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The discovery of CRISPR in archaea and bacteria
Open accessAbstract
CRISPR-Cas are self-/nonself-discriminating systems found in prokaryotic cells. They represent a remarkable example of molecular memory that is hereditarily transmitted. Their discovery can be considered as one of the first fruits of the systematic exploration of prokaryotic genomes. Although this genomic feature was serendipitously discovered in molecular biology studies, it was the availability of multiple complete genomes that shed light about their role as a genetic immune system. Here we tell the story of how this discovery originated and was slowly and painstakingly advanced to the point of understating the biological role of what initially was just an odd genomic feature.
Overview
AI snapshot
Written from the paper’s full text.
TL;DR
This is a historical account by Mojica and Rodríguez-Valera of how CRISPR was discovered in archaea and bacteria, beginning with an unexpected 30-bp repeat pattern in *Haloferax mediterranei* in 1992. It traces how exploratory prokaryotic genomics and spacer-matching analyses led to the recognition of CRISPR-Cas as an adaptive immune system.
Key findings
- The first CRISPR-like repeats were found serendipitously in *Haloferax mediterranei*: DNA segments 30 bp long repeated at regular distances, with at least 14 almost perfectly conserved repeats flanked at one end by a highly degenerated copy.
- Similar arrays were already known in bacteria: *E. coli* K12 had two DNA segments with 14 and 7 copies of a 29-bp sequence, and *Mycobacterium bovis* BCG had an array with 49 copies of a 36-bp direct repeat separated by 35–41 bp spacers.
- By the end of the century, regularly spaced repeats had been discovered in 12 species of archaea and bacteria, with open access to 26 completed microbial genomes; a comprehensive study showed wide distribution and hinted at ancestral origin and high biological relevance.
- Spacer analysis in *E. coli* showed that about 2% of spacers from 61 additional strains matched sequences in non-CRISPR loci, invariably in genetic elements of the corresponding spacer-carrier species, supporting CRISPR as an immunity system against foreign DNA.
Methods
- Historical narrative/perspective article, not a primary experimental study; it recounts the authors’ discovery process and the field’s development.
- Sources include the authors’ recollections, an unpublished Sanger sequencing gel dated 21/08/1992, an unpublished doctoral thesis, and published literature on CRISPR and prokaryotic genomes.
- Main analysis is chronological and descriptive, linking early repeat observations, genome sequencing advances, spacer database searches, and later experimental demonstrations by other groups.
Limitations
- Not stated in the paper: the article does not include a formal limitations section.
- Evident from the text: it is a retrospective personal account, so it may be shaped by recall and perspective rather than systematic review.
- Evident from the text: some reported experiments are unpublished results, and the authors describe publication rejections and lack of solid experimental evidence at the time, which limits the strength of the early immunity claims.
Model-written summary. Check it against the paper before relying on it.
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Claims the paper makes
42 Sources not found · 7 No basis given · 5 Own interpretation · 1 Own result
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In the paper
“When experiments equivalent to those previously performed in H. volcanii were replicated in E. coli, no clear phenotype was seen.”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
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In the paper
“DNA segments, 30 bp long, were repeated at regular distances (Fig. 2A).”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
What the sources say
- Not matchedcites [4]
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In the paper
“In the exceptional cases where the cell harboured one of these protospacer-carriers, the similarity between the spacer and its homolog segment was markedly diminished with respect to the protospacer consensus sequence.”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
What the sources say
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In the paper
“Firstly, the possibility that TREPs could serve as frequent recombination sites, and hence recombination as the main biological role of TREPs, was dismissed.”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
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In the paper
“additional sequencing experiments confirmed the presence in this region of at least 14 almost perfectly conserved (one occasional mismatch) repeats flanked at one end by a highly degenerated copy.”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
What the sources say
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In the paper
“They were located in a, seemingly, noncoding area next to open reading frames (ORFs) that did not show homology to any known protein [4].”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
What the sources say
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In the paper
“Moreover, additional studies did not provide any evidence of an involvement of the E. coli repeats in the partition apparatus.”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
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In the paper
“Moreover, plasmids or viruses containing spacer-matching sequences (named protospacers) were usually absent in the spacer-carrier.”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
What the sources say
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In the paper
“Even though salt-dependent transcription of genes surrounding the haloarchaeal repeats (by then called TREPs after Tandem REPeats) was detected, their implication in exclusively transcription regulation of a few genes was questionable due to the large size of the repeat loci.”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
What the sources say
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In the paper
“Then, three additional spacers were found to be similar to sequences in either that bacteriophage or in a conjugative plasmid of E. coli.”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
What the sources say
- Not matchedcites [11]
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plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Probably not a substantial claim. 8
