1887

Chapter 20 : Plasmids from

Authors: Patrick Forterre1, Mart Krupovic3, Kasie Raymann4, Nicolas Soler5
VIEW AFFILIATIONS HIDE AFFILIATIONS
Affiliations: 1: Institut Pasteur, 75015 Paris, France; 2: Institut de Génétique et Microbiologie, Université Paris-Sud 11, UMR 8621 CNRS, 91405 Orsay, France; 3: Institut Pasteur, 75015 Paris, France; 4: Institut Pasteur, 75015 Paris, France; 5: Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France; 6: INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
Content Type: Monograph
Publication Year: 2015

Category: Clinical Microbiology

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Preview Magnify
Zoom in
Zoomout

Plasmids from , Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818982/9781555818975_Chap20-1.gif /docserver/preview/fulltext/10.1128/9781555818982/9781555818975_Chap20-2.gif

Abstract:

Archaea were confused with bacteria, under the term , until their originality was recognized in 1977 by Carl Woese and his collaborators of the “Urbana school” ( ). The classification of all cellular organisms into three domains based on rRNA was later confirmed by comparative genomic analyses that have shown that most universal proteins exist in three versions ( Woese), one in each domain: , , and ( ). At the phenotypic level, archaea strikingly resemble bacteria in terms of size and shape, chromosome structure, and compact gene organization. However, when inspected at the molecular or biochemical level, archaea are either unique, for instance in terms of their lipids ( ), or rather similar to eukaryotes ( ). Archaea resemble eukarya with respect to both their informational systems (DNA replication, transcription, translation) and their operational systems (ATP production, protein secretion, vesicle formation, cytoskeleton, protein modification machinery) ( ). However, we will see in this chapter that archaeal plasmids (and mobilome in general) have a strong bacterial flavor, a paradox that remains to be explained ( ).

Citation: Forterre P, Krupovic M, Raymann K, Soler N. 2015. Plasmids from , p 349-377. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0027-2014
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Plasmids from Euryarchaeota
[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818982.chap20-1,webId=/content/author/10.1128/9781555818982.chap20-1,properties={foaf_givenname=Patrick, foaf_name=Patrick Forterre, foaf_surname=Forterre, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818982.chap20-aff1]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818982.chap20-2,webId=/content/author/10.1128/9781555818982.chap20-2,properties={foaf_givenname=Mart, foaf_name=Mart Krupovic, foaf_surname=Krupovic, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818982.chap20-aff3]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818982.chap20-3,webId=/content/author/10.1128/9781555818982.chap20-3,properties={foaf_givenname=Kasie, foaf_name=Kasie Raymann, foaf_surname=Raymann, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818982.chap20-aff4]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818982.chap20-4,webId=/content/author/10.1128/9781555818982.chap20-4,properties={foaf_givenname=Nicolas, foaf_name=Nicolas Soler, foaf_surname=Soler, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818982.chap20-aff5]]}]]
Citation: Forterre P, Krupovic M, Raymann K, Soler N. 2015. Plasmids from , p 349-377. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0027-2014
/content/10.1128/9781555818982.chap20.fig20-1
Figure 1
Phylogeny of . The tree is based on the concatenation of core DNA replication proteins present in the last archaeal common ancestor (adapted from reference ); for each order, the number of identified plasmids is indicated in brackets. All group I lack DNA gyrase (similarly to and ), whereas all group II contain a DNA gyrase gene of bacterial origin. The blue arrow indicates the acquisition of this gyrase gene. Right panel: topology of plasmids present in organisms with and without DNA gyrase. The difference in topology is illustrated by comparing the electrophoretic mobility of the same plasmid, pLC70, a derivative of pTN1 from , purified from (lacking DNA gyrase, upper picture) or from (a bacterium containing DNA gyrase); adapted from reference .
10.1128/9781555818982/fig20-1_thmb.gif
10.1128/9781555818982/fig20-1.gif
Image of Figure 1
Figure 1

Phylogeny of . The tree is based on the concatenation of core DNA replication proteins present in the last archaeal common ancestor (adapted from reference ); for each order, the number of identified plasmids is indicated in brackets. All group I lack DNA gyrase (similarly to and ), whereas all group II contain a DNA gyrase gene of bacterial origin. The blue arrow indicates the acquisition of this gyrase gene. Right panel: topology of plasmids present in organisms with and without DNA gyrase. The difference in topology is illustrated by comparing the electrophoretic mobility of the same plasmid, pLC70, a derivative of pTN1 from , purified from (lacking DNA gyrase, upper picture) or from (a bacterium containing DNA gyrase); adapted from reference .

Citation: Forterre P, Krupovic M, Raymann K, Soler N. 2015. Plasmids from , p 349-377. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0027-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
/content/10.1128/9781555818982.chap20.fig20-2
Figure 2
The wonderful world of euryarchaeal plasmids. General scheme representing most of the plasmids cited in the text. Relationships with viruses or other mobile elements are marked with green arrows. Dark grey lines link plasmids that are evolutionarily related. Keynote replication proteins are indicated by different colored symbols (Cf legend in the bottom-left box). The mode of replication of each plasmid is indicated in front of the plasmid names: RC, rolling-circle replication; θ, theta mode of replication; ?, undetermined or litigious mode of replication. Refer to tables for the size and host of the plasmids.
10.1128/9781555818982/fig20-2_thmb.gif
10.1128/9781555818982/fig20-2.gif
Image of Figure 2
Figure 2

The wonderful world of euryarchaeal plasmids. General scheme representing most of the plasmids cited in the text. Relationships with viruses or other mobile elements are marked with green arrows. Dark grey lines link plasmids that are evolutionarily related. Keynote replication proteins are indicated by different colored symbols (Cf legend in the bottom-left box). The mode of replication of each plasmid is indicated in front of the plasmid names: RC, rolling-circle replication; θ, theta mode of replication; ?, undetermined or litigious mode of replication. Refer to tables for the size and host of the plasmids.

Citation: Forterre P, Krupovic M, Raymann K, Soler N. 2015. Plasmids from , p 349-377. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0027-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
/content/10.1128/9781555818982.chap20.fig20-3
Figure 3
Analysis of archaeal RC-Rep proteins of superfamily I. Hand-made alignment of amino acid regions located around the four conserved previously known motifs (numbered 1 to 3) and the fourth motif detected in this analysis (motif 4). The cladogram was produced from this alignment (after concatenation) using the program Phylogeny.fr ( ).
10.1128/9781555818982/fig20-3_thmb.gif
10.1128/9781555818982/fig20-3.gif
Image of Figure 3
Figure 3

Analysis of archaeal RC-Rep proteins of superfamily I. Hand-made alignment of amino acid regions located around the four conserved previously known motifs (numbered 1 to 3) and the fourth motif detected in this analysis (motif 4). The cladogram was produced from this alignment (after concatenation) using the program Phylogeny.fr ( ).

