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single-stranded DNA binding protein

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https://www.readbyqxmd.com/read/29330047/an-intrinsically-disordered-domain-in-polaribacter-irgensii-kopri-22228-cspb-confers-extraordinary-freeze-tolerance
#1
Youn Hong Jung, Ji-Hyun Uh, Kyunghee Lee, Hana Im
Organisms living in extremely cold environments possess mechanisms to survive low temperatures. Among the known cold-induced genes, cold-shock proteins (Csps) are the most prominent. A csp-homologous gene, cspBPi, has been cloned from the Arctic bacterium Polaribacter irgensii KOPRI 22228, and overexpression of this gene greatly increased the freezing tolerance of its host. This protein consists of a unique N-terminal domain and a well conserved C-terminal cold shock domain. To elucidate the detailed mechanisms involved in the extraordinary freeze-tolerance conferred by CspBPi, we identified the responsible domain by mutational analysis...
January 9, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29326044/escherichia-coli-single-stranded-dna-binding-protein-ssb-promotes-alkb-mediated-dna-dealkylation-repair
#2
Richa Nigam, Roy Anindya
Repair of alkylation damage in DNA is essential for maintaining genome integrity. Escherichia coli (E.coli) protein AlkB removes various alkyl DNA adducts including N1-methyladenine (N1meA) and N3-methylcytosine (N3meC) by oxidative demethylation. Previous studies showed that AlkB preferentially removes N1meA and N3meC from single-stranded DNA (ssDNA). It can also remove N1meA and N3meC from double-stranded DNA by base-flipping. Notably, ssDNA produced during DNA replication and recombination, remains bound to E...
January 8, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29320733/dna-unwinding-is-the-primary-determinant-of-crispr-cas9-activity
#3
Shanzhong Gong, Helen Hong Yu, Kenneth A Johnson, David W Taylor
Bacterial adaptive immunity utilizes RNA-guided surveillance complexes comprising Cas proteins together with CRISPR RNAs (crRNAs) to target foreign nucleic acids for destruction. Cas9, a type II CRISPR-Cas effector complex, can be programed with a single-guide RNA that base pairs with the target strand of dsDNA, displacing the non-target strand to create an R-loop, where the HNH and the RuvC nuclease domains cleave opposing strands. While many structural and biochemical studies have shed light on the mechanism of Cas9 cleavage, a clear unifying model has yet to emerge...
January 9, 2018: Cell Reports
https://www.readbyqxmd.com/read/29290613/the-antiviral-and-cancer-genomic-dna-deaminase-apobec3h-is-regulated-by-an-rna-mediated-dimerization-mechanism
#4
Nadine M Shaban, Ke Shi, Kate V Lauer, Michael A Carpenter, Christopher M Richards, Daniel Salamango, Jiayi Wang, Michael W Lopresti, Surajit Banerjee, Rena Levin-Klein, William L Brown, Hideki Aihara, Reuben S Harris
Human APOBEC3H and homologous single-stranded DNA cytosine deaminases are unique to mammals. These DNA-editing enzymes function in innate immunity by restricting the replication of viruses and transposons. APOBEC3H also contributes to cancer mutagenesis. Here, we address the fundamental nature of RNA in regulating human APOBEC3H activities. APOBEC3H co-purifies with RNA as an inactive protein, and RNase A treatment enables strong DNA deaminase activity. RNA-binding-defective mutants demonstrate clear separation of function by becoming DNA hypermutators...
January 4, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29279380/atm-and-atr-play-complementary-roles-in-the-behavior-of-excitatory-and-inhibitory-vesicle-populations
#5
Aifang Cheng, Teng Zhao, Kai-Hei Tse, Hei-Man Chow, Yong Cui, Liwen Jiang, Shengwang Du, Michael M T Loy, Karl Herrup
ATM (ataxia-telangiectasia mutated) and ATR (ATM and Rad3-related) are large PI3 kinases whose human mutations result in complex syndromes that include a compromised DNA damage response (DDR) and prominent nervous system phenotypes. Both proteins are nuclear-localized in keeping with their DDR functions, yet both are also found in cytoplasm, including on neuronal synaptic vesicles. In ATM- or ATR-deficient neurons, spontaneous vesicle release is reduced, but a drop in ATM or ATR level also slows FM4-64 dye uptake...
