Identification of Linear DNA Plasmids of the YeastPichia pastoris

Banerjee, Hirendra Nath; Kopvak, C.; Curley, Dennis M.

doi:10.1006/plas.1998.1341

Cited by 7 publications

(6 citation statements)

References 7 publications

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“…However, none of the remaining ORFs could be identified as homologues of the K. lactis toxin gamma subunit or the anti-toxin protein. The lack of these proteins could potentially cause a loss of the killer phenotype and therefore provide support for the finding of Banerjee and colleagues (Banerjee et al, 1998; nath Banerjee and Verma, 2000). …”

Section: Resultssupporting

confidence: 79%

“…The K. lactis pGKL1/pGKL2 system has been extensively studied and resulted in the elucidation of plasmid encoded gene functions (Butler et al, 1991; Gunge and Kitada, 1988; Gunge, 1986; Kikuchi et al, 1984; Sor et al, 1983; Stam et al, 1986; Tokunaga et al, 1987). Banerjee and colleagues were the first to describe the presence of RNase resistant double stranded DNA molecules sensitive towards DNase I digestion in the methylotrophic yeast P. pastoris (Banerjee et al, 1998). …”

Section: Resultsmentioning

confidence: 99%

“…Neither ORF2, ORF3, ORF5 nor ORF6 could be identified as the killer toxin gamma subunit or anti-toxin protein. Although Banerjee and colleagues were able to isolate a DNase I digestible double stranded DNA fragment that was not susceptible to RNase degradation in P. pastoris (Banerjee et al, 1998) , evaluation of 14 different P. pastoris strains for their killer activity showed no killer phenotype (Banerjee and Verma, 2000). …”

Section: Resultsmentioning

confidence: 99%

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Refined Pichia pastoris reference genome sequence

Sturmberger

Chappell

Geier

et al. 2016

Journal of Biotechnology

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Strains of the species Komagataella phaffii are the most frequently used “Pichia pastoris” strains employed for recombinant protein production as well as studies on peroxisome biogenesis, autophagy and secretory pathway analyses. Genome sequencing of several different P. pastoris strains has provided the foundation for understanding these cellular functions in recent genomics, transcriptomics and proteomics experiments. This experimentation has identified mistakes, gaps and incorrectly annotated open reading frames in the previously published draft genome sequences. Here, a refined reference genome is presented, generated with genome and transcriptome sequencing data from multiple P. pastoris strains. Twelve major sequence gaps from 20 to 6000 base pairs were closed and 5111 out of 5256 putative open reading frames were manually curated and confirmed by RNA-seq and published LC-MS/MS data, including the addition of new open reading frames (ORFs) and a reduction in the number of spliced genes from 797 to 571. One chromosomal fragment of 76 kbp between two previous gaps on chromosome 1 and another 134 kbp fragment at the end of chromosome 4, as well as several shorter fragments needed re-orientation. In total more than 500 positions in the genome have been corrected. This reference genome is presented with new chromosomal numbering, positioning ribosomal repeats at the distal ends of the four chromosomes, and includes predicted chromosomal centromeres as well as the sequence of two linear cytoplasmic plasmids of 13.1 and 9.5 kbp found in some strains of P. pastoris.

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Section: Resultssupporting

confidence: 79%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Refined Pichia pastoris reference genome sequence

Sturmberger

Chappell

Geier

et al. 2016

Journal of Biotechnology

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“…Integrated cassettes appear to be quite stable in the P. pastoris genome which consists of four large chromosomes, ranging from 1.7 to 3.5 Mb depending on the strain, that can be resolved by pulsed-field gel electrophoresis and together represent 9.5 -9.8 Mb (7). Two linear plasmids of 11 and 8 kb have also been detected in one P. pastoris strain (8). Among recently characterised genes are five involved in the ER-to-Golgi transport (9), and we have isolated two genes encoding G-proteins that may also be active in protein transport (10).…”

mentioning

confidence: 95%

Characterization of a Gene Encoding a Pichia pastoris Protein Disulfide Isomerase

Warsame

Vad

Kristensen

et al. 2001

Biochemical and Biophysical Research Communications

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“…However, the number of discovered VLEs carrying strains is not very large. As a result of analysing over 1800 strains belonging to approximately 600 yeast species, molecules of this type have been found only in 40 strains [ 1 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 ]. Most of them belong to the Ascomycota phylum (34 strains) and the rest to the Basidiomycota phylum.…”

Section: Introductionmentioning

confidence: 99%

New Cytoplasmic Virus-Like Elements (VLEs) in the Yeast Debaryomyces hansenii

Połomska

Neuvéglise

Zyzak

et al. 2021

Toxins

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Yeasts can have additional genetic information in the form of cytoplasmic linear dsDNA molecules called virus-like elements (VLEs). Some of them encode killer toxins. The aim of this work was to investigate the prevalence of such elements in D. hansenii killer yeast deposited in culture collections as well as in strains freshly isolated from blue cheeses. Possible benefits to the host from harboring such VLEs were analyzed. VLEs occurred frequently among fresh D. hansenii isolates (15/60 strains), as opposed to strains obtained from culture collections (0/75 strains). Eight new different systems were identified: four composed of two elements and four of three elements. Full sequences of three new VLE systems obtained by NGS revealed extremely high conservation among the largest molecules in these systems except for one ORF, probably encoding a protein resembling immunity determinant to killer toxins of VLE origin in other yeast species. ORFs that could be potentially involved in killer activity due to similarity to genes encoding proteins with domains of chitin-binding/digesting and deoxyribonuclease NucA/NucB activity, could be distinguished in smaller molecules. However, the discovered VLEs were not involved in the biocontrol of Yarrowia lipolytica and Penicillium roqueforti present in blue cheeses.

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Identification of Linear DNA Plasmids of the YeastPichia pastoris

Cited by 7 publications

References 7 publications

Refined Pichia pastoris reference genome sequence

Refined Pichia pastoris reference genome sequence

Characterization of a Gene Encoding a Pichia pastoris Protein Disulfide Isomerase

New Cytoplasmic Virus-Like Elements (VLEs) in the Yeast Debaryomyces hansenii

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