1
|
Vignolini T, Couble JEC, Doré GRG, Baumgarten S. Transcript tinkering: RNA modifications in protozoan parasites. Curr Opin Microbiol 2024; 79:102477. [PMID: 38663181 DOI: 10.1016/j.mib.2024.102477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 03/19/2024] [Accepted: 04/03/2024] [Indexed: 06/11/2024]
Abstract
Apicomplexan and trypanosomatid parasites have evolved a wide range of post-transcriptional processes that allow them to replicate, differentiate, and transmit within and among multiple different tissue, host, and vector environments. In this review, we highlight the recent advances that point toward the regulatory potential of RNA modifications in mediating these processes on the coding and noncoding transcriptome throughout the life cycle of protozoan parasites. We discuss the recent technical advancements enabling the study of the 'epitranscriptome' and how parasites evolved RNA modification-mediated mechanisms adapted to their unique lifestyles.
Collapse
Affiliation(s)
- Tiziano Vignolini
- Institut Pasteur, Université Paris Cité, G5 Parasite RNA Biology, Department of Parasites and Insect Vectors, F-75015 Paris, France
| | - Justine E C Couble
- Institut Pasteur, Université Paris Cité, G5 Parasite RNA Biology, Department of Parasites and Insect Vectors, F-75015 Paris, France
| | - Grégory R G Doré
- Institut Pasteur, Université Paris Cité, G5 Parasite RNA Biology, Department of Parasites and Insect Vectors, F-75015 Paris, France
| | - Sebastian Baumgarten
- Institut Pasteur, Université Paris Cité, G5 Parasite RNA Biology, Department of Parasites and Insect Vectors, F-75015 Paris, France.
| |
Collapse
|
2
|
Guo G, Lin Y, Zhu X, Ding F, Xue X, Zhang Q. Emerging roles of the epitranscriptome in parasitic protozoan biology and pathogenesis. Trends Parasitol 2024; 40:214-229. [PMID: 38355313 DOI: 10.1016/j.pt.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 02/16/2024]
Abstract
RNA modifications (epitranscriptome) - such as N6-methyladenosine (m6A), 5-methylcytosine (m5C), and pseudouridine (Ψ) - modulate RNA processing, stability, interaction, and translation, thereby playing critical roles in the development, replication, virulence, metabolism, and life cycle adaptations of parasitic protozoa. Here, we summarize potential homologs of the major human RNA modification regulatory factors in parasites, outline current knowledge on how RNA modifications affect parasitic protozoa, highlight the regulation of RNA modifications and their crosstalk, and discuss current progress in exploring RNA modifications as potential drug targets. This review contributes to our understanding of epitranscriptomic regulation of parasitic protozoa biology and pathogenesis and provides new perspectives for the treatment of parasitic diseases.
Collapse
Affiliation(s)
- Gangqiang Guo
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yutong Lin
- First Clinical College, Wenzhou Medical University, Wenzhou, China
| | - Xinqi Zhu
- First Clinical College, Wenzhou Medical University, Wenzhou, China
| | - Feng Ding
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xiangyang Xue
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Qingfeng Zhang
- Laboratory of Molecular Parasitology, State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital; Clinical Center for Brain and Spinal Cord Research, School of Medicine, Tongji University, Shanghai 200120, China.
| |
Collapse
|
3
|
Soni A, Klebanov-Akopyan O, Erben E, Plaschkes I, Benyamini H, Mitesser V, Harel A, Yamin K, Onn I, Shlomai J. UMSBP2 is chromatin remodeler that functions in regulation of gene expression and suppression of antigenic variation in trypanosomes. Nucleic Acids Res 2023; 51:5678-5698. [PMID: 37207337 PMCID: PMC10287944 DOI: 10.1093/nar/gkad402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 05/03/2023] [Indexed: 05/21/2023] Open
Abstract
Universal Minicircle Sequence binding proteins (UMSBPs) are CCHC-type zinc-finger proteins that bind the single-stranded G-rich UMS sequence, conserved at the replication origins of minicircles in the kinetoplast DNA, the mitochondrial genome of kinetoplastids. Trypanosoma brucei UMSBP2 has been recently shown to colocalize with telomeres and to play an essential role in chromosome end protection. Here we report that TbUMSBP2 decondenses in vitro DNA molecules, which were condensed by core histones H2B, H4 or linker histone H1. DNA decondensation is mediated via protein-protein interactions between TbUMSBP2 and these histones, independently of its previously described DNA binding activity. Silencing of the TbUMSBP2 gene resulted in a significant decrease in the disassembly of nucleosomes in T. brucei chromatin, a phenotype that could be reverted, by supplementing the knockdown cells with TbUMSBP2. Transcriptome analysis revealed that silencing of TbUMSBP2 affects the expression of multiple genes in T. brucei, with a most significant effect on the upregulation of the subtelomeric variant surface glycoproteins (VSG) genes, which mediate the antigenic variation in African trypanosomes. These observations suggest that UMSBP2 is a chromatin remodeling protein that functions in the regulation of gene expression and plays a role in the control of antigenic variation in T. brucei.
Collapse
Affiliation(s)
- Awakash Soni
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel- Canada and the Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Olga Klebanov-Akopyan
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel- Canada and the Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Esteban Erben
- Heidelberg University Center for Molecular Biology at Heidelberg University, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Inbar Plaschkes
- The Info-Core Bioinformatics Unit, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Hadar Benyamini
- The Info-Core Bioinformatics Unit, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Vera Mitesser
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel- Canada and the Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Amnon Harel
- Azrieli Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold Street, Safed1311502, Israel
| | - Katereena Yamin
- Azrieli Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold Street, Safed1311502, Israel
| | - Itay Onn
- Azrieli Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold Street, Safed1311502, Israel
| | - Joseph Shlomai
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel- Canada and the Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| |
Collapse
|
4
|
Davis JA, Reyes AV, Nitika, Saha A, Wolfgeher DJ, Xu SL, Truman AW, Li B, Chakrabarti K. Proteomic analysis defines the interactome of telomerase in the protozoan parasite, Trypanosoma brucei. Front Cell Dev Biol 2023; 11:1110423. [PMID: 37009488 PMCID: PMC10061497 DOI: 10.3389/fcell.2023.1110423] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/03/2023] [Indexed: 03/17/2023] Open
Abstract
Telomerase is a ribonucleoprotein enzyme responsible for maintaining the telomeric end of the chromosome. The telomerase enzyme requires two main components to function: the telomerase reverse transcriptase (TERT) and the telomerase RNA (TR), which provides the template for telomeric DNA synthesis. TR is a long non-coding RNA, which forms the basis of a large structural scaffold upon which many accessory proteins can bind and form the complete telomerase holoenzyme. These accessory protein interactions are required for telomerase activity and regulation inside cells. The interacting partners of TERT have been well studied in yeast, human, and Tetrahymena models, but not in parasitic protozoa, including clinically relevant human parasites. Here, using the protozoan parasite, Trypanosoma brucei (T. brucei) as a model, we have identified the interactome of T. brucei TERT (TbTERT) using a mass spectrometry-based approach. We identified previously known and unknown interacting factors of TbTERT, highlighting unique features of T. brucei telomerase biology. These unique interactions with TbTERT, suggest mechanistic differences in telomere maintenance between T. brucei and other eukaryotes.
Collapse
Affiliation(s)
- Justin A. Davis
- Department of Biological Sciences, University of North Carolina, Charlotte, NC, United States
| | - Andres V. Reyes
- Department of Plant Biology and Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, CA, United States
| | - Nitika
- Department of Biological Sciences, University of North Carolina, Charlotte, NC, United States
| | - Arpita Saha
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Arts and Sciences, Cleveland State University, Cleveland, OH, United States
| | - Donald J. Wolfgeher
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, United States
| | - Shou-Ling Xu
- Department of Plant Biology and Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, CA, United States
| | - Andrew W. Truman
- Department of Biological Sciences, University of North Carolina, Charlotte, NC, United States
| | - Bibo Li
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Arts and Sciences, Cleveland State University, Cleveland, OH, United States
| | - Kausik Chakrabarti
- Department of Biological Sciences, University of North Carolina, Charlotte, NC, United States
| |
Collapse
|
5
|
Guerra-Slompo E, Cesaro G, Guimarães B, Zanchin N. Dissecting Trypanosoma brucei RRP44 function in the maturation of segmented ribosomal RNA using a regulated genetic complementation system. Nucleic Acids Res 2023; 51:396-419. [PMID: 36610751 PMCID: PMC9841430 DOI: 10.1093/nar/gkac1217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 11/29/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
Trypanosoma brucei belongs to a group of protozoans presenting fragmented large subunit rRNA. Its LSU rRNA equivalent to the 25S/28S rRNA of other eukaryotes is split into six fragments, requiring additional processing for removal of the extra spacer sequences. We have used a genetic complementation strategy to further investigate the T. brucei RRP44 nuclease in pre-rRNA maturation. TbRRP44 contains both a PIN and a RNB domain whose homologues are found in association with the exosome complex. We found that the exonucleolytic activity of the RNB domain as well as the physical presence of the PIN domain are essential for TbRRP44 function, while a catalytic site mutation in the PIN domain has no detectable effect on cell growth. A new endonucleolytic cleavage site in ITS1 was identified. In addition to the 5.8S rRNA 3'-end maturation, TbRRP44 is required for degradation of the excised 5'-ETS and for removal of part of ITS1 during maturation of the 18S rRNA 3'-end. TbRRP44 deficiency leads to accumulation of many LSU intermediate precursors, most of them not detected in control cells. TbRRP44 is also required for U3 snoRNA and spliced leader processing, indicating that TbRRP44 may have a wide role in RNA processing in T. brucei.
