Evolutionary constraints and expression analysis of gene duplications in Rhodobacter sphaeroides 2.4.1

BMC Research Notes

Madhusudan Choudhary¹  Hyuk Cho²  Anish Bavishi¹  Anne E Peters¹ 

[1] Department of Biological Sciences, Sam Houston State University, Huntsville, TX 77341, USA;Department of Computer Science, Sam Houston State University, Huntsville, TX 77341, USA

关键词: Rhodobacter sphaeroides;    Gene expression;    Microarray;    Out-paralog, Evolutionary constraint;    In-paralog;    Gene duplication;   

Others  :  1166494
DOI  :  10.1186/1756-0500-5-192

 received in 2011-10-29, accepted in 2012-04-05,  发布年份 2012

【 摘 要 】

Background

Gene duplication is a major force that contributes to the evolution of new metabolic functions in all organisms. Rhodobacter sphaeroides 2.4.1 is a bacterium that displays a wide degree of metabolic versatility and genome complexity and therefore is a fitting model for the study of gene duplications in bacteria. A comprehensive analysis of 234 duplicate gene-pairs in R. sphaeroides was performed using structural constraint and expression analysis.

Results

The results revealed that most gene-pairs in in-paralogs are maintained under negative selection (ω ≤ 0.3), but the strength of selection differed among in-paralog gene-pairs. Although in-paralogs located on different replicons are maintained under purifying selection, the duplicated genes distributed between the primary chromosome (CI) and the second chromosome (CII) are relatively less selectively constrained than the gene-pairs located within each chromosome. The mRNA expression patterns of duplicate gene-pairs were examined through microarray analysis of this organism grown under seven different growth conditions. Results revealed that ~62% of paralogs have similar expression patterns (cosine ≥ 0.90) over all of these growth conditions, while only ~7% of paralogs are very different in their expression patterns (cosine < 0.50).

Conclusions

The overall findings of the study suggest that only a small proportion of paralogs contribute to the metabolic diversity and the evolution of novel metabolic functions in R. sphaeroides. In addition, the lack of relationships between structural constraints and gene-pair expression suggests that patterns of gene-pair expression are likely associated with conservation or divergence of gene-pair promoter regions and other coregulation mechanisms.

【 授权许可】

   
2012 Peters et al.; licensee BioMed Central Ltd.

【 图 表 】

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