Ming Hammond

Associate Professor of Chemistry

Ming Hammond

B.S. California Institute of Technology

Ph.D. University of California, Berkeley

Research

References

ming.hammond@utah.edu

Ming Hammond's Lab Page

Ming Hammond's PubMed Literature Search

Biological Chemistry Program

Biosensors, RNA, Fluorescence Imaging, Bacterial and Immune Cell Signaling

Research

Molecular Imaging: RNA-based fluorescent biosensors

​We are one of the first labs to develop fluorescent biosensors made of RNA for live cell imaging of enzyme activity. These sensors are designed by combining a riboswitch domain, which is an RNA that changes conformation upon binding a small molecule ligand, and a fluorophore-binding domain. Ligand selectivity is dictated by the riboswitch domain and can even be reprogrammed with single nucleotide changes.

​Our lab has established allosteric stem design rules, novel designs, and optimization strategies for making RNA-based fluorescent biosensors from a variety of riboswitch folds. We have made biosensors with best-in-class sensitivity (sub-nanomolar limit of detection), selectivity (better than commercial monoclonal antibodies), and in vivo brightness (143% brighter than parent fluorophore-binding aptamer). We have applied these biosensors to visualize enzyme activity in both gram positive and gram negative bacteria, under aerobic and anaerobic conditions, via fluorescence microscopy and flow cytometry methods. We have 'watched' the chemical inhibition of an enzyme involved in biosynthesis of a quorum signaling molecule in live bacterial cells. We recently showed that the micronutrient zinc turns off a signaling enzyme that controls biofilm formation in E. coli, which helps to sensitize this common foodborne pathogen to antibiotics (Future of Biochemistry).

​Biosensor Papers: JACS 2013aJACS 2015JACS 2016NAR 2016Cell Chem Biol 2016Biochem 2018Methods 2018

Other Riboswitch-Based Methods Papers: JACS 2013bChem Biol 2013Anal Chem 2014RNA Biol 2015

Reviews: Methods Enz 2015Methods Mol Biol 2015Methods Mol Biol 2017Annu Rev Biochem 2017Microbiol Spec 2018

Signaling: Cyclic dinucleotides in bacteria and mammalian cells

​Cyclic dinucleotides are an emerging class of intracellular signaling molecules with diverse roles in bacteria and with newfound roles in innate immunity in mammalian cells. As second messengers, they are produced transiently in response to environmental stimuli and act inside the cell to change gene expression, physiology, and behavior. Given that three out of the four known cyclic dinucleotides were discovered in the past decade, much remains to be explored about their chemistry and biology. To study these chemical signals, our lab has developed fluorescent biosensors for each of the known cyclic dinucleotides. We also recently developed the first bioluminescent sensor for measuring cyclic dinucleotides in complex settings (Nat Chem Biol Research HighlightJGI Science Highlight).

​(i) Cyclic AMP-GMP (cAG) signaling: Using an in vitro biosensor assay, we discovered a cyclic AMP-GMP (cAG)-sensing riboswitch class, which was highlighted by Science Signaling as a Signaling Breakthrough of the Year. These newfound cAG riboswitches were identified in Geobacter bacteria and predicted to control these bacteria's unique ability to relay electrons outside the cell. By screening for enzyme activity using an in vivo biosensor assay, we subsequently discovered a G. sulfurreducens GGDEF enzyme that makes cAG, which is the founding member of Hypr GGDEF enzymes. This discovery is significant because for almost 30 years GGDEF enzymes were considered synonymous with the classical cyclic di-GMP signaling network; our result provides the first evidence that this enzyme class can make alternative cyclic dinucleotides to cyclic di-GMP (Berkeley news story). We are continuing to identify molecular components of the cAG signaling pathway and to understand its role in how bacteria like Geobacter sense and adapt to different kinds of surfaces. 

