Open Access Research article

Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria

Dmitry A Ravcheev12, Aaron A Best3, Natalia V Sernova2, Marat D Kazanov2, Pavel S Novichkov4 and Dmitry A Rodionov12*

Author Affiliations

1 Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA

2 A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia

3 Department of Biology, Hope College, Holland, MI, 49423, USA

4 Lawrence Berkeley National Laboratory, Berkeley, CA, 94710, USA

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BMC Genomics 2013, 14:94  doi:10.1186/1471-2164-14-94

Published: 12 February 2013

Additional files

Additional file 1:

Phylogenetic tree of 30 studied Lactobacillaceae genomes.- Description of data: Economic impact for each studied genome is shown in square brackets. The tree is based on approximately 78 universal prokaryotic proteins in the MicrobesOnline database: http://www.microbesonline.org/cgi-bin/speciesTree.cgi webcite.

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Additional file 2:

Repertoire of DNA-binding transcriptional factors identified in 15 Streptococcaceae genomes. Description of data: Orthologous groups are sorted by TF family and then by conservancy of each TF group. TFs with regulons reconstructed in this work are highlighted by light blue.

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Open Data

Additional file 3:

Repertoire of DNA-binding transcriptional factors identified in 15 Lactobacillaceae genomes. Description of data: Orthologous groups are sorted by TF family and then by conservancy of each TF group. TFs with regulons reconstructed in this work are highlighted by light blue.

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Open Data

Additional file 4:

Distribution of predicted DNA binding transcription factors in studied Lactobacillales genomes.

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Open Data

Additional file 5:

Collection of TF regulons reconstructed in Lactobacillales. Description of data: a Novel TF names introduced in this work are marked by asterisks. b Presence (+) or absence (−) of TFs orthologs. c Workflow 1, expansion and projection of a regulon previously characterized in model Lactobacillales organisms: (1a) TFBSs motif was known, (1b) TFBSs motif was predicted in present work; Workflow 2, projection of an orthologous regulon from B. subtilis or S. aureus; Workflow 3, ab initio regulon inference. Regulons previously studied in model organisms highlighted by green. Names of functional groups are highlighted in blue.

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Open Data

Additional file 6:

Functional content, experimental evidences and conservation for reconstructed regulons in Streptococcaceae. Description of data: Regulons are sorted by regulator names. Novel TF names introduced in this work are marked by asterisks. ‘Conservation of regulatory interaction’ column shows number of genomes with regulated gene/ operon (number of genomes having orthologs of operon).

Format: XLSX Size: 55KB Download file

Open Data

Additional file 7:

Functional content, experimental evidences and conservation for reconstructed regulons in Lactobacillaceae. Description of data: Regulons are sorted by regulator names. Novel TF names introduced in this work are marked by asterisks. ‘Conservation of regulatory interaction’ column shows number of genomes with regulated operon (number of genomes having orthologs of operon).

Format: XLSX Size: 37KB Download file

Open Data

Additional file 8:

Analysis of LacI family TFs in the studied Lactobacillales genomes.

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Additional file 9:

Comparison of predicted binding site motifs in Streptococcaceae and Lactobacillaceae genomes. Description of data: 1 Sequences Logos were constructed using WebLogo package (http://weblogo.berkeley.edu/logo.cgi) webcite. 2 NS, number of binding site sequences used to construct Logo. 3 Category reflects a conservancy between TFBS motifs in Streptococcaceae and Lactobacillaceae: I, highly conserved motifs; II, moderately different motifs; III, substantially different motifs. 4 Number of genomes that contain this regulon. 5 Average number of target operon in regulon per genome.

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Open Data