Publications by authors named "André Schneider"

129 Publications

Determinism and contingencies shaped the evolution of mitochondrial protein import.

Proc Natl Acad Sci U S A 2021 Feb;118(6)

Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, CH-3012 Bern, Switzerland;

Mitochondrial protein import requires outer membrane receptors that evolved independently in different lineages. Here we used quantitative proteomics and in vitro binding assays to investigate the substrate preferences of ATOM46 and ATOM69, the two mitochondrial import receptors of The results show that ATOM46 prefers presequence-containing, hydrophilic proteins that lack transmembrane domains (TMDs), whereas ATOM69 prefers presequence-lacking, hydrophobic substrates that have TMDs. Thus, the ATOM46/yeast Tom20 and the ATOM69/yeast Tom70 pairs have similar substrate preferences. However, ATOM46 mainly uses electrostatic, and Tom20 hydrophobic, interactions for substrate binding. In vivo replacement of ATOM46 by yeast Tom20 did not restore import. However, replacement of ATOM69 by the recently discovered Tom36 receptor of hydrogenosomes, while not allowing for growth, restored import of a large subset of trypanosomal proteins that lack TMDs. Thus, even though ATOM69 and Tom36 share the same domain structure and topology, they have different substrate preferences. The study establishes complementation experiments, combined with quantitative proteomics, as a highly versatile and sensitive method to compare in vivo preferences of protein import receptors. Moreover, it illustrates the role determinism and contingencies played in the evolution of mitochondrial protein import receptors.
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http://dx.doi.org/10.1073/pnas.2017774118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8017667PMC
February 2021

Cardiomyocytes-specific deletion of monoamine oxidase B reduces irreversible myocardial ischemia/reperfusion injury.

Free Radic Biol Med 2021 Mar 18;165:14-23. Epub 2021 Jan 18.

Justus-Liebig-University Giessen, Physiologisches Institut, Giessen, Germany.

Monoamine oxidase B (MAO-B), a protein localized at the outer mitochondrial membrane, catalyzes the oxidative deamination of biogenic amines thereby producing reactive oxygen species (ROS). Increased ROS formation contributes to myocardial ischemia/reperfusion (I/R); however, the importance of different ROS producing enzymes for increased I/R-induced ROS formation and the subsequent I/R injury is still a matter of debate. Here we describe the first cardiomyocytes-specific MAO-B knockout mouse and test the hypothesis that lack of cardiomyocyte MAO-B protects the heart from I/R injury. A cardiac-specific and tamoxifen-inducible MAO-B knockout mouse (MAO-B KO) was generated using the Cre/lox system; Cre-negative MAO-B littermates served as controls (WT). Lack of MAO-B was verified by Western blot and immunohistochemistry. Cardiac function of MAO-B KO and WT was analyzed by echocardiography, quantification of mitochondrial ROS production, and measurement of myocardial infarct size (in % of ventricle) in hearts exposed to global I/R using the Langendorff technique. MAO-B protein expression was significantly down-regulated in MAO-B KO mice after two weeks of tamoxifen feeding followed by ten weeks of feeding with normal chow. ROS formation stimulated by the MAO-B-specific substrate β-phenylethylamin (PEA; 250 μM) was significantly lower in mitochondria isolated from MAO-B KO compared to WT hearts (WT 4.5 ± 0.8 a. u.; MAO-B KO 1.2 ± 0.3 a. u.). Echocardiography revealed no significant differences in LV dimensions as well as ejection fraction (EF) between WT and MAO-B KO mice (EF: WT 67.3 ± 8.8%; MAO-B KO 67.7 ± 6.5%). After I/R, infarct size was significantly lower in MAO-B KO hearts (WT 69.3 ± 15.1%; MAO-B KO 46.8 ± 12.0%). CONCLUSION: Lack of cardiomyocytes-specific MAO-B reduces infarct size suggesting that MAO-B activity contributes to acute reperfusion injury.
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http://dx.doi.org/10.1016/j.freeradbiomed.2021.01.020DOI Listing
March 2021

tRNA 3' shortening by LCCR4 as a response to stress in Trypanosoma brucei.

Nucleic Acids Res 2021 02;49(3):1647-1661

Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.

Sensing of environmental cues is crucial for cell survival. To adapt to changes in their surroundings cells need to tightly control the repertoire of genes expressed at any time. Regulation of translation is key, especially in organisms in which transcription is hardly controlled, like Trypanosoma brucei. In this study, we describe the shortening of the bulk of the cellular tRNAs during stress at the expense of the conserved 3' CCA-tail. This tRNA shortening is specific for nutritional stress and renders tRNAs unsuitable substrates for translation. We uncovered the nuclease LCCR4 (Tb927.4.2430), a homologue of the conserved deadenylase Ccr4, as being responsible for tRNA trimming. Once optimal growth conditions are restored tRNAs are rapidly repaired by the trypanosome tRNA nucleotidyltransferase thus rendering the recycled tRNAs amenable for translation. This mechanism represents a fast and efficient way to repress translation during stress, allowing quick reactivation with a low energy input.
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http://dx.doi.org/10.1093/nar/gkaa1261DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7897491PMC
February 2021

BMP9 and BMP10 Act Directly on Vascular Smooth Muscle Cells for Generation and Maintenance of the Contractile State.

