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Hayashi M, Wada Y, Yamamura A, Inoue H, Yamashita N, Ichimura S, Iida Y. Evaluation of the enzymatic properties of DNA (cytosine-5)-methyltransferase M.ApeKI from archaea in the presence of metal ions. Biosci Biotechnol Biochem 2024; 88:1155-1163. [PMID: 39085041 DOI: 10.1093/bbb/zbae106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 07/16/2024] [Indexed: 08/02/2024]
Abstract
We previously identified M.ApeKI from Aeropyum pernix K1 as a highly thermostable DNA (cytosine-5)-methyltransferase. M.ApeKI uses the type II restriction-modification system (R-M system), among the best-studied R-M systems. Although endonucleases generally utilize Mg (II) as a cofactor, several reports have shown that MTases exhibit different reactions in the presence of metal ions. This study aim was to evaluate the enzymatic properties of DNA (cytosine-5)-methyltransferase M.ApeKI from archaea in the presence of metal ions. We evaluated the influence of metal ions on the catalytic activity and DNA binding of M.ApeKI. The catalytic activity was inhibited by Cu (II), Mg (II), Mn (II), and Zn (II), each at 5 m m. DNA binding was more strongly inhibited by 5 m m Cu (II) and 10 m m Zn (II). To our knowledge, this is the first report showing that DNA binding of type II MTase is inhibited by metal ions.
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Affiliation(s)
- Mao Hayashi
- Department of Applied Chemistry and Bioscience, Graduate School of Engineering, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
| | - Yoshinari Wada
- Department of Applied Bioscience, Faculty of Applied Bioscience, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
| | - Akira Yamamura
- Department of Applied Chemistry and Bioscience, Graduate School of Engineering, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
- Department of Applied Bioscience, Faculty of Applied Bioscience, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
| | - Hideki Inoue
- Department of Applied Chemistry and Bioscience, Graduate School of Engineering, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
- Department of Applied Bioscience, Faculty of Applied Bioscience, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
| | - Naoya Yamashita
- Department of Applied Chemistry and Bioscience, Graduate School of Engineering, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
- Department of Applied Bioscience, Faculty of Applied Bioscience, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
| | - Shigetoshi Ichimura
- Department of Applied Chemistry and Bioscience, Graduate School of Engineering, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
- Department of Applied Bioscience, Faculty of Applied Bioscience, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
| | - Yasuhiro Iida
- Department of Applied Chemistry and Bioscience, Graduate School of Engineering, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
- Department of Applied Bioscience, Faculty of Applied Bioscience, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
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Gulati P, Singh A, Patra S, Bhat S, Verma A. Restriction modification systems in archaea: A panoramic outlook. Heliyon 2024; 10:e27382. [PMID: 38644887 PMCID: PMC11033074 DOI: 10.1016/j.heliyon.2024.e27382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/19/2024] [Accepted: 02/28/2024] [Indexed: 04/23/2024] Open
Abstract
Restriction modification (RM) systems are one of the ubiquitous yet primitive defense responses employed by bacteria and archaea with the primary role of safeguarding themselves against invading bacteriophages. Protection of the host occurs by the cleavage of the invading foreign DNA via restriction endonucleases with concomitant methylation of host DNA with the aid of a methyltransferase counterpart. RM systems have been extensively studied in bacteria, however, in the case of archaea there are limited reports of RM enzymes that are investigated to date owing to their inhospitable growth demands. This review aims to broaden the knowledge about what is known about the diversity of RM systems in archaea and encapsulate the current knowledge on restriction and modification enzymes characterized in archaea so far and the role of RM systems in the milieu of archaeal biology.
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Affiliation(s)
- Pallavi Gulati
- Department of Microbiology, Ram Lal Anand College, University of Delhi South Campus, New Delhi 110021, India
| | - Ashish Singh
- Department of Microbiology, University of Delhi South Campus, New Delhi 110021, India
| | - Sandeep Patra
- Department of Microbiology, Ram Lal Anand College, University of Delhi South Campus, New Delhi 110021, India
| | - Shreyas Bhat
- Department of Microbiology, Ram Lal Anand College, University of Delhi South Campus, New Delhi 110021, India
| | - Anil Verma
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA-15213, USA
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Gulati P, Singh A, Goel M, Saha S. The extremophile Picrophilus torridus carries a DNA adenine methylase M.PtoI that is part of a Type I restriction-modification system. Front Microbiol 2023; 14:1126750. [PMID: 37007530 PMCID: PMC10050889 DOI: 10.3389/fmicb.2023.1126750] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 02/27/2023] [Indexed: 03/17/2023] Open
Abstract
DNA methylation events mediated by orphan methyltransferases modulate various cellular processes like replication, repair and transcription. Bacteria and archaea also harbor DNA methyltransferases that are part of restriction-modification systems, which serve to protect the host genome from being cleaved by the cognate restriction enzyme. While DNA methylation has been exhaustively investigated in bacteria it remains poorly understood in archaea. Picrophilus torridus is a euryarchaeon that can thrive under conditions of extremely low pH (0.7), and thus far no reports have been published regarding DNA methylation in this extremophile. This study reports the first experimentation examining DNA methylation in P. torridus. We find the genome to carry methylated adenine (m6A) but not methylated cytosine (m5C) residues. The m6A modification is absent at GATC sites, indicating the absence of an active Dam methylase even though the dam gene has been annotated in the genome sequence. Two other methylases have also been annotated in the P. torridus genome sequence. One of these is a part of a Type I restriction-modification system. Considering that all Type I modification methylases characterized to date target adenine residues, the modification methylase of this Type I system has been examined. The genes encoding the S subunit (that is responsible for DNA recognition) and M subunit (that is responsible for DNA methylation) have been cloned and the recombinant protein purified from E.coli, and regions involved in M-S interactions have been identified. The M.PtoI enzyme harbors all the motifs that typify Type I modification methylases, and displays robust adenine methylation in in vitro assays under a variety of conditions. Interestingly, magnesium is essential for enzyme activity. The enzyme displays substrate inhibition at higher concentrations of AdoMet. Mutational analyses reveal that Motif I plays a role in AdoMet binding, and Motif IV is critical for methylation activity. The data presented here lays the foundation for further research in the area of DNA methylation and restriction-modification research in this most unusual microorganism.
