Repeated capture of a cytoplasmic linear plasmid by the host nucleus in Debaryomyces hansenii

Yeast

Volumn 29, Issue 3-4, 2012, Pages 145-154

  Satwika, Dhira ^a,b   Klassen, Roland ^a,c   Meinhardt, Friedhelm ^a  

^a UNIVERSITY OF MÜNSTER   (Germany)

^b Duta Wacana Christian University   (Indonesia)

^c University of Texas Medical Branch School of Medicine   (United States)

Author keywords

Chitinase; DNA polymerase; Killer plasmid; NUPAVs; PDH1A

Indexed keywords

DNA POLYMERASE;

ARTICLE; DEBARYOMYCES HANSENII; GENETIC TRANSCRIPTION; KLUYVEROMYCES LACTIS; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PICHIA; PICHIA ACACIAE; PLASMID; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

AMINO ACID SEQUENCE; BASE SEQUENCE; CELL NUCLEUS; CHROMOSOMES, FUNGAL; CLONING, MOLECULAR; CYTOPLASM; DEBAROMYCES; DNA POLYMERASE BETA; ESCHERICHIA COLI; GENES, FUNGAL; KLUYVEROMYCES; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PHYLOGENY; PICHIA; PLASMIDS; RNA, FUNGAL; SPECIES SPECIFICITY; TRANSCRIPTION, GENETIC;

DEBARYOMYCES HANSENII; KLUYVEROMYCES LACTIS; PICHIA ACACIAE;

EID: 84859786167     PISSN: 0749503X     EISSN: 10970061     Source Type: Journal    
DOI: 10.1002/yea.2893     Document Type: Article

References (59)