Circulation 2021 Apr 18;143(14):1394-1410. Epub 2020 Dec 18.

Departments of Cardiac Development and Remodeling (L.W., M.R., S.S., F.W., T.B., M.W., A.S., T.B.).

Background: Vascular smooth muscle cells (VSMCs) show a remarkable phenotypic plasticity, allowing acquisition of contractile or synthetic states, but critical information is missing about the physiologic signals, promoting formation, and maintenance of contractile VSMCs in vivo. BMP9 and BMP10 (bone morphogenetic protein) are known to regulate endothelial quiescence after secretion from the liver and right atrium, whereas a direct role in the regulation of VSMCs was not investigated. We studied the role of BMP9 and BMP10 for controlling formation of contractile VSMCs.

Methods: We generated several cell type-specific loss- and gain-of-function transgenic mouse models to investigate the physiologic role of BMP9, BMP10, ALK1 (activin receptor-like kinase 1), and SMAD7 in vivo. Morphometric assessments, expression analysis, blood pressure measurements, and single molecule fluorescence in situ hybridization were performed together with analysis of isolated pulmonary VSMCs to unravel phenotypic and transcriptomic changes in response to absence or presence of BMP9 and BMP10.

Results: Concomitant genetic inactivation of in the germ line and in the right atrium led to dramatic changes in vascular tone and diminution of the VSMC layer with attenuated contractility and decreased systemic as well as right ventricular systolic pressure. On the contrary, overexpression of in endothelial cells of adult mice dramatically enhanced formation of contractile VSMCs and increased systemic blood pressure as well as right ventricular systolic pressure. Likewise, BMP9/10 treatment induced an ALK1-dependent phenotypic switch from synthetic to contractile in pulmonary VSMCs. Smooth muscle cell-specific overexpression of completely suppressed differentiation and proliferation of VSMCs and reiterated defects observed in adult double mutants. Deletion of in VSMCs recapitulated the phenotype in pulmonary but not in aortic and coronary arteries. Bulk expression analysis and single molecule RNA-fluorescence in situ hybridization uncovered vessel bed-specific, heterogeneous expression of BMP type 1 receptors, explaining phenotypic differences in different mutant vessel beds.

Conclusions: Our study demonstrates that BMP9 and BMP10 act directly on VSMCs for induction and maintenance of their contractile state. The effects of BMP9/10 in VSMCs are mediated by different combinations of BMP type 1 receptors in a vessel bed-specific manner, offering new opportunities to manipulate blood pressure in the pulmonary circulation.
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http://dx.doi.org/10.1161/CIRCULATIONAHA.120.047375DOI Listing
April 2021

A short history of guide RNAs: The intricate path that led to the discovery of a basic biological concept.

Authors:
André Schneider

EMBO Rep 2020 12 1;21(12):e51918. Epub 2020 Dec 1.

Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland.

This year's Nobel prize for the CRISPR/Cas system is an illustrative example of how scientific breakthroughs rests on preceding work: the discovery of guide RNAs in the 1990s.
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http://dx.doi.org/10.15252/embr.202051918DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7726800PMC
December 2020

tRNA import across the mitochondrial inner membrane in T. brucei requires TIM subunits but is independent of protein import.

Nucleic Acids Res 2020 12;48(21):12269-12281

Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.

Mitochondrial tRNA import is widespread, but mechanistic insights of how tRNAs are translocated across mitochondrial membranes remain scarce. The parasitic protozoan T. brucei lacks mitochondrial tRNA genes. Consequently, it imports all organellar tRNAs from the cytosol. Here we investigated the connection between tRNA and protein translocation across the mitochondrial inner membrane. Trypanosomes have a single inner membrane protein translocase that consists of three heterooligomeric submodules, which all are required for import of matrix proteins. In vivo depletion of individual submodules shows that surprisingly only the integral membrane core module, including the protein import pore, but not the presequence-associated import motor are required for mitochondrial tRNA import. Thus we could uncouple import of matrix proteins from import of tRNAs even though both substrates are imported into the same mitochondrial subcompartment. This is reminiscent to the outer membrane where the main protein translocase but not on-going protein translocation is required for tRNA import. We also show that import of tRNAs across the outer and inner membranes are coupled to each other. Taken together, these data support the 'alternate import model', which states that tRNA and protein import while mechanistically independent use the same translocation pores but not at the same time.
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http://dx.doi.org/10.1093/nar/gkaa1098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7708065PMC
December 2020

Structural Insights into the Mechanism of Mitoribosomal Large Subunit Biogenesis.

