Current Preprints

King, B.R., Sumida, K.H., Caruso, J.L., Baker, D., Zalatan, J.G. “Computational stabilization of a non-heme iron enzyme enables efficient evolution of new function.” bioRxiv 2024.04.18.590141

Fontana, J.*, Sparkman-Yager, D.*, Faulkner, I.*, Cardiff, R., Kiattisewee, C., Walls, A., Primo, T.G., Kinnunen, P.C., García Martín, H., Zalatan, J.G., Carothers, J.M. "Guide RNA structure design enables combinatorial CRISPRa programs for biosynthetic profiling." bioRxiv 2023.11.17.567465

Peer-Reviewed Research Publications

Cardiff, R., Faulkner, I., Beall, J., Carothers, J.M., Zalatan, J.G. "CRISPR-Cas tools for simultaneous transcription & translation control in bacteria." Nucleic Acids Res. 2024, gkae275.

Gavagan, M., Jameson, N., Zalatan, J.G. "The Axin scaffold protects the kinase GSK3β from cross-pathway inhibition." eLife 2023, 12:e85444.
bioRxiv preprint

Burbano, D. A., Cardiff, R.A.L., Tickman, B.I.; Kiattisewee, C., Maranas, C.J., Zalatan, J.G., Carothers, J.M. "Engineering Activatable Promoters for Scalable and Multi-Input CRISPRa/i Circuits." Proc. Natl. Acad. Sci. 2023, 120, e2220358120.

Kiattisewee, C.*, Karanjia, A.V.*, Legut, M., Daniloski, Z., Koplik, S.E., Nelson, J., Kleinstiver, B.P., Sanjana, N.E., Carothers, J.M., Zalatan, J.G. "Expanding the scope of bacterial CRISPR activation with PAM-flexible dCas9 variants." ACS Synth. Biol. 2022, 11, 4103-4122.
bioRxiv preprint.

Tickman, B.I.*, Burbano, D.A.*, Chavali, V.P., Kiattisewee, C., Fontana, J., Khakimzhan, A., Noireaux, V., Zalatan, J.G., Carothers, J.M. "Multi-layer CRISPRa/i circuits for dynamic genetic programs in cell-free and bacterial systems." Cell Systems 2022, 13, 215-229.

Cliff, E.R.*, Kirkpatrick, R.L.*, Cunningham-Bryant, D., Fernandez, B., Harman, J.L., Zalatan, J.G. "CRISPR-Cas-mediated tethering recruits the yeast HMR mating-type locus to the nuclear periphery but fails to silence gene expression." ACS Synth. Biol. 2021, 10, 2870-2877.
bioRxiv preprint.

Kiattisewee, C., Dong, C., Fontana, J., Sugianto, W., Peralta-Yahya, P., Carothers, J.M., Zalatan, J.G. "Portable bacterial CRISPR transcriptional activation enables metabolic engineering in Pseudomonas putida." Metab. Eng. 2021, 66, 283-295.

Kirkpatrick, R.L., Lewis, K., Langan, R.A., Lajoie, M.J., Boyken, S.E., Eakman, M., Baker, D., Zalatan, J.G. "Conditional recruitment to a DNA-bound CRISPR-Cas complex using a colocalization-dependent protein switch." ACS Synth. Biol. 2020, 9, 2316-2323.

Gavagan, M.*, Fagnan, E.*, Speltz, E.B., Zalatan, J.G. "The scaffold protein Axin promotes signaling specificity within the Wnt pathway by suppressing competing kinase reactions." Cell Systems 2020, 10, 515-525.
bioRxiv preprint.

Speltz, E.B. and Zalatan, J.G. “The relationship between effective molarity and affinity governs rate enhancements in tethered kinase-substrate reactions.” Biochemistry 2020, 59, 2182-2193.
bioRxiv preprint.

Fontana, J.*, Dong, C.*, Kiattisewee, C., Chavali, V.P., Tickman, B.I., Carothers, J.M., Zalatan, J.G. "Effective CRISPRa-mediated control of gene expression in bacteria must overcome stringent target site requirements." Nat. Commun. 2020, 11, 1618.
bioRxiv preprint.

Cunningham-Bryant, D., Sun, J., Fernandez, B., Zalatan, J.G. "CRISPR-Cas-mediated chemical control of transcriptional dynamics in yeast." ChemBioChem 2019, 20, 1519-1523.

Dong, C., Fontana, J., Patel, A., Carothers, J.M., Zalatan, J.G. "Synthetic CRISPR-Cas gene activators for transcriptional reprogramming in bacteria." Nat. Commun. 2018, 9, 2489.

