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C Saccone

Publications and source records attributed to C Saccone.

At least 91 records · Page 5Linked to original sources
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↗
PubMed1989

DNA microenvironments and the molecular clock.

A few years ago we presented a stationary Markov model of gene evolution according to which only homologous genes from not too divergent species obeying the condition of being stationary may behave as reliable molecular clocks. A compartmentalized model of the nuclear genome in which the genes are distributed in compartments, the isochores, defined by their G + C content has been proposed recently. We have found that only homologous gene pairs that are stationary, and belong to the same isochore, can be used consistently for the determination of phylogeny and base substitution rate. In particular, for the rodent-human couple, only about half of the homologous gene pairs are stationary. Stationary genes evolve at the third silent codon position with the same velocity independent of the genes and base composition. By contrast, nonstationary genes display apparent rate values (pseudovelocities) that are significantly higher. Our results cast doubt upon recent claims of a large acceleration in the rate of molecular evolution in rodents.

Biological Evolution↗
PubMed1989

The complete nucleotide sequence of the Rattus norvegicus mitochondrial genome: cryptic signals revealed by comparative analysis between vertebrates.

This paper reports the nucleotide sequence of rat mitochondrial DNA, only the fourth mammalian mitochondrial genome to be completely sequenced. Extensive comparative studies performed with similar genomes from other organisms revealed a number of interesting features. 1) Messenger RNA genes: the codon strategy is mainly dictated by the base compositional constraints of the corresponding codogenic DNA strand. The usage of the initiation and termination codons follows well-established rules. In general the canonical initiator, ATG, and terminators, TAA and TAG (in rat, only TAA), are always present when there is gene overlapping or when the mRNAs possess untranslated nucleotides at the 5' or 3' ends. 2) Transfer RNA genes: a number of features suggest the peculiar evolutionary behavior of this class of genes and confirm their role in the duplication and rearrangement processes that took place in the evolution of the animal mitochondrial genome. 3) Ribosomal RNA genes: accurate sequence analysis revealed a number of significant examples of complementarity between ribosomal and messenger RNAs. This suggests that they might play an important role in the regulation of mitochondrial translation and transcription mechanisms. The properties revealed by our work shed new light on the organization and evolution of the vertebrate mitochondrial genome and more importantly open up the way to clearly aimed experimental studies of the regulatory mechanisms in mitochondria.

Amino Acid Sequence↗
PubMed1989

Mitochondrial genome in animal cells. Structure, organization, and evolution.

In the past decade, the development of new DNA, RNA, and protein technologies has greatly incremented the knowledge about the organization and expression of mitochondrial DNA. The complete base sequence of mitochondrial DNA of several animals is known and many data are rapidly accumulating on the mitochondrial genomes of other systems. Here we discuss the results so far obtained that disclosed unexpected features of mitochondrial genetics. Furthermore, mitochondrial DNA has become established as a powerful tool for evolutionary studies in animals. Evidences are presented demonstrating that the evolution of mitochondrial DNA has proceeded in different ways in the various taxonomic groups. Data on heteroplasmic animals, which demonstrate the rapid evolution of mitochondrial DNA, are also presented.

Animals↗
PubMed1988

Clustering of tRNA genes in Paracentrotus lividus mitochondrial DNA.

We have determined the base sequence of the restriction fragment Bam1-2 (3,593) of Paracentrotus lividus (sea urchin) mtDNA. This fragment contains, in addition to genes previously identified (part of the 12S rRNA, ND1 and part of the ND2 mRNA), a cluster of 15 tRNA genes located between the 12S and ND1 genes. Also to be found in the tRNA gene cluster, between the tRNA(Thr) and tRNA(Pro) genes, is a sequence of 134 bp which constitutes the only non-coding region of this DNA so far identified. The distinctive organization of the tRNA genes and the extreme size reduction of the non-coding region suggest the existence of unique mechanisms for the regulation of gene expression in this organism.

Amino Acid Sequence↗
PubMed1987

Structural elements highly preserved during the evolution of the D-loop-containing region in vertebrate mitochondrial DNA.

A detailed comparative study of the regions surrounding the origin of replication in vertebrate mitochondrial DNA (mtDNA) has revealed a number of interesting properties. This region, called the D-loop-containing region, can be divided into three domains. The left (L) and right (R) domains, which have a low G content and contain the 5' and the 3' D-loop ends, respectively, are highly variable for both base sequence and length. They, however, contain thermodynamically stable secondary structures which include the conserved sequence blocks called CSB-1 and TAS which are associated with the start and stop sites, respectively, for D-loop strand synthesis. We have found that a "mirror symmetry" exists between the CSB-1 and TAS elements, which suggests that they can act as specific recognition sites for regulatory, probably dimeric, proteins. Long, statistically significant repeats are found in the L and R domains. Between the L and R domains we observed in all mtDNA sequences a region with a higher G content which was apparently free of complex secondary structure. This central domain, well preserved in mammals, contains an open reading frame of variable length in the organisms considered. The identification of common features well preserved in evolution despite the high primary structural divergence of the D-loop-containing region of vertebrate mtDNA suggests that these properties are of prime importance for the mitochondrial processes that occur in this region and may be useful for singling out the sites on which one should operate experimentally in order to discover functionally important elements.