Citation: Forterre P, Krupovic M, Raymann K, Soler N. 2015. Plasmids from , p 349-377. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0027-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
/content/10.1128/9781555818982.chap20.fig20-4
Figure 4
Schematic phylogeny of archaeal Cdc6/Orc1 proteins; see http://archaea.u-psud.fr/cdc6/cdc6.html for the original and complete phylogenies and reference for material and methods. The Cdc6/Orc1-1 and Cdc6/Orc1-2 groups (large dark triangles) contain representatives from most archaeal orders, and internal phylogenies are roughly congruent with archaeal phylogenies based on ribosomal proteins ( ). Other groups contain both plasmid-encoded members whose names are indicated beside the triangles (with haloarchaeal plasmids in bold) and chromosome-encoded members whose numbers are indicated in gray squares.
10.1128/9781555818982/fig20-4_thmb.gif
10.1128/9781555818982/fig20-4.gif
Image of Figure 4
Figure 4

Schematic phylogeny of archaeal Cdc6/Orc1 proteins; see http://archaea.u-psud.fr/cdc6/cdc6.html for the original and complete phylogenies and reference for material and methods. The Cdc6/Orc1-1 and Cdc6/Orc1-2 groups (large dark triangles) contain representatives from most archaeal orders, and internal phylogenies are roughly congruent with archaeal phylogenies based on ribosomal proteins ( ). Other groups contain both plasmid-encoded members whose names are indicated beside the triangles (with haloarchaeal plasmids in bold) and chromosome-encoded members whose numbers are indicated in gray squares.

