scholarly journals In Trypanosoma brucei RNA Editing, TbMP18 (Band VII) Is Critical for Editosome Integrity and for both Insertional and Deletional Cleavages

2006 ◽  
Vol 27 (2) ◽  
pp. 777-787 ◽  
Author(s):  
Julie A. Law ◽  
Sean O'Hearn ◽  
Barbara Sollner-Webb
Keyword(s):  
Rna Interference ◽  
Trypanosoma Brucei ◽  
Rna Editing ◽  
Protein Complex ◽  
Substrate Recognition ◽  
The Other ◽  
Major Protein

ABSTRACT In trypanosome RNA editing, uridylate (U) residues are inserted and deleted at numerous sites within mitochondrial pre-mRNAs by an ∼20S protein complex that catalyzes cycles of cleavage, U addition/U removal, and ligation. We used RNA interference to deplete TbMP18 (band VII), the last unexamined major protein of our purified editing complex, showing it is essential. TbMP18 is critical for the U-deletional and U-insertional cleavages and for integrity of the ∼20S editing complex, whose other major components, TbMP99, TbMP81, TbMP63, TbMP52, TbMP48, TbMP42 (bands I through VI), and TbMP57, instead sediment as ∼10S associations. Additionally, TbMP18 augments editing substrate recognition by the TbMP57 terminal U transferase, possibly aiding the recognition component, TbMP81. The other editing activities and their coordination in precleaved editing remain active in the absence of TbMP18. These data are reminiscent of the data on editing subcomplexes reported by A. Schnaufer et al. (Mol. Cell 12:307-319, 2003) and suggest that these subcomplexes are held together in the ∼20S complex by TbMP18, as was proposed previously. Our data additionally imply that the proteins are less long-lived in these subcomplexes than they are when held in the complete editing complex. The editing endonucleolytic cleavages being lost when the editing complex becomes fragmented, as upon TbMP18 depletion, should be advantageous to the trypanosome, minimizing broken mRNAs.

scholarly journals Distinct Functions of Two RNA Ligases in Active Trypanosoma brucei RNA Editing Complexes

2002 ◽  
Vol 22 (13) ◽  
pp. 4652-4660 ◽  
Author(s):  
Jorge Cruz-Reyes ◽  
Alevtina G. Zhelonkina ◽  
Catherine E. Huang ◽  
Barbara Sollner-Webb
Keyword(s):  
Genetic Analysis ◽  
Trypanosoma Brucei ◽  
Rna Editing ◽  
Protein Complex ◽  
Base Pairing ◽  
Guide Rnas ◽  
Single Protein ◽  
The Individual ◽  
Catalytic Functions

ABSTRACT Trypanosome RNA editing is a unique U insertion and U deletion process that involves cycles of pre-mRNA cleavage, terminal U addition or U removal, and religation. This editing can occur at massive levels and is directed by base pairing of trans-acting guide RNAs. Both U insertion and U deletion cycles are catalyzed by a single protein complex that contains only seven major proteins, band I through band VII. However, little is known about their catalytic functions, except that band IV and band V are RNA ligases and genetic analysis indicates that the former is important in U deletion. Here we establish biochemical approaches to distinguish the individual roles of these ligases, based on their distinctive ATP and pyrophosphate utilization. These in vitro analyses revealed that both ligases serve in RNA editing. Band V is the RNA editing ligase that functions very selectively to seal in U insertion (IREL), while band IV is the RNA editing ligase needed to seal in U deletion (DREL). In combination with our earlier findings about the cleavage and the U-addition/U-removal steps of U deletion and U insertion, these results show that all three steps of these editing pathways exhibit major differences and suggest that the editing complex could have physically separate regions for U deletion and U insertion.

scholarly journals In Trypanosoma brucei RNA Editing, Band II Enables Recognition Specifically at Each Step of the U Insertion Cycle

2005 ◽  
Vol 25 (7) ◽  
pp. 2785-2794 ◽  
Author(s):  
Julie A. Law ◽  
Catherine E. Huang ◽  
Sean F. O'Hearn ◽  
Barbara Sollner-Webb
Keyword(s):  
Rna Interference ◽  
Trypanosoma Brucei ◽  
Rna Editing ◽  
Cell Lines ◽  
Protein Recognition ◽  
Essential Nature ◽  
Insertion And Deletion ◽  
Insertion Sites

