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Prielhofer R, Cartwright SP, Graf AB, Valli M, Bill RM, Mattanovich D, Gasser B. Pichia pastoris regulates its gene-specific response to different carbon sources at the transcriptional, rather than the translational, level. BMC Genomics 2015; 16:167. [PMID: 25887254 PMCID: PMC4408588 DOI: 10.1186/s12864-015-1393-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 02/24/2015] [Indexed: 11/20/2022] Open
Abstract
Background The methylotrophic, Crabtree-negative yeast Pichia pastoris is widely used as a heterologous protein production host. Strong inducible promoters derived from methanol utilization genes or constitutive glycolytic promoters are typically used to drive gene expression. Notably, genes involved in methanol utilization are not only repressed by the presence of glucose, but also by glycerol. This unusual regulatory behavior prompted us to study the regulation of carbon substrate utilization in different bioprocess conditions on a genome wide scale. Results We performed microarray analysis on the total mRNA population as well as mRNA that had been fractionated according to ribosome occupancy. Translationally quiescent mRNAs were defined as being associated with single ribosomes (monosomes) and highly-translated mRNAs with multiple ribosomes (polysomes). We found that despite their lower growth rates, global translation was most active in methanol-grown P. pastoris cells, followed by excess glycerol- or glucose-grown cells. Transcript-specific translational responses were found to be minimal, while extensive transcriptional regulation was observed for cells grown on different carbon sources. Due to their respiratory metabolism, cells grown in excess glucose or glycerol had very similar expression profiles. Genes subject to glucose repression were mainly involved in the metabolism of alternative carbon sources including the control of glycerol uptake and metabolism. Peroxisomal and methanol utilization genes were confirmed to be subject to carbon substrate repression in excess glucose or glycerol, but were found to be strongly de-repressed in limiting glucose-conditions (as are often applied in fed batch cultivations) in addition to induction by methanol. Conclusions P. pastoris cells grown in excess glycerol or glucose have similar transcript profiles in contrast to S. cerevisiae cells, in which the transcriptional response to these carbon sources is very different. The main response to different growth conditions in P. pastoris is transcriptional; translational regulation was not transcript-specific. The high proportion of mRNAs associated with polysomes in methanol-grown cells is a major finding of this study; it reveals that high productivity during methanol induction is directly linked to the growth condition and not only to promoter strength. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1393-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roland Prielhofer
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria. .,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190, Vienna, Austria.
| | - Stephanie P Cartwright
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Alexandra B Graf
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190, Vienna, Austria. .,School of Bioengineering, University of Applied Sciences FH Campus Wien, Vienna, Austria.
| | - Minoska Valli
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria. .,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190, Vienna, Austria.
| | - Roslyn M Bill
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Diethard Mattanovich
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria. .,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190, Vienna, Austria.
| | - Brigitte Gasser
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria. .,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190, Vienna, Austria.
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Ravin NV, Eldarov MA, Kadnikov VV, Beletsky AV, Schneider J, Mardanova ES, Smekalova EM, Zvereva MI, Dontsova OA, Mardanov AV, Skryabin KG. Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1. BMC Genomics 2013; 14:837. [PMID: 24279325 PMCID: PMC3866509 DOI: 10.1186/1471-2164-14-837] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Accepted: 11/15/2013] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Hansenula polymorpha DL1 is a methylotrophic yeast, widely used in fundamental studies of methanol metabolism, peroxisome biogenesis and function, and also as a microbial cell factory for production of recombinant proteins and metabolic engineering towards the goal of high temperature ethanol production. RESULTS We have sequenced the 9 Mbp H. polymorpha DL1 genome and performed whole-genome analysis for the H. polymorpha transcriptome obtained from both methanol- and glucose-grown cells. RNA-seq analysis revealed the complex and dynamic character of the H. polymorpha transcriptome under the two studied conditions, identified abundant and highly unregulated expression of 40% of the genome in methanol grown cells, and revealed alternative splicing events. We have identified subtelomerically biased protein families in H. polymorpha, clusters of LTR elements at G + C-poor chromosomal loci in the middle of each of the seven H. polymorpha chromosomes, and established the evolutionary position of H. polymorpha DL1 within a separate yeast clade together with the methylotrophic yeast Pichia pastoris and the non-methylotrophic yeast Dekkera bruxellensis. Intergenome comparisons uncovered extensive gene order reshuffling between the three yeast genomes. Phylogenetic analyses enabled us to reveal patterns of evolution of methylotrophy in yeasts and filamentous fungi. CONCLUSIONS Our results open new opportunities for in-depth understanding of many aspects of H. polymorpha life cycle, physiology and metabolism as well as genome evolution in methylotrophic yeasts and may lead to novel improvements toward the application of H. polymorpha DL-1 as a microbial cell factory.
