Name: Author Spotlight: Direct Synthesis of EM-Visible Gold Nanoparticles in Cells for Protein Localization Analysis with Well-Preserved Ultrastructure
Uploaded: 2023-04-28T12:20:00
Description: Watch this Scientific Journal Video about Direct Synthesis of EM-Visible Gold Nanoparticles in Cells for Protein Localization Analysis with Well-Preserved Ultrastructure at JoVE.com

The protocol described here was derived from the article published by Jiang et al. (2020). This work was supported by grants from the MOST (973 Programs nos. 2011CB812502 and 2014CB849902) and by funding support from the Beijing Municipal Government.

All the supplies used in this experiment are listed in the Table of Materials. The step-by-step workflow of the current protocol is shown in Figure 1.
1. Cell culture on sapphire discs
<ol>
	<li>Transfer 3 mm x 0.16 mm sapphire discs to a 2 mL centrifuge tube containing 1 mL of ethanol, and sonicate in an ultrasonic cleaner for 10 min.</li>
	<li>Burn each sapphire disc in an alcohol lamp flame until there are no visible deposits...

Direct Synthesis of Gold Nanoparticles for Protein Localization Analysis

<ol>
	<li>Tsien, R. 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+green+fluorescent+protein.">The green fluorescent protein.</a> Annual Review of Biochemistry. 67, 509-544 (1998).</li><li>Shaner, N. C., Patterson, G. H., Davidson, M. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advances+in+fluorescent+protein+technology.">Advances in fluorescent protein technology.</a> Journal of Cell Science. 120, 4247-4260 (2007).</li><li>Masters, B. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=History+of+the+electron+microscope+in+cell+biology.">History of the electron microscope in cell biology.</a> Encylopedia of Life Sciences. , (2009).</li><li>Griffiths, G., Hoppeler, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitation+in+immunocytochemistry:+Correlation+of+immunogold+labeling+to+absolute+number+of+membrane+antigens.">Quantitation in immunocytochemistry: Correlation of immunogold labeling to absolute number of membrane antigens.</a> Journal of Histochemistry &amp; Cytochemistry. 34 (11), 1389-1398 (1986).</li><li>Tokuyasu, K. 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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=Engineered+ascorbate+peroxidase+as+a+genetically+encoded+reporter+for+electron+microscopy.">Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy.</a> Nature Biotechnology. 30 (11), 1143-1148 (2012).</li><li>Lam, S. 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=Directed+evolution+of+APEX2+for+electron+microscopy+and+proximity+labeling.">Directed evolution of APEX2 for electron microscopy and proximity labeling.</a> Nature Methods. 12 (1), 51-54 (2015).</li><li>Mavlyutov, T. A., 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=APEX2-enhanced+electron+microscopy+distinguishes+sigma-1+receptor+localization+in+the+nucleoplasmic+reticulum.">APEX2-enhanced electron microscopy distinguishes sigma-1 receptor localization in the nucleoplasmic reticulum.</a> Oncotarget. 8 (31), 51317-51330 (2017).</li><li>Wang, Q., Mercogliano, C. P., Lowe, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+ferritin-based+label+for+cellular+electron+cryotomography.">A ferritin-based label for cellular electron cryotomography.</a> Structure. 19 (2), 147-154 (2011).</li><li>Sano, T., Glazer, A. N., Cantor, C. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+streptavidin-metallothionein+chimera+that+allows+specific+labeling+of+biological+materials+with+many+different+heavy+metal+ions.">A streptavidin-metallothionein chimera that allows specific labeling of biological materials with many different heavy metal ions.</a> Proceedings of the National Academy of Sciences of the United States of America. 89 (5), 1534-1538 (1992).</li><li>Mercogliano, C. P., DeRosier, D. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gold+nanocluster+formation+using+metallothionein:+Mass+spectrometry+and+electron+microscopy.">Gold nanocluster formation using metallothionein: Mass spectrometry and electron microscopy.</a> Journal of Molecular Biology. 355 (2), 211-223 (2006).</li><li>Mercogliano, C. P., DeRosier, D. