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Bard JE, Tylec BL, Dubey AP, Lamb NA, Yergeau DA, Read LK. Life stage-specific poly(A) site selection regulated by Trypanosoma brucei DRBD18. Proc Natl Acad Sci U S A 2024; 121:e2403188121. [PMID: 38990950 PMCID: PMC11260167 DOI: 10.1073/pnas.2403188121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 06/07/2024] [Indexed: 07/13/2024] Open
Abstract
The kinetoplastid parasite, Trypanosoma brucei, undergoes a complex life cycle entailing slender and stumpy bloodstream forms in mammals and procyclic and metacyclic forms (MFs) in tsetse fly hosts. The numerous gene regulatory events that underlie T. brucei differentiation between hosts, as well as between active and quiescent stages within each host, take place in the near absence of transcriptional control. Rather, differentiation is controlled by RNA-binding proteins (RBPs) that associate with mRNA 3' untranslated regions (3'UTRs) to impact RNA stability and translational efficiency. DRBD18 is a multifunctional T. brucei RBP, shown to impact mRNA stability, translation, export, and processing. Here, we use single-cell RNAseq to characterize transcriptomic changes in cell populations that arise upon DRBD18 depletion, as well as to visualize transcriptome-wide alterations to 3'UTR length. We show that in procyclic insect stages, DRBD18 represses expression of stumpy bloodstream form and MF transcripts. Additionally, DRBD18 regulates the 3'UTR lengths of over 1,500 transcripts, typically promoting the use of distal polyadenylation sites, and thus the inclusion of 3'UTR regulatory elements. Remarkably, comparison of polyadenylation patterns in DRBD18 knockdowns with polyadenylation patterns in stumpy bloodstream forms shows numerous similarities, revealing a role for poly(A) site selection in developmental gene regulation, and indicating that DRBD18 controls this process for a set of transcripts. RNA immunoprecipitation supports a direct role for DRBD18 in poly(A) site selection. This report highlights the importance of alternative polyadenylation in T. brucei developmental control and identifies a critical RBP in this process.
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Affiliation(s)
- Jonathan E. Bard
- Genomics and Bioinformatics Core, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY14203
- Department of Biochemistry, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY14203
| | - Brianna L. Tylec
- Department of Microbiology and Immunology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY14203
| | - Ashutosh P. Dubey
- Department of Microbiology and Immunology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY14203
| | - Natalie A. Lamb
- Genomics and Bioinformatics Core, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY14203
| | - Donald A. Yergeau
- Genomics and Bioinformatics Core, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY14203
| | - Laurie K. Read
- Department of Microbiology and Immunology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY14203
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2
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Taheri T, Davarpanah E, Samimi-Rad K, Seyed N. PUF Proteins as Critical RNA-Binding Proteins in TriTryp Parasites: A Review Article. IRANIAN JOURNAL OF PARASITOLOGY 2024; 19:278-289. [PMID: 39318822 PMCID: PMC11417976 DOI: 10.18502/ijpa.v19i3.16386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 08/20/2024] [Indexed: 09/26/2024]
Abstract
In eukaryotes, translation is a fundamental step in the long pathway of protein synthesis within the cell. In this process, several proteins and factors have involved directly or indirectly, individually or in association with other elements to contact mRNA. For perfect translation, many essential modifications should be done, such as cis-splicing to remove introns and two main events for capping and poly A polymerization in 5' and 3' end of mRNA, respectively. Gene expression is then regulated at both translation and stability of the target mRNA molecule levels. Pumilio/FBFs (PUFs) are the main group of RNA-binding proteins which bind to the 3'-UTR of target RNA and thereby regulate the fate, stability and subcellular localization of mRNAs and adjust the translated protein level. PUF proteins have been found both in nucleus where that bind to precursor mRNA, for processing and maturation of rRNA, and in cytoplasm where that bind to mRNA, stall the ribosomes, suppress the translation and localization of the mRNA. They can regulate the expression of mRNAs through activation or suppression of translation. Therefore, these proteins have recently garnered much attention as new generation of therapeutic targets against diseases such as cancer and neurological disorders. In comparison to other eukaryotes, trypanosomatids have a high number of PUF proteins, which function not only as gene expression regulatory factors but also in several biological processes such as differentiation and life-cycle progression of the cells. Here, we review the molecular and biological roles of known PUF proteins in TriTryp parasites (Trypanosome brucei, T. cruzi and Leishmania) beside some other parasites.
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Affiliation(s)
- Tahereh Taheri
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
| | - Elaheh Davarpanah
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
| | - Katayon Samimi-Rad
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Negar Seyed
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
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Mejía-Jaramillo AM, Fernandez GJ, Ospina-Zapata H, Murillo AM, Jimenez DE, Gómez LA, Triana-Chávez O. PUF3 RNA binding protein of Trypanosoma cruzi regulates mitochondrial morphology and function. Heliyon 2024; 10:e32810. [PMID: 39022037 PMCID: PMC11252720 DOI: 10.1016/j.heliyon.2024.e32810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 07/20/2024] Open
Abstract
The RNA-binding PUF proteins are post-transcriptional regulators found throughout the eukaryotic domain. In Trypanosoma cruzi, ten Puf genes termed Puf1 to Puf10 have been identified. Considering that the control of gene expression in this parasite is mainly at the post-transcriptional level, we characterized the PUF3 protein by knocking out and overexpressing the gene in T. cruzi epimastigotes and studied different genetic and biological features. The RNA-seq analyses in both genotypes showed significant changes in the number of regulated transcripts compared with wild-type parasites. Thus, the number of differentially expressed genes in the knockout (ΔTcPuf3) and the overexpressor (pTEXTcPuf3) were 238 and 187, respectively. In the knockout, a more significant proportion of genes was negatively regulated (166 out of 238). In contrast, in the overexpressor, positively regulated genes were predominant (149 out of 170). Additionally, when we predicted the subcellular location of the differentially expressed genes, the results revealed an important representation of nuclear genes encoding mitochondrial proteins. Therefore, we determined whether overexpression or knockout of TcPuf3 could lead to changes in both mitochondrial structure and cellular respiration. When mitochondria from ΔTcPuf3 and pTEXTcPuf3 parasites were analyzed by transmission electron microscopy (TEM), it was observed that the overexpressor had an abnormal mitochondrial morphology, evidenced by swelling. The results associated with cellular respiration showed that both the ΔTcPuf3 and pTEXTcPuf3 had a lower efficiency in routine respiration and the electron transport system capacity. Likewise, the mitochondria from overexpressing parasites showed a slight hyperpolarization. Additionally, several biological features, depending on the function of the mitochondria, were altered, such as growth, cell division, metacyclogenesis, ROS production, and response to benznidazole. In conclusion, our results suggest that although PUF3 is not an essential protein in T. cruzi, it influences mitochondrial transcripts, affecting mitochondrial morphology and function.
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Affiliation(s)
| | - Geysson Javier Fernandez
- Biología y Control de Enfermedades Infecciosas, BCEI, Universidad de Antioquia, Medellín, Colombia
| | - Hader Ospina-Zapata
- Biología y Control de Enfermedades Infecciosas, BCEI, Universidad de Antioquia, Medellín, Colombia
| | - Ana Milena Murillo
- Biología y Control de Enfermedades Infecciosas, BCEI, Universidad de Antioquia, Medellín, Colombia
| | - Dianny Elizabeth Jimenez
- Biología y Control de Enfermedades Infecciosas, BCEI, Universidad de Antioquia, Medellín, Colombia
| | - Luis A. Gómez
- Área de Ciencias Fundamentales, Universidad Eafit, Medellín, Colombia
| | - Omar Triana-Chávez
- Biología y Control de Enfermedades Infecciosas, BCEI, Universidad de Antioquia, Medellín, Colombia
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Romagnoli BAA, Lucena ACR, Freire ER, Munhoz da Rocha IF, Alves LR, Goldenberg S. TcZC3HTTP, a regulatory element that contributes to Trypanosoma cruzi cell proliferation. Microbiol Spectr 2024; 12:e0288023. [PMID: 38270449 PMCID: PMC10913370 DOI: 10.1128/spectrum.02880-23] [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: 07/17/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024] Open
Abstract
Post-transcriptional regulation of gene expression is a critical process for adapting to and surviving Trypanosoma cruzi, a parasite with a complex life cycle. RNA-binding proteins (RBPs) are key players in this regulation, forming ribonucleoprotein complexes (messenger ribonucleoproteins) and RNA granules that control transcript stability, localization, degradation, and translation modulation. Understanding the specific roles of individual RBPs is crucial for unraveling the details of this regulatory network. In this study, we generated null mutants of the TcZC3HTTP gene, a specific RBP in the Trypanosoma family characterized by a C3H zinc finger and a DNAJ domain associated with RNA and protein binding, respectively. Through cell growth assays, we demonstrated that the absence of TcZC3HTTP or the expression of an additional tagged version impacted epimastigote growth, indicating its contribution to cell proliferation. TcZC3HTTP was found to associate with mRNAs involved in cell cycle and division in epimastigotes, while in nutritionally stressed parasites it exhibited associations with mRNAs coding for other RBPs and rRNA. Furthermore, our analysis identified that TcZC3HTTP protein partners were different during normal growth conditions compared to starvation conditions, with the latter showing enrichment of ribosomal proteins and other RBPs. Therefore, this study provides insights into TcZC3HTTP's role in the post-transcriptional regulation of gene expression during normal growth and nutritional stress in T. cruzi, uncovering its versatile functions in different cellular contexts.IMPORTANCEUnderstanding how Trypanosoma cruzi, the causative agent of Chagas disease, regulates gene expression is crucial for developing targeted interventions. In this study, we investigated the role of TcZC3HTTP, an RNA-binding protein, in post-transcriptional regulation. Our findings demonstrate that TcZC3HTTP is relevant for the growth and proliferation of epimastigotes, a stage of the parasite's life cycle. We identified its associations with specific mRNAs involved in cell cycle and division and its interactions with enzymes and other RNA-binding proteins (RBPs) under normal and starvation conditions. These insights shed light on the regulatory network underlying gene expression in T. cruzi and reveal the multifaceted functions of RBPs in this parasite. Such knowledge enhances our understanding of the parasite's biology and opens avenues for developing novel therapeutic strategies targeting post-transcriptional gene regulation in T. cruzi.
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Affiliation(s)
| | - Aline Castro Rodrigues Lucena
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Fiocruz PR, Curitiba, Paraná, Brazil
| | - Eden Ribeiro Freire
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, Fiocruz PR, Curitiba, Paraná, Brazil
| | | | - Lysangela Ronalte. Alves
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, Fiocruz PR, Curitiba, Paraná, Brazil
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity, CHU de Quebec Research Center, University Laval, Quebec, Canada
| | - Samuel Goldenberg
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, Fiocruz PR, Curitiba, Paraná, Brazil
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Ciganda M, Sotelo-Silveira J, Dubey AP, Pandey P, Smith JT, Shen S, Qu J, Smircich P, Read LK. Translational control by Trypanosoma brucei DRBD18 contributes to the maintenance of the procyclic state. RNA (NEW YORK, N.Y.) 2023; 29:1881-1895. [PMID: 37730435 PMCID: PMC10653379 DOI: 10.1261/rna.079625.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/24/2023] [Indexed: 09/22/2023]
Abstract
Trypanosoma brucei occupies distinct niches throughout its life cycle, within both the mammalian and tsetse fly hosts. The immunological and biochemical complexity and variability of each of these environments require a reshaping of the protein landscape of the parasite both to evade surveillance and face changing metabolic demands. In kinetoplastid protozoa, including T. brucei, posttranscriptional control mechanisms are the primary means of gene regulation, and these are often mediated by RNA-binding proteins. DRBD18 is a T. brucei RNA-binding protein that reportedly interacts with ribosomal proteins and translation factors. Here, we tested a role for DRBD18 in translational control. We validate the DRBD18 interaction with translating ribosomes and the translation initiation factor, eIF3a. We further show that DRBD18 depletion by RNA interference leads to altered polysomal profiles with a specific depletion of heavy polysomes. Ribosome profiling analysis reveals that 101 transcripts change in translational efficiency (TE) upon DRBD18 depletion: 41 exhibit decreased TE and 60 exhibit increased TE. A further 66 transcripts are buffered, that is, changes in transcript abundance are compensated by changes in TE such that the total translational output is expected not to change. In DRBD18-depleted cells, a set of transcripts that codes for procyclic form-specific proteins is translationally repressed while, conversely, transcripts that code for bloodstream form- and metacyclic form-specific proteins are translationally enhanced. RNA immunoprecipitation/qRT-PCR indicates that DRBD18 associates with members of both repressed and enhanced cohorts. These data suggest that DRBD18 contributes to the maintenance of the procyclic state through both positive and negative translational control of specific mRNAs.