Mol Cell 2020 08 16;79(4):629-644.e4. Epub 2020 Jul 16.

Department of Biology, ETH Zurich, Zurich 8093, Switzerland. Electronic address:

In contrast to the bacterial translation machinery, mitoribosomes and mitochondrial translation factors are highly divergent in terms of composition and architecture. There is increasing evidence that the biogenesis of mitoribosomes is an intricate pathway, involving many assembly factors. To better understand this process, we investigated native assembly intermediates of the mitoribosomal large subunit from the human parasite Trypanosoma brucei using cryo-electron microscopy. We identify 28 assembly factors, 6 of which are homologous to bacterial and eukaryotic ribosome assembly factors. They interact with the partially folded rRNA by specifically recognizing functionally important regions such as the peptidyltransferase center. The architectural and compositional comparison of the assembly intermediates indicates a stepwise modular assembly process, during which the rRNA folds toward its mature state. During the process, several conserved GTPases and a helicase form highly intertwined interaction networks that stabilize distinct assembly intermediates. The presented structures provide general insights into mitoribosomal maturation.
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http://dx.doi.org/10.1016/j.molcel.2020.06.030DOI Listing
August 2020

The single CCA-adding enzyme of has distinct functions in the cytosol and in mitochondria.

J Biol Chem 2020 05 31;295(18):6138-6150. Epub 2020 Mar 31.

Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern CH-3012, Switzerland. Electronic address:

tRNAs universally carry a CCA nucleotide triplet at their 3'-ends. In eukaryotes, the CCA is added post-transcriptionally by the CCA-adding enzyme (CAE). The mitochondrion of the parasitic protozoan lacks tRNA genes and therefore imports all of its tRNAs from the cytosol. This has generated interest in the tRNA modifications and their distribution in this organism, including how CCA is added to tRNAs. Here, using a BLAST search for genes encoding putative CAE proteins in , we identified a single ORF, Tb927.9.8780, as a potential candidate. Knockdown of this putative protein, termed TbCAE, resulted in the accumulation of truncated tRNAs, abolished translation, and inhibited both total and mitochondrial CCA-adding activities, indicating that TbCAE is located both in the cytosol and mitochondrion. However, mitochondrially localized tRNAs were much less affected by the TbCAE ablation than the other tRNAs. Complementation assays revealed that the N-terminal 10 amino acids of TbCAE are dispensable for its activity and mitochondrial localization and that deletion of 10 further amino acids abolishes both. A growth arrest caused by the TbCAE knockdown was rescued by the expression of the cytosolic isoform of yeast CAE, even though it was not imported into mitochondria. This finding indicated that the yeast enzyme complements the essential function of TbCAE by adding CCA to the primary tRNA transcripts. Of note, ablation of the mitochondrial TbCAE activity, which likely has a repair function, only marginally affected growth.
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http://dx.doi.org/10.1074/jbc.RA119.011877DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7196653PMC
May 2020

A Scalable Purification Method for Mitochondria from Trypanosoma brucei.

Methods Mol Biol 2020 ;2116:611-626

Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland.

Due to its unique biology the mitochondrion of Trypanosoma brucei has attracted a lot of interest since many decades, making it arguably the best studied mitochondrion outside yeast and mammals. Here we describe a method allowing purification of mitochondria from procyclic trypanosomes that yields highly enriched and functional organelles. The method is based on isotonic lysis of cells by nitrogen cavitation, DNase I digestion, differential centrifugation and Nycodenz gradient centrifugation. The method is scalable and can be adapted to culture volumes a small as 100 mL or as large as 24 L.
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http://dx.doi.org/10.1007/978-1-0716-0294-2_36DOI Listing
February 2021

Lexis and Grammar of Mitochondrial RNA Processing in Trypanosomes.

Trends Parasitol 2020 04 28;36(4):337-355. Epub 2020 Feb 28.

Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA 02118, USA.

Trypanosoma brucei spp. cause African human and animal trypanosomiasis, a burden on health and economy in Africa. These hemoflagellates are distinguished by a kinetoplast nucleoid containing mitochondrial DNAs of two kinds: maxicircles encoding ribosomal RNAs (rRNAs) and proteins and minicircles bearing guide RNAs (gRNAs) for mRNA editing. All RNAs are produced by a phage-type RNA polymerase as 3' extended precursors, which undergo exonucleolytic trimming. Most pre-mRNAs proceed through 3' adenylation, uridine insertion/deletion editing, and 3' A/U-tailing. The rRNAs and gRNAs are 3' uridylated. Historically, RNA editing has attracted major research effort, and recently essential pre- and postediting processing events have been discovered. Here, we classify the key players that transform primary transcripts into mature molecules and regulate their function and turnover.
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http://dx.doi.org/10.1016/j.pt.2020.01.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7083771PMC
April 2020

Evolution of mitochondrial protein import - lessons from trypanosomes.

Authors:
André Schneider

Biol Chem 2020 05;401(6-7):663-676

Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.

