Name: an in vitro assay to detect trna-isopentenyl transferase activity
Uploaded: 2018-10-08T13:00:00
Description: Watch this Scientific Journal Video about An In Vitro Assay to Detect tRNA-Isopentenyl Transferase Activity at JoVE.com

We would like to thank Dr. David Engelke for his guidance and helpful comments on this manuscript. PJS - Ball State University laboratory startup funds; DAB - grant 1R15AI130950-01.

NOTE: The protocol was adapted from Ref. 24.
1. Obtain RNA and Enzyme of Interest
<ol>
	<li>Use in vitro transcribed RNAs internally labeled with 32P, and recombinant His6-Mod5 expressed in and purified from E. coli, as previously described24.
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		<li>Introduce in vitro transcribed RNAs (section 3) using T7 RNA polymerase in the presence of unlabeled ATP, UTP, CTP, GTP and 10 &#181;Ci of gel-purified, e...

<ol>
	<li>Boccaletto, P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MODOMICS:+a+database+of+RNA+modification+pathways.+2017+update.">MODOMICS: a database of RNA modification pathways. 2017 update.</a> Nucleic Acids Research. 46 (D1), 303-307 (2018).</li><li>Lewis, C. J., Pan, T., Kalsotra, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA+modifications+and+structures+cooperate+to+guide+RNA-protein+interactions.">RNA modifications and structures cooperate to guide RNA-protein interactions.</a> Nature Reviews: Molecular and Cellular Biology. 18 (3), 202-210 (2017).</li><li>Soll, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enzymatic+modification+of+transfer+RNA.">Enzymatic modification of transfer RNA.</a> Science. 173 (3994), 293-299 (1971).</li><li>Schweizer, U., Bohleber, S., Fradejas-Villar, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+modified+base+isopentenyladenosine+and+its+derivatives+in+tRNA.">The modified base isopentenyladenosine and its derivatives in tRNA.</a> RNA Biology. 14 (9), 1197-1208 (2017).</li><li>Persson, B. C., Esberg, B., Olafsson, O., Bjork, G. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Synthesis+and+function+of+isopentenyl+adenosine+derivatives+in+tRNA.">Synthesis and function of isopentenyl adenosine derivatives in tRNA.</a> Biochimie. 76 (12), 1152-1160 (1994).</li><li>Urbonavicius, J., Qian, Q., Durand, J. M., Hagervall, T. G., Bjork, G. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Improvement+of+reading+frame+maintenance+is+a+common+function+for+several+tRNA+modifications.">Improvement of reading frame maintenance is a common function for several tRNA modifications.</a> EMBO Journal. 20 (17), 4863-4873 (2001).</li><li>Aubee, J. I., Olu, M., Thompson, K. 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+i6A37+tRNA+modification+is+essential+for+proper+decoding+of+UUX-Leucine+codons+during+rpoS+and+iraP+translation.">The i6A37 tRNA modification is essential for proper decoding of UUX-Leucine codons during rpoS and iraP translation.</a> RNA. 22 (5), 729-742 (2016).</li><li>Caillet, J., Droogmans, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+cloning+of+the+Escherichia+coli+miaA+gene+involved+in+the+formation+of+delta+2-isopentenyl+adenosine+in+tRNA.">Molecular cloning of the Escherichia coli miaA gene involved in the formation of delta 2-isopentenyl adenosine in tRNA.</a> Journal of Bacteriology. 170 (9), 4147-4152 (1988).</li><li>Soderberg, T., Poulter, C. D. <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+dimethylallyl+diphosphate:tRNA+dimethylallyltransferase:+essential+elements+for+recognition+of+tRNA+substrates+within+the+anticodon+stem-loop.">Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyltransferase: essential elements for recognition of tRNA substrates within the anticodon stem-loop.</a> Biochemistry. 39 (21), 6546-6553 (2000).</li><li>Dihanich, M. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+and+characterization+of+MOD5,+a+gene+required+for+isopentenylation+of+cytoplasmic+and+mitochondrial+tRNAs+of+Saccharomyces+cerevisiae.">Isolation and characterization of MOD5, a gene required for isopentenylation of cytoplasmic and mitochondrial tRNAs of Saccharomyces cerevisiae.</a> Molecular and Cellular Biology. 7 (1), 177-184 (1987).</li><li>Lemieux, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regulation+of+physiological+rates+in+Caenorhabditis+elegans+by+a+tRNA-modifying+enzyme+in+the+mitochondria.">Regulation of physiological rates in Caenorhabditis elegans by a tRNA-modifying enzyme in the mitochondria.</a> Genetics. 159 (1), 147-157 (2001).</li><li>Golovko, A., Sitbon, F., Tillberg, E., Nicander, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+a+tRNA+isopentenyltransferase+gene+from+Arabidopsis+thaliana.">Identification of a tRNA isopentenyltransferase gene from Arabidopsis thaliana.</a> Plant Molecular Biology. 49 (2), 161-169 (2002).</li><li>Warner, G. J., Rusconi, C. P., White, I. E., Faust, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+and+sequencing+of+two+isopentenyladenosine-modified+transfer+RNAs+from+Chinese+hamster+ovary+cells.">Identification and sequencing of two isopentenyladenosine-modified transfer RNAs from Chinese hamster ovary cells.</a> Nucleic Acids Research. 26 (23), 5533-5535 (1998).</li><li>Golovko, A., Hjalm, G., Sitbon, F., Nicander, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cloning+of+a+human+tRNA+isopentenyl+transferase.">Cloning of a human tRNA isopentenyl transferase.</a> Gene. 258 (1-2), 85-93 (2000).</li><li>Kernohan, K. D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Matchmaking+facilitates+the+diagnosis+of+an+autosomal-recessive+mitochondrial+disease+caused+by+biallelic+mutation+of+the+tRNA+isopentenyltransferase+(TRIT1)+gene.">Matchmaking facilitates the diagnosis of an autosomal-recessive mitochondrial disease caused by biallelic mutation of the tRNA isopentenyltransferase (TRIT1) gene.</a> Human Mutations. 38 (5), 511-516 (2017).</li><li>Yarham, J. W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Defective+i6A37+modification+of+mitochondrial+and+cytosolic+tRNAs+results+from+pathogenic+mutations+in+TRIT1+and+its+substrate+tRNA.">Defective i6A37 modification of mitochondrial and cytosolic tRNAs results from pathogenic mutations in TRIT1 and its substrate tRNA.</a> PLoS Genetics. 10 (6), 1004424 (2014).</li><li>Smaldino, P. J., Read, D. F., Pratt-Hyatt, M., Hopper, A. K., Engelke, D. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+cytoplasmic+and+nuclear+populations+of+the+eukaryote+tRNA-isopentenyl+transferase+have+distinct+functions+with+implications+in+human+cancer.">The cytoplasmic and nuclear populations of the eukaryote tRNA-isopentenyl transferase have distinct functions with implications in human cancer.