scholarly journals The Potential Functions of Protein Domains during COVID Infection; an Analysis and a Review

COVID ◽  
2021 ◽  
Vol 1 (1) ◽  
pp. 384-393
Author(s):  
Haitham Sobhy

Coronaviruses (CoVs) are a large viral family that can evolve rapidly emerging new strains that cause outbreaks and life-loss, including SARS-CoV, MERS-CoV, and SARS-CoV-2 (COVID-19). CoVs encode a diverse number of proteins, ranging from 5 proteins in bat CoV, to 14 in SARS CoV, which could have implication on viral tropism and pathogenicity. Here, we highlight the functional protein motifs (domains) that could contribute in the coronavirus infection and severity, including SARS-CoV-2. For this role, we used the experimentally validated domain (motif) datasets that are known to be crucial for viral infection. Then, we highlight the potential molecular pathways and interactions of SARS-CoV-2 proteins within human cells. Interestingly, the C-terminal of SARS-COV-2 nsp1 protein encodes MREL motif, which a signature motif of the tubulin superfamily, and regulate tubulin expression. The C-terminal region of nsp1 protein can bind to ribosome and regulation viral RNA translation.

Author(s):  
Haitham Sobhy

Although phylogenetic analysis shows coronaviruses (CoV) share similar genome sequences, CoVs encode different number of proteins (5 to 14), which has implication on viral pathogenicity and infection. Here, we aimed to identify (in-silico) the similarities between different members of coronavirus family. The analysis included 50 coronavirus proteomes, including SARS-CoV-2 (COVID-19), to find the variation of the number of protein functional motifs and domain in each coronavirus. For this role, we used the experimentally validated domain (motif) that known to be crucial for viral infection. Although human CoVs are classified within one genus, we found variations among them. SARS-CoV-1, SARS-CoV-2 and MERS-CoV encode different type of domains, which has implications on the molecular interactions triggered by each virus within human cells. Secondly, we used functional motifs to reconstruct the potential molecular pathways or interactions triggered by SARS-CoV-2 proteins within human cell.


Parasitology ◽  
2012 ◽  
Vol 139 (8) ◽  
pp. 998-1004 ◽  
Author(s):  
X. CUI ◽  
T. LEI ◽  
D. Y. YANG ◽  
P. HAO ◽  
Q. LIU

SUMMARYImmune mapped protein 1 (IMP1) is a newly discovered protein in Eimeria maxima. It is recognized as a potential vaccine candidate against E. maxima and a highly conserved protein in apicomplexan parasites. Although the Neospora caninum IMP1 (NcIMP1) orthologue of E. maxima IMP1 was predicted in the N. caninum genome, it was still not identified and characterized. In this study, cDNA sequence encoding NcIMP1 was cloned by RT-PCR from RNA isolated from Nc1 tachyzoites. NcIMP1 was encoded by an open reading frame of 1182 bp, which encoded a protein of 393 amino acids with a predicted molecular weight of 42·9 kDa. Sequence analysis showed that there was neither a signal peptide nor a transmembrane region present in the NcIMP1 amino acid sequence. However, several kinds of functional protein motifs, including an N-myristoylation site and a palmitoylation site were predicted. Recombinant NcIMP1 (rNcIMP1) was expressed in Escherichia coli and then purified rNcIMP1 was used to prepare specific antisera in mice. Mouse polyclonal antibodies raised against the rNcIMP1 recognized an approximate 43 kDa native IMP1 protein. Immunofluorescence analysis showed that NcIMP1 was localized on the membrane of N. caninum tachyzoites. The N-myristoylation site and the palmitoylation site were found to contribute to the localization of NcIMP1. Furthermore, the rNcIMP1-specific antibodies could inhibit cell invasion by N. caninum tachyzoites in vitro. All the results indicate that NcIMP1 is likely to be a membrane protein of N. caninum and may be involved in parasite invasion.


