The Variable Part of the dnaK Gene as an Alternative Marker for Phylogenetic Studies of Rhizobia and Related Alpha Proteobacteria

doi:10.1078/072320203770865765

Systematic and Applied Microbiology

Volume 26, Issue 4, 2003, Pages 483-494

https://doi.org/10.1078/072320203770865765 Get rights and content

Summary

DnaK is the 70 kDa chaperone that prevents protein aggregation and supports the refolding of damaged proteins. Due to sequence conservation and its ubiquity this chaperone has been widely used in phylogenetic studies. In this study, we applied the less conserved part that encodes the so-called α-subdomain of the substrate-binding domain of DnaK for phylogenetic analysis of rhizobia and related non-symbiotic alpha-Proteobacteria. A single 330 bp DNA fragment was routinely amplified from DNA templates isolated from the species of the genera, Azorhizobium, Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium, but also from some non-symbiotic alpha Proteobacteria such as Blastochloris, Chelatobacter and Chelatococcus. Phylogenetic analyses revealed high congruence between dnaK sequences and 16S rDNA trees, but they were not identical. In contrast, the partition homogeneity tests revealed that dnaK sequence data could be combined with other housekeeping genes such as recA, atpD or glnA. The dnaK trees exhibited good resolution in the cases of the genera Mesorhizobium, Sinorhizobium and Rhizobium, even better than usually shown by 16S rDNA phylogeny. The dnaK phylogeny supported the close phylogenetic relationship of Rhizobium galegae and Agrobacterium tumefaciens(R. radiobacter) C58, which together formed a separate branch within the fast-growing rhizobia, albeit closer to the genus Sinorhizobium. The Rhizobium and Sinorhizobium genera carried an insertion composed of two amino acids, which additionally supported the phylogenetic affinity of these two genera, as well as their distinctness from the Mesorhizobium genus. Consistently with the phylogeny shown by 16S–23S rDNA intergenic region sequences [62], the dnaK trees divided the genus Bradyrhizobium into three main lineages, corresponding to B. japonicum, B. elkanii, and photosynthetic Bradyrhizobium strains that infect Aeschynomene plants. Our results suggest that the 330 bp dnaK sequences could be used as an additional taxonomic marker for rhizobia and related species (alternatively to the 16S rRNA gene phylogeny).

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The Variable Part of the dnaK Gene as an Alternative Marker for Phylogenetic Studies of Rhizobia and Related Alpha Proteobacteria

Summary

Cell

Syst. Appl. Microbiol

Gene

Microb. Ecol.

Syst. Appl. Microbiol

FEMS Microbiol. Lett.

Syst. Appl. Microbiol

Currents protocols in molecular biology

Biodiversity of bradyrhizobia nodulating Lupinus spp. Int. J. Syst.

Bacteriol

Photosynthetic bradyrhizobia are natural endophytes of the African wild rice Oryza breviligulata. Appl. Environ

Microbiol

Ralstonia taiwanensis sp. nov., isolated from root nodules of Mimosa species and sputum of a cystic fibrosis patient

Int. J. Syst. Evol. Microbiol

Allorhizobium undicola gen. nov., sp. nov., nitrogen-fixing bacteria that efficiently nodulate Neptunia natans in Senegal. Int.

J. Syst. Bacteriol

Characterization of tropical tree rhizobia and description of Mesorhizobium plurifarium sp. nov.

Int. J. Syst. Bacteriol

Protein folding and degradation in bacteria: to degrade or not to degrade? That is the question

Cell Mol. Life Sci.

Functions of rhizobial nodulation genes

Characterization of Azorhizobium caulinodans gen. nov., sp. nov., a stem nodulating nitrogen fixing bacterium isolated from Sesbania rostrata

Int. J. Syst. Bacteriol

The RecA protein as a model molecule for molecular systematics studies ob bacteria: comparison of trees of RecA's and 16S rRNA's from the same species

J. Mol. Evol.

Distance methods for inferring phylogenies: a justification

Evolution

Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia

Int. J. Syst. Evol. Microbiol

Bradyrhizobium (Arachis) sp. strain NC92 contains two nodD genes involved in the repression of nodA and a nolA gene required for the efficient nodulation of host plants

J. Bacteriol

Discontinuous occurrence of the hsp70 (dnaK) gene among Archaea and sequence features of HSP70 suggest a novel outlook on phylogenies inferred from this protein

J. Bacteriol

Evolution of HSP70 gene and its implications regarding relationships between archaebacteria, eubacteria, and eukaryotes

J. Mol. Evol.

Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes

Microbiol Mol. Biol. Rev.

Transfer of the bacteriochlorophyll b-containing phototrophic bacteria Rhodopseudomonas viridis and Rhodopseudomonas sulfoviridis to the genus Blastochloris gen. nov.

Int. J. Syst. Bacteriol

Transfer of Rhizobium loti, Rhizobium huakuii, Rhizobium ciceri, Rhizobium mediterraneum, and Rhizobium tianshanense to Mesorhizobium gen. nov.

Int. J. Syst. Bact.

Transfer of Rhizobium japonicum Buchanan 1980 to Bradyrhizobium gen. nov., a genus of slow growing root nodule bacteria from leguminous plants

Int. J. Syst. Bacteriol

A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences

J. Mol. Evol.

Genetic diversity in Bradyrhizobium japonicum Jordan 1982 and a proposal for Bradyrhizobium elkanii sp. nov.

Can. J. Microbiol

Molecular diversity of rhizobia occurring on native shrubby legumes in southeastern australia

Appl. Environ. Microbiol

Gene conversion drives within genic sequences: concerted evolution of ribosomal RNA genes in bacteria and archaea

J. Mol. Evol.

The RDP-II (Ribosomal Database Project)

Nucleic Acids Res.

The RDP (Ribosomal Database Project)

Nucleic Acids Res.

Construction and analysis of hybrid Escherichia coli-Bacillus subtilis dnaK genes

J. Bacteriol

Photosynthetic bradyrhizobia from Aeschynomene spp. are specific to stem-nodulated species and form a separate 16S ribosomal DNA restriction fragment lenght polymorphism group

Appl. Environ. Microbiol

Nodulation of legumes by members of the Beta-subclass of Proteobacteria

Nature