December 26, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29278803/sorption-of-nucleic-acids-and-proteins-on-polyaniline-and-polyaramide-nano-coatings-as-studied-by-spectral-correlation-interferometry-in-a-real-time-mode
#6
Elena Yagudaeva, Dmitry Zybin, Alexander Vikhrov, Anna Prostyakova, Anatoly Ischenko, Vitaly Zubov, Dmitry Kapustin
Polyaniline (PANI) and polyaramides deposited on the surfaces of glass slides and particulate silica were studied as adsorbents of nucleic acids and proteins by flow-through spectral correlation interferometry and solid-state extraction using spin-cartridges. Double stranded DNA from E. coli as well as pepsin, bovine serum albumin and lysozyme were the analytes studied in contact with the polymer nanolayers in phosphate buffer solution, pH 7.2. None of the coated glass slides could bind the DNA, which passed them practically without adsorption...
December 15, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/29248151/protein-flexibility-and-synergy-of-hmg-domains-underlie-u-turn-bending-of-dna-by-tfam-in-solution
#7
Anna Rubio-Cosials, Federica Battistini, Alexander Gansen, Anna Cuppari, Pau Bernadó, Modesto Orozco, Jörg Langowski, Katalin Tóth, Maria Solà
Human mitochondrial transcription factor A (TFAM) distorts DNA into a U-turn, as shown by crystallographic studies. The relevance of this U-turn is associated with transcription initiation at the mitochondrial light strand promoter (LSP). However, it has not been yet discerned whether a tight U-turn or an alternative conformation, such as a V-shape, is formed in solution. Here, single-molecule FRET experiments on freely diffusing TFAM/LSP complexes containing different DNA lengths show that a DNA U-turn is induced by progressive and cooperative binding of the two TFAM HMG-box domains and the linker between them...
December 13, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29228259/the-non-specific-adenine-dna-methyltransferase-m-ecogii
#8
Iain A Murray, Richard D Morgan, Yvette Luyten, Alexey Fomenkov, Ivan R Corrêa, Nan Dai, Mohammed B Allaw, Xing Zhang, Xiaodong Cheng, Richard J Roberts
We describe the cloning, expression and characterization of the first truly non-specific adenine DNA methyltransferase, M.EcoGII. It is encoded in the genome of the pathogenic strain Escherichia coli O104:H4 C227-11, where it appears to reside on a cryptic prophage, but is not expressed. However, when the gene encoding M.EcoGII is expressed in vivo - using a high copy pRRS plasmid vector and a methylation-deficient E. coli host-extensive in vivo adenine methylation activity is revealed. M.EcoGII methylates adenine residues in any DNA sequence context and this activity extends to dA and rA bases in either strand of a DNA:RNA-hybrid oligonucleotide duplex and to rA bases in RNAs prepared by in vitro transcription...
December 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29227966/pot1-inhibits-the-efficiency-but-promotes-the-fidelity-of-nonhomologous-end-joining-at-non-telomeric-dna-regions
#9
Yang Yu, Rong Tan, Qian Ren, Boya Gao, Zhejin Sheng, Juanlian Zhang, Xiaoqing Zheng, Ying Jiang, Li Lan, Zhiyong Mao
Robust DNA double strand break (DSB) repair and stabilized telomeres help maintain genome integrity, preventing the onset of aging or tumorigenesis. POT1 is one of the six factors in the shelterin complex, which protects telomeres from being recognized as DNA damages. TRF1 and TRF2, two other shelterin proteins, have been shown to participate in DNA DSB repair at non-telomeric regions, but whether POT1, which binds to single strand telomeric DNA at chromosomal ends, is involved in DNA DSB repair has not been assessed...
December 8, 2017: Aging
https://www.readbyqxmd.com/read/29223826/modulation-effect-of-double-strand-dna-on-the-self-assembly-of-n-terminal-domain-of-euplotes-octocarinatus-centrin
#10
Wenlong Zhang, Enxian Shi, Yaqin Zhao, Binsheng Yang
Centrin is a member of the EF-hand super family of calcium-binding proteins, which can behave as a part of damage detector initiated the initiation of nucleotide excision repair (NER). Its self-assembly plays a causative role in fiber contraction associated with the cell division cycle and ciliogenesis. To explore the possible role of DNA in the process of centrin self-assembly, the aggregation properties of N-terminal domain of Euplotes octocarinatus centrin (N-EoCen) in the presence of DNA with or without metal ions are investigated...
