2021, Vol. 48扩展功能
文章信息
- 任鄄宝, 邹根, 张赫男, 龚明, 吴迪, 张忠, 杨焱
- REN Juanbao, ZOU Gen, ZHANG Henan, GONG Ming, WU Di, ZHANG Zhong, YANG Yan
- 微生物多糖合成关键基因挖掘的研究进展
- Summary of progress in mining crucial genes involved in microbial polysaccharides synthesis
- 微生物学通报, 2021, 48(6): 2131-2142
- Microbiology China, 2021, 48(6): 2131-2142
- DOI: 10.13344/j.microbiol.china.200886
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文章历史
- 收稿日期: 2020-09-02
- 接受日期: 2020-11-21
- 网络首发日期: 2021-03-11
任鄄宝, 邹根, 张赫男, 龚明, 吴迪, 张忠, 杨焱. 微生物多糖合成关键基因挖掘的研究进展[J]. 微生物学通报, 2021, 48(6): 2131-2142.
REN Juanbao, ZOU Gen, ZHANG Henan, GONG Ming, WU Di, ZHANG Zhong, YANG Yan. Summary of progress in mining crucial genes involved in microbial polysaccharides synthesis[J]. Microbiology China, 2021, 48(6): 2131-2142.
微生物多糖合成关键基因挖掘的研究进展
1. 国家食用菌工程技术研究中心 农业农村部南方食用菌资源利用重点实验室 上海市农业科学院食用菌研究所 上海 201403;
2. 上海海洋大学食品学院 上海 201306
2. 上海海洋大学食品学院 上海 201306
摘要: 随着分子生物学技术的快速发展，功能基因的挖掘在微生物高产多糖合成关键途径研究中变得越来越重要，不断发展的基因挖掘方法和基因组分析工具推进了研究的深入进行。本文主要综述了近年来报道的微生物多糖生物合成途径和多糖合成途径中的关键酶，以及利用多种技术手段和分析软件工具对多糖合成关键基因进行挖掘和验证的相关研究，为微生物多糖合成关键基因的验证以及微生物高产多糖菌株的制备提供参考。
关键词:
微生物多糖 多糖合成途径 基因挖掘 功能验证
Summary of progress in mining crucial genes involved in microbial polysaccharides synthesis
1. National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungal Resources and Utilization (South), Ministry of Agriculture and Rural Affairs, China, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China;
2. College of Food Science, Shanghai Ocean University, Shanghai 201306, China
2. College of Food Science, Shanghai Ocean University, Shanghai 201306, China
Abstract: Profiting from the rapid development of molecular biology technology, functional genomics plays an increasingly important role in analyzing microbial polysaccharide synthesis pathways. Various gene mining methods and genomics analysis tools facilitate the study of genes responsible for microbial polysaccharides synthesis. Here, we summarize the recent studies in biosynthetic pathway of versatile microbial polysaccharide biosynthesis and the key enzymes involved, the techniques and software package used for gene mining and function verification. This review will provide a reliable technical reference for crucial genes verification in microbial polysaccharide synthesis and feasible solutions in strain engineering with elevating production titer.
