Elongation factors EF-G from E. coli and mammalian mitochondria are not functionally interchangeable

Structural insights into mammalian mitochondrial translation elongation catalyzed by mtEFG1

Mitochondria are eukaryotic organelles of bacterial origin where respiration takes place to produce cellular chemical energy. These reactions are catalyzed by the respiratory chain complexes located in the inner mitochondrial membrane. Notably, key components of the respiratory chain complexes are encoded on the mitochondrial chromosome and their expression relies on a dedicated mitochondrial translation machinery. Defects in the mitochondrial gene expression machinery lead to a variety of diseases in humans mostly affecting tissues with high energy demand such as the nervous system, the heart, or the muscles. The mitochondrial translation system has substantially diverged from its bacterial ancestor, including alterations in the mitoribosomal architecture, multiple changes to the set of translation factors and striking reductions in otherwise conserved tRNA elements. Although a number of structures of mitochondrial ribosomes from different species have been determined, our mechanistic understanding of the mitochondrial translation cycle remains largely unexplored. Here, we present two cryo-EM reconstructions of human mitochondrial elongation factor G1 bound to the mammalian mitochondrial ribosome at two different steps of the tRNA translocation reaction during translation elongation. Our structures explain the mechanism of tRNA and mRNA translocation on the mitoribosome, the regulation of mtEFG1 activity by the ribosomal GTPase-associated center, and the basis of decreased susceptibility of mtEFG1 to the commonly used antibiotic fusidic acid.

Unique features of animal mitochondrial translation systems. The non-universal genetic code, unusual features of the translational apparatus and their relevance to human mitochondrial diseases

In animal mitochondria, several codons are non-universal and their meanings differ depending on the species. In addition, the tRNA structures that decipher codons are sometimes unusually truncated. These features seem to be related to the shortening of mitochondrial (mt) genomes, which occurred during the evolution of mitochondria. These organelles probably originated from the endosymbiosis of an aerobic eubacterium into an ancestral eukaryote. It is plausible that these events brought about the various characteristic features of animal mt translation systems, such as genetic code variations, unusually truncated tRNA and rRNA structures, unilateral tRNA recognition mechanisms by aminoacyl-tRNA synthetases, elongation factors and ribosomes, and compensation for RNA deficits by enlarged proteins. In this article, we discuss molecular mechanisms for these phenomena. Finally, we describe human mt diseases that are caused by modification defects in mt tRNAs.

Functional compatibility of elongation factors between mammalian mitochondrial and bacterial ribosomes: characterization of GTPase activity and translation elongation by hybrid ribosomes bearing heterologous L7/12 proteins

The mammalian mitochondrial (mt) ribosome (mitoribosome) is a bacterial-type ribosome but has a highly protein-rich composition. Almost half of the rRNA contained in the bacterial ribosome is replaced with proteins in the mitoribosome. Escherichia coli elongation factor G (EF-G Ec) has no translocase activity on the mitoribosome but EF-G mt is functional on the E.coli ribosome. To investigate the functional equivalency of the mt and E.coli ribosomes, we prepared hybrid mt and E.coli ribosomes. The hybrid mitoribosome containing E.coli L7/12 (L7/12 Ec) instead of L7/12 mt clearly activated the GTPase of EF-G Ec and efficiently promoted its translocase activity in an in vitro translation system. Thus, the mitoribosome is functionally equivalent to the E.coli ribosome despite their distinct compositions. The mt EF-Tu-dependent translation activity of the E.coli ribosome was also clearly enhanced by replacing the C-terminal domain (CTD) of L7/12 Ec with the mt counterpart (the hybrid E.coli ribosome). This strongly indicates that the CTD of L7/12 is responsible for EF-Tu function. These results demonstrate that functional compatibility between elongation factors and the L7/12 protein in the ribosome governs its translational specificity.

