Готові списки джерел за темами / Single Stranded DNA Binding Protein (SSBb)

Добірка наукової літератури з теми "Single Stranded DNA Binding Protein (SSBb)"

Автор: Grafiati
Опубліковано: 6 вересня 2023

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Статті в журналах з теми "Single Stranded DNA Binding Protein (SSBb)"

1

Chen, Kuan-Lin, Jen-Hao Cheng, Chih-Yang Lin, Yen-Hua Huang, and Cheng-Yang Huang. "Characterization of single-stranded DNA-binding protein SsbB fromStaphylococcus aureus: SsbB cannot stimulate PriA helicase." RSC Advances 8, no. 50 (2018): 28367–75. http://dx.doi.org/10.1039/c8ra04392b.

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2

Singh, Amandeep, Umesh Varshney, and M. Vijayan. "Structure of the second Single Stranded DNA Binding protein (SSBb) from Mycobacterium smegmatis." Journal of Structural Biology 196, no. 3 (December 2016): 448–54. http://dx.doi.org/10.1016/j.jsb.2016.09.012.

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3

Luo, Xiao, Uli Schwarz-Linek, Catherine H. Botting, Reinhard Hensel, Bettina Siebers, and Malcolm F. White. "CC1, a Novel Crenarchaeal DNA Binding Protein." Journal of Bacteriology 189, no. 2 (November 3, 2006): 403–9. http://dx.doi.org/10.1128/jb.01246-06.

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ABSTRACT The genomes of the related crenarchaea Pyrobaculum aerophilum and Thermoproteus tenax lack any obvious gene encoding a single-stranded DNA binding protein (SSB). SSBs are essential for DNA replication, recombination, and repair and are found in all other genomes across the three domains of life. These two archaeal genomes also have only one identifiable gene encoding a chromatin protein (the Alba protein), while most other archaea have at least two different abundant chromatin proteins. We performed a biochemical screen for novel nucleic acid binding proteins present in cell extracts of T. tenax. An assay for proteins capable of binding to a single-stranded DNA oligonucleotide resulted in identification of three proteins. The first protein, Alba, has been shown previously to bind single-stranded DNA as well as duplex DNA. The two other proteins, which we designated CC1 (for crenarchaeal chromatin protein 1), are very closely related to one another, and homologs are restricted to the P. aerophilum and Aeropyrum pernix genomes. CC1 is a 6-kDa, monomeric, basic protein that is expressed at a high level in T. tenax. This protein binds single- and double-stranded DNAs with similar affinities. These properties are consistent with a role for CC1 as a crenarchaeal chromatin protein.
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4

Grove, Diane E., Smaranda Willcox, Jack D. Griffith, and Floyd R. Bryant. "Differential Single-stranded DNA Binding Properties of the Paralogous SsbA and SsbB Proteins from Streptococcus pneumoniae." Journal of Biological Chemistry 280, no. 12 (March 2005): 11067–73. http://dx.doi.org/10.1074/jbc.m414057200.

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5

Jain, Samta, Maria Zweig, Eveline Peeters, Katja Siewering, Kathleen T. Hackett, Joseph P. Dillard, and Chris van der Does. "Characterization of the Single Stranded DNA Binding Protein SsbB Encoded in the Gonoccocal Genetic Island." PLoS ONE 7, no. 4 (April 19, 2012): e35285. http://dx.doi.org/10.1371/journal.pone.0035285.

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6

Xu, Longfu, Matthew T. J. Halma, and Gijs J. L. Wuite. "Unravelling How Single-Stranded DNA Binding Protein Coordinates DNA Metabolism Using Single-Molecule Approaches." International Journal of Molecular Sciences 24, no. 3 (February 1, 2023): 2806. http://dx.doi.org/10.3390/ijms24032806.

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Анотація:
Single-stranded DNA-binding proteins (SSBs) play vital roles in DNA metabolism. Proteins of the SSB family exclusively and transiently bind to ssDNA, preventing the DNA double helix from re-annealing and maintaining genome integrity. In the meantime, they interact and coordinate with various proteins vital for DNA replication, recombination, and repair. Although SSB is essential for DNA metabolism, proteins of the SSB family have been long described as accessory players, primarily due to their unclear dynamics and mechanistic interaction with DNA and its partners. Recently-developed single-molecule tools, together with biochemical ensemble techniques and structural methods, have enhanced our understanding of the different coordination roles that SSB plays during DNA metabolism. In this review, we discuss how single-molecule assays, such as optical tweezers, magnetic tweezers, Förster resonance energy transfer, and their combinations, have advanced our understanding of the binding dynamics of SSBs to ssDNA and their interaction with other proteins partners. We highlight the central coordination role that the SSB protein plays by directly modulating other proteins’ activities, rather than as an accessory player. Many possible modes of SSB interaction with protein partners are discussed, which together provide a bigger picture of the interaction network shaped by SSB.
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7

Jong, A. Y., M. W. Clark, M. Gilbert, A. Oehm, and J. L. Campbell. "Saccharomyces cerevisiae SSB1 protein and its relationship to nucleolar RNA-binding proteins." Molecular and Cellular Biology 7, no. 8 (August 1987): 2947–55. http://dx.doi.org/10.1128/mcb.7.8.2947-2955.1987.

