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Simoes-Barbosa A, Pinheiro J. Unconventional features in the transcription and processing of spliceosomal small nuclear RNAs in the protozoan parasite Trichomonas vaginalis. Int J Parasitol 2024; 54:257-266. [PMID: 38452964 DOI: 10.1016/j.ijpara.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/07/2024] [Accepted: 03/03/2024] [Indexed: 03/09/2024]
Abstract
Trichomonas vaginalis is a medically important protozoan parasite, and a deep-branching, evolutionarily divergent unicellular eukaryote that has conserved several key features of eukaryotic gene expression. Trichomonas vaginalis possesses a metazoan/plant-like capping apparatus, mRNAs with a cap 1 structure and spliceosomes containing the five small nuclear RNAs (snRNAs). However, in contrast to metazoan and plant snRNAs, the structurally conserved T. vaginalis snRNAs were initially identified as lacking the canonical guanosine cap nucleotide. To explain this unusual condition, we sought to investigate transcriptional and processing features of the spliceosomal snRNAs in this protist. Here, we show that T. vaginalis spliceosomal snRNA genes mostly lack typical eukaryotic promoters. In contrast to other eukaryotes, the putative TATA box in the T. vaginalis U6 snRNA gene was found to be dispensable for transcription or RNA polymerase selectivity. Moreover, U6 transcription in T. vaginalis was virtually insensitive to tagetitoxin compared with other cellular transcripts produced by the same RNA polymerase III. Most important and unexpected, snRNA transcription in T. vaginalis appears to bypass capping as we show that these transcripts retain their original 5'-triphosphate groups. In conclusion, transcription and processing of spliceosomal snRNAs in T. vaginalis deviate considerably from the conventional rules of other eukaryotes.
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Affiliation(s)
- Augusto Simoes-Barbosa
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland 1010, New Zealand.
| | - Jully Pinheiro
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland 1010, New Zealand
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León-Sicairos CR, Figueroa-Angulo EE, Calla-Choque JS, Arroyo R. The Non-Canonical Iron-Responsive Element of IRE-tvcp12 Hairpin Structure at the 3'-UTR of Trichomonas vaginalis TvCP12 mRNA That Binds TvHSP70 and TvACTN-3 Can Regulate mRNA Stability and Amount of Protein. Pathogens 2023; 12:pathogens12040586. [PMID: 37111472 PMCID: PMC10143249 DOI: 10.3390/pathogens12040586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Abstract
Trichomonas vaginalis is one of the most common sexually transmitted parasites in humans. This protozoan has high iron requirements for growth, metabolism, and virulence. However, iron concentrations also differentially modulate T. vaginalis gene expression as in the genes encoding cysteine proteinases TvCP4 and TvCP12. Our goal was to identify the regulatory mechanism mediating the upregulation of tvcp12 under iron-restricted (IR) conditions. Here, we showed by RT-PCR, Western blot, and immunocytochemistry assays that IR conditions increase mRNA stability and amount of TvCP12. RNA electrophoretic mobility shift assay (REMSA), UV cross-linking, and competition assays demonstrated that a non-canonical iron-responsive element (IRE)-like structure at the 3'-untranslated region of the tvcp12 transcript (IRE-tvcp12) specifically binds to human iron regulatory proteins (IRPs) and to atypical RNA-binding cytoplasmic proteins from IR trichomonads, such as HSP70 and α-Actinin 3. These data were confirmed by REMSA supershift and Northwestern blot assays. Thus, our findings show that a positive gene expression regulation under IR conditions occurs at the posttranscriptional level possibly through RNA-protein interactions between atypical RNA-binding proteins and non-canonical IRE-like structures at the 3'-UTR of the transcript by a parallel mechanism to the mammalian IRE/IRP system that can be applied to other iron-regulated genes of T. vaginalis.
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Affiliation(s)
- Claudia R León-Sicairos
- Department of Infectomics and Molecular Pathogenesis, Center of Research and Advanced Studies of IPN (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, Mexico City 07360, Mexico
| | - Elisa E Figueroa-Angulo
- Department of Infectomics and Molecular Pathogenesis, Center of Research and Advanced Studies of IPN (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, Mexico City 07360, Mexico
| | - Jaeson S Calla-Choque
- Department of Infectomics and Molecular Pathogenesis, Center of Research and Advanced Studies of IPN (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, Mexico City 07360, Mexico
| | - Rossana Arroyo
- Department of Infectomics and Molecular Pathogenesis, Center of Research and Advanced Studies of IPN (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, Mexico City 07360, Mexico
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Gaona-López C, Vazquez-Jimenez LK, Gonzalez-Gonzalez A, Delgado-Maldonado T, Ortiz-Pérez E, Nogueda-Torres B, Moreno-Rodríguez A, Vázquez K, Saavedra E, Rivera G. Advances in Protozoan Epigenetic Targets and Their Inhibitors for the Development of New Potential Drugs. Pharmaceuticals (Basel) 2023; 16:ph16040543. [PMID: 37111300 PMCID: PMC10143871 DOI: 10.3390/ph16040543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
Protozoan parasite diseases cause significant mortality and morbidity worldwide. Factors such as climate change, extreme poverty, migration, and a lack of life opportunities lead to the propagation of diseases classified as tropical or non-endemic. Although there are several drugs to combat parasitic diseases, strains resistant to routinely used drugs have been reported. In addition, many first-line drugs have adverse effects ranging from mild to severe, including potential carcinogenic effects. Therefore, new lead compounds are needed to combat these parasites. Although little has been studied regarding the epigenetic mechanisms in lower eukaryotes, it is believed that epigenetics plays an essential role in vital aspects of the organism, from controlling the life cycle to the expression of genes involved in pathogenicity. Therefore, using epigenetic targets to combat these parasites is foreseen as an area with great potential for development. This review summarizes the main known epigenetic mechanisms and their potential as therapeutics for a group of medically important protozoal parasites. Different epigenetic mechanisms are discussed, highlighting those that can be used for drug repositioning, such as histone post-translational modifications (HPTMs). Exclusive parasite targets are also emphasized, including the base J and DNA 6 mA. These two categories have the greatest potential for developing drugs to treat or eradicate these diseases.
