Refined Pichia pastoris reference genome sequence

Journal of Biotechnology

Volumn 235, Issue , 2016, Pages 121-131

  Sturmberger, Lukas ^a   Chappell, Thomas ^e   Geier, Martina ^a   Krainer, Florian ^d   Day, Kasey J ^f   Vide, Ursa ^d   Trstenjak, Sara ^d   Schiefer, Anja ^a   Richardson, Toby ^g   Soriaga, Leah ^g   Darnhofer, Barbara ^a,b,c   Birner Gruenberger, Ruth ^a,b,c   Glick, Benjamin S ^f   Tolstorukov, Ilya ^e,h   Cregg, James ^e,h   Madden, Knut ^e   Glieder, Anton ^a,d,i  

^a AUSTRIAN CENTRE OF INDUSTRIAL BIOTECHNOLOGY   (Austria)

^b MEDICAL UNIVERSITY OF GRAZ   (Austria)

^c BIOTECHMED GRAZ   (Austria)

^d GRAZ UNIVERSITY OF TECHNOLOGY   (Austria)

^e Biogrammatics Inc   (United States)

^f UNIVERSITY OF CHICAGO   (United States)

^g Synthetic Genomics Inc   (United States)

^h KECK GRADUATE INSTITUTE   (United States)

ⁱ bisy eU   (Austria)

Author keywords

Centromere; Genome; Killer plasmid; P. pastoris; RNA seq; Splicing

Indexed keywords

CABLE JOINTING; CYTOLOGY; GENETIC ENGINEERING; MOLECULAR BIOLOGY; RECOMBINANT PROTEINS; RNA; YEAST;

CELLULAR FUNCTION; CENTROMERE; KILLER PLASMID; OPEN READING FRAME; P. PASTORIS; PEROXISOME BIOGENESIS; RECOMBINANT PROTEIN PRODUCTIONS; SECRETORY PATHWAYS;

GENES;

FUNGAL DNA; FUNGAL RNA; TRANSCRIPTOME; HYBRID PROTEIN;

ALTERNATIVE RNA SPLICING; CENTROMERE; DNA EXTRACTION; DNA MODIFICATION; FUNGAL GENOME; FUNGAL STRAIN; FUNGUS IDENTIFICATION; GENE FUNCTION; GENE MAPPING; GENE SEQUENCE; GENETIC DATABASE; INTRON; KOMAGATAELLA PASTORIS; MOLECULAR GENETICS; NONHUMAN; PLASMID; PRIORITY JOURNAL; REFERENCE DATABASE; REVIEW; RNA EXTRACTION; SPECIES CULTIVATION; TRANSCRIPTOMICS; DNA SEQUENCE; GENETIC ENGINEERING; GENETICS; METABOLISM; PICHIA;

ALTERNATIVE SPLICING; CENTROMERE; DNA, FUNGAL; GENETIC ENGINEERING; GENOME, FUNGAL; PICHIA; PLASMIDS; RECOMBINANT FUSION PROTEINS; SEQUENCE ANALYSIS, DNA; TRANSCRIPTOME;

EID: 84969921373     PISSN: 01681656     EISSN: 18734863     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2016.04.023     Document Type: Article

References (78)

