly present in all bacterial species, except various Gram-positive bacteria, groups and green non-sulphur bacteria, provides evidence that does not belong to these taxa. A particularly useful signature consisting of a 4 aa insert is found in Ala-tRNA synthetase. This insert is present in all proteobacterial homologues as well as in homologues from species belonging to the and (CFB) groups, but it is not found in homologues from any other groups of bacteria. The presence of this insert in Ala-tRNA synthetase provides evidence that this species is related to these groups. However, two other signatures in CTP synthase and Hsp70 proteins, that are distinctive of the proteobacterial species, are not present in the homologues. These results provide evidence that does not belong to the proteobacterial division and thus should be placed in a similar position as the and CFB groups of species.

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Keyword(s): bacterial evolution , CFB, Cytophaga–Flavobacterium–Bacteroides , Fibrobacter succinogenes , fibrolytic bacteria , phylogenetic placement and phylogeny
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2001-09-01
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The use of signature sequences in different proteins to determine the relative branching order of bacterial divisions: evidence that Fibrobacter diverged at a similar time to Chlamydia and the Cytophaga–Flavobacterium–Bacteroides divisionThe GenBank accession numbers for the sequences reported in this paper are AY017380, AY017381, AY017382 and AY017383.
Microbiology 147, 2611 (2001); https://doi.org/10.1099/00221287-147-9-2611
/content/journal/micro/10.1099/00221287-147-9-2611
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