Amino Acid Sequence↗
PubMed1987

A simple quantitative model of the molecular clock.

We present the ideas, and their motivation, at the basis of a simple model of nucleic acid evolution: the stationary Markov process, or Markov clock. After a brief review of its relevant mathematical properties, the Markov clock is applied to nucleotide sequences from mitochondrial and nuclear genes of different species. Particular emphasis is given to the necessity of carrying out a correct statistical analysis, which allows us to check quantitatively the applicability of our model. We find evidence that the Markov clock ticks in many different processes, and that its limitations can be understood in terms of a simple idea that we call the "base-drift" hypothesis. This hypothesis correlates the deviations from the stationarity of the Markov process to the evolutionary distance dAB(p) of two species A and B, relative to the process P. We conclude by discussing the implications of our findings for future work.

Animals↗
PubMed1987

A novel gene order in the Paracentrotus lividus mitochondrial genome.

The mitochondrial DNA (mtDNA) from Paracentrotus lividus (sea urchin) eggs, a circular molecule of about 15,500 bp, has been cloned in plasmid vectors after cleavage with various restriction enzymes. By a combination of Northern blot hybridization and nucleotide sequence analysis we have characterized most of the P. lividus mitochondrial transcripts and determined the basic gene organization of the mtDNA. The nucleotide sequence of a gene for one NADH dehydrogenase (ND) subunit, ND4L, has also been determined. Our results show the existence of a novel gene order. The 12S and 16S rRNA genes are not contiguous but are separated from each other by ND1 and ND2 genes. The ND4L gene is not adjacent to ND4 but is located between the tRNAArg gene and the gene for subunit II of cytochrome oxidase (CoII). The tRNA genes are reshuffled and contrary to all vertebrate mitochondrial genomes studied so far, there are no intergenic regions between the tRNAPhe and the cytochrome b genes. These characteristics suggest a peculiar mechanism for the regulation of gene expression in this organism and provide information on the evolution of the mitochondrial genetic system in animal cells.

Animals↗
PubMed1986

Structural conservation and variation in the D-loop-containing region of vertebrate mitochondrial DNA.

The nucleotide sequences of the D-loop-containing regions of three rat mitochondrial DNAs (mtDNAs), two from the species Rattus norvegicus and one from R. rattus, were determined. Comparisons made among these sequences and with the mouse sequence showed that, on the basis of both base composition and frequency of nucleotide alterations, three domains could be defined within the D-loop-containing region: a central conserved segment, poor in L-strand adenine, flanked by two divergent, adenine-rich regions. Deletions and insertions were found to occur at an unexpectedly high frequency in these sequences and the conserved sequence block called CSB-1 was found not to be intact in the R. rattus sequence. Although in comparisons of more distantly related mtDNAs the D-loop region is the most divergent on the molecule, it does not diverge more than typical protein genes between R. norvegicus and R. rattus, and its central conserved domain appears to be one of the molecule's most conserved regions. The most variable domain borders the tRNAPhe gene and contains the L and H-strand promoters and the 5' terminus for H-strand DNA synthesis. Within this region we have found sequences in all the mtDNAs we have examined, including those of human, two artiodactyls and Xenopus, that are capable of folding into cloverleaf structures. In the other divergent domain of the same mtDNAs, we find sequences capable of assuming similar secondary structural configurations at or near the sites for the termination of D-loop DNA synthesis. The evolutionary preservation of the potential to form such structures despite the high primary-structural divergence of the regions they occur in, suggests the structures are of principal importance for some processes occurring in the D-loop-containing region.

Animals↗
PubMed1986

Transition and transversion rate in the evolution of animal mitochondrial DNA.

We present a further application of the stochastic model previously described (Lanave et al., 1984, 1985) for measuring the nucleotide substitution rate in the mammalian evolution of the mitochondrial DNA (mtDNA). The applicability of this method depends on the validity of "stationarity conditions" (equal nucleotide frequencies at first, second and third silent codon positions in homologous protein coding genes). In the comparison of homologous sequences satisfying the stationarity condition at the silent sites, only the four codon families (quartets) for which both transitions and transversions are silent at the third position are considered here. This has allowed us to estimate the transition and transversion rates for any pair of species. We have analyzed the third silent codon position of the triplet rat-mouse-cow, of a series of slightly divergent primates and of two Drosophila species. In terms of two external dating input we have then determined the phylogenetic trees for rat, mouse, and cow as well as for a number of primates including man. The phylogenetic tree that we have derived for the triplet rat, mouse and cow agrees with that we had previously determined by analyzing the first, second and third silent codon positions (in both duets and quartets) of mt genes (Lanave et al., 1985). For primates our method leads to the following branching order from the oldest to the most recent: Gibbon, Orangutan, Gorilla, Chimpanzee and Man. In absolute time, fixing the distance Chimpanzee-Man as 5 million years (Myr) we estimate the dating of the divergence nodes as: Gorilla 7 Myr; Orangutan 16 Myr; Gibbon 20 Myr. In all cases analyzed, the transition rate has been found to be substantially higher than the transversion rate. Moreover we have found that the transition/transversion ratio is different in the various lineages. We suggest that this fact is probably related to the nucleotide frequencies at the third silent codon position.

