Molecular signatures (unique proteins and conserved indels) that are specific for the epsilon proteobacteria (Campylobacterales)

Antonie van Leeuwenhoek

2011

Microbial systematics and phylogeny should form the foundation and guiding light for a comprehensive understanding of different aspects of microbiology. However, there are many critical issues in microbial systematics that are currently not resolved. Some of these include: how to define and delimit a prokaryotic species; development of rationale criteria for the assignment of higher taxonomic ranks; understanding what unique properties distinguish species from different groups; and understanding the branching order and interrelationship among higher prokaryotic clades. The sequencing of genomes from large numbers of cultured as well as uncultured microbes covering prokaryotic diversity provides unique means to achieve these important objectives. Prokaryotic genomes are found to be very diverse and dynamic and horizontal gene transfers (HGTs) are indicated to have played important role in species/genome evolution. Although HGT adds a layer of complexity in terms of understanding the genomes and species evolution, it is contended that vast majority of genes and genetic characteristics that are distinctive characteristics of higher prokaryotic taxa are vertically inherited and based on them a solid foundation for microbial systematics can be developed. We describe two kinds of molecular markers consisting of conserved indels in protein sequences and whole proteins that are specific for different groups that are proving particularly valuable in defining different prokaryotic groups in clear molecular terms and in understanding their interrelationships. The genetic and biochemical studies on these taxa-specific molecular markers also open the way to discover novel biochemical and physiological characteristics that are unique properties of these groups.

Section: Current Issues In Microbial Systematicsmentioning

confidence: 96%

Microbial systematics in the post-genomics era

Antonie van Leeuwenhoek

2011

“…The proteins that were of interest generally involved a large increase in E-values from the last gammaproteobacterial hit to the first hit from any other organism. Further, the E-values of these latter hits were generally higher than 10 23 , which indicates a weak level of similarity that could occur by chance (Gao et al, 2006;Gupta, 2006). However, higher or lower Evalues can sometimes be acceptable depending upon the length of the query sequence and that of the hit (Altschul et al, 1997).…”

Section: Methodsmentioning

confidence: 99%

“…This strategy has provided valuable insights into evolutionary relationships for a number of other groups/phyla of bacteria (for example, the Alphaproteobacteria, Epsilonproteobacteria, Chlamydiae, Actinobacteria and Bacteroidetes-Chlorobi) (Griffiths et al, 2006;Gao et al, 2006;Gupta, 2006;Gupta & Lorenzini, 2007;Gupta & Mok, 2007). In this work, we carried out detailed phylogenetic analyses on a broad range of gammaproteobacteria covering all the main orders of the class, based on concatenated sequences for 36 highly conserved and universally distributed proteins.…”

Section: Introductionmentioning

confidence: 99%

Phylogenomics and protein signatures elucidating the evolutionary relationships among the Gammaproteobacteria

Mohan

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

2009

The class Gammaproteobacteria, which forms one of the largest groups within bacteria, is currently distinguished from other bacteria solely on the basis of its branching in phylogenetic trees. No molecular or biochemical characteristic is known that is unique to the class Gammaproteobacteria or its different subgroups (orders). The relationship among different orders of gammaproteobacteria is also not clear. In this study, we present detailed phylogenomic and comparative genomic analyses on gammaproteobacteria that clarify some of these issues. Phylogenetic trees based on concatenated sequences for 13 and 36 universally distributed proteins were constructed for 45 members of the class Gammaproteobacteria covering 13 of its 14 orders. In these trees, species from a number of the subgroups formed distinct clades and their relative branching order was indicated as follows (from the most recent to the earliest diverging): Enterobacteriales .Pasteurellales .Vibrionales, Aeromonadales .Alteromonadales .Oceanospirillales, Pseudomonadales .Chromatiales, Legionellales, Methylococcales, Xanthomonadales, Cardiobacteriales, Thiotrichales. Four conserved indels in four widely distributed proteins that are specific for gammaproteobacteria are also described. A 2 aa deletion in 59-phosphoribosyl-5-aminoimidazole-4-carboxamide transformylase (AICAR transformylase; PurH) was a distinctive characteristic of all gammaproteobacteria (except Francisella tularensis). Two other conserved indels (a 4 aa deletion in RNA polymerase b-subunit and a 1 aa deletion in ribosomal protein L16) were found uniquely in various species of the orders Enterobacteriales, Pasteurellales, Vibrionales, Aeromonadales and Alteromonadales, but were not found in other gammaproteobacteria. Lastly, a 2 aa deletion in leucyl-tRNA synthetase was commonly present in the above orders of the class Gammaproteobacteria and also in some members of the order Oceanospirillales. The presence of the conserved indels in these gammaproteobacterial orders indicates that species from these orders shared a common ancestor that was separate from other bacteria, a suggestion that is supported by phylogenetic studies. Systematic BLASTP searches were also conducted on various open reading frames (ORFs) in the genome of Escherichia coli K-12. These analyses identified 75 proteins that were unique to most members of the class Gammaproteobacteria or were restricted to species from some of its main orders (Enterobacteriales; Enterobacteriales and Pasteurellales; Enterobacteriales, Pasteurellales, Vibrionales, Aeromonadales and Alteromonadales; and the Enterobacteriales, Pasteurellales, Vibrionales, Aeromonadales, Alteromonadales, Oceanospirillales and Pseudomonadales etc.). The genes for these proteins have evolved at various stages during the evolution of gammaproteobacteria and their species distribution pattern, in conjunction with other results presented here, provide valuable information regarding the evolutionary relationships among these bacteria.Abbreviations: AICAR transformy...

“…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).…”

mentioning

confidence: 99%

“…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.…”

mentioning

confidence: 99%

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

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

2009

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...