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Glukhov A, Marchenkov V, Dzhus U, Krutilina A, Selikhanov G, Gabdulkhakov A. Bacteriophage T5 dUTPase: Combination of Common Enzymatic and Novel Functions. Int J Mol Sci 2024; 25:892. [PMID: 38255966 PMCID: PMC10815766 DOI: 10.3390/ijms25020892] [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: 11/16/2023] [Revised: 12/26/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
The main function of dUTPases is to regulate the cellular levels of dUTP and dTTP, thereby playing a crucial role in DNA repair mechanisms. Despite the fact that mutant organisms with obliterated dUTPase enzymatic activity remain viable, it is not possible to completely knock out the dut gene due to the lethal consequences of such a mutation for the organism. As a result, it is considered that this class of enzymes performs an additional function that is essential for the organism's survival. In this study, we provide evidence that the dUTPase of bacteriophage T5 fulfills a supplemental function, in addition to its canonical role. We determined the crystal structure of bacteriophage T5 dUTPase with a resolution of 2.0 Å, and we discovered a distinct short loop consisting of six amino acid residues, representing a unique structural feature specific to the T5-like phages dUTPases. The removal of this element did not affect the overall structure of the homotrimer, but it had significant effects on the development of the phage. Furthermore, it was shown that the enzymatic function and the novel function of the bacteriophage T5 dUTPase are unrelated and independent from each other.
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Affiliation(s)
- Anatoly Glukhov
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (A.G.); (V.M.); (U.D.); (G.S.)
| | - Victor Marchenkov
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (A.G.); (V.M.); (U.D.); (G.S.)
| | - Ulyana Dzhus
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (A.G.); (V.M.); (U.D.); (G.S.)
| | - Antonina Krutilina
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (A.G.); (V.M.); (U.D.); (G.S.)
| | - Georgii Selikhanov
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (A.G.); (V.M.); (U.D.); (G.S.)
- International Institute “Solution Chemistry of Advanced Materials and Technologies”, ITMO University, 191002 St. Petersburg, Russia
- Almetyevsk State Petroleum Institute, 423450 Almetyevsk, Russia
| | - Azat Gabdulkhakov
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (A.G.); (V.M.); (U.D.); (G.S.)
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Structural basis of staphylococcal Stl inhibition on a eukaryotic dUTPase. Int J Biol Macromol 2021; 184:821-830. [PMID: 34171258 DOI: 10.1016/j.ijbiomac.2021.06.107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 11/22/2022]
Abstract
dUTPases are key enzymes in all life kingdoms. A staphylococcal repressor protein (Stl) inhibited dUTPases from multiple species to various extents. Understanding the molecular basis underlying the inhibition differences is crucial to develop effective proteinaceous inhibitors of dUTPases. Herein, we report the complex structure of Stl N-terminal domain (StlN-ter) and Litopenaeus vannamei dUTPase domain (lvDUT65-210). Stl inhibited lvDUT65-210 through its N-terminal domain. The lvDUT65-210-StlN-ter complex structure revealed a heterohexamer encompassing three StlN-ter monomers bound to one lvDUT65-210 trimer, generating two types of Stl-dUTPase interfaces. Interface I is formed by Stl interaction with the lvDUT65-210 active-site region that is contributed by motifs I-IV from its two subunits; interface II results from Stl binding to the C-terminal motif V of the third lvDUT65-210 subunit. Structural comparison revealed both conserved features and obvious differences in Stl-dUTPase interaction patterns, giving clues about the inhibition differences of Stl on dUTPases. Noticeably, interface II is only observed in lvDUT65-210-StlN-ter. The Stl-interacting residues of lvDUT65-210 are conserved in other eukaryotic dUTPases, particularly human dUTPase. Altogether, our study presents the first structural model of Stl interaction with eukaryotic dUTPase, contributing to a more complete view of Stl inhibition and facilitating the development of proteinaceous inhibitor for eukaryotic dUTPases.
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Cheng J, Li X. Development and Application of Activity-based Fluorescent Probes for High-Throughput Screening. Curr Med Chem 2021; 29:1739-1756. [PMID: 34036907 DOI: 10.2174/0929867328666210525141728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 11/22/2022]
Abstract
High-throughput screening facilitates the rapid identification of novel hit compounds; however, it remains challenging to design effective high-throughput assays, partially due to the difficulty of achieving sensitivity in the assay techniques. Among the various analytical methods that are used, fluorescence-based assays dominate owing to their high sensitivity and ease of operation. Recent advances in activity-based sensing/imaging have further expanded the availability of fluorescent probes as monitors for high-throughput screening of result outputs. In this study, we have reviewed various activity-based fluorescent probes used in high-throughput screening assays, emphasizing their structure-related working mechanisms. Moreover, we have explored the possibility of the development of additional and better probes to boost hit identification and drug development against various targets.
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Affiliation(s)
- Juan Cheng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xin Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
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4
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Weng GX, Ling T, Hou W, Li SN, Chen T, Zhang Z, Wang DD, Xu LG. Mitochondrial DUT-M potentiates RLR-mediated antiviral signaling by enhancing VISA and TRAF2 association. Mol Immunol 2021; 132:117-125. [PMID: 33582548 DOI: 10.1016/j.molimm.2021.01.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/09/2021] [Accepted: 01/19/2021] [Indexed: 11/19/2022]
Abstract
Upon recognition of intracytoplasmic viral RNA, activated RIG-I is recruited to the mitochondrion-located adaptor protein VISA (also known as MAVS, CARDIF, and IPS-1). VISA then acts as a central signaling platform for linking RIG-I and downstream signaling components, such as TRAF2, 5, and 6, TBK1, and IKK, leading to activation of the kinases TBK1 and IKK. These activated kinases further phosphorylate the transcription factors IRF3/7 and NF-κB, leading to the induction of downstream antiviral genes. Here, we report a mitochondrial isoform, deoxyuridine triphosphate nucleotidohydrolase (dUTPase), DUT-M, as a positive regulator in RLR-VISA-mediated antiviral signaling. DUT-M interacts with VISA and RIG-I to facilitate the assembly of the VISA-TRAF2 complex and to augment the polyubiquitination of TRAF2, leading to potentiated activation of IRF3 dimerization and phosphorylation of P65, and enhanced VISA-mediated innate immune response. RLR-VISA-mediated IRF3 dimerization and P65 phosphorylation, were inhibited in DUT-knockdown and DUT-deficient 293 cells. Thus, DUT-M is a positive regulator of the RIG-I-VISA-mediated innate immune response to RNA viruses.
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Affiliation(s)
- Guang-Xiu Weng
- Key Laboratory of Functional Small Organic Molecules, Ministry of Education and College of Life Science, Jiangxi Normal University, Nanchang, Jiangxi, 330022, China
| | - Ting Ling
- Key Laboratory of Functional Small Organic Molecules, Ministry of Education and College of Life Science, Jiangxi Normal University, Nanchang, Jiangxi, 330022, China
| | - Wen Hou
- Key Laboratory of Functional Small Organic Molecules, Ministry of Education and College of Life Science, Jiangxi Normal University, Nanchang, Jiangxi, 330022, China
| | - Sheng-Na Li
- Key Laboratory of Functional Small Organic Molecules, Ministry of Education and College of Life Science, Jiangxi Normal University, Nanchang, Jiangxi, 330022, China
| | - Tian Chen
- Key Laboratory of Functional Small Organic Molecules, Ministry of Education and College of Life Science, Jiangxi Normal University, Nanchang, Jiangxi, 330022, China
| | - Zhi Zhang
- Key Laboratory of Functional Small Organic Molecules, Ministry of Education and College of Life Science, Jiangxi Normal University, Nanchang, Jiangxi, 330022, China
| | - Dan-Dan Wang
- Key Laboratory of Functional Small Organic Molecules, Ministry of Education and College of Life Science, Jiangxi Normal University, Nanchang, Jiangxi, 330022, China
| | - Liang-Guo Xu
- Key Laboratory of Functional Small Organic Molecules, Ministry of Education and College of Life Science, Jiangxi Normal University, Nanchang, Jiangxi, 330022, China.