The evolution of mitochondrial protein import and the systems that mediate it marks the boundary between the endosymbiotic ancestor of mitochondria and a true organelle that is under the control of the nucleus. Protein import has been studied in great detail in Saccharomyces cerevisiae. More recently, it has also been extensively investigated in the parasitic protozoan Trypanosoma brucei, making it arguably the second best studied system. A comparative analysis of the protein import complexes of yeast and trypanosomes is provided. Together with data from other systems, this allows to reconstruct the ancestral features of import complexes that were present in the last eukaryotic common ancestor (LECA) and to identify which subunits were added later in evolution. How these data can be translated into plausible scenarios is discussed, providing insights into the evolution of (i) outer membrane protein import receptors, (ii) proteins involved in biogenesis of α-helically anchored outer membrane proteins, and (iii) of the intermembrane space import and assembly system. Finally, it is shown that the unusual presequence-associated import motor of trypanosomes suggests a scenario of how the two ancestral inner membrane protein translocases present in LECA evolved into the single bifunctional one found in extant trypanosomes.
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http://dx.doi.org/10.1515/hsz-2019-0444DOI Listing
May 2020

Homologue replacement in the import motor of the mitochondrial inner membrane of trypanosomes.

Elife 2020 02 27;9. Epub 2020 Feb 27.

Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland.

Many mitochondrial proteins contain N-terminal presequences that direct them to the organelle. The main driving force for their translocation across the inner membrane is provided by the presequence translocase-associated motor (PAM) which contains the J-protein Pam18. Here, we show that in the PAM of the function of Pam18 has been replaced by the non-orthologous euglenozoan-specific J-protein TbPam27. TbPam27 is specifically required for the import of mitochondrial presequence-containing but not for carrier proteins. Similar to yeast Pam18, TbPam27 requires an intact J-domain to function. Surprisingly, still contains a bona fide Pam18 orthologue that, while essential for normal growth, is not involved in protein import. Thus, during evolution of kinetoplastids, Pam18 has been replaced by TbPam27. We propose that this replacement is linked to the transition from two ancestral and functionally distinct TIM complexes, found in most eukaryotes, to the single bifunctional TIM complex present in trypanosomes.
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http://dx.doi.org/10.7554/eLife.52560DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7064343PMC
February 2020

Correlating Decoherence in Transmon Qubits: Low Frequency Noise by Single Fluctuators.

Phys Rev Lett 2019 Nov;123(19):190502

Institute of Physics, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany.

We report on long-term measurements of a highly coherent, nontunable superconducting transmon qubit, revealing low-frequency burst noise in coherence times and qubit transition frequency. We achieve this through a simultaneous measurement of the qubit's relaxation and dephasing rate as well as its resonance frequency. The analysis of correlations between these parameters yields information about the microscopic origin of the intrinsic decoherence mechanisms in Josephson qubits. Our results are consistent with a small number of microscopic two-level systems located at the edges of the superconducting film, which is further confirmed by a spectral noise analysis.
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http://dx.doi.org/10.1103/PhysRevLett.123.190502DOI Listing
November 2019

The highly diverged trypanosomal MICOS complex is organized in a nonessential integral membrane and an essential peripheral module.

Mol Microbiol 2019 12 3;112(6):1731-1743. Epub 2019 Oct 3.

Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern, CH-3012, Switzerland.

The mitochondrial contact site and cristae organization system (MICOS) mediates the formation of cristae, invaginations in the mitochondrial inner membrane. The highly diverged MICOS complex of the parasitic protist Trypanosoma brucei consists of nine subunits. Except for two Mic10-like and a Mic60-like protein, all subunits are specific for kinetoplastids. Here, we determined on a proteome-wide scale how ablation of individual MICOS subunits affects the levels of the other subunits. The results reveal co-regulation of TbMic10-1, TbMic10-2, TbMic16 and TbMic60, suggesting that these nonessential, integral inner membrane proteins form an interdependent network. Moreover, the ablation of TbMic34 and TbMic32 reveals another network consisting of the essential, intermembrane space-localized TbMic20, TbMic32, TbMic34 and TbMic40, all of which are peripherally associated with the inner membrane. The downregulation of TbMic20, TbMic32 and TbMic34 also interferes with mitochondrial protein import and reduces the size of the TbMic10-containing complexes. Thus, the diverged MICOS of trypanosomes contains two subcomplexes: a nonessential membrane-integrated one, organized around the conserved Mic10 and Mic60, that mediates cristae formation, and an essential membrane-peripheral one consisting of four kinetoplastid-specific subunits, that is required for import of intermembrane space proteins.
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http://dx.doi.org/10.1111/mmi.14389DOI Listing
December 2019

Mitoribosomal small subunit biogenesis in trypanosomes involves an extensive assembly machinery.

Science 2019 09;365(6458):1144-1149

Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, CH-8093 Zurich, Switzerland.

