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BIT publishes prospective review paper in Trends in Biotechnology

News Resource & Photographer: School of Life Science

Editor: News Agency of BIT

Translator: Huang Yuwei, News Agency of BIT

Recently, Professor Huo Yixin and his team, from School of Life Science of Beijing Institute of Technology (BIT), have published a prospective review paper titled “Constructing the transcription regulatory network to optimize resource allocation for robustness synthesis” in Trends in Biotechnology (IF="19.536) which is a top journal in the field of biotechnology. The paper reviews the cutting-edge progress of robust optimization of microbial cell factories from a new perspective of resource allocation, and proposes the concept of building a “production-oriented” cell factory. The corresponding author is Professor Huo Yixin of School of Life Science, the first author is Associate Researcher Ma Xiaoyan and the joint first author is PHD student Ma Lianjie. The first unit is the Key Laboratory of Molecular Medicine and Biological Diagnosis and Treatment, Ministry of Industry and Information Technology, School of Life Science.

The transformation of microorganisms into cell factories for chemical fermentation production is an effective means to realize green manufacturing and promote “carbon neutrality”. However, there is a fundamental contradiction between the natural mission of maximizing the growth of microorganisms and the artificial empowerment of efficient production, which greatly hinders the maximization of production and yield. The paper puts forward the concept of “valve” for strain allocation resources, discussing the engineering strategies of the central transcriptional regulatory machinery (RNA polymerase) and its subordinate modules of the modified strains from the four levels of the transcriptional regulatory network: Global, Local, Edge and Bottom nodes. It describes the forward-looking strategy of “modifying the transcriptional regulatory network to reconstruct the resource allocation model to build a production-oriented cell factory and fully release its capacity”.

The RNAP core enzyme is similar to a multiway valve that governs resource allocation to growth, maintenance and production. In order to build a robust microbial cell factory, the gene regulatory network can be modified with top-down approach, from the top RNAP core enzymes to σ factors and global transcription factors, and then to the functional genes at the lower layer, to realize the overall redistribution and local precise guidance of cell resources (Picture 1B). The review through summarizing the latest research progress of the RNAP core enzyme structure (Picture 1C), aiming at the two main regions (the β' coiled-coil and the β flap) where the core enzyme binds to the σ factor (Picture 1D), discusses three different strategies for regulating the distribution of σ factor in the holoenzyme, including altering the key area of the RNAP core enzyme that interacts with the σ factor (Picture 1E), changing the interaction between the RNAP core enzyme and the effector (Picture 1F), and controlling the RNAP core enzyme synthesis to realize the switching of resource allocation between growth (path A) and production (path B) (Picture 1G), which can finally achieve the reprogramming of the global transcriptional regulatory network by the engineering of restructuring the RNAP core enzyme (filled with slashes), and strengthen the expression of production-related modules (dark orange) (Picture 1A).

Picture 1 Realize the reprogramming of the global transcriptional regulatory network through engineering modification of the RNAP core enzyme

Associate Researcher, Ma Xiaoyan, the paper’s first author, and PHD student Ma Lianjie focus on the use of transcriptional control to improve the robustness of cell factories, making a series of research progress. In terms of global regulation, a continuous expression system for the synthetic pathway driven by σ54 RNA polymerase is established, which is the solution to the insufficient supply of σ70 holoenzyme in the growth stabilization period and under stress conditions, and realizes the self-response, self-activation and self-reinforcement of the synthetic pathway. It shows good resistance to stress conditions such as low pH and high osmotic pressure, and successfully achieves high-efficiency biosynthesis across the entire growth period and under stress conditions. Driving the biosynthesis of higher alcohols via the σ54-dependent promoter, the production capacity of higher alcohols continues to increase after the stable period of bacterial growth, and the output reaches 3 times that of the common σ70-dependent promoter (Biotechnol Biofuels. 2020, 13:29).

In terms of the network edge, a “coupling” strategy of the anti-stress module and the production module has been developed. The research has found that the glutamate-dependent antacid system of Escherichia coli can be transcribed by σ70 RNA polymerase and σ38 RNA polymerase which appears abundantly in the stable period and under stress conditions, featuring stable expression throughout the growth period. Coupling the transcriptional regulation mechanism of the system with the pathway of higher alcohols production, the strain's output in the stable phase is increased by 25%, and under acid stress it reaches 1.8 times that of the existing engineered strain. This transcriptional coupling strategy can effectively resist the replacement of intracellular s factor under stress conditions and drive the continuous synthesis of cell factories throughout the growth period (Appl Microbiol Biot. 2018, 102:6).

The above research has created a variety of metabolic flux deployment elements including growth-phase independent driving elements, resource diversion elements, expression intensity control elements and metabolic resource valves, which redirects the metabolic flux from growth and reproduction to product synthesis, providing a new tool for the robust improvement of current industrial strains.

Picture 2 The synthetic pathway of σN drive element increases the output of microbial factories


Paper link: https://www.cell.com/trends/biotechnology/fulltext/S0167-7799(21)00263-8#%20

Attached author's introduction:

Associate Researcher Ma Xiaoyan, PhD graduated from the University of Chinese Academy of Sciences, has long been engaged in research on the construction of high-efficiency microbial cell factories and the green synthesis of amino acids and their high value-added derivatives. He has published more than 20 papers in top journals such as Nat Commun, Engineering, Biotechnol Biofuels, Appl Microbiol Biot, and obtained multiple invention patents.

Professor Huo Yixin, dean-appointed professor and doctoral supervisor of School of Life Science of BIT, has mainly focused on “microbial refining and manufacturing of bulk chemicals” and achieved a series of scientific research results for industrial applications by means of synthetic biology, whose representative works have been published in top journals such as Science, Nat Biotechnol, Nat Commun, etc. He has published more than 40 high-level papers and authorized nearly ten international and internal patents in the past five years. Having presided over more than ten national, provincial or regional projects such as the National Natural Science Foundation of China and the National Key Research and Development Program, he is currently on the board of management of Chinese Society of Biotechnology, appointed to deputy director of the “Molecular Medicine and Biological Diagnosis and Treatment” Key Laboratory of Ministry of Industry and Information Technology of the People's Republic China, and professor chair of biotechnology at BIT.