JP5978132B2 - 酵母を用いるスクアレン生成のための方法および組成物 - Google Patents
酵母を用いるスクアレン生成のための方法および組成物 Download PDFInfo
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Description
本出願は、米国特許仮出願第61/263,775号(標題“Methods and Compositions for Producing Squalene Using Yeast”、2009年11月23日出願。参照によりその全体が全ての目的において本明細書に組み込まれる)に対する優先権を主張する。
酵母を用いるイソプレノイド(例えばスクアレン)の生成のための方法および組成物を提供する。
以下の発明の背景に関する記載は単に本発明に関する理解を促すために提供するものであり、本発明の従前技術を記述する、またはそれを構成すると認めるものではない。
本発明は、酵母からスクアレンを生成するための組成物および方法を提供する。
酵母の種類
本明細書に開示する組成物および方法は、多くの酵母種および株のうちの、任意のものに基づくことができる。ある態様では、酵母は油性酵母である。例えば酵母はCryptococcus curvatus(例えばATCC 20508)、Yarrowia lipolytica(例えばATCC 20688またはATCC 90811)、Rhodotorula glutinus(例えばATCC 10788またはATCC 204091)、およびRhorosporidium toruloidesであってもよい。発明者は、Cryptococcus curvatusおよびRhodotorula glutinisが他の酵母(例えばYarrowia lipolytica)と比較して、広範な基質上で非常に高密度まで増殖し、多くの培養条件下で多量の総脂質を産生することを発見した。従って、特定の態様では、Cryptococcus curvatusおよびRhodotorula glutinisは、本明細書に開示する組成物および方法に特に有益である。Yarrowia lipolyticaに特異的な多くの遺伝子ツール(例えば形質転換プロトコル、選択マーカー)が開発されている;そのため、ある態様では、Yarrowia lipolyticaは本明細書に開示する組成物および方法に特に有益である。本明細書に開示する組成物および方法のある態様では、酵母(遺伝子転換された酵母または遺伝子転換されていない酵母)はYarrowia lipolytica株、例えばATCC 20688、ATCC 90811、ATCC 90904、ATCC 90812、ATCC MYA-2613、またはYeastern polgであってもよい。
本発明は、以下に詳述するコンフォメーションおよび化学的性質を有する「遺伝子修復オリゴ核酸塩基」を用いて実施することができる。本発明の「遺伝子修復オリゴ核酸塩基」には、混合2本鎖オリゴヌクレオチド、ヌクレオチド非含有分子、1本鎖オリゴデオキシヌクレオチド、および以下に記載する特許および特許文献に記載される、他の遺伝子修復分子がある。本発明の「遺伝子修復オリゴ核酸塩基」は、公開されている科学文献および特許文献に、以下の別称でも記載されている:「遺伝子組換え(recombinagenic)オリゴヌクレオチド」、「RNA/DNAキメラオリゴヌクレオチド」、「キメラオリゴヌクレオチド」、「混合2本鎖オリゴヌクレオチド(MDON)」、「RNA DNAオリゴヌクレオチド(RDO)」「遺伝子ターゲッティング・オリゴヌクレオチド」、「ゲノプラスト(genoplast)」、「1本鎖改変型オリゴヌクレオチド」、「1本鎖オリゴデオキシヌクレオチド変異ベクター」、「2本鎖変異ベクター」、および「ヘテロ2本鎖変異ベクター」。
ある態様では、異種発現によって外来遺伝子または内在性遺伝子の過剰コピーを酵母(例えばYarrowia lipolytica)中で発現させる。酵母における異種発現は、当該分野で公知の方法を用いて行うことができる。異種発現を用いる酵母中での外来遺伝子または内在性遺伝子の過剰コピーの発現は、以下を含有するベクターの使用を伴ってもよい:(a)転写開始のためのプロモーター配列、(b)転写終了のための終結配列、および(c)選択マーカー。異種発現および発現ベクターは、例えば以下に報告されているものであってもよい:Madzak, C., Gaillardin, C.,およびBeckerich, J-M., 2004 Heterologous Protein Expression and Secretion in the Non-Conventional Yeast Yarrowia lipolytica: a review, Journal of Biotechnology 109:63-81。