合成生物学 ›› 2021, Vol. 2 ›› Issue (4): 598-611.DOI: 10.12211/2096-8280.2020-092
于慧敏, 郑煜堃, 杜岩, 王苗苗, 梁有向
收稿日期:
2020-12-30
修回日期:
2021-02-06
出版日期:
2021-09-10
发布日期:
2021-09-10
通讯作者:
于慧敏
作者简介:
基金资助:
Huimin YU, Yukun ZHENG, Yan DU, Miaomiao WANG, Youxiang LIANG
Received:
2020-12-30
Revised:
2021-02-06
Online:
2021-09-10
Published:
2021-09-10
Contact:
Huimin YU
摘要:
合成生物学研究对于我国绿色生物制造产业和可持续发展战略至关重要。启动子是合成生物学核心元件,是在转录水平上实现基因高效、精准表达调控的最关键因素之一。本文重点对原核微生物启动子工程研究的基本内容、研究进展及发展趋势进行了综述。首先概述了启动子序列基本特征及其受RNA聚合酶σ因子识别调控的一般规律;并以大肠杆菌乳糖操纵子为例简要介绍了诱导型启动子的负调控与正调控诱导机制。其次,分别从对靶基因自身内源启动子进行突变改造以及采用高效外源启动子进行替换改造这两个方面入手,阐述了启动子改造的常用策略。进一步对近年来公开报道的不同类型诱导型启动子进行了梳理,小结了代表性化学分子诱导剂以及物理信号诱导方式的种类及基本特征。简述了非模式和模式微生物组成型启动子的研究进展及研究侧重点。结合动态代谢调控技术及人工智能工具的突破性发展,提出具有动态调控功能的特殊启动子的发现与改造、全新性能启动子元件的人工智能设计与改造等将成为启动子工程研究的新方向与新前沿。最后分析了启动子工程领域存在的挑战性问题,展望了今后的研究重点,并结合合成生物学的发展,进一步强调了微生物启动子工程的重要作用。
中图分类号:
于慧敏, 郑煜堃, 杜岩, 王苗苗, 梁有向. 合成生物学研究中的微生物启动子工程策略[J]. 合成生物学, 2021, 2(4): 598-611.
Huimin YU, Yukun ZHENG, Yan DU, Miaomiao WANG, Youxiang LIANG. Microbial promoter engineering strategies in synthetic biology[J]. Synthetic Biology Journal, 2021, 2(4): 598-611.
σ 因子 | 微生物名称 | -35区 | -10区 | 参考 文献 |
---|---|---|---|---|
σ70 | 大肠杆菌 | TTGACA | TATAAT | [ |
σ70 | 枯草芽孢杆菌 | TTGACA | TATAAT | [ |
σA | 谷氨酸棒杆菌 | TTG(A/C)CA | TGN | [ |
σA | 红色红球菌 | TTGNNN | (T/C)GN | [ |
σA | 运动发酵单胞菌 | TTGNNN | TATNNN | [ |
σhrdB | 阿维链霉菌 | TTGACA | tAgATT | [ |
表1 几种模式/非模式微生物看家σ因子识别的启动子保守序列比较
Tab. 1 Some promoter consensus sequences for housekeeping σ factors of model/non-model microorganisms
σ 因子 | 微生物名称 | -35区 | -10区 | 参考 文献 |
---|---|---|---|---|
σ70 | 大肠杆菌 | TTGACA | TATAAT | [ |
σ70 | 枯草芽孢杆菌 | TTGACA | TATAAT | [ |
σA | 谷氨酸棒杆菌 | TTG(A/C)CA | TGN | [ |
σA | 红色红球菌 | TTGNNN | (T/C)GN | [ |
σA | 运动发酵单胞菌 | TTGNNN | TATNNN | [ |
