Archive for the ‘Genome organization’ Category

The transposable elements that transpose via an RNA intermediate are of two kinds: Retrotransposons and retroposons.

1) Retrotransposons: They resemble retroviruses and encode reverse transcriptase enzyme.

2) Retroposons: Neither do they resemble retroviruses nor do they code for their own reverse transcriptase.

Retrotransposons: The genetic information of retroviruses is encoded in RNA, which is transcribed into DNA by the action of reverse transcriptase after the virus infects a cell. The reverse transcribed viral DNA is then inserted into the genome of the host cell, where it utilizes host cell’s machinery to express its genes. HIV is an example of a retrovirus.

Retrotransposons are similar to retroviruses in many aspects. Both have a similar structural organization, and nucleotide sequences of the two are similar. This immediately suggests that retrotransposons originated as retroviruses. Some retrotransposons even encode structural proteins that form virus-like particles in the cells. However, the most important difference between retrotransposons and retroviruses is the inability of retrotransposons to leave cells as virus particle and infect other cells. Retrotransposons have lost the ability to infect other cells; they are maintained as part of the chromosomes in cells.

Yeast Ty elements and D. melanogaster copia elements are the two prominent examples of retrotransposons. Retrotransposons are bordered by long terminal repeats (LTRs). The repeats are longer than inverted terminal repeats of transposons. Retrotransposons carry gag and pol genes that are similar to same genes found in retroviruses. During the movement of a retrotransposon in the genome, first RNA polymerase II transcribes the retrotransposon DNA into an RNA, which is polyadenylated to become mRNA. The gag and pol mRNAs are translated into polyproteins, which are cleaved into several individual proteins. The gag polyprotein is cleaved into three proteins, which form a capsid-like structure surrounding the retrotransposon RNA. The pol polyprotein is cleaved into four enzymes: reverse transcriptase, RNase, protease and integrase. Protease cleaves the polyproteins into their individual proteins; the proteins and RNA assemble into a retrovirus-like particle. Reverse transcriptase forms a single- stranded DNA molecule from the retrotransposon RNA template; RNase removes the RNA. The DNA is circularized and complementary DNA strand is synthesized to create a double-stranded, circular copy of the retrotransposon. Integrase integrates this new retrotransposon copy into a new site on the cellular DNA.


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The transposase recognizes sequences at the inverted terminal repeats and excises the element at those sites. Ac produces functional transposase; Ds cannot produce the functional enzyme due to deletions. The inverted terminal repeats are the same in both Ac and Ds elements, and transposase recognizes them and transposes both Ac and Ds elements. If there is no Ac element in the the genome, no functional transposase is produced and thus no Ds element transposition takes place. To summarize,

1) Autonomous elements encode functional transposase; capable of self-transposition.

2) Nonautonomous elements cannot encode functional transposase; transpose only when an autonomous element is present.

When an Ac or Ds element inserts into a new site, the site is cut in staggered fashion; on either end of the cut site single-stranded portions of eight nucleotides are generated. DNA polymerase adds nucleotides to fill in the single-stranded DNA gaps. This leads to the creation of  short direct repeats of eight nucleotide pairs in the DNA sequences that flank the inverted repeats of the element. Or, the direct repeats are created at the either ends of the inserted transposable element. During the next transposition event, when the transposase excises the transposable element, some of the repeated sequence is left behind as a “footprint” where the transposable element once resided.

This is the last post describing “The Ac-Ds Transposon System”.

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Ds elements, unable to excise themselves, can be excised and moved to a new location if an Ac element is present somewhere in the genome. Thus an Ac (activator) element activates transposition of a Ds element. In the absence of an Ac element, a Ds element remains in the gene and the allele behaves like a recessive allele. The Ac element is an autonomous transposon because of its capability of self-transposition. the Ds element is called a nonautonomous transposon as it is incapable of self-transposition. However, the Ds element can be transposed if an autonomous transposon is present in the genome.

Ac and Ds elements transpose in somatic cells only; in germ line cells they transpose rarely. Several Ac and Ds elements have been cloned and sequenced by Nina Fedoroff and her colleagues. The nucleotide sequences of these elements have revealed two distinct features about the Ac element and other autonomous elements:

1) Each one is bordered by “imperfect inverted terminal repeats”.

