a) Bioengineering of Gas Vesicles
Gas vesicles (GVs) are a class of hollow gas-filled protein nanostructures evolved in photosynthetic microbes. They are hundreds of nanometers in size and possess a gaseous interior enclosed by a ~ 2 nm-thick protein shell that is permeable to air but excludes water (Fig. a-b). The native role of GVs is to regulate the buoyancy of their microbial hosts in bodies of water so that when the microbes need to increase their photosynthesis rate, they will express GVs to float to the surface of the water for an increasing amount of sunlight. GVs are encoded by a cluster of 8-14 genes, and transferring these genes from their native hosts to other organisms, such as E. coli Nissle 1917 (the common probiotic Mutaflor®), results in the expression of GVs in these cells (Fig. c).
What make GV an interesting target for bioengineers are their unique biochemical and physical properties. The change of acoustic impedance at the air-water interface allows their detection by ultrasound imaging; the differential magnetic susceptibility between air and water enables magnetic resonance imaging (MRI); and lastly, the fast diffusion of xenon molecules across GV shells permits HyperCEST 129Xe MRI. Although GVs have been studied for decades by biologists, these new engineering efforts occur over the past few years have rendered them a new utility as genetically encoded agents for biomedical imaging, diagnosis and therapy. For example, exploring GVs’ dual responsiveness to ultrasound and magnetic field, acoustically modulated MRI (AM-MRI) was developed in 2018 that enabled GVs as a new type of MRI contrast agents that could be turned off in situ by operators (Fig. d). Shortly before, E. coli and Salmonella typhimurium were genetically engineered to express a highly echogenic genotype of GVs, which rendered these cells to be imaged by ultrasound within the gastrointestinal tract and in tumors. In this nascent field, the biodiversity, biochemistry and physical properties of GVs provide rich opportunities for further exploration of their utilities towards noninvasive imaging and remote control of cellular functions.
b) Biomolecular Contrast Agents for MRI
Magnetic resonance imaging (MRI) is a widely established medical imaging modality that can observe tissue morphology at high spatiotemporal resolution inside living organisms. Additionally, magnetic field and radiofrequency waves utilized by MRI possess unlimited penetration depth for biological tissues, which is in contrast to ~ 1 mm penetration depth of light for optical imaging. However, compared to optical imaging, in which fluorescent protein reporters such as green fluorescent protein (GFP) are well developed for visualizing biological processes such as gene expression and neural activation, relatively few such reporters are available for MRI. This forms the main technological gap that prevents the wider utilities of MRI to image biological processes at molecular and cellular specificity. Here, we aim to bridge this gap by engineering special proteins and protein nanostructures that can interact with the magnetic field. As examples, the engineering of an iron-containing P450 enzyme enables the signal intensity of T1-weighted MRI images to correlate specifically to the concentration of dopamine in brains of living rats (see figure below), and more recently, the engineering of gas vesicles leads to the development of acoustically modulated MRI.
Read more: Nature Materials (2018) 17:456–463, Current Opinion in Chemical Biology (2018) 45:57-63, Progress in NMR spectroscopy (2017) 102-103:32-42, Nature Biotechnology (2010) 28:264-270, Science (2014) 344:533-535.
c) Solid-state NMR Spectroscopy on Membrane Protein
Nuclear magnetic resonance (NMR) spectroscopy, X-ray crystallography and cryo-electron microscopy are three main methods that can determine atomic-resolution protein structures. Unlike the other two, NMR is unique in its ability to study proteins in their native environment of pH, hydration and temperature, or even directly proteins in living cells. This is beneficial in scenarios where the cellular context is crucial for the correct folding, dynamics and function of the proteins.
NMR method can be subdivided into the more established solution NMR and solid-state NMR (ssNMR). ssNMR is not restricted by the requirement of fast isotropic tumbling of proteins in a solution. As an example, ssNMR can study membrane proteins reconstituted in native lipid bilayers, where the whole protein-lipid assembly does not undergo isotropic motion. Thus, ssNMR may provide atomic-resolution structure, dynamics and interaction information for membrane proteins, which compared to soluble proteins, are less understood due to the technical challenges to studying them by most of the structural biology methods.