Detection of intrinsic transcription termination sites in bacteria: consensus from hairpin detection approaches

Abstract

We compare the WebGeSTer and INtrinsic transcription TERmination hairPIN (INTERPIN) databases used for intrinsic transcription termination (ITT) site prediction in bacteria. The former deploys inverted nucleotide repeat detection for identification of RNA hairpin, while the latter a pair-potential function – the hairpin energy score evaluation being identical for both. We find INTERPIN more sensitive than WebGeSTer with about 6% and 51% additional predictions for ITTs in chromosomal and plasmid operons, respectively. INTERPIN hairpins are relatively shorter in length with ungapped stem, and even located in AT-rich segments, compared to GC-rich longer hairpins with a gapped stem in WebGeSTer. The GC%, length, and energy score from INTERPIN transcription units (TUs) are best inter-correlated while the lowest energy single hairpins from WebGeSTer, considered suitable for ITT, being the worst. Around 72% TUs from the two databases overlap, and ∼60% of all alternate ITT sites downstream of TUs overlap, of which 65% are cluster hairpins. This helps highlight hairpin features that can be used to identify termination sites in bacteria across different prediction methods. Overall, the pair-potential-function-based hairpins screened appear to be more consistent with the kinetic and thermodynamics processes of ITT known to date.

Communicated by Ramaswamy H. Sarma

Keywords:

• Intrinsic transcription termination
• bacteria
• hairpin detection
• database comparison

Acknowledgments

SG thanks the Department of Biotechnology (DBT), New Delhi for a fellowship. DP thanks the DBT for supporting the computational facilities.

Author contributions

Swati Gupta: Methodology, Software, data curation, writing-original draft preparation, Visualization, Investigation. Debnath Pal: Conceptualization, Methodology, writing- reviewing and editing.

Disclosure statement

None declared.

Additional information

Funding

The author(s) reported there is no funding associated with the work featured in this article.