2) Each element carries a gene encoding the transposase enzyme.

Ds elements, however, contain deletions which include part of the transposase gene. Thus each Ds element is unable to encode functional trasnposase; and therefore could not transpose independently.

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The Ac-Ds system of maize is a muatble allele system. It was on the basis of studies on this system that Barbara McClintock proposed the concept of transposable elements. She received the 1984 Nobel Prize in medicine for her pioneering work on transposons.

Transposons, by inserting themselves into genes, cause mutations, and disrupt the trasncription of normal mRNA. This kind of mutation is transposon-insertion mutation and it creates a recessive allele (as functional gene product is not produced). The mutations caused this way are unstable because the mobile transposon can be excised from the gene and it can restore the function of the gene. Recessive transposon-insertion alleles are known as mutable alleles as they revert to dominant alleles at rates higher than for recessive alleles that contain other types of mutations.

There are several Ac and Ds trasnposons cloned and sequenced. These are good examples of how many of the transposons work. Ac stands for activator and Ds for dissociator. Both of them represent transposons and are part of the same system. However, they function in different ways. The Ds element (found within the coding sequence of a gene) is incapable of excising itself from the gene and therefore mutant alleles harboring a Ds element are usually stable. Ac elements are capable of excising themselves from the position where they reside and move elsewhere, causing the allele to revert to the dominant type after excision. If they land up within a new gene after the trasnposition event, Ac elements create a mutation in the gene. This is now detected as a recessive allele.

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 Transposable elements fall under the category of dispersed sequence repeats. Transposable elements are the sections of DNA that move or transpose within the genome. They are also sometimes referred to as molecular parasites, as they exist only to maintain and propagate themselves and have no specific function in the biology of their host. However, some reports have shown that they are involved in the evolution  of genomes (PNAS, 2000). Reports have also shown that they are involved in some important cellular functions.  These elements are of two kinds: Transposons and retrotransposons.

Transposons are mobile DNA elements that transpose directly as DNA molecule. The Ac/Ds system (to be discussed in the next post) and the P elements of Drosophila are the two prominent examples of transposons. The transposase  enzyme is required for their movement.

Retrotransposons move via an RNA intermediate using the reverse transcriptase enzyme. The yeast Ty elements and the copia elements of Drosophila are the examples of retrotrasnposons.

Mobile elements are eliminated from the genome at a very slow rate. They are removed either by deletion of DNA segments carrying them or by accumulation of mutations. Mobile elements also show evidence of environmental regulation as seen for Tam elements in snapdragon  (Antirrhinum majus). The frequency of Tam element transposition increases by 1000-fold when snapdragon plants are shifted from 25°C temperature to 15°C.

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Not all repetitive DNA is noncoding. There are many gene families that consist of genes repeated several times in gene clusters or tandem repeats. Each gene within a cluster is individually regulated. The genes of these multigene families typically code for those proteins that are required in large amounts e.g. seed storage proteins, RuBisCO (Ribulose-1,5-bisphosphate carboxylase/oxygenase), cytoskeletal proteins, 70 kDa heat shock proteins (HSPs), α- and β-globin genes, LHC proteins, histone genes, rRNA genes. Frequently, the DNA that lies within 5-10 Kb of a particular gene has sequences that are inexact copies of the gene. And the two sequences are closely related. These DNA sequences many a time arise through gene duplication events, and are referred to as duplicated protein-coding genes

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Repetitive DNA is distributed into 1000 to 40,000 families. All the repetitive DNA present in the genome could be broadly categorized into two: tandem repeats and dispersed repeats. Centromeres, telomeres and chromosome knobs fall under tandem repetitive DNA; and transposons and retrotransposons under dispersed repeats. In tandemly repetitive DNA, the repeat sequences are present contiguously one after the other, where as the repeat sequences of dispersed repeats are scattered throughout the genome. The repetitive DNA contributes to the character and function of specialized structures and chromosomes. It also plays an important role in genome organization.

The noncoding tandem repetitive DNA is also known as satellite DNA, as it forms a separate zone from the rest of the DNA during the CsCl density gradient centrifugation. The satellite DNA of most animals and yeast tend to be AT-rich; however, in plants, it is generally GC-rich.  The satellite DNA is primarily associated with either the centromere or telomere. It is usually heterochromatic and condensed.

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