</a> Gene. 556 (1), 13-18 (2015).</li><li>Lamichhane, T. N., Mattijssen, S., Maraia, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Human+cells+have+a+limited+set+of+tRNA+anticodon+loop+substrates+of+the+tRNA+isopentenyltransferase+TRIT1+tumor+suppressor.">Human cells have a limited set of tRNA anticodon loop substrates of the tRNA isopentenyltransferase TRIT1 tumor suppressor.</a> Molecular and Cellular Biology. 33 (24), 4900-4908 (2013).</li><li>Swoboda, R. K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Antimelanoma+CTL+recognizes+peptides+derived+from+an+ORF+transcribed+from+the+antisense+strand+of+the+3'+untranslated+region+of+TRIT1.">Antimelanoma CTL recognizes peptides derived from an ORF transcribed from the antisense strand of the 3' untranslated region of TRIT1.</a> Molecular Therapy Oncolytics. 1, 14009 (2015).</li><li>Yue, Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+breast+cancer+candidate+genes+using+gene+co-expression+and+protein-protein+interaction+information.">Identification of breast cancer candidate genes using gene co-expression and protein-protein interaction information.</a> Oncotarget. 7 (24), 36092-36100 (2016).</li><li>Chen, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Association+of+polymorphisms+and+haplotype+in+the+region+of+TRIT1,+MYCL1+and+MFSD2A+with+the+risk+and+clinicopathological+features+of+gastric+cancer+in+a+southeast+Chinese+population.">Association of polymorphisms and haplotype in the region of TRIT1, MYCL1 and MFSD2A with the risk and clinicopathological features of gastric cancer in a southeast Chinese population.</a> Carcinogenesis. 34 (5), 1018-1024 (2013).</li><li>Spinola, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+and+functional+characterization+of+the+candidate+tumor+suppressor+gene+TRIT1+in+human+lung+cancer.">Identification and functional characterization of the candidate tumor suppressor gene TRIT1 in human lung cancer.</a> Oncogene. 24 (35), 5502-5509 (2005).</li><li>Spinola, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ethnic+differences+in+frequencies+of+gene+polymorphisms+in+the+MYCL1+region+and+modulation+of+lung+cancer+patients'+survival.">Ethnic differences in frequencies of gene polymorphisms in the MYCL1 region and modulation of lung cancer patients' survival.</a> Lung Cancer. 55 (3), 271-277 (2007).</li><li>Read, D. F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Aggregation+of+Mod5+is+affected+by+tRNA+binding+with+implications+for+tRNA+gene-mediated+silencing.">Aggregation of Mod5 is affected by tRNA binding with implications for tRNA gene-mediated silencing.</a> FEBS Letters. 591 (11), 1601-1610 (2017).</li><li>Waller, T. J., Read, D. F., Engelke, D. R., Smaldino, P. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+human+tRNA-modifying+protein,+TRIT1,+forms+amyloid+fibers+in+vitro.">The human tRNA-modifying protein, TRIT1, forms amyloid fibers in vitro.</a> Gene. 612, 19-24 (2017).</li><li>Suzuki, G., Shimazu, N., Tanaka, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+yeast+prion,+Mod5,+promotes+acquired+drug+resistance+and+cell+survival+under+environmental+stress.">A yeast prion, Mod5, promotes acquired drug resistance and cell survival under environmental stress.</a> Science. 336 (6079), 355-359 (2012).</li><li>Soderberg, T., Poulter, C. D. <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+dimethylallyl+diphosphate:tRNA+dimethylallyltransferase:+site-directed+mutagenesis+of+highly+conserved+residues.">Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyltransferase: site-directed mutagenesis of highly conserved residues.</a> Biochemistry. 40 (6), 1734-1740 (2001).</li><li>Lamichhane, T. N., Blewett, N. H., Maraia, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Plasticity+and+diversity+of+tRNA+anticodon+determinants+of+substrate+recognition+by+eukaryotic+A37+isopentenyltransferases.">Plasticity and diversity of tRNA anticodon determinants of substrate recognition by eukaryotic A37 isopentenyltransferases.</a> Rna. 17 (10), 1846-1857 (2011).</li><li>Lamichhane, T. N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lack+of+tRNA+modification+isopentenyl-A37+alters+mRNA+decoding+and+causes+metabolic+deficiencies+in+fission+yeast.">Lack of tRNA modification isopentenyl-A37 alters mRNA decoding and causes metabolic deficiencies in fission yeast.</a> Molecular and Cellular Biology. 33 (15), 2918-2929 (2013).</li><li>Laten, H., Gorman, J., Bock, R. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isopentenyladenosine+deficient+tRNA+from+an+antisuppressor+mutant+of+Saccharomyces+cerevisiae.">Isopentenyladenosine deficient tRNA from an antisuppressor mutant of Saccharomyces cerevisiae.</a> Nucleic Acids Research. 5 (11), 4329-4342 (1978).</li><li>Etcheverry, T., Colby, D., Guthrie, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+precursor+to+a+minor+species+of+yeast+tRNASer+contains+an+intervening+sequence.">A precursor to a minor species of yeast tRNASer contains an intervening sequence.</a> Cell. 18 (1), 11-26 (1979).</li><li>Yan, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+high-throughput+quantitative+approach+reveals+more+small+RNA+modifications+in+mouse+liver+and+their+correlation+with+diabetes.">A high-throughput quantitative approach reveals more small RNA modifications in mouse liver and their correlation with diabetes.</a> Analytical Chemistry. 85 (24), 12173-12181 (2013).</li><li>Su, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+analysis+of+ribonucleoside+modifications+in+tRNA+by+HPLC-coupled+mass+spectrometry.">Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry.</a> Nature Protocols. 9 (4), 828-841 (2014).</li><li>Jonkhout, N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+RNA+modification+landscape+in+human+disease.">The RNA modification landscape in human disease.</a> Rna. 23 (12), 1754-1769 (2017).</li><li>Dominissini, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+dynamic+N(1)-methyladenosine+methylome+in+eukaryotic+messenger+RNA.">The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA.</a> Nature. 530 (7591), 441-446 (2016).</li><li>Meyer, K. 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RNA modifications continue to be shown to play ever more important and diverse roles in cellular and organismal function. As such, the development of assays to interrogate RNA modifying enzymes is central to better understanding the fundamental aspects of biology. This protocol describes a high-resolution in vitro assay to characterize the tRNA modification activity of Mod5.
This protocol has the distinct advantage of providing a direct, and easily interpretable readout of isopentenyl...

