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https://www.readbyqxmd.com/read/28902898/identification-and-characterization-of-preferred-dna-binding-sites-for-the-thermus-thermophilus-transcriptional-regulator-fadr
#1
Minwoo Lee, Hyejin Um, Michael W Van Dyke
One of the primary transcriptional regulators of fatty acid homeostasis in many prokaryotes is the protein FadR. To better understand its biological function in the extreme thermophile Thermus thermophilus HB8, we sought to first determine its preferred DNA-binding sequences in vitro using the combinatorial selection method Restriction Endonuclease Protection, Selection, and Amplification (REPSA) and then use this information to bioinformatically identify potential regulated genes. REPSA determined a consensus FadR-binding sequence 5´-TTRNACYNRGTNYAA-3´, which was further characterized using quantitative electrophoretic mobility shift assays...
2017: PloS One
https://www.readbyqxmd.com/read/28871436/the-prevalence-of-medication-related-adverse-events-in-inpatients-a-systematic-review-and-meta-analysis
#2
REVIEW
Outi Laatikainen, J Miettunen, S Sneck, H Lehtiniemi, O Tenhunen, M Turpeinen
PURPOSE: Adverse drug events (ADEs) have been internationally recognized as a major threat to patient safety. The purpose of this study was to conduct a meta-analysis focusing on inpatient ADEs in the Western World to provide better estimate of the current state of medication safety in these countries. METHODS: The studies for meta-analysis were identified through electronic search in Cochrane, Scopus, Medline, and Web of science databases. Included articles focused on adult inpatient ADEs, had commonly accepted definition for ADE, and were conducted between 2000 and 2016...
September 5, 2017: European Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/28724694/role-of-long-chain-acyl-coas-in-the-regulation-of-mycolic-acid-biosynthesis-in-mycobacteria
#3
Yi Ting Tsai, Valentina Salzman, Matías Cabruja, Gabriela Gago, Hugo Gramajo
One of the dominant features of the biology of Mycobacterium tuberculosis, and other mycobacteria, is the mycobacterial cell envelope with its exceptional complex composition. Mycolic acids are major and very specific components of the cell envelope and play a key role in its architecture and impermeability. Biosynthesis of mycolic acid (MA) precursors requires two types of fatty acid synthases, FAS I and FAS II, which should work in concert in order to keep lipid homeostasis tightly regulated. Both FAS systems are regulated at their transcriptional level by specific regulatory proteins...
July 2017: Open Biology
https://www.readbyqxmd.com/read/28669634/structure-of-phytoene-desaturase-provides-insights-into-herbicide-binding-and-reaction-mechanisms-involved-in-carotene-desaturation
#4
Anton Brausemann, Sandra Gemmecker, Julian Koschmieder, Sandro Ghisla, Peter Beyer, Oliver Einsle
Cyanobacteria and plants synthesize carotenoids via a poly-cis pathway starting with phytoene, a membrane-bound C40 hydrocarbon. Phytoene desaturase (PDS) introduces two double bonds and concomitantly isomerizes two neighboring double bonds from trans to cis. PDS assembles into homo-tetramers that interact monotopically with membranes. A long hydrophobic tunnel is proposed to function in the sequential binding of phytoene and the electron acceptor plastoquinone. The herbicidal inhibitor norflurazon binds at a plastoquinone site thereby blocking reoxidation of FADred...