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Affiliation(s)
- Martin Ciganda
- Department of Microbiology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, USA
| | - José Sotelo-Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo 11600, Uruguay
| | - Ashutosh P Dubey
- Department of Microbiology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, USA
| | - Parul Pandey
- Department of Microbiology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, USA
| | - Joseph T Smith
- Department of Microbiology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, USA
| | - Shichen Shen
- Department of Pharmaceutical Sciences, University at Buffalo and NYS Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo and NYS Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, USA
| | - Pablo Smircich
- Laboratorio de Bioinformática, Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo 11600, Uruguay
- Sección Genómica Funcional, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - Laurie K Read
- Department of Microbiology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, USA
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6
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Reuter C, Hauf L, Imdahl F, Sen R, Vafadarnejad E, Fey P, Finger T, Jones NG, Walles H, Barquist L, Saliba AE, Groeber-Becker F, Engstler M. Vector-borne Trypanosoma brucei parasites develop in artificial human skin and persist as skin tissue forms. Nat Commun 2023; 14:7660. [PMID: 37996412 PMCID: PMC10667367 DOI: 10.1038/s41467-023-43437-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 11/08/2023] [Indexed: 11/25/2023] Open
Abstract
Transmission of Trypanosoma brucei by tsetse flies involves the deposition of the cell cycle-arrested metacyclic life cycle stage into mammalian skin at the site of the fly's bite. We introduce an advanced human skin equivalent and use tsetse flies to naturally infect the skin with trypanosomes. We detail the chronological order of the parasites' development in the skin by single-cell RNA sequencing and find a rapid activation of metacyclic trypanosomes and differentiation to proliferative parasites. Here we show that after the establishment of a proliferative population, the parasites enter a reversible quiescent state characterized by slow replication and a strongly reduced metabolism. We term these quiescent trypanosomes skin tissue forms, a parasite population that may play an important role in maintaining the infection over long time periods and in asymptomatic infected individuals.
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Affiliation(s)
- Christian Reuter
- Department of Cell and Developmental Biology, Biocenter, Julius-Maximilians-Universitaet of Wuerzburg, Wuerzburg, Germany
- Department of Tissue Engineering and Regenerative Medicine (TERM), University Hospital Wuerzburg, Wuerzburg, Germany
| | - Laura Hauf
- Department of Cell and Developmental Biology, Biocenter, Julius-Maximilians-Universitaet of Wuerzburg, Wuerzburg, Germany
| | - Fabian Imdahl
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Wuerzburg, Germany
- Core Unit Systems Medicine, Julius-Maximilians-Universitaet of Wuerzburg, Wuerzburg, Germany
| | - Rituparno Sen
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Wuerzburg, Germany
| | - Ehsan Vafadarnejad
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Wuerzburg, Germany
| | - Philipp Fey
- Translational Center Regenerative Therapies, Fraunhofer ISC, Wuerzburg, Germany
| | - Tamara Finger
- Translational Center Regenerative Therapies, Fraunhofer ISC, Wuerzburg, Germany
| | - Nicola G Jones
- Department of Cell and Developmental Biology, Biocenter, Julius-Maximilians-Universitaet of Wuerzburg, Wuerzburg, Germany
| | - Heike Walles
- Translational Center Regenerative Therapies, Fraunhofer ISC, Wuerzburg, Germany
- Core Facility Tissue Engineering, Otto-von-Guericke University, Magdeburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Wuerzburg, Germany
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Wuerzburg, Germany
- Institute of Molecular Infection Biology (IMIB), Faculty of Medicine, Julius-Maximilians-Universitaet of Wuerzburg, Wuerzburg, Germany
| | - Florian Groeber-Becker
- Department of Tissue Engineering and Regenerative Medicine (TERM), University Hospital Wuerzburg, Wuerzburg, Germany
- Translational Center Regenerative Therapies, Fraunhofer ISC, Wuerzburg, Germany
| | - Markus Engstler
- Department of Cell and Developmental Biology, Biocenter, Julius-Maximilians-Universitaet of Wuerzburg, Wuerzburg, Germany.
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Yin S, Liu H, Zhou Z, Xu X, Wang P, Chen W, Deng G, Wang H, Yu H, Gu L, Huo M, Li M, Zeng L, He Y, Zhang C. PUM1 Promotes Tumor Progression by Activating DEPTOR-Meditated Glycolysis in Gastric Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301190. [PMID: 37469018 PMCID: PMC10520643 DOI: 10.1002/advs.202301190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/05/2023] [Indexed: 07/21/2023]
Abstract
RNA-binding proteins (RBPs) play essential roles in tumorigenesis and progression, but their functions in gastric cancer (GC) remain largely elusive. Here, it is reported that Pumilio 1 (PUM1), an RBP, induces metabolic reprogramming through post-transcriptional regulation of DEP domain-containing mammalian target of rapamycin (mTOR)-interacting protein (DEPTOR) in GC. In clinical samples, elevated expression of PUM1 is associated with recurrence, metastasis, and poor survival. In vitro and in vivo experiments demonstrate that knockdown of PUM1 inhibits the proliferation and metastasis of GC cells. In addition, RNA-sequencing and bioinformatics analyses show that PUM1 is enriched in the glycolysis gene signature. Metabolomics studies confirm that PUM1 deficiency suppresses glycolytic metabolism. Mechanistically, PUM1 binds directly to DEPTOR mRNA pumilio response element to maintain the stability of the transcript and prevent DEPTOR degradation through post-transcriptional pathway. PUM1-mediated DEPTOR upregulation inhibits mTORC1 and alleviates the inhibitory feedback signal transmitted from mTORC1 to PI3K under normal conditions, thus activating the PI3K-Akt signal and glycolysis continuously. Collectively, these results reveal the critical epigenetic role of PUM1 in modulating DEPTOR-dependent GC progression. These conclusions support further clinical investigation of PUM1 inhibitors as a metabolic-targeting treatment strategy for GC.
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Affiliation(s)
- Songcheng Yin
- Digestive Diseases CenterGuangdong Provincial Key Laboratory of Digestive Cancer ResearchThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenGuangdong518107China
| | - Huifang Liu
- Digestive Diseases CenterGuangdong Provincial Key Laboratory of Digestive Cancer ResearchThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenGuangdong518107China
- Department of RadiotherapyAffiliated Cancer Hospital of Zhengzhou UniversityHenan Cancer HospitalZhengzhouHenan450000China
| | - Zhijun Zhou
- Department of MedicineThe University of Oklahoma Health Sciences CenterOklahoma CityOK 73104USA
| | - Xiaoyu Xu
- Department of Gynecology and ObstetricsThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenGuangdong518107China
| | - Pengliang Wang
- Department of Gastrointestinal SurgerySun Yat‐sen Memorial HospitalSun Yat‐sen UniversityGuangzhouGuangdong510120China
| | - Wei Chen
- Digestive Diseases CenterGuangdong Provincial Key Laboratory of Digestive Cancer ResearchThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenGuangdong518107China
| | - Guofei Deng
- Digestive Diseases CenterGuangdong Provincial Key Laboratory of Digestive Cancer ResearchThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenGuangdong518107China
| | - Han Wang
- Digestive Diseases CenterGuangdong Provincial Key Laboratory of Digestive Cancer ResearchThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenGuangdong518107China
| | - Hong Yu
- Digestive Diseases CenterGuangdong Provincial Key Laboratory of Digestive Cancer ResearchThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenGuangdong518107China
| | - Liang Gu
- Digestive Diseases CenterGuangdong Provincial Key Laboratory of Digestive Cancer ResearchThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenGuangdong518107China
| | - Mingyu Huo
- Digestive Diseases CenterGuangdong Provincial Key Laboratory of Digestive Cancer ResearchThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenGuangdong518107China
| | - Min Li
- Department of MedicineThe University of Oklahoma Health Sciences CenterOklahoma CityOK 73104USA
| | - Leli Zeng
- Digestive Diseases CenterGuangdong Provincial Key Laboratory of Digestive Cancer ResearchThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenGuangdong518107China
| | - Yulong He
- Digestive Diseases CenterGuangdong Provincial Key Laboratory of Digestive Cancer ResearchThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenGuangdong518107China
- Department of Gastrointestinal SurgeryThe First Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouGuangdong510062China
| | - Changhua Zhang
- Digestive Diseases CenterGuangdong Provincial Key Laboratory of Digestive Cancer ResearchThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenGuangdong518107China
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8
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Toh JY, Nkouawa A, Dong G, Kolev NG, Tschudi C. Two cold shock domain containing proteins trigger the development of infectious Trypanosoma brucei. PLoS Pathog 2023; 19:e1011438. [PMID: 37276216 PMCID: PMC10270622 DOI: 10.1371/journal.ppat.1011438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 05/22/2023] [Indexed: 06/07/2023] Open
Abstract
Cold shock proteins are members of a family of DNA- and RNA-binding proteins with one or more evolutionarily conserved cold shock domain (CSD). These proteins have a wide variety of biological functions, including DNA-damage repair, mRNA stability, and regulation of transcription, splicing and translation. We previously identified two CSD containing proteins, CSD1 and CSD2, in the protozoan parasite Trypanosoma brucei to be required for RBP6-driven metacyclic production, albeit at different steps of the developmental program. During metacyclogenesis T. brucei undergoes major morphological and metabolic changes that culminate in the establishment of quiescent metacyclic parasites and the acquisition of mammalian infectivity. To investigate the specific role of CSD1 and CSD2 in this process, we ectopically expressed CSD1 or CSD2 in non-infectious procyclic parasites and discovered that each protein is sufficient to produce infectious metacyclic parasites in 24 hours. Domain truncation assays determined that the N-terminal domain, but not the C-terminal domain, of CSD1 and CSD2 was required for metacyclic development. Furthermore, conserved amino acid residues in the CSD of CSD1 and CSD2, known to be important for binding nucleic acids, were found to be necessary for metacyclic production. Using single-end enhanced crosslinking and immunoprecipitation (seCLIP) we identified the specific binding motif of CSD1 and CSD2 as "ANACAU" and the bound mRNAs were enriched for biological processes, including lipid metabolism, microtubule-based movement and nucleocytoplasmic transport that are likely involved in the transition to bloodstream form-like cells.
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Affiliation(s)
- Justin Y Toh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Agathe Nkouawa
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Gang Dong
- Max Perutz Labs, Vienna Biocenter, Center for Medical Biochemistry, Medical University of Vienna, Vienna, Austria
| | - Nikolay G Kolev
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Christian Tschudi
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
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9
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Briggs EM, Marques CA, Oldrieve GR, Hu J, Otto TD, Matthews KR. Profiling the bloodstream form and procyclic form Trypanosoma brucei cell cycle using single-cell transcriptomics. eLife 2023; 12:e86325. [PMID: 37166108 PMCID: PMC10212563 DOI: 10.7554/elife.86325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/10/2023] [Indexed: 05/12/2023] Open
Abstract
African trypanosomes proliferate as bloodstream forms (BSFs) and procyclic forms in the mammal and tsetse fly midgut, respectively. This allows them to colonise the host environment upon infection and ensure life cycle progression. Yet, understanding of the mechanisms that regulate and drive the cell replication cycle of these forms is limited. Using single-cell transcriptomics on unsynchronised cell populations, we have obtained high resolution cell cycle regulated (CCR) transcriptomes of both procyclic and slender BSF Trypanosoma brucei without prior cell sorting or synchronisation. Additionally, we describe an efficient freeze-thawing protocol that allows single-cell transcriptomic analysis of cryopreserved T. brucei. Computational reconstruction of the cell cycle using periodic pseudotime inference allowed the dynamic expression patterns of cycling genes to be profiled for both life cycle forms. Comparative analyses identify a core cycling transcriptome highly conserved between forms, as well as several genes where transcript levels dynamics are form specific. Comparing transcript expression patterns with protein abundance revealed that the majority of genes with periodic cycling transcript and protein levels exhibit a relative delay between peak transcript and protein expression. This work reveals novel detail of the CCR transcriptomes of both forms, which are available for further interrogation via an interactive webtool.
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Affiliation(s)
- Emma M Briggs
- Institute for Immunology and Infection Research, School of Biological Sciences, University of EdinburghEdinburghUnited Kingdom
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, University of GlasgowGlasgowUnited Kingdom
| | - Catarina A Marques
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, University of GlasgowGlasgowUnited Kingdom
| | - Guy R Oldrieve
- Institute for Immunology and Infection Research, School of Biological Sciences, University of EdinburghEdinburghUnited Kingdom
| | - Jihua Hu
- Institute for Immunology and Infection Research, School of Biological Sciences, University of EdinburghEdinburghUnited Kingdom
| | - Thomas D Otto
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, University of GlasgowGlasgowUnited Kingdom
| | - Keith R Matthews
- Institute for Immunology and Infection Research, School of Biological Sciences, University of EdinburghEdinburghUnited Kingdom
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10
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Ciganda M, Sotelo-Silveira J, Smith JT, Shen S, Qu J, Smircich P, Read LK. Translational control by Trypanosoma brucei DRBD18 contributes to the maintenance of the procyclic state. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.08.527724. [PMID: 36798237 PMCID: PMC9934708 DOI: 10.1101/2023.02.08.527724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Trypanosoma brucei occupies distinct niches throughout its life cycle, within both the mammalian and tsetse fly hosts. The immunological and biochemical complexity and variability of each of these environments require a reshaping of the protein landscape of the parasite both to evade surveillance and face changing metabolic demands. Whereas most well-studied organisms rely on transcriptional control as the main regulator of gene expression, post-transcriptional control mechanisms are particularly important in T. brucei , and these are often mediated by RNA-binding proteins. DRBD18 is a T. brucei RNA-binding protein that interacts with ribosomal proteins and translation factors. Here, we tested a role for DRBD18 in translational control. We show that DRBD18 depletion by RNA interference leads to altered polysomal profiles with a specific depletion of heavy polysomes. Ribosome profiling analysis reveals that 101 transcripts change in translational efficiency (TE) upon DRBD18 depletion: 41 exhibit decreased TE and 60 exhibit increased TE. A further 66 transcripts are buffered, i.e . changes in transcript abundance are compensated by changes in TE such that the total translational output is expected not to change. Proteomic analysis validates these data. In DRBD18-depleted cells, a cohort of transcripts that codes for procyclic form-specific proteins is translationally repressed while, conversely, transcripts that code for bloodstream form- and metacyclic form-specific proteins are translationally enhanced. These data suggest that DRBD18 contributes to the maintenance of the procyclic state through both positive and negative translational control of specific mRNAs.
