scholarly journals Mapping the Non-Structural Transmembrane Proteins of SARS-CoV-2

2020 ◽  
Author(s):  
Sunil Thomas
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Drug Targets ◽  
Transmembrane Proteins ◽  
Host Immunity ◽  
Open Reading Frames ◽  
Structural Proteins ◽  
Wild Animals ◽  
Cell Organelles ◽  
Enveloped Virus ◽  
Reading Frames

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for the disease COVID-19 has wreaked havoc on the health and economy of humanity. In addition, the disease is observed in domestic and wild animals. The disease has impacted directly and indirectly every corner of the planet. Currently, there are no vaccines and effective therapies for COVID-19. SARS-CoV-2 is an enveloped virus with a single-stranded RNA genome of 29.8 kb. More than two-thirds of the genome comprises Orf1ab encoding 16 non-structural proteins (nsps) followed by mRNAs encoding structural proteins, spike (S), envelop (E), membrane (M), and nucleocapsid (N). These genes are interspaced with several accessory genes (open reading frames [Orf] 3a, 3b, 6, 7a, 7b, 8, 9b, 9c and 10). The functions of these proteins are of particular interest for understanding the pathogenesis of SARS-CoV-2. Several of the nsps (nsp3, nsp4, nsp6) and Orf3a are transmembrane proteins involved in regulating the host immunity, modifying host cell organelles for viral replication and escape and hence considered drug targets. In this paper we report mapping the transmembrane structure of the non-structural proteins of SARS-CoV-2.

scholarly journals Overexpression of 7a, a Protein Specifically Encoded by the Severe Acute Respiratory Syndrome Coronavirus, Induces Apoptosis via a Caspase-Dependent Pathway

2004 ◽  
Vol 78 (24) ◽  
pp. 14043-14047 ◽  
Author(s):  
Yee-Joo Tan ◽  
Burtram C. Fielding ◽  
Phuay-Yee Goh ◽  
Shuo Shen ◽  
Timothy H. P. Tan ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Cell Lines ◽  
Cellular Localization ◽  
Viral Proteins ◽  
Open Reading Frames ◽  
Structural Proteins ◽  
Dependent Pathway ◽  
Reading Frames ◽  
Viral Structural Proteins

ABSTRACT Besides genes that are homologous to proteins found in other coronaviruses, the severe acute respiratory syndrome coronavirus genome also contains nine other potential open reading frames. Previously, we have characterized the expression and cellular localization of two of these “accessory” viral proteins, 3a (previously termed U274) and 7a (previously termed U122). In this study, we further examined whether they can induce apoptosis, which has been observed clinically. We showed that the overexpression of 7a, but not of 3a or the viral structural proteins, nucleocapsid, membrane, and envelope, induces apoptosis. 7a induces apoptosis via a caspase-dependent pathway and in cell lines derived from different organs, including lung, kidney, and liver.

scholarly journals Novel open reading frames in human accelerated regions and transposable elements reveal new leads to understand schizophrenia and bipolar disorder

2021 ◽  
Author(s):  
Chaitanya Erady ◽  
Krishna Amin ◽  
Temiloluwa O. A. E. Onilogbo ◽  
Jakub Tomasik ◽  
Rebekah Jukes-Jones ◽  
...  
Keyword(s):  
Bipolar Disorder ◽  
Transposable Elements ◽  
Drug Targets ◽  
Rapid Evolution ◽  
Open Reading Frames ◽  
Biological Regulation ◽  
Genomic Features ◽  
Species Specific ◽  
Human Accelerated Regions ◽  
Reading Frames

AbstractSchizophrenia (SCZ) and bipolar disorder are debilitating neuropsychiatric disorders arising from a combination of environmental and genetic factors. Novel open reading frames (nORFs) are genomic loci that give rise to previously uncharacterized transcripts and protein products. In our previous work, we have shown that nORFs can be biologically regulated and that they may play a role in cancer and rare diseases. More importantly, we have shown that nORFs may emerge in accelerated regions of the genome giving rise to species-specific functions. We hypothesize that nORFs represent a potentially important group of biological factors that may contribute to SCZ and bipolar disorder pathophysiology. Human accelerated regions (HARs) are genomic features showing human-lineage-specific rapid evolution that may be involved in biological regulation and have additionally been found to associate with SCZ genes. Transposable elements (TEs) are another set of genomic features that have been shown to regulate gene expression. As with HARs, their relevance to SCZ has also been suggested. Here, nORFs are investigated in the context of HARs and TEs. This work shows that nORFs whose expression is disrupted in SCZ and bipolar disorder are in close proximity to HARs and TEs and that some of them are significantly associated with SCZ and bipolar disorder genomic hotspots. We also show that nORF encoded proteins can form structures and potentially constitute novel drug targets.

