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Chaudhuri M, Tripathi A, Gonzalez FS. Diverse Functions of Tim50, a Component of the Mitochondrial Inner Membrane Protein Translocase. Int J Mol Sci 2021; 22:7779. [PMID: 34360547 PMCID: PMC8346121 DOI: 10.3390/ijms22157779] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 12/17/2022] Open
Abstract
Mitochondria are essential in eukaryotes. Besides producing 80% of total cellular ATP, mitochondria are involved in various cellular functions such as apoptosis, inflammation, innate immunity, stress tolerance, and Ca2+ homeostasis. Mitochondria are also the site for many critical metabolic pathways and are integrated into the signaling network to maintain cellular homeostasis under stress. Mitochondria require hundreds of proteins to perform all these functions. Since the mitochondrial genome only encodes a handful of proteins, most mitochondrial proteins are imported from the cytosol via receptor/translocase complexes on the mitochondrial outer and inner membranes known as TOMs and TIMs. Many of the subunits of these protein complexes are essential for cell survival in model yeast and other unicellular eukaryotes. Defects in the mitochondrial import machineries are also associated with various metabolic, developmental, and neurodegenerative disorders in multicellular organisms. In addition to their canonical functions, these protein translocases also help maintain mitochondrial structure and dynamics, lipid metabolism, and stress response. This review focuses on the role of Tim50, the receptor component of one of the TIM complexes, in different cellular functions, with an emphasis on the Tim50 homologue in parasitic protozoan Trypanosoma brucei.
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Affiliation(s)
- Minu Chaudhuri
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN 37208, USA; (A.T.); (F.S.G.)
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Amodeo S, Kalichava A, Fradera-Sola A, Bertiaux-Lequoy E, Guichard P, Butter F, Ochsenreiter T. Characterization of the novel mitochondrial genome segregation factor TAP110 in Trypanosoma brucei. J Cell Sci 2021; 134:jcs.254300. [PMID: 33589495 PMCID: PMC7970207 DOI: 10.1242/jcs.254300] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/03/2021] [Indexed: 12/18/2022] Open
Abstract
Proper mitochondrial genome inheritance is important for eukaryotic cell survival. Trypanosoma brucei, a protozoan parasite, contains a singular mitochondrial genome, the kinetoplast (k)DNA. The kDNA is anchored to the basal body via the tripartite attachment complex (TAC) to ensure proper segregation. Several components of the TAC have been described; however, the connection of the TAC to the kDNA remains elusive. Here, we characterize the TAC-associated protein TAP110. We find that both depletion and overexpression of TAP110 leads to a delay in the separation of the replicated kDNA networks. Proteome analysis after TAP110 overexpression identified several kDNA-associated proteins that changed in abundance, including a TEX-like protein that dually localizes to the nucleus and the kDNA, potentially linking replication and segregation in the two compartments. The assembly of TAP110 into the TAC region seems to require the TAC but not the kDNA itself; however, once TAP110 has been assembled, it also interacts with the kDNA. Finally, we use ultrastructure expansion microscopy in trypanosomes for the first time, and reveal the precise position of TAP110 between TAC102 and the kDNA, showcasing the potential of this approach.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Simona Amodeo
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Ana Kalichava
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | | | - Eloïse Bertiaux-Lequoy
- Department of Cell Biology, University of Geneva, Sciences III, 1211 Geneva, Switzerland
| | - Paul Guichard
- Department of Cell Biology, University of Geneva, Sciences III, 1211 Geneva, Switzerland
| | - Falk Butter
- Institute of Molecular Biology, 55128 Mainz, Germany
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Singha UK, Tripathi A, Smith JT, Quinones L, Saha A, Singha T, Chaudhuri M. Novel IM-associated protein Tim54 plays a role in the mitochondrial import of internal signal-containing proteins in Trypanosoma brucei. Biol Cell 2021; 113:39-57. [PMID: 33084070 PMCID: PMC8265390 DOI: 10.1111/boc.202000054] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/28/2020] [Indexed: 01/16/2023]
Abstract
BACKGROUND The translocase of the mitochondrial inner membrane (TIM) imports most of the nucleus-encoded proteins that are destined for the matrix, inner membrane (IM) and the intermembrane space (IMS). Trypanosoma brucei, the infectious agent for African trypanosomiasis, possesses a unique TIM complex consisting of several novel proteins in association with a relatively conserved protein TbTim17. Tandem affinity purification of the TbTim17 protein complex revealed TbTim54 as a potential component of this complex. RESULTS TbTim54, a trypanosome-specific IMS protein, is peripherally associated with the IM and is present in a protein complex slightly larger than the TbTim17 complex. TbTim54 knockdown (KD) reduced the import of TbTim17 and compromised the integrity of the TbTim17 complex. TbTim54 KD inhibited the in vitro mitochondrial import and assembly of the internal signal-containing mitochondrial carrier proteins MCP3, MCP5 and MCP11 to a greater extent than TbTim17 KD. Furthermore, TbTim54 KD, but not TbTim17 KD, significantly hampered the mitochondrial targeting of ectopically expressed MCP3 and MCP11. These observations along with our previous finding that the mitochondrial import of N-terminal signal-containing proteins like cytochrome oxidase subunit 4 and MRP2 was affected to a greater extent by TbTim17 KD than TbTim54 KD indicating a substrate-specificity of TbTim54 for internal-signal containing mitochondrial proteins. In other organisms, small Tim chaperones in the IMS are known to participate in the translocation of MCPs. We found that TbTim54 can directly interact with at least two of the six known small TbTim proteins, TbTim11 and TbTim13, as well as with the N-terminal domain of TbTim17. CONCLUSION TbTim54 interacts with TbTim17. It also plays a crucial role in the mitochondrial import and complex assembly of internal signal-containing IM proteins in T. brucei. SIGNIFICANCE We are the first to characterise TbTim54, a novel TbTim that is involved primarily in the mitochondrial import of MCPs and TbTim17 in T. brucei.
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Mochizuki K, Inaoka DK, Mazet M, Shiba T, Fukuda K, Kurasawa H, Millerioux Y, Boshart M, Balogun EO, Harada S, Hirayama K, Bringaud F, Kita K. The ASCT/SCS cycle fuels mitochondrial ATP and acetate production in Trypanosoma brucei. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148283. [PMID: 32763239 PMCID: PMC7402102 DOI: 10.1016/j.bbabio.2020.148283] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 11/03/2022]
Abstract
Acetate:succinate CoA transferase (ASCT) is a mitochondrial enzyme that catalyzes the production of acetate and succinyl-CoA, which is coupled to ATP production with succinyl-CoA synthetase (SCS) in a process called the ASCT/SCS cycle. This cycle has been studied in Trypanosoma brucei (T. brucei), a pathogen of African sleeping sickness, and is involved in (i) ATP and (ii) acetate production and proceeds independent of oxygen and an electrochemical gradient. Interestingly, knockout of ASCT in procyclic form (PCF) of T. brucei cause oligomycin A-hypersensitivity phenotype indicating that ASCT/SCS cycle complements the deficiency of ATP synthase activity. In bloodstream form (BSF) of T. brucei, ATP synthase works in reverse to maintain the electrochemical gradient by hydrolyzing ATP. However, no information has been available on the source of ATP, although ASCT/SCS cycle could be a potential candidate. Regarding mitochondrial acetate production, which is essential for fatty acid biosynthesis and growth of T. brucei, ASCT or acetyl-CoA hydrolase (ACH) are known to be its source. Despite the importance of this cycle, direct evidence of its function is lacking, and there are no comprehensive biochemical or structural biology studies reported so far. Here, we show that in vitro–reconstituted ASCT/SCS cycle is highly specific towards acetyl-CoA and has a higher kcat than that of yeast and bacterial ATP synthases. Our results provide the first biochemical basis for (i) rescue of ATP synthase-deficient phenotype by ASCT/SCS cycle in PCF and (ii) a potential source of ATP for the reverse reaction of ATP synthase in BSF. First biochemical and structural characterization of mitochondrial ASCT/SCS cycle It is essential for mitochondrial acetate/ATP production and T. brucei BSF growth. TbASCT/SCS cycle shows higher kcat than that of yeast and bacterial ATP synthases. Detailed comparative biochemical analysis between ASCT and human SCOT Active site residue and X-CoA binding site determined by site-directed mutagenesis
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Affiliation(s)
- Kota Mochizuki
- Department of Immunogenetics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Japan; Graduate School of Biomedical Sciences, Nagasaki University, Japan
| | - Daniel Ken Inaoka
- Department of Molecular Infection Dynamics, Shionogi Global Infectious Diseases Division, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Japan; School of Tropical Medicine and Global Health, Nagasaki University, Japan; Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Japan.
| | - Muriel Mazet
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, CNRS UMR-5234, France
| | - Tomoo Shiba
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Japan.
| | - Keisuke Fukuda
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Japan
| | - Hana Kurasawa
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Japan
| | - Yoann Millerioux
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, CNRS UMR-5234, France
| | - Michael Boshart
- Fakultät für Biologie, Genetik, Ludwig-Maximilians-Universität München, Germany
| | - Emmanuel O Balogun
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Japan; Department of Biochemistry, Ahmadu Bello University, Nigeria
| | - Shigeharu Harada
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Japan
| | - Kenji Hirayama
- Department of Immunogenetics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Japan
| | - Frédéric Bringaud
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, CNRS UMR-5234, France
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, Japan; Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Japan; Department of Host - Defense Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Japan
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Causes and consequences of mitochondrial proteome size variation in animals. Mitochondrion 2020; 52:100-107. [DOI: 10.1016/j.mito.2020.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 12/23/2019] [Accepted: 02/13/2020] [Indexed: 12/25/2022]
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A Global Analysis of Enzyme Compartmentalization to Glycosomes. Pathogens 2020; 9:pathogens9040281. [PMID: 32290588 PMCID: PMC7237986 DOI: 10.3390/pathogens9040281] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 12/28/2022] Open
Abstract
In kinetoplastids, the first seven steps of glycolysis are compartmentalized into a glycosome along with parts of other metabolic pathways. This organelle shares a common ancestor with the better-understood eukaryotic peroxisome. Much of our understanding of the emergence, evolution, and maintenance of glycosomes is limited to explorations of the dixenous parasites, including the enzymatic contents of the organelle. Our objective was to determine the extent that we could leverage existing studies in model kinetoplastids to determine the composition of glycosomes in species lacking evidence of experimental localization. These include diverse monoxenous species and dixenous species with very different hosts. For many of these, genome or transcriptome sequences are available. Our approach initiated with a meta-analysis of existing studies to generate a subset of enzymes with highest evidence of glycosome localization. From this dataset we extracted the best possible glycosome signal peptide identification scheme for in silico identification of glycosomal proteins from any kinetoplastid species. Validation suggested that a high glycosome localization score from our algorithm would be indicative of a glycosomal protein. We found that while metabolic pathways were consistently represented across kinetoplastids, individual proteins within those pathways may not universally exhibit evidence of glycosome localization.
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Conserved motifs in nuclear genes encoding predicted mitochondrial proteins in Trypanosoma cruzi. PLoS One 2019; 14:e0215160. [PMID: 30964924 PMCID: PMC6456187 DOI: 10.1371/journal.pone.0215160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 03/27/2019] [Indexed: 11/19/2022] Open
Abstract
Trypanosoma cruzi, the protozoan parasite that causes Chagas’ disease, exhibits peculiar biological features. Among them, the presence of a unique mitochondrion is remarkable. Even though the mitochondrial DNA constitutes up to 25% of total cellular DNA, the structure and functionality of the mitochondrion are dependent on the expression of the nuclear genome. As in other eukaryotes, specific peptide signals have been proposed to drive the mitochondrial localization of a subset of trypanosomatid proteins. However, there are mitochondrial proteins encoded in the nuclear genome that lack of a peptide signal. In other eukaryotes, alternative protein targeting to subcellular organelles via mRNA localization has also been recognized and specific mRNA localization towards the mitochondria has been described. With the aim of seeking for mitochondrial localization signals in T. cruzi, we developed a strategy to build a comprehensive database of nuclear genes encoding predicted mitochondrial proteins (MiNT) in the TriTryps (T. cruzi, T. brucei and L. major). We found that approximately 15% of their nuclear genome encodes mitochondrial products. In T. cruzi the MiNT database reaches 1438 genes and a conserved peptide signal, M(L/F) R (R/S) SS, named TryM-TaPe is found in 60% of these genes, suggesting that the canonical mRNA guidance mechanism is present. In addition, the search for compositional signals in the transcripts of T. cruzi MiNT genes produce a list, being worth to note a conserved non-translated element represented by the consensus sequence DARRVSG. Taking into account its reported interaction with the T. brucei TRRM3 protein which is enriched in the mitochondrial membrane fraction, we here suggest a putative zip code role for this element. Globally, here we provide an inventory of the mitochondrial proteins in T. cruzi and give evidence for the existence of both peptide and mRNA signals specific to nuclear encoded mitochondrial proteins.
