Going Viral with Fluorescent Proteins

Abstract

Many longstanding questions about dynamics of virus-cell interactions can be answered by combining fluorescence imaging techniques with fluorescent protein (FP) tagging strategies. Successfully creating a FP fusion with a cellular or viral protein of interest first requires selecting the appropriate FP. However, while viral architecture and cellular localization often dictate the suitability of a FP, a FP's chemical and physical properties must also be considered. Here, we discuss the challenges of and offer suggestions for identifying the optimal FPs for studying the cell biology of viruses. Statements such as "my fluorescent virus can barely replicate" and "I cannot see my fluorescent protein fusion" are, unfortunately, not uncommon complaints about fusion proteins made with fluorescent proteins (FPs). In some cases, FPs are inappropriate for the system or question. Other times, FPs are incorporated in a haphazard manner. Finally, FPs may not perform as advertised or the investigator may not read the "fine print." In this review, we describe how to avoid common FP problems and how to select appropriate FPs for FP fusions.With multiple fluorescent labeling strategies available, why use FP tags? Generally, FPs have many desirable characteristics. They are genetically encoded, have sufficiently short sequences for incorporation into many viral genomes, and enable site-specific labeling of a viral or cellular protein of interest. Dye-labeling techniques often randomly label proteins and require extracellular delivery, and dye-labeled proteins cannot be delivered into subcellular organelles, such as the endoplasmic reticulum. Difficulties frequently arise when investigators expect FPs to be inert, well behaved in all environments, and provide a bright signal. While few, if any, FPs satisfy every item on a wish list, FPs are undeniably powerful cell biology tools. For a detailed list of virus-relevant methods that exploit FPs, see reference 1 (especially Tables 1 and 2). For basic considerations for developing FP fusion proteins, see reference 2. PHYSICAL PROPERTIES OF FLUORESCENT PROTEINSFirst, let us consider the general properties of FPs. They have short primary sequences but fold into proteins that are not small (ϳ5 nm in diameter) (3). FPs are evolved as soluble cytoplasmic proteins, with only the environmental considerations related to the pH-neutral cytoplasm as a selective pressure. Taken together, these properties suggest significant concerns when using FPs, such as the potential for steric hindrance in fusion proteins and for the performance of FPs in subcellular compartments. The photophysical characteristics of FPs range tremendously in brightness and photostability. Unless the investigator is studying isolated FPs or using advanced microscopy techniques, including total internal-reflection fluorescence (TIRF) (4) and photoactivated localization microscopy (PALM) (5), it is difficult to detect the signal of a single FP in the presence of the cellular autofluorescence background (2). The photophysical pr...

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