Using the biological taxonomy to access biological literature with PathBinderH

PathBinderH allows users to make queries that retrieve sentences and the abstracts containing them from PubMed. Another aspect of PathBinderH is that users can specify biological taxa in order to limit searches by mentioning either the specified taxa, or their subordinate taxa, in the biological taxonomy. Although the current project requires this function only for plant taxa, the principle is extensible to the entire taxonomy.

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www.plantgenomics.iastate.edu/PathBinderH. Source code and databases on request.

Molecular biology of acetyl-CoA metabolism

We have characterized the expression of potential acetyl-CoA-generating genes (acetyl-CoA synthetase, pyruvate decarboxylase, acetaldehyde dehydrogenase, plastidic pyruvate dehydrogenase complex and ATP-citrate lyase), and compared these with the expression of acetyl-CoA-metabolizing genes (heteromeric and homomeric acetyl-CoA carboxylase). These comparisons have led to the development of testable hypotheses as to how distinct pools of acetyl-CoA are generated and metabolized. These hypotheses are being tested by combined biochemical, genetic and molecular biological experiments, which is providing insights into how acetyl-CoA metabolism is regulated.

Molecular biology of cytosolic acetyl-CoA generation

ATP citrate lyase (ACL) catalyses the ATP-dependent reaction between citrate and CoA to form oxaloacetate and acetyl-CoA. Our molecular characterizations of the cDNAs and genes coding for the Arabidopsis ACL indicate that the plant enzyme is heteromeric, consisting of two dissimilar subunits. The A subunit is homologous to the N-terminal third of the animal ACL, and the B subunit is homologous to C-terminal two-thirds of the animal ACL. Using both ACL-A- and ACL-B-specific antibodies and activity assays we have shown that ACL is located in the cytosol, and is not detectable in the plastids, mitochondria or peroxisomes. During seed development, ACL-A and ACL-B mRNA accumulation is co-ordinated with the accumulation of the cytosolic homomeric acetyl-CoA carboxylase mRNA. Antisense Arabidopsis plants reduced in ATP citrate lyase activity show a complex phenotype, with miniaturized organs, small cell size, aberrant plastid morphology and reduced cuticular wax. Our results indicate that ACL generates the cytosolic pool of acetyl-CoA, which is the substrate required for the biosynthesis of a variety of phytochemicals, including cuticular waxes and flavonoids.

The role of pyruvate dehydrogenase and acetyl-coenzyme A synthetase in fatty acid synthesis in developing Arabidopsis seeds

Acetyl-coenzyme A (acetyl-CoA) formed within the plastid is the precursor for the biosynthesis of fatty acids and, through them, a range of important biomolecules. The source of acetyl-CoA in the plastid is not known, but two enzymes are thought to be involved: acetyl-CoA synthetase and plastidic pyruvate dehydrogenase. To determine the importance of these two enzymes in synthesizing acetyl-CoA during lipid accumulation in developing Arabidopsis seeds, we isolated cDNA clones for acetyl-CoA synthetase and for the ptE1alpha- and ptE1beta-subunits of plastidic pyruvate dehydrogenase. To our knowledge, this is the first reported acetyl-CoA synthetase sequence from a plant source. The Arabidopsis acetyl-CoA synthetase preprotein has a calculated mass of 76,678 D, an apparent plastid targeting sequence, and the mature protein is a monomer of 70 to 72 kD. During silique development, the spatial and temporal patterns of the ptE1beta mRNA level are very similar to those of the mRNAs for the plastidic heteromeric acetyl-CoA carboxylase subunits. The pattern of ptE1beta mRNA accumulation strongly correlates with the formation of lipid within the developing embryo. In contrast, the level of mRNA for acetyl-CoA synthetase does not correlate in time and space with lipid accumulation. The highest level of accumulation of the mRNA for acetyl-CoA synthetase during silique development is within the funiculus. These mRNA data suggest a predominant role for plastidic pyruvate dehydrogenase in acetyl-CoA formation during lipid synthesis in seeds.

Coordinate regulation of the nuclear and plastidic genes coding for the subunits of the heteromeric acetyl-coenzyme A carboxylase

Plastidic acetyl-coenzyme A (CoA) carboxylase (ACCase) catalyzes the first committed reaction of de novo fatty acid biosynthesis. This heteromeric enzyme is composed of one plastid-coded subunit (beta-carboxyltransferase) and three nuclear-coded subunits (biotin carboxy-carrier, biotin carboxylase, and alpha-carboxyltransferase). We report the primary structure of the Arabidopsis alpha-carboxyltransferase and beta-carboxyltransferase subunits deduced from nucleotide sequences of the respective genes and/or cDNA. Co-immunoprecipitation experiments confirm that the alpha-carboxyltransferase and beta-carboxyltransferase subunits are physically associated. The plant alpha-carboxyltransferases have gained a C-terminal domain relative to eubacteria, possibly via the evolutionary acquisition of a single exon. This C-terminal domain is divergent among plants and may have a structural function rather than being essential for catalysis. The four ACCase subunit mRNAs accumulate to the highest levels in tissues and cells that are actively synthesizing fatty acids, which are used either for membrane biogenesis in rapidly growing tissues or for oil accumulation in developing embryos. Development coordinately affects changes in the accumulation of the ACCase subunit mRNAs so that these four mRNAs maintain a constant molar stoichiometric ratio. These data indicate that the long-term, developmentally regulated expression of the heteromeric ACCase is in part controlled by a mechanism(s) that coordinately affects the steady-state concentrations of each subunit mRNA.

