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Vaysset H, Meers C, Cury J, Bernheim A, Sternberg SH. Evolutionary origins of archaeal and eukaryotic RNA-guided RNA modification in bacterial IS110 transposons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.599552. [PMID: 38948817 PMCID: PMC11213020 DOI: 10.1101/2024.06.21.599552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Transposase genes are ubiquitous in all domains of life and provide a rich reservoir for the evolution of novel protein functions. Here we report deep evolutionary links between bacterial IS110 transposases, which catalyze RNA-guided DNA recombination using bridge RNAs, and archaeal/eukaryotic Nop5-family proteins, which promote RNA-guided RNA 2'-O-methylation using C/D-box snoRNAs. Based on conservation in the protein primary sequence, domain architecture, and three-dimensional structure, as well as common architectural features of the non-coding RNA components, we propose that programmable RNA modification emerged via exaptation of components derived from IS110-like transposons. Alongside recent studies highlighting the origins of CRISPR-Cas9 and Cas12 in IS605-family transposons, these findings underscore how recurrent domestication events of transposable elements gave rise to complex RNA-guided biological mechanisms.
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Affiliation(s)
- Hugo Vaysset
- Institut Pasteur, CNRS UMR3525, Molecular Diversity of Microbes Lab, Paris, France
- AgroParisTech, Université Paris-Saclay, Paris, France
| | - Chance Meers
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Jean Cury
- Institut Pasteur, CNRS UMR3525, Molecular Diversity of Microbes Lab, Paris, France
| | - Aude Bernheim
- Institut Pasteur, CNRS UMR3525, Molecular Diversity of Microbes Lab, Paris, France
| | - Samuel H. Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
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2
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Łazowski K, Woodgate R, Fijalkowska IJ. Escherichia coli DNA replication: the old model organism still holds many surprises. FEMS Microbiol Rev 2024; 48:fuae018. [PMID: 38982189 PMCID: PMC11253446 DOI: 10.1093/femsre/fuae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/26/2024] [Accepted: 07/08/2024] [Indexed: 07/11/2024] Open
Abstract
Research on Escherichia coli DNA replication paved the groundwork for many breakthrough discoveries with important implications for our understanding of human molecular biology, due to the high level of conservation of key molecular processes involved. To this day, it attracts a lot of attention, partially by virtue of being an important model organism, but also because the understanding of factors influencing replication fidelity might be important for studies on the emergence of antibiotic resistance. Importantly, the wide access to high-resolution single-molecule and live-cell imaging, whole genome sequencing, and cryo-electron microscopy techniques, which were greatly popularized in the last decade, allows us to revisit certain assumptions about the replisomes and offers very detailed insight into how they work. For many parts of the replisome, step-by-step mechanisms have been reconstituted, and some new players identified. This review summarizes the latest developments in the area, focusing on (a) the structure of the replisome and mechanisms of action of its components, (b) organization of replisome transactions and repair, (c) replisome dynamics, and (d) factors influencing the base and sugar fidelity of DNA synthesis.
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Affiliation(s)
- Krystian Łazowski
- Laboratory of DNA Replication and Genome Stability, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, United States
| | - Iwona J Fijalkowska
- Laboratory of DNA Replication and Genome Stability, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
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3
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Moelling K. Epigenetics and transgenerational inheritance. J Physiol 2024; 602:2537-2545. [PMID: 37772441 DOI: 10.1113/jp284424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/15/2023] [Indexed: 09/30/2023] Open
Abstract
Epigenetic modifications can alter the function of genes. The epigenetics changes are caused by environmental effects, which lead to chemical modifications of the DNA or the chromatin. The mechanisms involve the influence of small interfering siRNAs on gene silencing. Epigenetic changes normally last only during the life-time of an individual and are erased in embryos and eggs for a naive progeny. The genomes are reprogrammed and the chemical modifications removed to restart the next generation. However, there are mechanisms that allow the genome to escape from such a clearing effect so that modifications can be transmitted to one or more subsequent generations. In the germline of animal cells small RNAs, including piRNAs, have evolved which guarantee a higher degree of fidelity for transmission of genetic information, guarding especially against the detrimental effect caused by transposon activity. piRNA is essential for transposon silencing for survival of a species and protection of subsequent generations. Inactivation of piRNA results in abundant transposon activity and sperm infertility. The effect in humans has been described but is less distinct. Some stress-induced epigenetic changes are transitory in mice and can be reversed by a change of environment or lifestyle.
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Affiliation(s)
- Karin Moelling
- Institute Medical Microbiology, University Zürich, Zurich, Switzerland
- Max Planck Institute of Molecular Genetics, Berlin, Germany
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4
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Teng M, Xia ZJ, Lo N, Daud K, He HH. Assembling the RNA therapeutics toolbox. MEDICAL REVIEW (2021) 2024; 4:110-128. [PMID: 38680684 PMCID: PMC11046573 DOI: 10.1515/mr-2023-0062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/29/2024] [Indexed: 05/01/2024]
Abstract
From the approval of COVID-19 mRNA vaccines to the 2023 Nobel Prize awarded for nucleoside base modifications, RNA therapeutics have entered the spotlight and are transforming drug development. While the term "RNA therapeutics" has been used in various contexts, this review focuses on treatments that utilize RNA as a component or target RNA for therapeutic effects. We summarize the latest advances in RNA-targeting tools and RNA-based technologies, including but not limited to mRNA, antisense oligos, siRNAs, small molecules and RNA editors. We focus on the mechanisms of current FDA-approved therapeutics but also provide a discussion on the upcoming workforces. The clinical utility of RNA-based therapeutics is enabled not only by the advances in RNA technologies but in conjunction with the significant improvements in chemical modifications and delivery platforms, which are also briefly discussed in the review. We summarize the latest RNA therapeutics based on their mechanisms and therapeutic effects, which include expressing proteins for vaccination and protein replacement therapies, degrading deleterious RNA, modulating transcription and translation efficiency, targeting noncoding RNAs, binding and modulating protein activity and editing RNA sequences and modifications. This review emphasizes the concept of an RNA therapeutic toolbox, pinpointing the readers to all the tools available for their desired research and clinical goals. As the field advances, the catalog of RNA therapeutic tools continues to grow, further allowing researchers to combine appropriate RNA technologies with suitable chemical modifications and delivery platforms to develop therapeutics tailored to their specific clinical challenges.
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Affiliation(s)
- Mona Teng
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ziting Judy Xia
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Nicholas Lo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Kashif Daud
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Housheng Hansen He
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
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5
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Zhang H, Vandesompele J, Braeckmans K, De Smedt SC, Remaut K. Nucleic acid degradation as barrier to gene delivery: a guide to understand and overcome nuclease activity. Chem Soc Rev 2024; 53:317-360. [PMID: 38073448 DOI: 10.1039/d3cs00194f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Gene therapy is on its way to revolutionize the treatment of both inherited and acquired diseases, by transferring nucleic acids to correct a disease-causing gene in the target cells of patients. In the fight against infectious diseases, mRNA-based therapeutics have proven to be a viable strategy in the recent Covid-19 pandemic. Although a growing number of gene therapies have been approved, the success rate is limited when compared to the large number of preclinical and clinical trials that have been/are being performed. In this review, we highlight some of the hurdles which gene therapies encounter after administration into the human body, with a focus on nucleic acid degradation by nucleases that are extremely abundant in mammalian organs, biological fluids as well as in subcellular compartments. We overview the available strategies to reduce the biodegradation of gene therapeutics after administration, including chemical modifications of the nucleic acids, encapsulation into vectors and co-administration with nuclease inhibitors and discuss which strategies are applied for clinically approved nucleic acid therapeutics. In the final part, we discuss the currently available methods and techniques to qualify and quantify the integrity of nucleic acids, with their own strengths and limitations.
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Affiliation(s)
- Heyang Zhang
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Kevin Braeckmans
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Stefaan C De Smedt
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Katrien Remaut
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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6
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McGregor L, Acajjaoui S, Desfosses A, Saïdi M, Bacia-Verloop M, Schwarz JJ, Juyoux P, von Velsen J, Bowler MW, McCarthy AA, Kandiah E, Gutsche I, Soler-Lopez M. The assembly of the Mitochondrial Complex I Assembly complex uncovers a redox pathway coordination. Nat Commun 2023; 14:8248. [PMID: 38086790 PMCID: PMC10716376 DOI: 10.1038/s41467-023-43865-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
The Mitochondrial Complex I Assembly (MCIA) complex is essential for the biogenesis of respiratory Complex I (CI), the first enzyme in the respiratory chain, which has been linked to Alzheimer's disease (AD) pathogenesis. However, how MCIA facilitates CI assembly, and how it is linked with AD pathogenesis, is poorly understood. Here we report the structural basis of the complex formation between the MCIA subunits ECSIT and ACAD9. ECSIT binding induces a major conformational change in the FAD-binding loop of ACAD9, releasing the FAD cofactor and converting ACAD9 from a fatty acid β-oxidation (FAO) enzyme to a CI assembly factor. We provide evidence that ECSIT phosphorylation downregulates its association with ACAD9 and is reduced in neuronal cells upon exposure to amyloid-β (Aβ) oligomers. These findings advance our understanding of the MCIA complex assembly and suggest a possible role for ECSIT in the reprogramming of bioenergetic pathways linked to Aβ toxicity, a hallmark of AD.
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Affiliation(s)
- Lindsay McGregor
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38043, Grenoble, France
| | - Samira Acajjaoui
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38043, Grenoble, France
| | - Ambroise Desfosses
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS (IBS), 38044, Grenoble, France
| | - Melissa Saïdi
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38043, Grenoble, France
| | - Maria Bacia-Verloop
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS (IBS), 38044, Grenoble, France
| | - Jennifer J Schwarz
- European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany
| | - Pauline Juyoux
- European Molecular Biology Laboratory (EMBL), 38043, Grenoble, France
| | - Jill von Velsen
- European Molecular Biology Laboratory (EMBL), 38043, Grenoble, France
| | - Matthew W Bowler
- European Molecular Biology Laboratory (EMBL), 38043, Grenoble, France
| | - Andrew A McCarthy
- European Molecular Biology Laboratory (EMBL), 38043, Grenoble, France
| | - Eaazhisai Kandiah
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38043, Grenoble, France
| | - Irina Gutsche
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS (IBS), 38044, Grenoble, France.
- Department of Chemistry, Umeå University, Umeå, Sweden.
| | - Montserrat Soler-Lopez
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38043, Grenoble, France.
