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Transcriptional plasticity through differential assembly of a multiprotein activation complex.

Cormier L, Barbey R, Kuras L - Nucleic Acids Res. (2010)

Bottom Line: Study of Cbf1 and Met31/32 association with PDC6 allowed us to find a new mechanism of recruitment of Met4, which allows PDC6 being differentially regulated compared to sulfur amino acid biosynthetic genes.Our findings provide a new example of mechanism allowing transcriptional plasticity within a regulatory network thanks to a definite toolbox comprising a unique master activator and several dedicated DNA-binding cofactors.We also show evidence suggesting that integration of PDC6 to the Met4 regulon may have occurred recently in the evolution of the Saccharomyces cerevisiae lineage.

View Article: PubMed Central - PubMed

Affiliation: CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France.

ABSTRACT
Cell adaptation to the environment often involves induction of complex gene expression programs under the control of specific transcriptional activators. For instance, in response to cadmium, budding yeast induces transcription of the sulfur amino acid biosynthetic genes through the basic-leucine zipper activator Met4, and also launches a program of substitution of abundant glycolytic enzymes by isozymes with a lower content in sulfur. We demonstrate here that transcriptional induction of PDC6, which encodes a pyruvate decarboxylase isoform with low sulfur content, is directly controlled by Met4 and its DNA-binding cofactors the basic-helix-loop-helix protein Cbf1 and the two homologous zinc finger proteins Met31 and Met32. Study of Cbf1 and Met31/32 association with PDC6 allowed us to find a new mechanism of recruitment of Met4, which allows PDC6 being differentially regulated compared to sulfur amino acid biosynthetic genes. Our findings provide a new example of mechanism allowing transcriptional plasticity within a regulatory network thanks to a definite toolbox comprising a unique master activator and several dedicated DNA-binding cofactors. We also show evidence suggesting that integration of PDC6 to the Met4 regulon may have occurred recently in the evolution of the Saccharomyces cerevisiae lineage.

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Transcriptional kinetics of PDC6 versus MET genes. (A) In response to cadmium. wild-type cells were grown to early log phase in YPD medium and exposed to 0.5 mM Cd2+. Total RNA was extracted from samples taken at the time points indicated. RNA levels were quantified by RT-real time PCR and normalized to 25S ribosomal RNA. For direct comparison among genes, the maximum value for each gene was set up to 1. Data represent the average of two independent experiments and average deviations were 25% at maximum (error bars were omitted for clarity). Numbers are given in Supplementary Table S1. (B) In response to sulfur limitation. Cells were cultivated and RNA was analyzed as in Figure 2A. (C) In the GAL1-MET4 met30Δ strain. Cells were cultivated and RNA was analyzed as in Figure 2B.
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Figure 8: Transcriptional kinetics of PDC6 versus MET genes. (A) In response to cadmium. wild-type cells were grown to early log phase in YPD medium and exposed to 0.5 mM Cd2+. Total RNA was extracted from samples taken at the time points indicated. RNA levels were quantified by RT-real time PCR and normalized to 25S ribosomal RNA. For direct comparison among genes, the maximum value for each gene was set up to 1. Data represent the average of two independent experiments and average deviations were 25% at maximum (error bars were omitted for clarity). Numbers are given in Supplementary Table S1. (B) In response to sulfur limitation. Cells were cultivated and RNA was analyzed as in Figure 2A. (C) In the GAL1-MET4 met30Δ strain. Cells were cultivated and RNA was analyzed as in Figure 2B.

Mentions: The unusual structure of PDC6 promoter raises the question of whether PDC6 and MET gene regulations are identical. To address this point, we compared the kinetics of induction of PDC6 in response to cadmium with that of known MET genes involved in sulfate assimilation, transsulfuration, glutathione biosynthesis, S-adenosylmethionine cycle, or uptake of sulfur compounds (Figure 8A and Supplementary Table S1). This study revealed that the majority of MET genes showed a similar profile of mRNA accumulation upon cadmium induction and, unquestionably, this profile was very different from the profile of PDC6. For most MET genes, the maximum level of transcription was reached within 30 min upon exposure to cadmium, whereas PDC6 was transcribed at only a few percents of its maximum level at this time point. Among MET genes, only AGP3, which encodes a methionine transporter, showed a notable delay in transcript accumulation, but this delay was still not as strong as in the case of PDC6. So, the whole sulfur metabolism gene network is induced in a quite synchronous manner and PDC6 clearly stands apart. We also analyzed the transcriptional kinetics of PDC6 and several representative MET genes in response to sulphur limitation as well as in the GAL1-MET4 met30Δ strain after addition of galactose (Figure 8B and C). We also observed a clear delay in accumulation of PDC6 transcripts compared to MET gene transcripts. Therefore the differential transcriptional kinetics of PDC6 and MET genes is not limited to the case where induction is triggered by cadmium.Figure 8.


