1
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von Känel C, Stettler P, Esposito C, Berger S, Amodeo S, Oeljeklaus S, Calderaro S, Durante IM, Rašková V, Warscheid B, Schneider A. Pam16 and Pam18 were repurposed during Trypanosoma brucei evolution to regulate the replication of mitochondrial DNA. PLoS Biol 2024; 22:e3002449. [PMID: 39146359 DOI: 10.1371/journal.pbio.3002449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 07/23/2024] [Indexed: 08/17/2024] Open
Abstract
Protein import and genome replication are essential processes for mitochondrial biogenesis and propagation. The J-domain proteins Pam16 and Pam18 regulate the presequence translocase of the mitochondrial inner membrane. In the protozoan Trypanosoma brucei, their counterparts are TbPam16 and TbPam18, which are essential for the procyclic form (PCF) of the parasite, though not involved in mitochondrial protein import. Here, we show that during evolution, the 2 proteins have been repurposed to regulate the replication of maxicircles within the intricate kDNA network, the most complex mitochondrial genome known. TbPam18 and TbPam16 have inactive J-domains suggesting a function independent of heat shock proteins. However, their single transmembrane domain is essential for function. Pulldown of TbPam16 identifies a putative client protein, termed MaRF11, the depletion of which causes the selective loss of maxicircles, akin to the effects observed for TbPam18 and TbPam16. Moreover, depletion of the mitochondrial proteasome results in increased levels of MaRF11. Thus, we have discovered a protein complex comprising TbPam18, TbPam16, and MaRF11, that controls maxicircle replication. We propose a working model in which the matrix protein MaRF11 functions downstream of the 2 integral inner membrane proteins TbPam18 and TbPam16. Moreover, we suggest that the levels of MaRF11 are controlled by the mitochondrial proteasome.
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Affiliation(s)
- Corinne von Känel
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Philip Stettler
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Carmela Esposito
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Stephan Berger
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Simona Amodeo
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Silke Oeljeklaus
- Faculty of Chemistry and Pharmacy, Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Salvatore Calderaro
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Ignacio M Durante
- Institute of Parasitology, Biology Centre, České Budějovice, Czech Republic
| | - Vendula Rašková
- Institute of Parasitology, Biology Centre, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Bettina Warscheid
- Faculty of Chemistry and Pharmacy, Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - André Schneider
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
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2
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Wenger C, Harsman A, Niemann M, Oeljeklaus S, von Känel C, Calderaro S, Warscheid B, Schneider A. The Mba1 homologue of Trypanosoma brucei is involved in the biogenesis of oxidative phosphorylation complexes. Mol Microbiol 2023; 119:537-550. [PMID: 36829306 DOI: 10.1111/mmi.15048] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023]
Abstract
Consistent with other eukaryotes, the Trypanosoma brucei mitochondrial genome encodes mainly hydrophobic core subunits of the oxidative phosphorylation system. These proteins must be co-translationally inserted into the inner mitochondrial membrane and are synthesized by the highly unique trypanosomal mitoribosomes, which have a much higher protein to RNA ratio than any other ribosome. Here, we show that the trypanosomal orthologue of the mitoribosome receptor Mba1 (TbMba1) is essential for normal growth of procyclic trypanosomes but redundant in the bloodstream form, which lacks an oxidative phosphorylation system. Proteomic analyses of TbMba1-depleted mitochondria from procyclic cells revealed reduced levels of many components of the oxidative phosphorylation system, most of which belong to the cytochrome c oxidase (Cox) complex, three subunits of which are mitochondrially encoded. However, the integrity of the mitoribosome and its interaction with the inner membrane were not affected. Pull-down experiments showed that TbMba1 forms a dynamic interaction network that includes the trypanosomal Mdm38/Letm1 orthologue and a trypanosome-specific factor that stabilizes the CoxI and CoxII mRNAs. In summary, our study suggests that the function of Mba1 in the biogenesis of membrane subunits of OXPHOS complexes is conserved among yeast, mammals and trypanosomes, which belong to two eukaryotic supergroups.
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Affiliation(s)
- Christoph Wenger
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Anke Harsman
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Moritz Niemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Silke Oeljeklaus
- Faculty of Chemistry and Pharmacy, Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Corinne von Känel
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Salvatore Calderaro
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Bettina Warscheid
- Faculty of Chemistry and Pharmacy, Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany.,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - André Schneider
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.,Institute for Advanced Study (Wissenschaftskolleg) Berlin, Berlin, Germany
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3
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Berná L, Greif G, Pita S, Faral-Tello P, Díaz-Viraqué F, Souza RDCMD, Vallejo GA, Alvarez-Valin F, Robello C. Maxicircle architecture and evolutionary insights into Trypanosoma cruzi complex. PLoS Negl Trop Dis 2021; 15:e0009719. [PMID: 34437557 PMCID: PMC8425572 DOI: 10.1371/journal.pntd.0009719] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 09/08/2021] [Accepted: 08/10/2021] [Indexed: 12/13/2022] Open
Abstract
We sequenced maxicircles from T. cruzi strains representative of the species evolutionary diversity by using long-read sequencing, which allowed us to uncollapse their repetitive regions, finding that their real lengths range from 35 to 50 kb. T. cruzi maxicircles have a common architecture composed of four regions: coding region (CR), AT-rich region, short (SR) and long repeats (LR). Distribution of genes, both in order and in strand orientation are conserved, being the main differences the presence of deletions affecting genes coding for NADH dehydrogenase subunits, reinforcing biochemical findings that indicate that complex I is not functional in T. cruzi. Moreover, the presence of complete minicircles into maxicircles of some strains lead us to think about the origin of minicircles. Finally, a careful phylogenetic analysis was conducted using coding regions of maxicircles from up to 29 strains, and 1108 single copy nuclear genes from all of the DTUs, clearly establishing that taxonomically T. cruzi is a complex of species composed by group 1 that contains clades A (TcI), B (TcIII) and D (TcIV), and group 2 (1 and 2 do not coincide with groups I and II described decades ago) containing clade C (TcII), being all hybrid strains of the BC type. Three variants of maxicircles exist in T. cruzi: a, b and c, in correspondence with clades A, B, and C from mitochondrial phylogenies. While A and C carry maxicircles a and c respectively, both clades B and D carry b maxicircle variant; hybrid strains also carry the b- variant. We then propose a new nomenclature that is self-descriptive and makes use of both the phylogenetic relationships and the maxicircle variants present in T. cruzi.
