Molecular Biology and Physiology
- Research Article | Molecular Biology and PhysiologyCombining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides
Knowledge about the role of genes under a particular growth condition is required for a holistic understanding of a bacterial cell and has implications for health, agriculture, and biotechnology. We developed the Tn-seq analysis software (TSAS) package to provide a flexible and statistically rigorous workflow for the high-throughput analysis of insertion mutant libraries, advanced the knowledge of gene essentiality in...
- Research Article | Molecular Biology and PhysiologyThe Protein Interactome of Streptococcus pneumoniae and Bacterial Meta-interactomes Improve Function Predictions
Identification of protein interactions in bacterial species can help define the individual roles that proteins play in cellular pathways and pathogenesis. Very few protein interactions have been identified for the important human pathogen S. pneumoniae. We used an experimental approach to identify over 2,000 new protein interactions for...
- Editor's Pick Research Article | Molecular Biology and PhysiologyQuantitative Proteomics Shows Extensive Remodeling Induced by Nitrogen Limitation in Prochlorococcus marinus SS120
Prochlorococcus is the most abundant photosynthetic organism on Earth, contributing significantly to global primary production and playing a prominent role in biogeochemical cycles. Here we study the effects of extreme nitrogen limitation, a feature of the oligotrophic oceans inhabited by this organism. Quantitative proteomics allowed an accurate quantification of the Prochlorococcus proteome, finding three main...
- Research Article | Molecular Biology and PhysiologyA Genome-Scale Model of Shewanella piezotolerans Simulates Mechanisms of Metabolic Diversity and Energy Conservation
The well-studied nature of the metabolic diversity of Shewanella bacteria makes species from this genus a promising platform for investigating the evolution of carbon metabolism and energy conservation. The Shewanella phylogeny is diverged into two major branches, referred to as group 1 and group 2. While the genotype-phenotype connections of group 2 species have been extensively studied with metabolic modeling, a...
- Research Article | Molecular Biology and PhysiologyMetatranscriptomics Supports the Mechanism for Biocathode Electroautotrophy by “Candidatus Tenderia electrophaga”
Bacteria that directly use electrodes as metabolic electron donors (biocathodes) have been proposed for applications ranging from microbial electrosynthesis to advanced bioelectronics for cellular communication with machines. However, just as we understand very little about oxidation of analogous natural insoluble electron donors, such as iron oxide, the organisms and extracellular electron transfer (EET) pathways underlying the...
- Research Article | Molecular Biology and PhysiologyTranscriptional Profiling of the Oral Pathogen Streptococcus mutans in Response to Competence Signaling Peptide XIP
Genetic competence provides bacteria with an opportunity to increase genetic diversity or acquire novel traits conferring a survival advantage. In the cariogenic pathogen Streptococcus mutans, DNA transformation is regulated by the competence stimulating peptide XIP (ComX-inducing p...
- Methods and Protocols | Molecular Biology and PhysiologyFrom Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer
Bacteria are ubiquitous in our ecosystem and have a major impact on human health, e.g., by supporting digestion in the human gut. Bacterial communities can also aid in biotechnological processes such as wastewater treatment or decontamination of polluted soils. Diverse bacteria contribute with their unique capabilities to the functioning of such ecosystems, but lab experiments to investigate those capabilities are labor-intensive. Major...
- Research Article | Molecular Biology and PhysiologyGenomewide Dam Methylation in Escherichia coli during Long-Term Stationary Phase
While it has been shown that methylation remains relatively constant into early stationary phase of E. coli, this study goes further through death phase and long-term stationary phase, a unique time in the bacterial life cycle due to nutrient limitation and strong selection for mutants with increased fitness. The absence of methylation at GATC sites can influence the...
- Research Article | Molecular Biology and PhysiologyA Metabolic Widget Adjusts the Phosphoenolpyruvate-Dependent Fructose Influx in Pseudomonas putida
The regulatory nodes that govern metabolic traffic in bacteria often show connectivities that could be deemed unnecessarily complex at a first glance. Being a soil dweller and plant colonizer, Pseudomonas putida frequently encounters fructose in the niches that it inhabits. As is the case with many other sugars, fructose is internalized by a dedicated...
- Research Article | Molecular Biology and PhysiologyGlobal Analysis and Comparison of the Transcriptomes and Proteomes of Group A Streptococcus Biofilms
Prokaryotes are thought to regulate their proteomes largely at the level of transcription. However, the results from this first set of global transcriptomic and proteomic analyses of paired microbial samples presented here show that this assumption is false for the majority of genes and their products in S. pyogenes. In addition, the tenuousness of the link between...