Molecular characterization of the non-biotin-containing subunit of 3-methylcrotonyl-CoA carboxylase

The biotin enzyme, 3-methylcrotonyl-CoA carboxylase (MCCase) (3-methylcrotonyl-CoA:carbon-dioxide ligase (ADP-forming), EC 6.4.1. 4), catalyzes a pivotal reaction required for both leucine catabolism and isoprenoid metabolism. MCCase is a heteromeric enzyme composed of biotin-containing (MCC-A) and non-biotin-containing (MCC-B) subunits. Although the sequence of the MCC-A subunit was previously determined, the primary structure of the MCC-B subunit is unknown. Based upon sequences of biotin enzymes that use substrates structurally related to 3-methylcrotonyl-CoA, we isolated the MCC-B cDNA and gene of Arabidopsis. Antibodies directed against the bacterially produced recombinant protein encoded by the MCC-B cDNA react solely with the MCC-B subunit of the purified MCCase and inhibit MCCase activity. The primary structure of the MCC-B subunit shows the highest similarity to carboxyltransferase domains of biotin enzymes that use methyl-branched thiol esters as substrate or products. The single copy MCC-B gene of Arabidopsis is interrupted by nine introns. MCC-A and MCC-B mRNAs accumulate in all cell types and organs, with the highest accumulation occurring in rapidly growing and metabolically active tissues. In addition, these two mRNAs accumulate coordinately in an approximately equal molar ratio, and they each account for between 0.01 and 0.1 mol % of cellular mRNA. The sequence of the Arabidopsis MCC-B gene has enabled the identification of animal paralogous MCC-B cDNAs and genes, which may have an impact on the molecular understanding of the lethal inherited metabolic disorder methylcrotonylglyciuria.

Geranoyl-CoA carboxylase: a novel biotin-containing enzyme in plants

Geranoyl-CoA carboxylase (EC 6.4.1.4) is a biotin-containing enzyme previously described in two genera of bacteria. Here we report the presence of geranoyl-CoA carboxylase in kingdom Plantae. Geranoyl-CoA carboxylase was purified 180-fold from maize leaves. The enzyme has a biotin-containing subunit of 122 kDa. The pH optimum for activity is 8.3. The apparent Km values for the substrates geranoyl-CoA, bicarbonate, and ATP are 64 +/- 5 microM, 0. 58 +/- 0.04 mM, and 8.4 +/- 0.4 microM, respectively. Subcellular fractionations indicate that geranoyl-CoA carboxylase is located in plastids. Geranoyl-CoA carboxylase activity is ubiquitous in organs of monocots and dicots and varies with development. We postulate that geranoyl-CoA carboxylase plays an important role in isoprenoid catabolism in plants, in a pathway analogous to that shown in Psuedomonas sp. In plants, this catabolic pathway would require the interaction of at least three subcellular compartments (plastids, microbodies, and mitochondria) and two biotin-containing enzymes, geranoyl-CoA carboxylase and 3-methylcrotonyl-CoA carboxylase.

3-Methylcrotonyl-coenzyme A carboxylase is a component of the mitochondrial leucine catabolic pathway in plants

3-Methylcrotonyl-coenzyme A carboxylase (MCCase) is a mitochondrial biotin-containing enzyme whose metabolic function is not well understood in plants. In soybean (Glycine max) seedlings the organ-specific and developmentally induced changes in MCCase expression are regulated by mechanisms that control the accumulation of MCCase mRNA and the activity of the enzyme. During soybean cotyledon development, when seed-storage proteins are degraded, leucine (Leu) accumulation peaks transiently at 8 d after planting. The coincidence between peak MCCase expression and the decline in Leu content provides correlative evidence that MCCase is involved in the mitochondrial catabolism of Leu. Direct evidence for this conclusion was obtained from radiotracer metabolic studies using extracts from isolated mitochondria. These experiments traced the metabolic fate of [U-14C]Leu and NaH14CO3, the latter of which was incorporated into methylglutaconyl-coenzyme A (CoA) via MCCase. These studies directly demonstrate that plant mitochondria can catabolize Leu via the following scheme: Leu --> alpha-ketoisocaproate --> isovaleryl-CoA --> 3-methylcrotonyl-CoA --> 3-methylglutaconyl-CoA --> 3-hydroxy-3-methylglutaryl-CoA --> acetoacetate + acetyl-CoA. These findings demonstrate for the first time, to our knowledge, that the enzymes responsible for Leu catabolism are present in plant mitochondria. We conclude that a primary metabolic role of MCCase in plants is the catabolism of Leu.

