About

Mark Goulian is the Charles and William L. Day Distinguished Professor in the Natural Sciences at the University of Pennsylvania's Department of Biology. His research interests focus on Microbiology, Genetics, Epigenetics, Genomics, and Computational Biology. He is based in the 204F Lynch Laboratory and can be contacted via goulian@sas.upenn.edu. The information provided highlights his distinguished professorship and his broad research focus within the biological sciences, particularly emphasizing microbial systems and genetic and computational approaches.

Research topics

• Biology
• Genetics
• Microbiology
• Biochemistry
• Cell biology
• Bioinformatics
• Ecology

Selected publications

• An <i>Escherichia coli</i> Phosphotransferase System Modulates Methylglyoxal Resistance by Regulating Intracellular Potassium

  Molecular Microbiology · 2026-04-10

  articleOpen accessSenior author

  ABSTRACT Methylglyoxal is a toxic aldehyde produced during cellular metabolism across all domains of life. To cope with methylglyoxal stress, Escherichia coli employs the glyoxalase detoxification pathway coupled with Kef‐mediated potassium/proton antiport. However, the Kef system is protective only when extracellular potassium is well below concentrations typically found in mammalian hosts. The regulatory phosphotransferase system (PTS) that is historically known as the nitrogen‐related PTS (PTS Ntr ) has previously been shown to modulate potassium homeostasis and other processes in E. coli . Here, we identified this regulatory PTS as a mediator of methylglyoxal resistance for potassium concentrations that are comparable to those encountered in the context of host colonization or infection. We found that loss of unphosphorylated PtsN increases survival in methylglyoxal, and that this depended on the potassium/proton antiporter YcgO, whose activity decreases intracellular potassium and pH. While cytoplasmic acidification has been hypothesized to underlie protection from methylglyoxal via potassium/proton antiport, our results suggest the effects of acidification and intracellular potassium cannot be easily separated. Loss of potassium import through Trk increased survival in methylglyoxal and decreased intracellular potassium with only a relatively small decrease in pH. Moreover, the addition of acetate, which acidifies the cytoplasm and protects cells from methylglyoxal, also decreased intracellular potassium. Our results demonstrate that for extracellular potassium levels relevant for host infection and colonization, PtsN modulates methylglyoxal resistance by regulating potassium transport, and that low intracellular potassium, in addition to acidification, could play a direct role in protecting against methylglyoxal stress.

  PublisherDOI

• A phosphohistidine phosphatase promotes starvation survival by dephosphorylating nucleoside diphosphate kinase

  Cell Reports · 2026-01-01

  articleOpen accessSenior author

  Nucleoside diphosphate kinase (Ndk) is a ubiquitous enzyme that maintains the cellular nucleoside triphosphate (NTP) pool and participates in many other pathways of eukaryotes and prokaryotes. Here, we show that in Escherichia coli, Ndk is regulated by dephosphorylation of its phosphohistidine intermediate via the phosphatase SixA, thereby inhibiting nucleotide phosphoryl transfer activity. We further show that loss of this regulation alters the metabolic state of E. coli in low-nutrient conditions and reduces survival in long-term stationary phase. Similar regulation of Ndk by a phosphohistidine phosphatase has been reported previously for human cells, although the molecular interactions differ. The prevalence of SixA and Ndk orthologs in prokaryotes and the appearance of this regulatory mechanism in both E. coli and humans suggest that phosphohistidine phosphatase-mediated control of nucleoside diphosphate kinases may be widespread.

  PublisherOA PDFDOI

• Bacterial cell widening alters periplasmic size and activates envelope stress responses

  The EMBO Journal · 2025-09-03 · 2 citations

  articleOpen access

  The Rcs signal transduction system is a phosphorelay responsible for sensing enterobacterial cell envelope stresses. In Escherichia coli, the Rcs system is required to survive treatment with A22 and mecillinam, antibiotics that perturb cell size. To test whether size changes are correlated with envelope damage and thereby sensed by the Rcs system, we tuned E. coli cell size via A22 treatment, mutations in the cell-shape determinant MreB, and mechanically confined growth. In all conditions, cell width was strongly correlated with Rcs activation, and RcsF, the outer-membrane-localized upstream component, was essential for responding to cell width changes. Several gene deletions that induce Rcs resulted in cells that were wider than wild-type. Cryo-electron microscopy revealed that the periplasm of a wide MreB mutant is ~3 nm thinner than in wild-type cells, bringing RcsF closer to the downstream, inner-membrane-localized components of the signaling cascade. Conversely, extending the RcsF linker region in wild-type cells by ~3 nm increased Rcs activity. Thus, we propose that the Rcs system responds to changes in cell width due to altered periplasmic thickness.

  PublisherOA PDFDOI

• Cryoelectron microscopy image of wild-type Escherichia coli cell

  EMPIAR dataset · 2025-06-27

  datasetOpen access

  EMPIAR, the Electron Microscopy Public Image Archive centered at EMBL-EBI, is a public resource for raw electron microscopy images related to EMDB, contains micrographs, particle sets and tilt-series.

  PublisherDOI

• Cryoelectron microscopy image of MreB R193C Escherichia coli cell

  EMPIAR dataset · 2025-06-30

  datasetOpen access

  EMPIAR, the Electron Microscopy Public Image Archive centered at EMBL-EBI, is a public resource for raw electron microscopy images related to EMDB, contains micrographs, particle sets and tilt-series.

  PublisherDOI

• 657: CARBOHYDRATE CONSUMPTION DRIVES ADAPTIVE MUTATIONS IN ESCHERICHIA COLI INCREASING THE RISK FOR SYSTEMIC INFECTIONS

  Gastroenterology · 2025-05-01

  article
  PublisherDOI

• Platelet factor 4 modulates endothelial cell antimicrobial activity to enhance bacterial clearance and improve sepsis outcomes

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-03

  preprintOpen access

  ABSTRACT Sepsis is a life-threatening condition characterized by dysregulated host responses to infection. Here, we identify platelet factor 4 (PF4) as a key mediator of vascular antimicrobial defense. In vitro, PF4 enhanced endothelial cell internalization of Escherichia coli via interactions with the PF4 receptor CXCR3 and the endothelial glycocalyx, directing bacteria to clathrin-mediated endocytosis and lysosomal degradation. In vivo, PF4 administration improved survival and reduced sepsis severity, bacterial burden, inflammation, and thrombosis in wild-type (WT) and PF4 knockout ( PF4 − / − ) mice challenged with systemic polymicrobial infection. Using intravital microscopy, we observed that infused bacteria were rapidly sequestered in the pulmonary microvasculature. However, PF4 − / − mice exhibited impaired bacterial clearance and increased microvascular platelet adhesion and aggregation. In the liver, following Kupffer cell depletion, PF4 − / − mice had increased sinusoidal platelet accumulation, larger bacterial aggregates, and elevated hepatic bacterial burden compared to WT controls. Collectively, these findings reveal that PF4 promotes bacterial clearance and restrains immunothrombosis during sepsis in part via endothelial cell uptake and destruction of microbes. By enhancing endothelial antimicrobial function, PF4 represents a significant yet previously underrecognized host defense mechanism that limits bacterial spread and alleviates vascular injury during infection. KEY POINTS In vitro, PF4 accelerates bacterial clearance by enhancing endothelial uptake of bacteria and promoting their trafficking to the lysosome. In murine sepsis, PF4 augments pathogen clearance to reduce infection severity, limit organ injury, and improve survival.

  PublisherOA PDFDOI

• Platelet factor 4 (PF4) modulates endothelial cell antimicrobial activity to enhance bacterial clearance and improve sepsis outcomes

  Blood · 2025-11-03

  articleOpen access

  Abstract Introduction: Upon sensing pathogens, platelets (plt) release high concentrations of the positively charged chemokine PF4 from their ⍺-granules. PF4 rapidly binds to endothelial chemokine receptor, CXCR3B, and forms electrostatic interactions with glycosaminoglycans (GAGs) on the endothelial cell (EC) glycocalyx. PF4 similarly forms complexes with anionic polymers in the bacterial cell wall, bridging bacteria to ECs. This study aims to investigate mechanisms by which ECs and plt collaborate to promote bacterial clearance, paving the way for translational studies on PF4-based therapeutics for sepsis. Methods: PF4-mediated bacterial aggregation: Escherichia (E) coli (K-12 strain) (1x108 colony forming unit (CFU)/mL) were incubated with PF4 (0-100µg/mL). Bacterial cluster size was quantified with scanning electron microscope (SEM). PF4 effects on in vitro EC-mediated bacterial clearance: Human umbilical vein ECs (HUVECs) were incubated with TNF⍺ (20ng/mL) to induce inflammation. A subset was then pre-treated with AMG-487 (20µg/mL), Dynasore (100µM), Pitstop (30µM), heparinases (1U/mL), or hydroxychloroquine (HCQ; 50µM). Prior to exposure to E coli at a multiplicity of infection of 10 ± PF4 (25µg/mL) for 1h at 37°C. ECs were then washed with PBS to remove unbound bacteria and incubated for up to 5h. HUVEC culture supernatant was collected every hour to quantify lactate dehydrogenase (LDH) release. Cells were treated with 1% penicillin-streptomycin for 1h at 37°C to kill extracellular bacteria and lysed for internalized CFU enumeration. PF4 effects on in vivo bacterial clearance: Twelve-to-16-week-old WT and PF4-/- mice on a C57BL/6J background received intravenous (I.V) injection of cecal slurry (CS; 20mg) ± PF4 (100µg). Sepsis severity and mortality were assessed up to 96h. Blood and organ homogenates were subjected to CFU enumeration at 24h. Visualizing PF4-mediated bacterial clearance in vivo: WT and PF4-/-mice received I.V infusions of GFP-expressing E coli (1x109 CFU) and underwent lung and liver intravital microscopy. Lung and liver CFUs were quantified at 15min and 2h. A subset of mice received intraperitoneal injections of clodronate liposomes to deplete Kupffer cells (KC) 3 days prior to imaging. Results: E. coli cluster size rose from 3.09µm2 at baseline to 4.06µm2 and 5.24µm2with 20 and 100µg/mL of PF4, respectively. Two hours post E coli exposure, HUVECs incubated with bacteria and PF4 exhibited higher intracellular CFUs, indicating enhanced uptake. LDH levels did not differ between groups suggesting increased bacterial uptake was not associated with EC injury. Surprisingly, from 3 to 5h, intracellular CFUs declined in PF4-treated group, falling below levels observed in untreated cells, suggesting accelerated intracellular bacterial clearance. CXCR3 inhibition, removing GAGs, and blocking endocytosis decreased E coli internalization. Lysosomal alkalinization resulted in a marked increase in intracellular E coli, suggesting that PF4 promotes bacterial uptake through interaction with endothelial CXCR3 and GAGs, leading to clathrin-mediated endocytosis, followed by trafficking to lysosomes for killing. CS-challenged PF4-/-mice had reduced survival compared to WT animals (100% vs 33% mortality). All of WT mice and 62.5% of PF4-/- mice that received CS+PF4 were protected from mortality. In both genotypes, PF4 significantly reduced CFUs in blood, lung, and liver compared to genotype-matched mice given CS alone. Intravital imaging studies revealed that PF4-/-mice exhibited higher E coli count, increased residual CFUs, and more pronounced plt aggregation in the pulmonary microvasculature. In the liver microcirculation of both genotypes, E coli was similarly sequestered by KC, suggesting that PF4 does not influence KC-mediated bacterial trapping despite higher residual CFUs in PF4-/- mice. Post KC-depletion, PF4-/- mice exhibitedlarger E coli aggregates and increased plt accumulation inthe hepatic sinusoids as compared to WT mice, suggesting that PF4 facilitates bacterial clearance in liver through a mechanism partly independent of KC phagocytic activity. Conclusion: This study uncovers a critical role for plt PF4 in enhancing host defense against bloodstream infections by promoting EC uptake and clearance of bacteria. Beyond expanding the known functions of PF4, our findings support a broader concept that ECs, long recognized as a passive barrier, actively contribute to innate immune defense during systemic infection.

