Genetically encoded reporters for hyperpolarized xenon magnetic resonance imaging

Journal name:
Nature Chemistry
Year published:
Published online


Magnetic resonance imaging (MRI) enables high-resolution non-invasive observation of the anatomy and function of intact organisms. However, previous MRI reporters of key biological processes tied to gene expression have been limited by the inherently low molecular sensitivity of conventional 1H MRI. This limitation could be overcome through the use of hyperpolarized nuclei, such as in the noble gas xenon, but previous reporters acting on such nuclei have been synthetic. Here, we introduce the first genetically encoded reporters for hyperpolarized 129Xe MRI. These expressible reporters are based on gas vesicles (GVs), gas-binding protein nanostructures expressed by certain buoyant microorganisms. We show that GVs are capable of chemical exchange saturation transfer interactions with xenon, which enables chemically amplified GV detection at picomolar concentrations (a 100- to 10,000-fold improvement over comparable constructs for 1H MRI). We demonstrate the use of GVs as heterologously expressed indicators of gene expression and chemically targeted exogenous labels in MRI experiments performed on living cells.

At a glance


  1. GVs produce HyperCEST contrast at picomolar concentrations.
    Figure 1: GVs produce HyperCEST contrast at picomolar concentrations.

    a, Diagram of 129Xe chemical exchange saturation transfer between bulk aqueous solvent (left) and GVs (hexagons) either in isolation or inside a cell (grey). Polarized 129Xe nuclei (black) exchange into GVs, where they have a unique NMR frequency (red) at which they can be saturated by RF pulses. Saturated (grey) xenon returns to the bulk, which causes a decrease in bulk 129Xe signal. b, NMR spectra of 129Xe in buffer that contained 400 pM GVs after saturation for the specified amount of time at 31.2 ppm. Spectra are offset for visibility. a.u., arbitrary units. c, Frequency-dependent saturation spectra for intact (red) and collapsed (black) GVs. Each spectrum is an average of two. d, Transmission electron micrographs of intact (left and centre) and collapsed (right) GVs used in this study. Scale bars, 200 nm. e, Concentration dependence of saturation contrast generated by GVs with saturation times that correspond colour-wise to those in b (n = 3 for each data point). Data are fitted with monoexponential curves as a visual aide. f, Saturation contrast image of a three-compartment phantom that contains 400 pM GVs, 100 pM GVs and buffer. RF saturation and image-averaging parameters are listed in Supplementary Tables 1 and 2. All the GVs used here were isolated from A. flos-aquae. Error bars represent s.e.m.

  2. GVs in different species of bacteria have distinct HyperCEST saturation frequencies, which enables multiplexed imaging.
    Figure 2: GVs in different species of bacteria have distinct HyperCEST saturation frequencies, which enables multiplexed imaging.

    a, Frequency-dependent saturation spectra for solutions of wild-type Halobacteria sp. NRC-1 (D600 = 0.01), Microcystis sp. (D600 = 0.36) and E. coli heterologously expressing the pNL29 GV gene cassette from B. megaterium (D600 = 4.46) (n = 3 for each data point). Colour triangles on the x axis indicate the frequency offsets of saturation applied to generate the images in bd. bd, Pseudocoloured saturation contrast images of a three-compartment phantom that contains Microcystis sp. (D600 = 1.2), E. coli expressing pNL29 (D600 = 5.8) and purified GVs from Halobacteria sp. NRC-1 (D500,PS = 0.32). Saturation was applied at offsets of 58.6 ppm (b), 30.6 ppm (c) and 9.0 ppm (d). e, Colour overlay of bd. RF saturation and image-averaging parameters are listed in Supplementary Tables 1 and 2.

  3. GVs as genetic reporters and biosensors.
    Figure 3: GVs as genetic reporters and biosensors.

    a, Diagram of inducible GV expression in E. coli. cells (grey ovals) contain the pNL29 gene cluster (red) under the control of an IPTG-inducible promoter (blue). GVs (black) are only produced when IPTG is present. b, Saturation contrast generated by E. coli (D600 = 0.32) that contained IPTG-inducible pNL29 after overnight supplementation with different quantities of IPTG (n = 4 for each data point). A straight line is fitted to the data as a visual aide. c, Saturation contrast image of a three-compartment phantom that contained E. coli (D600 = 1.6) carrying IPTG-inducible pNL29, with and without overnight induction with 50 µM IPTG, or an empty control vector induced with 50 µM IPTG. d, Diagram of cancer-cell labelling strategy. Anabaena flos-aquae GVs (black) are functionalized with anti-HER2 antibodies (orange) via biotin–avidin conjugation (grey, blue). The antibody recognizes the HER2 receptor (red) on SKBR3 cells. e, Saturation contrast generated by GV-labelled SKBR3 or Jurkat cells (n = 3 for each data point). f, Saturation contrast image of three-compartment phantom that contained SKBR3 cells labelled with antibody-functionalized GVs, similarly labelled Jurkat cells and unlabelled SKBR3 cells. RF saturation and image-averaging parameters are listed in Supplementary Tables 1 and 2. Error bars represent s.e.m.


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Author information


  1. Miller Research Institute, University of California, Berkeley, Berkeley, California 94720, USA

    • Mikhail G. Shapiro
  2. Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, USA

    • Mikhail G. Shapiro,
    • George Sun &
    • David V. Schaffer
  3. Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA

    • Mikhail G. Shapiro
  4. Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA

    • Mikhail G. Shapiro
  5. Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, USA

    • R. Matthew Ramirez,
    • Jinny Sun,
    • Alexander Pines &
    • Vikram S. Bajaj
  6. Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA

    • R. Matthew Ramirez,
    • Lindsay J. Sperling,
    • Alexander Pines &
    • Vikram S. Bajaj
  7. Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA

    • David V. Schaffer


M.G.S. conceived and directed the study. M.G.S., R.M.R., V.S.B. and L.J.S. designed the experiments. M.G.S., R.M.R., J.S. and L.J.S. performed NMR measurements. M.G.S. prepared the GVs, bacteria and mammalian cells. M.G.S. and G.S. generated E. coli genetic constructs. M.G.S., R.M.R. and J.S. analysed the data. M.G.S. wrote the manuscript with interpretation and input from all authors. M.G.S. and V.S.B. provided supervision with input from A.P. and D.V.S.

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