bims-mitran 2021-07-18 papers

bims-mitran

Biomed News

on Mitochondrial translation

Issue of 2021–07–18
twelve papers selected by
Andreas Kohler, Stockholm University

Preferential import of queuosine-modified tRNAs into Trypanosoma brucei mitochondrion is critical for organellar protein synthesis.
Tissue-specific expression atlas of murine mitochondrial tRNAs.
ALKBH7-mediated demethylation regulates mitochondrial polycistronic RNA processing.
Three human RNA polymerases interact with TFIIH via a common RPB6 subunit.
Quantitative Modeling of Protein Synthesis Using Ribosome Profiling Data.
A Complementary Mechanism of Bacterial mRNA Translation Inhibition by Tetracyclines.
Hibernation-Promoting Factor Sequesters Staphylococcus aureus Ribosomes to Antagonize RNase R-Mediated Nucleolytic Degradation.
Translational autoregulation of RF2 protein in E. coli through programmed frameshifting.
Reducing embryonic mtDNA copy number alters epigenetic profile of key hepatic lipolytic genes and causes abnormal lipid accumulation in adult mice.
Mistranslation reduces mutation load in evolving proteins through negative epistasis with DNA mutations.
capCLIP: a new tool to probe translational control in human cells through capture and identification of the eIF4E-mRNA interactome.
Allosteric transcription stimulation by RNA polymerase II super elongation complex.

Nucleic Acids Res. 2021 Jul 09. pii: gkab567. [Epub ahead of print]

Preferential import of queuosine-modified tRNAs into Trypanosoma brucei mitochondrion is critical for organellar protein synthesis.

Sneha Kulkarni, Mary Anne T Rubio, Eva Hegedűsová, Robert L Ross, Patrick A Limbach, Juan D Alfonzo, Zdeněk Paris.

Transfer RNAs (tRNAs) are key players in protein synthesis. To be fully active, tRNAs undergo extensive post-transcriptional modifications, including queuosine (Q), a hypermodified 7-deaza-guanosine present in the anticodon of several tRNAs in bacteria and eukarya. Here, molecular and biochemical approaches revealed that in the protozoan parasite Trypanosoma brucei, Q-containing tRNAs have a preference for the U-ending codons for asparagine, aspartate, tyrosine and histidine, analogous to what has been described in other systems. However, since a lack of tRNA genes in T. brucei mitochondria makes it essential to import a complete set from the cytoplasm, we surprisingly found that Q-modified tRNAs are preferentially imported over their unmodified counterparts. In turn, their absence from mitochondria has a pronounced effect on organellar translation and affects function. Although Q modification in T. brucei is globally important for codon selection, it is more so for mitochondrial protein synthesis. These results provide a unique example of the combined regulatory effect of codon usage and wobble modifications on protein synthesis; all driven by tRNA intracellular transport dynamics.

DOI: https://doi.org/10.1093/nar/gkab567
J Biol Chem. 2021 Jul 12. pii: S0021-9258(21)00760-2. [Epub ahead of print] 100960

Tissue-specific expression atlas of murine mitochondrial tRNAs.

Qiufen He, Xiao He, Yun Xiao, Qiong Zhao, Zhenzhen Ye, Limei Cui, Ye Chen, Min-Xin Guan.

  Mammalian mitochondrial tRNA (mt-tRNA) plays a central role in the synthesis of the 13 subunits of the oxidative phosphorylation complex system (OXPHOS). However, many aspects of the context-dependent expression of mt-tRNAs in mammals remains unknown. To investigate the tissue-specific effects of mt-tRNAs, we performed a comprehensive analysis of mitochondrial tRNA expression across 5 mice tissues (brain, heart, liver, skeletal muscle, and kidney) using Northern blot analysis. Striking differences in the tissue-specific expression of 22 mt-tRNAs were observed, in some cases differing by as much as ten-fold from lowest to highest expression levels among these 5 tissues. Overall, the heart exhibited the highest levels of mt-tRNAs, while the liver displayed markedly lower levels. Variations in the levels of mt-tRNAs showed significant correlations with total mitochondrial DNA (mtDNA) contents in these tissues. However, there were no significant differences observed in the 2-thiouridylation levels of tRNALys, tRNAGlu, and tRNAGln among these tissues. A wide range of aminoacylation levels for 15 mt-tRNAs occurred among these five tissues, with skeletal muscle and kidneys most notably displaying the highest and lowest tRNA aminoacylation levels, respectively. Among these tissues, there was a negative correlation between variations in mt-tRNA aminoacylation levels and corresponding variations in mitochondrial tRNA synthetases (mt-aaRS) expression levels. Furthermore, the variable levels of OXPHOS subunits, as encoded by mtDNA or nuclear genes may reflect differences in relative functional emphasis for mitochondria in each tissue. Our findings provide new insight into the mechanism of mt-tRNA tissue-specific effects on oxidative phosphorylation.