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Affiliation(s)
- Luisa Berná
- Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Sección Biomatemática—Unidad de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Gonzalo Greif
- Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Sebastián Pita
- Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Sección Genética, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Paula Faral-Tello
- Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Florencia Díaz-Viraqué
- Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | | | - Gustavo Adolfo Vallejo
- Laboratorio de investigaciones en Parasitología Tropical (LIPT), Facultad de Ciencias, Universidad del Tolima, Tolima, Colombia
| | - Fernando Alvarez-Valin
- Sección Biomatemática—Unidad de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Carlos Robello
- Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- * E-mail:
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4
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Gerasimov ES, Gasparyan AA, Afonin DA, Zimmer SL, Kraeva N, Lukeš J, Yurchenko V, Kolesnikov A. Complete minicircle genome of Leptomonas pyrrhocoris reveals sources of its non-canonical mitochondrial RNA editing events. Nucleic Acids Res 2021; 49:3354-3370. [PMID: 33660779 PMCID: PMC8034629 DOI: 10.1093/nar/gkab114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 02/03/2021] [Accepted: 02/09/2021] [Indexed: 01/24/2023] Open
Abstract
Uridine insertion/deletion (U-indel) editing of mitochondrial mRNA, unique to the protistan class Kinetoplastea, generates canonical as well as potentially non-productive editing events. While the molecular machinery and the role of the guide (g) RNAs that provide required information for U-indel editing are well understood, little is known about the forces underlying its apparently error-prone nature. Analysis of a gRNA:mRNA pair allows the dissection of editing events in a given position of a given mitochondrial transcript. A complete gRNA dataset, paired with a fully characterized mRNA population that includes non-canonically edited transcripts, would allow such an analysis to be performed globally across the mitochondrial transcriptome. To achieve this, we have assembled 67 minicircles of the insect parasite Leptomonas pyrrhocoris, with each minicircle typically encoding one gRNA located in one of two similar-sized units of different origin. From this relatively narrow set of annotated gRNAs, we have dissected all identified mitochondrial editing events in L. pyrrhocoris, the strains of which dramatically differ in the abundance of individual minicircle classes. Our results support a model in which a multitude of editing events are driven by a limited set of gRNAs, with individual gRNAs possessing an inherent ability to guide canonical and non-canonical editing.
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Affiliation(s)
- Evgeny S Gerasimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow 119435, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russia
| | - Anna A Gasparyan
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Dmitry A Afonin
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Sara L Zimmer
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, Duluth, MN 55812, USA
| | - Natalya Kraeva
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice (Budweis), Czech Republic
| | - Vyacheslav Yurchenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow 119435, Russia
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Alexander Kolesnikov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
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5
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Zigáčková D, Vaňáčová Š. The role of 3' end uridylation in RNA metabolism and cellular physiology. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0171. [PMID: 30397107 DOI: 10.1098/rstb.2018.0171] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2018] [Indexed: 12/14/2022] Open
Abstract
Most eukaryotic RNAs are posttranscriptionally modified. The majority of modifications promote RNA maturation, others may regulate function and stability. The 3' terminal non-templated oligouridylation is a widespread modification affecting many cellular RNAs at some stage of their life cycle. It has diverse roles in RNA metabolism. The most prevalent is the regulation of stability and quality control. On the cellular and organismal level, it plays a critical role in a number of pathways, such as cell cycle regulation, cell death, development or viral infection. Defects in uridylation have been linked to several diseases. This review summarizes the current knowledge about the role of the 3' terminal oligo(U)-tailing in biology of various RNAs in eukaryotes and describes key factors involved in these pathways.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
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Affiliation(s)
- Dagmar Zigáčková
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5/A35, Brno 625 00, Czech Republic
| | - Štěpánka Vaňáčová
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5/A35, Brno 625 00, Czech Republic
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6
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Zhang L, Sement FM, Suematsu T, Yu T, Monti S, Huang L, Aphasizhev R, Aphasizheva I. PPR polyadenylation factor defines mitochondrial mRNA identity and stability in trypanosomes. EMBO J 2017; 36:2435-2454. [PMID: 28684539 DOI: 10.15252/embj.201796808] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 05/10/2017] [Accepted: 05/22/2017] [Indexed: 11/09/2022] Open
Abstract
In Trypanosoma brucei, most mitochondrial mRNAs undergo internal changes by RNA editing and 3' end modifications. The temporally separated and functionally distinct modifications are manifested by adenylation prior to editing, and by post-editing extension of a short A-tail into a long A/U-heteropolymer. The A-tail stabilizes partially and fully edited mRNAs, while the A/U-tail enables mRNA binding to the ribosome. Here, we identify an essential pentatricopeptide repeat-containing RNA binding protein, kinetoplast polyadenylation factor 3 (KPAF3), and demonstrate its role in protecting pre-mRNA against degradation by the processome. We show that KPAF3 recruits KPAP1 poly(A) polymerase to the 3' terminus, thus leading to pre-mRNA stabilization, or decay depending on the occurrence and extent of editing. In vitro, KPAF3 stimulates KPAP1 activity and inhibits mRNA uridylation by RET1 TUTase. Our findings indicate that KPAF3 selectively directs pre-mRNA toward adenylation rather than uridylation, which is a default post-trimming modification characteristic of ribosomal and guide RNAs. As a quality control mechanism, KPAF3 binding ensures that mRNAs entering the editing pathway are adenylated and, therefore, competent for post-editing A/U-tailing and translational activation.
