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RNA-seq

  • Open Access
    Twists and Turns in the Salicylate Catabolism of <em>Aspergillus terreus</em>, Revealing New Roles of the 3-Hydroxyanthranilate Pathway
    Research Article | Molecular Biology and Physiology
    Twists and Turns in the Salicylate Catabolism of Aspergillus terreus, Revealing New Roles of the 3-Hydroxyanthranilate Pathway

    Aspergilli are versatile cell factories used in industry for the production of organic acids, enzymes, and pharmaceutical drugs. To date, bio-based production of organic acids relies on food substrates.

    Tiago M. Martins, Celso Martins, Paula Guedes, Cristina Silva Pereira
  • Open Access
    Nonadditive Transcriptomic Signatures of Genotype-by-Genotype Interactions during the Initiation of Plant-Rhizobium Symbiosis
    Research Article | Host-Microbe Biology
    Nonadditive Transcriptomic Signatures of Genotype-by-Genotype Interactions during the Initiation of Plant-Rhizobium Symbiosis

    A sustainable way for meeting the need of an increased global food demand should be based on a holobiont perspective, viewing crop plants as intimately associated with their microbiome, which helps improve plant nutrition, tolerance to pests, and adverse climate conditions. However, the genetic repertoire needed for efficient association with plants by the microbial symbionts is still poorly understood.

    Camilla Fagorzi, Giovanni Bacci, Rui Huang, Lisa Cangioli, Alice Checcucci, Margherita Fini, Elena Perrin, Chiara Natali, George Colin diCenzo, Alessio Mengoni
  • Open Access
    Transcription Inhibitors with XRE DNA-Binding and Cupin Signal-Sensing Domains Drive Metabolic Diversification in <em>Pseudomonas</em>
    Research Article | Molecular Biology and Physiology
    Transcription Inhibitors with XRE DNA-Binding and Cupin Signal-Sensing Domains Drive Metabolic Diversification in Pseudomonas

    Bacteria of the Pseudomonas genus, including the major human pathogen Pseudomonas aeruginosa, are known for their complex regulatory networks and high number of transcription factors, which contribute to their impressive adaptive ability. However, even in the most studied species, most of the regulators are still uncharacterized.

    Julian Trouillon, Michel Ragno, Victor Simon, Ina Attrée, Sylvie Elsen
  • Open Access
    Exometabolite Dynamics over Stationary Phase Reveal Strain-Specific Responses
    Editor's Pick Research Article | Applied and Environmental Science
    Exometabolite Dynamics over Stationary Phase Reveal Strain-Specific Responses

    Nongrowth states are common for bacteria that live in environments that are densely populated and predominantly nutrient exhausted, and yet these states remain largely uncharacterized in cellular metabolism and metabolite output. Here, we investigated and compared stationary-phase exometabolites and RNA transcripts for each of three environmental bacterial strains.

    John L. Chodkowski, Ashley Shade
  • Open Access
    Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in <span class="named-content genus-species" id="named-content-1">Yersinia pseudotuberculosis</span>
    Research Article | Host-Microbe Biology
    Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in Yersinia pseudotuberculosis

    The alternative sigma factor RpoN (σ54), which is widely distributed in eubacteria, has been implicated in controlling gene expression of importance for numerous functions including virulence. Proper responses to host environments are crucial for bacteria to establish infection, and regulatory mechanisms involved are therefore of high interest for development of future therapeutics. Little is known about the function of RpoN...

    A. K. M. Firoj Mahmud, Kristina Nilsson, Anna Fahlgren, Roberto Navais, Rajdeep Choudhury, Kemal Avican, Maria Fällman
  • Open Access
    Characterizing the Mechanism of Action of an Ancient Antimicrobial, Manuka Honey, against <span class="named-content genus-species" id="named-content-1">Pseudomonas aeruginosa</span> Using Modern Transcriptomics
    Research Article | Molecular Biology and Physiology
    Characterizing the Mechanism of Action of an Ancient Antimicrobial, Manuka Honey, against Pseudomonas aeruginosa Using Modern Transcriptomics

    The threat of antimicrobial resistance to human health has prompted interest in complex, natural products with antimicrobial activity. Honey has been an effective topical wound treatment throughout history, predominantly due to its broad-spectrum antimicrobial activity. Unlike traditional antibiotics, honey-resistant bacteria have not been reported; however, honey remains underutilized in the clinic in part due to a lack of...

