Publications by authors named "Coppee J"
Microbial pathogenesis is mediated by the expression of virulence genes. However, as microbes with identical virulence gene content can differ in their pathogenic potential, other virulence determinants must be involved. Here, by combining comparative genomics and transcriptomics of a large collection of isolates of the model pathogen Listeria monocytogenes, time-lapse microscopy, in vitro evolution and in vivo experiments, we show that the individual stress responsiveness of L.
View Article and Find Full Text PDFAlternative transcription start site (TSS) usage regulation has been identified as a major means of gene expression regulation in metazoans. However, in fungi, its impact remains elusive as its study has thus far been restricted to model yeasts. Here, we first re-analyzed TSS-seq data to define genuine TSS clusters in 2 species of pathogenic Cryptococcus.
View Article and Find Full Text PDFResistance to fluconazole (FLC), the most widely used antifungal drug, is typically achieved by altering the azole drug target and/or drug efflux pumps. Recent reports have suggested a link between vesicular trafficking and antifungal resistance. Here, we identified novel regulators of extracellular vesicle (EV) biogenesis that impact FLC resistance.
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- The study investigates additional Toxin/Antitoxin (TA) systems in the Vibrio cholerae N16961 genome, which already contains 18 known type II TA systems within its chromosomal superintegron.
- Researchers identified a new functional type II TA system (VCA0497-0498) and found that its antitoxin represses its own gene expression, while also linking it to a newly discovered superfamily of TA systems.
- Additionally, they uncovered a novel type I TA system (VCA0495) that includes antisense non-coding RNAs; silencing these RNAs caused cell death, indicating the functional role of this TA system, thereby increasing the total number to 19 within the
Article Synopsis
- The study investigates the relationship between bacteria, their viruses (bacteriophages), and human health, particularly how these populations coexist in the digestive tract.
- Researchers used RNA sequencing to identify genes in E. coli that changed expression in different environments, finding specific genes that affected how E. coli interacted with virulent phages.
- This research highlights the complex dynamics among bacteria, phages, and host organisms, showing that gene regulation impacts their interactions and overall balance in the intestines.
Article Synopsis
- The text discusses a genus of Amoebozoa that includes harmful species found in the intestines, focusing on gene regulation from an evolutionary viewpoint.
- Research involved profiling transcriptomes of closely related species, identifying transcription start sites (TSS) and polyadenylation sites (PAS) to analyze gene regulatory sequences.
- A key finding was the prevalence of antisense transcription within gene coding sequences, particularly in genes related to processes critical for species that infect the human intestine, hinting at a conserved gene regulatory system.
Article Synopsis
- * In a study with mice, it was found that these "trained" ILC3s not only survive for months after being activated but also have improved ability to multiply and produce interleukin-22 (IL-22) when faced with a second infection.
- * These findings suggest that temporary exposure to pathogens can lead to lasting enhancements in ILC3 functions, strengthening the immune response in the intestines over time.
Article Synopsis
- - Pathogenic Leptospira bacteria cause leptospirosis, a severe and widespread zoonotic disease, particularly affecting impoverished populations in sub-tropical regions.
- - Researchers identified a new PerR-like regulator called PerRB in L. interrogans, which, alongside another regulator PerRA, helps the bacteria adapt to oxidative stress during infection.
- - The study found that while single mutations in perRA or perRB increased tolerance to specific oxidants, a double mutation rendered the bacteria avirulent, highlighting the complex regulation of virulence through oxidative stress adaptation in pathogenic Leptospira.
Article Synopsis
- Spirochetes, like the bacteria Leptospira, have a unique spiral shape and specific flagella that are essential for movement, and this study examines the roles of two proteins, FlhF and FlhG, in controlling these flagella.*
- The research found that while FlhF is crucial for Leptospira's motility, mutations in FlhG resulted in decreased movement in both saprophytic and pathogenic strains, without causing hyperflagellation as seen in other bacteria.*
- Additionally, it was revealed through various tests that FlhG negatively regulates certain flagellar genes and that its function is not interchangeable across species, impacting the virulence of L. interrogans in a hamster model.*
Article Synopsis
- Indole secretion is triggered by low levels of tobramycin and helps bacteria survive aminoglycoside antibiotics by increasing the number of persister cells.
