This work was supported by the European Commission project Indox-FP7-KBBE-2013-7-613549; a Cost-Action CM1303-Systems Biocatalysis; and the National Projects Dewry [BIO201343407-R] and Cambios [RTC-2014-1777-3].

1. Construção do mutante Biblioteca <ol><li> Escolher as regiões a ser submetido à transição com a ajuda de algoritmos computacionais com base na estrutura de cristal ou homologia modelos disponíveis 18. <ol><li> Aqui, como alvo duas regiões de AAO de Pleurotus eryngii de mutagénese aleatória e recombinação (Met [α1] -Val109, Phe392-Gln566), enquanto amplifica o restante do gene (844 pb) por PCR de alta fidelidade (Figura 1). Nota: Vários segmentos podem ser estudados por MORPHING de forma independente ou combinada 16. </li></ol></li><li> Ampliar as áreas visadas por PCR mutagênico. Criar áreas entre os segmentos (~ 50 pb cada) sobreposto por sobreposição de reacções de PCR das regiões definidas. <ol><li> Prepare PCR mutagénica de segmentos-alvo num volume final de 50 uL contendo uma cadeia molde de ADN (0,92 ng / uL), 90 nM de senso de oligo (RMLN para o segmento de MI e AAO-PA para o segmento M-II), 90 nM de uminiciador ntisense (AAO-92C para o segmento de MI e rMLC para segmento H-II), dNTPs 0,3 mM (0,075 mM de cada), 3% (v / v) de dimetilsulfóxido (DMSO), MgCl 1,5 mM, MnCl2 0,05 mM de 2 e 0,05 U / ul de polimerase de ADN de Taq. Sequências de iniciadores são detalhadas na Figura 1. </li><li> Usar o seguinte programa de PCR: 95 ° C durante 2 min (1 ciclo); 95 ° C durante 45 seg, 50 ° C durante 45 seg, 74 ° C durante 45 segundos (28 ciclos); e 74 ° C durante 10 min (1 ciclo). </li></ol></li><li> Amplificar as regiões não-mutagénicos com ultra-alta polimerase fidelidade e incluem as áreas correspondentes que se sobrepõem os segmentos mutagénicos e / ou saliências vector linearizado. <ol><li> Prepare misturas reaccionais num volume final de 50 ul contendo: molde de ADN (de 0,2 ng / uL), 250 nM de oligo sentido HFF, 250 nM de oligo anti-sentido de HFR, dNTPs 0,8 mM (0,2 mM cada), 3% (v / v) de dimetilsulfóxido (DMSO) e 0,02 U / ul de polimerase de ADN iproof. sequências de iniciadores são detalhados em &lt;strong&gt; Figura 1. </li><li> Usar o seguinte programa de PCR: 98 ° C durante 30 seg (1 ciclo); 98 ° C durante 10 seg, 55 ° C durante 25 seg, 72 ° C durante 45 segundos (28 ciclos); e 72 ° C durante 10 min (1 ciclo). Nota: Com condições descritas no 1.2 e 1.3 sobreposições de 43 bp (região plasmídeo-M1); 46 bp (região de região-HF M1); 47 pb (região-M2 região HF) e 61 pb (M2 região plasmídeo) são concebidos (Figura 1) para favorecer no splicing in vivo em leveduras. </li><li> Purifica-se todos os fragmentos de PCR (mutagénicos e não mutagénicos) com um kit de extracção de gel comercial de acordo com o protocolo do fabricante. </li></ol></li><li> Linearizar o vector de modo a que as regiões de cerca de 50 pb que flanqueia são criados que são homólogas às 5&#39;- e 3&#39;- extremidades do gene alvo. <ol><li> Prepara-se uma mistura de reacção contendo linearização 2 ug de ADN, 7,5 U de BamHI, 7,5 L Xho I, 20 ug de BSA e 2 ul de tampão Bam HI 10x num volume final de 20 ul. </li><li> Incubar a mistura de reacção a 37 ° C durante 2 h e 40 min. Posteriormente, proceder a inactivação a 80 ° C durante 20 min. </li></ol></li><li> Purifica-se o vector linearizado por extracção em gel de agarose a fim de evitar a contaminação com o plasmídeo circular residual (Figura 2). <ol><li> Carregar a mistura reaccional para a digestão mega-poço de um baixo ponto de fusão do gel de agarose semi-preparativa (0,75%, w: v), bem como uma alíquota (5 pi) da mistura de reacção na adjacentes bem como um repórter. </li><li> eletroforese Run DNA (5 V / cm entre os eletrodos, 4 ᵒC) e separar o gel de agarose correspondente ao mega-bem e armazená-lo em 4 ᵒC em 1x TAE. </li><li> Manchar a faixa com a escada de peso molecular e o repórter. Visualizar as bandas sob a luz UV. Nick a posição onde os linearizadas lugares vetor. Observação: Como a qualidade do vector linearizado purificado é um critifator de cal para a recombinação de sucesso e montagem em levedura, evitar manchas gel para eletroforese de DNA semi-preparativa. O uso de corantes e exposição aos raios UV para a extração de gel pode afectar a estabilidade do vector de ADN, comprometer a eficiência de recombinação in vivo. Como alternativa aos corantes EtBr tóxicos, Gel corantes SYBR vermelha e são comumente usados ​​para a coloração do gel. </li><li> Na ausência de luz UV, identificar o vector linearizado no fragmento mega poço utilizando a orientação dos entalhes na pista repórter coradas de modo que ele pode ser isolado. </li><li> Extrair o vector linearizado a partir de agarose e purificá-lo com um gel extraction kit comercial de acordo com o protocolo do fabricante. Nota: O uso de altas cópia vectores vaivém epissomal com marcadores de antibióticos e de auxotrofia: Neste exemplo, aplicou-se o uracilo independente e resistência à ampicilina pJRoC30 vector, sob o controlo do promotor de levedura GAL1. </li></ol></li><li> Preparar um mi equimolarxture dos fragmentos de PCR e misturá-lo com o vector linearizado numa