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Yeast glucose pathways converge on the transcriptional regulation of trehalose biosynthesis.

Apweiler E, Sameith K, Margaritis T, Brabers N, van de Pasch L, Bakker LV, van Leenen D, Holstege FC, Kemmeren P - BMC Genomics (2012)

Bottom Line: In general, the mutations do not induce pathway-specific transcriptional responses.Epistasis analysis of tps2Δ double mutants supports this prediction.Although based on transcriptional changes only, these results suggest that all changes in perceived glucose levels ultimately lead to a shift in trehalose biosynthesis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Cancer Research, University Medical Centre Utrecht, Utrecht, the Netherlands.

ABSTRACT

Background: Cellular glucose availability is crucial for the functioning of most biological processes. Our understanding of the glucose regulatory system has been greatly advanced by studying the model organism Saccharomyces cerevisiae, but many aspects of this system remain elusive. To understand the organisation of the glucose regulatory system, we analysed 91 deletion mutants of the different glucose signalling and metabolic pathways in Saccharomyces cerevisiae using DNA microarrays.

Results: In general, the mutations do not induce pathway-specific transcriptional responses. Instead, one main transcriptional response is discerned, which varies in direction to mimic either a high or a low glucose response. Detailed analysis uncovers established and new relationships within and between individual pathways and their members. In contrast to signalling components, metabolic components of the glucose regulatory system are transcriptionally more frequently affected. A new network approach is applied that exposes the hierarchical organisation of the glucose regulatory system.

Conclusions: The tight interconnection between the different pathways of the glucose regulatory system is reflected by the main transcriptional response observed. Tps2 and Tsl1, two enzymes involved in the biosynthesis of the storage carbohydrate trehalose, are predicted to be the most downstream transcriptional components. Epistasis analysis of tps2Δ double mutants supports this prediction. Although based on transcriptional changes only, these results suggest that all changes in perceived glucose levels ultimately lead to a shift in trehalose biosynthesis.

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Transcriptional response mimicking either a high or a low glucose response. (A) Unsupervised hierarchical cluster diagram of all deletion mutants with gene expression changes differing from WT, i.e. twelve or more significant transcriptional changes, and all transcripts changing significantly in at least one of these mutants (p < 0.01, FC > 1.7). The dendrograms indicate relationships between transcripts (top) and mutants (right). The latter is colour-coded according to whether the mutants are part of the “high glucose” (red) or “low glucose” group (green). FC is indicated by the colour scale, with yellow for upregulation, blue for downregulation, and black for no change, versus the average WT. (B) Line graph of a time-course experiment in which glucose-depleted WT cells were inoculated into fresh media (SC, supplemented with 2% glucose) and their subsequent transcriptional output was monitored over a period of five hours. All transcripts differentially expressed between the “high glucose” and “low glucose” groups were split according to whether they were up- (left panel, yellow) or downregulated (right panel, blue) in the “low glucose” group. The average expression of the differentially expressed transcripts is indicated in black; all other transcripts are shown in grey.
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Figure 2: Transcriptional response mimicking either a high or a low glucose response. (A) Unsupervised hierarchical cluster diagram of all deletion mutants with gene expression changes differing from WT, i.e. twelve or more significant transcriptional changes, and all transcripts changing significantly in at least one of these mutants (p < 0.01, FC > 1.7). The dendrograms indicate relationships between transcripts (top) and mutants (right). The latter is colour-coded according to whether the mutants are part of the “high glucose” (red) or “low glucose” group (green). FC is indicated by the colour scale, with yellow for upregulation, blue for downregulation, and black for no change, versus the average WT. (B) Line graph of a time-course experiment in which glucose-depleted WT cells were inoculated into fresh media (SC, supplemented with 2% glucose) and their subsequent transcriptional output was monitored over a period of five hours. All transcripts differentially expressed between the “high glucose” and “low glucose” groups were split according to whether they were up- (left panel, yellow) or downregulated (right panel, blue) in the “low glucose” group. The average expression of the differentially expressed transcripts is indicated in black; all other transcripts are shown in grey.

Mentions: The relationships between the 45 mutants with significant gene expression changes were investigated by hierarchical clustering of the gene expression profiles (Figure 2A). Gene expression profiles of deletion mutants can be treated as detailed molecular phenotypes [17,18]. Deleting certain pathway members often results in the malfunctioning of the entire pathway, the effect of which can be a specific expression signature. Deletion mutants of the same pathway will therefore show the same expression signature. Deletion mutants of distinct pathways, such as the HOG or mating pathway [18], or chromatin interaction pathways [23], show an expression signature specific to the pathway they belong to. The glucose regulatory system is composed of the Ras/PKA, Gpr1/PKA, Sch9, Yak1, Snf1 and Snf3/Rgt2 signalling pathways, as well as metabolic pathways (Figure 1). Nevertheless, based on the hierarchical clustering, the mutants segregate into two distinct groups rather than according to specific pathway membership (Figure 2A). Essentially, the expression signature of all members within one group is highly similar and mostly opposite to that of the other group, indicating that the two expression signatures are mutually exclusive. Thus, disruption of any glucose pathway causes an invariable response differing only in terms of direction and magnitude. A likely interpretation is that the pathways are so tightly interconnected that upon perceived alterations to glucose levels, they ultimately end up in one of two possible steady-states.


