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Journal articles on the topic 'Single Stranded DNA Binding Protein (SSBb)'

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Published: 6 September 2023

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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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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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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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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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11

Hobbs, Michael D., Akiko Sakai, and Michael M. Cox. "SSB Protein Limits RecOR Binding onto Single-stranded DNA." Journal of Biological Chemistry 282, no. 15 (February 1, 2007): 11058–67. http://dx.doi.org/10.1074/jbc.m611007200.

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12

Tan, Changgeng, Tong Wang, Wenyi Yang, and Lei Deng. "PredPSD: A Gradient Tree Boosting Approach for Single-Stranded and Double-Stranded DNA Binding Protein Prediction." Molecules 25, no. 1 (December 26, 2019): 98. http://dx.doi.org/10.3390/molecules25010098.

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Interactions between proteins and DNAs play essential roles in many biological processes. DNA binding proteins can be classified into two categories. Double-stranded DNA-binding proteins (DSBs) bind to double-stranded DNA and are involved in a series of cell functions such as gene expression and regulation. Single-stranded DNA-binding proteins (SSBs) are necessary for DNA replication, recombination, and repair and are responsible for binding to the single-stranded DNA. Therefore, the effective classification of DNA-binding proteins is helpful for functional annotations of proteins. In this work, we propose PredPSD, a computational method based on sequence information that accurately predicts SSBs and DSBs. It introduces three novel feature extraction algorithms. In particular, we use the autocross-covariance (ACC) transformation to transform feature matrices into fixed-length vectors. Then, we put the optimal feature subset obtained by the minimal-redundancy-maximal-relevance criterion (mRMR) feature selection algorithm into the gradient tree boosting (GTB). In 10-fold cross-validation based on a benchmark dataset, PredPSD achieves promising performances with an AUC score of 0.956 and an accuracy of 0.912, which are better than those of existing methods. Moreover, our method has significantly improved the prediction accuracy in independent testing. The experimental results show that PredPSD can significantly recognize the binding specificity and differentiate DSBs and SSBs.

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13

Inoue, Jin, Takayuki Nagae, Masaki Mishima, Yutaka Ito, Takehiko Shibata, and Tsutomu Mikawa. "A Mechanism for Single-stranded DNA-binding Protein (SSB) Displacement from Single-stranded DNA upon SSB-RecO Interaction." Journal of Biological Chemistry 286, no. 8 (December 17, 2010): 6720–32. http://dx.doi.org/10.1074/jbc.m110.164210.

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14

Kozlov, Alexander G., Michael M. Cox, and Timothy M. Lohman. "Regulation of Single-stranded DNA Binding by the C Termini of Escherichia coli Single-stranded DNA-binding (SSB) Protein." Journal of Biological Chemistry 285, no. 22 (April 1, 2010): 17246–52. http://dx.doi.org/10.1074/jbc.m110.118273.

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15

Cai, Ying, Lalitha Nagarajan, and Stephen J. Brandt. "Single-Stranded DNA-Binding Proteins (SSBPs) Promote the Oligomerization of LIM-Domain Binding Protein Ldb1." Blood 112, no. 11 (November 16, 2008): 2437. http://dx.doi.org/10.1182/blood.v112.11.2437.2437.