1. Banerjee, H., Verma, M., Search for a novel killer toxin in yeast Pichia pastoris. Plasmid 43 (2000), 181–183.
2. Banerjee, H., Kopvak, C., Curley, D., Identification of linear DNA plasmids of the yeast Pichia pastoris. Plasmid 40 (1998), 58–60.
3. Bevis, B.J., Hammond, A.T., Reinke, C.A., Glick, B.S., De novo formation of transitional ER sites and Golgi structures in Pichia pastoris. Nat. Cell Biol. 4 (2002), 750–756.
4. Biggins, S., The composition, functions, and regulation of the budding yeast kinetochore. Genetics 194 (2013), 817–846.
5. Birney Clamp, M., Durbin, R.E., GeneWise and genomewise. Genome Res. 14 (2004), 988–995.
6. Butler, A.R., O'Donnell, R.W., Martin, V.J., Gooday, G.W., Stark, M.J., Kluyveromyces lactis toxin has an essential chitinase activity. Eur. J. Biochem. 199 (1991), 483–488.
7. Clarke, L., Carbon, J., The structure and function of yeast centromeres. Ann. Rev. Genet. 19 (1985), 29–56.
8. Cock, P.J.A., Fields, C.J., Goto, N., Heuer, M.L., Rice, P.M., The Sanger FASTQ file format for sequences with quality scores: and the solexa/illumina FASTQ variants. Nucleic Acids Res. 38 (2009), 1767–1771.
9. Cong, Y., Yarrow, D., Li, Y., Fukuhara, H., Debaryomyces hansenii and Wingea robertsiae. Yeast, 1994, 1327–1335.
10. Consortium, T.U., UniProt: a hub for protein information. Nucleic Acids Res. 43 (2015), D204–D212.
11. Cregg, J.M., Tolstorukov, I., Kusari, A., Sunga, J., Madden, K., Chappell, T., Chapter 13 Expression in the Yeast Pichia pastoris. Enzymology, R.R.B., M.P.D.B.T.-M, (eds.) Guide to Protein Purification, 2nd Edition, 2009, Academic Press, 169–189.
12. David, L., Huber, W., Granovskaia, M., Toedling, J., Palm, C.J., Bofkin, L., Jones, T., Davis, R.W., Steinmetz, L.M., A high-resolution map of transcription in the yeast genome. Proc. Natl. Acad. Sci. U. S. A. 103 (2006), 5320–5325.
13. De Schutter, K., Lin, Y.-C., Tiels, P., Van Hecke, A., Glinka, S., Weber-Lehmann, J., Rouzé, P., Van de Peer, Y., Callewaert, N., Genome sequence of the recombinant protein production host Pichia pastoris. Nat. Biotechnol. 27 (2009), 561–566.
14. Drinnenberg, I.A., Weinberg, D.E., Xie, K.T., Mower, J.P., Wolfe, K.H., Fink, G.R., Bartel, D.P., RNAi in budding yeast. Science 326:80 (2009), 544–550.
15. English, A.C., Richards, S., Han, Y., Wang, M., Vee, V., Qu, J., Qin, X., Muzny, D.M., Reid, J.G., Worley, K.C., Gibbs, R.A., Mind the gap: upgrading genomes with pacific biosciences RS long-read sequencing technology. PLoS One 7 (2012), 1–12.
16. Finn, R.D., Clements, J., Eddy, S.R., HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 39 (2011), 1–9.
17. Finn, R.D., Coggill, P., Eberhardt, R.Y., Eddy, S.R., Mistry, J., Mitchell, A.L., Potter, S.C., Punta, M., Qureshi, M., Sangrador-Vegas, A., Salazar, G.A., Tate, J., Bateman, A., The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res., 2015 (gkv1344).
18. Fitzgerald, I., Glick, B.S., Secretion of a foreign protein from budding yeasts is enhanced by cotranslational translocation and by suppression of vacuolar targeting. Microb. Cell Fact., 13, 2014, 125.
19. Geier, M., Fauland, P.C., Vogl, T., Glieder, A., Compact multi enzyme pathways in Pichia pastoris. Chem. Commun. 51 (2014), 1643–1646.
20. Geier, M., Brandner, C., Strohmeier, G., a Hall, M., Hartner, F.S., Glieder, A., Engineering Pichia pastoris for improved NADH regeneration: a novel chassis strain for whole-cell catalysis. Beilstein J. Org. Chem. 11 (2015), 1741–1748.
21. Geier, M., Fauland, P., Vogl, T., Glieder, A., Compact multi-enzyme pathways in P. pastoris. Chem. Commun. 51 (2015), 1643–1646.
