4601
|
Abstract
Human cytomegalovirus (HCMV) has become a paradigm for viral immune evasion due to its unique multitude of immune-modulatory strategies. HCMV modulates the innate as well as adaptive immune response at every step of its life cycle. It dampens the induction of antiviral interferon-induced genes by several mechanisms. Further striking is the multitude of genes and strategies devoted to modulating and escaping the cellular immune response. Several genes are independently capable of inhibiting antigen presentation to cytolytic T cells by downregulating MHC class I. Recent data revealed an astounding variety of methods in triggering or inhibiting activatory and inhibitory receptors found on NK cells, NKT cells, T cells as well as auxiliary cells of the immune system. The multitude and complexity of these mechanisms is fascinating and continues to reveal novel insights into the host-pathogen interaction and novel cell biological and immunological concepts.
Collapse
Affiliation(s)
- C Powers
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, OR 97201, USA
| | | | | | | |
Collapse
|
4602
|
Affiliation(s)
- Jay A Nelson
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, USA
| |
Collapse
|
4603
|
Abstract
Bioinformatic and direct cloning approaches have led to the identification of over 100 novel miRNAs expressed in DNA viruses, although the function of the majority of these small regulatory RNA molecules is unclear. Recently, a number of reports have now identified potential targets of viral miRNAs, including cellular and viral genes as well as an ortholog of an important immuno-regulatory cellular miRNA. In this review, we will cover the identification and characterization of miRNAs expressed in the herpesvirus family and discuss the potential significance of their role in viral infection.
Collapse
|
4604
|
Buck AH, Santoyo-Lopez J, Robertson KA, Kumar DS, Reczko M, Ghazal P. Discrete clusters of virus-encoded micrornas are associated with complementary strands of the genome and the 7.2-kilobase stable intron in murine cytomegalovirus. J Virol 2007; 81:13761-70. [PMID: 17928340 PMCID: PMC2168849 DOI: 10.1128/jvi.01290-07] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2007] [Accepted: 10/01/2007] [Indexed: 01/07/2023] Open
Abstract
The prevalence and importance of microRNAs (miRNAs) in viral infection are increasingly relevant. Eleven miRNAs were previously identified in human cytomegalovirus (HCMV); however, miRNA content in murine CMV (MCMV), which serves as an important in vivo model for CMV infection, has not previously been examined. We have cloned and characterized 17 novel miRNAs that originate from at least 12 precursor miRNAs in MCMV and are not homologous to HCMV miRNAs. In parallel, we applied a computational analysis, using a support vector machine approach, to identify potential precursor miRNAs in MCMV. Four of the top 10 predicted precursor sequences were cloned in this study, and the combination of computational and cloning analysis demonstrates that MCMV has the capacity to encode miRNAs clustered throughout the genome. On the basis of drug sensitivity experiments for resolving the kinetic class of expression, we show that the MCMV miRNAs are both early and late gene products. Notably, the MCMV miRNAs occur on complementary strands of the genome in specific regions, a feature which has not previously been observed for viral miRNAs. One cluster of miRNAs occurs in close proximity to the 5' splice site of the previously identified 7.2-kb stable intron, implying a variety of potential regulatory mechanisms for MCMV miRNAs.
Collapse
Affiliation(s)
- Amy H Buck
- Division of Pathway Medicine, University of Edinburgh, Edinburgh, United Kingdom.
| | | | | | | | | | | |
Collapse
|
4605
|
Abstract
Immune cells with specific functions and abilities are vital to cancer treatment prevention. Although there have been many accomplishments made in the areas of immunotherapy and immunobiology of myeloma, there are still many obstacles in the way of conceptualizing the interrelationships between immune cells and tumor cells. To provide better understanding of these concepts and to move toward improved therapies for myeloma, cell-based therapeutic approaches should be developed.
Collapse
Affiliation(s)
- Nikhil C. Munshi
- Associate Director, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA
- Associate Professor, Department of Medicine, Harvard Medical School, Boston, MA
- Staff Physician, VA Boston Healthcare System, Harvard Medical School, Boston, MA
| | - Rao H. Prabhala
- Instructor, Department of Medicine, Brigham and Women's Hospital/Dana Farber Cancer Institute, Boston, MA
- Research Health Scientist, VA Boston Healthcare System, Harvard Medical School, Boston, MA
| |
Collapse
|
4606
|
Haanstra JR, Stewart M, Luu VD, van Tuijl A, Westerhoff HV, Clayton C, Bakker BM. Control and regulation of gene expression: quantitative analysis of the expression of phosphoglycerate kinase in bloodstream form Trypanosoma brucei. J Biol Chem 2007; 283:2495-507. [PMID: 17991737 DOI: 10.1074/jbc.m705782200] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Isoenzymes of phosphoglycerate kinase in Trypanosoma brucei are differentially expressed in its two main life stages. This study addresses how the organism manages to make sufficient amounts of the isoenzyme with the correct localization, which processes (transcription, splicing, and RNA degradation) control the levels of mRNAs, and how the organism regulates the switch in isoform expression. For this, we combined new quantitative measurements of phosphoglycerate kinase mRNA abundance, RNA precursor stability, trans splicing, and ribosome loading with published data and made a kinetic computer model. For the analysis of regulation we extended regulation analysis. Although phosphoglycerate kinase mRNAs are present at surprisingly low concentrations (e.g. 12 molecules per cell), its protein is highly abundant. Substantial control of mRNA and protein levels was exerted by both mRNA synthesis and degradation, whereas splicing and precursor degradation had little control on mRNA and protein concentrations. Yet regulation of mRNA levels does not occur by transcription, but by adjusting mRNA degradation. The contribution of splicing to regulation is negligible, as for all cases where splicing is faster than RNA precursor degradation.
