Genome-wide analysis of myxobacterial two-component systems: genome relatedness and evolutionary changes

BMC Genomics

Research Article

David E. Whitworth¹ 

[1] Institute of Biological Environmental and Rural Sciences, Aberystwyth University, SY23 3DD, Ceredigion, UK;

关键词: Myxobacteria;    Myxococcus xanthus;    Histidine kinase;    Response regulator;    Mutation;    Comparative genomics;   

DOI  :  10.1186/s12864-015-2018-y

 received in 2015-04-28, accepted in 2015-10-08,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundTwo-component systems (TCSs) are abundant prokaryotic signaling pathways, whose evolution is of particular importance because of their role in bacterial pathogenicity. Comparative genomics can provide important insights into the evolution of these genes, but inferences are dependent on the relatedness of the compared genomes. This study investigated the relationship between evolutionary distance and TCS evolution in myxobacterial genomes, of which there are several sequenced examples, of varying relatedness, and which encode large numbers of TCSs.MethodsMyxobacterial TCS gene sets were compared, orthologues defined, and changes in TCS properties such as gene organisation, domain architecture and size identified. Results Genome relatedness/evolutionary distance was found to have a large effect on the apparent frequency of evolutionary events affecting TCS genes, but not on the relative dominance of different types of mutations. Large (≥1 gene) indels were the most common changes, often giving rise to gene organisation changes. Smaller indels were also common, sometimes changing domain architecture, and/or leading to pseudogene formation. Individuality of myxobacterial TCS gene sets seems primarily due to lineage specific gene loss. However, there is also evidence of extensive acquisition of genes by lateral transfer, with gene duplication also creating new TCS genes.ConclusionsThis study provides catalogues of myxobacterial TCS gene sets and their orthology relationships, benchmarked against genome relatedness. It also provides insights into the relationship between evolutionary distance and the inference of TCS estudies of TCS evolution beyond the myxobacteriavolution, which may be important for studies of TCS evolutiThe online version of this articleon beyond the myxobacteria.

【 授权许可】

CC BY   
© Whitworth. 2015