sRNATarBase: a comprehensive database of bacterial sRNA targets verified by experiments

Abstract

Bacterial sRNAs are an emerging class of small regulatory RNAs, 40-500 nt in length, which play a variety of important roles in many biological processes through binding to their mRNA or protein targets. A comprehensive database of experimentally confirmed sRNA targets would be helpful in understanding sRNA functions systematically and provide support for developing prediction models. Here we report on such a database--sRNATarBase. The database holds 138 sRNA-target interactions and 252 noninteraction entries, which were manually collected from peer-reviewed papers. The detailed information for each entry, such as supporting experimental protocols, BLAST-based phylogenetic analysis of sRNA-mRNA target interaction in closely related bacteria, predicted secondary structures for both sRNAs and their targets, and available binding regions, is provided as accurately as possible. This database also provides hyperlinks to other databases including GenBank, SWISS-PROT, and MPIDB. The database is available from the web page http://ccb.bmi.ac.cn/srnatarbase/.

FIGURE 1.

(A) The query interface for the database, from which users can search sRNA targets using a particular field or a combination of fields. (B) The part of the search results using default values, from which users can check detailed information on sRNA targets, such as sRNA sequence, target sequence, and supporting experimental protocols by clicking the hyperlinked “Detail.”

FIGURE 2.

Detailed information is displayed for a particular database entry, including general information (A), sRNA information (B), target information (C), and supporting information (D). Additionally, the links to the databases NCBI (A,B,D), MPID (C), and SWISS-PROT (C) are provided from which further information on the sRNA and its target can be accessed.

FIGURE 3.

The interface of BLAST-based phylogenetic analysis of an sRNA–mRNA target interaction is provided, through which the conservation of sRNA–mRNA target interaction or their binding regions can be checked among the closely related bacteria.

FIGURE 4.

The predicted secondary structure of sRNA DsrA and its binding information with target hns, as well as the binding region list of sRNA DsrA with other targets are displayed, from which the structure features of the binding regions between an sRNA and its targets can be explored.