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Ong SC, Luo HW, Cheng WH, Ku FM, Tsai CY, Huang PJ, Lee CC, Yeh YM, Lin R, Chiu CH, Tang P. The core exosome proteome of Trichomonas vaginalis. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2024; 57:246-256. [PMID: 38383245 DOI: 10.1016/j.jmii.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/15/2024] [Accepted: 02/13/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND Trichomonas vaginalis is parasitic protozoan that causes human urogenital infections. Accumulated reports indicated that exosomes released by this parasite play a crucial role in transmitting information and substances between cells during host-parasite interactions. Current knowledge on the protein contents in T. vaginalis exosome is mainly generated from three previous studies that used different T. vaginalis isolates as an experimental model. Whether T. vaginalis exosomes comprise a common set of proteins (core exosome proteome) is still unclear. METHODS To explore the core exosome proteome in T. vaginalis, we used liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify the contents of sucrose ultracentrifugation-enriched exosome and supernatant fractions isolated from six isolates. RESULTS Transmission electron microscopy (TEM) confirmed the presence of exosomes in the enriched fraction. Proteomic analysis identified a total of 1870 proteins from exosomal extracts. There were 1207 exosomal-specific proteins after excluding 436 'non-core exosomal proteins'. Among these, 72 common exosomal-specific proteins were expressed in all six isolates. Compared with three published T. vaginalis exosome proteome datasets, we identified 16 core exosomal-specific proteins. These core exosomal-specific proteins included tetraspanin (TvTSP1), the classical exosome marker, and proteins mainly involved in catalytic activity and binding such as ribosomal proteins, ras-associated binding (Rab) proteins, and heterotrimeric G proteins. CONCLUSIONS Our study highlighted the importance of using supernatant fraction from exosomal extract as a control to eliminate 'non-core exosomal proteins'. We compiled a reference core exosome proteome of T. vaginalis, which is essential for developing a fundamental understanding of exosome-mediated cell communication and host-parasite interaction.
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Affiliation(s)
- Seow-Chin Ong
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan.
| | - Hong-Wei Luo
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan.
| | - Wei-Hung Cheng
- Department of Parasitology, College of Medicine, National Cheng Kung University, Tainan City, Taiwan.
| | - Fu-Man Ku
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan.
| | - Chih-Yu Tsai
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan.
| | - Po-Jung Huang
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan; Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.
| | - Chi-Ching Lee
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan; Department of Computer Science and Information Engineering, College of Engineering, Chang Gung University, Guishan District, Taoyuan City, Taiwan.
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.
| | - Rose Lin
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan.
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan.
| | - Petrus Tang
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan; Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan.
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Dorantes-Palma D, Pérez-Mora S, Azuara-Liceaga E, Pérez-Rueda E, Pérez-Ishiwara DG, Coca-González M, Medel-Flores MO, Gómez-García C. Screening and Structural Characterization of Heat Shock Response Elements (HSEs) in Entamoeba histolytica Promoters. Int J Mol Sci 2024; 25:1319. [PMID: 38279319 PMCID: PMC10815948 DOI: 10.3390/ijms25021319] [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: 12/14/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/28/2024] Open
Abstract
Entamoeba histolytica (E. histolytica) exhibits a remarkable capacity to respond to thermal shock stress through a sophisticated genetic regulation mechanism. This process is carried out via Heat Shock Response Elements (HSEs), which are recognized by Heat Shock Transcription Factors (EhHSTFs), enabling fine and precise control of gene expression. Our study focused on screening for HSEs in the promoters of the E. histolytica genome, specifically analyzing six HSEs, including Ehpgp5, EhrabB1, EhrabB4, EhrabB5, Ehmlbp, and Ehhsp100. We discovered 2578 HSEs, with 1412 in promoters of hypothetical genes and 1166 in coding genes. We observed that a single promoter could contain anywhere from one to five HSEs. Gene ontology analysis revealed the presence of HSEs in essential genes for the amoeba, including cysteine proteinases, ribosomal genes, Myb family DNA-binding proteins, and Rab GTPases, among others. Complementarily, our molecular docking analyses indicate that these HSEs are potentially recognized by EhHSTF5, EhHSTF6, and EhHSTF7 factors in their trimeric conformation. These findings suggest that E. histolytica has the capability to regulate a wide range of critical genes via HSE-EhHSTFs, not only for thermal stress response but also for vital functions of the parasite. This is the first comprehensive study of HSEs in the genome of E. histolytica, significantly contributing to the understanding of its genetic regulation and highlighting the complexity and precision of this mechanism in the parasite's survival.
