Handling mammalian mitochondrial tRNAs and aminoacyl-tRNA synthetases for functional and structural characterization

The mammalian mitochondrial (mt) genome codes for only 13 proteins, which are essential components in the process of oxidative phosphorylation of ADP into ATP. Synthesis of these proteins relies on a proper mt translation machinery. While 22 tRNAs and 2 rRNAs are also coded by the mt genome, all other factors including the set of aminoacyl-tRNA synthetases (aaRSs) are encoded in the nucleus and imported. Investigation of mammalian mt aminoacylation systems (and mt translation in general) gains more and more interest not only in regard of evolutionary considerations but also with respect to the growing number of diseases linked to mutations in the genes of either mt-tRNAs, synthetases or other factors. Here we report on methodological approaches for biochemical, functional, and structural characterization of human/mammalian mt-tRNAs and aaRSs. Procedures for preparation of native and in vitro transcribed tRNAs are accompanied by recommendations for specific handling of tRNAs incline to structural instability and chemical fragility. Large-scale preparation of mg amounts of highly soluble recombinant synthetases is a prerequisite for structural investigations that requires particular optimizations. Successful examples leading to crystallization of four mt-aaRSs and high-resolution structures are recalled and limitations discussed. Finally, the need for and the state-of-the-art in setting up an in vitro mt translation system are emphasized. Biochemical characterization of a subset of mammalian aminoacylation systems has already revealed a number of unprecedented peculiarities of interest for the study of evolution and forensic research. Further efforts in this field will certainly be rewarded by many exciting discoveries.     

Dual mode recognition of two isoacceptor tRNAs by mammalian mitochondrial seryl-tRNA synthetase

Animal mitochondrial translation systems contain two serine tRNAs, corresponding to the codons AGY (Y = U and C) and UCN (N = U, C, A, and G), each possessing an unusual secondary structure; tRNA(GCU)(Ser) (for AGY) lacks the entire D arm, whereas tRNA(UGA)(Ser) (for UCN) has an unusual cloverleaf configuration. We previously demonstrated that a single bovine mitochondrial seryl-tRNA synthetase (mt SerRS) recognizes these topologically distinct isoacceptors having no common sequence or structure. Recombinant mt SerRS clearly footprinted at the TPsiC loop of each isoacceptor, and kinetic studies revealed that mt SerRS specifically recognized the TPsiC loop sequence in each isoacceptor. However, in the case of tRNA(UGA)(Ser), TPsiC loop-D loop interaction was further required for recognition, suggesting that mt SerRS recognizes the two substrates by distinct mechanisms. mt SerRS could slightly but significantly misacylate mitochondrial tRNA(Gln), which has the same TPsiC loop sequence as tRNA(UGA)(Ser), implying that the fidelity of mitochondrial translation is maintained by kinetic discrimination of tRNAs in the network of aminoacyl-tRNA synthetases.     

Functional defects of pathogenic human mitochondrial tRNAs related to structural fragility

Aminoacylation of transfer RNAs (tRNAs) is essential for protein synthesis. A growing number of human diseases correlate with point mutations in tRNA genes within the mitochondrial genome. These tRNAs have unique sequences that suggest they have fragile structures. However, the structural significance of pathology-related tRNA mutations and their effects on molecular function have not been explored. Here, opthalmoplegia related mutants of a human mitochondrial tRNA have been investigated. Each mutation replaces either an A-U or G-C pair in the predicted secondary structure with an A-C pair. Aminoacylation of each mutant tRNA was severely attenuated. Moreover, each strongly inhibited aminoacylation of the wild type substrate, suggesting that the effects of these mutations might not be bypassed in the potentially heteroplasmic environment of mitochondria. The function of mutant tRNAs was rescued by single compensatory mutations that restored Watson-Crick base pairing and reintroduced stability into regions of predicted secondary structure, even though the pairs introduced were different from those found in the wild type tRNA. Thus, functional defects caused by a subset of pathogenic mutations may result from the inherent structural fragility of human mitochondrial tRNAs.     

