1
|
Sandes JM, de Figueiredo RCBQ. The endoplasmic reticulum of trypanosomatids: An unrevealed road for chemotherapy. Front Cell Infect Microbiol 2022; 12:1057774. [PMID: 36439218 PMCID: PMC9684732 DOI: 10.3389/fcimb.2022.1057774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/24/2022] [Indexed: 01/04/2024] Open
Abstract
The endoplasmic reticulum (ER) of higher eukaryotic cells forms an intricate membranous network that serves as the main processing facility for folding and assembling of secreted and membrane proteins. The ER is a highly dynamic organelle that interacts with other intracellular structures, as well as endosymbiotic pathogenic and non-pathogenic microorganisms. A strict ER quality control (ERQC) must work to ensure that proteins entering the ER are folded and processed correctly. Unfolded or misfolded proteins are usually identified, selected, and addressed to Endoplasmic Reticulum-Associated Degradation (ERAD) complex. Conversely, when there is a large demand for secreted proteins or ER imbalance, the accumulation of unfolded or misfolded proteins activates the Unfold Protein Response (UPR) to restore the ER homeostasis or, in the case of persistent ER stress, induces the cell death. Pathogenic trypanosomatids, such as Trypanosoma cruzi, Trypanosoma brucei and Leishmania spp are the etiological agents of important neglected diseases. These protozoans have a complex life cycle alternating between vertebrate and invertebrate hosts. The ER of trypanosomatids, like those found in higher eukaryotes, is also specialized for secretion, and depends on the ERAD and non-canonical UPR to deal with the ER stress. Here, we reviewed the basic aspects of ER biology, organization, and quality control in trypanosomatids. We also focused on the unusual way by which T. cruzi, T. brucei, and Leishmania spp. respond to ER stress, emphasizing how these parasites' ER-unrevealed roads might be an attractive target for chemotherapy.
Collapse
Affiliation(s)
- Jana Messias Sandes
- Laboratório de Biologia Celular e Molecular de Patógenos, Departamento de Microbiologia, Instituto Aggeu Magalhães, Recife, Brazil
- Laboratório de Microscopia Eletrônica, Instituto Keizo Assami, Universidade Federal de Pernambuco, Recife, Brazil
| | | |
Collapse
|
2
|
Rajan KS, Adler K, Doniger T, Cohen-Chalamish S, Aharon-Hefetz N, Aryal S, Pilpel Y, Tschudi C, Unger R, Michaeli S. Identification and functional implications of pseudouridine RNA modification on small noncoding RNAs in the mammalian pathogen Trypanosoma brucei. J Biol Chem 2022; 298:102141. [PMID: 35714765 PMCID: PMC9283944 DOI: 10.1016/j.jbc.2022.102141] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/09/2022] [Accepted: 06/11/2022] [Indexed: 01/11/2023] Open
Abstract
Trypanosoma brucei, the parasite that causes sleeping sickness, cycles between an insect and a mammalian host. However, the effect of RNA modifications such as pseudouridinylation on its ability to survive in these two different host environments is unclear. Here, two genome-wide approaches were applied for mapping pseudouridinylation sites (Ψs) on small nucleolar RNA (snoRNA), 7SL RNA, vault RNA, and tRNAs from T. brucei. We show using HydraPsiSeq and RiboMeth-seq that the Ψ on C/D snoRNA guiding 2'-O-methylation increased the efficiency of the guided modification on its target, rRNA. We found differential levels of Ψs on these noncoding RNAs in the two life stages (insect host and mammalian host) of the parasite. Furthermore, tRNA isoform abundance and Ψ modifications were characterized in these two life stages demonstrating stage-specific regulation. We conclude that the differential Ψ modifications identified here may contribute to modulating the function of noncoding RNAs involved in rRNA processing, rRNA modification, protein synthesis, and protein translocation during cycling of the parasite between its two hosts.
Collapse
Affiliation(s)
- K. Shanmugha Rajan
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Katerina Adler
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Tirza Doniger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Smadar Cohen-Chalamish
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Noa Aharon-Hefetz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Saurav Aryal
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Christian Tschudi
- Department of Epidemiology and Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Ron Unger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel,For correspondence: Shulamit Michaeli
| |
Collapse
|
3
|
Soni K, Kempf G, Manalastas-Cantos K, Hendricks A, Flemming D, Guizetti J, Simon B, Frischknecht F, Svergun DI, Wild K, Sinning I. Structural analysis of the SRP Alu domain from Plasmodium falciparum reveals a non-canonical open conformation. Commun Biol 2021; 4:600. [PMID: 34017052 PMCID: PMC8137916 DOI: 10.1038/s42003-021-02132-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/22/2021] [Indexed: 12/25/2022] Open
Abstract
The eukaryotic signal recognition particle (SRP) contains an Alu domain, which docks into the factor binding site of translating ribosomes and confers translation retardation. The canonical Alu domain consists of the SRP9/14 protein heterodimer and a tRNA-like folded Alu RNA that adopts a strictly 'closed' conformation involving a loop-loop pseudoknot. Here, we study the structure of the Alu domain from Plasmodium falciparum (PfAlu), a divergent apicomplexan protozoan that causes human malaria. Using NMR, SAXS and cryo-EM analyses, we show that, in contrast to its prokaryotic and eukaryotic counterparts, the PfAlu domain adopts an 'open' Y-shaped conformation. We show that cytoplasmic P. falciparum ribosomes are non-discriminative and recognize both the open PfAlu and closed human Alu domains with nanomolar affinity. In contrast, human ribosomes do not provide high affinity binding sites for either of the Alu domains. Our analyses extend the structural database of Alu domains to the protozoan species and reveal species-specific differences in the recognition of SRP Alu domains by ribosomes.
Collapse
Affiliation(s)
- Komal Soni
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Georg Kempf
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | | | - Astrid Hendricks
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Dirk Flemming
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Julien Guizetti
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Bernd Simon
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Friedrich Frischknecht
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Klemens Wild
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany.
| |
Collapse
|
4
|
Wild K, Becker MM, Kempf G, Sinning I. Structure, dynamics and interactions of large SRP variants. Biol Chem 2019; 401:63-80. [DOI: 10.1515/hsz-2019-0282] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/09/2019] [Indexed: 12/11/2022]
Abstract
Abstract
Co-translational protein targeting to membranes relies on the signal recognition particle (SRP) system consisting of a cytosolic ribonucleoprotein complex and its membrane-associated receptor. SRP recognizes N-terminal cleavable signals or signal anchor sequences, retards translation, and delivers ribosome-nascent chain complexes (RNCs) to vacant translocation channels in the target membrane. While our mechanistic understanding is well advanced for the small bacterial systems it lags behind for the large bacterial, archaeal and eukaryotic SRP variants including an Alu and an S domain. Here we describe recent advances on structural and functional insights in domain architecture, particle dynamics and interplay with RNCs and translocon and GTP-dependent regulation of co-translational protein targeting stimulated by SRP RNA.