Biochemical and molecular biological characterization of CAC2, the Arabidopsis thaliana gene coding for the biotin carboxylase subunit of the plastidic acetyl-coenzyme A carboxylase

The biotin carboxylase subunit of the heteromeric chloroplastic acetyl-coenzyme A carboxylase (ACCase) of Arabidopsis thaliana is coded by a single gene (CAC2), which is interrupted by 15 introns. The cDNA encodes a deduced protein of 537 amino acids with an apparent N-terminal chloroplast-targeting transit peptide. Antibodies generated to a glutathione S-transferase-CAC2 fusion protein react solely with a 51-kD polypeptide of Arabidopsis; these antibodies also inhibit ACCase activity in extracts of Arabidopsis. The entire CAC2 cDNA sequence was expressed in Escherichia coli and the resulting recombinant biotin carboxylase was enzymatically active in carboxylating free biotin. The catalytic properties of the recombinant biotin carboxylase indicate that the activity of the heteromeric ACCase may be regulated by light-/dark-induced changes in stromal pH. The CAC2 gene is maximally expressed in organs and tissues that are actively synthesizing fatty acids for membrane lipids or oil deposition. The observed expression pattern of CAC2 mirrors that previously reported for the CAC1 gene (J.-K. Choi, F. Yu, E.S. Wurtele, B.J. Nikolau [1995] Plant Physiol 109: 619-625; J. Ke, J.-K. Choi, M. Smith, H.T. Horner, B.J. Nikolau, E.S. Wurtele [1997] Plant Physiol 113: 357-365), which codes for the biotin carboxyl carrier subunit of the heteromeric ACCase. This coordination is probably partially established by coordinate transcription of the two genes. This hypothesis is consistent with the finding that the CAC2 and CAC1 gene promoters share a common set of sequence motifs that may be important in guiding the transcription of these genes.

Zrp2: a novel maize gene whose mRNA accumulates in the root cortex and mature stems

A near full-length cDNA clone (pZRP2) was isolated from a cDNA library constructed from maize root mRNAs. The predicted polypeptide has a calculated molecular mass of 66,975 Da, is largely hydrophilic, and contains 26 repeats of a motif the consensus sequence of which is RKATTSYG[S][D/E][D/E][D/E][D/E][P]. The function of the putative protein remains to be elucidated. The ZRP2 mRNA accumulates to the highest levels in young roots, and is also present in mature roots and stems of maize. Further analysis of young roots indicates that the lowest level of ZRP2 mRNA is near the root tip, with relatively high levels throughout the remainder of the root. In situ hybridization reveals that ZRP2 mRNA accumulates predominantly in the cortical parenchyma cells of the root. In vitro nuclear run-on transcription experiments indicate a dramatically higher level of zrp2 gene transcription in 3-day old roots than in 5-day old leaves. A zrp2 genomic clone, which includes the transcribed region and 4.7 kb of upstream sequence, was isolated and characterized.

Structure of the CAC1 gene and in situ characterization of its expression. The Arabidopsis thaliana gene coding for the biotin-containing subunit of the plastidic acetyl-coenzyme A carboxylase

The CAC1 gene of Arabidopsis thaliana that codes for the biotin carboxyl-carrier subunit of the heteromeric acetyl-coenzyme A carboxylase was isolated and sequenced. CAC1 is a single-copy gene interrupted by six introns. Subcellular immunogold labeling indicates that the biotin carboxyl-carrier subunit is localized in the stroma of the plastids and chloroplasts. The CAC1 mRNA accumulates throughout developing embryos and ovules of siliques at a time of rapid growth and oil accumulation (7 d after flowering), but is present at much lower levels in wall cells and central septal cells of the silique. Immunolocalization studies show that the pattern of accumulation of the biotin carboxyl-carrier subunit within the siliques and leaves is similar to that of the CAC1 mRNA. These observations indicate that the cellular pattern of biotin carboxyl-carrier protein accumulation in the developing silique may be determined by the transcriptional activity of the CAC1 gene.

Characterization of the cDNA and gene coding for the biotin synthase of Arabidopsis thaliana

Biotin, an essential cofactor, is synthesized de novo only by plants and some microbes. An Arabidopsis thaliana expressed sequence tag that shows sequence similarity to the carboxyl end of biotin synthase from Escherichia coli was used to isolate a near-full-length cDNA. This cDNA was shown to code for the Arabidopsis biotin synthase by its ability to complement a bioB mutant of E. coli. Site-specific mutagenesis indicates that residue threonine-173, which is highly conserved in biotin synthases, is important for catalytic competence of the enzyme. The primary sequence of the Arabidopsis biotin synthase is most similar to biotin synthases from E. coli, Serratia marcescens, and Saccharomyces cerevisiae (about 50% sequence identity) and more distantly related to the Bacillus sphaericus enzyme (33% sequence identity). The primary sequence of the amino terminus of the Arabidopsis biotin synthase may represent an organelle-targeting transit peptide. The single Arabidopsis gene coding for biotin synthase, BIO2, was isolated and sequenced. The biotin synthase coding sequence is interrupted by five introns. The gene sequence upstream of the translation start site has several unusual features, including imperfect palindromes and polypyrimidine sequences, which may function in the transcriptional regulation of the BIO2 gene.

Reduction of growth and acetyl-CoA carboxylase activity by expression of a chimeric streptavidin gene in Escherichia coli

The streptavidin gene from Streptomyces avidinii was expressed in E. coli as a non-fusion protein and as a glutathione S-transferase fusion protein. The streptavidin protein accumulated primarily in the inclusion bodies and did not alter cell growth. In contrast, the glutathione-S-transferase-streptavidin fusion protein was soluble. Nondenaturing polyacrylamide gel electrophoresis indicated that the chimeric glutathione-S-transferase-streptavidin protein was present mostly as a monomer, with some detectable polymeric forms. Cells grown in the presence of [3H]-biotin had label specifically associated with the expressed glutathione-S-transferase-streptavidin fusion protein, indicating this protein bound biotin in vivo. The majority of the radiolabeled biotin was associated with polymeric forms of the glutathione-S-transferase-streptavidin protein. The growth rates of biotin auxotrophs of E. coli growing in biotin-deficient media were substantially decreased by the expression of the glutathione-S-transferase-streptavidin gene. The decreased growth rate correlated with a decrease in acetyl-CoA carboxylase activity.