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11
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Oliveira C, Holetz FB, Alves LR, Ávila AR. Modulation of Virulence Factors during Trypanosoma cruzi Differentiation. Pathogens 2022; 12:pathogens12010032. [PMID: 36678380 PMCID: PMC9865030 DOI: 10.3390/pathogens12010032] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
Chagas disease is a neglected tropical disease caused by Trypanosoma cruzi. This protozoan developed several mechanisms to infect, propagate, and survive in different hosts. The specific expression of proteins is responsible for morphological and metabolic changes in different parasite stages along the parasite life cycle. The virulence strategies at the cellular and molecular levels consist of molecules responsible for mediating resistance mechanisms to oxidative damage, cellular invasion, and immune evasion, performed mainly by surface proteins. Since parasite surface coat remodeling is crucial to invasion and infectivity, surface proteins are essential virulence elements. Understanding the factors involved in these processes improves the knowledge of parasite pathogenesis. Genome sequencing has opened the door to high-throughput technologies, allowing us to obtain a deeper understanding of gene reprogramming along the parasite life cycle and identify critical molecules for survival. This review therefore focuses on proteins regulated during differentiation into infective forms considered virulence factors and addresses the current known mechanisms acting in the modulation of gene expression, emphasizing mRNA signals, regulatory factors, and protein complexes.
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Affiliation(s)
- Camila Oliveira
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, Fiocruz Paraná, Curitiba 81350-010, Brazil
- Centre de Recherche CERVO, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Fabíola Barbieri Holetz
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, Fiocruz Paraná, Curitiba 81350-010, Brazil
| | - Lysangela Ronalte Alves
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, Fiocruz Paraná, Curitiba 81350-010, Brazil
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center, University Laval, Québec City, QC G1V 4G2, Canada
| | - Andréa Rodrigues Ávila
- Laboratório de Pesquisa em Apicomplexa, Instituto Carlos Chagas, Fiocruz Paraná, Curitiba 81350-010, Brazil
- Correspondence: ; Tel.: +55-41-33163230
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12
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Falk F, Melo Palhares R, Waithaka A, Clayton C. Roles and interactions of the specialized initiation factors EIF4E2, EIF4E5 and EIF4E6 in Trypanosoma brucei: EIF4E2 maintains the abundances of S-phase mRNAs. Mol Microbiol 2022; 118:457-476. [PMID: 36056730 DOI: 10.1111/mmi.14978] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/14/2022] [Accepted: 08/30/2022] [Indexed: 11/29/2022]
Abstract
Trypanosoma brucei has six versions of the cap-binding translation initiation factor EIF4E. We investigated the functions of EIF4E2, EIF4E3, EIF4E5 and EIF4E6 in bloodstream forms. We confirmed the protein associations previously found in procyclic forms, and detected specific co-purification of some RNA-binding proteins. Bloodstream forms lacking EIF4E5 grew normally and differentiated to replication-incompetent procyclic forms. Depletion of EIF4E6 inhibited bloodstream-form trypanosome growth and translation. EIF4E2 co-purified only the putative RNA binding protein SLBP2. Bloodstream forms lacking EIF4E2 multiplied slowly, had a low maximal cell density, and expressed the stumpy-form marker PAD1, but showed no evidence for enhanced stumpy-form signalling. EIF4E2 knock-out cells differentiated readily to replication-competent procyclic forms. EIF4E2 was strongly associated with a subset of mRNAs that are maximally abundant in S-phase, and these all had decreased abundances in EIF4E2 knock-out cells. Three EIF4E2 target mRNAs are also bound and stabilized by the Pumilio domain protein PUF9. Yeast 2-hybrid results suggested that PUF9 interacts directly with SLBP2, but PUF9 was not detected in EIF4E2 pull-downs. We speculate that the EIF4E2-SLBP2 complex might interact with its target mRNAs, perhaps via PUF9, only early during G1/S, stabilizing the mRNAs in preparation for translation later in S-phase or in early G2.
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Affiliation(s)
- Franziska Falk
- Heidelberg University Centre for Molecular Biology (ZMBH), Im Neuenheimer Feld, Heidelberg, Germany
| | - Rafael Melo Palhares
- Heidelberg University Centre for Molecular Biology (ZMBH), Im Neuenheimer Feld, Heidelberg, Germany.,Institut für Mikro- und Molekularbiologie, Justus-Liebig-Universität Giessen, IFZ, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Albina Waithaka
- Heidelberg University Centre for Molecular Biology (ZMBH), Im Neuenheimer Feld, Heidelberg, Germany
| | - Christine Clayton
- Heidelberg University Centre for Molecular Biology (ZMBH), Im Neuenheimer Feld, Heidelberg, Germany
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13
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Extensive Translational Regulation through the Proliferative Transition of Trypanosoma cruzi Revealed by Multi-Omics. mSphere 2021; 6:e0036621. [PMID: 34468164 PMCID: PMC8550152 DOI: 10.1128/msphere.00366-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Trypanosoma cruzi is the etiological agent for Chagas disease, a neglected parasitic disease in Latin America. Gene transcription control governs the eukaryotic cell replication but is absent in trypanosomatids; thus, it must be replaced by posttranscriptional regulatory events. We investigated the entrance into the T. cruzi replicative cycle using ribosome profiling and proteomics on G1/S epimastigote cultures synchronized with hydroxyurea. We identified 1,784 translationally regulated genes (change > 2, false-discovery rate [FDR] < 0.05) and 653 differentially expressed proteins (change > 1.5, FDR < 0.05), respectively. A major translational remodeling accompanied by an extensive proteome change is found, while the transcriptome remains largely unperturbed at the replicative entrance of the cell cycle. The differentially expressed genes comprise specific cell cycle processes, confirming previous findings while revealing candidate cell cycle regulators that undergo previously unnoticed translational regulation. Clusters of genes showing a coordinated regulation at translation and protein abundance share related biological functions such as cytoskeleton organization and mitochondrial metabolism; thus, they may represent posttranscriptional regulons. The translatome and proteome of the coregulated clusters change in both coupled and uncoupled directions, suggesting that complex cross talk between the two processes is required to achieve adequate protein levels of different regulons. This is the first simultaneous assessment of the transcriptome, translatome, and proteome of trypanosomatids, which represent a paradigm for the absence of transcriptional control. The findings suggest that gene expression chronology along the T. cruzi cell cycle is controlled mainly by translatome and proteome changes coordinated using different mechanisms for specific gene groups. IMPORTANCE Trypanosoma cruzi is an ancient eukaryotic unicellular parasite causing Chagas disease, a potentially life-threatening illness that affects 6 to 7 million people, mostly in Latin America. The antiparasitic treatments for the disease have incomplete efficacy and adverse reactions; thus, improved drugs are needed. We study the mechanisms governing the replication of the parasite, aiming to find differences with the human host, valuable for the development of parasite-specific antiproliferative drugs. Transcriptional regulation is essential for replication in most eukaryotes, but in trypanosomatids, it must be replaced by subsequent gene regulation steps since they lack transcription initiation control. We identified the genome-wide remodeling of mRNA translation and protein abundance during the entrance to the replicative phase of the cell cycle. We found that translation is strongly regulated, causing variation in protein levels of specific cell cycle processes, representing the first simultaneous study of the translatome and proteome in trypanosomatids.
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14
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Rico-Jiménez M, Ceballos-Pérez G, Gómez-Liñán C, Estévez AM. An RNA-binding protein complex regulates the purine-dependent expression of a nucleobase transporter in trypanosomes. Nucleic Acids Res 2021; 49:3814-3825. [PMID: 33744953 PMCID: PMC8053114 DOI: 10.1093/nar/gkab181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 12/13/2022] Open
Abstract
Post-transcriptional regulation of gene expression is particularly important in trypanosomatid protozoa. RNA-binding proteins (RBPs) regulate mRNA stability and translation, yet information about how RBPs are able to link environmental cues to post-transcriptional control is scarce. In Trypanosoma brucei, we have previously characterized a short RNA stem-loop cis-element (PuRE, Purine Responsive Element) within the 3'-UTR of the NT8 nucleobase transporter mRNA that is necessary and sufficient to confer a strong repression of gene expression in response to purines. In this study, we have identified a protein complex composed of two RNA-binding proteins (PuREBP1 and PuREBP2) that binds to the PuRE in vitro and to NT8 mRNA in vivo. Depletion of PuREBP1 by RNA interference results in the upregulation of just NT8 and the mRNAs encoding the amino acid transporter AATP6 paralogues. Moreover, we found that the PuREBP1/2 complex is associated with only a handful of mRNAs, and that it is responsible for the observed purine-dependent regulation of NT8 expression.
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Affiliation(s)
- Miriam Rico-Jiménez
- Instituto de Parasitología y Biomedicina 'López-Neyra', IPBLN-CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016 Armilla, Granada, Spain
| | - Gloria Ceballos-Pérez
- Instituto de Parasitología y Biomedicina 'López-Neyra', IPBLN-CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016 Armilla, Granada, Spain
| | - Claudia Gómez-Liñán
- Instituto de Parasitología y Biomedicina 'López-Neyra', IPBLN-CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016 Armilla, Granada, Spain
| | - Antonio M Estévez
- Instituto de Parasitología y Biomedicina 'López-Neyra', IPBLN-CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016 Armilla, Granada, Spain
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15
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Mwangi KW, Macharia RW, Bargul JL. Gene co-expression network analysis of Trypanosoma brucei in tsetse fly vector. Parasit Vectors 2021; 14:74. [PMID: 33482903 PMCID: PMC7821691 DOI: 10.1186/s13071-021-04597-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/13/2021] [Indexed: 01/14/2023] Open
Abstract
Background Trypanosoma brucei species are motile protozoan parasites that are cyclically transmitted by tsetse fly (genus Glossina) causing human sleeping sickness and nagana in livestock in sub-Saharan Africa. African trypanosomes display digenetic life cycle stages in the tsetse fly vector and in their mammalian host. Experimental work on insect-stage trypanosomes is challenging because of the difficulty in setting up successful in vitro cultures. Therefore, there is limited knowledge on the trypanosome biology during its development in the tsetse fly. Consequently, this limits the development of new strategies for blocking parasite transmission in the tsetse fly. Methods In this study, RNA-Seq data of insect-stage trypanosomes were used to construct a T. brucei gene co-expression network using the weighted gene co-expression analysis (WGCNA) method. The study identified significant enriched modules for genes that play key roles during the parasite’s development in tsetse fly. Furthermore, potential 3′ untranslated region (UTR) regulatory elements for genes that clustered in the same module were identified using the Finding Informative Regulatory Elements (FIRE) tool. Results A fraction of gene modules (12 out of 27 modules) in the constructed network were found to be enriched in functional roles associated with the cell division, protein biosynthesis, mitochondrion, and cell surface. Additionally, 12 hub genes encoding proteins such as RNA-binding protein 6 (RBP6), arginine kinase 1 (AK1), brucei alanine-rich protein (BARP), among others, were identified for the 12 significantly enriched gene modules. In addition, the potential regulatory elements located in the 3′ untranslated regions of genes within the same module were predicted. Conclusions The constructed gene co-expression network provides a useful resource for network-based data mining to identify candidate genes for functional studies. This will enhance understanding of the molecular mechanisms that underlie important biological processes during parasite’s development in tsetse fly. Ultimately, these findings will be key in the identification of potential molecular targets for disease control.![]()
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Affiliation(s)
- Kennedy W Mwangi
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100, Nairobi, Kenya. .,Jomo Kenyatta University of Agriculture and Technology, P.O. BOX 62000-00200, Nairobi, Kenya.
| | | | - Joel L Bargul
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100, Nairobi, Kenya.,Jomo Kenyatta University of Agriculture and Technology, P.O. BOX 62000-00200, Nairobi, Kenya
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16
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Melo do Nascimento L, Terrao M, Marucha KK, Liu B, Egler F, Clayton C. The RNA-associated proteins MKT1 and MKT1L form alternative PBP1-containing complexes in Trypanosoma brucei. J Biol Chem 2020; 295:10940-10955. [PMID: 32532821 DOI: 10.1074/jbc.ra120.013306] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/03/2020] [Indexed: 01/20/2023] Open
Abstract
Control of gene expression in kinetoplastids such as trypanosomes depends heavily on RNA-binding proteins that influence mRNA decay and translation. We previously showed that the trypanosome protein MKT1 forms a multicomponent protein complex: MKT1 interacts with PBP1, which in turn recruits LSM12 and poly(A)-binding protein. MKT1 is recruited to mRNAs by sequence-specific RNA-binding proteins, resulting in stabilization of the bound mRNA. We here show that PBP1, LSM12, and a 117-residue protein, XAC1 (Tb927.7.2780), are present in complexes that contain either MKT1 or an MKT1-like protein, MKT1L (Tb927.10.1490). All five proteins are present predominantly in the complexes, and we found evidence for a minor subset of complexes containing both MKT1 and MKT1L. XAC1-containing complexes reproducibly contained RNA-binding proteins that were previously found associated with MKT1. Moreover, XAC1- or MKT1-containing complexes specifically recruited one of the two poly(A)-binding proteins, PABP2, and one of the six cap-binding translation initiation complexes, EIF4E6-EIF4G5. Yeast two-hybrid assay results indicated that MKT1 directly interacts with EIF4G5. MKT1-PBP1 complexes can therefore interact with mRNAs via their poly(A) tails and caps, as well as through sequence-specific RNA-binding proteins. Correspondingly, MKT1 is associated with many mRNAs, although not with those encoding ribosomal proteins. Meanwhile, MKT1L resembles MKT1 at the C terminus but additionally features an N-terminal extension with low-complexity regions. Although MKT1L depletion inhibited cell proliferation, we found no evidence that it specifically interacts with RNA-binding proteins or mRNA. We speculate that MKT1L may compete with MKT1 for PBP1 binding and thereby modulate the function of MKT1-containing complexes.
