The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Short motif sequences determine the targets of the prokaryotic CRISPR defence system
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated CRISPR-associated sequence (CAS) proteins constitute a novel antiviral defence system that is widespread in prokaryotes. Repeats are separated by spacers, some of them homologous to sequences in mobile genetic elements. Although the whole process involved remains uncharacterized, it is known that new spacers are incorporated into CRISPR loci of the host during a phage challenge, conferring specific resistance against the virus. Moreover, it has been demonstrated that such interference is based on small RNAs carrying a spacer. These RNAs would guide the defence apparatus to foreign molecules carrying sequences that match the spacers. Despite this essential role, the spacer uptake mechanism has not been addressed. A first step forward came from the detection of motifs associated with spacer precursors (proto-spacers) of Streptococcus thermophilus , revealing a specific recognition of donor sequences in this species. Here we show that the conservation of proto-spacer adjacent motifs (PAMs) is a common theme for the most diverse CRISPR systems. The PAM sequence depends on the CRISPR-CAS variant, implying that there is a CRISPR-type-specific (motif-directed) choice of the spacers, which subsequently determines the interference target. PAMs also direct the orientation of spacers in the repeat arrays. Remarkably, observations based on such polarity argue against a recognition of the spacer precursors on transcript RNA molecules as a general rule.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Spacer acquisition in the E. coli type I-E CRISPR-Cas system begins with the recognition of PAM complementary sequences in ssDNA by Cas1a and Cas1a' subunits.
“Spacer acquisition in the E. coli type I-E CRISPR-Cas system begins with the recognition of PAM complementary sequences in ssDNA by Cas1a and Cas1a’ subunits [24].”
From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [24]
PAMs are short sequences (2-5 nucleotides), specific to each CRISPR-Cas subtype and bacteria, which determine the spacer alignment within the CRISPR array in type I and II systems.
“PAMs are short sequences (2–5 nucleotides), specific to each CRISPR-Cas subtype and bacteria, which determine the spacer alignment within the CRISPR array in type 1 and II systems, the better understood models of adaptation [24].”
From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [24]
Selection of protospacer sequences seems to be mediated by short motifs located near the target sequence, denominated protospacer adjacent motifs (PAMs).
“Selection of protospacer sequences seems to be mediated by short motifs located near the target sequence, denominated protospacer adjacent motifs (PAMs).”
From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [24]
CRISPR-Cas systems require a short PAM sequence next to the 3′ end of the target sequence.
“CRISPR-Cas systems require a short PAM sequence next to the 3′ end of the target sequence [24,37].”
From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [24]
Protospacers are DNA fragments attacked by the prokaryotic immune system, identical to corresponding spacers at the CRISPR locus except for the PAM motif.
“Protospacers are DNA fragments that are attacked by the immune system of prokaryotes, and are identical to the corresponding spacers at the CRISPR locus, except for the PAM motif.”
From CRISPR–Cas9: A History of Its Discovery and Ethical Considerations of Its Use in Genome Editing (2022) · cites this paper as [29]
Bolotin et al. discovered a specific pattern in the nucleotide sequences on one side of the described spacers of the CRISPR arrays, later understood as PAMs.
“Another important observation made by Bolotin et al. was the discovery of a specific pattern in the nucleotide sequences on one side of the described spacers of the CRISPR arrays, but the understanding of the role for this phenomenon was only revealed in later studies.”
From CRISPR–Cas9: A History of Its Discovery and Ethical Considerations of Its Use in Genome Editing (2022) · cites this paper as [29]
PAMs are short motifs adjacent to protospacers but absent in the original spacers of the CRISPR locus.
“Currently, short motifs adjacent to protospacers but absent in the original spacers of the CRISPR locus are called PAMs (protospacer adjacent motifs) [29].”
