An official website of the United States government
Chromosome architecture plays a crucial role in bacterial adaptation, yet its direct impact remains unclear. Different bacterial species and even strains within the same species exhibit diverse chromosomal configurations, including a single circular or linear chromosome, two circular chromosomes, or a circular-linear combination. To investigate how these architectures shape bacterial behavior, we generated near-isogenic strains representing each configuration inAgrobacterium tumefaciensC58, an important soil bacterium widely used for plant genetic transformation. Strains with a single-chromosome architecture, whether linear or circular, exhibited faster growth, enhanced stress tolerance, and greater interstrain competitiveness. In contrast, bipartite chromosome strains showed higher virulence gene expression and enhanced transient plant transformation efficiency, suggesting a pathogenic adaptation. Whole-transcriptome analysis revealed architecture-dependent gene expression patterns, underscoring the profound impact of chromosome organization onAgrobacteriumfitness and virulence. These findings highlight how chromosome structure influences bacterial adaptation and shapes evolutionary trajectories.
more »
« less
This content will become publicly available on June 11, 2026
Linear dicentric chromosomes in bacterial natural isolates reveal common constraints for replicon fusion
ABSTRACT Multipartite bacterial genome organization can confer advantages, including coordinated gene regulation and faster genome replication, but is challenging to maintain.Agrobacterium tumefacienslineages often contain a circular chromosome (Ch1), a linear chromosome (Ch2), and multiple plasmids. We previously observed that in some stocks of the C58 lab model, Ch1 and Ch2 were fused into a linear dicentric chromosome. Here we analyzedAgrobacteriumnatural isolates from the French Collection for Plant-Associated Bacteria and identified two strains distinct from C58 with fused chromosomes. Chromosome conformation capture identified integration junctions that were different from the C58 fusion strain. Genome-wide DNA replication profiling showed that both replication origins remained active. Transposon sequencing revealed that partitioning systems of both chromosome centromeres were essential. Importantly, the site-specific recombinase XerCD is required for the survival of the strains containing the fusion chromosome. Our findings show that replicon fusion occurs in natural environments and that balanced replication arm sizes and proper resolution systems enable the survival of such strains. IMPORTANCEMost bacterial genomes are monopartite with a single, circular chromosome. However, some species, likeAgrobacterium tumefaciens, carry multiple chromosomes. Emergence of multipartite genomes is often related to adaptation to specific niches, including pathogenesis or symbiosis. Multipartite genomes confer certain advantages; however, maintaining this complex structure can present significant challenges. We previously reported a laboratory-propagated lineage ofA. tumefaciensstrain C58 in which the circular and linear chromosomes fused to form a single dicentric chromosome. Here we discovered two geographically separated environmental isolates ofA. tumefacienscontaining fused chromosomes with integration junctions different from the C58 fusion chromosome, revealing the constraints and diversification of this process. We found that balanced replication arm sizes and the repurposing of multimer resolution systems enable the survival and stable maintenance of dicentric chromosomes. These findings reveal how multipartite genomes function across different bacterial species and the role of genomic plasticity in bacterial genetic diversification.
more »
« less
- Award ID(s):
- 2022049
- PAR ID:
- 10629078
- Editor(s):
- Komeili, Arash
- Publisher / Repository:
- American Society for Microbiology
- Date Published:
- Journal Name:
- mBio
- Volume:
- 16
- Issue:
- 6
- ISSN:
- 2150-7511
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Claesen, Jan (Ed.)ABSTRACT The human skin microbiome is a diverse ecosystem that can help prevent infections by producing biomolecules and peptides that inhibit growth and virulence of bacterial pathogens.Staphylococcus aureusis a major human pathogen responsible for diseases that range from acute skin and soft tissue infections to life-threatening septicemia. Its ability to form biofilms is a key virulence factor contributing to its success as a pathogen as well as to its increased antimicrobial resistance. Here, we investigated the ability of bacterial skin commensals to produce molecules that inhibitS. aureusbiofilm formation. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identified 77 human skin microbiome bacterial isolates fromStaphylococcusandBacillusgenera. Metabolites from cell-free concentrated media (CFCM) from 26 representative isolates were evaluated for their ability to inhibit biofilm formation by both methicillin-resistant (MRSA) and methicillin-sensitive (MSSA)S. aureusstrains. CFCM, derived from most of the isolates, inhibited biofilm formation to varying extents but did not inhibit planktonic growth ofS. aureus. Size fractionation of the CFCM of threeS.epidermidisisolates indicated that they produce different bioactive molecules. Cluster analysis, based on either MALDI-TOF mass spectra or whole-genome sequencing draft genomes, did not show clear clusters associated with levels of biofilm inhibition amongS. epidermidisstrains. Finally, similar biosynthetic gene clusters were detected in allS. epidermidisstrains analyzed. These