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Affiliation(s)
- Pallavi Gulati
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Ashish Singh
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Manisha Goel
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Swati Saha
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
- *Correspondence: Swati Saha, ;
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Evaluation of the Properties of the DNA Methyltransferase from Aeropyrum pernix K1. Microbiol Spectr 2021; 9:e0018621. [PMID: 34585946 PMCID: PMC8557920 DOI: 10.1128/spectrum.00186-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Little is known regarding the DNA methyltransferases (MTases) in hyperthermophilic archaea. In this study, we focus on an MTase from Aeropyrum pernix K1, a hyperthermophilic archaeon that is found in hydrothermal vents and whose optimum growth temperature is 90°C to 95°C. From genomic sequence analysis, A. pernix K1 has been predicted to have a restriction-modification system (R-M system). The restriction endonuclease from A. pernix K1 (known as ApeKI from New England BioLabs Inc. [catalog code R06435]) has been described previously, but the properties of the MTase from A. pernix K1 (M.ApeKI) have not yet been clarified. Thus, we demonstrated the properties of M.ApeKI. In this study, M.ApeKI was expressed in Escherichia coli strain JM109 and affinity purified using its His tag. The recognition sequence of M.ApeKI was determined by methylation activity and bisulfite sequencing (BS-seq). High-performance liquid chromatography (HPLC) was used to detect the position of the methyl group in methylated cytosine. As a result, it was clarified that M.ApeKI adds the methyl group at the C-5 position of the second cytosine in 5'-GCWGC-3'. Moreover, we also determined that the MTase optimum temperature was over 70°C and that it is strongly tolerant to high temperatures. M.ApeKI is the first highly thermostable DNA (cytosine-5)-methyltransferase to be evaluated by experimental evidence. IMPORTANCE In general, thermophilic bacteria with optimum growth temperatures over or equal to 60°C have been predicted to include only N4-methylcytosine or N6-methyladenine as methylated bases in their DNA, because 5-methylcytosine is susceptible to deamination by heat. However, from this study, A. pernix K1, with an optimum growth temperature at 95°C, was demonstrated to produce a DNA (cytosine-5)-methyltransferase. Thus, A. pernix K1 presumably has 5-methylcytosine in its DNA and may produce an original repair system for the expected C-to-T mutations. M.ApeKI was demonstrated to be tolerant to high temperatures; thus, we expect that M.ApeKI may be valuable for the development of a novel analysis system or epigenetic editing tool.
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The complex phylogenetic relationships of a 4mC/6mA DNA methyltransferase in prokaryotes. Mol Phylogenet Evol 2020; 149:106837. [PMID: 32304827 DOI: 10.1016/j.ympev.2020.106837] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 01/30/2020] [Accepted: 04/09/2020] [Indexed: 01/04/2023]
Abstract
DNA methyltransferases are proteins that modify DNA via attachment of methyl groups to nucleobases and are ubiquitous across the bacterial, archaeal, and eukaryotic domains of life. Here, we investigated the complex evolutionary history of the large and consequential 4mC/6mA DNA methyltransferase protein family using phylogenetic reconstruction of amino acid sequences. We present a well-supported phylogeny of this family based on systematic sampling of taxa across superphyla of bacteria and archaea. We compared the phylogeny to a current representation of the species tree of life and found that the 4mC/6mA methyltransferase family has a strikingly complex evolutionary history that likely began sometime after the last universal common ancestor of life diverged into the bacterial and archaeal lineages and probably involved many horizontal gene transfers within and between domains. Despite the complexity of its evolutionary history, we inferred that only one significant shift in molecular evolutionary rate characterizes the diversification of this protein family.
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6
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Mullins EA, Rodriguez AA, Bradley NP, Eichman BF. Emerging Roles of DNA Glycosylases and the Base Excision Repair Pathway. Trends Biochem Sci 2019; 44:765-781. [PMID: 31078398 DOI: 10.1016/j.tibs.2019.04.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 12/20/2022]
Abstract
The base excision repair (BER) pathway historically has been associated with maintaining genome integrity by eliminating nucleobases with small chemical modifications. In the past several years, however, BER was found to play additional roles in genome maintenance and metabolism, including sequence-specific restriction modification and repair of bulky adducts and interstrand crosslinks. Central to this expanded biological utility are specialized DNA glycosylases - enzymes that selectively excise damaged, modified, or mismatched nucleobases. In this review we discuss the newly identified roles of the BER pathway and examine the structural and mechanistic features of the DNA glycosylases that enable these functions.
