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Histone acetylation accompanied with promoter sequences displaying differential expression profiles of B-class MADS-box genes for phalaenopsis floral morphogenesis.

Hsu CC, Wu PS, Chen TC, Yu CW, Tsai WC, Wu K, Wu WL, Chen WH, Chen HH - PLoS ONE (2014)

Bottom Line: The amplified promoter sequences of PeMADS2∼6 could drive beta-glucuronidase (GUS) gene expression in all floral organs, similar to their expression at the floral primordia stage.The promoter sequence of PeMADS4, exclusively expressed in lip and column, showed a 1.6∼3-fold higher expression in lip/column than in sepal/petal.Furthermore, we noted a 4.9-fold increase in histone acetylation (H3K9K14ac) in the translation start region of PeMADS4 in lip as compared in petal.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.

ABSTRACT
Five B-class MADS-box genes, including four APETALA3 (AP3)-like PeMADS2∼5 and one PISTILLATA (PI)-like PeMADS6, specify the spectacular flower morphology in orchids. The PI-like PeMADS6 ubiquitously expresses in all floral organs. The four AP3-like genes, resulted from two duplication events, express ubiquitously at floral primordia and early floral organ stages, but show distinct expression profiles at late floral organ primordia and floral bud stages. Here, we isolated the upstream sequences of PeMADS2∼6 and studied the regulatory mechanism for their distinct gene expression. Phylogenetic footprinting analysis of the 1.3-kb upstream sequences of AP3-like PeMADS2∼5 showed that their promoter regions have sufficiently diverged and contributed to their subfunctionalization. The amplified promoter sequences of PeMADS2∼6 could drive beta-glucuronidase (GUS) gene expression in all floral organs, similar to their expression at the floral primordia stage. The promoter sequence of PeMADS4, exclusively expressed in lip and column, showed a 1.6∼3-fold higher expression in lip/column than in sepal/petal. Furthermore, we noted a 4.9-fold increase in histone acetylation (H3K9K14ac) in the translation start region of PeMADS4 in lip as compared in petal. All these results suggest that the regulation via the upstream sequences and increased H3K9K14ac level may act synergistically to display distinct expression profiles of the AP3-like genes at late floral organ primordia stage for Phalaenopsis floral morphogenesis.

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Visual representation of motifs in the 1.3-kb promoter sequences of PeMADS2∼5.FOOTPRINTER parameters: (A) motif size: 11, allowed mutations: 0, (B) motif size: 10, allowed mutations: 0. (C) Putative CArG boxes in the PeMADS promoter regions predicted with the homemade software (red box) and the PLACE database (blue box).
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pone-0106033-g002: Visual representation of motifs in the 1.3-kb promoter sequences of PeMADS2∼5.FOOTPRINTER parameters: (A) motif size: 11, allowed mutations: 0, (B) motif size: 10, allowed mutations: 0. (C) Putative CArG boxes in the PeMADS promoter regions predicted with the homemade software (red box) and the PLACE database (blue box).

Mentions: The conserved regulatory motifs are thought to be functional important for gene expression profiles [37]–[40]. However, multiple alignment of these promoter sequences using global alignment procedures was failed because the inversions often cause rearrangements of the regulatory elements [41]. Therefore, we examined the 1.3-kb upstream sequences of PeMADS2∼5 by phylogenetic footprinting, a method for discovering regulatory elements in a set of regulatory regions [32] and has been used to promoter analysis for MADS-box genes in Arabidopsis and Orchis italica and for bZIP genes in rice and sorghum [40], [42], [43]. With prediction of a conserved 11-bp motif with a 0-bp mutation allowance, conservation of four 11-bp motifs was identified between the promoter regions of PeMADS3 and PeMADS4 in different order (Fig. 2A), while no motifs were conserved between promoter regions of PeMADS2 and PeMADS5 (Fig. 2A). With prediction of conserved 10-bp motifs, increased conserved motifs were identified between the promoter regions of PeMADS3 and PeMADS4, and three motifs were lined up in those of PeMADS2 and PeMADS5 (Fig. 2B). Interestingly, we noticed that differential conserved 10-bp motif sets were detected between the promoter regions of PeMADS2/PeMADS5 and PeMADS3/PeMADS4 (Fig. 2B), which suggests that the two lineage of PeMADS2/5 and PeMADS3/4 have diverged for their subfuncationalization after gene duplication. Moreover, the CArG boxes were broadly distributed in the promoter regions of the four PeMADS genes, and no clear correlations of these CArG boxes were detected with their distinct expression profiles (Fig. 2C). Furthermore, with prediction of a conserved 12-bp motif with a 1-bp mutation allowance, motifs were identified between the promoter regions of PeMADS2 and PeMADS5, PeMADS3 and PeMADS4, and PeMADS6 and AtPI, but no motifs were present between the promoter sequences of AtAP3 and PeMADS2∼5 (Fig. 2D).


