bims-mitran 2021-06-13 papers

bims-mitran

Biomed News

on Mitochondrial translation

Issue of 2021–06–13
thirteen papers selected by
Andreas Kohler, Stockholm University

Mitochondrial mistranslation modulated by metabolic stress causes cardiovascular disease and reduced lifespan.
Targeting the Mitochondrial Genome Via a MITO-Porter : Evaluation of mtDNA and mtRNA Levels and Mitochondrial Function.
PCR-Based Determination of Mitochondrial DNA Copy Number in Multiple Species.
Sequence-Specific Control of Mitochondrial Gene Transcription Using Programmable Synthetic Gene Switches Called MITO-PIPs.
mRNA Targeting, Transport and Local Translation in Eukaryotic Cells: From the Classical View to a Diversity of New Concepts.
mTRIP, an Imaging Tool to Investigate Mitochondrial DNA Dynamics in Physiology and Disease at the Single-Cell Resolution.
Mechanisms of Cotranslational Protein Maturation in Bacteria.
A role for the ribosome-associated complex in activation of the IRE1 branch of UPR.
Ribosome-associated quality control mediates degradation of the premature translation termination product Orf1p of ODC antizyme mRNA.
GATA3 induces mitochondrial biogenesis in primary human CD4+ T cells during DNA damage.
Bacterial RF3 senses chaperone function in co-translational folding.
Perturbation of ribosomal subunits dynamics by inhibitors of tRNA translocation.
Translation and codon usage regulate Argonaute slicer activity to trigger small RNA biogenesis.

Aging Cell. 2021 Jun 07. e13408

Mitochondrial mistranslation modulated by metabolic stress causes cardiovascular disease and reduced lifespan.

Tara R Richman, Judith A Ermer, Stefan J Siira, Irina Kuznetsova, Christopher A Brosnan, Giulia Rossetti, Jessica Baker, Kara L Perks, Henrietta Cserne Szappanos, Helena M Viola, Nicola Gray, Mark Larance, Livia C Hool, Steven Zuryn, Oliver Rackham, Aleksandra Filipovska.

  Changes in the rate and fidelity of mitochondrial protein synthesis impact the metabolic and physiological roles of mitochondria. Here we explored how environmental stress in the form of a high-fat diet modulates mitochondrial translation and affects lifespan in mutant mice with error-prone (Mrps12ep / ep ) or hyper-accurate (Mrps12ha / ha ) mitochondrial ribosomes. Intriguingly, although both mutations are metabolically beneficial in reducing body weight, decreasing circulating insulin and increasing glucose tolerance during a high-fat diet, they manifest divergent (either deleterious or beneficial) outcomes in a tissue-specific manner. In two distinct organs that are commonly affected by the metabolic disease, the heart and the liver, Mrps12ep / ep mice were protected against heart defects but sensitive towards lipid accumulation in the liver, activating genes involved in steroid and amino acid metabolism. In contrast, enhanced translational accuracy in Mrps12ha / ha mice protected the liver from a high-fat diet through activation of liver proliferation programs, but enhanced the development of severe hypertrophic cardiomyopathy and led to reduced lifespan. These findings reflect the complex transcriptional and cell signalling responses that differ between post-mitotic (heart) and highly proliferative (liver) tissues. We show trade-offs between the rate and fidelity of mitochondrial protein synthesis dictate tissue-specific outcomes due to commonly encountered stressful environmental conditions or aging.

Keywords:  ageing; metabolism; mitochondria; protein synthesis

DOI:  https://doi.org/10.1111/acel.13408
Methods Mol Biol. 2021 ;2275 227-245

Targeting the Mitochondrial Genome Via a MITO-Porter : Evaluation of mtDNA and mtRNA Levels and Mitochondrial Function.

Yuma Yamada, Hideyoshi Harashima.

  Genetic mutations and defects in mitochondrial DNA (mtDNA) are associated with certain types of mitochondrial dysfunctions, ultimately resulting in the emergence of a variety of human diseases. To achieve an effective mitochondrial gene therapy, it will be necessary to deliver therapeutic agents to the innermost mitochondrial space (the mitochondrial matrix), which contains the mtDNA pool. We recently developed a MITO-Porter, a liposome-based nanocarrier that delivers cargo to mitochondria via a membrane-fusion mechanism. In this chapter, we discuss the methodology used to deliver bioactive molecules to the mitochondrial matrix using a Dual Function (DF)-MITO-Porter, a liposome-based nanocarrier that delivers it cargo by means of a stepwise process, and an evaluation of mtDNA levels and mitochondrial activities in living cells. We also discuss mitochondrial gene silencing by the mitochondrial delivery of antisense RNA oligonucleotide (ASO) targeting mtDNA-encoded mRNA using the MITO-Porter system.

