4.7 Article

In vitro characterization of a pAgo nuclease TtdAgo from Thermococcus thioreducens and evaluation of its effect in vivo

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

An Argonaute from Thermus parvatiensis exhibits endonuclease activity mediated by 5′ chemically modified DNA guides

Yingying Sun et al.

Summary: Ago nucleases from Thermus parvatiensis have been found to cleave DNA and RNA targets at high temperatures using 5' hydroxyl or phosphate DNA guides. They can also utilize various 5'-modified DNA guides for catalysis and perform programmable cleavage of double-stranded DNA at temperatures over 80 degrees C.

ACTA BIOCHIMICA ET BIOPHYSICA SINICA (2022)

Article Microbiology

A short prokaryotic Argonaute activates membrane effector to confer antiviral defense

Zhifeng Zeng et al.

Summary: This study reveals a short pAgo protein in the archaeon Sulfolobus islandicus, along with its genetically associated proteins Aga1 and Aga2, provide robust anti-viral protection through abortive infection. Aga2 is a toxic transmembrane effector that binds anionic phospholipids, resulting in membrane depolarization and cell killing. Ago and Aga1 form a stable complex with nucleic acid-directed recognition ability and directly interact with Aga2, suggesting an immune sensing mechanism.

CELL HOST & MICROBE (2022)

Article Biochemistry & Molecular Biology

A programmable pAgo nuclease with RNA target preference from the psychrotolerant bacterium Mucilaginibacter paludis

Wenqiang Li et al.

Summary: This study characterized a novel prokaryotic Ago protein, MbpAgo, from the psychrotolerant bacterium Mucilaginibacter paludis, which prefers cleaving RNA targets over DNA targets. MbpAgo is active at a wide range of temperatures and shows no obvious preference for the 5'-nucleotide of a guide.

NUCLEIC ACIDS RESEARCH (2022)

Article Biotechnology & Applied Microbiology

Characterization and application of a thermophilic Argonaute from archaeon Thermococcus thioreducens

Mengjun Fang et al.

Summary: This study reported the in vitro characterization of an Argonaute protein from Thermococcus thioreducens, demonstrating its application in hepatitis B virus DNA detection. The protein functions as a programmable DNA endonuclease with high efficiency and accuracy at certain temperatures, showing potential in DNA manipulation tools.

BIOTECHNOLOGY AND BIOENGINEERING (2022)

Article Biotechnology & Applied Microbiology

Molecular mechanism of enhanced ethanol tolerance associated with hfq overexpression in Zymomonas mobilis

Ying Tang et al.

Summary: This study investigated the role of Hfq in Z. mobilis and found that overexpression of hfq can enhance the ethanol tolerance of this microorganism. The study also demonstrated that Hfq may interact with heat shock proteins DnaK and DnaJ to mitigate the ethanol inhibition.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2022)

Article Biotechnology & Applied Microbiology

Endogenous CRISPR-assisted microhomology-mediated end joining enables rapid genome editing in Zymomonas mobilis

Xin Sui et al.

Summary: A novel gene deletion tool based on the endogenous subtype I-F CRISPR-Cas system and the MMEJ pathway was developed for Zymomonas mobilis, enabling the efficient deletion of single genes and large fragments. Modifications to the guide RNA expression cassette and target site selection further improved editing efficiency.

BIOTECHNOLOGY FOR BIOFUELS (2021)

Article Biochemistry & Molecular Biology

A programmable omnipotent Argonaute nuclease from mesophilic bacteria Kurthia massiliensis

Yang Liu et al.

Summary: Argonaute (Ago) proteins are conserved nucleic acid-guided proteins found in all domains of life. Eukaryotic Argonaute proteins play key roles in RNA interference pathways. Kurthia massiliensis (KmAgo) is a unique prokaryotic Argonaute protein that can utilize DNA and RNA guides to cleave DNA and RNA at different temperatures.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

CRISPR-mediated host genomic DNA damage is efficiently repaired through microhomology-mediated end joining in Zymomonas mobilis

Xiaojie Wang et al.

Summary: CRISPR-Cas systems provide adaptive immunity to bacteria and archaea by absorbing spacers, but self-derived spacers can cause CRISPR self-interference; the species efficiently repairs CRISPR-Cas system-mediated DNA breaks using the MMEJ pathway.

