Genome complexity: introners and introns (Introduction)

by David Turell , Thursday, March 30, 2023, 18:25 (386 days ago) @ David Turell

A totally new finding, introns everywhere:

https://www.quantamagazine.org/how-a-dna-parasite-may-have-fragmented-our-genes-20230330/

"In their DNA, the information about how to make proteins isn’t laid out in long coherent strings of bases. Instead, genes are split into segments, with intervening sequences, or “introns,” spacing out the exons that encode bits of the protein. When eukaryotes express their genes, their cells have to splice out RNA from the introns and stitch together RNA from the exons to reconstruct the recipes for their proteins.

"The mystery of why eukaryotes rely on this baroque system deepened with the discovery that the different branches of the eukaryotic family tree varied widely in the abundance of their introns. The genes of yeast, for instance, have very few introns, but those of land plants have many. Introns make up almost 25% of human DNA. How this tremendous, enigmatic variation in intron frequency evolved has stirred debate among scientists for decades.

"Answers may finally be emerging, however, from recent studies of genetic elements called introners that some scientists regard as a kind of genomic parasite. These pieces of DNA can slip into genomes and multiply there, leaving profusions of introns behind them. Last November, researchers presented evidence that introners have been doing this in diverse eukaryotes throughout evolution. Moreover, they showed that introners could explain why explosive gains in introns seem to have been particularly common in aquatic forms of life.

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"Because of the introns polka-dotting their DNA, if the genes of eukaryotes were translated directly into proteins, the resulting molecules would typically be nonfunctional garbage. For that reason, all eukaryotic cells are equipped with special genetic shears called spliceosomes. These protein complexes recognize the distinctive sequences that flank intron RNA and remove it from the preliminary RNA transcripts of active genes. Then they splice together the coding segments from exons to produce messenger RNA that can be translated into a working protein. (my bold)

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"Why natural selection in eukaryotes favored introns that needed to be removed by spliceosomes is unknown. But the key might be that such introns allow for alternative splicing, a phenomenon that dramatically increases the diversity of products that can arise from a single gene. When the intron RNA is clipped out, the exon RNA sequences can be strung together in a new order to make slightly different proteins, Corbett-Detig explained. (my bold)

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"The distinctive feature of introners is that they create introns. Introners copy and paste themselves into stretches of coding DNA that offer an appropriate splicing site. Then they move on, leaving behind a specific intron sequence flanked by splicing sites, which splits the coding DNA into two exons. This process can be repeated on a massive scale throughout a genome. In fungi, for example, introners appear to account for most of the intron gain during at least the last 100,000 years.

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"The work by Gozashti and his colleagues proved that introners are not distributed equally among eukaryotes. For example, introners are more than six times as likely to appear in the genomes of aquatic organisms as in those of terrestrial organisms. Moreover, nearly three-quarters of the genomes from aquatic species that contain introners host multiple introner families.

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"Although horizontal gene transfer and introners share a connection to the aquatic environment, the findings don’t yet show definitively that this is where introners come from. But the discovery of introners’ widespread influence does challenge some theories about how genomes — particularly eukaryotic genomes — have evolved.

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"The evolutionary arms race between invading genetic elements and the host may have a hand in generating a more complicated genome. The parasitic elements are in “constant conflict” with genetic elements that belong to the host, Gozashti explained, because they compete for genomic space. “All these moving pieces are constantly driving each other to evolve,” he said.

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"Feschotte thinks that profusions of introns might help drive the evolution of families of genes that can change rapidly. Stuffed with new introns, those genes could co-opt the new variability enabled by alternative splicing. (my bold)

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"Irina Arkhipova, a molecular evolutionary geneticist at the University of Chicago Marine Biological Laboratory, is interested in knowing more about how introners are spreading through the genome at such large scales. “It just leaves no trace of the enzyme that was responsible for this massive burst of mobility — that’s a mystery,” she said. “You basically have to catch it in the act while it’s still moving.”

Comment: my bolds show the increasing facility to make new proteins. A clever arrangement b y God, the designer.
Comment: my bolds show it is a neat trick to form more proteins.