中国化学工程学报 ›› 2025, Vol. 83 ›› Issue (7): 277-285.DOI: 10.1016/j.cjche.2025.03.013
Xinzhe Zhang, Aipeng Li, Xiaohan Huang, Qiang Fei
收稿日期:2025-01-05
修回日期:2025-03-16
接受日期:2025-03-24
出版日期:2025-07-28
发布日期:2025-07-28
通讯作者:
Qiang Fei,E-mail:feiqiang@xjtu.edu.cn
基金资助:Xinzhe Zhang, Aipeng Li, Xiaohan Huang, Qiang Fei
Received:2025-01-05
Revised:2025-03-16
Accepted:2025-03-24
Online:2025-07-28
Published:2025-07-28
Contact:
Qiang Fei,E-mail:feiqiang@xjtu.edu.cn
Supported by:摘要: One-carbon (C1) compounds, such as CO2, methane, and methanol, are emerging as promising feedstocks for next-generation biomanufacturing due to their abundance and low cost. In recent years, there has been growing interest in harnessing microorganisms to convert these carbon sources into valuable natural products (NPs), which offers great potential for sustainable development. This review systematically outlines recent advancements in biocatalysts, synthetic biology, and process optimization aimed at improving the feasibility and scalability of producing C1-based NPs. Current challenges and insights into NPs biomanufacturing from C1 compounds are thoroughly examined in the areas of multi-gene editing, metabolic regulation, and synthetic microbial consortium. With ongoing progress in biosynthetic tools and fermentation techniques, C1-based biomanufacturing is becoming a versatile and sustainable platform for generating diverse value-added products.
Xinzhe Zhang, Aipeng Li, Xiaohan Huang, Qiang Fei. Recent advances in the biosynthesis of natural products from C1 compounds[J]. 中国化学工程学报, 2025, 83(7): 277-285.
Xinzhe Zhang, Aipeng Li, Xiaohan Huang, Qiang Fei. Recent advances in the biosynthesis of natural products from C1 compounds[J]. Chinese Journal of Chemical Engineering, 2025, 83(7): 277-285.
| [1] R. Chen, G.M. Weng, Sustainable energy resources for driving methane conversion, Adv. Energy Mater. 13(36) (2023) 2301734. [2] S. O'Keeffe, L. Garcia, Y. Chen, R.C. Law, C. Liu, J.O. Park, Bringing carbon to life via one-carbon metabolism, Trends Biotechnol. 43(3) (2025) 572-585. [3] D. Laborde, A. Mamun, W. Martin, V. Pineiro, R. Vos, Agricultural subsidies and ~ global greenhouse gas emissions, Nat. Commun. 12(2021) 2601. [4] J.K. Jansson, K.S. Hofmockel, Soil microbiomes and climate change, Nat. Rev. Microbiol. 18(1) (2020) 35-46. [5] Y. Gao, J.J. Li, S.Y. Wang, J.J. Jia, F. Wu, G.R. Yu, Global inland water greenhouse gas (GHG) geographical patterns and escape mechanisms under different water level, Water Res. 269(2025) 122808. [6] L. Jeffry, M.Y. Ong, S. Nomanbhay, M. Mofijur, M. Mubashir, P.L. Show, Greenhouse gases utilization: a review, Fuel 301(2021) 121017. [7] L.Z. Hu, S.Q. Guo, B. Wang, R.Z. Fu, D.D. Fan, M. Jiang, Q. Fei, R. Gonzalez, Biovalorization of C1 gaseous substrates into bioalcohols: potentials and challenges in reducing carbon emissions, Biotechnol. Adv. 59(2022) 107954. [8] A. Gesicka, P. Oleskowicz-Popiel, M. Łe?zyk, Recent trends in methane to _ bioproduct conversion by methanotrophs, Biotechnol. Adv. 53(2021) 107861. [9] J. Yoon, M.K. Oh, Strategies for biosynthesis of C1 gas-derived polyhydroxyalkanoates: a review, Bioresour. Technol. 