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single-stranded DNA binding protein

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https://www.readbyqxmd.com/read/28100698/cdc45-induced-loading-of-human-rpa-onto-single-stranded-dna
#1
Anna Szambowska, Ingrid Tessmer, Piotr Prus, Bernhard Schlott, Helmut Pospiech, Frank Grosse
Cell division cycle protein 45 (Cdc45) is an essential component of the eukaryotic replicative DNA helicase. We found that human Cdc45 forms a complex with the single-stranded DNA (ssDNA) binding protein RPA. Moreover, it actively loads RPA onto nascent ssDNA. Pull-down assays and surface plasmon resonance studies revealed that Cdc45-bound RPA complexed with ssDNA in the 8-10 nucleotide binding mode, but dissociated when RPA covered a 30-mer. Real-time analysis of RPA-ssDNA binding demonstrated that Cdc45 catalytically loaded RPA onto ssDNA...
January 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28098260/hepatitis-b-virus-x-protein-is-capable-of-down-regulating-protein-level-of-host-antiviral-protein-apobec3g
#2
Ruidong Chen, Xue Zhao, Yongxiang Wang, Youhua Xie, Jing Liu
The apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) family proteins bind RNA and single-stranded DNA, and create C-to-U base modifications through cytidine deaminase activity. APOBEC3G restricts human immunodeficiency virus 1 (HIV-1) infection by creating hypermutations in proviral DNA, while HIV-1-encoded vif protein antagonizes such restriction by targeting APOBEC3G for degradation. APOBEC3G also inhibits hepatitis B virus (HBV): APOBEC3G co-expression inhibits HBV replication and evidences exist indicating APOBEC3G-mediated HBV hypermutations in patients...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28078722/ssb-and-the-recg-dna-helicase-an-intimate-association-to-rescue-a-stalled-replication-fork
#3
REVIEW
Piero R Bianco, Yuri L Lyubchenko
In E. coli, the regression of stalled DNA replication forks is catalyzed by the DNA helicase RecG. One means of gaining access to the fork is by binding to the single strand binding protein or SSB. This interaction occurs via the wedge domain of RecG and the intrinsically disordered linker (IDL) of SSB, in a manner similar to that of SH3 domains binding to PXXP motif-containing ligands in eukaryotic cells. During loading, SSB remodels the wedge domain so that the helicase domains bind to the parental, duplex DNA, permitting the helicase to translocate using thermal energy...
January 12, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28078720/the-intrinsically-disordered-linker-of-e-coli-ssb-is-critical-for-the-release-from-single-stranded-dna
#4
Hui Yin Tan, Luke A Wilczek, Sasheen Pottinger, Maria Manosas, Cong Yu, Trong Nguyenduc, Piero R Bianco
The Escherichia coli single stranded DNA binding protein (SSB) is crucial for DNA replication, recombination and repair. Within each process, it has two seemingly disparate roles: it stabilizes single-stranded DNA (ssDNA) intermediates generated during DNA processing and, forms complexes with a group of proteins known as the SSB-interactome. Key to both roles is the C-terminal, one-third of the protein, in particular the intrinsically disordered linker (IDL). Previously, we have shown using a series of linker deletion mutants that the IDL links both ssDNA and target protein binding by mediating interactions with the oligosaccharide/oligonucleotide binding fold in the target...
January 12, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28074284/high-affinity-rna-binding-by-a-hyperthermophilic-single-stranded-dna-binding-protein
#5
Michael J Morten, Roland Gamsjaeger, Liza Cubeddu, Ruvini Kariawasam, Jose Peregrina, J Carlos Penedo, Malcolm F White
Single-stranded DNA-binding proteins (SSBs), including replication protein A (RPA) in eukaryotes, play a central role in DNA replication, recombination, and repair. SSBs utilise an oligonucleotide/oligosaccharide-binding (OB) fold domain to bind DNA, and typically oligomerise in solution to bring multiple OB fold domains together in the functional SSB. SSBs from hyperthermophilic crenarchaea, such as Sulfolobus solfataricus, have an unusual structure with a single OB fold coupled to a flexible C-terminal tail...
