Abstract
Intrinsic transcription termination (ITT) sites are currently identified by locating single and double-adjacent RNA hairpins downstream of the stop codon. ITTs for a limited number of genes/operons in only a few bacterial genomes are currently known. This lack of coverage is a lacuna in the existing ITT inference methods. We have studied the inter-operon regions of 13 genomes covering all major phyla in bacteria, for which good quality public RNA-seq data exist. We identify ITT sites in 87% of cases by predicting hairpin(s) and validate against 81% of cases for which the RNA-seq derived sites could be calculated. We identify 72% of these sites correctly, with 98% of them located ≤ 80 bases downstream of the stop codon. The predicted hairpins form a cluster (when present < 15 bases) in two-thirds of the cases, the remaining being single hairpins. The largest number of clusters is formed by two hairpins, and the occurrence decreases exponentially with an increasing number of hairpins in the cluster. Our study reveals that hairpins form an effective ITT unit when they act in concert in a cluster. Their pervasiveness along with single hairpin terminators corroborates a wider utilization of ITT mechanisms for transcription control across bacteria.
Highlights
By our analysis and others[19,20,21], it was observed by computational as well as in vivo methods that poly U trail is not necessary for intrinsic transcription termination (ITT)
We look for the presence of an ITT site in the 13 bacterial genomes (Table 1)
Using the Interoperonic Region (IR; Fig. 1a) as the scan window, we individually identify a hairpin in either cluster or single, with the presence/ absence of poly U/A stretch
Summary
By our analysis and others[19,20,21], it was observed by computational as well as in vivo methods that poly U trail is not necessary for ITT. Other features in sequences downstream of the stop codon affect termination efficiency along with stemloop and poly U segment downstream of the hairpin stem This includes two G/C base pairs in the U-rich tract, an elemental pause sequence, or conserved sequences like TCTG downstream of hairpin[27,28]. The RNA hairpins far identified as transcription terminators have been classified in a bid to understand their secondary structure and function[18]. Classification labels such as I- and L-shape have been given to single hairpins where L shape hairpins are I hairpins extended by a poly-U trail. We can correctly identify that around three-fourths of all microbial operons/single genes have ITT sites without a bias towards the GC base composition
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