Histone acetylation accompanied with promoter sequences displaying differential expression profiles of B-class MADS-box genes for phalaenopsis floral morphogenesis.

Hsu CC, Wu PS, Chen TC, Yu CW, Tsai WC, Wu K, Wu WL, Chen WH, Chen HH - PLoS ONE (2014)

Visual representation of motifs in the 1.3-kb promoter sequences of PeMADS2∼5.FOOTPRINTER parameters: (A) motif size: 11, allowed mutations: 0, (B) motif size: 10, allowed mutations: 0. (C) Putative CArG boxes in the PeMADS promoter regions predicted with the homemade software (red box) and the PLACE database (blue box).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263434&req=5

pone-0106033-g002: Visual representation of motifs in the 1.3-kb promoter sequences of PeMADS2∼5.FOOTPRINTER parameters: (A) motif size: 11, allowed mutations: 0, (B) motif size: 10, allowed mutations: 0. (C) Putative CArG boxes in the PeMADS promoter regions predicted with the homemade software (red box) and the PLACE database (blue box).
Mentions: The conserved regulatory motifs are thought to be functional important for gene expression profiles [37]–[40]. However, multiple alignment of these promoter sequences using global alignment procedures was failed because the inversions often cause rearrangements of the regulatory elements [41]. Therefore, we examined the 1.3-kb upstream sequences of PeMADS2∼5 by phylogenetic footprinting, a method for discovering regulatory elements in a set of regulatory regions [32] and has been used to promoter analysis for MADS-box genes in Arabidopsis and Orchis italica and for bZIP genes in rice and sorghum [40], [42], [43]. With prediction of a conserved 11-bp motif with a 0-bp mutation allowance, conservation of four 11-bp motifs was identified between the promoter regions of PeMADS3 and PeMADS4 in different order (Fig. 2A), while no motifs were conserved between promoter regions of PeMADS2 and PeMADS5 (Fig. 2A). With prediction of conserved 10-bp motifs, increased conserved motifs were identified between the promoter regions of PeMADS3 and PeMADS4, and three motifs were lined up in those of PeMADS2 and PeMADS5 (Fig. 2B). Interestingly, we noticed that differential conserved 10-bp motif sets were detected between the promoter regions of PeMADS2/PeMADS5 and PeMADS3/PeMADS4 (Fig. 2B), which suggests that the two lineage of PeMADS2/5 and PeMADS3/4 have diverged for their subfuncationalization after gene duplication. Moreover, the CArG boxes were broadly distributed in the promoter regions of the four PeMADS genes, and no clear correlations of these CArG boxes were detected with their distinct expression profiles (Fig. 2C). Furthermore, with prediction of a conserved 12-bp motif with a 1-bp mutation allowance, motifs were identified between the promoter regions of PeMADS2 and PeMADS5, PeMADS3 and PeMADS4, and PeMADS6 and AtPI, but no motifs were present between the promoter sequences of AtAP3 and PeMADS2∼5 (Fig. 2D).

Bottom Line: The amplified promoter sequences of PeMADS2∼6 could drive beta-glucuronidase (GUS) gene expression in all floral organs, similar to their expression at the floral primordia stage.The promoter sequence of PeMADS4, exclusively expressed in lip and column, showed a 1.6∼3-fold higher expression in lip/column than in sepal/petal.Furthermore, we noted a 4.9-fold increase in histone acetylation (H3K9K14ac) in the translation start region of PeMADS4 in lip as compared in petal.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.

ABSTRACT
Five B-class MADS-box genes, including four APETALA3 (AP3)-like PeMADS2∼5 and one PISTILLATA (PI)-like PeMADS6, specify the spectacular flower morphology in orchids. The PI-like PeMADS6 ubiquitously expresses in all floral organs. The four AP3-like genes, resulted from two duplication events, express ubiquitously at floral primordia and early floral organ stages, but show distinct expression profiles at late floral organ primordia and floral bud stages. Here, we isolated the upstream sequences of PeMADS2∼6 and studied the regulatory mechanism for their distinct gene expression. Phylogenetic footprinting analysis of the 1.3-kb upstream sequences of AP3-like PeMADS2∼5 showed that their promoter regions have sufficiently diverged and contributed to their subfunctionalization. The amplified promoter sequences of PeMADS2∼6 could drive beta-glucuronidase (GUS) gene expression in all floral organs, similar to their expression at the floral primordia stage. The promoter sequence of PeMADS4, exclusively expressed in lip and column, showed a 1.6∼3-fold higher expression in lip/column than in sepal/petal. Furthermore, we noted a 4.9-fold increase in histone acetylation (H3K9K14ac) in the translation start region of PeMADS4 in lip as compared in petal. All these results suggest that the regulation via the upstream sequences and increased H3K9K14ac level may act synergistically to display distinct expression profiles of the AP3-like genes at late floral organ primordia stage for Phalaenopsis floral morphogenesis.

Show MeSH