The J-domain proteins of Arabidopsis thaliana: an unexpectedly large and diverse family of chaperones

Abstract

A total of 89 J-domain proteins were identified in the genome of the model flowering plant Arabidopsis thaliana. The deduced amino acid sequences of the J-domain proteins were analyzed for an assortment of structural features and motifs. Based on the results of sequence comparisons and structure and function predictions, 51 distinct families were identified. The families ranged in size from 1 to 6 members. Subcellular localizations of the A thaliana J-domain proteins were predicted; species were found in both the soluble and membrane compartments of all cellular organelles. Based on digital Northern analysis, the J-domain proteins could be separated into groups of low, medium, and moderate expression levels. This genomics-based analysis of the A thaliana J-domain proteins establishes a framework for detailed studies of biological function and specificity. It additionally provides a comprehensive basis for evolutionary comparisons.

Fig 1.

Phylogenetic relationships among the J-domain sequences of the A thaliana J-domain proteins. The sequences were manually aligned, then analyzed using SEQBOOT. The resulting cladogram was constructed using the PHYLIP program. Members of the clades, from top to bottom, are as follows: 1, A3, A2, B19, C29-2, B70, C21-2, B88; 2, C18, C35, C10, C46, B45, C7, C84, A30, B1, C74, B37, C6; 3, B13, B40, C72, B79, B66, C85, B87, B83, C82, B67, C4, C5, C59, C68; 4, C25, C20, C11, C41, C38, C8, C17, C21-1, C29-1, C64, C53, C55; 5, A36, B9, B60, B14, B22, C12, B23, B32, C33; 6, C61, C75, C31, B51, C34, B71, C77, B47, B73, B44, C76, C62, C27, C28, B78, B65, C49, B43, B48; 7, B86, B89, B80, C81, B57, C69, C58; 8, C50, C56, A52, A54, A26, A24; 9, B15, B16, C39, A63, B42

Fig 2.

Digital Northern analysis of the A thaliana J-domain proteins. The EST abundance in dbEST, as of January 2001, is presented. The histograms are, from bottom to top, atDjB1 to atDjC89. The shaded histogram, included for the sake of comparison, is for the plastidial enzyme dihydrolipoyl acetyltransferase. The differences between numbers, at the 95% confidence interval, are also presented. For a given EST number, indicated in the first column, the number of ESTs immediately beyond the confidence interval is indicated in the second column (Audic and Claverie 1997; Mekhedov et al 2000)