生物技术通报 ›› 2023, Vol. 39 ›› Issue (11): 123-136.doi: 10.13560/j.cnki.biotech.bull.1985.2023-0750
李昕悦1(), 周明海1, 樊亚超2, 廖莎2, 张风丽1, 刘晨光1, 孙悦3, 张霖2, 赵心清1()
收稿日期:
2023-08-09
出版日期:
2023-11-26
发布日期:
2023-12-20
通讯作者:
赵心清,女,博士,教授,研究方向:微生物合成生物学及酶和化学品生产;E-mail: xqzhao@sjtu.edu.cn作者简介:
李昕悦,男,博士研究生,研究方向:微物代谢工程;E-mail: lixinyue123@sjtu.edu.cn
基金资助:
LI Xin-yue1(), ZHOU Ming-hai1, FAN Ya-chao2, LIAO Sha2, ZHANG Feng-li1, LIU Chen-guang1, SUN Yue3, ZHANG Lin2, ZHAO Xin-qing1()
Received:
2023-08-09
Published:
2023-11-26
Online:
2023-12-20
摘要:
微生物细胞工厂广泛用于生物燃料以及高值化学品和大宗化学品的可持续生产,但是高浓度产物和底物以及多种环境胁迫条件会抑制菌株的发酵效率,降低生产的经济性。因此,增强菌株耐受性对于目的产物的高效和可持续生产至关重要。近年来,利用转运蛋白工程保护菌株免受毒性化合物的损害以提升菌株耐受性的策略日益受到研究者的关注。因此,本文总结了基于微生物转运蛋白工程改造提升菌株耐受性的研究进展,分析了目前微生物转运蛋白研究领域中存在的关键问题,并探讨了基于转运蛋白工程提升微生物菌株耐受性的策略,尤其对人工智能在转运蛋白功能注释、结构模拟和底物-转运蛋白互作预测中的应用进行了总结和展望,以期能够促进微生物在绿色生物制造领域的应用。
李昕悦, 周明海, 樊亚超, 廖莎, 张风丽, 刘晨光, 孙悦, 张霖, 赵心清. 基于转运蛋白工程提升微生物菌株耐受性和生物制造效率的研究进展[J]. 生物技术通报, 2023, 39(11): 123-136.
LI Xin-yue, ZHOU Ming-hai, FAN Ya-chao, LIAO Sha, ZHANG Feng-li, LIU Chen-guang, SUN Yue, ZHANG Lin, ZHAO Xin-qing. Research Progress in the Improvement of Microbial Strain Tolerance and Efficiency of Biological Manufacturing Based on Transporter Engineering[J]. Biotechnology Bulletin, 2023, 39(11): 123-136.
蛋白名称 Protein name | 转运蛋白类型 Type of transporter | 蛋白来源 Source of protein | 宿主 Host | 耐受类型 Tolerance type | 改进策略 Strategy | 结果 Result | 参考文献 Reference |
---|---|---|---|---|---|---|---|
木质纤维素水解液胁迫Stress of lignocellulosic hydrolysate | |||||||
ZMO0799, ZMO0800, ZMO1288, ZMO1856, ZMO0282, ZMO0798 | ATP-binding Cassette(ABC)Superfamily | Zymomonas mobilis | Z. mobilis | 酚醛 Phenolic aldehyde | 过表达,敲除Overexpression, knockout | 六种转运蛋白被认为与酚醛耐受性相关 | [ |
Pdr5, Snq2 | ABC Superfamily | S. cerevisiae | S. cerevisiae | 香草醛 Vanilline | 过表达 Overexpression | 菌体生长加快,菌株延滞期缩短 | [ |
Pdr5, Yor1, Snq2 | ABC Superfamily | S. cerevisiae | S. cerevisiae | 香草醛 Vanilline | 过表达 Overexpression | 菌株香兰素耐受性提升 | [ |
酸胁迫Acid stress | |||||||
Ady2 | Acetate Uptake Transporter Family | S. cerevisiae | S. cerevisiae | 乙酸 Acetic acid | 敲除 Knockout | 菌株在乙酸,过氧化氢,甲酸胁迫下的生长性能提升,ADY2敲除突变体在3.6 g/L乙酸胁迫条件下的乙醇生产强度提高了14.66% | [ |
