Back to the Soil: Retroviruses and Transposons

Abstract

Transposable elements (TEs) have exerted an impact on genome evolution that is at once substantial and fundamental. They have promoted phenotypic diversity because of their potential for effecting genetic alteration in a great variety of settings and with significant magnitude. Both ancient and omnipresent, TEs can benefit lineages while simultaneously proving detrimental to some individuals. Transposable elements play reformatting, building, and sculpting roles as they effect changes in the genome through both direct and indirect means. Thus, their impact on soil microbes can be substantial. As short DNA sequences, TEs possess the capability to migrate between diverse sites within the genome, a capacity that enables them to promote genomic mutations in a number of ways, ranging from the most limited regulatory mutations to the most extensive rearrangements of the genome. Scientists who pioneered the original discovery of TEs announced their potential roles in genomic adaptation, which was sharply contested by other theorists. Such was the misunderstanding of the beneficial roles of TEs that for over two decades they were regarded almost exclusively in a negative light as genome-damaging intragenomic parasites. A major watershed in TE research came when the Drosophila melanogaster genome was sequenced, which unleashed unprecedented analysis of TEs. This path breaking investigation resulted in the initial identification of TE-produced adaptations in Drosophila melanogaster. Subsequent studies illuminated the fundamental contributions of TEs in the processes of adaptive evolution. This important inference was the product of a methodical search of the entire genome that focused on adaptive insertions that resulted from TEs.

Appendix

Abbreviation	Term	Meaning
Ago	Argonaute protein	The catalytic core of RISC that binds short RNAs and, in many cases, displays RNase H-like mRNA-cleaving activity. Key domains include the PAZ (Piwi-Argonaute-Zwille) and Piwi domains. Ago is named after an Arabidopsis developmental mutant that resembles the tentacles of a paper nautilus (Argonautidae)
Dcr	Dicer protein	The RNase-III family ribonuclease that cleaves dsRNA into short RNAs. Key domains include a helicase C-terminal domain, dsRNA-binding domains, a PAZ domain and two RNase-III domains. Named for its “dicing” activity
dsRNA	Double-stranded RNA	Small double-stranded RNAs are the basic molecules involved in gene silencing, gene regulation and viral defense
endo-siRNA	Endogenous siRNA	A short RNA (other than an miRNA) that is derived from the host genome, rather than an exogenous source (e.g. a virus)
IS	Insertional sequences	The most basic of transposable element forms, which are part of practically every bacterial genome, are the insertion sequences
miRNA	microRNA	Single-stranded RNAs of 21–22 nt, derived from short fold-back hairpins (pre-miRNAs) and involved in translational control
piRNA	Piwi-interacting RNA	Single-stranded RNAs of 24–29 nt that function in complex with Piwi family Argonaute proteins in the animal germ line
rasiRNA	Repeat-associated siRNA	Short RNAs derived from repeat sequences, such as TEs, sometimes considered a subclass of piRNAs in Drosophila
RdRp	RNA-dependent RNA polymerase	RNA polymerase directed by RNA, especially eukaryotic polymerases involved in the amplification of RNAi in nematodes and plants
RISC	RNA-induced silencing complex	The complex comprising Argonaute, a short RNA, and several other proteins, which mediates RNAi through sequence-specific complementarity
RNAi	RNA interference	The class of processes that use short single-stranded RNA molecules in complex with an Argonaute protein to bind complementary nucleic acids and modify their action and/or processing
siRNA	Short interfering RNA	Single-stranded RNAs of 20–30 nt involved in RNAi (especially those not classed as microRNAs)
ncRNA	Small noncoding RNA	Small noncoding RNAs play a crucial role in molecular immunity based on sequence homology
SRNA	Small nucleolar-like RNA	The pre-RNA that are several hundred to thousand or so bp long and contain hairpin structure. These molecules are cut into smaller size and exported to cytoplasm by Exportin-5. Subsequently they take the shape of siRNA
TE	Transposable element	A stretch of DNA capable of moving around the genome, either by excision (cut-and-paste transposons) or through an RNA intermediate (retro-elements)
UTR	Untranslated region	Nonprotein-coding regions at the 5′ and 3′ ends of an mRNA
viRNA	Viral RNA	siRNAs derived from viral sequences
VSR	Viral suppressor of RNAi	Any viral gene that inhibits host RNAi function