Linked Life Data

11535801

Source:http://linkedlifedata.com/resource/pubmed/id/11535801

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
Pt 9
pubmed:dateCreated
2001-9-5
pubmed:databankReference
pubmed:abstractText
The phylogenetic placement of the rumen bacterium Fibrobacter succinogenes was determined using a signature sequence approach that allows determination of the relative branching order of the major divisions among Bacteria [Gupta, R. S. (2000) FEMS Microbiol Rev 24, 367-402]. For this purpose, segments of the Hsp60 (groEL), Hsp70 (dnaK), 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, 1.4 kb, 0.75 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 F. succinogenes Hsp70 supports its placement within the Gram-negative group of bacteria. A conserved insert in F. succinogenes Hsp60 that is commonly present in all bacterial species, except various Gram-positive bacteria, Deinococcus-Thermus groups and green non-sulphur bacteria, provides evidence that F. succinogenes 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 Chlamydia and Cytophaga-Flavobacterium- Bacteroides (CFB) groups, but it is not found in homologues from any other groups of bacteria. The presence of this insert in F. succinogenes 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 F. succinogenes homologues. These results provide evidence that F. succinogenes does not belong to the proteobacterial division and thus should be placed in a similar position as the Chlamydia and CFB groups of species.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Sep
pubmed:issn
1350-0872
pubmed:author
pubmed:issnType
Print
pubmed:volume
147
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
2611-22
pubmed:dateRevised
2009-11-19
pubmed:meshHeading
pubmed-meshheading:11535801-Alanine-tRNA Ligase, pubmed-meshheading:11535801-Amino Acid Sequence, pubmed-meshheading:11535801-Bacteria, pubmed-meshheading:11535801-Bacterial Proteins, pubmed-meshheading:11535801-Bacteroides, pubmed-meshheading:11535801-Base Sequence, pubmed-meshheading:11535801-Carbon-Nitrogen Ligases, pubmed-meshheading:11535801-Chaperonin 60, pubmed-meshheading:11535801-Chlamydia, pubmed-meshheading:11535801-Cytophaga, pubmed-meshheading:11535801-DNA, Bacterial, pubmed-meshheading:11535801-Escherichia coli Proteins, pubmed-meshheading:11535801-Flavobacterium, pubmed-meshheading:11535801-HSP70 Heat-Shock Proteins, pubmed-meshheading:11535801-Molecular Sequence Data, pubmed-meshheading:11535801-Phylogeny, pubmed-meshheading:11535801-Sequence Homology, Amino Acid, pubmed-meshheading:11535801-Time Factors
pubmed:year
2001
pubmed:articleTitle
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 division.
pubmed:affiliation
Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't