Dynamics of enzyme aggregates of carbon core metabolism in growing and starved cells / a. Interactome studies
Lead Research Organisation:
Newcastle University
Department Name: Inst for Cell and Molecular Biosciences
Abstract
The objective of this project is to develop an integrated understanding of the metabolic and genetic network that controls the transition from growth to glucose starvation in the model bacterium, Bacillus subtilis. In addition to serving as a model system, B. subtilis is an industrial workhorse for 'white biotechnology' since it serves is a primary producer of technical enzymes and other products (e.g. vitamins, antibiotics, flavour enhancers and biochemicals). The transition from growth to growth limitation is a fundamental ecophysiological response and is studied by academic researchers as a model for environmental signal processing and integration. Understanding this transition is also pivotal for industrial fermentations of Bacillus that occur predominantly under nutrient limitation. Our approach is to integrate biological data with mathematical models of the networks that regulate the transition from growth to starvation. The approach starts with quantitative monitoring of defined genetic and environmental perturbations under standardized growth conditions. These data are used for mathematical modelling of regulatory processes. As the programme develops, gaps in our understanding will be revealed by the failure of structural, genome-wide network analyses to describe the biological data. Our concept is to continuously probe model and data consistency in clearly defined (sub)projects, each involving an experimental and a modelling partner. The pivotal element is a model-driven experimental design, where model-based hypotheses are tested through targeted measurements of critical variables. Facilitated through standardized nomenclature, model formats, and defined input/output signals, modular mathematical models are then integrated into a consistent systems representation. In summary, the project will provide convincing evidence that close interactions between experimental and computational scientists on a well advanced model organism can significantly advance our quantitative understanding of, and eventually our ability to control, the highly dynamic and complex regulatory processes in microbes.
Technical Summary
The overall goal of Bacell-SysMo is the quantitative understanding of the interacting and dynamic regulatory processes that control the transition from growth to starvation - an essential issue for cell physiology and biotechnology. This goal will be accomplished through integrating quantitative data from a variety of post-genomic methods within mathematical models for data analyses, evaluation and prediction of systems behaviour. There are three integrative workpackages: WP1 will follow the dynamics of interacting components of metabolic and gene expression networks during the transition from growth to a glucose-starvation induced non-growing state. This WP is constructed as a series of partnerships between experimental and modelling groups that investigate specific cellular subsystems in an iterative procedure between model building/simulation and experiment, thereby fostering close collaborations. WP2 has the goal of integrating the modules into a consistent system representation on the background of a static genome-scale model of metabolism. While a whole cell model would be overly ambitious and problems with individual modules might arise, the integrated model will grow step-wise by integrating the functional modules. WP3 is the data generation platform that provides an inventory of the molecular architecture of growing and non-growing cells by using various omics approaches to provide global quantitative and structural data for modelling. These studies involve mRNA profiling, quantification of the level and synthesis rate of cellular proteins, their stability and sorting as well as integration into functional complexes, elucidation of the structure of the complexes and their in vivo assembly and localization.
People |
ORCID iD |
Colin Harwood (Principal Investigator) |
Publications
Newman JA
(2011)
Unusual, dual endo- and exonuclease activity in the degradosome explained by crystal structure analysis of RNase J1.
in Structure (London, England : 1993)
Newman JA
(2012)
Dissection of the network of interactions that links RNA processing with glycolysis in the Bacillus subtilis degradosome.
in Journal of molecular biology
Description | Bacteria have, for decades, been regarded simply as a bag of enzymes and proteins that facilitate various metabolic activities. In recent years a more detailed understanding of how the contents of bacterial cells are organised. In particular, there is emerging knowledge that the enzymes and proteins associated with various aspects of metabolism, such as the utilisation of simple sugars such as glucose, functional as multi protein complexes. It has also been shown that individual components can be shared between different complexes. This work has studied the complex involved in controlling the degradation of messenger RNA, a key intermediate in protein synthesis, that shares complaints with central carbon metabolism. |
Exploitation Route | The initial findings were expanded in a second project grant within the SysMo initiative. |
Sectors | Healthcare Manufacturing including Industrial Biotechology |
Description | The results of these studies have contributed to our knowledge of central carbon metabolism and the regulation of RNA stability and degradation. These are both important aspects of the metabolism of the majority of bacterial species. |
First Year Of Impact | 2011 |
Sector | Healthcare |
Impact Types | Societal |
Description | Modelling carbon core metabolism in Bacillus subtilis |
Organisation | University of Greifswald |
Country | Germany |
Sector | Academic/University |
PI Contribution | The production of proteins for protein:protein analysis and structural analysis |
Collaborator Contribution | Carbon core metabolism and identification of protein interactions |
Impact | This academic collaboration resulted in a number of papers in academic journals |
Start Year | 2009 |
Description | Modelling carbon core metabolism in Bacillus subtilis |
Organisation | University of Göttingen |
Department | Department of Microbiology |
Country | Germany |
Sector | Academic/University |
PI Contribution | The production of proteins for protein:protein analysis and structural analysis |
Collaborator Contribution | Carbon core metabolism and identification of protein interactions |
Impact | This academic collaboration resulted in a number of papers in academic journals |
Start Year | 2009 |
Description | CBMNet meeting Factories for advanced biomanufacturing, Sheffield |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | The imperative to revolutionise the chemicals industry by creating a sustainable bio-based future and the increasing importance of biologics in medicine pose major challenges to UK biotechnologists. The design and implementation of bespoke advanced microbial cell factories, that can reproducibly yield bio-based alternatives to the chemicals that underpin so much of modern infrastructure is a fundamental challenge. Chassis engineering represents the single most critical technology to revolutionise biomanufacturing by improving product yields, simplifying product recovery and improving sustainability through reduced materials use and waste, thereby enhancing process economics and commercial viability. With a strong research base already working on microbial chassis engineering, CBMNet is the natural progenitor for such an event centred on microbial chassis design. |
Year(s) Of Engagement Activity | 2017 |
URL | https://cbmnetnibb.group.shef.ac.uk/members-forum/event-reports/december-2017-factories-for-advanced... |
Description | European Bacillus meeting and Symposium on Central Carbon Metabolism, Paris |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | This is a long-standing series of meeting that I helped to establish in the 1990s and are still organised on an annual basis. I organised the meeting in Newcastle in 2015. The mission of the meeting is to bring together researchers from the European Bacillus community as well as members from several European consortia that perform fundamental and applied research on Bacillus subtilis and related Gram-positive bacteria. |
Year(s) Of Engagement Activity | 2016 |
URL | https://symposium.inra.fr/bacell2016/ |
Description | SynGen - Genomics and Synthetic Biology Conference, London |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | The SynGen Series UK, with over 600 senior-level delegates representing internationally renowned research & academic institutions, clinical research institutions and pharmaceutical companies. Over 20 case studies and presentations demonstrating the latest synthetic biology tools and their therapeutic applications, including 2 interactive streams: Synthetic Biology - Tool Development Synthetic Biology - Applications Co-located with the highly established Annual Next Generation Sequencing and Clinical Diagnostics Congress, Annual Single Cell Analysis Congress and the Annual Genome Editing Congress. Invited talk on The Bacillus Cell Factory: Recent advances in novel tool development and session chair |
Year(s) Of Engagement Activity | 2018 |
URL | https://www.oxfordglobal.co.uk/syntheticbiology-congress/ |