Molecular cloning and characterization of the cDNA coding for the biotin-containing subunit of the chloroplastic acetyl-coenzyme A carboxylase

We report the molecular cloning and sequence of the cDNA coding for the biotin-containing subunit of the chloroplastic acetylcoenzyme A (CoA) carboxylase (ACCase) of Arabidopsis thaliana (CAC1). The 3' end of the CAC1 sequence, coding for a peptide of 94 amino acids, which includes a putative biotinylation motif, was expressed in Escherichia coli as a glutathione-S-transferase (GST) fusion protein. The resulting GST-CAC1 fusion protein was biotinylated in vivo, indicating that CAC1 codes for a biotin-containing protein. Antibodies generated to the GST-CAC1 protein reacted solely with the 38-kD biotin-containing polypeptide of Arabidopsis. Furthermore, these antibodies inhibited ACCase activity in extracts from Arabidopsis leaves. The deduced amino acid sequence of CAC1 has an apparent N-terminal chloroplast-targeting transit peptide. The CAC1 protein is coded by a single Arabidopsis gene, and its mRNA accumulates to the highest levels in organs that are undergoing rapid growth. The amino acid sequence of the CAC1 protein is most similar to the biotin carboxyl-carrier protein component of eubacterial ACCases. These characterizations identify CAC1 as the biotin-containing subunit of the plastidic, heteromeric ACCase of Arabidopsis. The results support the ancient origin of the two structurally distinct ACCases of plants.

Regulation of [beta]-Methylcrotonyl-Coenzyme A Carboxylase Activity by Biotinylation of the Apoenzyme

Regulation of the expression of the gene(s) coding for the 78-kD, biotin-containing subunit of [beta]-methylcrotonyl-coenzyme A carboxylase (MCCase) was investigated in different organs of tomato (Lycopersicon esculantus) plants. The specific activity of MCCase is highest in extracts from roots, followed in descending order by ripe and ripening fruits, stems, and leaves. The specific activity is 10-fold higher in roots than in leaves. However, the steady-state levels of the 78-kD subunit of MCCase and its mRNA are approximately equal in both roots and leaves. Instead, the difference in MCCase activity between these two organs is directly correlated to the biotinylation status of the enzyme's biotin-containing subunit. Thus, the lower activity of MCCase in leaves is attributed to the reduced biotinylation of the biotin-containing subunit of the enzyme. Consistent with this model, a pool of nonbiotinylated enzyme is present in leaves, whereas the nonbiotinylated enzyme is undetectable in roots. The underbiotinylation of MCCase in leaves is not due to a lack of biotin in this organ, since the biotin concentration is 4- to 5-fold higher in leaves than in roots. These observations indicate that the posttranslational biotinylation of the biotin-containing sub-unit of MCCase is an important mechanism for regulating the organ-specific expression of MCCase activity.

Genomic organization of 251 kDa acetyl-CoA carboxylase genes in Arabidopsis: tandem gene duplication has made two differentially expressed isozymes

Acetyl-CoA carboxylase (ACCase) catalyzes the carboxylation of acetyl-CoA, forming malonyl-CoA a key intermediate in the biosynthesis of fatty acids and a variety of secondary metabolites. Based upon amino acid sequences conserved among rat, chicken, and E. coli ACCases, PCR-primers were used to amplify a genomic fragment which codes for an ACCase of Arabidopsis. The resulting fragment was used for isolation of genomic and cDNA clones. We have determined the complete cDNA sequence coding for an Arabidopsis ACCase consists of 2,254 amino acids with the molecular mass of 251 kDa. This enzyme contains no recognizable plastid transit-peptide sequence. Therefore, this ACCase is presumably the cytosolic isozyme. Southern analysis indicates that there are two ACCase genes in the Arabidopsis genome. Surprisingly, the results of RFLP analysis and physical mapping of the isolated genomic clones demonstrate that these two genes, acc1 and acc2, are contiguously located within a 25-kbp genomic region near the middle of chromosome 1. Both genes are transcriptionally active, as transcripts from each gene were detected by reverse transcription-PCR analysis using gene-specific primers. The acc1 and acc2 transcripts accumulate in leaves and seedlings but only the acc1 transcript accumulates in developing siliques, unexpectedly. The differences in the expression patterns may be indicative of the differential role of the two genes.

Molecular cloning and characterization of the cDNA coding for the biotin-containing subunit of 3-methylcrotonoyl-CoA carboxylase: identification of the biotin carboxylase and biotin-carrier domains

Soybean genomic clones were isolated based on hybridization to probes that code for the conserved biotinylation domain of biotin-containing enzymes. The corresponding cDNA was isolated and expressed in Escherichia coli through fusion to the bacterial trpE gene. The resulting chimeric protein was biotinylated in E. coli. Antibodies raised against the chimeric protein reacted specifically with an 85-kDa biotin-containing polypeptide from soybean and inhibited 3-methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) activity in cell-free extracts of soybean leaves. Thus, the isolated soybean gene and corresponding cDNA code for the 85-kDa biotin-containing subunit of 3-methylcrotonoyl-CoA carboxylase. The nucleotide sequence of the cDNA and portions of the genomic clones was determined. Comparison of the deduced amino acid sequence of the biotin-containing subunit of 3-methylcrotonoyl-CoA carboxylase with sequences of other biotin enzymes suggests that this subunit contains the functional domains for the first half-reaction catalyzed by all biotin-dependent carboxylases--namely, the carboxylation of biotin. These domains are arranged serially on the polypeptide, with the biotin carboxylase domain at the amino terminus and the biotin-carboxyl carrier domain at the carboxyl terminus.