Collapse
Affiliation(s)
- Eloise Pavão Guerra-Slompo
- Carlos Chagas Institute, Oswaldo Cruz Foundation, FIOCRUZ, R. Prof. Algacyr Munhoz Mader 3775, 81350-010, Curitiba-PR, Brazil
| | - Giovanna Cesaro
- Carlos Chagas Institute, Oswaldo Cruz Foundation, FIOCRUZ, R. Prof. Algacyr Munhoz Mader 3775, 81350-010, Curitiba-PR, Brazil,Biochemistry Postgraduate Program, Federal University of Paraná, Curitiba-PR, Brazil
| | - Beatriz Gomes Guimarães
- Carlos Chagas Institute, Oswaldo Cruz Foundation, FIOCRUZ, R. Prof. Algacyr Munhoz Mader 3775, 81350-010, Curitiba-PR, Brazil,Biochemistry Postgraduate Program, Federal University of Paraná, Curitiba-PR, Brazil
| | | |
Collapse
|
6
|
Current Status of Regulatory Non-Coding RNAs Research in the Tritryp. Noncoding RNA 2022; 8:ncrna8040054. [PMID: 35893237 PMCID: PMC9326685 DOI: 10.3390/ncrna8040054] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 11/23/2022] Open
Abstract
Trypanosomatids are protozoan parasites that cause devastating vector-borne human diseases. Gene expression regulation of these organisms depends on post-transcriptional control in responding to diverse environments while going through multiple developmental stages of their complex life cycles. In this scenario, non-coding RNAs (ncRNAs) are excellent candidates for a very efficient, quick, and economic strategy to regulate gene expression. The advent of high throughput RNA sequencing technologies show the presence and deregulation of small RNA fragments derived from canonical ncRNAs. This review seeks to depict the ncRNA landscape in trypanosomatids, focusing on the small RNA fragments derived from functional RNA molecules observed in RNA sequencing studies. Small RNA fragments derived from canonical ncRNAs (tsRNAs, snsRNAs, sdRNAs, and sdrRNAs) were identified in trypanosomatids. Some of these RNAs display changes in their levels associated with different environments and developmental stages, demanding further studies to determine their functional characterization and potential roles. Nevertheless, a comprehensive and detailed ncRNA annotation for most trypanosomatid genomes is still needed, allowing better and more extensive comparative and functional studies.
Collapse
|
7
|
Fibrillarin RNA methylase is an interacting protein of Cryptosporidium parvum calmodulin-like protein (CpCML). Microb Pathog 2022; 170:105679. [PMID: 35843442 DOI: 10.1016/j.micpath.2022.105679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 11/23/2022]
Abstract
Cryptosporidium parvum is an obligate protozoan parasite invading epithelial cells of small intestine of human and animals, and causing diarrheal disease. In apicomplexan parasites, calcium signaling can regulate many essential biological processes such as invasion and migration. As the main intracellular receptor for calcium ions, calmodulins control the activities of hundreds of enzymes and proteins. Calmodulin-like protein (CML) is an important member of the calmodulin family and may play a key role in C. parvum, however, the actual situation is still not clear. The present study aimed to identify the parasite interaction partner proteins of C. parvum calmodulin-like protein (CpCML). By constructing the cpcml bait plasmid, 5 potential CpCML - interacting proteins in C. parvum oocyst were screened by yeast-two-hybrid system (Y2H). Bimolecular fluorescence complementation (BiFC) and Co-immunoprecipitation (Co-IP) were performed as subsequent validations. Fibrillarin RNA methylase (FBL) was identified via this screening method as CpCML interacting protein in C. parvum. The identification of this interaction made it possible to get a further understanding of the function of CpCML and its contribution to the pathogenicity of C. parvum.
Collapse
|
8
|
Budzak J, Rudenko G. Pedal to the Metal: Nuclear Splicing Bodies Turbo-Charge VSG mRNA Production in African Trypanosomes. Front Cell Dev Biol 2022; 10:876701. [PMID: 35517511 PMCID: PMC9065277 DOI: 10.3389/fcell.2022.876701] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/18/2022] [Indexed: 11/18/2022] Open
Abstract
The African trypanosome Trypanosoma brucei is a parasite of the mammalian bloodstream and tissues, where an antigenically variable Variant Surface Glycoprotein (VSG) coat protects it from immune attack. This dense layer comprised of ∼107 VSG proteins, makes VSG by far the most abundant mRNA (7-10% total) and protein (∼10% total) in the bloodstream form trypanosome. How can such prodigious amounts of VSG be produced from a single VSG gene? Extremely high levels of RNA polymerase I (Pol I) transcription of the active VSG provide part of the explanation. However, recent discoveries highlight the role of pre-mRNA processing, both in maintaining high levels of VSG transcription, as well as its monoallelic expression. Trypanosome mRNAs are matured through trans-splicing a spliced leader (SL) RNA to the 5' end of precursor transcripts, meaning abundant SL RNA is required throughout the nucleus. However, requirement for SL RNA in the vicinity of the active VSG gene is so intense, that the cell reconfigures its chromatin architecture to facilitate interaction between the SL RNA genes and the active VSG. This presumably ensures that sufficient localised SL RNA is available, and not limiting for VSG mRNA expression. Recently, novel nuclear splicing bodies which appear to provide essential trans-splicing components, have been identified associating with the active VSG. These observations highlight the underappreciated role of pre-mRNA processing in modulating gene expression in trypanosomes. Dissecting the function of these nuclear RNA processing bodies should help us elucidate the mechanisms of both VSG expression and monoallelic exclusion in T. brucei.
Collapse
Affiliation(s)
| | - Gloria Rudenko
- Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, London, United Kingdom
| |
Collapse
|
9
|
Alm Rosenblad M, López MD, Samuelsson T. The enigmatic RNase MRP of kinetoplastids. RNA Biol 2021; 18:139-147. [PMID: 34308760 DOI: 10.1080/15476286.2021.1952758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
The ribonucleoprotein RNase MRP is responsible for the processing of ribosomal RNA precursors. It is found in virtually all eukaryotes that have been examined. In the Euglenozoa, including the genera Euglena, Diplonema and kinetoplastids, MRP RNA and protein subunits have so far escaped detection using bioinformatic methods. However, we now demonstrate that the RNA component is widespread among the Euglenozoa and that these RNAs have secondary structures that conform to the structure of all other phylogenetic groups. In Euglena, we identified the same set of P/MRP protein subunits as in many other protists. However, we failed to identify any of these proteins in the kinetoplastids. This finding poses interesting questions regarding the structure and function of RNase MRP in these species.
Collapse
Affiliation(s)
- Magnus Alm Rosenblad
- Department of Chemistry and Molecular Biology, National Infrastructure of Bioinformatics (NBIS), Lundberg Laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Marcela Dávila López
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Tore Samuelsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| |
Collapse
|
10
|
Matzov D, Taoka M, Nobe Y, Yamauchi Y, Halfon Y, Asis N, Zimermann E, Rozenberg H, Bashan A, Bhushan S, Isobe T, Gray MW, Yonath A, Shalev-Benami M. Cryo-EM structure of the highly atypical cytoplasmic ribosome of Euglena gracilis. Nucleic Acids Res 2020; 48:11750-11761. [PMID: 33091122 PMCID: PMC7672448 DOI: 10.1093/nar/gkaa893] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/21/2020] [Accepted: 10/21/2020] [Indexed: 12/11/2022] Open
Abstract
Ribosomal RNA is the central component of the ribosome, mediating its functional and architectural properties. Here, we report the cryo-EM structure of a highly divergent cytoplasmic ribosome from the single-celled eukaryotic alga Euglena gracilis. The Euglena large ribosomal subunit is distinct in that it contains 14 discrete rRNA fragments that are assembled non-covalently into the canonical ribosome structure. The rRNA is substantially enriched in post-transcriptional modifications that are spread far beyond the catalytic RNA core, contributing to the stabilization of this highly fragmented ribosome species. A unique cluster of five adenosine base methylations is found in an expansion segment adjacent to the protein exit tunnel, such that it is positioned for interaction with the nascent peptide. As well as featuring distinctive rRNA expansion segments, the Euglena ribosome contains four novel ribosomal proteins, localized to the ribosome surface, three of which do not have orthologs in other eukaryotes.