Collapse
Affiliation(s)
- Jurgen R Haanstra
- Vrije Universiteit, Biocentrum Amsterdam, De Boelelaan 1085, Amsterdam, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
4607
|
Elucidating the role of C/D snoRNA in rRNA processing and modification in Trypanosoma brucei. EUKARYOTIC CELL 2007; 7:86-101. [PMID: 17981991 DOI: 10.1128/ec.00215-07] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Most eukaryotic C/D small nucleolar RNAs (snoRNAs) guide 2'-O methylation (Nm) on rRNA and are also involved in rRNA processing. The four core proteins that bind C/D snoRNA in Trypanosoma brucei are fibrillarin (NOP1), NOP56, NOP58, and SNU13. Silencing of NOP1 by RNA interference identified rRNA-processing and modification defects that caused lethality. Systematic mapping of 2'-O-methyls on rRNA revealed the existence of hypermethylation at certain positions of the rRNA in the bloodstream form of the parasites, suggesting that this modification may assist the parasites in coping with the major temperature changes during cycling between their insect and mammalian hosts. The rRNA-processing defects of NOP1-depleted cells suggest the involvement of C/D snoRNA in trypanosome-specific rRNA-processing events to generate the small rRNA fragments. MRP RNA, which is involved in rRNA processing, was identified in this study in one of the snoRNA gene clusters, suggesting that trypanosomes utilize a combination of unique C/D snoRNAs and conserved snoRNAs for rRNA processing.
Collapse
|
4608
|
Mouse cytomegalovirus microRNAs dominate the cellular small RNA profile during lytic infection and show features of posttranscriptional regulation. J Virol 2007; 81:13771-82. [PMID: 17942535 DOI: 10.1128/jvi.01313-07] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
MicroRNAs (miRNAs) are small, noncoding RNA molecules that regulate gene expression at the posttranscriptional level. Originally identified in a variety of organisms ranging from plants to mammals, miRNAs have recently been identified in several viruses. Viral miRNAs may play a role in modulating both viral and host gene expression. Here, we report on the identification and characterization of 18 viral miRNAs from mouse fibroblasts lytically infected with the murine cytomegalovirus (MCMV). The MCMV miRNAs are expressed at early times of infection and are scattered in small clusters throughout the genome with up to four distinct miRNAs processed from a single transcript. No significant homologies to human CMV-encoded miRNAs were found. Remarkably, as soon as 24 h after infection, MCMV miRNAs constituted about 35% of the total miRNA pool, and at 72 h postinfection, this proportion was increased to more than 60%. However, despite the abundance of viral miRNAs during the early phase of infection, the expression of some MCMV miRNAs appeared to be regulated. Hence, for three miRNAs we observed polyuridylation of their 3' end, coupled to subsequent degradation. Individual knockout mutants of two of the most abundant MCMV miRNAs, miR-m01-4 and miR-M44-1, or a double knockout mutant of miR-m21-1 and miR-M23-2, incurred no or only a very mild growth deficit in murine embryonic fibroblasts in vitro.
Collapse
|
4609
|
Soifer HS, Rossi JJ, Saetrom P. MicroRNAs in disease and potential therapeutic applications. Mol Ther 2007; 15:2070-9. [PMID: 17878899 DOI: 10.1038/sj.mt.6300311] [Citation(s) in RCA: 289] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are 21-24 nucleotide (nt) duplex RNAs that are created from precursor transcripts by subsequent processing steps mediated by members of the RNAseIII family, Drosha and Dicer. One of the two strands is incorporated into the active sites of the Argonaute family of proteins, where it serves as a guide for Watson-Crick base pairing with complementary sequences in target messenger RNAs (mRNAs). In mammals, the majority of miRNAs guide the RNA-induced silencing complex (RISC) to the 3' untranslated regions (UTRs) of mRNA targets, with the consequence that translation of the target mRNAs is inhibited. The importance of miRNAs in normal cellular development and metabolism is only now being realized. miRNA deficiencies or excesses have been correlated with a number of clinically important diseases ranging from myocardial infarction to cancers. The loss or gain of miRNA function can be caused by a single point mutation in either the miRNA or its target or by epigenetic silencing of primary miRNA transcription units. This review summarizes miRNA biogenesis and biology, explores the potential roles miRNAs can play in a variety of diseases, and suggests some therapeutic applications for restoring or inhibiting miRNA function.
Collapse
Affiliation(s)
- Harris S Soifer
- 1Division of Molecular Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
| | | | | |
Collapse
|
4610
|
Abstract
Plants and invertebrates can protect themselves from viral infection through RNA silencing. This antiviral immunity involves production of virus-derived small interfering RNAs (viRNAs) and results in specific silencing of viruses by viRNA-guided effector complexes. The proteins required for viRNA production as well as several key downstream components of the antiviral immunity pathway have been identified in plants, flies, and worms. Meanwhile, viral mechanisms to suppress this small RNA-directed immunity by viruses are being elucidated, thereby illuminating an ongoing molecular arms race that likely impacts the evolution of both viral and host genomes.
Collapse
Affiliation(s)
- Shou-Wei Ding
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
- Correspondence: (S.W.D.), (O.V.)
| | - Olivier Voinnet
- Institut de Biologie Moléculaire des plantes, CNRS, Université Louis Pasteur, 67084 Strasbourg Cedex, France
- Correspondence: (S.W.D.), (O.V.)
| |
Collapse
|
4611
|
Ahmad S. Evasive manoeuvres. Nat Rev Immunol 2007. [DOI: 10.1038/nri2157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
4612
|
Research Highlights. Nat Immunol 2007. [DOI: 10.1038/ni0907-911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
4613
|
Evasive manoeuvres. Nat Rev Microbiol 2007. [DOI: 10.1038/nrmicro1735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
4614
|
Affiliation(s)
- Bryan R Cullen
- Center for Virology and Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27707, USA.