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“However, highly variable results were obtained upon deletion of phage-homologous spacers on susceptibility to infection, as well as when analysing transformation efficiency of recombinant plasmids containing spacer-matching sequences (unpublished results).”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
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In the paper
“Then, a reduction in cell viability detected in these cultures, concomitant with the appearance of cells with reduced chromosomal content, was seen as a sign of incompatibility between replicons containing the repeats, hinting at a role for TREPs in replicon partitioning [9].”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
What the sources say
- Not matchedcites [9]
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In the paper
“To corroborate this finding, the spacers of 61 additional strains, including all available complete genomes, were subjected to the same sort of analysis, turning out that about a 2% of them matched sequences in non-CRISPR loci, invariably in genetic elements of the corresponding spacer-carrier species [11].”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
What the sources say
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In the paper
“However, repeat binding proteins could not be recovered from cell extracts and topology of recombinant plasmids was not affected by the presence of repeat stretches.”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
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In the paper
“This comprehensive study demonstrated the wide distribution of this sort of redundant sequences across a wide microbial diversity, hinting at an ancestral origin and high biological relevance [13].”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
What the sources say
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In the paper
“TREP sequences were found in the chromosome and a large plasmid of both H. mediterranei and Haloferax volcanii, and hybridization assays disclosed the presence of similar repeats in a second haloarchaeal genus, Haloarcula.”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
What the sources say
- Not matchedcites [9]
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plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“Northern blots hybridized with probes of the repeat region revealed multiple transcripts, suggesting that highly processed RNAs derived from the repeat arrays (Fig. 3).”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
What the sources say
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hedgedcorrelationalSingle case- Asserted: passes — The authors put it forward as true.
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In the paper
“Together with the CRISPRassociated (Cas) proteins, they are the main constituents of the CRISPR-Cas systems that provide prokaryotes with acquired immunity and contribute other unrelated functions such as gene regulation.”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
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In the paper
“These signatures, today known as Protospacer Adjacent Motifs (PAMs), were afterwards shown to be a common feature in diverse CRISPR systems [22] where PAM recognition is a requisite for both spacer uptake and target interference [23].”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
What the sources say
- Not matchedcites [22]
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Not matchedcites [23]
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plaindirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Although this genomic feature was serendipitously discovered in molecular biology studies”
§ The discovery of CRISPR in archaea and bacteria > Abstract
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In the paper
“We know now that CRISPR can acquire spacers from, and eventually interfere with, RNA [32] and/or DNA molecules, depending on the particular system.”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
What the sources say
- Not matchedcites [32]
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plaindirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“They represent a remarkable example of molecular memory that is hereditarily transmitted.”
§ The discovery of CRISPR in archaea and bacteria > Abstract
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper may give no reason why it holds.
In the paper
“Taken together, these findings strongly supported a connection between CRISPR and immunity against foreign DNA, most likely guided by CRISPR-RNA molecules.”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
What the sources say
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Their existence proves that prokaryotic genomes are environment tuned.”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
boosteddirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Besides, target cleavage is not the only way CRISPR may act and roles beyond immunity, notably through regulation of gene expression [33], are played by specific systems.”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
What the sources say
- Not matchedcites [33]
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hedgedconditional- Asserted: passes — The authors put it forward as true.
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In the paper
“Whereas regularly spaced repeats had not been seen before in archaea, similarly arranged structures had been reported in the chromosome of Gram-negative (Escherichia coli) [5] and Grampositive (Mycobacterium spp.) [6] bacteria.”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
What the sources say
- Not matchedcites [5]
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
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In the paper
“not to mention the average 10% non-coding DNA [38] present in all these genomes.”
§ The discovery of CRISPR in archaea and bacteria > phenotypic properties in bacterial populations.
What the sources say
- Not matchedcites [38]
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plain- Asserted: passes — The authors put it forward as true.
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In the paper
“Clustered regularly interspaced short palindromic repeats, CRISPR for short, form arrays of up to several hundred units in the genome of many bacteria and archaea.”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“It seems appropriate to remember here that the great motor of molecular biology during the XX th century, molecular cloning, was made possible by restriction endonucleases and plasmid vectors, both derived from serendipitous discoveries of prokaryotic cell biology features involved in self/nonself discrimination as well.”
