Misplaced Pages

Virosphere

Article snapshot taken from Wikipedia with creative commons attribution-sharealike license. Give it a read and then ask your questions in the chat. We can research this topic together.
Viral part of the biosphere

Virosphere (virus diversity, virus world, global virosphere) was coined to refer to all those places in which viruses are found or which are affected by viruses. However, more recently virosphere has also been used to refer to the pool of viruses that occurs in all hosts and all environments, as well as viruses associated with specific types of hosts (prokaryotic virosphere, archaeal virosphere, Invertebrate  virosphere), type of genome  (RNA virosphere, dsDNA virosphere) or ecological niche (marine virosphere).

Viral genome diversity

The scope of viral genome diversity is enormous compared to cellular life. Cellular life including all known organisms have double stranded DNA genome. Whereas viruses have one of at least 7 different types of genetic information, namely dsDNA, ssDNA, dsRNA, ssRNA+, ssRNA-, ssRNA-RT, dsDNA-RT. Each type of genetic information has its specific manner of mRNA synthesis. Baltimore classification is a system providing overview on these mechanisms for each type of genome. Moreover, in contrast to cellular organisms, viruses don't have universally conserved sequences in their genomes to be compared by.

Viral genome size varies approximately 1000 fold. Smallest viruses may consist of only from 1–2 kb genome coding for 1 or 2 genes and it is enough for them to successfully evolve and travel through space and time by infecting and replicating (make copies of their own) in its host. Two most basic viral genes are replicase gene and capsid protein gene, as soon as virus has them it represents a biological entity able to evolve and reproduce in cellular life forms. Some viruses may have only replicase gene and use capsid gene of other e.g. endogenous virus. Most viral genomes are 10-100kb, whereas bacteriophages tend to have larger genomes carrying parts of genome translation machinery genes from their host. In contrast, RNA viruses have smaller genomes, with maximum 35kb by coronavirus. RNA genomes have higher mutation rate, that is why their genome has to be small enough in order not to harbour to many mutations, which would disrupt the essential genes or their parts. The function of the vast majority of viral genes remain unknown und the approaches to study have to be developed. The total number of viral genes is much higher, than the total number of genes of three domains of life all together, which practically means viruses encode most of the genetic diversity on the planet.

Viral host diversity

Viruses are cosmopolites, they are able to infect every cell and every organism on planet earth. However different viruses infect different hosts. Viruses are host specific as they need to replicate (reproduce) within a host cell. In order to enter the cell viral particle needs to interact with a receptor on the surface of its host cell. For the process of replication many viruses use their own replicases, but for protein synthesis they are dependent on their host cell protein synthesis machinery. Thus, host specificity is a limiting factor for viral reproduction.

Some viruses have extremely narrow host range and are able to infect only 1 certain strain of 1 bacterial species, whereas others are able to infect hundreds or even thousands of different hosts. For example cucumber mosaic virus (CMV) can use more than 1000 different plant species as a host. Members of viral families like Rhabdoviridae infect hosts from different kingdoms e.g. plants and vertebrates. And members of genera Psimunavirus and Myohalovirus infect hosts from different domains of life e.g. bacteria and archaea.

Viral capsid diversity

Capsid is the outer protecting shell or scaffold of a viral genome. Capsid enclosing viral nucleic acid make up viral particle or a virion. Capsid is made of protein and sometimes has lipid layer harboured from the host cell while exiting it. Capsid proteins are highly symmetrical and assemble within a host cell by their own due to the fact, that assembled capsid is more thermodynamically favourable state, than separate randomly floating proteins. The most viral capsids have icosahedral or helical symmetry, whereas bacteriophages have complex structure consisting of icosahedral head and helical tail including baseplate and fibers important for host cell recognition and penetration. Viruses of archaea infecting hosts living in extreme environments like boiling water, highly saline or acidic environments have totally different capsid shapes and structures. The variety of capsid structures of Archaeal viruses includes lemon shaped viruses Bicaudaviridae of family and Salterprovirus genus, spindle form Fuselloviridae, bottle shaped Ampullaviridae, egg shaped Guttaviridae.

