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Mitesser V, Simantov K, Dzikowski R. Time to switch gears: how long noncoding RNAs function as epigenetic regulators in Apicomplexan parasites. Curr Opin Microbiol 2024; 79:102484. [PMID: 38688159 DOI: 10.1016/j.mib.2024.102484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 04/08/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
Long noncoding RNAs (lncRNA) are emerging as important regulators of gene expression in eukaryotes. In recent years, a large repertoire of lncRNA were discovered in Apicomplexan parasites and were implicated in several mechanisms of gene expression, including marking genes for activation, contributing to the formation of subnuclear compartments and organization, regulating the deposition of epigenetic modifications, influencing chromatin and chromosomal structure and manipulating host gene expression. Here, we aim to update recent knowledge on the role of lncRNAs as regulators in Apicomplexan parasites and highlight the possible molecular mechanisms by which they function. We hope that some of the hypotheses raised here will contribute to further investigation and lead to new mechanistic insight and better understanding of the role of lncRNA in parasite's biology.
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Affiliation(s)
- Vera Mitesser
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Karina Simantov
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Ron Dzikowski
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
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Kent RS, Briggs EM, Colon BL, Alvarez C, Silva Pereira S, De Niz M. Paving the Way: Contributions of Big Data to Apicomplexan and Kinetoplastid Research. Front Cell Infect Microbiol 2022; 12:900878. [PMID: 35734575 PMCID: PMC9207352 DOI: 10.3389/fcimb.2022.900878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
In the age of big data an important question is how to ensure we make the most out of the resources we generate. In this review, we discuss the major methods used in Apicomplexan and Kinetoplastid research to produce big datasets and advance our understanding of Plasmodium, Toxoplasma, Cryptosporidium, Trypanosoma and Leishmania biology. We debate the benefits and limitations of the current technologies, and propose future advancements that may be key to improving our use of these techniques. Finally, we consider the difficulties the field faces when trying to make the most of the abundance of data that has already been, and will continue to be, generated.
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Affiliation(s)
- Robyn S. Kent
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, United States
| | - Emma M. Briggs
- Institute for Immunology and Infection Research, School of Biological Sciences, University Edinburgh, Edinburgh, United Kingdom
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Beatrice L. Colon
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Catalina Alvarez
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Sara Silva Pereira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Mariana De Niz
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
- Institut Pasteur, Paris, France
- *Correspondence: Mariana De Niz,
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Zeng Q, Hu B, Blanco AH, Zhang W, Zhao D, Martínez P, Hong Y. Full-Length Transcriptome Sequences Provide Insight Into Hermaphroditism of Freshwater Pearl Mussel Hyriopsis schlegelii. Front Genet 2022; 13:868742. [PMID: 35401664 PMCID: PMC8987123 DOI: 10.3389/fgene.2022.868742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
The freshwater mussel Hyriopsis schlegelii is a cultured bivalve in China, and the quality of the pearls produced is affected by the type of gonads. However, because of the lack of a published genome and the complexity of sex determination, research on sex reversal and development of this species is limited. In this study, Illumina RNA-seq and PacBio Isoform Sequencing (Iso-Seq) were combined to analyze the gonads of H. schlegelii. A total of 201,481 high-quality transcripts were generated. The study identified 7,922 differentially expressed genes in three comparison group (females versus males, hermaphrodites versus females, and hermaphrodites versus males). Twenty-four genes were identified as potential sex-related genes, including sox9 and wnt4 involved in sex determination, and vtg, cyp17a1 and 17β-hsd2 involved in gonadal development. We also speculated a possible pathways for the formation of hermaphroditism in H. schlegelii. The data provide a clear view of the transcriptome for H. schlegelii gonads and will be valuable in elucidating the mechanisms of gonad development.
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Affiliation(s)
- Qi Zeng
- School of Life Sciences, Nanchang University, Nanchang, China
- Key Lab of Aquatic Resources and Utilization of Jiangxi, Nanchang, China
| | - Beijuan Hu
- School of Life Sciences, Nanchang University, Nanchang, China
- Key Lab of Aquatic Resources and Utilization of Jiangxi, Nanchang, China
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang, China
| | - Andres Hortas Blanco
- Department of Zoology Genetics and Physical Anthropology, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
| | - Wanchang Zhang
- School of Life Sciences, Nanchang University, Nanchang, China
- Key Lab of Aquatic Resources and Utilization of Jiangxi, Nanchang, China
| | - Daxian Zhao
- School of Life Sciences, Nanchang University, Nanchang, China
- Key Lab of Aquatic Resources and Utilization of Jiangxi, Nanchang, China
| | - Paulino Martínez
- Department of Zoology Genetics and Physical Anthropology, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
| | - Yijiang Hong
- School of Life Sciences, Nanchang University, Nanchang, China
- Key Lab of Aquatic Resources and Utilization of Jiangxi, Nanchang, China
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang, China
- *Correspondence: Yijiang Hong,
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Olajide JS, Olopade B, Cai J. Functional Intricacy and Symmetry of Long Non-Coding RNAs in Parasitic Infections. Front Cell Infect Microbiol 2021; 11:751523. [PMID: 34692567 PMCID: PMC8531492 DOI: 10.3389/fcimb.2021.751523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/20/2021] [Indexed: 12/11/2022] Open
Abstract
RNAs are a class of molecules and the majority in eukaryotes are arbitrarily termed non- coding transcripts which are broadly classified as short and long non-coding RNAs. Recently, knowledge of the identification and functions of long non-coding RNAs have continued to accumulate and they are being recognized as important molecules that regulate parasite-host interface, parasite differentiation, host responses, and disease progression. Herein, we present and integrate the functions of host and parasite long non-coding RNAs during infections within the context of epigenetic re-programming and molecular crosstalk in the course of host-parasite interactions. Also, the modular range of parasite and host long non-coding RNAs in coordinated parasite developmental changes and host immune dynamic landscapes are discussed. We equally canvass the prospects of long non-coding RNAs in disease diagnosis and prognosis. Hindsight and suggestions are offered with the aim that it will bolster our understanding for future works on host and parasite long non-coding RNAs.
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Affiliation(s)
- Joshua Seun Olajide
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Institute of Veterinary Research Chinese Academy of Agricultural Sciences, Lanzhou, China.,Centre for Distance Learning, Obafemi Awolowo University, Ile-Ife, Nigeria.,Jiangsu Co-Innovation Center for Prevention and Control of Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Bolatito Olopade
- Department of Medical Microbiology and Parasitology, College of Health Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Jianping Cai
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Institute of Veterinary Research Chinese Academy of Agricultural Sciences, Lanzhou, China.,Jiangsu Co-Innovation Center for Prevention and Control of Animal Infectious Diseases and Zoonoses, Yangzhou, China
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The repertoire of serine rhomboid proteases of piroplasmids of importance to animal and human health. Int J Parasitol 2021; 51:455-462. [PMID: 33610524 DOI: 10.1016/j.ijpara.2020.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 10/24/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023]
Abstract
Babesia, Theileria and Cytauxzoon are tick-borne apicomplexan protozoans of the order Piroplasmida, notorious for the diseases they cause in livestock, pets and humans. Host cell invasion is their Achilles heel, allowing for the development of drug or vaccine-based therapies. In other apicomplexans, cleavage of the transmembrane domain of adhesins by the serine rhomboid proteinase ROM4 is required for successful completion of invasion. In this study, we record and classify the rhomboid repertoire encoded in the genomes of 10 piroplasmid species pertaining to the lineages Babesia sensu stricto (s.s., Clade VI), Theileria sensu stricto (Clade IV), Theileria equi (Clade IV), Cytauxzoon felis (Clade IIIb) and Babesia microti (Clade I), as defined by Schnittger et al. (2012). Fifty-six piroplasmid rhomboid-like proteins were assigned by phylogenetic analysis and bidirectional best hit to the ROM4, ROM6, ROM7 or ROM8 groups, and their crucial motifs for conformation and function were identified. Forty-four of these rhomboids had either been incorrectly classified or misannotated. Babesia s.s. encode five or three ROM4 proteinase paralogs, whereas the remaining piroplasmids encode two ROM4 paralogs. All piroplasmids encode a single ROM6, ROM7 and ROM8. Thus, an increased paralog number of ROM4 is the only feature distinguishing Babesia s.s. from other piroplasmid lineages. Piroplasmid ROM6 is related to the mammalian mitochondrial rhomboid and, accordingly, N-terminal mitochondrial targeting signal sequences was found in some cases. ROM6 is the only rhomboid encoded by piroplasmids that is ubiquitous in other organisms. ROM8 represents a pseudoproteinase that is highly conserved between studied piroplasmids, suggesting that it is important in regulatory functions. ROM4, ROM6, ROM7 and ROM8 are exclusively present in Aconoidasida, which comprises piroplasmids and Plasmodium, suggesting a relevant functional role in erythrocyte invasion. The correct classification and designation of piroplasmid rhomboids presented in this study facilitates an informed choice for future in-depth study of their functions.
