Developing a pathway-independent and full-autonomous global resource allocation strategy to dynamically switching phenotypic states

Junjun Wu,Peng Zhou,Caiwen Chen,Zhijun Zhao,Qianqian Zhuang,Shiyao Cheng,Meijiao Bao,Xuguo Duan,Jiahua Gao

doi:10.1038/s41467-020-19432-2

Abstract

A grand challenge of biological chemical production is the competition between synthetic circuits and host genes for limited cellular resources. Quorum sensing (QS)-based dynamic pathway regulations provide a pathway-independent way to rebalance metabolic flux over the course of the fermentation. Most cases, however, these pathway-independent strategies only have capacity for a single QS circuit functional in one cell. Furthermore, current dynamic regulations mainly provide localized control of metabolic flux. Here, with the aid of engineering synthetic orthogonal quorum-related circuits and global mRNA decay, we report a pathway-independent dynamic resource allocation strategy, which allows us to independently controlling two different phenotypic states to globally redistribute cellular resources toward synthetic circuits. The strategy which could pathway-independently and globally self-regulate two desired cell phenotypes including growth and production phenotypes could totally eliminate the need for human supervision of the entire fermentation.

Highlights

A grand challenge of biological chemical production is the competition between synthetic circuits and host genes for limited cellular resources
Previous studies mainly focused on characterizing Lux-like Quorum sensing (QS) systems from Gram-negative bacterium[11,12], each with a unique LuxR-like receptor and homoserine lactone (HSL) homologue, and found that hybrid tra and rpa QS systems, which were created by replacing lux-box-like sequences from Lux QS systems with tra-box and rpa-box, respectively, exhibited both signal and promoter orthogonality[12]
Developing strategies to switch between modes of growth and production for controlling resource economy of cells is a fundamental goal of biological chemical production[1]

Summary

Introduction

A grand challenge of biological chemical production is the competition between synthetic circuits and host genes for limited cellular resources. Quorum sensing (QS)-based dynamic pathway regulations provide a pathway-independent way to rebalance metabolic flux over the course of the fermentation Most cases, these pathway-independent strategies only have capacity for a single QS circuit functional in one cell. Promoter-regulator systems detecting acetyl phosphate[6], FadRbased sensors[7], stress-responsive promoters sensing farnesyl pyrophosphate[8], malonyl-CoA sensor-regulators, and bifunctional dynamic control regulating phosphoenolpyruvate metabolic nodes[2] have been designed to dynamically control the biosynthesis of lycopene, biodiesel, amorphadiene, fatty acids and muconic acid While these exciting achievements have been proven effective, such strategies require pathway- or metabolitespecific sensors, which are unknown for many metabolites or pathways that one might want to monitor, limiting their widespread use in other metabolic pathways or hosts[9]. Technologies should be developed to full-autonomously, genome-widely regulate gene expression patterns to minimize resource expenditure

Methods

Results

Conclusion