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Stevens M, Abdeen S, Salim N, Ray AM, Washburn A, Chitre S, Sivinski J, Park Y, Hoang QQ, Chapman E, Johnson SM. HSP60/10 chaperonin systems are inhibited by a variety of approved drugs, natural products, and known bioactive molecules. Bioorg Med Chem Lett 2019; 29:1106-1112. [PMID: 30852084 DOI: 10.1016/j.bmcl.2019.02.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/23/2019] [Accepted: 02/26/2019] [Indexed: 01/08/2023]
Abstract
All living organisms contain a unique class of molecular chaperones called 60 kDa heat shock proteins (HSP60 - also known as GroEL in bacteria). While some organisms contain more than one HSP60 or GroEL isoform, at least one isoform has always proven to be essential. Because of this, we have been investigating targeting HSP60 and GroEL chaperonin systems as an antibiotic strategy. Our initial studies focused on applying this antibiotic strategy for treating African sleeping sickness (caused by Trypanosoma brucei parasites) and drug-resistant bacterial infections (in particular Methicillin-resistant Staphylococcus aureus - MRSA). Intriguingly, during our studies we found that three known antibiotics - suramin, closantel, and rafoxanide - were potent inhibitors of bacterial GroEL and human HSP60 chaperonin systems. These findings prompted us to explore what other approved drugs, natural products, and known bioactive molecules might also inhibit HSP60 and GroEL chaperonin systems. Initial high-throughput screening of 3680 approved drugs, natural products, and known bioactives identified 161 hit inhibitors of the Escherichia coli GroEL chaperonin system (4.3% hit rate). From a purchased subset of 60 hits, 29 compounds (48%) re-confirmed as selective GroEL inhibitors in our assays, all of which were nearly equipotent against human HSP60. These findings illuminate the notion that targeting chaperonin systems might be a more common occurrence than we previously appreciated. Future studies are needed to determine if the in vivo modes of action of these approved drugs, natural products, and known bioactive molecules are related to GroEL and HSP60 inhibition.
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Affiliation(s)
- Mckayla Stevens
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States
| | - Sanofar Abdeen
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States
| | - Nilshad Salim
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States
| | - Anne-Marie Ray
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States
| | - Alex Washburn
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States
| | - Siddhi Chitre
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States
| | - Jared Sivinski
- The University of Arizona, College of Pharmacy, Department of Pharmacology and Toxicology, 1703 E. Mabel St., PO Box 210207, Tucson, AZ 85721, United States
| | - Yangshin Park
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States; Stark Neurosciences Research Institute, Indiana University School of Medicine. 320 W. 15th Street, Suite 414, Indianapolis, IN 46202, United States; Department of Neurology, Indiana University School of Medicine. 635 Barnhill Drive, Indianapolis, IN 46202, United States
| | - Quyen Q Hoang
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States; Stark Neurosciences Research Institute, Indiana University School of Medicine. 320 W. 15th Street, Suite 414, Indianapolis, IN 46202, United States; Department of Neurology, Indiana University School of Medicine. 635 Barnhill Drive, Indianapolis, IN 46202, United States
| | - Eli Chapman
- The University of Arizona, College of Pharmacy, Department of Pharmacology and Toxicology, 1703 E. Mabel St., PO Box 210207, Tucson, AZ 85721, United States
| | - Steven M Johnson
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States.
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Muthye V, Lavrov DV. Characterization of mitochondrial proteomes of nonbilaterian animals. IUBMB Life 2018; 70:1289-1301. [PMID: 30419142 DOI: 10.1002/iub.1961] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/08/2018] [Accepted: 09/29/2018] [Indexed: 12/18/2022]
Abstract
Mitochondria require ~1,500 proteins for their maintenance and proper functionality, which constitute the mitochondrial proteome (mt-proteome). Although a few of these proteins, mostly subunits of the electron transport chain complexes, are encoded in mitochondrial DNA (mtDNA), the vast majority are encoded in the nuclear genome and imported to the organelle. Previous studies have shown a continuous and complex evolution of mt-proteome among eukaryotes. However, there was less attention paid to mt-proteome evolution within Metazoa, presumably because animal mtDNA and, by extension, animal mitochondria are often considered to be uniform. In this analysis, two bioinformatic approaches (Orthologue-detection and Mitochondrial Targeting Sequence prediction) were used to identify mt-proteins in 23 species from four nonbilaterian phyla: Cnidaria, Ctenophora, Placozoa, and Porifera, as well as two choanoflagellates, the closest animal relatives. Our results revealed a large variation in mt-proteome in nonbilaterian animals in size and composition. Myxozoans, highly reduced cnidarian parasites, possessed the smallest inferred mitochondrial proteomes, while calcareous sponges possessed the largest. About 513 mitochondrial orthologous groups were present in all nonbilaterian phyla and human. Interestingly, 42 human mitochondrial proteins were not identified in any nonbilaterian species studied and represent putative innovations along the bilaterian branch. Several of these proteins were involved in apoptosis and innate immunity, two processes known to evolve within Metazoa. Conversely, several proteins identified as mitochondrial in nonbilaterian phyla and animal outgroups were absent in human, representing cases of possible loss. Finally, a few human cytosolic proteins, such as histones and cytosolic ribosomal proteins, were predicted to be targeted to mitochondria in nonbilaterian animals. Overall, our analysis provides the first step in characterization of mt-proteomes in nonbilaterian animals and understanding evolution of animal mt-proteome. © 2018 IUBMB Life, 70(12):1289-1301, 2018.
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Affiliation(s)
- Viraj Muthye
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Dennis V Lavrov
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
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Millerioux Y, Mazet M, Bouyssou G, Allmann S, Kiema TR, Bertiaux E, Fouillen L, Thapa C, Biran M, Plazolles N, Dittrich-Domergue F, Crouzols A, Wierenga RK, Rotureau B, Moreau P, Bringaud F. De novo biosynthesis of sterols and fatty acids in the Trypanosoma brucei procyclic form: Carbon source preferences and metabolic flux redistributions. PLoS Pathog 2018; 14:e1007116. [PMID: 29813135 PMCID: PMC5993337 DOI: 10.1371/journal.ppat.1007116] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 06/08/2018] [Accepted: 05/22/2018] [Indexed: 12/27/2022] Open
Abstract
De novo biosynthesis of lipids is essential for Trypanosoma brucei, a protist responsible for the sleeping sickness. Here, we demonstrate that the ketogenic carbon sources, threonine, acetate and glucose, are precursors for both fatty acid and sterol synthesis, while leucine only contributes to sterol production in the tsetse fly midgut stage of the parasite. Degradation of these carbon sources into lipids was investigated using a combination of reverse genetics and analysis of radio-labelled precursors incorporation into lipids. For instance, (i) deletion of the gene encoding isovaleryl-CoA dehydrogenase, involved in the leucine degradation pathway, abolished leucine incorporation into sterols, and (ii) RNAi-mediated down-regulation of the SCP2-thiolase gene expression abolished incorporation of the three ketogenic carbon sources into sterols. The SCP2-thiolase is part of a unidirectional two-step bridge between the fatty acid precursor, acetyl-CoA, and the precursor of the mevalonate pathway leading to sterol biosynthesis, 3-hydroxy-3-methylglutaryl-CoA. Metabolic flux through this bridge is increased either in the isovaleryl-CoA dehydrogenase null mutant or when the degradation of the ketogenic carbon sources is affected. We also observed a preference for fatty acids synthesis from ketogenic carbon sources, since blocking acetyl-CoA production from both glucose and threonine abolished acetate incorporation into sterols, while incorporation of acetate into fatty acids was increased. Interestingly, the growth of the isovaleryl-CoA dehydrogenase null mutant, but not that of the parental cells, is interrupted in the absence of ketogenic carbon sources, including lipids, which demonstrates the essential role of the mevalonate pathway. We concluded that procyclic trypanosomes have a strong preference for fatty acid versus sterol biosynthesis from ketogenic carbon sources, and as a consequence, that leucine is likely to be the main source, if not the only one, used by trypanosomes in the infected insect vector digestive tract to feed the mevalonate pathway.
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Affiliation(s)
- Yoann Millerioux
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, CNRS UMR-5234, Bordeaux, France
- Centre de Résonance Magnétique des Systèmes Biologiques (RMSB), Université de Bordeaux, CNRS UMR-5536, Bordeaux, France
| | - Muriel Mazet
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, CNRS UMR-5234, Bordeaux, France
- Centre de Résonance Magnétique des Systèmes Biologiques (RMSB), Université de Bordeaux, CNRS UMR-5536, Bordeaux, France
| | - Guillaume Bouyssou
- Membrane Biogenesis Laboratory, CNRS-University of Bordeaux, UMR-5200, INRA Bordeaux Aquitaine, Villenave d'Ornon, France
| | - Stefan Allmann
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, CNRS UMR-5234, Bordeaux, France
- Centre de Résonance Magnétique des Systèmes Biologiques (RMSB), Université de Bordeaux, CNRS UMR-5536, Bordeaux, France
| | - Tiila-Riikka Kiema
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Eloïse Bertiaux
- Trypanosome Transmission Group, Trypanosome Cell Biology Unit, Department of Parasites and Insect Vectors, INSERM U1201, Institut Pasteur, Paris, France
| | - Laetitia Fouillen
- Membrane Biogenesis Laboratory, CNRS-University of Bordeaux, UMR-5200, INRA Bordeaux Aquitaine, Villenave d'Ornon, France
- Metabolome Facility of Bordeaux, Functional Genomics Center, Villenave d'Ornon
| | - Chandan Thapa
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Marc Biran
- Centre de Résonance Magnétique des Systèmes Biologiques (RMSB), Université de Bordeaux, CNRS UMR-5536, Bordeaux, France
| | - Nicolas Plazolles
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, CNRS UMR-5234, Bordeaux, France
| | - Franziska Dittrich-Domergue
- Membrane Biogenesis Laboratory, CNRS-University of Bordeaux, UMR-5200, INRA Bordeaux Aquitaine, Villenave d'Ornon, France
| | - Aline Crouzols
- Trypanosome Transmission Group, Trypanosome Cell Biology Unit, Department of Parasites and Insect Vectors, INSERM U1201, Institut Pasteur, Paris, France
| | - Rik K. Wierenga
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Brice Rotureau
- Trypanosome Transmission Group, Trypanosome Cell Biology Unit, Department of Parasites and Insect Vectors, INSERM U1201, Institut Pasteur, Paris, France
| | - Patrick Moreau
- Membrane Biogenesis Laboratory, CNRS-University of Bordeaux, UMR-5200, INRA Bordeaux Aquitaine, Villenave d'Ornon, France
| | - Frédéric Bringaud
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, CNRS UMR-5234, Bordeaux, France
- Centre de Résonance Magnétique des Systèmes Biologiques (RMSB), Université de Bordeaux, CNRS UMR-5536, Bordeaux, France
- * E-mail:
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Amodeo S, Jakob M, Ochsenreiter T. Characterization of the novel mitochondrial genome replication factor MiRF172 in Trypanosoma brucei. J Cell Sci 2018; 131:jcs211730. [PMID: 29626111 PMCID: PMC5963845 DOI: 10.1242/jcs.211730] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 03/20/2018] [Indexed: 01/07/2023] Open
Abstract
The unicellular parasite Trypanosoma brucei harbors one mitochondrial organelle with a singular genome called the kinetoplast DNA (kDNA). The kDNA consists of a network of concatenated minicircles and a few maxicircles that form the kDNA disc. More than 30 proteins involved in kDNA replication have been described. However, several mechanistic questions are only poorly understood. Here, we describe and characterize minicircle replication factor 172 (MiRF172), a novel mitochondrial genome replication factor that is essential for cell growth and kDNA maintenance. By performing super-resolution microscopy, we show that MiRF172 is localized to the kDNA disc, facing the region between the genome and the mitochondrial membranes. We demonstrate that depletion of MiRF172 leads to a loss of minicircles and maxicircles. Detailed analysis suggests that MiRF172 is involved in the reattachment of replicated minicircles to the kDNA disc. Furthermore, we provide evidence that the localization of the replication factor MiRF172 not only depends on the kDNA itself, but also on the mitochondrial genome segregation machinery, suggesting an interaction between the two essential entities.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Simona Amodeo
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern CH-3012, Switzerland
| | - Martin Jakob
- Institute of Cell Biology, University of Bern, Bern, Switzerland
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12
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Morriswood B, Engstler M. Let's get fISSical: fast in silico synchronization as a new tool for cell division cycle analysis. Parasitology 2018; 145:196-209. [PMID: 28166845 PMCID: PMC5964468 DOI: 10.1017/s0031182017000038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/23/2016] [Accepted: 01/05/2017] [Indexed: 12/23/2022]
Abstract
Cell cycle progression is a question of fundamental biological interest. The coordinated duplication and segregation of all cellular structures and organelles is however an extremely complex process, and one which remains only partially understood even in the most intensively researched model organisms. Trypanosomes are in an unusual position in this respect - they are both outstanding model systems for fundamental questions in eukaryotic cell biology, and pathogens that are the causative agents of three of the neglected tropical diseases. As a failure to successfully complete cell division will be deleterious or lethal, analysis of the cell division cycle is of relevance both to basic biology and drug design efforts. Cell division cycle analysis is however experimentally challenging, as the analysis of phenotypes associated with it remains hypothesis-driven and therefore biased. Current methods of analysis are extremely labour-intensive, and cell synchronization remains difficult and unreliable. Consequently, there exists a need - both in basic and applied trypanosome biology - for a global, unbiased, standardized and high-throughput analysis of cell division cycle progression. In this review, the requirements - both practical and computational - for such a system are considered and compared with existing techniques for cell cycle analysis.