| |
Collapse
|
4615
|
Zamudio JR, Mittra B, Foldynová-Trantírková S, Zeiner GM, Lukes J, Bujnicki JM, Sturm NR, Campbell DA. The 2'-O-ribose methyltransferase for cap 1 of spliced leader RNA and U1 small nuclear RNA in Trypanosoma brucei. Mol Cell Biol 2007; 27:6084-92. [PMID: 17606627 PMCID: PMC1952150 DOI: 10.1128/mcb.00647-07] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
mRNA cap 1 2'-O-ribose methylation is a widespread modification that is implicated in processing, trafficking, and translational control in eukaryotic systems. The eukaryotic enzyme has yet to be identified. In kinetoplastid flagellates trans-splicing of spliced leader (SL) to polycistronic precursors conveys a hypermethylated cap 4, including a cap 0 m7G and seven additional methylations on the first 4 nucleotides, to all nuclear mRNAs. We report the first eukaryotic cap 1 2'-O-ribose methyltransferase, TbMTr1, a member of a conserved family of viral and eukaryotic enzymes. Recombinant TbMTr1 methylates the ribose of the first nucleotide of an m7G-capped substrate. Knockdowns and null mutants of TbMTr1 in Trypanosoma brucei grow normally, with loss of 2'-O-ribose methylation at cap 1 on substrate SL RNA and U1 small nuclear RNA. TbMTr1-null cells have an accumulation of cap 0 substrate without further methylation, while spliced mRNA is modified efficiently at position 4 in the absence of 2'-O-ribose methylation at position 1; downstream cap 4 methylations are independent of cap 1. Based on TbMTr1-green fluorescent protein localization, 2'-O-ribose methylation at position 1 occurs in the nucleus. Accumulation of 3'-extended SL RNA substrate indicates a delay in processing and suggests a synergistic role for cap 1 in maturation.
Collapse
Affiliation(s)
- Jesse R Zamudio
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, 609 Charles E. Young Drive East, University of California at Los Angeles, Los Angeles, CA 90095-1489, USA
| | | | | | | | | | | | | | | |
Collapse
|
4616
|
Pasternack DA, Sayegh J, Clarke S, Read LK. Evolutionarily divergent type II protein arginine methyltransferase in Trypanosoma brucei. EUKARYOTIC CELL 2007; 6:1665-81. [PMID: 17601874 PMCID: PMC2043365 DOI: 10.1128/ec.00133-07] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Protein arginine methylation is a posttranslational modification that impacts cellular functions, such as RNA processing, transcription, DNA repair, and signal transduction. The majority of our knowledge regarding arginine methylation derives from studies of yeast and mammals. Here, we describe a protein arginine N-methyltransferase (PRMT), TbPRMT5, from the early-branching eukaryote Trypanosoma brucei. TbPRMT5 shares the greatest sequence similarity with PRMT5 and Skb1 type II enzymes from humans and Schizosaccharomyces pombe, respectively, although it is significantly divergent at the amino acid level from its mammalian and yeast counterparts. Recombinant TbPRMT5 displays broad substrate specificity in vitro, including methylation of a mitochondrial-gene-regulatory protein, RBP16. TbPRMT5 catalyzes the formation of omega-N(G)-monomethylarginine and symmetric omega-N(G),N(G')-dimethylarginine and does not require trypanosome cofactors for this activity. These data establish that type II PRMTs evolved early in the eukaryotic lineage. In vivo, TbPRMT5 is constitutively expressed in the bloodstream form and procyclic-form (insect host) life stages of the parasite and localizes to the cytoplasm. Genetic disruption via RNA interference in procyclic-form trypanosomes indicates that TbPRMT5 is not essential for growth in this life cycle stage. TbPRMT5-TAP ectopically expressed in procyclic-form trypanosomes is present in high-molecular-weight complexes and associates with an RG domain-containing DEAD box protein related to yeast Ded1 and two kinetoplastid-specific proteins. Thus, TbPRMT5 is likely to be involved in novel methylation-regulated functions in trypanosomes, some of which may include RNA processing and/or translation.
Collapse
Affiliation(s)
- Deborah A Pasternack
- Department of Microbiology and Immunology and Witebsky Center for Microbial Pathogenesis and Immunology, State University of New York School of Medicine, Buffalo, New York 14214, USA
| | | | | | | |
Collapse
|
4617
|
Ruan JP, Ullu E, Tschudi C. Characterization of the Trypanosoma brucei cap hypermethylase Tgs1. Mol Biochem Parasitol 2007; 155:66-9. [PMID: 17610965 PMCID: PMC2075351 DOI: 10.1016/j.molbiopara.2007.05.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2007] [Revised: 05/04/2007] [Accepted: 05/17/2007] [Indexed: 10/23/2022]
Abstract
Many U-snRNAs contain a hypermodified 2,2,7-trimethylguanosine (TMG) cap structure, which is formed by post-transcriptional methylation of an m(7)G cap. At present, little is known about the maturation of U-snRNAs in trypanosomes. The current evidence is consistent with the primary transcript containing an m(7)G moiety, but it is not clear whether the conversion of m(7)G to TMG takes place in the cytoplasm or in the nucleus. To address this issue, we characterized the Trypanosoma brucei homologue of the trimethylguanosine synthase (TbTgs1), a 28kDa protein, which is mainly composed of the conserved catalytic domain and lacks a large N-terminal domain present in higher eukaryotes. A GFP fusion with TbTgs1 revealed that this protein localizes throughout the nucleoplasm, as well as in one or two dots outside the nucleolus and RNAi-mediated downregulation of TbTgs1 suggests that this protein is responsible for hypermethylation of the m(7)G cap of both snRNAs and snoRNAs.
Collapse
Affiliation(s)
- Jia-peng Ruan
- Department of Epidemiology and Public Health, Yale University Medical School, 295 Congress Avenue, New Haven, CT 06536-0812, USA
| | | | | |
Collapse
|
4618
|
Zhang H, Hou Y, Miranda L, Campbell DA, Sturm NR, Gaasterland T, Lin S. Spliced leader RNA trans-splicing in dinoflagellates. Proc Natl Acad Sci U S A 2007; 104:4618-23. [PMID: 17360573 PMCID: PMC1838650 DOI: 10.1073/pnas.0700258104] [Citation(s) in RCA: 290] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Indexed: 12/31/2022] Open
Abstract
Through the analysis of hundreds of full-length cDNAs from fifteen species representing all major orders of dinoflagellates, we demonstrate that nuclear-encoded mRNAs in all species, from ancestral to derived lineages, are trans-spliced with the addition of the 22-nt conserved spliced leader (SL), DCCGUAGCCAUUUUGGCUCAAG (D = U, A, or G), to the 5' end. SL trans-splicing has been documented in a limited but diverse number of eukaryotes, in which this process makes it possible to translate polycistronically transcribed nuclear genes. In SL trans-splicing, SL-donor transcripts (SL RNAs) contain two functional domains: an exon that provides the SL for mRNA and an intron that contains a spliceosomal (Sm) binding site. In dinoflagellates, SL RNAs are unusually short at 50-60 nt, with a conserved Sm binding motif (AUUUUGG) located in the SL (exon) rather than the intron. The initiation nucleotide is predominantly U or A, an unusual feature that may affect capping, and hence the translation and stability of the recipient mRNA. The core SL element was found in mRNAs coding for a diverse array of proteins. Among the transcripts characterized were three homologs of Sm-complex subunits, indicating that the role of the Sm binding site is conserved, even if the location on the SL is not. Because association with an Sm-complex often signals nuclear import for U-rich small nuclear RNAs, it is unclear how this Sm binding site remains on mature mRNAs without impeding cytosolic localization or translation of the latter. The sequences reported in this paper have been deposited in the GenBank database (accession nos. AF 512889, DQ 864761-DQ 864971, DQ 867053-DQ 867070, DQ 884413-DQ 884451, EF 133854-EF 133905, EF 133961-EF 134003, EF 134083-EF 134402, EF 141835, and EF 143070-EF 143105).
