passages: PMC-2677866-sec-12__text
passages: sec
passages: Nucleotide features of free-standing homing-endonucleases
  Gene control elements were identified for several members of each type of intervening homing endonuclease genes described in this study. In 15 out of 16, 5' untranslated regions of the endonucleases we identified RNA hairpin structures upstream of initiation codons (Figures 1 and 4A). This may be a translational regulatory hairpin structure known from various phage genes, including homing endonucleases (22,47-49). The hairpins we found are in fractured gene loci with different protein host types, including gp41, IMPDH, DnaE, NrdJ and NrdA. Ten of these hairpins also include a conserved sequence of Aeh1 phage late promoter element (TATAAATA), which was recently shown to inhibit the translation of a gene-fracturing endonuclease gene, by sequestering its ribosome binding site (22,23). Analysis of the endonuclease 5' untranslated regions revealed two conserved motifs (Figures 4A and Supplementary Figure S4), which usually complement each other on the stem of the conserved hairpin structures. 
  Figure 4.
  Nucleotide features of endonuclease genes. (A) RNA hairpin structures at the 5' untranslated region of endonuclease ORFs in the gp41-1 (representing the very similar sequences of gp41-1-7), nrdA-5 and DnaE-1 gene loci. Initiator codons are marked by arrows, conserved putative T4 late promoter elements are boxed, and conserved sequence motifs (Supplementary Figure S4) are highlighted in grey. The expected values for motifs 1 and 2 are 1.7-10 and 9.9-3, respectively. RNA structures were calculated using the Vienna package (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi), and sequence motifs were identified using the MEME program. (B) Overlapping#protein coding regions of endonuclease 3' termini and the 5' termini of their downstream genes.
  Additionally, 15 loci included an overlapping region of 6-69 bp between the coding regions of the probable endonuclease C-termini and the downstream N-termini of the split-intein part (Figures 1 and 4B). This overlap is present in both types of endonucleases, and is independent on the presence of a split-intein part in the fractured gene, also occurring in the putative sbcD DNA-repair gene that we found, as well as in the Aeh1 fractured nrdA found by Gibb and Edgell (22).
  