The role of conformational epitopes in the evolutionary divergence of enterovirus D68 clades: A bioinformatics-based study

2021 ◽  
pp. 104992
Author(s):  
Yulu Fang ◽  
Qin Chen ◽  
Hui Wang ◽  
Liping Wang ◽  
Hao Rong ◽  
...  
2017 ◽  
Vol 128 (12) ◽  
pp. e430
Author(s):  
M. Ceccanti ◽  
A. Rubino ◽  
F. Romanzi ◽  
E. Onesti ◽  
G. Tartaglia ◽  
...  

2017 ◽  
Vol 8 ◽  
Author(s):  
Marco Ceccanti ◽  
Emilia Sbardella ◽  
Federica Letteri ◽  
Manuela De Michele ◽  
Anne Falcou ◽  
...  

2019 ◽  
Author(s):  
Mohammed Yousuf Ansari ◽  
Sakshi D. Batra ◽  
Hina Ojha ◽  
Ashish ◽  
Jaya S. Tyagi ◽  
...  

AbstractMycobacterial GroELs namely GroEL1 and GroEL2 belong to the family of molecular chaperones, chaperonins. Chaperonins in Escherichia coli are termed as GroEL and GroES which are encoded by essential genes and are involved in cellular protein folding. GroEL1 has a characteristic Histidine-rich C-terminus contrary to its essential paralog GroEL2 and E. coli GroEL which have hydrophobic (GGM) repeats. Since Histidine richness is likely to be involved in metal binding, in this study we have attempted to decipher the role of GroEL1 protein in chelating metals and the consequent role on M. tuberculosis physiology. Using isothermal titration calorimetry (ITC), we found that GroEL1 binds copper, nickel and cobalt, with the highest binding affinity to copper. Since copper is known to be toxic at higher concentration, we cultured Wild Type M. tuberculosis H37Rv, groEL1 knock-out and groEL1-complemented strain with increasing concentrations of copper. We found that M. tuberculosis groEL1 knock out strain is more sensitive to copper than the wild type. Further hypothesizing that the probable mode of action of copper is by induction of oxidative stress, we attempted to understand the role of GroEL1 in redox silencing and hydroxyl radical mediated DNA damage. We interestingly found through our in vitro studies that GroEL1 is helpful in protection from copper stress through maintaining redox balance and free radical mediated DNA damage. Thus, these results indicate that the duplication of chaperonin genes in M. tuberculosis might have led to their evolutionary divergence and resulted in a functional divergence of chaperonins.


2019 ◽  
Vol 11 (7) ◽  
pp. 1813-1828 ◽  
Author(s):  
Pei-Chen Peng ◽  
Pierre Khoueiry ◽  
Charles Girardot ◽  
James P Reddington ◽  
David A Garfield ◽  
...  

Abstract Transcription factor (TF) binding is determined by sequence as well as chromatin accessibility. Although the role of accessibility in shaping TF-binding landscapes is well recorded, its role in evolutionary divergence of TF binding, which in turn can alter cis-regulatory activities, is not well understood. In this work, we studied the evolution of genome-wide binding landscapes of five major TFs in the core network of mesoderm specification, between Drosophila melanogaster and Drosophila virilis, and examined its relationship to accessibility and sequence-level changes. We generated chromatin accessibility data from three important stages of embryogenesis in both Drosophila melanogaster and Drosophila virilis and recorded conservation and divergence patterns. We then used multivariable models to correlate accessibility and sequence changes to TF-binding divergence. We found that accessibility changes can in some cases, for example, for the master regulator Twist and for earlier developmental stages, more accurately predict binding change than is possible using TF-binding motif changes between orthologous enhancers. Accessibility changes also explain a significant portion of the codivergence of TF pairs. We noted that accessibility and motif changes offer complementary views of the evolution of TF binding and developed a combined model that captures the evolutionary data much more accurately than either view alone. Finally, we trained machine learning models to predict enhancer activity from TF binding and used these functional models to argue that motif and accessibility-based predictors of TF-binding change can substitute for experimentally measured binding change, for the purpose of predicting evolutionary changes in enhancer activity.


