产生3‑羟基丙酸的重组酵母和使用其产生3‑羟基丙酸的方法与流程

本发明涉及产生3-羟基丙酸(3-hp)的重组酵母和使用其产生3-hp的方法，更具体地，涉及产生3-hp的重组酵母，其包含编码aadh的外源基因、编码acc的内源基因或外源基因、编码mcr的外源基因和编码hpdh的外源基因，并通过[丙酮酸(pyruvate)→乙醛→乙酰辅酶a→丙二酰辅酶a→丙二酸半醛→3-hp]的生物合成途径产生3-hp，以及使用该重组酵母产生3-hp的方法。
背景技术：
：：3-hp(3-羟基丙酸，c3)是乳酸(2-羟基丙酸)的异构体，在其两端具有羧酸基和羟基，因此是能够转化成各种化学品(如1,3-丙二醇、丙烯酸、丙烯酰胺、聚合物等)的有用材料。实际上，由于上述原因，2004年3-hp被美国能源部选为能够由生物质生产的有前途的化学品之一。特别地，作为用于涂料、粘合剂、添加剂、尿布等的高度市场化的材料，丙烯酸是3-hp的主要应用形式。3-hp理论上可以通过发酵从诸如葡萄糖的各种生物质中以100％的收率生产，使用微生物的发酵工艺适合于满足对生态环境友好和可再生材料的需求。还没有利用生物质商业生产3-hp的情况，但已经对各种方法进行了研究，获得经济的3-hp产生菌株成为主要障碍。细菌被公认为是产生有机酸的代表性微生物，并广泛用于工业如食品工业等。然而，将使用工业细菌(如大肠杆菌)的有机酸生产应用于大规模化学工业(如3-hp生产)存在缺点。随着有机酸的产量增加，氢化形式的酸增加，酸性增加(ph降低)，从而大多数大肠杆菌的活性降低。在生产高浓度的有机酸的情况下，细菌需要碱如氢氧化钠(naoh)和氢氧化铵(nh4oh)来保持中性ph。这导致依赖于注入的碱的发酵过程的成本增加，使提取和分离过程难以进行或者使成本显著增加。在最近的将有机酸生产应用于化学工业的情况中，使用酵母从葡萄糖生产有机酸。与细菌相比，酵母对有机酸具有高耐受性，因此即使在高酸性(低ph)下酵母的活性也不会被显著抑制，使得酵母成为更合适的用于生产有机酸的宿主。特别地，酵母已经被常规地、广泛地用作用于生产烈酒、工业乙醇等的工业生物催化剂，酵母可以被大规模地培养并且可以不被噬菌体污染，使得酵母与细菌相比在化学工业中的适用性更加优异。酵母具有产生有机酸的优点，但是使用酵母产生有机酸如3-hp存在几个缺点。首先，与细菌相比，对酵母进行基因修饰更为困难，为了表达特定的代谢酶，应当鉴定用于表达代谢途径以及特定代谢酶的亚细胞位置，这是由于其细胞形状与细菌不同，被分为细胞内结构体，例如线粒体、过氧化物酶体等。例如，代表性代谢中间体如乙酰辅酶a主要在酵母的线粒体中产生。然而，如果在胞质溶胶中产生目标产物，则也需要在胞质溶胶中产生乙酰辅酶a的方法。此外，由于在真菌界存在大量不同的酵母，并且所有酵母都不满足对高生产率、耐有机酸性和大规模培养的要求，因此应当有效地选择适于产生有机酸的宿主。已知一些酵母有效地从作为己糖的葡萄糖产生乙醇，一些酵母种类也产生有机酸。在进行修饰以使用微生物产生目标产物时，重要的是保持代谢反应的氧化和还原的整体平衡，并且由葡萄糖发酵生产乙醇的代谢反应是得到适当维持的反应。即使在基因修饰酵母以产生有机酸的情况下，也应当适当地保持上述平衡，并且在通过修饰酵母来生产乳酸的情况下，平衡地引入另一还原反应的乳酸脱氢酶(ldh)用于补充从乙醛生产乙醇的还原反应是重要的。已知在少数微生物例如橙色绿屈挠菌(chloroflexusaurantiacus)中产生少量3-hp，并且3-hp部分地由微生物如粪产碱杆菌(alcaligenesfaecalis)中的二甲基磺基丙酸分解过程或酵母中尿嘧啶的分解过程形成。通过发现如上所述的自然界中存在的3-hp，已经进行了3-hp代谢途径和相应的酶的研究，并且基于最近的研究，进行了对以下技术的研究：通过在大肠杆菌中引入3-hp生物合成所需的基因来产生3-hp或pha的技术，pha为3-hp的聚合物形式。另外，为了使在自然界中仅作为代谢中间体存在或仅少量产生的3-hp的生产率和产量最大化，必须使用诸如代谢工程技术、系统生物学技术、合成生物学技术等的技术。根据代谢工程技术的发展，预测使用微生物生产各种物质的生产途径成为可能，从葡萄糖生产3-hp的途径按照代谢中间体可以大致分为丙烯酰辅酶a途径、β-丙氨酸途径、丙二酰辅酶a途径和甘油途径。丙烯酰辅酶a途径是指将从葡萄糖糖酵解获得的丙酮酸或磷酸烯醇丙酮酸(pep)经由乳酸(lactate)或β-丙氨酸转化为丙烯酰辅酶a，然后通过水合反应和还原反应将丙烯酰辅酶a转化为3-hp的代谢途径(丙酮酸或pep→乳酸或β-丙氨酸→丙烯酰辅酶a→3-hp)。丙烯酰辅酶a是在丙酸的分解过程中观察到的代谢物，并且由于形成该代谢物的吉布斯自由能值为正，所以正向反应是不利的反应。此外，丙烯酰辅酶a硫酯酶的底物特异性低，使得丙烯酰辅酶a途径不适合作为大规模生产3-hp的代谢途径。β-丙氨酸途径是指通过转氨基反应将丙酮酸或草酰乙酸转化为氨基酸，最后通过转氨基反应经由β-丙氨酸转化为3-hp的代谢途径(丙酮酸或草酰乙酸→氨基酸→β-丙氨酸→3-hp；us2012/0135481a1)。由于β-丙氨酸向3-hp转化的转氨基反应经由对微生物具有高毒性的丙二酸半醛进行，因此需要具有高活性的3-hp脱氢酶。另外，通常，由于转氨基反应形成稳态的氨基酸分子结构的自由基形式，所以该反应的酶具有用于减轻自由基的反应性的结构。由于该自由基对氧具有强的反应性，因此对于平稳的转氨基反应，基本上需要厌氧条件或用于稳定自由基分子的辅酶。丙二酰辅酶a途径是通过羧化将乙酰辅酶a转化为丙二酰辅酶a，然后通过还原反应将丙二酰辅酶a转化为3-hp的代谢途径(乙酰辅酶a→丙二酰辅酶a→3-hp)，甘油途径是将葡萄糖转化为甘油，通过脱水反应将甘油转化为3-羟基丙醛，然后将3-羟基丙醛转化为3-hp的代谢途径(葡萄糖→甘油→3-羟基丙醛→3-hp)。由于丙二酰辅酶a途径和甘油途径经由通常由诸如大肠杆菌等的微生物产生的中间体进行，因此主要将这些途径作为3-hp生产途径进行研究(us2013/0071893a1)。由于可以通过丙二酸(malonate)还原酶和3-hp脱氢酶将丙二酰辅酶a转化为3-hp，并且可以通过甘油脱水酶和醛脱氢酶将甘油转化为3-hp，使用修饰的大肠杆菌将葡萄糖或甘油转化为3-hp的方法是众所周知的。与转氨基反应类似，甘油的脱水反应是伴随有自由基的反应，基本上需要辅酶b12以在氧的存在下进行反应。考虑到工业发酵，由于辅酶(如辅酶b12)的成本，难以使用其作为培养基的物质，并且微生物(例如酵母)不能在细胞中生物合成或吸收相应的物质，因此β-丙氨酸途径或甘油途径不适合作为使用酵母产生3-hp的代谢途径。最近，已经报道了修饰关键酶以克服该问题的研究。[us7,655,451b2]丙二酰辅酶a由胞质溶胶中的乙酰辅酶a合成，从而可以还原成3-hp。在细菌如大肠杆菌的情况下，乙酰辅酶a由胞质溶胶中的丙酮酸形成，因此可用作tca循环或其它代谢反应的底物。然而，如上所述，在具有独立的亚细胞区室的酵母中，通常在线粒体中合成乙酰辅酶a并将其用作tca循环的底物，并且胞质溶胶中的乙酰辅酶a通过乙酸产生反应或柠檬酸循环反应来产生，乙酸产生反应是乙醇产生反应的副反应。从乙酸或柠檬酸产生乙酰辅酶a的所有反应都是消耗atp的反应，并且由于与细菌相比，酵母还消耗能量以在胞质溶胶中获得乙酰辅酶a，所以酵母在能量学方面是不利的。在酵母中，诸如胞质溶胶的还原状态、蛋白质合成后的折叠、密码子使用等的环境与细菌中的环境不同，使得在表达来自细菌的外源酶时，不显示其活性或活性可能显著降低。