High-quality genome sequence of Pichia pastoris CBS7435

Küberl, Andreas; Schneider, Jessica; Thallinger, Gerhard G.; Anderl, Ingund; Wibberg, Daniel; Hajek, Tanja; Jaenicke, Sebastian; Brinkrolf, Karina; Goesmann, Alexander; Szczepanowski, Rafael; Pühler, Alfred; Schwab, Helmut; Glieder, Anton; Pichler, Harald

doi:10.1016/j.jbiotec.2011.04.014

Cited by 152 publications

(153 citation statements)

References 46 publications

Supporting

Mentioning

148

Contrasting

Unclassified

Order By: Relevance

“…The structure of P. pastoris chromosome 4 as represented in the genome sequences of CBS7435 (38) and GS115 (21) is alpha+ in the nomenclature used here. However, our laboratory stocks of CBS7435 and GS115 are both alpha− by PCR, indicating inversion or sequence misassembly across the inner IRs.…”

Section: Methodsmentioning

confidence: 99%

“…Species in the CTG clade have only one MAT-like locus and do not switch (36,37). More recently, genomes have been sequenced from a third clade within the Saccharomycotina which includes the methanol-assimilating species Hansenula polymorpha (20) and Pichia pastoris (21,38) and relatives such as Dekkera bruxellensis (22,23) and Kuraishia capsulata (24). For convenience we refer to this clade as the "methylotrophs."…”

Section: Significancementioning

confidence: 99%

“…The taxonomy of P. pastoris strains also has been revised recently, but all the strains we discuss here are from a single species that is properly called "Komagataella phaffii" (46). The genome sequence of strain CBS7435 (38) contains two MAT-like loci. One locus is close to the telomere of chromosome 4 and contains MATa1 and a2, whereas the other locus is 138 kb away and contains MATalpha1 and alpha2.…”

Section: P Pastoris Also Has Two Mat-like Loci At the Ends Of An Invmentioning

confidence: 99%

See 2 more Smart Citations

Mating-type switching by chromosomal inversion in methylotrophic yeasts suggests an origin for the three-locus Saccharomyces cerevisiae system

Hanson

Byrne

Wolfe

2014

Proc. Natl. Acad. Sci. U.S.A.

149

View full text Add to dashboard Cite

Saccharomyces cerevisiae has a complex system for switching the mating type of haploid cells, requiring the genome to have three mating-type (MAT)-like loci and a mechanism for silencing two of them. How this system originated is unknown, because the threelocus system is present throughout the family Saccharomycetaceae, whereas species in the sister Candida clade have only one locus and do not switch. Here we show that yeasts in a third clade, the methylotrophs, have a simpler two-locus switching system based on reversible inversion of a section of chromosome with MATa genes at one end and MATalpha genes at the other end. In Hansenula polymorpha the 19-kb invertible region lies beside a centromere so that, depending on the orientation, either MATa or MATalpha is silenced by centromeric chromatin. In Pichia pastoris, the orientation of a 138-kb invertible region puts either MATa or MATalpha beside a telomere and represses transcription of MATa2 or MATalpha2. Both species are homothallic, and inversion of their MAT regions can be induced by crossing two strains of the same mating type. The three-locus system of S. cerevisiae, which uses a nonconservative mechanism to replace DNA at MAT, likely evolved from a conservative two-locus system that swapped genes between expression and nonexpression sites by inversion. The increasing complexity of the switching apparatus, with three loci, donor bias, and cell lineage tracking, can be explained by continuous selection to increase sporulation ability in young colonies. Our results provide an evolutionary context for the diversity of switching and silencing mechanisms.Hansenula polymorpha | Pichia pastoris | yeast genetics | comparative genomics M ating-type switching in yeasts is a highly regulated process that converts a haploid cell of one mating type into a haploid of the opposite type (1-5). Switching involves the complete deactivation of one set of regulatory genes and activation of an alternative set, but, unlike most regulatory changes, the switch is achieved by physically replacing the DNA at an expression site that is shared by both types of cell. In Saccharomyces cerevisiae the switching system uses a menagerie of molecular components (3) including three mating-type (MAT)-like loci (the expressed MAT locus and the silent loci HML and HMR); an endonuclease (HO) that creates a double-strand break at the MAT locus, which then is repaired using HMLalpha or HMRa as a donor; a mechanism (Sir1 and Sir2/3/4 proteins) for repressing transcription and HO cleavage at the silent loci; two triplicated sequences (the Z and X regions) that guide repair of the dsDNA break; a donorbias mechanism (the recombination enhancer, RE) to ensure that switching happens in the correct direction; and a cell lineagetracking mechanism (Ash1 mRNA localization) to ensure that switching occurs only in particular cells. Most of these components have no function other than facilitating switching.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Significancementioning

