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Molecular Biology and Physiology

  • Open Access
    <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Has a Unique Transcriptional Program in Long-Term Stationary Phase Allowing Identification of Genes Important for Survival
    Editor's Pick Research Article | Molecular Biology and Physiology
    Escherichia coli Has a Unique Transcriptional Program in Long-Term Stationary Phase Allowing Identification of Genes Important for Survival

    Experimental 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...

    Karin E. Kram, Autumn L. Henderson, Steven E. Finkel
  • Open Access
    Coevolutionary Analysis Reveals a Conserved Dual Binding Interface between Extracytoplasmic Function σ Factors and Class I Anti-σ Factors
    Research Article | Molecular Biology and Physiology
    Coevolutionary Analysis Reveals a Conserved Dual Binding Interface between Extracytoplasmic Function σ Factors and Class I Anti-σ Factors

    In 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...

    Delia Casas-Pastor, Angelika Diehl, Georg Fritz
  • Open Access
    Systematic Analysis of REBASE Identifies Numerous Type I Restriction-Modification Systems with Duplicated, Distinct <em>hsdS</em> Specificity Genes That Can Switch System Specificity by Recombination
    Research Article | Molecular Biology and Physiology
    Systematic Analysis of REBASE Identifies Numerous Type I Restriction-Modification Systems with Duplicated, Distinct hsdS Specificity Genes That Can Switch System Specificity by Recombination

    Many 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...

    John M. Atack, Chengying Guo, Thomas Litfin, Long Yang, Patrick J. Blackall, Yaoqi Zhou, Michael P. Jennings
  • Open Access
    Proteomic Study of the Survival and Resuscitation Mechanisms of Filamentous Persisters in an Evolved <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Population from Cyclic Ampicillin Treatment
    Research Article | Molecular Biology and Physiology
    Proteomic Study of the Survival and Resuscitation Mechanisms of Filamentous Persisters in an Evolved Escherichia coli Population from Cyclic Ampicillin Treatment

    Persisters 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...

    Jordy Evan Sulaiman, Henry Lam
  • Open Access
    Genome-Scale Transcription-Translation Mapping Reveals Features of <span class="named-content genus-species" id="named-content-1">Zymomonas mobilis</span> Transcription Units and Promoters
    Research Article | Molecular Biology and Physiology
    Genome-Scale Transcription-Translation Mapping Reveals Features of Zymomonas mobilis Transcription Units and Promoters

    Efforts 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...

    Jessica M. Vera, Indro Neil Ghosh, Yaoping Zhang, Alex S. Hebert, Joshua J. Coon, Robert Landick
  • Open Access
    Tracking Recombination Events That Occur in Conjugative Virulence Plasmid p15WZ-82_Vir during the Transmission Process
    Research Article | Molecular Biology and Physiology
    Tracking Recombination Events That Occur in Conjugative Virulence Plasmid p15WZ-82_Vir during the Transmission Process

    Although 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...

    Xuemei Yang, Lianwei Ye, Edward Wai-Chi Chan, Rong Zhang, Sheng Chen
  • Open Access
    Data-Driven Models Reveal Mutant Cell Behaviors Important for Myxobacterial Aggregation
    Research Article | Molecular Biology and Physiology
    Data-Driven Models Reveal Mutant Cell Behaviors Important for Myxobacterial Aggregation

    Self-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...

    Zhaoyang Zhang, Christopher R. Cotter, Zhe Lyu, Lawrence J. Shimkets, Oleg A. Igoshin
  • Open Access
    A Comprehensive Coexpression Network Analysis in <span class="named-content genus-species" id="named-content-1">Vibrio cholerae</span>
    Resource Report | Molecular Biology and Physiology
    A Comprehensive Coexpression Network Analysis in Vibrio cholerae

    Cholera 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...

    Cory D. DuPai, Claus O. Wilke, Bryan W. Davies
  • 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
    GapMind: Automated Annotation of Amino Acid Biosynthesis
    Editor's Pick Research Article | Molecular Biology and Physiology
    GapMind: Automated Annotation of Amino Acid Biosynthesis

    Many 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,...

    Morgan N. Price, Adam M. Deutschbauer, Adam P. Arkin

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