Development of Pseudomonas putida as a genome mining host for antimicrobial discovery

Summer 2017

Andrew Wong : Molecular and Cell Biology

Mentor: Amin Zargar

With the increasing threat of antimicrobial resistance, there is great demand for the development of new antibiotics. Natural products, which are biologically produced substances, are used as the primary reference for the development of antibiotics and drug development.  Recent developments in metagenomics, the field of recovering genetic material from environmental samples, have allowed for the investigation of previously unexplored genomes. These genomes are potential sources for undiscovered natural products, and many have already been discovered through expressing environmental DNA (eDNA) in heterologous host vectors, such as E. coli and S. lividans. This method, however, suffers from low “hit-rates”, with at most 1 in 10000 clones producing an antimicrobial. This obstacle may be attributed to the intrinsic incapability of the heterologous hosts. E. coli suffers from a low tolerance for physicochemical stresses, a low-GC content compared to other bacteria, and a low xenobiotic tolerance. S. lividans is naturally more suitable for antibiotic production, but is far less genetically tractable and grows much more slowly than E. coli. This summer, I will contribute to the development of a chassis organism for the activation of biosynthetic gene clusters from actinobacteria, which are responsible for the majority of antimicrobials. Specifically, I will focus on working with Pseudomonas putida, which has the genetic tractability of E. coli and the high-GC content of S. lividans. This project will focus on the effectiveness of P. putida as a chassis compared to other candidates. This will be determined by transfecting eDNA into different heterologous hosts and performing a series of functional screens.  

Working under the funding of the SURF Rose Hills program has transformed my understanding and appreciation of scientific research. I had worked under my mentor during the academic year prior to my summer with this program and although I was fascinated with the science, I felt that I could not properly engage with the material. I felt it was difficult to delve into the material at a satisfactory level because it was difficult to manage the necessary literature reading alongside school and my part-time job. The funding that I was generously granted this summer gave me the opportunity to focus my energy on my development as a scientist. As a result, I have a much stronger understanding of how scientific research is conducted. By strengthening this foundation of understanding, I have grown to truly be excited for going into the laboratory -- I am now confident I want to continue scientific research throughout my future academic pursuits.