From Corynebacterium glutamicum to Mycobacterium tuberculosis--towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet.
Year by year, approximately two million people die from tuberculosis, a disease caused by the bacterium Mycobacterium tuberculosis. There is a tremendous need for new anti-tuberculosis therapies (antituberculotica) and drugs to cope with the spread of tuberculosis. Despite many efforts to obtain a better understanding of M. tuberculosis' pathogenicity and its survival strategy in humans, many questions are still unresolved. Among other cellular processes in bacteria, pathogenicity is controlled by transcriptional regulation. Thus, various studies on M. tuberculosis concentrate on the analysis of transcriptional regulation in order to gain new insights on pathogenicity and other essential processes ensuring mycobacterial survival. We designed a bioinformatics pipeline for the reliable transfer of gene regulations between taxonomically closely related organisms that incorporates (i) a prediction of orthologous genes and (ii) the prediction of transcription factor binding sites. In total, 460 regulatory interactions were identified for M. tuberculosis using our comparative approach. Based on that, we designed a publicly available platform that aims to data integration, analysis, visualization and finally the reconstruction of mycobacterial transcriptional gene regulatory networks: MycoRegNet. It is a comprehensive database system and analysis platform that offers several methods for data exploration and the generation of novel hypotheses. MycoRegNet is publicly available at http://mycoregnet.cebitec.uni-bielefeld.de.
Krawczyk
Justina
J
Computational Genomics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany and International Computer Science Institute, Berkeley, CA, USA.
Kohl
Thomas A
TA
Goesmann
Alexander
A
Kalinowski
Jörn
J
Baumbach
Jan
J
D001426:Bacterial Proteins / Q000378:metabolism; D001665:Binding Sites; D003196:Computer Graphics; D048230:Corynebacterium glutamicum / Q000235:genetics*; D030541:Databases, Genetic; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D020407:Internet; D009169:Mycobacterium tuberculosis / Q000235:genetics*; D018511:Systems Integration; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic; D014584:User-Computer Interface
D001426:Bacterial Proteins; C513697:CRP protein, Mycobacterium tuberculosis; D014157:Transcription Factors