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

Abstract

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.

Quantitative Proteomic Analysis of Alligator Weed Leaves Reveals That Cationic Peroxidase 1 Plays Vital Roles in the Potassium Deficiency Stress Response

“…Thus, in our study, the high expression of FPGS in the alligator weed leaves could improve the lignin content in the cell wall in order to protect cells under LK stress. Corbin et al reported that some direct proteins (DIRs) can be involved in secondary cell wall biosynthesis and plant defense in flax [24]. In our study, one DIR was up-regulated, underlying the universal roles DIRs play in plant abiotic stress response.…”

The Evolution of Flavonoid Biosynthesis: A Bryophyte Perspective

“…For MpMYB14, this includes the three DIR genes discussed earlier as well as other DIR genes that have been shown to be direct targets (Kubo et al, 2018). Co-expression analysis in flax found that MYB TFs were up-regulated along with DIR genes during secondary wall biosynthesis (Corbin et al, 2018), suggesting that MYB proteins could control DIR expression in both angiosperms and bryophytes.…”

“…The role of DIRs in determining stereospecificity has been best described in the formation of lignans, a class of 8-8' linked C 6 C 3 phenylpropanoid dimers involved in pathogen resistance, for example in the production of (+)-or (−)-pinoresinol compounds in flax (Linum usitatissimum) and pea (Pisum sativum) Corbin et al, 2018). The X-ray crystal structure of PsDRR206 involved in (+)-pinoresinol formation suggested that the active protein had a trimeric structure .…”

“…DIR gene families can be quite large, with 26 genes in Arabidopsis (Paniagua et al, 2017) and 44 genes in flax (of which seven appeared to be gene fragments or result from chromosomal rearrangements; Corbin et al, 2018). Of the 37 genes with classical DIR structure in flax, 15 paralogous gene pairs were identified.…”

Feasible Production of Lignans and Neolignans in Root-Derived In Vitro Cultures of Flax (Linum usitatissimum L.)

“…The early biosynthetic steps of lignans' formation have been well characterized [17]. First, a dirigent protein (DIR) (LuDIR1, LuDIR5 or LuDIR6 for in flax) directs the stereoselective radical-radical coupling of two E-coniferyl alcohol radical units into pinoresinol [18][19][20]. Pinoresinol is then reduced into secoisolariciresinol by a stereoselective pinoresinol-lariciresinol reductase (PLR) enzyme, via lariciresinol formation.…”