A genome-wide analysis of the flax (Linum usitatissimum L.) dirigent protein family: from gene identification and evolution to differential regulation

Corbin, Cyrielle; Drouet, Samantha; Markulin, Lucija; Auguin, Daniel; Lainé, Éric; Davin, Laurence B.; Cort, John R.; Lewis, Norman G.; Hano, Christophe

doi:10.1007/s11103-018-0725-x

A genome-wide analysis of the flax (Linum usitatissimum L.) dirigent protein family: from gene identification and evolution to differential regulation

Journal Article · Mon Apr 30 00:00:00 EDT 2018 · Plant molecular biology

DOI:https://doi.org/10.1007/s11103-018-0725-x· OSTI ID:1437532

Corbin, Cyrielle; Drouet, Samantha; Markulin, Lucija; Auguin, Daniel; Lainé, Éric; ; ; ;

Identification of DIR encoding genes in flax genome. Analysis of phylogeny, gene/protein structures and evolution. Identification of new conserved motifs linked to biochemical functions. Investigation of spatio-temporal gene expression and response to stress. Dirigent proteins (DIRs) were discovered during 8-8' lignan biosynthesis studies, through identification of stereoselective coupling to afford either (+)- or (-)-pinoresinols from E-coniferyl alcohol. DIRs are also involved or potentially involved in terpenoid, allyl/propenyl phenol lignan, pterocarpan and lignin biosynthesis. DIRs have very large multigene families in different vascular plants including flax, with most still of unknown function. DIR studies typically focus on a small subset of genes and identification of biochemical/physiological functions. Herein, a genome-wide analysis and characterization of the predicted flax DIR 44-membered multigene family was performed, this species being a rich natural grain source of 8-8' linked secoisolariciresinol-derived lignan oligomers. All predicted DIR sequences, including their promoters, were analyzed together with their public gene expression datasets. Expression patterns of selected DIRs were examined using qPCR, as well as through clustering analysis of DIR gene expression. These analyses further implicated roles for specific DIRs in (-)-pinoresinol formation in seed-coats, as well as (+)-pinoresinol in vegetative organs and/or specific responses to stress. Phylogeny and gene expression analysis segregated flax DIRs into six distinct clusters with new cluster-specific motifs identified. We propose that these findings can serve as a foundation to further systematically determine functions of DIRs, i.e. other than those already known in lignan biosynthesis in flax and other species. Given the differential expression profiles and inducibility of the flax DIR family, we provisionally propose that some DIR genes of unknown function could be involved in different aspects of secondary cell wall biosynthesis and plant defense.

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)

DOE Contract Number:: AC05-76RL01830

OSTI ID:: 1437532

Report Number(s):: PNNL-SA-131411; 48403; 49285; 44716; KP1704020

Journal Information:: Plant molecular biology, Journal Name: Plant molecular biology Journal Issue: 1-2 Vol. 97; ISSN 0167-4412

Publisher:: Springer

Country of Publication:: United States

Language:: English

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Eucalyptus hairy roots, a fast, efficient and versatile tool to explore function and expression of genes involved in wood formation Plasencia, Anna; Soler, Marçal; Dupas, Annabelle Plant Biotechnology Journal, Vol. 14, Issue 6 https://doi.org/10.1111/pbi.12502	journal	November 2015
Opposite Stereoselectivities of Dirigent Proteins in Arabidopsis and Schizandra Species Kim, Kye-Won; Moinuddin, Syed G. A.; Atwell, Kathleen M. Journal of Biological Chemistry, Vol. 287, Issue 41 https://doi.org/10.1074/jbc.M112.387423	journal	August 2012
Pinoresinol–lariciresinol reductase gene expression and secoisolariciresinol diglucoside accumulation in developing flax (Linum usitatissimum) seeds Hano, C.; Martin, I.; Fliniaux, O. Planta, Vol. 224, Issue 6 https://doi.org/10.1007/s00425-006-0308-y	journal	May 2006
The MYB36 transcription factor orchestrates Casparian strip formation Kamiya, Takehiro; Borghi, Monica; Wang, Peng Proceedings of the National Academy of Sciences, Vol. 112, Issue 33 https://doi.org/10.1073/pnas.1507691112	journal	June 2015
Casparian strip diffusion barrier in Arabidopsis is made of a lignin polymer without suberin Naseer, S.; Lee, Y.; Lapierre, C. Proceedings of the National Academy of Sciences, Vol. 109, Issue 25 https://doi.org/10.1073/pnas.1205726109	journal	June 2012
The AmMYB308 and AmMYB330 Transcription Factors from Antirrhinum Regulate Phenylpropanoid and Lignin Biosynthesis in Transgenic Tobacco Tamagnone, Lodovico; Merida, Angel; Parr, Adrian The Plant Cell, Vol. 10, Issue 2 https://doi.org/10.1105/tpc.10.2.135	journal	February 1998
Dirigent Protein-Mediated Lignan and Cyanogenic Glucoside Formation in Flax Seed: Integrated Omics and MALDI Mass Spectrometry Imaging Dalisay, Doralyn S.; Kim, Kye Won; Lee, Choonseok Journal of Natural Products, Vol. 78, Issue 6 https://doi.org/10.1021/acs.jnatprod.5b00023	journal	May 2015
Flaxseed as a functional food source Oomah, B. Dave Journal of the Science of Food and Agriculture, Vol. 81, Issue 9 https://doi.org/10.1002/jsfa.898	journal	January 2001
Plant cis-acting regulatory DNA elements (PLACE) database: 1999 Higo, K.; Ugawa, Y.; Iwamoto, M. Nucleic Acids Research, Vol. 27, Issue 1 https://doi.org/10.1093/nar/27.1.297	journal	January 1999
The cell biology of lignification in higher plants Barros, Jaime; Serk, Henrik; Granlund, Irene Annals of Botany, Vol. 115, Issue 7 https://doi.org/10.1093/aob/mcv046	journal	April 2015
The genome of flax ( Linum usitatissimum ) assembled de novo from short shotgun sequence reads Wang, Zhiwen; Hobson, Neil; Galindo, Leonardo The Plant Journal, Vol. 72, Issue 3 https://doi.org/10.1111/j.1365-313X.2012.05093.x	journal	August 2012

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Linum Lignan and Associated Biochemical Pathways in Human Health and Plant Defense

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A genome-wide analysis of the flax (Linum usitatissimum L.) dirigent protein family: from gene identification and evolution to differential regulation

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