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Affiliation(s)
- Brooke Morriswood
- Department of Cell & Developmental Biology,University of Würzburg,Biocentre, Am Hubland, 97074 Würzburg,Germany
| | - Markus Engstler
- Department of Cell & Developmental Biology,University of Würzburg,Biocentre, Am Hubland, 97074 Würzburg,Germany
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Zíková A, Verner Z, Nenarokova A, Michels PAM, Lukeš J. A paradigm shift: The mitoproteomes of procyclic and bloodstream Trypanosoma brucei are comparably complex. PLoS Pathog 2017; 13:e1006679. [PMID: 29267392 PMCID: PMC5739487 DOI: 10.1371/journal.ppat.1006679] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- * E-mail:
| | - Zdeněk Verner
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Sciences, Charles University, Prague, Czech Republic
| | - Anna Nenarokova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Paul A. M. Michels
- Centre for Immunity, Infection and Evolution, The University of Edinburgh, Edinburgh, United Kingdom
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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14
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Kessler RL, Pavoni DP, Krieger MA, Probst CM. Trypanosoma cruzi specific mRNA amplification by in vitro transcription improves parasite transcriptomics in host-parasite RNA mixtures. BMC Genomics 2017; 18:793. [PMID: 29037144 PMCID: PMC5644099 DOI: 10.1186/s12864-017-4163-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 10/05/2017] [Indexed: 11/25/2022] Open
Abstract
Background Trypanosomatids are a group of protozoan parasites that includes the etiologic agents of important human illnesses as Chagas disease, sleeping sickness and leishmaniasis. These parasites have a significant distinction from other eukaryotes concerning mRNA structure, since all mature mRNAs have an identical species-specific sequence of 39 nucleotides at the 5′ extremity, named spliced leader (SL). Considering this peculiar aspect of trypanosomatid mRNA, the aim of the present work was to develop a Trypanosoma cruzi specific in vitro transcription (IVT) linear mRNA amplification method in order to improve parasite transcriptomics analyses. Methods We designed an oligonucleotide complementary to the last 21 bases of T. cruzi SL sequence, bearing an upstream T7 promoter (T7SL primer), which was used to direct the synthesis of second-strand cDNA. Original mRNA was then amplified by IVT using T7 RNA polymerase. T7SL-amplified RNA from two distinct T. cruzi stages (epimastigotes and trypomastigotes) were deep sequenced in SOLiD platform. Usual poly(A) + RNA and and T7-oligo(dT) amplified RNA (Eberwine method) were also sequenced. RNA-Seq reads were aligned to our new and improved T. cruzi Dm28c genome assembly (PacBio technology) and resulting transcriptome pattern from these three RNA preparation methods were compared, mainly concerning the conservation of mRNA transcritional levels and DEGs detection between epimastigotes and trypomastigotes. Results T7SL IVT method detected more potential differentially expressed genes in comparison to either poly(A) + RNA or T7dT IVT, and was also able to produce reliable quantifications of the parasite transcriptome down to 3 ng of total RNA. Furthermore, amplification of parasite mRNA in HeLa/epimastigote RNA mixtures showed that T7SL IVT generates transcriptome quantification with similar detection of differentially expressed genes when parasite RNA mass was only 0.1% of the total mixture (R = 0.78 when compared to poly(A) + RNA). Conclusions The T7SL IVT amplification method presented here allows the detection of more potential parasite differentially expressed genes (in comparison to poly(A) + RNA) in host-parasite mixtures or samples with low amount of RNA. This method is especially useful for trypanosomatid transcriptomics because it produces less bias than PCR-based mRNA amplification. Additionally, by simply changing the complementary region of the T7SL primer, the present method can be applied to any trypanosomatid species. Electronic supplementary material The online version of this article (10.1186/s12864-017-4163-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rafael Luis Kessler
- Functional Genomics Laboratory, Instituto Carlos Chagas, FIOCRUZ, Curitiba, PR, Brazil
| | - Daniela Parada Pavoni
- Functional Genomics Laboratory, Instituto Carlos Chagas, FIOCRUZ, Curitiba, PR, Brazil
| | - Marco Aurelio Krieger
- Functional Genomics Laboratory, Instituto Carlos Chagas, FIOCRUZ, Curitiba, PR, Brazil
| | - Christian Macagnan Probst
- Functional Genomics Laboratory, Instituto Carlos Chagas, FIOCRUZ, Curitiba, PR, Brazil. .,Bioinformatics and Computational Biology Laboratory, Instituto Carlos Chagas, FIOCRUZ, Curitiba, PR, Brazil.
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Weems E, Singha UK, Smith JT, Chaudhuri M. The divergent N-terminal domain of Tim17 is critical for its assembly in the TIM complex in Trypanosoma brucei. Mol Biochem Parasitol 2017; 218:4-15. [PMID: 28965880 DOI: 10.1016/j.molbiopara.2017.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 09/18/2017] [Accepted: 09/25/2017] [Indexed: 10/18/2022]
Abstract
Trypanosoma brucei Tim17(TbTim17), the single member of the Tim17/23/22 protein family, is an essential component of the translocase of the mitochondrial inner membrane (TIM). In spite of the conserved secondary structure, the primary sequence of TbTim17, particularly the N-terminal hydrophilic region, is significantly divergent. In order to understand the function of this region we expressed two N-terminal deletion mutants (Δ20 and Δ30) of TbTim17 in T. brucei. Both of these mutants of TbTim17 were targeted to mitochondria, however, they failed to complement the growth defect of TbTim17 RNAi cells. In addition, the import defect of other nuclear encoded proteins into TbTim17 knockdown mitochondria were not restored by expression of the N-terminal deletion mutants but complemented by knock-in of the full-length protein. Further analysis revealed that Δ20-TbTim17 and Δ30-TbTim17 mutants were not localized in the mitochondrial inner membrane. Analysis of the protein complexes in the wild type and mutant mitochondria by two-dimensional Blue-native/SDS-PAGE revealed that none of these mutants are assembled into the TbTim17 protein complex. However, FL-TbTim17 was integrated into the mitochondrial inner membrane and assembled into TbTim17 complex. Co-immunoprecipitation analysis showed that unlike the FL-TbTim17, mutant proteins are not associated with the endogenous TbTim17 as well as its interacting partner TbTim62, a novel trypanosome specific Tim. Together, these results show that the N-terminal domain of TbTim17 plays unique and essential roles for its sorting and assembly into the TbTim17 protein complex.
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Affiliation(s)
- Ebony Weems
- Department of Microbiology and Immunology, Meharry Medical College, Nashville, TN, 37209, United States
| | - Ujjal K Singha
- Department of Microbiology and Immunology, Meharry Medical College, Nashville, TN, 37209, United States
| | - Joseph T Smith
- Department of Microbiology and Immunology, Meharry Medical College, Nashville, TN, 37209, United States
| | - Minu Chaudhuri
- Department of Microbiology and Immunology, Meharry Medical College, Nashville, TN, 37209, United States.
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Montenegro M, Cuervo C, Cardenas C, Duarte S, Díaz JR, Thomas MC, Lopez MC, Puerta CJ. Identification of a type I nitroreductase gene in non-virulent Trypanosoma rangeli. Mem Inst Oswaldo Cruz 2017; 112:504-509. [PMID: 28591312 PMCID: PMC5452488 DOI: 10.1590/0074-02760160532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 03/22/2017] [Indexed: 11/21/2022] Open
Abstract
Trypanosomatid type I nitroreductases (NTRs), i.e., mitochondrial enzymes that metabolise nitroaromatic pro-drugs, are essential for parasite growth, infection, and survival. Here, a type I NTR of non-virulent protozoan Trypanosoma rangeli is described and compared to those of other trypanosomatids. The NTR gene was isolated from KP1(+) and KP1(-) strains, and its corresponding transcript and 5’ untranslated region (5’UTR) were determined. Bioinformatics analyses and nitro-drug activation assays were also performed. The results indicated that the type I NTR gene is present in both KP1(-) and KP1(+) strains, with 98% identity. However, the predicted subcellular localisation of the protein differed among the strains (predicted as mitochondrial in the KP1(+) strain). Comparisons of the domains and 3D structures of the NTRs with those of orthologs demonstrated that the nitroreductase domain of T. rangeli NTR is conserved across all the strains, including the residues involved in the interaction with the FMN cofactor and in the tertiary structure characteristics of this oxidoreductase protein family. mRNA processing and expression were also observed. In addition, T. rangeli was shown to be sensitive to benznidazole and nifurtimox in a concentration-dependent manner. In summary, T. rangeli appears to have a newly discovered functional type I NTR.
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Affiliation(s)
- Marjorie Montenegro
- Pontificia Universidad Javeriana, Facultad de Ciencias, Departamento de Microbiología, Laboratorio de Parasitología Molecular, Bogotá, Colombia.,Consejo Superior de Investigaciones Científicas, Instituto de Parasitología y Biomedicina López Neyra, Granada, Spain
| | - Claudia Cuervo
- Pontificia Universidad Javeriana, Facultad de Ciencias, Departamento de Microbiología, Laboratorio de Parasitología Molecular, Bogotá, Colombia
| | - Constanza Cardenas
- Pontificia Universidad Católica de Valparaíso, Núcleo de Biotecnología Curauma, Valparaíso, Chile
| | - Silvia Duarte
- Pontificia Universidad Javeriana, Facultad de Ciencias, Departamento de Microbiología, Laboratorio de Parasitología Molecular, Bogotá, Colombia
| | - Jenny R Díaz
- Pontificia Universidad Javeriana, Facultad de Ciencias, Departamento de Microbiología, Laboratorio de Parasitología Molecular, Bogotá, Colombia
| | - M Carmen Thomas
- Consejo Superior de Investigaciones Científicas, Instituto de Parasitología y Biomedicina López Neyra, Granada, Spain
| | - Manuel C Lopez
- Consejo Superior de Investigaciones Científicas, Instituto de Parasitología y Biomedicina López Neyra, Granada, Spain
| | - Concepcion J Puerta
- Pontificia Universidad Javeriana, Facultad de Ciencias, Departamento de Microbiología, Laboratorio de Parasitología Molecular, Bogotá, Colombia
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Charting organellar importomes by quantitative mass spectrometry. Nat Commun 2017; 8:15272. [PMID: 28485388 PMCID: PMC5436138 DOI: 10.1038/ncomms15272] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 03/15/2017] [Indexed: 11/08/2022] Open
Abstract
Protein import into organelles is essential for all eukaryotes and facilitated by multi-protein translocation machineries. Analysing whether a protein is transported into an organelle is largely restricted to single constituents. This renders knowledge about imported proteins incomplete, limiting our understanding of organellar biogenesis and function. Here we introduce a method that enables charting an organelle's importome. The approach relies on inducible RNAi-mediated knockdown of an essential subunit of a translocase to impair import and quantitative mass spectrometry. To highlight its potential, we established the mitochondrial importome of Trypanosoma brucei, comprising 1,120 proteins including 331 new candidates. Furthermore, the method allows for the identification of proteins with dual or multiple locations and the substrates of distinct protein import pathways. We demonstrate the specificity and versatility of this ImportOmics method by targeting import factors in mitochondria and glycosomes, which demonstrates its potential for globally studying protein import and inventories of organelles. Knowing the specific protein content of individual organelles is necessary for an integrated understanding of cellular physiology. Here the authors describe a mass spectrometry-based approach to identify the substrates of distinct protein import pathways and define organellar proteomes.
