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Kit Pogliano

Research

Our research helped establish modern bacterial cell biology by revealing that bacteria and their viruses possess sophisticated intracellular organization once thought to be unique to eukaryotic cells. Using advanced imaging, genetics, and quantitative biology, we investigate how bacterial cells build, remodel, and evolve dynamic cellular architectures, while developing transformative technologies for antibiotic discovery and biotechnology.

Cellular Mechanisms of Bacillus subtilis Sporulation

The Bacillus subtilis sporulation pathway provides striking examples of bacterial cellular remodeling and differentiation. Our laboratory developed quantitative imaging and genetic approaches that provided the first mechanistic model for engulfment during sporulation, a phagocytosis-like process in which one cell surrounds another during endospore formation. These studies demonstrated that coordinated synthesis and degradation of peptidoglycan actively drive membrane migration around the developing spore and identified the SpoIIQ-SpoIIIAH (Q-A) complex as a molecular landmark and mechanical ratchet that facilitates this process.

More recently, we discovered that sporulation involves extensive metabolic specialization, with the forespore selectively dismantling central metabolic pathways and becoming dependent on the mother cell for biosynthetic precursors. Together, these studies are revealing unexpected parallels between bacterial differentiation and metabolic cooperation in multicellular organisms and demonstrated how conserved cellular processes can be repurposed to generate complex developmental programs.

Accelerating Antibiotic Discovery

Our laboratory co-invented Bacterial Cytological Profiling (BCP) and Rapid Inhibition Profiling, imaging-based platforms that transformed antibiotic mechanism-of-action studies by enabling rapid cellular classification of antimicrobial compounds and identification of antibiotics with new cellular targets. These widely adopted technologies accelerated antibiotic discovery in both academia and industry and established new approaches for linking cellular phenotypes with molecular mechanisms.

To broaden the reach of this technology, Joe Pogliano and I co-founded Linnaeus Bioscience, where our team integrates high-content imaging with AI-driven analysis to accelerate discovery of antibacterial, antifungal, and antimycobacterial therapeutics. Ongoing efforts focus on developing next-generation imaging and analytical technologies that connect antimicrobial phenotypes with molecular mechanisms in living cells.

Jumbo Phage and the Evolution of Cellular Complexity

Working with Joe Pogliano, Elizabeth Villa and collaborators, we discovered that certain jumbo bacteriophages construct nucleus-like compartments inside bacterial cells. These phages, known as the Chimalliviridae, assemble selectively permeable protein-bound organelles that compartmentalize viral DNA replication, transport proteins and RNA, and organize phage assembly in space and time. They also use tubulin-based systems for intracellular positioning and capsid trafficking, revealing an unexpected level of organization in bacterial viruses.

These discoveries overturned longstanding assumptions about the simplicity of prokaryotic viruses and established bacterial phage as powerful new models for understanding the evolution of cellular compartmentalization and intracellular organization. Ongoing work seeks to understand how these systems evolve and how they can be harnessed for phage therapeutics and synthetic biology.

Collectively, our studies continue to uncover sophisticated intracellular organization, differentiation, and compartmentalization in bacterial systems, revealing new principles underlying cellular complexity in bacteria and their viruses while enabling new technologies for antibiotic discovery and biotechnology.

Select Publications

Foundational contributions to bacterial cell biology and sporulation

  • Abanes-de Mello, A., Y.-L. Sun, S. Aung and K. Pogliano. (2002) A cytoskeleton-like role for the bacterial cell wall during engulfment of the B. subtilis forespore.  Genes & Development 16:3253-3264.
  • Sharp, M.D. and K. Pogliano. (2002) Role of cell-specific assembly of SpoIIIE in polarity of DNA transfer.  Science 295:137-139.
  • Broder, D. and K. Pogliano. (2006) Forespore engulfment mediated by a ratchet-like mechanism. Cell 126:917-928.
  • Ptacin, J., M. Nollmann, E.C. Becker, N.R. Cozzarelli, K. Pogliano and C. Bustamante. (2008) Sequence-directed DNA export guides chromosome translocation during sporulation in Bacillus subtilis. Nature Structural and Molecular Biology 15:485-493.
  • Ojkic, N, J. López-Garrido, K. Pogliano and R.G. Endres. (2016) Cell wall remodeling drives engulfment during Bacillus subtilis sporulation, eLife, Nov. 17, e18657
  • Riley, E.P., J. López-Garrido, J. Sugie, R.B. Liu and K. Pogliano. (2021) Metabolic differentiation and intercellular nurturing underpin bacterial endospore formation. Science Advances, 7:eabd6385.
  • Riley, E.P., J. Lydia, J. Octavio Reyes-Matte, J. Sugie, I.R. Kasu, E. Enustun, E.G. Armbruster, S. Ravishankar, R.L. Isaacson, A.H. Camp, J. López-Garrido, and K. Pogliano. (2025) Developmentally regulated proteolysis by MdfA and ClpCP mediates metabolic differentiation during Bacillus subtilis sporulation. Genes and Development 39:524–537

