Structure and function of initiator methionine tRNA from the mitochondria of Neurospora crassa

tRNA biology in mitochondria

Mitochondria are the powerhouses of eukaryotic cells. They are considered as semi-autonomous because they have retained genomes inherited from their prokaryotic ancestor and host fully functional gene expression machineries. These organelles have attracted considerable attention because they combine bacterial-like traits with novel features that evolved in the host cell. Among them, mitochondria use many specific pathways to obtain complete and functional sets of tRNAs as required for translation. In some instances, tRNA genes have been partially or entirely transferred to the nucleus and mitochondria require precise import systems to attain their pool of tRNAs. Still, tRNA genes have also often been maintained in mitochondria. Their genetic arrangement is more diverse than previously envisaged. The expression and maturation of mitochondrial tRNAs often use specific enzymes that evolved during eukaryote history. For instance many mitochondria use a eukaryote-specific RNase P enzyme devoid of RNA. The structure itself of mitochondrial encoded tRNAs is also very diverse, as e.g., in Metazoan, where tRNAs often show non canonical or truncated structures. As a result, the translational machinery in mitochondria evolved adapted strategies to accommodate the peculiarities of these tRNAs, in particular simplified identity rules for their aminoacylation. Here, we review the specific features of tRNA biology in mitochondria from model species representing the major eukaryotic groups, with an emphasis on recent research on tRNA import, maturation and aminoacylation.

Functional evidence for D- and T-loop interactions in tmRNA

During bacterial protein synthesis, stalled ribosomes can be rescued by tmRNA, a molecule with both tRNA and mRNA features. The tRNA region of tmRNA has sequence similarity with tRNA(Ala) and also has a clover-leaf structure folded similarly as in canonical tRNAs. Here we propose the L-shape of tmRNA to be stabilized by two tertiary interactions between its D- and T-loop on the basis of phylogenetic and experimental evidence. Mutational analysis clearly demonstrates a tertiary interaction between G(13) and U(342). Strikingly, this in evolution conserved interaction is not primarily important for tmRNA alanylation and for binding to elongation factor Tu, but especially for a proper functioning of SmpB.

Characterization of an unusual tRNA-like sequence found inserted in a Neurospora retroplasmid

We characterized an unusual tRNA-like sequence that had been found inserted in suppressive variants of the mitochondrial retroplasmid of Neurospora intermedia strain Varkud. We previously identified two forms of the tRNA-like sequence, one of 64 nt (TRL-64)and the other of 78 nt (TRL-78) containing a 14-nt internal insertion in the anticodon stem at a position expected for a nuclear tRNA intron. Here, we show that TRL-78 is encoded in Varkud mitochondrial (mt)DNA within a 7 kb sequence that is not present in Neurospora crassa wild-type 74A mtDNA. This 7-kb insertion also contains a perfectly duplicated tRNA(Trp)gene, segments of several mitochondrial plasmids and numerous GC-rich pallindromic sequences that are repeated elsewhere in the mtDNA. The mtDNA-encoded copy of TRL-78 is transcribed and apparently undergoes 5'- and 3'-end processing and 3' nucleotide addition by tRNA nucleotidyl transferase to yield a discrete tRNA-sized molecule. However, the 14 nt intron-like sequence in TRL-78, which is missing in the TRL-64 form, is not spliced detectably in vivo or in vitro. Our results show that TRL-78 is an unusual tRNA-like species that could be incorporated into suppressive retroplasmids by the same reverse transcription mechanism used to incorporate mt tRNAs. The tRNA-like sequence may have been derived from an intron-containing nuclear tRNA gene or it may serve some function, like tmRNA. Our results suggest that mtRNAs or tRNA-like species may be integrated into mtDNA via reverse transcription, analogous to SINE elements in animal cells.

