Using genomic resources to guide research directions. The arabinogalactan protein gene family as a test case

被引:186
作者
Schultz, CJ
Rumsewicz, MP
Johnson, KL
Jones, BJ
Gaspar, YM
Bacic, A
机构
[1] Univ Adelaide, Waite Agr Res Inst, Dept Plant Sci, Glen Osmond, SA 5064, Australia
[2] Univ Melbourne, Sch Bot, Plant Cell Biol Res Ctr, Melbourne, Vic 3010, Australia
关键词
D O I
10.1104/pp.003459
中图分类号
Q94 [植物学];
学科分类号
071001 ;
摘要
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.
引用
收藏
页码:1448 / 1463
页数:16
相关论文
共 68 条
[1]   Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].
Altschul, SF ;
Madden, TL ;
Schaffer, AA ;
Zhang, JH ;
Zhang, Z ;
Miller, W ;
Lipman, DJ .
NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402
[2]   A large scale analysis of cDNA in Arabidopsis thaliana:: Generation of 12,028 non-redundant expressed sequence tags from normalized and size-selected cDNA libraries [J].
Asamizu, E ;
Nakamura, Y ;
Sato, S ;
Tabata, S .
DNA RESEARCH, 2000, 7 (03) :175-180
[3]   Genome annotation [J].
Aubourg, S ;
Rouzé, P .
PLANT PHYSIOLOGY AND BIOCHEMISTRY, 2001, 39 (3-4) :181-193
[4]  
Bacic A, 2000, CELL AND DEVELOPMENTAL BIOLOGY OF ARABINOGALACTAN-PROTEINS, P11
[5]   Improved PCR-walking for large-scale isolation of plant T-DNA borders [J].
Balzergue, S ;
Dubreucq, B ;
Chauvin, S ;
Le-Clainche, I ;
Le Boulaire, F ;
de Rose, R ;
Samson, F ;
Biaudet, V ;
Lecharny, A ;
Cruaud, C ;
Weissenbach, J ;
Caboche, M ;
Lepiniec, L .
BIOTECHNIQUES, 2001, 30 (03) :496-+
[6]  
BORNER GHH, 2001, 9 INT CELL WALL M TO, P74
[7]   Functional genomics in plants [J].
Bouchez, D ;
Höfte, H .
PLANT PHYSIOLOGY, 1998, 118 (03) :725-732
[8]   Growth stage-based phenotypic analysis of arabidopsis:: A model for high throughput functional genomics in plants [J].
Boyes, DC ;
Zayed, AM ;
Ascenzi, R ;
McCaskill, AJ ;
Hoffman, NE ;
Davis, KR ;
Görlach, J .
PLANT CELL, 2001, 13 (07) :1499-1510
[9]   Occurrence of cell surface arabinogalactan-protein and extensin epitopes in relation to pericycle and vascular tissue development in the root apex of four species [J].
Casero, PJ ;
Casimiro, I ;
Knox, JP .
PLANTA, 1998, 204 (02) :252-259
[10]   MOLECULAR-CLONING OF A GENE ENCODING AN ARABINOGALACTAN PROTEIN FROM PEAR (PYRUS-COMMUNIS) CELL-SUSPENSION CULTURE [J].
CHEN, CG ;
PU, ZY ;
MORITZ, RL ;
SIMPSON, RJ ;
BACIC, A ;
CLARKE, AE ;
MAU, SL .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1994, 91 (22) :10305-10309