Biology subjects

Marquis, J.

Publications and source records attributed to Marquis, J..

5 recordsLinked to original sources

bioRxiv2026

Genome replication and cell division control by the methylation-sensitive GcrA regulator in Agrobacterium tumefaciens

Bacteria with complex genomes including secondary chromosomes and/or megaplasmids face unique challenges when controlling their cell cycle: they not only need to coordinate genome replication with other cell cycle events such as cell growth and cell division, but also to synchronize the replication of different replicons. In Alphaproteobacteria, replication and maintenance of large extrachromosomal replicons are usually dependent on RepABC modules, as seen for the plant pathogen Agrobacterium tumefaciens. In this study, we demonstrate that the conserved GcrA protein is an essential methylation-dependent transcriptional regulator playing at least two critical roles during the A. tumefaciens cell cycle. First, GcrA is required for the on-time and synchronized firing of the three RepABC-dependent origins of replication of A. tumefaciens that are needed for chromosomal and megaplasmid replication. Second, GcrA triggers the expression of several essential cell division genes for the timely assembly of a functional divisome. These findings highlight how this conserved global regulator can control and then synchronize a variety of essential cell cycle events in Alphaproteobacteria with complex genomes, notably coordinating the maintenance of several RepABC-dependent replicons with cell division. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=47 SRC="FIGDIR/small/728657v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@c7f0f7org.highwire.dtl.DTLVardef@9cf8f1org.highwire.dtl.DTLVardef@19baa05org.highwire.dtl.DTLVardef@b73437_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Cytosine methylation by ScmA contributes to the fitness of Caulobacter crescentus cells naturally expressing a Vsr-like protein

While methylated cytosines are known to play important roles in eukaryotes, their significance in bacteria remains poorly understood especially when they are added on genomes by DNA methyltransferases that are not parts of restriction-modification systems. The newly named ScmA protein of Caulobacter crescentus is one of these solitary cytosine methyltransferases. Here, we show that it methylates YGCCGGCR motifs introducing thousands of m5C bases on the C. crescentus genome. We also find that wild-type C. crescentus cells easily outcompete{Delta} scmA cells during competition experiments. Transcriptome comparisons and using single-cell fluorescent reporters reveal that a DNA damage response is turned on in a significant proportion of{Delta} scmA cells. We then show that this particular response is strictly dependent on the presence of a Vsr-like protein named VsrA. Eventhough the vsrA gene is surprisingly neither genetically linked with the scmA gene nor with another cytosine methyltransferase gene, VsrA is predicted to encode an endonuclease preventing m5C-to-T mutations. Fluorescence microscopy experiments then show that GFP-VsrA forms foci relatively frequently in stationary phase cells, which may correspond to active repair sites. We propose that VsrA may accidentally create double strand breaks when detecting mismatched bases on the genome of{Delta} scmA cells, leading to their observed loss of fitness. Thus, the presence of vsr-like genes can potentially stabilize genes encoding cytosine methyltransferases in bacterial genomes, providing a potential explanation for the relatively high prevalence of solitary cytosine methyltransferases in bacteria even if some of these do not appear to play an easily detectable regulatory role.

microbiology↗

bioRxiv2023

DNA methylation by CcrM contributes to genome maintenance in the Agrobacterium tumefaciens plant pathogen

The cell cycle-regulated DNA methyltransferase CcrM is conserved in most Alphaproteobacteria, but its role in bacteria with complex or multicentric genomes remains unexplored. Here, we compare the methylome, the transcriptome and the phenotypes of wild-type and CcrM-depleted Agrobacterium tumefaciens cells with a dicentric genome with two essential replication origins. We find that DNA methylation has a pleiotropic impact on motility, biofilm formation and viability. Remarkably, CcrM promotes the expression of the repABCCh2 operon, encoding proteins required for replication initiation/partitioning at ori2, and inhibits gcrA, encoding a conserved global cell cycle regulator. Imaging ori1 and ori2 in live cells, we show that replication from ori2 is often delayed in cells with a hypo-methylated genome, while ori2 over-initiates in cells with a hyper-methylated genome. We thus propose that methylation by CcrM stimulates RepABC-dependent chromosomal origins, uncovering a novel and original connection between CcrM-dependent DNA methylation and genome maintenance in an Alphaproteobacterial pathogen.

microbiology↗

bioRxiv2019

Modeling ribosome dwell times and relationships with tRNA loading and codon usage in mammals

Protein translation depends on mRNA-specific initiation, elongation and termination rates. While the regulation of ribosome elongation is well studied in bacteria and yeast, less is known in higher eukaryotes. Here, we combined ribosome and tRNA profiling to investigate the relations between ribosome elongation rates, (aminoacyl-) tRNA levels and codon usage in mammals. We modeled codon-specific ribosome dwell times and translation fluxes from ribosome profiling, considering pair-interactions between ribosome sites. In mouse liver, the model revealed site and codon specific dwell times, as well as codon pair-interactions clustering by amino acids. While translation fluxes varied significantly across diurnal time and feeding regimen, codon dwell times were highly stable, and conserved in human. Fasting had no effect on codon dwell times in mouse liver. Profiling of total and aminoacyl-tRNAs revealed highly heterogeneous levels that correlated with codon usage and showed specific isoacceptor patterns. tRNAs for several amino acids were lowly loaded, which was conserved in fasted mice. Finally, codons with low levels of charged tRNAs and high codon usage relative to tRNA abundance exhibited long dwell times. Together, these analyses pave the way towards understanding the complex interactions between tRNA loading, codon usage and ribosome dwell times in mammals.

systems biology↗

bioRxiv2017

Transcription factor activity rhythms and tissue-specific chromatin interactions explain circadian gene expression across organs.

AbstractTemporal control of physiology requires the interplay between gene networks involved in daily timekeeping and tissue function across different organs. How the circadian clock interweaves with tissue-specific transcriptional programs is poorly understood. Here we dissected temporal and tissue-specific regulation at multiple gene regulatory layers by examining mouse tissues with an intact or disrupted clock over time. Integrated analysis uncovered two distinct regulatory modes underlying tissue-specific rhythms: tissue-specific oscillations in transcription factor (TF) activity, which were linked to feeding-fasting cycles in liver and sodium homeostasis in kidney; and co-localized binding of clock and tissue-specific transcription factors at distal enhancers. Chromosome conformation capture (4C-Seq) in liver and kidney identified liver-specific chromatin loops that recruited clock-bound enhancers to promoters to regulate liver-specific transcriptional rhythms. Furthermore, this looping was remarkably promoter-specific on the scale of less than ten kilobases. Enhancers can contact a rhythmic promoter while looping out nearby nonrhythmic alternative promoters, confining rhythmic enhancer activity to specific promoters. These findings suggest that chromatin folding enables the clock to regulate rhythmic transcription of specific promoters to output temporal transcriptional programs tailored to different tissues.

genomics↗