Fontana, J., Dong, C., Ham, J.Y., Zalatan, J.G., Carothers, J.M. “Regulated expression of sgRNAs tunes CRISPRi in E. coli.” Biotechnol. J. 2018, 13, 1800069.

Saha, A., Johnston, T.G., Shafranek, R.T., Goodman, C.J., Zalatan, J.G., Storti, D.W., Ganter, M.A., Nelson, A. “Additive manufacturing of catalytically active living materials.” ACS Appl. Mater. Interfaces 2018, 10, 13373-13380.

Zalatan J.G., Lee M.E., Almeida R., Gilbert L.A., Whitehead E.H., La Russa M., Tsai J.C., Weissman J.S., Dueber J.E., Qi L.S., and Lim W.A. “Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds.” Cell 2015, 160, 339-350.
Featured on the cover of Cell.

Andrews L.D., Zalatan J.G., Herschlag D. “Probing the origins of catalytic discrimination between phosphate and sulfate monoester hydrolysis: comparative analysis of alkaline phosphatase and protein tyrosine phosphatases.” Biochemistry 2014, 53, 6811-6819.

Zalatan, J.G.,* Coyle, S.M.,* Rajan, S., Sidhu, S.S., and Lim, W.A. “Conformational control of the Ste5 scaffold protein insulates against MAP kinase misactivation.” Science 2012, 337, 1218-1222.

Zalatan, J.G., Fenn, T. D., and Herschlag, D. “Comparative enzymology in the alkaline phosphatase superfamily to determine the catalytic role of an active site metal ion.” J. Mol. Biol. 2008, 384, 1174-1189.

O’Brien, P.J., Lassila, J.K., Fenn, T.D., Zalatan, J.G., and Herschlag, D. “Arginine coordination in enzymatic phosphoryl transfer: Evaluation of the effect of Arg166 mutations in Escherichia coli alkaline phosphatase.” Biochemistry 2008, 47, 7663-7672.

Zalatan, J.G., Catrina, I., Mitchell, R., Grzyska, P.K., O’Brien, P.J., Herschlag, D., and Hengge, A.C. “Kinetic isotope effects for alkaline phosphatase reactions: Implications for the role of active site metal ions in catalysis.” J. Am. Chem. Soc. 2007, 129, 9789-9798.

Catrina, I., O’Brien, P.J., Purcell, J., Nikolic-Hughes, I., Zalatan, J.G., Hengge, A.C., and Herschlag, D. “Probing the origin of the compromised catalysis of E. coli alkaline phosphatase in its promiscuous sulfatase reaction.” J. Am. Chem. Soc. 2007, 129, 5760-5765.

Zalatan, J.G., Fenn, T.D., Brunger, A.T., and Herschlag, D. “Structural and functional comparisons of nucleotide pyrophosphatase/phosphodiesterase and alkaline phosphatase: Implications for mechanism and evolution.” Biochemistry 2006, 45, 9788-9803.

Zalatan, J.G., and Herschlag, D. “Alkaline phosphatase mono- and diesterase reactions: Comparative transition state analysis.” J. Am. Chem. Soc. 2006, 128, 1293-1303.

Other Publications (Reviews/Book Chapters)

Zalatan, J. G.; Petrini, L.; Geiger, R. "Engineering bacteria for cancer immunotherapy.". Curr. Opin. Biotechnol. 2024, 85, 103061.

Jameson, N., Gavagan, M., Zalatan, J.G. "A kinetic mechanism for systems-level behavior in GTPase signaling." Trends Biochem. Sci. 2022 47, 459-460.

Fontana, J.*, Sparkman-Yager, D.*, Zalatan, J.G., Carothers, J.M. "Challenges and opportunities with CRISPR activation in bacteria for data-driven metabolic engineering." Curr. Opin. Biotechnol. 2020, 64, 190-198.

Fontana, J., Voje, W.E., Zalatan, J.G., Carothers, J.M. “Prospects for engineering dynamic CRISPR-Cas transcriptional circuits to improve bioproduction.” J. Ind. Microbiol. Biotechnol. 2018, 45, 481-490.

Zalatan, J.G. “CRISPR-Cas RNA scaffolds for transcriptional programming in yeast.” Meth. Mol. Biol. 2017, 1632: 341-357.

Good, M.C., Zalatan, J.G., and Lim, W.A. “Scaffold proteins: Hubs for controlling the flow of cellular information.” Science 2011, 332, 680-686.

Lassila, J.K.,* Zalatan, J.G.,* and Herschlag D. “Biological phosphoryl-transfer reactions: Understanding mechanism and catalysis.” Annu. Rev. Biochem. 2011, 80, 669-702.

Zalatan, J.G. and Herschlag, D. “The far reaches of enzymology.” Nat. Chem. Biol. 2009, 5, 516-520.