热纤梭菌在生物质能源开发中的合成生物学研究进展

doi:10.12211/2096-8280.2023-046

合成生物学 ›› 2023, Vol. 4 ›› Issue (6): 1055-1081.DOI: 10.12211/2096-8280.2023-046

热纤梭菌在生物质能源开发中的合成生物学研究进展

肖艳¹^,²^,³^,⁴, 刘亚君¹^,²^,³^,⁴, 冯银刚¹^,²^,³^,⁴, 崔球¹^,²^,³^,⁴

^1.中国科学院青岛生物能源与过程研究所，中国科学院生物燃料重点实验室，山东省合成生物学重点实验室，山东青岛 266101
^2.山东省能源研究院，山东青岛 266101
^3.青岛新能源山东省实验室，山东青岛 266101
^4.中国科学院大学，北京 100049

收稿日期:2023-07-02 修回日期:2023-09-22 出版日期:2023-12-31 发布日期:2024-01-19
通讯作者: 冯银刚,崔球
作者简介:肖艳（1982—），女，博士，副研究员，硕士生导师。研究方向为能源微生物代谢机理与改造。E-mail：xiaoyan@qibebt.ac.cn
冯银刚（1977—），男，博士，研究员，博士生导师。研究方向为能源微生物的分子生理机制与合成生物学应用、工业酶催化机制与酶工程等。E-mail：fengyg@qibebt.ac.cn
崔球（1975—），男，博士，研究员，博士生导师。研究方向为基于代谢物组/代谢流组学的计算分析辅助能源微生物代谢工程设计、蛋白质结构功能研究。E-mail：cuiqiu@qibebt.ac.cn
基金资助:
国家自然科学基金(32070125);山东能源研究院(SEI I202106);山东省自然科学基金(ZR2022MC128)

Progress in synthetic biology research of Clostridium thermocellum for biomass energy applications

Yan XIAO¹^,²^,³^,⁴, Yajun LIU¹^,²^,³^,⁴, Yin′gang FENG¹^,²^,³^,⁴, Qiu CUI¹^,²^,³^,⁴

^1.Shandong Provincial Key Laboratory of Synthetic Biology，CAS Key Laboratory of Biofuels，Qingdao Institute of Bioenergy and Bioprocess Technology，Chinese Academy of Sciences，Qingdao 266101，Shandong，China
^2.Shandong Energy Institute，Qingdao 266101，Shandong，China
^3.Qingdao New Energy Shandong Laboratory，Qingdao 266101，Shandong，China
^4.University of Chinese Academy of Sciences，Beijing 100049，China

Received:2023-07-02 Revised:2023-09-22 Online:2023-12-31 Published:2024-01-19
Contact: Yin′gang FENG, Qiu CUI

摘要/Abstract

摘要：

农林废弃物、能源植物、微藻等生物质是唯一同时具备“能源”和“物质”双重属性的可再生资源，在替代不可再生的化石能源方面具有巨大的潜力。木质纤维素生物转化的核心之一在于高效生物催化剂的构建。热纤梭菌是高效降解木质纤维素的嗜热厌氧菌，是多种木质纤维素生物转化策略的理想底盘菌株，在生物质能源开发中具有重要价值。经过近二十年的研究和开发，针对热纤梭菌已经建立了多种遗传改造技术，并构建了可以生产多种能源分子及化学品的热纤梭菌细胞工厂。本文首先介绍了热纤梭菌及其纤维素降解与利用特性，简述了热纤梭菌的系统生物学研究和遗传改造工具开发的现状，随后重点回顾和总结了热纤梭菌在生产乙醇、丁醇、异丁醇、氢气、乳酸、中/短链脂肪酸酯和可发酵糖等生物能源开发中的合成生物学研究进展。最后对热纤梭菌的合成生物学发展方向进行了展望，并强调了合成生物学技术在未来生物质能源开发中的重要作用。

关键词: 生物能源, 热纤梭菌, 纤维素, 生物燃料, 纤维小体

Abstract:

Biomass, including agricultural and forestry waste, energy plants, and microalgae, possesses both "energy" and "substance" properties, making it a promising renewable resource that can potentially replace fossil fuels. The efficient lignocellulose bioconversion relies on the development of effective biocatalysts. Clostridium thermocellum (also known as Ruminiclostridium thermocellum, Hungateiclostridium thermocellum, and Acetivibrio thermocellus) is a thermophilic anaerobic bacterium that can efficiently degrade lignocellulosic biomass. Over the past two decades, extensive research and development have led to the potential of using C. thermocellum as a cell factory to produce various energy and chemicals from lignocellulose. C. thermocellum has been used to produce ethanol, butanol, isobutanol, hydrogen, lactic acid, medium/short-chain fatty acid esters, and fermentable sugars from lignocellulosic biomass. The degradation and utilization process of lignocellulosic biomass by C. thermocellum mainly involves substrate recognition and hydrolysis through the cellulosome, hydrolysate uptake through ABC transporters, and intracellular metabolism via atypical glycolytic pathways. C. thermocellum possesses dynamic regulation of cellulosome production adapting extracellular substrates, which enables thehigh capability of degrading various lignocellulosic substrates. The cellulosome consists of non-catalytic scaffoldins and multiple enzymatic subunits with distinct catalytic activities and has broad applications in synthetic biology as well as lignocellulose degradation. In addition to lignocellulose refinery, the thermophilic C. thermocellum also has great potential in synthetic biology research under high-temperature conditions. Several genetic manipulation tools have been developed for C. thermocellum, although greater challenges have been encountered compared to model organisms such as Escherichia coli. The genetic tools include homologous recombination technology, Thermotargetron technology, and CRISPR/Cas systems, which enable gene knockout, insertion, replacement, mutation, and expression regulation of target genes in the strain. C. thermocellum has been used as the whole-cell biocatalyst for lignocellulose bioconversion through consolidated bioprocessing (CBP) and consolidated bio-saccharification (CBS). CBS follows the concept of sugar platform construction and shows great potential in real-world applications. The synthetic biology research targeting the CBS strategy still requires future development. For example, we need to explore new genetic tools and thermophilic functional elements for C. thermocellum and improve the efficiency of gene editing. We need to strengthen research on the genetic, physiological, and metabolic aspects of C. thermocellum, and the molecular mechanisms underlying lignocellulose degradation. It is noteworthy that, as a strict anaerobe, C. thermocellum cannot be used as the chassis for catalyzing oxygen-involved reactions. Selecting suitable metabolic pathways and target products will be the focus in future developments of synthetic biology based on C. thermocellum. Therefore, we need to investigate additional target pathways and products for synthetic biology development. In recent years, automation methods and artificial intelligence (AI) technologies are being developed rapidly and have been applied in various synthetic biology research fields. Such technologies may also be employed to promote research on thermophilic and anaerobic microorganisms.

Key words: bioenergy, Clostridium thermocellum, cellulose, biofuels, cellulosome

中图分类号:

Q812

肖艳, 刘亚君, 冯银刚, 崔球. 热纤梭菌在生物质能源开发中的合成生物学研究进展[J]. 合成生物学, 2023, 4(6): 1055-1081.

Yan XIAO, Yajun LIU, Yin′gang FENG, Qiu CUI. Progress in synthetic biology research of Clostridium thermocellum for biomass energy applications[J]. Synthetic Biology Journal, 2023, 4(6): 1055-1081.

