transcriptomics
Research Article | Molecular Biology and PhysiologyIntegrative Analysis of Proteome and Transcriptome Dynamics during Bacillus subtilis Spore RevivalThis study demonstrated the progress of macromolecular synthesis during Bacillus subtilis spore germination and outgrowth. The transcriptome analysis has additionally allowed us to trace gene expression during this transformation process. For the first time, the basic survival kit for spore-based life has been identified. In addition, in this analysis based on...
Research Article | Ecological and Evolutionary ScienceThe Transcriptional Aftermath in Two Independently Formed Hybrids of the Opportunistic Pathogen Candida orthopsilosisHow new pathogens emerge is an important question that remains largely unanswered. Some emerging yeast pathogens are hybrids originated through the crossing of two different species, but how hybridization contributes to higher virulence is unclear. Here, we show that hybrids selectively retain gene regulation plasticity inherited from the two parents and that this plasticity affects genes involved in virulence.
Commentary | Host-Microbe BiologymSphere of Influence: Predicting Immune Responses and Susceptibility to Influenza Virus—May the Data Be with YouIrene Ramos works in the field of immunology to viral infections. In this mSphere of Influence article, she reflects on how “Global analyses of human immune variation reveal baseline predictors of postvaccination responses” by Tsang et al. (Cell 157:499–513, 2014, https://doi.org/10.1016/j.cell.2014.03.031) and “A crowdsourced analysis to identify ab initio molecular signatures...
Editor's Pick Research Article | Host-Microbe BiologyTranscriptomic and Proteomic Approaches to Finding Novel Diagnostic and Immunogenic Candidates in PneumocystisThe current report enhances our understanding of Pneumocystis biology in a number of ways. First, the current study provided a preliminary annotation of the Pneumocystis murina genome, addressing a long-standing issue in the field. Second, this study validated two novel transcripts enriched in the two predominant life forms of Pneumocystis. These...
Research Article | Host-Microbe BiologyAnalysis of the In Vivo Transcriptome of Bordetella pertussis during Infection of MiceIn vitro growth conditions for bacteria do not fully recapitulate the host environment. RNA sequencing transcriptome analysis allows for the characterization of the infection gene expression profiles of pathogens in complex environments. Isolation of the pathogen from infected tissues is critical because of the large amounts of host RNA present in crude lysates of infected organs. A filtration method was developed that enabled...
Research Article | Molecular Biology and PhysiologycsrB Gene Duplication Drives the Evolution of Redundant Regulatory Pathways Controlling Expression of the Major Toxic Secreted Metalloproteases in Vibrio tasmaniensis LGP32The conserved CsrB sRNAs are an example of sibling sRNAs, i.e., sRNAs which are present in multiple copies in genomes. This report illustrates how new copies arise through gene duplication events and highlights two evolutionary advantages of having such multiple copies: differential regulation of the multiple copies allows integration of different input signals into the regulatory network of which they are parts, and the high redundancy...
Research Article | Therapeutics and PreventionMechanism of High-Level Daptomycin Resistance in Corynebacterium striatumAntimicrobial resistance threatens the efficacy of antimicrobial treatment options, including last-line-of-defense drugs. Understanding how this resistance develops can help direct antimicrobial stewardship efforts and is critical to designing the next generation of antimicrobial therapies. Here we determine how Corynebacterium striatum, a skin commensal and...
Research Article | Host-Microbe BiologyShifts in the Gut Metabolome and Clostridium difficile Transcriptome throughout Colonization and Infection in a Mouse ModelClostridium difficile is a bacterial pathogen of global significance that is a major cause of antibiotic-associated diarrhea. Antibiotics deplete the indigenous gut microbiota and change the metabolic environment in the gut to one favoring C. difficile growth. Here we used metabolomics and...
Research Article | Molecular Biology and PhysiologySulfide Homeostasis and Nitroxyl Intersect via Formation of Reactive Sulfur Species in Staphylococcus aureusHydrogen sulfide (H2S) is a toxic molecule and a recently described gasotransmitter in vertebrates whose function in bacteria is not well understood. In this work, we describe the transcriptomic response of the major human pathogen Staphylococcus aureus to quantified changes in levels of cellular organic reactive sulfur species, which are effector molecules...
Research Article | Host-Microbe BiologyNew Insights into Autoinducer-2 Signaling as a Virulence Regulator in a Mouse Model of Pneumonic PlagueYersinia pestis is the bacterial agent that causes the highly fatal disease plague. The organism represents a significant concern because of its potential use as a bioterror agent, beyond the several thousand naturally occurring human infection cases occurring globally each year. While there has been development of effective antibiotics, the narrow therapeutic window...