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CRISPR-Cas Adaptive Immune Systems of the Sulfolobales: Unravelling Their Complexity and Diversity.

Garrett RA, Shah SA, Erdmann S, Liu G, Mousaei M, León-Sobrino C, Peng W, Gudbergsdottir S, Deng L, Vestergaard G, Peng X, She Q - Life (Basel) (2015)

Bottom Line: Recent work also supports critical roles for non-core Cas proteins, especially during Type III-directed interference, and this is consistent with these proteins tending to coevolve with core Cas proteins.Various novel aspects of CRISPR-Cas systems of the Sulfolobales are considered including an alternative spacer acquisition mechanism, reversible spacer acquisition, the formation and significance of antisense CRISPR RNAs, and a novel mechanism for avoidance of CRISPR-Cas defense.Finally, questions regarding the basis for the complexity, diversity, and apparent redundancy, of the intracellular CRISPR-Cas systems are discussed.

View Article: PubMed Central - PubMed

Affiliation: Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark. garrett@bio.ku.dk.

ABSTRACT
The Sulfolobales have provided good model organisms for studying CRISPR-Cas systems of the crenarchaeal kingdom of the archaea. These organisms are infected by a wide range of exceptional archaea-specific viruses and conjugative plasmids, and their CRISPR-Cas systems generally exhibit extensive structural and functional diversity. They carry large and multiple CRISPR loci and often multiple copies of diverse Type I and Type III interference modules as well as more homogeneous adaptation modules. These acidothermophilic organisms have recently provided seminal insights into both the adaptation process, the diverse modes of interference, and their modes of regulation. The functions of the adaptation and interference modules tend to be loosely coupled and the stringency of the crRNA-DNA sequence matching during DNA interference is relatively low, in contrast to some more streamlined CRISPR-Cas systems of bacteria. Despite this, there is evidence for a complex and differential regulation of expression of the diverse functional modules in response to viral infection. Recent work also supports critical roles for non-core Cas proteins, especially during Type III-directed interference, and this is consistent with these proteins tending to coevolve with core Cas proteins. Various novel aspects of CRISPR-Cas systems of the Sulfolobales are considered including an alternative spacer acquisition mechanism, reversible spacer acquisition, the formation and significance of antisense CRISPR RNAs, and a novel mechanism for avoidance of CRISPR-Cas defense. Finally, questions regarding the basis for the complexity, diversity, and apparent redundancy, of the intracellular CRISPR-Cas systems are discussed.

No MeSH data available.


Related in: MedlinePlus

Schematic diagrams of CRISPR-Cas interference complexes. (A) A Type I-A complex where the Cas3' and Cas3", but not Cas6, are associated with the interference complex of the crenarchaeon T. tenax [102]. The crRNA is oriented as shown earlier for the genetically modified E. coli Type I-E complex [105]. (B) Type III-B Cmr-α complex of S. islandicus based on published structures of related complexes [46,106]. This complex requires Csx1 for targeting transcripts and transcribing DNA [47,48]. (C) RNA targeting Type III-B Cmr-β complex of S. islandicus, extrapolating from the Type III-B structure of S. solfataricus in [44]. (D) A Type III-D complex of S. solfataricus [99]. Estimated binding regions of crRNAs are colour-coded brown. Subunits of the Type I-A and III-D complexes are assigned Cas protein numbers while Type III-B complexes are given Cmr protein numbers. In (C) 7 denotes non-core protein Cmr7 which forms a pseudo-hexameric structure in the Sulfolobales. In (A) the protein locations indicated for Cas3'/3'' are speculative, while the putative position of a Cas8'' dimer is deduced from the published structure of a Type I-E interference complex [105].
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life-05-00783-f006: Schematic diagrams of CRISPR-Cas interference complexes. (A) A Type I-A complex where the Cas3' and Cas3", but not Cas6, are associated with the interference complex of the crenarchaeon T. tenax [102]. The crRNA is oriented as shown earlier for the genetically modified E. coli Type I-E complex [105]. (B) Type III-B Cmr-α complex of S. islandicus based on published structures of related complexes [46,106]. This complex requires Csx1 for targeting transcripts and transcribing DNA [47,48]. (C) RNA targeting Type III-B Cmr-β complex of S. islandicus, extrapolating from the Type III-B structure of S. solfataricus in [44]. (D) A Type III-D complex of S. solfataricus [99]. Estimated binding regions of crRNAs are colour-coded brown. Subunits of the Type I-A and III-D complexes are assigned Cas protein numbers while Type III-B complexes are given Cmr protein numbers. In (C) 7 denotes non-core protein Cmr7 which forms a pseudo-hexameric structure in the Sulfolobales. In (A) the protein locations indicated for Cas3'/3'' are speculative, while the putative position of a Cas8'' dimer is deduced from the published structure of a Type I-E interference complex [105].

Mentions: Type I and Type III interference modules show major differences in their protein contents although some proteins are likely to be distant homologs [35,36,104]. Furthermore, their quaternary structures are distinct and diverse; a seahorse-like structure was first reported for the CASCADE complexes of E. coli Type I-E systems [105], whereas a low-resolution structure of an S. solfataricus Type III-B complex more closely resembled a “crab claw” [44]. The availability of higher resolution structures of additional Type I and III complexes suggest that they share a common central form that reconciles differences between the seahorse and crab-claw structures [46,99,105]. A schematic view of the most common Sulfolobus interference complexes based on results published for related systems is presented in Figure 6A–D.