(ii) Mammalian cGAMP signaling: The enzyme cyclic GMP-AMP synthase (cGAS) was discovered to be the innate immune sensor for cytosolic DNA, which may result from microbial infection or other pathophysiological conditions. Upon binding double-stranded DNA, cGAS produces the signaling molecule cGAMP, which activates the receptor protein, stimulator of interferon genes (STING). In collaboration with Russell Vance (UC Berkeley), we proved the chemical structure of cGAMP had a noncanonical 2'-5' linkage by NMR. We recently developed a biosensor-based platereader assay to quantitate cGAMP levels in DNA-stimulated mammalian cell lysates.

​(iii) Other cyclic dinucleotide signaling: We have analyzed the activity of cyclic di-GMP and cyclic di-AMP signaling enzymes using in vivo biosensor assays. For example, we have demonstrated that archaeal enzymes produce cyclic di-AMP. This result completed the set of experimental evidence that cyclic dinucleotide signaling extends to all three domains of life.

​cAG Signaling Papers: PNAS 2015Cell Reports 2015PNAS 2016

cGAMP Signaling Papers: Cell Reports 2013Cell Chem Biol 2016

Other CDN Biosensor Papers: JACS 2013aJACS 2015NAR 2016ACS Chem Bio 2018

Publications

  1. Wright, T. A., Jiang, L., Park, J. J., Anderson, W. A., Chen, G., Hallberg, Z. F., Nan, B., and Hammond, M. C. "Second messengers and divergent HD-GYP enzymes regulate 3',3'-cGAMP signaling" Submitted Preprint

  2. Wright, T. A., Dippel, A. B., Hammond, M. C. “Cyclic di-GMP signaling gone astray: cGAMP signaling via Hypr GGDEF and HD-GYP enzymes” In Chou, S.-H., Guilliani, N., Lee, V., Romling U. (ed), Microbial cyclic di-nucleotide signaling.  Accepted - in press (Invited Chapter)

  3. Dippel, A. B. and Hammond, M. C. "A poxin on both of your houses: Poxviruses degrade the immune signal cGAMP" Biochemistry (2019) 58, 19, 2387-2388  (Invited Viewpoint) Link

  4. Hallberg, Z. F.*, Chan, C. H.*, Wright, T. A., Park, J. J., Kranzusch, P. J., Doxzen, K., Bond,
    D. R., Hammond, M. C. “Structure and mechanism of a Hypr GGDEF enzyme that activates cGAMP signaling to control extracellular metal respiration” eLife (2019); e43959 Link *
    co-first authors

  5. Villa, J.*, Su, Y.*, Contreras, L. M., Hammond, M. C. “Synthetic biology of small RNAs and riboswitches” (2019) 527-545. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0007-2017 (Invited Book Chapter) Link *co-first authors

