Name: identifying protein-protein interaction in drosophila adult heads by tandem affinity purification (tap)
Uploaded: 2013-12-05T17:00:00
Description: Watch this Scientific Journal Video about Identifying Protein-protein Interaction in Drosophila Adult Heads by Tandem Affinity Purification TAP at JoVE.com

We thank EUROSARF for sending us yeast TAP expression plasmids. We are also grateful for editorial help from Ryan Labadens. This work was supported by a NIH/NINDS grant (R01NS070962) to C.W.

1. Generate UAS-TAP-tagged Transgenic Flies
<ol>
	<li>Generate pUAST-TAP-tagged DNA constructs.
	<ol>
		<li>Decide which side (N- or C-terminus) of the bait protein the TAP tag should be fused to, based on the protein&#39;s structure/function. See discussion for more details.</li>
		<li>Subclone the cDNA coding region of the gene of interest into the multiple cloning sites (MCS) of the pUAST-NTAP or pUAST-CTAP vectors to generate N- or C-terminal-tagged UAS-TAP transgenes, respectively. See Figure 1 fo...

<ol>
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Tandem affinity purification (TAP) method offers a dual purification protocol that allows the isolation and enrichment of protein complexes through two independent affinity purification steps. The design of the TAP tag is not restricted to what is presented in this protocol, other protein binding domains and motifs are also applicable if buffer conditions are adjusted accordingly. A good example of other TAP tags is the GS-TAP tag, a combination of a G protein and a streptavidin-binding motif, designed by Giulio Superti-...

Defining the molecular pathways or networks that mediate a particular biological process is one of the ultimate goals of biomedical research. Fly geneticists have depended heavily on forward genetics, especially modifier genetic screens (both enhancer and suppressor screens), to identify factors that work together, in parallel with, or upstream or downstream of a gene of interest. However, forward genetics screens often times fail to identify essential genes which, when mutated, cause lethality at early developmental stages, or genes with functional redundancy and compensation whose loss of function only cause subtle defects that are hard to score. One way to overcome this difficulty is to screen for direct protein-protein interactions. For more than a decade, a growing list of biochemical methods, including yeast two-hybrid, phage display, chemical cross-linking, Co-IP, Tandem Affinity Purification (TAP), etc.&#160;have been used to investigate protein-protein interactions. Each of these approaches has its own set of strengths and weaknesses in regards to sensitivity and specificity.&#160; Among them, the TAP method allows for detection of physical interaction under near-physiological conditions, &#160;preserves specificity and consistency2&#160;and includes the ability to extend to high-throughput analyses3,4.
The TAP method was originally developed in yeast by Rigautand colleagues1. In this method, a protein of interest is expressed with a TAP tag. The TAP tag harbors two independent affinity-binding domains: a Protein A domain that binds to IgG and a calmodulin-binding domain. The two domains are separated by a TEV (Tobacco Etch Virus) cleavage site. Such a combination allows for two independent rounds of affinity purifications to sufficiently reduce nonspecific bindings and enrich specific bindings1. For this instance, the TAP method is a very powerful method to identify in vivo interactions of a given protein, although overexpressing the exogenous protein may make it more prone to associate with proteins that normally don&#39;t complex with its endogenous counterpart. Since its development, the TAP method has been applied in many other systems, including cell-culture-based systems5,6 and other in vivo model systems6-9. Here we describe the adaptation of the TAP method in Drosophila. We first generate pUAST-NTAP and pUAST-CTAP vectors to facilitate cloning and fusion of the TAP tag to either the N- or C-terminal of the gene of interest. The UAS-TAP-tagged transgene is then expressed in the nervous system under the control of a neuronal GAL4 driver10. Next, a large number of adult fly heads will be collected, which have high content of neural cells and are easy to separate from other body parts after freezing based on size differences. The adult heads are homogenized and cleared by sequential centrifugations, and the supernatant is subject to a TAP procedure described below.

