JP5666908B2 - ゲノムdnaの大きな断片の捕捉および修飾、ならびに合成葉緑体を有する生物を構築するための系 - Google Patents
ゲノムdnaの大きな断片の捕捉および修飾、ならびに合成葉緑体を有する生物を構築するための系 Download PDFInfo
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Description
本出願は、米国仮出願番号第60/978124号(2007年10月5日出願)の優先権および利益を主張し、この仮出願は、参照により本明細書中に援用される。
本明細書において言及される全ての刊行物および特許出願は、個々の刊行物または特許出願の各々が、参照によって援用されるべきであることが具体的かつ個別に示されたのと同じ程度まで、参照によって本明細書中に援用される。
DNAは、当該分野において公知の方法に従って単離および分析される。
E.coli株DH10BまたはGenehogは、0.7のOD600まで細胞を増殖させることによってエレクトロコンピテントにされ、次いで、収集され、氷冷10%グリセロールで2回洗浄され、ドライアイスエタノール浴において急速冷凍され、−80℃で保存される。全酵母または藻類のDNAが調製され、例えば、Bio−Rad Gene Pulsar Electroporatorにおいて0.1cmキュベットを1,800V、200オーム、および25mFで使用することによってE.coli中にエレクトロポレーションされる。細胞は回収され、クローンは、カナマイシン(50μg/mL)、アンピシリン(100μg/mL)、ゲンタマイシン(50μg/mL)、テトラサイクリン(51μg/mL)またはクロラムフェニコール(34μg/mL)のような1種以上の抗生物質を含有する寒天増殖培地上で選択される。
この実施例において、系は葉緑体DNAを捕捉するためにハイブリッドギャップ充填ベクターを使用して確立される(図1)。ハイブリッドギャップ充填ベクターのバックボーンは、ベクターが酵母人工プラスミド(YAP)として機能することを可能にする酵母要素、およびベクターがプラスミド人工染色体(PAC)として機能することを可能にする細菌要素を含有する。酵母要素は、酵母選択マーカー配列(例えば、TRP1またhLEU2)、酵母動原体配列(CEN)、および酵母自己複製ヌクレオチド配列(ARS)を含む。細菌要素は、P1または細菌性複製起点配列、および細菌選択マーカー配列(例えば、Kanr)を含む。
しばしば、非相同DNAの大きな断片は、酵母または細菌のような宿主生物において不安定である。これは、限定されないが、毒性遺伝子産物またはコドンバイアスの存在、および/または選択圧の欠如を含む、複数の因子のためであり得る。したがって、シャトルベクター内の標的DNAは、酵母または細菌内で変更され得る。例えば、標的DNA配列の特定の部分(例えば、コード領域またはプロモーター)は、宿主生物内の組換えによって除去または移動され得る。同様に、標的DNAを担持するシャトルベクターが標的DNAを提供した生物(または近縁の種)に戻された場合、標的DNAは不安定になることができる。
安定化ベクター有りまたは無しでハイブリッドベクターを含有するC.reinhardtii葉緑体ゲノムを産生するために、pTRP−10−KanおよびpSE−3HB−Strep−AUは、藻細胞に形質転換された。pTRP−10−Kanは、葉緑体標的化要素が各末端にあるようにするためにベクターを線状にするためにNotIで消化された(図5)。pSE−3HB−Strep−AUは、環状DNAとして形質転換された。
この実施例において、C.reinhardtii葉緑体ゲノムは、上記に記載されるような標準的技術を使用して単離される。pSE−3HB−Strep−AU有りまたは無しでpTRP−10−Kanベクターを含有するC.reinhardtii葉緑体DNAは、細菌を形質転換するために使用された。エレクトロコンピテントE.coli株DH10BまたはGenehogは、形質転換され、カナマイシン(50mg/l)を有するLB寒天増殖培地上で選択された。個々のクローンからのDNAは、細胞を37℃でカナマイシン(50mg/l)を有するLB液体増殖培地において飽和まで増殖させることによって単離された。飽和された細胞培養物は、LB+Kan+IPTGにおいて1:20に希釈され、そして37℃で4時間増殖される。Plasmid Maxiキット(QIAGEN)は、単離されたクローンからプラスミドDNAを調製するために使用される。
これらの実験について、全ての形質転換は、内因性psbA遺伝子座由来のSAAを発現するC.reinhardtii株W1.1、または内因性psbA遺伝子座由来のLuxABを発現するW1−1のいずれかで実行される。W1.1とW1−1の両方が、16S rRNAにおいて変異を導入するp228の形質転換のおかげでスペクチノマイシンに対して耐性である。細胞は、100rpmに設定されたロータリーシェーカー上で450ルクスの連続照明下、23℃でTAP培地(GormanおよびLevine,Proc.Natl.Acad.Sci.,USA 54:1665−1669,1965,これは参照によって本明細書中に援用される)において後期対数期まで(およそ7日間)増殖される。4,000×g、23℃で5分間の遠心分離によって50mlの細胞が採取される。上清は静かに移され、細胞は、その後の粒子衝突(Cohenら(前出)、1998)による葉緑体形質転換のために4mlのHSM培地に再懸濁される。全ての形質転換は、HSM寒天上で実行される。
