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The reconstruction of condition-specific transcriptional modules provides new insights in the evolution of yeast AP-1 proteins.

Goudot C, Etchebest C, Devaux F, Lelandais G - PLoS ONE (2011)

Bottom Line: We developed a computational approach to infer condition-specific transcriptional modules associated to the orthologous AP-1 protein Yap1p, Cgap1p and Cap1p, in three yeast species: the model yeast Saccharomyces cerevisiae and two pathogenic species Candida glabrata and Candida albicans.In Candida glabrata, we found that Cgap1p, unlike Yap1p and Cap1p, recognizes YRE-O and YRE-A motifs.Thus, whereas arginine and lysine substitutions in Cgap1p and Yap1p proteins were reported as responsible for a specific YRE-O or YRE-A preference, our analyses rather suggest that the ancestral yeast AP-1 protein could recognize both YRE-O and YRE-A motifs and that the arginine/lysine exchange is not the only determinant of the specialization of modern Yaps for one motif or another.

View Article: PubMed Central - PubMed

Affiliation: Dynamique des Structures et Interactions des Macromolécules Biologiques, INSERM, U665 Paris, France.

ABSTRACT
AP-1 proteins are transcription factors (TFs) that belong to the basic leucine zipper family, one of the largest families of TFs in eukaryotic cells. Despite high homology between their DNA binding domains, these proteins are able to recognize diverse DNA motifs. In yeasts, these motifs are referred as YRE (Yap Response Element) and are either seven (YRE-Overlap) or eight (YRE-Adjacent) base pair long. It has been proposed that the AP-1 DNA binding motif preference relies on a single change in the amino acid sequence of the yeast AP-1 TFs (an arginine in the YRE-O binding factors being replaced by a lysine in the YRE-A binding Yaps). We developed a computational approach to infer condition-specific transcriptional modules associated to the orthologous AP-1 protein Yap1p, Cgap1p and Cap1p, in three yeast species: the model yeast Saccharomyces cerevisiae and two pathogenic species Candida glabrata and Candida albicans. Exploitation of these modules in terms of predictions of the protein/DNA regulatory interactions changed our vision of AP-1 protein evolution. Cis-regulatory motif analyses revealed the presence of a conserved adenine in 5' position of the canonical YRE sites. While Yap1p, Cgap1p and Cap1p shared a remarkably low number of target genes, an impressive conservation was observed in the YRE sequences identified by Yap1p and Cap1p. In Candida glabrata, we found that Cgap1p, unlike Yap1p and Cap1p, recognizes YRE-O and YRE-A motifs. These findings were supported by structural data available for the transcription factor Pap1p (Schizosaccharomyces pombe). Thus, whereas arginine and lysine substitutions in Cgap1p and Yap1p proteins were reported as responsible for a specific YRE-O or YRE-A preference, our analyses rather suggest that the ancestral yeast AP-1 protein could recognize both YRE-O and YRE-A motifs and that the arginine/lysine exchange is not the only determinant of the specialization of modern Yaps for one motif or another.

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Identification of cis-regulatory motifs in promoter sequences of AP-1 bTM genes.Yeast AP-1 bTMs were characterized using the procedure presented in Figure 1. They are represented here using the following color code: Yap1p bTM in S. cerevisiae (SCERE) in purple, Cgap1p bTM in C. glabrata (CGLAB) in orange, Cap1p bTM in C. albicans in green. Promoter sequences of genes were analyzing using a combination of five different algorithms (BEAM, PRISM, SPACER, Oligo-Analysis and MEME) and applying a filter procedure to select the most significant motifs (see Material and Methods and Text S3). 12 motifs were identified in SCERE, 7 motifs in CGLAB and 8 motifs in CALB. They are presented in Text S4. In each species, these motifs were combined and consensus sequences are shown here (SeqLogo representations). A unique consensus MTKASTMA was observed in promoters of SCERE and CALB genes and two consensuses (MTTASSTAA, ATTACHAAW) were observed in promoters of CGLAB genes (where M designates A or C, K designates G or T, S designates C or G and W designates A or T). Percentages of genes in each AP-1 bTMs that exhibit those consensuses are indicated below the SeqLogo representations, with the associated enrichment p-value (see Materials and Methods). Highly conserved positions between the consensuses are underlined. They are predicted to strongly interact with the TF DNA binding domain, based on structural inspection of the Pap1p/DNA complex (see Figure 4).
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pone-0020924-g003: Identification of cis-regulatory motifs in promoter sequences of AP-1 bTM genes.Yeast AP-1 bTMs were characterized using the procedure presented in Figure 1. They are represented here using the following color code: Yap1p bTM in S. cerevisiae (SCERE) in purple, Cgap1p bTM in C. glabrata (CGLAB) in orange, Cap1p bTM in C. albicans in green. Promoter sequences of genes were analyzing using a combination of five different algorithms (BEAM, PRISM, SPACER, Oligo-Analysis and MEME) and applying a filter procedure to select the most significant motifs (see Material and Methods and Text S3). 12 motifs were identified in SCERE, 7 motifs in CGLAB and 8 motifs in CALB. They are presented in Text S4. In each species, these motifs were combined and consensus sequences are shown here (SeqLogo representations). A unique consensus MTKASTMA was observed in promoters of SCERE and CALB genes and two consensuses (MTTASSTAA, ATTACHAAW) were observed in promoters of CGLAB genes (where M designates A or C, K designates G or T, S designates C or G and W designates A or T). Percentages of genes in each AP-1 bTMs that exhibit those consensuses are indicated below the SeqLogo representations, with the associated enrichment p-value (see Materials and Methods). Highly conserved positions between the consensuses are underlined. They are predicted to strongly interact with the TF DNA binding domain, based on structural inspection of the Pap1p/DNA complex (see Figure 4).