22. Goto, N., Prins, P., Nakao, M., Bonnal, R., Aerts, J., Katayama, T., BioRuby: bioinformatics software for the ruby programming language. Bioinformatics 26 (2010), 2617–2619.
23. Gouldi, S.J., Mccollum, D., Spong, A.P., Heyman, J.A., Development of the yeast Pichia pastoris as a model organism for a genetic and molecular analysis of peroxisome assembly. Yeast 8 (1992), 613–628.
24. Grabherr, M.G., Haas, B.J., Yassour, M., Levin, J.Z., Thompson, D.A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., Chen, Z., Mauceli, E., Hacohen, N., Gnirke, A., Rhind, N., di Palma, F., Birren, B.W., Nusbaum, C., Lindblad-Toh, K., Friedman, N., Regev, A., Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotech. 29 (2011), 644–652.
25. Grabherr, Manfred G., Haas, Brian J., Yassour, Moran, Levin, Joshua Z., Thompson, Dawn A., Amit, Ido, Adiconis, Xian, Fan, Lin, Raychowdhury, Raktima, Zeng, Qiandong, Chen, Zehua, Mauceli, Evan, Hacohen, Nir, Gnirke, Andreas, Rhind, Nicholas, di Palma, Federica, Bruce, W.N., Friedman, A.R., Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nat. Biotechnol. 29 (2013), 644–652.
26. Gunge, N., Kitada, K., Replication and maintenance of the Kluyveromyces linear pGKL plasmids. Eur. J. Epidemiol. 4 (1988), 409–414.
27. Gunge, N., Tamaru, A., Ozawa, F., Sakaguchi, K., Isolation and characterization of linear deoxyribonucleic acid plasmids from Kluyveromyces lactis and the plasmid- associated killer character. J. Bacteriol. 145 (1981), 382–390.
28. Gunge, N., Linear DNA killer plasmids from the yeast Kluyveromyces. Yeast 2 (1986), 153–162.
29. Haft, D.H., Selengut, J.D., White, O., The TIGRFAMs database of protein families. Nucleic Acids Res. 31 (2003), 371–373.
30. Hanson, S.J., Byrne, K.P., Wolfe, K.H., Mating-type switching by chromosomal inversion in methylotrophic yeasts suggests an origin for the three-locus Saccharomyces cerevisiae system. Proc. Natl. Acad. Sci. U. S. A., 2014, 1–8.
31. Hayman, G.T., Bolen, P.L., Linear DNA plasmids of Pichia inositovora are associated with a novel killer toxin activity. Curr. Genet. 19 (1991), 389–393.
32. Jung, G.H., Leavitt, M.C., Ito, J., Yeast killer plasmid pGKL1 encodes a DNA polymerase belonging to the family B DNA polymerases. Nucleic Acids Res., 15, 1987, 9088.
33. Küberl, A., Schneider, J., Thallinger, G.G., Anderl, I., Wibberg, D., Hajek, T., Jaenicke, S., Brinkrolf, K., Goesmann, A., Szczepanowski, R., Pühler, A., Schwab, H., Glieder, A., Pichler, H., High-quality genome sequence of Pichia pastoris CBS7435. J. Biotechnol. 154 (2011), 312–320.
34. Kikuchi, Y., Hirai, K., Hishinuma, F., The yeast linear DNA killer plasmids, pGKL1 and pGKL2: possess terminally attached proteins. Nucleic Acids Res. 12 (1984), 5685–5692.
35. Kurtzman, C.P., Description of Komagataella phaffii sp. nov. and the transfer of Pichia pseudopastoris to the methylotrophic yeast genus Komagataella. Int. J. Syst. Evol. Microbiol. 55 (2005), 973–976.
36. Kurtzman, C.P., Biotechnological strains of Komagataella (Pichia) pastoris are Komagataella phaffii as determined from multigene sequence analysis. J. Ind. Microbiol. Biotechnol. 36 (2009), 1435–1438.
37. Lardenois, A., Liu, Y., Walther, T., Chalmel, F., Evrard, B., Granovskaia, M., Chu, A., Davis, R.W., Steinmetz, L.M., Primig, M., Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6. Proc. Natl. Acad. Sci. U. S. A. 108 (2011), 1058–1063.
38. Larsen, M., Gunge, N., Meinhardt, F., Kluyveromyces lactis killer plasmid pGKL2: evidence for a viral-like capping enzyme encoded by ORF3. Plasmid 40 (1998), 243–246.
39. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., The sequence alignment/map format and SAMtools. Bioinformatics 25 (2009), 2078–2079.
40. Liang, S., Wang, B., Pan, L., Ye, Y., He, M., Han, S., Zheng, S., Wang, X., Lin, Y., Comprehensive structural annotation of Pichia pastoris transcriptome and the response to various carbon sources using deep paired-end RNA sequencing. BMC Genomics, 13, 2012, 1.
41. Luke, B., Panza, A., Redon, S., Iglesias, N., Li, Z., Lingner, J., The Rat1p 5′–3′ exonuclease degrades telomeric repeat-containing RNA and promotes telomere elongation in Saccharomyces cerevisiae. Mol. Cell 32 (2008), 465–477.
42. Malik, H.S., Henikoff, S., Major evolutionary transitions in centromere complexity. Cell 138 (2009), 1067–1082.
43. McFarlane, R.J., Humphrey, T.C., A role for recombination in centromere function. Trends Genet. 26 (2010), 209–213.
44. Mccarthy, A., Third generation DNA sequencing: pacific biosciences’ single molecule real time technology. Chem. Biol. 17 (2010), 675–676.
45. Meluh, P.B., Yang, P., Glowczewski, L., Koshland, D., Smith, M.M., Cse4p is a component of the core centromere of Saccharomyces cerevisiae. Cell 94 (1998), 607–613.
46. Näätsaari, L., Mistlberger, B., Ruth, C., Hajek, T., Hartner, F.S., Glieder, A., Deletion of the Pichia pastoris KU70 homologue facilitates platform strain generation for gene expression and synthetic biology. PLoS One, 7, 2012, e39720.
47. Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M., Snyder, M., The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:80 (2008), 1344–1349.
48. Noskov, V.N., Chuang, R.-Y., Gibson, D.G., Leem, S.-H., Larionov, V., Kouprina, N., Isolation of circular yeast artificial chromosomes for synthetic biology and functional genomics studies. Nat. Protoc. 6 (2010), 89–96.
49. Pearson, C.G., Maddox, P.S., Salmon, E.D.D., Bloom, K., Budding yeast chromosome structure and dynamics during mitosis. J. Cell Biol. 152 (2001), 1255–1266.
50. Papanikou, E., Day, K.J., Austin, J., Glick, B.S., COPI selectively drives maturation of the early Golgi. Elife, 4, 2015, e13232.
51. Quail, M., Smith, M.E., Coupland, P., Otto, T.D., Harris, S.R., Connor, T.R., Bertoni, A., Swerdlow, H.P., Gu, Y., A tale of three next generation sequencing platforms: comparison of ion torrent, pacific biosciences and illumina MiSeq sequencers. BMC Genomics, 13, 2012, 1.
52. Renuse, S., Madugundu, A.K., Kumar, P., Nair, B.G., Gowda, H., Prasad, T.S.K., Pandey, A., Proteomic analysis and genome annotation of Pichia pastoris, a recombinant protein expression host. Proteomics, 2014.
53. Roberts, R.J., Carneiro, M.O., Schatz, M.C., The advantages of SMRT sequencing. Genome Biol., 14, 2013, 405.
54. Robson, R.L., Jones, R., Robson, R.M., Schwartz, A., Richardson, T.H., Azotobacter genomes: the genome of azotobacter chroococcum NCIMB 8003 (ATCC 4412). PLoS One, 10, 2015, e0127997.
55. Rossanese, O.W., Soderholm, J., Bevis, B.J., Sears, I.B., O'Connor, J., Williamson, E.K., Glick, B.S., Golgi structure correlates with transitional endoplasmic reticulum organization in Pichia pastoris and Saccharomyces cerevisiae. J. Cell Biol. 145 (1999), 69–81.
56. Roy, B., Sanyal, K., Diversity in requirement of genetic and epigenetic factors for centromere function in fungi Eukaryot. Cell 10 (2011), 1384–1395.
57. Rustchenko, E.P., Curran, T.M., Sherman, F., Variations in the number of ribosomal DNA units in morphological mutants and normal strains of Candida albicans and in normal strains of Saccharomyces cerevisiae. J. Bacteriol. 175 (1993), 7189–7199.
