Nous remercions le Dr Michael Cashel (National Institutes of Health, Bethesda, MA, USA) pour nous envoyer des souches bactériennes, plasmides, et les protocoles nécessaires. Nous remercions le Dr John Glover (Département de biochimie, Université de Toronto) pour l&#39;utilisation du lecteur de plaque SpecraMax. Royaume-Uni est le destinataire d&#39;un en sciences naturelles et en génie du Canada, bourses d&#39;études supérieures du Canada (CRSNG), les Instituts canadiens de recherche en santé Programme stratégique de formation en biologie structurale des protéines membranaires liées aux maladies, et de l&#39;Université de Toronto Bourse ouverte. Ce travail a été soutenu par une subvention des Instituts canadiens de recherche en santé (MOP-67210) pour WAH.

1) Les réactifs et les équipements <ol><li> Tout d&#39;abord, préparer les trois solutions suivantes: 1 mL de la solution A qui est composé de 8 mM de L-lysine, 100 mM de sodium 2 - (N-morpholino) éthanesulfonique (MES) à pH 6,5, 0,2 mM de nucléotides, où le nucléotide est soit: guanosine diphosphate (PIB), guanosine triphosphate (GTP), la guanosine 5&#39;-diphosphate, 3&#39;-diphosphate (ppGpp), ou guanosine-5&#39;-triphosphate, 3&#39;-diphosphate (pppGpp), 0,1 mM de pyridoxal 5&#39;-phosphate (PLP), et 1 mM β-mercaptoéthanol / (β-ME). 1 mL de la solution B qui se compose de 100 mM de sodium MES pH 6,5, 0,1 mM PLP, 1 mM β-ME, et 50 LdcI nM. LdcI a été purifié comme décrit dans Snider et al. 6 et Kanjee et al. 14. 1 ml de solution C qui est identique à la solution B, mais ne contient pas LdcI. </li><li> Préparer 100 mL de la solution d&#39;arrêt composé de carbonate de sodium 1 M (10,6 g/100 ml) et 50 ul aliquotes dans chaque puits d&#39;une plaque de polystyrène de 96 puits à l&#39;aide d&#39;une pipette multi-canaux. Ajouter 30 uL d&#39;eau à la plaque, puis couvrir. Notez que la somme du volume d&#39;eau ajoutée et le volume de l&#39;échantillon extrait durant la réaction enzymatique doit être égal à 50 pl. Dans ce cas, 20 uL d&#39;échantillon réaction enzymatique sera supprimé. </li><li> Préparer 5 ml de solution de TNBS à 10 mM en diluant 294 uL de 5% (p / v) de bouillon de TNBS avec de l&#39;eau 4706 ul, l&#39;envelopper dans du papier d&#39;aluminium et de garder sur la glace. </li><li> Equilibrer le thermostat Eppendorf Plus à 37 ° C. Le Plus thermostat a 24 puits en 6 colonnes. Voir Figure 2 pour schématique. Étiquette de 1,5 mL tubes Eppendorf indiquant l&#39;identité du nucléotide qui sera testé (un par colonne): GTP (colonne A), le PIB (colonne B), ppGpp (colonne C), pppGpp (colonne D), aucun nucléotide (colonne E ), et des échantillons de protéines (colonne F). </li><li> Boîtes en rack plusieurs de ces 200 conseils uL que chaque rangée de remplacement est omise donne un total de quatre rangées de pointes. Cela est nécessaire pour l&#39;utilisation de la pipette multi-canaux avec le thermostat et heatblock pendant le dosage enzymatique. </li><li> Equilibrer numérique Heatblock (VWR) à 42 ° C. </li><li> Placer une plaque de 96 puits en polypropylène 2,0 ml sur la glace pour refroidir. </li></ol> 2) Dosage LdcI <ol><li> Aliquote de 50 ul de la solution A avec le nucléotide appropriées pour 1,5 mL tubes Eppendorf dans chacune des cinq colonnes du thermostat Eppendorf. </li><li> Ajouter 330 ul de la solution B pour trois tubes dans la colonne F et ajouter 330 ul de la solution C (le contrôle sans protéines) sur le tube de finale dans la colonne F. </li><li> Equilibrer les solutions à 37 ° C pendant cinq minutes. Astuce: après 5 minutes, couper les chapeaux des tubes dans le centre du système de chauffage-bloc pour les empêcher d&#39;interférer avec la pipette multicanaux à être utilisés suivant. </li><li> L&#39;utilisation d&#39;un 5-50 uL VWR multi-canal pipette, transférer 50 ul des tubes dans la colonne F dans chacun des tubes dans les colonnes AE. Démarrer le chronomètre dès que le premier tube est mélangé. </li><li> À 2, 4 et 6 minutes enlever 20 uL d&#39;échantillon à l&#39;aide de la pipette multi-canaux et ajouter à la solution d&#39;arrêt. </li><li> Note: les échantillons dans une solution d&#39;arrêt peuvent être couverts dans une pellicule plastique et congelés à -20 ° C pour un traitement ultérieur. Les plaques doivent être décongelés à température ambiante avant réaction avec le TNBS. </li></ol> 3) Réaction TNBS et le développement de couleurs <ol><li> Ajouter 50 uL de MM TNBS 10 solution à la solution d&#39;arrêt à l&#39;aide de la pipette multi-canaux et puis incuber à 42 ° C pendant 