proporção de 2: 1, com não menos do que 100 ng do plasmídeo linearizado (teste diferentes rácios de biblioteca equimolar / vector aberto para conseguir bons rendimentos de transformação). <ol><li> Medir a absorvância dos fragmentos de PCR e o vector linearizado a 260 nm e 280 nm para determinar a concentração e pureza. </li></ol></li><li> Transformar células competentes de levedura com a mistura de ADN utilizando um kit de transformação de levedura comercial (ver Tabela para o abastecimento) de acordo com as instruções do fabricante. <ol><li> Aqui, use uma protease deficiente e URA3 - S. dependentes cerevisiae, BJ5465. Transformar as células com o vector parental circularizado como um padrão interno durante o rastreio (ver abaixo). Além disso, o fundo vá transformando o vector linearizado na ausência de fragmentos de PCR. Nota: Em caso de detecção de níveis iniciais de secreção baixos, use S.cerevisiae protease estirpes deficientes como BJ5465 para promover o acúmulo de proteína ativa em sobrenadantes de cultura. Se a enzima alvo é submetido a hiperglicosilação, a utilização de estirpes de glicosilação-deficiente (por exemplo, Δ Kre2 que só é capaz de prender pequenas oligómeros de manose) poderia ser uma opção adequada. </li></ol></li><li> Placa as células transformadas em SC placas de abandono e incubar-los a 30 ° C durante três dias. Plate (em SC drop-out placas suplementadas com uracil) URA3 - S. cerevisiae células com falta do plasmídeo como um controlo negativo para o rastreio (ver abaixo). </li></ol> 2. Alto Throughput Screening Assay (Figura 3) <ol><li> Encher um número apropriado de placas de 96 poços estéreis (23 placas para analisar uma biblioteca de 2.000 clones) com 50 ul de meio mínimo por cavidade com a ajuda de um robot de pipetagem. </li><li> Escolha das colónias individuais a partir do SC-gota a placas e transferi-los para as placas de 96 poços. <ol><li> Em cada prato, inocular número da coluna 6 com o tipo parental como padrão interno e bem H1 com URA3 - S. cerevisiae (células em meio SC suplementado com uracilo) sem plasmídeo como um controlo negativo. Nota: Bem H1 é preenchido especificamente com os meios de abandono suplementadas com uracil. Um meio contendo bem em branco sem células também pode ser preparado como um controle adicional esterilidade. </li></ol></li><li> Cubra as placas com suas tampas e envolvê-los em Parafilm. Incubar as placas durante 48 h a 30 ° C, 225 rpm e 80% de humidade relativa num agitador húmido. </li><li> Remover o Parafilm, adicionar 160 uL de meio de expressão para cada cavidade com a ajuda do robot de pipetagem, voltar a selar as placas e incubar durante mais 24 h. Nota: Minimal médio e médio expressão são preparados como relatado em outros 19. níveis de secreção podem variar em função do gene em estudo e, consequentemente, tele incubação vezes tem de ser optimizada em cada caso, para sincronizar o crescimento celular em todas as cavidades. </li><li> Centrifugar as placas (placas mestres) a 2800 x g durante 10 min a 4 ° C. </li><li> Transferir 20 uL do sobrenadante dos poços na placa mestra para a placa réplica, utilizando um líquido de manuseamento de múltiplas robótico. Nota: Para favorecer a secreção de enzima é aconselhável substituir o péptido de sinal nativa da proteína alvo por péptidos de sinal vulgarmente utilizados para expressão heteróloga em levedura (por exemplo, o factor de prepro-α líder, o líder do K 1 da toxina assassina de S. cerevisiae, ou mesmo versões quiméricas de ambos os péptidos 13). Alternativamente, o péptido sinal nativo pode ser evoluído exclusivamente para a secreção em levedura. </li><li> Adicionar 20 ul de p -methoxybenzylalcohol 2 mM em 100 mM de tampão fosfato de sódio pH 6,0, com a ajuda do robot de pipetagem. Agitar as placas brevemente com uma de 96 nósLL misturador de placas e incubar durante 30 min à TA. </li><li> Com o robot de pipetagem, adicionar 160 ul do reagente FOX para cada placa de réplica e agita-se brevemente com o misturador (concentração final de mistura FOX no poço: 100 uM de xilenol laranja, 250 ^ M de Fe (NH 4) 2 (SO 4) 2 e mm H 25 2 SO 4). <ol><li> Adicionar vários aditivos para o reagente para aumentar a sensibilidade, tais como co-solventes orgânicos (DMSO, etanol, metanol) ou sorbitol 17. Aqui, amplificar a resposta por adição de sorbitol a uma concentração final de 100 mM (figura 4). </li></ol></li><li> Ler as placas (modo de ponto final, t 0) a 560 nm num leitor de placas. </li><li> Incubar as placas à temperatura ambiente até a cor se desenvolve e medir novamente a absorção (T 1). <ol><li> Calcula-se a actividade relativa da diferença entre o valor Abs após a incubação e a da medição inicial normalizada com base na pareTipo ntal para cada placa (Dt 1 - t 0). </li></ol></li><li> Sujeitar os melhores hits mutantes para dois re-exames consecutivos para excluir falsos positivos. Nota: Tipicamente, re-rastreios incluem isolamento de plasmídeos a partir de levedura, amplificação e purificação em Escherichia coli, seguido de transformação de células de levedura fresca com o plasmídeo 19. Cada clone seleccionado é re-exibido em pentaplicate. </li></ol>