Citation: Forterre P, Krupovic M, Raymann K, Soler N. 2015. Plasmids from , p 349-377. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0027-2014
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555818982.chap20
1. Sapp J,, Fox GE . 2013. The singular quest for a universal tree of life. Microbiol Mol Biol Rev 77 : 541– 550.[PubMed] [CrossRef]
2. Woese CR,, Fox EF . 1977. Phylogenetic structure of prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74 : 5088– 5090.[PubMed] [CrossRef]
3. Ciccarelli FD,, Doerks T,, von Mering C,, Creevey CJ,, Snel B,, Bork P . 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311 : 1283– 1287.[PubMed] [CrossRef]
4. Lombard J,, López-García P,, Moreira D . 2012. Phylogenomic investigation of phospholipid synthesis in Archaea . Archaea 2012 : 1– 13.[PubMed] [CrossRef]
5. Garrett R,, Klenk H-P . 2007. Archaea. Blackwell Publishing, Oxford, UK.
6. Brochier-Armanet C,, Forterre P,, Gribaldo S . 2011. Phylogeny and evolution of the Archaea: one hundred genomes later. Curr Opin Microbiol 14 : 274– 281.[PubMed] [CrossRef]
7. Forterre P . 2013. The common ancestor of Archaea and Eukarya was not an archaeon. Archaea 2013 : 1– 18.[PubMed] [CrossRef]
8. Reed CJ,, Lewis H,, Trejo E,, Winston V,, Evilia C . 2013. Protein adaptations in archaeal extremophiles. Archaea 2013 : 1– 14.[PubMed] [CrossRef]
9. Mardanov AV,, Ravin NV . 2012. The impact of genomics on research in diversity and evolution of archaea. Biochemistry (Mosc) 77 : 799– 812.[PubMed] [CrossRef]
10. Woese CR,, Kandler O,, Wheelis ML . Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya . Proc Natl Acad Sci USA 87 : 4576– 4579.[PubMed] [CrossRef]
11. Brochier-Armanet C,, Boussau B,, Gribaldo S,, Forterre P . 2008. Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota . Nat Rev Microbiol 6 : 245– 252.[PubMed] [CrossRef]
12. Brochier-Armanet C,, Gribaldo S,, Forterre P . 2012. Spotlight on the Thaumarchaeota . ISME J 6 : 227– 230.[PubMed] [CrossRef]
13. Brochier-Armanet C,, Gribaldo S,, Forterre P . 2008. A DNA topoisomerase IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya . Biol Direct 3 : 54. doi:10.1186/1745-6150-3-54. [PubMed] [CrossRef]
14. Krupovic M,, Spang A,, Gribaldo S,, Forterre P,, Schleper C . 2011. A thaumarchaeal provirus testifies for an ancient association of tailed viruses with archaea. Biochem Soc Trans 39 : 82– 88.[PubMed] [CrossRef]
15. Pina M,, Bize A,, Forterre P,, Prangishvili D . 2011. The archeoviruses. FEMS Microbiol Rev 35 : 1035– 1054.[PubMed] [CrossRef]
16. Pietilä MK,, Demina TA,, Atanasova NS,, Oksanen HM,, Bamford DH . 2014. Archaeal viruses and bacteriophages: comparisons and contrasts. Trends Microbiol 22 : 334– 344.[PubMed] [CrossRef]
17. Krupovič M,, Forterre P,, Bamford DH . 2010. Comparative analysis of the mosaic genomes of tailed archaeal viruses and proviruses suggests common themes for virion architecture and assembly with tailed viruses of bacteria. J Mol Biol 397 : 144– 160.[PubMed] [CrossRef]
18. Dridi B,, Henry M,, El Khéchine A,, Raoult D,, Drancourt M . 2009. High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol. PLoS ONE 4 : e7063. doi:10.1371/journal.pone.0007063. [PubMed] [CrossRef]
19. Huber H,, Hohn MJ,, Stetter KO,, Rachel R . 2003. The phylum Nanoarchaeota: present knowledge and future perspectives of a unique form of life. Res Microbiol 154 : 165– 171.[PubMed] [CrossRef]
20. Forterre P,, Gribaldo S,, Brochier-Armanet C . 2009. Happy together: genomic insights into the unique Nanoarchaeum/Ignicoccus association. J Biol 8 : 7. [PubMed] [CrossRef]
21. Comolli LR,, Baker BJ,, Downing KH,, Siegerist CE,, Banfield JF . 2009. Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon. ISME J 3 : 159– 167.[PubMed] [CrossRef]
22. Baker BJ,, Comolli LR,, Dick GJ,, Hauser LJ,, Hyatt D,, Dill BD,, Land ML,, VerBerkmoes NC,, Hettich RL,, Banfield JF . 2010. Enigmatic, ultrasmall, uncultivated Archaea . Proc Natl Acad Sci USA 107 : 8806– 8811.[PubMed] [CrossRef]
23. Narasingarao P,, Podell S,, Ugalde JA,, Brochier-Armanet C,, Emerson JB,, Brocks JJ,, Heidelberg KB,, Banfield JF,, Allen EE . 2012. De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J 6 : 81– 93.[PubMed] [CrossRef]
24. Schleper C,, Jurgens G,, Jonuscheit M . 2005. Genomic studies of uncultivated archaea. Nat Rev Microbiol 3 : 479– 488.[PubMed] [CrossRef]
25. Raymann K,, Forterre P,, Brochier-Armanet C,, Gribaldo S . 2014. Global phylogenomic analysis disentangles the complex evolutionary history of DNA replication in Archaea . Genome Biol Evol 6 : 192– 212.[PubMed] [CrossRef]
26. Bapteste É,, Brochier C,, Boucher Y . 2005. Higher-level classification of the Archaea: evolution of methanogenesis and methanogens. Archaea 1 : 353– 363.[PubMed] [CrossRef]
27. Borrel G,, O’Toole PW,, Harris HMB,, Peyret P,, Brugere J-F,, Gribaldo S . 2013. Phylogenomic data support a seventh order of methylotrophic methanogens and provide insights into the evolution of methanogenesis. Genome Biol Evol 5 : 1769– 1780.[PubMed] [CrossRef]
28. Sioud M,, Possot O,, Elie C,, Sibold L,, Forterre P . 1988. Coumarin and quinolone action in archaebacteria: evidence for the presence of a DNA gyrase-like enzyme. J Bacteriol 170 : 946– 953.[PubMed]
29. Holmes ML,, Dyall-Smith ML . 1991. Mutations in DNA gyrase result in novobiocin resistance in halophilic archaebacteria. J Bacteriol 173 : 642– 648.[PubMed]
30. Lopez-Garcia P,, Anton J,, Abad J,, Amils R . 1994. Halobacterial megaplasmids are negatively supercoiled. Mol Microbiol 11 : 421– 427.[PubMed] [CrossRef]
31. Lopez-Garcia P,, Forterre P,, van der Oost J,, Erauso G . 2000. Plasmid pGS5 from the hyperthermophilic archaeon Archaeoglobus profundus Is negatively supercoiled. J Bacteriol 182 : 4998– 5000.[PubMed] [CrossRef]
32. Sioud M,, Baldacci G,, de Recondo A-M,, Forterre P . 1988. Novobiocin induces positive supercoiling of small plasmids from halophilic archaebacteria in vivo . Nucleic Acids Res 16 : 1379– 1391.[PubMed] [CrossRef]
33. Charbonnier F,, Forterre P . 1994. Comparison of plasmid DNA topology among mesophilic and thermophilic eubacteria and archaebacteria. J Bacteriol 176 : 1251– 1259.[PubMed]
34. Gaudin M,, Gauliard E,, Schouten S,, Houel-Renault L,, Lenormand P,, Marguet E,, Forterre P . 2013. Hyperthermophilic archaea produce membrane vesicles that can transfer DNA: membrane vesicles from Thermococcales . Environ Microbiol Rep 5 : 109– 116.[PubMed] [CrossRef]
35. Soler N,, Marguet E,, Cortez D,, Desnoues N,, Keller J,, van Tilbeurgh H,, Sezonov G,, Forterre P . 2010. Two novel families of plasmids from hyperthermophilic archaea encoding new families of replication proteins. Nucleic Acids Res 38 : 5088– 5104.[PubMed] [CrossRef]
