私たちは、私たち菌株、プラスミド、および必要なプロトコルを送信するための博士マイケルキャシェル（国立衛生研究所、ベセスダ、MA、米国）を感謝。我々はSpecraMaxプレートリーダーを使用するためにドクタージョングローバー（生化学部、トロント大学を）感謝。英国では、国立科学およびカナダの工学研究審議会（NSERC）大学院奨学金、疾病へのリンク膜タンパク質の構造生物学、およびトロントオープンフェローシップの大学における保健研究戦略的トレーニングプログラムのカナダの協会の受信者です。この作品は、カナダ衛生研究所（MOP - 67210）からWAHへの助成金によって支えられている。

1）試薬および器具<ol><li>最初に、以下の3つのソリューションを準備する：溶液1 mLの8ミリL -リジン、100 mMリン酸ナトリウム2で構成されている - （N -モルホリノ）エタンスルホン酸（MES）pH6.5で、ヌクレオチドが塩基0.2mMの、どちらか：グアノシン二リン酸（GDP）、グアノシン三リン酸（GTP）、グアノシン5&#39; -二リン酸、3&#39; -二リン酸（ppGppの）、または5&#39; -三リン酸、3&#39; -二リン酸（pppGpp）グアノシン、0.1mMのピリドキサール5&#39; -リン酸（PLP）、および1mMβ-メルカプトエタノール/（β- ME）。 100mMの塩化ナトリウムMES pH6.5で、0.1mMのPLP、1mMのβ- ME、および50 nMのLdcIから成るソリューションBを1mL。スナイダーら 6 Kanjee らに説明したようにLdcIを精製した。14。 ソリューションBと同一だLdcIを含まない溶液Cの1mL。 </li><li>マルチチャンネルピペットを用いて96穴ポリスチレンプレートの各ウェルに、1Mの炭酸ナトリウム（10.6 g/100 mL）に、アリコート50μLから成る反応停止液100 mLを準備する。プレートに水30μLを追加してから、カバーしています。水の体積の和が追加され、酵素反応の間に抽出されたサンプルの量が50μLに等しくなければならないことに注意してください。この場合、酵素反応の試料の20μLを削除されます。 </li><li>アルミホイルで4706μL水、ラップで5％の294μL（w / v）のTNBSの株式を希釈して10 mMのでTNBS溶液5mlを調製し、氷上に置きます。 </li><li>エッペンドルフのサーモスタットを平衡化するプラス37℃サーモスタットプラス6列の24個のウェルを持っている。回路図、図2を参照してください。 （列ごと）にテストされるヌクレオチドの同一性を示すラベル1.5mLのエッペンドルフチュー​​ブ：GTP（列）、GDP（列B）、ppGppの（列C）、pppGpp（列D）、無ヌクレオチド（カ​​ラムE ）、およびタンパク質サンプル（列F）。 </li><li>各代替行がヒントの4行の合計を与えて省略されているように、200μLのヒントのラックいくつかの箱。これは、酵素アッセイの間にサーモスタットプラスheatblockとマルチチャンネルのピペットを使用するために必要です。 </li><li> 42でデジタルHeatblock（VWR）を平衡℃に</li><li>冷却するために氷上で96ウェル2.0mLのポリプロピレン板を置きます。 </li></ol> 2）LdcIアッセイ<ol><li>エッペンドルフのサーモスタットの5つの列のそれぞれに1.5mlのエッペンドルフチュー​​ブに適切なヌクレオチドと溶液のアリコート50μL。 </li><li> F列の3本のチューブに溶液B 330μLを追加し、列Fの最後のチューブに溶液C（無タンパク質の制御）330μLを加える</li><li> 37ソリューションを平衡℃で5分間。ヒント：5分後、次に使用するマルチチャンネルピペットが干渉するのを防ぐために、加熱ブロックの中心にチューブのキャップを切断。 </li><li>列AEの各チューブに50から50μLVWRマルチチャンネルピペット、F列の管からの転送50μLを使用する。とすぐに最初のチューブが混ざっているようにタイマーを開始します。 </li><li> 2、4、6分でマルチチャンネルピペットを用いて試料の20μLを削除し、ワンストップソリューションに追加します。 </li><li>注：停止溶液中の試料をプラスチック覆いで覆われ、その後の処理のために-20℃で凍結することができます。プレートは、TNBSと反応させる前に室温で解凍してください。 </li></ol> 3）TNBSの反応と色の開発<ol><li> 6分間後、マルチチャンネルピペットと42℃でインキュベートCを使用して停止液に10mMのTNBS溶液50μLを追加。 TNBSは、リジンとカダベリンと反応するようなソリューションでは、暗い黄色/オレンジ色に変わります。 </li><li> 6分後、反応を遅らせるために氷の上でプレートを冷却する。 </li><li>氷上で冷却し、2 mLのディープウェルプレートでVWR 20〜200μLマルチチャンネルピペットと場所を使用してサンプル100μLを削除します。 fumehoodにアイスバケットを転送する。 </li><li>よくHandyStep（ブランド）リピートピペッターと12.5 mLのピペットチップ（Plastibrand）を使用して、それぞれにトルエン500μLを追加。 </li><li>キムワイプを使用して余分なトルエンを拭うと包装テープのストリップとプレートをカバーしています。良好なシールを得るためにしっかりと下に押してください。平らな蓋付き96ウェルプレートをカバーし、1分30秒間激しく振る。 </li><li> 5分のために解決するソリューションを残す。 TNP -リジンは、水溶性のまま、TNP -カダベリンは、（図1参照）、上部のトルエン相に入りました。 </li><li>読書のための96ウェルプレートに20〜200μLマルチチャンネルのピペットを用いてトルエン200μLを削除します。注意：削除する各サンプルが明確であり、下部水相のいずれかを持っていないことを確認してください。注：トルエンによるマルチチャンネルピペットへの損傷を防止するために使用するバリアヒント。 </li><li> SpectraMax 340プレートリーダーで340nmの吸光度を読み取る。 </li><li>石英板をクリーニングするには、水とトルエンを洗い落として、大規模で石英板を配置ドラフト内でガラス皿。 70％（v / v）の硝酸の午前7時03分混合物を100mLの上に注ぐ：95％（v / v）エタノールをし、第2のガラストレイを持つ石英プレートをカバーしています。警告：反応は非常に発熱し、時には爆発的に摩耗適切な保護であるとヒュームフードのサッシが低い6&quot;レベルに設定されていることを確認冷却後、水で硝酸を洗い流し、その後95％エタノール。。 </li></ol> 4）代表者の結果 1）カダベリン標準曲線（図3） アッセイは、任意のL -リジンまたはLdcIなく説明するが、実行されたとカダベリンの代わりに種々の濃度は、経験的にアッセイの直線範囲を決定するために使用されていました。アッセイは、カダベリンの〜22ナノモル（図3）に対応する、0.25のOD 340まで線形であった。 LdcI 2）活性（図4） 単独でLdcIの活性は153.5（± 18.1）ナノモルカダベリン分-1μgのpH6.5のLdcI - 1と決定した。 LdcIの活動は、100μMのGTPまたはGDPの存在下で影響を受けることはありませんが強くpppGppとppGppの（図4）の存在下で（&gt; 10倍）抑制される。 <img src="/files/ftp_upload/2094/2094fig1.jpg" alt="図1" /> 図1。 LdcIの反応の模式図。CO 2及びカダベリンを生成するために、L -リジンの脱炭酸反応は、N、N&#39; - bistrinitrophenylcadaverine（TNP -カダベリン）とN、Nを生成するだけでなく、高pHでTNBSで次の反応を示されています&#39;- bistrinitrophenyllysine（TNP -リジン）。ファンティエットら11に基づいて<img src="/files/ftp_upload/2094/2094fig2.jpg" alt="図2" /> 図2。エッペンドルフのサーモスタットのセットアップ。24 -ウェルエッペンドルフサーモスタットのサンプルのレイアウトは、アッセイの手順の説明（太字で示されている）とともに示されています。矢印は、プロトコルに従って反応液の転送を示している。 96ウェルプレートでのワンストップソリューションへの反応液の除去にも示されています。 <img src="/files/ftp_upload/2094/2094fig3.jpg" alt="図3" /> 図3。カダベリン標準曲線。カダベリンのナノモルに対する340nmの吸光度のプロットが示されています。エラーバーは、少なくとも3つの独立した測定値の標準偏差を表しています。ベストフィットのラインも表示し、0.996のR2を持っています。 <img src="/files/ftp_upload/2094/2094fig4.jpg" alt="図4" /> 図4。 LdcIアッセイの結果。LdcIの活動の割合（ナノモルカダベリンのmin - 1μgの1 LdcIを生産）のプロットは、100μMのGTP、GDP、pppGpp、ppGppのと塩基の存在下での存在下で示されています。緊縮応答のヌクレオチド（P）ppGppのは著しく阻害LdcIの活動が可能です。エラーバーは、少なくとも6つの独立した測定値の標準偏差を表しています。

