bims-mitran 2021-06-06 papers

bims-mitran

Biomed News

on Mitochondrial Translation

Issue of 2021‒06‒06
thirteen papers selected by
Andreas Kohler

Mitochondrial DNA: cellular genotoxic stress sentinel.
Deep conservation of ribosome stall sites across RNA processing genes.
PINK1 and parkin shape the organism-wide distribution of a deleterious mitochondrial genome.
The Isolation and Deep Sequencing of Mitochondrial DNA.
Ribosome Biogenesis and Cancer: Overview on Ribosomal Proteins.
Identification of a Novel Variant in MT-CO3 Causing MELAS.
Expression and analysis of the SAM-dependent RNA methyltransferase Rsm22 from Saccharomyces cerevisiae.
Mitochondrial D-Loop Region Methylation and Copy Number in Peripheral Blood DNA of Parkinson's Disease Patients.
Reevaluating the role of human mitochondrial uL18m in the cytosolic stress response.
Allotopic Expression of ATP6 in Mouse as a Transgenic Model of Mitochondrial Disease.
Molecular engineering of a near-infrared fluorescent ligand for tracking mitochondrial DNA G-quadruplexes.
Pan-Mitogenomics Approach Discovers Diversity and Dynamism in the Prominent Brown Rot Fungal Pathogens.
Mitogenome Analysis of Four Lamiinae Species (Coleoptera: Cerambycidae) and Gene Expression Responses by Monochamus alternatus When Infected with the Parasitic Nematode, Bursaphelenchus mucronatus.

Trends Biochem Sci. 2021 Jun 01. pii: S0968-0004(21)00106-7. [Epub ahead of print]

Mitochondrial DNA: cellular genotoxic stress sentinel.

Zheng Wu, Alva G Sainz, Gerald S Shadel.

  High copy number, damage prone, and lean on repair mechanisms are unique features of mitochondrial DNA (mtDNA) that are hard to reconcile with its essentiality for oxidative phosphorylation, the primary function ascribed to this maternally inherited component of our genome. We propose that mtDNA is also a genotoxic stress sentinel, as well as a direct second messenger of this type of cellular stress. Here, we discuss existing evidence for this sentinel/effector role through the ability of mtDNA to escape the confines of the mitochondrial matrix and activate nuclear DNA damage/repair responses via interferon-stimulated gene products and other downstream effectors. However, this arrangement may come at a cost, leading to cancer chemoresistance and contributing to inflammation, disease pathology, and aging.

Keywords:  DNA repair; cGAS-STING; chemoresistance; interferon-stimulated gene (ISG); mtDNA; retrograde signaling

DOI:  https://doi.org/10.1016/j.tibs.2021.05.004
NAR Genom Bioinform. 2021 Jun;3(2): lqab038

Deep conservation of ribosome stall sites across RNA processing genes.

Katarzyna Chyżyńska, Kornel Labun, Carl Jones, Sushma N Grellscheid, Eivind Valen.

The rate of translation can vary depending on the mRNA template. During the elongation phase the ribosome can transiently pause or permanently stall. A pause can provide the nascent protein with the time to fold or be transported, while stalling can serve as quality control and trigger degradation of aberrant mRNA and peptide. Ribosome profiling has allowed for the genome-wide detection of such pauses and stalls, but due to library-specific biases, these predictions are often unreliable. Here, we take advantage of the deep conservation of protein synthesis machinery, hypothesizing that similar conservation could exist for functionally important locations of ribosome slowdown, here collectively called stall sites. We analyze multiple ribosome profiling datasets from phylogenetically diverse eukaryotes: yeast, fruit fly, zebrafish, mouse and human to identify conserved stall sites. We find thousands of stall sites across multiple species, with the enrichment of proline, glycine and negatively charged amino acids around conserved stalling. Many of the sites are found in RNA processing genes, suggesting that stalling might have a conserved role in RNA metabolism. In summary, our results provide a rich resource for the study of conserved stalling and indicate possible roles of stalling in gene regulation.

DOI: https://doi.org/10.1093/nargab/lqab038
Cell Rep. 2021 Jun 01. pii: S2211-1247(21)00552-0. [Epub ahead of print]35(9): 109203

PINK1 and parkin shape the organism-wide distribution of a deleterious mitochondrial genome.

