基因修饰苯丙酮酸脱羧酶、其制备方法和用途与流程

本专利申请要求2014年12月10日提交的名称为“基因修饰苯丙酮酸脱羧酶、其制备方法和其用途”的美国专利申请第62/089,912号的权益，所述专利申请以全文引用的方式并入本文中。本发明涉及在微生物中使用生物酶产生c6-c10化合物，如醇、羧酸和烷烃的领域。更确切地说，其涉及使用一或多种工程改造硫胺素依赖性脱羧酶转化给定2-酮酸底物的领域。表达如下文所描述的表示m461v变异体的本发明的基因修饰脱羧酶的一个特定实施例的微生物样品已于2015年12月9日寄存于美国组织类型收集(atcc)专利库,10801universityblvd.,manassas,va20110。地理政治和环境问题已激励全世界的研究人员追求使用可再生途径，包括(但不限于)使用微生物的发酵产生基于石化品的产品。但是，由于微生物通常未能在经济上可行的速率或产率下产生许多基于石化品的产品，代谢工程改造已广泛用于建立路径和/或朝向所关注的路径引导代谢物。当前，乙醇为使用微生物制得的最常见生物化学物质。但是，在生物燃料和化学行业中积极地追求产生较长链醇和羧酸的经济上可行的方法。通过微生物发酵产生天然氨基酸中的成功尤其在使用氨基酸生物合成路径产生所关注的化学品，包括较长链醇和羧酸中产生重大兴趣。参见例如becker,j.；wittmann,c.“用于氨基酸生产的系统和合成代谢工程改造-工业菌株发展的脉搏(systemsandsyntheticmetabolicengineeringforaminoacidproduction-theheartbeatofindustrialstraindevelopment),”《生物技术当前观点(curr.opinbiotechnol)》.,2012,23:718-726；和becker,j.；wittmann,c.“基于生物的化学品、材料和燃料的生产-谷氨酸棒状杆菌作为通用细胞工厂(bio-basedproductionofchemicals,materialsandfuels-corynebacteriumglutamicumasversatilecellfactory),”《现代生物技术观点(curr.opin.biotechnol.)》,2012,23:631-640。在氨基酸生物合成期间为关键中间物的2-酮酸能经受可用于细胞内部的化学物质的生物合成的不同类型的修饰。参见例如gronenberg,l.s.；marcheschi,r.j.；liao,j.c.“原核生物中的下一代生物燃料工程改造(nextgenerationbiofuelengineeringinprokaryotes),”《化学生物学新见(curr.opin.chem.biol.)》,2013,17:462-471。在一个实例中，美国专利8,232,089描述表达产生异丁醇的代谢路径的重组酵母菌，所述路径包括在与异丁醇产生基因共表达时将2-酮基异戊酸酯转化为异丁醛的巴西固氮螺菌脱羧酶。在另一实例中，美国专利8,298,798描述通过2-酮酸的脱羧，接着通过乳酸乳杆菌(l.lactis)酮基异戊酸酯脱羧酶和酵母菌醇脱氢酶adh6的表达来还原产生的醛而在大肠杆菌(e.coli)细胞中产生直链和分支链醇。也参见atsumi,s.；hanai,t.；liao,j.c.“用于合成分支链高级醇作为生物燃料的非发酵路径(non-fermentativepathwaysforsynthesisofbranched-chainhigheralcoholsasbiofuels)”《自然(nature)》,2008,451:86-89；marcheschi,r.j.；li,h.；zhang,k.；noey,e.l.；kim,s.；chaubey,a.；houk,k.n.；liao,j.c.“用于碳链延长的合成递归“+1”路径(syntheticrecursive“+1”pathwayforcarbonchainelongation),”《acs化学生物学(acschem.biol)》.,2012,7:689-697；和zhang,k.；sawaya,m.r.；eisenberg,d.s.；liao,j.c.“用于生物合成非天然醇的扩张代谢(expandingmetabolismforbiosynthesisofnonnaturalalcohols),”《美国国家科学院院刊(proc.natl.acad.sci.u.s.a.)》,2008,105:20653-20658。已经由脱羧酶和醛去氢酶的表达展示2-酮酸中间物在细胞内部转化为羧酸。参见例如xiong,m.；deng,j.；woodruff,a.p.；zhu,m.；zhou,j.；park,s.w.；li,h.；yao,f.“脂族酮的生物催化方法(abio-catalyticapproachtoaliphaticketones),”2012,《科学报导(sci.rep.)》2:311；和zhang,k.；woodruff,a.p.；xiong,m.；zhou,j.；dhande,.,k.“用于生产平台化学异丁酸的合成代谢路径(asyntheticmetabolicpathwayforproductionoftheplatformchemicalisobutyricacid),”《化学与可持续性、能源与材料(chemsuschem)》,2011,4:1068-1070。经由大肠杆菌的leua基因产物的工程改造延长细胞内部的2-酮酸的长度的可行性也已扩展可产生自2-酮酸的生物化学物质的范围。参见例如atsumi,s.,同上.,和zhang,k.,同上。在大肠杆菌中，leuabcd基因延长2-酮酸的长度一个碳单元，如在亮氨酸生物合成期间所观测，其中其共同起作用以将2-酮基异戊酸酯(5碳酸)转化为2-酮基异己酸酯(6碳酸)。marcheschi等人.《acs化学生物学》.,2012,7:689-697描述leua的活性位点的扩展和c4酮酸、2-酮基丁酸酸[2-酮基丁酸酯]延长为c9酮酸、2-酮基壬酸[2-酮基壬酸酯]。尽管有可能使用代谢工程改造在微生物中产生变化长度的醇和羧酸，但到目前为止尚未展示特定c6-c8醇或酸的产生，优选地以按总醇产物计的大于20重量％(wt％)、更优选地大于30wt％的量。若干因素似乎决定产生自细胞内部的2-酮酸的醇/酸的特异性。脱羧酶接受变化长度的2-酮酸的杂乱性导致变化长度的醛，其接着通过对应的共表达醛或醇脱氢酶氧化或还原。因此，较高水准的杂乱性，即较低水准的特异性导致较高数量的产物。这转而可意味着尤其所需的特定产物的较低产率。经由2-酮酸特定产生醇或羧酸也可受就leuabcd来说的脱羧酶的表达量不利地影响。较高水准的具有广泛底物特异性的脱羧酶倾向于与leua基因产物竞争2-酮酸中间物且进而限制路径延长2-酮酸的能力。这可导致形成比可能需要短的醇或羧酸，再次导致非所需产物和/或产物混合物。一般来说，改良工业微生物的方法从传统菌株改良(csi)的随机方法到代谢工程改造的高度合理方法变动。csi一般对于缓解产物抑制或提高产率有效，但在产生能够产生完全新颖产物的菌株中效果小得多。此外，csi为时间和资源密集型的。为了获得对于抑制性发酵产物具有高耐受性的菌株，有必要通过在增加的抑制剂浓度存在下在培养基中连续培养菌株而连续筛选和选择突变体。这通常与使用化学诱变剂和/或紫外线(uv)辐射的诱导性突变诱发结合进行。