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To better define the function of Saccharomyces cerevisiae SSB1, an abundant single-stranded nucleic acid-binding protein, we determined the nucleotide sequence of the SSB1 gene and compared it with those of other proteins of known function. The amino acid sequence contains 293 amino acid residues and has an Mr of 32,853. There are several stretches of sequence characteristic of other eucaryotic single-stranded nucleic acid-binding proteins. At the amino terminus, residues 39 to 54 are highly homologous to a peptide in calf thymus UP1 and UP2 and a human heterogeneous nuclear ribonucleoprotein. Residues 125 to 162 constitute a fivefold tandem repeat of the sequence RGGFRG, the composition of which suggests a nucleic acid-binding site. Near the C terminus, residues 233 to 245 are homologous to several RNA-binding proteins. Of 18 C-terminal residues, 10 are acidic, a characteristic of the procaryotic single-stranded DNA-binding proteins and eucaryotic DNA- and RNA-binding proteins. In addition, examination of the subcellular distribution of SSB1 by immunofluorescence microscopy indicated that SSB1 is a nuclear protein, predominantly located in the nucleolus. Sequence homologies and the nucleolar localization make it likely that SSB1 functions in RNA metabolism in vivo, although an additional role in DNA metabolism cannot be excluded.
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8

Jong, A. Y., M. W. Clark, M. Gilbert, A. Oehm, and J. L. Campbell. "Saccharomyces cerevisiae SSB1 protein and its relationship to nucleolar RNA-binding proteins." Molecular and Cellular Biology 7, no. 8 (August 1987): 2947–55. http://dx.doi.org/10.1128/mcb.7.8.2947.

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Анотація:
To better define the function of Saccharomyces cerevisiae SSB1, an abundant single-stranded nucleic acid-binding protein, we determined the nucleotide sequence of the SSB1 gene and compared it with those of other proteins of known function. The amino acid sequence contains 293 amino acid residues and has an Mr of 32,853. There are several stretches of sequence characteristic of other eucaryotic single-stranded nucleic acid-binding proteins. At the amino terminus, residues 39 to 54 are highly homologous to a peptide in calf thymus UP1 and UP2 and a human heterogeneous nuclear ribonucleoprotein. Residues 125 to 162 constitute a fivefold tandem repeat of the sequence RGGFRG, the composition of which suggests a nucleic acid-binding site. Near the C terminus, residues 233 to 245 are homologous to several RNA-binding proteins. Of 18 C-terminal residues, 10 are acidic, a characteristic of the procaryotic single-stranded DNA-binding proteins and eucaryotic DNA- and RNA-binding proteins. In addition, examination of the subcellular distribution of SSB1 by immunofluorescence microscopy indicated that SSB1 is a nuclear protein, predominantly located in the nucleolus. Sequence homologies and the nucleolar localization make it likely that SSB1 functions in RNA metabolism in vivo, although an additional role in DNA metabolism cannot be excluded.
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9

Myler, Logan R., Ignacio F. Gallardo, Yi Zhou, Fade Gong, Soo-Hyun Yang, Marc S. Wold, Kyle M. Miller, Tanya T. Paull, and Ilya J. Finkelstein. "Single-molecule imaging reveals the mechanism of Exo1 regulation by single-stranded DNA binding proteins." Proceedings of the National Academy of Sciences 113, no. 9 (February 16, 2016): E1170—E1179. http://dx.doi.org/10.1073/pnas.1516674113.

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Анотація:
Exonuclease 1 (Exo1) is a 5′→3′ exonuclease and 5′-flap endonuclease that plays a critical role in multiple eukaryotic DNA repair pathways. Exo1 processing at DNA nicks and double-strand breaks creates long stretches of single-stranded DNA, which are rapidly bound by replication protein A (RPA) and other single-stranded DNA binding proteins (SSBs). Here, we use single-molecule fluorescence imaging and quantitative cell biology approaches to reveal the interplay between Exo1 and SSBs. Both human and yeast Exo1 are processive nucleases on their own. RPA rapidly strips Exo1 from DNA, and this activity is dependent on at least three RPA-encoded single-stranded DNA binding domains. Furthermore, we show that ablation of RPA in human cells increases Exo1 recruitment to damage sites. In contrast, the sensor of single-stranded DNA complex 1—a recently identified human SSB that promotes DNA resection during homologous recombination—supports processive resection by Exo1. Although RPA rapidly turns over Exo1, multiple cycles of nuclease rebinding at the same DNA site can still support limited DNA processing. These results reveal the role of single-stranded DNA binding proteins in controlling Exo1-catalyzed resection with implications for how Exo1 is regulated during DNA repair in eukaryotic cells.
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10

