Introduction

Introduction

This database hosts up-to-date annotation information of the genome of the methylotrophic yeast Pichia pastoris (Komagataella spp.), containing the new manually achieved annotation of K. phaffii strain CBS7435, and basic sequence and annotation information taken from the GenBank data of various Komagataella strains and species. Additionally the sequence information of S. cerevisiae strain S288c is also available for comparison and homolog display. A JBrowse based genome browser is integrated into the annotation data website, displaying ORF annotation information, RNA-Seq data and flanking regions of particular features.

Taxonomy and natural isolates of Pichia pastoris

TextTaxonomy

Pichia pastoris was first isolated in 1920 from the exudate of a chestnut tree in France, and described by A. Guilliermond as Zygosaccharomyces pastori [1]. This isolate is the species type strain, CBS704, (= NRRL Y-1603) [1]. Further strains were isolated from trees in California by H. Phaff, who named the species Pichia pastoris in 1956 [2]. For several decades, only few isolates existed, of which the strain NRRL Y-11430 (CBS7435), isolated from black oak tree in California, was developed as a platform for single cell protein by Philips Petroleum. This strain was then used as a basis for a development of the protein production system [3].
Based on ribosomal gene sequence data, P. pastoris was re-classified in 1995 into a new phylogenetically distinct genus, Komagataella [4], which was later split into several species based on 26S rRNA sequencing data [5]. Currently six members of the genus Komagataella are described (K. pastoris, K. phaffii, K. pseudopastoris, K. poluli, K. ulmi, and K. kurtzmanii) [6]. The established Pichia pastoris protein production platforms are based on strains of either K. phaffii or K. pastoris [7]. According to the rules of biological taxonomy, the former type strain of the species P. pastoris CBS704 (NRRL Y-1603) remains the type strain of the genus Komagataella and of the species K. pastoris. The Californian isolates mentioned above differ enough in their 26S rRNA sequence to justify their allocation to a new species, K. phaffii [5].
Whole genome sequencing of K. pastoris CBS704 and K. phaffii CBS7435 ([8 – 10]) confirmed the presence of four chromosomes and a chromosome rearrangement between K. pastoris and K. phaffii, as identified by pulsed field gel electrophoresis [11]. It should be noted however that the members of the genus Komagataella are phenotypically very similar and cannot easily be distinguished from one another by routine fermentation and assimilation tests employed in yeast taxonomy, so that classification is mainly based on sequence comparisons of a limited number of genes. To avoid confusion and to include all strains employed in biotechnology we use the established name Pichia pastoris here as a synonym for all Komagataella species, giving reference to the different species for different strains, as listed in the table below.
  1. Guilliermond A. 1920. Zygosaccharomyces pastori, nouvelle espèce de levures copulation hétérogamique. Bulletin de la Société Mycologique de France 36:203-11.
  2. Phaff H, Miller M, Shifrine M. 1956. The taxonomy of yeasts isolated from Drosophila in the Yosemite region of California. Antonie Van Leeuwenhoek 22:145-61.
  3. Cregg JM, Barringer KJ, Hessler AY, Madden KR. 1985. Pichia pastoris as a host system for transformations. Mol Cell Biol 5:3376-85.
  4. Yamada Y, Matsuda M, Maeda K, Mikata K. 1995. The phylogenetic relationships of methanol-assimilating yeasts based on the partial sequences of 18S and 26S ribosomal RNAs: the proposal of Komagataella gen. nov. (Saccharomycetaceae). Biosci Biotechnol Biochem 59:439-44.
  5. Kurtzman C. 2005. Description of Komagataella phaffii sp. nov. and the transfer of Pichia pseudopastoris to the methylotrophic yeast genus Komagataella. Int J Syst Evol Microbiol 55:973-6.
  6. Naumov GI, Naumova ES, Tyurin OV, Kozlov DG. 2013. Komagataella kurtzmanii sp. nov., a new sibling species of Komagataella (Pichia) pastoris based on multigene sequence analysis. Antonie Van Leeuwenhoek 104:339-47.
  7. Kurtzman CP. 2009. Biotechnological strains of Komagataella (Pichia) pastoris are Komagataella phaffii as determined from multigene sequence analysis. J Ind Microbiol Biotechnol 36:1435-8.
  8. De Schutter K, Lin YC, Tiels P, Van Hecke A, Glinka S and others. 2009. Genome sequence of the recombinant protein production host Pichia pastoris. Nat Biotechnol 27:561-6.
  9. Mattanovich D, Graf A, Stadlmann J, Dragosits M, Redl A and others. 2009. Genome, secretome and glucose transport highlight unique features of the protein production host Pichia pastoris. Microb Cell Fact 8:29.
  10. Kuberl A, Schneider J, Thallinger GG, Anderl I, Wibberg D and others. 2011. High-quality genome sequence of Pichia pastoris CBS7435. J Biotechnol 154:312-20.
  11. Ohi H, Okazaki N, Uno S, Miura M, Hiramatsu R. 1998. Chromosomal DNA patterns and gene stability of Pichia pastoris. Yeast 14:895-903.

