The invisible dance of CRISPR-Cas9. Simulations unveil the molecular side of the gene-editing revolution

Evidence for scale-dependent root-antation feedback and its role in halting the spread of a pantropical shrub into an endemic sedge

Vegetation pattern formation is a widespread phenomenon in resource-limited environments, but the driving mechanisms are largely unconfirmed empirically. Combining results of field studies and mathematical modeling, empirical evidence for a generic pattern-formation mechanism is demonstrated with the clonal shrub Guilandina bonduc L. (hereafter Guilandina) on the Brazilian island of Trindade. The mechanism is associated with water conduction by laterally spread roots and root augmentation as the shoot grows-a crucial element in the positive feedback loop that drives spatial patterning. Assuming precipitation-dependent root-shoot relations, the model accounts for the major vegetation landscapes on Trindade Island, substantiating lateral root augmentation as the driving mechanism of Guilandina patterning. Guilandina expands into surrounding communities dominated by the Trindade endemic, Cyperus atlanticus Hemsl. (hereafter Cyperus). It appears to do so by decreasing the water potential in soils below Cyperus through its dense lateral roots, leaving behind a patchy Guilandina-only landscape. We use this system to highlight a novel form of invasion, likely to apply to many other systems where the invasive species is pattern-forming. Depending on the level of water stress, the invasion can take two distinct forms: (i) a complete invasion at low stress that culminates in a patchy Guilandina-only landscape through a spot-replication process, and (ii) an incomplete invasion at high stress that begins but does not spread, forming isolated Guilandina spots of fixed size, surrounded by bare-soil halos, in an otherwise uniform Cyperus grassland. Thus, drier climates may act selectively on pattern-forming invasive species, imposing incomplete invasion and reducing the negative effects on native species.

Decrypting the mechanistic basis of CRISPR/Cas9 protein

CRISPR/Cas system, a newly but extensively investigated genome-editing method, harbors practical solutions for various genetic problems. It relies on short guide RNAs (gRNAs) to recruit the Cas9 protein, a DNA cleaving enzyme, to its genomic target DNAs. The Cas9 enzyme exhibits some unique properties, like the ability to differentiate self vs. non-self - DNA strands using the base-pairing potential of crRNA, i.e., only CRISPR DNA is entirely complementary to the CRISPR repeat sequences at the crRNA whereas the presence of mismatches in the upstream region of the spacer permit CRISPR interference which is inhibited in case of CRISPR-DNA, allosteric regulation in its domains, and domain reorientation on sgRNA binding. Several groups have contributed their efforts in understanding the functioning of the CRISPR/Cas system, but even then, there is a lot more to explore in this area. The structural and sequence-based understanding of the whole CRISPR-associated bacterial ortholog family landscape is still ambiguous. A better understanding of the underlying energetics of the CRISPR/Cas9 system should reveal critical parameters to design better CRISPR/Cas9s.

Engineering and Design of Programmable Genome Editors

Programmable genome editors are enzymes that can be targeted to a specific location in the genome for making site-specific alterations or deletions. The engineering, design, and development of sequence-specific editors has resulted in a dramatic increase in the precision of editing for nucleotide sequences. These editors can target specific locations in a genome, in vivo. The genome editors are being deployed for the development of genetically modified organisms for agriculture and industry, and for gene therapy of inherited human genetic disorders, cancer, and immunotherapy. Experimental and computational studies of structure, binding, activity, dynamics, and folding, reviewed here, have provided valuable insights that have the potential for increasing the functional efficiency of these gene/genome editors. Biochemical and biophysical studies of the specificities of natural and engineered genome editors reveal that increased binding affinity can be detrimental because of the increase of off-target effects and that the engineering and design of genome editors with higher specificity may require modulation and control of the conformational dynamics.

