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CRISPR-Cas immunity and mobile DNA: a new superfamily of DNA transposons encoding a Cas1 endonuclease.

Hickman AB, Dyda F - Mob DNA (2014)

Bottom Line: Mobile genetic elements such as DNA transposons are a feature of most genomes.The existence of novel DNA transposons can be inferred when whole genome sequencing reveals the presence of hallmarks of mobile elements such as terminal inverted repeats (TIRs) flanked by target site duplications (TSDs).The data strongly suggests that these elements, designated 'casposons', are likely to be bona fide DNA transposons and that their Cas1 nucleases act as transposases and are possibly still active.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

ABSTRACT
Mobile genetic elements such as DNA transposons are a feature of most genomes. The existence of novel DNA transposons can be inferred when whole genome sequencing reveals the presence of hallmarks of mobile elements such as terminal inverted repeats (TIRs) flanked by target site duplications (TSDs). A recent report describes a new superfamily of DNA transposons in the genomes of a few bacteria and archaea that possess TIRs and TSDs, and encode several conserved genes including a cas1 endonuclease gene, previously associated only with CRISPR-Cas adaptive immune systems. The data strongly suggests that these elements, designated 'casposons', are likely to be bona fide DNA transposons and that their Cas1 nucleases act as transposases and are possibly still active.

No MeSH data available.


Related in: MedlinePlus

Properties of the family 2 casposons. (A) Predicted common protein-coding genes within family 2 casposons include a PolB family polymerase, an HNH family endonuclease, several HTH domains, and Cas1. The gene color code corresponds to that of Krupovic et al. The green arrows flanking the casposons indicate target site duplications (TSDs). (B) An alignment of the first 41 nucleotides (nt) of casposon family 2 Left End Terminal Inverted Repeats (TIRs) reveals conserved sequence motifs which could be the basis of transposase recognition. Green letters indicate the TSDs and black letters the TIR sequences identified by Krupovic et al., with apparently conserved patterns highlighted in red or blue. Bold black lettering corresponds to nts that were not included in the analysis of Krupovic et al. The aligned sequences and the Accession Number and coordinates for each are: MetFor-C1 [NC_019943;1964105..1964159], MetPsy-C1 [NC_018876;190336..190390], MetTin-C1 [NZ_AZAJ01000001; 3015399..3015453], MetMaz-C1 [NC_003901; 3946587..3946641], MetMah-C1[NC_014002; reverse complement of 1332841..1332895], MetLum-C1 [NZ_CAJE01000015; 159864..159918] AciBoo-C1 [NC_013926; 380309..380363], MetArv-C1 [NC_009464; 2695204..2695258].
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Figure 1: Properties of the family 2 casposons. (A) Predicted common protein-coding genes within family 2 casposons include a PolB family polymerase, an HNH family endonuclease, several HTH domains, and Cas1. The gene color code corresponds to that of Krupovic et al. The green arrows flanking the casposons indicate target site duplications (TSDs). (B) An alignment of the first 41 nucleotides (nt) of casposon family 2 Left End Terminal Inverted Repeats (TIRs) reveals conserved sequence motifs which could be the basis of transposase recognition. Green letters indicate the TSDs and black letters the TIR sequences identified by Krupovic et al., with apparently conserved patterns highlighted in red or blue. Bold black lettering corresponds to nts that were not included in the analysis of Krupovic et al. The aligned sequences and the Accession Number and coordinates for each are: MetFor-C1 [NC_019943;1964105..1964159], MetPsy-C1 [NC_018876;190336..190390], MetTin-C1 [NZ_AZAJ01000001; 3015399..3015453], MetMaz-C1 [NC_003901; 3946587..3946641], MetMah-C1[NC_014002; reverse complement of 1332841..1332895], MetLum-C1 [NZ_CAJE01000015; 159864..159918] AciBoo-C1 [NC_013926; 380309..380363], MetArv-C1 [NC_009464; 2695204..2695258].

Mentions: The work of Krupovic et al. builds on a previous report on the evolutionary history of Cas1 proteins which identified two groups of Cas1 proteins not associated with CRISPR loci [9]. One of these groups, designated the Cas1-solo group 2, has Cas1 genes in a conserved neighborhood that usually also contains genes for a B family DNA polymerase, an HNH nuclease, and several helix-turn-helix (HTH) domains (FigureĀ 1A). The current analysis reveals that this conserved region is contained between terminal inverted repeats (TIRs) and is flanked by target site duplications (TSDs), hallmarks of DNA transposons encoding RNase H-like transposases (reviewed in [15,16]). Krupovic et al. propose that these features suggest that these regions are mobile genetics elements, and that the Cas1 proteins are required for the integration step of transposition. They further propose that the location of this group of proteins within the Cas1 phylogeny indicates that they likely predate the development of CRISPR-Cas systems.


