Application of proteomics in biotechnology – Microbial proteomics

Proteomic Analysis of Anti-Cancerous Scopularide Production by a Marine Microascus brevicaulis Strain and Its UV Mutant

The marine fungus Microascus brevicaulis strain LF580 is a non-model secondary metabolite producer with high yields of the two secondary metabolites scopularides A and B, which exhibit distinct activities against tumour cell lines. A mutant strain was obtained using UV mutagenesis, showing faster growth and differences in pellet formation besides higher production levels. Here, we show the first proteome study of a marine fungus. Comparative proteomics were applied to gain deeper understanding of the regulation of production and of the physiology of the wild type strain and its mutant. For this purpose, an optimised protein extraction protocol was established. In total, 4759 proteins were identified. The central metabolic pathway of strain LF580 was mapped using the KEGG pathway analysis and GO annotation. Employing iTRAQ labelling, 318 proteins were shown to be significantly regulated in the mutant strain: 189 were down- and 129 upregulated. Proteomics are a powerful tool for the understanding of regulatory aspects: The differences on proteome level could be attributed to limited nutrient availability in the wild type strain due to a strong pellet formation. This information can be applied for optimisation on strain and process level. The linkage between nutrient limitation and pellet formation in the non-model fungus M. brevicaulis is in consensus with the knowledge on model organisms like Aspergillus niger and Penicillium chrysogenum.

After genomics, what proteomics tools could help us understand the antimicrobial resistance of Escherichia coli?

Proteomic approaches have been considerably improved during the past decade and have been used to investigate the differences in protein expression profiles of cells grown under a broad spectrum of growth conditions and with different stress factors including antibiotics. In Europe, the most significant disease threat remains the presence of microorganisms that have become resistant to antimicrobials and so it is important that different scientific tools are combined to achieve the largest amount of knowledge in this area of expertise. The emergence and spread of the antibiotic-resistant Gram-negative pathogens, such as Escherichia coli, can lead to serious problem public health in humans. E. coli, a very well described prokaryote, has served as a model organism for several biological and biotechnological studies increasingly so since the completion of the E. coli genome-sequencing project. The purpose of this review is to present an overview of the different proteomic approaches to antimicrobial-resistant E. coli that will be helpful to obtain a better knowledge of the antibiotic-resistant mechanism(s). This can also aid to understand the molecular determinants involved with pathogenesis, which is essential for the development of effective strategies to combat infection and to reveal new therapeutic targets. This article is part of a Special Issue entitled: Proteomics: The clinical link.

Therapeutic plasma proteins--application of proteomics in process optimization, validation, and analysis of the final product

An overview is given on the application of proteomic technology in the monitoring of different steps during the production of therapeutic proteins from human plasma. Recent advances in this technology enable the use of proteomics as an advantageous tool for the validation of already existing processes, the development and fine tuning of new production steps, the characterization and quality control of final products, the detection of both harmful impurities and modifications of the therapeutic protein and the auditing of batch-to-batch variations. Further, use of proteomics for preclinical testing of new products, which can be either recombinant or plasma-derived, is also discussed.

In-depth analysis of exoproteomes from marine bacteria by shotgun liquid chromatography-tandem mass spectrometry: the Ruegeria pomeroyi DSS-3 case-study

Microorganisms secrete into their extracellular environment numerous compounds that are required for their survival. Many of these compounds could be of great interest for biotechnology applications and their genes used in synthetic biology design. The secreted proteins and the components of the translocation systems themselves can be scrutinized in-depth by the most recent proteomic tools. While the secretomes of pathogens are well-documented, those of non-pathogens remain largely to be established. Here, we present the analysis of the exoproteome from the marine bacterium Ruegeria pomeroyi DSS-3 grown in standard laboratory conditions. We used a shotgun approach consisting of trypsin digestion of the exoproteome, and identification of the resulting peptides by liquid chromatography coupled to tandem mass spectrometry. Three different proteins that have domains homologous to those observed in RTX toxins were uncovered and were semi-quantified as the most abundantly secreted proteins. One of these proteins clearly stands out from the catalogue, representing over half of the total exoproteome. We also listed many soluble proteins related to ABC and TRAP transporters implied in the uptake of nutrients. The Ruegeria pomeroyi DSS-3 case-study illustrates the power of the shotgun nano-LC-MS/MS strategy to decipher the exoproteome from marine bacteria and to contribute to environmental proteomics.

