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An Arabidopsis gene regulatory network for secondary cell wall synthesis

Nature volume 517, pages 571–575 (2015)Cite this article

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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.

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Figure 1: Regulators of xylem development and secondary cell wall biosynthesis.
Figure 2: E2Fc represses secondary cell wall gene biosynthesis.
Figure 3: Tissue-specific VND7 regulation and VND7 targets.
Figure 4: Multiple transcription factors bind the CESA4 promoter.
Figure 5: The xylem-specific gene regulatory network is responsive to high salinity and iron deprivation.

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Acknowledgements

We thank M. Tierney (University of Vermont) for 35S::GFP seeds, T. Demura for VND7 resources, M.K. Barton for REV:GR seeds, E.P. Spalding for advice on manuscript revision, and C. Gutierrez for E2Fc RNAi and E2Fc N-terminal deletion overexpressor seeds and useful discussion. This research was supported by the Office of Science (BER) Department of Energy Grant DE-FG02-08ER64700DE (to S.P.H. and S.A.K.), National Institute of General Medical Sciences of the National Institutes of Health under award numbers RO1GM056006 and RC2GM092412 (to S.A.K.), National Institute of Health (R01GM107311) and National Science Foundation (IOS-1036491 and IOS-1352478) to K.D., USDA CRIS 1907-21000-030 to D.W. and L.F., a Royal Society UK Fellowship (to S.E.A.), and UC Davis Startup Funds and a Hellman Fellowship (to S.M.B).

Author information

Author notes

  1. L. Lin, G. Breton & S. A. Kay

    Present address: Present addresses: Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211, USA (L.L.); Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA (G.B.); Molecular and Computational Biology Section, University of Southern California, Los Angeles, California 90089, USA (S.A.K.).,

  2. M. Taylor-Teeples, L. Lin and M. de Lucas: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, California 95616, USA,

    M. Taylor-Teeples, M. de Lucas, G. Turco, T. W. Toal, A. Gaudinier, C. Wang, K. Dehesh & S. M. Brady

  2. Genome Center, University of California Davis, One Shields Avenue, Davis, California 95616, USA,

    M. Taylor-Teeples, M. de Lucas, G. Turco, T. W. Toal, A. Gaudinier, A. Tsoukalas, I. Tagkopoulos & S. M. Brady

  3. Biology Department, University of Massachusetts, Amherst, 01003, Massachusetts, USA

    L. Lin, N. F. Young, G. M. Trabucco, M. T. Veling, R. Lamothe, P. P. Handakumbura & S. P. Hazen

  4. Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, 94720, California, USA

    G. Xiong & M. Pauly

  5. Department of Plant Sciences, University of California Davis, One Shields Avenue, Davis, California 95616, USA,

    J. Corwin & D. J. Kliebenstein

  6. Department of Computer Science, University of California Davis, One Shields Avenue, Davis, California 95616, USA,

    A. Tsoukalas & I. Tagkopoulos

  7. Cold Spring Harbor Laboratory, Cold Spring Harbor, 11724, New York, USA

    L. Zhang & D. Ware

  8. US Department of Agriculture, Agricultural Research Service, Ithaca, 14853, New York, USA

    D. Ware

  9. Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, 92093, California, USA

    G. Breton, J. L. Pruneda-Paz & S. A. Kay

  10. Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK,

    S. E. Ahnert

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  1. M. Taylor-Teeples
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Contributions

M.T.-T., L.L. and M.d.L. contributed equally to this work. T.W.T. and A.G. contributed equally to this work. S.M.B. and S.P.H. contributed equally to this work. M.T.-T., L.L., M.d.L., S.M.B., and S.P.H. designed the research. M.T.-T., L.L., M.d.L., A.G., G.X., N.F.Y., G.M.T., M.T.V., R.L., P.P.H., C.W., and K.D. performed the research. M.T.-T., L.L., G.T., T.W.T., N.T., J.C., M.P., D.K., I.T., S.E.A., S.M.B. and S.P.H. analysed the data. L.Z., D.W., G.B., J.L.P.-P., and S.A.K. contributed new reagents/analytic tools. M.T.-T., L.L., G.M.T., S.M.B. and S.P.H. wrote the article. All authors discussed the results and commented on the manuscript.

Corresponding authors

Correspondence to S. P. Hazen or S. M. Brady.

