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Type: Journal article
Title: Using genomic resources to guide research directions. The arabinogalactan protein gene family as a test case
Author: Schultz, C.
Rumsewicz, M.
Johnson, K.
Jones, B.
Gaspar, Y.
Bacic, A.
Citation: Plant Physiology, 2002; 129(4):1448-1463
Publisher: Amer Soc Plant Physiologists
Issue Date: 2002
ISSN: 0032-0889
Statement of
Carolyn J. Schultz, Michael P. Rumsewicz, Kim L. Johnson, Brian J. Jones, Yolanda M. Gaspar and Antony Bacic
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.
Keywords: Arabidopsis
Plant Proteins
Arabidopsis Proteins
Oligonucleotide Array Sequence Analysis
Markov Chains
Contig Mapping
Gene Expression Regulation, Developmental
Gene Expression Regulation, Plant
Sequence Homology, Amino Acid
Multigene Family
Expressed Sequence Tags
Stress, Mechanical
Molecular Sequence Data
Description: © 2002 American Society of Plant Biologists
DOI: 10.1104/pp.003459
Published version:
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