A5046171773- CRISPR and Genetic Engineering
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Microbial Community Ecology and Physiology
- Insect symbiosis and bacterial influences
- Folate and B Vitamins Research
- Innovation and Socioeconomic Development
- Polyamine Metabolism and Applications
- Biochemical and Molecular Research
- Amino Acid Enzymes and Metabolism
- Bacteriophages and microbial interactions
- Chemical Analysis and Environmental Impact
- Retinal Development and Disorders
- Enzyme Structure and Function
- Epigenetics and DNA Methylation
- Peptidase Inhibition and Analysis
- Porphyrin Metabolism and Disorders
- Metalloenzymes and iron-sulfur proteins
- Evolution and Genetic Dynamics
- Genetics, Aging, and Longevity in Model Organisms
- Mosquito-borne diseases and control
- Advanced biosensing and bioanalysis techniques
- Biofuel production and bioconversion
- Anaerobic Digestion and Biogas Production
Mammoth Biosciences (United States)
2025
University of California, San Francisco
2016-2018
QB3
2018
Portland State University
2015-2018
Zogenix (United States)
2018
University of California System
2018
Quantitative BioSciences
2016-2017
Oregon Health & Science University
2014-2017
CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 gene editing technology is derived from a microbial adaptive immune system, where bacteriophages are often the intended target. Natural inhibitors of CRISPR-Cas9 enable phages to evade immunity and show promise in controlling Cas9-mediated human cells. However, mechanism inhibition not known, potential applications for Cas9 inhibitor proteins mammalian cells have been fully established. We that anti-CRISPR protein...
Bacterial CRISPR-Cas systems protect their host from bacteriophages and other mobile genetic elements. Mobile elements, in turn, encode various anti-CRISPR (Acr) proteins to inhibit the immune function of CRISPR-Cas. To date, Acr have been discovered for type I (subtypes I-D, I-E, I-F) II (II-A II-C) but not CRISPR systems. Here, we report discovery 12 acr genes, including inhibitors V-A I-C AcrVA1 inhibits a broad spectrum Cas12a (Cpf1) orthologs-including MbCas12a, Mb3Cas12a, AsCas12a,...
Abstract CRISPR gene editing is a transformative technology for addressing genetic diseases, but delivery constraints have largely limited its therapeutic applications to liver-targeted and ex vivo therapies. Here, we present the discovery engineering of NanoCas, an ultracompact nuclease capable extending CRISPR’s reach in beyond liver targets. We experimentally screened 176 systems found metagenomic data applied protein approaches enhance efficiency NanoCas. The optimized NanoCas exhibits...
The Methanocaldcoccus jannaschii tyrosyl-tRNA synthetase (TyrRS):tRNA(Tyr) cognate pair has been used to incorporate a large number of noncanonical amino acids (ncAAs) into recombinant proteins in Escherichia coli. However, the structural elements suppressor tRNA(Tyr) these experiments have not examined for optimal performance. Here, we evaluate steady-state kinetic parameters wild-type M. TyrRS and an evolved 3-nitrotyrosyl-tRNA (nitroTyrRS) toward several engineered suppressors, correlate...
The biosynthetic route for homocysteine, an intermediate in methionine biosynthesis, is unknown some methanogenic archaea because homologues of the canonical required genes cannot be identified. Here we demonstrate that Methanocaldococcus jannaschii can biosynthesize homocysteine from aspartate semialdehyde and hydrogen sulfide. Additionally, confirm involved this new pathway Methanosarcina acetivorans. A possible series reactions which a thioaldehyde formed then reduced to thiol are...
Summary The metabolic network for sulfide assimilation and trafficking in methanogens is largely unknown. To discover novel proteins required these processes, we used bioinformatics to identify genes co‐occurring with the protein biosynthesis enzyme SepCysS , which converts phosphoseryl‐ tRNA Cys cysteinyl‐ nearly all methanogens. Exhaustive analysis revealed three conserved families, each containing molecular signatures predicting function sulfur metabolism. One of classified within...
Conserved genes essential to sulfur assimilation and trafficking in aerobic organisms are missing many methanogens, most of which inhabit highly sulfidic, anaerobic environmental niches. This suggests that methanogens possess distinct pathways for the synthesis key metabolites intermediates, including cysteine, homocysteine, protein persulfide groups. Prior work identified a novel tRNA-dependent two-step pathway cysteine biosynthesis new metabolic transformation by is inserted into aspartate...
CRISPR-Cas9 gene editing technology is derived from a microbial adaptive immune system, where bacteriophages are often the intended target. Natural inhibitors of enable phages to evade immunity and show promise in controlling Cas9-mediated human cells. However, mechanism inhibition not known potential applications for Cas9 inhibitor proteins mammalian cells has fully been established. We here that anti-CRISPR protein AcrIIA4 binds only assembled Cas9-single guide RNA (sgRNA) complexes alone....
The methionine salvage pathway (MSP) is critical for regeneration of S-adenosyl-l-methionine (SAM), a widely used cofactor involved in many essential metabolic reactions. MSP has been completely elucidated aerobic organisms, and found to rely on molecular oxygen. Since anaerobic organisms do not use O2, an alternative pathway(s) must be operating. We sought evaluate whether the functions two annotated enzymes from Methanocaldococcus jannaschii, methylthioinosine phosphorylase (MTIP)...
The mechanisms of sulfur uptake and trafficking in methanogens inhabiting sulfidic environments are highly distinctive. In aerobes, transfers between proteins occur via persulfide relay, but direct evidence for persulfides has been lacking. Here, we use mass spectrometry to analyze tryptic peptides the Methanosarcina acetivorans SepCysS MA1821 purified anaerobically from methanogen cells. These enzymes insert sulfide into phosphoseryl(Sep)-tRNACys aspartate semialdehyde, respectively, form...
SUMMARY CRISPR–Cas immune systems utilize RNA-guided nucleases to protect bacteria from bacteriophage infection. Bacteriophages have in turn evolved inhibitory ‘anti-CRISPR’ (Acr) proteins, including six inhibitors (AcrIIA1-6) that can block DNA cutting and genome editing by type II-A CRISPR-Cas9 enzymes. We show here AcrIIA2 its homologue, AcrIIA2b, prevent Cas9 binding occluding protein residues required for binding. Cryo-EM-determined structures of or AcrIIA2b bound S. pyogenes reveal a...