A dicentric bacterial chromosome requires XerC/D site-specific recombinases for resolution

Liao, Qin; Ren, Zhenglong; Wiesler, Emma E.; Fuqua, Clay; Wang, Xindan

doi:10.1016/j.cub.2022.06.050

Cited by 10 publications

(17 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…1 B). Large genome rearrangements are often found between two laboratories working with the same organisms (Periwal and Scaria 2015 ; Guérillot et al 2019 ; Liao et al 2022 ), but to ensure that the ~ 80 kbp deletion was not important for the transformation phenotype we observe, we compared the natural transformation efficiency of KC13 to J901, a variant of the sequenced strain (Seyhan et al 2015 ). After transformation and selection, we observed that both strains were capable of DNA uptake with a similar efficiency (Figure S1), therefore the deletion present in strain KC13 was not considered further.…”

Section: Resultsmentioning

confidence: 99%

Random transposon mutagenesis identifies genes essential for transformation in Methanococcus maripaludis

et al. 2023

View full text Add to dashboard Cite

Natural transformation, the process whereby a cell acquires DNA directly from the environment, is an important driver of evolution in microbial populations, yet the mechanism of DNA uptake is only characterized in bacteria. To expand our understanding of natural transformation in archaea, we undertook a genetic approach to identify a catalog of genes necessary for transformation in Methanococcus maripaludis. Using an optimized method to generate random transposon mutants, we screened 6144 mutant strains for defects in natural transformation and identified 25 transformation-associated candidate genes. Among these are genes encoding components of the type IV-like pilus, transcription/translation associated genes, genes encoding putative membrane bound transport proteins, and genes of unknown function. Interestingly, similar genes were identified regardless of whether replicating or integrating plasmids were provided as a substrate for transformation. Using allelic replacement mutagenesis, we confirmed that several genes identified in these screens are essential for transformation. Finally, we identified a homolog of a membrane bound substrate transporter in Methanoculleus thermophilus and verified its importance for transformation using allelic replacement mutagenesis, suggesting a conserved mechanism for DNA transfer in multiple archaea. These data represent an initial characterization of the genes important for transformation which will inform efforts to understand gene flow in natural populations. Additionally, knowledge of the genes necessary for natural transformation may assist in identifying signatures of transformation machinery in archaeal genomes and aid the establishment of new model genetic systems for studying archaea.

show abstract

Section: Resultsmentioning

confidence: 99%

Random transposon mutagenesis identifies genes essential for transformation in Methanococcus maripaludis

et al. 2023

View full text Add to dashboard Cite

show abstract

“…This is in agreement with a recent study also suggesting a longitudinal oriter distribution of a natural cointegrate of the circular and linear chromosomes in A. tumefaciens. (23) In wild type and SmABCΔR, oriC and oriA/oriB occupied polar and subpolar areas, respectively (S11B Fig) . As expected from our filtering approach and in agreement with previous reports, (13,30) in both strains, the oriC signal showed a very low positional variance at one cell pole (S1 Table ). Subpolar localization of oriA and oriB signals with similar variances in both strains suggests a spatial confinement of these elements to this region of the cell (S1 Table ).…”

Section: Polar Localization Of Oric and Subpolar Localization Of Both...mentioning

confidence: 99%

“…(20) Cointegration events of two or three replicons, resulting in DNA molecules with two or three origins of replication, have been reported for natural strain isolates of the αproteobacteria S. meliloti, Sinorhizoium fredii and A. tumefaciens, as well as for the β-proteobacterium Cupriavidus necator and the -proteobacterium Vibrio cholerae. (21)(22)(23)(24)(25)(26)(27) In bacterial cells, the genomic DNA is highly organized, and replication and segregation are coordinated in space and time. (28) Tethering of the chromosomal origin and terminus regions to cell poles plays an important role for spatial chromosome organization and segregation.…”

Section: ◼ Introductionmentioning

confidence: 99%

Engineering aSinorhizobium melilotichassis with monopartite, single replicon genome configuration

