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Wang Q, Zhang J, Zhao Z, Li Y, You J, Wang Y, Li X, Xu M, Rao Z. Dual genetic level modification engineering accelerate genome evolution of Corynebacterium glutamicum. Nucleic Acids Res 2024:gkae577. [PMID: 38967005 DOI: 10.1093/nar/gkae577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/02/2024] [Accepted: 06/26/2024] [Indexed: 07/06/2024] Open
Abstract
High spontaneous mutation rate is crucial for obtaining ideal phenotype and exploring the relationship between genes and phenotype. How to break the genetic stability of organisms and increase the mutation frequency has become a research hotspot. Here, we present a practical and controllable evolutionary tool (oMut-Cgts) based on dual genetic level modification engineering for Corynebacterium glutamicum. Firstly, the modification engineering of transcription and replication levels based on RNA polymerase α subunit and DNA helicase Cgl0854 as the 'dock' of cytidine deaminase (pmCDA1) significantly increased the mutation rate, proving that the localization of pmCDA1 around transient ssDNA is necessary for genome mutation. Then, the combined modification and optimization of engineering at dual genetic level achieved 1.02 × 104-fold increased mutation rate. The genome sequencing revealed that the oMut-Cgts perform uniform and efficient C:G→T:A transitions on a genome-wide scale. Furthermore, oMut-Cgts-mediated rapid evolution of C. glutamicum with stress (acid, oxidative and ethanol) tolerance proved that the tool has powerful functions in multi-dimensional biological engineering (rapid phenotype evolution, gene function mining and protein evolution). The strategies for rapid genome evolution provided in this study are expected to be applicable to a variety of applications in all prokaryotic cells.
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Affiliation(s)
- Qing Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Institute of Future Food Technology, JITRI, Yixing 214200, China
| | - Jie Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Institute of Future Food Technology, JITRI, Yixing 214200, China
| | - Zhe Zhao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Institute of Future Food Technology, JITRI, Yixing 214200, China
| | - Yichen Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Institute of Future Food Technology, JITRI, Yixing 214200, China
| | - Jiajia You
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Institute of Future Food Technology, JITRI, Yixing 214200, China
| | - Yi Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Institute of Future Food Technology, JITRI, Yixing 214200, China
| | - Xiangfei Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Institute of Future Food Technology, JITRI, Yixing 214200, China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Institute of Future Food Technology, JITRI, Yixing 214200, China
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Institute of Future Food Technology, JITRI, Yixing 214200, China
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Tian S, Zhao G, Lv G, Wu C, Su R, Wang F, Wang Z, Liu Y, Chen N, Li Y. Efficient Fermentative Production of d-Alanine and Other d-Amino Acids by Metabolically Engineered Corynebacterium glutamicum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8039-8051. [PMID: 38545740 DOI: 10.1021/acs.jafc.4c00914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
d-Amino acids (d-AAs) have wide applications in industries such as pharmaceutical, food, and cosmetics due to their unique properties. Currently, the production of d-AAs has relied on chemical synthesis or enzyme catalysts, and it is challenging to produce d-AAs via direct fermentation from glucose. We observed that Corynebacterium glutamicum exhibits a remarkable tolerance to high concentrations of d-Ala, a crucial characteristic for establishing a successful fermentation process. By optimizing meso-diaminopilmelate dehydrogenases in different C. glutamicum strains and successively deleting l-Ala biosynthetic pathways, we developed an efficient d-Ala fermentation system. The d-Ala titer was enhanced through systems metabolic engineering, which involved strengthening glucose assimilation and pyruvate supply, reducing the formation of organic acid byproducts, and attenuating the TCA cycle. During fermentation in a 5-L bioreactor, a significant accumulation of l-Ala was observed in the broth, which was subsequently diminished by introducing an l-amino acid deaminase. Ultimately, the engineered strain DA-11 produced 85 g/L d-Ala with a yield of 0.30 g/g glucose, accompanied by an optical purity exceeding 99%. The fermentation platform has the potential to be extended for the synthesis of other d-AAs, as demonstrated by the production of d-Val and d-Glu.
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Affiliation(s)
- Siyu Tian
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Guihong Zhao
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Gengcheng Lv
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Chen Wu
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Rui Su
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Feiao Wang
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Zeting Wang
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Yuexiang Liu
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Ning Chen
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Yanjun Li
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
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Zhang Y, Xiao F, Zhang L, Ding Z, Shi G, Li Y. A New Mechanism of Carbon Metabolism and Acetic Acid Balance Regulated by CcpA. Microorganisms 2023; 11:2303. [PMID: 37764147 PMCID: PMC10535407 DOI: 10.3390/microorganisms11092303] [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: 08/17/2023] [Revised: 09/02/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Catabolite control protein A (CcpA) is a critical regulator in Gram-positive bacteria that orchestrates carbon metabolism by coordinating the utilization of different carbon sources. Although it has been widely proved that CcpA helps prioritize the utilization of glucose over other carbon sources, this global regulator's precise mechanism of action remains unclear. In this study, a mutant Bacillus licheniformis deleted for CcpA was constructed. Cell growth, carbon utilization, metabolites and the transcription of key enzymes of the mutant strain were compared with that of the wild-type one. It was found that CcpA is involved in the regulation of glucose concentration metabolism in Bacillus. At the same time, CcpA regulates glucose metabolism by inhibiting acetic acid synthesis and pentose phosphate pathway key gene zwF. The conversion rate of acetic acid is increased by about 3.5 times after ccpA is deleted. The present study provides a new mechanism of carbon metabolism and acetic acid balance regulated by CcpA. On the one hand, this work deepens the understanding of the regulatory function of CcpA and provides a new view on the regulation of glucose metabolism. On the other hand, it is helpful to the transformation of B. licheniformis chassis microorganisms.
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Affiliation(s)
- Yupeng Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.Z.); (F.X.); (L.Z.); (Z.D.); (G.S.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Fengxu Xiao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.Z.); (F.X.); (L.Z.); (Z.D.); (G.S.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Liang Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.Z.); (F.X.); (L.Z.); (Z.D.); (G.S.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Zhongyang Ding
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.Z.); (F.X.); (L.Z.); (Z.D.); (G.S.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Guiyang Shi
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.Z.); (F.X.); (L.Z.); (Z.D.); (G.S.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Youran Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.Z.); (F.X.); (L.Z.); (Z.D.); (G.S.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
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Kurpejović E, Wibberg D, Bastem GM, Burgardt A, Busche T, Kaya FEA, Dräger A, Wendisch VF, Akbulut BS. Can Genome Sequencing Coupled to Flux Balance Analyses Offer Precision Guidance for Industrial Strain Development? The Lessons from Carbon Trafficking in Corynebacterium glutamicum ATCC 21573. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:434-443. [PMID: 37707996 DOI: 10.1089/omi.2023.0098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Systems biology tools offer new prospects for industrial strain selection. For bacteria that are significant for industrial applications, whole-genome sequencing coupled to flux balance analysis (FBA) can help unpack the complex relationships between genome mutations and carbon trafficking. This work investigates the l-tyrosine (l-Tyr) overproducing model system Corynebacterium glutamicum ATCC 21573 with an eye to more rational and precision strain development. Using genome-wide mutational analysis of C. glutamicum, we identified 27,611 single nucleotide polymorphisms and 479 insertion/deletion mutations. Mutations in the carbon uptake machinery have led to phosphotransferase system-independent routes as corroborated with FBA. Mutations within the central carbon metabolism of C. glutamicum impaired the carbon flux, as evidenced by the lower growth rate. The entry to and flow through the tricarboxylic acid cycle was affected by mutations in pyruvate and α-ketoglutarate dehydrogenase complexes, citrate synthase, and isocitrate dehydrogenase. FBA indicated that the estimated flux through the shikimate pathway became larger as the l-Tyr production rate increased. In addition, protocatechuate export was probabilistically impossible, which could have contributed to the l-Tyr accumulation. Interestingly, aroG and cg0975, which have received previous attention for aromatic amino acid overproduction, were not mutated. From the branch point molecule, prephenate, the change in the promoter region of pheA could be an influential contributor. In summary, we suggest that genome sequencing coupled with FBA is well poised to offer rational guidance for industrial strain development, as evidenced by these findings on carbon trafficking in C. glutamicum ATCC 21573.
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Affiliation(s)
- Eldin Kurpejović
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Daniel Wibberg
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | | | - Arthur Burgardt
- Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Tobias Busche
- Technology Platform Genomics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Medical School East Westphalia-Lippe, Bielefeld University, Bielefeld, Germany
| | - Fatma Ece Altinisik Kaya
- Department of Bioengineering, Marmara University, Istanbul, Turkey
- Department of Computer Science, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Andreas Dräger
- Department of Computer Science, Eberhard Karl University of Tübingen, Tübingen, Germany
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
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Schmollack M, Werner F, Huber J, Kiefer D, Merkel M, Hausmann R, Siebert D, Blombach B. Metabolic engineering of Corynebacterium glutamicum for acetate-based itaconic acid production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:139. [PMID: 36517879 PMCID: PMC9753420 DOI: 10.1186/s13068-022-02238-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Itaconic acid is a promising platform chemical for a bio-based polymer industry. Today, itaconic acid is biotechnologically produced with Aspergillus terreus at industrial scale from sugars. The production of fuels but also of chemicals from food substrates is a dilemma since future processes should rely on carbon sources which do not compete for food or feed. Therefore, the production of chemicals from alternative substrates such as acetate is desirable to develop novel value chains in the bioeconomy. RESULTS In this study, Corynebacterium glutamicum ATCC 13032 was engineered to efficiently produce itaconic acid from the non-food substrate acetate. Therefore, we rewired the central carbon and nitrogen metabolism by inactivating the transcriptional regulator RamB, reducing the activity of isocitrate dehydrogenase, deletion of the gdh gene encoding glutamate dehydrogenase and overexpression of cis-aconitate decarboxylase (CAD) from A. terreus optimized for expression in C. glutamicum. The final strain C. glutamicum ΔramB Δgdh IDHR453C (pEKEx2-malEcadopt) produced 3.43 ± 0.59 g itaconic acid L-1 with a product yield of 81 ± 9 mmol mol-1 during small-scale cultivations in nitrogen-limited minimal medium containing acetate as sole carbon and energy source. Lowering the cultivation temperature from 30 °C to 25 °C improved CAD activity and further increased the titer and product yield to 5.01 ± 0.67 g L-1 and 116 ± 15 mmol mol-1, respectively. The latter corresponds to 35% of the theoretical maximum and so far represents the highest product yield for acetate-based itaconic acid production. Further, the optimized strain C. glutamicum ΔramB Δgdh IDHR453C (pEKEx2-malEcadopt), produced 3.38 ± 0.28 g itaconic acid L-1 at 25 °C from an acetate-containing aqueous side-stream of fast pyrolysis. CONCLUSION As shown in this study, acetate represents a suitable non-food carbon source for itaconic acid production with C. glutamicum. Tailoring the central carbon and nitrogen metabolism enabled the efficient production of itaconic acid from acetate and therefore this study offers useful design principles to genetically engineer C. glutamicum for other products from acetate.