Rta1 | Lipid-translocating Exporter Family | Cryptococcus humicola | S. cerevisiae | 酸 Acid | 异源表达 Heterologous expression | 重组菌株在酸铝胁迫下延滞期比对照减少12 h | [ |
ThiT | Vitamin Uptake Transporter Family | L. lactisNZ9000 | L. lactisNZ9000 | 酸 Acid | 过表达 Overexpression | 菌株在酸胁迫下最大存活率提升16.2倍 | [ |
Zrt3 | Zinc-Iron Permease Family | S. cerevisiae | S. cerevisiae | 乙酸 Acetic acid | 敲除 Knockout | 对乙酸介导的调节性细胞死亡具有高度抗性,液泡功能障碍减少 | [ |
Jen1 | Major Facilitator Superfamily(MFS) | S. cerevisiae | S. cerevisiae | L-乳酸 L-lactic acid | 过表达 Overexpression | 菌株乳酸产量从43.6 g/L提升到51.4 g/L | [ |
盐胁迫Salt stress | |||||||
Nha2 | Monovalent Cation: Proton Antiporter-1 Family | Y. lipolytica | S. cerevisiae | 钠盐 Na+ | 异源表达 Heterologous expression | 酿酒酵母中的Na+耐受性显著提升 | [ |
BusA | ABC Superfamily | Tetragenococcus halophilus | E. coli | 高浓度盐 High salinity | 异源表达 Heterologous expression | 大肠杆菌MKH13的盐耐受能力显著提升 | [ |
BmrA, BmrB | ABC Superfamily | Bifidobacterium longumBBMN68 | L. lactisNZ9000 | 胆汁盐 Bile salt | 异源表达 Heterologous expression | 菌株对牛胆汁(0.10%)的耐受性提高20.77倍 | [ |
HKT2;1 | K+ Transporter(Trk)Family | Aeluropus lagopoides | A. lagopoides | 钾盐 K+ | 异源表达Heterologous expression | 使K+吸收缺陷(WΔ6)和Na+敏感酵母突变体(G19)能够在>1 mmol/L KCl浓度下生长 | [ |
Trk1 | Trk Family | Candida glabrata | S. cerevisiae | 高浓度盐 High salinity | 异源表达 Heterologous expression | 细胞盐离子耐受性提升 | [ |
产物胁迫Product stress | |||||||
Abc2, Abc3 | ABC Superfamily | Y. lipolytica | S. cerevisiae | 烷烃 Alkane | 异源表达 Heterologous expression | 酿酒酵母对癸烷和十一烷的耐受性显著增加,ABC2转运蛋白将酿酒酵母对癸烷的耐受限度提高约80倍 | [ |
AcrE, MdtE, MdtC, Cmr | Membrane Fusion Protei Family; MFS | E. coli | E. coli | 脂肪酸 Fatty acid | 过表达 Overexpression | 菌株中链脂肪酸滴度增加两倍以上 | [ |
Abc2, Abc3 | ABC Superfamily | Grosmannia ciavigera, Y. Iipoiytica | S. cerevisiae | 桧烯, 青篙二烯Hinokiene, Pennyroyalene | 异源表达 Heterologous expression | ABC3的表达使桧烯的产量提高34.5%,表达ABC2使青蒿二烯产量提高24.6%,外排率提高16.0% | [ |
YALI0F19492g | Cor413im1 Family | Y. lipolytica | Y. lipolytica | 柠檬烯 Limonene | 过表达 Overexpression | 显著提高了菌株的柠檬烯耐受性 | [ |
Esbp6 | MFS | S. cerevisiae | S. cerevisiae | 香豆酸Coumaric acid | 过表达 Overexpression | 菌株对芳香酸的耐受性提升,菌株的香豆酸分泌显著改善 | [ |
Bpt1 | ABC Superfamily | S. cerevisiae | S. cerevisiae | 大麻二酚 Cannabidiol | 过表达 Overexpression | 大麻二酚产量达到6.92 mg/L,较出发菌株产量提高100倍 | [ |
