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Plant Physiol, February 2000, Vol. 122, pp. 389-402
Toward a Functional Catalog of the Plant Genome. A Survey of
Genes for Lipid Biosynthesis1
Sergei
Mekhedov,
Oskar Martínez
de
Ilárduya,2 and
John
Ohlrogge*
Department of Botany and Plant Pathology, Michigan State
University, East Lansing, Michigan 48824.
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.
1
This work was supported by grants from the
National Science Foundation (no. DCB90-05290) and from the Department
of Energy (no. DE-FG02-87ER12729). We also acknowledge the Michigan
Agricultural Experiment Station for its support of this research.
2
Present address: Department of Nematology, 2231 Spieth Hall, University of California, Riverside, CA 92521.
*
Corresponding author; e-mail ohlrogge{at}pilot.msu.edu; fax
517-353-1926.
© 2000 American Society of Plant Physiologists
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