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Molecular Biology and Physiology

  • Open Access
    Charting the Metabolic Landscape of the Facultative Methylotroph <span class="named-content genus-species" id="named-content-1">Bacillus methanolicus</span>
    Research Article | Molecular Biology and Physiology
    Charting the Metabolic Landscape of the Facultative Methylotroph Bacillus methanolicus

    Methanol is inexpensive, is easy to transport, and can be produced both from renewable and from fossil resources without mobilizing arable lands. As such, it is regarded as a potential carbon source to transition toward a greener industrial chemistry. Metabolic engineering of bacteria and yeast able to efficiently consume methanol is expected to provide cell factories that will transform methanol into higher-value chemicals in the so-...

    Baudoin Delépine, Marina Gil López, Marc Carnicer, Cláudia M. Vicente, Volker F. Wendisch, Stéphanie Heux
  • Open Access
    CRISPR-CBEI: a Designing and Analyzing Tool Kit for Cytosine Base Editor-Mediated Gene Inactivation
    Research Article | Molecular Biology and Physiology
    CRISPR-CBEI: a Designing and Analyzing Tool Kit for Cytosine Base Editor-Mediated Gene Inactivation

    Life science has been in pursuit of precise and efficient genome editing in living cells since the very beginning of the first restriction cloning attempt. The introduction of RNA-guided CRISPR-associated (Cas) nucleases contributed to this ultimate goal through their ability to deliver a double-strand break (DSB) to a precise target location in various species, obsoleting the preceding editing tools, such as zinc-finger nucleases (ZFNs...

    Haopeng Yu, Zhaowei Wu, Xiangdan Chen, Quanjiang Ji, Shiheng Tao
  • Open Access
    A Decrease in Transcription Capacity Limits Growth Rate upon Translation Inhibition
    Research Article | Molecular Biology and Physiology
    A Decrease in Transcription Capacity Limits Growth Rate upon Translation Inhibition

    Exposure of bacteria to sublethal concentrations of antibiotics can lead to bacterial adaptation and survival at higher doses of inhibitors, which in turn can lead to the emergence of antibiotic resistance. The presence of sublethal concentrations of antibiotics targeting translation results in an increase in the amount of ribosomes per cell but nonetheless a decrease in the cells’ growth rate. In this work, we have found that...

    Qing Zhang, Elisa Brambilla, Rui Li, Hualin Shi, Marco Cosentino Lagomarsino, Bianca Sclavi
  • Open Access
    Pivotal Roles for pH, Lactate, and Lactate-Utilizing Bacteria in the Stability of a Human Colonic Microbial Ecosystem
    Research Article | Molecular Biology and Physiology
    Pivotal Roles for pH, Lactate, and Lactate-Utilizing Bacteria in the Stability of a Human Colonic Microbial Ecosystem

    Lactate is formed by many species of colonic bacteria, and can accumulate to high levels in the colons of inflammatory bowel disease subjects. Conversely, in healthy colons lactate is metabolized by lactate-utilizing species to the short-chain fatty acids butyrate and propionate, which are beneficial for the host. Here, we investigated the impact of continuous lactate infusions (up to 20 mM) at two pH values (6.5 and 5.5) on human...

    Shui Ping Wang, Luis A. Rubio, Sylvia H. Duncan, Gillian E. Donachie, Grietje Holtrop, Galiana Lo, Freda M. Farquharson, Josef Wagner, Julian Parkhill, Petra Louis, Alan W. Walker, Harry J. Flint
  • Open Access
    Negative Interplay between Biofilm Formation and Competence in the Environmental Strains of <em>Bacillus subtilis</em>
    Research Article | Molecular Biology and Physiology
    Negative Interplay between Biofilm Formation and Competence in the Environmental Strains of Bacillus subtilis

    The soil bacterium Bacillus subtilis can form robust biofilms, which are important for its survival in the environment. B. subtilis also exhibits natural competence. By investigating competence development in B. subtilis in...