Trk1 | Trk Family | S. cerevisiae | S. cerevisiae | 丙酸Propionic acid | 适应性实验室进化 Adaptive laboratory evolution | 菌株对丙酸和多种有机酸的耐受能力提升 | [ |
YcjP | ABC Superfamily | E. coli | E. coli | 咖啡酸Caffeic acid | 过表达 Overexpression | 菌株的咖啡酸滴度达到 775.7 mg/L(对照589.9 mg/L) | [ |
表1 基于转运蛋白工程的菌株耐受性研究进展
Table 1 Research progress in strain tolerance based on transporter engineering
蛋白名称 Protein name | 转运蛋白类型 Type of transporter | 蛋白来源 Source of protein | 宿主 Host | 耐受类型 Tolerance type | 改进策略 Strategy | 结果 Result | 参考文献 Reference |
---|---|---|---|---|---|---|---|
木质纤维素水解液胁迫Stress of lignocellulosic hydrolysate | |||||||
ZMO0799, ZMO0800, ZMO1288, ZMO1856, ZMO0282, ZMO0798 | ATP-binding Cassette(ABC)Superfamily | Zymomonas mobilis | Z. mobilis | 酚醛 Phenolic aldehyde | 过表达,敲除Overexpression, knockout | 六种转运蛋白被认为与酚醛耐受性相关 | [ |
Pdr5, Snq2 | ABC Superfamily | S. cerevisiae | S. cerevisiae | 香草醛 Vanilline | 过表达 Overexpression | 菌体生长加快,菌株延滞期缩短 | [ |
Pdr5, Yor1, Snq2 | ABC Superfamily | S. cerevisiae | S. cerevisiae | 香草醛 Vanilline | 过表达 Overexpression | 菌株香兰素耐受性提升 | [ |
酸胁迫Acid stress | |||||||
Ady2 | Acetate Uptake Transporter Family | S. cerevisiae | S. cerevisiae | 乙酸 Acetic acid | 敲除 Knockout | 菌株在乙酸,过氧化氢,甲酸胁迫下的生长性能提升,ADY2敲除突变体在3.6 g/L乙酸胁迫条件下的乙醇生产强度提高了14.66% | [ |
Rta1 | Lipid-translocating Exporter Family | Cryptococcus humicola | S. cerevisiae | 酸 Acid | 异源表达 Heterologous expression | 重组菌株在酸铝胁迫下延滞期比对照减少12 h | [ |
ThiT | Vitamin Uptake Transporter Family | L. lactisNZ9000 | L. lactisNZ9000 | 酸 Acid | 过表达 Overexpression | 菌株在酸胁迫下最大存活率提升16.2倍 | [ |
Zrt3 | Zinc-Iron Permease Family | S. cerevisiae | S. cerevisiae | 乙酸 Acetic acid | 敲除 Knockout | 对乙酸介导的调节性细胞死亡具有高度抗性,液泡功能障碍减少 | [ |
Jen1 | Major Facilitator Superfamily(MFS) | S. cerevisiae | S. cerevisiae | L-乳酸 L-lactic acid | 过表达 Overexpression | 菌株乳酸产量从43.6 g/L提升到51.4 g/L | [ |
盐胁迫Salt stress | |||||||
Nha2 | Monovalent Cation: Proton Antiporter-1 Family | Y. lipolytica | S. cerevisiae | 钠盐 Na+ | 异源表达 Heterologous expression | 酿酒酵母中的Na+耐受性显著提升 | [ |
BusA | ABC Superfamily | Tetragenococcus halophilus | E. coli | 高浓度盐 High salinity | 异源表达 Heterologous expression | 大肠杆菌MKH13的盐耐受能力显著提升 | [ |