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Affiliation(s)
- Elwood A Mullins
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Alyssa A Rodriguez
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Noah P Bradley
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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Xiong L, Liu S, Chen S, Xiao Y, Zhu B, Gao Y, Zhang Y, Chen B, Luo J, Deng Z, Chen X, Wang L, Chen S. A new type of DNA phosphorothioation-based antiviral system in archaea. Nat Commun 2019; 10:1688. [PMID: 30975999 PMCID: PMC6459918 DOI: 10.1038/s41467-019-09390-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 03/07/2019] [Indexed: 01/21/2023] Open
Abstract
Archaea and Bacteria have evolved different defence strategies that target virtually all steps of the viral life cycle. The diversified virion morphotypes and genome contents of archaeal viruses result in a highly complex array of archaea-virus interactions. However, our understanding of archaeal antiviral activities lags far behind our knowledges of those in bacteria. Here we report a new archaeal defence system that involves DndCDEA-specific DNA phosphorothioate (PT) modification and the PbeABCD-mediated halt of virus propagation via inhibition of DNA replication. In contrast to the breakage of invasive DNA by DndFGH in bacteria, DndCDEA-PbeABCD does not degrade or cleave viral DNA. The PbeABCD-mediated PT defence system is widespread and exhibits extensive interdomain and intradomain gene transfer events. Our results suggest that DndCDEA-PbeABCD is a new type of PT-based virus resistance system, expanding the known arsenal of defence systems as well as our understanding of host-virus interactions.
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Affiliation(s)
- Lei Xiong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
- Taihe Hospital, Hubei University of Medicine, 442000, Shiyan, Hubei, China
- Brain Center, Zhongnan Hospital, Wuhan University, 430071, Wuhan, China
| | - Siyi Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
- Brain Center, Zhongnan Hospital, Wuhan University, 430071, Wuhan, China
| | - Si Chen
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, 430023, Wuhan, China
| | - Yao Xiao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
- Brain Center, Zhongnan Hospital, Wuhan University, 430071, Wuhan, China
| | - Bochen Zhu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
- Brain Center, Zhongnan Hospital, Wuhan University, 430071, Wuhan, China
| | - Yali Gao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
- Brain Center, Zhongnan Hospital, Wuhan University, 430071, Wuhan, China
| | - Yujing Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
- Brain Center, Zhongnan Hospital, Wuhan University, 430071, Wuhan, China
| | - Beibei Chen
- College of Life Sciences, Wuhan University, 430071, Wuhan, China
| | - Jie Luo
- Taihe Hospital, Hubei University of Medicine, 442000, Shiyan, Hubei, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
| | - Xiangdong Chen
- College of Life Sciences, Wuhan University, 430071, Wuhan, China
| | - Lianrong Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
- Taihe Hospital, Hubei University of Medicine, 442000, Shiyan, Hubei, China
- Brain Center, Zhongnan Hospital, Wuhan University, 430071, Wuhan, China
| | - Shi Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China.
- Taihe Hospital, Hubei University of Medicine, 442000, Shiyan, Hubei, China.
- Brain Center, Zhongnan Hospital, Wuhan University, 430071, Wuhan, China.
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8
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The Patchy Distribution of Restriction⁻Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria. Genes (Basel) 2019; 10:genes10030233. [PMID: 30893937 PMCID: PMC6471742 DOI: 10.3390/genes10030233] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 12/26/2022] Open
Abstract
Restriction⁻modification (RM) systems in bacteria are implicated in multiple biological roles ranging from defense against parasitic genetic elements, to selfish addiction cassettes, and barriers to gene transfer and lineage homogenization. In bacteria, DNA-methylation without cognate restriction also plays important roles in DNA replication, mismatch repair, protein expression, and in biasing DNA uptake. Little is known about archaeal RM systems and DNA methylation. To elucidate further understanding for the role of RM systems and DNA methylation in Archaea, we undertook a survey of the presence of RM system genes and related genes, including orphan DNA methylases, in the halophilic archaeal class Halobacteria. Our results reveal that some orphan DNA methyltransferase genes were highly conserved among lineages indicating an important functional constraint, whereas RM systems demonstrated patchy patterns of presence and absence. This irregular distribution is due to frequent horizontal gene transfer and gene loss, a finding suggesting that the evolution and life cycle of RM systems may be best described as that of a selfish genetic element. A putative target motif (CTAG) of one of the orphan methylases was underrepresented in all of the analyzed genomes, whereas another motif (GATC) was overrepresented in most of the haloarchaeal genomes, particularly in those that encoded the cognate orphan methylase.
