Name: using secm arrest sequence as a tool to isolate ribosome bound polypeptides
Uploaded: 2012-06-19T12:00:00
Description: Watch this Scientific Journal Video about Using SecM Arrest Sequence as a Tool to Isolate Ribosome Bound Polypeptides at JoVE.com

This work was funded by Human Frontier Science Program grant RGP0024.

1. DNA Template Preparation and in vitro Transcription
<ol>
 <li>The gene of interest is cloned in any T7 and/or e.g. SP6 promoter based plasmid. To obtain RNCs of interest, C-terminus of the target polypeptide is extended by adding arrest inducing sequence of SecM FXXXXWIXXXXGIRAGP7. In order to ensure that the polypeptide fragment of interest will extrude out of the ribosomal tunnel, the C-terminal part of the target protein has to be extended by at least 30 amino acids12-14. A flexible...

<ol>
	<li>Fedorov, A. N., Baldwin, T. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cotranslational+protein+folding.">Cotranslational protein folding.</a> J. Biol. Chem. 272, 32715-32718 (1997).</li><li>Hardesty, B., Kramer, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Folding+of+a+nascent+peptide+on+the+ribosome.">Folding of a nascent peptide on the ribosome.</a> Prog. Nucleic Acid Res. Mol. Biol. 66, 41-66 (2001).</li><li>Kramer, G., Boehringer, D., Ban, N., Bukau, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+ribosome+as+a+platform+for+co-translational+processing,+folding+and+targeting+of+newly+synthesized+proteins.">The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins.</a> Nat. Struct. Mol. Biol. 16, 589-597 (2009).</li><li>Komar, A. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+pause+for+thought+along+the+co-translational+folding+pathway.">A pause for thought along the co-translational folding pathway.</a> Trends Biochem. Sci. 34, 16-24 (2009).</li><li>Cabrita, L. D., Dobson, C. M., Christodoulou, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+folding+on+the+ribosome.">Protein folding on the ribosome.</a> Curr. Opin. Struct. Biol. 20, 33-45 (2010).</li><li>Oliver, D., Norman, J., Sarker, S. <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+Escherichia+coli+secA+by+cellular+protein+secretion+proficiency+requires+an+intact+gene+X+signal+sequence+and+an+active+translocon.">Regulation of Escherichia coli secA by cellular protein secretion proficiency requires an intact gene X signal sequence and an active translocon.</a> J. Bacteriol. 180, 5240-5242 (1998).</li><li>Nakatogawa, H., Ito, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+ribosomal+exit+tunnel+functions+as+a+discriminating+gate.">The ribosomal exit tunnel functions as a discriminating gate.</a> Cell. 108, 629-636 (2002).</li><li>Nakatogawa, H., Ito, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Secretion+monitor,+SecM,+undergoes+self-translation+arrest+in+the+cytosol.">Secretion monitor, SecM, undergoes self-translation arrest in the cytosol.</a> Mol. Cell. 7, 185-192 .</li><li>Muto, H., Nakatogawa, H., Ito, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genetically+encoded+but+non+polypeptide+prolyl-tRNA+functions+in+the+A+site+for+SecM-mediated+ribosomal+stall.">Genetically encoded but non polypeptide prolyl-tRNA functions in the A site for SecM-mediated ribosomal stall.</a> Mol. Cell. 22, 545-552 (2006).</li><li>Cabrita, L. D., Hsu, S. T., Launay, H., Dobson, C. M., Christodoulou, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Probing+ribosome-nascent+chain+complexes+produced+in+vivo+by+NMR+spectroscopy.">Probing ribosome-nascent chain complexes produced in vivo by NMR spectroscopy.</a> Proc. Natl. Acad. Sci. U.S.A. 106, 22239-22244 (2009).</li><li>Eichmann, C., Preissler, S., Riek, R., Deuerling, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cotranslational+structure+acquisition+of+nascent+polypeptides+monitored+by+NMR+spectroscopy.">Cotranslational structure acquisition of nascent polypeptides monitored by NMR spectroscopy.</a> Proc. Natl. Acad. Sci. USA. 107, 9111-9116 (2010).</li><li>Kolb, V. A., Makeyev, E. V., Spirin, A. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enzymatic+activity+of+the+ribosome-bound+nascent+polypeptide.">Enzymatic activity of the ribosome-bound nascent polypeptide.</a> FEBS Lett. 378, 166-170 (1996).</li><li>Ban, N., Nissen, P., Hansen, J., Moore, P. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+complete+atomic+structure+of+the+large+ribosomal+subunit+at+2.4+Å+resolution.">The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution.</a> Science. 289, 905-920 (2000).</li><li>Voss, N. R., Gerstein, M., Steitz, T. A., Moore, P. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+geometry+of+the+ribosomal+polypeptide+exit+tunnel.">The geometry of the ribosomal polypeptide exit tunnel.</a> J. Mol. Biol. 360, 893-906 (2006).</li><li>Sch&#228;gger, H., von Jagow, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tricine-sodium+dodecyl+sulfate-polyacrylamide+gel+electrophoresis+for+the+separation+of+proteins+in+the+range+from+1+to+100+kDa.">Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa.</a> Anal. Biochem. 166, 368-379 (1987).</li><li>Komar, A. A., Kommer, A., Krasheninnikov, I. A., Spirin, A. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cotranslational+folding+of+globin.">Cotranslational folding of globin.</a> J. Biol. Chem. 272, 10646-10651 (1997).</li><li>Keiler, K. C., Waller, P. R., Sauer, R. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Role+of+a+peptide+tagging+system+in+degradation+of+proteins+synthesized+from+damaged+messenger+RNA.">Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA.</a> Science. 271, 990-993 (1996).</li><li>Evans, M. S., Ugrinov, K. G., Frese, M. A., Clark, P. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Homogeneous+stalled+ribosome+nascent+chain+complexes+produced+in+vivo+or+in+vitro.">Homogeneous stalled ribosome nascent chain complexes produced in vivo or in vitro.</a> Nat. Methods. 2, 757-762 (2005).</li></ol>

