Using Genomic Resources to Guide Research Directions. The Arabinogalactan Protein Gene Family as a Test Case

Abstract

Arabinogalactan proteins (AGPs) are extracellular hydroxyproline-rich proteoglycans implicated in plant growth and development. The protein backbones of AGPs are rich in proline/hydroxyproline, serine, alanine, and threonine. Most family members have less than 40% similarity; therefore, finding family members using Basic Local Alignment Search Tool searches is difficult. As part of our systematic analysis of AGP function in Arabidopsis, we wanted to make sure that we had identified most of the members of the gene family. We used the biased amino acid composition of AGPs to identify AGPs and arabinogalactan (AG) peptides in the Arabidopsis genome. Different criteria were used to identify the fasciclin-like AGPs. In total, we have identified 13 classical AGPs, 10 AG-peptides, three basic AGPs that include a short lysine-rich region, and 21 fasciclin-like AGPs. To streamline the analysis of genomic resources to assist in the planning of targeted experimental approaches, we have adopted a flow chart to maximize the information that can be obtained about each gene. One of the key steps is the reformatting of the Arabidopsis Functional Genomics Consortium microarray data. This customized software program makes it possible to view the ratio data for all Arabidopsis Functional Genomics Consortium experiments and as many genes as desired in a single spreadsheet. The results for reciprocal experiments are grouped to simplify analysis and candidate AGPs involved in development or biotic and abiotic stress responses are readily identified. The microarray data support the suggestion that different AGPs have different functions.

Mucilage chemical profile and antioxidant properties of giant swamp taro tubers

“…Extraction of crude AGPs from GST flour The taro AGPs was extracted following the method of Schultz et al (2002). 5 g of taro flour were suspended in 5 mL of buffer solution (50 mM Tris-HCl pH 8, 10 mM EDTA, 0.1 % β-mercaptoéthanol, 1 % (w/v) Triton X 100) at 4°C for 4 h. The samples were centrifuged at 14 000 g for 10 min at 4°C and the resulting supernatant treated with 5 volumes of absolute ethanol for 24 h at 4°C before centrifuging at 14 000 g for 10 min at 4°C to obtain pellets which were then suspended in 5 mL of Tris-HCl solution (50 mM, pH8).…”

Poplar genes encoding fasciclin‐like arabinogalactan proteins are highly expressed in tension wood

“…Several PopFLAs are highly and specifically represented in tension wood Recently, Schultz et al (2002) classified 47 Arabidopsis glycosylphosphatidylinositol (GPI)-anchored AGPs into four groups: classical AGPs, AG-peptides, basic AGPs and fasciclin-like AGPs. Compared with the three other groups, the FLAs group is quite heterogeneous as it includes AGPs with one or two AGP-like domains and one or two fasciclinlike domains.…”

“…Numerous AGPs showing sequence similarities were identified in several plant species (Gaspar et al ., 2001;Schultz et al ., 2002). Deduced AGP protein backbones are designated as either 'classical' or 'nonclassical' AGP according to the organization into domains and motifs.…”

“…(2001) described the fasciclin-like AGPs (FLAs), a subclass of classical AGPs containing domain(s) similar to Drosophila melanogaster fasciclins cell adhesion molecules. A number of genes encoding FLA protein backbones have been identified in Arabidopsis (Schultz et al ., 2002) and in loblolly pine (Loopstra & Sederoff, 1995;Loopstra et al ., 2000;Zhang et al ., 2000). Some FLA proteins are associated with wood formation Whetten et al ., 2001;Lorenz & Dean, 2002).…”

The Organization Pattern of Root Border-Like Cells of Arabidopsis Is Dependent on Cell Wall Homogalacturonan

“…Arabinogalactan-proteins are highly glycosylated members of the Hyp-rich glycoprotein superfamily. Many of these glycoproteins, the so-called classical arabinogalactan-proteins, are anchored to the plasma membrane by a glycosylphosphatidylinositol anchor and have the potential to bind both cell wall components (Immerzeel et al, 2006) and cytosolic cortical microtubules (Schultz et al, 2002;Sardar et al, 2006;Nguema-Ona et al, 2007). These proteoglycans have been implicated in many aspects of plant life, including cell expansion, cell signaling and communication, embryogenesis, and wound response (Johnson et al, 2003;Seifert and Roberts, 2007;Driouich and Baskin, 2008).…”