2. • The domain Archaea was proposed about 40 years ago by Carl woese (1977) and the
study of viruses associated with it has used classical bacteriophage techniques.
• They may be almost as common as the Bacteria in oceans, soils and subterranean
environments and also show enormous diversity.They also occupy and can predominate
in so-called extreme environments, such as hot-springs, salt and soda lakes. Likewise,
there is every reason to assume that viruses of the Archaea are as numerous and
diverse as those of the bacteria.
2
3. Virus or Phage in archaea ?
• In fact, to date, there are no reports of any archaeal virus that can
infect Bacteria, nor any report of a bacterial phage that can
infect Archaea.
• Phages evolving genes that facilitate infection of the host of their
bacterial host.Thus, Bacteria are simply a vehicle to allow phages to
infect eukaryotes. But Archaea lack any canonical virulence factors.
• Most viruses infecting archaea have nothing in common with those
infecting bacteria, although they are still considered as
“bacteriophages” by many virologists, just because archaea and
bacteria are both prokaryotes (without nucleus).
The proportional lack of archaeal pathogens: Do viruses/phages hold the key? Erin E Gill, Fiona
Brinkman, Bioassay, 2011 apr, 33(4): 248–254.
3
4. • Though these archaeal viruses are clearly
different from bacterial phages, there are some
archaeal viruses associated with members of the
Euryarchaeota that belong to the myovirus and
siphovirus families. However, only three archaeal
myoviruses and siphoviruses have been
sequenced
• Phi Ch1 or ϕCh1 (myovirus)
• PsiM1 or ψM1 (siphovirus)
• PsiM100 or ψM100 (siphovirus)
Defining life: the virus viewpoint.Forterre P Orig Life Evol Biosph. 2013 Apr; 40(2):151-60.
4
5. • No viruses of the Archaea with an RNA genome have yet been identified,
but it would seem likely that they exist. just as they do in the domains
Bacteria and Eukarya. In fact archaeal viruses, which to date all have
dsDNA genomes, exhibit a range of virion morphotypes, most of which
have not been observed before for any dsDNA virus.
5
6. There are exceptional forms, including fusiforms, droplet and bottle
shapes, and linear and spherical virions. Moreover, genome-sequence
analyses have demonstrated that most of the archaeal viruses are
unrelated to other known viruses and suggest that they might have
different, and possibly multiple, evolutionary origins.
6
7. The viruses of Crenarchaeota
• Around 30 viruses infecting the Crenarchaeota have been
described not only for generally being isolated from
hyperthermophilic hosts growing at temperatures > 80°C but also for
an array of unusual morphologies not observed in viruses of the
Eukarya or Bacteria.
• SSV1 : The Fuselloviridae e.g. SSV1 virus, infecting members of the
genera Sulfolobus and possibly Acidianus, which have small circular
genomes from ∼15–24 kb
• SIRV: The rod shaped Rudiviridae, SIRV1 and SIRV2 viruses with 35
kb genomes, infect Sulfolobus species
• SIFV: an enveloped flexible filamentous virus with a 41 kb genome
infecting Sulfolobus, is a member of the Lipothrixviridae.
Redder P, Environ Microbiol. 2009 Nov; 11(11):2849-62.
A novel virus family, the Rudiviridae: Structure, virus-host interactions and genome variability of the
sulfolobus viruses SIRV1 and SIRV2.1999
A novel lipothrixvirus, SIFV, of the extremely thermophilic crenarchaeon Sulfolobus.2000 7
8. The viruses of Crenarchaeota
• SNDV: The Sulfolobus neozealandicus droplet shaped virions of
the Guttaviridae, all have circular genomes of around 20 kb.
• ABV: The Acidianus bottle shaped virion of Ampullaviridae, are
exemplified by which has a linear 24 kb genome.
• ATV: The Acidianus two tailed virion of the Bicaudaviridae has a
genome of 62 Kb
• PSV: The Pyrobaculum spherical virus of the Globuloviridae also
exist.