January 10, 2017: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/28063413/chronopotentiometric-sensing-of-specific-interactions-between-lysozyme-and-the-dna-aptamer
#6
Veronika Ostatná, Veronika Kasalová-Vargová, László Kékedy-Nagy, Hana Černocká, Elena E Ferapontova
Specific DNA-protein interactions are vital for cellular life maintenance processes, such as transcriptional regulation, chromosome maintenance, replication and DNA repair, and their monitoring gives valuable information on molecular-level organization of those processes. Here, we propose a new method of label-free electrochemical sensing of sequence specific binding between the lysozyme protein and a single stranded DNA aptamer specific for lysozyme (DNAapta) that exploits the constant current chronopotentiometric stripping (CPS) analysis at modified mercury electrodes...
December 23, 2016: Bioelectrochemistry
https://www.readbyqxmd.com/read/28053120/dna-flap-creation-by-the-rara-mgsa-protein-of-escherichia-coli
#7
Tyler H Stanage, Asher N Page, Michael M Cox
We identify a novel activity of the RarA (also MgsA) protein of Escherichia coli, demonstrating that this protein functions at DNA ends to generate flaps. A AAA(+) ATPase in the clamp loader clade, RarA protein is part of a highly conserved family of DNA metabolism proteins. We demonstrate that RarA binds to double-stranded DNA in its ATP-bound state and single-stranded DNA in its apo state. RarA ATPase activity is stimulated by single-stranded DNA gaps and double-stranded DNA ends. At these double-stranded DNA ends, RarA couples the energy of ATP binding and hydrolysis to separating the strands of duplex DNA, creating flaps...
January 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28049704/the-nucleotide-excision-repair-pathway-limits-l1-retrotransposition
#8
Geraldine Servant, Vincent A Streva, Rebecca S Derbes, Madushani I Wijetunge, Marc Neeland, Travis B White, Victoria P Belancio, Astrid M Roy-Engel, Prescott L Deininger
Long interspersed elements 1 (L1) are active mobile elements that constitute almost 17% of the human genome. They amplify through a "copy-and-paste" mechanism termed retrotransposition, and de novo insertions related to these elements have been reported to cause 0.2% of genetic diseases. Our previous data demonstrated that the endonuclease complex ERCC1-XPF, which cleaves a 3' DNA flap structure, limits L1 retrotransposition. Although the ERCC1-XPF endonuclease participates in several different DNA repair pathways, such as single-strand annealing, or in telomere maintenance, its recruitment to DNA lesions is best characterized in the nucleotide excision repair (NER) pathway...
January 2017: Genetics
https://www.readbyqxmd.com/read/28034956/dna-binding-specificities-of-escherichia-coli-cas1-cas2-integrase-drive-its-recruitment-at-the-crispr-locus
#9
Clara Moch, Michel Fromant, Sylvain Blanquet, Pierre Plateau
Prokaryotic adaptive immunity relies on the capture of fragments of invader DNA (protospacers) followed by their recombination at a dedicated acceptor DNA locus. This integrative mechanism, called adaptation, needs both Cas1 and Cas2 proteins. Here, we studied in vitro the binding of an Escherichia coli Cas1-Cas2 complex to various protospacer and acceptor DNA molecules. We show that, to form a long-lived ternary complex containing Cas1-Cas2, the acceptor DNA must carry a CRISPR locus, and the protospacer must not contain 3'-single-stranded overhangs longer than 5 bases...
December 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/28034301/mechanistic-differences-between-hiv-1-and-siv-nucleocapsid-proteins-and-cross-species-hiv-1-genomic-rna-recognition
#10
Klara Post, Erik D Olson, M Nabuan Naufer, Robert J Gorelick, Ioulia Rouzina, Mark C Williams, Karin Musier-Forsyth, Judith G Levin
BACKGROUND: The nucleocapsid (NC) domain of HIV-1 Gag is responsible for specific recognition and packaging of genomic RNA (gRNA) into new viral particles. This occurs through specific interactions between the Gag NC domain and the Psi packaging signal in gRNA. In addition to this critical function, NC proteins are also nucleic acid (NA) chaperone proteins that facilitate NA rearrangements during reverse transcription. Although the interaction with Psi and chaperone activity of HIV-1 NC have been well characterized in vitro, little is known about simian immunodeficiency virus (SIV) NC...
