Phylogenetic analysis of gram-positive bacteria based on grpE, encoded by the dnaK operon.

Abstract

The dnaK operon in Gram-positive bacteria includes grpE, dnaJ and, in some members, hrcA as well. Both DnaK and DnaJ have been utilized for constructing phylogenetic relationships among various organisms. Multiple copies exist for dnaK and dnaJ genes in some bacterial genera, as opposed to a single gene copy for grpE and for hrcA, according to the currently available data. Here, we present a partial protein-based phylogenetic tree for Grampositive bacteria, derived by using the amino acid sequence identity of GrpE ; the results are compared with the phylogenetic trees generated from 5S rRNA, 16S rRNA, dnaK and dnaJ sequences. Our results indicate three main groupings : two are within low-GMC DNA Gram-positive bacteria comprising Bacillus species and Staphylococcus aureus on the one hand and Streptococcus species/Lactococcus lactis/Enterococcus faecalis/Lactobacillus sakei on the other hand ; the Mycobacterium species and Streptomyces coelicolor, belonging to the high-GMC DNA Gram-positive bacteria, form the third cluster. This hierarchical arrangement is in close agreement with that obtained with 16S rRNA and DnaK sequences but not DnaJ-based phylogeny.

Determination of Enterococcus faecalis groESL Full-Length Sequence and Application for Species Identification

“…The data presented here suggest a close relationship between these organisms. This result is generally in agreement with the data obtained from 5S rRNA, 16s RNA and grpE reported by Ahmad et al (1) E. faecalis groES and groEL each have a ribosome-binding site. The putative ribosome-binding site sequence (GGAGG) of E. faecalis GroES was identical to that of S. pneumoniae.…”

Extracting phylogenetic information from whole-genome sequencing projects: the lactic acid bacteria as a test case

“…As mentioned above the topologies of the trees based on the 16S rRNA gene, gyrB, sodA, dnaK, recA and alaS were very similar, which is largely in agreement with previously published data for these and other bacteria (Eisen, 1995;Huang, 1996;Poyart et al, 1998;Diaz-Lazcoz et al, 1998;Ahmad et al, 2000). The extensive intraspecies and intragenus diversity observed in the ddl-based tree is most probably the result of a previously described hitchhiking effect driven by the penicillin-binding protein 2b gene (pbp2b): interspecies recombinational exchanges at the pbp2b locus (selected for by the use of penicillin) can extend into or through the nearby ddl gene (Enright & Spratt, 1999).…”

Phylogenetic, amino acid content and indel analyses of the beta subunit of DNA-dependent RNA polymerase of gram-positive and gram-negative bacteria.

“…The classification of Gram-positive bacteria into two groups based on DNA GjC content (high and low GjC) is, however, supported by all these chronometers, together with studies on the types of RNaseP (Haas et al, 1996) and DNA polymerase C (Huang & Ito, 1999) that they contain and the organization of their dnaK operons (Segal & Ron, 1996). Inferences within these groups are again varied, with phylogenetic studies on the HrcA (Ahmad et al, 1999) and GrpE (Ahmad et al, 2000) proteins suggesting two separate groups of low-GjC Gram-positive bacteria. The relationship of these two (three) Grampositive groups with the Gram-negative bacteria is also unclear, with the high-GjC group being more closely linked on the basis of RNaseP RNA type (Haas et al, 1996) and the presence of shared indels in S12 protein, dihydroorotate dehydrogenase and pyruvate kinase (Gupta, 1998), whilst the low-GjC group is more closely linked on the basis of shared indels in gyrase A (Gupta, 1998).…”

“…Phylogenetic trees based on various chronometers have indicated close relationships of Gram-positive bacteria to various groups of other bacteria including the cyanobacteria (Ahmad et al, 1999 ;Eisen, 1995), halobacteria (Gribaldo et al, 1999 ;Haas et al, 1996) and mycoplasmas (Weisburg et al, 1989a), whilst specific links have been suggested to Methanosarcina mazei (Gribaldo et al, 1999) and Borrelia burgdorferi (Eisen, 1995). Likewise, such chronometers also give variable phylogenetic positions for the clostridia (Ahmad et al, 1999(Ahmad et al, , 2000Gribaldo et al, 1999 ;Bustard & Gupta, 1997). Previously, we have sequenced the rpoC gene from various leuconostocs and performed a comparative phylogenetic analysis to discern relationships and the tenet of tachytelic evolution within this group of Gram-positive bacteria (Morse et al, 1996a).…”

“…Recently, however, systematists have begun to compare and contrast phylogenetic relationships inferred from other molecules with those of 16S rRNA (Gupta, 1998 ;Hansmann & Martin, 2000). Examples of such alternative chronometers include GrpE (Ahmad et al, 2000), ribosomal protein (Bocchetta et al, 2000), Hsp70 (Gribaldo et al, 1999), Hsp40 (Bustard & Gupta, 1997) and EF-G (Bocchetta et al, 1995). These studies have, with a few exceptions (Hasegawa & Hashimoto, 1993), demonstrated that 16S rRNA is an excellent A multiple alignment of the RNAP β subunit amino acid sequences deduced from the gene sequences is available as supplementary material in IJSEM Online (http://ijs.sgmjournals.org/).…”