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Affiliation(s)
- Marc Schmollack
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Uferstraße 53, 94315, Straubing, Germany
| | - Felix Werner
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Uferstraße 53, 94315, Straubing, Germany
| | - Janine Huber
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Uferstraße 53, 94315, Straubing, Germany
| | - Dirk Kiefer
- Institute of Food Science and Biotechnology, Department of Bioprocess Engineering, University of Hohenheim, Stuttgart, Germany
| | - Manuel Merkel
- Institute of Food Science and Biotechnology, Department of Bioprocess Engineering, University of Hohenheim, Stuttgart, Germany
| | - Rudolf Hausmann
- Institute of Food Science and Biotechnology, Department of Bioprocess Engineering, University of Hohenheim, Stuttgart, Germany
| | - Daniel Siebert
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Uferstraße 53, 94315, Straubing, Germany
- SynBiofoundry@TUM, Technical University of Munich, Straubing, Germany
| | - Bastian Blombach
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Uferstraße 53, 94315, Straubing, Germany.
- SynBiofoundry@TUM, Technical University of Munich, Straubing, Germany.
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Ricci L, Seifert A, Bernacchi S, Fino D, Pirri CF, Re A. Leveraging substrate flexibility and product selectivity of acetogens in two-stage systems for chemical production. Microb Biotechnol 2022; 16:218-237. [PMID: 36464980 PMCID: PMC9871533 DOI: 10.1111/1751-7915.14172] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/31/2022] [Accepted: 11/08/2022] [Indexed: 12/09/2022] Open
Abstract
Carbon dioxide (CO2 ) stands out as sustainable feedstock for developing a circular carbon economy whose energy supply could be obtained by boosting the production of clean hydrogen from renewable electricity. H2 -dependent CO2 gas fermentation using acetogenic microorganisms offers a viable solution of increasingly demonstrated value. While gas fermentation advances to achieve commercial process scalability, which is currently limited to a few products such as acetate and ethanol, it is worth taking the best of the current state-of-the-art technology by its integration within innovative bioconversion schemes. This review presents multiple scenarios where gas fermentation by acetogens integrate into double-stage biotechnological production processes that use CO2 as sole carbon feedstock and H2 as energy carrier for products' synthesis. In the integration schemes here reviewed, the first stage can be biotic or abiotic while the second stage is biotic. When the first stage is biotic, acetogens act as a biological platform to generate chemical intermediates such as acetate, formate and ethanol that become substrates for a second fermentation stage. This approach holds the potential to enhance process titre/rate/yield metrics and products' spectrum. Alternatively, when the first stage is abiotic, the integrated two-stage scheme foresees, in the first stage, the catalytic transformation of CO2 into C1 products that, in the second stage, can be metabolized by acetogens. This latter scheme leverages the metabolic flexibility of acetogens in efficient utilization of the products of CO2 abiotic hydrogenation, namely formate and methanol, to synthesize multicarbon compounds but also to act as flexible catalysts for hydrogen storage or production.
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Affiliation(s)
- Luca Ricci
- Department of Applied Science and TechnologyPolitecnico di TorinoTurinItaly,Centre for Sustainable Future TechnologiesFondazione Istituto Italiano di TecnologiaTurinItaly
| | | | | | - Debora Fino
- Department of Applied Science and TechnologyPolitecnico di TorinoTurinItaly,Centre for Sustainable Future TechnologiesFondazione Istituto Italiano di TecnologiaTurinItaly
| | - Candido Fabrizio Pirri
- Department of Applied Science and TechnologyPolitecnico di TorinoTurinItaly,Centre for Sustainable Future TechnologiesFondazione Istituto Italiano di TecnologiaTurinItaly
| | - Angela Re
- Department of Applied Science and TechnologyPolitecnico di TorinoTurinItaly,Centre for Sustainable Future TechnologiesFondazione Istituto Italiano di TecnologiaTurinItaly
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Mutyala S, Kim JR. Recent advances and challenges in the bioconversion of acetate to value-added chemicals. BIORESOURCE TECHNOLOGY 2022; 364:128064. [PMID: 36195215 DOI: 10.1016/j.biortech.2022.128064] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Acetate is a major byproduct of the bioconversion of the greenhouse gas carbon dioxide, pretreatment of lignocellulose biomass, and microbial fermentation. The utilization and valorization of acetate have been emphasized in transforming waste to clean energy and value-added platform chemicals, contributing to the development of a closed carbon loop toward a low-carbon circular bio-economy. Acetate has been used to produce several platform chemicals, including succinate, 3-hydroxypropionate, and itaconic acid, highlighting the potential of acetate to synthesize many biochemicals and biofuels. On the other hand, the yields and titers have not reached the theoretical maximum. Recently, recombinant strain development and pathway regulation have been suggested to overcome this limitation. This review provides insights into the important constraints limiting the yields and titers of the biochemical and metabolic pathways of bacteria capable of metabolizing acetate for acetate bioconversion. The current developments in recombinant strain engineering are also discussed.
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Affiliation(s)
- Sakuntala Mutyala
- School of Chemical Engineering, Pusan National University, 63 Busandeahak-ro, Geumjeong-Gu, Busan 46241, Republic of Korea
| | - Jung Rae Kim
- School of Chemical Engineering, Pusan National University, 63 Busandeahak-ro, Geumjeong-Gu, Busan 46241, Republic of Korea.
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Ray D, Anand U, Jha NK, Korzeniewska E, Bontempi E, Proćków J, Dey A. The soil bacterium, Corynebacterium glutamicum, from biosynthesis of value-added products to bioremediation: A master of many trades. ENVIRONMENTAL RESEARCH 2022; 213:113622. [PMID: 35710026 DOI: 10.1016/j.envres.2022.113622] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 05/05/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Ever since its discovery in 1957, Corynebacterium glutamicum has become a well-established industrial strain and is known for its massive capability of producing various amino acids (like L-lysine and L-glutamate) and other value-added chemicals. With the rising demand for these bio-based products, the revelation of the whole genome sequences of the wild type strains, and the astounding advancements made in the fields of metabolic engineering and systems biology, our perspective of C. glutamicum has been revolutionized and has expanded our understanding of its strain development. With these advancements, a new era for C. glutamicum supremacy in the field of industrial biotechnology began. This led to remarkable progress in the enhancement of tailor-made over-producing strains and further development of the substrate spectrum of the bacterium, to easily accessible, economical, and renewable resources. C. glutamicum has also been metabolically engineered and used in the degradation/assimilation of highly toxic and ubiquitous environmental contaminant, arsenic, present in water or soil. Here, we review the history, current knowledge, progress, achievements, and future trends relating to the versatile metabolic factory, C. glutamicum. This review paper is devoted to C. glutamicum which is one of the leading industrial microbes, and one of the most promising and versatile candidates to be developed. It can be used not only as a platform microorganism to produce different value-added chemicals and recombinant proteins, but also as a tool for bioremediation, allowing to enhance specific properties, for example in situ bioremediation.
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Affiliation(s)
- Durga Ray
- Department of Microbiology, St. Aloysius' College, Jabalpur, Madhya Pradesh, 482001, India.
| | - Uttpal Anand
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering & Technology, Sharda University, Greater Noida, 201310, Uttar Pradesh, India; Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, 140413, Punjab, India; Department of Biotechnology, School of Applied & Life Sciences, Uttaranchal University, Dehradun 248007, Uttarakhand, India
| | - Ewa Korzeniewska
- Department of Water Protection Engineering and Environmental Microbiology, The Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-719, Olsztyn, Poland
| | - Elza Bontempi
- INSTM and Chemistry for Technologies Laboratory, Department of Mechanical and Industrial Engineering, University of Brescia, Via Branze, 38, 25123, Brescia, Italy
| | - Jarosław Proćków
- Department of Plant Biology, Institute of Environmental Biology, Wrocław University of Environmental and Life Sciences, Kożuchowska 5b, 51-631, Wrocław, Poland.
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, West Bengal, India.
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Development of a novel platform for recombinant protein production in Corynebacterium glutamicum on ethanol. Synth Syst Biotechnol 2022; 7:765-774. [PMID: 35387228 PMCID: PMC8942793 DOI: 10.1016/j.synbio.2022.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 03/04/2022] [Accepted: 03/15/2022] [Indexed: 02/03/2023] Open
Abstract
Corynebacterium glutamicum represents an emerging recombinant protein expression factory due to its ideal features for protein secretion, but its applicability is harmed by the lack of an autoinduction system with tight regulation and high yield. Here, we propose a new recombinant protein manufacturing platform that leverages ethanol as both a delayed carbon source and an inducer. First, we reanalysed the native inducible promoter PICL from the acetate uptake operon and found that its limited capacity is the result of the inadequate translation initial architecture. The two strategies of bicistronic design and ribozyme-based insulator can ensure the high activity of this promoter. Next, through transcriptional engineering that alters transcription factor binding sites (TFBSs) and the first transcribed sequence, the truncated promoter PA256 with a dramatically higher transcription level was generated. When producing the superfolder green fluorescent protein (sfGFP) under 1% ethanol conditions, PA256 exhibited substantially lower protein accumulation in prophase but an approximately 2.5-fold greater final yield than the strong promoter PH36. This superior expression mode was further validated using two secreted proteins, camelid antibody fragment (VHH) and endoxylanase (XynA). Furthermore, utilizing CRISPRi technology, ethanol utilization blocking strains were created, and PA256 was shown to be impaired in the phosphotransacetylase (PTA) knockdown strains, indicating that ethanol metabolism into the tricarboxylic acid cycle is required for PA256 upregulation. Finally, this platform was applied to produce the “de novo design” protein NEO-2/15, and by introducing the N-propeptide of CspB, NEO-2/15 was effectively secreted with the accumulation 281 mg/L obtained after 24 h of shake-flask fermentation. To the best of our knowledge, this is the first report of NEO-2/15 secretory overexpression.
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10
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Adaptive Laboratory Evolution of Halomonas bluephagenesis Enhances Acetate Tolerance and Utilization to Produce Poly(3-hydroxybutyrate). Molecules 2022; 27:molecules27093022. [PMID: 35566371 PMCID: PMC9103988 DOI: 10.3390/molecules27093022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/02/2022] [Accepted: 05/06/2022] [Indexed: 11/17/2022] Open
Abstract
Acetate is a promising economical and sustainable carbon source for bioproduction, but it is also a known cell-growth inhibitor. In this study, adaptive laboratory evolution (ALE) with acetate as selective pressure was applied to Halomonas bluephagenesis TD1.0, a fast-growing and contamination-resistant halophilic bacterium that naturally accumulates poly(3-hydroxybutyrate) (PHB). After 71 transfers, the evolved strain, B71, was isolated, which not only showed better fitness (in terms of tolerance and utilization rate) to high concentrations of acetate but also produced a higher PHB titer compared with the parental strain TD1.0. Subsequently, overexpression of acetyl-CoA synthetase (ACS) in B71 resulted in a further increase in acetate utilization but a decrease in PHB production. Through whole-genome resequencing, it was speculated that genetic mutations (single-nucleotide variation (SNV) in phaB, mdh, and the upstream of OmpA, and insertion of TolA) in B71 might contribute to its improved acetate adaptability and PHB production. Finally, in a 5 L bioreactor with intermittent feeding of acetic acid, B71 was able to produce 49.79 g/L PHB and 70.01 g/L dry cell mass, which were 147.2% and 82.32% higher than those of TD1.0, respectively. These results highlight that ALE provides a reliable method to harness H. bluephagenesis to metabolize acetate for the production of PHB or other high-value chemicals more efficiently.
