Location is everything: protein translocations as a viral infection strategy

Abstract

Protein movement between different subcellular compartments is an essential aspect of biological processes, including transcriptional and metabolic regulation, and immune and stress responses. As obligate intracellular parasites, viruses are master manipulators of cellular composition and organization. Accumulating evidences have highlighted the importance of infection-induced protein translocations between organelles. Both directional and temporal, these translocation events facilitate localization-dependent protein interactions and changes in protein functions that contribute to either host defense or virus replication. The discovery and characterization of protein movement is technically challenging, given the necessity for sensitive detection and subcellular resolution. Here, we discuss infection-induced translocations of host and viral proteins, and the value of integrating quantitative proteomics with advanced microscopy for understanding the biology of human virus infections.

Figure 1

Movement of proteins across subcellular space is a fundamental aspect of biological processes. Examples of protein translocations necessary for cellular homeostasis and response to biological stimuli: (a)De novo formation of peroxisomes requires movement of ER and mitochondrial factors, and import of matrix proteins from the cytosol. (b) Neurotransmitter release relies on the nanometer-level spatial coordination of secretory, cytoskeletal, trafficking, docking and fusion machineries with calcium triggers. (c) Maintenance of mitochondrial dynamics via fission is a temporally-ordered process that involves contact of sub-mitochondrial domains with the ER and RAB7-coated lysosomes, as well as recruitment of cytosolic fission factors. (d) The synthesis and movement of proteins, such as integrins, through the secretory pathway is dependent on biochemical sorting signals, vesicle fission/fusion machineries, cargo-specific molecular motor adaptors, and cytoskeletal trafficking. (e) Pathogenic DNA and RNA trigger immune response in the cytoplasm to induce the expression of interferon (IFN) genes. (f) An accumulation of unfolded proteins, such as following oxidative stress or viral infection, activates the movement of ATF6 for expression of unfolded protein response (UPR) genes. Abbreviations: Rab3-interacting proteins (RIMs), RIM-binding proteins (RBPs), interferons (IFNs), stimulator of interferon genes (STING), mitochondrial antiviral-signaling protein (MAVS), site-2 protease (S2P).

Figure 2

Virus infection causes the translocations of both host and virus proteins. (a) Viruses have diverse spatial-temporal strategies to enter the cell, replicate their genomes, assemble virions, and egress to infect a new host. (b) Translocations of host and virus proteins are critical for using cellular machineries for virus replication, assembly, and egress. (c) Host antiviral signaling relies on protein translocations between organelles, and viruses can disrupt these movements or translocate viral proteins to attenuate immune response. Abbreviations: endosomal sorting complexes required for transport (ESCRTs), MHC class I polypeptide-related sequence A (MICA), signal transducer and activator of transcription (STAT).

Figure 3

Mass spectrometry and microscopy methods as tools for detecting and quantifying protein translocations. (a) Varying levels of spatial scope (i.e. single protein versus single organelle versus global cellular analysis) and temporal capability (i.e. one versus many time points of infection) provided by several mass spectrometry and microscopy methods. (b) Schematic representations of selected MS-based proteomic workflows and microscopy methods used in protein translocation studies. (c) Quantitative MS approaches can be used to monitor the abundance of proteins in spatial-temporal proteomic studies. Abbreviations: electron microscopy (EM), correlative light EM (CLEM), Förster resonance energy transfer (FRET), bi-molecular fluorescence complementation (BiFC), ascorbate peroxidase (APEX), chemical crosslinking (XL)-MS, immunoaffinity purification (IP)-MS, multiple reaction monitoring (MRM), selected reaction monitoring (SRM), parallel reaction monitoring (PRM), sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH), stable isotope labeling of amino acids in culture (SILAC), tandem mass tag (TMT), isobaric tags for relative and absolute quantitation (iTRAQ).