Dubiel, Katarzyna, Camille Henry, Lisanne M. Spenkelink, Alexander G. Kozlov, Elizabeth A. Wood, Slobodan Jergic, Nicholas E. Dixon, et al. "Development of a single-stranded DNA-binding protein fluorescent fusion toolbox." Nucleic Acids Research 48, no. 11 (May 6, 2020): 6053–67. http://dx.doi.org/10.1093/nar/gkaa320.

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Abstract Bacterial single-stranded DNA-binding proteins (SSBs) bind single-stranded DNA and help to recruit heterologous proteins to their sites of action. SSBs perform these essential functions through a modular structural architecture: the N-terminal domain comprises a DNA binding/tetramerization element whereas the C-terminus forms an intrinsically disordered linker (IDL) capped by a protein-interacting SSB-Ct motif. Here we examine the activities of SSB-IDL fusion proteins in which fluorescent domains are inserted within the IDL of Escherichia coli SSB. The SSB-IDL fusions maintain DNA and protein binding activities in vitro, although cooperative DNA binding is impaired. In contrast, an SSB variant with a fluorescent protein attached directly to the C-terminus that is similar to fusions used in previous studies displayed dysfunctional protein interaction activity. The SSB-IDL fusions are readily visualized in single-molecule DNA replication reactions. Escherichia coli strains in which wildtype SSB is replaced by SSB-IDL fusions are viable and display normal growth rates and fitness. The SSB-IDL fusions form detectible SSB foci in cells with frequencies mirroring previously examined fluorescent DNA replication fusion proteins. Cells expressing SSB-IDL fusions are sensitized to some DNA damaging agents. The results highlight the utility of SSB-IDL fusions for biochemical and cellular studies of genome maintenance reactions.
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Дисертації з теми "Single Stranded DNA Binding Protein (SSBb)"

1

Bain, Amanda Louise. "Investigation of the Physiological Role of Ssb1 using an in-vivo Targeted Mouse Model." Thesis, Griffith University, 2013. http://hdl.handle.net/10072/366937.

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Анотація:
Single-stranded DNA binding proteins (SSBs) are critical for binding, protecting and sequestering single-stranded DNA intermediates during multiple cellular transactions, including DNA replication, repair and transcription. The canonical SSB in eukaryotes, Replication Protein A (RPA), is a heterotrimeric protein essential for numerous cellular processes, including DNA repair by homologous recombination (HR). Recently, Richard et al. (2008) identified a novel human SSB, designated human Single-Stranded DNA Binding protein 1 (hSSB1), critical to DNA repair and the maintenance of genomic stability. siRNA-mediated depletion of hSSB1 led to attenuation of ATM signalling in response to DNA damage by ionizing radiation (IR), impairment of DNA repair by HR, and overall genetic instability. Moreover, hSSB1 was subsequently shown to itself function in a heterotrimeric complex in a manner analogous to RPA, with Integrator complex subunit 3 (INTS3), and a small, uncharacterised acidic protein C9Orf80/MISE/SSBIP1. siRNA-mediated depletion of these components led to similar DNA damage-related phenotypes to what has been observed for hSSB1 depletion alone, suggesting that complex formation may be important for hSSB1 functioning. Moreover, hSSB2, a homolog of hSSB1, was shown to be able to form a similar complex with INTS3 and C9Orf80 in place of hSSB1, suggesting an element of functional redundancy in the roles of hSSB1 and hSSB2.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Biomolecular and Physical Sciences
Science, Environment, Engineering and Technology
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2

Jordan, Christian. "Helicase-SSB Interactions In Recombination-Dependent DNA Repair and Replication." ScholarWorks @ UVM, 2014. http://scholarworks.uvm.edu/graddis/270.