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Affiliation(s)
- Liye Zhang
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA, USA.,Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Francois M Sement
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA, USA
| | - Takuma Suematsu
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA, USA
| | - Tian Yu
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA, USA
| | - Stefano Monti
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Lan Huang
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA, USA.,Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA, USA
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7
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Kirby LE, Sun Y, Judah D, Nowak S, Koslowsky D. Analysis of the Trypanosoma brucei EATRO 164 Bloodstream Guide RNA Transcriptome. PLoS Negl Trop Dis 2016; 10:e0004793. [PMID: 27399202 PMCID: PMC4939953 DOI: 10.1371/journal.pntd.0004793] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 05/31/2016] [Indexed: 12/04/2022] Open
Abstract
The mitochondrial genome of Trypanosoma brucei contains many cryptogenes that must be extensively edited following transcription. The RNA editing process is directed by guide RNAs (gRNAs) that encode the information for the specific insertion and deletion of uridylates required to generate translatable mRNAs. We have deep sequenced the gRNA transcriptome from the bloodstream form of the EATRO 164 cell line. Using conventionally accepted fully edited mRNA sequences, ~1 million gRNAs were identified. In contrast, over 3 million reads were identified in our insect stage gRNA transcriptome. A comparison of the two life cycle transcriptomes show an overall ratio of procyclic to bloodstream gRNA reads of 3.5:1. This ratio varies significantly by gene and by gRNA populations within genes. The variation in the abundance of the initiating gRNAs for each gene, however, displays a trend that correlates with the developmental pattern of edited gene expression. A comparison of related major classes from each transcriptome revealed a median value of ten single nucleotide variations per gRNA. Nucleotide variations were much less likely to occur in the consecutive Watson-Crick anchor region, indicating a very strong bias against G:U base pairs in this region. This work indicates that gRNAs are expressed during both life cycle stages, and that differential editing patterns observed for the different mitochondrial mRNA transcripts are not due to the presence or absence of gRNAs. However, the abundance of certain gRNAs may be important in the developmental regulation of RNA editing. Trypanosoma brucei is the causative agent of African sleeping sickness, a disease that threatens millions of people in sub-Saharan Africa. During its life cycle, Trypanosoma brucei lives in either its mammalian host or its insect vector. These environments are very different, and the transition between these environments is accompanied by changes in parasite energy metabolism, including distinct changes in mitochondrial gene expression. In trypanosomes, mitochondrial gene expression involves a unique RNA editing process, where U-residues are inserted or deleted to generate the mRNA’s protein code. The editing process is directed by a set of small RNAs called guide RNAs. Our lab has previously deep sequenced the gRNA transcriptome of the insect stage of T. brucei. In this paper, we present the gRNA transcriptome of the bloodstream stage. Our comparison of these two transcriptomes indicates that most gRNAs are present in both life cycle stages, even though utilization of the gRNAs differs greatly during the two life-cycle stages. These data provide unique insight into how RNA systems may allow for rapid adaptation to different environments and energy utilization requirements.
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Affiliation(s)
- Laura E. Kirby
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Yanni Sun
- Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - David Judah
- Merial Veterinary Scholars Program, Michigan State University, East Lansing, Michigan, United States of America
| | - Scooter Nowak
- Department of Entomology, Michigan State University, East Lansing, Michigan, United States of America
| | - Donna Koslowsky
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
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8
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Suematsu T, Zhang L, Aphasizheva I, Monti S, Huang L, Wang Q, Costello CE, Aphasizhev R. Antisense Transcripts Delimit Exonucleolytic Activity of the Mitochondrial 3' Processome to Generate Guide RNAs. Mol Cell 2016; 61:364-378. [PMID: 26833087 PMCID: PMC4744118 DOI: 10.1016/j.molcel.2016.01.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 11/16/2015] [Accepted: 12/24/2015] [Indexed: 12/21/2022]
Abstract
Small, noncoding RNA biogenesis typically involves cleavage of structured precursor by RNase III-like endonucleases. However, guide RNAs (gRNAs) that direct U-insertion/deletion mRNA editing in mitochondria of trypanosomes maintain 5' triphosphate characteristic of the transcription initiation and possess a U-tail indicative of 3' processing and uridylation. Here, we identified a protein complex composed of RET1 TUTase, DSS1 3'-5' exonuclease, and three additional subunits. This complex, termed mitochondrial 3' processome (MPsome), is responsible for primary uridylation of ∼800 nt gRNA precursors, their processive degradation to a mature size of 40-60 nt, and secondary U-tail addition. Both strands of the gRNA gene are transcribed into sense and antisense precursors of similar lengths. Head-to-head hybridization of these transcripts blocks symmetrical 3'-5' degradation at a fixed distance from the double-stranded region. Together, our findings suggest a model in which gRNA is derived from the 5' extremity of a primary molecule by uridylation-induced, antisense transcription-controlled 3'-5' exonucleolytic degradation.
