Biology subjects

Boccard, F.

Publications and source records attributed to Boccard, F..

8 recordsLinked to original sources

bioRxiv2026

Conserved lifestyle-associated chromosome architectures across mammalian symbionts

Bacterial chromosome biology has largely focused on bacteria that are either free-living or facultatively associated with eukaryotes. Therefore, it is not known how obligate animal symbionts organize their chromosomes. Here, we studied the chromosome organization of three species of multicellular Neisseriaceae that colonize the oral cavity of mammals, Alysiella filiformis, Simonsiella muelleri and Conchiformibius steedae. DNA fluorescence in situ hybridization showed that - irrespective of their ploidy - their chromosomes are longitudinally configured with the origin of DNA replication consistently localized at their host-attached poles throughout the cell cycle. Immunolocalization, ChIP-seq and EMSA implicated ParBS complexes in maintaining this stable chromosome orientation. Moreover, chromosome conformation capture across two species and three growth conditions further revealed conserved lifestyle-associated chromosome architectures, including planktonic-specific ParB-associated chromatin loops and condition-specific chromatin frontiers. Together, our findings show that obligate mammalian symbionts maintain stable longitudinal chromosome orientations irrespective of ploidy while remodeling higher-order chromosome architecture according to physiological state. Distinct yet conserved chromosome architectures characterize exponential, stationary and surface-associated growth, indicating that bacterial genome folding reflects lifestyle and environmental context.

microbiology↗

bioRxiv2025

Bacterial chromatin remodeling associated with transcription-induced domains at pathogenicity islands

The nucleoid-associated protein H-NS is a bacterial xenogeneic silencer responsible for preventing costly expression of genes acquired through horizontal gene transfer. H-NS silences several Salmonella Pathogenicity Islands (SPIs) essential for host infection. The stochastic expression of SPI-1 is required for invasion of host epithelial cells but complicates investigation of factors involved in SPI-1 chromatin structure and regulation. We performed functional genomics on sorted Salmonella populations expressing SPI-1 or not, to characterize how SPI-1 activation affects chromatin composition, DNA conformation, gene expression and SPI-1 subcellular localization. High H-NS occupancy co-exists with low spurious transcriptional activity and low RNA polymerase occupancy at silent SPIs. Upon SPI-1 activation, remodeling of H-NS occupancy defines a new chromatin landscape, which together with the master SPI-1 regulator HilD, facilitates transcription of SPI-1 genes. SPI-1 activation promotes formation of Transcription Induced Domains accompanied by repositioning SPI-1 close to the nucleoid periphery. We present a model for tightly regulated chromatin remodeling that minimizes the cost of pathogenicity island activation

microbiology↗

bioRxiv2023

Stable chromosome configuration and loop-based polarization in animal symbionts

Chromosome partitioning precedes the division of the cytoplasm, and its evolution is linked with the positioning of the division plane. So far, bacterial chromosome biology has heavily focused on transversally dividing, free-living ones. Here, we determined the chromosome organization of three longitudinally dividing Neisseriaceae exclusively inhabiting the oral cavity of mammals. We showed that in all three multicellular bacteria the origin of DNA replication is invariably located at the host-attached (proximal) pole. Next, 3C-seq revealed loop-based folding of the ori region in Alysiella filiformis and Simonsiella muelleri. Moreover, genes involved in cell motility, piliation and signal transduction mechanisms were specifically looped when transcriptionally and translationally active cells adhered to a substrate, but not when cultured in liquid. Overall, we propose that proximal positioning of the ori and loop-based folding of its surrounding DNA may mediate localized translation of proteins involved in host colonization.

genomics↗

bioRxiv2023

Activity of MukBEF for chromosome management in E. coli and its inhibition by MatP

Structural maintenance of chromosomes (SMC) complexes share conserved structures and serve a common role in maintaining chromosome architecture. In the bacterium Escherichia coli, the SMC complex MukBEF is necessary for rapid growth and the accurate segregation and positioning of the chromosome, although the specific molecular mechanisms involved are still unknown. Here we used a number of in vivo assays to reveal how MukBEF controls chromosome conformation and how the MatP/matS system prevents MukBEF activity. Our results indicate that the loading of MukBEF occurs preferentially on newly replicated DNA, at multiple loci on the chromosome where it can promote long-range contacts in cis even though MukBEF can promote long-range contacts in the absence of replication. Using HiC and ChIP-seq analyses in strains with rearranged chromosomes, the prevention of MukBEF activity increases with the number of matS sites and this effect likely results from the unloading of MukBEF by MatP. Altogether, our results reveal how MukBEF operates to control chromosome folding and segregation in E. coli.