At least 163 distinct posttranscriptional RNA modifications have been identified, with these modifications conferring diverse and context-dependent functions to RNAs, directly influencing RNA structure, and affecting interactions of RNA with other molecules1,2. As the appreciation for the number and variety of RNA modifications increases, it is critical to develop assays that can reliably interrogate both the RNA modifications and the enzymes that catalyze them.
One of the first RNA modifications to be identified occurs at base 37 in tRNAs, adjacent to the anti-codon on the 3&#39; side3,4. An isopentenyl group is transferred from dimethylallylpyrophosphate (DMAPP) to the N6 position of adenosine 37 (i6A37) 3,5 on a subset of both cytoplasmic and mitochondrial tRNAs. i6A37 improves translation fidelity and efficiency by increasing the tRNA&#39;s affinity for the ribosome4,6 and i6A37 is important for stress response in bacteria7. The enzymes that perform this modification are termed tRNA isopentenyl transferases and are highly conserved in bacteria8,9, fungi10, worms11, plants12, and higher eukaryotes13, including humans14.
Mutations in the human tRNA isopentenyl transferase gene, TRIT1, are associated with human disease. For example, a mutation in TRIT1 is correlated with a severe mitochondrial disease, likely caused by a defect in mitochondrial protein synthesis15,16. Furthermore, TRIT1 has been described as a tumor suppressor gene17,18 and is implicated in several types of cancers including melanoma19, breast20, gastric21, and lung cancers22,23. Finally, TRIT1 and Mod5 (Saccharomyces cerevisiae) isopentenyl transferases are aggregation-prone proteins that form prion-like amyloid fibers24,25,26. These observations potentially implicate tRNA isopentenyl transferases in neurodegenerative diseases, although direct evidence for this has not yet been shown.
Given the role that isopentenyl transferases play in translation and disease, methods that directly measure i6A isopentenyl transferase activity are important for a mechanistic understanding of these enzymes under normal and disease states. An increasing number of methods are available to detect i6A RNA modifications, including in vitro isopentenylation assays, positive hybridization in the absence of i6A (PHA6) assays, thin layer chromatography (TLC), amino acid acceptance activity assays, and mass spectrometry approaches (Reviewed in Ref. 4).
An in vitro isopentenylation assay has been described that utilizes 14C-DMAPP and unlabeled tRNAs. In this assay, radioactive carbon is transferred to RNA from 14C-DMAPP by the isopentenyl transferase. While this assay is highly sensitive, it is often difficult to determine the specific residue that is modified9,20,27. PHA6 assays rely on the bulky i6A modification interfering with hybridization of a 32P-labeled probe spanning the modified residue. As such, hybridization is greater in the absence of an i6A modification18,28,29. PHA6 assays are highly sensitive, and capable of analyzing total RNA extracted from cellular lysates. Additionally, the ability to design probes specific to the RNA of interest gives this method substantial target flexibility. However, PHA6 assays are limited to the characterization of modifications that occur on residues within the targeted region of the probe and therefore are less likely to identify novel modification sites. In addition, as absence of binding is indicative of modification, other modifications or mutations that affect RNA binding will confound data analysis.
Another approach combines benzyl DEAE cellulose (BD) cellulose chromatography with amino acid acceptance activity as a readout of i6A modifications in tRNA30. This approach directly assays the function of the i6A modification, but it is an indirect approach to detect i6A modification and lacks resolution to map modifications to a specific residue in the RNA. A TLC approach has been used to detect total tRNA i6A modifications. In this approach, internally 32P-labeled tRNAs are digested to single nucleotides and two-dimensional TLC analysis is used to identify isopentenylation. This approach is highly sensitive in detecting total i6A in a given RNA sample but upon digestion, all sequence information is lost; thus, the investigator has no way of determining which residues have been modified31.
More recently, liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods have been developed that quantitatively compare total RNA modifications between species, cell types, and experimental conditions32,33,34. A limitation of this methodology is that it is less able to determine the identity and position within the RNA from which the modified nucleoside was derived34. Furthermore, the expertise and equipment necessary to execute these experiments limit the practicality of this approach.
In addition, several next-generation sequencing technologies have been developed to map RNA modifications transcriptome-wide34. Immunoprecipitation of RNAs with antibodies specific to a particular modification (RIP-Seq) enable the investigator to identify all sequences containing a specific modification35,36. Additionally, reverse transcriptase-based approaches such as Chem-Seq and non-random mismatch sequencing rely on perturbations of the reverse transcription reaction at the modified residues37,38,39. Despite the advantage of these techniques to map RNA modifications transcriptome-wide, RIP-seq and Chem-Seq technologies are limited by the lack of reliable antibodies or reactive chemicals available for each specific modification, respectively34. Furthermore, reverse transcriptase enzymes required to perform Chem-Seq and non-random mismatch sequencing techniques can be impeded by stable RNA structures. The highly modified and structurally stable nature of tRNAs make them especially difficult to interrogate using these techniques. To date, next-generation sequencing-based technologies have not yet been utilized to map i6A modifications34.
Herein, we describe a simple and direct approach to detect i6A tRNA modifications in vitro. This method utilizes incubation of RNAs with recombinant S. cerevisiae isopentenyl transferase (Mod5), followed by RNase T1 digestion, and 1-dimensional gel electrophoresis analysis to map i6A modifications. This approach is direct and requires little specialized expertise to analyze the data. Furthermore, this method is adaptable to other RNA modifying enzymes, including enzymes that covalently change the molecular weight of RNA or an RNA&#39;s mobility through a gel.