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Abstract The multifunctional LIM domain-binding protein Ldb1 is important in multiple developmental programs, including hematopoiesis. An evolutionarily conserved family of proteins with single-stranded DNA-binding activity, the SSBPs, has been shown to act as Ldb1 partners and augment its biological actions. We recently established that Ssbp2 and Ssbp3 were components of an E-box-GATA DNA-binding complex in murine erythroid progenitors containing the LIM-only protein Lmo2 and transcription factors Tal1, E2A, and Gata1 and showed these SSBPs stimulated E box-GATA DNA-binding activity and inhibited Ldb1 ubiquitination and subsequent proteasomal degradation (Genes & Dev.21:942–955, 2007). As its SSBP interaction domain (Ldb1/Chip conserved domain or LCCD) is adjacent to Ldb1’s N-terminal dimerization domain (DD), we sought to determine whether SSBP binding affected Ldb1 dimerization. To investigate, the Ldb1 coding region was fused to the DNA-binding domain of the yeast transcription factor GAL4 (GAL4DBD) and in a second construct to the activation domain of herpesvirus VP16 (VP16AD). These fusion proteins were then expressed in mammalian cells with a luciferase reporter linked to a promoter with iterated GAL4 binding sites. Luciferase activity became detectable with coexpression of the VP16AD-Ldb1 and GAL4DBD-Ldb1 fusions, presumably from Ldb1 dimerization, which increased markedly with simultaneous expression of SSBP2. In contrast, SSBP2 (ΔLUFS) and Ldb1 (ΔLCCD) mutants incapable of interacting with Ldb1 and SSBPs, respectively, were inactive, suggesting that SSBP2 augmentation of Ldb1 dimerization involved direct protein-protein interactions. To exclude an effect of SSBP2 on turnover of Ldb1 fusion proteins, radiolabeled full-length Ldb1 and SSBP3 were prepared by in vitro transcription/translation, mixed, and subjected to chemical crosslinking. Addition of the crosslinker bis(sulfosuccinimidyl)-suberate (BS3) to Ldb1, but not SSBP3, led to the appearance of a radiolabeled protein with mobility in denaturing polyacrylamide gels approximately twice that of Ldb1, consistent with an Ldb1 homodimer. When SSBP3 and Ldb1 were mixed together and crosslinked, a dose-related increase was noted in a more retarded species predicted to contain two molecules each of Ldb1 and SSBP3, together with a decrease in monomeric Ldb1. Finally, two well-characterized dimerization-defective Ldb1 mutants, Ldb1(200–375) and Ldb1(50–375), failed to support the formation of the higher molecular weight species or to homodimerize. Thus, the SSBPs promoted assembly of ternary complexes incorporating both SSBP and Ldb1 in a manner dependent on Ldb1 dimerization. The failure to observe Ldb1-SSBP heterodimers in cross-linking experiments suggests, further, that the SSBPs interacted with preformed Ldb1 dimers. In summary, either through an allosteric effect on Ldb1’s DD or by altering the equilibrium between monomeric and dimeric species, the SSBPs promote Ldb1 oligomerization. Together with inhibition of Ldb1 ubiquitination and turnover, this would serve to augment Ldb1 function.

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16

Antony, Edwin, and Timothy M. Lohman. "Dynamics of E. coli single stranded DNA binding (SSB) protein-DNA complexes." Seminars in Cell & Developmental Biology 86 (February 2019): 102–11. http://dx.doi.org/10.1016/j.semcdb.2018.03.017.

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17

Rochester, S. Craig, and Paula Traktman. "Characterization of the Single-Stranded DNA Binding Protein Encoded by the Vaccinia Virus I3 Gene." Journal of Virology 72, no. 4 (April 1, 1998): 2917–26. http://dx.doi.org/10.1128/jvi.72.4.2917-2926.1998.

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ABSTRACT The 34-kDa protein encoded by the I3 gene of vaccinia virus is expressed at early and intermediate times postinfection and is phosphorylated on serine residues. Recombinant I3 has been expressed inEscherichia coli and purified to near homogeneity, as has the protein from infected cells. Both recombinant and endogenous I3 protein demonstrate a striking affinity for single-stranded, but not for double-stranded, DNA. The interaction with DNA is resistant to salt, exhibits low cooperativity, and appears to involve a binding site of approximately 10 nucleotides. Electrophoretic mobility shift assays indicate that numerous I3 molecules can bind to a template, reflecting the stoichiometric interaction of I3 with DNA. Sequence analysis reveals that a pattern of aromatic and charged amino acids common to many replicative single-stranded DNA binding proteins (SSBs) is conserved in I3. The inability to isolate viable virus containing an interrupted I3 allele provides strong evidence that the I3 protein plays an essential role in the viral life cycle. A likely role for I3 as an SSB involved in DNA replication and/or repair is discussed.

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18

Attaiech, Laetitia, Audrey Olivier, Isabelle Mortier-Barrière, Anne-Lise Soulet, Chantal Granadel, Bernard Martin, Patrice Polard, and Jean-Pierre Claverys. "Role of the Single-Stranded DNA–Binding Protein SsbB in Pneumococcal Transformation: Maintenance of a Reservoir for Genetic Plasticity." PLoS Genetics 7, no. 6 (June 30, 2011): e1002156. http://dx.doi.org/10.1371/journal.pgen.1002156.

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19

Jędrzejczak, Robert, Mirosława Dauter, Zbigniew Dauter, Marcin Olszewski, Anna Długołęcka, and Józef Kur. "Structure of the single-stranded DNA-binding protein SSB fromThermus aquaticus." Acta Crystallographica Section D Biological Crystallography 62, no. 11 (October 18, 2006): 1407–12. http://dx.doi.org/10.1107/s0907444906036031.

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20

Filipkowski, Paweł, Anna Duraj-Thatte, and Józef Kur. "Novel thermostable single-stranded DNA-binding protein (SSB) from Deinococcus geothermalis." Archives of Microbiology 186, no. 2 (June 21, 2006): 129–37. http://dx.doi.org/10.1007/s00203-006-0128-2.

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21

Hamon, L., D. Pastre, P. Dupaigne, C. L. Breton, E. L. Cam, and O. Pietrement. "High-resolution AFM imaging of single-stranded DNA-binding (SSB) protein--DNA complexes." Nucleic Acids Research 35, no. 8 (March 29, 2007): e58-e58. http://dx.doi.org/10.1093/nar/gkm147.

