Epigenetic regulation of lignin biosynthesis in wood formation

Abstract

Introduction

Lignin is a phenolic polymer and a major component of wood, constituting c. 20–30% of the wood biomass. It is the key limiting factor for wood conversion efficiency because it must be removed to extract the other two wood components, cellulose (40–50% of wood) and hemicelluloses (20–30% of wood), for paper making (Sarkanen, 1976; Chiang, 2002; Ragauskas et al., 2006). Wood cellulose and hemicelluloses are potentially commercial feedstock for biofuel production (Sarkanen, 1976). Lignin is synthesized through the polymerization of three canonical monolignols, p-coumaryl, coniferyl, and sinapyl alcohols, known as the p-hydroxyphenyl (H), guaiacyl (G), and syringyl (S) units, respectively (Freudenberg, 1965; Sarkanen & Ludwig, 1971; Higuchi, 1997). Monolignols are biosynthesized from phenylalanine through a complex network pathway mediated by > 20 pathway enzymes. The mediation requires combined catalysis functions of individual enzymes (Higuchi, 1997; Sulis et al., 2023; Li et al., 2024), enzyme complexes (Chen et al., 2011, 2014; Lin et al., 2015; Yan et al., 2018; X. Zhao et al., 2023), and protein phosphorylation (Wang et al., 2015) to produce monolignols for lignin polymerization.

At the genetic level, the expression of genes encoding pathway enzymes controls monolignol production, affecting lignin biosynthesis and thus the recalcitrance of wood to conversion. Transregulation of monolignol gene expression has been extensively studied. Approximately 50 transcription factors (TFs) belonging to MYB, NAC, WRKY, ERF, WBLH, TZF, HSF, MADS-box, and LBD families have been implicated in such regulation (Supporting Information Table S1; Li et al., 2024). Only a few TFs, such as PtoMYB221, PtrMYB092, PtrMYB161, PtrMYB189, PdMYB221/LTF1, BpNAC012, PtrHSFB3-1, and PagERF81, have been demonstrated to directly regulate monolignol biosynthesis genes (including COMT2, CAld5H1, CAld5H2, CCoAOMT2, CCoAOMT1, 4CL5, C3H3, C4H1, PAL2, PAL4, PAL5, CSE1, 4CL1, CCR2, and CCR1) (Tang et al., 2015; Gui et al., 2019; H. Chen et al., 2019; Hu et al., 2019; Wang et al., 2020; Liu et al., 2021; X. W. Zhao et al., 2023). These TFs bind to the promoters of monolignol genes and interact with other regulators to exert activating or repressive effects on lignin biosynthesis.

Gene expression can be controlled by histone modifications, including acetylation and methylation (Grunstein, 1997; Berger, 2002; Reyes et al., 2002; Kouzarides, 2007). Histone acetylation plays a crucial role in regulating gene expression during various developmental processes in plants. The dynamic balance of histone acetylation and deacetylation is regulated by histone acetyltransferases (HATs) (Balasubramanian et al., 2002; Berger, 2002) and histone deacetylases (HDAs or HDACs) (Roth & Allis, 1996; Kadosh & Struhl, 1997; Strahl & Allis, 2000). Histone acetylation is catalyzed by HAT complexes (Shahbazian & Grunstein, 2007), often containing GENERAL CONTROL NON-DEREPRESSIBLE5 (GCN5) as the catalytic subunit (Brownell et al., 1996) and ALTERATION/DEFICIENCY IN ACTIVATION2 (ADA2) as an adaptor protein (Grant et al., 1997). ADA2 enhances the HAT activity of GCN5 (Balasubramanian et al., 2002). Conversely, histone deacetylation is catalyzed not only by HDAC corepressor complexes (Rundlett et al., 1996; Long et al., 2006; Gonzalez et al., 2007; Krogan et al., 2012; Hung et al., 2018) but also primarily through direct interactions with certain transregulators (Liu et al., 2014; W. Q. Chen et al., 2019; Kumar et al., 2021).

Histone deacetylases were confirmed to suppress the expression of target genes (FLC, MAF4, AGL19, AG, AP3, SEP3, or HSL1) to regulate flowering time or development, or seed germination by interacting with various TFs and binding to these genes' promoters (Yu et al., 2011; Krogan et al., 2012; Kim et al., 2013; Zhou et al., 2013; Zeng et al., 2019). These HDACs also respond to abiotic stresses, exhibiting similar regulatory functions (Kim et al., 2008; Luo et al., 2012; Mehdi et al., 2015; Yang et al., 2020). HDA15, an essential HDAC, plays distinct roles in various plant developmental processes. It specifically interacts with PIF3, playing a role in photomorphogenesis in Arabidopsis (Liu et al., 2013). HDA15 forms a complex with the MYB96 protein to negatively regulate ABA signaling genes (ROP6, ROP10, and ROP11) by deacetylation H3 and H4 histones at their binding sites (Lee & Seo, 2019). However, the function of HDACs in regulating lignin biosynthesis remains largely unknown.

In this study, we report the discovery of epigenetic regulation that represses lignin biosynthesis during wood formation in Populus trichocarpa. The HDAC PtrHDA15 acts as an epigenetic inhibitor and is recruited by the key wood-forming TF PtrbZIP44-A1 to the promoter of the target monolignol genes, PtrCCoAOMT2 and PtrCCR2. This recruitment leads to chromatin histone modifications that suppress these genes, consequently reducing lignin content in wood.