Mentions: Compared with previous works, the yeast AP-1 bTMs defined in this study had the originality to arise from the combination of condition-specific transcriptome experiments and ChIP-chip data. Assuming that this approach resulted in a physiologically more relevant and accurate view of the yeast AP-1 target genes, we next investigated the regulatory mechanisms that guide the functioning of the yeast AP-1 proteins, analyzing cis-regulatory motifs in the promoter sequences of bTM-genes. We used an original procedure that combined five different motif discovery algorithms: BEAM [37], PRISM [38] and SPACER [39] (combined in the SCOPE program [40]), Oligo-Analysis [41] and MEME [42]. These algorithms were chosen because they use different theoretical background and hence were each designed to identify a particular class of motifs (short non-degenerate motifs, short-degenerate motifs, long highly degenerate motifs, motifs with non-contiguous critical residues, etc.). Promoter sequences of genes in yeast AP-1 bTMs were analyzed searching for potential regulatory motifs (see Materials and Methods). To combine and filter the results obtained with each algorithm we applied the global procedure illustrated in Text S3. To summarize, the approach consisted in (i) collecting all the motifs proposed by each algorithm, (ii) removing irrelevant motifs that were too short for being specifically recognized by AP-1 proteins (<7 base pairs) and motifs with more than three uncharacterized positions, (iii) ordering the remaining motifs according to their enrichment p-values and conserving the most significant ones, i.e. with a p-value<10−5, and (iv) selecting the motifs that agreed steps (i) to (iii) and that were identified with at least two different algorithms. As a result, 12 motifs were identified in S. cerevisiae, 7 motifs in C. glabrata and 8 motifs in C. albicans. Detailed motif information can be found in Text S4 and the corresponding consensus sequences together with sequence logos are presented in Figure 3. Interestingly, a unique consensus sequence MTKASTMA was enriched in promoter sequences of genes in both the Yap1p and Cap1p bTMs. The corresponding p-values were highly significant, at 4.10−19 (Yap1p bTM in S. cerevisiae) and 1.10−18 (Cap1p bTM in C. albicans). Notably this sequence (i) was present in more than 70% of the promoters of Yap1p- and Cap1p-dependent genes, (ii) included YRE-O motifs with in particular, the palindrome sequence TTA(C/G)TAA characterized previously as being the main benomyl response element (BRE) in these two species [16], [19], and (iii) exhibited a supplementary adenine (or to a less extend a cytosine) in 5′ position. In C. glabrata, the identified motifs could be combined into two different consensuses MTTASSTAA (p-value = 7.10−14) and ATTACHAAW (p-value = 2.10−6). These consensuses were 9 base pair long with again, A or C in the 5′ position. The MTTASSTAA consensus could be related to the YRE-A motifs, which were recently proposed to be the main Cgap1p DNA binding sequences [23]. Strikingly enough, this motif was present in only 24% of the promoters of Cgap1p-dependent genes. The second consensus ATTACHAAW could be related to YRE-O motifs and included the TTACAAA sequence, which was previously demonstrated to act as a BRE in C. glabrata [21]. This consensus sequence was found in 31% of Cgap1p-dependant gene promoters. All together, the MTTASSTAA and ATTACHAAW motifs were present in half of the genes composing the Cgap1 bTM.