Collapse
Affiliation(s)
- Klemens Wild
- Heidelberg University Biochemistry Center (BZH) , INF 328 , D-69120 Heidelberg , Germany
| | - Matthias M.M. Becker
- Heidelberg University Biochemistry Center (BZH) , INF 328 , D-69120 Heidelberg , Germany
| | - Georg Kempf
- Heidelberg University Biochemistry Center (BZH) , INF 328 , D-69120 Heidelberg , Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH) , INF 328 , D-69120 Heidelberg , Germany
| |
Collapse
|
5
|
Chiweshe SM, Steketee PC, Jayaraman S, Paxton E, Neophytou K, Erasmus H, Labuschagne M, Cooper A, MacLeod A, Grey FE, Morrison LJ. Parasite specific 7SL-derived small RNA is an effective target for diagnosis of active trypanosomiasis infection. PLoS Negl Trop Dis 2019; 13:e0007189. [PMID: 30779758 PMCID: PMC6413958 DOI: 10.1371/journal.pntd.0007189] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/12/2019] [Accepted: 01/25/2019] [Indexed: 12/19/2022] Open
Abstract
Human and animal African trypanosomiasis (HAT & AAT, respectively) remain a significant health and economic issue across much of sub-Saharan Africa. Effective control of AAT and potential eradication of HAT requires affordable, sensitive and specific diagnostic tests that can be used in the field. Small RNAs in the blood or serum are attractive disease biomarkers due to their stability, accessibility and available technologies for detection. Using RNAseq, we have identified a trypanosome specific small RNA to be present at high levels in the serum of infected cattle. The small RNA is derived from the non-coding 7SL RNA of the peptide signal recognition particle and is detected in the serum of infected cattle at significantly higher levels than in the parasite, suggesting active processing and secretion. We show effective detection of the small RNA in the serum of infected cattle using a custom RT-qPCR assay. Strikingly, the RNA can be detected before microscopy detection of parasitaemia in the blood, and it can also be detected during remission periods of infection when no parasitaemia is detectable by microscopy. However, RNA levels drop following treatment with trypanocides, demonstrating accurate prediction of active infection. While the small RNA sequence is conserved between different species of trypanosome, nucleotide differences within the sequence allow generation of highly specific assays that can distinguish between infections with Trypanosoma brucei, Trypanosoma congolense and Trypanosoma vivax. Finally, we demonstrate effective detection of the small RNA directly from serum, without the need for pre-processing, with a single step RT-qPCR assay. Our findings identify a species-specific trypanosome small RNA that can be detected at high levels in the serum of cattle with active parasite infections. This provides the basis for the development of a cheap, non-invasive and highly effective diagnostic test for trypanosomiasis. African trypanosomes cause significant disease in humans and animals across sub-Saharan Africa. For both human and animal infections diagnostics that can accurately identify an active infection are lacking–this is particularly the case in animal disease where most diagnosis is based upon clinical signs, which is not a specific or sensitive means of detecting infection. There is therefore a significant unmet need for a pathogen marker of active infection that accurately indicates whether an animal or human is currently infected. Through analysing the blood of cattle infected with trypanosomes, we identified a short sequence of RNA that was present at very high levels. This small RNA derives from the trypanosome genome, and we could identify its presence in the genome of all three species that are responsible for human and animal disease. We were able to design species-specific tests, and showed that in samples from infected animals the assays were more sensitive than the traditional microscope-based detection, importantly the signal disappeared relatively quickly after successful treatment, and when treatment failed, the assay was able to accurately identify when infection persisted. We also demonstrated that the causative agent of human trypanosomiasis secretes the marker at similar levels to that seen in the animal-infective trypanosomes. Therefore, we have discovered a marker of trypanosome infection that is present at high levels in the blood of infected animals, disappears quickly upon successful treatment, but is effective at detecting instances of unsuccessful treatment and persistent infection. This represents a potentially powerful diagnostic tool for human and animal trypanosomiasis.
Collapse
Affiliation(s)
- Stephen M Chiweshe
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Pieter C Steketee
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Siddharth Jayaraman
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Edith Paxton
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Kyriaki Neophytou
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Heidi Erasmus
- Clinvet Research Innovation, Uitzich Road, Bainsvlei, Bloemfontein, South Africa
| | - Michel Labuschagne
- Clinvet Research Innovation, Uitzich Road, Bainsvlei, Bloemfontein, South Africa
| | - Anneli Cooper
- Wellcome Centre for Molecular Parasitology, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary & Life Sciences, Bearsden Road, University of Glasgow, Glasgow, United Kingdom
| | - Annette MacLeod
- Wellcome Centre for Molecular Parasitology, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary & Life Sciences, Bearsden Road, University of Glasgow, Glasgow, United Kingdom
| | - Finn E Grey
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Liam J Morrison
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| |
Collapse
|
6
|
Van Puyenbroeck V, Vermeire K. Inhibitors of protein translocation across membranes of the secretory pathway: novel antimicrobial and anticancer agents. Cell Mol Life Sci 2018; 75:1541-1558. [PMID: 29305616 PMCID: PMC5897483 DOI: 10.1007/s00018-017-2743-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/15/2017] [Accepted: 12/27/2017] [Indexed: 12/22/2022]
Abstract
Proteins routed to the secretory pathway start their journey by being transported across biological membranes, such as the endoplasmic reticulum. The essential nature of this protein translocation process has led to the evolution of several factors that specifically target the translocon and block translocation. In this review, various translocation pathways are discussed together with known inhibitors of translocation. Properties of signal peptide-specific systems are highlighted for the development of new therapeutic and antimicrobial applications, as compounds can target signal peptides from either host cells or pathogens and thereby selectively prevent translocation of those specific proteins. Broad inhibition of translocation is also an interesting target for the development of new anticancer drugs because cancer cells heavily depend on efficient protein translocation into the endoplasmic reticulum to support their fast growth.
Collapse
Affiliation(s)
- Victor Van Puyenbroeck
- Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, 3000, Leuven, Belgium
| | - Kurt Vermeire
- Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, 3000, Leuven, Belgium.
| |
Collapse
|
7
|
Amin SV, Roberts JT, Patterson DG, Coley AB, Allred JA, Denner JM, Johnson JP, Mullen GE, O'Neal TK, Smith JT, Cardin SE, Carr HT, Carr SL, Cowart HE, DaCosta DH, Herring BR, King VM, Polska CJ, Ward EE, Wise AA, McAllister KN, Chevalier D, Spector MP, Borchert GM. Novel small RNA (sRNA) landscape of the starvation-stress response transcriptome of Salmonella enterica serovar typhimurium. RNA Biol 2016; 13:331-42. [PMID: 26853797 DOI: 10.1080/15476286.2016.1144010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Small RNAs (sRNAs) are short (∼50-200 nucleotides) noncoding RNAs that regulate cellular activities across bacteria. Salmonella enterica starved of a carbon-energy (C) source experience a host of genetic and physiological changes broadly referred to as the starvation-stress response (SSR). In an attempt to identify novel sRNAs contributing to SSR control, we grew log-phase, 5-h C-starved and 24-h C-starved cultures of the virulent Salmonella enterica subspecies enterica serovar Typhimurium strain SL1344 and comprehensively sequenced their small RNA transcriptomes. Strikingly, after employing a novel strategy for sRNA discovery based on identifying dynamic transcripts arising from "gene-empty" regions, we identify 58 wholly undescribed Salmonella sRNA genes potentially regulating SSR averaging an ∼1,000-fold change in expression between log-phase and C-starved cells. Importantly, the expressions of individual sRNA loci were confirmed by both comprehensive transcriptome analyses and northern blotting of select candidates. Of note, we find 43 candidate sRNAs share significant sequence identity to characterized sRNAs in other bacteria, and ∼70% of our sRNAs likely assume characteristic sRNA structural conformations. In addition, we find 53 of our 58 candidate sRNAs either overlap neighboring mRNA loci or share significant sequence complementarity to mRNAs transcribed elsewhere in the SL1344 genome strongly suggesting they regulate the expression of transcripts via antisense base-pairing. Finally, in addition to this work resulting in the identification of 58 entirely novel Salmonella enterica genes likely participating in the SSR, we also find evidence suggesting that sRNAs are significantly more prevalent than currently appreciated and that Salmonella sRNAs may actually number in the thousands.