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11
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Zhang S, Ma X, Yu H, Lu X, Liu J, Zhang L, Wang G, Ye J, Ning G. Silver(I) metal-organic framework-embedded polylactic acid electrospun fibrous membranes for efficient inhibition of bacteria. Dalton Trans 2022; 51:6673-6681. [PMID: 35411886 DOI: 10.1039/d1dt04234c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
With recent outbreaks of fatal strains of diseases and the emergency of antibiotic resistance, there is a pressing demand to discover bactericidal materials that can effectively reduce or prevent infections by pathogenic bacteria. Herein, silver(I) metal organic frameworks Ag2(HBTC) were embedded into biocompatible polylactic acid (PLA) fibrous membranes through an electrospinning process as an antibiotic-free material for effective bacterial killing. The as-synthesized Ag2(HBTC)/PLA composite membrane showed an inactivation efficiency of more than 99.9% against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) at a concentration of 200-250 mg L-1. Mechanistic investigation indicated that the steady release of Ag+ ions and ˙OH generation from the composites contributed to the efficient antibacterial activities through irreversible damage to the bacterial cell membranes. In-depth proteomic analysis demonstrated that Ag2(HBTC)/PLA exerted a biological effect towards bacterial cells through down-regulating functional proteins, thereby destroying the central biochemical pathways of the cellular energy metabolism process, reducing resistance to oxidative damage and inhibiting cell division. In general, this study shows a promising perspective on designing MOF/PLA membranes with broad-spectrum disinfection capability for potential environmental sterilization and public healthcare protection.
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Affiliation(s)
- Siqi Zhang
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning, 116024, PR China
| | - Xiao Ma
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning, 116024, PR China
| | - Hailong Yu
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning, 116024, PR China
| | - Xinyi Lu
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning, 116024, PR China.,CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, PR China.
| | - Jianhui Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, PR China.
| | - Lihua Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, PR China.
| | - Guangyao Wang
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning, 116024, PR China
| | - Junwei Ye
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning, 116024, PR China
| | - Guiling Ning
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning, 116024, PR China
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12
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Merkel M, Kiefer D, Schmollack M, Blombach B, Lilge L, Henkel M, Hausmann R. Acetate-based production of itaconic acid with Corynebacterium glutamicum using an integrated pH-coupled feeding control. BIORESOURCE TECHNOLOGY 2022; 351:126994. [PMID: 35288270 DOI: 10.1016/j.biortech.2022.126994] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
To date, most bio-based products of industrial biotechnology stem from sugar-based carbon sources originating from food and feed competing resources. Exemplary for bioproducts converted from glucose, the potential C5 platform chemical itaconic acid is presently produced by the filamentous fungus Aspergillus terreus. Here, an engineered strain of the industrial platform organism Corynebacterium glutamicum ATCC 13032 was used for acetate-based production of itaconic acid to overcome current production difficulties. For this purpose, C. glutamicum ICDR453C (pEKEx2-malEcadopt) with a mutated icd variant for reduced isocitrate dehydrogenase activity was constructed harbouring pEKEx2-malEcadopt, that includes a cis-aconitate dehydrogenase gene originating from A. terreus. Overall, a peak volumetric productivity of 1.01 gL-1h-1 was achieved resulting in an itaconate titer of 29.2 g/L, by using an integrated pH-coupled acetate feeding control in a fed-batch process without base titration. The results support the high potential of acetate as alternative substrate for bioproduction.
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Affiliation(s)
- Manuel Merkel
- University of Hohenheim, Institute of Food Science and Biotechnology, Department of Bioprocess Engineering, Fruwirthstrasse 12, 70599 Stuttgart, Germany
| | - Dirk Kiefer
- University of Hohenheim, Institute of Food Science and Biotechnology, Department of Bioprocess Engineering, Fruwirthstrasse 12, 70599 Stuttgart, Germany
| | - Marc Schmollack
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Straubing, Germany
| | - Bastian Blombach
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Straubing, Germany; SynBiofoundry@TUM, Technical University of Munich, Straubing, Germany
| | - Lars Lilge
- University of Hohenheim, Institute of Food Science and Biotechnology, Department of Bioprocess Engineering, Fruwirthstrasse 12, 70599 Stuttgart, Germany
| | - Marius Henkel
- University of Hohenheim, Institute of Food Science and Biotechnology, Department of Bioprocess Engineering, Fruwirthstrasse 12, 70599 Stuttgart, Germany.
| | - Rudolf Hausmann
- University of Hohenheim, Institute of Food Science and Biotechnology, Department of Bioprocess Engineering, Fruwirthstrasse 12, 70599 Stuttgart, Germany
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13
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Zannier F, Portero LR, Douki T, Gärtner W, Farías ME, Albarracín VH. Proteomic Signatures of Microbial Adaptation to the Highest Ultraviolet-Irradiation on Earth: Lessons From a Soil Actinobacterium. Front Microbiol 2022; 13:791714. [PMID: 35369494 PMCID: PMC8965627 DOI: 10.3389/fmicb.2022.791714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/26/2022] [Indexed: 11/13/2022] Open
Abstract
In the Central Andean region in South America, high-altitude ecosystems (3500-6000 masl) are distributed across Argentina, Chile, Bolivia, and Peru, in which poly-extremophilic microbes thrive under extreme environmental conditions. In particular, in the Puna region, total solar irradiation and UV incidence are the highest on Earth, thus, restraining the physiology of individual microorganisms and the composition of microbial communities. UV-resistance of microbial strains thriving in High-Altitude Andean Lakes was demonstrated and their mechanisms were partially characterized by genomic analysis, biochemical and physiological assays. Then, the existence of a network of physiological and molecular mechanisms triggered by ultraviolet light exposure was hypothesized and called "UV-resistome". It includes some or all of the following subsystems: (i) UV sensing and effective response regulators, (ii) UV-avoidance and shielding strategies, (iii) damage tolerance and oxidative stress response, (iv) energy management and metabolic resetting, and (v) DNA damage repair. Genes involved in the described UV-resistome were recently described in the genome of Nesterenkonia sp. Act20, an actinobacterium which showed survival to high UV-B doses as well as efficient photorepairing capability. The aim of this work was to use a proteomic approach together with photoproduct measurements to help dissecting the molecular events involved in the adaptive response of a model High-Altitude Andean Lakes (HAAL) extremophilic actinobacterium, Nesterenkonia sp. Act20, under artificial UV-B radiation. Our results demonstrate that UV-B exposure induced over-abundance of a well-defined set of proteins while recovery treatments restored the proteomic profiles present before the UV-challenge. The proteins involved in this complex molecular network were categorized within the UV-resistome subsystems: damage tolerance and oxidative stress response, energy management and metabolic resetting, and DNA damage repair.
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Affiliation(s)
- Federico Zannier
- Laboratorio de Microbiología Ultraestructural y Molecular, Centro Integral de Microscopía Electrónica, Facultad de Agronomía y Zootecnia, UNT y Centro Científico Tecnológico, CONICET NOASUR, San Miguel de Tucumán, Argentina
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales y Microbiológicos, Centro Científico Tecnológico, CONICET NOASUR, San Miguel de Tucumán, Argentina
| | - Luciano R. Portero
- Laboratorio de Microbiología Ultraestructural y Molecular, Centro Integral de Microscopía Electrónica, Facultad de Agronomía y Zootecnia, UNT y Centro Científico Tecnológico, CONICET NOASUR, San Miguel de Tucumán, Argentina
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales y Microbiológicos, Centro Científico Tecnológico, CONICET NOASUR, San Miguel de Tucumán, Argentina
| | - Thierry Douki
- Université Grenoble Alpes, Commissariat a l’Energie Atomique et aux Energies Alternatives, Centre National de la Recherche Scientifique, Institut de Recherche Interdisciplinaire de Grenoble–Systèmes Moléculaires et nanoMatériaux p our l’Énergie et la Santé, Grenoble, France
| | - Wolfgang Gärtner
- Institute of Analytical Chemistry, University of Leipzig, Leipzig, Germany
| | - María E. Farías
- Laboratorio de Microbiología Ultraestructural y Molecular, Centro Integral de Microscopía Electrónica, Facultad de Agronomía y Zootecnia, UNT y Centro Científico Tecnológico, CONICET NOASUR, San Miguel de Tucumán, Argentina
| | - Virginia H. Albarracín
- Laboratorio de Microbiología Ultraestructural y Molecular, Centro Integral de Microscopía Electrónica, Facultad de Agronomía y Zootecnia, UNT y Centro Científico Tecnológico, CONICET NOASUR, San Miguel de Tucumán, Argentina
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales y Microbiológicos, Centro Científico Tecnológico, CONICET NOASUR, San Miguel de Tucumán, Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
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14
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Wendisch VF, Nampoothiri KM, Lee JH. Metabolic Engineering for Valorization of Agri- and Aqua-Culture Sidestreams for Production of Nitrogenous Compounds by Corynebacterium glutamicum. Front Microbiol 2022; 13:835131. [PMID: 35211108 PMCID: PMC8861201 DOI: 10.3389/fmicb.2022.835131] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/13/2022] [Indexed: 01/06/2023] Open
Abstract
Corynebacterium glutamicum is used for the million-ton-scale production of amino acids. Valorization of sidestreams from agri- and aqua-culture has focused on the production of biofuels and carboxylic acids. Nitrogen present in various amounts in sidestreams may be valuable for the production of amines, amino acids and other nitrogenous compounds. Metabolic engineering of C. glutamicum for valorization of agri- and aqua-culture sidestreams addresses to bridge this gap. The product portfolio accessible via C. glutamicum fermentation primarily features amino acids and diamines for large-volume markets in addition to various specialty amines. On the one hand, this review covers metabolic engineering of C. glutamicum to efficiently utilize components of various sidestreams. On the other hand, examples of the design and implementation of synthetic pathways not present in native metabolism to produce sought after nitrogenous compounds will be provided. Perspectives and challenges of this concept will be discussed.