Capsid size of a virus differs dramatically depending on its genome size and capsid type.Icosahedral capsids are measured by diameter, whereas helical and complex are measured by length and diameter. Viruses differ in capsid size in a spectrum from 10 to more than 1000 nm. The smallest viruses are ssRNA viruses like Parvovirus. They have icosahedral capsid approximately 14 nm in diameter. Whereas the biggest currently known viruses are Pithovirus, Mamavirus and Pandoravirus. Pithovirus is a flask-shaped virus 1500 nm long and 500 nm in diameter, Pandoravirus is an oval-shaped virus1000nm (1 micron) long and Mamavirus is an icosahedral virus reaching approximately 500 nm in diameter. Example of how capsid size depends on the size of viral genome can be shown by comparing icosahedral viruses - the smallest viruses are 15-30 nm in diameter have genomes in range of 5 to 15 kb (kilo bases or kilo base pairs depending on type of genome), and the biggest are near 500 nm in diameter and their genomes are also the largest, they exceed1Mb (million base pairs).

Viral evolution

Viral evolution or evolution of viruses presumably started from the beginning of the second age of RNA world, when different types of viral genomes arose through the transition from RNA- RT –DNA, which also emphasises that viruses played a critical role in the emergence of DNA and predate LUCA The abundance and variety of viral genes also imply that their origin predates LUCA. As viruses do not share unifying common genes they are considered to be polyphyletic or having multiple origins as opposed to one common origin as all cellular life forms have. Virus evolution is more complex as it is highly prone to horizontal gene transfer, genetic recombination and reassortment. Moreover viral evolution should always be considered as a process of co-evolution with its host, as a host cell is inevitable for virus reproduction and hence, evolution.

Viral abundance

Viruses are the most abundant biological entities, there are 10^31 viruses on our planet. Viruses are capable of infecting all organisms on earth and they are able to survive in much harsher environments, than any cellular life form. As viruses can not be included in the tree of life there is no separate structure illustrating viral diversity and evolutionary relationships. However, viral ubiquity can be imagined as a virosphere covering the whole tree of life.

Nowadays we are entering the phase of exponential viral discovery. The genome sequencing technologies including high-throughput methods allow fast and cheap sequencing of environmental samples. The vast majority of the sequences from any environment, both from wild nature and human made, reservoirs are new. It practically means that during over 100 years of virus research from the discovery of bacteriophages - viruses of bacteria in 1917 until current time we only scratched on a surface of a great viral diversity. The classic methods like viral culture used previously allowed to observe physical virions or viral particles using electron microscope, they also allowed to gathering information about their physical and molecular properties. New methods deal only with the genetic information of viruses.

