Submitted to: Genome
Publication Type: Peer reviewed journal
Publication Acceptance Date: 4/11/2002
Publication Date: 8/6/2002
Citation: GRANGER, C.L., CORYELL, V., KHANNA, A., KEIM, P., VODKIN, L., SHOEMAKER, R.C. IDENTIFICATION, STRUCTURE, AND DIFFERENTIAL EXPRESSION OF MEMBERS OF A BURP DOMAIN CONTAINING PROTEIN FAMILY IN SOYBEAN. GENOME. 2002. v. 45. p. 693-701. Interpretive Summary: The evolution of many plants has resulted in more than one copy of many genes. Often these genes take an unique function. It is very expensive and time-consuming to measure levels of expression in each gene. However, many genomics projects are now producing vast collections of partial gene sequences generated from different organs, stages of development, and environmental conditions. In this paper the authors mine several public databases to estimate patterns of gene expression within a family of stress-related genes. They identify various forms of each gene and discovered that the gene forms are expressed differently in different tissues. This work demonstrates the usefulness of data-mining in understanding complex relationships within a gene family. These results will be used by scientists to design experiments to determine gene function in a more efficient and cost-effective manner.
Technical Abstract: Expressed sequence tags (ESTs) related to a desiccation-responsive gene (rd22) from Arabidopsis thaliana (L.) Heynh were identified from the Glycine max (L.) Merr, Medicago truncatula Gaertner, and Lycopersicon esculentum P. Mill EST databases. These ESTs were assembled into six (G. max), three (M. truncatula), and two (L. esculentum) contig(s). Consensus amino acid sequences generated from these contigs exhibit 31 to 65% identity to RD22. Together with RD22, the deduced proteins cluster as a subfamily within a superfamily of related proteins. Proteins in this superfamily have hydrophobic signaling sequences and remarkably similar C-terminal regions. However, in the N-terminal regions, members of the RD22-related subfamily have as many as four repeated sequences of 18 to 23 amino acids whose function is unknown. Unique expression patterns were observed for five of the rd22-related genes from G. max. Four genes were specifically expressed in either roots, seed coats, or senescing/drought-stressed leaves while one gene had a broader distribution. Expression patterns of the rd22-related G. max genes cluster with those of other dehydration-responsive genes as well as unknown genes that may be functionally related to the rd22 homologs. We discuss the functional and evolutionary implications of these findings as well as the utility of EST-based analyses for identifying and characterizing interspecies homologs.