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中国生物工程杂志

CHINA BIOTECHNOLOGY
中国生物工程杂志  2023, Vol. 43 Issue (11): 92-104    DOI: 10.13523/j.cb.2305009
综述     
进化工程在蓝细菌生物学和生物技术研究中的应用*
马依凡1,2,3,孙绘梨3,4,5,**(),毛绍名1,2,**(),栾国栋3,4,5,吕雪峰3,4,5
1 中南林业科技大学生命科学与技术学院 长沙 410004
2 中南林业科技大学 林业生物技术湖南省重点实验室 长沙 410004
3 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 青岛 266101
4 山东能源研究院 青岛 266101
5 青岛新能源山东省实验室 青岛 266101
Application of Evolutionary Engineering in Cyanobacterial Biology and Biotechnology Research
MA Yi-fan1,2,3,SUN Hui-li3,4,5,**(),MAO Shao-ming1,2,**(),LUAN Guo-dong3,4,5,LV Xue-feng3,4,5
1 College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
2 Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry & Technology, Changsha 410004, China
3 Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
4 Shandong Energy Institute, Qingdao 266101, China
5 Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
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摘要:

蓝细菌是光合作用、叶绿体起源和植物进化等基础生物学研究的重要模式生物,也作为极具潜力的微生物光合平台在固碳合成领域引起广泛关注。蓝细菌基础生物学研究和生物技术开发过程中面临大量的复杂生理和代谢表型改造需求,理性的靶向改造技术往往难以取得理想效果。进化工程不依赖于对微生物遗传背景和代谢网络的认识,在微生物复杂生理耐受表型改造和相关功能机制解析方面有着显著的技术优势,在蓝细菌基础生物学和生物技术研究中也发挥了重要作用。结合进化工程的技术特点和实施案例,在蓝细菌基础科学机制解析和光合生物制造技术开发两条路线上,对进化工程的应用进展进行了总结并对未来发展方向进行了展望。

关键词: 蓝细菌进化工程生理耐受性适应性进化光合作用    
Abstract:

Cyanobacteria have long been used as model organisms in basic biological research on topics such as photosynthesis, chloroplast origins and plant evolution. Additionally, due to their fast growth, simple culture techniques and convenient genetic manipulation, cyanobacteria have gained increasing attention in photosynthetic bio-manufacturing. One strategy for studying cyanobacteria is to first obtain mutants with specific phenotypes, and then further analyze their functional mutations and related mechanisms. Moreover, in the development of photosynthetic biomanufacturing technologies, enhancing the physiological tolerance of chassis cells is of significant importance for the large-scale application of cyanobacteria photosynthetic cell factories. Evolutionary engineering offers significant advantages in the acquisition of mutants and the optimization of complex physiological tolerance phenotypes, as it does not require knowledge of the microbial genetic background and metabolic network. This paper reviews the progress of evolutionary engineering in the analysis of cyanobacteria physiological metabolism mechanisms and the optimization of physiological tolerance in cyanobacteria photosynthetic biomanufacturing chassis, and meanwhile it also discusses the challenges and future directions of evolutionary engineering in cyanobacteria applications.

Key words: Cyanobacteria    Evolutionary engineering    Physiological tolerance    Adaptive evolution    Photosynthesis
收稿日期: 2023-05-06 出版日期: 2023-12-01
ZTFLH:  Q93-3  
基金资助: *国家自然科学基金(32270103);国家自然科学基金(32070084)
通讯作者: **孙绘梨,毛绍名     E-mail: sunhl@qibebt.ac.cn;msm526@163.com
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引用本文:

马依凡, 孙绘梨, 毛绍名, 栾国栋, 吕雪峰. 进化工程在蓝细菌生物学和生物技术研究中的应用*[J]. 中国生物工程杂志, 2023, 43(11): 92-104.

MA Yi-fan, SUN Hui-li, MAO Shao-ming, LUAN Guo-dong, LV Xue-feng. Application of Evolutionary Engineering in Cyanobacterial Biology and Biotechnology Research. China Biotechnology, 2023, 43(11): 92-104.

链接本文:

https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.2305009        https://manu60.magtech.com.cn/biotech/CN/Y2023/V43/I11/92