ABSTRACT Trypanosome RNA editing is the posttranscriptional insertion and deletion of uridylate (U) residues, often to a massive extent, through cycles of cleavage, U addition or U removal, and ligation. These editing cycles are catalyzed by a complex that we purified to seven major proteins (bands I through VII). Here we analyze the role of band II using extracts of clonal band II RNA interference (RNAi) cell lines prepared by a rapid protocol that enables retention of activities that are lost during traditional extract preparation. By individually scoring each step of editing, we show that band II is critical for all steps of U insertion but is not important for any of the steps of U deletion or for their coordination into the U deletion cycle. This specificity supports the long- standing model that U-insertional and U-deletional activities are separated within the editing complex. Furthermore, by assaying the basic activities of the enzymes that catalyze the steps of U insertion, independent of their action in editing, we show that band II is not any of those enzymes. Rather, band II enables endonuclease action at authentic U insertion sites, terminal-uridylyl-transferase (TUTase) action at cleaved U insertion sites, and U-insertion-specific ligase (band V/IREL) action in the editing complex. Thus, band II facilitates each step of U insertion by providing proper RNA and/or protein recognition. We propose that band II (TbMP81) be called IRER, indicating its essential nature in U-insertional RNA editing recognition.

scholarly journals Characterization of Two Mitochondrial Flavin Adenine Dinucleotide-Dependent Glycerol-3-Phosphate Dehydrogenases in Trypanosoma brucei

2013 ◽  
Vol 12 (12) ◽  
pp. 1664-1673 ◽  
Author(s):  
Ingrid Škodová ◽  
Zdeněk Verner ◽  
Fréderic Bringaud ◽  
Peter Fabian ◽  
Julius Lukeš ◽  
...  
Keyword(s):  
Rna Interference ◽  
Trypanosoma Brucei ◽  
Flavin Adenine Dinucleotide ◽  
The Other ◽  
Dihydroxyacetone Phosphate ◽  
Protein Overexpression ◽  
Content Type ◽  
Digitonin Permeabilization ◽  
Shed Light

ABSTRACT Glycerol-3-phosphate dehydrogenases (G3PDHs) constitute a shuttle that serves for regeneration of NAD + reduced during glycolysis. This NAD-dependent enzyme is employed in glycolysis and produces glycerol-3-phosphate from dihydroxyacetone phosphate, while its flavin adenine dinucleotide (FAD)-dependent homologue catalyzes a reverse reaction coupled to the respiratory chain. Trypanosoma brucei possesses two FAD-dependent G3PDHs. While one of them (mitochondrial G3PDH [mtG3PDH]) has been attributed to the mitochondrion and seems to be directly involved in G3PDH shuttle reactions, the function of the other enzyme (putative G3PDH [putG3PDH]) remains unknown. In this work, we used RNA interference and protein overexpression and tagging to shed light on the relative contributions of both FAD-G3PDHs to overall cellular metabolism. Our results indicate that mtG3PDH is essential for the bloodstream stage of T. brucei , while in the procyclic stage the enzyme is dispensable. Expressed putG3PDH-V5 was localized to the mitochondrion, and the data obtained by digitonin permeabilization, Western blot analysis, and immunofluorescence indicate that putG3PDH is located within the mitochondrion.

scholarly journals Atomic Force Microscopy Investigation of the Interactions between the MCM Helicase and DNA

Materials ◽  
2021 ◽  
Vol 14 (3) ◽  
pp. 687
Author(s):  
Amna Abdalla Mohammed Khalid ◽  
Pietro Parisse ◽  
Barbara Medagli ◽  
Silvia Onesti ◽  
Loredana Casalis
Keyword(s):  
Atomic Force Microscopy ◽  
Nucleic Acid ◽  
Single Molecule ◽  
Protein Complex ◽  
The Other ◽  
Contour Length ◽  
Force Microscopy ◽  
Atomic Force ◽  
Mcm Complex ◽  
Dna Double Helix

The MCM (minichromosome maintenance) protein complex forms an hexameric ring and has a key role in the replication machinery of Eukaryotes and Archaea, where it functions as the replicative helicase opening up the DNA double helix ahead of the polymerases. Here, we present a study of the interaction between DNA and the archaeal MCM complex from Methanothermobacter thermautotrophicus by means of atomic force microscopy (AFM) single molecule imaging. We first optimized the protocol (surface treatment and buffer conditions) to obtain AFM images of surface-equilibrated DNA molecules before and after the interaction with the protein complex. We discriminated between two modes of interaction, one in which the protein induces a sharp bend in the DNA, and one where there is no bending. We found that the presence of the MCM complex also affects the DNA contour length. A possible interpretation of the observed behavior is that in one case the hexameric ring encircles the dsDNA, while in the other the nucleic acid wraps on the outside of the ring, undergoing a change of direction. We confirmed this topographical assignment by testing two mutants, one affecting the N-terminal β-hairpins projecting towards the central channel, and thus preventing DNA loading, the other lacking an external subdomain and thus preventing wrapping. The statistical analysis of the distribution of the protein complexes between the two modes, together with the dissection of the changes of DNA contour length and binding angle upon interaction, for the wild type and the two mutants, is consistent with the hypothesis. We discuss the results in view of the various modes of nucleic acid interactions that have been proposed for both archaeal and eukaryotic MCM complexes.

