Transcription Profile of Thermus thermophilus CRISPR Systems after Phage Infection

CRISPR-Cas are prokaryotic adaptive immune systems that provide protection against bacteriophage (phage) and other parasites. Little is known about how CRISPR-Cas systems are regulated, preventing prediction of phage dynamics in nature and manipulation of phage resistance in clinical settings. Here, we show that the bacterium Pseudomonas aeruginosa PA14 uses the cell-cell communication process, called quorum sensing, to activate cas gene expression, to increase CRISPR-Cas targeting of foreign DNA, and to promote CRISPR adaptation, all at high cell density. This regulatory mechanism ensures maximum CRISPR-Cas function when bacterial populations are at highest risk for phage infection. We demonstrate that CRISPR-Cas activity and acquisition of resistance can be modulated by administration of proand antiquorum-sensing compounds. We propose that quorum-sensing inhibitors could be used to suppress the CRISPR-Cas adaptive immune system to enhance medical applications, including phage therapies.quorum sensing | CRISPR | immunity | phage | phage defense

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“…To limit fitness costs, some CRISPR-Cas systems are induced upon infection (11)(12)(13). Other environmental cues regulate CRISPR-Cas.…”

mentioning

confidence: 99%

Quorum sensing controls the Pseudomonas aeruginosa CRISPR-Cas adaptive immune system

Høyland‐Kroghsbo

Paczkowski

Mukherjee

et al. 2016

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

264

223

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“…The CRISPR locus is transcribed beginning in the leader sequence, which houses four promoters [122]. Although generally the transcription of the CRISPR locus occurs continuously at low levels, in Thermus thermophilus, the presence of foreign DNA can cause increased levels of expression of CRISPR-Cas elements [1]. The initial transcription of the CRISPR locus produces a long crRNA precursor that can contain an RNA transcript of the entire locus [12,101].…”

Section: Crrna Biogenesismentioning

confidence: 99%

“…In P. furiosus, the cleavage of the pre-crRNA is performed by Cas6 [16]. However, in E. Coli, the cascade complex, a protein complex composed of cse1, cse2, cse3, cse4, and cse5 (also known as CasA, B, C, D, and E), cleaves the pre-crRNA inside of the transcript resultant from the repeat sequence [1]. Cse3 cleaves at the 5 end of the new crRNA, and the 3 end is then processed via an unknown mechanism.…”

Section: Crrna Biogenesismentioning

confidence: 99%

Diversity, evolution, and therapeutic applications of small RNAs in prokaryotic and eukaryotic immune systems

Cooper

Overstreet

2014

Physics of Life Reviews

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Recent evidence supports that prokaryotes exhibit adaptive immunity in the form of CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats) and Cas (CRISPR associated proteins). The CRISPR-Cas system confers resistance to exogenous genetic elements such as phages and plasmids by allowing for the recognition and silencing of these genetic elements. Moreover, CRISPR-Cas serves as a memory of past exposures. This suggests that the evolution of the immune system has counterparts among the prokaryotes, not exclusively among eukaryotes. Mathematical models have been proposed which simulate the evolutionary patterns of CRISPR, however large gaps in our understanding of CRISPR-Cas function and evolution still exist. The CRISPR-Cas system is analogous to small RNAs involved in resistance mechanisms throughout the tree of life, and a deeper understanding of the evolution of small RNA pathways is necessary before the relationship between these convergent systems is to be determined. Presented in this review are novel RNAi therapies based on CRISPR-Cas analogs and the potential for future therapies based on CRISPR-Cas system components.

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“…Indeed, it has been shown that the expression of several cas genes as well as the CRISPR array can be repressed, with the system undergoing upregulation upon signs of phage infection. 65,66 Under this model, CRISPR spacers targeting the lysogenic phage would become lethal only when a prophage is induced, sacrificing the host but limiting the spread of the phage to adjacent cells. This hypothesis is supported by recent studies showing that type IIIB CRISPR/Cas requires active transcription of the DNA target in order to degrade it.…”

Section: Holding a Grudgementioning

confidence: 99%

Holding a grudge

2013

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T he CRISPR (clustered regularlyinterspaced short palindromic repeats)/Cas (CRISPR-associated) system of bacteria and archaea constitutes a mechanism of acquired adaptive immunity against phages, which is based on genome-encoded markers of previously infecting phage sequences ("spacers"). As a repository of phage sequences, these spacers make the system particularly suitable for elucidating phage-bacteria interactions in metagenomic studies. Recent metagenomic analyses of CRISPRs associated with the human microbiome intriguingly revealed conserved "memory spacers" shared by bacteria in multiple unrelated, geographically separated individuals. Here, we discuss possible avenues for explaining this phenomenon by integrating insights from CRISPR biology and phage-bacteria ecology, with a special focus on the human gut. We further explore the growing body of evidence for the role of CRISPR/Cas in regulating the interplay between bacteria and lysogenic phages, which may be intimately related to the presence of memory spacers and sheds new light on the multifaceted biological and ecological modes of action of CRISPR/Cas. IntroductionBacteriophages are known to play a crucial role in shaping the structure, diversity and evolution of microbial communities in various ecological niches. [1][2][3][4] The CRISPR (clustered regularly interspaced short palindromic repeats)/Cas Holding a grudgePersisting anti-phage CRISPR immunity in multiple human gut microbiomes (CRISPR-associated) system of bacteria and archaea constitutes a mechanism of acquired adaptive immunity against phages, which is based on genomeencoded markers of past infections. 5 The unique biology of this system has opened a window into the multifaceted interactions that take place in natural environments between microbial populations and their associated phages. At the same time, observation of these interactions raises intriguing questions about the underlying mechanistic activity of CRISPR/Cas. Here, we explore this reciprocity with a focus on the microbial community resident in the human gut.CRISPR loci are composed of a succession of short repeat sequences separated by unique "spacer" sequences, usually sized 24-50 bp. While the mechanism of action of the CRISPR/Cas system is not yet fully characterized and some specifics vary by subtype, it generally entails three processes: incorporation of fragments of phage or plasmid genomes as novel spacers in bacterial CRISPR arrays; transcription and processing of the array into small RNAs (crRNAs) and formation of a crRNA/Cas protein complex that recognizes foreign nucleic acids through sequence complementarity and interferes with phage replication. [6][7][8][9][10][11] Elucidation of the function of the CRISPR/Cas system has led to theoretical and experimental efforts at exploring the ecological impacts of CRISPR-mediated immunity, as well as the conditions under which its emergence would be favored. [12][13][14] However, this system provided an ©2012 Landes Bioscience. Do not distribute.

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Transcription Profile of Thermus thermophilus CRISPR Systems after Phage Infection

Cited by 121 publications

References 39 publications

Quorum sensing controls the Pseudomonas aeruginosa CRISPR-Cas adaptive immune system

Quorum sensing controls the Pseudomonas aeruginosa CRISPR-Cas adaptive immune system

Diversity, evolution, and therapeutic applications of small RNAs in prokaryotic and eukaryotic immune systems

Holding a grudge

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