Chapter 20. Gene creatures, partii: jumping genes and junk DNA. Prepared by Woojoo Choi

Transcription

1 Chapter 20. Gene creatures, partii: jumping genes and junk DNA Prepared by Woojoo Choi

2 1) Transposable elements (transposons): segment of DNA that can move as a unit from one location to another, but which always remains part of another DNA molecule and do not have own origin of replication 2) Some of these alter egos as viruses, whereas others only exist as chunks of integrated DNA. 3) Other stretches of parasitic DNA are stuck permanently where they are and are probably the remains of once mobile gene creatures. 4) They have degenerated into junk DNA.

3 Transposons 1) Transposons are always inserted into other DNA so they are never free as separate molecules. 2) Transposition: process by which a transposon moves itself from one host molecule of DNA to another 3) Simple transposons cannot replicate themselves. 4) As long as the DNA molecule of which the transposon is part gets replicated, the transposon will also be replicated.

4 The essential parts of a transposon 1) Insertion sequence: the simplest type of transposable element, consisting only of two terminal inverted repeats and a gene for the transposase enzyme 2) Insertion seqeunces have two vitally important characteristics. They have inverted repeats: Inverted repeats: two DNA sequences that are the same except that one is inverted relative to the other Inverted repeats are not quite exact repeats. Insertion sequences have just one gene that encodes the transposase, the enzyme needed for movement.

5 The essential parts of a transposon 3) Insertion sequences are found in the chromosomes of bacteria and also in the DNA of their plasmids and viruses. 4) To qualify as a genuine transposon, as opposed to a mere insertion sequence, one needs some extra genes which encode useful characteristics such as antibiotic resistance inside the inverted repeats.

6 1) The transposase is responsible for moving the transposon around. Movement of transposons

7 Movement of transposons 2) The transposase has two things to do: 1 It recognizes the inverted repeats at the transposon ends and this tells it which piece of DNA must be moved. 2 The transposase must also recognize a specific sequence on the DNA molecule it has chosen as its future home. Target sequence: short sequence of DNA which is recognized by the transposase and into which it inserts the transposon when it moves Transposases will often accept a target site with a sequence that is near match to the preferred target sequence.

8 Movement of transposons 3) Conservative transposition: The version of transposition in which the transposon is removed from its original location, so leaving a gap in the DNA, and is inserted unaltered into a new site 4) The process of consevative transposition The transposase starts the movement process by cutting the transposon loose from its original site.

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10 Movement of transposons Next, the tansposase grabs the molecule of DNA that will be the transposon s new home and makes a staggered cut. Then it sticks the transposon into the gap. Finally, the single stranded stretches of target sequence are filled in to make double stranded DNA.

11 Movement of transposons 5) When the transposon has cut itself out of its original home in the process of the conservative transposition, it leaves a double stranded break in the DNA. 6) This damaged DNA molecule will not get back together again and is doomed.

12 Replicative transposition 1) In replicative transposition, both the original home site and the newly selected location end up with a copy of the transposon. 2) The original home DNA is not destroyed unlike DNA in conservative transposition. 3) Complex transposon: type of transposon that leaves behind one copy in its original location when it moves, and inserts a second copy into the new location.

13 Replicative transposition 4) For replicative transposition they need resolvase and internal resolution site (IRS) Resolvase: enzyme needed by complex transposons to cup apart the fused intermediated formed during the transposition process into two separate DNA internal resolution site (IRS): DNA sequence which is recognized by the resolvase

14 Replicative transposition 5) However they are not replicons and did not make a new copy of itself. 6) They trick the host cell into duplicating them: 1 The transpose makes single stranded nicks at the end of both transposon and the target sequence. 2 It joins the loose ends to create a tangled mess in which both DNA molecules are linked via single strands of transposon DNA. 3 Host cell mends the single stranded region, thus duplication the transposon.

15 Replicative transposition 7) The function of resolvase is to resolve the mess and get the two DNA separated again. 8) It does this by recognizing two IRS sequences and carrying out recombination between them.

16 Composite transposons 1) Composite transposon: segment of DNA flanked by two insertion sequences that can jump as a complete unit 2) Let s surround a segment of DNA at both ends by two identical insertion sequences. 3) When transposition occurs, we have two possibilities.

17 Composite transposons 4) Many of the best known bacterial transposons which carry genes for antibiotic resistance or other useful properties are actually composite transposons. 5) Once a useful composite transposon has evolved, mutations inactivate the innermost pair of inverted repeats, which prevents the insertion sequences from jumping independently.

