Progress and perspectives on developing Zymomonas mobilis as a chassis cell

doi:10.12211/2096-8280.2020-071

Synthetic Biology Journal ›› 2021, Vol. 2 ›› Issue (1): 59-90.DOI: 10.12211/2096-8280.2020-071

• Invited Review • Previous Articles Next Articles

Progress and perspectives on developing Zymomonas mobilis as a chassis cell

Yongfu YANG¹, Binan GENG¹, Haoyue SONG¹, Qiaoning HE¹, Mingxiong HE², Jie BAO³, Fengwu BAI⁴, Shihui YANG¹

^1.State Key Laboratory of Biocatalysis and Enzyme Engineering，Environmental Microbial Technology Center of Hubei Province，School of Life Sciences，Hubei University，Wuhan 430062，Hubei，China
^2.Biomass Energy Technology Research Centre，Biogas Institute of Ministry of Agriculture，Chengdu 610041，Sichuan，China
^3.State Key Laboratory of Bioreactor Engineering，School of Biotechnology，East China University of Science and Technology，Shanghai 200237，China
^4.State Key Laboratory of Microbial Metabolism，School of Life Sciences and Biotechnology，Shanghai Jiao Tong University，Shanghai 200240，China

Received:2020-07-05 Revised:2020-10-01 Online:2021-03-12 Published:2021-03-22
Contact: Fengwu BAI, Shihui YANG

运动发酵单胞菌底盘细胞研究现状及展望

杨永富¹, 耿碧男¹, 宋皓月¹, 何桥宁¹, 何明雄², 鲍杰³, 白凤武⁴, 杨世辉¹

^1.湖北大学生命科学学院，省部共建生物催化与酶工程国家重点实验室，湖北省环境微生物工程技术研究中心，湖北武汉　430062
^2.农业农村部沼气科学研究所，生物质能技术研究中心，四川成都　610041
^3.华东理工大学生物工程学院，生物反应器工程国家重点实验室，上海　200237
^4.上海交通大学生命科学技术学院，微生物代谢国家重点实验室，上海　200240

通讯作者: 白凤武,杨世辉
作者简介:杨永富（1994—），男，博士研究生，研究方向为微生物系统生物学与合成生物学。E-mail：yongfu.yang@stu.hubu.edu.cn
耿碧男（1995—），女，博士研究生，研究方向为微生物基因组优化及合成生物学。E-mail：binangeng@stu.hubu.edu.cn
白凤武（1964—），男，博士,教授，研究方向为生物质资源生物炼制及微生物代谢工程。E-mail：fwbai@sjtu.edu.cn
杨世辉（1971—），男，博士,教授，研究方向为微生物代谢工程与合成生物学。E-mail：Shihui.Yang@hubu.edu.cn
基金资助:
国家自然科学基金(21978071);国家重点研发计划(2018YFA0900300);浙江省引进培育领军型创新创业团队项目(2018R01014)

Abstract

Abstract:

Zymomonas mobilis, the only microorganism known to use the Entner-Doudoroff (ED) pathway anaerobically, can produce ethanol naturally from glucose, fructose and sucrose with many desirable traits such as ethanol production at high rate and yield and merit with biosafety (generally regarded as safe, GRAS), which has attracted more attention to be engineered as cell factories to produce biofuels and other bio-based products from lignocellulosic biomass. With the rapid development of novel technologies such as next-generation sequencing (NGS) and CRISPR-Cas genome editing as well as the accumulation of knowledge from studies on its physiology and modifications through metabolic engineering and systems biology, it is necessary to summarize accomplishments achieved recently to further explore the advantages of Z. mobilis, expediting the development and deployment of the robust synthetic microbial chass for the goals of "build to understand" and "build to apply" in the systems and synthetic biology era. In this review, we critically comment on the unique physiological characteristics of Z. mobilis and its potentials as a synthetic chassis to be engineered as microbial cell factories for producing diverse biochemicals economically, with a focus on the advances and challenges of developing efficient and effective tools and techniques for engineering this bacterium, taking advantages of methodologies developed with system biology and synthetic biology as well as metabolic engineering. We also prospect on future research for developing Z. mobilis as an attractive microbial chassis to be able to fix CO₂ and N₂ for biochemical production through genome optimization and metabolic engineering to advance the principles of synthetic biology and explore its potentials on biotechnological applications, which need unceasing effort to improve, develop and deploy efficient and effective genome editing tools, strategies for fine-tuning metabolic and regulatory pathways timely and spatially, as well as automatic high-throughput screening and quantification approaches.

