Biology subjects

Orman, M. A.

Publications and source records attributed to Orman, M. A..

7 recordsLinked to original sources

bioRxiv2026

Glycerol-Driven Energy and Proteostasis Underpin Antibiotic Tolerance in Escherichia coli

Bacterial persisters are frequently described as metabolically dormant, yet the endogenous metabolic programs that sustain survival during prolonged nutrient limitation remain poorly understood. Here, using stationary-phase Escherichia coli as a model of antibiotic tolerance, we combine proteomics, genetics, metabolic phenotyping, and single-cell imaging to define a metabolic framework underlying persistence. Perturbation of tricarboxylic acid cycle function broadly reprogrammed stationary-phase physiology, suppressing lipid and glycerol metabolism, altering energy homeostasis and proteostasis, and reducing antibiotic tolerance. Systems-level analyses identified phospholipid-derived glycerol catabolism as a central metabolic node linking endogenous carbon recycling to persistence. Genetic disruption of glycerol utilization impaired proton motive force homeostasis, reduced formation of large polar protein aggregates, altered division-associated remodeling, and sensitized cells to antibiotic-induced lysis. Functional metabolic assays further revealed that persisters retain a selective capacity to utilize glycerol for rapid proton motive force restoration without growth resumption. Together, our findings support a model in which stationary-phase persisters are not metabolically inert but sustained through endogenous metabolic rewiring that coordinates energy maintenance, proteostasis, and antibiotic tolerance.

microbiology↗

bioRxiv2025

The Role of c-Jun Signaling in Cytidine Analog-Induced Cell Death in Melanoma

Melanoma stands as an increasingly pressing health concern. Enhanced mitochondrial metabolism has been reported in melanoma cells that survived treatment with traditional therapeutics, including cytidine analogs like gemcitabine (GEM). These findings suggest that chemotherapeutic drugs may play dual roles in promoting both cell survival and cell death, although the underlying mechanisms require further investigation. Herein, we conducted proteomics analysis on GEM-treated melanoma cells and found a drug-induced activation of DNA damage response and apoptosis, along with cell cycle arrest. Additionally, GEM treatment significantly altered protein networks related to mitochondrial ribosomal activity, the electron transport chain, and translation. Furthermore, we reported an upregulation of the JNK/c-Jun network in connection with the apoptotic proteins. Co-treatment with a Jun N-terminal Kinase (JNK) inhibitor, JNK-IN-8 (JNKi), significantly increased cell survival, suggesting the involvement of c-Jun signaling in GEM-induced cell death. Additionally, proteomics analysis revealed that JNKi downregulated apoptosis in co-treated cells, highlighting the potential role of the JNK/c-Jun network inhibition in chemotherapeutic tolerance. Collectively, our findings bridge gaps in understanding how melanoma cells respond to cytidine analogs by demonstrating the multifaceted effects of these agents in 1) inducing JNK-mediated apoptotic cell death, and 2) promoting a state of cell cycle inhibition.

cancer biology↗

bioRxiv2024

The Diverse Phenotypic and Mutational Landscape Induced by Fluoroquinolone Treatment

Despite extensive research on antibiotic resistance, the potential effects of antibiotic treatments on bacterial tolerance and resistance remain a significant concern. Although bacterial cells adopt a variety of mutational strategies to resist unfavorable circumstances, it is still unclear how antibiotic tolerance and resistance mechanisms affect bacterial fitness characteristics and whether evolved mutants exhibit similar properties across different cell populations subjected to the same conditions. Here, we used Escherichia coli, a fluoroquinolone antibiotic (ofloxacin), and adaptive laboratory evolutionary experiments to demonstrate that ofloxacin tolerance and resistance can evolve independently across different cell populations exposed to identical conditions. Fitness attributes, such as lag score, doubling time, competition score, and other metabolic features, were variably affected by antibiotic tolerance and resistance mechanisms. However, we did not observe strong and apparent correlations between fitness trade-offs and antibiotic tolerance and resistance. While our whole-genome sequencing identified some shared mutations, such as single nucleotide polymorphisms in the icd gene (a crucial citric acid cycle gene), evolved cell populations exhibited diverse genetic mutations without a clear pattern of a conserved evolutionary pathway. Our study also identifies unique phenotypes, such as those displaying significantly lower minimum inhibitory concentration levels compared to the parental strain yet showing remarkably high tolerance to the same antibiotic. Altogether, our study, examining the phenotypic and mutational landscapes of fluoroquinolone-induced strains, contributes to our understanding of complex bacterial adaptation mechanisms.

microbiology↗

bioRxiv2024

UV-Induced DNA Repair Mechanisms and Their Effects on Mutagenesis and Culturability in Escherichia coli

Ultraviolet-B (UV-B) radiation, intensified by ozone depletion, induces DNA damage and promotes mutagenesis, shaping evolution. While UV-induced SOS responses are well characterized in bacteria, the cellular consequences of prolonged UV-B exposure remain less clear. Prolonged UV-B exposure disrupts translation and RecA-mediated SOS induction without major changes in membrane permeability or reactive oxygen species. This impairs mutagenesis and induces a reversible loss of culturability. Genetic analysis reveals both redundant and differential roles for DNA repair pathways: homologous recombination (RecA, RecB), nucleotide excision repair (UvrA), and translesion synthesis (UmuC/D) are essential for maintaining mutagenesis and culturability, while others (RecN, RmuC) have limited impact. Notably, deletion of UvrD (a repair-associated helicase) intensifies transient non-culturability without affecting mutagenesis, underscoring complexity in repair networks. Overall, our findings reveal a dose-dependent trade-off: moderate UV-B promotes mutagenesis with minimal viability loss, whereas prolonged exposure suppresses mutagenesis via transient dormancy, reflecting an adaptive strategy with significant evolutionary implications.