CRISPR-Cas Adaptive Immune Systems of the Sulfolobales: Unravelling Their Complexity and Diversity.

Garrett RA, Shah SA, Erdmann S, Liu G, Mousaei M, León-Sobrino C, Peng W, Gudbergsdottir S, Deng L, Vestergaard G, Peng X, She Q - Life (Basel) (2015)

Schematic diagrams of CRISPR-Cas interference complexes. (A) A Type I-A complex where the Cas3' and Cas3", but not Cas6, are associated with the interference complex of the crenarchaeon T. tenax [102]. The crRNA is oriented as shown earlier for the genetically modified E. coli Type I-E complex [105]. (B) Type III-B Cmr-α complex of S. islandicus based on published structures of related complexes [46,106]. This complex requires Csx1 for targeting transcripts and transcribing DNA [47,48]. (C) RNA targeting Type III-B Cmr-β complex of S. islandicus, extrapolating from the Type III-B structure of S. solfataricus in [44]. (D) A Type III-D complex of S. solfataricus [99]. Estimated binding regions of crRNAs are colour-coded brown. Subunits of the Type I-A and III-D complexes are assigned Cas protein numbers while Type III-B complexes are given Cmr protein numbers. In (C) 7 denotes non-core protein Cmr7 which forms a pseudo-hexameric structure in the Sulfolobales. In (A) the protein locations indicated for Cas3'/3'' are speculative, while the putative position of a Cas8'' dimer is deduced from the published structure of a Type I-E interference complex [105].
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4390879&req=5

life-05-00783-f006: Schematic diagrams of CRISPR-Cas interference complexes. (A) A Type I-A complex where the Cas3' and Cas3", but not Cas6, are associated with the interference complex of the crenarchaeon T. tenax [102]. The crRNA is oriented as shown earlier for the genetically modified E. coli Type I-E complex [105]. (B) Type III-B Cmr-α complex of S. islandicus based on published structures of related complexes [46,106]. This complex requires Csx1 for targeting transcripts and transcribing DNA [47,48]. (C) RNA targeting Type III-B Cmr-β complex of S. islandicus, extrapolating from the Type III-B structure of S. solfataricus in [44]. (D) A Type III-D complex of S. solfataricus [99]. Estimated binding regions of crRNAs are colour-coded brown. Subunits of the Type I-A and III-D complexes are assigned Cas protein numbers while Type III-B complexes are given Cmr protein numbers. In (C) 7 denotes non-core protein Cmr7 which forms a pseudo-hexameric structure in the Sulfolobales. In (A) the protein locations indicated for Cas3'/3'' are speculative, while the putative position of a Cas8'' dimer is deduced from the published structure of a Type I-E interference complex [105].
Mentions: Type I and Type III interference modules show major differences in their protein contents although some proteins are likely to be distant homologs [35,36,104]. Furthermore, their quaternary structures are distinct and diverse; a seahorse-like structure was first reported for the CASCADE complexes of E. coli Type I-E systems [105], whereas a low-resolution structure of an S. solfataricus Type III-B complex more closely resembled a “crab claw” [44]. The availability of higher resolution structures of additional Type I and III complexes suggest that they share a common central form that reconciles differences between the seahorse and crab-claw structures [46,99,105]. A schematic view of the most common Sulfolobus interference complexes based on results published for related systems is presented in Figure 6A–D.

Bottom Line: Recent work also supports critical roles for non-core Cas proteins, especially during Type III-directed interference, and this is consistent with these proteins tending to coevolve with core Cas proteins.Various novel aspects of CRISPR-Cas systems of the Sulfolobales are considered including an alternative spacer acquisition mechanism, reversible spacer acquisition, the formation and significance of antisense CRISPR RNAs, and a novel mechanism for avoidance of CRISPR-Cas defense.Finally, questions regarding the basis for the complexity, diversity, and apparent redundancy, of the intracellular CRISPR-Cas systems are discussed.

View Article: PubMed Central - PubMed

Affiliation: Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark. garrett@bio.ku.dk.

ABSTRACT
The Sulfolobales have provided good model organisms for studying CRISPR-Cas systems of the crenarchaeal kingdom of the archaea. These organisms are infected by a wide range of exceptional archaea-specific viruses and conjugative plasmids, and their CRISPR-Cas systems generally exhibit extensive structural and functional diversity. They carry large and multiple CRISPR loci and often multiple copies of diverse Type I and Type III interference modules as well as more homogeneous adaptation modules. These acidothermophilic organisms have recently provided seminal insights into both the adaptation process, the diverse modes of interference, and their modes of regulation. The functions of the adaptation and interference modules tend to be loosely coupled and the stringency of the crRNA-DNA sequence matching during DNA interference is relatively low, in contrast to some more streamlined CRISPR-Cas systems of bacteria. Despite this, there is evidence for a complex and differential regulation of expression of the diverse functional modules in response to viral infection. Recent work also supports critical roles for non-core Cas proteins, especially during Type III-directed interference, and this is consistent with these proteins tending to coevolve with core Cas proteins. Various novel aspects of CRISPR-Cas systems of the Sulfolobales are considered including an alternative spacer acquisition mechanism, reversible spacer acquisition, the formation and significance of antisense CRISPR RNAs, and a novel mechanism for avoidance of CRISPR-Cas defense. Finally, questions regarding the basis for the complexity, diversity, and apparent redundancy, of the intracellular CRISPR-Cas systems are discussed.

No MeSH data available.


Related in: MedlinePlus