August 1, 2017: Structure
https://www.readbyqxmd.com/read/28536705/role-of-gntr-family-regulatory-gene-sco1678-in-gluconate-metabolism-in-streptomyces-coelicolor-m145
#5
Olga Tsypik, Roman Makitrynskyy, Agnieszka Bera, Lijiang Song, Wolfgang Wohlleben, Victor Fedorenko, Bohdan Ostash
Here we report functional characterization of the Streptomyces coelicolor M145 gene SCO1678, which encodes a GntR-like regulator of the FadR subfamily. Bioinformatic analysis suggested that SCO1678 is part of putative operon (gnt) involved in gluconate metabolism. Combining the results of SCO1678 knockout, transcriptional analysis of gnt operon, and Sco1678 protein-DNA electromobility shift assays, we established that Sco1678 protein controls the gluconate operon. It does so via repression of its transcription from a single promoter located between genes SCO1678 and SCO1679...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28160603/structural-basis-of-operator-sites-recognition-and-effector-binding-in-the-tetr-family-transcription-regulator-fadr
#6
Hyun Ku Yeo, Young Woo Park, Jae Young Lee
FadR is a fatty acyl-CoA dependent transcription factor that regulates genes encoding proteins involved in fatty-acid degradation and synthesis pathways. In this study, the crystal structures of Bacillus halodurans FadR, which belong to the TetR family, have been determined in three different forms: ligand-bound, ligand-free and DNA-bound at resolutions of 1.75, 2.05 and 2.80 Å, respectively. Structural and functional data showed that B. halodurans FadR was bound to its operator site without fatty acyl-CoAs...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28115548/the-fatty-acid-regulator-fadr-influences-the-expression-of-the-virulence-cascade-in-the-el-tor-biotype-of-vibrio-cholerae-by-modulating-the-levels-of-toxt-via-two-different-mechanisms
#7
Gabriela Kovacikova, Wei Lin, Ronald K Taylor, Karen Skorupski
FadR is a master regulator of fatty acid (FA) metabolism that coordinates the pathways of FA degradation and biosynthesis in enteric bacteria. We show here that a ΔfadR mutation in the El Tor biotype of Vibrio cholerae prevents the expression of the virulence cascade by influencing both the transcription and the posttranslational regulation of the master virulence regulator ToxT. FadR is a transcriptional regulator that represses the expression of genes involved in FA degradation, activates the expression of genes involved in unsaturated FA (UFA) biosynthesis, and also activates the expression of two operons involved in saturated FA (SFA) biosynthesis...
April 1, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/27761152/improvement-of-free-fatty-acid-production-using-a-mutant-acyl-coa-thioesterase-i-with-high-specific-activity-in-escherichia-coli
#8
Kwang Soo Shin, Sangwoo Kim, Sung Kuk Lee
BACKGROUND: Microbial production of oleochemicals has been actively studied in the last decade. Free fatty acids (FFAs) could be converted into a variety of molecules such as industrial products, consumer products, and fuels. FFAs have been produced in metabolically engineered Escherichia coli cells expressing a signal sequence-deficient acyl-CoA thioesterase I ('TesA). Nonetheless, increasing the expression level of 'TesA seems not to be an appropriate approach to scale up FFA production because a certain ratio of each component including fatty acid synthase and 'TesA is required for optimal production of FFAs...
2016: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/27466817/engineered-production-of-short-chain-fatty-acid-in-escherichia-coli-using-fatty-acid-synthesis-pathway
#9
Kamran Jawed, Anu Jose Mattam, Zia Fatma, Saima Wajid, Malik Z Abdin, Syed Shams Yazdani
Short-chain fatty acids (SCFAs), such as butyric acid, have a broad range of applications in chemical and fuel industries. Worldwide demand of sustainable fuels and chemicals has encouraged researchers for microbial synthesis of SCFAs. In this study we compared three thioesterases, i.e., TesAT from Anaerococcus tetradius, TesBF from Bryantella formatexigens and TesBT from Bacteroides thetaiotaomicron, for production of SCFAs in Escherichia coli utilizing native fatty acid synthesis (FASII) pathway and modulated the genetic and bioprocess parameters to improve its yield and productivity...
2016: PloS One
https://www.readbyqxmd.com/read/26944841/transcriptional-repression-of-the-vc2105-protein-by-vibrio-fadr-suggests-that-it-is-a-new-auxiliary-member-of-the-fad-regulon
#10
Rongsui Gao, Jingxia Lin, Han Zhang, Youjun Feng
UNLABELLED: Recently, our group along with others reported that the Vibrio FadR regulatory protein is unusual in that, unlike the prototypical fadR product of Escherichia coli, which has only one ligand-binding site, Vibrio FadR has two ligand-binding sites and represents a new mechanism for fatty acid sensing. The promoter region of the vc2105 gene, encoding a putative thioesterase, was mapped, and a putative FadR-binding site (AA CTG GTA AGA GCA CTT) was proposed. Different versions of the FadR regulatory proteins were prepared and purified to homogeneity...