Key words: Zymomonas mobilis, synthetics biology, chassis cell, systems biology, gene editing, non-model species

摘要：

运动发酵单胞菌（Zymomonas mobilis）是目前已知唯一能够在厌氧条件下利用Entner-Doudoroff（ED）途径代谢葡萄糖、果糖和蔗糖产乙醇的革兰氏阴性细菌，具有乙醇发酵速率高和对糖表观收率高、乙醇耐受性好及生物安全（generally regarded as safe，GRAS）等特点。基于合成生物学方法和代谢工程改造，可以作为纤维素乙醇及其他生物基产品生物炼制的细胞工厂。本文综述了运动发酵单胞菌独特的生理特点及其作为细胞工厂在不同领域的应用，重点介绍了构建运动发酵单胞菌作为底盘细胞，实现工业产品规模化经济生产涉及的系统生物学、合成生物学及代谢工程改造相关方法、技术与工具等方面的进展及瓶颈。同时探讨了持续开发、完善、应用高效精准的基因编辑技术、代谢途径精准时空调控方法及高通量自动筛选检测手段，在运动发酵单胞菌基因组精简优化以及生物固碳与固氮等方面取得的突破，推动合成生物学理论研究和实践应用的发展。

关键词: 运动发酵单胞菌, 合成生物学, 底盘细胞, 系统生物学, 基因编辑, 非模式微生物

CLC Number:

Q939.97

Yongfu YANG, Binan GENG, Haoyue SONG, Qiaoning HE, Mingxiong HE, Jie BAO, Fengwu BAI, Shihui YANG. Progress and perspectives on developing Zymomonas mobilis as a chassis cell[J]. Synthetic Biology Journal, 2021, 2(1): 59-90.

杨永富, 耿碧男, 宋皓月, 何桥宁, 何明雄, 鲍杰, 白凤武, 杨世辉. 运动发酵单胞菌底盘细胞研究现状及展望[J]. 合成生物学, 2021, 2(1): 59-90.

Figures/Tables 7

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化合物	产量	应用范围	文献
葡萄糖酸（gluconic acid）	541 g·L^-1	蛋白凝固剂和食品防腐剂	[75]
聚羟基丁酸（PHB）	0.7% DCW(DCW为细胞干重）	可降解生物塑料	[74]
L-乳酸（L-lactate）	10.8 g·L^-1	医疗，食品，化妆品，化工原料等	[73]
D-乳酸（D-lactate）	65.6 g·L^-1	医疗，食品，化妆品，化工原料等	[70]
果聚糖（levan）	40.2 g·L^-1	加工食品，常作为乳化稳定剂、气泡稳定剂	[72]
丁二酸（succinate）	2.8 g·L^-1	C₄ 平台化合物，有机化工原料及中间体	[71]
乙醇（ethanol）	136 g·L^-1	生物能源	[69]
山梨醇（sorbitol）	135.7 g·L^-1	保湿剂，软化剂，甜味剂	[68]
2,3-丁二醇（2,3-butanediol）	120 g·L^-1	平台大宗化合物，液体燃料	[65]
乙醛（acetaldehyde）	4.0 g·L^-1	化学工业平台化合物，重要的香味剂	[66]
乙烯（ethylene）	12.83 nmol/mL(OD₆₀₀)	基础化工原料，可用于合成橡胶、纤维、聚烯烃和聚氯乙烯塑料等	[67]
乳糖酸（lactobionic acid）	182.7 g·L^-1	精细化学品，医药中间体，材料中间体等	[64]
异丁醇（isobutanol）	4 g·L^-1	可再生生物能源，异丁烯前体物	[63]