Arnaud Ahier, Chuan-Yang Dai, Ina Kirmes, Nadia Cummins, Grace Ching Ching Hung, Jürgen Götz, Steven Zuryn.

  In multiple species, certain tissue types are prone to acquiring greater loads of mitochondrial genome (mtDNA) mutations relative to others, but the mechanisms that drive these heteroplasmy differences are unknown. We find that the conserved PTEN-induced putative kinase (PINK1/PINK-1) and the E3 ubiquitin-protein ligase parkin (PDR-1), which are required for mitochondrial autophagy (mitophagy), underlie stereotyped differences in heteroplasmy of a deleterious mitochondrial genome mutation (ΔmtDNA) between major somatic tissues types in Caenorhabditis elegans. We demonstrate that tissues prone to accumulating ΔmtDNA have lower mitophagy responses than those with low mutation levels. Moreover, we show that ΔmtDNA heteroplasmy increases when proteotoxic species that are associated with neurodegenerative disease and mitophagy inhibition are overexpressed in the nervous system. These results suggest that PINK1 and parkin drive organism-wide patterns of heteroplasmy and provide evidence of a causal link between proteotoxicity, mitophagy, and mtDNA mutation levels in neurons.

Keywords:  Alzheimer's disease; PINK1; heteroplasmy; mitochondria; mitophagy; mtDNA; parkin; polyglutamate; proteotoxicity; tau

DOI:  https://doi.org/10.1016/j.celrep.2021.109203
Methods Mol Biol. 2021 ;2277 433-447

The Isolation and Deep Sequencing of Mitochondrial DNA.

Alexander G Bury, Fiona M Robertson, Angela Pyle, Brendan A I Payne, Gavin Hudson.

  In recent years, next-generation sequencing (NGS) has become a powerful tool for studying both inherited and somatic heteroplasmic mitochondrial DNA (mtDNA) variation. NGS has proved particularly powerful when combined with single-cell isolation techniques, allowing the investigation of low-level heteroplasmic variants both between cells and within tissues. Nevertheless, there remain significant challenges, especially around the selective enrichment of mtDNA from total cellular DNA and the avoidance of nuclear pseudogenes. This chapter summarizes the techniques needed to enrich, amplify, sequence, and analyse mtDNA using NGS .

Keywords:  Massively parallel sequencing; Mitochondrial DNA; Mitochondrial isolation deep sequencing

DOI:  https://doi.org/10.1007/978-1-0716-1270-5_27
Int J Mol Sci. 2021 May 23. pii: 5496. [Epub ahead of print]22(11):

Ribosome Biogenesis and Cancer: Overview on Ribosomal Proteins.

Annalisa Pecoraro, Martina Pagano, Giulia Russo, Annapina Russo.

  Cytosolic ribosomes (cytoribosomes) are macromolecular ribonucleoprotein complexes that are assembled from ribosomal RNA and ribosomal proteins, which are essential for protein biosynthesis. Mitochondrial ribosomes (mitoribosomes) perform translation of the proteins essential for the oxidative phosphorylation system. The biogenesis of cytoribosomes and mitoribosomes includes ribosomal RNA processing, modification and binding to ribosomal proteins and is assisted by numerous biogenesis factors. This is a major energy-consuming process in the cell and, therefore, is highly coordinated and sensitive to several cellular stressors. In mitochondria, the regulation of mitoribosome biogenesis is essential for cellular respiration, a process linked to cell growth and proliferation. This review briefly overviews the key stages of cytosolic and mitochondrial ribosome biogenesis; summarizes the main steps of ribosome biogenesis alterations occurring during tumorigenesis, highlighting the changes in the expression level of cytosolic ribosomal proteins (CRPs) and mitochondrial ribosomal proteins (MRPs) in different types of tumors; focuses on the currently available information regarding the extra-ribosomal functions of CRPs and MRPs correlated to cancer; and discusses the role of CRPs and MRPs as biomarkers and/or molecular targets in cancer treatment.

Keywords:  cancer; cancer treatment; mitochondrial ribosomal proteins; mitoribosome biogenesis; ribosomal proteins; ribosome biogenesis

DOI:  https://doi.org/10.3390/ijms22115496
Front Genet. 2021 ;12 638749

Identification of a Novel Variant in MT-CO3 Causing MELAS.

Manting Xu, Robert Kopajtich, Matthias Elstner, Zhaoxia Wang, Zhimei Liu, Junling Wang, Holger Prokisch, Fang Fang.

  Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) is a maternally inherited mitochondrial disease. Most cases of MELAS are caused by the m.3243A > G variant in the MT-TL1 gene encoding tRNALeu(UUR). However, the genetic cause in 10% of patients with MELAS is unknown. We investigated the pathogenicity of the novel mtDNA variant m.9396G > A/MT-CO3 (p.E64K), which affects an extremely conserved amino acid in the CO3 subunit of mitochondrial respiratory chain (MRC) complex IV (CIV) in a patient with MELAS. Biochemical assays of a muscle biopsy confirmed remarkable CIV deficiency, and pathological examination showed ragged red fibers and generalized COX non-reactive muscle fibers. Transfer of the mutant mtDNA into cybrids impaired CIV assembly, followed by remarkable mitochondrial dysfunction and ROS production. Our findings highlight the pathogenicity of a novel m.9396G > A variant and extend the spectrum of pathogenic mtDNA variants.

Keywords:  MELAS; MT-CO3 gene; complex IV of respiratory chain; mitochondrial diseases; novel mitochondrial DNA variant

DOI:  https://doi.org/10.3389/fgene.2021.638749
Acta Crystallogr D Struct Biol. 2021 Jun 01. 77(Pt 6): 840-853

Expression and analysis of the SAM-dependent RNA methyltransferase Rsm22 from Saccharomyces cerevisiae.

Jahangir Alam, Farah Tazkera Rahman, Shiv K Sah-Teli, Rajaram Venkatesan, M Kristian Koski, Kaija J Autio, J Kalervo Hiltunen, Alexander J Kastaniotis.

  The Saccharomyces cerevisiae Rsm22 protein (Sc-Rsm22), encoded by the nuclear RSM22 (systematic name YKL155c) gene, is a distant homologue of Rsm22 from Trypanosoma brucei (Tb-Rsm22) and METTL17 from mouse (Mm-METTL17). All three proteins have been shown to be associated with mitochondrial gene expression, and Sc-Rsm22 has been documented to be essential for mitochondrial respiration. The Sc-Rsm22 protein comprises a polypeptide of molecular weight 72.2 kDa that is predicted to harbor an N-terminal mitochondrial targeting sequence. The precise physiological function of Rsm22-family proteins is unknown, and no structural information has been available for Sc-Rsm22 to date. In this study, Sc-Rsm22 was expressed and purified in monomeric and dimeric forms, their folding was confirmed by circular-dichroism analyses and their low-resolution structures were determined using a small-angle X-ray scattering (SAXS) approach. The solution structure of the monomeric form of Sc-Rsm22 revealed an elongated three-domain arrangement, which differs from the shape of Tb-Rsm22 in its complex with the mitochondrial small ribosomal subunit in T. brucei (PDB entry 6sg9). A bioinformatic analysis revealed that the core domain in the middle (Leu117-Asp462 in Sc-Rsm22) resembles the corresponding region in Tb-Rsm22, including a Rossmann-like methyltransferase fold followed by a zinc-finger-like structure. The latter structure is not present in this position in other methyltransferases and is therefore a unique structural motif for this family. The first half of the C-terminal domain is likely to form an OB-fold, which is typically found in RNA-binding proteins and is also seen in the Tb-Rsm22 structure. In contrast, the N-terminal domain of Sc-Rsm22 is predicted to be fully α-helical and shares no sequence similarity with other family members. Functional studies demonstrated that the monomeric variant of Sc-Rsm22 methylates mitochondrial tRNAs in vitro. These data suggest that Sc-Rsm22 is a new and unique member of the RNA methyltransferases that is important for mitochondrial protein synthesis.

Keywords:  Rsm22; SAXS structure; crystallization; methyltransferases; mitochondrial ribosomes

DOI:  https://doi.org/10.1107/S2059798321004149
Genes (Basel). 2021 May 12. pii: 720. [Epub ahead of print]12(5):

Mitochondrial D-Loop Region Methylation and Copy Number in Peripheral Blood DNA of Parkinson's Disease Patients.

Andrea Stoccoro, Adam R Smith, Filippo Baldacci, Claudia Del Gamba, Annalisa Lo Gerfo, Roberto Ceravolo, Katie Lunnon, Lucia Migliore, Fabio Coppedè.