Keywords:  MITO-Porter; Mitochondria; Mitochondrial DNA; Mitochondrial RNA knockdown; Mitochondrial drug delivery; Mitochondrial gene therapy; Mitochondrial matrix; Nucleic acid delivery

DOI:  https://doi.org/10.1007/978-1-0716-1262-0_14
Methods Mol Biol. 2021 ;2310 91-111

PCR-Based Determination of Mitochondrial DNA Copy Number in Multiple Species.

Tess C Leuthner, Jessica H Hartman, Ian T Ryde, Joel N Meyer.

  Mitochondrial DNA (mtDNA) copy number is a critical component of overall mitochondrial health. In this chapter, we describe methods for simultaneous isolation of mtDNA and nuclear DNA (nucDNA), and measurement of their respective copy numbers using quantitative PCR. Methods differ depending on the species and cell type of the starting material, and availability of specific PCR reagents. We also briefly describe factors that affect mtDNA copy number and discuss caveats to its use as a biomarker.

Keywords:  Copy number; Mitochondrial DNA; Mitochondrial disease; Mitochondrial toxicity; QPCR; mtDNA; mtDNA depletion

DOI:  https://doi.org/10.1007/978-1-0716-1433-4_8
Methods Mol Biol. 2021 ;2275 217-225

Sequence-Specific Control of Mitochondrial Gene Transcription Using Programmable Synthetic Gene Switches Called MITO-PIPs.

Takuya Hidaka, Hiroshi Sugiyama, Ganesh N Pandian.

  Mitochondria possess multiple copies of mitochondrial DNA (mtDNA) that encode 37 genes and their transcription and replication get controlled by unique molecular codes different from that in the nuclear DNA. The mtDNA has been gaining increased attention as one of the critical therapeutic targets as mutations in them impair the function of mitochondria and cause mitochondrial diseases like MELAS. In this chapter, we describe artificial control of mitochondrial transcription based on mtDNA sequence information with a new type of compounds termed MITO-PIPs, which encompasses two domains: pyrrole-imidazole polyamide as DNA recognition domain and mitochondrial penetrating peptide as the mitochondria-targeting domain. Because MITO-PIPs are amenable to tunability, they can be expanded as a synthetic strategy to modulate mitochondrial gene(s) on demand.

Keywords:  DNA binding ligand; Fmoc solid-phase synthesis; MITO-PIP; Mitochondrial DNA; Pyrrole–imidazole polyamide; Transcription

DOI:  https://doi.org/10.1007/978-1-0716-1262-0_13
Mol Biol. 2021 May 30. 1-31

mRNA Targeting, Transport and Local Translation in Eukaryotic Cells: From the Classical View to a Diversity of New Concepts.

Kseniya A Lashkevich, Sergey E Dmitriev.

  Spatial organization of protein biosynthesis in the eukaryotic cell has been studied for more than fifty years, thus many facts have already been included in textbooks. According to the classical view, mRNA transcripts encoding secreted and transmembrane proteins are translated by ribosomes associated with endoplasmic reticulum membranes, while soluble cytoplasmic proteins are synthesized on free polysomes. However, in the last few years, new data has emerged, revealing selective translation of mRNA on mitochondria and plastids, in proximity to peroxisomes and endosomes, in various granules and at the cytoskeleton (actin network, vimentin intermediate filaments, microtubules and centrosomes). There are also long-standing debates about the possibility of protein synthesis in the nucleus. Localized translation can be determined by targeting signals in the synthesized protein, nucleotide sequences in the mRNA itself, or both. With RNA-binding proteins, many transcripts can be assembled into specific RNA condensates and form RNP particles, which may be transported by molecular motors to the sites of active translation, form granules and provoke liquid-liquid phase separation in the cytoplasm, both under normal conditions and during cell stress. The translation of some mRNAs occurs in specialized "translation factories," assemblysomes, transperons and other structures necessary for the correct folding of proteins, interaction with functional partners and formation of oligomeric complexes. Intracellular localization of mRNA has a significant impact on the efficiency of its translation and presumably determines its response to cellular stress. Compartmentalization of mRNAs and the translation machinery also plays an important role in viral infections. Many viruses provoke the formation of specific intracellular structures, virus factories, for the production of their proteins. Here we review the current concepts of the molecular mechanisms of transport, selective localization and local translation of cellular and viral mRNAs, their effects on protein targeting and topogenesis, and on the regulation of protein biosynthesis in different compartments of the eukaryotic cell. Special attention is paid to new systems biology approaches, providing new cues to the study of localized translation.