2004 ◽  
Vol 78 (17) ◽  
pp. 9224-9232 ◽  
Author(s):  
Zhen-Yong Keck ◽  
Anne Op De Beeck ◽  
Kenneth G. Hadlock ◽  
Jinming Xia ◽  
Ta-Kai Li ◽  
...  

ABSTRACT Mechanisms of virion attachment, interaction with its receptor, and cell entry are poorly understood for hepatitis C virus (HCV) because of a lack of an efficient and reliable in vitro system for virus propagation. Infectious HCV retroviral pseudotype particles (HCVpp) were recently shown to express native E1E2 glycoproteins, as defined in part by HCV human monoclonal antibodies (HMAbs) to conformational epitopes on E2, and some of these antibodies block HCVpp infection (A. Op De Beeck, C. Voisset, B. Bartosch, Y. Ciczora, L. Cocquerel, Z. Y. Keck, S. Foung, F. L. Cosset, and J. Dubuisson, J. Virol. 78:2994-3002, 2004). Why some HMAbs are neutralizing and others are nonneutralizing is looked at in this report by a series of studies to determine the expression of their epitopes on E2 associated with HCVpp and the role of antibody binding affinity. Antibody cross-competition defined three E2 immunogenic domains with neutralizing HMAbs restricted to two domains that were also able to block E2 interaction with CD81, a putative receptor for HCV. HCVpp immunoprecipitation showed that neutralizing and nonneutralizing domains are expressed on E2 associated with HCVpp, and affinity studies found moderate-to-high-affinity antibodies in all domains. These findings support the perspective that HCV-specific epitopes are responsible for functional steps in virus infection, with specific antibodies blocking distinct steps of virus attachment and entry, rather than the perspective that virus neutralization correlates with increased antibody binding to any virion surface site, independent of the epitope recognized by the antibody. Segregation of virus neutralization and sensitivity to low pH to specific regions supports a model of HCV E2 immunogenic domains similar to the antigenic structural and functional domains of other flavivirus envelope E glycoproteins.


2009 ◽  
Vol 78 (1) ◽  
pp. 181-196 ◽  
Author(s):  
Alberto Pascual-García ◽  
David Abia ◽  
Raúl Méndez ◽  
Gonzalo S. Nido ◽  
Ugo Bastolla

2021 ◽  
Author(s):  
Kuohan Li ◽  
Jie Zheng ◽  
Melissa Wirawan ◽  
Trinh Mai Nguyen ◽  
Olga Fedorova ◽  
...  

DRH-3 belongs to the family of duplex RNA-dependent ATPases (DRAs), which include Dicer and RIG-I-like receptors (RLRs). DRH-3 is critically involved in germline development and RNAi-facilitated chromosome segregation via the 22G-siRNA pathway in C. elegans. The molecular understanding of DRH-3 and its function in endogenous RNAi pathways remains elusive. In this study, we solved the crystal structures of the DRH-3 N-terminal domain (NTD) and the C-terminal domains (CTDs) in complex with 5'-triphosphorylated RNAs. The NTD of DRH-3 adopts a distinct fold of tandem Caspase Activation and Recruitment Domains (CARDs) structurally similar to the CARDs of RIG-I and MDA5, suggesting a signaling function in the endogenous RNAi biogenesis. The CTD preferentially recognizes 5'-triphosphorylated double-stranded RNAs bearing the typical features of secondary siRNA transcripts. The full-length DRH-3 displays unique structural dynamics upon binding to RNA duplexes that differ from RIG-I or MDA5. These unique molecular features of DRH-3 help explain its function in RNAi in worms and the evolutionary divergence of the Dicer-like helicases.


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