Collapse
Affiliation(s)
- Donna Matzov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Yuko Nobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Yoshio Yamauchi
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Yehuda Halfon
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nofar Asis
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ella Zimermann
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Haim Rozenberg
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anat Bashan
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shashi Bhushan
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Michael W Gray
- Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1X5
| | - Ada Yonath
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Moran Shalev-Benami
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| |
Collapse
|
11
|
Differentially Expressed Homologous Genes Reveal Interspecies Differences of Paragonimus Proliferus based on Transcriptome Analysis. Helminthologia 2020; 57:196-210. [PMID: 32855607 PMCID: PMC7425231 DOI: 10.2478/helm-2020-0029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 04/01/2020] [Indexed: 01/23/2023] Open
Abstract
Paragonimus proliferus (P. proliferus), one of 46 Paragonimus species registered in the National Center for Biotechnology Information database, may be much more widely distributed in Southeast Asia than previously thought, as its reported natural foci have increased in the past decades. However, very little is known about its molecular biology, especially at the transcriptome level. For the first time, the transcriptome of this species was sequenced and compared with four other common Paragonimus species, namely Paragonimus skrjabini, Paragonimus kellicotti, Paragonimus miyazakii, and Paragonimus westermani, to predict homologous genes and differentially expressed homologous genes to explore interspecies differences of Paragonimus proliferus. A total of 7393 genes were found to be significantly differentially expressed. Of these, 49 were considered to be core genes because they were differentially expressed in all four comparison groups. Annotations revealed that these genes were related mainly to "duplication, transcription, or translation", energy or nutrient metabolism, and parasitic growth, proliferation, motility, invasion, adaptation to the host, or virulence. Interestingly, a majority (5601/7393) of the identified genes, and in particular the core genes (48/49), were expressed at lower levels in P. proliferus. The identified genes may play essential roles in the biological differences between Paragonimus species. This work provides fundamental background information for further research into the molecular biology of P. proliferus.
Collapse
|
12
|
Rajan KS, Zhu Y, Adler K, Doniger T, Cohen-Chalamish S, Srivastava A, Shalev-Benami M, Matzov D, Unger R, Tschudi C, Günzl A, Carmichael GG, Michaeli S. The large repertoire of 2'-O-methylation guided by C/D snoRNAs on Trypanosoma brucei rRNA. RNA Biol 2020; 17:1018-1039. [PMID: 32250712 DOI: 10.1080/15476286.2020.1750842] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The parasite Trypanosoma brucei cycles between insect and mammalian hosts, and is the causative agent of sleeping sickness. Here, we performed genome-wide mapping of 2'-O-methylations (Nms) on trypanosome rRNA using three high-throughput sequencing methods; RibOxi-seq, RiboMeth-seq and 2'-OMe-seq. This is the first study using three genome-wide mapping approaches on rRNA from the same species showing the discrepancy among the methods. RibOxi-seq detects all the sites, but RiboMeth-seq is the only method to evaluate the level of a single Nm site. The sequencing revealed at least ninety-nine Nms guided by eighty-five snoRNAs among these thirty-eight Nms are trypanosome specific sites. We present the sequence and target of the C/D snoRNAs guiding on rRNA. This is the highest number of Nms detected to date on rRNA of a single cell parasite. Based on RiboMeth-seq, several Nm sites were found to be differentially regulated at the two stages of the parasite life cycle, the insect procyclic form (PCF) versus the bloodstream form (BSF) in the mammalian host.
Collapse
Affiliation(s)
- K Shanmugha Rajan
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University , Ramat-Gan, Israel
| | - Yinzhou Zhu
- Department of Genetics and Genome Sciences, UConn Health , Farmington, CT, USA
| | - Katerina Adler
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University , Ramat-Gan, Israel
| | - Tirza Doniger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University , Ramat-Gan, Israel
| | - Smadar Cohen-Chalamish
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University , Ramat-Gan, Israel
| | - Ankita Srivastava
- Department of Genetics and Genome Sciences, UConn Health , Farmington, CT, USA
| | - Moran Shalev-Benami
- Department of Structural Biology, Weizmann Institute of Science , Rehovot, Israel
| | - Donna Matzov
- Department of Structural Biology, Weizmann Institute of Science , Rehovot, Israel
| | - Ron Unger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University , Ramat-Gan, Israel
| | - Christian Tschudi
- Departmentof Epidemiology and Microbial Diseases, Yale School of Public Health , New Haven, CT, USA
| | - Arthur Günzl
- Department of Genetics and Genome Sciences, UConn Health , Farmington, CT, USA
| | - Gordon G Carmichael
- Department of Genetics and Genome Sciences, UConn Health , Farmington, CT, USA
| | - Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University , Ramat-Gan, Israel
| |
Collapse
|
13
|
Unique Aspects of rRNA Biogenesis in Trypanosomatids. Trends Parasitol 2019; 35:778-794. [DOI: 10.1016/j.pt.2019.07.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 07/20/2019] [Accepted: 07/26/2019] [Indexed: 12/15/2022]
|
14
|
Martínez-Calvillo S, Florencio-Martínez LE, Nepomuceno-Mejía T. Nucleolar Structure and Function in Trypanosomatid Protozoa. Cells 2019; 8:cells8050421. [PMID: 31071985 PMCID: PMC6562600 DOI: 10.3390/cells8050421] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/26/2019] [Accepted: 04/28/2019] [Indexed: 12/12/2022] Open
Abstract
The nucleolus is the conspicuous nuclear body where ribosomal RNA genes are transcribed by RNA polymerase I, pre-ribosomal RNA is processed, and ribosomal subunits are assembled. Other important functions have been attributed to the nucleolus over the years. Here we review the current knowledge about the structure and function of the nucleolus in the trypanosomatid parasites Trypanosoma brucei, Trypanosoma cruzi and Leishmania ssp., which represent one of the earliest branching lineages among the eukaryotes. These protozoan parasites present a single nucleolus that is preserved throughout the closed nuclear division, and that seems to lack fibrillar centers. Trypanosomatids possess a relatively low number of rRNA genes, which encode rRNA molecules that contain large expansion segments, including several that are trypanosomatid-specific. Notably, the large subunit rRNA (28S-type) is fragmented into two large and four small rRNA species. Hence, compared to other organisms, the rRNA primary transcript requires additional processing steps in trypanosomatids. Accordingly, this group of parasites contains the highest number ever reported of snoRNAs that participate in rRNA processing. The number of modified rRNA nucleotides in trypanosomatids is also higher than in other organisms. Regarding the structure and biogenesis of the ribosomes, recent cryo-electron microscopy analyses have revealed several trypanosomatid-specific features that are discussed here. Additional functions of the nucleolus in trypanosomatids are also reviewed.
Collapse
Affiliation(s)
- Santiago Martínez-Calvillo
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla CP 54090, Estado de México, Mexico.
| | - Luis E Florencio-Martínez
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla CP 54090, Estado de México, Mexico.
| | - Tomás Nepomuceno-Mejía
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla CP 54090, Estado de México, Mexico.
| |
Collapse
|
15
|
Holden JM, Koreny L, Obado S, Ratushny AV, Chen WM, Bart JM, Navarro M, Chait BT, Aitchison JD, Rout MP, Field MC. Involvement in surface antigen expression by a moonlighting FG-repeat nucleoporin in trypanosomes. Mol Biol Cell 2019; 29:1100-1110. [PMID: 29496964 PMCID: PMC5921576 DOI: 10.1091/mbc.e17-06-0430] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The nuclear pore complex is an ancient component of the eukaryotic cell. We show here that an FG nucleoporin, TbNup53b, in trypanosomes has an association with the splicing machinery and roles in gene expression, indicating that moonlighting roles for nucleoporins are highly ancient and present in the earliest eukaryotes. Components of the nuclear periphery coordinate a multitude of activities, including macromolecular transport, cell-cycle progression, and chromatin organization. Nuclear pore complexes (NPCs) mediate nucleocytoplasmic transport, mRNA processing, and transcriptional regulation, and NPC components can define regions of high transcriptional activity in some organisms at the nuclear periphery and nucleoplasm. Lineage-specific features underpin several core nuclear functions and in trypanosomatids, which branched very early from other eukaryotes, unique protein components constitute the lamina, kinetochores, and parts of the NPCs. Here we describe a phenylalanine-glycine (FG)-repeat nucleoporin, TbNup53b, that has dual localizations within the nucleoplasm and NPC. In addition to association with nucleoporins, TbNup53b interacts with a known trans-splicing component, TSR1, and has a role in controlling expression of surface proteins including the nucleolar periphery-located, procyclin genes. Significantly, while several nucleoporins are implicated in intranuclear transcriptional regulation in metazoa, TbNup53b appears orthologous to components of the yeast/human Nup49/Nup58 complex, for which no transcriptional functions are known. These data suggest that FG-Nups are frequently co-opted to transcriptional functions during evolution and extend the presence of FG-repeat nucleoporin control of gene expression to trypanosomes, suggesting that this is a widespread and ancient eukaryotic feature, as well as underscoring once more flexibility within nucleoporin function.