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Affiliation(s)
- Takuma Suematsu
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA 02118, USA
| | - Liye Zhang
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA 02118, USA
| | - Stefano Monti
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Lan Huang
- Department of Physiology & Biophysics, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA
| | - Qi Wang
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Catherine E Costello
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA 02118, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA.
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9
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Dietrich A, Wallet C, Iqbal RK, Gualberto JM, Lotfi F. Organellar non-coding RNAs: Emerging regulation mechanisms. Biochimie 2015; 117:48-62. [DOI: 10.1016/j.biochi.2015.06.027] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/29/2015] [Indexed: 02/06/2023]
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10
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Greif G, Rodriguez M, Reyna-Bello A, Robello C, Alvarez-Valin F. Kinetoplast adaptations in American strains from Trypanosoma vivax. Mutat Res 2015; 773:69-82. [PMID: 25847423 DOI: 10.1016/j.mrfmmm.2015.01.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/06/2015] [Accepted: 01/17/2015] [Indexed: 05/24/2023]
Abstract
The mitochondrion role changes during the digenetic life cycle of African trypanosomes. Owing to the low abundance of glucose in the insect vector (tsetse flies) the parasites are dependent upon a fully functional mitochondrion, capable of performing oxidative phosphorylation. Nevertheless, inside the mammalian host (bloodstream forms), which is rich in nutrients, parasite proliferation relies on glycolysis, and the mitochondrion is partially redundant. In this work we perform a comparative study of the mitochondrial genome (kinetoplast) in different strains of Trypanosoma vivax. The comparison was conducted between a West African strain that goes through a complete life cycle and two American strains that are mechanically transmitted (by different vectors) and remain as bloodstream forms only. It was found that while the African strain has a complete and apparently fully functional kinetoplast, the American T. vivax strains have undergone a drastic process of mitochondrial genome degradation, in spite of the recent introduction of these parasites in America. Many of their genes exhibit different types of mutations that are disruptive of function such as major deletions, frameshift causing indels and missense mutations. Moreover, all but three genes (A6-ATPase, RPS12 and MURF2) are not edited in the American strains, whereas editing takes place normally in all (editable) genes from the African strain. Two of these genes, A6-ATPase and RPS12, are known to play an essential function during bloodstream stage. Analysis of the minicircle population shows that its diversity has been greatly reduced, remaining mostly those minicircles that carry guide RNAs necessary for the editing of A6-ATPase and RPS12. The fact that these two genes remain functioning normally, as opposed to that reported in Trypanosoma brucei-like trypanosomes that restrict their life cycle to the bloodstream forms, along with other differences, is indicative that the American T. vivax strains are following a novel evolutionary pathway.
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Affiliation(s)
- Gonzalo Greif
- Unidad de Biología Molecular, Institut Pasteur de Montevideo, Uruguay
| | - Matías Rodriguez
- Sección Biomatemática, Facultad de Ciencias, Universidad de la Republica, Uruguay
| | - Armando Reyna-Bello
- Departamento de Ciencias de la Vida, Carrera en Ingeniería en Biotecnología, Universidad de las Fuerzas Armadas, Ecuador; Centro de Estudios Biomédicos y Veterinarios, Universidad Nacional Experimental Simón Rodríguez-IDECYT, Caracas, Venezuela
| | - Carlos Robello
- Unidad de Biología Molecular, Institut Pasteur de Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República Uruguay
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11
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Verner Z, Basu S, Benz C, Dixit S, Dobáková E, Faktorová D, Hashimi H, Horáková E, Huang Z, Paris Z, Peña-Diaz P, Ridlon L, Týč J, Wildridge D, Zíková A, Lukeš J. Malleable mitochondrion of Trypanosoma brucei. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 315:73-151. [PMID: 25708462 DOI: 10.1016/bs.ircmb.2014.11.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The importance of mitochondria for a typical aerobic eukaryotic cell is undeniable, as the list of necessary mitochondrial processes is steadily growing. Here, we summarize the current knowledge of mitochondrial biology of an early-branching parasitic protist, Trypanosoma brucei, a causative agent of serious human and cattle diseases. We present a comprehensive survey of its mitochondrial pathways including kinetoplast DNA replication and maintenance, gene expression, protein and metabolite import, major metabolic pathways, Fe-S cluster synthesis, ion homeostasis, organellar dynamics, and other processes. As we describe in this chapter, the single mitochondrion of T. brucei is everything but simple and as such rivals mitochondria of multicellular organisms.
