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Chapter 46 : Archaeal Mobile DNA

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Abstract:

This chapter summarizes the different classes of mobile DNA elements of archaea and considers their impact on archaeal evolution. Several viruses and virus-like particles have been characterized for the archaea, although, with the exception of , no comprehensive studies have been performed to examine the diversity of viruses that are present. To date, although there is strong evidence for exchange of insertion elements (IS) elements between viruses and chromosomes, there is no direct evidence for chromosome integration of any euryarchaeal viruses. All of the crenarchaeal viruses that have been characterized so far carry double-stranded DNA genomes and differ in morphology from their euryarchaeal counterparts. Several plasmids have been isolated and characterized, at least partially, from both archaeal kingdoms. Conjugative plasmids in Archaea have so far been found only in closely related strains of , where they occur frequently. Putative large inserts, which resemble bacterial integrons, have been detected in archaeal chromosomes. Some archaeal genomes, and in particular those from some and species, are rich in IS elements, both in their chromosomes and in their extrachromosomal genetic elements, while others appear to contain very few. Several IS elements have also been detected in archaeal genetic elements. These include two copies of ISH1800 in each of the haloarchaeal viruses φH2 and φH5. Archaea carry introns in their tRNA, rRNA, and mRNA genes that are archaea-specific with respect to both the structures of their RNA intron-exon junctions and their splicing mechanism.

Citation: Redder P, Brügger K, She Q, Garrett R, Faguy D. 2002. Archaeal Mobile DNA, p 1060-1073. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch46

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Figures

Image of Figure 1.
Figure 1.

A model for the excision/integration of the putative plasmid pXQ1 in the chromosome of P2. The integrase target sites in the plasmid and chromosome are the 45-bp direct repeats, where L and R denote left and right, respectively. Excision and circularization produce an intact integrase gene (). The IS element ISC1439A interrupts A. Four ORFs from pXQ1 show high sequence similarity to genes of other members of the pRN family. and represent putative double-strand and single-strand origins of replication, respectively ( ).

Citation: Redder P, Brügger K, She Q, Garrett R, Faguy D. 2002. Archaeal Mobile DNA, p 1060-1073. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch46
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Image of Figure 2.
Figure 2.

(a) Consensus sequences of the aligned terminal inverted repeats for the MITE SM1 and its partner IS element ISC1048. The terminal inverted repeats are shaded, and capital letters indicate identical nucleotides. (b) Potentially mobile unit (800 bp) containing a copy of ISC1048 where the upstream half has been replaced by SM1 and the remainder contains a copy of SM2 ( ). The left inverted repeat (IR) of SM1 and the right IR of ISC1048 are complementary, as shown in panel a.

Citation: Redder P, Brügger K, She Q, Garrett R, Faguy D. 2002. Archaeal Mobile DNA, p 1060-1073. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch46
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Image of Figure 3.
Figure 3.

Distribution of SM elements in the chromosome of P2. The areas marked IS-1 to IS-4 represent high concentrations of IS and SM elements ( ).

Citation: Redder P, Brügger K, She Q, Garrett R, Faguy D. 2002. Archaeal Mobile DNA, p 1060-1073. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch46
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Tables

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Table 1

Euryarchaeal viruses

Citation: Redder P, Brügger K, She Q, Garrett R, Faguy D. 2002. Archaeal Mobile DNA, p 1060-1073. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch46
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Table 2

Crenarchaeal viruses

Citation: Redder P, Brügger K, She Q, Garrett R, Faguy D. 2002. Archaeal Mobile DNA, p 1060-1073. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch46
Generic image for table
Table 3

Crenarchaeal pRN plasmids

Citation: Redder P, Brügger K, She Q, Garrett R, Faguy D. 2002. Archaeal Mobile DNA, p 1060-1073. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch46
Generic image for table
Table 4

Crenarchaeal conjugative plasmids

Citation: Redder P, Brügger K, She Q, Garrett R, Faguy D. 2002. Archaeal Mobile DNA, p 1060-1073. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch46
Generic image for table
Table 6

Summary of the IS elements in the genome

Citation: Redder P, Brügger K, She Q, Garrett R, Faguy D. 2002. Archaeal Mobile DNA, p 1060-1073. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch46
Generic image for table
Table 7

SM elements found in the genome

Citation: Redder P, Brügger K, She Q, Garrett R, Faguy D. 2002. Archaeal Mobile DNA, p 1060-1073. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch46
Generic image for table
Table 5

Summary of IS elements and MITEs found in archaeal genomes

Citation: Redder P, Brügger K, She Q, Garrett R, Faguy D. 2002. Archaeal Mobile DNA, p 1060-1073. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch46
Generic image for table
Table 8

Archaeal rRNA introns

Citation: Redder P, Brügger K, She Q, Garrett R, Faguy D. 2002. Archaeal Mobile DNA, p 1060-1073. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch46

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