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			<td style="width:176px;">National Diagnostics</td>
			<td style="width:119px;">EC-833</td>
			<td>As part of a kit</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">UreaGel Buffer</td>
			<td style="width:176px;">National Diagnostics</td>
			<td style="width:119px;">EC-833</td>
			<td>As part of a kit</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">10x TBE</td>
			<td style="width:176px;">National Diagnostics</td>
			<td style="width:119px;">EC-833</td>
			<td>As part of a kit</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Ammonium persulfate (APS)</td>
			<td style="width:176px;">Sigma-Aldrich</td>
			<td style="width:119px;">7727-54-0</td>
			<td></td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">N,N,N&#8242;,N&#8242;-Tetramethylethylenediamine (TMED)</td>
			<td style="width:176px;">Sigma-Aldrich</td>
			<td style="width:119px;">T9281</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Tris base</td>
			<td style="width:176px;">Sigma-Aldrich</td>
			<td style="width:119px;">T1503</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Boric acid</td>
			<td style="width:176px;">Sigma-Aldrich</td>
			<td style="width:119px;">10043-35-3</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">EDTA</td>
			<td style="width:176px;">Sigma-Aldrich</td>
			<td style="width:119px;">60-00-4</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">ATP</td>
			<td style="width:176px;">Sigma-Aldrich</td>
			<td style="width:119px;">34369-07-8</td>
			<td></td>
		</tr>
		<tr height="25">
			<td height="25" style="height:25px;width:216px;">MgCl2</td>
			<td style="width:176px;">Sigma-Aldrich</td>
			<td style="width:119px;">7786-30-3</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">DMAPP</td>
			<td style="width:176px;">Caymen Chemical</td>
			<td style="width:119px;">1186-30-7</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Super RNaseIN</td>
			<td style="width:176px;">ThermoFisher Scientific</td>
			<td style="width:119px;">AM2694</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">2-mercaptoethanol</td>
			<td style="width:176px;">Sigma-Aldrich</td>
			<td style="width:119px;">60-24-2</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Ethanol</td>
			<td style="width:176px;">Sigma-Aldrich</td>
			<td style="width:119px;">64-17-5</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Sodiume acetate</td>
			<td style="width:176px;">Sigma-Aldrich</td>
			<td style="width:119px;">127-09-3</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Rnase T1</td>
			<td style="width:176px;">ThermoFisher Scientific</td>
			<td style="width:119px;">EN0541</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Glycerol</td>
			<td style="width:176px;">Sigma-Aldrich</td>
			<td style="width:119px;">56-81-5</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Xylene cyanol</td>
			<td style="width:176px;">Sigma-Aldrich</td>
			<td style="width:119px;">2650-17-1</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Equipment and Supplies</td>
			<td style="width:176px;"></td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Short glass plates (20-40 cm W x 40 cm L)</td>
			<td style="width:176px;">The Gel Company</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Long glass plates (20-40 cm W x 40 cm L)</td>
			<td style="width:176px;">The Gel Company</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Vertical gel apparatus</td>
			<td style="width:176px;">The Gel Company</td>
			<td style="width:119px;">S2-3040</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">50 mL disposable syringe</td>
			<td style="width:176px;">Fisher Scientific</td>
			<td style="width:119px;">03-377-26</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Stainless steel binder clips</td>
			<td style="width:176px;">Idea Scientific</td>
			<td style="width:119px;">1066</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Phosphoscreen</td>
			<td style="width:176px;">Sigma-Aldrich</td>
			<td style="width:119px;">28-9564-74</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Plastic wrap</td>
			<td style="width:176px;">(local grocery store)</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
	</tbody>
</table>

an in vitro assay to detect trna-isopentenyl transferase activity

N6-isopentenyladenosine RNA modifications are functionally diverse and highly conserved among prokaryotes and eukaryotes. One of the most highly conserved N6-isopentenyladenosine modifications occurs at the A37 position in a subset of tRNAs. This modification improves translation efficiency and fidelity by increasing the affinity of the tRNA for the ribosome. Mutation of enzymes responsible for this modification in eukaryotes are associated with several disease states, including mitochondrial dysfunction and cancer. Therefore, understanding the substrate specificity and biochemical activities of these enzymes is important for understanding of normal and pathologic eukaryotic biology. A diverse array of methods has been employed to characterize i6A modifications. Herein is described a direct approach for the detection of isopentenylation by Mod5. This method utilizes incubation of RNAs with a recombinant isopentenyl transferase, followed by RNase T1 digestion, and 1-dimensional gel electrophoresis analysis to detect i6A modifications. In addition, the potential adaptability of this protocol to characterize other RNA-modifying enzymes is discussed.

Mod5 was incubated with a tyrosine tRNA or serine tRNA in the presence or absence of DMAPP. Following the modification reaction, products were RNase T1-digested, which cleaves the 3&#39; end of all guanosines leaving a 3&#39; guanosine monophosphates (GMP)24 (Figure 1). Full digestion of the RNAs produces a predictable pattern of radiolabeled fragments (Figure 2A), which are then resolved ...

Watch this Scientific Journal Video about An In Vitro Assay to Detect tRNA-Isopentenyl Transferase Activity at JoVE.com

An In Vitro Assay to Detect tRNA-Isopentenyl Transferase Activity

Here, we describe a protocol for the biochemical characterization of the yeast RNA-modifying enzyme, Mod5, and discuss how this protocol could be applied to other RNA-modifying enzymes.