Mitochondrial ribosomes (mitoribosomes) are large ribonucleoprotein complexes that synthesize proteins encoded by the mitochondrial genome. An extensive cellular machinery responsible for ribosome assembly has been described only for eukaryotic cytosolic ribosomes. Here we report that the assembly of the small mitoribosomal subunit in involves a large number of factors and proceeds through the formation of assembly intermediates, which we analyzed by using cryo-electron microscopy. One of them is a 4-megadalton complex, referred to as the small subunit assemblosome, in which we identified 34 factors that interact with immature ribosomal RNA (rRNA) and recognize its functionally important regions. The assembly proceeds through large-scale conformational changes in rRNA coupled with successive incorporation of mitoribosomal proteins, providing an example for the complexity of the ribosomal assembly process in mitochondria.
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http://dx.doi.org/10.1126/science.aaw5570DOI Listing
September 2019

Inducible orthogonal aminoacylation demonstrates that charging is required for mitochondrial tRNA import in Trypanosoma brucei.

Sci Rep 2019 07 25;9(1):10836. Epub 2019 Jul 25.

Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern, CH-3012, Switzerland.

Orthogonal aminoacyl-tRNA synthetase/tRNA pairs have emerged as powerful means of site-specifically introducing non-standard amino acids into proteins in vivo. Using amino acids with crosslinking moieties this method allows the identification of transient protein-protein interactions. Here we have introduced a previously characterized evolved tyrosyl-tRNA synthetase/suppressor tRNA pair from E. coli into the parasitic protozoan Trypanosoma brucei. Upon addition of a suitable non-standard amino acid the suppressor tRNA was charged and allowed translation of a green fluorescent protein whose gene contained a nonsense mutation. - T. brucei is unusual in that its mitochondrion lacks tRNA genes indicating that all its organellar tRNAs are imported from the cytosol. Expression of the bacterial tyrosyl-tRNA synthetase in our system is tetracycline-inducible. We have therefore used it to demonstrate that cytosolic aminoacylation of the suppressor tRNA induces its import into the mitochondrion.
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http://dx.doi.org/10.1038/s41598-019-47268-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6658472PMC
July 2019

tRNA Biology in Trypanosomes.

Chimia (Aarau) 2019 May;73(6):395-405

Besides their medical importance, the parasitic protozoan and its relatives are experimentally highly accessible model systems for many cell biological processes. Trypanosomes are phylogenetically essentially unrelated to the popular model eukaryotes, such as yeast and animals, and thus show several unique features, many of which are connected to RNA. Here we review the tRNA biology of trypanosomes. Even though tRNAs were already discovered 60 years ago, owing to current technological advances in the field, research on tRNA biology has seen a Renaissance in recent years. First we discuss the extensive mitochondrial tRNA import process and the consequences it has for the parasite. Next we focus on trypanosomal aminoacyl-tRNA synthetases, some of which may be exploited as drug targets. Furthermore, we summarize what is known about trypanosomal tRNA modifications in both the cytosol and the mitochondrion. Finally, we provide an overview on the emerging field of tRNA-derived fragments and their possible function as translation regulators.
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http://dx.doi.org/10.2533/chimia.2019.395DOI Listing
May 2019

A tRNA half modulates translation as stress response in Trypanosoma brucei.

Nat Commun 2019 01 10;10(1):118. Epub 2019 Jan 10.

Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland.

In the absence of extensive transcription control mechanisms the pathogenic parasite Trypanosoma brucei crucially depends on translation regulation to orchestrate gene expression. However, molecular insight into regulating protein biosynthesis is sparse. Here we analyze the small non-coding RNA (ncRNA) interactome of ribosomes in T. brucei during different growth conditions and life stages. Ribosome-associated ncRNAs have recently been recognized as unprecedented regulators of ribosome functions. Our data show that the tRNA 3´half is produced during nutrient deprivation and becomes one of the most abundant tRNA-derived RNA fragments (tdRs). tRNA halves associate with ribosomes and polysomes and stimulate translation by facilitating mRNA loading during stress recovery once starvation conditions ceased. Blocking or depleting the endogenous tRNA halves mitigates this stimulatory effect both in vivo and in vitro. T. brucei and its close relatives lack the well-described mammalian enzymes for tRNA half processing, thus hinting at a unique tdR biogenesis in these parasites.
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http://dx.doi.org/10.1038/s41467-018-07949-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6328589PMC
January 2019

Mitochondrial protein import in trypanosomatids: Variations on a theme or fundamentally different?

Authors:
André Schneider

PLoS Pathog 2018 11 29;14(11):e1007351. Epub 2018 Nov 29.

Department of Chemistry and Biochemistry, University of Bern, Freiestrasse, Bern, Switzerland.

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http://dx.doi.org/10.1371/journal.ppat.1007351DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6264148PMC
November 2018

The Diverged Trypanosome MICOS Complex as a Hub for Mitochondrial Cristae Shaping and Protein Import.

