Sequential and Multistep Substrate Interrogation Provides the Scaffold for Specificity in Human Flap Endonuclease 1
Name:
Article-Cell_Repor-Sequential-2013-06-06.pdf
Size:
3.205Mb
Format:
PDF
Description:
Article - Full Text
Type
ArticleKAUST Department
Biological and Environmental Sciences and Engineering (BESE) DivisionBioscience Program
Enrichment Program
Laboratory of DNA Replication and Recombination
Physical Science and Engineering (PSE) Division
Date
2013-06-06Online Publication Date
2013-06-06Print Publication Date
2013-06Permanent link to this record
http://hdl.handle.net/10754/334510
Metadata
Show full item recordAbstract
Human flap endonuclease 1 (FEN1), one of the structure-specific 5' nucleases, is integral in replication, repair, and recombination of cellular DNA. The 5' nucleases share significant unifying features yet cleave diverse substrates at similar positions relative to 5' end junctions. Using single-molecule Förster resonance energy transfer, we find a multistep mechanism that verifies all substrate features before inducing the intermediary-DNA bending step that is believed to unify 5' nuclease mechanisms. This is achieved by coordinating threading of the 5' flap of a nick junction into the conserved capped-helical gateway, overseeing the active site, and bending by binding at the base of the junction. We propose that this sequential and multistep substrate recognition process allows different 5' nucleases to recognize different substrates and restrict the induction of DNA bending to the last common step. Such mechanisms would also ensure the protection ofDNA junctions from nonspecific bending and cleavage. 2013 The Authors.Citation
Sobhy MA, Joudeh LI, Huang X, Takahashi M, Hamdan SM (2013) Sequential and Multistep Substrate Interrogation Provides the Scaffold for Specificity in Human Flap Endonuclease 1. Cell Reports 3: 1785-1794. doi:10.1016/j.celrep.2013.05.001.Publisher
Elsevier BVJournal
Cell ReportsPubMed ID
23746444ae974a485f413a2113503eed53cd6c53
10.1016/j.celrep.2013.05.001
Scopus Count
The following license files are associated with this item:
Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by/3.0/
Related articles
- Flap endonuclease 1.
- Authors: Balakrishnan L, Bambara RA
- Issue date: 2013
- Single-molecule characterization of Fen1 and Fen1/PCNA complexes acting on flap substrates.
- Authors: Craggs TD, Hutton RD, Brenlla A, White MF, Penedo JC
- Issue date: 2014 Feb
- DNA and Protein Requirements for Substrate Conformational Changes Necessary for Human Flap Endonuclease-1-catalyzed Reaction.
- Authors: Algasaier SI, Exell JC, Bennet IA, Thompson MJ, Gotham VJ, Shaw SJ, Craggs TD, Finger LD, Grasby JA
- Issue date: 2016 Apr 8
- Human flap endonuclease structures, DNA double-base flipping, and a unified understanding of the FEN1 superfamily.
- Authors: Tsutakawa SE, Classen S, Chapados BR, Arvai AS, Finger LD, Guenther G, Tomlinson CG, Thompson P, Sarker AH, Shen B, Cooper PK, Grasby JA, Tainer JA
- Issue date: 2011 Apr 15
- Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1.
- Authors: Rashid F, Harris PD, Zaher MS, Sobhy MA, Joudeh LI, Yan C, Piwonski H, Tsutakawa SE, Ivanov I, Tainer JA, Habuchi S, Hamdan SM
- Issue date: 2017 Feb 23
Related items
Showing items related by title, author, creator and subject.
-
Antioxidant enzymes expression in lymphocytes of patients undergoing carotid endarterectomyObradovic, Milan; Zafirovic, Sonja; Essack, Magbubah; Dimitrov, Jelena; Zivkovic, Lada; Spremo-Potparevic, Biljana; Radak, Djordje; Bajic, Vladimir B.; Isenovic, Esma R. (Medical Hypotheses, Elsevier BV, 2019-10-03) [Article]To remedy carotid artery stenosis and prevent stroke surgical intervention is commonly used, and the gold standard being carotid endarterectomy (CEA). During CEA cerebrovascular hemoglobin oxygen saturation decreases and when this decrease reaches critical levels it leads to cerebral hypoxia that causes neuronal damage. One of the proposed mechanism that affects changes during CEA and contribute to acute brain ischemia (ABI) is oxidative stress. The increased production of reactive oxygen species and reactive nitrogen species during ABI may cause an unregulated inflammatory response and further lead to structural and functional injury of neurons. Antioxidant activity are involved in the protection against neuronal damage after cerebral ischemia. We hypothesized that neuronal injury and poor outcomes in patients undergoing CEA may be results of oxidative stress that disturbed function of antioxidant enzymes and contributed to the DNA damage in lymphocytes.
