Biology subjects

Wartel, M.

Publications and source records attributed to Wartel, M..

4 recordsLinked to original sources

bioRxiv2024

Systematic Characterization of Transport Regulation in Escherichia coli across defined environmental cues

Transport of small molecules across the bacterial cell envelope is essential to ensure nutrient uptake and protect bacteria from toxic compounds. Due to its decisive role, transport is controlled by complex regulatory networks, knowledge of which - in particular across external cues - remains poorly understood. Here we investigate transcriptional regulation of seven prominent transport genes in Escherichia coli across 94 defined chemical cues, and simultaneously map the contributions of the key regulators MarA, SoxS and Rob to promoter activity. One third of all tested compounds triggered transcriptional changes, the vast majority of which previously unknown. Importantly, we exposed main drivers of transport control in E. coli, e.g. bacteriostatic, but not bactericidal, antibiotics trigger expression of efflux pumps, and that Rob contributes to [~]1/3 of all measured transcriptional changes, thereby emerging as a more prominent transport regulator than previously thought. We showcase the potential of our resource by elucidating the molecular mechanism of antibiotic antagonisms with widely consumed caffeine in E. coli. Altogether, our resource capitalizes on providing a quantitative overview of transport determinants across environments, and brings perspective to long-term prevailing concepts in the field.

microbiology↗

bioRxiv2022

Bacterial cell widening alters periplasmic size and activates envelope stress responses

The Rcs signal transduction system is a phosphorelay responsible for sensing a wide variety of enterobacterial cell envelope stresses. In Escherichia coli, the Rcs system is required to survive A22 and mecillinam treatment, two drugs that perturb cell size. To test whether cell size changes might be correlated with envelope damage and thereby sensed by the Rcs system, we tuned E. coli cell size via drug inhibition with A22, point mutations to the cell-shape determinant MreB, and mechanically confined growth. In all conditions, cell width was strongly correlated with Rcs activation, with wider cells exhibiting more activation than wild-type. In all conditions, RcsF, the outer membrane-localized upstream component of the Rcs system, was essential for responding to cell width changes. Consistently, several envelope gene deletions known to induce the Rcs system via RcsF resulted in cells that were wider than wild-type. Cryo- electron microscopy revealed that the periplasm of a wide MreB mutant was on average [~]3 nm thinner than wild-type, thereby bringing RcsF closer to the downstream components of the signaling cascade in the inner membrane. Conversely, extending the flexible linker region of RcsF by [~]3 nm increased Rcs activity in wild-type cells. In summary, we propose that the Rcs system responds to changes in cell width because of altered periplasmic thickness.

microbiology↗

bioRxiv2019

The outer membrane lipoprotein NlpI nucleates hydrolases within peptidoglycan multi-enzyme complexes in Escherichia coli

The peptidoglycan (PG) sacculus provides bacteria with the mechanical strength to maintain cell shape and resist osmotic stress. Enlargement of the mesh-like sacculus requires the combined activity of PG synthases and hydrolases. In Escherichia coli, the activity of the two bifunctional PG synthases is driven by lipoproteins anchored in the outer membrane. However, the regulation of PG hydrolases is less well understood, with only regulators for PG amidases having been described. Here, we identify the lipoprotein NlpI as a general adaptor protein for PG hydrolases. NlpI binds to different classes of hydrolases and can specifically form multimeric complexes with various PG endopeptidases. In addition, NlpI seems to contribute both to PG elongation and cell division biosynthetic complexes based on its localization and genetic interactions. In line with such a role, we reconstitute PG multi-enzyme complexes containing NlpI, the PG synthesis regulator LpoA, its cognate bifunctional synthase, PBP1A, and different endopeptidases. Our results indicate that PG regulators and adaptors are part of PG biosynthetic multi-enzyme complexes, regulating and potentially coordinating the spatiotemporal action of PG synthases and hydrolases.\n\nSignificanceThe activity of PG hydrolases may cause lysis of the bacterial cell if left unregulated. Hence, the cell must have ways of regulating and coordinating their activities. Our current understanding of how this occurs is incomplete. In this work, we present the outer membrane (OM) anchored lipoprotein, NlpI, as a scaffold of peptidoglycan hydrolases. We propose that NlpI facilitates the formation of multi-enzyme complexes and that, along with other regulators, it coordinates a safe enlargement and separation of the PG layer in E. coli.

microbiology↗

bioRxiv2017

Phenotype prediction in an Escherichia coli strain panel

Understanding how genetic variation contributes to phenotypic differences is a fundamental question in biology. Here, we set to predict fitness defects of an individual using mechanistic models of the impact of genetic variants combined with prior knowledge of gene function. We assembled a diverse panel of 696 Escherichia coli strains for which we obtained genomes and measured growth phenotypes in 214 conditions. We integrated variant effect predictors to derive gene-level probabilities of loss of function for every gene across strains. We combined these probabilities with information on conditional gene essentiality in the reference K-12 strain to predict the strains growth defects, providing significant predictions for up to 38% of tested conditions. The putative causal variants were validated in complementation assays highlighting commonly perturbed pathways in evolution for the emergence of growth phenotypes. Altogether, our work illustrates the power of integrating high-throughput gene function assays to predict the phenotypes of individuals.\n\nHighlightsO_LIAssembled a reference panel of E. coli strains\nC_LIO_LIGenotyped and high-throughput phenotyped the E. coli reference strain panel\nC_LIO_LIReliably predicted the impact of genetic variants in up to 38% of tested conditions\nC_LIO_LIHighlighted common genetic pathways for the emergence of deleterious phenotypes\nC_LI

systems biology↗