scholarly journals Asymmetric Trimeric Ring Structure of the Nucleocapsid Protein of Tospovirus

2017 ◽  
Vol 91 (20) ◽  
Author(s):  
Keisuke Komoda ◽  
Masanori Narita ◽  
Keitaro Yamashita ◽  
Isao Tanaka ◽  
Min Yao

ABSTRACT Tomato spotted wilt virus (TSWV), belonging to the genus Tospovirus of the family Bunyaviridae, causes significant economic damage to several vegetables and ornamental plants worldwide. Similar to those of all other negative-strand RNA viruses, the nucleocapsid (N) protein plays very important roles in its viral life cycle. N proteins protect genomic RNAs by encapsidation and form a viral ribonucleoprotein complex (vRNP) with some RNA-dependent RNA polymerases. Here we show the crystal structure of the N protein from TSWV. Protomers of TSWV N proteins consist of three parts: the N arm, C arm, and core domain. Unlike N proteins of other negative-strand RNA viruses, the TSWV N protein forms an asymmetric trimeric ring. To form the trimeric ring, the N and C arms of the N protein interact with the core domains of two adjacent N proteins. By solving the crystal structures of the TSWV N protein with nucleic acids, we showed that an inner cleft of the asymmetric trimeric ring is an RNA-binding site. These characteristics are similar to those of N proteins of other viruses of the family Bunyaviridae. Based on these observations, we discuss possibilities of a TSWV encapsidation model. IMPORTANCE Tospoviruses cause significant crop losses throughout the world. Particularly, TSWV has an extremely wide host range (>1,000 plant species, including dicots and monocots), and worldwide losses are estimated to be in excess of $1 billion annually. Despite such importance, no proteins of tospoviruses have been elucidated so far. Among TSWV-encoded proteins, the N protein is required for assembling the viral genomic RNA into the viral ribonucleoprotein (vRNP), which is involved in various steps of the life cycle of these viruses, such as RNA replication, virus particle formation, and cell-to-cell movement. This study revealed the structure of the N protein, with or without nucleic acids, of TSWV as the first virus of the genus Tospovirus, so it completed our view of the N proteins of the family Bunyaviridae.

mBio ◽  
2020 ◽  
Vol 11 (3) ◽  
Author(s):  
Yukiyo Sato ◽  
Wajeeha Shamsi ◽  
Atif Jamal ◽  
Muhammad Faraz Bhatti ◽  
Hideki Kondo ◽  
...  

ABSTRACT The search for viruses infecting fungi, or mycoviruses, has extended our knowledge about the diversity of RNA viruses, as exemplified by the discovery of polymycoviruses, a phylogenetic group of multisegmented RNA viruses with unusual forms. The genomic RNAs of known polymycoviruses, which show a phylogenetic affinity for animal positive-sense single-stranded RNA [(+)RNA] viruses such as caliciviruses, are comprised of four conserved segments with an additional zero to four segments. The double-stranded form of polymycovirus genomic RNA is assumed to be associated with a virally encoded protein (proline-alanine-serine-rich protein [PASrp]) in either of two manners: a capsidless colloidal form or a filamentous encapsidated form. Detailed molecular characterizations of polymycoviruses, however, have been conducted for only a few strains. Here, a novel polymyco-related virus named Hadaka virus 1 (HadV1), from the phytopathogenic fungus Fusarium oxysporum, was characterized. The genomic RNA of HadV1 consisted of an 11-segmented positive-sense RNA with highly conserved terminal nucleotide sequences. HadV1 shared the three conserved segments with known polymycoviruses but lacked the PASrp-encoding segment. Unlike the known polymycoviruses and encapsidated viruses, HadV1 was not pelleted by conventional ultracentrifugation, possibly due to the lack of PASrp. This result implied that HadV1 exists only as a soluble form with naked RNA. Nevertheless, the 11 genomic segments of HadV1 have been stably maintained through host subculturing and conidiation. Taken together, the results of this study revealed a virus with a potential novel virus lifestyle, carrying many genomic segments without typical capsids or PASrp-associated forms. IMPORTANCE Fungi collectively host various RNA viruses. Examples include encapsidated double-stranded RNA (dsRNA) viruses with diverse numbers of genomic segments (from 1 to 12) and capsidless viruses with nonsegmented (+)RNA genomes. Recently, viruses with unusual intermediate features of an infectious entity between encapsidated dsRNA viruses and capsidless (+)RNA viruses were found. They are called polymycoviruses, which typically have four to eight dsRNA genomic segments associated with one of the virus-encoded proteins and are phylogenetically distantly related to animal (+)RNA caliciviruses. Here, we identified a novel virus phylogenetically related to polymycoviruses, from the phytopathogenic fungus Fusarium oxysporum. The virus, termed Hadaka virus 1 (HadV1), has 11 (+)RNA genomic segments, the largest number in known (+)RNA viruses. Nevertheless, HadV1 lacked a typical structural protein of polymycoviruses and was not pelleted by standard ultracentrifugation, implying an unusual capsidless nature of HadV1. This study reveals a potential novel lifestyle of multisegmented RNA viruses.