Keywords:  SARS-CoV-2 induced COVID-19; assemblysomes; endoplasmic reticulum; localized translation; mRNA transport; mitochondria; nuclear translation; stress granules; translation factories; viral factories

DOI:  https://doi.org/10.1134/S0026893321030080
Methods Mol Biol. 2021 ;2275 247-263

mTRIP, an Imaging Tool to Investigate Mitochondrial DNA Dynamics in Physiology and Disease at the Single-Cell Resolution.

Laurent Chatre, Miria Ricchetti.

  Mitochondrial physiology and metabolism are closely linked to replication and transcription of mitochondrial DNA (mtDNA). However, the characterization of mtDNA processing is poorly defined at the single-cell level. We developed mTRIP (mitochondrial Transcription and Replication Imaging Protocol), an imaging approach based on modified fluorescence in situ hybridization (FISH), which simultaneously reveals mitochondrial structures committed to mtDNA initiation of replication as well as the mitochondrial RNA (mtRNA) content at the single-cell level in human cells. Also specific RNA regions, rather than global RNA, can be tracked with mTRIP. In addition, mTRIP can be coupled to immunofluorescence for in situ protein tracking, or to MitoTracker, thereby allowing for simultaneous labeling of mtDNA, mtRNA, and proteins or mitochondria, respectively. Altogether, qualitative and quantitative alterations of the dynamics of mtDNA processing are detected by mTRIP in human cells undergoing physiological changes, as well as stress and dysfunction. mTRIP helped elucidating mtDNA processing alterations in cancer cells, and has a potential for diagnostic of mitochondrial diseases.

Keywords:  DNA replication; FISH; Imaging; Mitochondrial DNA; Mitochondrial disease; Single-cell; Transcription; mTRIP

DOI:  https://doi.org/10.1007/978-1-0716-1262-0_15
Front Mol Biosci. 2021 ;8 689755

Mechanisms of Cotranslational Protein Maturation in Bacteria.

Jiří Koubek, Jaro Schmitt, Carla Veronica Galmozzi, Günter Kramer.

  Growing cells invest a significant part of their biosynthetic capacity into the production of proteins. To become functional, newly-synthesized proteins must be N-terminally processed, folded and often translocated to other cellular compartments. A general strategy is to integrate these protein maturation processes with translation, by cotranslationally engaging processing enzymes, chaperones and targeting factors with the nascent polypeptide. Precise coordination of all factors involved is critical for the efficiency and accuracy of protein synthesis and cellular homeostasis. This review provides an overview of the current knowledge on cotranslational protein maturation, with a focus on the production of cytosolic proteins in bacteria. We describe the role of the ribosome and the chaperone network in protein folding and how the dynamic interplay of all cotranslationally acting factors guides the sequence of cotranslational events. Finally, we discuss recent data demonstrating the coupling of protein synthesis with the assembly of protein complexes and end with a brief discussion of outstanding questions and emerging concepts in the field of cotranslational protein maturation.

Keywords:  DnaK; chaperone recognition; cotranslational assembly; nascent chain processing; protein folding; ribosomal exit tunnel; trigger factor

DOI:  https://doi.org/10.3389/fmolb.2021.689755
Cell Rep. 2021 Jun 08. pii: S2211-1247(21)00568-4. [Epub ahead of print]35(10): 109217

A role for the ribosome-associated complex in activation of the IRE1 branch of UPR.

I-Hui Wu, Jae Seok Yoon, Qian Yang, Yi Liu, William Skach, Philip Thomas.