本明細書の組成物および方法のある態様では、ベクターはpYLEX1(Yeastern)である。使用できる選択マーカーの非制限的な例としてura3、lys5、trp1、leu2、ade1、ハイグロマイシン耐性をコードするE.coli hph、およびSaccharomyces cerevisiae由来のSUC2がある。使用できるプロモーターの非制限的な例としてpLEU2、pXPR2、pPOX2、pPOT1、pICL1、pG3P、pMTP、pTEF、およびpRPS7がある。ある態様では、プロモーターはhp4dプロモーターであり、これは強力な構成的ハイブリッド・プロモーターである(米国特許第6,083,717号(2000年7月4日出願))。使用できる終結配列の非制限的な例としてXPR2t、LIP2t、およびPHO5tがある。
本明細書に開示する改変型または変異型酵素は、塩基対の変更、挿入、置換などによって改変または変異させることができる。
任意の公知の方法を本発明の方法に使用して、酵母細胞を遺伝子修復オリゴ核酸塩基で形質転換することができる。代表的な方法として、エレクトロポレーション、LiOAc、遺伝子銃、スフェロプラスト、および/またはアグロバクテリウムの使用がある(例えばMcClelland, C.M., Chang, Y.C.,およびKwon-Chung, K.J. (2005) Fungal Genetics and Biology 42:904-913参照)。
改変型酵素を発現する酵母の同定は、多くの方法のいずれを用いて行うことができる。ある方法では、同一実験で選択可能な転換(すなわちマーカー)および選択不能な転換(例えば目的の標的遺伝子)の両方を標的とする遺伝子修復オリゴ核酸塩基(gene repair oligonucleobases;GRON)を用いる、同時転換法を行う。この方法では、GRONが送達されなかった、またはGRONによって指定された転換が伝達されなかった細胞が除去される。非関連遺伝子を標的とするGRONの送達は選択的ではないと考えられるので、ある程度の頻度で、うまく選択された転換を含有するコロニーは、他の標的遺伝子の1つにも転換を有すると考えられる。転換事象は一塩基多型(SNP)分析によって解析される。
Cryptococcus curvatus(ATCC株20508)およびRhodotorula glutinis(ATCC株10788および204091)形質転換系を作製するために、S. cerevisiaeにカナマイシン耐性を付与するKANMX発現カセット(プロモーター-遺伝子-ターミネーター)を選択マーカーとして用い、菌株をカナマイシン感受性から耐性に転換する(例えばBaudin, A.ら (1993) Nucleic Acids Research (21) 3329-3330参照)。菌株を、発現カセットのみ、並びに、DNA複製起点を含有するR. glutinusが報告するプラスミド(例えばOloke, J.K.およびGlick, B.R. (2006) African Journal of Biotechnology 5(4):327-332参照)の制限フラグメントにライゲートしたKANMXで形質転換した。エレクトロポレーション、LiOAc、遺伝子銃、スフェロプラスト、および/またはアグロバクテリウムによって、DNAをC. curvatusおよびR. glutinisに導入する(McClelland, C.M., Chang, Y.C.,およびKwon-Chung, K.J. (2005) Fungal Genetics and Biology 42:904-913)。
Cryptococcus curvatusおよびRhodotorula glutinisにおいてウラシル要求性変異株を作製するために、細胞を抗代謝物(5-フルオロオロチン酸)を含有する最少量の培地中で培養し、ura3またはura5遺伝子中に変異を有する耐性変異体を選択した。Cryptococcus curvatusの安定な5-FOARコロニー33個およびRhodotorula glutinisの安定な5-FOARコロニー20個をバンクに預託した。Cryptococcus curvatusおよびRhodotorula glutinis由来の野生型URA3遺伝子をクローニングし、5-FOAR分離株中の変異ura3遺伝子をシーケンシングした。
Yarrowia lipolytica株ATCC 90811(leu2-35 lys5-12 ura3-18 XPR2B)由来のleu2、lys5、およびura3遺伝子の対立遺伝子をPCRによってクローニングし、その配列を野生型対立遺伝子と比較して差異を同定した。
