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Yu Y, Li J, Wang W, Wang T, Qi W, Zheng X, Duan L, Chen J, Li S, Han X, Zhang W, Duan L. Transcriptome analysis uncovers the key pathways and candidate genes related to the treatment of Echinococcus granulosus protoscoleces with the repurposed drug pyronaridine. BMC Genomics 2021; 22:534. [PMID: 34256697 PMCID: PMC8276484 DOI: 10.1186/s12864-021-07875-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 07/01/2021] [Indexed: 11/10/2022] Open
Abstract
Background Cystic echinococcosis (CE) is a life-threatening zoonosis caused by the larval form of Echinococcus granulosus tapeworm. Our previous study showed that an approved drug pyronaridine (PND) is highly effective against CE, both in vitro and in an animal model. To identify possible target genes, transcriptome analysis was performed with E. granulosus sensu stricto protoscoleces treated with PND. Results A total of 1,321 genes were differentially expressed in protoscoleces treated with PND, including 541 upregulated and 780 downregulated genes. Gene ontology and KEGG analyses revealed that the spliceosome, mitogen-activated protein kinase (MAPK) pathway and ATP-binding cassette (ABC) transporters were the top three enriched pathways. Western blot analysis showed that PND treatment resulted in a dose-dependent increase in protein expression levels of EgMKK1 (MKK3/6-like) and EgMKK2 (MEK1/2-like), two members of MAPK cascades. Interestingly, several heat shock protein (HSP) genes were greatly downregulated including stress-inducible HSPs and their constitutive cognates, and some of them belong to Echinococcus-specific expansion of HSP70. Conclusions PND has a great impact on the spliceosome, MAPK pathway and ABC transporters, which may underline the mechanisms by which PND kills E. granulosus protoscoleces. In addition, PND downregulates HSPs expression, suggesting a close relationship between the drug and HSPs. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07875-w.
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Affiliation(s)
- Yingfang Yu
- NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 200025, Shanghai, China
| | - Jun Li
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, the First Affiliated Hospital of Xinjiang Medical University, 830054, Urumqi, China
| | - Weisi Wang
- NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 200025, Shanghai, China
| | - Tian Wang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, the First Affiliated Hospital of Xinjiang Medical University, 830054, Urumqi, China
| | - Wenjing Qi
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, the First Affiliated Hospital of Xinjiang Medical University, 830054, Urumqi, China
| | - Xueting Zheng
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, the First Affiliated Hospital of Xinjiang Medical University, 830054, Urumqi, China
| | - Lei Duan
- NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 200025, Shanghai, China
| | - Jiaxu Chen
- NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 200025, Shanghai, China
| | - Shizhu Li
- NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 200025, Shanghai, China
| | - Xiumin Han
- Qinghai Provincial People's Hospital, 810007, Xining, China
| | - Wenbao Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, the First Affiliated Hospital of Xinjiang Medical University, 830054, Urumqi, China.
| | - Liping Duan
- NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 200025, Shanghai, China. .,Qinghai Provincial People's Hospital, 810007, Xining, China.
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Gao L, Yuan Z, Yu S, Yang Y, Li Y, He C. Genome-wide identification of HSP70/110 genes in sea cucumber Apostichopus japonicus and comparative analysis of their involvement in aestivation. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 28:162-171. [PMID: 30265919 DOI: 10.1016/j.cbd.2018.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/09/2018] [Accepted: 07/09/2018] [Indexed: 12/18/2022]
Abstract
HSP70/110s are a subgroup of heat shock proteins and play crucial roles in protein homeostasis. HSP70/110s can enhance cell survival in response to a multitude of stressful stimuli, of which the most studied one is heat stress. To perform a systematic study of HSP70/110s in sea cucumber Apostichopus japonicus, 15 HSP70/110 genes, including 13 HSP70s and two HSP110s, were identified and characterized from the transcriptome and genome of sea cucumber. Moderate expansion and conserved structure were found by the phylogenetic and syntenic analysis. Differential expression patterns of HSP70/110s were observed in adult individuals during aestivation, with the comparison of juvenile individuals without aestivation in chronic heat stress. Tissue-specific expression profiles were found both in adult and juvenile individuals, which might indicate that the functional tissues (intestine and respiratory tree) could be restored to normal physiological activity prior to protecting and sporting tissues (body wall and muscle). Differential expression profiles were also observed between the adult and juvenile individuals, which was mainly due to the hypometabolism in aestivation. Taken together, tissue-specific pattern and individual-specific pattern were observed in the HSP70/110 expression profiles in sea cucumber during aestivation. These findings could provide early insight into the involvement of HSP70/110s in the aestivation of marine invertebrate.
