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Chapter 20 : Plasmids from

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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
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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
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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
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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
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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
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Tables

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
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
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
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

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