About

Mohammed Kaplan is an Assistant Professor of Microbiology at the University of Chicago within the Department of Microbiology. His research focuses on the in situ architecture of bacterial structures, including the endosymbiont Wolbachia pipientis, bacterial flagellar motors, and associated protein complexes. His work involves advanced imaging techniques such as cryo-electron tomography to reveal morphological remodeling during bacterial developmental cycles and to characterize the assembly and structure of bacterial motility apparatuses. Dr. Kaplan's contributions include discovering novel bacterial structures related to the flagellar Type III Secretion System, transient cytoplasmic rings that stabilize flagellar motors, and in situ imaging of outer membrane projections. He is actively involved in graduate programs across Microbiology, Biochemistry and Molecular Biophysics, and UChicago Biosciences, and maintains a research profile dedicated to understanding bacterial cell architecture and motility at nanometer resolution.

Research topics

• Chemistry
• Biology
• Physics
• Biochemistry
• Biophysics
• Cell biology
• Microbiology
• Genetics
• Materials science
• Nanotechnology
• Anatomy

Selected publications

• Dual membrane-spanning anti-sigma 2 controls OMV biogenesis and colonization fitness in <i>Bacteroides thetaiotaomicron</i>

  Journal of Bacteriology · 2026-03-05

  articleOpen access

  ABSTRACT Bacteroides spp . are gram-negative, gut commensals that shape the enteric landscape by producing o uter m embrane v esicles (OMVs) that degrade dietary fibers and traffic immunomodulatory biomolecules. Understanding the mechanism behind OMV biogenesis in Bacteroides spp . is necessary to determine their role in the gut. Recent studies showed that mutation of d ual m embrane-spanning a nti-sigma factor 1 (Dma1) increased OMV production in Bacteroides thetaiotaomicron ( Bt ) by modulating the expression of its downstream regulon. Additional members of the Dma family have been identified, but very little is known regarding their roles in Bt . Here, we investigate the role of Dma2 in controlling OMV biogenesis in Bt . We employ biochemical and proteomic analyses to show that mutation of dma2 increases OMV production. This induction is dependent on the expression of its cognate sigma factor, das2 , but the precise mechanism by which dma2 increases OMV biogenesis remains elusive. Transcriptome analyses revealed that Δdma2 displays decreased expression of select p olysaccharide u tilization l oci (PULs) that primarily target host-associated glycans. Follow-up comparative proteomics showed that the PUL repertoire was most impacted in the OMV fraction. In vitro growth assessments confirmed that Δdma2 exhibits delayed growth in the presence of select host-associated glycans. In vivo co-colonization studies in mice revealed that Δdma2 is outcompeted by the wild-type in the gut, which indicates that Dma2 is a key determinant of colonization fitness in Bt . Altogether, these findings expand our knowledge of the Dma family’s role in OMV biogenesis and demonstrate their importance in Bacteroides physiology. IMPORTANCE Dual membrane-spanning anti-sigma factors (Dma) are a novel class of regulatory proteins found solely among Bacteroidota. Previous studies demonstrated the importance of Dma1 in vesiculation, but the overall role of the Dma family in Bacteroides physiology remains poorly understood. Here, we show that Dma2 modulates vesiculation and the expression of select polysaccharide utilization loci (PULs) that target host-associated glycans in vitro . Mouse studies revealed that Dma2 is an important fitness determinant in vivo when competing against kin bacteria. This work begins characterizing the multifaceted involvement of Dma2 in OMV biogenesis, PUL regulation, and colonization fitness.