Molecular cloning of cDNAs and genes coding for beta-methylcrotonyl-CoA carboxylase of tomato

Tomato cDNA and genomic clones were isolated by using as a probe a cDNA clone that had originally been identified by its ability to direct the synthesis of a biotin-containing polypeptide in Escherichia coli. The nucleotide sequences of the newly isolated cDNAs indicate that they are clones of a single mRNA molecule. However, one of the cDNA clones contains an insertion of a sequence which we identified as an unspliced intron. The amino acid sequence deduced from the nucleotide sequence of the cDNAs showed similarity to regions of previously sequenced biotin enzymes, indicating that the isolated cDNAs code for a biotin-containing protein. Portions of the cDNAs were expressed in E. coli as glutathione S-transferase or beta-galactosidase fusion proteins. Each fusion protein was purified and used to immunize rabbits. The resulting antisera recognized a 78-kDa biotin-containing polypeptide in tomato leaf extracts. In addition, both antisera specifically inhibited beta-methylcrotonyl-CoA carboxylase activity in extracts from tomato leaves. These characterizations have identified the isolated tomato cDNAs and genes as coding for the 78-kDa biotin subunit of beta-methylcrotonyl-CoA carboxylase. Comparison of the deduced amino acid sequence of the biotin subunit of beta-methylcrotonyl-CoA carboxylase with other biotin enzymes suggest that this subunit contains the biotin carboxylase and biotin carboxyl-carrier domains.

Purification and characterization of 3-methylcrotonyl-coenzyme-A carboxylase from leaves of Zea mays

3-Methylcrotonyl-CoA carboxylase has been purified to near homogeneity from maize leaves. The resulting preparations of 3-methylcrotonyl-CoA carboxylase have a specific activity of between 200 and 600 nmol.min-1.mg-1 protein, representing an approximately 5000-fold purification of the enzyme. The purified 3-methylcrotonyl-CoA carboxylase has a molecular weight of 853,000 +/- 34,000 and is composed of two types of subunits, a biotin-containing subunit of 80 +/- 2 kDa and a non-biotin-containing subunit of 58.5 +/- 1.5 kDa. These data suggest that the enzyme has an alpha 6 beta 6 configuration. The optimum pH for activity is 8.0. The kinetic constants for the substrates 3-methylcrotonyl-CoA, ATP, and HCO3- are 11 microM, 20 microM, and 0.8 mM, respectively. Kinetic studies of the 3-methylcrotonyl-CoA carboxylase reaction with variable concentrations of two substrates confirmed that ATP and HCO3- bind sequentially to the enzyme and that ATP and 3-methylcrotonyl-CoA bind in ping-pong fashion. However, similar analyses indicate that the binding of HCO3- at the first site is affected by 3-methylcrotonyl-CoA. Kinetic studies of the role of Mg2+ in the 3-methylcrotonyl-CoA carboxylase reaction establish that Mg.ATP is the substrate for the enzyme, that free ATP is an inhibitor, and that free Mg2+ is an activator. Both Mn2+ and Co2+ can substitute somewhat for Mg2+, but Zn2+ is unable to do so. In addition to carboxylating 3-methylcrotonyl-CoA, the maize carboxylase can carboxylate crotonyl-CoA, but not acetoacetyl-CoA. In fact, acetoacetyl-CoA is a potent, noncompetitive inhibitor, which indicates that the enzyme contains an acetoacetyl-CoA binding site that is independent of the active sites. The monovalent cations K+, Cs+, Rb+, and NH4+ activated 3-methylcrotonyl-CoA carboxylase activity, with Rb+ being the most potent activator. The inhibition of 3-methylcrotonyl-CoA carboxylase by sulfhydryl and arginyl modifying reagents could be partly alleviated by the substrates ATP and 3-methylcrotonyl-CoA, which suggests that sulfhydryl and arginyl residues may be involved in catalysis.

Purification and characterization of 3-methylcrotonyl-CoA carboxylase from somatic embryos of Daucus carota

3-Methylcrotonyl-CoA carboxylase, a biotin enzyme, was purified from embryos of Daucus carota. Polyethylene glycol precipitation and monomeric avidin affinity chromatography were used to purify all biotin enzymes from cell-free extracts of embryos. The resulting 3-methylcrotonyl-CoA carboxylase preparation had a specific activity of 745 nmol/min.mg protein, representing a 3725-fold purification of the enzyme and a 135% recovery of activity. Fractionation of the purified biotin-containing proteins by anionic exchange chromatography using Q-Sepharose partially resolved the 3-methylcrotonyl-CoA carboxylase from the other biotin enzymes. 3-Methylcrotonyl-CoA carboxylase has a biotin-containing subunit with a molecular mass of about 78,000 Da and a non-biotin-containing subunit of about 65,000 Da. The native enzyme is 987,000 Da. The optimum pH for activity is between 8.0 and 8.4. The apparent Km values for the substrates 3-methylcrotonyl-CoA, sodium bicarbonate, and ATP are 42 +/- 2 microM, 4.0 +/- 0.9 mM, and 21 +/- 2 microM, respectively. The enzyme is inhibited by acetoacetyl-CoA and palmitoyl-CoA.