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Neste artigo, nós resumimos a maioria das dicas e truques empregados no nosso laboratório para projetar enzimas por evolução dirigida em S. cerevisiae (AAO utilizando como exemplo) de modo que eles podem ser adaptados para utilização com muitos outros sistemas enzima eucariótica, simplesmente seguindo a abordagem comum descrito aqui. Em termos de criação de biblioteca, Metamorfose é um método one-pot rápido para introduzir e recombinar mutações aleatórias em trechos d...

Evolução molecular dirigida é um método robusto, rápido e fiável para conceber enzimas 1, 2. Através de ciclos iterativos de aleatória mutação, recombinação e selecção, versões melhoradas das enzimas pode ser gerado que actuam sobre novos substratos, em novas reacções, em não-naturais ambientes, ou até mesmo para ajudar a célula de atingir novos objectivos metabólicas 3-5. Entre os anfitriões utilizados na evolução dirigida, levedura Saccharomyces cerevisiae da cervejaria oferece um repertório de soluções para a expressão funcional de proteínas eucarióticas complexas que não estejam disponíveis em vias procariotas 6,7. Utilizado exaustivamente em estudos de biologia celular, este pequeno modelo eucariótico tem muitas vantagens em termos de modificações pós-traducionais, a facilidade de manipulação e transformação eficiência, todos os quais são características importantes de engenheiro enzimas por evolução dirigida 8. Por outro lado, a alta frequênciarecombinação homóloga de ADN em S. cerevisiae acoplado ao seu aparelho à prova de leitura eficiente abre um vasto leque de possibilidades para a criação de biblioteca e montagem de gene in vivo, promovendo a evolução de diferentes sistemas de enzimas individuais para vias artificiais complexos 9-12. Nosso laboratório passou a última década projetando ferramentas e estratégias para a evolução molecular de diferentes ligninases em levedura (Oxirredutases envolvidas na degradação da lignina durante o decaimento de madeira natural) 13-14. Nesta comunicação, nós apresentamos um protocolo detalhado para preparar e bibliotecas mutantes tela em S. cerevisiae para um modelo flavooxidase, -aril-oxidase de álcool (AAO 15) -, que podem ser facilmente convertidos para muitas outras enzimas. O protocolo envolve um método evolução focada-dirigida (MORPHING: Processo mutagênicos Organizado recombinação homóloga in vivo pelo Agrupamento) assistida pelo aparelho celular de levedura 16, umda ensaio de rastreio muito sensível com base na reacção de Fenton, a fim de detectar a actividade AAO secretado para o caldo de cultura 17.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1. Culture media</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Ampicillin sodium salt</td>
			<td>Sigma-Aldrich</td>
			<td>A0166</td>
			<td>CAS N&#186; 69-52-3 M.W. 371.39</td>
		</tr>
		<tr>
			<td>Bacto Agar</td>
			<td>Difco</td>
			<td>214010</td>
			<td></td>
		</tr>
		<tr>
			<td>Cloramphenicol</td>
			<td>Sigma-Aldrich</td>
			<td>C-0378</td>
			<td>CAS N&#186; 56-75-7 M.W. 323.13</td>
		</tr>
		<tr>
			<td>D-(+)-Galactose</td>
			<td>Sigma-Aldrich</td>
			<td>G0750</td>
			<td>CAS N&#186; 59-23-4 M.W. 180.16</td>
		</tr>
		<tr>
			<td>D-(+)-Glucose</td>
			<td>Sigma-Aldrich</td>
			<td>G5767</td>
			<td>CAS N&#186; 50-99-7 M.W. 180.16</td>
		</tr>
		<tr>
			<td>D-(+)-Raffinose pentahydrate</td>
			<td>Sigma-Aldrich</td>
			<td>83400</td>
			<td>CAS N&#186; 17629-30-0 M.W. 594.51</td>
		</tr>
		<tr>
			<td>Peptone</td>
			<td>Difco</td>
			<td>211677</td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium phosphate monobasic</td>
			<td>Sigma-Aldrich</td>
			<td>P0662</td>
			<td>CAS N&#186; 7778-77-0 M.W. 136.09</td>
		</tr>
		<tr>
			<td>Uracil</td>
			<td>Sigma Aldrich</td>
			<td>U1128</td>
			<td></td>
		</tr>
		<tr>
			<td>Yeast Extract</td>
			<td>Difco</td>
			<td>212750</td>
			<td></td>
		</tr>
		<tr>
			<td>Yeast Nitrogen Base without Amino Acids</td>
			<td>Difco</td>
			<td>291940</td>
			<td></td>
		</tr>
		<tr>
			<td>Yeast Synthetic Drop-out Medium Supplements without uracil</td>
			<td>Sigma-Aldrich</td>
			<td>Y1501</td>
			<td></td>
		</tr>
		
