Intervening Sequences of Regularly Spaced Prokaryotic Repeats Derive from Foreign Genetic Elements

@article{Mojica2004InterveningSO,
  title={Intervening Sequences of Regularly Spaced Prokaryotic Repeats Derive from Foreign Genetic Elements},
  author={Francisco J. M. Mojica and Chcsar D{\'i}ez-Villase{\~n}or and Jes{\'u}s Garc{\'i}a-Mart{\'i}nez and Elena Soria},
  journal={Journal of Molecular Evolution},
  year={2004},
  volume={60},
  pages={174-182}
}
Prokaryotes contain short DNA repeats known as CRISPR, recognizable by the regular spacing existing between the recurring units. They represent the most widely distributed family of repeats among prokaryotic genomes, suggesting a biological function. The origin of the intervening sequences, at present unknown, could provide clues about their biological activities. Here we show that CRISPR spacers derive from preexisting sequences, either chromosomal or within transmissible genetic elements such… 
The Repetitive DNA Elements Called CRISPRs and Their Associated Genes: Evidence of Horizontal Transfer Among Prokaryotes
TLDR
A mechanism by which this HGT has occurred is suggested, namely, that the CRISPR loci can be carried between cells on megaplasmids ≥40 kb in length.
Short motif sequences determine the targets of the prokaryotic CRISPR defence system.
TLDR
It is shown that the conservation of proto-spacer adjacent motifs (PAMs) is a common theme for the most diverse CRISPR systems, implying that there is aCRISPR-type-specific (motif-directed) choice of the spacers, which subsequently determines the interference target.
Genome editing based on CRISPR/CAS systems: beginning of a new era of genetic manipulation and inheritance
TLDR
In 2002, Ruud Jansen found a 21-37 bp interspaced short sequence repeats distinctly spaced among several bacterial species, such as, Salmonella typhimurium and Streptococcus pyogenes, and referred to the phenomenon as Clustered Regularly Interspaced Short Palindormic Repeats (CRISPR).
The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes
TLDR
A comprehensive analysis of the spacers from all CRISPR-cas loci identified in bacterial and archaeal genomes found that nearly all spacers with matches originate from viral or plasmid genomes that are either free or have been integrated into the host genome.
The Role of CRISPR-Cas Systems in Virulence of Pathogenic Bacteria
TLDR
Recently reported cases of potential involvement of CRISPR-Cas systems in bacterial stress responses in general and bacterial virulence in particular are described.
The CRISPR spacer space is dominated by sequences from the species-specific mobilome
TLDR
Almost all spacers with identifiable protospacers target mobile genetic elements (MGE), and the GC-content, as well as dinucleotide and tetranucleotide compositions, of microbial genomes, their spacer complements, and the cognate viral genomes show a nearly perfect correlation and are almost identical.
Evolutionary Analysis of CRISPRs in Archaea: An Evidence for HorizontalGene Transfer
TLDR
The phylogenetic analysis sketched from theCRISPR sequences signifies a harmony along the direct repeats of the analyzed organisms with no trace of spacer similarity, which affirms huge variation within the CRISPR–CAS systems among different prokaryotes.
Sequences spanning the leader-repeat junction mediate CRISPR adaptation to phage in Streptococcus thermophilus
TLDR
It is found that sequences within 10 bp of the site of integration, in both the leader and repeat of the CRISPR, are required for the process of adaptation in this Type II-A system and likely otherCRISPR-Cas systems.
Diversity, Evolution, and Functionality of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Regions in the Fire Blight Pathogen Erwinia amylovora
TLDR
The aim of this work was to investigate CRISPR diversity in the highly homogeneous species Erwinia amylovora, the causal agent of fire blight, and found reciprocal exclusion was generally observed between plasmid content and cognate spacer sequences, supporting the role of theCRISPR/Cas system in protecting against foreign DNA elements.
Genetics of CRISPR arrays in Salmonella Typhimurium 14028 associated with foreign DNA decay
TLDR
The results demonstrate that the spacer sequence is dependent on genetic relations, especially for adaptive immunity against phage or foreign DNAs.
...
...

References

SHOWING 1-10 OF 43 REFERENCES
Identification of genes that are associated with DNA repeats in prokaryotes
TLDR
A novel family of repetitive DNA sequences that is present among both domains of the prokaryotes but absent from eukaryotes or viruses is studied, characterized by direct repeats, varying in size from 21 to 37 bp, interspaced by similarly sized non‐repetitive sequences.
Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria
TLDR
The SRSRs are widespread among the various physiological and phylogenetic groups, probably being present in all the Archaea and hyperthermophilic Bacteria, in at least some members of the cyanobacteria and proteobacteria lineages, as well as in the two subgroups of Gram-positive bacteria (the low and high GC content groups).
Archaeal integrative genetic elements and their impact on genome evolution.
Genetic profile of pNOB8 from Sulfolobus: the first conjugative plasmid from an archaeon
TLDR
The complete nucleotide sequence of the archaeal conjugative plasmid, pNOB8, from the Sulfolobus isolate NOB8-H2, was determined and it is inferred that the conjugatives mechanism for Sulfoobus differs considerably from known bacterial mechanisms.
Prophage Genomics
TLDR
Analysis of the prophages suggested that after being integrated into bacterial genomes, they undergo a complex decay process consisting of inactivating point mutations, genome rearrangements, modular exchanges, invasion by further mobile DNA elements, and massive DNA deletion.
pING Family of Conjugative Plasmids from the Extremely Thermophilic Archaeon Sulfolobus islandicus: Insights into Recombination and Conjugation in Crenarchaeota
TLDR
The small defective but mobile variants pING2 and -3, which both lack a cluster of highly conserved ORFs probably involved in plasmid transfer, were shown to be formed in vivo by recombinative deletion of the larger part of the genomes of pING4 and pING6, respectively.
Genetic evidence of a coupling role for the TraG protein family in bacterial conjugation
TLDR
It is suggested that the factors that determine the frequencies of transfer of different MOB regions are the differential interactions of TrwB with pilus and relaxosome.
Lateral gene transfer and the origins of prokaryotic groups.
TLDR
Evidence for an important role of LGT in the evolution of photosynthesis, aerobic respiration, nitrogen fixation, sulfate reduction, methylotrophy, isoprenoid biosynthesis, quorum sensing, flotation (gas vesicles), thermophily, and halophily is reviewed.
A multicopy plasmid of the extremely thermophilic archaeon Sulfolobus effects its transfer to recipients by mating
TLDR
A plasmid of 45 kb, designated pNOB8, was found in high copy number in a new heterotrophic Sulfolobus isolate, NOB8H2, from Japan, and horizontal transfer of pNob8 was proved by isolating transcipients from mating mixtures via single colonies.
...
...