Collapse
Affiliation(s)
| | - Ludek Koreny
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | | | - Alexander V Ratushny
- Center for Infectious Disease Research (formerly Seattle Biomed) and Institute for Systems Biology, Seattle, WA 98109-5234
| | - Wei-Ming Chen
- Center for Infectious Disease Research (formerly Seattle Biomed) and Institute for Systems Biology, Seattle, WA 98109-5234
| | - Jean-Mathieu Bart
- Instituto de Parasitología y Biomedicina "López-Neyra," Consejo Superior de Investigaciones Científicas, 18016 Armilla (Granada), Spain
| | - Miguel Navarro
- Instituto de Parasitología y Biomedicina "López-Neyra," Consejo Superior de Investigaciones Científicas, 18016 Armilla (Granada), Spain
| | | | - John D Aitchison
- Center for Infectious Disease Research (formerly Seattle Biomed) and Institute for Systems Biology, Seattle, WA 98109-5234
| | | | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| |
Collapse
|
16
|
Chikne V, Shanmugha Rajan K, Shalev-Benami M, Decker K, Cohen-Chalamish S, Madmoni H, Biswas VK, Kumar Gupta S, Doniger T, Unger R, Tschudi C, Ullu E, Michaeli S. Small nucleolar RNAs controlling rRNA processing in Trypanosoma brucei. Nucleic Acids Res 2019; 47:2609-2629. [PMID: 30605535 PMCID: PMC6411936 DOI: 10.1093/nar/gky1287] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 12/04/2018] [Accepted: 12/20/2018] [Indexed: 12/19/2022] Open
Abstract
In trypanosomes, in contrast to most eukaryotes, the large subunit (LSU) ribosomal RNA is fragmented into two large and four small ribosomal RNAs (srRNAs) pieces, and this additional processing likely requires trypanosome-specific factors. Here, we examined the role of 10 abundant small nucleolar RNAs (snoRNAs) involved in rRNA processing. We show that each snoRNA involved in LSU processing associates with factors engaged in either early or late biogenesis steps. Five of these snoRNAs interact with the intervening sequences of rRNA precursor, whereas the others only guide rRNA modifications. The function of the snoRNAs was explored by silencing snoRNAs. The data suggest that the LSU rRNA processing events do not correspond to the order of rRNA transcription, and that srRNAs 2, 4 and 6 which are part of LSU are processed before srRNA1. Interestingly, the 6 snoRNAs that affect srRNA1 processing guide modifications on rRNA positions that span locations from the protein exit tunnel to the srRNA1, suggesting that these modifications may serve as check-points preceding the liberation of srRNA1. This study identifies the highest number of snoRNAs so far described that are involved in rRNA processing and/or rRNA folding and highlights their function in the unique trypanosome rRNA maturation events.
Collapse
Affiliation(s)
- Vaibhav Chikne
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - K Shanmugha Rajan
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Moran Shalev-Benami
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Kathryn Decker
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Smadar Cohen-Chalamish
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Hava Madmoni
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Viplov K Biswas
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Sachin Kumar Gupta
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Tirza Doniger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Ron Unger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Christian Tschudi
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06536, USA
| | - Elisabetta Ullu
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06536, USA
| | - Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900 Israel
| |
Collapse
|
17
|
Andersen KL, Nielsen H. Knock-Down of a Novel snoRNA in Tetrahymena Reveals a Dual Role in 5.8S rRNA Processing and Generation of a 26S rRNA Fragment. Biomolecules 2018; 8:E128. [PMID: 30380771 PMCID: PMC6315972 DOI: 10.3390/biom8040128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/24/2018] [Accepted: 10/25/2018] [Indexed: 11/30/2022] Open
Abstract
In eukaryotes, 18S, 5.8S, and 28S rRNAs are transcribed as precursor molecules that undergo extensive modification and nucleolytic processing to form the mature rRNA species. Central in the process are the small nucleolar RNAs (snoRNAs). The majority of snoRNAs guide site specific chemical modifications but a few are involved in defining pre-rRNA cleavages. Here, we describe an unusual snoRNA (TtnuCD32) belonging to the box C/D subgroup from the ciliate Tetrahymena thermophila. We show that TtnuCD32 is unlikely to function as a modification guide snoRNA and that it is critical for cell viability. Cell lines with genetic knock-down of TtnuCD32 were impaired in growth and displayed two novel and apparently unrelated phenotypes. The most prominent phenotype is the accumulation of processing intermediates of 5.8S rRNA. The second phenotype is the decrease in abundance of a ~100 nt 26S rRNA fragment of unknown function. Sequence analysis demonstrated that TtnuCD32 share features with the essential snoRNA U14 but an alternative candidate (TtnuCD25) was more closely related to other U14 sequences. This, together with the fact that the observed rRNA processing phenotypes were not similar to what has been observed in U14 depleted cells, suggests that TtnuCD32 is a U14 homolog that has gained novel functions.
Collapse
MESH Headings
- Base Sequence
- Cell Survival
- Conserved Sequence
- Gene Expression Regulation
- Gene Knockdown Techniques
- Genome
- Methylation
- Nucleic Acid Conformation
- Protozoan Proteins/chemistry
- Protozoan Proteins/metabolism
- RNA Processing, Post-Transcriptional/genetics
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 5.8S/chemistry
- RNA, Ribosomal, 5.8S/genetics
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- Tetrahymena/genetics
- RNA, Guide, CRISPR-Cas Systems
Collapse
Affiliation(s)
- Kasper L Andersen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200N Copenhagen, Denmark.
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Blegdamsvej 5b, DK-2200N Copenhagen, Denmark.
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Blegdamsvej 5b, DK-2200N Copenhagen, Denmark.
| |
Collapse
|
18
|
TbUTP10, a protein involved in early stages of pre-18S rRNA processing in Trypanosoma brucei. Mol Biochem Parasitol 2018; 225:84-93. [PMID: 30248370 DOI: 10.1016/j.molbiopara.2018.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 08/28/2018] [Accepted: 09/15/2018] [Indexed: 12/19/2022]
Abstract
Ribosome biosynthesis, best studied in opisthokonts, is a highly complex process involving numerous protein and RNA factors. Yet, very little is known about the early stages of pre-18S rRNA processing even in these model organisms, let alone the conservation of this mechanism in other eukaryotes. Here we extend our knowledge of this process by identifying and characterizing the essential protein TbUTP10, a homolog of yeast U3 small nucleolar RNA-associated protein 10 - UTP10 (HEATR1 in human), in the excavate parasitic protist Trypanosoma brucei. We show that TbUTP10 localizes to the nucleolus and that its ablation by RNAi knock-down in two different T. brucei life cycle stages results in similar phenotypes: a disruption of pre-18S rRNA processing, exemplified by the accumulation of rRNA precursors, a reduction of mature 18S rRNA, and also a decrease in the level of U3 snoRNA. Moreover, polysome profiles of the RNAi-induced knock-down cells show a complete disappearance of the 40S ribosomal subunit, and a prominent accumulation of the 60S large ribosomal subunit, reflecting impaired ribosome assembly. Thus, TbUTP10 is an important protein in the processing of 18S rRNA.
Collapse
|
19
|
Yadav S, Shekhawat M, Jahagirdar D, Kumar Sharma N. Natural and artificial small RNAs: a promising avenue of nucleic acid therapeutics for cancer. Cancer Biol Med 2017; 14:242-253. [PMID: 28884041 PMCID: PMC5570601 DOI: 10.20892/j.issn.2095-3941.2017.0038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/22/2017] [Indexed: 01/02/2023] Open
Abstract
Since the failure of traditional therapy, gene therapy using functional DNA sequence and small RNA/DNA molecules (oligonucleotide) has become a promising avenue for cancer treatment. The discovery of RNA molecules has impelled researchers to investigate small regulatory RNA from various natural and artificial sources and determine a cogent target for controlling tumor progression. Small regulatory RNAs are used for therapeutic silencing of oncogenes and aberrant DNA repair response genes. Despite their advantages, therapies based on small RNAs exhibit limitations in terms of stability of therapeutic drugs, precision-based delivery in tissues, precision-based intercellular and intracellular targeting, and tumor heterogeneity-based responses. In this study, we summarize the potential and drawbacks of small RNAs in nucleic acid therapeutics for cancer.
