Biology:Picornavirus

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Picornaviruses are a group of related nonenveloped RNA viruses which infect vertebrates including fish,[1] mammals, and birds. They are viruses that represent a large family of small, positive-sense, single-stranded RNA viruses with a 30 nm icosahedral capsid. The viruses in this family can cause a range of diseases including the common cold, poliomyelitis, meningitis, hepatitis, and paralysis.[2][3][4][5]

Picornaviruses constitute the family Picornaviridae, order Picornavirales, and realm Riboviria. There are 159 species in this family, assigned to 68 genera, most of which belong to 5 subfamilies. Notable examples are genera Enterovirus (including Rhinovirus and Poliovirus), Aphthovirus, Cardiovirus, and Hepatovirus.[6][7]

Etymology

The name "picornavirus" has a dual etymology. Firstly, the name derives from picorna- which is an acronym for "poliovirus, insensitivity to ether, coxsackievirus, orphan virus, rhinovirus, and ribonucleic acid". Secondly, the name derives from pico-, which designates a very small unit of measurement (equivalent to 10−12), combined with rna to describe this group of very small RNA viruses.[8]

History

The first animal virus discovered (1897) was the foot-and-mouth disease virus (FMDV). It is the prototypic member of the genus Aphthovirus in the Picornaviridae family.[4] The plaque assay was developed using poliovirus; the discovery of viral replication in culture was also with poliovirus in 1949. This was the first time that infectious virus had been produced in cultured cells.[9] Polyprotein synthesis, internal ribosome entry sites, and uncapped mRNA were all discovered by studying poliovirus infected cells, and a poliovirus clone was the first infectious DNA clone made of an RNA virus in animals. Along with rhinovirus, poliovirus was the first animal virus to have its structure determined by x-ray crystallography. RNA dependent RNA polymerase was discovered in Mengovirus, a genus of picornaviruses.[10]

Virology

Structure

FMDV structural proteins VP1, VP2, VP3, and VP4 form the biological protomer and icosahedral capsid.


Many picornaviruses have a deep cleft formed by around each of the 12 vertices of icosahedrons. The outer surface of the capsid is composed of regions of VP1, VP2, and VP3. Around each of the vertices is a canyon lined with the C termini of VP1 and VP3. The interior surface of the capsid is composed of VP4 and the N termini of VP1. J. Esposito and Frederick A. Murphy demonstrates cleft structure referred to as canyons, using X-ray crystallography and cryoelectron microscopy.[9]


Genome

Genome organization and proteins of enteroviruses and aphthoviruses

Picornaviruses are classed under Baltimore's viral classification system as group IV viruses, as they contain a single-stranded, positive-sense RNA genome. Their genome ranges between 6.7 and 10.1 (kilobases) in length.[7] Like most positive-sense RNA genomes, the genetic material alone is infectious; although substantially less virulent than if contained within the viral particle, the RNA can have increased infectivity when transfected into cells. The genome RNA is unusual because it has a protein on the 5' end that is used as a primer for transcription by RNA polymerase. This primer is called VPg genome, and it ranges between 2 and 3 kb. VPg contain tyrosine residue at the 3' end. Tyrosine as a –OH source for covalently linked to 5' end of RNA.[9][11]


The 1A, 1B, 1C, and 1D proteins are the capsid proteins VP4, VP2, VP3, and VP1, respectively. Virus-coded proteases perform the cleavages, some of which are intramolecular. The polyprotein is first cut to yield P1, P2, and P3. P1 becomes myristylated at the N terminus before being cleaved to VP0, VP3, and VP1, the proteins that will form procapsids; VP0 will later be cleaved to produce VP2 and VP4. Other cleavage products include 3B (VPg), 2C (an ATPase), and 3D (the RNA polymerase).[9][12]

Replication

RNA elements

Foot-and-mouth disease virus genome and RNA structural elements

Genomic RNAs of picornaviruses possess multiple RNA elements, and they are required for both negative- and positive-strand RNA synthesis. The cis-acting replication element (CRE) is required for replication. The stem-loop-structure that contains the CRE is independent of position, but changes with location between virus types when it has been identified. Also, the 3' end elements of viral RNA are significant and efficient for RNA replication of picornaviruses. The 3' end of picornavirus contains a poly(A) tract, which is required for infectivity. RNA synthesis, though, is hypothesized to occur in this region. The 3' end NCR of poliovirus is not necessary for negative-strand synthesis, but is important element for positive–strand synthesis. Additionally, the 5' end NCR that contains secondary structural elements is required for RNA replication and poliovirus translation initiation. Internal ribosome entry sites are RNA structures that allow cap-independent initiation of translation, and are able to initiate translation in the middle of a messenger RNA.[13]