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Affiliation(s)
- Carlos Gaona-López
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | - Lenci K Vazquez-Jimenez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | - Alonzo Gonzalez-Gonzalez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | - Timoteo Delgado-Maldonado
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | - Eyrá Ortiz-Pérez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | - Benjamín Nogueda-Torres
- Departamento de Parasitología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Adriana Moreno-Rodríguez
- Laboratorio de Estudios Epidemiológicos, Clínicos, Diseños Experimentales e Investigación, Facultad de Ciencias Químicas, Universidad Autónoma "Benito Juárez" de Oaxaca, Avenida Universidad S/N, Ex Hacienda Cinco Señores, Oaxaca 68120, Mexico
| | - Karina Vázquez
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma de Nuevo León, Francisco Villa 20, General Escobedo 66054, Mexico
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City 14080, Mexico
| | - Gildardo Rivera
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
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In-depth comparative analysis of Tritrichomonas foetus transcriptomics reveals novel genes linked with adaptation to feline host. Sci Rep 2022; 12:10057. [PMID: 35710931 PMCID: PMC9203502 DOI: 10.1038/s41598-022-14310-x] [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: 01/08/2022] [Accepted: 06/06/2022] [Indexed: 11/09/2022] Open
Abstract
Tritrichomonas foetus is a flagellated parasite able to infect cattle, cats, and pigs. Despite its prevalence, feline tritrichomonosis has received markedly less attention than venereal infection, and little information about the molecular mechanisms that participate in feline host infection is available. Through a bioinformatics approach, we integrated public transcriptomic data for three T. foetus isolates and explored the differences at transcript level with a focus on pathogenesis and adaptation processes, particularly for the feline isolate. Our analysis revealed higher abundance levels of predicted virulence factors, such as proteases and surface antigens. Additionally, by a comparative and expression analysis of T. foetus genes, we proposed putative virulence factors that could be involved in feline infection. Finally, we identified a great proportion of predicted transcription factors of the MYB protein family and, by a promoter analysis, we revealed that MYB-related proteins could participate in the regulation of gene transcription in T. foetus. In conclusion, this integrated approach is a valuable resource for future studies of host–pathogen interactions and identifying new gene targets for improved feline tritrichomonosis diagnosis and treatment.
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Abstract
Trichomonas vaginalis is an anaerobic/microaerophilic protist parasite which causes trichomoniasis, one of the most prevalent sexually transmitted diseases worldwide. T. vaginalis not only is important as a human pathogen but also is of great biological interest because of its peculiar cell biology and metabolism, in earlier times fostering the erroneous notion that this microorganism is at the root of eukaryotic evolution. This review summarizes the major advances in the last five years in the T. vaginalis field with regard to genetics, molecular biology, ecology, and pathogenicity of the parasite.
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Affiliation(s)
- David Leitsch
- Department of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Vienna, Austria
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Lizarraga A, Muñoz D, Strobl-Mazzulla PH, de Miguel N. Toward incorporating epigenetics into regulation of gene expression in the parasite Trichomonas vaginalis. Mol Microbiol 2021; 115:959-967. [PMID: 33599017 DOI: 10.1111/mmi.14704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 02/13/2021] [Indexed: 12/11/2022]
Abstract
Trichomonas vaginalis is an extracellular parasite that colonizes the human urogenital tract, causing a highly prevalent sexually transmitted infection. The parasite must change its transcriptional profile in order to establish and maintain infection. However, few core regulatory elements and transcription factors have been identified to date and little is known about other mechanisms that may control these rapid changes in gene expression during parasite infection. In the last years, epigenetic mechanisms involved in the regulation of gene expression have been gaining major attention in this parasite. In this review, we summarize and discuss the major advances of the last few years with regard to epigenetics (DNA methylation, post-translational histone modifications, and histone variants) in the parasite T. vaginalis. These studies can shed light into our current understanding of this parasite's biology with far-reaching implications for the prognosis and treatment of trichomoniasis.
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Affiliation(s)
- Ayelen Lizarraga
- Laboratorio de Parásitos Anaerobios, Instituto Tecnológico Chascomús (INTECH), CONICET-UNSAM, Chascomús, Argentina
| | - Daniela Muñoz
- Laboratorio de Parásitos Anaerobios, Instituto Tecnológico Chascomús (INTECH), CONICET-UNSAM, Chascomús, Argentina
| | - Pablo H Strobl-Mazzulla
- Laboratorio de Biología del Desarrollo, Instituto Tecnológico Chascomús (INTECH), CONICET-UNSAM, Chascomús, Argentina
| | - Natalia de Miguel
- Laboratorio de Parásitos Anaerobios, Instituto Tecnológico Chascomús (INTECH), CONICET-UNSAM, Chascomús, Argentina
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Parra-Marín O, López-Pacheco K, Hernández R, López-Villaseñor I. The highly diverse TATA box-binding proteins among protists: A review. Mol Biochem Parasitol 2020; 239:111312. [PMID: 32771681 DOI: 10.1016/j.molbiopara.2020.111312] [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] [Received: 02/20/2020] [Revised: 06/28/2020] [Accepted: 07/22/2020] [Indexed: 10/23/2022]
Abstract
Transcription is the first step of gene expression regulation and is a fundamental mechanism for establishing the viability and development of a cell. The TATA box-binding protein (TBP) interaction with a TATA box in a promoter is one of the best studied mechanisms in transcription initiation. TBP is a transcription factor that is highly conserved from archaea to humans and is essential for the transcription initiated by each of the three RNA polymerases. In addition, the discovery of TBP-related factor 1 (TRF1) and other factors related to TBP shed light on the variability among transcription initiation complexes, thus demonstrating that the compositions of these complexes are, in fact, more complicated than originally believed. Despite these facts, the majority of studies on transcription have been performed on animal, plant and fungal cells, which serve as canonical models, and information regarding protist cells is relatively scarce. The aim of this work is to review the diversity of the TBPs that have been documented in protists and describe some of the specific features that differentiate them from their counterparts in higher eukaryotes.