scholarly journals A Novel Severe Acute Respiratory Syndrome Coronavirus Protein, U274, Is Transported to the Cell Surface and Undergoes Endocytosis

2004 ◽  
Vol 78 (13) ◽  
pp. 6723-6734 ◽  
Author(s):  
Yee-Joo Tan ◽  
Eileen Teng ◽  
Shuo Shen ◽  
Timothy H. P. Tan ◽  
Phuay-Yee Goh ◽  
...  
Keyword(s):  
Amino Acids ◽  
Severe Acute Respiratory Syndrome ◽  
Cell Surface ◽  
Open Reading Frames ◽  
Structural Proteins ◽  
Replicase Gene ◽  
Subgenomic Rna ◽  
C Terminus ◽  
Infected Cells ◽  
Potential Orfs

ABSTRACT The severe acute respiratory syndrome coronavirus (SARS-CoV) genome contains open reading frames (ORFs) that encode for several genes that are homologous to proteins found in all known coronaviruses. These are the replicase gene 1a/1b and the four structural proteins, nucleocapsid (N), spike (S), membrane (M), and envelope (E), and these proteins are expected to be essential for the replication of the virus. In addition, this genome also contains nine other potential ORFs varying in length from 39 to 274 amino acids. The largest among these is the first ORF of the second longest subgenomic RNA, and this protein (termed U274 in the present study) consists of 274 amino acids and contains three putative transmembrane domains. Using antibody specific for the C terminus of U274, we show U274 to be expressed in SARS-CoV-infected Vero E6 cells and, in addition to the full-length protein, two other processed forms were also detected. By indirect immunofluorescence, U274 was localized to the perinuclear region, as well as to the plasma membrane, in both transfected and infected cells. Using an N terminus myc-tagged U274, the topology of U274 and its expression on the cell surface were confirmed. Deletion of a cytoplasmic domain of U274, which contains Yxxφ and diacidic motifs, abolished its transport to the cell surface. In addition, U274 expressed on the cell surface can internalize antibodies from the culture medium into the cells. Coimmunoprecipitation experiments also showed that U274 could interact specifically with the M, E, and S structural proteins, as well as with U122, another protein that is unique to SARS-CoV.

scholarly journals Identification of Trichoplusia ni ascovirus 2c virion structural proteins

2007 ◽  
Vol 88 (8) ◽  
pp. 2194-2197 ◽  
Author(s):  
Liwang Cui ◽  
Xiaowen Cheng ◽  
Lianchao Li ◽  
Jianyong Li
Keyword(s):  
Mass Spectrometry ◽  
Trichoplusia Ni ◽  
Major Capsid Protein ◽  
Protein Sequences ◽  
Open Reading Frames ◽  
Structural Proteins ◽  
Tandem Mass ◽  
Double Stranded Dna ◽  
Coomassie Blue ◽  
Reading Frames

Ascoviruses are a family of insect viruses with circular, double-stranded DNA genomes. With the sequencing of the Trichoplusia ni ascovirus 2c (TnAV-2c) genome, the virion structural proteins were identified by using tandem mass spectrometry. From at least eight protein bands visible on a Coomassie blue-stained gel of TnAV-2c virion proteins, seven bands generated protein sequences that matched predicted open reading frames (ORFs) in the genome, i.e. ORFs 2, 43, 115, 141, 142, 147 and 153. Among these ORFs, only ORF153, encoding the major capsid protein, has been characterized previously.

scholarly journals The SARS-CoV-2 antibody landscape is lower in magnitude for structural proteins, diversified for accessory proteins and stable long-term in children

2021 ◽  
Author(s):  
Asmaa Hachim ◽  
Haogao Gu ◽  
Otared Kavian ◽  
Mike YW Kwan ◽  
Wai-hung Chan ◽  
...  
Keyword(s):  
Antibody Response ◽  
Principal Component ◽  
Humoral Response ◽  
Open Reading Frames ◽  
Clinical Severity ◽  
Structural Proteins ◽  
Accessory Proteins ◽  
Longitudinal Sampling ◽  
Reading Frames

