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Chapter 17 : Archaeal Plasmids

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Abstract:

Our knowledge of archaeal plasmids is still sketchy compared to that of bacteria and eukarya, and most of it has been accrued quite recently. Moreover, while many archaeal plasmids have been isolated, and several have been sequenced, very few functional studies have been performed, and little is known about their mechanisms of replication, copy-number control, maintenance, partition, or conjugation. Nevertheless, several archaeal plasmids have now been classified with cryptic or conjugative phenotypes, some of which are integrative, and detailed studies on their molecular biology are in progress. This chapter summarizes recent advances in our knowledge of known classes of archaeal plasmids and emphasizes the insights gained into their molecular mechanisms of replication, maintenance, copy-number control, conjugation, and integration, all of which have special archaeal characteristics. The pNRC100 and pNRC200 plasmids have been classified as minichromosomes because they carry essential chromosomal genes including the Cdc6 protein located adjacent to putative multiple replication origins. Few investigations have been reported on the replication mechanisms of archaeal plasmids. The archaeal plasmids that encode integrases and exist in free or integrated states are listed. and chromosomes each exhibit two (N)’s, overlapping downstream halves of tRNA genes, and one and two copies of (C), respectively. Research into archaeal plasmids is entering an exciting phase. The first results reinforce the view emerging from studies of other archaeal systems that they have diverged greatly from corresponding bacterial systems.

Citation: Garrett R, Redder P, Greve B, Brügger K, Chen L, She Q. 2004. Archaeal Plasmids, p 377-392. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch17

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Figures

Image of Figure 1.
Figure 1.

Linear genome maps of some pRN plasmids. Blackened arrows: ORFs present in all free pRN plasmids, PlrA, CopG, and RepA. ORFA is conserved and often located adjacent to or in a similar position to CopG ORFs. White arrows: ORFs ( > 50 aa) showing no significant sequence similarity to the other plasmid ORFs. Patterned arrows indicate ORFs that are conserved in one or more pRN plasmids. (A) Free pRN plasmids. Diagonal-lined arrows indicate ORFs in pSSVx homologous to SSV2 viral ORFs. Dotted arrows indicate a conserved region with homologous ORFs shared by pDI.10 and pHF.N7. R denotes the putative recombination motifs. Shaded bars indicate sequence regions that show similarity to single-stranded and doublestranded origins of bacterial rolling-circle plasmids (see text). (B) Integrated pRN-type plasmids. Integrase genes responsible for the chromosome insertion of the plasmids are partitioned during the integration of pSTl and pXQI. The gene of pXQl contains an IS element, ISC1439. tRNA genes that function as target sites for the integrases are indicated.

Citation: Garrett R, Redder P, Greve B, Brügger K, Chen L, She Q. 2004. Archaeal Plasmids, p 377-392. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch17
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Image of Figure 2.
Figure 2.

Putative recombination mechanism shared by plasmids. The diagram shows how the transition may occur between (A) pHEN7-type plasmids and (B) the smaller pRN-l and pRN-2-type plasmids. A deletion mechanism is depicrcd for the former where the putative cutting sites, within two loop regions, are indicated by arrows. Five conserved nucleotides bordering the recombination R motifs are bold-faced.

Citation: Garrett R, Redder P, Greve B, Brügger K, Chen L, She Q. 2004. Archaeal Plasmids, p 377-392. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch17
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Image of Figure 3.
Figure 3.

Sequence alignment of PlrA proteins. The PlrA proteins are encoded in the pRN-type and conjugative plasmids listed in Tables 1 and 2 and in the chromosome The protein is highly conserved in both sequence and length. X's indicate conserved amino acids in a possible leucine zipper, which, in contrast to other known leucine zipper motifs, is located at the N terminus of the protein ( ). The alignment was drawn using t_coffee and BOX shade software (http://www.ch.embnet.org/software/BOX_form.html) where black and gray boxes, respectively, indicate identical and a similar amino acids.