类型 策略 优点 缺点
自发突变 在选择压力下进行长期连续传代以积累自发突变 利用自然存在的变异机制,无须额外实验干预,技术难度低 1.进化周期长;2.人力成本较高;3.变异位点随机,无法控制变异范围
理化诱变 使用最佳剂量的UV、MNNG、MMS或EMS对细胞进行诱变处理,然后在特定选择压力下筛选或在逐渐升高的选择压力下进行传代,在传代中通常结合多种理化诱变因子进行多轮处理 丰富变异类型,提高突变频率 1.造成大量细胞损伤,降低效率;2.引入大量变异,其中可能包括较多的无用或不利突变;3.变异位点随机,无法控制变异范围
转座子诱变 构建体内转座子标记诱变系统,然后在特定选择压力下筛选,或直接观测特定表型并筛选 1.可以引发随机或定向突变;2.便于定位转座子的插入基因或位置 1.转座子插入位置可能具有一定偏好性,限制突变范围;2.多数会导致基因表达中断,偶尔会引发蛋白质功能改变,因此变异类型有限;3.对基因组进行饱和突变的成本较高
CRISPRi
抑制文库
合成针对目标基因或目标途径的gRNA,构建CRISPRi文库并转化蓝细菌构建突变体文库。然后在特定选择压力下筛选,或直接观测特定表型并筛选 能够对特定基因或途径进行精确抑制 1.只能导致基因抑制;2.针对大范围基因设计合成gRNA的成本较高
超突变技术 敲除或过表达细胞复制保真机制中的关键基因,并使用环境胁迫诱发细胞的超突变状态,然后在特定选择压力下筛选,或在逐渐升高的选择压力下进行传代培养 1.较高突变率可以缩短进化周期,并提高进化效率;2.边诱变边筛选的体内连续诱变方式减少了人工干预;3.引入突变的方式较为温和,筛选获得的进化藻株中无用或不利突变较少 1.变异位点随机,无法控制变异范围;2.面对不同胁迫类型和胁迫强度,需要探索适配的突变率强度
表1  不同变异引入方法的优缺点比较
图1  理化诱变、转座子诱变、CRISPRi抑制文库和超突变进化原理示意图
出发藻株 胁迫因素 改造情况 传代时长 进化方法 引文
Synechocystis sp. PCC 6803 微氧条件 微氧条件下生长缺陷 - 转座子诱变 [25]
Leptolyngbya boryana 固氮异常 微氧固氮下生长缺陷 - 转座子诱变 [26]
Synechococcus sp. PCC 7942 DCMU 在1 μmol/L DCMU条件下存活 - MNNG诱变 [36]
Synechococcus sp. PCC 7942 Cyanobacterin 4.7 μmol/L Cyanobacterin条件下生长没有受到抑制 MNNG诱变 [37]
Synechococcus sp. PCC 7942 Bentazone 在含有0.1 mmol/L Bentazone的固体培养基中存活 MNNG诱变 [38]
Synechococcus leopoliensisAnabaena variabilis 高浓度CO2 失败 750代 自发突变 [39]
Trichodesmium erytheum 高浓度CO2 固氮速率和生长速率提高 4.5年 自发突变 [40]
Nodularia spumigena
strain AV2
噬藻体 在噬藻体存在条件下不发生裂解 22周 自发突变 [41]
Synechocystis sp. PCC 6803 有毒氨基酸 在含有1 mmol/L精氨酸、组氨酸、赖氨酸、甲硫氨酸、苯丙氨酸、苏氨酸的TCM培养基中维持正常生长速率 160天 自发突变 [42]
Synechococcus sp. PCC 7942 2-nonanone 在100 μmol/L 2-壬烷酮条件下存活 - 转座子诱变 [28]
Synechococcus sp. PCC 7942 缺氮或缺硫 缺氮或缺硫条件下呈现非漂白表型 - 转座子诱变 [8]
Microcystis aeruginosa 高盐 对NaCl的耐受性从10 g/L提高至14 g/L 约160天 自发突变 [43]
表2  进化工程在蓝细菌基础生物学的应用
出发藻株 改造表型 改造情况 改造时长 进化方法 引用
Synechocystis sp. PCC 6803 丁醇 在0.5%(V/V)丁醇浓度下的生长没有受到抑制 395天 自发突变 [48]
异丁醇 在5 g/L异丁醇条件下能够生长 76天 自发突变 [49]
高盐 3% NaCl条件下的生长速率最高为野生型的150% 303天 自发突变 [50]
高光 能够在9 000 μmol photons/(m2·s)光照下生长 52天 自发突变 [52]
高光 能够在3 000 μmol photons/(m2·s)光照下生长 900多天 UV和MMS诱变结合适应性进化 [23]
高温 能够在45℃/23~26℃的日夜循环条件下稳定生长 1年 适应性进化结合MMS诱变和UV诱变 [53]
能在pH 5.5条件下生长 3个月 自发突变 [51]
Synechococcus sp. PCC 7942 高温高光 极端温度和光照条件下[45℃、1 500 μmol photons/(m2·s)]快速生长 2周内 超突变系统体内连续诱变 [31]
Synechococcus elongatus PCC11801 正丁醇和
2,3-丁二醇
正丁醇耐受进化藻株表现出对乙醇(22 g/L)、异丙醇(18 g/L)、异丁醇(8 g/L)的交叉耐受性,2,3-丁二醇耐受进化藻株表现出对乙醇(22 g/L)、异丙醇(15 g/L)、正丁醇(4 g/L)、异丁醇(7 g/L)、叔丁醇(15 g/L)、异戊醇(5 g/L)的交叉耐受性 500多天 自发突变 [61]
Anabaena sp. PCC 7120, Anabaena variabilis ATCC 29413, Nostoc punctiforme ATCC 29133 法呢烯、
月桂烯、
芳樟醇
和柠檬烯
Anabaena sp. PCC 7120对法呢烯的耐受性提高至0.32 g/L,Anabaena variabilis ATCC 29413对芳樟醇的耐受性提高至0.72 g/L,Nostoc punctiforme ATCC 29133对芳樟醇的耐受性提高至0.54 g/L - 自发突变 [65]
Fremyella diplosiphon 高盐 在20 g/L NaCl液体培养基中的生长没有受到抑制 - 高温诱导突变 [66]
表3  进化工程在蓝细菌生理耐受性优化方面的应用
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