Lifecycle

Picornavirus life cycle

The viral particle binds to cell surface receptors. Cell surface receptors are characterized for each serotype of picornaviruses. For example, poliovirus receptor is glycoprotein CD155, which is special receptor for human and some other primate species. For this reason, poliovirus could not be made in many laboratories until transgenic mice having a CD155 receptor on their cell surfaces were developed in the 1990s. These animals can be infected and used for studies of replication and pathogenesis.[9] Binding causes a conformational change in the viral capsid proteins, and myristic acid is released. The acid forms a pore in the cell membrane through which RNA is injected.[14]

While the prototype poliovirus model relies on a single receptor (CD155) to trigger both attachment and uncoating, many enteroviruses utilize a multi-step, multi-protein mechanism for entry. For instance, several serotypes of Echovirus (such as Echovirus 7 and 11) bind to decay-accelerating factor (DAF; also known as CD55) on the host cell surface [15]. Structural and biochemical analyses demonstrate that CD55 acts strictly as an attachment factor rather than a true uncoating receptor; binding occurs outside the viral canyon near the icosahedral twofold axes and does not catalyze the destabilization of the native virion or the formation of 135S "A-particles" [16]. Internalization and subsequent genome uncoating require the virus to engage secondary extracellular and intracellular factors. Early research in 1999 established that physiological concentrations of serum albumin actively regulate this pathway, with normal, fatty-acid loaded albumin reversibly blocking echovirus uncoating and protecting the particle in extracellular spaces; this may be a key factor in viral tropism[17]. Moreover, this albumin blocking affect on viral infection is an early example of a protein corona that pre dates the term 'Viral Protein Corona ' as now used in nanoscience where these viruses are considered as nano particles. [1] Conversely, interaction with modified or fatty-acid-depleted albumin can prime the virus, releasing the hydrophobic "pocket factor" and shifting the capsid into a metastable, fenestrated intermediate state that prepares the genome for release upon encountering endosomal ionic environments [18] [19]. In 2019, independent studies identified the neonatal Fc receptor (FcRn)—a cell-surface glycoprotein that physiologically binds and regulates albumin and IgG homeostasis as a pan-echovirus and primary uncoating receptor for major Enterovirus B species [20]. Virus pre- primed by fatty acid deplete albumin, induces binding of FcRn inside the viral canyon, and forces further structural transitions, prompting viral uncoating[21]


Translation takes place by -1 ribosomal frameshifting, viral initiation, and ribosomal skipping. The virus exits in host cell by lysis, and viroporins. Vertebrates serve as the natural hosts. Transmission routes are fecal-oral, contact, ingestion, and air-borne particles.[3]

Viral protein (VPg)