捕捉された葉緑体ゲノムDNAをキシラナーゼの生成のために修飾するために、藻発現カセットが、実施例4に記載される酵母マーカーベクター中にクローニングされた。簡単には、C.reinhardtii葉緑体発現ベクターは、C.reinhardtii由来のpsbD遺伝子について5’UTRによって調節され、そしてC.reinhardtii由来のpsbA遺伝子について3’UTRで調節されるT.reeseiからキシラーゼを有するDNAのフラグメント(配列番号18)を遊離するためにSpeIで消化された。フラグメントは、平滑末端を作製するためにKlenowフラグメントで処理され、pUC1−URA3/ADE2、pUC3−URA3/LEU2、およびpUC4−URA3/HIS3において酵母マーカー間でSmaI(XmaI)部位中にクローニングされた。図10Aは、新しいベクターにおける種々の要素の配列を示す。
捕捉された葉緑体ゲノムDNAをFPPシンターゼの生成のために修飾するために、藻発現カセットが、実施例4に記載される酵母マーカーベクター中にクローニングされた。簡単には、C.reinhardtii葉緑体発現ベクターは、C.reinhardtii由来のpsbD遺伝子について5’UTRによって調節され、そしてC.reinhardtii由来のpsbA遺伝子について3’UTRで調節されるG.gallusからFPPシンターゼを有するDNAのフラグメント(配列番号19)を遊離するためにSpeIで消化された。フラグメントは、平滑末端を作製するためにKlenowフラグメントで処理され、pUC1−URA3/ADE2、pUC3−URA3/LEU2、およびpUC4−URA3/HIS3において酵母マーカー間でSmaI(XmaI)部位中にクローニングされた。図10Aは、新しいベクターにおける種々の要素の配列を示す。
この実施例において、系は、酵母における組換えによって葉緑体DNAを捕捉するためにハイブリッドギャップ充填ベクターを使用して確立される(図13)。ハイブリッドギャップ充填ベクターを葉緑体DNAを捕捉するように適合させるために、ベクターpDOCI−B5A10(配列番号20)が産生された。C.reinhardtii葉緑体ゲノムの一部が、psbD遺伝子(A10、配列番号27および28)およびpsbH遺伝子(B5、配列番号787および788)付近に隣接する領域に特異的な2つのプライマー対を使用してPCR増幅された。各PCR産物は、NotIおよびI−SceIで消化され、I−SceIで消化されてpDOCI−B5A10(配列番号20)を形成するpDOCI(配列番号1)に連結された。
この実施例において、系は、酵母における組換えによって完全な葉緑体ゲノムを捕捉するためにハイブリッドギャップ充填ベクターを使用して確立される(図14)。葉緑体DNAを捕捉するためのギャップ充填ベクターpTRP−10は、酵母における組換えを使用して構築された。簡単には、pDOCI−10(実施例3に記載される配列番号3)が、葉緑体ゲノム特異的要素をハイブリッドギャップ充填ベクター中に導入するカセットを遊離するために、PacIおよびAscIで消化された。このカセットは、酢酸リチウム法を使用して酵母株YPH858中にpTRP−AUと共に形質転換された。相同組換えは、形質転換された酵母細胞においてインビボで起こる。カセットと正しく一体化された形質転換体は、5−フルオロオロチン酸(5−FOA)を含有するCSM−Trp寒天培地上の増殖に基づいて、および赤色によって単離された。5−FOAは、機能的URA3遺伝子を欠くクローンおよびADE2遺伝子が除去される場合に生じる赤色を選択する。プラスミドDNAは、CSM−Trp液体培地において増殖され、かつE.coli(DH10B)に形質転換された酵母クローンから単離された。大量のpTRP−10−Kanを産生するために、pTRP−10−Kanを含むDH10B細胞が、LB+Kan(50μg/mL)において37℃で飽和まで増殖され、次いで、LB+Kan+IPTGにおいて1:20に希釈され、37℃で4時間増殖された。DNAは、Plasmid Maxiキット(QIAGEN)を使用して細菌培養物から調製された。
葉緑体ゲノムDNAの領域を除去するベクターを産生するために、葉緑体ゲノムDNAの800〜1000bp領域が、図4において示される部位に隣接する5’領域および3’領域にアニールするPCRプライマー対(1−5’部位、配列番号1079および1080;1−3’部位、配列番号1125および1126;3−5’部位、配列番号1083および1084;3−3’部位、配列番号1129および1130;4−5’部位、配列番号1087および1088;4−3’部位、配列番号1133および1134;5−5’部位、配列番号789および790;5−3’部位、配列番号787および788;ならびに7−5’部位、配列番号1091および1092;7−3’部位、配列番号1089および1090)を使用して増幅される。異なる部位に対する5’領域および3’領域からのPCR産物の対は、NotIおよびI−SceIで消化され、NotIで消化されたpUC−SE(配列番号2)に連結される。(実施例4に記載される)酵母選択マーカーの対は、SalIを使用して5’フラグメントおよび3’フラグメント間でクローニングされる。
