The mitochondrial genome almost exclusively encodes a handful of transmembrane constituents of the oxidative phosphorylation (OXPHOS) system. Coordinated expression of these genes ensures the correct stoichiometry of the system’s components. Translation initiation in mitochondria is assisted by two general initiation factors mIF2 and mIF3, orthologues of which in bacteria are indispensible for protein synthesis and viability. mIF3 was thought to be absent in Saccharomyces cerevisiae until we recently identified mitochondrial protein Aim23 as the missing orthologue. Here we show that, surprisingly, loss of mIF3/Aim23 in S. cerevisiae does not indiscriminately abrogate mitochondrial translation but rather causes an imbalance in protein production: the rate of synthesis of the Atp9 subunit of F1F0 ATP synthase (complex V) is increased, while expression of Cox1, Cox2 and Cox3 subunits of cytochrome c oxidase (complex IV) is repressed. Our results provide one more example of deviation of mitochondrial translation from its bacterial origins.

Mitochondrial genome has undergone significant reduction in a course of evolution; however, it still contains a set of protein-encoding genes and requires translational machinery for their expression. Mitochondrial translation is of the prokaryotic type with several remarkable differences. This review is dedicated to one of the most puzzling features of mitochondrial protein synthesis, namely, the system of translational activators, i.e., proteins that specifically regulate translation of individual mitochondrial mRNAs and couple protein biosynthesis with the assembly of mitochondrial respiratory chain complexes. The review does not claim to be a comprehensive analysis of all published data; it is rather focused on the idea of the "core component" of the translational activator system.

A strain of a hyperthermophilic filamentous archaeon was isolated from a sample of Kamchatka hot spring sediment. Isolate 1807-2 grew optimally at 85 °C, pH 6.0-6.5, the parameters being close to those at the sampling site. 16S rRNA gene sequence analysis placed the novel isolate in the crenarchaeal genus Thermofilum; Thermofilum pendens was its closest valid relative (95.7 % of sequence identity). Strain 1807-2 grew organothrophically using polysaccharides (starch and glucomannan), yeast extract or peptone as substrates. The addition of other crenarchaea culture broth filtrates was obligatory required for growth and could not be replaced by the addition of these organisms’ cell wall fractions, as it was described for T. pendens. The genome of strain 1807-2 was sequenced using Illumina and PGM technologies. The average nucleotide identities between genome of strain 1807-2 and T. pendens strain HRK 5T and “T. adornatus” strain 1910b were 85 and 82 %, respectively. On the basis of 16S rRNA gene sequence phylogeny, ANI calculations and phenotypic differences we propose a novel species Thermofilum uzonense with the type strain 1807-2T (= DSM 28062T = JCM 19810T). Project information and genome sequence was deposited in Genbank under IDs PRJNA262459 and CP009961, respectively.Electronic supplementary materialThe online version of this article (doi:10.1186/s40793-015-0105-y) contains supplementary material, which is available to authorized users.

Protein biosynthesis in mitochondria is organized in a bacterial manner. However, during evolution, mitochondrial translation mechanisms underwent many organelle-specific changes. In particular, almost all mitochondrial translation factors, being orthologous to bacterial proteins, are characterized by some unique elements of primary or secondary structure. In the case of the organellar initiation factor 3 (IF3), these elements are several dozen amino acids long N- and C-terminal extensions. This study focused on the terminal extensions of baker’s yeast mitochondrial IF3, Aim23p. By in vivo deletion and complementation analysis, we show that at least one extension is necessary for Aim23p function. At the same time, human mitochondrial IF3 is fully functional in yeast mitochondria even without both terminal extensions. While Escherichia coli IF3 itself is poorly active in yeast mitochondria, adding Aim23p terminal extensions makes the resulting chimeric protein as functional as the cognate factor. Our results show that the terminal extensions of IF3 have evolved as the “adaptors” that accommodate the translation factor of bacterial origin to the evolutionary changed protein biosynthesis system in mitochondria.

The complete genomic sequence of a novel hyperthermophilic crenarchaeon, strain 1910bT, was determined. The genome comprises a 1,750,259-bp circular chromosome containing single copies of 3 rRNA genes, 43 tRNA genes, and 1,896 protein-coding sequences. In silico genome-genome hybridization suggests the proposal of a novel species, “Thermofilum adornatus” strain 1910bT.

The processes of association and dissociation of ribosomal subunits are of great importance for the protein biosynthesis. The mechanistic details of these processes, however, are not well known. In bacteria, upon translation termination, the ribosome dissociates into subunits which is necessary for its further involvement into new initiation step. The dissociated state of the ribosome is maintained by initiation factor 3 (IF3) which binds to free small subunits and prevents their premature association with large subunits. In this work, we have exchanged IF3 in Escherichia coli cells by its ortholog from Saccharomyces cerevisiae mitochondria (Aim23p) and showed that yeast protein cannot functionally substitute the bacterial one and is even slightly toxic for bacterial cells. Our in vitro experiments have demonstrated that Aim23p does not split E. coli ribosomes into subunits. Instead, it fixes a state of ribosomes characterized by sedimentation coefficient about 60S which is not a stable structure but rather reflects a shift of dynamic equilibrium between associated and dissociated states of the ribosome. Mitochondria-specific terminal extensions of Aim23p are necessary for “60S state” formation, and molecular modeling results point out that these extensions might stabilize the position of the protein on the bacterial ribosome.

No abstract

The processes of association and dissociation of ribosomal subunits are of great importance for the protein biosynthesis. The mechanistic details of these processes, however, are not well known. In bacteria, upon translation termination, ribosome dissociates into subunits which is necessary for its further involvement into new initiation step. The dissociated state of ribosome is maintained by initiation factor 3 (IF3) which binds to free small subunits and prevents their premature association with the large subunits. In this work, we have exchanged IF3 in E.coli cells by its ortholog from Saccharomyces cerevisiae mitochondria (Aim23p) and showed that yeast protein cannot functionally substitute the bacterial one and is even slightly toxic for bacterial cells. 49 binds to the small subunit in order to keep it apart from the large one . This 50 stage is, in fact, the very first stage of the translation initiation process; 30S•IF3 complex 51 becomes the basis for the full-size initiatory complex formation which includes Shine-Dalgarno 52 sequence of mRNA, initiator tRNA, and initiation factors 1 and 2. It is worth mentioning that 53 anti-association activity of IF3 is definitely of passive mode: it does not promote dissociation of 54 the ribosome into subunits but instead binds to free small subunit and prevents its re-association 55 with the large one (Gualerzi et al. 1977) (Gottleib et al. 1975). 56The exact mechanism of ribosome dissociation into subunits remains not clear. This is 57 due to methodological complications of studying this fast and dynamic process. In kinetic study, 58 a model was proposed that assumed the existence of several consecutive conformations of 70S 59 ribosome in course of its dissociation; IF3 was hypothesized to be a potential effector of 60 corresponding conformational changes which could shift the equilibria between different states 61 of dissociating ribosome (Goss et al. 1980). It can be assumed that these conformations might be 62 characterized by different sedimentation coefficients, less than 70S but probably more than 50S.