  The ubiquitous ribosome-associated complex (RAC) is a chaperone that spans ribosomes, making contacts near both the polypeptide exit tunnel and the decoding center, a position prime for sensing and coordinating translation and folding. Loss of RAC is known to result in growth defects and sensitization to translational and osmotic stresses. However, the physiological substrates of RAC and the mechanism(s) by which RAC is involved in responding to specific stresses in higher eukaryotes remain obscure. The data presented here uncover an essential function of mammalian RAC in the unfolded protein response (UPR). Knockdown of RAC sensitizes mammalian cells to endoplasmic reticulum (ER) stress and selectively interferes with IRE1 branch activation. Higher-order oligomerization of the inositol-requiring enzyme 1α (IRE1α) kinase/endoribonuclease depends upon RAC. These results reveal a surveillance function for RAC in the UPR, as follows: modulating IRE1α clustering as required for endonuclease activation and splicing of the substrate Xbp1 mRNA.

Keywords:  IRE1 foci; UPR; Xbp1 mRNA; chaperone; ribosome stalling; ribosome-associated complex; translation

DOI:  https://doi.org/10.1016/j.celrep.2021.109217
FEBS Lett. 2021 Jun 10.

Ribosome-associated quality control mediates degradation of the premature translation termination product Orf1p of ODC antizyme mRNA.

Ashis Kumar Pradhan, Ganapathi Kandasamy, Upasana Chatterjee, Anushree Bharadwaj, Sam J Mathew, R Jürgen Dohmen, R Palanimurugan.

  Decoding of ornithine decarboxylase (ODC) antizyme 1 (OAZ1) mRNA, which harbours two open reading frames (ORF1 and ORF2) interrupted by a naturally occurring Premature Termination Codon (PTC), produces an 8 kDa truncated polypeptide termed Orf1p, unless the PTC is bypassed by +1 ribosomal frameshifting. In this study, we identified Orf1p as an endogenous ubiquitin-dependent substrate of the 26S proteasome both in yeast and mammalian cells. Surprisingly, we found that the ribosome-associated quality control factor Rqc1 and the ubiquitin ligase Ltn1 are critical for Orf1p degradation. In addition, the cytosolic protein quality control chaperone system Hsp70/Hsp90 and their corresponding co-chaperones Sse1, Fes1, Sti1, and Cpr7 are also required for Orf1p proteolysis. Our study finds that Orf1p, which is naturally synthesized as a result of a premature translation termination event, requires the coordinated role of both ribosome-associated and cytosolic protein quality control factors for its degradation.

Keywords:  Antizyme; Ubiquitin/Proteasome System (UPS); protein degradation; ribosomal frameshifting; ribosome-associated protein quality control (RQC)

DOI:  https://doi.org/10.1002/1873-3468.14147
Nat Commun. 2021 06 07. 12(1): 3379

GATA3 induces mitochondrial biogenesis in primary human CD4+ T cells during DNA damage.

Lauren A Callender, Johannes Schroth, Elizabeth C Carroll, Conor Garrod-Ketchley, Lisa E L Romano, Eleanor Hendy, Audrey Kelly, Paul Lavender, Arne N Akbar, J Paul Chapple, Sian M Henson.

GATA3 is as a lineage-specific transcription factor that drives the differentiation of CD4+ T helper 2 (Th2) cells, but is also involved in a variety of processes such as immune regulation, proliferation and maintenance in other T cell and non-T cell lineages. Here we show a mechanism utilised by CD4+ T cells to increase mitochondrial mass in response to DNA damage through the actions of GATA3 and AMPK. Activated AMPK increases expression of PPARG coactivator 1 alpha (PPARGC1A or PGC1α protein) at the level of transcription and GATA3 at the level of translation, while DNA damage enhances expression of nuclear factor erythroid 2-related factor 2 (NFE2L2 or NRF2). PGC1α, GATA3 and NRF2 complex together with the ATR to promote mitochondrial biogenesis. These findings extend the pleotropic interactions of GATA3 and highlight the potential for GATA3-targeted cell manipulation for intervention in CD4+ T cell viability and function after DNA damage.

DOI: https://doi.org/10.1038/s41467-021-23715-7
Mol Cell. 2021 Jun 02. pii: S1097-2765(21)00400-7. [Epub ahead of print]

Bacterial RF3 senses chaperone function in co-translational folding.

Liang Zhao, Marie-Pierre Castanié-Cornet, Sneha Kumar, Pierre Genevaux, Manajit Hayer-Hartl, F Ulrich Hartl.