Keywords:
microbial polysaccharides polysaccharide synthesis pathway gene mining function verification
微生物多糖是微生物在新陈代谢过程中产生的生物高聚物[1]，主要包含细菌脂多糖、酵母菌多糖、大型真菌多糖等[2]。微生物多糖从形态上又可分为胞内多糖、胞壁多糖和胞外多糖[3]。微生物多糖有着安全稳定、应用面广等多种优点，可在人工控制条件下大批量生产，在未来健康医药工业领域有广阔的应用前景。
20世纪70年代以来，大量研究证实微生物多糖是微生物生命活动中产生的具有保护作用的高聚化合物，是其行使正常生理功能所不可或缺的组成部分[4]，如作为细胞壁的主要成分等[5]。此外，大量研究表明微生物多糖在不同程度上表现出免疫调节[6-11]、抗氧化[12-14]、调节糖脂代谢[15-16]、抗肿瘤[17-19]、抗癌[20-21]、抗炎[22]、抗疲劳[23]、保肝护胃[24]等多种生物学活性，在医药[25-26]、材料[27]、食品、化妆品等领域具有广泛应用价值。随着微生物多糖潜在用途的不断开发，其应用范围也更加广泛，尤其是食用菌多糖在很多方面都发挥着重要的作用，如作为保健药品的蛹虫草多糖[28]、作为抗肿瘤辅助用药的灵芝多糖[29]、作为功能饮料成分的猴头菇多糖[30]、作为饲料喂养牲畜的酵母多糖[31]、作为化妆品活性成分的银耳多糖[32]等。随着微生物多糖的应用越来越广，其需求量也在逐年增大，因此，对微生物多糖合成途径的研究也受到更多研究者的关注[33]。在此基础之上，本综述对有关微生物多糖合成途径及关键基因的挖掘和验证工作进行总结，以期为食用菌多糖合成关键基因的发现以及食用菌高产多糖菌株的制备提供参考。
1 微生物多糖的合成途径对于多糖的合成途径而言，细菌中多糖合成途径的研究已经有一些报道，但对真菌多糖的研究却鲜有报道[34]。然而，真菌与细菌的多糖合成基本途径具有一定的相似度，基本合成途径分为前体的供给、合成的起始、单糖聚合和多糖输出[35-37]。
有研究人员利用同位素示踪法对多糖合成途径进行研究[38]，也有研究人员运用基因过表达等分子手段进行相关研究[39]。图 1对已发表论文中微生物多糖合成的主要途径进行了概括。微生物生长主要利用的底物葡萄糖，在葡糖激酶作用下生成葡萄糖-6-磷酸，进而在不同关键酶作用下生成不同的核苷酸糖，作为多糖合成的前体物质。这个过程中包括多种代谢途径和关键酶的作用：(1) 葡萄糖-6-磷酸在α-磷酸葡糖变位酶的作用下和乳糖经酶系11作用生成葡萄糖-1-磷酸，进而在UDP-葡萄糖焦磷酸化酶、UDP-葡萄糖-4-差向异构酶、NAD连接的脱氢酶等关键酶作用下生成了UDP-葡萄糖、UDP-半乳糖等[40-42]；(2) 葡萄糖-6-磷酸转化为甘露糖-6-磷酸后，在磷酸甘露糖变位酶、GDP-甘露糖焦磷酸化酶、脱水酶和GDP-岩藻糖合成酶等作用下生成了GDP-甘露糖和GDP-岩藻糖，为多糖的合成提供了前体物质[43-44]；(3) 葡萄糖-6-磷酸在磷酸葡糖异构酶作用下及果糖为碳源时都生成了果糖-6-磷酸，进而在相关关键酶作用下生成GDP-果糖和UDP-N-乙酰半乳糖胺[45]；(4) 葡萄糖-6-磷酸代谢过程中生成的部分果糖-6-磷酸在机体需要时会转化为丙酮酸进入厌氧途径生成乳酸，或进入TCA循环生成ATP、辅酶等其他产物，为多糖合成提供能量保证，进而在葡聚糖合成酶的作用下利用多糖合成前体合成多糖[46]。因为微生物多糖合成途径的相似性，可以重点关注合成通路里的关键酶，通过调控关键酶的表达水平，促进特定结构多糖的合成代谢流，进而提高多糖的产量。
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| 图 1 微生物中多糖合成的主要途径 Figure 1 Diagrammatic sketch of microbial polysaccharides synthesis pathway 注：1：葡糖激酶；2：α-磷酸葡糖变位酶；3：UDP-葡萄糖焦磷酸化酶；4：UDP-葡萄糖-4-差向异构酶；5：NAD连接的脱氢酶；6：葡萄糖-1-磷酸胸苷转移酶；7：鼠李糖合成酶系；8：磷酸甘露糖变位酶和GDP-甘露糖焦磷酸化酶；9：脱水酶和GDP-岩藻糖合成酶；10：磷酸葡糖异构酶；11：乳糖转化为1-磷酸-葡萄糖酶系 Note: 1: Glucokinase; 2: α-phosphate glucose