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Shi K, Li J, Lv J, Liu P, Li J, Li S. Full-length transcriptome sequences of ridgetail white prawn Exopalaemon carinicauda provide insight into gene expression dynamics during thermal stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 747:141238. [PMID: 32799022 DOI: 10.1016/j.scitotenv.2020.141238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/10/2020] [Accepted: 07/23/2020] [Indexed: 06/11/2023]
Abstract
Marine heat waves and extreme high temperature become more frequent and intense in these years, which affected the survival of aquaculture animals. The ridgetail white prawn Exopalaemon carinicauda is an important economic species in eastern China, which has remarkable thermal tolerance. However, there has been little study of its thermal-adaptation mechanisms due to the complex genetic structure and unknown genome. To better understand the molecular mechanisms of E. carinicauda to adapt to the changing temperature, a combination of Illumina-based short reads RNA-seq and single molecule real-time-based full-length transcriptome sequencing was used in this study. In total, 17,212 unigenes from high-quality transcripts of E. carinicauda were generated and 14,663 complete ORFs were detected with an average length of 1980 bp. In addition, the transcriptome profiles of E. carinicauda treated with 34 °C heat stress for 6 and 24 h were analyzed. These differentially expressed genes were primarily enriched in oxidation-reduction process (Gene Ontology enrichment, GO) and the pathways of starch and sucrose metabolism (Kyoto Encyclopedia of Genes and Genomes enrichment, KEGG) after 6 h thermal stress, which indicated that E. carinicauda was suffering the attack by reactive oxygen species. After 24 h thermal stress, these differentially expressed genes were enriched in the pathway of lysosome, glycine, serine and threonine metabolism, fatty acid metabolism (KEGG), which indicated the oxidative stress was decreased. Interestingly, 40 genes for hemocyanin were found to be downregulated after 6 h heat stress, which indicated that the immunocompetence of E. carinicauda decreased after short term thermal stress (6 h). After 24 h thermal stress, E. carinicauda showed transcriptional adaptation to high temperature by upregulating of 11 genes encoding molecular chaperones, including HSP40 and HSP90 which were firstly reported to be related to thermal stress in E. carinicauda. These results promote a better understanding of the thermal-adaptation mechanism of E. carinicauda.
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Affiliation(s)
- Kunpeng Shi
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Jitao Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Jianjian Lv
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Ping Liu
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Jian Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China.
| | - Sedong Li
- Guangdong Evergreen Ltd. Corporation, Zhanjiang, PR China
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Zhou CX, Xie SC, Li MY, Huang CQ, Zhou HY, Cong H, Zhu XQ, Cong W. Analysis of the serum peptidome associated with Toxoplasma gondii infection. J Proteomics 2020; 222:103805. [PMID: 32387797 DOI: 10.1016/j.jprot.2020.103805] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 04/26/2020] [Accepted: 05/01/2020] [Indexed: 01/27/2023]
Abstract
Toxoplasma gondii is an obligate intracellular parasite that can cause severe disease in immunocompromised individuals and congenitally infected neonates. In order to determine whether serum peptide profile could reveal disease markers or allow determination of toxoplasmosis aggressiveness, mouse sera were collected from acutely infected, chronically infected and control subjects, and analyzed by a quantitative label-free pepdomics approach (LC-MS/MS). Six hundred and seven endogenous peptides were identified among all samples, with peptide profiling of difference that readily distinguished between acutely infected samples and other samples. Among these peptides detected in this study, 81 and 68 differentially expressed peptides (DEPs) were found in the acute and chronic infection stages, respectively. Through Gene Ontology analysis, most of the precursor proteins of these DEPs were associated with biological regulation and binding activity. These findings in this study will help in the search of peptide targets with a key role in disease diagnosis and create new opportunities for the development of better means for the prevention and control of toxoplasmosis. SIGNIFICANCE: Toxoplasma gondii is an unicellular parasite which infects humans and a wide range of warm-blooded animals. The serum peptidome contains a large set of low molecular weight endogenous peptides derived from secretion, protease activity and PTMs. In the present study we quantified the effects of T. gondii infection on the serum peptidome to identify novel disease regulated secretory factors. We developed an optimized label-free LC-MS/MS method to analyze endogenous peptides during toxoplasmosis progression. This resulted in quantification of 607 unique peptides at both acute and chronic infection stages. Collectively, our deep peptidomic analysis of serum revealed that peptide variations were affected by disease development, and peptidomics is an ideal method for quantifying changes in circulating factors on a global scale in response to pathophysiological perturbations such as T. gondii infection.
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Affiliation(s)
- Chun-Xue Zhou
- Department of Pathogen Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province 250012, PR China
| | - Shi-Chen Xie
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China
| | - Man-Yao Li
- Marine College, Shandong University, Weihai, Shandong Province 264209, PR China
| | - Cui-Qin Huang
- College of Life Sciences and Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan University, Longyan, Fujian Province 364012, PR China
| | - Huai-Yu Zhou
- Department of Pathogen Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province 250012, PR China
| | - Hua Cong
- Department of Pathogen Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province 250012, PR China
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China.
| | - Wei Cong
- Marine College, Shandong University, Weihai, Shandong Province 264209, PR China.
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Abstract
Toxoplasma gondii is a ubiquitous, intracellular protozoan parasite with a broad range of intermediate hosts, including humans and rodents. In many hosts, T. gondii establishes a latent long-term infection by converting from its rapidly dividing or lytic form to its slowly replicating and encysting form. In humans and rodents, the major organ for encystment is the central nervous system (CNS), which has led many to investigate how this persistent CNS infection might influence rodent and human behavior and, more recently, neurodegenerative diseases. Toxoplasma gondii is a ubiquitous, intracellular protozoan parasite with a broad range of intermediate hosts, including humans and rodents. In many hosts, T. gondii establishes a latent long-term infection by converting from its rapidly dividing or lytic form to its slowly replicating and encysting form. In humans and rodents, the major organ for encystment is the central nervous system (CNS), which has led many to investigate how this persistent CNS infection might influence rodent and human behavior and, more recently, neurodegenerative diseases. Given the interest in this topic, here we seek to take a global approach to the data for and against the effects of latent T. gondii on behavior and neurodegeneration and the proposed mechanisms that might underlie behavior modifications.