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Abstract
African swine fever virus (ASFV), an Asfivirus affecting pigs and wild boars with up to 100% case fatality rate, is currently rampaging throughout China and some other countries in Asia. There is an urgent need to develop therapeutic and preventive reagents against the virus. Our crystallographic and biochemical studies reveal that ASFV E165R is a member of trimeric dUTP nucleotidohydrolase (dUTPase) family that catalyzes the hydrolysis of dUTP into dUMP. Our apo-E165R and E165R-dUMP structures reveal the constitutive residues and the configuration of the active center of this enzyme in rich detail and give evidence that the active center of E165R is very similar to that of dUTPases from Plasmodium falciparum and Mycobacterium tuberculosis, which have already been used as targets for designing drugs. Therefore, our high-resolution structures of E165R provide useful structural information for chemotherapeutic drug design. E165R, a highly specific dUTP nucleotidohydrolase (dUTPase) encoded by the African swine fever virus (ASFV) genome, is required for productive replication of ASFV in swine macrophages. Here, we solved the high-resolution crystal structures of E165R in its apo state and in complex with its product dUMP. Structural analysis explicitly defined the architecture of the active site of the enzyme as well as the interaction between the active site and the dUMP ligand. By comparing the ASFV E165R structure with dUTPase structures from other species, we found that the active site of E165R is highly similar to those of dUTPases from Mycobacterium tuberculosis and Plasmodium falciparum, against which small-molecule chemicals have been developed, which could be the potential drug or lead compound candidates for ASFV. Our results provide important basis for anti-ASFV drug design by targeting E165R.
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Abstract
ABSTRACT
Pathogenicity islands are members of a vast collection of genomic islands that encode important virulence, antibiotic resistance and other accessory functions and have a critical role in bacterial gene transfer.
Staphylococcus aureus
is host to a large family of such islands, known as SaPIs, which encode super antigen and other virulence determinants, are mobilized by helper phages and transferred at extremely high frequencies. They benefit their host cells by interfering with phage predation and enhancing horizontal gene transfer. This chapter describes their life cycle, the bases of their phage interference mechanisms, their transfer system and their conversion to antibacterial agents for treatment ofstaphylococcal infections.
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Cui J, Gizzi A, Stivers JT. Deoxyuridine in DNA has an inhibitory and promutagenic effect on RNA transcription by diverse RNA polymerases. Nucleic Acids Res 2019; 47:4153-4168. [PMID: 30892639 PMCID: PMC6486633 DOI: 10.1093/nar/gkz183] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/04/2019] [Accepted: 03/09/2019] [Indexed: 12/16/2022] Open
Abstract
dUTP is a close structural congener of dTTP and can be readily incorporated into DNA opposite to adenine during DNA replication leading to non-mutagenic dU/A base pairs ('uracilation'). We find that dU/A pairs located within DNA transcriptional templates optimized for either T7 RNA polymerase (T7 RNAP) or human RNA polymerase II (pol II) have inhibitory and mutagenic effects on transcription. The data for T7 RNAP establishes that even a single dU/A pair can inhibit promoter binding and transcription initiation up to 30-fold, and that inhibitory effects on transcription elongation are also possible. Sequencing of the mRNA transcribed from uniformly uracilated DNA templates by T7 RNAP indicated an increased frequency of transversion and insertion mutations compared to all T/A templates. Strong effects of dU/A pairs on cellular transcription activity and fidelity were also observed with RNA pol II using uracil base excision repair (UBER)-deficient human cells. At the highest levels of template uracilation, transcription by RNA pol II was completely blocked. We propose that these effects arise from the decreased thermodynamic stability and increased dynamics of dU/A pairs in DNA. The potential implications of these findings on gene regulation and disease are discussed.
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Affiliation(s)
- Junru Cui
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
| | - Anthony Gizzi
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
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Zhou DR, Eid R, Miller KA, Boucher E, Mandato CA, Greenwood MT. Intracellular second messengers mediate stress inducible hormesis and Programmed Cell Death: A review. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:773-792. [DOI: 10.1016/j.bbamcr.2019.01.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 01/25/2019] [Accepted: 01/29/2019] [Indexed: 12/11/2022]
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9
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Zhou DR, Eid R, Boucher E, Miller KA, Mandato CA, Greenwood MT. Stress is an agonist for the induction of programmed cell death: A review. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:699-712. [DOI: 10.1016/j.bbamcr.2018.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/17/2018] [Accepted: 12/01/2018] [Indexed: 02/07/2023]
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10
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Wang M, Jiang S, Wu W, Yu F, Chang W, Li P, Wang K. Non-coding RNAs Function as Immune Regulators in Teleost Fish. Front Immunol 2018; 9:2801. [PMID: 30546368 PMCID: PMC6279911 DOI: 10.3389/fimmu.2018.02801] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/13/2018] [Indexed: 12/13/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are functional RNA molecules that are transcribed from DNA but not translated into proteins. ncRNAs function as key regulators of gene expression and chromatin modification. Recently, the functional role of ncRNAs in teleost fish has been extensively studied. Teleost fish are a highly diverse group among the vertebrate lineage. Fish are also important in terms of aquatic ecosystem, food production and human life, being the source of animal proteins worldwide and models of biomedical research. However, teleost fish always suffer from the invasion of infectious pathogens including viruses and bacteria, which has resulted in a tremendous economic loss to the fishing industry worldwide. Emerging evidence suggests that ncRNAs, especially miRNAs and lncRNAs, may serve as important regulators in cytokine and chemokine signaling, antigen presentation, complement and coagulation cascades, and T cell response in teleost fish. In this review, we summarize current knowledge and understanding of the roles of both miRNAs and lncRNAs in immune regulation in teleost fish. Molecular mechanism insights into the function of ncRNAs in fish immune response may contribute to the development of potential biomarkers and therapeutic targets for the prevention and treatment of fish diseases.
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Affiliation(s)
- Man Wang
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Shuai Jiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Wei Wu
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Fei Yu
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Wenguang Chang
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Kun Wang
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
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11
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Wanat P, Kasprzyk R, Kopcial M, Sikorski PJ, Strzelecka D, Jemielity J, Kowalska J. ExciTides: NTP-derived probes for monitoring pyrophosphatase activity based on excimer-to-monomer transitions. Chem Commun (Camb) 2018; 54:9773-9776. [PMID: 30105342 DOI: 10.1039/c8cc04968h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe a new type of nucleotide-derived fluorescent probe designed for monitoring pyrophosphatase activity based on excimer-to-monomer transitions, called ExciTide. The nucleotides were designed with two self-interacting dye moieties and synthesised using copper-catalysed azide-alkyne cycloaddition click chemistry. We applied these probes for enzyme activity monitoring and inhibitor evaluation. Some of the probes permeated into living cells, yielding interesting prospects for future applications.
