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PubMed1981

On the origin of biological systems and the role of poly-nucleotides -- the initiation of evolution, the structural basis of the genetic code and the mechanism of protein biosynthesis.

There is much information on the nature and function of biological systems in the structures of the small molecules that affect them and in the biosynthetic and other reactions in which they are involved. Combining this with biochemical and polynucleotide sequence information allows us to derive explanations for a number of biological problems that earlier were unclear or even quite obscure. Thus polynucleotide systems give a good account of the origin of life, of the genetic code and of the function of the ribosomal mechanism of protein biosynthesis. It is apparent that polynucleotides play a more important role than has been fully appreciated.

Biological Evolution↗
PubMed1982

Globular proteins, GU wobbling, and the evolution of the genetic code.

It has previously been shown that the formation of GU base pairs in RNA copying processes leads to an accumulation of G and U in both strands of the replicating RNA, which results in a non-random distribution of base triplets. In the present paper, this distribution is calculated, and, using the X2-test, a correlation between the distribution of triplets and the amino acid composition of the evolutionarily conservative interior regions of selected globular proteins is established. It is suggested that GU wobbling in early replication of RNA could have led to the observed amino acid composition of present-day protein interiors. If this hypothesis is correct, then GU wobbling must have been very extensive in the imprecisely replicating RNA, even reaching values close to the critical for stability of its double-helical structure. Implications of the hypothesis both for the evolution of the genetic code and of proteins are discussed.

Biological Evolution↗
PubMed1987

Isolation of a rat mitochondrial release factor. Accommodation of the changed genetic code for termination.

A single release factor has been isolated and partially purified from rat mitochondria. It requires ethanol in addition to the specific termination codon when assayed in a heterologous system with Escherichia coli ribosomes. The factor recognizes the codons UAA and UAG but not UGA, and therefore it has been designated mtRF-1. A factor of the bacterial RF-2 type, which in E. coli recognizes UGA, or of the mammalian type, which recognizes all three termination codons, has not been detected in mitochondria. The absence of a factor responding to UGA accommodates the use of this codon as a signal for tryptophan in the rat mitochondrial genetic code. The mtRF-1 could translate all of the known termination codons in the rat mitochondrial genome. It does not respond to AGG and AGA which in bovine and human mitochondrial DNA code for termination but which in rat mitochondria may not code for either an amino acid or for termination.

Animals↗
PubMed1975

Replication of picornaviruses. I. Evidence from in vitro RNA synthesis that poly(A) of the poliovirus genome is genetically coded.

A crude replication complex has been isolated from poliovirus-infected HeLa cells and used for synthesis of poliovirus replicative intermediate (RI) RNA, replicative form (RF) RNA, and single-stranded (SS) RNA in vitro. All three classes of virus-specific RNA synthesized in vitro are shown to contain poly(A). Poly(A) of RF and of SS RNA [RF-poly(A) and SS-poly(A)] has a chain length (50 to 70 nucleotides) that is shorter than that of poly(A) of in vivo-synthesized RNAs. Poly(A) of RI [RI-poly(A),] however, is at least 200 nucleotides long and, therefore, larger than poly(A) of RI isolated from HeLa cells 4 h after infection. The crude membrane-bound replication complex contains a terminal adenylate transferase activity that is stimulated by Mn2+ and the addition of an (Ap)2AOH primer. This transferase activity is found also in extracts of mock-infected cells. Partial purificaiton of the replication complex in a stepwise sucrose gradient, in which the viral replicase is associated with the smooth cytoplasmic membrane fraction, does not remove the terminal transferase. However, when the partially purified replication complex is treated with deoxycholate and sedimented through a sucrose gradient, a soluble replication complex can be isolated that is free from terminal adenylate transferase. This soluble replication complex was found to synthesize viral RNA-linked poly(A) longer in chain length than that synthesized by the crude replication complex. Taking into account the 5'-terminal poly(U) in poliovirus minus strands, our data suggest that polyadenylation of poliovirus RNA occurs by transcription and not by end addition. When compared to other viral systems, poliovirus and, probably, all picornaviruses appear to be unique in that the poly(A) of their genome is genetically coded.