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Affiliation(s)
- David Dorantes-Palma
- Laboratorio de Biomedicina Molecular 1, ENMyH, Instituto Politécnico Nacional, Mexico City 07320, Mexico; (D.D.-P.); (S.P.-M.); (D.G.P.-I.); (M.C.-G.); (M.O.M.-F.)
| | - Salvador Pérez-Mora
- Laboratorio de Biomedicina Molecular 1, ENMyH, Instituto Politécnico Nacional, Mexico City 07320, Mexico; (D.D.-P.); (S.P.-M.); (D.G.P.-I.); (M.C.-G.); (M.O.M.-F.)
| | - Elisa Azuara-Liceaga
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City 03100, Mexico;
| | - Ernesto Pérez-Rueda
- Unidad Académica del Estado de Yucatán, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Mexico City 97302, Mexico;
| | - David Guillermo Pérez-Ishiwara
- Laboratorio de Biomedicina Molecular 1, ENMyH, Instituto Politécnico Nacional, Mexico City 07320, Mexico; (D.D.-P.); (S.P.-M.); (D.G.P.-I.); (M.C.-G.); (M.O.M.-F.)
| | - Misael Coca-González
- Laboratorio de Biomedicina Molecular 1, ENMyH, Instituto Politécnico Nacional, Mexico City 07320, Mexico; (D.D.-P.); (S.P.-M.); (D.G.P.-I.); (M.C.-G.); (M.O.M.-F.)
| | - María Olivia Medel-Flores
- Laboratorio de Biomedicina Molecular 1, ENMyH, Instituto Politécnico Nacional, Mexico City 07320, Mexico; (D.D.-P.); (S.P.-M.); (D.G.P.-I.); (M.C.-G.); (M.O.M.-F.)
| | - Consuelo Gómez-García
- Laboratorio de Biomedicina Molecular 1, ENMyH, Instituto Politécnico Nacional, Mexico City 07320, Mexico; (D.D.-P.); (S.P.-M.); (D.G.P.-I.); (M.C.-G.); (M.O.M.-F.)
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Guo T, Modi OL, Hirano J, Guzman HV, Tsuboi T. Single-chain models illustrate the 3D RNA folding shape during translation. BIOPHYSICAL REPORTS 2022; 2:100065. [PMID: 36425329 PMCID: PMC9680788 DOI: 10.1016/j.bpr.2022.100065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/19/2022] [Indexed: 06/16/2023]
Abstract
The three-dimensional conformation of RNA is important in the function and fate of the molecule. The common conformation of mRNA is formed based on the closed-loop structure and internal base pairings with the activity of the ribosome movements. However, recent reports suggest that the closed-loop structure might not be formed in many mRNAs. This implies that mRNA can be considered as a single polymer in the cell. Here, we introduce the Three-dimensional RNA Illustration Program (TRIP) to model the three-dimensional RNA folding shape based on single-chain models and angle restriction of each bead component from previously reported single-molecule fluorescence in situ hybridization (smFISH) experimental data. This simulation method was able to recapitulate the mRNA conformation change of the translation activity and three-dimensional positional interaction between an organelle and its localized mRNAs as end-to-end distances. Within the analyzed cases, base-pairing interactions only have minor effects on the three-dimensional mRNA conformation, and instead single-chain polymer characteristics have a more significant impact on the conformation. This top-down method will be used to interpret the aggregation mechanism of mRNA under different cellular conditions such as nucleolus and phase-separated granules.