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Affiliation(s)
- Przemyslaw Wanat
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
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12
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Shoguchi E, Beedessee G, Tada I, Hisata K, Kawashima T, Takeuchi T, Arakaki N, Fujie M, Koyanagi R, Roy MC, Kawachi M, Hidaka M, Satoh N, Shinzato C. Two divergent Symbiodinium genomes reveal conservation of a gene cluster for sunscreen biosynthesis and recently lost genes. BMC Genomics 2018; 19:458. [PMID: 29898658 PMCID: PMC6001144 DOI: 10.1186/s12864-018-4857-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/06/2018] [Indexed: 11/10/2022] Open
Abstract
Background The marine dinoflagellate, Symbiodinium, is a well-known photosynthetic partner for coral and other diverse, non-photosynthetic hosts in subtropical and tropical shallows, where it comprises an essential component of marine ecosystems. Using molecular phylogenetics, the genus Symbiodinium has been classified into nine major clades, A-I, and one of the reported differences among phenotypes is their capacity to synthesize mycosporine-like amino acids (MAAs), which absorb UV radiation. However, the genetic basis for this difference in synthetic capacity is unknown. To understand genetics underlying Symbiodinium diversity, we report two draft genomes, one from clade A, presumed to have been the earliest branching clade, and the other from clade C, in the terminal branch. Results The nuclear genome of Symbiodinium clade A (SymA) has more gene families than that of clade C, with larger numbers of organelle-related genes, including mitochondrial transcription terminal factor (mTERF) and Rubisco. While clade C (SymC) has fewer gene families, it displays specific expansions of repeat domain-containing genes, such as leucine-rich repeats (LRRs) and retrovirus-related dUTPases. Interestingly, the SymA genome encodes a gene cluster for MAA biosynthesis, potentially transferred from an endosymbiotic red alga (probably of bacterial origin), while SymC has completely lost these genes. Conclusions Our analysis demonstrates that SymC appears to have evolved by losing gene families, such as the MAA biosynthesis gene cluster. In contrast to the conservation of genes related to photosynthetic ability, the terminal clade has suffered more gene family losses than other clades, suggesting a possible adaptation to symbiosis. Overall, this study implies that Symbiodinium ecology drives acquisition and loss of gene families. Electronic supplementary material The online version of this article (10.1186/s12864-018-4857-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
| | - Girish Beedessee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Ipputa Tada
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.,Present address: Department of Genetics, School of Life Science, The Graduate University for Advanced Studies, 1111, Yata, Mishima-shi, Shizuoka, 411-8540, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Takeshi Kawashima
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.,Present address: Center for Information Biology, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Nana Arakaki
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Manabu Fujie
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Ryo Koyanagi
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Michael C Roy
- Instrumental Analysis Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, 305-8506, Japan
| | - Michio Hidaka
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan. .,Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwanoha, Kashiwa, 277-8564, Japan.
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13
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Baranowski MR, Nowicka A, Jemielity J, Kowalska J. A fluorescent HTS assay for phosphohydrolases based on nucleoside 5'-fluorophosphates: its application in screening for inhibitors of mRNA decapping scavenger and PDE-I. Org Biomol Chem 2018; 14:4595-604. [PMID: 27031609 DOI: 10.1039/c6ob00492j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Several nucleotide-specific phosphohydrolases can cleave P-F bonds in substrate analogues containing a fluorophosphate moiety to release fluoride ions. In this work, by employing a fluoride-sensitive molecular sensor, we harnessed this cleavage reaction to develop a fluorescence assay to screen for phosphohydrolase inhibitors. The assay is rapid, sensitive, and based on simple and synthetically available reagents. The assay was adapted to the high-throughput screening (HTS) format and its utility was demonstrated by screening an 'in-house' library of small nucleotides against two enzymes: DcpS, a metal-independent mRNA decapping pyrophosphatase of the histidine triad (HIT) family; and PDE-I, a divalent cation-dependent nuclease. Our screening results agreed with the known specificities of DcpS and PDE-I, and led to the selection of several inhibitors featuring low-micromolar IC50 values. For DcpS, we also verified the results by using an alternative method with the natural substrate. Notably, the assay presented here is the first fluorescence-based HTS-adaptable assay for DcpS, an established therapeutic target for spinal muscular atrophy. The assay should be useful for phosphohydrolase specificity profiling and inhibitor discovery, particularly in the context of DcpS and other HIT-family enzymes, which play key roles in maintaining cellular functions and have been linked to disease development.
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Affiliation(s)
- M R Baranowski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland.
| | - A Nowicka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland. and Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - J Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - J Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland.
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14
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Zang K, Li F, Ma Q. The dUTPase of white spot syndrome virus assembles its active sites in a noncanonical manner. J Biol Chem 2017; 293:1088-1099. [PMID: 29187596 DOI: 10.1074/jbc.m117.815266] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/14/2017] [Indexed: 01/04/2023] Open
Abstract
dUTPases are essential enzymes for maintaining genome integrity and have recently been shown to play moonlighting roles when containing extra sequences. Interestingly, the trimeric dUTPase of white spot syndrome virus (wDUT) harbors a sequence insert at the position preceding the C-terminal catalytic motif V (pre-V insert), rarely seen in other dUTPases. However, whether this extra sequence endows wDUT with additional properties is unknown. Herein, we present the crystal structures of wDUT in both ligand-free and ligand-bound forms. We observed that the pre-V insert in wDUT forms an unusual β-hairpin structure in the domain-swapping region and thereby facilitates a unique orientation of the adjacent C-terminal segment, positioning the catalytic motif V onto the active site of its own subunit instead of a third subunit. Consequently, wDUT employs two-subunit active sites, unlike the widely accepted paradigm that the active site of trimeric dUTPase is contributed by all three subunits. According to results from local structural comparisons, the active-site configuration of wDUT is similar to that of known dUTPases. However, we also found that residues in the second-shell region of the active site are reconfigured in wDUT as an adaption to its unique C-terminal orientation. We also show that deletion of the pre-V insert significantly reduces wDUT's enzymatic activity and thermal stability. We hypothesize that this rare structural arrangement confers additional functionality to wDUT. In conclusion, our study expands the structural diversity in the conserved dUTPase family and illustrates how sequence insertion and amino acid substitution drive protein evolution cooperatively.
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Affiliation(s)
- Kun Zang
- From the Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China.,the Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China, and.,the University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fuhua Li
- From the Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China.,the Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China, and
| | - Qingjun Ma
- From the Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China, .,the Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China, and
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15
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Alite C, Humphrey S, Donderis J, Maiques E, Ciges-Tomas JR, Penadés JR, Marina A. Dissecting the link between the enzymatic activity and the SaPI inducing capacity of the phage 80α dUTPase. Sci Rep 2017; 7:11234. [PMID: 28894239 PMCID: PMC5593958 DOI: 10.1038/s41598-017-11234-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/22/2017] [Indexed: 11/09/2022] Open
Abstract
The trimeric staphylococcal phage-encoded dUTPases (Duts) are signalling molecules that induce the cycle of some Staphylococcal pathogenicity islands (SaPIs) by binding to the SaPI-encoded Stl repressor. To perform this regulatory role, these Duts require an extra motif VI, as well as the Dut conserved motifs IV and V. While the apo form of Dut is required for the interaction with the Stl repressor, usually only those Duts with normal enzymatic activity can induce the SaPI cycle. To understand the link between the enzymatic activities and inducing capacities of the Dut protein, we analysed the structural, biochemical and physiological characteristics of the Dut80α D95E mutant, which loses the SaPI cycle induction capacity despite retaining enzymatic activity. Asp95 is located at the threefold central channel of the trimeric Dut where it chelates a divalent ion. Here, using state-of-the-art techniques, we demonstrate that D95E mutation has an epistatic effect on the motifs involved in Stl binding. Thus, ion binding in the central channel correlates with the capacity of motif V to twist and order in the SaPI-inducing disposition, while the tip of motif VI is disturbed. These alterations in turn reduce the affinity for the Stl repressor and the capacity to induce the SaPI cycle.