但是，常规的培养物筛选过程是冗长、耗时并且通常徒劳的。代谢修饰一般在创造产生新产物的菌株中更有效。这是因为基因，且在一些情况下甚至整个路径可在生物体之间转移(重组方法)和/或酶可经修饰(工程改造方法)。这些方法避免csi的一些缺点。包含重组和工程改造方法两者的术语代谢工程改造为广泛用于设计菌株以通过代谢通量分布的改变而实现代谢物过度产生中的较高效率的定向且通常较快的方法。到目前为止此操作的大部分是关于使用具有充分研究的遗传学和生理学的生物体(例如大肠杆菌、酵母菌和融合瘤细胞)来产生次级代谢物(如抗生素)、氨基酸(例如赖氨酸)和异源蛋白质。代谢通量分布的化学计量分析提供适当代谢修饰、最优培养基调配和馈入策略和生物工艺优化的指导。但是，此方法仍需要发酵细胞中的代谢和调节网络的深入知识。尽管这些合理方法已在涉及单个基因或单一基因簇内的若干基因的情况下取得成功，但其通常在涉及更复杂或在很大程度上未知的代谢途径的情况下无效。这是因为这通常每次靶向一个基因，且因此未能预测给定路径中的多个基因之间的复杂相互作用。通过修饰基因密码的所述部分，即生物体dna进行酶修饰，其对应于酶的表达。酶修饰可产生完全新颖的官能团且可用于提高所需中间物或产物的特异性或效率。另外，已知某些酶为杂乱的且可发现进行超出其已知自然角色的任务。此类酶也可经修饰以进行新转化，但到目前为止，此方法的成功频繁地限于在商业上不可行的产率。参见例如zhang,k.,同上。在路径中修饰多个酶可理论上用作使特异性和/或催化效率最大化的技术。已知在某些条件下产生辛醇的生物体的一个实例为梭菌属(clostridium)。梭菌属的各种物种(例如丙酮丁醇梭菌(c.acetobutylicum)、艰难梭菌(c.difficile)和克氏梭菌(c.kluyveri))用于wo2012135731中。公开案描述通过工程改造的梭菌属物种产生少量正辛醇，连同其它产物，且将对于正辛醇的不佳特异性归因于生物体表达或过度表达β-酮硫解酶(例如bktb)、乙酰基coa乙酰基转移酶(例如atob)、3-羟基丁酰基-coa去氢酶(例如来自梭菌属的hbd，或paahi)巴豆酸酶(例如crt)和反烯酰基-coa还原酶(例如ter)的能力。一般来说，工程改造修饰是针对生物体的coa路径以产生高级醇，且此路径避免发现于许多梭菌属物种中的涉及氧敏感性酶和中间物的丁醇产生路径。显示为已经由本发明产生的正辛醇的量太小而在商业上不可行。也参见例如lee,j.y.；jang,y.s.；lee,j.；papoutsakis,e.t.；lee,s.y.“丙酮丁醇梭杆菌m5的代谢工程改造以用于高度选择性丁醇生产(metabolicengineeringofclostridiumacetobutylicumm5forhighlyselectivebutanolproduction),”《生物技术学刊(biotechnol.)》2009,4:1432-1440；和wang,y.；blaschek,h.p.“通过用拜氏梭菌发酵而优化从热带玉米秆汁的丁醇生产(optimizationofbutanolproductionfromtropicalmaizestalkjuicebyfermentationwithclostridiumbeijerinckii),”《生物资源技术(bioresour.technol.)》,2011,102:9985-9990。当前研究的基因工程改造的一种应用是在能源领域。关于未来获得和使用化石燃料的稀缺、成本和环境影响的担忧已刺激在采用廉价、可再生生物质作为由其制得的燃料和化学品两者的替代来源中的兴趣。由于原油价格变得更易变，基于生物的化学品和工业产品已变为其石油衍生性对应物的有吸引力的替代方案。使用厌氧微生物的发酵方法提供将生物质和农业废弃物转化为有用产物的有前景的途径，且同时整改可在处置低价值农业商品和食品加工副产物/废弃物中遇到的问题。可由低成本生物质进料制备的有用产物中的一些为有机酸和醇，包括辛醇。c6-c10醇尤其用作制备作为许多行业中的高度所需进料化学品的烷烃、烯烃和醛的低成本起始物质。这些行业包括用作溶液聚合的共单体，和洗涤剂行业，其使用烷基化酚的这些前驱物来生产洗涤剂前驱物。这些醇也可用作表面活性剂；润肤剂；化妆品和食品行业种的增稠剂；杀虫剂；和多种其它应用。在一个实施例中，本发明提供一种基因修饰微生物的方法，其包含(a)选择产生c7-c112-酮酸的微生物；和(b)插入编码对应于seqid4、8、14、16、18、28、30、32、34、36、38、40、42、46、52、54、56、62、64、66、68或76的氨基酸序列，或与其至少90％同源的氨基酸序列的非天然核酸序列；使得非天然苯丙酮酸脱羧酶表达于微生物中。在另一实施例中，本发明提供基因修饰微生物。在另一实施例中，本发明提供一种制备c6-c10醛、c6-c10醇、c6-c10羧酸或c6-c10烷烃的方法，其包含以下步骤：(a)使2-酮基丁酸酯或2-酮基异戊酸酯、异丙基苹果酸合成酶、异丙基苹果酸异构酶和异丙基苹果酸去氢酶在使得2-酮基丁酸酯或2-酮基异戊酸酯转化为c7-c112-酮酸的条件下接触；(b)使c7-c112-酮酸与苯丙酮酸脱羧酶在使得c7-c112-酮酸转化为碳原子比转化的c7-c112-酮酸少一个的c6-c10醛的条件下接触，所述苯丙酮酸脱羧酶由编码对应于seqid4、8、14、16、18、28、30、32、34、36、38、40、42、46、52、54、56、62、64、66、68或76的氨基酸序列，或与其至少90％同源的氨基酸序列的非天然核酸序列表示；和(c)任选地使c6-c10醛与(1)醇脱氢酶在形成c6-c10醇的条件下接触；或(2)醛去氢酶在形成c6-c10羧酸的条件下接触；或(3)脂肪醛脱羧酶在形成c6-c10烷烃的条件下接触；进行所述方法以使得在微生物内部或外部和好氧或厌氧条件下独立地进行每一步骤和子步骤。在另一实施例中，本发明提供一种多肽，其包含对应于seqid8、14、16、18、28、30、32、34、36、38、40、42、46、52、54、56、62、64、66、68或76，或与其至少90％同源的氨基酸序列，主要由所述氨基酸序列组成，或由所述氨基酸序列组成。在另一实施例中，本发明提供一种基因修饰微生物，其包含(a)2-酮酸源；(b)将2-酮酸转化为c7-c11醛的野生型代谢路径；和(c)由编码与基因库寄存编号l26240对应的氨基酸序列，或与其至少80％同源的氨基酸序列的核酸序列表示的非天然苯丙酮酸脱羧酶；此类序列任选地经以下各者修饰：(1)经缬氨酸取代met-380；或(2)经缬氨酸、亮氨酸或异亮氨酸取代phe-385；或(3)经缬氨酸、亮氨酸、丙氨酸或半胱氨酸取代met-461；或(4)经缬氨酸或亮氨酸取代phe-465；或(5)经甘氨酸、丙氨酸、缬氨酸或亮氨酸取代phe-532；或(6)经缬氨酸、亮氨酸、异亮氨酸、丙氨酸或甘氨酸取代gln-536；或(7)如(1)-(6)中所述的两个或三个取代的任何组合对于下文描述的序列，每一奇数编号的序列标识号(seqid)显示核苷酸或核酸序列，且每一偶数编号的seqid显示对应编码的氨基酸序列。核酸序列编码氨基酸序列，其中术语“氨基酸序列”等效于“多肽”或“蛋白质”。所有提到的蛋白质(偶数编号的)seqid承认有可能使用替代密码子产生给定氨基酸序列的事实。