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Dda, one of three helicases encoded by bacteriophage T4, has been well- characterized biochemically but its biological role remains unclear. It is thought to be involved in origin-dependent replication, recombination-dependent replication, anti- recombination, recombination repair, as well as in replication fork progression past template-bound nucleosomes and RNA polymerase. One of the proteins that most strongly interacts with Dda, Gp32, is the only single-stranded DNA binding protein (SSB) encoded by T4, is essential for DNA replication, recombination, and repair. Previous studies have shown that Gp32 is essential for Dda stimulation of replication fork progression. Our studies show that interactions between Dda and Gp32 play a critical role in regulating replication fork restart during recombination repair. When the leading strand polymerase stalls at a site of ssDNA damage and the lagging strand machinery continues, Gp32 binds the resulting ssDNA gap ahead of the stalled leading strand polymerase. We found that a Gp32 cluster on leading strand ssDNA blocks Dda loading on the lagging strand ssDNA, blocks stimulation of fork progression by Dda, and stimulates Dda to displace the stalled polymerase and the 3' end of the daughter strand. This unwinding generates conditions necessary for polymerase template switching in order to regress the DNA damage-stalled replication fork. Helicase trafficking by Gp32 could play a role in preventing premature fork progression until the events required for error-free translesion DNA synthesis have taken place. Interestingly, we found that Dda helicase activity is strongly stimulated by the N-terminal deletion mutant Gp32-B, suggesting the N-terminal truncation to generate Gp32-B reveals a cryptic helicase stimulatory activity of Gp32 that may be revealed in the context of a moving polymerase, or through direct interactions of Gp32 with other replisome components. Additionally, our findings support a role for Dda-Gp32 interactions in double strand break (DSB) repair by homology-directed repair (HDR), which relies on homologous recombination and the formation of a displacement loop (D-loop) that can initiate DNA synthesis. We examined the D-loop unwinding activity of Dda, Gp41, and UvsW, the D-loop strand extension activity of Gp43 polymerase, and the effect of the helicases and their modulators on D-loop extension. Dda and UvsW, but not Gp41, catalyze D-loop invading strand by DNA unwinding. The relationship between Dda and Gp43 was modulated by the presence of Gp32. Dda D-loop unwinding competes with D- loop extension by Gp43 only in the presence of Gp32, resulting in a decreased frequency of invading strand extension when all three proteins are present. These data suggest Dda functions as an antirecombinase and negatively regulates the replicative extension of D- loops. Invading strand extension is observed in the presence of Dda, indicating that invading strand extension and unwinding can occur in a coordinated manner. The result is a translocating D-loop, called bubble migration synthesis, a hallmark of break-induced repair (BIR) and synthesis dependent strand annealing (SDSA). Gp41 did not unwind D- loops studied and may serve as a secondary helicase loaded subsequent to D-loop processing by Dda. Dda is proposed to be a mixed function helicase that can work both as an antirecombinase and to promote recombination-dependent DNA synthesis, consistent with the notion that Dda stimulates branch migration. These results have implications on the repair of ssDNA damage, DSB repair, and replication fork regulation, which are highly conserved processes sustained in all organisms.
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3

In, Junghoon Erie Dorothy A. "Structure-function studies of late stages of E. Coli MMR interaction of DNA helicase II with single-stranded DNA binding protein SSB and MutL /." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2008. http://dc.lib.unc.edu/u?/etd,2053.

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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2008.
Title from electronic title page (viewed Feb. 17, 2009). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Curriculum in Applied and Material Sciences." Discipline: Applied and Materials Sciences; Department/School: Applied and Materials Sciences.
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4

Nag, Purba. "Delineating the overlapping roles of the single-stranded DNA binding proteins Ssb1 and Ssb2 in the maintenance of genomic stability and intestinal homeostasis." Thesis, Griffith University, 2019. http://hdl.handle.net/10072/384796.