Overview Taxonomy

Species name* CBS DSMZ ATCC NRRL Location deposited by Isolation Genome sequence
Komagataella ulmi CBS 12361 YB-407 USA, Illinois, Peoria C. Kurtzman, July 2011 exudate, elm tree( Ulmus americana) Type strain of Komagataella ulmi
Komagataella populi CBS 12362 YB-455 USA, Illinois, Peoria C. Kurtzman, July 2011 exudate, cottonwood tree( Populus deltoides) Type strain of Komagataella populi
Komagataella kurtzmanii CBS 12817 Y-63667 USA, Arizona, Catalina mountains I. Naumov, April 2013 fir flux Type strain of Komagataella kurtzmanii
Komagataella phaffii Kurtzman CBS 2612 Y-7556 USA, California H.J. Phaff, K 239 Quercus kelloggii (black oak) Type strain of Komagataella phaffii
Komagataella pastoris (Guilliermond) Y. Yamada et al. CBS 704 70382 28485 Y-1603 France, near Lyon A. Guilliermond exudate from chestnut tree Mattanovich et al. 2009 Type strain of genus Komagataella; Type strain of Komagatella pastoris
Komagataella phaffii Kurtzman CBS 7435 76273 Y-11430 Phillips Petroleum Co. 21-1 Kueberl et al. 2011
Komagataella pseudopastoris (Dlauchy, Tornai-Lehoczki, Fülöp & Péter) Kurtzman CBS 9187 Y-27603 Hungary, Dorog Gábor Péter rotten wood material in a cavity of a Salix alba Type strain of Komagataella pseudopastoris
Komagataella phaffii Kurtzman Y-12729 Etienne, IMP, Mexico
Komagataella phaffii Kurtzman (2005) Y-17741 Tucson, Arizona, USA Starmer, Syracuse University, NY FLX, sap flux, Emory oak (Quercus emoryi)
Komagataella phaffii Kurtzman (2005) YB-4289 YB-4290 California, USA Phaff, University of CA, Davis, CA HTR, Black oak, (Quercus kelloggii)
Komagataella pastoris (Guilliermond) Y. Yamada et al. 70877 Germany S. Windisch, Pi-0704 <- W. Henninger beech slime flux
X-33 Komagataella phaffii Invitrogen; revertant of GS115
GS115 [AOX1 his4- ] Komagataella phaffii 20864 Invitrogen; nitrosoguanidine mutant of NRRL Y-11430 De Schutter et al. 2009
KM71 [his4 aox1]Komagataella phaffii 201178 Invitrogen
SMD1168 [pep4 his4] Invitrogen
Komagataella spp. (species unnown) 76274 Y-11431 Phillips Petroleum Co. 21-2
*Please note that in some databases and strain collections species names have not been updated yet, and the species name is still Pichia pastoris. In some cases, K. phaffii has erroneously been named K. pastoris.

Sources

Genome Database of the Pichia pastoris
Hosted by the University of Natural Resources and Applied Life Sciences, Vienna - working group Mattanovich - in collaboration with the Austrian Center of Industrial Biotechnology (acib)

The DSMZ 70382 strain was sequenced by the University of Natural Resources and Applied Life Sciences, Vienna, Department of Applied Microbiology.
Reference: Mattanovich et al., Genome, secretome and glucose transport highlight unique features of the protein production host Pichia pastoris, Microbial Cell Factories 2009, 8:29

The GS115 strain was sequenced by the VIB Ghent, Department of Biomedical Molecular Biology.
Reference: De Schutter et al.,Genome sequence of the recombinant protein production host Pichia pastoris, Nature Biotechnology 27, 561 - 566 (2009)

The CBS7435 strain was sequenced by the Institute for Genomics and Bioinformatics, Graz University of Technology (Austria).
Reference: High-quality genome sequence of Pichia pastoris CBS7435, Journal of Biotechnology 2011, 154(4):312-20

The Saccharomyces cerevisiae S288c sequence was taken from the SGD in February 2016.