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7
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Gruber C, Gursinsky T, Gago-Zachert S, Pantaleo V, Behrens SE. Effective Antiviral Application of Antisense in Plants by Exploiting Accessible Sites in the Target RNA. Int J Mol Sci 2023; 24:17153. [PMID: 38138982 PMCID: PMC10743417 DOI: 10.3390/ijms242417153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/24/2023] Open
Abstract
Antisense oligodeoxynucleotides (ASOs) have long been used to selectively inhibit or modulate gene expression at the RNA level, and some ASOs are approved for clinical use. However, the practicability of antisense technologies remains limited by the difficulty of reliably predicting the sites accessible to ASOs in complex folded RNAs. Recently, we applied a plant-based method that reproduces RNA-induced RNA silencing in vitro to reliably identify sites in target RNAs that are accessible to small interfering RNA (siRNA)-guided Argonaute endonucleases. Here, we show that this method is also suitable for identifying ASOs that are effective in DNA-induced RNA silencing by RNases H. We show that ASOs identified in this way that target a viral genome are comparably effective in protecting plants from infection as siRNAs with the corresponding sequence. The antiviral activity of the ASOs could be further enhanced by chemical modification. This led to two important conclusions: siRNAs and ASOs that can effectively knock down complex RNA molecules can be identified using the same approach, and ASOs optimized in this way could find application in crop protection. The technology developed here could be useful not only for effective RNA silencing in plants but also in other organisms.
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Affiliation(s)
- Cornelia Gruber
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany; (C.G.); (T.G.); (S.G.-Z.)
| | - Torsten Gursinsky
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany; (C.G.); (T.G.); (S.G.-Z.)
| | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany; (C.G.); (T.G.); (S.G.-Z.)
| | - Vitantonio Pantaleo
- Institute for Sustainable Plant Protection, Department of Biology, Agricultural and Food Sciences National Research Council, Bari Unit, I-70126 Bari, Italy;
| | - Sven-Erik Behrens
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany; (C.G.); (T.G.); (S.G.-Z.)
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8
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Altae-Tran H, Shmakov SA, Makarova KS, Wolf YI, Kannan S, Zhang F, Koonin EV. Diversity, evolution, and classification of the RNA-guided nucleases TnpB and Cas12. Proc Natl Acad Sci U S A 2023; 120:e2308224120. [PMID: 37983496 PMCID: PMC10691335 DOI: 10.1073/pnas.2308224120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/19/2023] [Indexed: 11/22/2023] Open
Abstract
The TnpB proteins are transposon-associated RNA-guided nucleases that are among the most abundant proteins encoded in bacterial and archaeal genomes, but whose functions in the transposon life cycle remain unknown. TnpB appears to be the evolutionary ancestor of Cas12, the effector nuclease of type V CRISPR-Cas systems. We performed a comprehensive census of TnpBs in archaeal and bacterial genomes and constructed a phylogenetic tree on which we mapped various features of these proteins. In multiple branches of the tree, the catalytic site of the TnpB nuclease is rearranged, demonstrating structural and probably biochemical malleability of this enzyme. We identified numerous cases of apparent recruitment of TnpB for other functions of which the most common is the evolution of type V CRISPR-Cas effectors on about 50 independent occasions. In many other cases of more radical exaptation, the catalytic site of the TnpB nuclease is apparently inactivated, suggesting a regulatory function, whereas in others, the activity appears to be retained, indicating that the recruited TnpB functions as a nuclease, for example, as a toxin. These findings demonstrate remarkable evolutionary malleability of the TnpB scaffold and provide extensive opportunities for further exploration of RNA-guided biological systems as well as multiple applications.
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Affiliation(s)
- Han Altae-Tran
- HHMI, Cambridge, MA02139
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Sergey A. Shmakov
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD20894
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD20894
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD20894
| | - Soumya Kannan
- HHMI, Cambridge, MA02139
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Feng Zhang
- HHMI, Cambridge, MA02139
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD20894
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9
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Smug BJ, Szczepaniak K, Rocha EPC, Dunin-Horkawicz S, Mostowy RJ. Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with bacterial hosts. Nat Commun 2023; 14:7460. [PMID: 38016962 PMCID: PMC10684548 DOI: 10.1038/s41467-023-43236-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 11/03/2023] [Indexed: 11/30/2023] Open
Abstract
Biological modularity enhances evolutionary adaptability. This principle is vividly exemplified by bacterial viruses (phages), which display extensive genomic modularity. Phage genomes are composed of independent functional modules that evolve separately and recombine in various configurations. While genomic modularity in phages has been extensively studied, less attention has been paid to protein modularity-proteins consisting of distinct building blocks that can evolve and recombine, enhancing functional and genetic diversity. Here, we use a set of 133,574 representative phage proteins and highly sensitive homology detection to capture instances of domain mosaicism, defined as fragment sharing between two otherwise unrelated proteins, and to understand its relationship with functional diversity in phage genomes. We discover that unrelated proteins from diverse functional classes frequently share homologous domains. This phenomenon is particularly pronounced within receptor-binding proteins, endolysins, and DNA polymerases. We also identify multiple instances of recent diversification via domain shuffling in receptor-binding proteins, neck passage structures, endolysins and some members of the core replication machinery, often transcending distant taxonomic and ecological boundaries. Our findings suggest that ongoing diversification via domain shuffling is reflective of a co-evolutionary arms race, driven by the need to overcome various bacterial resistance mechanisms against phages.
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Affiliation(s)
- Bogna J Smug
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Stanislaw Dunin-Horkawicz
- Institute of Evolutionary Biology, Faculty of Biology & Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Rafał J Mostowy
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
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10
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Xiang K, Puzakov M, Shi S, Diaby M, Ullah N, Gao B, Song C. Mosquito ( MS), a DD37E Family of Tc1/ Mariner, Displaying a Distinct Evolution Profile from DD37E/ TRT and DD37E/ L18. Genes (Basel) 2023; 14:1379. [PMID: 37510284 PMCID: PMC10379824 DOI: 10.3390/genes14071379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/26/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Diverse Tc1/mariner elements with the DD37E signature have been detected. However, their evolutionary relationship and profiles are largely unknown. Using bioinformatics methods, we defined the evolution profile of a Tc1/Mariner family, which harbors the catalytic domain with the DD37E signature, and renamed it DD37E/Mosquito (MS). MS transposons form a separate monophyletic clade in the phylogenetic tree, distinct from the other two groups of elements with the DD37E signature, DD37E/L18 and DD37E/TRT (transposon related to Tc1), and represent a very different taxonomic distribution from that of DD37E/TRT. MS is only detected in invertebrate and is mostly present in Arthropoda, as well as in Cnidaria, Ctenophora, Mollusca, Nematoda, and Platyhelminthes, with a total length of about 1.3 kb, containing an open reading frame (ORF) encoding about 340 amino acids transposases, with a conserved DD37E catalytic domain. The terminal inverted repeat (TIR) lengths range from 19 bp to 203 bp, and the target site duplication (TSD) is TA. We also identified few occurrences of MS horizontal transfers (HT) across lineages of diptera. In this paper, the distribution characteristics, structural characteristics, phylogenetic evolution, and horizontal transfer of the MS family are fully analyzed, which is conducive to supplementing and improving the Tc1/Mariner superfamily and excavating active transposons.
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Affiliation(s)
- Kuilin Xiang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Mikhail Puzakov
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Lenninsky Ave, 38, Moscow 119991, Russia
| | - Shasha Shi
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Mohamed Diaby
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Numan Ullah
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Bo Gao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
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11
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Fernandez M, Shkumatov AV, Liu Y, Stulemeijer C, Derclaye S, Efremov R, Hallet B, Alsteens D. AFM-based force spectroscopy unravels stepwise formation of the DNA transposition complex in the widespread Tn3 family mobile genetic elements. Nucleic Acids Res 2023; 51:4929-4941. [PMID: 37026471 PMCID: PMC10250215 DOI: 10.1093/nar/gkad241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/03/2023] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
Transposon Tn4430 belongs to a widespread family of bacterial transposons, the Tn3 family, which plays a prevalent role in the dissemination of antibiotic resistance among pathogens. Despite recent data on the structural architecture of the transposition complex, the molecular mechanisms underlying the replicative transposition of these elements are still poorly understood. Here, we use force-distance curve-based atomic force microscopy to probe the binding of the TnpA transposase of Tn4430 to DNA molecules containing one or two transposon ends and to extract the thermodynamic and kinetic parameters of transposition complex assembly. Comparing wild-type TnpA with previously isolated deregulated TnpA mutants supports a stepwise pathway for transposition complex formation and activation during which TnpA first binds as a dimer to a single transposon end and then undergoes a structural transition that enables it to bind the second end cooperatively and to become activated for transposition catalysis, the latter step occurring at a much faster rate for the TnpA mutants. Our study thus provides an unprecedented approach to probe the dynamic of a complex DNA processing machinery at the single-particle level.
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Affiliation(s)
- Maricruz Fernandez
- NanoBioPhysics lab, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
- Biochemistry and Genetics of Microorganisms, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Alexander V Shkumatov
- Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Yun Liu
- Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Claire Stulemeijer
- Biochemistry and Genetics of Microorganisms, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Sylvie Derclaye
- NanoBioPhysics lab, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Rouslan G Efremov
- Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Bernard Hallet
- Biochemistry and Genetics of Microorganisms, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - David Alsteens
- NanoBioPhysics lab, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
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12
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Nety SP, Altae-Tran H, Kannan S, Demircioglu FE, Faure G, Hirano S, Mears K, Zhang Y, Macrae RK, Zhang F. The Transposon-Encoded Protein TnpB Processes Its Own mRNA into ωRNA for Guided Nuclease Activity. CRISPR J 2023; 6:232-242. [PMID: 37272862 PMCID: PMC10278001 DOI: 10.1089/crispr.2023.0015] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/21/2023] [Indexed: 06/06/2023] Open
Abstract
TnpB is a member of the Obligate Mobile Element Guided Activity (OMEGA) RNA-guided nuclease family, is harbored in transposons, and likely functions to maintain the transposon in genomes. Previously, it was shown that TnpB cleaves double- and single-stranded DNA substrates in an RNA-guided manner, but the biogenesis of the TnpB ribonucleoprotein (RNP) complex is unknown. Using in vitro purified apo TnpB, we demonstrate the ability of TnpB to generate guide omegaRNA (ωRNA) from its own mRNA through 5' processing. We also uncover a potential cis-regulatory mechanism whereby a region of the TnpB mRNA inhibits DNA cleavage by the RNP complex. We further expand the characterization of TnpB by examining ωRNA processing and RNA-guided nuclease activity in 59 orthologs spanning the natural diversity of the TnpB family. This work reveals a new functionality, ωRNA biogenesis, of TnpB, and characterizes additional members of this biotechnologically useful family of programmable enzymes.
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Affiliation(s)
- Suchita P. Nety
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Han Altae-Tran
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Soumya Kannan
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - F. Esra Demircioglu
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Guilhem Faure
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Seiichi Hirano
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kepler Mears
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Yugang Zhang
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Rhiannon K. Macrae
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Feng Zhang
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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13
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Kitagawa Y, Liao Z, Morikawa K, Oda M. Metal-binding and folding thermodynamics of Escherichia coli ribonuclease HI related to its catalytic function. Biophys Chem 2023; 295:106961. [PMID: 36736006 DOI: 10.1016/j.bpc.2023.106961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/30/2023]
Abstract
Escherichia coli ribonuclease HI (RNH) hydrolyzes the RNA strands of RNA/DNA hybrids in the presence of Mg2+ at the highest level, relative to other metal ions. The Mg2+ binding affinity was 8.39 × 103 M-1, which was lower than those of other metal ions. The low-affinity binder can express the maximum catalytic activity of RNH. The stability of RNH increased with increasing metal ion concentration, except for Zn2+. The thermodynamic origin for enhancing the stability of RNH with Mg2+ was more favorable entropy compared to those with other metal ions, indicating that Mg2+ binding changes the RNH structure while maintaining flexibility. Upon H124A mutation, the metal ion binding affinities decreased for Mn2+ and Zn2+ to a relatively large extent. The present thermodynamic analyses provide information on the structural dynamics of RNH with metal ion exchangeable binding, which can reasonably explain the metal-ion-dependent catalytic activity.