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Affiliation(s)
- Nikolai V Ravin
- Centre “Bioengineering” of RAS, Prosp. 60-let Oktyabrya, bld. 7-1, Moscow 117312, Russia
| | - Michael A Eldarov
- Centre “Bioengineering” of RAS, Prosp. 60-let Oktyabrya, bld. 7-1, Moscow 117312, Russia
| | - Vitaly V Kadnikov
- Centre “Bioengineering” of RAS, Prosp. 60-let Oktyabrya, bld. 7-1, Moscow 117312, Russia
| | - Alexey V Beletsky
- Centre “Bioengineering” of RAS, Prosp. 60-let Oktyabrya, bld. 7-1, Moscow 117312, Russia
| | - Jessica Schneider
- Institute for Bioinformatics, Center for Biotechnology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Eugenia S Mardanova
- Centre “Bioengineering” of RAS, Prosp. 60-let Oktyabrya, bld. 7-1, Moscow 117312, Russia
| | - Elena M Smekalova
- Faculty of Chemistry, Lomonosov Moscow State University, 119999 Moscow, Russia and Belozersky Institute, Moscow State University, Leninskie Gory 1, Bldg. 40, 119991 Moscow, Russia
| | - Maria I Zvereva
- Faculty of Chemistry, Lomonosov Moscow State University, 119999 Moscow, Russia and Belozersky Institute, Moscow State University, Leninskie Gory 1, Bldg. 40, 119991 Moscow, Russia
| | - Olga A Dontsova
- Faculty of Chemistry, Lomonosov Moscow State University, 119999 Moscow, Russia and Belozersky Institute, Moscow State University, Leninskie Gory 1, Bldg. 40, 119991 Moscow, Russia
| | - Andrey V Mardanov
- Centre “Bioengineering” of RAS, Prosp. 60-let Oktyabrya, bld. 7-1, Moscow 117312, Russia
| | - Konstantin G Skryabin
- Centre “Bioengineering” of RAS, Prosp. 60-let Oktyabrya, bld. 7-1, Moscow 117312, Russia
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Gvozdev AR, Tukhvatullin IA, Gvozdev RI. Quinone-dependent alcohol dehydrogenases and FAD-dependent alcohol oxidases. BIOCHEMISTRY (MOSCOW) 2013; 77:843-56. [PMID: 22860906 DOI: 10.1134/s0006297912080056] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This review considers quinone-dependent alcohol dehydrogenases and FAD-dependent alcohol oxidases, enzymes that are present in numerous methylotrophic eu- and prokaryotes and significantly differ in their primary and quaternary structure. The cofactors of the enzymes are bound to the protein polypeptide chain through ionic and hydrophobic interactions. Microorganisms containing these enzymes are described. Methods for purification of the enzymes, their physicochemical properties, and spatial structures are considered. The supposed mechanism of action and practical application of these enzymes as well as their producers are discussed.
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Affiliation(s)
- A R Gvozdev
- Biosensor AN Ltd., pr. Akademika Semenova 1, 142432 Chernogolovka, Moscow Region, Russia.
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4
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Characterization of alcohol dehydrogenase 3 of the thermotolerant methylotrophic yeast Hansenula polymorpha. Appl Microbiol Biotechnol 2012; 96:697-709. [DOI: 10.1007/s00253-011-3866-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 12/20/2011] [Accepted: 12/22/2011] [Indexed: 10/14/2022]
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5
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Yeast methylotrophy: metabolism, gene regulation and peroxisome homeostasis. Int J Microbiol 2011; 2011:101298. [PMID: 21754936 PMCID: PMC3132611 DOI: 10.1155/2011/101298] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 05/09/2011] [Indexed: 11/18/2022] Open
Abstract
Eukaryotic methylotrophs, which are able to obtain all the carbon and energy needed for growth from methanol, are restricted to a limited number of yeast species. When these yeasts are grown on methanol as the sole carbon and energy source, the enzymes involved in methanol metabolism are strongly induced, and the membrane-bound organelles, peroxisomes, which contain key enzymes of methanol metabolism, proliferate massively. These features have made methylotrophic yeasts attractive hosts for the production of heterologous proteins and useful model organisms for the study of peroxisome biogenesis and degradation. In this paper, we describe recent insights into the molecular basis of yeast methylotrophy.
