Characterization of the archaeal, plasmid-encoded type II restriction-modification system MthTI from Methanobacterium thermoformicicum THF: homology to the bacterial NgoPII system from Neisseria gonorrhoeae

Nölling, J; Vos, Willem M. de

doi:10.1128/jb.174.17.5719-5726.1992

Cited by 47 publications

(33 citation statements)

References 49 publications

(54 reference statements)

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“…The rm genes on conjugative plasmids are mobile, and those on the chromosomes may be mobile by transformation, transduction, or other means. It appears that some rm gene pairs were added to the genome by horizontal transfer (1,9,12,14,35,36). This potential mobility is consistent with the tight linkage of r and m genes (1).…”

Section: Discussionsupporting

confidence: 55%

Restriction-modification systems as genomic parasites in competition for specific sequences.

Kusano

Naito

Handa

et al. 1995

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

102

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Restriction-modification (RM) systems are believed to have evolved to protect cells from foreign DNA. However, this hypothesis may not be sufficient to explain the diversity and specificity in sequence recognition, as well as other properties, of these systems. We report that the EcoRI restriction endonuclease-modification methylase (rm) gene pair stabilizes plasmids that carry it and that this stabilization is blocked by an RM of the same sequence specificity (EcoRI or its isoschizomer, Rsr I) but not by an RM of a different specificity (PaeR7I) on another plasmid. The PaeR7I rm likewise stabilizes plasmids, unless an rm gene pair with identical sequence specificity is present. Our analysis supports the following model for stabilization and incompatibility: the descendants of cells that have lost an rm gene pair expose the recognition sites in their chromosomes to lethal attack by any remaining restriction enzymes unless modification by another RM system of the same specificity protects these sites. Competition for specific sequences among these selfish genes may have generated the great diversity and specificity in sequence recognition among RM systems. Such altruistic suicide strategies, similar to those found in virusinfected cells, may have allowed selfish RM systems to spread by effectively competing with other selfish genes.A type II restriction endonuclease makes a double-strand break within or near a specific recognition sequence in duplex DNA. A cognate modification enzyme methylates the recognition sequence to protect it from the cleavage (1, 2). It is widely accepted that the evolution and maintenance of restriction-modification (RM) systems have been driven by the protection from foreign DNA that they afford to cells. The RM systems do protect cells from infection with some viruses by cleaving their DNA (for example, see ref.3) and are likely to be responsible both for the evolution of antirestriction mechanisms and for the paucity of some restriction sites in certain viruses and plasmids (4).Recent experimental and theoretical analyses (5, 6), however, seem to us to bring into question the efficacy of virusmediated selection for RM systems. Defense by RM systems is short-lived because invading viral DNA will occasionally escape restriction and will become modified, thus affording protection from restriction to itself and its descendants (5, 6). Bacteria will more likely develop other, longer-lasting means of resistance to viruses, such as alterations in the receptor required for infection (5, 6). Although RM systems can provide bacteria with advantage when they are invading new habitats full of phages, it is not clear whether such colonization selection is realistic under natural conditions (5, 6).It is also unclear whether the above "cellular defense" hypothesis can account for the following properties of type II RM systems (1, 2). (i) Their individual high specificity and collective wide diversity in the sequence recognition. (ii) The tight linkage of cognate restriction and modification ...

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Section: Discussionsupporting

confidence: 55%

Restriction-modification systems as genomic parasites in competition for specific sequences.

Kusano

Naito

Handa

et al. 1995

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

102

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“…Furthermore, methanogenic plasmids pFV1, pFZ1, and pFZ2 from M. thermoformicicum were found to carry different type II R-M systems (198), such as MthTI, a GGCC-recognizing R-M system (33), and MthZI and MthFI, both of which are CTAGrecognizing R-M systems (34). The genomes of these archaeal plasmids are thus methylated by the encoded MTases, which allow them to escape host restriction.…”