2021 ◽  
Author(s):  
Jianxing Song ◽  
Mei Dang

Abstract Great efforts have led to successfully developing the spike-based vaccines but challenges still exist to completely terminate the SARS-CoV-2 pandemic. SARS-CoV-2 nucleocapsid (N) protein plays the essential roles in almost all key steps of the viral life cycle, thus representing a top drug target. Almost all key functions of N protein including liquid-liquid phase separation (LLPS) depend on its capacity in interacting with nucleic acids. Therefore, only the variants with their N proteins functional in binding nucleic acids might survive and spread in evolution and indeed, the residues critical for binding nucleic acids are highly conserved. Very recently, hydroxychloroquine (HCQ) was shown to prevent the transmission in a large-scale clinical study in Singapore but so far, no specific SARS-CoV-2 protein was experimentally identified to be targeted by HCQ. Here by NMR, we unambiguously decode that HCQ specifically binds NTD and CTD of SARS- CoV-2 N protein with Kd of 112.1 and 57.1 μM respectively to inhibit their interaction with nucleic acid, as well as to disrupt LLPS essential for the viral life cycle. Most importantly, HCQ-binding residues are identical in SARS-CoV-2 variants and therefore HCQ is likely effective to them all. The results not only provide a structural basis for the anti-SARS-CoV-2 activity of HCQ, but also renders HCQ to be the first known drug capable of targeting LLPS. Furthermore, the unique structure of the HCQ-CTD complex decodes a promising strategy for further design of better anti-SARS-CoV-2 drugs from HCQ. Therefore, HCQ is a promising candidate to help terminate the pandemic.


2019 ◽  
Vol 94 (4) ◽  
Author(s):  
Yingying Cong ◽  
Mustafa Ulasli ◽  
Hein Schepers ◽  
Mario Mauthe ◽  
Philip V’kovski ◽  
...  

ABSTRACT Coronavirus (CoV) nucleocapsid (N) proteins are key for incorporating genomic RNA into progeny viral particles. In infected cells, N proteins are present at the replication-transcription complexes (RTCs), the sites of CoV RNA synthesis. It has been shown that N proteins are important for viral replication and that the one of mouse hepatitis virus (MHV), a commonly used model CoV, interacts with nonstructural protein 3 (nsp3), a component of the RTCs. These two aspects of the CoV life cycle, however, have not been linked. We found that the MHV N protein binds exclusively to nsp3 and not other RTC components by using a systematic yeast two-hybrid approach, and we identified two distinct regions in the N protein that redundantly mediate this interaction. A selective N protein variant carrying point mutations in these two regions fails to bind nsp3 in vitro, resulting in inhibition of its recruitment to RTCs in vivo. Furthermore, in contrast to the wild-type N protein, this N protein variant impairs the stimulation of genomic RNA and viral mRNA transcription in vivo and in vitro, which in turn leads to impairment of MHV replication and progeny production. Altogether, our results show that N protein recruitment to RTCs, via binding to nsp3, is an essential step in the CoV life cycle because it is critical for optimal viral RNA synthesis. IMPORTANCE CoVs have long been regarded as relatively harmless pathogens for humans. Severe respiratory tract infection outbreaks caused by severe acute respiratory syndrome CoV and Middle East respiratory syndrome CoV, however, have caused high pathogenicity and mortality rates in humans. These outbreaks highlighted the relevance of being able to control CoV infections. We used a model CoV, MHV, to investigate the importance of the recruitment of N protein, a central component of CoV virions, to intracellular platforms where CoVs replicate, transcribe, and translate their genomes. By identifying the principal binding partner at these intracellular platforms and generating a specific mutant, we found that N protein recruitment to these locations is crucial for promoting viral RNA synthesis. Moreover, blocking this recruitment strongly inhibits viral infection. Thus, our results explain an important aspect of the CoV life cycle and reveal an interaction of viral proteins that could be targeted in antiviral therapies.