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Affiliation(s)
- Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - K Madhavan Nampoothiri
- Microbial Processes and Technology Division, Council of Scientific and Industrial Research-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, India
| | - Jin-Ho Lee
- Department of Food Science & Biotechnology, Kyungsung University, Busan, South Korea
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15
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Wang R, Bu W, Yang Y. Identification of Metabolism-Related Genes Influencing Prognosis of Multiple Myeloma Patients. JOURNAL OF HEALTHCARE ENGINEERING 2021; 2021:6574491. [PMID: 34956573 PMCID: PMC8694996 DOI: 10.1155/2021/6574491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/19/2021] [Accepted: 11/25/2021] [Indexed: 11/17/2022]
Abstract
Multiple myeloma (MM) is the second most commonly diagnosed hematological malignancy. Understanding the basic mechanisms of the metabolism in MM may lead to new therapies that benefit patients. We collected the gene expression profile data of GSE39754 and performed differential analysis. Furthermore, identify the candidate genes that affect the prognosis of the differentially expressed genes (DEGs) related to the metabolism. Enrichment analysis is used to identify the biological effects of candidate genes. Perform coexpression analysis on the verified DEGs. In addition, the candidate genes are used to cluster MM into different subtypes through consistent clustering. Use LASSO regression analysis to identify key genes, and use Cox regression analysis to evaluate the prognostic effects of key genes. Evaluation of immune cell infiltration in MM is by CIBERSORT. We identified 2821 DEGs, of which 348 genes were metabolic-related prognostic genes and were considered candidate genes. Enrichment analysis revealed that the candidate genes are mainly related to the proteasome, purine metabolism, and cysteine and methionine metabolism signaling pathways. According to the consensus clustering method, we identified the two subtypes of group 1 and group 2 that affect the prognosis of MM patients. Using the LASSO model, we have identified 10 key genes. The prognosis of the high-risk group identified by Cox regression analysis is worse than that of the low-risk group. Among them, PKLR has a greater impact on the prognosis of MM, and the prognosis of MM patients is poor when the expression is high. In addition, the level of immune cell infiltration in the high-risk group is higher than that in the low-risk group. In the summary, metabolism-related genes significantly affect the prognosis of MM patients through the metabolic process of MM patients. PKLR may be a prognostic risk factor for MM patients.
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Affiliation(s)
- Rui Wang
- Department of Hematology, People's Hospital of Lianshui, Lianshui 223400, Huai'an, China
| | - Wenxuan Bu
- Department of Hematology, People's Hospital of Lianshui, Lianshui 223400, Huai'an, China
| | - Yang Yang
- Department of Hematology, People's Hospital of Lianshui, Lianshui 223400, Huai'an, China
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16
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Ji JJ, Sun QM, Nie DY, Wang Q, Zhang H, Qin FF, Wang QS, Lu SF, Pang GM, Lu ZG. Probiotics protect against RSV infection by modulating the microbiota-alveolar-macrophage axis. Acta Pharmacol Sin 2021; 42:1630-1641. [PMID: 33495515 PMCID: PMC8463687 DOI: 10.1038/s41401-020-00573-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/04/2020] [Indexed: 02/06/2023] Open
Abstract
Respiratory syncytial virus (RSV) is leading cause of respiratory tract infections in early childhood. Gut microbiota is closely related with the pulmonary antiviral immunity. Recent evidence shows that gut dysbiosis is involved in the pathogenesis of RSV infection. Therefore; pharmacological and therapeutic strategies aiming to readjust the gut dysbiosis are increasingly important for the treatment of RSV infection. In this study, we evaluated the therapeutic effects of a probiotic mixture on RSV-infected mice. This probiotic mixture consisted of Lactobacillus rhamnosus GG, Escherichia coli Nissle 1917 and VSL#3 was orally administered to neonatal mice on a daily basis either for 1 week in advance or for 3 days starting from the day of RSV infection. We showed that administration of the probiotics protected against RSV-induced lung pathology by suppressing RSV infection and exerting an antiviral response via alveolar macrophage (AM)-derived IFN-β. Furthermore, administration of the probiotics reversed gut dysbiosis and significantly increased the abundance of short-chain fatty acid (SCFA)-producing bacteria in RSV-infected mice, which consequently led to elevated serum SCFA levels. Moreover, administration of the probiotics restored lung microbiota in RSV-infected mice. We demonstrated that the increased production of IFN-β in AMs was attributed to the increased acetate in circulation and the levels of Corynebacterium and Lactobacillus in lungs. In conclusion, we reveal that probiotics protect against RSV infection in neonatal mice through a microbiota-AM axis, suggesting that the probiotics may be a promising candidate to prevent and treat RSV infection, and deserve more research and development in future.
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Affiliation(s)
- Jian-Jian Ji
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Qin-Mei Sun
- The First School of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Deng-Yun Nie
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Qian Wang
- International Education College, Nanjing University of Chinese Medicine, Nanjing, 210000, China
| | - Han Zhang
- The First School of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Fen-Fen Qin
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Qi-Sheng Wang
- The First School of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Sheng-Feng Lu
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Guo-Ming Pang
- Kaifeng Hospital of Traditional Chinese Medicine, Kaifeng, 475000, China.
| | - Zhi-Gang Lu
- The First School of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
- International Education College, Nanjing University of Chinese Medicine, Nanjing, 210000, China.
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
- Kaifeng Hospital of Traditional Chinese Medicine, Kaifeng, 475000, China.
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17
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Recent progress in metabolic engineering of Corynebacterium glutamicum for the production of C4, C5, and C6 chemicals. KOREAN J CHEM ENG 2021. [DOI: 10.1007/s11814-021-0788-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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Kim Y, Lama S, Agrawal D, Kumar V, Park S. Acetate as a potential feedstock for the production of value-added chemicals: Metabolism and applications. Biotechnol Adv 2021; 49:107736. [PMID: 33781888 DOI: 10.1016/j.biotechadv.2021.107736] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 02/22/2021] [Accepted: 03/19/2021] [Indexed: 10/21/2022]
Abstract
Acetate is regarded as a promising carbon feedstock in biological production owing to its possible derivation from C1 gases such as CO, CO2 and methane. To best use of acetate, comprehensive understanding of acetate metabolisms from genes and enzymes to pathways and regulations is needed. This review aims to provide an overview on the potential of acetate as carbon feedstock for industrial biotechnology. Biochemical, microbial and biotechnological aspects of acetate metabolism are described. Especially, the current state-of-the art in the production of value-added chemicals from acetate is summarized. Challenges and future perspectives are also provided.
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Affiliation(s)
- Yeonhee Kim
- School of Energy and Chemical Engineering, UNIST, 50, UNIST-gil, Ulsan 44919, Republic of Korea
| | - Suman Lama
- School of Energy and Chemical Engineering, UNIST, 50, UNIST-gil, Ulsan 44919, Republic of Korea
| | - Deepti Agrawal
- Biochemistry and Biotechnology Area, Material Resource Efficiency Division, CSIR- Indian Institute of Petroleum, Mohkampur, Dehradun 248005, India
| | - Vinod Kumar
- Centre for Climate and Environmental Protection, School of Water, Energy and Environment, Cranfield University, Cranfield, MK430AL, United Kingdom.
| | - Sunghoon Park
- School of Energy and Chemical Engineering, UNIST, 50, UNIST-gil, Ulsan 44919, Republic of Korea.
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19
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Zhang Y, Xiong H, Chen Z, Fu Y, Xu Q, Chen N. Effect of fed-batch and chemostat cultivation processes of C. glutamicum CP for L-leucine production. Bioengineered 2021; 12:426-439. [PMID: 33470174 PMCID: PMC8806242 DOI: 10.1080/21655979.2021.1874693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Most of the current industrial processes for L-leucine production are based on fermentation, usually in fed-batch operation mode. Although the culture technology has advanced in recent decades, the process still has significant drawbacks. To solve these problems, we investigated the effects of chemostat culture conditions on the production of L-leucine by Corynebacterium glutamicum CP. The dilution rate, the nitrogen source, and the carbon–nitrogen ratio of the medium were optimized. With the addition of ammonium acetate to the chemostat medium, the initial C/N ratio was adjusted to 57.6, and the L-leucine titer reached the highest level at the optimal dilution rate of 0.04 h−1. Compared with fed-batch culture, the L-leucine titer was reduced (from 53.0 to 24.8 g L−1), but the yield from glucose was increased by 10.0% (from 0.30 to 0.33 mol mol−1) and productivity was increased by 58.3% (from 1.2 to 1.9 g L−1 h−1). Moreover, the titer of the by-product L-alanine was significantly reduced (from 8.9 to 0.8 g L−1). In addition, gene expression levels and activity of key enzymes in the synthesis of L-leucine and L-alanine were analyzed to explain the difference of production performance between chemostat culture and fed-batch culture. The results indicate that chemostat culture has great potential to increase the industrial production of L-leucine compared to current fed-batch approaches.
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Affiliation(s)
- Yufu Zhang
- College of Biotechnology, Tianjin University of Science & Technology , Tianjin, P. R. China.,Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science & Technology, Ministry of Education , Tianjin, P. R. China.,Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science & Technology , Tianjin, P. R. China
| | - Haibo Xiong
- College of Biotechnology, Tianjin University of Science & Technology , Tianjin, P. R. China.,Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science & Technology, Ministry of Education , Tianjin, P. R. China.,Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science & Technology , Tianjin, P. R. China
| | - Zhichao Chen
- College of Biotechnology, Tianjin University of Science & Technology , Tianjin, P. R. China.,Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science & Technology, Ministry of Education , Tianjin, P. R. China.,Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science & Technology , Tianjin, P. R. China
| | - Yunpeng Fu
- College of Biotechnology, Tianjin University of Science & Technology , Tianjin, P. R. China.,Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science & Technology, Ministry of Education , Tianjin, P. R. China.,Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science & Technology , Tianjin, P. R. China
| | - Qingyang Xu
- College of Biotechnology, Tianjin University of Science & Technology , Tianjin, P. R. China.,Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science & Technology, Ministry of Education , Tianjin, P. R. China.,Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science & Technology , Tianjin, P. R. China
| | - Ning Chen
- College of Biotechnology, Tianjin University of Science & Technology , Tianjin, P. R. China.,Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science & Technology, Ministry of Education , Tianjin, P. R. China.,Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science & Technology , Tianjin, P. R. China
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20
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Kuprat T, Johnsen U, Ortjohann M, Schönheit P. Acetate Metabolism in Archaea: Characterization of an Acetate Transporter and of Enzymes Involved in Acetate Activation and Gluconeogenesis in Haloferax volcanii. Front Microbiol 2020; 11:604926. [PMID: 33343547 PMCID: PMC7746861 DOI: 10.3389/fmicb.2020.604926] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/13/2020] [Indexed: 02/01/2023] Open
Abstract
The haloarchaeon Haloferax volcanii grows on acetate as sole carbon and energy source. The genes and proteins involved in uptake and activation of acetate and in gluconeogenesis were identified and analyzed by characterization of enzymes and by growth experiments with the respective deletion mutants. (i) An acetate transporter of the sodium: solute-symporter family (SSF) was characterized by kinetic analyses of acetate uptake into H. volcanii cells. The functional involvement of the transporter was proven with a Δssf mutant. (ii) Four paralogous AMP-forming acetyl-CoA synthetases that belong to different phylogenetic clades were shown to be functionally involved in acetate activation. (iii) The essential involvement of the glyoxylate cycle as an anaplerotic sequence was concluded from growth experiments with an isocitrate lyase knock-out mutant excluding the operation of the methylaspartate cycle reported for Haloarcula species. (iv) Enzymes involved in phosphoenolpyruvate synthesis from acetate, namely two malic enzymes and a phosphoenolpyruvate synthetase, were identified and characterized. Phylogenetic analyses of haloarchaeal malic enzymes indicate a separate evolutionary line distinct from other archaeal homologs. The exclusive function of phosphoenolpyruvate synthetase in gluconeogenesis was proven by the respective knock-out mutant. Together, this is a comprehensive study of acetate metabolism in archaea.