Collapse
Affiliation(s)
- Huan Zhang
- *Department of Marine Sciences, University of Connecticut, 1080 Shennecossett Road, Groton, CT 06340
| | - Yubo Hou
- *Department of Marine Sciences, University of Connecticut, 1080 Shennecossett Road, Groton, CT 06340
| | - Lilibeth Miranda
- *Department of Marine Sciences, University of Connecticut, 1080 Shennecossett Road, Groton, CT 06340
| | - David A. Campbell
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, 609 Charles Young Drive, Los Angeles, CA 90095; and
| | - Nancy R. Sturm
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, 609 Charles Young Drive, Los Angeles, CA 90095; and
| | - Terry Gaasterland
- Scripps Institution of Oceanography, University of California at San Diego, 8602 La Jolla Shores Drive, La Jolla, CA 92037
| | - Senjie Lin
- *Department of Marine Sciences, University of Connecticut, 1080 Shennecossett Road, Groton, CT 06340
| |
Collapse
|
4619
|
Tkacz ID, Lustig Y, Stern MZ, Biton M, Salmon-Divon M, Das A, Bellofatto V, Michaeli S. Identification of novel snRNA-specific Sm proteins that bind selectively to U2 and U4 snRNAs in Trypanosoma brucei. RNA (NEW YORK, N.Y.) 2007; 13:30-43. [PMID: 17105994 PMCID: PMC1705756 DOI: 10.1261/rna.174307] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In eukaryotes the seven Sm core proteins bind to U1, U2, U4, and U5 snRNAs. In Trypanosoma brucei, Sm proteins have been implicated in binding both spliced leader (SL) and U snRNAs. In this study, we examined the function of these Sm proteins using RNAi silencing and protein purification. RNAi silencing of each of the seven Sm genes resulted in accumulation of SL RNA as well as reduction of several U snRNAs. Interestingly, U2 was unaffected by the loss of SmB, and both U2 and U4 snRNAs were unaffected by the loss of SmD3, suggesting that these snRNAs are not bound by the heptameric Sm complex that binds to U1, U5, and SL RNA. RNAi silencing and protein purification showed that U2 and U4 snRNAs were bound by a unique set of Sm proteins that we termed SSm (specific spliceosomal Sm proteins). This is the first study that identifies specific core Sm proteins that bind only to a subset of spliceosomal snRNAs.
Collapse
Affiliation(s)
- Itai Dov Tkacz
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | | | | | | | | | | | | | | |
Collapse
|
4620
|
Biton M, Mandelboim M, Arvatz G, Michaeli S. RNAi interference of XPO1 and Sm genes and their effect on the spliced leader RNA in Trypanosoma brucei. Mol Biochem Parasitol 2006; 150:132-43. [PMID: 16916550 DOI: 10.1016/j.molbiopara.2006.07.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2006] [Revised: 07/03/2006] [Accepted: 07/11/2006] [Indexed: 12/30/2022]
Abstract
In trypanosomes, trans-splicing is a major essential RNA-processing mechanism that involves the addition of a spliced leader sequence to all mRNAs from a small RNA species, known as the spliced leader RNA (SL RNA). SL RNA maturation is poorly understood and it is not clear where assembly with Sm proteins takes place. In this study, we followed the localization of the SL RNA during knockdown of Sm proteins and XPO1, which in metazoa functions in transport of mRNA and U snRNAs from the nucleus to the cytoplasm. We found that XPO1 has no role in SL RNA biogenesis in wild-type cells, or when the cells are depleted of Sm proteins. During Sm depletion, 'defective' SL RNA lacking cap modification at position +4 first accumulates in the nucleus, suggesting that Sm assembly on SL RNA most probably takes place in this compartment. Only after massive nuclear accumulation is the 'defective' SL RNA exported to the cytoplasm to form SL RNP-C, which may be a route to dispose of SL RNA when its normal biogenesis is blocked.
