NCBI Special Seminar
Bldg 38a, 5th floor Conference room
Friday January 26, 2 PM

(apologies for the short notice)

Toward a Functional Catalog of the Plant Genome. A Survey of Genes for 
Lipid Biosynthesis

Sergei Mekhedov

MSU-DOE Plant Research Laboratory, Michigan State University

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, the first plant member of a gene family similar to animal, 
bacterial and fungal acyl desaturases was identified as the gene for 
palmitate-specific monogalactosyldiacylglycerol desaturase. The first 
plant gene for an enzyme of fatty acid biosynthesis in mitochondria was 
identified.

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. 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.

A considerable number of errors have been detected in GenBank files. In 
at least one case a careful examination of genes that are incorrectly 
annotated made it possible to identify two genes for putative 
bifunctional proteins with a protein kinase-like and an acyl-CoA 
interacting domains. These proteins are candidates for protein kinases 
regulating fatty acid biosynthesis.

Plant Physiol, February 2000, Vol. 122, pp. 389-402


-- 
Eugene V. Koonin, PhD
National Center for Biotechnology Information
National Library of Medicine
National Institutes of Health, Bldg. 38A, Rm. 5N503 (5th floor)
8600 Rockville Pike
Bethesda, MD 20894, USA
Voice: (301)435-5913
Fax: (301)435-7794 or (301)480-9241
email koonin@ncbi.nlm.nih.gov