Honors & Awards


  • Mona M. Burgess Graduate Fellow, Bio-X SIGF, Stanford University (2018 Sept - 2021)
  • CMAD Fellow, The Center for Molecular Analysis and Design, Stanford University (2016 July - 2018 June)

Education & Certifications


  • B.Sc, University of Michigan, Biochemistry summa cum laude (2014)

All Publications


  • Identification of PAmKate as a Red Photoactivatable Fluorescent Protein for Cryogenic Super-Resolution Imaging. Journal of the American Chemical Society Dahlberg, P. D., Sartor, A. M., Wang, J., Saurabh, S., Shapiro, L., Moerner, W. E. 2018; 140 (39): 12310–13

    Abstract

    Single-molecule super-resolution fluorescence microscopy conducted in vitrified samples at cryogenic temperatures offers enhanced localization precision due to reduced photobleaching rates, a chemical-free and rapid fixation method, and the potential of correlation with cryogenic electron microscopy. Achieving cryogenic super-resolution microscopy requires the ability to control the sparsity of emissive labels at cryogenic temperatures. Obtaining this control presents a key challenge for the development of this technique. In this work, we identify a red photoactivatable protein, PAmKate, which remains activatable at cryogenic temperatures. We characterize its activation as a function of temperature and find that activation is efficient at cryogenic and room temperatures. We perform cryogenic super-resolution experiments in situ, labeling PopZ, a protein known to assemble into a microdomain at the poles of the model bacterium Caulobacter crescentus. We find improved localization precision at cryogenic temperatures compared to room temperature by a factor of 4, attributable to reduced photobleaching.

    View details for DOI 10.1021/jacs.8b05960

    View details for PubMedID 30222332

  • Spatial organization and dynamics of RNase E and ribosomes in Caulobacter crescentus PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Bayas, C. A., Wang, J., Lee, M. K., Schrader, J. M., Shapiro, L., Moerner, W. E. 2018; 115 (16): E3712–E3721

    Abstract

    We report the dynamic spatial organization of Caulobacter crescentus RNase E (RNA degradosome) and ribosomal protein L1 (ribosome) using 3D single-particle tracking and superresolution microscopy. RNase E formed clusters along the central axis of the cell, while weak clusters of ribosomal protein L1 were deployed throughout the cytoplasm. These results contrast with RNase E and ribosome distribution in Escherichia coli, where RNase E colocalizes with the cytoplasmic membrane and ribosomes accumulate in polar nucleoid-free zones. For both RNase E and ribosomes in Caulobacter, we observed a decrease in confinement and clustering upon transcription inhibition and subsequent depletion of nascent RNA, suggesting that RNA substrate availability for processing, degradation, and translation facilitates confinement and clustering. Importantly, RNase E cluster positions correlated with the subcellular location of chromosomal loci of two highly transcribed rRNA genes, suggesting that RNase E's function in rRNA processing occurs at the site of rRNA synthesis. Thus, components of the RNA degradosome and ribosome assembly are spatiotemporally organized in Caulobacter, with chromosomal readout serving as the template for this organization.

    View details for DOI 10.1073/pnas.1721648115

    View details for Web of Science ID 000430191900016

    View details for PubMedID 29610352

    View details for PubMedCentralID PMC5910860

  • Mg2+ Shifts Ligand-Mediated Folding of a Riboswitch from Induced-Fit to Conformational Selection JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Suddala, K. C., Wang, J., Hou, Q., Water, N. G. 2015; 137 (44): 14075-14083

    Abstract

    Bacterial riboswitches couple small-molecule ligand binding to RNA conformational changes that widely regulate gene expression, rendering them potential targets for antibiotic intervention. Despite structural insights, the ligand-mediated folding mechanisms of riboswitches are still poorly understood. Using single-molecule fluorescence resonance energy transfer (smFRET), we have investigated the folding mechanism of an H-type pseudoknotted preQ1 riboswitch in dependence of Mg(2+) and three ligands of distinct affinities. We show that, in the absence of Mg(2+), both weakly and strongly bound ligands promote pseudoknot docking through an induced-fit mechanism. By contrast, addition of as low as 10 μM Mg(2+) generally shifts docking toward conformational selection by stabilizing a folded-like conformation prior to ligand binding. Supporting evidence from transition-state analysis further highlights the particular importance of stacking interactions during induced-fit and of specific hydrogen bonds during conformational selection. Our mechanistic dissection provides unprecedented insights into the intricate synergy between ligand- and Mg(2+)-mediated RNA folding.

    View details for DOI 10.1021/jacs.5b09740

    View details for Web of Science ID 000364727600019

    View details for PubMedID 26471732

  • Meeting Report: SMART Timing-Principles of Single Molecule Techniques Course at the University of Michigan 2014 BIOPOLYMERS Bartke, R. M., Cameron, E. L., Cristie-David, A. S., Custer, T. C., Denies, M. S., Daher, M., Dhakal, S., Ghosh, S., Heinicke, L. A., Hoff, J. D., Hou, Q., Kahlscheuer, M. L., Karslake, J., Krieger, A. G., Li, J., Li, X., Lund, P. E., Vo, N. N., Park, J., Pitchiaya, S., Rai, V., Smith, D. J., Suddala, K. C., Wang, J., Widom, J. R., Walter, N. G. 2015; 103 (5): 296-302

    Abstract

    Four days after the announcement of the 2014 Nobel Prize in Chemistry for "the development of super-resolved fluorescence microscopy" based on single molecule detection, the Single Molecule Analysis in Real-Time (SMART) Center at the University of Michigan hosted a "Principles of Single Molecule Techniques 2014" course. Through a combination of plenary lectures and an Open House at the SMART Center, the course took a snapshot of a technology with an especially broad and rapidly expanding range of applications in the biomedical and materials sciences. Highlighting the continued rapid emergence of technical and scientific advances, the course underscored just how brightly the future of the single molecule field shines.

    View details for DOI 10.1002/bip.22603

    View details for Web of Science ID 000350306700005

    View details for PubMedID 25546606

  • Recent Advances in Radical SAM Enzymology: New Structures and Mechanisms ACS CHEMICAL BIOLOGY Wang, J., Woldring, R. P., Roman-Melendez, G. D., McClain, A. M., Alzua, B. R., Marsh, E. N. 2014; 9 (9): 1929-1938

    Abstract

    The radical S-adenosylmethionine (SAM) superfamily of enzymes catalyzes an amazingly diverse variety of reactions ranging from simple hydrogen abstraction to complicated multistep rearrangements and insertions. The reactions they catalyze are important for a broad range of biological functions, including cofactor and natural product biosynthesis, DNA repair, and tRNA modification. Generally conserved features of the radical SAM superfamily include a CX3CX2C motif that binds an [Fe4S4] cluster essential for the reductive cleavage of SAM. Here, we review recent advances in our understanding of the structure and mechanisms of these enzymes that, in some cases, have overturned widely accepted mechanisms.

    View details for DOI 10.1021/cb5004674

    View details for Web of Science ID 000342121200003

    View details for PubMedID 25009947