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	<li>Gale, E. F., Epps, H. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+effect+of+the+pH+of+the+medium+during+growth+on+the+enzymic+activities+of+bacteria+(Escherichia+coli+and+Micrococcus+lysodeikticus)+and+the+biological+significance+of+the+changes+produced.">The effect of the pH of the medium during growth on the enzymic activities of bacteria (Escherichia coli and Micrococcus lysodeikticus) and the biological significance of the changes produced.</a> Biochem J. 36, 600-618 (1942).</li><li>Foster, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Escherichia+coli+acid+resistance:+tales+of+an+amateur+acidophile.">Escherichia coli acid resistance: tales of an amateur acidophile.</a> Nat Rev Microbiol. 2, 898-907 (2004).</li><li>Castanie-Cornet, M. P., Penfound, T. A., Smith, D., Elliott, J. F., Foster, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Control+of+acid+resistance+in+Escherichia+coli.">Control of acid resistance in Escherichia coli.</a> J Bacteriol. 181, 3525-3535 (1999).</li><li>Iyer, R., Williams, C., Miller, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Arginine-agmatine+antiporter+in+extreme+acid+resistance+in+Escherichia+coli.">Arginine-agmatine antiporter in extreme acid resistance in Escherichia coli.</a> J Bacteriol. 185, 6556-6561 (2003).</li><li>Sabo, D. L., Boeker, E. A., Byers, B., Waron, H., Fischer, E. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Purification+and+physical+properties+of+inducible+Escherichia+coli+lysine+decarboxylase.">Purification and physical properties of inducible Escherichia coli lysine decarboxylase.</a> Biochemistry. 13, 662-670 (1974).</li><li>Snider, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Formation+of+a+distinctive+complex+between+the+inducible+bacterial+lysine+decarboxylase+and+a+novel+AAA++ATPase.">Formation of a distinctive complex between the inducible bacterial lysine decarboxylase and a novel AAA+ ATPase.</a> J Biol Chem. 281, 1532-1546 (2006).</li><li>Kashiwagi, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Coexistence+of+the+genes+for+putrescine+transport+protein+and+ornithine+decarboxylase+at+16+min+on+Escherichia+coli+chromosome.">Coexistence of the genes for putrescine transport protein and ornithine decarboxylase at 16 min on Escherichia coli chromosome.</a> J Biol Chem. 266, 20922-20927 (1991).</li><li>Schneider, G., Kack, H., Lindqvist, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+manifold+of+vitamin+B6+dependent+enzymes.">The manifold of vitamin B6 dependent enzymes.</a> Structure. 8, 1-6 (2000).</li><li>Cashel, M., Gentry, D. 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A., A, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Linkage+between+the+Bacterial+Acid+Stress+and+Stringent+Responses+Revealed+by+the+Structure+of+the+Inducible+Lysine+Decarboxylase.">Linkage between the Bacterial Acid Stress and Stringent Responses Revealed by the Structure of the Inducible Lysine Decarboxylase.</a> EMBO Journal. 30, 931-944 (2011).</li></ol>

利害の衝突は宣言されません。

リジン脱炭酸酵素のアッセイでは、TNBSは、TNP -リジンとTNP -カダベリン付加体（図1）を形成するために、L -リジンとカダベリンの第一級アミンと反応させる。 TNP -カダベリンは、カルボン酸基を欠く、トルエン11に分割することができる間、TNP -リジン上にカルボン酸基の存在のために、この付加物は水に可溶のまま。このタイプのアッセイは、カルボン酸基の消失が反応中に発生す?...

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		<div>
		<table border="1">
		<thead>
		<tr>
		<th>Material Name</th>
		<th>Type</th>
		<th>Company</th>
		<th>Catalogue Number</th>
		<th>Comment</th>
		</tr>
		</thead>
		<tbody>
		
<tr>
<td>2,4,6-trinitrobenzensulfonic acid </td>
<td>&nbsp;</td>
<td>Sigma Aldrich</td>
<td>P2297</td>
<td>&nbsp;</td>
<tr>
<td>0.1 mM pyridoxal 5'-phosphate (PLP)</td>
<td>&nbsp;</td>
<td>Sigma Aldrich</td>
<td>P9255</td>
<td>&nbsp;</td>
<tr>
<td>Cadaverine</td>
<td>&nbsp;</td>
<td>Sigma Aldrich</td>
<td>D22606</td>
<td>&nbsp;</td>
<tr>
<td>96 well polystyrene plates</td>
<td>&nbsp;</td>
<td>Sarstedt</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>96-well quartz plate</td>
<td>&nbsp;</td>
<td>Hellma</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>VWR Digital Heatblock</td>
<td>&nbsp;</td>
<td>VWR</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>ThermoStat Plus</td>
<td>&nbsp;</td>
<td>Eppendorf</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>2.0 mL 96-well polypropylene plates</td>
<td>&nbsp;</td>
<td>Axygen</td>
<td>P-DW-20-C</td>
<td>&nbsp;</td>
<tr>
<td>Handy Step Repeat Pipettor</td>
<td>&nbsp;</td>
<td>Brand</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>12.5 mL Repeat Pipettor Tips</td>
<td>&nbsp;</td>
<td>Brand (Plastibrand)</td>
<td>702378</td>
<td>&nbsp;</td>
<tr>
<td>SpectraMax 340PC Plate Reader</td>
<td>&nbsp;</td>
<td>SpectraMax</td>
<td>&nbsp;</td>
<td>&nbsp;</td>		</tbody>
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an assay for measuring the activity of escherichia coli inducible lysine decarboxyase