Adenosine Monophosphate↗
PubMed1987

Unusual genetic codes and a novel gene structure for tRNA(AGYSer) in starfish mitochondrial DNA.

The nucleotide sequence of a 3849-bp fragment of starfish mitochondrial genome was determined. The genes for NADH dehydrogenase subunits 3, 4, 5, and COIII, and three kinds of (tRNA(UCNSer), tRNA(His), and tRNA(AGYSer) were identified by comparing with the genes of other animal mitochondria so far elucidated. The gene arrangement of starfish mitochondrial genome was different from those of vertebrate and insect mitochondrial genomes. Comparison of the protein-encoding nucleotide sequences of starfish mitochondria with those of other animal mitochondria suggested a unique genetic code in starfish mitochondrial genome; both AGA and AGG (arginine in the universal code) code for serine, AUA (isoleucine in the universal code but methionine in most mitochondrial systems) for isoleucine, and AAA (lysine) for asparagine. It was also inferred that these AGA and AGG codons are decoded by serine tRNA(AGYSer) originally corresponding to AGC and AGU codons. This situation is similar to the case of Drosophila mitochondrial genome. Variations in the use of AGA and AGG codons were discussed on the basis of the evolution of animals and decoding capacity of various tRNA(AGYSer) species possessing different sizes of the dihydrouridine (D) arm.

Animals↗
PubMed1985

The mitochondrial DNA molecular of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code.

The sequence of the 16,019 nucleotide-pair mitochondrial DNA (mtDNA) molecule of Drosophila yakuba is presented. This molecule contains the genes for two rRNAs, 22 tRNAs, six identified proteins [cytochrome b, cytochrome c oxidase subunits I, II, and III (COI-III), and ATPase subunits 6 and 8] and seven presumptive proteins (URF1-6 and URF4L). Replication originates within a region of 1077 nucleotides that is 92.8% A + T and lacks any open reading frame larger than 123 nucleotides. An equivalent to the sequence found in all mammalian mtCDNAs that is associated with initiation of second-strand DNA synthesis is not present in D. yakuba mtDNA. Introns are absent from D. yakuba mitochondrial genes and there are few (0-31) intergenic nucleotides. The genes found in D. yakuba and mammalian mtDNAs are the same, but there are differences in their arrangement and in the relative proportions of the complementary strands of the molecule that serve as templates for transcription. Although the D. yakuba small and large mitochondrial rRNA genes are exceptionally low in G and C and are shorter than any other metazoan rRNA genes reported, they can be folded into secondary structures remarkably similar to the secondary structures proposed for mammalian mitochondrial rRNAs. D. yakuba mitochondrial tRNA genes, like their mammalian counterparts, are more variable in sequence than nonorganelle tRNAs. In mitochondrial protein genes ATG, ATT, ATA, and in one case (COI) ATAA appear to be used as translation initiation codons. The only termination codon found in these genes is TAA. In the D. yakuba mitochondrial genetic code, AGA, ATA, and TGA specify serine, isoleucine, and tryptophan, respectively. Fifty-nine types of sense condon are used in the D. yakuba mitochondrial protein genes, but 93.8% of all codons end in A or T. Codon-anticodon interactions may include both G-A and C-A pairing in the wobble position. Evidence is summarized that supports the hypothesis that A and T nucleotides are favored at all locations in the D. yakuba mtDNA molecule where these nucleotides are compatible with function.

Adenosine Triphosphatases↗
PubMed1989

The complete nucleotide sequence, gene organization, and genetic code of the mitochondrial genome of Paracentrotus lividus.