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Анотація:
Single stranded DNA (ssDNA) binding proteins (SSBPs), are known key players of DNA damage response (DDR) pathway and play an essential role in stabilising fragile ssDNA generated during DNA replication, transcription and repair. The canonical SSBP is the heterotrimeric Replication Protein A (RPA) which is involved in a number of key cellular processes including replication and repair via Homologous Recombination (HR) in the course of DNA damage. Our lab recently described two new SSBPs, termed SSB1 and SSB2 (also known as NABP2/OBFC2B/SOSS-B1 and NABP1/OBFC2A/SOSSB-2, respectively) which form independent co-complexes with two additional proteins, the Integrator complex subunit 3 (INTS3) and the chromosome 9 open reading frame 80 (C9ORF80), a small acidic 104 residue polypeptide. Previously, we demonstrated that whilst Ssb1/Nabp2 KO in mouse caused perinatal lethality, Ssb2/Nabp1 KO did not lead to any phenotypic abnormalities. Interestingly, ablation of Ssb1 led to stabilisation of Ssb2 and vice-versa, indicating functional redundancy between these two proteins. This was recently demonstrated in-vivo by the generation of Ssb1 and Ssb2 (together referred as Ssb1/2) double-knockout (DKO) mice, which caused early embryonic lethality in a constitutive model and acute bone marrow failure and intestinal atrophy using the inducible Rosa26-CreERT2 system. To delineate the functional redundancy between these two proteins at the molecular level, we have generated inducible DKO mouse embryonic fibroblasts (MEFs) using the Rosa26-CreERT2 system, which will be described in the first research chapter. We found that cumulative loss of Ssb1/2 in the primary as well as SV40-immortalised MEFs led to acute proliferation arrest and cell death following TAM administration. This was associated with accumulation of genomic instability via endogenous replication stress. Although loss of Ssb1/2 in-vivo and in-vitro is associated with accumulation of R-loops, the overall DKO phenotype was not able to be rescued with overexpression of RNaseH1, which resolves R-loops. Additionally, we investigated the roles of Ssb1/2 following treatment with different DNA damaging agents to determine their roles in the DDR system. Interestingly, DDR signalling in DKO was normal following ionizing radiation, ultraviolet C and camptothecin but with hydroxyurea treatment that causes replication stress, we observed a delayed signalling response in DKO. Together, this chapter defines the phenotypic changes that take place in-vitro when Ssb1 and Ssb2 are deleted. The second research chapter describes our finding that loss of Ssb1 and Ssb2 together leads to reduced levels of several Integrator components and thus, has an equivalent profound effect on the misprocessing of the Sm- associated small nuclear RNAs (snRNAs) to that of the Integrator catalytic components- IntS9 and IntS11. Here, we show that upregulated snRNAs are not only misprocessed, but extend up to several hundred to a thousand base pairs past their native termination site, and are polyadenylated. Additionally, we demonstrate that loss of Ssb1/2 led to changes in the dynamics of alternative splicing, likely due to perturbation of the splicing machinery by aberrant snRNAs. We further show that a number of regulators of transcription and the cell cycle are affected by these changes, which might contribute to the loss of viability observed in DKO cells. Together, these findings reveal the critical role of Ssb1/2 and their association with the Integrator complex in regulating cellular proliferation and spliceosomal function. The third chapter of this thesis further investigates the intestinal atrophy observed upon loss of Ssb1 and Ssb2 in the DKO mice from our lab. For this, we have generated a small intestine (SI) specific Ssb1/2 DKO mouse- the VillinCreERT2 Ssb1flox/flox; Ssb2flox/flox model. This mouse model is a unique system to study the undefined roles of Ssb1/2 in the small intestine (SI) by bypassing the confounding effects of the bone marrow phenotype in the ubiquitous Rosa26-CreERT2 DKO model. We have found that loss of intestinal Ssb1/2 leads to exhaustion of the stem cells in the crypts, resulting in loss of the normal crypt-villus axis anatomy which causes acute morbidity within six days of induction. Interestingly, the stem cells are pushed to proliferate immediately after the loss of Ssb1 and Ssb2, followed by the exhaustion of these cells. This is demonstrated by sequential proliferation studies using the known thymidine analogue 5-bromo-2’deoxyuridine (BrdU) as well as quantitative reverse transcription polymerase chain reaction (qRT-PCR). Therefore through this model, we have demonstrated a fundamental role of Ssb1/2 in the maintenance of intestinal homeostasis. In conclusion, through the inducible abrogation of two SSBPs- Ssb1 and Ssb2 together, we have demonstrated several novel roles of these proteins in the maintenance of genomic stability both in-vitro and in-vivo that were previously masked in single KO studies. Further, we have defined the molecular mechanisms underlying the acute lethality observed upon abrogation of these two proteins.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Environment and Sc
Science, Environment, Engineering and Technology
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5

Johnson, Vinu. "Structural and Biophysical Studies of Single-Stranded DNA Binding Proteins and dnaB Helicases, Proteins Involved in DNA Replication and Repair." University of Toledo / OhioLINK, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1198939056.

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6

Howland, Christopher James. "The single-stranded DNA-binding protein gene of plasmid Colib-P9." Thesis, University of Leicester, 1989. http://hdl.handle.net/2381/34428.

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The Incil plasmid Colib-P9 was found to carry a single-stranded DNA-binding protein gene (ssb), and the cloned gene was able to suppress the UV and temperature-sensitivity of an ssb-l strain of Escherichia coli K-12. Determination of the nucleotide sequence of Colib ssb demonstrated that the gene shows considerable homology to the ssb gene of plasmid F. In contrast, Southern hybridization techniques indicated that the IncP plasmid RP4 lacks a gene with any extensive homology to F ssb. It was shown that the direction of transfer of Colib-P9 is such that the Colib ssb gene, which lies approximately 11 kb from the origin of transfer, is located within the region transferred early during conjugation. The Colib and F ssb genes are therefore similarly located on their respective plasmids. The Colib ssb gene was shown to be coordinately expressed with the transfer (tra) genes, suggesting that the Colib SSB protein may participate in the conjugative process. However, a mutant Colibdrd-1 derivative carrying a Tn903-derived insertion in ssb showed no defect in tests of conjugative efficiency and was apparently maintained stably both following mating and during vegetative growth. Thus no biological role for the Colib SSB protein was detected. However, unlike the parental plasmid, the Colib ssb mutants conferred a marked Psi- (plasmid- mediated SOS inhibition) phenotype on recA441 and recA730 strains. This may result from high level expression of a psi gene due to readthrough from the Tn903 insertion. It is now apparent that many conjugative plasmids previously thought to be unrelated may be derived from a common ancestral plasmid which possessed both ssb and psi genes. It is speculated that the function of the SSB proteins of conjugative plasmids such as Colib and F may subsequently have been duplicated by analogues derived from newly aquired conjugation systems.
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7