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22

Huang, Yen-Hua, and Cheng-Yang Huang. "The glycine-rich flexible region in SSB is crucial for PriA stimulation." RSC Advances 8, no. 61 (2018): 35280–88. http://dx.doi.org/10.1039/c8ra07306f.

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23

Cai, Ying, Lalitha Nagarajan, and Stephen J. Brandt. "Single-Stranded DNA Binding Proteins (SSBPs) Interact with LDB1 Homodimers to Facilitate DNA Looping." Blood 114, no. 22 (November 20, 2009): 1469. http://dx.doi.org/10.1182/blood.v114.22.1469.1469.

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Abstract Abstract 1469 Poster Board I-492 The LIM domain binding protein LDB1 is an essential cofactor of LIM-homeodomain (LIM-HD) and LIM-only (LMO) proteins in hematopoiesis and other developmental programs. We have shown that LDB1 and its LIM-HD and LMO interaction partners are protected from ubiquitylation by a small family of SSBPs. Recently, we demonstrated that these SSBPs bind to LDB1 homodimers to promote formation of a ternary complex containing two molecules of LDB1 and SSBP. This was dependent on an intact LDB1 dimerization domain (DD) and produced a shift, directly or indirectly, in the equilibrium between LDB1 monomer and dimer. In the present study, we introduced a 24-glycine linker between two full-length LDB1 peptide-coding sequences and expressed this forced or tethered LDB1 dimer (TD-LDB1) in vitro and in vivo. First, both TD-LDB1, introduced into cells by transfection, and endogenous LDB1 were found to have the same turnover rate, indicating that protection from ubiquitylation was independent of dimerization status. Second, TD-LDB1 was fused to the DNA binding domain of GAL4 (GAL4DBD) and in a second construct to the activation domain of herpesvirus VP16 (VP16AD) and these constructs were expressed in cells with a GAL4 reporter plasmid. Co-expression of GAL4-LDB1 and VP16-LDB1 significantly increased reporter luciferase activity as a result of dimerization, while co-expression of GAL4-TD-LDB1 with VP16-LDB1 did not, ruling out formation of LDB1 trimers. Likewise, co-expression of GAL4-TD-LDB1 with VP16-TD-LDB1 did not significantly affect luciferase activity, indicating that LDB1 also cannot form protein tetramers. In contrast, TD-LDB1 was able to bind SSBP2 and SSBP3 in both chemical cross-linking and mammalian two-hybrid assays, consistent with the SSBP interacting with preformed LDB1 dimers. Finally, the complete 200-amino acid DD of LDB1, reported as necessary and sufficient for protein dimerization, was confirmed in cross-linking analysis to act as a dominant negative inhibitor of LDB1 dimerization. When the DD was introduced into Lhx2-, Ldb1-, and Ssbp3-expressing cells, application of a modified electrophoretic mobility assay that can detect linking of two DNA probes in solution revealed that the DD reduced formation of a ‘looped’ complex containing two DNA probes and led to the appearance of a new complex containing Lhx2, Ssbp3, and Ldb1, apparently in a monomeric form. In summary, this work elucidates a novel function of SSBPs in enhancing LDB1 dimerization and, ultimately, long-range communication between cis regulatory regions in genes. In addition, it suggests that SSBPs bind dimeric LDB1 and induce an allosteric change in the adjacent SSBP interaction domain rather than vice versa. Finally, these results lead to the prediction that an SSBP- and LDB1-containing complex could promote looping between promoter-proximal and promoter-distal LIM-HD binding elements. Disclosures: No relevant conflicts of interest to declare.

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24

Cai, Ying, Zhixiong Xu, Lalitha Nagarajan, and Stephen J. Brandt. "Single-Stranded DNA-Binding Proteins (SSBPs) Regulate the Abundance of the LIM-Homeodomain Protein LHX2 and Augment Its Transcriptional Activity." Blood 110, no. 11 (November 16, 2007): 1239. http://dx.doi.org/10.1182/blood.v110.11.1239.1239.