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Boothroyd JC. What a Difference 30 Years Makes! A Perspective on Changes in Research Methodologies Used to Study Toxoplasma gondii. Methods Mol Biol 2020; 2071:1-25. [PMID: 31758444 DOI: 10.1007/978-1-4939-9857-9_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Toxoplasma gondii is a remarkable species with a rich cell, developmental, and population biology. It is also sometimes responsible for serious disease in animals and humans and the stages responsible for such disease are relatively easy to study in vitro or in laboratory animal models. As a result of all this, Toxoplasma has become the subject of intense investigation over the last several decades, becoming a model organism for the study of the phylum of which it is a member, Apicomplexa. This has led to an ever-growing number of investigators applying an ever-expanding set of techniques to dissecting how Toxoplasma "ticks" and how it interacts with its many hosts. In this perspective piece I first wind back the clock 30 years and then trace the extraordinary pace of methodologies that have propelled the field forward to where we are today. In keeping with the theme of this collection, I focus almost exclusively on the parasite, rather than host side of the equation. I finish with a few thoughts about where the field might be headed-though if we have learned anything, the only sure prediction is that the pace of technological advance will surely continue to accelerate and the future will give us still undreamed of methods for taking apart (and then putting back together) this amazing organism with all its intricate biology. We have so far surely just scratched the surface.
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Affiliation(s)
- John C Boothroyd
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
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Abstract
Alternative splicing is a widespread, essential, and complex component of gene regulation. Apicomplexan parasites have long been recognized to produce alternatively spliced transcripts for some genes and can produce multiple protein products that are essential for parasite growth. Alternative splicing is a widespread, essential, and complex component of gene regulation. Apicomplexan parasites have long been recognized to produce alternatively spliced transcripts for some genes and can produce multiple protein products that are essential for parasite growth. Recent approaches are now providing more wide-ranging surveys of the extent of alternative splicing; some indicate that alternative splicing is less widespread than in other model eukaryotes, whereas others suggest levels comparable to those of previously studied groups. In many cases, apicomplexan alternative splicing events appear not to generate multiple alternative proteins but instead produce aberrant or noncoding transcripts. Nonetheless, appropriate regulation of alternative splicing is clearly essential in Plasmodium and Toxoplasma parasites, suggesting a biological role for at least some of the alternative splicing observed. Several studies have now disrupted conserved regulators of alternative splicing and demonstrated lethal effects in apicomplexans. This minireview discusses methods to accurately determine the extent of alternative splicing in Apicomplexa and discuss potential biological roles for this conserved process in a phylum of parasites with compact genomes.
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Chen LF, Han XL, Li FX, Yao YY, Fang JP, Liu XJ, Li XC, Wu K, Liu M, Chen XG. Comparative studies of Toxoplasma gondii transcriptomes: insights into stage conversion based on gene expression profiling and alternative splicing. Parasit Vectors 2018; 11:402. [PMID: 29996885 PMCID: PMC6042387 DOI: 10.1186/s13071-018-2983-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/27/2018] [Indexed: 11/19/2022] Open
Abstract
Background Toxoplasma gondii is one of the most important apicomplexan parasites and infects one-third of the human population worldwide. Transformation between the tachyzoite and bradyzoite stages in the intermediate host is central to chronic infection and life-long risk. There have been some transcriptome studies on T. gondii; however, we are still early in our understanding of the kinds and levels of gene expression that occur during the conversion between stages. Results We used high-throughput RNA-sequencing data to assemble transcripts using genome-based and de novo strategies. The expression-level analysis of 6996 T. gondii genes showed that over half (3986) were significantly differentially expressed during stage conversion, whereas 2205 genes were upregulated, and 1778 genes were downregulated in tachyzoites compared with bradyzoites. Several important gene families were expressed at relatively high levels. Comprehensive functional annotation and gene ontology analysis revealed that stress response-related genes are important for survival of bradyzoites in immune-competent hosts. We compared Trinity-based de novo and genome-based strategies, and found that the de novo assembly strategy compensated for the defects of the genome-based strategy by filtering out several transcripts with low expression or those unannotated on the genome. We also found some inaccuracies in the ToxoDB gene models. In addition, our analysis revealed that alternative splicing can be differentially regulated in response to life-cycle change. In depth analysis revealed a 20-nt, AG-rich sequence, alternative splicing locus from alt_acceptor motif search in tachyzoite. Conclusion This study represents the first large-scale effort to sequence the transcriptome of bradyzoites from T. gondii tissue cysts. Our data provide a comparative view of the tachyzoite and bradyzoite transcriptomes to allow a more complete dissection of all the molecular regulation mechanisms during stage conversions. A better understanding of the processes regulating stage conversion may guide targeted interventions to disrupt the transmission of T. gondii. Electronic supplementary material The online version of this article (10.1186/s13071-018-2983-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Long-Fei Chen
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou North Avenue No.1838, Guangzhou, 510515, Guangdong, China
| | - Xiao-Long Han
- Department of Bioinformatics, School of Basic Medicine School of Basic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Fen-Xiang Li
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou North Avenue No.1838, Guangzhou, 510515, Guangdong, China
| | - Yun-Ying Yao
- Epidemiology and Infection Control Branch, Shenzhen Guangming District Center for Disease Control and Prevention, Shenzhen, 518106, Guangdong, China
| | - Jin-Ping Fang
- First Clinical Medical College, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Xiao-Ju Liu
- First Clinical Medical College, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Xiao-Cong Li
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou North Avenue No.1838, Guangzhou, 510515, Guangdong, China
| | - Kun Wu
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou North Avenue No.1838, Guangzhou, 510515, Guangdong, China
| | - Min Liu
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou North Avenue No.1838, Guangzhou, 510515, Guangdong, China.
| | - Xiao-Guang Chen
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou North Avenue No.1838, Guangzhou, 510515, Guangdong, China.
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Hassan MA, Vasquez JJ, Guo-Liang C, Meissner M, Nicolai Siegel T. Comparative ribosome profiling uncovers a dominant role for translational control in Toxoplasma gondii. BMC Genomics 2017; 18:961. [PMID: 29228904 PMCID: PMC5725899 DOI: 10.1186/s12864-017-4362-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 12/01/2017] [Indexed: 11/17/2022] Open
Abstract
Background The lytic cycle of the protozoan parasite Toxoplasma gondii, which involves a brief sojourn in the extracellular space, is characterized by defined transcriptional profiles. For an obligate intracellular parasite that is shielded from the cytosolic host immune factors by a parasitophorous vacuole, the brief entry into the extracellular space is likely to exert enormous stress. Due to its role in cellular stress response, we hypothesize that translational control plays an important role in regulating gene expression in Toxoplasma during the lytic cycle. Unlike transcriptional profiles, insights into genome-wide translational profiles of Toxoplasma gondii are lacking. Methods We have performed genome-wide ribosome profiling, coupled with high throughput RNA sequencing, in intracellular and extracellular Toxoplasma gondii parasites to investigate translational control during the lytic cycle. Results Although differences in transcript abundance were mostly mirrored at the translational level, we observed significant differences in the abundance of ribosome footprints between the two parasite stages. Furthermore, our data suggest that mRNA translation in the parasite is potentially regulated by mRNA secondary structure and upstream open reading frames. Conclusion We show that most of the Toxoplasma genes that are dysregulated during the lytic cycle are translationally regulated. Electronic supplementary material The online version of this article (10.1186/s12864-017-4362-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Musa A Hassan
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, UK. .,The Centre for Tropical Livestock Genetics and Health, The Roslin Institute, University of Edinburgh, Edinburgh, UK.