§ The discovery of CRISPR in archaea and bacteria > phenotypic properties in bacterial populations.
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“CRISPR-Cas are self/non-self discriminating systems found in prokaryotic cells.”
§ The discovery of CRISPR in archaea and bacteria > Abstract
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper may give no reason why it holds.
In the paper
“Nonetheless, given that protospacers were also detected in chromosomal regions, a regulatory role for CRISPR was inferred, resembling the eukaryotic RNA interference (RNAi) mechanism [11].”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
What the sources say
- Not matchedcites [11]
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hedgedconditional- Asserted: passes — The authors put it forward as true.
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In the paper
“There are orphan CRISPR arrays in prokaryotic genomes and viruses [34,35], as well as CRISPR-like stretches in eukaryotic viruses [36] and mitochondria [13], most of which are enigmatic regarding their activity or function.”
§ The discovery of CRISPR in archaea and bacteria > Accepted Article
What the sources say
- Not matchedcites [34]
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- Not matchedcites [35]
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- Not matchedcites [13]
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plain- Asserted: passes — The authors put it forward as true.
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The paper relies on this without support.
The four selected microorganisms (E. coli, Streptococcus pyogenes, Sulfolobus, and Methanothermobacter thermoautotrophicum) are representative of their respective prokaryotic groups such that common observations about their CRISPR loci apply to prokaryotes in general.
“Four microorganisms were selected, as representatives of their respective prokaryotic groups, for further analysis: E. coli (Gram-negative bacteria), Streptococcus pyogenes (Gram-positive bacteria), Sulfolobus (crenarchaea) and Methanothermobacter thermoautotrophicum (euryarchaea).”
“Hence, common observations related to their CRISPR loci would provide conclusions applying to the prokaryotes in general.”
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Cited works that were retracted
Works this paper cites that were later retracted, from the retraction notices publishers deposit. Major when the notice came out before this paper was published.
A note, not an issue: for example, a cited work that was retracted only after this paper was published, which its authors could not have known.
In the paper
“10.1038/nbt.3547”
Cited work 10.1038/nbt.3547 · retracted 2017-07-26 · notice 10.1038/nbt0817-797a · this paper published 2016-06-15
Citations
Cites
1 retracted
DNA-guided genome editing using the Natronobacterium gregoryi Argonaute
Gao, F., Shen, X. Z., Jiang, F., Wu, Y., & Han, C. (2016) · Nature Biotechnology · doi:10.1038/nbt.3547 · Cited by 170
RetractedCRISPR Provides Acquired Resistance Against Viruses in Prokaryotes
Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., Romero, D. A., & Horvath, P. (2007) · Science · doi:10.1126/science.1138140 · Cited by 5,947
An updated evolutionary classification of CRISPR–Cas systems
Makarova, K. S., Wolf, Y. I., Alkhnbashi, O. S., Costa, F., Shah, S. A., Saunders, S. J., Barrangou, R., Brouns, S. J. J., Charpentier, E., Haft, D. H., et al. (2015) · Nature Reviews Microbiology · doi:10.1038/nrmicro3569 · Cited by 2,480
Self-citationSmall CRISPR RNAs Guide Antiviral Defense in Prokaryotes
Brouns, S. J. J., Jore, M. M., Lundgren, M., Westra, E. R., Slijkhuis, R. J. H., Snijders, A. P. L., Dickman, M. J., Makarova, K. S., Koonin, E. V., & van der Oost, J. (2008) · Science · doi:10.1126/science.1159689 · Cited by 2,460
Ishino, Y., Shinagawa, H., Makino, K., Amemura, M., & Nakata, A. (1987) · Journal of Bacteriology · doi:10.1128/jb.169.12.5429-5433.1987 · Cited by 2,421
The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA
Garneau, J. E., Dupuis, M.-È., Villion, M., Romero, D. A., Barrangou, R., Boyaval, P., Fremaux, C., Horvath, P., Magadán, A. H., & Moineau, S. (2010) · Nature · doi:10.1038/nature09523 · Cited by 2,336
Evolution and classification of the CRISPR–Cas systems
Makarova, K. S., Haft, D. H., Barrangou, R., Brouns, S. J. J., Charpentier, E., Horvath, P., Moineau, S., Mojica, F. J. M., Wolf, Y. I., Yakunin, A. F., et al. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2577 · Cited by 2,331
Self-citationComplete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii
Bult, C. J., White, O. R., Olsen, G. J., Zhou, L., Fleischmann, R. D., Sutton, G. G., Blake, J. A., Fitzgerald, L. M., Clayton, R. A., Gocayne, J. D., et al. (1996) · Science · doi:10.1126/science.273.5278.1058 · Cited by 2,086
Intervening Sequences of Regularly Spaced Prokaryotic Repeats Derive from Foreign Genetic Elements