Stroud, A. L. "Genetic analysis of RPA single-stranded DNA binding protein in Haloferax volcanii." Thesis, University of Nottingham, 2012. http://eprints.nottingham.ac.uk/12623/.

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Replication protein A (RPA) is a single-stranded DNA-binding protein that is present in all three domains of life. The roles of RPA include stabilising and protecting single- stranded DNA from nuclease degradation during DNA replication and repair. To achieve this, RPA uses an oligosaccharide-binding fold (OB fold) to bind single- stranded DNA. Haloferax volcanii encodes three RPAs – RPA1, RPA2 and RPA3, of which rpa1 and rpa3 are in operons with genes encoding associated proteins (APs). The APs belong to the COG3390 group of proteins found in Euryarchaeota and feature an OB fold. Genetic analysis of deletion mutants was employed to determine if all three RPAs are essential for cell viability, and if there is an element of redundancy between RPA1 and RPA3. The hypothesis that the RPAs form a complex with their respective APs, as opposed to a heterotrimeric RPA complex, was also investigated. Furthermore, it was tested whether the RPAs and their respective APs are specific for each other, or whether they are interchangeable. The genetic analysis showed that RPA2 is essential for cell viability, but that neither RPA1 nor RPA3 are. The rpa3, rpa3ap and the rpa3 operon deletion mutants showed sensitivity to DNA damage but only a slight growth defect. By contrast, the rpa1, rpa1ap, rpe and rpa1 operon mutants did not show any DNA damage sensitivity and an even milder growth defect. The double rpa1 rpa3 operon deletion was difficult to generate but unexpectedly lacked a significant DNA damage sensitivity and growth defect. The inability to make the double rpa1 rpa3ap and rpa1ap rpa3 deletion mutants suggests that the APs are specific for their respective RPAs. Biochemical analysis involving histidine-tagged RPAs and APs was used to confirm the conclusions of the genetic analysis. The RPAs did not interact with each other, but instead co-purified with their respective APs. This finding reiterates that the RPAs do not form a heterotrimeric complex, as seen in eukaryotes, but instead form a novel complex with their respective APs.
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8

Morten, Michael J. "Developing novel single molecule analyses of the single-stranded DNA binding protein from Sulfolobus solfataricus." Thesis, University of St Andrews, 2015. http://hdl.handle.net/10023/7568.

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Single-stranded DNA binding proteins (SSB) bind to single-stranded DNA (ssDNA) that is generated by molecular machines such as helicases and polymerases. SSBs play crucial roles in DNA translation, replication and repair and their importance is demonstrated by their inclusion across all domains of life. The homotetrameric E. coli SSB and the heterotrimeric human RPA demonstrate how SSBs can vary structurally, but all fulfil their roles by employing oligonucleotide/oligosaccharide binding (OB) folds. Nucleofilaments of SSB proteins bound to ssDNA sequester the ssDNA strands, and in doing so protect exposed bases, keep the ssDNA in conformations favoured by other proteins that metabolise DNA and also recruit other proteins to bind to ssDNA. This thesis focuses on the SSB from the archaeon S. solfataricus (SsoSSB), and has found SsoSSB to be a monomer that binds cooperatively to ssDNA with a binding site size of 4-5 nucleotides. Tagging ssDNA and SsoSSB with fluorescent labels allowed the real time observation of single molecule interactions during the initial nucleation event and subsequent binding of an adjacent SsoSSB monomer. This was achieved by interpreting fluorescent traces that have recorded combinations of FRET, protein induced fluorescent enhancement (PIFE) and quenching events. This novel analysis gave precise measurements of the dynamics of the first and second monomers binding to ssDNA, which allowed affinity and cooperativity constants to be quantified for this important molecular process. SsoSSB was also found to have a similar affinity for RNA, demonstrating a promiscuity not found in other SSBs and suggesting further roles for SsoSSB in the cell - possibly exploiting its capacity to protect nucleic acids from degradation. The extreme temperatures that S. solfataricus experiences and the strength of the interaction with ssDNA and RNA make exploring the application of SsoSSB for industrial uses an interesting prospect; and its rare monomeric structure provides an opportunity to investigate the action of OB folds in a more isolated environment than in higher order structures.
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9

Dodd, Isabel. "Characterisation of the single-stranded DNA binding protein encoded by Kaposi's sarcoma herpesvirus." Thesis, Cranfield University, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.421241.

