scholarly journals Characterization of an SSB–dT25 complex: structural insights into the S-shaped ssDNA binding conformation

RSC Advances ◽  
2019 ◽  
Vol 9 (69) ◽  
pp. 40388-40396 ◽  
Author(s):  
Yen-Hua Huang ◽  
I-Chen Chen ◽  
Cheng-Yang Huang

Single-stranded DNA (ssDNA)-binding proteins (SSBs) play an important role in all DNA-dependent cellular processes, such as DNA replication, recombination, repair, and replication restart.

2021 ◽  
Author(s):  
Simona Graziano ◽  
Nuria Coll-Bonfill ◽  
Barbara Teodoro-Castro ◽  
Sahiti Kuppa ◽  
Jessica Jackson ◽  
...  

Lamins provide a nuclear scaffold for compartmentalization of genome function that is important for genome integrity. The mechanisms whereby lamins regulate genome stability remain poorly understood. Here, we demonstrate a crucial role for A-type lamins preserving the integrity of the replication fork (RF) during replication stress (RS). We find that lamins bind to nascent DNA strands, especially during RS, and ensure the recruitment of fork protective factors RPA and RAD51. These ssDNA-binding proteins, considered the first and second responders to RS respectively, play crucial roles in the stabilization, remodeling and repair of the stalled fork to ensure proper restart and genome stability. Reduced recruitment of RPA and RAD51 upon lamins depletion elicits replication fork instability (RFI) depicted by MRE11 nuclease-mediated degradation of nascent DNA, RS-induced accumulation of DNA damage, and increased sensitivity to replication inhibitors. Importantly, in contrast to cells deficient in various homology recombination repair proteins, the RFI phenotype of lamins-depleted cells is not linked to RF reversal. This suggests that the point of entry of nucleases is not the reversed fork, but regions of ssDNA generated during RS that are not protected by RPA and RAD51. Consistently, RFI in lamins-depleted cells is rescued by forced elevation of the heterotrimeric RPA complex or RAD51. These data unveil a clear involvement of structural nuclear proteins in the protection of ssDNA from the action of nucleases during RS by warranting proper recruitment of ssDNA binding proteins RPA and RAD51 to stalled RFs. In support of this model, we show physical interaction between RPA and lamins. Our study also suggests that RS is a major source of genomic instability in laminopathies and in lamins-depleted tumors.


Author(s):  
Tzu-Yu Lee ◽  
Yi-Ching Li ◽  
Min-Guan Lin ◽  
Chwan-Deng Hsiao ◽  
Hung-Wen Li

DNA damages lead to stalled or collapsed replication forks. Replication restart primosomes re-initiate DNA synthesis at these stalled or collapsed DNA replication forks, which is important for bacterial survival. Primosomal...


2014 ◽  
Vol 70 (a1) ◽  
pp. C1510-C1510
Author(s):  
Maria Miller

The basic region:leucine zipper (bZIP) DNA-binding protein, C/EBPbeta, plays a central role in many vital cellular processes, but is also implicated in tumorigenesis, tumor progression, as well as viral replication within cells. C/EBPbeta binds to specific DNA sites as homo- or hetero-dimers and interacts with other transcription factors to control the transcription of a number of eukaryotic genes. C/EBPbeta is an intrinsically repressed protein that is activated in response to growth factors. This study employs a variety of techniques such as sequence analysis, molecular modeling, X-ray crystallography, and mutagenesis to provide structural insights into the mechanisms that modulate the biological activities of C/EBPbeta. Analysis of the primary structure indicates that C/EBPbeta is a largely disordered protein that consists of unstructured regions that have the potential to fold upon binding to molecular partners as well as regions that retain irregular conformations regardless of their environment. Here, a model of the auto-inhibited form of C/EBPbeta is presented as well as the structural basis of its specific dimerization, DNA-binding, and interactions with the p300 transcriptional co-activator.


2006 ◽  
Vol 27 (5) ◽  
pp. 1592-1601 ◽  
Author(s):  
Naduparambil K. Jacob ◽  
Rachel Lescasse ◽  
Benjamin R. Linger ◽  
Carolyn M. Price