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Affiliation(s)
- Christian Alite
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Jaume Roig 11, 46010, Valencia, Spain
| | - Suzanne Humphrey
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Jordi Donderis
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Jaume Roig 11, 46010, Valencia, Spain
| | - Elisa Maiques
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Jaume Roig 11, 46010, Valencia, Spain.,Departamento de Ciencias Biomédicas, Universidad CEU Cardenal Herrera, 46115, Alfara del Patriarca, Valencia, Spain
| | - J Rafael Ciges-Tomas
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Jaume Roig 11, 46010, Valencia, Spain
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK.
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Jaume Roig 11, 46010, Valencia, Spain.
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16
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Donderis J, Bowring J, Maiques E, Ciges-Tomas JR, Alite C, Mehmedov I, Tormo-Mas MA, Penadés JR, Marina A. Convergent evolution involving dimeric and trimeric dUTPases in pathogenicity island mobilization. PLoS Pathog 2017; 13:e1006581. [PMID: 28892519 PMCID: PMC5608427 DOI: 10.1371/journal.ppat.1006581] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 09/21/2017] [Accepted: 08/15/2017] [Indexed: 11/18/2022] Open
Abstract
The dUTPase (Dut) enzymes, encoded by almost all free-living organisms and some viruses, prevent the misincorporation of uracil into DNA. We previously proposed that trimeric Duts are regulatory proteins involved in different cellular processes; including the phage-mediated transfer of the Staphylococcus aureus pathogenicity island SaPIbov1. Recently, it has been shown that the structurally unrelated dimeric Dut encoded by phage ϕNM1 is similarly able to mobilize SaPIbov1, suggesting dimeric Duts could also be regulatory proteins. How this is accomplished remains unsolved. Here, using in vivo, biochemical and structural approaches, we provide insights into the signaling mechanism used by the dimeric Duts to induce the SaPIbov1 cycle. As reported for the trimeric Duts, dimeric Duts contain an extremely variable region, here named domain VI, which is involved in the regulatory capacity of these enzymes. Remarkably, our results also show that the dimeric Dut signaling mechanism is modulated by dUTP, as with the trimeric Duts. Overall, our results demonstrate that although unrelated both in sequence and structure, dimeric and trimeric Duts control SaPI transfer by analogous mechanisms, representing a fascinating example of convergent evolution. This conserved mode of action highlights the biological significance of Duts as regulatory molecules.
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Affiliation(s)
- Jorge Donderis
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Janine Bowring
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Elisa Maiques
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - J. Rafael Ciges-Tomas
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Christian Alite
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Iltyar Mehmedov
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - María Angeles Tormo-Mas
- Departamento de Ciencias Biomédicas, Universidad CEU Cardenal Herrera, Moncada, Valencia, Spain
| | - José R. Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- * E-mail: (AM); (JRP)
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
- * E-mail: (AM); (JRP)
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17
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Bowring J, Neamah MM, Donderis J, Mir-Sanchis I, Alite C, Ciges-Tomas JR, Maiques E, Medmedov I, Marina A, Penadés JR. Pirating conserved phage mechanisms promotes promiscuous staphylococcal pathogenicity island transfer. eLife 2017; 6:26487. [PMID: 28826473 PMCID: PMC5779228 DOI: 10.7554/elife.26487] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 08/07/2017] [Indexed: 11/15/2022] Open
Abstract
Targeting conserved and essential processes is a successful strategy to combat enemies. Remarkably, the clinically important Staphylococcus aureus pathogenicity islands (SaPIs) use this tactic to spread in nature. SaPIs reside passively in the host chromosome, under the control of the SaPI-encoded master repressor, Stl. It has been assumed that SaPI de-repression is effected by specific phage proteins that bind to Stl, initiating the SaPI cycle. Different SaPIs encode different Stl repressors, so each targets a specific phage protein for its de-repression. Broadening this narrow vision, we report here that SaPIs ensure their promiscuous transfer by targeting conserved phage mechanisms. This is accomplished because the SaPI Stl repressors have acquired different domains to interact with unrelated proteins, encoded by different phages, but in all cases performing the same conserved function. This elegant strategy allows intra- and inter-generic SaPI transfer, highlighting these elements as one of nature’s most fascinating subcellular parasites. Many harmful microbes can produce different molecules that make them more effective in causing and spreading diseases. These molecules can also be obtained from ‘mobile genetic elements’ that can be transferred between bacteria within a population. Pathogenicity islands are one such type of mobile genetic element and are very common among bacteria known as staphylococci. They spread toxin-encoding genes between bacteria, including one that can lead to a condition called toxic shock syndrome in humans. Pathogenicity islands are normally found within the DNA of the bacteria, where they are deactivated by specific repressor proteins. However, in the presence of another type of mobile genetic element – the bacteriophages – the repressor proteins start to interact with specific proteins encoded by the bacteriophages. This allows the pathogenicity islands to become active and spread to other bacteria. Previous research has shown that in the bacterium known as Staphylococcus aureus, different pathogenicity islands have different repressors. Scientists therefore assumed that the repressors are only able to interact with certain bacteriophage proteins. However, since pathogenicity islands are widespread in nature, it could be possible that they use other ways to hijack the bacteriophage machinery to ensure their transfer. To test this hypothesis, Bowring et al. studied two types of pathogenicity islands in S. aureus and revealed that their two different repressors did not interact with specific bacteriophage proteins as previously hypothesized. Instead, each repressor could interact with multiple bacteriophage proteins that had a variety of different structures, including proteins from completely different bacteriophages. Bowring et al. also discovered that each of the analyzed repressor proteins did not actually recognize any specific shared structural features on the bacteriophage proteins, but rather evolved to target proteins that play the same role in various bacteriophages. This suggests the repressors target a specific process rather than a single protein. This strategy allows them to be transferred within the same species, but also between different ones. A next step will be to better understand how a repressor can recognize structurally unrelated proteins, and establish what evolutionary forces are driving this phenomenon. A deeper knowledge of how pathogenicity islands spread between staphylococci is vital to understand how these bacteria can become resistant to treatments such as antibiotics.