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>2. PCR Reactions</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>dNTP Mix</td>
			<td>Agilent genomics</td>
			<td>200415-51</td>
			<td>25 mM each</td>
		</tr>
		<tr>
			<td>iProof High-Fidelity DNA polymerase</td>
			<td>Bio-rad</td>
			<td>172-5301</td>
			<td></td>
		</tr>
		<tr>
			<td>Manganese(II) chloride tetrahydrate</td>
			<td>Sigma-Aldrich</td>
			<td>M8054</td>
			<td>CAS N&#186; 13446-34-9 M.W. 197.91</td>
		</tr>
		<tr>
			<td>Taq DNA Polymerase</td>
			<td>Sigma-Aldrich</td>
			<td>D4545</td>
			<td>For error prone PCR</td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>3. Plasmid linearization</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>BamHI restriction enzyme</td>
			<td>New England Biolabs</td>
			<td>R0136S</td>
			<td></td>
		</tr>
		<tr>
			<td>Bovine Serum Albumin</td>
			<td>New England Biolabs</td>
			<td>B9001S</td>
			<td></td>
		</tr>
		<tr>
			<td>XhoI restriction enzyme</td>
			<td>New England Biolabs</td>
			<td>R0146S</td>
			<td></td>
		</tr>
		<tr>
			<td>Gel Red</td>
			<td>Biotium</td>
			<td>41003</td>
			<td>For staining DNA</td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>4. FOX assays</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Ammonium iron(II) sulfate hexahydrate</td>
			<td>Sigma-Aldrich</td>
			<td>F3754</td>
			<td>CAS N&#186; 7783-85-9 M.W. 392.14</td>
		</tr>
		<tr>
			<td>Anysil Alcohol</td>
			<td>Sigma Aldrich</td>
			<td>W209902</td>
			<td>CAS N&#186; 105-13-5 M.W. 138.16</td>
		</tr>
		<tr>
			<td>D-Sorbitol</td>
			<td>Sigma-Aldrich</td>
			<td>S1876</td>
			<td>CAS N&#186; 50-70-4 M.W. 182.17</td>
		</tr>
		<tr>
			<td>Hydrogen peroxide 30%</td>
			<td>Merck Millipore</td>
			<td>1072090250</td>
			<td>FOX standard curve</td>
		</tr>
		<tr>
			<td>Xylenol Orange disodium salt</td>
			<td>Sigma-Aldrich</td>
			<td>52097</td>
			<td>CAS N&#186; 1611-35-4 M.W. 716.62</td>
		</tr>
		<tr>
			<td>Agarose gel stuff</td>
			<td>-</td>
			<td>-</td>
			<td>-</td>
		</tr>
		<tr>
			<td>Agarose</td>
			<td>Norgen</td>
			<td>28035</td>
			<td>CAS N&#186; 9012-36-6</td>
		</tr>
		<tr>
			<td>Gel Red</td>
			<td>Biotium</td>
			<td>41003</td>
			<td>DNA analysis dye</td>
		</tr>
		<tr>
			<td>GeneRuler 1Kb Ladder</td>
			<td>Thermo Scientific</td>
			<td>SM0311</td>
			<td>DNA M.W. standard</td>
		</tr>
		<tr>
			<td>Loading Dye 6x</td>
			<td>Thermo Scientific</td>
			<td>R0611</td>
			<td></td>
		</tr>
		<tr>
			<td>Low-melting temperature agarose</td>
			<td>Bio-rad</td>
			<td>161-3112</td>
			<td>CAS N&#186; 39346-81-1</td>
		</tr>
	
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>5. Kits and cells</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>S. cerevisiae strain BJ5465</td>
			<td>LGC Promochem, Spain</td>
			<td>ATTC 208289</td>
			<td>Protease deficient strain with genotype: MAT&#945; ura3-52 trp1 leu2-delta1 his3-delta200 pep4::HIS3 prb1-delta1.6R can1 GAL</td>
		</tr>
		<tr>
			<td>E. coli XL2-Blue competent cells</td>
			<td>Agilent genomics</td>
			<td>200150</td>
			<td>For plasmid purification and amplification</td>
		</tr>
		<tr>
			<td>NucleoSpin Gel and PCR Clean-up Kit</td>
			<td>Macherey-Nagel</td>
			<td>740,609,250</td>
			<td>DNA gel extraction</td>
		</tr>
		<tr>
			<td>NucleoSpin Plasmid Kit</td>
			<td>Macherey-Nagel</td>
			<td>740,588,250</td>
			<td>Column miniprep Kit</td>
		</tr>
		<tr>
			<td>Yeast Transformation Kit</td>
			<td>Sigma-Aldrich</td>
			<td>YEAST1-1KT</td>
			<td>Included DNA carrier (Salmon testes)</td>
		</tr>
		<tr>
			<td>Zymoprep yeast plasmid miniprep I</td>
			<td>Zymo research</td>
			<td>D2001</td>
			<td>Plasmid extraction from yeast</td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>6. Plates</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>96-well plates</td>
			<td>Greioner Bio-One</td>
			<td>655101</td>
			<td>Clear, non-sterile, Polystyrene (for activity measurements)</td>
		</tr>
		<tr>
			<td>96-well plates</td>
			<td>Greioner Bio-One</td>
			<td>655161</td>
			<td>Clear, sterile, Polystyrene (for microfermentations)</td>
		</tr>
		<tr>
			<td>96-well plate lid</td>
			<td>Greioner Bio-One</td>
			<td>656171</td>
			<td>Clear, sterile, Polystyrene (for microfermentations)</td>
		</tr>
	</tbody>
</table>

directed evolution method in saccharomyces cerevisiae: mutant library creation and screening