Altered hepatic mitochondrial ribosome structure following chronic ethanol consumption

Chronic ethanol consumption decreases the synthesis of all 13 polypeptides encoded by the hepatic mitochondrial genome. This alteration in mitochondrial protein synthesis is due to modifications in mitochondrial ribosomes. In the current study, the nature of these alterations was investigated by determining some of the hydrodynamic properties, namely sedimentation coefficient, shape, and mass of mitochondrial ribosomes. The effect of ethanol consumption on the capacity for mitochondrial ribosomes to translate proteins was also determined using an in vitro Poly (U) assay system. Rats were fed the Lieber-DeCarli diet for 31 days with ethanol as 36% of total calories. The sedimentation coefficient, measured by sedimentation velocity analyses, was slightly, but significantly lower in ethanol mitochondrial ribosomes (53.2 +/- 0.5S) when compared with pair-fed controls (54.1 +/- 0.5S) (P = 0.04). Mitochondrial ribosomes from ethanol-fed animals also had a greater tendency to dissociate into subunits. The diffusion coefficient, determined by dynamic light scattering, was lower in mitochondrial ribosomes from ethanol-fed rats than pair-fed controls and this indicated a significantly greater diameter for ethanol ribosomes (42.1 +/- 0.2 nm) than for preparations from pair-fed controls (39.1 +/- 0.5 nm; P = 0.008). These alterations to ethanol mitochondrial ribosomes occurred despite no change in molecular mass, which suggested a significant ethanol-related shape change in the ribosomes. The translation capacity of mitochondrial ribosome preparations from ethanol-fed animals was markedly reduced due to dissociation of the monosome into light and heavy subunits. In summary, these observations demonstrate that chronic ethanol consumption causes significant structural and functional alterations to mitochondrial ribosomes. The loss in ribosome function leads to impaired mitochondrial polypeptide synthesis and is an example of a pathology giving rise to an alteration in the mitochondrial ribosome structure.

Bovine mitochondrial initiation and elongation factors

The procedures summarized above provide nearly homogeneous preparations of IF-2mt, EF-Tu. Tsmt, and EF-Gmt. The scheme developed for IF-2mr leads to a 24,000-fold purification of this factor with a 26% recovery of activity. Analysis by SDS-polyacrylamide gel electrophoresis and gel filtration chromatography indicates that this factor functions as a monomer with a molecular weight of about 85,000. The scheme developed EF-Tu.Tsmt provides a 10,000-fold purification with an overall yield of about 10%. The EF-Tumt component in this complex has a molecular weight of about 46,000, whereas EF-Tsmt has a molecular weight of about 32,000 on SDS-polyacrylamide gel electrophoresis. The EF-Tu. Tsmt complex is tightly associated and appears to have a native molecular weight of about 70,000. The five-step purification procedure outlined above for EF-Gmt results in a 14,000-fold purification of EF-Gmt with a 2-5% recovery of activity. Analysis by SDS-polyacrylamide gel electrophoresis and gel filtration chromatography indicates that EF-Gmt functions as a monomeric protein with an apparent molecular weight of about 80,000.

Effect of chronic ethanol consumption on hepatic mitochondrial transcription and translation

Liver mitochondria from ethanol-fed rats display an impaired ability for protein synthesis in vitro. Studies were conducted to explore the possible mechanisms which might account for this impaired capacity of ethanol mitochondria for protein synthesis. The present studies did not demonstrate any significant ethanol-induced lesion in mitochondrial nucleic acid metabolism in organelles isolated from ethanol-fed rats for any of the parameters investigated (mtDNA content, steady-state mtRNA concentration, mtRNA polymerase activity, concentration of specific mRNAs and rRNAs, mtRNA processing). An investigation of ribosome function in isolated mitochondria demonstrated significant decreases in the number of active ribosomes (55% fewer) in mitochondria from ethanol-fed rats. Initiation of protein synthesis was also significantly depressed (46%) in ethanol mitochondria. In addition, the yield of ribosomal particles from ethanol mitochondria was decreased 32% as compared to the yield of ribosomal particles from control mitochondria. However, isolated ribosomes from ethanol mitochondria were determined to be fully functional in a poly(U)-directed phenylalanine polymerization system. Soluble translation factors from ethanol mitochondria were also found to support full activity of control ribosomes in a poly(U)-directed phenylalanine polymerization system. These results suggest strongly that the ethanol-induced depression of mitochondrial protein synthesis is due to a decrease in the number of competent ribosomes in hepatic mitochondria from chronically ethanol-fed rats.

The translation system of mammalian mitochondria

Oligoribonucleotides and mRNA were used to define properties of the bovine mitoribosomal mRNA binding site. The RNA binding domain on the 28 S subunit spans approx. 80 nucleotides of the template, based on ribosome protection experiments, but the major interaction with the ribosome occurs over a 30 nucleotide stretch. The binding site for E. coli IF3 is conserved in bovine mitoribosomes, but mitochondrial factors appear essential for proper interaction of mRNA with mitoribosomes. The small subunit of bovine mitoribosomes contains a high-affinity binding site for guanyl nucleotides, further indication of specialized mechanisms for initiation complex formation and function of mammalian mitochondrial ribosomes.

