Chance and Necessity: Evolution guided antibiotic improvement and discovery

Streptomyces is a harmless bacterium that is found in soil. Competition for nutrients in soil is intense and it is thought that Streptomyces produce antibiotics to harm competing organisms, such as other bacteria. It is these antibiotics that we exploit in human medicine, where almost two-thirds of our clinically used antibiotics are made naturally by Streptomyces bacteria. The rise in antibiotic resistant infections in recent years has indicated that there is an urgent need for us to discover new antibiotics and increase the production efficiency of existing antibiotics to help us combat the resistance crisis. Understanding how antibiotic producing bacteria regulate the production of antibiotics and what genes are involved in production is important for us to be able to better exploit Streptomyces and their antibiotics in human medicine.
When we produce antibiotics at industrial scale, we use Streptomyces bacteria whose DNA has been modified through a process called 'random mutagenesis' - this mutagenesis process creates strains of bacteria that are better adapted to growing in the fermenters and produce more antibiotics that they would naturally. This process essentially accelerates evolution, where scientists select the fittest or best strains for industrial production of antibiotics - but it is time consuming and difficult to direct. Bacteria undergo a similar process to evolve, adapt and survive in their natural soil environment. In this proposal, we wish to study a natural adaptation process in Streptomyces and how its genome adapts to grow in a nutrient rich broth in the laboratory. We also wish to look at the genomes several strains of an industrial Streptomyces species that have been used to make an antibiotic commercially to see how the random mutagenesis process has forced them to adapt to the conditions and make industrial amounts of antibiotic. We hypothesise that the genes acted upon by evolution (either forced or natural) are likely to be similar and as strains adapt, they will lose the activity of genes that are no longer required, such as those for degrading nutrients that they no longer encounter, genes involved in certain stress responses or the ability to form spores. Sequencing the genomes of Streptomyces allows us to look at the genes responsible for the production of antibiotics, and how they have changed during adaptation.
If we can understand the mechanisms that drive the adaptation of strains, we will understand what mutations are beneficial and those which are deleterious for surviving in fermenters, adapting to an environment and producing antibiotics. This work will also allow us to understand how different genes interact and if certain combinations of mutations are particularly advantageous or deleterious. This is important because adaptation and the generation of industrial strains is time consuming and labour intensive, but if we understand the order and the kinds of mutations that occur in strains that are high-yielding, then we can rapidly make these mutations in new strains. This will make it easier and quicker to bring new antibiotics to the clinic in the future to combat the growing antimicrobial resistant infection crisis.

Evolutionary adaptation is driven by the accumulation of mutations, but the temporal dynamics of this process are difficult to observe directly. This is also true during the random mutagenesis process used to enhance industrial production of natural products such as antibiotics, where strains are subjected to iterative rounds of mutagenesis and selection to identify better performing strains. This proposal is focused on understanding how Streptomyces species adapt to their environment during the strain improvement process and how repeatable the mutational process is which hones the genome, resulting in better industrial performance and antibiotic production. Using a combination of Long-Term Experimental Evolution (LTEE) studies (the first in Streptomyces), molecular genetics and genomics we will study adaptive mutations and the epistatic interactions that shape the Streptomyces genome. We will use the model strain S. coelicolor for our LTEE and an authentic, industrially improved lineage of the oxytetracycline producer S. rimosus to study how strains adapt to new environments and culture conditions with a view to enhancing antibiotic production. The accumulation of mutations and the genetic drift observed during adaptation and strain improvement will reveal the undelaying mutational rate for strains, never previously calculated for industrial Streptomyces strains, and will reveal details about the underlying strain stability, which is vital for robust industrial processes. This evolutionary approach will increase our understanding of adaptive responses in Streptomyces and the industrial strain improvement process which is vital to future industrial competitiveness. Ultimately, this approach will facilitate more rapid industrial strain improvement processes and rational strain design strategies for Streptomyces.

The rise of antibiotic resistance (AMR) and the recognition that it represents one of the greatest threats to human health has increased the need for innovative ways to discover new antimicrobial drugs and develop methods to efficiently produce existing molecules. Bacteria that belong to the genus Streptomyces produce over two-thirds of our current, clinically used antimicrobial drugs. Studies on antibiotics are a research priority and there is still lots of novel and exploitable biology to be discovered in this area. Using an evolutionary guided approach to reveal novel aspects of antibiotic production, we believe that we can improve the speed and efficiency of industrial strain development. In this proposal, we seek to establish a fundamental understanding of adaptation in Streptomyces revealing the order, nature and repeatability of adaptive evolution using a combination of a long-term evolution experiments and an authentic lineage of an industrial Streptomyces strain.
A long-term and continued investment in to Streptomyces research by RCUK and now UKRI has continued to make a significant impact on the UK economy and on human and animal health. For example creation of five spin-out companies founded by Streptomyces researchers, including one that was sold for ~£120m and another which established a ~£123m licensing deal (https://bbsrc.ukri.org/documents/streptomyces-case-study-pdf/) . The investment from RCUK (UKRI) has also trained and supported a highly-skilled work force in the UK and internationally. Research has often been closely linked to industry, including a £1.6m iUK/BBSRC grant to Hoskisson in collaboration with GSK to develop industrial Streptomyces fermentations. The continued training of early career researchers in this field is key to continued exploitation of these bacteria in the future. High quality training, mentorship and development programmes for researchers is required for capacity building in this area.

Industrial applications: The wider biotechnology market in the UK has recently been estimated at £81 billion per annum, employing 800,000 people across the pharmaceutical, food & drink, bioconversion and waste-treatment industries. The Hoskisson laboratory has long standing industrial links with companies engaged in antibiotic discovery and development with Acies Bio (Slovenia) and GSK. Hoskisson has recently been involved in the development of sustainable industrial fermentation processes for antibiotics with GSK and with 3f Bio for human and animal foods. The 3f Bio project recently secured >£6m in financing to further develop the process (http://www.3fbio.com/3f-bio-ltd-confirms-a-6-16m-series-a-financing-round/). Long-term and continued industrial links demonstrate that Hoskisson is able to realise the potential of discoveries and to implement these in a form that is attractive to industry.

Agricultural applications: A greater understanding of Streptomyces evolution has implications for understanding plant-microbe interactions. Streptomyces represent potential biocontrol organisms for use in sustainable agriculture, enhancing plant growth, suppressing disease and increasing nutrient availability. For example in the UK, potatoes alone are worth £780 million annually to the economy. The rising importance of global food security studies such as this can have significant impact on our understanding and the exploitation of these processes.

Outreach/public engagement: The AMR crisis facing the global human population captures the public's imagination and demonstrates how basic science, such as how and why bacteria produce antibiotics can be transformed in to tangible outputs for industry (antibiotic discovery) and agriculture (plant growth promotion/disease suppression). The programme developed here will engage the public at a range of levels (Big Bang festival, outreach events, social media and stop-motion animations) to reinforce the impacts of the work.