Collapse
Affiliation(s)
- Shivam V Amin
- a Department of Biology , University of South Alabama , Mobile , AL
| | - Justin T Roberts
- a Department of Biology , University of South Alabama , Mobile , AL
| | | | | | | | - Jason M Denner
- a Department of Biology , University of South Alabama , Mobile , AL
| | - Justin P Johnson
- a Department of Biology , University of South Alabama , Mobile , AL
| | | | - Trenton K O'Neal
- a Department of Biology , University of South Alabama , Mobile , AL
| | - Jason T Smith
- a Department of Biology , University of South Alabama , Mobile , AL
| | - Sara E Cardin
- a Department of Biology , University of South Alabama , Mobile , AL
| | - Hank T Carr
- a Department of Biology , University of South Alabama , Mobile , AL
| | - Stacie L Carr
- a Department of Biology , University of South Alabama , Mobile , AL
| | - Holly E Cowart
- a Department of Biology , University of South Alabama , Mobile , AL
| | - David H DaCosta
- a Department of Biology , University of South Alabama , Mobile , AL
| | | | - Valeria M King
- a Department of Biology , University of South Alabama , Mobile , AL
| | | | - Erin E Ward
- a Department of Biology , University of South Alabama , Mobile , AL
| | - Alice A Wise
- a Department of Biology , University of South Alabama , Mobile , AL
| | | | - David Chevalier
- c Department of Biology , East Georgia State College , Swainsboro , GA
| | - Michael P Spector
- b Department of Biomedical Sciences , University of South Alabama , Mobile , AL
| | - Glen M Borchert
- a Department of Biology , University of South Alabama , Mobile , AL.,d Department of Pharmacology , USA College of Medicine , Mobile , AL
| |
Collapse
|
8
|
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
|
9
|
Liu N, Niu G, Xie Z, Chen Z, Itzek A, Kreth J, Gillaspy A, Zeng L, Burne R, Qi F, Merritt J. The Streptococcus mutans irvA gene encodes a trans-acting riboregulatory mRNA. Mol Cell 2015; 57:179-90. [PMID: 25574948 DOI: 10.1016/j.molcel.2014.11.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 09/12/2014] [Accepted: 11/04/2014] [Indexed: 02/08/2023]
Abstract
In both prokaryotes and eukaryotes, insight into gene function is typically obtained by in silico homology searches and/or phenotypic analyses of strains bearing mutations within open reading frames. However, the studies herein illustrate how mRNA function is not limited to the expression of a cognate protein. We demonstrate that a stress-induced protein-encoding mRNA (irvA) from the dental caries pathogen Streptococcus mutans directly modulates target mRNA (gbpC) stability through seed pairing interactions. The 5' untranslated region of irvA mRNA is a trans riboregulator of gbpC and a critical activator of the DDAG stress response, whereas IrvA functions independently in the regulation of natural competence. The irvA riboregulatory domain controls GbpC production by forming irvA-gbpC hybrid mRNA duplexes that prevent gbpC degradation by an RNase J2-mediated pathway. These studies implicate a potentially ubiquitous role for typical protein-encoding mRNAs as riboregulators, which could alter current concepts in gene regulation.
Collapse
Affiliation(s)
- Nan Liu
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA
| | - Guoqing Niu
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA
| | - Zhoujie Xie
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA
| | - Zhiyun Chen
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA
| | - Andreas Itzek
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA
| | - Jens Kreth
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA; Division of Oral Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Allison Gillaspy
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA
| | - Lin Zeng
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
| | - Robert Burne
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
| | - Fengxia Qi
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA; Division of Oral Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Justin Merritt
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA; Division of Oral Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
| |
Collapse
|
10
|
Abstract
The Alu domain of the signal recognition particle (SRP) arrests protein biosynthesis by competition with elongation factor binding on the ribosome. The mammalian Alu domain is a protein-RNA complex, while prokaryotic Alu domains are protein-free with significant extensions of the RNA. Here we report the crystal structure of the complete Alu domain of Bacillus subtilis SRP RNA at 2.5 Å resolution. The bacterial Alu RNA reveals a compact fold, which is stabilized by prokaryote-specific extensions and interactions. In this 'closed' conformation, the 5' and 3' regions are clamped together by the additional helix 1, the connecting 3-way junction and a novel minor groove interaction, which we term the 'minor-saddle motif' (MSM). The 5' region includes an extended loop-loop pseudoknot made of five consecutive Watson-Crick base pairs. Homology modeling with the human Alu domain in context of the ribosome shows that an additional lobe in the pseudoknot approaches the large subunit, while the absence of protein results in the detachment from the small subunit. Our findings provide the structural basis for purely RNA-driven elongation arrest in prokaryotes, and give insights into the structural adaption of SRP RNA during evolution.
Collapse
Affiliation(s)
- Georg Kempf
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Klemens Wild
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| |
Collapse
|
11
|
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
|
12
|
Functional analysis of noncoding RNAs in trypanosomes: RNA walk, a novel approach to study RNA-RNA interactions between small RNA and its target. Methods Mol Biol 2011; 718:245-57. [PMID: 21370053 DOI: 10.1007/978-1-61779-018-8_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The recent discovery of thousands of small noncoding RNAs (ncRNAs), in many different organisms, has led to the need for methods to study their function. One way to help understand their function is to determine what other RNAs interact with the ncRNAs. We have developed a novel method to investigate the RNA-RNA interactions between a small RNA and its target that we termed "RNA walk." The method is based on UV-induced AMT cross-linking in vivo followed by affinity selection of the hybrid molecules and mapping the intermolecular adducts by RT-PCR. Domains carrying the cross-linked adducts are less efficiently amplified than domains that are not cross-linked. Real-time PCR is used to quantify the results. Further mapping of the interactions is performed by primer extension to determine the exact cross-linked adduct.
Collapse
|
13
|
Abstract
Assembly of ribonucleoprotein complexes is a facilitated quality-controlled process that typically includes modification to the RNA component from precursor to mature form. The SRP (signal recognition particle) is a cytosolic ribonucleoprotein that catalyses protein targeting to the endoplasmic reticulum. Assembly of SRP is largely nucleolar, and most of its protein components are required to generate a stable complex. A pre-SRP is exported from the nucleus to the cytoplasm where the final protein, Srp54p, is incorporated. Although this outline of the SRP assembly pathway has been determined, factors that facilitate this and/or function in quality control of the RNA are poorly understood. In the present paper, the SRP assembly pathway is summarized, and evidence for the involvement of both the Rex1p and nuclear exosome nucleases and the TRAMP (Trf4-Air2-Mtr4p polyadenylation) adenylase in quality control of SRP RNA is discussed. The RNA component of SRP is transcribed by RNA polymerase III, and both La, which binds all newly transcribed RNAs generated by this enzyme, and the nuclear Lsm complex are implicated in SRP RNA metabolism.