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Ouellette M, Gogarten JP, Lajoie J, Makkay AM, Papke RT. Characterizing the DNA Methyltransferases of Haloferax volcanii via Bioinformatics, Gene Deletion, and SMRT Sequencing. Genes (Basel) 2018; 9:genes9030129. [PMID: 29495512 PMCID: PMC5867850 DOI: 10.3390/genes9030129] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 02/16/2018] [Accepted: 02/19/2018] [Indexed: 12/31/2022] Open
Abstract
DNA methyltransferases (MTases), which catalyze the methylation of adenine and cytosine bases in DNA, can occur in bacteria and archaea alongside cognate restriction endonucleases (REases) in restriction-modification (RM) systems or independently as orphan MTases. Although DNA methylation and MTases have been well-characterized in bacteria, research into archaeal MTases has been limited. A previous study examined the genomic DNA methylation patterns (methylome) of the halophilic archaeon Haloferax volcanii, a model archaeal system which can be easily manipulated in laboratory settings, via single-molecule real-time (SMRT) sequencing and deletion of a putative MTase gene (HVO_A0006). In this follow-up study, we deleted other putative MTase genes in H. volcanii and sequenced the methylomes of the resulting deletion mutants via SMRT sequencing to characterize the genes responsible for DNA methylation. The results indicate that deletion of putative RM genes HVO_0794, HVO_A0006, and HVO_A0237 in a single strain abolished methylation of the sole cytosine motif in the genome (Cm4TAG). Amino acid alignments demonstrated that HVO_0794 shares homology with characterized cytosine CTAG MTases in other organisms, indicating that this MTase is responsible for Cm4TAG methylation in H. volcanii. The CTAG motif has high density at only one of the origins of replication, and there is no relative increase in CTAG motif frequency in the genome of H. volcanii, indicating that CTAG methylation might not have effectively taken over the role of regulating DNA replication and mismatch repair in the organism as previously predicted. Deletion of the putative Type I RM operon rmeRMS (HVO_2269-2271) resulted in abolished methylation of the adenine motif in the genome (GCAm6BN₆VTGC). Alignments of the MTase (HVO_2270) and site specificity subunit (HVO_2271) demonstrate homology with other characterized Type I MTases and site specificity subunits, indicating that the rmeRMS operon is responsible for adenine methylation in H. volcanii. Together with HVO_0794, these genes appear to be responsible for all detected methylation in H. volcanii, even though other putative MTases (HVO_C0040, HVO_A0079) share homology with characterized MTases in other organisms. We also report the construction of a multi-RM deletion mutant (ΔRM), with multiple RM genes deleted and with no methylation detected via SMRT sequencing, which we anticipate will be useful for future studies on DNA methylation in H. volcanii.
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Affiliation(s)
- Matthew Ouellette
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06268, USA.
| | - J Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06268, USA.
| | - Jessica Lajoie
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06268, USA.
| | - Andrea M Makkay
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06268, USA.
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06268, USA.
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Couturier M, Lindås AC. The DNA Methylome of the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius. Front Microbiol 2018; 9:137. [PMID: 29472906 PMCID: PMC5809426 DOI: 10.3389/fmicb.2018.00137] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/22/2018] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is the most common epigenetic modification observed in the genomic DNA (gDNA) of prokaryotes and eukaryotes. Methylated nucleobases, N6-methyl-adenine (m6A), N4-methyl-cytosine (m4C), and 5-methyl-cytosine (m5C), detected on gDNA represent the discrimination mark between self and non-self DNA when they are part of restriction-modification systems in prokaryotes (Bacteria and Archaea). In addition, m5C in Eukaryotes and m6A in Bacteria play an important role in the regulation of key cellular processes. Although archaeal genomes present modified bases as in the two other domains of life, the significance of DNA methylations as regulatory mechanisms remains largely uncharacterized in Archaea. Here, we began by investigating the DNA methylome of Sulfolobus acidocaldarius. The strategy behind this initial study entailed the use of combined digestion assays, dot blots, and genome resequencing, which utilizes specific restriction enzymes, antibodies specifically raised against m6A and m5C and single-molecule real-time (SMRT) sequencing, respectively, to identify DNA methylations occurring in exponentially growing cells. The previously identified restriction-modification system, specific of S. acidocaldarius, was confirmed by digestion assay and SMRT sequencing while, the presence of m6A was revealed by dot blot and identified on the characteristic Dam motif by SMRT sequencing. No m5C was detected by dot blot under the conditions tested. Furthermore, by comparing the distribution of both detected methylations along the genome and, by analyzing DNA methylation profiles in synchronized cells, we investigated in which cellular pathways, in particular the cell cycle, this m6A methylation could be a key player. The analysis of sequencing data rejected a role for m6A methylation in another defense system and also raised new questions about a potential involvement of this modification in the regulation of other biological functions in S. acidocaldarius.
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Affiliation(s)
- Mohea Couturier
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ann-Christin Lindås
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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11
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Zhang Y, Matsuzaka T, Yano H, Furuta Y, Nakano T, Ishikawa K, Fukuyo M, Takahashi N, Suzuki Y, Sugano S, Ide H, Kobayashi I. Restriction glycosylases: involvement of endonuclease activities in the restriction process. Nucleic Acids Res 2017; 45:1392-1403. [PMID: 28180312 PMCID: PMC5388411 DOI: 10.1093/nar/gkw1250] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/23/2016] [Accepted: 12/12/2016] [Indexed: 11/18/2022] Open
Abstract
All restriction enzymes examined are phosphodiesterases generating 3΄-OH and 5΄-P ends, but one restriction enzyme (restriction glycosylase) excises unmethylated bases from its recognition sequence. Whether its restriction activity involves endonucleolytic cleavage remains unclear. One report on this enzyme, R.PabI from a hyperthermophile, ascribed the breakage to high temperature while another showed its weak AP lyase activity generates atypical ends. Here, we addressed this issue in mesophiles. We purified R.PabI homologs from Campylobacter coli (R.CcoLI) and Helicobacter pylori (R.HpyAXII) and demonstrated their DNA cleavage, DNA glycosylase and AP lyase activities in vitro at 37°C. The AP lyase activity is more coupled with glycosylase activity in R.CcoLI than in R.PabI. R.CcoLI/R.PabI expression caused restriction of incoming bacteriophage/plasmid DNA and endogenous chromosomal DNA within Escherichia coli at 37°C. The R.PabI-mediated restriction was promoted by AP endonuclease action in vivo or in vitro. These results reveal the role of endonucleolytic DNA cleavage in restriction and yet point to diversity among the endonucleases. The cleaved ends are difficult to repair in vivo, which may indicate their biological significance. These results support generalization of the concept of restriction–modification system to the concept of self-recognizing epigenetic system, which combines any epigenetic labeling and any DNA damaging.