seqid1和2表示附接于氨基酸序列的起点的13个氨基酸的组氨酸标签。seqid3和4表示对应于基因库寄存编号l26240的野生型巴西固氮螺菌(azospirillumbrasilense)苯丙酮酸脱羧酶基因。seqid5和6表示seqid3和4的基因序列，但abppdc中的met-380在位置380处经缬氨酸置换(基于无his-tag的氨基酸序列；在13个氨基酸的his-tag的情况下，这将为位置393)。修饰带有名称m380v，因此遵守行业标准，其中氨基酸修饰定义为原始单字母氨基酸密码，接着为氨基酸位置，接着为新氨基酸单字母密码。seqid7和8表示f385l。seqid9和10表示f385v。seqid11和12表示f385i。seqid13和14表示m461c。seqid15和16表示m461v。seqid17和18表示m461l。seqid19和20表示m461a。seqid21和22表示f465l。seqid23和24表示f532a。seqid25和26表示f532g。seqid27和28表示f532v。seqid29和30表示f532l。seqid31和32表示q536g。seqid33和34表示q536a。seqid35和36表示q536l。seqid37和38表示q536i。seqid39和40表示q536v。seqid41和42表示f532v/q536v。seqid43和44表示m380l/m461v。seqid45和46表示m380v/m461v。seqid47和48表示f385v/m461v。seqid49和50表示f385l/m461v。seqid51和52表示f532a/q536v。seqid53和54表示f532v/q536a。seqid55和56表示f385l/q536v。seqid57和58表示f385v/q536v。seqid59和60表示m461v/q536v。seqid61和62表示m461l/q536v。seqid63和64表示m461a/q536v。seqid65和66表示m461v/f532v。seqid67和68表示f465l/q536v。seqid69和70表示f465v/q536v。seqid71和72表示f465l/f532v。seqid73和74表示f532a/q536a。seqid75和76表示m461v/f532v/q536v。seqid77和78表示m380v/m461v/q536v。seqid79和80表示f385l/m461l/q536v。seqid81和82表示m380v/f385v/m461v。图1说明通过递归(迭代)活性，接着脱羧为比迭代路径中在其之前的2-酮酸短一个碳原子的醛的链延长。图2说明使用异丙基苹果酸合成酶、异丙基苹果酸异构酶、异丙基苹果酸去氢酶和醇脱氢酶(adh6)以及abppdc的f385l变异体(seqid8)的组合从2-酮基丁酸酯体外产生直链c5-c8醇。图3说明使用异丙基苹果酸合成酶、异丙基苹果酸异构酶、异丙基苹果酸去氢酶和醇脱氢酶(adh6)以及abppdc的f385l变异体(seqid8)的组合从2-酮基异戊酸酯体外产生分支链c5-c8醇。图4说明使用异丙基苹果酸合成酶、异丙基苹果酸异构酶、异丙基苹果酸去氢酶和醇脱氢酶(adh6)以及abppdc的f385l变异体(seqid8)的组合从3-甲基-2-酮基戊酸酯体外产生分支链c5-c8醇。图5说明含有“+1路径”酶以及abppdc野生型(wt)、abppdc变异体、kivdwt(雷特氏乳球菌酮基异戊酸酯脱羧酶)且不含脱羧酶的大肠杆菌的血清瓶发酵的平均醇分布。adh6也包含于所有菌株构筑体中。一般来说，本发明尤其包括新苯丙酮酸脱羧酶的两个特定实施例，其可在第一实施例中为对应于基因库寄存编号l26240的获自巴西固氮螺菌(a.brasilense)或与其至少80百分比(％)同源的氨基酸序列的表达。在第二实施例中，本发明包括先前定义的基因修饰苯丙酮酸脱羧酶，但具有另外的有意基因工程改造以在序列内插入特定氨基酸的一个、两个或三个修饰，其同样用于以在许多情况下在进行多种生物合成(其中苯丙酮酸脱羧酶参与)中有利的方式修改苯丙酮酸脱羧酶的催化效率。确切地说，野生型或核酸修饰的巴西固氮螺菌苯丙酮酸脱羧酶可与异丙基苹果酸合成酶、异丙基苹果酸异构酶和异丙基苹果酸去氢酶组合以产生醇、羧酸或烷烃。如将在本文中显示，相比于所选宿主微生物的野生型酶具有改进的特性的新苯丙酮酸脱羧酶是通过以描述于本文中的多种方式中的一种进行基因修饰而产生；或为由巴西固氮螺菌苯丙酮酸脱羧酶至少80％同源且包括相同修饰的氨基酸序列表示的酶；经由重组、工程改造或组合重组和工程改造方法的技术制造其的方法；使用野生型或新苯丙酮酸脱羧酶制造c6-c10醇、羧酸和烷烃的方法；以及可表达或过度表达此酶且可用于产生c6-c10醇、羧酸和烷烃的基因修饰微生物有机体。在本文使用所述术语时，同源性是指序列中列出的氨基酸在其给定位置的80％或更大的一致或功能对应。新苯丙酮酸脱羧酶可在某些特定实施例中用作或表示为以下代谢路径的一部分：经由合成代谢(例如伍德-永达尔(wood-ljundahl))或分解代谢(例如糖酵解或磷酸戊糖路径)途径产生乙酰基co-a，且最终参与c7-c112-酮酸的转化以形成少一个碳的对应c6-10醛。在一些实施例中，c6-c10醛可进一步反应以形成c6-c10醇、羧酸或烷烃。本发明的基因修饰苯丙酮酸脱羧酶由于描述于本文中的其氨基酸序列中的特异性改变而提供对各种底物的特异性中的一些显著差异，且特异性的此改变提供就产物产率和减少或消除非所需和/或竞争副产物来说的重要优点。本发明包括巴西固氮螺菌苯丙酮酸脱羧酶的多种改变的氨基酸序列，其已鉴别为相比于seqid4中显示的对应于基因库寄存编号l26240的野生型巴西固氮螺菌氨基酸序列展现改进的c7-c112-酮酸的脱羧。野生型序列内的六个位点已鉴别为对于获得所述改进至关重要。这些为met-380、phe-385、met-461、phe-465、phe-532、gln-536和其组合。在每一改变中作出变化，其中缬氨酸、亮氨酸、丙氨酸、甘氨酸或异亮氨酸在野生型氨基酸的鉴别位点处经取代，其中取代从单位点(即，构成三个碱基对单一氨基酸)取代到多种定义为优选地2到3个鉴别位点的“组合”的多位点(2到5个位点)取代改变。seqid3-82显示包括指定的取代中的一或多者的产生的许多变化形式的氨基酸序列。取代可概述如下：(1)用缬氨酸取代met-380；或(2)用缬氨酸、亮氨酸或异亮氨酸取代phe-385；或(3)用缬氨酸、亮氨酸、丙氨酸或半胱氨酸取代met-461；或(4)用缬氨酸或亮氨酸取代phe-465；或(5)用甘氨酸、丙氨酸、缬氨酸或亮氨酸取代phe-532；或(6)用缬氨酸、亮氨酸、异亮氨酸、丙氨酸或甘氨酸取代gln-536；或(7)如(1)-(6)中所述的三种取代的任何组合；所属领域的技术人员应了解，本发明的基因修饰苯丙酮酸脱羧酶可在体内(即，通过基因修饰微生物)或体外使用。鉴于此，如本文所用的术语“经基因修饰”或“经修饰”是指具有刻意改变的氨基酸序列，即“非野生型”氨基酸序列的本发明苯丙酮酸脱羧酶的群组，或具有关于(至少)在本文中描述和定义为发明性的特定经修饰脱羧酶已刻意改变的基因组的微生物(取决于作为形容词的任一术语的放置)。此类改变可经由重组技术实现，其中一或多种基因从第二不同微生物转移至目标微生物中；或工程改造技术，其中目标微生物内的核酸一般经由定点突变诱发改变，导致至少一种核酸转化为不同核酸并且因此修饰一或多种酶。