| | - Juan J Vasquez
- Research Centre for Infectious Diseases, University of Wuerzburg, Wuerzburg, 97080, Germany.,Present address: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Chew Guo-Liang
- Computational Biology Program, Basic Sciences and Public Health Sciences Division, Fred Hutchinson Cancer Research Centre, Seattle, WA, 98105, USA
| | - Markus Meissner
- Wellcome Centre for Molecular Parasitology, University of Glasgow, Glasgow, UK.,Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität, München, 80802, Munich, Germany
| | - T Nicolai Siegel
- Research Centre for Infectious Diseases, University of Wuerzburg, Wuerzburg, 97080, Germany.,Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität, München, 80802, Munich, Germany.,Biomedical Center Munich, Physiological Chemistry, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
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13
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Wiedmer S, Erdbeer A, Volke B, Randel S, Kapplusch F, Hanig S, Kurth M. Identification and analysis of Eimeria nieschulzi gametocyte genes reveal splicing events of gam genes and conserved motifs in the wall-forming proteins within the genus Eimeria (Coccidia, Apicomplexa). ACTA ACUST UNITED AC 2017; 24:50. [PMID: 29210668 PMCID: PMC5718062 DOI: 10.1051/parasite/2017049] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/09/2017] [Indexed: 01/07/2023]
Abstract
The genus Eimeria (Apicomplexa, Coccidia) provides a wide range of different species with different hosts to study common and variable features within the genus and its species. A common characteristic of all known Eimeria species is the oocyst, the infectious stage where its life cycle starts and ends. In our study, we utilized Eimeria nieschulzi as a model organism. This rat-specific parasite has complex oocyst morphology and can be transfected and even cultivated in vitro up to the oocyst stage. We wanted to elucidate how the known oocyst wall-forming proteins are preserved in this rodent Eimeria species compared to other Eimeria. In newly obtained genomics data, we were able to identify different gametocyte genes that are orthologous to already known gam genes involved in the oocyst wall formation of avian Eimeria species. These genes appeared putatively as single exon genes, but cDNA analysis showed alternative splicing events in the transcripts. The analysis of the translated sequence revealed different conserved motifs but also dissimilar regions in GAM proteins, as well as polymorphic regions. The occurrence of an underrepresented gam56 gene version suggests the existence of a second distinct E. nieschulzi genotype within the E. nieschulzi Landers isolate that we maintain.
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Affiliation(s)
- Stefanie Wiedmer
- Institute for Zoology, Technische Universität Dresden, Helmholtzstraße 10, 01062 Dresden, Germany
| | - Alexander Erdbeer
- Institute for Zoology, Technische Universität Dresden, Helmholtzstraße 10, 01062 Dresden, Germany
| | - Beate Volke
- Institute for Zoology, Technische Universität Dresden, Helmholtzstraße 10, 01062 Dresden, Germany
| | - Stephanie Randel
- Institute for Zoology, Technische Universität Dresden, Helmholtzstraße 10, 01062 Dresden, Germany
| | - Franz Kapplusch
- Institute for Zoology, Technische Universität Dresden, Helmholtzstraße 10, 01062 Dresden, Germany
| | - Sacha Hanig
- Institute for Zoology, Technische Universität Dresden, Helmholtzstraße 10, 01062 Dresden, Germany
| | - Michael Kurth
- Institute for Zoology, Technische Universität Dresden, Helmholtzstraße 10, 01062 Dresden, Germany
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14
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Liu G, Zhang H, Sun G, Zhao C, Shang S, Gao X, Xia T, Yang X. Characterization of the peripheral blood transcriptome and adaptive evolution of the MHC I and TLR gene families in the wolf (Canis lupus). BMC Genomics 2017; 18:584. [PMID: 28784091 PMCID: PMC5545864 DOI: 10.1186/s12864-017-3983-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 08/01/2017] [Indexed: 01/25/2023] Open
Abstract
Background The wolf (Canis lupus) is one of the most widely distributed terrestrial mammals, because it is well adapted to various ecological niches and their corresponding pathogen environments. Immunological competence is a crucial factor involved in adapting to a changing environment and fighting pathogen infection in animals. In this study, the peripheral blood transcriptome of wolves was generated via RNA-seq to advance understanding of the wolf immunome, with a special focus on the major histocompatibility complex class I (MHC I) and toll-like receptor (TLR) gene families, which are involved in pathogen recognition and defense. Results The blood transcriptomic libraries of eight wolves originating from Tibet and Inner Mongolia were sequenced, and approximately 383 million reads were generated. Using a genome-guided assembly strategy, we obtained 123,851 unigenes, with a mean length of 845 bp and an N50 length of 1121 bp. On the basis of BLAST searches against the NCBI non-redundant protein database (Nr), a total of 36,192 (29.22%) unigenes were annotated. For functional classification, 24,663 unigenes were assigned to 13,016 Gene Ontology (GO) terms belonging to 51 sub-categories of the three main GO categories. Additionally, 7682 unigenes were classified into 6 Kyoto Encyclopedia of Genes and Genomes (KEGG) categories, in which the most represented functional sub-categories were signal transduction and the immune system, and 16,238 unigenes were functionally classified into 25 Eukaryotic Orthologous Groups (KOG) categories. We observed an overall higher ω (dN/dS) value at antigen-binding sites (ABSs) than at non-ABS regions as well as clear evidence of intergenic/intragenic recombination events at wolf MHC I loci. Additionally, our analysis revealed that carnivorous TLRs were dominated by purifying selection, with mean ω values at each TLR locus ranging from 0.173 to 0.527. However, we also found significant instances of positive selection that acted on several codons in pathogen recognition domains and were linked to species-specific differences in pathogen recognition. Conclusions This study represents the first attempt to characterize the blood transcriptome of the wolf and to highlight the value of investigating the immune system. Balancing selection and recombination have contributed to the historical evolution of wolf MHC I genes. Moreover, TLRs in carnivores have undergone adaptive evolution against the background of purifying selection, and a high level of adaptive evolution was detected in the wolf TLR system. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3983-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guangshuai Liu
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
| | - Honghai Zhang
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China.
| | - Guolei Sun
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
| | - Chao Zhao
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
| | - Shuai Shang
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
| | - Xiaodong Gao
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
| | - Tian Xia
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
| | - Xiufeng Yang
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
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15
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Palmieri N, Shrestha A, Ruttkowski B, Beck T, Vogl C, Tomley F, Blake DP, Joachim A. The genome of the protozoan parasite Cystoisospora suis and a reverse vaccinology approach to identify vaccine candidates. Int J Parasitol 2017; 47:189-202. [PMID: 28161402 PMCID: PMC5354109 DOI: 10.1016/j.ijpara.2016.11.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/17/2016] [Accepted: 11/20/2016] [Indexed: 12/16/2022]
Abstract
Vaccine development targeting protozoan parasites remains challenging, partly due to the complex interactions between these eukaryotes and the host immune system. Reverse vaccinology is a promising approach for direct screening of genome sequence assemblies for new vaccine candidate proteins. Here, we applied this paradigm to Cystoisospora suis, an apicomplexan parasite that causes enteritis and diarrhea in suckling piglets and economic losses in pig production worldwide. Using Next Generation Sequencing we produced an ∼84Mb sequence assembly for the C. suis genome, making it the first available reference for the genus Cystoisospora. Then, we derived a manually curated annotation of more than 11,000 protein-coding genes and applied the tool Vacceed to identify 1,168 vaccine candidates by screening the predicted C. suis proteome. To refine the set of candidates, we looked at proteins that are highly expressed in merozoites and specific to apicomplexans. The stringent set of candidates included 220 proteins, among which were 152 proteins with unknown function, 17 surface antigens of the SAG and SRS gene families, 12 proteins of the apicomplexan-specific secretory organelles including AMA1, MIC6, MIC13, ROP6, ROP12, ROP27, ROP32 and three proteins related to cell adhesion. Finally, we demonstrated in vitro the immunogenic potential of a C. suis-specific 42kDa transmembrane protein, which might constitute an attractive candidate for further testing.
