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Deantas-Jahn C, Mendoza SN, Licona-Cassani C, Orellana C, Saa PA. Metabolic modeling of Halomonas campaniensis improves polyhydroxybutyrate production under nitrogen limitation. Appl Microbiol Biotechnol 2024; 108:310. [PMID: 38662130 PMCID: PMC11045607 DOI: 10.1007/s00253-024-13111-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 02/25/2024] [Accepted: 03/18/2024] [Indexed: 04/26/2024]
Abstract
Poly-hydroxybutyrate (PHB) is an environmentally friendly alternative for conventional fossil fuel-based plastics that is produced by various microorganisms. Large-scale PHB production is challenging due to the comparatively higher biomanufacturing costs. A PHB overproducer is the haloalkaliphilic bacterium Halomonas campaniensis, which has low nutritional requirements and can grow in cultures with high salt concentrations, rendering it resistant to contamination. Despite its virtues, the metabolic capabilities of H. campaniensis as well as the limitations hindering higher PHB production remain poorly studied. To address this limitation, we present HaloGEM, the first high-quality genome-scale metabolic network reconstruction, which encompasses 888 genes, 1528 reactions (1257 gene-associated), and 1274 metabolites. HaloGEM not only displays excellent agreement with previous growth data and experiments from this study, but it also revealed nitrogen as a limiting nutrient when growing aerobically under high salt concentrations using glucose as carbon source. Among different nitrogen source mixtures for optimal growth, HaloGEM predicted glutamate and arginine as a promising mixture producing increases of 54.2% and 153.4% in the biomass yield and PHB titer, respectively. Furthermore, the model was used to predict genetic interventions for increasing PHB yield, which were consistent with the rationale of previously reported strategies. Overall, the presented reconstruction advances our understanding of the metabolic capabilities of H. campaniensis for rationally engineering this next-generation industrial biotechnology platform. KEY POINTS: A comprehensive genome-scale metabolic reconstruction of H. campaniensis was developed. Experiments and simulations predict N limitation in minimal media under aerobiosis. In silico media design increased experimental biomass yield and PHB titer.
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Affiliation(s)
- Carolina Deantas-Jahn
- Departamento de Ingeniería Química y Bioprocesos, Escuela de Ingeniería, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Sebastián N Mendoza
- Departamento de Ingeniería Química y Bioprocesos, Escuela de Ingeniería, Pontificia Universidad Católica de Chile, Santiago, Chile
- Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Cuauhtemoc Licona-Cassani
- Núcleo de Innovación de Sistemas Biológicos (NISB), FEMSA Biotechnology Center, Tecnológico de Monterrey, Monterrey, Mexico
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Monterrey, Mexico
| | - Camila Orellana
- Departamento de Ingeniería Química y Bioprocesos, Escuela de Ingeniería, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pedro A Saa
- Departamento de Ingeniería Química y Bioprocesos, Escuela de Ingeniería, Pontificia Universidad Católica de Chile, Santiago, Chile.
- Instituto de Ingeniería Matemática y Computacional, Pontificia Universidad Católica de Chile, Santiago, Chile.
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Leandro T, Oliveira MC, da Fonseca MMR, Cesário MT. Co-Production of Poly(3-hydroxybutyrate) and Gluconic Acid from Glucose by Halomonas elongata. Bioengineering (Basel) 2023; 10:643. [PMID: 37370574 DOI: 10.3390/bioengineering10060643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/10/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
Polyhydroxyalkanoates (PHA) are biopolyesters regarded as an attractive alternative to petroleum-derived plastics. Nitrogen limitation and phosphate limitation in glucose cultivations were evaluated for poly(3-hydroxybutyrate) (P(3HB)) production by Halomonas elongata 1H9T, a moderate halophilic strain. Co-production of P(3HB) and gluconic acid was observed in fed-batch glucose cultivations under nitrogen limiting conditions. A maximum P(3HB) accumulation of 53.0% (w/w) and a maximum co-production of 133 g/L of gluconic acid were attained. Fed-batch glucose cultivation under phosphate limiting conditions resulted in a P(3HB) accumulation of only 33.3% (w/w) and no gluconic acid production. As gluconic acid is a valuable organic acid with extensive applications in several industries, this work presents an interesting approach for the future development of an industrial process aiming at the co-production of an intracellular biopolymer, P(3HB), and a value-added extracellular product, gluconic acid.