genomics↗

bioRxiv2022

Ribosomal RNA operons define a central functional compartment in the Streptomyces chromosome

Streptomyces are prolific producers of specialized metabolites with applications in medicine and agriculture. These bacteria possess a large linear chromosome genetically compartmentalized: core genes are grouped in the central part, while terminal regions are populated by poorly conserved genes and define the chromosomal arms. In exponentially growing cells, chromosome conformation capture unveiled sharp boundaries formed by ribosomal RNA (rrn) operons that segment the chromosome into multiple domains. The first and last rrn operons delimit the highly expressed central compartment and the rather transcriptionally silent terminal compartments. Here we further explore the link between the genetic distribution of rrn operons and Streptomyces genomic compartmentalization. A large panel of genomes of species representative of the genus diversity revealed that rrn operons and core genes form a central skeleton, the former being identifiable from their core gene environment. We implemented a new nomenclature for Streptomyces genomes and trace their rrn-based evolutionary history. Remarkably, rrn operons are close to pericentric inversions. Moreover, the central compartment delimited by rrn operons has a very dense, nearly invariant core gene content. Finally, this compartment harbors genes with the highest expression levels, regardless of gene persistence and distance to the origin of replication. Our results highlight that rrn operons define the structural boundaries of a central functional compartment prone to transcription in Streptomyces.

genomics↗

bioRxiv2020

Dynamics of the compartmentalized Streptomyces chromosome during metabolic differentiation

Streptomyces are among the most prolific bacterial producers of specialized metabolites, including antibiotics. The linear chromosome is partitioned into a central region harboring core genes and two extremities enriched in specialized metabolite biosynthetic gene clusters (SMBGCs). The molecular mechanisms governing structure and function of these compartmentalized genomes remain mostly unknown. Here we show that in exponential phase, chromosome structure correlates with genetic compartmentalization: conserved, large and highly transcribed genes form boundaries that segment the central part of the chromosome into domains, whereas the terminal ends are transcriptionally, largely quiescent compartments with different structural features. Onset of metabolic differentiation is accompanied by remodeling of chromosome architecture from an open to a rather closed conformation, in which the SMBGCs are expressed forming new boundaries. Altogether, our results reveal that S. ambofaciens linear chromosome is partitioned into structurally distinct entities, indicating a link between chromosome folding, gene expression and genome evolution.

microbiology↗

bioRxiv2020

Fine-tuning of the Smc flux facilitates chromosome organization in B. subtilis

SMC complexes are widely conserved ATP-powered loop extrusion motors indispensable for the faithful segregation of chromosomes during cell division. How SMC complexes translocate along DNA for loop extrusion and what happens when two complexes meet on the same DNA molecule is largely unknown. Revealing the origins and the consequences of SMC encounters is crucial for understanding the folding process not only of bacterial, but also of eukaryotic chromosomes. Here, we uncover several factors that influence bacterial chromosome organization by modulating the probability of such clashes. These factors include the number, the strength and the distribution of Smc loading sites, the residence time on the chromosome, the translocation rate, and the cellular abundance of Smc complexes. By studying various mutants, we show that these parameters are fine-tuned to reduce the frequency of encounters between Smc complexes, presumably as a risk mitigation strategy. Mild perturbations hamper chromosome organization by causing Smc collisions, implying that the cellular capacity to resolve them is rather limited. Altogether, we identify mechanisms that help to avoid Smc collisions and their resolution by Smc traversal or other potentially risky molecular transactions.

cell biology↗

bioRxiv2020

Distinct activities of bacterial condensins for chromosome management in Pseudomonas aeruginosa.

Bacteria encompass three types of structurally related SMC complexes referred to as condensins. Smc-ScpAB is present in most bacteria while MukBEF is found in enterobacteria and MksBEF is scattered over the phylogenic tree. The contributions of these condensins to chromosome management were characterized in Pseudomonas aeruginosa that carries both Smc-ScpAB and MksBEF. In this bacterium, SMC-ScpAB controls chromosome disposition by juxtaposing chromosome arms. In contrast, MksBEF is critical for chromosome segregation in the absence of the main segregation system and affects the higher-order architecture of the chromosome by promoting DNA contacts in the megabase range. Strikingly, our results reveal a prevalence of Smc-ScpAB over MksBEF involving a coordination of their activities with the DNA replication process. They also show that E. coli MukBEF can substitute for MksBEF in P. aeruginosa while prevailing over Smc-ScpAB. Altogether, our results reveal a hierarchy between activities of bacterial condensins on the same chromosome.

microbiology↗