A putative viral defence mechanism in archaeal cells

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/.

Knowledge-based discovery for designing CRISPR-CAS systems against invading mobilomes in thermophiles

“…Therefore, the cas genes of most thermophilic genomes have appeared in the order of cas5-cas3-cas1-cas2. It also reports that a superoperon (cas6-cas4-cas1-cas2-csh1-csh2-cas5-cas3) is identified and typically established in the genome of T. lettingae as similar to earlier findings (Lillestol et al 2006). Very often, superoperons are absent in the chromosomes of T. acidophilum and P. abyssi and of their plasmids, pNOB8 and pKEF9.…”

“…RNA-directed defense mechanisms in the genomes of thermophilic bacteria and archaea have evolved like a prokaryotic genome to cope with the constant threat of genome invaders (Chellapandi and Ranjani 2011;Makarova et al 2012;Weinberger et al 2012;Vestergaard et al 2014). The existence of this pathway in these genomes has been hypothesized to parallel the eukaryotic RNAi pathway known as Clustered regularly interspaced short palindromic repeats-CRISPR-associated sequences (CRISPR-CAS) system or prokaryotic RNAi (pRNAi) (Lillestol et al 2006;Makarova et al 2006;Tomoyasu et al 2008). The common structural characteristics of CRISPR loci are: (1) multiple short direct repeats (2) non-repetitive spacer sequences between the repeats of similar size (3) a common leader sequence of a few hundred base pairs harboring multiple CRISPR loci and (4) accompanied by cas gene families.…”

CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea

“…The observation that only 2% of all spacers match any known sequence presumably reflect the general under-sampling of phage sequence space, and is in agreement with recent estimates of huge untapped phage environmental diversity 26 . Indeed, in lactic acid bacteria such as S. thermophilus, for which more than a dozen phage genomes have been isolated and sequenced, ~40% of the spacers had a homologue, matching either phage (75%) or plasmid (20%) sequences 20 .Spacers seem to be evenly distributed across the phage genomes and derive both from the sense (coding) and antisense (non-coding) orientations 18,19,21,25 , although one report suggested a preference towards spacers derived from one strand of the phage 20 . Two recent studies have reported on a short motif present in phage genomes 1-2 nucleotides 4 downstream to spacer-matching sequences [49][50] .…”

Diversity, evolution, and therapeutic applications of small RNAs in prokaryotic and eukaryotic immune systems

“…There is great variation in the size of the locus, which can be as short as a single spacer sandwiched by two repeats or as long as 375 spacers [90,119]. Over time, the CRISPR locus can mutate by undergoing sequence deletions, duplications, or recombinations.…”

“…However, there appears to be strong selective pressure against the insertion of these elements [90]. The CRISPR locus is rarely targeted by integrative genetic elements, even in species in which genetic shuffling caused by these mobile sequences is common.…”