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Affiliation(s)
- Yumi Kitagawa
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Shimogamo Hangi-cho, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan
| | - Zengwei Liao
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Shimogamo Hangi-cho, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan; Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kosuke Morikawa
- Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan
| | - Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Shimogamo Hangi-cho, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan.
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14
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IS481EU Shows a New Connection between Eukaryotic and Prokaryotic DNA Transposons. BIOLOGY 2023; 12:biology12030365. [PMID: 36979057 PMCID: PMC10045372 DOI: 10.3390/biology12030365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/03/2023] [Accepted: 02/24/2023] [Indexed: 03/03/2023]
Abstract
DDD/E transposase gene is the most abundant gene in nature and many DNA transposons in all three domains of life use it for their transposition. A substantial number of eukaryotic DNA transposons show similarity to prokaryotic insertion sequences (ISs). The presence of IS481-like DNA transposons was indicated in the genome of Trichomonas vaginalis. Here, we surveyed IS481-like eukaryotic sequences using a bioinformatics approach and report a group of eukaryotic IS481-like DNA transposons, designated IS481EU, from parabasalids including T. vaginalis. The lengths of target site duplications (TSDs) of IS481EU are around 4 bps, around 15 bps, or around 25 bps, and strikingly, these discrete lengths of TSDs can be observed even in a single IS481EU family. Phylogenetic analysis indicated the close relationships of IS481EU with some of the prokaryotic IS481 family members. IS481EU was not well separated from IS3EU/GingerRoot in the phylogenetic analysis, but was distinct from other eukaryotic DNA transposons including Ginger1 and Ginger2. The unique characteristics of IS481EU in protein sequences and the distribution of TSD lengths support its placement as a new superfamily of eukaryotic DNA transposons.
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15
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Devate NB, Krishna H, Mishra CN, Manjunath KK, Sunilkumar VP, Chauhan D, Singh S, Sinha N, Jain N, Singh GP, Singh PK. Genetic dissection of marker trait associations for grain micro-nutrients and thousand grain weight under heat and drought stress conditions in wheat. FRONTIERS IN PLANT SCIENCE 2023; 13:1082513. [PMID: 36726675 PMCID: PMC9885108 DOI: 10.3389/fpls.2022.1082513] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/15/2022] [Indexed: 06/18/2023]
Abstract
Introduction Wheat is grown and consumed worldwide, making it an important staple food crop for both its calorific and nutritional content. In places where wheat is used as a staple food, suboptimal micronutrient content levels, especially of grain iron (Fe) and zinc (Zn), can lead to malnutrition. Grain nutrient content is influenced by abiotic stresses, such as drought and heat stress. The best method for addressing micronutrient deficiencies is the biofortification of food crops. The prerequisites for marker-assisted varietal development are the identification of the genomic region responsible for high grain iron and zinc contents and an understanding of their genetics. Methods A total of 193 diverse wheat genotypes were evaluated under drought and heat stress conditions across the years at the Indian Agricultural Research Institute (IARI), New Delhi, under timely sown irrigated (IR), restricted irrigated (RI) and late sown (LS) conditions. Grain iron content (GFeC) and grain zinc content (GZnC) were estimated from both the control and treatment groups. Genotyping of all the lines under study was carried out with the single nucleotide polymorphisms (SNPs) from Breeder's 35K Axiom Array. Result and Discussion Three subgroups were observed in the association panel based on both principal component analysis (PCA) and dendrogram analysis. A large whole-genome linkage disequilibrium (LD) block size of 3.49 Mb was observed. A genome-wide association study identified 16 unique stringent marker trait associations for GFeC, GZnC, and 1000-grain weight (TGW). In silico analysis demonstrated the presence of 28 potential candidate genes in the flanking region of 16 linked SNPs, such as synaptotagmin-like mitochondrial-lipid-binding domain, HAUS augmin-like complex, di-copper center-containing domain, protein kinase, chaperonin Cpn60, zinc finger, NUDIX hydrolase, etc. Expression levels of these genes in vegetative tissues and grain were also found. Utilization of identified markers in marker-assisted breeding may lead to the rapid development of biofortified wheat genotypes to combat malnutrition.
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Affiliation(s)
- Narayana Bhat Devate
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, India
| | - Hari Krishna
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, India
| | | | | | - V. P. Sunilkumar
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, India
| | - Divya Chauhan
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, India
| | - Shweta Singh
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, India
| | - Nivedita Sinha
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, India
| | - Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, India
| | | | - Pradeep Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, India
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16
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Wang Q, Liu Z, Tang S, Wu Z. Morphine suppresses the immune function of lung cancer by up-regulating MAEL expression. BMC Pharmacol Toxicol 2022; 23:92. [PMID: 36476246 PMCID: PMC9730686 DOI: 10.1186/s40360-022-00632-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Patients with cancer rely on morphine for analgesia, while studies have indicated morphine can induce immunosuppression in cancer. Therefore, investigating the immunosuppressive roles and molecular mechanism of morphine on lung cancer progression is imperative. METHODS Lactate dehydrogenase (LDH) release assay was used to determine the cytotoxicity of morphine to lung cancer cells. The percentage of CD4+ and CD8+ T cells was detected by flow cytometry. In addition, Maelstrom (MAEL), Nrf2, and PTEN were determined by western blot and RT-qPCR. Immune factors programmed death-ligand 1 (PD-L1), transforming growth factor (TGF-β), interleukin (IL)-10, and IL-2 were determined by western blot and ELISA assay. RESULTS Morphine increased the levels of PD-L1, TGF-β, and IL-10, while decreased IL-2 level. Morphine enhanced MAEL expression in A549 cells and H460 cells. Morphine up-regulated Nrf2 and down-regulated PTEN, and morphine-induced MAEL up-regulation was reversed by PTEN. However, MAEL silencing inhibited the enhanced effects of morphine on cell viability and proliferation of A549 cells. Furthermore, morphine treatment reduced the LDH release and the percentage of CD8+ T cells, and increased the ratio of CD4+/CD8+ T cells and tumor weight. Meanwhile, MAEL silencing reversed the effects of morphine on immune factors (PD-L1, TGF-β, IL-10, and IL-2), the percentage of CD8+ T cells, and the ratio of CD4+/CD8+ T cells. CONCLUSION Morphine activated MAEL in lung cancer cells by Nrf2/PTEN pathway and regulated the immune factors, thereby promoting tumor immune escape.
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Affiliation(s)
- Qichao Wang
- grid.411634.50000 0004 0632 4559Department of Oncology II, Dalian Fifth People’s Hospital, No. 890, Huanghe Road, Shahekou District, Dalian City, 116021 Liaoning Province China
| | - Zhenfu Liu
- Department of Anesthesiology, Zaozhuang Hospital of Zaozhuang Mining Group, No. 188, Shengli Road, Zaozhuang City, 277100 Shandong Province China
| | - Shuhong Tang
- grid.411634.50000 0004 0632 4559Department of Oncology II, Dalian Fifth People’s Hospital, No. 890, Huanghe Road, Shahekou District, Dalian City, 116021 Liaoning Province China
| | - Zhen Wu
- grid.452582.cDepartment of Anesthesiology, The Fourth Hospital of Hebei Medical University, No.12, Jiankang Road, Shijiazhuang City, 050000 Hebei Province China
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17
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He T, Edwards TC, Majima R, Jung E, Kankanala J, Xie J, Geraghty RJ, Wang Z. Repurposing N-hydroxy thienopyrimidine-2,4-diones (HtPD) as inhibitors of human cytomegalovirus pUL89 endonuclease: Synthesis and biological characterization. Bioorg Chem 2022; 129:106198. [PMID: 36265353 PMCID: PMC9643671 DOI: 10.1016/j.bioorg.2022.106198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 11/02/2022]
Abstract
The terminase complex of human cytomegalovirus (HCMV) is required for viral genome packaging and cleavage. Critical to the terminase functions is a metal-dependent endonuclease at the C-terminus of pUL89 (pUL89-C). We have previously reported metal-chelating N-hydroxy thienopyrimidine-2,4-diones (HtPD) as inhibitors of human immunodeficiency virus 1 (HIV-1) RNase H. In the current work, we have synthesized new analogs and resynthesized known analogs of two isomeric HtPD subtypes, anti-HtPD (13), and syn-HtPD (14), and characterized them as inhibitors of pUL89-C. Remarkably, the vast majority of analogs strongly inhibited pUL89-C in the biochemical endonuclease assay, with IC50 values in the nM range. In the cell-based antiviral assay, a few analogs inhibited HCMV in low μM concentrations. Selected analogs were further characterized in a biophysical thermal shift assay (TSA) and in silico molecular docking, and the results support pUL89-C as the protein target of these inhibitors. Collectively, the biochemical, antiviral, biophysical, and in silico data reported herein indicate that the isomeric HtPD chemotypes 13-14 can serve as valuable chemical platforms for designing improved inhibitors of HCMV pUL89-C.
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Affiliation(s)
- Tianyu He
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Tiffany C Edwards
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ryuichi Majima
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Eunkyung Jung
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jayakanth Kankanala
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jiashu Xie
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert J Geraghty
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA.
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18
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A widespread group of large plasmids in methanotrophic Methanoperedens archaea. Nat Commun 2022; 13:7085. [PMID: 36400771 PMCID: PMC9674854 DOI: 10.1038/s41467-022-34588-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 10/31/2022] [Indexed: 11/19/2022] Open
Abstract
Anaerobic methanotrophic (ANME) archaea obtain energy from the breakdown of methane, yet their extrachromosomal genetic elements are little understood. Here we describe large plasmids associated with ANME archaea of the Methanoperedens genus in enrichment cultures and other natural anoxic environments. By manual curation we show that two of the plasmids are large (155,605 bp and 191,912 bp), circular, and may replicate bidirectionally. The plasmids occur in the same copy number as the main chromosome, and plasmid genes are actively transcribed. One of the plasmids encodes three tRNAs, ribosomal protein uL16 and elongation factor eEF2; these genes appear to be missing in the host Methanoperedens genome, suggesting an obligate interdependence between plasmid and host. Our work opens the way for the development of genetic vectors to shed light on the physiology and biochemistry of Methanoperedens, and potentially genetically edit them to enhance growth and accelerate methane oxidation rates.