December 29, 2016: Retrovirology
https://www.readbyqxmd.com/read/28028224/ape2-zf-grf-facilitates-3-5-resection-of-dna-damage-following-oxidative-stress
#11
Bret D Wallace, Zachary Berman, Geoffrey A Mueller, Yunfeng Lin, Timothy Chang, Sara N Andres, Jessica L Wojtaszek, Eugene F DeRose, C Denise Appel, Robert E London, Shan Yan, R Scott Williams
The Xenopus laevis APE2 (apurinic/apyrimidinic endonuclease 2) nuclease participates in 3'-5' nucleolytic resection of oxidative DNA damage and activation of the ATR-Chk1 DNA damage response (DDR) pathway via ill-defined mechanisms. Here we report that APE2 resection activity is regulated by DNA interactions in its Zf-GRF domain, a region sharing high homology with DDR proteins Topoisomerase 3α (TOP3α) and NEIL3 (Nei-like DNA glycosylase 3), as well as transcription and RNA regulatory proteins, such as TTF2 (transcription termination factor 2), TFIIS, and RPB9...
December 27, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28028171/single-strand-dna-binding-by-the-helix-hairpin-helix-domain-of-xpf-contributes-to-substrate-specificity-of-ercc1-xpf
#12
Devashish Das, Maryam Faridounnia, Lidija Kovacic, Robert Kaptein, Rolf Boelens, Gert E Folkers
The nucleotide excision repair protein complex ERCC1-XPF is required for incision of DNA upstream of the DNA damage. Functional studies have provided insight into the binding of ERCC1-XPF to various DNA substrates. However, since no structure for the ERCC1-XPF-DNA complex has been determined, the mechanism of substrate recognition remains elusive. Here we biochemically characterize the substrate preferences of the Helix-hairpin-Helix domains of XPF and ERCC-XPF and show that the binding to ss/dsDNA junctions is dependent on joint binding to the DNA binding domain of ERCC1 and XPF...
December 27, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28012548/facilitated-dissociation-kinetics-of-dimeric-nucleoid-associated-proteins-follow-a-universal-curve
#13
Katelyn Dahlke, Charles E Sing
Recent experimental work has demonstrated facilitated dissociation of certain nucleoid-associated proteins that exhibit an unbinding rate that depends on the concentration of freely diffusing proteins or DNA in solution. This concentration dependence arises due to binding competition with these other proteins or DNA. The identity of the binding competitor leads to different qualitative trends, motivating an investigation to understand observed differences in facilitated dissociation. We use a coarse-grained simulation that takes into account the dimeric nature of many nucleoid-associated proteins by allowing an intermediate binding state...
December 21, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/28009302/rpa-stabilization-of-single-stranded-dna-is-critical-for-break-induced-replication
#14
Patrick Ruff, Roberto A Donnianni, Eleanor Glancy, Julyun Oh, Lorraine S Symington
DNA double-strand breaks (DSBs) are cytotoxic lesions that must be accurately repaired to maintain genome stability. Replication protein A (RPA) plays an important role in homology-dependent repair of DSBs by protecting the single-stranded DNA (ssDNA) intermediates formed by end resection and by facilitating Rad51 loading. We found that hypomorphic mutants of RFA1 that support intra-chromosomal homologous recombination are profoundly defective for repair processes involving long tracts of DNA synthesis, in particular break-induced replication (BIR)...
December 20, 2016: Cell Reports
https://www.readbyqxmd.com/read/28000228/differential-regulation-of-ssb-genes-in-the-nitrogen-fixing-cyanobacterium-anabaena-sp-strain-pcc7120
#15
Anurag Kirti, Arvind Kumar, Hema Rajaram
Anabaena sp. PCC7120 possesses three genes coding for single-stranded DNA-binding (SSB) protein, of which ssb1 was a single gene, and ssb2 and ssb3, the first gene of their corresponding operons. Regulation of the truncated ssb genes, ssb1 (alr0088) and ssb2 (alr7559) were unaffected by N-status of growth. They were negatively regulated by the SOS-response regulatory protein LexA, as indicated by the (i) binding of Anabaena LexA to the LexA-box of regulatory regions of ssb1 and ssb2, and (ii) decreased expression of the downstream gfp reporter gene in E...