BmrA, BmrB | ABC Superfamily | Bifidobacterium longumBBMN68 | L. lactisNZ9000 | 胆汁盐 Bile salt | 异源表达 Heterologous expression | 菌株对牛胆汁(0.10%)的耐受性提高20.77倍 | [ |
HKT2;1 | K+ Transporter(Trk)Family | Aeluropus lagopoides | A. lagopoides | 钾盐 K+ | 异源表达Heterologous expression | 使K+吸收缺陷(WΔ6)和Na+敏感酵母突变体(G19)能够在>1 mmol/L KCl浓度下生长 | [ |
Trk1 | Trk Family | Candida glabrata | S. cerevisiae | 高浓度盐 High salinity | 异源表达 Heterologous expression | 细胞盐离子耐受性提升 | [ |
产物胁迫Product stress | |||||||
Abc2, Abc3 | ABC Superfamily | Y. lipolytica | S. cerevisiae | 烷烃 Alkane | 异源表达 Heterologous expression | 酿酒酵母对癸烷和十一烷的耐受性显著增加,ABC2转运蛋白将酿酒酵母对癸烷的耐受限度提高约80倍 | [ |
AcrE, MdtE, MdtC, Cmr | Membrane Fusion Protei Family; MFS | E. coli | E. coli | 脂肪酸 Fatty acid | 过表达 Overexpression | 菌株中链脂肪酸滴度增加两倍以上 | [ |
Abc2, Abc3 | ABC Superfamily | Grosmannia ciavigera, Y. Iipoiytica | S. cerevisiae | 桧烯, 青篙二烯Hinokiene, Pennyroyalene | 异源表达 Heterologous expression | ABC3的表达使桧烯的产量提高34.5%,表达ABC2使青蒿二烯产量提高24.6%,外排率提高16.0% | [ |
YALI0F19492g | Cor413im1 Family | Y. lipolytica | Y. lipolytica | 柠檬烯 Limonene | 过表达 Overexpression | 显著提高了菌株的柠檬烯耐受性 | [ |
Esbp6 | MFS | S. cerevisiae | S. cerevisiae | 香豆酸Coumaric acid | 过表达 Overexpression | 菌株对芳香酸的耐受性提升,菌株的香豆酸分泌显著改善 | [ |
Bpt1 | ABC Superfamily | S. cerevisiae | S. cerevisiae | 大麻二酚 Cannabidiol | 过表达 Overexpression | 大麻二酚产量达到6.92 mg/L,较出发菌株产量提高100倍 | [ |
Trk1 | Trk Family | S. cerevisiae | S. cerevisiae | 丙酸Propionic acid | 适应性实验室进化 Adaptive laboratory evolution | 菌株对丙酸和多种有机酸的耐受能力提升 | [ |
YcjP | ABC Superfamily | E. coli | E. coli | 咖啡酸Caffeic acid | 过表达 Overexpression | 菌株的咖啡酸滴度达到 775.7 mg/L(对照589.9 mg/L) | [ |
模型 Model | 功能 Function | AI算法 AI method | 特征提取方法 Feature extraction method | 数据集 Data set | 年份Year | 参考文献Reference |
---|---|---|---|---|---|---|
转运蛋白分类和功能注释Classification and functional annotation of transporters | ||||||
ISTRF | 鉴定蔗糖转运蛋白 | 随机森林 Random Forest | k-separated-bigrams-PSSM | 382个SUT蛋白(蔗糖转运蛋白)和911个非SUT蛋白 | 2022 | [ |
Fiamenghi’s model | 鉴定木糖转运蛋白 | 梯度提升决策树 Gradient Boosting Decision Tree Classifier | HMM and PSSM profiles | 396个蛋白质(其中25个能够转运木糖) | 2022 | [ |