36. Cortez D,, Forterre P,, Gribaldo S . 2009. A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes. Genome Biol 10 : R65. [PubMed] [CrossRef]
37. Fukui T . 2005. Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. Genome Res 15 : 352– 363.[PubMed] [CrossRef]
38. She Q,, Peng X,, Zillig W,, Garrett RA . 2001. Genome evolution: gene capture in archaeal chromosomes. Nature 409 : 478. [PubMed] [CrossRef]
39. Serre M-C . 2002. Cleavage properties of an archaeal site-specific recombinase, the SSV1 integrase. J Biol Chem 277 : 16758– 16767.[PubMed] [CrossRef]
40. Lepage E,, Marguet E,, Geslin C,, Matte-Tailliez O,, Zillig W,, Forterre P,, Tailliez P . 2004. Molecular diversity of new Thermococcales isolates from a single area of hydrothermal deep-sea vents as revealed by randomly amplified polymorphic DNA fingerprinting and 16S rRNA gene sequence analysis. Appl Environ Microbiol 70 : 1277– 1286.[PubMed] [CrossRef]
41. Farkas JA,, Picking JW,, Santangelo TJ . 2013. Genetic techniques for the Archaea . Annu Rev Genet 47 : 539– 561.[PubMed] [CrossRef]
42. Leigh JA,, Albers S-V,, Atomi H,, Allers T . 2011. Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales: archaeal model organisms. FEMS Microbiol Rev 35 : 577– 608.[PubMed] [CrossRef]
43. Thiel A,, Michoud G,, Moalic Y,, Flament D,, Jebbar M . 2014. Genetic manipulations of the hyperthermophilic piezophilic archaeon Thermococcus barophilus . Appl Environ Microbiol 80 : 2299– 2306.[PubMed] [CrossRef]
44. Hileman TH,, Santangelo TJ . 2012. Genetics techniques for Thermococcus kodakaraensis . Front Microbiol 3 : 195. doi:10.3389/fmicb.2012.00195. [CrossRef]
45. Imanaka T . 2011. Molecular bases of thermophily in hyperthermophiles. Proc Jpn Acad Ser B 87 : 587– 602.[CrossRef]
46. Kim M-S,, Bae SS,, Kim YJ,, Kim TW,, Lim JK,, Lee SH,, Choi AR,, Jeon JH,, Lee J-H,, Lee HS,, Kang SG . 2013. CO-dependent H2 production by genetically engineered Thermococcus onnurineus NA1. Appl Environ Microbiol 79 : 2048– 2053.[PubMed] [CrossRef]
47. Geslin C,, Le Romancer M,, Erauso G,, Gaillard M,, Perrot G,, Prieur D . 2003. PAV1, the first virus-like particle isolated from a hyperthermophilic euryarchaeote, “ Pyrococcus abyssi.” J Bacteriol 185 : 3888– 3894.[PubMed] [CrossRef]
48. Geslin C,, Gaillard M,, Flament D,, Rouault K,, Le Romancer M,, Prieur D,, Erauso G . 2007. Analysis of the first genome of a hyperthermophilic marine virus-like particle, PAV1, isolated from Pyrococcus abyssi . J Bacteriol 189 : 4510– 4519.[PubMed] [CrossRef]
49. Gorlas A,, Koonin EV,, Bienvenu N,, Prieur D,, Geslin C . 2012. TPV1, the first virus isolated from the hyperthermophilic genus Thermococcus: characterization of a new hyperthermophilic virus TPV1. Environ Microbiol 14 : 503– 516.[PubMed] [CrossRef]
50. Krupovic M,, Quemin ERJ,, Bamford DH,, Forterre P,, Prangishvili D . 2014. Unification of the globally distributed spindle-shaped viruses of the Archaea . J Virol 88 : 2354– 2358.[PubMed] [CrossRef]
51. Bath C,, Cukalac T,, Porter K,, Dyall-Smith ML . 2006. His1 and His2 are distantly related, spindle-shaped haloviruses belonging to the novel virus group, Salterprovirus . Virology 350 : 228– 239.[PubMed] [CrossRef]
52. Gonnet M,, Erauso G,, Prieur D,, Le Romancer M . 2011. pAMT11, a novel plasmid isolated from a Thermococcus sp. strain closely related to the virus-like integrated element TKV1 of the Thermococcus kodakaraensis genome. Res Microbiol 162 : 132– 143.[PubMed] [CrossRef]
53. Gaudin M,, Krupovic M,, Marguet E,, Gauliard E,, Cvirkaite-Krupovic V,, Le Cam E,, Oberto J,, Forterre P . 2013. Extracellular membrane vesicles harbouring viral genomes: viral vesicles. Environ Microbiol. doi:10.1111/1462–2920.12235. [PubMed] [CrossRef]
54. Erauso G,, Marsin S,, Benbouzid-Rollet N,, Baucher M-F,, Barbeyron T,, Zivanovic Y,, Prieur D,, Forterre P . 1996. Sequence of plasmid pGT5 from the archaeon Pyrococcus abyssi: evidence for rolling-circle replication in a hyperthermophile. J Bacteriol 178 : 3232– 3237.[PubMed]
55. Soler N,, Justome A,, Quevillon-Cheruel S,, Lorieux F,, Le Cam E,, Marguet E,, Forterre P . 2007. The rolling-circle plasmid pTN1 from the hyperthermophilic archaeon Thermococcus nautilus . Mol Microbiol 66 : 357– 370.[PubMed] [CrossRef]
56. Gorlas A,, Krupovic M,, Forterre P,, Geslin C . 2013. Living side by side with a virus: characterization of two novel plasmids from Thermococcus prieurii, a host for the spindle-shaped virus TPV1. Appl Environ Microbiol 79 : 3822– 3828.[PubMed] [CrossRef]
57. Ilyina TV,, Koonin EV . 1992. Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria. Nucleic Acids Res 20 : 3279– 3285.[PubMed] [CrossRef]
58. Marsin S,, Forterre P . 1998. A rolling circle replication initiator protein with a nucleotidyl-transferase activity encoded by the plasmid pGT5 from the hyperthermophilic archaeon Pyrococcus abyssi . Mol Microbiol 27 : 1183– 1192.[PubMed] [CrossRef]
59. Khan SA . 1997. Rolling-circle replication of bacterial plasmids. Microbiol Mol Biol Rev 61 : 442– 455.[PubMed]
60. Marsin S,, Forterre P . 2001. pGT5 replication initiator protein Rep75 from Pyrococcus abyssi . Methods Enzymol 334 : 193– 204.[PubMed] [CrossRef]
61. Santangelo TJ,, Cubonova L,, Reeve JN . 2008. Shuttle vector expression in Thermococcus kodakaraensis: contributions of cis elements to protein synthesis in a hyperthermophilic archaeon. Appl Environ Microbiol 74 : 3099– 3104.[PubMed] [CrossRef]
62. Pietila MK,, Atanasova NS,, Manole V,, Liljeroos L,, Butcher SJ,, Oksanen HM,, Bamford DH . 2012. Virion architecture unifies globally distributed pleolipoviruses infecting halophilic archaea. J Virol 86 : 5067– 5079.[PubMed] [CrossRef]
63. Krupovic M,, Gonnet M,, Hania WB,, Forterre P,, Erauso G . 2013. Insights into dynamics of mobile genetic elements in hyperthermophilic environments from five new thermococcus plasmids. PLoS ONE 8 : e49044. doi:10.1371/journal.pone.0049044. [PubMed] [CrossRef]
64. Soler N,, Gaudin M,, Marguet E,, Forterre P . 2011. Plasmids, viruses and virus-like membrane vesicles from Thermococcales . Biochem Soc Trans 39 : 36– 44.[PubMed] [CrossRef]
65. Vannier P,, Marteinsson VT,, Fridjonsson OH,, Oger P,, Jebbar M . 2011. Complete genome sequence of the hyperthermophilic, piezophilic, heterotrophic, and carboxydotrophic archaeon Thermococcus barophilus MP. J Bacteriol 193 : 1481– 1482.[PubMed] [CrossRef]
66. Iyer LM . 2005. Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members. Nucleic Acids Res 33 : 3875– 3896.[PubMed] [CrossRef]
67. Gill S,, Krupovic M,, Desnoues N,, Beguin P,, Sezonov G,, Forterre P . 2014. A highly divergent archaeo-eukaryotic primase from the Thermococcus nautilus plasmid, pTN2. Nucleic Acids Res 42 : 3707– 3719.[PubMed] [CrossRef]