From CRISPR–Cas9: A History of Its Discovery and Ethical Considerations of Its Use in Genome Editing (2022) · cites this paper as [29]
Citations
Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Flagged first, then by citations
Research works printed but not linked: 31
- Barrangou, 2007, CRISPR provides acquired resistance against viruses in prokaryotes, Science, 315, 1709, 10.1126/science.1138140 · DOI · Paper page
- Beloglazova, 2008, A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats, J Biol Chem, 283, 20361, 10.1074/jbc.M803225200 · DOI
- Bolotin, 2005, Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin, Microbiology, 151, 2551, 10.1099/mic.0.28048-0 · DOI
- Brennecke, 2007, Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila, Cell, 128, 1089, 10.1016/j.cell.2007.01.043 · DOI · Paper page
- Brouns, 2008, Small CRISPR RNAs guide antiviral defense in prokaryotes, Science, 321, 960, 10.1126/science.1159689 · DOI · Paper page
- Crooks, 2004, WebLogo: a sequence logo generator, Genome Res, 14, 1188, 10.1101/gr.849004 · DOI
- DeBoy, 2006, Chromosome evolution in the Thermotogales: large-scale inversions and strain diversification of CRISPR sequences, J Bacteriol, 188, 2364, 10.1128/JB.188.7.2364-2374.2006 · DOI
- Deveau, 2008, Phage response to CRISPR-encoded resistance in Streptococcus thermophilus, J Bacteriol, 190, 1390, 10.1128/JB.01412-07 · DOI
- Ebihara, 2006, Crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 reveals a new protein family with an RNA recognition motif-like domain, Protein Sci, 15, 1494, 10.1110/ps.062131106 · DOI
- Haft, 2005, A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes, PLoS Comput Biol, 1, e60, 10.1371/journal.pcbi.0010060 · DOI
- Horvath, 2008, Diversity, activity and evolution of CRISPR loci in Streptococcus thermophilus, J Bacteriol, 190, 1401, 10.1128/JB.01415-07 · DOI
- Ishino, 1987, Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product, J Bacteriol, 169, 5429, 10.1128/JB.169.12.5429-5433.1987 · DOI · Paper page
- Jansen, 2002, Identification of genes that are associated with DNA repeats in prokaryotes, Mol Microbiol, 43, 1565, 10.1046/j.1365-2958.2002.02839.x · DOI · Paper page
- Kawaji, 2008, Exploration of small RNAs, PLoS Genet, 4, e22, 10.1371/journal.pgen.0040022 · DOI
- Kojima, 2008, Systematic survey for novel types of prokaryotic retroelements based on gene neighbourhood and protein architecture, Mol Biol Evol, 25, 1395, 10.1093/molbev/msn081 · DOI
- Kunin, 2007, Evolutionary conservation of sequence and secondary structures in CRISPR repeats, Genome Biol, 8, R61, 10.1186/gb-2007-8-4-r61 · DOI
- Lillestøl, 2006, A putative viral defence mechanism in archaeal cells, Archaea, 2, 59, 10.1155/2006/542818 · DOI
- Makarova, 2002, A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis, Nucleic Acids Res, 30, 482, 10.1093/nar/30.2.482 · DOI
- Makarova, 2006, A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action, Biol Direct, 1
- Mandin, 2007, Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets, Nucleic Acids Res, 35, 962, 10.1093/nar/gkl1096 · DOI
- Mojica, 1995, Long stretches of short tandem repeats are present in the largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning, Mol Microbiol, 17, 85, 10.1111/j.1365-2958.1995.mmi_17010085.x · DOI
- Mojica, 2000, Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria, Mol Microbiol, 36, 244, 10.1046/j.1365-2958.2000.01838.x · DOI
- Mojica, 2005, Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements, J Mol Evol, 60, 174, 10.1007/s00239-004-0046-3 · DOI · Paper page
- Ochman, 1984, Standard reference strains of Escherichia coli from natural populations, J Bacteriol, 157, 690, 10.1128/jb.157.2.690-693.1984 · DOI
- Pourcel, 2005, CRISPR elements in Y ersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies, Microbiology, 151, 653, 10.1099/mic.0.27437-0 · DOI · Paper page
- Riehle, 2001, Genetic architecture of thermal adaptation in Escherichia coli, Proc Natl Acad Sci U S A, 98, 525, 10.1073/pnas.98.2.525 · DOI
- Schneider, 1990, Sequence logos: a new way to display consensus sequences, Nucleic Acids Res, 18, 6097, 10.1093/nar/18.20.6097 · DOI
- Sorek, 2008, CRISPR – a widespread system that provides acquired resistance against phages in bacteria and archaea, Nat Rev Microbiol, 6, 181, 10.1038/nrmicro1793 · DOI
- Tang, 2002, Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus, Proc Natl Acad Sci U S A, 99, 7536, 10.1073/pnas.112047299 · DOI
