Archaea :Mobile Genetic Elements : Viruses, Plasmids, and Transposons


Definitions and Concepts:

Viruses are extracellular versions of plasmids. They have protein and/or membrane envelopes that allow them to infect other cells.

Plasmids are Non Chromosomal Superintegron versions of Transposons. They are also internal cellular mobile genetic elements that lack encapsulation by capsid proteins

Transposons are evolved versions of Insertion Sequence Elements.

Insertion Sequence elements are evolved versions of Group II Introns and Ribozymes

Group II Introns and Ribozymes come from the RNA-protein world

These mobile genetic elements inherit genes for replication, integration, toxin-antitoxins, capsids and other functions. They transfer these genes to host cells.

The genetic mutation rate for mobile genetic elements is orders of magnitude faster than those of cells.


Archean Mobile Genetic Elements can be Classified as RNA dependent Polymerase agents , Reverse Transcriptase Dependent Agents, or DNA Polymerase dependent agents.

The DNA viruses can be subclassified into vertex protein containing versus nonvertex protein containing, Present in both Euryarchaea + Crenarchea versus those present in just one phylum. An analysis of these classifications results in identification of ancestors versus descendants. These ancestors provide clues to the origin of major protein families, processes of LUCA genesis, and geochemistry at the time of cellular life's origin.

Historical patterns of gene gain and gene loss suggest worlds existed with more gene familys than those on Earth Today. This suggests complex ancestors with more genes than todays cellular systems. However, this analysis may be ignoring the noncoding DNA history of recently evolved beings. The history of life may be one of nc gene gains and losses which are impacted by collision events. The canonical paradigm has been the opposite of what research is suggesting. One school of thought prefers to view ancestral life forms as simplified versions of todays life forms., Whereas the other prefers the opposite. The middle ground is to accept cycles of more primitive or descendant based on 2 points in the cycle history. The cycle periods for these gains and losses my be predicatable. Viruses inform us of the pros and cons of the more advanced versus the more primitive ancestor arguments.


DNA Viruses: ( possible morphological evolution pathways)



  Family, Group, or Species Vertex Proteins Present In All Archaea In All Archaea and Eubacteria

Ligamenviralis - infects thermophillic crenarchaea ds linear DNA

Lipothrixviridae protein attached to linear ds DNA , contains a membrane ie. AFV1


Rudiviridae -- linear dsDNA without a membrane Rolling circle hairpin mode of replication usuing Rep. , DNA primase, and Resolvase

  yes. used for viral escape from cell    
yes no no

alpha lipothrix

beta lipothrix

gamma lipothrix

delta lipothrix

yes no- C no

Bicaudaviridae - enveloped circular dsDNA lysogenic or lytic (tails develop outside of the host)

Bicauda - Eury
?early version    

Fuselloviridae -- circular ds DNA positive supercoiled. Lysogenic in crenarchaea and possible single stranded DNA versions

ssDNA Salterprovirus HIS1 spindle shaped

Fusello - STSV1-Cren
yes yes no

Ampullaviridae - linear ds DNA (? vertex at tip for injection into host)

yes ? no

Guttaviridae - enveloped circular dsDNA lysogenic hypermethylated ABV1 SNDV APSV1 , APOV1

yes no no

Clavaviridae - circular ds DNA 5278bp APBV1 ?nonlysogenic (? Vertex tip for entry into cells. ? outer capsid and internal membrane?)

yes no no

STIV- family circular/linear ds DNA (ie. SH1, SNJ1 , STIV (uses vertex structure to egress from host) Capsid Related to Tectoviridae/PRD1 (uses vertex for release and dna injection into cells) , Adenovirus, and PBCV )

2 MCP SH1 Group is related to :

Thermus thermophilus phage P23-77 , Thermus aquaticus phage ?IN93, Salisaeta icosahedral phage 1 ([SSIP-1], Haloarcula plasmid pHH205 and proviruses


2 MCPs






STIV , STIV2- Cren


yes yes relatives yes
yes ? ?

Caudoviralis - linear ds DNA without membrane

Myoviridae phiCh1(ch1 sequence), phiH-like


Siphoviridae M1/2 , Nvie-Pro1 -Thaumarcheota


Unassigned HF1, and HF2

Myo -Eury


p24, soc

yes yes

Sipho - HRTV1- Eury


HSTV-1 Eury


orf 50 for BJ1

yes yes

Bacillus phage p29 like

group I F29, PZA, F15 and BS32, group II B103, Nf and M2Y, and group III GA-1

Podoviridae (not yet identified in archaea)



Globuloviridae - linear dsDNA enveloped and with helical nucleocapsid

Globulo- Cren



no ? no

Pleolipoviruses- enveloped circular ssDNA and dsDNA with gaps ie. His2 lysogenic with type B DNA polymerase

HRPV-1a 7048 ssDNA 54.2%
HHPV-1b 8082 dsDNA 55.8%
HRPV-2 10656 ssDNA 63.7%
HRPV-3 8770 dsDNA 58.3%
HRPV-6 8549 ssDNA 62.7%
HGPV-1 9694 dsDNA 61.6%


Group I


Group II


Group III

no ? no

ACV circular ssDNA hyperthermophile 24.8K nt

?ORF273 possible helix forming protein with binding sites for glycerol and sulfate

superhelical rod shaped cylinder with dna wrapped inside nucleocapsid helical fiber. Cylinder appears hollow ?

