dnaJ is a useful phylogenetic marker for alphaproteobacteria

Abstract

In the past, bacterial phylogeny relied almost exclusively on 16S rRNA gene sequence analysis. More recently, multilocus sequence analysis has been used to infer organismal phylogenies. In this study, the dnaJ chaperone gene was investigated as a marker for phylogeny studies in alphaproteobacteria. Preliminary analysis of G+C contents and G+C3s contents (the G+C content of the synonymous third codon position) showed no clear evidence of horizontal transfer of this gene in proteobacteria. dnaJ-based phylogenies were then analysed at three taxonomic levels: the Proteobacteria, the Alphaproteobacteria and the genus Mesorhizobium. Dendrograms based on DnaJ and 16S rRNA gene sequences revealed the same topology described previously for the Proteobacteria. These results indicate that the DnaJ phylogenetic signal is able to reproduce the accepted relationships among the five classes of the Proteobacteria. At a lower taxonomic level, using 20 alphaproteobacteria, the 16S rRNA gene-based phylogeny is distinct from the one based on DnaJ sequence analysis. Although the same clusters are generated, only the topology of the DnaJ tree is consistent with broader phylogenies from recent studies based on concatenated alignments of multiple core genes. For example, the DnaJ tree shows the two clusters within the Rhizobiales as closely related, as expected, while the 16S rRNA gene-based phylogeny shows them as distantly related. In order to evaluate the phylogenetic performance of dnaJ at the genus level, a multilocus analysis based on five housekeeping genes (atpD, gapA, gyrB, recA and rplB) was performed for ten Mesorhizobium species. In contrast to the 16S rRNA gene, the DnaJ sequence analysis generated a tree similar to the multilocus dendrogram. For identification of chickpea mesorhizobium isolates, a dnaJ nucleotide sequence-based tree was used. Despite different topologies, 16S rRNA gene-and dnaJ-based trees led to the same species identification. This study suggests that the dnaJ gene is a good phylogenetic marker, particularly for the class Alphaproteobacteria, since its phylogeny is consistent with phylogenies based on multilocus approaches. INTRODUCTIONThe phylum Proteobacteria is composed of five classes, the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria and Epsilonproteobacteria (Garrity et al., 2005;Stackebrandt et al., 1988). By the end of 2008, more than 380 complete genomes of proteobacteria were available in public databases (http://www. ncbi.nlm.nih.gov/genomes/lproks.cgi). Alphaproteobacteria exhibit an enormous diversity in their morphological and metabolic characteristics and the class is presently recognized solely as a clade in the 16S rRNA gene-based phylogeny (Stackebrandt et al., 1988). Based on 16S rRNA gene trees, the Alphaproteobacteria has been divided into seven orders: Caulobacterales, Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Parvularculales (Kersters et al., 2006). The Alphaproteobacteria includes important bacteria tha...

Following phylogenetic tracks of Astragalus cicer microsymbionts

“…Taking this into consideration, we decided to additionally determine the evolutionary history of two other conserved core genes i.e. atpD and glnII, according to the standard practice in the modern-day prokaryotic phylogeny and taxonomy (Gaunt et al 2001;Turner and Young 2000;Alexandre et al 2008).…”

“…Presently, genes coding e.g. RecA, b-subunit ATPase, the elongation factor Tu, DnaK, DnaJ, and glutamine synthetase (GS) are used as alternative phylogenetic markers (Maiden 2006;Stępkowski et al 2003Stępkowski et al , 2005Alexandre et al 2008). Glutamine synthetase is a key enzyme in nitrogen assimilation encoded by gene gln that is duplicated and conserved in the function.…”

Transmission of Intestinal Bifidobacterium longum subsp. longum Strains from Mother to Infant, Determined by Multilocus Sequencing Typing and Amplified Fragment Length Polymorphism

“…Seven housekeeping genes encoding proteins were chosen for analysis as previously described (2,8,30,36). The selected genes encode the following proteins: class III stress response-related ATPase with chaperone activity (clpC), DNA primase (dnaG), chaperone protein DnaJ (dnaJ), GTP-binding protein chain elongation factor G (fusA), the ␤ subunit of DNA gyrase (gyrB), amidophosphoribosyltransferase (purF), and the ␤ subunit of RNA polymerase (rpoB) ( Table 1).…”

hsp60 and 16S rRNA gene sequence relationships among species of the genus Bacteroides with the finding that Bacteroides suis and Bacteroides tectus are heterotypic synonyms of Bacteroides pyogenes

“…To date, a multilocus sequence typing (MLST) approach has been widely used to infer the phylogeny of organisms (Alexandre et al, 2008; Itoh et al, 2006;Shah et al, 2007;Yamamoto & Harayama, 1995). However, only limited information has been accumulated for species of the genus Bacteroides.…”

“…The taxonomy of the genus Bacteroides has undergone significant changes in the last two decades (Dewhirst et al, 1990;Moore & Moore, 1994;Rautio et al, 2003;Sakamoto et al, 2002Sakamoto et al, , 2007Sakamoto & Benno, 2006;Shah & Collins, 1988. It has also been reported that 16S rRNA gene sequencing is useful for the identification of isolates of clinically significant species of the genus Bacteroides (Song et al, 2005).To date, a multilocus sequence typing (MLST) approach has been widely used to infer the phylogeny of organisms (Alexandre et al, 2008; Itoh et al, 2006;Shah et al, 2007;Yamamoto & Harayama, 1995). However, only limited information has been accumulated for species of the genus Bacteroides.…”