Collapse
Affiliation(s)
- Sunny Yadav
- Cancer and Translational Research Lab, Dr. D.Y Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune 411033, Maharashtra, India
| | - Mamta Shekhawat
- Cancer and Translational Research Lab, Dr. D.Y Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune 411033, Maharashtra, India
| | - Devashree Jahagirdar
- Cancer and Translational Research Lab, Dr. D.Y Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune 411033, Maharashtra, India
| | - Nilesh Kumar Sharma
- Cancer and Translational Research Lab, Dr. D.Y Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune 411033, Maharashtra, India
| |
Collapse
|
20
|
A pseudouridylation switch in rRNA is implicated in ribosome function during the life cycle of Trypanosoma brucei. Sci Rep 2016; 6:25296. [PMID: 27142987 PMCID: PMC4855143 DOI: 10.1038/srep25296] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/14/2016] [Indexed: 12/27/2022] Open
Abstract
The protozoan parasite Trypanosoma brucei, which causes devastating diseases in humans and animals in sub-Saharan Africa, undergoes a complex life cycle between the mammalian host and the blood-feeding tsetse fly vector. However, little is known about how the parasite performs most molecular functions in such different environments. Here, we provide evidence for the intriguing possibility that pseudouridylation of rRNA plays an important role in the capacity of the parasite to transit between the insect midgut and the mammalian bloodstream. Briefly, we mapped pseudouridines (Ψ) on rRNA by Ψ-seq in procyclic form (PCF) and bloodstream form (BSF) trypanosomes. We detected 68 Ψs on rRNA, which are guided by H/ACA small nucleolar RNAs (snoRNA). The small RNome of both life cycle stages was determined by HiSeq and 83 H/ACAs were identified. We observed an elevation of 21 Ψs modifications in BSF as a result of increased levels of the guiding snoRNAs. Overexpression of snoRNAs guiding modification on H69 provided a slight growth advantage to PCF parasites at 30 °C. Interestingly, these modifications are predicted to significantly alter the secondary structure of the large subunit (LSU) rRNA suggesting that hypermodified positions may contribute to the adaption of ribosome function during cycling between the two hosts.
Collapse
|
21
|
A tRNA methyltransferase paralog is important for ribosome stability and cell division in Trypanosoma brucei. Sci Rep 2016; 6:21438. [PMID: 26888608 PMCID: PMC4757839 DOI: 10.1038/srep21438] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/18/2016] [Indexed: 02/06/2023] Open
Abstract
Most eukaryotic ribosomes contain 26/28S, 5S, and 5.8S large subunit ribosomal RNAs (LSU rRNAs) in addition to the 18S rRNA of the small subunit (SSU rRNA). However, in kinetoplastids, a group of organisms that include medically important members of the genus Trypanosoma and Leishmania, the 26/28S large subunit ribosomal RNA is uniquely composed of 6 rRNA fragments. In addition, recent studies have shown the presence of expansion segments in the large ribosomal subunit (60S) of Trypanosoma brucei. Given these differences in structure, processing and assembly, T. brucei ribosomes may require biogenesis factors not found in other organisms. Here, we show that one of two putative 3-methylcytidine methyltransferases, TbMTase37 (a homolog of human methyltransferase-like 6, METTL6), is important for ribosome stability in T. brucei. TbMTase37 localizes to the nucleolus and depletion of the protein results in accumulation of ribosomal particles lacking srRNA 4 and reduced levels of polysome associated ribosomes. We also find that TbMTase37 plays a role in cytokinesis, as loss of the protein leads to multi-flagellated and multi-nucleated cells.
Collapse
|
22
|
Eliaz D, Doniger T, Tkacz ID, Biswas VK, Gupta SK, Kolev NG, Unger R, Ullu E, Tschudi C, Michaeli S. Genome-wide analysis of small nucleolar RNAs of Leishmania major reveals a rich repertoire of RNAs involved in modification and processing of rRNA. RNA Biol 2015; 12:1222-55. [PMID: 25970223 DOI: 10.1080/15476286.2015.1038019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Trypanosomatids are protozoan parasites and the causative agent of infamous infectious diseases. These organisms regulate their gene expression mainly at the post-transcriptional level and possess characteristic RNA processing mechanisms. In this study, we analyzed the complete repertoire of Leishmania major small nucleolar (snoRNA) RNAs by performing RNA-seq analysis on RNAs that were affinity-purified using the C/D snoRNA core protein, SNU13, and the H/ACA core protein, NHP2. This study revealed a large collection of C/D and H/ACA snoRNAs, organized in gene clusters generally containing both snoRNA types. Abundant snoRNAs were identified and predicted to guide trypanosome-specific rRNA cleavages. The repertoire of snoRNAs was compared to that of the closely related Trypanosoma brucei, and 80% of both C/D and H/ACA molecules were found to have functional homologues. The comparative analyses elucidated how snoRNAs evolved to generate molecules with analogous functions in both species. Interestingly, H/ACA RNAs have great flexibility in their ability to guide modifications, and several of the RNA species can guide more than one modification, compensating for the presence of single hairpin H/ACA snoRNA in these organisms. Placing the predicted modifications on the rRNA secondary structure revealed hypermodification regions mostly in domains which are modified in other eukaryotes, in addition to trypanosome-specific modifications.
Collapse
Affiliation(s)
- Dror Eliaz
- a The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute ; Bar-Ilan University ; Ramat-Gan , Israel
| | - Tirza Doniger
- a The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute ; Bar-Ilan University ; Ramat-Gan , Israel
| | - Itai Dov Tkacz
- a The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute ; Bar-Ilan University ; Ramat-Gan , Israel
| | - Viplov Kumar Biswas
- a The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute ; Bar-Ilan University ; Ramat-Gan , Israel
| | - Sachin Kumar Gupta
- a The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute ; Bar-Ilan University ; Ramat-Gan , Israel
| | - Nikolay G Kolev
- b Department of Epidemiology of Microbial Diseases ; Yale University School of Public Health ; New Haven , CT USA
| | - Ron Unger
- a The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute ; Bar-Ilan University ; Ramat-Gan , Israel
| | - Elisabetta Ullu
- c Department of Internal Medicine and Cell Biology ; Yale University Medical School ; New Haven , CT USA.,d Cell Biology ; Yale University Medical School ; New Haven , CT USA
| | - Christian Tschudi
- b Department of Epidemiology of Microbial Diseases ; Yale University School of Public Health ; New Haven , CT USA
| | - Shulamit Michaeli
- a The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute ; Bar-Ilan University ; Ramat-Gan , Israel
| |
Collapse
|
23
|
Michaeli S. Non-coding RNA and the complex regulation of the trypanosome life cycle. Curr Opin Microbiol 2014; 20:146-52. [DOI: 10.1016/j.mib.2014.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Revised: 06/12/2014] [Accepted: 06/13/2014] [Indexed: 11/26/2022]
|
24
|
Gupta SK, Chikne V, Eliaz D, Tkacz ID, Naboishchikov I, Carmi S, Waldman Ben-Asher H, Michaeli S. Two splicing factors carrying serine-arginine motifs, TSR1 and TSR1IP, regulate splicing, mRNA stability, and rRNA processing in Trypanosoma brucei. RNA Biol 2014; 11:715-31. [PMID: 24922194 DOI: 10.4161/rna.29143] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In trypanosomes, mRNAs are processed by trans-splicing; in this process, a common exon, the spliced leader, is added to all mRNAs from a small RNA donor, the spliced leader RNA (SL RNA). However, little is known regarding how this process is regulated. In this study we investigated the function of two serine-arginine-rich proteins, TSR1 and TSR1IP, implicated in trans-splicing in Trypanosoma brucei. Depletion of these factors by RNAi suggested their role in both cis- and trans-splicing. Microarray was used to examine the transcriptome of the silenced cells. The level of hundreds of mRNAs was changed, suggesting that these proteins have a role in regulating only a subset of T. brucei mRNAs. Mass-spectrometry analyses of complexes associated with these proteins suggest that these factors function in mRNA stability, translation, and rRNA processing. We further demonstrate changes in the stability of mRNA as a result of depletion of the two TSR proteins. In addition, rRNA defects were observed under the depletion of U2AF35, TSR1, and TSR1IP, but not SF1, suggesting involvement of SR proteins in rRNA processing.
Collapse
Affiliation(s)
- Sachin Kumar Gupta
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, Israel
| | - Vaibhav Chikne
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, Israel
| | - Dror Eliaz
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, Israel
| | - Itai Dov Tkacz
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, Israel
| | - Ilana Naboishchikov
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, Israel
| | - Shai Carmi
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, Israel
| | - Hiba Waldman Ben-Asher
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, Israel
| | - Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, Israel
| |
Collapse
|
25
|
Abstract
snoRNAs (small nucleolar RNAs) constitute one of the largest and best-studied classes of non-coding RNAs that confer enzymatic specificity. With associated proteins, these snoRNAs form ribonucleoprotein complexes that can direct 2'-O-methylation or pseudouridylation of target non-coding RNAs. Aided by computational methods and high-throughput sequencing, new studies have expanded the diversity of known snoRNA functions. Complexes incorporating snoRNAs have dynamic specificity, and include diverse roles in RNA silencing, telomerase maintenance and regulation of alternative splicing. Evidence that dysregulation of snoRNAs can cause human disease, including cancer, indicates that the full scope of snoRNA roles remains an unfinished story. The diversity in structure, genomic origin and function between snoRNAs found in different complexes and among different phyla illustrates the surprising plasticity of snoRNAs in evolution. The ability of snoRNAs to direct highly specific interactions with other RNAs is a consistent thread in their newly discovered functions. Because they are ubiquitous throughout Eukarya and Archaea, it is likely they were a feature of the last common ancestor of these two domains, placing their origin over two billion years ago. In the present chapter, we focus on recent advances in our understanding of these ancient, but functionally dynamic RNA-processing machines.