6 minutes. La solution prend une couleur jaune foncé / orange comme le TNBS réagit avec la lysine et la cadavérine. </li><li> Après 6 minutes, refroidir la plaque sur la glace pour ralentir la réaction. </li><li> Retirer 100 pi d&#39;échantillon en utilisant un VWR 20-200 uL pipette multi-canaux et la place dans la plaque de 2 mL puits profond qui a été refroidi sur la glace. Transfert seau à glace à la hotte. </li><li> Ajouter 500 ul de toluène à chaque puits en utilisant un HandyStep (Marque) pipeteur répéter et 12,5 mL pipette (Plastibrand). </li><li> Essuyer tout excès de toluène en utilisant un Kimwipe et couvrir la plaque avec des bandes de ruban d&#39;emballage. Assurez-vous d&#39;appuyer fermement pour obtenir une bonne étanchéité. Recouvrir la plaque de 96 puits avec un couvercle plat et ensuite agiter vigoureusement pendant 1 minute et 30 secondes. </li><li> Laissez les solutions pour régler pendant 5 minutes. Le TNP-cadavérine est maintenant dans la phase supérieure du toluène, tandis que le TNP-lysine reste soluble dans l&#39;eau (voir figure 1). </li><li> Retirer 200 ul de toluène en utilisant les 20 à 200 uL multi-canal pipette dans une plaque de 96 puits pour la lecture. Remarque: veillez à vérifier que chaque échantillon étant enlevée est claire et n&#39;a pas de la phase aqueuse inférieure. Remarque: l&#39;utilisation des conseils barrière pour éviter d&#39;endommager la pipette multi-canaux par le toluène. </li><li> Lire l&#39;absorbance à 340 nm dans un lecteur de plaque de SpectraMax 340. </li><li> Pour nettoyer la plaque de quartz, rincer le toluène avec de l&#39;eau et placez la plaque de quartz dans un grandplateau en verre dans la hotte. Verser sur 100 mL d&#39;un mélange 7:3 de 70% (v / v) d&#39;acide nitrique: 95% (v / v) d&#39;éthanol et de recouvrir la plaque de quartz avec un plateau en verre secondes. Attention: la réaction est fortement exothermique protection contre l&#39;usure et parfois explosives appropriées et s&#39;assurer que la ceinture hotte est d&#39;abaisser le 6 &quot;niveau Après refroidissement, laver l&#39;acide nitrique à l&#39;eau puis 95% d&#39;éthanol.. </li></ol> Résultats Représentant 4) 1) Cadaverine standard courbe (figure 3) Le test a été réalisé comme décrit, mais sans aucune L-lysine ou LdcI et des concentrations différentes, au lieu de cadavérine ont été utilisés pour déterminer empiriquement la gamme linéaire du dosage. Le test est linéaire jusqu&#39;à une DO 340 de 0,25, correspondant à ~ 22 nmoles de cadavérine (figure 3). 2) Activité des LdcI (figure 4) L&#39;activité de LdcI seul a été établi à 153,5 (± 18,1) nmol cadavérine min-1 ug LdcI-1 à pH 6,5. L&#39;activité de LdcI est insensible à la présence de 100 uM GTP ou le PIB, mais est fortement inhibée (&gt; 10 fois), en présence de pppGpp et ppGpp (figure 4). <img src="/files/ftp_upload/2094/2094fig1.jpg" alt="Figure 1" /> Figure 1. Schéma de la réaction LdcI. La réaction de décarboxylation de la L-lysine pour générer du CO 2 et la cadavérine est indiqué ainsi que la réaction ultérieure avec le TNBS à pH élevé pour générer N, N&#39;-bistrinitrophenylcadaverine (TNP-cadavérine) et le N, N &#39;-bistrinitrophenyllysine (TNP-lysine). Basé sur Phan et al.11 <img src="/files/ftp_upload/2094/2094fig2.jpg" alt="Figure 2" /> Figure 2. Installation du thermostat Eppendorf. La disposition des échantillons dans le thermostat de 24 puits Eppendorf est montré avec la description des étapes de l&#39;essai (indiqués en gras). Les flèches indiquent le transfert de solutions de réaction selon le protocole. Retrait de la solution de réaction à la solution d&#39;arrêt dans la plaque de 96 puits est également indiquée. <img src="/files/ftp_upload/2094/2094fig3.jpg" alt="Figure 3" /> Figure 3. Cadaverine standard courbe. Une parcelle de l&#39;absorbance à 340 nm par rapport nmoles de cadavérine est montré. Les barres d&#39;erreur représentent la déviation standard d&#39;au moins trois mesures indépendantes. La ligne de meilleur ajustement est également représenté et a un R2 de 0,996. <img src="/files/ftp_upload/2094/2094fig4.jpg" alt="Figure 4" /> Figure 4. Résultats du dosage LdcI. Une parcelle du taux d&#39;activité LdcI (en nmoles cadavérine produite min-1 ug-1 LdcI) est indiqué dans la présence de 100 uM, GTP PIB, pppGpp, ppGpp et en l&#39;absence de nucléotide. Les nucléotides de réponse sévères (p) ppGpp sont capables d&#39;activité significative LdcI inhibant. Les barres d&#39;erreur représentent la déviation standard d&#39;au moins six mesures indépendantes.