Transcriptional plasticity through differential assembly of a multiprotein activation complex.

Cormier L, Barbey R, Kuras L - Nucleic Acids Res. (2010)

Transcriptional kinetics of PDC6 versus MET genes. (A) In response to cadmium. wild-type cells were grown to early log phase in YPD medium and exposed to 0.5 mM Cd2+. Total RNA was extracted from samples taken at the time points indicated. RNA levels were quantified by RT-real time PCR and normalized to 25S ribosomal RNA. For direct comparison among genes, the maximum value for each gene was set up to 1. Data represent the average of two independent experiments and average deviations were 25% at maximum (error bars were omitted for clarity). Numbers are given in Supplementary Table S1. (B) In response to sulfur limitation. Cells were cultivated and RNA was analyzed as in Figure 2A. (C) In the GAL1-MET4 met30Δ strain. Cells were cultivated and RNA was analyzed as in Figure 2B.
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Figure 8: Transcriptional kinetics of PDC6 versus MET genes. (A) In response to cadmium. wild-type cells were grown to early log phase in YPD medium and exposed to 0.5 mM Cd2+. Total RNA was extracted from samples taken at the time points indicated. RNA levels were quantified by RT-real time PCR and normalized to 25S ribosomal RNA. For direct comparison among genes, the maximum value for each gene was set up to 1. Data represent the average of two independent experiments and average deviations were 25% at maximum (error bars were omitted for clarity). Numbers are given in Supplementary Table S1. (B) In response to sulfur limitation. Cells were cultivated and RNA was analyzed as in Figure 2A. (C) In the GAL1-MET4 met30Δ strain. Cells were cultivated and RNA was analyzed as in Figure 2B.
Mentions: The unusual structure of PDC6 promoter raises the question of whether PDC6 and MET gene regulations are identical. To address this point, we compared the kinetics of induction of PDC6 in response to cadmium with that of known MET genes involved in sulfate assimilation, transsulfuration, glutathione biosynthesis, S-adenosylmethionine cycle, or uptake of sulfur compounds (Figure 8A and Supplementary Table S1). This study revealed that the majority of MET genes showed a similar profile of mRNA accumulation upon cadmium induction and, unquestionably, this profile was very different from the profile of PDC6. For most MET genes, the maximum level of transcription was reached within 30 min upon exposure to cadmium, whereas PDC6 was transcribed at only a few percents of its maximum level at this time point. Among MET genes, only AGP3, which encodes a methionine transporter, showed a notable delay in transcript accumulation, but this delay was still not as strong as in the case of PDC6. So, the whole sulfur metabolism gene network is induced in a quite synchronous manner and PDC6 clearly stands apart. We also analyzed the transcriptional kinetics of PDC6 and several representative MET genes in response to sulphur limitation as well as in the GAL1-MET4 met30Δ strain after addition of galactose (Figure 8B and C). We also observed a clear delay in accumulation of PDC6 transcripts compared to MET gene transcripts. Therefore the differential transcriptional kinetics of PDC6 and MET genes is not limited to the case where induction is triggered by cadmium.Figure 8.

Bottom Line: Study of Cbf1 and Met31/32 association with PDC6 allowed us to find a new mechanism of recruitment of Met4, which allows PDC6 being differentially regulated compared to sulfur amino acid biosynthetic genes.Our findings provide a new example of mechanism allowing transcriptional plasticity within a regulatory network thanks to a definite toolbox comprising a unique master activator and several dedicated DNA-binding cofactors.We also show evidence suggesting that integration of PDC6 to the Met4 regulon may have occurred recently in the evolution of the Saccharomyces cerevisiae lineage.

View Article: PubMed Central - PubMed

Affiliation: CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France.

ABSTRACT
Cell adaptation to the environment often involves induction of complex gene expression programs under the control of specific transcriptional activators. For instance, in response to cadmium, budding yeast induces transcription of the sulfur amino acid biosynthetic genes through the basic-leucine zipper activator Met4, and also launches a program of substitution of abundant glycolytic enzymes by isozymes with a lower content in sulfur. We demonstrate here that transcriptional induction of PDC6, which encodes a pyruvate decarboxylase isoform with low sulfur content, is directly controlled by Met4 and its DNA-binding cofactors the basic-helix-loop-helix protein Cbf1 and the two homologous zinc finger proteins Met31 and Met32. Study of Cbf1 and Met31/32 association with PDC6 allowed us to find a new mechanism of recruitment of Met4, which allows PDC6 being differentially regulated compared to sulfur amino acid biosynthetic genes. Our findings provide a new example of mechanism allowing transcriptional plasticity within a regulatory network thanks to a definite toolbox comprising a unique master activator and several dedicated DNA-binding cofactors. We also show evidence suggesting that integration of PDC6 to the Met4 regulon may have occurred recently in the evolution of the Saccharomyces cerevisiae lineage.

Show MeSH
Related in: MedlinePlus