2019 ◽  
Author(s):  
Adam M. Dinan ◽  
Nina I. Lukhovitskaya ◽  
Ingrida Olendraite ◽  
Andrew E. Firth

ABSTRACTPositive-sense single-stranded RNA viruses form the largest and most diverse group of eukaryote-infecting viruses. Their genomes comprise one or more segments of coding-sense RNA that function directly as messenger RNAs upon release into the cytoplasm of infected cells. Positive-sense RNA viruses are generally accepted to encode proteins solely on the positive strand. However, we previously identified a surprisingly long (~1000 codons) open reading frame (ORF) on the negative strand of some members of the familyNarnaviridaewhich, together with RNA bacteriophages of the familyLeviviridae, form a sister group to all other positive-sense RNA viruses. Here, we completed the genomes of three mosquito-associated narnaviruses, all of which have the long reverse-frame ORF. We systematically identified narnaviral sequences in public data sets from a wide range of sources, including arthropod, fungi and plant transcriptomic datasets. Long reverse-frame ORFs are widespread in one clade of narnaviruses, where they frequently occupy >95% of the genome. The reverse-frame ORFs correspond to a specific avoidance of CUA, UUA and UCA codons (i.e. stop codon reverse complements) in the forward-frame RNA-dependent RNA polymerase ORF. However, absence of these codons cannot be explained by other factors such as inability to decode these codons or GC3 bias. Together with other analyses, we provide the strongest evidence yet of coding capacity on the negative strand of a positive-sense RNA virus. As these ORFs comprise some of the longest known overlapping genes, their study may be of broad relevance to understanding overlapping gene evolution andde novoorigin of genes.


2011 ◽  
Vol 80 (1) ◽  
pp. 169-174 ◽  
Author(s):  
Luis M. De Pablos ◽  
Antonio Osuna

ABSTRACTThe MASP gene family is the second most widely represented gene family in the genome ofTrypanosoma cruzi. One of its main characteristics is that its 5′ and 3′ regions are highly conserved. We assessed the expression of these conserved regions as a marker forT. cruziand also analyzed the expression of themaspgenes and MASP proteins. In parasite strains CL-Brener (DTUVI lineage) and PAN4 (DTUI lineage),maspgenes were expressed at different levels both with regard to the two strains and between stages in the parasite's life cycle. We also studied the expression of the family during the intracellular cycle ofT. cruzi, using antibodies against the conserved MASP signal peptide (SP). Fluorescence intensity showed an increase in expression from 24 h onwards, with a peak in intensity at 72 h postinfection. After 24 and 48 h, the MASP proteins were expressed in 33.33% and 57.14% of the amastigotes, respectively. Our data show that not only the extracellular forms ofT. cruzibut also the intracellular phases express this type of protein, though to different extents in the various forms of the parasite.


2015 ◽  
Vol 90 (2) ◽  
pp. 715-724 ◽  
Author(s):  
Shihong Qiu ◽  
Minako Ogino ◽  
Ming Luo ◽  
Tomoaki Ogino ◽  
Todd J. Green

ABSTRACTViruses have various mechanisms to duplicate their genomes and produce virus-specific mRNAs. Negative-strand RNA viruses encode their own polymerases to perform each of these processes. For the nonsegmented negative-strand RNA viruses, the polymerase is comprised of the large polymerase subunit (L) and the phosphoprotein (P). L proteins from members of theRhabdoviridae,Paramyxoviridae, andFiloviridaeshare sequence and predicted secondary structure homology. Here, we present the structure of the N-terminal domain (conserved region I) of the L protein from a rhabdovirus, vesicular stomatitis virus, at 1.8-Å resolution. The strictly and strongly conserved residues in this domain cluster in a single area of the protein. Serial mutation of these residues shows that many of the amino acids are essential for viral transcription but not for mRNA capping. Three-dimensional alignments show that this domain shares structural homology with polymerases from other viral families, including segmented negative-strand RNA and double-stranded RNA (dsRNA) viruses.IMPORTANCENegative-strand RNA viruses include a diverse set of viral families that infect animals and plants, causing serious illness and economic impact. The members of this group of viruses share a set of functionally conserved proteins that are essential to their replication cycle. Among this set of proteins is the viral polymerase, which performs a unique set of reactions to produce genome- and subgenome-length RNA transcripts. In this article, we study the polymerase of vesicular stomatitis virus, a member of the rhabdoviruses, which has served in the past as a model to study negative-strand RNA virus replication. We have identified a site in the N-terminal domain of the polymerase that is essential to viral transcription and that shares sequence homology with members of the paramyxoviruses and the filoviruses. Newly identified sites such as that described here could prove to be useful targets in the design of new therapeutics against negative-strand RNA viruses.