December 21, 2016: Journal of Phycology
https://www.readbyqxmd.com/read/27993012/rational-design-of-small-molecules-targeting-oncogenic-noncoding-rnas-from-sequence
#16
Matthew D Disney, Alicia J Angelbello
The discovery of RNA catalysis in the 1980s and the dissemination of the human genome sequence at the start of this century inspired investigations of the regulatory roles of noncoding RNAs in biology. In fact, the Encyclopedia of DNA Elements (ENCODE) project has shown that only 1-2% of the human genome encodes protein, yet 75% is transcribed into RNA. Functional studies both preceding and following the ENCODE project have shown that these noncoding RNAs have important roles in regulating gene expression, developmental timing, and other critical functions...
December 20, 2016: Accounts of Chemical Research
https://www.readbyqxmd.com/read/27992233/using-multiorder-time-correlation-functions-tcfs-to-elucidate-biomolecular-reaction-pathways-from-microsecond-single-molecule-fluorescence-experiments
#17
Carey Phelps, Brett Israels, Morgan C Marsh, Peter H von Hippel, Andrew H Marcus
Recent advances in single-molecule fluorescence imaging have made it possible to perform measurements on microsecond time scales. Such experiments have the potential to reveal detailed information about the conformational changes in biological macromolecules, including the reaction pathways and dynamics of the rearrangements involved in processes, such as sequence-specific DNA "breathing" and the assembly of protein-nucleic acid complexes. Because microsecond-resolved single-molecule trajectories often involve "sparse" data, that is, they contain relatively few data points per unit time, they cannot be easily analyzed using the standard protocols that were developed for single-molecule experiments carried out with tens-of-millisecond time resolution and high "data density...
December 29, 2016: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/27984589/replication-protein-a-presents-canonical-functions-and-is-also-involved-in-the-differentiation-capacity-of-trypanosoma-cruzi
#18
Raphael Souza Pavani, Marcelo Santos da Silva, Carlos Alexandre Henrique Fernandes, Flavia Souza Morini, Christiane Bezerra Araujo, Marcos Roberto de Mattos Fontes, Osvaldo Augusto Sant'Anna, Carlos Renato Machado, Maria Isabel Cano, Stenio Perdigão Fragoso, Maria Carolina Elias
Replication Protein A (RPA), the major single stranded DNA binding protein in eukaryotes, is composed of three subunits and is a fundamental player in DNA metabolism, participating in replication, transcription, repair, and the DNA damage response. In human pathogenic trypanosomatids, only limited studies have been performed on RPA-1 from Leishmania. Here, we performed in silico, in vitro and in vivo analysis of Trypanosoma cruzi RPA-1 and RPA-2 subunits. Although computational analysis suggests similarities in DNA binding and Ob-fold structures of RPA from T...
December 2016: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/27974460/metnase-mediates-loading-of-exonuclease-1-onto-single-strand-overhang-dna-for-end-resection-at-stalled-replication-forks
#19
Hyun-Suk Kim, Elizabeth A Williamson, Jac A Nickoloff, Robert A Hromas, Suk-Hee Lee
Stalling at DNA replication forks generates stretches of single-stranded (ss) DNA on both strands that are exposed to nucleolytic degradation, potentially compromising genome stability. One enzyme crucial for DNA replication fork repair and restart of stalled forks in human is Metnase (also known as SETMAR), a chimeric fusion protein consisting of a SET histone methylase and transposase nuclease domain. We previously showed that Metnase possesses a unique fork cleavage activity necessary for its function in replication restart and that its SET domain is essential for recovery from hydroxyurea-induced DNA damage...
December 14, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27974172/advances-in-structural-studies-of-recombination-mediator-proteins
#20
S Korolev
Recombination mediator proteins (RMPs) are critical for genome integrity in all organisms. They include phage UvsY, prokaryotic RecF, -O, -R (RecFOR) and eukaryotic Rad52, Breast Cancer susceptibility 2 (BRCA2) and Partner and localizer of BRCA2 (PALB2) proteins. BRCA2 and PALB2 are tumor suppressors implicated in cancer. RMPs regulate binding of RecA-like recombinases to sites of DNA damage to initiate the most efficient non-mutagenic repair of broken chromosome and other deleterious DNA lesions. Mechanistically, RMPs stimulate a single-stranded DNA (ssDNA) hand-off from ssDNA binding proteins (ssbs) such as gp32, SSB and RPA, to recombinases, activating DNA repair only at the time and site of the damage event...
December 6, 2016: Biophysical Chemistry
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