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Abstract A small family of proteins with putative single-stranded DNA-binding activity has been shown to augment the biological actions of LIM-homeodomain (LIM-HD) transcription factors through the mediation of the LIM domain-binding protein LDB1. We recently established that two of these SSBPs, Ssbp2 and Ssbp3, were components of an E-box-GATA DNA-binding complex in murine erythroid progenitors containing transcription factors Tal1, E2A, and Gata-1 and LIM-only protein Lmo2 and showed that Ssbp2 stimulated E box-GATA DNA-binding activity by inhibiting Ldb1 ubiquitination and Ldb1 and Lmo2 turnover (Genes & Dev.21:942–955, 2007). Since LIM-HD proteins are substrates of different E3 ubiquitin ligases than LIM-only proteins and have the additional property of binding DNA, we sought to determine the effect of SSBPs on LIM-HD expression and function. Using the prototype LIM-HD protein Lhx2 and one of its best-characterized target genes, Cga, for analysis, we found that an Ssbp3-, Ldb1-, and Lhx2-containing complex associated with an Lhx2 binding element in the Cga promoter in vitro and in mouse pituitary cells (alphaT3-1 cell line) in vivo. We then showed that enforced expression of Ssbp2 and Ssbp3 in alphaT3-1 cells increased Lhx2 and Ldb1 protein abundance, Lhx2 DNA-binding activity, and Cga expression and augmented Lhx2 transcriptional activity in an Ldb1-dependent fashion. While Lhx2-Ldb1-Ssbp3 DNA-binding activity increased in Ssbp3- relative to vector-transfected cells, the affinity of this complex for DNA was unaltered. Similar to the effect of Ssbp2 on Lmo2 in murine erythroleukemia (MEL) cells, overexpressed Ssbp3 reduced Lhx2 protein turnover in cycloheximide-treated alphaT3-1 cells without affecting Lhx2 RNA levels. In contrast, knockdown of endogenous Ssbp3, but not Ssbp2 which is expressed at much lower levels in these cells, reduced Lhx2 and Ldb1 abundance, Lhx2 DNA-binding activity, Lhx2, Ldb1, and Ssbp3 loading onto the Cga promoter, Cga promoter activity, and endogenous Cga gene expression. Significantly, neither overexpression nor knockdown of Ssbp2 in MEL cells, which express both the LIM-only protein Lmo2 and LIM-HD protein Lhx2, affected Lhx2 protein abundance, and Lhx2 DNA-binding activity was undetectable in nuclear extracts from these cells despite the presence of immunoreactive Lhx2. These studies indicate that SSBP augmentation of LIM-HD function results from Ldb1-mediated inhibition of LIM-HD protein turnover and increased assembly of a LIM-HD/LDB1/SSBP DNA-binding complex. The much greater affinity for LDB1 of LIM-only compared to LIM-HD proteins is likely a major determinant of the SSBP effect on LIM-HD protein abundance. Finally, these findings are consistent with cell type-specific contributions of different SSBPs, even for similar LDB1-dependent actions.

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25

Nigam, Richa, and Roy Anindya. "Escherichia coli single-stranded DNA binding protein SSB promotes AlkB-mediated DNA dealkylation repair." Biochemical and Biophysical Research Communications 496, no. 2 (February 2018): 274–79. http://dx.doi.org/10.1016/j.bbrc.2018.01.043.

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26

Harami, Gábor M., Zoltán J. Kovács, Rita Pancsa, János Pálinkás, Veronika Baráth, Krisztián Tárnok, András Málnási-Csizmadia, and Mihály Kovács. "Phase separation by ssDNA binding protein controlled via protein−protein and protein−DNA interactions." Proceedings of the National Academy of Sciences 117, no. 42 (October 5, 2020): 26206–17. http://dx.doi.org/10.1073/pnas.2000761117.

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Bacterial single-stranded (ss)DNA-binding proteins (SSB) are essential for the replication and maintenance of the genome. SSBs share a conserved ssDNA-binding domain, a less conserved intrinsically disordered linker (IDL), and a highly conserved C-terminal peptide (CTP) motif that mediates a wide array of protein−protein interactions with DNA-metabolizing proteins. Here we show that theEscherichia coliSSB protein forms liquid−liquid phase-separated condensates in cellular-like conditions through multifaceted interactions involving all structural regions of the protein. SSB, ssDNA, and SSB-interacting molecules are highly concentrated within the condensates, whereas phase separation is overall regulated by the stoichiometry of SSB and ssDNA. Together with recent results on subcellular SSB localization patterns, our results point to a conserved mechanism by which bacterial cells store a pool of SSB and SSB-interacting proteins. Dynamic phase separation enables rapid mobilization of this protein pool to protect exposed ssDNA and repair genomic loci affected by DNA damage.

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27

Nai, Yi Heng, Egan H. Doeven, and Rosanne M. Guijt. "An improved nucleic acid sequence-based amplification method mediated by T4 gene 32 protein." PLOS ONE 17, no. 3 (March 24, 2022): e0265391. http://dx.doi.org/10.1371/journal.pone.0265391.