ABSTRACT The POT1/TEBP telomere proteins are a group of single-stranded DNA (ssDNA)-binding proteins that have long been assumed to protect the G overhang on the telomeric 3′ strand. We have found that the Tetrahymena thermophila genome contains two POT1 gene homologs, POT1a and POT1b. The POT1a gene is essential, but POT1b is not. We have generated a conditional POT1a cell line and shown that POT1a depletion results in a monster cell phenotype and growth arrest. However, G-overhang structure is essentially unchanged, indicating that POT1a is not required for overhang protection. In contrast, POT1a is required for telomere length regulation. After POT1a depletion, most telomeres elongate by 400 to 500 bp, but some increase by up to 10 kb. This elongation occurs in the absence of further cell division. The growth arrest caused by POT1a depletion can be reversed by reexpression of POT1a or addition of caffeine. Thus, POT1a is required to prevent a cell cycle checkpoint that is most likely mediated by ATM or ATR (ATM and ATR are protein kinases of the PI-3 protein kinase-like family). Our findings indicate that the essential function of POT1a is to prevent a catastrophic DNA damage response. This response may be activated when nontelomeric ssDNA-binding proteins bind and protect the G overhang.


RSC Advances ◽  
2018 ◽  
Vol 8 (50) ◽  
pp. 28367-28375 ◽  
Author(s):  
Kuan-Lin Chen ◽  
Jen-Hao Cheng ◽  
Chih-Yang Lin ◽  
Yen-Hua Huang ◽  
Cheng-Yang Huang

Single-stranded DNA-binding proteins (SSBs) are essential to cells as they participate in DNA metabolic processes, such as DNA replication, repair, and recombination.


2002 ◽  
Vol 30 (4) ◽  
pp. 397-401 ◽  
Author(s):  
M. Zannis-Hadjopoulos ◽  
O. Novac ◽  
D. Alvarez ◽  
G. B. Price

14-3-3 proteins are conserved multifunctional molecules, involved in many biological processes. Several 14-3-3 isoforms were recently shown to be cruciform DNA-binding proteins, which is a new activity ascribed to the 14-3-3 family. As cruciform-binding proteins, 14-3-3 proteins are putatively involved in the regulation of DNA replication. Inverted repeat sequences that are able to extrude into cruciform structures are a common feature of replication origins in both prokaryotes and eukaryotes. The involvement of cruciform structures in the initiation of DNA replication has been demonstrated. A leading model of 14-3-3 function proposes that they facilitate critical protein-protein interactions, thus serving as a central component of a wide variety of cellular processes.


2018 ◽  
Author(s):  
Jeffrey M. Schaub ◽  
Hongshan Zhang ◽  
Michael M. Soniat ◽  
Ilya J. Finkelstein

AbstractSingle-stranded DNA (ssDNA) is a critical intermediate in all DNA transactions. As ssDNA is more flexible than double-stranded (ds)DNA, interactions with ssDNA-binding proteins (SSBs) may significantly compact or elongate the ssDNA molecule. Here, we develop and characterize low-complexity ssDNA curtains, a high-throughput single-molecule assay to simultaneously monitor protein binding and correlated ssDNA length changes on supported lipid bilayers. Low-complexity ssDNA is generated via rolling circle replication of short synthetic oligonucleotides, permitting control over the sequence composition and secondary structure-forming propensity. One end of the ssDNA is functionalized with a biotin, while the second is fluorescently labeled to track the overall DNA length. Arrays of ssDNA molecules are organized at microfabricated barriers for high-throughput single-molecule imaging. Using this assay, we demonstrate that E. coli SSB drastically and reversibly compacts ssDNA templates upon changes in NaCl concentration. We also examine the interactions between a phosphomimetic RPA and ssDNA. Our results indicate that RPA-ssDNA interactions are not significantly altered by these modifications. We anticipate low-complexity ssDNA curtains will be broadly useful for single-molecule studies of ssDNA-binding proteins involved in DNA replication, transcription and repair.


2020 ◽  
Author(s):  
Olga M. Mazina ◽  
Srinivas Somarowthu ◽  
Lyudmila Y. Kadyrova ◽  
Andrey G. Baranovskiy ◽  
Tahir H. Tahirov ◽  
...  

SUMMARYReplication protein A (RPA), a major eukaryotic ssDNA-binding protein, is essential for all metabolic processes that involve ssDNA including DNA replication, repair, and damage signaling. Surprisingly, we found here that RPA binds RNA in vitro with high affinity. Using native RIP method, we isolated RNA-RPA complexes from human cells. Furthermore, RPA promotes R-loop formation between RNA and homologous dsDNA. R-loops, the three-stranded nucleic acid structure consisting of an RNA-DNA hybrid and the displaced ssDNA strand, are common in human genome. R-loops may play an important role in transcription-coupled homologous recombination and DNA replication restart. We reconstituted the process of replication restart in vitro using RPA-generated R-loops and human DNA polymerases. These findings indicate that RPA may play a role in RNA metabolism and suggest a mechanism of genome maintenance that depends on RPA and RNA.


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