Evolução dirigida em Saccharomyces cerevisiae oferece muitas vantagens atraentes no projecto enzimas para aplicações biotecnológicas, um processo que envolve a construção, clonagem e expressão de bibliotecas de mutantes, acoplada a alta frequência de recombinação homóloga de ADN in vivo. Aqui, apresentamos um protocolo para criar e bibliotecas mutantes tela em leveduras com base no exemplo de um fúngica oxidase aril-álcool (AAO) para melhorar a sua actividade total. Dois segmentos de proteína foram sujeitos a evolução focalizado dirigido por mutagénese aleatória de ADN e na recombinação in vivo. Saliências de ~ 50 pb que flanqueia cada segmento permitiu a remontagem correcta do gene AAO-fusão num vector linearizado dando origem a um total de plasmídeo de replicação autónoma. Bibliotecas mutantes enriquecidos com variantes funcionais da AAO foram rastreados em S. cerevisiae sobrenadantes com um ensaio de elevado débito sensível com base na reacção de Fenton. O processo geral dea construção da biblioteca em S. cerevisiae aqui descrito pode ser facilmente aplicado a evoluir muitos outros genes eucarióticos, evitando reacções adicionais de PCR in vitro de recombinação de DNA e ligação etapas.

AAO de P. eryngii é um flavooxidase extracelular que abastece as peroxidases fúngicas com H 2 O 2 para começar a atacar a lignina. Dois segmentos de AAO foram submetidos a evolução focada-dirigido por MORPHING, a fim de melhorar a sua actividade e a sua expressão em S. cerevisiae 19. Independentemente das enzimas estrangeiras abrigadas por S. cerevisiae, o problema mais crítico, quando a construção de bibliotecas de mut...

Watch this Scientific Journal Video about Directed Evolution Method in Saccharomyces cerevisiae: Mutant Library Creation and Screening at JoVE.com

Directed Evolution Method in Saccharomyces cerevisiae: Mutant Library Creation and Screening

We present a detailed protocol to construct and screen mutant libraries for directed evolution campaigns in Saccharomyces cerevisiae.

Dirigido Método Evolução<em&gt; Saccharomyces cerevisiae</em&gt;: Mutant Biblioteca Criação e Triagem

Directed evolution in Saccharomyces cerevisiae offers many attractive advantages when designing enzymes for biotechnological applications, a process that ...

directed-evolution-method-saccharomyces-cerevisiae-mutant-library

Research

JoVE Journal

Biology

Directed Evolution Method in Saccharomyces cerevisiae: Mutant Library Creation and Screening

10.8K visualizações.  Institute of Catalysis, CSIC. We present a detailed protocol to construct and screen mutant libraries for directed evolution campaigns in Saccharomyces cerevisiae. 

Vídeo: Directed Evolution Method in Saccharomyces cerevisiae: Mutant Library Creation and Screening

Dissection of Saccharomyces Cerevisiae Asci

Yeast is a highly tractable model system that is used to study many different cellular processes. The common laboratory strain Saccharomyces cerevisiae exists in either a haploid or diploid state. The ability to combine alleles from two haploids and the ability to introduce modifications to the genome requires the production and dissection of asci. Asci production from haploid cells begins with the mating of two yeast haploid strains with compatible mating types to produce a diploid strain. This can be accomplished in a number of ways either on solid medium or in liquid. It is advantageous to select for the diploids in medium that selectively promotes their growth compared to either of the haploid strains. The diploids are then allowed to sporulate on nutrient-poor medium to form asci, a bundle of four haploid daughter cells resulting from meiotic reproduction of the diploid. A mixture of vegetative cells and asci is then treated with the enzyme zymolyase to digest away the membrane sac surrounding the ascospores of the asci. Using micromanipulation with a microneedle under a dissection microscope one can pick up individual asci and separate and relocate the four ascopores. Dissected asci are grown for several days and tested for the markers or alleles of interest by replica plating onto appropriate selective media.

Dissection of Saccharomyces Cerevisiae Asci

Micromanipulation of yeast cells is needed for meiotic genetic analysis or to select diploid zygotes. These micromanipulations are carried out using the microneedle of a dissection microscope. The microneedle is used to relocate cells and is controlled by a micromanipulator which are available with various degrees of automation.

Dissecção da Saccharomyces cerevisiae Asci

Yeast is a highly tractable model system that is used to study many different cellular processes. The common laboratory strain Saccharomyces cerevisiae ...

Biologia

Quantitative Phosphoproteomics in Fatty Acid Stimulated Saccharomyces cerevisiae

This protocol describes the growth and stimulation, with the fatty acid oleate, of isotopically heavy and light S. cerevisiae cells. Cells are ground using a cryolysis procedure in a ball mill grinder and the resulting grindate brought into solution by urea solubilization. This procedure allows for the lysis of the cells in a metabolically inactive state, preserving phosphorylation and preventing reorientation of the phosphoproteome during cell lysis.  Following reduction, alkylation, trypsin digestion of the proteins, the samples are desalted on C18 columns and the sample complexity reduced by fractionation using hydrophilic interaction chromatography (HILIC). HILIC columns preferentially retain hydrophilic molecules which is well suited for phosphoproteomics.  Phosphorylated peptides tend to elute later in the chromatographic profile than the non phosphorylated counterparts. After fractionation, phosphopeptides are enriched using immobilized metal chromatography, which relies on charge-based affinities for phosphopeptide enrichment. At the end of this procedure the samples are ready to be quantitatively analyzed by mass spectrometry.