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Affiliation(s)
- Olivia Parra-Marín
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Karla López-Pacheco
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Roberto Hernández
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Imelda López-Villaseñor
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, Mexico.
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Wang SE, Brooks AES, Poole AM, Simoes-Barbosa A. Determinants of translation efficiency in the evolutionarily-divergent protist Trichomonas vaginalis. BMC Mol Cell Biol 2020; 21:54. [PMID: 32689943 PMCID: PMC7370421 DOI: 10.1186/s12860-020-00297-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 06/29/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Trichomonas vaginalis, the causative agent of a prevalent urogenital infection in humans, is an evolutionarily divergent protozoan. Protein-coding genes in T. vaginalis are largely controlled by two core promoter elements, producing mRNAs with short 5' UTRs. The specific mechanisms adopted by T. vaginalis to fine-tune the translation efficiency (TE) of mRNAs remain largely unknown. RESULTS Using both computational and experimental approaches, this study investigated two key factors influencing TE in T. vaginalis: codon usage and mRNA secondary structure. Statistical dependence between TE and codon adaptation index (CAI) highlighted the impact of codon usage on mRNA translation in T. vaginalis. A genome-wide interrogation revealed that low structural complexity at the 5' end of mRNA followed closely by a highly structured downstream region correlates with TE variation in this organism. To validate these findings, a synthetic library of 15 synonymous iLOV genes was created, representing five mRNA folding profiles and three codon usage profiles. Fluorescence signals produced by the expression of these synonymous iLOV genes in T. vaginalis were consistent with and validated our in silico predictions. CONCLUSIONS This study demonstrates the role of codon usage bias and mRNA secondary structure in TE of T. vaginalis mRNAs, contributing to a better understanding of the factors that influence, and possibly regulate, gene expression in this human pathogen.
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Affiliation(s)
- Shuqi E Wang
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, USA
| | - Anna E S Brooks
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Anthony M Poole
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Bioinformatics Institute, The University of Auckland, Auckland, New Zealand
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Adenine DNA methylation, 3D genome organization, and gene expression in the parasite Trichomonas vaginalis. Proc Natl Acad Sci U S A 2020; 117:13033-13043. [PMID: 32461362 DOI: 10.1073/pnas.1917286117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Trichomonas vaginalis is a common sexually transmitted parasite that colonizes the human urogenital tract causing infections that range from asymptomatic to highly inflammatory. Recent works have highlighted the importance of histone modifications in the regulation of transcription and parasite pathogenesis. However, the nature of DNA methylation in the parasite remains unexplored. Using a combination of immunological techniques and ultrahigh-performance liquid chromatography (UHPLC), we analyzed the abundance of DNA methylation in strains with differential pathogenicity demonstrating that N6-methyladenine (6mA), and not 5-methylcytosine (5mC), is the main DNA methylation mark in T. vaginalis Genome-wide distribution of 6mA reveals that this mark is enriched at intergenic regions, with a preference for certain superfamilies of DNA transposable elements. We show that 6mA in T. vaginalis is associated with silencing when present on genes. Interestingly, bioinformatics analysis revealed the presence of transcriptionally active or repressive intervals flanked by 6mA-enriched regions, and results from chromatin conformation capture (3C) experiments suggest these 6mA flanked regions are in close spatial proximity. These associations were disrupted when parasites were treated with the demethylation activator ascorbic acid. This finding revealed a role for 6mA in modulating three-dimensional (3D) chromatin structure and gene expression in this divergent member of the Excavata.
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Translation initiation factors GleIF4E2 and GleIF4A can interact directly with the components of the pre-initiation complex to facilitate translation initiation in Giardia lamblia. Mol Biochem Parasitol 2020; 236:111258. [DOI: 10.1016/j.molbiopara.2020.111258] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 12/31/2019] [Accepted: 01/13/2020] [Indexed: 01/20/2023]
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Karnkowska A, Treitli SC, Brzoň O, Novák L, Vacek V, Soukal P, Barlow LD, Herman EK, Pipaliya SV, Pánek T, Žihala D, Petrželková R, Butenko A, Eme L, Stairs CW, Roger AJ, Eliáš M, Dacks JB, Hampl V. The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion. Mol Biol Evol 2019; 36:2292-2312. [PMID: 31387118 PMCID: PMC6759080 DOI: 10.1093/molbev/msz147] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The discovery that the protist Monocercomonoides exilis completely lacks mitochondria demonstrates that these organelles are not absolutely essential to eukaryotic cells. However, the degree to which the metabolism and cellular systems of this organism have adapted to the loss of mitochondria is unknown. Here, we report an extensive analysis of the M. exilis genome to address this question. Unexpectedly, we find that M. exilis genome structure and content is similar in complexity to other eukaryotes and less "reduced" than genomes of some other protists from the Metamonada group to which it belongs. Furthermore, the predicted cytoskeletal systems, the organization of endomembrane systems, and biosynthetic pathways also display canonical eukaryotic complexity. The only apparent preadaptation that permitted the loss of mitochondria was the acquisition of the SUF system for Fe-S cluster assembly and the loss of glycine cleavage system. Changes in other systems, including in amino acid metabolism and oxidative stress response, were coincident with the loss of mitochondria but are likely adaptations to the microaerophilic and endobiotic niche rather than the mitochondrial loss per se. Apart from the lack of mitochondria and peroxisomes, we show that M. exilis is a fully elaborated eukaryotic cell that is a promising model system in which eukaryotic cell biology can be investigated in the absence of mitochondria.