- Tang, 2005, Identification of novel non-coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus, Mol Microbiol, 55, 469, 10.1111/j.1365-2958.2004.04428.x · DOI
- Willkomm, 2005, Experimental RNomics in Aquifex aeolicus: identification of small non-coding RNAs and the putative 6S RNA homolog, Nucleic Acids Res, 33, 1949, 10.1093/nar/gki334 · DOI
Cited by
Sorted by citations
A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012) · Science · doi:10.1126/science.1225829 · Cited by 17,116
Multiplex Genome Engineering Using CRISPR/Cas Systems
Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., et al. (2013) · Science · doi:10.1126/science.1231143 · Cited by 15,339
Gasiunas, G., Barrangou, R., Horvath, P., & Siksnys, V. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1208507109 · Cited by 2,769
Crystal structure of Cas9 in complex with guide RNA and target DNA
Nishimasu, H., Ran, F. A., Hsu, P. D., Konermann, S., Shehata, S. I., Dohmae, N., Ishitani, R., Zhang, F., & Nureki, O. (2014) · Cell · doi:10.1016/j.cell.2014.02.001 · Cited by 2,306
RNA-guided genetic silencing systems in bacteria and archaea
Wiedenheft, B., Sternberg, S. H., & Doudna, J. A. (2012) · Nature · doi:10.1038/nature10886 · Cited by 1,851
Engineered CRISPR-Cas9 nucleases with altered PAM specificities
Kleinstiver, B. P., Prew, M. S., Tsai, S. Q., Topkar, V. V., Nguyen, N. T., Zheng, Z., Gonzales, A. P. W., Li, Z., Peterson, R. T., Yeh, J.-R. J., et al. (2015) · Nature · doi:10.1038/nature14592 · Cited by 1,624
CRISPR-Cas guides the future of genetic engineering
Knott, G. J., & Doudna, J. A. (2018) · Science · doi:10.1126/science.aat5011 · Cited by 1,410
Off-target Effects in CRISPR/Cas9-mediated Genome Engineering
Zhang, X.-H., Tee, L. Y., Wang, X.-G., Huang, Q.-S., & Yang, S.-H. (2015) · Molecular Therapy - Nucleic Acids · doi:10.1038/mtna.2015.37 · Cited by 1,273
Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants
Walton, R. T., Christie, K. A., Whittaker, M. N., & Kleinstiver, B. P. (2020) · Science · doi:10.1126/science.aba8853 · Cited by 1,233
Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells
Wu, X., Scott, D. A., Kriz, A. J., Chiu, A. C., Hsu, P. D., Dadon, D. B., Cheng, A. W., Trevino, A. E., Konermann, S., Chen, S., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2889 · Cited by 944
CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation
Bhaya, D., Davison, M., & Barrangou, R. (2011) · Annual Review of Genetics · doi:10.1146/annurev-genet-110410-132430 · Cited by 914
Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation
Dominguez, A. A., Lim, W. A., & Qi, L. S. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2015.2 · Cited by 832
CRISPR-mediated adaptive immune systems in bacteria and archaea
Sorek, R., Lawrence, C. M., & Wiedenheft, B. (2013) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-072911-172315 · Cited by 668
Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis
Hou, Z., Zhang, Y., Propson, N. E., Howden, S. E., Chu, L.-F., Sontheimer, E. J., & Thomson, J. A. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1313587110 · Cited by 681
Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition
Kleinstiver, B. P., Prew, M. S., Tsai, S. Q., Nguyen, N. T., Topkar, V. V., Zheng, Z., & Joung, J. K. (2015) · Nature Biotechnology · doi:10.1038/nbt.3404 · Cited by 611
CRISPR/Cas9 systems targeting β-globin and CCR5 genes have substantial off-target activity
Cradick, T. J., Fine, E. J., Antico, C. J., & Bao, G. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt714 · Cited by 590
Classification and evolution of type II CRISPR-Cas systems
Chylinski, K., Makarova, K. S., Charpentier, E., & Koonin, E. V. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku241 · Cited by 498
A compact, high-accuracy Cas9 with a dinucleotide PAM for in vivo genome editing
Edraki, A., Mir, A., Ibraheim, R., Gainetdinov, I., Yoon, Y., Song, C.-Q., Cao, Y., Gallant, J., Xue, W., Rivera-Pérez, J. A., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2018.12.003 · Cited by 265
Streptococcus thermophilus CRISPR-cas9 systems enable specific editing of the human genome
Müller, M., Lee, C. M., Gasiunas, G., Davis, T. H., Cradick, T. J., Siksnys, V., Bao, G., Cathomen, T., & Mussolino, C. (2016) · Molecular Therapy · doi:10.1038/mt.2015.218 · Cited by 254
CRISPR–Cas9: A History of Its Discovery and Ethical Considerations of Its Use in Genome Editing