1と、信じられないほど、低いとpHが落ちることができる哺乳類の胃の通過を含む極端な酸応力に耐えることができるか- 大腸菌では、pH値（9 pHは5）の広い範囲で成長することができる腸内細菌です。 2 2 - pHを1として。酸性pHの生存、E.のような広い範囲を有効にするには大腸菌は、プロトン依存的に脱炭酸、その基質のアミノ酸はこのように内部のpHを上げることつの異なる誘導アミノ酸decarboxylasesを持っています。 decarboxylasesはグルタミン酸decarboxylasesガダとGadB 3、アルギニンデカルボキシラーゼ不透過4、リジン脱炭酸酵素LdcI 5、6、オルニチンデカルボキシラーゼSPEF 7を含める。これらの酵素のすべてが新鮮な基板2と引き換えに、外部媒体への脱炭酸の製品を削除する内側の膜基板-製品のアンチポーターと一緒にコファクター8および関数としてピリドキサール5&#39; - phospateを利用する。 LdcIの場合には、リジン-カダベリンアンチポーターはCADBと呼ばれています。最近、我々は、2.0 ÅにLdcIのX線結晶構造を決定し、そして我々はLdcI厳しいレスポンスレギュレーターのグアノシン5&#39; -二リン酸、3&#39; -二リン酸（ppGppの）14に結合した新規の低分子化合物を発見した。指数関数的に成長する細胞が栄養枯渇や他のストレス9の数字のいずれかが発生するときに緊縮応答が発生します。その結果、細胞が定常期の成長率は10〜急激な成長からのシフトで最高潮に達するシグナル伝達カスケードにつながるppGppのを作り出す。我々は、ppGppのはLdcI 14の特異的阻害剤であることが実証されている。ここでは、ファンティエットらによって開発されたアッセイから変更。11、我々はLdcIの活動とその活動上pppGpp / ppGppのの効果を決定するために使用されていることを、リジン脱炭酸酵素のアッセイを説明します。 LdcIの脱炭酸反応は、L -リジンのα-カルボキシ基を除去し、二酸化炭素とポリアミンカダベリン（1,5 -ジアミノペンタン）5を生成します。 L -リジンとカダベリンは、それぞれ、N、N&#39; - bistrinitrophenylcadaverine（TNP -カダベリン）とN、N&#39; - bistrinitrophenyllysine（TNP -リジン）を生成するために、高pHで2,4,6 - trinitrobenzensulfonic酸（TNBS）と反応させることができます。 11。後者は（図1参照）ではない。前者はトルエンなどの有機溶媒に可溶であるとしてTNP -カダベリンは、TNP -リジンから分離することができる。アッセイの直線範囲は、経験的に精製カダベリンを用いて決定した。

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An Assay for Measuring the Activity of Escherichia coli Inducible Lysine Decarboxyase

誘導性リジン脱炭酸酵素の活性は、基質のL -リジンとトルエンで、差動溶解度を持っている付加体を形成するために、2,4,6 - trinitrobenzensulfonic酸による製品のカダベリンを反応させることによって監視されます。

の活性を測定するアッセイ大腸菌誘導性リジンDecarboxyase

Escherichia coli is an enteric bacterium that is capable of growing over a wide range of pH values (pH 5 - 9)1 and, incredibly, is able to survive extreme ...

an-assay-for-measuring-activity-escherichia-coli-inducible-lysine

Research

JoVE Journal

Biology

An Assay for Measuring the Activity of Escherichia coli Inducible Lysine Decarboxyase

14.1K ビュー.  University of Toronto. 誘導性リジン脱炭酸酵素の活性は、基質のL -リジンとトルエンで、差動溶解度を持っている付加体を形成するために、2,4,6 - trinitrobenzensulfonic酸による製品のカダベリンを反応させることによって監視されます。

ビデオ: An Assay for Measuring the Activity of Escherichia coli Inducible Lysine Decarboxyase

Measuring the Bending Stiffness of Bacterial Cells Using an Optical Trap

We developed a protocol to measure the bending rigidity of filamentous rod-shaped bacteria. Forces are applied with an optical trap, a microscopic three-dimensional spring made of light that is formed when a high-intensity laser beam is focused to a very small spot by a microscope's objective lens. To bend a cell, we first bind live bacteria to a chemically-treated coverslip. As these cells grow, the middle of the cells remains bound to the coverslip but the growing ends are free of this restraint. By inducing filamentous growth with the drug cephalexin, we are able to identify cells in which one end of the cell was stuck to the surface while the other end remained unattached and susceptible to bending forces. A bending force is then applied with an optical trap by binding a polylysine-coated bead to the tip of a growing cell. Both the force and the displacement of the bead are recorded and the bending stiffness of the cell is the slope of this relationship.