<ol>
	<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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K., Bearson, B., Bang, S. H., Bang, I. S., 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=Internal+pH+crisis,+lysine+decarboxylase+and+the+acid+tolerance+response+of+Salmonella+typhimurium.">Internal pH crisis, lysine decarboxylase and the acid tolerance response of Salmonella typhimurium.</a> Mol Microbiol. 20, 605-611 (1996).</li><li>Merrell, D. S., Camilli, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+cadA+gene+of+Vibrio+cholerae+is+induced+during+infection+and+plays+a+role+in+acid+tolerance.">The cadA gene of Vibrio cholerae is induced during infection and plays a role in acid tolerance.</a> Mol Microbiol. 34, 836-849 (1999).</li><li>Kanjee, U., Gutsche, I., Alexopoulos, E., Zhao, B., Bakkouri, M. E. l., Thibault, G., Liu, K., Ramachandran, S., Snider, J., Pai, E. F., Houry, W. 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>

Dans le dosage de la lysine décarboxylase, TNBS réagit avec les amines primaires de L-lysine et la cadavérine pour former le TNP-lysine et la cadavérine TNP-adduits (figure 1). En raison de la présence du groupe acide carboxylique sur le TNP-lysine, cet adduit reste soluble dans l&#39;eau tandis que le TNP-cadavérine, manquant le groupe acide carboxylique, est capable de partitionnement dans le toluène 11. Ce type de test peut être utilisé plus largement sur d&#39;autres types d&#39;acides aminés, o...

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		<th>Material Name</th>
		<th>Type</th>
		<th>Company</th>
		<th>Catalogue Number</th>
		<th>Comment</th>
		</tr>
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<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>
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an assay for measuring the activity of escherichia coli inducible lysine decarboxyase