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Affiliation(s)
| | - Monica Terrao
- Heidelberg University Centre for Molecular Biology (ZMBH), Heidelberg, Germany
| | | | - Bin Liu
- Heidelberg University Centre for Molecular Biology (ZMBH), Heidelberg, Germany
| | - Franziska Egler
- Heidelberg University Centre for Molecular Biology (ZMBH), Heidelberg, Germany
| | - Christine Clayton
- Heidelberg University Centre for Molecular Biology (ZMBH), Heidelberg, Germany
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17
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Roles of the Pumilio domain protein PUF3 in Trypanosoma brucei growth and differentiation. Parasitology 2020; 147:1171-1183. [PMID: 32513341 DOI: 10.1017/s003118202000092x] [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: 12/14/2022]
Abstract
Trypanosomes strongly rely on post-transcriptional mechanisms to control gene expression. Several Opisthokont Pumilio domain proteins are known to suppress expression when bound to mRNAs. The Trypanosoma brucei Pumilio domain protein PUF3 is a cytosolic mRNA-binding protein that suppresses expression when tethered to a reporter mRNA. RNA-binding studies showed that PUF3 preferentially binds to mRNAs with a classical Pumilio-domain recognition motif, UGUA[U/C]AUU. RNA-interference-mediated reduction of PUF3 in bloodstream forms caused a minor growth defect, but the transcriptome was not affected. Depletion of PUF3 also slightly delayed differentiation to the procyclic form. However, both PUF3 genes could be deleted in cultured bloodstream- and procyclic-form trypanosomes. Procyclic forms without PUF3 also grew somewhat slower than wild-type, but ectopic expression of C-terminally tagged PUF3 impaired their viability. PUF3 was not required for RBP10-induced differentiation of procyclic forms to bloodstream forms. Mass spectrometry revealed no PUF3 binding partners that might explain its suppressive activity. We conclude that PUF3 may have a role in fine-tuning gene expression. Since PUF3 is conserved in all Kinetoplastids, including those that do not infect vertebrates, we suggest that it might confer advantages within the invertebrate host.
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18
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Miller JC, Delzell SB, Concepción-Acevedo J, Boucher MJ, Klingbeil MM. A DNA polymerization-independent role for mitochondrial DNA polymerase I-like protein C in African trypanosomes. J Cell Sci 2020; 133:jcs.233072. [PMID: 32079654 DOI: 10.1242/jcs.233072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 02/10/2020] [Indexed: 01/01/2023] Open
Abstract
Mitochondrial DNA of Trypanosoma brucei and related parasites is a catenated network containing thousands of minicircles and tens of maxicircles, called kinetoplast DNA (kDNA). Replication of a single nucleoid requires at least three DNA polymerase I-like proteins (i.e. POLIB, POLIC and POLID), each showing discrete localizations near the kDNA during S phase. POLIB and POLID have roles in minicircle replication but the specific role of POLIC in kDNA maintenance is less clear. Here, we use an RNA interference (RNAi)-complementation system to dissect the functions of two distinct POLIC regions, i.e. the conserved family A DNA polymerase (POLA) domain and the uncharacterized N-terminal region (UCR). While RNAi complementation with wild-type POLIC restored kDNA content and cell cycle localization of kDNA, active site point mutations in the POLA domain impaired minicircle replication similar to that of POLIB and POLID depletions. Complementation with POLA domain alone abolished the formation of POLIC foci and partially rescued the RNAi phenotype. Furthermore, we provide evidence that the UCR is crucial in cell cycle-dependent protein localization and facilitates proper distribution of progeny networks. This is the first report of a DNA polymerase that impacts on mitochondrial nucleoid distribution.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Jonathan C Miller
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Stephanie B Delzell
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Jeniffer Concepción-Acevedo
- Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, 1600 Clifton Road, Atlanta, GA 30329, USA
| | - Michael J Boucher
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Michele M Klingbeil
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA .,Division of Foodborne,Waterborne, and Environmental Diseases, The Institute of Applied Life Sciences, University of Massachusetts, Amherst, MA 01003, USA
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19
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Romagnoli BAA, Holetz FB, Alves LR, Goldenberg S. RNA Binding Proteins and Gene Expression Regulation in Trypanosoma cruzi. Front Cell Infect Microbiol 2020; 10:56. [PMID: 32154189 PMCID: PMC7045066 DOI: 10.3389/fcimb.2020.00056] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/03/2020] [Indexed: 01/24/2023] Open
Abstract
The regulation of gene expression in trypanosomatids occurs mainly at the post-transcriptional level. In the case of Trypanosoma cruzi, the characterization of messenger ribonucleoprotein (mRNP) particles has allowed the identification of several classes of RNA binding proteins (RBPs), as well as non-canonical RBPs, associated with mRNA molecules. The protein composition of the mRNPs as well as the localization and functionality of the mRNAs depend on their associated proteins. mRNPs can also be organized into larger complexes forming RNA granules, which function as stress granules or P-bodies depending on the associated proteins. The fate of mRNAs in the cell, and consequently the genes expressed, depends on the set of proteins associated with the messenger molecule. These proteins allow the coordinated expression of mRNAs encoding proteins that are related in function, resulting in the formation of post-transcriptional operons. However, the puzzle posed by the combinatorial association of sets of RBPs with mRNAs and how this relates to the expressed genes remain to be elucidated. One important tool in this endeavor is the use of the CRISPR/CAS system to delete genes encoding RBPs, allowing the evaluation of their effect on the formation of mRNP complexes and associated mRNAs in the different compartments of the translation machinery. Accordingly, we recently established this methodology for T. cruzi and deleted the genes encoding RBPs containing zinc finger domains. In this manuscript, we will discuss the data obtained and the potential of the CRISPR/CAS methodology to unveil the role of RBPs in T. cruzi gene expression regulation.
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Affiliation(s)
- Bruno A A Romagnoli
- Gene Expression Regulation Laboratory, Institute Carlos Chagas, Curitiba, Brazil
| | - Fabiola B Holetz
- Gene Expression Regulation Laboratory, Institute Carlos Chagas, Curitiba, Brazil
| | - Lysangela R Alves
- Gene Expression Regulation Laboratory, Institute Carlos Chagas, Curitiba, Brazil
| | - Samuel Goldenberg
- Gene Expression Regulation Laboratory, Institute Carlos Chagas, Curitiba, Brazil
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20
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Benz C, Urbaniak MD. Organising the cell cycle in the absence of transcriptional control: Dynamic phosphorylation co-ordinates the Trypanosoma brucei cell cycle post-transcriptionally. PLoS Pathog 2019; 15:e1008129. [PMID: 31830130 PMCID: PMC6907760 DOI: 10.1371/journal.ppat.1008129] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/07/2019] [Indexed: 11/18/2022] Open
Abstract
The cell division cycle of the unicellular eukaryote Trypanosome brucei is tightly regulated despite the paucity of transcriptional control that results from the arrangement of genes in polycistronic units and lack of dynamically regulated transcription factors. To identify the contribution of dynamic phosphorylation to T. brucei cell cycle control we have combined cell cycle synchronisation by centrifugal elutriation with quantitative phosphoproteomic analysis. Cell cycle regulated changes in phosphorylation site abundance (917 sites, average 5-fold change) were more widespread and of a larger magnitude than changes in protein abundance (443 proteins, average 2-fold change) and were mostly independent of each other. Hierarchical clustering of co-regulated phosphorylation sites according to their cell cycle profile revealed that a bulk increase in phosphorylation occurs across the cell cycle, with a significant enrichment of known cell cycle regulators and RNA binding proteins (RBPs) within the largest clusters. Cell cycle regulated changes in essential cell cycle kinases are temporally co-ordinated with differential phosphorylation of components of the kinetochore and eukaryotic initiation factors, along with many RBPs not previously linked to the cell cycle such as eight PSP1-C terminal domain containing proteins. The temporal profiles demonstrate the importance of dynamic phosphorylation in co-ordinating progression through the cell cycle, and provide evidence that RBPs play a central role in post-transcriptional regulation of the T. brucei cell cycle. Data are available via ProteomeXchange with identifier PXD013488.
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Affiliation(s)
- Corinna Benz
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom
| | - Michael D. Urbaniak
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom
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21
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Functions, mechanisms and regulation of Pumilio/Puf family RNA binding proteins: a comprehensive review. Mol Biol Rep 2019; 47:785-807. [PMID: 31643042 DOI: 10.1007/s11033-019-05142-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 10/15/2019] [Indexed: 12/16/2022]
Abstract
The Pumilio (Pum)/Puf family proteins are ubiquitously present across eukaryotes, including yeast, plants and humans. They generally bind to the 3' untranslated regions of single stranded RNA targets in a sequence specific manner and destabilize them, although a few reports suggest their role in stabilizing the target transcripts. The Pum isoforms are implicated in a wide array of biological processes including stem cell maintenance, development, ribosome biogenesis as well as human diseases. Further studies on Pum would be interesting and important to understand their evolutionarily conserved and divergent features across species, which can have potential implications in medicine, plant sciences as well as basic molecular and cell biological studies. A large number of research reports exists, pertaining to various aspects of Pum, in individual experimental systems. This review is a comprehensive summary of the functions, types, mechanism of action as well as the regulation of Pum in various species. Also, the research questions to be addressed in future are discussed.
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22
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Trenaman A, Glover L, Hutchinson S, Horn D. A post-transcriptional respiratome regulon in trypanosomes. Nucleic Acids Res 2019; 47:7063-7077. [PMID: 31127277 PMCID: PMC6648352 DOI: 10.1093/nar/gkz455] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/25/2019] [Accepted: 05/10/2019] [Indexed: 12/21/2022] Open
Abstract
Post-transcriptional regulons coordinate the expression of groups of genes in eukaryotic cells, yet relatively few have been characterized. Parasitic trypanosomatids are particularly good models for studies on such mechanisms because they exhibit almost exclusive polycistronic, and unregulated, transcription. Here, we identify the Trypanosoma brucei ZC3H39/40 RNA-binding proteins as regulators of the respiratome; the mitochondrial electron transport chain (complexes I-IV) and the FoF1-ATP synthase (complex V). A high-throughput RNAi screen initially implicated both ZC3H proteins in variant surface glycoprotein (VSG) gene silencing. This link was confirmed and both proteins were shown to form a cytoplasmic ZC3H39/40 complex. Transcriptome and mRNA-interactome analyses indicated that the impact on VSG silencing was indirect, while the ZC3H39/40 complex specifically bound and stabilized transcripts encoding respiratome-complexes. Quantitative proteomic analyses revealed specific positive control of >20 components from complexes I, II and V. Our findings establish a link between the mitochondrial respiratome and VSG gene silencing in bloodstream form T. brucei. They also reveal a major respiratome regulon controlled by the conserved trypanosomatid ZC3H39/40 RNA-binding proteins.
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Affiliation(s)
- Anna Trenaman
- The Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Lucy Glover
- The Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Sebastian Hutchinson
- The Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - David Horn
- The Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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Abstract
In trypanosomes, RNA polymerase II transcription is polycistronic and individual mRNAs are excised by trans-splicing and polyadenylation. The lack of individual gene transcription control is compensated by control of mRNA processing, translation and degradation. Although the basic mechanisms of mRNA decay and translation are evolutionarily conserved, there are also unique aspects, such as the existence of six cap-binding translation initiation factor homologues, a novel decapping enzyme and an mRNA stabilizing complex that is recruited by RNA-binding proteins. High-throughput analyses have identified nearly a hundred regulatory mRNA-binding proteins, making trypanosomes valuable as a model system to investigate post-transcriptional regulation.
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Affiliation(s)
- Christine Clayton
- University of Heidelberg Center for Molecular Biology (ZMBH), Im Neuenheimer Feld 282, D69120 Heidelberg, Germany
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24
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In-depth analysis of the genome of Trypanosoma evansi, an etiologic agent of surra. SCIENCE CHINA-LIFE SCIENCES 2019; 62:406-419. [PMID: 30685829 DOI: 10.1007/s11427-018-9473-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 12/29/2018] [Indexed: 12/16/2022]
Abstract
Trypanosoma evansi is the causative agent of the animal trypanosomiasis surra, a disease with serious economic burden worldwide. The availability of the genome of its closely related parasite Trypanosoma brucei allows us to compare their genetic and evolutionarily shared and distinct biological features. The complete genomic sequence of the T. evansi YNB strain was obtained using a combination of genomic and transcriptomic sequencing, de novo assembly, and bioinformatic analysis. The genome size of the T. evansi YNB strain was 35.2 Mb, showing 96.59% similarity in sequence and 88.97% in scaffold alignment with T. brucei. A total of 8,617 protein-coding genes, accounting for 31% of the genome, were predicted. Approximately 1,641 alternative splicing events of 820 genes were identified, with a majority mediated by intron retention, which represented a major difference in post-transcriptional regulation between T. evansi and T. brucei. Disparities in gene copy number of the variant surface glycoprotein, expression site-associated genes, microRNAs, and RNA-binding protein were clearly observed between the two parasites. The results revealed the genomic determinants of T. evansi, which encoded specific biological characteristics that distinguished them from other related trypanosome species.
