The Prokaryotes Vol 6 Proteobacteria Gamma Subclass Pdf Download |LINK|
Microbial oxidation of geothermally produced reduced sulfur compounds is at the nexus of the biogeochemical carbon and sulfur cycles at deep-sea hydrothermal vents. Available information indicates that microbial symbionts and free- living gammaproteobacteria of the genera Thiomicrospira, Halothiobacillus, and Beggiatoa are important sulfur-oxidizers above the seafloor at these systems. In addition, bacteria belonging to the Epsilonproteobacteria have been identified as a major component of microbial communities at deep-sea vents. We have previously identified a novel sulfuroxidizing epsilonproteobacterium, Candidatus Arcobacter sulfidicus, which produces sulfur in filamentous form that is morphologically and chemically similar to material observed before and after submarine volcanic eruptions. In the meantime, many autotrophic epsilonproteobacteria have been isolated and characterized from deep-sea vents, providing further evidence that these organisms play an important role in sulfur and carbon cycling in these environments.
The Prokaryotes Vol 6 Proteobacteria Gamma Subclass Pdf Download
A genome-wide analysis of sequences similar to TnpAIS200 and TnpAREP in prokaryotes revealed a large number of family members with a wide taxonomic distribution. These can be arranged into three distinct classes and 12 subclasses based on sequence similarity. One subclass includes sequences similar to TnpAIS200. Proteins from other subclasses are not associated with typical insertion sequence features. These are characterized by specific additional domains possibly involved in protein/DNA or protein/protein interactions. Their genes are found in more than 25% of species analyzed. They exhibit a patchy taxonomic distribution consistent with dissemination by horizontal gene transfers followed by loss. The tnpAREP genes of five subclasses are flanked by typical REP sequences in a REPtron-like arrangement. Four distinct REP types were characterized with a subclass specific distribution. Other subclasses are not associated with REP sequences but have a large conserved domain located in C-terminal end of their sequence. This unexpected diversity suggests that, while most likely involved in processing single-strand DNA, proteins from different subfamilies may play a number of different roles.
The tree was computed on a subset of our initial sample composed of potentially functional proteins with a complete catalytic core domain. To obtain a global view of subclass distribution across bacterial phyla, we compiled the results from the original sample, retaining only one strain per species. Among the 1354 species, 57.2% do not encode a tnpAY1 gene, 25.6% encode at least one member of class 1 (with 21.5% at least one member of subclass 1.1), 25.4% encode at least one member of class 2 and 0.3% at least a member of class 3. Multiple different class 2 genes can co-occur in several species. Of these, we have distinguished up to four genes from different class 2 subclasses in 12 of the species in the library. Figure 4 shows the presence or absence of subclass members in each strain. Subclass 1.1 members are well distributed throughout, with a few strongly represented phyla (e.g. Cyanobacteria, Clostridia...). Members of the other subclasses show sparse distribution but with a tendency to co-occur in the same genera genome set (Cyanobacteria, Bacteroidetes, Epsilon-, Delta-, Beta- and Gamma-proteobacteria). Subclass 2.8 appears restricted to Cyanobacteria. The assembled Tenericute genomes, represented by 35 Mollicute species in our sample, do not exhibit tnpAY1 homologs (although a number of IS200/IS605 can be found in unassembled genomes). Class 3, enlarged to 24 proteins, is principally present in Planctomycetes (11), Acidobacteria (6) and Proteobacteria (5).
A more parsimonious model is to assume that dissemination of class 2 genes occurred by multiple horizontal gene transfers (HGTs). Support for this hypothesis comes from the observation of tnpAREP gene transfer from a Pseudomonad to marine gammaproteobacteria  and evidence that HGT is likely to have occurred between fluorescent pseudomonad strains . In the absence of formal evidence for autonomous mobility of these elements, tnpAREP genes might use the same routes as accessory genes for transfer (e.g. transformation , conjugation , transduction , and gene transfer agents [55, 56]). The taxonomic distribution of class 2 genes (Fig. 4) is consistent with the observation that HGT events are more frequent between closely related species . Indeed, except for subclass 2.1, and to a lesser extent for subclass 2.4, tnpAREP genes are mostly confined to a specific taxonomic group. This proximity would also favour integration of class 2 proteins into host cell metabolism by, for example, providing domains for interaction with other host proteins or influencing gene expression. The observation here, that intra-genome gene copies belonging to the same subclass are distantly related (see Additional file 1: Figure S13), is also compatible with multiple HGTs. Gene loss should also be considered as an evolutionary force since such events are suspected in genomes encoding REP sequences in the absence of tnpAREP gene  and is well documented in E. coli strains, where the REPtron locus had been replaced by an operon encoding toxin/antitoxin genes . Gene loss may have occurred after the acquisition of tnpAREP by HGT in the ancestor. The contribution of HGT and gene loss can be estimated with reconciliation methods that compare gene trees and species trees to recover the history of gene families , but this is outside the scope of this work. 350c69d7ab