Pathogens 2013, 2(4), 627-635; doi:10.3390/pathogens2040627
Article

Whole-Proteome Analysis of Twelve Species of Alphaproteobacteria Links Four Pathogens

1email, 1,2,3email and 1,2,3,* email
Received: 1 August 2013; in revised form: 19 November 2013 / Accepted: 20 November 2013 / Published: 26 November 2013
(This article belongs to the Special Issue Bacterial Pathogenomics: From Technology to Application)
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Abstract: Thousands of whole-genome and whole-proteome sequences have been made available through advances in sequencing technology, and sequences of millions more organisms will become available in the coming years. This wealth of genetic information will provide numerous opportunities to enhance our understanding of these organisms including a greater understanding of relationships among species. Researchers have used 16S rRNA and other gene sequences to study the evolutionary origins of bacteria, but these strategies do not provide insight into the sharing of genes among bacteria via horizontal transfer. In this work we use an open source software program called pClust to cluster proteins from the complete proteomes of twelve species of Alphaproteobacteria and generate a dendrogram from the resulting orthologous protein clusters. We compare the results with dendrograms constructed using the 16S rRNA gene and multiple sequence alignment of seven housekeeping genes. Analysis of the whole proteomes of these pathogens grouped Rickettsia typhi with three other animal pathogens whereas conventional sequence analysis failed to group these pathogens together. We conclude that whole-proteome analysis can give insight into relationships among species beyond their phylogeny, perhaps reflecting the effects of horizontal gene transfer and potentially providing insight into the functions of shared genes by means of shared phenotypes.
Keywords: whole-proteome sequences; Alphaproteobacteria; bacterial pathogens; bacterial phenotypes; pClust
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Zhou, Y.; Call, D.R.; Broschat, S.L. Whole-Proteome Analysis of Twelve Species of Alphaproteobacteria Links Four Pathogens. Pathogens 2013, 2, 627-635.

AMA Style

Zhou Y, Call DR, Broschat SL. Whole-Proteome Analysis of Twelve Species of Alphaproteobacteria Links Four Pathogens. Pathogens. 2013; 2(4):627-635.

Chicago/Turabian Style

Zhou, Yunyun; Call, Douglas R.; Broschat, Shira L. 2013. "Whole-Proteome Analysis of Twelve Species of Alphaproteobacteria Links Four Pathogens." Pathogens 2, no. 4: 627-635.

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