σhrdB | 阿维链霉菌 | TTGACA | tAgATT | [ |
图2 诱导型启动子的负调控与正调控诱导机制以及大肠杆菌乳糖操纵子负调控的典型序列(a)无诱导剂条件下的基因调控;(b)诱导剂加入条件下的基因调控;(c) β-半乳糖苷酶(LacZ)启动子的乳糖操纵子负调控区域DNA序列。LacI—阻遏蛋白;lacO—操纵序列;SD序列—基因的核糖体结合位点(也称为RBS);Inducer—乳糖操纵子的lacI-lacO体系诱导剂,通常为异丙基-β-D-硫代吡喃半乳糖苷(IPTG)或乳糖(实际为1,6-别乳糖,乳糖的代谢物)
Fig. 2 Negative and positive regulation mechanism of inducible promoters and the partial sequence of lactose operon (lacO) of E. coli.(a, b) gene regulation mode under inducer-free or inducer-present condition, respectively. (c) partial DNA sequence of inducible promoter of β-galactosidase (LacZ) with negative regulation. LacI—inhibitor (repressor) protein; lacO—operator sequence for repressor binding; SD—Shine-Dalgarno sequence as ribosome biding site (RBS); Inducer—for lacI-lacO system, common inducer is isopropyl-β-D-thiogalactopyranoside (IPTG) or lactose (1,6-allolactose in fact, a metabolite of lactose), respectively
图3 启动子改造的常用有效策略-35和-10—启动子核心区;+1—转录起始位点;RBS—核糖体结合位点;ATG—翻译起始密码子
Fig. 3 Common efficient strategies for promoter engineering-35 and -10—core elements of promoter; +1— transcription initiation site; RBS— ribosome binding site; ATG— start codon of enzyme translation
诱导类型 | 诱导剂 | 相关微生物 | 启动子特征 | 参考 文献 |
---|---|---|---|---|
化学信号 | IPTG/乳糖 | 大肠杆菌;谷氨酸棒杆菌;枯草芽孢杆菌等 | Plac、Ptac;广谱性好、诱导强度较高;诱导剂价格高;基于LacI阻遏蛋白(负调控蛋白)的负调控机制 | [ |
IPTG | 大肠杆菌 | T7启动子,噬菌体来源;pET表达系统;常与溶源化宿主菌(即T7 RNA聚合酶基因插入在宿主菌基因组中)联用;诱导强度高、广谱性好;诱导剂价格高;基于阻遏蛋白的负调控机制 | [ | |
L-鼠李糖/ L-阿拉伯糖 | 大肠杆菌;红球菌等 | rhaPBAD/araPBAD启动子;AraC正/负调控蛋白;pBAD表达系统;诱导剂价格较高;诱导强度较高;广谱性较好;其中rhaPBAD为基于正调控蛋白的正调控机制;araPBAD为基于阻遏蛋白的负调控机制 | [ | |
木糖 | 枯草芽孢杆菌;酵母菌等 | Pxyl;诱导剂价格高;基于阻遏蛋白的负调控机制 | [ | |
蔗糖 | 枯草芽孢杆菌等 | PsacB/PsacP;强度低,易泄露表达;基于不依赖于ρ因子的RNA抗终止子序列的负调控机制 | [ | |
四环素/脱水四环素 | 浑浊红球菌;丙酮丁醇梭菌等 | Ptet;诱导剂用量低;基于TetR阻遏蛋白的负调控机制 | [ | |