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The uptake of Nucleic Acid Sequence-Based Amplification (NASBA) for point of care testing may be hindered by a complexity in the workflow due the requirement of a thermal denaturation step to initiate the cyclic isothermal amplification before the addition of the amplification enzymes. Despite reports of successful enhancement of other DNA and RNA amplification methods using DNA and RNA binding proteins, this has not been reported for NASBA. Here, three single-stranded binding proteins, RecA, Extreme Thermostable Single-stranded binding protein (ET SSB) and T4 gene gp32 protein (gp32), were incorporated in NASBA protocol and used for single pot, one-step NASBA at 41 °C. Indeed, all SSBs showed significantly improved amplifications compared with the 2-step process, but only gp32 showed no non-specific aberrant amplification, and slightly improved the time-to-positivity in comparison with the conventional NASBA. For synthetic HIV-1 RNA, gp32 was found to improve the time-to-positivity (ttp) by average of 13.6% of one-step NASBA and 6.7% of conventional NASBA for the detection of HIV-1 RNA, showing its potential for simplifying the workflow as desirable for point of care applications of NASBA.

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Steffen, Scott E., Francine S. Katz, and Floyd R. Bryant. "Complete Inhibition ofStreptococcus pneumoniaeRecA Protein-catalyzed ATP Hydrolysis by Single-stranded DNA-binding Protein (SSB Protein)." Journal of Biological Chemistry 277, no. 17 (February 19, 2002): 14493–500. http://dx.doi.org/10.1074/jbc.m112444200.

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Iftode, C., and J. A. Borowiec. "Denaturation of the simian virus 40 origin of replication mediated by human replication protein A." Molecular and Cellular Biology 17, no. 7 (July 1997): 3876–83. http://dx.doi.org/10.1128/mcb.17.7.3876.

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The initiation of simian virus 40 (SV40) replication requires recognition of the viral origin of replication (ori) by SV40 T antigen, followed by denaturation of ori in a reaction dependent upon human replication protein A (hRPA). To understand how origin denaturation is achieved, we constructed a 48-bp SV40 "pseudo-origin" with a central 8-nucleotide (nt) bubble flanked by viral sequences, mimicking a DNA structure found within the SV40 T antigen-ori complex. hRPA bound the pseudo-origin with similar stoichiometry and an approximately fivefold reduced affinity compared to the binding of a 48-nt single-stranded DNA molecule. The presence of hRPA not only distorted the duplex DNA flanking the bubble but also resulted in denaturation of the pseudo-origin substrate in an ATP-independent reaction. Pseudo-origin denaturation occurred in 7 mM MgCl2, distinguishing this reaction from Mg2+-independent DNA-unwinding activities previously reported for hRPA. Tests of other single-stranded DNA-binding proteins (SSBs) revealed that pseudo-origin binding correlates with the known ability of these SSBs to support the T-antigen-dependent origin unwinding activity. Our results suggest that hRPA binding to the T antigen-ori complex induces the denaturation of ori including T-antigen recognition sequences, thus releasing T antigen from ori to unwind the viral DNA. The denaturation activity of hRPA has the potential to play a significant role in other aspects of DNA metabolism, including DNA repair.

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Brill, Steven J., and Suzanne Bastin-Shanower. "Identification and Characterization of the Fourth Single-Stranded-DNA Binding Domain of Replication Protein A." Molecular and Cellular Biology 18, no. 12 (December 1, 1998): 7225–34. http://dx.doi.org/10.1128/mcb.18.12.7225.

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ABSTRACT Replication protein A (RPA), the heterotrimeric single-stranded-DNA (ssDNA) binding protein (SSB) of eukaryotes, contains two homologous ssDNA binding domains (A and B) in its largest subunit, RPA1, and a third domain in its second-largest subunit, RPA2. Here we report that Saccharomyces cerevisiae RPA1 contains a previously undetected ssDNA binding domain (domain C) lying in tandem with domains A and B. The carboxy-terminal portion of domain C shows sequence similarity to domains A and B and to the region of RPA2 that binds ssDNA (domain D). The aromatic residues in domains A and B that are known to stack with the ssDNA bases are conserved in domain C, and as in domain A, one of these is required for viability in yeast. Interestingly, the amino-terminal portion of domain C contains a putative Cys4-type zinc-binding motif similar to that of another prokaryotic SSB, T4 gp32. We demonstrate that the ssDNA binding activity of domain C is uniquely sensitive to cysteine modification but that, as with gp32, ssDNA binding is not strictly dependent on zinc. The RPA heterotrimer is thus composed of at least four ssDNA binding domains and exhibits features of both bacterial and phage SSBs.

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Lindner, Cordula, Reindert Nijland, Mariska van Hartskamp, Sierd Bron, Leendert W. Hamoen, and Oscar P. Kuipers. "Differential Expression of Two Paralogous Genes of Bacillus subtilis Encoding Single-Stranded DNA Binding Protein." Journal of Bacteriology 186, no. 4 (February 15, 2004): 1097–105. http://dx.doi.org/10.1128/jb.186.4.1097-1105.2004.

