Abstract
DNA methylation plays an important role in the gene-silencing network of higher eukaryotes. We have analyzed the 21.5-kb maintenance methyltransferase (M-MTase) gene, met1, of the multicellular green alga Volvox carteri. The met1 transcript was detected only during the period when DNA replication and cell division are taking place. It encodes a 238 kDa protein containing eight C-terminal activity domains typical of M-MTases, plus upstream DNA-binding domains including the ProDom domain PD003757, which experimental analyses in animal systems have indicated is required for targeting the enzyme to DNA-replication foci. Several insertions of unknown function make Volvox Met1 the largest known member of the Met1/Dnmt1 family. Here we also show that several endogenous transposon families are CpG-methyated in Volvox, which we think causes them to be inactive. This view is supported by the observation that an in vitro CpG-methylated gene introduced into Volvox was maintained in the methylated and silent state over >100 generations. Thus, we believe that Met1 recognizes and perpetuates the in vitro methylation signal, and that the silencing machinery is then able to transduce such a methylation-only signal into a stable heterochromatic (and silent) state.
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Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
Amann K (2002) Identifizierung neuer regA-kontrollierter Gene bei der grünen Kugelalge Volvox carteri. Diploma thesis. University of Regensburg
Amati BB, Goldschmidt-Clermont M, Wallace CJ, Rochaix JD (1988) cDNA and deduced amino acid sequences of cytochrome c from Chlamydomonas reinhardtii: unexpected functional and phylogenetic implications. J Mol Evol 28:151–160
Aufsatz W, Mette MF, Matzke AJ, Matzke M (2004) The role of MET1 in RNA-directed de novo and maintenance methylation of CG dinucleotides. Plant Mol Biol 54:793–804
Babinger P, Kobl I, Mages W, Schmitt R (2001) A link between DNA methylation and epigenetic silencing in transgenic Volvox carteri. Nucleic Acids Res 29:1261–1271
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL (2005) GenBank. Nucleic Acids Res 33:D34–D38
Bernstein E, Allis CD (2005) RNA meets chromatin. Genes Dev 19:1635–1655
Bird A (2001) Methylation talk between histones and DNA. Science 294:2113–2115
Callebaut I, Courvalin JC, Mornon JP (1999) The BAH (bromo-adjacent homology) domain: a link between DNA methylation, replication and transcriptional regulation. FEBS Lett 446:189–193
Cao X, Jacobsen SE (2002) Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc Natl Acad Sci USA 99(Suppl 4):16491–16498
Cheng Q, Fowler R, Tam LW, Edwards L, Miller SM (2003) The role of GlsA in the evolution of asymmetric cell division in the green alga Volvox carteri. Dev Genes Evol 213:328–335
Cline J, Braman JC, Hogrefe HH (1996) PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acids Res 24:3546–35451
Cole DG, Reedy MV (2003) Algal morphogenesis: how Volvox turns itself inside-out. Curr Biol 13:R770–R772
Cresnar B, Mages W, Müller K, Salbaum JM, Schmitt R (1990) Structure and expression of a single actin gene in Volvox carteri. Curr Genet 18:337–346
Davies JP, Weeks DP, Grossman AR (1992) Expression of the arylsulfatase gene from the beta 2-tubulin promoter in Chlamydomonas reinhardtii. Nucleic Acids Res 20:2959–2965
Duncan L, Bouckaert K, Yeh F, Kirk DL (2002) kangaroo, a Mobile Element From Volvox carteri, is a member of a newly recognized third class of retrotransposons. Genetics 162:1617–1630
Finnegan EJ, Kovac KA (2000) Plant DNA methyltransferases. Plant Mol Biol 43:189–201
Freitag M, Selker EU (2005) Controlling DNA methylation: many roads to one modification. Curr Opin Genet Dev 15:191–199
Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CL (1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci USA 89:1827–1831
Gruber H, Kirzinger SH, Schmitt R (1996) Expression of the Volvox gene encoding nitrate reductase: mutation-dependent activation of cryptic splice sites and intron-enhanced gene expression from a cDNA. Plant Mol Biol 31:1–12
Hermann A, Gowher H, Jeltsch A (2004) Biochemistry and biology of mammalian DNA methyltransferases. Cell Mol Life Sci 61:2571–2587
Kirk DL, Kirk MM (1983) Protein synthetic patterns during the asexual life cycle of Volvox carteri. Dev Biol 96:493–506
