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Open Access Research article

Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in Streptomyces coelicolor

Mohammad Tauqeer Alam12, Eriko Takano3 and Rainer Breitling12*

Author Affiliations

1 Institute of Molecular, Cell and Systems Biology College of Medical, Veterinary and Life Sciences, Joseph Black Building B3.10, University of Glasgow, G12 8QQ, Glasgow, UK

2 Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands

3 Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands

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BMC Research Notes 2011, 4:325  doi:10.1186/1756-0500-4-325

Published: 7 September 2011

Abstract

Background

Streptomyces coelicolor, a model organism of antibiotic producing bacteria, has one of the largest genomes of the bacterial kingdom, including 7825 predicted protein coding genes. A large number of these genes, nearly 34%, are functionally orphan (hypothetical proteins with unknown function). However, in gene expression time course data, many of these functionally orphan genes show interesting expression patterns.

Results

In this paper, we analyzed all functionally orphan genes of Streptomyces coelicolor and identified a list of "high priority" orphans by combining gene expression analysis and additional phylogenetic information (i.e. the level of evolutionary conservation of each protein).

Conclusions

The prioritized orphan genes are promising candidates to be examined experimentally in the lab for further characterization of their function.