离子液体 | 木质素分解肠杆菌;大肠杆菌;酿酒酵母等 | eilAR表达盒;EilA表达离子液体自诱导内膜转运蛋白;EilR为负调控蛋白;负调控机制 | [ | |
尿酸 | 耐辐射奇球菌;大肠杆菌等 | 基于HucR阻遏蛋白的负调控机制;强度与pBAD/pET系统相当 | [ | |
巴豆酰胺/ 甲基丙烯酰胺 | 红球菌等 | 红球菌适用;基于正负调控蛋白协同作用的复合调控机制 | [ | |
联苯 | 红球菌RHA1;红串红球菌 | 基于BphS-BphT两组分调控元件的正调控机制 | [ | |
ε-己内酰胺/十几种腈类 | 链霉菌;红球菌等 | PnitA-NitR杂合元件;强启动高表达;基于NitR正调控蛋白的正调控机制 | [ | |
尿素 | 红色红球菌 | Pnh,Pami,Pa2;基于正负调控蛋白协同作用的调控机制,具体调控机制尚未解析 | [ | |
铁离子 | 多能硫碱弧菌;大肠杆菌等 | P3AF启动子,携带19 bp大肠杆菌铁摄取调节子蛋白基因fur的核心区序列,铁离子严谨调控 | [ | |
碱性染料 | 大肠杆菌;恶臭假单胞菌;苜蓿中华根瘤菌;新月柄杆菌等 | 基于EilR阻遏蛋白-操纵序列的负调控机制;结晶紫等廉价、严谨、高效诱导;微生物广谱适用性;低成本 | [ | |
丙烯酸盐/葡萄糖酸/红霉素/柚皮素 | 大肠杆菌;类球红细菌;恶臭假单胞菌 | 属于TetR家族阻遏蛋白的AcuR/MphR/TtgR等调控蛋白;CdaR,转录激活蛋白;响应4种代谢物的生物传感器性能,分别为负调控和正调控机制;不同诱导信号的正交效果 | [ | |
甲醇 | 红串红球菌;毕赤酵母等 | 异柠檬酸裂解酶基因(iclRe)上游序列;基于RamBRe阻遏蛋白的负调控机制 | [ | |
乙醇 | 运动发酵单胞菌等 | P0405、P0435和P0038启动子,调控机制尚未明确 | [ | |
对异丙苯甲酸酯/间苯二酚 | 链霉菌;放线菌 | 负调控机制;对异丙苯甲酸酯诱导,P21启动子-CymR调控蛋白;间苯二酚,PA3启动子-RolR调控蛋白 | [ | |
磷酸盐饥饿 | 大肠杆菌 | 磷酸盐饥饿诱导;基于PhoB激活的正调控机制 | [ | |
氮饥饿 | 三角褐指藻 | 铵转运蛋白AMT基因启动子;氮饥饿条件强诱导;机制尚未报道 | [ | |
低溶氧 | 大肠杆菌;谷氨酸棒杆菌;盐单胞菌等 | vgb启动子;nar启动子;响应低溶氧条件启动转录 | [ | |
低pH | 黑曲霉 | Pgas,低pH诱导(pH2.0/3.0);受未知功能双调控蛋白调控 | [ | |
物理信号 | 高温 | 大肠杆菌;枯草芽孢杆菌等 | pR/pL,受温敏型阻遏蛋白CI857调控;P2和P7等 | [ |
低温(-15 ℃) | 大肠杆菌 | PcspA耦合LacI负调控;杂合启动子,严谨低温调控,pCold载体效率与pET14相当 | [ | |
低温(-30 ℃) | 大肠杆菌 | 整合多个温敏转录开关与蛋白降解模块;从37 ℃到30 ℃严谨调控;复合调控机制 | [ | |
光 | 大肠杆菌;酵母菌等 | 10余种光敏调控蛋白Cph8/OmpR;YF1/FixJ;EL222等;白光诱导、蓝光诱导、黑暗诱导等 | [ |
表2 近年来报道的一些不同微生物来源、不同类型的诱导型启动子
Tab. 2 Some inducible promoters reported recently from different microorganisms with diverse mechanisms
诱导类型 | 诱导剂 | 相关微生物 | 启动子特征 | 参考 文献 |
---|---|---|---|---|
化学信号 | IPTG/乳糖 | 大肠杆菌;谷氨酸棒杆菌;枯草芽孢杆菌等 | Plac、Ptac;广谱性好、诱导强度较高;诱导剂价格高;基于LacI阻遏蛋白(负调控蛋白)的负调控机制 | [ |
IPTG | 大肠杆菌 | T7启动子,噬菌体来源;pET表达系统;常与溶源化宿主菌(即T7 RNA聚合酶基因插入在宿主菌基因组中)联用;诱导强度高、广谱性好;诱导剂价格高;基于阻遏蛋白的负调控机制 | [ | |