化合物	产量	应用范围	文献
葡萄糖酸（gluconic acid）	541 g·L^-1	蛋白凝固剂和食品防腐剂	[75]
聚羟基丁酸（PHB）	0.7% DCW(DCW为细胞干重）	可降解生物塑料	[74]
L-乳酸（L-lactate）	10.8 g·L^-1	医疗，食品，化妆品，化工原料等	[73]
D-乳酸（D-lactate）	65.6 g·L^-1	医疗，食品，化妆品，化工原料等	[70]
果聚糖（levan）	40.2 g·L^-1	加工食品，常作为乳化稳定剂、气泡稳定剂	[72]
丁二酸（succinate）	2.8 g·L^-1	C₄ 平台化合物，有机化工原料及中间体	[71]
乙醇（ethanol）	136 g·L^-1	生物能源	[69]
山梨醇（sorbitol）	135.7 g·L^-1	保湿剂，软化剂，甜味剂	[68]
2,3-丁二醇（2,3-butanediol）	120 g·L^-1	平台大宗化合物，液体燃料	[65]
乙醛（acetaldehyde）	4.0 g·L^-1	化学工业平台化合物，重要的香味剂	[66]
乙烯（ethylene）	12.83 nmol/mL(OD₆₀₀)	基础化工原料，可用于合成橡胶、纤维、聚烯烃和聚氯乙烯塑料等	[67]
乳糖酸（lactobionic acid）	182.7 g·L^-1	精细化学品，医药中间体，材料中间体等	[64]
异丁醇（isobutanol）	4 g·L^-1	可再生生物能源，异丁烯前体物	[63]

研究内容	年份	方法	数据序列号	参考文献
ZM4基因组与比较基因组	2005	基因组（随机鸟枪测序法）比较基因组（芯片技术）	AE008692；E-MEXP-217	[97]
结合系统生物学数据更新ZM4基因组注释	2009	基因组（454焦磷酸测序）	SRP000908	[98]
有氧与无氧条件下ZM4转录组与代谢组	2009	转录组（芯片技术）；代谢组（GC、GC-MS、HPLC）	GSE10302	[101]
Ac^R菌株基因型与表型关联及比较基因组	2010	基因组（454焦磷酸测序）；比较基因组（芯片技术）；转录组（芯片技术）	GSE18106	[57]
絮凝菌株ZM401重测序	2012	基因组（Illumina）	AMSR00000000	[109]
絮凝菌株ZM401 转录组分析	2012	转录组（芯片技术）	GU560731-7	[53]
ZM4在5%（体积分数）乙醇压力下的转录组	2012	转录组（芯片技术）	GSE39558	[102]
ZM4在1 g/L糠醛压力下的转录组	2012	转录组（芯片技术）	GSE37848	[102]
ZM4在6%（体积分数）乙醇压力下的转录组、蛋白组和代谢组	2013	转录组（芯片技术）；蛋白组（鸟枪法蛋白质测序）；代谢组（GC-MS、HPLC）	GSE21165	[103]
ZM4 sRNA转录组	2014	转录组（sRNA-Seq）	GSE57773	[110]
