Continuing fascination of exploration in natural substances from microorganisms†

In the search for novel organic compounds, I think it is of paramount importance not to overlook the pursuit of microorganism diversity and the abilities those microorganisms hold as a resource. In commemoration of Professor Satoshi ōmura’s Nobel Prize in Physiology or Medicine, I will briefly describe the microorganism that produces avermectin and then discuss how innovating isolation methods and pioneering isolation sources have opened the door to numerous new microorganism resources. Furthermore, as exploratory research of substances views the world from many different angles—from biological activity to a compound’s physiochemical properties—it is possible to discover a novel compound from a well-known microorganism. Based on this, I will discuss the future prospects of exploratory research.     

Improving the ‘tool box’ for robust industrial enzymes

The speed of sequencing of microbial genomes and metagenomes is providing an ever increasing resource for the identification of new robust biocatalysts with industrial applications for many different aspects of industrial biotechnology. Using ‘natures catalysts’ provides a sustainable approach to chemical synthesis of fine chemicals, general chemicals such as surfactants and new consumer-based materials such as biodegradable plastics. This provides a sustainable and ‘green chemistry’ route to chemical synthesis which generates no toxic waste and is environmentally friendly. In addition, enzymes can play important roles in other applications such as carbon dioxide capture, breakdown of food and other waste streams to provide a route to the concept of a ‘circular economy’ where nothing is wasted. The use of improved bioinformatic approaches and the development of new rapid enzyme activity screening methodology can provide an endless resource for new robust industrial biocatalysts.This mini-review will discuss several recent case studies where industrial enzymes of ‘high priority’ have been identified and characterised. It will highlight specific hydrolase enzymes and recent case studies which have been carried out within our group in Exeter.

     

Microbial hydantoinases – industrial enzymes from the origin of life?

Hydantoinases are valuable enzymes for the production of optically pure d- and l-amino acids. They catalyse the reversible hydrolytic ring cleavage of hydantoin or 5′-monosubstituted hydantoins and are therefore classified in the EC nomenclature as cyclic amidases (EC 3.5.2.). In the EC nomenclature, four different hydantoin-cleaving enzymes are described: dihydropyrimidinase (3.5.2.2), allantoinase (EC 3.5.2.5), carboxymethylhydantoinase (EC 3.5.2.4), and N-methylhydantoinase (EC 3.5.2.14). Beside these, other hydantoinases with known metabolic functions, such as imidase and carboxyethylhydantoinase and enzymes with unknown metabolic function, are described in the literature and have not yet been classified. An important question is whether the distinct hydantoinases, which are frequently classified as l-, d-, and non-selective hydantoinases depending on their substrate specificity and stereoselectivity, are related to each other. In order to investigate the evolutionary relationship, amino acid sequence data can be used for a phylogenetic analysis. Although most of these enzymes only share limited sequence homology (identity<15%) and therefore are only distantly related, it can be shown (i) that most of them are members of a broad set of amidases with similarities to ureases and build a protein superfamily, whereas ATP-dependent hydantoinases are not related, (ii) that the urease-related amidases have evolved divergently from a common ancestor and (iii) that they share a metal-binding motif consisting of conserved histidine residues. The difference in enantioselectivity used for the classification of hydantoinases on the basis of their biotechnological value does not reflect their evolutionary relationship, which is to a more diverse group of enzymes than was assumed earlier. This protein superfamily probably has its origin in the prebiotic conditions of the primitive earth. Received: 24 August 1998 / Received revision: 9 November 1998 / Accepted: 21 November 1998     

β-Diglycosidases from microorganisms as industrial biocatalysts: biochemical characteristics and potential applications

Flavonoid glycoside degradation can proceed through two alternative enzymatic pathways: one that is mediated by monoglycosidases, and the other catalyzed by a diglycosidase. β-Diglycosidase performs the flavonoid deglycosylation in a single reaction. The characterized β-diglycosidase activities recognize the following disaccharidic sugar moieties: β-primeverose, acuminose, vicianose, and β-rutinose. The present paper reviews the biochemical characteristics and potential industrial applications of microbial β-diglycosidases that break down plant diglycoconjugated flavonoids.

