Biology subjects

Fatima, R.

Publications and source records attributed to Fatima, R..

7 recordsLinked to original sources

bioRxiv2026

Growth phase-dependent priming of galactose metabolism in Escherichia coli

Bacteria routinely respond to changing environments, with vastly different with nutrient availability. When nutritional changes are predictable, bacteria can deploy mechanisms to anticipate them. In these cases, an organism's past environment can shape its response to its current environment, which is often referred to as a history-dependent behaviour (HDB). Using nutritional shift assays, we investigated how prior growth phase influences subsequent growth across different carbon sources. Here, we show evidence of a novel HDB regulating galactose metabolism in Escherichia coli, where previous growth to exponential phase leads to a growth advantage in a galactose environment, with no comparable effect observed in all other carbon environments tested. We demonstrate a role of the galactose repressors, GalR and GalS, in regulating this behaviour, as it is lost in strains deficient in either repressor. Further, we show how this HDB is generalizable across a collection of E. coli isolates, but not Salmonella - a closely related species with a similar natural history. Together, these findings build on the existing knowledge of HDBs governing carbohydrate metabolism by demonstrating how growth phase history can influence an organism's response to fluctuating nutritional environments.

microbiology↗

bioRxiv2025

High-throughput screening reveals diverse lambdoid prophage inducers

Prophages; dormant bacteriophage genomes integrated within the bacterial chromosome, play pivotal roles in shaping microbial communities when awakened. Our current understanding of prophage activation is largely shaped by a narrow set of traditional DNA-damaging inducers, such as mitomycin C and ciprofloxacin, which trigger the bacterial SOS response. This study employed high-throughput screening of 3,921 compounds to identify novel prophage inducers using model lambdoid prophage HK97. We identified multiple new inducers across diverse pharmacological classes, including dietary supplements and therapeutics. Despite the variety in compounds, all acted through SOS-dependent pathways. However, bleomycin, an antineoplastic antibiotic, demonstrated broad-spectrum and potent prophage induction exceeding standard inducers, with activity validated across multiple phages and bacterial hosts. These findings expand the repertoire of prophage inducers into commonly ingested xenobiotics, and introduce Bleomycin as a powerful, cost-effective tool for prophage research.

microbiology↗

bioRxiv2024

Temperate phages increase antibiotic effectiveness in a Caenorhabditis elegans infection model

The bactericidal nature of obligately lytic bacterial viruses (phages) is of increasing interest for the treatment of drug-resistant bacterial infections, either administered alone or in combination with antibiotics. In contrast, temperate phages are largely ignored in a therapeutic context due to their ability to lie dormant within the bacterial host. However, these phages often undergo a lytic cycle. Furthermore, even in their dormant state they can be a considerable burden to the bacterium - most famously by their ability to switch to lytic replication in response to environmental triggers, such as antibiotics, that stress the bacterial host. Recent reports of antibiotics synergizing with temperate phages in vitro, termed "temperate phage antibiotic synergy" (tPAS), present a potentially scalable opportunity to make use of these abundant entities for the treatment of bacterial infections. Here we employ Caenorhabditis elegans as a robust in vivo animal model for testing the efficacy of temperate phages as adjuvants to antibiotics. In vivo, temperate phage Hali alone results in 60% dormancy in the bacterial survivors. However, the antibiotic ciprofloxacin can abolish dormancy of temperate phage Hali - infecting a ciprofloxacin resistant Pseudomonas aeruginosa clinical strain. The phage Hali-ciprofloxacin pairing increased the lifespan of P. aeruginosa infected worms to that of the uninfected control, at doses where neither the phage nor the antibiotic had any effect alone. Complete rescue was also observed in worms infected with a phage-carrying strain treated with the otherwise ineffective antibiotic, supporting that the phage - even in its dormant form - can greatly enhance antibiotic effectiveness. This illustrates potential "accidental" phage therapy when antibiotics are prescribed. Our work establishes C. elegans as a suitable model for studying the in vivo efficacy of tPAS and is the first in vivo demonstration of this synergy, greatly expanding the therapeutic potential of temperate phages.

microbiology↗

bioRxiv2024

Temperate phage-antibiotic synergy is widespread, but varies by phage, host, and antibiotic pairing

With a decline in antibiotic effectiveness, there is a renewed interest in bacteriophage (phage) therapy. Phages are bacterial-specific viruses that can be used alone or with antibiotics to reduce bacterial load. Most phages are unsuitable for therapy because they are temperate and can integrate into the host genome, forming a lysogen which is protected from subsequent phage infections. However, integrated phages can be awakened by stressors such as antibiotics. This interaction was previously reported to result in a potent synergy between antibiotic classes and a model E. coli temperate phage, which can readily eradicate the bacterium at sub-lethal concentrations of antibiotics, despite the poor effectiveness of the phage alone. Here we explore the generalizability of this synergy to a clinically relevant pathogen: Pseudomonas aeruginosa. Thirty-six temperate phages isolated from clinical strains were screened for synergy with six antibiotics (ciprofloxacin, levofloxacin, meropenem, piperacillin, tobramycin, polymyxin B), using checkerboard assays. Interestingly, our screen identified phages that can synergize with each antibiotic, despite their widely differing targets - however, these are highly phage-antibiotic and phage-host pairing specific. Screening the strongest pairings across multiple clinical strains reveal that these phages can reduce the antibiotic minimum inhibitory concentration up to 32-fold, even in a resistant isolate, functionally re-sensitizing the bacterium to the antibiotic. When meropenem and tobramycin were effective synergistic agents, they did not reduce the frequency of lysogens, suggesting a mechanism of action independent of the temperate nature of the phages. In contrast, ciprofloxacin and piperacillin were able to reduce the frequency of lysogeny, the former by inducing phages - as previously reported in E. coli. Curiously, synergy with piperacillin reduced the frequency of lysogeny, but not by inducing the phages, and therefore likely acts by biasing the phage away from lysogeny in the initial infection. Overall, our findings indicate that temperate phages can act as adjuvants to antibiotics in clinically relevant pathogens, even in the presence of antibiotic resistance, thereby drastically expanding their therapeutic potential.

