Publication

Adaptation of Hansenula polymorpha to methanol: A transcriptome analysis

van Zutphen, T., Baerends, R. J. S., Susanna, K., de Jong, A., Kuipers, O. P., Veenhuis, M. & van der Klei, I. J., 4-Jan-2010, In : BMC Genomics. 11, 1, 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

APA

van Zutphen, T., Baerends, R. J. S., Susanna, K., de Jong, A., Kuipers, O. P., Veenhuis, M., & van der Klei, I. J. (2010). Adaptation of Hansenula polymorpha to methanol: A transcriptome analysis. BMC Genomics, 11(1). https://doi.org/10.1186/1471-2164-11-1

Author

van Zutphen, T. ; Baerends, R.J S ; Susanna, Kim ; de Jong, Anne ; Kuipers, O.P. ; Veenhuis, M ; van der Klei, I.J. / Adaptation of Hansenula polymorpha to methanol : A transcriptome analysis. In: BMC Genomics. 2010 ; Vol. 11, No. 1.

Harvard

van Zutphen, T, Baerends, RJS, Susanna, K, de Jong, A, Kuipers, OP, Veenhuis, M & van der Klei, IJ 2010, 'Adaptation of Hansenula polymorpha to methanol: A transcriptome analysis', BMC Genomics, vol. 11, no. 1. https://doi.org/10.1186/1471-2164-11-1

Standard

Adaptation of Hansenula polymorpha to methanol : A transcriptome analysis. / van Zutphen, T.; Baerends, R.J S; Susanna, Kim; de Jong, Anne; Kuipers, O.P.; Veenhuis, M; van der Klei, I.J.

In: BMC Genomics, Vol. 11, No. 1, 04.01.2010.

Research output: Contribution to journalArticleAcademicpeer-review

Vancouver

van Zutphen T, Baerends RJS, Susanna K, de Jong A, Kuipers OP, Veenhuis M et al. Adaptation of Hansenula polymorpha to methanol: A transcriptome analysis. BMC Genomics. 2010 Jan 4;11(1). https://doi.org/10.1186/1471-2164-11-1


BibTeX

@article{8632d276629d47b79e1e0db01a5b6cb5,
title = "Adaptation of Hansenula polymorpha to methanol: A transcriptome analysis",
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 (t(d) glucose 1 h vs t(d) methanol 4.5 h).",
keywords = "METHYLOTROPHIC YEAST, PICHIA-PASTORIS, SACCHAROMYCES-CEREVISIAE, CANDIDA-BOIDINII, DNA MICROARRAYS, IDENTIFY GENES, FATTY-ACID, EXPRESSION, PROTEIN, PEROXISOMES",
author = "{van Zutphen}, T. and Baerends, {R.J S} and Kim Susanna and {de Jong}, Anne and O.P. Kuipers and M Veenhuis and {van der Klei}, I.J.",
year = "2010",
month = "1",
day = "4",
doi = "10.1186/1471-2164-11-1",
language = "English",
volume = "11",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "BioMed Central Ltd.",
number = "1",

}

RIS

TY - JOUR

T1 - Adaptation of Hansenula polymorpha to methanol

T2 - A transcriptome analysis

AU - van Zutphen, T.

AU - Baerends, R.J S

AU - Susanna, Kim

AU - de Jong, Anne

AU - Kuipers, O.P.

AU - Veenhuis, M

AU - van der Klei, I.J.

PY - 2010/1/4

Y1 - 2010/1/4

N2 - 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 (t(d) glucose 1 h vs t(d) methanol 4.5 h).

AB - 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 (t(d) glucose 1 h vs t(d) methanol 4.5 h).

KW - METHYLOTROPHIC YEAST

KW - PICHIA-PASTORIS

KW - SACCHAROMYCES-CEREVISIAE

KW - CANDIDA-BOIDINII

KW - DNA MICROARRAYS

KW - IDENTIFY GENES

KW - FATTY-ACID

KW - EXPRESSION

KW - PROTEIN

KW - PEROXISOMES

U2 - 10.1186/1471-2164-11-1

DO - 10.1186/1471-2164-11-1

M3 - Article

VL - 11

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - 1

ER -

ID: 1892441