  Molecular chaperones assist with protein folding by interacting with nascent polypeptide chains (NCs) during translation. Whether the ribosome can sense chaperone defects and, in response, abort translation of misfolding NCs has not yet been explored. Here we used quantitative proteomics to investigate the ribosome-associated chaperone network in E. coli and the consequences of its dysfunction. Trigger factor and the DnaK (Hsp70) system are the major NC-binding chaperones. HtpG (Hsp90), GroEL, and ClpB contribute increasingly when DnaK is deficient. Surprisingly, misfolding because of defects in co-translational chaperone function or amino acid analog incorporation results in recruitment of the non-canonical release factor RF3. RF3 recognizes aberrant NCs and then moves to the peptidyltransferase site to cooperate with RF2 in mediating chain termination, facilitating clearance by degradation. This function of RF3 reduces the accumulation of misfolded proteins and is critical for proteostasis maintenance and cell survival under conditions of limited chaperone availability.

Keywords:  ClpB; DnaJ; DnaK; GroEL; GrpE; Hsp70; Hsp90; HtpG; PrfC (RF3); co-translational protein folding; molecular chaperones; proteomics; translation termination; trigger factor

DOI:  https://doi.org/10.1016/j.molcel.2021.05.016
RNA. 2021 Jun 11. pii: rna.078758.121. [Epub ahead of print]

Perturbation of ribosomal subunits dynamics by inhibitors of tRNA translocation.

Riccardo Belardinelli, Heena Sharma, Frank Peske, Marina V Rodnina.

  Many antibiotics that bind to the ribosome inhibit translation by blocking the movement of tRNAs and mRNA or interfering with ribosome dynamics, which impairs the formation of essential translocation intermediates. Here we show how translocation inhibitors viomycin (Vio), neomycin (Neo), paromomycin (Par), kanamycin (Kan), spectinomycin (Spc), hygromycin B (HygB), and streptomycin (Str, an antibiotic that does not inhibit tRNA movement), affect principal motions of the small ribosomal subunits (SSU) during EF-G-promoted translocation. Using ensemble kinetics, we studied the SSU body domain rotation and SSU head domain swiveling in real time. We show that although antibiotics binding to the ribosome can favor a particular ribosome conformation in the absence of EF-G, their kinetic effect on the EF-G-induced transition to the rotated/swiveled state of the SSU is moderate. The antibiotics mostly inhibit backward movements of the SSU body and/or the head domains. Vio, Spc and high concentrations of Neo completely inhibit the backward movements of the SSU body and head domain. Kan, Par, HygB and low concentrations of Neo slow down both movements, but their sequence and coordination are retained. Finally, Str has very little effect on the backward rotation of the SSU body domain, but retards the SSU head movement. The data underscore the importance of ribosome dynamics for tRNA-mRNA translocation and provide new insights into the mechanism of antibiotic action.

Keywords:  EF-G; rapid kinetics,; ribosome head domain swiveling; ribosome subunit rotation,; translation elongation;

DOI:  https://doi.org/10.1261/rna.078758.121
Nat Commun. 2021 06 09. 12(1): 3492

Translation and codon usage regulate Argonaute slicer activity to trigger small RNA biogenesis.

Meetali Singh, Eric Cornes, Blaise Li, Piergiuseppe Quarato, Loan Bourdon, Florent Dingli, Damarys Loew, Simone Proccacia, Germano Cecere.

In the Caenorhabditis elegans germline, thousands of mRNAs are concomitantly expressed with antisense 22G-RNAs, which are loaded into the Argonaute CSR-1. Despite their essential functions for animal fertility and embryonic development, how CSR-1 22G-RNAs are produced remains unknown. Here, we show that CSR-1 slicer activity is primarily involved in triggering the synthesis of small RNAs on the coding sequences of germline mRNAs and post-transcriptionally regulates a fraction of targets. CSR-1-cleaved mRNAs prime the RNA-dependent RNA polymerase, EGO-1, to synthesize 22G-RNAs in phase with translating ribosomes, in contrast to other 22G-RNAs mostly synthesized in germ granules. Moreover, codon optimality and efficient translation antagonize CSR-1 slicing and 22G-RNAs biogenesis. We propose that codon usage differences encoded into mRNA sequences might be a conserved strategy in eukaryotes to regulate small RNA biogenesis and Argonaute targeting.

DOI: https://doi.org/10.1038/s41467-021-23615-w