图/表 5

参考文献 183

1	LI F H, LI Y W, NOVOSELOV K S, et al. Bioresource upgrade for sustainable energy, environment, and biomedicine[J]. Nano-Micro Letters, 2023, 15(1): 35.
2	LYND L R, BECKHAM G T, GUSS A M, et al. Toward low-cost biological and hybrid biological/catalytic conversion of cellulosic biomass to fuels[J]. Energy & Environmental Science, 2022, 15(3): 938-990.
3	KEASLING J, GARCIA MARTIN H, LEE T S, et al. Microbial production of advanced biofuels[J]. Nature Reviews Microbiology, 2021, 19(11): 701-715.
4	LIU Y J, LI B, FENG Y G, et al. Consolidated bio-saccharification: leading lignocellulose bioconversion into the real world[J]. Biotechnology Advances, 2020, 40: 107535.
5	ZHANG H Y, HAN L J, DONG H M. An insight to pretreatment, enzyme adsorption and enzymatic hydrolysis of lignocellulosic biomass: experimental and modeling studies[J]. Renewable and Sustainable Energy Reviews, 2021, 140: 110758.
6	RE A, MAZZOLI R. Current progress on engineering microbial strains and consortia for production of cellulosic butanol through consolidated bioprocessing[J]. Microbial Biotechnology, 2023, 16(2): 238-261.
7	LYND L R, VAN ZYL W H, MCBRIDE J E, et al. Consolidated bioprocessing of cellulosic biomass: an update[J]. Current Opinion in Biotechnology, 2005, 16(5): 577-583.
8	LIN P P, MI L, MORIOKA A H, et al. Consolidated bioprocessing of cellulose to isobutanol using Clostridium thermocellum [J]. Metabolic Engineering, 2015, 31: 44-52.
9	KOTHARI N, BHAGIA S, PU Y Q, et al. The effect of switchgrass plant cell wall properties on its deconstruction by thermochemical pretreatments coupled with fungal enzymatic hydrolysis or Clostridium thermocellum consolidated bioprocessing[J]. Green Chemistry, 2020, 22(22): 7924-7945.
10	PERIYASAMY S, BEULA ISABEL J, KAVITHA S, et al. Recent advances in consolidated bioprocessing for conversion of lignocellulosic biomass into bioethanol — a review[J]. Chemical Engineering Journal, 2023, 453: 139783.
11	DEMAIN A L, NEWCOMB M, DAVID WU J H. Cellulase, Clostridia, and ethanol[J]. Microbiology and Molecular Biology Reviews, 2005, 69(1): 124-154.
12	OLSON D G, HÖRL M, FUHRER T, et al. Glycolysis without pyruvate kinase in Clostridium thermocellum [J]. Metabolic Engineering, 2017, 39: 169-180.
13	LAMED R, BAYER E A. Cellulosomes from Clostridium thermocellum [J]. Methods in Enzymology, 1988, 160: 472-482.
14	HOLWERDA E K, WORTHEN R S, KOTHARI N, et al. Multiple levers for overcoming the recalcitrance of lignocellulosic biomass[J]. Biotechnology for Biofuels, 2019, 12: 15.
15	ARTZI L, BAYER E A, MORAÏS S. Cellulosomes: bacterial nanomachines for dismantling plant polysaccharides[J]. Nature Reviews Microbiology, 2017, 15(2): 83-95.
16	ZHANG Y H P, LYND L R. Cellulose utilization by Clostridium thermocellum: bioenergetics and hydrolysis product assimilation[J]. Proceedings of the National Academy of Sciences of the United States of America, 2005, 102(20): 7321-7325.
17	YAN F, DONG S, LIU Y J, et al. Deciphering cellodextrin and glucose uptake in Clostridium thermocellum [J]. mBio, 2022, 13(5): e01476-22.
18	MAZZOLI R, OLSON D G. Clostridium thermocellum: a microbial platform for high-value chemical production from lignocellulose[M/OL]//Advances in Applied Microbiology. Amsterdam: Elsevier, 2020: 111-161 [2023-06-01]. .
19	LIU Y J, ZHANG Y D, CHI F, et al. Integrated lactic acid production from lignocellulosic agricultural wastes under thermal conditions[J]. Journal of Environmental Management, 2023, 342: 118281.
20	LIU G L, BU X Y, CHEN C Y, et al. Bioconversion of non-food corn biomass to polyol esters of fatty acid and single-cell oils[J]. Biotechnology for Biofuels and Bioproducts, 2023, 16(1): 9.
21	LIU G L, ZHAO X X, CHEN C, et al. Robust production of pigment-free pullulan from lignocellulosic hydrolysate by a new fungus co-utilizing glucose and xylose[J]. Carbohydrate Polymers, 2020, 241: 116400.
22	LÓPEZ-MONDÉJAR R, ALGORA C, BALDRIAN P. Lignocellulolytic systems of soil bacteria: a vast and diverse toolbox for biotechnological conversion processes[J]. Biotechnology Advances, 2019, 37(6): 107374.
23	XIONG W, REYES L H, MICHENER W E, et al. Engineering cellulolytic bacterium Clostridium thermocellum to co-ferment cellulose- and hemicellulose-derived sugars simultaneously[J]. Biotechnology and Bioengineering, 2018, 115(7): 1755-1763.
24	JOHNSON E A, REESE E T, DEMAIN A. Inhibition of Clostridium thermocellum cellulase by end products of cellulolysis[J]. Journal of Applied Biochemistry, 1982, 4: 64-71.
25	BROWN S D, GUSS A M, KARPINETS T V, et al. Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum [J]. Proceedings of the National Academy of Sciences of the United States of America, 2011, 108(33): 13752-13757.
26	HAMILTON-BREHM S D, MOSHER J J, VISHNIVETSKAYA T, et al. Caldicellulosiruptor obsidiansis sp. nov., an anaerobic, extremely thermophilic, cellulolytic bacterium isolated from obsidian pool, Yellowstone National Park[J]. Applied and Environmental Microbiology, 2010, 76(4): 1014-1020.
27	DESVAUX M, GUEDON E, PETITDEMANGE H. Cellulose catabolism by Clostridium cellulolyticum growing in batch culture on defined medium[J]. Applied and Environmental Microbiology, 2000, 66(6): 2461-2470.
28	TINDALL B J. The names Hungateiclostridium Zhanget al. 2018, Hungateiclostridium thermocellum (Viljoenet al. 1926) Zhanget al. 2018, Hungateiclostridium cellulolyticum (Patelet al. 1980) Zhanget al. 2018, Hungateiclostridium aldrichii (Yanget al. 1990) Zhanget al. 2018, Hungateiclostridium alkalicellulosi (Zhilinaet al. 2006) Zhanget al. 2018, Hungateiclostridium clariflavum (Shiratoriet al. 2009) Zhanget al. 2018, Hungateiclostridium straminisolvens (Katoet al. 2004) Zhanget al. 2018 and Hungateiclostridium saccincola (Koecket al. 2016) Zhanget al. 2018 contravene Rule 51b of the International Code of Nomenclature of Prokaryotes and require replacement names in the genus Acetivibrio Patelet al. 1980[J/OL]. International Journal of Systematic and Evolutionary Microbiology, 2019, 69(12): 3927-3932[2023-06-01]. .
29	AKINOSHO H, YEE K, CLOSE D, et al. The emergence of Clostridium thermocellum as a high utility candidate for consolidated bioprocessing applications[J]. Frontiers in Chemistry, 2014, 2: 66.
30	FEINBERG L, FODEN J, BARRETT T, et al. Complete genome sequence of the cellulolytic thermophile Clostridium thermocellum DSM 1313[J]. Journal of Bacteriology, 2011, 193(11): 2906-2907.
31	TRIPATHI S A, OLSON D G, ARGYROS D A, et al. Development of pyrF-based genetic system for targeted gene deletion in Clostridium thermocellum and creation of a pta mutant[J]. Applied and Environmental Microbiology, 2010, 76(19): 6591-6599.
32	OLSON D G, LYND L R. Transformation of Clostridium thermocellum by electroporation[M/OL]. Methods in enzymology, 2012, 510: 317-330[2023-06-01]. .
33	RILEY L A, JI L X, SCHMITZ R J, et al. Rational development of transformation in Clostridium thermocellum ATCC 27405 via complete methylome analysis and evasion of native restriction-modification systems[J]. Journal of Industrial Microbiology and Biotechnology, 2019, 46(9/10): 1435-1443.
34	BAYER E A, BELAICH J P, SHOHAM Y, et al. The cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides[J]. Annual Review of Microbiology, 2004, 58: 521-554.
35	HONG W, ZHANG J, FENG Y G, et al. The contribution of cellulosomal scaffoldins to cellulose hydrolysis by Clostridium thermocellum analyzed by using thermotargetrons[J]. Biotechnology for Biofuels, 2014, 7: 80.
36	冯银刚, 刘亚君, 崔球. 纤维小体在合成生物学中的应用研究进展[J]. 合成生物学, 2022, 3(1): 138-154.
	FENG Y G, LIU Y J, CUI Q. Research progress in cellulosomes and their applications in synthetic biology[J]. Synthetic Biology Journal, 2022, 3(1): 138-154.