在当今dna合成技术的情况下，重组技术也可使用完全合成dna实现，所述dna使用常规方法转移至目标微生物。也可采用以上方法中的任一种的组合。本发明进一步包括一种制备c6-c10醛、c6-c10羧酸、c6-c10烷烃和c6-10醇(如己醇、庚醇和/或1-辛醇)的方法，其经由起始底物与包括本发明的基因修饰苯丙酮酸脱羧酶中的一或多种的一系列酶之间的接触以使用另外的酶和步骤将底物最终转化为所需c6-c10醛、醇、羧酸或烷烃。此方法可在非天然存在，即基因工程改造的细胞的所描述实施例中的一个中，即在非天然存在的微生物中以生物合成方式进行；或c6-c10醇、羧酸或烷烃的生产可经由体外方法进行，通常从不包括微生物的起始点开始。为了获得本发明的经修饰苯丙酮酸脱羧酶的群组，在一个实施例中需要与下文所描述类似地执行方案。一般来说，实例显示涉及改变给定密码子中的一或多个核酸碱基以改变核酸碱基为一部分的酶的工程改造的基因修饰。这可仅用于产生用于例如体外分析目的的改变的酶。相比之下，宿主微生物的基因组可优选地经改变以用于较大规模生产株。可如所属领域的技术人员一般理解地进行被设计用于体外酶生产的以下方法。一般来说，适合的数据库(如基因库(genbank))用于获得用于野生型酶的基因编码，接着识别适合于修饰的密码子。此识别可用作蛋白质工程的技术已知方法的基础，其中计算机分子建模鉴别可有效地采用酶/底物界面的修饰的结构位置并且使得能够区别所述结构位置。接着使用分子生物学技术进行给定所需修饰，其中经由定点突变诱发进行一或多个核酸碱基的改变。变异型酶必须接着经受纯化以分离出非目标蛋白质，留下将展现高于野生型的催化效率的纯化酶。这可根据最适合于给定特定酶的方法经恰当地体外分析。显示具有所需催化效率水准的分析的酶进而确认为所需基因修饰的产物，且可用于体外生产方法，如将c7-c112-酮酸体外转化为少一个碳的对应c6-c10醛(例如将2-酮基壬酸酯转化为辛醛，或将2-酮基辛酸酯转化为庚醛)，其可接着在一个实施例中通过与适当野生型或非野生型醇脱氢酶接触而还原，以形成对应c6-c10醇。如上文所提到，可在体内或体外进行本发明。体内方法可对于商业规模生产为优选的，而在一些情况下，体外方法可适合于商业规模生产。通常，体外方法可尤其便于实验室和一般研究目的，以便进行酶分析。举例来说，可制备适用于酶促产物大规模或商业规模发酵生产，如在某些特定实施例中，c6-c10醇或c6-c10醇的组合的所需微生物有机体。此类制备可如下进行：通过使用重组技术将来自第一微生物的编码所需改进的酶的dna或dna片段插入至第二“宿主”微生物的基因组中，已知或相信所述第二“宿主”微生物具有一或多个所需代谢路径和/其它所需特征，如耐抑制发酵能力。一般来说，体内方法采用此类微生物野生型代谢路径在不同步数中首先将适合的含碳底物转化为丙酮酸酯，且接着将丙酮酸酯转化为2-酮基丁酸酯，或者，2-酮基异戊酸酯。举例来说，在一个实施例中，适合的含碳底物，如c5或c6糖(例如葡萄糖、蔗糖、戊糖或其组合)可经由分解代谢或合成代谢路径中的一个，如糖酵解或磷酸戊糖路径直接转化为丙酮酸盐。此后，丙酮酸盐可经由pc(丙酮酸羧化酶)；aat(天冬氨酸转氨酶)；thrabc(thra，其为双官能天冬氨酸激酶/高丝氨酸去氢酶；thrb，其为高丝氨酸激酶；thrc，其为苏氨酸合成酶；且asd，其为天冬氨酸半醛去氢酶)首先转化为l-苏氨酸。l-苏氨酸接着经由ilva(苏氨酸脱水酶)转化为2-酮基丁酸酯。在一替代实施例中，丙酮酸盐可经由亮氨酸生物合成中的ilvbn/ilvgm、ilvc和ilvd的活性转化为2-酮基异戊酸酯。另外参见zhang,k.；sawaya,m.r.等人,同上。从这个角度，涉及拉长2-酮酸的亮氨酸生物合成路径内的野生型或基因修饰形式的三种酶中的一或多者经操作以将2-酮基丁酸酯或2-酮基异戊酸酯转化为c7-c112-酮酸。在不提及任何特定微生物的情况下，这些酶一般称为异丙基苹果酸合成酶、异丙基苹果酸异构酶和异丙基苹果酸去氢酶。但是，特定在大肠杆菌中，其分别称为leua(基因库寄存编号nc000913.3，基因标识：947465)、leub(基因库寄存编号nc000913.3，基因标识：944798)和leucd(基因库寄存编号nc000913.3，基因标识945076和基因标识：945642)。此链延长的一个实例显示于图1中，其中2-酮基丁酸酯经由称为“+1路径”的多个步骤转化为c7-c112-酮酸2-酮基壬酸酯。在某些特定实施例中，涉及延伸2-酮酸的的亮氨酸生物合成路径的野生型酶可尤其通过包括至少一种外源酶、酶复合物或其组合而修饰以在发生链延长时将2-酮基丁酸酯首先转化为2-酮基戊酸酯，接着转化为2-酮基己酸酯，接着转化为2-酮基庚酸酯且必要时继续转化为另一延长的2-酮酸直至转化为2-酮基十一酸酯，即所需c7-c112-酮酸。但是，任选地可能仅修饰酶、酶复合物或其组合中的一个或两个以便获得可接受或所需产量的c7-c112-酮酸。这些酶可包括如上文所提及的leua、leub和/或leucd。尤其适用于路径的此部分的修饰的为2014年12月10日提交的同在申请中的国际专利申请序号pct/us14/69438(代理人案号75413-wo-pct)的公开内容，所述专利申请要求2013年12月12日提交的美国临时专利申请第61/915,040号(代理人案号75413-us-psp)的权益，其均以全文引用的方式并入本文中。在某些实施例中，至少选择经修饰的异丙基苹果酸去氢酶变异体(其为大肠杆菌中的leub基因的产物)，或在其它实施例中，至少包括经修饰的leua(leua')和leub'变异体，其优选地但未必如引用的专利申请中的一个或两个中所述。也优选地采用leua'、leub'和经修饰的leucd(leucd')酶/酶复合物的其它组合。同样，应注意“leu”+字母(a、b、cd)名称为大肠杆菌中的异丙基苹果酸合成酶、异丙基苹果酸异构酶和异丙基苹果酸去氢酶的亮氨酸路径酶的特定名称，而其它生物体的亮氨酸路径中的相同或等效酶可具有不同名称。最后，本发明的基因修饰苯丙酮酸脱羧酶可在此特定实施例中用以将c7-c112-酮酸转化为比底物2-酮酸少一个碳的醛。在各种实施例中，所得c6-c10醛可发现多种用途，作为产物本身或作为用于生产包括c6-c10醇的产物的起始或中间产物。可经由c6-c10醛通过适当野生型或基因修饰醇脱氢酶的转化实现c6-c10醇的制备，但其它产物，如c6-c10烷烃也可经由脂肪醛脱羧酶的作用或表达制备，或c6-10羧酸可通过醛去氢酶的作用或表达制备。参见例如choi,y.j.；lee,s.y.“短链烷烃的微生物生产(microbialproductionofshort-chainalkanes)”,《自然(nature)》,2013,502:571-574。因此，c6-10醛在工业上高度适用作用于制备多种其它产物的极佳中间产物。因此，预期本发明的基因修饰苯丙酮酸脱羧酶家族将可适用于多种行业。此类行业可包括(例如)在燃料、塑料、食品、包装、化妆品、香料、制药、清洁材料、污染控制、香料、药物和许多其它行业中的用途。尽管存在多种完全属于本发明的权利要求的范围内的可能的氨基酸序列，但应注意，通过序列标识号(seqid)鉴别为选自seqid34、36、38、40、42、46、62、68和76的某些氨基酸序列就对c7-c112-酮酸脱羧基来说是尤其适合和优选的。