December 5, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/29208763/characterization-of-the-catalytic-signature-of-scabin-toxin-a-dna-targeting-adp-ribosyltransferase
#11
Bronwyn Lyons, Miguel R Lugo, Stephanie Carlin, Taylor Lidster, A Rod Merrill
Scabin was previously identified as a novel DNA-targeting mono-ADP-ribosyltransferase toxin from the plant pathogen 87.22 strain of Streptomyces scabies Scabin is a member of the Pierisin-like subgroup of mono-ADP-ribosyltransferase toxins, since it targets DNA. An in-depth characterization of both the glycohydrolase and transferase enzymatic activities of Scabin was conducted. Several protein variants were developed based on an initial Scabin·DNA molecular model. Consequently, three residues were deemed important for DNA binding and transferase activity...
December 5, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/29202219/direct-single-molecule-observation-of-mode-and-geometry-of-reca-mediated-homology-search
#12
Andrew James Lee, Masayuki Endo, Jamie Kayne Hobbs, Christoph Walti
Genomic integrity, when compromised by accrued DNA lesions, is maintained through efficient repair via homologous recombination. For this process the ubiquitous Recombinase A (RecA), and its homologues such as the human Rad51, are of central importance, able to align and exchange homologous sequences within single-stranded and double-stranded DNA in order to swap out defective regions. Here, we directly observe the widely debated mechanism of RecA homology searching at a single molecule level using high-speed atomic force microscopy (HS-AFM) in combination with tailored DNA origami frames to present the reaction targets in a way suitable for AFM-imaging...
December 4, 2017: ACS Nano
https://www.readbyqxmd.com/read/29198584/aptamers-targeting-cell-surface-proteins
#13
REVIEW
Masaki Takahashi
High affinity binders targeting specific cell surface proteins are vital for developing basic and applied biosciences. However, despite sustained efforts to generate such binders by chemicals and antibodies, there are still many cell surface proteins that lack high affinity binders. Nucleic acids, referred to as aptamers, appear to be potential binders to capture cell surface proteins because single-strand DNA/RNA can form distinct structures of high affinity and specificity to a wide range of targets. Aptamers are isolated from large combinatorial libraries using a unique iterative selection-amplification process known as systematic evolution of ligands by exponential enrichment (SELEX)...
November 30, 2017: Biochimie
https://www.readbyqxmd.com/read/29197718/the-mechanisms-of-k-lactis-cdc13-in-telomere-dna-binding-and-telomerase-regulation
#14
Min Hsu, Neal F Lue
Eukaryotic chromosome ends, or telomeres, are essential for genome stability and are protected by an intricate nucleoprotein assembly. Cdc13, the major single-strand telomere-binding protein in budding yeasts, mediates critical functions in both telomere protection and telomere elongation by telomerase. In particular, the interaction between S. cerevisiae Cdc13 and telomerase subunit Est1 has long served as a paradigm for telomerase regulation. However, despite extensive investigations, the role of this interaction in regulating telomerase recruitment or activation remains controversial...
November 28, 2017: DNA Repair
https://www.readbyqxmd.com/read/29197185/structure-and-interaction-of-corynebacterium-pseudotuberculosis-cold-shock-protein-a-with-y-box-single-stranded-dna-fragment
#15
Ícaro P Caruso, Vineet Panwalkar, Monika A Coronado, Andrew J Dingley, Marinônio L Cornélio, Dieter Willbold, Raghuvir K Arni, Raphael J Eberle
Cold shock proteins (Csps) function to preserve cell viability at low temperatures by binding to nucleic acids and consequently control gene expression. The mesophilic bacterium Corynebacterium pseudotuberculosis is the causative agent of caseous lymphadenitis in animals, and infection to livestock is a considerable economic burden worldwide. In this report, the structure of cold shock protein A from C. pseudotuberculosis (Cp-CspA) and biochemical analysis of its temperature-dependent interaction with a Y-box single-stranded DNA (ssDNA) motif is presented...
December 2, 2017: FEBS Journal
https://www.readbyqxmd.com/read/29191792/the-binding-efficiency-of-rpa-to-telomeric-g-strands-folded-into-contiguous-g-quadruplexes-is-independent-of-the-number-of-g4-units
#16
Astrid Lancrey, Layal Safa, Jean Chatain, Emmanuelle Delagoutte, Jean-François Riou, Patrizia Alberti, Carole Saintomé
Replication protein A (RPA) is a single-stranded DNA binding protein involved in replication and in telomere maintenance. During telomere replication, G-quadruplexes (G4) can accumulate on the lagging strand template and need to be resolved. It has been shown that human RPA is able to unfold a single G4. Nevertheless, the G-strand of human telomeres is prone to fold into higher-order structures formed by contiguous G-quadruplexes. To understand how RPA deals with these structures, we studied its interaction with telomeric G-strands folding into an increasing number of contiguous G4s...
