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https://www.readbyqxmd.com/read/29136175/structural-basis-of-effector-and-operator-recognition-by-the-phenolic-acid-responsive-transcriptional-regulator-padr
#1
Sun Cheol Park, Yun Mi Kwak, Wan Seok Song, Minsun Hong, Sung-Il Yoon
The PadR family is a large group of transcriptional regulators that function as environmental sensors. PadR negatively controls the expression of phenolic acid decarboxylase, which detoxifies harmful phenolic acids. To identify the mechanism by which PadR regulates phenolic acid-mediated gene expression, we performed structural and mutational studies of effector and operator recognition by Bacillus subtilis PadR. PadR contains an N-terminal winged helix-turn-helix (wHTH) domain (NTD) and a C-terminal homodimerization domain (CTD) and dimerizes into a dolmen shape...
November 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29070902/mycobacterium-smegmatis-pafbc-is-involved-in-regulation-of-dna-damage-response
#2
Begonia Fudrini Olivencia, Andreas U Müller, Bernd Roschitzki, Sibylle Burger, Eilika Weber-Ban, Frank Imkamp
Two genes, pafB and pafC, are organized in an operon with the Pup-ligase gene pafA, which is part of the Pup-proteasome system (PPS) present in mycobacteria and other actinobacteria. The PPS is crucial for Mycobacterium tuberculosis resistance towards reactive nitrogen intermediates (RNI). However, pafB and pafC apparently play only a minor role in RNI resistance. To characterize their function, we generated a pafBC deletion in Mycobacterium smegmatis (Msm). Proteome analysis of the mutant strain revealed decreased cellular levels of various proteins involved in DNA damage repair, including recombinase A (RecA)...
October 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29040945/quercetin-protects-mouse-liver-against-triptolide-induced-hepatic-injury-by-restoring-th17-treg-balance-through-tim-3-and-tlr4-myd88-nf-%C3%AE%C2%BAb-pathway
#3
Cai-Bing Wei, Kun Tao, Rong Jiang, Lian-Di Zhou, Qi-Hui Zhang, Chun-Su Yuan
Triptolide (TP) is a diterpene triepoxide with various biological activities, but its clinical applications have been limited by potential hepatotoxicity, which can be attributed to T helper 17 (Th17)/T regulatory (Treg) cell imbalance. Quercetin (QE), a natural flavonoid, has been reported to have many benefits and medicinal properties, including hepatoprotective activity against TP-induced liver injury. However, the hepatoprotection mechanisms have not been clarified. The present study was designed to explore the protective effect and the mechanism of QE against TP-induced liver injury...
October 14, 2017: International Immunopharmacology
https://www.readbyqxmd.com/read/28745822/dnri-of-streptomyces-peucetius-binds-to-the-resistance-genes-drrab-and-drrc-but-is-activated-by-daunorubicin
#4
Francis Prija, Padmanabhan Srinivasan, Subhadeep Das, Karuppasamy Kattusamy, Ranjan Prasad
The master regulator, DnrI of Streptomyces peucetius is a member of the family of transcriptional activator, Streptomyces antibiotic regulatory proteins (SARP), which controls the biosynthesis of antitumor anthracycline, daunorubicin (DNR) and doxorubicin (DXR). The binding of DnrI to the heptameric repeat sequence found within the -35 promoter region of biosynthetic gene, dpsE activates it. To combat the increased level of intracellular DNR, the cell has developed self resistance mechanism mediated by drrAB and drrC genes which are regulated by regulatory genes...
July 26, 2017: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/28670937/marr-family-transcription-factors-dynamic-variations-on-a-common-scaffold
#5
Dinesh K Deochand, Anne Grove
Members of the multiple antibiotic resistance regulator (MarR) family of transcription factors are critical for bacterial cells to respond to chemical signals and to convert such signals into changes in gene activity. Obligate dimers belonging to the winged helix-turn-helix protein family, they are critical for regulation of a variety of functions, including degradation of organic compounds and control of virulence gene expression. The conventional regulatory paradigm is based on a genomic locus in which the gene encoding the MarR protein is divergently oriented from a gene under its control; MarR binding to the intergenic region controls expression of both genes by changing the interaction of RNA polymerase with gene promoters...