A structural model for the large subunit of the mammalian mitochondrial ribosome

Protein translation is essential for all forms of life and is conducted by a macromolecular complex, the ribosome. Evolutionary changes in protein and RNA sequences can affect the 3D organization of structural features in ribosomes in different species. The most dramatic changes occur in animal mitochondria, whose genomes have been reduced and altered significantly. The RNA component of the mitochondrial ribosome (mitoribosome) is reduced in size, with a compensatory increase in protein content. Until recently, it was unclear how these changes affect the 3D structure of the mitoribosome. Here, we present a structural model of the large subunit of the mammalian mitoribosome developed by combining molecular modeling techniques with cryo-electron microscopic data at 12.1A resolution. The model contains 93% of the mitochondrial rRNA sequence and 16 mitochondrial ribosomal proteins in the large subunit of the mitoribosome. Despite the smaller mitochondrial rRNA, the spatial positions of RNA domains known to be involved directly in protein synthesis are essentially the same as in bacterial and archaeal ribosomes. However, the dramatic reduction in rRNA content necessitates evolution of unique structural features to maintain connectivity between RNA domains. The smaller rRNA sequence also limits the likelihood of tRNA binding at the E-site of the mitoribosome, and correlates with the reduced size of D-loops and T-loops in some animal mitochondrial tRNAs, suggesting co-evolution of mitochondrial rRNA and tRNA structures.     

Complete sequence of bovine mitochondrial DNA conserved features of the mammalian mitochondrial genome

We present here the complete 16,338 nucleotide DNA sequence of the bovine mitochondrial genome. This sequence is homologous to that of the human mitochondrial genome (Anderson et al., 1981) and the genes are organized in virtually identical fashion. The bovine mitochondrial protein genes are 63 to 79% homologous to their human counterparts, and most of the nucleotide differences occur in the third positions of codons. The minimum rate of base substitution that accounts for the nucleotide differences in the codon third positions is very high: at least 6 × 10^?9 changes per position per year. The bovine and human mitochondrial transfer RNA genes exhibit more interspecies variation than do their cytoplasmic counterparts, with the “TΨC” loop being the most variable part of the molecule. The bovine 12 S and 16 S ribosomal RNA genes, when compared with those from human mitochondrial DNA, show conserved features that are consistent with proposed secondary structure models for the ribosomal RNAs. Unlike the pattern of moderate-to-high homology between the bovine and human mitochondrial DNAs found over most of the genome, the DNA sequence in the bovine D-loop region is only slightly homologous to the corresponding region in the human mitochondrial genome. This region is also quite variable in length, and accounts for the bulk of the size difference between the human and bovine mitochondrial DNAs.     

