Riboregulation in bacteria: From general principles to novel mechanisms of the trp attenuator and its sRNA and peptide products

E Evguenieva‐Hackenberg - Wiley Interdisciplinary Reviews …, 2022 - Wiley Online Library
Gene expression strategies ensuring bacterial survival and competitiveness rely on cis‐and
trans‐acting RNA‐regulators (riboregulators). Among the cis‐acting riboregulators are …

Thirty Years of sRNA-Mediated Regulation in Staphylococcus aureus: From Initial Discoveries to In Vivo Biological Implications

G Menard, C Silard, M Suriray, A Rouillon… - International Journal of …, 2022 - mdpi.com
Staphylococcus aureus is a widespread livestock and human pathogen that colonizes
diverse microenvironments within its host. Its adaptation to the environmental conditions …

Freiburg RNA tools: a central online resource for RNA-focused research and teaching

M Raden, SM Ali, OS Alkhnbashi, A Busch… - Nucleic acids …, 2018 - academic.oup.com
The Freiburg RNA tools webserver is a well established online resource for RNA-focused
research. It provides a unified user interface and comprehensive result visualization for …

Riboregulation in nitrogen-fixing endosymbiotic bacteria

M Robledo, NI García-Tomsig, JI Jiménez-Zurdo - Microorganisms, 2020 - mdpi.com
Small non-coding RNAs (sRNAs) are ubiquitous components of bacterial adaptive
regulatory networks underlying stress responses and chronic intracellular infection of …

[HTML][HTML] Differential expression of small RNAs in biofilm-producing clinical methicillin-susceptible Staphylococcus aureus recovered from human urine

SU Jones, BP Kee, CH Chew, CC Yeo, KH Chua… - Heliyon, 2024 - cell.com
Bacterial small RNAs (sRNAs) play crucial roles in coordinating gene regulatory networks in
various physiological processes, including biofilm formation. In this study, RNA sequencing …

Structure and interaction prediction in prokaryotic RNA biology

PR Wright, M Mann, R Backofen - Regulating with RNA in …, 2018 - Wiley Online Library
For over a decade, prokaryotic and eukaryotic RNA biology exploration has unveiled the
multifaceted and central contribution of RNA‐based control in all domains of life. RNA …

The impact of various seed, accessibility and interaction constraints on sRNA target prediction-a systematic assessment

M Raden, T Müller, S Mautner, R Gelhausen… - BMC …, 2020 - Springer
Background Seed and accessibility constraints are core features to enable highly accurate
sRNA target screens based on RNA-RNA interaction prediction. Currently, available tools …

A framework for the computational prediction and analysis of non-coding RNAs in microbial environmental populations and their experimental validation

SC Lott, K Voigt, SJ Lambrecht, WR Hess… - The ISME …, 2020 - academic.oup.com
Small regulatory RNAs and antisense RNAs play important roles in the regulation of gene
expression in bacteria but are underexplored, especially in natural populations. While …

An integrated database of small RNAs and their interplay with transcriptional gene regulatory networks in Corynebacteria

MTD Parise, D Parise, FF Aburjaile… - Frontiers in …, 2021 - frontiersin.org
Small RNAs (sRNAs) are one of the key players in the post-transcriptional regulation of
bacterial gene expression. These molecules, together with transcription factors, form …

GLASSgo in Galaxy: high-throughput, reproducible and easy-to-integrate prediction of sRNA homologs

RA Schäfer, SC Lott, J Georg, BA Grüning… - …, 2020 - academic.oup.com
Motivation The correct prediction of bacterial sRNA homologs is a prerequisite for many
downstream analyses based on comparative genomics, but it is frequently challenging due …