    Qianxuan She, Evan Hunter, Yuxuan Qin, Samantha Nicolau, Eliza A. Zalis, Hongkai Wang, Yun Chen, Yunrong Chai
  • Open Access
    Benchmarking Bacterial Promoter Prediction Tools: Potentialities and Limitations
    Methods and Protocols | Molecular Biology and Physiology
    Benchmarking Bacterial Promoter Prediction Tools: Potentialities and Limitations

    The correct mapping of promoter elements is a crucial step in microbial genomics. Also, when combining new DNA elements into synthetic sequences, predicting the potential generation of new promoter sequences is critical. Over the last years, many bioinformatics tools have been created to allow users to predict promoter elements in a sequence or genome of interest. Here, we assess the predictive power of some of the main prediction tools...

    Murilo Henrique Anzolini Cassiano, Rafael Silva-Rocha
  • Open Access
    Bioinformatic Mapping of Opine-Like Zincophore Biosynthesis in Bacteria
    Research Article | Molecular Biology and Physiology
    Bioinformatic Mapping of Opine-Like Zincophore Biosynthesis in Bacteria

    Bacteria must acquire essential nutrients, including zinc, from their environment. For bacterial pathogens, this necessitates overcoming the host metal-withholding response known as nutritional immunity. A novel type of zinc uptake mechanism that involves the bacterial production of a small zinc-scavenging molecule was recently described in the human pathogens Staphylococcus...

    Jacqueline R. Morey, Thomas E. Kehl-Fie
  • Open Access
    Systematic Reconstruction of the Complete Two-Component Sensorial Network in <span class="named-content genus-species" id="named-content-1">Staphylococcus aureus</span>
    Research Article | Molecular Biology and Physiology
    Systematic Reconstruction of the Complete Two-Component Sensorial Network in Staphylococcus aureus

    Bacteria are able to sense environmental conditions and respond accordingly. Their sensorial system relies on pairs of sensory and regulatory proteins, known as two-component systems (TCSs). The majority of bacteria contain dozens of TCSs, each of them responsible for sensing and responding to a different range of signals. Traditionally, the function of each TCS has been determined by analyzing the changes in gene expression caused by...

    B. Rapun-Araiz, A. F. Haag, V. De Cesare, C. Gil, P. Dorado-Morales, J. R. Penades, I. Lasa
  • Open Access
    Development of a Counterselectable Transposon To Create Markerless Knockouts from an 18,432-Clone Ordered <span class="named-content genus-species" id="named-content-1">Mycobacterium bovis</span> Bacillus Calmette-Guérin Mutant Resource
    Editor's Pick Research Article | Molecular Biology and Physiology
    Development of a Counterselectable Transposon To Create Markerless Knockouts from an 18,432-Clone Ordered Mycobacterium bovis Bacillus Calmette-Guérin Mutant Resource

    While speeding up research for many fields of biology (e.g., yeast, plant, and Caenorhabditis elegans), genome-wide ordered mutant collections are still elusive in mycobacterial research. We developed methods to generate such resources in a time- and cost-effective manner and developed a newly engineered transposon from which unmarked mutants can be efficiently...

    Katlyn Borgers, Kristof Vandewalle, Annelies Van Hecke, Gitte Michielsen, Evelyn Plets, Loes van Schie, Sandrine Vanmarcke, Laurent Schindfessel, Nele Festjens, Nico Callewaert
  • Open Access
    Genome-Wide Analysis of RNA Decay in the Cyanobacterium <em>Synechococcus</em> sp. Strain PCC 7002
    Research Article | Molecular Biology and Physiology
    Genome-Wide Analysis of RNA Decay in the Cyanobacterium Synechococcus sp. Strain PCC 7002

    RNA degradation is an important process that affects the final concentration of individual mRNAs, affecting protein expression and cellular physiology. Studies of how RNA is degraded increase our knowledge of this fundamental process as well as enable the creation of genetic tools to manipulate RNA stability. By studying global transcript turnover, we searched for sequence elements that correlated with transcript (in)stability and used...

    Gina C. Gordon, Jeffrey C. Cameron, Sanjan T. P. Gupta, Michael D. Engstrom, Jennifer L. Reed, Brian F. Pfleger

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