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9. LTR retrotransposons.pdf

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Biology (Sci)
BIOL 200
Richard Roy

Naveen Sooknanan McGill Fall 2011 LTR retrotransposons, LINEs and SINEs: While DNA Transposons move using a “cut and paste mechanism”, LTR retrotransposons move through and RNA intermediate, much like retroviruses.  In fact, retrotransposons use a reverse transcriptase enzyme in order to reincorporate themselves into the genome, which can use RNA or DNA as a template  They have a very small gene length, approximately 6-11 kbp (although they can be considerably larger), and have a very high copy number, almost half a million  LTR retrotransposons can be found in small number in the human genome, but are much more predominant in plant genomes like wheat and flowers The structure of an LTR is almost identical to that of a retrovirus in its proviral form.  They both have noncoding target-site direct repeats at the very ends of the transposon (which are part of the normal genome)  They both also have a protein coding region, although they proteins for which they code are slightly different  They both also contain an LTR region The protein coding region of the retroviral ORF contains a series of exons coding for 5 different polypeptides.  The gag region codes for a group specific antigen  The pol region codes for a polymerase regions which synthesizes various enzymes involved in the transcription process o Within this region, PR codes for protease, RT for reverse transcriptase and IN for integrase o This region form one long mRNA molecule involving all of these polypeptides but are then cleaved post transcriptionally in order to separate the polypeptide chain into functional proteins  The env region codes for an envelope which allows the retrovirus to escape the cell and complete its life cycle The ORF order of an LTR retrotransposon are almost the same as the proviral ORF, except that they have no env region. This means that the LTR retrotransposon is not allowed to leave the cell (i.e. it is not infectious like a retrovirus). Due to the vast similarities between these two species, there is a debate as to which came first in the evolutionary process: LTR retrotransposons or retroviruses.  One argument states that the retroviruses could have entered the host cell (which is possible as there are many retroviruses littering the genome) and lost their env region disabling their infectious properties  The counterargument involves the capturing of an LTR retrotransposon by a host cell (which is not uncommon) and somehow gained an env region from the host cell, thus gaining retroviral properties 1element m Results in golottose Primary transcript Transposed (a) A transposon (b) Retrotransposon Donor DNA element m Results in golottose Primary transcript Transposed (a) A transposon (b) Retrotransposon Donor DNANaveen Sooknanan McGill Fall 2011 o Capturing genes is not uncommon; oncoviruses are capable of capturing host DNA and host enzymes The experiment above proved that LTR retrotransposons move through and RNA intermediate. The engineered plasmids used in this experiment have a Gal responsive Ty (LTR retrotransposon) gene which means the cells only grow in the presence of galactose.  In the first experiment, these plasmids were allowed to grow in a galactose containing medium o As expected, the number of Ty mRNA molecules synthesized increased as well as the number of transposed Ty elements  In the second experiment, an intron extracted from another source was introduced into the Ty region of the plasmid and the same experiment took place o The transposed Ty molecule synthesized, unlike what was expected, did not contain the intron present in the original gene which means mRNA processing must have occurred o The original Ty gene formed a primary transcript containing the intron, but was removed by mRNA slicing and then was reverse transcribed into the transposed element  If the LTR retrotransposon was moved by a DNA intermediate, there would be no mRNA processing and the final transposed element would still contain the intron from the original plasmid The transformation of an LTR retrotransposon’s RNA intermediate into a DNA molecule is exactly the same as that of a retrovirus: The integration of the DNA intermediate of the LTR retrotransposon into the genome is facilitated by the enzyme integrase, which is coded for by the transposon itself.  It inserts it way into the genome the same way that a DNA transposon does, by a process called gap filling. The main difference between a DNA transposon and an LTR retrotransposon is the involvement of reverse transcriptase and an RNA intermediate  While the DNA transposon physically leaved the donor DNA by a cut and paste mechanism, the LTR retrotransposon never leaves its stop in the host genome o This allows the LTR retrotransposon to have a much higher copy number increase rate than DNA transposons because it just needs to increase the transcription rate of the host gene  Both of these mobile elements use gap filling to incorporate themselves into the target gene Non LTR retrotransposons are another form of mobile elements which make up one third of the human genome, making them the most abundant mobile elements foun
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