实例1设计对于2-酮基壬酸脱羧具有较高催化效率的巴西固氮螺菌苯丙酮酸脱羧酶(abppdc)变异体abppdc与3-脱氮-硫胺素二磷酸酯和5-苯基-2-氧代戊酸(pdb标识码2q5q)的三元复合物的晶体结构模型用于鉴别加衬abppdc的活性位点内的2-酮酸结合袋的残基。参见例如versees,w.；spaepen,s.；wood,m.d.；leeper,f.j.；vanderleyden,j.；steyaert,j.“二磷酸硫胺素依赖性脱羧酶中的异位底物活化的分子机制(molecularmechanismofallostericsubstrateactivationinathiaminediphosphate-dependentdecarboxylase)”,《生物化学杂志(j.biol.chem.)》,2007,282:35269-35278。将命名为met-380、met-461、phe-385、phe-465、gln-536和phe-532的氨基酸位点基于其与5-苯基-2-氧代戊酸的关系选择用于取代实验。如表1中所列地进行一或多个位点的取代且制备变异体。酶f532v以缬氨酸置换abppdc中的phe-532，而酶f532l以亮氨酸置换phe-532。酶f385l/m461v以亮氨酸置换phe-385且以缬氨酸置换met-461。表1中的其余的巴西固氮螺菌苯丙酮酸脱羧酶(abppdc)变异体是根据氨基酸(第一个字母，其中“f”表示“苯丙氨酸[phe]”；“m”表示“甲硫氨酸”[met]；且“q”表示“谷氨酰胺”[gln])、其在氨基酸序列中的位置(编号)和用作替换的氨基酸(最后一个字母，其中“l”表示“亮氨酸”；“v”表示“缬氨酸”；“a”表示“丙氨酸”；“c”表示“半胱氨酸”；“i”表示“异亮氨酸”；且“g”表示“甘氨酸”)命名。经修饰abppdc变异体中的每一个经表达和纯化，且接着测试针对三种底物的活性，所述底物为2-酮基己酸酯(2-kh)、2-酮基辛酸酯(2-ko)和2-酮基壬酸酯(2-kn)。将预期2-kh、2-ko和2-kn在通过abppdc脱羧时分别形成戊醛、庚醛和辛醛。使用下文描述的高通量酶分析在两个步骤中进行abppdc变异体的评估。起初，测试所有变异体针对单一高浓度(2mm)的2-kh和2-kn的活性(如表1中所示)。在初始评估之后，对于选择数目的变异体进行详细动力学分析以测定最大速率(kcat)、产生半最大速率(k0.5，酶在michaelis-menten动力学之后的km的等效物)的底物浓度和酶针对2-ko和2-kn的催化效率(kcat/k0.5)(如表2中所示)。对于2-kn具有较高特异性(较高kcat/k0.5)的abppdc变异体将在细胞内部产生衍生自其的辛醛和化学物质中有效。表1.abppdc变异体的序列清单和活性seqid4为巴西固氮螺菌苯丙酮酸脱羧酶(基因库寄存编号l26240)的氨基酸序列。seqid6-82为设计和表示于本发明中的蛋白质的序列。本发明中表示的所有蛋白质在n端具有13个以组氨酸标签形式添加的额外氨基酸(显示于seqid2中)。实例2a.巴西固氮螺菌苯丙酮酸脱羧酶(abppdc)和其工程改造变异体在大肠杆菌中的异源表达为了评估表1中列出的野生型abppdc和其变异体的底物特异性，所有蛋白质的基因分别表达于大肠杆菌细胞中且蛋白质产物与细胞分离。从ncbi数据库下载巴西固氮螺菌苯丙酮酸脱羧酶(基因库寄存编号l26240)的基因序列。将包括六个(6)组氨酸(his)的13个额外氨基酸的密码子添加到abppdc基因序列的met-1密码子的上游。此类修饰允许具有13个额外氨基酸的组氨酸标记的abppdc在n端上的表达。额外氨基酸以使用ni-nta色谱在单一步骤中纯化蛋白质的辅助的形式附接。具有13个额外氨基酸的整个abppdc序列(seqid2)经化学合成且接着克隆到syntheticgenomics,inc.(sandiego,ca)的t7聚合酶促进剂下游的prsfduet-1载体(emdbiosciences)中。最终载体在装运之前由syntheticgenomics,inc.定序。使用newenglandbiolab的q5定点突变诱发试剂盒(目录号e0554s)化学合成或产生表1中列出的abppdc变异体的基因且克隆至prsfduet-1载体中。含有abppdc或abppdc变异体基因的prsfduet-1载体如下所述地转化成大肠杆菌、abppdc或其变异体，接着表达且最终纯化。接着使用获自emdbiosciences的感受态bl21(de3)细胞进行大肠杆菌表达研究。根据试剂盒说明书进行转化且涉及混合50微升(μl)等分试样的感受态细胞与1μl载体。使用康霉素作为生长培养基中的标记物选择含有abppdc表达载体的细胞。接着在含有50微克/毫升(μg/ml)康霉素的卢里亚-贝尔塔尼(luria-bertani；lb)培养液琼脂板上选择含有abppdc或abppdc变异体表达载体的大肠杆菌转化体。在37摄氏度(℃)下培育所述板16小时(h)。通过将单一群落的转化体转移至50毫升(ml)含有50μg/ml康霉素的lb培养基中且在37℃下在振荡的情况下以220转/分(rpm)培育过夜而开始起子培养。次日，将7ml起子培养物接种至800mlterrificbroth(tb)中且在37℃下培育培养物直至培养物达到0.5的600纳米下的光学密度(od600nm)。添加1mm的最终浓度下的异丙基β-d-1-硫代哌喃半乳糖苷(iptg)以诱发abppdc或abppdc变异体基因的表达且将培养物转移至15℃恒温箱后维持16小时(h)。在16h结束时，培养物在8000转/分(rpm)下离心以使细胞粒化。将细胞团分成两个等分试样且储存于-80℃下过夜，随后纯化。获自400ml表达培养物的大肠杆菌细胞团悬浮于含有1μg/mldna酶(thermofisherscientific,inc.,rockford,il)、1μg/ml溶菌酶(thermofisherscientific,inc.,rockford,il)、1毫摩尔(mm)二硫苏糖醇和蛋白酶抑制剂混合液(rpicorp.,mountprospect,il)的b-per试剂(thermofisherscientific,inc.,rockford,il)中。将悬浮液在室温下平缓地摇动30分钟(min)且在15,000倍重力(×g)下离心20min以使细胞碎片粒化。分离上清液且与5mlco-nta树脂(thermofisherscientific,inc.,rockford,il)一起培育，所述树脂已用平衡缓冲液(50mm磷酸钠，ph8.0，含有300mm氯化钠、20mm咪唑、50μl蛋白酶抑制剂混合液和15％甘油)预平衡。在4℃下的1h的培育期之后，用5倍体积的平衡缓冲液洗涤酶结合树脂。abppdc或其变异体用过含有200mm咪唑的平衡缓冲液从co-nta树脂洗脱。洗脱的蛋白质相对于磷酸盐缓冲盐水渗析且以20％甘油溶液的形式储存于-20℃下。b.测定abppdc和abppdc变异体的底物特异性使用如在实例1中详细描述的方法进行abppdc变异体的底物特异性的评估。进行高通量abppdc偶合酶分析以评估abppdc变异体的底物特异性。分析涉及使用醇脱氢酶(adh6，基因库寄存编号np014051.3)减少产生自abppdc介导的2-酮酸脱羧的醛。