8b在不同碳源下外加乙酸的转录组	2014	转录组（芯片技术）	GSE57553	[106]
Ac^R菌株在10 g/L乙酸钠的转录组与蛋白组	2014	转录组（芯片技术）；蛋白组（LC-MS/MS ）	GSE25443	[107]
ZM4基因转座子突变体文库的表型适应检测	2014	突变体文库适应检测	GSE51870	[111]
ZM4五碳糖重组自然进化菌株（KLD1，KLD2）重测序	2015	基因组（Illumina）	NA	[112]
ZM4添加5 mmol/L酚醛抑制物的转录组	2015	转录组（芯片技术）	NA	[108]
ZM4在220g/L葡萄糖添加山梨醇（10 mmol/L）的转录组	2015	转录组（芯片技术）	GSE49620	[48]
ZM4质粒序列更新及8b、2032基因组序列	2018	基因组（Illumina）；转录组（RNA-Seq）	PRJNA391970	[99]
ZM4在多种抑制物环境下的蛋白组和代谢组	2018	蛋白组（RPLC-MS/MS）；代谢组（GC-MS）	NA	[113]
耐低pH（pH 3.5）菌株（PH1 -29）重测序	2019	基因组（Illumina）	GDMCC60258；GDMCC60260	[51]
乙酸及糠醛耐受菌株532与533重测序	2019	基因组（Illumina）	GDMCC60526；GDMCC60527	[58]
²H和¹³C代谢组学研究ZM4 ED途径热力学	2019	代谢组（LC-MS、NMR）	NA	[114]
ZM4在无氧、好氧和固氮条件的磷酸化蛋白质组	2019	蛋白组（LC-MS/MS）	PXD014065	[115]
氧暴露对ZM4类异戊二烯生成的影响	2019	转录组（RNA-Seq）；蛋白组（LC-MS/MS）；代谢组（LC-MS、NMR）	GSE125123	[25]
2032菌株利用合成水解液中葡萄糖与木糖	2019	转录组（RNA-Seq）；蛋白组（LC-MS/MS）；代谢组（IP-LC-MS、GC-MS、AEX-LC-MS、HILIC-MS）	GSE135718；PXD015007	[116]
ZM4葡萄糖与木糖共利用菌株AD50重测序	2020	基因组（Illumina）	NA	[31]
ZM4耐低pH菌株3.6M和3.5M重测序及转录组	2020	基因组（Illumina）;转录组（RNA-Seq）	PRJNA590883；PRJNA553033	[18]
8b在3 g/L糠醛短期刺激或2 g/L糠醛长期胁迫下的转录组	2020	转录组（芯片技术、RNA-Seq）	GSE63540	[105]
ZM4过表达sRNA(Zms4与Zms6)的转录组	2020	转录组（RNA-Seq）	GSE107219	[117]
Mg²⁺对 ZM4细胞生长影响的转录组	2020	转录组（RNA-Seq）	PRJNA601020	[118]
代谢活跃非生长Zm6菌株适应氧供应变化代谢组学	2020	代谢组（CIC-MS）	NA	[119]

