A Comprehensive Expression Analysis of all Members of a Gene Family Encoding Cell-Wall Enzymes Allowed us to Predict cis-Regulatory Regions Involved in Cell-Wall Construction in Specific Organs of Arabidopsis

Abstract

The Arabidopsis thaliana genome sequencing project has revealed that multigene families, such as those generated by genome duplications, are more abundant among plant genomes than among animal genomes. To gain insight into the evolutionary implications of the multigene families in higher plants, we examined the XTH gene family, a group of genes encoding xyloglucan endotransglucosylase/hydrolase, which are responsible for cell-wall construction in plants. Expression analysis of all members (33 genes) of this family, using quantitative real-time RT-PCR, revealed that most members exhibit distinct expression profiles in terms of tissue specificity and responses to hormonal signals, with some members exhibiting similar expression patterns. By comparing the flanking sequences of individual genes, we identified four sets of large-segment duplications and two sets of solitary gene duplications. In each set of gene duplicates, long nucleotide sequences, ranging from one to two hundred base pairs, are conserved. Furthermore, gene duplicates exhibit similar organ-specific expression profiles. These facts allowed us to predict putative cis-regulatory regions, particularly those responsible for cell-wall construction, and hence for morphogenesis, that are specific for certain organs or tissues in plants.

The Galactose Residues of Xyloglucan Are Essential to Maintain Mechanical Strength of the Primary Cell Walls in Arabidopsis during Growth

“…In Arabidopsis, these enzymes are encoded by a XTH gene family (Rose et al, 2002) comprising nearly three dozen members in at least three subclasses (Campbell and Braam, 1999;Yokoyama and Nishitani, 2001;Rose et al, 2002). The numerous XTH isoforms suggest a multiplicity of roles in cell development (Yokoyama and Nishitani, 2001). Thus, if members of some classes of XTH function in polymer elongation, as has been suggested ( Thompson and Fry, 2001), then Gal residues are not essential for these particular reactions.…”

“…No less than 10 XTHs are highly expressed in Arabidopsis roots (Yokoyama and Nishitani, 2001), although the number expressed specifically in hypocotyls is unknown. Redundancy of expression of several XTHs with similar function in any one cell may explain the difficulty using this approach to characterize gene function (Campbell and Braam, 1999;Yokoyama and Nishitani, 2001). In the experiments described here, the alteration of a common substrate has been more informative than underexpression of a single XTH gene.…”

Group III-AXTHGenes of Arabidopsis Encode Predominant Xyloglucan Endohydrolases That Are Dispensable for Normal Growth

“…Thirty-three members of the XTH gene family have been found previously (Yokoyama and Nishitani, 2001) in the genome of Arabidopsis (Arabidopsis Genome Initiative, 2000). Of these, only two, AtXTH31 (locus At3g44990) and AtXTH32 (locus At2g36870), encode proteins belonging to group III-A (Eklöf and Brumer, 2010) in the updated phylogeny proposed by Baumann et al (2007).…”

Organelle–nucleus cross-talk regulates plant intercellular communication via plasmodesmata

“…Three CSLD genes (CSLD2, CSLD3, and CSLD5) and one CSLA gene (CSLA9) also show altered expression in ise1 and ise2 mutants ( Table 2). A large family of 33 XyG endotransglucosylase/hydrolase (XTH) enzymes is involved in XyG modification in A. thaliana, and the expression of XTH genes is tissue-specific (35). Eight of these genes are differentially regulated in ise1 and/or ise2 compared with WT (Table 2).…”