Keywords:  Mitochondrial tRNA; murine; oxidative phosphorylation; tissue specific expression; translation

DOI:  https://doi.org/10.1016/j.jbc.2021.100960
Nat Cell Biol. 2021 Jul;23(7): 684-691

ALKBH7-mediated demethylation regulates mitochondrial polycistronic RNA processing.

Li-Sheng Zhang, Qing-Ping Xiong, Sonia Peña Perez, Chang Liu, Jiangbo Wei, Cassy Le, Linda Zhang, Bryan T Harada, Qing Dai, Xinran Feng, Ziyang Hao, Yuru Wang, Xueyang Dong, Lulu Hu, En-Duo Wang, Tao Pan, Arne Klungland, Ru-Juan Liu, Chuan He.

Members of the mammalian AlkB family are known to mediate nucleic acid demethylation1,2. ALKBH7, a mammalian AlkB homologue, localizes in mitochondria and affects metabolism3, but its function and mechanism of action are unknown. Here we report an approach to site-specifically detect N1-methyladenosine (m1A), N3-methylcytidine (m3C), N1-methylguanosine (m1G) and N2,N2-dimethylguanosine (m22G) modifications simultaneously within all cellular RNAs, and discovered that human ALKBH7 demethylates m22G and m1A within mitochondrial Ile and Leu1 pre-tRNA regions, respectively, in nascent polycistronic mitochondrial RNA4-6. We further show that ALKBH7 regulates the processing and structural dynamics of polycistronic mitochondrial RNAs. Depletion of ALKBH7 leads to increased polycistronic mitochondrial RNA processing, reduced steady-state mitochondria-encoded tRNA levels and protein translation, and notably decreased mitochondrial activity. Thus, we identify ALKBH7 as an RNA demethylase that controls nascent mitochondrial RNA processing and mitochondrial activity.

DOI: https://doi.org/10.1038/s41556-021-00709-7
Nucleic Acids Res. 2021 Jul 16. pii: gkab612. [Epub ahead of print]

Three human RNA polymerases interact with TFIIH via a common RPB6 subunit.

Masahiko Okuda, Tetsufumi Suwa, Hidefumi Suzuki, Yuki Yamaguchi, Yoshifumi Nishimura.

In eukaryotes, three RNA polymerases (RNAPs) play essential roles in the synthesis of various types of RNA: namely, RNAPI for rRNA; RNAPII for mRNA and most snRNAs; and RNAPIII for tRNA and other small RNAs. All three RNAPs possess a short flexible tail derived from their common subunit RPB6. However, the function of this shared N-terminal tail (NTT) is not clear. Here we show that NTT interacts with the PH domain (PH-D) of the p62 subunit of the general transcription/repair factor TFIIH, and present the structures of RPB6 unbound and bound to PH-D by nuclear magnetic resonance (NMR). Using available cryo-EM structures, we modelled the activated elongation complex of RNAPII bound to TFIIH. We also provide evidence that the recruitment of TFIIH to transcription sites through the p62-RPB6 interaction is a common mechanism for transcription-coupled nucleotide excision repair (TC-NER) of RNAPI- and RNAPII-transcribed genes. Moreover, point mutations in the RPB6 NTT cause a significant reduction in transcription of RNAPI-, RNAPII- and RNAPIII-transcribed genes. These and other results show that the p62-RPB6 interaction plays multiple roles in transcription, TC-NER, and cell proliferation, suggesting that TFIIH is engaged in all RNAP systems.

DOI: https://doi.org/10.1093/nar/gkab612
Front Mol Biosci. 2021 ;8 688700

Quantitative Modeling of Protein Synthesis Using Ribosome Profiling Data.

Vandana Yadav, Inayat Ullah Irshad, Hemant Kumar, Ajeet K Sharma.