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Affiliation(s)
- Yingbiao Zhang
- Department of Computational Biology and Medical Sciences (formerly Department of Medical Genome Sciences), Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan
| | - Tomoyuki Matsuzaka
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University Higashi-Hiroshima 739-8526, Japan
| | - Hirokazu Yano
- Department of Computational Biology and Medical Sciences (formerly Department of Medical Genome Sciences), Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Yoshikazu Furuta
- Department of Computational Biology and Medical Sciences (formerly Department of Medical Genome Sciences), Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Toshiaki Nakano
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University Higashi-Hiroshima 739-8526, Japan
| | - Ken Ishikawa
- National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Noriko Takahashi
- Department of Computational Biology and Medical Sciences (formerly Department of Medical Genome Sciences), Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences (formerly Department of Medical Genome Sciences), Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan
| | - Sumio Sugano
- Department of Computational Biology and Medical Sciences (formerly Department of Medical Genome Sciences), Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan
| | - Hiroshi Ide
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University Higashi-Hiroshima 739-8526, Japan
| | - Ichizo Kobayashi
- Department of Computational Biology and Medical Sciences (formerly Department of Medical Genome Sciences), Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
- Faculty of Medicine, Kyorin University, Mitaka, Tokyo 181-8611, Japan
- Institut for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette 91198, France
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560 064, India
- To whom correspondence should be addressed. Tel: +81 90 2487 7510; ; ;
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Kojima KK, Kobayashi I. Transmission of the PabI family of restriction DNA glycosylase genes: mobility and long-term inheritance. BMC Genomics 2015; 16:817. [PMID: 26481899 PMCID: PMC4615327 DOI: 10.1186/s12864-015-2021-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 10/07/2015] [Indexed: 02/08/2023] Open
Abstract
Background R.PabI is an exceptional restriction enzyme that functions as a DNA glycosylase. The enzyme excises an unmethylated base from its recognition sequence to generate apurinic/apyrimidinic (AP) sites, and also displays AP lyase activity, cleaving the DNA backbone at the AP site to generate the 3’-phospho alpha, beta-unsaturated aldehyde end in addition to the 5’-phosphate end. The resulting ends are difficult to religate with DNA ligase. The enzyme was originally isolated in Pyrococcus, a hyperthermophilic archaeon, and additional homologs subsequently identified in the epsilon class of the Gram-negative bacterial phylum Proteobacteria, such as Helicobacter pylori. Results Systematic analysis of R.PabI homologs and their neighboring genes in sequenced genomes revealed co-occurrence of R.PabI with M.PabI homolog methyltransferase genes. R.PabI and M.PabI homolog genes are occasionally found at corresponding (orthologous) loci in different species, such as Helicobacter pylori, Helicobacter acinonychis and Helicobacter cetorum, indicating long-term maintenance of the gene pair. One R.PabI and M.PabI homolog gene pair is observed immediately after the GMP synthase gene in both Campylobacter and Helicobacter, representing orthologs beyond genera. The mobility of the PabI family of restriction-modification (RM) system between genomes is evident upon comparison of genomes of sibling strains/species. Analysis of R.PabI and M.PabI homologs in H. pylori revealed an insertion of integrative and conjugative elements (ICE), and replacement with a gene of unknown function that may specify a membrane-associated toxin (hrgC). In view of the similarity of HrgC with toxins in type I toxin-antitoxin systems, we addressed the biological significance of this substitution. Our data indicate that replacement with hrgC occurred in the common ancestor of hspAmerind and hspEAsia. Subsequently, H. pylori with and without hrgC were intermixed at this locus, leading to complex distribution of hrgC in East Asia and the Americas. In Malaysia, hrgC was horizontally transferred from hspEAsia to hpAsia2 strains. Conclusions The PabI family of RM system behaves as a mobile, selfish genetic element, similar to the other families of Type II RM systems. Our analysis additionally revealed some cases of long-term inheritance. The distribution of the hrgC gene replacing the PabI family in the subpopulations of H. pylori, hspAmerind, hspEAsia and hpAsia2, corresponds to the two human migration events, one from East Asia to Americas and the other from China to Malaysia. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2021-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kenji K Kojima
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan. .,Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan. .,Genetic Information Research Institute, Los Altos, CA, 94022, USA.
| | - Ichizo Kobayashi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan. .,Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan.
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Abstract
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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Ouellette M, Jackson L, Chimileski S, Papke RT. Genome-wide DNA methylation analysis of Haloferax volcanii H26 and identification of DNA methyltransferase related PD-(D/E)XK nuclease family protein HVO_A0006. Front Microbiol 2015; 6:251. [PMID: 25904898 PMCID: PMC4389544 DOI: 10.3389/fmicb.2015.00251] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 03/13/2015] [Indexed: 01/16/2023] Open
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.
