Structural and dynamic insights into the role of conformational switching in the nuclease activity of the Xanthomonas albilineans Cas2 in CRISPR-mediated adaptive immunity.

Donghyun Ka,Euiyoung Bae,Migyeong Jeong,Jeong-Yong Suh,Suji Hong,Nayoung Suh,Ugeene Jeong

doi:10.1063/1.4984052

Abstract

Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins constitute a microbial, adaptive immune system countering invading nucleic acids. Cas2 is a universal Cas protein found in all types of CRISPR-Cas systems, and its role is implicated in new spacer acquisition into CRISPR loci. In subtype I-C CRISPR-Cas systems, Cas2 proteins are metal-dependent double-stranded DNA (dsDNA) nucleases, and a pH-dependent conformational transition has been proposed as a prerequisite for catalytic action. Here, we report the crystal structure of Xanthomonas albilineans Cas2 (XaCas2) and provide experimental evidence of a pH-dependent conformational change during functional activation. XaCas2 crystallized at an acidic pH represented a catalytically inactive conformational state in which two Asp8 residues were too far apart to coordinate a single catalytic metal ion. Consistently, XaCas2 exhibited dsDNA nuclease activity only under neutral and basic conditions. Despite the overall structural similarity of the two protomers, significant conformational heterogeneity was evident in the putative hinge regions, suggesting that XaCas2 engages in hinge-bending conformational switching. The presence of a Trp residue in the hinge region enabled the investigation of hinge dynamics by fluorescence spectroscopy. The pH dependence of the fluorescence intensity overlapped precisely with that of nuclease activity. Mutational analyses further suggested that conformational activation proceeded via a rigid-body hinge-bending motion as both D8E and hinge mutations significantly reduced nuclease activity. Together, our results reveal strong correlations between the conformational states, catalytic activity, and hinge dynamics of XaCas2, and provide structural and dynamic insights into the conformational activation of the nuclease function of Cas2.

Highlights

Repeat sequences interspaced with sized variable spacer sequences derived from foreign nucleic acids.6–8 Clustered regularly interspaced short palindromic repeats (CRISPRs)-associated genes lie adjacent to the clustered regularly interspaced short palindromic repeats (CRISPR) loci and encode a series of conserved proteins exhibiting nucleic acid-related functions.9–11 The CRISPR array and the Cas proteins constitute an adaptive immune system in bacteria and archaea, countering invasion by phages and plasmids.12–15 During the adaptation stage of CRISPR-mediated adaptive immunity, new spacers are acquired from foreign nucleic acids and integrated into the CRISPR loci of the host genome
Cas2 is a universal Cas protein found in all types of CRISPR-Cas systems, and its role is implicated in new spacer acquisition into CRISPR loci
Cas2 is a universal Cas protein found in all types of CRISPR-Cas systems,15–17,19 and plays a role in new spacer acquisition during the adaptation stage of CRISPR-Cas immunity

Summary

Introduction

Repeat sequences interspaced with sized variable spacer sequences derived from foreign nucleic acids. CRISPR-associated (cas) genes lie adjacent to the CRISPR loci and encode a series of conserved proteins exhibiting nucleic acid-related functions. The CRISPR array and the Cas proteins constitute an adaptive immune system in bacteria and archaea, countering invasion by phages and plasmids. During the adaptation stage of CRISPR-mediated adaptive immunity, new spacers are acquired from foreign nucleic acids and integrated into the CRISPR loci of the host genome. The Cas proteins of Desulfovibrio vulgaris (DvCas2) and Thermococcus onnurineus did not exhibit nuclease functions.19,26 It has been shown in various systems that Cas interacts with Cas to form a stable heterohexameric complex, in which a central Cas dimer connects two Cas dimers.. The recent structural and mechanistic studies, much of which are about the subtype I-E CRISPR-Cas system from Escherichia coli, revealed that the Cas1-Cas complex plays crucial roles in several processes of the CRISPR adaptation, including the foreign DNA capture, the recognition of the CRISPR locus, and the integration of new spacers into the CRISPR array.. The Cas1-Cas adaptation complexes are capable of independently recognizing the integration sites within the CRISPR loci based on their intrinsic affinities, whereas the integration host factor, a host protein assisting the recognition of the CRISPR array, was discovered in E. coli.. It has been shown in various systems that Cas interacts with Cas to form a stable heterohexameric complex, in which a central Cas dimer connects two Cas dimers. The recent structural and mechanistic studies, much of which are about the subtype I-E CRISPR-Cas system from Escherichia coli, revealed that the Cas1-Cas complex plays crucial roles in several processes of the CRISPR adaptation, including the foreign DNA capture, the recognition of the CRISPR locus, and the integration of new spacers into the CRISPR array. The Cas proteins in the complex show affinity for DNA segments complementary to the specific target recognition motif, called a protospacer-adjacent motif. Upon the DNA binding, the Cas1-Cas complex undergoes a significant conformational change. In several systems, the Cas1-Cas adaptation complexes are capable of independently recognizing the integration sites within the CRISPR loci based on their intrinsic affinities, whereas the integration host factor, a host protein assisting the recognition of the CRISPR array, was discovered in E. coli. The Cas1-Cas complex functions as a “molecular ruler” to control the length of spacers, and generates free 30-OH ends of the bound DNA substrate required for the nucleophilic attacks to the CRISPR array for the spacer insertion.

Methods

Results

Conclusion