Citation: Garrett R, Redder P, Greve B, Brügger K, Chen L, She Q. 2004. Archaeal Plasmids, p 377-392. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch17
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Image of Figure 4.
Figure 4.

Gene maps of conjugative plasmids free and integrated in genomes. ORFs are shaded and labeled where homologues are found in other bacterial or archaeal plasmids. The putative recombination sites (Rm) are shown as multiple vertical lines crossing the gene map. (A) Alignment of pNOB8 and the related integrated plasmid in the genome. The location of the plasmid in the genome is indicated. The SRSR cluster in pNOB8 is shown, and arrows indicate the position of the duplicated R m sites where recombination occurs in plNG4 to yield pINGl ( ). (B) Alignment of pARN4 and the plasmid in the genome. (C) A summary of ORFs that are present in all sequenced free conjugative plasmids superimposed on the pNOB8 gene map.

Citation: Garrett R, Redder P, Greve B, Brügger K, Chen L, She Q. 2004. Archaeal Plasmids, p 377-392. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch17
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Image of Figure 5.
Figure 5.

TraG sequence alignment. Partial alignment of the putative archaeal TraG proteins with selected members of the TraG superfamily. Arch, archaeal sequences; bact, bacterial sequences. Proteins of the TraG superfamily contain two functional domains that probably form a nucleotide-binding domain. Conserved motifs are denoted above the alignment. Black background, amino acids identical in at least 50% of the sequences; shaded background, amino acids similar in at least 50% of the sequences. The alignment was prepared using the BOX shade program (http://www.ch.embnet.org/software/ BOX_form.html). (A) Domain 1 contains the conserved ATP-binding motif I. (B) N-terminal part of domain 2 exhibits the conserved motifs II (NTP-binding) and III (unknown function). GenBank sequence accession numbers are: pINGl, Q9C4Y4; pNOBS, 093672 ; pARN4/2, pARN3/2, pKEF9/l, and pHVE14 (B. Greve and R. A. Garrett, unpublished results); ST1326 , Q971N4; TraG , Q8R8F9; TrsK (pMRCOl, , 087219; TrwB (pR388, ), Q04230; VirD4 (pTiC58, ), P18594; TraG , Q8XW89; A1I8037 ( sp.), Q8YK80; MobC ), Q9ZF54.

Citation: Garrett R, Redder P, Greve B, Brügger K, Chen L, She Q. 2004. Archaeal Plasmids, p 377-392. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch17
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Image of Figure 6.
Figure 6.

SRSR alignment. Alignment of SRSR direct repeat sequences in the conjugative plasmids pNOB8 and pKEF9/1. Arrows indicate imperfect inverted repeats. Conserved sequences are shown.

Citation: Garrett R, Redder P, Greve B, Brügger K, Chen L, She Q. 2004. Archaeal Plasmids, p 377-392. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch17
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Image of Figure 7.
Figure 7.

Model for insertion of pXQl into the P2 chromosome. The integrase target site in the plasmid and chromosome is the 45-bp site indicated by a blackened bar ( ). In the integrated form the integrase gene is partitioned into and pXQl carries four ORFs that are homologous to those of other pRN plasmids ( Fig. 1 ). IS element ISC1439 interrupts ( ).

Citation: Garrett R, Redder P, Greve B, Brügger K, Chen L, She Q. 2004. Archaeal Plasmids, p 377-392. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch17
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Tables

Generic image for table
Table 1.

Crenarchaeal pRN plasmids

Citation: Garrett R, Redder P, Greve B, Brügger K, Chen L, She Q. 2004. Archaeal Plasmids, p 377-392. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch17
Generic image for table
Table 2.

Crenarchaeal conjugative plasmids

Citation: Garrett R, Redder P, Greve B, Brügger K, Chen L, She Q. 2004. Archaeal Plasmids, p 377-392. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch17
Generic image for table
Table 3.

Integrative plasmids in archaea

Citation: Garrett R, Redder P, Greve B, Brügger K, Chen L, She Q. 2004. Archaeal Plasmids, p 377-392. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch17

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