  Altered mitochondrial DNA (mtDNA) methylation has been detected in several human pathologies, although little attention has been given to neurodegenerative diseases. Recently, altered methylation levels of the mitochondrial displacement loop (D-loop) region, which regulates mtDNA replication, were observed in peripheral blood cells of Alzheimer's disease and amyotrophic lateral sclerosis patients. However, nothing is yet known about D-loop region methylation levels in peripheral blood of Parkinson's disease (PD) patients. In the current study, we investigated D-loop methylation levels and mtDNA copy number in peripheral blood of 30 PD patients and 30 age- and sex-matched control subjects. DNA methylation analyses have been performed by means of methylation-sensitive high-resolution melting (MS-HRM) and pyrosequencing techniques, while mtDNA copy number was analyzed by quantitative PCR. MS-HRM and pyrosequencing analyses provided very similar D-loop methylation levels in PD patients and control subjects, and no differences between the two groups have been observed. Treatment with L-dopa and duration of the disease had no effect on D-loop methylation levels in PD patients. Additionally, mtDNA copy number did not differ between PD patients and control subjects. Current results suggest that D-loop methylation levels are not altered in peripheral blood of PD patients nor influenced by dopaminergic treatment.

Keywords:  D-loop region; DNA methylation; Mitoepigenetics; Parkinson’s disease

DOI:  https://doi.org/10.3390/genes12050720
Nat Struct Mol Biol. 2021 May 31.

Reevaluating the role of human mitochondrial uL18m in the cytosolic stress response.

Austin Choi, Antoni Barrientos.

DOI: https://doi.org/10.1038/s41594-021-00599-1
Methods Mol Biol. 2021 ;2277 1-13

Allotopic Expression of ATP6 in Mouse as a Transgenic Model of Mitochondrial Disease.

David A Dunn, Carl A Pinkert.

  Progress in animal modeling of polymorphisms and mutations in mitochondrial DNA (mtDNA) is not as developed as nuclear transgenesis due to a host of cellular and physiological distinctions. mtDNA mutation modeling is of critical importance as mutations in the mitochondrial genome give rise to a variety of pathological conditions and play a contributing role in many others. Nuclear localization and transcription of mtDNA genes followed by cytoplasmic translation and transport into mitochondria (allotopic expression, AE) provide an opportunity to create in vivo modeling of a targeted mutation in mitochondrial genes. Accordingly, such technology has been suggested as a strategy for gene replacement therapy in patients harboring mitochondrial DNA mutations. Here, we use our AE approach to transgenic mouse modeling of the pathogenic human T8993G mutation in mtATP6 as a case study for designing AE animal models.

Keywords:  ATP6; Allotopic expression; Animal modeling; Mitochondrial disease; Transgenic mouse; mtDNA

DOI:  https://doi.org/10.1007/978-1-0716-1270-5_1
Anal Chim Acta. 2021 Jul 18. pii: S0003-2670(21)00426-8. [Epub ahead of print]1169 338600

Molecular engineering of a near-infrared fluorescent ligand for tracking mitochondrial DNA G-quadruplexes.

Ming-Hao Hu.

  G-quadruplexes are supposed to exist in mitochondrial DNA, which may participate in the regulation of mitochondrial metabolism. However, their formation dynamics and cellular roles are still unknown, calling for the development of promising small-molecule fluorescent probes for detecting mitochondrial DNA (mtDNA) G4s in live cells. In this study, we engineered a NIR fluorescent probe termed IZIN-1 by conjugating a typical G4 ligand and a mitochondrion-targeting AIE luminogen, which was then found to be able to emit NIR fluorescence by binding to mtDNA G4s via a distinctive mode. Cell-based experiments demonstrated that IZIN-1 may track mtDNA G4 formation in live cells. Collectively, this work provides a promising example about how to design a fluorescent probe targeting mtDNA G4s, and also offers a feasible chemical tool for investigating mtDNA G4s in live cells.

Keywords:  Engineering; Fluorescent; G-quadruplex; Mitochondria; Near-infrared

DOI:  https://doi.org/10.1016/j.aca.2021.338600
Front Microbiol. 2021 ;12 647989

Pan-Mitogenomics Approach Discovers Diversity and Dynamism in the Prominent Brown Rot Fungal Pathogens.

Gozde Yildiz, Hilal Ozkilinc.

