Origin of noncoding DNA sequences: molecular fossils of genome evolution.

Abstract

The total amount of noncoding sequences on chromosomes of contemporary organisms varies significantly from species to species. We propose a hypothesis for the origin of these noncoding sequences that assumes that (a) an -0.55-kilobase (kb)-long reading frame composed the primordial gene and (it) a 20-kb-long single-stranded polynucleotide is the longest molecule (as a genome) that was polymerized at random and without a specific template in the primordial soup/cell. The statistical distribution of stop codons allows examination of the probability of generating reading frames of =0.55 kb in this primordial polynucleotide. This analysis reveals that with three stop codons, a run of at least 0.55-kb equivalent length of nonstop codons would occur in 4.6% of 20-kb-long polynucleotide molecules. We attempt to estimate the total amount of noncoding sequences that would be present on the chromosomes of contemporary species assuming that present-day chromosomes retain the prototype primordial genome structure. Theoretical estimates thus obtained for most eukaryotes do not differ significantly from those reported for these specific organisms, with only a few exceptions. Furthermore, analysis of possible stop-codon distributions suggests that life on earth would not exist, at least in its present form, had two or four stop codons been selected early in evolution.

Statistical analysis and prediction of the exonic structure of human genes

“…Genes evolved by exon shuffling should have most introns belonging to the same class (Patthy 1987). It was shown that the exon size is distributed approximately as the size of open reading frames in random sequences (Senapatby 1986;Naora et al 1987;Smith 1988;H6glund et al 1990), although the observations on exon lengths are not stable and depend on the sample (e.g., cf. results by Deacon 1982 andby Hawkins 1988;Smith 1988;H6glund et al 1990).…”

The role of metal ions in biological oxidation - the past and the present

“…They directly protect metal ions within the cell, as well as the extracellular proteins, albumin and transferrin, which are essential for metal transport in blood. Metal ions are also responsible for controlling the expression of these proteins in cells (Naora et al 1987, Ayensu and Tchounwou 2006, Mounicou et al 2009, Mü ller 2010.…”

“…Metal ions are often responsible for the damage and protection of biological systems (Dovinová et al 1999). Fenton and the Fenton-like reactions can play a central role the oxidative stress and can be catalyzed by transition metal ions and their complexes (Naora et al 1987, Kleczkowski et al 2002, Ayensu and Tchounwou 2006, Hud 2008, Mounicou et al 2009, Mü ller 2010.…”

Detection of fundamental principles and a level of order for large-scale gene clustering on the Escherichia coli chromosome

“…(17) Naora et al (1987) reported that the relationship between the total sizes of noncoding DNA sequences and the genome sizes of contemporary eukaryotic chromosomes was linear log-log. They proposed that noncoding region size could be approximated by m = N(20-0.55) kb, where N was an estimate of the total number of genes in a genome, and (20--0.55) kb was an estimate of noncoding region length in a postulated primordial chromosome.…”

“…By inspection of their data (Fig. 1, Naora et al 1987), we inferred the relationship shown by equation 13, log(NS) = odog(GS)…”