Characterization of two forms of the multifunctional protein acting in fatty acid beta-oxidation

Peroxisome biogenesis and function

Peroxisomes are small and single membrane-delimited organelles that execute numerous metabolic reactions and have pivotal roles in plant growth and development. In recent years, forward and reverse genetic studies along with biochemical and cell biological analyses in Arabidopsis have enabled researchers to identify many peroxisome proteins and elucidate their functions. This review focuses on the advances in our understanding of peroxisome biogenesis and metabolism, and further explores the contribution of large-scale analysis, such as in sillco predictions and proteomics, in augmenting our knowledge of peroxisome function In Arabidopsis.

Seed storage oil mobilization

Storage oil mobilization starts with the onset of seed germination. Oil bodies packed with triacylglycerol (TAG) exist in close proximity with glyoxysomes, the single membrane-bound organelles that house most of the biochemical machinery required to convert fatty acids derived from TAG to 4-carbon compounds. The 4-carbon compounds in turn are converted to soluble sugars that are used to fuel seedling growth. Biochemical analysis over the last 50 years has identified the main pathways involved in this process, including beta-oxidation, the glyoxylate cycle, and gluconeogenesis. In the last few years molecular genetic dissection of the overall process in the model oilseed species Arabidopsis has provided new insight into its complexity, particularly with respect to the specific role played by individual enzymatic steps and the subcellular compartmentalization of the glyoxylate cycle. Both abscisic acid (ABA) and sugars inhibit storage oil mobilization and a substantial degree of the control appears to operate at the transcriptional level.

Peroxisomal beta-oxidation--a metabolic pathway with multiple functions

Fatty acid degradation in most organisms occurs primarily via the beta-oxidation cycle. In mammals, beta-oxidation occurs in both mitochondria and peroxisomes, whereas plants and most fungi harbor the beta-oxidation cycle only in the peroxisomes. Although several of the enzymes participating in this pathway in both organelles are similar, some distinct physiological roles have been uncovered. Recent advances in the structural elucidation of numerous mammalian and yeast enzymes involved in beta-oxidation have shed light on the basis of the substrate specificity for several of them. Of particular interest is the structural organization and function of the type 1 and 2 multifunctional enzyme (MFE-1 and MFE-2), two enzymes evolutionarily distant yet catalyzing the same overall enzymatic reactions but via opposite stereochemistry. New data on the physiological roles of the various enzymes participating in beta-oxidation have been gathered through the analysis of knockout mutants in plants, yeast and animals, as well as by the use of polyhydroxyalkanoate synthesis from beta-oxidation intermediates as a tool to study carbon flux through the pathway. In plants, both forward and reverse genetics performed on the model plant Arabidopsis thaliana have revealed novel roles for beta-oxidation in the germination process that is independent of the generation of carbohydrates for growth, as well as in embryo and flower development, and the generation of the phytohormone indole-3-acetic acid and the signal molecule jasmonic acid.

The Arabidopsis thaliana multifunctional protein gene (MFP2) of peroxisomal beta-oxidation is essential for seedling establishment

The multifunctional protein (MFP) of peroxisomal beta-oxidation catalyses four separate reactions, two of which (2-trans enoyl-CoA hydratase and L-3-hydroxyacyl-CoA dehydrogenase) are core activities required for the catabolism of all fatty acids. We have isolated and characterized five Arabidopsis thaliana mutants in the MFP2 gene that is expressed predominantly in germinating seeds. Seedlings of mfp2 require an exogenous supply of sucrose for seedling establishment to occur. Analysis of mfp2-1 seedlings revealed that seed storage lipid was catabolized more slowly, long-chain acyl-CoA substrates accumulated and there was an increase in peroxisome size. Despite a reduction in the rate of beta-oxidation, mfp2 seedlings are not resistant to the herbicide 2,4-dichlorophenoxybutyric acid, which is catabolized to the auxin 2,4-dichlorophenoxyacetic acid by beta-oxidation. Acyl-CoA feeding experiments show that the MFP2 2-trans enoyl-CoA hydratase only exhibits activity against long chain (C18:0) substrates, whereas the MFP2 L-3-hydroxyacyl-CoA dehydrogenase is active on C6:0, C12:0 and C18:0 substrates. A mutation in the abnormal inflorescence meristem gene AIM1, the only homologue of MFP2, results in an abnormal inflorescence meristem phenotype in mature plants (Richmond and Bleecker, Plant Cell 11, 1999, 1911) demonstrating that the role of these genes is very different. The mfp2-1 aim1double mutant aborted during the early stages of embryo development showing that these two proteins share a common function that is essential for this key stage in the life cycle.