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Affiliation(s)
- Nicola Palmieri
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine, Veterinärplatz 1, A-1210 Vienna, Austria.
| | - Aruna Shrestha
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Bärbel Ruttkowski
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Tomas Beck
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Claus Vogl
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Fiona Tomley
- Department of Pathology and Pathogen Biology, Royal Veterinary College, Hatfield, Hawkshead Lane, North Mymms AL9 7TA, UK
| | - Damer P Blake
- Department of Pathology and Pathogen Biology, Royal Veterinary College, Hatfield, Hawkshead Lane, North Mymms AL9 7TA, UK
| | - Anja Joachim
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine, Veterinärplatz 1, A-1210 Vienna, Austria
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16
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Singh R, Lawal HM, Schilde C, Glöckner G, Barton GJ, Schaap P, Cole C. Improved annotation with de novo transcriptome assembly in four social amoeba species. BMC Genomics 2017; 18:120. [PMID: 28143409 PMCID: PMC5282741 DOI: 10.1186/s12864-017-3505-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 01/14/2017] [Indexed: 11/27/2022] Open
Abstract
Background Annotation of gene models and transcripts is a fundamental step in genome sequencing projects. Often this is performed with automated prediction pipelines, which can miss complex and atypical genes or transcripts. RNA sequencing (RNA-seq) data can aid the annotation with empirical data. Here we present de novo transcriptome assemblies generated from RNA-seq data in four Dictyostelid species: D. discoideum, P. pallidum, D. fasciculatum and D. lacteum. The assemblies were incorporated with existing gene models to determine corrections and improvement on a whole-genome scale. This is the first time this has been performed in these eukaryotic species. Results An initial de novo transcriptome assembly was generated by Trinity for each species and then refined with Program to Assemble Spliced Alignments (PASA). The completeness and quality were assessed with the Benchmarking Universal Single-Copy Orthologs (BUSCO) and Transrate tools at each stage of the assemblies. The final datasets of 11,315-12,849 transcripts contained 5,610-7,712 updates and corrections to >50% of existing gene models including changes to hundreds or thousands of protein products. Putative novel genes are also identified and alternative splice isoforms were observed for the first time in P. pallidum, D. lacteum and D. fasciculatum. Conclusions In taking a whole transcriptome approach to genome annotation with empirical data we have been able to enrich the annotations of four existing genome sequencing projects. In doing so we have identified updates to the majority of the gene annotations across all four species under study and found putative novel genes and transcripts which could be worthy for follow-up. The new transcriptome data we present here will be a valuable resource for genome curators in the Dictyostelia and we propose this effective methodology for use in other genome annotation projects. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3505-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Reema Singh
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, UK.,Cell and Development Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, UK
| | - Hajara M Lawal
- Cell and Development Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, UK
| | - Christina Schilde
- Cell and Development Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, UK
| | - Gernot Glöckner
- Institute of Biochemistry I, Medical Faculty, University of Cologne, D-50931, Cologne, Germany.,Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, D-12587, Berlin, Germany
| | - Geoffrey J Barton
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, UK
| | - Pauline Schaap
- Cell and Development Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, UK
| | - Christian Cole
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, UK.
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17
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Gissot M, Hovasse A, Chaloin L, Schaeffer-Reiss C, Van Dorsselaer A, Tomavo S. An evolutionary conserved zinc finger protein is involved inToxoplasma gondiimRNA nuclear export. Cell Microbiol 2016; 19. [DOI: 10.1111/cmi.12644] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 06/20/2016] [Accepted: 07/02/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Mathieu Gissot
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille; U1019, UMR 8204, CIIL, Centre d'Infection et d'Immunité de Lille; F-59000 Lille France
| | - Agnès Hovasse
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC, CNRS; Université de Strasbourg; Strasbourg France
| | - Laurent Chaloin
- CPBS, CNRS UMR 5236; Université de Montpellier; Montpellier France
| | - Christine Schaeffer-Reiss
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC, CNRS; Université de Strasbourg; Strasbourg France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC, CNRS; Université de Strasbourg; Strasbourg France
| | - Stanislas Tomavo
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille; U1019, UMR 8204, CIIL, Centre d'Infection et d'Immunité de Lille; F-59000 Lille France
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18
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Matsubayashi M, Kawahara F, Hatta T, Yamagishi J, Miyoshi T, Anisuzzaman, Sasai K, Isobe T, Kita K, Tsuji N. Transcriptional profiles of virulent and precocious strains of Eimeria tenella at sporozoite stage; novel biological insight into attenuated asexual development. INFECTION GENETICS AND EVOLUTION 2016; 40:54-62. [DOI: 10.1016/j.meegid.2016.02.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 02/17/2016] [Accepted: 02/19/2016] [Indexed: 10/22/2022]
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19
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Antisense technologies in the studying of Toxoplasma gondii. J Microbiol Methods 2015; 138:93-99. [PMID: 26724749 DOI: 10.1016/j.mimet.2015.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 11/13/2015] [Accepted: 12/17/2015] [Indexed: 11/23/2022]
Abstract
This review covers a brief history of antisense RNAs and its applications, and summarizes the current stage of antisense technologies used in Toxoplasma gondii, a fascinating model organism with a unique characteristic blend of genetic regulatory systems normally found in plants or animals. Based on the current knowledge of regulatory RNAs and non-coding RNA (ncRNA), the antisense technologies are reviewed according to the classification of ncRNAs, which are roughly categorized into small, ranging from ~20-200 nucleotides in length, and long >200 nucleotides. Techniques utilizing small regulatory RNAs such as siRNA, miRNA, antagomirs, ribozymes and morpholino oligomers are discussed along with long non-coding RNA (lncRNA) including antisense and double stranded. These antisense technologies can be used in forward and reverse genetics studies. The future of technologies is limitless, particularly by combining these technologies with conventional methods, and should allow for ever greater understanding of gene regulation of the organism and related pathogenic microorganisms.
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20
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de Monerri NCS, Weiss LM. Integration of RNA-seq and proteomics data with genomics for improved genome annotation in Apicomplexan parasites. Proteomics 2015; 15:2557-9. [PMID: 26152714 PMCID: PMC4552184 DOI: 10.1002/pmic.201500253] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 07/02/2015] [Indexed: 11/07/2022]
Abstract
While high quality genomic sequence data is available for many pathogenic organisms, the corresponding gene annotations are often plagued with inaccuracies that can hinder research that utilizes such genomic data. Experimental validation of gene models is clearly crucial in improving such gene annotations; the field of proteogenomics is an emerging area of research wherein proteomic data is applied to testing and improving genetic models. Krishna et al. [Proteomics 2015, 15, 2618-2628] investigated whether incorporation of RNA-seq data into proteogenomics analyses can contribute significantly to validation studies of genome annotation, in two important parasitic organisms Toxoplasma gondii and Neospora caninum. They applied a systematic approach to combine new and previously published proteomics data from T. gondii and N. caninum with transcriptomics data, leading to substantially improved gene models for these organisms. This study illustrates the importance of incorporating experimental data from both proteomics and RNA-seq studies into routine genome annotation protocols.
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Affiliation(s)
- Natalie C. Silmon de Monerri
- Department of Pathology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Room 504 Forchheimer, Bronx, NY, 10461
| | - Louis M. Weiss
- Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Room 504 Forchheimer, Bronx, NY, 10461
- Department of Pathology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Room 504 Forchheimer, Bronx, NY, 10461
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21
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Alternative splicing mechanisms orchestrating post-transcriptional gene expression: intron retention and the intron-rich genome of apicomplexan parasites. Curr Genet 2015; 62:31-8. [PMID: 26194054 DOI: 10.1007/s00294-015-0506-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 07/09/2015] [Accepted: 07/09/2015] [Indexed: 12/13/2022]
Abstract
Apicomplexan parasites including Toxoplasma gondii and Plasmodium species have complex life cycles that include multiple hosts and differentiation through several morphologically distinct stages requiring marked changes in gene expression. This review highlights emerging evidence implicating regulation of mRNA splicing as a mechanism to prime these parasites for rapid gene expression upon differentiation. We summarize the most important insights in alternative splicing including its role in regulating gene expression by decreasing mRNA abundance via 'Regulated Unproductive Splicing and Translation'. As a related but less well-understood mechanism, we discuss also our recent work suggesting a role for intron retention for precluding translation of stage specific isoforms of T. gondii glycolytic enzymes. We additionally provide new evidence that intron retention might be a widespread mechanism during parasite differentiation. Supporting this notion, recent genome-wide analysis of Toxoplasma and Plasmodium suggests intron retention is more pervasive than heretofore thought. These findings parallel recent emergence of intron retention being more prevalent in mammals than previously believed, thereby adding to the established roles in plants, fungi and unicellular eukaryotes. Deeper mechanistic studies of intron retention will provide important insight into its role in regulating gene expression in apicomplexan parasites and more general in eukaryotic organisms.