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19
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Shkumatov AV, Aryanpour N, Oger CA, Goossens G, Hallet BF, Efremov RG. Structural insight into Tn3 family transposition mechanism. Nat Commun 2022; 13:6155. [PMID: 36257990 PMCID: PMC9579193 DOI: 10.1038/s41467-022-33871-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 10/05/2022] [Indexed: 12/24/2022] Open
Abstract
Transposons are diverse mobile genetic elements that play the critical role as genome architects in all domains of life. Tn3 is a widespread family and among the first identified bacterial transposons famed for their contribution to the dissemination of antibiotic resistance. Transposition within this family is mediated by a large TnpA transposase, which facilitates both transposition and target immunity. Howtever, a structural framework required for understanding the mechanism of TnpA transposition is lacking. Here, we describe the cryo-EM structures of TnpA from Tn4430 in the apo form and paired with transposon ends before and after DNA cleavage and strand transfer. We show that TnpA has an unusual architecture and exhibits a family specific regulatory mechanism involving metamorphic refolding of the RNase H-like catalytic domain. The TnpA structure, constrained by a double dimerization interface, creates a peculiar topology that suggests a specific role for the target DNA in transpososome assembly and activation.
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Affiliation(s)
- Alexander V. Shkumatov
- grid.11486.3a0000000104788040Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium ,grid.8767.e0000 0001 2290 8069Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium ,Present Address: Confo Therapeutics, Brussels, Belgium
| | - Nicolas Aryanpour
- grid.7942.80000 0001 2294 713XLouvain Institue of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud 4/5, 1348 Louvain-la-Neuve, Belgium
| | - Cédric A. Oger
- grid.7942.80000 0001 2294 713XLouvain Institue of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud 4/5, 1348 Louvain-la-Neuve, Belgium
| | - Gérôme Goossens
- grid.7942.80000 0001 2294 713XLouvain Institue of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud 4/5, 1348 Louvain-la-Neuve, Belgium ,Present Address: Thermo Fisher Scientific, Seneffe, Belgium
| | - Bernard F. Hallet
- grid.7942.80000 0001 2294 713XLouvain Institue of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud 4/5, 1348 Louvain-la-Neuve, Belgium
| | - Rouslan G. Efremov
- grid.11486.3a0000000104788040Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium ,grid.8767.e0000 0001 2290 8069Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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20
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Huang Y, Dong H, Mou C, Wang P, Hao Q, Zhang M, Wu H, Zhang F, Ma T, Miao R, Fu K, Chen Y, Zhu Z, Chen C, Tong Q, Wang Z, Zhou S, Liu X, Liu S, Tian Y, Jiang L, Wan J. Ribonuclease H-like gene SMALL GRAIN2 regulates grain size in rice through brassinosteroid signaling pathway. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1883-1900. [PMID: 35904032 DOI: 10.1111/jipb.13333] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Grain size is a key agronomic trait that determines the yield in plants. Regulation of grain size by brassinosteroids (BRs) in rice has been widely reported. However, the relationship between the BR signaling pathway and grain size still requires further study. Here, we isolated a rice mutant, named small grain2 (sg2), which displayed smaller grain and a semi-dwarf phenotype. The decreased grain size was caused by repressed cell expansion in spikelet hulls of the sg2 mutant. Using map-based cloning combined with a MutMap approach, we cloned SG2, which encodes a plant-specific protein with a ribonuclease H-like domain. SG2 is a positive regulator downstream of GLYCOGEN SYNTHASE KINASE2 (GSK2) in response to BR signaling, and its mutation causes insensitivity to exogenous BR treatment. Genetical and biochemical analysis showed that GSK2 interacts with and phosphorylates SG2. We further found that BRs enhance the accumulation of SG2 in the nucleus, and subcellular distribution of SG2 is regulated by GSK2 kinase activity. In addition, Oryza sativa OVATE family protein 19 (OsOFP19), a negative regulator of grain shape, interacts with SG2 and plays an antagonistic role with SG2 in controlling gene expression and grain size. Our results indicated that SG2 is a new component of GSK2-related BR signaling response and regulates grain size by interacting with OsOFP19.
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Affiliation(s)
- Yunshuai Huang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hui Dong
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Changling Mou
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ping Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qixian Hao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Min Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hongmin Wu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fulin Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tengfei Ma
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rong Miao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kai Fu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yaping Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ziyan Zhu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Cheng Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qikai Tong
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhuoran Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shirong Zhou
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shijia Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunlu Tian
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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21
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Current medicinal chemistry strategies in the discovery of novel HIV-1 ribonuclease H inhibitors. Eur J Med Chem 2022; 243:114760. [PMID: 36152387 DOI: 10.1016/j.ejmech.2022.114760] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/29/2022] [Accepted: 09/06/2022] [Indexed: 11/23/2022]
Abstract
During HIV-1 genome replication, the viral reverse transcriptase-associated ribonuclease H (RT-associated RNase H) activity hydrolyzes the RNA strand of RNA/DNA heteroduplex intermediates. As of today, HIV-1 RNase H inhibitors (RHIs) remain at an investigational level, although none of them reached clinical trials. Therefore, RNase H remains as an attractive target for drug design and development. In this paper, we review the current status of medicinal chemistry strategies aimed at the discovery of novel RHIs, while discussing problems encountered in their characterization and further development, thereby providing an update on recent progress in the field.
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22
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Biochemical and Structural Study of RuvC and YqgF from Deinococcus radiodurans. mBio 2022; 13:e0183422. [PMID: 36000732 DOI: 10.1128/mbio.01834-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Deinococcus radiodurans possesses robust DNA damage response and repair abilities, and this is mainly due to its efficient homologous recombination repair system, which incorporates an uncharacterized Holliday junction (HJ) resolution process. D. radiodurans encodes two putative HJ resolvase (HJR) homologs: RuvC (DrRuvC) and YqgF (DrYqgF). Here, both DrRuvC and DrYqgF were identified as essential proteins for the survival of D. radiodurans. The crystal structures and the biochemical properties of DrRuvC and DrYqgF were also studied. DrRuvC crystallized as a homodimer, while DrYqgF crystallized as a monomer. DrRuvC could preferentially cleave HJ at the consensus 5'-(G/C)TC↓(G/C)-3' sequence and could prefer using Mn2+ for catalysis in vitro, which would be different from the preferences of the other previously characterized RuvCs. On the other hand, DrYqgF was identified as a Mn2+-dependent RNA 5'-3' exo/endonuclease with a sequence preference for poly(A) and without any HJR activity. IMPORTANCE Deinococcus radiodurans is one of the most radioresistant bacteria in the world due to its robust DNA damage response and repair abilities, which are contributed by its efficient homologous recombination repair system. However, the late steps of homologous recombination, especially the Holliday junction (HJ) resolution process, have not yet been well-studied in D. radiodurans. We characterized the structural and biochemical features of the two putative HJ resolvases, DrRuvC and DrYqgF, in D. radiodurans. It was identified that DrRuvC and DrYqgF exhibit HJ resolvase (HJR) activity and RNA exo/endonuclease activity, respectively. Furthermore, both DrRuvC and DrYqgF digest substrates in a sequence-specific manner with a preferred sequence that is different from those of the other characterized RuvCs or YqgFs. Our findings provide new insights into the HJ resolution process and reveal a novel RNase involved in RNA metabolism in D. radiodurans.
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Thakur M, Parulekar RS, Barale SS, Sonawane KD, Muniyappa K. Interrogating the substrate specificity landscape of UvrC reveals novel insights into its non-canonical function. Biophys J 2022; 121:3103-3125. [PMID: 35810330 PMCID: PMC9463653 DOI: 10.1016/j.bpj.2022.07.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 05/23/2022] [Accepted: 07/07/2022] [Indexed: 11/29/2022] Open
Abstract
Although it is relatively unexplored, accumulating data highlight the importance of tripartite crosstalk between nucleotide excision repair (NER), DNA replication, and recombination in the maintenance of genome stability; however, elucidating the underlying mechanisms remains challenging. While Escherichia coli uvrA and uvrB can fully complement polAΔ cells in DNA replication, uvrC attenuates this alternative DNA replication pathway, but the exact mechanism by which uvrC suppresses DNA replication is unknown. Furthermore, the identity of bona fide canonical and non-canonical substrates for UvrCs are undefined. Here, we reveal that Mycobacterium tuberculosis UvrC (MtUvrC) strongly binds to, and robustly cleaves, key intermediates of DNA replication/recombination as compared with the model NER substrates. Notably, inactivation of MtUvrC ATPase activity significantly attenuated its endonuclease activity, thus suggesting a causal link between these two functions. We built an in silico model of the interaction of MtUvrC with the Holliday junction (HJ), using a combination of homology modeling, molecular docking, and molecular dynamic simulations. The model predicted residues that were potentially involved in HJ binding. Six of these residues were mutated either singly or in pairs, and the resulting MtUvrC variants were purified and characterized. Among them, residues Glu595 and Arg597 in the helix-hairpin-helix motif were found to be crucial for the interaction between MtUvrC and HJ; consequently, mutations in these residues, or inhibition of ATP hydrolysis, strongly abrogated its DNA-binding and endonuclease activities. Viewed together, these findings expand the substrate specificity landscape of UvrCs and provide crucial mechanistic insights into the interplay between NER and DNA replication/recombination.
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Affiliation(s)
- Manoj Thakur
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India.
| | | | - Sagar S Barale
- Structural Bioinformatics Unit, Shivaji University, Kolhapur, India
| | - Kailas D Sonawane
- Department of Microbiology, Shivaji University, Kolhapur, India; Structural Bioinformatics Unit, Shivaji University, Kolhapur, India
| | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India.
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24
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Noor E, Flamholz AI, Jayaraman V, Ross BL, Cohen Y, Patrick WM, Gruic‐Sovulj I, Tawfik DS. Uniform binding and negative catalysis at the origin of enzymes. Protein Sci 2022; 31:e4381. [PMID: 35900021 PMCID: PMC9281367 DOI: 10.1002/pro.4381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/06/2022] [Accepted: 06/15/2022] [Indexed: 11/06/2022]
Abstract
Enzymes are well known for their catalytic abilities, some even reaching "catalytic perfection" in the sense that the reaction they catalyze has reached the physical bound of the diffusion rate. However, our growing understanding of enzyme superfamilies has revealed that only some share a catalytic chemistry while others share a substrate-handle binding motif, for example, for a particular phosphate group. This suggests that some families emerged through a "substrate-handle-binding-first" mechanism ("binding-first" for brevity) instead of "chemistry-first" and we are, therefore, left to wonder what the role of non-catalytic binders might have been during enzyme evolution. In the last of their eight seminal, back-to-back articles from 1976, John Albery and Jeremy Knowles addressed the question of enzyme evolution by arguing that the simplest mode of enzyme evolution is what they defined as "uniform binding" (parallel stabilization of all enzyme-bound states to the same degree). Indeed, we show that a uniform-binding proto-catalyst can accelerate a reaction, but only when catalysis is already present, that is, when the transition state is already stabilized to some degree. Thus, we sought an alternative explanation for the cases where substrate-handle-binding preceded any involvement of a catalyst. We find that evolutionary starting points that exhibit negative catalysis can redirect the reaction's course to a preferred product without need for rate acceleration or product release; that is, if they do not stabilize, or even destabilize, the transition state corresponding to an undesired product. Such a mechanism might explain the emergence of "binding-first" enzyme families like the aldolase superfamily.