Collapse
MESH Headings
- Active Transport, Cell Nucleus
- Animals
- Autoantigens/genetics
- Autoantigens/physiology
- Cell Nucleus/chemistry
- Cell Nucleus/metabolism
- Cytoplasm/metabolism
- Fatty Acids, Unsaturated/pharmacology
- Karyopherins/genetics
- Karyopherins/physiology
- Kinetics
- Protozoan Proteins/genetics
- Protozoan Proteins/physiology
- RNA Interference
- RNA Processing, Post-Transcriptional/physiology
- RNA, Protozoan/analysis
- RNA, Protozoan/metabolism
- RNA, Spliced Leader/analysis
- RNA, Spliced Leader/metabolism
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/physiology
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/physiology
- Trans-Splicing
- Trypanosoma brucei brucei/genetics
- Trypanosoma brucei brucei/physiology
- snRNP Core Proteins
- Exportin 1 Protein
Collapse
Affiliation(s)
- Moshe Biton
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | | | | | | |
Collapse
|
4621
|
Yoffe Y, Zuberek J, Lerer A, Lewdorowicz M, Stepinski J, Altmann M, Darzynkiewicz E, Shapira M. Binding specificities and potential roles of isoforms of eukaryotic initiation factor 4E in Leishmania. EUKARYOTIC CELL 2006; 5:1969-79. [PMID: 17041189 PMCID: PMC1694823 DOI: 10.1128/ec.00230-06] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The 5' cap structure of trypanosomatid mRNAs, denoted cap 4, is a complex structure that contains unusual modifications on the first four nucleotides. We examined the four eukaryotic initiation factor 4E (eIF4E) homologues found in the Leishmania genome database. These proteins, denoted LeishIF4E-1 to LeishIF4E-4, are located in the cytoplasm. They show only a limited degree of sequence homology with known eIF4E isoforms and among themselves. However, computerized structure prediction suggests that the cap-binding pocket is conserved in each of the homologues, as confirmed by binding assays to m(7)GTP, cap 4, and its intermediates. LeishIF4E-1 and LeishIF4E-4 each bind m(7)GTP and cap 4 comparably well, and only these two proteins could interact with the mammalian eIF4E binding protein 4EBP1, though with different efficiencies. 4EBP1 is a translation repressor that competes with eIF4G for the same residues on eIF4E; thus, LeishIF4E-1 and LeishIF4E-4 are reasonable candidates for serving as translation factors. LeishIF4E-1 is more abundant in amastigotes and also contains a typical 3' untranslated region element that is found in amastigote-specific genes. LeishIF4E-2 bound mainly to cap 4 and comigrated with polysomal fractions on sucrose gradients. Since the consensus eIF4E is usually found in 48S complexes, LeishIF4E-2 could possibly be associated with the stabilization of trypanosomatid polysomes. LeishIF4E-3 bound mainly m(7)GTP, excluding its involvement in the translation of cap 4-protected mRNAs. It comigrates with 80S complexes which are resistant to micrococcal nuclease, but its function is yet unknown. None of the isoforms can functionally complement the Saccharomyces cerevisiae eIF4E, indicating that despite their structural conservation, they are considerably diverged.
Collapse
Affiliation(s)
- Yael Yoffe
- Department of Life Sciences, Ben Gurion University, P.O. Box 653, Beer Sheva 84105, Israel
| | | | | | | | | | | | | | | |
Collapse
|
4622
|
Zamudio JR, Mittra B, Zeiner GM, Feder M, Bujnicki JM, Sturm NR, Campbell DA. Complete cap 4 formation is not required for viability in Trypanosoma brucei. EUKARYOTIC CELL 2006; 5:905-15. [PMID: 16757738 PMCID: PMC1489268 DOI: 10.1128/ec.00080-06] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In kinetoplastids spliced leader (SL) RNA is trans-spliced onto the 5' ends of all nuclear mRNAs, providing a universal exon with a unique cap. Mature SL contains an m(7)G cap, ribose 2'-O methylations on the first four nucleotides, and base methylations on nucleotides 1 and 4 (AACU). This structure is referred to as cap 4. Mutagenized SL RNAs that exhibit reduced cap 4 are trans-spliced, but these mRNAs do not associate with polysomes, suggesting a direct role in translation for cap 4, the primary SL sequence, or both. To separate SL RNA sequence alterations from cap 4 maturation, we have examined two ribose 2'-O-methyltransferases in Trypanosoma brucei. Both enzymes fall into the Rossmann fold class of methyltransferases and model into a conserved structure based on vaccinia virus homolog VP39. Knockdown of the methyltransferases individually or in combination did not affect growth rates and suggests a temporal placement in the cap 4 formation cascade: TbMT417 modifies A(2) and is not required for subsequent steps; TbMT511 methylates C(3), without which U(4) methylations are reduced. Incomplete cap 4 maturation was reflected in substrate SL and mRNA populations. Recombinant methyltransferases bind to a methyl donor and show preference for m(7)G-capped RNAs in vitro. Both enzymes reside in the nucleoplasm. Based on the cap phenotype of substrate SL stranded in the cytosol, A(2), C(3), and U(4) methylations are added after nuclear reimport of Sm protein-complexed substrate SL RNA. As mature cap 4 is dispensable for translation, cap 1 modifications and/or SL sequences are implicated in ribosomal interaction.
Collapse
Affiliation(s)
- Jesse R Zamudio
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095-1489, USA
| | | | | | | | | | | | | |
Collapse
|
4623
|
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
|
4624
|
Arhin GK, Li H, Ullu E, Tschudi C. A protein related to the vaccinia virus cap-specific methyltransferase VP39 is involved in cap 4 modification in Trypanosoma brucei. RNA (NEW YORK, N.Y.) 2006; 12:53-62. [PMID: 16301606 PMCID: PMC1370885 DOI: 10.1261/rna.2223406] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The spliced-leader (SL) RNA plays a key role in the biogenesis of mRNA in trypanosomes by providing the m(7)G-capped SL sequence to the 5' end of every mRNA. The cap structure of the SL RNA is unique in eukaryotes with 4 nucleotides after the cap carrying a total of seven methyl groups and by convention is referred to as "cap 4". Although the enzymatic machinery for cap addition has been characterized in several organisms, including Trypanosoma brucei, the identification of methyltransferases dedicated to the generation of higher order cap structures has lagged behind, except in viruses. Here we describe T. brucei MT57 (TbMT57), a primarily nuclear polypeptide with structural and functional similarities to vaccinia virus VP39, a bifunctional protein acting at the mRNA 5' end as a cap-specific 2'-O-methyltransferase. Down-regulation by RNAi or genetic ablation of TbMT57 resulted in the accumulation of SL RNA missing 2'-O-methyl groups at positions +3 and +4 and thus bearing a cap 2 rather than a cap 4. Furthermore, competitive binding studies indicated that modifications at the +3 and +4 positions are important for binding to the nuclear cap-binding complex. Genetic ablation of MT57 resulted in viable cells with no apparent defect in SL RNA trans-splicing, suggesting that MT57 is not essential or that trypanosomes have developed alternate mechanisms to counteract the absence of this protein. Interestingly, MT57 homologs are only found in trypanosomatid protozoa that have a cap 4 structure and in poxviruses, of which vaccinia virus is a prototype.