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van Zutphen T, Baerends RJS, Susanna KA, de Jong A, Kuipers OP, Veenhuis M, van der Klei IJ. Adaptation of Hansenula polymorpha to methanol: a transcriptome analysis. BMC Genomics 2010; 11:1. [PMID: 20044946 PMCID: PMC2827406 DOI: 10.1186/1471-2164-11-1] [Citation(s) in RCA: 148] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 01/04/2010] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Methylotrophic yeast species (e.g. Hansenula polymorpha, Pichia pastoris) can grow on methanol as sole source of carbon and energy. These organisms are important cell factories for the production of recombinant proteins, but are also used in fundamental research as model organisms to study peroxisome biology. During exponential growth on glucose, cells of H. polymorpha typically contain a single, small peroxisome that is redundant for growth while on methanol multiple, enlarged peroxisomes are present. These organelles are crucial to support growth on methanol, as they contain key enzymes of methanol metabolism.In this study, changes in the transcriptional profiles during adaptation of H. polymorpha cells from glucose- to methanol-containing media were investigated using DNA-microarray analyses. RESULTS Two hours after the shift of cells from glucose to methanol nearly 20% (1184 genes) of the approximately 6000 annotated H. polymorpha genes were significantly upregulated with at least a two-fold differential expression. Highest upregulation (> 300-fold) was observed for the genes encoding the transcription factor Mpp1 and formate dehydrogenase, an enzyme of the methanol dissimilation pathway. Upregulated genes also included genes encoding other enzymes of methanol metabolism as well as of peroxisomal beta-oxidation.A moderate increase in transcriptional levels (up to 4-fold) was observed for several PEX genes, which are involved in peroxisome biogenesis. Only PEX11 and PEX32 were higher upregulated. In addition, an increase was observed in expression of the several ATG genes, which encode proteins involved in autophagy and autophagy processes. The strongest upregulation was observed for ATG8 and ATG11.Approximately 20% (1246 genes) of the genes were downregulated. These included glycolytic genes as well as genes involved in transcription and translation. CONCLUSION Transcriptional profiling of H. polymorpha cells shifted from glucose to methanol showed the expected downregulation of glycolytic genes together with upregulation of the methanol utilisation pathway. This serves as a confirmation and validation of the array data obtained. Consistent with this, also various PEX genes were upregulated. The strong upregulation of ATG genes is possibly due to induction of autophagy processes related to remodeling of the cell architecture required to support growth on methanol. These processes may also be responsible for the enhanced peroxisomal beta-oxidation, as autophagy leads to recycling of membrane lipids. The prominent downregulation of transcription and translation may be explained by the reduced growth rate on methanol (td glucose 1 h vs td methanol 4.5 h).
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Affiliation(s)
- Tim van Zutphen
- Molecular Cell Biology, University of Groningen, Haren, the Netherlands
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Qian W, Song H, Liu Y, Zhang C, Niu Z, Wang H, Qiu B. Improved gene disruption method and Cre-loxP mutant system for multiple gene disruptions in Hansenula polymorpha. J Microbiol Methods 2009; 79:253-9. [PMID: 19765620 DOI: 10.1016/j.mimet.2009.09.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 08/17/2009] [Accepted: 09/02/2009] [Indexed: 11/27/2022]
Abstract
In H. polymorpha, there is still a lack of a highly efficient gene disruption method. To help address this issue, we presented a simple and efficient method for both single and multiple gene disruptions in H. polymorpha. The knockout system combined a variation of sticky-end polymerase chain reaction method (SEP), split marker deletion method, co-transformation of single-stranded DNA and mutant Cre-loxP system. Using a slightly modified LiAc/SS-DNA/PEG procedure, the co-transformation double-stranded split marker constructs together with single-stranded split marker constructs resulted in at least 70% homologous recombination events when the homologous genomic DNA fragment had a size of approximately 500bp. Our evidence suggested that single-stranded DNA may be responsible for the increased gene disruption efficiency. We demonstrated the effectiveness of the method for gene disruption by constructing both single and double gene disruptions at the ALG3 and URA5 loci in the same genetic background. The method described here presents an improved strategy for gene disruption and a potential application for investigation of biological processes in other yeast strains.