The reconstruction of condition-specific transcriptional modules provides new insights in the evolution of yeast AP-1 proteins.

Goudot C, Etchebest C, Devaux F, Lelandais G - PLoS ONE (2011)

Identification of cis-regulatory motifs in promoter sequences of AP-1 bTM genes.Yeast AP-1 bTMs were characterized using the procedure presented in Figure 1. They are represented here using the following color code: Yap1p bTM in S. cerevisiae (SCERE) in purple, Cgap1p bTM in C. glabrata (CGLAB) in orange, Cap1p bTM in C. albicans in green. Promoter sequences of genes were analyzing using a combination of five different algorithms (BEAM, PRISM, SPACER, Oligo-Analysis and MEME) and applying a filter procedure to select the most significant motifs (see Material and Methods and Text S3). 12 motifs were identified in SCERE, 7 motifs in CGLAB and 8 motifs in CALB. They are presented in Text S4. In each species, these motifs were combined and consensus sequences are shown here (SeqLogo representations). A unique consensus MTKASTMA was observed in promoters of SCERE and CALB genes and two consensuses (MTTASSTAA, ATTACHAAW) were observed in promoters of CGLAB genes (where M designates A or C, K designates G or T, S designates C or G and W designates A or T). Percentages of genes in each AP-1 bTMs that exhibit those consensuses are indicated below the SeqLogo representations, with the associated enrichment p-value (see Materials and Methods). Highly conserved positions between the consensuses are underlined. They are predicted to strongly interact with the TF DNA binding domain, based on structural inspection of the Pap1p/DNA complex (see Figure 4).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3111461&req=5

pone-0020924-g003: Identification of cis-regulatory motifs in promoter sequences of AP-1 bTM genes.Yeast AP-1 bTMs were characterized using the procedure presented in Figure 1. They are represented here using the following color code: Yap1p bTM in S. cerevisiae (SCERE) in purple, Cgap1p bTM in C. glabrata (CGLAB) in orange, Cap1p bTM in C. albicans in green. Promoter sequences of genes were analyzing using a combination of five different algorithms (BEAM, PRISM, SPACER, Oligo-Analysis and MEME) and applying a filter procedure to select the most significant motifs (see Material and Methods and Text S3). 12 motifs were identified in SCERE, 7 motifs in CGLAB and 8 motifs in CALB. They are presented in Text S4. In each species, these motifs were combined and consensus sequences are shown here (SeqLogo representations). A unique consensus MTKASTMA was observed in promoters of SCERE and CALB genes and two consensuses (MTTASSTAA, ATTACHAAW) were observed in promoters of CGLAB genes (where M designates A or C, K designates G or T, S designates C or G and W designates A or T). Percentages of genes in each AP-1 bTMs that exhibit those consensuses are indicated below the SeqLogo representations, with the associated enrichment p-value (see Materials and Methods). Highly conserved positions between the consensuses are underlined. They are predicted to strongly interact with the TF DNA binding domain, based on structural inspection of the Pap1p/DNA complex (see Figure 4).
Mentions: Compared with previous works, the yeast AP-1 bTMs defined in this study had the originality to arise from the combination of condition-specific transcriptome experiments and ChIP-chip data. Assuming that this approach resulted in a physiologically more relevant and accurate view of the yeast AP-1 target genes, we next investigated the regulatory mechanisms that guide the functioning of the yeast AP-1 proteins, analyzing cis-regulatory motifs in the promoter sequences of bTM-genes. We used an original procedure that combined five different motif discovery algorithms: BEAM [37], PRISM [38] and SPACER [39] (combined in the SCOPE program [40]), Oligo-Analysis [41] and MEME [42]. These algorithms were chosen because they use different theoretical background and hence were each designed to identify a particular class of motifs (short non-degenerate motifs, short-degenerate motifs, long highly degenerate motifs, motifs with non-contiguous critical residues, etc.). Promoter sequences of genes in yeast AP-1 bTMs were analyzed searching for potential regulatory motifs (see Materials and Methods). To combine and filter the results obtained with each algorithm we applied the global procedure illustrated in Text S3. To summarize, the approach consisted in (i) collecting all the motifs proposed by each algorithm, (ii) removing irrelevant motifs that were too short for being specifically recognized by AP-1 proteins (<7 base pairs) and motifs with more than three uncharacterized positions, (iii) ordering the remaining motifs according to their enrichment p-values and conserving the most significant ones, i.e. with a p-value<10−5, and (iv) selecting the motifs that agreed steps (i) to (iii) and that were identified with at least two different algorithms. As a result, 12 motifs were identified in S. cerevisiae, 7 motifs in C. glabrata and 8 motifs in C. albicans. Detailed motif information can be found in Text S4 and the corresponding consensus sequences together with sequence logos are presented in Figure 3. Interestingly, a unique consensus sequence MTKASTMA was enriched in promoter sequences of genes in both the Yap1p and Cap1p bTMs. The corresponding p-values were highly significant, at 4.10−19 (Yap1p bTM in S. cerevisiae) and 1.10−18 (Cap1p bTM in C. albicans). Notably this sequence (i) was present in more than 70% of the promoters of Yap1p- and Cap1p-dependent genes, (ii) included YRE-O motifs with in particular, the palindrome sequence TTA(C/G)TAA characterized previously as being the main benomyl response element (BRE) in these two species [16], [19], and (iii) exhibited a supplementary adenine (or to a less extend a cytosine) in 5′ position. In C. glabrata, the identified motifs could be combined into two different consensuses MTTASSTAA (p-value = 7.10−14) and ATTACHAAW (p-value = 2.10−6). These consensuses were 9 base pair long with again, A or C in the 5′ position. The MTTASSTAA consensus could be related to the YRE-A motifs, which were recently proposed to be the main Cgap1p DNA binding sequences [23]. Strikingly enough, this motif was present in only 24% of the promoters of Cgap1p-dependent genes. The second consensus ATTACHAAW could be related to YRE-O motifs and included the TTACAAA sequence, which was previously demonstrated to act as a BRE in C. glabrata [21]. This consensus sequence was found in 31% of Cgap1p-dependant gene promoters. All together, the MTTASSTAA and ATTACHAAW motifs were present in half of the genes composing the Cgap1 bTM.