Collapse
|
26
|
Gupta SK, Kolet L, Doniger T, Biswas VK, Unger R, Tzfati Y, Michaeli S. The Trypanosoma brucei
telomerase RNA (TER) homologue binds core proteins of the C/D snoRNA family. FEBS Lett 2013; 587:1399-404. [DOI: 10.1016/j.febslet.2013.03.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Revised: 03/06/2013] [Accepted: 03/07/2013] [Indexed: 12/16/2022]
|
27
|
Gupta SK, Carmi S, Waldman Ben-Asher H, Tkacz ID, Naboishchikov I, Michaeli S. Basal splicing factors regulate the stability of mature mRNAs in trypanosomes. J Biol Chem 2013; 288:4991-5006. [PMID: 23283975 DOI: 10.1074/jbc.m112.416578] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Gene expression in trypanosomes is mainly regulated post-transcriptionally. Genes are transcribed as polycistronic mRNAs that are dissected by the concerted action of trans-splicing and polyadenylation. In trans-splicing, a common exon, the spliced leader, is added to all mRNAs from a small RNA. In this study, we examined by microarray analysis the transcriptome following RNAi silencing of the basal splicing factors U2AF65, SF1, and U2AF35. The transcriptome data revealed correlations between the affected genes and their splicing and polyadenylation signaling properties, suggesting that differential binding of these factors to pre-mRNA regulates trans-splicing and hence expression of specific genes. Surprisingly, all these factors were shown to affect not only splicing but also mRNA stability. Affinity purification of SF1 and U2AF35 complexes supported their role in mRNA stability. U2AF35 but not SF1 was shown to bind to ribosomes. To examine the role of splicing factors in mRNA stability, mutations were introduced into the polypyrimidine tract located in the 3' UTR of a mini-gene, and the results demonstrate that U2AF65 binds to such a site and controls the mRNA stability. We propose that transcripts carrying splicing signals in their 3' UTR bind the splicing factors and control their stability.
Collapse
Affiliation(s)
- Sachin Kumar Gupta
- Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
| | | | | | | | | | | |
Collapse
|
28
|
Early evolution of eukaryote feeding modes, cell structural diversity, and classification of the protozoan phyla Loukozoa, Sulcozoa, and Choanozoa. Eur J Protistol 2012; 49:115-78. [PMID: 23085100 DOI: 10.1016/j.ejop.2012.06.001] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 06/21/2012] [Accepted: 06/26/2012] [Indexed: 11/21/2022]
Abstract
I discuss how different feeding modes and related cellular structures map onto the eukaryote evolutionary tree. Centrally important for understanding eukaryotic cell diversity are Loukozoa: ancestrally biciliate phagotrophic protozoa possessing a posterior cilium and ventral feeding groove into which ciliary currents direct prey. I revise their classification by including all anaerobic Metamonada as a subphylum and adding Tsukubamonas. Loukozoa, often with ciliary vanes, are probably ancestral to all protozoan phyla except Euglenozoa and Percolozoa and indirectly to kingdoms Animalia, Fungi, Plantae, and Chromista. I make a new protozoan phylum Sulcozoa comprising subphyla Apusozoa (Apusomonadida, Breviatea) and Varisulca (Diphyllatea; Planomonadida, Discocelida, Mantamonadida; Rigifilida). Understanding sulcozoan evolution clarifies the origins from them of opisthokonts (animals, fungi, Choanozoa) and Amoebozoa, and their evolutionary novelties; Sulcozoa and their descendants (collectively called podiates) arguably arose from Loukozoa by evolving posterior ciliary gliding and pseudopodia in their ventral groove. I explain subsequent independent cytoskeletal modifications, accompanying further shifts in feeding mode, that generated Amoebozoa, Choanozoa, and fungi. I revise classifications of Choanozoa, Conosa (Amoebozoa), and basal fungal phylum Archemycota. I use Choanozoa, Sulcozoa, Loukozoa, and Archemycota to emphasize the need for simply classifying ancestral (paraphyletic) groups and illustrate advantages of this for understanding step-wise phylogenetic advances.
Collapse
|
29
|
Collins LJ. Characterizing ncRNAs in Human Pathogenic Protists Using High-Throughput Sequencing Technology. Front Genet 2011; 2:96. [PMID: 22303390 PMCID: PMC3268645 DOI: 10.3389/fgene.2011.00096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2011] [Accepted: 12/07/2011] [Indexed: 11/16/2022] Open
Abstract
ncRNAs are key genes in many human diseases including cancer and viral infection, as well as providing critical functions in pathogenic organisms such as fungi, bacteria, viruses, and protists. Until now the identification and characterization of ncRNAs associated with disease has been slow or inaccurate requiring many years of testing to understand complicated RNA and protein gene relationships. High-throughput sequencing now offers the opportunity to characterize miRNAs, siRNAs, small nucleolar RNAs (snoRNAs), and long ncRNAs on a genomic scale, making it faster and easier to clarify how these ncRNAs contribute to the disease state. However, this technology is still relatively new, and ncRNA discovery is not an application of high priority for streamlined bioinformatics. Here we summarize background concepts and practical approaches for ncRNA analysis using high-throughput sequencing, and how it relates to understanding human disease. As a case study, we focus on the parasitic protists Giardia lamblia and Trichomonas vaginalis, where large evolutionary distance has meant difficulties in comparing ncRNAs with those from model eukaryotes. A combination of biological, computational, and sequencing approaches has enabled easier classification of ncRNA classes such as snoRNAs, but has also aided the identification of novel classes. It is hoped that a higher level of understanding of ncRNA expression and interaction may aid in the development of less harsh treatment for protist-based diseases.
Collapse
Affiliation(s)
- Lesley Joan Collins
- Institute of Fundamental Sciences, Massey University Palmerston North, New Zealand
| |
Collapse
|
30
|
Chawla B, Jhingran A, Panigrahi A, Stuart KD, Madhubala R. Paromomycin affects translation and vesicle-mediated trafficking as revealed by proteomics of paromomycin -susceptible -resistant Leishmania donovani. PLoS One 2011; 6:e26660. [PMID: 22046323 PMCID: PMC3203147 DOI: 10.1371/journal.pone.0026660] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 09/30/2011] [Indexed: 02/03/2023] Open
Abstract
Leishmania donovani is a protozoan parasite that causes visceral leishmaniasis (VL) and is responsible for significant mortality and morbidity. Increasing resistance towards antimonial drugs poses a great challenge in chemotherapy of VL. Paromomycin is an aminoglycosidic antibiotic and is one of the drugs currently being used in the chemotherapy of cutaneous and visceral leishmaniasis. To understand the mode of action of this antibiotic at the molecular level, we have investigated the global proteome differences between the wild type AG83 strain and a paromomycin resistant (PRr) strain of L. donovani. Stable isotope labeling of amino acids in cell culture (SILAC) followed by quantitative mass spectrometry of the wild type AG83 strain and the paromomycin resistant (PRr) strain identified a total of 226 proteins at ≥95% confidence. Data analysis revealed upregulation of 29 proteins and down-regulation of 21 proteins in the PRr strain. Comparative proteomic analysis of the wild type and the paromomycin resistant strains showed upregulation of the ribosomal proteins in the resistant strain indicating role in translation. Elevated levels of glycolytic enzymes and stress proteins were also observed in the PRr strain. Most importantly, we observed upregulation of proteins that may have a role in intracellular survival and vesicular trafficking in the PRr strain. Furthermore, ultra-structural analysis by electron microscopy demonstrated increased number of vesicular vacuoles in PRr strain when compared to the wild-type strain. Drug affinity pull-down assay followed by mass spectrometery identified proteins in L. donovani wild type strain that were specifically and covalently bound to paromomycin. These results provide the first comprehensive insight into the mode of action and underlying mechanism of resistance to paromomycin in Leishmania donovani.
