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Review
, 7, 167

Molecular Signatures (Unique Proteins and Conserved Indels) That Are Specific for the Epsilon Proteobacteria (Campylobacterales)

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Review

Molecular Signatures (Unique Proteins and Conserved Indels) That Are Specific for the Epsilon Proteobacteria (Campylobacterales)

Radhey S Gupta. BMC Genomics.

Abstract

Background: The epsilon proteobacteria, which include many important human pathogens, are presently recognized solely on the basis of their branching in rRNA trees. No unique molecular or biochemical characteristics specific for this group are known.

Results: Comparative analyses of proteins in the genomes of Wolinella succinogenes DSM 1740 and Campylobacter jejuni RM1221 against all available sequences have identified a large number of proteins that are unique to various epsilon proteobacteria (Campylobacterales), but whose homologs are not detected in other organisms. Of these proteins, 49 are uniquely found in nearly all sequenced epsilon-proteobacteria (viz. Helicobacter pylori (26695 and J99), H. hepaticus, C. jejuni (NCTC 11168, RM1221, HB93-13, 84-25, CF93-6, 260.94, 11168 and 81-176), C. lari, C. coli, C. upsaliensis, C. fetus, W. succinogenes DSM 1740 and Thiomicrospira denitrificans ATCC 33889), 11 are unique for the Wolinella and Helicobacter species (i.e. Helicobacteraceae family) and many others are specific for either some or all of the species within the Campylobacter genus. The primary sequences of many of these proteins are highly conserved and provide novel resources for diagnostics and therapeutics. We also report four conserved indels (i.e. inserts or deletions) in widely distributed proteins (viz. B subunit of exinuclease ABC, phenylalanyl-tRNA synthetase, RNA polymerase beta '-subunit and FtsH protein) that are specific for either all epsilon proteobacteria or different subgroups. In addition, a rare genetic event that caused fusion of the genes for the largest subunits of RNA polymerase (rpoB and rpoC) in Wolinella and Helicobacter is also described. The inter-relationships amongst Campylobacterales as deduced from these molecular signatures are in accordance with the phylogenetic trees based on the 16S rRNA and concatenated sequences for nine conserved proteins.

Conclusion: These molecular signatures provide novel tools for identifying and circumscribing species from the Campylobacterales order and its subgroups in molecular terms. Although sequence information for these signatures is presently limited to Campylobacterales species, it is likely that many of them will also be found in other epsilon proteobacteria. Functional studies on these proteins and conserved indels should reveal novel biochemical or physiological characteristics that are unique to these groups of epsilon proteobacteria.

Figures

Figure 1
Figure 1
Partial nucleotide sequence alignment for an ε-proteobacterial specific protein WS0086. The initial part of this alignment, which is less conserved and some of which is also missing in C. lari, is not shown. The asterisks (*) denote residues that are completely conserved. A number of conserved regions that are suitable for designing PCR primers or other diagnostic probes are boxed.
Figure 2
Figure 2
Partial sequence alignments of the B protein from exinuclease ABC complex (A) and phenylalanyl-tRNA synthetase (B) showing two conserved indels that are specific for ε-Proteobacteria and not found in other organisms. The dashes (-) in the alignment show identity with the amino acid on the top line. The accession numbers of the sequences (second column) and position of the sequence in C. jejuni homolog (on top) are indicated. Sequence information for only representative species is shown.
Figure 3
Figure 3
Partial sequence alignments of the FtsH protease (A) and RNA polymerase β' subunit (B) showing two conserved indels that are specific for the indicated subgroups of ε-Proteobacteria. The dashes (-) denote identity with the amino acid on the top line. Sequence information for only representative species is shown.
Figure 4
Figure 4
Diagrammatic representation of the arrangements of two largest subunits of RNA polymerase, i.e. β subunit (RpoB) and β' subunit (RpoC) in different bacteria. In contrast to other bacteria where these proteins are made as distinct polypeptides, in Helicobacter and Wolinella a rare genetic event has led to fusion/joining of the genes for these proteins so that they are now made as a single large polypeptide.
Figure 5
Figure 5
Phylogenetic trees based on (A) 16S rRNA and (B) concatenated sequences for 9 proteins (AlaRS, Gyrase A, Gyrase B, EF-Tu, EF-G, Hsp60, Hsp70, RpoB and RpoC) containing 7919 aligned positions. The sequences were bootstrapped either 100 (A) or 500 times (B) and bootstrap scores for all nodes above 50% are shown. (C) A model depicting the evolutionary stages where different Campylobacterales- (or ε-proteobacteria) specific proteins and other RGCs were introduced.

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