此外，由于氧或其它金属离子的存在或不存在可以显著改变所述活性，即使在具有相同功能的外源酶的情况下，其在酵母中的表达结果会根据酶的来源而不同。实际上，在木糖代谢中的重要酶即木糖异构酶(xi)的情况下，当在酵母中表达来自细菌的xi时，通常其活性明显较低，但是证明了通过引入来自厌氧真菌的xi，酵母被成功修饰从而以相对高的活性进行木糖代谢。因此，在酵母中引入来自细菌或古生菌的代谢途径(如丙二酰辅酶a途径)的情况下，应通过发挥相同功能的各种来源的基因来获得具有高活性的基因。存在与基因修饰各种酵母菌株中的酿酒酵母(saccharomycescerevisiae)以产生3-hp的方法相关的各种文献和专利，但是在酿酒酵母的情况下，由于3-hp通过[丙酮酸→乙醛→乙酸→乙酰辅酶a→丙二酰辅酶a→丙二酸半醛→3-hp]途径生产，存在该产生3-hp的代谢途径复杂、3-hp的生产率相对低的问题(us2010/0248233a1；y.chen等人，metabolicengineering，22:104-109,2014)。因此，作为解决上述问题的努力的结果，为了克服酵母在获得胞质溶胶中乙酰辅酶a的过程中消耗atp的缺点，本发明人想到更短的代谢途径：[丙酮酸→乙醛→乙酰辅酶a→丙二酰辅酶a→丙二酸半醛→3-hp]，该代谢途径不经过乙酸中间体而直接将乙醛转化为乙酰辅酶a，并且证实在使用包含该途径的重组酵母的情况下，与使用大肠杆菌的情况不同，不仅减少了ph调节物质的使用(从而减少了盐的产生)，而且即使在低的ph下也可以以高浓度和高产率从生物质产生3-hp，从而完成本发明。技术实现要素：技术问题本发明的目的是提供包含[丙酮酸→乙醛→乙酰辅酶a→丙二酰辅酶a→丙二酸半醛→3-hp]的主动3-hp生物合成途径的重组酵母，其不经由乙酸而将乙醛直接转化为乙酰辅酶a。本发明的另一个目的是提供使用该重组酵母产生3-hp的方法。问题的解决方案为了实现上述目的，本发明提供了一种包含[丙酮酸→乙醛→乙酰辅酶a→丙二酰辅酶a→丙二酸半醛→3-hp]的主动3-hp生物合成途径的重组酵母，其中该酵母包含：编码aadh的外源基因；编码acc的内源基因或外源基因；编码mcr的外源基因；和编码hpdh的外源基因。在本发明中，所述酵母是耐酸的，并且选自例如酵母属(saccharomyces)、kazachstania属和假丝酵母(candida)属。特别感兴趣的酵母种包括酿酒酵母(saccharomycescerevisiae)、kazachstaniaexigua、kazachstaniabulderi和小假丝酵母(candidahumilis)，但种类不仅限于此。此外，本发明提供了制备3-hp的方法，其包括：(a)在包含至少一种碳源的培养基中培养权利要求1-10中任一项所述的重组酵母，从而产生3-hp；以及(b)从培养物中分离3-hp。附图说明图1示出了本发明的重组酵母从葡萄糖产生3-hp的途径(修饰的丙二酰辅酶a代谢途径)和主要的酶。图2示出了乙酰辅酶a羧化酶的acc1活性的相对排名。图3示出了对古细菌mcr变体的相对活性(左图)和表达水平(sds-page)(右图)的确认结果。图4示出了用于表达与3-hp途径相关的酶的酵母表达质粒psk-084和psk-085。图5示出了对可以影响3-hp生产水平的培养条件的测试结果。图6示出了使用补料分批(片剂掺加(tabletspiking))培养条件时更成熟的3-hp生产菌株的3-hp生产量。具体实施方式除非另有定义，本文使用的所有技术和科学术语具有与本发明所属领域的技术人员通常理解的相同的含义。通常，本文使用的命名法是本领域公知的并且通常使用的。通常，在酵母中，由于乙酰辅酶a通过[乙醛→乙酸→乙酰辅酶a]途径制备，并且在酵母的胞质溶胶中产生乙酸，因此在生产乙酰辅酶a的过程中atp通过转化为amp而被消耗掉(图1；y.chen等人,metabolicengineering,22:104-109,2014)。然而，在本发明中，设计并应用了一种途径(图1)，在产生胞质溶胶中的乙酰辅酶a的过程中，该途径通过不经由乙酸而由乙醛直接制备乙酰辅酶a来克服和改善酵母消耗atp的缺点。结果，在使用本发明的重组酵母的情况下，证明了即使在低ph下，也以高浓度和高产率由葡萄糖产生3-hp。因此，一方面，本发明涉及包含[丙酮酸→乙醛→乙酰辅酶a→丙二酰辅酶a→丙二酸半醛→3-hp]的主动3-hp生物合成途径的重组酵母，其中该酵母包含：编码aadh的外源基因；编码acc的内源基因或外源基因；编码mcr的外源基因；和编码hpdh的外源基因。[丙酮酸→乙醛→乙酰辅酶a→丙二酰辅酶a→丙二酸半醛→3-hp]的3-hp生物合成途径是从诸如葡萄糖等的碳源产生3-hp的途径。“丙酮酸→乙醛”是指使用丙酮酸脱羧酶(pdc)由丙酮酸生产乙醛而不产生中间体的途径；(ii)“乙醛→乙酰辅酶a”是指使用乙酰化乙醛脱氢酶(acetylatingacetaldehydedehydrogenase，aadh)由乙醛生产乙酰辅酶a而不产生诸如乙酸的中间体的途径；(iii)“乙酰辅酶a→丙二酰辅酶a”是指使用乙酰辅酶a羧化酶(acc)由乙酰辅酶a生产丙二酰辅酶a而不产生中间体的途径；(iv)“丙二酰辅酶a→3-hp或丙二酰辅酶a→丙二酸半醛→3-hp”是指使用双功能丙二酰辅酶a还原酶(mcr)由丙二酰辅酶a生产3-hp而不产生中间体的途径，或通过使用单功能丙二酰辅酶a还原酶生物合成丙二酸半醛从而由丙二酸半醛产生3-hp的途径(图1)。在本发明中，pdc基因不是工程化的，但是可以例如通过扩增酵母中存在的pdc基因、通过应用本
技术领域：
：熟知的现有技术来工程化pdc基因以增加3-hp生产率。在本发明的一个示例性实施方案中，通过生物信息学基因组挖掘途径酶候选物来提取编码具有特殊功能的途径酶的基因。本发明包括编码aadh的外源基因。在一个实施方案中，编码aadh的基因为编码下述aadh的核酸：aadh具有与选自以下表1-3中所示的氨基酸序列的aadh氨基酸序列具有至少60％，优选至少70％、80％、90％、91％、92％、93％、94％、95％、96％、97％、99％或100％的序列同一性的氨基酸序列，但编码aadh的基因不限于此，只要其具有由乙醛生物合成乙酰辅酶a的功能即可。表1aadh(adhe型)表2aadh(eute型)表3aadh本发明包括编码acc的基因。在一个实施方案中，编码acc的基因为编码下述acc的核酸，该acc具有与选自下表4所示的氨基酸序列的acc氨基酸序列具有至少60％，优选至少70％、80％、90％、91％、92％、93％、94％、95％、96％、97％、99％或100％的序列同一性的氨基酸序列，但编码acc的基因不限于此，只要其具有由乙酰辅酶a生物合成丙二酰辅酶a的功能即可。表4acc(真核多结构域型)本发明包括编码mcr的基因。在一个实施方案中，mcr可以是双功能mcr，其具有将丙二酰辅酶a转化为丙二酸半醛的功能和将丙二酸半醛转化为3-hp的功能；或者是单功能mcr，其具有将丙二酰辅酶a转化为丙二酸半醛的功能。在本发明中，编码所述双功能mcr的基因为编码下述mcr的核酸：mcr具有与选自下表5中所示的氨基酸序列的mcr氨基酸序列具有至少60％，优选至少70％、80％、90％、91％、92％、93％、94％、95％、96％、97％、99％或100％的序列同一性的氨基酸序列，但编码所述双功能的基因不限于此，只要其同时具有将丙二酰辅酶a转化为丙二酸半醛的功能和将丙二酸半醛转化为3-hp的功能即可。