We present a protocol for bending filamentous bacterial cells attached to a cover-slip surface with an optical trap to measure the cellular bending stiffness.

光トラップを用いた細菌細胞の曲げ剛性の測定

We developed a protocol to measure the bending rigidity of filamentous rod-shaped bacteria. Forces are applied with an optical trap, a microscopic ...

生物学

High Throughput Screening of Fungal Endoglucanase Activity in Escherichia coli

Cellulase enzymes (endoglucanases, cellobiohydrolases, and &beta;-glucosidases) hydrolyze cellulose into component sugars, which in turn can be converted into fuel alcohols1. The potential for enzymatic hydrolysis of cellulosic biomass to provide renewable energy has intensified efforts to engineer cellulases for economical fuel production2. Of particular interest are fungal cellulases3-8, which are already being used industrially for foods and textiles processing.
Identifying active variants among a library of mutant cellulases is critical to the engineering process; active mutants can be further tested for improved properties and/or subjected to additional mutagenesis. Efficient engineering of fungal cellulases has been hampered by a lack of genetic tools for native organisms and by difficulties in expressing the enzymes in heterologous hosts. Recently, Morikawa and coworkers developed a method for expressing in E. coli the catalytic domains of endoglucanases from H. jecorina3,9, an important industrial fungus with the capacity to secrete cellulases in large quantities. Functional E. coli expression has also been reported for cellulases from other fungi, including Macrophomina phaseolina10 and Phanerochaete chrysosporium11-12. 
We present a method for high throughput screening of fungal endoglucanase activity in E. coli. (Fig 1) This method uses the common microbial dye Congo Red (CR) to visualize enzymatic degradation of carboxymethyl cellulose (CMC) by cells growing on solid medium. The activity assay requires inexpensive reagents, minimal manipulation, and gives unambiguous results as zones of degradation (&#x201C;halos&#x201D;) at the colony site. Although a quantitative measure of enzymatic activity cannot be determined by this method, we have found that halo size correlates with total enzymatic activity in the cell. Further characterization of individual positive clones will determine , relative protein fitness. 
Traditional bacterial whole cell CMC/CR activity assays13 involve pouring agar containing CMC onto colonies, which is subject to cross-contamination, or incubating cultures in CMC agar wells, which is less amenable to large-scale experimentation. Here we report an improved protocol that modifies existing wash methods14 for cellulase activity: cells grown on CMC agar plates are removed prior to CR staining. Our protocol significantly reduces cross-contamination and is highly scalable, allowing the rapid screening of thousands of clones. In addition to H. jecorina enzymes, we have expressed and screened endoglucanase variants from the Thermoascus aurantiacus and Penicillium decumbens (shown in Figure 2), suggesting that this protocol is applicable to enzymes from a range of organisms.

High Throughput Screening of Fungal Endoglucanase Activity in Escherichia coli

We describe a low cost, high throughput method to screen for fungal endoglucanase activity in E. coli. The method relies on a simple visual readout of substrate degradation, does not require enzyme purification, and is highly scalable. This allows for the rapid screening of large libraries of enzyme variants.

における真菌エンドグルカナーゼ活性のハイスループットスクリーニング大腸菌</em

Cellulase enzymes (endoglucanases, cellobiohydrolases, and &beta;-glucosidases) hydrolyze cellulose into component sugars, which in turn can be converted ...

Application of MassSQUIRM for Quantitative Measurements of Lysine Demethylase Activity

Recently, epigenetic regulators have been discovered as key players in many different diseases 1-3. As a result, these enzymes are prime targets for small molecule studies and drug development 4. Many epigenetic regulators have only recently been discovered and are still in the process of being classified. Among these enzymes are lysine demethylases which remove methyl groups from lysines on histones and other proteins. Due to the novel nature of this class of enzymes, few assays have been developed to study their activity. This has been a road block to both the classification and high throughput study of histone demethylases. Currently, very few demethylase assays exist. Those that do exist tend to be qualitative in nature and cannot simultaneously discern between the different lysine methylation states (un-, mono-, di- and tri-). Mass spectrometry is commonly used to determine demethylase activity but current mass spectrometric assays do not address whether differentially methylated peptides ionize differently. Differential ionization of methylated peptides makes comparing methylation states difficult and certainly not quantitative (Figure 1A). Thus available assays are not optimized for the comprehensive analysis of demethylase activity.
Here we describe a method called MassSQUIRM (mass spectrometric quantitation using isotopic reductive methylation) that is based on reductive methylation of amine groups with deuterated formaldehyde to force all lysines to be di-methylated, thus making them essentially the same chemical species and therefore ionize the same (Figure 1B). The only chemical difference following the reductive methylation is hydrogen and deuterium, which does not affect MALDI ionization efficiencies. The MassSQUIRM assay is specific for demethylase reaction products with un-, mono- or di-methylated lysines. The assay is also applicable to lysine methyltransferases giving the same reaction products. Here, we use a combination of reductive methylation chemistry and MALDI mass spectrometry to measure the activity of LSD1, a lysine demethylase capable of removing di- and mono-methyl groups, on a synthetic peptide substrate 5. This assay is simple and easily amenable to any lab with access to a MALDI mass spectrometer in lab or through a proteomics facility. The assay has ~8-fold dynamic range and is readily scalable to plate format 5.

