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

Gupta, S and Pal, D (2024) Detection of intrinsic transcription termination sites in bacteria: consensus from hairpin detection approaches. In: Journal of Biomolecular Structure and Dynamics .

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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. © 2024 Informa UK Limited, trading as Taylor & Francis Group.

Item Type:	Journal Article
Publication:	Journal of Biomolecular Structure and Dynamics
Publisher:	Taylor and Francis Ltd.
Additional Information:	The copyright for this article belongs to Taylor and Francis Ltd.
Department/Centre:	Division of Interdisciplinary Sciences > Computational and Data Sciences
Date Deposited:	25 May 2024 12:38
Last Modified:	25 May 2024 12:38
URI:	https://eprints.iisc.ac.in/id/eprint/84880

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