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18
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Mantilla BS, Marchese L, Casas-Sánchez A, Dyer NA, Ejeh N, Biran M, Bringaud F, Lehane MJ, Acosta-Serrano A, Silber AM. Proline Metabolism is Essential for Trypanosoma brucei brucei Survival in the Tsetse Vector. PLoS Pathog 2017; 13:e1006158. [PMID: 28114403 PMCID: PMC5289646 DOI: 10.1371/journal.ppat.1006158] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 02/02/2017] [Accepted: 12/29/2016] [Indexed: 01/18/2023] Open
Abstract
Adaptation to different nutritional environments is essential for life cycle completion by all Trypanosoma brucei sub-species. In the tsetse fly vector, L-proline is among the most abundant amino acids and is mainly used by the fly for lactation and to fuel flight muscle. The procyclic (insect) stage of T. b. brucei uses L-proline as its main carbon source, relying on an efficient catabolic pathway to convert it to glutamate, and then to succinate, acetate and alanine as the main secreted end products. Here we investigated the essentiality of an undisrupted proline catabolic pathway in T. b. brucei by studying mitochondrial Δ1-pyrroline-5-carboxylate dehydrogenase (TbP5CDH), which catalyzes the irreversible conversion of gamma-glutamate semialdehyde (γGS) into L-glutamate and NADH. In addition, we provided evidence for the absence of a functional proline biosynthetic pathway. TbP5CDH expression is developmentally regulated in the insect stages of the parasite, but absent in bloodstream forms grown in vitro. RNAi down-regulation of TbP5CDH severely affected the growth of procyclic trypanosomes in vitro in the absence of glucose, and altered the metabolic flux when proline was the sole carbon source. Furthermore, TbP5CDH knocked-down cells exhibited alterations in the mitochondrial inner membrane potential (ΔΨm), respiratory control ratio and ATP production. Also, changes in the proline-glutamate oxidative capacity slightly affected the surface expression of the major surface glycoprotein EP-procyclin. In the tsetse, TbP5CDH knocked-down cells were impaired and thus unable to colonize the fly’s midgut, probably due to the lack of glucose between bloodmeals. Altogether, our data show that the regulated expression of the proline metabolism pathway in T. b. brucei allows this parasite to adapt to the nutritional environment of the tsetse midgut. Bloodsucking insects play a major role in the transmission of pathogens that cause major tropical diseases. Their capacity to transmit these diseases is directly associated with the availability and turnover of energy sources. Proline is the main readily-mobilizable fuel of the tsetse fly, which is the vector of sub-species of Trypanosoma brucei parasites that cause human sleeping sickness and are partly responsible for animal trypanosomiasis (Nagana disease) in sub-Saharan Africa. Once trypanosomes are ingested from an infected host by the tsetse, the parasites encounter an environment that is poor in glucose (as it is rapidly metabolized by the fly) but rich in proline, which then becomes the main carbon source once the parasite differentiates into the first insect (procyclic) stage. In this work, we provide evidence on the essentiality of T. b. brucei proline catabolism for procyclic survival within the tsetse’s digestive tract, as this organism is unable to synthesize this amino acid and strictly depends on the proline provided by the fly. We also show that parasites deficient in TbP5CDH, a mitochondrial enzyme involved in the proline degradative pathway, failed to proliferate in vitro, showed a diminished respiratory capacity, and showed compromised maintenance of energy levels and metabolic flux when proline was offered as the main carbon source. Thus, the integrity of the trypanosome proline degradation pathway is needed to maintain essential functions related to parasite bioenergetics, replication and infectivity within the insect host. Our observations answer a long-standing question on the role of parasite proline metabolism in tsetse-trypanosome interplay.
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Affiliation(s)
- Brian S. Mantilla
- Laboratory of Biochemistry of Tryps - LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Letícia Marchese
- Laboratory of Biochemistry of Tryps - LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Aitor Casas-Sánchez
- Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Naomi A. Dyer
- Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Nicholas Ejeh
- Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Marc Biran
- Centre de Résonance Magnétique des Systemes Biologiques, Université Bordeaux, Bordeaux, France
| | - Frédéric Bringaud
- Centre de Résonance Magnétique des Systemes Biologiques, Université Bordeaux, Bordeaux, France
| | - Michael J. Lehane
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Alvaro Acosta-Serrano
- Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- * E-mail: (AMS); (AAS)
| | - Ariel M. Silber
- Laboratory of Biochemistry of Tryps - LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- * E-mail: (AMS); (AAS)
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Batista M, Kugeratski FG, de Paula Lima CV, Probst CM, Kessler RL, de Godoy LM, Krieger MA, Marchini FK. The MAP kinase MAPKLK1 is essential to Trypanosoma brucei proliferation and regulates proteins involved in mRNA metabolism. J Proteomics 2016; 154:118-127. [PMID: 28039027 DOI: 10.1016/j.jprot.2016.12.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/23/2016] [Accepted: 12/21/2016] [Indexed: 10/20/2022]
Abstract
Protein phosphorylation and dephosphorylation events regulate many cellular processes. The identification of all phosphorylation sites and their association to a respective protein kinase or phosphatase is a challenging and crucial step to have a deeper understanding of the effects of signaling networks on cells. Pathogenic trypanosomatids have a large number of protein kinases and phosphatases in comparison to other organisms, which reinforces the relevance of the phosphorylation process in these early eukaryotes, nevertheless little is known about protein phosphorylation in these protozoa. In this context, the role of a MAP kinase-like kinase (MAPKLK1), observed to be essential to proliferation of procyclic Trypanosoma brucei, was studied. After silencing MAPKLK1 expression by RNAi, the cells were evaluated by SILAC MS-based proteomics and RNA-Seq. We identified 1756 phosphorylation sites of which 384 were not previously described in T. brucei. Despite being essential, few modulations were observed at the phosphorylation patterns and gene expression levels of MAPKLK1 knockdown. These indirect targets and potential substrates of MAPKLK1 are related to key cellular processes enriched to mRNA processing and stability control. SIGNIFICANCE The field of cell signaling is a promising topic of study for trypanosomatids, since little is known about this topic and the gene expression regulation occurs at post-transcriptional level. In this sense, the present work increases the knowledge on protein phosphorylation process in Trypanosoma brucei. We depleted one MAP kinase (MAPKLK1) of T. brucei and evaluated the effects on the cell. We showed that MAPKLK1 is essential to the cell, while few modulations on phosphoproteome, proteome and transcriptome are observed with its depletion. Although in low number, the changes in phosphoproteome were significant, presenting possible substrate candidates of MAPKLK1 and indirect targets related to mRNA processing and stability control, metabolic pathways, among others. This result provides insights in the phosphorylation network of T. brucei, a model organism that impacts human and animal health.
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Affiliation(s)
- Michel Batista
- Functional Genomics Laboratory, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil; Mass Spectrometry Facility RPT02H, Carlos Chagas Institute, Fiocruz, Parana, Brazil
| | - Fernanda G Kugeratski
- Functional Genomics Laboratory, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil
| | - Carla V de Paula Lima
- Functional Genomics Laboratory, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil
| | - Christian M Probst
- Functional Genomics Laboratory, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil
| | - Rafael L Kessler
- Functional Genomics Laboratory, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil
| | - Lyris M de Godoy
- Functional Genomics Laboratory, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil
| | - Marco A Krieger
- Functional Genomics Laboratory, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil
| | - Fabricio K Marchini
- Functional Genomics Laboratory, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil; Mass Spectrometry Facility RPT02H, Carlos Chagas Institute, Fiocruz, Parana, Brazil.
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20
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Surve SV, Jensen BC, Heestand M, Mazet M, Smith TK, Bringaud F, Parsons M, Schnaufer A. NADH dehydrogenase of Trypanosoma brucei is important for efficient acetate production in bloodstream forms. Mol Biochem Parasitol 2016; 211:57-61. [PMID: 27717801 PMCID: PMC5225879 DOI: 10.1016/j.molbiopara.2016.10.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/29/2016] [Accepted: 10/03/2016] [Indexed: 11/29/2022]
Abstract
Various genetic mutants of NDH2 were created in bloodstream form Trypanosoma brucei. NDH2 null mutants showed a substantial reduction in growth. NDH2 ablation in a complex I deficient background led to severe growth restriction. Upon prolonged culture, parasites partially compensated for NDH2 deficiency. Loss of NDH2 led to reduced acetate, potentially contributing to the growth defect.
In the slender bloodstream form, Trypanosoma brucei mitochondria are repressed for many functions. Multiple components of mitochondrial complex I, NADH:ubiquinone oxidoreductase, are expressed in this stage, but electron transfer through complex I is not essential. Here we investigate the role of the parasite’s second NADH:ubiquinone oxidoreductase, NDH2, which is composed of a single subunit that also localizes to the mitochondrion. While inducible knockdown of NDH2 had a modest growth effect in bloodstream forms, NDH2 null mutants, as well as inducible knockdowns in a complex I deficient background, showed a greater reduction in growth. Altering the NAD+/NADH balance would affect numerous processes directly and indirectly, including acetate production. Indeed, loss of NDH2 led to reduced levels of acetate, which is required for several essential pathways in bloodstream form T. brucei and which may have contributed to the observed growth defect. In conclusion our study shows that NDH2 is important, but not essential, in proliferating bloodstream forms of T. brucei, arguing that the mitochondrial NAD+/NADH balance is important in this stage, even though the mitochondrion itself is not actively engaged in the generation of ATP.
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Affiliation(s)
- Sachin V Surve
- Center for Infectious Disease Research (Formerly Seattle Biomedical Research Institute), 307 Westlake Ave. N., Seattle, WA, 98109, USA
| | - Bryan C Jensen
- Center for Infectious Disease Research (Formerly Seattle Biomedical Research Institute), 307 Westlake Ave. N., Seattle, WA, 98109, USA
| | - Meredith Heestand
- Center for Infectious Disease Research (Formerly Seattle Biomedical Research Institute), 307 Westlake Ave. N., Seattle, WA, 98109, USA
| | - Muriel Mazet
- Centre de Résonance Magnétique des Systèmes Biologiques (RMSB), UMR5536, Université de Bordeaux, CNRS, Bordeaux, France
| | - Terry K Smith
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St. Andrews KY16 9ST, United Kingdom
| | - Frédéric Bringaud
- Centre de Résonance Magnétique des Systèmes Biologiques (RMSB), UMR5536, Université de Bordeaux, CNRS, Bordeaux, France
| | - Marilyn Parsons
- Center for Infectious Disease Research (Formerly Seattle Biomedical Research Institute), 307 Westlake Ave. N., Seattle, WA, 98109, USA; Dept. of Global Health, University of Washington, Seattle, WA, 98195, USA.
| | - Achim Schnaufer
- Institute of Immunology & Infection Research and Centre of Immunity, Infection & Evolution, The University of Edinburgh, Edinburgh, EH9 3FL, United Kingdom.
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Abdeen S, Salim N, Mammadova N, Summers CM, Goldsmith-Pestana K, McMahon-Pratt D, Schultz PG, Horwich AL, Chapman E, Johnson SM. Targeting the HSP60/10 chaperonin systems of Trypanosoma brucei as a strategy for treating African sleeping sickness. Bioorg Med Chem Lett 2016; 26:5247-5253. [PMID: 27720295 DOI: 10.1016/j.bmcl.2016.09.051] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 09/19/2016] [Accepted: 09/20/2016] [Indexed: 10/21/2022]
Abstract
Trypanosoma brucei are protozoan parasites that cause African sleeping sickness in humans (also known as Human African Trypanosomiasis-HAT). Without treatment, T. brucei infections are fatal. There is an urgent need for new therapeutic strategies as current drugs are toxic, have complex treatment regimens, and are becoming less effective owing to rising antibiotic resistance in parasites. We hypothesize that targeting the HSP60/10 chaperonin systems in T. brucei is a viable anti-trypanosomal strategy as parasites rely on these stress response elements for their development and survival. We recently discovered several hundred inhibitors of the prototypical HSP60/10 chaperonin system from Escherichia coli, termed GroEL/ES. One of the most potent GroEL/ES inhibitors we discovered was compound 1. While examining the PubChem database, we found that a related analog, 2e-p, exhibited cytotoxicity to Leishmania major promastigotes, which are trypanosomatids highly related to Trypanosoma brucei. Through initial counter-screening, we found that compounds 1 and 2e-p were also cytotoxic to Trypanosoma brucei parasites (EC50=7.9 and 3.1μM, respectively). These encouraging initial results prompted us to develop a library of inhibitor analogs and examine their anti-parasitic potential in vitro. Of the 49 new chaperonin inhibitors developed, 39% exhibit greater cytotoxicity to T. brucei parasites than parent compound 1. While many analogs exhibit moderate cytotoxicity to human liver and kidney cells, we identified molecular substructures to pursue for further medicinal chemistry optimization to increase the therapeutic windows of this novel class of chaperonin-targeting anti-parasitic candidates. An intriguing finding from this study is that suramin, the first-line drug for treating early stage T. brucei infections, is also a potent inhibitor of GroEL/ES and HSP60/10 chaperonin systems.