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Concatenated+metallothionein+as+a+clonable+gold+label+for+electron+microscopy.">Concatenated metallothionein as a clonable gold label for electron microscopy.</a> Journal of Structural Biology. 160 (1), 70-82 (2007).</li><li>Morphew, M. 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=Metallothionein+as+a+clonable+tag+for+protein+localization+by+electron+microscopy+of+cells.">Metallothionein as a clonable tag for protein localization by electron microscopy of cells.</a> Journal of Microscopy. 260 (1), 20-29 (2015).</li><li>Nishino, Y., Yasunaga, T., Miyazawa, 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+genetically+encoded+metallothionein+tag+enabling+efficient+protein+detection+by+electron+microscopy.">A genetically encoded metallothionein tag enabling efficient protein detection by electron microscopy.</a> Journal of Electron Microscopy. 56 (3), 93-101 (2007).</li><li>Bouchet-Marquis, C., Pagratis, M., Kirmse, R., Hoenger, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Metallothionein+as+a+clonable+high-density+marker+for+cryo-electron+microscopy.">Metallothionein as a clonable high-density marker for cryo-electron microscopy.</a> Journal of Structural Biology. 177 (1), 119-127 (2012).</li><li>Fukunaga, Y., 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=Electron+microscopic+analysis+of+a+fusion+protein+of+postsynaptic+density-95+and+metallothionein+in+cultured+hippocampal+neurons.">Electron microscopic analysis of a fusion protein of postsynaptic density-95 and metallothionein in cultured hippocampal neurons.</a> Journal of Electron Microscopy. 56 (4), 119-129 (2007).</li><li>Diestra, E., Fontana, J., Guichard, P., Marco, S., Risco, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Visualization+of+proteins+in+intact+cells+with+a+clonable+tag+for+electron+microscopy.">Visualization of proteins in intact cells with a clonable tag for electron microscopy.</a> Journal of Structural Biology. 165 (3), 157-168 (2009).</li><li>Risco, C., 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=sensitive,+high-resolution+detection+of+protein+molecules+in+eukaryotic+cells+using+metal-tagging+transmission+electron+microscopy.">sensitive, high-resolution detection of protein molecules in eukaryotic cells using metal-tagging transmission electron microscopy.</a> Structure. 20 (5), 759-766 (2012).</li><li>Ding, S. -. 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=Noncanonical+role+for+the+host+Vps4+AAA++ATPase+ESCRT+protein+in+the+formation+of+tomato+bushy+stunt+virus+replicase.">Noncanonical role for the host Vps4 AAA+ ATPase ESCRT protein in the formation of tomato bushy stunt virus replicase.</a> PLoS Pathogens. 10 (4), e1004087 (2014).</li><li>Jiang, 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=Direct+synthesis+of+gold+nanoparticles+on+cysteine-rich+tags+in+yeast+cells.">Direct synthesis of gold nanoparticles on cysteine-rich tags in yeast cells.</a> Protocol Exchange. , (2020).</li><li>Jiang, 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=Direct+synthesis+of+gold+nanoparticles+on+cysteine-rich+tags+in+mammalian+cells.">Direct synthesis of gold nanoparticles on cysteine-rich tags in mammalian cells.</a> Protocol Exchange. , (2020).</li><li>Jiang, 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=Genetically+encoded+tags+for+direct+synthesis+of+EM-visible+gold+nanoparticles+in+cells.">Genetically encoded tags for direct synthesis of EM-visible gold nanoparticles in cells.</a> Nature Methods. 17 (9), 937-946 (2020).</li><li>Brust, M., Walker, M., Bethell, D., Schiffrin, D. 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The study presents here a robust clonable EM labeling technology for the single-molecule visualization of protein molecules within the cellular environment with ultrastructural resolution. The AuNPs directly synthesized on genetically encoded cysteine-rich tags provide unambiguous and precise localization of the target proteins. High-pressure freezing and freeze-substitution technique excellently preserve the ultrastructure of biological samples. Taken together, the clonable electron microscopy labeling technology presen...

