First published online August 1, 2002; 10.1104/pp.003459
Plant Physiol, August 2002, Vol. 129, pp. 1448-1463
Using Genomic Resources to Guide Research Directions. The
Arabinogalactan Protein Gene Family as a Test Case1
Carolyn J.
Schultz,*
Michael P.
Rumsewicz,
Kim L.
Johnson,
Brian J.
Jones,
Yolanda M.
Gaspar, and
Antony
Bacic
Department of Plant Science, Waite Agricultural Research Institute,
The University of Adelaide, RMB1, Glen Osmond, South Australia 5064, Australia (C.J.S.); 13 Riverway, Fulham Gardens, South Australia 5024, Australia (M.P.R.); and Plant Cell Biology Research Centre, School of
Botany, University of Melbourne, Victoria 3010, Australia (K.L.J.,
B.J.J., Y.M.G., A.B.)
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.
1
This work was supported by the Australian
Research Council (Large Grant no. A10020017) and by the University of
Melbourne (research scholarships to K.L.J. and Y.M.G.).
*
Corresponding author; e-mail carolyn.schultz{at}adelaide.edu.au;
fax 61-8-8303-7102.
© 2002 American Society of Plant Physiologists
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