SNDV, a novel virus of the extremely thermophilic and acidophilic archaeon Sulfolobus.2000
Viral diversity in hot springs of Pozzuoli, Italy, and characterization of a unique archaeal virus,
Acidianus bottle-shaped virus, from a new family, the Ampullaviridae.2005
Structural and genomic properties of the hyperthermophilic archaeal virus ATV with an
extracellular stage of the reproductive cycle.2006
Morphology and genome organization of the virus PSV of the hyperthermophilic archaeal genera
Pyrobaculum and Thermoproteus: a novel virus family, the Globuloviridae.2004
8
9. The viruses of Euryarchaeota
• Euryarchaeota predominate in high salt environments and also
contains metanogens.
• About 20 viruses have been studied from salt environments, infecting
members of the genera Halobacteriales (Halophiles).
• The temperate myovirus ϕCh1 virus which has a 58.5 kb linear
genome, and infects the haloalkaliphilic host Natrialba magadii
• The lytic viruses HF1 virus and the closely related HF2 virus, have
linear genomes of 75.9 kb and 77.7 kb and infect the Haloferax
lucentense and Halorubrum coriense, respectively.
• BJ1 virus with a 43 kb genome infects Halorubrum kocuri.
Sequence analysis of an Archaeal virus isolated from a hypersaline lake in Inner Mongolia, China.2007
Halorubrum kocurii sp. nov., an archaeon isolated from a saline lake.2008
9
10. The viruses of Euryarchaeota
• A lytic icosahedral SH1 virus having a linear genome of 31 kb
infects Haloarcula hispanica.
• The Salterprovirus include His1 and His2 viruses have linear
genomes of 14.5 and 16 kb respectively with lacking integrase
gene that infect Haloarcula hispanica.
• The only archaeal virus thus far identified not having a dsDNA
genome is the (HRPV-1) virus or Halorubrum pleomorphic virus
1 which has a ssDNA genome 7048 nucleotides in size.
SH1: A novel, spherical halovirus isolated from an Australian hypersaline lake.2015
His1 and His2 are distantly related, spindle-shaped haloviruses belonging to the novel
virus group, Salterprovirus.2016
An ssDNA virus infecting archaea: a new lineage of viruses with a membrane
envelope.2009 10
11. The Euryarchaeotal methanogens also have identified viruses,
like Psi M1 (ψM1) virus with a linear dsDNA 30 kb genome
isolated from:
Methanothermobacter marburgensis
Figure: FISH image of Methanothermobacter by MiDAS field guide
Molecular analysis of Methanobacterium phage psiM2.Pfister P, Wasserfallen A,
Stettler R, Leisinger T Mol Microbiol. 2008 Oct; 30(2):233-44.
12. The (SSV1) : Sulfolobus spindle-shaped virus 1
The virus of Crenarchaeota.
Its circular genome is positively supercoiled,
and during infection it integrates into a tRNA gene in
the host chromosome (Sulfolobus and possibly Acidianus),
and Producing partitioned integrase gene while the tRNA
gene remains intact
UV irradiation or mytomycin treatment induce viral
replication and temporarily inhibit the growth of
lysogens for causing their lysis.
Nadal, Positively supercoiled DNA in a viruslike particle of an archaebacterium. Nature 321, 256–258 (2006).
SSV1-encoded site-specific recombination system in Sulfolobus.2013
Martin, A. et al. SAV1, a temperate u.v.-inducible DNA virus-like particle from the archaebacterium Sulfolobus
acidocaldarius isolate B12. EMBO J. 3, 2165–2168 (2014). 12
13. The (SSV1) : Sulfolobus spindle-shaped virus 1
13
The Figures are courtesy of W. Zillig.
14. The (ATV): Acidianus two-tailed virus
ATV virus is the only known virus of the acidophilic,
hyperthermophilic Crenarchaea (Acidianus) that is
capable of host lysis. Its reproductive cycle has some
unique features.