  Monilinia fructicola and Monilinia laxa species are the most destructive and economically devastating fungal plant pathogens causing brown rot disease on stone and pome fruits worldwide. Mitochondrial genomes (mitogenomes) play critical roles influencing the mechanisms and directions of the evolution of fungal pathogens. The pan-mitogenomics approach predicts core and accessory regions of the mitochondrial genomes and explains the gain or loss of variation within and between species. The present study is a fungal pan-mitogenome of M. fructicola (N = 8) and M. laxa (N = 8) species. The completely sequenced and annotated mitogenomes showed high variability in size within and between the species. The mitogenomes of M. laxa were larger, ranging from 178,351 to 179,780bp, than the mitogenomes of M. fructicola, ranging from 158,607 to 167,838bp. However, size variation within the species showed that M. fructicola isolates were more variable in the size range than M. laxa isolates. All the mitogenomes included conserved mitochondrial genes, as well as variable regions including different mobile introns encoding homing endonucleases or maturase, non-coding introns, and repetitive elements. The linear model analysis supported the hypothesis that the mitogenome size expansion is due to presence of variable (accessory) regions. Gene synteny was mostly conserved among all samples, with the exception for order of the rps3 in the mitogenome of one isolate. The mitogenomes presented AT richness; however, A/T and G/C skew varied among the mitochondrial genes. The purifying selection was detected in almost all the protein-coding genes (PCGs) between the species. However, cytochrome b was the only gene showing a positive selection signal among the total samples. Combined datasets of amino acid sequences of 14 core mitochondrial PCGs and rps3 obtained from this study together with published mitochondrial genome sequences from some other species from Heliotales were used to infer a maximum likelihood (ML) phylogenetic tree. ML tree indicated that both Monilinia species highly diverged from each other as well as some other fungal species from the same order. Mitogenomes harbor much information about the evolution of fungal plant pathogens, which could be useful to predict pathogenic life strategies.

Keywords:  Monilinia species; brown rot; evolution; mitogenome; pan-mitogenomics

DOI:  https://doi.org/10.3389/fmicb.2021.647989
Insects. 2021 May 14. pii: 453. [Epub ahead of print]12(5):

Mitogenome Analysis of Four Lamiinae Species (Coleoptera: Cerambycidae) and Gene Expression Responses by Monochamus alternatus When Infected with the Parasitic Nematode, Bursaphelenchus mucronatus.

Zi-Yi Zhang, Jia-Yin Guan, Yu-Rou Cao, Xin-Yi Dai, Kenneth B Storey, Dan-Na Yu, Jia-Yong Zhang.

  We determined the mitochondrial gene sequence of Monochamus alternatus and three other mitogenomes of Lamiinae (Insect: Coleoptera: Cerambycidae) belonging to three genera (Aulaconotus, Apriona and Paraglenea) to enrich the mitochondrial genome database of Lamiinae and further explore the phylogenetic relationships within the subfamily. Phylogenetic trees of the Lamiinae were built using the Bayesian inference (BI) and maximum likelihood (ML) methods and the monophyly of Monochamus, Anoplophora, and Batocera genera was supported. Anoplophora chinensis, An. glabripennis and Aristobia reticulator were closely related, suggesting they may also be potential vectors for the transmission of the pine wood pathogenic nematode (Bursaphelenchus xylophilus) in addition to M. alternatus, a well-known vector of pine wilt disease. There is a special symbiotic relationship between M. alternatus and Bursaphelenchus xylophilus. As the native sympatric sibling species of B. xylophilus, B. mucronatus also has a specific relationship that is often overlooked. The analysis of mitochondrial gene expression aimed to explore the effect of B. mucronatus on the energy metabolism of the respiratory chain of M. alternatus adults. Using RT-qPCR, we determined and analyzed the expression of eight mitochondrial protein-coding genes (COI, COII, COIII, ND1, ND4, ND5, ATP6, and Cty b) between M. alternatus infected by B. mucronatus and M. alternatus without the nematode. Expression of all the eight mitochondrial genes were up-regulated, particularly the ND4 and ND5 gene, which were up-regulated by 4-5-fold (p < 0.01). Since longicorn beetles have immune responses to nematodes, we believe that their relationship should not be viewed as symbiotic, but classed as parasitic.

Keywords:  Bursaphelenchus mucronatus; Lamiinae; Monochamus alternatus; mitochondrial gene expression; mitochondrial genome; phylogeny

DOI:  https://doi.org/10.3390/insects12050453