Transformative technologies for antibiotic discovery 

  • Lamsa, A., W.-T. Liu, P.C. Dorrestein and K. Pogliano. (2012) The Bacillus subtilis cannibalism toxin SDP collapses the proton motive force and induces autolysis. Molecular Microbiology 84:486-500.
  • Nonejuie, P., M. Burkhart, K. Pogliano and J. Pogliano. (2013) Bacterial cytological profiling rapidly identifies the cellular pathways targeted by antibacterial molecules. Proc. Natl. Acad. Sci., USA 110:16169-16174.
  • Lamsa, A., J. López-Garrido, D.T. Quach, E.P. Riley, J. Pogliano and K. Pogliano. (2016) Rapid inhibition profiling in Bacillus subtilis to identify the mechanism of action of new antimicrobials, American Chemical Society Chemical Biology, 11:2222-2231
  • Nonejuie, G.L., R. Trial, G.L. Newton, A. Lamsa, V.R. Perera, J. Aguilar, W.-T. Liu, P.C. Dorrestein, J. Pogliano and K. Pogliano. (2016) Application of bacterial cytological profiling to crude natural product extracts reveals the antibacterial arsenal of Bacillus subtilis, Journal of Antibiotics.69:353-361

Jumbo Phage and cellular complexity

  • Chaikeeratisak, V., K.T. Nguyen, K. Khanna, A.F. Brilot, M.L. Erb, J.K.C. Coker, A. Vavilina, G.L. Newton, R. Buschauer, K. Pogliano, E. Villa, D.A. Agard and J. Pogliano. (2017) Assembly of a nucleus-like structure during viral replication in bacteria, Science 355:194-197.
  • Chaikeeratisak, V., K. Khanna, M. Egan, M.L. Erb, A. Vavilina, K.T. Nguyen, P. Nonejuie, E. Niewglowska, A.F. Brilot, K. Pogliano, D.A. Agard, E. Villa, and J. Pogliano. (2019) Viral capsid trafficking along tubulin filaments in bacteria. Cell 177:1771-1780.
  • Birkholz EA, Morgan CJ, Laughlin TG, Lau RK, Prichard A, Rangarajan S, Meza GN, Lee J, Armbruster EG, Suslov S, Pogliano K, Meyer JR, Villa E, Corbett KD, Pogliano J. (2024) A mobile intron facilitates interference competition between co-infecting viruses. Science, 385:105-112.
  • Armbruster EG, Lee J, Hutchings J, VanderWal AR, Enustun E, Adler BA, Aindow A, Deep A, Rodriguez ZK, Morgan CJ, Ghassemian M, Charles E, Cress BF, Savage DF, Doudna JA, Pogliano K, Corbett KD, Villa E, Pogliano J. (2025) Sequential membrane- and protein-bound organelles compartmentalize genomes during phage infection. Cell Host and Microbe 33(4):484-497.

Biography

Kit Pogliano received her Ph.D. from Harvard Medical School and completed postdoctoral training at Harvard University as a Damon Runyon-Walter Winchell Fellow. She joined the faculty at University of California San Diego in 1996 and became Dean of Biological Sciences in 2018, leading one of the nation’s premier biology programs, recognized for its distinguished faculty, pioneering research, and leadership in biological education and innovation.  Pogliano is the recipient of the Searle Scholar and Beckman Young Investigator awards and is an elected Fellow of the American Academy of Microbiology and the American Association for the Advancement of Science. 

For complete list of publications see: https://scholar.google.com/citations?user=BTJdkLwAAAAJ&hl=en

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