scholarly journals A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation

2021 ◽  
Author(s):  
Lin Kang ◽  
Guijuan He ◽  
Amanda K. Sharp ◽  
Xiaofeng Wang ◽  
Anne M. Brown ◽  
...  
Keyword(s):  
Selective Sweep ◽  
Rna Virus ◽  
Critical Role ◽  
Glycosylation Site ◽  
Human Cells ◽  
Interspecies Transmission ◽  
Genetic Changes ◽  
Spike Gene ◽  
Synonymous Change ◽  
Virus Genomes

SummaryWhile SARS-CoV-2 likely has animal origins1, the viral genetic changes necessary to adapt this animal-derived ancestral virus to humans are largely unknown, mostly due to low levels of sequence polymorphism and the notorious difficulties in experimental manipulations of coronavirus genomes. We scanned more than 182,000 SARS-CoV-2 genomes for selective sweep signatures and found that a distinct footprint of positive selection is located around a non-synonymous change (A1114G; T372A) within the Receptor-Binding Domain of the Spike protein, which likely played a critical role in overcoming species barriers and accomplishing interspecies transmission from animals to humans. Structural analysis indicated that the substitution of threonine with an alanine in SARS-CoV-2 concomitantly removes a predicted glycosylation site at N370, resulting in more favorable binding predictions to human ACE2, the cellular receptor. Using a novel bacteria-free cloning system for manipulating RNA virus genomes, we experimentally validated that this SARS-CoV-2-unique substitution significantly increases replication in human cells relative to its putative ancestral variant. Notably, this mutation’s impact on virus replication in human cells was much greater than that of the Spike D614G mutant, which has been widely reported to have been selected for during human-to-human transmission2,3.

Molecular Mechanisms of Complement System Proteins and Matrix Metalloproteinases in the Pathogenesis of Age-Related Macular Degeneration

2019 ◽  
Vol 19 (10) ◽  
pp. 705-718 ◽  
Author(s):  
Naima Mansoor ◽  
Fazli Wahid ◽  
Maleeha Azam ◽  
Khadim Shah ◽  
Anneke I. den Hollander ◽  
...  
Keyword(s):  
Matrix Metalloproteinases ◽  
Macular Degeneration ◽  
Complement System ◽  
Molecular Mechanisms ◽  
Critical Role ◽  
Age Related Macular Degeneration ◽  
Genetic Changes ◽  
Complement System Proteins ◽  
Age Related ◽  
Common Genetic Variants

: Age-related macular degeneration (AMD) is an eye disorder affecting predominantly the older people above the age of 50 years in which the macular region of the retina deteriorates, resulting in the loss of central vision. The key factors associated with the pathogenesis of AMD are age, smoking, dietary, and genetic risk factors. There are few associated and plausible genes involved in AMD pathogenesis. Common genetic variants (with a minor allele frequency of >5% in the population) near the complement genes explain 40–60% of the heritability of AMD. The complement system is a group of proteins that work together to destroy foreign invaders, trigger inflammation, and remove debris from cells and tissues. Genetic changes in and around several complement system genes, including the CFH, contribute to the formation of drusen and progression of AMD. Similarly, Matrix metalloproteinases (MMPs) that are normally involved in tissue remodeling also play a critical role in the pathogenesis of AMD. MMPs are involved in the degradation of cell debris and lipid deposits beneath retina but with age their functions get affected and result in the drusen formation, succeeding to macular degeneration. In this review, AMD pathology, existing knowledge about the normal and pathological role of complement system proteins and MMPs in the eye is reviewed. The scattered data of complement system proteins, MMPs, drusenogenesis, and lipofusogenesis have been gathered and discussed in detail. This might add new dimensions to the understanding of molecular mechanisms of AMD pathophysiology and might help in finding new therapeutic options for AMD.

scholarly journals Essential role of IPS-1 in innate immune responses against RNA viruses

2006 ◽  
Vol 203 (7) ◽  
pp. 1795-1803 ◽  
Author(s):  
Himanshu Kumar ◽  
Taro Kawai ◽  
Hiroki Kato ◽  
Shintaro Sato ◽  
Ken Takahashi ◽  
...  
Keyword(s):  
Rna Viruses ◽  
Rna Virus ◽  
Critical Role ◽  
Nuclear Factor Κb ◽  
Type I ◽  
Innate Immune Responses ◽  
Antiviral Responses ◽  
Deficient Mice