An mRNA putatively coding for an O-methyltransferase accumulates preferentially in maize roots and is located predominantly in the region of the endodermis

ZRP4, a 1.4-kb mRNA that preferentially accumulates in roots of young Zea mays L. plants, was identified by isolation of the corresponding cDNA clone. Genomic Southern analysis indicates that the zrp4 gene is represented once in the corn genome. The deduced ZRP4 polypeptide of 39,558 D is rich in leucine, serine, and alanine. Comparison of the deduced ZRP4 polypeptide sequence to polypeptide sequences of previously cloned plant and animal genes indicates that ZRP4 may be an O-methyltransferase. The ZRP4 mRNA preferentially accumulates in young roots and can be detected only at low levels in leaf, stem, and other shoot organs. ZRP4 mRNA accumulation is developmentally regulated within the root, with very low levels of accumulation in the meristematic region, higher levels in the regions of cell elongation, highest levels in the region of cell maturation, and low levels in the mature regions of the root. ZRP4 mRNA is predominantly located in the endodermis, with lower levels in the exodermis. An intriguing possibility is that the ZRP4 mRNA may code for an O-methyltransferase involved in suberin biosynthesis.

Characterization of a gene that is expressed early in somatic embryogenesis of Daucus carota

The EMB-1 mRNA of carrot (Daucus carota) was isolated as an embryo abundant cDNA clone (T.H. Ulrich, E.S. Wurtele, B.J. Nikolau [1990] Nucleic Acids Res 18: 2826). Northern analyses of RNA isolated from embryos, cultured cells, and a variety of vegetative organs indicate that the EMB-1 mRNA specifically accumulates in embryos, beginning at the early stages of embryo development. In situ hybridization with both zygotic and somatic embryos show that the EMB-1 mRNA begins to accumulate at low levels throughout globular embryos. Accumulation of EMB-1 mRNA increases and becomes more localized as embryos mature; in torpedo embryos, EMB-1 mRNA preferentially accumulates in the meristematic regions, particularly the procambium. The similarity in distribution of EMB-1 mRNA in both zygotic and somatic embryos indicates that much of the spatial pattern of expression of the emb-1 gene is dependent on the developmental program of the carrot embryo and does not require maternal or endosperm factors. The EMB-1 protein (relative molecular weight 9910) is a very hydrophilic protein that is a member of a class of highly conserved proteins (typified also by the Em protein of wheat and the Lea D19 protein of cotton) that may be ubiquitous among angiosperm embryos but whose functions are as yet unknown. The carrot genome appears to contain one or two copies of the emb-1 gene. A 1313-base pair DNA fragment of the carrot genome containing the emb-1 gene was isolated and sequenced. The gene is interrupted by a single intron of 99 base pairs. Primer extension experiments identify two EMB-1 mRNAs, differing by 6 bases at their 5' ends that are transcribed from this gene.

Differential Accumulation of Biotin Enzymes during Carrot Somatic Embryogenesis

The activities of four biotin enzymes, acetyl-coenzyme A (CoA) carboxylase, 3-methylcrotonyl-CoA carboxylase, pyruvate carboxylase, and propionyl-CoA carboxylase, and the accumulation of six biotin-containing polypeptides were determined during development of somatic embryos of carrot (Daucus carota). Acetyl-CoA carboxylase activity increased more than sevenfold, whereas the activities of 3-methylcrotonyl-CoA carboxylase, pyruvate carboxylase, and propionyl-CoA carboxylase were relatively unaltered. An increase also occurred in the accumulation of three of the biotin-containing polypeptides (molecular masses of 220, 62, and 34 kilodaltons). Of these, the most dramatic change was in the accumulation of the 62-kilodalton biotin-containing polypeptide, which increased by at least 50-fold as embryogenic cell clusters developed into torpedo embryos.

Plants contain multiple biotin enzymes: discovery of 3-methylcrotonyl-CoA carboxylase, propionyl-CoA carboxylase and pyruvate carboxylase in the plant kingdom

Acetyl-CoA carboxylase is the sole biotin enzyme previously reported in plants. Western analysis with 125I-streptavidin of proteins extracted from carrot somatic embryos visualized six biotin-containing polypeptides, the relative molecular masses of which are 210,000, 140,000, 73,000, 50,000, 39,000, and 34,000. This multiplicity of the biotin-containing polypeptides can be partly explained by the discovery of 3-methylcrotonyl-CoA carboxylase, propionyl-CoA carboxylase, and pyruvate carboxylase in extracts of somatic carrot embryos, biotin enzymes previously unknown in the plant kingdom. These biotin enzymes seem to be widely distributed in the plant kingdom.