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Extended data figures and tables

Extended Data Figure 1 Number of novel and previously described protein–DNA interactions and transcription factors involved in secondary cell wall biosynthesis and xylem development.

a, b, Venn diagrams of overlap between previously reported19 interactions (a) or transcription factors (b) and those of the xylem-specific gene regulatory network. *Includes genes that were not included in the yeast one hybrid screen.

Extended Data Figure 2 Activation or repression of VND7 by E2Fc is dynamic and dose-dependent.

a, Intensity of LUC bioluminescence quantified using Andor Solis image analysis software. Data are means ± s.d. (n = 20). Asterisks denote significance at P < 0.05 determined by Student’s t-test. b, Quantitative PCR with reverse transcription of E2Fc and VND7 transcripts in ΔN-E2Fc (E2Fc overexpressor line lacking the N-terminal domain) expressing plants versus Col-0 control. Red dashed line marks the point at which VND7 is unchanged compared to control. Each data point is an individual biological replicate with 3 technical replicates. c, 3-week-old tobacco leaves were infiltrated with the p19 silencing inhibitor and either the reporter VND7p::GUS or VND7p::GUS and either 35S::E2Fc::MYC or 35S::RBR::GFP, or both. Extracted protein was then used in a quantitative MUG fluorescent assay, where relative fluorescence was measured 60 min after incubation with substrate. Data are means ± s.d., n = 3.

Extended Data Figure 3 Binding of NST2 and SND1 to fragments of CESA7, CESA8, and KOR promoters.

a–f, Electrophoretic mobility shift assays showing NST2 (a–d) and SND1 (e–f) protein specifically binds the promoters of cellulose-associated genes. Probe was incubated in the absence or presence of GST or GST:SND1 protein extracts. The arrowheads indicate the specific protein–DNA complexes, while arrows indicate free probe.

Extended Data Figure 4 Sub-networks of network genes differentially expressed in response to iron deprivation of high salinity.

a, b, Sub-network of genes with q values of ≤ 0.01 and whose fold change between mean expression values was ≥ 1.5 in either direction in iron deprivation (a) or high NaCl (b) stress microarray data set. Nodes are coloured according to in-degree as shown on scale bars below sub-networks. Transcription factors with the highest in-degree are labelled and indicated with a black circle.

Extended Data Figure 5 The reconstructed gene regulatory consensus network based on analysis of the iron-deprivation expression data set by different network inference methods.

a, Unsupervised; b, supervised in the first pass; c, supervised after the validated two connections have been added in the training set. Edge transparency denotes P ≤ 0.06 for the Pearson correlation coefficient (PCC); edge width is proportional to PCC; edge value corresponds to the total edge score; a greater value corresponds to a more significant score. Yellow and red nodes correspond to transcription factor and target gene nodes, respectively; black and blue edges denote Y1H-derived and inferred interactions, respectively.

Extended Data Figure 6 Iron deprivation and NaCl stress influences lignin and phenylpropanoid biosynthesis associated gene expression.

a, No change was observed in the expression of 4CL1::GFP in 4 days after imbibition (DAI) roots transferred to a control media (left, n = 4) or media with 140 mM NaCl for 48 h (right, n = 4). b, Increased fuchsin staining of xylem cells as well as of cell walls of non-vascular cells in 4 DAI roots transferred to a control media (left) or media with an iron chelator for 72 h (right). c, No change was observed in the expression of VND7::YFP in 4 DAI roots transferred to a control media (left, n = 4) or media with an iron chelator for 72 h (right, n = 5).

Extended Data Figure 7 The reconstructed gene regulatory consensus network based on analysis of the salt-stress expression data set by different network inference methods.

a, Unsupervised; b, supervised in the first pass; c, supervised after the validated two connections have been added in the training set. Edge transparency denotes P ≤ 0.06 for the Pearson correlation coefficient (PCC); edge width is proportional to PCC; edge value corresponds to the total edge score; a greater value corresponds to a more significant score. Yellow and red nodes correspond to transcription factor and target gene nodes, respectively; black and blue edges denote Y1H-derived and inferred interactions, respectively.

Extended Data Figure 8 Schematic diagram of dual-luciferase reporter vector development.

a, Three distinct donor vectors harbouring either the transcription factor, VP64 activation domain fused to the 35S minimal promoter, or a promoter fragment. b, The dual reporter vector, pLAH-LARm, is then recombined with the three donor vectors to generate the single reporter vector (c).

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Taylor-Teeples, M., Lin, L., de Lucas, M. et al. An Arabidopsis gene regulatory network for secondary cell wall synthesis. Nature 517, 571–575 (2015). https://doi.org/10.1038/nature14099

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