Dynamic bacterial genome organization

Kolstø, Anne‐Brit

doi:10.1046/j.1365-2958.1997.3501715.x

Cited by 105 publications

(69 citation statements)

References 45 publications

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“…According to the annotation (source organism) in the description of registered amino acid sequences, we sorted members of the ParAB families into chromosome-derived (genes located on chromosomes) and plasmid-derived (on plasmid and phages) groups. A chromosome is defined by a replicon that has housekeeping genes (22,23).…”

Section: Methodsmentioning

confidence: 99%

Active segregation by the Bacillus subtilis partitioning system in Escherichia coli

Yamaichi

Niki

2000

Proc. Natl. Acad. Sci. U.S.A.

151

160

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Bacterial genes required for proper partitioning consist of two transacting genes that encode proteins and a cis-acting gene that functions like a centromere. Plasmids actively partitioning by means of these genes migrate from midcell to the cell quarters and are tethered to these sites until the cells divide. Previously the partitioning genes were mainly found on plasmids and phages in Escherichia coli. However, progress in genome sequencing reveals that partitioning genes are ubiquitous in many bacterial plasmids and chromosomes. Each homologue of the two transacting genes belongs to a family, ParA or ParB. Moreover, phylogenic analysis of members of the ParA and ParB families indicates that each member falls into a chromosomal group or an extrachromosomal group. It is known that the parAB genes in the chromosomal group are located on relatively conserved chromosomal regions in several bacterial species. This suggests that the parAB genes were transferred from a chromosome to plasmids and phages, so the genes have diverged among bacterial species. To support this possibility, we show that the Bacillus subtilis Soj and Spo0J members of the ParAB families are responsible for the specific localization of plasmids at cell quarters in E. coli and can function as partition proteins. Host factors to tether actively partitioning plasmids at subcellular sites may be conserved in Gram-negative and Grampositive bacteria so that phages and plasmids with the ParAB partitioning system can be stably inherited in host cells across bacterial species. L ow copy-number plasmids are stably maintained in host Escherichia coli cells because of active partitioning mechanisms; in the cases of F plasmid and P1 phage, which is a plasmid in lysogenized host cells, these are specified by the sopABC and parABS genes, respectively (1). SopA and P1͞ParA are similar in amino acid sequence and function, as are SopB and P1͞ParB. Both sopC and parS are cis-acting sites that function as centromere-like elements. In the case of the sopABC mechanism, the SopB protein binds to sopC. SopA interacts with the SopB-sopC complex to ensure proper segregation. Plasmids actively partitioned by the sopABC or parABS systems are localized at specific subcellular sites throughout the cell-division cycle (2-4). In newborn cells, the plasmids are localized at midcell. Replicated plasmids are then rapidly relocalized at the 1͞4 and 3͞4 positions of cell length. The SopAB-sopC complex probably binds to unidentified host factors that localize at the cell quarters, tethering actively partitioning plasmids at these specific subcellular sites.Many homologues of SopAB and P1͞ParAB have been identified in various plasmids and phages, and in fact several members are involved in the accurate partitioning of extrachromosomal elements (1, 5-7). We therefore call these homologues the ParA and ParB families. Recent genome searches have revealed that genes of members of both families are found in many bacterial genomes (8, 9). Homologues of the parAB genes are often located in...

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Section: Methodsmentioning

confidence: 99%

Active segregation by the Bacillus subtilis partitioning system in Escherichia coli

Yamaichi

Niki

2000

Proc. Natl. Acad. Sci. U.S.A.

151

160

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“…Chromosomal rearrangements are largely dependent on the activity of repeated and mobile elements such as insertion sequences (ISs), transposons, prophage sequences, and plasmids (233). Bacterial genomes containing a higher repeat density have higher rates of rearrangements, leading to an accelerated loss of gene order (371).…”

Section: Evolution and Dynamics Of Bacterial Genomesmentioning

confidence: 99%

Genomics ofActinobacteria: Tracing the Evolutionary History of an Ancient Phylum

Ventura

Canchaya

Tauch

et al. 2007

Microbiol Mol Biol Rev

946

638

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SUMMARY Actinobacteria constitute one of the largest phyla among Bacteria and represent gram-positive bacteria with a high G+C content in their DNA. This bacterial group includes microorganisms exhibiting a wide spectrum of morphologies, from coccoid to fragmenting hyphal forms, as well as possessing highly variable physiological and metabolic properties. Furthermore, Actinobacteria members have adopted different lifestyles, and can be pathogens (e.g., Corynebacterium, Mycobacterium, Nocardia, Tropheryma, and Propionibacterium), soil inhabitants (Streptomyces), plant commensals (Leifsonia), or gastrointestinal commensals (Bifidobacterium). The divergence of Actinobacteria from other bacteria is ancient, making it impossible to identify the phylogenetically closest bacterial group to Actinobacteria. Genome sequence analysis has revolutionized every aspect of bacterial biology by enhancing the understanding of the genetics, physiology, and evolutionary development of bacteria. Various actinobacterial genomes have been sequenced, revealing a wide genomic heterogeneity probably as a reflection of their biodiversity. This review provides an account of the recent explosion of actinobacterial genomics data and an attempt to place this in a biological and evolutionary context.

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“…Comparative genomics of bacteria and archaea (collectively, prokaryotes) reveals extensive variation of gene repertoires, which is thought to reflect a highly dynamic regime of genome evolution [1][2][3][4][5][6]. Prokaryotic genomes present a wide variety of genome sizes, from approximately 150 kb in some intracellular endosymbionts of insects [7] to approximately 13 Mb in the largest cyanobacteria [8] and myxobacteria [9].…”

Section: Introductionmentioning

confidence: 99%

Genomes in turmoil: Quantification of genome dynamics in prokaryote supergenomes

et al. 2014

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Background: Genomes of bacteria and archaea (collectively, prokaryotes) appear to exist in incessant flux, expanding via horizontal gene transfer and gene duplication, and contracting via gene loss. However, the actual rates of genome dynamics and relative contributions of different types of event across the diversity of prokaryotes are largely unknown, as are the sizes of microbial supergenomes, i.e. pools of genes that are accessible to the given microbial species.

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Dynamic bacterial genome organization

Cited by 105 publications

References 45 publications

Active segregation by the Bacillus subtilis partitioning system in Escherichia coli

Active segregation by the Bacillus subtilis partitioning system in Escherichia coli

Genomics ofActinobacteria: Tracing the Evolutionary History of an Ancient Phylum

Genomes in turmoil: Quantification of genome dynamics in prokaryote supergenomes

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