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Affiliation(s)
- Janine Bowring
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Maan M Neamah
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.,Department of Microbiology, Faculty of Veterinary Medicine, University of Kufa, Kufa, Iraq
| | - Jorge Donderis
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras, Valencia, Spain
| | - Ignacio Mir-Sanchis
- Departamento de Ciencias Biomédicas, Universidad CEU Cardenal Herrera, Valencia, Spain
| | - Christian Alite
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras, Valencia, Spain
| | - J Rafael Ciges-Tomas
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras, Valencia, Spain
| | - Elisa Maiques
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras, Valencia, Spain.,Departamento de Ciencias Biomédicas, Universidad CEU Cardenal Herrera, Valencia, Spain
| | - Iltyar Medmedov
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras, Valencia, Spain
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras, Valencia, Spain
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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18
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Dos Santos RS, Daures M, Philippi A, Romero S, Marselli L, Marchetti P, Senée V, Bacq D, Besse C, Baz B, Marroquí L, Ivanoff S, Masliah-Planchon J, Nicolino M, Soulier J, Socié G, Eizirik DL, Gautier JF, Julier C. dUTPase ( DUT) Is Mutated in a Novel Monogenic Syndrome With Diabetes and Bone Marrow Failure. Diabetes 2017; 66:1086-1096. [PMID: 28073829 DOI: 10.2337/db16-0839] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 01/05/2017] [Indexed: 11/13/2022]
Abstract
We describe a new syndrome characterized by early-onset diabetes associated with bone marrow failure, affecting mostly the erythrocytic lineage. Using whole-exome sequencing in a remotely consanguineous patient from a family with two affected siblings, we identified a single homozygous missense mutation (chr15.hg19:g.48,626,619A>G) located in the dUTPase (DUT) gene (National Center for Biotechnology Information Gene ID 1854), affecting both the mitochondrial (DUT-M p.Y142C) and the nuclear (DUT-N p.Y54C) isoforms. We found the same homozygous mutation in an unrelated consanguineous patient with diabetes and bone marrow aplasia from a family with two affected siblings, whereas none of the >60,000 subjects from the Exome Aggregation Consortium (ExAC) was homozygous for this mutation. This replicated observation probability was highly significant, thus confirming the role of this DUT mutation in this syndrome. DUT is a key enzyme for maintaining DNA integrity by preventing misincorporation of uracil into DNA, which results in DNA toxicity and cell death. We showed that DUT silencing in human and rat pancreatic β-cells results in apoptosis via the intrinsic cell death pathway. Our findings support the importance of tight control of DNA metabolism for β-cell integrity and warrant close metabolic monitoring of patients treated by drugs affecting dUTP balance.
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Affiliation(s)
| | - Mathilde Daures
- INSERM UMRS 958, Faculté de Médecine Paris Diderot, Université Paris Diderot-Paris 7, Université Sorbonne Paris Cité, Paris, France
| | - Anne Philippi
- INSERM UMRS 958, Faculté de Médecine Paris Diderot, Université Paris Diderot-Paris 7, Université Sorbonne Paris Cité, Paris, France
| | - Sophie Romero
- INSERM UMRS 958, Faculté de Médecine Paris Diderot, Université Paris Diderot-Paris 7, Université Sorbonne Paris Cité, Paris, France
| | - Lorella Marselli
- Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, Pisa, Italy
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, Pisa, Italy
| | - Valérie Senée
- INSERM UMRS 958, Faculté de Médecine Paris Diderot, Université Paris Diderot-Paris 7, Université Sorbonne Paris Cité, Paris, France
| | - Delphine Bacq
- Centre National de Génotypage, Institut de Génomique, Commissariat à l'Energie Atomique, Evry, France
| | - Céline Besse
- Centre National de Génotypage, Institut de Génomique, Commissariat à l'Energie Atomique, Evry, France
| | - Baz Baz
- Hôpital Lariboisière, Assistance Publique-Hôpitaux de Paris, Department of Diabetes and Endocrinology, Université Paris Diderot-Paris 7, Université Sorbonne Paris Cité, Paris, France
| | - Laura Marroquí
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Sarah Ivanoff
- Aplastic Anemia Reference Centre, Hematology Laboratory, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, INSERM U944, Université Paris Diderot-Paris 7, Université Sorbonne Paris Cité, Paris, France
| | - Julien Masliah-Planchon
- Aplastic Anemia Reference Centre, Hematology Laboratory, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, INSERM U944, Université Paris Diderot-Paris 7, Université Sorbonne Paris Cité, Paris, France
| | - Marc Nicolino
- Hôpital Femme-Mère-Enfant, Division of Pediatric Endocrinology, Hospices Civils de Lyon, Université Lyon 1, Lyon, France
| | - Jean Soulier
- Aplastic Anemia Reference Centre, Hematology Laboratory, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, INSERM U944, Université Paris Diderot-Paris 7, Université Sorbonne Paris Cité, Paris, France
| | - Gérard Socié
- Hematology Transplantation, Department of Hematology, Immunology and Oncology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Decio L Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Jean-François Gautier
- Hôpital Lariboisière, Assistance Publique-Hôpitaux de Paris, Department of Diabetes and Endocrinology, Université Paris Diderot-Paris 7, Université Sorbonne Paris Cité, Paris, France
| | - Cécile Julier
- INSERM UMRS 958, Faculté de Médecine Paris Diderot, Université Paris Diderot-Paris 7, Université Sorbonne Paris Cité, Paris, France
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19
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Podolny Y, Herzig E, Hizi A. Insights into the molecular and biological features of the dUTPase-related gene of bovine immunodeficiency virus. Virology 2017; 506:55-63. [PMID: 28342388 DOI: 10.1016/j.virol.2017.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/06/2017] [Accepted: 03/16/2017] [Indexed: 01/20/2023]
Abstract
This study was stimulated by our previous research of the dUTPase-related protein from bovine immunodeficiency virus (BIV) (Voronin et al., 2014). Despite the lack of detectable enzymatic BIV dUTPase activity (both of the recombinant protein and in virions), mutating the dUTPase gene was deleterious to viral production. However, cDNA synthesis and integration were apparently unaffected. Consequently, we have studied here two important issues. First, we showed that in cDNA produced by the dUTPase-mutated virions, the incidence of mutations was not higher than that found in wild-type BIV-infected cells. Second, single mutations, introduced in preserved dUTPase residues Asp48 and Asn57 (in the putative dUTPase active site or close to it), have led to abortive BIV infections (except for the conservative Asp48Glu mutation). Therefore, we postulate that the BIV dUTPase-related protein has a critical role in retroviral replication at steps that take place after viral cDNA synthesis and integration.
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Affiliation(s)
- Yulia Podolny
- From the Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Eytan Herzig
- From the Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Amnon Hizi
- From the Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
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20
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Pramono AK, Kuwahara H, Itoh T, Toyoda A, Yamada A, Hongoh Y. Discovery and Complete Genome Sequence of a Bacteriophage from an Obligate Intracellular Symbiont of a Cellulolytic Protist in the Termite Gut. Microbes Environ 2017; 32:112-117. [PMID: 28321010 PMCID: PMC5478533 DOI: 10.1264/jsme2.me16175] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Termites depend nutritionally on their gut microbes, and protistan, bacterial, and archaeal gut communities have been extensively studied. However, limited information is available on viruses in the termite gut. We herein report the complete genome sequence (99,517 bp) of a phage obtained during a genome analysis of “Candidatus Azobacteroides pseudotrichonymphae” phylotype ProJPt-1, which is an obligate intracellular symbiont of the cellulolytic protist Pseudotrichonympha sp. in the gut of the termite Prorhinotermes japonicus. The genome of the phage, designated ProJPt-Bp1, was circular or circularly permuted, and was not integrated into the two circular chromosomes or five circular plasmids composing the host ProJPt-1 genome. The phage was putatively affiliated with the order Caudovirales based on sequence similarities with several phage-related genes; however, most of the 52 protein-coding sequences had no significant homology to sequences in the databases. The phage genome contained a tRNA-Gln (CAG) gene, which showed the highest sequence similarity to the tRNA-Gln (CAA) gene of the host “Ca. A. pseudotrichonymphae” phylotype ProJPt-1. Since the host genome lacked a tRNA-Gln (CAG) gene, the phage tRNA gene may compensate for differences in codon usage bias between the phage and host genomes. The phage genome also contained a non-coding region with high nucleotide sequence similarity to a region in one of the host plasmids. No other phage-related sequences were found in the host ProJPt-1 genome. To the best of our knowledge, this is the first report of a phage from an obligate, mutualistic endosymbiont permanently associated with eukaryotic cells.