Yeast glucose pathways converge on the transcriptional regulation of trehalose biosynthesis.

Apweiler E, Sameith K, Margaritis T, Brabers N, van de Pasch L, Bakker LV, van Leenen D, Holstege FC, Kemmeren P - BMC Genomics (2012)

Transcriptional response mimicking either a high or a low glucose response. (A) Unsupervised hierarchical cluster diagram of all deletion mutants with gene expression changes differing from WT, i.e. twelve or more significant transcriptional changes, and all transcripts changing significantly in at least one of these mutants (p < 0.01, FC > 1.7). The dendrograms indicate relationships between transcripts (top) and mutants (right). The latter is colour-coded according to whether the mutants are part of the “high glucose” (red) or “low glucose” group (green). FC is indicated by the colour scale, with yellow for upregulation, blue for downregulation, and black for no change, versus the average WT. (B) Line graph of a time-course experiment in which glucose-depleted WT cells were inoculated into fresh media (SC, supplemented with 2% glucose) and their subsequent transcriptional output was monitored over a period of five hours. All transcripts differentially expressed between the “high glucose” and “low glucose” groups were split according to whether they were up- (left panel, yellow) or downregulated (right panel, blue) in the “low glucose” group. The average expression of the differentially expressed transcripts is indicated in black; all other transcripts are shown in grey.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Figure 2: Transcriptional response mimicking either a high or a low glucose response. (A) Unsupervised hierarchical cluster diagram of all deletion mutants with gene expression changes differing from WT, i.e. twelve or more significant transcriptional changes, and all transcripts changing significantly in at least one of these mutants (p < 0.01, FC > 1.7). The dendrograms indicate relationships between transcripts (top) and mutants (right). The latter is colour-coded according to whether the mutants are part of the “high glucose” (red) or “low glucose” group (green). FC is indicated by the colour scale, with yellow for upregulation, blue for downregulation, and black for no change, versus the average WT. (B) Line graph of a time-course experiment in which glucose-depleted WT cells were inoculated into fresh media (SC, supplemented with 2% glucose) and their subsequent transcriptional output was monitored over a period of five hours. All transcripts differentially expressed between the “high glucose” and “low glucose” groups were split according to whether they were up- (left panel, yellow) or downregulated (right panel, blue) in the “low glucose” group. The average expression of the differentially expressed transcripts is indicated in black; all other transcripts are shown in grey.
Mentions: The relationships between the 45 mutants with significant gene expression changes were investigated by hierarchical clustering of the gene expression profiles (Figure 2A). Gene expression profiles of deletion mutants can be treated as detailed molecular phenotypes [17,18]. Deleting certain pathway members often results in the malfunctioning of the entire pathway, the effect of which can be a specific expression signature. Deletion mutants of the same pathway will therefore show the same expression signature. Deletion mutants of distinct pathways, such as the HOG or mating pathway [18], or chromatin interaction pathways [23], show an expression signature specific to the pathway they belong to. The glucose regulatory system is composed of the Ras/PKA, Gpr1/PKA, Sch9, Yak1, Snf1 and Snf3/Rgt2 signalling pathways, as well as metabolic pathways (Figure 1). Nevertheless, based on the hierarchical clustering, the mutants segregate into two distinct groups rather than according to specific pathway membership (Figure 2A). Essentially, the expression signature of all members within one group is highly similar and mostly opposite to that of the other group, indicating that the two expression signatures are mutually exclusive. Thus, disruption of any glucose pathway causes an invariable response differing only in terms of direction and magnitude. A likely interpretation is that the pathways are so tightly interconnected that upon perceived alterations to glucose levels, they ultimately end up in one of two possible steady-states.

Bottom Line: In general, the mutations do not induce pathway-specific transcriptional responses.Epistasis analysis of tps2Δ double mutants supports this prediction.Although based on transcriptional changes only, these results suggest that all changes in perceived glucose levels ultimately lead to a shift in trehalose biosynthesis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Cancer Research, University Medical Centre Utrecht, Utrecht, the Netherlands.

ABSTRACT

Background: Cellular glucose availability is crucial for the functioning of most biological processes. Our understanding of the glucose regulatory system has been greatly advanced by studying the model organism Saccharomyces cerevisiae, but many aspects of this system remain elusive. To understand the organisation of the glucose regulatory system, we analysed 91 deletion mutants of the different glucose signalling and metabolic pathways in Saccharomyces cerevisiae using DNA microarrays.

Results: In general, the mutations do not induce pathway-specific transcriptional responses. Instead, one main transcriptional response is discerned, which varies in direction to mimic either a high or a low glucose response. Detailed analysis uncovers established and new relationships within and between individual pathways and their members. In contrast to signalling components, metabolic components of the glucose regulatory system are transcriptionally more frequently affected. A new network approach is applied that exposes the hierarchical organisation of the glucose regulatory system.

Conclusions: The tight interconnection between the different pathways of the glucose regulatory system is reflected by the main transcriptional response observed. Tps2 and Tsl1, two enzymes involved in the biosynthesis of the storage carbohydrate trehalose, are predicted to be the most downstream transcriptional components. Epistasis analysis of tps2Δ double mutants supports this prediction. Although based on transcriptional changes only, these results suggest that all changes in perceived glucose levels ultimately lead to a shift in trehalose biosynthesis.

Show MeSH