Virions are extruded from host cells as tail-less,
fusiform particles, which then develop long tails at
each pointed end at temperatures above 75°C, close to
the temperature of the natural habitat of the host
One function of the elongated, flexible tails might be
to enhance the probability of virion adsorption to a
new host cell.
• Haring, M. et al. Virology: independent virus development outside a host. Nature 436, 1101–1102 (2005).
• Prangishvili, D.ATV with an extracellular stage of the reproductive cycle. Mol. Biol. 359, 1203–1216 (2006). 14
16. The Salterprovirus (His 1 and His 2 viruses)
• His1 and His2 viruses infect strains of the extremely
halophilic genus Haloarcula of the Euryarchaeota.
Both viruses are lytic and the linear genomes show
no sequence similarity to the circular genomes of
the other fusiform viruses.
• The virions of these viruses are similar in size (44 ×
67–77 nm) but, despite pronounced morphological
similarities, their major structural proteins are not
orthologous. Each of the viruses encodes a DNA
polymerase which might be primed by proteins
attached to the termini of their linear genomes.
• Bath, C.His1 and His2 are distantly related, spindle-shaped haloviruses belonging to the novel
virus group, Salterprovirus. Virology 350, 228–239 (2006).
16
18. The ABV virus – bottle shape
• The Acidianus bottle-shaped virus (ABV) has a complex form
resembling a Bottle infects the hyperthermophilic Acidianus genus
and has been assigned to the new family ‘Ampullaviridae. The virion
has no elements of icosahedral or helical symmetry and differs in its
basic architecture from any known virus.
18
Figure is reproduced with permission from REF. 31 c (2005) American Society for
Microbiology.
19. 19
The SNDV virus
The Sulfolobus neozealandicus droplet-shaped virus (SNDV): a novel virus of
the extremely thermophilic and acidophilic crenarchaeon Sulfolobus and is the
sole member of the family Guttaviridae.
• The circular dsDNA genome of 20 kb, which is modified by dam-like methylation.
It is cleaved by only a few type II restriction enzymes e.g. DpnI but not Mbol,
demonstrating an N(6)-methylation of the adenine residue in GATC. sequences.
Zillig, SNDV, Virology (2010).
a: SSV1, b: ATV, c: ABV, d: SNDV
20. The Linear Archaeaviruses
• Linear particles are the main virion type found in
terrestrial hot environments (>80°C) where
crenarchaea of the genera Sulfolobus, Acidianus
and Thermoproteus predominate.
(SIRV): Sulfolobus islandicus rod-shaped virus
(AFV): Acidianus filamentous virus
(SIFV): Sulfolobus islandicus filamentous virus
(TTV): Thermoproteus tenax virus
20
21. 21
Electron Micrographs of Sulfolobus islandicus rod-shaped viruses SIRV5 (a) and SIRV8
(b) stained with 2% uranyl acetate. Scale bar 100 nm.
The SIRV virus: rod virus of Sulfolobus
islandicus
22. 22
AFV: Electron micrographs of 2-μm-long filamentous viruses from a hot spring at Pozzuoli,
Italy. Journal of Virology, American society of microbiology.2008
The AFV virus: filamentous virus of Acidianus sp.
28. SH1 virus: spherical virus of Haloarcula hispanica
28
Figure: PMID 18515426, EMDB EMD 2008
29. Electron micrographs of linear and spherical viruses of the archaea
29
a | Sulfolobus islandicus rod-shaped virus 1 (SIRV1)
b | Acidianus filamentous virus 1 (AFV1)
c | Acidianus filamentous virus 2 (AFV2) (with terminal structures
d | Pyrobaculum spherical virus (PSV)
e | Haloarcula hispanica virus (SH1)
Figure: By David Prangishvili , Viruses of the Archaea: a
unifying view
30. The Head-tail viruses
They are non-enveloped virions carrying icosahedral heads and helical tails .