1. Altschul SF, Madden TL, Schäffer AA, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
2. Blaisonneau J, Nosek J, Fukuhara H. 1999. Linear DNA plasmid pPK2 of Pichia kluyveri: distinction between cytoplasmic and mitochondrial linear plasmids in yeasts. Yeast 15: 781-791.
3. Bolen PL, Kurtzman CP, Ligon JM, et al. 1992. Physical and genetic characterization of linear DNA plasmids from the heterothallic yeast Saccharomycopsis crataegensis. Antonie van Leuwenhoek 61: 195-205.
4. Breuer U, Harms H. 2006. Debaryomyces hansenii - an extremophilic yeast with biotechnological potential. Yeast 23: 415-437.
5. Challberg MD, Kelly TJ. 1979. Adenovirus DNA replication in vitro. Proc Natl Acad Sci USA 76: 655-659.
6. Cong YS, Yarrow D, Li YY, Fukuhara H. 1994. Linear DNA plasmids from Pichia etchellsii, Debaryomyces hansenii and Wingea robertsiae. Microbiology 140: 1327-1335.
7. Dufour E, Rodriguez I, Lazaro JM, et al. 2003. A conserved insertion in protein-primed DNA polymerases is involved in primer terminus stabilisation. J Mol Biol 304: 289-300.
8. Dujon B, Sherman D, Fischer G, et al. 2004. Genome evolution in yeasts. Nature 430: 35-44.
9. Frank AC, Wolfe KH. 2009. Evolutionary capture of viral and plasmid DNA by yeast nuclear chromosomes. Eukaryot Cell 8: 1521-1531.
10. Fukuda K, Maebuchi M, Takata H, Gunge N. 1997. The linear plasmid pDHL1 from Debaryomyces hansenii encodes a protein highly homologous to the pGKL1-plasmid DNA polymerase. Yeast 13: 613-620.
11. Fukuhara H. 1995. Linear DNA plasmids of yeasts. FEMS Microbiol Lett 131: 1-9.
12. Gunge N, Sakaguchi K. 1981. Intergeneric transfer of deoxyribonucleic acid killer plasmids, pGKl1 and pGKl2, from Kluyveromyces lactis into Saccharomyces cerevisiae by cell fusion. J Bacteriol 147: 155-160.
13. Hishinuma F, Hirai K. 1991. Genome organization of the linear plasmid pSKL, isolated from Saccharomyces kluyveri. Mol Gen Genet 226: 97-106.
14. Hishinuma F, Nakamura K, Hirai K, et al. 1984. Cloning and nucleotide sequence of the DNA killer plasmids from yeast. Nucleic Acids Res 12: 7581-7597.
15. Glu wobble uridine methylation by Trm9 identifies Elongator's key role for zymocin-induced cell death in yeast. Mol Microbiol 59: 677-688.
16. Jeske S, Meinhardt F. 2006. Autonomous cytoplasmic linear plasmid pPac1-1 of Pichia acaciae: molecular structure and expression studies. Yeast 23: 479-486.
17. Jeske S, Meinhardt F, Klassen R. 2006a. Extranuclear inheritance: virus-like DNA elements in yeast. In Progress in Botany, vol 68, Esser K, Lüttge U, Beyschlag W, Murata J (eds). Springer: Berlin, Heidelberg, New York; 98-129.
18. Jeske S, Tiggemann M, Meinhardt F. 2006b. Yeast autonomous linear plasmid pGKL2: ORF9 is an actively transcribed essential gene with multiple transcription start points. FEMS Microbiol Lett 255: 321-327.
19. Kämper J, Meinhardt F, Gunge N, Esser K. 1989a. In vivo construction of linear vectors based on killer plasmids from Kluyveromyces lactis: selection of a nuclear gene results in attachment of telomeres. Mol Cell Biol 9: 3931-3937.
20. Kämper J, Meinhardt F, Gunge N, Esser K. 1989b. New recombinant linear DNA elements derived from Kluyveromyces lactis killer plasmids. Nucleic Acids Res 17: 1781.
21. Kempken F, Hermanns J, Osiewacz HD. 1992. Evolution of linear plasmids. J Mol Evol 35: 502-513.
22. Kitada K, Hishinuma H. 1987. A new linear plasmid isolated from the yeast Saccharomyces kluyveri. Mol Gen Genet 206: 377-381.
23. Klassen R, Meinhardt F. 2002. Linear plasmids pWR1A and pWR1B of the yeast Wingea robertsiae are associated with a killer phenotype. Plasmid 48: 142-148.
24. Klassen R, Meinhardt F. 2003. Structural and functional analysis of the killer element pPin1-3 from Pichia inositovora. Mol Genet Genom 270: 190-199.
25. Klassen R, Meinhardt F. 2005. Induction of DNA damage and apoptosis in Saccharomyces cerevisiae by a yeast killer toxin. Cell Microbiol 7: 393-401.
26. Klassen R, Meinhardt F. 2007. Linear protein-primed replicating plasmids in eukaryotic microbes. In Microbial Linear Plasmids, Meinhardt F, Klassen R (eds). Microbiology Monographs, vol 7. Springer: Berlin, Heidelberg; 187-226.
27. Klassen R, Tontsidou L, Larsen M, Meinhardt F. 2001. Genome organization of the linear cytoplasmic element pPE1B from Pichia etchellsii. Yeast 18: 953-961.
28. Klassen R, Jablonowski D, Schaffrath R, Meinhardt F. 2002. Genome organization of the linear Pichia etchellsii plasmid pPE1A: evidence for expression of an extracellular chitin-binding protein homologous to the α-subunit of the Kluyveromyces lactis killer toxin. Plasmid 47: 224-233.