344(Pt B) (2022) 126307. [10] J.M. Clomburg, A.M. Crumbley, R. Gonzalez, Industrial biomanufacturing: the future of chemical production, Science 355(6320) (2017) aag0804. [11] L. Chistoserdova, Applications of methylotrophs: can single carbon be harnessed for biotechnology? Curr. Opin. Biotechnol. 50(2018) 189-194. [12] C. Cannavacciuolo, S. Pagliari, R. Celano, L. Campone, L. Rastrelli, Critical analysis of green extraction techniques used for botanicals: trends, priorities, and optimization strategies-a review, Trac. Trends Anal. Chem. 173(2024) 117627. [13] F. Barzegar, S. Nabizadeh, M. Kamankesh, J.B. Ghasemi, A. Mohammadi, Recent advances in natural product-based nanoemulsions as promising substitutes for hazardous synthetic food additives: a new revolution in food processing, Food Bioprocess Technol. 17(5) (2024) 1087-1108. [14] W.B. Qiao, S.J. Xu, Z.H. Liu, X.Y. Fu, H.M. Zhao, S.B. Shi, Challenges and opportunities in C1-based biomanufacturing, Bioresour. Technol. 364(2022) 128095. [15] X.Q. Lv, W.W. Yu, C.Y. Zhang, P. Ning, J.H. Li, Y.F. Liu, G.C. Du, L. Liu, C1-based biomanufacturing: advances, challenges and perspectives, Bioresour. Technol. 367(2023) 128259. [16] C.W. Koo, A.C. Rosenzweig, Biochemistry of aerobic biological methane oxidation, Chem. Soc. Rev. 50(5) (2021) 3424-3436. [17] A.D. Nguyen, E.Y. Lee, Engineered methanotrophy: a sustainable solution for methane-based industrial biomanufacturing, Trends Biotechnol. 39(4) (2021) 381-396. [18] D.H.A. Mai, T.T. Nguyen, E.Y. Lee, The ethylmalonyl-CoA pathway for methane-based biorefineries: a case study of using Methylosinus trichosporium OB3b, an alpha-proteobacterial methanotroph, for producing 2-hydroxyisobutyric acid and 1,3-butanediol from methane, Green Chem. 23(19) (2021) 7712-7723. [19] M.I.S. Naduthodi, N.J. Claassens, S. D'Adamo, J. van der Oost, M.J. Barbosa, Synthetic biology approaches to enhance microalgal productivity, Trends Biotechnol. 39(10) (2021) 1019-1036. [20] C.A. Henard, C. Wu, W. Xiong, J.M. Henard, B. Davidheiser-Kroll, F.D. Orata, M. T. Guarnieri, Ribulose-1, 5-bisphosphate carboxylase/oxygenase (RubisCO) is essential for growth of the methanotroph Methylococcus capsulatus strain bath, Appl. Environ. Microbiol. 87(18) (2021) e0088121. [21] X.J. Yuan, W.J. Chen, Z.X. Ma, Q.Q. Yuan, M. Zhang, L. He, X.H. Mo, C. Zhang, C.T. Zhang, M.Y. Wang, X.H. Xing, S. Yang, Rewiring the native methanol assimilation metabolism by incorporating the heterologous ribulose monophosphate cycle into Methylorubrum extorquens, Metab. Eng. 64(2021) 95-110. [22] X. Wang, X.L. Wang, X.L. Lu, C. Ma, K.Q. Chen, P.K. Ouyang, Methanol fermentation increases the production of NAD(P)H-dependent chemicals in synthetic methylotrophic Escherichia coli, Biotechnol. Biofuels 12(2019) 17. [23] L. Nikkanen, D. Solymosi, M. Jokel, Y. Allahverdiyeva, Regulatory electron transport pathways of photosynthesis in cyanobacteria and microalgae: recent advances and biotechnological prospects, Physiol Plant 173(2) (2021) 514-525. [24] A. Burlacot, O. Dao, P. Auroy, S. Cuine, Y. Li-Beisson, G. Peltier, Alternative photosynthesis pathways drive the algal CO2-concentrating mechanism, Nature 605(7909) (2022) 366-371. [25] A.D. Nguyen, D. Kim, E.Y. Lee, Unlocking the biosynthesis of sesquiterpenoids from methane via the methylerythritol phosphate pathway in methanotrophic bacteria, using a-humulene as a model compound, Metab. Eng. 61(2020) 69-78. [26] G. Emelianov, D.U. Song, N. Jang, M. Ko, S.K. Kim, E. Rha, J. Shin, K.K. Kwon, H. Kim, D.H. Lee, H. Lee, S.G. Lee, Engineered Methylococcus capsulatus bath for efficient methane conversion to isoprene, Bioresour. Technol. 