See also

References

  1. "World Wide Words: Virosphere". World Wide Words. Retrieved 2023-04-13.
  2. Suttle, Curtis (2005). "The viriosphere: the greatest biological diversity on Earth and driver of global processes". Environmental Microbiology. 7 (4): 481–482. Bibcode:2005EnvMi...7..481S. doi:10.1111/j.1462-2920.2005.803_11.x. ISSN 1462-2912. PMID 15816923. S2CID 40555592.
  3. Abroi, Aare; Gough, Julian (2011). "Are viruses a source of new protein folds for organisms? – Virosphere structure space and evolution". BioEssays. 33 (8): 626–635. doi:10.1002/bies.201000126. ISSN 1521-1878. PMID 21633962. S2CID 6680980.
  4. Krupovic, Mart; Prangishvili, David; Hendrix, Roger W.; Bamford, Dennis H. (2011). "Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere". Microbiology and Molecular Biology Reviews. 75 (4): 610–635. doi:10.1128/mmbr.00011-11. PMC 3232739. PMID 22126996.
  5. ^ Prangishvili, David; Bamford, Dennis H.; Forterre, Patrick; Iranzo, Jaime; Koonin, Eugene V.; Krupovic, Mart (December 2017). "The enigmatic archaeal virosphere". Nature Reviews Microbiology. 15 (12): 724–739. doi:10.1038/nrmicro.2017.125. ISSN 1740-1534. PMID 29123227. S2CID 21789564.
  6. Shi, Mang; Lin, Xian-Dan; Tian, Jun-Hua; Chen, Liang-Jun; Chen, Xiao; Li, Ci-Xiu; Qin, Xin-Cheng; Li, Jun; Cao, Jian-Ping; Eden, John-Sebastian; Buchmann, Jan (December 2016). "Redefining the invertebrate RNA virosphere". Nature. 540 (7634): 539–543. Bibcode:2016Natur.540..539S. doi:10.1038/nature20167. ISSN 1476-4687. PMID 27880757. S2CID 1198891.
  7. Urayama, Syun-ichi; Takaki, Yoshihiro; Nishi, Shinro; Yoshida-Takashima, Yukari; Deguchi, Shigeru; Takai, Ken; Nunoura, Takuro (2018). "Unveiling the RNA virosphere associated with marine microorganisms". Molecular Ecology Resources. 18 (6): 1444–1455. doi:10.1111/1755-0998.12936. ISSN 1755-0998. PMID 30256532. S2CID 52821905.
  8. Iranzo, Jaime; Krupovic, Mart; Koonin, Eugene V. (2016). "The Double-Stranded DNA Virosphere as a Modular Hierarchical Network of Gene Sharing". mBio. 7 (4). doi:10.1128/mbio.00978-16. PMC 4981718. PMID 27486193.
  9. Mizuno, Carolina Megumi; Rodriguez-Valera, Francisco; Kimes, Nikole E.; Ghai, Rohit (2013-12-12). "Expanding the Marine Virosphere Using Metagenomics". PLOS Genetics. 9 (12): e1003987. doi:10.1371/journal.pgen.1003987. ISSN 1553-7404. PMC 3861242. PMID 24348267.
  10. Holmes, Edward C. (2010-01-26). "The comparative genomics of viral emergence". Proceedings of the National Academy of Sciences. 107 (suppl 1): 1742–1746. doi:10.1073/pnas.0906193106. PMC 2868293. PMID 19858482.
  11. Hurwitz, Bonnie L.; U'Ren, Jana M.; Youens-Clark, Ken (May 2016). Millard, Andrew (ed.). "Computational prospecting the great viral unknown". FEMS Microbiology Letters. 363 (10): fnw077. doi:10.1093/femsle/fnw077. ISSN 1574-6968. PMID 27030726.
  12. Rohwer, Forest; Barott, Katie (2013-03-01). "Viral information". Biology & Philosophy. 28 (2): 283–297. doi:10.1007/s10539-012-9344-0. ISSN 1572-8404. PMC 3585991. PMID 23482918.
  13. Palukaitis, Peter; Roossinck, Marilyn J.; Dietzgen, Ralf G.; Francki, Richard I.B. (1992-01-01). "Cucumber MOSAIC Virus". Advances in Virus Research. 41: 281–348. doi:10.1016/S0065-3527(08)60039-1. ISBN 9780120398416. ISSN 0065-3527. PMID 1575085.
  14. Hogenhout, Saskia A.; Redinbaugh, Margaret G.; Ammar, El-Desouky (June 2003). "Plant and animal rhabdovirus host range: a bug's view". Trends in Microbiology. 11 (6): 264–271. doi:10.1016/s0966-842x(03)00120-3. ISSN 0966-842X. PMID 12823943.
