Journal of Molecular Evolution

, Volume 74, Issue 3–4, pp 187–205 | Cite as

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

  • Julia Krushkal
  • Yanhua Qu
  • Derek R. Lovley
  • Ronald M. Adkins
Article

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.

Keywords

Geobacter sulfurreducens LysR LTTR Phylogenetic tree Operon Transcriptional regulation 

Supplementary material

239_2012_9498_MOESM1_ESM.nwk (1.1 mb)
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 (138 kb)
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 (2.4 mb)
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 (130 kb)
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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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Julia Krushkal
    • 1
  • Yanhua Qu
    • 1
  • Derek R. Lovley
    • 2
  • Ronald M. Adkins
    • 3
  1. 1.Department of Preventive MedicineThe University of Tennessee Health Science CenterMemphisUSA
  2. 2.Department of MicrobiologyThe University of MassachusettsAmherstUSA
  3. 3.Department of PediatricsThe University of Tennessee Health Science CenterMemphisUSA

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