18.4 Genetics

Which of the following is the most common transposable element in humans? a. copia b. Alu c. Acd. Ty e. P

b. Alu

How do insertion sequences and composite transposons differ?

(1) Insertion sequences contain genes required for transposition (e.g., transposase) and reinsertion flanked by inverted terminal repeats. Insertion sequences only carry genes required for transposition and reinsertion, and are thus relatively short sequences. (2) Composite transposons are complex transposons that are generally any sequence of DNA flanked by two insertion sequences. Composite transposons can be up to thousands of base pairs long and carry various genes, such as antibiotic resistance genes. One or both of the insertion sequences contains the transposase that enables the transposon to excise and reintegrate elsewhere within the genome.

Which of the following transposable elements have indirect repeats at each end? -Ac in maize -Ty in yeast -copia in Drosophila -Alu in humans -All of the above have indirect repeats.

-Ac in maize

Consider two theoretical transposable elements in yeast, A and B. Each contains an intron and each transposed to a new location in the yeast genome. Suppose you then examine the transposons for the presence of the intron. In the new locations, you find that A has no intron but B does. From these facts, what can you conclude about the mechanisms of transposition for the two transposable elements? -B probably makes a transposase. -A probably has inverted repeats at each end of the element. -B probably uses RNA as an intermediate in the transposition event. -B probably makes a reverse transcriptase. -A probably doesn't create a duplication of the host genome target sequence.

-B probably makes a transposase.

Which of the following pairs of sequences would you expect to be found in the same transposable element? -Inverted repeats and a gene for transposase -Long terminal repeats and a gene for transposase -Inverted repeats and a gene for reverse transcriptase -A gene for transposase and a gene for reverse transcriptase -Both B and C are both correct.

-Inverted repeats and a gene for transposase

Which of the following characterizes the mode of transposition of retrotransposons? -It involves a RNA intermediate. -It involves the initial synthesis of transposase. -It involves the production of a protein repressor. -It only occurs in nondividing host genomes. -It requires inverted repeats at each end of the retrotransposon.

-It involves a RNA intermediate.

Which of the following is characteristic of retrotransposons? -They use transposase to transpose to new sites. -They have inverted repeats at each of their ends. -They transpose through an RNA intermediate -They make transposase. -They are found only in prokaryotes.

-They transpose through an RNA intermediate

Give the inverted repeat of the following sequences 5-ATCCGCT-3 3-TAGGCGA-5 5-AAATTT-3 3-TTTAAA-5 5-GGAATTCC-3 3-CCTTAAGG-5

5-AGCGGAT-33-TCGCCTA-5 (inverted; non-palindrome) 5-AAATTT-33-TTTAAA-5 (inverted; palindrome) 5-GGAATTCC-33-CCTTAAGG-5 (inverted; palindrome)

Which of the following is required for an IS element in E. coli to be able to transpose? -A gene for reverse transcriptase and long terminal repeats -A gene for reverse transcriptase and inverted repeats -A gene for transposase and inverted repeats -A gene for transposase and long terminal repeats -A gene for DNA polymerase and long terminal repeats

A gene for transposase and inverted repeats

Transposable elements that transpose through an RNA intermediate are retrotransposons. There are two types of retrotransposons, those that have direct repeats at each end, often called long terminal repeats (LTRs), and those that do not have these repeats. Pick an example of each type of retrotransposon and give: (1) its basic structure, and (2) its possible evolutionary history.

A prominent example of the first type of retrotransposon is the Ty element in yeast. It is about 6300 nucleotides in size and contains direct repeats, called deltas, of about 330 nucleotides. It also contains homologous genes to the gag and pol genes of retroviruses. The pol gene encodes a reverse transcriptase, which it can use for transposition. Ty is clearly evolutionarily related to retroviruses, which also contain direct repeats (or LTRs) and gag and pol genes. In addition, most retroviruses contain an env gene (Chapter 8), which Ty doesn't have. Whether Ty evolved from a retrovirus or vice versa or whether they both evolved from some other entity is not known. The copia element of Drosophila could also be used as an example of this class.An example of the second type of retrotransposon would be the Alu element in primates including humans. Alu is about 300 nucleotides in size although many copies of Alu are smaller than this. There are no direct repeats nor are there pol or gag genes. Therefore, Alu elements must utilize some other source of reverse transcriptase in the cell to facilitate transposition. There are over a million copies of the Alu element in humans, scattered throughout the genome as a prominent SINE (short interspersed element).The Alu sequence seems to be related to the 7SL RNA gene, which has an internal promoter, and Alu has been referred to as a "pseudogene." Presumably, transcription of the Alu sequence leads to an RNA that can sometimes be converted to a DNA sequence with the ability to integrate throughout the genome. Presently, it appears that few Alu copies in humans are active in transposition but some are, as evidenced by genetic disorders caused by an inappropriate integration of an Alu copy. The LINE L1 could also be used as an example of this type of retrotransposon.L1 is quite different from Alu is that it contains a gene for reverse transcriptase and is not a pseudogene.