Identification of a rice RNA- and microtubule-binding protein as the multifunctional protein, a peroxisomal enzyme involved in the beta -oxidation of fatty acids

The control of subcellular mRNA localization and translation is often mediated by protein factors that are directly or indirectly associated with the cytoskeleton. We report the identification and characterization of a rice seed protein that possesses both RNA and microtubule binding activities. In vitro UV cross-linking assays indicated that this protein binds to all mRNA sequences tested, although there was evidence for preferential binding to RNAs that contained A-C nucleotide sequence motifs. The protein was purified to homogeneity using a two-step procedure, and amino acid sequencing identified it as the multifunctional protein (MFP), a peroxisomal enzyme known to possess a number of activities involved in the beta-oxidation of fatty acids. The recombinant version of this rice MFP binds to RNA in UV cross-linking and gel mobility shift experiments, co-sediments specifically with microtubules, and possesses at least two enzymatic activities involved in peroxisomal fatty acid beta-oxidation. Taken together these data suggest that MFP has an important role in mRNA physiology in the cytoplasm, perhaps in regulating the localization or translation of mRNAs through an interaction with microtubules, in addition to its peroxisomal function.

Requirement for 3-ketoacyl-CoA thiolase-2 in peroxisome development, fatty acid beta-oxidation and breakdown of triacylglycerol in lipid bodies of Arabidopsis seedlings

3-ketoacyl-CoA thiolase (KAT) (EC: 2.3.1.16) catalyses a key step in fatty acid beta-oxidation. Expression of the Arabidopsis thaliana KAT gene on chromosome 2 (KAT2), which encodes a peroxisomal thiolase, is activated in early seedling growth. We identified a T-DNA insertion in this gene which abolishes its expression and eliminates most of the thiolase activity in seedlings. In the homozygous kat2 mutant, seedling growth is dependent upon exogenous sugar, and storage triacylglycerol (TAG) and lipid bodies persist in green cotyledons. The peroxisomes in cotyledons of kat2 seedlings are very large, the total peroxisomal compartment is dramatically increased, and some peroxisomes contain unusual membrane inclusions. The size and number of plastids and mitochondria are also modified. Long-chain (C16 to C20) fatty acyl-CoAs accumulate in kat2 seedlings, indicating that the mutant lacks long-chain thiolase activity. In addition, extracts from kat2 seedlings have significantly decreased activity with aceto-acetyl CoA, and KAT2 appears to be the only thiolase gene expressed at significant levels during germination and seedling growth, indicating that KAT2 has broad substrate specificity. The kat2 phenotype can be complemented by KAT2 or KAT5 cDNAs driven by the CaMV 35S promoter, showing that these enzymes are functionally equivalent, but that expression of the KAT5 gene in seedlings is too low for effective catabolism of TAG. By comparison with glyoxylate cycle mutants, it is concluded that while gluconeogenesis from fatty acids is not absolutely required to support Arabidopsis seedling growth, peroxisomal beta-oxidation is essential, which is in turn required for breakdown of TAG in lipid bodies.

The membrane-bound DnaJ protein located at the cytosolic site of glyoxysomes specifically binds the cytosolic isoform 1 of Hsp70 but not other Hsp70 species

DnaJ proteins are located in various compartments of the eukaryotic cell. As previously shown, peroxisomes and glyoxysomes possess a membrane-anchored form of DnaJ protein located on the cytosolic face. Hints as to how the membrane-bound co-chaperone interacts with cytosolic soluble chaperones were obtained by examining the affinity between the DnaJ protein and various potential partners of the Hsp70 family. Two genes encoding cytosolic Hsp70 isoforms were isolated and characterized from cucumber cotyledons. In addition, cDNAs encoding Hsp70 forms attributed to the cytosol, plastids and the lumen of the endoplasmic reticulum were prepared. His-tagged DnaJ proteins and glutathione S-transferase-Hsp70 fusion proteins were constructed. Using these tools, it was demonstrated that the soluble His-tagged form of DnaJ protein exclusively binds the cytosolic isoform 1 of Hsp70. This interaction was further analyzed by characterizing the interaction between the glyoxysome-bound form of the DnaJ protein and various isoforms of Hsp70. Specific binding to the glyoxysomal surface was only observed in the case of cytosolic isoform 1 of Hsp70. This interaction was strictly dependent on the presence of ADP. Glyoxysomes did not bind other cytosolic or plastidic isoforms or the BiP-related form of Hsp70. Analyzing the enzymatic properties of cytosolic Hsp70s, we showed that the ATPase-modulating activity of DnaJ was highest when isoform 1 was assayed. Collectively, the data indicate that the partner of the DnaJ protein anchored at the glyoxysomal membrane is the cytosolic isoform 1 of Hsp70. In addition to the chaperones located at the surface of glyoxysomes, two isoforms of Hsp70 and one soluble form of DnaJ protein were detected in the glyoxysomal matrix.