Atomic-scale insights into allosteric inhibition and evolutional rescue mechanism of Streptococcus thermophilus Cas9 by the anti-CRISPR protein AcrIIA6

CRISPR-Cas systems are prokaryotic adaptive immunity against invading phages and plasmids. Phages have evolved diverse protein inhibitors of CRISPR-Cas systems, called anti-CRISPR (Acr) proteins, to neutralize this CRISPR machinery. In response, bacteria have co-evolved Cas variants to escape phage's anti-CRISPR strategies, called anti-anti-CRISPR systems. Here we explore the anti-CRISPR allosteric inhibition and anti-anti-CRISPR rescue mechanisms between Streptococcus thermophilus Cas9 (St1Cas9) and the anti-CRISPR protein AcrIIA6 at the atomic level, by generating mutants of key residues in St1Cas9. Extensive unbiased molecular dynamics simulations show that the functional motions of St1Cas9 in the presence of AcrIIA6 differ substantially from those of St1Cas9 alone. AcrIIA6 binding triggers a shift of St1Cas9 conformational ensemble towards a less catalytically competent state; this state significantly compromises protospacer adjacent motif (PAM) recognition and nuclease activity by altering interdependently conformational dynamics and allosteric signals among nuclease domains, PAM-interacting (PI) regions, and AcrIIA6 binding motifs. Via in vitro DNA cleavage assays, we further elucidate the rescue mechanism of efficiently escaping AcrIIA6 inhibition harboring St1Cas9 triple mutations (G993K/K1008M/K1010E) in the PI domain and identify the evolutionary landscape of such mutational escape within species. Our results provide mechanistic insights into Acr proteins as natural brakes for the CRISPR-Cas systems and a promising potential for the design of allosteric Acr peptidomimetics.

Establishing the allosteric mechanism in CRISPR-Cas9

Allostery is a fundamental property of proteins, which regulates biochemical information transfer between spatially distant sites. Here, we report on the critical role of molecular dynamics (MD) simulations in discovering the mechanism of allosteric communication within CRISPR-Cas9, a leading genome editing machinery with enormous promises for medicine and biotechnology. MD revealed how allostery intervenes during at least three steps of the CRISPR-Cas9 function: affecting DNA recognition, mediating the cleavage and interfering with the off-target activity. An allosteric communication that activates concerted DNA cleavages was found to led through the L1/L2 loops, which connect the HNH and RuvC catalytic domains. The identification of these "allosteric transducers" inspired the development of novel variants of the Cas9 protein with improved specificity, opening a new avenue for controlling the CRISPR-Cas9 activity. Discussed studies also highlight the critical role of the recognition lobe in the conformational activation of the catalytic HNH domain. Specifically, the REC3 region was found to modulate the dynamics of HNH by sensing the formation of the RNA:DNA hybrid. The role of REC3 was revealed to be particularly relevant in the presence of DNA mismatches. Indeed, interference of REC3 with the RNA:DNA hybrid containing mismatched pairs at specific positions resulted in locking HNH in an inactive "conformational checkpoint" conformation, thereby hampering off-target cleavages. Overall, MD simulations established the fundamental mechanisms underlying the allosterism of CRISPR-Cas9, aiding engineering strategies to develop new CRISPR-Cas9 variants for improved genome editing.

CRISPR-Cas9 Genome Interrogation: A Facilitated Subdiffusive Target Search Strategy

The functional application of RNA-guided CRISPR-associated Cas9 protein, a bacterial immune system-based protein complex, via which in vivo, highly specific, and well-regulated, gene-editing processes are being monitored at an unprecedented level, has led to remarkable progress in genetic engineering and technology. The complicated in vivo process of genome interrogation followed by gene editing by the Cas9 complex was recently reported by Knight et al. (Science, 2015, 350, 823-826) using an elegant single-particle tracking method, aided by the two-photon fluorescence correlation spectroscopic technique. In contrast to the usually observed fast target-searching and protein-binding events in biophysical systems, an interesting slow genome-interrogation process by the RNA-guided CRISPR-Cas9 system through a crowded chromatin environment of a mammalian cell has been revealed in Knight et al.'s study. Motivated by this experiment, in this paper, we provide a generalized theoretical framework to capture this particular target-searching mechanism of the CRISPR-Cas9 protein complex. We show that an analysis on the basis of 3D subdiffusion under a cylindrical volume, created by several nonspecific off-target interactions from the DNA strands, can capture the essential details of the process. Moreover, on the basis of this model, we quantify the dynamics of this process and estimate the survival probability, first passage time, and the intensity correlation function of the tagged proteins of the experiment. The results from our theoretical predictions are found to be consistent with the experimental observations, and hence, seem to provide a plausible microscopic picture of the process.