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Antagonistic and cooperative AGO2-PUM interactions in regulating mRNAs. Sci Rep 2018; 8:15316. [PMID: 30333515 PMCID: PMC6192998 DOI: 10.1038/s41598-018-33596-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/27/2018] [Indexed: 12/14/2022] Open
Abstract
Approximately 1500 RNA-binding proteins (RBPs) profoundly impact mammalian cellular function by controlling distinct sets of transcripts, often using sequence-specific binding to 3′ untranslated regions (UTRs) to regulate mRNA stability and translation. Aside from their individual effects, higher-order combinatorial interactions between RBPs on specific mRNAs have been proposed to underpin the regulatory network. To assess the extent of such co-regulatory control, we took a global experimental approach followed by targeted validation to examine interactions between two well-characterized and highly conserved RBPs, Argonaute2 (AGO2) and Pumilio (PUM1 and PUM2). Transcriptome-wide changes in AGO2-mRNA binding upon PUM knockdown were quantified by CLIP-seq, and the presence of PUM binding on the same 3′UTR corresponded with cooperative and antagonistic effects on AGO2 occupancy. In addition, PUM binding sites that overlap with AGO2 showed differential, weakened binding profiles upon abrogation of AGO2 association, indicative of cooperative interactions. In luciferase reporter validation of candidate 3′UTR sites where AGO2 and PUM colocalized, three sites were identified to host antagonistic interactions, where PUM counteracts miRNA-guided repression. Interestingly, the binding sites for the two proteins are too far for potential antagonism due to steric hindrance, suggesting an alternate mechanism. Our data experimentally confirms the combinatorial regulatory model and indicates that the mostly repressive PUM proteins can change their behavior in a context-dependent manner. Overall, the approach underscores the importance of further elucidation of complex interactions between RBPs and their transcriptome-wide extent.
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26
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Goldstrohm AC, Hall TMT, McKenney KM. Post-transcriptional Regulatory Functions of Mammalian Pumilio Proteins. Trends Genet 2018; 34:972-990. [PMID: 30316580 DOI: 10.1016/j.tig.2018.09.006] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/10/2018] [Accepted: 09/19/2018] [Indexed: 01/18/2023]
Abstract
Mammalian Pumilio proteins, PUM1 and PUM2, are members of the PUF family of sequence-specific RNA-binding proteins. In this review, we explore their mechanisms, regulatory networks, biological functions, and relevance to diseases. Pumilio proteins bind an extensive network of mRNAs and repress protein expression by inhibiting translation and promoting mRNA decay. Opposingly, in certain contexts, they can activate protein expression. Pumilio proteins also regulate noncoding (nc)RNAs. The ncRNA, ncRNA activated by DNA damage (NORAD), can in turn modulate Pumilio activity. Genetic analysis provides new insights into Pumilio protein function. They are essential for growth and development. They control diverse processes, including stem cell fate, and neurological functions, such as behavior and memory formation. Novel findings show that their dysfunction contributes to neurodegeneration, epilepsy, movement disorders, intellectual disability, infertility, and cancer.
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Affiliation(s)
- Aaron C Goldstrohm
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Katherine M McKenney
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
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27
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Abstract
Cells must make careful use of the resources available to them. A key area of cellular regulation involves the biogenesis of ribosomes. Transcriptional regulation of ribosome biogenesis factor genes through alterations in histone acetylation has been well studied. This work identifies a post-transcriptional mechanism of ribosome biogenesis regulation by Puf protein control of mRNA stability. Puf proteins are eukaryotic mRNA binding proteins that play regulatory roles in mRNA degradation and translation via association with specific conserved elements in the 3' untranslated region (UTR) of target mRNAs and with degradation and translation factors. We demonstrate that several ribosome biogenesis factor mRNAs in Saccharomyces cerevisiae containing a canonical Puf4p element in their 3' UTRs are destabilized by Puf2p, Puf4, and Puf5p, yet stabilized by Puf1p and Puf3p. In the absence of all Puf proteins, these ribosome biogenesis mRNAs are destabilized by a secondary mechanism involving the same 3' UTR element. Unlike other targets of Puf4p regulation, the decay of these transcripts is not altered by carbon source. Overexpression of Puf4p results in delayed ribosomal RNA processing and altered ribosomal subunit trafficking. These results represent a novel role for Puf proteins in yeast as regulators of ribosome biogenesis transcript stability.
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Affiliation(s)
- Anthony D Fischer
- a Department of Biology , University of Missouri-St. Louis , St. Louis , MO , USA
| | - Wendy M Olivas
- a Department of Biology , University of Missouri-St. Louis , St. Louis , MO , USA
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28
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Liang X, Hart KJ, Dong G, Siddiqui FA, Sebastian A, Li X, Albert I, Miao J, Lindner SE, Cui L. Puf3 participates in ribosomal biogenesis in malaria parasites. J Cell Sci 2018; 131:jcs.212597. [PMID: 29487181 DOI: 10.1242/jcs.212597] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 02/16/2018] [Indexed: 12/11/2022] Open
Abstract
In this study, we characterized the Puf family gene member Puf3 in the malaria parasites Plasmodium falciparum and Plasmodium yoelii Secondary structure prediction suggested that the RNA-binding domains of the Puf3 proteins consisted of 11 pumilio repeats that were similar to those in the human Puf-A (also known as PUM3) and Saccharomyces cerevisiae Puf6 proteins, which are involved in ribosome biogenesis. Neither P. falciparum (Pf)Puf3 nor P. yoelii (Py)Puf3 could be genetically disrupted, suggesting they may be essential for the intraerythrocytic developmental cycle. Cellular fractionation of PfPuf3 in the asexual stages revealed preferential partitioning to the nuclear fraction, consistent with nuclear localization of PfPuf3::GFP and PyPuf3::GFP as detected by immunofluorescence. Furthermore, PfPuf3 colocalized with the nucleolar marker PfNop1, demonstrating that PfPuf3 is a nucleolar protein in the asexual stages. We found, however, that PyPuf3 changed its localization from being nucleolar to being present in cytosolic puncta in the mosquito and liver stages, which may reflect alternative functions in these stages. Affinity purification of molecules that associated with a PTP-tagged variant of PfPuf3 revealed 31 proteins associated with the 60S ribosome, and an enrichment of 28S rRNA and internal transcribed spacer 2 sequences. Taken together, these results suggest an essential function for PfPuf3 in ribosomal biogenesis.
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Affiliation(s)
- Xiaoying Liang
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA
| | - Kevin J Hart
- Department of Biochemistry and Molecular Biology, Center for Malaria Research, Pennsylvania State University, University Park, PA 16802, USA
| | - Gang Dong
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, 1030 Vienna, Austria
| | - Faiza A Siddiqui
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA
| | - Aswathy Sebastian
- Bioinformatics Consulting Center, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Xiaolian Li
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA
| | - Istvan Albert
- Bioinformatics Consulting Center, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Jun Miao
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA
| | - Scott E Lindner
- Department of Biochemistry and Molecular Biology, Center for Malaria Research, Pennsylvania State University, University Park, PA 16802, USA
| | - Liwang Cui
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA
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29
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Crozier TWM, Tinti M, Wheeler RJ, Ly T, Ferguson MAJ, Lamond AI. Proteomic Analysis of the Cell Cycle of Procylic Form Trypanosoma brucei. Mol Cell Proteomics 2018; 17:1184-1195. [PMID: 29555687 PMCID: PMC5986242 DOI: 10.1074/mcp.ra118.000650] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/01/2018] [Indexed: 12/24/2022] Open
Abstract
We describe a single-step centrifugal elutriation method to produce synchronous Gap1 (G1)-phase procyclic trypanosomes at a scale amenable for proteomic analysis of the cell cycle. Using ten-plex tandem mass tag (TMT) labeling and mass spectrometry (MS)-based proteomics technology, the expression levels of 5325 proteins were quantified across the cell cycle in this parasite. Of these, 384 proteins were classified as cell-cycle regulated and subdivided into nine clusters with distinct temporal regulation. These groups included many known cell cycle regulators in trypanosomes, which validates the approach. In addition, we identify 40 novel cell cycle regulated proteins that are essential for trypanosome survival and thus represent potential future drug targets for the prevention of trypanosomiasis. Through cross-comparison to the TrypTag endogenous tagging microscopy database, we were able to validate the cell-cycle regulated patterns of expression for many of the proteins of unknown function detected in our proteomic analysis. A convenient interface to access and interrogate these data is also presented, providing a useful resource for the scientific community. Data are available via ProteomeXchange with identifier PXD008741 (https://www.ebi.ac.uk/pride/archive/).
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Affiliation(s)
- Thomas W M Crozier
- From the ‡Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.,§Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Michele Tinti
- From the ‡Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Richard J Wheeler
- ‖Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Tony Ly
- §Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Michael A J Ferguson
- From the ‡Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK;
| | - Angus I Lamond
- §Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK;
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The Trypanosoma cruzi RNA-binding protein RBP42 is expressed in the cytoplasm throughout the life cycle of the parasite. Parasitol Res 2018; 117:1095-1104. [PMID: 29473141 DOI: 10.1007/s00436-018-5787-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 01/25/2018] [Indexed: 01/12/2023]
Abstract
Trypanosoma cruzi, the protozoan parasite that causes Chagas disease in humans, has a complex life cycle that promotes survival in disparate environments. In each environment, the parasite must fine-tune its metabolic pathways to divide and multiply. In the absence of recognizable transcriptional gene regulation, it is apparent that protein levels are determined by post-transcriptional mechanisms. Post-transcriptional gene control is influenced by RNA-binding proteins that target mRNAs in the cell's cytoplasm. To initiate the study of post-transcriptional activities in T. cruzi, we studied this organism's ortholog of RBP42, a trypanosomal RNA-binding protein. RBP42 was originally detected in Trypanosoma brucei and was shown to target a subset of mRNAs that encode proteins governing central carbon metabolism. T. cruzi RBP42 structurally resembles T. brucei RBP42, sharing an NTF2 domain at its amino terminus and a single RNA-binding domain (specifically, the RNA recognition motif, or RRM), at its carboxy terminus. A phylogenetic analysis reveals that an NTF2 and a single RRM are distinguishing features of all RBP42 orthologs within the broad kinetoplastid grouping. T. cruzi RBP42 is expressed in all life cycle stages of the parasite as determined by immunoblot and immunofluorescence microscopy. In each case, the protein is localized to the cytoplasm, indicating a role for T. cruzi RBP42 in post-transcriptional activities in all stages of the parasite life cycle. We speculate that RBP42 influences the dynamic metabolic pathways responsible for parasite infection and transmission.
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Morriswood B, Engstler M. Let's get fISSical: fast in silico synchronization as a new tool for cell division cycle analysis. Parasitology 2018; 145:196-209. [PMID: 28166845 PMCID: PMC5964468 DOI: 10.1017/s0031182017000038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/23/2016] [Accepted: 01/05/2017] [Indexed: 12/23/2022]
Abstract
Cell cycle progression is a question of fundamental biological interest. The coordinated duplication and segregation of all cellular structures and organelles is however an extremely complex process, and one which remains only partially understood even in the most intensively researched model organisms. Trypanosomes are in an unusual position in this respect - they are both outstanding model systems for fundamental questions in eukaryotic cell biology, and pathogens that are the causative agents of three of the neglected tropical diseases. As a failure to successfully complete cell division will be deleterious or lethal, analysis of the cell division cycle is of relevance both to basic biology and drug design efforts. Cell division cycle analysis is however experimentally challenging, as the analysis of phenotypes associated with it remains hypothesis-driven and therefore biased. Current methods of analysis are extremely labour-intensive, and cell synchronization remains difficult and unreliable. Consequently, there exists a need - both in basic and applied trypanosome biology - for a global, unbiased, standardized and high-throughput analysis of cell division cycle progression. In this review, the requirements - both practical and computational - for such a system are considered and compared with existing techniques for cell cycle analysis.
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Affiliation(s)
- Brooke Morriswood
- Department of Cell & Developmental Biology,University of Würzburg,Biocentre, Am Hubland, 97074 Würzburg,Germany
| | - Markus Engstler
- Department of Cell & Developmental Biology,University of Würzburg,Biocentre, Am Hubland, 97074 Würzburg,Germany
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32
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Erben ED. High-throughput Methods for Dissection of Trypanosome Gene Regulatory Networks. Curr Genomics 2018; 19:78-86. [PMID: 29491736 PMCID: PMC5814965 DOI: 10.2174/1389202918666170815125336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 12/22/2016] [Accepted: 02/03/2017] [Indexed: 12/24/2022] Open
Abstract
From synthesis to decay, mRNA associates with RNA-binding proteins (RBPs) establishing dynamic ribonucleoprotein particles (RNPs). Understanding the composition and function of RNPs is fundamental to understanding how eukaryotic mRNAs are controlled. This is especially relevant for trypanosomes and related kinetoplastid parasites, which mostly rely on post-transcriptional mechanisms to control gene expression. Crucial for trypanosome differentiation, development, or even response to heat shock, RBPs are known to be essential modulators of diverse molecular processes. The recent application of large-scale quantitative methods, such as Next-Generation Sequencing (NGS) and quantitative mass spectrometry, has revealed new exciting features about the parasite RNA-related metabolism. Novel proteins carrying RNA-binding activity, including many proteins without RNA-related ontology were discovered setting a necessary groundwork to get in insights into RNA biology. Conclusion: This review aims to give the reader an understanding of current trypanosome RNP research, highlighting the progress made using high-throughput approaches.