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Affiliation(s)
- Matthew Ouellette
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Laura Jackson
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Scott Chimileski
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
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15
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Fukuyo M, Nakano T, Zhang Y, Furuta Y, Ishikawa K, Watanabe-Matsui M, Yano H, Hamakawa T, Ide H, Kobayashi I. Restriction-modification system with methyl-inhibited base excision and abasic-site cleavage activities. Nucleic Acids Res 2015; 43:2841-52. [PMID: 25697504 PMCID: PMC4357717 DOI: 10.1093/nar/gkv116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The restriction-modification systems use epigenetic modification to distinguish between self and nonself DNA. A modification enzyme transfers a methyl group to a base in a specific DNA sequence while its cognate restriction enzyme introduces breaks in DNA lacking this methyl group. So far, all the restriction enzymes hydrolyze phosphodiester bonds linking the monomer units of DNA. We recently reported that a restriction enzyme (R.PabI) of the PabI superfamily with half-pipe fold has DNA glycosylase activity that excises an adenine base in the recognition sequence (5′-GTAC). We now found a second activity in this enzyme: at the resulting apurinic/apyrimidinic (AP) (abasic) site (5′-GT#C, # = AP), its AP lyase activity generates an atypical strand break. Although the lyase activity is weak and lacks sequence specificity, its covalent DNA–R.PabI reaction intermediates can be trapped by NaBH4 reduction. The base excision is not coupled with the strand breakage and yet causes restriction because the restriction enzyme action can impair transformation ability of unmethylated DNA even in the absence of strand breaks in vitro. The base excision of R.PabI is inhibited by methylation of the target adenine base. These findings expand our understanding of genetic and epigenetic processes linking those in prokaryotes and eukaryotes.
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Affiliation(s)
- Masaki Fukuyo
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan Department of Evolutionary Studies of Biosystems, School of Advanced Sciences, The Graduate University for Advanced Studies (SOKENDAI), Hayama, Kanagawa 240-0193, Japan Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Toshiaki Nakano
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University Higashi-Hiroshima 739-8526, Japan
| | - Yingbiao Zhang
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Yoshikazu Furuta
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Ken Ishikawa
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo 113-8654, Japan
| | - Miki Watanabe-Matsui
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Hirokazu Yano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Takeshi Hamakawa
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University Higashi-Hiroshima 739-8526, Japan
| | - Hiroshi Ide
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University Higashi-Hiroshima 739-8526, Japan
| | - Ichizo Kobayashi
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo 113-8654, Japan
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Pingoud A, Wilson GG, Wende W. Type II restriction endonucleases--a historical perspective and more. Nucleic Acids Res 2014; 42:7489-527. [PMID: 24878924 PMCID: PMC4081073 DOI: 10.1093/nar/gku447] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 05/02/2014] [Accepted: 05/07/2014] [Indexed: 12/17/2022] Open
Abstract
This article continues the series of Surveys and Summaries on restriction endonucleases (REases) begun this year in Nucleic Acids Research. Here we discuss 'Type II' REases, the kind used for DNA analysis and cloning. We focus on their biochemistry: what they are, what they do, and how they do it. Type II REases are produced by prokaryotes to combat bacteriophages. With extreme accuracy, each recognizes a particular sequence in double-stranded DNA and cleaves at a fixed position within or nearby. The discoveries of these enzymes in the 1970s, and of the uses to which they could be put, have since impacted every corner of the life sciences. They became the enabling tools of molecular biology, genetics and biotechnology, and made analysis at the most fundamental levels routine. Hundreds of different REases have been discovered and are available commercially. Their genes have been cloned, sequenced and overexpressed. Most have been characterized to some extent, but few have been studied in depth. Here, we describe the original discoveries in this field, and the properties of the first Type II REases investigated. We discuss the mechanisms of sequence recognition and catalysis, and the varied oligomeric modes in which Type II REases act. We describe the surprising heterogeneity revealed by comparisons of their sequences and structures.
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Affiliation(s)
- Alfred Pingoud
- Institute of Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
| | - Geoffrey G Wilson
- New England Biolabs Inc., 240 County Road, Ipswich, MA 01938-2723, USA
| | - Wolfgang Wende
- Institute of Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
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Direct and continuous fluorescence-based measurements of Pyrococcus horikoshii DNA N-6 adenine methyltransferase activity. Anal Biochem 2011; 418:204-12. [PMID: 21839719 DOI: 10.1016/j.ab.2011.07.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 07/20/2011] [Indexed: 12/18/2022]
Abstract
N-6 methylation of adenine destabilises duplex DNA and this can increase the proportion of DNA that dissociates into single strands. We have investigated utilising this property to measure the DNA adenine methyltransferase-catalyzed conversion of hemimethylated to fully methylated DNA through a simple, direct, fluorescence-based assay. The effects of methylation on the kinetics and thermodynamics of hybridisation were measured by comparing a fully methylated oligonucleotide product and a hemimethylated oligonucleotide substrate using a 13-bp duplex labeled on adjacent strands with a fluorophore (fluorescein) and quencher (dabcyl). Enzymatic methylation of the hemimethylated GATC site resulted in destabilisation of the duplex, increasing the proportion of dissociated DNA, and producing an observable increase in fluorescence. The assay provides a direct measurement of methylation rate in real time and is highly reproducible, with a coefficient of variance over 48 independent measurements of 3.6%. DNA methylation rates can be measured as low as 3.55 ± 1.84 fmols(-1) in a 96-well plate format, and the assay has been used to kinetically characterise the Pyrococcus horikoshii DNA adenine methyltransferase.