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Affiliation(s)
- Tom Kuprat
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität, Kiel, Germany
| | - Ulrike Johnsen
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität, Kiel, Germany
| | - Marius Ortjohann
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität, Kiel, Germany
| | - Peter Schönheit
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität, Kiel, Germany
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21
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Sakarika M, Candry P, Depoortere M, Ganigué R, Rabaey K. Impact of substrate and growth conditions on microbial protein production and composition. BIORESOURCE TECHNOLOGY 2020; 317:124021. [PMID: 32829116 DOI: 10.1016/j.biortech.2020.124021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/10/2020] [Accepted: 08/12/2020] [Indexed: 06/11/2023]
Abstract
Production of microbial protein (MP) from recovered resources - e.g. CO2-sourced formate and acetate - could provide protein while enabling CO2 capture. To assess the protein quality obtained from this process, pure cultures and enriched communities were selected and characterized kinetically, stoichiometrically and nutritionally. Growth on acetate resulted in up to 5.3 times higher maximum specific growth rate (μmax) than formate (i.e. 0.15-0.41 h-1 for acetate compared to 0.061-0.29 h-1 for formate at pH = 7). The protein content was a function of the growth phase, with the highest values during stationary phase, ranging between 18 and 82%CDW protein depending on the organism and substrate. The negative correlation between biomass productivity and protein content indicated a trade-off between production rate and product quality. The final product (i.e. dried MP) quality was in most cases superior to soybean and all cultures were rich in threonine, phenylalanine and tyrosine, regardless of the carbon source.
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Affiliation(s)
- Myrsini Sakarika
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering Ghent University, Coupure Links 653, 9000 Gent, Belgium; Center for Advanced Process Technology for Urban Resource recovery (CAPTURE), Belgium(1)
| | - Pieter Candry
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering Ghent University, Coupure Links 653, 9000 Gent, Belgium; Center for Advanced Process Technology for Urban Resource recovery (CAPTURE), Belgium(1)
| | - Mathilde Depoortere
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering Ghent University, Coupure Links 653, 9000 Gent, Belgium; Center for Advanced Process Technology for Urban Resource recovery (CAPTURE), Belgium(1)
| | - Ramon Ganigué
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering Ghent University, Coupure Links 653, 9000 Gent, Belgium; Center for Advanced Process Technology for Urban Resource recovery (CAPTURE), Belgium(1)
| | - Korneel Rabaey
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering Ghent University, Coupure Links 653, 9000 Gent, Belgium; Center for Advanced Process Technology for Urban Resource recovery (CAPTURE), Belgium(1).
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22
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Seong W, Han GH, Lim HS, Baek JI, Kim SJ, Kim D, Kim SK, Lee H, Kim H, Lee SG, Lee DH. Adaptive laboratory evolution of Escherichia coli lacking cellular byproduct formation for enhanced acetate utilization through compensatory ATP consumption. Metab Eng 2020; 62:249-259. [PMID: 32931907 DOI: 10.1016/j.ymben.2020.09.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/18/2020] [Accepted: 09/08/2020] [Indexed: 10/23/2022]
Abstract
Acetate has attracted great attention as a carbon source to develop economically feasible bioprocesses for sustainable bioproducts. Acetate is a less-preferred carbon source and a well-known growth inhibitor of Escherichia coli. In this study, we carried out adaptive laboratory evolution of an E. coli strain lacking four genes (adhE, pta, ldhA, and frdA) involved in acetyl-CoA consumption, allowing the efficient utilization of acetate as its sole carbon and energy source. Four genomic mutations were found in the evolved strain through whole-genome sequencing, and two major mutations (in cspC and patZ) mainly contributed to efficient utilization of acetate and tolerance to acetate. Transcriptomic reprogramming was examined by analyzing the genome-wide transcriptome with different carbon sources. The evolved strain showed high levels of intracellular ATP by upregulation of genes involved in NADH and ATP biosynthesis, which facilitated the production of enhanced green fluorescent protein, mevalonate, and n-butanol using acetate alone. This new strain, given its high acetate tolerance and high ATP levels, has potential as a starting host for cell factories targeting the production of acetyl-CoA-derived products from acetate or of products requiring high ATP levels.
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Affiliation(s)
- Wonjae Seong
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Gui Hwan Han
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Center for Industrialization of Agricultural and Livestock Microorganism (CIALM), Jeongeup, 56212, Republic of Korea
| | - Hyun Seung Lim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Ji In Baek
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Soo-Jung Kim
- Department of Integrative Food, Bioscience and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Seong Keun Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Hyewon Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Haseong Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Seung-Goo Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
| | - Dae-Hee Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
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23
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Vo CH, Goyal N, Karimi IA, Kraft M. First Observation of an Acetate Switch in a Methanogenic Autotroph ( Methanococcus maripaludis S2). Microbiol Insights 2020; 13:1178636120945300. [PMID: 32843840 PMCID: PMC7416134 DOI: 10.1177/1178636120945300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/01/2020] [Indexed: 11/17/2022] Open
Abstract
The transition from acetate production by a microorganism in its early growth phase to acetate re-uptake in its late growth phase has been termed acetate switch. It has been observed in several heterotrophic prokaryotes, but not in an autotroph. Furthermore, all reports hitherto have involved the tricarboxylic acid cycle. This study reports the first observation of acetate switch in a methanogenic autotroph Methanococcus maripaludis S2, which uses the Wolfe cycle for its anaerobic respiration. When grown in minimal medium with carbon dioxide as the sole carbon source, and either ammonium or dinitrogen as the sole nitrogen source, M. maripaludis S2 dissimilated acetate in the early growth phase and assimilated it back in the late growth phase. The acetate switch was more pronounced in the dinitrogen-grown cultures. We postulate that the acetate dissimilation in M. maripaludis S2 may serve as a metabolic outlet for the carbon overflow in the early growth phase, and the assimilation in the late growth phase may be due to the scarcity of the carbon source. Based on the primary and secondary protein structures, we propose that MMP0253 may function as the adenosine diphosphate (ADP)-forming acetyl-CoA synthetase to catalyse acetate formation from acetyl-CoA. To verify this, we produced MMP0253 via the ligation-independent cloning technique in Escherichia coli strain Rosetta (DE3) using pNIC28-Bsa4 as the vector. The recombinant protein showed catalytic activity, when added into a mixture of acetyl-CoA, ADP, and inorganic phosphate (Pi). The concentration profile of acetate, together with the enzymatic activity of MMP0253, shows that M. maripaludis S2 can produce acetate and exhibit an acetate switch.
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Affiliation(s)
- Chi Hung Vo
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore.,Cambridge Centre for Advanced Research and Education in Singapore Ltd, Singapore
| | - Nishu Goyal
- Department of Chemical Engineering, University of Petroleum and Energy Studies, Dehradun, India
| | - Iftekhar A Karimi
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore.,Cambridge Centre for Advanced Research and Education in Singapore Ltd, Singapore
| | - Markus Kraft
- Cambridge Centre for Advanced Research and Education in Singapore Ltd, Singapore.,Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK.,School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore
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24
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Siebert D, Busche T, Metz AY, Smaili M, Queck BAW, Kalinowski J, Eikmanns BJ. Genetic Engineering of Oligotropha carboxidovorans Strain OM5-A Promising Candidate for the Aerobic Utilization of Synthesis Gas. ACS Synth Biol 2020; 9:1426-1440. [PMID: 32379961 DOI: 10.1021/acssynbio.0c00098] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Due to climate change and worldwide pollution, development of highly sustainable routes for industrial production of basic and specialty chemicals is critical nowadays. One possible approach is the use of CO2- and CO-utilizing microorganisms in biotechnological processes to produce value-added compounds from synthesis gas (mixtures of CO2, CO, and H2) or from C1-containing industrial waste gases. Such syngas fermentation processes have already been established, e.g., biofuel production using strictly anaerobic acetogenic bacteria. However, aerobic processes may be favorable for the formation of more costly (ATP-intensive) products. Oligotropha carboxidovorans strain OM5 is an aerobic carboxidotrophic bacterium and potentially a promising candidate for such processes. We here performed RNA-Seq analysis comparing cells of this organism grown heterotrophically with acetate or autotrophically with CO2, CO, and H2 as carbon and energy source and found a variety of chromosomally and of native plasmid-encoded genes to be highly differentially expressed. In particular, genes and gene clusters encoding proteins required for autotrophic growth (CO2 fixation via Calvin-Benson-Bassham cycle), for CO metabolism (CO dehydrogenase), and for H2 utilization (hydrogenase), all located on megaplasmid pHCG3, were much higher expressed during autotrophic growth with synthesis gas. Furthermore, we successfully established reproducible transformation of O. carboxidovorans via electroporation and developed gene deletion and gene exchange protocols via two-step recombination, enabling inducible and stable expression of heterologous genes as well as construction of defined mutants of this organism. Thus, this study marks an important step toward metabolic engineering of O. carboxidovorans and effective utilization of C1-containing gases with this organism.
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Affiliation(s)
- Daniel Siebert
- Institute of Microbiology and Biotechnology, Ulm University, 89069 Ulm, Germany
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, 94315 Straubing, Germany
| | - Tobias Busche
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Aline Y. Metz
- Institute of Microbiology and Biotechnology, Ulm University, 89069 Ulm, Germany
| | - Medina Smaili
- Institute of Microbiology and Biotechnology, Ulm University, 89069 Ulm, Germany
| | - Bastian A. W. Queck
- Institute of Microbiology and Biotechnology, Ulm University, 89069 Ulm, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
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25
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Nieto-Domínguez M, Nikel PI. Intersecting Xenobiology and Neometabolism To Bring Novel Chemistries to Life. Chembiochem 2020; 21:2551-2571. [PMID: 32274875 DOI: 10.1002/cbic.202000091] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/09/2020] [Indexed: 12/19/2022]
Abstract
The diversity of life relies on a handful of chemical elements (carbon, oxygen, hydrogen, nitrogen, sulfur and phosphorus) as part of essential building blocks; some other atoms are needed to a lesser extent, but most of the remaining elements are excluded from biology. This circumstance limits the scope of biochemical reactions in extant metabolism - yet it offers a phenomenal playground for synthetic biology. Xenobiology aims to bring novel bricks to life that could be exploited for (xeno)metabolite synthesis. In particular, the assembly of novel pathways engineered to handle nonbiological elements (neometabolism) will broaden chemical space beyond the reach of natural evolution. In this review, xeno-elements that could be blended into nature's biosynthetic portfolio are discussed together with their physicochemical properties and tools and strategies to incorporate them into biochemistry. We argue that current bioproduction methods can be revolutionized by bridging xenobiology and neometabolism for the synthesis of new-to-nature molecules, such as organohalides.