In this group, primer-dependent RNA synthesis uses a small 22– to 25-amino acid-long viral protein linked to the VPg[22] to initiate polymerase activity, where the primer is covalently bound to the 5' end of the RNA template.[23] The uridylylation occurs at a tyrosine residue at the third position of the VPg. A CRE, which is a RNA stem loop structure, serves as a template for the uridylylation of VPg, resulting in the synthesis of VPgpUpUOH. Mutations within the CRE-RNA structure prevent VPg uridylylation, and mutations within the VPg sequence can severely diminish RdRp catalytic activity.[24] While the tyrosine hydroxyl of VPg can prime negative-strand RNA synthesis in a CRE- and VPgpUpUOH-independent manner, CRE-dependent VPgpUpUOH synthesis is absolutely required for positive-strand RNA synthesis. CRE-dependent VPg uridylylation lowers the Km of UTP required for viral RNA replication and CRE-dependent VPgpUpUOH synthesis, and is required for efficient negative-strand RNA synthesis, especially when UTP concentrations are limiting.[25] The VPgpUpUOH primer is transferred to the 3’ end of the RNA template for elongation, which can continue by addition of nucleotide bases by RdRp. Partial crystal structures for VPgs of foot and mouth disease virus[26] and coxsackie virus B3[27] suggest that there may be two sites on the viral polymerase for the small VPgs of the picornaviruses. NMR solution structures of poliovirus VPg[28] and VPgpU[29] show that uridylylation stabilizes the structure of the VPg, which is otherwise quite flexible in solution. The second site may be used for uridylylation, after which the VPgpU can initiate RNA synthesis. The VPg primers of caliciviruses, whose structures are only beginning to be revealed,[30] are much larger than those of the picornaviruses. Mechanisms for uridylylation and priming may be quite different in all of these groups. VPg uridylylation may include the use of precursor proteins, allowing for the determination of a possible mechanism for the location of the diuridylylated, VPg-containing precursor at the 3' end of positive- or negative-strand RNA for production of full-length RNA. Determinants of VPg uridylylation efficiency suggest formation and/or collapse or release of the uridylylated product as the rate-limiting step in vitro depending upon the VPg donor employed.[31] Precursor proteins also have an effect on VPg-CRE specificity and stability.[32] The upper RNA stem loop, to which VPg binds, has a significant impact on both retention, and recruitment, of VPg and Pol. The stem loop of CRE will partially unwind, allowing the precursor components to bind and recruit VPg and Pol4. The CRE loop has a defined consensus sequence to which the initiation components bind, but no consensus sequence exists for the supporting stem, which suggests that only the structural stability of the CRE is important.[33]

Assembly and organization of the picornavirus VPg ribonucleoprotein complex

  1. Two 3CD (VPg complex) molecules bind to CRE with the 3C domains (VPg domain) contacting the upper stem and the 3D domains (VPg domain) contacting the lower stem.
  2. The 3C dimer opens the RNA stem by forming a more stable interaction with single strands forming the stem.
  3. 3Dpol is recruited to and retained in this complex by a physical interaction between the back-of-the-thumb subdomain of 3Dpol and a surface of one or both 3C subdomains of 3CD.

VPg may also play an important role in specific recognition of viral genome by movement proteins (MP), which are nonstructural proteins encoded by many, if not all, plant viruses to enable their movement from one infected cell to neighboring cells.[34] MP and VPg interact to provide specificity for the transport of viral RNA from cell to cell. To fulfill energy requirements, MP also interacts with P10, which is a cellular ATPase.

Diseases

Taxonomy

The family Picornaviridae contains five subfamilies that contain 66 genera. Another two genera are unassigned to subfamilies. These taxa are listed hereafter (-virinae denotes subfamily and -virus denotes genus).[6]