In the postgenomic era, the development of green fluorescent protein (GFP) as a single-molecule reporter for light microscopy has revolutionized the field of modern life science research1,2. For decades, electron microscopy (EM) has been a powerful tool for intuitively observing the cellular ultrastructure with nanoscale resolution3; however, the precise identification and localization of protein molecules remain challenging.
The most commonly used EM labeling technique is the immunoelectron microscopy (IEM) labeling technique, which is based on the antigen-antibody reaction. However, although many techniques have been developed in the field of IEM labeling, including pre-embedding IEM and post-embedding IEM (on resin sections or hydrated cryosections), it still suffers from low labeling efficiency (&#60;10%)4,5, which is related to the sample preparation and antibody quality. To overcome these limitations, developing genetically encoded tags has great application potential.
Two main types of EM tags have been thoroughly explored in recent years. One type is the DAB staining method, which utilizes tags such as APEX2 to oxidize 3,3&#39;-diaminobenzidine (DAB) to osmiophilic polymers for EM visualization6,7,8,9,10,11,12. It enables the labeling of high-abundance proteins in subcellular regions but is not suitable for single-molecule counting. The other type utilizes metal-binding proteins, such as ferritin13 and metallothionein (MT)14,15,16,17,18,19,20,21,22,23,24,25,26, to generate electron-dense metal deposits in situ for EM visualization. Only the latter has real potential for single-molecule visualization and counting. The molecular size of ferritin is too large (~450 kD) for it to be used as a promising tag, whereas the small size (~5 kD) of MT and its ability to bind various ions through its 20 cysteines have attracted great attention. Several labs have tried to label purified MT-fusion proteins or MT-expressing cells by incubating directly with Au+. These attempts have initially proved that MT tags can bind gold ions to form high-contrast signals, but none have really achieved the effective identification of individual proteins in cells, and they are not widely applicable14,15,16,17,18,19,20,21,22,23.
The ANSM-based AuNP synthesis technique, which involves synthesizing 2-6 nm-sized AuNPs directly on cysteine-rich tags (e.g., MT, the MT variants MTn and MT&#945;, AFP) as electron-dense labels for EM visualization, is the first reliable and applicable approach for protein labeling and single molecule detection in cells24,25,26. It allows for the specific synthesis of AuNPs on isolated tag fusion proteins and has achieved an unprecedented labeling efficiency in nonfixed or chemically fixed prokaryotic (E. coli) and eukaryotic (S. pombe) cells. However, implementing the same protocol in more advanced systems such as mammalian cells or even tissues involves additional challenges, such as the more complex intracellular redox homeostasis and more fragile cellular structure.
This study presents a clonable EM labeling technology, which combines the novel ANSM-based AuNP synthesis technique for labeling genetically encoded cysteine-rich tags (MT) with the HPF/FSF-rehydration-HPF/FSF sample preparation method, enables the unambiguous single-molecule identification of tagged proteins in the ER membrane, ER lumen, and mitochondrial matrix in HeLa cells. The current method combines the characteristics of high labeling efficiency, a high signal-to-noise ratio, single-molecule labeling, and strong universality, and this method has broad application prospects in life science research.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>0.025 mm/0.275 mm Aluminum carrier</td>