An In Vitro Assay to Detect tRNA-Isopentenyl Transferase Activity

N6-isopentenyladenosine RNA modifications are functionally diverse and highly conserved among prokaryotes and eukaryotes. One of the most highly conserved ...

The overall goal of this protocol is to biochemically characterize tRNA-Isopentenyl Transferase Activity In Vitro. This method is useful for the in-vitro detection and characterization of tRNA-isopentenyl transferase activity of purified recombinant enzymes. The main advantage of this technique is that it is a simple and direct assay used to detect a covalent RNA modification.Though this method provides insight to tRNA-isopentenyl transferase activity, it's potentially adaptable for the biochemical characterization of wide range or RNA modifying enzymes. The first step in this procedure is to thoroughly clean the glass plates that will be used for casting the gel. Wash the plates with soap and water, rinse well with deionized water, and then clean the plates with isopropanol and lint-free wipes.Next, assemble the plates and spacers. Mix the following reagents to make a 100 milliliter 20%acrylamide, 7.5 molar urea, 1x TBE gel. 80 milliliters of urea gel concentrate, 10 milliliters of urea gel diluent, and 10 milliliters of urea gel buffer.Add 40 microliters of T-med and 800 microliters of freshly prepared 10%ammonium persulfate to the mixture. Draw the gel solution up into a large syringe and dispense the gel solution between the glass plates tapping on the glass while dispensing the solution to prevent bubble formation. Allow the gel to solidify at room temperature for 30 minutes.After the gel has solidified, plant the gel onto a vertical gel apparatus. Fill the upper and lower buffer chambers with 1x TBE. Two hours prior to loading the gel, pre-run the gel at 20 milliamps for two hours to allow the buffer boundary to out run the smallest oligonucleotides.Prepare each reaction for the RNA isopentenylation assay in a final volume of 17 microliters. Add to each tube 50 millimolor Tris-HCl, pH 7.2, 1.2 millimolar ATP, 5.8 millimolar magnesium chloride, 0.2 millimolar DMAPP, 10 units RNase inhibitor, 40, 000 CPM internally 32P labeled RNA, 5.3 micromolar Mod5, and 1.2 millimolar 2-mercaptoethanol. Incubate the reactions at 37 degrees Celsius for one hour.After one hour, ethanol precipitate the RNase using 2.5 volume of 100%ethanol and 1/10 volume of 3.5 molar sodium acetate pH 5.5, and place it negative 20 degrees Celsius for one hour overnight. Next, centrifuge the RNA samples at 15, 400 g's and four degrees Celsius for 20 minutes. Carefully remove the supernatant and wash each RNA pellet with 500 microliters of 70%ethanol.Centrifuge the samples at 15, 400 g's and four degrees Celsius for five minutes. Carefully remove the supernatant and air dry the RNA pellets for 15 minutes or until all ethanol has evaporated. Next re-suspend each RNA pellet in 10 microliters of eight molar urea.Add 150 units of RNase T1 to each sample and incubate at 37 degrees Celsius overnight. On the following day, add two microliters of 6x loading buffer to each sample. Load 10 microliters of each RNA sample on a pre-run, 20%polyacrylamide, 7.5 molar urea gel.Run the gel at 25 milliamps for two hours. After two hours, stop the electrophoresis and remove the gel from the apparatus. Break the seal between the two glass plates and carefully remove one of the glass plates with the gel remaining on either plate.Place a layer of plastic wrap over the gel and expose on a phosphorus screen for three hours. This protocol reliably detects isopentenylation of both canonical and noncanonical tRNA residues modified by the S.cerevisiae isopentenyl tranferase Mod5. In this example tyrosine tRNA was internally labeled with 32P-adenosine and Mod5 was incubated with RNase in the presence or absence of DMAPP.The RNAs were digested with RNase T1 and resolved on a denaturing polyacrylamide gel. Mod5 modifies the predicted residue in the presence of DMAPP and indicated by the shifted 10 nucleotide, triple adenosine containing fragment at nucleoside positions 36 through 38 contain fragment in the tyrosine tRNA. The modified adenosine 37 reside is indicated with an asterisk.Similarly when the serine tRNA is incubated with Mod5 and DMAPP, a complete shift of the 10 nucleotide triple adenosine containing fragment at nucleoside position 36 through 38 is observed. Interestingly, a partial shift of a seven nucleotide fragment is observed that does not contain the triple adenosine containing fragment at nucleoside positions 36 through 38, suggesting that the triple adenosine containing fragment at nucleoside position 36 through 38 sequence and structure may not be required for Mod5 in vitro activity. Once mastered this technique will take two, four to six hour days if it is performed properly.Well attempting this procedure it is important to remember to maintain and monitor the integrity of the RNA, because RNA degradation could effect the RNA modification and will confound data interpretation. Following this procedure mutational studies using your enzyme of interest, could be done to determine specific residues or domains required for enzymatic activity. After its development, this technique paved the way for researchers in the field of RNA biology, to say tRNA-isopentenyl transferase activities of prokaryotic and eukaryotic enzymes.After watching this video, you should have a good understanding of how to carryout the protocol for the detection of isopentenyl transferase activity of your enzyme of interest. Don't forget that working with radioactivity can be extremely hazardous and precautions such as wearing proper PPE, using adequate shielding, and disposing of radioactivity properly should always be taken while performing this procedure.

an-in-vitro-assay-to-detect-trna-isopentenyl-transferase-activity

Research

JoVE Journal

Biochemistry

Detection of the pH-dependent Activity of Escherichia coli Chaperone HdeB In Vitro and In Vivo