mutase; 3: UDP-glucose pyrophosphorylase; 4: UDP-glucose-4-epimerase; 5: NAD-linked dehydrogenase; 6: Glucose-1-phosphothymidine transferase; 7: Rhamnose synthase system; 8: Mannose phosphate mutase and GDP-mannose pyrophosphorylase; 9: Dehydrase and GDP-fucose synthase; 10: Phosphoglucose isomerase; 11: Enzymes responsible for converting into 1-phospho-glucose |
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基因挖掘验证的一般技术路线主要有3个环节：基于生物信息学的基因挖掘、基于遗传转化、异源表达的基因验证和转化后的产物分析。如图 2所示，首先是在多组学数据和生物信息学分析的基础上，通过各种分析软件和工具对目标基因进行筛选，获得具有研究价值的关键基因；然后利用沉默、异源表达等多种分子生物学手段对关键基因进行功能验证分析，通过构建不同功能的基因表达载体，在模式菌株中进行基因水平、蛋白水平和酶活水平的验证；最后再通过在本物种内同源表达并对产物进行深入分析，获得相关基因表达量、产物、组分和生物活性分析等多种结果，从产物层次进行综合分析验证，以期获得促进多糖合成的关键基因。基因簇挖掘技术的不断发展，大大促进了新的功能基因研究、新型天然产物的发现和生物功能信息分析等的发展。
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| 图 2 基因挖掘验证的一般技术路线 Figure 2 Flowchart of gene mining and verifying |
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生物信息学分析是对所研究物种进行全基因组测序后，通过生物信息学分析网站和软件对潜在的基因进行功能片段分析预测，进而聚焦到目标基因簇。由于多糖类物质合成过程复杂，涉及的关键酶和基因较多，往往需要进行多组学的整合分析预测，进而挖掘出部分多糖合成关键基因并进行实验验证，从而确定其在多糖合成中的作用[47]。
随着当今大数据的快速发展，不断更新的数据库为我们进行数据挖掘提供了充分的便利。如Carbohydrate-Active Enzymes Database (CAZy，http://www.cazy.org)中就收录了75个真核生物和2 870个细菌的全基因组测序结果。多个实验结果表明，尽管细菌多糖的种类很多，结构复杂多变，但其生物合成机制却具有一定的相似性[48]。
利用三代测序技术进行关键基因挖掘是生物信息学分析的实践应用典范。在对基因组、转录组和蛋白质组的多组学分析后，利用表 1中程序和数据库对基因进行比对，初步确定未知基因在生物体内的功能，为目的基因的发现提供方向。如Wang等的研究中，通过生物信息学分析手段确定了一个胞外多糖合成相关基因(epsN)，表明其在胞外多糖合成途径中起关键作用，并利用分子遗传学技术对其进行了验证分析[49]。
表 1 基因组挖掘中的生物信息学分析工具和数据库
Table 1 Bioinformatics analysis tools and databases for genome mining
| 程序和数据库 Programs and databases |
功能简介 Brief introduction of the function |
内容相关网址 Content-related website |
| BLAST | BLAST可以把测定的氨基酸或核苷酸序列提交到数据库进行比对分析, 并在一定的要求范围下计算相似度, 可用于菌种的鉴定、结构域定位和功能注释等 BLAST can submit the amino acid or nucleotide sequence to the database for comparative analysis, and calculate the similarity within a certain range of requirements.It can be used for species identification, domain location and functional annotation, etc |