Early structural features in mammalian prion conformation conversion

The conversion to a disease-associated conformer (PrP^Sc) of the cellular prion protein (PrP^C) is the central event in prion diseases. Wild-type PrP^C converts to PrP^Sc in the sporadic forms of the disorders through an unknown mechanism. These forms account for up to 85% of all human (Hu) occurrences; the infectious types contribute for less than 1%, while genetic incidence of the disease is about 15%. Familial Hu prion diseases are associated with about 40 point mutations of the gene coding for the PrP denominated PRNP. Most of the variants associated with these mutations are located in the globular domain of the protein. In a recent work in collaboration with the German Research School for Simulation Science, in Jülich, Germany, we performed molecular dynamics simulations for each of these mutants to investigate their structure in aqueous solution. Structural analysis of the various point mutations present in the globular domain unveiled common folding traits that may allow a better understanding of the early conformational changes leading to the formation of monomeric PrP^Sc. Recent experimental data support these findings, thus opening novel approaches to determine initial structural determinants of prion formation.Key words: prions, prion protein, human, pathogenic mutations, structure, molecular dynamics, nuclear magnetic resonancePrion diseases have attracted much attention from researchers with different scientific backgrounds and coming from various areas of expertise. Many questions still remain unanswered in the study of these rare and yet unique neurodegenerative disorders. Central to understanding the disease is deciphering the nature of the causative agent of these disorders: the prion. In fact, the mechanism by which a prion (PrP^Sc) is formed and the structure of the latter, have posed major challenges to this field. Indeed, prion research has achieved a great deal of detailed information in understanding the pathogenesis of the disease, but until now the early events leading to the conformational change harboring prions have remained elusive.¹ In an attempt to learning how the protein may undergo this conformational rearrangement, my group and the group of Paolo Carloni at the German Research School for Simulation Science, in Jülich, Germany, reasoned that some clues might come from the study of pathogenic mutants in HuPrP. At the time of beginning our work the structures of few mutants were known.² The structure of HuPrP was used as template for our studies.³ We therefore performed molecular dynamics (MD) simulations for each of these mutants to investigate their structure in aqueous solution. In total, almost 2 µs MD data were obtained. The calculations were based on the AMBER(parm99) force field, which has been shown to reproduce very accurately the structural features of the wild-type HuPrP and a few variants for which experimental structural information was available.⁴ All the variants present structural features different from those of wild-type HuPrP and the protective dominant negative polymorphism HuPrP(E219K). These characteristics include loss of salt bridges in the α₂–α₃ regions and the loss of π-stacking interactions in the β₂-α₂ loop. In addition, in the majority of the mutants analyzed, the α₃ helix is more flexible and the residue Tyr169 is more exposed to the aqueous solvent. The biological relevance of these findings is of utmost importance. The presence of similar traits in this large spectrum of mutations hints to a role of these characteristics in their known capabilities to generate disease-causing properties. Overall, we concluded that the regions most affected by disease-linked mutations in terms of structure and/or flexibility might be those involved in the pathogenic conversion of PrP^C to the scrapie form of the protein, and ultimately, in the interaction with cellular partners.Recent reports have indicated that the alteration of PRNP sequence by pathological mutations is sufficient to generate prions in transgenic mice.⁵ Therefore, solution-state NMR studies on PrP mutants may help identifying critical regions in PrP^C structure involved in the conversion. The comparison between the structures of Q212P and V210I mutants with the wild-type HuPrP revealed that, although structures share similar globular architecture, mutations introduce novel local structural differences.⁶ The observed variations are mostly clustered in the β₂-α₂-loop region and in the α₂–α₃ inter-helical interfaces. In contrast to the wild-type protein, where the structures of Q212P and V210I mutants point to the interruption of aromatic and hydrophobic interactions between residues located at the interface of the β₂-α₂ loop and the C-terminal end of α₃ helix. A loss of contacts between the β₂-α₂-loop and the α₃ helix in the mutants results in higher exposure of hydrophobic residues to solvent. Similar findings have also been reported in the NMR structure of the E200K mutant,⁷ X-ray structures of F198S and D178N mutants⁸ and in independent MD studies.^9–11 In addition, in the two mutants here considered side chains of Phe141 and Tyr149 adopt different orientation. Our findings indicate that the structural disorder of the β₂-α₂-loop together with the increased distance between the loop and α₃ helix represent key pathological structural features and may shed light on critical epitopes on the HuPrP structure possibly involved in the conversion to PrP^Sc.Different experimental studies suggested that the conformation of the β₂-α₂-loop plays a role in the prion disease transmission and susceptibility. Several studies have indicated that mammals carrying a flexible β₂-α₂ loop could be easily infected by prions, whereas prions are poorly transmissible to animals carrying a rigid loop.¹² Importantly, horse and rabbit have so far displayed resistance to prion infections and there are no reports of these species developing spontaneous prion diseases. NMR studies showed that their PrP structures are characterized by a rigid β₂-α₂ loop and by closer contacts between the loop and α₃ helix.^13,14 Thus, it seems that prion resistance is enciphered by the amino acidic composition of the β₂-α₂-loop and its long-range interactions with the C-terminal end of the α₃ helix.Interestingly, it has been proposed a role of α₁ helix as a promoter of PrP^C aggregation.¹⁵ In support, Tyr149 in α₁ helix is part of a motif, which may be solvent exposed in PrP^Sc and involved in structural rearrangements during fibril formation.¹⁶ Pronounced stabilization of α₁ helix in the protein may represent another important factor in the prevention of spontaneous PrP^Sc formation.Comparing the structures of the wild-type protein and the mutants enabled us to detect regions on HuPrP structure that may play a key role in the pathogenic conversion. The obtained structural data indicate that the β₂-α₂ loop and, in particular, interactions of this loop with residues in the C-terminal part of α₃ helix determine the extent of exposure of hydrophobic surface to solvent, and thus could influence propensity of PrP^C for intermolecular interactions. Moreover, our results highlight the significance of the α₁ helix and its tertiary contacts in overall stabilization of HuPrP folding.Overall, the many features discussed here involve the most important regions that confer stability to wild-type HuPrP, although the mutations considered are different for position and characteristics. In particular, the β₂-α₂-loop and the α₂–α₃ regions are the most affected in terms of structural organization and flexibility of the molecule. These two subdomains are crucial for the stability of the wild-type HuPrP^C fold¹⁷ and might play a prominent role in the early unfolding events leading to PrP^Sc conversion.     