AbstractBackgroundChildren are less clinically affected by SARS-CoV-2 infection than adults with the majority of cases being mild or asymptomatic and the differences in infection outcomes are poorly understood. The kinetics, magnitude and landscape of the antibody response may impact the clinical severity and serological diagnosis of COVID-19. Thus, a comprehensive investigation of the antibody landscape in children and adults is needed.MethodsWe tested 254 plasma from 122 children with symptomatic and asymptomatic SARS-CoV-2 infections in Hong Kong up to 206 days post symptom onset, including 146 longitudinal samples from 58 children. Adult COVID-19 patients and pre-pandemic controls were included for comparison. We assessed antibodies to a 14-wide panel of SARS-CoV-2 structural and accessory proteins by Luciferase Immunoprecipitation System (LIPS).FindingsChildren have lower levels of Spike and Nucleocapsid antibodies than adults, and their cumulative humoral response is more expanded to accessory proteins (NSP1 and Open Reading Frames (ORFs)). Sensitive serology using the three N, ORF3b, ORF8 antibodies can discriminate COVID-19 in children. Principal component analysis revealed distinct serological signatures in children and the highest contribution to variance were responses to non-structural proteins ORF3b, NSP1, ORF7a and ORF8. Longitudinal sampling revealed maintenance or increase of antibodies for at least 6 months, except for ORF7b antibodies which showed decline. It was interesting to note that children have higher antibody responses towards known IFN antagonists: ORF3b, ORF6 and ORF7a. The diversified SARS-CoV-2 antibody response in children may be an important factor in driving control of SARS-CoV-2 infection.

scholarly journals Characterization of accessory genes in coronavirus genomes

2020 ◽  
Author(s):  
Christian Jean Michel ◽  
Claudine Mayer ◽  
Olivier Poch ◽  
Julie Dawn Thompson
Keyword(s):  
Drug Targets ◽  
Variable Number ◽  
Open Reading Frames ◽  
Accessory Proteins ◽  
Accessory Genes ◽  
Genome Annotations ◽  
Virus Genomes ◽  
Potential Orfs ◽  
Reading Frames

Abstract Background: The Covid19 infection is caused by the SARS-CoV-2 virus, a novel member of the coronavirus (CoV) family. CoV genomes code for a ORF1a / ORF1ab polyprotein and four structural proteins widely studied as major drug targets. The genomes also contain a variable number of open reading frames (ORFs) coding for accessory proteins that are not essential for virus replication, but appear to have a role in pathogenesis. The accessory proteins have been less well characterized and are difficult to predict by classical bioinformatics methods.Methods: We propose a computational tool GOFIX to characterize potential ORFs in virus genomes. In particular, ORF coding potential is estimated by searching for enrichment in motifs of the X circular code, that is known to be over-represented in the reading frames of viral genes.Results: We applied GOFIX to study the SARS-CoV-2 and related genomes including SARS-CoV and SARS-like viruses from bat, civet and pangolin hosts, focusing on the accessory proteins. Our analysis provides evidence supporting the presence of overlapping ORFs 7b, 9b and 9c in all the genomes and thus helps to resolve some differences in current genome annotations. In contrast, we predict that ORF3b is not functional in all genomes. Novel putative ORFs were also predicted, including a truncated form of the ORF10 previously identified in SARS-CoV-2 and a little known ORF overlapping the Spike protein in Civet-CoV and SARS-CoV.Conclusions: Our findings contribute to characterizing sequence properties of accessory genes of SARS coronaviruses, and especially the newly acquired genes making use of overlapping reading frames.

scholarly journals Genome Sequences of Two GH Clade SARS-CoV-2 Strains Isolated from Patients with COVID-19 in South Korea

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Minwoo Kim ◽  
Youn-Jung Lee ◽  
Jae Sun Yoon ◽  
Jin Young Ahn ◽  
Jung Ho Kim ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
South Korea ◽  
Open Reading Frames ◽  
Untranslated Regions ◽  
Genome Sequences ◽  
Nonsynonymous Substitutions ◽  
Sequence Identity ◽  
Reading Frames

ABSTRACT We report the genome sequences of two GH clade severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains isolated from nasopharyngeal swabs from patients with coronavirus disease 2019 (COVID-19) in South Korea. These strains had two mutations in the untranslated regions and seven nonsynonymous substitutions in open reading frames, compared with Wuhan/Hu-1/2019, showing 99.96% sequence identity.

scholarly journals Characterization of Nora Virus Structural Proteins via Western Blot Analysis