- The research shows that the molecule RaiA plays a key role in this process by managing ribosomes, leading to a significant increase in persisters when overexpressed, while its deletion disrupts this ability.
- The study suggests that under stress, bacteria store ribosomes in an inactive state (termed "sleeping ribosomes") and can quickly reactivate them when the stress is removed, providing insights into how bacterial persistence works during antibiotic treatment.
Metatranscriptomic outlook on green and brown food webs in acid mine drainage.
Environ Microbiol Rep
October 2021
Article Synopsis
- Acid mine drainages (AMDs) are acidic, metal-rich waters from mining that support diverse microorganisms and affect ecosystem processes like primary production and litter decomposition.
- The study found that in AMD sediments, a mutual relationship exists between green (plant-based) and brown (decomposer-based) food webs due to low carbon and available nutrients, while disturbances like plant debris can shift growth dynamics.
- In contrast, the nearby unpolluted Amous River shows dominance of the green food web, with freshwater organisms enhancing phytoplankton growth, suggesting that factors like pH, metal levels, and nutrient availability significantly shape microbial communities.
Article Synopsis
- - Queuosine, a modified ribonucleoside found in tRNA, is essential for certain eukaryotic parasites and must be sourced through diet or gut bacteria, as eukaryotes can't synthesize it.
- - Queuine boosts the parasite's resistance to oxidative stress and enhances the expression of protective genes like heat shock proteins, while simultaneously reducing the expression of virulence-related genes.
- - Silencing the gene responsible for queuine incorporation into tRNAs significantly hinders the parasite's growth and reduces its ability to withstand oxidative stress, highlighting its crucial role in both survival and virulence.
Article Synopsis
- Influenza A viruses (IAVs) disrupt cellular gene expression by affecting mRNA splicing in human lung cells, leading to increased exon inclusion and decreased intron retention.
- More than half of the altered mRNAs in IAV-infected cells show splicing changes without significant shifts in overall abundance, indicating IAVs specifically manipulate this process.
- The study also highlights that certain alternative splicing events are unique to IAV infection and suggests that IAVs may hijack specific cellular proteins, like RED, to enhance viral mRNA splicing at the expense of host mRNA processing.
Article Synopsis
- Researchers studied how a specific DNA methyltransferase in the Leptospira bacterium affects cellular processes, particularly focusing on the modification 4-methylcytosine (4mC).
- When they inhibited this enzyme, it completely blocked the methylation of a specific DNA sequence (CTAG), leading to widespread changes in gene expression.
- The resulting bacteria showed growth problems, reduced ability to attach to host cells, increased vulnerability to antibiotics, and loss of virulence in infection models, underlining the crucial role of 4mC in their physiology.
Article Synopsis
- The study investigates natural antisense transcripts (NAT) in the unicellular parasite Entamoeba histolytica, revealing that about 28% of its protein-coding genes show significant transcription on the opposite strand.
- It finds that the location of transcription start and polyadenylation sites for these NATs is influenced by specific motifs encoded on the opposite strand, suggesting a compact regulatory system for gene expression.
- Additionally, NATs are shown to be up-regulated under multiple environmental stresses, indicating a potential regulatory role in the gene expression of E. histolytica that requires further exploration.
Article Synopsis
- Bacteria at acid mine drainage sites play a crucial role in water remediation by converting arsenite to arsenate, which helps in the removal of arsenic from contaminated water.
- After exposure to arsenite, certain bacterial strains can develop resistant variants, particularly when grown in biofilms, and these variants increase in prevalence with higher arsenite concentrations.
- The study identified that genes related to DNA repair were upregulated in resistant bacteria, and multiple mutations accumulated, particularly in a genomic island associated with arsenic resistance, shedding light on bacterial adaptation and genome evolution in toxic environments.
Article Synopsis
- Pathogenic Leptospira spp. cause leptospirosis and face challenges like reactive oxygen species (ROS) from host immunity, necessitating evolved defenses for persistence.