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Affiliation(s)
- Zdeněk Verner
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Present address: Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Present address: Faculty of Sciences, Charles University, Prague, Czech Republic
| | - Somsuvro Basu
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic; Present address: Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Germany
| | - Corinna Benz
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Sameer Dixit
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Eva Dobáková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Present address: Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Drahomíra Faktorová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Hassan Hashimi
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Eva Horáková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic
| | - Zhenqiu Huang
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Zdeněk Paris
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic
| | - Priscila Peña-Diaz
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic
| | - Lucie Ridlon
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic; Present address: Salk Institute, La Jolla, San Diego, USA
| | - Jiří Týč
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - David Wildridge
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic
| | - Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
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12
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Carnes J, Lerch M, Kurtz I, Stuart K. Bloodstream form Trypanosoma brucei do not require mRPN1 for gRNA processing. RNA (NEW YORK, N.Y.) 2015; 21:28-35. [PMID: 25404564 PMCID: PMC4274635 DOI: 10.1261/rna.045708.114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 10/06/2014] [Indexed: 06/04/2023]
Abstract
Mitochondrial RNA processing in the kinetoplastid parasite Trypanosoma brucei involves numerous specialized catalytic activities that are incompletely understood. The mitochondrial genome consists of maxicircles that primarily encode rRNAs and mRNAs, and minicircles that encode a diverse array of guide RNAs (gRNAs). RNA editing uses these gRNAs as templates to recode mRNAs by insertion and deletion of uridine (U) residues. While the multiprotein complex that catalyzes RNA editing has been extensively studied, other players involved in mitochondrial RNA processing have remained enigmatic. The proteins required for processing mitochondrial polycistronic transcripts into mature species was essentially unknown until an RNase III endonuclease, called mRPN1, was reported to be involved in gRNA processing in procyclic form parasites. In this work, we examine the role of mRPN1 in gRNA processing in bloodstream form parasites, and show that complete elimination of mRPN1 by gene knockout does not alter gRNA maturation. These results indicate that another enzyme must be involved in gRNA processing.
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Affiliation(s)
- Jason Carnes
- Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
| | - Melissa Lerch
- Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
| | - Irina Kurtz
- Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
| | - Ken Stuart
- Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
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13
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Koslowsky D, Sun Y, Hindenach J, Theisen T, Lucas J. The insect-phase gRNA transcriptome in Trypanosoma brucei. Nucleic Acids Res 2014; 42:1873-86. [PMID: 24174546 PMCID: PMC3919587 DOI: 10.1093/nar/gkt973] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 09/30/2013] [Accepted: 10/01/2013] [Indexed: 11/13/2022] Open
Abstract
One of the most striking examples of small RNA regulation of gene expression is the process of RNA editing in the mitochondria of trypanosomes. In these parasites, RNA editing involves extensive uridylate insertions and deletions within most of the mitochondrial messenger RNAs (mRNAs). Over 1200 small guide RNAs (gRNAs) are predicted to be responsible for directing the sequence changes that create start and stop codons, correct frameshifts and for many of the mRNAs generate most of the open reading frame. In addition, alternative editing creates the opportunity for unprecedented protein diversity. In Trypanosoma brucei, the vast majority of gRNAs are transcribed from minicircles, which are approximately one kilobase in size, and encode between three and four gRNAs. The large number (5000-10,000) and their concatenated structure make them difficult to sequence. To identify the complete set of gRNAs necessary for mRNA editing in T. brucei, we used Illumina deep sequencing of purified gRNAs from the procyclic stage. We report a near complete set of gRNAs needed to direct the editing of the mRNAs.
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Affiliation(s)
- Donna Koslowsky
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA, Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Yanni Sun
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA, Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jordan Hindenach
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA, Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Terence Theisen
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA, Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jasmin Lucas
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA, Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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14
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Kolesnikov AA, Gerasimov ES. Diversity of mitochondrial genome organization. BIOCHEMISTRY (MOSCOW) 2013; 77:1424-35. [PMID: 23379519 DOI: 10.1134/s0006297912130020] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In this review, we discuss types of mitochondrial genome structural organization (architecture), which includes the following characteristic features: size and the shape of DNA molecule, number of encoded genes, presence of cryptogenes, and editing of primary transcripts.
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Affiliation(s)
- A A Kolesnikov
- Biological Faculty, Lomonosov Moscow State University, Moscow, 119234, Russia.
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15
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Madina BR, Kuppan G, Vashisht AA, Liang YH, Downey KM, Wohlschlegel JA, Ji X, Sze SH, Sacchettini JC, Read LK, Cruz-Reyes J. Guide RNA biogenesis involves a novel RNase III family endoribonuclease in Trypanosoma brucei. RNA (NEW YORK, N.Y.) 2011; 17:1821-30. [PMID: 21810935 PMCID: PMC3185915 DOI: 10.1261/rna.2815911] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 06/29/2011] [Indexed: 05/29/2023]
Abstract
The mitochondrial genome of kinetoplastids, including species of Trypanosoma and Leishmania, is an unprecedented DNA structure of catenated maxicircles and minicircles. Maxicircles represent the typical mitochondrial genome encoding components of the respiratory complexes and ribosomes. However, most mRNA sequences are cryptic, and their maturation requires a unique U insertion/deletion RNA editing. Minicircles encode hundreds of small guide RNAs (gRNAs) that partially anneal with unedited mRNAs and direct the extensive editing. Trypanosoma brucei gRNAs and mRNAs are transcribed as polycistronic precursors, which undergo processing preceding editing; however, the relevant nucleases are unknown. We report the identification and functional characterization of a close homolog of editing endonucleases, mRPN1 (mitochondrial RNA precursor-processing endonuclease 1), which is involved in gRNA biogenesis. Recombinant mRPN1 is a dimeric dsRNA-dependent endonuclease that requires Mg(2+), a critical catalytic carboxylate, and generates 2-nucleotide 3' overhangs. The cleavage specificity of mRPN1 is reminiscent of bacterial RNase III and thus is fundamentally distinct from editing endonucleases, which target a single scissile bond just 5' of short duplexes. An inducible knockdown of mRPN1 in T. brucei results in loss of gRNA and accumulation of precursor transcripts (pre-gRNAs), consistent with a role of mRPN1 in processing. mRPN1 stably associates with three proteins previously identified in relatively large complexes that do not contain mRPN1, and have been linked with multiple aspects of mitochondrial RNA metabolism. One protein, TbRGG2, directly binds mRPN1 and is thought to modulate gRNA utilization by editing complexes. The proposed participation of mRPN1 in processing of polycistronic RNA and its specific protein interactions in gRNA expression are discussed.