Collapse
|
14
|
Bibi E. Early targeting events during membrane protein biogenesis in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1808:841-50. [PMID: 20682283 DOI: 10.1016/j.bbamem.2010.07.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2010] [Revised: 07/21/2010] [Accepted: 07/22/2010] [Indexed: 10/19/2022]
Abstract
All living cells have co-translational pathways for targeting membrane proteins. Co-translation pathways for secretory proteins also exist but mostly in eukaryotes. Unlike secretory proteins, the biosynthetic pathway of most membrane proteins is conserved through evolution and these proteins are usually synthesized by membrane-bound ribosomes. Translation on the membrane requires that both the ribosomes and the mRNAs be properly localized. Theoretically, this can be achieved by several means. (i) The current view is that the targeting of cytosolic mRNA-ribosome-nascent chain complexes (RNCs) to the membrane is initiated by information in the emerging hydrophobic nascent polypeptides. (ii) The alternative model suggests that ribosomes may be targeted to the membrane also constitutively, whereas the appropriate mRNAs may be carried on small ribosomal subunits or targeted by other cellular factors to the membrane-bound ribosomes. Importantly, the available experimental data do not rule out the possibility that cells may also utilize both pathways in parallel. In any case, it is well documented that a major player in the targeting pathway is the signal recognition particle (SRP) system composed of the SRP and its receptor (SR). Although the functional core of the SRP system is evolutionarily conserved, its composition and biological practice come with different flavors in various organisms. This review is dedicated mainly to the Escherichia (E.) coli SRP, where the biochemical and structural properties of components of the SRP system have been relatively characterized, yielding essential information about various aspects of the pathway. In addition, several cellular interactions of the SRP and its receptor have been described in E. coli, providing insights into their spatial function. Collectively, these in vitro studies have led to the current view of the targeting pathway [see (i) above]. Interestingly, however, in vivo studies of the role of the SRP and its receptor, with emphasis on the temporal progress of the pathway, elicited an alternative hypothesis [see (ii) above]. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes.
Collapse
Affiliation(s)
- Eitan Bibi
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.
| |
Collapse
|
15
|
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
|
16
|
Lustig Y, Wachtel C, Safro M, Liu L, Michaeli S. 'RNA walk' a novel approach to study RNA-RNA interactions between a small RNA and its target. Nucleic Acids Res 2009; 38:e5. [PMID: 19854950 PMCID: PMC2800229 DOI: 10.1093/nar/gkp872] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
In this study we describe a novel method to investigate the RNA–RNA interactions between a small RNA and its target that we termed ‘RNA walk’. The method is based on UV-induced AMT cross-linking in vivo followed by affinity selection of the hybrid molecules and mapping the intermolecular adducts by RT–PCR or real-time PCR. Domains carrying the cross-linked adducts fail to efficiently amplify by PCR compared with non-cross-linked domains. This method was calibrated and used to study the interaction between a special tRNA-like molecule (sRNA-85) that is part of the trypanosome signal recognition particle (SRP) complex and the ribosome. Four contact sites between sRNA-85 and rRNA were identified by ‘RNA walk’ and were further fine-mapped by primer extension. Two of the contact sites are expected; one contact site mimics the interaction of the mammalian Alu domain of SRP with the ribosome and the other contact sites include a canonical tRNA interaction. The two other cross-linked sites could not be predicted. We propose that ‘RNA walk, is a generic method to map target RNA small RNAs interactions in vivo.
Collapse
Affiliation(s)
- Yaniv Lustig
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
| | | | | | | | | |
Collapse
|
17
|
Abstract
The Signal Recognition Particle (SRP) plays a critical role in the sorting of nascent secretory and membrane proteins. Remarkably, this function has been conserved from bacteria, where SRP delivers proteins to the inner membrane, through to eukaryotes, where SRP is required for targeting of proteins to the endoplasmic reticulum. This review focuses on present understanding of SRP structure and function and the relationship between the two. Furthermore, the similarities and differences in the structure, function and cellular role of SRP in bacteria, chloroplasts, fungi and mammals will be stressed.
Collapse
Affiliation(s)
- Martin R Pool
- Faculty of Life Sciences, University of Manchester, Manchester, UK.
| |
Collapse
|
18
|
Field MC, Lumb JH, Adung'a VO, Jones NG, Engstler M. Chapter 1 Macromolecular Trafficking and Immune Evasion in African Trypanosomes. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2009; 278:1-67. [DOI: 10.1016/s1937-6448(09)78001-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
19
|
Trypanosome spliced-leader-associated RNA (SLA1) localization and implications for spliced-leader RNA biogenesis. EUKARYOTIC CELL 2008; 8:56-68. [PMID: 19028994 DOI: 10.1128/ec.00322-08] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Spliced-leader-associated RNA (SLA1) guides the pseudouridylation at position -12 (relative to the 5' splice site) of the spliced-leader (SL) RNA in all trypanosomatid species. Nevertheless, the exact role of this RNA is currently unknown. Here, we demonstrate that the absence of pseudouridine on Leptomonas collosoma SL RNA has only a minor effect on the ability of this RNA to function in trans splicing in vivo. To investigate the possible role of SLA1 during SL RNA biogenesis, the structure of the SL RNA was examined in permeable Trypanosoma brucei cells depleted for CBF5, the H/ACA pseudouridine synthase, lacking SLA1. Our results suggest that in the absence of SLA1, the SL RNA secondary structure is changed, as was detected by differential sensitivity to oligonucleotide-directed RNase H cleavage, suggesting that the association of SLA1 maintains the SL RNA in a structural form which is distinct from the structure of the SL RNA in the steady state. In T. brucei cells depleted for the SL RNA core protein SmD1, SL RNA first accumulates in large amounts in the nucleus and then is expelled to the cytoplasm. Here, we demonstrate by in vivo aminomethyltrimethyl UV cross-linking studies that under SmD1 depletion, SLA1 remains bound to SL RNA and escorts the SL RNA to the cytoplasm. In situ hybridization with SLA1 and SL RNA demonstrates colocalization between SLA1 and the SL RNA transcription factor tSNAP42, as well as with Sm proteins, suggesting that SLA1 associates with SL RNA early in its biogenesis. These results demonstrate that SLA1 is a unique chaperonic RNA that functions during the early biogenesis of SL RNA to maintain a structure that is most probably suitable for cap 4 modification.