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Affiliation(s)
- Elad Noor
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Avi I. Flamholz
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
- Resnick Sustainability InstituteCalifornia Institute of TechnologyPasadenaCAUSA
| | - Vijay Jayaraman
- Department of Molecular Cell BiologyWeizmann Institute of ScienceRehovotIsrael
| | - Brian L. Ross
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Yair Cohen
- Department of Caltech Environmental Science and EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Wayne M. Patrick
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Ita Gruic‐Sovulj
- Department of Chemistry, Faculty of ScienceUniversity of ZagrebZagrebCroatia
| | - Dan S. Tawfik
- Department of Molecular Cell BiologyWeizmann Institute of ScienceRehovotIsrael
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25
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Jung E, Majima R, Edwards TC, Soto-Acosta R, Geraghty RJ, Wang Z. 8-Hydroxy-1,6-naphthyridine-7-carboxamides as Inhibitors of Human Cytomegalovirus pUL89 Endonuclease. ChemMedChem 2022; 17:e202200334. [PMID: 35879245 PMCID: PMC9463105 DOI: 10.1002/cmdc.202200334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Indexed: 11/10/2022]
Abstract
Human cytomegalovirus (HCMV) replication requires a metal-dependent endonuclease at the C-terminus of pUL89 (pUL89-C) for viral genome packaging and cleavage. We have previously shown that pUL89-C can be pharmacologically inhibited with designed metal-chelating compounds. We report herein the synthesis of a few 8-hydroxy-1,6-naphthyridine subtypes, including 5-chloro (subtype 15), 5-aryl (subtype 16), and 5-amino (subtype 17) variants. Analogs were studied for the inhibition of pUL89-C in a biochemical endonuclease assay, a biophysical thermal shift assay (TSA), in silico molecular docking, and for the antiviral potential against HCMV in cell-based assays. These studies identified eight analogs of 8-hydroxy-1,6-naphthyridine-7-carboxamide subtypes for further characterization, most of which inhibited pUL89-C with single-digit μM IC50 values, and conferred antiviral activity in μM range. TSA and molecular modeling of selected analogs corroborate their binding to pUL89-C. Collectively, our biochemical, antiviral, biophysical and in silico data suggest that 8-hydroxy-1,6-naphthyridine-7-carboxamide subtypes can be used for designing inhibitors of HCMV pUL89-C.
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Affiliation(s)
- Eunkyung Jung
- University of Minnesota College of Pharmacy, Center for Drug Design, UNITED STATES
| | - Ryuichi Majima
- University of Minnesota College of Pharmacy, Center for Drug Design, UNITED STATES
| | - Tiffany C Edwards
- University of Minnesota College of Pharmacy, Center for Drug Design, UNITED STATES
| | - Ruben Soto-Acosta
- University of Minnesota College of Pharmacy, Center for Drug Design, UNITED STATES
| | - Robert J Geraghty
- University of Minnesota College of Pharmacy, Center for Drug Design, UNITED STATES
| | - Zhengqiang Wang
- University of Minnesota Twin Cities, Center for Drug Design, 516 Delaware St Se, 55455, Minneapolis, UNITED STATES
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26
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Wright LR, Wright DL, Weller SK. Viral Nucleases from Herpesviruses and Coronavirus in Recombination and Proofreading: Potential Targets for Antiviral Drug Discovery. Viruses 2022; 14:v14071557. [PMID: 35891537 PMCID: PMC9324378 DOI: 10.3390/v14071557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 02/05/2023] Open
Abstract
In this review, we explore recombination in two very different virus families that have become major threats to human health. The Herpesviridae are a large family of pathogenic double-stranded DNA viruses involved in a range of diseases affecting both people and animals. Coronaviridae are positive-strand RNA viruses (CoVs) that have also become major threats to global health and economic stability, especially in the last two decades. Despite many differences, such as the make-up of their genetic material (DNA vs. RNA) and overall mechanisms of genome replication, both human herpes viruses (HHVs) and CoVs have evolved to rely heavily on recombination for viral genome replication, adaptation to new hosts and evasion of host immune regulation. In this review, we will focus on the roles of three viral exonucleases: two HHV exonucleases (alkaline nuclease and PolExo) and one CoV exonuclease (ExoN). We will review the roles of these three nucleases in their respective life cycles and discuss the state of drug discovery efforts against these targets.
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Affiliation(s)
- Lee R. Wright
- Department of Pharmaceutical Sciences, University of Connecticut School of Pharmacy, Storrs, CT 06269, USA; (L.R.W.); (D.L.W.)
| | - Dennis L. Wright
- Department of Pharmaceutical Sciences, University of Connecticut School of Pharmacy, Storrs, CT 06269, USA; (L.R.W.); (D.L.W.)
| | - Sandra K. Weller
- Department of Molecular Biology and Biophysics, University of Connecticut School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA
- Correspondence: ; Tel.: +1-(860)-679-2310; Fax: +1-(860)-679-1239
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27
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He T, Edwards TC, Xie J, Aihara H, Geraghty RJ, Wang Z. 4,5-Dihydroxypyrimidine Methyl Carboxylates, Carboxylic Acids, and Carboxamides as Inhibitors of Human Cytomegalovirus pUL89 Endonuclease. J Med Chem 2022; 65:5830-5849. [PMID: 35377638 PMCID: PMC9441020 DOI: 10.1021/acs.jmedchem.2c00203] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human cytomegalovirus (HCMV) terminase complex entails a metal-dependent endonuclease at the C-terminus of pUL89 (pUL89-C). We report herein the design, synthesis, and characterization of dihydroxypyrimidine (DHP) acid (14), methyl ester (13), and amide (15) subtypes as inhibitors of HCMV pUL89-C. All analogs synthesized were tested in an endonuclease assay and a thermal shift assay (TSA) and subjected to molecular docking to predict binding affinity. Although analogs inhibiting pUL89-C in the sub-μM range were identified from all three subtypes, acids (14) showed better overall potency, substantially larger thermal shift, and considerably better docking scores than esters (13) and amides (15). In the cell-based antiviral assay, six analogs inhibited HCMV with moderate activities (EC50 = 14.4-22.8 μM). The acid subtype (14) showed good in vitro ADME properties, except for poor permeability. Overall, our data support the DHP acid subtype (14) as a valuable scaffold for developing antivirals targeting HCMV pUL89-C.
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Affiliation(s)
- Tianyu He
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Tiffany C Edwards
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jiashu Xie
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Robert J Geraghty
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
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28
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Senaweera S, Edwards TC, Kankanala J, Wang Y, Sahani RL, Xie J, Geraghty RJ, Wang Z. Discovery of N-benzyl hydroxypyridone carboxamides as a novel and potent antiviral chemotype against human cytomegalovirus (HCMV). Acta Pharm Sin B 2022; 12:1671-1684. [PMID: 35847513 PMCID: PMC9279720 DOI: 10.1016/j.apsb.2021.08.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/05/2021] [Accepted: 08/17/2021] [Indexed: 12/29/2022] Open
Abstract
Current drugs for treating human cytomegalovirus (HCMV) infections are limited by resistance and treatment-associated toxicities. In developing mechanistically novel HCMV antivirals, we discovered an N-benzyl hydroxypyridone carboxamide antiviral hit (8a) inhibiting HCMV in submicromolar range. We describe herein the structure–activity relationship (SAR) for 8a, and the characterization of potent analogs for cytotoxicity/cytostatic property, the preliminary mechanism of action, and the absorption, distribution, metabolism and excretion (ADME) properties. The SAR revealed a few pharmacophore features conferring optimal antiviral profile, including the 5-OH, the N-1 benzyl, at least one –CH2− in the linker, and a di-halogen substituted phenyl ring in the amide moiety. In the end, we identified numerous analogs with sub-micromolar antiviral potency and good selectivity index. The preliminary mechanism of action characterization used a pUL89-C biochemical endonuclease assay, a virus entry assay, a time-of-addition assay, and a compound withdrawal assay. ADME profiling measuring aqueous solubility, plasma and liver microsomal stability, and parallel artificial membrane permeability assay (PAMPA) permeability demonstrated largely favorable drug-like properties. Together, these studies validate the N-benzyl hydroxypyridone carboxamide as a viable chemotype for potent and mechanistically distinct antivirals against HCMV.
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29
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Liao Z, Oyama T, Kitagawa Y, Katayanagi K, Morikawa K, Oda M. Pivotal role of a conserved histidine in Escherichia coli ribonuclease HI as proposed by X-ray crystallography. Acta Crystallogr D Struct Biol 2022; 78:390-398. [PMID: 35234152 PMCID: PMC8900815 DOI: 10.1107/s2059798322000870] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/24/2022] [Indexed: 11/10/2022] Open
Abstract
The ribonuclease (RNase) H family of enzymes catalyze the specific cleavage of RNA strands of RNA/DNA hybrid duplexes and play an important role in DNA replication and repair. Since the first report of the crystal structure of RNase HI, its catalytic mechanisms, which require metal ions, have been discussed based on numerous structural and functional analyses, including X-ray crystallography. In contrast, the function of the conserved histidine residue (His124 in Escherichia coli) in the flexible loop around the active site remains poorly understood, although an important role was suggested by NMR analyses. Here, novel high-resolution X-ray crystal structures of E. coli RNase HI are described, with a particular focus on the interactions of divalent cations with His124 oriented towards the active site. The enzyme–Mg2+ complex contains two metal ions in the active site, one of which has previously been observed. The second ion lies alongside the first and binds to His124 in an octahedral coordination scheme. In the enzyme–Zn2+ complex a single metal ion was found to bind to the active site, showing a tetrahedral coordination geometry with the surrounding atoms, including His124. These results provide structural evidence that His124 plays a crucial role in the catalytic activity of RNase HI by interacting weakly and transiently with metal ions in the catalytic center.
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Abstract
The majority of drug discovery efforts against herpesviruses have focused on nucleoside analogs that target viral DNA polymerases, agents that are associated with dose-limiting toxicity and/or a narrow spectrum of activity. We are pursuing a strategy based on targeting two-metal ion-dependent (TMID) viral enzymes. This family of enzymes consists of structurally related proteins that share common active sites containing conserved carboxylates predicted to coordinate divalent cations essential for catalysis. Compounds that target TMID enzymes, such as HIV integrase and influenza endoribonuclease, have been successfully developed for clinical use. HIV integrase inhibitors have been reported to inhibit replication of herpes simplex virus (HSV) and other herpesviruses; however, the molecular targets of their antiviral activities have not been identified. We employed a candidate-based approach utilizing several two-metal-directed chemotypes and the potential viral TMID enzymatic targets in an effort to correlate target-based activity with antiviral potency. The panel of compounds tested included integrase inhibitors, the anti-influenza agent baloxavir, three natural products previously shown to exhibit anti-HSV activity, and two 8-hydroxyquinolines (8-HQs), AK-157 and AK-166, from our in-house program. The integrase inhibitors exhibited weak overall anti-HSV-1 activity, while the 8-HQs were shown to inhibit both HSV-1 and cytomegalovirus (CMV). Target-based analysis demonstrated that none of the antiviral compounds acted by inhibiting ICP8, contradicting previous reports. On the other hand, baloxavir inhibited the proofreading exonuclease of HSV polymerase, while AK-157 and AK-166 inhibited the alkaline exonuclease UL12. In addition, AK-157 also inhibited the catalytic activity of the HSV polymerase, which provides an opportunity to potentially develop dual-targeting agents against herpesviruses. IMPORTANCE Human herpesviruses (HHVs) establish lifelong latent infections, which undergo periodic reactivation and remain a major cause of morbidity and mortality, especially in immunocompromised individuals. Currently, HHV infections are treated primarily with agents that target viral DNA polymerase, including nucleoside analogs; however, long-term treatment can be complicated by the development of drug resistance. New therapies with novel modes of action would be important not only for the treatment of resistant viruses but also for use in combination therapy to reduce dose-limiting toxicities and potentially eliminate infection. Since many essential HHV proteins are well conserved, inhibitors of novel targets would ideally exhibit broad-spectrum activity against multiple HHVs.