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Affiliation(s)
- Anna Karnkowska
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
- Department of Molecular Phylogenetics and Evolution, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Sebastian C Treitli
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Ondřej Brzoň
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Lukáš Novák
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Vojtěch Vacek
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Petr Soukal
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Lael D Barlow
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Canada
| | - Emily K Herman
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Canada
| | - Shweta V Pipaliya
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Canada
| | - Tomáš Pánek
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - David Žihala
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Romana Petrželková
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Anzhelika Butenko
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Laura Eme
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Courtney W Stairs
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Joel B Dacks
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Canada
| | - Vladimír Hampl
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
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An in vitro characterisation of the Trichomonas vaginalis TATA box-binding proteins (TBPs). Parasitol Res 2019; 118:3019-3031. [DOI: 10.1007/s00436-019-06438-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/22/2019] [Indexed: 10/26/2022]
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13
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Wang SE, Amir AS, Nguyen T, Poole AM, Simoes-Barbosa A. Spliceosomal introns in Trichomonas vaginalis revisited. Parasit Vectors 2018; 11:607. [PMID: 30482228 PMCID: PMC6260720 DOI: 10.1186/s13071-018-3196-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/09/2018] [Indexed: 11/16/2022] Open
Abstract
Background The human protozoan parasite Trichomonas vaginalis is an organism of interest for understanding eukaryotic evolution. Despite having an unusually large genome and a rich gene repertoire among protists, spliceosomal introns in T. vaginalis appear rare: only 62 putative introns have been annotated in this genome, and little or no experimental evidence exists to back up these predictions. Results This study revisited the 62 annotated introns of T. vaginalis derived from the genome sequencing plus previous publications. After experimental validation and a new genome-wide search, we confirmed the presence of introns in 32 genes and 18 others were concluded to be intronless. Sequence analyses classified the validated introns into two types, based on distinctive features such as length and conservation of splice site motifs. Conclusions Our study provides an updated list of intron-containing genes in the genome of T. vaginalis. Our findings suggests the existence of two intron ‘families’ spread among T. vaginalis protein-coding genes. Additional studies are needed to understand the functional separation of these two classes of introns and to assess the existence of further introns in the T. vaginalis genome. Electronic supplementary material The online version of this article (10.1186/s13071-018-3196-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shuqi E Wang
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Abdul S Amir
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Tai Nguyen
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Anthony M Poole
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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Mirasol-Meléndez E, Brieba LG, Díaz-Quezada C, López-Hidalgo M, Figueroa-Angulo EE, Ávila-González L, Arroyo-Verástegui R, Benítez-Cardoza CG. Characterization of multiple enolase genes from Trichomonas vaginalis. Potential novel targets for drug and vaccine design. Parasitol Int 2018; 67:444-453. [DOI: 10.1016/j.parint.2018.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 03/10/2018] [Accepted: 04/11/2018] [Indexed: 10/17/2022]
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Singh M, Beri D, Nageshan RK, Chavaan L, Gadara D, Poojary M, Subramaniam S, Tatu U. A secreted Heat shock protein 90 of Trichomonas vaginalis. PLoS Negl Trop Dis 2018; 12:e0006493. [PMID: 29768419 PMCID: PMC5973626 DOI: 10.1371/journal.pntd.0006493] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 05/29/2018] [Accepted: 05/03/2018] [Indexed: 11/18/2022] Open
Abstract
Trichomonas vaginalis is a causative agent of Trichomoniasis, a leading non-viral sexually transmitted disease worldwide. In the current study, we show Heat shock protein 90 is essential for its growth. Upon genomic analysis of the parasite, it was found to possess seven ORFs which could potentially encode Hsp90 isoforms. We identified a cytosolic Hsp90 homolog, four homologs which can align to truncated cytosolic Hsp90 gene products along with two Grp94 homologs (ER isoform of Hsp90). However, both Grp94 orthologs lacked an ER retention motif. In cancer cells, it is very well established that Hsp90 is secreted and regulates key clients involved in metastases, migration, and invasion. Since Trichomonas Grp94 lacks ER retention motif, we examined the possibility of its secretion. By using cell biology and biochemical approaches we show that the Grp94 isoform of Hsp90 is secreted by the parasite by the classical ER-Golgi pathway. This is the first report of a genome encoded secreted Hsp90 in a clinically important parasitic protozoan. Hsp90 is an essential chaperone in eukaryotes and it is often described as a master regulator of cellular homeostasis. In addition to its well-known functions inside the cell, extracellular Hsp90 has also been implicated in migration and invasion of tumor cells. We have, for the first time, identified the presence of an extracellular Hsp90 in a parasitic protozoan, Trichomonas vaginalis. The extracellular Hsp90 is a Grp94 homolog that lacks a canonical ER retention signal. Our analysis of Grp94 sequences from protozoa shows that it is uncommon for a Grp94 to lack ER retention signal. In the current study, we characterized the biochemical parameters and established the extracellular localization of this Hsp90 paralog. This secreted Hsp90 in Trichomonas can potentially modulate host-pathogen interaction.
