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RNA-seq

  • Open Access
    Genome-Wide Analysis of Transcriptional Changes and Genes That Contribute to Fitness during Degradation of the Anthropogenic Pollutant Pentachlorophenol by <span class="named-content genus-species" id="named-content-1">Sphingobium chlorophenolicum</span>
    Research Article | Molecular Biology and Physiology
    Genome-Wide Analysis of Transcriptional Changes and Genes That Contribute to Fitness during Degradation of the Anthropogenic Pollutant Pentachlorophenol by Sphingobium chlorophenolicum

    Phenolic compounds such as pentachlorophenol (PCP), triclosan, and 2,4-dichlorophenoxyacetic acid (2,4-D) represent a common class of anthropogenic biocides. Despite the novelty of these compounds, many can be degraded by microbes isolated from contaminated sites. However, degradation of this class of chemicals often generates toxic intermediates, which may contribute to their recalcitrance to biodegradation. We have addressed the...

    Jake J. Flood, Shelley D. Copley
  • Open Access
    Arabinose-Induced Catabolite Repression as a Mechanism for Pentose Hierarchy Control in <em>Clostridium acetobutylicum</em> ATCC 824
    Research Article | Molecular Biology and Physiology
    Arabinose-Induced Catabolite Repression as a Mechanism for Pentose Hierarchy Control in Clostridium acetobutylicum ATCC 824

    Clostridium acetobutylicum can ferment a wide variety of carbohydrates to the commodity chemicals acetone, butanol, and ethanol. Recent advances in genetic engineering have expanded the chemical production repertoire of C. acetobutylicum using synthetic biology. Due to its natural properties and...

    Matthew D. Servinsky, Rebecca L. Renberg, Matthew A. Perisin, Elliot S. Gerlach, Sanchao Liu, Christian J. Sund
  • Open Access
    Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium <span class="named-content genus-species" id="named-content-1">Thioalkalivibrio thiocyanoxidans</span> ARh 2<sup>T</sup> Using Transcriptomics
    Research Article | Molecular Biology and Physiology
    Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium Thioalkalivibrio thiocyanoxidans ARh 2T Using Transcriptomics

    Thiocyanate is a moderately toxic and chemically stable sulfur compound that is produced by both natural and industrial processes. Despite its significance as a pollutant, knowledge of the microbial degradation of thiocyanate is very limited. Therefore, investigation of thiocyanate oxidation in haloalkaliphiles such as the genus Thioalkalivibrio may lead to improved biotechnological applications in wastewater remediation.

    ...
    Tom Berben, Cherel Balkema, Dimitry Y. Sorokin, Gerard Muyzer
  • Open Access
    Transcriptome Analysis of Polyhydroxybutyrate Cycle Mutants Reveals Discrete Loci Connecting Nitrogen Utilization and Carbon Storage in <em>Sinorhizobium meliloti</em>
    Research Article | Molecular Biology and Physiology
    Transcriptome Analysis of Polyhydroxybutyrate Cycle Mutants Reveals Discrete Loci Connecting Nitrogen Utilization and Carbon Storage in Sinorhizobium meliloti

    The ability of bacteria to store carbon and energy as intracellular polymers uncouples cell growth and replication from nutrient uptake and provides flexibility in the use of resources as they are available to the cell. The impact of carbon storage on cellular metabolism would be reflected in global transcription patterns. By investigating the transcriptomic effects of genetically disrupting genes involved in the PHB carbon storage...

    Maya D’Alessio, Ricardo Nordeste, Andrew C. Doxey, Trevor C. Charles
  • Open Access
    Biphasic Metabolism and Host Interaction of a Chlamydial Symbiont
    Editor's Pick Research Article | Host-Microbe Biology
    Biphasic Metabolism and Host Interaction of a Chlamydial Symbiont

    Chlamydiae are known as major bacterial pathogens of humans, causing the ancient disease trachoma, but they are also frequently found in the environment where they infect ubiquitous protists such as amoebae. All known chlamydiae require a eukaryotic host cell to thrive. Using the environmental chlamydia Protochlamydia amoebophila within its natural host, Acanthamoeba castellanii, we investigated gene expression...

    Lena König, Alexander Siegl, Thomas Penz, Susanne Haider, Cecilia Wentrup, Julia Polzin, Evelyne Mann, Stephan Schmitz-Esser, Daryl Domman, Matthias Horn
  • Open Access
    Global Analysis and Comparison of the Transcriptomes and Proteomes of Group A <em>Streptococcus</em> Biofilms
    Research Article | Molecular Biology and Physiology
    Global 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...

    Jeffrey A. Freiberg, Yoann Le Breton, Bao Q. Tran, Alison J. Scott, Janette M. Harro, Robert K. Ernst, Young Ah Goo, Emmanuel F. Mongodin, David R. Goodlett, Kevin S. McIver, Mark E. Shirtliff
  • Open Access
    RNA Sequencing-Based Genome Reannotation of the Dermatophyte <em>Arthroderma benhamiae</em> and Characterization of Its Secretome and Whole Gene Expression Profile during Infection
    Research Article | Host-Microbe Biology
    RNA Sequencing-Based Genome Reannotation of the Dermatophyte Arthroderma benhamiae and Characterization of Its Secretome and Whole Gene Expression Profile during Infection
    Van Du T. Tran, Niccolò De Coi, Marc Feuermann, Emanuel Schmid-Siegert, Elena-Tatiana Băguţ, Bernard Mignon, Patrice Waridel, Corinne Peter, Sylvain Pradervand, Marco Pagni, Michel Monod

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