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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

Alignment of locus E leaders from S. solfataricus strains P2 and 98/2 and S. islandicus strain LD.8.5 (SislLD) together with a selection of closely similar CRISPR leaders from different S. islandicus strains [55,87]. The number following the strain indicates the number of repeats in the CRISPR array. Position -1 lies adjacent to the first repeat. Conserved sequence positions are indicated by asterisks.
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life-05-00783-f005: Alignment of locus E leaders from S. solfataricus strains P2 and 98/2 and S. islandicus strain LD.8.5 (SislLD) together with a selection of closely similar CRISPR leaders from different S. islandicus strains [55,87]. The number following the strain indicates the number of repeats in the CRISPR array. Position -1 lies adjacent to the first repeat. Conserved sequence positions are indicated by asterisks.

Mentions: Locus E of S. solfataricus strains P1, P2 and 98/2 carries 6 spacers and the spacer and repeat sequences are identical, with the exception of the most leader-distal spacer of strain 98/2, and strain P3 carries four additional spacers (Figure 4) [42]. The mechanism of de novo spacer acquisition in locus E in strain P2 differed from that observed for the other active CRISPR loci in that spacers were inserted throughout the locus, albeit with a strong bias to repeat 4 (56%) and lesser bias to repeats 1, 3 and 6 (11%–17%). Moreover, only a single spacer insertion was observed for each clone [75]. An explanation for this apparent anomaly may lie in the sequence of the locus E leader which differs from those of other leaders in strain P2 and more closely resembles leaders of several S. islandicus strains, except that it carries a 25 bp deletion upstream from position -46 (Figure 5) [75,76]. Possibly, absence of this sequence impairs the specificity of the spacer insertion process.


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)

Alignment of locus E leaders from S. solfataricus strains P2 and 98/2 and S. islandicus strain LD.8.5 (SislLD) together with a selection of closely similar CRISPR leaders from different S. islandicus strains [55,87]. The number following the strain indicates the number of repeats in the CRISPR array. Position -1 lies adjacent to the first repeat. Conserved sequence positions are indicated by asterisks.
© Copyright Policy
Related In: Results  -  Collection

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

life-05-00783-f005: Alignment of locus E leaders from S. solfataricus strains P2 and 98/2 and S. islandicus strain LD.8.5 (SislLD) together with a selection of closely similar CRISPR leaders from different S. islandicus strains [55,87]. The number following the strain indicates the number of repeats in the CRISPR array. Position -1 lies adjacent to the first repeat. Conserved sequence positions are indicated by asterisks.
Mentions: Locus E of S. solfataricus strains P1, P2 and 98/2 carries 6 spacers and the spacer and repeat sequences are identical, with the exception of the most leader-distal spacer of strain 98/2, and strain P3 carries four additional spacers (Figure 4) [42]. The mechanism of de novo spacer acquisition in locus E in strain P2 differed from that observed for the other active CRISPR loci in that spacers were inserted throughout the locus, albeit with a strong bias to repeat 4 (56%) and lesser bias to repeats 1, 3 and 6 (11%–17%). Moreover, only a single spacer insertion was observed for each clone [75]. An explanation for this apparent anomaly may lie in the sequence of the locus E leader which differs from those of other leaders in strain P2 and more closely resembles leaders of several S. islandicus strains, except that it carries a 25 bp deletion upstream from position -46 (Figure 5) [75,76]. Possibly, absence of this sequence impairs the specificity of the spacer insertion process.

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