Initiation of protein synthesis in Saccharomyces cerevisiae mitochondria without formylation of the initiator tRNA

Protein synthesis in eukaryotic organelles such as mitochondria and chloroplasts is widely believed to require a formylated initiator methionyl tRNA (fMet-tRNA(fMet)) for initiation. Here we show that initiation of protein synthesis in yeast mitochondria can occur without formylation of the initiator methionyl-tRNA (Met-tRNA(fMet)). The formylation reaction is catalyzed by methionyl-tRNA formyltransferase (MTF) located in mitochondria and uses N(10)-formyltetrahydrofolate (10-formyl-THF) as the formyl donor. We have studied yeast mutants carrying chromosomal disruptions of the genes encoding the mitochondrial C(1)-tetrahydrofolate (C(1)-THF) synthase (MIS1), necessary for synthesis of 10-formyl-THF, and the methionyl-tRNA formyltransferase (open reading frame YBL013W; designated FMT1). A direct analysis of mitochondrial tRNAs using gel electrophoresis systems that can separate fMet-tRNA(fMet), Met-tRNA(fMet), and tRNA(fMet) shows that there is no formylation in vivo of the mitochondrial initiator Met-tRNA in these strains. In contrast, the initiator Met-tRNA is formylated in the respective "wild-type" parental strains. In spite of the absence of fMet-tRNA(fMet), the mutant strains exhibited normal mitochondrial protein synthesis and function, as evidenced by normal growth on nonfermentable carbon sources in rich media and normal frequencies of generation of petite colonies. The only growth phenotype observed was a longer lag time during growth on nonfermentable carbon sources in minimal media for the mis1 deletion strain but not for the fmt1 deletion strain.

Functional interaction of an arginine conserved in the sixteen amino acid insertion module of Escherichia coli methionyl-tRNA formyltransferase with determinants for formylation in the initiator tRNA

Formylation of initiator methionyl-tRNA by methionyl-tRNA formyltransferase (MTF) is important for initiation of protein synthesis in eubacteria. The determinants for formylation are clustered mostly in the acceptor stem of the initiator tRNA. Previous studies suggested that a 16 amino acid insertion loop, present in all eubacterial MTF's (residues 34-49 in the E. coli enzyme), plays an important role in specific recognition of the initiator tRNA. Here, we have analyzed the effect of site-specific mutations of amino acids within this region. We show that an invariant arginine at position 42 within the loop plays a very important role both in the steps of substrate binding and in catalysis. The kinetic parameters of the R42K and R42L mutant enzymes using acceptor stem mutant initiator tRNAs as substrates suggest that arginine 42 makes functional contacts with the determinants at the 3:70 and possibly also the 2:71 base pairs in the acceptor stem of the initiator tRNA. The kinetic parameters of the G41R/R42L double mutant enzyme are essentially the same as those of R42L mutant, suggesting that the requirement for arginine at position 42 cannot be fulfilled by an arginine at position 41. Along with other data, this result suggests that the insertion loop, which is normally unstructured and flexible, adopts a defined conformation upon binding to the tRNA.

Mitochondrial DNA sequence analysis of the cytochrome oxidase subunit I and II genes, the ATPase9 gene, the NADH dehydrogenase ND4L and ND5 gene complex, and the glutaminyl, methionyl and arginyl tRNA genes from Trichophyton rubrum

In this paper, we present the nucleotide sequence of a 5248 bp-long region of the mitochondrial (mt) genome of the dermatophyte Trichophyton rubrum. This region which represents about 1/4 of the total mt genome of this species reveals a compact organization of genes including: the glutaminyl tRNA, the methionyl tRNA, the cytochrome oxidase subunit I gene, the arginyl tRNA, the mitochondrial version of the ATPase subunit 9 gene, the cytochrome oxidase subunit II gene and a part of the NADH dehydrogenase ND4L and ND5 gene "complex". The main features of the part of mt DNA sequenced is the non-interrupted COXI gene and the presence in the mitochondrial version of the ATPase 9 gene of a small group IA intron. The extensive amino-acid sequence similarity with the equivalent gene in Aspergillus nidulans and Neuropora crassa indicates that this gene codes for a dicyclohexylcarbodiimide binding protein. The conserved arrangement of this portion of the mt genome and the presence of tRNAs between the protein-coding genes are compatible with a large polycistronic transcript processed by the excision of tRNAs, or similar secondary structures, as proposed for other fungal or mammalian mt DNAS.

The complete DNA sequence of the mitochondrial genome of Podospora anserina

The complete 94,192 bp sequence of the mitochondrial genome from race s of Podospora anserina is presented (1 kb = 10(3) base pairs). Three regions unique to race A are also presented bringing the size of this genome to 100,314 bp. Race s contains 31 group I introns (33 in race A) and 2 group II introns (3 in race A). Analysis shows that the group I introns can be categorized according to families both with regard to secondary structure and their open reading frames. All identified genes are transcribed from the same strand. Except for the lack of ATPase 9, the Podospora genome contains the same genes as its fungal counterparts, N. crassa and A. nidulans. About 20% of the genome has not yet been identified. DNA sequence studies of several excision-amplification plasmids demonstrate a common feature to be the presence of short repeated sequences at both termini with a prevalence of GGCGCAAGCTC.