  PublisherDOI

• Diel remodeling and cellular integration of the nitroplast

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-14

  articleOpen accessSenior authorCorresponding

  Abstract Nitrogen-fixing eukaryotes were not believed to exist in nature until the recent discovery of a N 2 -fixing organelle, or nitroplast, in the marine microalga Braarudosphaera bigelowii . This nitroplast (formerly known as UCYN-A2) has long been recognized as key cyanobacterial contributor to global oceanic N₂ fixation. However, how this novel organelle is integrated and regulated within the architecture of a eukaryotic cell remains unclear. Here, we combine multiscale volumetric imaging with cryo–electron tomography to resolve the native architecture, cellular integration, and diel remodeling of the nitroplast in cultured and environmental cells. We find that the nitroplast occupies up to 10% of the cell volume and exhibits close interfaces with multiple host organelles through membrane contact sites, while integration of this metabolically demanding compartment does not disrupt global scaling of host organelles. Interestingly, the chloroplast-to-nitroplast volume ratio is conserved across distinct life stages. Cryo-electron tomography reveals that the nitroplast retains a reinforced four-layer cyanobacterial envelope and is additionally surrounded by two host-derived layers that remodel across the day–night cycle. During daytime N₂ fixation, these host-derived barriers become locally discontinuous and the organelle interface becomes enriched with two distinct vesicle populations. Our findings suggest that dynamic control of organelle accessibility through transient membrane gating represents a fundamental strategy by which eukaryotic cells could domesticate new endosymbiotic functions during early organellogenesis.

  PublisherOA PDFDOI

• Distinct motors, shared mechanics: unifying principles of microbial gliding

  Journal of Bacteriology · 2026-04-01

  articleOpen access

  Gliding motility is one of the more elegant tricks in the microbial playbook, allowing cells to move smoothly along an external surface. Unlike swimming in bulk fluid, gliding requires contact with a biotic or abiotic surface, imposing strong physical constraints on how forces are generated, transmitted, and dissipated. It is an active, energy-dependent process that operates without flagella, instead relying on specialized molecular machines that couple dynamic surface adhesins to motion. In this mini-review, we summarize recent advances that illuminate how distinct molecular motors converge on common mechanical principles to drive microbial gliding motility.

  PublisherDOI

• Author response for "Structural differences in the outer membrane‐associated flagellar rings between sheathed and unsheathed flagella"

  2025-01-15

  peer-reviewSenior author
  PublisherDOI

• Contributors

  Elsevier eBooks · 2025-01-01

  book-chapter
  PublisherDOI

• <i>In situ</i> architecture of the endosymbiont <i>Wolbachia pipientis</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-29

  preprintOpen accessSenior author

  ABSTRACT Hidden within host cells, the endosymbiont Wolbachia pipientis is the most prevalent bacterial infection in the animal kingdom. Scientific breakthroughs over the past century yielded fundamental mechanisms by which Wolbachia controls arthropod reproduction to shape dynamic ecological and evolutionary trajectories. However, the structure and spatial organization of symbiont machineries that underpin intracellular colonization and orchestrate maternal inheritance remain unknown. Here, we used cryo-electron tomography to directly image the nanoscale architecture of bacterial tools deployed for host manipulation and germline transmission. We discovered that Wolbachia assembles multiple structures at the host-endosymbiont interface including a filamentous ladder-like framework hypothesized to serve as a specialized motility mechanism that enables bacterial translocation to specific host cell compartments during embryogenesis and somatic tissue dissemination. In addition, we present the first in situ structure of the Rickettsiales vir homolog type IV secretion system ( rvh T4SS). We provide evidence that the rvh T4SS nanomachine exhibits architectural similarities to the pED208-encoded T4SS apparatus including the biogenesis of rigid conjugative pili extending hundreds of nanometers beyond the bacterial cell surface. Coupled with integrative structural modeling, we demonstrate that in contrast to canonical T4SS architectures, the α-proteobacterial T4SS outer membrane complex assembles a periplasmic baseplate structure predicted to comprise VirB9 oligomers complexed with cognate VirB10 subunits that form extended antennae projections surrounding the translocation channel pore. Collectively, these studies provide an unprecedented view into Wolbachia structural cell biology and unveil the molecular blueprints for architectural paradigms that reinforce ancient host-microbe symbioses.

  PublisherOA PDFDOI

• Structural differences in the outer membrane‐associated flagellar rings between sheathed and unsheathed flagella

  FEBS Letters · 2025-02-20 · 1 citations

  articleOpen accessSenior authorCorresponding

  The bacterial flagellar motor generates a torque to move the bacterium in its environment. Despite sharing a conserved core, flagellar motors of different species exhibit structural diversity with species-specific embellishments. These embellishments are classified into various types, including integrated (spanning the whole periplasmic space) or outer membrane (OM)-associated ones. Here, we used cryo-electron tomography to investigate the structural differences between the embellishments of sheathed and unsheathed flagella in various species. We discovered that the integrated embellishments of sheathed flagella have disks and rings with a constant diameter, while those of unsheathed flagella have components that vary significantly in diameter. Both unsheathed and sheathed flagella with OM-associated embellishments have components with constant diameter with a subset of motors having an additional extracellular ring. In this Hypothesis article, we propose that these differences may play a role in the formation of the sheath, as having large protein disks of various diameters underneath the OM may interfere with membrane bending to form the sheath.

