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

Mekhedov, Sergei; Ilárduya, Oskar Martı́nez de; Ohlrogge, John B.

doi:10.1104/pp.122.2.389

Cited by 199 publications

(141 citation statements)

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“…To demonstrate the differential expression of a gene, its EST assembly must be composed of more than four ESTs to be considered as having greater than a basal level of expression. Using Audic and Claverie's statistical approach, Ewing et al (1999) and Mekhedov et al (2000) analyzed public databases of Arabidopsis and rice to identify genes with differential expression in either selected tissues or between the species. In this work, we attempted to assess the validity of our digital northern data by experimental approach.…”

Section: Discussionmentioning

confidence: 99%

“…In silico-based gene discovery and tissue profiling were performed to study plant fatty acid and lipid metabolism, cell wall biosynthesis, and seed oil production ( Van de Loo et al, 1995;Allona et al, 1998;Sterky et al, 1998;Cahoon et al, 1999;Mekhedov et al, 2000;White et al, 2000). Such analyses were made possible through accumulation of large numbers of ESTs, where the gene expression level can be deduced in silico by calculating EST frequencies in different cDNA libraries.…”

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confidence: 99%

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Genome-Wide Identification of Nodule-Specific Transcripts in the Model Legume Medicago truncatula

et al. 2002

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The Medicago truncatula expressed sequence tag (EST) database (Gene Index) contains over 140,000 sequences from 30 cDNA libraries. This resource offers the possibility of identifying previously uncharacterized genes and assessing the frequency and tissue specificity of their expression in silico. Because M. truncatula forms symbiotic root nodules, unlike Arabidopsis, this is a particularly important approach in investigating genes specific to nodule development and function in legumes. Our analyses have revealed 340 putative gene products, or tentative consensus sequences (TCs), expressed solely in root nodules. These TCs were represented by two to 379 ESTs. Of these TCs, 3% appear to encode novel proteins, 57% encode proteins with a weak similarity to the GenBank accessions, and 40% encode proteins with strong similarity to the known proteins. Nodule-specific TCs were grouped into nine categories based on the predicted function of their protein products. Besides previously characterized nodulins, other examples of highly abundant nodule-specific transcripts include plantacyanin, agglutinin, embryo-specific protein, and purine permease. Six nodule-specific TCs encode calmodulin-like proteins that possess a unique cleavable transit sequence potentially targeting the protein into the peribacteroid space. Surprisingly, 114 nodule-specific TCs encode small Cys cluster proteins with a cleavable transit peptide. To determine the validity of the in silico analysis, expression of 91 putative nodule-specific TCs was analyzed by macroarray and RNA-blot hybridizations. Nodule-enhanced expression was confirmed experimentally for the TCs composed of five or more ESTs, whereas the results for those TCs containing fewer ESTs were variable. , and organ development (Ruan et al., 1998;Girke et al., 2000; Zhu and Wang, 2000). Although Arabidopsis serves as the model system for most plant processes, it suffers from two major weaknesses in consideration of plant-microbe interactions: the absence of symbiotic associations with mycorrhizal fungi and with rhizobia.In recent years, Medicago truncatula and Lotus japonicus have emerged as model systems for genomic approaches to plant-microbe symbiotic associations (Barker et al., 1990;Handberg and Stougaard, 1992; Cook et al., 1997; Cook, 1999;Oldroyd and Geurts, 2001;Thoquet et al., 2002). Both species possess small genomes, are diploid, have fast generation times, and can be transformed with Agrobacterium tumefaciens and regenerated (Handberg and Stougaard, 1992; Blondon et al., 1994;Handberg et al., 1994; Chabaud et al., 1996;Jiang and Gresshoff, 1997;Stiller et al., 1997;Trinh et al., 1998;Trieu et al., 2000). Currently, both functional and structural genomics approaches are being pursued within each of these species. Covitz et al. (1998) reported the sequencing of about 900 cDNA tags from the M. truncatula root hairs. In addition, hundreds more expressed sequence tags (ESTs) have been isolated and characterized from effective root nodules of L. japonicus and M. truncatula, and a ...