     

Protoplast fusion — a tool for genetic manipulation and breeding in industrial microorganisms

Protoplasts can be isolated from microbial cells by enzymatic digestion of the cell wall, in the presence of an osmotic stabilizer. Such protoplasts can be induced to fuse in the presence of agents such as the poly (ethylene glycols). When suitably selected auxotrophic strains are used, the fusion products can be recovered by selection on the basis of nutritional complementation. Cultivation of the protoplasts on a hypertonic growth medium induces regeneration of new cell wall material and their subsequent reversion to the normal cell form of the organism. The protoplast fusion technique has been applied sucessfully to both bacterial and fungal systems leading to the recovery of recombinant progeny. In the fungi, the recovery of non-parental segregants from inter-species crosses has also been demonstrated. In assessing the value of the fusion technique, caution may be necessary at this stage in its application to genetic mapping in bacteria. The behaviour of protoplasts, especially with respect to reversion, could be an additional factor that operates during selection, distorting recombination frequencies. However, the fusion technique, in providing a mechanism by which genetic recombination can be readily achieved, should be of great potential in empirical breeding and strain improvement. These aspects are reviewed.     

The quest for a vaccine against Helicobacter pylori: how to move from mouse to man?

Several lines of evidence from experimental animal models of infection have clearly demonstrated the feasibility of a prophylactic and therapeutic vaccine against Helicobacter pylori. However, comparatively few clinical studies have been carried out to evaluate whether the positive results obtained in animals can be reproduced in humans. The preliminary results obtained with single component, mucosally delivered vaccines have shown very limited results thus far. Very good immunogenicity and safety profiles are now being obtained with parenterally delivered, aluminium hydroxide-adjuvanted multicomponent candidate vaccines. For sure, better vaccine formulations, better antigen preparation(s), better adjuvants, and better delivery systems have to be designed and tested for safety and immunogenicity. These studies are also needed for deciphering those aspects of the effector immune responses that correlate with protection against H. pylori infection and disease.     

The quest for a mechanistic understanding of biodiversity–ecosystem services relationships

Ecosystem services (ES) approaches to biodiversity conservation are currently high on the ecological research and policy agendas. However, despite a wealth of studies into biodiversity''s role in maintaining ES (B–ES relationships) across landscapes, we still lack generalities in the nature and strengths of these linkages. Reasons for this are manifold, but can largely be attributed to (i) a lack of adherence to definitions and thus a confusion between final ES and the ecosystem functions (EFs) underpinning them, (ii) a focus on uninformative biodiversity indices and singular hypotheses and (iii) top-down analyses across large spatial scales and overlooking of context-dependency. The biodiversity–ecosystem functioning (B–EF) field provides an alternate context for examining biodiversity''s mechanistic role in shaping ES, focusing on species'' characteristics that may drive EFs via multiple mechanisms across contexts. Despite acknowledgements of a need for B–ES research to look towards underlying B–EF linkages, the connections between these areas of research remains weak. With this review, we pull together recent B–EF findings to identify key areas for future developments in B–ES research. We highlight a means by which B–ES research may begin to identify how and when multiple underlying B–EF relationships may scale to final ES delivery and trade-offs.     

The effect of β-glucosidase on some assays for cellulolytic enzymes

The effect of -glucosidase on three assays for cellulolytic enzymes, i. e. the activities against dyed Avicel, hydroxyethylcellulose (HEC) and filter paper (FPU), was studied using cellulase enzyme derived from Trichoderma reesei VTT-D-80133. The dyed Avicel and HEC assays were only slightly affected by -glucosidase, whereas the FPU assay was linearly dependent on the level of -glucosidase over a wide range of activity of this enzyme.     

The successful quest for oral factor Xa inhibitors; learnings for all of medicinal chemistry?