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Affiliation(s)
- Sanofar Abdeen
- Indiana University, School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States
| | - Nilshad Salim
- Indiana University, School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States
| | - Najiba Mammadova
- Indiana University, School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States
| | - Corey M Summers
- Indiana University, School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States
| | - Karen Goldsmith-Pestana
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, 60 College St., New Haven, CT 06520, United States
| | - Diane McMahon-Pratt
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, 60 College St., New Haven, CT 06520, United States
| | - Peter G Schultz
- The Scripps Research Institute, Department of Chemistry, 10550 North Torrey Pines Rd., La Jolla, CA 92037, United States
| | - Arthur L Horwich
- HHMI, Department of Genetics, Yale School of Medicine, Boyer Center for Molecular Medicine, 295 Congress Ave., New Haven, CT 06510, United States
| | - Eli Chapman
- The University of Arizona, College of Pharmacy, Department of Pharmacology and Toxicology, 1703 E. Mabel St., Tucson, AZ 85721, United States
| | - Steven M Johnson
- Indiana University, School of Medicine, Department of Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202, United States.
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22
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TAC102 Is a Novel Component of the Mitochondrial Genome Segregation Machinery in Trypanosomes. PLoS Pathog 2016; 12:e1005586. [PMID: 27168148 PMCID: PMC4864229 DOI: 10.1371/journal.ppat.1005586] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 03/30/2016] [Indexed: 11/19/2022] Open
Abstract
Trypanosomes show an intriguing organization of their mitochondrial DNA into a catenated network, the kinetoplast DNA (kDNA). While more than 30 proteins involved in kDNA replication have been described, only few components of kDNA segregation machinery are currently known. Electron microscopy studies identified a high-order structure, the tripartite attachment complex (TAC), linking the basal body of the flagellum via the mitochondrial membranes to the kDNA. Here we describe TAC102, a novel core component of the TAC, which is essential for proper kDNA segregation during cell division. Loss of TAC102 leads to mitochondrial genome missegregation but has no impact on proper organelle biogenesis and segregation. The protein is present throughout the cell cycle and is assembled into the newly developing TAC only after the pro-basal body has matured indicating a hierarchy in the assembly process. Furthermore, we provide evidence that the TAC is replicated de novo rather than using a semi-conservative mechanism. Lastly, we demonstrate that TAC102 lacks an N-terminal mitochondrial targeting sequence and requires sequences in the C-terminal part of the protein for its proper localization. Proper segregation of the mitochondrial genome during cell division is a prerequisite of healthy eukaryotic cells. However, the mechanism underlying the segregation process is only poorly understood. We use the single celled parasite Trypanosoma brucei, which, unlike most model organisms, harbors a single large mitochondrion with a single mitochondrial genome, also called kinetoplast DNA (kDNA), to study this question. In trypanosomes, kDNA replication and segregation are tightly integrated into the cell cycle and thus can be studied alongside cell cycle markers. Furthermore, previous studies using electron microscopy have characterized the tripartite attachment complex (TAC) as a structural element of the mitochondrial genome segregation machinery. Here, we characterize TAC102, a novel trypanosome protein localized to the TAC. The protein is essential for proper kDNA segregation and cell growth. We analyze the presence of this protein using super resolution microscopy and show that TAC102 is a mitochondrial protein localized between the kDNA and the basal body of the cell’s flagellum. In addition, we characterize different parts of the protein and show that the C-terminus of TAC102 is important for its proper localization. The data and resources presented will allow a more detailed characterization of the dynamics and hierarchy of the TAC in the future and might open new avenues for drug discovery targeting this structure.
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Alves e Silva TL, Savage AF, Aksoy S. Transcript Abundance of Putative Lipid Phosphate Phosphatases During Development of Trypanosoma brucei in the Tsetse Fly. Am J Trop Med Hyg 2016; 94:890-3. [PMID: 26856918 DOI: 10.4269/ajtmh.15-0566] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 12/22/2015] [Indexed: 01/28/2023] Open
Abstract
African trypanosomes (Trypanosoma brucei spp.) cause devastating diseases in sub-Saharan Africa. Trypanosomes differentiate repeatedly during development in tsetse flies before gaining mammalian infectivity in fly salivary glands. Lipid phosphate phosphatases (LPPs) are involved in diverse biological processes, such as cell differentiation and cell migration. Gene sequences encoding two putative T. brucei LPP proteins were used to search the T. brucei genome, revealing two additional putative family members. Putative structural features and transcript abundance during parasite development in tsetse fly were characterized. Three of the four LPP proteins are predicted to have six transmembrane domains, while the fourth shows only one. Semiquantitative gene expression revealed differential regulation of LPPs during parasite development. Transcript abundance for three of the four putative LPP genes was elevated in parasites infecting salivary glands, but not mammalian-infective metacyclic cells in fly saliva, indicating a potential role of this family in parasite establishment in tsetse salivary glands.
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Affiliation(s)
- Thiago Luiz Alves e Silva
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland; Department of Epidemiology of Microbial Diseases, Yale University School of Public Heath, New Haven, Connecticut; National Institute of Science and Technology in Molecular Entomology, Rio de Janeiro, Brazil; Department of Biology, Bard College, Annandale-on-Hudson, New York
| | - Amy F Savage
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland; Department of Epidemiology of Microbial Diseases, Yale University School of Public Heath, New Haven, Connecticut; National Institute of Science and Technology in Molecular Entomology, Rio de Janeiro, Brazil; Department of Biology, Bard College, Annandale-on-Hudson, New York
| | - Serap Aksoy
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland; Department of Epidemiology of Microbial Diseases, Yale University School of Public Heath, New Haven, Connecticut; National Institute of Science and Technology in Molecular Entomology, Rio de Janeiro, Brazil; Department of Biology, Bard College, Annandale-on-Hudson, New York
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24
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Singha UK, Hamilton V, Chaudhuri M. Tim62, a Novel Mitochondrial Protein in Trypanosoma brucei, Is Essential for Assembly and Stability of the TbTim17 Protein Complex. J Biol Chem 2015; 290:23226-39. [PMID: 26240144 DOI: 10.1074/jbc.m115.663492] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Indexed: 11/06/2022] Open
Abstract
Trypanosoma brucei, the causative agent of human African trypanosomiasis, possesses non-canonical mitochondrial protein import machinery. Previously, we characterized the essential translocase of the mitochondrial inner membrane (TIM) consisting of Tim17 in T. brucei. TbTim17 is associated with TbTim62. Here we show that TbTim62, a novel protein, is localized in the mitochondrial inner membrane, and its import into mitochondria depends on TbTim17. Knockdown (KD) of TbTim62 decreased the steady-state levels of TbTim17 post-transcriptionally. Further analysis showed that import of TbTim17 into mitochondria was not inhibited, but its half-life was reduced >4-fold due to TbTim62 KD. Blue-native gel electrophoresis revealed that TbTim62 is present primarily in ∼150-kDa and also in ∼1100-kDa protein complexes, whereas TbTim17 is present in multiple complexes within the range of ∼300 to ∼1100 kDa. TbTim62 KD reduced the levels of both TbTim62 as well as TbTim17 protein complexes. Interestingly, TbTim17 was accumulated as lower molecular mass complexes in TbTim62 KD mitochondria. Furthermore, depletion of TbTim62 hampered the assembly of the ectopically expressed TbTim17-2X-myc into TbTim17 protein complex. Co-immunoprecipitation analysis revealed that association of TbTim17 with mHSP70 was markedly reduced in TbTim62 KD mitochondria. All together our results demonstrate that TbTim62, a unique mitochondrial protein in T. brucei, is required for the formation of a stable TbTim17 protein complex. TbTim62 KD destabilizes this complex, and unassembled TbTim17 degrades. Therefore, TbTim62 acts as a novel regulatory factor to maintain the levels of TIM in T. brucei mitochondria.
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Affiliation(s)
- Ujjal K Singha
- From the Department of Microbiology and Immunology, Meharry Medical College, Nashville, Tennessee 37208
| | - VaNae Hamilton
- From the Department of Microbiology and Immunology, Meharry Medical College, Nashville, Tennessee 37208
| | - Minu Chaudhuri
- From the Department of Microbiology and Immunology, Meharry Medical College, Nashville, Tennessee 37208
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25
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Abstract
Reductive evolution during the adaptation to obligate parasitism and expansions of gene families encoding virulence factors are characteristics evident to greater or lesser degrees in all parasitic protists studied to date. Large evolutionary distances separate many parasitic protists from the yeast and animal models upon which classic views of eukaryotic biochemistry are often based. Thus a combination of evolutionary divergence, niche adaptation and reductive evolution means the biochemistry of parasitic protists is often very different from their hosts and to other eukaryotes generally, making parasites intriguing subjects for those interested in the phenomenon of moonlighting proteins. In common with other organisms, the contribution of protein moonlighting to parasite biology is only just emerging, and it is not without controversy. Here, an overview of recently identified moonlighting proteins in parasitic protists is provided, together with discussion of some of the controversies.
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26
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Mbang-Benet DE, Sterkers Y, Crobu L, Sarrazin A, Bastien P, Pagès M. RNA interference screen reveals a high proportion of mitochondrial proteins essential for correct cell cycle progress in Trypanosoma brucei. BMC Genomics 2015; 16:297. [PMID: 25888089 PMCID: PMC4445814 DOI: 10.1186/s12864-015-1505-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 03/30/2015] [Indexed: 12/20/2022] Open
Abstract
Background Trypanosomatid parasites possess a single mitochondrion which is classically involved in the energetic metabolism of the cell, but also, in a much more original way, through its single and complex DNA (termed kinetoplast), in the correct progress of cell division. In order to identify proteins potentially involved in the cell cycle, we performed RNAi knockdowns of 101 genes encoding mitochondrial proteins using procyclic cells of Trypanosoma brucei. Results A major cell growth reduction was observed in 10 cases and a moderate reduction in 29 other cases. These data are overall in agreement with those previously obtained by a case-by-case approach performed on chromosome 1 genes, and quantitatively with those obtained by “high-throughput phenotyping using parallel sequencing of RNA interference targets” (RIT-seq). Nevertheless, a detailed analysis revealed many qualitative discrepancies with the RIT-seq-based approach. Moreover, for 37 out of 39 mutants for which a moderate or severe growth defect was observed here, we noted abnormalities in the cell cycle progress, leading to increased proportions of abnormal cell cycle stages, such as cells containing more than 2 kinetoplasts (K) and/or more than 2 nuclei (N), and modified proportions of the normal phenotypes (1N1K, 1N2K and 2N2K). Conclusions These data, together with the observation of other abnormal phenotypes, show that all the corresponding mitochondrial proteins are involved, directly or indirectly, in the correct progress or, less likely, in the regulation, of the cell cycle in T. brucei. They also show how post-genomics analyses performed on a case-by-case basis may yield discrepancies with global approaches. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1505-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diane-Ethna Mbang-Benet
- Université Montpellier 1, UFR Médecine, Laboratoire de Parasitologie-Mycologie, CHRU de Montpellier, 39, Avenue Charles Flahault, 34295, Montpellier, Cedex 5, France. .,CNRS 5290 - IRD 224 - Université Montpellier (UMR "MiVEGEC"), Montpellier, France.
| | - Yvon Sterkers
- Université Montpellier 1, UFR Médecine, Laboratoire de Parasitologie-Mycologie, CHRU de Montpellier, 39, Avenue Charles Flahault, 34295, Montpellier, Cedex 5, France. .,CNRS 5290 - IRD 224 - Université Montpellier (UMR "MiVEGEC"), Montpellier, France. .,Département de Parasitologie-Mycologie, CHRU (Centre Hospitalier Universitaire de Montpellier), Montpellier, France.
| | - Lucien Crobu
- CNRS 5290 - IRD 224 - Université Montpellier (UMR "MiVEGEC"), Montpellier, France.
| | - Amélie Sarrazin
- Montpellier RIO Imaging Facility, Montpellier BIOCAMPUS, UMS3426, Arnaud de Villeneuve Campus Imaging Facility - Institut de Génétique Humaine-CNRS, Montpellier, France.
| | - Patrick Bastien
- Université Montpellier 1, UFR Médecine, Laboratoire de Parasitologie-Mycologie, CHRU de Montpellier, 39, Avenue Charles Flahault, 34295, Montpellier, Cedex 5, France. .,CNRS 5290 - IRD 224 - Université Montpellier (UMR "MiVEGEC"), Montpellier, France. .,Département de Parasitologie-Mycologie, CHRU (Centre Hospitalier Universitaire de Montpellier), Montpellier, France.
| | - Michel Pagès
- Université Montpellier 1, UFR Médecine, Laboratoire de Parasitologie-Mycologie, CHRU de Montpellier, 39, Avenue Charles Flahault, 34295, Montpellier, Cedex 5, France. .,CNRS 5290 - IRD 224 - Université Montpellier (UMR "MiVEGEC"), Montpellier, France.