2018 ◽  
Vol 92 (17) ◽  
Author(s):  
Rhys Parry ◽  
Sassan Asgari

ABSTRACTInsect-specific viruses (ISVs) of the yellow fever mosquitoAedes aegyptihave been demonstrated to modulate transmission of arboviruses such as dengue virus (DENV) and West Nile virus by the mosquito. The diversity and composition of the virome ofA. aegypti, however, remains poorly understood. In this study, we characterized Aedes anphevirus (AeAV), a negative-sense RNA virus from the orderMononegavirales. AeAV identified fromAedescell lines was infectious to bothA. aegyptiandAedes albopictuscells but not to three mammalian cell lines. To understand the incidence and genetic diversity of AeAV, we assembled 17 coding-complete and two partial genomes of AeAV from available transcriptome sequencing (RNA-Seq) data. AeAV appears to transmit vertically and be present in laboratory colonies, wild-caught mosquitoes, and cell lines worldwide. Phylogenetic analysis of AeAV strains indicates that as theA. aegyptimosquito has expanded into the Americas and Asia-Pacific, AeAV has evolved into monophyletic African, American, and Asia-Pacific lineages. The endosymbiotic bacteriumWolbachia pipientisrestricts positive-sense RNA viruses inA. aegypti. Reanalysis of a small RNA library ofA. aegypticells coinfected with AeAV andWolbachiaproduces an abundant RNA interference (RNAi) response consistent with persistent virus replication. We foundWolbachiaenhances replication of AeAV compared to a tetracycline-cleared cell line, and AeAV modestly reduces DENV replicationin vitro. The results from our study improve understanding of the diversity and evolution of the virome ofA. aegyptiand adds to previous evidence that showsWolbachiadoes not restrict a range of negative-strand RNA viruses.IMPORTANCEThe mosquitoAedes aegyptitransmits a number of arthropod-borne viruses (arboviruses), such as dengue virus and Zika virus. Mosquitoes also harbor insect-specific viruses that may affect replication of pathogenic arboviruses in their body. Currently, however, there are only a few insect-specific viruses described fromA. aegyptiin the literature. Here, we characterize a novel negative-strand virus, AeAV. Meta-analysis ofA. aegyptisamples showed that it is present inA. aegyptimosquitoes worldwide and is vertically transmitted.Wolbachia-transinfected mosquitoes are currently being used in biocontrol, as they effectively block transmission of several positive-sense RNA viruses in mosquitoes. Our results demonstrate thatWolbachiaenhances the replication of AeAV and modestly reduces dengue virus replication in a cell line model. This study expands our understanding of the virome inA. aegyptias well as providing insight into the complexity of theWolbachiavirus restriction phenotype.


2015 ◽  
Vol 90 (2) ◽  
pp. 659-669 ◽  
Author(s):  
Mang Shi ◽  
Xian-Dan Lin ◽  
Nikos Vasilakis ◽  
Jun-Hua Tian ◽  
Ci-Xiu Li ◽  
...  