表5mcr(双功能型)在另一个实施方案中，所述mcr基因可以是具有将丙二酰辅酶a转化为丙二酸半醛的功能的单功能基因，可以进一步包含编码可以将丙二酸半醛转化为3-hp的酶的基因。在本发明中，所述编码单功能mcr的基因为编码下述mcr的核酸：该mcr具有与选自下表6中所示的氨基酸序列的mcr氨基酸序列具有至少60％，优选至少70％、80％、90％、91％、92％、93％、94％、95％、96％、97％、99％或100％的序列同一性的氨基酸序列，但编码所述单功能mcr的基因不限于此，只要其具有将丙二酰辅酶a转化为丙二酸半醛的功能即可。表6mcr在本发明中，编码将丙二酸半醛转化为3-hp的酶的基因是编码下述酶的核酸：该酶具有与选自下表7-10所示的氨基酸序列的hpdh、hibadh、hbdh或bdh氨基酸序列具有至少60％，优选至少70％、80％、90％、91％、92％、93％、94％、95％、96％、97％、99％或100％的序列同一性的氨基酸序列，但所述编码酶的基因不限于此，只要该蛋白编码基因具有从丙二酸半醛生物合成3-hp的功能即可。下表7中所示的hpdh氨基酸序列、下表8中所示的hibadh氨基酸序列、下表9中所示的hbdh氨基酸序列和下表10中所示的bdh-氨基酸序列为具有从丙二酸半醛生物合成3-hp的功能的蛋白质的氨基酸序列。表7hpdh表8hibadh表9hbdh表10bdh在本发明的一个具体实施方案中，包含主动3-hp生物合成途径的重组酵母可以具有表11中所列的基因，例如编码具有选自seqidno:74-98的氨基酸序列的aadh的外源基因、编码具有选自seqidno:99-106的氨基酸序列的acc的内源基因或外源基因、编码具有选自seqidno:107-116的氨基酸序列的mcr的外源基因以及编码具有选自seqidno：117-144的氨基酸序列的hpdh的外源基因。表11在本发明中，酵母可以是耐酸的，并且所述耐酸酵母可以选自例如酵母属、kazachstania属和假丝酵母属。特别感兴趣的酵母种包括酿酒酵母、kazachstaniaexigua、kazachstaniabulderi和小假丝酵母，但不限于此。根据本发明，重组酵母可以是耐酸的，为了制备耐酸重组酵母，优选使用对有机酸(特别是3-hp和/或制备3-hp时作为副产物产生有机酸)具有耐酸性的酵母宿主。耐酸性酵母可以选自酿酒酵母、kazachstaniaexigua、kazachstaniabulderi和小假丝酵母，但不限于此。本说明书中使用的术语“耐酸性酵母”是指对有机酸如3-hp等具有耐酸性的酵母，耐酸性可以通过确认在含有各种浓度的有机酸的培养基上的生长来评价。在这种情况下，“耐酸性酵母”可以是当在含有高浓度有机酸的培养基中生长时与一般酵母相比表现出高生长速率和高生物质消耗速率的酵母。根据本发明，耐酸性酵母可以是在含有超过1m或更多有机酸(特别是3-hp)的培养基中、在小于有机酸(特别是3-hp)的pka值的ph下，与在不含有机酸的培养基中生长的酵母相比，能够维持至少10％的葡萄糖(或类似物)消耗速率或至少10％的比生长速率的酵母。根据本发明，耐酸性酵母可以是在ph2-4下，与在ph7下相比，可以维持至少10％的葡萄糖(或类似物)消耗速率或至少10％的比生长速率的酵母。本发明的经基因修饰的微生物可以通过将基因插入微生物的染色体或将经修饰的载体引入微生物中来制备。通常使用dna引入效率高且引入的dna的表达效率高的宿主作为所述经修饰的微生物，在本发明的一个示例性实施方案中，使用酵母，但不限于此，只要能充分表达靶dna，可以使用任何种类的微生物。所述经修饰的微生物可以通过任何转化方法制备。“转化”是指将dna引入宿主，从而dna能够作为染色体的因子或通过整合染色体而复制，这是人为引起基因改变的现象。在常见的转化方法中，存在电穿孔、乙酸锂-peg方法等。另外，在本发明中，可以使用一般公知的基因工程方法作为向宿主微生物的染色体中引入基因的方法，例如存在使用逆转录病毒载体、腺病毒载体、腺伴随病毒载体、单纯疱疹病毒载体、痘病毒载体、慢病毒载体、非病毒载体等的方法。“载体”是指包含待可操作地连接到合适的控制序列的、能够在宿主内部表达dna的dna序列的dna构建体。载体可以是质粒、噬菌体颗粒或简单的潜在基因组插入片段。当载体转化到合适的宿主中时，其可以被复制或发挥功能而不管宿主基因组如何，或在一些情况下，其可以整合到基因组本身中。质粒是最常用作载体的类型。可用于该目的的典型质粒载体的结构包含(a)允许有效进行复制以使每个宿主细胞包含质粒载体的复制起点，(b)抗生素抗性基因或营养缺陷型标记基因，其允许选择用质粒载体转化的宿主细胞，和(c)可以插入外源dna片段的限制酶限制性位点。即使不存在合适的限制酶限制性位点，当使用根据一般方法的接头或合成的寡核苷酸衔接子(adaptor)时，可以容易地将载体和外源dna连接。当核酸与其他核酸序列以功能关系排列时，其是“可操作地连接的”。它可以是：当适当分子(例如转录激活蛋白)连接到控制序列时在能够进行基因表达的过程中连接的基因和控制序列。例如，当表达参与多肽分泌的前蛋白时，前序列或分泌前导序列的dna可操作地连接至多肽的dna；在影响序列的转录时启动子或增强子可操作地连接至编码序列；当影响序列的转录时，核糖体结合结构域可操作地连接至编码序列；或当核糖体结合结构域被设置为易于被翻译时，其与编码序列可操作地连接。通常，“可操作地连接”是指连接的dna序列的接触，或分泌前导序列在前导框中接触和呈递。然而，增强子不需要接触。增强子序列的连接通过在方便的限制酶位点处的连接来进行。当不存在该结构域时，使用根据一般方法的合成寡核苷酸衔接子或接头。当然，应当理解，所有载体都不能等同地发挥作用以表达根据本发明的dna序列。同样地，所有宿主细胞对于相同的表达系统也不是等同地起作用。然而，在不脱离本发明的范围且没有过度的实验的情况下，本领域技术人员可以适当地选择载体、表达控制序列和宿主细胞。例如，在选择载体时，必须考虑宿主细胞。这是因为载体应当在宿主细胞中复制。此外，还应当考虑复制数量和控制载体的复制数量的能力以及由载体编码的其它蛋白质(例如抗生素标记物)的表达。在另一方面，本发明涉及制备3-hp的方法，其包括：(a)在包含至少一种碳源的培养基中培养权利要求1-10中任一项所述的重组酵母，从而产生3-hp；以及(b)从培养物中分离3-hp。在本发明中，碳源可以是选自葡萄糖、木糖、阿拉伯糖、蔗糖、果糖、纤维素、葡萄糖低聚物和甘油中的一种或多种，但不限于此。在本发明中，培养优选在微生物如大肠杆菌不再工作(例如产生代谢物等)的条件下进行。在实施方案中，在ph1.0-6.5，优选在ph1.0-6.0，更优选在ph2.6-4.0下进行培养，但不限于此。具体实施方式在下文中，将参考以下实施例更详细地描述本发明。然而，以举例的方式提供以下实施例是为了容易地解释对本发明技术精神的描述和本发明技术精神的范围。因此，本发明的范围不限于此或不由此改变。另外，本发明所属领域的技术人员可根据本说明书的描述进行各种修改和改变。实施例1基于对3-hp的耐受性选择宿主酵母菌株生产3-hp的生物体的基本特征是对高浓度3-hp的良好耐受性，这使得在发酵期间产物能够积累，同时菌株性能损失最小。对一个718个野生型酵母菌株组成的大的、多样化的组(set)进行筛选以鉴定在低ph下能够耐受高浓度3-hp并且在这些条件下可以生长和代谢葡萄糖的那些菌株(表12)。最初使用许多基于琼脂板和液体培养基微量滴定板的生长测定来筛选整组菌株的耐酸性。然后，评价菌株亚组(subset)在摇瓶培养中在低ph下耐受大量3-hp的能力。