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27
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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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28
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Fadda A, Ryten M, Droll D, Rojas F, Färber V, Haanstra JR, Merce C, Bakker BM, Matthews K, Clayton C. Transcriptome-wide analysis of trypanosome mRNA decay reveals complex degradation kinetics and suggests a role for co-transcriptional degradation in determining mRNA levels. Mol Microbiol 2014; 94:307-26. [PMID: 25145465 PMCID: PMC4285177 DOI: 10.1111/mmi.12764] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2014] [Indexed: 01/14/2023]
Abstract
African trypanosomes are an excellent system for quantitative modelling of post-transcriptional mRNA control. Transcription is constitutive and polycistronic; individual mRNAs are excised by trans splicing and polyadenylation. We here measure mRNA decay kinetics in two life cycle stages, bloodstream and procyclic forms, by transcription inhibition and RNASeq. Messenger RNAs with short half-lives tend to show initial fast degradation, followed by a slower phase; they are often stabilized by depletion of the 5′–3′ exoribonuclease XRNA. Many longer-lived mRNAs show initial slow degradation followed by rapid destruction: we suggest that the slow phase reflects gradual deadenylation. Developmentally regulated mRNAs often show regulated decay, and switch their decay pattern. Rates of mRNA decay are good predictors of steady state levels for short mRNAs, but mRNAs longer than 3 kb show unexpectedly low abundances. Modelling shows that variations in splicing and polyadenylation rates can contribute to steady-state mRNA levels, but this is completely dependent on competition between processing and co-transcriptional mRNA precursor destruction.
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Affiliation(s)
- Abeer Fadda
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany
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29
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Freire ER, Vashisht AA, Malvezzi AM, Zuberek J, Langousis G, Saada EA, Nascimento JDF, Stepinski J, Darzynkiewicz E, Hill K, De Melo Neto OP, Wohlschlegel JA, Sturm NR, Campbell DA. eIF4F-like complexes formed by cap-binding homolog TbEIF4E5 with TbEIF4G1 or TbEIF4G2 are implicated in post-transcriptional regulation in Trypanosoma brucei. RNA (NEW YORK, N.Y.) 2014; 20:1272-86. [PMID: 24962368 PMCID: PMC4105752 DOI: 10.1261/rna.045534.114] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 05/12/2014] [Indexed: 05/19/2023]
Abstract
Members of the eIF4E mRNA cap-binding family are involved in translation and the modulation of transcript availability in other systems as part of a three-component complex including eIF4G and eIF4A. The kinetoplastids possess four described eIF4E and five eIF4G homologs. We have identified two new eIF4E family proteins in Trypanosoma brucei, and define distinct complexes associated with the fifth member, TbEIF4E5. The cytosolic TbEIF4E5 protein binds cap 0 in vitro. TbEIF4E5 was found in association with two of the five TbEIF4Gs. TbIF4EG1 bound TbEIF4E5, a 47.5-kDa protein with two RNA-binding domains, and either the regulatory protein 14-3-3 II or a 117.5-kDa protein with guanylyltransferase and methyltransferase domains in a potentially dynamic interaction. The TbEIF4G2/TbEIF4E5 complex was associated with a 17.9-kDa hypothetical protein and both 14-3-3 variants I and II. Knockdown of TbEIF4E5 resulted in the loss of productive cell movement, as evidenced by the inability of the cells to remain in suspension in liquid culture and the loss of social motility on semisolid plating medium, as well as a minor reduction of translation. Cells appeared lethargic, as opposed to compromised in flagellar function per se. The minimal use of transcriptional control in kinetoplastids requires these organisms to implement downstream mechanisms to regulate gene expression, and the TbEIF4E5/TbEIF4G1/117.5-kDa complex in particular may be a key player in that process. We suggest that a pathway involved in cell motility is affected, directly or indirectly, by one of the TbEIF4E5 complexes.
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Affiliation(s)
- Eden R Freire
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Ajay A Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Amaranta M Malvezzi
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, USA Department of Microbiology, Centro de Pesquisas Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco 50670-420, Brazil
| | - Joanna Zuberek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
| | - Gerasimos Langousis
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Edwin A Saada
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Janaína De F Nascimento
- Department of Microbiology, Centro de Pesquisas Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco 50670-420, Brazil
| | - Janusz Stepinski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
| | - Edward Darzynkiewicz
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland
| | - Kent Hill
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Osvaldo P De Melo Neto
- Department of Microbiology, Centro de Pesquisas Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco 50670-420, Brazil
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Nancy R Sturm
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - David A Campbell
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, USA
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30
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Mulindwa J, Fadda A, Merce C, Matovu E, Enyaru J, Clayton C. Methods to determine the transcriptomes of trypanosomes in mixtures with mammalian cells: the effects of parasite purification and selective cDNA amplification. PLoS Negl Trop Dis 2014; 8:e2806. [PMID: 24743343 PMCID: PMC3990519 DOI: 10.1371/journal.pntd.0002806] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 03/09/2014] [Indexed: 11/19/2022] Open
Abstract
Patterns of gene expression in cultured Trypanosoma brucei bloodstream and procyclic forms have been extensively characterized, and some comparisons have been made with trypanosomes grown to high parasitaemias in laboratory rodents. We do not know, however, to what extent these transcriptomes resemble those in infected Tsetse flies - or in humans or cattle, where parasitaemias are substantially lower. For clinical and field samples it is difficult to characterize parasite gene expression because of the large excess of host cell RNA. We have here examined two potential solutions to this problem for bloodstream form trypanosomes, assaying transcriptomes by high throughput cDNA sequencing (RNASeq). We first purified the parasites from blood of infected rats. We found that a red blood cell lysis procedure affected the transcriptome substantially more than purification using a DEAE cellulose column, but that too introduced significant distortions and variability. As an alternative, we specifically amplified parasite sequences from a mixture containing a 1000-fold excess of human RNA. We first purified polyadenylated RNA, then made trypanosome-specific cDNA by priming with a spliced leader primer. Finally, the cDNA was amplified using nested primers. The amplification procedure was able to produce samples in which 20% of sequence reads mapped to the trypanosome genome. Synthesis of the second cDNA strand with a spliced leader primer, followed by amplification, is sufficiently reproducible to allow comparison of different samples so long as they are all treated in the same way. However, SL priming distorted the abundances of the cDNA products and definitely cannot be used, by itself, to measure absolute mRNA levels. The amplification method might be suitable for clinical samples with low parasitaemias, and could also be adapted for other Kinetoplastids and to samples from infected vectors. Most experiments on African trypanosomes - including those designed to look for new drugs - have studied parasites either from culture, or from laboratory rodents. We are interested in comparing these parasites that grow in man and domestic animals, where the parasites generally have different nutrient concentrations and much lower parasitaemias than in experimental models. The most accessible way to make the comparison is to measure the amounts of mRNAs. In this paper we describe how methods that are used to purify the parasites from human cells can change the relative amounts of mRNA. We also describe a method to examine RNA from relatively small numbers of parasites that are mixed with host cells.
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Affiliation(s)
- Julius Mulindwa
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Abeer Fadda
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Clementine Merce
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Enoch Matovu
- College of Veterinary Medicine, Animal Resources & Biosecurity, Makerere University, Kampala, Uganda
| | - John Enyaru
- College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Christine Clayton
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- * E-mail:
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Mbang-Benet DE, Sterkers Y, Morelle C, Kebe NM, Crobu L, Portalès P, Coux O, Hernandez JF, Meghamla S, Pagès M, Bastien P. The bacterial-like HslVU protease complex subunits are involved in the control of different cell cycle events in trypanosomatids. Acta Trop 2014; 131:22-31. [PMID: 24299926 DOI: 10.1016/j.actatropica.2013.11.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 11/16/2013] [Accepted: 11/21/2013] [Indexed: 02/08/2023]
Abstract
The trypanosomatid parasites Leishmania and Trypanosoma are responsible for the most important WHO-designated neglected tropical diseases, for which the need for cost-effective new drugs is urgent. In addition to the classical eukaryotic 20S and 26S proteasomes, these unconventional eukaryotes possess a bacterial-like protease complex, HslVU, made of proteolytic (HslV) and regulatory (HslU) subunits. In trypanosomatids, two paralogous genes are co-expressed: HslU1 and HslU2. Conflicting reports have been published with respect to subcellular localization, functional redundancy and putative roles of the different subunits of this complex in trypanosomatids. Here, we definitively established the mitochondrial localization of HslVU in L. major procyclic promastigotes and of HslV in T. brucei bloodstream trypomastigotes, the latter being the form responsible for the disease in the mammalian host. Moreover, our data demonstrate for the first time the essential nature of HslVU in the bloodstream trypomastigotes of T. brucei, in spite of mitochondrial repression at this stage. Interestingly, our work also allows distinguishing a specific role for the different members of the complex, as HslV and HslU1 appear to be involved in the control of different cell cycle events. Finally, these data validate HslVU as a promising drug target against these parasitic diseases of wide medical and economical importance.
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Mazet M, Morand P, Biran M, Bouyssou G, Courtois P, Daulouède S, Millerioux Y, Franconi JM, Vincendeau P, Moreau P, Bringaud F. Revisiting the central metabolism of the bloodstream forms of Trypanosoma brucei: production of acetate in the mitochondrion is essential for parasite viability. PLoS Negl Trop Dis 2013; 7:e2587. [PMID: 24367711 PMCID: PMC3868518 DOI: 10.1371/journal.pntd.0002587] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 10/30/2013] [Indexed: 11/24/2022] Open
Abstract
Background The bloodstream forms of Trypanosoma brucei, the causative agent of sleeping sickness, rely solely on glycolysis for ATP production. It is generally accepted that pyruvate is the major end-product excreted from glucose metabolism by the proliferative long-slender bloodstream forms of the parasite, with virtually no production of succinate and acetate, the main end-products excreted from glycolysis by all the other trypanosomatid adaptative forms, including the procyclic insect form of T. brucei. Methodology/Principal Findings A comparative NMR analysis showed that the bloodstream long-slender and procyclic trypanosomes excreted equivalent amounts of acetate and succinate from glucose metabolism. Key enzymes of acetate production from glucose-derived pyruvate and threonine are expressed in the mitochondrion of the long-slender forms, which produces 1.4-times more acetate from glucose than from threonine in the presence of an equal amount of both carbon sources. By using a combination of reverse genetics and NMR analyses, we showed that mitochondrial production of acetate is essential for the long-slender forms, since blocking of acetate biosynthesis from both carbon sources induces cell death. This was confirmed in the absence of threonine by the lethal phenotype of RNAi-mediated depletion of the pyruvate dehydrogenase, which is involved in glucose-derived acetate production. In addition, we showed that de novo fatty acid biosynthesis from acetate is essential for this parasite, as demonstrated by a lethal phenotype and metabolic analyses of RNAi-mediated depletion of acetyl-CoA synthetase, catalyzing the first cytosolic step of this pathway. Conclusions/Significance Acetate produced in the mitochondrion from glucose and threonine is synthetically essential for the long-slender mammalian forms of T. brucei to feed the essential fatty acid biosynthesis through the “acetate shuttle” that was recently described in the procyclic insect form of the parasite. Consequently, key enzymatic steps of this pathway, particularly acetyl-CoA synthetase, constitute new attractive drug targets against trypanosomiasis. Many protists, including parasitic helminthes, trichomonads and trypanosomatids, produce acetate in their mitochondrion or mitochondrion-like organelle, which is excreted as a main metabolic end-product of their energy metabolism. We have recently demonstrated that mitochondrial production of acetate is essential for fatty acid biosynthesis and ATP production in the procyclic insect form of T. brucei. However, acetate metabolism has not been investigated in the long-slender bloodstream forms of the parasite, the proliferative forms responsible for the sleeping sickness. In contrast to the current view, we showed that the bloodstream forms produce almost as much acetate from glucose than the procyclic parasites. Acetate production from glucose and threonine is synthetically essential for growth and de novo synthesis of fatty acids of the bloodstream trypanosomes. These data highlight that the central metabolism of the bloodstream forms contains unexpected essential pathways, although minor in terms of metabolic flux, which could be targeted for the development of trypanocidal drugs.
