Do Transcription Factors Play Special Roles in Adaptive Variation?

Martin, Cathie; Ellis, Noel; Rook, Fred

doi:10.1104/pp.110.161331

Cited by 34 publications

(26 citation statements)

References 57 publications

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“…Martin demonstrated that the regulatory sequences of most plant genes resided within a region 500 bp upstream of the start codon [56]. Accordingly, a promoter analysis of the 50 cotton MDH genes using the PlantCARE database revealed that most of the cis -regulatory elements were conserved in the 1500 bp upstream of the translational start site (S6 Table).…”

Section: Resultsmentioning

confidence: 99%

Comparative Genome-Wide Analysis of the Malate Dehydrogenase Gene Families in Cotton

2016

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Malate dehydrogenases (MDHs) play crucial roles in the physiological processes of plant growth and development. In this study, 13 and 25 MDH genes were identified from Gossypium raimondii and Gossypium hirsutum, respectively. Using these and 13 previously reported Gossypium arboretum MDH genes, a comparative molecular analysis between identified MDH genes from G. raimondii, G. hirsutum, and G. arboretum was performed. Based on multiple sequence alignments, cotton MDHs were divided into five subgroups: mitochondrial MDH, peroxisomal MDH, plastidial MDH, chloroplastic MDH and cytoplasmic MDH. Almost all of the MDHs within the same subgroup shared similar gene structure, amino acid sequence, and conserved motifs in their functional domains. An analysis of chromosomal localization suggested that segmental duplication played a major role in the expansion of cotton MDH gene families. Additionally, a selective pressure analysis indicated that purifying selection acted as a vital force in the evolution of MDH gene families in cotton. Meanwhile, an expression analysis showed the distinct expression profiles of GhMDHs in different vegetative tissues and at different fiber developmental stages, suggesting the functional diversification of these genes in cotton growth and fiber development. Finally, a promoter analysis indicated redundant but typical cis-regulatory elements for the potential functions and stress activity of many MDH genes. This study provides fundamental information for a better understanding of cotton MDH gene families and aids in functional analyses of the MDH genes in cotton fiber development.

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Section: Resultsmentioning

confidence: 99%

Comparative Genome-Wide Analysis of the Malate Dehydrogenase Gene Families in Cotton

2016

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“…It was proposed that the regulatory sequences for most plant genes are within 500 bp (or more conservatively, the length of the target gene) upstream from the start codon (Martin et al 2010). To study the cis-regulatory structures of melon PSYs, DNA sequences that are 1.34 and 1.65 Kb upstream of the translational start of CmPSY1 and CmPSY2 were obtained by inverse PCR.…”

Section: Cis-regulatory Structures Of Cmpsy1 and Cmpsy2mentioning

confidence: 99%

Expression, subcellular localization, and cis-regulatory structure of duplicated phytoene synthase genes in melon (Cucumis melo L.)

Qin

Coku

Inoue

et al. 2011

Planta

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Carotenoids perform many critical functions in plants, animals, and humans. It is therefore important to understand carotenoid biosynthesis and its regulation in plants. Phytoene synthase (PSY) catalyzes the first committed and rate-limiting step in carotenoid biosynthesis. While PSY is present as a single copy gene in Arabidopsis, duplicated PSY genes have been identified in many economically important monocot and dicot crops. CmPSY1 was previously identified from melon (Cucumis melo L.), but was not functionally characterized. We isolated a second PSY gene, CmPSY2, from melon in this work. CmPSY2 possesses a unique intron/exon structure that has not been observed in other plant PSYs. Both CmPSY1 and CmPSY2 are functional in vitro, but exhibit distinct expression patterns in different melon tissues and during fruit development, suggesting differential regulation of the duplicated melon PSY genes. In vitro chloroplast import assays verified the plastidic localization of CmPSY1 and CmPSY2 despite the lack of an obvious plastid target peptide in CmPSY2. Promoter motif analysis of the duplicated melon and tomato PSY genes and the Arabidopsis PSY revealed distinctive cis-regulatory structures of melon PSYs and identified gibberellin-responsive motifs in all PSYs except for SlPSY1, which has not been reported previously. Overall, these data provide new insights into the evolutionary history of plant PSY genes and the regulation of PSY expression by developmental and environmental signals that may involve different regulatory networks.

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“…One explanation is regulation. Clearly dispersed genes can be coregulated through a common transcription factor, and there are some excellent examples of coordinate regulation of unlinked genes for metabolic pathways in plants (Martin et al, 2010). However, physical clustering of functionally related genes in eukaryotes has the potential to add another tier to the hierarchy of gene regulation, providing mechanisms for the coordinated regulation of gene expression at the levels of nuclear organization and/or chromatin (Hurst et al, 2004;Sproul et al, 2005;Osbourn and Field, 2009).…”

Section: What Is the Significance Of Clustering?mentioning

confidence: 99%

Gene Clusters for Secondary Metabolic Pathways: An Emerging Theme in Plant Biology

Osbourn

2010

Plant Physiology

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Do Transcription Factors Play Special Roles in Adaptive Variation?

Cited by 34 publications

References 57 publications

Comparative Genome-Wide Analysis of the Malate Dehydrogenase Gene Families in Cotton

Comparative Genome-Wide Analysis of the Malate Dehydrogenase Gene Families in Cotton

Expression, subcellular localization, and cis-regulatory structure of duplicated phytoene synthase genes in melon (Cucumis melo L.)

Gene Clusters for Secondary Metabolic Pathways: An Emerging Theme in Plant Biology

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