Different mitochondrial gene orders among insects: exchanged tRNA gene positions in the COII/COIII region between an orthopteran and a dipteran species

We have cloned and sequenced a 2.65 kb segment of the mtDNA molecule of the orthopteran insect Locusta migratoria. It harbors the genes for four mitochondrial tRNAs, for cytochrome c oxidase subunits II and III and for ATPase subunits 6 and 8. The order of the locust genes resembles that of Drosophila yakuba: in both insects the genes for COII and ATPase 8 are separated from each other by the genes encoding tRNA(lys) and tRNA(asp), but in the locust, the positions of the two tRNA genes are reversed. This leads to a different mitochondrial gene order in the two insects.

Sequence and structure of a methionine transfer RNA from mosquito mitochondria

We have sequenced a methionine tRNA from mosquito mitochondria, and examined its structure using nucleases S1 and T1 under non-denaturing conditions. The sequence is highly homologous to a putative initiator methionine tRNA gene from Drosophila mitochondria. Its anticodon stem contains a run of three G-C base pairs that is characteristic of conventional initiator tRNAs; however, nuclease S1 analysis suggested an anticodon loop configuration characteristic of conventional elongator tRNAs. We propose that this tRNA can assume both initiator and elongator roles.

Nonsense suppression in Schizosaccharomyces pombe: the S. pombe Sup3-e tRNASerUGA gene is active in S. cerevisiae

The gene encoding the efficient UGA suppressor sup3-e of Schizosaccharomyces pombe was isolated by in vivo transformation of Saccharomyces cerevisiae UGA mutants with S. pombe sup3-e DNA. DNA from a clone bank of EcoRI fragments from a S. pombe sup3-e strain in the hybrid yeast vector YRp17 was used to transform the S. cerevisiae multiple auxotroph his4-260 leu2-2 trp1-1 to prototrophy. Transformants were isolated at a low frequency; they lost the ability to grow in minimal medium after passaging in non-selective media. This suggested the presence of the suppressor gene on the non-integrative plasmid. Plasmid DNA, isolated from the transformed S. cerevisiae cells and subsequently amplified in E. coli, transformed S. cerevisiae his4-260 leu2-2 trp1-1 to prototrophy. In this way a 2.4 kb S. pombe DNA fragment carrying the sup3-e gene was isolated. Sequence analysis revealed the presence of two tRNA coding regions separated by a spacer of only seven nucleotides. The sup3-e tRNASerUGA tRNA gene is followed by a sequence coding for the initiator tRNAMet. The transformation results demonstrate that the cloned S. pombe UGA suppressor is active in S. cerevisiae UGA mutant strains.

Highly conserved GC-rich palindromic DNA sequences flank tRNA genes in Neurospora crassa mitochondria

In sequencing a 2200 bp region of the Neurospora crassa mitochondrial DNA encoding the 3' end of the large rRNA gene and a cluster of six tRNA genes, we have found that the tRNA genes are flanked by highly conserved GC-rich palindromic DNA sequences. An 18 bp long core sequence, 5'-CC CTGCAG TA CTGCAG GG-3', containing two closely spaced Pst I sites, is common to all these palindromic sequences. Each of the eight Pst I sites mapped in the 2200 bp region consists of two closely spaced Pst I sites; thus this 2200 bp long segment actually contains 16 Pst I sites. Between 5-10% of the N. crassa DNA may consist of these GC-rich palindromic sequences that include the 18 base long core sequence. The same core sequence is present within both the 5' and 3' side of the intervening sequence of the large rRNA gene, close to, but not at, the intron-exon boundaries. We discuss probable roles for these sequences in N. crassa mitochondrial function, including their role as signals either in the synthesis or processing (or both) of RNA in the mitochondria.