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Affiliation(s)
- Muriel Mazet
- Centre de Résonance Magnétique des Systèmes Biologiques (RMSB), UMR5536, Université Bordeaux Segalen, CNRS, Bordeaux, France
| | - Pauline Morand
- Centre de Résonance Magnétique des Systèmes Biologiques (RMSB), UMR5536, Université Bordeaux Segalen, CNRS, Bordeaux, France
| | - Marc Biran
- Centre de Résonance Magnétique des Systèmes Biologiques (RMSB), UMR5536, Université Bordeaux Segalen, CNRS, Bordeaux, France
| | - Guillaume Bouyssou
- Laboratoire de Biogenèse Membranaire, UMR5200 Université Bordeaux Segalen, CNRS, Bâtiment A3, INRA Bordeaux Aquitaine, Villenave d'Ornon, France
| | - Pierrette Courtois
- Laboratoire de Parasitologie, UMR177 IRD CIRAD, Université Bordeaux Segalen, BP 43, Bordeaux, France
| | - Sylvie Daulouède
- Laboratoire de Parasitologie, UMR177 IRD CIRAD, Université Bordeaux Segalen, BP 43, Bordeaux, France
| | - Yoann Millerioux
- Centre de Résonance Magnétique des Systèmes Biologiques (RMSB), UMR5536, Université Bordeaux Segalen, CNRS, Bordeaux, France
| | - Jean-Michel Franconi
- Centre de Résonance Magnétique des Systèmes Biologiques (RMSB), UMR5536, Université Bordeaux Segalen, CNRS, Bordeaux, France
| | - Philippe Vincendeau
- Laboratoire de Parasitologie, UMR177 IRD CIRAD, Université Bordeaux Segalen, BP 43, Bordeaux, France
| | - Patrick Moreau
- Laboratoire de Biogenèse Membranaire, UMR5200 Université Bordeaux Segalen, CNRS, Bâtiment A3, INRA Bordeaux Aquitaine, Villenave d'Ornon, France
| | - Frédéric Bringaud
- Centre de Résonance Magnétique des Systèmes Biologiques (RMSB), UMR5536, Université Bordeaux Segalen, CNRS, Bordeaux, France
- * E-mail: .
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Milone M, Wong LJ. Diagnosis of mitochondrial myopathies. Mol Genet Metab 2013; 110:35-41. [PMID: 23911206 DOI: 10.1016/j.ymgme.2013.07.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Revised: 07/10/2013] [Accepted: 07/10/2013] [Indexed: 01/01/2023]
Abstract
Mitochondria are ubiquitous organelles and play crucial roles in vital functions, most importantly, the oxidative phosphorylation and energy metabolism. Therefore, mitochondrial dysfunction can affect multiple tissues, with muscle and nerve preferentially affected. Mitochondrial myopathy is a common clinical phenotype, which is characterized by early fatigue and/or fixed muscle weakness; rhabdomyolysis can seldom occur. Muscle biopsy often identifies signs of diseased mitochondria by morphological studies, while biochemical analysis may identify respiratory chain deficiencies. The clinical, morphological and biochemical data guide molecular analysis. Being the mitochondrial function under the control of both mitochondrial DNA and nuclear DNA, the search for mitochondrial DNA mutations and mitochondrial DNA quantitation, may not be sufficient for the molecular diagnosis of mitochondrial myopathies. Approximately 1500 nuclear genes can affect mitochondrial structure and function and the targeting of such genes may be necessary to reach the diagnosis. The identification of causative molecular defects in nuclear or mitochondrial genome leads to the definite diagnosis of mitochondrial myopathy.
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Affiliation(s)
- Margherita Milone
- Department of Neurology, Neuromuscular Division, Mayo Clinic, Rochester, MN, USA
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Regulation of Trypanosoma brucei Total and Polysomal mRNA during Development within Its Mammalian Host. PLoS One 2013; 8:e67069. [PMID: 23840587 PMCID: PMC3694164 DOI: 10.1371/journal.pone.0067069] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 05/14/2013] [Indexed: 11/25/2022] Open
Abstract
The gene expression of Trypanosoma brucei has been examined extensively in the blood of mammalian hosts and in forms found in the midgut of its arthropod vector, the tsetse fly. However, trypanosomes also undergo development within the mammalian bloodstream as they progress from morphologically ‘slender forms’ to transmissible ‘stumpy forms’ through morphological intermediates. This transition is temporally progressive within the first wave of parasitaemia such that gene expression can be monitored in relatively pure slender and stumpy populations as well as during the progression between these extremes. The development also represents the progression of cells from translationally active forms adapted for proliferation in the host to translationally quiescent forms, adapted for transmission. We have used metabolic labelling to quantitate translational activity in slender forms, stumpy forms and in forms undergoing early differentiation to procyclic forms in vitro. Thereafter we have examined the cohort of total mRNAs that are enriched throughout development in the mammalian bloodstream (slender, intermediate and stumpy forms), irrespective of strain, revealing those that exhibit consistent developmental regulation rather than sample specific changes. Transcripts that cosediment with polysomes in stumpy forms and slender forms have also been enriched to identify transcripts that escape translational repression prior to transmission. Combined, the expression and polysomal association of transcripts as trypanosomes undergo development in the mammalian bloodstream have been defined, providing a resource for trypanosome researchers. This facilitates the identification of those that undergo developmental regulation in the bloodstream and therefore those likely to have a role in the survival and capacity for transmission of stumpy forms.
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Zhang X, Shen Y, Ding G, Tian Y, Liu Z, Li B, Wang Y, Jiang C. TFPP: an SVM-based tool for recognizing flagellar proteins in Trypanosoma brucei. PLoS One 2013; 8:e54032. [PMID: 23349782 PMCID: PMC3547966 DOI: 10.1371/journal.pone.0054032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 12/07/2012] [Indexed: 11/18/2022] Open
Abstract
Trypanosoma brucei is a unicellular flagellated eukaryotic parasite that causes African trypanosomiasis in human and domestic animals with devastating health and economic consequences. Recent studies have revealed the important roles of the single flagellum of T. brucei in many aspects, especially that the flagellar motility is required for the viability of the bloodstream form T. brucei, suggesting that impairment of the flagellar function may provide a promising cure for African sleeping sickness. Knowing the flagellum proteome is crucial to study the molecular mechanism of the flagellar functions. Here we present a novel computational method for identifying flagellar proteins in T. brucei, called trypanosome flagellar protein predictor (TFPP). TFPP was developed based on a list of selected discriminating features derived from protein sequences, and could predict flagellar proteins with ∼92% specificity at a ∼84% sensitivity rate. Applied to the whole T. brucei proteome, TFPP reveals 811 more flagellar proteins with high confidence, suggesting that the flagellar proteome covers ∼10% of the whole proteome. Comparison of the expression profiles of the whole T. brucei proteome at three typical life cycle stages found that ∼45% of the flagellar proteins were significantly changed in expression levels between the three life cycle stages, indicating life cycle stage-specific regulation of flagellar functions in T. brucei. Overall, our study demonstrated that TFPP is highly effective in identifying flagellar proteins and could provide opportunities to study the trypanosome flagellar proteome systematically. Furthermore, the web server for TFPP can be freely accessed at http:/wukong.tongji.edu.cn/tfpp.
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Affiliation(s)
- Xiaobai Zhang
- Department of Bioinformatics, the School of Life Sciences and Technology, Tongji University, Shanghai, China
- * E-mail: (XZ); (CJ)
| | - Yuefeng Shen
- Department of Bioinformatics, the School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Guitao Ding
- Department of Bioinformatics, the School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yi Tian
- Department of Bioinformatics, the School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zhenping Liu
- Department of Bioinformatics, the School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Bing Li
- Department of Bioinformatics, the School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yun Wang
- Department of Bioinformatics, the School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Cizhong Jiang
- Department of Bioinformatics, the School of Life Sciences and Technology, Tongji University, Shanghai, China
- * E-mail: (XZ); (CJ)
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Serricchio M, Bütikofer P. Phosphatidylglycerophosphate synthase associates with a mitochondrial inner membrane complex and is essential for growth ofTrypanosoma brucei. Mol Microbiol 2012. [DOI: 10.1111/mmi.12116] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Mauro Serricchio
- Institute of Biochemistry & Molecular Medicine; University of Bern; Bern; Switzerland
| | - Peter Bütikofer
- Institute of Biochemistry & Molecular Medicine; University of Bern; Bern; Switzerland
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Duncan MR, Fullerton M, Chaudhuri M. Tim50 in Trypanosoma brucei possesses a dual specificity phosphatase activity and is critical for mitochondrial protein import. J Biol Chem 2012; 288:3184-97. [PMID: 23212919 DOI: 10.1074/jbc.m112.436378] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
In eukaryotes, proteins are imported into mitochondria via multiprotein translocases of the mitochondrial outer and inner membranes, TOM and TIM, respectively. Trypanosoma brucei, a hemoflagellated parasitic protozoan and the causative agent of African trypanosomiasis, imports about a thousand proteins into the mitochondrion; however, the mitochondrial protein import machinery in this organism is largely unidentified. Here, we characterized a homolog of Tim50 that is localized in the mitochondrial membrane in T. brucei. Similar to Tim50 proteins from fungi and mammals, Tim50 in T. brucei (TbTim50) possesses a mitochondrial targeting signal at its N terminus and a C-terminal domain phosphatase motif at its C terminus. Knockdown of TbTim50 reduced cell growth and inhibited import of proteins that contain N-terminal targeting signals. Co-immunoprecipitation analysis revealed that TbTim50 interacts with TbTim17. Unlike its fungal counterpart but similar to the human homolog of Tim50, recombinant TbTim50 possesses a dual specificity phosphatase activity with a greater affinity for protein tyrosine phosphate than for protein serine/threonine phosphate. Mutation of the aspartic acid residues to alanine in the C-terminal domain phosphatase motif (242)DXDX(V/T)(246) abolished activity for both type of substrates. TbTim50 knockdown increased and its overexpression decreased the level of voltage-dependent anion channel (VDAC). However, the VDAC level was unaltered when the phosphatase-inactive mutant of TbTim50 was overexpressed, suggesting that the phosphatase activity of TbTim50 plays a role in regulation of VDAC expression. In contrast, phosphatase activity of the TbTim50 is required neither for mitochondrial protein import nor for its interaction with TbTim17. Overall, our results show that TbTim50 plays additional roles in mitochondrial activities besides preprotein translocation.
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Affiliation(s)
- Melanie R Duncan
- Department of Microbiology and Immunology, Meharry Medical College, Nashville, Tennessee 37208, USA
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Fisk JC, Li J, Wang H, Aletta JM, Qu J, Read LK. Proteomic analysis reveals diverse classes of arginine methylproteins in mitochondria of trypanosomes. Mol Cell Proteomics 2012; 12:302-11. [PMID: 23152538 DOI: 10.1074/mcp.m112.022533] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Arginine (arg) methylation is a widespread posttranslational modification of proteins that impacts numerous cellular processes such as chromatin remodeling, RNA processing, DNA repair, and cell signaling. Known arg methylproteins arise mostly from yeast and mammals, and are almost exclusively nuclear and cytoplasmic. Trypanosoma brucei is an early branching eukaryote whose genome encodes five putative protein arg methyltransferases, and thus likely contains a plethora of arg methylproteins. Additionally, trypanosomes and related organisms possess a unique mitochondrion that undergoes dramatic developmental regulation and uses novel RNA editing and mitochondrial DNA replication mechanisms. Here, we performed a global mass spectrometric analysis of the T. brucei mitochondrion to identify new arg methylproteins in this medically relevant parasite. Enabling factors of this work are use of a combination digestion with two orthogonal enzymes, an efficient offline two dimensional chromatography separation, and high-resolution mass spectrometry analysis with two complementary activations. This approach led to the comprehensive, sensitive and confident identification and localization of methylarg at a proteome level. We identified 167 arg methylproteins with wide-ranging functions including metabolism, transport, chaperoning, RNA processing, translation, and DNA replication. Our data suggest that arg methylproteins in trypanosome mitochondria possess both trypanosome-specific and evolutionarily conserved modifications, depending on the protein targeted. This study is the first comprehensive analysis of mitochondrial arg methylation in any organism, and represents a significant advance in our knowledge of the range of arg methylproteins and their sites of modification. Moreover, these studies establish T. brucei as a model organism for the study of posttranslational modifications.