confidence: 99%

Section: P Pastoris Also Has Two Mat-like Loci At the Ends Of An Invmentioning

confidence: 99%

See 1 more Smart Citation

Mating-type switching by chromosomal inversion in methylotrophic yeasts suggests an origin for the three-locus Saccharomyces cerevisiae system

Hanson

Byrne

Wolfe

2014

Proc. Natl. Acad. Sci. U.S.A.

149

View full text Add to dashboard Cite

show abstract

“…Zonadhesin is known as a predicted protein with characteristic repeats of Thr, Ser, Val, and Ala residues at the C-terminal domain in analogy with adhesion molecules of Candida albicans and Saccharomyces cerevisiae (33,35). Amino acid sequences with homology to zonadhesin occur in peptidases and few other proteins of P. pastoris.…”

Section: Discussionmentioning

confidence: 99%

Crystal structure of linoleate 13R-manganese lipoxygenase in complex with an adhesion protein

Chen

Wennman

Karkehabadi

et al. 2016

Journal of Lipid Research

View full text Add to dashboard Cite

“…Pichia pastoris CBS7435 is the parent strain of all P. pastoris recombinant protein production hosts. Its genome sequence was annotated automatically to yield 5,007 protein-coding genes, 124 tRNAs and 29 rRNAs and the complete DNA sequence of the first mitochondrial genome of a methylotrophic yeast (Kuberl et al 2011).…”

Section: Methodsmentioning

confidence: 99%

Reconstruction and visualization of carbohydrate, N-glycosylation pathways in Pichia pastoris CBS7435 using computational and system biology approaches

2012

View full text Add to dashboard Cite

Pichia pastoris is an efficient expression system for production of recombinant proteins. To understand its physiology for building novel applications it is important to understand and reconstruct its metabolic network. The metabolic reconstruction approach connects genotype with phenotype. Here, we have attempted to reconstruct carbohydrate metabolism pathways responsible for high biomass density and N-glycosylation pathways involved in the post translational modification of proteins of P. pastoris CBS7435. Both these metabolic pathways play a crucial role in heterologous protein production. We report novel, missing and unannotated enzymes involved in the target metabolic pathways. A strong possibility of cellulose and xylose metabolic processes in P. pastoris CBS7435 suggests its use in the area of biofuels. The reconstructed metabolic networks can be used for increased yields and improved product quality, for designing appropriate growth medium, for production of recombinant therapeutics and for making biofuels.

show abstract

High-quality genome sequence of Pichia pastoris CBS7435

Cited by 152 publications

References 46 publications

Mating-type switching by chromosomal inversion in methylotrophic yeasts suggests an origin for the three-locus Saccharomyces cerevisiae system

Mating-type switching by chromosomal inversion in methylotrophic yeasts suggests an origin for the three-locus Saccharomyces cerevisiae system

Crystal structure of linoleate 13R-manganese lipoxygenase in complex with an adhesion protein

Reconstruction and visualization of carbohydrate, N-glycosylation pathways in Pichia pastoris CBS7435 using computational and system biology approaches

Contact Info

Product

Resources

About