Strategies for the sustainable production of new biodegradable polyesters in plants: a review

In this study we review relevant pathways with regard to the production of poly(3-hydroxyalkanoates) (PHA) with medium chain length monomers in higher plants. On the basis of what is known of the genetics and the biochemistry of PHA formation in bacteria, and of fatty acid metabolism in various organisms, a number of possibilities for PHA production in model plants and in economically important crop plants are listed. Along with the molecular biology of PHA synthesis and fatty acid metabolism, we discuss theoretical and environmental considerations, metabolic engineering strategies, and plant transformation systems.Key words: polyhydroxyalkanoate, fatty acid, starch, potato, Arabidopsis.

Changing stereochemistry for a metabolic pathway in vivo. Experiments with the peroxisomal beta-oxidation in yeast

The biosphere is inherently built of chiral molecules, and once their metabolism is established, the stereochemical course of the reactions involved is seen to remain highly conserved. However, by replacing the yeast peroxisomal multifunctional enzyme (MFE), which catalyzes the second and third reactions of beta-oxidation of fatty acids via D-3-hydroxyacyl-CoA intermediates, with rat peroxisomal MFE, which catalyzes the same reactions via L-3-hydroxy intermediates, it was possible to change the chiralities of the intermediates in a major metabolic pathway in vivo. Both stereochemical alternatives allowed the yeast cells to grow on oleic acid, implying that when the beta-oxidation pathways evolved, the overall function was the determining factor for the acquisition of MFEs and not the stereospecificities of the reactions themselves.

Fatty acid beta-oxidation in glyoxysomes. Characterization of a new tetrafunctional protein (MFP III)

We describe a new form of a multifunctional protein possessing the enzyme activities of delta 3, delta 2-enoyl-CoA isomerase, 3-hydroxyacyl-CoA epimerase, L-3-hydroxyacyl-CoA dehydrogenase and L-3-hydroxyacyl-CoA forming 2-trans-enoyl-CoA hydratase. This isoform, characterized by a molecular mass of 81 kDa and an isoelectric point above pH 9, was designated MFP III. Along with the tetrafunctional 76.5 kDa MFP II and the trifunctional 74 kDa MFP I, MFP III participates in degradation of fatty acid in glyoxysomes during mobilization of fat reserves. In combination with thiolase, MFP III encompasses all activities to degrade 3-cis-enoyl-CoAs to acetyl-CoA.

Evidence for domain structures of the trifunctional protein and the tetrafunctional protein acting in glyoxysomal fatty acid beta-oxidation

In plant glyoxysomes, an enzyme activity responsible for a particular step in the fatty acid beta-oxidation is located on more than one protein species. Various monofunctional enzymes and two forms of a multifunctional protein are involved in the degradation of cis-unsaturated fatty acids. delta 3, delta 2-Enoyl-CoA isomerase activity, previously found to be located on a monofunctional dimeric protein, is attributable to one form of the monomeric multifunctional protein (MFP). The presence or absence of isomerase activity allows us to differentiate between the tetrafunctional 76.5-kDa isoform (MFP II) and the trifunctional 74-kDa isoform (MFP I) in cucumber (Cucumis sativus) cotyledons. Both MFP I and MFP II exhibited blocked N-terminal structures. MFP I and MFP II are distinguishable from each other by their susceptibility to limited proteolysis. A series of examples is presented describing the preparation of enzymically active proteolytic fragments. We demonstrate that both forms of the monomeric MFP are composed of domains separable from each other without loss of activity. By fragmentation of MFP I and subsequent chromatography, a 60-kDa peptide was purified retaining hydratase and epimerase activity but lacking dehydrogenase activity. In addition, a highly positively charged fragment was observed carrying solely dehydrogenase activity. From MFP II, a 36-kDa fragment with hydratase activity was characterized. An enzymically inactive 46-kDa fragment was prepared from MFP II and sequenced at its unblocked N-terminus.