68. Keller J,, Leulliot N,, Soler N,, Collinet B,, Vincentelli R,, Forterre P,, van Tilbeurgh H . 2009. A protein encoded by a new family of mobile elements from euryarchaea exhibits three domains with novel folds. Protein Sci 18 : 850– 855.[PubMed]
69. Oberto J,, Gaudin M,, Cossu M,, Gorlas A,, Slesarev A,, Marguet E,, Forterre P . 2014. Genome sequence of a hyperthermophilic archaeon, Thermococcus nautili 30-1, that produces viral vesicles. Genome Announc 2 : e00243–14. doi:10.1128/genomeA.00243-14. [PubMed] [CrossRef]
70. Krupovič M,, Bamford DH . 2008. Archaeal proviruses TKV4 and MVV extend the PRD1-adenovirus lineage to the phylum Euryarchaeota . Virology 375 : 292– 300.[PubMed] [CrossRef]
71. Krupovic M,, Gribaldo S,, Bamford DH,, Forterre P . 2010. The evolutionary history of archaeal MCM helicases: a case study of vertical evolution combined with hitchhiking of mobile genetic elements. Mol Biol Evol 27 : 2716– 2732.[PubMed] [CrossRef]
72. Ward DE,, Revet IM,, Nandakumar R,, Tuttle JH,, de Vos WM,, van der Oost J,, DiRuggiero J . 2002. Characterization of plasmid pRT1 from Pyrococcus sp. strain JT1. J Bacteriol 184 : 2561– 2566.[CrossRef]
73. Liu Y,, Whitman WB . 2008. Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann NY Acad Sci 1125 : 171– 189.[PubMed] [CrossRef]
74. Eiserling F,, Pushkin A,, Gingery M,, Bertani G . 1999. Bacteriophage-like particles associated with the gene transfer agent of methanococcus voltae PS. J Gen Virol 80 : 3305– 3308.[PubMed]
75. Lang AS,, Zhaxybayeva O,, Beatty JT . 2012. Gene transfer agents: phage-like elements of genetic exchange. Nat Rev Microbiol 10 : 472– 482.[PubMed]
76. Wood AG,, Whitman WB,, Konisky J . 1989. Isolation and characterization of an archaebacterial viruslike particle from Methanococcus voltae A3. J Bacteriol 171 : 93– 98.[PubMed]
77. Bult CJ,, White O,, Olsen GJ,, Zhou L,, Fleischmann RD,, Sutton GG,, Blake JA,, FitzGerald LM,, Clayton RA,, Gocayne JD . 1996. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii . Science 273 : 1058– 1073.[PubMed] [CrossRef]
78. Tumbula DL,, Bowen TL,, Whitman WB . 1997. Characterization of pURB500 from the archaeon Methanococcus maripaludis and construction of a shuttle vector. J Bacteriol 179 : 2976– 2986.[PubMed]
79. Wolfe RS . 1992. Biochemistry of methanogenesis. Biochem Soc Symp 58 : 41– 49.[PubMed]
80. Pfister P,, Wasserfallen A,, Stettler R,, Leisinger T . 1998. Molecular analysis of Methanobacterium phage ΨM2. Mol Microbiol 30 : 233– 244.[PubMed] [CrossRef]
81. Luo Y,, Pfister P,, Leisinger T,, Wasserfallen A . 2001. The genome of archaeal prophage M100 encodes the lytic enzyme responsible for autolysis of Methanothermobacter wolfeii . J Bacteriol 183 : 5788– 5792.[PubMed] [CrossRef]
82. Luo Y,, Leisinger T,, Wasserfallen A . 2001. Comparative sequence analysis of plasmids pME2001 and pME2200 of Methanothermobacter marburgensis strains Marburg and ZH3. Plasmid 45 : 18– 30.[PubMed] [CrossRef]
83. Meile L,, Kiener A,, Leisinger T . 1983. A plasmid in the archaebacterium Methanobacterium thermoautotrophicum . Mol Gen Genet 191 : 480– 484.[PubMed] [CrossRef]
84. Nölling J,, van Eeden FJ,, Eggen RI,, de Vos WM . 1992. Modular organization of related archaeal plasmids encoding different restriction-modification systems in Methanobacterium thermoformicicum . Nucleic Acids Res 20 : 6501– 6507.[PubMed] [CrossRef]
85. Kosaka T,, Toh H,, Toyoda A . 2013. Complete genome sequence of a thermophilic hydrogenotrophic methanogen, Methanothermobacter sp. strain CaT2. Genome Announc 1 : e00672–13. doi:10.1128/genomeA.00672-13. [PubMed] [CrossRef]
86. Lopez P,, Philippe H,, Myllykallio H,, Forterre P . 1999. Identification of putative chromosomal origins of replication in archaea. Mol Microbiol 32 : 883– 886.[PubMed] [CrossRef]
87. Nelson-Sathi S,, Dagan T,, Landan G,, Janssen A,, Steel M,, McInerney JO,, Deppenmeier U,, Martin WF . 2012. Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of haloarchaea. Proc Natl Acad Sci USA 109 : 20537– 20542.[PubMed] [CrossRef]
88. Pawlowski A,, Rissanen I,, Bamford JKH,, Krupovic M,, Jalasvuori M . 2014. Gammasphaerolipovirus, a newly proposed bacteriophage genus, unifies viruses of halophilic archaea and thermophilic bacteria within the novel family Sphaerolipoviridae . Arch Virol 159 : 1541– 1554. doi:10.1007/s00705-013-1970-6.Epub2014.
89. Dyall-Smith M,, Tang S-L,, Bath C . 2003. Haloarchaeal viruses: how diverse are they? Res Microbiol 154 : 309– 313.[CrossRef]
90. Torsvik T,, Dundas I . 1974. Bacteriophage of Halobacterium salinarum . Nature 248 : 680– 681.[CrossRef]
91. Stolt P,, Zillig W . 1994. Transcription of the halophage ɸH repressor gene is abolished by transcription from an inversely oriented lytic promoter. FEBS Lett 344 : 125– 128.[CrossRef]
92. Senčilo A,, Jacobs-Sera D,, Russell DA,, Ko C-C,, Bowman CA,, Atanasova NS,, Österlund E,, Oksanen HM,, Bamford DH,, Hatfull GF,, Roine E,, Hendrix RW . 2013. Snapshot of haloarchaeal tailed virus genomes. RNA Biol 10 : 803– 816.[PubMed] [CrossRef]
93. Pietila MK,, Laurinmaki P,, Russell DA,, Ko C-C,, Jacobs-Sera D,, Hendrix RW,, Bamford DH,, Butcher SJ . 2013. Structure of the archaeal head-tailed virus HSTV-1 completes the HK97 fold story. Proc Natl Acad Sci USA 110 : 10604– 10609.[PubMed] [CrossRef]
94. Porter K,, Tang S-L,, Chen C-P,, Chiang P-W,, Hong M-J,, Dyall-Smith M . 2013. PH1: An archaeovirus of Haloarcula hispanica related to SH1 and HHIV-2. Archaea 2013 : 1– 17.[PubMed] [CrossRef]
95. Roine E,, Kukkaro P,, Paulin L,, Laurinavicius S,, Domanska A,, Somerharju P,, Bamford DH . 2010. New, closely related haloarchaeal viral elements with different nucleic acid types. J Virol 84 : 3682– 3689.[PubMed] [CrossRef]
96. Pietila MK,, Laurinavicius S,, Sund J,, Roine E,, Bamford DH . 2010. The single-stranded DNA genome of novel archaeal virus halorubrum pleomorphic virus 1 is enclosed in the envelope decorated with glycoprotein spikes. J Virol 84 : 788– 798.[PubMed] [CrossRef]
97. Krupovic M,, Bamford DH . 2010. Order to the viral universe. J Virol 84 : 12476– 12479.[PubMed] [CrossRef]
98. Wu Z,, Liu H,, Liu J,, Liu X,, Xiang H . 2012. Diversity and evolution of multiple orc/cdc6-adjacent replication origins in haloarchaea. BMC Genomics 13 : 478. [PubMed] [CrossRef]
99. Harrison PW,, Lower RPJ,, Kim NKD,, Young JPW . 2010. Introducing the bacterial “chromid”: not a chromosome, not a plasmid. Trends Microbiol 18 : 141– 148.[PubMed] [CrossRef]
100. Filee J,, Siguier P,, Chandler M . 2007. Insertion sequence diversity in archaea. Microbiol Mol Biol Rev 71 : 121– 157.[PubMed] [CrossRef]
101. Rosenshine I,, Tchelet R,, Mevarech M . 1989. The mechanism of DNA transfer in the mating system of an archaebacterium. Science 245 : 1387– 1389.[PubMed] [CrossRef]