2015 ◽  
Vol 89 (8) ◽  
pp. 4237-4248 ◽  
Author(s):  
Jane Besong-Ndika ◽  
Konstantin I. Ivanov ◽  
Anders Hafrèn ◽  
Thierry Michon ◽  
Kristiina Mäkinen

ABSTRACTPotato virus A(PVA) is a single-stranded positive-sense RNA virus and a member of the familyPotyviridae. The PVA coat protein (CP) has an intrinsic capacity to self-assemble into filamentous virus-like particles, but the mechanism responsible for the initiation of viral RNA encapsidationin vivoremains unclear. Apart from virion assembly, PVA CP is also involved in the inhibition of viral RNA translation. In this study, we show that CP inhibits PVA RNA translation in a dose-dependent manner, through a mechanism involving the CP-encoding region. Analysis of this region, however, failed to identify any RNA secondary structure(s) preferentially recognized by CP, suggesting that the inhibition depends on CP-CP rather than CP-RNA interactions. In agreement with this possibility, insertion of an in-frame stop codon upstream of the CP sequence led to a marked decrease in the inhibition of viral RNA translation. Based on these results, we propose a model in which the cotranslational interactions between excess CP accumulating intransand CP translated from viral RNA incisare required to initiate the translational repression. This model suggests a mechanism for how viral RNA can be sequestered from translation and specifically selected for encapsidation at the late stages of viral infection.IMPORTANCEThe main functions of the CP during potyvirus infection are to protect viral RNA from degradation and to transport it locally, systemically, and from host to host. Although virion assembly is a key step in the potyviral infectious cycle, little is known about how it is initiated and how viral RNA is selected for encapsidation. The results presented here suggest that CP-CP rather than CP-RNA interactions are predominantly involved in the sequestration of viral RNA away from translation. We propose that the cotranslational nature of these interactions may represent a mechanism for the selection of viral RNA for encapsidation. A better understanding of the mechanism of virion assembly may lead to development of crops resistant to potyviruses at the level of viral RNA encapsidation, thereby reducing the detrimental effects of potyvirus infections on food production.


2021 ◽  
Vol 25 (1) ◽  
pp. 16-24
Author(s):  
O. B. Tamrazova ◽  
A. S. Stadnikova ◽  
E. V. Rudikova

In late 2019, a new viral infection appeared in China, which spread around the world, causing a pandemic. The causative agent of the new coronavirus infection COVID-19 is the SARS-CoV-2 coronavirus. The review presents modern data on the epidemiology, pathogenesis and course of the novel coronavirus infection COVID-19 in children. Chinese, American and European scientists have described a variety of cutaneous manifestations in children with COVID-19. The article provides a literature review of the cutaneous manifestations of COVID-19 coronavirus infection in children. During our own observation of 301 patients with coronavirus infection COVID-19 caused by SARS-CoV-2 at the Bashlyaevs Children Hospital in Moscow from May 17 to November 16, 2020, it was revealed that 39 (13 %) patients had skin manifestations. The article presents a classification of skin manifestations characteristic of COVID-19. A brief description of each group is given.


Author(s):  
I. E. Khoroshilov

The new coronavirus infection COVID-19 that appeared at the end of 2019 is signifi cantly different from the viral infections that existed previously. The new SARS-CoV-2 coronavirus combines two transmission routes—aerosol and oral-intestinal. The targets for this virus are both cells of the respiratory system and the human gastrointestinal tract. Along with the classical form of this disease, the so-called “gastrointestinal” form is described, in which the clinical picture is dominated by signs of damage to the gastrointestinal tract (diarrhea, vomiting, anorexia). These symptoms are detected, in general, in 20% of patients with COVID-19. More than 80% of patients have mild forms, a third of these individuals had diarrhea. Although SARSCoV-2 viral RNA is detected in faeces samples of patients with COVID-19, it does not carry an infectious onset, and not a single case of fecal-oral transmission has been confi rmed. Since the intestines are the most powerful organ of our immune system, we can introduce SARS-CoV-2 viral RNA into the gastrointestinal tract to ensure the formation of immunity to this infection.