Srinivasan’s model | 鉴定托烷生物碱(TA)转运蛋白 | 监督分类器 Supervised Classifier Models | 基因的序列信息 | 15个TA和15 333个非TA基因 | 2021 | [ |
GT-Finder | 葡萄糖转运蛋白家族的分类 | BERT语言模型 Pre-trained BERT Language Models | 使用预训练的BERT模型生成上下文相关的词嵌入 | 510个GLUT、225个SGLT和190个SWEET葡萄糖转运蛋白 | 2021 | [ |
TooT-T | 鉴别转运蛋白与非转运蛋白 | 支持向量机 Support Vector Machine | 位置特异性迭代氨基酸组成、成对氨基酸组成和伪氨基酸组成 | 900个转运蛋白与660个非转运蛋白 | 2020 | [ |
膜转运蛋白的结构预测Structure prediction of transporters | ||||||
Bergman’s model | 研究底物结合诱导的ω-3脂肪酸转运蛋白MFSD2A中的构象转变 | 深度神经网络分类算法 Deep Neural Network(DNN)Classification Algorithm | 将每个轨迹帧转换为适合输入到DNN的视觉表示 | 分子动力学模拟的数据,4 000个轨迹帧(步幅160 ps)表示OFS集合和4 000帧(步幅为160 ps)表示选择的OcS状态集合 | 2023 | [ |
Mitrovic’s model | 研究糖转运蛋白超家族转运周期中的构象变化 | 卷积神经网络 Convolutional Neural Network | 通过协同进化得分过滤实验接触图 | 实验确定的结构的接触图 | 2023 | [ |
底物与转运蛋白相互作用预测Prediction of the interactions between substrates and transporters | ||||||
Denger’s model | 预测大肠杆菌、拟南芥、酿酒酵母以及人类膜转运蛋白的底物 | 支持向量机 Support Vector Machine | 氨基酸组成、PSSM | 具有已知底物的膜转运蛋白的数据集来自手动策划的Swiss-Prot数据库 | 2022 | [ |
Nguyen’s model | 鉴定转运蛋白的底物特异性 | 神经网络 Neural Network | 使用词嵌入向量作为蛋白质的特征 | 1 197个转运蛋白,其中73个氨基酸转运蛋白、221个电子转运蛋白、88个氢离子转运蛋白、78个脂质转运蛋白、455个蛋白质/mRNA转运蛋白,84个糖转运蛋白,198种其他转运蛋白和1 050种膜蛋白 | 2019 | [ |
表2 基于人工智能研究转运蛋白功能的研究范例
Table 2 Research examples of transporter function based on artificial intelligence
模型 Model | 功能 Function | AI算法 AI method | 特征提取方法 Feature extraction method | 数据集 Data set | 年份Year | 参考文献Reference |
---|---|---|---|---|---|---|
转运蛋白分类和功能注释Classification and functional annotation of transporters | ||||||
ISTRF | 鉴定蔗糖转运蛋白 | 随机森林 Random Forest | k-separated-bigrams-PSSM | 382个SUT蛋白(蔗糖转运蛋白)和911个非SUT蛋白 | 2022 | [ |
Fiamenghi’s model | 鉴定木糖转运蛋白 | 梯度提升决策树 Gradient Boosting Decision Tree Classifier | HMM and PSSM profiles | 396个蛋白质(其中25个能够转运木糖) | 2022 | [ |
Srinivasan’s model | 鉴定托烷生物碱(TA)转运蛋白 | 监督分类器 Supervised Classifier Models | 基因的序列信息 | 15个TA和15 333个非TA基因 | 2021 | [ |
GT-Finder | 葡萄糖转运蛋白家族的分类 | BERT语言模型 Pre-trained BERT Language Models | 使用预训练的BERT模型生成上下文相关的词嵌入 | 510个GLUT、225个SGLT和190个SWEET葡萄糖转运蛋白 | 2021 | [ |
TooT-T | 鉴别转运蛋白与非转运蛋白 | 支持向量机 Support Vector Machine | 位置特异性迭代氨基酸组成、成对氨基酸组成和伪氨基酸组成 | 900个转运蛋白与660个非转运蛋白 | 2020 | [ |
膜转运蛋白的结构预测Structure prediction of transporters | ||||||
