Tuesday, November 3, 2009

Interesting Elements # 2: MINE, WEIRD and MGL

Figure 1. Sizes are relative and not to scale. UTR-untranslated region; APE-apurinic/apyrimidinic endonuclease;RT-reverse transcriptase; RNH-RNase H

This weeks entry deals with several inter-related retrotransposons from the rice blast fungus Magnaporthe grisea, a pathogenic fungus which infects not only rice but other species of plants. Many of the retrotransposons, and DNA transposons, from M. grisea were discovered when researchers were trying to determine the molecular reasons for it's resistance to certain biological counter-measures produced by the plants it infects. Often this was caused by the insertion of various TEs into so-called avirulence genes in the M. grisea genome.

Two SINEs (Short Interspersed Elements) from M. grisea were characterized in 1995, Mg-SINE and Ch-SINE ( Kachroo et al., 1995). The former is around 472 bp long, has a tRNA-derived 5' end and it's 3' end is 99% similar to the 3' end of the LINE element MGL from the same species (Thon et al., 2004). The latter also have a 3' end very similar to MGL which indicates that both SINEs are probably reverse transcribed and inserted into the genome by the proteins MGL encodes (Okada et al., 1997).

So far this story isn't too weird( <---- inadvertent foreshadowing, I swear) because LINE-SINE pairs have been found many times in different genomes. Where it does get weird is with an element discovered several years later named MINE ( Fudal et al., 2005). MINE consists of a non-coding sequence at the 5' end termed WEIRD fused to various 5' truncated MGL elements. Some ~30 individual loci were found, nearly all of which had different truncated MGL elements fused to the standard WEIRD sequence which never varied. How do fusions like this occur you might ask? Well, they are typically thought to occur through a process known as template jumping. A retrotransposon replicates by making a complementary DNA, or cDNA, copy of it's RNA using the reverse transcriptase it encodes. During this process the reverse transcriptase can sometimes jump from one RNA template to another and keep on copying, effectively making a cDNA which is a fusion or chimera of several different RNA templates. If while an MGL element was creating a cDNA itself a WEIRD RNA was close by, the RT could jump from the MGL to the WEIRD and create the fusion product. This gets integrated back into the genome because it has the special sequence of the MGL 3' end and voila, you have a MINE insertion.

The most interesting thing about MINE is the fact that there are so many insertions that seemed to have come from independent template jumping events. Some of the MINE insertions were of the same copy but most of them had unique 5' truncated MGL sequences at their 3'ends, suggesting that for whatever reason this WEIRD sequence keeps getting fused to MGL again, and again and again. They found at least 30 instances of this.

The authors describe finding expressed sequence tags, or ESTs, of WEIRD and MINE elements in the EST database for M. grisea. Basically this means that WEIRD and some MINEs are actually being expressed, like genes would be, by the M. grisea genome. What they couldn't find however were any WEIRD sequences on their own, but this may have been due to the fact that the genome sequence data wasn't complete yet (Gogvadze et al., 2007). They found WEIRD transcripts mainly in cells during the process of infecting a host suggesting that this WEIRD sequence might actually be a functionally important RNA for the fungus. Wherever this WEIRD is coming from it seems that it either has a very high propensity for being fused to MGL or it is present in such high concentrations that the creation of these MINE insertions is very common. Gogvadze et al. also found two other insertion that were due to template jumping composed of, respectively, a WEIRD-Mg-SINE-MGL fusion and a WEIRD-Mg-SINE fusion.

Unlike other instances of template jumping, where the point in the non-LTR sequence where the new sequence begins, in MGL the authors appear to have identified jumping hot spots. They found a preponderance of WEIRD sequences joining MGL sequences near predicted hairpin structures in the MGL mRNA (Gogvadze et al., 2007). They thought that these hairpins might be acting like blocks which stall the RT enzyme just enough so that another template like WEIRD can sneak in.

What interest me about this system is the number of independent fusion events that ocurred. We could be seeing something analogous to the initial formative steps of something like a new SINE, although we can't exactly call it a Short Interspersed Element, and Long Interspersed is already taken :P If certain insertions can make full-length transcripts and can continue to parasitize the proteins of MGL with enough frequency and efficiency it very well could be.

Fudal, I., H.U. Böhnert, D. Tharreau, and M.-H. Lebrun. 2005. Transposition of MINE, a composite retrotransposon, in the avirulence gene ACE1 of the rice blast fungus Magnaporthe grisea. Fungal Genetics and Biology 42: 761-772.

Gogvadze, E., C. Barbisan, M.-H. Lebrun, and A. Buzdin. 2007. Tripartite chimeric pseudogene from the genome of rice blast fungus Magnaporthe grisea suggests double template jumps during long interspersed nuclear element (LINE) reverse transcription. BMC Genomics 8: 10.1186/1471-2164-1188-1360.

Kachroo, P., S.A. Leong, and B.B. Chattoo. 1995. Mg-SINE: A short interspersed nuclear element from the rice blast fungus, Magnaporthe grisea. Proceedings of the National Academy of Sciences of the United States of America 92: 11125-11129.

Okada, N., M. Hamada, I. Ogiwara, and K. Oshima. 1997. SINEs and LINEs share common 3' sequences: a review. Gene 205: 229-243.

Thon, M.R., S.L. Martin, S. Goff, R.A. Wing, and R.A. Dean. 2004. BAC end sequences and a physical map reveal transposable element content and clustering patterns in the genome of Magnaporthe grisea. Fungal Genetics and Biology 41: 657-666.