A systems approach to understanding metabolic switching in Streptomyces coelicolor

Lead Research Organisation: University of Warwick
Department Name: Biological Sciences

Abstract

Bacteria found in soil have been exploited for their ability to produce antibiotics for over 60 years. This resulted in the effective treatment of diseases such as TB, bacterial pneumonia, sepsis and a wide range of infections which previously resulted in death or had a very low survival rate. Recently the alarming rise in antibiotic resistant pathogens especially those acquired in hospitals has reduced the efficacy of our existing armoury of drugs and new antibiotics are badly needed. In addition there are a number of emerging pathogens for which existing drugs are not effective. Antibiotics are made during the second phase of growth when there is a transition in metabolism from primary metabolism to secondary metabolism. Primary metabolism is growth related and involves all the normal cellular activities associated with cell growth and division. Whereas secondary metabolism is non-growth linked and is non-essential but many important activities occur during this phase which help the bacterium survive and compete in its natural environment. One of these activities is antibiotic production and is widespread in streptomycetes found in most soils. These bacteria have a fascinating life history and are abundant producers of biologically active compounds many of which have been exploited for their anti-tumour, anti-bacteria and anti-fungal activity. Our research will greatly improve our understanding of how these bacteria regulate the transitions from primary to secondary metabolism and provide mathematical models to simulate the metabolic switch of life styles. The overall approach is regarded as a 'systems' analysis where a model is built of the whole metabolism and it can predict outcomes that will not have been determined previously by experimental methods. A range of modelling tools will be provided and these will be available for use with many other projects involved in a systems approach to biology. The fuller understanding of the metabolic switch and the elucidation of how and why certain antibiotics are made under defined growth conditions will be vital for the full exploitation of these bacteria. Many tools are available to manipulate bacterial genomes and with an understanding of the metabolism it will be possible to discover and manipulate growth in order to produce novel antibiotics.

Technical Summary

Genetic and physiological manipulations of Streptomyces are essential for new drug discovery and production development. Predictive manipulation of metabolism will not only help to increase production of existing antibiotics but will also facilitate combinatorial biosynthesis of antibiotic pathway enzymes to generate novel secondary metabolites and provide new opportunities for the expression of hitherto cryptic secondary metabolite pathways. The main aim of the project is to facilitate integration and coordination of theoretical and experimental work elucidating metabolic regulation in a complex oligotroph Streptomyces coelicolor. A working model of the transition from primary to secondary phases of metabolism will be produced, interfacing growth related processes with non-growth linked productivity. The proposal consists of 7 work packages (WPs), WP 1, 4, and 7 (project 1) will be done at Warwick and WP6 at Aberdeen, the remaining WPs are part of the transnational component based in Norway, Germany, Netherlands and Spain. WP 1 is co-ordination and provision of real time PCR, programs for Qiagen BioRobot Universal and its application to the project work. WP 4 will conduct gene network inference, analysis and data integration of metabolic reprogramming and WP 7 encompasses analysis of global carbon (project 1), nitrogen and phosphate regulation: the central pathways of assimilation in Streptomyces coelicolor. Only Project 1 (the pathways of carbon assimilation during transitioantibiotic production on the level of the systemn phase and anaplerosis) of WP7 will be done at Warwick. Transcriptomics (WP5), proteomics (WP6), and metabolomics (WP2; provision of cell pastes and metabolomics, WP3 metabolic flux analysis and computational modelling of metabolism) each provide a different view on the organism's response to a changing environment, we will integrate these datasets into a consistent view of the key players for antibiotic production at the system level.

Publications

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Arabnia, Hamid R.; Tran, Quoc-Nam Professor (2011) Software Tools and Algorithms for Biological Systems

 
Description During the lifetime of a fermenter culture, the soil bacterium Streptomyces coelicolor undergoes a major metabolic switch from exponential growth to antibiotic production. We have studied gene expression patterns during this switch, using a specifically designed Affymetrix genechip and a high-resolution time-series of fermenter-grown samples. Surprisingly, we find that the metabolic switch actually consists of multiple finely orchestrated switching events. Strongly coherent clusters of genes show drastic changes in gene expression already many hours before the classically defined transition phase where the switch from primary to secondary metabolism was expected. The main switch in gene expression takes only 2 hours, and changes in antibiotic biosynthesis genes are delayed relative to the metabolic rearrangements. Furthermore, global variation in morphogenesis genes indicates an involvement of cell differentiation pathways in the decision phase leading up to the commitment to antibiotic biosynthesis. Our study provides the first detailed insights into the complex sequence of early regulatory events during and preceding the major metabolic switch in S. coelicolor, which will form the starting point for future attempts at engineering antibiotic production in a biotechnological setting.
Exploitation Route Regulatory nodes can be exploited and studied further for regulation of antibiotic biosynthesis in the pharmaceutical industry.
Sectors Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

 
Description Provision of a gene regulatory network for the switch-on of secondary metabolism and antibiotic production
First Year Of Impact 2011
Sector Pharmaceuticals and Medical Biotechnology
Impact Types Economic

 
Description (CARTNET) - Combatting Antimicrobial Resistance Training Network
Amount € 3,445,596 (EUR)
Funding ID 765147 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 01/2018 
End 12/2021
 
Description Innovation fund A
Amount £40,000 (GBP)
Funding ID MyP 838 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 03/2013 
End 06/2015
 