  6. Dippel, A. D., Anderson, W. A., Evans, R. S., Deutsch, S., Hammond, M. C. "Luminescent biosensors for detection of second  messenger  cyclic di-GMP" ACS Chem Bio (2018) 13, 1872-1879 (Invited Paper) Link   Related Highlights: "Sensors" special issue; Research Highlight in Nat Chem BiolJGI Science Highlight
  7. Truong, J., Hsieh, Y.-F., Truong, L., Jia, G., Hammond, M.C. "Designing fluorescent biosensors using circular permutations of riboswitches", Methods (2018) 143, 102-109. (Invited Paper) Link 
  8. Villa, J. K.*, Su, Y.*, Contreras, L. M., Hammond, M. C. "Synthetic biology of small RNAs and riboswitches” Microbiol Spectr (2018) 6, doi: 10.1128/microbiolspec.RWR-0007-2017. (Invited Review) Link 
  9. Yeo, J., Dippel, A. B., Wang, X. C., Hammond, M. C. "In Vivo Biochemistry: Single-cell dynamics of cyclic di-GMP in E. coli in response to zinc overload" Biochemistry (2018) 57, 108-116. Link 
    Related Highlights: Future of Biochemistry special issueCollege of Chemistry news story
  10. Yeo, J., Wang, X. C., Hammond, M. C. "Live flow cytometry analysis of c-di-GMP levels in single cell populations" Methods Mol Biol (2017) 1657, 111-130. Link to Book
  11. Hallberg, Z. F., Su, Y., Kitto, R. Z., Hammond, M. C. "Engineering and in vivo applications of riboswitches" Annual Rev Biochem (2017) 86, 515-539. Link
  12. Bose, D.*, Su, Y.*, Marcus, A., Raulet, D. H., Hammond, M. C. "An RNA-based fluorescent biosensor for high-throughput analysis of the cGAS-cGAMP-STING pathway" Cell Chem Biol (2016) 23, 1539-1549. Link
  13. Wang, X. C., Wilson, S. C., Hammond, M. C. "Next-generation RNA-based fluorescent biosensors enable anaerobic detection of cyclic di-GMP" Nucleic Acids Res (2016) 44, e139. Link
  14. Su, Y., Hickey, S. F., Keyser, S. G. L., Hammond, M. C. "In vitro and in vivo enzyme activity screening via RNA-based fluorescent biosensors for S-adenosyl-L-homocysteine (SAH)" J Am Chem Soc (2016) 138, 7040-7047. Link
  15. Hallberg, Z. F., Wang, X. C., Wright, T. A., Nan, B., Ad, O., Yeo, J., Hammond, M. C. "Hybrid promiscuous (Hypr) GGDEF enzymes produce cyclic AMP-GMP (3', 3'-cGAMP)" Proc Natl Acad Sci (2016) 113, 1790-1795. Link Related Highlights: 2015 NIH High Risk-High Reward SymposiumBerkeley news story
  16. Muller, R. Y., Hammond, M. C., Rio, D. C., Lee, Y. J. "An efficient method for electroporation of small interfering RNAs (siRNAs) into ENCODE Project Tier 1 GM12878 and K562 cell lines" J Biomol Tech (2015) 26, 142-149. Link
  17. Gonzalez, T. L., Liang, Y., Nguyen, B., Staskawicz, B. J., Loque, D., Hammond, M. C. "Tight regulation of plant immune responses by combining promoter and suicide exon elements" Nucleic Acids Res (2015) 43, 7152-7161. Link
  18. Kellenberger, C. A., Sales-Lee, J., Pan, Y., Gassaway, M. M., Herr, A. E., Hammond, M. C. "A minimalist biosensor: quantitation of cyclic di-GMP using the conformational change of a riboswitch aptamer" RNA Biol (2015) 12, 1189-1197. Link
  19. Kellenberger, C. A.*, Chen, C.*, Whiteley, A. T., Portnoy, D. A., Hammond, M. C. "RNA-based fluorescent biosensors for live cell imaging of second messenger cyclic di-AMP" J Am Chem Soc (2015) 137, 6432-6435. Link
  20. Ren, A., Wang, X. C., Kellenberger, C. A., Rajashankar, J. R., Jones, R., Hammond, M. C., Patel, D. J. "Structural basis for molecular discrimination by a 3', 3'-cGAMP sensing riboswitch" Cell Reports (2015), 11, 1-12. Open Access PDF
  21. Kellenberger, C. A.*, Wilson, S. C.*, Hickey, S. F., Gonzalez, T. L., Su, Y., Hallberg, Z. F., Brewer, T. F., Iavarone, A. T., Carlson, H. K., Hsieh, Y. F., Hammond, M. C. "GEMM-I riboswitches from Geobacter sense the bacterial second messenger c-AMP-GMP" Proc Natl Acad Sci (2015) 112, 5383-5388. Link Related Highlights: 2015 Signaling Breakthroughs of the Year
