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VIPER is a genetically encoded peptide tag for fluorescence and electron microscopy

Significance We are entering a new era in cell cartography, wherein proteins and multiprotein complexes will be mapped with nanoscale precision using advanced instrumentation. The central obstacle hindering progress in this area is the shortage of methods for labeling proteins for imaging by both fluorescence microscopy and electron microscopy. In this report, we describe a technology for tracking and mapping proteins by multiscale microscopy. To do this, we developed an innovative technology called VIPER. VIPER consists of a heterodimeric coiled-coil between a genetically encoded peptide tag (CoilE) and a reporter-conjugated peptide (CoilR). The key finding is that VIPER delivers a variety of chemical reporters, thus enabling effortless switching from fluorescence microscopy to high-resolution electron microscopy imaging without changing the genetically encoded tag. Many discoveries in cell biology rely on making specific proteins visible within their native cellular environment. There are various genetically encoded tags, such as fluorescent proteins, developed for fluorescence microscopy (FM). However, there are almost no genetically encoded tags that enable cellular proteins to be observed by both FM and electron microscopy (EM). Herein, we describe a technology for labeling proteins with diverse chemical reporters, including bright organic fluorophores for FM and electron-dense nanoparticles for EM. Our technology uses versatile interacting peptide (VIP) tags, a class of genetically encoded tag. We present VIPER, which consists of a coiled-coil heterodimer formed between the genetic tag, CoilE, and a probe-labeled peptide, CoilR. Using confocal FM, we demonstrate that VIPER can be used to highlight subcellular structures or to image receptor-mediated iron uptake. Additionally, we used VIPER to image the iron uptake machinery by correlative light and EM (CLEM). VIPER compared favorably with immunolabeling for imaging proteins by CLEM, and is an enabling technology for protein targets that cannot be immunolabeled. VIPER is a versatile peptide tag that can be used to label and track proteins with diverse chemical reporters observable by both FM and EM instrumentation.