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Affiliation(s)
- Meetali Singh
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Divya Beri
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | | | - Leena Chavaan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Darshak Gadara
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Mukta Poojary
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Suraj Subramaniam
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Utpal Tatu
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
- * E-mail:
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16
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Mancilla-Olea MI, Ortega-López J, Figueroa-Angulo EE, Avila-González L, Cárdenas-Guerra RE, Miranda-Ozuna JF, González-Robles A, Hernández-García MS, Sánchez-Ayala L, Arroyo R. Trichomonas vaginalis cathepsin D-like aspartic proteinase (Tv-CatD) is positively regulated by glucose and degrades human hemoglobin. Int J Biochem Cell Biol 2018; 97:1-15. [DOI: 10.1016/j.biocel.2018.01.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 01/15/2018] [Accepted: 01/22/2018] [Indexed: 01/07/2023]
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17
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Puente-Rivera J, Villalpando JL, Villalobos-Osnaya A, Vázquez-Carrillo LI, León-Ávila G, Ponce-Regalado MD, López-Camarillo C, Elizalde-Contreras JM, Ruiz-May E, Arroyo R, Alvarez-Sánchez ME. The 50 kDa metalloproteinase TvMP50 is a zinc-mediated Trichomonas vaginalis virulence factor. Mol Biochem Parasitol 2017; 217:32-41. [DOI: 10.1016/j.molbiopara.2017.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 08/28/2017] [Accepted: 09/01/2017] [Indexed: 12/18/2022]
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18
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Wang SE, Brooks AES, Cann B, Simoes-Barbosa A. The fluorescent protein iLOV outperforms eGFP as a reporter gene in the microaerophilic protozoan Trichomonas vaginalis. Mol Biochem Parasitol 2017; 216:1-4. [PMID: 28602728 DOI: 10.1016/j.molbiopara.2017.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 06/06/2017] [Accepted: 06/07/2017] [Indexed: 01/31/2023]
Abstract
Trichomonas vaginalis is a flagellated protozoan causing a notorious urogenital infection in humans. Due to its anaerobic metabolism, an alternative fluorescent protein that can be readily expressed in oxygen-deprived conditions is ideal. This study assessed the performance of iLOV, which does not require oxygen to function, as compared to the conventional enhanced green fluorescent protein (eGFP) in T. vaginalis. The results indicated that iLOV outperforms eGFP in both transient and stable expression, being detectable earlier and producing higher fluorescent intensity than eGFP in T. vaginalis. This finding facilitates forthcoming genetic studies that will advance the knowledge on this human parasitic infection.
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Affiliation(s)
- Shuqi E Wang
- School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
| | - Anna E S Brooks
- School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand; Maurice Wilkins Centre, University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
| | - Bronwyn Cann
- School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
| | - Augusto Simoes-Barbosa
- School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand.
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19
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Pachano T, Nievas YR, Lizarraga A, Johnson PJ, Strobl-Mazzulla PH, de Miguel N. Epigenetics regulates transcription and pathogenesis in the parasite Trichomonas vaginalis. Cell Microbiol 2017; 19:e12716. [PMID: 28054438 DOI: 10.1111/cmi.12716] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/14/2016] [Accepted: 12/21/2016] [Indexed: 12/21/2022]
Abstract
Trichomonas vaginalis is a common sexually transmitted parasite that colonizes the human urogenital tract. Infections range from asymptomatic to highly inflammatory, depending on the host and the parasite strain. Different T. vaginalis strains vary greatly in their adherence and cytolytic capacities. These phenotypic differences might be attributed to differentially expressed genes as a consequence of extra-genetic variation, such as epigenetic modifications. In this study, we explored the role of histone acetylation in regulating gene transcription and pathogenesis in T. vaginalis. Here, we show that histone 3 lysine acetylation (H3KAc) is enriched in nucleosomes positioned around the transcription start site of active genes (BAP1 and BAP2) in a highly adherent parasite strain; compared with the low acetylation abundance in contrast to that observed in a less-adherent strain that expresses these genes at low levels. Additionally, exposition of less-adherent strain with a specific histone deacetylases inhibitor, trichostatin A, upregulated the transcription of BAP1 and BAP2 genes in concomitance with an increase in H3KAc abundance and chromatin accessibility around their transcription start sites. Moreover, we demonstrated that the binding of initiator binding protein, the transcription factor responsible for the initiation of transcription of ~75% of known T. vaginalis genes, depends on the histone acetylation state around the metazoan-like initiator to which initiator binding protein binds. Finally, we found that trichostatin A treatment increased parasite aggregation and adherence to host cells. Our data demonstrated for the first time that H3KAc is a permissive histone modification that functions to mediate both transcription and pathogenesis of the parasite T. vaginalis.
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Affiliation(s)
- Tomas Pachano
- Laboratorio de Parásitos Anaerobios, Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico Chascomús (IIB-INTECH), CONICET-UNSAM, Chascomús, Argentina
| | - Yesica R Nievas
- Laboratorio de Parásitos Anaerobios, Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico Chascomús (IIB-INTECH), CONICET-UNSAM, Chascomús, Argentina
| | - Ayelen Lizarraga
- Laboratorio de Parásitos Anaerobios, Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico Chascomús (IIB-INTECH), CONICET-UNSAM, Chascomús, Argentina
| | - Patricia J Johnson
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, USA
| | - Pablo H Strobl-Mazzulla
- Laboratorio de Biología del Desarrollo, Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico Chascomús (IIB-INTECH), CONICET-UNSAM, Chascomús, Argentina
| | - Natalia de Miguel
- Laboratorio de Parásitos Anaerobios, Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico Chascomús (IIB-INTECH), CONICET-UNSAM, Chascomús, Argentina
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Abstract
The microaerophilic protist parasite Trichomonas vaginalis is occurring globally and causes infections in the urogenital tract in humans, a condition termed trichomoniasis. In fact, trichomoniasis is the most prevalent non-viral sexually transmitted disease with more than 250 million people infected every year. Although trichomoniasis is not life threatening in itself, it can be debilitating and increases the risk of adverse pregnancy outcomes, HIV infection, and, possibly, neoplasias in the prostate and the cervix. Apart from its role as a pathogen, T. vaginalis is also a fascinating organism with a surprisingly large genome for a parasite, i. e. larger than 160 Mb, and a physiology adapted to its microaerophilic lifestyle. In particular, the hydrogenosome, a mitochondria-derived organelle that produces hydrogen, has attracted much interest in the last few decades and rendered T. vaginalis a model organism for eukaryotic evolution. This review will give a succinct overview of the major advances in the T. vaginalis field in the last few years.