Section: Restriction-modification Systemsmentioning

confidence: 99%

“…This led to the immediate isolation of several plasmids from different archaeal hosts. Five of them were from methanogens, including pMP1, pME2001, and pME2200 from Methanobacterium thermoautotrophicum (31)(32)(33)(34) and pFV1 and pFZ1 from Methanobacterium thermoformicicum (34). Two plasmids were isolated from hyperthermophilic archaea: pDL10 from Acidianus ambivalens, a thermophilic crenarchaeon isolated from a hot spring in Iceland (35), and pGT5 from Pyrococcus abyssi, a hyperthermophilic euryarchaeon isolated from a deep sea hydrothermal vent (36).…”

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confidence: 99%

Archaeal Extrachromosomal Genetic Elements

Wang

Peng

Shah

et al. 2015

Microbiol Mol Biol Rev

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SUMMARY Research on archaeal extrachromosomal genetic elements (ECEs) has progressed rapidly in the past decade. To date, over 60 archaeal viruses and 60 plasmids have been isolated. These archaeal viruses exhibit an exceptional diversity in morphology, with a wide array of shapes, such as spindles, rods, filaments, spheres, head-tails, bottles, and droplets, and some of these new viruses have been classified into one order, 10 families, and 16 genera. Investigation of model archaeal viruses has yielded important insights into mechanisms underlining various steps in the viral life cycle, including infection, DNA replication and transcription, and virion egression. Many of these mechanisms are unprecedented for any known bacterial or eukaryal viruses. Studies of plasmids isolated from different archaeal hosts have also revealed a striking diversity in gene content and innovation in replication strategies. Highly divergent replication proteins are identified in both viral and plasmid genomes. Genomic studies of archaeal ECEs have revealed a modular sequence structure in which modules of DNA sequence are exchangeable within, as well as among, plasmid families and probably also between viruses and plasmids. In particular, it has been suggested that ECE-host interactions have shaped the coevolution of ECEs and their archaeal hosts. Furthermore, archaeal hosts have developed defense systems, including the innate restriction-modification (R-M) system and the adaptive CRISPR (clustered regularly interspaced short palindromic repeats) system, to restrict invasive plasmids and viruses. Together, these interactions permit a delicate balance between ECEs and their hosts, which is vitally important for maintaining an innovative gene reservoir carried by ECEs. In conclusion, while research on archaeal ECEs has just started to unravel the molecular biology of these genetic entities and their interactions with archaeal hosts, it is expected to accelerate in the next decade.

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“…Type II restriction enzyme systems [176] Methanococcus jannaschii Informational genes resistance to eukaryotes than bacteria. Operational genes closely related to E. coli and Synechocystis.…”

Section: Methanobacterium Thermoformicium and Neisseria Gonorhoeaementioning

confidence: 99%

Phylogeny vs genome reshuffling: horizontal gene transfer

2008

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The evolutionary events in organisms can be tracked to the transfer of genetic material. The inheritance of genetic material among closely related organisms is a slow evolutionary process. On the other hand, the movement of genes among distantly related species can account for rapid evolution. The later process has been quite evident in the appearance of antibiotic resistance genes among human and animal pathogens. Phylogenetic trees based on such genes and those involved in metabolic activities refl ect the incongruencies in comparison to the 16S rDNA gene, generally used for taxonomic relationships. Such discrepancies in gene inheritance have been termed as horizontal gene transfer (HGT) events. In the post-genomic era, the explosion of known sequences through large-scale sequencing projects has unraveled the weakness of traditional 16S rDNA gene tree based evolutionary model. Various methods to scrutinize HGT events include atypical composition, abnormal sequence similarity, anomalous phylogenetic distribution, unusual phyletic patterns, etc. Since HGT generates greater genetic diversity, it is likely to increase resource use and ecosystem resilience.

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Characterization of the archaeal, plasmid-encoded type II restriction-modification system MthTI from Methanobacterium thermoformicicum THF: homology to the bacterial NgoPII system from Neisseria gonorrhoeae

Cited by 47 publications

References 49 publications

Restriction-modification systems as genomic parasites in competition for specific sequences.

Restriction-modification systems as genomic parasites in competition for specific sequences.

Archaeal Extrachromosomal Genetic Elements

Phylogeny vs genome reshuffling: horizontal gene transfer

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