Taming of the Streptomycete: Understanding the rules of domestication in antibiotic-producing bacteria

Streptomyces are bacteria that make antibiotics to enable them to survive in soil. It is these molecules that comprise around two-thirds of our clinically used antibiotics, without which modern medicine would cease to function. They are used to treat infections, but they are also used extensively prior to surgery and in immunocompromised patients (cancer, transplant patients, HIV/AIDS etc) to prevent infections. The rise in antibiotic resistant infections in recent years has indicated that there is an urgent need for us to increase the production efficiency of existing antibiotics to help combat the resistance crisis.
Industrial production of antibiotics is achieved by growing Streptomyces in large fermenters using specialised media. The bacteria used are not the wild-type Streptomyces, but strains that have undergone extensive rounds of 'improvement' to help them efficiently make more antibiotics. The 'improvement' process for Streptomyces can be thought of like a selective breeding or domestication process for plants or animals, where those exhibiting the best traits are selected for future breeding. This means that each generation is better adapted for growth in the fermenter, rather than soil, and produces more antibiotics. To generate the improved strains, the Streptomyces are exposed to chemicals that bring about changes (mutations) in their DNA, and the resulting strains which show an increase in antibiotic production are chosen for further rounds of improvement (also known as mutagenesis and selection). This has been done for all industrial Streptomyces strains, yet we have very little understanding or knowledge of the kinds of changes the best strains have and therefore what makes them good overproducers of antibiotics. This means that every new antibiotic has to undergo a long and laborious process to produce commercial amounts of antibiotic.
GSK have been performing mutagenesis and selection with a strain of Streptomyces for more than 35 years that makes an important antibiotic called clavulanic acid (CA). The World Health Organisation consider CA as one of its essential medicines and understanding the production of CA is important in the fight against antimicrobial resistance.
Understanding how antibiotic-producing bacteria can increase the production of antibiotics is important for us to be able to better exploit Streptomyces for human medicine and agriculture. To achieve this, we have been analysing the genomes of the GSK CA-producing lineage of Streptomyces and identifying the mutations that allow them to produce up to five-times more CA than the wild-type strain.
We will experimentally test each of these mutations to see which are responsible for the increase in CA production and if any of the mutations limit how much CA can be produced. It may be that while overall the mutations help increase CA production, some mutations may damage certain parts of metabolism, preventing strains from reaching their full potential. It is also possible that the order in which these mutations occurred could determine how good at producing CA the Streptomyces can become. We will use genome editing to test if the mutations need to accumulate in a specific order to have a beneficial effect. Finally, once we have identified some important mutations for increasing CA production, we will try and make the same mutations in other industrially important Streptomyces to see if these changes also increase antibiotic production. We believe that this is possible because the building blocks for many antibiotics are derived from the same parts of metabolism as the building blocks for CA.
We believe this approach will make it easier and quicker to bring new antibiotics to the clinic in the future to help combat the growing antimicrobial resistant infection crisis.

Streptomyces bacteria are the industrial workhorses for the production of numerous pharmaceutically useful metabolites such as antibiotics. Traditionally, strains of Streptomyces that are high producers of antibiotics have been developed via random mutagenesis and selection. Whilst this approach to strain improvement is successful at yielding high-producing strains, it is often time consuming and can take years to yield commercially viable results, such that greater insight into the genomic changes that give rise to increased production levels will help in the design of rational approaches to strain improvement and enable the rapid generation of new strains. This proposal is focused on analysis of a bona fide industrial lineage of Streptomyces to understand the nature of mutations, the importance of the order in which mutations accumulate and finally if some mutations can be broadly applied to other industrially important Streptomyces strains. Moreover, we will determine if all mutations present in the industrial strains are beneficial in production, as some may limit the metabolic flexibility of advanced industrial producing strains. We believe this approach will offer rapid pathways to strain improvement of industrial Streptomyces, reducing the discovery to profit timeline new molecules and expediting profitability.