scholarly journals TbUNC119 and Its Binding Protein Complex Are Essential for Propagation, Motility, and Morphogenesis of Trypanosoma brucei Procyclic Form Cells

PLoS ONE ◽  
2010 ◽  
Vol 5 (12) ◽  
pp. e15577 ◽  
Author(s):  
Shigeru Ohshima ◽  
Mitsuko Ohashi-Suzuki ◽  
Yutaka Miura ◽  
Yoshisada Yabu ◽  
Noriko Okada ◽  
...  
Keyword(s):  
Trypanosoma Brucei ◽  
Protein Complex ◽  
Binding Protein ◽  
Procyclic Form

Localization, turnover and conservation of gp15/400 in different stages ofBrugia malayi

Parasitology ◽  
1993 ◽  
Vol 107 (4) ◽  
pp. 449-457 ◽  
Author(s):  
M. E. Selkirk ◽  
W. F. Gregory ◽  
R. E. Jenkins ◽  
R. M. Maizels
Keyword(s):  
Protein Complex ◽  
Cdna Probe ◽  
The Body ◽  
Mammalian Host ◽  
Major Protein ◽  
Homologous Genes ◽  
Acanthocheilonema Viteae ◽  
Filarial Nematodes ◽  
The Matrix

SUMMARYThe expression of a protein complex designated gp15/400, previously identified via extrinsic iodination of adultBrugia malayi, was examined by labelling all stages found in the mammalian host and immunoprecipitation with a specific antibody raised to a recombinant protein. In this way, gp15/400 could be detected in L3, L4, adult worms and microfilariae recovered from jirds and labelled with Bolton–Hunter reagent. Metabolic labelling indicated that gp15/400 was released into culture medium when adult worms were maintainedin vitro, but at a rate slower than that of gp29, the major soluble cuticular glycoprotein. Immuno-electron microscopy showed that the protein complex was broadly distributed in different tissues, although it was not detectable in the cuticle of adult worms. Dense labelling was observed in the matrix of the basal laminae bordering the hypodermis, somatic musculature and oesophagus, and lower but significant labelling was seen in the cells overlying these extracellular matrices. Hybridization of genomic DNA with a cDNA probe encoding gp15/400 indicated that homologous genes were present inDirofilaria immitisandAcanthocheilonema viteae. The failure to detect related genes in non-filarial nematodes was presumed to be due to divergence beyond the practical limits of detection by nucleic acid probes, as antibody reagents showed that the protein cross-reacted immunologically with ABA-1, a major protein allergen from the body fluid ofAscaris.

scholarly journals Mitochondrial DNAs provide insight into trypanosome phylogeny and molecular evolution

2020 ◽  
Author(s):  
Christopher Kay ◽  
Tom A Williams ◽  
Wendy Gibson
Keyword(s):  
Molecular Evolution ◽  
Trypanosoma Brucei ◽  
Rna Editing ◽  
Phylogenetic Trees ◽  
Nucleotide Composition ◽  
Sub Saharan Africa ◽  
African Trypanosomes ◽  
Animal Pathogens ◽  
Recent Emergence ◽  
The Impact

Abstract Background: Trypanosomes are single-celled eukaryotic parasites characterised by the unique biology of their mitochondrial DNA (mtDNA). African livestock trypanosomes impose a major burden on agriculture across sub-Saharan Africa, but are poorly understood compared to those that cause sleeping sickness and Chagas disease in humans. Here we explore the potential of trypanosome mtDNA to study the evolutionary history of trypanosomes and the molecular evolution of their mtDNAs.Results: We used long-read sequencing to completely assemble mtDNAs from four previously uncharacterized African trypanosomes, and leveraged these assemblies to scaffold and assemble a further 103 trypanosome mtDNAs from published short-read data. While synteny was largely conserved, there were repeated, independent losses of Complex I genes. Comparison of edited and non-edited genes revealed the impact of RNA editing on nucleotide composition, with non-edited genes approaching the limits of GC loss. African tsetse-transmitted trypanosomes showed high levels of RNA editing compared to other trypanosomes. Whole mtDNA coding regions were used to construct time-resolved phylogenetic trees, revealing deep divergence events among isolates of the pathogens Trypanosoma brucei and T. congolense .Conclusions: Our mtDNA data represents a new resource for experimental and evolutionary analyses of trypanosome phylogeny, molecular evolution and function. Molecular clock analyses yielded a timescale for trypanosome evolution congruent with major biogeographical events in Africa and revealed the recent emergence of Trypanosoma brucei gambiense and T. equiperdum , major human and animal pathogens.

Analysis of Gene Function in Trypanosoma brucei Using RNA Interference

2004 ◽  
pp. 73-83 ◽  
Author(s):  
Appolinaire Djikeng ◽  
Shuiyuan Shen ◽  
Christian Tschudi ◽  
Elisabetta Ullu
Keyword(s):  
Rna Interference ◽  
Trypanosoma Brucei ◽  
Gene Function
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