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Banerjee A, Rao DN. Functional analysis of an acid adaptive DNA adenine methyltransferase from Helicobacter pylori 26695. PLoS One 2011; 6:e16810. [PMID: 21347417 PMCID: PMC3036652 DOI: 10.1371/journal.pone.0016810] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 01/13/2011] [Indexed: 11/18/2022] Open
Abstract
HP0593 DNA-(N(6)-adenine)-methyltransferase (HP0593 MTase) is a member of a Type III restriction-modification system in Helicobacter pylori strain 26695. HP0593 MTase has been cloned, overexpressed and purified heterologously in Escherichia coli. The recognition sequence of the purified MTase was determined as 5'-GCAG-3'and the site of methylation was found to be adenine. The activity of HP0593 MTase was found to be optimal at pH 5.5. This is a unique property in context of natural adaptation of H. pylori in its acidic niche. Dot-blot assay using antibodies that react specifically with DNA containing m6A modification confirmed that HP0593 MTase is an adenine-specific MTase. HP0593 MTase occurred as both monomer and dimer in solution as determined by gel-filtration chromatography and chemical-crosslinking studies. The nonlinear dependence of methylation activity on enzyme concentration indicated that more than one molecule of enzyme was required for its activity. Analysis of initial velocity with AdoMet as a substrate showed that two molecules of AdoMet bind to HP0593 MTase, which is the first example in case of Type III MTases. Interestingly, metal ion cofactors such as Co(2+), Mn(2+), and also Mg(2+) stimulated the HP0593 MTase activity. Preincubation and isotope partitioning analyses clearly indicated that HP0593 MTase-DNA complex is catalytically competent, and suggested that DNA binds to the MTase first followed by AdoMet. HP0593 MTase shows a distributive mechanism of methylation on DNA having more than one recognition site. Considering the occurrence of GCAG sequence in the potential promoter regions of physiologically important genes in H. pylori, our results provide impetus for exploring the role of this DNA MTase in the cellular processes of H. pylori.
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Affiliation(s)
- Arun Banerjee
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Desirazu N. Rao
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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Ishikawa K, Fukuda E, Kobayashi I. Conflicts targeting epigenetic systems and their resolution by cell death: novel concepts for methyl-specific and other restriction systems. DNA Res 2010; 17:325-42. [PMID: 21059708 PMCID: PMC2993543 DOI: 10.1093/dnares/dsq027] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Epigenetic modification of genomic DNA by methylation is important for defining the epigenome and the transcriptome in eukaryotes as well as in prokaryotes. In prokaryotes, the DNA methyltransferase genes often vary, are mobile, and are paired with the gene for a restriction enzyme. Decrease in a certain epigenetic methylation may lead to chromosome cleavage by the partner restriction enzyme, leading to eventual cell death. Thus, the pairing of a DNA methyltransferase and a restriction enzyme forces an epigenetic state to be maintained within the genome. Although restriction enzymes were originally discovered for their ability to attack invading DNAs, it may be understood because such DNAs show deviation from this epigenetic status. DNAs with epigenetic methylation, by a methyltransferase linked or unlinked with a restriction enzyme, can also be the target of DNases, such as McrBC of Escherichia coli, which was discovered because of its methyl-specific restriction. McrBC responds to specific genome methylation systems by killing the host bacterial cell through chromosome cleavage. Evolutionary and genomic analysis of McrBC homologues revealed their mobility and wide distribution in prokaryotes similar to restriction–modification systems. These findings support the hypothesis that this family of methyl-specific DNases evolved as mobile elements competing with specific genome methylation systems through host killing. These restriction systems clearly demonstrate the presence of conflicts between epigenetic systems.
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Affiliation(s)
- Ken Ishikawa
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan
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20
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Bheemanaik S, Sistla S, Krishnamurthy V, Arathi S, Desirazu NR. Kinetics of Methylation by EcoP1I DNA Methyltransferase. Enzyme Res 2010; 2010:302731. [PMID: 21048863 PMCID: PMC2962900 DOI: 10.4061/2010/302731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2010] [Accepted: 06/21/2010] [Indexed: 11/20/2022] Open
Abstract
EcoP1I DNA MTase (M.EcoP1I), an N6-adenine MTase from bacteriophage P1, is a part of the EcoP1I restriction-modification (R-M) system which belongs to the Type III R-M system. It recognizes the sequence 5′-AGACC-3′ and methylates the internal adenine. M.EcoP1I requires Mg2+ for the transfer of methyl groups to DNA. M.EcoP1I is shown to exist as dimer in solution, and even at high salt concentrations (0.5 M) the dimeric M.EcoP1I does not dissociate into monomers suggesting a strong interaction between the monomer subunits. Preincubation and isotope partitioning studies with M.EcoP1I indicate a kinetic mechanism where the duplex DNA binds first followed by AdoMet. Interestingly, M.EcoP1I methylates DNA substrates in the presence of Mn2+ and Ca2+ other than Mg2+ with varying affinities. Amino acid analysis and methylation assays in the presence of metal ions suggest that M.EcoP1I has indeed two metal ion-binding sites [358ID(x)n … ExK401 and 600DxDxD604 motif]. EcoP1I DNA MTase catalyzes the transfer of methyl groups using a distributive mode of methylation on DNA containing more than one recognition site. A chemical modification of EcoP1I DNA MTase using N-ethylmaleimide resulted in an irreversible inactivation of enzyme activity suggesting the possible role of cysteine residues in catalysis.