November 27, 2017: Biochimie
https://www.readbyqxmd.com/read/29186920/rna-chaperone-function-of-a-universal-stress-protein-in-arabidopsis-confers-enhanced-cold-stress-tolerance-in-plants
#17
Sarah Mae Boyles Melencion, Yong Hun Chi, Thuy Thi Pham, Seol Ki Paeng, Seong Dong Wi, Changyu Lee, Seoung Woo Ryu, Sung Sun Koo, Sang Yeol Lee
The physiological function of Arabidopsis thaliana universal stress protein (AtUSP) in plant has remained unclear. Thus, we report here the functional role of the Arabidopsis universal stress protein, AtUSP (At3g53990). To determine how AtUSP affects physiological responses towards cold stress, AtUSP overexpression (AtUSP OE) and T-DNA insertion knock-out (atusp, SALK_146059) mutant lines were used. The results indicated that AtUSP OE enhanced plant tolerance to cold stress, whereas atusp did not. AtUSP is localized in the nucleus and cytoplasm, and cold stress significantly affects RNA metabolism such as by misfolding and secondary structure changes of RNA...
November 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29175904/cohesin-sa2-is-a-sequence-independent-dna-binding-protein-that-recognizes-dna-replication-and-repair-intermediates
#18
Preston Countryman, Yanlin Fan, Aparna Gorthi, Hai Pan, Jack Strickland, Parminder Kaur, Xuechun Wang, Jianggguo Lin, Xiaoying Lei, Christian White, Changjiang You, Nicolas Wirth, Ingrid Tessmer, Jacob Pieler, Robert Riehn, Alexander J R Bishop, Yizhi Jane Tao, Hong Wang
Proper chromosome alignment and segregation during mitosis depend on cohesion between sister chromatids, mediated by the cohesin protein complex, which also plays crucial roles in diverse genome maintenance pathways. Current models attribute DNA binding by cohesin to entrapment of dsDNA by the cohesin ring subunits (SMC1, SMC3, and RAD21 in humans). However, the biophysical properties and activities of the fourth core cohesin subunit SA2 (STAG2) are largely unknown. Here, using single molecule atomic force and fluorescence microscopy imaging as well as fluorescence anisotropy measurements, we established that SA2 binds to both dsDNA and ssDNA, albeit with a higher binding affinity for ssDNA...
November 24, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29168694/the-mechanism-of-variability-in-transcription-start-site-selection
#19
Libing Yu, Jared Winkelman, Chirangini Pukhrambam, Terence Strick, Bryce E Nickels, Richard H Ebright
During transcription initiation, RNA polymerase (RNAP) binds to promoter DNA, unwinds promoter DNA to form an RNAP-promoter open complex (RPo) containing a single-stranded 'transcription bubble,' and selects a transcription start site (TSS). TSS selection occurs at different positions within the promoter region, depending on promoter sequence and initiating-substrate concentration. Variability in TSS selection has been proposed to involve DNA 'scrunching' and 'anti-scrunching,' the hallmarks of which are: (i) forward and reverse movement of the RNAP leading edge, but not trailing edge, relative to DNA, and (ii) expansion and contraction of the transcription bubble...
November 23, 2017: ELife
https://www.readbyqxmd.com/read/29163424/the-bacillus-subtilis-conjugative-plasmid-pls20-encodes-two-ribbon-helix-helix-type-auxiliary-relaxosome-proteins-that-are-essential-for-conjugation
#20
Andrés Miguel-Arribas, Jian-An Hao, Juan R Luque-Ortega, Gayetri Ramachandran, Jorge Val-Calvo, César Gago-Córdoba, Daniel González-Álvarez, David Abia, Carlos Alfonso, Ling J Wu, Wilfried J J Meijer
Bacterial conjugation is the process by which a conjugative element (CE) is transferred horizontally from a donor to a recipient cell via a connecting pore. One of the first steps in the conjugation process is the formation of a nucleoprotein complex at the origin of transfer (oriT), where one of the components of the nucleoprotein complex, the relaxase, introduces a site- and strand specific nick to initiate the transfer of a single DNA strand into the recipient cell. In most cases, the nucleoprotein complex involves, besides the relaxase, one or more additional proteins, named auxiliary proteins, which are encoded by the CE and/or the host...
2017: Frontiers in Microbiology
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