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Affiliation(s)
- Tianze Guo
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Olivia L. Modi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Jillian Hirano
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Horacio V. Guzman
- Department of Theoretical Physics, Jozef Stefan Institute, Ljubljana, Slovenia
| | - Tatsuhisa Tsuboi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen, Guangdong, China
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Weber R, McCullagh M. Role of ATP in the RNA Translocation Mechanism of SARS-CoV-2 NSP13 Helicase. J Phys Chem B 2021; 125:8787-8796. [PMID: 34328740 PMCID: PMC8353885 DOI: 10.1021/acs.jpcb.1c04528] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 07/21/2021] [Indexed: 11/29/2022]
Abstract
The COVID-19 pandemic has demonstrated the need to develop potent and transferable therapeutics to treat coronavirus infections. Numerous antiviral targets are being investigated, but nonstructural protein 13 (nsp13) stands out as a highly conserved and yet understudied target. Nsp13 is a superfamily 1 (SF1) helicase that translocates along and unwinds viral RNA in an ATP-dependent manner. Currently, there are no available structures of nsp13 from SARS-CoV-1 or SARS-CoV-2 with either ATP or RNA bound, which presents a significant hurdle to the rational design of therapeutics. To address this knowledge gap, we have built models of SARS-CoV-2 nsp13 in Apo, ATP, ssRNA and ssRNA+ATP substrate states. Using 30 μs of a Gaussian-accelerated molecular dynamics simulation (at least 6 μs per substrate state), these models were confirmed to maintain substrate binding poses that are similar to other SF1 helicases. A Gaussian mixture model and linear discriminant analysis structural clustering protocol was used to identify key structural states of the ATP-dependent RNA translocation mechanism. Namely, four RNA-nsp13 structures are identified that exhibit ATP-dependent populations and support the inchworm mechanism for translocation. These four states are characterized by different RNA-binding poses for motifs Ia, IV, and V and suggest a power stroke-like motion of domain 2A relative to domain 1A. This structural and mechanistic insight of nsp13 RNA translocation presents novel targets for the further development of antivirals.
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Affiliation(s)
- Ryan Weber
- Department
of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Martin McCullagh
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74074, United States
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5
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Wei Q, Geng J, Chen Y, Lin H, Wang J, Fang Z, Wang F, Zhang Z. Structure and function of DEAH-box helicase 32 and its role in cancer. Oncol Lett 2021; 21:382. [PMID: 33777205 PMCID: PMC7988694 DOI: 10.3892/ol.2021.12643] [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: 08/16/2020] [Accepted: 12/23/2020] [Indexed: 11/06/2022] Open
Abstract
DEAH-box helicase 32 (DHX32) is an RNA helicase with unique structural characteristics that is involved in numerous biological processes associated with RNA, including ribosome biosynthesis, transcription, mRNA splicing and translation. Increasing evidence suggests that abnormal DHX32 expression contributes to cancer initiation and development, due to dysregulated cell proliferation, differentiation, apoptosis and other processes. In the current review, the discovery, structure and function of DHX32, as well as the association between abnormal DHX32 expression and tumors are discussed. DHX32 expression is downregulated in acute lymphoblastic leukemia, but upregulated in solid tumors, including colorectal and breast cancer. Furthermore, DHX32 expression levels are associated with the pathological and clinical features of the cancer. Therefore, DHX32 may serve as a novel liquid biopsy marker for auxiliary diagnosis and prognosis screening, as well as a possible target for cancer therapy. The molecular mechanism underlying the contribution of DHX32 towards the initiation and development of cancer requires further investigation for the development of anticancer treatments based on manipulating DHX32 expression and function.