Collapse
Affiliation(s)
- George K Arhin
- Department of Epidemiology and Public Health, Yale University Medical School, 295 Congress Avenue, New Haven, CT 06536-0812, USA
| | | | | | | |
Collapse
|
4625
|
Liang XH, Liu Q, Liu L, Tschudi C, Michaeli S. Analysis of spliceosomal complexes in Trypanosoma brucei and silencing of two splicing factors Prp31 and Prp43. Mol Biochem Parasitol 2005; 145:29-39. [PMID: 16219373 DOI: 10.1016/j.molbiopara.2005.09.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Accepted: 09/06/2005] [Indexed: 11/21/2022]
Abstract
In trypanosomatids all mRNAs undergo trans-splicing, whereas cis-splicing is restricted to a few transcripts. Trans-splicing is mechanistically similar to cis-splicing, however, little is known about the trans-splicing machinery and its underlying mechanism. In this study, we examined the involvement of splicing factors in cis- and trans-splicing by RNA interference (RNAi). Two factors (Prp31 and Prp43) were found to be essential for both pathways, suggesting that splicing factors are shared by these two reactions. We identified a 45S complex carrying pre-mRNA and all the U-snRNAs, including U1 and the SL RNA, suggesting that a single spliceosomal complex may potentially conduct both trans- and cis-splicing.
Collapse
Affiliation(s)
- Xue-hai Liang
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | | | | | | | | |
Collapse
|
4626
|
Foldynová-Trantírková S, Paris Z, Sturm NR, Campbell DA, Lukes J. The Trypanosoma brucei La protein is a candidate poly(U) shield that impacts spliced leader RNA maturation and tRNA intron removal. Int J Parasitol 2005; 35:359-66. [PMID: 15777912 DOI: 10.1016/j.ijpara.2004.12.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2004] [Revised: 12/17/2004] [Accepted: 12/17/2004] [Indexed: 10/25/2022]
Abstract
By virtue of its preferential binding to poly(U) tails on small RNA precursors and nuclear localisation motif, the La protein has been implicated for a role in the stabilisation and nuclear retention of processing intermediates for a variety of small RNAs in eukaryotic cells. As the universal substrate for trans-splicing, the spliced leader RNA is transcribed as a precursor with just such a tail. La protein was targeted for selective knockdown by inducible RNA interference in Trypanosoma brucei. Of three RNA interference strategies employed, a p2T7-177 vector was the most effective in reducing both the La mRNA as well as the protein itself from induced cells. In the relative absence of La protein T. brucei cells were not viable, in contrast to La gene knockouts in yeast. A variety of potential small RNA substrates were examined under induction, including spliced leader RNA, spliced leader associated RNA, the U1, U2, U4, and U6 small nuclear RNAs, 5S ribosomal RNA, U3 small nucleolar RNA, and tRNATyr. None of these molecules showed significant variance in size or abundance in their mature forms, although a discrete subset of intermediates appear for spliced leader RNA and tRNATyr intron splicing under La depletion conditions. 5'-end methylation in the spliced leader RNA and U1 small nuclear RNA was unaffected. The immediate cause of lethality in T. brucei was not apparent, but may represent a cumulative effect of multiple defects including processing of spliced leader RNA, tRNATyr and other unidentified RNA substrates. This study indicates that La protein binding is not essential for maturation of the spliced leader RNA, but does not rule out the presence of an alternative processing pathway that could compensate for the absence of normally-associated La protein.
Collapse
Affiliation(s)
- Silvie Foldynová-Trantírková
- Institute of Parasitology, Czech Academy of Sciences, Faculty of Biology, University of South Bohemia, 37005 Ceské Budejovice, Czech Republic
| | | | | | | | | |
Collapse
|
4627
|
Barth S, Hury A, Liang XH, Michaeli S. Elucidating the role of H/ACA-like RNAs in trans-splicing and rRNA processing via RNA interference silencing of the Trypanosoma brucei CBF5 pseudouridine synthase. J Biol Chem 2005; 280:34558-68. [PMID: 16107339 DOI: 10.1074/jbc.m503465200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Most pseudouridinylation in eukaryotic rRNA and small nuclear RNAs is guided by H/ACA small nucleolar RNAs. In this study, the Trypanosoma brucei pseudouridine synthase, Cbf5p, a snoRNP protein, was identified and silenced by RNAi. Depletion of this protein destabilized all small nucleolar RNAs of the H/ACA-like family. Following silencing, defects in rRNA processing, such as accumulation of precursors and inhibition of cleavages to generate the mature rRNA, were observed. snR30, an H/ACA RNA involved in rRNA maturation, was identified based on prototypical conserved domains characteristic of this RNA in other eukaryotes. The silencing of CBF5 also eliminated the spliced leader-associated (SLA1) RNA that directs pseudouridylation on the spliced leader RNA (SL RNA), which is the substrate for the trans-splicing reaction. Surprisingly, the depletion of Cbf5p not only eliminated the pseudouridine on the SL RNA but also abolished capping at the fourth cap-4 nucleotide. As a result of defects in the SL RNA and decreased modification on the U small nuclear RNA, trans-splicing was inhibited at the first step of the reaction, providing evidence for the essential role of H/ACA RNAs and the modifications they guide on trans-splicing.