Primary sequence of wheat mitochondrial 5S ribosomal ribonucleic acid: functional and evolutionary implications

Using the procedures of Donis-Keller et al. [Donis-Keller, H., Maxam, A. M., & Gilbert, W. (1977) Nucleic Acids Res. 4, 2527--2538 (1977)] and Peattie [Peattie, D. A. (1979) Proc. Natl. Acad. Sci. U.S.A. 76, 1760--1764], we have determined the nucleotide sequence of wheat mitochondrial 5S ribosomal ribonucleic acid (rRNA). This sequence [Formula: see text] is the first to be reported for a plant mitochondrial RNA. A highly conserved region (underlined) readily identifies the molecule as a structural homologue of other 5S rRNAs, as do potential base-paired regions which are characteristic of all known (prokaryotic, chloroplast, eukaryotic cytosol) 5S rRNA sequences. However, when assessed in terms of those structural features which distinguish prokaryotic from eukaryotic 5S rRNAs, wheat mitochondrial 5S rRNA cannot be classified readily as one or the other but instead displays characteristics of both types. In addition, the mitochondrial 5S rRNA has several unusual features, including (i) a variable number (two to three) of A residues at both the 5' and 3' ends, (ii) a unique sequence (CGACC, italic) in place of the prokaryotic sequence (CGAAC) which has been postulated to interact with aminoacyl-tRNA during translation, and (iii) a novel sequence, AUAUAUAU, immediately following the highly conserved sequence. In terms of overall primary sequence, wheat mitochondrial and cytosol 5S rRNAs seem to be slightly more divergent from each other than either is from Escherichia coli 5S rRNA, with which they are about equally homologous. From these observations, we propose that wheat mitochondrial 5S rRNA represents a distinct class of 5S rRNA. Our observations raise a number of questions about the evolutionary origin and functional role(s) of plant mitochondrial 5S rRNA.

Transfer-RNA: the early adaptor

Evolutionary history of tRNA is studied by comparative sequence analysis of two specified tRNA's at various phylogenetic levels and of tRNA families within four different species. Criteria are developed that allow 1) to distinguish between convergent and divergent evolution, 2) to determine the mechanism of divergence and 3) to estimate the degree of randomization of the variable parts of the sequences. The conclusion of these investigations is that tRNA's represent ancient molecules that existed in the form of a mutant distribution prior to their integration into genomes.

The nucleotide sequence of spinach chloroplast methionine elongator tRNA

The nucleotide sequence of spinach chloroplast methionine elongator tRNA (sp. chl. tRNAm Met) has been determined. This tRNA is considerably more homologous to E. coli tRNAm Met (67% homology) than to the three known eukaryotic tRNAm Met (50-55% homology). Sp. chl. tRNAm Met, like the eight other chloroplast tRNAs sequenced, contains a methylated GG sequence in the dihydrouridine loop and lacks unusual structural features which have been found in several mitochondrial tRNAs.

Are archaebacteria merely derived 'prokaryotes'?

The archaebacteria are a group of prokaryotes which seem as distinct from the true bacteria (eubacteria) as they are from eukaryotes. The evidence on which this conclusion rests is of two types: genotypic (quantitative)--that is, comparative sequence studies, and phenotypic (qualitative)--that is, differences in various organismal characteristics. The differences between archaebacteria and true bacteria are so great, both quantitatively and qualitatively, that the two bacterial groups should be considered as representing separate primary lines of descent, each tracing directly back to the universal ancestor. Furthermore, this ancestor itself seems not to be a prokaryote; rather it was a far simpler type of organism, one properly called a progenote. If this is true, the discovery of archaebacteria marks a major advance in the biologist's attempts to understand the basis for the evolution of the cell.

The nucleotide sequence of a small (3S) seryl-tRNA (anticodon GCU) from beef heart mitochondria

The primary structure of a 3S serine tRNA from beef heart mitochondria has been determined using our new two-dimensional "read-off" sequencing method (Tanaka, Y., Dyer, T.A. and Brownlee, G.G (1980) Nucleic Acids Res. 8, 1259-1272). When arranged in the "cloverleaf" form it shows unique features since (i) it completely lacks the dihydrouridine arm, (ii) it has an extended "T gamma" loop, but lacks the T and gamma residues, and (iii) it has only one minor base, N6(N-threonylcarbamoyl)adenosine, next to the anticodon.

