Transposable elements: possible catalysts of organismic evolution

doi:10.1016/S0169-5347(00)89012-6

Trends in Ecology & Evolution

Volume 10, Issue 3, March 1995, Pages 123-126

https://doi.org/10.1016/S0169-5347(00)89012-6 Get rights and content

Abstract

Mutation is the ultimate source of all genetic variation in natural populations and is generally considered a prerequisite for evolution. Although transposable elements are acknowledged as a major source of spontaneous mutations, the evolutionary significance of these mobile pieces of DNA remains the subjects of some debate. In this perspective, I discuss the biology of transposable elements with particular emphasis on their potential to produce mutations that have dramatic effecs on organismic evolution.

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Cited by (108)

Distribution patterns and impact of transposable elements in genes of green algae
2016, Gene
Citation Excerpt :
The preeminent feature of mobile elements in the evolutionary question is related with their transposition capability. In fact, as a result of a TE insertion, genes might have their structure or regulation modified, as well can be induced to silence or function disruption (Feschotte, 2008; Jurka et al., 2007; Kazazian, 2004; Levin and Moran, 2011; McDonald, 1995). Despite the likely deleterious effect, a TE insertion into coding region might change or adapt the original function of the gene in an advantageous manner (Krom et al., 2007; Lopes et al., 2008; Nekrutenko and Li, 2001).
Transposable elements (TEs) are DNA sequences able to transpose in the host genome, a remarkable feature that enables them to influence evolutive trajectories of species. An investigation about the TE distribution and TE impact in different gene regions of the green algae species Chlamydomonas reinhardtii and Volvox carteri was performed. Our results indicate that TEs are very scarce near introns boundaries, suggesting that insertions in this region are negatively selected. This contrasts with previous results showing enrichment of tandem repeats in introns boundaries and suggests that different evolutionary forces are acting in these different classes of repeats. Despite the relatively low abundance of TEs in the genome of green algae when compared to mammals, the proportion of poly(A) sites derived from TEs found in C. reinhardtii was similar to that described in human and mice. This fact, associated with the enrichment of TEs in gene 5′ and 3′ flanks of C. reinhardtii, opens up the possibility that TEs may have considerably contributed for gene regulatory sequences evolution in this species. Moreover, it was possible identify several instances of TE exonization for C. reinhardtii, with a particularly interesting case from a gene coding for Condensin II, a protein involved in the maintenance of chromosomal structure, where the addition of a transposomal PHD finger may contribute to binding specificity of this protein. Taken together, our results suggest that the low abundance of TEs in green algae genomes is correlated with a strict negative selection process, combined with the retention of copies that contribute positively with gene structures.
Characterization of arrangement and expression of the beta-2 microglobulin locus in the sandbar and nurse shark
2010, Developmental and Comparative Immunology
Beta 2 microglobulin (β2m) is an essential subunit of major histocompatibility complex (MHC) type I molecules. In this report, β2m cDNAs were identified and sequenced from sandbar shark spleen cDNA library. Sandbar shark β2m gene encodes one amino acid less than most teleost β2m genes, and 3 amino acids less than mammal β2m genes. Although sandbar shark β2m protein contains one β sheet less than that of human in the predicted protein structure, the overall structure of β2m proteins is conserved during evolution. Germline gene for the β2m in sandbar and nurse shark is present as a single locus. It contains three exons and two introns. CpG sites are evenly distributed in the shark β2m loci. Several DNA repeat elements were also identified in the shark β2m loci. Sequence analysis suggests that the β2m locus is not linked to the MHC I loci in the shark genome.
The adaptive role of transposable elements in the Drosophila genome
2009, Gene
Transposable elements (TEs) are short DNA sequences with the capacity to move between different sites in the genome. This ability provides them with the capacity to mutate the genome in many different ways, from subtle regulatory mutations to gross genomic rearrangements. The potential adaptive significance of TEs was recognized by those involved in their initial discovery although it was hotly debated afterwards. For more than two decades, TEs were considered to be intragenomic parasites leading to almost exclusively detrimental effects to the host genome. The sequencing of the Drosophila melanogaster genome provided an unprecedented opportunity to study TEs and led to the identification of the first TE-induced adaptations in this species. These studies were followed by a systematic genome-wide search for adaptive insertions that allowed for the first time to infer that TEs contribute substantially to adaptive evolution. This study also revealed that there are at least twice as many TE-induced adaptations that remain to be identified. To gain a better understanding of the adaptive role of TEs in the genome we clearly need to (i) identify as many adaptive TEs as possible in a range of Drosophila species as well as (ii) carry out in-depth investigations of the effects of adaptive TEs on as many phenotypes as possible.
Spip and Squiq, two novel rice non-autonomous LTR retro-element families related to RIRE3 and RIRE8
2007, Plant Science