Collapse
|
20
|
Goldshmidt H, Sheiner L, Bütikofer P, Roditi I, Uliel S, Günzel M, Engstler M, Michaeli S. Role of protein translocation pathways across the endoplasmic reticulum in Trypanosoma brucei. J Biol Chem 2008; 283:32085-98. [PMID: 18768469 DOI: 10.1074/jbc.m801499200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The translocation of secretory and membrane proteins across the endoplasmic reticulum (ER) membrane is mediated by co-translational (via the signal recognition particle (SRP)) and post-translational mechanisms. In this study, we investigated the relative contributions of these two pathways in trypanosomes. A homologue of SEC71, which functions in the post-translocation chaperone pathway in yeast, was identified and silenced by RNA interference. This factor is essential for parasite viability. In SEC71-silenced cells, signal peptide (SP)-containing proteins traversed the ER, but several were mislocalized, whereas polytopic membrane protein biogenesis was unaffected. Surprisingly trypanosomes can interchangeably utilize two of the pathways to translocate SP-containing proteins except for glycosylphosphatidylinositol-anchored proteins, whose level was reduced in SEC71-silenced cells but not in cells depleted for SRP68, an SRP-binding protein. Entry of SP-containing proteins to the ER was significantly blocked only in cells co-silenced for the two translocation pathways (SEC71 and SRP68). SEC63, a factor essential for both translocation pathways in yeast, was identified and silenced by RNA interference. SEC63 silencing affected entry to the ER of both SP-containing proteins and polytopic membrane proteins, suggesting that, as in yeast, this factor is essential for both translocation pathways in vivo. This study suggests that, unlike bacteria or other eukaryotes, trypanosomes are generally promiscuous in their choice of mechanism for translocating SP-containing proteins to the ER, although the SRP-independent pathway is favored for glycosylphosphatidylinositol-anchored proteins, which are the most abundant surface proteins in these parasites.
Collapse
Affiliation(s)
- Hanoch Goldshmidt
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Lakkaraju AKK, Mary C, Scherrer A, Johnson AE, Strub K. SRP keeps polypeptides translocation-competent by slowing translation to match limiting ER-targeting sites. Cell 2008; 133:440-51. [PMID: 18455985 DOI: 10.1016/j.cell.2008.02.049] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2007] [Revised: 01/08/2008] [Accepted: 02/14/2008] [Indexed: 11/18/2022]
Abstract
SRP is essential for targeting nascent chains to the endoplasmic reticulum, and it delays nascent chain elongation in cell-free translation systems. However, the significance of this function has remained unclear. We show that efficient protein translocation into the ER is incompatible with normal cellular translation rates due to rate-limiting concentrations of SRP receptor (SR). We complemented mammalian cells depleted of SRP14 by expressing mutant versions of the protein lacking the elongation arrest function. The absence of a delay caused inefficient targeting of preproteins leading to defects in secretion, depletion of proteins in the endogenous membranes, and reduced cell growth. The detrimental effects were reversed by either reducing the cellular protein synthesis rate or increasing SR expression. SRP therefore ensures that nascent chains remain translocation competent during the targeting time window dictated by SR. Since SRP-signal sequence affinities vary, the delay may also regulate which proteins are preferentially targeted.
Collapse
Affiliation(s)
- Asvin K K Lakkaraju
- Département de biologie cellulaire, Université de Genève, Sciences III, 1211 Geneva, Switzerland
| | | | | | | | | |
Collapse
|
22
|
Patrick KL, Luz PM, Ruan JP, Shi H, Ullu E, Tschudi C. Genomic rearrangements and transcriptional analysis of the spliced leader-associated retrotransposon in RNA interference-deficient Trypanosoma brucei. Mol Microbiol 2007; 67:435-47. [PMID: 18067542 DOI: 10.1111/j.1365-2958.2007.06057.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The Trypanosoma brucei genome is colonized by the site-specific non-LTR retrotransposon SLACS, or spliced leader-associated conserved sequence, which integrates exclusively into the spliced leader (SL) RNA genes. Although there is evidence that the RNA interference (RNAi) machinery regulates SLACS transcript levels, we do not know whether RNAi deficiency affects the genomic stability of SLACS, nor do we understand the mechanism of SLACS transcription. Here, we report that prolonged culturing of RNAi-deficient T. brucei cells, but not wild-type cells, results in genomic rearrangements of SLACS. Furthermore, two populations of SLACS transcripts persist in RNAi-deficient cells: a full-length transcript of approximately 7 kb and a heterogeneous population of small SLACS transcripts ranging in size from 450 to 550 nt. We provide evidence that SLACS transcription initiates at the +1 of the interrupted SL RNA gene and proceeds into the 5' UTR and open reading frame 1 (ORF1). This transcription is carried out by an RNA polymerase with alpha-amanitin sensitivity reminiscent of SL RNA synthesis and is dependent on the SL RNA promoter. Additionally, we show that both sense and antisense small SLACS transcripts originate from ORF1 and that they are associated with proteins in vivo. We speculate that the small SLACS transcripts serve as substrates for the production of siRNAs to regulate SLACS expression.
Collapse
Affiliation(s)
- Kristin L Patrick
- Department of Epidemiology and Public Health, Yale University Medical School, 295 Congress Avenue, New Haven, CT 06536-0812, USA
| | | | | | | | | | | |
Collapse
|
23
|
Dieci G, Fiorino G, Castelnuovo M, Teichmann M, Pagano A. The expanding RNA polymerase III transcriptome. Trends Genet 2007; 23:614-22. [PMID: 17977614 DOI: 10.1016/j.tig.2007.09.001] [Citation(s) in RCA: 376] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Revised: 09/14/2007] [Accepted: 09/17/2007] [Indexed: 11/19/2022]
Abstract
The role of RNA polymerase (Pol) III in eukaryotic transcription is commonly thought of as being restricted to a small set of highly expressed, housekeeping non-protein-coding (nc)RNA genes. Recent studies, however, have remarkably expanded the set of known Pol III-synthesized ncRNAs, suggesting that gene-specific Pol III regulation is more common than previously appreciated. Newly identified Pol III transcripts include small nucleolar RNAs, microRNAs, short interspersed nuclear element-encoded or tRNA-derived RNAs and novel classes of ncRNA that can display significant sequence complementarity to protein-coding genes and might thus regulate their expression. The extent of the Pol III transcriptome, the complexity of its regulation and its influence on cell physiology, development and disease are emerging as new areas for future research.
Collapse
Affiliation(s)
- Giorgio Dieci
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, Viale G.P. Usberti 23/A, 43100 Parma, Italy.
| | | | | | | | | |
Collapse
|
24
|
Lustig Y, Vagima Y, Goldshmidt H, Erlanger A, Ozeri V, Vince J, McConville MJ, Dwyer DM, Landfear SM, Michaeli S. Down-regulation of the trypanosomatid signal recognition particle affects the biogenesis of polytopic membrane proteins but not of signal peptide-containing proteins. EUKARYOTIC CELL 2007; 6:1865-75. [PMID: 17715370 PMCID: PMC2043396 DOI: 10.1128/ec.00134-07] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Protein translocation across the endoplasmic reticulum is mediated by the signal recognition particle (SRP). In this study, the SRP pathway in trypanosomatids was down-regulated by two approaches: RNA interference (RNAi) silencing of genes encoding SRP proteins in Trypanosoma brucei and overexpression of dominant-negative mutants of 7SL RNA in Leptomonas collosoma. The biogenesis of both signal peptide-containing proteins and polytopic membrane proteins was examined using endogenous and green fluorescent protein-fused proteins. RNAi silencing of SRP54 or SRP68 in T. brucei resulted in reduced levels of polytopic membrane proteins, but no effect on the level of signal peptide-containing proteins was observed. When SRP deficiency was achieved in L. collosoma by overexpression of dominant-negative mutated 7SL RNA, a major effect was observed on polytopic membrane proteins but not on signal peptide-containing proteins. This study included two trypanosomatid species, tested various protein substrates, and induced depletion of the SRP pathway by affecting either the levels of SRP binding proteins or that of SRP RNA. Our results demonstrate that, as in bacteria but in contrast to mammalian cells, the trypanosome SRP is mostly essential for the biogenesis of membrane proteins.