https://blast.ncbi.nlm.nih.gov/Blast.cgi |
| Metascape | Metascape数据库覆盖面相当广泛, 整合了GO、KEGG和DrugBank等多个权威的数据资源, 不仅能完成通路富集和生物过程注释, 还能做基因相关的蛋白质网络分析和涉及的药物分析等 The Metascape database covers a wide range of data sources, including GO, KEGG and DrugBank.It not only completes pathway enrichment and annotation of biological processes, but also performs gene-related protein network analysis and drug analysis |
http://metascape.org/gp/index.html |
| HMMER | HMMER可以对未知功能的蛋白序列在数据库中进行比对、分析及注释, 而且蛋白家族数据库Pfam和InterPro也都使用了HMMER的算法进行数据分析 HMMER can compare, analyze and annotate the unknown protein sequences in the database.HMMER's algorithm was also used in both Pfam and InterPro databases for data analysis |
https://myhits.isb-sib.ch/cgi-bin/hmmer3_search |
| 北京大学生物信息学中心 Bioinformatics Center, Peking University |
欧洲分子生物学组织的中国国家节点, 而且与多个国外生物信息中心建立了合作关系, 是目前国内数据库种类最多、数据量最大的生物信息站点 It is the National node of the European Organization for Molecular Biology.Besides, it has established cooperative relations with many foreign biological information centers, and is the biological information site with the most kinds of databases and the largest amount of data in China |
http://www.cbi.pku.edu.cn/ |
| CAZy | CAZy是着重于分析碳水化合物活性酶基因组的专家数据库, 可以通过比对碳水化合物活性酶的基因组内容来获取数据 CAZy is an expert database focusing on the analysis of the genome of active carbohydrate enzymes.Data can be obtained by comparing the genome contents of active carbohydrate enzymes |
http://www.cazy.org/ |
分子遗传学是一门着重研究基因结构及其功能的学科，倾向于研究基因在分子遗传学系统中的储存、复制、表达及其调控过程。自21世纪以来，随着DNA测序方法和PCR技术的建立和快速发展，限制酶和同源重组连接酶的接连发现，为基因功能的验证提供了更加强有力的帮助。
2.2.1 微生物多糖合成通路关键基因验证(1) 基因敲除
基因敲除是在生物信息学预测基础上直接对基因功能进行验证的实验研究，利用同源重组原理在基因组上定点缺失目的基因，通过抑制目的基因的正常表达，进而检测基因缺失菌株各项生理数据的变化，推断该基因的生物学功能，验证生物信息学预测的结果。