The 15,697-nucleotide sequence of Paracentrotus lividus mitochondrial DNA is reported. This genome codes for 2 rRNAs, 22 tRNAs, and 12 mRNAs which specify 13 subunits of the mitochondrial inner membrane respiratory complexes. The gene arrangement differs from that of other animal species. The two ribosomal genes 16 S and 12 S are separated by a stretch of about 3.3 kilobase pairs which contains the ND1 and ND2 genes and a cluster of 15 tRNA genes. The ND4L coding sequence is not contained in the ND4 mRNA but has its own mRNA which maps between the tRNA(Arg) and the Co II genes. The main noncoding region, located in the tRNA gene cluster, is only 132 nucleotides long, but contains sequences homologous to the mammalian displacement loop. Other short noncoding sequences are interspersed in the genome: they contain a conserved AT consensus which probably has a role in transcription or RNA processing. As regards the mitochondrial genetic code, the codons AGA and AGG specify serine and are recognized by a tRNA with a GCU anticodon, whereas AUA and AAA code for isoleucine and asparagine rather than for methionine and lysine. Except for ND4L which starts with AUC and ATPase 8 which starts with GUG, AUG is used as the initiation codon. In 11 out of 13 cases the genes terminate with the canonical stop codons UAA or UAG. These observations suggest that during invertebrate evolution each lineage developed its own mechanism of mitochondrial DNA replication and transcription and of RNA processing and translation.

Amino Acid Sequence↗
PubMed1990

Evolution of the mitochondrial genetic code. III. Reassignment of CUN codons from leucine to threonine during evolution of yeast mitochondria.

Yeast mitochondria use UUR as the sole leucine codons. CUN, universal leucine codons, are read as threonine by aberrant threonine tRNA with anticodon sequence (UAG). The reassignment of CUN codons to threonine during yeast mitochondrial evolution could have proceeded by the disappearance of CUN codons from the reading frames of messenger RNA, through mutation mainly to UUR leucine codons as a result of AT pressure. We suggest that this was accompanied by a loss of leucine-accepting ability of tRNA Leu(UAG). This tRNA could have then acquired threonine-accepting activity through the appearance of an additional threonyl-tRNA synthetase. CUN codons that subsequently appeared from mutations of various other codons would have been translated as threonine. This change in the yeast mitochondrial genetic code is likely to have evolved through a series of nondisruptive nucleotide substitutions that produced no widespread replacement of leucine by threonine in proteins as a consequence.

Adenine↗
PubMed1995

Codon usage, genetic code and phylogeny of Dictyostelium discoideum mitochondrial DNA as deduced from a 7.3-kb region.

We have sequenced a region (7,376-bp) of the mitochondrial (mt) DNA (54 kb) of the cellular slime mold, Dictyostelium discoideum. From the DNA and amino-acid sequence comparisons with known sequences, genes for ATPase subunit 9 (ATP9), cytochrome b (CYTB), NADH dehydrogenase subunits 1, 3 and 6 (ND1, ND3 and ND6), small subunit rRNA (SSU rRNA) and seven tRNAs (Arg, Asn, Cys, Lys, f-Met, Met and Pro) have been identified. The sequenced region of the mtDNA has a high average A + T-content (70.8%). The A + T-content of protein-genes (73.6%) is considerably higher than that of RNA genes (61.3%). Even with the strong AT-bias, the genetic code employed is most probably the universal one. All seven tRNAs are able to form typical clover leaf structures. The molecular phylogenetic trees of CYTB and SSU rRNA suggest that D. discoideum is closer to green plants than to animals and fungi.

Amino Acid Sequence↗
PubMed1995

Structure, function and evolution of seryl-tRNA synthetases: implications for the evolution of aminoacyl-tRNA synthetases and the genetic code.