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ABSTRACT The Bacillus subtilis genome comprises two paralogous single-stranded DNA binding protein (SSB) genes, ssb and ywpH, which show distinct expression patterns. The main ssb gene is strongly expressed during exponential growth and is coregulated with genes encoding the ribosomal proteins S6 and S18. The gene organization rpsF-ssb-rpsR as observed in B. subtilis is found in many gram-positive as well as some gram-negative bacteria, but not in Escherichia coli. The ssb gene is essential for cell viability, and like other SSBs its expression is elevated during SOS response. In contrast, the paralogous ywpH gene is transcribed from its own promoter at the onset of stationary phase in minimal medium only. Its expression is ComK dependent and its gene product is required for optimal natural transformation.

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Myers, T. W., and L. J. Romano. "Mechanism of stimulation of T7 DNA polymerase by Escherichia coli single-stranded DNA binding protein (SSB)." Journal of Biological Chemistry 263, no. 32 (November 1988): 17006–15. http://dx.doi.org/10.1016/s0021-9258(18)37490-8.

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Cheng, Zishuo, Aimee Caillet, Binbin Ren, and Huangen Ding. "Stimulation ofEscherichia coliDNA damage inducible DNA helicase DinG by the single-stranded DNA binding protein SSB." FEBS Letters 586, no. 21 (October 1, 2012): 3825–30. http://dx.doi.org/10.1016/j.febslet.2012.09.032.

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Huang, Yen-Hua, and Cheng-Yang Huang. "SAAV2152 is a single-stranded DNA binding protein: the third SSB in Staphylococcus aureus." Oncotarget 9, no. 29 (February 5, 2018): 20239–54. http://dx.doi.org/10.18632/oncotarget.24427.

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Huang, Yen-Hua, Hong-Hsiang Guan, Chun-Jung Chen, and Cheng-Yang Huang. "Staphylococcus aureus single-stranded DNA-binding protein SsbA can bind but cannot stimulate PriA helicase." PLOS ONE 12, no. 7 (July 27, 2017): e0182060. http://dx.doi.org/10.1371/journal.pone.0182060.

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Harami, Gabor, Zoltan J. Kovacs, János Pálinkás, Rita Pancsa, Veronika Baráth, Krisztián Tárnok, Hajnalka Harami-Papp, Andras Malnasi-Csizmadia, and Mihaly Kovacs. "E. coli Single-Stranded DNA Binding (SSB) Protein Undergoes Dynamic Liquid-Liquid Phase Separation Controlled via Protein-Protein and Protein-DNA Interactions." Biophysical Journal 118, no. 3 (February 2020): 484a. http://dx.doi.org/10.1016/j.bpj.2019.11.2680.

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Tiranti, Valeria, Mariano Rocchi, Stefano DiDonato, and Massimo Zeviani. "Cloning of human and rat cDNAs encoding the mitochondrial single-stranded DNA-binding protein (SSB)." Gene 126, no. 2 (April 1993): 219–25. http://dx.doi.org/10.1016/0378-1119(93)90370-i.

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Huang, Yen-Hua, and Cheng-Yang Huang. "C-Terminal Domain Swapping of SSB Changes the Size of the ssDNA Binding Site." BioMed Research International 2014 (2014): 1–16. http://dx.doi.org/10.1155/2014/573936.

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Single-stranded DNA-binding protein (SSB) plays an important role in DNA metabolism, including DNA replication, repair, and recombination, and is therefore essential for cell survival. Bacterial SSB consists of an N-terminal ssDNA-binding/oligomerization domain and a flexible C-terminal protein-protein interaction domain. We characterized the ssDNA-binding properties ofKlebsiella pneumoniaeSSB (KpSSB),Salmonella entericaSerovar Typhimurium LT2 SSB (StSSB),Pseudomonas aeruginosaPAO1 SSB (PaSSB), and two chimeric KpSSB proteins, namely, KpSSBnStSSBc and KpSSBnPaSSBc. The C-terminal domain of StSSB or PaSSB was exchanged with that of KpSSB through protein chimeragenesis. By using the electrophoretic mobility shift assay, we characterized the stoichiometry of KpSSB, StSSB, PaSSB, KpSSBnStSSBc, and KpSSBnPaSSBc, complexed with a series of ssDNA homopolymers. The binding site sizes were determined to be26±2,21±2,29±2,21±2, and29±2nucleotides (nt), respectively. Comparison of the binding site sizes of KpSSB, KpSSBnStSSBc, and KpSSBnPaSSBc showed that the C-terminal domain swapping of SSB changes the size of the binding site. Our observations suggest that not only the conserved N-terminal domain but also the C-terminal domain of SSB is an important determinant for ssDNA binding.