Bacteria are frequently exposed to environmental changes, such as alterations in pH, temperature, redox status, light exposure or mechanical force. Many of these conditions cause protein unfolding in the cell and have detrimental impact on the survival of the organism. A group of unrelated, stress-specific molecular chaperones have been shown to play essential roles in the survival of these stress conditions. While fully folded and chaperone-inactive before stress, these proteins rapidly unfold and become chaperone-active under specific stress conditions. Once activated, these conditionally disordered chaperones bind to a large number of different aggregation-prone proteins, prevent their aggregation and either directly or indirectly facilitate protein refolding upon return to non-stress conditions. The primary approach for gaining a more detailed understanding about the mechanism of their activation and client recognition involves the purification and subsequent characterization of these proteins using in vitro chaperone assays. Follow-up in vivo stress assays are absolutely essential to independently confirm the obtained in vitro results.
This protocol describes in vitro and in vivo methods to characterize the chaperone activity of E. coli HdeB, an acid-activated chaperone. Light scattering measurements were used as a convenient read-out for HdeB&#39;s capacity to prevent acid-induced aggregation of an established model client protein, MDH, in vitro. Analytical ultracentrifugation experiments were applied to reveal complex formation between HdeB and its client protein LDH, to shed light into the fate of client proteins upon their return to non-stress conditions. Enzymatic activity assays of the client proteins were conducted to monitor the effects of HdeB on pH-induced client inactivation and reactivation. Finally, survival studies were used to monitor the influence of HdeB&#39;s chaperone function in vivo.

Detection of the pH-dependent Activity of Escherichia coli Chaperone HdeB In Vitro and In Vivo

This study describes biophysical, biochemical and molecular techniques to characterize the chaperone activity of Escherichia coli HdeB under acidic pH conditions. These methods have been successfully applied for other acid-protective chaperones such as HdeA and can be modified to work for other chaperones and stress conditions.

Bacteria are frequently exposed to environmental changes, such as alterations in pH, temperature, redox status, light exposure or mechanical force. Many ...

A Fluorescence-based Assay of Phospholipid Scramblase Activity

Scramblases translocate phospholipids across the membrane bilayer bidirectionally in an ATP-independent manner. The first scramblase to be identified and biochemically verified was opsin, the apoprotein of the photoreceptor rhodopsin. Rhodopsin is a G protein-coupled receptor localized in rod photoreceptor disc membranes of the retina where it is responsible for the perception of light. Rhodopsin&#39;s scramblase activity does not depend on its ligand 11-cis-retinal, i.e., the apoprotein opsin is also active as a scramblase. Although constitutive and regulated phospholipid scrambling play an important role in cell physiology, only a few phospholipid scramblases have been identified so far besides opsin. Here we describe a fluorescence-based assay of opsin&#39;s scramblase activity. Opsin is reconstituted into large unilamellar liposomes composed of phosphatidylcholine, phosphatidylglycerol and a trace quantity of fluorescent NBD-labeled PC (1-palmitoyl-2-{6-[7-nitro-2-1,3-benzoxadiazole-4-yl)amino]hexanoyl}-sn-glycero-3-phosphocholine). Scramblase activity is determined by measuring the extent to which NBD-PC molecules located in the inner leaflet of the vesicle are able to access the outer leaflet where their fluorescence is chemically eliminated by a reducing agent that cannot cross the membrane. The methods we describe have general applicability and can be used to identify and characterize scramblase activities of other membrane proteins.

We describe a fluorescence-based assay to measure phospholipid scrambling in large unilamellar liposomes reconstituted with opsin.

Scramblases translocate phospholipids across the membrane bilayer bidirectionally in an ATP-independent manner. The first scramblase to be identified and ...

Identification of Cyclin-dependent Kinase 1 Specific Phosphorylation Sites by an In Vitro Kinase Assay

Cyclin-dependent kinase 1 (Cdk1) is a master controller for the cell cycle in all eukaryotes and phosphorylates an estimated 8 - 13% of the proteome; however, the number of identified targets for Cdk1, particularly in human cells is still low. The identification of Cdk1-specific phosphorylation sites is important, as they provide mechanistic insights into how Cdk1 controls the cell cycle. Cell cycle regulation is critical for faithful chromosome segregation, and defects in this complicated process lead to chromosomal aberrations and cancer.
Here, we describe an in vitro kinase assay that is used to identify Cdk1-specific phosphorylation sites. In this assay, a purified protein is phosphorylated in vitro by commercially available human Cdk1/cyclin B. Successful phosphorylation is confirmed by SDS-PAGE, and phosphorylation sites are subsequently identified by mass spectrometry. We also describe purification protocols that yield highly pure and homogeneous protein preparations suitable for the kinase assay, and a binding assay for the functional verification of the identified phosphorylation sites, which probes the interaction between a classical nuclear localization signal (cNLS) and its nuclear transport receptor karyopherin &#945;. To aid with experimental design, we review approaches for the prediction of Cdk1-specific phosphorylation sites from protein sequences. Together these protocols present a very powerful approach that yields Cdk1-specific phosphorylation sites and enables mechanistic studies into how Cdk1 controls the cell cycle. Since this method relies on purified proteins, it can be applied to any model organism and yields reliable results, especially when combined with cell functional studies.

Identification of Cyclin-dependent Kinase 1 Specific Phosphorylation Sites by an In Vitro Kinase Assay

Cyclin-dependent kinase 1 (Cdk1) is activated in the G2 phase of the cell cycle and regulates many cellular pathways. Here, we present a protocol for an in vitro kinase assay with Cdk1, which allows the identification of Cdk1-specific phosphorylation sites for establishing cellular targets of this important kinase.

Cyclin-dependent kinase 1 (Cdk1) is a master controller for the cell cycle in all eukaryotes and phosphorylates an estimated 8 - 13% of the proteome; ...