Animals↗
PubMed1985

Multisequence comparisons in protein coding genes. Search for functional constraints.

A very powerful method for detecting functional constraints operative in biological macromolecules is presented. This method entails performing a base permanence analysis of protein coding genes at each codon position simultaneously in different species. It calculates the degree of permanence of subregions of the gene by dividing it into segments, c codons long, counting how many sites remain unchanged in each segment among all species compared. By comparing the base permanence among several sequences with the expectations based on a stochastic evolutionary process, gene regions showing different degrees of conservation can be selected. This means that wherever the permanence deviates significantly from the expected value generated by the simulation, the corresponding regions are considered "constrained" or "hypervariable". The constrained regions are of two types: alpha and beta. The alpha regions result from constraints at the amino acid level, whereas the beta regions are those probably involved in "control" processing. The method has been applied to mitochondrial genes coding for subunit 6 of the ATPase and subunit 1 of the cytochrome oxidase in four mammalian species: human, rat, mouse, and cow. In the two mitochondrial genes a few regions that are highly conserved in all codon positions have been identified. Among these regions a sequence, common to both genes, that is complementary to a strongly conserved region of 12S rRNA has been found. This method can also be of great help in studying molecular evolution mechanisms.

Amino Acid Sequence↗
PubMed1984

Cloning of mitochondrial DNA from Paracentrotus lividus.

In order to study the gene organization and sequence of the mt DNA from sea urchin Paracentrotus lividus, we have cloned the two Bam HI fragments of 12 Kb and 4 Kb in the plasmid vectors pAT 153 and pBR 322 respectively. The cloning has been tested by hybridizing the DNA extracted from the recombinant plasmids with sea urchin mt DNA and by comparing the restriction patterns of the cloned fragments with those shown by fragment isolated from sea urchin mt DNA. This has allowed the determination of the size of sea urchin mt DNA that results to be about 15.000 base pairs, similar to that already reported for other animal mt DNA.

Animals↗
PubMed1984

Determination of some mitochondrial RNAs concentration in adult rat liver.

A method has been developed to accurately measure steady state concentrations of mitochondrial transcripts in adult rat liver. Total mitochondrial RNA has been hybridized with an excess of labelled mitochondrial DNA fragments coding for a single gene or a piece of it. The results obtained show that each mitochondrion contains 36 molecules of 16S rRNA, 81 of 12S rRNA and about 8 molecules of mRNAs coding for identified and unidentified reading frames. Thus, the rRNA/mRNA ratio in rat liver differs from that reported in HeLa cell mitochondria. These results are discussed in the light of mitochondrial DNA transcription regulation.

Animals↗
PubMed1984

A new method for calculating evolutionary substitution rates.

In this paper we present a new method for analysing molecular evolution in homologous genes based on a general stationary Markov process. The elaborate statistical analysis necessary to apply the method effectively has been performed using Monte Carlo techniques. We have applied our method to the silent third position of the codon of the five mitochondrial genes coding for identified proteins of four mammalian species (rat, mouse, cow and man). We found that the method applies satisfactorily to the three former species, while the last appears to be outside the scope of the present approach. The method allows one to calculate the evolutionarily effective silent substitution rate (vs) for mitochondrial genes, which in the species mentioned above is 1.4 X 10(-8) nucleotide substitutions per site per year. We have also determined the divergence time ratios between the couples mouse-cow/rat-mouse and rat-cow/rat-mouse. In both cases this value is approximately 1.4.

Animals↗
PubMed1984

Transport of proteins into mitochondria.

There is still much that is obscure concerning the transport of proteins into or through the mitochondrial membrane systems. In addition, as pointed out previously, it is unlikely that the details of the process are the same for proteins destined for different compartments of the organelle. A brief summary of the process for matrix proteins might be as follows: The proteins are synthesized on free polysomes as precursors of higher molecular weight than the native forms. These precursors are liberated into the cell cytosol and subsequently translocated into the mitochondria. This timing might be different in yeast under some circumstances, synthesis being completed in association with the mitochondria. The precursors interact with a receptor in the outer mitochondrial membrane interaction being mediated by the presequences of the precursors. The presequences therefore act as addressing signals as well as possibly playing a role in one or all of (a) solubilization of precursors, (b) prevention of premature assembly into multimeric structures, or (c) maintenance of nonnative configurations required for transport. Interaction occurs with a second receptor, this time in the inner membrane of the mitochondria, interaction being with multiple sites in the polypeptide chain. Transport across the inner membrane then occurs, this transport depending on a transmembrane electrochemical gradient of which the proton component is the essential part. Transport is accompanied or followed by proteolysis of the prepiece, and formation of the native structure. While steps 1 and 2 of this sequence can be considered well established, the remaining steps are still poorly understood or purely hypothetical. Nevertheless, this sequence of events is consistent with known facts about the process and provides a framework for future investigations.

Animals↗