			<td>Beijing Wulundes Biotech Ltd., or Engineering Office of M. Wohlwend</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>0.2 M HEPES buffer</td>
			<td></td>
			<td></td>
			<td>Dissolve HEPES (0.2 M) in 980 mL of ddH2O, then add 10 mL of 100 mM MgCl2 and 10 mL of 100 mM CaCl2 (final concentration 1 mM), respectively, adjust pH to 5.5</td>
		</tr>
		<tr>
			<td>1.5 mL MaxyClear snaplock microtube</td>
			<td>Axygen Scientific</td>
			<td>MCT150C</td>
			<td></td>
		</tr>
		<tr>
			<td>2 mL polypropylene screw cap microtubes</td>
			<td>Biologix</td>
			<td>81-0204</td>
			<td></td>
		</tr>
		<tr>
			<td>200 mesh hexagonal copper grid</td>
			<td>Tedpella inc</td>
			<td>G200HEX</td>
			<td></td>
		</tr>
		<tr>
			<td>2-mercaptoethanol</td>
			<td>Amresco</td>
			<td>0482-250ML</td>
			<td></td>
		</tr>
		<tr>
			<td>35 mm cell culture dishes</td>
			<td>Corning</td>
			<td>430165</td>
			<td></td>
		</tr>
		<tr>
			<td>50 mL polypropylene centrifuge tubes</td>
			<td>Corning</td>
			<td>430928</td>
			<td></td>
		</tr>
		<tr>
			<td>Acetone</td>
			<td>Beiijng Tong Guang Fine Chemicals Company</td>
			<td>31025</td>
			<td></td>
		</tr>
		<tr>
			<td>Automated freeze substitution machine</td>
			<td>Leica</td>
			<td>AFS2</td>
			<td></td>
		</tr>
		<tr>
			<td>Customized 3.05 mm x 0.66 mm specimen holders for HPF</td>
			<td>Beijing Wulundes Biotech Ltd.</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>D-penicillamine</td>
			<td>TCI</td>
			<td>P0147</td>
			<td></td>
		</tr>
		<tr>
			<td>Dulbecco&#8217;s modified Eagle medium</td>
			<td>GBICO</td>
			<td>C11965500BT</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal bovine serum</td>
			<td>GBICO</td>
			<td>10099-141C</td>
			<td></td>
		</tr>
		<tr>
			<td>Flat bottom embedding capsule</td>
			<td>Tedpella inc</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Foam cryobox</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Formvar 15/95 resin</td>
			<td>Electron Microscopy Sciences</td>
			<td>15800</td>
			<td></td>
		</tr>
		<tr>
			<td>HAuCl4</td>
			<td>Sigma</td>
			<td>4022-1G</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>sigma&#160;</td>
			<td>H3375-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>HPF machine</td>
			<td>Wohlwend&#160;</td>
			<td>HPF compact01</td>
			<td></td>
		</tr>
		<tr>
			<td>Methonal&#160;</td>
			<td>Beiijng Tong Guang Fine Chemicals Company</td>
			<td>12397</td>
			<td></td>
		</tr>
		<tr>
			<td>NaBH4</td>
			<td>Sigma</td>
			<td>480886-25G</td>
			<td></td>
		</tr>
		<tr>
			<td>OsO4</td>
			<td>Electron Microscopy Sciences</td>
			<td>19110</td>
			<td></td>
		</tr>
		<tr>
			<td>PBS-A buffer</td>
			<td></td>
			<td></td>
			<td>Dissolve NaH2PO4 (1.125 mM), Na2HPO4 (3.867 mM), NaCl (100 mM) in 1 L of ddH2O, adjust to pH 7.4</td>
		</tr>
		<tr>
			<td>Qualitative filter paper (medium speed)</td>
			<td>Beyotime Biotechnology</td>
			<td>FFT08</td>
			<td></td>
		</tr>
		<tr>
			<td>Sapphire discs</td>
			<td>Beijing Wulundes Biotech Ltd., or Engineering Office of M. Wohlwend</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Solvent resistant pen</td>
			<td>Electron Microscopy Sciences</td>
			<td>62053-B</td>
			<td></td>
		</tr>
		<tr>
			<td>SPI-Pon 812 resin</td>
			<td>SPI Inc</td>
			<td>02659-AB</td>
			<td></td>
		</tr>
		<tr>
			<td>Transmission electron microscopy</td>
			<td>FEI</td>
			<td>Tecnai G2 spirit</td>
			<td></td>
		</tr>
		<tr>
			<td>Trypsin-EDTA</td>
			<td>GBICO</td>
			<td>C25200-056</td>
			<td></td>
		</tr>
		<tr>
			<td>Tweezers</td>
			<td>Dumont</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Ultramictotome</td>
			<td>Leica</td>
			<td>FC7</td>
			<td></td>
		</tr>
		<tr>
			<td>Uranyl acetate</td>
			<td>Electron Microscopy Sciences</td>
			<td>22400</td>
			<td></td>
		</tr>
	</tbody>
</table>

