Stability domains of actin genes and genomic evolution

In eukaryotic genes, the protein coding sequence is split into several fragments, the exons, separated by noncoding DNA stretches, the introns. Prokaryotes do not have introns in their genomes. We report calculations of the stability domains of actin genes for various organisms in the animal, plant, and fungi kingdoms. Actin genes have been chosen because they have been highly conserved during evolution. In these genes, all introns were removed so as to mimic ancient genes at the time of the early eukaryotic development, i.e., before intron insertion. Common stability boundaries are found in evolutionarily distant organisms, which implies that these boundaries date from the early origin of eukaryotes. In general, the boundaries correspond with intron positions in the actins of vertebrates and other animals, but not much for plants and fungi. The sharpest boundary is found in a locus where fungi, algae, and animals have introns in positions separated by one nucleotide only, which identifies a hot spot for insertion. These results suggest that some introns may have been incorporated into the genomes through a thermodynamically driven mechanism, in agreement with previous observations on human genes. They also suggest a different mechanism for intron insertion in plants and animals.

Figure 1

(Color online) Through the mechanism of alternative splicing different RNAs and thus different proteins can be obtained from the same intron-containing DNA sequence. Typically, these different RNAs are synthesized in different tissues. In the example shown here, three different RNAs are formed from the same DNA sequence: exons are colored, while introns are white. (a) Exons are assembled following the same order as in the DNA sequence. (b) Exon 2 is skipped. (c) Exons 2 and 3 are in reversed order compared to the DNA sequence.

Figure 2

(Color online) Melting domains for H. sapiens actins. GenBank entries: (a) NM_001101 (actin $\beta$, ACTB), (b) NM_001100 (actin ${\alpha }_1$, skeletal muscle ACTA1), (c) NM_005159 (actin $\alpha$, cardiac muscle, ACTC1) (d) NM_001613 (actin ${\alpha }_2$, ACTA2) (e) NM_001614 (actin ${\gamma }_1$, ACTG1) (f) NM_001615 (actin ${\gamma }_2$, ACTG2). The sequences have high similarity to those of all other vertebrate actins, for which almost identical melting patterns are found. Hence only human actins are shown as representatives of those of all the vertebrates. In the plots the temperature is on the $x$ axis and the sequence position on the $y$ axis. The thick solid lines separate the low-temperature helix domain from the high-temperature coiled state. Horizontal dashed lines indicate the boundaries of the CDS and the solid lines the intron positions for the given sequence. Arrows point to the intron positions found in homologous sequences.

Figure 3

(Color online) Melting domains for actin genes of D. melanogaster. (a),(b) and C. elegans (c). GenBank entries: (a) NM_169525 (Act87E), (b) NM_079643 (Act88F), and (c) NM_073416. The area descriptions are the same as in Fig. 2.

Figure 4

(Color online) Melting domains for actin sequences of A. thaliana. The area descriptions are the same as in Fig. 2. GenBank entries: (a) M20016 (AAc1), (b) NM_180280 (ACT2), (c) U39480 (ACT3), (d) U27980 (ACT4), (e) U27811 (ACT7), (f) U42007 (ACT8), (g) U27981 (ACT11), (h) U27982 (ACT12), and (i) U37281 (actin 2).

Figure 5

(Color online) Average melting curves from 21 green plant actin genes. The axes of the diagram are swapped compared to those in Figs. 2, 3, 4. The horizontal axis is given in codon position; only the coding sequence is shown. The four vertical lines denote the four major intron positions found to correlate with stability boundaries in vertebrates.

Figure 6

(Color online) Melting domains for actin sequences of fungi. The area descriptions are the same as in Fig. 2. (a) S. cerevisiae (yeast), (b) N. crassa, and (c) C. albicans. GenBank entries: (a) X61502 (Act2), (b) U78026, and (c) X16377 (act1).

Figure 7

Possible scenarios of gene evolution. (I),(II) introns late and (III) introns early perspectives. The scheme (I) is the insertion driven by thermodynamics, supported by the analysis of stability regions reported in this paper. The scheme (II) suggests the appearance of a thermal boundary after intron insertion, a scenario not supported by the results presented in this paper. Finally, the scheme (III) takes into account the introns early perspective, in which the ancient exons had already different stability properties.