• 特约评述 •
石婷1,2,3, 宋展1,2,3,4, 宋世怡1,2,5, 张以恒1,2,3
收稿日期:
2024-01-07
修回日期:
2024-03-11
出版日期:
2024-04-10
通讯作者:
张以恒
作者简介:
基金资助:
Ting SHI1,2,3, Zhan SONG1,2,3,4, Shiyi SONG1,2,5, Yi-Heng P. Job ZHANG1,2,3
Received:
2024-01-07
Revised:
2024-03-11
Online:
2024-04-10
Contact:
Yi-Heng P. Job ZHANG
摘要:
人类社会的重大挑战(如粮食安全、能源安全、气候变化与双碳目标等)驱动全社会寻求创新型技术解决方案。体外生物转化(in vitro BioTransformation,ivBT)是介于微生物发酵与酶催化之间的新质生物制造平台,多酶分子机器是其超限生物催化剂。它基于大道至简原则,利用多个天然酶、人工酶以及(仿生/天然)辅酶等重构生化途径,摆脱生物体生存局限(如细胞复制、基础代谢、复杂调控和能量供给等),超越细胞合成极限,实现重要生物转化与超限能量转换,尤其是生产低值大宗产品与新能源产品等。工业生物制造的三个平台技术分别是基于细胞工厂的发酵、基于酶分子的生物催化与基于多酶分子机器的ivBT。本综述对ivBT给出明确定义,阐明其多酶途径设计原则与产业化技术研发路径,比较该平台与现有生物制造平台相似性与不同点,介绍多个代表性案例,以及讨论其未来的机会与挑战。ivBT技术发展采用设计-构建-判决-优化的线性策略,开发能够满足国家需求的超高效多酶分子机器。利用ivBT有望形成超过30万亿元生物产品的工业生物制造,助力实现人类社会的多项重要需求,如粮食安全、新型能源体系等。人造淀粉不仅将帮助中国端牢粮食饭碗,而且将是一个全新且安全的高密度储氢载体(比压缩氢气高2.5倍)与高能储电介质(比锂电池高10倍)。
中图分类号:
石婷, 宋展, 宋世怡, 张以恒. 体外生物转化(in vitro BioTransformation,ivBT):生物制造的新前沿[J]. 合成生物学, DOI: 10.12211/2096-8280.2024-004.
Ting SHI, Zhan SONG, Shiyi SONG, Yi-Heng P. Job ZHANG. In vitro BioTransformation (ivBT): new frontier of industrial biomanufacturing[J]. Synthetic Biology Journal, DOI: 10.12211/2096-8280.2024-004.
生物制造平台 | 微生物发酵 (Fermentation) | 酶催化 (Biocatalysis) | 体外生物转化 (ivBT) |
---|---|---|---|
催化剂 | 细胞工厂 | 酶分子、级联多酶 | 多酶分子机器 |
标志性产品 | 初级代谢产物 次级代谢产物 生物大分子 微生物蛋白 | 果葡糖浆 生物质糖 医药原料 NMN | 肌醇、塔格糖 合成淀粉 糖水制绿氢 糖酶燃料电池 |
产品种类 | 极多 | 较多 | 较少 |
优选水解、异构、手性合成等方式合成产品 | 优选异构、糖苷键重排、分解与合成代谢等方式合成产品 | ||
产品规模 | 小、中、大 | 小 | 超大(如能源、粮食) |
浓度(Titer) | 低 | 高 | 高 |
得率(Yield) | 较低 | 高 | 高 |
速率(Rate) | 低 | 最高 | 高 |
生物安全 | 有挑战、强监管 | 好 | 最好 |
技术壁垒 | 低 | 高 | 最高 |
表1 生物制造平台的比较
Table 1 Comparison of biomanufacturing platforms
生物制造平台 | 微生物发酵 (Fermentation) | 酶催化 (Biocatalysis) | 体外生物转化 (ivBT) |
---|---|---|---|
催化剂 | 细胞工厂 | 酶分子、级联多酶 | 多酶分子机器 |
