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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

Comparison of CRISPR loci of S. solfataricus strains P1, P2, P3 and 98/2. Spacers are coloured to identify virus and plasmid sequences with the best match. A significant match was defined as a maximum of 10 mismatches with no more than two in the critical annealing region from positions 3–7 (Section 6.2). Each locus is oriented with the leader on the left. Colour-coding of virus and plasmid matches is indicated. The large arrowheads in loci D and F represent irregularities in the spacer-repeat structures (Section 4.5). Regions shaded in specific colours are identical in sequence. In the original publication of Lillestøl et al. [29], some parts of the CRISPR arrays were inadvertently inverted relative to the leader [57] and were later corrected in [37].
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life-05-00783-f004: Comparison of CRISPR loci of S. solfataricus strains P1, P2, P3 and 98/2. Spacers are coloured to identify virus and plasmid sequences with the best match. A significant match was defined as a maximum of 10 mismatches with no more than two in the critical annealing region from positions 3–7 (Section 6.2). Each locus is oriented with the leader on the left. Colour-coding of virus and plasmid matches is indicated. The large arrowheads in loci D and F represent irregularities in the spacer-repeat structures (Section 4.5). Regions shaded in specific colours are identical in sequence. In the original publication of Lillestøl et al. [29], some parts of the CRISPR arrays were inadvertently inverted relative to the leader [57] and were later corrected in [37].

Mentions: Bioinformatical analyses of CRISPR loci of the Sulfolobales revealed many potentially significant spacer sequence matches to viruses or conjugative plasmids and they were identified earlier for the large CRISPR loci of S. solfataricus P1 and P2 and different S. islandicus strains [29,37,53,54,55,56]. The S. solfataricus matches are presented here (Figure 4) together with those of the more recently sequenced CRISPR loci of strains P3 and 98/2 employing more rigorous stringency criteria than used earlier.


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)

Comparison of CRISPR loci of S. solfataricus strains P1, P2, P3 and 98/2. Spacers are coloured to identify virus and plasmid sequences with the best match. A significant match was defined as a maximum of 10 mismatches with no more than two in the critical annealing region from positions 3–7 (Section 6.2). Each locus is oriented with the leader on the left. Colour-coding of virus and plasmid matches is indicated. The large arrowheads in loci D and F represent irregularities in the spacer-repeat structures (Section 4.5). Regions shaded in specific colours are identical in sequence. In the original publication of Lillestøl et al. [29], some parts of the CRISPR arrays were inadvertently inverted relative to the leader [57] and were later corrected in [37].
© Copyright Policy
Related In: Results  -  Collection

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

life-05-00783-f004: Comparison of CRISPR loci of S. solfataricus strains P1, P2, P3 and 98/2. Spacers are coloured to identify virus and plasmid sequences with the best match. A significant match was defined as a maximum of 10 mismatches with no more than two in the critical annealing region from positions 3–7 (Section 6.2). Each locus is oriented with the leader on the left. Colour-coding of virus and plasmid matches is indicated. The large arrowheads in loci D and F represent irregularities in the spacer-repeat structures (Section 4.5). Regions shaded in specific colours are identical in sequence. In the original publication of Lillestøl et al. [29], some parts of the CRISPR arrays were inadvertently inverted relative to the leader [57] and were later corrected in [37].
Mentions: Bioinformatical analyses of CRISPR loci of the Sulfolobales revealed many potentially significant spacer sequence matches to viruses or conjugative plasmids and they were identified earlier for the large CRISPR loci of S. solfataricus P1 and P2 and different S. islandicus strains [29,37,53,54,55,56]. The S. solfataricus matches are presented here (Figure 4) together with those of the more recently sequenced CRISPR loci of strains P3 and 98/2 employing more rigorous stringency criteria than used earlier.

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