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Affiliation(s)
- Bhaskara Reddy Madina
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
| | - Gokulan Kuppan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
| | - Ajay A. Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095-1737, USA
| | - Yu-He Liang
- Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Kurtis M. Downey
- Department of Microbiology and Immunology, University at Buffalo, State University of New York, Buffalo, New York 14214, USA
| | - James A. Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095-1737, USA
| | - Xinhua Ji
- Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Sing-Hoi Sze
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - James C. Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
| | - Laurie K. Read
- Department of Microbiology and Immunology, University at Buffalo, State University of New York, Buffalo, New York 14214, USA
| | - Jorge Cruz-Reyes
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
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16
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Aphasizhev R, Aphasizheva I. Mitochondrial RNA processing in trypanosomes. Res Microbiol 2011; 162:655-63. [PMID: 21596134 DOI: 10.1016/j.resmic.2011.04.015] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Accepted: 04/04/2011] [Indexed: 01/20/2023]
Abstract
The mitochondrial genome of trypanosomes is composed of ∼50 maxicircles and thousands of minicircles. Maxi-(∼25 kb) and mini-(∼1 kb)circles are catenated and packed into a dense structure called a kinetoplast. Both types of circular DNA are transcribed by a phage-like RNA polymerase: maxicircles yield multicistronic rRNA and mRNA precursors, while guide RNA (gRNA) precursors are produced from minicircles. To function in mitochondrial translation, pre-mRNAs must undergo a nucleolytic processing and 3' modifications, and often uridine insertion/deletion editing. gRNAs, which represent short (50-60 nt) RNAs directing editing reactions, are produced by 3' nucleolytic processing of a much longer precursor followed by 3' uridylation. Ribosomal RNAs are excised from precursors and their 3' ends are also trimmed and uridylated. All tRNAs are imported from the cytoplasm and some are further modified and edited in the mitochondrial matrix. Historically, the fascinating phenomenon of RNA editing has been extensively studied as an isolated pathway in which nuclear-encoded proteins mediate interactions of maxi- and minicircle transcripts to create open reading frames. However, recent studies unraveled a highly integrated network of mitochondrial genome expression including critical pre- and post-editing 3' mRNA processing, and gRNA and rRNA maturation steps. Here we focus on RNA 3' adenylation and uridylation as processes essential for biogenesis, stability and functioning of mitochondrial RNAs.
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Affiliation(s)
- Ruslan Aphasizhev
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, B240 Medical Sciences I, Irvine, CA 92697, USA.
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17
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Aphasizheva I, Aphasizhev R. RET1-catalyzed uridylylation shapes the mitochondrial transcriptome in Trypanosoma brucei. Mol Cell Biol 2010; 30:1555-67. [PMID: 20086102 PMCID: PMC2832499 DOI: 10.1128/mcb.01281-09] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 10/30/2009] [Accepted: 01/05/2010] [Indexed: 01/25/2023] Open
Abstract
RNA uridylylation is critical for the expression of the mitochondrial genome in trypanosomes. Short U tails are added to guide RNAs and rRNAs, while long A/U heteropolymers mark 3' ends of most mRNAs. Three divergent mitochondrial terminal uridylyl transferases (TUTases) are known: RET1 catalyzes guide RNA (gRNA) uridylylation, RET2 executes U insertion mRNA editing, and MEAT1 associates with the editosome-like complex. However, the activities responsible for 3' uridylylation of rRNAs and mRNAs, and the roles of these modifications, are unclear. To dissect the functions of mitochondrial TUTases, we investigated the effects of their repression and overexpression on abundance, processing, 3'-end status, and in vivo stability of major mitochondrially encoded RNA classes. We show that RET1 adds U tails to gRNAs, rRNAs, and select mRNAs and contributes U's into A/U heteropolymers. Furthermore, RET1's TUTase activity is required for the nucleolytic processing of gRNA, rRNA, and mRNA precursors. The U tail's presence does not affect the stability of gRNAs and rRNAs, while transcript-specific uridylylation triggers 3' to 5' mRNA decay. We propose that the minicircle-encoded antisense transcripts, which are stabilized by RET1-catalyzed uridylylation, may direct a nucleolytic cleavage of multicistronic precursors.
