scholarly journals Site-Specific Topoisomerase I-Mediated DNA Cleavage Induced by Nogalamycin:  A Potential Role of Ligand-Induced DNA Bending at a Distal Site†

Biochemistry ◽  
2000 ◽  
Vol 39 (32) ◽  
pp. 9928-9934 ◽  
Author(s):  
Sai-Peng Sim ◽  
Daniel S. Pilch ◽  
Leroy F. Liu
Keyword(s):  
Dna Cleavage ◽  
Topoisomerase I ◽  
Potential Role ◽  
Dna Bending ◽  
Site Specific ◽  
Distal Site

scholarly journals Real-time observation of flexible domain movements in Cas9

2017 ◽  
Author(s):  
Saki Osuka ◽  
Kazushi Isomura ◽  
Shohei Kajimoto ◽  
Tomotaka Komori ◽  
Hiroshi Nishimasu ◽  
...  
Keyword(s):  
Single Molecule ◽  
Dna Cleavage ◽  
Potential Role ◽  
Domain Architecture ◽  
Guide Rna ◽  
Single Molecule Fret ◽  
Target Dna ◽  
Time Observation ◽  
Real Time Observation

ABSTRACTThe CRISPR-associated protein Cas9 is a widely used genome editing tool that recognizes and cleaves target DNA through the assistance of a single-guide RNA (sgRNA). Structural studies have demonstrated the multi-domain architecture of Cas9 and sequential domain movements upon binding to the sgRNA and the target DNA. These studies also hinted at the flexibility between domains, but whether these flexible movements occur in solution is unclear. Here, we directly observed dynamic fluctuations of multiple Cas9 domains, using single-molecule FRET. The flexible domain movements allow Cas9 to adopt transient conformations beyond those captured in the crystal structures. Importantly, the HNH nuclease domain in Cas9 only accessed the DNA cleavage position during such flexible movements, suggesting the importance of this flexibility in the DNA cleavage process. Our FRET data also revealed the conformational flexibility of apo-Cas9, which may play a role in the assembly with the sgRNA. Collectively, our results highlight the potential role of domain fluctuations in driving Cas9-catalyzed DNA cleavage.

scholarly journals A conserved SUMO pathway repairs topoisomerase DNA-protein cross-links by engaging ubiquitin-mediated proteasomal degradation

2020 ◽  
Vol 6 (46) ◽  
pp. eaba6290 ◽  
Author(s):  
Yilun Sun ◽  
Lisa M. Miller Jenkins ◽  
Yijun P. Su ◽  
Karin C. Nitiss ◽  
John L. Nitiss ◽  
...  
Keyword(s):  
Ubiquitin Ligase ◽  
Dna Cleavage ◽  
Topoisomerase I ◽  
Human Cells ◽  
Sumo Modification ◽  
Sumo Ligase ◽  
Subsequent Degradation ◽  
Cross Links ◽  
Sumo Pathway

Topoisomerases form transient covalent DNA cleavage complexes to perform their reactions. Topoisomerase I cleavage complexes (TOP1ccs) are trapped by camptothecin and TOP2ccs by etoposide. Proteolysis of the trapped topoisomerase DNA-protein cross-links (TOP-DPCs) is a key step for some pathways to repair these lesions. We describe a pathway that features a prominent role of the small ubiquitin-like modifier (SUMO) modification for both TOP1- and TOP2-DPC repair. Both undergo rapid and sequential SUMO-2/3 and SUMO-1 modifications in human cells. The SUMO ligase PIAS4 is required for these modifications. RNF4, a SUMO-targeted ubiquitin ligase (STUbL), then ubiquitylates the TOP-DPCs for their subsequent degradation by the proteasome. This pathway is conserved in yeast with Siz1 and Slx5-Slx8, the orthologs of human PIAS4 and RNF4.

DYNAMICS OF ENZYME-INDUCED DNA BENDING

2006 ◽  
Vol 01 (04) ◽  
pp. 343-352
Author(s):  
PETER LENZ ◽  
JEAN-FRANÇOIS JOANNY ◽  
JACQUES PROST
Keyword(s):  
Dna Cleavage ◽  
Dna Bending ◽  
Adsorption Site ◽  
Time Dependent ◽  
Cleavage Rate ◽  
Quasistatic Approximation ◽  
Stress Propagation ◽  
Dna Shape ◽  
Surrounding Fluid

We theoretically study the role of enzyme-induced bending in DNA-cleavage processes. In our model the enzyme bends DNA at its adsorption site leading to stress propagation along the filaments. Since this process is slow the time-dependent DNA-shape can be calculated in a quasistatic approximation. This allows to determine the range of parameters for which strong DNA bending occurs. For enzymes which cut by bending only the cleavage rate is found to depend crucially on the viscosity of the surrounding fluid and the length of the cut DNA segment.