  Quantitative prediction on protein synthesis requires accurate translation initiation and codon translation rates. Ribosome profiling data, which provide steady-state distribution of relative ribosome occupancies along a transcript, can be used to extract these rate parameters. Various methods have been developed in the past few years to measure translation-initiation and codon translation rates from ribosome profiling data. In the review, we provide a detailed analysis of the key methods employed to extract the translation rate parameters from ribosome profiling data. We further discuss how these approaches were used to decipher the role of various structural and sequence-based features of mRNA molecules in the regulation of gene expression. The utilization of these accurate rate parameters in computational modeling of protein synthesis may provide new insights into the kinetic control of the process of gene expression.

Keywords:  codon translation rate; codon usage bias; quantitative modeling of protein synthesis; ribo-seq; ribosome profiling; translation-initiation rate

DOI:  https://doi.org/10.3389/fmolb.2021.688700
Front Microbiol. 2021 ;12 682682

A Complementary Mechanism of Bacterial mRNA Translation Inhibition by Tetracyclines.

Victor Barrenechea, Maryhory Vargas-Reyes, Miguel Quiliano, Pohl Milón.

  Tetracycline has positively impacted human health as well as the farming and animal industries. Its extensive usage and versatility led to the spread of resistance mechanisms followed by the development of new variants of the antibiotic. Tetracyclines inhibit bacterial growth by impeding the binding of elongator tRNAs to the ribosome. However, a small number of reports indicated that Tetracyclines could also inhibit translation initiation, yet the molecular mechanism remained unknown. Here, we use biochemical and computational methods to study how Oxytetracycline (Otc), Demeclocycline (Dem), and Tigecycline (Tig) affect the translation initiation phase of protein synthesis. Our results show that all three Tetracyclines induce Initiation Factor IF3 to adopt a compact conformation on the 30S ribosomal subunit, similar to that induced by Initiation Factor IF1. This compaction was faster for Tig than Dem or Otc. Furthermore, all three tested tetracyclines affected IF1-bound 30S complexes. The dissociation rate constant of IF1 in early 30S complexes was 14-fold slower for Tig than Dem or Otc. Late 30S initiation complexes (30S pre-IC or IC) exhibited greater IF1 stabilization by Tig than for Dem and Otc. Tig and Otc delayed 50S joining to 30S initiation complexes (30S ICs). Remarkably, the presence of Tig considerably slowed the progression to translation elongation and retained IF1 in the resulting 70S initiation complex (70S IC). Molecular modeling of Tetracyclines bound to the 30S pre-IC and 30S IC indicated that the antibiotics binding site topography fluctuates along the initiation pathway. Mainly, 30S complexes show potential contacts between Dem or Tig with IF1, providing a structural rationale for the enhanced affinity of the antibiotics in the presence of the factor. Altogether, our data indicate that Tetracyclines inhibit translation initiation by allosterically perturbing the IF3 layout on the 30S, retaining IF1 during 70S IC formation, and slowing the transition toward translation elongation. Thus, this study describes a new complementary mechanism by which Tetracyclines may inhibit bacterial protein synthesis.

Keywords:  antibiotic; initiation factor; ribosome; tetracycline; tigecycline; translation initiation

DOI:  https://doi.org/10.3389/fmicb.2021.682682
mBio. 2021 Jul 13. e0033421

Hibernation-Promoting Factor Sequesters Staphylococcus aureus Ribosomes to Antagonize RNase R-Mediated Nucleolytic Degradation.

Anna Lipońska, Mee-Ngan F Yap.