102. Zhou M,, Xiang H,, Sun C,, Tan H . 2004. Construction of a novel shuttle vector based on an RCR-plasmid from a haloalkaliphilic archaeon and transformation into other haloarchaea. Biotechnol Lett 26 : 1107– 1113.[PubMed] [CrossRef]
103. Holmes ML,, Dyall-Smith ML . 1990. A plasmid vector with a selectable marker for halophilic archaebacteria. J Bacteriol 172 : 756– 761.[PubMed]
104. Kagramanova VK,, Derckacheva NI,, Mankin AS . 1988. The complete nucleotide sequence of the archaebacterial plasmid pHSB from Halobacterium, strain SB3. Nucleic Acids Res 16 : 4158. [PubMed] [CrossRef]
105. Hall MJ,, Hackett NR . 1989. DNA sequence of a small plasmid from Halobacterium strain GN101. Nucleic Acids Res 17 : 10501. [PubMed] [CrossRef]
106. Hackett NR,, Krebs MP,, DasSarma S,, Goebel W,, RajBhandary UL,, Khorana HG . 1990. Nucleotide sequence of a high copy number plasmid from Halobacterium strain GRB. Nucleic Acids Res 18 : 3408. [PubMed] [CrossRef]
107. Akhmanova AS,, Kagramanova VK,, Mankin AS . 1993. Heterogeneity of small plasmids from halophilic archaea. J Bacteriol 175 : 1081– 1086.[PubMed]
108. Zhou L,, Zhou M,, Sun C,, Han J,, Lu Q,, Zhou J,, Xiang H . 2008. Precise determination, cross-recognition, and functional analysis of the double-strand origins of the rolling-circle replication plasmids in haloarchaea. J Bacteriol 190 : 5710– 5719.[PubMed] [CrossRef]
109. Sioud M,, Forterre P,, de Recondo A-M . 1987. Effects of the antitumor drug VP16 (etoposide) on the archaebacterial Halobacterium GRB 1.7 kb plasmid in vivo . Nucleic Acids Res 15 : 8217– 8234.[PubMed] [CrossRef]
110. Sioud M,, Baldacci G,, Foeterre P,, de Recondo A-M . 1988. Novobiocin induces accumulation of a single strand of plasmid pGRB-1 in the archaebacterium Halobacterium GRB. Nucleic Acids Res 16 : 7833– 7842.[PubMed] [CrossRef]
111. Zhou M,, Xiang H,, Sun C,, Li Y,, Liu J,, Tan H . 2004. Complete sequence and molecular characterization of pNB101, a rolling-circle replicating plasmid from the haloalkaliphilic archaeon Natronobacterium sp. strain AS7091. Extremophiles 8 : 91– 98.[PubMed] [CrossRef]
112. Holmes M,, Pfeifer F,, Dyall-Smith ML . 1995. Analysis of the halobacterial plasmid pHK2 minimal replicon. Gene 153 : 117– 121.[PubMed] [CrossRef]
113. Sun C,, Zhou M,, Li Y,, Xiang H . 2006. Molecular characterization of the minimal replicon and the unidirectional theta replication of pSCM201 in extremely halophilic archaea. J Bacteriol 188 : 8136– 8144.[PubMed] [CrossRef]
114. Zhou L,, Zhou M,, Sun C,, Xiang H,, Tan H . 2007. Genetic analysis of a novel plasmid pZMX101 from Halorubrum saccharovorum: determination of the minimal replicon and comparison with the related haloarchaeal plasmid pSCM201. FEMS Microbiol Lett 270 : 104– 108.[PubMed] [CrossRef]
115. Pfeifer F,, Weidinger G,, Goebel W . 1981. Characterization of plasmids in halobacteria. J Bacteriol 145 : 369– 374.[PubMed]
116. Weidinger G,, Klotz G,, Goebel W . 1979. A large plasmid from Halobacterium halobium carrying genetic information for gas vacuole formation. Plasmid 2 : 377– 386.[PubMed] [CrossRef]
117. Ng W-L,, DasSarma S . 1993. Minimal replication origin of the 200-kilobase Halobacterium plasmid pNRC100. J Bacteriol 175 : 4584– 4596.[PubMed]
118. Pfeifer F,, Ghahraman P . 1993. Plasmid pHH1 of Halobacterium salinarium: characterization of the replicon region, the gas vesicle gene cluster and insertion elements. Mol Gen Genet 238 : 193– 200.[PubMed]
119. Charlebois RL,, Lam WL,, Cline SW,, Doolittle WF . 1987. Characterization of pHV2 from Halobacterium volcanii and its use in demonstrating transformation of an archaebacterium. Proc Natl Acad Sci USA 84 : 8530– 8534.[PubMed] [CrossRef]
120. Ng WV,, Kennedy SP,, Mahairas GG,, Berquist B,, Pan M,, Shukla HD,, Lasky SR,, Baliga NS,, Thorsson V,, Sbrogna J . 2000. Genome sequence of Halobacterium species NRC-1. Proc Natl Acad Sci USA 97 : 12176– 12181.[PubMed] [CrossRef]
121. Klein R,, Beranyl U,, Rossler N,, Greineder B,, Scholz H,, Witte A . Natrialba magadii virus phiCh1: first complete nucleotide sequence and functional organization of a virus infecting a haloalkaliphilic archaeon. Mol Microbiol 45 : 851– 863.[PubMed] [CrossRef]
122. Ye X,, Ou J,, Ni L,, Shi W,, Shen P . 2003. Characterization of a novel plasmid from extremely halophilic Archaea: nucleotide sequence and function analysis. FEMS Microbiol Lett 221 : 53– 57.[PubMed] [CrossRef]
123. Zhang Z,, Liu Y,, Wang S,, Yang D,, Cheng Y,, Hu J,, Chen J,, Mei Y,, Shen P,, Bamford DH,, Chen X . 2012. Temperate membrane-containing halophilic archaeal virus SNJ1 has a circular dsDNA genome identical to that of plasmid pHH205. Virology 434 : 233– 241.[PubMed] [CrossRef]
124. Falb M,, Pfeiffer F,, Palm P,, Rodewald K,, Hickmann V,, Tittor J,, Oesterhelt D . 2005. Living with two extremes: conclusions from the genome sequence of Natrono…monas pharaonis . Genome Res 15 : 1336– 1343.[PubMed] [CrossRef]
125. Dyall-Smith ML,, Pfeiffer F,, Klee K,, Palm P,, Gross K,, Schuster SC,, Rampp M,, Oesterhelt D . 2011. Haloquadratum walsbyi: limited diversity in a global pond. PLoS ONE 6 : e20968. doi:10.1371/journal.pone.0020968. [PubMed] [CrossRef]
126. Metcalf WW,, Zhang JK,, Apolinario E,, Sowers KR,, Wolfe RS . 1997. A genetic system for Archaea of the genus Methanosarcina: liposome-mediated transformation and construction of shuttle vectors. Proc Natl Acad Sci USA 94 : 2626– 2631.[PubMed] [CrossRef]
127. Maeder DL,, Anderson I,, Brettin TS,, Bruce DC,, Gilna P,, Han CS,, Lapidus A,, Metcalf WW,, Saunders E,, Tapia R,, Sowers KR . 2006. The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes. J Bacteriol 188 : 7922– 7931.[PubMed] [CrossRef]
128. Zhu J,, Zheng H,, Ai G,, Zhang G,, Liu D,, Liu X,, Dong X . 2012. The genome characteristics and predicted function of methyl-group oxidation pathway in the obligate aceticlastic methanogens, Methanosaeta spp. PLoS ONE 7 : e36756. doi:10.1371/journal.pone.0036756. [CrossRef]
129. Lipps G . 2011. Structure and function of the primase domain of the replication protein from the archaeal plasmid pRN1. Biochem Soc Trans 39 : 104– 106.[PubMed] [CrossRef]
130. Barber RD,, Zhang L,, Harnack M,, Olson MV,, Kaul R,, Ingram-Smith C,, Smith KS . 2011. Complete genome sequence of Methanosaeta concilii, a specialist in aceticlastic methanogenesis. J Bacteriol 193 : 3668– 3669.[PubMed] [CrossRef]
131. Yamashiro K,, Yokobori S,, Oshima T,, Yamagishi A . 2006. Structural analysis of the plasmid pTA1 isolated from the thermoacidophilic archaeon Thermoplasma acidophilum . Extremophiles 10 : 327– 335.[PubMed] [CrossRef]
132. Angelov A,, Voss J,, Liebl W . 2011. Characterization of plasmid pPO1 from the hyperacidophile Picrophilus oshimae . Archaea 2011 : 1– 4.[PubMed] [CrossRef]