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Affiliation(s)
- Manuel Nieto-Domínguez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
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26
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Menendez-Gil P, Caballero CJ, Catalan-Moreno A, Irurzun N, Barrio-Hernandez I, Caldelari I, Toledo-Arana A. Differential evolution in 3'UTRs leads to specific gene expression in Staphylococcus. Nucleic Acids Res 2020; 48:2544-2563. [PMID: 32016395 PMCID: PMC7049690 DOI: 10.1093/nar/gkaa047] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 12/05/2019] [Accepted: 01/16/2020] [Indexed: 12/16/2022] Open
Abstract
The evolution of gene expression regulation has contributed to species differentiation. The 3' untranslated regions (3'UTRs) of mRNAs include regulatory elements that modulate gene expression; however, our knowledge of their implications in the divergence of bacterial species is currently limited. In this study, we performed genome-wide comparative analyses of mRNAs encoding orthologous proteins from the genus Staphylococcus and found that mRNA conservation was lost mostly downstream of the coding sequence (CDS), indicating the presence of high sequence diversity in the 3'UTRs of orthologous genes. Transcriptomic mapping of different staphylococcal species confirmed that 3'UTRs were also variable in length. We constructed chimeric mRNAs carrying the 3'UTR of orthologous genes and demonstrated that 3'UTR sequence variations affect protein production. This suggested that species-specific functional 3'UTRs might be specifically selected during evolution. 3'UTR variations may occur through different processes, including gene rearrangements, local nucleotide changes, and the transposition of insertion sequences. By extending the conservation analyses to specific 3'UTRs, as well as the entire set of Escherichia coli and Bacillus subtilis mRNAs, we showed that 3'UTR variability is widespread in bacteria. In summary, our work unveils an evolutionary bias within 3'UTRs that results in species-specific non-coding sequences that may contribute to bacterial diversity.
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Affiliation(s)
- Pilar Menendez-Gil
- Instituto de Agrobiotecnología (IdAB), CSIC-UPNA-Gobierno de Navarra, 31192-Mutilva, Navarra, Spain
| | - Carlos J Caballero
- Instituto de Agrobiotecnología (IdAB), CSIC-UPNA-Gobierno de Navarra, 31192-Mutilva, Navarra, Spain
| | - Arancha Catalan-Moreno
- Instituto de Agrobiotecnología (IdAB), CSIC-UPNA-Gobierno de Navarra, 31192-Mutilva, Navarra, Spain
| | - Naiara Irurzun
- Instituto de Agrobiotecnología (IdAB), CSIC-UPNA-Gobierno de Navarra, 31192-Mutilva, Navarra, Spain
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Isabelle Caldelari
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR9002, F-67000-Strasbourg, France
| | - Alejandro Toledo-Arana
- Instituto de Agrobiotecnología (IdAB), CSIC-UPNA-Gobierno de Navarra, 31192-Mutilva, Navarra, Spain
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27
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Wolf N, Bussmann M, Koch-Koerfges A, Katcharava N, Schulte J, Polen T, Hartl J, Vorholt JA, Baumgart M, Bott M. Molecular Basis of Growth Inhibition by Acetate of an Adenylate Cyclase-Deficient Mutant of Corynebacterium glutamicum. Front Microbiol 2020; 11:87. [PMID: 32117117 PMCID: PMC7026483 DOI: 10.3389/fmicb.2020.00087] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/15/2020] [Indexed: 01/02/2023] Open
Abstract
In Corynebacterium glutamicum, cyclic adenosine monophosphate (cAMP) serves as an effector of the global transcriptional regulator GlxR. Synthesis of cAMP is catalyzed by the membrane-bound adenylate cyclase CyaB. In this study, we investigated the consequences of decreased intracellular cAMP levels in a ΔcyaB mutant. While no growth defect of the ΔcyaB strain was observed on glucose, fructose, sucrose, or gluconate alone, the addition of acetate to these growth media resulted in a severe growth inhibition, which could be reversed by plasmid-based cyaB expression or by supplementation of the medium with cAMP. The effect was concentration- and pH-dependent, suggesting a link to the uncoupling activity of acetate. In agreement, the ΔcyaB mutant had an increased sensitivity to the protonophore carbonyl cyanide m-chlorophenyl hydrazone (CCCP). The increased uncoupler sensitivity correlated with a lowered membrane potential of acetate-grown ΔcyaB cells compared to wild-type cells. A reduced membrane potential affects major cellular processes, such as ATP synthesis by F1F O -ATP synthase and numerous transport processes. The impaired membrane potential of the ΔcyaB mutant could be due to a decreased expression of the cytochrome bc 1-aa 3 supercomplex, which is the major contributor of proton-motive force in C. glutamicum. Expression of the supercomplex genes was previously reported to be activated by GlxR-cAMP. A suppressor mutant of the ΔcyaB strain with improved growth on acetate was isolated, which carried a single mutation in the genome leading to an Ala131Thr exchange in GlxR. Introduction of this point mutation into the original ΔcyaB mutant restored the growth defect on acetate. This supported the importance of GlxR for the phenotype of the ΔcyaB mutant and, more generally, of the cAMP-GlxR system for the control of energy metabolism in C. glutamicum.
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Affiliation(s)
- Natalie Wolf
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Michael Bussmann
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Abigail Koch-Koerfges
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Nino Katcharava
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Julia Schulte
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Tino Polen
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Johannes Hartl
- Institute of Microbiology, ETH Zürich, Zurich, Switzerland
| | | | - Meike Baumgart
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
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28
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Engineering Corynebacterium glutamicum for the Efficient Production of 3-Hydroxypropionic Acid from a Mixture of Glucose and Acetate via the Malonyl-CoA Pathway. Catalysts 2020. [DOI: 10.3390/catal10020203] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
3-Hydroxypropionic acid (3-HP) has been recognized as one of the top value-added building block chemicals, due to its numerous potential applications. Over the past decade, biosynthesis of 3-HP via the malonyl-CoA pathway has been increasingly favored because it is balanced in terms of ATP and reducing equivalents, does not require the addition of costly coenzymes, and can utilize renewable lignocellulosic biomass. In this study, gene mcr encoding malonyl-CoA reductase from Chloroflexus aurantiacus was introduced into Corynebacterium glutamicum ATCC13032 to construct the strain Cgz1, which accumulated 0.30 g/L 3-HP. Gene ldhA encoding lactate dehydrogenase was subsequently deleted to eliminate lactate accumulation, but this decreased 3-HP production and greatly increased acetate accumulation. Then, different acetate utilization genes were overexpressed to reuse the acetate, and the best candidate Cgz5 expressing endogenous gene pta could effectively reduce the acetate accumulation and produced 0.68 g/L 3-HP. To enhance the supply of the precursor acetyl-CoA, acetate was used as an ancillary carbon source to improve the 3-HP production, and 1.33 g/L 3-HP could be produced from a mixture of glucose and acetate, with a 2.06-fold higher yield than from glucose alone. Finally, to inhibit the major 3-HP competing pathway-fatty acid synthesis, 10 μM cerulenin was added and strain Cgz5 produced 3.77 g/L 3-HP from 15.47 g/L glucose and 4.68 g/L acetate with a yield of 187 mg/g substrate in 48 h, which was 12.57-fold higher than that of Cgz1. To our best knowledge, this is the first report on engineering C. glutamicum to produce 3-HP via the malonyl-CoA pathway. The results indicate that the innocuous biosafety level I microorganism C. glutamicum is a potential industrial 3-HP producer.
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29
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Improved Astaxanthin Production with Corynebacterium glutamicum by Application of a Membrane Fusion Protein. Mar Drugs 2019; 17:md17110621. [PMID: 31683510 PMCID: PMC6891673 DOI: 10.3390/md17110621] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 12/19/2022] Open
Abstract
Astaxanthin is one of the strongest natural antioxidants and a red pigment occurring in nature. This C40 carotenoid is used in a broad range of applications such as a colorant in the feed industry, an antioxidant in cosmetics or as a supplement in human nutrition. Natural astaxanthin is on the rise and, hence, alternative production systems are needed. The natural carotenoid producer Corynebacterium glutamicum is a potent host for industrial fermentations, such as million-ton scale amino acid production. In C. glutamicum, astaxanthin production was established through heterologous overproduction of the cytosolic lycopene cyclase CrtY and the membrane-bound β-carotene hydroxylase and ketolase, CrtZ and CrtW, in previous studies. In this work, further metabolic engineering strategies revealed that the potential of this GRAS organism for astaxanthin production is not fully exploited yet. It was shown that the construction of a fusion protein comprising the membrane-bound β-carotene hydroxylase and ketolase (CrtZ~W) significantly increased astaxanthin production under high glucose concentration. An evaluation of used carbon sources indicated that a combination of glucose and acetate facilitated astaxanthin production. Moreover, additional overproduction of cytosolic carotenogenic enzymes increased the production of this high value compound. Taken together, a seven-fold improvement of astaxanthin production was achieved with 3.1 mg/g CDW of astaxanthin.
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30
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Mindt M, Heuser M, Wendisch VF. Xylose as preferred substrate for sarcosine production by recombinant Corynebacterium glutamicum. BIORESOURCE TECHNOLOGY 2019; 281:135-142. [PMID: 30818264 DOI: 10.1016/j.biortech.2019.02.084] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/17/2019] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
The aim of this work was to study the fermentative production of the N-methylated amino acid sarcosine by C. glutamicum. Characterization of the imine reductase DpkA from Pseudomonas putida revealed that it catalyses N-methylamination of glyoxylate to sarcosine. Heterologous expression of dpkA in a C. glutamicum strain engineered for glyoxylate overproduction enabled fermentative production of sarcosine from sugars and monomethylamine. Glucose-based fermentation reached sarcosine production titers of 2.4 ± 0.1 g L-1. Sarcosine production based on the second generation feedstocks xylose and arabinose led to higher product titers of 2.7 ± 0.1 g L-1 and 3.4 ± 0.3 g L-1, respectively, than glucose-based production. Optimization of production conditions with xylose and potassium acetate blends increased sarcosine titers to 8.7 ± 0.2 g L-1 with a yield of 0.25 g g-1. This is the first example in which a C. glutamicum process using lignocellulosic pentoses is superior to glucose-based production.
