Bacterial NO synthases

Unlike mammalian NO synthases, bacterial NO synthases do not contain a reductase domain. The only exception from this rule is the NO synthase from myxobacterium Sorangium cellulosum, but its reductase domain has unusual structure and location in the enzyme molecule. Recent achievements in bacterial genome sequencing have revealed the gene coding NO synthase (represented as an oxygenase domain) in some bacteria and have advanced the study of structure and functions of bacterial NO synthases. Important features of structure, sources of reducing equivalents, evolutionary connections, and functions of bacterial NO synthases (i.e. participation in nitration of the indole ring of Trp, in reparation of UV-radiation damage, role in adaptation of bacteria to oxidative stress, participation in the synthesis of cGMP, and resistance of bacteria against antibiotics) are described.     

Isoprenyl diphosphate synthases

Isoprenyl diphosphate synthases catalyze consecutive condensations of isopentenyl diphosphates with allylic primer substrates to form linear backbones for all isoprenoid compounds including cholesterol. These synthases are classified according to the final chain length of their end products and the stereochemistry of the newly formed double bonds. Mutagenesis and X-ray crystallography data have uncovered the basic catalytic and chain length determination mechanisms of E-isoprenyl diphosphate synthases and shed light on their possible evolutionary course. Although much less is known about the Z-isoprenyl diphosphate synthase family, successful cloning and subsequent crystallizations in the near future will no doubt bring more insight as researchers begin to unravel the essential components and precise reaction mechanisms of this cellular machinery.     

Mammalian hyaluronan synthases

Three mammalian hyaluronan (HA) synthase genes, HAS1, HAS2, and HAS3, have been cloned and expressed, allowing the mechanisms for regulation of HA biosynthesis and function to be studied. The hyaluronan synthase (HAS) isoforms differ in kinetic characteristics and product size. The expression of each HAS isoform is controlled in a different fashion when mammalian cells are stimulated by various cytokines and the expression patterns are both spatially and temporally regulated during embryonic development. The existence of three different HAS isoforms with different characteristics implies that the broad range of biological and physiological roles performed by HA are regulated by controlling the activities and expression of the HAS isoforms. This review focuses on recent findings on the regulatory mechanisms for controlling HA biosynthesis and provides new insights into the enzymic basis for the functional regulation of HA.     

Multi-tasking phytochelatin synthases

Phytochelatins are essential for cadmium and arsenic detoxification in plants, some fungi, and animals. It is mysterious, that the responsible enzymes, phytochelatin synthases (PCS), are constitutively expressed and so widespread in nature. Phylogenetic analysis indicates multiple horizontal transfers of PCS genes, but a bacterial origin appears unlikely. Differences between bacterial and eukaryotic PCS proteins in structure and activity had indicated bi-functionality of phytochelatin synthases as peptidases and transpeptidases. Recent observations indicate that PCS indeed serve physiological functions that most likely are much more prevalent than cadmium or arsenic detoxification. First, PCS-deficient Arabidopsis thaliana mutants are hypersensitive to zinc suggesting a role of phytochelatin synthesis, i.e. the formation of metal-binding peptides from glutathione in a transpeptidase reaction, in Zn homeostasis. Second, these mutants are also impaired in defense responses conferring resistance to incompatible pathogens (= nonhost resistance). The latter is hypothesized to be attributable to an involvement of PCS as a peptidase in indole glucosinolate metabolism. Possibly, micronutrient homeostasis and nonhost resistance are closely connected as PCS are not the only proteins involved in both processes.     

Mechanisms of acetohydroxyacid synthases

Acetohydroxyacid synthases are thiamin diphosphate- (ThDP-) dependent biosynthetic enzymes found in all autotrophic organisms. Over the past 4-5 years, their mechanisms have been clarified and illuminated by protein crystallography, engineered mutagenesis and detailed single-step kinetic analysis. Pairs of catalytic subunits form an intimate dimer containing two active sites, each of which lies across a dimer interface and involves both monomers. The ThDP adducts of pyruvate, acetaldehyde and the product acetohydroxyacids can be detected quantitatively after rapid quenching. Determination of the distribution of intermediates by NMR then makes it possible to calculate individual forward unimolecular rate constants. The enzyme is the target of several herbicides and structures of inhibitor-enzyme complexes explain the herbicide-enzyme interaction.     