abppdc催化反应的初始速度测定自在醛的adh6催化的还原期间发生的还原烟酰胺腺嘌呤二核苷酸磷酸(nadph)的氧化的速率。htp筛选分析涉及用含0.5mm二磷酸硫胺素、0.35mmnadph、4.7微克(μg)酵母菌adh6(基因库寄存编号np014051.3)和0.3毫克/毫升(mg/ml)牛血清白蛋白(bsa)的abppdc分析缓冲液(50mm3-(n-吗啉基)丙磺酸，ph6.8，含有2.5mm氯化镁(mgcl2))在30℃下培育2mm2-kh或2mm2-kn。反应通过在30℃下添加含有0.5μg至3.5μg稀释于含有1mg/mlbsa的abppdc分析缓冲液中的abppdc变异体的工作酶储备液而开始。含有200μl反应混合物的所述板在2500×g下离心15秒且在30℃下预平衡的biotektm板读取器上在340nm处以分光光度法追踪反应混合物的吸收率变化。使用340nm处的nadph消耗速率和nadph的消光系数(6.22mm-1cm-1)计算酶反应的初始速度。所有变异体的活性以存在于反应混合物中的酶的量标准化且表示为纳摩尔/分钟/毫克(nmol.min-1.mg-1)。使用购自thermofisherscientific,inc.的来自piercebiotechnologyinc.的660nm总蛋白质分析试剂盒，使用bsa作为标准物测定用于使活性标准化的蛋白质浓度。2-酮基辛酸酯(2-ko)和2-酮基壬酸酯(2-kn)通过abppdc和其变异体的脱羧的动力学参数也使用相同htpabppdc偶合酶分析测定，除了2-ko或2-kn的浓度从0变为4mm。对于展现底物活化的abppdc变异体，如从相对于底物浓度曲线的初始速度的s形曲线显而易见，通过使用非线性回归将数据拟合至希尔方程式(hillequation)(表2的图例中示出)获得2-酮基酸脱羧的动力学参数(kcat、k0.5和kcat/k0.5)。对于遵循正态饱和动力学的变异体，通过使用非线性回归将初始速度拟合至michaelis-menten方程式而动力学参数(kcat、km和kcat/km)。使用graphpadprismtm软件进行非线性回归。表2列出通过abppdc和其变异体的2-ko和2-kn脱羧的动力学参数。使用piercebiotechnologyinc.tm660nm总蛋白质分析试剂盒且使用bsa作为标准物来测定反应混合物中的酶的量。预期使abppdc的底物特异性变窄会改进特定醛和其下游产物的积聚。一般来说，abppdc偏好更庞大2-酮酸，如5-苯基-2-酮基戊酸酯和苯基丙酮酸，如通过关于那些底物的高催化效率证明(参见例如spaepen,s.；versees,w.；gocke,d.；pohl,m.；steyaert,j.；vanderleyden,j.“参与巴西固氮螺菌的生长素生产的苯丙酮酸脱羧酶的表征(characterizationofphenylpyruvatedecarboxylase,involvedinauxinproductionofazospirillumbrasilense),”《细菌学杂志(j.bacteriol.)》,2007,189:7626-7633)。对表1中列出的abppdc和变异体筛选针对作为底物的2mm2-酮基己酸酯(2-kh)和2mm2-酮基壬酸酯(2-kn)的活性。筛选展现野生型abppdc催化2-kn的脱羧，但在分析条件下展现针对2-kh的不佳活性。所有abppdc变异体也催化2-kn的脱羧，且展现针对2-kh的相对低活性(表1)。gln-536经丙氨酸、缬氨酸、异亮氨酸或亮氨酸的取代相比于野生型酶增加2-kn脱羧基活性，但也改进针对作为底物的2-kh的活性。这些结果表明表1中列出的所有abppdc变异体可以活性形式表达于异源系统中。此外，其全部具有相比于2-kh显著较高的针对2-kn的活性，表明本文所述的abppdc和变异体偏好>c62-酮酸。对所有酶进行详细稳态动力学分析以测定对2-酮基辛酸酯(2-ko)和2-酮基壬酸酯(2-kn)脱羧的最大速率和催化效率。两种底物均展现如从表2显而易见的双曲线和非双曲线动力学。对于显示非双曲线动力学的abppdc变异体，将2-ko和2-kn的脱羧的速度拟合至hill方程式(表2图例)且如表2中所示地计算最大速率和催化效率(kcat/k0.5)。大于1的希尔系数表明存在通过2-ko和2-kn的底物活化。已在abppdc和其它脱羧酶的情况下报导底物活化。另外参见spaepen,s.,同上。如从表2显而易见，氨基酸取代以不同方式影响捕获2-ko和2-kn用于催化中的变异体的催化效率。对于一些变异体，例如f532v，2-kn和2-ko的脱羧的催化效率分别为相比于野生型abppdc的180％和45％。这表明f532v取代增加2-kn的底物特异性，同时减少2-ko的底物特异性。通过采用变异体的催化效率的比率计算相比于2-ko的abppdc变异体对于2-kn的偏好且显示于表2中。如表2中所证明，abppdc和f532v的特异性分别为1.8和5.6，指示其对2-kn脱羧的催化效率高于对2-ko脱羧的效率1.8倍和5.6倍。这也指示相比于abppdc，f532v变异体在相比于2-ko偏好2-k中的特异性高3倍。类似地，相比于2-ko的f385l对于2-kn的偏好比abppdc高5倍。此数据表明相比于较短2-酮酸(例如2-ko)，f385l和f532v取代改进较长2-酮酸(例如2-kn)的底物特异性。因此，当使用“+1路径”延长2-酮酸时，f385l和f532v变异体将改进基于较长(c7-c10)醛的产物的积聚(图1)。类似地，m461l、f532l、q536g、q536l、f532v/q536v、m380v/m461v、f532a/q536v、f532v/q536a、f385l/q536v、m461v/f532v和m461v/f532v/q536v变异体对于2-kn的特异性相比于每一变异体对于2-ko的特异性分别为3.3、4.3、4.8、2.7、3.6、2.7、6.8、4.6、4.3、5.4和2.1。这表明所有这些变异体在捕获2-kn用于催化中比abppdc更具特异性。除abppdc变异体对于2-kn的特异性以外，辛醛和衍生自其的生物化学品的最大积聚也将取决于相对于abppdc变异体的2-kn产生路径的相对效率。举例来说，当产生2-kn中的工程改造的2-酮酸链延长路径(涉及三种酶，异丙基苹果酸合成酶、异丙基苹果酸异构酶和异丙基苹果酸去氢酶)的效率相比于产生2-ko相对较低时，将由于2-ko通过abppdc变异体的脱羧以及细胞内部基于辛醛的化学物质的积聚的减少而导致庚醛形成。在这些情形下，如f385l的abppdc变异体将基于其相对高特异性(9.1)，以及其减小的作为2-kn脱羧催化剂的效率(表2)而为优选的脱羧酶。结果也显示经疏水性氨基酸(即，甘氨酸、丙氨酸、缬氨酸、亮氨酸或异亮氨酸)取代gln-536改进abppdc的催化效率和如表2中所示的其它特异性增强取代。q536v变异体分别在对2-ko和2-kn脱羧中比野生型酶高效8倍和5.7倍(表2)。类似地，m461v/f532v/q536v变异体分别在对2-ko和2-kn脱羧中比m461v/f532v变异体高效27倍和10倍(表2)。m461v/f532v/q536v变异体为分别在对2-ko和2-kn脱羧中比野生型酶高效约17倍和20倍的酶(表2)。