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Affiliation(s)
- Melanie Mindt
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Maria Heuser
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
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31
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Xu Q, Bai C, Liu Y, Song L, Tian L, Yan Y, Zhou J, Zhou X, Zhang Y, Cai M. Modulation of acetate utilization in Komagataella phaffii by metabolic engineering of tolerance and metabolism. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:61. [PMID: 30936941 PMCID: PMC6427870 DOI: 10.1186/s13068-019-1404-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 03/11/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Acetate, an economical industrial chemical, which is also the precursor of acetyl-CoA, could serve as an alternative substrate for biomanufacturing. This nontraditional substrate can be widely produced from syngas via hydrolysis or pyrolysis of the cellulosic biomass, chemical or microbial catalysis, anaerobic fermentation in treated wastewater, etc. However, the toxicity of acetate to microorganisms has held back its utilization, especially for the eukaryotes that are good hosts for production of complicated pharmaceuticals or chemicals. This study seeks to improve acetate utilization in a widely used yeast host, Komagataella phaffii (previously Pichia pastoris), by metabolic engineering of acetate tolerance, transport, and metabolism. RESULTS A kinase-deficient library of K. phaffii was firstly used to screen acetate-resistant kinases. The HRK1 knockout strain was sensitive to acetate and overexpression of this gene improved acetate tolerance and cell growth of the strain. Also, overexpression of HRK1 caused a 55% productivity improvement of acetyl-CoA-dependent 6-methylsalicylic acid (6-MSA). However, activation of Hrk1 on membrane H(+)-ATPase Pma1 seemed not to work in the engineered strain. Acetate transporter gene ScFPS1* was further overexpressed, despite of not improving 6-MSA biosynthesis. To enhance acetate metabolism, acetyl-CoA synthesizing related genes, yeast PpACS1, ScACS1*, and E. coli ackA/pta were overexpressed separately. Introduction of PpACS1 and ScACS1* each increased biosynthesis of 6-MSA by approximately 20% on 20 mM acetate. Finally, co-overexpression of HRK1 and ScACS1* improved 6-MSA productivity by 51% on 20 mM acetate, despite that a low expression level of HRK1 happened when genes were expressed under the same promoter. CONCLUSIONS HRK1 screened by K. phaffii kinase-deficient library played an important role in acetate tolerance and was proved to profit the biosynthesis of acetyl-CoA-derived chemicals. It could be a potential target for metabolic engineering of acetate utilization in other eukaryotic hosts as well. A combined strategy of introducing genes for acetate tolerance and metabolism further improved biosynthesis of acetyl-CoA derived reporter compound in K. phaffii. This makes it a good choice for acetyl-CoA-derived chemicals with acetate as substrate or precursor in K. phaffii, which would also extend the use of this chassis host.
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Affiliation(s)
- Qin Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Chenxiao Bai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Yiqi Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Lili Song
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Lin Tian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Yunfeng Yan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Jinfeng Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Xiangshan Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
- Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, 200237 China
| | - Menghao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
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Tenhaef N, Brüsseler C, Radek A, Hilmes R, Unrean P, Marienhagen J, Noack S. Production of d-xylonic acid using a non-recombinant Corynebacterium glutamicum strain. BIORESOURCE TECHNOLOGY 2018; 268:332-339. [PMID: 30092487 DOI: 10.1016/j.biortech.2018.07.127] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 05/22/2023]
Abstract
It was found that Corynebacterium glutamicum ΔiolR devoid of the transcriptional regulator IolR accumulates high amounts of d-xylonate when cultivated in the presence of d-xylose. Detailed analyses of constructed deletion mutants revealed that the putative myo-inositol 2-dehydrogenase IolG also acts as d-xylose dehydrogenase and is mainly responsible for d-xylonate oxidation in this organism. Process development for d-xylonate production was initiated by cultivating C. glutamicum ΔiolR on defined d-xylose/d-glucose mixtures under batch and fed-batch conditions. The resulting yield matched the theoretical maximum of 1 mol mol-1 and high volumetric productivities of up to 4 g L-1 h-1 could be achieved. Subsequently, a novel one-pot sequential hydrolysis and fermentation process based on optimized medium containing hydrolyzed sugarcane bagasse was developed. Cost-efficiency and abundance of second-generation substrates, good performance indicators, and enhanced market access using a non-recombinant strain open the perspective for a commercially viable bioprocess for d-xylonate production in the near future.
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Affiliation(s)
- Niklas Tenhaef
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany; Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Christian Brüsseler
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany; Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Andreas Radek
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany; Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - René Hilmes
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany; Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Pornkamol Unrean
- National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany; Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany; Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich D-52425, Germany.
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Wei H, Ma Y, Chen Q, Cui Y, Du L, Ma Q, Li Y, Xie X, Chen N. Identification and application of a novel strong constitutive promoter in Corynebacterium glutamicum. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1344-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022] Open
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The RamA regulon: complex regulatory interactions in relation to central metabolism in Corynebacterium glutamicum. Appl Microbiol Biotechnol 2018; 102:5901-5910. [DOI: 10.1007/s00253-018-9085-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/07/2018] [Accepted: 05/08/2018] [Indexed: 12/16/2022]
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Wen J, Xiao Y, Liu T, Gao Q, Bao J. Rich biotin content in lignocellulose biomass plays the key role in determining cellulosic glutamic acid accumulation by Corynebacterium glutamicum. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:132. [PMID: 29760774 PMCID: PMC5944095 DOI: 10.1186/s13068-018-1132-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 04/28/2018] [Indexed: 05/30/2023]
Abstract
BACKGROUND Lignocellulose is one of the most promising alternative feedstocks for glutamic acid production as commodity building block chemical, but the efforts by the dominant industrial fermentation strain Corynebacterium glutamicum failed for accumulating glutamic acid using lignocellulose feedstock. RESULTS We identified the existence of surprisingly high biotin concentration in corn stover hydrolysate as the determining factor for the failure of glutamic acid accumulation by Corynebacterium glutamicum. Under excessive biotin content, induction by penicillin resulted in 41.7 ± 0.1 g/L of glutamic acid with the yield of 0.50 g glutamic acid/g glucose. Our further investigation revealed that corn stover contained 353 ± 16 μg of biotin per kg dry solids, approximately one order of magnitude greater than the biotin in corn grain. Most of the biotin remained stable during the biorefining chain and the rich biotin content in corn stover hydrolysate almost completely blocked the glutamic acid accumulation. This rich biotin existence was found to be a common phenomenon in the wide range of lignocellulose biomass and this may be the key reason why the previous studies failed in cellulosic glutamic acid fermentation from lignocellulose biomass. The extended recording of the complete members of all eight vitamin B compounds in lignocellulose biomass further reveals that the major vitamin B members were also under the high concentration levels even after harsh pretreatment. CONCLUSIONS The high content of biotin in wide range of lignocellulose biomass feedstocks and the corresponding hydrolysates was discovered and it was found to be the key factor in determining the cellulosic glutamic acid accumulation. The highly reserved biotin and the high content of their other vitamin B compounds in biorefining process might act as the potential nutrients to biorefining fermentations. This study creates a new insight that lignocellulose biorefining not only generates inhibitors, but also keeps nutrients for cellulosic fermentations.
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Affiliation(s)
- Jingbai Wen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Yanqiu Xiao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Ting Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Qiuqiang Gao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Jie Bao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
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Metabolic engineering of Corynebacterium glutamicum for fermentative production of chemicals in biorefinery. Appl Microbiol Biotechnol 2018; 102:3915-3937. [DOI: 10.1007/s00253-018-8896-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 01/22/2023]
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37
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Wang X, Khushk I, Xiao Y, Gao Q, Bao J. Tolerance improvement of Corynebacterium glutamicum on lignocellulose derived inhibitors by adaptive evolution. Appl Microbiol Biotechnol 2017; 102:377-388. [DOI: 10.1007/s00253-017-8627-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 10/24/2017] [Accepted: 11/06/2017] [Indexed: 01/09/2023]
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38
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The linkage between nutrient supply, intracellular enzyme abundances and bacterial growth: New evidences from the central carbon metabolism of Corynebacterium glutamicum. J Biotechnol 2017. [DOI: 10.1016/j.jbiotec.2017.06.407] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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39
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Ren GX, Guo XP, Sun YC. Regulatory 3' Untranslated Regions of Bacterial mRNAs. Front Microbiol 2017; 8:1276. [PMID: 28740488 PMCID: PMC5502269 DOI: 10.3389/fmicb.2017.01276] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/26/2017] [Indexed: 12/11/2022] Open
Abstract
The untranslated regions (UTRs) of mRNA contain important features that are relevant to the post-transcriptional and translational regulation of gene expression. Most studies of bacterial UTRs have focused on the 5′regions; however, 3′UTRs have recently emerged as a new class of post-transcriptional regulatory elements. 3′UTRs were found to regulate the decay and translation initiation in their own mRNAs. In addition, 3′UTRs constitute a rich reservoir of small regulatory RNAs, regulating target gene expression. In the current review, we describe several recently discovered examples of bacterial regulatory 3′UTRs, discuss their modes of action, and illustrate how they facilitate gene regulation in various environments.
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Affiliation(s)
- Gai-Xian Ren
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Xiao-Peng Guo
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Yi-Cheng Sun
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
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40
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Huang Q, Liang L, Wu W, Wu S, Huang J. Metabolic engineering of Corynebacterium glutamicum to enhance L-leucine production. ACTA ACUST UNITED AC 2017. [DOI: 10.5897/ajb2017.15911] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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41
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Harst A, Albaum SP, Bojarzyn T, Trötschel C, Poetsch A. Proteomics of FACS-sorted heterogeneous Corynebacterium glutamicum populations. J Proteomics 2017; 160:1-7. [PMID: 28323243 DOI: 10.1016/j.jprot.2017.03.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/26/2017] [Accepted: 03/13/2017] [Indexed: 01/20/2023]
Abstract
The metabolic status of individual cells in microbial cultures can differ, being relevant for biotechnology, environmental and medical microbiology. However, it is hardly understood in molecular detail due to limitations of current analytical tools. Here, we demonstrate that FACS in combination with proteomics can be used to sort and analyze cell populations based on their metabolic state. A previously established GFP reporter system was used to detect and sort single Corynebacterium glutamicum cells based on the concentration of branched chain amino acids (BCAA) using FACS. A proteomics workflow optimized for small cell numbers was used to quantitatively compare proteomes of a ΔaceE mutant, lacking functional pyruvate dehydrogenase (PD), and the wild type. About 800 proteins could be quantified from 1,000,000 cells. In the ΔaceE mutant BCAA production was coordinated with upregulation of the glyoxylate cycle and TCA cycle to counter the lack of acetyl CoA resulting from the deletion of aceE. BIOLOGICAL SIGNIFICANCE Metabolic pathways in C. glutamicum WT and ΔaceE, devoid of functional pyruvate dehydrogenase, were compared to understand proteome changes that contribute to the high production of branched chain amino acids (BCAA) in the ΔaceE strain. The data complements previous metabolome studies and corroborates the role of malate provided by the glyoxylate cycle and increased activity of glycolysis and pyruvate carboxylase reaction to replenish the TCA cycle. A slight increase in acetohydroxyacid synthase (ILV subunit B) substantiates the previously reported increased pyruvate pool in C. glutamicumΔaceE, and the benefit of additional ilv gene cluster overexpression for BCAA production.