We present a method for using MALDI mass spectrometry and reductive methylation chemistry to quantify changes in lysine methylation.

リジン脱メチル化酵素活性の定量測定のためのMassSQUIRMのアプリケーション

Recently, epigenetic regulators have been discovered as key players in many different diseases 1-3. As a result, these enzymes are prime targets for small ...

Rapid Protocol for Preparation of Electrocompetent Escherichia coli and Vibrio cholerae

Electroporation has become a widely used method for rapidly and efficiently introducing foreign DNA into a wide range of cells. Electrotransformation has become the method of choice for introducing DNA into prokaryotes that are not naturally competent. Electroporation is a rapid, efficient, and streamlined transformation method that, in addition to purified DNA and competent bacteria, requires commercially available gene pulse controller and cuvettes. In contrast to the pulsing step, preparation of electrocompetent cells is time consuming and labor intensive involving repeated rounds of centrifugation and washes in decreasing volumes of sterile, cold water, or non-ionic buffers of large volumes of cultures grown to mid-logarithmic phase of growth. Time and effort can be saved by purchasing electrocompetent cells from commercial sources, but the selection is limited to commonly employed E. coli laboratory strains. We are hereby disseminating a rapid and efficient method for preparing electrocompetent E. coli, which has been in use by bacteriology laboratories for some time, can be adapted to V. cholerae and other prokaryotes. While we cannot ascertain whom to credit for developing the original technique, we are hereby making it available to the scientific community.

Rapid Protocol for Preparation of Electrocompetent Escherichia coli and Vibrio cholerae

Electroporation is a commonly employed method for introducing DNA into bacteria in a process known as transformation. Traditional protocols for the preparation of electrocompetent cells are time consuming and labor intensive. This article describes an alternate, rapid, and efficient method for the preparation of electrocompetent cells presently employed by some laboratories.

エレクトロ作成のための迅速なプロトコル<em&gt;エシェリヒア·コリ</em&gt;と<em&gt;コレラ菌</em

Electroporation has become a widely used method for rapidly and efficiently introducing foreign DNA into a wide range of cells. Electrotransformation has ...

Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology

Ideal cell-free expression systems can theoretically emulate an in vivo cellular environment in a controlled in vitro platform.1 This is useful for expressing proteins and genetic circuits in a controlled manner as well as for providing a prototyping environment for synthetic biology.2,3 To achieve the latter goal, cell-free expression systems that preserve endogenous Escherichia coli transcription-translation mechanisms are able to more accurately reflect in vivo cellular dynamics than those based on T7 RNA polymerase transcription. We describe the preparation and execution of an efficient endogenous E. coli based transcription-translation (TX-TL) cell-free expression system that can produce equivalent amounts of protein as T7-based systems at a 98% cost reduction to similar commercial systems.4,5 The preparation of buffers and crude cell extract are described, as well as the execution of a three tube TX-TL reaction. The entire protocol takes five days to prepare and yields enough material for up to 3000 single reactions in one preparation. Once prepared, each reaction takes under 8 hr from setup to data collection and analysis. Mechanisms of regulation and transcription exogenous to E. coli, such as lac/tet repressors and T7 RNA polymerase, can be supplemented.6 Endogenous properties, such as mRNA and DNA degradation rates, can also be adjusted.7 The TX-TL cell-free expression system has been demonstrated for large-scale circuit assembly, exploring biological phenomena, and expression of proteins under both T7- and endogenous promoters.6,8 Accompanying mathematical models are available.9,10 The resulting system has unique applications in synthetic biology as a prototyping environment, or "TX-TL biomolecular breadboard."

Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology

This five-day protocol outlines all steps, equipment, and supplemental software necessary for creating and running an efficient endogenous Escherichia coli based TX-TL cell-free expression system from scratch. With reagents, the protocol takes 8 hours or less to setup a reaction, collect, and process data.

実装するためのプロトコル<em&gt;エシェリヒア·コリ</em合成生物学のための&gt;に基づくTX-TLの無細胞発現系

Ideal cell-free expression systems can theoretically emulate an in vivo cellular environment in a controlled in vitro platform.1 This is useful for ...