Interaction of bovine mitochondrial ribosomes with Escherichia coli initiation factor 3 (IF3)

Mammalian mitochondrial ribosomes are distinguished from their bacterial and eukaryotic-cytoplasmic counterparts, as well as from mitochondrial ribosomes of lower eukaryotes, by their physical and chemical properties and their high protein content. However, they do share more functional homologies with bacterial ribosomes than with cytoplasmic ribosomes. To search for possible homologies between mammalian mitochondrial ribosomes and bacterial ribosomes at the level of initiation factor binding sites, we studied the interaction of Escherichia coli initiation factor 3 (IF3) with bovine mitochondrial ribosomes. Bacterial IF3 was found to bind to the small subunit of bovine mitochondrial ribosomes with an affinity of the same order of magnitude as that for bacterial ribosomes, suggesting that most of the functional groups contributing to the IF3 binding site in bacterial ribosomes are conserved in mitochondrial ribosomes. Increasing ionic strength affects binding to both ribosomes similarly and suggests a large electrostatic contribution to the reaction. Furthermore, bacterial IF3 inhibits the Mg2+-dependent association of mitochondrial ribosomal subunits, suggesting that the bacterial IF3 binds to mitochondrial small subunits in a functional way.

RNA binding proteins of the large subunit of bovine mitochondrial ribosomes

RNA binding properties of proteins from the large subunit of bovine mitochondrial ribosomes were studied using four different approaches: binding of radiolabeled RNA to western blotted proteins; disassembly of the intact 39 S ribosomal subunits with urea; binding of ribosomal proteins to RNA in the presence of urea; and binding of proteins extracted with lithium chloride to RNA. Results from these four approaches allowed us to identify a set of six proteins (L7, L13, L14, L21, L26, and L44) which appear to be strong RNA binding proteins. Seven additional proteins (L8, L11, L28, L35, L40, L49, and L50) were identified as secondary RNA binding proteins. RNA binding properties of the proteins in both of these sets were compared with the topographic disposition and susceptibility towards lithium chloride extraction of the individual proteins. Proteins from the first set are good candidates for early assembly proteins since they have a high affinity for RNA, are generally found in 4M lithium chloride core particles, and are among the most buried proteins in the 39 S subunit.

Ribosome specificity of archaebacterial elongation factor 2. Studies with hybrid polyphenylalanine synthesis systems

Polyphenylalanine synthesis with ribosomes and two separated, partially purified elongation factors (EF) was measured in cell-free systems from the archaebacteria Thermoplasma acidophilum and Methanococcus vannielii, in an eukaryotic system from rat liver and an eubacterial one with Escherichia coli ribosomes and factors from Thermus thermophilus. By substitution of heterologous EF-2 or EF-G, respectively, for the homologous factors, ribosome specificity was shown to be restricted to factors from the same kingdom. In contrast, EF-1 from T. thermophilus significantly cooperated with ribosomes from T. acidophilum.

Inhibition of mitochondrial protein synthesis and energy coupling by fragment A of diphtheria toxin

The effect of intact diphtheria toxin and its fragment A on energy-dependent functions in mouse liver mitochondria/mitoplasts has been studied. Fragment A was found to inhibit protein synthesis in mitoplasts to the same extent (approximately 80%) as the uncoupler carbonylcyanide p-trifluoromethoxyphenylhydrazone, but had no similar effect in lysed mitoplasts. Intact diphtheria toxin had no effect in either case. Fragment A was found to function as a potent uncoupler in isolated mitochondria and mitoplasts, inhibiting oxidative phosphorylation by approximately 80% at a concentration (2 micrograms fragment A/mg of protein) that did not inhibit protein synthesis. In contrast, intact toxin slightly increased the tightness of energy coupling in isolated mitoplasts. 125I-labelled intact diphtheria toxin was bound to mitoplasts to about the same extent as labelled fragment A. At concentrations which efficiently inhibited mitochondrial protein synthesis, fragment A had no effect on the intramitochondrial concentration of nicotinamide adenine dinucleotides, nor was it capable of ADP-ribosylating mitochondrial proteins, indicating that the well known enzymatic activity of fragment A is not involved in the observed effect in mitochondria. The results indicate that fragment A of diphtheria toxin inhibits protein synthesis in mitochondria and mitoplasts by inhibiting mitochondrial energy transduction. The detailed mechanism of the uncoupling effect and its possible significance in intact cells remain to be elucidated.