IFN-β promoter stimulator (IPS)-1 was recently identified as an adapter for retinoic acid–inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (Mda5), which recognize distinct RNA viruses. Here we show the critical role of IPS-1 in antiviral responses in vivo. IPS-1–deficient mice showed severe defects in both RIG-I– and Mda5-mediated induction of type I interferon and inflammatory cytokines and were susceptible to RNA virus infection. RNA virus–induced interferon regulatory factor-3 and nuclear factor κB activation was also impaired in IPS-1–deficient cells. IPS-1, however, was not essential for the responses to either DNA virus or double-stranded B-DNA. Thus, IPS-1 is the sole adapter in both RIG-I and Mda5 signaling that mediates effective responses against a variety of RNA viruses.

scholarly journals A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation

Cell ◽  
2021 ◽  
Author(s):  
Lin Kang ◽  
Guijuan He ◽  
Amanda K. Sharp ◽  
Xiaofeng Wang ◽  
Anne M. Brown ◽  
...  
Keyword(s):  
Selective Sweep ◽  
Human Adaptation ◽  
Spike Gene

Genetic changes during immortalization of human cells

1995 ◽  
Vol 3 (6) ◽  
pp. 299-306
Author(s):  
Roger R. Reddel ◽  
Tracy M. Bryan ◽  
Eileen M. Rogan ◽  
Jane R. Noble ◽  
Kenneth Maclean ◽  
...  
Keyword(s):  
Human Cells ◽  
Genetic Changes

scholarly journals Extrachromosomal Histone H2B Mediates Innate Antiviral Immune Responses Induced by Intracellular Double-Stranded DNA

2009 ◽  
Vol 84 (2) ◽  
pp. 822-832 ◽  
Author(s):  
Kouji Kobiyama ◽  
Fumihiko Takeshita ◽  
Nao Jounai ◽  
Asako Sakaue-Sawano ◽  
Atsushi Miyawaki ◽  
...  
Keyword(s):  
Immune Responses ◽  
Rna Virus ◽  
Cellular Signaling ◽  
Helical Structure ◽  
Human Cells ◽  
Type I Interferons ◽  
Type I ◽  
Histone H2b ◽  
Dna Viruses ◽  
Double Stranded Dna

ABSTRACT Fragments of double-stranded DNA (dsDNA) forming a right-handed helical structure (B-DNA) stimulate cells to produce type I interferons (IFNs). While an adaptor molecule, IFN-β promoter stimulator 1 (IPS-1), mediates dsDNA-induced cellular signaling in human cells, the underlying molecular mechanism is not fully understood. Here, we demonstrate that the extrachromosomal histone H2B mediates innate antiviral immune responses in human cells. H2B physically interacts with IPS-1 through the association with a newly identified adaptor, CIAO (COOH-terminal importin 9-related adaptor organizing histone H2B and IPS-1), to transmit the cellular signaling for dsDNA but not immunostimulatory RNA. Extrachromosomal histone H2B was biologically crucial for cell-autonomous responses to protect against multiplication of DNA viruses but not an RNA virus. Thus, the present findings provide evidence indicating that the extrachromosomal histone H2B is engaged in the signaling pathway initiated by dsDNA to trigger antiviral innate immune responses.

scholarly journals Critical Role of Apoptotic Speck Protein Containing a Caspase Recruitment Domain (ASC) and NLRP3 in Causing Necrosis and ASC Speck Formation Induced byPorphyromonas gingivalisin Human Cells

2009 ◽  
Vol 182 (4) ◽  
pp. 2395-2404 ◽  
Author(s):  
Max Tze-Han Huang ◽  
Debra J. Taxman ◽  
Elizabeth A. Holley-Guthrie ◽  
Chris B. Moore ◽  
Stephen B. Willingham ◽  
...  
Keyword(s):  
Critical Role ◽  
Human Cells ◽  
Caspase Recruitment Domain

scholarly journals Viral strategies of manipulating autophagy to benefit infection

2019 ◽  
Author(s):  
Ho Him Wong ◽  
Sumana Sanyal
Keyword(s):  
Rna Virus ◽  
Critical Role ◽  
Intracellular Pathogens ◽  
Virus Infections ◽  
Central Process ◽  
Conservation Of Energy ◽  
Evolutionarily Conserved ◽  
Cellular Defence ◽  
Host Metabolism ◽  
Fine Tune

