Solitary restriction endonucleases in prokaryotic genomes

Ershova, Anna S.; Karyagina, A. S.; Vasiliev, Mikhail O.; Lyashchuk, A. M.; Лунин, В. Г.; Spirin, Sergei A.; Alexeevski, Andrei V.

doi:10.1093/nar/gks853

Cited by 15 publications

(18 citation statements)

References 40 publications

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“…90 genome contains 31 RM systems, which function as microbial defence systems against foreign DNAs [57]. Type I, II, III and IV RM systems were annotated from the Anabaena sp.…”

Section: Discussionmentioning

confidence: 99%

Genome-derived insights into the biology of the hepatotoxic bloom-forming cyanobacterium Anabaena sp. strain 90

et al. 2012

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BackgroundCyanobacteria can form massive toxic blooms in fresh and brackish bodies of water and are frequently responsible for the poisoning of animals and pose a health risk for humans. Anabaena is a genus of filamentous diazotrophic cyanobacteria commonly implicated as a toxin producer in blooms in aquatic ecosystems throughout the world. The biology of bloom-forming cyanobacteria is poorly understood at the genome level.ResultsHere, we report the complete sequence and comprehensive annotation of the bloom-forming Anabaena sp. strain 90 genome. It comprises two circular chromosomes and three plasmids with a total size of 5.3 Mb, encoding a total of 4,738 genes. The genome is replete with mobile genetic elements. Detailed manual annotation demonstrated that almost 5% of the gene repertoire consists of pseudogenes. A further 5% of the genome is dedicated to the synthesis of small peptides that are the products of both ribosomal and nonribosomal biosynthetic pathways. Inactivation of the hassallidin (an antifungal cyclic peptide) biosynthetic gene cluster through a deletion event and a natural mutation of the buoyancy-permitting gvpG gas vesicle gene were documented. The genome contains a large number of genes encoding restriction-modification systems. Two novel excision elements were found in the nifH gene that is required for nitrogen fixation.ConclusionsGenome analysis demonstrated that this strain invests heavily in the production of bioactive compounds and restriction-modification systems. This well-annotated genome provides a platform for future studies on the ecology and biology of these important bloom-forming cyanobacteria.

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“…90 genome contains 31 RM systems, which function as microbial defence systems against foreign DNAs [57]. Type I, II, III and IV RM systems were annotated from the Anabaena sp.…”

Section: Discussionmentioning

confidence: 99%

Genome-derived insights into the biology of the hepatotoxic bloom-forming cyanobacterium Anabaena sp. strain 90

et al. 2012

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“…Subtypes of the type II systems are primarily based on cleavage specificity (138). The type II systems consist solely of the methyltransferase-REase pair that is typically encoded within the same operon, although cases of apparent disjointed localization of the two genes have been reported (40). The most complex, ATP-dependent type I RM systems encompass three genes that encode the R (restriction), M (modification), and S (specificity) subunits of the RMS complex; the R subunit, in addition to REase, also contains a distinct ATPase domain that belongs to helicase superfamily II (15, 99, 163).…”

Section: Innate Immunitymentioning

confidence: 99%

Evolutionary Genomics of Defense Systems in Archaea and Bacteria

Koonin

Makarova²,

Wolf³

2017

Annu. Rev. Microbiol.

285

235

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Evolution of bacteria and archaea involves an incessant arms race against an enormous diversity of genetic parasites. Accordingly, a substantial fraction of the genes in most bacteria and archaea are dedicated to antiparasite defense. The functions of these defense systems follow several distinct strategies, including innate immunity; adaptive immunity; and dormancy induction, or programmed cell death. Recent comparative genomic studies taking advantage of the expanding database of microbial genomes and metagenomes, combined with direct experiments, resulted in the discovery of several previously unknown defense systems, including innate immunity centered on Argonaute proteins, bacteriophage exclusion, and new types of CRISPR-Cas systems of adaptive immunity. Some general principles of function and evolution of defense systems are starting to crystallize, in particular, extensive gain and loss of defense genes during the evolution of prokaryotes; formation of genomic defense islands; evolutionary connections between mobile genetic elements and defense, whereby genes of mobile elements are repeatedly recruited for defense functions; the partially selfish and addictive behavior of the defense systems; and coupling between immunity and dormancy induction/programmed cell death.

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“…The Type II R-M systems have been further classified into several subtypes, primarily on the basis of cleavage specificity (41). The Type II systems consist solely of the MTase–REase pair that is typically encoded within the same operon, although some cases of apparent disjointed localization of the two genes have been reported (43). The most complex ATP-dependent Type I R-M systems encompass three genes, which encode the R (restriction), M (modification) and S (specificity) subunits of the R-MA complex; the R subunit also contains a distinct ATPase domain that belongs to the helicase Superfamily II (42,44,45).…”

Section: Defense Mechanisms In Bacteria and Archaeamentioning

confidence: 99%

Comparative genomics of defense systems in archaea and bacteria

Makarova

Wolf

Koonin

2013

Nucleic Acids Research

387

402

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Our knowledge of prokaryotic defense systems has vastly expanded as the result of comparative genomic analysis, followed by experimental validation. This expansion is both quantitative, including the discovery of diverse new examples of known types of defense systems, such as restriction-modification or toxin-antitoxin systems, and qualitative, including the discovery of fundamentally new defense mechanisms, such as the CRISPR-Cas immunity system. Large-scale statistical analysis reveals that the distribution of different defense systems in bacterial and archaeal taxa is non-uniform, with four groups of organisms distinguishable with respect to the overall abundance and the balance between specific types of defense systems. The genes encoding defense system components in bacterial and archaea typically cluster in defense islands. In addition to genes encoding known defense systems, these islands contain numerous uncharacterized genes, which are candidates for new types of defense systems. The tight association of the genes encoding immunity systems and dormancy- or cell death-inducing defense systems in prokaryotic genomes suggests that these two major types of defense are functionally coupled, providing for effective protection at the population level.

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Solitary restriction endonucleases in prokaryotic genomes

Cited by 15 publications

References 40 publications

Genome-derived insights into the biology of the hepatotoxic bloom-forming cyanobacterium Anabaena sp. strain 90

Genome-derived insights into the biology of the hepatotoxic bloom-forming cyanobacterium Anabaena sp. strain 90

Evolutionary Genomics of Defense Systems in Archaea and Bacteria

Comparative genomics of defense systems in archaea and bacteria

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