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Affiliation(s)
- Weidong Qian
- Center for Agricultural Biotechnology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Beijing 100101, People's Republic of China
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8
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Reconstructing generalized logical networks of transcriptional regulation in mouse brain from temporal gene expression data. EURASIP JOURNAL ON BIOINFORMATICS & SYSTEMS BIOLOGY 2009:545176. [PMID: 19300527 PMCID: PMC3171431 DOI: 10.1155/2009/545176] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2008] [Revised: 09/08/2008] [Accepted: 12/12/2008] [Indexed: 02/02/2023]
Abstract
Gene expression time course data can be used not only to detect differentially expressed genes but also to find temporal associations among genes. The problem of reconstructing generalized logical networks to account for temporal dependencies among genes and environmental stimuli from transcriptomic data is addressed. A network reconstruction algorithm was developed that uses statistical significance as a criterion for network selection to avoid false-positive interactions arising from pure chance. The multinomial hypothesis testing-based network reconstruction allows for explicit specification of the false-positive rate, unique from all extant network inference algorithms. The method is superior to dynamic Bayesian network modeling in a simulation study. Temporal gene expression data from the brains of alcohol-treated mice in an analysis of the molecular response to alcohol are used for modeling. Genes from major neuronal pathways are identified as putative components of the alcohol response mechanism. Nine of these genes have associations with alcohol reported in literature. Several other potentially relevant genes, compatible with independent results from literature mining, may play a role in the response to alcohol. Additional, previously unknown gene interactions were discovered that, subject to biological verification, may offer new clues in the search for the elusive molecular mechanisms of alcoholism.
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9
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Krikken AM, Veenhuis M, van der Klei IJ. Hansenula polymorpha pex11 cells are affected in peroxisome retention. FEBS J 2009; 276:1429-39. [DOI: 10.1111/j.1742-4658.2009.06883.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Bener Aksam E, Jungwirth H, Kohlwein SD, Ring J, Madeo F, Veenhuis M, van der Klei IJ. Absence of the peroxiredoxin Pmp20 causes peroxisomal protein leakage and necrotic cell death. Free Radic Biol Med 2008; 45:1115-24. [PMID: 18694816 DOI: 10.1016/j.freeradbiomed.2008.07.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Revised: 07/01/2008] [Accepted: 07/08/2008] [Indexed: 11/30/2022]
Abstract
We analyzed the role of the peroxisomal peroxiredoxin Pmp20 of the yeast Hansenula polymorpha. Cells of a PMP20 disruption strain (pmp20) grew normally on substrates that are not metabolized by peroxisomal enzymes, but showed a severe growth defect on methanol, the metabolism of which involves a hydrogen peroxide producing peroxisomal oxidase. This growth defect was paralleled by leakage of peroxisomal matrix proteins into the cytosol. Methanol-induced pmp20 cells accumulated enhanced levels of reactive oxygen species and lipid peroxidation products. Moreover, the fatty acid composition of methanol-induced pmp20 cells differed relative to WT controls, suggesting an effect on fatty acid homeostasis. Plating assays and FACS-based analysis of cell death markers revealed that pmp20 cells show loss of clonogenic efficiency and membrane integrity, when cultured on methanol. We conclude that the absence of the peroxisomal peroxiredoxin leads to loss of peroxisome membrane integrity and necrotic cell death.