Quantitative Phosphoproteomics in Fatty Acid Stimulated Saccharomyces cerevisiae

Description of a quantitative phosphorylation procedure using cryolysis, urea solubilziation, HILIC fractionation and IMAC enrichment of phosphorylated peptides.

Phosphoproteomics quantitativa em ácidos graxos estimulada Saccharomyces cerevisiae</em

This protocol describes the growth and stimulation, with the fatty acid oleate, of isotopically heavy and light S. cerevisiae cells. Cells are ground ...

Mutagenesis and Functional Selection Protocols for Directed Evolution of Proteins in E. coli

The efficient generation of genetic diversity represents an invaluable molecular tool that can be used to label DNA synthesis, to create unique molecular signatures, or to evolve proteins in the laboratory. Here, we present a protocol that allows the generation of large (>1011) mutant libraries for a given target sequence. This method is based on replication of a ColE1 plasmid encoding the desired sequence by a low-fidelity variant of DNA polymerase I (LF-Pol I). The target plasmid is transformed into a mutator strain of E. coli and plated on solid media, yielding between 0.2 and 1 mutations/kb, depending on the location of the target gene. Higher mutation frequencies are achieved by iterating this process of mutagenesis. Compared to alternative methods of mutagenesis, our protocol stands out for its simplicity, as no cloning or PCR are involved. Thus, our method is ideal for mutational labeling of plasmids or other Pol I templates or to explore large sections of sequence space for the evolution of activities not present in the original target. The tight spatial control that PCR or randomized oligonucleotide-based methods offer can also be achieved through subsequent cloning of specific sections of the library. Here we provide protocols showing how to create a random mutant library and how to establish drug-based selections in E. coli to identify mutants exhibiting new biochemical activities.

Mutagenesis and Functional Selection Protocols for Directed Evolution of Proteins in E. coli

Here we demonstrate a simple protocol to create a random mutant library for a given target sequence. We show how this method, which is performed in vivo in Escherichia coli, can be coupled with functional selections to evolve new enzymatic activities.

Mutagênese e Funcional Protocolos de Seleção para a Evolução Dirigida de proteínas em E. coli</em

The efficient generation of genetic diversity represents an invaluable molecular tool that can be used to label DNA synthesis, to create unique molecular ...

Microarray Analysis for Saccharomyces cerevisiae

In this protocol, gene expression in yeast (Saccharomyces cerevisiae) is changed after exposure to oxidative stress induced by the addition of hydrogen peroxide (H2O2), an oxidizing agent. In the experiment, yeast is grown for 48 hours in 1/2X YPD broth containing 3X glucose. The culture is split into a control and treated group. The experiment culture is treated with 0.5 mM H2O2 in Hanks Buffered Saline (HBSS) for 1 hour. The control culture is treated with HBSS only. Total RNA is extracted from both cultures and is converted to a biotin-labeled cRNA product through a multistep process. The final synthesis product is taken back to the UVM Microarray Core Facility and hybridized to the Affymetrix yeast GeneChips. The resulting gene expression data are uploaded into bioinformatics data analysis software.

Microarray Analysis for Saccharomyces cerevisiae

In this protocol, gene expression in yeast (Saccharomyces cerevisiae) is changed after exposure to oxidative stress induced by the addition of hydrogen peroxide (H2O2), an oxidizing agent.

Microarray Analysis for Saccharomyces cerevisiae</em

In this protocol, gene expression in yeast (Saccharomyces cerevisiae) is changed after exposure to oxidative stress induced by the addition of hydrogen ...

A Fluorescence Microscopy Assay for Monitoring Mitophagy in the Yeast Saccharomyces cerevisiae

Autophagy is important for turnover of cellular components under a range of different conditions. It serves an essential homeostatic function as well as a quality control mechanism that can target and selectively degrade cellular material including organelles1-4. For example, damaged or redundant mitochondria (Fig. 1), not disposed of by autophagy, can represent a threat to cellular homeostasis and cell survival. In the yeast, Saccharomyces cerevisiae, nutrient deprivation (e.g., nitrogen starvation) or damage can promote selective turnover of mitochondria by autophagy in a process termed mitophagy 5-9.
We describe a simple fluorescence microscopy approach to assess autophagy. For clarity we restrict our description here to show how the approach can be used to monitor mitophagy in yeast cells. The assay makes use of a fluorescent reporter, Rosella, which is a dual-emission biosensor comprising a relatively pH-stable red fluorescent protein linked to a pH-sensitive green fluorescent protein. The operation of this reporter relies on differences in pH between the vacuole (pH ~ 5.0-5.5) and mitochondria (pH ~ 8.2) in living cells. Under growing conditions, wild type cells exhibit both red and green fluorescence distributed in a manner characteristic of the mitochondria. Fluorescence emission is not associated with the vacuole. When subjected to nitrogen starvation, a condition which induces mitophagy, in addition to red and green fluorescence labeling the mitochondria, cells exhibit the accumulation of red, but not green fluorescence, in the acidic vacuolar lumen representing the delivery of mitochondria to the vacuole. Scoring cells with red, but not green fluorescent vacuoles can be used as a measure of mitophagic activity in cells5,10-12.

