Due to the high exposition to changing environmental conditions, bacteria have developed many mechanisms enabling immediate adjustments of gene expression. In many cases, the required speed and plasticity of the response are provided by RNA-dependent regulatory mechanisms. This is possible due to the very high dynamics and flexibility of an RNA structure, which provide the necessary sensitivity and specificity for efficient sensing and transduction of environmental signals. In this review, we will discuss the current knowledge about known bacterial regulatory mechanisms which rely on RNA structure. To better understand the structure-driven modulation of gene expression, we describe the basic theory on RNA structure folding and dynamics. Next, we present examples of multiple mechanisms employed by RNA regulators in the control of bacterial transcription and translation.

Background: Streptococcus agalactiae, referred to as Group B Streptococcus (GBS), is a prominent bacterium causing life-threatening neonatal infections. Although antibiotics are efficient against GBS, growing antibiotic resistance forces the search for alternative treatments and/or prevention approaches. Antimicrobial photodynamic inactivation (aPDI) appears to be a potent alternative non-antibiotic strategy against GBS. Methods: The effect of rose bengal aPDI on various GBS serotypes, Lactobacillus species, human eukaryotic cell lines and microbial vaginal flora composition was evaluated. Results: RB-mediated aPDI was evidenced to exert high bactericidal efficacy towards S. agalactiae in vitro (>4 log₁₀ units of viability reduction for planktonic and >2 log₁₀ units for multispecies biofilm culture) and in vivo (ca. 2 log₁₀ units of viability reduction in mice vaginal GBS colonization model) in microbiological and metagenomic analyses. At the same time, RB-mediated aPDI was evidenced to be not mutagenic and safe for human vaginal cells, as well as capable of maintaining the balance and viability of vaginal microbial flora. Conclusions: aPDI can efficiently kill GBS and serve as an alternative approach against GBS vaginal colonization and/or infections.

The recent development of high-throughput workflows in genomics and transcriptomics revealed that efficient annotation of such results is essential for researchers to draw conclusions from obtained results. Although some tools are available, their functionality is limited. Here, we present AGouTI–a universal tool for flexible annotation of any genomic or transcriptomic coordinates using known genomic features deposited in different publicly available databases in the form of GTF or GFF files. In contrast to currently available tools, AGouTI is designed to provide a flexible selection of genomic features overlapping or adjacent to annotated intervals and can be used on custom column-based text files obtained from different data analysis pipelines. Although providing many unique options, AGouTI is straightforward in installation and usage, enabling effortless integration into existing data analysis workflows.

Summary: The recent development of high-throughput workflows in genomics and transcriptomics revealed that efficient annotation is essential for effective data processing and analysis. Although a variety of tools dedicated to this purpose is available, their functionality is limited. Here, we present AGouTI – a universal tool for flexible annotation of any genomic or transcriptomic coordinates using known genomic features deposited in different publicly available databases in the form of GTF or GFF files. In contrast to currently available tools, AGouTI is designed to provide a flexible selection of genomic features overlapping or adjacent to annotated intervals, can be used on custom column-based text files obtained from different data analysis pipelines, and supports operations on transcriptomic coordinate systems. Availability and Implementation: AGouTI was implemented using Python 3 and is freely available on GitHub ( https://github.com/zywicki-lab/agouti ), from the Python Package Index ( https://pypi.org/project/AGouTI/ ) or Anaconda Cloud ( https://anaconda.org/bioconda/agouti ). We also provide a Galaxy wrapper available from the Galaxy Tool Shed ( https://toolshed.g2.bx.psu.edu/view/janktoolshed/agouti/c204da8f836d ). Supplementary information: Supplementary Data are available at Publisher site online. Files for replicating the use-case scenario described in Supplementary Data are available at Zenodo: https://doi.org/10.5281/zenodo.7317210 . Contact: Marek.Zywicki@amu.edu.pl

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 .