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Affiliation(s)
- Lei Gao
- Key Laboratory of Marine Fishery Molecular Biology of Liaoning Province, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, China.
| | - Zihao Yuan
- The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Simeng Yu
- Key Laboratory of Marine Fishery Molecular Biology of Liaoning Province, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, China
| | - Yujia Yang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Yunfeng Li
- Key Laboratory of Marine Fishery Molecular Biology of Liaoning Province, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, China
| | - Chongbo He
- Key Laboratory of Marine Fishery Molecular Biology of Liaoning Province, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, China
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Koziol U, Radio S, Smircich P, Zarowiecki M, Fernández C, Brehm K. A Novel Terminal-Repeat Retrotransposon in Miniature (TRIM) Is Massively Expressed in Echinococcus multilocularis Stem Cells. Genome Biol Evol 2015; 7:2136-53. [PMID: 26133390 PMCID: PMC4558846 DOI: 10.1093/gbe/evv126] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2015] [Indexed: 12/14/2022] Open
Abstract
Taeniid cestodes (including the human parasites Echinococcus spp. and Taenia solium) have very few mobile genetic elements (MGEs) in their genome, despite lacking a canonical PIWI pathway. The MGEs of these parasites are virtually unexplored, and nothing is known about their expression and silencing. In this work, we report the discovery of a novel family of small nonautonomous long terminal repeat retrotransposons (also known as terminal-repeat retrotransposons in miniature, TRIMs) which we have named ta-TRIM (taeniid TRIM). ta-TRIMs are only the second family of TRIM elements discovered in animals, and are likely the result of convergent reductive evolution in different taxonomic groups. These elements originated at the base of the taeniid tree and have expanded during taeniid diversification, including after the divergence of closely related species such as Echinococcus multilocularis and Echinococcus granulosus. They are massively expressed in larval stages, from a small proportion of full-length copies and from isolated terminal repeats that show transcriptional read-through into downstream regions, generating novel noncoding RNAs and transcriptional fusions to coding genes. In E. multilocularis, ta-TRIMs are specifically expressed in the germinative cells (the somatic stem cells) during asexual reproduction of metacestode larvae. This would provide a developmental mechanism for insertion of ta-TRIMs into cells that will eventually generate the adult germ line. Future studies of active and inactive ta-TRIM elements could give the first clues on MGE silencing mechanisms in cestodes.
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Affiliation(s)
- Uriel Koziol
- Institute of Hygiene and Microbiology, University of Würzburg, Germany Sección Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Santiago Radio
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Pablo Smircich
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Magdalena Zarowiecki
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Cecilia Fernández
- Cátedra de Inmunología, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Klaus Brehm
- Institute of Hygiene and Microbiology, University of Würzburg, Germany
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Abstract
The genomes of more than 20 helminths have now been sequenced. Here we perform a meta-analysis of all sequenced genomes of nematodes and Platyhelminthes, and attempt to address the question of what are the defining characteristics of helminth genomes. We find that parasitic worms lack systems for surface antigenic variation, instead maintaining infections using their surfaces as the first line of defence against the host immune system, with several expanded gene families of genes associated with the surface and tegument. Parasite excretory/secretory products evolve rapidly, and proteases even more so, with each parasite exhibiting unique modifications of its protease repertoire. Endoparasitic flatworms show striking losses of metabolic capabilities, not matched by nematodes. All helminths do however exhibit an overall reduction in auxiliary metabolism (biogenesis of co-factors and vitamins). Overall, the prevailing pattern is that there are few commonalities between the genomes of independently evolved parasitic worms, with each parasite having undergone specific adaptations for their particular niche.