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22
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Ramaprasad A, Mourier T, Naeem R, Malas TB, Moussa E, Panigrahi A, Vermont SJ, Otto TD, Wastling J, Pain A. Comprehensive evaluation of Toxoplasma gondii VEG and Neospora caninum LIV genomes with tachyzoite stage transcriptome and proteome defines novel transcript features. PLoS One 2015; 10:e0124473. [PMID: 25875305 PMCID: PMC4395442 DOI: 10.1371/journal.pone.0124473] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 03/02/2015] [Indexed: 11/25/2022] Open
Abstract
Toxoplasma gondii is an important protozoan parasite that infects all warm-blooded animals and causes opportunistic infections in immuno-compromised humans. Its closest relative, Neospora caninum, is an important veterinary pathogen that causes spontaneous abortion in livestock. Comparative genomics of these two closely related coccidians has been of particular interest to identify genes that contribute to varied host cell specificity and disease. Here, we describe a manual evaluation of these genomes based on strand-specific RNA sequencing and shotgun proteomics from the invasive tachyzoite stages of these two parasites. We have corrected predicted structures of over one third of the previously annotated gene models and have annotated untranslated regions (UTRs) in over half of the predicted protein-coding genes. We observe distinctly long UTRs in both the organisms, almost four times longer than other model eukaryotes. We have also identified a putative set of cis-natural antisense transcripts (cis-NATs) and long intergenic non-coding RNAs (lincRNAs). We have significantly improved the annotation quality in these genomes that would serve as a manually curated dataset for Toxoplasma and Neospora research communities.
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Affiliation(s)
- Abhinay Ramaprasad
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Raeece Naeem
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia
| | - Tareq B. Malas
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia
| | - Ehab Moussa
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia
| | - Aswini Panigrahi
- Bioscience Core Laboratory (BCL), King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia
| | - Sarah J. Vermont
- Institute of Infection and Global Health and School of Veterinary Science, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, Merseyside, United Kingdom
| | - Thomas D. Otto
- Parasite Genomics Group, Wellcome Trust Sanger Institute (WTSI), Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jonathan Wastling
- Institute of Infection and Global Health and School of Veterinary Science, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, Merseyside, United Kingdom
| | - Arnab Pain
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia
- * E-mail:
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23
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Yeoh LM, Goodman CD, Hall NE, van Dooren GG, McFadden GI, Ralph SA. A serine-arginine-rich (SR) splicing factor modulates alternative splicing of over a thousand genes in Toxoplasma gondii. Nucleic Acids Res 2015; 43:4661-75. [PMID: 25870410 PMCID: PMC4482073 DOI: 10.1093/nar/gkv311] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 03/27/2015] [Indexed: 11/12/2022] Open
Abstract
Single genes are often subject to alternative splicing, which generates alternative mature mRNAs. This phenomenon is widespread in animals, and observed in over 90% of human genes. Recent data suggest it may also be common in Apicomplexa. These parasites have small genomes, and economy of DNA is evolutionarily favoured in this phylum. We investigated the mechanism of alternative splicing in Toxoplasma gondii, and have identified and localized TgSR3, a homologue of ASF/SF2 (alternative-splicing factor/splicing factor 2, a serine-arginine–rich, or SR protein) to a subnuclear compartment. In addition, we conditionally overexpressed this protein, which was deleterious to growth. qRT-PCR was used to confirm perturbation of splicing in a known alternatively-spliced gene. We performed high-throughput RNA-seq to determine the extent of splicing modulated by this protein. Current RNA-seq algorithms are poorly suited to compact parasite genomes, and hence we complemented existing tools by writing a new program, GeneGuillotine, that addresses this deficiency by segregating overlapping reads into distinct genes. In order to identify the extent of alternative splicing, we released another program, JunctionJuror, that detects changes in intron junctions. Using this program, we identified about 2000 genes that were constitutively alternatively spliced in T. gondii. Overexpressing the splice regulator TgSR3 perturbed alternative splicing in over 1000 genes.
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Affiliation(s)
- Lee M Yeoh
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Christopher D Goodman
- School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nathan E Hall
- Department of Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Carlton, Victoria 3010, Australia
| | - Giel G van Dooren
- Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
| | - Geoffrey I McFadden
- School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Stuart A Ralph
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
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24
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Odell AV, Tran F, Foderaro JE, Poupart S, Pathak R, Westwood NJ, Ward GE. Yeast three-hybrid screen identifies TgBRADIN/GRA24 as a negative regulator of Toxoplasma gondii bradyzoite differentiation. PLoS One 2015; 10:e0120331. [PMID: 25789621 PMCID: PMC4366382 DOI: 10.1371/journal.pone.0120331] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 02/06/2015] [Indexed: 12/17/2022] Open
Abstract
Differentiation of the protozoan parasite Toxoplasma gondii into its latent bradyzoite stage is a key event in the parasite's life cycle. Compound 2 is an imidazopyridine that was previously shown to inhibit the parasite lytic cycle, in part through inhibition of parasite cGMP-dependent protein kinase. We show here that Compound 2 can also enhance parasite differentiation, and we use yeast three-hybrid analysis to identify TgBRADIN/GRA24 as a parasite protein that interacts directly or indirectly with the compound. Disruption of the TgBRADIN/GRA24 gene leads to enhanced differentiation of the parasite, and the TgBRADIN/GRA24 knockout parasites show decreased susceptibility to the differentiation-enhancing effects of Compound 2. This study represents the first use of yeast three-hybrid analysis to study small-molecule mechanism of action in any pathogenic microorganism, and it identifies a previously unrecognized inhibitor of differentiation in T. gondii. A better understanding of the proteins and mechanisms regulating T. gondii differentiation will enable new approaches to preventing the establishment of chronic infection in this important human pathogen.