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Affiliation(s)
- Eda Bener Aksam
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
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Nagotu S, Krikken AM, Otzen M, Kiel JAKW, Veenhuis M, van der Klei IJ. Peroxisome Fission inHansenula polymorphaRequires Mdv1 and Fis1, Two Proteins Also Involved in Mitochondrial Fission. Traffic 2008; 9:1471-84. [DOI: 10.1111/j.1600-0854.2008.00772.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Trm1p, a Zn(II)2Cys6-type transcription factor, is a master regulator of methanol-specific gene activation in the methylotrophic yeast Candida boidinii. EUKARYOTIC CELL 2008; 7:527-36. [PMID: 18203863 DOI: 10.1128/ec.00403-07] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The methylotrophic yeasts are commonly used as hosts for heterologous gene expression. In this study, we describe a novel gene, TRM1, in Candida boidinii, responsible for the transcriptional activation of several methanol-inducible promoters. The encoded protein, Trm1p, is a Zn(II)2Cys6-type zinc cluster protein. Deletion of TRM1 completely inhibits growth on methanol but causes no growth defect on glucose or other nonfermentative carbon sources, glycerol, ethanol, or oleate. Trm1p is responsible for transcriptional activation of five methanol-inducible promoters tested, but not for peroxisome assembly or peroxisomal protein transport. Expression of the TRM1 gene was constitutive, and Trm1p localizes to the nuclei regardless of the carbon source. Two cis-acting methanol response elements (MREs), MRE1 and MRE2 are present in the promoter of the dihydroxyacetone synthase gene. Trm1p is shown to be required for MRE1-dependent methanol-inducible gene expression. Chromatin immunoprecipitation assays reveal that Trm1p binds to five methanol-inducible promoters upon methanol induction but does not bind in glucose-grown cells. Thus, the TRM1 gene encodes a master transcriptional regulator responsible for methanol-specific gene activation in the methylotrophic yeasts.
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Nagotu S, Saraya R, Otzen M, Veenhuis M, van der Klei IJ. Peroxisome proliferation in Hansenula polymorpha requires Dnm1p which mediates fission but not de novo formation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2007; 1783:760-9. [PMID: 18060881 DOI: 10.1016/j.bbamcr.2007.10.018] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Revised: 10/26/2007] [Accepted: 10/29/2007] [Indexed: 11/28/2022]
Abstract
We show that the dynamin-like proteins Dnm1p and Vps1p are not required for re-introduction of peroxisomes in Hansenula polymorpha pex3 cells upon complementation with PEX3-GFP. Instead, Dnm1p, but not Vps1p, plays a crucial role in organelle proliferation via fission. In H. polymorpha DNM1 deletion cells (dnm1) a single peroxisome is present that forms long extensions, which protrude into developing buds and divide during cytokinesis. Budding pex11.dnm1 double deletion cells lack these peroxisomal extensions, suggesting that the peroxisomal membrane protein Pex11p is required for their formation. Life cell imaging revealed that fluorescent Dnm1p-GFP spots fluctuate between peroxisomes and mitochondria. On the other hand Pex11p is present over the entire organelle surface, but concentrates during fission at the basis of the organelle extension in dnm1 cells. Our data indicate that peroxisome fission is the major pathway for peroxisome multiplication in H. polymorpha.
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Affiliation(s)
- Shirisha Nagotu
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Haren, The Netherlands
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Sasano Y, Yurimoto H, Sakai Y. Gene-tagging mutagenesis in the methylotrophic yeast Candida boidinii. J Biosci Bioeng 2007; 104:86-9. [PMID: 17697989 DOI: 10.1263/jbb.104.86] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2007] [Accepted: 04/13/2007] [Indexed: 11/17/2022]
Abstract
A gene-tagging mutagenesis method by random integration of linear DNA fragments was developed and used in the methylotrophic yeast Candida boidinii to isolate mutants defective in methanol-inducible gene expression. A large number of mutants were obtained, indicating that this method is a powerful tool for random mutagenesis in C. boidinii.
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Affiliation(s)
- Yu Sasano
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Kyoto, Japan
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Hartner FS, Glieder A. Regulation of methanol utilisation pathway genes in yeasts. Microb Cell Fact 2006; 5:39. [PMID: 17169150 PMCID: PMC1781073 DOI: 10.1186/1475-2859-5-39] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Accepted: 12/14/2006] [Indexed: 11/10/2022] Open
Abstract
Methylotrophic yeasts such as Candida boidinii, Hansenula polymorpha, Pichia methanolica and Pichia pastoris are an emerging group of eukaryotic hosts for recombinant protein production with an ever increasing number of applications during the last 30 years. Their applications are linked to the use of strong methanol-inducible promoters derived from genes of the methanol utilisation pathway. These promoters are tightly regulated, highly repressed in presence of non-limiting concentrations of glucose in the medium and strongly induced if methanol is used as carbon source. Several factors involved in this tight control and their regulatory effects have been described so far. This review summarises available data about the regulation of promoters from methanol utilisation pathway genes. Furthermore, the role of cis and trans acting factors (e.g. transcription factors, glucose processing enzymes) in the expression of methanol utilisation pathway genes is reviewed both in the context of the native cell environment as well as in heterologous hosts.