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Leitner M, Etebari K, Asgari S. Transcriptional response of Wolbachia-transinfected Aedes aegypti mosquito cells to dengue virus at early stages of infection. J Gen Virol 2022; 103. [PMID: 35006065 PMCID: PMC8895618 DOI: 10.1099/jgv.0.001694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mosquito-borne flaviviruses are responsible for viral infections and represent a considerable public health burden. Aedes aegypti is the principal vector of dengue virus (DENV), therefore understanding the intrinsic virus-host interactions is vital, particularly in the presence of the endosymbiont Wolbachia, which blocks virus replication in mosquitoes. Here, we examined the transcriptional response of Wolbachia-transinfected Ae. aegypti Aag2 cells to DENV infection. We identified differentially expressed immune genes that play a key role in the activation of anti-viral defence such as the Toll and immune deficiency pathways. Further, genes encoding cytosine and N6-adenosine methyltransferases and SUMOylation, involved in post-transcriptional modifications, an antioxidant enzyme, and heat-shock response were up-regulated at the early stages of DENV infection and are reported here for the first time. Additionally, several long non-coding RNAs were among the differentially regulated genes. Our results provide insight into Wolbachia-transinfected Ae. aegypti's initial virus recognition and transcriptional response to DENV infection.
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Affiliation(s)
- Michael Leitner
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Kayvan Etebari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Sassan Asgari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Australia
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32
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Aguirre-Ramirez E, Velasco-Cuervo S, Toro-Perea N. Genomic Traces of the Fruit Fly Anastrepha obliqua Associated with Its Polyphagous Nature. INSECTS 2021; 12:1116. [PMID: 34940204 PMCID: PMC8704581 DOI: 10.3390/insects12121116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/24/2021] [Accepted: 11/27/2021] [Indexed: 12/23/2022]
Abstract
Anastrepha obliqua (Macquart) (Diptera: Tephritidae) is an important pest in the neotropical region. It is considered a polyphagous insect, meaning it infests plants of different taxonomic families and readily colonizes new host plants. The change to new hosts can lead to diversification and the formation of host races. Previous studies investigating the effect of host plants on population structure and selection in Anastrepha obliqua have focused on the use of data from the mitochondrial DNA sequence and microsatellite markers of nuclear DNA, and there are no analyses at the genomic level. To better understand this issue, we used a pooled restriction site-associated DNA sequencing (pooled RAD-seq) approach to assess genomic differentiation and population structure across sympatric populations of Anastrepha obliqua that infest three host plants-Spondias purpurea (red mombin), Mangifera indica (mango) of the family Anacardiaceae and Averrhoa carambola (carambola) of the family Oxalidaceae-in sympatric populations of the species Anastrepha obliqua of Inter-Andean Valley of the Cauca River in southwestern Colombia. Our results show genomic differentiation of populations from carambola compared to mango and red mombin populations, but the genetic structure was mainly established by geography rather than by the host plant. On the other hand, we identified 54 SNPs in 23 sequences significantly associated with the use of the host plant. Of these 23 sequences, we identified 17 candidate genes and nine protein families, of which four protein families are involved in the nutrition of these flies. Future studies should investigate the adaptive processes undergone by phytophagous insects in the Neotropics, using fruit flies as a model and state-of-the-art molecular tools.
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Affiliation(s)
- Elkin Aguirre-Ramirez
- Grupo de Estudios Ecogenéticos y Biología Molecular, Departamento de Biología, Universidad del Valle, Cali 760032, Colombia; (S.V.-C.); (N.T.-P.)
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33
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Ilina TV, Brosenitsch T, Sluis-Cremer N, Ishima R. Retroviral RNase H: Structure, mechanism, and inhibition. Enzymes 2021; 50:227-247. [PMID: 34861939 DOI: 10.1016/bs.enz.2021.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
All retroviruses encode the enzyme, reverse transcriptase (RT), which is involved in the conversion of the single-stranded viral RNA genome into double-stranded DNA. RT is a multifunctional enzyme and exhibits DNA polymerase and ribonuclease H (RNH) activities, both of which are essential to the reverse-transcription process. Despite the successful development of polymerase-targeting antiviral drugs over the last three decades, no bona fide inhibitor against the RNH activity of HIV-1 RT has progressed to clinical evaluation. In this review article, we describe the retroviral RNH function and inhibition, with primary consideration of the structural aspects of inhibition.
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Affiliation(s)
- Tatiana V Ilina
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Teresa Brosenitsch
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Nicolas Sluis-Cremer
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.
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34
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Handsel J, Matthews B, Knight NJ, Coles SJ. Translating the InChI: adapting neural machine translation to predict IUPAC names from a chemical identifier. J Cheminform 2021; 13:79. [PMID: 34620215 PMCID: PMC8496104 DOI: 10.1186/s13321-021-00535-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/20/2021] [Indexed: 11/10/2022] Open
Abstract
We present a sequence-to-sequence machine learning model for predicting the IUPAC name of a chemical from its standard International Chemical Identifier (InChI). The model uses two stacks of transformers in an encoder-decoder architecture, a setup similar to the neural networks used in state-of-the-art machine translation. Unlike neural machine translation, which usually tokenizes input and output into words or sub-words, our model processes the InChI and predicts the IUPAC name character by character. The model was trained on a dataset of 10 million InChI/IUPAC name pairs freely downloaded from the National Library of Medicine's online PubChem service. Training took seven days on a Tesla K80 GPU, and the model achieved a test set accuracy of 91%. The model performed particularly well on organics, with the exception of macrocycles, and was comparable to commercial IUPAC name generation software. The predictions were less accurate for inorganic and organometallic compounds. This can be explained by inherent limitations of standard InChI for representing inorganics, as well as low coverage in the training data.
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Affiliation(s)
- Jennifer Handsel
- Scientific Computing Department, Science and Technology Facilities Council, Didcot, OX11 0FA, UK.
| | - Brian Matthews
- Scientific Computing Department, Science and Technology Facilities Council, Didcot, OX11 0FA, UK
| | - Nicola J Knight
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Simon J Coles
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK
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Altae-Tran H, Kannan S, Demircioglu FE, Oshiro R, Nety SP, McKay LJ, Dlakić M, Inskeep WP, Makarova KS, Macrae RK, Koonin EV, Zhang F. The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases. Science 2021; 374:57-65. [PMID: 34591643 PMCID: PMC8929163 DOI: 10.1126/science.abj6856] [Citation(s) in RCA: 165] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
IscB proteins are putative nucleases encoded in a distinct family of IS200/IS605 transposons and are likely ancestors of the RNA-guided endonuclease Cas9, but the functions of IscB and its interactions with any RNA remain uncharacterized. Using evolutionary analysis, RNA sequencing, and biochemical experiments, we reconstructed the evolution of CRISPR-Cas9 systems from IS200/IS605 transposons. We found that IscB uses a single noncoding RNA for RNA-guided cleavage of double-stranded DNA and can be harnessed for genome editing in human cells. We also demonstrate the RNA-guided nuclease activity of TnpB, another IS200/IS605 transposon-encoded protein and the likely ancestor of Cas12 endonucleases. This work reveals a widespread class of transposon-encoded RNA-guided nucleases, which we name OMEGA (obligate mobile element–guided activity), with strong potential for developing as biotechnologies.
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Affiliation(s)
- Han Altae-Tran
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Soumya Kannan
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - F. Esra Demircioglu
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rachel Oshiro
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Suchita P. Nety
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Luke J. McKay
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA
- Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717
| | - Mensur Dlakić
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - William P. Inskeep
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA
- Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Rhiannon K. Macrae
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Feng Zhang
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Gao J, Zhang P, Li X, Wu W, Wei H, Zhang W. Toward an understanding of the detection and function of R-loops in plants. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6110-6122. [PMID: 34115858 DOI: 10.1093/jxb/erab280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 06/10/2021] [Indexed: 06/12/2023]
Abstract
Although lagging behind studies in humans and other mammals, studies of R-loops in plants have recently entered an exciting stage in which the roles of R-loops in gene expression, genome stability, epigenomic signatures, and plant development and stress responses are being elucidated. Here, we review the strengths and weaknesses of existing methodologies, which were largely developed for R-loop studies in mammals, and then discuss the potential challenges of applying these methodologies to R-loop studies in plants. We then focus on recent advances in the functional characterization of R-loops in Arabidopsis thaliana and rice. Recent studies in plants indicate that there are coordinated relationships between R-loops and gene expression, and between R-loops and epigenomic signatures that depend, in part, on the types of R-loops involved. Finally, we discuss the emerging roles of R-loops in plants and directions for future research.
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Affiliation(s)
- Jingjing Gao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Pengyue Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Xinxu Li
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Wenqi Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
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An efficient metatranscriptomic approach for capturing RNA virome and its application to SARS-CoV-2. J Genet Genomics 2021; 48:860-862. [PMID: 34438048 PMCID: PMC8380547 DOI: 10.1016/j.jgg.2021.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/09/2021] [Accepted: 08/16/2021] [Indexed: 11/23/2022]
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Leitner M, Bishop C, Asgari S. Transcriptional Response of Wolbachia to Dengue Virus Infection in Cells of the Mosquito Aedes aegypti. mSphere 2021; 6:e0043321. [PMID: 34190587 PMCID: PMC8265661 DOI: 10.1128/msphere.00433-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/07/2021] [Indexed: 11/20/2022] Open
Abstract
Aedes aegypti transmits one of the most significant mosquito-borne viruses, dengue virus (DENV). The absence of effective vaccines and clinical treatments and the emergence of insecticide resistance in A. aegypti necessitate novel vector control strategies. A new approach uses the endosymbiotic bacterium Wolbachia pipientis to reduce the spread of arboviruses. However, the Wolbachia-mediated antiviral mechanism is not well understood. To shed light on this mechanism, we investigated an unexplored aspect of Wolbachia-virus-mosquito interaction. We used RNA sequencing to examine the transcriptional response of Wolbachia to DENV infection in A. aegypti Aag2 cells transinfected with the wAlbB strain of Wolbachia. Our results suggest that genes encoding an endoribonuclease (RNase HI), a regulator of sigma 70-dependent gene transcription (6S RNA), essential cellular, transmembrane, and stress response functions and primary type I and IV secretion systems were upregulated, while a number of transport and binding proteins of Wolbachia, ribosome structure, and elongation factor-associated genes were downregulated due to DENV infection. Furthermore, bacterial retrotransposon, transposable, and phage-related elements were found among the up- and downregulated genes. We show that Wolbachia elicits a transcriptional response to virus infection and identify differentially expressed Wolbachia genes mostly at the early stages of virus infection. These findings highlight Wolbachia's ability to alter its gene expression in response to DENV infection of the host cell. IMPORTANCE Aedes aegypti is a vector of several pathogenic viruses, including dengue, Zika, chikungunya, and yellow fever viruses, which are of importance to human health. Wolbachia is an endosymbiotic bacterium currently used in transinfected mosquitoes to suppress replication and transmission of dengue viruses. However, the mechanism of Wolbachia-mediated virus inhibition is not fully understood. While several studies have shown mosquitoes' transcriptional responses to dengue virus infection, none have investigated these responses in Wolbachia, which may provide clues to the inhibition mechanism. Our results suggest changes in the expression of a number of functionally important Wolbachia genes upon dengue virus infection, including those involved in stress responses, providing insights into the endosymbiont's reaction to virus infection.