Gostimskaya, I. (2022) · Biochemistry (Moscow) · doi:10.1134/s0006297922080090 · Cited by 224
A Thermostable Cas9 with Increased Lifetime in Human Plasma
Harrington, L. B., Paez-Espino, D., Staahl, B. T., Chen, J. S., Ma, E., Kyrpides, N. C., & Doudna, J. A. (2017) · Nature Communications · doi:10.1038/s41467-017-01408-4 · Cited by 205
The discovery of CRISPR in archaea and bacteria
Mojica, F. J. M., & Rodriguez‐Valera, F. (2016) · The FEBS Journal · doi:10.1111/febs.13766 · Cited by 207
Self-citationThe CRISPR/Cas9 system and its applications in crop genome editing
Bao, A., Burritt, D. J., Chen, H., Zhou, X., Cao, D., & Tran, L.-S. P. (2019) · Critical Reviews in Biotechnology · doi:10.1080/07388551.2018.1554621 · Cited by 185
Structural basis for the altered PAM specificities of engineered CRISPR-cas9
Hirano, S., Nishimasu, H., Ishitani, R., & Nureki, O. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.02.018 · Cited by 152
Type III CRISPR-Cas immunity: major differences brushed aside
Tamulaitis, G., Venclovas, Č., & Siksnys, V. (2017) · Trends in Microbiology · doi:10.1016/j.tim.2016.09.012 · Cited by 126
RNA Interference (RNAi) Screening in Drosophila
Heigwer, F., Port, F., & Boutros, M. (2018) · Genetics · doi:10.1534/genetics.117.300077 · Cited by 125
Loureiro, A., & da Silva, G. J. (2019) · Antibiotics · doi:10.3390/antibiotics8010018 · Cited by 129
Archaeal CRISPR-based immune systems: exchangeable functional modules
Garrett, R. A., Vestergaard, G., & Shah, S. A. (2011) · Trends in Microbiology · doi:10.1016/j.tim.2011.08.002 · Cited by 98
CRISPR-based genome editing in wheat: a comprehensive review and future prospects
Kumar, R., Kaur, A., Pandey, A., Mamrutha, H. M., & Singh, G. P. (2019) · Molecular Biology Reports · doi:10.1007/s11033-019-04761-3 · Cited by 70
Characterization and Repurposing of Type I and Type II CRISPR–Cas Systems in Bacteria
Hidalgo-Cantabrana, C., Goh, Y. J., & Barrangou, R. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.09.013 · Cited by 63
Pride, D. T., Salzman, J., & Relman, D. A. (2012) · Environmental Microbiology · doi:10.1111/j.1462-2920.2012.02775.x · Cited by 60
PAM-flexible genome editing with an engineered chimeric Cas9
Zhao, L., Koseki, S. R. T., Silverstein, R. A., Amrani, N., Peng, C., Kramme, C., Savic, N., Pacesa, M., Rodríguez, T. C., Stan, T., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-41829-y · Cited by 59
Vamsi Krishna, K., Bharathi, N., George Shiju, S., Alagesan Paari, K., & Malaviya, A. (2022) · Environmental Science and Pollution Research · doi:10.1007/s11356-022-20637-9 · Cited by 51
CRISPR-Cas systems in multicellular cyanobacteria
Hou, S., Brenes-Álvarez, M., Reimann, V., Alkhnbashi, O. S., Backofen, R., Muro-Pastor, A. M., & Hess, W. R. (2019) · RNA Biology · doi:10.1080/15476286.2018.1493330 · Cited by 47
Yang, C., Lin, F., Li, Q., Li, T., & Zhao, J. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00394 · Cited by 44
Umeyama, T., Hayashi, Y., Shimosaka, H., Inukai, T., Yamagoe, S., Takatsuka, S., Hoshino, Y., Nagi, M., Nakamura, S., Kamei, K., et al. (2018) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00894-18 · Cited by 43
CRISPR/Cas9-Mediated Phage Resistance Is Not Impeded by the DNA Modifications of Phage T4
Yaung, S. J., Esvelt, K. M., & Church, G. M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0098811 · Cited by 39
Insights into the CRISPR/Cas system of Gardnerella vaginalis
Pleckaityte, M., Zilnyte, M., & Zvirbliene, A. (2012) · BMC Microbiology · doi:10.1186/1471-2180-12-301 · Cited by 33
Lohia, A., Sahel, D. K., Salman, M., Singh, V., Mariappan, I., Mittal, A., & Chitkara, D. (2022) · Asian Journal of Pharmaceutical Sciences · doi:10.1016/j.ajps.2022.02.001 · Cited by 33
PAM binding ensures orientational integration during Cas4-Cas1-Cas2-mediated CRISPR adaptation
Dhingra, Y., Suresh, S. K., Juneja, P., & Sashital, D. G. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.09.030 · Cited by 21
Metadata
- Authors
- Mojica, F. J. M., Díez-Villaseñor, C., García-Martínez, J., & Almendros, C.
- Affiliations
- Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, E-03080 Alicante, Spain
- Venue
- Microbiology
- Publisher
- Microbiology Society
- Published
- 2009-03-01
- Volume
- 155
- Issue
- 3
- Pages
- 733-740
- ISSN
- 1350-0872
- 1465-2080
- Cited by
- 1,426
- References
- 1
- Language
- en
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.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
