title: An Arabidopsis gene regulatory network for secondary cell wall synthesis.
abstract: The plant cell wall is an important factor for determining cell shape, function and response to the environment. Secondary cell walls, such as those found in xylem, are composed of cellulose, hemicelluloses and lignin and account for the bulk of plant biomass. The coordination between transcriptional regulation of synthesis for each polymer is complex and vital to cell function. A regulatory hierarchy of developmental switches has been proposed, although the full complement of regulators remains unknown. Here we present a protein-DNA network between Arabidopsis thaliana transcription factors and secondary cell wall metabolic genes with gene expression regulated by a series of feed-forward loops. This model allowed us to develop and validate new hypotheses about secondary wall gene regulation under abiotic stress. Distinct stresses are able to perturb targeted genes to potentially promote functional adaptation. These interactions will serve as a foundation for understanding the regulation of a complex, integral plant component.
authors.affiliation: 1] Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, California 95616, USA [2] Genome Center, University of California Davis, One Shields Avenue, Davis, California 95616, USA.
authors.forename: M
authors.initials: M
authors.lastname: Taylor-Teeples
authors.affiliation: Biology Department, University of Massachusetts, Amherst, Massachusetts 01003, USA.
authors.forename: L
authors.initials: L
authors.lastname: Lin
authors.affiliation: 1] Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, California 95616, USA [2] Genome Center, University of California Davis, One Shields Avenue, Davis, California 95616, USA.
authors.forename: M
authors.initials: M
authors.lastname: de Lucas
authors.affiliation: 1] Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, California 95616, USA [2] Genome Center, University of California Davis, One Shields Avenue, Davis, California 95616, USA.
authors.forename: G
authors.initials: G
authors.lastname: Turco
authors.affiliation: 1] Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, California 95616, USA [2] Genome Center, University of California Davis, One Shields Avenue, Davis, California 95616, USA.
authors.forename: T W
authors.initials: TW
authors.lastname: Toal
authors.affiliation: 1] Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, California 95616, USA [2] Genome Center, University of California Davis, One Shields Avenue, Davis, California 95616, USA.
authors.forename: A
authors.initials: A
authors.lastname: Gaudinier
authors.affiliation: Biology Department, University of Massachusetts, Amherst, Massachusetts 01003, USA.
authors.forename: N F
authors.initials: NF
authors.lastname: Young
authors.affiliation: Biology Department, University of Massachusetts, Amherst, Massachusetts 01003, USA.
authors.forename: G M
authors.initials: GM
authors.lastname: Trabucco
authors.affiliation: Biology Department, University of Massachusetts, Amherst, Massachusetts 01003, USA.
authors.forename: M T
authors.initials: MT
authors.lastname: Veling
authors.affiliation: Biology Department, University of Massachusetts, Amherst, Massachusetts 01003, USA.
authors.forename: R
authors.initials: R
authors.lastname: Lamothe
authors.affiliation: Biology Department, University of Massachusetts, Amherst, Massachusetts 01003, USA.
authors.forename: P P
authors.initials: PP
authors.lastname: Handakumbura
authors.affiliation: Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720, USA.
authors.forename: G
authors.initials: G
authors.lastname: Xiong
authors.affiliation: Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, California 95616, USA.
authors.forename: C
authors.initials: C
authors.lastname: Wang
authors.affiliation: Department of Plant Sciences, University of California Davis, One Shields Avenue, Davis, California 95616, USA.
authors.forename: J
authors.initials: J
authors.lastname: Corwin
authors.affiliation: 1] Genome Center, University of California Davis, One Shields Avenue, Davis, California 95616, USA [2] Department of Computer Science, University of California Davis, One Shields Avenue, Davis, California 95616, USA.
authors.forename: A
authors.initials: A
authors.lastname: Tsoukalas
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
authors.forename: L
authors.initials: L
authors.lastname: Zhang
authors.affiliation: 1] Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA [2] US Department of Agriculture, Agricultural Research Service, Ithaca, New York 14853, USA.
authors.forename: D
authors.initials: D
authors.lastname: Ware
authors.affiliation: Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720, USA.
authors.forename: M
authors.initials: M
authors.lastname: Pauly
authors.affiliation: Department of Plant Sciences, University of California Davis, One Shields Avenue, Davis, California 95616, USA.
authors.forename: D J
authors.initials: DJ
authors.lastname: Kliebenstein
authors.affiliation: Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, California 95616, USA.
authors.forename: K
authors.initials: K
authors.lastname: Dehesh
authors.affiliation: 1] Genome Center, University of California Davis, One Shields Avenue, Davis, California 95616, USA [2] Department of Computer Science, University of California Davis, One Shields Avenue, Davis, California 95616, USA.
authors.forename: I
authors.initials: I
authors.lastname: Tagkopoulos
authors.affiliation: Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA.
authors.forename: G
authors.initials: G
authors.lastname: Breton
authors.affiliation: Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA.
authors.forename: J L
authors.initials: JL
authors.lastname: Pruneda-Paz
authors.affiliation: Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK.
authors.forename: S E
authors.initials: SE
authors.lastname: Ahnert
authors.affiliation: Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA.
authors.forename: S A
authors.initials: SA
authors.lastname: Kay
authors.affiliation: Biology Department, University of Massachusetts, Amherst, Massachusetts 01003, USA.
authors.forename: S P
authors.initials: SP
authors.lastname: Hazen
authors.affiliation: 1] Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, California 95616, USA [2] Genome Center, University of California Davis, One Shields Avenue, Davis, California 95616, USA.
authors.forename: S M
authors.initials: SM
authors.lastname: Brady
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D002473:Cell Wall / Q000378:metabolism*; D018744:DNA, Plant / Q000235:genetics / Q000378:metabolism; D050684:E2F Transcription Factors / Q000378:metabolism; D005246:Feedback; D018507:Gene Expression Regulation, Developmental / Q000235:genetics; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D053263:Gene Regulatory Networks / Q000235:genetics*; D000090463:Iron Deficiencies; D009928:Organ Specificity; D011401:Promoter Regions, Genetic / Q000235:genetics; D015203:Reproducibility of Results; D054712:Salinity; D013997:Time Factors; D014157:Transcription Factors / Q000378:metabolism*; D052584:Xylem / Q000235:genetics / Q000254:growth & development / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; D018744:DNA, Plant; D050684:E2F Transcription Factors; C514752:E2FC protein, Arabidopsis; D014157:Transcription Factors; C583237:VND7 protein, Arabidopsis