Biology subjects

Redder, P.

Publications and source records attributed to Redder, P..

5 recordsLinked to original sources

bioRxiv2026

Intrinsic features of the RNase E membrane targeting sequence specify RNA degradosome organisation and activity

In bacteria, transcription and RNA degradation are physically separated via segregation of the main ribonucleolytic machinery - the RNA degradosome - into phase-separated or membrane-anchored molecular assemblies driven by RNase E. Despite the widespread conservation of an amphipathic membrane anchor (MTS) in RNase E, the regulatory information embedded within this sequence and its biological importance remain poorly understood. Here, we have studied the importance of the Pseudomonas aeruginosa RNase E MTS for bacterial fitness or virulence and assessed its interchangeability. We show that amphipathicity is dispensable for foci scaffolding but necessary for proper foci morphology, dynamics, and localisation, although sequence modulates foci behaviour. Loss of the MTS additionally causes a drastic sensitivity to high salinity and a consistent virulence defect in Galleria mellonella larvae. Moreover, transcriptomics and analysis of mRNA spatial organisation reveal that the MTS mutant has specific stabilisation of localised membrane protein-encoding transcripts, together with abnormal operon processing. Altogether, our study highlights the elegant MTS-mediated control of spatial organisation and target selection, shaping the transcriptome and bacterial stress response.

microbiology↗

bioRxiv2025

rnaends: an R package targeted to study the exact RNA ends at the nucleotide resolution

AO_SCPLOWBSTRACTC_SCPLOW5 and 3 RNA-end sequencing protocols have unlocked new opportunities to study aspects of RNA metabolism such as synthesis, maturation and degradation, by enabling the quantification of exact ends of RNA molecules in vivo. From RNA-Seq data that have been generated with one of the specialized protocols, it is possible to identify transcription start sites (TSS) and/or endoribonucleolytic cleavage sites, and even, in some cases, co-translational 5 to 3 degradation dynamics. Furthermore, post-transcriptional addition of ribonucleotides at the 3 end of RNA can be studied at the nucleotide resolution. While different RNA-end sequencing library protocols exist that have been adapted to a specific organism (prokaryote or eukaryote) or specific biological question, the generated RNA-Seq data are very similar and share common processing steps. Most importantly, the major aspect of RNA-end sequencing is that only the 5 or 3 end mapped location is of interest, contrary to conventional RNA sequencing that considers genomic ranges for gene expression analysis. This translates to a simple representation of the quantitative data as a count matrix of RNA-end location on the reference sequences. This representation seems under-exploited and is, to our knowledge, not available in a generic package focused on the analyses on the exact transcriptome ends. Here, we present the rnaends R package which is dedicated to RNA-end sequencing analysis. It offers functions for raw read pre-processing, RNA-end mapping and quantification, RNA-end count matrix post-processing, and further downstream count matrix analyses such as TSS identification, fast Fourier transform for signal periodic pattern analysis, or differential proportion of RNA-end analysis. The use of rnaends is illustrated here with applications in RNA metabolism studies through selected rnaends workflows on published RNA-end datasets: (i) TSS identification, (ii) ribosome translation speed and co-translational degradation, (iii) post-transcriptional modification analysis and differential proportion analysis.

bioinformatics↗

bioRxiv2023

Critical factors for precise and efficient RNA cleavage by RNase Y in Staphylococcus aureus

Cellular processes require precise and specific gene regulation, in which continuous mRNA degradation is a major element. The mRNA degradation mechanisms should be able to degrade a wide range of different RNA substrates with high efficiency, but should at the same time be limited, to avoid killing the cell by elimination of all cellular RNA. RNase Y is a major endoribonuclease found in most Firmicutes, including Bacillus subtilis and Staphylococcus aureus. However, the molecular interactions that direct RNase Y to cleave the correct RNA molecules at the correct position remain unknown. In this work we have identified transcripts that are homologs in S. aureus and B. subtilis, and are RNase Y targets in both bacteria. Two such transcript pairs were used as models to show a functional overlap between the S. aureus and the B. subtilis RNase Y, which highlighted the importance of the nucleotide sequence of the RNA molecule itself in the RNase Y targeting process. Cleavage efficiency is driven by the primary nucleotide sequence immediately downstream of the cleavage site and base-pairing in a secondary structure a few nucleotides downstream. Cleavage positioning is roughly localised by the downstream secondary structure and fine-tuned by the nucleotide immediately upstream of the cleavage. The identified elements were sufficient for RNase Y-dependent cleavage, since the sequence elements from one of the model transcripts were able to convert an exogenous non-target transcript into a target for RNase Y. Author summaryIn order to correctly regulate the level of RNAs, bacteria require their RNA to be continuously synthesised and degraded. However, even related bacterial species can have different sets of ribonucleases, each with their own target criteria. Here we explore which sequence elements of an RNA are important for being targeted by the endoribonuclese RNase Y in the two bacteria, Staphylococcus aureus and Bacillus subtilis. We specifically examine the RNase Y dependent cleavage of two transcripts that have homologs in both bacteria. We identify a short single-stranded regions immediately downstream of the cleavage position can be modified to change the cleavage efficiency up to 20-fold. We furthermore discover that a secondary structure a few nucleotides downstream of the cleavage is required for cleavage and that the positioning of the cleavage can be modulated by moving this structure.

