Mechanisms for intron loss and gain

           This fifth article, Evolution of the mechanisms of intron loss and gain in the social amoebae Dicytostelium, by Ma et al. looks at introns in a fashion completely different from the previous articles in this blog. The authors wanted to explore the mechanisms of intron loss and gain through Dictyostelium, particularly Dictyostelium discoideum and Dictyostelium purpureum. The authors chose Dictyostelium because it breaks away from the typical mold of eukaryotes studied for introns and it has characteristics that make it useful for studying intron evolution. The first characteristic is the amount of simple sequence repeats (SSRs) and the second being 16 new genes Dictyostelium has acquired from bacteria by horizontal gene transfer.

            The authors wanted to test three possible models from the mechanisms of intron gain or loss. The first is the reverse transcription model, in which introns are deleted from the genome by recombination of cDNA and genomic DNA. The second model is simple genomic deletion, which introns are lost regardless of location on the gene. The third model is one where introns are lost during non-homologous end joining repair of DNA.

            After experimentation, the authors found Dictyostelium discoideum had 441 intron losses and 40 intron gains and Dictyostelium purpureum had 202 intron losses and 58 intron gains. These observations maintain the simple genomic deletion theory but do not support the homologous end joining model for intron loss. Next they wanted to figure out why there was more itron loss in one but not the other. Two explanations based on reverse transcription were tested. The first is that D. discoideum had shorter introns and more suitable for recombination. The second is that D. discoideum had higher reverse transcriptase activity than D. purpureum. The second explanation held up as D. discoideum has many more reverse transcriptase genes than D. purpureum.

            The authors also cited how natural selection can show the variations in intron loss and gain. The two species of Dictyostelium separated hundreds of million years ago meaning that that natural selection selected differently for the unique characteristics of each Dictyostelium.

            The explanation for the intron loss mechanism is explained and studied thoroughly the mechanism for intron gain is cloudier. Finding the source sequences for intron has been incredibly difficult as another study was only able to locate one of seven intron gain source sequences. A possibility for this difficulty is that viruses may have contributed exogenous sequences onto the Dictyostelium, this could explain intron gains without having that sequence in the original DNA strand.

            The authors finished their study by stating that the mechanisms for intron loss are very similar to the mechanisms found in animals and fungi. The intron loss found in Dictyostelium was due to the genomic conversion between genomic DNA and cDNA reverse transcribed from mature mRNA.

            This journal successfully provided mechanisms for intron loss but not for intron gains. Despite the intron gains, this study was a success. It was interesting to see how the authors tied in the mechanisms with natural selection to better explain their findings along the results of their experimentation.

Source

Ma, M., Che, X., Porceddu, A., & Niu, D. (2015). Evolution of the mechanisms of intron loss and gain in the social amoebae Dictyostelium. BMC Evolutionary Biology. 15: 286.