Phylogenetic Classification of Diverse LysR-Type Transcriptional Regulators of a Model Prokaryote Geobacter sulfurreducens
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The protein family of LysR-type transcriptional regulators (LTTRs) is highly abundant among prokaryotes. We analyzed 10,145 non-redundant microbial sequences with homology to eight LysR family regulators of a model prokaryote, Geobacter sulfurreducens, and employed phylogenetic tree inference for LTTR classification. We also analyzed the arrangement of genome clusters containing G. sulfurreducens LTTR genes and searched for LTTR regulatory motifs, suggesting likely regulatory targets of G. sulfurreducens LTTRs. This is the first study to date providing a detailed classification of LTTRs in the deltaproteobacterial family Geobacteraceae.
KeywordsGeobacter sulfurreducens LysR LTTR Phylogenetic tree Operon Transcriptional regulation
This research was supported by the Office of Science (BER), U.S. Department of Energy, Cooperative Agreement No. DEFC02-02ER63446. Additional support for this study was provided by the Office of Research at the University of Tennessee Health Science Center. We thank Dr. M. Aklujkar (University of Massachusetts) for access to the functional annotation of the G. sulfurreducens genome and for helpful discussions about functional roles of genes and operons. We also thank Dr. P. Brown (University of Massachusetts) for development and computational support of the Geobacter Project web site, which was used to search for the functional roles of the G. sulfurreducens LTTRs. We thank Dr. K. Zengler (University of California, San Diego) for sharing information on experimentally derived operon organization of G. sulfurreducens and RpoN-dependent regulation. We are grateful to J. Peeples (The University of Tennessee Health Science Center) for editorial assistance.
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