37	ZVERLOV V V, KELLERMANN J, SCHWARZ W H. Functional subgenomics of Clostridium thermocellum cellulosomal genes: identification of the major catalytic components in the extracellular complex and detection of three new enzymes[J]. Proteomics, 2005, 5(14): 3646-3653.
38	KUROKAWA J, HEMJINDA E, ARAI T, et al. Clostridium thermocellum cellulase CelT, a family 9 endoglucanase without an Ig-like domain or family 3c carbohydrate-binding module[J]. Applied Microbiology and Biotechnology, 2002, 59(4): 455-461.
39	ZVERLOV V V, SCHANTZ N, SCHWARZ W H. A major new component in the cellulosome of Clostridium thermocellum is a processive endo-β-1, 4-glucanase producing cellotetraose[J]. FEMS Microbiology Letters, 2005, 249(2): 353-358.
40	YE X H, ZHU Z G, ZHANG C M, et al. Fusion of a family 9 cellulose-binding module improves catalytic potential of Clostridium thermocellum cellodextrin phosphorylase on insoluble cellulose[J]. Applied Microbiology and Biotechnology, 2011, 92(3): 551-560.
41	ANBAR M, GUL O, LAMED R, et al. Improved thermostability of Clostridium thermocellum endoglucanase Cel8A by using consensus-guided mutagenesis[J]. Applied and Environmental Microbiology, 2012, 78(9): 3458-3464.
42	LEIS B, HELD C, BERGKEMPER F, et al. Comparative characterization of all cellulosomal cellulases from Clostridium thermocellum reveals high diversity in endoglucanase product formation essential for complex activity[J]. Biotechnology for Biofuels, 2017, 10: 240.
43	YUAN S F, WU T H, LEE H L, et al. Biochemical characterization and structural analysis of a bifunctional cellulase/xylanase from Clostridium thermocellum [J]. The Journal of Biological Chemistry, 2015, 290(9): 5739-5748.
44	OLSON D G, TRIPATHI S A, GIANNONE R J, et al. Deletion of the Cel48S cellulase from Clostridium thermocellum [J]. Proceedings of the National Academy of Sciences of the United States of America, 2010, 107(41): 17727-17732.
45	LIU Y J, LIU S Y, DONG S, et al. Determination of the native features of the exoglucanase Cel48S from Clostridium thermocellum [J]. Biotechnology for Biofuels, 2018, 11: 6.
46	EIBINGER M, GANNER T, PLANK H, et al. A biological nanomachine at work: watching the cellulosome degrade crystalline cellulose[J]. ACS Central Science, 2020, 6(5): 739-746.
47	DING S Y, BAYER E A. Understanding cellulosome interaction with cellulose by high-resolution imaging[J]. ACS Central Science, 2020, 6(7): 1034-1036.
48	WEI Z, CHEN C, LIU Y J, et al. Alternative σ^I/anti-σ^I factors represent a unique form of bacterial σ/anti-σ complex[J]. Nucleic Acids Research, 2019, 47(11): 5988-5997.
49	SMITH S P, BAYER E A. Insights into cellulosome assembly and dynamics: from dissection to reconstruction of the supramolecular enzyme complex[J]. Current Opinion in Structural Biology, 2013, 23(5): 686-694.
50	NATAF Y, BAHARI L, KAHEL-RAIFER H, et al. Clostridium thermocellum cellulosomal genes are regulated by extracytoplasmic polysaccharides via alternative σ factors[J]. Proceedings of the National Academy of Sciences of the United States of America, 2010, 107(43): 18646-18651.
51	STEVENSON D M, WEIMER P J. Expression of 17 genes in Clostridium thermocellum ATCC 27405 during fermentation of cellulose or cellobiose in continuous culture[J]. Applied and Environmental Microbiology, 2005, 71(8): 4672-4678.
52	KAHEL-RAIFER H, JINDOU S, BAHARI L, et al. The unique set of putative membrane-associated anti-σ factors in Clostridium thermocellum suggests a novel extracellular carbohydrate-sensing mechanism involved in gene regulation[J]. FEMS Microbiology Letters, 2010, 308(1): 84-93.
53	GRINBERG I R, YANIV O, DE ORA L O, et al. Distinctive ligand-binding specificities of tandem PA14 biomass-sensory elements from Clostridium thermocellum and Clostridium clariflavum [J]. Proteins: Structure, Function, and Bioinformatics, 2019, 87(11): 917-930.
54	ORTIZ DE ORA L, LAMED R, LIU Y J, et al. Regulation of biomass degradation by alternative σ factors in cellulolytic clostridia[J]. Scientific Reports, 2018, 8: 11036.
55	CHEN C, DONG S, YU Z L, et al. Essential autoproteolysis of bacterial anti-σ factor RsgI for transmembrane signal transduction[J]. Science Advances, 2023, 9(27): eadg4846.
56	NATAF Y, YARON S, STAHL F, et al. Cellodextrin and laminaribiose ABC transporters in Clostridium thermocellum [J]. Journal of Bacteriology, 2009, 191(1): 203-209.
57	JACOBSON T B, KOROSH T K, STEVENSON D M, et al. In vivo thermodynamic analysis of glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum using ¹³C and ²H tracers[J]. mSystems, 2020, 5(2): e00736-e19.
58	DENG Y, OLSON D G, ZHOU J L, et al. Redirecting carbon flux through exogenous pyruvate kinase to achieve high ethanol yields in Clostridium thermocellum [J]. Metabolic Engineering, 2013, 15: 151-158.
59	XIONG W, LIN P P, MAGNUSSON L, et al. CO₂-fixing one-carbon metabolism in a cellulose-degrading bacterium Clostridium thermocellum [J]. Proceedings of the National Academy of Sciences of the United States of America, 2016, 113(46): 13180-13185.
60	BROWN S D, RAMAN B, MCKEOWN C K, et al. Construction and evaluation of a Clostridium thermocellum ATCC 27405 whole-genome oligonucleotide microarray[J]. Applied Biochemistry and Biotechnology, 2007, 137: 663-674.
61	GOLD N D, MARTIN V J J. Global view of the Clostridium thermocellum cellulosome revealed by quantitative proteomic analysis[J]. Journal of Bacteriology, 2007, 189(19): 6787-6795.
62	ROBERTS S B, GOWEN C M, BROOKS J P, et al. Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production[J]. BMC Systems Biology, 2010, 4: 31.
63	RIEDERER A, TAKASUKA T E, MAKINO S I, et al. Global gene expression patterns in Clostridium thermocellumas as determined by microarray analysis of chemostat cultures on cellulose or cellobiose[J]. Applied and Environmental Microbiology, 2011, 77(4): 1243-1253.
64	WILSON C M, RODRIGUEZ M, JOHNSON C M, et al. Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass[J]. Biotechnology for Biofuels, 2013, 6: 179.
65	HOLWERDA E K, THORNE P G, OLSON D G, et al. The exometabolome of Clostridium thermocellum reveals overflow metabolism at high cellulose loading[J]. Biotechnology for Biofuels, 2014, 7: 155.
66	CHOU W C, MA Q, YANG S H, et al. Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum [J]. Nucleic Acids Research, 2015, 43(10): e67.
67	XU Q, RESCH M G, PODKAMINER K, et al. Dramatic performance of Clostridium thermocellum explained by its wide range of cellulase modalities[J]. Science Advances, 2016, 2(2): e1501254.
68	POUDEL S, GIANNONE R J, RODRIGUEZ M, et al. Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass[J]. Biotechnology for Biofuels, 2017, 10: 14.
69	DASH S, KHODAYARI A, ZHOU J L, et al. Development of a core Clostridium thermocellum kinetic metabolic model consistent with multiple genetic perturbations[J]. Biotechnology for Biofuels, 2017, 10: 108.
70	DUMITRACHE A, KLINGEMAN D M, NATZKE J, et al. Specialized activities and expression differences for Clostridium thermocellum biofilm and planktonic cells[J]. Scientific Reports, 2017, 7: 43583.
71	WHITHAM J M, MOON J W, RODRIGUEZ M JR, et al. Clostridium thermocellum LL 1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics[J]. Biotechnology for Biofuels, 2018, 11: 98.
72	TAFUR RANGEL A E, CROFT T, GONZÁLEZ BARRIOS A F, et al. Transcriptomic analysis of a Clostridium thermocellum strain engineered to utilize xylose: responses to xylose versus cellobiose feeding[J]. Scientific Reports, 2020, 10: 14517.
73	FOSTER C, BOORLA V S, DASH S, et al. Assessing the impact of substrate-level enzyme regulations limiting ethanol titer in Clostridium thermocellum using a core kinetic model[J]. Metabolic Engineering, 2022, 69: 286-301.
