Arabidopsis genes IRREGULAR XYLEM (IRX15) and IRX15L encode DUF579‐containing proteins that are essential for normal xylan deposition in the secondary cell wall

Abstract

SUMMARYThere are 10 genes in the Arabidopsis genome that contain a domain described in the Pfam database as domain of unknown function 579 (DUF579). Although DUF579 is widely distributed in eukaryotic species, there is no direct experimental evidence to assign a function to it. Five of the 10 Arabidopsis DUF579 family members are co-expressed with marker genes for secondary cell wall formation. Plants in which two closely related members of the DUF579 family have been disrupted by T-DNA insertions contain less xylose in the secondary cell wall as a result of decreased xylan content, and exhibit mildly distorted xylem vessels. Consequently we have named these genes IRREGULAR XYLEM 15 (IRX15) and IRX15L. These mutant plants exhibit many features of previously described xylan synthesis mutants, such as the replacement of glucuronic acid side chains with methylglucuronic acid side chains. By contrast, immunostaining of xylan and transmission electron microscopy (TEM) reveals that the walls of these irx15 irx15l double mutants are disorganized, compared with the wild type or other previously described xylan mutants, and exhibit dramatic increases in the quantity of sugar released in cell wall digestibility assays. Furthermore, localization studies using fluorescent fusion proteins label both the Golgi and also an unknown intracellular compartment. These data are consistent with irx15 and irx15l defining a new class of genes involved in xylan biosynthesis. How these genes function during xylan biosynthesis and deposition is discussed.

Putative Glycosyltransferases and Other Plant Golgi Apparatus Proteins Are Revealed by LOPIT Proteomics

“…Consistent with high pectin synthesis in the callus cells, we identified GAUT1, GAUT7, and many other GAUT family members in GT8 (Sterling et al, 2006;Atmodjo et al, 2011) as well as ARAD1 and XGD1 in GT47, involved in arabinan and xylogalacturonan synthesis, respectively (Harholt et al, 2006;Jensen et al, 2008). We also detected enzymes likely involved in primary cell wall glucuronoarabinoxylan synthesis: IRX10-L, IRX14, and two IRX15/DUF579 homologs (Brown et al, 2009(Brown et al, , 2011Wu et al, 2010;Jensen et al, 2011), and GUX3, a homolog of the GUX1 and GUX2 xylan glucuronosyltransferases (Mortimer et al, 2010). Proteins of extensin glycosylation (RRA3 and XEG113; Velasquez et al, 2011) and possibly glucomannan synthesis (CslD2 and CslD3; Yin et al, 2011) were identified as well, indicating that LOPIT also detects proteins synthesizing relatively minor cell wall components.…”

An Arabidopsis Cell Wall Proteoglycan Consists of Pectin and Arabinoxylan Covalently Linked to an Arabinogalactan Protein

“…Pectin and xylan synthesis occurs in the Golgi (Mohnen, 2008;Brown et al, 2011), and AGP synthesis initiates in the endoplasmic reticulum and continues in the Golgi (Oka et al, 2010;Wu et al, 2010). Thus, one possible mechanism for APAP1 biosynthesis is the addition of glycans onto AGP57C by either the consecutive addition of one residue at a time or by block addition, possibly occurring within the Golgi apparatus (Atmodjo et al, 2011(Atmodjo et al, , 2013.…”

Systematic Identification of Functional Plant Modules through the Integration of Complementary Data Sources

“…6A), is derived from the GO term "chitin metabolic process" and also includes some PPIs, TF targets, and AraNet edges. The module contains five true-positive genes, MYB DOMAIN PROTEIN63 (MYB63; Zhou et al, 2009), IRREGULAR XYLEM15 (IRX15) and IRX15-L (Brown et al, 2011), NAC DOMAIN CONTAINING PROTEIN73 (ANAC073) (Zhong et al, 2008), and REDUCED WALL ACETYLATION1 (RWA1) (Lee et al, 2011), all of which were correctly predicted to be involved in cell wall biogenesis. MYB63 and ANAC073 are a MYB and a NAC TF, respectively, and whereas MYB63 was known to be involved in JA/SA response pathways (Yanhui et al, e Genes that were present in both conserved and nonconserved modules could gain a prediction by both.…”