Biotechnological applications of microbial proteomes

Advances in proteomic technologies have led to the creation of large-scale proteome databases that can be used to elucidate invaluable information on the dynamics of the metabolic, signaling and regulatory networks and to aid understanding of physiological changes. In particular, proteomics can have practical applications, for example, through the identification of proteins that may be potential targets for the biotechnology industry, and through the extension of our understanding of the physiological action of these proteins. In this review, we describe proteomic approaches for the discovery of targets that have potential biotechnological applications. These targets include promoters, chaperones, soluble fusion partners, anchoring motifs, and excretion fusion partners. In addition, we discuss the potential applications of proteomic techniques for the design of future bioprocesses and the optimization of existing ones. Successful applications of proteomic information have proven to have enormous value for both scientific and practical applications.

Use of proteomics for validation of the isolation process of clotting factor IX from human plasma

The use of proteomic techniques in the monitoring of different production steps of plasma-derived clotting factor IX (pd F IX) was demonstrated. The first step, solid-phase extraction with a weak anion-exchange resin, fractionates the bulk of human serum albumin (HSA), immunoglobulin G, and other non-binding proteins from F IX. The proteins that strongly bind to the anion-exchange resin are eluted by higher salt concentrations. In the second step, anion-exchange chromatography, residual HSA, some proteases and other contaminating proteins are separated. In the last chromatographic step, affinity chromatography with immobilized heparin, the majority of the residual impurities are removed. However, some contaminating proteins still remain in the eluate from the affinity column. The next step in the production process, virus filtration, is also an efficient step for the removal of residual impurities, mainly high molecular weight proteins, such as vitronectin and inter-alpha inhibitor proteins. In each production step, the active component, pd F IX and contaminating proteins are monitored by biochemical and immunochemical methods and by LC-MS/MS and their removal documented. Our methodology is very helpful for further process optimization, rapid identification of target proteins with relatively low abundance, and for the design of subsequent steps for their removal or purification.

Proteomics in South Africa: current status, challenges and prospects

Proteomics is a biotechnology research area that is generally defined as the large-scale study of protein expression, structure and functions. Primarily, proteomics is used to study relative cellular, subcellular and extracellular abundances of proteins expressed at a defined physiological state on a large scale. In contrast to the analysis of mRNA expression studies, generally referred to as transcriptomics, proteomics approaches take into consideration the post-transcriptional, translational and post-translational modifications of polypeptides. Over the past 10 years, the proteomics field has been growing tremendously and contributing positively to biotechnology, particularly in North America, Europe and Asia. Research output in Africa is still very low in comparison. This article reviews proteomics capacity as well as research activities in South Africa. We highlight, with examples, the potential that this technology has in the acceleration of disease biomarker discovery and its role in drug design. Our ultimate objective is to promote further developments, research and applications of proteomics in South Africa, aiming for the generation of new scientific knowledge for our continent and for the rest of the world.

Proteomics as a tool for optimization of human plasma protein separation

The application of proteomics technology in purification of proteins from human plasma and for characterization of plasma-derived therapeutics has been recently discussed. However, until now, the impact of this technology on the plasma protein fractionation and analysis of the final product has not been realized. In the present work, we demonstrate the use of proteomic techniques the monitoring of the first step of the plasma fractionation by use of anion-exchange chromatography. This chromatographic method is frequently used in the purification scheme for isolation of vitamin K dependent clotting factors II, VII, IX and X, and clotting inhibitors protein C and protein S, as well as inter-alpha inhibitor proteins (IaIp). After the removal of immunoglobulin G and non-binding proteins in the flow-through fraction, albumin and weakly bound proteins were eluted with low concentration of sodium chloride. The proteins that strongly bind to the anion-exchange column were eluted by higher salt concentrations. The fractions of interest were analyzed, and proteins were identified by LC-ESI-MS/MS. By use of this method, not only candidates for therapeutic concentrates, but also some potentially harmful components were identified. This strategy was very helpful for further process optimization, fast identification of target proteins with relatively low abundance, and for the design of subsequent steps in their removal or purification.