Segregation but Not Replication of the
            <i>Pseudomonas aeruginosa</i>
            Chromosome Terminates at
            <i>Dif</i>

Bhowmik, Bijit K.; Clevenger, April L.; Zhao, Hang; Rybenkov, Valentin V.

doi:10.1128/mbio.01088-18

Cited by 14 publications

(21 citation statements)

References 56 publications

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“…A major feature differing genomes of PAO1 derivatives MPAO1 and PAO1-DSM, is the lack of a large inversion resulting from the homologous recombination between two rRNA operons rrnA and rrnB [5], which is present in the reference PAO1-UW genome [7]. Despite an asymmetrical positioning of the dif region in PAO1-UW, this inversion does not seem to affect chromosome segregation and such large rearrangements might be common among bacteria [8]. Remarkably, recent analyses indicated that sequence variation including singlenucleotide polymorphisms (SNPs), multiple-nucleotide polymorphisms (MNPs) and indels could lead to major variations in e.g.…”

Section: Introductionmentioning

confidence: 99%

Genome sequence of Pseudomonas aeruginosa PAO1161, a PAO1 derivative with the ICEPae1161 integrative and conjugative element

et al. 2020

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Background: Pseudomonas aeruginosa is a cause of nosocomial infections, especially in patients with cystic fibrosis and burn wounds. PAO1 strain and its derivatives are widely used to study the biology of this bacterium, however recent studies demonstrated differences in the genomes and phenotypes of derivatives from different laboratories. Results: Here we report the genome sequence of P. aeruginosa PAO1161 laboratory strain, a leu-, Rif R , restrictionmodification defective PAO1 derivative, described as the host of IncP-8 plasmid FP2, conferring the resistance to mercury. Comparison of PAO1161 genome with PAO1-UW sequence revealed lack of an inversion of a large genome segment between rRNA operons and 100 nucleotide polymorphisms, short insertions and deletions. These included a change in leuA, resulting in E108K substitution, which caused leucine auxotrophy and a mutation in rpoB, likely responsible for the rifampicin resistance. Nonsense mutations were detected in PA2735 and PA1939 encoding a DNA methyltransferase and a putative OLD family endonuclease, respectively. Analysis of revertants in these two genes showed that PA2735 is a component of a restriction-modification system, independent of PA1939. Moreover, a 12 kb RPG42 prophage and a novel 108 kb PAPI-1 like integrative conjugative element (ICE) encompassing a mercury resistance operon were identified. The ICEPae1161 was transferred to Pseudomonas putida cells, where it integrated in the genome and conferred the mercury resistance. Conclusions: The high-quality P. aeruginosa PAO1161 genome sequence provides a reference for further research including e.g. investigation of horizontal gene transfer or comparative genomics. The strain was found to carry ICEPae1161, a functional PAPI-1 family integrative conjugative element, containing loci conferring mercury resistance, in the past attributed to the FP2 plasmid of IncP-8 incompatibility group. This indicates that the only known member of IncP-8 is in fact an ICE.

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Section: Introductionmentioning

confidence: 99%

Genome sequence of Pseudomonas aeruginosa PAO1161, a PAO1 derivative with the ICEPae1161 integrative and conjugative element

et al. 2020

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“…Subsequent experiments were carried out with cells grown in minimal medium, with replication initiated only once per cell cycle. The oriC-proximal region was tagged with tetO repeats and visualized using a fluorescent repressor operator system (FROS) as previously described (27,28). Its location was followed in parental PAO1-UW cells and in cells deficient in one or both condensins.…”

Section: Resultsmentioning

confidence: 99%

“…To evaluate this possibility, we explored chromosome segregation in condensin mutants using marker frequency analysis. To this end, chromosomal DNA of the mutant cells was subjected to deep sequencing, and the relative abundances of genomic loci fit to a model that postulates up to two replication start events at the oriC during the lifetime of the cell (28). This analysis quantifies duplication of genomic loci following the passage of a replication fork, which leads to a higher copy number of origin-proximal DNA fragments (Fig.…”

Section: Resultsmentioning

confidence: 99%

Alternating Dynamics of oriC , SMC, and MksBEF in Segregation of Pseudomonas aeruginosa Chromosome