74	SCHROEDER W L, KUIL T, VAN MARIS A J A, et al. A detailed genome-scale metabolic model of Clostridium thermocellum investigates sources of pyrophosphate for driving glycolysis[J]. Metabolic Engineering, 2023, 77: 306-322.
75	RAMAN B, PAN C L, HURST G B, et al. Impact of pretreated switchgrass and biomass carbohydrates on Clostridium thermocellum ATCC 27405 cellulosome composition: a quantitative proteomic analysis[J]. PLoS One, 2009, 4(4): e5271.
76	BURTON E, MARTIN V J J. Proteomic analysis of Clostridium thermocellum ATCC 27405 reveals the upregulation of an alternative transhydrogenase-malate pathway and nitrogen assimilation in cells grown on cellulose[J]. Canadian Journal of Microbiology, 2012, 58(12): 1378-1388.
77	WEI H, FU Y, MAGNUSSON L, et al. Comparison of transcriptional profiles of Clostridium thermocellum grown on cellobiose and pretreated yellow poplar using RNA-Seq[J]. Frontiers in Microbiology, 2014, 5: 142.
78	YOAV S, BARAK Y, SHAMSHOUM M, et al. How does cellulosome composition influence deconstruction of lignocellulosic substrates in Clostridium (Ruminiclostridium) thermocellum DSM 1313?[J]. Biotechnology for Biofuels, 2017, 10: 222.
79	DE CAMARGO B R, STEINDORFF A S, SILVA L A DA, et al. Expression profiling of Clostridium thermocellum B8 during the deconstruction of sugarcane bagasse and straw[J]. World Journal of Microbiology and Biotechnology, 2023, 39(4): 105.
80	RAMAN B, MCKEOWN C K, RODRIGUEZ M, et al. Transcriptomic analysis of Clostridium thermocellum ATCC 27405 cellulose fermentation[J]. BMC Microbiology, 2011, 11: 134.
81	RYDZAK T, MCQUEEN P D, KROKHIN O V, et al. Proteomic analysis of Clostridium thermocellum core metabolism: relative protein expression profiles and growth phase-dependent changes in protein expression[J]. BMC Microbiology, 2012, 12: 214.
82	YANG S H, GIANNONE R J, DICE L, et al. Clostridium thermocellum ATCC 27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress[J]. BMC Genomics, 2012, 13: 336.
83	WILSON C M, YANG S H, RODRIGUEZ M, et al. Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress[J]. Biotechnology for Biofuels, 2013, 6: 131.
84	SANDER K, WILSON C M, RODRIGUEZ M, et al. Clostridium thermocellum DSM 1313 transcriptional responses to redox perturbation[J]. Biotechnology for Biofuels, 2015, 8: 211.
85	TIAN L, PEROT S J, STEVENSON D, et al. Metabolome analysis reveals a role for glyceraldehyde 3-phosphate dehydrogenase in the inhibition of C. thermocellum by ethanol[J]. Biotechnology for Biofuels, 2017, 10: 276.
86	LI H Y, PAN Y L, CHANG S, et al. Transcriptomic analysis of Clostridium thermocellum in cellulolytic consortium after artificial reconstruction to enhance ethanol production[J]. BioResources, 2015, 10(4): 7105-7122.
87	LINVILLE J L, RODRIGUEZ M JR, LAND M, et al. Industrial robustness: understanding the mechanism of tolerance for the Populus hydrolysate-tolerant mutant strain of Clostridium thermocellum [J]. PLoS One, 2013, 8(10): e78829.
88	LINVILLE J L, RODRIGUEZ M, BROWN S D, et al. Transcriptomic analysis of Clostridium thermocellum Populus hydrolysate-tolerant mutant strain shows increased cellular efficiency in response to Populus hydrolysate compared to the wild type strain[J]. BMC Microbiology, 2014, 14: 215.
89	THOMPSON R A, LAYTON D S, GUSS A M, et al. Elucidating central metabolic redox obstacles hindering ethanol production in Clostridium thermocellum [J]. Metabolic Engineering, 2015, 32: 207-219.
90	THOMPSON R A, DAHAL S, GARCIA S, et al. Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome[J]. Biotechnology for Biofuels, 2016, 9: 194.
91	GARCIA S, THOMPSON R A, GIANNONE R J, et al. Development of a genome-scale metabolic model of Clostridium thermocellum and its applications for integration of multi-omics datasets and computational strain design[J]. Frontiers in Bioengineering and Biotechnology, 2020, 8: 772.
92	MOHR G, HONG W, ZHANG J E, et al. A targetron system for gene targeting in thermophiles and its application in Clostridium thermocellum [J]. PLoS One, 2013, 8(7): e69032.
93	WALKER J E, LANAHAN A A, ZHENG T Y, et al. Development of both type I-B and type Ⅱ CRISPR/Cas genome editing systems in the cellulolytic bacterium Clostridium thermocellum [J]. Metabolic Engineering Communications, 2020, 10: e00116.
94	GANGULY J, MARTIN-PASCUAL M, VAN KRANENBURG R. CRISPR interference (CRISPRi) as transcriptional repression tool for Hungateiclostridium thermocellum DSM 1313[J]. Microbial Biotechnology, 2020, 13(2): 339-349.
95	GUSS A M, OLSON D G, CAIAZZA N C, et al. Dcm methylation is detrimental to plasmid transformation in Clostridium thermocellum [J]. Biotechnology for Biofuels, 2012, 5(1): 30.
96	ZHANG J, LIU S Y, LI R M, et al. Efficient whole-cell-catalyzing cellulose saccharification using engineered Clostridium thermocellum [J]. Biotechnology for Biofuels, 2017, 10: 124.
97	ARGYROS D A, TRIPATHI S A, BARRETT T F, et al. High ethanol titers from cellulose by using metabolically engineered thermophilic, anaerobic microbes[J]. Applied and Environmental Microbiology, 2011, 77(23): 8288-8294.
98	KWON S W, PAARI K A, MALAVIYA A, et al. Synthetic biology tools for genome and transcriptome engineering of solventogenic Clostridium [J]. Frontiers in Bioengineering and Biotechnology, 2020, 8: 282.
99	KUEHNE S A, MINTON N P. ClosTron-mediated engineering of Clostridium [J]. Bioengineered, 2012, 3(4): 247-254.
100	HEAP J T, PENNINGTON O J, CARTMAN S T, et al. The ClosTron: a universal gene knock-out system for the genus Clostridium [J]. Journal of Microbiological Methods, 2007, 70(3): 452-464.
101	PARK S K, MOHR G, YAO J, et al. Group Ⅱ intron-like reverse transcriptases function in double-strand break repair[J]. Cell, 2022, 185(20): 3671-3688.e23.
102	CUI G Z, HONG W, ZHANG J, et al. Targeted gene engineering in Clostridium cellulolyticum H10 without methylation[J]. Journal of Microbiological Methods, 2012, 89(3): 201-208.
103	ENYEART P J, CHIRIELEISON S M, DAO M N, et al. Generalized bacterial genome editing using mobile group Ⅱ introns and Cre-lox[J]. Molecular Systems Biology, 2013, 9: 685.
104	ADLI M. The CRISPR tool kit for genome editing and beyond[J]. Nature Communications, 2018, 9: 1911.
105	OLSON D G, MCBRIDE J E, SHAW A JOE, et al. Recent progress in consolidated bioprocessing[J]. Current Opinion in Biotechnology, 2012, 23(3): 396-405.
106	MCALLISTER K N, SORG J A. CRISPR genome editing systems in the genus Clostridium: a timely advancement[J]. Journal of Bacteriology, 2019, 201(16): e00219.
107	PYNE M E, BRUDER M R, MOO-YOUNG M, et al. Harnessing heterologous and endogenous CRISPR-Cas machineries for efficient markerless genome editing in Clostridium [J]. Scientific Reports, 2016, 6: 25666.
108	RICHTER H, ZOEPHEL J, SCHERMULY J, et al. Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis [J]. Nucleic Acids Research, 2012, 40(19): 9887-9896.
109	RICHTER H, ROMPF J, WIEGEL J, et al. Fragmentation of the CRISPR-Cas Type I-B signature protein Cas8b[J]. Biochimica et Biophysica Acta (BBA)-General Subjects, 2017, 1861(11): 2993-3000.
110	ZHAO H, SUN Y J, PETERS J M, et al. Depletion of undecaprenyl pyrophosphate phosphatases disrupts cell envelope biogenesis in Bacillus subtilis [J]. Journal of Bacteriology, 2016, 198: 2925-2935.
111	LIU X, GALLAY C, KJOS M, et al. High-throughput CRISPRi phenotyping identifies new essential genes in Streptococcus pneumoniae [J]. Molecular Systems Biology, 2017, 13(5): 931.