Claims (24)
- 環状葉緑体ゲノムを組み立てる方法であって、
全体で光合成の実施に必要とされる全ての葉緑体遺伝子を含む、複数のベクターを取得する工程;
ここで前記複数のベクター中の各ベクターが、前記複数のベクターの1つ又は2つの他のベクターと相同組換えを行うための相同な領域を共有し、
ここで前記複数のベクターの1つ以上のベクターが、1つの酵母DNA複製要素を含み、ここで前記複数のベクターの1つ以上のベクターが、1つの細菌DNA複製要素を含み、且つ
ここで前記複数のベクターの1つ以上のベクターが、1つ以上の酵母選択マーカーを含む1つの酵母安定要素を含む;
前記複数のベクターを酵母に導入して、相同組換えで前記複数のベクターを組み立てることにより、組み立てられた環状葉緑体ゲノムを作製する工程;並びに
前記1つ以上の安定要素の存在を選別することにより、前記環状葉緑体ゲノムの完全な組み立てを選別する工程;
を含む、前記方法。 - 前記複数のベクターが、2つのベクターを含み、当該各ベクターが、他方のベクターと組換えを行うための相同な領域を共有する、請求項1に記載の方法。
- 前記酵母DNA複製要素が、酵母動原体、酵母自己複製配列、又はそれらの両方である、請求項1又は2に記載の方法。
- 前記細菌DNA複製要素が、P1複製配列又はF因子複製配列である、請求項1又は2に記載の方法。
- 前記組み立てられた環状葉緑体ゲノムが、単一の酵母動原体を含む、請求項1〜4のいずれか1項に記載の方法。
- 前記酵母DNA複製要素及び前記細菌DNA複製要素が、同一のベクター中に含まれる、請求項1〜5のいずれか1項に記載の方法。
- 前記組み立てられた環状葉緑体ゲノムが、140kb以上のDNAを含む、請求項1〜6のいずれか1項に記載の方法。
- 前記ベクターの1つ以上が、合成されたDNAを含む、請求項1〜7のいずれか1項に記載の方法。
- 前記ベクターの1つ以上が、光合成生物由来のゲノム葉緑体DNAを含む、請求項1〜7のいずれか1項に記載の方法。
- 前記光合成生物が藻類である、請求項9に記載の方法。
- 前記藻類が微細藻である、請求項10に記載の方法。
- 前記微細藻が、クラミドモナス種(Chlamydomonas sp.)、クロレラ種(Chorella sp.)、ドゥナリエラ種(Dunaliella sp.)、ヘマトコッカス種(Haematococcus sp.)、セネデスムス種(Scenedesmus sp.)のいずれかである、請求項11に記載の方法。
- 前記光合成生物由来のゲノム葉緑体DNAが修飾される、請求項9に記載の方法。
- 前記修飾が、非相同または相同ポリヌクレオチドの挿入によって、1個以上の核酸塩基の欠失によって、1個以上の核酸塩基の突然変異によって、1個以上のポリヌクレオチドの再配列によって、またはそれらの組み合わせによってなされる、請求項13に記載の方法。
- 前記酵母安定要素が、1対の酵母選択マーカーを含む、請求項1〜14のいずれか1項に記載の方法。
- 前記1対の選択マーカーが、URA3遺伝子及び追加の酵母選択マーカーである、請求項15に記載の方法。
- 前記追加のマーカーがADE2遺伝子、LEU2遺伝子、HIS3遺伝子、LYS2遺伝子又はG418遺伝子である、請求項16に記載の方法。
- 酵母安定要素を含む各ベクターにおいて、当該酵母安定要素が、異なる対の酵母選択マーカーを含む、請求項17に記載の方法。
- 前記組み立てられた環状葉緑体ゲノムを宿主生物に導入する工程を更に含む、請求項1〜18のいずれか1項に記載の方法。
- 前記宿主生物が、真核生物、酵母又は藻類である、請求項19に記載の方法。
- 前記環状葉緑体ゲノムの完全な組み立てを選別する工程の後に、前記1つ以上の酵母安定要素を除去する工程を更に含む、請求項1〜20のいずれか1項に記載の方法。
- 全ての手順が終了した後に、前記酵母及び細菌複製要素を除去する工程を含む、請求項1〜21のいずれか1項に記載の方法。
- 組み立てられた環状葉緑体ゲノムであって、
全体で光合成に必要とされる全ての葉緑体遺伝子を含む、複数のベクター;
を含み、請求項1〜22のいずれか1項に記載の方法により組み立てられる、前記ゲノム。 - 組み立てられた環状葉緑体ゲノムであって、
全体で光合成の実施に必要とされる全ての葉緑体遺伝子を含む、複数のベクター;
前記複数のベクター中の各ベクターが、前記複数のベクターの1つ又は2つの他のベクターと相同組換えを行うための相同な領域を共有し、
前記複数のベクターの1つ以上のベクターが、1つの酵母DNA複製要素を含み、ここで前記複数のベクターの1つ以上のベクターが、1つの細菌DNA複製要素を含み、かつ
前記複数のベクターの1つ以上のベクターが、1つ以上の酵母選択マーカーを含む1つの酵母安定要素を含む;
を含む、当該環状葉緑体ゲノム。
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CN109536525B (zh) * | 2019-02-20 | 2019-08-23 | 中国科学院烟台海岸带研究所 | 一种杜氏盐藻叶绿体同源重组空载体及其应用 |
