Genome-wide searches for cis-regulatory motifs orthologous to Ruegeria pomeroyi DSS-3 in bacterial genomes

Contributors: Leong-Keat Chan, XiaoJia Tang, Shalabh Sharma, Ryan J Newton, Qin Ma, Ying Xu, and Mary Ann Moran

Contact: MA Moran, Department of Marine Sciences, University of Georgia, Marine Science Building, Athens, GA 30602-3636, USA. Email: mmoran@uga.edu; Fax: 1-706-542-5888; Phone: 1-706-542-6481

Data submission date: October 01, 2011

Data last update date: October 01, 2011

Publication referencing this database: Manuscript in preparation

Methods summary: The program BoBro (Li et al., 2010) was used to identified cis-regulatory motifs in the 5’ DNA regulatory regions (DNA sequences up to 300 nt upstream from the transcriptional start site in the intergenic region and into the first 25 nt in the coding region) of R. pomeroyi DSS-3 genes that were transcriptionally perturbed under steady-state macronutrient limitations (Chan et al., 2012). Motifs with P-values <10^-6 were considered significant (Li et al., 2010). These analyses resulted in the identification of 14 R. pomeroyi DSS-3 motifs. Using the program BoBro Based Searching/Scanning (BBS) tool, the 14 motifs were used as queries in subsequent genome-wide searches for orthologous motifs in the 5’ DNA regulatory regions associated with all protein-coding genes of 36 Roseobacter genomes, including R. pomeroyi, and in six non-Roseobacter (i.e., control) genomes: two distantly related marine bacteria in the Alphaproteobacteria lineage, two marine bacteria in Gammaproteobacteria, one marine bacterium in the Bacteroidetes lineage, and E. coli, a non-marine Gammaproteobacterium. Motif searches were considered significant if the resultant P-value was <10^-7 and Z-score (Xie et al., 2005; Xie et al., 2007)>20. Bacterial genomes were downloaded from GenBank (as of May 2011).

Computational program:: BoBro and BBS are available for download at http://csbl.bmb.uga.edu/~maqin/motif_finding/. Please contact Prof. Ying Xu (email: xyn@bmb.uga.edu; website: http://csbl.bmb.uga.edu/~xyn/) for questions related to the program.

Information for downloadable files: For each queried bacterial genome, two files are available: 1) a FASTA file contains the input 5’ DNA regulatory sequences used for genome-wide motif searches, and 2) a text file contains the resultant significant motifs. Header for the 5’ DNA regulatory sequence file has locus tag and the location of the queried regulatory sequence numbered according to the actual position in the genome. Header for the resultant significant motif file has this information: Gene, locus tag; Offset, location (in nt) of the motif start site from the transcriptional start site (+, upstream; -, downstream); Pos, start location of the motif sequence numbered according to the actual position in the genome; Motif, motif sequence; Score, see (Li et al., 2010); Intergenic, queried regulatory region length; Info, locus tag and the location of the motif sequence numbered according to the actual position in the genome.

Literature references:
Chan, L.K., Newton, R.J., Sharma, S., Smith, C.B., Rayapati, P., Limardo, A.J. et al. (2012) Transcriptional changes underlying elemental stoichiometry shifts in a marine heterotrophic bacterium. Front Microbiol. 3:159.

Li, G., Liu, B., Ma, Q., and Xu, Y. (2010) A new framework for identifying cis-regulatory motifs in prokaryotes. Nucleic Acids Res. 39:e42.

Xie, X.H., Mikkelsen, T.S., Gnirke, A., Lindblad-Toh, K., Kellis, M., and Lander, E.S. (2007) Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites. Proc Natl Acad Sci U S A. 104:7145-7150.

Xie, X.H., Lu, J., Kulbokas, E.J., Golub, T.R., Mootha, V., Lindblad-Toh, K. et al. (2005) Systematic discovery of regulatory motifs in human promoters and 3 ' UTRs by comparison of several mammals. Nature. 434:338-345.

  Download Individual File (includes both text and fasta files)

Roseobacters
Citreicella SE45	Phaeobacter gallaeciensis 2.10	Roseovarius nubinhibens ISM
Dinoroseobacter shibae DFL 12	Phaeobacter sp. Y4I	Roseovarius sp. TM1035
Jannaschia sp. CCS1	Rhodobacterales bacterium KLH11	Roseovarius sp. 217
Loktanella vestfoldensis SKA53	Rhodobacterales bacterium HTCC2083	Ruegeria lacuscaerulensis ITI-1157
Maritimibacter alkaliphilus HTCC2654	Rhodobacterales bacterium HTCC2150	Ruegeria pomeroyi DSS-3
Oceanibulbus indolifex HEL45	Roseobacter denitrificans OCh 114	Ruegeria sp. TM1040
Oceanicola batsensis HTCC2597	Roseobacter litoralis Och 149	Ruegeria sp. Trich CH4B
Oceanicola granulosus HTCC2516	Roseobacter sp. AzwK-3b	Ruegeria sp. R11
Octadecabacter arcticus 238	Roseobacter sp. CCS2	Sagittula stellata E-37
Octadecabacter antarcticus 307	Roseobacter sp. GAI101	Sulfitobacter sp. EE-36
Pelagibaca bermudensis HTCC2601	Roseobacter sp. MED193	Sulfitobacter NAS-14.1
Phaeobacter gallaeciensis BS107	Roseobacter sp. SK209-2-6	Thalassiobium R2A62
Controls
Candidatus Pelagibacter ubique HTCC1062	Escherichia coli str. K-12 substr. MG165	Marine gamma Proteobacterium HTCC2080
Candidatus Puniceispirillum marinum IMCC1322	Maribacter sp. HTCC2170	Marine gamma Proteobacterium HTCC2148
Download all files as one zip file (11.4 MB)

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