393(2024) 130098. [27] C.F. Li, L.J. Yin, J.W. Wang, H.T. Zheng, J. Ni, Light-driven biosynthesis of volatile, unstable and photosensitive chemicals from CO2, Nat. Synth. 2(2023) 960-971. [28] D.N. Pham, A.D. Nguyen, S.H. Oh, E.Y. Lee, Bypassing the bottlenecks in the shikimate and methylerythritol phosphate pathways for enhancing the production of natural products from methane in Methylotuvimicrobium alcaliphilum 20Z, Green Chem. 24(7) (2022) 2893-2903. [29] B.R. Lichman, The scaffold-forming steps of plant alkaloid biosynthesis, Nat. Prod. Rep. 38(1) (2021) 103-129. [30] J.C. Sun, W.T. Sun, G.L. Zhang, B. Lv, C. Li, High efficient production of plant flavonoids by microbial cell factories: challenges and opportunities, Metab. Eng. 70(2022) 143-154. [31] S. Dinday, S. Ghosh, Recent advances in triterpenoid pathway elucidation and engineering, Biotechnol. Adv. 68(2023) 108214. [32] M.E. Bergman, R.W.J. Kortbeek, M. Gutensohn, N. Dudareva, Plant terpenoid biosynthetic network and its multiple layers of regulation, Prog. Lipid Res. 95(2024) 101287. [33] A.D. Nguyen, D.N. Pham, T.H.T. Chau, E.Y. Lee, Enhancing sesquiterpenoid production from methane via synergy of the methylerythritol phosphate pathway and a short-cut route to 1-deoxy-D-xylulose 5-phosphate in methanotrophic bacteria, Microorganisms 9(6) (2021) 1236. [34] S.E. Lim, S. Cho, Y. Choi, J.G. Na, J. Lee, High production of ectoine from methane in genetically engineered Methylomicrobium alcaliphilum 20Z by preventing ectoine degradation, Microb. Cell Fact. 23(1) (2024) 127. [35] D.N. Pham, D.H.A. Mai, A.D. Nguyen, T.H.T. Chau, E.Y. Lee, Development of an engineered methanotroph-based microbial platform for biocatalytic conversion of methane to phytohormone for sustainable agriculture, Chem. Eng. J. 429(2022) 132522. [36] C.K. Kang, S.W. Jeong, J.H. Jo, J.H. Park, M.S. Kim, J.E. Yang, Y.J. Choi, High-level squalene production from methane using a metabolically engineered Methylomonas sp. DH-1 strain, ACS Sustainable Chem. Eng. 9(48) (2021) 16485-16493. [37] H.T. Quynh Le, D.H. Anh Mai, J.G. Na, E.Y. Lee, Development of Methylorubrum extorquens AM1 as a promising platform strain for enhanced violacein production from co-utilization of methanol and acetate, Metab. Eng. 72(2022) 150-160. [38] B.J. Zhao, Y. Li, Y. Zhang, M.X. Pan, G.S. Zhao, Y.B. Guo, Low-carbon and overproduction of cordycepin from methanol using engineered Pichia pastoris cell factory, Bioresour. Technol. 