For reproducible results, quality and concentration of the components used for in vitro transcription and translation are critical. We have used commercially available in vitro transcription and translation extracts and they give efficient and reproducible results, if handled carefully. Quality of mRNA can affect the translation, so it is of utmost importance to test the integrity of mRNA before using it for in vitro translation. Incubation time for in vitro translation varies with the...

<table border="1">
	<tbody>
		<tr>
			<td>Name of reagent/ Kit</td>
			<td>Company</td>
			<td>Catalogue number</td>
		</tr>
		<tr>
			<td>MEGAscript T7 High yield Transcription Kit</td>
			<td>Ambion</td>
			<td>AM1333</td>
		</tr>
		<tr>
			<td>RTS 100 E.coli HY Kit</td>
			<td>5 Prime</td>
			<td>2401100</td>
		</tr>
		<tr>
			<td>Ribonuclease Inhibitor</td>
			<td>Invitrogen</td>
			<td>15518012</td>
		</tr>
		<tr>
			<td>Trans [35S]-Label</td>
			<td>MP Biomedicals</td>
			<td>0151006</td>
		</tr>
		<tr>
			<td>Amicon Ultra-4 Centrifugal Filter Unit</td>
			<td>Millipore</td>
			<td>UFC801008</td>
		</tr>
		<tr>
			<td>Storage phosphor autoradiography</td>
			<td>GE Healthcare</td>
			<td>Typhoon 9410 variable mode imager</td>
		</tr>
		<tr>
			<td>Density Gradient Fractionation Systems</td>
			<td>Teledyne Isco, Inc.</td>
			<td>ISCO Programmable Density Gradient System</td>
		</tr>
		<tr>
			<td>Sucrose Gradient Centrifugation</td>
			<td>Beckman Coulter</td>
			<td>Optima L-90 K Preparative Ultracentrifuge</td>
		</tr>
	</tbody>
</table>

using secm arrest sequence as a tool to isolate ribosome bound polypeptides

Extensive research has provided ample evidences suggesting that protein folding in the cell is a co-translational process1-5. However, the exact pathway that polypeptide chain follows during co-translational folding to achieve its functional form is still an enigma. In order to understand this process and to determine the exact conformation of the co-translational folding intermediates, it is essential to develop techniques that allow the isolation of RNCs carrying nascent chains of predetermined sizes to allow their further structural analysis.
SecM (secretion monitor) is a 170 amino acid E. coli protein that regulates expression of the downstream SecA (secretion driving) ATPase in the secM-secA operon6. Nakatogawa and Ito originally found that a 17 amino acid long sequence (150-FSTPVWISQAQGIRAGP-166) in the C-terminal region of the SecM protein is sufficient and necessary to cause stalling of SecM elongation at Gly165, thereby producing peptidyl-glycyl-tRNA stably bound to the ribosomal P-site7-9. More importantly, it was found that this 17 amino acid long sequence can be fused to the C-terminus of virtually any full-length and/or truncated protein thus allowing the production of RNCs carrying nascent chains of predetermined sizes7. Thus, when fused or inserted into the target protein, SecM stalling sequence produces arrest of the polypeptide chain elongation and generates stable RNCs both in vivo in E. coli cells and in vitro in a cell-free system. Sucrose gradient centrifugation is further utilized to isolate RNCs.
The isolated RNCs can be used to analyze structural and functional features of the co-translational folding intermediates. Recently, this technique has been successfully used to gain insights into the structure of several ribosome bound nascent chains10,11. Here we describe the isolation of bovine Gamma-B Crystallin RNCs fused to SecM and generated in an in vitro translation system.

Watch this Scientific Journal Video about Using SecM Arrest Sequence as a Tool to Isolate Ribosome Bound Polypeptides at JoVE.com

Using SecM Arrest Sequence as a Tool to Isolate Ribosome Bound Polypeptides

We describe here a technique that is now routinely used to isolate stably bound ribosome nascent chain complexes (RNCs). This technique takes advantage of the discovery that a 17 amino acid long SecM "arrest sequence" can halt translation elongation in a prokaryotic (E. coli) system, when inserted into (or fused to the C-terminus) of virtually any protein.

Extensive research has provided ample evidences suggesting that protein folding in the cell is a co-translational process1-5. However, the exact pathway ...

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