这些筛选方法中没有一个孤立地是工业环境中3-hp耐受性的完美指标，但是许多方法的组合提供了一种全面而稳健的确定有前途的产生3-hp酵母菌株的方法。最初，在含有不同量的3-hp的固体ypd基琼脂培养基上评估718个酵母菌株的生长，其中3-hp的量为：0g/l3-hp(ph6.62)、50g/l3-hp(ph3.44)、75g/l3-hp(ph3.28)、100g/l3-hp(ph3.17)和125g/l3-hp(ph3.08)。然后基于它们在该筛选测定中耐受不同量的3-hp的能力对菌株进行评分。然后使用可以自动孵育、摇动和测量培养物浊度的bioscreenc机器在不存在3-hp(基于scd的培养基，0g/l3-hp，ph6.0)或存在3-hp(基于scd的培养基，70g/l3-hp，ph3.5)的情况下在微量滴定板液体培养物中评估718个酵母菌株的生长。然后采用现有的用于建模微生物生长曲线的软件在每个实验条件下为每个菌株确定滞后期、最大生长速率和最终细胞密度。对于该筛选测定，基于其在不存在3-hp时的最大生长速率、其在3-hp存在下的最大生长速率和这两个最大生长速率值之间的相对差对每个菌株进行评分。使用液体处理自动控制仪器(robot)，在微量滴定板中在含有85g/l3-hp(ph3.5)的基于ypd的液体培养基中评估718个酵母菌株的生长和葡萄糖利用率。使用自动化工作流程(work-flow)来接种生长平板、在指定时间点稀释样品用于od测量并离心和收集上清用于hplc分析，hplc分析用于测定指定时间点处残留葡萄糖量。与bioscreenc生长测定相反，自动操作(robotic)微量滴定板生长测定允许实现更多的通气和更高的最大细胞密度，同时还允许评估葡萄糖利用率，而不像之前的两种测定一样仅评估生长速率。对于该筛选测定，基于在3-hp存在下获得的菌株最大细胞密度和菌株在3-hp存在下在低ph条件下消耗葡萄糖的能力对每个菌株进行评分。将来自各种3-hp耐受性评估测定的个体评分一起取平均值以获得每种菌株的最终3-hp耐受性评分(表12)。这些筛选表明，在低ph和不同条件下，以下酵母种类具有对3-hp的良好的一般耐受性：蜂生假丝酵母(candidaapicola)、小假丝酵母、东方伊萨酵母(issatchenkiaorientalis)、kazachstaniabulderi、kazachstaniaexigua、膜璞毕赤酵母(pichiamembranifaciens)、酿酒酵母和解脂耶氏酵母(yarrowialipolytica)。然后在摇瓶培养中在低ph下进一步分析这8种3-hp耐受性酵母种对3-hp的耐受性。对于这些培养(定义的基于scd的培养基，高初始生物质，低通风)，在以下不同的ph值和不同水平的3-hp存在下评估菌株生长、消耗葡萄糖和产生乙醇的能力：100g/l3-hp(ph4.0)、100g/l3-hp(ph3.5)、100g/l3-hp(ph3.0)和80g/l3-hp(ph2.6)。这些摇瓶培养显示某些小假丝酵母(c.humilis)、k.bulderi、k.exigua和酿酒酵母菌株在低ph下对高水平的3-hp具有非常强的耐受性，因为在各种酵母菌株中它们在这些苛刻条件下具有最快的葡萄糖利用率、生物质产生速率和乙醇产生速率。另一方面，在这些非常受限的生长条件下，蜂生假丝酵母、东方伊萨酵母、膜璞毕赤酵母和解脂耶氏酵母菌株不能良好地表现。这些使用各种摇瓶培养的详细后续分析证实某些小假丝酵母、k.bulderi、k.exigua和酿酒酵母菌株显示出作为3-hp产生宿主的巨大潜力，因为它们显示出在工业相关条件下对3-hp的高的天然耐受性。表12酵母菌株对3-hp的耐受性实施例2生物信息学基因组挖掘以获得途径酶候选物进行基于同源性的数据库搜索以鉴定用于特定功能的候选酶。在每种情况下，用多个查询序列搜索数据库。此外，相关蛋白家族的成员基于interpro结构域注释从uniprot/swissprot中检索。使用blastp针对uniprot(swissprot和trembl)和genbank蛋白质数据库(nr，pat和env_nr)，以及使用tblastn针对genbank核苷酸数据库(tsa_nt，env_nt和pat)进行基于同源性的搜索。提取e值小于1e-30的序列；然而，在一些情况下，对e值小于1e-80的序列进行额外的分析。使用查询序列作为翻译中的指导，用genewise将命中的核苷酸翻译成蛋白质序列。对于genewise而言，翻译长acc序列的任务太困难，因此，从blast-xml输出中提取蛋白质序列(与查询序列匹配的部分)。为了去除冗余序列，使用blastclust或cd-hit将检索的序列集中(clustered)成含有彼此具有80％以上同一性的序列的集合(cluster)。从每个集合仅保留一个代表性序列。将非冗余的序列组要么与蛋白质家族的pfam结构域比对要么通过使用mafft进行比对。在蛋白质家族不与任何pfam相关的情况下或者如果蛋白质的序列被分割成几个pfam结构域，则创建mafft的全局比对。基于使用phylip或fasttree的多序列比对生成系统发生树。该树用e.c.数、生物体名称、blaste值注释，并使用geneious软件可视化。2-1：乙酰化乙醛脱氢酶乙醛还原为乙酰辅酶a可以通过乙酰化乙醛脱氢酶(aadh，e.c.1.2.1.10)完成。aadh可以分为三组功能同源物(wei等人，nat.commun.4：2580,2013)，包括1)具有aadh和醇脱氢酶活性的双功能蛋白(大肠杆菌adhe型基因，genbankno.：np_415757，查询序列)，2)参与乙醇胺分解代谢的蛋白质(大肠杆菌eute型基因，genbankno.：aag57564，查询序列)和3)双功能蛋白质，其是参与4-羟基-2-酮戊酸分解代谢的醛缩酶-脱氢酶复合物的一部分(大肠杆菌mphf型基因，genbankno.：np_414885)。特别感兴趣的是第1组(adhe型)和第2组(eute型)的酶。adhe蛋白的n-末端结构域与醛:nad+氧化还原酶高度同源，而c末端区与fe2+-依赖性乙醇:nad+氧化还原酶家族同源(membrillo-hernandez等人，j.biol.chem.275:33869-33875,2000)。乙酰化乙醛脱氢酶活性也可以通过去除醇脱氢酶结构域来截短双功能adhe蛋白从而仅具有n-末端醛还原酶结构域而引入细胞。基于生物信息学分析和序列同源性推断具有这种双功能aadh活性的其他基因。各种基因总结在表1中。许多肠杆菌可以利用乙醇胺作为碳源和氮源(stojiljkovic等人，j.bacteriol.177:1357-1366,1995)。该分解代谢途径包括通过乙酰化乙醛脱氢酶eute将乙醛转化为乙酰辅酶a的步骤。基于生物信息学分析和序列同源性推断具有这种aadh活性的新基因。各种基因总结在表2中。此外，基于生物信息学分析和与adhe以及eute型基因的序列同源性，存在一组注释为醛脱氢酶的基因，可以推断其具有aadh活性。各种基因总结在表3中。2-2：真核乙酰辅酶a羧化酶乙酰辅酶a羧化酶(acc，ec6.4.1.2)是多功能生物素依赖性羧化酶，是脂肪酸生物合成的关键酶。它使用辅因子atp和生物素催化乙酰辅酶a转化为丙二酰辅酶a。该反应分两步进行。首先，生物素羧化酶催化生物素与碳酸氢盐的atp依赖性羧化。然后，羧基转移酶将羧基从生物素转移到乙酰辅酶a以形成丙二酰辅酶a。真核生物酶是大的多结构域酶，而相应的原核生物酶由由不同基因编码的多个亚基组成。