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Affiliation(s)
- Qingchun Wei
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian 361102, P.R. China
| | - Jinting Geng
- Xiamen Key Laboratory of Biomarker Translational Medicine, Center of Medical Laboratory of Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
| | - Yongquan Chen
- Xiamen Key Laboratory of Biomarker Translational Medicine, Center of Medical Laboratory of Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
| | - Huayue Lin
- Center of Clinical Laboratory, Xiamen University Affiliated Zhongshan Hospital, Xiamen, Fujian 361104, P.R. China
| | - Jiajia Wang
- Center of Clinical Laboratory, Xiamen University Affiliated Zhongshan Hospital, Xiamen, Fujian 361104, P.R. China
| | - Zanxi Fang
- Center of Clinical Laboratory, Xiamen University Affiliated Zhongshan Hospital, Xiamen, Fujian 361104, P.R. China
| | - Fen Wang
- Center for Cancer and Stem Cell Biology, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX 77030, USA
| | - Zhongying Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian 361102, P.R. China
- Xiamen Key Laboratory of Biomarker Translational Medicine, Center of Medical Laboratory of Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
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6
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Abdelkrim YZ, Banroques J, Kyle Tanner N. Known Inhibitors of RNA Helicases and Their Therapeutic Potential. Methods Mol Biol 2021; 2209:35-52. [PMID: 33201461 DOI: 10.1007/978-1-0716-0935-4_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
RNA helicases are proteins found in all kingdoms of life, and they are associated with all processes involving RNA from transcription to decay. They use NTP binding and hydrolysis to unwind duplexes, to remodel RNA structures and protein-RNA complexes, and to facilitate the unidirectional metabolism of biological processes. Viral, bacterial, and eukaryotic parasites have an intimate need for RNA helicases in their reproduction. Moreover, various disorders, like cancers, are often associated with a perturbation of the host's helicase activity. Thus, RNA helicases provide a rich source of targets for the development of therapeutic or prophylactic drugs. In this review, we provide an overview of the different targeting strategies against helicases, the different types of compounds explored, the proposed inhibitory mechanisms of the compounds on the proteins, and the therapeutic potential of these compounds in the treatment of various disorders.
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Affiliation(s)
- Yosser Zina Abdelkrim
- Expression Génétique Microbienne, UMR8261 CNRS, Institut de Biologie Physico-Chimique, Université de Paris, Paris, France.,Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis/Université de Tunis el Manar, Tunis-Belvédère, Tunisia
| | - Josette Banroques
- Expression Génétique Microbienne, UMR8261 CNRS, Institut de Biologie Physico-Chimique, Université de Paris, Paris, France.,PSL Research University, Paris, France
| | - N Kyle Tanner
- Expression Génétique Microbienne, UMR8261 CNRS, Institut de Biologie Physico-Chimique, Université de Paris, Paris, France.
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7
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Yasmin R, Kaur I, Tuteja R. Plasmodium falciparum DDX55 is a nucleocytoplasmic protein and a 3'-5' direction-specific DNA helicase. PROTOPLASMA 2020; 257:1049-1067. [PMID: 32125511 DOI: 10.1007/s00709-020-01495-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 02/19/2020] [Indexed: 06/10/2023]
Abstract
Malaria is one of the major causes of mortality as well as morbidity in many tropical and subtropical countries around the world. Although artemisinin combination therapies (ACTs) are contributing to substantial decline in the worldwide malaria burden, it is becoming vulnerable by the emergence of artemisinin resistance in Plasmodium falciparum leading to clinical failure of ACTs in Southeast Asia. Helicases play important role in nucleic acid metabolic processes and have been also identified as therapeutic drug target for different diseases. Previously, it has been reported that P. falciparum contains a group of DEAD-box family of helicases which are homologous to Has1 family of yeast. Here, we present the characterization of a member of Has1 family (PlasmoDB number PF3D7_1419100) named as PfDDX55. The biochemical characterization of PfDDX55C revealed that it contains both DNA- and RNA-dependent ATPase activity. PfDDX55C unwinds partially duplex DNA in 3' to 5' direction and utilizes mainly ATP or dATP for its activity. The immunofluorescence assay and q-RT PCR analysis show that PfDDX55 is a nucleocytoplasmic protein expressed in all the intraerythrocytic development of P. falciparum 3D7 strain with maximum expression level in trophozoite stage. The LC-MS/MS experiment results and STRING analysis show that PfDDX55 interacts with AAA-ATPase which has been shown to be involved in ribosomal biogenesis.