Transposable elements are the main components of complex genomes. Their impact on the genomes in terms of structural changes during evolution is thus one of the main focuses of today's structural genomics. Although non-autonomous transposable elements have been known for a long time, their contribution to genome evolution is poorly understood. Our present study describes two new non-autonomous LTR retrotransposons in the rice (Oryza sativa L) genome, Spip and Squiq, the LTR of which are closely related to those of the gypsy-like RIRE3 and RIRE8 LTR retrotransposon families, respectively, but the internal region of which is completely different and harbours none of the characteristic coding domains of LTR retrotransposons. Spip and Squiq thus belong to the class of LArge Retrotransposon Derivatives (LARDs).
A phylogenetic study based on the sequence alignment of the LTRs of Spip/RIRE3, and of Squiq/RIRE8 show that both Spip and Squiq elements are of monophyletic origin. In addition, the estimation of the date of insertion of the copies suggests that Spip and Squiq families are of recent origin (that is, they amplified mainly within the last 2 My).
Spip and Squiq are the fourth and fifth LARD families to be described in the rice genome, suggesting that this type of sequences is not rare. Moreover, these two families appear to be as numerous as their autonomous counterparts, suggesting that they have played an equivalent role in the recent history of rice.
Cloning of a CACTA transposon-like insertion in intron I of tomato invertase Lin5 gene and identification of transposase-like sequences of Solanaceae species
2006, Journal of Plant Physiology
Very few CACTA transposon-like sequences have been described in Solanaceae species. Sequence information has been restricted to partial transposase (TPase)-like fragments, and no target gene of CACTA-like transposon insertion has been described in tomato to date. In this manuscript, we report on a CACTA transposon-like insertion in intron I of tomato (Lycopersicon esculentum) invertase gene Lin5 and TPase-like sequences of several Solanaceae species. Consensus primers deduced from the TPase region of the tomato CACTA transposon-like element allowed the amplification of similar sequences from various Solanaceae species of different subfamilies including Solaneae (Solanum tuberosum), Cestreae (Nicotiana tabacum) and Datureae (Datura stramonium). This demonstrates the ubiquitous presence of CACTA-like elements in Solanaceae genomes. The obtained partial sequences are highly conserved, and allow further detection and detailed analysis of CACTA-like transposons throughout Solanaceae species. CACTA-like transposon sequences make possible the evaluation of their use for genome analysis, functional studies of genes and the evolutionary relationships between plant species.
Heat-shock promoters: Targets for evolution by P transposable elements in Drosophila
2006, PLoS Genetics
Transposable elements are potent agents of genomic change during evolution, but require access to chromatin for insertion—and not all genes provide equivalent access. To test whether the regulatory features of heat-shock genes render their proximal promoters especially susceptible to the insertion of transposable elements in nature, we conducted an unbiased screen of the proximal promoters of 18 heat-shock genes in 48 natural populations of Drosophila. More than 200 distinctive transposable elements had inserted into these promoters; greater than 96% are P elements. By contrast, few or no P element insertions segregate in natural populations in a “negative control” set of proximal promoters lacking the distinctive regulatory features of heat-shock genes. P element transpositions into these same genes during laboratory mutagenesis recapitulate these findings. The natural P element insertions cluster in specific sites in the promoters, with up to eight populations exhibiting P element insertions at the same position; laboratory insertions are into similar sites. By contrast, a “positive control” set of promoters resembling heat-shock promoters in regulatory features harbors few P element insertions in nature, but many insertions after experimental transposition in the laboratory. We conclude that the distinctive regulatory features that typify heat-shock genes (in Drosophila) are especially prone to mutagenesis via P elements in nature. Thus in nature, P elements create significant and distinctive variation in heat-shock genes, upon which evolutionary processes may act.
Transposable elements can be a major source of evolutionary change. Their insertion can directly affect the genes into, or next to, which they insert. To insert, however, they must first gain access to the host gene. The authors reasoned that, because the DNA in the promoters (i.e., regulatory regions) of heat-shock genes is unusually accessible, these genes might harbor many transposable elements. With a technique that can detect any insertion into a gene, they discovered more than 200 distinctive transposable elements in the promoter regions of heat-shock genes in fruit flies from the wild—but few or none in the promoter regions of more typical genes. Surprisingly, out of the one hundred kinds of transposable elements in fruit flies, almost all were P elements. P elements are remarkable because they invaded the fruit fly genome only during the last century. These findings imply that the combination of accessible DNA and the recent invasion of P elements have left a distinctive imprint on the promoters of heat-shock genes.

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Trends in Ecology & Evolution

PerspectiveTransposable elements: possible catalysts of organismic evolution

Abstract

Curr. Opin. Genet. Dev.

Mol. Biol.

Mol. Immunol.

Mobile DNA

EMBO J.

Mol. Biol. Evol.

Nucleic Acids Res.

Genet. Res.

Genet. Res.

Annu. Rev. Genet.

Perspective
Transposable elements: possible catalysts of organismic evolution