112	WANG M, HAN J, DUNN J B, et al. Well-to-wheels energy use and greenhouse gas emissions of ethanol from corn, sugarcane and cellulosic biomass for US use[J]. Environmental Research Letters, 2012, 7(4): 045905.
113	LI J J, ZHANG Y L, YANG Y L, et al. Life cycle assessment and techno-economic analysis of ethanol production via coal and its competitors: a comparative study[J]. Applied Energy, 2022, 312: 118791.
114	KANNUCHAMY S, MUKUND N, SALEENA L M. Genetic engineering of Clostridium thermocellum DSM 1313 for enhanced ethanol production[J]. BMC Biotechnology, 2016, 16(): 34.
115	DIEN B S, COTTA M A, JEFFRIES T W. Bacteria engineered for fuel ethanol production: current status[J]. Applied Microbiology and Biotechnology, 2003, 63(3): 258-266.
116	RYDZAK T, LYND L R, GUSS A M. Elimination of formate production in Clostridium thermocellum [J]. Journal of Industrial Microbiology & Biotechnology, 2015, 42(9): 1263-1272.
117	RYDZAK T, GARCIA D, STEVENSON D M, et al. Deletion of Type Ⅰ glutamine synthetase deregulates nitrogen metabolism and increases ethanol production in Clostridium thermocellum [J]. Metabolic Engineering, 2017, 41: 182-191.
118	BISWAS R, ZHENG T Y, OLSON D G, et al. Elimination of hydrogenase active site assembly blocks H₂ production and increases ethanol yield in Clostridium thermocellum [J]. Biotechnology for Biofuels, 2015, 8: 20.
119	LI H F, KNUTSON B L, NOKES S E, et al. Metabolic control of Clostridium thermocellum via inhibition of hydrogenase activity and the glucose transport rate[J]. Applied Microbiology and Biotechnology, 2012, 93(4): 1777-1784.
120	LO J, OLSON D G, MURPHY S J L, et al. Engineering electron metabolism to increase ethanol production in Clostridium thermocellum [J]. Metabolic Engineering, 2017, 39: 71-79.
121	ZHENG T Y, OLSON D G, TIAN L, et al. Cofactor specificity of the bifunctional alcohol and aldehyde dehydrogenase (AdhE) in wild-type and mutant Clostridium thermocellum and Thermoanaerobacterium saccharolyticum [J]. Journal of Bacteriology, 2015, 197(15): 2610-2619.
122	TIAN L, PAPANEK B, OLSON D G, et al. Simultaneous achievement of high ethanol yield and titer in Clostridium thermocellum [J]. Biotechnology for Biofuels, 2016, 9: 116.
123	HOLWERDA E K, OLSON D G, RUPPERTSBERGER N M, et al. Metabolic and evolutionary responses of Clostridium thermocellum to genetic interventions aimed at improving ethanol production[J]. Biotechnology for Biofuels, 2020, 13: 40.
124	WILLIAMS T I, COMBS J C, LYNN B C, et al. Proteomic profile changes in membranes of ethanol-tolerant Clostridium thermocellum [J]. Applied Microbiology and Biotechnology, 2007, 74(2): 422-432.
125	KIM S K, WESTPHELING J. Engineering a spermidine biosynthetic pathway in Clostridium thermocellum results in increased resistance to furans and increased ethanol production[J]. Metabolic Engineering, 2018, 49: 267-274.
126	HERRING C D, KENEALY W R, SHAW A JOE, et al. Strain and bioprocess improvement of a thermophilic anaerobe for the production of ethanol from wood[J]. Biotechnology for Biofuels, 2016, 9: 125.
127	BERI D, HERRING C D, BLAHOVA S, et al. Coculture with hemicellulose-fermenting microbes reverses inhibition of corn fiber solubilization by Clostridium thermocellum at elevated solids loadings[J]. Biotechnology for Biofuels, 2021, 14(1): 24.
128	CHEN S T, XU Z X, DING B N, et al. Big data mining, rational modification, and ancestral sequence reconstruction inferred multiple xylose isomerases for biorefinery[J]. Science Advances, 2023, 9(5): eadd8835.
129	CHEN X W, KUHN E, JENNINGS E W, et al. DMR (deacetylation and mechanical refining) processing of corn stover achieves high monomeric sugar concentrations (230 g·L^-1) during enzymatic hydrolysis and high ethanol concentrations (>10% v/v) during fermentation without hydrolysate purification or concentration[J]. Energy & Environmental Science, 2016, 9(4): 1237-1245.
130	GHOSH I N, LANDICK R. OptSSeq: high-throughput sequencing readout of growth enrichment defines optimal gene expression elements for homoethanologenesis[J]. ACS Synthetic Biology, 2016, 5(12): 1519-1534.
131	KHANA D B, CALLAGHAN M M, AMADOR-NOGUEZ D. Novel computational and experimental approaches for investigating the thermodynamics of metabolic networks[J]. Current Opinion in Microbiology, 2022, 66: 21-31.
132	BHANDIWAD A, SHAW A J, GUSS A, et al. Metabolic engineering of Thermoanaerobacterium saccharolyticum for n-butanol production[J]. Metabolic Engineering, 2014, 21: 17-25.
133	KELLER M W, LIPSCOMB G L, LODER A J, et al. A hybrid synthetic pathway for butanol production by a hyperthermophilic microbe[J]. Metabolic Engineering, 2015, 27: 101-106.
134	TIAN L, CONWAY P M, CERVENKA N D, et al. Metabolic engineering of Clostridium thermocellum for n-butanol production from cellulose[J]. Biotechnology for Biofuels, 2019, 12: 186.
135	TIAN L, CERVENKA N D, LOW A M, et al. A mutation in the AdhE alcohol dehydrogenase of Clostridium thermocellum increases tolerance to several primary alcohols, including isobutanol, n-butanol and ethanol[J]. Scientific Reports, 2019, 9: 1736.
136	PINTO T, FLORES-ALSINA X, GERNAEY K V, et al. Alone or together? A review on pure and mixed microbial cultures for butanol production[J]. Renewable and Sustainable Energy Reviews, 2021, 147: 111244.
137	KIYOSHI K, FURUKAWA M, SEYAMA T, et al. Butanol production from alkali-pretreated rice straw by co-culture of Clostridium thermocellum and Clostridium saccharoperbutylacetonicum [J]. Bioresource Technology, 2015, 186: 325-328.
138	WEN Z Q, WU M B, LIN Y J, et al. A novel strategy for sequential co-culture of Clostridium thermocellum and Clostridium beijerinckii to produce solvents from alkali extracted corn cobs[J]. Process Biochemistry, 2014, 49(11): 1941-1949.
139	BEGUM S, DAHMAN Y. Enhanced biobutanol production using novel clostridial fusants in simultaneous saccharification and fermentation of green renewable agriculture residues[J]. Biofuels, Bioproducts and Biorefining, 2015, 9(5): 529-544.
140	LAKSHMI N M, BINOD P, SINDHU R, et al. Microbial engineering for the production of isobutanol: current status and future directions[J]. Bioengineered, 2021, 12(2): 12308-12321.
141	HON S, HOLWERDA E K, WORTHEN R S, et al. Expressing the Thermoanaerobacterium saccharolyticum pforA in engineered Clostridium thermocellum improves ethanol production[J]. Biotechnology for Biofuels, 2018, 11: 242.
142	LIN P P, RABE K S, TAKASUMI J L, et al. Isobutanol production at elevated temperatures in thermophilic Geobacillus thermoglucosidasius [J]. Metabolic Engineering, 2014, 24: 1-8.
143	DONG H J, ZHAO C H, ZHANG T R, et al. A systematically chromosomally engineered Escherichia coli efficiently produces butanol[J]. Metabolic Engineering, 2017, 44: 284-292.
144	ZHAO C H, SINUMVAYO J P, ZHANG Y P, et al. Design and development of a "Y-shaped" microbial consortium capable of simultaneously utilizing biomass sugars for efficient production of butanol[J]. Metabolic Engineering, 2019, 55: 111-119.
145	ZHAN Y Y, XU Y, LU X C, et al. Metabolic engineering of Bacillus licheniformis for sustainable production of isobutanol[J]. ACS Sustainable Chemistry & Engineering, 2021, 9(51): 17254-17265.
146	BAEZ A, CHO K M, LIAO J C. High-flux isobutanol production using engineered Escherichia coli: a bioreactor study with in situ product removal[J]. Applied Microbiology and Biotechnology, 2011, 90(5): 1681-1690.
147	DODDS P E, STAFFELL I, HAWKES A D, et al. Hydrogen and fuel cell technologies for heating: a review[J]. International Journal of Hydrogen Energy, 2015, 40(5): 2065-2083.
148	OLADOKUN O, AHMAD A, ABDULLAH T A T, et al. Biohydrogen production from Imperata cylindrica bio-oil using non-stoichiometric and thermodynamic model[J]. International Journal of Hydrogen Energy, 2017, 42(14): 9011-9023.