The medicinal chemistry of oral small molecule factor Xa inhibitors is discussed, highlighting key advances that led to clinical candidates and the first licensed medicines. Identification of neutral ligands for the primary specificity pocket was a key discovery; capitalised upon by structure based design and combinatorial methods to deliver many variations on the theme; but it was good medicinal chemistry practice, in the optimisation of physical properties, which ultimately delivered efficacious compounds with adequate oral exposure. As a retrospective appraisal, representative compounds were profiled using the more contemporary concepts of Ligand Efficiency and Property Forecast Indices; which gave clear indications of the value of these principles.     

Purification and characterization of β-mannanase from Bacillus licheniformis for industrial use

An easily scaled-up technique has been designed to purify -mannanase from Bacillus licheniformis. Using flocculation, ultrafiltration and ion-exchange chromatography, the enzyme was purified 33-fold with a final recovery of 47% and a specific activity of 4341 U mg^–1protein. The enzyme had maximum activity at 60 °C and pH 7.0. It was stable at 50 °C and pH 6.0 for 6 h, but lost all of its activity when held at 70 °C and pH 6.0 for 1 h.     

Balancing the protection of marine ecosystems with economic benefits from land‐based activities: The quest for international legal barriers

The major threats to the health, productivity, and biodiversity of the marine environment result from human activities on land. National laws have failed to provide an adequate response. In conformity with the obligations contained in the 1982 Law of the Sea Convention, in recent years states have launched new legislative attempts that have as their stated objective to give more priority to protection of the marine ecosystem from land‐based activities. The 1995 Global Programme of Action as well as regional treaties and programs provide for a wide variety of alternative strategies, including monitoring, economic instruments, raising of awareness, and capability‐building that all as a matter or urgency need to be pursued. This article discusses what has become the dominant substantive strategy: development and imple‐mentation of best available techniques and best management practices. The article describes the rationale underlying the application of these approaches in international law and examines how recent treaties and action programs have incorporated them. The article concludes that in several respects the law is inadequate, but that the main problem is the lack of commitment of states to accept obligations to apply technology‐based standards or practices that are sufficiently responsive to the need for protection of the marine ecosystem.     

The quest for an AIDS vaccine: is the CD8+ T-cell approach feasible?

The rationale for developing anti-HIV vaccines that stimulate cytotoxic T-lymphocyte responses is given. We argue that such vaccines will work, provided that attention is paid to the development of memory T-cell responses that are strong and preferably activated. Furthermore, the vaccine should match the prevailing virus clade as closely as possible. Vaccines will have to stimulate a wide range of responses, but it is not clear how this can be achieved.     

Protocatechuate 3,4-Dioxygenase from Nocardia erythropolis†

Protocatechuate 3,4-dioxygenase was isolated from a gram-positive bacterium, Nocardia erythropolis, the enzyme participates in the phthalate ester metabolism in the bacterium. Cultural conditions for production of the enzyme, the purification procedure, and some properties of the enzyme were studied. A bouillon (beef) medium was the most effective among those tested for cell growth and enzyme formation. The effect was due to the ring closure type of creatine compounds. Protocatechuate 3,4-dioxygenase was purified from the cell-free extract ca. 1,400-fold and it gave a single band on polyacrylamide gel electrophoresis. The molecular weight was estimated to be ca. 150,000. The optimal pH and temperature were pH 8.0 and 40°C, respectively. The enzyme was stable in a pH range from 7.6 to 8.6 and below 42°C. The enzyme was inhibited by several metals such as Pb²⁺ , Cd²⁺ and Hg²⁺ . The enzyme was active on a wide range of o-dihydroxyphenyl compounds, in contrast to the high specificity of similar enzymes from gram-negative bacteria (Pseudomonas). The enzyme had a broad absorption band in the visible region with a peak around 450 nm, suggesting the presence of non-heme ion(s) bound to the enzyme as a cofactor. The spectrum changed markedly upon addition of the substrate, possibly showing the formation of an enzyme-substrate complex.