See also

  • Animal viruses

References

  1. ↑ "A highly divergent picornavirus infecting the Gut Epithelia of Zebrafish (Danio rerio) in research institutions worldwide". Zebrafish 16 (3): 291–299. 2019. doi:10.1089/zeb.2018.1710. PMID 30939077. 
  2. ↑ "Chapter 11 – Picornavirus". Molecular virology of human pathogenic viruses.. Korea: Academic Press. 2016. pp. 153–64. doi:10.1016/b978-0-12-800838-6.00011-4. ISBN 978-0-12-800838-6. 
  3. ↑ 3.0 3.1 "Viral Zone". ExPASy. http://viralzone.expasy.org/all_by_species/33.html. 
  4. ↑ 4.0 4.1 "Foot-and-Mouth Disease Virus". Animal Viruses: Molecular Biology. Norfolk, UK: Caister Academic Press. 2008. ISBN 978-1-904455-22-6. https://www.caister.com/avir. 
  5. ↑ "Complete genome analysis of three novel picornaviruses from diverse bat species". Journal of Virology 85 (17): 8819–28. September 2011. doi:10.1128/JVI.02364-10. PMID 21697464. 
  6. ↑ 6.0 6.1 Cite error: Invalid <ref> tag; no text was provided for refs named ICTV1
  7. ↑ 7.0 7.1 "Picornaviridae - Picornaviridae - Picornavirales" (in en). https://talk.ictvonline.org/ictv-reports/ictv_online_report/positive-sense-rna-viruses/picornavirales/w/picornaviridae. 
  8. ↑ "Picornaviridae" (in en). October 2017. https://talk.ictvonline.org/ictv-reports/ictv_online_report/positive-sense-rna-viruses/picornavirales/w/picornaviridae. 
  9. ↑ 9.0 9.1 9.2 9.3 9.4 Carter, John B.; Saunders, Venetia A. (2007). "Picornaviruses (and other plus-strand RNA viruses)". Virology: Principles and applications. Chichester, England: John Wiley & Sons. pp. 160–65. ISBN 978-0-470-02386-0. 
  10. ↑ Knipe, David M.; Howley, Peter (2013). Fields Virology. Lippincott Williams & Wilkins. ISBN 978-1-4698-3066-7. https://books.google.com/books?id=dxIrrMrot3gC. 
  11. ↑ "Cowpea mosaic virus VPg: sequencing of radiochemically modified protein allows mapping of the gene on B RNA". The EMBO Journal 3 (7): 1629–34. July 1984. doi:10.1002/j.1460-2075.1984.tb02021.x. PMID 16453534. 
  12. ↑ Acheson, Nicholas H (2011). Fundamentals of Molecular Virology (2nd ed.). John Wiley & Sons, Inc.. ISBN 978-0470900598. 
  13. ↑ "Mechanistic intersections between picornavirus translation and RNA replication". Advances in Virus Research 80: 1–24. 2011. doi:10.1016/B978-0-12-385987-7.00001-4. ISBN 9780123859877. PMID 21762819. 
  14. ↑ "Pathology, Microbiology and Immunology - School of Medicine Columbia | University of South Carolina". http://pathmicro.med.sc.edu/virol/polio.htm. 
  15. ↑ Ward, T.; Pipkin, P. A.; Clarkson, N. A.; Stone, D. M.; Minor, P. D.; Almond, J. W. (1994-11-01). "Decay-accelerating factor CD55 is identified as the receptor for echovirus 7 using CELICS, a rapid immuno-focal cloning method". The EMBO Journal 13 (21): 5070–5074. doi:10.1002/j.1460-2075.1994.tb06836.x. ISSN 0261-4189. PMID 7525274. 
  16. ↑ He, Yongning; Lin, Feng; Chipman, Paul R.; Bator, Carol M.; Baker, Timothy S.; Shoham, Menachem; Kuhn, Richard J.; Medof, M. Edward et al. (2002-08-06). "Structure of decay-accelerating factor bound to echovirus 7: A virus-receptor complex". Proceedings of the National Academy of Sciences 99 (16): 10325–10329. doi:10.1073/pnas.152161599. PMID 12119400. Bibcode: 2002PNAS...9910325H. 
  17. ↑ Ward, T.; Powell, R. M.; Evans, D. J.; Almond, J. W. (February 1999). "Serum albumin inhibits echovirus 7 uncoating". The Journal of General Virology 80 ( Pt 2) (2): 283–290. doi:10.1099/0022-1317-80-2-283. ISSN 0022-1317. PMID 10073686. 
  18. ↑ Ward, T.; Powell, R. M.; Chaudhry, Y.; Meredith, J.; Almond, J. W.; Kraus, W.; Nelsen-Salz, B.; Eggers, H. J. et al. (April 2000). "Fatty acid-depleted albumin induces the formation of echovirus A particles". Journal of Virology 74 (7): 3410–3412. doi:10.1128/jvi.74.7.3410-3412.2000. ISSN 0022-538X. PMID 10708459. 
  19. ↑ Ruokolainen, Visa; Domanska, Aušra; Laajala, Mira; Pelliccia, Maria; Butcher, Sarah J.; Marjomäki, Varpu (2019-09-01). "Extracellular Albumin and Endosomal Ions Prime Enterovirus Particles for Uncoating That Can Be Prevented by Fatty Acid Saturation". Journal of Virology 93 (17): e00599–19. doi:10.1128/JVI.00599-19. ISSN 1098-5514. PMID 31189702. 