标志性产品 | 初级代谢产物 次级代谢产物 生物大分子 微生物蛋白 | 果葡糖浆 生物质糖 医药原料 NMN | 肌醇、塔格糖 合成淀粉 糖水制绿氢 糖酶燃料电池 |
产品种类 | 极多 | 较多 | 较少 |
优选水解、异构、手性合成等方式合成产品 | 优选异构、糖苷键重排、分解与合成代谢等方式合成产品 | ||
产品规模 | 小、中、大 | 小 | 超大(如能源、粮食) |
浓度(Titer) | 低 | 高 | 高 |
得率(Yield) | 较低 | 高 | 高 |
速率(Rate) | 低 | 最高 | 高 |
生物安全 | 有挑战、强监管 | 好 | 最好 |
技术壁垒 | 低 | 高 | 最高 |
体外生物转化(ivBT) | 多酶级联催化(CEB) | 无细胞蛋白质合成(CFPS) | |
---|---|---|---|
目标 | 大规模生物制造 产品规模:>1万吨,甚至10亿吨级 | 精细生物制造 精细产品:~1000公斤级, <100吨 | 研究工具 特殊制造(快速生产克级蛋白质) |
代表性产品 | 粮食、能源、材料 (如淀粉、绿氢、肌醇、塔格糖) | 药物中间体(NMN) | 疫苗合成 |
产品市场规模 (每个产品) | 5亿(最小市场) →100亿(塔格糖) →10万亿(绿氢) | 千万(最大市场低于5亿) | NA |
目标产品数目 | ~100(粮食、能源等大宗产品) | ~10,000(精细化学品) | NA |
原料成本/ 产品价格 | >50%→90%(最大) | 5%→20% | NA |
合成途径设计 | 非天然途径与人造电子传递链 | 主反应与辅酶再生,利用部分天然途径 | 利用天然合成途径 |
催化元件 | 天然(超稳)酶、人工酶、固定化多酶、(仿生)辅酶再生 | 天然(常温)酶、改造酶、固定化酶、辅酶再生 | 细胞裂解液或纯化元件、外加氨基酸、ATP供体、DNA模板 |
元件需求 | 超低成本酶、超稳定固定化酶、价廉且稳定(仿生)辅酶 | 酶成本不敏感,利用天然辅酶 | 利用细胞裂解液中的有效成分 |
生产周期 | 天、周、月(多次,连续) | 小时、天(一次,极少多次) | 小时(一次) |
表2 ivBT 与相似技术的区分
Table 2 Comparison of ivBT with similar biotechnologies
体外生物转化(ivBT) | 多酶级联催化(CEB) | 无细胞蛋白质合成(CFPS) | |
---|---|---|---|
目标 | 大规模生物制造 产品规模:>1万吨,甚至10亿吨级 | 精细生物制造 精细产品:~1000公斤级, <100吨 | 研究工具 特殊制造(快速生产克级蛋白质) |
代表性产品 | 粮食、能源、材料 (如淀粉、绿氢、肌醇、塔格糖) | 药物中间体(NMN) | 疫苗合成 |
产品市场规模 (每个产品) | 5亿(最小市场) →100亿(塔格糖) →10万亿(绿氢) | 千万(最大市场低于5亿) | NA |
目标产品数目 | ~100(粮食、能源等大宗产品) | ~10,000(精细化学品) | NA |
原料成本/ 产品价格 | >50%→90%(最大) | 5%→20% | NA |
合成途径设计 | 非天然途径与人造电子传递链 | 主反应与辅酶再生,利用部分天然途径 | 利用天然合成途径 |
催化元件 | 天然(超稳)酶、人工酶、固定化多酶、(仿生)辅酶再生 | 天然(常温)酶、改造酶、固定化酶、辅酶再生 | 细胞裂解液或纯化元件、外加氨基酸、ATP供体、DNA模板 |
元件需求 | 超低成本酶、超稳定固定化酶、价廉且稳定(仿生)辅酶 | 酶成本不敏感,利用天然辅酶 | 利用细胞裂解液中的有效成分 |
生产周期 | 天、周、月(多次,连续) | 小时、天(一次,极少多次) | 小时(一次) |
图4 ivBT 的体外肌醇合成途径(A) αGP—α-葡聚糖磷酸化酶;PGM—葡萄糖 6-磷酸异构酶;IPS—肌醇 3-磷酸合成酶;IMP—肌醇单磷酸磷酸酶; IA—异淀粉酶;(B)首个 ivBT 肌醇工业化生产工厂图片
