New directions in metabolic engineering

Perspectives in metabolic engineering: understanding cellular regulation towards the control of metabolic routes

Metabolic engineering seeks to redirect metabolic pathways through the modification of specific biochemical reactions or the introduction of new ones with the use of recombinant technology. Many of the chemicals synthesized via introduction of product-specific enzymes or the reconstruction of entire metabolic pathways into engineered hosts that can sustain production and can synthesize high yields of the desired product as yields of natural product-derived compounds are frequently low, and chemical processes can be both energy and material expensive; current endeavors have focused on using biologically derived processes as alternatives to chemical synthesis. Such economically favorable manufacturing processes pursue goals related to sustainable development and "green chemistry". Metabolic engineering is a multidisciplinary approach, involving chemical engineering, molecular biology, biochemistry, and analytical chemistry. Recent advances in molecular biology, genome-scale models, theoretical understanding, and kinetic modeling has increased interest in using metabolic engineering to redirect metabolic fluxes for industrial and therapeutic purposes. The use of metabolic engineering has increased the productivity of industrially pertinent small molecules, alcohol-based biofuels, and biodiesel. Here, we highlight developments in the practical and theoretical strategies and technologies available for the metabolic engineering of simple systems and address current limitations.

Surmounting antimicrobial resistance in the Millennium Superbug: Staphylococcus aureus

Staphylococcus aureus is the third most dreaded pathogen posing a severe threat due to its refractory behavior against the current armamentarium of antimicrobial drugs. This is attributed to the evolution of an array of resistance mechanisms responsible for morbidity and mortality globally. Local and international travel has resulted in the movement of drug resistant S. aureus clones from hospitals into communities and further into different geographical areas where they have been responsible for epidemic outbreaks. Thus, there is a dire necessity to refrain further cross movement of these multidrug resistant clones across the globe. The plausible alternative to prevent this situation is by thorough implementation of regulatory aspects of sanitation, formulary usage and development of new therapeutic interventions. Various strategies like exploring novel antibacterial targets, high throughput screening of microbes, combinatorial and synthetic chemistry, combinatorial biosynthesis and vaccine development are being extensively sought to overcome multidrug resistant chronic Staphylococcal infections. The majority of the antibacterial drugs are of microbial origin and are prone to being resisted. Anti-staphylococcal plant natural products that may provide a new alternative to overcome the refractory S.aureus under clinical settings have grossly been unnoticed. The present communication highlights the new chemical entities and therapeutic modalities that are entering the pharmaceutical market or are in the late stages of clinical evaluation to overcome multidrug resistant Staphylococcal infections. The review also explores the possibility of immunity and enzyme-based interventions as new therapeutic modalities and highlights the regulatory concerns on the prescription, usage and formulary development in the developed and developing world to keep the new chemical entities and therapeutic modalities viable to overcome antimicrobial resistance in S. aureus.

Engineering primary metabolic pathways of industrial micro-organisms

Metabolic engineering is a powerful tool for the optimisation and the introduction of new cellular processes. This is mostly done by genetic engineering. Since the introduction of this multidisciplinary approach, the success stories keep accumulating. The primary metabolism of industrial micro-organisms has been studied for long time and most biochemical pathways and reaction networks have been elucidated. This large pool of biochemical information, together with data from proteomics, metabolomics and genomics underpins the strategies for design of experiments and choice of targets for manipulation by metabolic engineers. These targets are often located in the primary metabolic pathways, such as glycolysis, pentose phosphate pathway, the TCA cycle and amino acid biosynthesis and mostly at major branch points within these pathways. This paper describes approaches taken for metabolic engineering of these pathways in bacteria, yeast and filamentous fungi.

Synthetic biology

Synthetic biologists come in two broad classes. One uses unnatural molecules to reproduce emergent behaviours from natural biology, with the goal of creating artificial life. The other seeks interchangeable parts from natural biology to assemble into systems that function unnaturally. Either way, a synthetic goal forces scientists to cross uncharted ground to encounter and solve problems that are not easily encountered through analysis. This drives the emergence of new paradigms in ways that analysis cannot easily do. Synthetic biology has generated diagnostic tools that improve the care of patients with infectious diseases, as well as devices that oscillate, creep and play tic-tac-toe.