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Ashton, Nicholas W. "Characterisation of human single-stranded DNA-binding protein 1 (hSSB1) regulation by post-translational modifications." Thesis, Queensland University of Technology, 2016. https://eprints.qut.edu.au/98660/1/Nicholas_Ashton_Thesis.pdf.

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Human single-stranded DNA-binding protein 1 (hSSB1) is required for the timely repair of double-strand DNA breaks, as well as the stabilisation and restart of stalled replication forks. In this work, evidence is provided that cellular survival in response to replication stress is promoted by dynamic phosphorylation of hSSB1 by the DNA-dependent protein kinase (DNA-PK) and PPP-family protein phosphatases. These data provide insight into the functional regulation of hSSB1 following replication fork disruption.
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Книги з теми "Single Stranded DNA Binding Protein (SSBb)"

1

Erdeniz, Naz. Rsp5, a ubiquitin protein ligase, is involved in degradation of the single-stranded DNA binding protein, Rfa1, in Saccharomyces cerevisiae. 1998.

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2

Smith, Julianne M. Characterization of the role of Saccharomyces cerevisiae single-stranded DNA binding protein RP-A in direct repeat recombination. 1996.

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3

Choi, Mieyoung. Sequencing and cloning of the N4-coded single-stranded DNA binding protein gene: Identification and functional analysis of active domains. 1992.

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Частини книг з теми "Single Stranded DNA Binding Protein (SSBb)"

1

Page, Asher N., and Nicholas P. George. "Methods for Analysis of SSB–Protein Interactions by SPR." In Single-Stranded DNA Binding Proteins, 169–74. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-032-8_12.

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2

Inoue, Jin, and Tsutomu Mikawa. "Use of Native Gels to Measure Protein Binding to SSB." In Single-Stranded DNA Binding Proteins, 175–82. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-032-8_13.

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3

Bernstein, Douglas A. "Identification of Small Molecules That Disrupt SSB–Protein Interactions Using a High-Throughput Screen." In Single-Stranded DNA Binding Proteins, 183–91. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-032-8_14.

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4

Vujaklija, Dusica, and Boris Macek. "Detecting Posttranslational Modifications of Bacterial SSB Proteins." In Single-Stranded DNA Binding Proteins, 205–18. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-032-8_16.

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Ryzhikov, Mikhail, and Sergey Korolev. "Structural Studies of SSB Interaction with RecO." In Single-Stranded DNA Binding Proteins, 123–31. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-032-8_7.

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Kozlov, Alexander G., and Timothy M. Lohman. "SSB Binding to ssDNA Using Isothermal Titration Calorimetry." In Single-Stranded DNA Binding Proteins, 37–54. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-032-8_3.

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7

Kozlov, Alexander G., Roberto Galletto, and Timothy M. Lohman. "SSB–DNA Binding Monitored by Fluorescence Intensity and Anisotropy." In Single-Stranded DNA Binding Proteins, 55–83. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-032-8_4.

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Marceau, Aimee H. "Ammonium Sulfate Co-precipitation of SSB and Interacting Proteins." In Single-Stranded DNA Binding Proteins, 151–53. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-032-8_9.

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9

Zhou, Ruobo, and Taekjip Ha. "Single-Molecule Analysis of SSB Dynamics on Single-Stranded DNA." In Single-Stranded DNA Binding Proteins, 85–100. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-032-8_5.

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10

Hedgethorne, Katy, and Martin R. Webb. "Fluorescent SSB as a Reagentless Biosensor for Single-Stranded DNA." In Single-Stranded DNA Binding Proteins, 219–33. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-032-8_17.

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Тези доповідей конференцій з теми "Single Stranded DNA Binding Protein (SSBb)"

1

Casas-Finet, Jose R. "Fluorimetric characterization of tryptophan residues in Escherichia coli single-stranded DNA-binding (SSB) protein and its poly(dT) complex." In OE/LASE '94, edited by Joseph R. Lakowicz. SPIE, 1994. http://dx.doi.org/10.1117/12.182709.

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2

Holden, Todd, G. Tremberger, Jr., E. Cheung, R. Subramaniam, N. Gadura, P. Schneider, R. Sullivan, A. Flamholz, D. Lieberman, and T. D. Cheung. "Nucleotide fluctuation of radiation-resistant Halobacterium sp. NRC-1 single-stranded DNA-binding protein (RPA) genes." In SPIE Optical Engineering + Applications, edited by Richard B. Hoover, Gilbert V. Levin, Alexei Y. Rozanov, and Kurt D. Retherford. SPIE, 2009. http://dx.doi.org/10.1117/12.825827.