Collapse
Affiliation(s)
- Yaniv Lustig
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel
| | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Lustig Y, Sheiner L, Vagima Y, Goldshmidt H, Das A, Bellofatto V, Michaeli S. Spliced-leader RNA silencing: a novel stress-induced mechanism in Trypanosoma brucei. EMBO Rep 2007; 8:408-13. [PMID: 17347669 PMCID: PMC1852752 DOI: 10.1038/sj.embor.7400930] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Revised: 01/23/2007] [Accepted: 01/23/2007] [Indexed: 11/09/2022] Open
Abstract
The signal-recognition particle (SRP) mediates the translocation of membrane and secretory proteins across the endoplasmic reticulum upon interaction with the SRP receptor. In trypanosomes, the main RNA molecule is the spliced-leader (SL) RNA, which donates the SL sequence to all messenger RNA through trans-splicing. Here, we show that RNA interference silencing of the SRP receptor (SRalpha) in Trypanosoma brucei caused the accumulation of SRP on ribosomes and triggered silencing of SL RNA (SLS). SLS was elicited due to the failure of the SL RNA-specific transcription factor tSNAP42 to bind to its promoter. SL RNA reduction, in turn, eliminated mRNA processing and resulted in a significant reduction of all mRNA tested. SLS was also induced under pH stress and might function as a master regulator in trypanosomes. SLS is reminiscent of, but distinct from, the unfolded protein response and can potentially act as a new target for parasite eradication.
Collapse
MESH Headings
- Animals
- Hydrogen-Ion Concentration
- Promoter Regions, Genetic
- Protozoan Proteins/analysis
- Protozoan Proteins/genetics
- Protozoan Proteins/metabolism
- RNA Interference
- RNA, Messenger/metabolism
- RNA, Spliced Leader/antagonists & inhibitors
- RNA, Spliced Leader/genetics
- RNA, Spliced Leader/physiology
- Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/physiology
- Receptors, Peptide/antagonists & inhibitors
- Receptors, Peptide/genetics
- Receptors, Peptide/physiology
- Ribosomes/metabolism
- Transcription Factors/analysis
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Trypanosoma brucei brucei/chemistry
- Trypanosoma brucei brucei/genetics
- Trypanosoma brucei brucei/growth & development
Collapse
Affiliation(s)
- Yaniv Lustig
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Lilach Sheiner
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Yaron Vagima
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Hanoch Goldshmidt
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Anish Das
- Department of Microbiology and Molecular Genetics, UMDNJ-New Jersey Medical School, Newark, NJ, USA
| | - Vivian Bellofatto
- Department of Microbiology and Molecular Genetics, UMDNJ-New Jersey Medical School, Newark, NJ, USA
| | - Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
- Tel: +972 3 5318068; Fax: +972 3 7384058; E-mail:
| |
Collapse
|
26
|
Zaitseva L, Myers R, Fassati A. tRNAs promote nuclear import of HIV-1 intracellular reverse transcription complexes. PLoS Biol 2006; 4:e332. [PMID: 17020411 PMCID: PMC1584419 DOI: 10.1371/journal.pbio.0040332] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Accepted: 08/08/2006] [Indexed: 11/19/2022] Open
Abstract
Infection of non-dividing cells is a biological property of HIV-1 crucial for virus transmission and AIDS pathogenesis. This property depends on nuclear import of the intracellular reverse transcription and pre-integration complexes (RTCs/PICs). To identify cellular factors involved in nuclear import of HIV-1 RTCs, cytosolic extracts were fractionated by chromatography and import activity examined by the nuclear import assay. A near-homogeneous fraction was obtained, which was active in inducing nuclear import of purified and labeled RTCs. The active fraction contained tRNAs, mostly with defective 3' CCA ends. Such tRNAs promoted HIV-1 RTC nuclear import when synthesized in vitro. Active tRNAs were incorporated into and recovered from virus particles. Mutational analyses indicated that the anticodon loop mediated binding to the viral complex whereas the T-arm may interact with cellular factors involved in nuclear import. These tRNA species efficiently accumulated into the nucleus on their own in a energy- and temperature-dependent way. An HIV-1 mutant containing MLV gag did not incorporate tRNA species capable of inducing HIV-1 RTC nuclear import and failed to infect cell cycle-arrested cells. Here we provide evidence that at least some tRNA species can be imported into the nucleus of human cells and promote HIV-1 nuclear import.
Collapse
Affiliation(s)
- Lyubov Zaitseva
- Wohl Virion Centre, London, United Kingdom
- Medical Research Council Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Richard Myers
- Medical Research Council Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London, United Kingdom
- Centre of Postgenomic Virology, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Ariberto Fassati
- Wohl Virion Centre, London, United Kingdom
- Medical Research Council Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London, United Kingdom
| |
Collapse
|
27
|
Andersen ES, Rosenblad MA, Larsen N, Westergaard JC, Burks J, Wower IK, Wower J, Gorodkin J, Samuelsson T, Zwieb C. The tmRDB and SRPDB resources. Nucleic Acids Res 2006; 34:D163-8. [PMID: 16381838 PMCID: PMC1347504 DOI: 10.1093/nar/gkj142] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Maintained at the University of Texas Health Science Center at Tyler, Texas, the tmRNA database (tmRDB) is accessible at the URL http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html with mirror sites located at Auburn University, Auburn, Alabama (http://www.ag.auburn.edu/mirror/tmRDB/) and the Royal Veterinary and Agricultural University, Denmark (http://tmrdb.kvl.dk/). The signal recognition particle database (SRPDB) at http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html is mirrored at http://srpdb.kvl.dk/ and the University of Goteborg (http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html). The databases assist in investigations of the tmRNP (a ribonucleoprotein complex which liberates stalled bacterial ribosomes) and the SRP (a particle which recognizes signal sequences and directs secretory proteins to cell membranes). The curated tmRNA and SRP RNA alignments consider base pairs supported by comparative sequence analysis. Also shown are alignments of the tmRNA-associated proteins SmpB, ribosomal protein S1, alanyl-tRNA synthetase and Elongation Factor Tu, as well as the SRP proteins SRP9, SRP14, SRP19, SRP21, SRP54 (Ffh), SRP68, SRP72, cpSRP43, Flhf, SRP receptor (alpha) and SRP receptor (beta). All alignments can be easily examined using a new exploratory browser. The databases provide links to high-resolution structures and serve as depositories for structures obtained by molecular modeling.
