A5080723359- CRISPR and Genetic Engineering
- RNA and protein synthesis mechanisms
- Advanced biosensing and bioanalysis techniques
- Bacterial Genetics and Biotechnology
- Bacteriophages and microbial interactions
- RNA regulation and disease
- Cytomegalovirus and herpesvirus research
- Protein Structure and Dynamics
- DNA Repair Mechanisms
- Microbial Community Ecology and Physiology
- Machine Learning in Bioinformatics
- Viral Infections and Immunology Research
- Plant Virus Research Studies
- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Molecular Junctions and Nanostructures
- Evolution and Genetic Dynamics
- Mosquito-borne diseases and control
- Enzyme Structure and Function
- Genetics and Neurodevelopmental Disorders
- Vibrio bacteria research studies
- Insect symbiosis and bacterial influences
- Virus-based gene therapy research
- Protist diversity and phylogeny
- Epigenetics and DNA Methylation
Vilnius University
2014-2024
Czech Academy of Sciences, Institute of Biotechnology
2013-2024
Aarhus University
2023
Great Ormond Street Hospital
2023
University College London
2023
Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research
2023
Bar-Ilan University
2023
St. Jude Children's Research Hospital
2023
Novo Nordisk (Denmark)
2021
University of Copenhagen
2021
Clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide adaptive immunity against viruses and plasmids in bacteria archaea. The silencing of invading nucleic acids is executed by ribonucleoprotein complexes preloaded with small, interfering CRISPR RNAs (crRNAs) that act as guides for targeting degradation foreign acid. Here, we demonstrate the Cas9–crRNA complex Streptococcus thermophilus CRISPR3/Cas system introduces vitro a double-strand...
The CRISPR/Cas adaptive immune system provides resistance against phages and plasmids in Archaea Bacteria.CRISPR loci integrate short DNA sequences from invading genetic elements that provide small RNA-mediated interference subsequent exposure to matching nucleic acids.In Streptococcus thermophilus, it was previously shown the CRISPR1/Cas can immunity by integrating novel spacers following these foreign subsequently direct specific cleavage of invasive homologous sequences.Here, we show S....
Clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems protect bacteria and archaea from infection by viruses plasmids. Central to this defense is a ribonucleoprotein complex that produces RNA-guided cleavage of foreign nucleic acids. In DNA-targeting CRISPR-Cas systems, the RNA component encodes target recognition forming site-specific hybrid (R-loop) with its complement (protospacer) on an invading DNA while displacing noncomplementary strand....
RNA-guided nucleases (RGNs) based on the type II CRISPR-Cas9 system of Streptococcus pyogenes (Sp) have been widely used for genome editing in experimental models. However, nontrivial level off-target activity reported several human cells may hamper clinical translation. RGN specificity depends both guide RNA (gRNA) and protospacer adjacent motif (PAM) recognized by Cas9 protein. We hypothesized that more stringent PAM requirements reduce occurrence mutagenesis. To test this postulation, we...
The Cas9-crRNA complex of the Streptococcus thermophilus DGCC7710 CRISPR3-Cas system functions as an RNA-guided endonuclease with crRNA-directed target sequence recognition and protein-mediated DNA cleavage. We show here that additional RNA molecule, tracrRNA (trans-activating CRISPR RNA), co-purifies Cas9 protein isolated from heterologous E. coli strain carrying S. system. provide experimental evidence is required for Cas9-mediated interference both in vitro vivo. specifically promotes...
To expand the repertoire of Cas9s available for genome targeting, we present a new in vitro method simultaneous examination guide RNA and protospacer adjacent motif (PAM) requirements. The relies on cleavage plasmid libraries containing randomized PAM as function Cas9-guide complex concentration. Using this method, accurately reproduce canonical preferences Streptococcus pyogenes, thermophilus CRISPR3 (Sth3), CRISPR1 (Sth1). Additionally, sgRNA solutions novel Cas9 protein from Brevibacillus...
Abstract Bacterial Cas9 nucleases from type II CRISPR-Cas antiviral defence systems have been repurposed as genome editing tools. Although these proteins are found in many microbes, only a handful of variants used for applications. Here, we use bioinformatic and biochemical analyses to explore this largely uncharacterized diversity. We apply cell-free screens assess the protospacer adjacent motif (PAM) guide RNA (gRNA) requirements 79 proteins, thus identifying at least 7 distinct gRNA...
Abstract Motivation Reliable prediction of protein thermostability from its sequence is valuable for both academic and industrial research. This problem can be tackled using machine learning by taking advantage the recent blossoming deep methods analysis. These facilitate training on more data and, possibly, enable development versatile predictors multiple ranges temperatures. Results We applied principle transfer to predict embeddings generated language models (pLMs) an input sequence. used...
CRISPR and associated Cas proteins function as an adaptive immune system in prokaryotes to combat bacteriophage infection. During the immunization step, new spacers are acquired by machinery, but molecular mechanism of spacer capture remains enigmatic. We show that Cas9, Cas1, Cas2, Csn2 a Streptococcus thermophilus type II-A CRISPR-Cas form complex provide cryoelectron microscopy (cryo-EM) structures three different assemblies. The predominant form, with stoichiometry Cas18-Cas24-Csn28,...
Abstract A key aim in exploiting CRISPR–Cas is gRNA engineering to introduce additional functionalities, ranging from individual nucleotide changes that increase efficiency of on-target binding the inclusion larger functional RNA aptamers or ribonucleoproteins (RNPs). Cas9–gRNA interactions are crucial for complex assembly, but several distinct regions amenable modification. We used vitro ensemble and single-molecule assays assess impact structural alterations on RNP formation, R-loop...
Article21 October 2022Open Access Source DataTransparent process A new family of CRISPR-type V nucleases with C-rich PAM recognition Tomas Urbaitis CasZyme, Vilnius, Lithuania Institute Biotechnology, Vilnius University, Contribution: Conceptualization, Data curation, Formal analysis, Validation, Investigation, Visualization, Methodology, Writing - original draft, review & editing Search for more papers by this author Giedrius Gasiunas Corresponding Author [email protected]...
The genomic characterization of novel cyanophage vB_AphaS-CL131 and the analysis its features in context other viruses, metagenomic data, host CRISPR-Cas systems contribute toward a better understanding aquatic viral diversity distribution general brackish-water cyanophages infecting filamentous diazotrophic cyanobacteria Baltic Sea particular. results this study revealed previously undescribed genomes (e.g., self-excising intein-containing putative dCTP deaminase cyanophage-encoded...