Flavones and flavone synthases

Within the secondary metabolite class of flavonoids which consist of more than 9000 known structures, flavones define one of the largest subgroups. Their natural distribution is demonstrated for almost all plant tissues. Various flavone aglyca and their O- or C-glycosides have been described in the literature. The diverse functions of flavones in plants as well as their various roles in the interaction with other organisms offer many potential applications, not only in plant breeding but also in ecology, agriculture and human nutrition and pharmacology. In this context, the antioxidative activity of flavones, their use in cancer prevention and treatment as well as the prevention of coronary heart disease should be emphasized. The therapeutic potential of flavones makes these compounds valuable targets for drug design, including recombinant DNA approaches. The biosynthesis of flavones in plants was found to be catalyzed by two completely different flavone synthase proteins (FNS), a unique feature within the flavonoids. The first, FNS I, a soluble dioxygenase, was only described for members of the Apiaceae family so far. The second, FNS II, a membrane bound cytochrome P450 enzyme, has been found in all other flavone accumulating tissues. This phenomenon is particularly of interest from the evolutionary point of view concerning the flavone biosynthesis and functions in plants. Recently, FNS I and FNS II genes have been cloned from a number of plant species. This now enables detailed biochemical and molecular characterizations and also the development of direct metabolic engineering strategies for modifications of flavone synthesis in plants to improve their nutritional and/or biopharmaceutical value.     

Higher plant cellulose synthases

Cellulose, an aggregate of unbranched polymers of β-1,4-linked glucose residues, is the major component of wood and thus paper, and is synthesized by plants, most algae, some bacteria and fungi, and even some animals. The genes that synthesize cellulose in higher plants differ greatly from the well-characterized genes found in Acetobacter and Agrobacterium sp. More correctly designated as 'cellulose synthase catalytic subunits', plant cellulose synthase (CesA) proteins are integral membrane proteins, approximately 1,000 amino acids in length. The sequences for more than 20 full-length CesA genes are available, and they show high similarity to one another across the entire length of the encoded protein, except for two small regions of variability. There are a number of highly conserved residues, including several motifs shown to be necessary for processive glycosyltransferase activity. No crystal structure is known for cellulose synthase proteins, and the exact enzymatic mechanism is unknown. There are a number of mutations in cellulose synthase genes in the model organism Arabidopsis thaliana. Some of these mutants show altered morphology due to the lack of a properly developed primary or secondary cell wall. Others show resistance to well-characterized cellulose biosynthesis inhibitors.     

Mammalian nitric oxide synthases.

The nitric oxide (NO) synthase family of enzymes generate NO from L-arginine, which acts as a biologic effector molecule in a broad number of settings. This report summarizes some of the current information regarding NO synthase structure-function, reaction mechanism, control of catalysis, and protein interactions.     

Building-block selectivity of polyketide synthases

For the past decade, polyketide synthases have presented an exciting paradigm for the controlled manipulation of complex natural product structure. These multifunctional enzymes catalyze the biosynthesis of polyketide natural products by stepwise condensation and modification of metabolically derived building blocks. In particular, regioselective modification of polyketide structure is possible by alterations in either intracellular acyl-CoA pools or, more commonly, by manipulation of acyl transferases that act as the primary gatekeepers for building blocks.     

Inhibitors of specific ceramide synthases

Ceramide synthases (CerSs) are key enzymes in the biosynthesis of ceramides and display a group of at least six different isoenzymes (CerS1-6). Ceramides itself are bioactive molecules. Ceramides with different N-acyl side chains (C_14:0-Cer – C_26:0-Cer) possess distinct roles in cell signaling. Therefore, the selective inhibition of specific CerSs which are responsible for the formation of a specific ceramide holds promise for a number of new clinical treatment strategies, e.g., cancer. Here, we identified four of hitherto unknown functional inhibitors of CerSs derived from the FTY720 (Fingolimod) lead structure and showed their inhibitory effectiveness by two in vitro CerS activity assays. Additionally, we tested the substances in two cell lines (HCT-116 and HeLa) with different ceramide patterns. In summary, the in vitro activity assays revealed out that ST1058 and ST1074 preferentially inhibit CerS2 and CerS4, while ST1072 inhibits most potently CerS4 and CerS6. Importantly, ST1060 inhibits predominately CerS2. First structure–activity relationships and the potential biological impact of these compounds are discussed.     