CRISPR-Cas immunity and mobile DNA: a new superfamily of DNA transposons encoding a Cas1 endonuclease.

Hickman AB, Dyda F - Mob DNA (2014)

Properties of the family 2 casposons. (A) Predicted common protein-coding genes within family 2 casposons include a PolB family polymerase, an HNH family endonuclease, several HTH domains, and Cas1. The gene color code corresponds to that of Krupovic et al. The green arrows flanking the casposons indicate target site duplications (TSDs). (B) An alignment of the first 41 nucleotides (nt) of casposon family 2 Left End Terminal Inverted Repeats (TIRs) reveals conserved sequence motifs which could be the basis of transposase recognition. Green letters indicate the TSDs and black letters the TIR sequences identified by Krupovic et al., with apparently conserved patterns highlighted in red or blue. Bold black lettering corresponds to nts that were not included in the analysis of Krupovic et al. The aligned sequences and the Accession Number and coordinates for each are: MetFor-C1 [NC_019943;1964105..1964159], MetPsy-C1 [NC_018876;190336..190390], MetTin-C1 [NZ_AZAJ01000001; 3015399..3015453], MetMaz-C1 [NC_003901; 3946587..3946641], MetMah-C1[NC_014002; reverse complement of 1332841..1332895], MetLum-C1 [NZ_CAJE01000015; 159864..159918] AciBoo-C1 [NC_013926; 380309..380363], MetArv-C1 [NC_009464; 2695204..2695258].
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4150552&req=5

Figure 1: Properties of the family 2 casposons. (A) Predicted common protein-coding genes within family 2 casposons include a PolB family polymerase, an HNH family endonuclease, several HTH domains, and Cas1. The gene color code corresponds to that of Krupovic et al. The green arrows flanking the casposons indicate target site duplications (TSDs). (B) An alignment of the first 41 nucleotides (nt) of casposon family 2 Left End Terminal Inverted Repeats (TIRs) reveals conserved sequence motifs which could be the basis of transposase recognition. Green letters indicate the TSDs and black letters the TIR sequences identified by Krupovic et al., with apparently conserved patterns highlighted in red or blue. Bold black lettering corresponds to nts that were not included in the analysis of Krupovic et al. The aligned sequences and the Accession Number and coordinates for each are: MetFor-C1 [NC_019943;1964105..1964159], MetPsy-C1 [NC_018876;190336..190390], MetTin-C1 [NZ_AZAJ01000001; 3015399..3015453], MetMaz-C1 [NC_003901; 3946587..3946641], MetMah-C1[NC_014002; reverse complement of 1332841..1332895], MetLum-C1 [NZ_CAJE01000015; 159864..159918] AciBoo-C1 [NC_013926; 380309..380363], MetArv-C1 [NC_009464; 2695204..2695258].
Mentions: The work of Krupovic et al. builds on a previous report on the evolutionary history of Cas1 proteins which identified two groups of Cas1 proteins not associated with CRISPR loci [9]. One of these groups, designated the Cas1-solo group 2, has Cas1 genes in a conserved neighborhood that usually also contains genes for a B family DNA polymerase, an HNH nuclease, and several helix-turn-helix (HTH) domains (FigureĀ 1A). The current analysis reveals that this conserved region is contained between terminal inverted repeats (TIRs) and is flanked by target site duplications (TSDs), hallmarks of DNA transposons encoding RNase H-like transposases (reviewed in [15,16]). Krupovic et al. propose that these features suggest that these regions are mobile genetics elements, and that the Cas1 proteins are required for the integration step of transposition. They further propose that the location of this group of proteins within the Cas1 phylogeny indicates that they likely predate the development of CRISPR-Cas systems.

Bottom Line: Mobile genetic elements such as DNA transposons are a feature of most genomes.The existence of novel DNA transposons can be inferred when whole genome sequencing reveals the presence of hallmarks of mobile elements such as terminal inverted repeats (TIRs) flanked by target site duplications (TSDs).The data strongly suggests that these elements, designated 'casposons', are likely to be bona fide DNA transposons and that their Cas1 nucleases act as transposases and are possibly still active.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

ABSTRACT
Mobile genetic elements such as DNA transposons are a feature of most genomes. The existence of novel DNA transposons can be inferred when whole genome sequencing reveals the presence of hallmarks of mobile elements such as terminal inverted repeats (TIRs) flanked by target site duplications (TSDs). A recent report describes a new superfamily of DNA transposons in the genomes of a few bacteria and archaea that possess TIRs and TSDs, and encode several conserved genes including a cas1 endonuclease gene, previously associated only with CRISPR-Cas adaptive immune systems. The data strongly suggests that these elements, designated 'casposons', are likely to be bona fide DNA transposons and that their Cas1 nucleases act as transposases and are possibly still active.

No MeSH data available.


Related in: MedlinePlus