58. Schaffrath, R., Meacock, P.A., An SSB encoded by and operating on linear killer plasmids from Kluyveromyces lactis. Yeast 18 (2001), 1239–1247.
59. Schickel, J., Helmig, C., Meinhardt, F., Kluyveromyces lactis killer system: analysis of cytoplasmic promoters of the linear plasmids. Nucleic Acids Res. 24 (1996), 1879–1886.
60. Schutter, K., De Lin, Y. Tiels, P. Hecke, A. Van, Glinka S., Peer Y. Van De, Callewaert N., Weber-lehmann J., Rouze, P., 2009. Genome sequence of the recombinant protein production host Pichia pastoris.
61. Sonnhammer, E.L.L., B.E.E.S, Multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res. 26 (1998), 320–322.
62. Sor, F., Wèsolowski, M., Fukuhara, H., Inverted terminal repetitions of the two linear DNA associated with the killer character of the yeast Kluyveromyces lactis. Nucleic Acids Res. 11 (1983), 5037–5044.
63. Stam, J.C., Kwakman, J., Meijer, M., Stuitje, A.R., 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 (1986), 6871–6884.
64. Stanke, M., Diekhans, M., Baertsch, R., Haussler, D., Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24 (2008), 637–644.
65. Stark, M.J., Boyd, A., The killer toxin of Kluyveromyces lactis: characterization of the toxin subunits and identification of the genes which encode them. EMBO J. 5 (1986), 1995–2002.
66. Thompson, D.M., Parker, R., Cytoplasmic decay of intergenic transcripts in Saccharomyces cerevisiae. Mol. Cell. Biol. 27 (2007), 92–101.
67. Tokunaga, M., Wada, N., Hishinuma, F., Expression and identification of immunity determinants on linear DNA killer plasmids pGKL1 and pGKL2 in Kluyveromyces lactis. Nucleic Acids Res. 15 (1987), 1031–1046.
68. Trapnell, C., Pachter, L., Salzberg, S.L., TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25 (2009), 1105–1111.
69. Varoquaux, N., Liachko, I., Ay, F., Burton, J.N., Shendure, J., Dunham, M.J., Vert, J.P., Noble, W.S., Accurate identification of centromere locations in yeast genomes using Hi-C. Nucleic Acids Res. 43 (2015), 5331–5339.
70. Volpe, T., Schramke, V., Hamilton, G.L., White, S.A., Teng, G., Martienssen, R.A., Allshire, R.C., RNA interference is required for normal centromere function in fission yeast. Chromosom. Res. 11 (2003), 137–146.
71. Wickner, R.B., Leibowitz, M.J., Chromosomal genes essential for replication of a double-stranded RNA plasmid of Saccharomyces cerevisiae: the killer character of yeast. J. Mol. Biol. 105 (1976), 427–443.
72. Wickner, R.B., The killer double-stranded RNA plasmids of yeast. Plasmid 2 (1979), 303–322.
73. Wilhelm, B.T., Marguerat, S., Watt, S., Schubert, F., Wood, V., Goodhead, I., Penkett, C.J., Rogers, J., Bähler, J., Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453 (2008), 1239–1243.
74. Wilson, D.W., Meacock, P.A., Extranuclear gene expression in yeast: evidence for a plasmid-encoded RNA polymerase of unique structure. Nucleic Acids Res. 16 (1988), 8097–8112.
75. Worsham, P.L., Bolen, P.L., Killer toxin production in Pichia acaciae is associated with linear DNA plasmids. Curr. Genet. 18 (1990), 77–80.
76. Wu, J., Delneri, D., Keefe, R.T.O., Non-coding RNAs in Saccharomyces cerevisiae: What is the function?. Biochem. Soc. Trans. 40 (2012), 907–911.
77. Zerbino, D.R., Birney, E., Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18 (2008), 821–829.
78. van Dijk, E.L., Chen, C.L., d'Aubenton-Carafa, Y., Gourvennec, S., Kwapisz, M., Roche, V., Bertrand, C., Silvain, M., Legoix-Né, P., Loeillet, S., Nicolas, A., Thermes, C., Morillon, A., XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast. Nature 475 (2011), 114–117.