Mojica, F. J. M., D�ez-Villase�or, C., Garc�a-Mart�nez, J., & Soria, E. (2005) · Journal of Molecular Evolution · doi:10.1007/s00239-004-0046-3 · Cited by 2,042
Self-citationIdentification of genes that are associated with DNA repeats in prokaryotes
Jansen, R., Embden, J. D. A. V., Gaastra, W., & Schouls, L. M. (2002) · Molecular Microbiology · doi:10.1046/j.1365-2958.2002.02839.x · Cited by 1,802
CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA
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Short motif sequences determine the targets of the prokaryotic CRISPR defence system
Mojica, F. J. M., Díez-Villaseñor, C., García-Martínez, J., & Almendros, C. (2009) · Microbiology · doi:10.1099/mic.0.023960-0 · Cited by 1,426
Self-citationPourcel, C., Salvignol, G., & Vergnaud, G. (2005) · Microbiology · doi:10.1099/mic.0.27437-0 · Cited by 1,201
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Mojica, F. J. M., Díez‐Villaseñor, C., Soria, E., & Juez, G. (2000) · Molecular Microbiology · doi:10.1046/j.1365-2958.2000.01838.x · Cited by 821
Self-citationInsights from 20 years of bacterial genome sequencing
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Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities
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Evolutionary conservation of sequence and secondary structures in CRISPR repeats
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Self-citationProtospacer recognition motifs: Mixed identities and functional diversity
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Self-citationCRISPR–Cas systems: beyond adaptive immunity
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Self-citationHalobacterium mediterranei spec, nov., a New Carbohydrate-Utilizing Extreme Halophile
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Direct CRISPR spacer acquisition from RNA by a natural reverse transcriptase–Cas1 fusion protein
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Shuttle vectors for the archaebacterium Halobacterium volcanii.
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Identification of a Novel Family of Sequence Repeats among Prokaryotes
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Unusual nucleotide arrangement with repeated sequences in the Escherichia coli K-12 chromosome
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MIMIVIRE is a defence system in mimivirus that confers resistance to virophage
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Reconstructing Viral Genomes from the Environment Using Fosmid Clones: The Case of Haloviruses
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Localized domains of DNA supercoiling: topological coupling between promoters
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Self-citationIn vivo supercoiling of plasmid and chromosomal DNA in an Escherichia coli hns mutant
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Self-citationDiscovery and Seminal Developments in the CRISPR Field
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Self-citationThe on–off switch of CRISPR immunity against phages in Escherichia coli
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Self-citation
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CRISPR–Cas9 Structures and Mechanisms
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Methodologies for Improving HDR Efficiency
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In vivo somatic cell base editing and prime editing
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Metadata
- Authors
- Mojica, F. J. M., & Rodriguez‐Valera, F.
- Affiliations
- University of Alicante (ES)
- Evolutionary Genomics Group Universidad Miguel Hernandez Alicante Spain
- Corresponding author
- Mojica, Francisco J. M.
- Venue
- The FEBS Journal
- Publisher
- Wiley
- Published
- 2016-06-15
- Volume
- 283
- Issue
- 17
- Pages
- 3162-3169
- ISSN
- 1742-464X (ISSN-L)
- 1742-4658
- OpenAlex
- W2397372517
- Cited by
- 207
- References
- 39
- Citations by year
- 2026: 10 · 2025: 24 · 2024: 27 · 2023: 22 · 2022: 36 · 2021: 26 · 2020: 19 · 2019: 11 · 2018: 18 · 2017: 11 · 2016: 3
- FWCI
- 1.24
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- FEBS Journal (publishedVersion, other-oa)
- PubMed (publishedVersion)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion)
- Repositorio Institucional de la Universidad de Alicante (Universidad de Alicante) (submittedVersion)
- Funders
- European Commission (291815)
- Seventh Framework Programme
- Generalitat Valenciana
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Structural Characterization
- Keywords
- CRISPR-Cas, archaea, bacteria, self/non-self discrimination, molecular memory, adaptive immunity
- MeSH terms
- Archaea, Bacteria, Genome, Bacterial, Genome, Archaeal, Genomics, CRISPR-Cas Systems
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-11-08, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-11-08 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
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