m461v/f532v/q536v变异体的较高催化效率允许2-ko在比野生型酶低17倍的胞内含量下的有效脱羧且促进细胞内部的庚醛衍生性化学品，如庚醇(经由与醇脱氢酶的共表达)或庚酸盐(经由醛去氢酶的共表达)的积聚。也改进脱羧的催化效率的gln-536的其它取代(如经甘氨酸、丙氨酸、亮氨酸或异亮氨酸)也将改进特异性增强取代的催化效率。这通过q536a取代展现，其在添加到f532v变异体(对于2-ko，kcat/k0.5＝4.8mm-1min-1且对于2-kn，kcat/k0.5＝27mm-1min-1)中时产生针对2-ko和2-kn的催化效率分别高72％和40％的f532v/q536a变异体(对于2-ko，kcat/k0.5＝8.3mm-1min-1和对于2-kn，kcatk0.5＝38mm-1min-1)。总体来说，结果表明abppdc和其基因修饰变异体的表达允许c7-c11(且在此实例中尤其为c7-c9)2-酮酸在体内的有效脱羧，且进而允许例如衍生自醛的化学物质，如己醛、庚醛和/或辛醛在细胞内部的积聚。此外，单独或组合形式的f532、f385、q536、m380、m461、f465的修饰可产生在细胞内部展现例如类似地衍生的化学物质的尤其改进的积聚的微生物。表2.abppdc和其变异体的动力学表征**使用本文中描述的htp偶合分析测定初始速度研究。除了通过§指示的所有酶的初始速度使用graphpadprismtm软件拟合至希尔方程式(v为给定底物浓度s下的初始速度)。kcat、k0.5、h和kcat/k0.5分别为最大速度、最大速度的一半处的底物浓度、希尔系数和催化效率。结果为2-3个独立实验的平均值±标准误差。通过取用关于2-kn与2-ko的变异体的催化效率比(kcat/k0.5)计算abppdc变异体的特异性。1应用的命名规则为第一个字母指示已改变的氨基酸残基。f＝苯丙氨酸[phe]；q＝谷氨酰胺[gln]；m＝甲硫氨酸[met]。数字指示氨基酸序列中的位置(显示的相应为位置380、385、461、465、532和536)。最后一个字母指示在所述位置处经取代的氨基酸残基。g＝甘氨酸；a＝丙氨酸；i＝异亮氨酸；v＝缬氨酸；l＝亮氨酸。§这些变异体的初始速度拟合至经典michaelis-menton方程式。实例3用巴西固氮螺菌苯丙酮酸脱羧酶(abppdc)的f385l变异体(seqid.8)体外合成c5-c9醇如下进行用f385l变异体体外合成直链醇：用含0.5mm二磷酸硫胺素、2.5mmnad+、0.2毫克/毫升(0.2mg/ml)牛血清白蛋白(bsa)、5mm乙酰基辅酶a、0.036mg/ml大肠杆菌异丙基苹果酸合成酶的h97a/s139g/n167g/p169a/g462d变异体(由marcheschi,r.j.等人.“用于碳链延长的合成递归“+1”路径(asyntheticrecursive“+1”pathwayforcarbonchainelongation)”《acs化学生物学(acschem.biol.)》7:689-697,2012)、0.16mg/ml异丙基苹果酸异构酶的leuc亚单元(基因库寄存编号nc000913.3，基因标识：945076)和0.21mg/ml异丙基苹果酸异构酶的leud亚单元(基因库寄存编号nc000913.3，基因标识：945642)、0.264mg/ml大肠杆菌异丙基苹果酸去氢酶(leub；基因库寄存编号nc_000913.3，基因标识：944798)、0.192mg/ml异丙基苹果酸去氢酶的l96g/v198a变异体(报导于wo2015089127a1中)、0.025mg/ml酿酒酵母醇脱氢酶(adh6，基因库寄存编号np_014051.3)和0.0054mg/mlf385l变异体(seqid8)的体外合成缓冲液(50mm2-[4-(2-羟乙基)哌嗪-1-基]乙磺酸，ph7.5，含有30mm氯化钾(kcl)和5mm氯化镁(mgcl2))培育0.5mm2-酮基丁酸酯(2-kb)。反应通过添加2-酮基丁酸酯至反应混合物的其余部分而起始。相同体积的分析级甲苯(用于hplc的chromosolvplustm，≥99％，产品目录编号650579)覆加在反应混合物的顶部上且在30℃下培育溶液。在30℃下培育2.5小时之后，添加nadph至水层直到1mm的最终浓度。在30℃下培育6小时之后，添加额外nadph至水层直到2mm的最终浓度。在30℃下再培育反应物18小时，接着通过在-20℃下冷冻30分钟而停止。去除甲苯层的一部分且使用装备有火焰电离检测器(fid)的气相色谱仪分析。通过在以上反应混合物中用0.5mm2-酮基异戊酸酯(2-kiv)或0.5mm3-甲基-2-酮基戊酸酯(3m-2kp)置换2-酮基丁酸酯且如上文所述地进行实验而进行f385l变异体的分支链醇的体外合成。使用装备有火焰电离检测器(fid)、g1513a型号自动注射器和gc自动取样器控制器的hewlettpackard(hp)6890系列气相色谱仪对醇进行定量。使用agilentj&wdb-ffap毛细管gc柱(30m×0.320mmid×0.25μm膜厚度；产品目录编号123-3232，agilenttechnologies,inc.,wilmington,de19808)分离分析物。初始gc烘箱温度为40℃，其保持1.50分钟，接着以40℃/分钟梯度增加至235℃。此梯度给出6.38分钟的总运行时间。柱流动速率为4.0ml/min，其中氦气作为载气。注入体积为1μl。注射器和检测器的温度设定为225℃。产生自这些体外合成反应的醇效价显示于图2、3和4中。结果指示f385l变异体与大肠杆菌异丙基苹果酸合成酶(leua)、大肠杆菌异丙基苹果酸异构酶(leucd)、野生型和经修饰大肠杆菌异丙基苹果酸去氢酶(leub)以及醇脱氢酶(adh6)的h97a/s139g/n167g/-p169a/g462d变异体组合，在与2-酮基丁酸酯、2-酮基异戊酸酯或3-甲基-2-酮基戊酸酯一起培育后产生延长的c5-c9醇。此外，结果展示f385l变异体对于较长直链醇的特异性，其中1-辛醇表示在与2-酮基丁酸酯一起培育后产生的总醇的大致60％。在分支链2-酮酸(2-酮基异戊酸酯(kiv)和3-甲基-2-酮基戊酸酯(3m-2-kp))的情况下，在与2-酮基异戊酸酯一起培育后产生大致等效量的5-甲基-1-己醇和6-甲基-1-庚醇，且在与3-甲基-2-酮基戊酸酯一起培育后产生大致等效量的3-甲基-1-戊醇和5-甲基-1-庚醇。这些结果展示f385l变异体接受直链以及分支链2-酮酸作为底物且可产生对应直链和分支链醛，其可随后转化为其它产物，如醇、羧酸或烷烃。实例4使用野生型abppdc和其变异体以及“+1路径”酶在大肠杆菌的工程改造菌株中体内产生c5-c8醇大肠杆菌(e.coli)mg1655经工程改造以促进长链直链醇产生且使得能够从t7启动子进行基因表达。为了改进直链醇生产，ilvbn和ilvih经由λred介导的同源重组不活化，如datsenko,ka,wanner,bl,“大肠杆菌k-12中的染色体基因使用pcr产物的单步不活化(one-stepinactivationofchromosomalgenesinescherichiacolik-12usingpcrproducts),”《美国国家科学院院刊(proc.natl.acad.sci.u.s.a.)》2000,97(12),6640-6645所描述。