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Choi, Woong, Jonghyeon Son, Aekyung Park, Hongshi Jin, Seung Chul Shin, Jun Hyuck Lee, T. Doohun Kim, and Han-Woo Kim. "Identification, Characterization, and Preliminary X-ray Diffraction Analysis of a Single Stranded DNA Binding Protein (LjSSB) from Psychrophilic Lacinutrix jangbogonensis PAMC 27137." Crystals 12, no. 4 (April 11, 2022): 538. http://dx.doi.org/10.3390/cryst12040538.

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Single-stranded DNA-binding proteins (SSBs) are essential for DNA metabolism, including repair and replication, in all organisms. SSBs have potential applications in molecular biology and in analytical methods. In this study, for the first time, we purified, structurally characterized, and analyzed psychrophilic SSB (LjSSB) from Lacinutrix jangbogonensis PAMC 27137 isolated from the Antarctic region. LjSSB has a relatively short amino acid sequence, consisting of 111 residues, with a molecular mass of 12.6 kDa. LjSSB protein was overexpressed in Escherichia coli BL21 (DE3) and analyzed for binding affinity using 20- and 35-mer deoxythymidine oligonucleotides (dT). In addition, the crystal structure of LjSSB at a resolution 2.6 Å was obtained. The LjSSB protein crystal belongs to the space group C222 with the unit cell parameters of a = 106.58 Å, b = 234.14 Å, c = 66.14 Å. The crystal structure was solved using molecular replacement, and subsequent iterative structure refinements and model building are currently under progress. Further, the complete structural information of LjSSB will provide a novel strategy for protein engineering and for the application on molecular biological techniques.

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Paradzik, Tina, Nives Ivic, Zelimira Filic, Babu A. Manjasetty, Paul Herron, Marija Luic, and Dusica Vujaklija. "Structure–function relationships of two paralogous single-stranded DNA-binding proteins from Streptomyces coelicolor: implication of SsbB in chromosome segregation during sporulation." Nucleic Acids Research 41, no. 6 (February 6, 2013): 3659–72. http://dx.doi.org/10.1093/nar/gkt050.

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41

Lee, I.-Ren, Teckla Akinyi, and Taekjip Ha. "Single Molecule Observation of Direct Transfer of Escherichia Coli Single-Strand Binding Protein (SSB) between Single-Stranded DNA Molecules." Biophysical Journal 104, no. 2 (January 2013): 73a. http://dx.doi.org/10.1016/j.bpj.2012.11.443.

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42

Skaar, Jeffrey R., Derek J. Richard, Anita Saraf, Alfredo Toschi, Emma Bolderson, Laurence Florens, Michael P. Washburn, Kum Kum Khanna, and Michele Pagano. "INTS3 controls the hSSB1-mediated DNA damage response." Journal of Cell Biology 187, no. 1 (September 28, 2009): 25–32. http://dx.doi.org/10.1083/jcb.200907026.

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Human SSB1 (single-stranded binding protein 1 [hSSB1]) was recently identified as a part of the ataxia telangiectasia mutated (ATM) signaling pathway. To investigate hSSB1 function, we performed tandem affinity purifications of hSSB1 mutants mimicking the unphosphorylated and ATM-phosphorylated states. Both hSSB1 mutants copurified a subset of Integrator complex subunits and the uncharacterized protein LOC58493/c9orf80 (henceforth minute INTS3/hSSB-associated element [MISE]). The INTS3–MISE–hSSB1 complex plays a key role in ATM activation and RAD51 recruitment to DNA damage foci during the response to genotoxic stresses. These effects on the DNA damage response are caused by the control of hSSB1 transcription via INTS3, demonstrating a new network controlling hSSB1 function.

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Kovacs, Zoltan J., Ágnes Hubert, Veronika Baráth, Lili Farkas, Yeonee Seol, Keir C. Neuman, Gabor Harami, and Mihaly Kovacs. "Probing and Visualization of the RecQ Helicase-Induced DNA Binding Mode Change of the Bacterial Single-Stranded DNA Binding (SSB) Protein." Biophysical Journal 118, no. 3 (February 2020): 373a. http://dx.doi.org/10.1016/j.bpj.2019.11.2136.

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44

Benam, Afsaneh V., Emma Lång, Kristian Alfsnes, Burkhard Fleckenstein, Alexander D. Rowe, Eirik Hovland, Ole Herman Ambur, Stephan A. Frye, and Tone Tønjum. "Structure–function relationships of the competence lipoprotein ComL and SSB in meningococcal transformation." Microbiology 157, no. 5 (May 1, 2011): 1329–42. http://dx.doi.org/10.1099/mic.0.046896-0.