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Affiliation(s)
- John C Fisk
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14124, USA
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Gunasekera K, Wüthrich D, Braga-Lagache S, Heller M, Ochsenreiter T. Proteome remodelling during development from blood to insect-form Trypanosoma brucei quantified by SILAC and mass spectrometry. BMC Genomics 2012; 13:556. [PMID: 23067041 PMCID: PMC3545838 DOI: 10.1186/1471-2164-13-556] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 10/11/2012] [Indexed: 12/12/2022] Open
Abstract
Background Trypanosoma brucei is the causative agent of human African sleeping sickness and Nagana in cattle. In addition to being an important pathogen T. brucei has developed into a model system in cell biology. Results Using Stable Isotope Labelling of Amino acids in Cell culture (SILAC) in combination with mass spectrometry we determined the abundance of >1600 proteins in the long slender (LS), short stumpy (SS) mammalian bloodstream form stages relative to the procyclic (PC) insect-form stage. In total we identified 2645 proteins, corresponding to ~30% of the total proteome and for the first time present a comprehensive overview of relative protein levels in three life stages of the parasite. Conclusions We can show the extent of pre-adaptation in the SS cells, especially at the level of the mitochondrial proteome. The comparison to a previously published report on monomorphic in vitro grown bloodstream and procyclic T. brucei indicates a loss of stringent regulation particularly of mitochondrial proteins in these cells when compared to the pleomorphic in vivo situation. In order to better understand the different levels of gene expression regulation in this organism we compared mRNA steady state abundance with the relative protein abundance-changes and detected moderate but significant correlation indicating that trypanosomes possess a significant repertoire of translational and posttranslational mechanisms to regulate protein abundance.
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Editosome accessory factors KREPB9 and KREPB10 in Trypanosoma brucei. EUKARYOTIC CELL 2012; 11:832-43. [PMID: 22562468 DOI: 10.1128/ec.00046-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Multiprotein complexes, called editosomes, catalyze the uridine insertion and deletion RNA editing that forms translatable mitochondrial mRNAs in kinetoplastid parasites. We have identified here two new U1-like zinc finger proteins that associate with editosomes and have shown that they are related to KREPB6, KREPB7, and KREPB8, and thus we have named them Kinetoplastid RNA Editing Proteins, KREPB9 and KREPB10. They are conserved and syntenic in trypanosomatids although KREPB10 is absent in Trypanosoma vivax and both are absent in Leishmania. Tandem affinity purification (TAP)-tagged KREPB9 and KREPB10 incorporate into ~20S editosomes and/or subcomplexes thereof and preferentially associate with deletion subcomplexes, as do KREPB6, KREPB7, and KREPB8. KREPB10 also associates with editosomes that are isolated via a chimeric endonuclease, KREN1 in KREPB8 RNA interference (RNAi) cells, or MEAT1. The purified complexes have precleaved editing activities and endonuclease cleavage activity that appears to leave a 5' OH on the 3' product. RNAi knockdowns did not affect growth but resulted in relative reductions of both edited and unedited mitochondrial mRNAs. The similarity of KREPB9 and KREPB10 to KREPB6, KREPB7, and KREPB8 suggests they may be accessory factors that affect editing endonuclease activity and as a consequence may affect mitochondrial mRNA stability. KREPB9 and KREPB10, along with KREPB6, KREPB7, and KREPB8, may enable the endonucleases to discriminate among and accurately cleave hundreds of different editing sites and may be involved in the control of differential editing during the life cycle of T. brucei.
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An essential bacterial-type cardiolipin synthase mediates cardiolipin formation in a eukaryote. Proc Natl Acad Sci U S A 2012; 109:E954-61. [PMID: 22451910 DOI: 10.1073/pnas.1121528109] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cardiolipin is important for bacterial and mitochondrial stability and function. The final step in cardiolipin biosynthesis is catalyzed by cardiolipin synthase and differs mechanistically between prokaryotes and eukaryotes. To study the importance of cardiolipin synthesis for mitochondrial integrity, membrane protein complex formation, and cell proliferation in the human and animal pathogenic protozoan parasite, Trypanosoma brucei, we generated conditional cardiolipin synthase-knockout parasites. We found that cardiolipin formation in T. brucei procyclic forms is catalyzed by a bacterial-type cardiolipin synthase, providing experimental evidence for a prokaryotic-type cardiolipin synthase in a eukaryotic organism. Ablation of enzyme expression resulted in inhibition of de novo cardiolipin synthesis, reduction in cellular cardiolipin levels, alterations in mitochondrial morphology and function, and parasite death in culture. By using immunofluorescence microscopy and blue-native gel electrophoresis, cardiolipin synthase was shown to colocalize with inner mitochondrial membrane proteins and to be part of a large protein complex. During depletion of cardiolipin synthase, the levels of cytochrome oxidase subunit IV and cytochrome c1, reflecting mitochondrial respiratory complexes IV and III, respectively, decreased progressively.
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Singha UK, Hamilton V, Duncan MR, Weems E, Tripathi MK, Chaudhuri M. Protein translocase of mitochondrial inner membrane in Trypanosoma brucei. J Biol Chem 2012; 287:14480-93. [PMID: 22408251 DOI: 10.1074/jbc.m111.322925] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Translocases of mitochondrial inner membrane (TIMs) are multiprotein complexes. The only Tim component so far characterized in kinetoplastid parasites such as Trypanosoma brucei is Tim17 (TbTim17), which is essential for cell survival and mitochondrial protein import. Here, we report that TbTim17 is present in a protein complex of about 1,100 kDa, which is much larger than the TIM complexes found in fungi and mammals. Depletion of TbTim17 in T. brucei impairs the mitochondrial import of cytochrome oxidase subunit IV, an N-terminal signal-containing protein. Pretreatment of isolated mitoplasts with the anti-TbTim17 antibody inhibited import of cytochrome oxidase subunit IV, indicating a direct involvement of the TbTim17 in the import process. Purification of the TbTim17-containing protein complex from the mitochondrial membrane of T. brucei by tandem affinity chromatography revealed that TbTim17 associates with seven unique as well as a few known T. brucei mitochondrial proteins. Depletion of three of these novel proteins, i.e. TbTim47, TbTim54, and TbTim62, significantly decreased mitochondrial protein import in vitro. In vivo targeting of a newly synthesized mitochondrial matrix protein, MRP2, was also inhibited due to depletion of TbTim17, TbTim54, and TbTim62. Co-precipitation analysis confirmed the interaction of TbTim54 and TbTim62 with TbTim17 in vivo. Overall, our data reveal that TbTim17, the single homolog of Tim17/22/23 family proteins, is present in a unique TIM complex consisting of novel proteins in T. brucei and is critical for mitochondrial protein import.
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Affiliation(s)
- Ujjal K Singha
- Department of Microbiology and Immunology, Meharry Medical College, Nashville, Tennessee 37208, USA
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Kramer S. Developmental regulation of gene expression in the absence of transcriptional control: The case of kinetoplastids. Mol Biochem Parasitol 2012; 181:61-72. [PMID: 22019385 DOI: 10.1016/j.molbiopara.2011.10.002] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 10/03/2011] [Accepted: 10/04/2011] [Indexed: 11/25/2022]
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Abstract
The diseases caused by trypanosomes are medically and economically devastating to the population of Sub-Saharan Africa. Parasites of the genus Trypanosoma infect both humans, causing African sleeping sickness, and livestock, causing Nagana. The development of effective treatment strategies has suffered from severe side effects of approved drugs, resistance and major difficulties in delivering drugs. Antimicrobial peptides (AMPs) are ubiquitous components of immune defence and are being rigorously pursued as novel sources of new therapeutics for a variety of pathogens. Here, we review the role of AMPs in the innate immune response of the tsetse fly to African trypanosomes, catalogue trypanocidal AMPs from diverse organisms and highlight the susceptibility of bloodstream form African trypanosomes to killing by unconventional toxic peptides.
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Affiliation(s)
- J M Harrington
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA. )
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Manful T, Fadda A, Clayton C. The role of the 5'-3' exoribonuclease XRNA in transcriptome-wide mRNA degradation. RNA (NEW YORK, N.Y.) 2011; 17:2039-2047. [PMID: 21947264 PMCID: PMC3198596 DOI: 10.1261/rna.2837311] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 08/16/2011] [Indexed: 05/31/2023]
Abstract
The steady-state level of each mRNA in a cell is a balance between synthesis and degradation. Here, we use high-throughput RNA sequencing (RNASeq) to determine the relationship between mRNA degradation and mRNA abundance on a transcriptome-wide scale. The model organism used was the bloodstream form of Trypanosoma brucei, a protist that lacks regulation of RNA polymerase II initiation. The mRNA half-lives varied over two orders of magnitude, with a median half-life of 13 min for total (rRNA-depleted) mRNA. Data for poly(A)+ RNA yielded shorter half-lives than for total RNA, indicating that removal of the poly(A) tail was usually the first step in degradation. Depletion of the major 5'-3' exoribonuclease, XRNA, resulted in the stabilization of most mRNAs with half-lives under 30 min. Thus, on a transcriptome-wide scale, degradation of most mRNAs is initiated by deadenylation. Trypanosome mRNA levels are strongly influenced by gene copy number and mRNA half-life: Very abundant mRNAs that are required throughout the life-cycle may be encoded by multicopy genes and have intermediate-to-long half-lives; those encoding ribosomal proteins, with one to two gene copies, are exceptionally stable. Developmentally regulated transcripts with a lower abundance in the bloodstream forms than the procyclic forms had half-lives around the median, whereas those with a higher abundance in the bloodstream forms than the procyclic forms, such as those encoding glycolytic enzymes, had longer half-lives.
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Affiliation(s)
- Theresa Manful
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, D69120 Heidelberg, Germany
| | - Abeer Fadda
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, D69120 Heidelberg, Germany
| | - Christine Clayton
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, D69120 Heidelberg, Germany
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After half a century mitochondrial calcium in- and efflux machineries reveal themselves. EMBO J 2011; 30:4119-25. [PMID: 21934651 DOI: 10.1038/emboj.2011.337] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 08/26/2011] [Indexed: 12/19/2022] Open
Abstract
Mitochondrial Ca(2+) uptake and release play a fundamental role in the control of different physiological processes, such as cytoplasmic Ca(2+) signalling, ATP production and hormone metabolism, while dysregulation of mitochondrial Ca(2+) handling triggers the cascade of events that lead to cell death. The basic mechanisms of mitochondrial Ca(2+) homeostasis have been firmly established for decades, but the molecular identities of the channels and transporters responsible for Ca(2+) uptake and release have remained mysterious until very recently. Here, we briefly review the main findings that have led to our present understanding of mitochondrial Ca(2+) homeostasis and its integration in cell physiology. We will then discuss the recent work that has unravelled the biochemical identity of three key molecules: NCLX, the mitochondrial Na(+)/Ca(2+) antiporter, MCU, the pore-forming subunit of the mitochondrial Ca(2+) uptake channel, and MICU1, one of its regulatory subunits.
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Gene expression in Trypanosoma brucei: lessons from high-throughput RNA sequencing. Trends Parasitol 2011; 27:434-41. [PMID: 21737348 DOI: 10.1016/j.pt.2011.05.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 05/13/2011] [Accepted: 05/17/2011] [Indexed: 11/23/2022]
Abstract
Trypanosoma brucei undergoes major biochemical and morphological changes during its development from the bloodstream form in the mammalian host to the procyclic form in the midgut of its insect host. The underlying regulation of gene expression, however, is poorly understood. More than 60% of the predicted genes remain annotated as hypothetical, and the 5' and 3' untranslated regions important for regulation of gene expression are unknown for >90% of the genes. In this review, we compare the data from four recently published high-throughput RNA sequencing studies in light of the different experimental setups and discuss how these data can enhance genome annotation and give insights into the regulation of gene expression in T. brucei.
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Dimitriadis D, Koumandou VL, Trimpalis P, Kossida S. Protein functional links in Trypanosoma brucei, identified by gene fusion analysis. BMC Evol Biol 2011; 11:193. [PMID: 21729286 PMCID: PMC3155505 DOI: 10.1186/1471-2148-11-193] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 07/05/2011] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Domain or gene fusion analysis is a bioinformatics method for detecting gene fusions in one organism by comparing its genome to that of other organisms. The occurrence of gene fusions suggests that the two original genes that participated in the fusion are functionally linked, i.e. their gene products interact either as part of a multi-subunit protein complex, or in a metabolic pathway. Gene fusion analysis has been used to identify protein functional links in prokaryotes as well as in eukaryotic model organisms, such as yeast and Drosophila. RESULTS In this study we have extended this approach to include a number of recently sequenced protists, four of which are pathogenic, to identify fusion linked proteins in Trypanosoma brucei, the causative agent of African sleeping sickness. We have also examined the evolution of the gene fusion events identified, to determine whether they can be attributed to fusion or fission, by looking at the conservation of the fused genes and of the individual component genes across the major eukaryotic and prokaryotic lineages. We find relatively limited occurrence of gene fusions/fissions within the protist lineages examined. Our results point to two trypanosome-specific gene fissions, which have recently been experimentally confirmed, one fusion involving proteins involved in the same metabolic pathway, as well as two novel putative functional links between fusion-linked protein pairs. CONCLUSIONS This is the first study of protein functional links in T. brucei identified by gene fusion analysis. We have used strict thresholds and only discuss results which are highly likely to be genuine and which either have already been or can be experimentally verified. We discuss the possible impact of the identification of these novel putative protein-protein interactions, to the development of new trypanosome therapeutic drugs.
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