Kirk MM, Stark K, Miller SM, Müller W, Taillon BE, Gruber H, Schmitt R, Kirk DL (1999) regA, a Volvox gene that plays a central role in germ-soma differentiation, encodes a novel regulatory protein. Development 126:639–647
Köhl G (1997) Eigenschaften und Verbreitung typischer Transposons der Grünalge Volvox carteri f. nagariensis: Lückenbüßer und Jordan-2. PhD thesis. University of Regensburg
Leonhardt H, Page AW, Weier HU, Bestor TH (1992) A targeting sequence directs DNA methyltransferase to sites of DNA replication in mammalian nuclei. Cell 71:865–873
Lindauer A, Fraser D, Brüderlein M, Schmitt R (1993) Reverse transcriptase families and a copia-like retrotransposon, Osser, in the green alga Volvox carteri. FEBS Lett 319:261–266
Liu Y, Oakeley EJ, Sun L, Jost JP (1998) Multiple domains are involved in the targeting of the mouse DNA methyltransferase to the DNA replication foci. Nucleic Acids Res 26:1038–1045
Mages W, Salbaum JM, Harper JF, Schmitt R (1988) Organization and structure of Volvox alpha-tubulin genes. Mol Gen Genet 213:449–458
Miller SM, Kirk DL (1999) glsA, a Volvox gene required for asymmetric division and germ cell specification, encodes a chaperone-like protein. Development 126:649–658
Miller SM, Schmitt R, Kirk DL (1993) Jordan, an active Volvox transposable element similar to higher plant transposons. Plant Cell 5:1125–1138
Miura A, Yonebayashi S, Watanabe K, Toyama T, Shimada H, Kakutani T (2001) Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411:212–214
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, Gough J, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McDowall J, Mitchell A, Nikolskaya AN, Orchard S, Pagni M, Ponting CP, Quevillon E, Selengut J, Sigrist CJ, Silventoinen V, Studholme DJ, Vaughan R, Wu CH (2005) InterPro, progress and status in 2005. Nucleic Acids Res 33:D201–D205
Qu GZ, Ehrlich M (1999) Demethylation and expression of methylated plasmid DNA stably transfected into HeLa cells. Nucleic Acids Res 27:2332–2338
Robertson KD (2002) DNA methylation and chromatin—unraveling the tangled web. Oncogene 21:5361–5379
Sambrook J, Russell DW (2001) Molecular Cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
Schiedlmeier B, Schmitt R, Müller W, Kirk MM, Gruber H, Mages W, Kirk DL (1994) Nuclear transformation of Volvox carteri. Proc Natl Acad Sci USA 91:5080–5084
Schmitt R (2003) Differentiation of germinal and somatic cells in Volvox carteri. Curr Opin Microbiol 6:608–613
Schmitt R, Fabry S, Kirk DL (1992) In search of molecular origins of cellular differentiation in Volvox and its relatives. Int Rev Cytol 139:189–265
Schmitt R, Stark K, Fabry S, Kirk DL (1998) Phylogenetic relationship of volvocine algae to plants and animals. In: M Syvanen, C Kado (eds) Horizontal Gene Transfer. Chapman & Hall, London, pp 338–348
Servant F, Bru C, Carrere S, Courcelle E, Gouzy J, Peyruc D, Kahn D (2002) ProDom: automated clustering of homologous domains. Brief Bioinform 3:246–251
Sonnhammer EL, Durbin R (1995) A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 167:GC1–GC10
Stark K, Kirk DL, Schmitt R (2001) Two enhancers and one silencer located in the introns of regA control somatic cell differentiation in Volvox carteri. Genes Dev 15:1449–1460
Stark K, Schmitt R (2002) Genetic control of germ-soma differentiation in Volvox carteri. Protist 153:99–107
Tam LW, Kirk DL (1991) Identification of cell-type-specific genes of Volvox carteri and characterization of their expression during the asexual life cycle. Dev Biol 145:51–66
Tariq M, Paszkowski J (2004) DNA and histone methylation in plants. Trends Genet 20:244–251
Wassenegger M (2005) The role of the RNAi machinery in heterochromatin formation. Cell 122:13–16
Yoder JA, Walsh CP, Bestor TH (1997) Cytosine methylation and the ecology of intragenomic parasites. Trends Genet 13:335–340
Zdobnov EM, Apweiler R (2001) InterProScan—an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17:847–848
Acknowledgments
This work was supported by Deutsche Forschungsgemeinschaft (SFB 521/B1). We thank Manuela De Lazzer for technical help and David Kirk for critical review of the manuscript.
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Babinger, P., Völkl, R., Cakstina, I. et al. Maintenance DNA methyltransferase (Met1) and silencing of CpG-methylated foreign DNA in Volvox carteri . Plant Mol Biol 63, 325–336 (2007). https://doi.org/10.1007/s11103-006-9091-1
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DOI: https://doi.org/10.1007/s11103-006-9091-1