Which of the following best describes the Activator (Ac) and Dissociation (Ds) transposable elements in maize (corn)? -Ac elements cannot transpose unless a Ds element is present. -Ac contains a functional transposase gene; Ds lacks a functional transposase gene. -Ds contains a functional transposase gene; Ac lacks a functional transposase gene. -Both Ac and Ds have functional transposase genes. -Neither Ac nor Ds contains functional transposase genes.

Ac contains a functional transposase gene; Ds lacks a functional transposase gene.

Which of the following transposable elements are flanked by direct repeats of a short portion of the host genome? Tn10 L1 Activator (Ac) Alu All of the above

All of the above

Explain how transposable elements might play a role in studying gene function.

Because some transposable elements insert randomly throughout the genome and because the element has a known sequence, researchers can use the elements as a way to tag a gene in which that element has caused a disruption in that gene's function.

Explain how bacterial resistance to antibiotics can be efficiently transmitted by transposons.

Composite transposons can carry antibiotic resistance genes and can be transferred via conjugation, transduction (phage infection), and transformation. Transposable elements can also excise and insert into plasmid elements, which can be subsequently transferred by various means to different cells. Transposable elements can undergo homologous recombination with plasmids or other DNA sites within a cell containing the same transposable elements sequence, and be transferred via conjugation, transduction, and so forth. Under the selective pressure antibiotic treatment, resistance will, of course, be highly advantageous to those bacterial cells containing resistance genes, and thus antibiotic resistance can spread very rapidly in bacterial populations.

Practically all transposable elements that have studied are associated with which of the following? -Indirect repeats at each end -A gene for transposase -A gene for reverse transcriptase -A gene for RNA polymerase -Flanking direct repeats

Flanking direct repeats

Why don't transposable elements that move through replicative transposition eventually take over the genome completely?

Organisms have evolved mechanisms to regulate transposition, either by controlling the amount of transposase produced or by direct inhibition of the transposition event. The transposable elements themselves have also evolved mechanisms to limit their own level of transposition. The long-term well being of the transposon is often dependent upon the long-term survival of its host. For example, the promoters of some transposase genes are often weak with low levels of expression.

What would be the result of a large deletion in the resolvase gene of a transposable element?

Resolvase is an enzyme carried by some transposable elements that use a replicative transposition process. A transposable elements with a deletion in its resolvase gene would not be able to resolve the cointegrate molecule formed during the transposition process into two separate transposable elements. Instead, a single cointegrate molecule containing two copies of the transposable elements would be formed.

Most transposable elements are flanked by direct DNA repeats. What is the significance of these direct repeats?

The direct repeats indicate that staggered cuts are made in the target DNA sequence when transposable genetic elements insert themselves. The direct repeats are a consequence of repairing the staggered cuts after insertion.

A transposable element is found to use RNA as an intermediate in transposition. On the basis of this information which of the following would you expect to be correct? -The transposable element also probably makes transposase. -The transposable element may encode a reverse transcriptase. -The transposable element is probably located in a bacterial genome. -The transposable element probably contains inverted repeats at each end. -The transposable element will not be able to transpose without a second copy also present in the genome.

The transposable element may encode a reverse transcriptase.

In a eukaryotic cell, two different transposable elements, each containing an intron, excise and insert in different locations within the genome. After transposition, the transposable elements are sequenced at their new sites. Explain the following sequencing results: Neither of the translocated transposable elements contains any intron sequences. One of the transposable elements contains the intron, but the other transposable elements do not

The transposition process itself must result in loss of the introns. It is therefore likely that, in this case, the transposition process involves transcription, and the elements moved via RNA intermediates (e.g., retrotransposons). Retention of the intron in one transposable element suggests that this particular transposable element moved through a DNA intermediate (i.e., not transcription dependent) and therefore didn't require an RNA intermediate. This would likely be a class II transposable element and would make transposase. The other transposable element is likely a retrotransposon.

Do you believe that transposable elements (TEs) are best described as "parasitic" DNA sequences, simply using the host genome as a means to replicate and spread and providing no benefit for the host, or do you believe that they provide some adaptive advantage for the host genomes that house them? Explain. If you believe that TEs are advantageous to the host, give some specific examples to support this conclusion.