L-鼠李糖/ L-阿拉伯糖 | 大肠杆菌;红球菌等 | rhaPBAD/araPBAD启动子;AraC正/负调控蛋白;pBAD表达系统;诱导剂价格较高;诱导强度较高;广谱性较好;其中rhaPBAD为基于正调控蛋白的正调控机制;araPBAD为基于阻遏蛋白的负调控机制 | [ | |
木糖 | 枯草芽孢杆菌;酵母菌等 | Pxyl;诱导剂价格高;基于阻遏蛋白的负调控机制 | [ | |
蔗糖 | 枯草芽孢杆菌等 | PsacB/PsacP;强度低,易泄露表达;基于不依赖于ρ因子的RNA抗终止子序列的负调控机制 | [ | |
四环素/脱水四环素 | 浑浊红球菌;丙酮丁醇梭菌等 | Ptet;诱导剂用量低;基于TetR阻遏蛋白的负调控机制 | [ | |
离子液体 | 木质素分解肠杆菌;大肠杆菌;酿酒酵母等 | eilAR表达盒;EilA表达离子液体自诱导内膜转运蛋白;EilR为负调控蛋白;负调控机制 | [ | |
尿酸 | 耐辐射奇球菌;大肠杆菌等 | 基于HucR阻遏蛋白的负调控机制;强度与pBAD/pET系统相当 | [ | |
巴豆酰胺/ 甲基丙烯酰胺 | 红球菌等 | 红球菌适用;基于正负调控蛋白协同作用的复合调控机制 | [ | |
联苯 | 红球菌RHA1;红串红球菌 | 基于BphS-BphT两组分调控元件的正调控机制 | [ | |
ε-己内酰胺/十几种腈类 | 链霉菌;红球菌等 | PnitA-NitR杂合元件;强启动高表达;基于NitR正调控蛋白的正调控机制 | [ | |
尿素 | 红色红球菌 | Pnh,Pami,Pa2;基于正负调控蛋白协同作用的调控机制,具体调控机制尚未解析 | [ | |
铁离子 | 多能硫碱弧菌;大肠杆菌等 | P3AF启动子,携带19 bp大肠杆菌铁摄取调节子蛋白基因fur的核心区序列,铁离子严谨调控 | [ | |
碱性染料 | 大肠杆菌;恶臭假单胞菌;苜蓿中华根瘤菌;新月柄杆菌等 | 基于EilR阻遏蛋白-操纵序列的负调控机制;结晶紫等廉价、严谨、高效诱导;微生物广谱适用性;低成本 | [ | |
丙烯酸盐/葡萄糖酸/红霉素/柚皮素 | 大肠杆菌;类球红细菌;恶臭假单胞菌 | 属于TetR家族阻遏蛋白的AcuR/MphR/TtgR等调控蛋白;CdaR,转录激活蛋白;响应4种代谢物的生物传感器性能,分别为负调控和正调控机制;不同诱导信号的正交效果 | [ | |
甲醇 | 红串红球菌;毕赤酵母等 | 异柠檬酸裂解酶基因(iclRe)上游序列;基于RamBRe阻遏蛋白的负调控机制 | [ | |
乙醇 | 运动发酵单胞菌等 | P0405、P0435和P0038启动子,调控机制尚未明确 | [ | |
对异丙苯甲酸酯/间苯二酚 | 链霉菌;放线菌 | 负调控机制;对异丙苯甲酸酯诱导,P21启动子-CymR调控蛋白;间苯二酚,PA3启动子-RolR调控蛋白 | [ | |
磷酸盐饥饿 | 大肠杆菌 | 磷酸盐饥饿诱导;基于PhoB激活的正调控机制 | [ | |
氮饥饿 | 三角褐指藻 | 铵转运蛋白AMT基因启动子;氮饥饿条件强诱导;机制尚未报道 | [ | |
低溶氧 | 大肠杆菌;谷氨酸棒杆菌;盐单胞菌等 | vgb启动子;nar启动子;响应低溶氧条件启动转录 | [ | |
低pH | 黑曲霉 | Pgas,低pH诱导(pH2.0/3.0);受未知功能双调控蛋白调控 | [ | |
物理信号 | 高温 | 大肠杆菌;枯草芽孢杆菌等 | pR/pL,受温敏型阻遏蛋白CI857调控;P2和P7等 | [ |
低温(-15 ℃) | 大肠杆菌 | PcspA耦合LacI负调控;杂合启动子,严谨低温调控,pCold载体效率与pET14相当 | [ | |
低温(-30 ℃) | 大肠杆菌 | 整合多个温敏转录开关与蛋白降解模块;从37 ℃到30 ℃严谨调控;复合调控机制 | [ | |
光 | 大肠杆菌;酵母菌等 | 10余种光敏调控蛋白Cph8/OmpR;YF1/FixJ;EL222等;白光诱导、蓝光诱导、黑暗诱导等 | [ |
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