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Affiliation(s)
- Ajeng K Pramono
- Department of Biological Sciences, Tokyo Institute of Technology
| | | | - Takehiko Itoh
- Department of Biological Information, Tokyo Institute of Technology
| | | | - Akinori Yamada
- Department of Biological Sciences, Tokyo Institute of Technology.,Division of Marine Biomaterial Science, Graduate School of Fisheries Science and Environmental Studies, Nagasaki University
| | - Yuichi Hongoh
- Department of Biological Sciences, Tokyo Institute of Technology
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21
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Eid R, Arab NTT, Greenwood MT. Iron mediated toxicity and programmed cell death: A review and a re-examination of existing paradigms. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1864:399-430. [PMID: 27939167 DOI: 10.1016/j.bbamcr.2016.12.002] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/08/2016] [Accepted: 12/04/2016] [Indexed: 12/11/2022]
Abstract
Iron is an essential micronutrient that is problematic for biological systems since it is toxic as it generates free radicals by interconverting between ferrous (Fe2+) and ferric (Fe3+) forms. Additionally, even though iron is abundant, it is largely insoluble so cells must treat biologically available iron as a valuable commodity. Thus elaborate mechanisms have evolved to absorb, re-cycle and store iron while minimizing toxicity. Focusing on rarely encountered situations, most of the existing literature suggests that iron toxicity is common. A more nuanced examination clearly demonstrates that existing regulatory processes are more than adequate to limit the toxicity of iron even in response to iron overload. Only under pathological or artificially harsh situations of exposure to excess iron does it become problematic. Here we review iron metabolism and its toxicity as well as the literature demonstrating that intracellular iron is not toxic but a stress responsive programmed cell death-inducing second messenger.
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Affiliation(s)
- Rawan Eid
- Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Kingston, Ontario, Canada
| | - Nagla T T Arab
- Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Kingston, Ontario, Canada
| | - Michael T Greenwood
- Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Kingston, Ontario, Canada.
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22
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Mota CS, Gonçalves AMD, de Sanctis D. Deinococcus radiodurans DR2231 is a two-metal-ion mechanism hydrolase with exclusive activity on dUTP. FEBS J 2016; 283:4274-4290. [PMID: 27739259 DOI: 10.1111/febs.13923] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/27/2016] [Accepted: 10/11/2016] [Indexed: 02/04/2023]
Abstract
DR2231 from Deinococcus radiodurans was previously functionally and structurally characterized as an all-α NTP pyrophosphohydrolase with specific dUTPase activity. dUTPases have a central role in the regulation of dUTP intracellular levels and dTTP nucleotide metabolism. DR2231 presents a conserved dimetal catalytic site, similar to all-α dimeric dUTPases, but contrary to these enzymes, it is unable to process dUDP. In this article, we present functional and structural evidence of single-point mutations that affect directly or indirectly the enzyme catalysis and provide a complete description of the all-α NTP pyrophosphohydrolase mechanism. Activity assays, isothermal titration calorimetry and the crystal structures of these mutants obtained in complex with dUMP or a dUTP analogue aid in probing the reaction mechanism. Our results demonstrate that the two metals are necessary for enzyme processing and also important to modulate the substrate binding affinity. Single-point mutations located in a structurally mobile lid-like loop show that the interactions with the nucleoside monophosphate are essential for induction of the closed conformation and ultimately for substrate processing. β- and γ-phosphates are held in place through coordination with the second metal, which is responsible for the substrate 'gauche' orientation in the catalytic position. The lack of sufficient contacts to orient the dUDP β-phosphate for hydrolysis explains DR2231 preference towards dUTP. Sequence and structural similarities with MazG proteins suggest that a similar mechanism might be conserved within the protein family. DATABASE Structural data are available in the PDB under the accession numbers 5HVA, 5HWU, 5HX1, 5HYL, 5I0J, 5HZZ, 5I0M.
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Affiliation(s)
| | - Ana Maria D Gonçalves
- Macromolecular Crystallography Unit, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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23
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Ardisson-Araújo DMP, Lima RN, Melo FL, Clem RJ, Huang N, Báo SN, Sosa-Gómez DR, Ribeiro BM. Genome sequence of Perigonia lusca single nucleopolyhedrovirus: insights into the evolution of a nucleotide metabolism enzyme in the family Baculoviridae. Sci Rep 2016; 6:24612. [PMID: 27273152 PMCID: PMC4895240 DOI: 10.1038/srep24612] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 04/01/2016] [Indexed: 12/19/2022] Open
Abstract
The genome of a novel group II alphabaculovirus, Perigonia lusca single nucleopolyhedrovirus (PeluSNPV), was sequenced and shown to contain 132,831 bp with 145 putative ORFs (open reading frames) of at least 50 amino acids. An interesting feature of this novel genome was the presence of a putative nucleotide metabolism enzyme-encoding gene (pelu112). The pelu112 gene was predicted to encode a fusion of thymidylate kinase (tmk) and dUTP diphosphatase (dut). Phylogenetic analysis indicated that baculoviruses have independently acquired tmk and dut several times during their evolution. Two homologs of the tmk-dut fusion gene were separately introduced into the Autographa californica multiple nucleopolyhedrovirus (AcMNPV) genome, which lacks tmk and dut. The recombinant baculoviruses produced viral DNA, virus progeny, and some viral proteins earlier during in vitro infection and the yields of viral occlusion bodies were increased 2.5-fold when compared to the parental virus. Interestingly, both enzymes appear to retain their active sites, based on separate modeling using previously solved crystal structures. We suggest that the retention of these tmk-dut fusion genes by certain baculoviruses could be related to accelerating virus replication and to protecting the virus genome from deleterious mutation.
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Affiliation(s)
- Daniel M P Ardisson-Araújo
- Laboratory of Baculovirus, Cell Biology Department, University of Brasília, Brasília, DF, Brazil.,Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Rayane Nunes Lima
- Laboratory of Baculovirus, Cell Biology Department, University of Brasília, Brasília, DF, Brazil
| | - Fernando L Melo
- Laboratory of Baculovirus, Cell Biology Department, University of Brasília, Brasília, DF, Brazil
| | - Rollie J Clem
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Ning Huang
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Sônia Nair Báo
- Laboratory of Baculovirus, Cell Biology Department, University of Brasília, Brasília, DF, Brazil
| | | | - Bergmann M Ribeiro
- Laboratory of Baculovirus, Cell Biology Department, University of Brasília, Brasília, DF, Brazil
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24
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Maiques E, Quiles-Puchalt N, Donderis J, Ciges-Tomas JR, Alite C, Bowring JZ, Humphrey S, Penadés JR, Marina A. Another look at the mechanism involving trimeric dUTPases in Staphylococcus aureus pathogenicity island induction involves novel players in the party. Nucleic Acids Res 2016; 44:5457-69. [PMID: 27112567 PMCID: PMC4914113 DOI: 10.1093/nar/gkw317] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 04/13/2016] [Indexed: 12/14/2022] Open
Abstract
We have recently proposed that the trimeric staphylococcal phage encoded dUTPases (Duts) are signaling molecules that act analogously to eukaryotic G-proteins, using dUTP as a second messenger. To perform this regulatory role, the Duts require their characteristic extra motif VI, present in all the staphylococcal phage coded trimeric Duts, as well as the strongly conserved Dut motif V. Recently, however, an alternative model involving Duts in the transfer of the staphylococcal islands (SaPIs) has been suggested, questioning the implication of motifs V and VI. Here, using state-of the-art techniques, we have revisited the proposed models. Our results confirm that the mechanism by which the Duts derepress the SaPI cycle depends on dUTP and involves both motifs V and VI, as we have previously proposed. Surprisingly, the conserved Dut motif IV is also implicated in SaPI derepression. However, and in agreement with the proposed alternative model, the dUTP inhibits rather than inducing the process, as we had initially proposed. In summary, our results clarify, validate and establish the mechanism by which the Duts perform regulatory functions.