Quantification of Hypopigmentation Activity In Vitro

This study presents laboratory methods for the quantification of hypopigmentation activity in vitro. Melanin, the major pigment in melanocytes, is synthesized in response to multiple cellular and environmental factors. Melanin protects skin cells from ultraviolet damage, but also has biophysical and biochemical functions. Excessive production or accumulation of melanin in melanocytes can cause dermatological problems, such as freckles, dark spots, melasma, and moles. Therefore, the control of melanogenesis with hypopigmentation agents is important in individuals with clinical or cosmetic needs. Melanin is primarily synthesized in the melanosomes of melanocytes in a complex biochemical process called melanogenesis, which is influenced by extrinsic and intrinsic factors, such as hormones, inflammation, age, and ultraviolet light exposure. We describe three methods to determine the hypopigmentation activity of chemicals or natural substances in melanocytes: measurement of the 1) cellular tyrosinase activity and 2) melanin content, and 3) staining and quantifying cellular melanin with image analysis.
In melanogenesis, tyrosinase catalyzes the rate-limiting step that converts L-tyrosine into 3,4-dihydroxyphenylalanine (L-DOPA) and then into dopaquinone. Therefore, the inhibition of tyrosinase is a primary hypopigmentation mechanism. In cultured melanocytes, tyrosinase activity can be quantified by adding L-DOPA as a substrate and measuring dopaquinone production by spectrophotometry. Melanogenesis can also be measured by quantifying the melanin content. The melanin-containing cellular fraction is extracted with NaOH and melanin is quantified spectrophotometrically. Finally, the melanin content can be quantified by image analysis following Fontana-Masson staining of melanin. Although the results of these in vitro assays may not always be reproduced in human skin, these methods are widely used in melanogenesis research, especially as the initial step to identify potential hypopigmentation activity. These methods can also be used to assess melanocyte activity, growth, and differentiation. Consistent results with the three different methods ensure the validity of the effects.

We describe three experimental methods for evaluating the hypopigmentation activity of chemicals in vitro: quantification of 1) cellular tyrosinase activity and 2) melanin content, and 3) measurement of melanin by cellular melanin staining and image analysis.

This study presents laboratory methods for the quantification of hypopigmentation activity in vitro. Melanin, the major pigment in melanocytes, is ...

A Fluorogenic Peptide Cleavage Assay to Screen for Proteolytic Activity: Applications for coronavirus spike protein activation

Enveloped viruses such as coronaviruses or influenza virus require proteolytic cleavage of their fusion protein to be able to infect the host cell. Often viruses exhibit cell and tissue tropism and are adapted to specific cell or tissue proteases. Moreover, these viruses can introduce mutations or insertions into their genome during replication that may affect the cleavage, and thus can contribute to adaptations to a new host. Here, we present a fluorogenic peptide cleavage assay that allows a rapid screening of peptides mimicking the cleavage site of viral fusion proteins. The technique is very flexible and can be used to investigate the proteolytic activity of a single protease on many different substrates, and in addition, it also allows exploration of the activity of multiple proteases on one or more peptide substrates. In this study, we used peptides mimicking the cleavage site motifs of the coronavirus spike protein. We tested human and camel derived Middle East Respiratory Syndrome coronaviruses (MERS-CoV) to demonstrate that single and double substitutions in the cleavage site can alter the activity of furin and dramatically change cleavage efficiency. We also used this method in combination with bioinformatics to test furin cleavage activity of feline coronavirus spike proteins from different serotypes and strains. This peptide-based method is less labor- and time intensive than conventional methods used for the analysis of proteolytic activity for viruses, and results can be obtained within a single day.

We present a fluorogenic peptide cleavage assay that allows a rapid screening of the proteolytic activity of proteases on peptides representing the cleavage site of viral fusion peptides. This method can also be used on any other amino acid motif within a protein sequence to test for the protease activity.

Enveloped viruses such as coronaviruses or influenza virus require proteolytic cleavage of their fusion protein to be able to infect the host cell. Often ...

A Colorimetric Assay of Citrate Synthase Activity in Drosophila Melanogaster

Mitochondria play the most prominent roles in cellular metabolism by producing ATP through oxidative phosphorylation and regulating a variety of physiological processes. Mitochondrial dysfunction is a primary cause of a number of metabolic and neurodegenerative diseases. Intact mitochondria are critical for their proper functioning. The enzyme citrate synthase is localized in the mitochondrial matrix and thus can be used as a quantitative enzyme marker of intact mitochondrial mass. Given that many molecules and pathways that have important functions in mitochondria are highly conserved between humans and Drosophila, and that an array of powerful genetic tools are available in Drosophila, Drosophila serves as a good model system for studying mitochondrial function. Here, we present a protocol for fast and simple measurement of citrate synthase activity in tissue homogenate from adult flies without isolating mitochondria. This protocol is also suitable for measuring citrate synthase activity in larvae, cultured cells, and mammalian tissues.

A Colorimetric Assay of Citrate Synthase Activity in Drosophila Melanogaster

We present a protocol for a colorimetric assay of citrate synthase activity for quantification of intact mitochondrial mass in Drosophila tissue homogenates.

Mitochondria play the most prominent roles in cellular metabolism by producing ATP through oxidative phosphorylation and regulating a variety of ...

An In Vitro Single-Molecule Imaging Assay for the Analysis of Cap-Dependent Translation Kinetics

Cap-dependent protein synthesis is the predominant translation pathway in eukaryotic cells. While various biochemical and genetic approaches have allowed extensive studies of cap-dependent translation and its regulation, high resolution kinetic characterization of this translation pathway is still lacking. Recently, we developed an in vitro assay to measure cap-dependent translation kinetics with single-molecule resolution. The assay is based on fluorescently labeled antibody binding to nascent epitope-tagged polypeptide. By imaging the binding and dissociation of antibodies to and from nascent peptide&#8211;ribosome&#8211;mRNA complexes, the translation progression on individual mRNAs can be tracked. Here, we present a protocol for establishing this assay, including mRNA and PEGylated slide preparations, real-time imaging of translation, and analysis of single molecule trajectories. This assay enables tracking of individual cap-dependent translation events and resolves key translation kinetics, such as initiation and elongation rates. The assay can be widely applied to distinct translation systems and should broadly benefit in vitro studies of cap-dependent translation kinetics and translational control mechanisms.

An In Vitro Single-Molecule Imaging Assay for the Analysis of Cap-Dependent Translation Kinetics

Tracking individual translation events allows for high-resolution kinetic studies of cap-dependent translation mechanisms. Here we demonstrate an in vitro single-molecule assay based on imaging interactions between fluorescently labeled antibodies and epitope-tagged nascent peptides. This method enables single-molecule characterization of initiation and peptide elongation kinetics during active in vitro cap-dependent translation.

