IS-Linked Movement of a Restriction-Modification System

Takahashi, Noriko; Ohashi, Seishi; Sadykov, Marat R.; Mizutani-Ui, Yoko; Kobayashi, Ichizo

doi:10.1371/journal.pone.0016554

Cited by 17 publications

(13 citation statements)

References 43 publications

(84 reference statements)

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“…Similar clustering of defense genes has been observed in other studies; in particular, diverse genomic islands carrying RM systems have been described (39). Furthermore, involvement of transposable elements in the horizontal transfer of defense systems has been demonstrated (23,36,83). An additional twist in the relationships between transposable elements and defense systems is added by the demonstration that mobile elements, in particular retroelements, can function as Abi systems and are also associated with CRISPR-Cas systems (14,45,53).…”

supporting

confidence: 80%

Defense Islands in Bacterial and Archaeal Genomes and Prediction of Novel Defense Systems

et al. 2011

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The arms race between cellular life forms and viruses is a major driving force of evolution. A substantial fraction of bacterial and archaeal genomes is dedicated to antivirus defense. We analyzed the distribution of defense genes and typical mobilome components (such as viral and transposon genes) in bacterial and archaeal genomes and demonstrated statistically significant clustering of antivirus defense systems and mobile genes and elements in genomic islands. The defense islands are enriched in putative operons and contain numerous overrepresented gene families. A detailed sequence analysis of the proteins encoded by genes in these families shows that many of them are diverged variants of known defense system components, whereas others show features, such as characteristic operonic organization, that are suggestive of novel defense systems. Thus, genomic islands provide abundant material for the experimental study of bacterial and archaeal antivirus defense. Except for the CRISPR-Cas systems, different classes of defense systems, in particular toxin-antitoxin and restriction-modification systems, show nonrandom clustering in defense islands. It remains unclear to what extent these associations reflect functional cooperation between different defense systems and to what extent the islands are genomic "sinks" that accumulate diverse nonessential genes, particularly those acquired via horizontal gene transfer. The characteristics of defense islands resemble those of mobilome islands. Defense and mobilome genes are nonrandomly associated in islands, suggesting nonadaptive evolution of the islands via a preferential attachment-like mechanism underpinned by the addictive properties of defense systems such as toxinsantitoxins and an important role of horizontal mobility in the evolution of these islands.

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confidence: 80%

Defense Islands in Bacterial and Archaeal Genomes and Prediction of Novel Defense Systems

et al. 2011

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“…International Journal of Genomics 7 International Journal of Genomics be mediated by MGE, such as phage [37] and insertion sequence [38]. However, there seem to be no phages or MGEs involved in these acquired genes, consistent with a previous finding in Arthrospira platensis [39].…”

supporting

confidence: 85%

Comparative Genomic Analysis of Rhodococcus equi: An Insight into Genomic Diversity and Genome Evolution

Ying

et al. 2019

International Journal of Genomics

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Rhodococcus equi, a member of the Rhodococcus genus, is a gram-positive pathogenic bacterium. Rhodococcus possesses an open pan-genome that constitutes the basis of its high genomic diversity and allows for adaptation to specific niche conditions and the changing host environments. Our analysis further showed that the core genome of R. equi contributes to the pathogenicity and niche adaptation of R. equi. Comparative genomic analysis revealed that the genomes of R. equi shared identical collinearity relationship, and heterogeneity was mainly acquired by means of genomic islands and prophages. Moreover, genomic islands in R. equi were always involved in virulence, resistance, or niche adaptation and possibly working with prophages to cause the majority of genome expansion. These findings provide an insight into the genomic diversity, evolution, and structural variation of R. equi and a valuable resource for functional genomic studies.

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“…Therefore, it is highly probable that the loss of the activity of the TA system is compensated by the presence of the functional PamI 'stabilizing' system. This form of 'symbiosis' between an R-M system and its host plasmid may promote the spread, and therefore, the long-term persistence of R-M complexes in a wide range of bacteria (Takahashi et al, 2011).…”

Section: Discussionmentioning

confidence: 99%

Functional characterization of the type II PamI restriction-modification system derived from plasmid pAMI7 of Paracoccus aminophilusJCM 7686

Dziewit

Kuczkowska

Adamczuk

et al. 2011

FEMS Microbiol Lett

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Plasmid pAMI7 of the methylotrophic bacterium Paracoccus aminophilus JCM 7686 (Alphaproteobacteria) encodes a functional type II restriction-modification (R-M) system designated PamI. Homologous systems were identified in the genomes of distinct taxonomic groups of Bacteria and Archaea, which provides evidence that horizontal gene transfer has contributed to the wide dissemination of R-M modules - even between domains. Analysis of the cleavage specificity of the R.PamI endonuclease revealed that this protein is an isoschizomer of restriction enzyme NcoI. Interestingly, bioinformatic analyses suggest that R.PamI and NcoI are accompanied by methyltransferases of different methylation specificities (C5-methylcytosine and N4-methylcytosine methyltransferases, respectively), which possibly exemplifies recombinational shuffling of genes coding for individual components of R-M systems. The PamI system can stabilize plasmid pAMI7 in a bacterial population, most probably at the postsegregational level. Therefore, it functions in an analogous manner to plasmid-encoded toxin-antitoxin (TA) systems. Since the TA system of pAMI7 is nonfunctional, it is highly probable that this lack is compensated by the stabilizing activity of PamI. This indicates the crucial role of the analyzed R-M system in the stable maintenance of pAMI7, which is, to our knowledge, the first report of 'symbiosis' between a R-M system and a plasmid in the Alphaproteobacteria.

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IS-Linked Movement of a Restriction-Modification System

Cited by 17 publications

References 43 publications

Defense Islands in Bacterial and Archaeal Genomes and Prediction of Novel Defense Systems

Defense Islands in Bacterial and Archaeal Genomes and Prediction of Novel Defense Systems

Comparative Genomic Analysis of Rhodococcus equi: An Insight into Genomic Diversity and Genome Evolution

Functional characterization of the type II PamI restriction-modification system derived from plasmid pAMI7 of Paracoccus aminophilusJCM 7686

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