direct synthesis of em-visible gold nanoparticles in cells for protein localization analysis with well-preserved ultrastructure

Analyzing the precise localization of protein molecules in cells with ultrastructural resolution is of great significance for the study of various physiological or pathological processes in all living organisms. Therefore, the development of clonable tags that can be used as electron microscopy probes is of great value, just as fluorescent proteins have played a crucial role in the field of optical imaging. The autonucleation suppression mechanism (ANSM) was recently uncovered, which allows for the specific synthesis of gold nanoparticles (AuNPs) on cysteine-rich tags, such as metallothionein (MT) and antifreeze protein (AFP).
Based on the ANSM, an electron microscopy labeling technology was developed, which enables the specific detection of tagged proteins in prokaryotic and eukaryotic cells with an unprecedented labeling efficiency. This study illustrates a protocol for the detection of MTn (an engineered MT variant lacking aldehyde-reactive residues) fusion proteins in mammalian cells with well-preserved ultrastructure. In this protocol, high-pressure freezing and freeze-substitution fixation were performed using non-aldehyde fixatives (such as tannic acid, uranyl acetate) to preserve near-native ultrastructure and avoid damage to the tag activity caused by aldehyde crosslinking.
A simple one-step rehydration was used prior to the ANSM-based AuNP synthesis. The results showed that the tagged proteins targeted various organelles, including the membranes and the lumen of the endoplasmic reticulum (ER), and mitochondrial matrices were detected with high efficiency and specificity. This research provides biologists with a robust protocol to address an enormous range of biological questions at the single-molecule level in cellular ultrastructural contexts.

Author Spotlight: Direct Synthesis of EM-Visible Gold Nanoparticles in Cells for Protein Localization Analysis with Well-Preserved Ultrastructure  

Direct Synthesis of EM-Visible Gold Nanoparticles in Cells for Protein Localization Analysis with Well-Preserved Ultrastructure

Protein detection and localization are essential in biological research. Our protocol describes a novel EM-labeling technology using genetically-encoded tags which allows single-molecule visualization in situ with well-preserved ultrastructure. It is crucial to avoid over-fixation.The labeling method is based on the activity of cysteines in the tags, which are highly sensitive to aldehyde cross-linking. Our protocol avoids use of aldehyde fixatives and preserves the tag activity and ultrastructure. at the same time.EM labeling has always been challenging, suffering from poor morphology or inefficient labeling. Our protocols synthesizes in situ nanoparticles directly on individual proteins to provide clear and precise localization of the target proteins, with a high signal-to-noise ratio, high efficiency, and specificity. We have so far achieved excellent labeling in isolated proteins, E.coli cells, yeast cells, and HeLa cells.We will explore and optimize the method for application to tissue samples. Combining the prevailing cryo-FIB and cryo-EM technologies will allow us to address important biological questions.

The ANSM-based AuNP synthesis technique is an extremely useful tool for labeling and detecting MT-tagged proteins with TEM26. To validate its robustness in mammalian cells, three stable cell lines expressing EGFP-MTn-KDEL, Ost4-EGFP-MTn, or Mito-acGFP-MTn in Hela cells were generated. KDEL is a canonical C-terminal endoplasmic reticulum (ER) retention/retrieval sequence, which maintains the fusion protein EGFP-MTn-KDEL within the ER lumen or the perinuclear space of the nuclear envelope (NE). Ost4...

Watch this Scientific Journal Video about Direct Synthesis of EM-Visible Gold Nanoparticles in Cells for Protein Localization Analysis with Well-Preserved Ultrastructure at JoVE.com

The present protocol describes a clonable electron microscopy labeling technology for detecting metallothionein-tagged proteins in cells using a novel autonucleation suppression mechanism-based gold nanoparticle synthesis technique.