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Affiliation(s)
- David Leitsch
- Institute of Parasitology, Vetsuisse Faculty of the University of Bern, University of Bern, Längassstrasse, Bern, 3012, Switzerland
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21
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Figueroa-Angulo EE, Calla-Choque JS, Mancilla-Olea MI, Arroyo R. RNA-Binding Proteins in Trichomonas vaginalis: Atypical Multifunctional Proteins. Biomolecules 2015; 5:3354-95. [PMID: 26703754 PMCID: PMC4693282 DOI: 10.3390/biom5043354] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/07/2015] [Accepted: 11/12/2015] [Indexed: 01/08/2023] Open
Abstract
Iron homeostasis is highly regulated in vertebrates through a regulatory system mediated by RNA-protein interactions between the iron regulatory proteins (IRPs) that interact with an iron responsive element (IRE) located in certain mRNAs, dubbed the IRE-IRP regulatory system. Trichomonas vaginalis, the causal agent of trichomoniasis, presents high iron dependency to regulate its growth, metabolism, and virulence properties. Although T. vaginalis lacks IRPs or proteins with aconitase activity, possesses gene expression mechanisms of iron regulation at the transcriptional and posttranscriptional levels. However, only one gene with iron regulation at the transcriptional level has been described. Recently, our research group described an iron posttranscriptional regulatory mechanism in the T. vaginalis tvcp4 and tvcp12 cysteine proteinase mRNAs. The tvcp4 and tvcp12 mRNAs have a stem-loop structure in the 5'-coding region or in the 3'-UTR, respectively that interacts with T. vaginalis multifunctional proteins HSP70, α-Actinin, and Actin under iron starvation condition, causing translation inhibition or mRNA stabilization similar to the previously characterized IRE-IRP system in eukaryotes. Herein, we summarize recent progress and shed some light on atypical RNA-binding proteins that may participate in the iron posttranscriptional regulation in T. vaginalis.
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Affiliation(s)
- Elisa E Figueroa-Angulo
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, CP 07360 México, D.F., Mexico.
| | - Jaeson S Calla-Choque
- Laboratorio de Inmunopatología en Neurocisticercosis, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, Urb. Ingeniería, S.M.P., Lima 15102, Peru.
| | - Maria Inocente Mancilla-Olea
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, CP 07360 México, D.F., Mexico.
| | - Rossana Arroyo
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, CP 07360 México, D.F., Mexico.
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Trichomonas vaginalis Cysteine Proteinases: Iron Response in Gene Expression and Proteolytic Activity. BIOMED RESEARCH INTERNATIONAL 2015; 2015:946787. [PMID: 26090464 PMCID: PMC4450334 DOI: 10.1155/2015/946787] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 03/09/2015] [Indexed: 12/29/2022]
Abstract
We focus on the iron response of Trichomonas vaginalis to gene family products such as the cysteine proteinases (CPs) involved in virulence properties. In particular, we examined the effect of iron on the gene expression regulation and function of cathepsin L-like and asparaginyl endopeptidase-like CPs as virulence factors. We addressed some important aspects about CPs genomic organization and we offer possible explanations to the fact that only few members of this large gene family are expressed at the RNA and protein levels and the way to control their proteolytic activity. We also summarized all known iron regulations of CPs at transcriptional, posttranscriptional, and posttranslational levels along with new insights into the possible epigenetic and miRNA processes.
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23
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Woehle C, Kusdian G, Radine C, Graur D, Landan G, Gould SB. The parasite Trichomonas vaginalis expresses thousands of pseudogenes and long non-coding RNAs independently from functional neighbouring genes. BMC Genomics 2014; 15:906. [PMID: 25326207 PMCID: PMC4223856 DOI: 10.1186/1471-2164-15-906] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 10/09/2014] [Indexed: 12/11/2022] Open
Abstract
Background The human pathogen Trichomonas vaginalis is a parabasalian flagellate that is estimated to infect 3% of the world’s population annually. With a 160 megabase genome and up to 60,000 genes residing in six chromosomes, the parasite has the largest genome among sequenced protists. Although it is thought that the genome size and unusual large coding capacity is owed to genome duplication events, the exact reason and its consequences are less well studied. Results Among transcriptome data we found thousands of instances, in which reads mapped onto genomic loci not annotated as genes, some reaching up to several kilobases in length. At first sight these appear to represent long non-coding RNAs (lncRNAs), however, about half of these lncRNAs have significant sequence similarities to genomic loci annotated as protein-coding genes. This provides evidence for the transcription of hundreds of pseudogenes in the parasite. Conventional lncRNAs and pseudogenes are expressed in Trichomonas through their own transcription start sites and independently from flanking genes in Trichomonas. Expression of several representative lncRNAs was verified through reverse-transcriptase PCR in different T. vaginalis strains and case studies exclude the use of alternative start codons or stop codon suppression for the genes analysed. Conclusion Our results demonstrate that T. vaginalis expresses thousands of intergenic loci, including numerous transcribed pseudogenes. In contrast to yeast these are expressed independently from neighbouring genes. Our results furthermore illustrate the effect genome duplication events can have on the transcriptome of a protist. The parasite’s genome is in a steady state of changing and we hypothesize that the numerous lncRNAs could offer a large pool for potential innovation from which novel proteins or regulatory RNA units could evolve. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-906) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Sven B Gould
- Institute of Molecular Evolution, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.
