Molecular Biology and Physiology
Editor's Pick Research Article | Molecular Biology and PhysiologyEscherichia coli Has a Unique Transcriptional Program in Long-Term Stationary Phase Allowing Identification of Genes Important for SurvivalExperimental evolution studies have elucidated evolutionary processes, but usually in chemically well-defined and/or constant environments. Using complex environments is important to begin to understand how evolution may occur in natural environments, such as soils or within a host. However, characterizing the stresses that cells experience in these complex environments can be challenging. One way to approach this is by determining how...
Research Article | Molecular Biology and PhysiologyCoevolutionary Analysis Reveals a Conserved Dual Binding Interface between Extracytoplasmic Function σ Factors and Class I Anti-σ FactorsIn the bacterial world, extracytoplasmic function σ factors (ECFs) are the most widespread family of alternative σ factors, mediating many cellular responses to environmental cues, such as stress. This work uses a computational approach to investigate how these σ factors interact with class I anti-σ factors—the most abundant regulators of ECF activity. By comprehensively classifying the anti-σs into phylogenetic groups and by comparing...
Research Article | Molecular Biology and PhysiologySystematic Analysis of REBASE Identifies Numerous Type I Restriction-Modification Systems with Duplicated, Distinct hsdS Specificity Genes That Can Switch System Specificity by RecombinationMany bacterial species contain DNA methyltransferases that have random on/off switching of expression. These systems, called phasevarions (phase-variable regulons), control the expression of multiple genes by global methylation changes. In every previously characterized phasevarion, genes involved in pathobiology, antibiotic resistance, and potential vaccine candidates are randomly varied in their expression, commensurate with...
Research Article | Molecular Biology and PhysiologyProteomic Study of the Survival and Resuscitation Mechanisms of Filamentous Persisters in an Evolved Escherichia coli Population from Cyclic Ampicillin TreatmentPersisters are a subpopulation of cells with enhanced survival toward antibiotic treatment and have the ability to resume normal growth when the antibiotic stress is lifted. Although proteomics is the most suitable tool to study them from a system-level perspective, the number of persisters that present naturally is too few for proteomics analysis, and thus the complex mechanisms through which they are able to survive antibiotic...
Research Article | Molecular Biology and PhysiologyGenome-Scale Transcription-Translation Mapping Reveals Features of Zymomonas mobilis Transcription Units and PromotersEfforts to rationally engineer synthetic pathways in Zymomonas mobilis are impeded by a lack of knowledge and tools for predictable and quantitative programming of gene regulation at the transcriptional, posttranscriptional, and posttranslational levels. With the detailed functional characterization of the...
Research Article | Molecular Biology and PhysiologyTracking Recombination Events That Occur in Conjugative Virulence Plasmid p15WZ-82_Vir during the Transmission ProcessAlthough they are often nonconjugative, large virulence plasmids are increasingly detected in clinical K. pneumoniae and contribute to the hypervirulence phenotype of this organism. In this study, we demonstrated that the virulence-encoding region that originated from virulence plasmid pLVPK actively interacted with different types of plasmids via homologous...
Research Article | Molecular Biology and PhysiologyData-Driven Models Reveal Mutant Cell Behaviors Important for Myxobacterial AggregationSelf-organization into spatial patterns is evident in many multicellular phenomena. Even for the best-studied systems, our ability to dissect the mechanisms driving coordinated cell movement is limited. While genetic approaches can identify mutations perturbing multicellular patterns, the diverse nature of the signaling cues coupled to significant heterogeneity of individual cell behavior impedes our ability to mechanistically connect...
Resource Report | Molecular Biology and PhysiologyA Comprehensive Coexpression Network Analysis in Vibrio choleraeCholera is a devastating illness that kills tens of thousands of people annually. Vibrio cholerae, the causative agent of cholera, is an important model organism to investigate both bacterial pathogenesis and the impact of horizontal gene transfer on the emergence and dissemination of new virulent strains. Despite the importance of this pathogen, roughly one-third of...
Research Article | Molecular Biology and PhysiologyCharacterizing the Mechanism of Action of an Ancient Antimicrobial, Manuka Honey, against Pseudomonas aeruginosa Using Modern TranscriptomicsThe 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...
Editor's Pick Research Article | Molecular Biology and PhysiologyGapMind: Automated Annotation of Amino Acid BiosynthesisMany microbes can make all of the amino acids (the building blocks of proteins). In principle, we should be able to predict which amino acids a microbe can make, and which it requires as nutrients, by checking its genome sequence for all of the necessary genes. However, in practice, it is difficult to check for all of the alternative pathways. Furthermore, new pathways and enzymes are still being discovered. We built an automated tool,...