Staphylococcus regulatory RNA database (SRD)

Staphylococcus regulatory RNA database (SRD) catalogs regulatory small RNAs (sRNAs) from staphylococci, annotating sequences and genomic locations, recording experimental support, and providing structural and target predictions to support studies of bacterial gene regulation.

Key Features:

• srn identifier system: A simplified identifier scheme assigns srn names based on genetic location in the Staphylococcus aureus strain N315 reference genome.
• Dataset compilation and deduplication: An initial compilation of 894 sequences was curated and redundant entries removed to yield 575 unique srn.
• Experimental support annotations: Each sRNA entry includes details on experimental support to enable evaluation of evidence.
• RNA-seq analyses: RNA-seq data from S. aureus strains N315, NCTC8325, and Newman were used during annotation and identified an additional 159 sRNAs reported as transcribed independent of RNA-seq data.
• Cross-strain and cross-species prediction: The database predicts the number and genomic locations of srn across 18 S. aureus strains and 10 other staphylococcal species.
• Comparative genomics: Comparative analysis across 32 staphylococcal genomes documents variability and poor conservation of srn between species.
• Secondary-structure prediction: sRNA secondary structures are predicted using MFold.
• Sequence similarity search: Integrated BLAST searches allow sequence-based comparison and retrieval.
• Target prediction: intaRNA is used to predict potential RNA–RNA interactions and targets.

Scientific Applications:

• Bacterial gene regulation studies: Enables analysis of sRNA sequences, genomic context, and experimental evidence to investigate regulatory roles in S. aureus and related staphylococci.
• sRNA discovery and annotation: Supports identification and curation of sRNAs by integrating compiled sequences and RNA-seq data.
• Comparative genomics of staphylococci: Facilitates cross-strain and cross-species comparisons to assess sRNA conservation and variability.
• Structure and target inference: Provides MFold-based secondary-structure predictions and intaRNA-based target predictions to inform functional hypotheses.

Methodology:

Compilation of 894 sequences with redundancy removal to 575 unique srn; assignment of srn identifiers based on genetic location in S. aureus strain N315; RNA-seq analyses on N315, NCTC8325, and Newman with identification of 159 additional sRNAs transcribed independent of RNA-seq data; prediction of srn number and location across 18 S. aureus strains and 10 other staphylococcal species; comparative analysis across 32 staphylococcal genomes; sRNA secondary-structure prediction using MFold; sequence similarity searches with BLAST; target prediction using intaRNA.