149	LEVIN D B, ISLAM R, CICEK N, et al. Hydrogen production by Clostridium thermocellum 27405 from cellulosic biomass substrates[J]. International Journal of Hydrogen Energy, 2006, 31(11): 1496-1503.
150	TIAN Q Q, LIANG L, ZHU M J. Enhanced biohydrogen production from sugarcane bagasse by Clostridium thermocellum supplemented with CaCO₃ [J]. Bioresource Technology, 2015, 197: 422-428.
151	KIM D H, SHIN H S, KIM S H. Enhanced H₂ fermentation of organic waste by CO₂ sparging[J]. International Journal of Hydrogen Energy, 2012, 37(20): 15563-15568.
152	KIM C, WOLF I, DOU C, et al. Coupling gas purging with inorganic carbon supply to enhance biohydrogen production with Clostridium thermocellum [J]. Chemical Engineering Journal, 2023, 456: 141028.
153	LEE H S, VERMAAS W F J, RITTMANN B E. Biological hydrogen production: prospects and challenges[J]. Trends in Biotechnology, 2010, 28(5): 262-271.
154	LI Q, LIU C Z. Co-culture of Clostridium thermocellum and Clostridium thermosaccharolyticum for enhancing hydrogen production via thermophilic fermentation of cornstalk waste[J]. International Journal of Hydrogen Energy, 2012, 37(14): 10648-10654.
155	AN Q, BU J, CHENG J R, et al. Biological saccharification by Clostridium thermocellum and two-stage hydrogen and methane production from hydrogen peroxide-acetic acid pretreated sugarcane bagasse[J]. International Journal of Hydrogen Energy, 2020, 45(55): 30211-30221.
156	ALVES DE OLIVEIRA R, KOMESU A, ROSSELL C E VAZ, et al. Challenges and opportunities in lactic acid bioprocess design—from economic to production aspects[J]. Biochemical Engineering Journal, 2018, 133: 219-239.
157	TARRARAN L, MAZZOLI R. Alternative strategies for lignocellulose fermentation through lactic acid bacteria: the state of the art and perspectives[J]. FEMS Microbiology Letters, 2018, 365(15): fny126.
158	LO J, ZHENG T Y, HON S, et al. The bifunctional alcohol and aldehyde dehydrogenase gene, adhE, is necessary for ethanol production in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum [J]. Journal of Bacteriology, 2015, 197(8): 1386-1393.
159	MAZZOLI R, OLSON D G, LYND L R. Construction of lactic acid overproducing Clostridium thermocellum through enhancement of lactate dehydrogenase expression[J]. Enzyme and Microbial Technology, 2020, 141: 109645.
160	SUBRAMANIAN M R, TALLURI S, CHRISTOPHER L P. Production of lactic acid using a new homofermentative Enterococcus faecalis isolate[J]. Microbial Biotechnology, 2015, 8(2): 221-229.
161	WEN Z Q, LEDESMA-AMARO R, LU M R, et al. Combined evolutionary engineering and genetic manipulation improve low pH tolerance and butanol production in a synthetic microbial Clostridium community[J]. Biotechnology and Bioengineering, 2020, 117(7): 2008-2022.
162	MAZZOLI R, OLSON D G, CONCU A M, et al. In vivo evolution of lactic acid hyper-tolerant Clostridium thermocellum [J]. New Biotechnology, 2022, 67: 12-22.
163	KRUIS A J, BOHNENKAMP A C, PATINIOS C, et al. Microbial production of short and medium chain esters: enzymes, pathways, and applications[J]. Biotechnology Advances, 2019, 37(7): 107407.
164	RODRIGUEZ G M, TASHIRO Y, ATSUMI S. Expanding ester biosynthesis in Escherichia coli [J]. Nature Chemical Biology, 2014, 10(4): 259-265.
165	SEO H, LEE J W, GARCIA S, et al. Single mutation at a highly conserved region of chloramphenicol acetyltransferase enables isobutyl acetate production directly from cellulose by Clostridium thermocellum at elevated temperatures[J]. Biotechnology for Biofuels, 2019, 12: 245.
166	SEO H, NICELY P N, TRINH C T. Endogenous carbohydrate esterases of Clostridium thermocellum are identified and disrupted for enhanced isobutyl acetate production from cellulose[J]. Biotechnology and Bioengineering, 2020, 117(7): 2223-2236.
167	SEO H, LEE J W, GIANNONE R J, et al. Engineering promiscuity of chloramphenicol acetyltransferase for microbial designer ester biosynthesis[J]. Metabolic Engineering, 2021, 66: 179-190.
168	SEO H, SINGH P, WYMAN C E, et al. Rewiring metabolism of Clostridium thermocellum for consolidated bioprocessing of lignocellulosic biomass poplar to produce short-chain esters[J]. Bioresource Technology, 2023, 384: 129263.
169	LIU S Y, LIU Y J, FENG Y G, et al. Construction of consolidated bio-saccharification biocatalyst and process optimization for highly efficient lignocellulose solubilization[J]. Biotechnology for Biofuels, 2019, 12: 35.
170	QI K, CHEN C, YAN F, et al. Coordinated β-glucosidase activity with the cellulosome is effective for enhanced lignocellulose saccharification[J]. Bioresource Technology, 2021, 337: 125441.
171	OLGUIN-MACIEL E, SINGH A, CHABLE-VILLACIS R, et al. Consolidated bioprocessing, an innovative strategy towards sustainability for biofuels production from crop residues: an overview[J]. Agronomy, 2020, 10(11): 1834.
172	PATEL A, SHAH A R. Integrated lignocellulosic biorefinery: gateway for production of second generation ethanol and value added products[J]. Journal of Bioresources and Bioproducts, 2021, 6(2): 108-128.
173	ARORA R, SINGH P, SARANGI P K, et al. A critical assessment on scalable technologies using high solids loadings in lignocellulose biorefinery: challenges and solutions[J/OL]. Critical Reviews in Biotechnology, 2023[2023-06-01]. .
174	REIS C E R, LIBARDI N, BENTO H B S, et al. Process strategies to reduce cellulase enzyme loading for renewable sugar production in biorefineries[J]. Chemical Engineering Journal, 2023, 451: 138690.
175	ICHIKAWA S, ICHIHARA M, ITO T, et al. Glucose production from cellulose through biological simultaneous enzyme production and saccharification using recombinant bacteria expressing the β-glucosidase gene[J]. Journal of Bioscience and Bioengineering, 2019, 127(3): 340-344.
176	DASH S, OLSON D G, CHAN S H J, et al. Thermodynamic analysis of the pathway for ethanol production from cellobiose in Clostridium thermocellum [J]. Metabolic Engineering, 2019, 55: 161-169.
177	HON S, OLSON D G, HOLWERDA E K, et al. The ethanol pathway from Thermoanaerobacterium saccharolyticum improves ethanol production in Clostridium thermocellum [J]. Metabolic Engineering, 2017, 42: 175-184.
178	SANDER K, ASANO K G, BHANDARI D, et al. Targeted redox and energy cofactor metabolomics in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum [J]. Biotechnology for Biofuels, 2017, 10: 270.
179	CUI J X, OLSON D G, LYND L R. Characterization of the Clostridium thermocellum AdhE, NfnAB, ferredoxin and Pfor proteins for their ability to support high titer ethanol production in Thermoanaerobacterium saccharolyticum [J]. Metabolic Engineering, 2019, 51: 32-42.
180	CHIRANIA P, HOLWERDA E K, GIANNONE R J, et al. Metaproteomics reveals enzymatic strategies deployed by anaerobic microbiomes to maintain lignocellulose deconstruction at high solids[J]. Nature Communications, 2022, 13: 3870.
181	BALCH M L, HOLWERDA E K, DAVIS M F, et al. Lignocellulose fermentation and residual solids characterization for senescent switchgrass fermentation by Clostridium thermocellum in the presence and absence of continuous in situ ball-milling[J]. Energy & Environmental Science, 2017, 10(5): 1252-1261.
182	YAN F, WEI R, CUI Q, et al. Thermophilic whole-cell degradation of polyethylene terephthalate using engineered Clostridium thermocellum [J]. Microbial Biotechnology, 2021, 14(2): 374-385.
183	XIAO Y, DONG S, LIU Y J, et al. Key roles of β-glucosidase BglA for the catabolism of both laminaribiose and cellobiose in the lignocellulolytic bacterium Clostridium thermocellum [J]. International Journal of Biological Macromolecules, 2023, 250: 126226.

