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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

Domain architecture and multiple alignment of Type IIG homologs. (A) The position of predicted domains present within HVO_A0006 (accession number ADE01899) homologs is shown, including experimentally characterized DNA methyltransferases from B. burgdorferi and H. pylori and several annotated methyltransferases from archaeal species. The common regions of homology between all proteins are shown in gray. Detected s-adenosyl-L-methionine-dependent methyltransferase superfamily domains (SSF53335) are shown in light blue, along with N6 adenine specific DNA methlytransferase signatures (IPR002296; dark blue). The conserved structural core (αβββαβ) of a PD-(D/E)XK nuclease domain is shown in purple. All sequences shown contained a PD-(D/E)XK motif with a confidence score of 1.0 (Laganeckas et al., 2011). (B) Multiple alignment of HVO_A0006 homologs. Predicted DNA methlytransferase signatures (blue) and PD-(D/E)XK signatures (purple) from part A are highlighted. Conserved secondary structure predictions are shown above: as red boxes for α-helices and yellow arrows for β-sheets. Components of the conserved αβββαβ core of the predicted PD-(D/E)XK nuclease domain shown in part A are outlined in black. Amino acid shading represents Clustal sequence similarity. All sequences other than HVO_A0006 are truncated (see Figure S1 for entire alignment).
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Figure 2: Domain architecture and multiple alignment of Type IIG homologs. (A) The position of predicted domains present within HVO_A0006 (accession number ADE01899) homologs is shown, including experimentally characterized DNA methyltransferases from B. burgdorferi and H. pylori and several annotated methyltransferases from archaeal species. The common regions of homology between all proteins are shown in gray. Detected s-adenosyl-L-methionine-dependent methyltransferase superfamily domains (SSF53335) are shown in light blue, along with N6 adenine specific DNA methlytransferase signatures (IPR002296; dark blue). The conserved structural core (αβββαβ) of a PD-(D/E)XK nuclease domain is shown in purple. All sequences shown contained a PD-(D/E)XK motif with a confidence score of 1.0 (Laganeckas et al., 2011). (B) Multiple alignment of HVO_A0006 homologs. Predicted DNA methlytransferase signatures (blue) and PD-(D/E)XK signatures (purple) from part A are highlighted. Conserved secondary structure predictions are shown above: as red boxes for α-helices and yellow arrows for β-sheets. Components of the conserved αβββαβ core of the predicted PD-(D/E)XK nuclease domain shown in part A are outlined in black. Amino acid shading represents Clustal sequence similarity. All sequences other than HVO_A0006 are truncated (see Figure S1 for entire alignment).

Mentions: A blastp search indicated that HVO_A0006 is a rare protein among the sequenced Halobacteria. The only significant hit within this group was an annotated adenine specific DNA methyltransferase domain protein belonging to Halorubrum sp. AJ67 (Table 4). Out of the top 10 significant hits only a few belonged to archaeal species and the rest were bacterial (Table 4). The blastp analysis also found homologs experimentally characterized as methyltransferases from Borrelia burgdorferi and Helicobacter pylori (Rego et al., 2011; Krebes et al., 2014). However, those homologs are much larger than HVO_A0006, spanning between 700 and 1000 amino acids (Figure 2). A reciprocal blastp of those hits against the H. volcanii DS2 and Halorubrum sp. AJ67 genomes revealed there are additional homologs. One is H. volcanii gene HVO_A0237 (accession number ADE02204), also annotated as an adenine methyltransferase, listed in REBASE as HvoDSORF237P, and located on pHV4 231 genes downstream from HVO_A0006. Another identified homolog is a small annotated adenine methyltransferase in Halorubrum sp. AJ67.


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)

Domain architecture and multiple alignment of Type IIG homologs. (A) The position of predicted domains present within HVO_A0006 (accession number ADE01899) homologs is shown, including experimentally characterized DNA methyltransferases from B. burgdorferi and H. pylori and several annotated methyltransferases from archaeal species. The common regions of homology between all proteins are shown in gray. Detected s-adenosyl-L-methionine-dependent methyltransferase superfamily domains (SSF53335) are shown in light blue, along with N6 adenine specific DNA methlytransferase signatures (IPR002296; dark blue). The conserved structural core (αβββαβ) of a PD-(D/E)XK nuclease domain is shown in purple. All sequences shown contained a PD-(D/E)XK motif with a confidence score of 1.0 (Laganeckas et al., 2011). (B) Multiple alignment of HVO_A0006 homologs. Predicted DNA methlytransferase signatures (blue) and PD-(D/E)XK signatures (purple) from part A are highlighted. Conserved secondary structure predictions are shown above: as red boxes for α-helices and yellow arrows for β-sheets. Components of the conserved αβββαβ core of the predicted PD-(D/E)XK nuclease domain shown in part A are outlined in black. Amino acid shading represents Clustal sequence similarity. All sequences other than HVO_A0006 are truncated (see Figure S1 for entire alignment).
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Related In: Results  -  Collection

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Figure 2: Domain architecture and multiple alignment of Type IIG homologs. (A) The position of predicted domains present within HVO_A0006 (accession number ADE01899) homologs is shown, including experimentally characterized DNA methyltransferases from B. burgdorferi and H. pylori and several annotated methyltransferases from archaeal species. The common regions of homology between all proteins are shown in gray. Detected s-adenosyl-L-methionine-dependent methyltransferase superfamily domains (SSF53335) are shown in light blue, along with N6 adenine specific DNA methlytransferase signatures (IPR002296; dark blue). The conserved structural core (αβββαβ) of a PD-(D/E)XK nuclease domain is shown in purple. All sequences shown contained a PD-(D/E)XK motif with a confidence score of 1.0 (Laganeckas et al., 2011). (B) Multiple alignment of HVO_A0006 homologs. Predicted DNA methlytransferase signatures (blue) and PD-(D/E)XK signatures (purple) from part A are highlighted. Conserved secondary structure predictions are shown above: as red boxes for α-helices and yellow arrows for β-sheets. Components of the conserved αβββαβ core of the predicted PD-(D/E)XK nuclease domain shown in part A are outlined in black. Amino acid shading represents Clustal sequence similarity. All sequences other than HVO_A0006 are truncated (see Figure S1 for entire alignment).
Mentions: A blastp search indicated that HVO_A0006 is a rare protein among the sequenced Halobacteria. The only significant hit within this group was an annotated adenine specific DNA methyltransferase domain protein belonging to Halorubrum sp. AJ67 (Table 4). Out of the top 10 significant hits only a few belonged to archaeal species and the rest were bacterial (Table 4). The blastp analysis also found homologs experimentally characterized as methyltransferases from Borrelia burgdorferi and Helicobacter pylori (Rego et al., 2011; Krebes et al., 2014). However, those homologs are much larger than HVO_A0006, spanning between 700 and 1000 amino acids (Figure 2). A reciprocal blastp of those hits against the H. volcanii DS2 and Halorubrum sp. AJ67 genomes revealed there are additional homologs. One is H. volcanii gene HVO_A0237 (accession number ADE02204), also annotated as an adenine methyltransferase, listed in REBASE as HvoDSORF237P, and located on pHV4 231 genes downstream from HVO_A0006. Another identified homolog is a small annotated adenine methyltransferase in Halorubrum sp. AJ67.

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