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Bedulina DS, Evgen'ev MB, Timofeyev MA, Protopopova MV, Garbuz DG, Pavlichenko VV, Luckenbach T, Shatilina ZM, Axenov-Gribanov DV, Gurkov AN, Sokolova IM, Zatsepina OG. Expression patterns and organization of thehsp70genes correlate with thermotolerance in two congener endemic amphipod species (Eulimnogammarus cyaneusandE. verrucosus) from Lake Baikal. Mol Ecol 2013; 22:1416-30. [DOI: 10.1111/mec.12136] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 10/09/2012] [Accepted: 10/10/2012] [Indexed: 12/14/2022]
Affiliation(s)
- D. S. Bedulina
- Irkutsk State University; Karl-Marx str. 1 Irkutsk 664003 Russia
- Baikal Research Centre; Lenina str. 3 Irkutsk 664003 Russia
| | - M. B. Evgen'ev
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; Vaviolva str. 32 Moscow 119991 Russia
- Institute of Cell Biophysics; Russian Academy of Sciences; Institutskaya str. 3 Pushchino 142290 Russia
| | - M. A. Timofeyev
- Irkutsk State University; Karl-Marx str. 1 Irkutsk 664003 Russia
- Baikal Research Centre; Lenina str. 3 Irkutsk 664003 Russia
| | - M. V. Protopopova
- Irkutsk State University; Karl-Marx str. 1 Irkutsk 664003 Russia
- Siberian Institute of Plant Physiology and Biochemistry; Siberian Branch Russian Academy of Sciences; Lermontov str. 132 Irkutsk 664033 Russia
| | - D. G. Garbuz
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; Vaviolva str. 32 Moscow 119991 Russia
| | - V. V. Pavlichenko
- Irkutsk State University; Karl-Marx str. 1 Irkutsk 664003 Russia
- Siberian Institute of Plant Physiology and Biochemistry; Siberian Branch Russian Academy of Sciences; Lermontov str. 132 Irkutsk 664033 Russia
| | - T. Luckenbach
- UFZ Helmholtz Centre for Environmental Research; Department of Bioanalytical Ecotoxicology; Permoserstr.15 Leipzig 04318 Germany
| | - Z. M. Shatilina
- Irkutsk State University; Karl-Marx str. 1 Irkutsk 664003 Russia
- Baikal Research Centre; Lenina str. 3 Irkutsk 664003 Russia
| | - D. V. Axenov-Gribanov
- Irkutsk State University; Karl-Marx str. 1 Irkutsk 664003 Russia
- Baikal Research Centre; Lenina str. 3 Irkutsk 664003 Russia
| | - A. N. Gurkov
- Irkutsk State University; Karl-Marx str. 1 Irkutsk 664003 Russia
- Baikal Research Centre; Lenina str. 3 Irkutsk 664003 Russia
| | - I. M. Sokolova
- Department of Biology; University of North Carolina at Charlotte; 9201 University City Blvd. Charlotte NC 28223 USA
| | - O. G. Zatsepina
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; Vaviolva str. 32 Moscow 119991 Russia
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Olson PD, Zarowiecki M, Kiss F, Brehm K. Cestode genomics - progress and prospects for advancing basic and applied aspects of flatworm biology. Parasite Immunol 2012; 34:130-50. [PMID: 21793855 DOI: 10.1111/j.1365-3024.2011.01319.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Characterization of the first tapeworm genome, Echinococcus multilocularis, is now nearly complete, and genome assemblies of E. granulosus, Taenia solium and Hymenolepis microstoma are in advanced draft versions. These initiatives herald the beginning of a genomic era in cestodology and underpin a diverse set of research agendas targeting both basic and applied aspects of tapeworm biology. We discuss the progress in the genomics of these species, provide insights into the presence and composition of immunologically relevant gene families, including the antigen B- and EG95/45W families, and discuss chemogenomic approaches toward the development of novel chemotherapeutics against cestode diseases. In addition, we discuss the evolution of tapeworm parasites and introduce the research programmes linked to genome initiatives that are aimed at understanding signalling systems involved in basic host-parasite interactions and morphogenesis.
