SubtiWiki 2.0—an integrated database for the model organismBacillus subtilis

Abstract

To understand living cells, we need knowledge of each of their parts as well as about the interactions of these parts. To gain rapid and comprehensive access to this information, annotation databases are required. Here, we present SubtiWiki 2.0, the integrated database for the model bacterium Bacillus subtilis (http://subtiwiki.uni-goettingen.de/). SubtiWiki provides text-based access to published information about the genes and proteins of B. subtilis as well as presentations of metabolic and regulatory pathways. Moreover, manually curated protein-protein interactions diagrams are linked to the protein pages. Finally, expression data are shown with respect to gene expression under 104 different conditions as well as absolute protein quantification for cytoplasmic proteins. To facilitate the mobile use of SubtiWiki, we have now expanded it by Apps that are available for iOS and Android devices. Importantly, the App allows to link private notes and pictures to the gene/protein pages. Today, SubtiWiki has become one of the most complete collections of knowledge on a living organism in one single resource.

Large-scale reduction of the Bacillus subtilis genome: consequences for the transcriptional network, resource allocation, and metabolism

“…The highly increased transcription of the MhqR regulon is also the reason for the overrepresentation of the functional category Lifestyle in protein resource allocation (see above). This category includes the stress proteins and thus also the proteins involved in resistance against oxidative and electrophile stress (see http://subtiwiki.unigoettingen.de/wiki/index.php/Resistance_against_ oxidative_and_electrophile_stress) (Michna et al 2016).…”

Gene expression regulation in the plant growth promoting Bacillus atrophaeus UCMB-5137 stimulated by maize root exudates

“…The 2 folds threshold was used in this case to make the results comparable with the stress response regulation patterns published by Sappa et al (2013) and Kohlstedt et al (2014). Operon predictions and their transcriptional regulations were checked by using the SubtiWiki Web-based resource (Michna et al, 2015). Putative transcription regulation binding sites were identified by using the software tools provided by DBTBS server (Sierro et al, 2008; http://dbtbs.hgc.jp/).…”

“…To avoid false-positive identification of untranslated regions (5'-UTR) as ncRNA, only the loci flanked by oppositely regulated genes were considered in this work. Identified sequences were compared to the records of ncRNA in SubtiWiki database (Michna et al, 2015) and those reported by Fan et al (2015) in Bacillus amyloliquefaciens FZB42. The level of sequence conservation of predicted ncRNA was checked by BLASTN search through the complete genome DNA sequences of B. subtilis ssp.…”

“…There were many other down-regulated intergenic spacer loci; however, since it was difficult to distinguish them from putative 5'-UTR as they were surrounded by down-regulated neighbor genes, these loci were not considered in this study. (Michna et al, 2015) and DBTBS databases (Sierro et al, 2008). Both species belonged to the same group of related organisms, which were not easily distinguished even by the 16S rRNA sequences (Safronova et al, 2012).…”

Bacillus subtilis, the model Gram‐positive bacterium: 20 years of annotation refinement

“…This resource is now routinely used by the community, providing text‐based access to published information about the genes and proteins of B. subtilis as well as presentations of its metabolic and regulatory pathways (Michna et al ., 2016). …”