A putative viral defence mechanism in archaeal cells

Reidun Lillestøl,Kim Brügger,Roger A Garrett,Peter Redder

doi:10.1155/2006/542818

Abstract

Clusters of regularly spaced direct repeats, separated by unconserved spacer sequences, are ubiquitous in archaeal chromosomes and occur in some plasmids. Some clusters constitute around 1% of chromosomal DNA. Similarly structured clusters, generally smaller, also occur in some bacterial chromosomes. Although early studies implicated these clusters in segregation/partition functions, recent evidence suggests that the spacer sequences derive from extrachromosomal elements, and, primarily, viruses. This has led to the proposal that the clusters provide a defence against viral propagation in cells, and that both the mode of inhibition of viral propagation and the mechanism of adding spacer-repeat units to clusters, are dependent on RNAs transcribed from the clusters. Moreover, the putative inhibitory apparatus (piRNA-based) may be evolutionarily related to the interference RNA systems (siRNA and miRNA), which are common in eukarya. Here, we analyze all the current data on archaeal repeat clusters and provide some new insights into their diverse structures, transcriptional properties and mode of structural development. The results are consistent with larger cluster transcripts being processed at the centers of the repeat sequences and being further trimmed by exonucleases to yield a dominant, intracellular RNA species, which corresponds approximately to the size of a spacer. Furthermore, analysis of the extensive clusters of Sulfolobus solfataricus strains P1 and P2B provides support for the presence of a flanking sequence adjoining a cluster being a prerequisite for the incorporation of new spacer-repeat units, which occurs between the flanking sequence and the cluster. An archaeal database summarizing the data will be maintained at http://dac.molbio.ku.dk/dbs/SRSR/.

Highlights

Clusters of regularly spaced repeats were first detected in Escherichia coli (Ishino et al 1987), and were later found in archaea, both in chromosomes of the Haloferax genus of the kingdom Euryarchaeota (Mojica et al 1993, 1995) and in conjugative plasmids of the Sulfolobus genus of the kingdom Crenarchaeota (She et al 1998, Greve et al 2004)
Sequencing of clusters in S. solfataricus P1 Long range PCR products were obtained across the chromosomal cluster regions of strain P1, which differ in sequence from those of strain P2, using the Herculase II kit
Genome sequences were downloaded from National Center for Biotechnology Information (NCBI), except that of Haloferax volcanii, which was obtained from The Institute for Genomic Research, and the Hyperthermus butylicus sequence

Summary

Introduction

Clusters of regularly spaced repeats were first detected in Escherichia coli (Ishino et al 1987), and were later found in archaea, both in chromosomes of the Haloferax genus of the kingdom Euryarchaeota (Mojica et al 1993, 1995) and in conjugative plasmids of the Sulfolobus genus of the kingdom Crenarchaeota (She et al 1998, Greve et al 2004). With the rapid progress in whole genome sequencing, it is clear that repeat clusters are ubiquitous in the sequenced archaeal chromosomes, except that of Halobacterium sp. Striking for the Archaea, is that the chromosomal clusters are often both multiple and very large, such that in some Sulfolobus species, they constitute > 1% of the genome (Kawarabayasi et al 2001, She et al 2001)

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Conclusion