413(2024) 131446. [39] T.T. Niu, X.G. Yan, J.R. Wang, H.J. Song, Y. Cui, X.P. Cai, A.K. Chang, J.J. Qiao, M. Z. Wen, J.W. He, Engineering of Pichia pastoris for the De novo synthesis of the sesquiterpene Zealexin A1 from methanol, ACS Sustainable Chem. Eng. 12(34) (2024) 12786-12794. [40] L.H. Gao, R. Hou, P. Cai, L. Yao, X.Y. Wu, Y.X. Li, L.H. Zhang, Y.J. Zhou, Engineering yeast peroxisomes for a-bisabolene production from sole methanol with the aid of proteomic analysis, JACS Au 4(7) (2024) 2474-2483. [41] J.J. Li, J.Q. Gao, M. Ye, P. Cai, W. Yu, X.X. Zhai, Y.J. Zhou, Engineering yeast for high-level production of b-farnesene from sole methanol, Metab. Eng. 85(2024) 194-200. [42] H.J. Lee, J.I. Choi, H.M. Woo, Biocontainment of engineered Synechococcus elongatus PCC 7942 for photosynthetic production of a-farnesene from CO2, J. Agric. Food Chem. 69(2) (2021) 698-703. [43] J.S. Rodrigues, P. Lindberg, Metabolic engineering of Synechocystis sp. PCC 6803 for improved bisabolene production, Metab. Eng. Commun. 12(2020) e00159. [44] B. Pattanaik, E. Englund, N. Nolte, P. Lindberg, Introduction of a green algal squalene synthase enhances squalene accumulation in a strain of Synechocystis sp. PCC 6803, Metab. Eng. Commun. 10(2020) e00125. [45] T. Hasunuma, A. Takaki, M. Matsuda, Y. Kato, C.J. Vavricka, A. Kondo, Singlestage astaxanthin production enhances the nonmevalonate pathway and photosynthetic central metabolism in Synechococcus sp. PCC 7002, ACS Synth. Biol. 8(12) (2019) 2701-2709. [46] H.L. Wu, H.J. Pan, Z.J. Li, T.F. Liu, F.L. Liu, S.Y. Xiu, J. Wang, H.Q. Wang, Y. Hou, B. Yang, L.C. Lei, J.Z. Lian, Efficient production of lycopene from CO2 via microbial electrosynthesis, Chem. Eng. J. 430(2022) 132943. [47] J.H. Chen, Y. Kato, M. Matsuda, C.Y. Chen, D. Nagarajan, T. Hasunuma, A. Kondo, J.S. Chang, Lutein production with Chlorella sorokiniana MB-1-M12 using novel two-stage cultivation strategies - metabolic analysis and process improvement, Bioresour. Technol. 334(2021) 125200. [48] B.S. Yu, Y.J. Sung, H.I. Choi, R. Sirohi, S.J. Sim, Concurrent enhancement of CO2 fixation and productivities of omega-3 fatty acids and astaxanthin in Haematococcus pluvialis culture via calcium-mediated homeoviscous adaptation and biomineralization, Bioresour. Technol. 340(2021) 125720. [49] P.C. Lin, F.Z. Zhang, H.B. Pakrasi, Enhanced limonene production in a fastgrowing cyanobacterium through combinatorial metabolic engineering, Metab. Eng. Commun. 12(2021) e00164. [50] A.P. Li, X.P. Cao, R.Z. Fu, S.Q. Guo, Q. Fei, Biocatalysis of CO2 and CH4: key enzymes and challenges, Biotechnol. Adv. 72(2024) 108347. [51] L.Z. Hu, S.Q. Guo, X. Yan, T.Q. Zhang, J. Xiang, Q. Fei, Exploration of an efficient electroporation system for heterologous gene expression in the genome of methanotroph, Front. Microbiol. 12(2021) 717033. [52] K. Schultenkäamper, D.D. Gütle, M.G. Lopez, L.B. Keller, L. Zhang, O. Einsle, J.P. Jacquot, V.F. Wendisch, Interrogating the role of the two distinct fructosebisphosphate aldolases of Bacillus methanolicus by site-directed mutagenesis of key amino acids and gene repression by CRISPR interference, Front. Microbiol. 12(2021) 669220. [53] X.H. Mo, H. Zhang, T.M. Wang, C. Zhang, C. Zhang, X.H. Xing, S. Yang, Establishment of CRISPR interference in Methylorubrum extorquens and application of rapidly mining a new phytoene desaturase involved in carotenoid biosynthesis, Appl. Microbiol. Biotechnol. 104(10) (2020) 4515-4532. [54] T. Tapscott, M.T. Guarnieri, C.A. Henard, Development of a CRISPR/Cas9 system for methylococcus capsulatus in vivo gene editing, Appl. Environ. Microbiol. 