I’ve been working with (or close to) Drosophila transposable elements (TEs) for more than 10 years and at some point after looking at a hundred different TE names that pop up in one analysis or another for the hundredth time, I started wondering why they were called that. Today, I’m starting a series of posts describing the origins of some of the most famous TEs’ discovery and naming. I’ll start with the first identified TEs, but it quickly becomes hard to keep everything strictly chronological, so I’ll follow what feels natural and what best reflects the naming conventions.
Transposons were discovered in maize (McClintock, 1950). In animals, Drosophila became the proving ground once cloning took off in the late 1970s. Two “repeated gene families” were the gateway: copia and 412 (Finnegan et al., 1978). Copia means “plenty” in Latin, and 412 is named after the plasmid clone cDm412 that carried it. The original paper already noticed terminal redundancy in 412 - well before “LTR retrotransposon” became standard parlance.
After that paper, there was a boom in mobile element identification. With this knowledge in place, Gerald Rubin and colleagues were able to pinpoint the P-M hybrid dysgenesis phenomenon to a single repeated mobile element, the P-element. To remind you what hybrid dysgenesis is: researchers identified two D. melanogaster strains that showed unusual behaviour when crossed. If fathers came from the P (paternal) strain and mothers from the M (maternal) strain, the offspring had severe defects such as increased recombination in males (which is in theory impossible, because in this species males do not have crossing over during meiosis) and female sterility. However, if mothers were from P and fathers from M, the offspring were healthy and viable. Rubin and colleagues identified the 2.9 kb P element as the root cause, since removing the P-element abrogated the defects. Not only did the P-element explain the puzzling hybrid dysgenesis, it also became a powerful instrument that let scientists do what they had long wanted to do: clone a gene into a eukaryotic organism. I will make a separate article on the P-element later this year, so I will not go into more detail here.
There is another mobile element that got its name from a dysgenesis system, called I–R dysgenesis. I stands for inducer and R for reactor fly strains. The dysgenesis was described in 1971 by Picard and L’Héritier, and the mobile element, a LINE-like retrotransposon, was later called I or the I-element (Bucheton et al., 1984).
At approximately the same time, in the early 1980s, a group of Soviet scientists in the lab of Georgi Georgiev used the same general approach as Rubin and identified additional mobile genomic elements by clone hybridization with polytene chromosomes. They gave these an unimaginative collective name, mobile dispersed genes: mdg1, mdg2, mdg3, and mdg4.
Later it was shown that mdg2 was actually none other than dm412, so the name was dropped. mdg4 was the last mobile element that got the mdg label (Bayev et al, 1984). It turned out that this was the same TE as gypsy, discovered a year earlier (Modolell, Bender and Meselson, 1983). Since then, even Soviet molecular biologists shifted to more interesting names.
In general, one of the first trends for naming a TE was to use the number of a plasmid or a phage clone from genomic libraries. I already mentioned 412. 297 was found in a library made by Pieter Wensink. 17.6 was found in a phage clone designed to study the histone genes (Kugimiya et al., 1983). 1731 denotes a phage clone used in the screening for ecdysone-modulated genes (Peronnet et al., 1986).
One notable exception is the DNA transposon 1360. Found in the YDm12 clone from the Y-chromosome and published from Igor Zhimulev’s lab as one of the shortest TEs in Drosophila at that time, the naming choice itself is enigmatic (Kholodilov et al., 1988).
That’s it for today. In the next issue, I’m going to talk about TEs with wandering names: hobo, Burdock, rover, and so on.
| Element | Year | Naming reason | Key references |
|---|---|---|---|
| copia | 1978 | Latin “copia” meaning abundance; highly expressed repeated family | Finnegan et al., 1978 (link to pdf) |
| 412 (Dm412) | 1978 | From defining clone cDm412; terminal redundancy noted in original paper | Finnegan et al., 1978 |
| P-element | 1982-1983 | From the P–M dysgenesis system; “P” strain | Bingham, Kidwell & Rubin, 1982 (DOI) |
| I-element | 1984 | From I-R dysgenesis; “Inducer” strain | Bucheton et al., 1984 (DOI) |
| mdg1 to mdg4 | 1980-1984 | “mobile dispersed genes” cataloged in Georgiev’s lab | Ilyin et al., 1980 (DOI); Bayev et al., 1984 (DOI) |
| mdg4 = gypsy | 1983-1984 | gypsy described in 1983; mdg4 published in 1984; same element | Modolell, Bender & Meselson, 1983 (DOI); Bayev et al., 1984 |
| 297 | 1979-1982 | Numeric clone or library identifier (Wensink library) | Potter et al., 1979 (DOI) |
| 17.6 | 1983-1984 | Phage clone near histone genes | Ikenaga & Saigo, 1982 (DOI); Kugimiya et al., 1983 (DOI) |
| 1731 | 1986 | Phage clone 1731 from an ecdysone-regulated screen | Peronnet et al., 1986 (DOI) |
| 1360 (Hoppel) | 1988 | Found in YDm12 Y-chromosome clone; name origin not stated | Kholodilov et al., 1988 (DOI) |