Publications 2026 Bhattarai N, Moore JP, Payne S, Harshey RM (2026). Aer is a bidirectional redox sensor mediating negative chemotaxis to antibiotic-induced ROS in Escherichia coli. mBio 0:e00381-26. https://journals.asm.org/doi/10.1128/mbio.00381-26 Ho, K. & Harshey, R. M. (2026). Phage Mu enlists the β-sliding clamp for late gene transcription. Proceedings of the National Academy of Sciences 123, e2519494123. https://www.pnas.org/doi/10.1073/pnas.2519494123 2025 Bhattarai N, Guo W, Partridge JD, Harshey RM. (2025). Texas 2-step: a new model for YcgR::c-di-GMP action at the flagellar motor. J Bacteriol 0:e00353-25. https://doi.org/10.1128/jb.00353-25 Hwang Y, Perez M, Holzel R, Harshey RM. (2025). c-di-GMP is required for swarming in E. coli, producing colanic acid that acts as surfactant. mBio 0:e00916-25. https://doi.org/10.1128/mbio.00916-25 Ho K, Harshey RM. (2025) Membrane-associated σ factors disrupt rRNA operon clustering in Escherichia coli. PLOS Biology 23(4): e3003113. https://doi.org/10.1371/journal.pbio.3003113 2024 Bhattacharyya, Souvik & Lopez, Shelby & Singh, Abhyudai & Harshey, Rasika. (2024). Flagellar motility is mutagenic. Proceedings of the National Academy of Sciences. 121. 10.1073/pnas.2412541121. Partridge, Jonathan & Harshey, Rasika. (2024). Flagellar protein FliL: A many‐splendored thing. Molecular Microbiology. 122. 447-454. 10.1111/mmi.15301. 2023 Bhattacharyya, Souvik & Bhattarai, Nabin & Pfannenstiel, Dylan & Wilkins, Brady & Singh, Abhyudai & Harshey, Rasika. (2023). A heritable iron memory enables decision-making in Escherichia coli. Proceedings of the National Academy of Sciences. 120. 10.1073/pnas.2309082120. Partridge, Jonathan & Dufour, Yann & Hwang, YuneSahng & Harshey, Rasika. (2023). Flagellar motor remodeling during swarming requires FliL. Molecular Microbiology. 120. n/a-n/a. 10.1111/mmi.15148. Hwang, YuneSahng & Harshey, Rasika. (2023). A Second Role for the Second Messenger Cyclic-di-GMP in E. coli: Arresting Cell Growth by Altering Metabolic Flow. mBio. 14. e0061923. 10.1128/mbio.00619-23. 2022 Bhattacharyya, S. et al. Efflux-linked accelerated evolution of antibiotic resistance at a population edge. Mol Cell 82, 4368-4385.e6. dio: 10.1016/j.molcel.2022.10.024 2021 Ho, K. & Harshey, R. M. Goodbye PAM: Phage λ’s Red recombination system cripples PAMs and helps dodge CRISPR attacks. Cell Host & Microbe 29, 1469–1471. doi: 10.1016/j.chom.2021.09.011 2020 Bhattacharyya S., Walker, D.M. and Harshey, R.M. Dead cells release a ‘necrosignal’ that activates antibiotic survival pathways in bacterial swarming. Nature Comm. 11(1):4157. doi: 10.1038/s41467-020-17709-0. Walker D.M. and Harshey R.M. Deep sequencing reveals new roles for MuB in transposition immunity and target-capture, and redefines the insular Ter region of E. coli Mob DNA. 11:26. doi: 10.1186/s13100-020-00217-9. Partridge, J.D., Nhu, N.T.Q., Dufour, Y. and Harshey, R.M. Tumble Suppression is a Conserved Feature of Swarming Motility. mBio. doi: 10.1128/mBio.01189-20 Partridge, J.D. and Harshey, R.M. Investigating Flagella-Driven Motility in Escherichia coli by Applying Three Estalished Techniques in a series. J. Vis. Exp. doi: 10.3791/61364. Walker, D.M., Freddolino, P.L. and Harshey, R.M. A Well-Mixed E. coli Genome: Widespread Contacts Revealed by Tracking Mu Transposition. Cell. doi: 10.1016/j.cell.2020.01.031 2019 Nieto, V., Partridge, J.D., Severin, G.B., Lai, R.Z., Waters, C.M., Parkinson, J.S. and Harshey, R.M. Under Elevated c-di-GMP in Escherichia coli, YcgR Alters Flagellar Motor Bias and Speed Sequentially, with Additional Negative Control of the Flagellar Regulon via the Adaptor Protein RssB. J. Bacteriol. doi: 10.1128/JB.00578-19 Partridge, J.D., Nhu, N.T.Q., Dufour, Y.S., and Harshey, R.M. Escherichia coli remodels the chemotaxis pathway for swarming. mBio. Mar 10;2: doi: 10.1128/mBio.00316-19 2018 Bhattacharyya, S., Soniat, M.M., Walker, D., Jang, S., Finkelstein, I.J., and Harshey, R.M. Phage Mu Gam protein promotes NHEJ in concert with Escherichia coli ligase. Proc. Natl. Acad. Sci. Dec 11;115(50): E11614-E11622. doi: 10.1073/pnas.1816606115 Partridge, J.D., Ariel, G., Schvartz, O., Harshey, R.M., and Be’er, A. The 2D architecture of a bacterial swarm has implications for antibiotic tolerance. Sci. Rep. Oct 25;8(1): 15823. doi: 10.1038/s41598-018-34192-22016 H. K. Kim and R. M. Harshey. A diguanylate cyclase acts as a cell