- The study used RNA sequencing to assess how L. interrogans responds to varying levels of hydrogen peroxide and to identify the role of the peroxide stress regulator, PerR, in managing oxidative stress.
- Key findings include the involvement of specific peroxidase enzymes, heat shock response proteins, and a PerR-independent regulatory network that aids in Leptospira’s tolerance to oxidative damage, potentially revealing new avenues for understanding its virulence strategies.
Article Synopsis
- Human leishmaniases are caused by parasites that infect immune cells called dendritic cells (DCs), which are crucial for immune response initiation.
- The study investigates how these parasites influence DC maturation, finding that DCs infected with non-opsonized amastigotes stayed immature, while those with opsonized ones showed a semi-mature state.
- Transcriptomic analyses revealed that infections triggered specific gene expressions related to antigen presentation and immune signaling, highlighting a unique behavior of opsonized parasitic infections in altering DC functionality.
Article Synopsis
- BAHD1 is a newly identified factor involved in heterochromatin formation and is associated with histone deacetylases, but its functions are not fully understood.
- A study found that mice lacking BAHD1 did not have obvious brain structure issues, but RNA analysis showed around 2500 genes were deregulated, affecting areas like nervous system development and behavior.
- Mice with partial BAHD1 deficiency exhibited anxiety-like behavior, linking BAHD1's gene regulation role to potential psychiatric disorders in humans.
Article Synopsis
- Bacterial persister cells are a type of bacteria that temporarily stop growing and can tolerate antibiotics, posing challenges in treatment.
- Recent research shows that Staphylococcus aureus can exist as persister cells inside infected host cells, surviving antibiotic treatment and entering a non-dividing state.
- These persister cells are metabolically active but undergo stress responses, making them potentially responsible for recurring infections and leading to treatment failures.
Article Synopsis
- Researchers adapted a human in vitro microfold (M) cell model to study how pathogens interact with these cells during infections using advanced imaging techniques.
- They focused on the intracellular pathogen Shigella flexneri and discovered it can either quickly spread from M cells or take longer to break out, while also showing that it and Listeria monocytogenes can avoid being transcytosed and instead spread directly to neighboring cells.
- The findings suggest that these pathogens have a unique method to bypass immune detection, contradicting previous beliefs about how they are processed by M cells.
Article Synopsis
- Entamoeba histolytica causes amebiasis, primarily affecting the intestines and liver in humans, with most infections being silent and 10% resulting in invasive disease.
- Researchers utilized tissue engineering to create a realistic 3D-intestinal model that mimics human colon characteristics, which includes a layered structure with immune cells.
- The study revealed dynamic interactions between the parasite and the model, identifying known virulence factors and uncovering new molecules and regulatory components involved in the invasion process.
Article Synopsis
- Free-living amoebae provide an environment where bacteria like Mycobacterium abscessus can develop resistance and possibly become pathogenic.
- The study focused on the gene expression differences between M. abscessus in amoeba and murine macrophages, comparing it with the less pathogenic Mycobacterium chelonae.
- Findings revealed that certain upregulated genes in M. abscessus help it survive environmental stress and switch to different metabolic processes, and when these genes were manipulated, it affected the bacteria's virulence and survival in host cells.
Article Synopsis
- Research indicates that metals like cobalt (Co) can hinder iron (Fe) acquisition in bacteria by interfering with the action of siderophores, which are molecules that help microbes gather Fe.
- In Pseudomonas aeruginosa, Co is incorporated into the cell via a siderophore called pyochelin (PCH) through a specific transporter, leading to decreased production of PCH.
- The study reveals that this reduction in PCH production is caused not by the typical regulatory mechanism involving the Fur protein, but instead by competition between PCH-Co and PCH-Fe for a key transcriptional activator (PchR), which is necessary for PCH gene expression.
Article Synopsis
- * The study focuses on how two Mycobacterium tuberculosis strains respond to delamanid, a recently approved drug, revealing that its action is similar to another drug, pretomanid, in the same drug class.
- * While delamanid inhibits cell wall synthesis, the study found that its most significant impact is on aerobic respiration, indicating that respiratory poisoning is key to its effectiveness, especially noting the role of poorly understood genes in its action.