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Affiliation(s)
- Franz S Hartner
- Research Centre Applied Biocatalysis GmbH, Petersgasse 14/2, 8010 Graz, Austria
| | - Anton Glieder
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria
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16
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van der Klei IJ, Yurimoto H, Sakai Y, Veenhuis M. The significance of peroxisomes in methanol metabolism in methylotrophic yeast. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1763:1453-62. [PMID: 17023065 DOI: 10.1016/j.bbamcr.2006.07.016] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2006] [Accepted: 07/26/2006] [Indexed: 11/22/2022]
Abstract
The capacity to use methanol as sole source of carbon and energy is restricted to relatively few yeast species. This may be related to the low efficiency of methanol metabolism in yeast, relative to that of prokaryotes. This contribution describes the details of methanol metabolism in yeast and focuses on the significance of compartmentalization of this metabolic pathway in peroxisomes.
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Affiliation(s)
- Ida J van der Klei
- Eukaryotic Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, P.O. Box 14, NL-9750 AA Haren, The Netherlands
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17
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Stevens P, Monastyrska I, Leão-Helder AN, van der Klei IJ, Veenhuis M, Kiel JAKW. Vam7p is required for macropexophagy. FEMS Yeast Res 2005; 5:985-97. [PMID: 16269391 DOI: 10.1016/j.femsyr.2005.02.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2005] [Revised: 02/23/2005] [Accepted: 02/24/2005] [Indexed: 10/25/2022] Open
Abstract
We have analyzed the functions of two vacuolar t-SNAREs, Vam3p and Vam7p, in peroxisome degradation in the methylotrophic yeast Hansenula polymorpha. A Hp-vam7 mutant was strongly affected in peroxisome degradation by selective macropexophagy as well as non-selective microautophagy. Deletion of Hp-Vam3p function had only a minor effect on peroxisome degradation processes. Both proteins were located at the vacuolar membrane, with Hp-Vam7p also having a partially cytosolic location. Previously, in baker's yeast Vam3p and Vam7p have been demonstrated to be components of a t-SNARE complex essential for vacuole biogenesis. We speculate that the function of this complex in macropexophagy includes a role in membrane fusion processes between the outer membrane layer of sequestered peroxisomes and the vacuolar membrane. Our data suggest that Hp-Vam3p may be functionally redundant in peroxisome degradation. Remarkably, deletion of Hp-VAM7 also significantly affected peroxisome biogenesis and resulted in organelles with multiple, membrane-enclosed compartments. These morphological defects became first visible in cells that were in the mid-exponential growth phase of cultivation on methanol, and were correlated with accumulation of electron-dense extensions that were connected to mitochondria.
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Affiliation(s)
- Patricia Stevens
- Eukaryotic Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, P.O. Box 14, 9751 AA Haren, The Netherlands
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18
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Ozimek P, Veenhuis M, van der Klei IJ. Alcohol oxidase: a complex peroxisomal, oligomeric flavoprotein. FEMS Yeast Res 2005; 5:975-83. [PMID: 16169288 DOI: 10.1016/j.femsyr.2005.06.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2005] [Revised: 06/07/2005] [Accepted: 06/07/2005] [Indexed: 10/25/2022] Open
Abstract
Alcohol oxidase (AO) is the key enzyme of methanol metabolism in methylotrophic yeast species. It catalyses the first step of methanol catabolism, namely its oxidation to formaldehyde with concomitant production of hydrogen peroxide. In its mature active form, AO is a molecule of high molecular mass (600 kDa) that consists of eight identical subunits, each of which carry one non-covalently bound flavin adenine nucleotide (FAD) molecule as the prosthetic group. In vivo, the protein is compartmentalized into special cell organelles, termed peroxisomes. AO is an abundant protein and its synthesis is strictly regulated by repression/derepression and induction mechanisms that occur at the transcriptional level. Various aspects of its sorting and assembly/activation render AO a unique protein. Recent developments of AO synthesis, sorting and assembly/activation are highlighted in this paper.
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Affiliation(s)
- Paulina Ozimek
- Eukaryotic Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, P.O. Box 14, 9750 AA Haren, The Netherlands
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Current awareness on yeast. Yeast 2004; 21:1233-40. [PMID: 15580707 DOI: 10.1002/yea.1096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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