HPH2/C/42/5'Cy3/3'idC
5’Cy3-GAACTCACCGCGACGTCTGTCGAGAAGTTTCTGATCGAAAAG-3’idC
HPH2/NC/42/5'Cy3/3'idC
5’Cy3-HCTTTTCGATCAGAAACTTCTCGACAGACGTCGCGGTGAGTTC-3’idC
E12stopK13stopを修復して野生型とするGRON(T34G T37A)
HPH3/C/43/5'Cy3/3'idC
5’Cy3-CTCACCGCGACGTCTGTCGAGAAGTTTCTGATCGAAAAGTTCG-3’idC
HPH3/NC/43/5'Cy3/3'idC
5’Cy3-CGAACTTTTCGATCAGAAACTTCTCGACAGACGTCGCGGTGAG-3’idC
NCBIデータベースに収録されているSaccharomycesおよび他の酵母由来のACCase、HMGR、スクアレンシンターゼ、およびスクアレンエポキシダーゼの配列をPCRプライマー源として使用し、対応する遺伝子をCryptococcus curvatusおよびRhodotorula glutinisから、それらに対応する調節領域(プロモーター、ターミネーター)と共にクローニングした。プロモーターの「亢進」変異および「抑制」変異(それぞれ、転写を増加または低下させる)を同定するために、これら4つの遺伝子のプロモーターを相対的に誤りがちな(error-prone)DNAポリメラーゼを用いてクローニングし、プロモーター中に点変異を作製し、それらのフラグメントを、緑色蛍光タンパク質(GFP)またはβガラクトシダーゼレポーター遺伝子と融合させたベクターにクローニングし、S. cerevisiaeまたはE. coliにおけるインビトロ試験に使用した。プロモーターの「亢進」変異はRTDSによってHMGRおよびスクアレンシンターゼゲノム配列に再導入し、「抑制」変異はゲノムACCaseおよびスクアレンエポキシダーゼ配列中で作製する。R. glutinisおよびC. curvatus中の必須遺伝子(例えばGAPDH、アクチン)由来のプロモーターをクローニングし、外来遺伝子発現に使用する。PCRクローニング用のプライマーは、S. cerevisiae中のこれらの遺伝子との相同性から設計する。
ACCase。R. glutinis、C. curvatus、およびそれ以外の酵母中のACCase遺伝子のコピー数を測定する。RTDSを利用し、過剰コピー中の翻訳開始位置の直後に終結コドンを導入することによってACCase発現を低下させる。
Cryptococcus curvatuの増殖を測定し、培地中の細胞量を最大にするのに最適な炭素源を検討した。酵母抽出物に基づくリッチな培地(10g/L 酵母抽出物、20g/L ペプトン)中で、C. curvatusは2-20% w/v グルコースの存在下で良好に増殖し、16% w/v グルコース以上では、4日後に最大レベル55g/Lの細胞乾燥重量(CDW)を得た。同様に、C. curvatusは同じ培地中、3-12% w/v グルコースの存在下でも増殖し、12% w/v グルコースでは、5日後のCDWは40g/Lであった。C. curvatusは、最大3.5% w/vのバイオディーゼルグリセロール(Imperial Western Products社。カリフォルニア州コーチェラ)中でも増殖し、CDWは23g/Lであった。
スクアレンの正味の生成量を増加させるために環境操作についての検討を行った。それらには以下がある:(a)オレイン酸、オリーブもしくは他の植物油(単数または複数)、イノシトール、コリン、ソラフェン、フルアジホップ、およびクレトジム、または他のACCase阻害性除草剤を用いるACCaseの発現および/または活性の阻害、(b)テルビナフィン、トルナフテート、およびエルゴステロール、または他のスクアレンエポキシダーゼ阻害性防かび剤を用いるスクアレンエポキシダーゼの発現および/または活性の阻害、(c)(出発培地または追加培地中の)グリセロールに基づく培地のC/N比の操作、(d)培地中の窒素源の変更(有機対無機対単体/複合体)、(e)炭素添加方式の変更(例えばバッチ対流加)、(f)炭素源以外の栄養素を枯渇させた場合の影響の検討、(g)糖、糖アルコール、アルコール、多価アルコール、および有機酸の混合物に添加する炭素源の変更、(h)HMGR阻害性化合物、例えばロバスタチン、または他のスタチン系阻害剤上での増殖に関する選択、および(i)親油性色素もしくは染料の使用、および/または(例えば重量分析法またはガスクロマトグラフィー分析法による)抽出可能な脂質の分析による、培地中での高油生成量に関する選択。