29. Klassen R, Teichert S, Meinhardt F. 2004. Novel yeast killer toxins provoke S-phase arrest and DNA damage checkpoint activation. Mol Microbiol 53: 263-273.
30. Klassen R, Fricke J, Pfeiffer A, Meinhardt F. 2008a. A modified DNA isolation protocol for obtaining pure RT-PCR grade RNA. Biotechnol Lett 30: 1041-1044.
31. Gln. Mol Microbiol 69: 681-697.
32. Larkin MA, Blackshields G, Brown NP, et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
33. Larsen M, Meinhardt F. 2000. Kluyveromyces lactis killer system: identification of a new gene encoded by pGKL2. Curr Genet 38: 271-275.
34. Lépingle A, Casaregola S, Neuveglise C, et al. 2000. Genomic exploration of the hemiascomycetous yeasts: 14. Debaryomyces hansenii var. hansenii. FEBS Lett 487: 82-86.
35. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964.
36. Lu J, Huang B, Esberg A, et al. 2005. The Kluyveromyces lactis γ toxin targets tRNA anticodons. RNA 11: 1648-1654.
37. Meijer WJJ, Horcajadas JA, Salas M. 2001. Φ29 Family of phages. Microbiol Mol Biol Rev 65: 261-287.
38. Meinhardt F, Klassen R. 2009. Yeast killer toxins: fundamentals and applications. In The Mycota, vol 15, Anke T, Weber D (eds). Springer: Berlin, Heidelberg; 107-130.
39. Meinhardt F, Kempken F, Esser K. 1986. Proteins are attached to the ends of a linear plasmid in the filamentous fungus Ascobolus immersus. Curr Genet 11: 243-246.
40. Meinhardt F, Kempken F, Kämper J, Esser K. 1990. Linear plasmids among eukaryotes: fundamentals and applications. Curr Genet 17: 89-95.
41. Meinhardt F, Schaffrath R, Larsen M. 1997. Microbial linear plasmids. Appl Microbiol Biotechnol 47: 329-336.
42. Paluszynski JP, Klassen R, Meinhardt F. 2007. The Pichia acaciae killer system: genetic analysis of toxin immunity. Appl Environ Microbiol 73: 4373-4378.
43. Rohe M, Schründer J, Tudzynski P, Meinhardt F. 1992. Phylogenetic relationships of linear, protein-primed replicating genomes. Curr Genet 21: 173-176.
44. Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY.
45. Sanger F, Nicklen S, Coulsen AR. 1977. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74: 5463-5467.
46. Schaffrath R, Meacock PA. 1995. Kluyveromyces lactis killer plasmid pGKL2: molecular analysis of an essential gene, ORF 5. Yeast 11: 615-628.
47. Schaffrath R, Meinhardt F. 2005. Kluyveromyces lactis zymocin and other plasmid-encoded yeast killer toxins. In Topics in Current Genetics, vol 11, Microbial Protein Toxins, Schmitt MJ, Schaffrath R (eds). Springer: Berlin, Heidelberg; 337-352.
48. Schaffrath R, Stark MJR, Gunge N, Meinhardt F. 1992. Kluyveromyces lactis killer system: ORF1 of pGKL2 has no function in immunity expression and is dispensable for killer plasmid replication and maintenance. Curr Genet 21: 357-363.
49. Schaffrath R, Soond SM, Meacock PA. 1995. The DNA and RNA polymerase genes of yeast plasmid pGKL2 are essential loci for plasmid integrity and maintenance. Microbiology 141: 2591-2599.
50. Schickel J, Helmig C, Meinhardt F. 1996. Kluyveromyces lactis killer system: analysis of cytoplasmic promoters of the linear plasmids. Nucleic Acids Res 24: 1879-1886.
51. Stam JC, Kwakman J, Meijer M, Stuitje AR. 1986. Efficient isolation of the linear DNA killer plasmid of Kluyveromyces lactis: evidence for location and expression in the cytoplasm and characterization of their terminally bound proteins. Nucleic Acids Res 14: 6871-6884.
52. Stark MJR, Boyd A, Mileham AJ, Romanos MA. 1990. The plasmid-encoded killer system of Kluyveromyces lactis: a review. Yeast 6: 1-29.
53. Tamura K, Peterson D, Peterson N, et al. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
54. Tiggemann M, Jeske S, Larsen M, Meinhardt F. 2001. Kluyveromyces lactis cytoplasmic plasmid pGKL2: heterologous expression of Orf3p and proof of guanylyltransferase and mRNA-triphosphatase activities. Yeast 18: 815-825.
55. Tokunaga T, Wada N, Hishinuma F. 1987. Expression and identification of immunity determinants on linear DNA killer plasmids pGKL1 and pGKL2 in Kluyveromyces lactis. Nucleic Acids Res 15: 1031-1046.
56. Tommasino M, Ricci S, Galeotti C. 1988. Genome organisation of the plasmid pGKL2 from Kluyveromyces lactis. Nucleic Acids Res 16: 5863-5878.
57. Worsham PL, Bolen PL. 1990. Killer toxin production in Pichia acaciae is associated with linear DNA plasmids. Curr Genet 18: 77-80.
58. Yanisch-Perron C, Vieira J, Messing J. 1985. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33: 103-119.
59. Young TW. 1987. Killer yeasts. In The Yeasts, vol 2, 2nd edn, Rose AH, Harrison JS (eds). Academic Press: London; 131-164.