Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups

Gupta, Radhey S.; Mok, Amy

doi:10.1186/1471-2180-7-106

Cited by 131 publications

(133 citation statements)

References 83 publications

Supporting

Mentioning

120

Contrasting

Order By: Relevance

“…CGH profile analysis suggested that the absence of GIs on the genome types 122 and 6 in B. japonicum extends to non-Bj strains (Figure 1). So far, the GI sequences have proven specific for B. japonicum USDA110 by our BLAST search (http://www.ncbi.nlm.nih.gov/ blast) of data on the genomes of 10 strains of the family Bradyrhizobiaceae (Gupta and Mok, 2007), although we found partial homologous sequences within the GIs in Bradyrhizobium sp. BTAi1 and ORS278, R. palustris CGA009, BisA53, BisB18, BisB5 and HaA2, and Rhizobium leguminosarum bv.…”

Section: Discussionmentioning

confidence: 53%

“…Bradyrhizobium japonicum is a member of the family Bradyrhizobiaceae, which belongs to the order Rhizobiales in the Alphaproteobacteria (Gupta and Mok, 2007). Members of Bradyrhizobiaceae include a number of nonsymbiotic bacteria with diverse biochemical functions such as photosynthesis (Molouba et al, 1999;Larimer et al, 2004;Giraud et al, 2007), oligotrophy (Saito et al, 1998;King, 2007), 2,4-dichlorophenoxyacetic acid degradation (Kamagata et al, 1997) and nitrification (Starkenburg et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members

et al. 2008

View full text Add to dashboard Cite

Comparative genomic hybridization (CGH) was performed with nine strains of Bradyrhizobium japonicum (a symbiotic nitrogen-fixing bacterium associated with soybean) and eight other members of the Bradyrhizobiaceae by DNA macroarray of B. japonicum USDA110. CGH clearly discriminated genomic variations in B. japonicum strains, but similar CGH patterns were observed in other members of the Bradyrhizobiaceae. The most variable regions were 14 genomic islands (4-97 kb) and low G þ C regions on the USDA110 genome, some of which were missing in several strains of B. japonicum and other members of the Bradyrhizobiaceae. The CGH profiles of B. japonicum were classified into three genome types: 110, 122 and 6. Analysis of DNA sequences around the boundary regions showed that at least seven genomic islands were missing in genome type 122 as compared with type 110. Phylogenetic analysis for internal transcribed sequences revealed that strains belonging to genome types 110 and 122 formed separate clades. Thus genomic islands were horizontally inserted into the ancestor genome of type 110 after divergence of the type 110 and 122 strains. To search for functional relationships of variable genomic islands, we conducted linear models of the correlation between the existence of genomic regions and the parameters associated with symbiotic nitrogen fixation in soybean. Variable genomic regions including genomic islands were associated with the enhancement of symbiotic nitrogen fixation in B. japonicum USDA110.

show abstract

Section: Discussionmentioning

confidence: 53%

Section: Introductionmentioning

confidence: 99%

Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members

et al. 2008

View full text Add to dashboard Cite

show abstract

“…Therefore, a bacterial population related to rhizobia may be passively affected by a part of the autoregulation systems for regulating rhizobia. In fact, the three genera (Aurantimonas, Methylobacterium and Rhizobium) in Rhizobiales found in the present study are all closely related to Bradyrhizobium spp., endosymbionts of soybeans (Gupta and Mok, 2007). Another surprising finding was the high similarity observed for the population shifts of Alpha-and Gammaproteobacteria between two different environmental factors: the effects of genotypes under SN fertilization and the effects of the nitrogen fertilization under the HN fertilization condition.…”

Section: Discussionmentioning

confidence: 92%

Community shifts of soybean stem-associated bacteria responding to different nodulation phenotypes and N levels

et al. 2009

View full text Add to dashboard Cite

The diversity of stem-associated bacteria of non-nodulated (Nod À ), wild-type nodulated (Nod þ ) and hypernodulated (Nod þ þ ) soybeans were evaluated by clone library analyses of the 16S ribosomal RNA gene. Soybeans were dressed with standard nitrogen (SN) fertilization (15 kg N ha -1 ) and heavy nitrogen (HN) fertilization (615 kg N ha -1 ). The relative abundance of Alphaproteobacteria in Nod þ soybeans (66%) was smaller than that in Nod À and Nod þ þ soybeans (75-76%) under SN fertilization, whereas that of Gammaproteobacteria showed the opposite pattern (23% in Nod þ and 12-16% in Nod À and Nod þ þ soybeans). Principal coordinate analysis showed that the bacterial communities of Nod À and Nod þ þ soybeans were more similar to each other than to that of Nod þ soybeans under SN fertilization. HN fertilization increased the relative abundance of Gammaproteobacteria in all nodulation phenotypes (33-57%) and caused drastic shifts of the bacterial community. The clustering analyses identified a subset of operational taxonomic units (OTUs) at the species level in Alpha-and Gammaproteobacteria responding to both the nodulation phenotypes and nitrogen fertilization levels. Meanwhile, the abundance of Betaproteobacteria was relatively constant in all libraries constructed under these environmental conditions. The relative abundances of two OTUs in Alphaproteobacteria (Aurantimonas sp. and Methylobacterium sp.) were especially sensitive to nodulation phenotype and were drastically decreased under HN fertilization. These results suggested that a subpopulation of proteobacteria in soybeans is controlled in a similar manner through both the regulation systems of plant-rhizobia symbiosis and the nitrogen signaling pathway in plants.