  20. ↑ Zhao, Xin; Zhang, Guigen; Liu, Sheng; Chen, Xiangpeng; Peng, Ruchao; Dai, Lianpan; Qu, Xiao; Li, Shihua et al. (2019-05-30). "Human Neonatal Fc Receptor Is the Cellular Uncoating Receptor for Enterovirus B" (in English). Cell 177 (6): 1553–1565.e16. doi:10.1016/j.cell.2019.04.035. ISSN 0092-8674. PMID 31104841. 
  21. ↑ Morosky, S.; Wells, A. I.; Lemon, K.; Evans, A. S.; Schamus, S.; Bakkenist, C. J.; Coyne, C. B. (2019). "PNAS" (in en). Proceedings of the National Academy of Sciences of the United States of America 116 (9): 3758–3763. doi:10.1073/pnas.1817341116. PMID 30808762. 
  22. ↑ "Poliovirus-specific primer-dependent RNA polymerase able to copy poly(A)". Proceedings of the National Academy of Sciences of the United States of America 74 (9): 3677–80. September 1977. doi:10.1073/pnas.74.9.3677. PMID 198796. Bibcode: 1977PNAS...74.3677F. 
  23. ↑ "Protein is linked to the 5' end of poliovirus RNA by a phosphodiester linkage to tyrosine". The Journal of Biological Chemistry 253 (15): 5263–66. August 1978. doi:10.1016/S0021-9258(17)30361-7. PMID 209034. 
  24. ↑ "Structure-function analysis of mutant RNA-dependent RNA polymerase complexes with VPg". Biochemistry. Biokhimiia 74 (10): 1132–41. October 2009. doi:10.1134/S0006297909100095. PMID 19916926. 
  25. ↑ "Poliovirus cis-acting replication element-dependent VPg Uridylylation lowers the Km of the initiating nucleoside triphosphate for viral RNA replication". Journal of Virology 82 (19): 9400–08. October 2008. doi:10.1128/JVI.00427-08. PMID 18653453. 
  26. ↑ "The structure of a protein primer-polymerase complex in the initiation of genome replication". The EMBO Journal 25 (4): 880–88. February 2006. doi:10.1038/sj.emboj.7600971. PMID 16456546. 
  27. ↑ "The crystal structure of coxsackievirus B3 RNA-dependent RNA polymerase in complex with its protein primer VPg confirms the existence of a second VPg binding site on Picornaviridae polymerases". Journal of Virology 82 (19): 9577–90. October 2008. doi:10.1128/JVI.00631-08. PMID 18632861. 
  28. ↑ "NMR structure of the viral peptide linked to the genome (VPg) of poliovirus". Peptides 27 (7): 1676–84. July 2006. doi:10.1016/j.peptides.2006.01.018. PMID 16540201. 
  29. ↑ "NMR solution structure of poliovirus uridylyated peptide linked to the genome (VPgpU)". Peptides 31 (8): 1441–48. August 2010. doi:10.1016/j.peptides.2010.04.021. PMID 20441784. 
  30. ↑ "Structures of the compact helical core domains of feline calicivirus and murine norovirus VPg proteins". Journal of Virology 87 (10): 5318–30. May 2013. doi:10.1128/JVI.03151-12. PMID 23487472. PMC 3648151. http://spiral.imperial.ac.uk/bitstream/10044/1/11699/4/Leen_etal_JVirol_2013.pdf. Retrieved 4 November 2018. 
  31. ↑ "Picornavirus genome replication: roles of precursor proteins and rate-limiting steps in oriI-dependent VPg uridylylation". The Journal of Biological Chemistry 283 (45): 30677–88. November 2008. doi:10.1074/jbc.M806101200. PMID 18779320. 
  32. ↑ "Human Rhinovirus Type 14 Gain-of-Function Mutants for oriI Utilization Define Residues of 3C(D) and 3Dpol That Contribute to Assembly and Stability of the Picornavirus VPg Uridylylation Complex". J. Virol. 81 (22): 12485–95. November 2007. doi:10.1128/JVI.00972-07. PMID 17855535. 
  33. ↑ "Sequence requirements for viral RNA replication and VPg uridylylation directed by the internal cis-acting replication element (CRE) of human rhinovirus type 14". Journal of Virology 76 (15): 7485–94. August 2002. doi:10.1128/JVI.76.15.7485-7494.2002. PMID 12097561. 
  34. ↑ "Interaction of Sesbania mosaic virus movement protein with VPg and P10: implication to specificity of genome recognition". PLOS ONE 6 (1). January 2011. doi:10.1371/journal.pone.0015609. PMID 21246040. Bibcode: 2011PLoSO...615609R. 

Further reading

Wikidata ☰ Q936600 entry



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