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

Title: 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.

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Research Organization:: Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)

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

DOE Contract Number:: AC05-76RL01830

OSTI ID:: 1437532

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

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

Publisher:: Springer

Country of Publication:: United States

Language:: English

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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
The roles of ABA in plant–pathogen interactions Cao, Feng Yi; Yoshioka, Keiko; Desveaux, Darrell Journal of Plant Research, Vol. 124, Issue 4 https://doi.org/10.1007/s10265-011-0409-y	journal	March 2011
Characterization of cis-elements required for vascular expression of the Cinnamoyl CoA Reductase gene and for protein-DNA complex formation Lacombe, Eric; Van Doorsselaere, Jan; Boerjan, Wout The Plant Journal, Vol. 23, Issue 5 https://doi.org/10.1046/j.1365-313x.2000.00838.x	journal	September 2000
Disruption of Mediator rescues the stunted growth of a lignin-deficient Arabidopsis mutant Bonawitz, Nicholas D.; Kim, Jeong Im; Tobimatsu, Yuki Nature, Vol. 509, Issue 7500, p. 376-380 https://doi.org/10.1038/nature13084	journal	March 2014
Pinoresinol-Lariciresinol Reductases with Opposite Enantiospecificity Determine the Enantiomeric Composition of Lignans in the Different Organs of Linum usitatissimum L. Hemmati, Shiva; Heimendahl, Cosima; Klaes, Michael Planta Medica, Vol. 76, Issue 09 https://doi.org/10.1055/s-0030-1250036	journal	May 2010
Knots in trees – A new rich source of lignans Holmbom, Bjarne; Eckerman, Christer; Eklund, Patrik Phytochemistry Reviews, Vol. 2, Issue 3 https://doi.org/10.1023/B:PHYT.0000045493.95074.a8	journal	January 2003
SMART: recent updates, new developments and status in 2015 Letunic, Ivica; Doerks, Tobias; Bork, Peer Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku949	journal	October 2014
MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0 Tamura, Koichiro; Stecher, Glen; Peterson, Daniel Molecular Biology and Evolution, Vol. 30, Issue 12 https://doi.org/10.1093/molbev/mst197	journal	October 2013
Dirigent Proteins from Cotton ( Gossypium sp.) for the Atropselective Synthesis of Gossypol Effenberger, Isabelle; Zhang, Bin; Li, Ling Angewandte Chemie International Edition, Vol. 54, Issue 49 https://doi.org/10.1002/anie.201507543	journal	October 2015

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