Synthetic biology of polyketide synthases

Complex reduced polyketides represent the largest class of natural products that have applications in medicine, agriculture, and animal health. This structurally diverse class of compounds shares a common methodology of biosynthesis employing modular enzyme systems called polyketide synthases (PKSs). The modules are composed of enzymatic domains that share sequence and functional similarity across all known PKSs. We have used the nomenclature of synthetic biology to classify the enzymatic domains and modules as parts and devices, respectively, and have generated detailed lists of both. In addition, we describe the chassis (hosts) that are used to assemble, express, and engineer the parts and devices to produce polyketides. We describe a recently developed software tool to design PKS system and provide an example of its use. Finally, we provide perspectives of what needs to be accomplished to fully realize the potential that synthetic biology approaches bring to this class of molecules.     

Metabolic control of hyaluronan synthases

Hyaluronan (HA) is a glycosaminoglycan composed by repeating units of D-glucuronic acid (GlcUA) and N-acetylglucosamine (GlcNAc) that is ubiquitously present in the extracellular matrix (ECM) where it has a critical role in the physiology and pathology of several mammalian tissues. HA represents a perfect environment in which cells can migrate and proliferate. Moreover, several receptors can interact with HA at cellular level triggering multiple signal transduction responses. The control of the HA synthesis is therefore critical in ECM assembly and cell biology; in this review we address the metabolic regulation of HA synthesis. In contrast with other glycosaminoglycans, which are synthesized in the Golgi apparatus, HA is produced at the plasma membrane by HA synthases (HAS1-3), which use cytoplasmic UDP-glucuronic acid and UDP-N-acetylglucosamine as substrates. UDP-GlcUA and UDP-hexosamine availability is critical for the synthesis of GAGs, which is an energy consuming process. AMP activated protein kinase (AMPK), which is considered a sensor of the energy status of the cell and is activated by low ATP:AMP ratio, leads to the inhibition of HA secretion by HAS2 phosphorylation at threonine 110. However, the most general sensor of cellular nutritional status is the hexosamine biosynthetic pathway that brings to the formation of UDP-GlcNAc and intracellular protein glycosylation by O-linked attachment of the monosaccharide β-N-acetylglucosamine (O-GlcNAcylation) to specific aminoacid residues. Such highly dynamic and ubiquitous protein modification affects serine 221 residue of HAS2 that lead to a dramatic stabilization of the enzyme in the membranes.     

Non-modular polyketide synthases in myxobacteria

Myxobacteria are prolific producers of a wide variety of secondary metabolites. The vast majority of these compounds are complex polyketides which are biosynthesised by multimodular polyketide synthases (PKSs). In contrast, few myxobacterial metabolites isolated to date are derived from non-modular PKSs, in particular type III PKSs. This review reports our progress on the characterisation of type III PKSs in myxobacteria. We also summarize current knowledge on bacterial type III PKSs, with a special focus on the evolutionary relationship between plant and bacterial enzymes. The biosynthesis of a quinoline alkaloid in Stigmatella aurantiaca by a non-modular PKS is also discussed.     

Cellulose synthases and related enzymes

The discovery of a large number of genes encoding cellulose synthases and related glycosyltransferases in plants has led to a renewed interest in the biosynthesis of cell-wall polysaccharides. A number of approaches, including virus-induced gene silencing have proven useful in the functional analysis of these genes. X-ray analysis of the structures of a few glycosyltransferases has led to the identification and confirmation of the role of conserved residues within this group of enzymes. Analysis of related enzymes has provided useful information on the possible domain organization of cellulose synthases and the requirement for at least two separate glycosyltransferase activities in the processive synthesis of sugar chains.