Dimeric transfer RNA precursors in S. pombe

Sequence analysis of a Schizosaccharomyces pombe DNA fragment revealed two tRNA coding regions separated by a seven nucleotide spacer. the 5'-proximal tRNA gene encodes a tRNAUCGSer sequence, which is interrupted by a 16 nucleotide intron at the 3' side of the base adjacent to the anticodon. The second tRNA gene encodes an initiator tRNAMet sequence. This DNA fragment, cloned into pBR322, was used as template for in vitro transcription in a nuclear extract of Xenopus oocytes. The tRNA genes were transcribed into one RNA precursor which contained both tRNA sequences. The primary transcription product initiates with pppG, contains a 9 nucleotide leader sequence, a 16 nucleotide intron, a 7 nucleotide spacer between the two tRNA molecules and an 8--9 nucleotide trailer sequence. RNA initiation was only observed upstream of the 5'-proximal tRNASer. We used RNA analysis to establish a sequence of the enzymatic steps of tRNA maturation in the nuclear extract. The first step in processing the dimeric precursor is an endonuclease cleavage which generates the mature 5' end of the tRNAMet. Further steps include the removal of the flanking sequences and addition of the CCAOH 3' terminus. The last step is the splicing of the tRNASer precursor to remove the intervening sequence.

Distinctive sequence of human mitochondrial ribosomal RNA genes

The nucleotide sequence spanning the ribosomal RNA (rRNA) genes of cloned human mitochondrial DNA reveals an extremely compact genome organization wherein the putative tRNA genes are probably 'butt-jointed' around the two rRNA genes. The sequences of the rRNA genes are significantly homologous in some regions to eukaryotic and prokaryotic sequences, but distinctive; the tRNA genes also have unusual nucleotide sequences. It seems that human mitochondria did not originate from recognizable relatives of present day organisms.

Codon recognition rules in yeast mitochondria

The mitochondrial genome of Saccharomyces cerevisiae codes for 24 tRNAs. The nucleotide sequences of the tRNA genes suggest a unique set of rules that govern the decoding of the mitochondrial genetic code. The four codons of unmixed fmilies are recognized by single tRNAs that always have a U in the wobble position of the anticodon. The codons of the mixed families are read by two different tRNAs. Codons terminating in a C or U are recognized by tRNAs with a G and codons terminating in a G or A are recognized by tRNAs with a U in the corresponding positions of the anticodons. There are two exceptions to these rules. In the AUN family for isoleucine and methionine, the isoleucine tRNA has a G and the methionine tRNA has a C in the wobble position. The tRNA for the arginine CGN family also has an A in the wobble position of the anticodon. It is of interest that the CGN codons have not been found in the mitochondrial genes sequenced to date. The simplified decoding system of yeast mitochondria allows all the codons to be recognized by only 24 tRNAs.

Novel features in the genetic code and codon reading patterns in Neurospora crassa mitochondria based on sequences of six mitochondrial tRNAs

We report the sequences of Neurospora crassa mitochondrial alanine, leucine(1), leucine(2), threonine, tryptophan, and valine tRNAs. On the basis of the anticodon sequences of these tRNAs and of a glutamine tRNA, whose sequence analysis is nearly complete, we infer the following: (i) The N. crassa mitochondrial tRNA species for alanine, leucine(2), threonine, and valine, amino acids that belong to four-codon families (GCN, CUN, ACN, and GUN, respectively; N = U, C, A, or G) all contain an unmodified U in the first position of the anticodon. In contrast, tRNA species for glutamine, leucine(1), and tryptophan, amino acids that use codons ending in purines (CA(G) (A), UU(G) (A), and UG(G) (A), respectively) contain a modified U derivative in the same position. These findings and the fact that we have not detected any other isoacceptor tRNAs for these amino acids suggest that N. crassa mitochondrial tRNAs containing U in the first position of the anticodon are capable of reading all four codons of a four-codon family whereas those containing a modified U are restricted to reading codons ending in A or G. Such an expanded codon-reading ability of certain mitochondrial tRNAs will explain how the mitochondrial protein-synthesizing system operates with a much lower number of tRNA species than do systems present in prokaryotes or in eukaryotic cytoplasm. (ii) The anticodon sequence of the N. crassa mitochondrial tryptophan tRNA is U(*)CA and not CCA or CmCA as is the case with tryptophan tRNAs from prokaryotes or from eukaryotic cytoplasm. Because a tRNA with U(*)CA in the anti-codon would be expected to read the codon UGA, as well as the normal tryptophan codon UGG, this suggests that in N. crassa mitochondria, as in yeast and in human mitochondria, UGA is a codon for tryptophan and not a signal for chain termination. (iii) The anticodon sequences of the two leucine tRNAs indicate that N. crassa mitochondria use both families of leucine codons (UU(A) (G) and CUN; N = U, C, A, or G) for leucine, in contrast to yeast mitochondria [Li, M. & Tzagoloff, A. (1979) Cell 18, 47-53] in which the CUA leucine codon and possibly the entire CUN family of leucine codons may be translated as threonine.

