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https://www.readbyqxmd.com/read/28631437/control-of-virulence-gene-transcription-by-indirect-readout-in-vibrio-cholerae-and-salmonella-enterica-serovar-typhimurium
#1
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...
June 19, 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
#2
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
#3
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
#4
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...
May 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28436329/molecular-mechanisms-underlying-the-function-diversity-of-arsr-family-metalloregulator
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
https://www.readbyqxmd.com/read/27303893/structural-basis-for-dna-recognition-by-the-transcription-regulator-metr
#16
Avinash S Punekar, Jonathan Porter, Stephen B Carr, Simon E V Phillips
MetR, a LysR-type transcriptional regulator (LTTR), has been extensively studied owing to its role in the control of methionine biosynthesis in proteobacteria. A MetR homodimer binds to a 24-base-pair operator region of the met genes and specifically recognizes the interrupted palindromic sequence 5'-TGAA-N5-TTCA-3'. Mechanistic details underlying the interaction of MetR with its target DNA at the molecular level remain unknown. In this work, the crystal structure of the DNA-binding domain (DBD) of MetR was determined at 2...
June 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27279732/a-novel-approach-to-predict-core-residues-on-cancer-related-dna-binding-domains
#17
Ka-Chun Wong
Protein-DNA interactions are involved in different cancer pathways. In particular, the DNA-binding domains of proteins can determine where and how gene regulatory regions are bound in different cell lines at different stages. Therefore, it is essential to develop a method to predict and locate the core residues on cancer-related DNA-binding domains. In this study, we propose a computational method to predict and locate core residues on DNA-binding domains. In particular, we have selected the cancer-related DNA-binding domains for in-depth studies, namely, winged Helix Turn Helix family, homeodomain family, and basic Helix-Loop-Helix family...
2016: Cancer Informatics
https://www.readbyqxmd.com/read/27171430/structural-analysis-and-insights-into-the-oligomeric-state-of-an-arginine-dependent-transcriptional-regulator-from-bacillus-halodurans
#18
Young Woo Park, Jina Kang, Hyun Ku Yeo, Jae Young Lee
The arginine repressor (ArgR) is an arginine-dependent transcription factor that regulates the expression of genes encoding proteins involved in the arginine biosynthesis and catabolic pathways. ArgR is a functional homolog of the arginine-dependent repressor/activator AhrC from Bacillus subtilis, and belongs to the ArgR/AhrC family of transcriptional regulators. In this research, we determined the structure of the ArgR (Bh2777) from Bacillus halodurans at 2.41 Å resolution by X-ray crystallography. The ArgR from B...
2016: PloS One
https://www.readbyqxmd.com/read/27085804/molecular-insights-into-dna-binding-and-anchoring-by-the-bacillus-subtilis-sporulation-kinetochore-like-raca-protein
#19
Maria A Schumacher, Jeehyun Lee, Wenjie Zeng
During Bacillus subtilis sporulation, segregating sister chromosomes are anchored to cell poles and the chromosome is remodeled into an elongated structure called the axial filament. Data indicate that a developmentally regulated protein called RacA is involved in these functions. To gain insight into how RacA performs these diverse processes we performed a battery of structural and biochemical analyses. These studies show that RacA contains an N-terminal winged-helix-turn-helix module connected by a disordered region to a predicted coiled-coil domain...
June 20, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/26953603/regulatory-pan-genome-of-an-obligate-intracellular-pathogen-in-the-pvc-superphylum
#20
Marie de Barsy, Antonio Frandi, Gaël Panis, Laurence Théraulaz, Trestan Pillonel, Gilbert Greub, Patrick H Viollier
Like other obligate intracellular bacteria, the Chlamydiae feature a compact regulatory genome that remains uncharted owing to poor genetic tractability. Exploiting the reduced number of transcription factors (TFs) encoded in the chlamydial (pan-)genome as a model for TF control supporting the intracellular lifestyle, we determined the conserved landscape of TF specificities by ChIP-Seq (chromatin immunoprecipitation-sequencing) in the chlamydial pathogen Waddlia chondrophila. Among 10 conserved TFs, Euo emerged as a master TF targeting >100 promoters through conserved residues in a DNA excisionase-like winged helix-turn-helix-like (wHTH) fold...
September 2016: ISME Journal
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