Cap-dependent protein synthesis is the predominant translation pathway in eukaryotic cells. While various biochemical and genetic approaches have allowed ...

A High-Throughput Enzyme-Coupled Activity Assay to Probe Small Molecule Interaction with the dNTPase SAMHD1

Sterile alpha motif and HD domain-containing protein 1 (SAMHD1) is a pivotal regulator of intracellular deoxynucleoside triphosphate (dNTP) pools, as this enzyme can hydrolyze dNTPs into their corresponding nucleosides and inorganic triphosphates. Due to its critical role in nucleotide metabolism, its association to several pathologies, and its role in therapy resistance, intense research is currently being carried out for a better understanding of both the regulation and cellular function of this enzyme. For this reason, development of simple and inexpensive high-throughput amenable methods to probe small molecule interaction with SAMHD1, such as allosteric regulators, substrates, or inhibitors, is vital. To this purpose, the enzyme-coupled malachite green assay is a simple and robust colorimetric assay that can be deployed in a 384-microwell plate format allowing the indirect measurement of SAMHD1 activity. As SAMHD1 releases the triphosphate group from nucleotide substrates, we can couple a pyrophosphatase activity to this reaction, thereby producing inorganic phosphate, which can be quantified by the malachite green reagent through the formation of a phosphomolybdate malachite green complex. Here, we show the application of this methodology to characterize known inhibitors of SAMHD1 and to decipher the mechanisms involved in SAMHD1 catalysis of non-canonical substrates and regulation by allosteric activators, exemplified by nucleoside-based anticancer drugs. Thus, the enzyme-coupled malachite green assay is a powerful tool to study SAMHD1, and furthermore, could also be utilized in the study of several enzymes which release phosphate species.

SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase with critical roles in human health and disease. Here we present a versatile enzyme-coupled SAMHD1 activity assay, deployed in a 384-well microplate format, that allows for the evaluation of small molecules and nucleotide analogues as SAMHD1 substrates, activators, and inhibitors.

Sterile alpha motif and HD domain-containing protein 1 (SAMHD1) is a pivotal regulator of intracellular deoxynucleoside triphosphate (dNTP) pools, as this ...

Continuous Fluorescence-Based Endonuclease-Coupled DNA Methylation Assay to Screen for DNA Methyltransferase Inhibitors

DNA methylation, a form of epigenetic gene regulation, is important for normal cellular function. In cells, proteins called DNA methyltransferases (DNMTs) establish and maintain the DNA methylation pattern. Changes to the normal DNA methylation pattern are linked to cancer development and progression, making DNMTs potential cancer drug targets. Thus, identifying and characterizing novel small molecule inhibitors of these enzymes is of great importance. This paper presents a protocol that can be used to screen for DNA methyltransferase inhibitors. The continuous coupled kinetics assay allows for initial velocities of DNA methylation to be determined in the presence and absence of potential small molecule inhibitors. The assay uses the methyl-sensitive endonuclease Gla I to couple methylation of a hemimethylated DNA substrate to fluorescence generation.
This continuous assay allows for enzyme activity to be monitored in real time. Conducting the assay in small volumes in microtiter plates reduces the cost of reagents. Using this assay, a small example screen was conducted for inhibitors of DNMT1, the most abundant DNMT isozyme in humans. The highly substituted anthraquinone natural product, laccaic acid A, is a potent, DNA-competitive inhibitor of DNMT1. Here, we examine three potential small molecule inhibitors &#8212; anthraquinones or anthraquinone-like molecules with one to three substituents &#8212; at two concentrations to describe the assay protocol. Initial velocities are used to calculate the percent activity observed in the presence of each molecule. One of three compounds examined exhibits concentration-dependent inhibition of DNMT1 activity, indicating that it is a potential inhibitor of DNMT1.

DNA methyltransferases are potential cancer drug targets. Here, a protocol is presented to assess small molecules for DNA methyltransferase inhibition. This assay utilizes an endonuclease to couple DNA methylation to fluorescence generation and allows for enzyme activity to be monitored in real time.&#160;

DNA methylation, a form of epigenetic gene regulation, is important for normal cellular function. In cells, proteins called DNA methyltransferases (DNMTs) ...

DetectSyn: A Rapid, Unbiased Fluorescent Method to Detect Changes in Synapse Density

Synapses are the site of communication between neurons. Neuronal circuit strength is related to synaptic density, and the breakdown of synapses is characteristic of disease states like major depressive disorder (MDD) and Alzheimer's disease. Traditional techniques to investigate synapse numbers include genetic expression of fluorescent markers (e.g., green fluorescent protein (GFP)), dyes that fill a neuron (e.g., carbocyanine dye, DiI), and immunofluorescent detection of spine markers (e.g., postsynaptic density 95 (PSD95)). A major caveat to these proxy techniques is that they only identify postsynaptic changes. Yet, a synapse is a connection between a presynaptic terminal and a postsynaptic spine. The gold standard for measuring synapse formation/elimination requires time-consuming electron microscopy or array tomography techniques. These techniques require specialized training and costly equipment. Further, only a limited number of neurons can be assessed and are used to represent changes to an entire brain region. DetectSyn is a rapid fluorescent technique that identifies changes to synapse formation or elimination due to a disease state or drug activity. DetectSyn utilizes a rapid proximity ligation assay to detect juxtaposed pre- and postsynaptic proteins and standard fluorescent microscopy, a technique readily available to most laboratories. Fluorescent detection of the resulting puncta allows for quick and unbiased analysis of experiments. DetectSyn provides more representative results than electron microscopy because larger areas can be analyzed than a limited number of fluorescent neurons. Moreover, DetectSyn works for in vitro cultured neurons and fixed tissue slices. Finally, a method is provided to analyze the data collected from this technique. Overall, DetectSyn offers a procedure for detecting relative changes in synapse density across treatments or disease states and is more accessible than traditional techniques.

DetectSyn is an unbiased, rapid fluorescent assay that measures changes in relative synapse (pre- and postsynaptic engagement) number across treatments or disease states. This technique utilizes a proximity ligation technique that can be used both in cultured neurons and fixed tissue.