Escherichia coli est une bactérie entérique qui est capable de croître sur un large éventail de valeurs de pH (pH 5 - 9) 1 et, incroyablement, est capable de survivre à l&#39;acide extrêmes souligne notamment le passage par l&#39;estomac des mammifères où le pH peut descendre jusqu&#39;à comme un pH de 1 - 2 2. Pour permettre un tel éventail de survie pH acide, E. coli possède quatre différents décarboxylases inductible acide aminé qui décarboxyler leurs acides aminés dans un substrat de manière à protons dépend donc élever le pH interne. Le décarboxylases inclure le glutamique décarboxylases Gada et BDAG 3, le arginine décarboxylase Adia 4, la lysine décarboxylase LdcI 5, 6 et l&#39;ornithine décarboxylase SPEF 7. Toutes ces enzymes utilisent le pyridoxal-5&#39;-phosphate comme un co-facteur 8 et fonctionnent ensemble avec intérieur de la membrane du substrat sous-produits qui éliminent les produits antiporteurs décarboxylation au milieu extérieur, en échange de substrat frais 2. Dans le cas de LdcI, le antiporteur lysine cadavérine est appelé CADB. Récemment, nous avons déterminé la structure cristalline aux rayons X des LdcI à 2,0 Å, et nous avons découvert un petit roman-molécule liée à la guanosine LdcI réponse strictes régulateur de 5&#39;-diphosphate, 3&#39;-diphosphate (ppGpp) 14. La réponse sévères survient lorsque des cellules en croissance exponentielle expérience de privation des éléments nutritifs ou l&#39;un des nombreux autres types de stress 9. En conséquence, les cellules produisent ppGpp qui conduit à une cascade de signalisation aboutissant à l&#39;évolution de la croissance exponentielle de la croissance en phase stationnaire 10. Nous avons démontré que ppGpp est un inhibiteur spécifique de LdcI 14. Nous décrivons ici le dosage lysine décarboxylase, modifié par le dosage développée par Phan et al. 11, que nous avons utilisée pour déterminer l&#39;activité de LdcI et l&#39;effet de pppGpp / ppGpp sur cette activité. La réaction de décarboxylation LdcI supprime le groupe α-carboxy de la L-lysine et produit du dioxyde de carbone et la cadavérine polyamine (1,5-diaminopentane) 5. L-lysine et la cadavérine peuvent réagir avec l&#39;acide 2,4,6-trinitrobenzensulfonic (TNBS) à pH élevé pour générer N, N&#39;-bistrinitrophenylcadaverine (TNP-cadavérine) et N, N&#39;-bistrinitrophenyllysine (TNP-lysine), respectivement 11. Le TNP-cadavérine peuvent être séparés du TNP-lysine que l&#39;ancien est soluble dans les solvants organiques tels que le toluène et le second l&#39;est pas (voir figure 1). La gamme linéaire du dosage a été déterminée empiriquement en utilisant purifiée cadavérine.

Watch this Scientific Journal Video about An Assay for Measuring the Activity of Escherichia coli Inducible Lysine Decarboxyase at JoVE.com

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

L&#39;activité de la décarboxylase inductible lysine est contrôlée par la réaction du substrat L-lysine et la cadavérine produit avec l&#39;acide 2,4,6-trinitrobenzensulfonic pour former des adduits qui ont une solubilité différentielle dans le toluène.

Un test pour mesurer l&#39;activité des Escherichia coli Inductible Lysine 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 vues.  University of Toronto. L'activité de la décarboxylase inductible lysine est contrôlée par la réaction du substrat L-lysine et la cadavérine produit avec l'acide 2,4,6-trinitrobenzensulfonic pour former des adduits qui ont une solubilité différentielle dans le toluène.

Vidéo: 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.

Mesure de la rigidité à la flexion des cellules bactériennes utilisant un piège optique

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

Recherche

Biologie

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.

Criblage à haut débit activité endoglucanase fongique dans les Escherichia coli</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.

Application de la MassSQUIRM pour des mesures quantitatives de l&#39;activité Déméthylase Lysine

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.

Protocole rapide pour la préparation de électrocompétentes<em&gt; Escherichia coli</em&gt; Et<em&gt; Vibrio cholerae</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.

Protocoles pour la mise en œuvre d&#39;un<em&gt; Escherichia coli</em&gt; Sur la base du système d&#39;expression cellulaire gratuit TX-TL pour la biologie synthétique

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

Détection de Live<em&gt; Escherichia coli</em&gt; O157: H7 par les cellules 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. ...

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.

Green Fluorescent Protein base Expression dépistage des protéines membranaires dans<em&gt; Escherichia coli</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.

Les avantages multiples de la protéine co-expression dans<em&gt; Escherichia coli</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.

Incorporation spécifiques résidus de noncanonical acides aminés en protéines de modèle à l&#39;aide d&#39;un<em&gt; Escherichia coli</em&gt; Système de transcription-traduction libre Cell-

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.

Mesure de l’activité enzymatique Lactase dans le laboratoire d’enseignement

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