CN110669789B (zh) * | 2019-12-04 | 2020-04-14 | 中国科学院烟台海岸带研究所 | 一种雨生红球藻叶绿体表达系统及其应用 |
CN111440733A (zh) * | 2020-02-07 | 2020-07-24 | 天津大学 | 产松油醇的重组酿酒酵母及构建方法及应用 |
CN115948450B (zh) * | 2022-08-01 | 2024-02-13 | 深圳大学 | 一种莱茵衣藻叶绿体-酿酒酵母-大肠杆菌穿梭载体及其构建方法与应用 |
CN115807021A (zh) * | 2022-08-01 | 2023-03-17 | 深圳大学 | 一种莱茵衣藻人工叶绿体基因组合成组装与功能测试的方法 |
CN116218750A (zh) * | 2022-10-14 | 2023-06-06 | 天津科技大学 | 一种解淀粉芽孢杆菌底盘菌及其构建方法与应用 |
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US7129391B1 (en) * | 1988-09-26 | 2006-10-31 | Auburn University | Universal chloroplast integration and expression vectors, transformed plants and products thereof |
US5866404A (en) * | 1995-12-06 | 1999-02-02 | Yale University | Yeast-bacteria shuttle vector |
US5976846A (en) * | 1996-01-13 | 1999-11-02 | Passmore; Steven E. | Method for multifragment in vivo cloning and mutation mapping |
EP2319933B1 (en) * | 1997-08-07 | 2014-10-15 | Auburn University | Universal chloroplast integration and expression vectors, transformed plants and products thereof |
US6670154B1 (en) * | 1998-07-27 | 2003-12-30 | Ronald A. Hitzeman | Automatic eukaryotic artificial chromosome vector |
US7083971B1 (en) * | 1999-06-07 | 2006-08-01 | Cell Genesys, Inc. | Hybrid yeast-bacteria cloning system and uses thereof |
BRPI0508271A (pt) * | 2004-03-03 | 2007-08-07 | Nat Univ Corp Nara Inst | método para aumentar a produtividade de plantas por tecnologia de cloroplasto |
CN1981039A (zh) * | 2004-05-10 | 2007-06-13 | 巴斯福植物科学有限公司 | 组装多表达构建体的方法 |
CA2692893C (en) * | 2007-06-01 | 2015-06-23 | The Scripps Research Institute | High throughput screening of genetically modified photosynthetic organisms |
US20090209015A1 (en) * | 2008-02-15 | 2009-08-20 | Ramesha Chakkodabylu S | Compositions and methods for production of biofuels |
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NZ583682A (en) | 2012-07-27 |
GB2453648A (en) | 2009-04-15 |
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GB2460351A (en) | 2009-12-02 |
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AU2008307471B2 (en) | 2013-05-02 |
DK2195426T3 (da) | 2013-09-08 |
KR101389254B1 (ko) | 2014-04-24 |
GB2453648A8 (en) | 2010-11-17 |
CN101939423A (zh) | 2011-01-05 |
KR20100085930A (ko) | 2010-07-29 |
GB2453648C2 (en) | 2012-12-19 |
JP2010539979A (ja) | 2010-12-24 |
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