  22. Kellenberger, C. A., Hallberg, Z. F., Hammond, M. C. "Live cell imaging using riboswitch-Spinach tRNA fusions as metabolite-sensing fluorescent biosensors" Methods in Mol Biol (2015) 1316, 87-103. Link to Chapter
  23. Kellenberger, C. A., Hammond, M. C. "In vitro analysis of riboswitch-Spinach aptamer fusions as metabolite-sensing fluorescent biosensors" Methods Enz (2015) 550, 147-172. Link to Chapter
  24. Pan, Y., Duncombe, T. A., Kellenberger, C. A., Hammond, M. C., Herr, A. E. "High-throughput electrophoretic mobility shift assays for quantitative analysis of molecular binding reactions" Analytical Chem (2014) 86, 10357-10364. Link
  25. Wilson, S. C., Cohen, D. T., Wang, X. C., Hammond, M. C. "A neutral pH thermal hydrolysis method for quantification of structured RNAs" RNA (2014) 20, 1153-1160. Link
  26. Hickey, S. F., Hammond, M. C. "Structure-guided design of fluorescent S-adenosylmethionine analogs for a high-throughput screen to target SAM-I riboswitch RNAs" Chem Biol (2014) 21, 345-356. Link
  27. Sadhu, M. J., Guan, Q., Li, F., Sales-Lee, J., Iavarone, A. T., Hammond, M. C., Cande, W. Z., Rine, J."Nutritional control of epigenetic processes in yeast and human cells" Genetics (2013) 195, 831-844. Link
  28. Diner, E. J., Burdette, D. L., Wilson, S. C., Monroe, K. M., Kellenberger, C. A., Hyodo, M., Hayakawa, Y., Hammond, M. C., Vance, R. E. "The innate immune DNA sensor cGAS produces a noncanonical cyclic dinucleotide that activates human STING" Cell Reports (2013), 3, 1355-1361. Link
  29. Leppek, K., Schott, J., Reitter, S., Poetz, F., Hammond, M. C., Stoecklin, G. "Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs" Cell (2013) 153, 869-881. Link
  30. Kellenberger, C. A., Wilson, S. C., Sales-Lee, J., Hammond, M. C. "RNA-based fluorescent biosensors for live cell imaging of second messengers cyclic di-GMP and cyclic AMP-GMP" J Am Chem Soc (2013) 135, 4906-4909. Link
  31. Karns, K., Vogan, J. M., Qin, Q., Hickey, S. F., Wilson, S. C., Hammond, M. C., Herr, A. E."Microfluidic screening of electrophoretic mobility shifts elucidates riboswitch binding function" J Am Chem Soc (2013), 135, 3136-3143. Link
  32. Hickey, S. F., Sridhar, M., Westermann, A. J., Qin, Q., Vijayendra, P., Liou, G., Hammond, M. C."Transgene regulation in plants by alternative splicing of a suicide exon" Nucleic Acids Res (2012), 40, 4701-4710. Link Selected by NAR editors as a Featured Article
  33. Hammond, M. C. "A tale of two riboswitches" Nat Chem Biol (2011), 7, 342-3. Link 
  34. Meyer, M. M., Hammond, M. C., Salinas, Y., Roth, A., Sudarsan, N., Breaker, R. R. "Challenges of ligand identification for riboswitch candidates" RNA Biol (2011), 8, 5-10. Link
  35. Block, K. F., Hammond, M. C., Breaker, R. R. "Evidence for widespread gene control function by the ydaO riboswitch candidate" J Bacter (2010), 192, 3983-9. Link
  36. Hammond, M. C., Wachter, A., Breaker, R. R. "A plant 5S rRNA mimic regulates alternative splicing of transcription factor IIIA pre-mRNAs" Nat Struct and Mol Biol (2009), 16, 541-9. Link
  37. Weinberg, Z., Regulski, E. E., Hammond, M. C., Barrick, J. E., Yao, Z., Ruzzo, W. L., Breaker, R. R. "The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches" RNA (2008), 14, 822-8. Link
  38. Hammond, M. C., Bartlett, P. A. "Synthesis of amino acid-derived cyclic acyl amidines for use in beta-strand peptidomimetics" J Org Chem (2007), 72, 3104-07. Link
  39. Hammond, M. C., Harris, B. Z.; Lim, W. A., Bartlett, P. A. "Beta-strand peptidomimetics as potent PDZ ligands" Chem Biol (2006), 13, 1247-51. Link
  40. Sudarsan, N.*, Hammond, M. C.*, Block, K. F., Welz, R., Barrick, J. E., Roth, A., Breaker, R. R. "Tandem riboswitch architectures exhibit complex gene control functions" Science (2006), 314, 300-304.
    *co-first authors Link

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Last Updated: 7/10/19