A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action

Makarova, Kira S.; Grishin, Nick V.; Shabalina, Svetlana A.; Wolf, Yuri I.; Koonin, Eugene V.

doi:10.1186/1745-6150-1-7

Cited by 986 publications

(684 citation statements)

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“…The spacers sometimes show good sequence matches with extrachromosomal elements which propagate in the same genus (19). It has been suggested (17,18,19) and was recently confirmed (3) that these DNA fragments were trans- 5) and their homologs in AFV6, AFV7, and AFV8. In Fig.…”

Section: Resultsmentioning

confidence: 88%

Structure of the Acidianus Filamentous Virus 3 and Comparative Genomics of Related Archaeal Lipothrixviruses

Vestergaard

Aramayo

Basta

et al. 2008

J Virol

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Four novel filamentous viruses with double-stranded DNA genomes, namely, Acidianus filamentous virus 3 (AFV3), AFV6, AFV7, and AFV8, have been characterized from the hyperthermophilic archaeal genus Acidianus, and they are assigned to the Betalipothrixvirus genus of the family Lipothrixviridae. The structures of the approximately 2-m-long virions are similar, and one of them, AFV3, was studied in detail. It consists of a cylindrical envelope containing globular subunits arranged in a helical formation that is unique for any known double-stranded DNA virus. The envelope is 3.1 nm thick and encases an inner core with two parallel rows of protein subunits arranged like a zipper. Each end of the virion is tapered and carries three short filaments. Two major structural proteins were identified as being common to all betalipothrixviruses. The viral genomes were sequenced and analyzed, and they reveal a high level of conservation in both gene content and gene order over large regions, with this similarity extending partly to the earlier described betalipothrixvirus Sulfolobus islandicus filamentous virus. A few predicted gene products of each virus, in addition to the structural proteins, could be assigned specific functions, including a putative helicase involved in Holliday junction branch migration, a nuclease, a protein phosphatase, transcriptional regulators, and glycosyltransferases. The AFV7 genome appears to have undergone intergenomic recombination with a large section of an AFV2-like viral genome, apparently resulting in phenotypic changes, as revealed by the presence of AFV2-like termini in the AFV7 virions. Shared features of the genomes include (i) large inverted terminal repeats exhibiting conserved, regularly spaced direct repeats; (ii) a highly conserved operon encoding the two major structural proteins; (iii) multiple overlapping open reading frames, which may be indicative of gene recoding; (iv) putative 12-bp genetic elements; and (v) partial gene sequences corresponding closely to spacer sequences of chromosomal repeat clusters.

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Section: Resultsmentioning

confidence: 88%

Structure of the Acidianus Filamentous Virus 3 and Comparative Genomics of Related Archaeal Lipothrixviruses

Vestergaard

Aramayo

Basta

et al. 2008

J Virol

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“…SRSR clusters have been suggested to act as possible centromer-like elements during archaeal chromosome segregation (30,31), and the induction of an SRSR-binding protein agrees with this suggestion, although an RNAi-like function for SRSR clusters recently was proposed (32). The Pelota protein (33) is implicated in spindle formation and nuclear envelope breakdown in Drosophila (34), and the late induction is in line with a cell-cycle-related function also in archaea, as is the induction of the Saci0053 gene, suggested to be involved in chromosome segregation (19), in addition to DNA repair.…”

Section: Discussionmentioning

confidence: 87%

Genome-wide transcription map of an archaeal cell cycle

Lundgren

Bernander

2007

Proc. Natl. Acad. Sci. U.S.A.

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Relative RNA abundance was measured at different cell-cycle stages in synchronized cultures of the hyperthermophilic archaeon Sulfolobus acidocaldarius. Cyclic induction was observed for >160 genes, demonstrating central roles for transcriptional regulation and cell-cycle-specific gene expression in archaeal cell-cycle progression. Many replication genes were induced in a cell-cyclespecific manner, and novel replisome components are likely to be among the genes of unknown function with similar induction patterns. Candidate genes for the unknown genome segregation and cell division machineries were also identified, as well as seven transcription factors likely to be involved in cell-cycle control. Two serine-threonine protein kinases showed distinct cell-cycle-specific induction, suggesting regulation of the archaeal cell cycle also through protein modification. Two candidate recognition elements, CCR boxes, for transcription factors in control of cell-cycle regulons were identified among gene sets with similar induction kinetics. The results allow detailed characterization of the genome segregation, division, and replication processes and may, because of the extensive homologies between the archaeal and eukaryotic information machineries, also be applicable to core features of the eukaryotic cell cycle.Archaea ͉ chromosome replication ͉ microarrays ͉ mitosis ͉ Sulfolobus

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“…The CRISPR-associated protein Cas9 that belongs to the type II CRISPR/ Cas system has attracted much attention due to its potential use in genomic engineering. Cas9 contains one HNH motif and three RuvC-like motifs, homologous to HNH and RuvC endonucleases, respectively (Supplementary information, Figure S1) [4][5][6][7][8]. Recent studies showed that Cas9 displayed strong DNA cleavage activity in bacteria and in test tubes.…”

Section: Dear Editormentioning

confidence: 99%