Genome‐wide expression profiling of the osmoadaptation response of <i>Debaryomyces hansenii</i>

González, Nancy Arroyo; Vázquez, Adrinel; Ortíz-Zuazaga, Humberto; Sen, Arup; Olvera, Hugo Luna; Ortı́z, Sandra Peña de; Govind, Nadathur S.

doi:10.1002/yea.1656

Cited by 20 publications

(13 citation statements)

References 52 publications

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“…Only recently, species-specific DNA microarray studies have been presented for e.g. Debaryomyces hansenii [40] and P. pastoris [41]. For H. polymorpha , Oh et al , [42] presented a partial, DNA microarray study, followed by a full DNA microarray analysis describing the transcriptional response of H. polymorpha to exposure to cadmium [43].…”

Section: Resultsmentioning

confidence: 99%

Adaptation of Hansenula polymorpha to methanol: a transcriptome analysis

et al. 2010

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BackgroundMethylotrophic 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.ResultsTwo 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 β-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.ConclusionTranscriptional 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 β-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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Section: Resultsmentioning

confidence: 99%

Adaptation of Hansenula polymorpha to methanol: a transcriptome analysis

et al. 2010

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“…The up-regulation of genes involved in protein synthesis during osmotic stress has been reported for the salt-tolerant yeasts H. werneckii and D. hansenii [30,50]. Furthermore, studies on brewing strains of S. cerevisiae concluded that the faster adaption to higher salt concentration compared to a laboratory strain was achieved by higher expression levels of genes involved in protein synthesis [51].…”

Section: Discussionmentioning

confidence: 97%

The response to unfolded protein is involved in osmotolerance of Pichia pastoris

et al. 2010

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BackgroundThe effect of osmolarity on cellular physiology has been subject of investigation in many different species. High osmolarity is of importance for biotechnological production processes, where high cell densities and product titers are aspired. Several studies indicated that increased osmolarity of the growth medium can have a beneficial effect on recombinant protein production in different host organisms. Thus, the effect of osmolarity on the cellular physiology of Pichia pastoris, a prominent host for recombinant protein production, was studied in carbon limited chemostat cultures at different osmolarities. Transcriptome and proteome analyses were applied to assess differences upon growth at different osmolarities in both, a wild type strain and an antibody fragment expressing strain. While our main intention was to analyze the effect of different osmolarities on P. pastoris in general, this was complemented by studying it in context with recombinant protein production.ResultsIn contrast to the model yeast Saccharomyces cerevisiae, the main osmolyte in P. pastoris was arabitol rather than glycerol, demonstrating differences in osmotic stress response as well as energy metabolism. 2D Fluorescence Difference Gel electrophoresis and microarray analysis were applied and demonstrated that processes such as protein folding, ribosome biogenesis and cell wall organization were affected by increased osmolarity. These data indicated that upon increased osmolarity less adaptations on both the transcript and protein level occurred in a P. pastoris strain, secreting the Fab fragment, compared with the wild type strain. No transcriptional activation of the high osmolarity glycerol (HOG) pathway was observed at steady state conditions. Furthermore, no change of the specific productivity of recombinant Fab was observed at increased osmolarity.ConclusionThese data point out that the physiological response to increased osmolarity is different to S. cerevisiae. Increased osmolarity resulted in an unfolded protein response (UPR) like response in P. pastoris and lead to pre-conditioning of the recombinant Fab producing strain of P. pastoris to growth at high osmolarity. The current data demonstrate a strong similarity of environmental stress response mechanisms and recombinant protein related stresses. Therefore, these results might be used in future strain and bioprocess engineering of this biotechnologically relevant yeast.

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“…Debaryomyces hansenii is a highly extremophilic yeast. However, unlike in the case of osmotolerance (Arroyo Gonzalez et al 2009), resistance to concentrations of cobalt that are toxic to other similar organisms does not seem to be a pre-adapted characteristic. This is supported by the fact that there is an initial shock when D. hansenni is exposed to Co (II), as indicated by the observation that many of the genes that are upregulated several fold are involved in DNA synthesis and repair.…”

Section: Cell Division and Growthmentioning

confidence: 88%

“…Debaryomyces hansenii is an extremophilic yeast that has been studied for its osmotic stress tolerance, its lipid accumulation and storage, its ability to synthesize various chemicals and enzymes important for industrial applications, and its capability to survive toxic concentrations of the heavy metal cobalt (Breuer and Harms 2006;Seda-Miró et al 2007;Arroyo Gonzalez et al 2009). It is also a highly heterogeneous yeast strain, with two major varieties described, namely, var.…”

Section: Introductionmentioning

confidence: 99%

“…The genomic sequences of only two strains are so far available -CBS 767 and MTCC 234 (Dujon et al 2004;Kumar et al 2012;Keeling et al 2014). Earlier studies in our laboratory showed a lack of cross-reactivity in microarrays made from the genome of CBS 767 with mRNA of the J6 strain (Arroyo Gonzalez et al 2009). In order to overcome this constraint, a transcriptome analysis was carried out which utilized RNA-seq data to elucidate the response of D. hansenii to heavy metal stress.…”

Section: Introductionmentioning

confidence: 99%

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Transcriptomic analysis of cobalt stress in the marine yeastDebaryomyces hansenii

Gumá-Cintrón

Bandyopadhyay

Rosado

et al. 2015

FEMS Yeast Research

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The yeast Debaryomyces hansenii overproduces riboflavin upon exposure to subtoxic levels of cobalt (Co(+2)). However, mechanisms for survival have yet to be studied and have been hindered by D. hansenii's high genetic heterogeneity among strains. In this study, we used transcriptomic analyses and RNA-seq in order to identify differentially expressed genes in D. hansenii in response to cobalt exposure. Highly upregulated genes under this condition were identified to primarily comprise DNA damage and repair genes, oxidative stress response genes, and genes for cell wall integrity and growth. The main response of D. hansenii to heavy metal stress is the activation of non-enzymatic oxidative stress response mechanisms and control of biological production of reactive oxygen species. Our results indicate that D. hansenii does not seem to be pre-adapted to survive high concentrations of heavy metals. These organisms appear to possess genetic survival and detoxification mechanisms that enable the cells to recover from heavy metal stress.

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Genome‐wide expression profiling of the osmoadaptation response of Debaryomyces hansenii

Cited by 20 publications

References 52 publications

Adaptation of Hansenula polymorpha to methanol: a transcriptome analysis

Adaptation of Hansenula polymorpha to methanol: a transcriptome analysis

The response to unfolded protein is involved in osmotolerance of Pichia pastoris

Transcriptomic analysis of cobalt stress in the marine yeastDebaryomyces hansenii

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