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Affiliation(s)
- Anahi V Odell
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, United States of America
| | - Fanny Tran
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St Andrews, Fife, Scotland, United Kingdom
| | - Jenna E Foderaro
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, United States of America
| | - Séverine Poupart
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St Andrews, Fife, Scotland, United Kingdom
| | - Ravi Pathak
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St Andrews, Fife, Scotland, United Kingdom
| | - Nicholas J Westwood
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St Andrews, Fife, Scotland, United Kingdom
| | - Gary E Ward
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, United States of America
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Du L, Li W, Fan Z, Shen F, Yang M, Wang Z, Jian Z, Hou R, Yue B, Zhang X. First insights into the giant panda (Ailuropoda melanoleuca) blood transcriptome: a resource for novel gene loci and immunogenetics. Mol Ecol Resour 2015; 15:1001-13. [DOI: 10.1111/1755-0998.12367] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 12/22/2014] [Accepted: 12/26/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Lianming Du
- Key Laboratory of Bio-resources and Eco-environment; Ministry of Education; College of Life Science; Sichuan University; Chengdu Sichuan 610064 China
| | - Wujiao Li
- Key Laboratory of Bio-resources and Eco-environment; Ministry of Education; College of Life Science; Sichuan University; Chengdu Sichuan 610064 China
| | - Zhenxin Fan
- Key Laboratory of Bio-resources and Eco-environment; Ministry of Education; College of Life Science; Sichuan University; Chengdu Sichuan 610064 China
| | - Fujun Shen
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife; Chengdu Research Base of Giant Panda Breeding; Chengdu Sichuan 610081 China
| | - Mingyu Yang
- Key Laboratory of Bio-resources and Eco-environment; Ministry of Education; College of Life Science; Sichuan University; Chengdu Sichuan 610064 China
| | - Zili Wang
- Key Laboratory of Bio-resources and Eco-environment; Ministry of Education; College of Life Science; Sichuan University; Chengdu Sichuan 610064 China
| | - Zuoyi Jian
- Key Laboratory of Bio-resources and Eco-environment; Ministry of Education; College of Life Science; Sichuan University; Chengdu Sichuan 610064 China
| | - Rong Hou
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife; Chengdu Research Base of Giant Panda Breeding; Chengdu Sichuan 610081 China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment; Ministry of Education; College of Life Science; Sichuan University; Chengdu Sichuan 610064 China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment; Ministry of Education; College of Life Science; Sichuan University; Chengdu Sichuan 610064 China
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26
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Hassan MA, Saeij JP. Incorporating alternative splicing and mRNA editing into the genetic analysis of complex traits. Bioessays 2014; 36:1032-40. [PMID: 25171292 PMCID: PMC4280019 DOI: 10.1002/bies.201400079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The nomination of candidate genes underlying complex traits is often focused on genetic variations that alter mRNA abundance or result in non-conservative changes in amino acids. Although inconspicuous in complex trait analysis, genetic variants that affect splicing or RNA editing can also generate proteomic diversity and impact genetic traits. Indeed, it is known that splicing and RNA editing modulate several traits in humans and model organisms. Using high-throughput RNA sequencing (RNA-seq) analysis, it is now possible to integrate the genetics of transcript abundance, alternative splicing (AS) and editing with the analysis of complex traits. We recently demonstrated that both AS and mRNA editing are modulated by genetic and environmental factors, and potentially engender phenotypic diversity in a genetically segregating mouse population. Therefore, the analysis of splicing and RNA editing can expand not only the regulatory landscape of transcriptome and proteome complexity, but also the repertoire of candidate genes for complex traits.
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Affiliation(s)
- Musa A. Hassan
- Massachusetts Institute of Technology, Department of Biology, Cambridge, MA, USA
| | - Jeroen P.J. Saeij
- Massachusetts Institute of Technology, Department of Biology, Cambridge, MA, USA
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Pittman KJ, Aliota MT, Knoll LJ. Dual transcriptional profiling of mice and Toxoplasma gondii during acute and chronic infection. BMC Genomics 2014; 15:806. [PMID: 25240600 PMCID: PMC4177681 DOI: 10.1186/1471-2164-15-806] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 09/17/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The obligate intracellular parasite Toxoplasma gondii establishes a life-long chronic infection within any warm-blooded host. After ingestion of an encysted parasite, T. gondii disseminates throughout the body as a rapidly replicating form during acute infection. Over time and after stimulation of the host immune response, T. gondii differentiates into a slow growing, cyst form that is the hallmark of chronic infection. Global transcriptome analysis of both host and parasite during the establishment of chronic T. gondii infection has not yet been performed. Here, we conducted a dual RNA-seq analysis of T. gondii and its rodent host to better understand host and parasite responses during acute and chronic infection. RESULTS We obtained nearly one billion paired-end RNA sequences from the forebrains of uninfected, acutely and chronically infected mice, then aligned them to the genomic reference files of both T. gondii and Mus musculus. Gene ontology (GO) analysis of the 100 most highly expressed T. gondii genes showed less than half were shared between acute and chronic infection. The majority of the highly expressed genes common in both acute and chronic infection were involved in transcription and translation, underscoring that parasites in both stages are actively synthesizing proteins. Similarly, most of the T. gondii genes highly expressed during chronic infection were involved in metabolic processes, again highlighting the activity of the cyst stage at 28 days post-infection. Comparative analyses of host genes using uninfected forebrain revealed over twice as many immune regulatory genes were more abundant during chronic infection compared to acute. This demonstrates the influence of parasite development on host gene transcription as well as the influence of the host environment on parasite gene transcription. CONCLUSIONS RNA-seq is a valuable tool to simultaneously analyze host and microbe transcriptomes. Our data shows that T. gondii is metabolically active and synthesizing proteins at 28 days post-infection and that a distinct subset of host genes associated with the immune response are more abundant specifically during chronic infection. These data suggest host and pathogen interplay is still present during chronic infection and provides novel T. gondii targets for future drug and vaccine development.
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Affiliation(s)
| | | | - Laura J Knoll
- Department of Medical Microbiology and Immunology, University of Wisconsin - Madison, 1550 Linden Drive, Madison, WI 53706, USA.
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Transcript maturation in apicomplexan parasites. Curr Opin Microbiol 2014; 20:82-7. [PMID: 24934558 DOI: 10.1016/j.mib.2014.05.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/19/2014] [Accepted: 05/20/2014] [Indexed: 01/21/2023]
Abstract
The complex life cycles of apicomplexan parasites are associated with dynamic changes of protein repertoire. In Toxoplasma gondii, global analysis of gene expression demonstrates that dynamic changes in mRNA levels unfold in a serial cascade during asexual replication and up to 50% of encoded genes are unequally expressed in development. Recent studies indicate transcription and mRNA processing have important roles in fulfilling the 'just-in-time' delivery of proteins to parasite growth and development. The prominence of post-transcriptional mechanisms in the Apicomplexa was demonstrated by mechanistic studies of the critical RNA-binding proteins and regulatory kinases. However, it is still early in our understanding of how transcription and post-transcriptional mechanisms are balanced to produce adequate numbers of specialized forms that is required to complete the parasite life cycle.
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Liao Q, Shen J, Liu J, Sun X, Zhao G, Chang Y, Xu L, Li X, Zhao Y, Zheng H, Zhao Y, Wu Z. Genome-wide identification and functional annotation of Plasmodium falciparum long noncoding RNAs from RNA-seq data. Parasitol Res 2014; 113:1269-81. [PMID: 24522451 DOI: 10.1007/s00436-014-3765-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 01/10/2014] [Indexed: 11/25/2022]
Abstract
The life cycle of Plasmodium falciparum is very complex, with an erythrocytic stage that involves the invasion of red blood cells and the survival and growth of the parasite within the host. Over the past several decades, numbers of studies have shown that proteins exported by P. falciparum to the surface of infected red blood cells play a critical role in recognition and interaction with host receptors and are thus essential for the completion of the life cycle of P. falciparum. However, little is known about long noncoding RNAs (lncRNAs). In this study, we designed a computational pipeline to identify new lncRNAs of P. falciparum from published RNA-seq data and analyzed their sequences and expression features. As a result, 164 novel lncRNAs were found. The sequences and expression features of P. falciparum lncRNAs were similar to those of humans and mice: there was a lack of sequence conservation, low expression levels, and high expression coefficient of variance and co-expression with nearby coding sequences in the genome. Next, a coding/noncoding gene co-expression network for P. falciparum was constructed to further annotate the functions of novel and known lncRNAs. In total, the functions of 69 lncRNAs, including 44 novel lncRNAs, were annotated. The main functions of the lncRNAs included metabolic processes, biosynthetic processes, regulation of biological processes, establishment of localization, catabolic processes, cellular component organization, and interspecies interactions between organisms. Our results will provide clues to further the investigation of interactions between human hosts and parasites and the mechanisms of P. falciparum infection.