ABSTRACTViruses of the familyFlaviviridaeare important pathogens of humans and other animals and are currently classified into four genera. To better understand their diversity, evolutionary history, and genomic flexibility, we used transcriptome sequencing (RNA-seq) to search for the viruses related to theFlaviviridaein a range of potential invertebrate and vertebrate hosts. Accordingly, we recovered the full genomes of five segmented jingmenviruses and 12 distant relatives of the knownFlaviviridae(“flavi-like” viruses) from a range of arthropod species. Although these viruses are highly divergent, they share a similar genomic plan and common ancestry with theFlaviviridaein the NS3 and NS5 regions. Remarkably, although these viruses fill in major gaps in the phylogenetic diversity of theFlaviviridae, genomic comparisons reveal important changes in genome structure, genome size, and replication/gene regulation strategy during evolutionary history. In addition, the wide diversity of flavi-like viruses found in invertebrates, as well as their deep phylogenetic positions, suggests that they may represent the ancestral forms from which the vertebrate-infecting viruses evolved. For the vertebrate viruses, we expanded the previously mammal-only pegivirus-hepacivirus group to include a virus from the graceful catshark (Proscyllium habereri), which in turn implies that these viruses possess a larger host range than is currently known. In sum, our data show that theFlaviviridaeinfect a far wider range of hosts and exhibit greater diversity in genome structure than previously anticipated.IMPORTANCEThe familyFlaviviridaeof RNA viruses contains several notorious human pathogens, including dengue virus, West Nile virus, and hepatitis C virus. To date, however, our understanding of the biodiversity and evolution of theFlaviviridaehas largely been directed toward vertebrate hosts and their blood-feeding arthropod vectors. Therefore, we investigated an expanded group of potential arthropod and vertebrate host species that have generally been ignored by surveillance programs. Remarkably, these species contained diverse flaviviruses and related viruses that are characterized by major changes in genome size and genome structure, such that these traits are more flexible than previously thought. More generally, these data suggest that arthropods may be the ultimate reservoir of theFlaviviridaeand related viruses, harboring considerable genetic and phenotypic diversity. In sum, this study revises the traditional view on the evolutionary history, host range, and genomic structures of a major group of RNA viruses.


2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Salma Damak ◽  
Hela Ben Mbarek ◽  
Issal Haj-Salem

Purpose The purpose of this study is to investigate R&D investments in family firms. Design/methodology/approach The socio-emotional wealth (SEW) perspective, considered as a dominant paradigm in the family business field, is the theoretical framework used to report different behaviors ascertained within family firms. This paper focuses on two dimensions of the SEW, namely, family control and influence and family identity. A suspected moderating role played by the firm’s life cycle stage on the dimensions is also investigated using panel data. To analyze the results, this paper uses the Smart PLS software on secondary data collected for 76 German family firms. Findings The empirical results reveal a negative influence of SEW on R&D investments. The prominent effect of the family control and influence dimension on R&D is higher in the first part of a firm life cycle. Research limitations/implications The analysis of this study is subject to several caveats. First, to measure the R&D investment, this paper used R&D intensity computed as the total annual R&D expenses by total sales. Except for the fact that the use of proxies received several criticizes from scholars (Berrone et al., 2012) claiming how they do not directly relate to the essence of the dimensions measured. Second, this paper used two out of five FIBER dimensions only in the study. This paper took the right direction, but still, the complexity of SEW may not be fully captured following this approach (Berrone et al., 2012). Originality/value This study could be considered as an important extension of prior research investigating R&D in family firms. The authors provide a valid empirical construct, the FIBER scale, to capture non-monotonic behaviors in family firms and an enlargement of the family firms and innovation management field of research.


2022 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Beatriz Adriana López-Chávez ◽  
César Maldonado-Alcudia

PurposeThe aim of this paper is to analyze the life cycle of family-owned hotels in the maturity phase from the integration of theoretical models for family-owned tourism businesses.Design/methodology/approachA qualitative multiple case study was used to analyze four mature family-owned hotels through eight interviews and four observation guides with an abductive method. Three axes were analyzed; the ownership with the Gersick model, the family with the Tobak and Nábradí model and the business with the Butler tourist areas model to identify whether they are going through the consolidation stage, stagnation, rejuvenation or decline within its maturity.FindingsThe cases studied evolve in the three axes. In the business axes, two go through the stagnation stage, another in decline and the last in consolidation; all remain under controlling owners. In the family, there are different generations in charge. The boost to the destination plays a key role as a force for deterministic change in the internal transformation of these organizations, and to remain in consolidation, discontinuous changes and voluntaristic actions are necessary.Originality/valueFamily businesses seek longevity, although a low percentage reaches maturity. This research proposes the integration of life cycle models to understand its development in the axes of family, ownership and business, where aspects of the tourism industry are considered and allow the stage identification through which it passes in maturity, supporting internal decision making.


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