    Daniel Bouzo, Nural N. Cokcetin, Liping Li, Giulia Ballerin, Amy L. Bottomley, James Lazenby, Cynthia B. Whitchurch, Ian T. Paulsen, Karl A. Hassan, Elizabeth J. Harry
  • Open Access
    Isolation and Characterization of the Novel Phage JD032 and Global Transcriptomic Response during JD032 Infection of <span class="named-content genus-species" id="named-content-1">Clostridioides difficile</span> Ribotype 078
    Research Article | Therapeutics and Prevention
    Isolation and Characterization of the Novel Phage JD032 and Global Transcriptomic Response during JD032 Infection of Clostridioides difficile Ribotype 078

    C. difficile is one of the most clinically significant intestinal pathogens. Although phages have been shown to effectively control C. difficile infection, the host responses to phage predation have not been fully studied. In this study, we reported the isolation and characterization of a new phage...

    Tinghua Li, Yan Zhang, Ke Dong, Chih-Jung Kuo, Chong Li, Yong-Qiang Zhu, Jinhong Qin, Qing-Tian Li, Yung-Fu Chang, Xiaokui Guo, Yongzhang Zhu
  • Open Access
    Global Network Analysis of <span class="named-content genus-species" id="named-content-1">Neisseria gonorrhoeae</span> Identifies Coordination between Pathways, Processes, and Regulators Expressed during Human Infection
    Research Article | Molecular Biology and Physiology
    Global Network Analysis of Neisseria gonorrhoeae Identifies Coordination between Pathways, Processes, and Regulators Expressed during Human Infection

    Neisseria gonorrhoeae is the causative agent of the sexually transmitted infection (STI) gonorrhea, a disease with high morbidity worldwide with an estimated 87 million cases annually. Current therapeutic and pharmacologic approaches to treat gonorrhea have been compromised by increased antibiotic resistance worldwide, including to the most recent FDA-approved...

    Ryan McClure, Ashwini Sunkavalli, Phillip M. Balzano, Paola Massari, Christine Cho, William M. Nauseef, Michael A. Apicella, Caroline A. Genco
  • Open Access
    Drug Repurposing of Bromodomain Inhibitors as Potential Novel Therapeutic Leads for Lymphatic Filariasis Guided by Multispecies Transcriptomics
    Research Article | Host-Microbe Biology
    Drug Repurposing of Bromodomain Inhibitors as Potential Novel Therapeutic Leads for Lymphatic Filariasis Guided by Multispecies Transcriptomics

    The current treatment regimen for lymphatic filariasis is mostly microfilaricidal. In an effort to identify new drug candidates for lymphatic filariasis, we conducted a three-way transcriptomics/systems biology study of one of the causative agents of lymphatic filariasis, Brugia malayi, its Wolbachia endosymbiont wBm, and its vector host...

    Matthew Chung, Laura E. Teigen, Silvia Libro, Robin E. Bromley, Dustin Olley, Nikhil Kumar, Lisa Sadzewicz, Luke J. Tallon, Anup Mahurkar, Jeremy M. Foster, Michelle L. Michalski, Julie C. Dunning Hotopp
  • Open Access
    Changes in the Composition of the Gut Microbiota and the Blood Transcriptome in Preterm Infants at Less than 29 Weeks Gestation Diagnosed with Bronchopulmonary Dysplasia
    Research Article | Host-Microbe Biology
    Changes in the Composition of the Gut Microbiota and the Blood Transcriptome in Preterm Infants at Less than 29 Weeks Gestation Diagnosed with Bronchopulmonary Dysplasia

    Bronchopulmonary dysplasia (BPD) is a serious inflammatory condition of the lung and is the most common complication associated with preterm birth. A large body of evidence now suggests that the gut microbiota can influence immunity and inflammation systemically; however, the role of the gut microbiota in BPD has not been evaluated to date. Here, we report that there are significant differences in the gut microbiota of infants born at...

    Feargal J. Ryan, Damian P. Drew, Chloe Douglas, Lex E. X. Leong, Max Moldovan, Miriam Lynn, Naomi Fink, Anastasia Sribnaia, Irmeli Penttila, Andrew J. McPhee, Carmel T. Collins, Maria Makrides, Robert A. Gibson, Geraint B. Rogers, David J. Lynn

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