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	<tbody>
		<tr height="42">
			<td height="42" style="height:42px;width:307px;">U.S.A. standard test sieve No. 25</td>
			<td style="width:104px;">Fisher Scientific&#160;</td>
			<td style="width:119px;">04-881-18&#160;</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">U.S.A. standard test sieve No. 40</td>
			<td style="width:104px;">Fisher Scientific&#160;</td>
			<td style="width:119px;">04-881-21</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">&#160;Kontes Dounce Tissue Grinders 15 ml</td>
			<td>Kimble Chase</td>
			<td>885300-0015</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:307px;"></td>
			<td style="width:104px;"></td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">IgG sepharose beads</td>
			<td>Pharmacia</td>
			<td style="width:119px;">17-0969-01</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Econo-column 0.7 cm x 20 cm</td>
			<td style="width:104px;">Bio-Rad</td>
			<td style="width:119px;">737-4721</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Econo-column 0.5 cm x 15 cm</td>
			<td style="width:104px;">Bio-Rad</td>
			<td style="width:119px;">737-4716</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Calmodulin beads</td>
			<td style="width:104px;">Stratagene</td>
			<td style="width:119px;">214303</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Coors Mortar and Pestle</td>
			<td style="width:104px;">CoorsTek</td>
			<td>60311</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">AcTEV Protease</td>
			<td style="width:104px;">Invitrogen</td>
			<td style="width:119px;">12575-015</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Protease Inhibitor Cocktail</td>
			<td style="width:104px;">Roche</td>
			<td style="width:119px;">11836153001</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Protease Inhibitor Mix</td>
			<td style="width:104px;">Sigma</td>
			<td style="width:119px;">P8340</td>
			<td></td>
		</tr>
	</tbody>
</table>

identifying protein-protein interaction in drosophila adult heads by tandem affinity purification (tap)

Genetic screens conducted using Drosophila melanogaster (fruit fly) have made numerous milestone discoveries in the advance of biological sciences. However, the use of biochemical screens aimed at extending the knowledge gained from genetic analysis was explored only recently. Here we describe a method to purify the protein complex that associates with any protein of interest from adult fly heads. This method takes advantage of the Drosophila GAL4/UAS system to express a bait protein fused with a Tandem Affinity Purification (TAP) tag in fly neurons in vivo, and then implements two rounds of purification using a TAP procedure similar to the one originally established in yeast1 to purify the interacting protein complex. At the end of this procedure, a mixture of multiple protein complexes is obtained whose molecular identities can be determined by mass spectrometry. Validation of the candidate proteins will benefit from the resource and ease of performing loss-of-function studies in flies. Similar approaches can be applied to other fly tissues. We believe that the combination of genetic manipulations and this proteomic approach in the fly model system holds tremendous potential for tackling fundamental problems in the field of neurobiology and beyond.

Here we demonstrate our effort in identifying Highwire-interacting proteins in the fly brain. Highwire (Hiw) and its vertebrate and invertebrate homologues are huge ubiquitin ligases that regulate the development and repair of the nervous system14. They share a number of highly conserved functional domains.&#160;However, their molecular actions are not entirely clear. Work done in worm, fly and mouse led to the current working model that Hiw functions as an E3 ligase and as a scaffolding protein to facilitate ...

Watch this Scientific Journal Video about Identifying Protein-protein Interaction in Drosophila Adult Heads by Tandem Affinity Purification TAP at JoVE.com

Identifying Protein-protein Interaction in Drosophila Adult Heads by Tandem Affinity Purification TAP

Drosophila is famous for its powerful genetic manipulation, but not for its suitability of in-depth biochemical analysis. Here we present a TAP-based procedure to identify interacting partners of any protein of interest from the fly brain. This procedure can potentially lead to new avenues of research.

Identifying Protein-protein Interaction in Drosophila Adult Heads by Tandem Affinity Purification (TAP)

Genetic screens conducted using Drosophila melanogaster (fruit fly) have made numerous milestone discoveries in the advance of biological sciences. ...

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