4.8 Article

RNA-triggered protein cleavage and cell growth arrest by the type III-E CRISPR nuclease-protease

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biotechnology & Applied Microbiology

Programmable eukaryotic protein synthesis with RNA sensors by harnessing ADAR

Kaiyi Jiang et al.

Summary: We developed a programmable RNA sensing technology that utilizes ADAR to control the translation of a target protein. Through sensor engineering, we achieved a 277-fold improvement in sensor activation and designed RADARS with diverse cargo proteins, enabling detection at low levels of endogenous transcript expression.

NATURE BIOTECHNOLOGY (2023)

Article Biotechnology & Applied Microbiology

RNA-responsive elements for eukaryotic translational control

Evan M. Zhao et al.

Summary: The use of eukaryotic toehold switches (eToeholds) allows for efficient induction of gene translation in eukaryotic cells, capable of distinguishing the presence of RNA transcripts under various circumstances. Through optimization of RNA annealing, up to 16-fold induction of transgene expression was achieved.

NATURE BIOTECHNOLOGY (2022)

Article Multidisciplinary Sciences

Fungal gasdermin-like proteins are controlled by proteolytic cleavage

Corinne Clave et al.

Summary: Gasdermins are a family of proteins that control cell death reactions in both mammals and fungi. This study reveals the proteolytic regulation of Gasdermins in fungi, showing an evolutionary parallel between fungal and mammalian cell death pathways.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

Article Multidisciplinary Sciences

Bacterial gasdermins reveal an ancient mechanism of cell death

Alex G. Johnson et al.

Summary: Gasdermin proteins play important roles in immune regulation and induction of cell death in human cells by forming membrane pores. Similar proteins encoded by bacteria have been found to defend against phages and execute cell death.

SCIENCE (2022)

Article Biochemistry & Molecular Biology

Structure and engineering of the type III-E CRISPR-Cas7-11 effector complex

Kazuki Kato et al.

Summary: This study reports a new type III-E CRISPR-Cas effector, Cas7-11, with dual RNase activities for precursor CRISPR RNA (pre-crRNA) processing and crRNA-guided target RNA cleavage, providing a new platform for RNA targeting in bacteria and mammals. The cryoelectron microscopy structure of Cas7-11 in complex with a crRNA and its target RNA was determined at a resolution of 2.5 angstroms. Rational engineering of a compact Cas7-11 variant, Cas7-11S, enabled in vivo applications for transcript knockdown in human cells.
Article Biochemical Research Methods

ColabFold: making protein folding accessible to all

Milot Mirdita et al.

Summary: ColabFold combines fast homology search and optimized model utilization to offer accelerated prediction of protein structures and complexes, with a processing speed that is 40-60 times faster. It serves as a free and accessible platform for protein folding, capable of predicting close to 1,000 structures per day.

NATURE METHODS (2022)

Article Biology

DeepEMhancer: a deep learning solution for cryo-EM volume post-processing

Ruben Sanchez-Garcia et al.

Summary: Sanchez-Garcia et al. introduce DeepEMhancer, a deep learning-based method for automatic post-processing of raw cryo-electron microscopy density maps. It globally improves local quality of density maps and shows potential as a useful tool for structures without readily available PDB models.

COMMUNICATIONS BIOLOGY (2021)

Article Biochemistry & Molecular Biology

UCSF ChimeraX: Structure visualization for researchers, educators, and developers

Eric F. Pettersen et al.

Summary: UCSF ChimeraX is a powerful visualization program with enhanced performance and graphics, offering new tools and analysis features, support for various areas like virtual reality, and improved ease of use, along with an app store for researchers to contribute new tools.

PROTEIN SCIENCE (2021)

Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

Article Multidisciplinary Sciences

Structural basis of human separase regulation by securin and CDK1-cyclin B1

Jun Yu et al.

Summary: The structures of separase in complex with either securin or cyclin B-CDK1 reveal the diverse array of mechanisms by which they bind and inhibit separase, shedding light on the regulation of chromosome separation during the cell cycle.

NATURE (2021)

Article Multidisciplinary Sciences

Programmable RNA targeting with the single-protein CRISPR effector Cas7-11

Ahsen Ozcan et al.

Summary: The study revealed that Cas7-11 from class 1 CRISPR-Cas systems is a single-protein effector with RNA interference capability. It can process pre-CRISPR RNA into mature crRNA with high specificity, and has potential applications in RNA knockdown and editing in mammalian cells. The findings provide a basis for developing new programmable RNA-targeting tools that are free of collateral activity and cell toxicity.