Detection of Live Escherichia coli O157:H7 Cells by PMA-qPCR

A unique open reading frame (ORF) Z3276 was identified as a specific genetic marker for E. coli O157:H7. A qPCR assay was developed for detection of E. coli O157:H7 by targeting ORF Z3276. With this assay, we can detect as low as a few copies of the genome of DNA of E. coli O157:H7. The sensitivity and specificity of the assay were confirmed by intensive validation tests with a large number of E. coli O157:H7 strains (n = 369) and non-O157 strains (n = 112). Furthermore, we have combined propidium monoazide (PMA) procedure with the newly developed qPCR protocol for selective detection of live cells from dead cells. Amplification of DNA from PMA-treated dead cells was almost completely inhibited in contrast to virtually unaffected amplification of DNA from PMA-treated live cells. Additionally, the protocol has been modified and adapted to a 96-well plate format for an easy and consistent handling of a large number of samples. This method is expected to have an impact on accurate microbiological and epidemiological monitoring of food safety and environmental source.

Detection of Live Escherichia coli O157:H7 Cells by PMA-qPCR

A qPCR assay was developed for detection of Escherichia coli O157:H7 targeting a unique genetic marker, Z3276. The qPCR was combined with propidium monoazide (PMA) treatment for live cell detection. This protocol has been modified and adapted to a 96-well plate format for easy and consistent handling of numerous samples

ライブの検出<em&gt;エシェリヒア·コリ</em&gt; O157：PMA-qPCRによりH7細胞

A unique open reading frame (ORF) Z3276 was identified as a specific genetic marker for E. coli O157:H7. A qPCR assay was developed for detection of E. ...

Green Fluorescent Protein-based Expression Screening of Membrane Proteins in Escherichia coli

The production of recombinant membrane proteins for structural and functional studies remains technically challenging due to low levels of expression and the inherent instability of many membrane proteins once solubilized in detergents. A protocol is described that combines ligation independent cloning of membrane proteins as GFP fusions with expression in Escherichia coli detected by GFP fluorescence. This enables the construction and expression screening of multiple membrane protein/variants to identify candidates suitable for further investment of time and effort. The GFP reporter is used in a primary screen of expression by visualizing GFP fluorescence following SDS polyacrylamide gel electrophoresis (SDS-PAGE). Membrane proteins that show both a high expression level with minimum degradation as indicated by the absence of free GFP, are selected for a secondary screen. These constructs are scaled and a total membrane fraction prepared and solubilized in four different detergents. Following ultracentrifugation to remove detergent-insoluble material, lysates are analyzed by fluorescence detection size exclusion chromatography (FSEC). Monitoring the size exclusion profile by GFP fluorescence provides information about the mono-dispersity and integrity of the membrane proteins in different detergents. Protein: detergent combinations that elute with a symmetrical peak with little or no free GFP and minimum aggregation are candidates for subsequent purification. Using the above methodology, the heterologous expression in E. coli of SED (shape, elongation, division, and sporulation) proteins from 47 different species of bacteria was analyzed. These proteins typically have ten transmembrane domains and are essential for cell division. The results show that the production of the SEDs orthologues in E. coli was highly variable with respect to the expression levels and integrity of the GFP fusion proteins. The experiment identified a subset for further investigation.

Green Fluorescent Protein-based Expression Screening of Membrane Proteins in Escherichia coli

A streamlined approach to screening for the expression of recombinant membrane proteins in Escherichia coli based on fusion to green fluorescent protein is presented.

膜タンパク質の緑色蛍光タンパク質ベースの発現スクリーニングで<em&gt;エシェリヒア·コリ</em

The production of recombinant membrane proteins for structural and functional studies remains technically challenging due to low levels of expression and ...

The Multifaceted Benefits of Protein Co-expression in Escherichia coli

We report here that the expression of protein complexes in vivo in Escherichia coli can be more convenient than traditional reconstitution experiments in vitro. In particular, we show that the poor solubility of Escherichia coli DNA polymerase III &#949; subunit (featuring 3&#8217;-5&#8217; exonuclease activity) is highly improved when the same protein is co-expressed with the &#945; and &#952; subunits (featuring DNA polymerase activity and stabilizing &#949;, respectively). We also show that protein co-expression in E. coli can be used to efficiently test the competence of subunits from different bacterial species to associate in a functional protein complex. We indeed show that the &#945; subunit of Deinococcus radiodurans DNA polymerase III can be co-expressed in vivo with the &#949; subunit of E. coli. In addition, we report on the use of protein co-expression to modulate mutation frequency in E. coli. By expressing the wild-type &#949; subunit under the control of the araBAD promoter (arabinose-inducible), and co-expressing the mutagenic D12A variant of the same protein, under the control of the lac promoter (inducible by isopropyl-thio-&#946;-D-galactopyranoside, IPTG), we were able to alter the E. coli mutation frequency using appropriate concentrations of the inducers arabinose and IPTG. Finally, we discuss recent advances and future challenges of protein co-expression in E. coli.