findings indicate that several bacterial constituents of the human skin microbiome display antibiofilmin vitroactivity, warranting further investigation on their potential as novel therapeutic agents. IMPORTANCEThe skin is constantly exposed to the environment and consequently to numerous pathogens. The bacterial community that colonizes healthy skin is thought to play an important role in protecting us against infections.S. aureusis a leading cause of death worldwide and is frequently involved in several types of infections, including skin and soft tissue infections. Its ability to adhere to surfaces and produce biofilms is considered an important virulence factor. Here, we analyzed the activity of different species of bacteria isolated from healthy skin onS. aureusbiofilm formation. We found that some species ofStaphylococcusandBacilluscan reduceS. aureusbiofilm formation, although a generally lower level of inhibitory activity was observed compared toS. epidermidisisolates. AmongS. epidermidisisolates, strength of activity was dependent on the strain. Our data highlight the importance of mining the skin microbiome for isolates that could help combat skin pathogens.more » « less
-
Roux, Simon (Ed.)ABSTRACT We isolated seven endospore-forming bacteria from campus woodland and sequenced their genomes using Illumina NextSeq. We share the draft genome assemblies for strainsBacillus wiedmanii_SC129,Bacillus pseudomycoides_SC131,Bacillus pumilis_SC133,Peribacillus butanolivorans_SC135,Bacillus thuringiensis_SC136,Priestia megaterium_SC138, andBacillus wiedmanii_SC141. Draft genome sizes range from 3,645,032 to 5,969,865 bp, with GC content between 34.8% and 41.2%.more » « less
-
The underlying factors that lead to specific strains within a species to emerge as human pathogens remain mostly enigmatic. The diarrheal disease cholera is caused by strains from a phylogenetically confined group within theVibrio choleraespecies, the pandemic cholera group (PCG), making it an ideal model system to tackle this puzzling phenomenon. Comprehensive analyses of over 1,840V. choleraegenomes, including environmental isolates from this study, reveal that the species consists of eleven groups, with the PCG belonging to the largest and located within a lineage shared with environmental strains. This hierarchical classification provided us with a framework to unravel the ecoevolutionary dynamics of the genetic determinants associated with the emergence of toxigenicV. cholerae. Our analyses indicate that this phenomenon is largely dependent on the acquisition of unique modular gene clusters and allelic variations that confer a competitive advantage during intestinal colonization. We determined that certain PCG-associated alleles are essential for successful colonization whereas others provide a nonlinear competitive advantage, acting as a critical bottleneck that clarifies the isolated emergence of PCG. For instance, toxigenic strains encoding non-PCG alleles of a)tcpFor b) a sextuple allelic exchange mutant for genestcpA,toxT,VC0176,VC1791,rfbT,andompU, lose their ability to colonize the intestine. Interestingly, these alleles do not play a role in the colonization of newly established model environmental reservoirs. Our study uncovers the evolutionary roots of toxigenicV. choleraeoffering a tractable approach for investigating the emergence of pathogenic clones within an environmental population.more » « less
-
Ciliates are a model lineage for studies of genome architecture given their unusual genome structures. All ciliates have both somatic macronuclei (MAC) and germline micronuclei (MIC), both of which develop from a zygotic nucleus following sex (i.e., conjugation). Nuclear developmental stages are not well documented among non-model ciliates, includingChilodonella uncinata(class Phyllopharyngea), the focus of our work. Here, we characterize nuclear architecture and genome dynamics inC. uncinataby combining 4′,6-diamidino-2-phenylindole (DAPI) staining and fluorescencein situhybridization (FISH) techniques with confocal microscopy. We developed a telomere probe for staining, which alongside DAPI allows for the identification of fragmented somatic chromosomes among the total DNA in the nuclei. We quantify both total DNA and telomere-bound signals from more than 250 nuclei sampled from 116 individual cells, and analyze changes in DNA content and nuclear architecture acrossChilodonella’s nuclear life cycle. Specifically, we find that MAC developmental stages in the ciliateC. uncinataare different from those reported from other ciliate species. These data provide insights into nuclear dynamics during development and enrich our understanding of genome evolution in non-model ciliates. IMPORTANCECiliates are a clade of diverse single-celled eukaryotic microorganisms that contain at least one somatic macronucleus (MAC) and germline micronucleus (MIC) within each cell/organism. Ciliates rely on complex genome rearrangements to generate somatic genomes from a zygotic nucleus. However, the development of somatic nuclei has only been documented for a few model ciliate genera, includingParamecium,Tetrahymena, andOxytricha. Here, we study the MAC developmental process in the non-model ciliate,C. uncinata. We analyze both total DNA and the generation of gene-sized somatic chromosomes using a laser scanning confocal microscope to describeC. uncinata’s nuclear life cycle. We show that DNA content changes dramatically during their life cycle and in a manner that differs from previous studies on model ciliates. Our study expands knowledge of genome dynamics in ciliates and among eukaryotes more broadly.more » « less