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

Genome-Wide Identification of Nodule-Specific Transcripts in the Model Legume Medicago truncatula

et al. 2002

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“…Table I presents the results of a more detailed survey of proteins predicted or known to be involved in plant lipid metabolism (the search was carried out using our database of predicted lipid-related genes in Arabidopsis (Mekhedov et al, 2000;F. Beisson and J.B. Ohlrogge, unpublished data).…”

Section: Plastid Envelope Membrane Protein Candidatesmentioning

confidence: 99%

“…Jackson-Constan and Keegstra (2001). b Arabidopsis glycerolipid biosynthetic enzyme candidates were searched using our database of lipid metabolism-related genes in Arabidopsis (Mekhedov et al, 2000;F. Beisson and J.B. Ohlrogge, unpublished data).…”

Section: Plastid Envelope Membrane Protein Candidatesmentioning

confidence: 99%

The Predicted Candidates of Arabidopsis Plastid Inner Envelope Membrane Proteins and Their Expression Profiles,

Koo

Ohlrogge

2002

Plant Physiology

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Plastid envelope proteins from the Arabidopsis nuclear genome were predicted using computational methods. Selection criteria were: first, to find proteins with NH 2 -terminal plastid-targeting peptides from all annotated open reading frames from Arabidopsis; second, to search for proteins with membrane-spanning domains among the predicted plastidial-targeted proteins; and third, to subtract known thylakoid membrane proteins. Five hundred forty-one proteins were selected as potential candidates of the Arabidopsis plastid inner envelope membrane proteins (AtPEM candidates). Only 34% (183) of the AtPEM candidates could be assigned to putative functions based on sequence similarity to proteins of known function (compared with the 69% function assignment of the total predicted proteins in the genome). Of the 183 candidates with assigned functions, 40% were classified in the category of "transport facilitation," indicating that this collection is highly enriched in membrane transporters. Information on the predicted proteins, tissue expression data from expressed sequence tags and microarrays, and publicly available T-DNA insertion lines were collected. The data set complements proteomic-based efforts in the increased detection of integral membrane proteins, low-abundance proteins, or those not expressed in tissues selected for proteomic analysis. Digital northern analysis of expressed sequence tags suggested that the transcript levels of most AtPEM candidates were relatively constant among different tissues in contrast to stroma and the thylakoid proteins. However, both digital northern and microarray analyses identified a number of AtPEM candidates with tissue-specific expression patterns.Plastids exist in a wide range of differential forms, including proplastids, chloroplasts, etioplasts, amyloplasts, leucoplasts, and chromoplasts, depending on the developmental stage and function of the plant cells in which they reside. To a large extent, the types of plastids that are carried by cells determine the metabolic function and products of the particular plant tissue (Kirk and Tilney-Bassett, 1978).One constant feature among the various types of plastids is the double membrane envelope structure that surrounds the organelle. The envelope, especially the inner envelope, effectively separates plastid metabolism from that of the cytosol. At the same time, almost all carbon and a major flux of other metabolites, various polypeptides, and signals must move through the envelope to coordinate and integrate metabolism with the entire cell. Plastid envelopes contain protein transport machinery (Schnell, 1995;Cline and Henry, 1996;Heins et al., 1998), and are a major site for membrane biogenesis. Metabolite transporters from chloroplast and/or nongreen plastids accommodate the requirements of the different photosynthetic or heterotrophic tissues (Kammerer et al., 1998;Neuhaus and Emes, 2000). Membrane constituents (glycerolipids, pigments, and prenylquinones) are synthesized on the envelope membrane as well as the porphyrin ring ...