Heat shock enhances the amount of prenylated Dnaj protein at membranes of glyoxysomes

Proteins similar to the bacterial Dnaj protein have been implicated as molecular chaperones in different compartments of eukaryots. A plant equivalent is now described in tissues of dark-grown cucumber seedlings. Using a cucumber Dnaj protein produced by expression in bacteria, we raised polyclonal antibodies against the protein and used them for localization studies. In etiolated cucumber seedlings, both cotyledons and hypocotyledons were found to contain Dnaj proteins. Cell fractionation of etiolated cotyledons showed that Dnaj proteins were detectable mainly in the postnuclear cell fraction after sedimentation at 10,000 x g, and in the microsomes. Following subfractionation by sucrose density gradient centrifugation and analysis by immunoblotting, a 53-kDa protein was attributed to the glyoxysomal fraction and an 80-kDa protein to the mitochondrial fraction. The glyoxysomal Dnaj protein behaved as a membrane-bound form. Upon heat shock, a slight increase in the content of the glyoxysomal Dnaj protein was found. When glyoxysomes were treated with protease and subsequently isolated by gradient centrifugation, virtually all immunologically detectable Dnaj protein was removed. Administration of radiolabelled mevalonic acid to cotyledons and isolation of glyoxysomes yielded labelled Dnaj protein which remained membrane bound during the purification of glyoxysomal membranes by floatation in a density gradient.

Peroxisomal beta-oxidation of polyunsaturated fatty acids

Peroxisomes have been shown to play an important role in the oxidative degradation of (poly)unsaturated fatty acids, and contain the enzyme activities needed for the metabolism of double bonds of unsaturated fatty acids in connection with this physiological function. Our understanding of the metabolic pathways and enzyme activities involved in the degradation of unsaturated acyl-CoAs has undergone a re-evaluation recently, and though many open questions still remain significant progress has been made, especially concerning the reactions metabolizing double bonds. The enzyme activities to be discussed here are 2,4-dienoyl-CoA reductase; 3/2-enoyl-CoA isomerase; 2-enoyl-CoA hydratase 2; 5-enoyl-CoA reductase and 3,5/2,4-dienoyl-CoA isomerase. Some of these activities are integral parts of the multifunctional proteins of beta-oxidation systems, which must also be taken into account in this context.

Fatty acid degradation in plant peroxisomes: function and biosynthesis of the enzymes involved

In plants, the fatty acid oxidation enzyme apparatus is exclusively located within glyoxysomes or peroxisomes. Following the formation of the CoA-ester, the machinery for the degradation of endogenous fatty acids consists of acyl-CoA oxidase, D-3-hydroxyacyl-CoA hydrolyase, 2,3-enoyl-CoA isomerase, isoenzymes of the multifunctional protein and thiolase. The multiple location of particular enzyme activities on different species of protein is discussed in detail. In cucumber cotyledons, the multifunctional protein exhibits a C-terminal targeting signal, -PRM like other glyoxysomal or leaf peroxisomal proteins. In contrast, proteolytic modification takes place at the N-terminus of thiolase and malate dehydrogenase. Thus, distinct mechanisms are envisaged to take place during the transfer of the cytosolic precursor into glyoxysomes prior to the intra-organellar assembly of the mature enzyme.

Evidence for a peroxisomal fatty acid beta-oxidation involving D-3-hydroxyacyl-CoAs. Characterization of two forms of hydro-lyase that convert D-(-)-3-hydroxyacyl-CoA into 2-trans-enoyl-CoA

A novel D-(-)-3-hydroxyacyl-CoA hydro-lyase, forming 2-trans-enoyl-CoA and formerly designated as epimerase (EC 5.1.2.3), was extracted from fat-degrading cotyledons of cucumber seedlings. The enzyme, called D-3-hydroxyacyl-CoA hydro-lyase or D-specific 2-trans-enoyl-CoA hydratase, is shown to be required for the degradation of unsaturated fatty acids that contain double bonds extending from even-numbered C atoms. The D-3-hydroxyacyl-CoA hydro-lyase was exclusively localized within peroxisomes. A 10,000-fold purification by chromatography on a hydrophobic matrix, a cation exchanger, on hydroxyapatite and Mono S led to two proteins of apparent homogeneity, both exhibiting Mr of 65,000. The D-3-hydroxyacyl-CoA hydro-lyases are homodimers with slightly differing isoelectric points around pH = 9.0. They catalyze the conversion of 2-trans-enoyl-CoA into D-3-hydroxyacyl-CoA. The reverse reaction was observed but no reaction with 2-cis-enoyl-CoAs or L-3-hydroxyacyl-CoAs. 2-trans-Decenoyl-CoA was converted 10-times faster than 2-trans-butenoyl-CoA. The conversion of 4-cis-decenoyl-CoA into octenoyl-CoA was demonstrated in vitro with purified proteins with an assay mixture containing acyl-CoA oxidase, multifunctional protein, thiolase and the D-3-hydroxyacyl-CoA hydro-lyase. Comparisons of enzyme activities present in the cotyledons or isolated peroxisomes clearly show that the pathway via dienoyl-CoA reductase is much less effective than the sequence involving D-3-hydroxyacyl-CoA hydro-lyase.