Collapse
MESH Headings
- Alternative Splicing
- Animals
- Base Sequence
- Blotting, Northern
- Gene Deletion
- Gene Silencing
- Hydro-Lyases/chemistry
- Hydro-Lyases/genetics
- Hydro-Lyases/metabolism
- Microtubule-Associated Proteins/genetics
- Microtubule-Associated Proteins/metabolism
- Models, Genetic
- Molecular Sequence Data
- Oligonucleotides/chemistry
- Oligonucleotides/genetics
- Phenotype
- Pseudouridine/chemistry
- RNA/metabolism
- RNA Interference
- RNA Splicing
- RNA, Messenger/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/metabolism
- RNA, Small Nuclear/metabolism
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/metabolism
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Ribonucleoproteins, Small Nucleolar/genetics
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Temperature
- Time Factors
- Transfection
- Trypanosoma/metabolism
- Trypanosoma brucei brucei/enzymology
- Trypanosoma brucei brucei/genetics
- Tubulin/chemistry
Collapse
Affiliation(s)
- Sarit Barth
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | | | | | | |
Collapse
|
4628
|
Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S. A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA modification. RNA (NEW YORK, N.Y.) 2005; 11:619-45. [PMID: 15840815 PMCID: PMC1370750 DOI: 10.1261/rna.7174805] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2004] [Accepted: 01/17/2005] [Indexed: 05/19/2023]
Abstract
Small nucleolar RNAs (snoRNAs) constitute newly discovered noncoding small RNAs, most of which function in guiding modifications such as 2'-O-ribose methylation and pseudouridylation on rRNAs and snRNAs. To investigate the genome organization of Trypanosoma brucei snoRNAs and the pattern of rRNA modifications, we used a whole-genome approach to identify the repertoire of these guide RNAs. Twenty-one clusters encoding for 57 C/D snoRNAs and 34 H/ACA-like RNAs, which have the potential to direct 84 methylations and 32 pseudouridines, respectively, were identified. The number of 2'-O-methyls (Nms) identified on rRNA represent 80% of the expected modifications. The modifications guided by these RNAs suggest that trypanosomes contain many modifications and guide RNAs relative to their genome size. Interestingly, approximately 40% of the Nms are species-specific modifications that do not exist in yeast, humans, or plants, and 40% of the species-specific predicted modifications are located in unique positions outside the highly conserved domains. Although most of the guide RNAs were found in reiterated clusters, a few single-copy genes were identified. The large repertoire of modifications and guide RNAs in trypanosomes suggests that these modifications possibly play a central role in these parasites.
Collapse
Affiliation(s)
- Xue-Hai Liang
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | | | | | | | | | | | | |
Collapse
|
4629
|
Li H, Tschudi C. Novel and essential subunits in the 300-kilodalton nuclear cap binding complex of Trypanosoma brucei. Mol Cell Biol 2005; 25:2216-26. [PMID: 15743819 PMCID: PMC1061625 DOI: 10.1128/mcb.25.6.2216-2226.2005] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
One of the unique aspects of RNA processing in trypanosomatid protozoa is the presence of a cap 4 structure (m7Gpppm2(6)AmpAmpCmpm3Um) at the 5' end of all mRNAs. The cap 4 becomes part of the mRNA through trans-splicing of a 39-nucleotide-long sequence donated by the spliced leader RNA. Although the cap 4 modifications are required for trans-splicing to occur, the underlying mechanism remains to be determined. We now describe an unconventional nuclear cap binding complex (CBC) in Trypanosoma brucei with an apparent molecular mass of 300 kDa and consisting of five protein components: the known CBC subunits CBP20 and importin-alpha and three novel proteins that are only present in organisms featuring a cap 4 structure and trans-splicing. Competitive binding studies are consistent with a specific interaction between the CBC and the cap 4 structure. Downregulation of several individual components of the T. brucei CBC by RNA interference demonstrated an essential function at an early step in trans-splicing. Thus, our studies are consistent with the CBC providing a mechanistic link between cap 4 modifications and trans-splicing.
Collapse
Affiliation(s)
- Hongjie Li
- Department of Epidemiology and Public Health, Yale University Medical School, BCMM 136C, 295 Congress Ave., New Haven, CT 06536-0812, USA
| | | |
Collapse
|
4630
|
Zeiner GM, Hitchcock RA, Sturm NR, Campbell DA. 3'-End polishing of the kinetoplastid spliced leader RNA is performed by SNIP, a 3'-->5' exonuclease with a Motley assortment of small RNA substrates. Mol Cell Biol 2005; 24:10390-6. [PMID: 15542846 PMCID: PMC529039 DOI: 10.1128/mcb.24.23.10390-10396.2004] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In all trypanosomatids, trans splicing of the spliced leader (SL) RNA is a required step in the maturation of all nucleus-derived mRNAs. The SL RNA is transcribed with an oligo-U 3' extension that is removed prior to trans splicing. Here we report the identification and characterization of a nonexosomal, 3'-->5' exonuclease required for SL RNA 3'-end formation in Trypanosoma brucei. We named this enzyme SNIP (for snRNA incomplete 3' processing). The central 158-amino-acid domain of SNIP is related to the exonuclease III (ExoIII) domain of the 3'-->5' proofreading epsilon subunit of Escherichia coli DNA polymerase III holoenzyme. SNIP had a preference for oligo(U) 3' extensions in vitro. RNA interference-mediated knockdown of SNIP resulted in a growth defect and correlated with the accumulation of one- to two- nucleotide 3' extensions of SL RNA, U2 and U4 snRNAs, a five-nucleotide extension of 5S rRNA, and the destabilization of U3 snoRNA and U2 snRNA. SNIP-green fluorescent protein localized to the nucleoplasm, and substrate SL RNA derived from SNIP knockdown cells showed wild-type cap 4 modification, indicating that SNIP acts on SL RNA after cytosolic trafficking. Since the primary SL RNA transcript was not the accumulating species in SNIP knockdown cells, SL RNA 3'-end formation is a multistep process in which SNIP provides the ultimate 3'-end polishing. We speculate that SNIP is part of an organized nucleoplasmic machinery responsible for processing of SL RNA.