division inhibitor in a two-step response to reductive and envelope stresses. MBio. Aug 9;7(4). pii: e00822-16. doi: 10.1128/mBio.00822-16 2015 G. Ariel, A. Rabani, S. Benisty, J. D. Partridge, R. M. Harshey and A. Be’er. Swarming Bacteria Migrate by Levy Walk. Nature Comm. Sep 25;6:8396. doi: 10.1038/ncomms9396 R. M. Harshey and J. D. Partridge. Shelter in a Swarm. J. Mol. Biol. Aug 12. pii: S0022-2836(15)00448-9. doi: 10.1016/j.jmb.2015.07.025 S. Jang and R. M. Harshey. Repair of transposable phage Mu DNA insertions begins only when the E. coli replisome collides with the trasnpososome. Mol. Microbiol. Aug;97(4):746-58. doi: 10.1111/mmi.13061 J. D. Partridge, V. Nieto and R. M. Harshey. A new player at the flagellar motor: FliL controls both motor output and bias. MBio. Feb 24;6(2):e02367. doi: 10.1128/mBio.02367-14 J. Lee, A. F. Monzingo, A. T. Keatinge-Clay and R. M. Harshey. Structure of Salmonella FlhE, conserved member of a flagellar type III secretion operon. J. Mol. Biol. Mar;427:1254062 doi: 10.1016/j.jmb.2014.11.022 2014 R.M. Harshey. Transposable Phage Mu. Microbiol. Spectr. Oct;2(5) doi: 10.1128/microbiolspec.MDNA3-0007-2014 W. Choi, S. Jang and R. M. Harshey. Mu transpososome and RecBCD nuclease collaborate in the repair of simple Mu insertions. Proc. Natl. Acad. Sci. USA. Sep 30;111(39):14112-7. doi: 10.1073/pnas.1407562111 W. Choi, R. P. Saha, S. Jang and R. M. Harshey. Controlling DNA degradation from a distance: a new role for the Mu transposition enhancer. Mol. Microbial. Nov;94(3):595-608. doi: 10.1111/mmi.12781 2013 R. P. Saha, Z. Lou, L. Meng and R. M. Harshey. Transposable prophage Mu is organized as a stable chromosomal domain of E. coli. Plos Genetics. Nov;9(11):e1003902. doi: 10.1371/journal.pgen.1003902 J. D. Partridge and R. M. Harshey. Swarming: flexible roaming plans. J. Bacteriol. Mar;195(5):909-18. doi: 10.1128/JB.02063-12 J. D. Partridge and R. M. Harshey. More than motility: Salmonella flagella contribue to overriding friction and facilitating colony hydration during swarming. J. Bacteriol. Mar;195(5):919-29. doi: 10.1128/JB.02064-12 2012 M. D. Lazova, M. T. Butler, T. S. Shimizu and R. M. Harshey. Salmonella chemoreceptors McpB and McpC mediate a repellent response to L-cystine: a potential mechanism to avoid oxidative conditions. Mol. Microbiol. May;84(4):697-711. doi: 10.1111/j.1365-2958.2012.08051.x Harhsey, R.M. The Mu story: how a maverick phage moved the field forward. Mob DNA. Dec 5;3(1):21. doi: 10.1186/1759-8753-3-21 S. Jang. S. J. Sandler and R. M. Harshey. Mu insertions are repaired by the double strand break repair pathway of E. coli. PLoS Genetics. Apr;8(4):e1002642. doi: 10.1371/journal.pgen.1002642 J. Lee, and R. M. Harshey. Loss of FlhE in the flagellar type III secretion system allows proton inflx into Salmonella and E. coli. Mol Microbial. May;84(3):550-65. doi: 10.1111/j.1365-2958.2012.08043 2011 A. Be’er and R. M. Harshey. Collective motion of surfactant-producing bacteria imparts superdiffusivity to their upper surface. Biophys. J. 101:1017-24. doi: 10.1016/j.bpj.2011.07.019 J. Ge, Z. Lou, H. Cui, L. Shang and R. M. Harshey. Analysis of phage Mu DNA transposition by whole-genome E. coli tiling arrays reveals a complex relationship to distribution of large selection protein B, transcription and chromosome architectural elements. J. Biosci. Sep;36(4):587-601. PubMed PMID: 21857106 2010 K. Paul. V. Nieto, W. C. Carliquist, D. F. Blair and R. M. Harshey. The c-di-GMP binding protein YcgR controls flagellar motor direction and speed to affect chemotaxis by a ‘backstop break’ mechanism. Mol. Cell. Apr 9;38(1):128-39. doi: 10.1016/j.molcel.2010.03.001 W. Choi and R. M. Harshey. DNA repair by the cryptic endonuclease activity of Mu transposase. Proc. Natl. Acad. Sci. USA. Jun 1;107(22):10014-9. doi: 10.1073/pnas.0912615107 M. Butler, Q. Wang and R. M. Harshey. Cell density and mobility protect swarming bacteria against antibiotic., Proc. Natl. Acad. Sci. USA. Feb 23;107(8):3776-81. doi: 10.1073/pnas.0910934107 R. P. Alexander, A. C. Lowenthal, R. M. Harshey and K. M. Ottemann. CheV: CheW-like coupling proteins at the core of the chemotaxis signaling network. Trends Microbial. Nov;18(11):494-503. doi: 10.1016/j.tim.2010.07.004 J. Ge, Z. Lou and R. M. Harshey. Immunity of replicating Mu to self-integration: a novel mechanism employing MuB protein. Mob DNA. Feb 1;1(1):8. doi: 10.1186/1759-8753-1-8