18 Transposons come in 57 different flavors Table 20.1 The variety of transposable elements Insertion sequence Composite transposon Complex transposon Retroposon Retron Simplest kind of transposable element, with two terminal inverted repeats and a gene for transposase Segment of DNA flanked by two insertion seqeunces which jumps as a complete unit Type of transposon which gets duplicated during transposition Transposon resembling a retrovirus in having reverse transcriptase and having an RNA phase Element found in bacteria which has reverse transcriptase and makes an RNA/DNA hybrid molecule

19 Transposons in higher life forms 1) Ac/Ds family of transposon: a family of transposons found in multiple copies, some of which are damaged, in cells of the maize (corn) plant Ac element is 4,500 bp long and is a fully functional transposon with the ability to move itself. The Ds elements vary in size and are defective. They are derived from Ac by deletion of part or all of the transposase gene. So they cannot move by themselves. To remain mobile, the Ds elements must keep the inverted repeats which the Ac transposase will recogzine.

20 Transposons in higher life forms 2) If a cell contains an Ac element anywhere in its DNA, then the transposase enzyme made by Ac can also move the Ds elements around.

21 Transposons in higher life forms 3) Ac/Ds produces a mottled kernel of corn.

22 Retro(trans)posons 1) Retrotransposon: transposon that resembles a retrovirus in having reverse transcriptase and which moves by making an intermediate RNA copy 2) TY-1 (Transposon Yeast No. 1): around 6,000 bp long

23 Moderately repetitive DNA of mammals 1) A substantial portion of the DNA of both animal and plants consists of repeated sequences that may be derived from retrotransposons. 2) In mammals, there are two classes: SINES: the short interspersed sequences making up much of the moderately repetitive DNA of mammals LINES: the long interspersed sequences making up much of the moderately repetitive DNA of mammals

24 Moderately repetitive DNA of mammals 3) Many of the repeats are defective and finding the complete version of a repeated sequence with a fully reverse transcriptase is not always easy. 4) In humans the LINES-1 is present in 50,000 to 100,000 copies. 5) However, only about 3,000 of the LINES-1 sequences are full length and most of these are crippled by point mutations.

25 Moderately repetitive DNA of mammals 6) Very rarely LINES-1 makes a new copy of itself and inserts it somewhere else in the DNA. 7) A few very rare cases of hemophilia are due to the insertion of a LINES-1 into the gene for blood clotting factor VII on the X-chromosome.

26 Moderately repetitive DNA of mammals

27 Retrons 1) Retron: genetic element found in bacteria whose mechanism of movement is still unknown but which has reverse transcriptase and uses it to make a bizarre RNA/DNA hybrid molecule 2) They have just one gene which makes a stretch of untranslated RNA followed by the coding region for reverse transcriptase.

28 Retrons 3) Retrons use their reverse transcriptase to manufacture lots of copies of a bizarre molecule that is part RNA and part DNA. 4) This does not reintegrate into the chromosome, and there is only a single copy of each retron in the bacterial chromosome.

29 Junk DNA and selfish DNA 1) Selfish DNA: Any region of DNA that manages to replicate, but which is of no use to the host cell it inhibits

30 Junk DNA and selfish DNA 2) Junk DNA: defective selfish DNA of no use to the host cell it inhibits and which is no longer capable of either moving or expressing its genes

31 Inteins and the splicing of proteins 1) Intein: the protion of a protein that removes itself after translation 2) Extein: the protion of a protein that remains after intein removal

32 Inteins and the splicing of proteins 3) No processing enzymes are necessary. 4) The intein segment is responsible for its own release as a separate protein molecule.

33 Inteins and the splicing of proteins 5) Usually there is just a single intein per protein, but one example is known where two inteins are inserted into the same host protein. 6) More bizzare is the case of dnae gene of Synechocystis.

34 Inteins and the splicing of proteins 7) The spliced-out intein polypeptide is not just a waste product; it is a deoxyribonuclease (DNase). If a sudden mutation occurs and the intein DNA is removed from the middle of the host gene, the intein protein tried to kill the cell by cutting the DNA double helix at this point. Any bacterial cell that deletes the useless intein DNA will be killed out of spite by the intein protein.

35 Inteins and the splicing of proteins

36 Inteins and the splicing of proteins 1) Yeast cells can mend doublestranded breaks in their DNA by a special form of recombination Gene conversion: the repaired copy of the gene is converted to the same sequence as the undamaged copy

37 Gene creatures and the evolution of higher organisms 1) The various gene creatures have had a major influence on the evolution of higher organism. 2) We may consider three main effects: 1 Diseases caused by them have killed large number of higher organisms. Individuals resistant to these diseases have been selected. This led to the development of a complex immune system and a whole range of modifications to avoid infection.

38 Gene creatures and the evolution of higher organisms 2 In a somewhat more positive vein, useful genes may be provided to their host cells by gene creatures (eg, antibiotic resistance) 3 The DNA of higher organisms is mostly non-coding and it could be worse. Most of this junk DNA consists of repetitive sequences derived from transpons and integrated virus genomes from retroviruses and retrotransposons.