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Affiliation(s)
- Michael Leitner
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Cameron Bishop
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Sassan Asgari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Australia
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Dürr SL, Bohuszewicz O, Berta D, Suardiaz R, Jambrina PG, Peter C, Shao Y, Rosta E. The Role of Conserved Residues in the DEDDh Motif: the Proton-Transfer Mechanism of HIV-1 RNase H. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01493] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Simon L. Dürr
- Department of Chemistry, King’s College London, London SE1 1DB, U.K
- Department of Chemistry, University of Konstanz, Konstanz 78457, Germany
| | - Olga Bohuszewicz
- Department of Chemistry, King’s College London, London SE1 1DB, U.K
| | - Dénes Berta
- Department of Physics and Astronomy, University College London; London WC1E 6BT, U.K
| | - Reynier Suardiaz
- Department of Chemistry, King’s College London, London SE1 1DB, U.K
| | | | - Christine Peter
- Department of Chemistry, University of Konstanz, Konstanz 78457, Germany
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019-5251, United States
| | - Edina Rosta
- Department of Chemistry, King’s College London, London SE1 1DB, U.K
- Department of Physics and Astronomy, University College London; London WC1E 6BT, U.K
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Metal binding 6-arylthio-3-hydroxypyrimidine-2,4-diones inhibited human cytomegalovirus by targeting the pUL89 endonuclease of the terminase complex. Eur J Med Chem 2021; 222:113640. [PMID: 34147908 DOI: 10.1016/j.ejmech.2021.113640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/18/2022]
Abstract
The genome packaging of human cytomegalovirus (HCMV) requires a divalent metal-dependent endonuclease activity localized to the C-terminus of pUL89 (pUL89-C), which is reminiscent of RNase H-like enzymes in active site structure and catalytic mechanism. Our previous work has shown that metal-binding small molecules can effectively inhibit pUL89-C while conferring significant antiviral activities. In this report we generated a collection of 43 metal-binding small molecules by repurposing analogs of the 6-arylthio-3-hydroxypyrimidine-2,4-dione chemotype previously synthesized for targeting HIV-1 RNase H, and by chemically synthesizing new N-1 analogs. The analogs were subjected to two parallel screening assays: the pUL89-C biochemical assay and the HCMV antiviral assay. Compounds with significant inhibition from each assay were further tested in a dose-response fashion. Single dose cell viability and PAMPA cell permeability were also conducted and considered in selecting compounds for the dose-response antiviral testing. These assays identified a few analogs displaying low μM inhibition against pUL89-C in the biochemical assay and HCMV replication in the antiviral assay. The target engagement was further evaluated via a thermal shift assay using recombinant pUL89-C and molecular docking. Overall, our current work identified novel inhibitors of pUL89-C with significant antiviral activities and further supports targeting pUL89-C with metal-binding small molecules as an antiviral approach against HCMV.
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Sharma V, Thakore P, Majumdar S. THAP9 Transposase Cleaves DNA via Conserved Acidic Residues in an RNaseH-Like Domain. Cells 2021; 10:cells10061351. [PMID: 34072453 PMCID: PMC8230255 DOI: 10.3390/cells10061351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
The catalytic domain of most 'cut and paste' DNA transposases have the canonical RNase-H fold, which is also shared by other polynucleotidyl transferases such as the retroviral integrases and the RAG1 subunit of V(D)J recombinase. The RNase-H fold is a mixture of beta sheets and alpha helices with three acidic residues (Asp, Asp, Glu/Asp-DDE/D) that are involved in the metal-mediated cleavage and subsequent integration of DNA. Human THAP9 (hTHAP9), homologous to the well-studied Drosophila P-element transposase (DmTNP), is an active DNA transposase that, although domesticated, still retains the catalytic activity to mobilize transposons. In this study we have modeled the structure of hTHAP9 using the recently available cryo-EM structure of DmTNP as a template to identify an RNase-H like fold along with important acidic residues in its catalytic domain. Site-directed mutagenesis of the predicted catalytic residues followed by screening for DNA excision and integration activity has led to the identification of candidate Ds and Es in the RNaseH fold that may be a part of the catalytic triad in hTHAP9. This study has helped widen our knowledge about the catalytic activity of a functionally uncharacterized transposon-derived gene in the human genome.
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digIS: towards detecting distant and putative novel insertion sequence elements in prokaryotic genomes. BMC Bioinformatics 2021; 22:258. [PMID: 34016050 PMCID: PMC8147514 DOI: 10.1186/s12859-021-04177-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/09/2021] [Indexed: 12/02/2022] Open
Abstract
Background The insertion sequence elements (IS elements) represent the smallest and the most abundant mobile elements in prokaryotic genomes. It has been shown that they play a significant role in genome organization and evolution. To better understand their function in the host genome, it is desirable to have an effective detection and annotation tool. This need becomes even more crucial when considering rapid-growing genomic and metagenomic data. The existing tools for IS elements detection and annotation are usually based on comparing sequence similarity with a database of known IS families. Thus, they have limited ability to discover distant and putative novel IS elements. Results In this paper, we present digIS, a software tool based on profile hidden Markov models assembled from catalytic domains of transposases. It shows a very good performance in detecting known IS elements when tested on datasets with manually curated annotation. The main contribution of digIS is in its ability to detect distant and putative novel IS elements while maintaining a moderate level of false positives. In this category it outperforms existing tools, especially when tested on large datasets of archaeal and bacterial genomes. Conclusion We provide digIS, a software tool using a novel approach based on manually curated profile hidden Markov models, which is able to detect distant and putative novel IS elements. Although digIS can find known IS elements as well, we expect it to be used primarily by scientists interested in finding novel IS elements. The tool is available at https://github.com/janka2012/digIS. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04177-6.
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Lee MR, Kim JC, Park SE, Lee SJ, Kim WJ, Lee DH, Kim JS. Interactive Gene Expression Between Metarhizium anisopliae JEF-290 and Longhorned Tick Haemaphysalis longicornis at Early Stage of Infection. Front Physiol 2021; 12:643389. [PMID: 34093222 PMCID: PMC8170561 DOI: 10.3389/fphys.2021.643389] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/22/2021] [Indexed: 12/12/2022] Open
Abstract
The longhorned tick, Haemaphysalis longicornis (Acari: Ixodidae), is a hard tick and a vector for severe fever with thrombocytopenia syndrome (SFTS) virus. The number of patients infected with SFTS is rapidly increasing. Recently, the invertebrate pathogen Metarhizium anisopliae JEF-290 was reported to be useful to control the tick as an alternative to chemical acaricides, which are not easily applicable in human living areas where the tick is widely spread. In this study, we analyzed how the tick and the fungal pathogen interact at the transcriptional level. Field-collected tick nymphs were treated with JEF-290 conidia at 1 × 108 conidia/ml. In the early stage of infection with 2.5% mortality, the infected ticks were subjected to RNA sequencing, and non-infected ticks and fungal masses served as controls. Fungus and tick genes were mostly up-regulated at the early stage of infection. In the gene set enrichment analysis of the infecting fungus, catabolic processes that included lipids, phospholipids, and detoxification processes, the response to oxidative stress, and toxic substances were significantly up-regulated. In this fungal up-regulation, various lipase, antioxidant enzyme, and hydrolase genes were highly transcribed. The gene set enrichment analysis of the infected tick showed that many peptide synthesis processes including translation, peptide metabolism, ribonucleotide metabolism, and energy production processes that included ATP generation and ADP metabolism were significantly up-regulated. Structurally, mitochondria and ribosome subunit genes in ticks were highly transcribed to upregulate these processes. Together these results indicate that JEF-290 initiates process that infects the tick while the tick actively defends against the fungal attack. This work provides background to improve our understanding of the early stage of fungal infection in longhorned tick.
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Affiliation(s)
- Mi Rong Lee
- Department of Agricultural Biology, College of Agriculture and Life Sciences, Jeonbuk National University, Jeonju, South Korea
| | - Jong Cheol Kim
- Department of Agricultural Biology, College of Agriculture and Life Sciences, Jeonbuk National University, Jeonju, South Korea
| | - So Eun Park
- Department of Agricultural Biology, College of Agriculture and Life Sciences, Jeonbuk National University, Jeonju, South Korea
| | - Se Jin Lee
- Department of Agricultural Biology, College of Agriculture and Life Sciences, Jeonbuk National University, Jeonju, South Korea
| | - Woo Jin Kim
- Department of Agricultural Biology, College of Agriculture and Life Sciences, Jeonbuk National University, Jeonju, South Korea
| | - Doo-Hyung Lee
- Department of Life Sciences, College of Bionano, Gachon University, Seongnam, South Korea
| | - Jae Su Kim
- Department of Agricultural Biology, College of Agriculture and Life Sciences, Jeonbuk National University, Jeonju, South Korea.,Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, South Korea
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Thakur M, Mohan D, Singh AK, Agarwal A, Gopal B, Muniyappa K. Novel insights into ATP-Stimulated Cleavage of branched DNA and RNA Substrates through Structure-Guided Studies of the Holliday Junction Resolvase RuvX. J Mol Biol 2021; 433:167014. [PMID: 33933468 DOI: 10.1016/j.jmb.2021.167014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/05/2021] [Accepted: 04/23/2021] [Indexed: 11/18/2022]
Abstract
Much of our understanding of the homologous recombination (HR) machinery hinges on studies using Escherichia coli as a model organism. Interestingly enough, studies on the HR machinery in different bacterial species casts doubt on the universality of the E. coli paradigm. The human pathogen Mycobacterium tuberculosis encodes two Holliday junction (HJ)-resolvase paralogues, namely RuvC and RuvX; however, insights into their structural features and functional relevance is still limited. Here, we report on structure-guided functional studies of the M. tuberculosis RuvX HJ resolvase (MtRuvX). The crystalline MtRuvX is a dimer in the asymmetric unit, and each monomer has a RNAse H fold vis-à-vis RuvC-like nucleases. Interestingly, MtRuvX also contains some unique features, including the residues essential for ATP binding/coordination of Mg2+ ions. Indeed, MtRuvX exhibited an intrinsic, robust ATPase activity, which was further accentuated by DNA cofactors. Structure-guided substitutions of single residues at the ATP binding/Mg2+coordination sites while markedly attenuating the ATPase activity completely abrogated HJ cleavage, indicating an unanticipated relationship between ATP hydrolysis and DNA cleavage. However, the affinity of ATPase-deficient mutants for the HJ was not impaired. Contrary to RuvC, MtRuvX exhibits relaxed substrate specificity, cleaving a variety of branched DNA/RNA substrates. Notably, ATP hydrolysis plays a regulatory role, rendering MtRuvX from a canonical HJ resolvase to a DNA/RNA non-sequence specific endonuclease, indicating a link between HJ resolvase and nucleic acid metabolism. These findings provide novel insights into the structure and dual-functional activities of MtRuvX, and suggest that it may play an important role in DNA/RNA metabolism.
