DNA Habitats and its RNA Inhabitants
The shifting perspective from a read-only-memory genome with copying errors to a read- and-write genome with competent change operators is fundamental: For decades it was assumed that driving force of evolution is mutation (error) and selection. Now it is recognized that errors cannot explain genetic novelty and complexity.
A variety of RNA based agents play essential roles in evolution and regulation in all DNA/Protein based life: basic non-coding RNA secondary structures built of (paired) stems and (not-paired) loops. RNA stem-loop swarms such as group I introns, group II introns, viroids, viral (RNA viruses, retrotransposons, LTRs, non-LTRs) and subviral networks (SINEs, LINEs, Alus) cooperate within cellular genomes as modular tools with its abundance of regulatory functions. Some noncoding RNAs built complementary consortia such as rRNAs, tRNAs, spliceosomes, editosomes, and other RNPs. Additionally counterbalancing modules such as toxin/antitoxin (TA) -, restriction/modification (RM) -, and insertion/deletion (INDEL) – modules assure identity (self/non-self) of cells, tissues, organs and even organisms.
Infectious RNAgents manipulate host genomes for (i) selfish replicative purposes or (ii) persistent co-evolutionary integration. The latter in most cases remain as defectives,
i.e. abundance of parts that now serve as co-opted modular tools for cellular needs or as full function elements that regulate complex developmental processes such as placentation in mammals. Also mixed consortia of RNA- and DNA virus-derived parts that integrate in host genomes have been found.
All fine-tuned steps and substeps of key cellular processes such as gene expression, transcription, translation, DNA recombination and repair, epigenetic imprinting (memory, learning), as well as various forms of innate and adaptive immunity are essentially constituted by such natural genetic content operators.
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