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Archaeal DNA alkylation repair conducted by DNA glycosylase and methyltransferase

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2023)

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Review Biochemistry & Molecular Biology

Archaea as a Model System for Molecular Biology and Biotechnology

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Summary: Archaea is the third domain of life and has a closer relationship with eukaryotes than bacteria. They are valuable model systems for molecular biology and biotechnology. Methanogens, halophiles, thermophilic euryarchaeota, and crenarchaeota are four groups of archaea with established genetic systems, making them suitable for studying archaeal genes' functions. Thermophiles are also used to investigate various aspects of archaeal biology and are a valuable source for biotechnological applications.

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Article Genetics & Heredity

The dual role of DNA repair protein MGMT in cancer prevention and treatment

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Summary: Alkylating agents are genotoxic chemicals that induce and treat cancer by bonding with cellular macromolecules, particularly DNA. O6-alkylguanine (O6-AlkylG) adducts are the most potent DNA lesions. If not repaired correctly, these adducts can cause DNA mutations, chromosome aberrations, and cell death. O6-methylguanine-DNA methyltransferase (MGMT) can remove alkyl groups from O6-AlkylG adducts and prevent the adverse biological effects. However, MGMT can also protect tumor cells from chemotherapy. It is important to explore the clinical exploitation of MGMT as a therapeutic target.

DNA REPAIR (2023)

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Article Biochemistry & Molecular Biology

A thermophilic 8-oxoguanine DNA glycosylase from Thermococcus barophiluss Ch5 is a new member of AGOG DNA glycosylase family

Lei Wang et al.

Summary: This study reveals the mechanism of AGOG enzyme (Tb-AGOG) from the archaeon Thermo Coccus barophilus Ch5 in excising 8oxoG from DNA at high temperatures. The residue D41 and E79 were found to play key roles in excision and intermediate formation.

ACTA BIOCHIMICA ET BIOPHYSICA SINICA (2022)

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Article Multidisciplinary Sciences

Resolving the subtle details of human DNA alkyltransferase lesion search and repair mechanism by single-molecule studies

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Summary: AGT is an important DNA repair protein that repairs highly mutagenic and cytotoxic alkylguanine lesions. Studies have revealed the interactions of AGT with alkyl lesions and its role in DNA repair mechanism. Surprisingly, AGT clusters do not enhance DNA translocation speed, suggesting a different role in AGT function.

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Article Chemistry, Medicinal

DNA Deformation Exerted by Regulatory DNA-Binding Motifs in Human Alkyladenine DNA Glycosylase Promotes Base Flipping

Lingyan Wang et al.

Summary: This study reveals the mechanism of human alkyladenine DNA glycosylase (AAG) in repairing alkylated nucleobases in damaged DNA through extensive molecular dynamics simulations and Markov state model. The results show that AAG extrudes the target base from the DNA and cleaves the glycosidic bond for repair. Key motifs in AAG play important roles in the extrusion process. These findings provide important insights into the function and mechanism of AAG and other related enzymes.

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Article Biotechnology & Applied Microbiology

Biochemical and functional characterization of an endonuclease III from Thermococcus barophilus Ch5

Chengxuan Tang et al.

Summary: In this study, we characterized an EndoIII enzyme from a hyperthermophilic archaeon and demonstrated its ability to excise Tg from DNA. We also found that this enzyme has unique thermostability and salt requirement compared to other archaeal EndoIII homologues. Our study provides insights into the additional function and catalytic mechanism of archaeal EndoIII.

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Review Microbiology

The cell biology of archaea

Marleen van Wolferen et al.

Summary: This review explores archaeal morphology, internal organization, and cell division, and discusses their importance in ecology, biotechnology, and human health. Recent studies have revealed the diversity and ubiquity of archaea in nature, expanding the phylogenetic scope of archaea and shedding light on their role in the evolutionary origins of eukaryotes. Advances in culturing and live imaging techniques have contributed to a better understanding of archaeal biology. The review also highlights technical challenges and discusses the potential of new technologies to address key unanswered questions.

NATURE MICROBIOLOGY (2022)

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First thermostable CLIP-tag by rational design applied to an archaeal O6-alkyl-guanine-DNA-alkyl-transferase

Rosa Merlo et al.

Summary: Self-labelling protein tags (SLPs) are versatile tools for sensor imaging that can be genetically fused with any protein of interest. Through computational and structural approaches, a thermostable CLIP-tag named SsOGT-MC8 was developed, which can covalently react with specific substrates at high temperatures.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2022)

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Review Biotechnology & Applied Microbiology

Archaea Biotechnology

Kevin Pfeifer et al.