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“…By contrast, the FATB class prefers saturated acyl-ACP substrates but also shows activity for oleoyl-ACPs (Doermann et al, 1995;Voelker et al, 1997;Salas and Ohlrogge, 2002). The Arabidopsis genome encodes two FATA genes and a single FATB gene (Mekhedov et al, 2000;Beisson et al, 2003). We previously described the isolation and analysis of an Arabidopsis mutant disrupted in the FATB gene ( fatb-ko; Bonaventure et al, 2003).…”

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Metabolic Responses to the Reduction in Palmitate Caused by Disruption of the FATB Gene in Arabidopsis

et al. 2004

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Disruption of the FATB gene in Arabidopsis results in a two-thirds reduction in saturated fatty acids, largely palmitate, in the leaf extra-plastidic phospholipids and a reduction in the growth rate of the mutant compared to wild type (Bonaventure G, Salas JJ, Pollard MR, Ohlrogge JB [2003] Plant Cell 15: 1020-1033. In this study, we report that although fatb-ko seedlings grow more slowly than wild type, the rate of fatty acid synthesis in leaves of the mutant increases by 40%. This results in approximately the same amount of palmitate exported from the plastid as in wild type but an increase in oleate export of about 55%. To maintain constant amounts of fatty acids in leaves, thereby counterbalancing their higher rate of production, the mutant also increases its rate of fatty acid degradation. Although fatb-ko leaves have higher rates of fatty acid synthesis and turnover, the relative proportions of membrane lipids are similar to wild type. Thus, homeostatic mechanisms to preserve membrane compositions compensate for substantial changes in rates of fatty acid and glycerolipid metabolism in the mutant. Pulse-chase labeling studies show that in fatb-ko leaves there is a net increase in the synthesis of both prokaryotic and eukaryotic lipids and consequently of their turnover. The net loss of palmitate from phosphatidylcholine plus phosphatidylethanolamine is similar for wild type and mutant, suggesting that mechanisms are not present that can preferentially preserve the saturated fatty acids. In summary, the leaf cell responds to the loss of saturated fatty acid production in the fatb-ko mutant by increasing both fatty acid synthesis and degradation, but in doing so the mechanisms for increased fatty acid turnover contribute to the lowering of the percentage of saturated fatty acids found in eukaryotic lipids.In plants, the major site for de novo fatty acid synthesis (FAS) occurs in the plastid (Ohlrogge et al., 1979). Fatty acids are either utilized in this organelle or exported to supply diverse cytoplasmic biosynthetic pathways and cellular processes. Production of fatty acids for export depends on the activity of acyl-ACP thioesterases (FATs) that hydrolyze acyl-acyl carrier protein (acyl-ACP) to release free fatty acids and ACP (for review, see Voelker et al., 1997). After export, the free fatty acids are re-esterified to CoA to form the cytosolic acyl-CoA pool (Pollard and Ohlrogge, 1999). In mesophyll cells, acyl-CoAs are primarily used for the biosynthesis of membrane glycerolipids in the endoplasmic reticulum (Browse and Somerville, 1991). However, in other cell types exported fatty acids have different fates. For example, in embryo cells of oilseeds, the major fraction is incorporated into triacylglycerols, while in epidermal cells a large fraction is utilized for the synthesis of waxes and cutin (Post-Beittenmiller, 1996;Kolattukudy, 2003). Furthermore, all cells synthesize sphingolipids (Lynch, 1993), and we recently estimated that as much as 30% to 40% of exported palmitate is needed for sphingoid ba...

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

Cited by 199 publications

References 64 publications

Genome-Wide Identification of Nodule-Specific Transcripts in the Model Legume Medicago truncatula

Genome-Wide Identification of Nodule-Specific Transcripts in the Model Legume Medicago truncatula

The Predicted Candidates of Arabidopsis Plastid Inner Envelope Membrane Proteins and Their Expression Profiles,

Metabolic Responses to the Reduction in Palmitate Caused by Disruption of the FATB Gene in Arabidopsis

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