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Affiliation(s)
- Elisa Maiques
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain
| | - Nuria Quiles-Puchalt
- Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad CEU Cardenal Herrera, 46113 Moncada, Valencia, Spain Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Jorge Donderis
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain
| | - J Rafael Ciges-Tomas
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain
| | - Christian Alite
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain
| | - Janine Z Bowring
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Suzanne Humphrey
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain
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Frígols B, Quiles-Puchalt N, Mir-Sanchis I, Donderis J, Elena SF, Buckling A, Novick RP, Marina A, Penadés JR. Virus Satellites Drive Viral Evolution and Ecology. PLoS Genet 2015; 11:e1005609. [PMID: 26495848 PMCID: PMC4619825 DOI: 10.1371/journal.pgen.1005609] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 09/25/2015] [Indexed: 12/18/2022] Open
Abstract
Virus satellites are widespread subcellular entities, present both in eukaryotic and in prokaryotic cells. Their modus vivendi involves parasitism of the life cycle of their inducing helper viruses, which assures their transmission to a new host. However, the evolutionary and ecological implications of satellites on helper viruses remain unclear. Here, using staphylococcal pathogenicity islands (SaPIs) as a model of virus satellites, we experimentally show that helper viruses rapidly evolve resistance to their virus satellites, preventing SaPI proliferation, and SaPIs in turn can readily evolve to overcome phage resistance. Genomic analyses of both these experimentally evolved strains as well as naturally occurring bacteriophages suggest that the SaPIs drive the coexistence of multiple alleles of the phage-coded SaPI inducing genes, as well as sometimes selecting for the absence of the SaPI depressing genes. We report similar (accidental) evolution of resistance to SaPIs in laboratory phages used for Staphylococcus aureus typing and also obtain the same qualitative results in both experimental evolution and phylogenetic studies of Enterococcus faecalis phages and their satellites viruses. In summary, our results suggest that helper and satellite viruses undergo rapid coevolution, which is likely to play a key role in the evolution and ecology of the viruses as well as their prokaryotic hosts. Satellites are defined as viruses that have a life cycle dependent on a helper virus. Thus, they can be considered as parasites of parasites. In addition to their fascinating life cycle, these widespread infectious elements, present both in eukaryotic and prokaryotic cells, have a dramatic role in virulence by controlling the symptoms induced by their eukaryotic helper viruses or by encoding key bacterial virulence genes. While satellites can play an important role in the ecology of the viruses they parasitise, the evolutionary impact on their helper viruses is unclear. Here we show that staphylococcal pathogenicity islands (SaPIs), an example of a virus satellite, are a major selective force on the viruses (bacteriophages) they parasitise. Using both bioinformatic and experimental evolution data we have been able to confirm that pathogenicity islands are a major selective pressure enhancing the diversity of both genes and gene content in Staphylococcus aureus phages. Since SaPIs exploit the life cycle of their helper phages to enable their rapid replication and promiscuous spread, these strategies are mechanisms that reduce SaPI interference, thus facilitating the infectivity and dissemination of the helper phages in nature.
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Affiliation(s)
| | - Nuria Quiles-Puchalt
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Jorge Donderis
- Instituto de Biomedicina de Valencia (CSIC), Valencia, Spain
| | - Santiago F. Elena
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Angus Buckling
- Department of Biosciences, Center for Ecology and Conservation, School of Biosciences, University of Exeter, Cornwall Campus, Penryn, United Kingdom
| | - Richard P. Novick
- Skirball Institute Program in Molecular Pathogenesis and Departments of Microbiology and Medicine, New York University Medical Center, New York, New York, United States of America
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (CSIC), Valencia, Spain
| | - José R. Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- * E-mail:
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Hizi A, Herzig E. dUTPase: the frequently overlooked enzyme encoded by many retroviruses. Retrovirology 2015; 12:70. [PMID: 26259899 PMCID: PMC4531489 DOI: 10.1186/s12977-015-0198-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 08/04/2015] [Indexed: 11/13/2022] Open
Abstract
Retroviruses are among the best studied viruses in last decades due to their pivotal involvement in cellular processes and, most importantly, in causing human diseases, most notably-acquired immunodeficiency syndrome (AIDS) that is triggered by human immunodeficiency viruses types 1 and 2 (HIV-1 and HIV-2, respectively). Numerous studied were conducted to understand the involvement of the three cardinal retroviral enzymes, reverse transcriptase, integrase and protease, in the life cycle of the viruses. These studies have led to the development of many inhibitors of these enzymes as anti-retroviral specific drugs that are used for routine treatments of HIV/AIDS patients. Interestingly, a fourth virus-encoded enzyme, the deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) is also found in several major retroviral groups. The presence and the importance of this enzyme to the life cycle of retroviruses were usually overlooked by most retrovirologists, although the occurrence of dUTPases, particularly in beta-retroviruses and in non-primate retroviruses, is known for more than 20 years. Only more recently, retroviral dUTPases were brought into the limelight and were shown in several cases to be essential for viral replication. Therefore, it is likely that future studies on this enzyme will advance our knowledge to a level that will allow designing novel, specific and potent anti-dUTPase drugs that are effective in combating retroviral diseases. The aim of this review is to give concise background information on dUTPases in general and to summarize the most relevant data on retroviral dUTPases and their involvement in the replication processes and pathogenicity of the viruses, as well as in possibly-associated human diseases.
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Affiliation(s)
- Amnon Hizi
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel.
| | - Eytan Herzig
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel.