85(11) (2019) e0034019. [55] M.G. Cheng, D.M. Pei, L. He, Q. Fei, X. Yan, Cre/lox-mediated CRISPRi library reveals core genome of a type I methanotroph Methylotuvimicrobium buryatense 5GB1C, Appl. Environ. Microbiol. 89(1) (2023) e0188322. [56] J. Wang, C.Y. Li, T. Jiang, Y.J. Yan, Biosensor-assisted titratable CRISPRi highthroughput (BATCH) screening for over-production phenotypes, Metab. Eng. 75(2023) 58-67. [57] Q.Q. Peng, W.W. Bao, B.N. Geng, S.H. Yang, Biosensor-assisted CRISPRi highthroughput screening to identify genetic targets in Zymomonas mobilis for high d-lactate production, Synth. Syst. Biotechnol. 9(2) (2024) 242-249. [58] X. Chen, F.R. Li, X.W. Li, M. Otto, Y. Chen, V. Siewers, Model-assisted CRISPRi/a library screening reveals central carbon metabolic targets for enhanced recombinant protein production in yeast, Metab. Eng. 88(2025) 1-13. [59] H. Xiao, H.R. Hu, Y.J. Guo, J. Li, W.B. Zeng, M.H. Luo, M.L. Wang, Z.H. Hu, Efficient strategy for synthesizing vector-free and oncolytic herpes simplex type 1 viruses, ACS Synth. Biol. 13(10) (2024) 3268-3280. [60] E.H. Wilson, J.D. Groom, M. Claire Sarfatis, S.M. Ford, M.E. Lidstrom, D.A.C. Beck, A computational framework for identifying promoter sequences in nonmodel organisms using RNA-seq data sets, ACS Synth. Biol. 10(6) (2021) 1394-1405. [61] J.M. Vento, N. Crook, C.L. Beisel, Barriers to genome editing with CRISPR in bacteria, J. Ind. Microbiol. Biotechnol. 46(9-10) (2019) 1327-1341. [62] V. Ganesan, L. Monteiro, D. Pedada, A. Stohr, M. Blenner, High-efficiency multiplexed cytosine base editors for natural product synthesis in Yarrowia lipolytica, ACS Synth. Biol. 12(10) (2023) 3082-3091. [63] H. Xiao, Y. Zhang, M. Wang, Discovery and engineering of cytochrome P450s for terpenoid biosynthesis, Trends Biotechnol. 37(6) (2019) 618-631. [64] M. Poborsky, C. Crocoll, M.S. Motawie, B.A. Halkier, Systematic engineering pinpoints a versatile strategy for the expression of functional cytochrome P450 enzymes in Escherichia coli cell factories, Microb. Cell Fact. 22(1) (2023) 219. [65] R.W. Wang, X. Liu, B. Lv, W.T. Sun, C. Li, Designing intracellular compartments for efficient engineered microbial cell factories, ACS Synth. Biol. 12(5) (2023) 1378-1395. [66] M. Nogueira, E.M.A. Enfissi, R. Welsch, P. Beyer, M.D. Zurbriggen, P.D. Fraser, Construction of a fusion enzyme for astaxanthin formation and its characterisation in microbial and plant hosts: a new tool for engineering ketocarotenoids, Metab. Eng. 52(2019) 243-252. [67] X. Wang, J.H. Pereira, S. Tsutakawa, X. Fang, P.D. Adams, A. Mukhopadhyay, T. S. Lee, Efficient production of oxidized terpenoids via engineering fusion proteins of terpene synthase and cytochrome P450, Metab. Eng. 64(2021) 41-51. [68] Y.K. Li, R. Li, J.J. Ge, S.X. Nie, R.Q. Chen, X.G. Yan, J.J. Qiao, Comprehensive engineering strategies for heterologous production of Zealexin A1 in Saccharomyces cerevisiae, J. Agric. Food Chem. 72(34) (2024) 19071-19080. [69] W. Kang, T. Ma, M. Liu, J. Qu, Z. Liu, H. Zhang, B. Shi, S. Fu, J. Ma, L.T.F. Lai, S. He, J. Qu, S. Wing-Ngor Au, B.H. Kang, W.C. Yu Lau, Z. Deng, J. Xia, T. Liu, Modular enzyme assembly for enhanced cascade biocatalysis and metabolic flux, Nat. Commun. 