There is no correct answer to this question and there is little agreement even among experts in this field. As far as being parasitic and possibly detrimental to the host, TEs do create random mutations and chromosomal rearrangements. Most of these events would be expected to be either neutral or even detrimental to the host and very few would be advantageous. Host genomes have evolved mechanisms to silence or at least reduce the activity of TEs such as DNA methylation and other epigenetic mechanisms. This suggests that the activities of TEs can be harmful unless controlled by the host. TEs may be beneficial to the host in several ways. Sometimes the creation of genetic variability could be useful to the host genome. In a rapidly changing environment or even a somewhat static environment, a rare beneficial mutation may be so valuable that the species would be willing to trade the many deleterious mutations for a very few beneficial ones. In these cases, any mechanism that increases genetic variation may be valuable and this would include TEs In addition, TEs themselves may evolve into a useful component of the host genome. The gene that makes the enzyme that replicates telomeres (telomerase, Chapter 12) may have come from a TE. In one plant a TE gene product has become a regulatory protein of plant genes and in vertebrates, part of the immune system seems to have come from a TE. As often happens in these types of controversies, it may turn out both points of view are somewhat valid. TEs may be somewhat parasitic and capable of causing harm if left unchecked. Hosts have evolved mechanisms to reduce the transposition activity of TEs but have not eliminated them completely from their genomes. Possibly, most genomes are in some kind of equilibrium with their resident TEs with a minimum of harm being done by them and an occasional useful adaptation coming from their presence.

Composite transposons in bacteria are characterized by which of the following? -They are composites of Ac and Ds elements. -Each has the ability to transpose either by replicative transposition or nonreplicative transposition. -They contain all deleted transposase genes. -They contain more than one gene. -None of the above is correct.

They contain more than one gene.

Which of the following describes the possible parasitic nature of transposable elements? -Transposable elements can increase in number within genomes without providing an advantage to the host. -Transposable elements are collected within their genomes by host organisms so that the host will benefit, but not the transposable elements. -Transposable elements will provide an evolutionary advantage to host organisms by transposing as often as possible. -Transposable elements will enhance their expression of transposase so that the hosts can evolve more quickly. -Transposable elements will add methyl groups to their own DNA to reduce their own rate of transposition.

Transposable elements can increase in number within genomes without providing an advantage to the host.

Bacterial insertion sequences encode which of the following gene products? Reverse transcriptase DNA polymerase Transposase Repressor Insertase

Transposase

Transposition can involve exchange of DNA sequences and recombination, which often leads to DNA a. acetylation. b. rearrangements. c. condensation. d. repair. e. replication.

b. rearrangements.

Upon transposing to a new site, transposable elements -add methyl groups to bases of the surrounding DNA. -delete about 100 base pairs of DNA on each side of them. -duplicate their transposase gene. -express a gene that confers sensitivity to some common antibiotics. -create a duplication of a target sequence on each side of them.

create a duplication of a target sequence on each side of them.

A new IS element is found in bacteria. Which of the following pairs of DNA sequences would most likely be found at each end of the IS element? (Only one of the two DNA strands is given.) a. 5 ́-GAGACTCTAC-3 ́ and 5 ́-GAGACTCTAC-3 ́ b. 5 ́-GAGACTCTAC-3 ́ and 5 ́-CATCTCAGAG-3 ́ c. 5 ́-GAGACTCTAC-3 ́ and 5 ́-CTCTGAGATG-3 ́ d. 5 ́-GAGACTCTAC-3 ́ and 5 ́-GTAGAGTCTC-3 ́ e. 5 ́-GAGACTCTAC-3 ́ and 5 ́-CAGACTCTAG-3 ́

d. 5 ́-GAGACTCTAC-3 ́ and 5 ́-GTAGAGTCTC-3 ́

It is estimated that transposable elements compose approximately what percent of the human genome? a. <1% b. 1% c. 10% d. 50% e. 99%

d. 50%

Transposable elements are found mainly in higher plants. mainly in animals, particularly in mammals. mainly in eukaryotes. mainly in prokaryotes. in practically all organisms.

in practically all organisms.

Hybrid dysgenesis in Drosphila occurs -when a male and a female, each carrying a copia element, mate and produce offspring that have numerous mutations. -in the offspring of a cross between a male that carries a copia element and a female that carries a P element. -in the offspring of a cross between a male that carries a Ty element and a female that carries an Ac element. -in the offspring of a cross between a male that carries a P element and a female that does not carry a P element. -in the offspring of a cross between a male that carries a Alu element and a female that carries a Ty element.

in the offspring of a cross between a male that carries a P element and a female that does not carry a P element.