研究内容	年份	方法	数据序列号	参考文献
ZM4基因组与比较基因组	2005	基因组（随机鸟枪测序法）比较基因组（芯片技术）	AE008692；E-MEXP-217	[97]
结合系统生物学数据更新ZM4基因组注释	2009	基因组（454焦磷酸测序）	SRP000908	[98]
有氧与无氧条件下ZM4转录组与代谢组	2009	转录组（芯片技术）；代谢组（GC、GC-MS、HPLC）	GSE10302	[101]
Ac^R菌株基因型与表型关联及比较基因组	2010	基因组（454焦磷酸测序）；比较基因组（芯片技术）；转录组（芯片技术）	GSE18106	[57]
絮凝菌株ZM401重测序	2012	基因组（Illumina）	AMSR00000000	[109]
絮凝菌株ZM401 转录组分析	2012	转录组（芯片技术）	GU560731-7	[53]
ZM4在5%（体积分数）乙醇压力下的转录组	2012	转录组（芯片技术）	GSE39558	[102]
ZM4在1 g/L糠醛压力下的转录组	2012	转录组（芯片技术）	GSE37848	[102]
ZM4在6%（体积分数）乙醇压力下的转录组、蛋白组和代谢组	2013	转录组（芯片技术）；蛋白组（鸟枪法蛋白质测序）；代谢组（GC-MS、HPLC）	GSE21165	[103]
ZM4 sRNA转录组	2014	转录组（sRNA-Seq）	GSE57773	[110]
8b在不同碳源下外加乙酸的转录组	2014	转录组（芯片技术）	GSE57553	[106]
Ac^R菌株在10 g/L乙酸钠的转录组与蛋白组	2014	转录组（芯片技术）；蛋白组（LC-MS/MS ）	GSE25443	[107]
ZM4基因转座子突变体文库的表型适应检测	2014	突变体文库适应检测	GSE51870	[111]
ZM4五碳糖重组自然进化菌株（KLD1，KLD2）重测序	2015	基因组（Illumina）	NA	[112]
ZM4添加5 mmol/L酚醛抑制物的转录组	2015	转录组（芯片技术）	NA	[108]
ZM4在220g/L葡萄糖添加山梨醇（10 mmol/L）的转录组	2015	转录组（芯片技术）	GSE49620	[48]
ZM4质粒序列更新及8b、2032基因组序列	2018	基因组（Illumina）；转录组（RNA-Seq）	PRJNA391970	[99]
ZM4在多种抑制物环境下的蛋白组和代谢组	2018	蛋白组（RPLC-MS/MS）；代谢组（GC-MS）	NA	[113]
耐低pH（pH 3.5）菌株（PH1 -29）重测序	2019	基因组（Illumina）	GDMCC60258；GDMCC60260	[51]
乙酸及糠醛耐受菌株532与533重测序	2019	基因组（Illumina）	GDMCC60526；GDMCC60527	[58]
²H和¹³C代谢组学研究ZM4 ED途径热力学	2019	代谢组（LC-MS、NMR）	NA	[114]
ZM4在无氧、好氧和固氮条件的磷酸化蛋白质组	2019	蛋白组（LC-MS/MS）	PXD014065	[115]
氧暴露对ZM4类异戊二烯生成的影响	2019	转录组（RNA-Seq）；蛋白组（LC-MS/MS）；代谢组（LC-MS、NMR）	GSE125123	[25]
2032菌株利用合成水解液中葡萄糖与木糖	2019	转录组（RNA-Seq）；蛋白组（LC-MS/MS）；代谢组（IP-LC-MS、GC-MS、AEX-LC-MS、HILIC-MS）	GSE135718；PXD015007	[116]
ZM4葡萄糖与木糖共利用菌株AD50重测序	2020	基因组（Illumina）	NA	[31]
ZM4耐低pH菌株3.6M和3.5M重测序及转录组	2020	基因组（Illumina）;转录组（RNA-Seq）	PRJNA590883；PRJNA553033	[18]
8b在3 g/L糠醛短期刺激或2 g/L糠醛长期胁迫下的转录组	2020	转录组（芯片技术、RNA-Seq）	GSE63540	[105]
ZM4过表达sRNA(Zms4与Zms6)的转录组	2020	转录组（RNA-Seq）	GSE107219	[117]
Mg²⁺对 ZM4细胞生长影响的转录组	2020	转录组（RNA-Seq）	PRJNA601020	[118]
代谢活跃非生长Zm6菌株适应氧供应变化代谢组学	2020	代谢组（CIC-MS）	NA	[119]

菌株	模型名称	模型尺度	参考文献
Z. mobilis	基于酶的动力学模型	ED 和 PPP途径	[130]
Z. mobilis	基于线性规划的计量学模型	79个反应与77个代谢物	[131]
Z. mobilis	中心代谢的计量学模型	96 个反应	[132]
Z. mobilis ATCC29191 (Zm6)	ED 途径的动力学模型	ED 途径	[133]
Z. mobilis	多种方法的中心代谢模型	中等规模	[134]
Z. mobilis ATCC31821 (ZM4)	ZmoMBEL601代谢网络模型	基因组尺度：348个基因、601个反应和579个代谢物	[128]
Z. mobilis ATCC31821 (ZM4)	iZM363代谢网络模型	基因组尺度：363个基因、747个反应和704个代谢物	[127]
Z. mobilis ATCC10988 (ZM1)	iEM439代谢网络模型	基因组尺度：439个基因、692个反应和658个代谢物	[126]
Z. mobilis ATCC31821 (ZM4)	iHN446代谢网络模型	基因组尺度：446个基因、859个反应和894个代谢物	[129]

Progress and perspectives on developing Zymomonas mobilis as a chassis cell

运动发酵单胞菌底盘细胞研究现状及展望

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