All are associated with the kingdom Euryarchaeota and they exclusively infect
extreme halophiles or methanogens that are either mesophilic or moderately
thermophilic.
Bacteriophages and archaeal head-tailed viruses share a common architectural
principle but their genome is so different.
30
Electron micrographs of head-tail viruses of
archaea and bacteria.
a | The haloarchaeal virus φH1.
b | The bacteriophage P2.
Both are negatively stained with uranyl
acetate.
32. The ecology of the archaeal viruses
• Despite the widespread presence of archaea on our
planet, specific screening for archaeal viruses so far has
only been done in extreme hydrothermal and hypersaline
environments.
• The most subsets of known morphotypes of archaeal
viruses have been observed at geothermal environments
• Iceland
• Eastern Russia (the Kamchatka peninsula),
• The Naples region of Italy
• Yellowstone National Park in the USA
• in deep-sea hydrothermal vents
32
34. Conclusion:
• The environment in which phages and their hosts
inhabit and have evolved in, may have shaped their
evolutionary trajectories such as their life cycle and
gene content.
• Although it has been shown that, archaeal viruses
show lytic, temperate and chronic life styles, few
studies have looked at the impact that the viruses have
on their host diversity and population structure.
• It has been suggested that the archaea following phage
exposure over time has multiple resistance
mechanisms to the phage they were exposed to.
34
35. • Metagenomic data will determine which genes in
phage-host interaction or cooperation are the most
important.
• Hopefully a fuller understanding of phage dynamics in
natural systems will assist in programmes to exploit
phages for example as therapeutic agents with which
to control bacterial pathogens.
• Detailed information about replication and virion
structures are only just starting to emerge in archaeal
phages and these are all largely questions for future
study. Exciting discoveries of novel biology can be
expected by science enthusiasts.
35
36. References:
• The proportional lack of archaeal pathogens: Do viruses/phages hold the
key? Erin E. Gill and Fiona S. L. Brinkman. Bioessays 33: 248–254, 2011.
• Prangishvili D, Forterre P, Garrett RA. 2006. Viruses of the archaea: a
unifying view. Nat Rev Microbiol 4: 837–48
• Liu Y, Whitman WB. 2008. Metabolic, phylogenetic and ecological diversity
of the methanogenic archaea. Ann NY Acad Sci 1125: 171–89.
• Phages in nature, Martha R.J. Clokie, Bacteriophage 1:1, 31-45;
January/February 2011; c 2011 Landes Bioscience
• Lawrence CM. Structural and functional studies of archaeal viruses. J Biol
Chem 2009:12599-603; PMID: 19158076.
• Mochizuki T, Diversity of viruses of the hyperthermophilic archaeal genus
Aeropyrum, and isolation of the Aeropyrum pernix bacilliform virus 1,
APBV1, the first representative of the family Clavaviridae. Virology 2010;
402:347-54; PMID: 20430412
• Eukaryotic-Like Virus Budding in Archaea.Quemin ER et al, MBIOSep.
2016
36
37. • Haring M, Viral diversity in hot springs of Pozzuoli, Italy, and
characterization of a unique archaeal virus, acidianus bottle-
shaped virus, from a new family, the Ampullaviridae. J Virol
2005; 79:9904-11; PMID: 16014951
• Prangishvili D, Structural and genomic properties of the
hyperthermophilic archaeal virus ATV with an extracellular
stage of the reproductive cycle. J Mol Biol 2006; 359:1203-16;
PMID: 16677670
• Marine archaea and archaeal viruses under global change.
Danovaro R et al. 2017 Jul , PMID: 29034077
• Structure and mechanisms of viral transcription factors
in archaea. Sheppard C, Warner F, Extremophiles. 2017 jul 5
• Haring M, Morphology and genome organization of the virus
PSV of the hyperthermophilic archaeal genera Pyrobaculum and
Thermoproteus: a novel virus family, the Globuloviridae.
Virology 2004; 323:233-42; PMID: 15193919
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