microbiology↗

bioRxiv2022

Systematic Design of Pulse Dosing to Eradicate Persister Bacteria

A small fraction of infectious bacteria use persistence as a strategy to survive exposure to antibiotics. Periodic pulse dosing of antibiotics has long been considered a potentially effective strategy towards eradication of persisters. Recent studies have demonstrated through in vitro experiments that it is indeed feasible to achieve such effectiveness. However, systematic design of periodic pulse dosing regimens to treat persisters is currently lacking. Here we rigorously develop a methodology for the systematic design of optimal periodic pulse dosing strategies for rapid eradication of persisters. A key outcome of the theoretical analysis, on which the proposed methodology is based, is that bactericidal effectiveness of periodic pulse dosing depends mainly on the ratio of durations of the corresponding on and off parts of the pulse. Simple formulas for critical and optimal values of this ratio are derived. The proposed methodology is supported by computer simulations and in vitro experiments. Author SummaryAdministering antibiotics in periodic pulses that alternate between high and low concentration has long been known as a possible dosing strategy to treat stubborn infections caused by bacteria known as persisters. Such bacteria use clever mechanisms to survive otherwise lethal temporary exposure to antibiotics and to resume normal activity upon antibiotic removal. Persisters pose a serious health problem. Recent studies have elucidated mechanisms of persistence and have confirmed that pulse dosing, if designed appropriately, can indeed be effective. However, effective pulse dosing design has been mainly handled by trial and error, requiring relatively extensive experimentation. Here we develop a method for rapid systematic design of effective pulse dosing. The method relies on a simple mathematical model and a minimal amount of standard experimental data. We derive corresponding design formulas that explicitly characterize the shape of generally effective or optimal periodic pulses. We tested our method through computer simulations and in vitro experiments, as well as on prior literature data. In all cases, the outcomes on persister bacteria eradication predicted by our method were confirmed. These results pave the way for ultimately developing effective pulse dosing regimens in realistic situations in vivo.

systems biology↗

bioRxiv2021

LON DELETION IMPAIRS PERSISTER CELL RESUSCITATION IN ESCHERICHIA COLI

Bacterial persisters are non-growing cells that are highly tolerant to bactericidal antibiotics. However, this tolerance is reversible and not mediated by heritable genetic changes. Lon, an ATP-dependent protease, has repeatedly been shown to play a critical role in fluoroquinolone persistence. Although lon deletion ({Delta}lon) is thought to kill persister cells via accumulation of the cell division inhibitor protein SulA, the exact mechanism underlying this phenomenon has yet to be elucidated. Here, we show that Lon is an important regulatory protein for the resuscitation of the fluoroquinolone persisters in Escherichia coli, and lon deletion impairs the ability of persister cells to form colonies during recovery, without killing these cells, through a sulA- and ftsZ-dependent mechanism. Notably, this observed non-culturable state of antibiotic-tolerant {Delta}lon cells is transient, as environmental conditions, such as starvation, can restore their culturability. Our data further indicate that starvation-induced SulA degradation or expression of Lon during recovery facilitates Z-ring formation in {Delta}lon persisters. Calculating the ratio of the cell length (L in {micro}m) to the number of Z-rings (Z) for each ofloxacin-treated intact cell analyzed has revealed a strong correlation between persister resuscitation and calculated L/Z values, which represents a potential biomarker for {Delta}lon persisters that are transitioning to the normal cell state under the conditions studied here.

microbiology↗

bioRxiv2019

INVESTIGATING THE EFFECTS OF OSMOLYTES AND ENVIRONMENTAL pH ON BACTERIAL PERSISTERS

Bacterial persisters are phenotypic variants that temporarily demonstrate an extraordinary tolerance towards antibiotics. Persisters have been linked to the recalcitrance of biofilm related infections; hence, a complete understanding of the physiology of persisters can lead to improvement of therapeutic strategies associated with such infections. Mechanisms pertaining to persister formation are known to be related to stress response pathways triggered from intra- or extra-cellular stress factors. Unfortunately, studies demonstrating the effects of osmolyte- and/or pH- induced stresses on bacterial persistence are largely missing. To fill this knowledge gap within the field, here we studied the effects of various osmolytes and pH conditions on Escherichia coli persistence with the use of phenotype microarrays and antibiotic tolerance assays. Although we found that a number of chemicals and pH environments, including urea, sodium nitrite and acidic pH, significantly reduced persister formation in E. coli compared to no-osmolyte/no-buffer controls, this reduction in persister levels was lessened in late-stationary-phase cultures. Our results further demonstrated a positive correlation between cell growth and persister formation, which challenges the general notion in the field that slow-growing cultures have more persister cells than fast-growing cultures.

microbiology↗