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Affiliation(s)
- Inna Aphasizheva
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, California 92697
| | - Ruslan Aphasizhev
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, California 92697
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18
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Guo X, Ernst NL, Carnes J, Stuart KD. The zinc-fingers of KREPA3 are essential for the complete editing of mitochondrial mRNAs in Trypanosoma brucei. PLoS One 2010; 5:e8913. [PMID: 20111718 PMCID: PMC2811742 DOI: 10.1371/journal.pone.0008913] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Accepted: 12/30/2009] [Indexed: 01/16/2023] Open
Abstract
Most mitochondrial mRNAs in trypanosomes undergo uridine insertion/deletion editing that is catalyzed by ∼20S editosomes. The editosome component KREPA3 is essential for editosome structural integrity and its two zinc finger (ZF) motifs are essential for editing in vivo but not in vitro. KREPA3 function was further explored by examining the consequence of mutation of its N- and C- terminal ZFs (ZF1 and ZF2, respectively). Exclusively expressed myc-tagged KREPA3 with ZF2 mutation resulted in lower KREPA3 abundance and a relative increase in KREPA2 and KREL1 proteins. Detailed analysis of edited RNA products revealed the accumulation of partially edited mRNAs with less insertion editing compared to the partially edited mRNAs found in the cells with wild type KREPA3 expression. Mutation of ZF1 in TAP-tagged KREPA3 also resulted in accumulation of partially edited mRNAs that were shorter and only edited in the 3′-terminal editing region. Mutation of both ZFs essentially eliminated partially edited mRNA. The mutations did not affect gRNA abundance. These data indicate that both ZFs are essential for the progression of editing and perhaps its accuracy, which suggests that KREPA3 plays roles in the editing process via its ZFs interaction with editosome proteins and/or RNA substrates.
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Affiliation(s)
- Xuemin Guo
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Nancy Lewis Ernst
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Jason Carnes
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Kenneth D. Stuart
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- * E-mail:
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19
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Koslowsky DJ. Complex interactions in the regulation of trypanosome mitochondrial gene expression. Trends Parasitol 2009; 25:252-5. [PMID: 19443271 DOI: 10.1016/j.pt.2009.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Revised: 03/13/2009] [Accepted: 03/19/2009] [Indexed: 02/04/2023]
Abstract
Trypanosomes undergo extreme physiological changes to adapt to different environments as they cycle between hosts. Adaptation to the different environments has evolved an energy metabolism involving a mitochondrion with an unusual genome. Recently, Aphasizhev and colleagues have identified two new protein complexes, a mitochondrial polyadenylation complex and a guide RNA stabilization complex, that provide novel insights into the coordinated expression of the mitochondrial genome.
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Affiliation(s)
- Donna J Koslowsky
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
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Aphasizhev R, Aphasizheva I. Terminal RNA uridylyltransferases of trypanosomes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2007; 1779:270-80. [PMID: 18191648 DOI: 10.1016/j.bbagrm.2007.12.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Revised: 12/10/2007] [Accepted: 12/13/2007] [Indexed: 12/14/2022]
Abstract
Terminal RNA uridylyltransferases (TUTases) are functionally and structurally diverse nucleotidyl transferases that catalyze template-independent 3' uridylylation of RNAs. Within the DNA polymerase beta-type superfamily, TUTases are closely related to non-canonical poly(A) polymerases. Studies of U-insertion/deletion RNA editing in mitochondria of trypanosomatids identified the first TUTase proteins and their cellular functions: post-transcriptional uridylylation of guide RNAs by RNA editing TUTase 1 (RET1) and U-insertion mRNA editing by RNA editing TUTase 2 (RET2). The editing TUTases possess conserved catalytic and nucleotide base recognition domains, yet differ in quaternary structure, substrate specificity and processivity. The cytosolic TUTases TUT3 and TUT4 have also been identified in trypanosomes but their biological roles remain to be established. Structural analyses have revealed a mechanism of cognate nucleoside triphosphate selection by TUTases, which includes protein-UTP contacts as well as contribution of the RNA substrate. This review focuses on biological functions and structures of trypanosomal TUTases.
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Affiliation(s)
- Ruslan Aphasizhev
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697-4025, USA.
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A population study of the minicircles in Trypanosoma cruzi: predicting guide RNAs in the absence of empirical RNA editing. BMC Genomics 2007; 8:133. [PMID: 17524149 PMCID: PMC1892023 DOI: 10.1186/1471-2164-8-133] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Accepted: 05/24/2007] [Indexed: 02/08/2023] Open
Abstract
Background The structurally complex network of minicircles and maxicircles comprising the mitochondrial DNA of kinetoplastids mirrors the complexity of the RNA editing process that is required for faithful expression of encrypted maxicircle genes. Although a few of the guide RNAs that direct this editing process have been discovered on maxicircles, guide RNAs are mostly found on the minicircles. The nuclear and maxicircle genomes have been sequenced and assembled for Trypanosoma cruzi, the causative agent of Chagas disease, however the complement of 1.4-kb minicircles, carrying four guide RNA genes per molecule in this parasite, has been less thoroughly characterised. Results Fifty-four CL Brener and 53 Esmeraldo strain minicircle sequence reads were extracted from T. cruzi whole genome shotgun sequencing data. With these sequences and all published T. cruzi minicircle sequences, 108 unique guide RNAs from all known T. cruzi minicircle sequences and two guide RNAs from the CL Brener maxicircle were predicted using a local alignment algorithm and mapped onto predicted or experimentally determined sequences of edited maxicircle open reading frames. For half of the sequences no statistically significant guide RNA could be assigned. Likely positions of these unidentified gRNAs in T. cruzi minicircle sequences are estimated using a simple Hidden Markov Model. With the local alignment predictions as a standard, the HMM had an ~85% chance of correctly identifying at least 20 nucleotides of guide RNA from a given minicircle sequence. Inter-minicircle recombination was documented. Variable regions contain species-specific areas of distinct nucleotide preference. Two maxicircle guide RNA genes were found. Conclusion The identification of new minicircle sequences and the further characterization of all published minicircles are presented, including the first observation of recombination between minicircles. Extrapolation suggests a level of 4% recombinants in the population, supporting a relatively high recombination rate that may serve to minimize the persistence of gRNA pseudogenes. Characteristic nucleotide preferences observed within variable regions provide potential clues regarding the transcription and maturation of T. cruzi guide RNAs. Based on these preferences, a method of predicting T. cruzi guide RNAs using only primary minicircle sequence data was created.