Bergman’s model | 研究底物结合诱导的ω-3脂肪酸转运蛋白MFSD2A中的构象转变 | 深度神经网络分类算法 Deep Neural Network(DNN)Classification Algorithm | 将每个轨迹帧转换为适合输入到DNN的视觉表示 | 分子动力学模拟的数据,4 000个轨迹帧(步幅160 ps)表示OFS集合和4 000帧(步幅为160 ps)表示选择的OcS状态集合 | 2023 | [ |
Mitrovic’s model | 研究糖转运蛋白超家族转运周期中的构象变化 | 卷积神经网络 Convolutional Neural Network | 通过协同进化得分过滤实验接触图 | 实验确定的结构的接触图 | 2023 | [ |
底物与转运蛋白相互作用预测Prediction of the interactions between substrates and transporters | ||||||
Denger’s model | 预测大肠杆菌、拟南芥、酿酒酵母以及人类膜转运蛋白的底物 | 支持向量机 Support Vector Machine | 氨基酸组成、PSSM | 具有已知底物的膜转运蛋白的数据集来自手动策划的Swiss-Prot数据库 | 2022 | [ |
Nguyen’s model | 鉴定转运蛋白的底物特异性 | 神经网络 Neural Network | 使用词嵌入向量作为蛋白质的特征 | 1 197个转运蛋白,其中73个氨基酸转运蛋白、221个电子转运蛋白、88个氢离子转运蛋白、78个脂质转运蛋白、455个蛋白质/mRNA转运蛋白,84个糖转运蛋白,198种其他转运蛋白和1 050种膜蛋白 | 2019 | [ |
数据库 Database | 网址 Website | 参考文献 Reference |
---|---|---|
TCDB | https://tcdb.org/ | [ |
VARIDT | http://varidt.idrblab.net/ | [ |
Membranome | http://membranome.org/ | [ |
PDBTM | http://pdbtm.enzim.hu/ | [ |
MPAD | https://web.iitm.ac.in/bioinfo2/mpad | [ |
MPtopo | http://blanco.biomol.uci.edu/mptopo | [ |
SoyTD | http://artemis.cyverse.org/soykb_dev/SoyTD/ | [ |
MTDB | http://bioinformatics.cau.edu.cn/MtTransporter/ | [ |
UCSF-FDA TransPortal | https://transportal.compbio.ucsf.edu/ | [ |
Metrabase | http://www-metrabase.ch.cam.ac.uk | [ |
TP-Search | http://togodb.dbcls.jp/tpsearch | [ |
ABCdb | https://www-abcdb.biotoul.fr/ | [ |
表3 转运蛋白相关数据库
Table 3 Transporter-related databases
数据库 Database | 网址 Website | 参考文献 Reference |
---|---|---|
TCDB | https://tcdb.org/ | [ |
VARIDT | http://varidt.idrblab.net/ | [ |
Membranome | http://membranome.org/ | [ |
PDBTM | http://pdbtm.enzim.hu/ | [ |
MPAD | https://web.iitm.ac.in/bioinfo2/mpad | [ |
MPtopo | http://blanco.biomol.uci.edu/mptopo | [ |
SoyTD | http://artemis.cyverse.org/soykb_dev/SoyTD/ | [ |
MTDB | http://bioinformatics.cau.edu.cn/MtTransporter/ | [ |
UCSF-FDA TransPortal | https://transportal.compbio.ucsf.edu/ | [ |
Metrabase | http://www-metrabase.ch.cam.ac.uk | [ |
TP-Search | http://togodb.dbcls.jp/tpsearch | [ |
ABCdb | https://www-abcdb.biotoul.fr/ | [ |
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