The Multifaceted Benefits of Protein Co-expression in Escherichia coli

Protein co-expression is a powerful alternative to the reconstitution in vitro of protein complexes, and is of help in performing biochemical and genetic tests in vivo. Here we report on the use of protein co-expression in Escherichia coli to obtain protein complexes, and to tune the mutation frequency of cells.

タンパク質の共発現の多面的メリットで<em&gt;エシェリヒア·コリ</em

We report here that the expression of protein complexes in vivo in Escherichia coli can be more convenient than traditional reconstitution experiments in ...

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System

The canonical set of amino acids leads to an exceptionally wide range of protein functionality. Nevertheless, the set of residues still imposes limitations on potential protein applications. The incorporation of noncanonical amino acids can enlarge this scope. There are two complementary approaches for the incorporation of noncanonical amino acids. For site-specific incorporation, in addition to the endogenous canonical translational machineries, an orthogonal aminoacyl-tRNA-synthetase-tRNA pair must be provided that does not interact with the canonical ones. Consequently, a codon that is not assigned to a canonical amino acid, usually a stop codon, is also required. This genetic code expansion enables the incorporation of a noncanonical amino acid at a single, given site within the protein. The here presented work describes residue-specific incorporation where the genetic code is reassigned within the endogenous translational system. The translation machinery accepts the noncanonical amino acid as a surrogate to incorporate it at canonically prescribed locations, i.e., all occurrences of a canonical amino acid in the protein are replaced by the noncanonical one. The incorporation of noncanonical amino acids can change the protein structure, causing considerably modified physical and chemical properties. Noncanonical amino acid analogs often act as cell growth inhibitors for expression hosts since they modify endogenous proteins, limiting in vivo protein production. In vivo incorporation of toxic noncanonical amino acids into proteins remains particularly challenging. Here, a cell-free approach for a complete replacement of L-arginine by the noncanonical amino acid L-canavanine is presented. It circumvents the inherent difficulties of in vivo expression. Additionally, a protocol to prepare target proteins for mass spectral analysis is included. It is shown that L-lysine can be replaced by L-hydroxy-lysine, albeit with lower efficiency. In principle, any noncanonical amino acid analog can be incorporated using the presented method as long as the endogenous in vitro translation system recognizes it.

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System

An easy-to-use, cell-free expression protocol for the residue-specific incorporation of noncanonical amino acid analogs into proteins, including downstream analysis, is presented for medical, pharmaceutic, structural and functional studies.

使用モデルタンパク質への非標準アミノ酸の残基特異的取り込み<em&gt;エシェリヒア・コリ</em&gt;無細胞転写翻訳システム

The canonical set of amino acids leads to an exceptionally wide range of protein functionality. Nevertheless, the set of residues still imposes ...

Measuring Lactase Enzymatic Activity in the Teaching Lab

Understanding how enzymes work, and relating this to real life examples, is critical to a wide range of undergraduate degrees in the biological and biomedical sciences. This easy to follow protocol was developed for first year undergraduate pharmacy students and provides an entry-level introduction to enzyme reactions and analytical procedures for enzyme analysis. The enzyme of choice is lactase, as this represents an example of a commercially available enzyme relevant to human disease/pharmaceutical practice. Lactase is extracted from dietary supplement tablets, and assessed using a colorimetric assay based upon hydrolysis of an artificial substrate for lactase (ortho-nitrophenol-beta-D-galactopyranoside, ONPG). Release of ortho-nitrophenol following the hydrolytic cleavage of ONPG by lactase is measured by a change in absorbance at 420 nm, and the effect of the temperature on the enzymatic reaction is evaluated by carrying out the reaction on ice, at room temperature and at 37 &#176;C. More advanced analysis can be implemented using this protocol by assessing the enzyme activity under different conditions and using different reagents.

The enzymatic activity of lactase is essential for the catabolic processing of the disaccharide lactose. Here, the activity of lactase found in dietary supplements is assayed using a colorimetric assay. This provides students with an experimental platform for understanding the activity of lactase and enzyme kinetics.

教育実習でラクターゼ酵素活性の測定

Understanding how enzymes work, and relating this to real life examples, is critical to a wide range of undergraduate degrees in the biological and ...

の活性を測定するアッセイ大腸菌誘導性リジンDecarboxyase

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光トラップを用いた細菌細胞の曲げ剛性の測定

における真菌エンドグルカナーゼ活性のハイスループットスクリーニング大腸菌

リジン脱メチル化酵素活性の定量測定のためのMassSQUIRMのアプリケーション

エレクトロ作成のための迅速なプロトコル

実装するためのプロトコル

ライブの検出

膜タンパク質の緑色蛍光タンパク質ベースの発現スクリーニングで

タンパク質の共発現の多面的メリットで

使用モデルタンパク質への非標準アミノ酸の残基特異的取り込み

教育実習でラクターゼ酵素活性の測定