molecular biology↗

bioRxiv2020

Occurrence and distribution of fecal indicators and pathogenic bacteria in seawater and Perna perna mussel in the Gulf of Annaba (Southern Mediterranean)

The brown mussel Perna perna is a marine bivalve that is widely distributed and consumed along the east coast of Algeria. Due to its filter-feeding capacity, this mollusk can accumulate large quantities of pathogenic microorganisms from the surrounding waters, thus acting as bio-indicator of coastal environments. The objective of this study is to investigate the occurrence and distribution of fecal indicators and pathogenic bacteria in seawaters and mussels collected from four different sites in the Gulf of Annaba through physicochemical, biochemical and molecular analysis. The obtained results revealed that the levels of fecal indicator bacteria (FIB) were alarmingly high at Sidi Salem and Rezgui Rachid when compared with the two other sites (p < 0.05) and largely exceeded the permissible limits. Besides, P. perna collected from all sites were several fold more contaminated by these germs than seawater samples, notably, during the warm season of the study period. Biochemical and molecular analysis showed that isolated bacteria from both environmental compartments were mostly potentially pathogenic species such as E. coli, Salmonella, Staphylococcus, Klebsiella, Pseudomonas and Proteus. These principal findings demonstrate the strong involvement of anthropogenic activities on the microbiological quality of the Gulf and highlight the role of P. perna as an effective bio-indicator of the bacteriological quality of coastal waters.

ecology↗

bioRxiv2016

Cell Cycle Constraints and Environmental Control of Local DNA Hypomethylation in Alpha-Proteobacteria

Heritable DNA methylation imprints are ubiquitous and underlie genetic variability from bacteria to humans. In microbial genomes, DNA methylation has been implicated in gene transcription, DNA replication and repair, nucleoid segregation, transposition and virulence of pathogenic strains. Despite the importance of local (hypo)methylation at specific loci, how and when these patterns are established during the cell cycle remains poorly characterized. Taking advantage of the small genomes and the synchronizability of -proteobacteria, we discovered that conserved determinants of the cell cycle transcriptional circuitry establish specific hypomethylation patterns in the cell cycle model system Caulobacter crescentus. We used genome-wide methyl-N6-adenine (m6A-) analyses by restriction-enzyme-cleavage sequencing (REC-Seq) and single-molecule real-time (SMRT) sequencing to show that MucR, a transcriptional regulator that represses virulence and cell cycle genes in S-phase but no longer in G1-phase, occludes 5-GANTC-3 sequence motifs that are methylated by he DNA adenine methyltransferase CcrM. Constitutive expression of CcrM or heterologous methylases in at least two different -proteobacteria homogenizes m6A patterns even when MucR is present and affects promoter activity. Environmental stress (phosphate limitation) can override and reconfigure local hypomethylation patterns imposed by the cell cycle circuitry that dictate when and where local hypomethylation is instated.\n\nAuthor SummaryDNA methylation is the post-replicative addition of a methyl group to a base by a methyltransferase that recognise a specific sequence, and represents an epigenetic regulatory mechanism in both eukaryotes and prokaryotes. In microbial genomes, DNA methylation has been implicated in gene transcription, DNA replication and repair, nucleoid segregation, transposition and virulence of pathogenic strains. CcrM is a conserved, cell cycle regulated adenine methyltransferase that methylates GANTC sites in -proteobacteria. N6-methyl-adenine (m6A) patterns generated by CcrM can change the affinity of a given DNA-binding protein for its target sequence, and therefore affect gene expression. Here, we combine restriction enzyme cleavage-deep sequencing (REC-Seq) with SMRT sequencing to identify hypomethylated 5-GANTC-3 (GANTCs) in -proteobacterial genomes instated by conserved cell cycle factors. By comparing SMRT and REC-Seq data with chromatin immunoprecipitation-deep sequencing data (ChIP-Seq) we show that a conserved transcriptional regulator, MucR, induces local hypomethylation patterns by occluding GANTCs to the CcrM methylase and we provide evidence that this competition occurs during S-phase, but not in G1-phase cells. Furthermore, we find that environmental signals (such as phosphate depletion) are superimposed to the cell cycle control mechanism and can override the specific hypomethylation pattern imposed by the cell cycle transcriptional circuitry.

microbiology↗