acc的活性在转录水平上以及在转录后水平上受控(例如通过磷酸化和聚集)以维持乙酰辅酶a动态平衡。在不同酵母种中的acc工程化导致acc活性增加和丙二酰辅酶a衍生产物的产量增加。已证明或假定在酿酒酵母(genbankno.：caa96294.1，查询序列)、解脂耶氏酵母(genbankno.：xp_501721.1，查询序列)和卷枝毛霉(mucorcircinelloides)(genbankno.：epb82652.1，查询序列)中存在编码具有acc活性的酶的基因。在kazachstaniaexigua(seqidno：1)和小假丝酵母(seqidno：2)的新测序的基因组中鉴定候选乙酰辅酶a羧化酶基因并克隆到我们的酵母表达质粒中。基于生物信息学分析和序列同源性推断具有acc活性的其它基因。各种真核多结构域acc基因总结在表4中。2-3：双功能丙二酰辅酶a还原酶丙二酰辅酶a还原成3-hp(经由丙二酸半醛中间体)可以通过大的双功能丙二酰辅酶a还原酶完成，其具有c末端醛脱氢酶结构域和n-末端醇脱氢酶结构域的双功能。具有这种活性的、高度底物特异性的、nadph依赖性酶的特征在于参与称为3-羟基丙酸循环的自养co2固定途径的光营养型绿色无硫细菌橙色绿屈挠菌(chloroflexusaurantiacus)(genbankno.：aas20429.1；查询序列)(hugler等人，j.bacteriol.184:2404-2410,2002)。基于生物信息学分析和序列同源性推断具有该双功能丙二酰辅酶a还原酶活性的其他基因。各种基因总结在表5中。2-4：丙二酰辅酶a还原酶与上面讨论的双功能丙二酰辅酶a还原酶相反，丙二酰辅酶a也可以通过两种单独的酶催化成3-hp。通过该途径，丙二酰辅酶a首先通过丙二酰辅酶a还原酶(mcr；ec1.2.1.75)或辅酶a酰化丙二酸半醛脱氢酶还原为丙二酸半醛，然后通过3-羟基丙酸脱氢酶(3-hpdh；ec1.1.1.59或ec1.1.1.298)还原为3-hp。mcr是一种nadph依赖性酶，其被一些嗜热嗜酸性古细菌用于经由3-羟基丙酸/4-羟基丁酸循环自养地将碳固定到有机物质中(berg等人，science，318:1782-1786,2007)。编码具有这种mcr活性的酶的基因被表征存在于勤奋金属球菌(metallosphaerasedula)(genbankno.：abp94884.1，查询序列)和头寇岱硫化叶菌(genbankno.：bab67276.1，查询序列)中。虽然这些mcr都具有与橙色绿屈挠菌双功能丙二酰辅酶a还原酶类似的醛脱氢酶活性，但它们没有表现出任何显著的序列相似性，表明绿屈挠菌属和硫化叶菌科中的自养途径趋同进化，并且募集不同的基因以在这些分类群中执行相似的代谢过程(alber等人，j.bacteriol.188:8551-8559,2006)。特别地，古细菌mcr显示出与天冬氨酸-半醛脱氢酶的高的序列相似性。基于生物信息学分析和序列同源性推断具有该mcr活性的其他基因。各种基因总结在表6中。2-5：3-羟基丙酸脱氢酶丙二酸半醛可通过可逆的3-羟基丙酸脱氢酶(hpdh；ec1.1.1.59，nadh依赖性的)或丙二酸半醛还原酶(ec1.1.1.298，nadph依赖性的)还原为3-hp。这些酶天然参与细菌和植物中的β-丙氨酸代谢、丙酸代谢或尿嘧啶降解。此外，一些嗜热嗜酸性古细菌需要这些酶以通过3-羟基丙酸/4-羟基丁酸循环固定碳(kockelkorn和fuchs，j.bacteriol.191:6352-6362,2009)。已证明或假定在大肠杆菌(genbankno.：efv00080.1，查询序列)、酿酒酵母(genbankno.：daa10125.1，查询序列)、勤奋金属球菌(genbankno.：abp96133.1，查询序列)、头寇岱硫化叶菌(genbankno.：bak54608.1，查询序列)和大肠杆菌(genbankno.：acr64730.1，查询序列)中存在编码具有3-羟基丙酸脱氢酶或丙二酸半醛还原酶活性的酶的基因。基于生物信息学分析和序列同源性推断具有3-羟基丙酸脱氢酶或丙二酸半醛还原酶活性的其它基因。各种基因总结在表7中。2-6：3-羟基异丁酸脱氢酶3-羟基异丁酸脱氢酶(hibadh；ec1.1.1.31)是参与缬氨酸和其它支链氨基酸的代谢的关键酶。hibadh催化3-羟基异丁酸向甲基丙二酸半醛的nadh依赖性或nadph依赖性可逆转化。然而，由于其广泛的底物特异性，还已表明hibadh通过将丙二酸半醛转化为3-hp显示出3-羟基丙酸脱氢酶活性(即ec1.1.1.59)(yao等人，appl.bio.biotechnol.160:694-703,2010)。在恶臭假单胞菌(genbankno.：adr61938.1，查询序列)、绿脓杆菌(genbankno.：aag06957.1，查询序列)、蜡样芽胞杆菌(genbankno.：aap10961.1，查询序列)和粪产碱杆菌(genbankno.：ejc65559.1，查询序列)中鉴定了具有hibadh活性的酶。基于生物信息学分析和序列同源性推断具有该hibadh活性的其他基因。各种基因总结在表8中。2-7：4-羟基丁酸脱氢酶4-羟基丁酸脱氢酶(hbdh；ec1.1.1.61)是天然参与丁酸代谢的酶。hbdh催化4-羟基丁酸向琥珀酸半醛的可逆nad+依赖性转化。然而，因为酶反应相似，hbdh也可以将丙二酸半醛转化为3-hp。已经在钩虫贪铜菌(genbankno.：aac41425.1，查询序列)和克氏梭菌(genbankno.：edk35022.1，查询序列)中鉴定了具有hbdh活性的酶。基于生物信息学分析和序列同源性推断具有该hbdh活性的其它基因。各种基因总结在表9中。2-8：3-羟基丁酸脱氢酶3-羟基丁酸脱氢酶(bdh；ec1.1.1.30)是天然参与丁酸代谢的酶。bdh催化3-羟基丁酸向乙酰乙酸酯的可逆nad+依赖性转化，但其也可氧化其它3-羟基一元羧酸。例如，因为酶反应是类似的，bdh可以将丙二酸半醛转化为3-hp。已经在绿脓杆菌(genbankno.：gaa17557.1，查询序列)中鉴定了具有bdh活性的酶。基于生物信息学分析和序列同源性推断具有该bdh活性的其他基因。各种基因总结在表10中。实施例3酶活性的测量acc分光光度酶测定分光光度acc测定是偶联测定，其中由acc反应产生的产物在需要辅因子nad(p)h的反应中被进一步消耗掉，可以用分光光度计监测辅因子nad(p)h的氧化。kroeger等人(2011，anal.biochem.411：100-105)描述了偶联测定，其中由acc1产生的丙二酰辅酶a通过纯化的丙二酰辅酶a还原酶(mcr)在需要nadph作为辅因子的反应中进一步转化为丙二酸半醛。acc活性通过以下nadph氧化来测量。diacovich等人(2002，j.biol.chem.277:31228-31236)将adp转化(在acc反应中用作辅因子的atp的水解产物)与需要adp的丙酮酸激酶反应结合，该丙酮酸激酶反应进一步与使用乳酸脱氢酶形成丙酮酸的反应偶联。后一种酶需要nadh作为辅因子，随后该辅因子被氧化。acc放射性酶测定最常用的体外acc测定是基于放射性14c碳酸盐的使用。随后是将放射性碳酸盐掺入酸和非挥发性物质(即丙二酰辅酶a)中。通过酸和热处理将未转化为丙二酰辅酶a的14c标记的碳酸氢钠除去，酸和热处理将剩余的nah14co3和可能的反应副产物转化为14c标记的co2。