-
Discovering, Characterizing, and Applying Acyl Homoserine Lactone-Quenching Enzymes to Mitigate Microbe-Associated Problems Under Saline ConditionsWang, Tian-Nyu; Guan, Qingtian; Pain, Arnab; Kaksonen, Anna H.; Hong, Pei-Ying (Frontiers in Microbiology, Frontiers Media SA, 2019-04-17) [Article]Quorum quenching (QQ) is proposed as a new strategy for mitigating microbe-associated problems (e.g., fouling, biocorrosion). However, most QQ agents reported to date have not been evaluated for their quenching efficacies under conditions representative of seawater desalination plants, cooling towers or marine aquaculture. In this study, bacterial strains were isolated from Saudi Arabian coastal environments and screened for acyl homoserine lactone (AHL)-quenching activities. Five AHL quenching bacterial isolates from the genera Pseudoalteromonas, Pontibacillus, and Altererythrobacter exhibited high AHL-quenching activity at a salinity level of 58 g/L and a pH of 7.8 at 50°C. This result demonstrates the potential use of these QQ bacteria in mitigating microbe-associated problems under saline and alkaline conditions at high (>37°C) temperatures. Further characterizations of the QQ efficacies revealed two bacterial isolates, namely, Pseudoalteromonas sp. L11 and Altererythrobacter sp. S1-5, which could possess enzymatic QQ activity. The genome sequences of L11 and S1-5 with a homologous screening against reported AHL quenching genes suggest the existence of four possible QQ coding genes in each strain. Specifically, two novel AHL enzymes, AiiAS1-5 and EstS1-5 from Altererythrobacter sp. S1-5, both contain signal peptides and exhibit QQ activity over a broad range of pH, salinity, and temperature values. In particular, AiiAS1-5 demonstrated activity against a wide spectrum of AHL molecules. When tested against three bacterial species, namely, Aeromonas hydrophila, Pseudomonas aeruginosa, and Vibrio alginolyticus, AiiAS1-5 was able to inhibit the motility of all three species under saline conditions. The biofilm formation associated with P. aeruginosa was also significantly inhibited by AiiAS1-5. AiiAS1-5 also reduced the quorum sensing-mediated virulence traits of A. hydrophila, P. aeruginosa, and V. alginolyticus during the mid and late exponential phases of cell growth. The enzyme did not impose any detrimental effects on cell growth, suggesting a lower potential for the target bacterium to develop resistance over long-term exposure. Overall, this study suggested that some QQ enzymes obtained from the bacteria that inhabit saline environments under high temperatures have potential applications in the mitigation of microbe-associated problems.
-
Digestive peptidase evolution in holometabolous insects led to a divergent group of enzymes in LepidopteraDias, Renata O.; Via, Allegra; Brandão, Marcelo M.; Tramontano, Anna; Silva-Filho, Marcio C. (Insect Biochemistry and Molecular Biology, Elsevier BV, 2015-03) [Article]© 2015 Elsevier Ltd. Trypsins and chymotrypsins are well-studied serine peptidases that cleave peptide bonds at the carboxyl side of basic and hydrophobic l-amino acids, respectively. These enzymes are largely responsible for the digestion of proteins. Three primary processes regulate the activity of these peptidases: secretion, precursor (zymogen) activation and substrate-binding site recognition. Here, we present a detailed phylogenetic analysis of trypsins and chymotrypsins in three orders of holometabolous insects and reveal divergent characteristics of Lepidoptera enzymes in comparison with those of Coleoptera and Diptera. In particular, trypsin subsite S1 was more hydrophilic in Lepidoptera than in Coleoptera and Diptera, whereas subsites S2-S4 were more hydrophobic, suggesting different substrate preferences. Furthermore, Lepidoptera displayed a lineage-specific trypsin group belonging only to the Noctuidae family. Evidence for facilitated trypsin auto-activation events were also observed in all the insect orders studied, with the characteristic zymogen activation motif complementary to the trypsin active site. In contrast, insect chymotrypsins did not seem to have a peculiar evolutionary history with respect to their mammal counterparts. Overall, our findings suggest that the need for fast digestion allowed holometabolous insects to evolve divergent groups of peptidases with high auto-activation rates, and highlight that the evolution of trypsins led to a most diverse group of enzymes in Lepidoptera.