133. Forterre P,, Gadelle D . 2009. Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms. Nucleic Acids Res 37 : 679– 692.[PubMed] [CrossRef]
134. Forterre P . 2002. A hot story from comparative genomics: reverse gyrase is the only hyperthermophile-specific protein. Trends Genet 18 : 236– 237.[PubMed] [CrossRef]
135. Brochier-Armanet C,, Forterre P . 2006. Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers. Archaea 2 : 83– 93.[CrossRef]
136. Atomi H,, Matsumi R,, Imanaka T . 2004. Reverse gyrase is not a prerequisite for hyperthermophilic life. J Bacteriol 186 : 4829– 4833.[PubMed] [CrossRef]
137. Guipaud O,, Marguet E,, Noll KM,, De La Tour CB,, Forterre P . 1997. Both DNA gyrase and reverse gyrase are present in the hyperthermophilic bacterium Thermotoga maritima . Proc Natl Acad Sci USA 94 : 10606– 10611.[CrossRef]
138. Marguet E,, Forterre P . 1994. DNA stability at temperatures typical for hyperthermophiles. Nucleic Acids Res 22 : 1681– 1686.[CrossRef]
139. Mojica FJ,, Charbonnier F,, Juez G,, Rodriguez-Valera F,, Forterre P . 1994. Effects of salt and temperature on plasmid topology in the halophilic archaeon Haloferax volcanii . J Bacteriol 176 : 4966– 4973.[PubMed]
140. Marguet E,, Zivanovic Y,, Forterre P . 1996. DNA topological change in the hyperthermophilic archaeon Pyrococcus abyssi exposed to low temperature. FEMS Microbiol Lett 142 : 31– 36.[CrossRef]
141. Lopez-Garcia P,, Forterre P . 1997. DNA topology in hyperthermophilic archaea: reference states and their variation with growth phase, growth temperature, and temperature stresses. Mol Microbiol 23 : 1267– 1279.[PubMed] [CrossRef]
142. Lopez-Garcia P,, Forterre P . 2000. DNA topology and the thermal stress response, a tale from mesophiles and hyperthermophiles. BioEssays 22 : 738– 746.[PubMed] [CrossRef]
143. Gardner WL,, Whitman WB . 1999. Expression vectors for Methanococcus maripaludis: overexpression of acetohydroxyacid synthase and β-galactosidase. Genetics 152 : 1439– 1447.[PubMed]
144. Guss AM,, Rother M,, Zhang JK,, Kulkkarni G,, Metcalf WW . 2008. New methods for tightly regulated gene expression and highly efficient chromosomal integration of cloned genes for Methanosarcina species. Archaea 2 : 193– 203.[PubMed] [CrossRef]
145. Dodsworth JA,, Leigh JA . 2006. Regulation of nitrogenase by 2-oxoglutarate-reversible, direct binding of a PII-like nitrogen sensor protein to dinitrogenase. Proc Natl Acad Sci USA 103 : 9779– 9784.[PubMed] [CrossRef]
146. Norais C,, Hawkins M,, Hartman AL,, Eisen JA,, Myllykallio H,, Allers T . 2007. Genetic and physical mapping of DNA replication origins in Haloferax volcanii . PLoS Genet 3 : e77. doi:10.1371/journal.pgen.0030077. [PubMed] [CrossRef]
147. DasSarma S,, Arora P,, Lin F,, Molinari E,, Yin LR . 1994. Wild-type gas vesicle formation requires at least ten genes in the gvp gene cluster of Halobacterium halobium plasmid pNRC100. J Bacteriol 176 : 7646– 7652.[PubMed]
148. Blaseio U,, Pfeifer F . 1990. Transformation of Halobacterium halobium: development of vectors and investigation of gas vesicle synthesis. Proc Natl Acad Sci USA 87 : 6772– 6776.[PubMed] [CrossRef]
149. Krebs MP,, Hauss T,, Heyn MP,, RajBhandary UL,, Khorana HG . 1991. Expression of the bacterioopsin gene in Halobacterium halobium using a multicopy plasmid. Proc Natl Acad Sci USA 88 : 859– 863.[PubMed] [CrossRef]
150. Lucas S,, Toffin L,, Zivanovic Y,, Charlier D,, Moussard H,, Forterre P,, Prieur D,, Erauso G . 2002. Construction of a shuttle vector for, and spheroplast transformation of, the hyperthermophilic archaeon Pyrococcus abyssi . Appl Environ Microbiol 68 : 5528– 5536.[PubMed] [CrossRef]
151. Waege I,, Schmid G,, Thumann S,, Thomm M,, Hausner W . 2010. Shuttle vector-based transformation system for Pyrococcus furiosus . Appl Environ Microbiol 76 : 3308– 3313.[PubMed] [CrossRef]
152. Koonin EV,, Dolja VV . 2013. A virocentric perspective on the evolution of life. Curr Opin Virol 3 : 546– 557.[PubMed] [CrossRef]
153. López-García P,, Moreira D . 2008. Tracking microbial biodiversity through molecular and genomic ecology. Res Microbiol 159 : 67– 73.[PubMed] [CrossRef]
154. Forterre P,, Prangishvili D . 2013. The major role of viruses in cellular evolution: facts and hypotheses. Curr Opin Virol 3 : 558– 565.[PubMed] [CrossRef]
155. Hawkins M,, Malla S,, Blythe MJ,, Nieduszynski CA,, Allers T . 2013. Accelerated growth in the absence of DNA replication origins. Nature 503 : 544– 547.[PubMed] [CrossRef]
156. Forterre P . 2002. The origin of DNA genomes and DNA replication proteins. Curr Opin Microbiol 5 : 525– 532.[PubMed] [CrossRef]
157. DasSarma S,, Damerval T,, Jones J,, Tandeau de Marsac N . 1987. A plasmid-encoded gas vesicle protein gene in a halophilic archaebacterium. Mol Microbiol 1 : 365– 370.[PubMed] [CrossRef]
158. Pfeifer F,, Blaseio U,, Horne M . 1989. Genome structure of Halobacterium halobium: plasmid dynamics in gas vacuole deficient mutants. Can J Microbiol 35 : 96– 100.[PubMed] [CrossRef]
159. Ng W-L,, Kothakota S,, DasSarma S . 1991. Structure of the gas vesicle plasmid in Halobacterium halobium: inversion isomers, inverted repeats, and insertion sequences. J Bacteriol 173 : 1958– 1964.[PubMed]
160. Li N,, Cannon MC . 1998. Gas vesicle genes identified in Bacillus megaterium and functional expression in Escherichia coli . J Bacteriol 180 : 2450– 2458.[PubMed]
161. Soler N,, Marguet E,, Verbavatz J-M,, Forterre P . 2008. Virus-like vesicles and extracellular DNA produced by hyperthermophilic archaea of the order Thermococcales . Res Microbiol 159 : 390– 399.[PubMed] [CrossRef]
162. Stahl DA,, de la Torre JR . 2012. Physiology and diversity of ammonia-oxidizing archaea. Annu Rev Microbiol 66 : 83– 101.[PubMed] [CrossRef]
163. Forterre P . 2012. Darwin’s goldmine is still open: variation and selection run the world. Front Cell Infect Microbiol 2 : 106. doi:10.3389/fcimb.2012.00106. [PubMed] [CrossRef]
164. Dodsworth JA,, Li L,, Wei S,, Hedlund BP,, Leigh JA,, de Figueiredo P . 2010. Interdomain conjugal transfer of DNA from bacteria to archaea. Appl Environ Microbiol 76 : 5644– 5647.[PubMed] [CrossRef]
165. Forterre P . 2013. Why are there so many diverse replication machineries? J Mol Biol 425 : 4714– 4726.[PubMed] [CrossRef]
166. Dereeper A,, Guignon V,, Blanc G,, Audic S,, Buffet S,, Chevenet F,, Dufayard J-F,, Guindon S,, Lefort V,, Lescot M,, Claverie J-M,, Gascuel O . 2008. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 36 : W465– W469.[PubMed] [CrossRef]
167. Greve B,, Jensen S,, Brügger K,, Zillig W,, Garrett RA . 2004. Genomic comparison of archaeal conjugative plasmids from Sulfolobus. Archaea 1( 4) : 231– 239.[PubMed] [CrossRef]