A Fluorescence Microscopy Assay for Monitoring Mitophagy in the Yeast Saccharomyces cerevisiae

A robust approach to monitor the delivery of organelles to the acidic lumen of the yeast vacuole for degradation and recycling is described. The method relies on the specific labeling of target organelles with a genetically encoded dual-emission fluorescence pH-biosensor, and visualization of individual cells using fluorescence microscopy.

Um Ensaio de microscopia de fluorescência para Mitophagy Monitoramento no fermento Saccharomyces cerevisiae

Autophagy is important for turnover of cellular components under a range of different conditions. It serves an essential homeostatic function as well as a ...

MISSION LentiPlex Pooled shRNA Library Screening in Mammalian Cells

RNA interference (RNAi) is an intrinsic cellular mechanism for the regulation of gene expression. Harnessing the innate power of this system enables us to knockdown gene expression levels in loss of gene function studies.
There are two main methods for performing RNAi. The first is the use of small interfering RNAs (siRNAs) that are chemically synthesized, and the second utilizes short-hairpin RNAs (shRNAs) encoded within plasmids 1. The latter can be transfected into cells directly or packaged into replication incompetent lentiviral particles. The main advantages of using lentiviral shRNAs is the ease of introduction into a wide variety of cell types, their ability to stably integrate into the genome for long term gene knockdown and selection, and their efficacy in conducting high-throughput loss of function screens. To facilitate this we have created the LentiPlex pooled shRNA library.
The MISSION LentiPlex Human shRNA Pooled Library is a genome-wide lentiviral pool produced using a proprietary process. The library consists of over 75,000 shRNA constructs from the TRC collection targeting 15,000+ human genes 2. Each library is tested for shRNA representation before product release to ensure robust library coverage. The library is provided in a ready-to-use lentiviral format at titers of at least 5 x 108 TU/ml via p24 assay and is pre-divided into ten subpools of approximately 8,000 shRNA constructs each. Amplification and sequencing primers are also provided for downstream target identification.
Previous studies established a synergistic antitumor activity of TRAIL when combined with Paclitaxel in A549 cells, a human lung carcinoma cell line 3, 4. In this study we demonstrate the application of a pooled LentiPlex shRNA library to rapidly conduct a positive selection screen for genes involved in the cytotoxicity of A549 cells when exposed to TRAIL and Paclitaxel. One barrier often encountered with high-throughput screens is the cost and difficulty in deconvolution; we also detail a cost-effective polyclonal approach utilizing traditional sequencing.

Here we use a human LentiPlex pooled library and traditional sequencing methods to identify gene targets promoting cell survival. We demonstrate how to set up and deconvolute a LentiPlex screen and validate the results.

LentiPlex MISSÃO Pooled shRNA Screening Biblioteca em células de mamíferos

RNA interference (RNAi) is an intrinsic cellular mechanism for the regulation of gene expression. Harnessing the innate power of this system enables us to ...

Expression and Purification of the Cystic Fibrosis Transmembrane Conductance Regulator Protein in Saccharomyces cerevisiae

The cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel, that when mutated, can give rise to cystic fibrosis in humans.There is therefore considerable interest in this protein, but efforts to study its structure and activity have been hampered by the difficulty of expressing and purifying sufficient amounts of the protein1-3. Like many 'difficult' eukaryotic membrane proteins, expression in a fast-growing organism is desirable, but challenging, and in the yeast S. cerevisiae, so far low amounts were obtained and rapid degradation of the recombinant protein was observed 4-9. Proteins involved in the processing of recombinant CFTR in yeast have been described6-9 .In this report we describe a methodology for expression of CFTR in yeast and its purification in significant amounts. The protocol describes how the earlier proteolysis problems can be overcome and how expression levels of CFTR can be greatly improved by modifying the cell growth conditions and by controlling the induction conditions, in particular the time period prior to cell harvesting. The reagants associated with this protocol (murine CFTR-expressing yeast cells or yeast plasmids) will be distributed via the US Cystic Fibrosis Foundation, which has sponsored the research. An article describing the design and synthesis of the CFTR construct employed in this report will be published separately (Urbatsch, I.; Thibodeau, P. et al., unpublished). In this article we will explain our method beginning with the transformation of the yeast cells with the CFTR construct - containing yeast plasmid (Fig. 1). The construct has a green fluorescent protein (GFP) sequence fused to CFTR at its C-terminus and follows the system developed by Drew et al. (2008)10. The GFP allows the expression and purification of CFTR to be followed relatively easily. The JoVE visualized protocol finishes after the preparation of microsomes from the yeast cells, although we include some suggestions for purification of the protein from the microsomes. Readers may wish to add their own modifications to the microsome purification procedure, dependent on the final experiments to be carried out with the protein and the local equipment available to them. The yeast-expressed CFTR protein can be partially purified using metal ion affinity chromatography, using an intrinsic polyhistidine purification tag. Subsequent size-exclusion chromatography yields a protein that appears to be &gt;90% pure, as judged by SDS-PAGE and Coomassie-staining of the gel.

