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      Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development

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          Abstract

          Transcript abundance of roughly a third of expressed Arabidopsis thaliana genes is circadian-regulated.

          Abstract

          Background

          As nonmotile organisms, plants must rapidly adapt to ever-changing environmental conditions, including those caused by daily light/dark cycles. One important mechanism for anticipating and preparing for such predictable changes is the circadian clock. Nearly all organisms have circadian oscillators that, when they are in phase with the Earth's rotation, provide a competitive advantage. In order to understand how circadian clocks benefit plants, it is necessary to identify the pathways and processes that are clock controlled.

          Results

          We have integrated information from multiple circadian microarray experiments performed on Arabidopsis thaliana in order to better estimate the fraction of the plant transcriptome that is circadian regulated. Analyzing the promoters of clock-controlled genes, we identified circadian clock regulatory elements correlated with phase-specific transcript accumulation. We have also identified several physiological pathways enriched for clock-regulated changes in transcript abundance, suggesting they may be modulated by the circadian clock.

          Conclusion

          Our analysis suggests that transcript abundance of roughly one-third of expressed A. thaliana genes is circadian regulated. We found four promoter elements, enriched in the promoters of genes with four discrete phases, which may contribute to the time-of-day specific changes in the transcript abundance of these genes. Clock-regulated genes are over-represented among all of the classical plant hormone and multiple stress response pathways, suggesting that all of these pathways are influenced by the circadian clock. Further exploration of the links between the clock and these pathways will lead to a better understanding of how the circadian clock affects plant growth and leads to improved fitness.

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          Most cited references83

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          Gene Ontology: tool for the unification of biology

          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            Multiple sequence alignment with the Clustal series of programs.

            R Chenna (2003)
            The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also the robustness, portability and user-friendliness of the programs. New features include NEXUS and FASTA format output, printing range numbers and faster tree calculation. Although, Clustal was originally developed to run on a local computer, numerous Web servers have been set up, notably at the EBI (European Bioinformatics Institute) (http://www.ebi.ac.uk/clustalw/).
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              Jasmonates: an update on biosynthesis, signal transduction and action in plant stress response, growth and development.

              Jasmonates are ubiquitously occurring lipid-derived compounds with signal functions in plant responses to abiotic and biotic stresses, as well as in plant growth and development. Jasmonic acid and its various metabolites are members of the oxylipin family. Many of them alter gene expression positively or negatively in a regulatory network with synergistic and antagonistic effects in relation to other plant hormones such as salicylate, auxin, ethylene and abscisic acid. This review summarizes biosynthesis and signal transduction of jasmonates with emphasis on new findings in relation to enzymes, their crystal structure, new compounds detected in the oxylipin and jasmonate families, and newly found functions. Crystal structure of enzymes in jasmonate biosynthesis, increasing number of jasmonate metabolites and newly identified components of the jasmonate signal-transduction pathway, including specifically acting transcription factors, have led to new insights into jasmonate action, but its receptor(s) is/are still missing, in contrast to all other plant hormones.
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                Author and article information

                Journal
                Genome Biol
                Genome Biology
                BioMed Central
                1465-6906
                1465-6914
                2008
                18 August 2008
                : 9
                : 8
                : R130
                Affiliations
                [1 ]Department of Plant Biology, College of Biological Sciences, One Shields Avenue, University of California, Davis, California 95616, USA
                [2 ]Present address: Department of Biochemistry and Cell Biology, Rice University, Main Street, Houston, Texas 77005, USA
                [3 ]Center for Biomathematical Technology, Box 800735, University of Virginia Health Sciences System, Charlottesville, Virginia 22908, USA
                [4 ]Present address: Customized Online Biomathematical Research Applications, Glenaire Drive, Charlottesville, Virginia 22901, USA
                [5 ]Department of Biochemistry, The Scripps Research Institute, North Torrey Pines Road, La Jolla, California 92037, USA
                [6 ]Present address: Section of Cell and Developmental Biology, University of California at San Diego, Gilman Drive, La Jolla, California 92093, USA
                Article
                gb-2008-9-8-r130
                10.1186/gb-2008-9-8-r130
                2575520
                18710561
                3233627b-629f-469f-a384-9836ea7e9ec2
                Copyright © 2008 Covington et al.; licensee BioMed Central Ltd.

                This is an open access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 30 June 2008
                : 7 August 2008
                : 18 August 2008
                Categories
                Research

                Genetics
                Genetics

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