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Affiliation(s)
- Tânia Leandro
- IBB-Institute for Bioengineering and Biosciences, Bioengineering Department, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - M Conceição Oliveira
- Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - M Manuela R da Fonseca
- IBB-Institute for Bioengineering and Biosciences, Bioengineering Department, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - M Teresa Cesário
- IBB-Institute for Bioengineering and Biosciences, Bioengineering Department, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
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Ye JW, Lin YN, Yi XQ, Yu ZX, Liu X, Chen GQ. Synthetic biology of extremophiles: a new wave of biomanufacturing. Trends Biotechnol 2023; 41:342-357. [PMID: 36535816 DOI: 10.1016/j.tibtech.2022.11.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/12/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022]
Abstract
Microbial biomanufacturing, powered by the advances of synthetic biology, has attracted growing interest for the production of diverse products. In contrast to conventional microbes, extremophiles have shown better performance for low-cost production owing to their outstanding growth and synthesis capacity under stress conditions, allowing unsterilized fermentation processes. We review increasing numbers of products already manufactured utilizing extremophiles in recent years. In addition, genetic parts, molecular tools, and manipulation approaches for extremophile engineering are also summarized, and challenges and opportunities are predicted for non-conventional chassis. Next-generation industrial biotechnology (NGIB) based on engineered extremophiles promises to simplify biomanufacturing processes and achieve open and continuous fermentation, without sterilization, and utilizing low-cost substrates, making NGIB an attractive green process for sustainable manufacturing.
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Affiliation(s)
- Jian-Wen Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China; Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yi-Na Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China; Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xue-Qing Yi
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhuo-Xuan Yu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Xu Liu
- PhaBuilder Biotech Company, Shunyi District, Zhaoquan Ying, Beijing 101309, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; Ministry of Education (MOE) Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing, China.
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Tsuji A, Takei Y, Azuma Y. Establishment of genetic tools for genomic DNA engineering of Halomonas sp. KM-1, a bacterium with potential for biochemical production. Microb Cell Fact 2022; 21:122. [PMID: 35725447 PMCID: PMC9208146 DOI: 10.1186/s12934-022-01797-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/13/2022] [Indexed: 01/09/2023] Open
Abstract
Halomonas species are halophilic and alkaliphilic bacteria, which exhibit potential for industrial production of a variety of chemicals, such as polyhydroxyalkanoates and ectoine, by fermentation because of their favorable characteristics, including high-density culturing capacity and low risk of contamination. However, genetic tools to modify the metabolism of Halomonas for suitable fermentation performance are limited. In this study, we developed two independent basic vectors for Halomonas, named pUCpHAw and pHA1AT_32, consisting of ori regions from two plasmids isolated from Halomonas sp. A020, and chloramphenicol- and tetracycline-resistant genes as cloning markers, respectively. These vectors can independently transform and co-transform the Halomonas sp. KM-1 (KM-1). A protein that was highly and constitutively accumulated was identified as a hemolysin coregulated protein (Hcp) based on proteome analysis of KM-1. Using the hcp promoter, various genes, such as phaA and EGFP, were highly expressed. To establish a gene disruption system, the Streptococcus pyogenes cas9 gene and guide RNA for the pyrF gene, a yeast URA3 homologue, were expressed in pUCpHAw and pHA1AT_32, respectively. As a result, gene disruption mutants were isolated based on phenotypes, 5-fluoroorotic acid resistance, and uracil auxotrophy. A combination of KM-1 and these vectors could be a suitable platform for industrial chemical and protein production.
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Affiliation(s)
- Ayaka Tsuji
- Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Yasuko Takei
- Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Yoshinao Azuma
- Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan.
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