Biology subjects

Schelling, M. A.

Publications and source records attributed to Schelling, M. A..

4 recordsLinked to original sources

bioRxiv2024

CRISPR-Cas9 target-strand nicking provides phage resistance by inhibiting replication

Cas endonucleases, like Cas9 and Cas12a, are RNA-guided immune effectors that provide bacterial defense against bacteriophages. Cas endonucleases rely on divalent metal ions for their enzymatic activities and to facilitate conformational changes that are required for specific recognition and cleavage of target DNA. While Cas endonucleases typically produce double-strand breaks (DSBs) in DNA targets, reduced, physiologically relevant Mg2+ concentrations and target mismatches can result in incomplete second-strand cleavage, resulting in the production of a nicked DNA. It remains poorly understood whether nicking by Cas endonucleases is sufficient to provide protection against phage. To address this, we tested phage protection by Cas9 nickases, in which only one of two nuclease domains is catalytically active. By testing a large panel of guide RNAs, we find that target strand nicking can be sufficient to provide immunity, while non-target nicking does not provide any additional protection beyond Cas9 binding. Target-strand nicking inhibits phage replication and can reduce the susceptibility of Cas9 to viral escape when targeting non-essential regions of the genome. Cleavage of the non- target strand by the RuvC domain is strongly impaired at low Mg2+ concentrations. As a result, fluctuations in the concentration of other biomolecules that can compete for binding of free Mg2+ strongly influences the ability of Cas9 to form a DSB at targeted sites. Overall, our results suggest that Cas9 may only nick DNA during CRISPR-mediated immunity, especially under conditions of low Mg2+ availability in cells.

biochemistry↗

bioRxiv2023

CRISPR-Cas12a exhibits metal-dependent specificity switching

Cas12a is the immune effector of type V-A CRISPR-Cas systems and has been co-opted for genome editing and other biotechnology tools. The specificity of Cas12a has been the subject of extensive investigation both in vitro and in genome editing experiments. However, in vitro studies have often been performed at high magnesium ion concentrations that are inconsistent with the free Mg2+ concentrations that would be present in cells. By profiling the specificity of Cas12a orthologs at a range of Mg2+ concentrations, we find that Cas12a switches its specificity depending on metal ion concentration. Lowering Mg2+ concentration decreases cleavage defects caused by seed mismatches, while increasing the defects caused by PAM-distal mismatches. We show that Cas12a can bind seed mutant targets more rapidly at low Mg2+ concentrations, resulting in faster cleavage. In contrast, PAM-distal mismatches cause substantial defects in cleavage following formation of the Cas12a-target complex at low Mg2+ concentrations. We observe differences in Cas12a specificity switching between three orthologs that results in variations in the routes of phage escape from Cas12a-mediated immunity. Overall, our results reveal the importance of physiological metal ion conditions on the specificity of Cas effectors that are used in different cellular environments.

biochemistry↗

bioRxiv2022

CRISPR-Cas effector specificity and target mismatches determine phage escape outcomes

CRISPR-mediated interference relies on complementarity between a guiding CRISPR RNA (crRNA) and target nucleic acids to provide defense against bacteriophage. Phages escape CRISPR-based immunity mainly through mutations in the PAM and seed regions. However, previous specificity studies of Cas effectors, including the class 2 endonuclease Cas12a, have revealed a high degree of tolerance of single mismatches. The effect of this mismatch tolerance has not been extensively studied in the context of phage defense. Here, we tested defense against lambda phage provided by Cas12a-crRNAs containing pre-existing mismatches against the genomic targets in phage DNA. We observe a correlation between Cas12a mismatch tolerance in vitro and phage defense on solid media. However, in liquid media, we find that most pre-existing crRNA mismatches lead to phage escape and lysis, regardless of whether the mismatches ablate Cas12a cleavage in vitro. We used high-throughput sequencing to examine the target regions of phage genomes following CRISPR challenge. Mismatches at all locations in the target accelerated emergence of mutant phage, including mismatches that greatly slowed cleavage in vitro. Mutations arose near the existing mismatch, in some cases resulting in multiple PAM-distal mismatches allowing for phage escape. Similar experiments with Cas9 showed the location of emergent target mutations was unaffected by pre-existing crRNA-target mismatches. Expression of multiple mismatched crRNAs prevented new mutations from arising in multiple targeted locations, allowing Cas12a mismatch tolerance to provide stronger and longer term protection. These results demonstrate that Cas effector mismatch tolerance and existing target mismatches strongly influence phage evolution.

microbiology↗

bioRxiv2020

Evaluation of the functional role of the maize Glossy2 and Glossy2-like genes in cuticular lipid deposition

Plant epidermal cells express unique molecular machinery that juxtapose the assembly of intracellular lipid components and the unique extracellular cuticular lipids that are unidirectionally secreted to plant surfaces. In maize (Zea mays L.), mutations at the glossy2 (gl2) locus affect the deposition of extracellular cuticular lipids. Sequence-based genome scanning identified a novel gl2 homolog in the maize genome, Gl2-like. Sequence homology identifies that both the Gl2-like and Gl2 genes are members of the BAHD superfamily of acyltransferases, with close sequence homology to the Arabidopsis CER2 gene. Transgenic experiments demonstrate that Gl2-like and Gl2 functionally complement the Arabidopsis cer2 mutation, with differential impacts on the cuticular lipids and the lipidome of the plant, particularly affecting the longer alkyl chain acyl lipids, particularly at the 32-carbon chain length. Site-directed mutagenesis of the putative BAHD catalytic HXXXDX-motif indicates that Gl2-like requires this catalytic capability to fully complement the cer2 function, but Gl2 can accomplish this without the need for this catalytic motif. These findings demonstrate that both Gl2 and Gl2-like overlap in their cuticular lipid function, however the two genes have evolutionary diverged to acquire non-overlapping functions. One-sentence summaryTransgenesis dissection of the functional roles of the maize Glossy2 and Glossy2-Like genes in cuticular lipid deposition.

biochemistry↗