May 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/26476644/improving-alkane-synthesis-in-escherichia-coli-via-metabolic-engineering
#11
Xuejiao Song, Haiying Yu, Kun Zhu
Concerns about energy security and global petroleum supply have made the production of renewable biofuels an industrial imperative. The ideal biofuels are n-alkanes in that they are chemically and structurally identical to the fossil fuels and can "drop in" to the transportation infrastructure. In this work, an Escherichia coli strain that produces n-alkanes was constructed by heterologous expression of acyl-acyl carrier protein (ACP) reductase (AAR) and aldehyde deformylating oxygenase (ADO) from Synechococcus elongatus PCC7942...
January 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/26460058/assessment-of-bacterial-acyltransferases-for-an-efficient-lipid-production-in-metabolically-engineered-strains-of-e-coli
#12
Annika Röttig, Paul Jannis Zurek, Alexander Steinbüchel
Microbially produced lipids like triacylglycerols or fatty acid ethyl esters are currently of great interest as fuel replacements or other industrially relevant compounds. They can even be produced by non-oleaginous microbes, like Escherichia coli, upon metabolic engineering. However, there is still much room for improvement regarding the yield for a competitive microbial production of lipids or biofuels. We genetically engineered E. coli by expressing fadD, fadR, pgpB, plsB and 'tesA in combination with atfA from Acinetobacter baylyi...
November 2015: Metabolic Engineering
https://www.readbyqxmd.com/read/26433722/transcriptional-regulators-of-gntr-family-in-streptomyces-coelicolor-a3-2-analysis-in-silico-and-in-vivo-of-ytra-subfamily
#13
O Tsypik, O Yushchuk, N Zaburannyi, K Flärdh, S Walker, V Fedorenko, B Ostash
Transcriptional factors of the GntR family regulate numerous physiological and morphological processes in response to the nutrient state of bacterial cells. The number of GntR transcriptional factors in genomes of soil-dwelling actinomycetes is one of the highest among bacteria, reflecting both the large size of their chromosomes and the complex ecological niche that they occupy. However, very little is known about the roles of GntRs in actinomycete biology. Here, we analyzed the genome of model actinomycete, Streptomyces coelicolor A3(2), in an attempt to gain new insights into the function of GntR family...
May 2016: Folia Microbiologica
https://www.readbyqxmd.com/read/26385696/modulation-of-fadr-binding-capacity-for-acyl-coa-fatty-acids-through-structure-guided-mutagenesis
#14
John-Paul Bacik, Chris M Yeager, Scott N Twary, Ricardo Martí-Arbona
FadR is a versatile global regulator in Escherichia coli that controls fatty acid metabolism and thereby modulates the ability of this bacterium to grow using fatty acids or acetate as the sole carbon source. FadR regulates fatty acid metabolism in response to intra-cellular concentrations of acyl-CoA lipids. The ability of FadR to bind acyl-CoA fatty acids is thus of significant interest for the engineering of biosynthetic pathways for the production of lipid-based biofuels and commodity chemicals. Based on the available crystal structure of E...
October 2015: Protein Journal
https://www.readbyqxmd.com/read/26358622/expression-of-shewanella-frigidimarina-fatty-acid-metabolic-genes-in-e-coli-by-crispr-cas9-coupled-lambda-red-recombineering
#15
Jun Xia, Ling Wang, Jian-bo Zhu, Cheng-jun Sun, Ming-gang Zheng, Li Zheng, Ying-hua Lou, Lei Shi
OBJECTIVE: To construct a clustered, regularly interspaced, short palindromic repeats (CRISPR)/cas9 system and use this system to obtain a recombinant Escherichia coli strain possessing the fatty acid metabolism genes from a lipid-rich marine bacterium. RESULTS: The fatty acid regulatory transcription factor (fadR), delta9 (Δ(9) desaturase) and acetyl-CoA carboxylase (acc) genes were cloned from Shewanella frigidimarina. The fatty acid regulatory transcription factor (fadD) and phosphoenolpyruvate carboxylase inactivated strains were used to construct the fadR/delta9 and acc knock-in strains, which are both markerless and "scar"-less, and identified the change in fatty acid composition in the recombinant strains...