  Bacterial and eukaryotic hibernation factors prevent translation by physically blocking the decoding center of ribosomes, a phenomenon called ribosome hibernation that often occurs in response to nutrient deprivation. The human pathogen Staphylococcus aureus lacking the sole hibernation factor HPF undergoes massive ribosome degradation via an unknown pathway. Using genetic and biochemical approaches, we find that inactivating the 3'-to-5' exonuclease RNase R suppresses ribosome degradation in the Δhpf mutant. In vitro cell-free degradation assays confirm that 30S and 70S ribosomes isolated from the Δhpf mutant are extremely susceptible to RNase R, in stark contrast to nucleolytic resistance of the HPF-bound 70S and 100S complexes isolated from the wild type. In the absence of HPF, specific S. aureus 16S rRNA helices are sensitive to nucleolytic cleavage. These RNase hot spots are distinct from that found in the Escherichia coli ribosomes. S. aureus RNase R is associated with ribosomes, but unlike the E. coli counterpart, it is not regulated by general stressors and acetylation. The results not only highlight key differences between the evolutionarily conserved RNase R homologs but also provide direct evidence that HPF preserves ribosome integrity beyond its role in translational avoidance, thereby poising the hibernating ribosomes for rapid resumption of translation. IMPORTANCE Ribosome hibernation is pivotal for the rapid recovery of translation after quiescence in both bacteria and eukaryotes. Ribosome hibernation factors sterically occlude the entry of mRNA and tRNA and are thought to primarily maintain ribosomes in a translation-repressive state, thereby providing a pool of readily recyclable 70S or 80S complexes upon dissociation of the hibernation factors. Ribosomes in Staphylococcus aureus cells lacking the sole hibernation factor HPF are extremely unstable. Here, we show that HPF binding inhibits ribosome degradation by the evolutionarily conserved exoribonuclease RNase R. The data not only uncover a direct protective role of HPF in ribosome stability but also reinforce the versatility of RNase R in RNA processing, decay, and ribosome quality control.

Keywords:  RNase; Staphylococcus aureus; hibernation; ribosome; stress response

DOI:  https://doi.org/10.1128/mBio.00334-21
Phys Rev E. 2021 Jun;103(6-1): 062412

Translational autoregulation of RF2 protein in E. coli through programmed frameshifting.

Ajeet K Sharma.

Various feedback mechanisms regulate the expression of different genes to ensure the required protein levels inside a cell. In this paper, we develop a kinetic model for one such mechanism that autoregulates RF2 protein synthesis in E. coli through programmed frameshifting. The model finds that the programmed frameshifting autoregulates RF2 protein synthesis by two independent mechanisms. First, it increases the rate of RF2 synthesis from each mRNA transcript at low RF2 concentration. Second, programmed frameshifting can dramatically increase the lifetime of RF2 transcripts when RF2 protein levels are lower than a threshold. This sharp increase in mRNA lifetime is caused by a first-order phase transition from a low to a high ribosome density on an RF2 transcript. The high ribosome density prevents the transcript's degradation by shielding it from nucleases, which increases its average lifetime and hence RF2 protein levels. Our study identifies this quality control mechanism that regulates the cellular protein levels by breaking the hierarchy of processes involved in gene expression.

DOI: https://doi.org/10.1103/PhysRevE.103.062412
FEBS J. 2021 Jul 14.

Reducing embryonic mtDNA copy number alters epigenetic profile of key hepatic lipolytic genes and causes abnormal lipid accumulation in adult mice.

Yakun Wang, Xuan Wang, Qiaoming Long, Yuanwu Liu, Tao Yin, Inna Sirota, Fazheng Ren, Zhenglong Gu, Junjie Luo.

  Adverse fetal environment, in particular a shortage or excess of nutrients, is associated with increased risks of metabolic diseases later in life. However, the molecular mechanisms underlying this developmental origin of adult diseases remain unclear. Here, we directly tested the role of mitochondrial stress in mediating fetal programming in mice by enzymatically depleting mitochondrial DNA (mtDNA) in zygotes. mtDNA-targeted plasmid microinjection is used to reduce embryonic mtDNA copy number directly, followed by embryo transfer. Mice with reduced zygote mtDNA copy number were born morphologically normal and showed no accelerated body weight gain. However, at five-month of age these mice showed markedly increased hepatic lipidosis and became glucose intolerant. Hepatic mRNA and protein expression of peroxisome proliferator-activated receptor α (Pparα), a key transcriptional regulator of lipid metabolism, were significantly decreased as a result of increased DNA methylation in its proximal regulatory region. These results indicate that perturbation of mitochondrial function around the periconceptional period causes hypermethylation and thus suppressed expression of PPARα in fetal liver, leading to impaired hepatic lipid metabolism. Our findings provide the first direct evidence that mitochondrial stress mediates epigenetic changes associated with fetal programming of adult diseases in a mammalian system.

Keywords:  DNA methylation; Lipid metabolism; PPARα signaling; Preimplantation embryo; mtDNA copy number

DOI:  https://doi.org/10.1111/febs.16121
Mol Biol Evol. 2021 Jul 13. pii: msab206. [Epub ahead of print]

Mistranslation reduces mutation load in evolving proteins through negative epistasis with DNA mutations.

Jia Zheng, Ning Guo, Andreas Wagner.

