A5037294200- CRISPR and Genetic Engineering
- RNA and protein synthesis mechanisms
- Advanced biosensing and bioanalysis techniques
- Insect symbiosis and bacterial influences
- Bacteriophages and microbial interactions
- RNA modifications and cancer
- Biochemical and Molecular Research
- Bacterial Genetics and Biotechnology
- Micro and Nano Robotics
- Innovation and Socioeconomic Development
- Plant Virus Research Studies
- Click Chemistry and Applications
- RNA regulation and disease
- Bacterial biofilms and quorum sensing
- Microtubule and mitosis dynamics
- HIV/AIDS drug development and treatment
- DNA and Nucleic Acid Chemistry
- Protist diversity and phylogeny
- Viral Infections and Immunology Research
- Cell Adhesion Molecules Research
- Adenosine and Purinergic Signaling
- Evolution and Genetic Dynamics
- Microfluidic and Bio-sensing Technologies
- Catalytic Processes in Materials Science
- Evolutionary Game Theory and Cooperation
Vilnius University
2022-2024
Innovative Genomics Institute
2019-2022
University of California, Berkeley
2019-2022
Loewe Center for Synthetic Microbiology
2014-2021
Philipps University of Marburg
2015-2016
Compact defense system in bacteriophages The CRISPR-Cas system, naturally found many prokaryotes, is widely used for genome editing. CRISPR arrays the bacterial genome, derived from of invading viruses, are to generate a RNA that guides Cas enzyme destroy repeat viral invaders. Recently, an unexpectedly compact was identified huge bacteriophages. Pausch et al . show even though this lacks commonly accessory proteins, it functional. In addition array, only component called CasF, which uses...
Adaptive immunity of prokaryotes is mediated by CRISPR-Cas systems that employ a large variety Cas protein effectors to identify and destroy foreign genetic material. The different targeting mechanisms proteins rely on the proper protection host genome sequence while allowing for efficient detection target sequences, termed protospacers. A short DNA sequence, protospacer-adjacent motif (PAM), frequently used mark sites. have evolved multitude PAM-interacting domains, which enables them cope...
CRISPR-Cas systems are host-encoded pathways that protect microbes from viral infection using an adaptive RNA-guided mechanism. Using genome-resolved metagenomics, we find CRISPR also encoded in diverse bacteriophages, where they occur as divergent and hypercompact anti-viral systems. Bacteriophage-encoded belong to all six known types, though some lack crucial components, suggesting alternate functional roles or host complementation. We describe multiple new Cas9-like proteins 44 families...
Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) systems have been developed as important tools for plant genome engineering. Here, we demonstrate that the hypercompact CasΦ nuclease is able to generate stably inherited gene edits in Arabidopsis , guide RNAs can be expressed with either Pol-III U6 promoter or a Pol-II together ribozyme mediated RNA processing. Using fwa epiallele, show displays higher editing efficiency when target locus...
Abstract Exponentially growing yeast cells produce every minute >160,000 ribosomal proteins. Owing to their difficult physicochemical properties, the synthesis of assembly-competent proteins represents a major challenge. Recent evidence highlights that dedicated chaperone recognize N-terminal regions and promote soluble expression delivery assembly site. Here we explore intuitive possibility are captured by chaperones in co-translational manner. Affinity purification four (Rrb1, Syo1,...
Ribosomes are the highly complex macromolecular assemblies dedicated to synthesis of all cellular proteins from mRNA templates. The main principles underlying making ribosomes conserved across eukaryotic organisms and this process has been studied in most detail yeast Saccharomyces cerevisiae. Yeast composed four ribosomal RNAs (rRNAs) 79 (r-proteins). Most r-proteins need be transported cytoplasm nucleus where they get incorporated into evolving pre-ribosomal particles. Due high abundance...
Shewanella putrefaciens CN-32 contains a single Type I-Fv CRISPR-Cas system which confers adaptive immunity against bacteriophage infection. Three Cas proteins (Cas6f, Cas7fv, Cas5fv) and mature CRISPR RNAs were shown to be required for the assembly of an interference complex termed Cascade. The protein-CRISPR RNA interaction sites within this identified via mass spectrometry. Additional proteins, commonly described as large small subunits, that are present in all other investigated Cascade...
The stringent response enables metabolic adaptation of bacteria under stress conditions and is governed by RelA/SpoT Homolog (RSH)-type enzymes. Long RSH-type enzymes encompass an N-terminal domain (NTD) harboring the second messenger nucleotide (p)ppGpp hydrolase synthetase activity a stress-perceiving regulatory C-terminal (CTD). CTD-mediated binding Rel to stalled ribosomes boosts synthesis. However, how opposing activities NTD are controlled in absence was poorly understood. Here, we...
Abstract CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated (Cas9, Cas12 Cas13 families), have been deployed numerous research, clinical agricultural applications. However, immense genetic biochemical diversity of these proteins in public domain poses a barrier researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), Cas Protein...
The growing demand for 4′-modified nucleoside analogs in medicinal and biological chemistry is contrasted by the challenging synthetic access to these molecules lack of efficient diversification strategies. Herein, we report development a biocatalytic approach based on phosphorylases, which allows straightforward installation variety pyrimidine purine nucleobases 4′-alkylated sugar scaffold. Following identification suitable biocatalyst as well its characterization with kinetic experiments...
CRISPR-Cas mediated DNA-interference typically relies on sequence-specific binding and nucleolytic degradation of foreign genetic material. Type IV-A systems diverge from this general mechanism, using a nuclease-independent interference pathway to suppress gene expression for regulation plasmid competition. To understand how the type system associated effector complex achieves interference, we determine cryo-EM structures two evolutionarily distinct complexes (types IV-A1 IV-A3) bound...
Selection for a certain trait in microbes depends on the genetic background of strain and selection pressure environmental conditions acting cells. In contrast to sessile state biofilm, various bacterial cells employ flagellum-dependent motility under planktonic suggesting that two phenotypes are mutually exclusive. However, flagellum dependent facilitates prompt establishment floating biofilms air-medium interface, called pellicles. Previously, pellicles B. subtilis were shown be preferably...
Emerging data have highlighted a correlation between microbiome composition and cancer immunotherapy outcome. While commensal bacteria their metabolites are known to modulate the host environment, contradictory effects lack of mechanistic understanding impede translation microbiome-based therapies into clinic. In this study, we demonstrate that abundance metabolite pentanoate is predictive for survival chimeric antigen receptor (CAR) T cell patients in two independent cohorts. Its...
ABSTRACT Type IV-A CRISPR-Cas systems are primarily encoded on plasmids and form multi-subunit ribonucleoprotein complexes with unknown biological functions. In contrast to other types, they lack the archetypical CRISPR acquisition module encode a DinG helicase instead of nuclease component. IV-A3 carried by large conjugative that often harbor multiple antibiotic-resistance genes. Although their array contents suggest role in inter-plasmid conflicts, this function underlying mechanisms have...
CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated (Cas9, Cas12 Cas13 families), have been deployed numerous research, clinical agricultural applications. However, immense genetic biochemical diversity of these proteins in public domain poses a barrier researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), Cas Protein Effector...