Collapse
Affiliation(s)
- Bhavna Chawla
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Anupam Jhingran
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | | | - Rentala Madhubala
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- * E-mail:
| |
Collapse
|
31
|
Michaeli S, Doniger T, Gupta SK, Wurtzel O, Romano M, Visnovezky D, Sorek R, Unger R, Ullu E. RNA-seq analysis of small RNPs in Trypanosoma brucei reveals a rich repertoire of non-coding RNAs. Nucleic Acids Res 2011; 40:1282-98. [PMID: 21976736 PMCID: PMC3273796 DOI: 10.1093/nar/gkr786] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The discovery of a plethora of small non-coding RNAs (ncRNAs) has fundamentally changed our understanding of how genes are regulated. In this study, we employed the power of deep sequencing of RNA (RNA-seq) to examine the repertoire of ncRNAs present in small ribonucleoprotein particles (RNPs) of Trypanosoma brucei, an important protozoan parasite. We identified new C/D and H/ACA small nucleolar RNAs (snoRNAs), as well as tens of putative novel non-coding RNAs; several of these are processed from trans-spliced and polyadenylated transcripts. The RNA-seq analysis provided information on the relative abundance of the RNAs, and their 5'- and 3'-termini. The study demonstrated that three highly abundant snoRNAs are involved in rRNA processing and highlight the unique trypanosome-specific repertoire of these RNAs. Novel RNAs were studied using in situ hybridization, association in RNP complexes, and 'RNA walk' to detect interaction with their target RNAs. Finally, we showed that the abundance of certain ncRNAs varies between the two stages of the parasite, suggesting that ncRNAs may contribute to gene regulation during the complex parasite's life cycle. This is the first study to provide a whole-genome analysis of the large repertoire of small RNPs in trypanosomes.
Collapse
Affiliation(s)
- Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel.
| | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Schnare MN, Gray MW. Complete modification maps for the cytosolic small and large subunit rRNAs of Euglena gracilis: functional and evolutionary implications of contrasting patterns between the two rRNA components. J Mol Biol 2011; 413:66-83. [PMID: 21875598 DOI: 10.1016/j.jmb.2011.08.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 08/15/2011] [Accepted: 08/16/2011] [Indexed: 10/17/2022]
Abstract
In the protist Euglena gracilis, the cytosolic small subunit (SSU) rRNA is a single, covalently continuous species typical of most eukaryotes; in contrast, the large subunit (LSU) rRNA is naturally fragmented, comprising 14 separate RNA molecules instead of the bipartite (28S+5.8S) eukaryotic LSU rRNA typically seen. We present extensively revised secondary structure models of the E. gracilis SSU and LSU rRNAs and have mapped the positions of all of the modified nucleosides in these rRNAs (88 in SSU rRNA and 262 in LSU rRNA, with only 3 LSU rRNA modifications incompletely characterized). The relative proportions of ribose-methylated nucleosides and pseudouridine (∼60% and ∼35%, respectively) are closely similar in the two rRNAs; however, whereas the Euglena SSU rRNA has about the same absolute number of modifications as its human counterpart, the Euglena LSU rRNA has twice as many modifications as the corresponding human LSU rRNA. The increased levels of rRNA fragmentation and modification in E. gracilis LSU rRNA are correlated with a 3-fold increase in the level of mispairing in helical regions compared to the human LSU rRNA. In contrast, no comparable increase in mispairing is seen in helical regions of the SSU rRNA compared to its homologs in other eukaryotes. In view of the reported effects of both ribose-methylated nucleoside and pseudouridine residues on RNA structure, these correlations lead us to suggest that increased modification in the LSU rRNA may play a role in stabilizing a 'looser' structure promoted by elevated helical mispairing and a high degree of fragmentation.
Collapse
Affiliation(s)
- Murray N Schnare
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | |
Collapse
|
33
|
Názer E, Verdún RE, Sánchez DO. Nucleolar localization of RNA binding proteins induced by actinomycin D and heat shock in Trypanosoma cruzi. PLoS One 2011; 6:e19920. [PMID: 21629693 PMCID: PMC3101214 DOI: 10.1371/journal.pone.0019920] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 04/14/2011] [Indexed: 11/18/2022] Open
Abstract
In this work we show that under Actinomycin D (ActD) treatment, several RNA Binding Proteins (RBPs) involved in mRNA metabolism are relocalized into the nucleolus in Trypanosoma cruzi as a specific stress response. ATP depletion as well as kinase inhibition markedly reduced the nucleolar localization response, suggesting that an energy-dependent transport modulated by the phosphorylation status of the parasite might be required. Deletion analyses in one of such proteins, TcSR62, showed that a domain bearing basic amino acids located in the COOH terminal region was sufficient to promote its nucleolar relocalization. Interestingly, we showed that in addition to RBPs, poly(A)+ RNA is also accumulated into the nucleolus in response to ActD treatment. Finally, we found out that nucleolar relocalization of RBPs is also triggered by severe heat shock in a reversible way. Together, these results suggest that the nucleolus of an early divergent eukaryote is either able to sequester key factors related to mRNA metabolism in response to transcriptional stress or behaves as a RBP processing center, arguing in favour to the hypothesis that the non-traditional features of the nucleolus could be acquired early during evolution.
Collapse
Affiliation(s)
- Ezequiel Názer
- Instituto de Investigaciones Biotecnólogicas-Instituto Tecnológico Chascomús, UNSAM-CONICET, San Martín, Provincia de Buenos Aires, Argentina
| | - Ramiro E. Verdún
- Leonard M. Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Daniel O. Sánchez
- Instituto de Investigaciones Biotecnólogicas-Instituto Tecnológico Chascomús, UNSAM-CONICET, San Martín, Provincia de Buenos Aires, Argentina
- * E-mail:
| |
Collapse
|
34
|
Doniger T, Katz R, Wachtel C, Michaeli S, Unger R. A comparative genome-wide study of ncRNAs in trypanosomatids. BMC Genomics 2010; 11:615. [PMID: 21050447 PMCID: PMC3091756 DOI: 10.1186/1471-2164-11-615] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 11/04/2010] [Indexed: 01/18/2023] Open
Abstract
Background Recent studies have provided extensive evidence for multitudes of non-coding RNA (ncRNA) transcripts in a wide range of eukaryotic genomes. ncRNAs are emerging as key players in multiple layers of cellular regulation. With the availability of many whole genome sequences, comparative analysis has become a powerful tool to identify ncRNA molecules. In this study, we performed a systematic genome-wide in silico screen to search for novel small ncRNAs in the genome of Trypanosoma brucei using techniques of comparative genomics. Results In this study, we identified by comparative genomics, and validated by experimental analysis several novel ncRNAs that are conserved across multiple trypanosomatid genomes. When tested on known ncRNAs, our procedure was capable of finding almost half of the known repertoire through homology over six genomes, and about two-thirds of the known sequences were found in at least four genomes. After filtering, 72 conserved unannotated sequences in at least four genomes were found, 29 of which, ranging in size from 30 to 392 nts, were conserved in all six genomes. Fifty of the 72 candidates in the final set were chosen for experimental validation. Eighteen of the 50 (36%) were shown to be expressed, and for 11 of them a distinct expression product was detected, suggesting that they are short ncRNAs. Using functional experimental assays, five of the candidates were shown to be novel H/ACA and C/D snoRNAs; these included three sequences that appear as singletons in the genome, unlike previously identified snoRNA molecules that are found in clusters. The other candidates appear to be novel ncRNA molecules, and their function is, as yet, unknown. Conclusions Using comparative genomic techniques, we predicted 72 sequences as ncRNA candidates in T. brucei. The expression of 50 candidates was tested in laboratory experiments. This resulted in the discovery of 11 novel short ncRNAs in procyclic stage T. brucei, which have homologues in the other trypansomatids. A few of these molecules are snoRNAs, but most of them are novel ncRNA molecules. Based on this study, our analysis suggests that the total number of ncRNAs in trypanosomatids is in the range of several hundred.
Collapse
Affiliation(s)
- Tirza Doniger
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | | | | | | | | |
Collapse
|
35
|
Clayton C, Michaeli S. 3' processing in protists. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 2:247-55. [PMID: 21957009 DOI: 10.1002/wrna.49] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Molecular biologists have traditionally focused on the very small corner of eukaryotic evolution that includes yeast and animals; even plants have been neglected. In this article, we describe the scant information that is available concerning RNA processing in the other four major eukaryotic groups, especially pathogenic protists. We focus mainly on polyadenylation and nuclear processing of stable RNAs. These processes have--where examined--been shown to be conserved, but there are many novel details. We also briefly mention other processing reactions such as splicing.
Collapse
Affiliation(s)
- Christine Clayton
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg, Germany.
| | | |
Collapse
|
36
|
Gupta SK, Hury A, Ziporen Y, Shi H, Ullu E, Michaeli S. Small nucleolar RNA interference in Trypanosoma brucei: mechanism and utilization for elucidating the function of snoRNAs. Nucleic Acids Res 2010; 38:7236-47. [PMID: 20601683 PMCID: PMC2978370 DOI: 10.1093/nar/gkq599] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Expression of dsRNA complementary to small nucleolar RNAs (snoRNAs) in Trypanosoma brucei results in snoRNA silencing, termed snoRNAi. Here, we demonstrate that snoRNAi requires the nuclear TbDCL2 protein, but not TbDCL1, which is involved in RNA interference (RNAi) in the cytoplasm. snoRNAi depends on Argonaute1 (Slicer), and on TbDCL2, suggesting that snoRNA dicing and slicing takes place in the nucleus, and further suggesting that AGO1 is active in nuclear silencing. snoRNAi was next utilized to elucidate the function of an abundant snoRNA, TB11Cs2C2 (92 nt), present in a cluster together with the spliced leader associated RNA (SLA1) and snR30, which are both H/ACA RNAs with special nuclear functions. Using AMT-UV cross-linking and RNaseH cleavage, we provide evidence for the interaction of TB11Cs2C2 with the small rRNAs, srRNA-2 and srRNA-6, which are part of the large subunit (LSU) rRNA. snoRNAi of TB11Cs2C2 resulted in defects in generating srRNA-2 and LSUβ rRNA. This is the first snoRNA described so far to engage in trypanosome-specific processing events.