  Translational errors during protein synthesis cause phenotypic mutations that are several orders of magnitude more frequent than DNA mutations. Such phenotypic mutations may affect adaptive evolution through their interactions with DNA mutations. To study how mistranslation may affect the adaptive evolution of evolving proteins, we evolved populations of green fluorescent protein (GFP) in either high-mistranslation or low-mistranslation E.coli hosts. In both hosts, we first evolved GFP under purifying selection for the ancestral phenotype green fluorescence, and then to directional selection towards the new phenotype yellow fluorescence. High-mistranslation populations evolved modestly higher yellow fluorescence during each generation of evolution than low-mistranslation populations. We demonstrate by high-throughput sequencing that elevated mistranslation reduced the accumulation of deleterious DNA mutations under both purifying and directional selection. It did so by amplifying the fitness effects of deleterious DNA mutations through negative epistasis with phenotypic mutations. In contrast, mistranslation did not affect the incidence of beneficial mutations. Our findings show that phenotypic mutations interact epistatically with DNA mutations. By reducing a population's mutation load, mistranslation can affect an important determinant of evolvability.

Keywords:  Molecular evolution; mistranslation; mutation load; negative epistasis; phenotypic mutations

DOI:  https://doi.org/10.1093/molbev/msab206
Nucleic Acids Res. 2021 Jul 13. pii: gkab604. [Epub ahead of print]

capCLIP: a new tool to probe translational control in human cells through capture and identification of the eIF4E-mRNA interactome.

Kirk B Jensen, B Kate Dredge, John Toubia, Xin Jin, Valentina Iadevaia, Gregory J Goodall, Christopher G Proud.

Translation of eukaryotic mRNAs begins with binding of their m7G cap to eIF4E, followed by recruitment of other translation initiation factor proteins. We describe capCLIP, a novel method to comprehensively capture and quantify the eIF4E (eukaryotic initiation factor 4E) 'cap-ome' and apply it to examine the biological consequences of eIF4E-cap binding in distinct cellular contexts. First, we use capCLIP to identify the eIF4E cap-omes in human cells with/without the mTORC1 (mechanistic target of rapamycin, complex 1) inhibitor rapamycin, there being an emerging consensus that rapamycin inhibits translation of TOP (terminal oligopyrimidine) mRNAs by displacing eIF4E from their caps. capCLIP reveals that the representation of TOP mRNAs in the cap-ome is indeed systematically reduced by rapamycin, thus validating our new methodology. capCLIP also refines the requirements for a functional TOP sequence. Second, we apply capCLIP to probe the consequences of phosphorylation of eIF4E. We show eIF4E phosphorylation reduces overall eIF4E-mRNA association and, strikingly, causes preferential dissociation of mRNAs with short 5'-UTRs. capCLIP is a valuable new tool to probe the function of eIF4E and of other cap-binding proteins such as eIF4E2/eIF4E3.

DOI: https://doi.org/10.1093/nar/gkab604
Mol Cell. 2021 Jul 12. pii: S1097-2765(21)00499-8. [Epub ahead of print]

Allosteric transcription stimulation by RNA polymerase II super elongation complex.

Ying Chen, Seychelle M Vos, Christian Dienemann, Momchil Ninov, Henning Urlaub, Patrick Cramer.

  The super elongation complex (SEC) contains the positive transcription elongation factor b (P-TEFb) and the subcomplex ELL2-EAF1, which stimulates RNA polymerase II (RNA Pol II) elongation. Here, we report the cryoelectron microscopy (cryo-EM) structure of ELL2-EAF1 bound to a RNA Pol II elongation complex at 2.8 Å resolution. The ELL2-EAF1 dimerization module directly binds the RNA Pol II lobe domain, explaining how SEC delivers P-TEFb to RNA Pol II. The same site on the lobe also binds the initiation factor TFIIF, consistent with SEC binding only after the transition from transcription initiation to elongation. Structure-guided functional analysis shows that the stimulation of RNA elongation requires the dimerization module and the ELL2 linker that tethers the module to the RNA Pol II protrusion. Our results show that SEC stimulates elongation allosterically and indicate that this stimulation involves stabilization of a closed conformation of the RNA Pol II active center cleft.

Keywords:  EAF1; ELL2; P-TEFb; RNA Pol II lobe and protrusion; RNA polymerase II; TFIIF; stimulation of transcription elongation; super elongation complex; transcription

DOI:  https://doi.org/10.1016/j.molcel.2021.06.019