经过略微的改变，已将由diacovich等人(2002,j.biol.chem.277:31228-31236)描述的测定用于检测酵母溶解产物的acc活性(shi等人2014,mbio5:3e01130-14)。由在指数期晚期或稳定期收获的酵母细胞制备细胞溶解产物。洗涤细胞，然后重悬于含有100mmph7.5的磷酸钾、2mmmgcl2、1mm二硫苏糖醇和1×edta游离的完整蛋白酶抑制剂(roche)的裂解缓冲液中。通过玻璃珠破碎细胞，并在4℃下离心后收集上清液。acc酶测定反应混合物包括100mm磷酸钾(ph8.0)、300μgbsa、3mmatp、5mmmgcl2、10mmnah4co3[比活性200μcimmol-1(7400kbqmmol)]和0.5mm乙酰辅酶a。该反应的总体积为100μl，包括20μl的细胞提取物。将反应在30℃下孵育15分钟，并通过加入50μl的5mhcl终止反应。将管内容物在95℃下蒸发至干，使残余物重悬于100μl水中，并与3ml闪烁混合液(scintillationcocktail)(ultimagoldab，perkinelmer)混合。使用液体闪烁计数器(perkinelmertri-carb2810tr)测定样品的14c含量。aadh酶测定按照kozak等人(2014,metab.eng.21:46-59)的描述通过在30℃下在340nm处监测nad+的还原来测量aadh活性。收集用于获得细胞溶解产物的酵母细胞，用水洗涤，然后重悬于含有100mmtris-hcl缓冲液(ph7.5)和1×edta游离蛋白酶抑制剂混合物(roche)的裂解缓冲液中。将细胞在precellys24均质器中以5500rpm的速度用玻璃珠破碎3×40秒，在各轮破碎之间将细胞保持在冰上。将溶解产物于4℃下以16000g离心20分钟，收集上清液。使用bradford方法测定总蛋白浓度。酶测定反应混合物在200μl的总反应体积中含有0.1mm辅酶a、50mmches缓冲液(ph9.5)、0.8mmnad+、0.2mmdtt和10μl细胞提取物。通过加入10mm新制备的乙醛溶液开始反应，随后使用thermokonelab20xt分析仪跟踪nad+的还原。酵母细胞溶解产物的mcr酶测定根据经过略微改变的chen等人(2014，metab.eng.22:104-109)描述的方法测量mcr酶活性。该方法以在340nm处监测nad(p)h的氧化为基础。收集细胞并用含有20mmtris-hcl(ph7.5)、20mmnan3的冷的洗涤缓冲液洗涤，然后重悬浮于含有50mmhepes(ph7.5)、150mmkcl、1mmdtt、1mmedta、0.5％tritonx-100和1×edta游离蛋白酶抑制剂混合物(roche)的1ml破碎缓冲液。将细胞在precellys24均质器中以5500rpm的速度用玻璃珠破碎3×40秒，在各轮破碎之间将细胞保持在冰上。将溶解产物在4℃下以16000g离心20分钟，收集上清液。使用bradford方法测定总蛋白浓度。mcr测定混合物含有50mmtris-hcl缓冲液(ph8.0)、5mmmgcl2和0.3mmnadph或nadh。在将20μl细胞溶解产物加入到200μl的总反应体积中后，将反应在30℃下预孵育5分钟，之后通过加入0.15mm丙二酰辅酶a开始反应。使用thermokonelab20xt分析仪在340nm监测测定。酵母表达载体的产生产生一系列酵母表达质粒以评估候选基因在酵母中的表达和活性能力。首先，设计了新的基于pbluescript的多克隆位点(mcs)，使得可以利用所有可能的限制酶(re)位点组合。然后将该修饰的mcs置于基于prs的系列酵母着丝粒和多拷贝质粒中。之后，使用一组10个独特的re位点，将九个不同组的启动子和终止子克隆到这些基于prs的酵母表达载体中。因此，可以利用该质粒系统在合适的酵母菌株中要么以低拷贝数要么以高拷贝数同时组成型表达多达9个基因，以评价用于产生3-hp的多种途径酶组合。acc基因的克隆已经转化到具有和不具有snf1缺失的工业酿酒酵母vsk-128菌株的acc1基因示于表13中。acc基因从多拷贝质粒表达，其中它们在pdc1启动子的控制下。在shi等人的出版物(2014)中描述的突变acc1sc基因是用quikchangeii定点诱变试剂盒(安捷伦科技有限公司)构建的。表13转化到酿酒酵母vsk-128的乙酰辅酶a羧化酶基因acc酶测定在文献中，分光光度测定法已经用于用纯化的或部分纯化的acc酶检测acc酶活性。用分光光度测定测试其中acc过表达的酵母细胞溶解产物，但是与对照相比没有检测到吸光度变化。放射性acc酶测定是非常敏感的，甚至可以检测pmol/mg/min活性。首先用市售的纯化的人acc酶测试该方法。当检测到明显的活性时，进一步优化该方法以检测酵母细胞溶解产物的acc活性。测定表13中列出的菌株的acc1活性，并基于该结果制作描述acc1的相对排名的列表(图2)。对最有前途的候选者accyl进行更多的研究，酿酒酵母s-128野生型菌株的结果和其中acc1已被过表达的相同菌株的结果显示在表14中。表14acc1基因的过表达导致acc1酶活性是野生型酿酒酵母vsk-128菌株的内源acc1活性的2.9倍。aadh体外酶活性测定最初选择了5种aadh基因(即adhepm、adheec、eutec、eutdz和lin1129li)，并转化到cen.pk实验室菌株中。这些aadh从多拷贝质粒表达，其中它们在tef1启动子的控制下。所有五个aadh基因显示aadh活性，但是与adhe型aadh(即adhepm和adheec)相比，三种eute型aadh基因(即eutec、eutdz和lin1129li)在酵母中给出高得多的aadh活性。从基因组挖掘分析中选择20个其他新aadh基因以评估酵母中的表达和酶活性。测试这二十个新的aadh基因的体外酶活性，其中四个(即aadhmm、aadhab、aadhbw和aadhvs)显示具有aadh活性。aadh体内生长测定从工业酿酒酵母vsk-128菌株中删除所有acs2基因拷贝以产生具有缺陷型pdh旁路的菌株，该菌株在基于葡萄糖的培养基上不能生长。然后将携带25种不同aadh变体的表达载体转化到该acs2缺失菌株中，以评价它们恢复该菌株在葡萄糖上的生长的能力。基于菌株在葡萄糖基琼脂平板上生长的能力，12种不同的aadh变体(即euteec、eutedz、lin1129li、aadhmm、aadht1、aadhab、aadhta、aadhbs、aadhbw、aadhvs、aadhhs和adheec)能够恢复acs2-缺失菌株的生长。体外aadh酶活性测定和体内生长恢复分析之间存在良好的相关性。然后在液体摇瓶培养中评估被发现能够恢复acs2缺失菌株生长的前九个aadh变体菌株的生长速率，并与含有完整pdh旁路的野生型菌株进行比较。当在葡萄糖上生长时，所有9个这些aadh变体都能够维持>50％的酿酒酵母vsk-128菌株有氧生长速率，并且这些aadh变体中的6个能够维持≥80％的酿酒酵母vsk-128菌株有氧生长速率。酵母中的mcr酶测定将八个全长绿屈挠菌属mcr同源物截短成它们的两个功能结构域，并且测定mcr特异性结构域以及六个古细菌mcr在酵母中的酶活性。这些mcr从多拷贝质粒表达，其中它们在tef1启动子的控制下并转化到cen.pk实验室菌株中。当利用nadph作为辅因子时，mcrca(橙色绿屈挠菌)及其同源物mcrrc(光合玫瑰弯菌)是仅有的两种给出比野生型菌株更高的mcr酶活性的绿屈挠菌属mcr同源物。