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Miyazono KI, Watanabe M, Kosinski J, Ishikawa K, Kamo M, Sawasaki T, Nagata K, Bujnicki JM, Endo Y, Tanokura M, Kobayashi I. Novel protein fold discovered in the PabI family of restriction enzymes. Nucleic Acids Res 2007; 35:1908-18. [PMID: 17332011 PMCID: PMC1874622 DOI: 10.1093/nar/gkm091] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Revised: 02/01/2007] [Accepted: 02/01/2007] [Indexed: 11/14/2022] Open
Abstract
Although structures of many DNA-binding proteins have been solved, they fall into a limited number of folds. Here, we describe an approach that led to the finding of a novel DNA-binding fold. Based on the behavior of Type II restriction-modification gene complexes as mobile elements, our earlier work identified a restriction enzyme, R.PabI, and its cognate modification enzyme in Pyrococcus abyssi through comparison of closely related genomes. While the modification methyltransferase was easily recognized, R.PabI was predicted to have a novel 3D structure. We expressed cytotoxic R.PabI in a wheat-germ-based cell-free translation system and determined its crystal structure. R.PabI turned out to adopt a novel protein fold. Homodimeric R.PabI has a curved anti-parallel beta-sheet that forms a 'half pipe'. Mutational and in silico DNA-binding analyses have assigned it as the double-strand DNA-binding site. Unlike most restriction enzymes analyzed, R.PabI is able to cleave DNA in the absence of Mg(2+). These results demonstrate the value of genome comparison and the wheat-germ-based system in finding a novel DNA-binding motif in mobile DNases and, in general, a novel protein fold in horizontally transferred genes.
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Affiliation(s)
- Ken-ichi Miyazono
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113-8657, Japan, Department of Medical Genome Sciences, Graduate School of Frontier Science, University of Tokyo, Tokyo 108-8639, Japan, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland, Department of Applied Chemistry, Faculty of Engineering, Ehime University, Matsuyama 790-8577, Japan, Graduate Program in Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo 108-8639, Japan and Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Miki Watanabe
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113-8657, Japan, Department of Medical Genome Sciences, Graduate School of Frontier Science, University of Tokyo, Tokyo 108-8639, Japan, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland, Department of Applied Chemistry, Faculty of Engineering, Ehime University, Matsuyama 790-8577, Japan, Graduate Program in Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo 108-8639, Japan and Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Jan Kosinski
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113-8657, Japan, Department of Medical Genome Sciences, Graduate School of Frontier Science, University of Tokyo, Tokyo 108-8639, Japan, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland, Department of Applied Chemistry, Faculty of Engineering, Ehime University, Matsuyama 790-8577, Japan, Graduate Program in Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo 108-8639, Japan and Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Ken Ishikawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113-8657, Japan, Department of Medical Genome Sciences, Graduate School of Frontier Science, University of Tokyo, Tokyo 108-8639, Japan, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland, Department of Applied Chemistry, Faculty of Engineering, Ehime University, Matsuyama 790-8577, Japan, Graduate Program in Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo 108-8639, Japan and Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Masayuki Kamo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113-8657, Japan, Department of Medical Genome Sciences, Graduate School of Frontier Science, University of Tokyo, Tokyo 108-8639, Japan, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland, Department of Applied Chemistry, Faculty of Engineering, Ehime University, Matsuyama 790-8577, Japan, Graduate Program in Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo 108-8639, Japan and Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Tatsuya Sawasaki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113-8657, Japan, Department of Medical Genome Sciences, Graduate School of Frontier Science, University of Tokyo, Tokyo 108-8639, Japan, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland, Department of Applied Chemistry, Faculty of Engineering, Ehime University, Matsuyama 790-8577, Japan, Graduate Program in Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo 108-8639, Japan and Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Koji Nagata
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113-8657, Japan, Department of Medical Genome Sciences, Graduate School of Frontier Science, University of Tokyo, Tokyo 108-8639, Japan, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland, Department of Applied Chemistry, Faculty of Engineering, Ehime University, Matsuyama 790-8577, Japan, Graduate Program in Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo 108-8639, Japan and Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Janusz M. Bujnicki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113-8657, Japan, Department of Medical Genome Sciences, Graduate School of Frontier Science, University of Tokyo, Tokyo 108-8639, Japan, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland, Department of Applied Chemistry, Faculty of Engineering, Ehime University, Matsuyama 790-8577, Japan, Graduate Program in Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo 108-8639, Japan and Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Yaeta Endo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113-8657, Japan, Department of Medical Genome Sciences, Graduate School of Frontier Science, University of Tokyo, Tokyo 108-8639, Japan, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland, Department of Applied Chemistry, Faculty of Engineering, Ehime University, Matsuyama 790-8577, Japan, Graduate Program in Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo 108-8639, Japan and Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113-8657, Japan, Department of Medical Genome Sciences, Graduate School of Frontier Science, University of Tokyo, Tokyo 108-8639, Japan, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland, Department of Applied Chemistry, Faculty of Engineering, Ehime University, Matsuyama 790-8577, Japan, Graduate Program in Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo 108-8639, Japan and Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Ichizo Kobayashi
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113-8657, Japan, Department of Medical Genome Sciences, Graduate School of Frontier Science, University of Tokyo, Tokyo 108-8639, Japan, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland, Department of Applied Chemistry, Faculty of Engineering, Ehime University, Matsuyama 790-8577, Japan, Graduate Program in Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo 108-8639, Japan and Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
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