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Donohoe OH, Henshilwood K, Way K, Hakimjavadi R, Stone DM, Walls D. Identification and Characterization of Cyprinid Herpesvirus-3 (CyHV-3) Encoded MicroRNAs. PLoS One 2015; 10:e0125434. [PMID: 25928140 PMCID: PMC4416013 DOI: 10.1371/journal.pone.0125434] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/17/2015] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs involved in post-transcriptional gene regulation. Some viruses encode their own miRNAs and these are increasingly being recognized as important modulators of viral and host gene expression. Cyprinid herpesvirus 3 (CyHV-3) is a highly pathogenic agent that causes acute mass mortalities in carp (Cyprinus carpio carpio) and koi (Cyprinus carpio koi) worldwide. Here, bioinformatic analyses of the CyHV-3 genome suggested the presence of non-conserved precursor miRNA (pre-miRNA) genes. Deep sequencing of small RNA fractions prepared from in vitro CyHV-3 infections led to the identification of potential miRNAs and miRNA–offset RNAs (moRNAs) derived from some bioinformatically predicted pre-miRNAs. DNA microarray hybridization analysis, Northern blotting and stem-loop RT-qPCR were then used to definitively confirm that CyHV-3 expresses two pre-miRNAs during infection in vitro. The evidence also suggested the presence of an additional four high-probability and two putative viral pre-miRNAs. MiRNAs from the two confirmed pre-miRNAs were also detected in gill tissue from CyHV-3-infected carp. We also present evidence that one confirmed miRNA can regulate the expression of a putative CyHV-3-encoded dUTPase. Candidate homologues of some CyHV-3 pre-miRNAs were identified in CyHV-1 and CyHV-2. This is the first report of miRNA and moRNA genes encoded by members of the Alloherpesviridae family, a group distantly related to the Herpesviridae family. The discovery of these novel CyHV-3 genes may help further our understanding of the biology of this economically important virus and their encoded miRNAs may have potential as biomarkers for the diagnosis of latent CyHV-3.
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Affiliation(s)
- Owen H. Donohoe
- Marine Institute, Rinville, Oranmore, Co. Galway, Ireland
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin, Ireland
| | | | - Keith Way
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), The Nothe, Weymouth, Dorset, the United Kingdom
| | - Roya Hakimjavadi
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin, Ireland
| | - David M. Stone
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), The Nothe, Weymouth, Dorset, the United Kingdom
| | - Dermot Walls
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin, Ireland
- * E-mail:
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28
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Ardisson-Araújo DMP, de Melo FL, Andrade MDS, Sihler W, Báo SN, Ribeiro BM, de Souza ML. Genome sequence of Erinnyis ello granulovirus (ErelGV), a natural cassava hornworm pesticide and the first sequenced sphingid-infecting betabaculovirus. BMC Genomics 2014; 15:856. [PMID: 25280947 PMCID: PMC4192325 DOI: 10.1186/1471-2164-15-856] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Accepted: 09/25/2014] [Indexed: 12/03/2022] Open
Abstract
Background Cassava (Manihot esculenta) is the basic source for dietary energy of 500 million people in the world. In Brazil, Erinnyis ello ello (Lepidoptera: Sphingidae) is a major pest of cassava crops and a bottleneck for its production. In the 1980s, a naturally occurring baculovirus was isolated from E. ello larva and successfully applied as a bio-pesticide in the field. Here, we described the structure, the complete genome sequence, and the phylogenetic relationships of the first sphingid-infecting betabaculovirus. Results The baculovirus isolated from the cassava hornworm cadavers is a betabaculovirus designated Erinnyis ello granulovirus (ErelGV). The 102,759 bp long genome has a G + C content of 38.7%. We found 130 putative ORFs coding for polypeptides of at least 50 amino acid residues. Only eight genes were found to be unique. ErelGV is closely related to ChocGV and PiraGV isolates. We did not find typical homologous regions and cathepsin and chitinase homologous genes are lacked. The presence of he65 and p43 homologous genes suggests horizontal gene transfer from Alphabaculovirus. Moreover, we found a nucleotide metabolism-related gene and two genes that could be acquired probably from Densovirus. Conclusions The ErelGV represents a new virus species from the genus Betabaculovirus and is the closest relative of ChocGV. It contains a dUTPase-like, a he65-like, p43-like genes, which are also found in several other alpha- and betabaculovirus genomes, and two Densovirus-related genes. Importantly, recombination events between insect viruses from unrelated families and genera might drive baculovirus genomic evolution. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-856) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Bergmann Morais Ribeiro
- Cell Biology Department, Laboratory of Baculovirus, University of Brasília, 70910-900 Brasília, DF, Brazil.
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Eid R, Sheibani S, Gharib N, Lapointe JF, Horowitz A, Vali H, Mandato CA, Greenwood MT. Human ribosomal protein L9 is a Bax suppressor that promotes cell survival in yeast. FEMS Yeast Res 2013; 14:495-507. [DOI: 10.1111/1567-1364.12121] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 10/21/2013] [Accepted: 10/24/2013] [Indexed: 11/27/2022] Open
Affiliation(s)
- Rawan Eid
- Department of Chemistry and Chemical Engineering; Royal Military College; Kingston ON Canada
| | - Sara Sheibani
- Department of Chemistry and Chemical Engineering; Royal Military College; Kingston ON Canada
| | - Nada Gharib
- Department of Chemistry and Chemical Engineering; Royal Military College; Kingston ON Canada
| | - Jason F. Lapointe
- Department of Anatomy and Cell Biology; McGill University; Montreal QC Canada
| | - Avital Horowitz
- Department of Chemistry and Chemical Engineering; Royal Military College; Kingston ON Canada
- Department of Anatomy and Cell Biology; McGill University; Montreal QC Canada
| | - Hojatollah Vali
- Department of Anatomy and Cell Biology; McGill University; Montreal QC Canada
| | - Craig A. Mandato
- Department of Anatomy and Cell Biology; McGill University; Montreal QC Canada
| | - Michael T. Greenwood
- Department of Chemistry and Chemical Engineering; Royal Military College; Kingston ON Canada
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30
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The human septin7 and the yeast CDC10 septin prevent Bax and copper mediated cell death in yeast. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:3186-3194. [DOI: 10.1016/j.bbamcr.2013.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 09/08/2013] [Accepted: 09/10/2013] [Indexed: 01/18/2023]
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Kelly WJ, Altermann E, Lambie SC, Leahy SC. Interaction between the genomes of Lactococcus lactis and phages of the P335 species. Front Microbiol 2013; 4:257. [PMID: 24009606 PMCID: PMC3757294 DOI: 10.3389/fmicb.2013.00257] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Accepted: 08/13/2013] [Indexed: 11/28/2022] Open
Abstract
Phages of the P335 species infect Lactococcus lactis and have been particularly studied because of their association with strains of L. lactis subsp. cremoris used as dairy starter cultures. Unlike other lactococcal phages, those of the P335 species may have a temperate or lytic lifestyle, and are believed to originate from the starter cultures themselves. We have sequenced the genome of L. lactis subsp. cremoris KW2 isolated from fermented corn and found that it contains an integrated P335 species prophage. This 41 kb prophage (Φ KW2) has a mosaic structure with functional modules that are highly similar to several other phages of the P335 species associated with dairy starter cultures. Comparison of the genomes of 26 phages of the P335 species, with either a lytic or temperate lifestyle, shows that they can be divided into three groups and that the morphogenesis gene region is the most conserved. Analysis of these phage genomes in conjunction with the genomes of several L. lactis strains shows that prophage insertion is site specific and occurs at seven different chromosomal locations. Exactly how induced or lytic phages of the P335 species interact with carbohydrate cell surface receptors in the host cell envelope remains to be determined. Genes for the biosynthesis of a variable cell surface polysaccharide and for lipoteichoic acids (LTAs) are found in L. lactis and are the main candidates for phage receptors, as the genes for other cell surface carbohydrates have been lost from dairy starter strains. Overall, phages of the P335 species appear to have had only a minor role in the adaptation of L. lactis subsp. cremoris strains to the dairy environment, and instead they appear to be an integral part of the L. lactis chromosome. There remains a great deal to be discovered about their role, and their contribution to the evolution of the bacterial genome.
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Affiliation(s)
- William J Kelly
- AgResearch Limited, Grasslands Research Centre Palmerston North, New Zealand
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