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24
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Puente-Rivera J, de los Ángeles Ramón-Luing L, Figueroa-Angulo EE, Ortega-López J, Arroyo R. Trichocystatin-2 (TC-2): An endogenous inhibitor of cysteine proteinases in Trichomonas vaginalis is associated with TvCP39. Int J Biochem Cell Biol 2014; 54:255-65. [DOI: 10.1016/j.biocel.2014.04.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 03/10/2014] [Accepted: 04/04/2014] [Indexed: 12/24/2022]
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Maritz JM, Land KM, Carlton JM, Hirt RP. What is the importance of zoonotic trichomonads for human health? Trends Parasitol 2014; 30:333-41. [PMID: 24951156 PMCID: PMC7106558 DOI: 10.1016/j.pt.2014.05.005] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/16/2014] [Accepted: 05/18/2014] [Indexed: 12/17/2022]
Abstract
Trichomonads represent emerging species of medical and veterinary importance. Clinical and molecular evidence suggest a zoonotic potential for trichomonads. Close relationship between avian and human trichomonads revealed in outbreaks.
Trichomonads are common parasites of many vertebrate and invertebrate species, with four species classically recognized as human parasites: Dientamoeba fragilis, Pentatrichomonas hominis, Trichomonas vaginalis, and Trichomonas tenax. The latter two species are considered human-specific; by contrast, D. fragilis and P. hominis have been isolated from domestic and farm mammals, demonstrating a wide host range and potential zoonotic origin. Several new studies have highlighted the zoonotic dimension of trichomonads. First, species typically known to infect birds and domestic mammals have been identified in human clinical samples. Second, several phylogenetic analyses have identified animal-derived trichomonads as close sister taxa of the two human-specific species. It is our opinion, therefore, that these observations prompt further investigation into the importance of zoonotic trichomonads for human health.
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Affiliation(s)
- Julia M Maritz
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Kirkwood M Land
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, USA
| | - Jane M Carlton
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Robert P Hirt
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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Gould SB, Woehle C, Kusdian G, Landan G, Tachezy J, Zimorski V, Martin WF. Deep sequencing of Trichomonas vaginalis during the early infection of vaginal epithelial cells and amoeboid transition. Int J Parasitol 2013; 43:707-19. [DOI: 10.1016/j.ijpara.2013.04.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 04/08/2013] [Accepted: 04/09/2013] [Indexed: 01/15/2023]
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Roy S, Poidevin L, Jiang T, Judelson HS. Novel core promoter elements in the oomycete pathogen Phytophthora infestans and their influence on expression detected by genome-wide analysis. BMC Genomics 2013; 14:106. [PMID: 23414203 PMCID: PMC3599244 DOI: 10.1186/1471-2164-14-106] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 01/31/2013] [Indexed: 12/19/2022] Open
Abstract
Background The core promoter is the region flanking the transcription start site (TSS) that directs formation of the pre-initiation complex. Core promoters have been studied intensively in mammals and yeast, but not in more diverse eukaryotes. Here we investigate core promoters in oomycetes, a group within the Stramenopile kingdom that includes important plant and animal pathogens. Prior studies of a small collection of genes proposed that oomycete core promoters contain a 16 to 19 nt motif bearing an Initiator-like sequence (INR) flanked by a novel sequence named FPR, but this has not been extended to whole-genome analysis. Results We used expectation maximization to find over-represented motifs near TSSs of Phytophthora infestans, the potato blight pathogen. The motifs corresponded to INR, FPR, and a new element found about 25 nt downstream of the TSS called DPEP. TATA boxes were not detected. Assays of DPEP function by mutagenesis were consistent with its role as a core motif. Genome-wide searches found a well-conserved combined INR+FPR in only about 13% of genes after correcting for false discovery, which contradicted prior reports that INR and FPR are found together in most genes. INR or FPR were found alone near TSSs in 18% and 7% of genes, respectively. Promoters lacking the motifs had pyrimidine-rich regions near the TSS. The combined INR+FPR motif was linked to higher than average mRNA levels, developmentally-regulated transcription, and functions related to plant infection, while DPEP and FPR were over-represented in constitutively-expressed genes. The INR, FPR, and combined INR+FPR motifs were detected in other oomycetes including Hyaloperonospora arabidopsidis, Phytophthora sojae, Pythium ultimum, and Saprolegnia parasitica, while DPEP was found in all but S. parasitica. Only INR seemed present in a non-oomycete stramenopile. Conclusions The absence of a TATA box and presence of novel motifs show that the oomycete core promoter is diverged from that of model systems, and likely explains the lack of activity of non-oomycete promoters in Phytophthora transformants. The association of the INR+FPR motif with developmentally-regulated genes shows that oomycete core elements influence stage-specific transcription in addition to regulating formation of the pre-initiation complex.
