CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies

Pourcel, Christine; Salvignol, Grégory; Vergnaud, Gilles

doi:10.1099/mic.0.27437-0

Cited by 1,126 publications

(733 citation statements)

References 29 publications

(29 reference statements)

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“…These variable sequences, known as spacers, are juxtaposed between 2 neighboring repeats and have been shown to be highly homologous to phages or foreign genetic elements. [5][6][7][8] Thus, the CRISPR loci are described as the genetic retention of historical infections. In addition, over 45 CRISPR-associated (cas) gene families have been identified.…”

Section: Introductionmentioning

confidence: 99%

Crystal structures of CRISPR-associated Csx3 reveal a manganese-dependent deadenylation exoribonuclease

2015

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In prokaryotes, the CRISPR/Cas system is known to target and degrade invading phages and foreign genetic elements upon subsequent infection. However, the structure and function of many Cas proteins remain largely unknown, due to the high diversity of Cas proteins. Here we report 3 crystal structures of Archaeoglobus fulgidus Csx3 (AfCsx3) in free form, in complex with manganese ions and in complex with a single-stranded RNA (ssRNA) fragment, respectively. AfCsx3 harbors a ferredoxin-like fold and forms dimer both in the crystal and in solution. Our structurebased biochemical analysis demonstrates that the RNA binding sites and cleavage sites are located at 2 separate surfaces within the AfCsx3 dimer, suggesting a model to bind, tether and cleave the incoming RNA substrate. In addition, AfCsx3 displays robust 3 0 -deadenylase activity in the presence of manganese ions, which strongly suggests that AfCsx3 functions as a deadenylation exonuclease. Taken together, our results indicate that AfCsx3 is a Cas protein involved in RNA deadenylation and provide a framework for understanding the role of AfCsx3 in the Type III-B CRISPR/ Cas system.

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Section: Introductionmentioning

confidence: 99%

Crystal structures of CRISPR-associated Csx3 reveal a manganese-dependent deadenylation exoribonuclease

2015

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“…For a small fraction of the spacers, protospacers have been reported, often in viral and plasmid genomes, but the substantial majority of the spacers remain without a match, representing vast CRISPR "dark matter" (43)(44)(45)(46)(47)(48)(49).…”

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The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes

Shmakov

Sitnik

Makarova

et al. 2017

mBio

198

195

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Clustered regularly interspaced short palindromic repeats and CRISPRassociated protein (CRISPR-Cas) systems store the memory of past encounters with foreign DNA in unique spacers that are inserted between direct repeats in CRISPR arrays. For only a small fraction of the spacers, homologous sequences, called protospacers, are detectable in viral, plasmid, and microbial genomes. The rest of the spacers remain the CRISPR "dark matter." We performed a comprehensive analysis of the spacers from all CRISPR-cas loci identified in bacterial and archaeal genomes, and we found that, depending on the CRISPR-Cas subtype and the prokaryotic phylum, protospacers were detectable for 1% to about 19% of the spacers (~7% global average). Among the detected protospacers, the majority, typically 80 to 90%, originated from viral genomes, including proviruses, and among the rest, the most common source was genes that are integrated into microbial chromosomes but are involved in plasmid conjugation or replication. Thus, almost all spacers with identifiable protospacers target mobile genetic elements (MGE). The GC content, as well as dinucleotide and tetranucleotide compositions, of microbial genomes, their spacer complements, and the cognate viral genomes showed a nearly perfect correlation and were almost identical. Given the near absence of self-targeting spacers, these findings are most compatible with the possibility that the spacers, including the dark matter, are derived almost completely from the species-specific microbial mobilomes. IMPORTANCEThe principal function of CRISPR-Cas systems is thought to be protection of bacteria and archaea against viruses and other parasitic genetic elements. The CRISPR defense function is mediated by sequences from parasitic elements, known as spacers, that are inserted into CRISPR arrays and then transcribed and employed as guides to identify and inactivate the cognate parasitic genomes. However, only a small fraction of the CRISPR spacers match any sequences in the current databases, and of these, only a minority correspond to known parasitic elements. We show that nearly all spacers with matches originate from viral or plasmid genomes that are either free or have been integrated into the host genome. We further demonstrate that spacers with no matches have the same properties as those of identifiable origins, strongly suggesting that all spacers originate from mobile elements.KEYWORDS CRISPR-Cas, bacteriophages, mobilome, oligonucleotide composition, spacer acquisition C RISPR-Cas (clustered regularly interspaced palindromic repeats and CRISPRassociated proteins) systems are adaptive (acquired) immune systems of archaea and bacteria that store memory of past encounters with foreign DNA in unique spacer Citation Shmakov SA, Sitnik V, Makarova KS, Wolf YI, Severinov KV, Koonin EV. 2017. The CRISPR spacer space is dominated by sequences from species-specific mobilomes.

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“…However, in addition to the matches with MGEs, spacers were also found that target sites on the bacterial or archaeal genome. For example, in Yersinia spp., of 36 spacers analyzed, the majority were of bacteriophage origin, but 8 spacers matched sequences on the Yersinia chromosome (13). A similar pattern was observed in a broader analysis of 4,500 spacers across archaea and bacteria, in which 35% of the spacers that matched sequences in the NCBI database were derived from chromosomal DNA and apparently were not related to foreign elements or prophages (12).…”

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confidence: 49%

“…Analysis of the sequences of spacers from a given CRISPR array can serve as a history of previous CRISPR-Cas interactions with invading MGEs. The first evidence that CRISPRCas systems function as an immune system came from such an analysis, when in 2005, three separate groups examined a variety of CRISPR arrays and found that spacers matched sequences found in phages and plasmids (11)(12)(13). However, in addition to the matches with MGEs, spacers were also found that target sites on the bacterial or archaeal genome.…”

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confidence: 99%

Friendly Fire: Biological Functions and Consequences of Chromosomal Targeting by CRISPR-Cas Systems

Heussler

O’Toole

2016

J Bacteriol

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Clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) systems in bacteria and archaea target foreign elements, such as bacteriophages and conjugative plasmids, through the incorporation of short sequences (termed spacers) from the foreign element into the CRISPR array, thereby allowing sequence-specific targeting of the invader. Thus, CRISPR-Cas systems are typically considered a microbial adaptive immune system. While many of these incorporated spacers match targets on bacteriophages and plasmids, a noticeable number are derived from chromosomal DNA. While usually lethal to the self-targeting bacteria, in certain circumstances, these self-targeting spacers can have profound effects in regard to microbial biology, including functions beyond adaptive immunity. In this minireview, we discuss recent studies that focus on the functions and consequences of CRISPR-Cas self-targeting, including reshaping of the host population, group behavior modification, and the potential applications of CRISPR-Cas self-targeting as a tool in microbial biotechnology. Understanding the effects of CRISPRCas self-targeting is vital to fully understanding the spectrum of function of these systems.

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CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies

Cited by 1,126 publications

References 29 publications

Crystal structures of CRISPR-associated Csx3 reveal a manganese-dependent deadenylation exoribonuclease

Crystal structures of CRISPR-associated Csx3 reveal a manganese-dependent deadenylation exoribonuclease

The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes

Friendly Fire: Biological Functions and Consequences of Chromosomal Targeting by CRISPR-Cas Systems

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