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Affiliation(s)
- Esteban D Erben
- Zentrum fur Molekulare Biologie der Universitet Heidelberg (ZMBH), Im Neuenheimer Feld 282, 69120Heidelberg, Germany
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33
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Belew AT, Junqueira C, Rodrigues-Luiz GF, Valente BM, Oliveira AER, Polidoro RB, Zuccherato LW, Bartholomeu DC, Schenkman S, Gazzinelli RT, Burleigh BA, El-Sayed NM, Teixeira SMR. Comparative transcriptome profiling of virulent and non-virulent Trypanosoma cruzi underlines the role of surface proteins during infection. PLoS Pathog 2017; 13:e1006767. [PMID: 29240831 PMCID: PMC5746284 DOI: 10.1371/journal.ppat.1006767] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 12/28/2017] [Accepted: 11/22/2017] [Indexed: 01/23/2023] Open
Abstract
Trypanosoma cruzi, the protozoan that causes Chagas disease, has a complex life cycle involving several morphologically and biochemically distinct stages that establish intricate interactions with various insect and mammalian hosts. It has also a heterogeneous population structure comprising strains with distinct properties such as virulence, sensitivity to drugs, antigenic profile and tissue tropism. We present a comparative transcriptome analysis of two cloned T. cruzi strains that display contrasting virulence phenotypes in animal models of infection: CL Brener is a virulent clone and CL-14 is a clone that is neither infective nor pathogenic in in vivo models of infection. Gene expression analysis of trypomastigotes and intracellular amastigotes harvested at 60 and 96 hours post-infection (hpi) of human fibroblasts revealed large differences that reflect the parasite’s adaptation to distinct environments during the infection of mammalian cells, including changes in energy sources, oxidative stress responses, cell cycle control and cell surface components. While extensive transcriptome remodeling was observed when trypomastigotes of both strains were compared to 60 hpi amastigotes, differences in gene expression were much less pronounced when 96 hpi amastigotes and trypomastigotes of CL Brener were compared. In contrast, the differentiation of the avirulent CL-14 from 96 hpi amastigotes to extracellular trypomastigotes was associated with considerable changes in gene expression, particularly in gene families encoding surface proteins such as trans-sialidases, mucins and the mucin associated surface proteins (MASPs). Thus, our comparative transcriptome analysis indicates that the avirulent phenotype of CL-14 may be due, at least in part, to a reduced or delayed expression of genes encoding surface proteins that are associated with the transition of amastigotes to trypomastigotes, an essential step in the establishment of the infection in the mammalian host. Confirming the role of members of the trans-sialidase family of surface proteins for parasite differentiation, transfected CL-14 constitutively expressing a trans-sialidase gene displayed faster kinetics of trypomastigote release in the supernatant of infected cells compared to wild type CL-14. Chagas disease, caused by the protozoan parasite Trypanosoma cruzi, is an infection that occurs in several Latin American countries, resulting in a mild illness or in severe damage of the heart and intestinal tract. Such a broad spectrum of clinical manifestations observed in Chagas disease patients is likely due to differences in host susceptibility as well as to a large heterogeneity among T. cruzi isolates. The identification of virulence factors that are differentially expressed in the parasite population is a valuable strategy for understanding of the distinct interactions that occur between this pathogen and its host, which may or may not lead to pathogenesis. By comparing the gene expression profiles of two T. cruzi strains that display contrasting virulence phenotypes in animal models of infection, we identified a central role for genes encoding surface proteins that is associated with the differentiation from intracellular replicative amastigotes to infective trypomastigotes. We showed that the expression of these genes occurs differentially within the two strains and this difference may be a factor that impacts parasite survival and dissemination in the mammalian host.
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Affiliation(s)
- A. Trey Belew
- Department of Cell Biology and Molecular Genetics and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Caroline Junqueira
- Centro de Pesquisas Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Gabriela F. Rodrigues-Luiz
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Bruna M. Valente
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Antonio Edson R. Oliveira
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rafael B. Polidoro
- Departmento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Luciana W. Zuccherato
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Daniella C. Bartholomeu
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Sergio Schenkman
- Departmento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Ricardo T. Gazzinelli
- Centro de Pesquisas Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Barbara A. Burleigh
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Najib M. El-Sayed
- Department of Cell Biology and Molecular Genetics and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
- * E-mail: (SMRT); (NES)
| | - Santuza M. R. Teixeira
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- * E-mail: (SMRT); (NES)
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Azizi H, Dumas C, Papadopoulou B. The Pumilio-domain protein PUF6 contributes to SIDER2 retroposon-mediated mRNA decay in Leishmania. RNA (NEW YORK, N.Y.) 2017; 23:1874-1885. [PMID: 28877997 PMCID: PMC5689007 DOI: 10.1261/rna.062950.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/05/2017] [Indexed: 06/07/2023]
Abstract
Leishmania and other trypanosomatid protozoa lack control at the level of transcription initiation and regulate gene expression exclusively post-transcriptionally. We have reported previously that Leishmania harbors a unique class of short interspersed degenerate retroposons (SIDERs) that are predominantly located within 3'UTRs and play a major role in post-transcriptional control. We have shown that members of the SIDER2 subfamily initiate mRNA decay through endonucleolytic cleavage within the second conserved 79-nt signature sequence of SIDER2 retroposons. Here, we have developed an optimized MS2 coat protein tethering system to capture trans-acting factor(s) regulating SIDER2-mediated mRNA decay. Tethering of the MS2 coat protein to a reporter RNA harboring two MS2 stem-loop aptamers and the cognate SIDER2-containing 3'UTR in combination with immunoprecipitation and mass spectrometry analysis led to the identification of RNA-binding proteins with known functions in mRNA decay. Among the candidate SIDER2-interacting proteins that were individually tethered to a SIDER2 reporter RNA, the Pumilio-domain protein PUF6 was shown to enhance degradation and reduce transcript half-life. Furthermore, we showed that PUF6 binds to SIDER2 sequences that include the regulatory 79-nt signature motif, hence contributing to the mRNA decay process. Consistent with a role of PUF6 in SIDER2-mediated decay, genetic inactivation of PUF6 resulted in increased accumulation and higher stability of endogenous SIDER2-bearing transcripts. Overall, these studies provide new insights into regulated mRNA decay pathways in Leishmania controlled by SIDER2 retroposons and propose a broader role for PUF proteins in mRNA decay within the eukaryotic kingdom.
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Affiliation(s)
- Hiva Azizi
- Research Center in Infectious Diseases, CHU de Quebec Research Center-Laval University, Quebec, QC, G1V 4G2 Canada
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Laval University, Quebec, QC, G1V 0A6 Canada
| | - Carole Dumas
- Research Center in Infectious Diseases, CHU de Quebec Research Center-Laval University, Quebec, QC, G1V 4G2 Canada
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Laval University, Quebec, QC, G1V 0A6 Canada
| | - Barbara Papadopoulou
- Research Center in Infectious Diseases, CHU de Quebec Research Center-Laval University, Quebec, QC, G1V 4G2 Canada
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Laval University, Quebec, QC, G1V 0A6 Canada
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Chávez S, Eastman G, Smircich P, Becco LL, Oliveira-Rizzo C, Fort R, Potenza M, Garat B, Sotelo-Silveira JR, Duhagon MA. Transcriptome-wide analysis of the Trypanosoma cruzi proliferative cycle identifies the periodically expressed mRNAs and their multiple levels of control. PLoS One 2017; 12:e0188441. [PMID: 29182646 PMCID: PMC5705152 DOI: 10.1371/journal.pone.0188441] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 11/07/2017] [Indexed: 12/02/2022] Open
Abstract
Trypanosoma cruzi is the protozoan parasite causing American trypanosomiasis or Chagas disease, a neglected parasitosis with important human health impact in Latin America. The efficacy of current therapy is limited, and its toxicity is high. Since parasite proliferation is a fundamental target for rational drug design, we sought to progress into its understanding by applying a genome-wide approach. Treating a TcI linage strain with hydroxyurea, we isolated epimastigotes in late G1, S and G2/M cell cycle stages at 70% purity. The sequencing of each phase identified 305 stage-specific transcripts (1.5-fold change, p≤0.01), coding for conserved cell cycle regulated proteins and numerous proteins whose cell cycle dependence has not been recognized before. Comparisons with the parasite T. brucei and the human host reveal important differences. The meta-analysis of T. cruzi transcriptomic and ribonomic data indicates that cell cycle regulated mRNAs are subject to sub-cellular compartmentalization. Compositional and structural biases of these genes- including CAI, GC content, UTR length, and polycistron position- may contribute to their regulation. To discover nucleotide motifs responsible for the co-regulation of cell cycle regulated genes, we looked for overrepresented motifs at their UTRs and found a variant of the cell cycle sequence motif at the 3' UTR of most of the S and G2 stage genes. We additionally identified hairpin structures at the 5' UTRs of a high proportion of the transcripts, suggesting that periodic gene expression might also rely on translation initiation in T. cruzi. In summary, we report a comprehensive list of T. cruzi cell cycle regulated genes, including many previously unstudied proteins, we show evidence favoring a multi-step control of their expression, and we identify mRNA motifs that may mediate their regulation. Our results provide novel information of the T. cruzi proliferative proteins and the integrated levels of their gene expression control.
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Affiliation(s)
- Santiago Chávez
- Laboratory of Molecular Interactions, School of Sciences, Universidad de la República, Montevideo, Uruguay
- Department of Genetics, School of Medicine, Universidad de la República, Montevideo, Uruguay
| | - Guillermo Eastman
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Pablo Smircich
- Laboratory of Molecular Interactions, School of Sciences, Universidad de la República, Montevideo, Uruguay
- Department of Genetics, School of Medicine, Universidad de la República, Montevideo, Uruguay
| | - Lorena Lourdes Becco
- Laboratory of Molecular Interactions, School of Sciences, Universidad de la República, Montevideo, Uruguay
| | - Carolina Oliveira-Rizzo
- Laboratory of Molecular Interactions, School of Sciences, Universidad de la República, Montevideo, Uruguay
- Department of Genetics, School of Medicine, Universidad de la República, Montevideo, Uruguay
| | - Rafael Fort
- Laboratory of Molecular Interactions, School of Sciences, Universidad de la República, Montevideo, Uruguay
- Department of Genetics, School of Medicine, Universidad de la República, Montevideo, Uruguay
| | - Mariana Potenza
- Institute for Research in Genetic Engineering and Molecular Biology 'Dr. N.H. Torres', Buenos Aires, Argentina
| | - Beatriz Garat
- Laboratory of Molecular Interactions, School of Sciences, Universidad de la República, Montevideo, Uruguay
| | - José Roberto Sotelo-Silveira
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
- Department of Cell and Molecular Biology, School of Sciences, Universidad de la República, Montevideo, Uruguay
| | - María Ana Duhagon
- Laboratory of Molecular Interactions, School of Sciences, Universidad de la República, Montevideo, Uruguay
- Department of Genetics, School of Medicine, Universidad de la República, Montevideo, Uruguay
- * E-mail:
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Expression of the RNA-binding protein RBP10 promotes the bloodstream-form differentiation state in Trypanosoma brucei. PLoS Pathog 2017; 13:e1006560. [PMID: 28800584 PMCID: PMC5568443 DOI: 10.1371/journal.ppat.1006560] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 08/23/2017] [Accepted: 07/29/2017] [Indexed: 01/06/2023] Open
Abstract
In nearly all eukaryotes, cellular differentiation is governed by changes in transcription, and stabilized by chromatin and DNA modification. Gene expression control in the pathogen Trypanosoma brucei, in contrast, relies almost exclusively on post-transcriptional mechanisms, so RNA binding proteins must assume the burden that is usually borne by transcription factors. T. brucei multiply in the blood of mammals as bloodstream forms, and in the midgut of Tsetse flies as procyclic forms. We show here that a single RNA-binding protein, RBP10, promotes the bloodstream-form trypanosome differentiation state. Depletion of RBP10 from bloodstream-form trypanosomes gives cells that can grow only as procyclic forms; conversely, expression of RBP10 in procyclic forms converts them to bloodstream forms. RBP10 binds to procyclic-specific mRNAs containing an UAUUUUUU motif, targeting them for translation repression and destruction. Products of RBP10 target mRNAs include not only the major procyclic surface protein and enzymes of energy metabolism, but also protein kinases and stage-specific RNA-binding proteins: this suggests that alterations in RBP10 trigger a regulatory cascade.
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García-Huertas P, Mejía-Jaramillo AM, González L, Triana-Chávez O. Transcriptome and Functional Genomics Reveal the Participation of Adenine Phosphoribosyltransferase inTrypanosoma cruziResistance to Benznidazole. J Cell Biochem 2017; 118:1936-1945. [DOI: 10.1002/jcb.25978] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/06/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Paola García-Huertas
- Grupo Biología y Control de Enfermedades Infecciosas-BCEI; Universidad de Antioquia; UdeA Medellín Colombia
| | - Ana María Mejía-Jaramillo
- Grupo Biología y Control de Enfermedades Infecciosas-BCEI; Universidad de Antioquia; UdeA Medellín Colombia
| | - Laura González
- Grupo Biología y Control de Enfermedades Infecciosas-BCEI; Universidad de Antioquia; UdeA Medellín Colombia
| | - Omar Triana-Chávez
- Grupo Biología y Control de Enfermedades Infecciosas-BCEI; Universidad de Antioquia; UdeA Medellín Colombia
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PUMILIO/FOXP1 signaling drives expansion of hematopoietic stem/progenitor and leukemia cells. Blood 2017; 129:2493-2506. [PMID: 28232582 DOI: 10.1182/blood-2016-10-747436] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 02/20/2017] [Indexed: 12/13/2022] Open
Abstract
RNA-binding proteins (RBPs) have emerged as important regulators of invertebrate adult stem cells, but their activities remain poorly appreciated in mammals. Using a short hairpin RNA strategy, we demonstrate here that the 2 mammalian RBPs, PUMILIO (PUM)1 and PUM2, members of the PUF family of posttranscriptional regulators, are essential for hematopoietic stem/progenitor cell (HSPC) proliferation and survival in vitro and in vivo upon reconstitution assays. Moreover, we found that PUM1/2 sustain myeloid leukemic cell growth. Through a proteomic approach, we identified the FOXP1 transcription factor as a new target of PUM1/2. Contrary to its canonical repressive activity, PUM1/2 rather promote FOXP1 expression by a direct binding to 2 canonical PUM responsive elements present in the FOXP1-3' untranslated region (UTR). Expression of FOXP1 strongly correlates with PUM1 and PUM2 levels in primary HSPCs and myeloid leukemia cells. We demonstrate that FOXP1 by itself supports HSPC and leukemic cell growth, thus mimicking PUM activities. Mechanistically, FOXP1 represses the expression of the p21-CIP1 and p27-KIP1 cell cycle inhibitors. Enforced FOXP1 expression reverses shPUM antiproliferative and proapoptotic activities. Altogether, our results reveal a novel regulatory pathway, underscoring a previously unknown and interconnected key role of PUM1/2 and FOXP1 in regulating normal HSPC and leukemic cell growth.
