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Genome-wide DNA methylation analysis of Haloferax volcanii H26 and identification of DNA methyltransferase related PD-(D/E)XK nuclease family protein HVO_A0006.

Ouellette M, Jackson L, Chimileski S, Papke RT - Front Microbiol (2015)

Bottom Line: Further bioinformatic analysis of the HVO_A0006 gene demonstrated that the gene is rare among the Halobacteria.It is surrounded by two transposition genes suggesting that HVO_A0006 is a fragment of a Type IIG RM gene, which has likely been acquired through gene transfer, and affects restriction-modification activity by interacting with another RM system component(s).Here, we present the first genome-wide characterization of DNA methylation in an archaeal species and examine the function of a DNA methyltransferase related gene HVO_A0006.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA.

ABSTRACT
Restriction-modification (RM) systems have evolved to protect the cell from invading DNAs and are composed of two enzymes: a DNA methyltransferase and a restriction endonuclease. Although RM systems are present in both archaeal and bacterial genomes, DNA methylation in archaea has not been well defined. In order to characterize the function of RM systems in archaeal species, we have made use of the model haloarchaeon Haloferax volcanii. A genomic DNA methylation analysis of H. volcanii strain H26 was performed using PacBio single molecule real-time (SMRT) sequencing. This analysis was also performed on a strain of H. volcanii in which an annotated DNA methyltransferase gene HVO_A0006 was deleted from the genome. Sequence analysis of H26 revealed two motifs which are modified in the genome: C(m4)TAG and GCA(m6)BN6VTGC. Analysis of the ΔHVO_A0006 strain indicated that it exhibited reduced adenine methylation compared to the parental strain and altered the detected adenine motif. However, protein domain architecture analysis and amino acid alignments revealed that HVO_A0006 is homologous only to the N-terminal endonuclease region of Type IIG RM proteins and contains a PD-(D/E)XK nuclease motif, suggesting that HVO_A0006 is a PD-(D/E)XK nuclease family protein. Further bioinformatic analysis of the HVO_A0006 gene demonstrated that the gene is rare among the Halobacteria. It is surrounded by two transposition genes suggesting that HVO_A0006 is a fragment of a Type IIG RM gene, which has likely been acquired through gene transfer, and affects restriction-modification activity by interacting with another RM system component(s). Here, we present the first genome-wide characterization of DNA methylation in an archaeal species and examine the function of a DNA methyltransferase related gene HVO_A0006.

No MeSH data available.


Related in: MedlinePlus

Diagram of the genomic neighborhood for H. volcanii HVO_A0006 (A) and HVO_A0237 (B). Genes are depicted along with two upstream and downstream flanking genes, with annotated functional predictions below. Gene sizes and intergenic spaces are shown in nucleotides. Both regions shown are found on replicon pHV4.
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Figure 3: Diagram of the genomic neighborhood for H. volcanii HVO_A0006 (A) and HVO_A0237 (B). Genes are depicted along with two upstream and downstream flanking genes, with annotated functional predictions below. Gene sizes and intergenic spaces are shown in nucleotides. Both regions shown are found on replicon pHV4.

Mentions: The gene neighborhoods of HVO_A0006 and HVO_A0237 were examined. Analysis of the surrounding genomic region of HVO_A0006 (Figure 3A) revealed that the gene is flanked by three transposition genes: a XerC/D-like integrase and two putative transposases. A putative transposase was also found directly upstream of HVO_A0237 (Figure 3B). This predicted protein (HVO_A0238) is the same length and 100% identical to the ISH5 transposase adjacent to HVO_A0006: HVO_A0007 (Figure 3).


Genome-wide DNA methylation analysis of Haloferax volcanii H26 and identification of DNA methyltransferase related PD-(D/E)XK nuclease family protein HVO_A0006.

Ouellette M, Jackson L, Chimileski S, Papke RT - Front Microbiol (2015)

Diagram of the genomic neighborhood for H. volcanii HVO_A0006 (A) and HVO_A0237 (B). Genes are depicted along with two upstream and downstream flanking genes, with annotated functional predictions below. Gene sizes and intergenic spaces are shown in nucleotides. Both regions shown are found on replicon pHV4.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4389544&req=5

Figure 3: Diagram of the genomic neighborhood for H. volcanii HVO_A0006 (A) and HVO_A0237 (B). Genes are depicted along with two upstream and downstream flanking genes, with annotated functional predictions below. Gene sizes and intergenic spaces are shown in nucleotides. Both regions shown are found on replicon pHV4.
Mentions: The gene neighborhoods of HVO_A0006 and HVO_A0237 were examined. Analysis of the surrounding genomic region of HVO_A0006 (Figure 3A) revealed that the gene is flanked by three transposition genes: a XerC/D-like integrase and two putative transposases. A putative transposase was also found directly upstream of HVO_A0237 (Figure 3B). This predicted protein (HVO_A0238) is the same length and 100% identical to the ISH5 transposase adjacent to HVO_A0006: HVO_A0007 (Figure 3).

Bottom Line: Further bioinformatic analysis of the HVO_A0006 gene demonstrated that the gene is rare among the Halobacteria.It is surrounded by two transposition genes suggesting that HVO_A0006 is a fragment of a Type IIG RM gene, which has likely been acquired through gene transfer, and affects restriction-modification activity by interacting with another RM system component(s).Here, we present the first genome-wide characterization of DNA methylation in an archaeal species and examine the function of a DNA methyltransferase related gene HVO_A0006.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA.

ABSTRACT
Restriction-modification (RM) systems have evolved to protect the cell from invading DNAs and are composed of two enzymes: a DNA methyltransferase and a restriction endonuclease. Although RM systems are present in both archaeal and bacterial genomes, DNA methylation in archaea has not been well defined. In order to characterize the function of RM systems in archaeal species, we have made use of the model haloarchaeon Haloferax volcanii. A genomic DNA methylation analysis of H. volcanii strain H26 was performed using PacBio single molecule real-time (SMRT) sequencing. This analysis was also performed on a strain of H. volcanii in which an annotated DNA methyltransferase gene HVO_A0006 was deleted from the genome. Sequence analysis of H26 revealed two motifs which are modified in the genome: C(m4)TAG and GCA(m6)BN6VTGC. Analysis of the ΔHVO_A0006 strain indicated that it exhibited reduced adenine methylation compared to the parental strain and altered the detected adenine motif. However, protein domain architecture analysis and amino acid alignments revealed that HVO_A0006 is homologous only to the N-terminal endonuclease region of Type IIG RM proteins and contains a PD-(D/E)XK nuclease motif, suggesting that HVO_A0006 is a PD-(D/E)XK nuclease family protein. Further bioinformatic analysis of the HVO_A0006 gene demonstrated that the gene is rare among the Halobacteria. It is surrounded by two transposition genes suggesting that HVO_A0006 is a fragment of a Type IIG RM gene, which has likely been acquired through gene transfer, and affects restriction-modification activity by interacting with another RM system component(s). Here, we present the first genome-wide characterization of DNA methylation in an archaeal species and examine the function of a DNA methyltransferase related gene HVO_A0006.

No MeSH data available.


Related in: MedlinePlus