江军等比对了副猪嗜血杆菌(Haemophilus parasuis)野生菌株和iscR基因(编码转录调节因子iscR蛋白)缺失株内胞外多糖(Exopolysaccharides，EPS)合成基因簇中capD (编码多糖生物合成蛋白)基因表达量的变化，经体外培养发现iscR缺失株的capD基因表达量显著降低，透射电镜观察到在外部刺激下野生菌株荚膜厚度约有95 nm，而iscR缺失株无明显荚膜生成，由此推测iscR基因可能是表面荚膜多糖的合成关键基因[33]。
Guo等运用分子生物学技术敲除了柑橘溃疡病菌(Xanthomonas citri subsp. citri)的UDP-葡萄糖焦磷酸化酶(Uridine Diphosphate Glucose Pyrophosphorylase) ugp基因后，检测UDP-葡萄糖(Uridine Diphosphate Glucose，UDP-Glc)含量后发现，与出发菌株相比，敲除ugp基因后菌株的UDP-Glc含量大量减少，导致多糖合成途径中前体物质供给减少，因此可以判断ugp基因是多糖合成途径中的关键基因[50]。Daran等通过构建磷酸葡萄糖变位酶(Phosphoglucomutase) pgm基因敲除载体，在对胞外液成分检测后发现，pgm基因敲除载体菌株的葡萄糖水平是其他菌株的3倍；结果表明，由于磷酸葡萄糖变位酶的缺失，减缓了葡萄糖-6-磷酸到葡萄糖-1-磷酸的转化过程，使得葡萄糖-6-磷酸大量沉积，进而减少了培养基中葡萄糖的利用，侧证了葡萄糖-6-磷酸转化为葡萄糖-1-磷酸的通路及关键基因[51]。
近年来，基于CRISPR/Cas9基因编辑技术的飞速发展，我们研究团队也最早在丝状真菌建立了该技术体系，并在真菌基因研究方面上取得了很多的成果[52-54]。但对多糖合成相关基因的研究还是鲜有发表，因此，利用基因编辑技术对多糖合成关键基因进行挖掘验证有望成为更快速省力的方法。
(2) 基因过表达验证
基因过表达是将生物信息学分析获得的可能目的基因重组到人工过表达载体上，使目的基因调控的产物得到充分表达，进而通过测定多糖合成途径中的前体物质和产物的含量来进行综合分析。
利用基因过表达方法对基因功能进行分析也有着事半功倍的效果。如Rodríguez-Díaz等通过构建重组过表达菌株，在干酪乳杆菌(Lactobacillus casei)中同源过表达了BL23基因(编码ugp)，在后续的酶活检测中发现其酶活提高了约70倍，UDP-Glc的浓度也提升了8.5倍，因此推断BL23基因是UDP-葡萄糖合成途径中的关键基因[55]。
已有研究报道，通过过表达灵芝多糖合成途径中的关键基因，可以显著提高多糖的合成产率。如Xu等在灵芝中过表达pgm基因，与出发菌株相比，胞内多糖(Intercellular Polysaccharide，IPS)和EPS的最大产量分别提高了40.5%和44.3%；灵芝多糖合成相关基因pgm和ugp的转录水平与出发菌株相比分别提高了4.77倍和1.51倍[56]。Ji等在灵芝中高表达了ugp基因，与出发菌株相比，IPS和EPS分别提高了42%和36%；pgm和ugp基因的转录水平分别提高了1.6倍和2.6倍[57]。此外，曹春红等构建了过表达pgm2基因的酿酒酵母重组菌株AYPGM，与出发菌株各项指标比对发现，pgm2基因的过表达明显降低了葡萄糖的阻遏效应，使发酵时间缩短了25%，表明pgm2基因在酿酒酵母多糖合成中发挥关键作用[58]。
(3) 基因沉默验证
基因沉默是在RNA水平上通过控制mRNA的翻译进而调控目的基因表达的一种方式。近几年来，通过人工合成miRNA或者构建RNA沉默载体等高效特异地抑制某一mRNA的翻译，从而了解基因的生物学功能和对细胞生长分化的作用。
基因沉默技术给目的基因的挖掘提供了新的方法。如Bouazzaoui等应用反义RNA沉默鼠李糖乳杆菌(Lactobacillus rhamnosus)中糖基转移酶基因，通过检测结果发现突变体中的糖基转移酶含量大大减少，产生了新的不同分子量的EPS，从而确定糖基转移酶基因在EPS合成过程中发挥着不可替代的作用[59]。
我们团队首次克隆鉴定了灰树花中的葡聚糖合酶基因(Grifola frondosa Glucan Synthase，gfgls)，通过构建的双启动子RNA沉默载体获得了转化株igfgls-3，定量PCR显示gfgls基因的转录表达水平降低了26.1%，而且菌丝体生物量和EPS分别下降至5.02 g/L和0.38 g/L，这些结果表明gfgls基因在菌丝体生长和胞外多糖的合成中有着重要作用[60]。Malinova等利用amiRNA (Artificial microRNA)技术沉默了拟南芥的pgm基因后，沉默突变体中的葡萄糖、葡萄糖-6-磷酸和果糖-6-磷酸的含量都显著高于出发菌株，对实验结果分析后可以看出，由于沉默突变体自身缺少了磷酸葡糖异构酶，使得突变体对葡萄糖的利用率大大降低，所吸收的葡萄糖也因此转向了果糖-6-磷酸通路[61]。