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Affiliation(s)
- Rahena Yasmin
- Parasite Biology Group, ICGEB, P. O. Box 10504, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Inderjeet Kaur
- Malaria Biology Group, ICGEB, P. O. Box 10504, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Renu Tuteja
- Parasite Biology Group, ICGEB, P. O. Box 10504, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Lalle M, Fiorillo A. The protein 14-3-3: A functionally versatile molecule in Giardia duodenalis. ADVANCES IN PARASITOLOGY 2019; 106:51-103. [PMID: 31630760 DOI: 10.1016/bs.apar.2019.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Giardia duodenalis is a cosmopolitan zoonotic protozoan parasite causing giardiasis, one of the most common diarrhoeal diseases in human and animals. Beyond its public health relevance, Giardia represents a valuable and fascinating model microorganism. The deep-branching phylogenetic position of Giardia, its simple life cycle and its minimalistic genomic and cellular organization provide a unique opportunity to define basal and "ancestral" eukaryotic functions. The eukaryotic 14-3-3 protein family represents a distinct example of phosphoserine/phosphothreonine-binding proteins. The extended network of protein-protein interactions established by 14-3-3 proteins place them at the crossroad of multiple signalling pathways that regulate physiological and pathological cellular processes. Despite the remarkable insight on 14-3-3 protein in different organisms, from yeast to humans, so far little attention was given to the study of this protein in protozoan parasites. However, in the last years, research efforts have provided evidences on unique properties of the single 14-3-3 protein of Giardia and on its association in key aspects of Giardia life cycle. In the first part of this chapter, a general overview of the features commonly shared among 14-3-3 proteins in different organisms (i.e. structure, target recognition, mode of action and regulatory mechanisms) is included. The second part focus on the current knowledge on the biochemistry and biology of the Giardia 14-3-3 protein and on the possibility to use this protein as target to propose new strategies for developing innovative antigiardial therapy.
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Affiliation(s)
- Marco Lalle
- Department of Infectious Diseases, European Union Reference Laboratory for Parasites, Istituto Superiore di Sanità, Rome, Italy.
| | - Annarita Fiorillo
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
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Plasmodium falciparum specific helicase 2 is a dual, bipolar helicase and is crucial for parasite growth. Sci Rep 2019; 9:1519. [PMID: 30728406 PMCID: PMC6365506 DOI: 10.1038/s41598-018-38032-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 12/19/2018] [Indexed: 12/24/2022] Open
Abstract
Human malaria infection is a major challenge across the globe and is responsible for millions of deaths annually. Rapidly emerging drug resistant strains against the new class of anti-malarial drugs are major threat to control the disease burden worldwide. Helicases are present in every organism and have important role in various nucleic acid metabolic processes. Previously we have reported the presence of three parasite specific helicases (PSH) in Plasmodium falciparum 3D7 strain. Here we present the detailed biochemical characterization of PfPSH2. PfPSH2 is DNA and RNA stimulated ATPase and is able to unwind partially duplex DNA and RNA substrates. It can translocate in both 3' to 5' and 5' to 3' directions. PfPSH2 is expressed in all the stages of intraerythrocytic development and it is localized in cytoplasm in P. falciparum 3D7 strain. The dsRNA mediated inhibition study suggests that PfPSH2 is important for the growth and survival of the parasite. This study presents the detailed characterization of PfPSH2 and lays the foundation for future development of PfPSH2 as drug target.
