Research Interest

Translate Microbial Natural Products into drugs for life-threatening diseases. Our research is focused on:

• Diversifying marine microbial natural product strains and extract libraries, while decreasing genetic and chemical redundancy.
• Screening for synergistic medicines in a high throughput manner.
• Increasing the production of drugable secondary metabolites from microbial producers by genetic engineering.

Research Highligts

Porphyrins and their derivatives find extensive applications in medicine, food, energy and materials. In this study, we produced porphyrin compounds by combining Rhodobacter sphaeroides as an efficient cell factory with enzymatic catalysis. Genome-wide CRISPRi-based screening in R. sphaeroides identifies hemN as a target for improved coproporphyrin III (CPIII) production, and exploiting phosphorylation of PrrA further improves the production of bioactive CPIII to 16.5 g L⁻¹ by fed-batch fermentation. Subsequent screening and engineering high-activity metal chelatases and coproheme decarboxylase results in the synthesis of various metalloporphyrins, including heme and the anti-tumor agent zincphyrin. After pilot-scale fermentation (200 L) and setting up the purification process for CPIII (purity >95%), we scaled up the production of heme and zincphyrin through enzymatic catalysis in a 5-L bioreactor, with CPIII achieving respective enzyme conversion rates of 63% and 98% and yielding 10.8 g L⁻¹ and 21.3 g L⁻¹, respectively. Our strategy offers a solution for high-yield bioproduction of heme and other valuable porphyrins with substantial industrial and medical applications. Nat Biotechnol (2024).

FtmOx1 is a non-heme iron (NHFe) endoperoxidase, catalyzing three disparate reactions, endoperoxidation, alcohol de-hydrogenation, and dealkylation, under in vitro conditions; the diversity complicates its mechanistic studies. Recently, we used substrate analogs to simplify the FtmOx1-catalyzed reaction from a very complicated system with three reactions to predominantly either the dealkylation or an alcohol dehydrogenation reaction. These simplified systems served as excellent models for FtmOx1 mechanistic characterizations using kinetic/spectroscopic/structural methods, and the results are more consistent with the COX-like model. JACS Au (2022).

Polyketides are mainly produced as secondary metabolites during the stationary phase of growth of Streptomyces species. The source of intracellular metabolites that are funneled into polyketide biosynthesis has proven elusive. We applied multi-omics to reveal that intracellular triacylglycerols (TAGs), which accumulates in primary metabolism, are degraded during stationary phase. This process could channel carbon flux from intracellular TAGs and extracellular substrates into polyketide biosynthesis. We devised a strategy named ‘dynamic degradation of TAG’ (ddTAG) to mobilize the TAG pool and increase polyketide biosynthesis. Our strategy could improve polyketide titers for pharmaceutical production. Nat Biotechnol (2020).

Besides genome editing, CRISPR-Cas12a has recently been used for DNA detection applications with attomolar sensitivity but, to our knowledge, it has not been used for the detection of small molecules. Bacterial allosteric transcription factors (aTFs) have evolved to sense and respond sensitively to a variety of small molecules to benefit bacterial survival. By combining the single-stranded DNA cleavage ability of CRISPR-Cas12a and the competitive binding activities of aTFs for small molecules and double-stranded DNA, here we develop a simple, supersensitive, fast and high-throughput platform for the detection of small molecules, designated CaT-SMelor (CRISPR-Cas12a- and aTF-mediated small molecule detector). CaT-SMelor is successfully evaluated by detecting nanomolar levels of various small molecules, including uric acid and p-hydroxybenzoic acid among their structurally similar analogues. We also demonstrate that our CaT-SMelor directly measured the uric acid concentration in clinical human blood samples, indicating a great potential of CaT-SMelor in the detection of small molecules. Nat Commun (2019).

There is a great demand for precisely quantitating the expression of genes of interest in synthetic and systems biotechnology as new and fascinating insights into the genetics of streptomycetes have come to light. Here, we developed, for the first time to our knowledge, a quantitative method based on flow cytometry and a superfolder green fluorescent protein (sfGFP) at single-cell resolution in Streptomyces. Single cells of filamentous bacteria were obtained by releasing the protoplasts from the mycelium, and the dead cells could be distinguished from the viable ones by propidium iodide (PI) staining. With this sophisticated quantitative method, some 200 native or synthetic promoters and 200 ribosomal binding sites (RBSs) were characterized in a high-throughput format. Furthermore, an insulator (RiboJ) was recruited to eliminate the interference between promoters and RBSs and improve the modularity of regulatory elements. Seven synthetic promoters with gradient strength were successfully applied in a proof-of-principle approach to activate and overproduce the cryptic lycopene in a predictable manner in Streptomyces avermitilis. Our work therefore presents a quantitative strategy and universal synthetic modular regulatory elements, which will facilitate the functional optimization of gene clusters and the drug discovery process in Streptomyces. PNAS (2015).

Biography

Prof. Lixin Zhang served as the Director of National Key Laboratory of Bioreactor Engineering at East China University of Science and Technology. His research focused on: Taxonomy guided diversification of a marine microbial natural product library; screening for synergistic medicines in a high throughput manner; increasing the production of drugable secondary metabolites from microbial producers by synthetic biology. His Avermectin project won a National Award for “Excellence to improve science and technologies” in 2017. He was a Chief Scientist of a “973 Program” and an Awardee of the National Science Fund for Distinguished Young Scholars, China. He worked in 3 pharmaceutical companies in USA and published seven books, 288 papers and holds 28 Chinese patents and 16 PCT patents. He served as the President of the International Chemical Biology Society (ICBS) during 2016-8. He has been appointed as an Editor-in-Chief for “Synthetic and Systems Biotechnology”. He also served as an Executive Board Member of International Committee on the Biology of Actinomycetes (ISBA) and the GIM (Genetics of Industrial Microorganisms). He is also on the SYNBIOCHEM External Advisory Board for the Manchester Institute of Biotechnology.