Curr Biol 2018 11 25;28(21):3393-3407.e5. Epub 2018 Oct 25.

Institute of Parasitology, Biology Center, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic. Electronic address:

The mitochondrial contact site and cristae organization system (MICOS) is a multiprotein complex responsible for cristae formation. Even though cristae are found in all mitochondria capable of oxidative phosphorylation, only Mic10 and Mic60 appear to be conserved throughout eukaryotes. The remaining 4 or 5 known MICOS subunits are specific to the supergroup Opisthokonta, which includes yeast and mammals that are the only organisms in which this complex has been analyzed experimentally. We have isolated the MICOS from Trypanosoma brucei, a member of the supergroup Excavata that is profoundly diverged from opisthokonts. We show that it is required for the maintenance of the unique discoidal cristae that typify excavates, such as euglenids and kinetoplastids, the latter of which include trypanosomes. The trypanosome MICOS consists of 9 subunits, most of which are essential for normal growth. Unlike in opisthokonts, it contains two distinct Mic10 orthologs and an unconventional putative Mic60 that lacks a mitofilin domain. Interestingly, one of the essential trypanosomatid-specific MICOS subunits called TbMic20 is a thioredoxin-like protein that appears to be involved in import of intermembrane space proteins, including respiratory chain complex assembly factors. This result points to trypanosome MICOS coordinating cristae shaping and population of its membrane with proteins involved in respiration, the latter via the catalytic activity of TbMic20. Thus, trypanosome MICOS allows us to define which of its features are conserved in all eukaryotes and decipher those that represent lineage-specific adaptations.
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http://dx.doi.org/10.1016/j.cub.2018.09.008DOI Listing
November 2018

Failure is not an option - mitochondrial genome segregation in trypanosomes.

J Cell Sci 2018 09 17;131(18). Epub 2018 Sep 17.

Institute of Cell Biology, University of Bern, Baltzerstrasse 4, Bern CH-3012, Switzerland

Unlike most other model eukaryotes, and its relatives have a single mitochondrion with a single-unit mitochondrial genome that is termed kinetoplast DNA (kDNA). Replication of the kDNA is coordinated with the cell cycle. During binary mitochondrial fission and prior to cytokinesis, the replicated kDNA has to be faithfully segregated to the daughter organelles. This process depends on the tripartite attachment complex (TAC) that physically links the kDNA across the two mitochondrial membranes with the basal body of the flagellum. Thus, the TAC couples segregation of the replicated kDNA with segregation of the basal bodies of the old and the new flagellum. In this Review, we provide an overview of the role of the TAC in kDNA inheritance in We focus on recent advances regarding the molecular composition of the TAC, and discuss how the TAC is assembled and how its subunits are targeted to their respective TAC subdomains. Finally, we will contrast the segregation of the single-unit kDNA in trypanosomes to mitochondrial genome inheritance in yeast and mammals, both of which have numerous mitochondria that each contain multiple genomes.
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http://dx.doi.org/10.1242/jcs.221820DOI Listing
September 2018

Evolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes.

Science 2018 10 13;362(6413). Epub 2018 Sep 13.

Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland.

Ribosomal RNA (rRNA) plays key functional and architectural roles in ribosomes. Using electron microscopy, we determined the atomic structure of a highly divergent ribosome found in mitochondria of , a unicellular parasite that causes sleeping sickness in humans. The trypanosomal mitoribosome features the smallest rRNAs and contains more proteins than all known ribosomes. The structure shows how the proteins have taken over the role of architectural scaffold from the rRNA: They form an autonomous outer shell that surrounds the entire particle and stabilizes and positions the functionally important regions of the rRNA. Our results also reveal the "minimal" set of conserved rRNA and protein components shared by all ribosomes that help us define the most essential functional elements.
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http://dx.doi.org/10.1126/science.aau7735DOI Listing
October 2018

Independent evolution of functionally exchangeable mitochondrial outer membrane import complexes.

Elife 2018 06 20;7. Epub 2018 Jun 20.

Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.

Assembly and/or insertion of a subset of mitochondrial outer membrane (MOM) proteins, including subunits of the main MOM translocase, require the fungi-specific Mim1/Mim2 complex. So far it was unclear which proteins accomplish this task in other eukaryotes. Here, we show by reciprocal complementation that the MOM protein pATOM36 of trypanosomes is a functional analogue of yeast Mim1/Mim2 complex, even though these proteins show neither sequence nor topological similarity. Expression of pATOM36 rescues almost all growth, mitochondrial biogenesis, and morphology defects in yeast cells lacking Mim1 and/or Mim2. Conversely, co-expression of Mim1 and Mim2 restores the assembly and/or insertion defects of MOM proteins in trypanosomes ablated for pATOM36. Mim1/Mim2 and pATOM36 form native-like complexes when heterologously expressed, indicating that additional proteins are not part of these structures. Our findings indicate that Mim1/Mim2 and pATOM36 are the products of convergent evolution and arose only after the ancestors of fungi and trypanosomatids diverged.
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http://dx.doi.org/10.7554/eLife.34488DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6010339PMC
June 2018

Comparison between numeric and approximate analytic solutions for the prediction of soil metal uptake by roots. Example of cadmium.