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Reddy S, Singh S. Investigation of hub genes and their nonsynonymous single nucleotide polymorphism analysis in Plasmodium falciparum for designing therapeutic methodologies using next-generation sequencing approach. Indian J Pharmacol 2019; 51:389-399. [PMID: 32029961 PMCID: PMC6984025 DOI: 10.4103/ijp.ijp_535_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/18/2019] [Accepted: 12/23/2019] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND: Incidences of resistance to current drugs by Plasmodium is increasing, hence, it is necessary to investigate and explore new drug targets to combat malarial disease. OBJECTIVE: Analysis of the transcriptome sequence information to characterize hub genes and their nonsynonymous single nucleotide polymorphisms (nsSNPs) to derive therapeutic objectives for Plasmodium falciparum. MATERIALS AND METHODS: Differentially expressed genes between Ring and other stages of P. falciparum were identified using Cufflinks tool. Using DAVID and KAAS programs, the gene ontology and pathway analysis were performed. The networks of protein-protein interaction (PPI) were developed by Search Tool for the Retrieval of Interacting Genes/Proteins and Cytoscape, and the node degree in the network was calculated by using Network Analyzer, and MCODE plugins of Cytoscape. SIFT, PROVEAN, and PredictSNP programs were used to study the genetic variations, which affect protein functions. RESULTS: A list of 4196 nonredundant genes was used for functional annotation cluster analysis, and 8 significant hub genes have been picked from the PPI network using MCODE plugins of Cytoscape. Various nsSNPs were identified in these 8 hub genes and were investigated both for its native and mutant stage for solvent accessibility and alteration in secondary structure protein residues. CONCLUSION: Hub genes identified in this study serve as potential targets to develop therapy to suppress the pathogenic action of P. falciprum through experimental techniques.
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Abdelkrim YZ, Harigua-Souiai E, Barhoumi M, Banroques J, Blondel A, Guizani I, Tanner NK. The steroid derivative 6-aminocholestanol inhibits the DEAD-box helicase eIF4A (LieIF4A) from the Trypanosomatid parasite Leishmania by perturbing the RNA and ATP binding sites. Mol Biochem Parasitol 2018; 226:9-19. [PMID: 30365976 DOI: 10.1016/j.molbiopara.2018.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/01/2018] [Accepted: 10/19/2018] [Indexed: 11/20/2022]
Abstract
The antifungal agent 6-aminocholestanol targets the production of ergosterol, which is the principle sterol in many fungi and protozoans; ergosterol serves many of the same roles as cholesterol in animals. We found that it also is an effective inhibitor of the translation-initiation factor eIF4AI from mouse (eIF4AIMus) and the Trypanosomatid parasite Leishmania (LieIF4A). The eIF4A proteins belong to the DEAD-box family of RNA helicases, which are ATP-dependent RNA-binding proteins and RNA-dependent ATPases. DEAD-box proteins contain a commonly-shared core structure consisting of two linked domains with structural homology to that of recombinant protein A (RecA) and that contain conserved motifs that are involved in RNA and ATP binding, and in the enzymatic activity. The compound inhibits both the ATPase and helicase activities by perturbing ATP and RNA binding, and it is capable of binding other proteins containing nucleic acid-binding sites as well. We undertook kinetic analyses and found that the Leishmania LieIF4A protein binds 6-aminocholestanol with a higher apparent affinity than for ATP, although multiple binding sites were probably involved. Competition experiments with the individual RecA-like domains indicate that the primary binding sites are on RecA-like domain 1, and they include a cavity that we previously identified by molecular modeling of LieIF4A that involve conserved RNA-binding motifs. The compound affects the mammalian and Leishmania proteins differently, which indicates the binding sites and affinities are not the same. Thus, it is possible to develop drugs that target DEAD-box proteins from different organisms even when they are implicated in the same biological process.