Pathogenic mutations in antisense mitochondrial tRNAs

Pathogenic mutations in mitochondrial tRNAs are 6.5 times more frequent than in other mitochondrial genes. This suggests that tRNA mutations perturb more than one function. A potential additional tRNA gene function is that of templating for antisense tRNAs. Pathogenic mutations weaken cloverleaf secondary structures of sense tRNAs. Analyses here show similar effects for most antisense tRNAs, especially after adjusting for associations between sense and antisense cloverleaf stabilities. These results imply translational activity by antisense tRNAs. For sense tRNAs Ala and Ser UCN, pathogenicity associates as much with sense as with antisense cloverleaf formation. For tRNA Pro, pathogenicity seems associated only with antisense, not sense tRNA cloverleaf formation. Translational activity by antisense tRNAs is expected for the 11 antisense tRNAs processed by regular sense RNA maturation, those recognized by their cognate amino acid’s tRNA synthetase, and those forming relatively stable cloverleaves as compared to their sense counterpart. Most antisense tRNAs probably function routinely in translation and extend the tRNA pool (extension hypothesis); others do not (avoidance hypothesis). The greater the expected translational activity of an antisense tRNA, the more pathogenic mutations weaken its cloverleaf secondary structure. Some evidence for RNA interference, a more classical role for antisense tRNAs, exists only for tRNA Ser UCN. Mutation pathogenicity probably frequently results from a mixture of effects due to sense and antisense tRNA translational activity for many mitochondrial tRNAs. Genomic studies should routinely explore for translational activity by antisense tRNAs.     

Tissue-specific expression atlas of murine mitochondrial tRNAs

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 remain unknown. To investigate the tissue-specific effects of mt-tRNAs, we performed a comprehensive analysis of mitochondrial tRNA expression across five 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 tenfold from lowest to highest expression levels among these five 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 tRNA^Lys, tRNA^Glu, and tRNA^Gln 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.     

Novel amber suppressor tRNAs of mammalian origin.

Two amber suppressor tRNAs have been isolated from calf liver. They are different from previously identified naturally occurring amber suppressors of eukaryotes in so far as they are neither tRNATyr nor tRNAGln. They are leucine iso-acceptors and their nucleotide sequence indicates that they harbour a CAA and a CAG anticodon respectively. Both species are functional as amber suppressors as demonstrated by readthrough of the amber codon which terminates the 126 kd protein gene of tobacco mosaic virus RNA. The results bring new information in the discussion of codon-anticodon recognition and regulation of termination in eukaryotic protein synthesis.     

Computational exploration of structural hypotheses for an additional sequence in a mammalian mitochondrial protein

Background

Proteins involved in mammalian mitochondrial translation, when compared to analogous bacterial proteins, frequently have additional sequence regions whose structural or functional roles are not always clear. For example, an additional short insert sequence in the bovine mitochondrial initiation factor 2 (IF2_mt) seems sufficient to fulfill the added role of eubacterial initiation factor IF1. Prior to our recent cryo-EM study that showed IF2_mt to structurally occupy both the IF1 and IF2 binding sites, the spatial separation of these sites, and the short length of the insert sequence, posed ambiguity in whether it could perform the role of IF1 through occupation of the IF1 binding site on the ribosome.

Results

The present study probes how well computational structure prediction methods can a priori address hypothesized roles of such additional sequences by creating quasi-atomic models of IF2_mt using bacterial IF2 cryo-EM densities (that lack the insert sequences). How such initial IF2_mt predictions differ from the observed IF2_mt cryo-EM map and how they can be suitably improved using further sequence analysis and flexible fitting are analyzed.

Conclusions

By hypothesizing that the insert sequence occupies the IF1 binding site, continuous IF2_mt models that occupy both the IF2 and IF1 binding sites can be predicted computationally. These models can be improved by flexible fitting into the IF2_mt cryo-EM map to get reasonable quasi-atomic IF2_mt models, but the exact orientation of the insert structure may not be reproduced. Specific eukaryotic insert sequence conservation characteristics can be used to predict alternate IF2_mt models that have minor secondary structure rearrangements but fewer unusually extended linker regions. Computational structure prediction methods can thus be combined with medium-resolution cryo-EM maps to explore structure-function hypotheses for additional sequence regions and to guide further biochemical experiments, especially in mammalian systems where high-resolution structures are difficult to determine.     

The structural features of beef heart mitochondrial creatine kinase.

Two forms of mitochondrial creatine kinase (Mi-CK) having Mr 320 kDa and 240 kDa as determined by gel-filtration on Sephacryl S-300 in 0.1 M Tris-HCl pH 7.4 were investigated. The sedimentation coefficient values for these two forms were found to be identical and equal to 12.3 S. When studied by electron microscopy the main type of images for the 320 kDa and 240 kDa Mi-CK appeared as annular particles, 12-14 nm in diameter, with a well-detected subunit structure and a central hollow, 3-4nm in diameter filled with the dye. The results of the averaging of the main type of individual Mi-CK images and particles of the two-dimensional crystal layer point to the overall geometry of the Mi-CK molecule structure as containing eight subunits arranged by a 4-fold symmetry around the central hollow. It may be that the eight identical subunits of crystalline Mi-CK are arranged with a P422 symmetry. However in both cases the averaged main images do not show a mirror symmetry. The multiplicity of the observed projections close to annular one provides additional evidence in favour of the great lability and structural mobility of the Mi-CK subunits. It allows to assume that two forms (320 kDa and 240 kDa) are not the different oligomers but they are two functionally distinct conformational states of octameric molecule of Mi-CK.     