  15. Dyall-Smith, Mike; Palm, Peter; Wanner, Gerhard; Witte, Angela; Oesterhelt, Dieter; Pfeiffer, Friedhelm (March 2019). "Halobacterium salinarum virus ChaoS9, a Novel Halovirus Related to PhiH1 and PhiCh1". Genes. 10 (3): 194. doi:10.3390/genes10030194. PMC 6471424. PMID 30832293.
  16. Kizziah, James L.; Manning, Keith A.; Dearborn, Altaira D.; Dokland, Terje (2020-02-18). "Structure of the host cell recognition and penetration machinery of a Staphylococcus aureus bacteriophage". PLOS Pathogens. 16 (2): e1008314. doi:10.1371/journal.ppat.1008314. ISSN 1553-7374. PMC 7048315. PMID 32069326.
  17. Abergel, Chantal; Legendre, Matthieu; Claverie, Jean-Michel (2015-11-01). "The rapidly expanding universe of giant viruses: Mimivirus, Pandoravirus, Pithovirus and Mollivirus". FEMS Microbiology Reviews. 39 (6): 779–796. doi:10.1093/femsre/fuv037. ISSN 0168-6445. PMID 26391910.
  18. Holmes, Edward C. (2011). "What Does Virus Evolution Tell Us about Virus Origins?". Journal of Virology. 85 (11): 5247–5251. doi:10.1128/jvi.02203-10. PMC 3094976. PMID 21450811.
  19. Krupovic, Mart; Dolja, Valerian V.; Koonin, Eugene V. (November 2020). "The LUCA and its complex virome". Nature Reviews Microbiology. 18 (11): 661–670. doi:10.1038/s41579-020-0408-x. ISSN 1740-1534. PMID 32665595. S2CID 220516514.
  20. Edwards, Robert A.; Rohwer, Forest (June 2005). "Viral metagenomics". Nature Reviews Microbiology. 3 (6): 504–510. doi:10.1038/nrmicro1163. ISSN 1740-1534. PMID 15886693. S2CID 8059643.
  21. Iranzo, Jaime; Krupovic, Mart; Koonin, Eugene V. (2017-03-04). "A network perspective on the virus world". Communicative & Integrative Biology. 10 (2): e1296614. doi:10.1080/19420889.2017.1296614. ISSN 1942-0889. PMC 5398231. PMID 28451057.
  22. Krupovic, Mart; Dolja, Valerian V.; Koonin, Eugene V. (July 2019). "Origin of viruses: primordial replicators recruiting capsids from hosts". Nature Reviews Microbiology. 17 (7): 449–458. doi:10.1038/s41579-019-0205-6. ISSN 1740-1534. PMID 31142823. S2CID 169035711.
  23. Suttle, Curtis A. (October 2007). "Marine viruses — major players in the global ecosystem". Nature Reviews Microbiology. 5 (10): 801–812. doi:10.1038/nrmicro1750. ISSN 1740-1534. PMID 17853907. S2CID 4658457.
  24. Breitbart, Mya; Rohwer, Forest (June 2005). "Here a virus, there a virus, everywhere the same virus?". Trends in Microbiology. 13 (6): 278–284. doi:10.1016/j.tim.2005.04.003. ISSN 0966-842X. PMID 15936660.
  25. "V-table – the interactive structured virosphere" (PDF). dpublication.com. 6 December 2019. Retrieved 18 September 2021.
  26. Gulino, K.; Rahman, J.; Badri, M.; Morton, J.; Bonneau, R.; Ghedin, E. (2020-06-30). Gilbert, Jack A. (ed.). "Initial Mapping of the New York City Wastewater Virome". mSystems. 5 (3). doi:10.1128/mSystems.00876-19. ISSN 2379-5077. PMC 7300365. PMID 32546676.
  27. Labonté, Jessica M.; Suttle, Curtis A. (November 2013). "Previously unknown and highly divergent ssDNA viruses populate the oceans". The ISME Journal. 7 (11): 2169–2177. Bibcode:2013ISMEJ...7.2169L. doi:10.1038/ismej.2013.110. ISSN 1751-7370. PMC 3806263. PMID 23842650.

External links

Microbiology: Virus
Components
Viral life cycle
Genetics
By host
Other
Self-replicating organic structures
Cellular life
Virus
Subviral
agents
Viroid
Helper-virus
dependent
Satellite
  • ssRNA satellite virus
  • dsDNA satellite virus (Virophage)
  • ssDNA satellite virus
  • ssDNA satellite
  • dsRNA satellite
  • ssRNA satellite (Virusoid)
  • Satellite-like nucleic acids
    • RNA
    • DNA
Other
Prion
Nucleic acid
self-replication
Mobile genetic
elements
Other aspects
Endosymbiosis
Abiogenesis
See also
Categories: