Era7
era7

bacterial genomics

Bacterial genomics is one of the fundamental research lines of Era7 Bioinformatics Unit. Era7 participates actively in this research area.

 

Era7 Bioinformatics is annotating the genome of E Coli strain causing EU outbreak.

We are annotating the draft sequences from BGI based in an assembly from Nick Loman: http://pathogenomics.bham.ac.uk/blog/2011/06/ehec-genome-assembly/

 

Within this line, we focus on

 

transcriptional regulation
We have developed ExtraTrain, a database focused on bacterial transcriptional factors and we have research interests in specific features of the different families of regulators and their DNA-binding sites.  We also are working in new paradigms to represent and analyze transcriptional networks from a systems biology point of view.
extragenic space: palindromes and repeats
Within bacterial genomics and related to transcriptional regulation we are studying the extragenic space of bacterial genomes, since within non-coding sequences are included the most important regulatory signals. Palindromicity is one feature of DNA binding-sites and other repetitive extragenic sequences that we are paying attention to.

Publications

The innate immunity role of cathepsin-D is linked to Trp-491 and Trp-492 residues of listeriolysin O.
Carrasco-Marín E, Madrazo-Toca F, de Los Toyos JR, Cacho-Alonso E, Tobes R, Pareja E, Paradela A, Albar JP, Chen W, Gomez-Lopez MT, Alvarez-Dominguez C.
Mol Microbiol. 2009 Apr 6.
Characterization of a Listeria monocytogenes protein interfering with Rab5a.
Alvarez-Dominguez C, Madrazo-Toca F, Fernandez-Prieto L, Vandekerckhove J, Pareja E, Tobes R, Gomez-Lopez MT, Del Cerro-Vadillo E, Fresno M, Leyva-Cobián F, Carrasco-Marín E.
Traffic. 2008 Mar;9(3):325-37.
Cutting edge: natural DNA repetitive extragenic sequences from gram-negative pathogens strongly stimulate TLR9.
Magnusson M, Tobes R, Sancho J, Pareja E.
J Immunol. 2007 Jul 1;179(1):31-5.
Bacterial repetitive extragenic palindromic sequences are DNA targets for Insertion Sequence elements.
Tobes R, Pareja E.
BMC Genomics. 2006 Mar 24;7:62. Review.
ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organisms.
Pareja E, Pareja-Tobes P, Manrique M, Pareja-Tobes E, Bonal J, Tobes R.
BMC Microbiol. 2006 Mar 15;6:29.
Repetitive extragenic palindromic sequences in the Pseudomonas syringae pv. tomato DC3000 genome: extragenic signals for genome reannotation.
Tobes R, Pareja E.
Res Microbiol. 2005 Apr;156(3):424-33. Epub 2005 Jan 28.
Growth phase-dependent expression of the Pseudomonas putida KT2440 transcriptional machinery analysed with a genome-wide DNA microarray.
Yuste L, Hervás AB, Canosa I, Tobes R, Jiménez JI, Nogales J, Pérez-Pérez MM, Santero E, Díaz E, Ramos JL, de Lorenzo V, Rojo F.
Environ Microbiol. 2006 Jan;8(1):165-77
The TetR family of transcriptional repressors.
Ramos JL, Martínez-Bueno M, Molina-Henares AJ, Terán W, Watanabe K, Zhang X, Gallegos MT, Brennan R, Tobes R.
Microbiol Mol Biol Rev. 2005 Jun;69(2):326-56
REP code: defining bacterial identity in extragenic space.
Tobes R, Ramos JL.
Environ Microbiol. 2005 Feb;7(2):225-8.
BacTregulators: a database of transcriptional regulators in bacteria and archaea.
Martínez-Bueno M, Molina-Henares AJ, Pareja E, Ramos JL, Tobes R.
Bioinformatics. 2004 Nov 1;20(16):2787-91
Detection of multiple extracytoplasmic function (ECF) sigma factors in the genome of Pseudomonas putida KT2440 and their counterparts in Pseudomonas aeruginosa PA01.
Martínez-Bueno MA, Tobes R, Rey M, Ramos JL.
Environ Microbiol. 2002 Dec;4(12):842-55.
Species-specific repetitive extragenic palindromic (REP) sequences in Pseudomonas putida.
Aranda-Olmedo I, Tobes R, Manzanera M, Ramos JL, Marqués S.
Nucleic Acids Res. 2002 Apr 15;30(8):1826-33.
AraC-XylS database: a family of positive transcriptional regulators in bacteria.
Tobes R, Ramos JL.
Nucleic Acids Res. 2002 Jan 1;30(1):318-21.