A comparison of mitochondrial tRNAs in five vertebrates

Sequences of several vertebrate mitochondrial tRNAs were aligned and compared. The comparisons were made in pairs of the tRNAs for an identical amino acid. There are 22 genes for different tRNAs in each vertebrate mitochondrial DNA. The closest similarities were between rat and mouse, the next were between mammals, and the widest difference was between human or rat and Xenopus laevis. However, there were very wide variations between different amino acids in each set of comparisons. The time lapse for each percent of difference greatly increased with evolutionary separation. Most of the nucleotide substitutions appeared to be neutral in character.Based on a presentation made at a workshop- Aminoacyl-tRNA Synthetases and the Evolution of the Genetic Code-held at Berkeley, CA, July 17–20, 1994     

Recognition of tRNAs by Methionyl-tRNA transformylase from mammalian mitochondria

Protein synthesis involves two methionine-isoaccepting tRNAs, an initiator and an elongator. In eubacteria, mitochondria, and chloroplasts, the addition of a formyl group gives its full functional identity to initiator Met-tRNA(Met). In Escherichia coli, it has been shown that the specific action of methionyl-tRNA transformylase on Met-tRNA(f)(Met) mainly involves a set of nucleotides in the acceptor stem, particularly a C(1)A(72) mismatch. In animal mitochondria, only one tRNA(Met) species has yet been described. It is admitted that this species can engage itself either in initiation or elongation of translation, depending on the presence or absence of a formyl group. In the present study, we searched for the identity elements of tRNA(Met) that govern its formylation by bovine mitochondrial transformylase. The main conclusion is that the mitochondrial formylase preferentially recognizes the methionyl moiety of its tRNA substrate. Moreover, the relatively small importance of the tRNA acceptor stem in the recognition process accounts for the protection against formylation of the mitochondrial tRNAs that share with tRNA(Met) an A(1)U(72) motif.     

The mitochondrial tRNAs of Trypanosoma brucei are nuclear encoded

The mitochondrial DNA of Trypanosoma brucei is organized as a catenated network of maxicircles and minicircles. The maxicircles are equivalent to the typical mitochondrial genome except that the genes for the mitochondrial tRNAs have not been identified by sequence analysis of the maxicircle DNA. The apparent absence of tRNA genes in the maxicircle DNA suggests that the mitochondrial tRNAs are encoded by either the minicircle or the nuclear DNA. In order to determine their genomic origin, we isolated and identified the mitochondrial tRNAs of T. brucei. We show that these mitochondrial tRNAs are truly mitochondrially located in vivo and that they are free from detectable contamination by cytosolic RNAs. By hybridization analysis, using mitochondrial tRNAs as the probe, we determined that the mitochondrial tRNAs are encoded by nuclear DNA. This implies that RNAs, like proteins, are imported into the mitochondria. We investigated the relationship between the cytosolic and the mitochondrial tRNA genes and show that there are unique cytosolic tRNA genes, unique mitochondrial tRNA genes, and tRNA genes which appear to be shared and whose products are therefore targeted to both the cytosol and the mitochondrion.     

Search for structural similarity in proteins

MOTIVATION: The expanding protein sequence and structure databases await methods allowing rapid similarity search. Geometric parameters-dihedral angle between two sequential peptide bond planes (V) and radius of curvature (R) as they appear in pentapeptide fragments in polypeptide chains-are proposed for use in evaluating structural similarity in proteins (VeaR). The parabolic (empirical) function expressing the radius of curvature's dependence on the V-angle in model polypeptides is altered in real proteins in a form characteristic for a particular protein. This can be used as a criterion for judging similarity. RESULTS: A structural comparison of proteins representing a wide spectrum of structures was assessed versus sequence similarity analysis based on the genetic semihomology algorithm. The term 'consensus structure', analogous to 'consensus sequence', was introduced for the serpine family. AVAILABILITY: Semihom-sequence comparison freely available on request from J. Leluk. VeaR-structural comparison freely available on request from I. Roterman.