show abstract

“…The proteins that were of interest generally involved a large increase in the expected values (E-values) from the last hit for the cluster I clostridia to the first hit from any other organism. Further, the E-values of these latter hits were generally greater than 10 23 , which indicates a weak level of similarity that can occur by chance (Gao et al, 2006;Gupta, 2006;Gupta & Mok, 2007). All promising proteins were further analysed using the PSI-BLAST program (Schaffer et al, 2001) to confirm their group specificity.…”

Section: R S Gupta and B Gao 286mentioning

confidence: 99%

“…Alphaproteobacteria, Epsilonproteobacteria, Chlamydia, Actinobacteria, Cyanobacteria, Deinococcus-Thermus, Bacteroidetes, etc. ; Griffiths et al, 2006;Gao et al, 2006;Gupta, 2006;Gupta & Lorenzini, 2007;Gupta & Mok, 2007). These newly discovered molecular markers provide valuable tools for biochemical, diagnostic, taxonomic and evolutionary studies on these bacteria (Koonin & Galperin, 1997;Binnewies et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I)

Gupta

Gao

2009

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

View full text Add to dashboard Cite

The species of Clostridium comprise a very heterogeneous assemblage of bacteria that do not form a phylogenetically coherent group. It has been proposed previously that only a subset of the species of Clostridium that form a distinct cluster in the 16S rRNA tree (cluster I) should be regarded as the true representatives of the genus Clostridium (i.e. Clostridium sensu stricto). However, this cluster is presently defined only in phylogenetic terms, and no biochemical, molecular or phenotypic characteristic is known that is unique to species from this cluster. We report here phylogenomic and comparative analyses based on sequenced clostridial genomes in an attempt to bridge this gap and to clarify the evolutionary relationships among species of clostridia. In phylogenetic trees for species of clostridia based on concatenated sequences for 37 highly conserved proteins, the species of Clostridium cluster I formed a strongly supported clade that was separated from all other clostridia by a long branch. Several other Clostridium species that are not part of this cluster grouped reliably with other species of clostridia in a number of wellresolved clades. Our comparative genomic analyses have identified three conserved indels in three highly conserved proteins (a 4 aa insert in DNA gyrase A, a 1 aa deletion in ATP synthase beta subunit and a 1 aa insert in ribosomal protein S2) that are unique to the species of Clostridium cluster I and are not found in any other bacteria. BLASTP searches on various proteins in the genomes of Clostridium tetani E88 and Clostridium perfringens SM101 have also identified more than 10 proteins that are found uniquely in the cluster I species. These results provide evidence that the species of Clostridium cluster I not only are phylogenetically distinct but also share many unique molecular characteristics. These newly identified molecular markers provide useful tools to define and circumscribe the genus Clostridium sensu stricto in more definitive terms. We have also identified a 7-9 aa conserved insert in the enzyme phosphoglycerate dehydrogenase that is uniquely found in the Clostridium thermocellum, Thermoanaerobacter pseudethanolicus, Thermoanaerobacter tengcogensis and Caldicellulosiruptor saccharolyticus homologues, and is absent from all other bacteria. These species form a well-defined clade in the phylogenetic trees and this indel provides a potential molecular marker for this clostridial cluster. INTRODUCTIONThe species belonging to the genus Clostridium comprise a heterogeneous assemblage that does not form a monophyletic grouping in phylogenetic trees based on different gene/protein sequences (Cato et al., 1986;Lawson et al., 1993;Stackebrandt et al., 1999;Finegold et al., 2002;Wiegel et al., 2006). Many species were originally assigned to this genus based on their being Gram-positive, anaerobic rods that are capable of endospore formation (Cato et al., 1986;Cato & Stackebrandt, 1989;Lawson et al., 1993;Finegold et al., 2002;Rood, 2006). However, these criteria led to the place...

show abstract

Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups

Cited by 131 publications

References 83 publications

Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members

Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members

Community shifts of soybean stem-associated bacteria responding to different nodulation phenotypes and N levels

Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I)

Contact Info

Product

Resources

About