July 3, 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28631437/control-of-virulence-gene-transcription-by-indirect-readout-in-vibrio-cholerae-and-salmonella-enterica-serovar-typhimurium
#6
REVIEW
Charles J Dorman, Matthew J Dorman
Indirect readout mechanisms of transcription control rely on the recognition of DNA shape by transcription factors (TFs). TFs may also employ a direct readout mechanism that involves the reading of the base sequence in the DNA major groove at the binding site. TFs with winged helix-turn-helix (wHTH) motifs use an alpha helix to read the base sequence in the major groove while inserting a beta sheet 'wing' into the adjacent minor groove. Such wHTH proteins are important regulators of virulence gene transcription in many pathogens; they also control housekeeping genes...
October 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28628237/wing-phosphorylation-is-a-major-functional-determinant-of-the-lrs14-type-biofilm-and-motility-regulator-abfr1-in-sulfolobus-acidocaldarius
#7
Lingling Li, Ankan Banerjee, Lisa Franziska Bischof, Hassan Ramadan Maklad, Lena Hoffmann, Anna-Lena Henche, Fabian Veliz, Wolfgang Bildl, Uwe Schulte, Alvaro Orell, Lars-Oliver Essen, Eveline Peeters, Sonja-Verena Albers
In response to a variety of environmental cues, prokaryotes can switch between a motile and a sessile, biofilm-forming mode of growth. The regulatory mechanisms and signaling pathways underlying this switch are largely unknown in archaea but involve small winged helix-turn-helix DNA-binding proteins of the archaea-specific Lrs14 family. Here, we study the Lrs14 member AbfR1 of Sulfolobus acidocaldarius. Small-angle X-ray scattering data are presented, which are consistent with a model of dimeric AbfR1 in which dimerization occurs via an antiparallel coiled coil as suggested by homology modeling...
June 19, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28621532/synthesis-of-luminescent-platinum-ii-2-6-bis-n-dodecylbenzimidazol-2-yl-pyridine-foldamers-and-their-supramolecular-assembly-and-metallogel-formation
#8
Michael Ho-Yeung Chan, Maggie Ng, Sammual Yu-Lut Leung, Wai Han Lam, Vivian Wing-Wah Yam
Dinuclear alkynylplatinum(II) metallofoldamers with an oligomeric m-phenyleneethynylene backbone have been designed with the incorporation of a sterically undemanding, π-conjugated, and hydrophobic 2,6-bis(N-dodecylbenzimidazol-2'-yl)pyridine pincer ligand. The complex with the optimal chain length has been found to exhibit gelation behavior via stabilization by noncovalent Pt···Pt and π-π stacking interactions in the hierarchical architecture constructed from the single-turn helix. The chain lengths of the complexes have been found to be a critical determinant for their gelation behavior, conformations, and morphologies...
June 16, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28486695/full-shut-off-of-escherichia-coli-rna-polymerase-by-t7-phage-requires-a-small-phage-encoded-dna-binding-protein
#9
Aline Tabib-Salazar, Bing Liu, Andrey Shadrin, Lynn Burchell, Zhexin Wang, Zhihao Wang, Moran G Goren, Ido Yosef, Udi Qimron, Konstantin Severinov, Steve J Matthews, Sivaramesh Wigneshweraraj
Infection of Escherichia coli by the T7 phage leads to rapid and selective inhibition of the bacterial RNA polymerase (RNAP) by the 7 kDa T7 protein Gp2. We describe the identification and functional and structural characterisation of a novel 7 kDa T7 protein, Gp5.7, which adopts a winged helix-turn-helix-like structure and specifically represses transcription initiation from host RNAP-dependent promoters on the phage genome via a mechanism that involves interaction with DNA and the bacterial RNAP. Whereas Gp2 is indispensable for T7 growth in E...
July 27, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28436329/molecular-mechanisms-underlying-the-function-diversity-of-arsr-family-metalloregulator
#10
REVIEW
Sai Ren, Qiming Li, Longxiang Xie, Jianping Xie
The ArsR family of transcriptional regulators are widespread among microorganisms and are involved in various important cellular events, such as metal ion homeostasis, biofilm formation, primary and secondary metabolism, symbiosis, response to adverse condition, and virulence. Its N-terminus contains a winged helix-turn-helix DNA-binding domain that can repress or activate transcription by binding to downstream target promoters. With the increasing number of members in this family identified over the past few decades, the ArsR family members have been intensively explored...