  PublisherOA PDFDOI

• 248: DETERMINANTS OF TRIMETHYLAMINE-N-OXIDE (TMAO) FECAL LEVELS AT THE INTERFACE BETWEEN DIET, THE GUT MICROBIOTA, AND BOTH THE MOUSE AND HUMAN HOSTS

  Gastroenterology · 2025-05-01

  article
  PublisherDOI

• Carbohydrate consumption drives adaptive mutations in <i>Escherichia coli</i> associated with increased risk for systemic infection

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-03-26 · 1 citations

  preprintOpen access

  Abstract Dissemination of organisms from the gut microbiota is a major contributor to sepsis and critical illness. Patients with cirrhosis are prone to systemic infections and are commonly prescribed the carbohydrate lactulose to manage hepatic encephalopathy (HE) 1 . Commensal metabolism of lactulose is believed to reduce pathobiont colonization through short-chain fatty acid production, but its direct effects on gut pathobionts remain unexplored 2 . Here, we show that lactulose consumption unexpectedly selects for mutations in Escherichia coli lactose (lac) operon regulation, enhancing its metabolic fitness and colonization capacity. This is mediated by selection for constitutive expression of the lac operon through mutations in its regulatory components. Using in vitro systems, murine models, and clinical samples, we demonstrate that these mutations enable E. coli to exploit lactulose as a carbon source, bypassing host carbohydrate metabolism and increasing its intestinal colonization. Despite its long-standing use in HE treatment, we find that lactulose has a paradoxical association with risk of infection hospitalization in patients with cirrhosis in a large epidemiologic study. The emergence of lactulose-adapted E. coli strains could be suppressed by a dietary oligosaccharide that competitively inhibits lactulose uptake. These findings reveal a mechanism by which dietary substrates exert selective pressure on the microbiome, with implications for diet-based strategies to modulate microbial evolution and infection risk.

  PublisherOA PDFDOI

Recent grants

• NIH Grant T32AI060516

  NIH · $2.0M · 2017

• Oxygen-dependent bacterial signaling

  NIH · $3.7M · 2007–2021

• NIH Grant R21AI125814

  NIH · $443k · 2019

• Imaging Two-Component Systems in E. Coli

  NSF · $426k · 2006–2010

Frequent coauthors

• Manuela Roggiani

  University of Pennsylvania

  33 shared

• Srujana S. Yadavalli

  Rutgers Sexual and Reproductive Health and Rights

  17 shared

• Kathleen J. Stebe

  University of Pennsylvania

  15 shared

• Gary D. Wu

  University of Pennsylvania

  15 shared

• Jun Zhu

  University of Pennsylvania

  14 shared

• Daeyeon Lee

  University of Pennsylvania

  14 shared

• Kandace Gollomp

  Children's Hospital of Philadelphia

  13 shared

• Sarah D. Hann

  California University of Pennsylvania

  11 shared

Awards & honors

• Charles and William L. Day Distinguished Professor in the Na…