JOURNAL OF GENETICS AND GENOMICS (2021)

Article Biochemistry & Molecular Biology

A programmable pAgo nuclease with universal guide and target specificity from the mesophilic bacterium Kurthia massiliensis

Ekaterina Kropocheva et al.

Summary: Argonaute proteins are programmable nucleases found in both eukaryotes and prokaryotes, with a newly discovered pAgo nuclease, KmAgo, showing unique properties of being able to cleave both DNA and RNA targets with no strict sequence specificity, making it potentially useful for highly specific nucleic acid detection and cleavage.

NUCLEIC ACIDS RESEARCH (2021)

Article Chemistry, Analytical

Pyrococcus furiosus Argonaute coupled with modified ligase chain reaction for detection of SARS-CoV-2 and HPV

Longyu Wang et al.

Summary: The PLCR method utilizes PfAgo and LCR technologies to detect DNA or RNA with attomolar sensitivities and distinguish single-base mismatches. The method can rapidly and accurately detect pathogenic microorganisms and achieve multiplexed detection.

TALANTA (2021)

Article Biochemistry & Molecular Biology

Profiling Thermus thermophilus Argonaute Guide DNA Sequence Preferences by Functional Screening

Eric A. Hunt et al.

Summary: Research on the Argonaute protein from Thermus thermophilus has revealed specific preferences for guide sequences, which can be used to enhance guide design for molecular applications. Notable preferences include a strong cleavage enhancement from a first position dT independent of target sequence, a significant decrease in activity with dA at position 12, and an impact of GC dinucleotides at positions 10 and 11. This approach could potentially be extended to characterize other variants and improve their utility in biology and genome editing applications.

FRONTIERS IN MOLECULAR BIOSCIENCES (2021)

Article Biotechnology & Applied Microbiology

Investigation of the impact of a broad range of temperatures on the physiological and transcriptional profiles of Zymomonas mobilis ZM4 for high-temperature-tolerant recombinant strain development

Runxia Li et al.

Summary: The model ethanologenic bacterium Zymomonas mobilis exhibits temperature-dependent effects on cell growth, glucose utilization, ethanol production, and gene expression. Extreme temperatures can hinder efficient glucose utilization and ethanol production. High temperature affects the transcriptional profiles of Z. mobilis, leading to changes in growth and morphology. Several candidate genes associated with heat tolerance in Z. mobilis have been identified, indicating potential for genetic improvement in industrial strains.

BIOTECHNOLOGY FOR BIOFUELS (2021)

Article Microbiology

A Hyperthermophilic Argonaute From Ferroglobus placidus With Specificity on Guide Binding Pattern

Xiang Guo et al.

Summary: Argonaute proteins from hyperthermophilic archaea, specifically Ferroglobus placidus, exhibit a unique DNA-guided DNA endonuclease activity, with precise cleavage regulated by specific temperatures and divalent cations. FpAgo shows tolerance for guide/target mismatch in the seed region but sensitivity to mismatches in the 3'-guide region. Structural modeling analysis suggests the PAZ domain of FpAgo plays a role in guide length specificity. This study expands understanding of thermophilic Agos and their potential in DNA manipulation.

FRONTIERS IN MICROBIOLOGY (2021)

Article Biochemistry & Molecular Biology

Argonaute integrated single-tube PCR system enables supersensitive detection of rare mutations

Qian Liu et al.

Summary: The A-Star system, utilizing PfAgo for efficient detection of rare DNA mutations, greatly improves the enrichment efficiency of rare mutations and enables simultaneous detection of multiple oncogenes. It shows promising potential for both research and therapeutic applications in nucleic acid detection.

NUCLEIC ACIDS RESEARCH (2021)

Article Biotechnology & Applied Microbiology

Metabolic engineering of Zymomonas mobilis for anaerobic isobutanol production

Mengyue Qiu et al.

BIOTECHNOLOGY FOR BIOFUELS (2020)

Article Biochemistry & Molecular Biology

Thermus thermophilus Argonaute Functions in the Completion of DNA Replication

Samson M. Jolly et al.

Article Biotechnology & Applied Microbiology

Regulated redirection of central carbon flux enhances anaerobic production of bioproducts in Zymomonas mobilis

Yang Liu et al.