Description KTP No 3356
Amount £250,000 (GBP)
Funding ID KTP No 3356 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2013 
End 06/2016
 
Description MRC-KHIDI UK-KOREA PARTNERING AWARDS
Amount £35,000 (GBP)
Funding ID MC_PC_18006 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 07/2018 
End 11/2018
 
Description New approaches to resolving community metaproteomes: ComProt
Amount £50,401 (GBP)
Funding ID NE/S013539/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 01/2019 
End 12/2019
 
Description SEVENTH FRAMEWORK PROGRAMME EU Initial Training Network
Amount € 320,000 (EUR)
Funding ID 289285 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 01/2012 
End 12/2015
 
Description The farm environment: an overlooked source of Mycobacterium bovis?
Amount £938,378 (GBP)
Funding ID BB/N004655/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2016 
End 12/2019
 
Description Collaboration with Prof Chris Quince on recovering genomes from metagenomes 
Organisation University of Warwick
Department Warwick Medical School
Country United Kingdom 
Sector Academic/University 
PI Contribution Provision of data and metagenomes, experimental and field work expertise.
Collaborator Contribution Expertise in bioinformatics
Impact Data base of metagenomes to be added to EBI metagenomes portal and also for use with workshops on analysis of metagenomes in ComMet workshop
Start Year 2016
 
Description Collaboration with Sanofi and grant from Warwick University Research Development Fund (RDF) 
Organisation Sanofi
Department Sanofi Research Division
Country France 
Sector Private 
PI Contribution Discovery of bioactive bacterial non-ribosomal peptide in a rhizosphere bacterium
Collaborator Contribution Interest in detailed characterization and further screening for activities unique to the peptide.
Impact Collaboration may provide novel antibiotic and teh study involves natural product chemists and microbiologists
Start Year 2016
 
Description Korean partnering on metagenomics and microbiome analysis 
Organisation Chung-Ang University
Country Korea, Republic of 
Sector Academic/University 
PI Contribution Understanding the risk posed by the widespread dissemination of antimicrobial resistant bacteria (AMRB) and pathogenic variants (AMRP) in the environment depends on persistence of the bacteria and the resistance genes (ARGs). ARGs can move into indigenous environmental bacteria but risks of infection will be reduced or removed. What has been observed is the high diversity of resistance genotypes in waste water polluted environments coupled with the expansive diversity of the environmental resistome and so the extensive mixing of human and animal wastes with environmental bacteria particularly in the presence of antibiotics could produce AMRP capable of extensive resistance phenotypes. Uncertainty exists over the longevity and activity of AMRP in the environment outside of their hosts and to what extent they may participate in gene exchange so current work in both the Cha and Wellington groups is focused on this aspect and finding new ways of monitoring AMRP and their activities. Thus we identified two major challenges in understanding risk in environmental exposure to AMRP which relates to viability and ARG acquisition. In the form of two workshops and exchange of personnel the Wellington group members Dr Chiara Borsetto and Dr Robert James demonstrated their methods for using long read sequencing to gain an improved analysis of resistance genes in the environmental resistome, Chiara Borsetto talked about using mesocosms to establish if sublethal levels of antibiotics in the environment select for resistance phenotypes or are simply collocated with already resistant bacteria in waste water effluent. By characterizing the host genome it is possible to establish if the resistant bacteria are human adapted or environmental bacteria. From our work on river flumes used to model impact of waste water effluent in UK rivers it appears that sublethal antibiotic has a distinct impact on the prevalence of the relevant resistance genes.
Collaborator Contribution Professor Chang-Jun Cha's group have expertise in bioinformatics and hold a resistance gene database in addition to having a WaferGen SmartChip machine and the arrays which can detect very sensitively over 300 types of resistance genes using PCR conducted in hundreds of minicells.We were given access to this machine and were able to compare results and also establish diversity and new combinations of various mobile genetic elements. We aim to write a position paper comparing our results on anthropogenic impacts on Thames riverine microbiome compared with the study they are conducting on the Han river in South Korea. They provided access to databases and SmartChips plus shared sequences and databases.
Impact Two papers are in progress and one submitted currently: Submission no: ENVINT_2019_218, Submission title: A novel sulfonamide resistance mechanism by two-component flavin-dependent monooxygenase system in sulfonamide-degrading actinobacteria Corresponding author: Professor Chang-Jun Cha, Listed co-author(s): Dr Kihyun Lee, Dr Cung Nawl Thawng, Professor Elizabeth Wellington, Dr Dae-Wi Kim.
Start Year 2018
 
Description TRAIN-ASAP 
Organisation University of Copenhagen
Country Denmark 
Sector Academic/University 
PI Contribution Discovery of antibiotic producers was extended to the uncultured fraction, which represents over 90% of the total bacterial population. Novel approaches were used to obtain HMW DNA from habitats where unique bacterial diversity has been detected either by functional or phylogenetic analysis of total community DNA. Both direct approaches to recover pathway DNA and indirect approach by capture of cells containing markers for functional genetic diversity were developed. Both served as sources of clustered genes for candidates to express pathways in selected engineered expression hosts. Warwick provided libraries of cloned natural product synthetic capacity, analysis and expression is currently taking place.
Collaborator Contribution Other partners in EU ITN provided expertise in antibiotic discovery and phenotypic expression screening.
Impact Multidisciplinary approach to treating bacterial infections in animals. Vets, chemists, biochemists, microbiologists were all involved.
Start Year 2011