Autophagy is an evolutionarily conserved central process in host metabolism. Among its major functions are conservation of energy during starvation, recycling organelles, and turnover of long-lived proteins. Besides, autophagy plays a critical role in removing intracellular pathogens and very likely represents a primordial intrinsic cellular defence mechanism. More recent findings indicate that it has not only retained its ability to degrade intracellular pathogens, but also functions to augment and fine tune antiviral immune responses. Interestingly, viruses have also co-evolved strategies to manipulate this pathway and use it to their advantage. Particularly intriguing is infection-dependent activation of autophagy with positive stranded (+)RNA virus infections, which benefit from the pathway without succumbing to lysosomal degradation. In this review we summarise recent data on viral manipulation of autophagy, with a particular emphasis on +RNA viruses and highlight key unanswered questions in the field that we believe merit further attention.

scholarly journals A functional investigation of the suppression of CpG and UpA dinucleotide frequencies in plant RNA virus genomes

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ahmad Ibrahim ◽  
Jelke Fros ◽  
Andre Bertran ◽  
Ferdyansyah Sechan ◽  
Valerie Odon ◽  
...  
Keyword(s):  
Rna Virus ◽  
Plant Viruses ◽  
Tobacco Plants ◽  
Protein Coding ◽  
Antiviral Responses ◽  
Fold Reduction ◽  
Analogous Process ◽  
Systemic Spread ◽  
Functional Investigation ◽  
Virus Genomes

AbstractFrequencies of CpG and UpA dinucleotides in most plant RNA virus genomes show degrees of suppression comparable to those of vertebrate RNA viruses. While pathways that target CpG and UpAs in HIV-1 and echovirus 7 genomes and restrict their replication have been partly characterised, whether an analogous process drives dinucleotide underrepresentation in plant viruses remains undetermined. We examined replication phenotypes of compositionally modified mutants of potato virus Y (PVY) in which CpG or UpA frequencies were maximised in non-structural genes (including helicase and polymerase encoding domains) while retaining protein coding. PYV mutants with increased CpG dinucleotide frequencies showed a dose-dependent reduction in systemic spread and pathogenicity and up to 1000-fold attenuated replication kinetics in distal sites on agroinfiltration of tobacco plants (Nicotiana benthamiana). Even more extraordinarily, comparably modified UpA-high mutants displayed no pathology and over a million-fold reduction in replication. Tobacco plants with knockdown of RDP6 displayed similar attenuation of CpG- and UpA-high mutants suggesting that restriction occurred independently of the plant siRNA antiviral responses. Despite the evolutionary gulf between plant and vertebrate genomes and encoded antiviral strategies, these findings point towards the existence of novel virus restriction pathways in plants functionally analogous to innate defence components in vertebrate cells.

scholarly journals Autophagy is involved in assisting the replication of Bamboo mosaic virus in Nicotiana benthamiana

2019 ◽  
Vol 70 (18) ◽  
pp. 4657-4670 ◽  
Author(s):  
Ying-Ping Huang ◽  
Ying-Wen Huang ◽  
Yung-Jen Hsiao ◽  
Siou-Cen Li ◽  
Yau-Huei Hsu ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Nicotiana Benthamiana ◽  
Fluorescent Protein ◽  
Rna Virus ◽  
Critical Role ◽  
Viral Rna ◽  
Autophagosome Formation ◽  
Orange Fluorescent Protein ◽  
Positive Sense ◽  
Trigger Cell Death

Abstract Autophagy plays a critical role in plants under biotic stress, including the response to pathogen infection. We investigated whether autophagy-related genes (ATGs) are involved in infection with Bamboo mosaic virus (BaMV), a single-stranded positive-sense RNA virus. Initially, we observed that BaMV infection in Nicotiana benthamiana leaves upregulated the expression of ATGs but did not trigger cell death. The induction of ATGs, which possibly triggers autophagy, increased rather than diminished BaMV accumulation in the leaves, as revealed by gene knockdown and transient expression experiments. Furthermore, the inhibitor 3-methyladenine blocked autophagosome formation and the autophagy inducer rapamycin, which negatively and positively affected BaMV accumulation, respectively. Pull-down experiments with an antibody against orange fluorescent protein (OFP)-NbATG8f, an autophagosome marker protein, showed that both plus- and minus-sense BaMV RNAs could associate with NbATG8f. Confocal microscopy revealed that ATG8f-enriched vesicles possibly derived from chloroplasts contained both the BaMV viral RNA and its replicase. Thus, BaMV infection may induce the expression of ATGs possibly via autophagy to selectively engulf a portion of viral RNA-containing chloroplast. Virus-induced vesicles enriched with ATG8f could provide an alternative site for viral RNA replication or a shelter from the host silencing mechanism.

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