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Affiliation(s)
- Yosser Zina Abdelkrim
- Expression Génétique Microbienne, CNRS UMR8261/Université Paris Diderot-Paris 7 & Paris Sciences et Lettres Research University, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis/Université de Tunis el Manar, 13 Place Pasteur, BP74 Tunis-Belvédère, 1002 Tunisia; Faculté des Sciences de Bizerte, Université de Carthage, 7021 Zarzouna-Bizerte, Tunisia
| | - Emna Harigua-Souiai
- Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis/Université de Tunis el Manar, 13 Place Pasteur, BP74 Tunis-Belvédère, 1002 Tunisia
| | - Mourad Barhoumi
- Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis/Université de Tunis el Manar, 13 Place Pasteur, BP74 Tunis-Belvédère, 1002 Tunisia
| | - Josette Banroques
- Expression Génétique Microbienne, CNRS UMR8261/Université Paris Diderot-Paris 7 & Paris Sciences et Lettres Research University, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Arnaud Blondel
- Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Institut Pasteur, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Ikram Guizani
- Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis/Université de Tunis el Manar, 13 Place Pasteur, BP74 Tunis-Belvédère, 1002 Tunisia.
| | - N Kyle Tanner
- Expression Génétique Microbienne, CNRS UMR8261/Université Paris Diderot-Paris 7 & Paris Sciences et Lettres Research University, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
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Fei J, Wu H, Su J, Jin C, Li N, Guo Y, Feng Y, Xiao L. Characterization of MEDLE-1, a protein in early development of Cryptosporidium parvum. Parasit Vectors 2018; 11:312. [PMID: 29792229 PMCID: PMC5966890 DOI: 10.1186/s13071-018-2889-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/07/2018] [Indexed: 11/10/2022] Open
Abstract
Background Cryptosporidium spp. are important diarrhea-causing pathogens in humans and animals. Comparative genomic analysis indicated that Cryptosporidium-specific MEDLE family proteins may contribute to host adaptation of Cryptosporidium spp., and a recent study of one member of this family, CpMEDLE-2 encoded by cgd5_4590, has provided evidence supporting this hypothesis. In this study, another member of the protein family, CpMEDLE-1 of Cryptosporidium parvum encoded by cgd5_4580, which is distinct from CpMEDLE-2 and has no signature motif MEDLE, was cloned, expressed and characterized to understand its function. Methods CpMEDLE-1 was expressed in Escherichia coli and polyclonal antibodies against the recombinant CpMEDLE-1 protein were prepared in rabbits. Quantitative PCR was used to analyze the expression profile of cgd5_4580 in C. parvum culture. Immunofluorescence staining was used to locate CpMEDLE-1 expression in life-cycle stages, and in vitro neutralization assay with antibodies was adopted to assess the role of the protein in C. parvum invasion. Results The results indicated that cgd5_4580 had a peak expression at 2 h of C. parvum culture. CpMEDLE-1 was located in the mid-anterior region of sporozoites, probably within the dense granules. The neutralization efficiency of anti-CpMEDLE-1 antibodies was approximately 40%. Conclusions The differences in protein and gene expression profiles between CpMEDLE-1 and CpMEDLE-2 suggest that MEDLE proteins have different subcellular locations, are developmentally regulated, could be potentially involved in the transcriptional regulation of the expression of parasite or host proteins and may exert their functions in different stages of the invasion and development process.