热纤梭菌菌株	主要方法	研究内容、结果或结论	年份	文献
F7 (VKMB 2203)	蛋白质组	在热纤梭菌基因组草图中发现了超过71个编码纤维小体蛋白的基因；蛋白质组鉴定了纤维小体中含量较高的13个组分	2005	[37]
ATCC 27405	转录组	建立了有效的微阵列方法用于热纤梭菌的转录组研究	2007	[60]
ATCC 27405	蛋白质组	多通过蛋白质组分析了热纤梭菌纤维小体的组分以及在纤维素和二糖上生长时的变化	2007	[61]
ATCC 27405	构建代谢模型	构建了基因组尺度代谢模型iSR432，包含了577个反应	2010	[62]
DSM 1313	基因组	热纤梭菌DSM1313基因组测序结果	2011	[30]
ATCC 27405	转录组	对比纤维素和纤维二糖稳态培养的基因表达对比分析。3189个基因中检测到2846个，分析了底物依赖的基因表达变化	2011	[63]
ATCC 27405	转录组	在稀酸预处理的杨树和柳枝稷上生长的不同时间（12 h和37 h）的热纤梭菌的基因转录	2013	[64]
DSM 1313	代谢组	高纤维素载量（50～100 g/L）下的热纤梭菌胞外代谢产物分析	2014	[65]
ATCC 27405	通过机器学习预测转录单元	根据转录组数据，使用机器学习方法预测了2590个转录单元，44%有多基因	2015	[66]
DSM 1313突变株	转录组，蛋白质组	在热纤梭菌中敲除不同脚架蛋白后，检测热纤梭菌的各种基因表达变化，揭示各种脚架蛋白的重要性以及与其他基因之间的耦联关系	2016	[67]
ATCC 27405	转录组，代谢组，蛋白质组	稀酸预处理的柳枝稷上生长的不同时间下三种组学的情况，分析在降解过程中抑制物造成的代谢变化	2017	[68]
DSM 1313	构建代谢模型	建立基因组尺度代谢模型iCth446，并在此基础上构建了核心代谢动力学模型k-ctherm118	2017	[69]
ATCC 27405	转录组，蛋白质组	分析了纤维素附着细胞和游动细胞的基因表达和蛋白差异	2017	[70]
DSM1313 Δhpt ΔhydG Δldh Δpfl Δpta-ack	转录组，代谢组	分析了当时已知的产乙醇最高的菌株在不同pH稳态培养下的代谢物和基因表达变化	2018	[71]
KJ335(整合了木糖利用基因的工程菌株，来自DSM 1313)	转录组	分析了木糖利用工程菌株的在木糖和纤维二糖上的转录组差异，揭示了木糖的转运与代谢相关基因以及热纤梭菌趋化与运动相关基因的表达变化	2020	[72]
DSM 1313	代谢流分析、构建动力学模型	基于代谢流分析建立核心代谢动力学模型k-ctherm138，鉴定了限制乙醇生产的67种底物水平抑制机制	2022	[73]
DSM 1313	构建代谢模型	构建基因组尺度代谢模型iCTH669，包含了913个代谢反应，837种代谢物，669个基因，模型的可靠性得到巨大的提升	2023	[74]