慣例的な菌株選択法を油性酵母に使用し、正味のスクアレン生産性を増加させる。UV、ニトロソグアニジン、またはエタンスルホン酸メチルによって変異させた菌株を高スクアレン蓄積量でスクリーニングおよび/または選択した。また、菌株を逐次選択圧(例えば3%グリセロール含有YEP(15g/L酵母抽出物、5g/Lペプトン)培地またはロバスタチンおよび他の公知のHMGR阻害剤を含有する培地での反復継代培養)に施与する。また、菌株を、種々の量のグリセロールおよび/またはグルコースを含有するCYM001培地、あるいは、ロバスタチンおよび/もしくは他の公知のHMGR阻害剤および/またはスクアレンシンターゼ阻害剤を含有する培地で反復継代し、HMGRおよび/またはスクアレンシンターゼ活性が高い自然発生突然変異体を得る。それらの変異はHMGR、スクアレンシンターゼ、または他の遺伝子中に存在してもよい(「第2部位変異」)。
Claims (11)
- 遺伝子改変された酵母または遺伝子改変されていない酵母によるスクアレンの生成法であって、該方法は、酵母を抗真菌剤と共に培養することを含む方法であり、
該酵母は、ATCC 20688、ATCC 90811、ATCC 90904、ATCC 90812、ATCC MYA-2613およびYeastern polgから成る群から選択されるYarrowia lipolytica株であり、
抗真菌剤は、アリルアミン抗真菌剤であり、
前記酵母が、遺伝子改変された酵母である場合には、
方法は、そのイソプレノイド生合成経路中の1つまたはそれ以上の酵素の活性または発現を増加または低下させることを含み、
(i) 前記酵素は、メバロン酸キナーゼであり、メバロン酸キナーゼが、増加した活性または発現を示すか、
(ii) 前記酵素は、アセチルCoAカルボキシラーゼであり、アセチルCoAカルボキシラーゼが、低減した活性または発現を示すか、
(iii) 前記酵素は、HMG-CoAレダクターゼであり、HMG-CoAレダクターゼが、増加した活性または発現を示すか、
(iv) 前記酵素は、スクアレンエポキシダーゼであり、スクアレンエポキシダーゼが、低減した活性または発現を示すか、
(v) 前記酵素は、スクアレンシンターゼまたはATPクエン酸リアーゼであり、スクアレンシンターゼまたはATPクエン酸リアーゼが、増加した活性または発現を示すか、
(vi) 前記酵素は、ATPクエン酸シンターゼであり、ATPクエン酸シンターゼが、増加した活性または発現を示すか、
(vii) 前記酵素は、グリセロールキナーゼであり、グリセロールキナーゼが、増加した活性または発現を示すか、または
(viii) 前記酵素は、5-アミノレブリン酸シンターゼであり、5-アミノレブリン酸シンターゼが、低減した活性または発現を示す、
方法。 - 請求項1に記載の方法であって、
該酵素の活性または発現は1つまたはそれ以上の意図的変異によって増加または低下され、該1つまたはそれ以上の意図的変異は該酵素中の所定の位置に存在し、該遺伝子改変された酵母は野生型酵母に比較して多量のイソプレノイドを産生する、方法。 - 請求項1または2に記載の方法であって、アリルアミン抗真菌剤が、10〜15μg/mLの濃度である、方法。
- (i) 前記酵素がメバロン酸キナーゼであり、メバロン酸キナーゼが、増加した活性または発現を示す、請求項1〜3のいずれか一項に記載の方法。
- (ii) 前記酵素がアセチルCoAカルボキシラーゼであり、アセチルCoAカルボキシラーゼが、低減した活性または発現を示す、請求項1〜3のいずれか一項に記載の方法。
- (iii) 前記酵素がHMG-CoAレダクターゼであり、HMG-CoAレダクターゼが、増加した活性または発現を示す、請求項1〜3のいずれか一項に記載の方法。
- (iv) 前記酵素がスクアレンエポキシダーゼであり、スクアレンエポキシダーゼが、低減した活性または発現を示す、請求項1〜3のいずれか一項に記載の方法。
- (v) 前記酵素がスクアレンシンターゼまたはATPクエン酸リアーゼであり、スクアレンシンターゼまたはATPクエン酸リアーゼが、増加した活性または発現を示す、請求項1〜3のいずれか一項に記載の方法。
- (vi) 前記酵素がATPクエン酸シンターゼであり、ATPクエン酸シンターゼが、増加した活性または発現を示す、請求項1〜3のいずれか一項に記載の方法。
- (vii) 前記酵素がグリセロールキナーゼであり、グリセロールキナーゼが、増加した活性または発現を示す、請求項1〜3のいずれか一項に記載の方法。
- (viii) 前記酵素が5-アミノレブリン酸シンターゼであり、5-アミノレブリン酸シンターゼが、低減した活性または発現を示す、請求項1〜3のいずれか一項に記載の方法。
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