Introducing the bacterial ‘chromid’: not a chromosome, not a plasmid

Harrison, Peter W.; Lower, Ryan P. J.; Kim, Nayoung K.D.; Young, Ji

doi:10.1016/j.tim.2009.12.010

Cited by 346 publications

(437 citation statements)

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“…Interestingly, a genomic architecture involving three large replication units (that is, chromosome, chromid(s) and/or megaplasmid) has evolved several times during the diversification of bacterial lineages (Harrison et al, 2010). In Burkholderia, Chain et al (2006) also showed that the different replication units are evolving under independent evolutionary dynamics.…”

Section: Discussionmentioning

confidence: 99%

“…The genomes of S. meliloti 1021 and S. medicae WSM 419 share similar architectures. Both include three main replication units: (i) a chromosome which harbours most of the housekeeping genes; (ii) a chromid (Harrison et al, 2010), where many genes involved in polysaccharide synthesis are clustered (pSMED01 for S. medicae WSM 419 and pSymB for S. meliloti 1021); and (iii) a megaplasmid, where nod genes and genes involved in nitrogen fixation are located (pSMED02 for WSM 419 and pSymA for 1021). The genome of S. medicae WSM 419 also includes a 219-kb plasmid called pSMED03.…”

Section: Introductionmentioning

confidence: 99%

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Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates

et al. 2011

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We investigated the genomic diversity of a local population of the symbiotic bacterium Sinorhizobium medicae, isolated from the roots of wild Medicago lupulina plants, in order to assess genomic diversity, to identify genomic regions influenced by duplication, deletion or strong selection, and to explore the composition of the pan-genome. Partial genome sequences of 12 isolates were obtained by Roche 454 shotgun sequencing (average 5.3 Mb per isolate) and compared with the published sequence of S. medicae WSM 419. Homologous recombination appears to have less impact on the polymorphism patterns of the chromosome than on the chromid pSMED01 and megaplasmid pSMED02. Moreover, pSMED02 is a hot spot of insertions and deletions. The whole chromosome is characterized by low sequence polymorphism, consistent with the high density of housekeeping genes. Similarly, the level of polymorphism of symbiosis genes (low) and of genes involved in polysaccharide synthesis (high) may reflect different selection. Finally, some isolates carry genes that may confer adaptations that S. medicae WSM 419 lacks, including homologues of genes encoding rhizobitoxine synthesis, iron uptake, response to autoinducer-2, and synthesis of distinct polysaccharides. The presence or absence of these genes was confirmed by PCR in each of these 12 isolates and a further 27 isolates from the same population. All isolates had rhizobitoxine genes, while the other genes were co-distributed, suggesting that they may be on the same mobile element. These results are discussed in relation to the ecology of Medicago symbionts and in the perspective of population genomics studies.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates

et al. 2011

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“…Notably, some genes essential for the glycolysis, pentose phosphate, and Calvin-Benson-Bassham pathways, and for the fermentation of pyruvate to acetate (see later), are found only on the smaller chromosome (Supplementary Figure S1). The term 'chromid' has been suggested as a term to describe additional bacterial chromosomes, given that they share characteristics with both chromosomes and plasmids (Harrison et al, 2010). Chromids are often seen in bacteria, being estimated to constitute approximately 1 in 10 of the available genomes from multiple phyla, including Chloroflexi members (Harrison et al, 2010;Jha et al, 2012).…”

Section: Resultsmentioning

confidence: 99%

“…The term 'chromid' has been suggested as a term to describe additional bacterial chromosomes, given that they share characteristics with both chromosomes and plasmids (Harrison et al, 2010). Chromids are often seen in bacteria, being estimated to constitute approximately 1 in 10 of the available genomes from multiple phyla, including Chloroflexi members (Harrison et al, 2010;Jha et al, 2012). What advantage the split genome has for the Cfx-K species is unclear, with the role of such an arrangement in bacteria being generally poorly understood (Egan et al, 2005;Jha et al, 2012).…”

Section: Resultsmentioning

confidence: 99%

Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge

et al. 2016

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Overgrowth of filamentous bacteria in activated sludge wastewater treatment plants (WWTPs) leads to impaired sludge settleability, a condition known as bulking, which is a common operational problem worldwide. Filaments with the Eikelboom 0092 morphotype are commonly associated with such bulking episodes. Members of the uncultured B45 phylotype, which is embraced within the phylum Chloroflexi, were recently shown to exhibit this morphology. Although these organisms are among the most abundant populations recorded in activated sludge processes, nothing is known about their metabolic characteristics. In this study, a genome sequence, representing the B45 phylotype, was retrieved from a metagenome generated from an activated sludge WWTP. The genome consisted of two chromosomes and one plasmid, which were 4.0, 1.0 and 0.04 Mbps in size, respectively. A metabolic model was constructed for this organism, based on annotation of its genome, showing its ability to generate energy by respiration, utilizing oxygen, nitrite or nitrous oxide as electron acceptors, or by fermentation of sugars. The ability of B45 members to ferment sugars under anaerobic conditions was validated in situ with microautoradiography-fluorescence in situ hybridization. The provisional name of 'Candidatus Promineofilum breve' is proposed for this species. This study represents the first detailed information on an uncultured genus of filamentous organisms from activated sludge.

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“…Chromosomes are distinguished from plasmids by the localization of essential genes (1,2). In general, main and second chromosomes are larger (>0.5 Mb) than coresident plasmids, have similar guanine+cytosine (G+C) contents to each other, and are maintained by cell cycle-linked replication and active partitioning systems, whereas plasmids are diverse in that some (i) can be conjugally mobilized, (ii) can replicate within one genus or within many genera (i.e., have a broad host range), (iii) are present in high copy numbers and are segregated stochastically, and (iv) have lower G+C contents than their host chromosomes (1)(2)(3). One of the practical ways of designating a replicon as a "chromosome" has been to examine the localization of the rRNA (rrn) operon, which encodes rRNAs (16S, 23S, and 5S rRNAs), because of its functional importance in protein synthesis.…”

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confidence: 99%

Bacterial clade with the ribosomal RNA operon on a small plasmid rather than the chromosome

Anda

Ohtsubo

Okubo

et al. 2015

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

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rRNA is essential for life because of its functional importance in protein synthesis. The rRNA (rrn) operon encoding 16S, 23S, and 5S rRNAs is located on the "main" chromosome in all bacteria documented to date and is frequently used as a marker of chromosomes. Here, our genome analysis of a plant-associated alphaproteobacterium, Aureimonas sp. AU20, indicates that this strain has its sole rrn operon on a small (9.4 kb), high-copy-number replicon. We designated this unusual replicon carrying the rrn operon on the background of an rrn-lacking chromosome (RLC) as the rrn-plasmid. Four of 12 strains close to AU20 also had this RLC/rrn-plasmid organization. Phylogenetic analysis showed that those strains having the RLC/rrn-plasmid organization represented one clade within the genus Aureimonas. Our finding introduces a previously unaddressed viewpoint into studies of genetics, genomics, and evolution in microbiology and biology in general.ribosomal RNA operon | chromosome | plasmid | genome rearrangement | Aureimonas

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Introducing the bacterial ‘chromid’: not a chromosome, not a plasmid

Cited by 346 publications

References 39 publications

Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates

Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates

Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge

Bacterial clade with the ribosomal RNA operon on a small plasmid rather than the chromosome

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