Isolation and characterization of a tomato cDNA clone which codes for a salt-induced protein

The cDNA clone (pNP24) coding for a protein induced by exogenous NaCl has been isolated from a tomato root cDNA library with the use of an inosine containing synthetic oligomer. The authenticity of the clone has been established by comparing the sequence of the clone to the NH2-terminal sequence of the protein which has been purified to homogeneity by HPLC. The nucleotide sequence of pNP24 reveals a 5' signal sequence, an open reading frame of 718 nucleotides, a 3' AT rich untranslated region containing a probable polyadenylation signal sequence, and a poly A stretch. The mature polypeptide sequence as deduced from the nucleotide sequence reveals a protein with a molecular weight of 24226. This protein has been named NP24. It is slightly basic and has an unusually high number of cysteines (15). Northern blot analyses reveal that the abundance of mRNA for NP24 is at least 100-fold greater in tomato suspension cells in log phase grown in medium with NaCl than in cells grown in the control medium. The mRNA for NP24 is below the level of detection in roots of young control tomato plants until several weeks after germination but it is induced earlier and to higher levels in roots stressed by 0.171 M NaCl. Thus salt stress accelerates the accumulation of message in tomato roots. A comparison of the steady state levels of mRNA for NP24 to the accumulation of NP24 by immuno analyses indicates that the accumulation of this protein is determined by its mRNA level. The protein is not secreted and is localized within the cytoplasm or the soluble fraction of the nucleus, vacuole, or microbodies. NP24 has a high degree of homology (58%) with thaumatin, a protein which has considerable value as an artificial sweetener.

Comparison of Starch and ADP-Glucose Pyrophosphorylase Levels in Nonembryogenic Cells and Developing Embryos from Induced Carrot Cultures

Cultures of carrot (Daucus carota L.) in a medium without added 2,4-dichlorophenoxyacetic acid were separated into fractions of embryos at different stages of development (large globular and heart, torpedo, and germinating) and nonembryogenic cells. The average starch content per cell in these fractions was similar. However, due to the smaller sizes of the cells of the embryos relative to the nonembryogenic cells, starch content per weight of tissue was higher in the embryos. The ADP-glucose pyrophosphorylase activity per cell in the nonembryogenic cells was double that of the embryo cells. Furthermore, the ratio of ADP-glucose pyrophosphorylase to starch was over 2-fold higher in the nonembryogenic cells, indicating that starch content is not simply determined by ADP-glucose pyrophosphorylase levels. ADP-glucose pyrophosphorylase activity of all culture fractions was directly proportional to the level of a single 50 kilodalton polypeptide detected by immunoblot analysis, using antiserum raised to the purified spinach leaf enzyme. In the same immunoblot analysis, novel polypeptides of 63 and 100 kilodalton were detected in embryos but were absent from nonembryogenic cells. This is one of the few reported examples of specific proteins which differentially accumulate in embryos and nonembryogenic cells.

Enzymes of Glucose Oxidation in Leaf Tissues : The Distribution of the Enzymes of Glycolysis and the Oxidative Pentose Phosphate Pathway between Epidermal and Mesophyll Tissues of C(3)-Plants and Epidermal, Mesophyll, and Bundle Sheath Tissues of C(4)-Plants

The distribution of the glycolytic enzymes, phosphofructokinase, aldolase, triosephosphate isomerase, phosphoglycerate kinase, pyruvate kinase, and the oxidative pentose phosphate pathway enzymes, glucose 6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase, was determined in the leaf tissues of two C(3)-plants, pea and leek, and two C(4)-plants, maize and sorghum. All enzymes examined were found in epidermal tissue. In pea, maize, and sorghum leaves, the specific activities of these enzymes were usually higher in the nonphotosynthetic epidermal tissue than in the photosynthetic tissues of the leaves. In leek leaves, which were etiolated, specific activities were similar in both epidermal and mesophyll tissue. The distribution of the rate limiting enzymes of glycolysis and the oxidative pentose phosphate pathways probably reflects the capacity of each tissue to generate NADH, NADPH, and ATP from the oxidation of glucose. This capacity appears to be greater in leaf tissues unable to generate reducing equivalents and ATP by photosynthesis, that is, in epidermal tissues and etiolated mesophyll tissue.

Use of streptavidin to detect biotin-containing proteins in plants

A procedure to detect biotinyl proteins after fractionation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis was developed. Proteins were immobilized on nitrocellulose and biotin-containing proteins were detected by probing with 125I-streptavidin. Using this procedure a small survey of biotinyl protein in plants was undertaken. In total four biotin-containing proteins were detected in higher plants of molecular weights 62,000, 50,000, 34,000, and 31,000. These biotinyl proteins were not ubiquitous in the plants surveyed. In the cyanobacterium Anabeana variabilis, a single biotin-containing protein of 21,000 Da was detected. In isolated spinach chloroplasts, the two biotinyl proteins detected were soluble. The results are discussed in relation to acetyl-CoA carboxylase.

Natural plant chemicals: sources of industrial and medicinal materials

Many higher plants produce economically important organic compounds such as oils, resins, tannins, natural rubber, gums, waxes, dyes, flavors and fragrances, pharmaceuticals, and pesticides. However, most species of higher plants have never been described, much less surveyed for chemical or biologically active constituents, and new sources of commercially valuable materials remain to be discovered. Advances in biotechnology, particularly methods for culturing plant cells and tissues, should provide new means for the commercial processing of even rare plants and the chemicals they produce. These new technologies will extend and enhance the usefulness of plants as renewable resources of valuable chemicals. In the future, biologically active plant-derived chemicals can be expected to play an increasingly significant role in the commercial development of new products for regulating plant growth and for insect and weed control.

