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)
?early version Fuselloviridae -- circular ds DNA positive supercoiled. Lysogenic in crenarchaea and possible single stranded DNA versions
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
SH1/STIV-family
2 MCPs
SH1-Eury
PH1-eury
HHIV-2-eury
SNJ1-eury
1 MCP
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
yes
p24, soc
yes yes yes
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
PSV
TTSV-1
no ? no Pleolipoviruses- enveloped circular ssDNA and dsDNA with gaps ie. His2 lysogenic with type B DNA polymerase
Pleolipo
Group I
HHPV-1HRPV-2HRPV-6Group II
HGPV-1HRPV-3Group III
HIS-2no ? 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 drcarr@telemedical.com.
References:
Source images linked to respective copyright owners Text and original diagrams ©1994-2012 Foster P. Carr MD all rights reserved