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Neisseria meningitidis, the meningococcus, is naturally competent for transformation throughout its growth cycle. The uptake of exogenous DNA into the meningococcus cell during transformation is a multi-step process. Beyond the requirement for type IV pilus expression for efficient transformation, little is known about the neisserial proteins involved in DNA binding, uptake and genome integration. This study aimed to identify and characterize neisserial DNA binding proteins in order to further elucidate the multi-factorial transformation machinery. The meningococcus inner membrane and soluble cell fractions were searched for DNA binding components by employing 1D and 2D gel electrophoresis approaches in combination with a solid-phase overlay assay with DNA substrates. Proteins that bound DNA were identified by MS analysis. In the membrane fraction, multiple components bound DNA, including the neisserial competence lipoprotein ComL. In the soluble fraction, the meningococcus orthologue of the single-stranded DNA binding protein SSB was predominant. The DNA binding activity of the recombinant ComL and SSB proteins purified to homogeneity was verified by electromobility shift assay, and the ComL–DNA interaction was shown to be Mg2+-dependent. In 3D models of the meningococcus ComL and SSB predicted structures, potential DNA binding sites were suggested. ComL was found to co-purify with the outer membrane, directly interacting with the secretin PilQ. The combined use of 1D/2D solid-phase overlay assays with MS analysis was a useful strategy for identifying DNA binding components. The ComL DNA binding properties and outer membrane localization suggest that this lipoprotein plays a direct role in neisserial transformation, while neisserial SSB is a DNA binding protein that contributes to the terminal part of the transformation process.

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Fedorov, R., G. Witte, C. Urbanke, D. J. Manstein, and U. Curth. "3D structure of Thermus aquaticus single-stranded DNA-binding protein gives insight into the functioning of SSB proteins." Nucleic Acids Research 34, no. 22 (November 27, 2006): 6708–17. http://dx.doi.org/10.1093/nar/gkl1002.

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46

Richard, D. J. "Physical and functional interaction of the archaeal single-stranded DNA-binding protein SSB with RNA polymerase." Nucleic Acids Research 32, no. 3 (February 13, 2004): 1065–74. http://dx.doi.org/10.1093/nar/gkh259.

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47

Singh, Amandeep, M. Vijayan, and Umesh Varshney. "Distinct properties of a hypoxia specific paralog of single stranded DNA binding (SSB) protein in mycobacteria." Tuberculosis 108 (January 2018): 16–25. http://dx.doi.org/10.1016/j.tube.2017.10.002.

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48

Greipel, J., G. Maass, and F. Mayer. "Complexes of the single-stranded DNA-binding protein from Escherichia coli (Eco SSB) with poly(dT)." Biophysical Chemistry 26, no. 2-3 (May 1987): 149–61. http://dx.doi.org/10.1016/0301-4622(87)80018-2.

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49

Mohan, Monisha, Vishal Pandya, and Roy Anindya. "Escherichia coli AlkB and single-stranded DNA binding protein SSB interaction explored by Molecular Dynamics Simulation." Journal of Molecular Graphics and Modelling 84 (September 2018): 29–35. http://dx.doi.org/10.1016/j.jmgm.2018.05.007.

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50

Voter, Andrew F., Michael P. Killoran, Gene E. Ananiev, Scott A. Wildman, F. Michael Hoffmann, and James L. Keck. "A High-Throughput Screening Strategy to Identify Inhibitors of SSB Protein–Protein Interactions in an Academic Screening Facility." SLAS DISCOVERY: Advancing the Science of Drug Discovery 23, no. 1 (June 1, 2017): 94–101. http://dx.doi.org/10.1177/2472555217712001.

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Antibiotic-resistant bacterial infections are increasingly prevalent worldwide, and there is an urgent need for novel classes of antibiotics capable of overcoming existing resistance mechanisms. One potential antibiotic target is the bacterial single-stranded DNA binding protein (SSB), which serves as a hub for DNA repair, recombination, and replication. Eight highly conserved residues at the C-terminus of SSB use direct protein–protein interactions (PPIs) to recruit more than a dozen important genome maintenance proteins to single-stranded DNA. Mutations that disrupt PPIs with the C-terminal tail of SSB are lethal, suggesting that small-molecule inhibitors of these critical SSB PPIs could be effective antibacterial agents. As a first step toward implementing this strategy, we have developed orthogonal high-throughput screening assays to identify small-molecule inhibitors of the Klebsiella pneumonia SSB-PriA interaction. Hits were identified from an initial screen of 72,474 compounds using an AlphaScreen (AS) primary screen, and their activity was subsequently confirmed in an orthogonal fluorescence polarization (FP) assay. As an additional control, an FP assay targeted against an unrelated eukaryotic PPI was used to confirm specificity for the SSB-PriA interaction. Nine potent and selective inhibitors produced concentration–response curves with IC50 values of <40 μM, and two compounds were observed to directly bind to PriA, demonstrating the success of this screen strategy.

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