2018 ◽  
Author(s):  
Manish Kumar Johri ◽  
Hiren Vasantrai Lashkari ◽  
Dhiviya Vedagiri ◽  
Divya Gupta ◽  
Krishnan Harinivas Harshan

ABSTRACTMechanistic target of rapamycin (mTOR) is an important kinase that assimilates several upstream signals including viral infection and facilitates appropriate response by the cell through two unique complexes mTORC1 and mTORC2. Here, we demonstrate that mTORC1 is activated early during HCV infection as antiviral response. Pharmacological inhibition of mTORC1 promoted HCV replication as suggested by elevated levels of HCV (+) and (-) RNA strands. This was accompanied by significant drop in extracellular HCV RNA levels indicating defective post-replication stages. The increase in viral RNA levels failed to augment intracellular infectious virion levels, suggesting that mTORC1 inhibition is detrimental to post-replication steps. Lower infectivity of the supernatant confirmed this observation. Depletion of Raptor and ULK1 accurately reproduced these results suggesting that mTORC1 imparted these effects on HCV through mTORC1-ULK1 arm. Interestingly, ULK1 depletion resulted in increased levels of miR-122, a critical host factor for HCV replication, thus revealing a new mechanism of regulation by ULK1. The binary effect of mTORC1 on HCV replication and egress suggests that mTORC1-ULK1 could be critical in replication: egress balance. Interestingly we discover that ULK1 depletion did not interfere with autophagy in Huh7.5 cells and hence the effects on HCV replication and post-replication events are not resultant of involvement of autophagy. Our studies demonstrate an overall ULK1 mediated anti-HCV function of mTORC1 and identifies an ULK1-independent autophagy that allows HCV replication in spite of mTORC1 activation.


2018 ◽  
Vol 92 (16) ◽  
Author(s):  
Saskia D. van Asten ◽  
Matthijs Raaben ◽  
Benjamin Nota ◽  
Robbert M. Spaapen

ABSTRACT Cellular antiviral programs can efficiently inhibit viral infection. These programs are often initiated through signaling cascades induced by secreted proteins, such as type I interferons, interleukin-6 (IL-6), or tumor necrosis factor alpha (TNF-α). In the present study, we generated an arrayed library of 756 human secreted proteins to perform a secretome screen focused on the discovery of novel modulators of viral entry and/or replication. The individual secreted proteins were tested for the capacity to inhibit infection by two replication-competent recombinant vesicular stomatitis viruses (VSVs) with distinct glycoproteins utilizing different entry pathways. Fibroblast growth factor 16 (FGF16) was identified and confirmed as the most prominent novel inhibitor of both VSVs and therefore of viral replication, not entry. Importantly, an antiviral interferon signature was completely absent in FGF16-treated cells. Nevertheless, the antiviral effect of FGF16 is broad, as it was evident on multiple cell types and also on infection by coxsackievirus. In addition, other members of the FGF family also inhibited viral infection. Thus, our unbiased secretome screen revealed a novel protein family capable of inducing a cellular antiviral state. This previously unappreciated role of the FGF family may have implications for the development of new antivirals and the efficacy of oncolytic virus therapy. IMPORTANCE Viruses infect human cells in order to replicate, while human cells aim to resist infection. Several cellular antiviral programs have therefore evolved to resist infection. Knowledge of these programs is essential for the design of antiviral therapeutics in the future. The induction of antiviral programs is often initiated by secreted proteins, such as interferons. We hypothesized that other secreted proteins may also promote resistance to viral infection. Thus, we tested 756 human secreted proteins for the capacity to inhibit two pseudotypes of vesicular stomatitis virus (VSV). In this secretome screen on viral infection, we identified fibroblast growth factor 16 (FGF16) as a novel antiviral against multiple VSV pseudotypes as well as coxsackievirus. Subsequent testing of other FGF family members revealed that FGF signaling generally inhibits viral infection. This finding may lead to the development of new antivirals and may also be applicable for enhancing oncolytic virus therapy.


mBio ◽  
2019 ◽  
Vol 10 (6) ◽  
Author(s):  
Yize Li ◽  
Beihua Dong ◽  
Zuzhang Wei ◽  
Robert H. Silverman ◽  
Susan R. Weiss