  PublisherOA PDFDOI

• Dual Membrane-spanning Anti-Sigma 2 Controls OMV biogenesis and Colonization Fitness in <i>Bacteroides thetaiotaomicron</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-27

  preprintOpen access

  Abstract Bacteroides spp. are Gram-negative, gut commensals that shape the enteric landscape by producing o uter m embrane v esicles (OMVs) that degrade dietary fibers and traffic immunomodulatory biomolecules. Understanding the mechanism behind OMV biogenesis in Bacteroides spp. is necessary to determine their role in the gut. Recent studies showed that mutation of D ual M embrane-spanning A nti-sigma factor 1 increased OMV production in Bacteroides thetaiotaomicron ( Bt ) by regulating members of its downstream regulon. Additional members of the Dma family have been identified, but very little is known regarding their roles in Bt . Here, we investigate the role of D ual M embrane-spanning A nti-sigma factor 2 (Dma2 ) in controlling OMV biogenesis in Bt . We employ biochemical and proteomic analyses to show that mutation of dma2 increases OMV production in a manner that is dependent on the expression of its cognate sigma factor, das2 . The precise mechanism by which dma2 increases OMV biogenesis remains elusive. However, transcriptome analyses revealed that Δdma2 has decreased expression of select p olysaccharide u tilization loci (PULs) that primarily target host-associated glycans. Follow-up comparative proteomics showed that the PUL repertoire was most impacted in the OMV fraction. In vitro growth assessments showed that Δdma2 exhibits delayed growth in the presence of select host-associated glycans. Colonization studies in mice revealed that Δdma2 is outcompeted by the wild-type in the gut, which indicates that dma2 is a key determinant of colonization fitness in Bt . Altogether, these findings expand our knowledge of the Dma family’s role in OMV biogenesis and demonstrates their importance in Bacteroides physiology. Importance D ual m embrane-spanning a nti-sigma factors (Dma) are a novel class of regulatory system found solely amongst Bacteroidota. Previous studies have demonstrated the role of Dma1 in vesiculation, but the overall role of the Dma family in Bacteroides physiology remains poorly understood. Here, we demonstrate that Dma2 modulates vesiculation and regulates the expression of select p olysaccharide u tilization loci (PULs) that target host-associated glycans. In vivo studies revealed that Dma2 is an important fitness determinant when competing against kin bacteria. This work begins characterizing the multifaceted involvement of Dma2 in OMV biogenesis, PUL regulation, and colonization fitness.

  PublisherOA PDFDOI

• Preparing bacterial cells for cryo-electron tomography

  Elsevier eBooks · 2025-01-01

  book-chapter1st authorCorresponding
  PublisherDOI

• MotorBench: A Cryo-Electron Tomography Dataset of Bacterial Flagellar Motors for Testing Detection Algorithms

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-23

  preprintOpen access

  Abstract Understanding bacterial nanomachines like flagellar motors, which are crucial for pathogenic bacteria motility, is vital for microbiological and therapeutic research. Cryogenic electron tomography (cryo-ET) enables visualization of these structures within cells at near-native conditions. But manual identification remains challenging due to low contrast, limited resolution, and crowded in vivo environments. To address this, we introduce MotorBench, an expert-annotated dataset of bacterial flagellar motors that has been curated as part of a Kaggle competition BYU - Locating Bacterial Flagellar Motors 2025 , engaging data scientists globally to create automated detection algorithms. MotorBench and its accompanying tools are intended to serve as a benchmark for evaluating and comparing future algorithms in automated cryo-ET analysis.

  PublisherOA PDFDOI

Frequent coauthors

• Grant J. Jensen

  Brigham Young University

  73 shared

• Georges Chreifi

  California Institute of Technology

  23 shared

• Yi‐Wei Chang

  19 shared

• Qing Yao

  18 shared

• Catherine M. Oikonomou

  California Institute of Technology

  15 shared

• Yu-xi Liu

  13 shared

• Nancy Meyer

  Oregon Health & Science University

  13 shared

• Debnath Ghosal

  University of Melbourne

  12 shared