Zhao

Bhowmik

Petrushenko

et al. 2020

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Mechanisms that define the chromosome as a structural entity remain unknown. Key elements in this process are condensins, which globally organize chromosomes and contribute to their segregation. This study characterized condensin and chromosome dynamics in Pseudomonas aeruginosa, which harbors condensins from two major protein superfamilies, SMC and MksBEF. The study revealed that both proteins play a dual role in chromosome maintenance by spatially organizing the chromosomes and guiding their segregation but can substitute for each other in some activities. The timing of chromosome, SMC, and MksBEF relocation was highly ordered and interdependent, revealing causative relationships in the process. Moreover, MksBEF produced clusters at the site of chromosome replication that survived cell division and remained in place until replication was complete. Overall, these data delineate the functions of condensins from the SMC and MksBEF superfamilies, reveal the existence of a chromosome organizing center, and suggest a mechanism that might explain the biogenesis of chromosomes.

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“…In Mycobacterium smegmatis, the oriC was found to be localized slightly off-center with respect to midcell (18). In Pseudomonas aeruginosa (19), the origin is localized at the cell center, as observed in E. coli (1). In the case of Streptomyces coelicolor, multiple copies of linear chromosomes have been demonstrated in hyphal cells (20).…”

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confidence: 84%

Rhodoccoccus erythropolis Is Different from Other Members of Actinobacteria : Monoploidy, Overlapping Replication Cycle, and Unique Segregation Pattern

et al. 2019

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Among actinomycetes, chromosome organization and segregation studies have been limited to Streptomyces coelicolor, Corynebacterium glutamicum, and Mycobacterium spp. There are differences with respect to ploidy and chromosome organization pattern in these bacteria. Here, we report on chromosome replication, organization, and segregation in Rhodococcus erythropolis PR4, which has a circular genome of 6.5 Mbp. The origin of replication of R. erythropolis PR4 was identified, and the DNA content in the cell under different growth conditions was determined. Our results suggest that the number of origins increases as the growth medium becomes rich, suggesting an overlapping replication cell cycle in this bacterium. Subcellular localization of the origin region revealed polar positioning in minimal and rich media. The terminus, which is the last region to be replicated and segregated, was found to be localized at the cell center in large cells. The middle markers corresponding to the 1.5-Mb and 4.7-Mb loci did not overlap, suggesting discontinuity in the segregation of the two arms of the chromosome. Chromosome segregation was not affected by inhibiting cell division. Deletion of parA or parB affected chromosome segregation. Unlike in C. glutamicum and Streptomyces spp., diploidy or polyploidy was not observed in R. erythropolis PR4. Our results suggest that R. erythropolis is different from other members of Actinobacteria; it is monoploid and has a unique chromosome segregation pattern. This is the first report on chromosome organization, replication, and segregation in R. erythropolis PR4. IMPORTANCE Rhodococci are highly versatile Gram-positive bacteria with high bioremediation potential. Some rhodococci are pathogenic and have been suggested as emerging threats. No studies on the replication, segregation, and cell cycle of these bacteria have been reported. Here, we demonstrate that the genus Rhodococcus is different from other actinomycetes, such as members of the genera Corynebacterium, Mycobacterium, and Streptomyces, with respect to ploidy and chromosome organization and segregation. Such studies will be useful not only in designing better therapeutics pathogenic strains in the future but also for studying genome maintenance in strains used for bioremediation.

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Segregation but Not Replication of the Pseudomonas aeruginosa Chromosome Terminates at Dif

Cited by 14 publications

References 56 publications

Genome sequence of Pseudomonas aeruginosa PAO1161, a PAO1 derivative with the ICEPae1161 integrative and conjugative element

Genome sequence of Pseudomonas aeruginosa PAO1161, a PAO1 derivative with the ICEPae1161 integrative and conjugative element

Alternating Dynamics of oriC , SMC, and MksBEF in Segregation of Pseudomonas aeruginosa Chromosome

Rhodoccoccus erythropolis Is Different from Other Members of Actinobacteria : Monoploidy, Overlapping Replication Cycle, and Unique Segregation Pattern

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