Summary: Archaea have significant potential in biotechnology, with advantages including the ability to be cultivated under non-sterile conditions, utilization of inexpensive feedstocks, and reduced cultivation costs. Some commercially available products from archaeal cell factories are bacterioruberin, squalene, bacteriorhodopsin, and diether-/tetraether-lipids, with other products like carotenoids, biohydrogen, polyhydroxyalkanoates, and methane in various stages of development.

BIOTECHNOLOGY ADVANCES (2021)

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Article Genetics & Heredity

Biochemical characterization and mutational studies of a novel 3-meth-lyadenine DNA glycosylase II from the hyperthermophilic Thermococcus gammatolerans

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Summary: This study reports the biochemical characterization and catalytic mechanism of Tg-AlkA from the hyperthermophilic and radioresistant euryarchaeon Thermococcus gammatolerans. Tg-AlkA is a bi-functional glycosylase with distinct features, and mutational studies reveal crucial catalytic residues and conformational flexibility.

DNA REPAIR (2021)

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Article Genetics & Heredity

Structure, function and evolution of the Helix-hairpin-Helix DNA glycosylase superfamily: Piecing together the evolutionary puzzle of DNA base damage repair mechanisms

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Summary: The Base Excision Repair (BER) pathway is a highly conserved DNA repair system that targets chemical base modifications. Among the DNA glycosylases (DGs) involved, the Helix-hairpin-Helix (HhH) superfamily stands out for its versatile substrate recognition abilities, shaped by motif and domain acquisitions during evolution.

DNA REPAIR (2021)

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Review Biochemistry & Molecular Biology

DNA alkylation lesion repair: outcomes and implications in cancer chemotherapy

Yihan Peng et al.

Summary: Repairing alkylated DNA lesions is crucial for cells, as they can be cytotoxic and potentially mutagenic. Various repair pathways exist, including base excision, nucleotide excision repair, direct reversal, and dealkylation. Maintaining a proper balance between these pathways is important for the organism's favorable response to alkylating agents.

JOURNAL OF ZHEJIANG UNIVERSITY-SCIENCE B (2021)

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Biochemical characterization and mutational studies of a thermostable endonuclease III from Sulfolobus islandicus REY15A

Likui Zhang et al.

Summary: Endonuclease III (EndoIII) from the hyperthermophilic crenarchaeon Sulfolobus islandicus REY15A is capable of removing Tg from DNA at high temperature, with optimal temperature and pH at around 70 degrees C and 7.0-8.0, respectively. It is a bifunctional enzyme with glycosylase and AP lyase activities, and forms a covalent intermediate with Tg-containing dsDNA, with specific residues responsible for its catalytic functions.

INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES (2021)

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Roles of the hydroxy group of tyrosine in crystal structures of Sulfurisphaera tokodaii O6-methylguanine-DNA methyltransferase

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Summary: This study investigated the function of tyrosine in the MGMT enzyme by comparing crystal structures of mutants and their complexes with substrate analogs. The results suggest that the highly conserved tyrosine may prevent oxidants from entering the active site and play a role in protecting MGMTs from deactivation after repairing alkyl adducts. This provides insights into the molecular mechanisms by which conserved amino acids ensure enzyme integrity and activity.

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Repair of Hypoxanthine in DNA Revealed by DNA Glycosylases and Endonucleases From Hyperthermophilic Archaea

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Summary: DNA glycosylases and endonucleases from hyperthermophilic Archaea play critical roles in repairing hypoxanthine (Hx) in DNA, triggering base excision repair (BER) or alternative excision repair (AER) processes. Repair processes involve excision, cleavage of DNA strands, and generation of double-stranded breaks, which may be repaired through homologous recombination or a combination of enzymatic activities such as DNA polymerase and DNA ligase.

FRONTIERS IN MICROBIOLOGY (2021)

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Zhenxiao Yu et al.

Summary: CRISPR-Cas systems provide adaptive immunity against invasive genetic elements in archaea and bacteria. Sulfolobales organisms usually contain both type I and type III CRISPR-Cas systems, with common subtypes including I-A, I-D, III-B, and III-D. Genetic assays have been developed to study the mechanisms of adaptation and interference, demonstrating PAM-dependent DNA interference and multiple interference activities by different CRISPR-Cas systems. Biochemical characterization of ribonucleoprotein effector complexes in Sulfolobales III-B and III-D systems has enriched our understanding of the molecular mechanisms of antiviral immune responses.

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FOLIA MICROBIOLOGICA (2020)

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Review Biochemistry & Molecular Biology

O6-alkylguanine-DNA Alkyltransferases in Microbes Living on the Edge: From Stability to Applicability

Rosanna Mattossovich et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

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NATURE MICROBIOLOGY (2020)

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PLOS ONE (2017)

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