当利用nadh作为辅因子时，没有观察到这八种绿屈挠菌属mcr同源物的酶活性。当利用nadph作为辅因子时，三个古细菌mcr[sulfolobalesarchaeon、嗜酸热硫化叶菌(x2)]给出了比野生型菌株高的mcr酶活性，使用nadh作为辅因子时，所有六个古细菌mcr都给出比野生型菌株高的mcr酶活性。古细菌mcr的异源表达和表征为四种不同的古细菌mcr(勤奋金属球菌(mcrms)、头寇岱硫化叶菌(mcrst)，candidatuscaldiarchaeum(mcrcc)和古菌硫化叶菌(mcrsa1))制备基于pbatt7启动子的表达构建体。这些构建体不含有纯化标签，是大肠杆菌密码子优化的且在本报告前面所述的条件下表达(表15)。表15用于在大肠杆菌中表达的古细菌mcr构建体的概述(ca-橙色绿屈挠菌，ms-勤奋金属球菌，st-头寇岱硫化叶菌，cc-candidatuscaldiarchaeum，sa1-古菌硫化叶菌，sa2-嗜酸热硫化叶菌)使用以下测定条件分析它们的活性：0.4mmnad(p)h，0.15mm丙二酰辅酶a，tris-hclph7，2mmmgcl2。在室温下以微量滴定板(mtp)形式对20倍稀释的溶解产物进行测定。随后及时追踪a365处的nadph或nadh氧化。在测试的四个古细菌基因中，mcrsa1和mcrst显示最高的mcr活性。然而，mcr活性小于测量的标记的mcrca的活性。对于candidatuscaldiarchaeummcr(mcrcc)，没有测量到对nadph或nadh的活性(在大肠杆菌细胞溶解产物中)。当使用sds-page凝胶分析这些构建体时，mcrsa1在大肠杆菌溶解产物中显示最高的表达水平，而mcrcc不能以可溶形式表达；参见凝胶(sa1>ca>st>ms>cc)(图3)。构建体mcrsa1和mcrst似乎具有双重辅因子偏好，并且与测量到的对nadph的活性相比，显示出约40-50％的相对nadh活性。就比活性而言，mcrst可以是所测试的四种古细菌mcr中活性最高的酶，因为它在相对低的表达水平下显示相对高的活性水平。实施例4通过培养重组酵母产生3-hp酿酒酵母的摇瓶培养从在选择性琼脂基平板上新生长的菌株中取出一小圈细胞，用于接种在250ml烧瓶中的20ml选择性sc基培养基(20g/l葡萄糖)，并生长2天(30℃，250rpm)，直到所有葡萄糖和乙醇已被消耗。测定最终细胞密度，将培养物在4000rpm离心5分钟。然后通过hplc或gc/ms分析上清液以确定培养物上清液中3-hp和其它主要代谢物的积累。然而，还根据具体菌株和目的来测试其他培养条件(例如葡萄糖的起始量、通气量、培养基的类型和向培养基中加入另外的物质等)。实施例5酿酒酵母的生物反应器培养在含有250-500ml培养基的multifors生物反应器(最大工作体积500ml，24叶片rusthon涡轮叶轮，inforsht，瑞士)中进行培养。最初将培养物维持在30℃，300或900-950rpm，1.2、2.4或3.6体积气体(体积培养)-1min-1(vvm)。通过加入无菌2mnaoh或2mh3po4使培养物ph在ph5.5±0.2处恒定。加入clerolfba3107消泡剂(cognisfrance，ponthierryparis；0.03％v/v)以控制泡沫产生。在用含3％co2的ar；含5％co2、0.99％ar、15％o2的n2；含20％o2加20％ar的n2；含0.04％乙醇的n2校准的primaproprocess质谱仪(thermoscientific，英国)中连续分析气体浓度(co2、o2、n2和ar)。将菌株在摇动的烧瓶中在scd基选择性培养基中预生长过夜，并用于接种生物反应器。使分批培养阶段(20g/l初始葡萄糖)持续14至20小时，并且仅在葡萄糖已被消耗后开始葡萄糖进料，但葡萄糖进料在乙醇已被消耗之前或之后开始(取决于培养目的)。葡萄糖进料速率保持在0.38-0.65gl-1h-1(取决于培养目的)。然后通过hplc分析上清液样品，以确定培养物中3-hp和其他主要代谢物的积累。实施例6通过hplc对细胞培养物上清液进行3-hp分析用watersalliancee2695hplc系统(waters，美国米尔福德)分析培养物上清液样品，其中注射体积为10μl。使用与fastacidanalysiscolumn(100mm×7.8mm)(bio-rad，美国)连接的aminexhpx-87horganicacidcolumn(300mm×7.8mm)(bio-rad，美国)作为hplc的固定相。将柱保持在+55℃，并使用5.0mmh2so4(merckkgaa，德国)作为洗脱液，流速为0.3mlmin-1或0.5mlmin-1。使用waters2489双波长uv(210nm)检测器(waters，美国米尔福德)和waters2414差示折射计(waters，美国米尔福德)检测3-羟基丙酸、葡萄糖、乙酸、琥珀酸、丙酮酸、甘油和乙醇。实施例7通过gc/ms对细胞培养物上清液进行3-hp分析按以下方式制备测试样品并制作标准曲线：用50μlhcl(6n)酸化上清液(0.5ml)，并掺加3-hpa(tci)标准品(在乙酸乙酯中)。加入5μl的乳酸内标溶液(sigmaaldrich(isotec)l-乳酸钠-3,3,3-d398原子％；5.5g/l)和约0.2g的nacl。由于标记的3-hp不可商购获得，因此选择该乳酸稳定同位素产品作为内标，因为该产品是可获得的、在样品基质中不存在、与3-hp在结构/化学方面最相似的化合物。将混合物在涡旋混合器中振荡约3分钟。然后采用0.5ml乙酸乙酯通过在涡旋混合器中混合约3分钟萃取样品两次。通过在10000rpm离心5分钟分离各层。将上层收集到gc小瓶中并蒸发。通过在60℃下孵育1小时，用含有1％tmcs的mstfa(50μl)将干燥的残余物衍生化。以与样品相同的方式提取校准曲线的标准品以使误差最小化。在与agilent5973质量选择性检测器(msd)结合的agilent6890气相色谱仪(gc)上运行样品。注射器(注射体积1μl，分流比20:1)和msd界面温度为280℃，并且炉温程序为以20℃/min的速率从50℃升至280℃。在agilenthp-5ms毛细管柱(30m，id200μm，膜厚度0.25μm；agilent19091s-433)上进行分析。化合物的鉴定基于对nist文库的光谱搜索。通过监测m/z147和m/z219检测3-hp，通过监测m/z177检测3-hp二聚体。通过利用3-hp响应(responses)构建5点校准曲线(c＝1-400mg/l)，并使用内标归一化。证明在该浓度范围内的定量是线性的。空白样品与样品一起分析。实施例8酿酒酵母质粒表达菌株的评价3-hp质粒表达菌株同时从两种不同的表达质粒(即psk-084和/或psk-085)表达一种、两种或三种3-hp途径酶(即aadh、acc1、mcr和hpdh)(图4)。这些菌株用于评价不同的3-hp途径酶(和这些酶的组合)对vsk-128耐酸酿酒酵母菌株中3-hp的产量的影响。将菌株在250ml烧瓶中的20ml选择性sc基培养基(20g/l葡萄糖)中培养，并生长2天(30℃，250rpm)直到所有葡萄糖和乙醇被消耗掉。实施例9体内途径酶活性分析的总结对表16中的25个aadh、8个acc1、10个双功能hpdh-mcr、6个古细菌mcr和28个hpdh在各种酿酒酵母菌株中产生3-hp的能力进行分析，如果需要，所述酿酒酵母菌株也表达额外的3-hp途径酶。