microbiology↗

bioRxiv2019

NK cells negatively regulate CD8 T cells to promote immune exhaustion and chronic Toxoplasma gondii infection

NK cells regulate CD4+ and CD8+ T cells in acute viral infection, vaccination and the tumor microenvironment. NK cells also become exhausted in chronic activation settings. The mechanisms causing these ILC responses and their impact on adaptive immunity are unclear. CD8+ T cell exhaustion develops during chronic Toxoplasma gondii (T. gondii) infection resulting in parasite reactivation and death. How chronic T. gondii infection impacts the NK cell compartment is not known. We demonstrate that NK cells do not exhibit hallmarks of exhaustion. Their numbers are stable and they do not express high PD1 or LAG3. NK cell depletion with anti-NK1.1 is therapeutic and rescues chronic T. gondii infected mice from CD8+ T cell exhaustion dependent death, increases survival after lethal secondary challenge and reduces parasite reactivation. Anti-NK1.1 treatment increased polyfunctional CD8+ T cell responses in spleen and brain and reduced CD8+ T cell apoptosis. Chronic T. gondii infection promotes the development of a modified NK cell compartment, which does not exhibit normal NK cell behavior. This splenic CD49a-CD49b+NKp46+ NK cell population develops during the early chronic phase of infection and increases through the late chronic phase of infection. They are Ly49 and TRAIL negative and are enriched for expression of CD94/NKG2A and KLRG1. They do not produce IFN{gamma}, are IL-10 negative, do not increase PDL1 expression, but do increase CD107a on their surface. They are also absent from brain. Based on the NK cell receptor phenotype we observed NKp46 and CD94-NKG2A cognate ligands were measured. Activating NKp46 (NCR1-ligand) ligand increased and NKG2A ligand Qa-1b expression was reduced. Blockade of NKp46 also rescued the chronically infected mice from death. Immunization with a single dose non-persistent 100% protective T. gondii vaccination did not induce this cell population in the spleen, suggesting persistent infection is essential for their development. We hypothesize chronic T. gondii infection induces an NKp46 dependent modified NK cell population that reduces functional CD8+ T cells to promote persistent parasite infection in the brain. NK cell targeted therapies could enhance immunity in people with chronic infections, chronic inflammation and cancer.

immunology↗

bioRxiv2019

scribble abrogation induces tumor growth through JNK-Wnt pathways depending on cellular-microenvironment in Drosophila wing imaginal tissue

scribble (scrib) is a cell-polarity determinant in Drosophila and human. Cell polarity plays a crucial role in the maintenance of tissue homeostasis and its disruption leads to neoplastic cancer progression. However, the underlying mechanisms by which loss of cell-polarity regulators drives cancer progression are poorly known. In this study, we have explored the tumor progression mechanisms upon scrib knockdown in Drosophila wing imaginal disc using UASRNAi-GAL4 approach. We have found that scrib knockdown in wing disc leads to tumor growth with disrupted actin cytoskeleton, loss of cell-polarity and elevated JNK signalling, resulting in absolute early pupal lethality. Further, scrib abrogated cells in a large area of the disc are capable of invading the surrounding wild type cells and inducing apoptosis along with compensatory proliferation through JNK-Wnt pathways. Moreover, JNK pathway upstream candidate hep (JNKK) knockdown in scrib abrogated cells rescues the cell polarity defects, actin cytoskeleton disruption and tumor growth, while constitutive hep activation further aggravates the tumor phenotype. Interestingly, generation of undead cells by apoptosis inhibition in these hep knockdown cells by p35 expression further leads to tumor development. Hence, we conclude that scrib knockdown in a large area of wing disc might have a group-protection and undead-cells microenvironment that modulates the action of JNK signalling resulting in tumor formation. Furthermore, JNK dependent activation of Wnt/Ca2+ signalling also supports the tumor growth and actin cytoskeleton disruption. Thus, our results importantly highlight the role of JNK signalling in tumor progression upon scrib loss of function depending on cellular-microenvironment.

cancer biology↗

bioRxiv2018

A novel enhancer RNA, Hmrhl, positively regulates its host gene, phkb, in Chronic Myelogenous Leukemia

Noncoding RNAs are increasingly being accredited with key roles in gene regulation during development and disease. Here we report the discovery and characterization of a novel long noncoding RNA, Hmrhl, which shares synteny and partial sequence similarity with the mouse lncRNA, Mrhl. The human homolog, Hmrhl, transcribed from intron 14 of phkb gene, is 5.5kb in size, expressed in all tissues examined and has acquired additional repeat elements. Analysis of Hmrhl locus using ENCODE database revealed that it is associated with hallmarks of enhancers like the open chromatin configuration, binding of transcription factors, enhancer specific histone signature etc. in the K562 Chronic Myelogenous Leukemia (CML) cells. We compared the expression of Hmrhl in the normal lymphoblast cell line, GM12878, with that of K562 cells and lymphoma samples and show that it is highly upregulated in leukemia as well as several cases of lymphoma. We validated the enhancer properties of Hmrhl locus in K562 cells with the help of Luciferase assay. Moreover, siRNA mediated down-regulation of Hmrhl in K562 cells leads to a concomitant down regulation of its parent gene, phkb, showing that Hmrhl functions as an enhancer RNA and positively regulates its host gene, phkb, in chronic myelogenous leukemia.

cancer biology↗