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Affiliation(s)
- P D Olson
- Department of Zoology, The Natural History Museum, London, UK
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Cai P, Hou N, Piao X, Liu S, Liu H, Yang F, Wang J, Jin Q, Wang H, Chen Q. Profiles of small non-coding RNAs in Schistosoma japonicum during development. PLoS Negl Trop Dis 2011; 5:e1256. [PMID: 21829742 PMCID: PMC3149011 DOI: 10.1371/journal.pntd.0001256] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 06/14/2011] [Indexed: 12/25/2022] Open
Abstract
Background The gene regulation mechanism along the life cycle of the genus Schistosoma is complex. Small non-coding RNAs (sncRNAs) are essential post transcriptional gene regulation elements that affect gene expression and mRNA stability. Preliminary studies indicated that sncRNAs in schistosomal parasites are generated through different pathways, which are developmentally regulated. However, the data of sncRNAs of schistosomal parasites are still fragmental and a complete expression profile of sncRNAs during the parasite development requires a deep investigation. Methodology/Principal Findings We employed high-throughput genome-wide transcriptome analytic techniques to explore the dynamic expression of microRNAs (miRNAs) and endogenous siRNAs (endo-siRNAs) of Schistosoma japonicum covering the free-living cercarial stage and all stages in the definitive host. This led us to analyze over 70 million clean reads represented both high and low abundance of the small RNA population. Patterns of differential expression of miRNAs and endo-siRNAs were observed. MiRNAs was twice more than endo-siRNAs in cercariae, but gradually decreased along with the development of the parasite. Both small RNA types were presented in equal aboudance in lung-stage schistosomula, while endo-siRNAs accumulated to 6 times more than miRNAs in adult female worms and hepatic eggs. Further, miRNAs were found mainly derived from genes located in the intergenic regions, while endo-siRNAs were mainly generated from transposable elements (TEs). The expression pattern of TE-siRNAs, as well as the pseudogene-derived siRNAs clustered in mRNAs of cytoskeletal proteins, stress proteins, enzymes related to energy metabolism also revealed distinction throughout different developmental stages. Natural antisense transcripts (NATs)-related siRNAs accounted for minor proportion of the endo-siRNAs which were dominantly expressed in cercariae. Conclusions/Significance Our results represented a comprehensive expression profile of sncRNAs in various developmental stages of S. japonicum with high accuracy and coverage. The data would facilitate a deep understanding of the parasite biology and potential discovery of novel targets for the design of anti-parasite drugs. Schistosomiasis, a debilitating disease, caused by agents of the genus Schistosoma afflicts more than 200 million people worldwide. Schistosomes could serve as an interesting model to explore gene regulation due to its evolutional position, complex life cycle and sexual dimorphism. We previously indicated that sncRNA profile in the parasite S. japonicum was developmentally regulated in hepatic and adult stages. In this study, we systematically investigated mircoRNA (miRNA) and endogenous siRNA (endo-siRNA) profile in this parasite in more detailed developmental stages (cercariae, lung-stage schistosomula, separated adult worms, and liver tissue-trapped eggs) using high-throughput RNA sequencing technology. We observed that the ratio of miRNAs to endo-siRNAs was dynamically changed throughout different developmental stages of the parasite. MiRNAs were expressed dominantly in cercariae, while endo-siRNAs accumulated in adult female worms and hepatic eggs. We demonstrated that miRNAs were mostly derived from intergenic regions whereas siRNAs were mostly derived from transposable elements. We also annotated miRNAs and siRNAs with stage- and gender- biased expression. Our findings would facilitate to understand the gene regulation mechanism of this parasite and discover novel targets for anti-parasite drugs.
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Affiliation(s)
- Pengfei Cai
- Laboratory of Parasitology, Institute of Pathogen Biology/Institute of Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Nan Hou
- Laboratory of Parasitology, Institute of Pathogen Biology/Institute of Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xianyu Piao
- Laboratory of Parasitology, Institute of Pathogen Biology/Institute of Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shuai Liu
- Laboratory of Parasitology, Institute of Pathogen Biology/Institute of Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haiying Liu
- Laboratory of Parasitology, Institute of Pathogen Biology/Institute of Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fan Yang
- Laboratory of Parasitology, Institute of Pathogen Biology/Institute of Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianwei Wang
- Laboratory of Parasitology, Institute of Pathogen Biology/Institute of Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qi Jin
- Laboratory of Parasitology, Institute of Pathogen Biology/Institute of Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Heng Wang
- Laboratory of Parasitology, Institute of Pathogen Biology/Institute of Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- * E-mail: (QC); (HW)
| | - Qijun Chen
- Laboratory of Parasitology, Institute of Pathogen Biology/Institute of Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, China
- * E-mail: (QC); (HW)
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