Subcellular and Developmental Distribution of beta-Cyanoalanine Synthase in Barley Leaves

The subcellular and developmental distribution of beta-cyanoalanine synthase (EC 4.4.1.9), which catalyzes the reaction between cysteine and HCN to form beta-cyanoalanine and H(2)S, were investigated in barley (Hordeum vulgare) leaves. Total leaf activity was 1.1 micromoles per minute per gram fresh weight. Sucrose density gradients of lysed mesophyll protoplasts of barley revealed the exclusive or predominant localization of beta-cyanoalanine synthase in the mitochondria. The enzyme was absent from both vacuole and chloroplast fractions.beta-Cyanoalanine synthase activity was distributed over the entire length of the barley leaf. Activity was dependent on the developmental stage, with a 3.5-fold higher activity in the oldest (apical) compared to the youngest (basal) parts of the leaf. The corresponding difference in activity for mesophyll protoplasts isolated from these parts was 7.5-fold. In younger leaf seagments, the nonchlorophyllous tissues accounted for up to 70% of the total beta-cyanoalanine synthase activity. These results are discussed with reference to the formation of HCN as a substrate in barley leaves.

Subcellular distribution of acetyl-coenzyme A carboxylase in mesophyll cells of barley and sorghum leaves

The subcellular distribution of acetyl-CoA carboxylase [acetyl-CoA-carbon dioxide ligase (ADP-forming), EC 6.4.1.2] was determined in mesophyll protoplasts isolation from barley, a C3 plant, and sorghum, a C4 plant. In both species, all of the mesophyll acetyl-CoA carboxylase was demonstrated to be chloroplastic. In barley leaves and mesophyll protoplasts, a single biotinyl protein of 60,000 Da was identified by a modified Western-blotting procedure. The subcellular distribution of this biotinyl protein was identical to that found for acetyl-CoA carboxylase. These results are discussed in relation to the compartmentation of reactions requiring malonyl-CoA as a substrate.

Tissue Distribution of beta-Cyanoalanine Synthase in Leaves

beta-Cyanoalanine synthase, which catalyzes the reaction between cysteine and HCN to form beta-cyanoalanine and H(2)S, was assayed in leaf tissues from cyanogenic (Sorghum bicolor x Sorghum sudanense [sorghum]) and noncyanogenic (Pisum sativum [pea], Zea mays [maize], and Allium porrum [leek]) plants. The activity in whole leaf extracts ranged from 33 nanomoles per gram fresh weight per minute in leeks, to 1940 nanomoles per gram fresh weight per minute in sorghum. The specific activities of beta-cyanoalanine synthase in epidermal protoplasts from maize and sorghum and in epidermal tissues from peas were in each case greater than the corresponding values for mesophyll protoplasts or tissues, or for strands of bundle sheath cells.THE TISSUE DISTRIBUTIONS FOR THIS ENZYME WERE DETERMINED FOR PEA, LEEK, AND SORGHUM: the mesophyll protoplasts and tissues in these three plants contained 65% to 78% of the enzyme, while epidermal protoplasts and tissues contained 10% to 35% of the total leaf activity. In sorghum, the bundle sheath strands contained 13% of the leaf activity. The presence of beta-cyanoalanine synthase in all tissues and species studied suggests a fundamental role for this enzyme in plant metabolism.

Tissue distribution of acetyl-coenzyme a carboxylase in leaves

Acetyl-CoA carboxylase [acetyl-CoA-carbon dioxide ligase (ADP forming), EC 6.4.1.2] is a biotin-containing enzyme catalyzing the formation of malonyl-CoA. The tissue distribution of this enzyme was determined for leaves of C(3)- and C(4)-plants. The mesophyll tissues of the C(3)-plants Pisum sativum and Allium porrum contained 90% of the leaf acetyl-CoA carboxylase activity, with the epidermal tissues containing the remainder. Western blotting of proteins fractionated by sodium dodecyl sulfate polyacrylamide gel electrophoresis, using (125)I-streptavidin as a probe, revealed biotinyl proteins of molecular weights 62,000, 51,000, and 32,000 in P. sativum and 62,000, 34,000, and 32,000 in A. porrum.In the C(4)-plant sorghum, epidermal protoplasts, mesophyll protoplasts and strands of bundle sheath cells contained 35, 47, and 17%, respectively, of the total leaf acetyl-CoA carboxylase activity. In Zea mays leaves the respective figures were 10% for epidermal protoplasts, 56% for mesophyll protoplasts, and 32% for bundle sheath strands. Biotinyl proteins of molecular weights 62,000 and 51,000 were identified in leaves of sorghum and Z. mays.The results are discussed with respect to each tissue's requirements for malonyl-CoA for various metabolic pathways.

Subcellular Localization of a UDP-Glucose:Aldehyde Cyanohydrin beta-Glucosyl Transferase in Epidermal Plastids of Sorghum Leaf Blades

Epidermal and mesophyll protoplasts, prepared from leaf blades of 6-day-old light-grown Sorghum bicolor seedlings were separated by differential sedimentation and assayed for a number of enzymes. The epidermal protoplasts contained higher levels of NADPH-cytochrome c reductase (EC 1.6.2.4), triose phosphate isomerase (EC 5.3.1.1), phosphoenolpyruvate carboxylase (EC 4.1.1.31), and a UDP-glucose:cyanohydrin beta-glucosyl transferase (EC 2.4.1.85), but lower levels of NADP(+) triosephosphate dehydrogenase (EC 1.2.1.13) than did mesophyll protoplasts. When protoplast preparations were lysed and applied to linear sucrose density gradients, triosephosphate isomerase was found to be present in epidermal plastids. A significant fraction (41%) of the glucosyl transferase activity was also associated with the epidermal plastids.