? contributes to the sheath protein of myoviruses or to podophage injection system


Positive Strand RNA virus capsid protein similar to nodaviruses, tetraviruses, and birnaviruses

virus from metagenomic information. structure yet to be elucidated. However it might be inferred based on similar capsid protein in other viruses. Contains an RdRp gene





Archael Plasmids -


pHH205 genome identical to SNJ1 virus

Crenarchaea Plasmids:

Theta Replication

PNOB8 like 24-36 kb 40-50 proteins transposase integrase not disrupted - pAH1 (mobilized by lipothrix AFV1) DNA primase, polymerase, helicase SFII,

Rolling Circle Replication

pRN type 5-14kb repa protien gag + prla +integrase - PTIK4, PTau4, PXZ1 (mcm helicase) , pSSVx packaged with fusellovirus SSV type integrase with internal insetion sites inside,

Conugative plasmids TraG, TraE

Plasmids- Euryarchaea

less than 5Kb RC replication pGT5 and pTN1 rep 75 and 74 related to transposases of IS 91, 1294, 801 , pRT1 Rep without sequence matches probable RC mode

pTN2 13kb Rep is a new DNA polymerase probable Theta mode of replication. pP12-1, PT26-2 20kb Rep has a new helicase

Thermococcus Plasmids 2 Groups: pTN2-like and pEXT9a-like.

Transposons and proviruses

NVie Pro1 Prophage in Thaumarchaea

SP01-like prohage in Korarchaea

Mu provirus in Thaumarchean


Topics for f Exploration:

1. Evolution of the Vertex Pyrimidal Proteins for Virus Release and Virus Entry ? Giant NCLDVs ----> small NCLDVs or vice versa

2. Evolution of Capsid proteins

3 Evolution of Family A, B, and C polymerases contained in viruses.

4. Evolution of tail measurement poteins.

5. Evolution of RdRps in Archael and Eubacterial Viruses

6. Evolution of membranes in Archael and Eubacterial Viruses

7. Evolution of membrane proteins in Archael and Eubacterial Viruses

8. Evolution of Tail Proteins.

9. Evolution of Viral Tail Fibers

10. Evoultion of viral baseplate proteins.

11. Evolution of external petidoglycans in archael and eubacterial viruses

12. Evolution of Insertion Sequences and Transposons in Archael and Eubacterial Viruses.

13. Timing of evolutionary and revolutionary biological inventions. (From the perspective of archaea and eubacteria)

14. Evolution of protein superfamily folds and domains in Archaea , Eubacteria, and their Viruses.

15. Metabolic and energy requirements of Archael and Eubacterial Viruses.

16. Fossil evidence of pre-LUCA chronocytes, pre-LECA cells and their viruses. ? Related to Acritarch findings.

17. Correlations of Evolution with Planet Formation related Impacts.

18. Correlations of Evolution with Geochemical History.

19. Correlation of Evolution with Radiation/Radioactivity Histories.

If you are interested in collaborating on these topics then please send an email to



Archaeal viruses—novel, diverse and enigmatic

Viruses of the Archaea: a unifying view

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

Phages in Nature

Common Origin of Four Diverse Families of Large Eukaryotic DNA Viruses

A thaumarchaeal provirus testifies for an ancient association of tailed viruses with archaea

Uniprot Taxonomy

Classification of Myoviridae bacteriophages using protein sequence similarity.

Bacteriophage SPO1 structure and morphogenesis. II. Head structure and DNA size.

The genome of Bacillus subtilis bacteriophage SPO1

Labome: Archael Viruses

The archeoviruses.

Virion architecture unifies globally distributed pleolipoviruses infecting halophilic archaea.

Identification of novel positive-strand RNA viruses by metagenomic analysis of archaea-dominated Yellowstone hot springs.

Small RNAs for defence and regulation in archaea.

Related haloarchaeal pleomorphic viruses contain different genome types

Virion architecture unifies globally distributed pleolipoviruses infecting halophilic archaea.

An ssDNA virus infecting archaea: a new lineage of viruses with a membrane envelope


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