Collapse
Affiliation(s)
| | - Magnus Alm Rosenblad
- Department of Medical Biochemistry, Goteborg UniversityBox 440, SE-405 30 Goteborg, Sweden
- SWEGENE Bioinformatics, Goteborg UniversityBox 413, SE-405 30 Goteborg, Sweden
| | - Niels Larsen
- Danish Genome InstituteGustav Wieds vej 10 C, DK-8000 Aarhus C, Denmark
| | - Jesper Cairo Westergaard
- Department of Natural Sciences, The Royal Veterinary and Agricultural UniversityThorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Jody Burks
- Department of Animal Sciences, Auburn UniversityAuburn, AL 36849-5415, USA
| | - Iwona K. Wower
- Department of Animal Sciences, Auburn UniversityAuburn, AL 36849-5415, USA
| | - Jacek Wower
- Department of Animal Sciences, Auburn UniversityAuburn, AL 36849-5415, USA
| | - Jan Gorodkin
- Center for Bioinformatics and Division of Genetics, IBHV, The Royal Veterinary and Agricultural UniversityGroennegaardsvej 3, 1870 Frederiksberg C, Denmark
| | - Tore Samuelsson
- Department of Medical Biochemistry, Goteborg UniversityBox 440, SE-405 30 Goteborg, Sweden
| | - Christian Zwieb
- Department of Molecular Biology, The University of Texas Health Science Center at Tyler11937 US Highway 271, Tyler, TX 75708-3154, USA
- To whom correspondence should be addressed. Tel: +1 903 877 7689; Fax: +1 903 877 5731;
| |
Collapse
|
28
|
Lustig Y, Goldshmidt H, Uliel S, Michaeli S. The Trypanosoma brucei signal recognition particle lacks the Alu-domain-binding proteins: purification and functional analysis of its binding proteins by RNAi. J Cell Sci 2006; 118:4551-62. [PMID: 16179612 DOI: 10.1242/jcs.02578] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Trypanosomes are protozoan parasites that have a major impact on human health and that of livestock. These parasites represent a very early branch in the eukaryotic lineage, and possess unique RNA processing mechanisms. The trypanosome signal recognition particle (SRP) is also unusual in being the first signal recognition particle described in nature to be comprised of two RNA molecules, the 7SL RNA and a tRNA-like molecule. In this study, we further elucidated the unique properties of this particle. The genes encoding three SRP proteins (SRP19, SRP72 and SRP68) were identified by bioinformatics analysis. Silencing of these genes by RNAi suggests that the SRP-mediated protein translocation pathway is essential for growth. The depletion of SRP72 and SRP68 induced sudden death, most probably as a result of toxicity due to the accumulation of the pre-SRP in the nucleolus. Purification of the trypanosome particle to homogeneity, by TAP-tagging, identified four SRP proteins (SRP72, SRP68, SRP54 and SRP19), but no Alu-domain-binding protein homologs. This study highlights the unique features of the trypanosome SRP complex and further supports the hypothesis that the tRNA-like molecule present in this particle may replace the function of the Alu-domain-binding proteins present in many eukaryotic SRP complexes.
Collapse
Affiliation(s)
- Yaniv Lustig
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | | | | | | |
Collapse
|
29
|
Ivens AC, Peacock CS, Worthey EA, Murphy L, Aggarwal G, Berriman M, Sisk E, Rajandream MA, Adlem E, Aert R, Anupama A, Apostolou Z, Attipoe P, Bason N, Bauser C, Beck A, Beverley SM, Bianchettin G, Borzym K, Bothe G, Bruschi CV, Collins M, Cadag E, Ciarloni L, Clayton C, Coulson RMR, Cronin A, Cruz AK, Davies RM, De Gaudenzi J, Dobson DE, Duesterhoeft A, Fazelina G, Fosker N, Frasch AC, Fraser A, Fuchs M, Gabel C, Goble A, Goffeau A, Harris D, Hertz-Fowler C, Hilbert H, Horn D, Huang Y, Klages S, Knights A, Kube M, Larke N, Litvin L, Lord A, Louie T, Marra M, Masuy D, Matthews K, Michaeli S, Mottram JC, Müller-Auer S, Munden H, Nelson S, Norbertczak H, Oliver K, O'neil S, Pentony M, Pohl TM, Price C, Purnelle B, Quail MA, Rabbinowitsch E, Reinhardt R, Rieger M, Rinta J, Robben J, Robertson L, Ruiz JC, Rutter S, Saunders D, Schäfer M, Schein J, Schwartz DC, Seeger K, Seyler A, Sharp S, Shin H, Sivam D, Squares R, Squares S, Tosato V, Vogt C, Volckaert G, Wambutt R, Warren T, Wedler H, Woodward J, Zhou S, Zimmermann W, Smith DF, Blackwell JM, Stuart KD, Barrell B, Myler PJ. The genome of the kinetoplastid parasite, Leishmania major. Science 2005; 309:436-42. [PMID: 16020728 PMCID: PMC1470643 DOI: 10.1126/science.1112680] [Citation(s) in RCA: 1043] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Leishmania species cause a spectrum of human diseases in tropical and subtropical regions of the world. We have sequenced the 36 chromosomes of the 32.8-megabase haploid genome of Leishmania major (Friedlin strain) and predict 911 RNA genes, 39 pseudogenes, and 8272 protein-coding genes, of which 36% can be ascribed a putative function. These include genes involved in host-pathogen interactions, such as proteolytic enzymes, and extensive machinery for synthesis of complex surface glycoconjugates. The organization of protein-coding genes into long, strand-specific, polycistronic clusters and lack of general transcription factors in the L. major, Trypanosoma brucei, and Trypanosoma cruzi (Tritryp) genomes suggest that the mechanisms regulating RNA polymerase II-directed transcription are distinct from those operating in other eukaryotes, although the trypanosomatids appear capable of chromatin remodeling. Abundant RNA-binding proteins are encoded in the Tritryp genomes, consistent with active posttranscriptional regulation of gene expression.
Collapse
MESH Headings
- Animals
- Chromatin/genetics
- Chromatin/metabolism
- Gene Expression Regulation
- Genes, Protozoan
- Genes, rRNA
- Genome, Protozoan
- Glycoconjugates/biosynthesis
- Glycoconjugates/metabolism
- Leishmania major/chemistry
- Leishmania major/genetics
- Leishmania major/metabolism
- Leishmaniasis, Cutaneous/parasitology
- Lipid Metabolism
- Membrane Proteins/biosynthesis
- Membrane Proteins/chemistry
- Membrane Proteins/genetics
- Membrane Proteins/metabolism
- Molecular Sequence Data
- Multigene Family
- Protein Biosynthesis
- Protein Processing, Post-Translational
- Protozoan Proteins/biosynthesis
- Protozoan Proteins/chemistry
- Protozoan Proteins/genetics
- Protozoan Proteins/metabolism
- RNA Processing, Post-Transcriptional
- RNA Splicing
- RNA, Protozoan/genetics
- RNA, Protozoan/metabolism
- Sequence Analysis, DNA
- Transcription, Genetic
Collapse
Affiliation(s)
- Alasdair C Ivens
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Rubio MAT, Alfonzo JD. Editing and modification in trypanosomatids: the reshaping of non-coding RNAs. FINE-TUNING OF RNA FUNCTIONS BY MODIFICATION AND EDITING 2005. [DOI: 10.1007/b106363] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
|
31
|
Huck L, Scherrer A, Terzi L, Johnson AE, Bernstein HD, Cusack S, Weichenrieder O, Strub K. Conserved tertiary base pairing ensures proper RNA folding and efficient assembly of the signal recognition particle Alu domain. Nucleic Acids Res 2004; 32:4915-24. [PMID: 15383645 PMCID: PMC519120 DOI: 10.1093/nar/gkh837] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Proper folding of the RNA is an essential step in the assembly of functional ribonucleoprotein complexes. We examined the role of conserved base pairs formed between two distant loops in the Alu portion of the mammalian signal recognition particle RNA (SRP RNA) in SRP assembly and functions. Mutations disrupting base pairing interfere with folding of the Alu portion of the SRP RNA as monitored by probing the RNA structure and the binding of the protein SRP9/14. Complementary mutations rescue the defect establishing a role of the tertiary loop-loop interaction in RNA folding. The same mutations in the Alu domain have no major effect on binding of proteins to the S domain suggesting that the S domain can fold independently. Once assembled into a complete SRP, even particles that contain mutant RNA are active in arresting nascent chain elongation and translocation into microsomes, and, therefore, tertiary base pairing does not appear to be essential for these activities. Our results suggest a model in which the loop-loop interaction and binding of the protein SRP9/14 play an important role in the early steps of SRP RNA folding and assembly.