(4) 异源表达
在利用分子遗传验证时按照宿主的不同分为同源表达和异源表达[62]。由于大型真菌遗传转化体系的构建尚不够成熟，在大多数同源菌中进行基因的遗传验证较为困难，所以在异源或者模式菌株中进行遗传验证，能更有效地进行目的基因的功能检测，以便于微生物基因资源的开发利用[63]。
因为异源表达的可操作性较强，所以有很多研究学者在此方向上取得了不错的研究成果[64]。如Stingele等在嗜热链球菌Sfi6中克隆了一个15 kb的EPS基因簇，其可编码多个与多糖合成密切相关基因，并且成功地在乳酸乳球菌MG1363中进行了异源表达，取得了理想的结果[65]。李阳等在大肠杆菌E. coli BL21(DE3)中对pgm进行了异源表达，并探究了其相关酶学性质，为灵芝多糖合成发酵策略的高效制定提供了依据[66]。
2.2.2 微生物多糖合成旁路关键基因验证在挖掘多糖合成关键基因时发现，多糖合成不仅与合成途径中的关键酶有密切的关联，糖代谢中能量的传递和底物的供给等也同样发挥着重要的作用，因此部分研究人员从这个角度进行基因挖掘，得到部分关键基因的生物学作用，以期促进微生物多糖产率的增加。
(1) 利用其他底物合成多糖的拯救途径
刘现伟发现了一种糖核苷供体拯救途径的相关酶GDP-岩藻糖焦磷酸化酶(GDP-Fucose Pyrophosphorylase，FKP)，并对其在大肠杆菌中进行了重组过量表达；当大肠杆菌菌株的GDP-Fuc合成途径失效后，大肠杆菌可以从培养基中直接吸收利用岩藻糖类似物或其他单糖用于糖核苷合成，进而作为细菌表面多糖的供体[67]。
(2) 通过控制细胞生长来促进多糖合成的途径
有研究表明除了多糖合成途径中的关键基因以外，持家基因也与多糖的合成密切相关，它们的表达量也会对多糖合成产生一定的影响[68-70]。因此，利用分子生物学技术对这类基因进行实验研究，验证其对多糖合成的促进作用，可从多方面提升多糖产率。
如Li等构建了甘油-3-磷酸脱氢酶基启动子和透明颤菌血红蛋白(Vitreoscilla Globin) vgb基因的重组载体并成功转入灵芝，结果显示IPS和EPS分别为26.4 mg/100 mg和0.83 g/L，分别比野生型菌株提高30.5%和88.2%，pgm和ugp的转录水平分别上调了1.51倍和1.55倍，证实了透明质酸的过量表达对灵芝高产多糖的促进作用[71]。Liu等也进行了相似的实验并获得了同样的结果[72]。董玉国等将vgb基因导入到短密青霉ATCC16024中用于改善菌体对氧的摄取能力，发酵结果表明vgb基因在短密青霉中成功获得了表达，而且大大提高了短密青霉的菌体密度，比原始菌株提高了约27.5%[70]。
(3) 改变调控因子和辅酶水平从而促进多糖合成
有研究表明通过调节调控因子的水平，使相关基因表达量上升[73-74]或提高辅酶水平使菌株产生更高的能量代谢流，进而提高多糖合成的产率是可行的。因此，Li等利用分子生物学技术在干酪乳杆菌中过表达NADH氧化酶，使得菌株的多糖产量提高46%[75]；在对铜绿假单胞菌分别过表达调控因子CupB5和ClpXP基因后，使得海藻糖的产量提高了20%和22%，极大地提升了菌株的多糖合成产量[76-77]。
3 展望近年来，随着基因组测序技术的快速发展和基因挖掘方法的不断更新，微生物多糖合成关键基因的挖掘工作有了更多的技术支撑，并不断取得新突破。微生物尤其是真菌产生的多糖作为一种天然免疫调节剂具有多种生物学功能，而通过菌株发酵的工业化生产获得这些物质更是未来发展的趋势。通过生物信息学和分子生物学技术整合，阐明多糖的合成代谢通路及调控的关键基因，对获得多糖高产菌株的分子育种及代谢通路调控具有重要的科学意义，也是具有潜力的研究方向[78-79]。
多糖合成途径研究已经在酵母菌、乳酸菌等微生物中获得了一些成果，而在大型真菌中几乎还是空白。因此，以微生物多糖合成代谢中发现的通路和关键基因为基础，继续对香菇、猴头菌、灵芝等食药用菌多糖的合成途径进行深入挖掘将是未来的研究方向。而利用分子生物学技术进行高产多糖优势菌株关键基因的挖掘验证，可为构建微生物高产多糖菌株奠定理论基础。
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