METABOLIC ENGINEERING (2020)

Article Biochemistry & Molecular Biology

DNA-guided DNA cleavage at moderate temperatures by Clostridium butyricum Argonaute

Jorrit W. Hegge et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

Programmable DNA cleavage by Ago nucleases from mesophilic bacteria Clostridium butyricum and Limnothrix rosea

Anton Kuzmenko et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biotechnology & Applied Microbiology

Establishment and application of a CRISPR-Cas12a assisted genome-editing system in Zymomonas mobilis

Wei Shen et al.

MICROBIAL CELL FACTORIES (2019)

Article Chemistry, Multidisciplinary

Pyrococcus furiosus Argonaute-mediated nucleic acid detection

Ruyi He et al.

CHEMICAL COMMUNICATIONS (2019)

Review Biotechnology & Applied Microbiology

Advances and prospects in metabolic engineering of Zymomonas mobilis

Xia Wang et al.

METABOLIC ENGINEERING (2018)

Article Biochemistry & Molecular Biology

Argonaute-based programmable RNase as a tool for cleavage of highly-structured RNA

Daniel M. Dayeh et al.

NUCLEIC ACIDS RESEARCH (2018)

Review Multidisciplinary Sciences

DNA interference and beyond: structure and functions of prokaryotic Argonaute proteins

Lidiya Lisitskaya et al.

NATURE COMMUNICATIONS (2018)

Article Biochemistry & Molecular Biology

Using the CRISPR/Cas9 system to eliminate native plasmids of Zymomonas mobilis ZM4

Qing-Hua Cao et al.

BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY (2017)

Article Biochemical Research Methods

Programmable DNA-Guided Artificial Restriction Enzymes

Behnam Enghiad et al.

ACS SYNTHETIC BIOLOGY (2017)

Article Microbiology

Structural and mechanistic insights into an archaeal DNA-guided Argonaute protein

Sarah Willkomm et al.

NATURE MICROBIOLOGY (2017)

Article Biotechnology & Applied Microbiology

Metabolic engineering of Zymomonas mobilis for 2,3-butanediol production from lignocellulosic biomass sugars

Shihui Yang et al.

BIOTECHNOLOGY FOR BIOFUELS (2016)

Article Biotechnology & Applied Microbiology

Systematic comparison of CRISPR/Cas9 and RNAi screens for essential genes

David W. Morgens et al.

NATURE BIOTECHNOLOGY (2016)

Article Multidisciplinary Sciences

Structural basis for the recognition of guide RNA and target DNA heteroduplex by Argonaute

Tomohiro Miyoshi et al.

NATURE COMMUNICATIONS (2016)

Review Biotechnology & Applied Microbiology

Zymomonas mobilis as a model system for production of biofuels and biochemicals

Shihui Yang et al.

MICROBIAL BIOTECHNOLOGY (2016)

Article Biochemistry & Molecular Biology

Argonaute of the archaeon Pyrococcus furiosus is a DNA-guided nuclease that targets cognate DNA

Daan C. Swarts et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Multidisciplinary Sciences

DNA-guided DNA interference by a prokaryotic Argonaute

Daan C. Swarts et al.

NATURE (2014)

Review Biochemistry & Molecular Biology

The evolutionary journey of Argonaute proteins

Daan C. Swarts et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2014)

Article Multidisciplinary Sciences

Structure of yeast Argonaute with guide RNA

Kotaro Nakanishi et al.

NATURE (2012)

Article Multidisciplinary Sciences

Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes

Yanli Wang et al.

NATURE (2009)

Article Biochemical Research Methods

Enzymatic assembly of DNA molecules up to several hundred kilobases

Daniel G. Gibson et al.

NATURE METHODS (2009)

Article Genetics & Heredity

Attenuation of Zinc Finger Nuclease Toxicity by Small-Molecule Regulation of Protein Levels

Shondra M. Pruett-Miller et al.

PLOS GENETICS (2009)

Article Biochemistry & Molecular Biology

Purified Argonaute2 and an siRNA form recombinant human RISC

FV Rivas et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2005)

Article Multidisciplinary Sciences

Crystal structure of argonaute and its implications for RISC slicer activity

JJ Song et al.

SCIENCE (2004)