ABSTRACT Bats are reservoirs for many RNA viruses that are highly pathogenic in humans yet relatively apathogenic in the natural host. It has been suggested that differences in innate immunity are responsible. The antiviral OAS-RNase L pathway is well characterized in humans, but there is little known about its activation and antiviral activity in bats. During infection, OASs, upon sensing double-stranded RNA (dsRNA), produce 2′-5′ oligoadenylates (2-5A), leading to activation of RNase L which degrades viral and host RNA, limiting viral replication. Humans encode three active OASs (OAS1 to -3). Analysis of the Egyptian Rousette bat genome combined with mRNA sequencing from bat RoNi/7 cells revealed three homologous OAS proteins. Interferon alpha treatment or viral infection induced all three OAS mRNAs, but RNase L mRNA is constitutively expressed. Sindbis virus (SINV) or vaccinia virus (VACVΔE3L) infection of wild-type (WT) or OAS1-KO (knockout), OAS2-KO, or MAVS-KO RoNi/7 cells, but not RNase L-KO or OAS3-KO cells, induces robust RNase L activation. SINV replication is 100- to 200-fold higher in the absence of RNase L or OAS3 than in WT cells. However, MAVS-KO had no detectable effect on RNA degradation or replication. Thus, in RoNi/7 bat cells, as in human cells, activation of RNase L during infection and its antiviral activity are dependent primarily on OAS3 while MAVS signaling is not required for the activation of RNase L and restriction of infection. Our findings indicate that OAS proteins serve as pattern recognition receptors (PRRs) to recognize viral dsRNA and that this pathway is a primary response to virus rather than a secondary effect of interferon signaling. IMPORTANCE Many RNA viruses that are highly pathogenic in humans are relatively apathogenic in their bat reservoirs, making it important to compare innate immune responses in bats to those well characterized in humans. One such antiviral response is the OAS-RNase L pathway. OASs, upon sensing dsRNA, produce 2-5A, leading to activation of RNase L which degrades viral and host RNA, limiting viral replication. Analysis of Egyptian Rousette bat sequences revealed three OAS genes expressing OAS1, OAS2, and OAS3 proteins. Interferon treatment or viral infection induces all three bat OAS mRNAs. In these bat cells as in human cells, RNase L activation and its antiviral activity are dependent primarily on OAS3 while MAVS signaling is not required. Importantly, our findings indicate the OAS-RNase L system is a primary response to virus rather than a secondary effect of interferon signaling and therefore can be activated early in infection or while interferon signaling is antagonized.


2003 ◽  
Vol 77 (10) ◽  
pp. 5649-5656 ◽  
Author(s):  
Kensuke Hirasawa ◽  
Angus Kim ◽  
Hye-Seung Han ◽  
Jaeseok Han ◽  
Hee-Sook Jun ◽  
...  

ABSTRACT Cellular phosphorylation events during viral infection are necessary for effective viral replication. Encephalomyocarditis (EMC) virus has been used for studies on the molecular mechanisms of viral replication, but little is known about the cellular signaling pathways involved. This investigation was initiated to determine whether mitogen-activated protein kinases (MAPKs), which are central components of signal transduction pathways in the regulation of cell proliferation, play a role in the replication of EMC virus. We examined the phosphorylation of MAPKs, including extracellular signal-regulated kinase (ERK1/2), p38 MAPK, and stress-activated protein kinase 1/c-Jun NH2-terminal kinase (SAPK/JNK) in EMC virus-infected L929 cells and found that p38 MAPK and SAPK-JNK, but not ERK1/2, were activated during viral infection. We then examined the effect of these kinases on the replication of EMC virus in L929 cells by using specific inhibitors, including genistein or herbimycin A for tyrosine kinase, SB203580 or SB202190 for p38 MAPK, and PD98059 for ERK1/2. We found that the tyrosine kinase and p38 MAPK inhibitors, but not the ERK1/2 inhibitor, suppressed viral replication and that the inhibitory effect was primarily on viral protein synthesis. Finally, we examined whether p38 MAPK is involved in the translation of EMC viral transcripts by using L929 cells transfected with a gene construct containing the internal ribosomal entry site (IRES) of EMC virus and a luciferase reporter gene. We found that the p38 MAPK inhibitor suppressed the translation of EMC viral RNA. On the basis of these observations, we conclude that p38 MAPK plays a critical role in the replication of EMC virus, probably in the translation of viral RNA.


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