10(1) (2019) 4248. [70] A.A. Bedekar, A. Deewan, S.S. Jagtap, D.A. Parker, P. Liu, R.I. Mackie, C.V. Rao, Transcriptional and metabolomic responses of Methylococcus capsulatus bath to nitrogen source and temperature downshift, Front. Microbiol. 14(2023) 1259015. [71] C. Xie, N. An, L. Zhou, X.L. Shen, J. Wang, Y.J. Yan, X.X. Sun, Q.P. Yuan, Establishing a coumarin production platform by protein and metabolic engineering, Metab. Eng. 86(2024) 89-98. [72] Q.F. Li, T. Jiang, R. Liu, X.D. Feng, C. Li, Tuning the pH profile of b-glucuronidase by rational site-directed mutagenesis for efficient transformation of glycyrrhizin, Appl. Microbiol. Biotechnol. 103(12) (2019) 4813-4823. [73] F.J. Tucci, A.C. Rosenzweig, Direct methane oxidation by copper- and iron-dependent methane monooxygenases, Chem. Rev. 124(3) (2024) 1288-1320. [74] J.L. Krüsemann, V. Rainaldi, C.A. Cotton, N.J. Claassens, S.N. Lindner, The cofactor challenge in synthetic methylotrophy: bioengineering and industrial applications, Curr. Opin. Biotechnol. 82(2023) 102953. [75] K.D. Cocon, P. Luis, The potential of RuBisCO in CO2 capture and utilization, Prog. Energy Combust. Sci. 105(2024) 101184. [76] N. Prywes, N.R. Phillips, L.M. Oltrogge, S. Lindner, L.J. Taylor-Kearney, Y.C. Tsai, B. de Pins, A.E. Cowan, H.A. Chang, R.Z. Wang, L.N. Hall, D. Bellieny-Rabelo, H. M. Nisonoff, R.F. Weissman, A.I. Flamholz, D. Ding, A.Y. Bhatt, O. Mueller-Cajar, P.M. Shih, R. Milo, D.F. Savage, A map of the rubisco biochemical landscape, Nature 638(8051) (2025) 823-828. [77] C.W. Koo, F.J. Tucci, Y. He, A.C. Rosenzweig, Recovery of particulate methane monooxygenase structure and activity in a lipid bilayer, Science 375(6586) (2022) 1287-1291. [78] W.D. Jang, G.B. Kim, Y. Kim, S.Y. Lee, Applications of artificial intelligence to enzyme and pathway design for metabolic engineering, Curr. Opin. Biotechnol. 73(2022) 101-107. [79] J.H. Zhou, M.L. Huang, Navigating the landscape of enzyme design: from molecular simulations to machine learning, Chem. Soc. Rev. 53(16) (2024) 8202-8239. [80] W.C. Chen, Y.K. Park, L. Studena, D. Bell, P. Hapeta, J. Fu, P.J. Nixon, R. Ledesma- Amaro, Synthetic, marine, light-driven, autotroph-heterotroph co-culture system for sustainable b-caryophyllene production, Bioresour. Technol. 410(2024) 131232. [81] Z.X. Gao, S.Q. Guo, Y.H. Chen, H.S. Chen, R.Z. Fu, Q.Q. Song, S. Li, W.Y. Lou, D.D. Fan, Y. Li, S.H. Yang, R. Gonzalez, Q. Fei, A novel nutritional induction strategy flexibly switching the biosynthesis of food-like products from methane by a methanotrophic bacterium, Green Chem. 26(12) (2024) 7048-7058. [82] Z.T. Qiu, X. Liu, J. Li, B. Qiao, G.R. Zhao, Metabolic division in an Escherichia coli coculture system for efficient production of kaempferide, ACS Synth. Biol. 11(3) (2022) 1213-1227. [83] Z.H. Li, X.N. Wang, H.R. Zhang, Balancing the non-linear rosmarinic acid biosynthetic pathway by modular co-culture engineering, Metab. Eng. 54(2019) 1-11. [84] Y. Du, B.R. Yang, Z.Q. Yi, L.L. Hu, M. Li, Engineering Saccharomyces cerevisiae coculture platform for the production of flavonoids, J. Agric. Food Chem. 68(7) (2020) 2146-2154. |
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