2017: Critical Reviews in Eukaryotic Gene Expression
https://www.readbyqxmd.com/read/28432336/structure-function-analysis-of-the-dna-binding-domain-of-a-transmembrane-transcriptional-activator
#11
Andreas Schlundt, Sophie Buchner, Robert Janowski, Thomas Heydenreich, Ralf Heermann, Jürgen Lassak, Arie Geerlof, Ralf Stehle, Dierk Niessing, Kirsten Jung, Michael Sattler
The transmembrane DNA-binding protein CadC of E. coli, a representative of the ToxR-like receptor family, combines input and effector domains for signal sensing and transcriptional activation, respectively, in a single protein, thus representing one of the simplest signalling systems. At acidic pH in a lysine-rich environment, CadC activates the transcription of the cadBA operon through recruitment of the RNA polymerase (RNAP) to the two cadBA promoter sites, Cad1 and Cad2, which are directly bound by CadC...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28396405/structure-of-a-dna-glycosylase-that-unhooks-interstrand-cross-links
#12
Elwood A Mullins, Garrett M Warren, Noah P Bradley, Brandt F Eichman
DNA glycosylases are important editing enzymes that protect genomic stability by excising chemically modified nucleobases that alter normal DNA metabolism. These enzymes have been known only to initiate base excision repair of small adducts by extrusion from the DNA helix. However, recent reports have described both vertebrate and microbial DNA glycosylases capable of unhooking highly toxic interstrand cross-links (ICLs) and bulky minor groove adducts normally recognized by Fanconi anemia and nucleotide excision repair machinery, although the mechanisms of these activities are unknown...
April 25, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28073944/a-novel-bifunctional-transcriptional-regulator-of-riboflavin-metabolism-in-archaea
#13
Irina A Rodionova, Matthew W Vetting, Xiaoqing Li, Steven C Almo, Andrei L Osterman, Dmitry A Rodionov
Riboflavin (vitamin B2) is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide, which are essential coenzymes in all free-living organisms. Riboflavin biosynthesis in many Bacteria but not in Archaea is controlled by FMN-responsive riboswitches. We identified a novel bifunctional riboflavin kinase/regulator (RbkR), which controls riboflavin biosynthesis and transport genes in major lineages of Crenarchaeota, Euryarchaeota and Thaumarchaeota. RbkR proteins are composed of the riboflavin kinase domain and a DNA-binding winged helix-turn-helix-like domain...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28031373/the-replication-initiator-of-the-cholera-pathogen-s-second-chromosome-shows-structural-similarity-to-plasmid-initiators
#14
Natalia Orlova, Matthew Gerding, Olha Ivashkiv, Paul Dominic B Olinares, Brian T Chait, Matthew K Waldor, David Jeruzalmi
The conserved DnaA-oriC system is used to initiate replication of primary chromosomes throughout the bacterial kingdom; however, bacteria with multipartite genomes evolved distinct systems to initiate replication of secondary chromosomes. In the cholera pathogen, Vibrio cholerae, and in related species, secondary chromosome replication requires the RctB initiator protein. Here, we show that RctB consists of four domains. The structure of its central two domains resembles that of several plasmid replication initiators...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28011634/structure-of-the-branched-chain-amino-acid-and-gtp-sensing-global-regulator-cody-from-bacillus-subtilis
#15
Vladimir M Levdikov, Elena Blagova, Vicki L Young, Boris R Belitsky, Andrey Lebedev, Abraham L Sonenshein, Anthony J Wilkinson
CodY is a branched-chain amino acid (BCAA) and GTP sensor and a global regulator of transcription in low G + C Gram-positive bacteria. It controls the expression of over 100 genes and operons, principally by repressing during growth genes whose products are required for adaptations to nutrient limitation. However, the mechanism by which BCAA binding regulates transcriptional changes is not clear. It is known that CodY consists of a GAF (cGMP-stimulated phosphodiesterases, adenylate cyclases, FhlA) domain that binds BCAAs and a winged helix-turn-helix (wHTH) domain that binds to DNA, but the way in which these domains interact and the structural basis of the BCAA dependence of this interaction are unknown...
