CRISPR analysis suggests that small circular single-stranded DNA smacoviruses infect Archaea instead of humans

Figures

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  Fig. 1. Clustered Interspaced Short Palindromic Repeats (CRISPR)-Cas Subtype I-B in Candidatus M. intestinalis and its targets in smacoviruses. The CRISPR-Cas subtype I-B in Ca. M. intestinalis is represented. Related cas genes are grouped and coloured according to functional categories: adaptation (cas1–2 and cas4), target cleavage (cas3) and formation of interference complex (cas6, cas8a1, cas7 and cas5). Cas8a1 would belong to subtype I-A. Two repetitive arrays are found in opposite orientations, here named B1 (112 repeats) and B2 (3 repeats), with putative leader sequences, from where transcription would start. Array B1 is amplified and similarities of spacers to sequences in smacoviruses indicated. A smacovirus 'archetype' is depicted where targets are represented with their relative positions to genes (see Methods). Similar sequences that are in the same orientation of spacers point right and vice versa. Smacoviruses are circular single-stranded DNA (ssDNA) virus with just two genes (rep and cap). Targets in the ssDNA are represented below the viral genome, and targets in the complementary strand above. Targets in red were found with local–global alignments, while targets in grey…

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  Fig. 2. Sequence conservation in flanking regions of smacoviral Candidatus M. intestinalis Clustered Interspaced Short Palindromic Repeats (CRISPR) targets. Sequence logos represent conservation of 10 bases, in non-target strand, upstream (5' end of corresponding spacer in CRISPR RNA (crRNA)) (a, c) and downstream (b, d) from sequences targeted by the spacer in Ca. M. intestinalis. Up (a, b), conservation around the six matches identical to spacers. Down (c, d), conservation in best matches to each 23 spacers. e Representation of an R-loop, where crRNA from spacer 6 hybridizes to target double-stranded DNA (dsDNA) protospacer in smacoviurs. f Part of life cycle of a Circular Rep Encoding Single-Stranded DNA (CRESS-DNA) virus showcasing presence of dsDNA, targeted presumably by the Type I CRISPR-Cas system, after synthesis of complementary strand, and in replication. In e, f the viral strand is represented in blue, complimentary in garnet and RNA in black

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  Fig. 3. Stop codons usage of Smacoviridae compared to Circular Rep Encoding Single-Stranded DNA (CRESS-DNA) viruses and possible hosts. In organisms, such as Candidatus M. intestinalis, that use amber (UAG) codon to codify pyrrolysine, its use for translation termination is reduced. Bars represent the percentage of coding sequences ending in one of the standard termination codons that end with amber, opal (UGA) or ochre (UAA) codons for a set of CRESS-DNA virus, a set of smacoviruses, Ca. M. intestinalis genome and human genome (see details in Methods section). Only percentages of amber codon are shown