1887

Abstract

The class , 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 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 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): , , , , , , , . Four conserved indels in four widely distributed proteins that are specific for gammaproteobacteria are also described. A 2 aa deletion in 5′-phosphoribosyl-5-aminoimidazole-4-carboxamide transformylase (AICAR transformylase; PurH) was a distinctive characteristic of all gammaproteobacteria (except ). Two other conserved indels (a 4 aa deletion in RNA polymerase -subunit and a 1 aa deletion in ribosomal protein L16) were found uniquely in various species of the orders , , , and , 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 and also in some members of the order . 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 searches were also conducted on various open reading frames (ORFs) in the genome of K-12. These analyses identified 75 proteins that were unique to most members of the class or were restricted to species from some of its main orders (; and , , and ; and the , , , , and 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.

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2009-02-01
2019-10-22
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List of proteins used in the phylogenetic analysis. [ PDF] 111 KB

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Bacterial strains used to produce the set I and set II concatenated alignments. [ PDF] 129 KB

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Concatenated sequence alignment of 36 proteins, after processing with the Gblock 0.91b program. [ PDF] 433 KB

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A neighbour-joining distance tree for gammaproteobacteria based on concatenated sequences for 36 proteins. [ PDF] 237 KB

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Branching pattern of gammaproteobacteria in ML/MP trees based on concatenated sequences for 13 proteins. [ PDF] 136 KB

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Partial sequence alignments of the ribosomal protein L16 showing a 1 aa deletion that is uniquely found in various species from the orders , , and also many , but absent in all other Gammaproteobacteria or other bacteria. [ PDF] 27 KB

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