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Madej MJ, Alfonzo JD, Hüttenhofer A. Small ncRNA transcriptome analysis from kinetoplast mitochondria of Leishmania tarentolae. Nucleic Acids Res 2007; 35:1544-54. [PMID: 17287292 PMCID: PMC1865066 DOI: 10.1093/nar/gkm004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Revised: 12/21/2006] [Accepted: 12/22/2006] [Indexed: 11/12/2022] Open
Abstract
Gene expression in mitochondria of kinetoplastid protozoa requires RNA editing, a post-transcriptional process which involves insertion or deletion of uridine residues at specific sites within mitochondrial pre-mRNAs. Sequence specificity of the RNA editing process is mediated by oligo-uridylated small, non-coding RNAs, designated as guide RNAs (gRNAs). In this study, we have analyzed the small ncRNA transcriptome from kinetoplast mitochondria of Leishmania tarentolae by generating specialized cDNA libraries encoding size-selected RNA species. Through this screen, a significant number of novel oligo-uridylated RNA species, which we have termed oU-RNAs, has been identified. Most novel oU-RNAs are present as stable RNA species in mitochondria as assessed by northern blot analysis. Thereby, novel oU-RNAs show similar expression levels and sizes as previously reported for canonical gRNAs. Several oU-RNAs are transcribed from both strands of the maxicircle and minicircles components of the mitochondrial genome, from regions where up till now no transcription has been reported. Two stable oU-RNAs exhibit an anchor sequence in antisense orientation to known gRNAs and thus might regulate editing of respective pre-mRNAs. A number of oU-RNAs map in antisense orientation to non-edited protein-coding genes suggesting that they might function by a different mechanism. In addition, our screen shows that all kinetoplast-derived RNAs are prone to some degree of uridylation.
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MESH Headings
- Animals
- Cells, Cultured
- DNA, Circular/chemistry
- Gene Library
- Leishmania/genetics
- Leishmania/metabolism
- Mitochondria/genetics
- Mitochondria/metabolism
- Oligoribonucleotides/analysis
- Protozoan Proteins/genetics
- RNA/biosynthesis
- RNA/chemistry
- RNA/genetics
- RNA, Antisense/genetics
- RNA, Guide, Kinetoplastida/biosynthesis
- RNA, Guide, Kinetoplastida/chemistry
- RNA, Guide, Kinetoplastida/genetics
- RNA, Mitochondrial
- RNA, Untranslated/genetics
- Sequence Analysis, DNA
- Transcription, Genetic
- Uracil Nucleotides/analysis
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Affiliation(s)
- Monika J. Madej
- Innsbruck Biocenter, Division of Genomics and RNomics, Innsbruck Medical University, Fritz-Pregl-Strasse. 3, 6020 Innsbruck, Austria and Department of Microbiology, Ohio State Biochemistry Program and The RNA Group, The Ohio State University, 484 West 12th Ave., Columbus, OH 43210, USA
| | - Juan D. Alfonzo
- Innsbruck Biocenter, Division of Genomics and RNomics, Innsbruck Medical University, Fritz-Pregl-Strasse. 3, 6020 Innsbruck, Austria and Department of Microbiology, Ohio State Biochemistry Program and The RNA Group, The Ohio State University, 484 West 12th Ave., Columbus, OH 43210, USA
| | - Alexander Hüttenhofer
- Innsbruck Biocenter, Division of Genomics and RNomics, Innsbruck Medical University, Fritz-Pregl-Strasse. 3, 6020 Innsbruck, Austria and Department of Microbiology, Ohio State Biochemistry Program and The RNA Group, The Ohio State University, 484 West 12th Ave., Columbus, OH 43210, USA
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23
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Lukes J, Hashimi H, Zíková A. Unexplained complexity of the mitochondrial genome and transcriptome in kinetoplastid flagellates. Curr Genet 2005; 48:277-99. [PMID: 16215758 DOI: 10.1007/s00294-005-0027-0] [Citation(s) in RCA: 145] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2005] [Revised: 09/03/2005] [Accepted: 09/07/2005] [Indexed: 10/25/2022]
Abstract
Kinetoplastids are flagellated protozoans, whose members include the pathogens Trypanosoma brucei, T. cruzi and Leishmania species, that are considered among the earliest diverging eukaryotes with a mitochondrion. This organelle has become famous because of its many unusual properties, which are unique to the order Kinetoplastida, including an extensive kinetoplast DNA network and U-insertion/deletion type RNA editing of its mitochondrial transcripts. In the last decade, considerable progress has been made in elucidating the complex machinery of RNA editing. Moreover, our understanding of the structure and replication of kinetoplast DNA has also dramatically improved. Much less however, is known, about the developmental regulation of RNA editing, its integration with other RNA maturation processes, stability of mitochondrial mRNAs, or evolution of the editing process itself. Yet the profusion of genomic data recently made available by sequencing consortia, in combination with methods of reverse genetics, hold promise in understanding the complexity of this exciting organelle, knowledge of which may enable us to fight these often medically important protozoans.
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Affiliation(s)
- Julius Lukes
- Institute of Parasitology, Czech Academy of Sciences, Faculty of Biology, University of South Bohemia, Branisovská 31, 37005, Ceské Budejovice, Czech Republic.
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