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Affiliation(s)
- Jilan Fei
- State Key Laboratory of Bioreactor Engineering, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Haizhen Wu
- School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Jiayuan Su
- State Key Laboratory of Bioreactor Engineering, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Chanchan Jin
- State Key Laboratory of Bioreactor Engineering, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Na Li
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Yaqiong Guo
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Yaoyu Feng
- State Key Laboratory of Bioreactor Engineering, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China. .,Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
| | - Lihua Xiao
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
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13
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Chauhan M, Tarique M, Tuteja R. Plasmodium falciparum specific helicase 3 is nucleocytoplasmic protein and unwinds DNA duplex in 3' to 5' direction. Sci Rep 2017; 7:13146. [PMID: 29030567 PMCID: PMC5640622 DOI: 10.1038/s41598-017-12927-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/20/2017] [Indexed: 02/08/2023] Open
Abstract
Plasmodium falciparum is responsible for most dangerous and prevalent form of malaria. The emergence of multi drug resistant parasite hindered the prevention of malaria burden worldwide. Helicases are omnipresent enzymes, which play important role in nucleic acid metabolism and can be used as potential targets for development of novel therapeutics. The genome wide analysis of P. falciparum 3D7 strain revealed some novel parasite specific helicases, which are not present in human host. Here we report the detailed biochemical characterization of P. falciparum parasite specific helicase 3 (PfPSH3). The characteristic ATPase and helicase activities of PfPSH3 reside in its N-terminal region (PfPSH3N) as it contains all the conserved signature motifs whereas the C-terminal does not show any detectable biochemical activity. PfPSH3N also shows DNA helicase activity in the 3′–5′ direction. The immunofluorescence microscopy results show that PSH3 is localized in nucleus as well as in cytoplasm during different stages such as trophozoite and early schizont stages of intraerythrocytic development. This report sets the foundation for further study of parasite specific helicases and will be helpful in understanding the parasite biology.
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Affiliation(s)
- Manish Chauhan
- Parasite Biology Group, International Centre for Genetic Engineering and Biotechnology, P. O. Box 10504, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mohammed Tarique
- Parasite Biology Group, International Centre for Genetic Engineering and Biotechnology, P. O. Box 10504, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Renu Tuteja
- Parasite Biology Group, International Centre for Genetic Engineering and Biotechnology, P. O. Box 10504, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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14
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da Costa KS, Galúcio JMP, Leonardo ES, Cardoso G, Leal É, Conde G, Lameira J. Structural and evolutionary analysis of Leishmania Alba proteins. Mol Biochem Parasitol 2017; 217:23-31. [PMID: 28847609 DOI: 10.1016/j.molbiopara.2017.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/23/2017] [Accepted: 08/18/2017] [Indexed: 01/10/2023]
Abstract
The Alba superfamily proteins share a common RNA-binding domain. These proteins participate in a variety of regulatory pathways by controlling developmental gene expression. They also interact with ribosomal subunits, translation factors, and other RNA-binding proteins. The Leishmania infantum genome encodes two Alba-domain proteins, LiAlba1 and LiAlba3. In this work, we used homology modeling, protein-protein docking, and molecular dynamics (MD) simulations to explore the details of the Alba1-Alba3-RNA complex from Leishmania infantum at the molecular level. In addition, we compared the structure of LiAlba3 with the human ribonuclease P component, Rpp20. We also mapped the ligand-binding residues on the Alba3 surface to analyze its druggability and performed mutational analyses in Alba3 using alanine scanning to identify residues involved in its function and structural stability. These results suggest that the RGG-box motif of LiAlba1 is important for protein function and stability. Finally, we discuss the function of Alba proteins in the context of pathogen adaptation to host cells. The data provided herein will facilitate further translational research regarding Alba structure and function.
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Affiliation(s)
- Kauê Santana da Costa
- Institute of Biodiversity, Federal University of West of Pará, Santarém, Pará, Brazil
| | | | - Elvis Santos Leonardo
- Institute of Biodiversity, Federal University of West of Pará, Santarém, Pará, Brazil
| | - Guelber Cardoso
- Institute of Biological Sciences, Federal University of Pará, 66075-110 Belém, Pará, Brazil
| | - Élcio Leal
- Institute of Biological Sciences, Federal University of Pará, 66075-110 Belém, Pará, Brazil
| | - Guilherme Conde
- Institute of Biodiversity, Federal University of West of Pará, Santarém, Pará, Brazil
| | - Jerônimo Lameira
- Institute of Biological Sciences, Federal University of Pará, 66075-110 Belém, Pará, Brazil.
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