January 2016: Biotechnology Letters
https://www.readbyqxmd.com/read/26151451/gntr-family-of-bacterial-transcription-factors-and-their-dna-binding-motifs-structure-positioning-and-co-evolution
#16
Inna A Suvorova, Yuri D Korostelev, Mikhail S Gelfand
The GNTR family of transcription factors (TFs) is a large group of proteins present in diverse bacteria and regulating various biological processes. Here we use the comparative genomics approach to reconstruct regulons and identify binding motifs of regulators from three subfamilies of the GNTR family, FADR, HUTC, and YTRA. Using these data, we attempt to predict DNA-protein contacts by analyzing correlations between binding motifs in DNA and amino acid sequences of TFs. We identify pairs of positions with high correlation between amino acids and nucleotides for FADR, HUTC, and YTRA subfamilies and show that the most predicted DNA-protein interactions are quite similar in all subfamilies and conform well to the experimentally identified contacts formed by FadR from E...
2015: PloS One
https://www.readbyqxmd.com/read/26147209/phytoene-desaturase-from-oryza-sativa-oligomeric-assembly-membrane-association-and-preliminary-3d-analysis
#17
Sandra Gemmecker, Patrick Schaub, Julian Koschmieder, Anton Brausemann, Friedel Drepper, Marta Rodriguez-Franco, Sandro Ghisla, Bettina Warscheid, Oliver Einsle, Peter Beyer
Recombinant phytoene desaturase (PDS-His6) from rice was purified to near-homogeneity and shown to be enzymatically active in a biphasic, liposome-based assay system. The protein contains FAD as the sole protein-bound redox-cofactor. Benzoquinones, not replaceable by molecular oxygen, serve as a final electron acceptor defining PDS as a 15-cis-phytoene (donor):plastoquinone oxidoreductase. The herbicidal PDS-inhibitor norflurazon is capable of arresting the reaction by stabilizing the intermediary FAD(red), while an excess of the quinone acceptor relieves this blockage, indicating competition...
2015: PloS One
https://www.readbyqxmd.com/read/26051676/experimental-null-method-to-guide-the-development-of-technical-procedures-and-to-control-false-positive-discovery-in-quantitative-proteomics
#18
Xiaomeng Shen, Qiang Hu, Jun Li, Jianmin Wang, Jun Qu
Comprehensive and accurate evaluation of data quality and false-positive biomarker discovery is critical to direct the method development/optimization for quantitative proteomics, which nonetheless remains challenging largely due to the high complexity and unique features of proteomic data. Here we describe an experimental null (EN) method to address this need. Because the method experimentally measures the null distribution (either technical or biological replicates) using the same proteomic samples, the same procedures and the same batch as the case-vs-contol experiment, it correctly reflects the collective effects of technical variability (e...
October 2, 2015: Journal of Proteome Research
https://www.readbyqxmd.com/read/26050090/binding-of-shewanella-fadr-to-the-faba-fatty-acid-biosynthetic-gene-implications-for-contraction-of-the-fad-regulon
#19
Huimin Zhang, Beiwen Zheng, Rongsui Gao, Youjun Feng
The Escherichia coli fadR protein product, a paradigm/prototypical FadR regulator, positively regulates fabA and fabB, the two critical genes for unsaturated fatty acid (UFA) biosynthesis. However the scenario in the other Ɣ-proteobacteria, such as Shewanella with the marine origin, is unusual in that Rodionov and coworkers predicted that only fabA (not fabB) has a binding site for FadR protein. It raised the possibility of fad regulon contraction. Here we report that this is the case. Sequence alignment of the FadR homologs revealed that the N-terminal DNA-binding domain exhibited remarkable similarity, whereas the ligand-accepting motif at C-terminus is relatively-less conserved...
September 2015: Protein & Cell
https://www.readbyqxmd.com/read/25938298/crystal-structure-of-fad35r-from-mycobacterium-tuberculosis-h37rv-in-the-apo-state
#20
Appu Kumar Singh, Babu Manjasetty, G L Balasubramani, Sukirte Koul, Abhishek Kaushik, Mary Krishna Ekka, Vijay Singh, S Kumaran
Fad35R from Mycobacterium tuberculosis binds to the promoter site of Fad35 operon and its DNA binding activities are reduced in the presence of tetracycline and palmitoyl-CoA. We resolved the crystal structure of Fad35R using single-wavelength anomalous diffraction method (SAD). Fad35R comprises canonical DNA binding domain (DBD) and ligand binding domain (LBD), but displays several distinct structural features. Two recognition helices of two monomers in the homodimer are separated by ~ 48 Å and two core triangle-shaped ligand binding cavities are well exposed to solvent...
2015: PloS One
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