NATURE (2021)

Article Multidisciplinary Sciences

The gRAMP CRISPR-Cas effector is an RNA endonuclease complexed with a caspase-like peptidase

Sam P. B. van Beljouw et al.

Summary: The study presents a novel type III-E effector, Sb-gRAMP, which uses CRISPR RNA to guide target RNA recognition and cleavage, and potentially gains viral immunity through target RNA-induced protease activity.

SCIENCE (2021)

Article Biotechnology & Applied Microbiology

Proteogenomic Insights into the Physiology of Marine,Sulfate-Reducing, Filamentous Desulfonema limicola and Desulfonema magnum

Vanessa Schnaars et al.

Summary: The genus Desulfonema, belonging to the family Desulfobacteraceae, comprises marine, sulfate-reducing bacteria that form filaments and move by gliding. The genomes of Dn. limicola and Dn. magnum show similarities in catabolic networks, but Dn. magnum demonstrates specific capacity for aromatic compound degradation.

MICROBIAL PHYSIOLOGY (2021)

Article Biochemistry & Molecular Biology

CDD/SPARCLE: the conserved domain database in 2020

Shennan Lu et al.

NUCLEIC ACIDS RESEARCH (2020)

Review Microbiology

Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants

Kira S. Makarova et al.

NATURE REVIEWS MICROBIOLOGY (2020)

Article Biochemical Research Methods

Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction

Ali Punjani et al.

NATURE METHODS (2020)

Article Multidisciplinary Sciences

Cas13-induced cellular dormancy prevents the rise of CRISPR-resistant bacteriophage

Alexander J. Meeske et al.

NATURE (2019)

Article Biochemical Research Methods

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

Dorothee Liebschner et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2019)

Article Biochemical Research Methods

Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs

Tristan Bepler et al.

NATURE METHODS (2019)

Article Biochemistry & Molecular Biology

MolProbity: More and better reference data for improved all-atom structure validation

Christopher J. Williams et al.

PROTEIN SCIENCE (2018)

Review Biochemistry & Molecular Biology

The Biology of CRISPR-Cas: Backward and Forward

Frank Hille et al.

Article Biochemical Research Methods

Real-space refinement in PHENIX for cryo-EM and crystallography

Pavel V. Afonine et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2018)

Article Multidisciplinary Sciences

Programmable protein circuits in living cells

Xiaojing J. Gao et al.

SCIENCE (2018)

Article Biochemical Research Methods

New tools for the analysis and validation of cryo-EM maps and atomic models

Pavel V. Afonine et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2018)

Article Multidisciplinary Sciences

Type III CRISPR-Cas systems produce cyclic oligoadenylate second messengers

Ole Niewoehner et al.

NATURE (2017)

Article Multidisciplinary Sciences

RNA targeting with CRISPR-Cas13

Omar O. Abudayyeh et al.

NATURE (2017)

Article Biochemical Research Methods

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

Ali Punjani et al.

NATURE METHODS (2017)

Article Biochemical Research Methods

Addressing preferred specimen orientation in single-particle cryo-EM through tilting

Yong Zi Tan et al.

NATURE METHODS (2017)

Article Multidisciplinary Sciences

A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems

Migle Kazlauskiene et al.

SCIENCE (2017)

Article Multidisciplinary Sciences

Nucleic acid detection with CRISPR-Cas13a/C2c2

Jonathan S. Gootenberg et al.

SCIENCE (2017)

Article Multidisciplinary Sciences

Architecture of the type IVa pilus machine

Yi-Wei Chang et al.

SCIENCE (2016)

Article Biochemical Research Methods

EMRinger: side chain directed model and map validation for 3D cryo-electron microscopy

Benjamin A. Barad et al.

NATURE METHODS (2015)

Review Biochemistry & Molecular Biology

Structural and Functional Discussion of the Tetra-Trico-Peptide Repeat, a Protein Interaction Module

Natalie Zeytuni et al.

STRUCTURE (2012)

Article Biochemical Research Methods

Features and development of Coot

P. Emsley et al.

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2010)

Article Biochemistry & Molecular Biology

Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy

PB Rosenthal et al.

JOURNAL OF MOLECULAR BIOLOGY (2003)

Article Biochemistry & Molecular Biology

Crystal structure of Escherichia coli σE with the cytoplasmic domain of its anti-σ RseA

EA Campbell et al.

MOLECULAR CELL (2003)