Trends in Genetics
Volume 22, Issue 5, May 2006, Pages 260-267
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Do transposable elements really contribute to proteomes?

https://doi.org/10.1016/j.tig.2006.03.006Get rights and content

Recent studies indicate that the initial classification of transposable elements (TEs) as ‘useless’, ‘selfish’ or ‘junk’ pieces of DNA is not an accurate one. TEs seem to have complex regulatory functions and contribute to the coding regions of many genes. Because this contribution had been documented only at transcript level, we searched for evidence that would also support the translation of TE cassettes. Our findings suggest that the proportion of proteins with TE-encoded fragments (∼0.1%), although probably underestimated, is much less than what the data at transcript level suggest (∼4%). In all cases, the TE cassettes are derived from old TEs, consistent with the idea that incorporation (exaptation) of TE fragments into functional proteins requires long evolutionary periods. We therefore argue that functional proteins are unlikely to contain TE cassettes derived from young TEs, the role of which is probably limited to regulatory functions.

Introduction

It is widely accepted that transposable elements (TEs; see Glossary) have had a major impact on the evolution of mammalian genomes. A well-documented example is that of the human genome, almost half of its sequence being derived from TEs [1]. TEs were initially regarded as ‘junk’ [2], ‘selfish’, and ‘parasite’ pieces of DNA 3, 4, 5. Gradually, scientists realized that TEs should be regarded as ‘seeds of evolution’ [6] and ‘genomic treasures’ [7] because they seem to enhance the organisms' evolvability in many ways. TEs are active genomic components that can promote recombination 8, 9 and provide ready-to-use motifs, such as transcriptional regulatory elements, polyadenylation and splicing signals, and even protein coding sequences 10, 11, 12, 13, 14.

The contribution of TEs to coding regions is of particular interest, because they can directly influence the phenotype by altering protein sequences. This aspect was documented, however, only at the transcript level, and the presence of TE-encoded fragments was not confirmed at the protein level [15]. Because of the important evolutionary implications, we attempted to clarify the issue of TE contribution to metazoan proteomes using computational methods and publicly available data by searching for TE cassettes in functionally well-characterized proteins. We found evidence indicating that functional proteins can indeed contain TE cassettes, but only those derived from old TEs. Those derived from young TEs, such as Alu short interspersed elements (SINEs) and L1 long interspersed elements (LINE1s), seem to disrupt the functionality of the proteins into which they are inserted.

Section snippets

TE fragments were found in coding regions of many transcripts but not in functional proteins

More than a decade ago, a few studies reported that some mRNAs contain TE cassettes in their coding regions 16, 17, 18 that sometimes resulted in disease phenotypes such as the gyrate atrophy of the choroid and retina [19]. These observations led to the hypothesis that, in other cases, TE exaptation could have neutral effects or even enhance fitness and, therefore, might increase protein variability with positive evolutionary consequences [20]. Since then, several studies discovered TE

Identifying proteins with TE-encoded fragments

We searched for TE cassettes only in functionally well-characterized proteins, to eliminate the uncertainty of translation associated with most transcripts (see the online supplementary material for more details). Among the 3764 Protein Databank (PDB; http://www.rcsb.org/pdb/) entries with non-redundant protein chains, we found only 24 proteins with fragments encoded by putative TE cassettes (Tables 1, S1 in the online supplementary material). No additional examples were identified in the

TE exaptation: when did it happen?

A second argument supporting the validity of the L3 cassette is provided by the origin of PTPN1. It is known that PTP diversification occurred by a series of duplication events during early vertebrate evolution 37, 38, 39. This can explain why PTPN1 is located ∼7.3-Mb apart from PTPRT on chromosome 20q, similar to their closest homologs, PTPN2 and PTPRM, respectively (Ref. [39]; Figure 2), which are located ∼4.4-Mb-apart on chromosome 18p. The most likely scenario is that an intra-chromosomal

TE exaptation: how did it happen?

According to Ohno [40], gene duplications create the raw material for evolutionary ‘innovations’. He argues that newly duplicated genes are free of functional constraints and can undergo significant changes until they acquire new specific functions. Provided that duplications are the documented source for PTP diversification as discussed earlier, it is easy to imagine that the future PTPN1 could have easily acquired a TE fragment after the activation of a cryptic splice site in a manner similar

Concluding remarks and directions for further research

The confirmation that TEs are present at the protein level is by no means a surprise, and they are certainly not the only category of DNA sequence to be exapted successfully into functional proteins. Hayashi et al. showed that any random sequence could acquire biological functions if it had sufficient time to evolve [43]. It is, however, their prevalence and mobility within genomes that make TEs important players in molecular and genomic evolution.

Acknowledgements

We thank Dimitra Chalkia for her contribution to the construction of MME and ARFIP2 phylogenies, and her constructive criticisms on the initial versions of the article. We are grateful to Vamsi Veeramachaneni for setting up the initial protein data set; to Jordi Bella and Paul McEwan for their help with protein structure visualization tools; to Nikolas Nikolaidis, Jongmin Nam and Arthur Lesk for critically reading the article; and to the reviewers for their useful comments and suggestions. V.G.

Glossary

Transposable elements (TEs):
all DNA segments that have the ability to move or multiply within genomes generating self-copies interspersed with non-repetitive DNA. The term is often used for referring to copies of such elements that lost the ability to move or multiply once integrated at a new genomic location because of either mutation or fragmentation. For those segments, ‘TE-derived sequences’ or ‘transposed elements’ would better describe the current status of the sequence. The more general

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