Collapse
Affiliation(s)
- Gusti M Zeiner
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, 609 Charles E. Young Dr. East, Los Angeles, CA 90095-1489, USA
| | | | | | | |
Collapse
|
4631
|
Yoffe Y, Zuberek J, Lewdorowicz M, Zeira Z, Keasar C, Orr-Dahan I, Jankowska-Anyszka M, Stepinski J, Darzynkiewicz E, Shapira M. Cap-binding activity of an eIF4E homolog from Leishmania. RNA (NEW YORK, N.Y.) 2004; 10:1764-1775. [PMID: 15388875 PMCID: PMC1370664 DOI: 10.1261/rna.7520404] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2004] [Accepted: 08/10/2004] [Indexed: 05/24/2023]
Abstract
All eukaryotic mRNAs possess a 5'-cap (m(7)GpppN) that is recognized by a family of cap-binding proteins. These participate in various processes, such as RNA transport and stabilization, as well as in assembly of the translation initiation complex. The 5'-cap of trypanosomatids is complex; in addition to 7-methyl guanosine, it includes unique modifications on the first four transcribed nucleotides, and is thus denoted cap-4. Here we analyze a cap-binding protein of Leishmania, in an attempt to understand the structural features that promote its binding to this unusual cap. LeishIF4E-1, a homolog of eIF4E, contains the conserved cap-binding pocket, similar to its mouse counterpart. The mouse eIF4E has a higher K(as) for all cap analogs tested, as compared with LeishIF4E-1. However, whereas the mouse eIF4E shows a fivefold higher affinity for m(7)GTP than for a chemically synthesized cap-4 structure, LeishIF4E-1 shows similar affinities for both ligands. A sequence alignment shows that LeishIF4E-1 lacks the region that parallels the C terminus in the murine eIF4E. Truncation of this region in the mouse protein reduces the difference that is observed between its binding to m(7)GTP and cap-4, prior to this deletion. We hypothesize that variations in the structure of LeishIF4E-1, possibly also the absence of a region that is homologous to the C terminus of the mouse protein, promote its ability to interact with the cap-4 structure. LeishIF4E-1 is distributed in the cytoplasm, but its function is not clear yet, because it cannot substitute the mammalian eIF4E in a rabbit reticulocyte in vitro translation system.
Collapse
Affiliation(s)
- Yael Yoffe
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O.B. 653, Beer Sheva 84105, Israel
| | | | | | | | | | | | | | | | | | | |
Collapse
|
4632
|
Lewdorowicz M, Yoffe Y, Zuberek J, Jemielity J, Stepinski J, Kierzek R, Stolarski R, Shapira M, Darzynkiewicz E. Chemical synthesis and binding activity of the trypanosomatid cap-4 structure. RNA (NEW YORK, N.Y.) 2004; 10:1469-78. [PMID: 15273325 PMCID: PMC1370633 DOI: 10.1261/rna.7510504] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Leishmania and other trypanosomatids are early eukaryotes that possess unusual molecular features, including polycistronic transcription and trans-splicing of pre-mRNAs. The spliced leader RNA (SL RNA) is joined to the 5' end of all mRNAs, thus donating a 5' cap that is characterized by complex modifications. In addition to the conserved m7GTP, linked via a 5'-5'-triphosphate bound to the first nucleoside of the mRNA, the trypanosomatid 5' cap includes 2'-O methylations on the first four ribose moieties and unique base methylations on the first adenine and the fourth uracil, resulting in the cap-4 structure, m7Gpppm3(6,6,2')Apm2'Apm2' Cpm2(3,2')U, as reported elsewhere previously. A library of analogs that mimic the cap structure to different degrees has been synthesized. Their differential affinities to the cap binding proteins make them attractive compounds for studying the molecular basis of cap recognition, and in turn, they may have potential therapeutic significance. The interactions between cap analogs and eIF4E, a cap-binding protein that plays a key role in initiation of translation, can be monitored by measuring intrinsic fluorescence quenching of the tryptophan residues. In the present communication we describe the multistep synthesis of the trypanosomatid cap-4 structure. The 5' terminal mRNA tetranucleotide fragment (pm3(6,6,2')Apm2'Apm2'Cpm2(3,2')U) was synthesized by the phosphoramidite solid phase method. After deprotection and purification, the 5'-phosphorylated tetranucleotide was chemically coupled with m7GDP to yield the cap-4 structure. Biological activity of this newly synthesized compound was confirmed in binding studies with eIF4E from Leishmania that we recently cloned (LeishIF4E-1), using the fluorescence time-synchronized titration method.
Collapse
Affiliation(s)
- Magdalena Lewdorowicz
- Department of Biophysics, Institute of Experimental Physics, Warsaw University, 93 Zwirki and Wigury St., 02-089, Poland
| | | | | | | | | | | | | | | | | |
Collapse
|
4633
|
Hitchcock RA, Zeiner GM, Sturm NR, Campbell DA. The 3â² termini of small RNAs in Trypanosoma brucei. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09629.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
4634
|
Liu Q, Liang XH, Uliel S, Belahcen M, Unger R, Michaeli S. Identification and functional characterization of lsm proteins in Trypanosoma brucei. J Biol Chem 2004; 279:18210-9. [PMID: 14990572 DOI: 10.1074/jbc.m400678200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RNA interference of Sm proteins in Trypanosoma brucei demonstrated that the stability of the small nuclear RNAs (U1, U2, U4, U5) and the spliced leader RNA, but not U6 RNA, were affected upon Sm depletion (Mandelboim, M., Barth, S., Biton, M., Liang, X. H., and Michaeli, S. (2003) J. Biol. Chem. 278, 51469-51478), suggesting that Lsm proteins that bind and stabilize U6 RNA in other eukaryotes should exist in trypanosomes. In this study, we identified seven Lsm proteins (Lsm2p to Lsm8p) and examined the function of Lsm3p and Lsm8p by RNA interference silencing. Both Lsm proteins were found to be essential for U6 stability and mRNA decay. Silencing was lethal, and cis- and trans-splicing were inhibited. Importantly, silencing also affected the level of U4.U6 and the U4.U6/U5 tri-small nuclear ribonucleoprotein complexes. The presence of Lsm proteins in trypanosomes that diverged early in the eukaryotic lineage suggests that these proteins are highly conserved in both structure and function among eukaryotes. Interestingly, however, Lsm1p that is specific to the mRNA decay complex was not identified in the genome data base of any kinetoplastidae, and the Lsm8p that in other eukaryotes exclusively functions in U6 stability was found to function in trypanosomes also in mRNA decay. These data therefore suggest that in trypanosomes only a single Lsm complex may exist.
Collapse
MESH Headings
- Amino Acid Sequence
- Animals
- Databases, Genetic
- Gene Silencing
- Protozoan Proteins/metabolism
- Protozoan Proteins/physiology
- RNA Splicing
- RNA Stability
- RNA, Small Interfering/pharmacology
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear/genetics
- Ribonucleoprotein, U4-U6 Small Nuclear/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear/physiology
- Ribonucleoprotein, U5 Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/physiology
- Sequence Alignment
- Trypanosoma brucei brucei/chemistry
Collapse
Affiliation(s)
- Qing Liu
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | | | | | | | | | | |
Collapse
|