Research

The goal of the concerted projects in the Forschergruppe is to unravel the recently discovered prokaryotic immune system CRISPR/Cas in Bacteria and Archaea (for a recent review see (Al-Attar et al., 2011; Marraffini & Sontheimer, 2010)). The CRISPR/Cas system (CRISPR: clustered regularly interspaced short palindromic repeats, Cas: CRISPR-associated) is an adaptive and heritable resistance mechanism against foreign genetic elements. The CRISPR/Cas system consists of clusters of repetitive DNA in which short palindromic DNA repeats are separated by short spacers, the latter being sequences derived from the invader. In addition, a set of proteins, the Cas proteins, is involved. The system is in some parts functionally analogous to RNA interference in eukaryotes and it will be very interesting to unravel the prokaryotic mechanism and to compare it to the eukaryotic one.

Previous work showed that CRISPR/Cas ribonucleoprotein complexes target homologous nucleic acids: DNA in case of bacterial CRISPR interference system and RNA in case of the archaeal CRISPR-RAMP subtype. However, this major difference is based on observations in a single archaeal species (Pyrococcus furiosus) and a few selected bacteria only, and a clear link to the respective relevant protein components is missing so far. Furthermore, the identity of the target, and how targeted invading elements are inactivated or even destroyed, remains unknown. Similarly, it is not known how the spacer sequences are selected, acquired and incorporated.

The CRISPR/Cas system in prokaryotes has some conserved features but seems to be also highly variable. The CRISPR spacer and repeat sequences have different sequences and lengths. The Cas proteins belong to approximately 45 different protein families. For most of these proteins the functional assignment is missing. Moreover, bioinformatics analyses suggest the presence of certain protein components in cyanobacteria and some chloroflexi, which otherwise occur exclusively in Archaea. Despite the progress made in understanding CRISPR function, many questions regarding the structure and function of its key components remain to be answered.

Several reviews are available for further reading, some of which we are listing here below:

Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes.
Al-Attar S, Westra ER, van der Oost J, Brouns SJ.
Biol Chem. 2011; 392 :277-89.

CRISPR/Cas and CRISPR/Cmr Immune Systems of Archaea
Shah, S. A., Vestergaard, G. and Garrett, R. A. (2011), in Regulatory RNAs in Prokaryotes eds Hess, W.R. and Marchfelder, A., Springer Verlag, Wien, pp 163-181

CRISPR/Cas system and its role in phage-bacteria interactions.
Deveau H, Garneau JE, Moineau S.
Annu Rev Microbiol. 2010; 64:475-93.

CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea.
Marraffini LA, Sontheimer EJ.
Nat Rev Genet. 2010; 11:181-90.

CRISPR/Cas, the immune system of bacteria and archaea.
Horvath P, Barrangou R.
Science. 2010; 327:167-70.