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. 2000 Feb;122(2):389-402.
doi: 10.1104/pp.122.2.389.

Toward a functional catalog of the plant genome. A survey of genes for lipid biosynthesis

S Mekhedov  1 , O M de Ilárduya, J Ohlrogge
Affiliations

Toward a functional catalog of the plant genome. A survey of genes for lipid biosynthesis

S Mekhedov et al. Plant Physiol. 2000 Feb.

Abstract

Public databases now include vast amounts of recently acquired DNA sequences that are only partially annotated and, furthermore, are often annotated by automated methods that are subject to errors. Maximum information value of these databases can be derived only by further detailed analyses that frequently require careful examination of records in the context of biological functions. In this study we present an example of such an analysis focused on plant glycerolipid synthesis. Public databases were searched for sequences corresponding to 65 plant polypeptides involved in lipid metabolism. Comprehensive search results and analysis of genes, cDNAs and expressed sequence tags (ESTs) are available online (http://www.canr.msu.edu/lgc). Multiple alignments provided a method to estimate the number of genes in gene families. Further analysis of sequences allowed us to tentatively identify several previously undescribed genes in Arabidopsis. For example, two genomic sequences were identified as candidates for the palmitate-specific monogalactosyldiacylglycerol desaturase (FAD5). A candidate genomic sequence for 3-ketoacyl-acyl-carrier protein (ACP) synthase involved in mitochondrial fatty acid biosynthesis was also identified. Biotin carboxyl carrier protein (BCCP) in Arabidopsis is encoded by at least two genes, but the most abundant BCCP transcript so far has not been characterized. The large number (>165,000) of plant ESTs also provides an opportunity to perform "digital northern" comparisons of gene expression levels across many genes. EST abundance in general correlated with biochemical and flux characteristics of the enzymes in Arabidopsis leaf tissue. In a few cases, statistically significant differences in EST abundance levels were observed for enzymes that catalyze similar reactions in fatty acid metabolism. For example, ESTs for the FatB acyl-ACP thioesterase occur 21 times compared with 7 times for FatA acyl-ACP thioesterase, although flux through the FatA reaction is several times higher than through FatB. Such comparisons may provide initial clues toward previously undescribed regulatory phenomena. The abundance of ESTs for ACP compared with that of stearoyl-ACP desaturase and FatB acyl-ACP thioesterase suggests that concentrations of some enzymes of fatty acid synthesis may be higher than their acyl-ACP substrates.

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Figures

Figure 1
Figure 1
Abbreviated diagram of glycerolipid synthesis in Arabidopsis leaves. Widths of the arrows show the relative fluxes through different reactions. Adapted from Browse and Somerville (1991) with permission of Annual Reviews. Numbers of reactions correspond to those in Table I of the present paper and in tables 1 and 4 of the website. Abbreviations for the lipid structures: fatty acids, X:Y, a fatty acyl group containing X carbon atoms and Y cis double bonds; t16:1, hexadec-3trans-enoic acid; G3P, glycerol-3-phosphate; LPA, 1-acyl-glycerol-3-phosphate; PA, phosphatidic acid; DAG, dyacylglycerol; CDP-DAG, cytidine-5′-diphosphate-diacylglycerol; PG, phosphatidylglycerol; PG-P, phosphatidylglycerol-3-phosphate; MGDG, monogalactosyldiacylglycerol; DGDG, digalactosyldiacylglycerol; SL, sulfoguinovosyldiacylglycerol; PC, phosphatidylcholine; PI, phosphatidylinositol; PE, phosphatidylethanolamine.
Figure 2
Figure 2
EST abundance for lipid metabolism enzymes and proteins in Arabidopsis and rice in dbEST as of August 1999. EST numbers for all plant species are shown in red beneath the x axis. Enzymes and proteins encoded by gene families are marked with asterisks. The inset shows 95% confidence intervals in the differences between EST numbers. For a given number of ESTs for a protein shown in the first column, the second column shows the number of ESTs immediately outside the confidence interval (first significantly different values) for the 95% confidence levels (based on table I from Audic and Claverie [1997]). For example, if one protein is represented by 20 ESTs, then for another protein, EST numbers ≤9 or ≥35 are considered different at the 95% confidence level. Proteins listed in Table I but not expected in Arabidopsis and rice, (Legend continues on facing page.)e.g. Δ12 fatty acid epoxydase as well as proteins for which sequences are unknown are not included in this comparison. Putative Arabidopsis wax synthase ESTs (4) may correspond to a hypothetical gene located immediately upstream of the wax synthase gene cluster.
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