Scientifica ◽  
2016 ◽  
Vol 2016 ◽  
pp. 1-8 ◽  
Author(s):  
Brad L. Ericson ◽  
Darby J. Carlson ◽  
Kimberly A. Carlson
Keyword(s):  
Western Blot ◽  
Open Reading Frames ◽  
Structural Proteins ◽  
Polypeptide Composition ◽  
Virus Particles ◽  
E Coli ◽  
Nora Virus ◽  
Monospecific Antisera ◽  
Reading Frames

Nora virus is a single stranded RNA picorna-like virus with four open reading frames (ORFs). The coding potentials of the ORFs are not fully characterized, but ORF3 and ORF4 are believed to encode the capsid proteins (VP3, VP4a, VP4b, and VP4c) comprising the virion. To determine the polypeptide composition of Nora virus virions, polypeptides from purified virus were compared to polypeptides detected in Nora virus infectedDrosophila melanogaster. Nora virus was purified from infected flies and used to challenge mice for the production of antisera.ORF3,ORF4a,ORF4b, andORF4cwere individually cloned and expressed inE. coli; resultant recombinant proteins purified and were used to make monospecific antisera. Antisera were evaluated via Western blot against whole virus particles and Nora virus infected fly lysates. Viral purification yielded two particle types with densities of ~1.31 g/mL (empty particles) and ~1.33 g/mL (complete virions). Comparison of purified virus polypeptide composition to Nora virus infectedD. melanogasterlysate showed the number of proteins in infected cell lysates is less than purified virus. Our results suggest the virion is composed of 6 polypeptides, VP3, VP4a, two forms of VP4b, and two forms of VP4c. This polypeptide composition is similar to other small RNA insect viruses.

scholarly journals The R-Type Pyocin of Pseudomonas aeruginosa C Is a Bacteriophage Tail-Like Particle That Contains Single-Stranded DNA

1999 ◽  
Vol 67 (2) ◽  
pp. 717-725 ◽  
Author(s):  
Frank K. N. Lee ◽  
Kathleen C. Dudas ◽  
Julie A. Hanson ◽  
M. Bud Nelson ◽  
Philip T. LoVerde ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Genomic Dna ◽  
Open Reading Frames ◽  
Structural Proteins ◽  
Chromosomal Dna ◽  
Unusual Structure ◽  
Single Stranded Dna ◽  
Complementary Oligonucleotide ◽  
Oligonucleotide Hybridization ◽  
Reading Frames

ABSTRACT Pseudomonas aeruginosa R-type pyocin particles have been described as bacteriocins that resemble bacteriophage tail-like structures. Because of their unusual structure, we reexamined whether they contained nucleic acids. Our data indicated that pyocin particles isolated from P. aeruginosa C (pyocin C) contain DNA. Probes generated from this DNA by the random-primer extension method hybridized to distinct bands in restriction endonuclease-digestedP. aeruginosa C genomic DNA. These probes also hybridized to genomic DNA from 6 of 18 P. aeruginosa strains that produced R-type pyocins. Asymmetric PCR, complementary oligonucleotide hybridization, and electron microscopy indicated that pyocin C particles contained closed circular single-stranded DNA, approximately 4.0 kb in length. Examination of total intracellular DNA from mitomycin C-induced cultures revealed the presence of two extrachromosomal DNA molecules, a double-stranded molecule and a single-stranded molecule, which hybridized to pyocin DNA. Sequence analysis of 7,480 nucleotides of P. aeruginosa C chromosomal DNA containing the pyocin DNA indicated the presence of pyocin open reading frames with similarities to open reading frames from filamentous phages and cryptic phage elements. We did not observe any similarities to known phage structural proteins or previously characterized pseudomonalprt genes expressing R-type pyocin structural proteins. These studies demonstrate that pyocin particles from P. aeruginosa C are defective phages that contain a novel closed circular single-stranded DNA and that this DNA was derived from the chromosome of P. aeruginosa C.

scholarly journals Genomic variance of Open Reading Frames (ORFs) and Spike protein in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

2020 ◽  
Vol 83 (8) ◽  
pp. 725-732
Author(s):  
Ping-Hsing Tsai ◽  
Mong-Lien Wang ◽  
De-Ming Yang ◽  
Kung-How Liang ◽  
Shih-Jie Chou ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Open Reading Frames ◽  
Spike Protein ◽  
Genomic Variance ◽  
Reading Frames
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