Yeast mitochondrial methionine initiator tRNA: characterization and nucleotide sequence

Two methionine tRNAs from yeast mitochondria have been purified. The mitochondrial initiator tRNA has been identified by formylation using a mitochondrial enzyme extract. E. coli transformylase however, does not formylate the yeast mitochondrial initiator tRNA. The sequence was determined using both 32P-in vivo labeled and 32P-end labeled mt tRNAf(Met). This tRNA, unlike N. crassa mitochondrial tRNAf(Met), has two structural features typical of procaryotic initiator tRNAs: (i) it lacks a Watson-Crick base-pair at the end of the acceptor stem and (ii) has a T-psi-C-A sequence in loop IV. However, both yeast and N. crassa mitochondrial initiator tRNAs have a U11:A24 base-pair in the D-stem unlike procaryotic initiator tRNAs which have A11:U24. Interestingly, both mitochondrial initiator tRNAs, as well as bean chloroplast tRNAf(Met), have only two G:C pairs next to the anticodon loop, unlike any other initiator tRNA whatever its origin. In terms of overall sequence homology, yeast mitochondrial tRNA(Met)f differs from both procaryotic or eucaryotic initiator tRNAs, showing the highest homology with N. crassa mitochondrial initiator tRNA.

The nucleotide sequence of phenylalanine tRNA from the cytoplasm of Neurospora crassa

The phenylalanine tRNA from the cytoplasm of Neurospora crassa has been purified and sequenced. The sequence is: pGCGGGUUUAm2GCUCA (N) GDDGGGAGAGCm22GpsiCAGACmUGmAAYApsim5CUGAAGm7GDm5CGUGUGTpsiCGm1AUCCACACAAACCGCACCAOH. Both in the nature of modified nucleotides which are present in this tRNA and in the overall sequence, this tRNA resembles more closely phenylalanine tRNAs of eukaryotic cytoplasm than those of prokaryotes. The sequence of this tRNA differs from those of the corresponding tRNAs of wheat germ and yeast by only 6 and 7 nucleotides respectively out of 76 nucleotides.U

The tRNAAGYSer and tRNACGYArg genes from a gene cluster in yeast mitochondrial DNA

Yeast mitochondrial DNA-pBR322 recombinant DNA molecules screened for rRNA genes were used as a source of DNA for mitochondrial tRNA gene sequence analysis. We report here the sequences of yeast mitochondrial tRNA genes coding for a tRNAAGYSer and a tRNACGYArg. The tRNAAGYSer sequence deduced from the gene is the first reported sequence of a yeast tRNAAGYSer. It is also the second yeast mitochondrial tRNASer gene to be sequenced, and demonstrates unequivocally the presence of mitochondrial encoded serine tRNA isoacceptors. The tRNACGYArg sequence deduced from the gene is the most AT-rich (82%) tRNA sequence ever reported. Whereas all the mitochondrial genes sequenced to date exist singly on the genome and are separated by long stretches of AT-rich DNA, the tRNAACYSer and tRNAcgyarg genes exist in tandem, separated by only 3 bp. This gene arrangement strongly suggests that mitochondrial tRNA genes may be transcribed into multicistronic precursors.

Evolution of methionine initiator and phenylalanine transfer RNAs

Sequence data from methionine initiator and phenylalanine transfer RNAs were used to construct phylogenetic trees by the maximum parsimony method. Although eukaryotes, prokaryotes and chloroplasts appear related to a common ancestor, no firm conclusion can be drawn at this time about mitochondrial-coded transfer RNAs. tRNA evolution is not appropriately described by random hit models, since the various regions of the molecule differ sharply in their mutational fixation rates. "Hot" mutational spots are identified in the Tpsic, the amino acceptor and the upper anticodon stems; the D arm and the loop areas on the other hand are highly conserved. Crucial tertiary interactions are thus essentially preserved while most of the double helical domain undergoes base pair interchange. Transitions are about half as costly as transversions, suggesting that base pair interchanges proceed mostly through G-U and A-C intermediates. There is a preponderance of replacements starting from G and C but this bias appears to follow the high G + C content of the easily mutated base paired regions.