Fig. 4 Inositol synthesis pathway of ivBT(A) αGP—α-glucan phosphorylase; PGM—phosphoglucomutase; IPS—inositol 3-phosphate synthase; IMP—inositol monophosphatase; IA—isoamylase; (B)Image of the first large-scale inositol factory
图5 ivBT 利用淀粉合成健康糖的人工合成途径αGP、PGM、IPS、IMP 同肌醇合成途径。PGI—葡萄糖 6-磷酸异构酶;FPP—果糖 6-磷酸磷酸酶;TPE—塔格糖 6-磷酸 4-差向异构酶;TPP—塔格糖 6-磷酸磷酸酶;MPI—甘露糖 6-磷酸异构酶;MPP—甘露糖 6-磷酸磷酸酶;API—阿洛酮糖 6-磷酸异构酶;APP—阿洛酮糖 6-磷酸磷酸酶
Fig. 5 Rare sugars artificial synthesis pathway of ivBTEnzymes of αGP, PGM, IPS, IMP are the same as inositol synthesis pathway. PGI—phosphoglucose isomerase; FPP—fructose 6-phosphatase; TPE—tagatose 6-phosphate 4-epimerase; TPP—tagatose 6-phosphatase; MPI—mannose 6-phosphate isomerase; MPP—mannose 6-phosphatase; API—allulose 6-phosphate isomerase; APP—allulose 6-phosphatase
图 6 ivBT 的体外纤维素合成淀粉途径EG—内切葡聚糖酶;CBH—纤维二糖水解酶;CBP—纤维二糖磷酸化酶;PGP—马铃薯 α-葡聚糖磷酸化酶
Fig. 6 Cellulose-amylose synthesis pathway of ivBTEG—endoglucanase; CBH—cellobiohydrolase; CBP—cellobiose phosphorylase; PGP—potato α-glucan phosphorylase
图7 ivBT 的体外 CO2 合成淀粉途径[96]AOX—醇氧化酶;FIS—甲醛酶;DAK—二羟基丙酮激酶;TIM—磷酸甘油醛异构酶;ALD—果糖 1,6-二磷酸醛缩酶;FBP—果糖 1,6-二磷酸酶;PGI—葡萄糖 6-磷酸异构酶;PGM—葡萄糖6-磷酸变位酶;AGP—ADP-葡萄糖焦磷酸化酶;SS—淀粉合成酶;CAT—过氧化氢酶;PPK—多聚磷酸激酶;PPA—焦磷酸酶
Fig. 7 CO2-Starch synthesis pathway of ivBT[96]AOX—alcohol oxidase; FIS—formolase; DAK—dihydroxyacetone kinase; TIM—triose phosphate isomerase; ALD—fructose-bisphosphate aldolase; FBP—fructose bisphosphatase; PGI—phosphoglucose isomerase; PGM—phosphoglucomutase; AGP—ADP-glucose pyrophosphorylase; SS—starch synthase; CAT—catalase; PPK—polyphosphate kinase; PPA—pyrophosphatase
图8 淀粉体外合成氢气途径αGP 和 PGM 同肌醇合成途径。G6PDH—葡萄糖 6-磷酸脱氢酶;6PGL—6-磷酸葡萄糖内酯酶;6PGDH—6-磷酸葡萄糖酸脱氢酶;RPI—核糖 5-磷酸异构酶;RPE—核酮糖 5-磷酸 3-差向异构酶;TK—转酮酶;TAL—转醛酶;TIM—磷酸甘油醛异构酶;ALD—果糖1,6-二磷酸醛缩酶;FBP—果糖1,6-二磷酸酶;PGI—葡萄糖6-磷酸异构酶;SHI—氢酶;NROR—NADPH-红氧还蛋白氧化还原酶;DI—心肌黄酶。代谢物:g1p—葡萄糖 1-磷酸;g6p—葡萄糖 6-磷酸;ru5p—核酮糖 5-磷酸;x5p—木糖 5-磷酸;r5p—核糖 5-磷酸;s7p—景天庚酮糖 7-磷酸;g3p—甘油醛 3-磷酸;e4p—赤藓糖 4-磷酸;dhap—磷酸二羟丙酮;fdp—果糖1,6-二磷酸;f6p—果糖 6-磷酸。
