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Marco Archetti

Publications and source records attributed to Marco Archetti.

8 recordsLinked to original sources
PubMed2006

The evolution of the genetic code took place in an anaerobic environment.

We have compared orthologous proteins from an aerobic organism, Cytophaga hutchinsonii, and from an obligate anaerobe, Bacteroides thetaiotaomicron. This comparison allows us to define the oxyphobic ranks of amino acids, i.e. a scale of the relative sensitivity to oxygen of the amino acid residues. The oxyphobic index (OI), which can be simply obtained from the amino acids' oxyphobic ranks, can be associated to any protein and therefore to the genetic code, if the number of synonymous codons attributed to the amino acids in the code is assumed to be the frequency with which the amino acids appeared in ancestral proteins. Sampling of the OI variable from the proteins of obligate anaerobes and aerobes has established that the OI value of the genetic code is not significantly different from the mean OI value of anaerobe proteins, while it is different from that of aerobe proteins. This observation would seem to suggest that the terminal phases of the evolution of genetic code organization took place in an anaerobic environment. This result is discussed in the framework of hypotheses suggested to explain the timing of the evolutionary appearance of the aerobic metabolism.

Amino Acid Substitution↗
PubMed2006

Autumn colours and the nutrient retranslocation hypothesis: a theoretical assessment.

The adaptive value of the bright colours of leaves in autumn is still debated. It is possible that autumn colours are an adaptation to protect the tree against photoinibition and photooxidation, which allows a more efficient recovery of nutrients. It has been proposed that the preference of aphids for trees that retranslocate nitrogen more efficiently can explain the high diversity of aphids on tree species with bright autumn colours. This scenario however does not take into account the impact of insects on the fitness of the trees and has not been analysed theoretically. Its assumptions and predictions, therefore, remain uncertain. I show with a model of insect-tree interaction that the system can actually evolve under particular conditions. I discuss the differences with the coevolution theory of autumn colours, available evidence and possible tests.

Adaptation, Physiological↗
PubMed2004

The coevolution theory of autumn colours.

According to the coevolution theory of autumn colours, the bright colours of leaves in autumn are a warning signal to insects that lay their eggs on the trees in that season. If the colour is linked to the level of defensive commitment of the tree and the insects learn to avoid bright colours, this may lead to a coevolutionary process in which bright trees reduce their parasite load and choosy insects locate the most profitable hosts for the winter. We try to clarify what the theory actually says and to correct some misunderstandings that have been put forward. We also review current research on autumn colours and discuss what needs to be done to test the theory.

Animals↗
PubMed2004

Codon usage bias and mutation constraints reduce the level of error minimization of the genetic code.

Studies on the origin of the genetic code compare measures of the degree of error minimization of the standard code with measures produced by random variant codes but do not take into account codon usage, which was probably highly biased during the origin of the code. Codon usage bias could play an important role in the minimization of the chemical distances between amino acids because the importance of errors depends also on the frequency of the different codons. Here I show that when codon usage is taken into account, the degree of error minimization of the standard code may be dramatically reduced, and shifting to alternative codes often increases the degree of error minimization. This is especially true with a high CG content, which was probably the case during the origin of the code. I also show that the frequency of codes that perform better than the standard code, in terms of relative efficiency, is much higher in the neighborhood of the standard code itself, even when not considering codon usage bias; therefore alternative codes that differ only slightly from the standard code are more likely to evolve than some previous analyses suggested. My conclusions are that the standard genetic code is far from being an optimum with respect to error minimization and must have arisen for reasons other than error minimization.

Base Composition↗
PubMed2004

Selection on codon usage for error minimization at the protein level.

Given the structure of the genetic code, synonymous codons differ in their capacity to minimize the effects of errors due to mutation or mistranslation. I suggest that this may lead, in protein-coding genes, to a preference for codons that minimize the impact of errors at the protein level. I develop a theoretical measure of error minimization for each codon, based on amino acid similarity. This measure is used to calculate the degree of error minimization for 82 genes of Drosophila melanogaster and 432 rodent genes and to study its relationship with CG content, the degree of codon usage bias, and the rate of nucleotide substitution. I show that (i) Drosophila and rodent genes tend to prefer codons that minimize errors; (ii) this cannot be merely the effect of mutation bias; (iii) the degree of error minimization is correlated with the degree of codon usage bias; (iv) the amino acids that contribute more to codon usage bias are the ones for which synonymous codons differ more in the capacity to minimize errors; and (v) the degree of error minimization is correlated with the rate of nonsynonymous substitution. These results suggest that natural selection for error minimization at the protein level plays a role in the evolution of coding sequences in Drosophila and rodents.

Amino Acids↗
PubMed2003

A selfish origin for recombination.

Recent findings of molecular biology show that recombination is initiated by interactions between homologous chromosomes and that an allele can induce the initiation of recombination on the homolog. Since gene conversion at the site of initiation is strong enough to promote the transmission of that allele, recombination may be a way for a self-promoting element to spread, even if it gives no advantage to the individual or to the population. I develop a simple model and discuss available molecular evidence in support of this hypothesis. A consequent argument is that with asexual reproduction the evolution of recombination leads to an intragenomic conflict, and a possible outcome of this conflict may be the origin of sexual reproduction.

Animals↗