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Affiliation(s)
- Qi Liao
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, People's Republic of China
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Dalmasso MC, Carmona SJ, Angel SO, Agüero F. Characterization of Toxoplasma gondii subtelomeric-like regions: identification of a long-range compositional bias that is also associated with gene-poor regions. BMC Genomics 2014; 15:21. [PMID: 24417889 PMCID: PMC4008256 DOI: 10.1186/1471-2164-15-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 01/02/2014] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Chromosome ends are composed of telomeric repeats and subtelomeric regions, which are patchworks of genes interspersed with repeated elements. Although chromosome ends display similar arrangements in different species, their sequences are highly divergent. In addition, these regions display a particular nucleosomal composition and bind specific factors, therefore producing a special kind of heterochromatin. Using data from currently available draft genomes we have characterized these putative Telomeric Associated Sequences in Toxoplasma gondii. RESULTS An all-vs-all pairwise comparison of T. gondii assembled chromosomes revealed the presence of conserved regions of ∼ 30 Kb located near the ends of 9 of the 14 chromosomes of the genome of the ME49 strain. Sequence similarity among these regions is ∼ 70%, and they are also highly conserved in the GT1 and VEG strains. However, they are unique to Toxoplasma with no detectable similarity in other Apicomplexan parasites. The internal structure of these sequences consists of 3 repetitive regions separated by high-complexity sequences without annotated genes, except for a gene from the Toxoplasma Specific Family. ChIP-qPCR experiments showed that nucleosomes associated to these sequences are enriched in histone H4 monomethylated at K20 (H4K20me1), and the histone variant H2A.X, suggesting that they are silenced sequences (heterochromatin). A detailed characterization of the base composition of these sequences, led us to identify a strong long-range compositional bias, which was similar to that observed in other genomic silenced fragments such as those containing centromeric sequences, and was negatively correlated to gene density. CONCLUSIONS We identified and characterized a region present in most Toxoplasma assembled chromosomes. Based on their location, sequence features, and nucleosomal markers we propose that these might be part of subtelomeric regions of T. gondii. The identified regions display a unique trinucleotide compositional bias, which is shared (despite the lack of any detectable sequence similarity) with other silenced sequences, such as those making up the chromosome centromeres. We also identified other genomic regions with this compositional bias (but no detectable sequence similarity) that might be functionally similar.
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Affiliation(s)
| | | | - Sergio O Angel
- Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús, UNSAM - CONICET, Sede Chascomús, Av, Intendente Marino Km 8, 2 CC 164, B 7130 IWA, Chascomús, Argentina.
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Rupp O, Becker J, Brinkrolf K, Timmermann C, Borth N, Pühler A, Noll T, Goesmann A. Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines. PLoS One 2014; 9:e85568. [PMID: 24427317 PMCID: PMC3888431 DOI: 10.1371/journal.pone.0085568] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 12/03/2013] [Indexed: 11/19/2022] Open
Abstract
Chinese hamster ovary (CHO) cell lines represent the most commonly used mammalian expression system for the production of therapeutic proteins. In this context, detailed knowledge of the CHO cell transcriptome might help to improve biotechnological processes conducted by specific cell lines. Nevertheless, very few assembled cDNA sequences of CHO cells were publicly released until recently, which puts a severe limitation on biotechnological research. Two extended annotation systems and web-based tools, one for browsing eukaryotic genomes (GenDBE) and one for viewing eukaryotic transcriptomes (SAMS), were established as the first step towards a publicly usable CHO cell genome/transcriptome analysis platform. This is complemented by the development of a new strategy to assemble the ca. 100 million reads, sequenced from a broad range of diverse transcripts, to a high quality CHO cell transcript set. The cDNA libraries were constructed from different CHO cell lines grown under various culture conditions and sequenced using Roche/454 and Illumina sequencing technologies in addition to sequencing reads from a previous study. Two pipelines to extend and improve the CHO cell line transcripts were established. First, de novo assemblies were carried out with the Trinity and Oases assemblers, using varying k-mer sizes. The resulting contigs were screened for potential CDS using ESTScan. Redundant contigs were filtered out using cd-hit-est. The remaining CDS contigs were re-assembled with CAP3. Second, a reference-based assembly with the TopHat/Cufflinks pipeline was performed, using the recently published draft genome sequence of CHO-K1 as reference. Additionally, the de novo contigs were mapped to the reference genome using GMAP and merged with the Cufflinks assembly using the cuffmerge software. With this approach 28,874 transcripts located on 16,492 gene loci could be assembled. Combining the results of both approaches, 65,561 transcripts were identified for CHO cell lines, which could be clustered by sequence identity into 17,598 gene clusters.
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Affiliation(s)
- Oliver Rupp
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Cell Culture Technology, Bielefeld University, Bielefeld, Germany
- Bioinformatics and Systems Biology, Justus-Liebig-University, Giessen, Germany
- * E-mail:
| | - Jennifer Becker
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Cell Culture Technology, Bielefeld University, Bielefeld, Germany
| | - Karina Brinkrolf
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | | | - Nicole Borth
- Department for Biotechnology, Universität für Bodenkultur Wien, Vienna, Austria
- ACIB, Austrian Center of Industrial Biotechnology, Graz and Vienna, Austria
| | - Alfred Pühler
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Thomas Noll
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Cell Culture Technology, Bielefeld University, Bielefeld, Germany
| | - Alexander Goesmann
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Bioinformatics and Systems Biology, Justus-Liebig-University, Giessen, Germany
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Catania F, Lynch M. A simple model to explain evolutionary trends of eukaryotic gene architecture and expression: how competition between splicing and cleavage/polyadenylation factors may affect gene expression and splice-site recognition in eukaryotes. Bioessays 2013; 35:561-70. [PMID: 23568225 DOI: 10.1002/bies.201200127] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Enormous phylogenetic variation exists in the number and sizes of introns in protein-coding genes. Although some consideration has been given to the underlying role of the population-genetic environment in defining such patterns, the influence of the intracellular environment remains virtually unexplored. Drawing from observations on interactions between co-transcriptional processes involved in splicing and mRNA 3'-end formation, a mechanistic model is proposed for splice-site recognition that challenges the commonly accepted intron- and exon-definition models. Under the suggested model, splicing factors that outcompete 3'-end processing factors for access to intronic binding sites concurrently favor the recruitment of 3'-end processing factors at the pre-mRNA tail. This hypothesis sheds new light on observations such as the intron-mediated enhancement of gene expression and the negative correlation between intron length and levels of gene expression.
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Affiliation(s)
- Francesco Catania
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.
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Langevin SA, Bent ZW, Solberg OD, Curtis DJ, Lane PD, Williams KP, Schoeniger JS, Sinha A, Lane TW, Branda SS. Peregrine: A rapid and unbiased method to produce strand-specific RNA-Seq libraries from small quantities of starting material. RNA Biol 2013; 10:502-15. [PMID: 23558773 PMCID: PMC3710357 DOI: 10.4161/rna.24284] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Use of second generation sequencing (SGS) technologies for transcriptional profiling (RNA-Seq) has revolutionized transcriptomics, enabling measurement of RNA abundances with unprecedented specificity and sensitivity and the discovery of novel RNA species. Preparation of RNA-Seq libraries requires conversion of the RNA starting material into cDNA flanked by platform-specific adaptor sequences. Each of the published methods and commercial kits currently available for RNA-Seq library preparation suffers from at least one major drawback, including long processing times, large starting material requirements, uneven coverage, loss of strand information and high cost. We report the development of a new RNA-Seq library preparation technique that produces representative, strand-specific RNA-Seq libraries from small amounts of starting material in a fast, simple and cost-effective manner. Additionally, we have developed a new quantitative PCR-based assay for precisely determining the number of PCR cycles to perform for optimal enrichment of the final library, a key step in all SGS library preparation workflows.
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Affiliation(s)
- Stanley A Langevin
- Biotechnology and Bioengineering, Sandia National Laboratories, Livermore, CA, USA
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