Molecular biology of the plant cell wall: searching for the genes that define structure, architecture and dynamics

Carpita, Nick; Tierney, Mary L.; Campbell, Malcolm M.

doi:10.1007/978-94-010-0668-2_1

Cited by 60 publications

(80 citation statements)

References 3 publications

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“…These families tend to be large. For example, the ␣-expansins consist of 26 family members (Lee et al, 2001) and the cellulose synthase family is represented by at least 10 CesA-type genes and 41 Csl (cellulose synthase-like) genes (Richmond and Somerville, 2000;Carpita et al, 2001;Desprez et al, 2002). Here, we report that COBRA is part of a new multigene family with the identification of 11 new family members.…”

mentioning

confidence: 79%

The COBRA Family of Putative GPI-Anchored Proteins in Arabidopsis. A New Fellowship in Expansion

et al. 2002

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Identification of regulatory molecules that determine the extent and direction of expansion is necessary to understand how cell morphogenesis is controlled in plants. We recently identified COB (COBRA) as a key regulator of the orientation of cell expansion in the root. Analysis of the Arabidopsis genome sequence indicated that COB belongs to a multigene family consisting of 12 members, all predicted to encode glycosylphosphatidylinositol-anchored proteins. All but two of the COBL (COB-like) genes are expressed in most organs examined, suggesting possible redundancy. Sequence comparisons, phylogenetic analyses, and exon-intron positions revealed that the COB family is composed of two main subgroups sharing a common architecture, one subgroup being characterized by an additional N-terminal domain. Identification of expressed sequence tags corresponding to potential orthologs in other plant species suggested that COB-related functions are required in all vascular plants. Together, these results indicate that COB family members are likely to be important new players at the plasma membrane-cell wall interface.Cell morphogenesis is heavily influenced and restricted by the presence of an extracellular network of carbohydrates and proteins, the cell wall. Far from being an inert and stable exoskeleton, the primary wall is a highly dynamic extracellular matrix characterized by plastic, elastic, and viscous physical properties. These properties are conferred by the nature of the different constituent polymers, a load-bearing cellulose/xyloglucan (hemicellulose) array, and a compression-resistant pectin gel (Roberts, 1994). The developmental regulation of cell wall dynamics required for cell expansion and cell shape modeling must be directed by proteins capable of organizing, loosening, and rearranging the different polysaccharide networks and incorporating newly synthesized material. More than 17% of Arabidopsis genes contain a signal peptide sequence and over 400 proteins are annotated as being localized in the cell wall (Arabidopsis Genome Initiative [AGI], 2000), suggesting the possibility that more than 1,000 genes are implicated in wall biogenesis and modification .Proteins localized to the cell wall, such as the Hyp-, Pro-, or Gly-rich proteins, arabinogalactan proteins, and expansins, were originally identified through assays for biochemical and/or biophysical activities. More recently, forward and reverse genetic approaches have led to the identification of new classes of cell wall modifiers such as cellulose synthases (Arioli et al., 1998; Fagard et al., 2000), endo-␤-1,4-glucanases (Nicol et al., 1998), and wall-associated kinases (Kohorn, 2001). By analyzing Arabidopsis mutants exhibiting abnormal cell expansion during root development (Benfey et al., 1993;Hauser et al., 1995), COBRA was identified as an essential player in the regulation of the orientation of cell expansion (Schindelman et al., 2001). Reduced levels of crystalline cellulose microfibrils in the mutant suggested a role for COBRA in cellulose de...

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confidence: 79%

The COBRA Family of Putative GPI-Anchored Proteins in Arabidopsis. A New Fellowship in Expansion

et al. 2002

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“…When using the 415 CAZy classified Arabidopsis GTs as an estimate of the total number of glycosidic bondforming enzymes, in plant this number is 1.6%, partly due to the existence of the highly complex CW. Based on the number of Arabidopsis genes that are predicted to possess signal peptides, it has been estimated that well over 2,000 genes are likely to participate in biosynthesis, assembly, and modification of CWs during plant development (Carpita et al, 2001). If soluble enzymes that participate in generation of substrates and the integral membrane-associated biosynthetic CW proteins, such as the cellulose synthase, are included, it has been estimated that some 15% of the Arabidopsis genome is dedicated to CW biogenesis and modification (Carpita et al, 2001).…”

Section: Discussionmentioning

confidence: 99%

“…Although composition of the major CW polysaccharides is reasonably well described (Carpita et al, 2001), only a handful of the biosynthetic genes have been identified. All of the seven known GTs, i.e.…”

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confidence: 99%

A Complementary Bioinformatics Approach to Identify Potential Plant Cell Wall Glycosyltransferase-Encoding Genes

Egelund¹,

Skjøt²,

Geshi³

et al. 2004

Plant Physiology

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Plant cell wall (CW) synthesizing enzymes can be divided into the glycan (i.e. cellulose and callose) synthases, which are multimembrane spanning proteins located at the plasma membrane, and the glycosyltransferases (GTs), which are Golgi localized single membrane spanning proteins, believed to participate in the synthesis of hemicellulose, pectin, mannans, and various glycoproteins. At the Carbohydrate-Active enZYmes (CAZy) database where e.g. glucoside hydrolases and GTs are classified into gene families primarily based on amino acid sequence similarities, 415 Arabidopsis GTs have been classified. Although much is known with regard to composition and fine structures of the plant CW, only a handful of CW biosynthetic GT genes-all classified in the CAZy system-have been characterized. In an effort to identify CW GTs that have not yet been classified in the CAZy database, a simple bioinformatics approach was adopted. First, the entire Arabidopsis proteome was run through the Transmembrane Hidden Markov Model 2.0 server and proteins containing one or, more rarely, two transmembrane domains within the N-terminal 150 amino acids were collected. Second, these sequences were submitted to the SUPERFAMILY prediction server, and sequences that were predicted to belong to the superfamilies NDP-sugartransferase, UDP-glycosyltransferase/glucogen-phosphorylase, carbohydrate-binding domain, Gal-binding domain, or Rossman fold were collected, yielding a total of 191 sequences. Fifty-two accessions already classified in CAZy were discarded. The resulting 139 sequences were then analyzed using the Three-Dimensional-Position-Specific Scoring Matrix and mGenTHREADER servers, and 27 sequences with similarity to either the GT-A or the GT-B fold were obtained. Proof of concept of the present approach has to some extent been provided by our recent demonstration that two members of this pool of 27 non-CAZy-classified putative GTs are xylosyltransferases involved in synthesis of pectin rhamnogalacturonan II

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“…Even highly heritable traits such as wood quality are expected to be influenced by variation in hundred of cell wall genes (Carpita et al 2001). To capture a large proportion of trait variation, the number of candidate genes examined needs to be increased substantially.…”

Section: Gene Discovery and Association Geneticsmentioning

confidence: 99%

Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus

Grattapaglia

Vaillancourt

Shepherd

et al. 2012

Tree Genetics & Genomes

228

188

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Molecular biology of the plant cell wall: searching for the genes that define structure, architecture and dynamics

Cited by 60 publications

References 3 publications

The COBRA Family of Putative GPI-Anchored Proteins in Arabidopsis. A New Fellowship in Expansion

The COBRA Family of Putative GPI-Anchored Proteins in Arabidopsis. A New Fellowship in Expansion

A Complementary Bioinformatics Approach to Identify Potential Plant Cell Wall Glycosyltransferase-Encoding Genes

Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus

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