Bacteria remain one of the main threats to human health and well-being, particularly in the light of increasing resistance to antimicrobials. More constructively, however, they also have the capacity to provide products (antibiotics, vaccines and biotherapeutics) that have a positive influence on human health. Thus, bacteria are both the targets for, and producers of, biopharmaceuticals that influence human health. BACELL HEALTH is a research and technological development (RTD) project designed to gain new knowledge in the field of bacterial cell biology for the development of new products and processes. The project aims to address both the harmful and beneficial characteristics of bacterial behaviour by undertaking an integrated and in-depth study of the response of Gram-positive bacteria to stress. The ability of bacteria to detect, respond to and resist environmental insult is crucial for their survival in the host during infection and to their productivity in industrial bioprocesses. The physical and chemical insults to which bacteria may be subject, range from generic environmental stresses to specific stresses encountered by pathogens during infection (e.g. host-mediated innate immune responses) or by engineered strains during industrial fermentations.
Pre-genomic research in cell biology has yielded a wealth of knowledge about individual regulatory pathways and metabolic processes that are obligatory for the survival of pathogens in their host and for the productivity of microbes in industrial bioprocesses. The major challenge for the BACELL HEALTH consortium, using state-of-the-art post-genomic technologies, is to understand how individual regulatory pathways are networked to maintain cellular homeostasis. We refer to this as the: Cell Stress Management System.
The networking of individual regulatory pathways ensures that the cell provides a balanced response to stress, sensing both the magnitude of the stress and the effectiveness of the response. In the case of pathogens, the identification of key nodes in these regulatory networks will provide new targets for the development of antimicrobial compounds that perturb or disrupt the cell stress management system. In the case of industrial production strains, the inactivation of stress-induced processes that limit the production of heterologous proteins will lead to the development of a new generation of host/vector systems for the production of pharmaceutically-active proteins.
The primary objective of the BACELL HEALTH project is to develop a detailed understanding of the integrative cell management system and associated stress resistance processes that are essential for sustaining bacteria as effective pathogens or producers of pharmaceutically-active proteins and peptides. Generic studies are carried out on the genetically highly amenable model bacterium Bacillus subtilis, but are extended with highly specific studies on pathogens in the same genus (e.g. B. anthracis, B. cereus), and related genera (e.g. Listeria monocytogenes, Mycobacterium tuberculosis, Staphylococcus aureus, Streptococcus pneumoniae).
Specifically, BACELL Health aims to:
The BACELL HEALTH project is divided into four experimental workpackages (WP), each with specific milestones and deliverables. WP1 focuses on a detailed understanding of how B. subtilis regulates its metabolism in response to environmental stresses. The stresses that have been chosen (e.g. pH, oxidative, iron and secretion stress) are those encountered by pathogens during the innate immune's response to infection. The aim is to understand the level of stress that is tolerated by an environmental organism as compared to that of a pathogen. WP2 aims to unravel the regulatory and biochemical processes that pathogens related to B. subtilis (see above) need to "top-up" these responses, in order avoid being killed by the innate immune response. Understanding these processes provides us with a novel set potential targets for antimicrobial chemotherapy: while conventional antibiotics are aimed at killing or inhibiting bacterial growth, anti-infective drugs aimed at these new targets are designed to undermine the ability of the bacterium to resist or subvert the host's innate immune response.
WP3 is aimed at improving the ability of commercial strains of B. subtilis and it close relatives to produce biopharmaceuticals. On the one hand it aims to improve the organism's survival during commercial fermentations by identifying stress pathways (e.g. oxidative and secretion stress) that limit product formation, and on the other by engineering commercial strains to improve their production of bioactive proteins and antimicrobial peptides.
WP4 focuses on comparative genomics and network modelling. As the networks regulating the response of B. subtilis to stress are being established and verified, comparative genomics techniques are being used to identify corresponding components in closely related Gram-positive bacteria. The web-accessible Microbase provides a repository for whole microbial genome comparisons that harnesses the computational power and data integration capabilities of the Grid networking technology. A dataset is provided that combines a microbial proteome comparison in combination with a high-resolution whole-genome nucleotide comparison. This provides a number of standard algorithms for genome comparisons, including characterisation of the phenotypic effects, changes in gene order, detection and characterisation of inserted genomic islands and algorithms for phylogenetic inference. However, the real power of the system lies in its ability to provide an environment for the remote execution of user-defined algorithms for specific problem domains. Specific algorithms are being developed for the comparison and characterisation of genomic regions encoding genes involved in stress response mechanisms.
The topology of regulatory networks involved in stress are being established from experimental data in WPs 1-3, including transcriptomic data from the wild- type and knockout mutants, the scientific literature and proteomics studies. Petri Net analysis techniques will then be applied to the resulting networks in order to model and verify the architecture of the regulatory circuits. The knowledge obtained for the modelling of the regulatory systems of B. subtilis will be used to assess the virulence and infection stress responses of pathogens.
Secreted proteins play an important part in the virulence of pathogens and again their synthesis provides targets for either antimicrobial or immune therapy. Algorithms have been developed to predict to predict the full complement of protein secreted by B. anthracis and B. cereus. These algorithms are being used to develop a web-based prediction service for the identification of secretory proteins from any Gram-positive bacterium with a known genome sequence.
The project will develop an understanding of the regulatory networks that underlie the response of environmental bacteria and pathogens to stresses encountered during infection and commercial bioprocesses.
Potential new targets for antimicrobial drugs, improved production of bioactive proteins and peptides, improved commercial production strains.