Tables

Plasmids from Euryarchaeota
[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818982.chap20-1,webId=/content/author/10.1128/9781555818982.chap20-1,properties={foaf_givenname=Patrick, foaf_name=Patrick Forterre, foaf_surname=Forterre, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818982.chap20-aff1]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818982.chap20-2,webId=/content/author/10.1128/9781555818982.chap20-2,properties={foaf_givenname=Mart, foaf_name=Mart Krupovic, foaf_surname=Krupovic, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818982.chap20-aff3]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818982.chap20-3,webId=/content/author/10.1128/9781555818982.chap20-3,properties={foaf_givenname=Kasie, foaf_name=Kasie Raymann, foaf_surname=Raymann, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818982.chap20-aff4]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818982.chap20-4,webId=/content/author/10.1128/9781555818982.chap20-4,properties={foaf_givenname=Nicolas, foaf_name=Nicolas Soler, foaf_surname=Soler, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818982.chap20-aff5]]}]]
Citation: Forterre P, Krupovic M, Raymann K, Soler N. 2015. Plasmids from , p 349-377. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0027-2014
/content/10.1128/9781555818982.chap20.tab20-1
Table 1
Rolling circle plasmids from
Generic image for table
Table 1

Rolling circle plasmids from

Citation: Forterre P, Krupovic M, Raymann K, Soler N. 2015. Plasmids from , p 349-377. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0027-2014
/content/10.1128/9781555818982.chap20.tab20-2
Table 2
Plasmids from group I replicating (putatively) via the theta mechanism
Generic image for table
Table 2

Plasmids from group I replicating (putatively) via the theta mechanism

Citation: Forterre P, Krupovic M, Raymann K, Soler N. 2015. Plasmids from , p 349-377. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0027-2014
/content/10.1128/9781555818982.chap20.tab20-3
Table 3
Plasmids from group II replicating (putatively) via the theta mechanism
Generic image for table
Table 3

Plasmids from group II replicating (putatively) via the theta mechanism

Citation: Forterre P, Krupovic M, Raymann K, Soler N. 2015. Plasmids from , p 349-377. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0027-2014
/content/10.1128/9781555818982.chap20.tab20-4
Table 4
Large plasmids from haloarchaea encoding RepH and/or replication proteins homologous from cellular ones
Generic image for table
Table 4

Large plasmids from haloarchaea encoding RepH and/or replication proteins homologous from cellular ones

Citation: Forterre P, Krupovic M, Raymann K, Soler N. 2015. Plasmids from , p 349-377. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0027-2014

Back to top
This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error