Sci Total Environ 2018 Apr 29;619-620:1194-1205. Epub 2017 Nov 29.

INRA, UMR 1391 ISPA, 71, avenue Edouard Bourlaux, CS 20032, 33882 Villenave-d'Ornon cedex, France; Bordeaux Sciences Agro, UMR 1391 ISPA, 33170 Gradignan, France. Electronic address:

The dissociation of metal complexes in the soil solution can increase the availability of metals for root uptake. When it is accounted for in models of bioavailability of soil metals, the number of partial differential equations (PDEs) increases and the computation time to numerically solve these equations may be problematic when a large number of simulations are required, for example for sensitivity analyses or when considering root architecture. This work presents analytical solutions for the set of PDEs describing the bioavailability of soil metals including the kinetics of complexation for three scenarios where the metal complex in solution was fully inert, fully labile, or partially labile. The analytical solutions are only valid i) at steady-state when the PDEs become ordinary differential equations, the transient phase being not covered, ii) when diffusion is the major mechanism of transport and therefore, when convection is negligible, iii) when there is no between-root competition. The formulation of the analytical solutions is for cylindrical geometry but the solutions rely on the spread of the depletion profile around the root, which was modelled assuming a planar geometry. The analytical solutions were evaluated by comparison with the corresponding PDEs for cadmium in the case of the French agricultural soils. Provided that convection was much lower than diffusion (Péclet's number<0.02), the cumulative uptakes calculated from the analytic solutions were in very good agreement with those calculated from the PDEs, even in the case of a partially labile complex. The analytic solutions can be used instead of the PDEs to predict root uptake of metals. The analytic solutions were also used to build an indicator of the contribution of a complex to the uptake of the metal by roots, which can be helpful to predict the effect of soluble organic matter on the bioavailability of soil metals.
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http://dx.doi.org/10.1016/j.scitotenv.2017.11.069DOI Listing
April 2018

The pseudo-dimeric tyrosyl-tRNA synthetase of T. brucei aminoacylates cytosolic and mitochondrial tRNA and requires both monomeric units for activity.

Mol Biochem Parasitol 2018 04 23;221:52-55. Epub 2018 Mar 23.

Department of Chemistry and Biochemistry, University of Bern, Freiestr. 3, CH-3012 Bern, Switzerland. Electronic address:

Aminoacyl-tRNA synthetases are essential for protein synthesis. The single-copy tyrosyl-tRNA synthetase (Tb-TyrRS) of T. brucei has an unusual structure and forms a pseudo-dimer. It is therefore twice the size than tyrosyl-tRNA synthetases of most other organisms. Here we show by inducible RNAi that Tb-TyrRS is essential for normal growth of procyclic T. brucei. Furthermore we demonstrate that Tb-TyrRS aminoacylates cytosolic as well as mitochondrial tRNA indicating that it is dually localized. Finally we show that individual deletion of the 36 N- or C-terminal amino acids abolishes the function of Tb-TyrRS. This indicates that both monomeric units of the enzyme, the C-terminal one of which is predicted to lack enzymatic activity, are essential for Tb-TyrRS function. In summary our results together with previous studies support the notion that Tb-TyrRS might be a suitable drug target.
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http://dx.doi.org/10.1016/j.molbiopara.2018.03.004DOI Listing
April 2018

COX-2-derived PGE triggers hyperplastic renin expression and hyperreninemia in aldosterone synthase-deficient mice.

Pflugers Arch 2018 07 17;470(7):1127-1137. Epub 2018 Feb 17.

Institute of Physiology, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany.

Pharmacological inhibition or genetic loss of function defects of the renin angiotensin aldosterone system (RAAS) causes compensatory renin cell hyperplasia and hyperreninemia. The triggers for the compensatory stimulation of renin synthesis and secretion in this situation may be multimodal. Since cyclooxygenase-2 (COX-2) expression in the macula densa is frequently increased in states of a defective RAAS, we have investigated a potential role of COX-2 and its derived prostaglandins for renin expression and secretion in aldosterone synthase-deficient mice (AS) as a model for a genetic defect of the RAAS. In comparison with wild-type mice (WT), AS mice had 9-fold and 30-fold increases of renin mRNA and of plasma renin concentrations (PRC), respectively. Renin immunoreactivity in the kidney cortex of AS mice was 10-fold higher than in WT. Macula densa COX-2 expression was 5-fold increased in AS kidneys relative to WT kidneys. Treatment of AS mice with the COX-2 inhibitor SC-236 for 1 week lowered both renal renin mRNA and PRC by 70%. Hyperplastic renin cells in AS kidneys were found to express the prostaglandin E receptors EP2 and EP4. Global deletion of EP2 receptors did not alter renin mRNA nor PRC values in AS mice. Renin cell-specific inducible deletion of the EP4 receptor lowered renin mRNA and PRC by 25% in AS mice. Renin cell-specific inducible deletion of the EP4 receptor in combination with global deletion of the EP2 receptor lowered renin mRNA and PRC by 70-75% in AS mice. Lineage tracing of renin-expressing cells revealed that deletion of EP2 and EP4 leads to a preferential downregulation of perivascular renin expression. Our findings suggest that increased macula densa COX-2 activity in AS mice triggers perivascular renin expression and secretion via prostaglandin E.
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http://dx.doi.org/10.1007/s00424-018-2118-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6013527PMC
July 2018

