A long-term growth stable Halomonas sp. deleted with multiple transposases guided by its metabolic network model Halo-ecGEM
Journal article, 2024

Microbial instability is a common problem during bio-production based on microbial hosts. Halomonas bluephagenesis has been developed as a chassis for next generation industrial biotechnology (NGIB) under open and unsterile conditions. However, the hidden genomic information and peculiar metabolism have significantly hampered its deep exploitation for cell-factory engineering. Based on the freshly completed genome sequence of H. bluephagenesis TD01, which reveals 1889 biological process-associated genes grouped into 84 GO-slim terms. An enzyme constrained genome-scale metabolic model Halo-ecGEM was constructed, which showed strong ability to simulate fed-batch fermentations. A visible salt-stress responsive landscape was achieved by combining GO-slim term enrichment and CVT-based omics profiling, demonstrating that cells deploy most of the protein resources by force to support the essential activity of translation and protein metabolism when exposed to salt stress. Under the guidance of Halo-ecGEM, eight transposases were deleted, leading to a significantly enhanced stability for its growth and bioproduction of various polyhydroxyalkanoates (PHA) including 3-hydroxybutyrate (3HB) homopolymer PHB, 3HB and 3-hydroxyvalerate (3HV) copolymer PHBV, as well as 3HB and 4-hydroxyvalerate (4HB) copolymer P34HB. This study sheds new light on the metabolic characteristics and stress-response landscape of H. bluephagenesis, achieving for the first time to construct a long-term growth stable chassis for industrial applications. For the first time, it was demonstrated that genome encoded transposons are the reason for microbial instability during growth in flasks and fermentors.

PHB

Enzyme-constrained GEM

Halomonas

Multiomics analysis

Polyhydroxyalkanoates

Microbial stability

GO-Slim term

Next generation industrial biotechnology

Author

Lizhan Zhang

Tsinghua University

Jian Wen Ye

Tsinghua University

Gang Li

Chalmers, Life Sciences, Systems and Synthetic Biology

Helen Park

Tsinghua University

Hao Luo

Chalmers, Life Sciences, Systems and Synthetic Biology

Yina Lin

Tsinghua University

Shaowei Li

Tsinghua University

Weinan Yang

Tsinghua University

Yuying Guan

Tsinghua University

Fuqing Wu

Center for Life Sciences

Tsinghua University

Wuzhe Huang

PhaBuilder Biotech Co. Ltd.

Qiong Wu

Tsinghua University

Nigel S. Scrutton

Faculty of Science and Engineering

Jens B Nielsen

Chalmers, Life Sciences, Systems and Synthetic Biology

BioInnovation Institute

Guo Qiang Chen

Tsinghua University

Center for Life Sciences

Metabolic Engineering

1096-7176 (ISSN) 1096-7184 (eISSN)

Vol. 84 95-108

Subject Categories

Microbiology

DOI

10.1016/j.ymben.2024.06.004

More information

Latest update

7/25/2024