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Affiliation(s)
- Andreas Harst
- Department of Plant Biochemistry, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Stefan P Albaum
- Bioinformatics Resource Facility, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Tanja Bojarzyn
- Department of Plant Biochemistry, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Christian Trötschel
- Department of Plant Biochemistry, Ruhr-University Bochum, 44801 Bochum, Germany.
| | - Ansgar Poetsch
- Department of Plant Biochemistry, Ruhr-University Bochum, 44801 Bochum, Germany; School of Biomedical and Healthcare Sciences, Plymouth University, Plymouth PL4 8AA, United Kingdom.
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42
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Im DK, Yun SH, Jung JY, Lee J, Oh MK. Comparison of metabolite profiling of Ralstonia eutropha H16 phaBCA mutants grown on different carbon sources. KOREAN J CHEM ENG 2017. [DOI: 10.1007/s11814-016-0333-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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43
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Zhang Y, Cai J, Shang X, Wang B, Liu S, Chai X, Tan T, Zhang Y, Wen T. A new genome-scale metabolic model of Corynebacterium glutamicum and its application. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:169. [PMID: 28680478 PMCID: PMC5493880 DOI: 10.1186/s13068-017-0856-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/22/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Corynebacterium glutamicum is an important platform organism for industrial biotechnology to produce amino acids, organic acids, bioplastic monomers, and biofuels. The metabolic flexibility, broad substrate spectrum, and fermentative robustness of C. glutamicum make this organism an ideal cell factory to manufacture desired products. With increases in gene function, transport system, and metabolic profile information under certain conditions, developing a comprehensive genome-scale metabolic model (GEM) of C. glutamicum ATCC13032 is desired to improve prediction accuracy, elucidate cellular metabolism, and guide metabolic engineering. RESULTS Here, we constructed a new GEM for ATCC13032, iCW773, consisting of 773 genes, 950 metabolites, and 1207 reactions. Compared to the previous model, iCW773 supplemented 496 gene-protein-reaction associations, refined five lumped reactions, balanced the mass and charge, and constrained the directionality of reactions. The simulated growth rates of C. glutamicum cultivated on seven different carbon sources using iCW773 were consistent with experimental values. Pearson's correlation coefficient between the iCW773-simulated and experimental fluxes was 0.99, suggesting that iCW773 provided an accurate intracellular flux distribution of the wild-type strain growing on glucose. Furthermore, genetic interventions for overproducing l-lysine, 1,2-propanediol and isobutanol simulated using OptForceMUST were in accordance with reported experimental results, indicating the practicability of iCW773 for the design of metabolic networks to overproduce desired products. In vivo genetic modifications of iCW773-predicted targets resulted in the de novo generation of an l-proline-overproducing strain. In fed-batch culture, the engineered C. glutamicum strain produced 66.43 g/L l-proline in 60 h with a yield of 0.26 g/g (l-proline/glucose) and a productivity of 1.11 g/L/h. To our knowledge, this is the highest titer and productivity reported for l-proline production using glucose as the carbon resource in a minimal medium. CONCLUSIONS Our developed iCW773 serves as a high-quality platform for model-guided strain design to produce industrial bioproducts of interest. This new GEM will be a successful multidisciplinary tool and will make valuable contributions to metabolic engineering in academia and industry.
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Affiliation(s)
- Yu Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jingyi Cai
- Beijing University of Chemical Technology, Beijing, 100029 China
| | - Xiuling Shang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Bo Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Shuwen Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xin Chai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Tianwei Tan
- Beijing University of Chemical Technology, Beijing, 100029 China
| | - Yun Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Tingyi Wen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049 China
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Becker J, Wittmann C. Industrial Microorganisms: Corynebacterium glutamicum. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Judith Becker
- Saarland University; Institute of Systems Biotechnology; Campus A 15 66123 Saarbrücken Germany
| | - Christoph Wittmann
- Saarland University; Institute of Systems Biotechnology; Campus A 15 66123 Saarbrücken Germany
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45
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Affiliation(s)
- Volker F. Wendisch
- Bielefeld University; Genetics of Prokaryotes, Faculty of Biology and CeBiTec; Postfach 100131 33501 Bielefeld Germany
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46
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Li Y, Huang B, Wu H, Li Z, Ye Q, Zhang YHP. Production of Succinate from Acetate by Metabolically Engineered Escherichia coli. ACS Synth Biol 2016; 5:1299-1307. [PMID: 27088218 DOI: 10.1021/acssynbio.6b00052] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Acetate, a major component of industrial biological wastewater and of lignocellulosic biomass hydrolysate, could potentially be a less costly alternative carbon source. Here we engineered Escherichia coli MG1655 strain for succinate production from acetate as the sole carbon source. Strategies of metabolic engineering included the blockage of the TCA cycle, redirection of the gluconeogenesis pathway, and enhancement of the glyoxylate shunt. The engineered strain MG03 featuring the deletion of genes: succinate dehydrogenase (sdhAB), isocitrate lyase regulator (iclR), and malic enzymes (maeB) accumulated 6.86 mM of succinate in 72 h. MG03(pTrc99a-gltA) overexpressing citrate synthase (gltA) accumulated 16.45 mM of succinate and the yield reached 0.46 mol/mol, about 92% of the maximum theoretical yield. Resting-cell was adopted for the conversion of acetate to succinate, and the highest concentration of succinate achieved 61.7 mM.
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Affiliation(s)
- Yunjie Li
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Bing Huang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Hui Wu
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Zhimin Li
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qin Ye
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Y-H Percival Zhang
- Biological
Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia 24061, United States
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
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47
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Jorge JMP, Nguyen AQD, Pérez-García F, Kind S, Wendisch VF. Improved fermentative production of gamma-aminobutyric acid via the putrescine route: Systems metabolic engineering for production from glucose, amino sugars, and xylose. Biotechnol Bioeng 2016; 114:862-873. [PMID: 27800627 DOI: 10.1002/bit.26211] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/04/2016] [Accepted: 10/28/2016] [Indexed: 11/07/2022]
Abstract
Gamma-aminobutyric acid (GABA) is a non-protein amino acid widespread in Nature. Among the various uses of GABA, its lactam form 2-pyrrolidone can be chemically converted to the biodegradable plastic polyamide-4. In metabolism, GABA can be synthesized either by decarboxylation of l-glutamate or by a pathway that starts with the transamination of putrescine. Fermentative production of GABA from glucose by recombinant Corynebacterium glutamicum has been described via both routes. Putrescine-based GABA production was characterized by accumulation of by-products such as N-acetyl-putrescine. Their formation was abolished by deletion of the spermi(di)ne N-acetyl-transferase gene snaA. To improve provision of l-glutamate as precursor 2-oxoglutarate dehydrogenase activity was reduced by changing the translational start codon of the chromosomal gene for 2-oxoglutarate dehydrogenase subunit E1o to the less preferred TTG and by maintaining the inhibitory protein OdhI in its inhibitory form by changing amino acid residue 15 from threonine to alanine. Putrescine-based GABA production by the strains described here led to GABA titers up to 63.2 g L-1 in fed-batch cultivation at maximum volumetric productivities up to 1.34 g L-1 h-1 , the highest volumetric productivity for fermentative GABA production reported to date. Moreover, GABA production from the carbon sources xylose, glucosamine, and N-acetyl-glucosamine that do not have competing uses in the food or feed industries was established. Biotechnol. Bioeng. 2017;114: 862-873. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- João M P Jorge
- Faculty of Biology and CeBiTec, Genetics of Prokaryotes, Bielefeld University, Universitätsstr. 25, Bielefeld 33615, Germany
| | - Anh Q D Nguyen
- Faculty of Biology and CeBiTec, Genetics of Prokaryotes, Bielefeld University, Universitätsstr. 25, Bielefeld 33615, Germany.,evocatal GmbH, Monheim, Germany
| | - Fernando Pérez-García
- Faculty of Biology and CeBiTec, Genetics of Prokaryotes, Bielefeld University, Universitätsstr. 25, Bielefeld 33615, Germany
| | | | - Volker F Wendisch
- Faculty of Biology and CeBiTec, Genetics of Prokaryotes, Bielefeld University, Universitätsstr. 25, Bielefeld 33615, Germany
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48
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Application of CRISPRi in Corynebacterium glutamicum for shikimic acid production. Biotechnol Lett 2016; 38:2153-2161. [PMID: 27623797 DOI: 10.1007/s10529-016-2207-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 08/31/2016] [Indexed: 10/21/2022]
Abstract
OBJECTIVES To construct, test and exploit the CRISPRi system for enhancement of shikimic acid production with Corynebacterium glutamicum. RESULTS The CRISPRi system was used to regulate C. glutamicum gene expression at the transcriptional level. Hfq protein-mediated small regulatory RNAs system was compared with CRISPRi system. The more efficient CRISPRi system was used to adjust the metabolic flux involving the shikimic acid (SA) synthetic pathway. In 11 candidate genes, including transcription regulator, three targets were effective for increasing SA production. Through over-expression of ncgl1512 and down-regulating the expression of ncgl2008, ncgl2809, ncgl1856, the titers of SA increased 115 % to 7.76 g/l in 250 ml flasks and 23.8 g/l in 5 l fermentor, which is the highest shikimic acid yield reported for C. glutamicum. CONCLUSIONS CRISPRi system was constructed and is a high-performance and time-saving method to manipulate multiple genes in C. glutamicum for shikimic acid production. Moreover, CRISPRi-system was also effective in regulating the expression of a transcription regulator.
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Updates on industrial production of amino acids using Corynebacterium glutamicum. World J Microbiol Biotechnol 2016; 32:105. [DOI: 10.1007/s11274-016-2060-1] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/27/2016] [Indexed: 12/14/2022]
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Usuda Y, Hara Y, Kojima H. Toward Sustainable Amino Acid Production. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 159:289-304. [PMID: 27872964 DOI: 10.1007/10_2016_36] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Because the global amino acid production industry has been growing steadily and is expected to grow even more in the future, efficient production by fermentation is of great importance from economic and sustainability viewpoints. Many systems biology technologies, such as genome breeding, omics analysis, metabolic flux analysis, and metabolic simulation, have been employed for the improvement of amino acid-producing strains of bacteria. Synthetic biological approaches have recently been applied to strain development. It is also important to use sustainable carbon sources, such as glycerol or pyrolytic sugars from cellulosic biomass, instead of conventional carbon sources, such as glucose or sucrose, which can be used as food. Furthermore, reduction of sub-raw substrates has been shown to lead to reduction of environmental burdens and cost. Recently, a new fermentation system for glutamate production under acidic pH was developed to decrease the amount of one sub-raw material, ammonium, for maintenance of culture pH. At the same time, the utilization of fermentation coproducts, such as cells, ammonium sulfate, and fermentation broth, is a useful approach to decrease waste. In this chapter, further perspectives for future amino acid fermentation from one-carbon compounds are described.
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Affiliation(s)
- Yoshihiro Usuda
- Institute for Innovation, Ajinomoto Co. Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki, 210-8681, Japan.
| | - Yoshihiko Hara
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1 Suzukicho, Kawasaki-ku, Kawasaki, 210-8681, Japan
| | - Hiroyuki Kojima
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1 Suzukicho, Kawasaki-ku, Kawasaki, 210-8681, Japan
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