热纤梭菌菌株	主要方法	研究内容、结果或结论	年份	文献
F7 (VKMB 2203)	蛋白质组	在热纤梭菌基因组草图中发现了超过71个编码纤维小体蛋白的基因；蛋白质组鉴定了纤维小体中含量较高的13个组分	2005	[37]
ATCC 27405	转录组	建立了有效的微阵列方法用于热纤梭菌的转录组研究	2007	[60]
ATCC 27405	蛋白质组	多通过蛋白质组分析了热纤梭菌纤维小体的组分以及在纤维素和二糖上生长时的变化	2007	[61]
ATCC 27405	构建代谢模型	构建了基因组尺度代谢模型iSR432，包含了577个反应	2010	[62]
DSM 1313	基因组	热纤梭菌DSM1313基因组测序结果	2011	[30]
ATCC 27405	转录组	对比纤维素和纤维二糖稳态培养的基因表达对比分析。3189个基因中检测到2846个，分析了底物依赖的基因表达变化	2011	[63]
ATCC 27405	转录组	在稀酸预处理的杨树和柳枝稷上生长的不同时间（12 h和37 h）的热纤梭菌的基因转录	2013	[64]
DSM 1313	代谢组	高纤维素载量（50～100 g/L）下的热纤梭菌胞外代谢产物分析	2014	[65]
ATCC 27405	通过机器学习预测转录单元	根据转录组数据，使用机器学习方法预测了2590个转录单元，44%有多基因	2015	[66]
DSM 1313突变株	转录组，蛋白质组	在热纤梭菌中敲除不同脚架蛋白后，检测热纤梭菌的各种基因表达变化，揭示各种脚架蛋白的重要性以及与其他基因之间的耦联关系	2016	[67]
ATCC 27405	转录组，代谢组，蛋白质组	稀酸预处理的柳枝稷上生长的不同时间下三种组学的情况，分析在降解过程中抑制物造成的代谢变化	2017	[68]
DSM 1313	构建代谢模型	建立基因组尺度代谢模型iCth446，并在此基础上构建了核心代谢动力学模型k-ctherm118	2017	[69]
ATCC 27405	转录组，蛋白质组	分析了纤维素附着细胞和游动细胞的基因表达和蛋白差异	2017	[70]
DSM1313 Δhpt ΔhydG Δldh Δpfl Δpta-ack	转录组，代谢组	分析了当时已知的产乙醇最高的菌株在不同pH稳态培养下的代谢物和基因表达变化	2018	[71]
KJ335(整合了木糖利用基因的工程菌株，来自DSM 1313)	转录组	分析了木糖利用工程菌株的在木糖和纤维二糖上的转录组差异，揭示了木糖的转运与代谢相关基因以及热纤梭菌趋化与运动相关基因的表达变化	2020	[72]
DSM 1313	代谢流分析、构建动力学模型	基于代谢流分析建立核心代谢动力学模型k-ctherm138，鉴定了限制乙醇生产的67种底物水平抑制机制	2022	[73]
DSM 1313	构建代谢模型	构建基因组尺度代谢模型iCTH669，包含了913个代谢反应，837种代谢物，669个基因，模型的可靠性得到巨大的提升	2023	[74]

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热纤梭菌在生物质能源开发中的合成生物学研究进展

Progress in synthetic biology research of Clostridium thermocellum for biomass energy applications

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