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REVIEW: Type III CRISPR-Cas Systems: Deciphering the Most Complex Prokaryotic Immune System

Matvey V. Kolesnik1,a*, Iana Fedorova2,3,b, Karyna A. Karneyeva1,c, Daria N. Artamonova1,d, and Konstantin V. Severinov1,3,4,e*

1Center of Life Science, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia

2Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia

3Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia

4Waksman Institute of Microbiology, Piscataway, NJ 08854, USA

* To whom correspondence should be addressed.

Received June 1, 2021; Revised August 24, 2021; Accepted August 30, 2021
The emergence and persistence of selfish genetic elements is an intrinsic feature of all living systems. Cellular organisms have evolved a plethora of elaborate defense systems that limit the spread of such genetic parasites. CRISPR-Cas are RNA-guided defense systems used by prokaryotes to recognize and destroy foreign nucleic acids. These systems acquire and store fragments of foreign nucleic acids and utilize the stored sequences as guides to recognize and destroy genetic invaders. CRISPR-Cas systems have been extensively studied, as some of them are used in various genome editing technologies. Although Type III CRISPR-Cas systems are among the most common CRISPR-Cas systems, they are also some of the least investigated ones, mostly due to the complexity of their action compared to other CRISPR-Cas system types. Type III effector complexes specifically recognize and cleave RNA molecules. The recognition of the target RNA activates the effector large subunit – the so-called CRISPR polymerase – which cleaves DNA and produces small cyclic oligonucleotides that act as signaling molecules to activate auxiliary effectors, notably non-specific RNases. In this review, we provide a historical overview of the sometimes meandering pathway of the Type III CRISPR research. We also review the current data on the structures and activities of Type III CRISPR-Cas systems components, their biological roles, and evolutionary history. Finally, using structural modeling with AlphaFold2, we show that the archaeal HRAMP signature protein, which heretofore has had no assigned function, is a degenerate relative of Type III CRISPR-Cas signature protein Cas10, suggesting that HRAMP systems have descended from Type III CRISPR-Cas systems or their ancestors.
KEY WORDS: CRISPR-Cas Type III, prokaryotic immunity, RNA-guided defense, cyclic oligonucleotides, CRISPR evolution, HRAMP

DOI: 10.1134/S0006297921100114