Molecular model of the mitochondrial genome segregation machinery in .

Proc Natl Acad Sci U S A 2018 02 6;115(8):E1809-E1818. Epub 2018 Feb 6.

Institute of Cell Biology, University of Bern, CH-3012 Bern, Switzerland;

In almost all eukaryotes, mitochondria maintain their own genome. Despite the discovery more than 50 y ago, still very little is known about how the genome is correctly segregated during cell division. The protozoan parasite contains a single mitochondrion with a singular genome, the kinetoplast DNA (kDNA). Electron microscopy studies revealed the tripartite attachment complex (TAC) to physically connect the kDNA to the basal body of the flagellum and to ensure correct segregation of the mitochondrial genome via the basal bodies movement, during the cell cycle. Using superresolution microscopy, we precisely localize each of the currently known TAC components. We demonstrate that the TAC is assembled in a hierarchical order from the base of the flagellum toward the mitochondrial genome and that the assembly is not dependent on the kDNA itself. Based on the biochemical analysis, the TAC consists of several nonoverlapping subcomplexes, suggesting an overall size of the TAC exceeding 2.8 mDa. We furthermore demonstrate that the TAC is required for correct mitochondrial organelle positioning but not for organelle biogenesis or segregation.
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http://dx.doi.org/10.1073/pnas.1716582115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5828607PMC
February 2018

Biogenesis of the mitochondrial DNA inheritance machinery in the mitochondrial outer membrane of Trypanosoma brucei.

PLoS Pathog 2017 12 29;13(12):e1006808. Epub 2017 Dec 29.

Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland.

Mitochondria cannot form de novo but require mechanisms that mediate their inheritance to daughter cells. The parasitic protozoan Trypanosoma brucei has a single mitochondrion with a single-unit genome that is physically connected across the two mitochondrial membranes with the basal body of the flagellum. This connection, termed the tripartite attachment complex (TAC), is essential for the segregation of the replicated mitochondrial genomes prior to cytokinesis. Here we identify a protein complex consisting of three integral mitochondrial outer membrane proteins-TAC60, TAC42 and TAC40-which are essential subunits of the TAC. TAC60 contains separable mitochondrial import and TAC-sorting signals and its biogenesis depends on the main outer membrane protein translocase. TAC40 is a member of the mitochondrial porin family, whereas TAC42 represents a novel class of mitochondrial outer membrane β-barrel proteins. Consequently TAC40 and TAC42 contain C-terminal β-signals. Thus in trypanosomes the highly conserved β-barrel protein assembly machinery plays a major role in the biogenesis of its unique mitochondrial genome segregation system.
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http://dx.doi.org/10.1371/journal.ppat.1006808DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5764417PMC
December 2017

Analog quantum simulation of the Rabi model in the ultra-strong coupling regime.

Nat Commun 2017 10 3;8(1):779. Epub 2017 Oct 3.

Physikalisches Institut, Karlsruhe Institute of Technology, Wolfgang-Gaede-Straße 1, 76131, Karlsruhe, Germany.

The quantum Rabi model describes the fundamental mechanism of light-matter interaction. It consists of a two-level atom or qubit coupled to a quantized harmonic mode via a transversal interaction. In the weak coupling regime, it reduces to the well-known Jaynes-Cummings model by applying a rotating wave approximation. The rotating wave approximation breaks down in the ultra-strong coupling regime, where the effective coupling strength g is comparable to the energy ω of the bosonic mode, and remarkable features in the system dynamics are revealed. Here we demonstrate an analog quantum simulation of an effective quantum Rabi model in the ultra-strong coupling regime, achieving a relative coupling ratio of g/ω ~ 0.6. The quantum hardware of the simulator is a superconducting circuit embedded in a cQED setup. We observe fast and periodic quantum state collapses and revivals of the initial qubit state, being the most distinct signature of the synthesized model.An analog quantum simulation scheme has been explored with a quantum hardware based on a superconducting circuit. Here the authors investigate the time evolution of the quantum Rabi model at ultra-strong coupling conditions, which is synthesized by slowing down the system dynamics in an effective frame.
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http://dx.doi.org/10.1038/s41467-017-00894-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5626763PMC
October 2017