显示许多新的3-hp途径酶(从基因组挖掘分析获得)在酵母中是有活性的，并且与先前公开的3-hp途径酶相比，它们中的许多具有更优异的性质(即更高的活性，更好的辅因子偏好)。表16实施例10用于3-hp生产的酿酒酵母摇瓶培养试验培养条件在一对早期测试菌株上评价各种不同的培养条件，以观察各种培养条件如何影响菌株产生3-hp的能力。酿酒酵母vsk-128(δura3，δhis3)菌株表达两种质粒，其中一种质粒含有hibadhpa或hpdhec基因，第二种质粒含有mcrsa2基因。两种菌株在培养期间表现相似，并且具有非常相似的代谢物谱图。测试六种不同的摇瓶培养条件：1.有氧，分批法，高初始葡萄糖(120g/l)。在第3天再加入100g/l葡萄糖。2.无氧，分批法，高初始葡萄糖(100g/l)。将烧瓶密封并且摇动更慢，速度为100rpm。3.有氧，分批法，重复掺加葡萄糖(glucosespiking)。初始葡萄糖为20g/l，然后每隔一天加入40g/l。4.有氧，模拟分批补料法，许多初始葡萄糖片。最初加入5片，在第3天再加入5片。每天加入不同量的酶a溶液(50-150μl/天)。5.有氧，模拟分批补料法，重复掺加葡萄糖片。最初加入1片，在第1天和第2天加入2片，在第3天和第4天加入3片。每天加入不同量的酶a溶液(50-150μl/天)。6.好氧，分批法，重复掺加半乳糖。初始半乳糖为20g/l，然后每隔一天加入40g/l。对于模拟补料分批培养，每个片剂被认为释放0.5g葡萄糖(对于25-ml培养体积而言，其相当于20g/l葡萄糖)。片剂基本上由葡萄糖(即淀粉)组成，酶a溶液(即淀粉酶)允许在摇瓶培养期间将葡萄糖受控地缓慢释放到培养基中。假设葡萄糖受限的补料分批条件可以促进生长和随后的3-hp生产的效率(flux)。细胞生长所有正常的基于葡萄糖的培养均类似地生长，并且半乳糖补料培养生长更慢。另一方面，与其他培养条件相比，分批补料条件促进更多的细胞生长。特别地，分批补料(片剂掺加)条件在培养早期的确促进了大量生长。3-hp生产对于这些培养，大多数生长通常在第2天结束时发生，并且绝大多数3-hp也在第2天生成，因此表明生长和3-hp产生彼此相关。分批补料(片剂掺加)培养条件产生最多的3-hp(～0.85g/l)，半乳糖进料培养产生最少量的3-hp(～0.12g/l)，其他培养条件全部产生约0.3-0.4g/l的3-hp。这些结果表明培养条件可对3-hp产生水平有大的影响(图5)。葡萄糖消耗在所有培养试验中葡萄糖被快速消耗直到第2-3天，然后葡萄糖消耗速率随着生长和3-hp产生显著降低(在第4-5天期间)。对于补料分批培养，似乎葡萄糖的消耗与其从片剂释放一样快，表明这些培养在葡萄糖受限的条件下进行。甘油、乙酸和乙醇积累对于葡萄糖进料培养，甘油积累是相当高的，对于半乳糖进料培养而言甘油积累则低得多。乙酸积累在不同的培养条件中相当相似，但是补料分批(许多片剂)条件产生更多的乙酸。对于这些摇瓶培养中的大部分，特别是对于葡萄糖分批培养和葡萄糖掺加培养，存在大量的乙醇累积。补料分批培养旨在代表葡萄糖受限条件以减少过量溢流代谢生成乙醇，并且这种方法似乎已经取得成功，因为在补料分批培养中乙醇积累显著较低。培养更成熟的3-hp产生菌株按照最有前途的补料分批(片剂掺加)培养条件培养其他3-hp生产菌株[(euteec、hpdh-mcrca、acc1sc_s1157a)和(hibadhpa、mcrsa2)]以检查其性能。同样，大部分生长发生在第3天，大部分3-hp产生发生在第3天。在该培养条件下，该菌株的3-hp产量超过1.2g/l(图6)。尽管详细描述了本发明的具体实施方案，但是对于本领域技术人员来说显而易见的是，具体描述仅仅是令人满意的示例性实施方案，并且不应被解释为限制本发明的范围。因此，本发明的实质范围由所附权利要求及其等同物限定。工业适用性使用本发明的重组酵母和制备3-hp的方法使得能够以高浓度和高收率在低ph下从有用的糖(如葡萄糖)生产3-hp，从而极大地有助于从生物质经济地生产3-hp及其应用产品。序列表<110>sk新技术株式会社<120>产生3-羟基丙酸的重组酵母和使用其产生3-羟基丙酸的方法<130>pf-b1841<140>pct/kr2015/009061<141>2015-08-28<150>10-2014-0114505<151>2014-08-29<160>144<170>patentinversion3.2<210>1<211>2248<212>prt<213>kazachstaniaexigua<400>1metserglugluasnleuphegluaspserseralalysargglntyr151015gluilethrasptyrserlyslyshislysalaleualaprohisphe202530valglyleuasnthrleuasplysvalglugluserproleulysasp354045phevallysserhisglyglyhisthrvalileserlysileleuile505560alaasnasnglyilealaalavallysgluileargservalarglys65707580trpsertyrgluthrpheglyaspgluargthrvalglnphevalala859095metalathrprogluaspleuglnalaasnserglutyrileargmet100105110alaaspglntyrvalgluvalproglyglythrasnasnasnasntyr115120125alaasnvalaspleuilevalaspvalalagluargthraspvalasp130135140alavaltrpalaglytrpglyhisalasergluasnprohisleupro145150155160glulysleualaalaserlysarglysileilepheileglypropro165170175glyseralametargserleuglyasplysileserserthrileval180185190alaglnhisalalysvalprocysileprotrpserglythrglyile195200205asplysvalhisvalaspgluthrserglyleuvalservalaspasp210215220aspvaltyrglnglnglycyscysglnserprogluaspglyleuala225230235240lysalalysglnileglypheprovalmetilelysalaserglugly245250255glyglyglylysglyileargglnvalgluargglugluasppheile260265270alaleutyrhisglnalaalaasngluileproglyserproilephe275280285ilemetlysleualaglylysalaarghisleugluvalglnleuleu290295300alaaspglntyrglythrasnileserleupheglyargaspcysser305310315320valglnargarghisglnlysileilegluglualaprovalthrile325330335alaasnasngluthrpheasplysmetalaasnalaalavalarg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