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Affiliation(s)
- Manoj Thakur
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Disha Mohan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Ankur Kumar Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Ankit Agarwal
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | | | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India.
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Nilavar NM, Raghavan SC. HIV integrase inhibitors that inhibit strand transfer interact with RAG1 and hamper its activities. Int Immunopharmacol 2021; 95:107515. [PMID: 33735713 DOI: 10.1016/j.intimp.2021.107515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/08/2021] [Accepted: 02/15/2021] [Indexed: 12/16/2022]
Abstract
Multiple steps of the retroviral infection process have been targeted over the years to develop therapeutic approaches, starting from the entry of the virus into the cell till the viral DNA integration to host genome. Inhibitors against the Human Immunodeficiency Virus (HIV) integrase is the newest among the therapies employed against HIV. Recombination activating gene 1 (RAG1) is an integral protein involved in the generation of diversity of antibodies and T-cell receptors and is one of the partners of the RAG complex. Studies have shown structural and functional similarities between the HIV integrase and RAG1. Recently, we and others have shown that some of the integrase inhibitors can interfere with RAG binding and cleavage, hindering its physiological functions. This mini review focuses on the HIV integrase, integrase inhibitors and their effect on RAG activities.
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Affiliation(s)
- Namrata M Nilavar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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Zhao C, Sahni S. Linear space string correction algorithm using the Damerau-Levenshtein distance. BMC Bioinformatics 2020; 21:4. [PMID: 33297940 PMCID: PMC7724867 DOI: 10.1186/s12859-019-3184-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 10/30/2019] [Indexed: 11/16/2022] Open
Abstract
Background The Damerau-Levenshtein (DL) distance metric has been widely used in the biological science. It tries to identify the similar region of DNA,RNA and protein sequences by transforming one sequence to the another using the substitution, insertion, deletion and transposition operations. Lowrance and Wagner have developed an O(mn) time O(mn) space algorithm to find the minimum cost edit sequence between strings of length m and n, respectively. In our previous research, we have developed algorithms that run in O(mn) time using only O(s∗min{m,n}+m+n) space, where s is the size of the alphabet comprising the strings, to compute the DL distance as well as the corresponding edit sequence. These are so far the fastest and most space efficient algorithms. In this paper, we focus on the development of algorithms whose asymptotic space complexity is linear. Results We develop linear space algorithms to compute the Damerau-Levenshtein (DL) distance between two strings and determine the optimal trace (corresponding edit operations.)Extensive experiments conducted on three computational platforms–Xeon E5 2603, I7-x980 and Xeon E5 2695–show that, our algorithms, in addition to using less space, are much faster than earlier algorithms. Conclusion Besides using less space than the previously known algorithms,significant run-time improvement was seen for our new algorithms on all three of our experimental platforms. On all platforms, our linear-space cache-efficient algorithms reduced run time by as much as 56.4% and 57.4% in respect to compute the DL distance and an optimal edit sequences compared to previous algorithms. Our multi-core algorithms reduced the run time by up to 59.3% compared to the best previously known multi-core algorithms.
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Affiliation(s)
- Chunchun Zhao
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, 32611, FL, USA.
| | - Sartaj Sahni
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, 32611, FL, USA
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An RNA Repair Operon Regulated by Damaged tRNAs. Cell Rep 2020; 33:108527. [PMID: 33357439 PMCID: PMC7790460 DOI: 10.1016/j.celrep.2020.108527] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 11/03/2020] [Accepted: 11/23/2020] [Indexed: 12/11/2022] Open
Abstract
Many bacteria contain an RNA repair operon, encoding the RtcB RNA ligase and the RtcA RNA cyclase, that is regulated by the RtcR transcriptional activator. Although RtcR contains a divergent version of the CARF (CRISPR-associated Rossman fold) oligonucleotide-binding regulatory domain, both the specific signal that regulates operon expression and the substrates of the encoded enzymes are unknown. We report that tRNA fragments activate operon expression. Using a genetic screen in Salmonella enterica serovar Typhimurium, we find that the operon is expressed in the presence of mutations that cause tRNA fragments to accumulate. RtcA, which converts RNA phosphate ends to 2′, 3′-cyclic phosphate, is also required. Operon expression and tRNA fragment accumulation also occur upon DNA damage. The CARF domain binds 5′ tRNA fragments ending in cyclic phosphate, and RtcR oligomerizes upon binding these ligands, a prerequisite for operon activation. Our studies reveal a signaling pathway involving broken tRNAs and implicate the operon in tRNA repair. Hughes et al. demonstrate that a bacterial RNA repair operon, containing the RtcB RNA ligase and the RtcA RNA cyclase, is regulated by binding of 5′ tRNA halves ending in 2′, 3′-cyclic phosphate to the RtcR transcriptional activator. These studies show how tRNA fragments can regulate bacterial gene expression.
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Layton E, Fairhurst AM, Griffiths-Jones S, Grencis RK, Roberts IS. Regulatory RNAs: A Universal Language for Inter-Domain Communication. Int J Mol Sci 2020; 21:E8919. [PMID: 33255483 PMCID: PMC7727864 DOI: 10.3390/ijms21238919] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/16/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022] Open
Abstract
In eukaryotes, microRNAs (miRNAs) have roles in development, homeostasis, disease and the immune response. Recent work has shown that plant and mammalian miRNAs also mediate cross-kingdom and cross-domain communications. However, these studies remain controversial and are lacking critical mechanistic explanations. Bacteria do not produce miRNAs themselves, and therefore it is unclear how these eukaryotic RNA molecules could function in the bacterial recipient. In this review, we compare and contrast the biogenesis and functions of regulatory RNAs in eukaryotes and bacteria. As a result, we discovered several conserved features and homologous components in these distinct pathways. These findings enabled us to propose novel mechanisms to explain how eukaryotic miRNAs could function in bacteria. Further understanding in this area is necessary to validate the findings of existing studies and could facilitate the use of miRNAs as novel tools for the directed remodelling of the human microbiota.
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Affiliation(s)
- Emma Layton
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; (E.L.); (S.G.-J.)
| | - Anna-Marie Fairhurst
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, Singapore 138673, Singapore;
| | - Sam Griffiths-Jones
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; (E.L.); (S.G.-J.)
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Richard K. Grencis
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; (E.L.); (S.G.-J.)
| | - Ian S. Roberts
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; (E.L.); (S.G.-J.)
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Durnaoglu S, Kim HS, Ahnn J, Lee SK. Human Endogenous Retrovirus K (HERV-K) can drive gene expression as a promoter in Caenorhabditis elegans. BMB Rep 2020; 53:521-526. [PMID: 32867919 PMCID: PMC7607151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/05/2020] [Accepted: 08/20/2020] [Indexed: 08/04/2024] Open
Abstract
Endogenous retroviruses (ERVs) are retrotransposons present in various metazoan genomes and have been implicated in metazoan evolution as well as in nematodes and humans. The long terminal repeat (LTR) retrotransposons contain several regulatory sequences including promoters and enhancers that regulate endogenous gene expression and thereby control organismal development and response to environmental change. ERVs including the LTR retrotransposons constitute 8% of the human genome and less than 0.6% of the Caenorhabditis elegans (C. elegans) genome, a nematode genetic model system. To investigate the evolutionarily conserved mechanism behind the transcriptional activity of retrotransposons, we generated a transgenic worm model driving green fluorescent protein (GFP) expression using Human endogenous retroviruses (HERV)-K LTR as a promoter. The promoter activity of HERV-K LTR was robust and fluorescence was observed in various tissues throughout the developmental process. Interestingly, persistent GFP expression was specifically detected in the adult vulva muscle. Using deletion constructs, we found that the region from positions 675 to 868 containing the TATA box was necessary for promoter activity driving gene expression in the vulva. Interestingly, we found that the promoter activity of the LTR was dependent on che-1 transcription factor, a sensory neuron driver, and lin-15b, a negative regulator of RNAi and germline gene expression. These results suggest evolutionary conservation of the LTR retrotransposon activity in transcriptional regulation as well as the possibility of che-1 function in non-neuronal tissues. [BMB Reports 2020; 53(10): 521-526].
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Affiliation(s)
- Serpen Durnaoglu
- Department of Life Science, Busan 46241, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Korea
| | - Joohong Ahnn
- Department of Life Science, Busan 46241, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Sun-Kyung Lee
- Department of Life Science, Busan 46241, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
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50
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Durnaoglu S, Kim HS, Ahnn J, Lee SK. Human Endogenous Retrovirus K (HERV-K) can drive gene expression as a promoter in Caenorhabditis elegans. BMB Rep 2020. [PMID: 32867919 PMCID: PMC7607151 DOI: 10.5483/bmbrep.2020.53.10.150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Endogenous retroviruses (ERVs) are retrotransposons present in various metazoan genomes and have been implicated in metazoan evolution as well as in nematodes and humans. The long terminal repeat (LTR) retrotransposons contain several regulatory sequences including promoters and enhancers that regulate endogenous gene expression and thereby control organismal development and response to environmental change. ERVs including the LTR retrotransposons constitute 8% of the human genome and less than 0.6% of the Caenorhabditis elegans (C.elegans) genome, a nematode genetic model system. To investigate the evolutionarily conserved mechanism behind the transcriptional activity of retrotransposons, we generated a transgenic worm model driving green fluorescent protein (GFP) expression using Human endogenous retroviruses (HERV)-K LTR as a promoter. The promoter activity of HERV-K LTR was robust and fluorescence was observed in various tissues throughout the developmental process. Interestingly, persistent GFP expression was specifically detected in the adult vulva muscle. Using deletion constructs, we found that the region from positions 675 to 868 containing the TATA box was necessary for promoter activity driving gene expression in the vulva. Interestingly, we found that the promoter activity of the LTR was dependent on che-1 transcription factor, a sensory neuron driver, and lin-15b, a negative regulator of RNAi and germline gene expression. These results suggest evolutionary conservation of the LTR retrotransposon activity in transcriptional regulation as well as the possibility of che-1 function in non-neuronal tissues.
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Affiliation(s)
- Serpen Durnaoglu
- Department of Life Science, Seoul 04763, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Korea
| | - Joohong Ahnn
- Department of Life Science, Seoul 04763, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Sun-Kyung Lee
- Department of Life Science, Seoul 04763, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
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