Download BIMM 122 Dr. Milton Saier The CRISPR

BIMM 122
The CRISPR-Cas
System of Bacterial Immunity
Dr. Milton Saier
“Man's mind, once stretched by a new idea, never regains its original dimensions.”
– Oliver Wendell Holmes
1. Clustered regulatory interspaced short palindromic repeats (CRISPRs) target
invading phage and plasmids.
2. They are found in many bacteria and most archaea.
3. They deal with environmental stressors including invading viruses.
4. It is described as the “bacterial immune system.”
5. The CRISPR repeats incorporate “spacers” homologous to fragments of the alien
viral or plasmid genomes.
6. Possibly, the host incorporates short sequences from invading genetic elements
(DNA) (virus or plasmid) into the CRISPR region.
7. The mechanism might comprise a constantly changing, co-evolutionary “arms
race” between the host and invading agents.
8. The CRISPR and cas genes appear to evolve rapidly, accounting for their
tremendous sequence divergence.
9. The process is sequence-specific, involving a variable cassette of CRISPRassociated (cas) genes.
10. There are at least four cas genes that are unique to and may be conserved in
microorganisms having the CRISPR system.
11. The 4 Cas proteins of Yersinia (Csy 1-4) assemble into a 350 kDa
ribonucleoprotein complex; some other bacteria/archaea have more cas genes.
12. Cas proteins from various organisms may be homologous, having common
origins and structures.
13. Sequence similarity between these systems is meager, but they have conserved
structural features.
14. There appear to be three phylogenetically distinct groups of these systems, all
possibly related.
15. This complex facilitates target nucleic acid recognition by the CRISPR-Cas
system.
16. This occurs because of sequence-specific hybridization between the CRISPRRNA
17. Target recognition is enthalpically driven.
18. Target recognition is localized to a “seed sequence” at the 5’ end of the CRISPR
RNA spacer.
19. The Cas complex is a crescent shaped particle in many bacteria including E. coli.
20. When these sequences are transcribed and processed with small (s)RNAs, they
guide the Cas system to recognize, bind to and cleave the invading genetic
material.
21. This “adaptive immunity system” (at the nucleic acid rather than the protein
levels) uses a library of small non-coding RNAs as a potential weapon against
fast-evolving viruses and plasmids.
22. The system reveals the increasingly dynamic nature of prokaryotic genomes.
23. There are CRISPR polymerases, and “Repeat-associated Mysterious Proteins”
(RAMPs), containing RNA recognition motif (RRM) domains.
24. CRISPR-Cas promotors are regulated, among other regulators, by H-NS, which is
involved in induction, and by a chaperone protein, HtpG.
25. It has been suggested that these systems utilizes a (poorly defined) Lamarckian
mechanism.
“Evolution, like the tinker, does not produce innovations from scratch. It works on what
already exists, transforming a system to give a new function, or combining several
systems to produce a more complex one.”
- F. Jacob from “The Possible and the Actual”
References
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archaea: versatile small RNAs for adaptive defense and regulation. Annu Rev Genet
45, 273-297.
Makarova, K.S., Aravind, L., Wolf, Y.I., and Koonin, E.V. (2011). Unification of Cas
protein families and a simple scenario for the origin and evolution of CRISPR-Cas
systems. Biol Direct 6, 38.
Makarova, K.S., Haft, D.H., Barrangou, R., Brouns, S.J., Charpentier, E., Horvath, P.,
Moineau, S., Mojica, F.J., Wolf, Y.I., Yakunin, A.F., et al. (2011). Evolution and
classification of the CRISPR-Cas systems. Nat Rev Microbiol 9, 467-477.
Makarova, K.S., Wolf, Y.I., Snir, S., and Koonin, E.V. (2011). Defense islands in
bacterial and archaeal genomes and prediction of novel defense systems. J Bacteriol
193, 6039-6056.
Pul, U., Wurm, R., Arslan, Z., Geissen, R., Hofmann, N., and Wagner, R. (2010).
Identification and characterization of E. coli CRISPR-cas promoters and their
silencing by H-NS. Mol Microbiol 75, 1495-1512.
Takeuchi, N., Wolf, Y.I., Makarova, K.S., and Koonin, E.V. (2011). Nature and Intensity
of Selection Pressure on CRISPR-Associated Genes. J Bacteriol.
Wiedenheft, B., van Duijn, E., Bultema, J.B., Waghmare, S.P., Zhou, K., Barendregt, A.,
Westphal, W., Heck, A.J., Boekema, E.J., Dickman, M.J., et al. (2011). RNAguided complex from a bacterial immune system enhances target recognition
through seed sequence interactions. Proc Natl Acad Sci U S A 108, 10092-10097.
Yosef, I., Goren, M.G., Kiro, R., Edgar, R., and Qimron, U. (2011). High-temperature
protein G is essential for activity of the Escherichia coli clustered regularly
interspaced short palindromic repeats (CRISPR)/Cas system. Proc Natl Acad Sci
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