Fig. 8 Hydrogen synthesis pathway of ivBTEnzymes of αGP and PGM are the same as inositol synthesis pathway. G6PDH—glucose 6-phosphate dehydrogenase; 6PGL—6-phosphogluconolactonase; 6PGDH—6-phosphogluconate dehydrogenase; RPI—ribose 5-phosphate isomerase; RPE—ribulose 5-phosphate 3-epimerase; TK—transketolase; TAL—transaldolase; TIM—triose phosphate isomerase; ALD—fructose-bisphosphate aldolase; FBP—fructosebisphosphatase; PGI—phosphoglucose isomerase; SHI—soluble hydrogenase I; NROR—NADPH rubredoxin oxidoreductase; DI—diaphorase. The metabolites are: g1p—glucose 1-phosphate; g6p—glucose 6-phosphate; ru5p—ribulose 5-phosphate; x5p—xylulose 5-phosphate; r5p—ribose 5-phosphate; s7p—sedoheptulose 7-phosphate; g3p—glyceraldehyde 3-phosphate; e4p—erythrose 4-phosphate; dhap—dihydroxacetone phosphate; fdp—fructose 1,6-diphosphate; f6p—fructose 6-phosphate.
细胞工厂的局限 | 体外生物转化的优势 | |
---|---|---|
生长偶联 | 细胞生长繁殖与产品制造的耦合,存在有限资源竞争、分配与调控等难题 | 催化剂合成与产品制造时空分离,产品制造是唯一目标 |
产品得率 | 产品得率低(由于细胞繁殖、副产物生成等问题) | 近理论得率 |
能量限制 | 生物能量学限制,需 ATP与还原力的净合成 | ATP 与还原力的平衡,不浪费生物能量 |
反应速率 | 反应速度(Rxn)低 | Rxn提升10倍以上 |
生物大分子 合成 | 生物大分子不能通过细胞 | 没有细胞膜,大分子降解与合成耦合 |
特殊极性分 子合成 | 特殊极性分子合成如磷酸糖不能过细胞膜 | 没有细胞膜,自由扩散 |
三传限制 | 细胞体内三传“动量传递、热量传递、质量传递”限制 | 超限制造(微通道反应器)超越传统“三传”限制 |
表3 ivBT 作为工业生物制造平台的技术优势
Table 3 Advantages of ivBT for biomanufacturing
细胞工厂的局限 | 体外生物转化的优势 | |
---|---|---|
生长偶联 | 细胞生长繁殖与产品制造的耦合,存在有限资源竞争、分配与调控等难题 | 催化剂合成与产品制造时空分离,产品制造是唯一目标 |
产品得率 | 产品得率低(由于细胞繁殖、副产物生成等问题) | 近理论得率 |
能量限制 | 生物能量学限制,需 ATP与还原力的净合成 | ATP 与还原力的平衡,不浪费生物能量 |
反应速率 | 反应速度(Rxn)低 | Rxn提升10倍以上 |
生物大分子 合成 | 生物大分子不能通过细胞 | 没有细胞膜,大分子降解与合成耦合 |
特殊极性分 子合成 | 特殊极性分子合成如磷酸糖不能过细胞膜 | 没有细胞膜,自由扩散 |
三传限制 | 细胞体内三传“动量传递、热量传递、质量传递”限制 | 超限制造(微通道反应器)超越传统“三传”限制 |
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