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Affiliation(s)
- Sourav Roy
- Department of Plant Pathology and Microbiology, University of California, 92521, Riverside, CA 92521, USA
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Pearson RJ, Morf L, Singh U. Regulation of H2O2 stress-responsive genes through a novel transcription factor in the protozoan pathogen Entamoeba histolytica. J Biol Chem 2012; 288:4462-74. [PMID: 23250742 DOI: 10.1074/jbc.m112.423467] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Outcome of infection depends upon complex interactions between the invading pathogen and the host. As part of the host's innate immune response, the release of reactive oxygen and nitrogen species by phagocytes represents a major obstacle to the establishment of infection. The ability of the human parasite Entamoeba histolytica to survive reactive oxygen and nitrogen species is central to its pathogenic potential and contributes to disease outcome. In order to define the transcriptional network associated with oxidative stress, we utilized the MEME and MAST programs to analyze the promoter regions of 57 amoebic genes that had increased expression specifically in response to H(2)O(2) exposure. We functionally characterized an H(2)O(2)-regulatory motif (HRM) ((1)AAACCTCAATGAAGA(15)), which was enriched in these promoters and specifically bound amoebic nuclear protein(s). Assays with promoter-luciferase fusions established the importance of key residues and that the HRM motif directly impacted the ability of H(2)O(2)-responsive promoters to drive gene expression. DNA affinity chromatography and mass spectrometry identified EHI_108720 as an HRM DNA-binding protein. Overexpression and down-regulation of EHI_108720 demonstrated the specificity of EHI_108720 protein binding to the HRM, and overexpression increased basal expression from an H(2)O(2)-responsive wild-type promoter but not from its mutant counterpart. Thus, EHI_108720, or HRM-binding protein, represents a new stress-responsive transcription factor in E. histolytica that controls a transcriptional regulatory network associated with oxidative stress. Overexpression of EHI_108720 increased parasite virulence. Insight into how E. histolytica responds to oxidative stress increases our understanding of how this important human pathogen establishes invasive disease.
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Affiliation(s)
- Richard J Pearson
- Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
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The effects of environmental factors on the virulence of Trichomonas vaginalis. Microbes Infect 2012; 14:1411-27. [DOI: 10.1016/j.micinf.2012.09.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 07/26/2012] [Accepted: 09/02/2012] [Indexed: 11/21/2022]
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Horváthová L, Šafaríková L, Basler M, Hrdy I, Campo NB, Shin JW, Huang KY, Huang PJ, Lin R, Tang P, Tachezy J. Transcriptomic identification of iron-regulated and iron-independent gene copies within the heavily duplicated Trichomonas vaginalis genome. Genome Biol Evol 2012; 4:1017-29. [PMID: 22975721 PMCID: PMC3490414 DOI: 10.1093/gbe/evs078] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Gene duplication is an important evolutionary mechanism and no eukaryote has more duplicated gene families than the parasitic protist Trichomonas vaginalis. Iron is an essential nutrient for Trichomonas and plays a pivotal role in the establishment of infection, proliferation, and virulence. To gain insight into the role of iron in T. vaginalis gene expression and genome evolution, we screened iron-regulated genes using an oligonucleotide microarray for T. vaginalis and by comparative EST (expressed sequence tag) sequencing of cDNA libraries derived from trichomonads cultivated under iron-rich (+Fe) and iron-restricted (−Fe) conditions. Among 19,000 ESTs from both libraries, we identified 336 iron-regulated genes, of which 165 were upregulated under +Fe conditions and 171 under −Fe conditions. The microarray analysis revealed that 195 of 4,950 unique genes were differentially expressed. Of these, 117 genes were upregulated under +Fe conditions and 78 were upregulated under −Fe conditions. The results of both methods were congruent concerning the regulatory trends and the representation of gene categories. Under +Fe conditions, the expression of proteins involved in carbohydrate metabolism, particularly in the energy metabolism of hydrogenosomes, and in methionine catabolism was increased. The iron–sulfur cluster assembly machinery and certain cysteine proteases are of particular importance among the proteins upregulated under −Fe conditions. A unique feature of the T. vaginalis genome is the retention during evolution of multiple paralogous copies for a majority of all genes. Although the origins and reasons for this gene expansion remain unclear, the retention of multiple gene copies could provide an opportunity to evolve differential expression during growth in variable environmental conditions. For genes whose expression was affected by iron, we found that iron influenced the expression of only some of the paralogous copies, whereas the expression of the other paralogs was iron independent. This finding indicates a very stringent regulation of the differentially expressed paralogous genes in response to changes in the availability of exogenous nutrients and provides insight into the evolutionary rationale underlying massive paralog retention in the Trichomonas genome.
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Affiliation(s)
- Lenka Horváthová
- Department of Parasitology, Charles University in Prague, Prague 2, Czech Republic
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Hirt RP, de Miguel N, Nakjang S, Dessi D, Liu YC, Diaz N, Rappelli P, Acosta-Serrano A, Fiori PL, Mottram JC. Trichomonas vaginalis pathobiology new insights from the genome sequence. ADVANCES IN PARASITOLOGY 2012; 77:87-140. [PMID: 22137583 DOI: 10.1016/b978-0-12-391429-3.00006-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The draft genome of the common sexually transmitted pathogen Trichomonas vaginalis encodes one of the largest known proteome with 60,000 candidate proteins. This provides parasitologists and molecular cell biologists alike with exciting, yet challenging, opportunities to unravel the molecular features of the parasite's cellular systems and potentially the molecular basis of its pathobiology. Here, recent investigations addressing selected aspects of the parasite's molecular cell biology are discussed, including surface and secreted virulent factors, membrane trafficking, cell signalling, the degradome, and the potential role of RNA interference in the regulation of gene expression.
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Affiliation(s)
- Robert P Hirt
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
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Smith A, Johnson P. Gene expression in the unicellular eukaryote Trichomonas vaginalis. Res Microbiol 2011; 162:646-54. [DOI: 10.1016/j.resmic.2011.04.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 03/02/2011] [Indexed: 02/01/2023]
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