Purification and characterization of a plant peroxisomal delta 2, delta 3-enoyl-CoA isomerase acting on 3-cis-enoyl-CoA and 3-trans-enoyl-CoA

A delta 3, delta 2-enoyl-CoA isomerase was extracted from fat-degrading cotyledons of cucumber seedlings. The enzyme is required for the degradation of cis-unsaturated fatty acids, e.g. linoleic acid being present in the storage tissue of cucumber seedlings in high amounts. The delta 3, delta 2-enoyl-CoA isomerase was exclusively localized within peroxisomes. Its purification included chromatography on a hydrophobic matrix, a cation exchanger, and on hydroxylapatite. 17,000-fold purification yielded a protein of apparent homogeneity. The isomerase is a homodimer with a Mr of 50,000 and an isoelectric point of pH approximately 8.1. Delta 3, delta 2-Enoyl-CoA isomerase reversibly catalyzes the conversion of both cis-3-enoyl-CoA and trans-3-enoyl-CoA into trans-2-enoyl-CoA. The isomerase exhibited optimal activity at pH 9 and was active with 3-enoyl-CoA species having chain lengths of C6-C12, with cis-hexanoyl-CoA being the most effective substrate. The purified enzyme did not show enoyl-CoA hydratase activity.

Transition form of microbodies. Overlapping of two sets of marker proteins during the rearrangement of glyoxysomes into leaf peroxisomes

Several forms of microbodies have been characterized on the basis of their biochemical functions. We have investigated cucumber cotyledons which house two different microbody forms during their development. In these cells, a shift from organelles with the enzymes of beta-oxidation and glyoxylate cycle to peroxisomes with the enzymes of the photosynthetic C2-cycle can be induced by light. The transition state and the time course of changes was studied at different levels of gene expression during the first 2 days of illumination, by quantifying the rate of de novo protein synthesis in cotyledons and by measuring the mRNA activities in vitro. Synthesis and turnover of particular proteins were determined during the transition stage by immunoprecipitation of malate synthase, isocitrate lyase, catalase, multifunctional protein, and thiolase, and quantified by fluorography. From the mRNA activities and the rate of protein synthesis, gene expression for enzymes of the glyoxylate cycle and beta-oxidation started to decrease 24-36 h after onset of continuous light. At that time the rate of synthesis of glycolate oxidase, a leaf peroxisomal marker, is already maximal. By pulse-chase experiments 0-48 h after the onset of light the speed and intensity of protein turnover were measured. Rates of proteolytic degradation of individual enzymes indicated that the different enzymes were not lost simultaneously or all at once. This excludes a destruction of the whole organelle by the lytic compartment.

The glyoxysomal beta-oxidation system in cucumber seedlings: identification of enzymes required for the degradation of unsaturated fatty acids

Fat-degrading cotyledons from cucumber seedlings were investigated with respect to the enzymes metabolizing cis-unsaturated fatty acids. Isolated glyoxysomes degrade linoleic acid, the dominating fatty acid in the storage tissue of the seed. Glyoxysomes were shown to be the sole intracellular site of enzymes responsible for the degradation of unsaturated fatty acids. All three auxiliary enzyme activities discussed for the degradation of polyunsaturated fatty acids, 2,4-dienoyl-CoA reductase, enoyl-CoA isomerase, and 3-hydroxyacyl-CoA epimerase were localized within the matrix of glyoxysomes. They were not found in mitochondria. Separation of glyoxysomal matrix proteins on CM-cellulose revealed that epimerase activity was attributable to the multifunctional protein and also to another protein which apparently exhibited no other beta-oxidation activity. Furthermore, on the basis of the high epimerase activity present in glyoxysomes compared to a much lower 2,4-dienoyl-CoA reductase activity, the metabolism of unsaturated fatty acids via delta 2-cis-enoyl-CoA is considered as alternative to the reductase-dependent pathway.