Two aspects of the evolution of aminoacyl-tRNA synthetases are discussed. Firstly, using recent crystal structure information on seryl-tRNA synthetase and its substrate complexes, the coevolution of the mode of recognition between seryl-tRNA synthetase and tRNA(ser) in different organisms is reviewed. Secondly, using sequence alignments and phylogenetic trees, the early evolution of class 2 aminoacyl-tRNA synthetases is traced. Arguments are presented to suggest that synthetases are not the oldest of protein enzymes, but survived as RNA enzymes during the early period of the evolution of protein catalysts. In this view, the relatedness of the current synthetases, as evidenced by the division into two classes with their associated subclasses, reflects the replacement of RNA synthetases by protein synthetases. This process would have been triggered by the acquisition of tRNA 3' end charging activity by early proteins capable of activating small molecules (e.g., amino acids) with ATP. If these arguments are correct, the genetic code was essentially frozen before the protein synthetases that we know today came into existence.

Acylation↗
PubMed1993

Transfer RNAs with complementary anticodons: could they reflect early evolution of discriminative genetic code adaptors?

In accordance with the hypercycle theory of M. Eigen and P. Schuster [(1979) Hypercycle: A Principle of Natural Self-Organization (Springer, New York)], the ancestors of modern tRNAs appear to have emerged via the shortest possible way, both complementary strands of a short symmetrical double helix serving as pre-tRNAs with complementary anticodons. This conclusion is based upon results of comparative sequence analysis of the 17-base-long anticodon loop and stem of tRNAs totaling 896 and especially of 22 pairs of consensus tRNAs with complementary or quasi-complementary anticodons. With regard to the anticodon loop and stem of pairs of consensus tRNAs, complementary distances were considerably less than direct distances--i.e., antiparallel pairing invariably yielded fewer mismatches than direct pairing. Furthermore, the smallest complementary distance was detected when two antiparallel sequences formed irregular G-U bonds in their anticodon triplets. The above implies that pre-tRNAs in peribiotic times were long hairpin structures having 73 bases or more, the middle base of an anticodon being the center of symmetry. Accordingly, each pair of pre-tRNAs with complementary anticodons should have been almost identical with each other except for their three central bases. The above situation appears to have dictated the early establishment of direct links between anticodons and the type of amino acids with which tRNAs are to be charged. This direct link is still maintained between modern aminoacyl-tRNA synthetases and anticodons. Replication of the double helices concertedly generated new codons for the same pair of amino acids. Thus, occurrence of synonymous as well as certain "palindromic" features of the genetic code table might have been determined by this mechanism.

Anticodon↗
PubMed1981

Periodic correlations in DNA sequences and evidence suggesting their evolutionary origin in a comma-less genetic code.

Strong rhythms with a period of three bases have been seen while correlating the relative positions of purines and pyrimidines and of the four individual bases in the complete DNA sequence of the viruses phi X174, G4 and fd. Generally weaker variations of the same type have been found in the DNA virus SV40, the plasmid pBR322, the RNA virus MS2, and elsewhere in procaryotes and eucaryotes (e.g. in a ribosomal protein gene cluster of E. coli and the sea urchin histone genes). From the interrelation of four-base with purine-pyrimidine rhythms it seems that the purine-pyrimidine relationships have a basic significance. An explanation is proposed in terms of the former use of a comma-less genetic code (i.e. readable only in one frame) of the general form RNY (R = purine, Y = pyrimidine and N = purine or pyrimidine). In spite of subsequent mutation, there appears to be still enough of the primitive messages remaining to produce these periodic variations with their characteristic properties in phase and amplitude. Particularly good evidence for this hypothesis is provided by the fact that the phases for the stronger rhythms are the same in all the genomes tested and can be successfully predicted by a simple consideration of the original RNY pattern. With regard to amplitude it can be similarly foreseen which variations will be more clearly marked than others. The observed behaviour of the amplitude as the separation between correlated bases increases is also explained by the insertions, deletions and point mutations which have occurred. Additionally it is possible to account for some notable features of the non-random use of codons for the same amino acid by this theory.

Base Sequence↗