February 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27988294/role-of-the-recognition-helix-of-response-regulator-walr-from-bacillus-anthracis-in-dna-binding-and-specificity
#16
Alisha Dhiman, Amit Rahi, Monisha Gopalani, Sailesh Bajpai, Sonika Bhatnagar, Rakesh Bhatnagar
WalRK two-component system of Bacillus anthracis potentially regulates multiple genes spanning diverse cellular functions. Its constituent response regulator (RR), WalR belongs to the OmpR/PhoB family which possesses a winged helix-turn-helix motif for DNA binding. An in silico knowledge based model of WalR C-terminal DNA binding domain in complex with its ftsE promoter region binding motif was used to identify specific residues of the recognition helix important for DNA binding. The model was validated by mutagenesis in conjunction with in vitro DNA binding analysis...
March 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/27668276/data-from-computational-analysis-of-the-peptide-linkers-in-the-mocr-bacterial-transcriptional-regulators
#17
Sebastiana Angelaccio, Teresa Milano, Angela Tramonti, Martino Luigi Di Salvo, Roberto Contestabile, Stefano Pascarella
Detailed data from statistical analyses of the structural properties of the inter-domain linker peptides of the bacterial regulators of the family MocR are herein reported. MocR regulators are a recently discovered subfamily of bacterial regulators possessing an N-terminal domain, 60 residue long on average, folded as the winged-helix-turn-helix architecture responsible for DNA recognition and binding, and a large C-terminal domain (350 residue on average) that belongs to the fold type-I pyridoxal 5'-phosphate (PLP) dependent enzymes such aspartate aminotransferase...
December 2016: Data in Brief
https://www.readbyqxmd.com/read/27446613/a-bioinformatics-analysis-reveals-a-group-of-mocr-bacterial-transcriptional-regulators-linked-to-a-family-of-genes-coding-for-membrane-proteins
#18
Teresa Milano, Sebastiana Angelaccio, Angela Tramonti, Martino Luigi Di Salvo, Roberto Contestabile, Stefano Pascarella
The MocR bacterial transcriptional regulators are characterized by an N-terminal domain, 60 residues long on average, possessing the winged-helix-turn-helix (wHTH) architecture responsible for DNA recognition and binding, linked to a large C-terminal domain (350 residues on average) that is homologous to fold type-I pyridoxal 5'-phosphate (PLP) dependent enzymes like aspartate aminotransferase (AAT). These regulators are involved in the expression of genes taking part in several metabolic pathways directly or indirectly connected to PLP chemistry, many of which are still uncharacterized...
2016: Biochemistry Research International
https://www.readbyqxmd.com/read/27403582/diverse-architectural-properties-of-sso10a-proteins-evidence-for-a-role-in-chromatin-compaction-and-organization
#19
Rosalie P C Driessen, Szu-Ning Lin, Willem-Jan Waterreus, Alson L H van der Meulen, Ramon A van der Valk, Niels Laurens, Geri F Moolenaar, Navraj S Pannu, Gijs J L Wuite, Nora Goosen, Remus T Dame
Sso10a proteins are small DNA-binding proteins expressed by the crenarchaeal model organism Sulfolobus solfataricus. Based on the structure of Sso10a1, which contains a winged helix-turn-helix motif, it is believed that Sso10a proteins function as sequence-specific transcription factors. Here we show that Sso10a1 and Sso10a2 exhibit different distinct DNA-binding modes. While the ability to bend DNA is shared between the two proteins, DNA bridging is observed only for Sso10a1 and only Sso10a2 exhibits filament formation along DNA...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27362745/conformational-dynamics-and-the-binding-of-specific-and-nonspecific-dna-by-the-autoinhibited-transcription-factor-ets-1
#20
Geneviève Desjardins, Mark Okon, Barbara J Graves, Lawrence P McIntosh
The affinity of the Ets-1 transcription factor for DNA is autoinhibited by an intrinsically disordered serine-rich region (SRR) and a helical inhibitory module (IM) appended to its winged helix-turn-helix ETS domain. Using NMR spectroscopy, we investigated how Ets-1 recognizes specific versus nonspecific DNA, with a focus on the roles of protein dynamics and autoinhibition in these processes. Upon binding either DNA, the two marginally stable N-terminal helices of the IM predominantly unfold, but still sample partially ordered conformations...
July 26, 2016: Biochemistry
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