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3

Ma, Xiao, and Pranav Shrotriya. "Study on Specific Binding Interaction Between Protein and DNA Aptamer via Dynamic Force Spectroscopy." In ASME 2013 2nd Global Congress on NanoEngineering for Medicine and Biology. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/nemb2013-93119.

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Recently the need to design nanoscale, sensitive and flexible bio-sensors or biotic-abiotic interface keeps increasing. One of the essential challenges on this objective is to grasp a thorough understanding of the mechanism governing binding interaction between bio-molecules. In this study we aim to demonstrate the binding specificity and reveal force interaction between the anti-coagulation protein thrombin and the single-stranded DNA thrombin aptamer by application of Atomic Force Microscopy (AFM). The thiolated aptamer was deposited onto gold substrate, and then repeatedly brought into contact with a thrombin-coated AFM tip, and force drop-offs during the pull-off were measured to determine the unbinding force between the thrombin-aptamer pair. The results from experiment show that the thrombin-aptamer pair has specific binding and the force between the pair exhibits loading rate dependence. It was shown that the binding forces of the thrombin-aptamer interaction increases with growth of loading rates. The average binding force for a single thrombin/aptamer pair increased from 20 pN to 40 pN, with loading rate changes from 500pN/s to 13500pN/s. Distribution of the unbinding forces measured for each loading rate can be explained on the basis of single energy barrier model for molecular bond breakage.
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Звіти організацій з теми "Single Stranded DNA Binding Protein (SSBb)"

1

Elbaum, Michael, and Peter J. Christie. Type IV Secretion System of Agrobacterium tumefaciens: Components and Structures. United States Department of Agriculture, March 2013. http://dx.doi.org/10.32747/2013.7699848.bard.

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Objectives: The overall goal of the project was to build an ultrastructural model of the Agrobacterium tumefaciens type IV secretion system (T4SS) based on electron microscopy, genetics, and immunolocalization of its components. There were four original aims: Aim 1: Define the contributions of contact-dependent and -independent plant signals to formation of novel morphological changes at the A. tumefaciens polar membrane. Aim 2: Genetic basis for morphological changes at the A. tumefaciens polar membrane. Aim 3: Immuno-localization of VirB proteins Aim 4: Structural definition of the substrate translocation route. There were no major revisions to the aims, and the work focused on the above questions. Background: Agrobacterium presents a unique example of inter-kingdom gene transfer. The process involves cell to cell transfer of both protein and DNA substrates via a contact-dependent mechanism akin to bacterial conjugation. Transfer is mediated by a T4SS. Intensive study of the Agrobacterium T4SS has made it an archetypal model for the genetics and biochemistry. The channel is assembled from eleven protein components encoded on the B operon in the virulence region of the tumor-inducing plasmid, plus an additional coupling protein, VirD4. During the course of our project two structural studies were published presenting X-ray crystallography and three-dimensional reconstruction from electron microscopy of a core complex of the channel assembled in vitro from homologous proteins of E. coli, representing VirB7, VirB9, and VirB10. Another study was published claiming that the secretion channels in Agrobacterium appear on helical arrays around the membrane perimeter and along the entire length of the bacterium. Helical arrangements in bacterial membranes have since fallen from favor however, and that finding was partially retracted in a second publication. Overall, the localization of the T4SS within the bacterial membranes remains enigmatic in the literature, and we believe that our results from this project make a significant advance. Summary of achievements : We found that polar inflations and other membrane disturbances relate to the activation conditions rather than to virulence protein expression. Activation requires low pH and nutrient-poor medium. These stress conditions are also reflected in DNA condensation to varying degrees. Nonetheless, they must be considered in modeling the T4SS as they represent the relevant conditions for its expression and activity. We identified the T4SS core component VirB7 at native expression levels using state of the art super-resolution light microscopy. This marker of the secretion system was found almost exclusively at the cell poles, and typically one pole. Immuno-electron microscopy identified the protein at the inner membrane, rather than at bridges across the inner and outer membranes. This suggests a rare or transient assembly of the secretion-competent channel, or alternatively a two-step secretion involving an intermediate step in the periplasmic space. We followed the expression of the major secreted effector, VirE2. This is a single-stranded DNA binding protein that forms a capsid around the transferred oligonucleotide, adapting the bacterial conjugation to the eukaryotic host. We found that over-expressed VirE2 forms filamentous complexes in the bacterial cytoplasm that could be observed both by conventional fluorescence microscopy and by correlative electron cryo-tomography. Using a non-retentive mutant we observed secretion of VirE2 from bacterial poles. We labeled the secreted substrates in vivo in order detect their secretion and appearance in the plant cells. However the low transfer efficiency and significant background signal have so far hampered this approach.
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