Application of combinatorial chemistry to antimicrobial drug discovery

The emergence of pathogens resistant to currently available treatments is seen as a public health crisis. Since few new classes of antimicrobial drugs have been developed in the last two decades, it is becoming increasingly probable that healthcare providers will be faced with infections for which no chemotherapeutic agent is available. A renewed emphasis is being placed on employing the most advanced drug discovery technologies in the development of new antimicrobials. The recently introduced technologies of combinatorial chemistry offer new sources of chemical diversity, as well as methods with which to produce and rapidly test them. In the last few years, many groups have adopted a number of approaches in order to apply combinatorial chemistry to antimicrobial drug discovery. These combinatorial strategies, and the manner in which they are used to develop new screening formats or to identify new chemical leads are, reviewed.

Metabolic engineering

Metabolic engineering is the science that combines systematic analysis of metabolic and other pathways with molecular biological techniques to improve cellular properties by designing and implementing rational genetic modifications. As such, metabolic engineering deals with the measurement of metabolic fluxes and elucidation of their control as determinants of metabolic function and cell physiology. A novel aspect of metabolic engineering is that it departs from the traditional reductionist paradigm of cellular metabolism, taking instead a holistic view. In this sense, metabolic engineering is well suited as a framework for the analysis of genome-wide differential gene expression data, in combination with data on protein content and in vivo metabolic fluxes. The insights of the integrated view of metabolism generated by metabolic engineering will have profound implications in biotechnological applications, as well as in devising rational strategies for target selection for screening candidate drugs or designing gene therapies. In this article we review basic concepts of metabolic engineering and provide examples of applications in the production of primary and secondary metabolites, improving cellular properties, and biomedical engineering.

Biochemical engineering of natural product biosynthesis pathways

Metabolic engineering of natural products is a science that has been built on the goals of traditional strain improvement with the availability of modern molecular biological technologies. In the past 15 years, the state of the art in metabolic engineering of natural products has advanced from the first proof-of-principle experiment based on minimal known genetics to a commonplace event using highly specific and sophisticated gene manipulation methods. With the availability of genes, host organisms, vector systems, and standard molecular biological tools, it is expected that metabolic engineering will be translated into industrial reality.

Will genomics revolutionize antimicrobial drug discovery?

Utilizing genome sequence data from bacterial and fungal pathogens for the discovery of new antimicrobial agents has received considerable attention, both practical and critical, from the pharmaceutical and biotechnological communities. Although no new drugs derived from genomics-based discovery have been reported to be in a development pipeline, the utilization of genomics has revolutionized many aspects of drug discovery. The application, utility, opportunity, and challenges afforded by many of these new approaches are discussed.

Enhancing therapeutic glycoprotein production in Chinese hamster ovary cells by metabolic engineering endogenous gene control with antisense DNA and gene targeting

Recombinant glycoprotein therapeutics have proven to be invaluable pharmaceuticals for the treatment of chronic and life-threatening diseases. Although these molecules are extraordinarily efficacious, many diseases have high dosage requirements of several hundred milligrams of protein for each administration. Multiple doses at this level are often required for treatment. One of the major challenges currently facing the biotechnology industry is the development of large-scale, cost-effective production and manufacturing processes of these biologically synthesized molecules. Metabolic engineering of animal cell expression hosts promises to address this challenge by substantially enhancing recombinant protein quality, productivity, and biological activity. In this report, we describe a novel approach to metabolic engineering in Chinese hamster ovary cells by control of endogenous gene expression. Analysis of the advantages and limitations of using antisense DNA and gene targeting as a means of control are discussed and several gene candidates for regulation with these techniques are identified. Practical considerations for using these technologies to reduce the levels of the CHO cell sialidase (Warner et al., Glycobiology, 3, 455-463, 1993) as a model gene system for regulation are also presented.