Biology subjects

Ranaweera, S.

Publications and source records attributed to Ranaweera, S..

2 recordsLinked to original sources

bioRxiv2025

EXPRESSION OF CONJUGATION GENES IS CONTROLLED BY PROCESSIVE ANTITERMINATION AND A NOVEL ZIPPER-TYPE TRANSCRIPTIONAL ATTENUATION MECHANISM

Proper expression of genes clustered in operons, particularly large operons, can be complex, often consisting of multiple regulatory switches. The conjugation operon present on the Bacillus subtilis conjugative plasmid pLS20 is over 32 kb long. This operon starts with a 456 nt leader region, which is followed by the first two genes of the operon, encoding a two-component processive antitermination system. Here, we demonstrate that the long leader region encodes a transcriptional attenuator that we named cATTpLS20. In vivo and in vitro analyses showed that the attenuator is composed of three segments: a stem-loop structure with a long imperfect stem that is preceded by a sequence that may form a weak stem-loop and followed by a sequence that may form an intrinsic terminator. Sequences of the upstream stem loop and downstream terminator are complementary, allowing further extension of the long stem, thereby generating an antiterminator conformation. Based on similarity with a zipper we coined this the zipper-type attenuator. Similar zipper-type attenuators are present upstream of the first genes of conjugation operons of all pLS20 family plasmids, as well as on many other conjugative plasmids in Gram-positive bacteria, suggesting that a common attenuation mechanism regulates expression of many conjugative operons. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/689506v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@a86a7eorg.highwire.dtl.DTLVardef@e787f8org.highwire.dtl.DTLVardef@8fdb75org.highwire.dtl.DTLVardef@90f842_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2024

Characterization of bacterial intrinsic transcription terminators identified with TERMITe - a novel method for comprehensive analysis of Term-seq data

In recent years, Term-seq became a standard experimental approach for high-throughput identification of 3 ends of bacterial transcripts. It was widely adopted to study transcription termination events and 3 maturation of bacterial RNAs. Despite widespread utilization, a universal bioinformatics toolkit for comprehensive analysis of Term-seq sequencing data is still lacking. Here, we describe TERMITe, a novel method for the identification of stable 3 RNA ends based on bacterial Term-seq data. TERMITe works with data obtained from both currently available Term-seq protocols and provides robust identification of the 3 RNA termini. Unique features of TERMITe include the calculation of the transcription termination efficiency using matched RNA-seq data and the comprehensive annotation of the identified 3 RNA ends, allowing functional analysis of the results. We have applied TERMITe to the comparative analysis of experimentally validated intrinsic terminators spanning different species across the bacterial domain of life, revealing substantial differences in their sequence and secondary structure. We also provide a complete atlas of experimentally validated intrinsic transcription termination sites for 13 bacterial species, including Escherichia coli, Bacillus subtilis, Listeria monocytogenes, Enterococcus faecalis, Synechocystis sp., Streptomyces clavuligerus, Streptomyces griseus, Streptomyces coelicolor, Streptomyces avermitilis, Streptomyces lividans, Streptomyces tsukubaensis, Streptomyces venezuelae, and Zymomonas mobilis.

bioinformatics↗