Wagner

Döhlemann

Geisel

et al. 2022

Preprint

View full text Add to dashboard Cite

While the vast majority of bacterial genomic DNA molecules contain a single origin of replication, some natural isolates and engineered strains were reported to contain chromosomes derived from cointegration events of multiple replicons. We investigated effects of multiple DNA replication origins and terminus regions on spatial DNA organization and spatiotemporal replicon segregation in the alphaproteobacterium Sinorhizobium meliloti. Strains with a bi- and monopartite genome configuration were constructed by Cre/lox-mediated site-specific fusions of the secondary replicons pSymA and pSymB, and of the chromosome, pSymA and pSymB. The design of these strains maintained replichore ratios, GC skew, as well as distribution and orientation of KOPS and coding sequences. Growth of these strains was essentially unaffected, except for high salt conditions. Replication initiation at the three origins as well as key features of spatial organization and spatiotemporal segregation were maintained in the triple-replicon fusion strain. Cell growth was slowed down by deleting, either individually or together, the pSymA- and pSymB-derived replication initiator encoding repC genes with their intrinsic origin of replication from the dual or triple replicon cointegrates, respectively. Replication of the triple cointegrate, characterized by the chromosomal oriC as sole origin and a strongly disbalanced replichore ratio, terminated in the original chromosomal terC region, suggesting a replication trap. Progression of replication of the longer replichore was not blocked but impaired, possibly due to the retained secondary replicon’s terminus regions and reverse alignment of replichore-orienting sequence features following from the deletion of replication origins. Moreover, during the cell cycle of this strain, oriC aberrantly localized and served as replication initiation site in the mid cell area of the cell with the oldest cell pole. Growth deficiency of this strain was attenuated by a suppressor mutation causing amino acid substitution R436H in the cell cycle histidine kinase CckA.

show abstract

“…However, a very recent study from 2022 showed that many of the C58 strains used in laboratories over the world carry a unique dicentric linear chromosome instead of two distinct chromosomes (Fig. 1a, left side) 28 . Still, even in such strains, the repABC Ch2 module (including ori2) appears to remain essential for survival since it could not be disrupted during Tn-seq experiments and since the repB Ch2 gene could not be deleted 28 , showing that initiation at ori2 and/or ori2 partitioning are essential in the two described A. tumefaciens C58 strains.…”

Section: Introductionmentioning

confidence: 99%

“…1a, left side) 28 . Still, even in such strains, the repABC Ch2 module (including ori2) appears to remain essential for survival since it could not be disrupted during Tn-seq experiments and since the repB Ch2 gene could not be deleted 28 , showing that initiation at ori2 and/or ori2 partitioning are essential in the two described A. tumefaciens C58 strains.…”

Section: Introductionmentioning

confidence: 99%

DNA methylation by CcrM contributes to genome maintenance in theAgrobacterium tumefaciensplant pathogen

Martin,

Fournes,

Ambrosini

et al. 2023

Preprint

View full text Add to dashboard Cite

Thecellcycle-regulated DNAmethyltransferase CcrM is conserved in mostAlphaproteobacteria, 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-depletedAgrobacterium tumefacienscells 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 therepABCCh2operon, encoding proteins required for replication initiation/partitioning atori2, and inhibitsgcrA, encoding a conservedglobalcell cycle regulator. Imagingori1andori2in live cells, we show that replication fromori2is often delayed in cells with a hypo-methylated genome, whileori2over-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 anAlphaproteobacterialpathogen.

show abstract

A dicentric bacterial chromosome requires XerC/D site-specific recombinases for resolution

Cited by 10 publications

References 57 publications

Random transposon mutagenesis identifies genes essential for transformation in Methanococcus maripaludis

Random transposon mutagenesis identifies genes essential for transformation in Methanococcus maripaludis

Engineering aSinorhizobium melilotichassis with monopartite, single replicon genome configuration

DNA methylation by CcrM contributes to genome maintenance in theAgrobacterium tumefaciensplant pathogen

Contact Info

Product

Resources

About