The Role of DNA Bending in Flp-mediated Site-specific Recombination

1995 ◽  
Vol 251 (4) ◽  
pp. 493-506 ◽  
Author(s):  
Karen H. Luetke ◽  
Paul D. Sadowski
Keyword(s):  
Dna Bending ◽  
Site Specific ◽  
Site Specific Recombination

scholarly journals Geotourism and Climate Change

2014 ◽  
Vol 29 (2) ◽  
pp. 77-86 ◽  
Author(s):  
C. Michael Hall ◽  
Jarkko Saarinen
Keyword(s):  
Climate Change ◽  
Potential Role ◽  
Polar Regions ◽  
Geological Time ◽  
Specific Level ◽  
Site Specific ◽  
Physical Systems ◽  
Geomorphological Heritage ◽  
A Site

Geotourism has achieved considerable prominence since the early 1990s as a means of conserving geological and geomorphological heritage. However, most accounts of the effects of geotourism are at a site-specific level while interpretation tends to focus on deep geological time rather than the Anthropocene. This restriction in consideration of time and space has meant that the broader effects of geotourism-related travel throughout the tourism system have been ignored, along with the potential role of climate change in affecting geosites and attractions. These issues are discussed with respect to the paradoxes of geotourism in polar regions with the polar cryospheric environment being both threatened by climate change yet simultaneously becoming more accessible and attractive to tourists. The article concludes that, like any form of tourism, geotourism needs to be understood within the broader context of tourism and physical systems rather than in isolation in order to fully access its contribution to geoconservation.

scholarly journals Syringopeptin Contributes to the Virulence of Pseudomonas fuscovaginae, Based on sypA Biosynthesis Mutant Analysis

2020 ◽  
Vol 110 (4) ◽  
pp. 780-789 ◽  
Author(s):  
Nirodha Weeraratne ◽  
Benjamin J. Stodart ◽  
Vittorio Venturi ◽  
Monica Hofte ◽  
Gia Khuong Hoang Hua ◽  
...  
Keyword(s):  
Potential Role ◽  
Brown Rot ◽  
Limited Information ◽  
Rice Seedlings ◽  
Site Specific ◽  
Disease Symptoms ◽  
Chromatography Analysis ◽  
Stages Of Growth ◽  
A Site

Pseudomonas fuscovaginae, first reported from Japan in 1976, is now present in many agroecological regions around the world; it causes sheath brown rot of rice and is reported as a pathogen of a broad range of hosts. The pathogen can infect rice plants at all stages of growth and is known to cause significant losses due to grain discoloration, poor spike emergence and panicle sterility. Limited information is available on the virulence and mechanisms of pathogenicity for P. fuscovaginae. To address this, an analysis of genomes was conducted, which identified the presence of a gene showing homology to one of the genes contributing to syringopeptin synthetase (sypA) of P. syringae pv. syringae. To study the potential role of this gene in the virulence and pathogenicity of P. fuscovaginae, a site-specific mutation was created. Following inoculation of seeds and plantlets of rice and wheat with P. fuscovaginae wild types and their respective mutants, we demonstrated that the mutation significantly reduced virulence. This was evident on rice and wheat inoculated with mutants causing a significantly higher number of roots, length of roots and seedling height compared with their respective wild types. Characteristic disease symptoms of necrotic lesions were significantly less in rice seedlings infected with bacterial suspensions of mutants indicating a reduction in virulence. Chromatography analysis of bacterial exudates showed suppression of synthesis of metabolites analogous to syringopeptin in the mutants. These data demonstrate that the protein encoded by this sypA homolog gene is a major virulence determinant of P. fuscovaginae.

POPDC proteins and cardiac function

2019 ◽  
Vol 47 (5) ◽  
pp. 1393-1404 ◽  
Author(s):  
Thomas Brand
Keyword(s):  
Potential Role ◽  
Striated Muscle ◽  
Short Review ◽  
Effector Proteins ◽  
Muscle Disease ◽  
Disease Genes ◽  
Protein Protein Interaction ◽  
Interaction Partners ◽  
And Function

Abstract The Popeye domain-containing gene family encodes a novel class of cAMP effector proteins in striated muscle tissue. In this short review, we first introduce the protein family and discuss their structure and function with an emphasis on their role in cyclic AMP signalling. Another focus of this review is the recently discovered role of POPDC genes as striated muscle disease genes, which have been associated with cardiac arrhythmia and muscular dystrophy. The pathological phenotypes observed in patients will be compared with phenotypes present in null and knockin mutations in zebrafish and mouse. A number of protein–protein interaction partners have been discovered and the potential role of POPDC proteins to control the subcellular localization and function of these interacting proteins will be discussed. Finally, we outline several areas, where research is urgently needed.

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