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Phylogenetic Classification of Diverse LysR-Type Transcriptional Regulators of a Model Prokaryote Geobacter sulfurreducens

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Abstract

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.

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Notes

  1. http://geobacter.org/.

  2. http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene.

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Acknowledgments

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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Authors and Affiliations

  1. Department of Preventive Medicine, The University of Tennessee Health Science Center, 66 N. Pauline Blvd. Ste. 633, Memphis, TN, 38163, USA

    Julia Krushkal & Yanhua Qu

  2. Department of Microbiology, The University of Massachusetts, Amherst, MA, 01003, USA

    Derek R. Lovley

  3. Department of Pediatrics, The University of Tennessee Health Science Center, Memphis, TN, USA

    Ronald M. Adkins

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  1. Julia Krushkal
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Correspondence to Julia Krushkal.

Electronic supplementary material

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239_2012_9498_MOESM1_ESM.nwk

Supplementary Figure 1. The neighbor-joining tree NJ-10145 inferred from 10,145 LTTRs with ≥90% coverage of the length of the G. sulfurreducens query sequences. The tree was inferred using Poisson correction for multiple hits and uniform distribution of substitution rates among sites. A. A text file containing the entire tree in the Newick format. (NWK 1172 kb)

239_2012_9498_MOESM2_ESM.pdf

Supplementary Figure 1. The neighbor-joining tree NJ-10145 inferred from 10,145 LTTRs with ≥90% coverage of the length of the G. sulfurreducens query sequences. The tree was inferred using Poisson correction for multiple hits and uniform distribution of substitution rates among sites. A. A text file containing the entire tree in the Newick format. B. A graphical overview of the tree NJ-10145, presented using the Dendroscope software as an unrooted radial phylogram. Due to a very large number of sequences in the tree, only selected representative sequence names are shown for groups of closely related lineages. Five names of sequences of G. sulfurreducens LTTRs representing the five phylogenetic clusters containing all eight LTTRs of G. sulfurreducens are shown in red color. (PDF 137 kb)

239_2012_9498_MOESM3_ESM.pdf

Supplementary Figure 2. Protein sequence alignment of 591 LTTRs containing eight G. sulfurreducens LTTRs and their close homologs, which were included in phylogenetic inference of the tree NJ-591. This alignment was generated by Clustal X and further manually edited and visually presented using Jalview (JV2) multiple sequence analysis software. (PDF 2445 kb)

239_2012_9498_MOESM4_ESM.pdf

Supplementary Figure 3. Detailed view of the phylogenetic tree NJ-591, inferred from 591 LTTRs family regulators, presented using the MEGA software. The tree was inferred using the neighbor-joining method, with Poisson correction for multiple hits and uniform distribution of substitution rates among sites. The tree was midpoint rooted. Numbers show bootstrap support (%) for individual tree nodes, computed using 500 bootstrap replications. (PDF 129 kb)

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Krushkal, J., Qu, Y., Lovley, D.R. et al. Phylogenetic Classification of Diverse LysR-Type Transcriptional Regulators of a Model Prokaryote Geobacter sulfurreducens . J Mol Evol 74, 187–205 (2012). https://doi.org/10.1007/s00239-012-9498-z

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