Bottom Line: We developed a computational approach to infer condition-specific transcriptional modules associated to the orthologous AP-1 protein Yap1p, Cgap1p and Cap1p, in three yeast species: the model yeast Saccharomyces cerevisiae and two pathogenic species Candida glabrata and Candida albicans.In Candida glabrata, we found that Cgap1p, unlike Yap1p and Cap1p, recognizes YRE-O and YRE-A motifs.Thus, whereas arginine and lysine substitutions in Cgap1p and Yap1p proteins were reported as responsible for a specific YRE-O or YRE-A preference, our analyses rather suggest that the ancestral yeast AP-1 protein could recognize both YRE-O and YRE-A motifs and that the arginine/lysine exchange is not the only determinant of the specialization of modern Yaps for one motif or another.

View Article: PubMed Central - PubMed

Affiliation: Dynamique des Structures et Interactions des Macromolécules Biologiques, INSERM, U665 Paris, France.

ABSTRACT
AP-1 proteins are transcription factors (TFs) that belong to the basic leucine zipper family, one of the largest families of TFs in eukaryotic cells. Despite high homology between their DNA binding domains, these proteins are able to recognize diverse DNA motifs. In yeasts, these motifs are referred as YRE (Yap Response Element) and are either seven (YRE-Overlap) or eight (YRE-Adjacent) base pair long. It has been proposed that the AP-1 DNA binding motif preference relies on a single change in the amino acid sequence of the yeast AP-1 TFs (an arginine in the YRE-O binding factors being replaced by a lysine in the YRE-A binding Yaps). We developed a computational approach to infer condition-specific transcriptional modules associated to the orthologous AP-1 protein Yap1p, Cgap1p and Cap1p, in three yeast species: the model yeast Saccharomyces cerevisiae and two pathogenic species Candida glabrata and Candida albicans. Exploitation of these modules in terms of predictions of the protein/DNA regulatory interactions changed our vision of AP-1 protein evolution. Cis-regulatory motif analyses revealed the presence of a conserved adenine in 5' position of the canonical YRE sites. While Yap1p, Cgap1p and Cap1p shared a remarkably low number of target genes, an impressive conservation was observed in the YRE sequences identified by Yap1p and Cap1p. In Candida glabrata, we found that Cgap1p, unlike Yap1p and Cap1p, recognizes YRE-O and YRE-A motifs. These findings were supported by structural data available for the transcription factor Pap1p (Schizosaccharomyces pombe). Thus, whereas arginine and lysine substitutions in Cgap1p and Yap1p proteins were reported as responsible for a specific YRE-O or YRE-A preference, our analyses rather suggest that the ancestral yeast AP-1 protein could recognize both YRE-O and YRE-A motifs and that the arginine/lysine exchange is not the only determinant of the specialization of modern Yaps for one motif or another.

Show MeSH