Collapse
Affiliation(s)
- Laurent Huck
- Département de Biologie Cellulaire, Université de Genève, CH-1211 Genève 4, Switzerland
| | | | | | | | | | | | | | | |
Collapse
|
32
|
Rosenblad MA, Zwieb C, Samuelsson T. Identification and comparative analysis of components from the signal recognition particle in protozoa and fungi. BMC Genomics 2004; 5:5. [PMID: 14720308 PMCID: PMC331402 DOI: 10.1186/1471-2164-5-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2003] [Accepted: 01/13/2004] [Indexed: 11/30/2022] Open
Abstract
Background The signal recognition particle (SRP) is a ribonucleoprotein complex responsible for targeting proteins to the ER membrane. The SRP of metazoans is well characterized and composed of an RNA molecule and six polypeptides. The particle is organized into the S and Alu domains. The Alu domain has a translational arrest function and consists of the SRP9 and SRP14 proteins bound to the terminal regions of the SRP RNA. So far, our understanding of the SRP and its evolution in lower eukaryotes such as protozoa and yeasts has been limited. However, genome sequences of such organisms have recently become available, and we have now analyzed this information with respect to genes encoding SRP components. Results A number of SRP RNA and SRP protein genes were identified by an analysis of genomes of protozoa and fungi. The sequences and secondary structures of the Alu portion of the RNA were found to be highly variable. Furthermore, proteins SRP9/14 appeared to be absent in certain species. Comparative analysis of the SRP RNAs from different Saccharomyces species resulted in models which contain features shared between all SRP RNAs, but also a new secondary structure element in SRP RNA helix 5. Protein SRP21, previously thought to be present only in Saccharomyces, was shown to be a constituent of additional fungal genomes. Furthermore, SRP21 was found to be related to metazoan and plant SRP9, suggesting that the two proteins are functionally related. Conclusions Analysis of a number of not previously annotated SRP components show that the SRP Alu domain is subject to a more rapid evolution than the other parts of the molecule. For instance, the RNA portion is highly variable and the protein SRP9 seems to have evolved into the SRP21 protein in fungi. In addition, we identified a secondary structure element in the Sacccharomyces RNA that has been inserted close to the Alu region. Together, these results provide important clues as to the structure, function and evolution of SRP.
Collapse
Affiliation(s)
- Magnus Alm Rosenblad
- Department of Medical Biochemistry, Goteborg University, Box 440, SE-405 30 Goteborg, Sweden
| | - Christian Zwieb
- Department of Molecular Biology, The University of Texas Health Science Center at Tyler, 11937 US Highway 271, Tyler TX 75708-3154, U.S.A
| | - Tore Samuelsson
- Department of Medical Biochemistry, Goteborg University, Box 440, SE-405 30 Goteborg, Sweden
| |
Collapse
|
33
|
Van Nues RW, Brown JD. Saccharomyces SRP RNA secondary structures: a conserved S-domain and extended Alu-domain. RNA (NEW YORK, N.Y.) 2004; 10:75-89. [PMID: 14681587 PMCID: PMC1370520 DOI: 10.1261/rna.5137904] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2003] [Accepted: 09/22/2003] [Indexed: 05/20/2023]
Abstract
The contribution made by the RNA component of signal recognition particle (SRP) to its function in protein targeting is poorly understood. We have generated a complete secondary structure for Saccharomyces cerevisiae SRP RNA, scR1. The structure conforms to that of other eukaryotic SRP RNAs. It is rod-shaped with, at opposite ends, binding sites for proteins required for the SRP functions of signal sequence recognition (S-domain) and translational elongation arrest (Alu-domain). Micrococcal nuclease digestion of purified S. cerevisiae SRP separated the S-domain of the RNA from the Alu-domain as a discrete fragment. The Alu-domain resolved into several stable fragments indicating a compact structure. Comparison of scR1 with SRP RNAs of five yeast species related to S. cerevisiae revealed the S-domain to be the most conserved region of the RNA. Extending data from nuclease digestion with phylogenetic comparison, we built the secondary structure model for scR1. The Alu-domain contains large extensions, including a sequence with hallmarks of an expansion segment. Evolutionarily conserved bases are placed in the Alu- and S-domains as in other SRP RNAs, the exception being an unusual GU(4)A loop closing the helix onto which the signal sequence binding Srp54p assembles (domain IV). Surprisingly, several mutations within the predicted Srp54p binding site failed to disrupt SRP function in vivo. However, the strength of the Srp54p-scR1 and, to a lesser extent, Sec65p-scR1 interaction was decreased in these mutant particles. The availability of a secondary structure for scR1 will facilitate interpretation of data from genetic analysis of the RNA.
Collapse
Affiliation(s)
- Rob W Van Nues
- School of Cell and Molecular Biosciences, The Medical School, University of Newcastle, Newcastle Upon Tyne, NE2 4HH, UK
| | | |
Collapse
|
34
|
Mandelboim M, Barth S, Biton M, Liang XH, Michaeli S. Silencing of Sm proteins in Trypanosoma brucei by RNA interference captured a novel cytoplasmic intermediate in spliced leader RNA biogenesis. J Biol Chem 2003; 278:51469-78. [PMID: 14532264 DOI: 10.1074/jbc.m308997200] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In Trypanosoma brucei the small nuclear (sn) RNAs U1, U2, U4, and U5, as well as the spliced leader (SL) RNA, bind the seven Sm canonical proteins carrying the consensus Sm motif. To determine the function of these proteins in snRNA and SL RNA biogenesis, two of the Sm core proteins, SmE and SmD1, were silenced by RNAi. Surprisingly, whereas the level of all snRNAs, including U1, U2, U4, and U5 was reduced during silencing, the level of SL RNA was dramatically elevated, but the levels of U6 and spliced leader-associated RNA (SLA1) remained unchanged. The SL RNA that had accumulated in silenced cells lacked modification at the cap4 nucleotide but harbored modifications at the cap1 and cap2 nucleotides and carried the characteristic psi. This SL RNA possessed a longer tail and had accumulated in the cytoplasm in 10 and 50 S particles that were found by in situ hybridization to be present in "speckles." We propose a model for SL RNA biogenesis involving a cytoplasmic phase and suggest that the trypanosome-specific "cap4" nucleotides function as a signal for export and import of SL RNA out and into the nucleus. The SL RNA biogenesis pathway differs from that of U sn ribonucleoproteins (RNPs) in that it is the only RNA that binds Sm proteins that were stabilized under Sm depletion in a novel RNP, which we termed SL RNP-C.
Collapse
Affiliation(s)
- Michal Mandelboim
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | | | | | | | | |
Collapse
|