Expression and Purification of the Cystic Fibrosis Transmembrane Conductance Regulator Protein in Saccharomyces cerevisiae

Attempts to express the cystic fibrosis transmembrane conductance regulator (CFTR) in Saccharomyces cerevisiae have, until now, yielded relatively low amounts of protein. This protocol and the associated reagents distributed via the Cystic Fibrosis Foundation should allow the preparation of milligram amounts of this 'difficult' eukaryotic membrane protein.

Expressão e purificação do Fibrose Cística proteína transmembranar regulador da condutância na Saccharomyces cerevisiae

The  cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride  channel, that when mutated, can give rise to cystic fibrosis in  ...

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

The Fluorescence in situ Hybridization (FISH) method allows one to detect nucleic acids in the native cellular environment. Here we provide a protocol for using FISH to quantify the number of mRNAs in single yeast cells. Cells can be grown in any condition of interest and then fixed and made permeable. Subsequently, multiple single-stranded deoxyoligonucleotides conjugated to fluorescent dyes are used to label and visualize mRNAs. Diffraction-limited fluorescence from single mRNA molecules is quantified using a spot-detection algorithm to identify and count the number of mRNAs per cell. While the more standard quantification methods of northern blots, RT-PCR and gene expression microarrays provide information on average mRNAs in the bulk population, FISH facilitates both the counting and localization of these mRNAs in single cells at single-molecule resolution.

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

This protocol describes an experimental procedure for performing Fluorescence in situ Hybridization (FISH) for counting mRNAs in single cells at single-molecule resolution.

Visualização e análise de moléculas de mRNA Usando Fluorescência<em&gt; In Situ</em&gt; A hibridação em<em&gt; Saccharomyces cerevisiae</em

The Fluorescence in situ Hybridization (FISH) method allows one to detect nucleic acids in the native cellular environment. Here we provide a protocol for ...

Coupled Assays for Monitoring Protein Refolding in Saccharomyces cerevisiae

Proteostasis, defined as the combined processes of protein folding/biogenesis, refolding/repair, and degradation, is a delicate cellular balance that must be maintained to avoid deleterious consequences 1. External or internal factors that disrupt this balance can lead to protein aggregation, toxicity and cell death. In humans this is a major contributing factor to the symptoms associated with neurodegenerative disorders such as Huntington's, Parkinson's, and Alzheimer's diseases 10. It is therefore essential that the proteins involved in maintenance of proteostasis be identified in order to develop treatments for these debilitating diseases. This article describes techniques for monitoring in vivo protein folding at near-real time resolution using the model protein firefly luciferase fused to green fluorescent protein (FFL-GFP). FFL-GFP is a unique model chimeric protein as the FFL moiety is extremely sensitive to stress-induced misfolding and aggregation, which inactivates the enzyme 12. Luciferase activity is monitored using an enzymatic assay, and the GFP moiety provides a method of visualizing soluble or aggregated FFL using automated microscopy. These coupled methods incorporate two parallel and technically independent approaches to analyze both refolding and functional reactivation of an enzyme after stress. Activity recovery can be directly correlated with kinetics of disaggregation and re-solubilization to better understand how protein quality control factors such as protein chaperones collaborate to perform these functions. In addition, gene deletions or mutations can be used to test contributions of specific proteins or protein subunits to this process. In this article we examine the contributions of the protein disaggregase Hsp104 13, known to partner with the Hsp40/70/nucleotide exchange factor (NEF) refolding system 5, to protein refolding to validate this approach.

Coupled Assays for Monitoring Protein Refolding in Saccharomyces cerevisiae

This article describes the use of a firefly luciferase-GFP fusion protein to investigate in vivo protein folding in Saccharomyces cerevisiae. Using this reagent, refolding of a model heat-denatured protein can be monitored simultaneously by fluorescence microscopy and an enzymatic assay to probe the roles of proteostasis network components in protein quality control.

Ensaios para Monitoramento juntamente redobramento de proteínas em<em&gt; Saccharomyces cerevisiae</em

Proteostasis, defined as the combined processes of protein folding/biogenesis, refolding/repair, and degradation, is a delicate cellular balance that must ...

Rapid Identification of Chemical Genetic Interactions in Saccharomyces cerevisiae

Determining the mode of action of bioactive chemicals is of interest to a broad range of academic, pharmaceutical, and industrial scientists. Saccharomyces cerevisiae, or budding yeast, is a model eukaryote for which a complete collection of ~6,000 gene deletion mutants and hypomorphic essential gene mutants are commercially available. These collections of mutants can be used to systematically detect chemical-gene interactions, i.e. genes necessary to tolerate a chemical. This information, in turn, reports on the likely mode of action of the compound. Here we describe a protocol for the rapid identification of chemical-genetic interactions in budding yeast. We demonstrate the method using the chemotherapeutic agent 5-fluorouracil (5-FU), which has a well-defined mechanism of action. Our results show that the nuclear TRAMP RNA exosome and DNA repair enzymes are needed for proliferation in the presence of 5-FU, which is consistent with previous microarray based bar-coding chemical genetic approaches and the knowledge that 5-FU adversely affects both RNA and DNA metabolism. The required validation protocols of these high-throughput screens are also described.

Rapid Identification of Chemical Genetic Interactions in Saccharomyces cerevisiae

Here we present a cost-effective method for defining chemical-genetic interactions in budding yeast. The approach is built on fundamental techniques in yeast molecular biology and is well suited for the mechanistic interrogation of small to medium collections of chemicals and other media environments.