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Savage AF, Kolev NG, Franklin JB, Vigneron A, Aksoy S, Tschudi C. Transcriptome Profiling of Trypanosoma brucei Development in the Tsetse Fly Vector Glossina morsitans. PLoS One 2016; 11:e0168877. [PMID: 28002435 PMCID: PMC5176191 DOI: 10.1371/journal.pone.0168877] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 12/07/2016] [Indexed: 01/10/2023] Open
Abstract
African trypanosomes, the causative agents of sleeping sickness in humans and nagana in animals, have a complex digenetic life cycle between a mammalian host and an insect vector, the blood-feeding tsetse fly. Although the importance of the insect vector to transmit the disease was first realized over a century ago, many aspects of trypanosome development in tsetse have not progressed beyond a morphological analysis, mainly due to considerable challenges to obtain sufficient material for molecular studies. Here, we used high-throughput RNA-Sequencing (RNA-Seq) to profile Trypanosoma brucei transcript levels in three distinct tissues of the tsetse fly, namely the midgut, proventriculus and salivary glands. Consistent with current knowledge and providing a proof of principle, transcripts coding for procyclin isoforms and several components of the cytochrome oxidase complex were highly up-regulated in the midgut transcriptome, whereas transcripts encoding metacyclic VSGs (mVSGs) and the surface coat protein brucei alanine rich protein or BARP were extremely up-regulated in the salivary gland transcriptome. Gene ontology analysis also supported the up-regulation of biological processes such as DNA metabolism and DNA replication in the proventriculus transcriptome and major changes in signal transduction and cyclic nucleotide metabolism in the salivary gland transcriptome. Our data highlight a small repertoire of expressed mVSGs and potential signaling pathways involving receptor-type adenylate cyclases and members of a surface carboxylate transporter family, called PADs (Proteins Associated with Differentiation), to cope with the changing environment, as well as RNA-binding proteins as a possible global regulators of gene expression.
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Affiliation(s)
- Amy F. Savage
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, Connecticut, United States of America
| | - Nikolay G. Kolev
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, Connecticut, United States of America
| | - Joseph B. Franklin
- Department of Cell Biology, School of Medicine, Yale University, New Haven, Connecticut, United States of America
| | - Aurelien Vigneron
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, Connecticut, United States of America
| | - Serap Aksoy
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, Connecticut, United States of America
- * E-mail: (SA); (CT)
| | - Christian Tschudi
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, Connecticut, United States of America
- * E-mail: (SA); (CT)
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Shrestha S, Li X, Ning G, Miao J, Cui L. The RNA-binding protein Puf1 functions in the maintenance of gametocytes in Plasmodium falciparum. J Cell Sci 2016; 129:3144-52. [PMID: 27383769 DOI: 10.1242/jcs.186908] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 07/01/2016] [Indexed: 01/17/2023] Open
Abstract
Translation control plays an important role in the regulation of gene expression in the malaria parasite Plasmodium falciparum, especially in transition stages between the vertebrate host and mosquito vector. Here, we determined the function of the Puf-family member Puf1 (denoted as PfPuf1 for the P. falciparum protein) during P. falciparum sexual development. We show that PfPuf1 was expressed in all gametocyte stages and at higher levels in female gametocytes. PfPuf1 disruption did not interfere with the asexual erythrocyte cycle of the parasite but resulted in an approximately tenfold decrease of mature gametocytes. In the PfPuf1-disrupted lines, gametocytes appeared normal before stage III but subsequently exhibited a sharp decline in gametocytemia. This was accompanied by a concomitant accumulation of dead and dying late-stage gametocytes, which retained normal gross morphology. In addition, significantly more female gametocytes were lost in the PfPuf1-disrupted lines during development, resulting in a reversed male-to-female sex ratio. These results indicate that PfPuf1 is important for the differentiation and maintenance of gametocytes, especially female gametocytes.
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Affiliation(s)
- Sony Shrestha
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Xiaolian Li
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Gang Ning
- Microscopy and Cytometry Facility, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jun Miao
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Liwang Cui
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802, USA
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TAC102 Is a Novel Component of the Mitochondrial Genome Segregation Machinery in Trypanosomes. PLoS Pathog 2016; 12:e1005586. [PMID: 27168148 PMCID: PMC4864229 DOI: 10.1371/journal.ppat.1005586] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 03/30/2016] [Indexed: 11/19/2022] Open
Abstract
Trypanosomes show an intriguing organization of their mitochondrial DNA into a catenated network, the kinetoplast DNA (kDNA). While more than 30 proteins involved in kDNA replication have been described, only few components of kDNA segregation machinery are currently known. Electron microscopy studies identified a high-order structure, the tripartite attachment complex (TAC), linking the basal body of the flagellum via the mitochondrial membranes to the kDNA. Here we describe TAC102, a novel core component of the TAC, which is essential for proper kDNA segregation during cell division. Loss of TAC102 leads to mitochondrial genome missegregation but has no impact on proper organelle biogenesis and segregation. The protein is present throughout the cell cycle and is assembled into the newly developing TAC only after the pro-basal body has matured indicating a hierarchy in the assembly process. Furthermore, we provide evidence that the TAC is replicated de novo rather than using a semi-conservative mechanism. Lastly, we demonstrate that TAC102 lacks an N-terminal mitochondrial targeting sequence and requires sequences in the C-terminal part of the protein for its proper localization. Proper segregation of the mitochondrial genome during cell division is a prerequisite of healthy eukaryotic cells. However, the mechanism underlying the segregation process is only poorly understood. We use the single celled parasite Trypanosoma brucei, which, unlike most model organisms, harbors a single large mitochondrion with a single mitochondrial genome, also called kinetoplast DNA (kDNA), to study this question. In trypanosomes, kDNA replication and segregation are tightly integrated into the cell cycle and thus can be studied alongside cell cycle markers. Furthermore, previous studies using electron microscopy have characterized the tripartite attachment complex (TAC) as a structural element of the mitochondrial genome segregation machinery. Here, we characterize TAC102, a novel trypanosome protein localized to the TAC. The protein is essential for proper kDNA segregation and cell growth. We analyze the presence of this protein using super resolution microscopy and show that TAC102 is a mitochondrial protein localized between the kDNA and the basal body of the cell’s flagellum. In addition, we characterize different parts of the protein and show that the C-terminus of TAC102 is important for its proper localization. The data and resources presented will allow a more detailed characterization of the dynamics and hierarchy of the TAC in the future and might open new avenues for drug discovery targeting this structure.
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42
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Lueong S, Merce C, Fischer B, Hoheisel JD, Erben ED. Gene expression regulatory networks in Trypanosoma brucei: insights into the role of the mRNA-binding proteome. Mol Microbiol 2016; 100:457-71. [PMID: 26784394 DOI: 10.1111/mmi.13328] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2016] [Indexed: 12/11/2022]
Abstract
Control of gene expression at the post-transcriptional level is essential in all organisms, and RNA-binding proteins play critical roles from mRNA synthesis to decay. To fully understand this process, it is necessary to identify the complete set of RNA-binding proteins and the functional consequences of the protein-mRNA interactions. Here, we provide an overview of the proteins that bind to mRNAs and their functions in the pathogenic bloodstream form of Trypanosoma brucei. We describe the production of a small collection of open-reading frames encoding proteins potentially involved in mRNA metabolism. With this ORFeome collection, we used tethering to screen for proteins that play a role in post-transcriptional control. A yeast two-hybrid screen showed that several of the discovered repressors interact with components of the CAF1/NOT1 deadenylation complex. To identify the RNA-binding proteins, we obtained the mRNA-bound proteome. We identified 155 high-confidence candidates, including many not previously annotated as RNA-binding proteins. Twenty seven of these proteins affected reporter expression in the tethering screen. Our study provides novel insights into the potential trypanosome mRNPs composition, architecture and function.
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Affiliation(s)
- Smiths Lueong
- Functional Genome Analysis, Deutsche Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Clementine Merce
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282
| | - Bernd Fischer
- Computational Genome Biology, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg
| | - Jörg D Hoheisel
- Functional Genome Analysis, Deutsche Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Esteban D Erben
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282
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Grewal JS, McLuskey K, Das D, Myburgh E, Wilkes J, Brown E, Lemgruber L, Gould MK, Burchmore RJ, Coombs GH, Schnaufer A, Mottram JC. PNT1 Is a C11 Cysteine Peptidase Essential for Replication of the Trypanosome Kinetoplast. J Biol Chem 2016; 291:9492-500. [PMID: 26940875 PMCID: PMC4850289 DOI: 10.1074/jbc.m116.714972] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Indexed: 11/16/2022] Open
Abstract
The structure of a C11 peptidase PmC11 from the gut bacterium, Parabacteroides merdae, has recently been determined, enabling the identification and characterization of a C11 orthologue, PNT1, in the parasitic protozoon Trypanosoma brucei. A phylogenetic analysis identified PmC11 orthologues in bacteria, archaea, Chromerids, Coccidia, and Kinetoplastida, the latter being the most divergent. A primary sequence alignment of PNT1 with clostripain and PmC11 revealed the position of the characteristic His-Cys catalytic dyad (His99 and Cys136), and an Asp (Asp134) in the potential S1 binding site. Immunofluorescence and cryoelectron microscopy revealed that PNT1 localizes to the kinetoplast, an organelle containing the mitochondrial genome of the parasite (kDNA), with an accumulation of the protein at or near the antipodal sites. Depletion of PNT1 by RNAi in the T. brucei bloodstream form was lethal both in in vitro culture and in vivo in mice and the induced population accumulated cells lacking a kinetoplast. In contrast, overexpression of PNT1 led to cells having mislocated kinetoplasts. RNAi depletion of PNT1 in a kDNA independent cell line resulted in kinetoplast loss but was viable, indicating that PNT1 is required exclusively for kinetoplast maintenance. Expression of a recoded wild-type PNT1 allele, but not of an active site mutant restored parasite viability after induction in vitro and in vivo confirming that the peptidase activity of PNT1 is essential for parasite survival. These data provide evidence that PNT1 is a cysteine peptidase that is required exclusively for maintenance of the trypanosome kinetoplast.
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Affiliation(s)
- Jaspreet S Grewal
- From the Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom, the Department of Biology, Centre for Immunology and Infection, University of York, Wentworth Way, Heslington, York YO10 5DD, United Kingdom
| | - Karen McLuskey
- From the Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Debanu Das
- the Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025
| | - Elmarie Myburgh
- From the Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom, the Department of Biology, Centre for Immunology and Infection, University of York, Wentworth Way, Heslington, York YO10 5DD, United Kingdom
| | - Jonathan Wilkes
- From the Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Elaine Brown
- From the Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom, the Department of Biology, Centre for Immunology and Infection, University of York, Wentworth Way, Heslington, York YO10 5DD, United Kingdom
| | - Leandro Lemgruber
- From the Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Matthew K Gould
- the Institute of Immunology and Infection Research and Centre for Immunity, Infection, and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Richard J Burchmore
- From the Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Graham H Coombs
- the Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, United Kingdom
| | - Achim Schnaufer
- the Institute of Immunology and Infection Research and Centre for Immunity, Infection, and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Jeremy C Mottram
- From the Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom, the Department of Biology, Centre for Immunology and Infection, University of York, Wentworth Way, Heslington, York YO10 5DD, United Kingdom,
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De Gaudenzi JG, Jäger AV, Izcovich R, Campo VA. Insights into the Regulation of mRNA Processing of Polycistronic Transcripts Mediated by DRBD4/PTB2, a Trypanosome Homolog of the Polypyrimidine Tract-Binding Protein. J Eukaryot Microbiol 2016; 63:440-52. [PMID: 26663092 DOI: 10.1111/jeu.12288] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/11/2015] [Accepted: 12/02/2015] [Indexed: 12/13/2022]
Abstract
Trypanosomes regulate gene expression mostly by posttranscriptional mechanisms, including control of mRNA turnover and translation efficiency. This regulation is carried out via certain elements located at the 3'-untranslated regions of mRNAs, which are recognized by RNA-binding proteins. In trypanosomes, trans-splicing is of central importance to control mRNA maturation. We have previously shown that TcDRBD4/PTB2, a trypanosome homolog of the human polypyrimidine tract-binding protein splicing regulator, interacts with the intergenic region of one specific dicistronic transcript, referred to as TcUBP (and encoding for TcUBP1 and TcUBP2, two closely kinetoplastid-specific proteins). In this work, a survey of TcUBP RNA processing revealed certain TcDRBD4/PTB2-regulatory elements within its intercistronic region, which are likely to influence the trans-splicing rate of monocistronic-derived transcripts. Furthermore, TcDRBD4/PTB2 overexpression in epimastigote cells notably decreased both UBP1 and UBP2 protein expression. This type of posttranscriptional gene regulatory mechanism could be extended to other transcripts as well, as we identified several other RNA precursor molecules that specifically bind to TcDRBD4/PTB2. Altogether, these findings support a model in which TcDRBD4/PTB2-containing ribonucleoprotein complexes can prevent trans-splicing. This could represent another stage of gene expression regulation mediated by the masking of trans-splicing/polyadenylation signals.
