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      Rex in Caldicellulosiruptor bescii: Novel regulon members and its effect on the production of ethanol and overflow metabolites

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          Rex is a global redox‐sensing transcription factor that senses and responds to the intracellular [ NADH]/[ NAD +] ratio to regulate genes for central metabolism, and a variety of metabolic processes in Gram‐positive bacteria. We decipher and validate four new members of the Rex regulon in Caldicellulosiruptor bescii; a gene encoding a class V aminotransferase, the HydG FeFe Hydrogenase maturation protein, an oxidoreductase, and a gene encoding a hypothetical protein. Structural genes for the NiFe and FeFe hydrogenases, pyruvate:ferredoxin oxidoreductase, as well as the rex gene itself are also members of this regulon, as has been predicted previously in different organisms. A C. bescii rex deletion strain constructed in an ethanol‐producing strain made 54% more ethanol (0.16 mmol/L) than its genetic parent after 36 hr of fermentation, though only under nitrogen limited conditions. Metabolomic interrogation shows this rex‐deficient ethanol‐producing strain synthesizes other reduced overflow metabolism products likely in response to more reduced intracellular redox conditions and the accumulation of pyruvate. These results suggest ethanol production is strongly dependent on the native intracellular redox state in C. bescii, and highlight the combined promise of using this gene and manipulation of culture conditions to yield strains capable of producing ethanol at higher yields and final titer.

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            KEGG as a reference resource for gene and protein annotation

            KEGG ( or is an integrated database resource for biological interpretation of genome sequences and other high-throughput data. Molecular functions of genes and proteins are associated with ortholog groups and stored in the KEGG Orthology (KO) database. The KEGG pathway maps, BRITE hierarchies and KEGG modules are developed as networks of KO nodes, representing high-level functions of the cell and the organism. Currently, more than 4000 complete genomes are annotated with KOs in the KEGG GENES database, which can be used as a reference data set for KO assignment and subsequent reconstruction of KEGG pathways and other molecular networks. As an annotation resource, the following improvements have been made. First, each KO record is re-examined and associated with protein sequence data used in experiments of functional characterization. Second, the GENES database now includes viruses, plasmids, and the addendum category for functionally characterized proteins that are not represented in complete genomes. Third, new automatic annotation servers, BlastKOALA and GhostKOALA, are made available utilizing the non-redundant pangenome data set generated from the GENES database. As a resource for translational bioinformatics, various data sets are created for antimicrobial resistance and drug interaction networks.
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              Consolidated bioprocessing of cellulosic biomass: an update.

              Biologically mediated processes seem promising for energy conversion, in particular for the conversion of lignocellulosic biomass into fuels. Although processes featuring a step dedicated to the production of cellulase enzymes have been the focus of most research efforts to date, consolidated bioprocessing (CBP)--featuring cellulase production, cellulose hydrolysis and fermentation in one step--is an alternative approach with outstanding potential. Progress in developing CBP-enabling microorganisms is being made through two strategies: engineering naturally occurring cellulolytic microorganisms to improve product-related properties, such as yield and titer, and engineering non-cellulolytic organisms that exhibit high product yields and titers to express a heterologous cellulase system enabling cellulose utilization. Recent studies of the fundamental principles of microbial cellulose utilization support the feasibility of CBP.

                Author and article information

                John Wiley and Sons Inc. (Hoboken )
                23 May 2018
                February 2019
                : 8
                : 2 ( doiID: 10.1002/mbo3.2019.8.issue-2 )
                [ 1 ] Department of Chemical and Biomolecular Engineering University of Tennessee Knoxville Tennessee
                [ 2 ] Bredesen Center for Interdisciplinary Graduate Research and Education University of Tennessee Knoxville Tennessee
                [ 3 ] BioEnergy Sciences Center Oak Ridge National Laboratory Oak Ridge Tennessee
                [ 4 ] Department of Genetics University of Georgia Athens Georgia
                [ 5 ] Biosciences Division Oak Ridge National Laboratory Oak Ridge Tennessee
                [ 6 ]Present address: National Renewable Energy Laboratory Golden CO
                [ 7 ]Present address: LanzaTech Skokie IL
                Author notes
                [* ] Correspondence

                Steven D. Brown, Bredesen Center for Interdisciplinary Graduate Research and Education, University of Tennessee, Knoxville, TN.

                Email: steve.brown@

                © 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                Figures: 7, Tables: 2, Pages: 15, Words: 10266
                Funded by: Office of Biological and Environmental Research in the DOE Office of Science
                Funded by: U.S. Department of Energy Bioenergy Research Center
                Funded by: BioEnergy Science Center (BESC)
                Original Article
                Original Articles
                Custom metadata
                February 2019
                Converter:WILEY_ML3GV2_TO_NLMPMC version:5.6.0 mode:remove_FC converted:26.02.2019

                Microbiology & Virology

                rex, caldicellulosiruptor bescii, consolidated bioprocessing, ethanol


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