ilvbn和ilvih基因参与分支链氨基酸产生，因此这些基因的不活化消除分支链醇的产生。参与2-酮基丁酸酯生产的ilva基因通过经由λred介导的同源重组用强力组成性启动子和强力核糖体结合位点置换其天然促进剂和核糖体结合位点而上调，如datsenko和wanner,同上所描述。为了使得能够从t7启动子进行基因表达，使用λde3溶原化试剂盒(emdmillipore目录编号69734)将de3溶源整合到mg1655中。所得菌株基因型为mg1655(de3)δilvbnδilvihilvaup。经由八种蛋白质的表达在经工程化大肠杆菌菌株中产生c5-c8醇：(1)大肠杆菌异丙基苹果酸合成酶(leua)；(2)工程改造异丙基苹果酸合成酶(由marcheschi等人《acs化学生物学(acschem.biol.)》2012,7,689-697)；(3)和(4)大肠杆菌异丙基苹果酸异构酶(leucd)的两个次单元；(5)异丙基苹果酸去氢酶(leub)；(6)大肠杆菌异丙基苹果酸去氢酶的l96g/v198a变异体(如2014年12月10日提交的同在申请中的国际专利申请序号pct/us14/69438(代理人案号75413-wo-pct)中较详细描述，所述专利申请要求2013年12月12日提交的美国临时专利申请第61/915,040号(代理人案号75413-us-psp)的权益，两者均以全文引用的方式并入本文中)；(7)abppdc或其变异体；和(8)酿酒酵母醇脱氢酶(adh6)。总计产生十一个菌株。产生仅含有野生型abppdc的一个菌株。作为阴性对照，也产生不具有ppdc的菌株。也产生含有abppdc变异体f532v、f358l、f385v、f532vq536v、m461c、m461v、f385vm461c和f385lm461v的八个菌株。最后，产生含有野生型雷特氏乳球菌(lactococcuslactis)酮基异戊酸酯脱羧酶(kivd；基因寄存编号aj746364)作为比较，因为先前操作已显示kivd能够产生与“+1路径”酶组合的长链醇。参见例如marcheschi等人,同上。允许使用四种相容质体同时表达八种基因的novagenduetvector系统(emdmillipore目录编号71146、71341、71340和71147)用于表达上文所提及的基因。四种duet载体中的每一者用t7启动子下游的八种基因中的两种克隆，且四种duet载体转化成经工程化大肠杆菌菌株。带有所有质体的重组菌株关于使用抗生素(25微克/毫升(μg/ml)下的安比西林(ampicillin)、17μg/ml下的氯胺苯醇、25μg/ml下的大观霉素(spectinomycin)和15μg/ml下的康霉素)而选择且使用所属领域的技术人员已知的方法以聚合酶链反应(pcr)确认。在每一固体和液体培养步骤添加抗生素以确保质体的维持。在转型、板选择和pcr确认之后，菌株起初在37℃下生长的卢里亚-贝尔塔尼(lb)琼脂板上培养。单一琼脂板群落用于接种250ml摇瓶中的50mllb培养基，其使用设定于200rpm下的恒温箱振荡器在37℃下好氧地培养。在lb摇瓶中培养12-16小时之后，在1％v/v下接种血清瓶以评估醇生产。使用根据表1中示出的浓度的去离子水制备血清瓶发酵培养基。培养基经过滤灭菌，且将20ml培养基添加至丁基橡胶塞住的125ml血清瓶中。在培养基添加之前，血清瓶通过使用sterisamscocenturysv-160hprevac灭菌器在125℃下高压灭菌30分钟而预灭菌。表1.用于展示来自经重组工程改造以含有“+1路径”以及巴西固氮螺菌脱羧酶(abppdc)或其变异体的大肠杆菌的醇生产的培养基组成。组分浓度(g/l)mops缓冲液26.2甘油20胰蛋白胨10酵母提取物5泛酸钙1.19na2hpo40.105(nh4)2so40.661nh4cl1.6在接种之后，在37℃下在200rpm于恒温箱振荡器中振荡的情况下培养血清瓶培养物。在接种之后大致三小时，使用0.1mm异丙基β-d-1-硫代半乳糖苷(iptg)诱导培养物以确保所有基因的表达。在诱导之后24小时收获发酵物用于分析。在发酵结束时，血清瓶通过置于冷冻机中20-30分钟而紧接着冷却至4℃。将血清瓶去瓶盖，且将发酵培养液快速倒入含有1ml饱和氯化钠溶液和2ml分析级甲苯(用于hplc的chromosolvplustm，≥99.9％，产品目录编号650579)的50ml锥形管中。培养液-氯化钠-甲苯混合物经涡旋30秒。接着将甲苯萃取物的300μl等分试样提交至如实例3中所述地使用gc/fid进行分析。血清瓶的平均醇分布显示于图5中。结果指示与“+1路径”基因和adh6组合的野生型巴西固氮螺菌(abppdc)的表达导致用于产生介于戊醇至辛醇范围内的直链醇的功能路径。未在无abppdc的菌株中检测到c5-c8醇，证实此基因的存在对长链醇产生至关重要。此外，结果展示含有野生型abppdc的菌株比含有kivd的菌株累积基本上更多的己醇、庚醇和辛醇。未在kivd菌株中检测到己醇、庚醇或辛醇产生，但abppdcwt菌株分别产生>2mg/l、>3mg/l和>0.1mg/l的己醇、庚醇和辛醇。醇生产的大致50％为庚醇和辛醇，其为相比于主要导致戊醇和己醇生产的其它脱羧酶的情况下的前述成果的显著改进(marcheschi等人《acs化学生物学》2012,7:689-697)。因此，使用abppdc脱羧酶似乎将醇生产转化至较长链长度，其结果与实例1和2内包含的体外数据一致。图5中的额外数据表明所有abppdc变异体具有产生c5-c8醇的能力。三种abppdc变异体m461c、m461v和f385l/m461v展示相比于野生型abppdc的c5-c8醇产生的显著改进。abppdc变异体m461c产生>3mg/l己醇和>5mg/l庚醇，表示相比于野生型abppdc的大于40％改进。最印象深刻地，abppdc变异体m461v显示相比于野生型abppdc的戊醇、己醇和庚醇产生的大于2倍改进。m461v变异体也显示相对于野生型abppdc的就辛醇效价来说的30％改进。含有m461v变异体的此菌株产生具有约9mg/l己醇和约8.5mg/l庚醇的最高效价。变异体f532v、f385l、f532vq536v、m461c、m461v和f385lm461v全部显示相比于kivd和abppdc野生型基因的1-辛醇效价的改进。最后，abppdc变异体f385l/m461v显示相比于abppdc野生型的己醇和庚醇产生的约60％改进。序列表<110>陶氏环球技术有限责任公司p·c·桑格哈尼c·c·斯托尔斯e·c·史乐s·a·格林沃尔特<120>基因修饰苯丙酮酸脱羧酶、其制备方法和用途<130>77272-wo-pct<140>tobeassigned<141>2015-12-03<150>62/089,912<151>2014-12-10<160>82<170>patentinversion3.5<210>1<211>39<212>dna<213>人工序列<220><223>表达的abppdc变异体的n端处的his-tag的13氨基酸序列<220><221>cds<222>(1)..(39)<400>1atgg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