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Affiliation(s)
- Javier G De Gaudenzi
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, UNSAM-CONICET, Sede San Martín, Prov. de Buenos Aires, Argentina
| | - Adriana V Jäger
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, UNSAM-CONICET, Sede San Martín, Prov. de Buenos Aires, Argentina
| | - Ronan Izcovich
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, UNSAM-CONICET, Sede San Martín, Prov. de Buenos Aires, Argentina
| | - Vanina A Campo
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, UNSAM-CONICET, Sede San Martín, Prov. de Buenos Aires, Argentina
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Mulindwa J, Mercé C, Matovu E, Enyaru J, Clayton C. Transcriptomes of newly-isolated Trypanosoma brucei rhodesiense reveal hundreds of mRNAs that are co-regulated with stumpy-form markers. BMC Genomics 2015; 16:1118. [PMID: 26715446 PMCID: PMC4696300 DOI: 10.1186/s12864-015-2338-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 12/22/2015] [Indexed: 12/02/2022] Open
Abstract
Background During natural Trypanosoma brucei infections, the parasites differentiate spontaneously into a non-dividing “stumpy” form when a certain level of parasitaemia is attained. This form is metabolically adapted for rapid further differentiation into procyclic forms upon uptake by Tsetse flies. Results We describe here four central Ugandan isolates of Trypanosoma brucei rhodesiense that have undergone only three rodent passages since isolation from human patients. As expected, SNP analysis shows that these isolates are more closely related to each other than to the commonly used strains Lister 427, Antat1.1, and TREU927. TREU927 generally has smaller copy numbers of repeated genes than the other strains, while Lister 427 trypanosomes with a 30-year history of in vitro culture and cloning have more histone genes than the other isolates. The recently isolated trypanosomes were grown in rats, and their transcriptomes characterised. In comparison with cultured procyclic and bloodstream forms, there were increases in mRNAs encoding the stumpy-form markers ESAG9 and PIP39, with coordinated alterations in the levels of over 600 additional mRNAs. Numerous mRNAs encoding proteins of no known function were either increased or decreased. The products of the mRNAs that were increased in parallel with PIP39 included not only enzymes of procyclic-form metabolism, but also components of the translational and RNA control machineries. Many of the mRNAs that were decreased in cells with elevated PIP39 reflected reduced cell division. Conclusions These transcriptomes suggest new avenues for research into the regulation of trypanosome differentiation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2338-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julius Mulindwa
- Department of Biochemistry and Sports Science, College of Natural Sciences, Makerere University, P.O.Box 7062, Kampala, Uganda. .,Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120, Heidelberg, Germany.
| | - Clémentine Mercé
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120, Heidelberg, Germany.
| | - Enock Matovu
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O.Box 7062, Kampala, Uganda.
| | - John Enyaru
- Department of Biochemistry and Sports Science, College of Natural Sciences, Makerere University, P.O.Box 7062, Kampala, Uganda.
| | - Christine Clayton
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120, Heidelberg, Germany.
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Glucose-Regulated Phosphorylation of the PUF Protein Puf3 Regulates the Translational Fate of Its Bound mRNAs and Association with RNA Granules. Cell Rep 2015; 11:1638-50. [PMID: 26051939 DOI: 10.1016/j.celrep.2015.05.014] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 03/04/2015] [Accepted: 05/06/2015] [Indexed: 01/07/2023] Open
Abstract
PUF proteins are post-transcriptional regulators that bind to the 3' UTRs of mRNA transcripts. Herein, we show how a yeast PUF protein, Puf3p, responds to glucose availability to switch the fate of its bound transcripts that encode proteins required for mitochondrial biogenesis. Upon glucose depletion, Puf3p becomes heavily phosphorylated within its N-terminal region of low complexity, associates with polysomes, and promotes translation of its target mRNAs. Such nutrient-responsive phosphorylation toggles the activity of Puf3p to promote either degradation or translation of these mRNAs according to the needs of the cell. Moreover, activation of translation of pre-existing mRNAs might enable rapid adjustment to environmental changes without the need for de novo transcription. Strikingly, a Puf3p phosphomutant no longer promotes translation but becomes trapped in intracellular foci in an mRNA-dependent manner. Our findings suggest that the inability to properly resolve Puf3p-containing RNA-protein granules via a phosphorylation-based mechanism might be toxic to a cell.
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Lott K, Mukhopadhyay S, Li J, Wang J, Yao J, Sun Y, Qu J, Read LK. Arginine methylation of DRBD18 differentially impacts its opposing effects on the trypanosome transcriptome. Nucleic Acids Res 2015; 43:5501-23. [PMID: 25940618 PMCID: PMC4477658 DOI: 10.1093/nar/gkv428] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/22/2015] [Indexed: 12/30/2022] Open
Abstract
Arginine methylation is a posttranslational modification that impacts wide-ranging cellular functions, including transcription, mRNA splicing and translation. RNA binding proteins (RBPs) represent one of the largest classes of arginine methylated proteins in both mammals and the early diverging parasitic protozoan, Trypanosoma brucei. Here, we report the effects of arginine methylation on the functions of the essential and previously uncharacterized T. brucei RBP, DRBD18. RNAseq analysis shows that DRBD18 depletion causes extensive rearrangement of the T. brucei transcriptome, with increases and decreases in hundreds of mRNAs. DRBD18 contains three methylated arginines, and we used complementation of DRBD18 knockdown cells with methylmimic or hypomethylated DRBD18 to assess the functions of these methylmarks. Methylmimic and hypomethylated DRBD18 associate with different ribonucleoprotein complexes. These altered macromolecular interactions translate into differential impacts on the T. brucei transcriptome. Methylmimic DRBD18 preferentially stabilizes target RNAs, while hypomethylated DRBD18 is more efficient at destabilizing RNA. The protein arginine methyltransferase, TbPRMT1, interacts with DRBD18 and knockdown of TbPRMT1 recapitulates the effects of hypomethylated DRBD18 on mRNA levels. Together, these data support a model in which arginine methylation acts as a switch that regulates T. brucei gene expression.
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Affiliation(s)
- Kaylen Lott
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Shreya Mukhopadhyay
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jun Li
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jie Wang
- Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jin Yao
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Yijun Sun
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Laurie K Read
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
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Abstract
TbRRM1 of Trypanosoma brucei is a nucleoprotein that was previously identified in a search for splicing factors in T. brucei. We show that TbRRM1 associates with mRNAs and with the auxiliary splicing factor polypyrimidine tract-binding protein 2, but not with components of the core spliceosome. TbRRM1 also interacts with several retrotransposon hot spot (RHS) proteins and histones. RNA immunoprecipitation of a tagged form of TbRRM1 from procyclic (insect) form trypanosomes identified ca. 1,500 transcripts that were enriched and 3,000 transcripts that were underrepresented compared to cellular mRNA. Enriched transcripts encoded RNA-binding proteins, including TbRRM1 itself, several RHS transcripts, mRNAs with long coding regions, and a high proportion of stage-regulated mRNAs that are more highly expressed in bloodstream forms. Transcripts encoding ribosomal proteins, other factors involved in translation, and procyclic-specific transcripts were underrepresented. Knockdown of TbRRM1 by RNA interference caused widespread changes in mRNA abundance, but these changes did not correlate with the binding of the protein to transcripts, and most splice sites were unchanged, negating a general role for TbRRM1 in splice site selection. When changes in mRNA abundance were mapped across the genome, regions with many downregulated mRNAs were identified. Two regions were analyzed by chromatin immunoprecipitation, both of which exhibited increases in nucleosome occupancy upon TbRRM1 depletion. In addition, subjecting cells to heat shock resulted in translocation of TbRRM1 to the cytoplasm and compaction of chromatin, consistent with a second role for TbRRM1 in modulating chromatin structure. Trypanosoma brucei, the parasite that causes human sleeping sickness, is transmitted by tsetse flies. The parasite progresses through different life cycle stages in its two hosts, altering its pattern of gene expression in the process. In trypanosomes, protein-coding genes are organized as polycistronic units that are processed into monocistronic mRNAs. Since genes in the same unit can be regulated independently of each other, it is believed that gene regulation is essentially posttranscriptional. In this study, we investigated the role of a nuclear RNA-binding protein, TbRRM1, in the insect stage of the parasite. We found that TbRRM1 binds nuclear mRNAs and also affects chromatin status. Reduction of nuclear TbRRM1 by RNA interference or heat shock resulted in chromatin compaction. We propose that TbRRM1 regulates RNA polymerase II-driven gene expression both cotranscriptionally, by facilitating transcription and efficient splicing, and posttranscriptionally, via its interaction with nuclear mRNAs.
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Blackinton JG, Keene JD. Post-transcriptional RNA regulons affecting cell cycle and proliferation. Semin Cell Dev Biol 2014; 34:44-54. [PMID: 24882724 PMCID: PMC4163074 DOI: 10.1016/j.semcdb.2014.05.014] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 05/21/2014] [Indexed: 01/19/2023]
Abstract
The cellular growth cycle is initiated and maintained by punctual, yet agile, regulatory events involving modifications of cell cycle proteins as well as coordinated gene expression to support cyclic checkpoint decisions. Recent evidence indicates that post-transcriptional partitioning of messenger RNA subsets by RNA-binding proteins help physically localize, temporally coordinate, and efficiently translate cell cycle proteins. This dynamic organization of mRNAs encoding cell cycle components contributes to the overall economy of the cell cycle consistent with the post-transcriptional RNA regulon model of gene expression. This review examines several recent studies demonstrating the coordination of mRNA subsets encoding cell cycle proteins during nuclear export and subsequent coupling to protein synthesis, and discusses evidence for mRNA coordination of p53 targets and the DNA damage response pathway. We consider how these observations may connect to upstream and downstream post-transcriptional coordination and coupling of splicing, export, localization, and translation. Published examples from yeast, nematode, insect, and mammalian systems are discussed, and we consider genetic evidence supporting the conclusion that dysregulation of RNA regulons may promote pathogenic states of growth such as carcinogenesis.
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Affiliation(s)
- Jeff G Blackinton
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Box 3020, Durham, NC 27710, USA
| | - Jack D Keene
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Box 3020, Durham, NC 27710, USA.
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Erben ED, Fadda A, Lueong S, Hoheisel JD, Clayton C. A genome-wide tethering screen reveals novel potential post-transcriptional regulators in Trypanosoma brucei. PLoS Pathog 2014; 10:e1004178. [PMID: 24945722 PMCID: PMC4055773 DOI: 10.1371/journal.ppat.1004178] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 04/28/2014] [Indexed: 12/23/2022] Open
Abstract
In trypanosomatids, gene expression is regulated mainly by post-transcriptional mechanisms, which affect mRNA processing, translation and degradation. Currently, our understanding of factors that regulate either mRNA stability or translation is rather limited. We know that often, the regulators are proteins that bind to the 3′-untranslated region; they presumably interact with ribonucleases and translation factors. However, very few such proteins have been characterized in any detail. Here we describe a genome-wide screen to find proteins implicated in post-transcriptional regulation in Trypanosoma brucei. We made a library of random genomic fragments in a plasmid that was designed for expression of proteins fused to an RNA-binding domain, the lambda-N peptide. This was transfected into cells expressing mRNAs encoding a positive or negative selectable marker, and bearing the “boxB” lambda-N recognition element in the 3′-untranslated region. The screen identified about 300 proteins that could be implicated in post-transcriptional mRNA regulation. These included known regulators, degradative enzymes and translation factors, many canonical RNA-binding proteins, and proteins that act via multi-protein complexes. However there were also nearly 150 potential regulators with no previously annotated function, or functions unrelated to mRNA metabolism. Almost 50 novel regulators were shown to bind RNA using a targeted proteome array. The screen also provided fine structure mapping of the hit candidates' functional domains. Our findings not only confirm the key role that RNA-binding proteins play in the regulation of gene expression in trypanosomatids, but also suggest new roles for previously uncharacterized proteins. Survival and adaptation of trypanosomatids to new surroundings requires activation of specific gene networks. This is mainly achieved by post-transcriptional mechanisms, and proteins that bind to specific mRNAs, and influence degradation or translation, are known to be important. However, only few such proteins have been characterized to date. The trypanosome genome encodes over 150 proteins with conserved RNA-binding domains, and it is very likely that additional proteins that do not have such domains could also modulate mRNA fate. Here, we report the results of a genome-wide screen to identify mRNA-fate regulators in Trypanosoma brucei. We used a method called “tethering” to artificially attach protein fragments to an mRNA. Our findings confirmed the role of RNA-binding proteins in the regulation of mRNA fate, and also suggested such roles for many other proteins, including some metabolic enzymes. Our results should serve as a useful resource. Moreover, the tethering screen approach could readily be adapted for use in other organisms.
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Affiliation(s)
- Esteban D. Erben
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- * E-mail:
| | - Abeer Fadda
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Smiths Lueong
- Division of Functional Genome Analysis, Deutsche Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Jörg D. Hoheisel
- Division of Functional Genome Analysis, Deutsche Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Christine Clayton
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
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