Collapse
Affiliation(s)
- Sachin Kumar Gupta
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900 Israel
| | | | | | | | | | | |
Collapse
|
37
|
Tkacz ID, Gupta SK, Volkov V, Romano M, Haham T, Tulinski P, Lebenthal I, Michaeli S. Analysis of spliceosomal proteins in Trypanosomatids reveals novel functions in mRNA processing. J Biol Chem 2010; 285:27982-99. [PMID: 20592024 DOI: 10.1074/jbc.m109.095349] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In trypanosomatids, all mRNAs are processed via trans-splicing, although cis-splicing also occurs. In trans-splicing, a common small exon, the spliced leader (SL), which is derived from a small SL RNA species, is added to all mRNAs. Sm and Lsm proteins are core proteins that bind to U snRNAs and are essential for both these splicing processes. In this study, SmD3- and Lsm3-associated complexes were purified to homogeneity from Leishmania tarentolae. The purified complexes were analyzed by mass spectrometry, and 54 and 39 proteins were purified from SmD3 and Lsm complexes, respectively. Interestingly, among the proteins purified from Lsm3, no mRNA degradation factors were detected, as in Lsm complexes from other eukaryotes. The U1A complex was purified and mass spectrometry analysis identified, in addition to U1 small nuclear ribonucleoprotein (snRNP) proteins, additional co-purified proteins, including the polyadenylation factor CPSF73. Defects observed in cells silenced for U1 snRNP proteins suggest that the U1 snRNP functions exclusively in cis-splicing, although U1A also participates in polyadenylation and affects trans-splicing. The study characterized several trypanosome-specific nuclear factors involved in snRNP biogenesis, whose function was elucidated in Trypanosoma brucei. Conserved factors, such as PRP19, which functions at the heart of every cis-spliceosome, also affect SL RNA modification; GEMIN2, a protein associated with SMN (survival of motor neurons) and implicated in selective association of U snRNA with core Sm proteins in trypanosomes, is a master regulator of snRNP assembly. This study demonstrates the existence of trypanosomatid-specific splicing factors but also that conserved snRNP proteins possess trypanosome-specific functions.
Collapse
Affiliation(s)
- Itai Dov Tkacz
- Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Simo G, Herder S, Cuny G, Hoheisel J. Identification of subspecies specific genes differentially expressed in procyclic forms of Trypanosoma brucei subspecies. INFECTION GENETICS AND EVOLUTION 2010; 10:229-37. [DOI: 10.1016/j.meegid.2009.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Revised: 10/29/2009] [Accepted: 11/03/2009] [Indexed: 11/30/2022]
|
39
|
Nocua P, Gómez C, Cuervo C, Puerta C. Cl gene cluster encoding several small nucleolar RNAs: a comparison amongst trypanosomatids. Mem Inst Oswaldo Cruz 2009; 104:473-80. [PMID: 19547875 DOI: 10.1590/s0074-02762009000300013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Accepted: 03/03/2009] [Indexed: 11/22/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are small non-coding RNAs that modify RNA molecules such as rRNA and snRNA by guiding 2'-O-ribose methylation (C/D box snoRNA family) and pseudouridylation reactions (H/ACA snoRNA family). H/ACA snoRNAs are also involved in trans-splicing in trypanosomatids. The aims of this work were to characterise the Cl gene cluster that encodes several snoRNAs in Trypanosoma rangeli and compare it with clusters from Trypanosoma cruzi, Trypanosoma brucei, Leishmania major, Leishmania infantum, Leishmania braziliensis and Leptomonas collosoma. The T. rangeli Cl gene cluster is an 801 base pair (bp) repeat sequence that encodes three C/D (Cl1, Cl2 and Cl4) and three H/ACA (Cl3, Cl5 and Cl6) snoRNAs. In contrast to T. brucei, the Cl3 and Cl5 homologues have not been annotated in the Leishmania or T. cruzi genome projects (http//:www.genedb.org). Of note, snoRNA transcribed regions have a high degree of sequence identity among all species and share gene synteny. Collectively, these findings suggest that the Cl cluster could constitute an interesting target for therapeutic (gene silencing) or diagnostic intervention strategies (PCR-derived tools).
Collapse
Affiliation(s)
- Paola Nocua
- Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | | | | | | |
Collapse
|
40
|
Makarova JA, Kramerov DA. Analysis of C/D box snoRNA genes in vertebrates: The number of copies decreases in placental mammals. Genomics 2009; 94:11-9. [PMID: 19272437 DOI: 10.1016/j.ygeno.2009.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Revised: 02/26/2009] [Accepted: 02/27/2009] [Indexed: 12/31/2022]
Abstract
C/D box small nucleolar RNAs (snoRNAs) guide site-specific 2'-O-methylation of RNAs. Nearly all C/D box snoRNAs with known targets are involved in rRNA modification. In vertebrates, snoRNAs are encoded in introns of various genes and their processing is coupled with splicing of host gene pre-mRNA. Here, the genes encoding C/D box snoRNAs that guide 2'-O-methylation of rRNA were identified and analyzed in vertebrate genomes. The number of copies of most C/D box snoRNA genes proved to be lower in placental mammals compared to other vertebrates. This can be due to smaller oocytes and accordingly lower number of ribosomes in them in eutherians. The targets of snoRNAs encoded by single-copy and multiple-copy genes proved to have different distribution in rRNAs. The causes of this difference are discussed. In some cases, the transcripts of homologous C/D box RNA genes were shown to guide the modification of neighboring nucleotides in rRNA. C/D box snoRNA pseudogenes were found in all vertebrate classes. Three novel C/D box snoRNAs were found in Xenopus tropicalis that may guide 2'-O-methylation of Xenopus-specific rRNA sites. A list of 922 annotated C/D box snoRNA genes is presented.
Collapse
Affiliation(s)
- Julia A Makarova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia
| | | |
Collapse
|
41
|
Myslyuk I, Doniger T, Horesh Y, Hury A, Hoffer R, Ziporen Y, Michaeli S, Unger R. Psiscan: a computational approach to identify H/ACA-like and AGA-like non-coding RNA in trypanosomatid genomes. BMC Bioinformatics 2008; 9:471. [PMID: 18986541 PMCID: PMC2613932 DOI: 10.1186/1471-2105-9-471] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Accepted: 11/05/2008] [Indexed: 11/12/2022] Open
Abstract
Background Detection of non coding RNA (ncRNA) molecules is a major bioinformatics challenge. This challenge is particularly difficult when attempting to detect H/ACA molecules which are involved in converting uridine to pseudouridine on rRNA in trypanosomes, because these organisms have unique H/ACA molecules (termed H/ACA-like) that lack several of the features that characterize H/ACA molecules in most other organisms. Results We present here a computational tool called Psiscan, which was designed to detect H/ACA-like molecules in trypanosomes. We started by analyzing known H/ACA-like molecules and characterized their crucial elements both computationally and experimentally. Next, we set up constraints based on this analysis and additional phylogenic and functional data to rapidly scan three trypanosome genomes (T. brucei, T. cruzi and L. major) for sequences that observe these constraints and are conserved among the species. In the next step, we used minimal energy calculation to select the molecules that are predicted to fold into a lowest energy structure that is consistent with the constraints. In the final computational step, we used a Support Vector Machine that was trained on known H/ACA-like molecules as positive examples and on negative examples of molecules that were identified by the computational analyses but were shown experimentally not to be H/ACA-like molecules. The leading candidate molecules predicted by the SVM model were then subjected to experimental validation. Conclusion The experimental validation showed 11 molecules to be expressed (4 out of 25 in the intermediate stage and 7 out of 19 in the final validation after the machine learning stage). Five of these 11 molecules were further shown to be bona fide H/ACA-like molecules. As snoRNA in trypanosomes are organized in clusters, the new H/ACA-like molecules could be used as starting points to manually search for additional molecules in their neighbourhood. All together this study increased our repertoire by fourteen H/ACA-like and six C/D snoRNAs molecules from T. brucei and L. Major. In addition the experimental analysis revealed that six ncRNA molecules that are expressed are not downregulated in CBF5 silenced cells, suggesting that they have structural features of H/ACA-like molecules but do not have their standard function. We termed this novel class of molecules AGA-like, and we are exploring their function. This study demonstrates the power of tight collaboration between computational and experimental approaches in a combined effort to reveal the repertoire of ncRNA molecles.
Collapse
Affiliation(s)
- Inna Myslyuk
- Faculty of Life Science, Bar-Ilan University, Ramat-Gan, Israel.
| | | | | | | | | | | | | | | |
Collapse
|