Adapting to life at the end of the line: How Drosophila telomeric retrotransposons cope with their job

Abstract

Drosophila telomeres are remarkable because they are maintained by telomere-specific retrotransposons, rather than the enzyme telomerase that maintains telomeres in almost every other eukaryotic organism. Successive transpositions of the Drosophila retrotransposons onto chromosome ends produce long head-to-tail arrays that are analogous in form and function to the long arrays of short repeats produced by telomerase in other organisms. Nevertheless, Drosophila telomere repeats are retrotransposons, complex entities three orders of magnitude longer than simple telomerase repeats. During the >40-60 My they have been coevolving with their host, these retrotransposons perforce have evolved a complex relationship with Drosophila cells to maintain populations of active elements while carrying out functions analogous to those of telomerase repeats in other organisms. Although they have assumed a vital role in maintaining the Drosophila genome, the three Drosophila telomere-specific elements are non-LTR retrotransposons, closely related to some of the best known non-telomeric elements in the Drosophila genome. Thus, these elements offer an opportunity to study ways in which retrotransposons and their host cells can coevolve cooperatively. The telomere-specific elements display several characteristics that appear important to their roles at the telomere; for example, we have recently reported that they have evolved at least two innovative mechanisms for protecting essential sequence on their 5'ends. Because every element serves as the end of the chromosome immediately after it transposes, its 5'end is subject to chromosomal erosion until it is capped by a new transposition. These two mechanisms make it possible for at least a significant fraction of elements to survive their initial time as the chromosome end without losing sequence necessary to be competent for subsequent transposition. Analysis of sequence from >90 kb of assembled telomere array shows that these mechanisms for small scale sequence protection are part of a unified set which maintains telomere length homeostasis. Here we concentrate on recently elucidated mechanisms that have evolved to provide this small scale 5' protection.

Figure 1

Model for the extension of chromosomes by telomere-specific retrotransposons. Arrows represent the head-to-tail array of complete and 5′truncated HeT-A (blue) and TART (green) that makes up the telomere. (Actual telomeres typically have more elements than shown here). Transcription of an element in the array provides sense strand RNA (wavy magenta line) that is translated in the cytoplasm to yield Gag protein. This protein associates with the RNA and delivers it to the chromosome end where the RNA is reverse-transcribed onto the chromosome. Analogy with retroviruses suggests that reverse transcriptase is included in the Gag-RNA complex; however there is no evidence on this point. Magenta (A)_n, 3′ poly(A) tail of RNA; black (A)_n, oligoA at 3′end of each element in chromosomal DNA. This results from reverse transcriptase beginning DNA synthesis within the poly(A) tail of the RNA. Those oligoA terminations vary in length but are generally much shorter than their parent poly(A) tails. Modified from reference by copyright permission of the Rockefeller University Press.

Figure 2

Mechanisms for adding buffering 5′ sequence to transposing elements. (A) Using sequence copied from upstream neighbor. Used by HeTA^mel and TART^vir. Telomere segment with a complete HeT-A^mel flanked by other elements (top) and TART^vir (bottom) flanked by other elements. (Other elements are shown as gray when they could be either HeT-A or TART, but note that for these elements the immediately upstream element must be a sister element to provide a transcription start site). HeT-A^mel UTRs are magenta with lighter box at 5′end of 5′UTR representing string of variably truncated Tags. TART^vir UTRs are lavender with darker box on 5′UTR representing Tag string. For both elements transcription starts at the bent arrow in the upstream element and continues through the complete downstream element. The resulting RNA (black line) has a new Tag consisting of the last nucleotides of the upstream element (short colored line and (A)_n on 5′end of RNA). When the RNA is reverse transcribed onto the chromosome this new Tag becomes the 5′end of the newly transposed element, undergoes erosion, and if the element transposes again, will be internalized into the string of variably eroded Tags indicated by the 5′ box on the complete element. (B) Using sequence copied from the 3′UTR of transposing RNA. Used by TART^mel. Telomere segment with a complete TART^mel (purple UTRs) flanked by other elements (gray boxes). (A)_n, 3′ oligoA in DNA; AAAAAA, 3′polyA tail on RNA; Gold arrows, PNTRs. Transcription starts at the bent arrow, producing an RNA with a very short 5′UTR. When this is reverse transcribed onto the chromosome end, the reverse transcriptase jumps back to identical sequence in the 3′ UTR and copies sequence to extend the 5′UTR, providing sacrificial DNA to buffer essential 5′ sequence.