Biology subjects

Boudvillain, M.

Publications and source records attributed to Boudvillain, M..

4 recordsLinked to original sources

bioRxiv2026

Distinct spatial organisation of Rho and RNA Polymerase in Salmonella cells

Rho is a conserved, ATP-dependent RNA translocase that terminates transcription at hundreds of sites across bacterial genomes. Although the molecular mechanism of Rho-dependent termination is well characterized, its spatial interplay with RNA polymerase (RNAP) within bacterial cells remains elusive. To address this question, we constructed intragenic, in-frame fusions inserting mCherry or sfGFP 48 amino acid residues downstream of the N-terminus of Rho in Salmonella. Strikingly, mCherry - but not sfGFP - renders the first 48 residues of Rho dispensable. Rho{Delta}48::mCherry is viable in single copy and exhibits wild-type termination activity in vitro, whereas the full-length Rho::sfGFP fusion, although viable, slows growth and shows strongly reduced activity. Structured illumination microscopy (SIM) revealed that, despite these functional differences, both constructs exhibit similar localisation patterns relative to fluorescently tagged RNAP in single cells. During exponential growth, both Rho and RNAP form discrete clusters, but with markedly distinct spatial organisations: RNAP clusters associate with the nucleoid, whereas Rho is distributed throughout the cell body. This spatial partitioning persists in stationary phase, where RNAP becomes diffusely associated with a compacted nucleoid while Rho accumulates at the cell periphery. The widespread distribution of Rho at cytoplasmic locations is unexpected and suggests participation in cellular functions beyond its canonical role in transcription termination.

microbiology↗

bioRxiv2024

Evolution of pH-sensitive transcription termination during adaptation to repeated long-term starvation.

Fluctuating environments that consist of regular cycles of co-occurring stress are a common challenge faced by cellular populations. For a population to thrive in constantly changing conditions, an ability to coordinate a rapid cellular response is essential. Here, we identify a mutation conferring an arginine-to-histidine (Arg to His) substitution in the transcription terminator Rho. The rho R109H mutation frequently arose in E. coli populations experimentally evolved under repeated long-term starvation conditions, during which feast and famine result in drastic environmental pH fluctuations. Metagenomic sequencing revealed that populations containing the rho mutation also possess putative loss-of-function mutations in ydcI, which encodes a recently characterized transcription factor associated with pH homeostasis. Genetic reconstructions of these mutations show that the rho allele confers a plastic alkaline-induced reduction of Rho function that, when found in tandem with a {Delta}ydcI allele, leads to intracellular alkalinization and genetic assimilation of Rho mutant function. We further identify Arg to His substitutions at analogous sites in rho alleles from species originating from fluctuating alkaline environments. Our results suggest that Arg to His substitutions in global regulators of gene expression can serve to rapidly coordinate complex responses through pH sensing and shed light on how cellular populations across the tree of life use environmental cues to coordinate rapid responses to complex, fluctuating environments.

microbiology↗

bioRxiv2022

Post-transcriptional regulation by copper with a new upstream Open Reading Frame

Copper is essential to most living beings but also toxic. Bacteria have thus developed homeostatic mechanisms to tightly control its intracellular concentration. The 3-gene operon bp2923-bfrG-bp2921 is down-regulated by copper and notably encodes a TonB-dependent transporter in Bordetella pertussis. We show that the protein encoded by bp2923, which is a member of the DUF2946 family, represents a new type of upstream Open Reading Frame (uORF) involved in post-transcriptional regulation of the downstream genes. In the absence of copper, the entire operon is transcribed and translated. Perception of copper by the nascent bp2923-coded protein via its conserved CXXC motif triggers Rho-dependent transcription termination between the first and second genes by relieving translation arrest on a conserved C-terminal RAPP motif. Homologues of bp2923 are widespread in bacterial genomes, where they head operons predicted to participate in copper homeostasis. This work has unveiled an original mode of genetic regulation by a transition metal and identified a regulatory function for a member of an uncharacterized family of bacterial proteins that we have named CruR, for copper-responsive upstream regulator.

microbiology↗

bioRxiv2021

Cryo-EM structure of the transcription termination factor Rho from Mycobacterium tuberculosis reveals mechanism of resistance to bicyclomycin

The bacterial Rho factor is a ring-shaped motor triggering genome-wide transcription termination and R-loop dissociation. Rho is essential in many species, including in Mycobacterium tuberculosis where rho gene inactivation leads to rapid death. Yet, the M. tuberculosis Rho [MtbRho] factor displays poor NTPase and helicase activities, and resistance to the natural Rho inhibitor bicyclomycin [BCM] that remain unexplained. Here, we address these unusual features by solving the cryo-EM structure of MtbRho at 3.3 [A] resolution, providing a new framework for future antibiotic development. The MtbRho hexamer is poised into a pre-catalytic, open-ringed state wherein specific contacts stabilize ATP in intersubunit ATPase pockets, thereby explaining the cofactor preference of MtbRho. We reveal a leucine-to-methionine substitution that creates a steric bulk in BCM binding cavities near the positions of ATP {gamma}-phosphates, and confers resistance to BCM at the expense of motor efficiency.

molecular biology↗