Transcript No Slide Title

Jumping
s
Gene
Mobile &
Transposable Elements
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Ethnobotany
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mosaic kernels
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1938: Marcus Rhoades reported odd
phenotypic ratios in corn.
Self pollination of a
pigmented corn kernel
yielded:
12 : 3 : 1
pigmented : dotted : colorless
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A hypothesis:
Two mutations at
unlinked loci: 1. pigment
gene A1 mutated to
colorless mutant a1, and
2. a dominant allele for
dotting (Dt) appeared.
The presence of the Dt
allele caused spots of
pigment to appear.
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Barbara McClintock
1902-1992
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Barbara McClintock
1902-1992
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Transposition = the movement
of genetic information from one
chromosomal location, the
donor site, to another, the
target site.
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DNA sequences that can change
their genomic location
intragenomically either
autonomously or non-autonomously
are called transposable elements.
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“copy-and-paste”
“cut-and-paste”
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Retrotransposons can be divided into five
orders on the basis of their mechanistic
features, sequence organization, and reverse
transcriptase phylogeny: LTR
retrotransposons, DIRS-like elements,
Penelope-like elements, LINEs, and SINEs.
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When a transposable element is inserted
into a host genome, a small segment of the
host DNA (usually 4-12 bp) is duplicated at
the insertion site.
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Transposition = the movement
of genetic information from one
chromosomal location, the
donor site, to another, the
target site.
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DNA sequences that can change
their genomic location
intragenomically either
autonomously or non-autonomously
are called transposable elements.
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Classifications of
Transposable Elements
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Transposition may be replicative or
conservative. Replicative transposition
will result in two copies of the element,
one at the donor site and one at the
target site. Following conservative
transposition the transposable element
will only be found at the target site, with
no change in copy number.
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Conservative transposition =
“cut-and-paste” transposition
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Duplicative transposition =
“copy-and-paste” transposition
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DNA-mediated and RNA-mediated
transposable elements:
1.Class I transposable elements
(retrotransposons).
2.Class II transposable elements (DNA
transposons).
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Autonomous and nonautonomous transposable elements
Autonomous transposable elements encode all the
components of the transposition machinery.
Nonautonomous transposable elements appropriate the
transposition machinery of autonomous transposable
elements.
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Active and fossil transposable elements
A transposable element is defined as active if it contains
all the necessary sequence elements for either
autonomous or nonautonomous transposition.
Active elements may be rendered defective by different
types of mutation, in which case they are referred to as
fossil transposable elements.
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Active and fossil transposable elements
A transposable-element family may contain different
combinations of active autonomous, active
nonautonomous, fossil autonomous, and fossil
nonautonomous transposable elements.
For example, the human genome contains approximately
50,000 fossil autonomous and 200,000 fossil
nonautonomous DNA transposons.
Intriguingly, the human genome seems to contain NO
active DNA transposons.
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According to the numbers and kinds of
genes they contain, DNA-mediated
transposable elements are divided into
insertion sequences and transposons.
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Found in Escherichia coli and Shigella dysinteria.
Length = 770 nucleotides, including two inverted
terminal repeats, 23 bp each.
Contains two out-of-phase reading frames, insA and
insB, from which a single protein is produced by
translational frameshifting at a run of adenines.
The N-terminal is an inhibitor of transposition; the Cterminal is a transposase, an enzyme that catalyzes the
insertion of transposable elements into insertion sites.
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Carriers and non-carriers of the insertion sequence can
be separated by centrifugation because the carriers are
heavier.
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INSERTION SEQUENCES (IS)
Insertion sequences were first discovered in the gal
operon of E. coli.
Galactose (gal) operon
galE
galT
galK
galM
galE = UDP-galactose 4-epimerase
galT = galactose-l-phosphate uridylyltransferase
galK = galactokinase
galM = mutarotase
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Galactose (gal) operon
galT
galE
galK
galM
IS
Insertion of an IS affects only the transcription of the genes
downstream from the insertion. For example, if the IS occurs
in the galT gene, the galT, galK and galM genes will be
disrupted, but galE will not be.
This phenomenon is known as a POLAR mutation.
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Stupidity
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Composite
Hypercomposite transposons contain two or
more transposons.
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(symmetrical-inverted) Tn3 from E. coli confers
streptomycin resistance. tnpR and bla are transcribed on
one strand; tnpA on the other. Tn3 is flanked by 38-bplong inverted repeats.
(asymmetrical) Tn554 from Staphylococcus aureus lacks
terminal repeats and contains 8 protein-coding genes.
Three of the genes are transcribed as a unit and encode
transposases (tnpA, tnpB, and tnpO). The spc and ermA
genes confer spectinomycin and erythromycin resistance,
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respectively.
Composite transposon Tn9 from
Escherichia coli contains two copies
of IS1 flanking the cat gene, which
encodes a chloramphenicol-resistance
protein.
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Some mobile elements can transpose
themselves in all cells; others are cellspecific.
Tc1 elements in the nematode
Caenorhabditis elegans and P elements
in Drosophila melanogaster are usually
mobile only in germ cells.
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Transposition of many elements is
regulated by developmental stage.
From an evolutionary point of
view, the developmental timing of
transposition is particularly
important, because it affects the
propagation of the transposable
element to future generations.
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LINE-1 transposable elements in mammals are
particularly active during leptotene and
zygotene, when DNA-strand breakages occur.
This offers an opportunity for transposable
elements to insert themselves into new sites.
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Genomic locations of target sites for
transposition:
Exclusive genomic preference: In the vast majority
of cases IS4 incorporates itself in the galactosidase operon
of Escherichia coli, and thus each bacterium contains
mostly one copy of IS4.
Complete randomness: Bacteriophage Mu transposes
itself at random within the genome.
Intermediate genomic preference: 40% of all Tn10
transposons in E. coli are found in the lacZ gene, which
constitutes a minute fraction of the host genome.
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Genomic locations of target sites for
transposition:
Affinity for a particular nucleotide
composition: IS1 favors AT-rich sites.
Affinity for a particular sequence: IS630 has a
special affinity for 5'—CTAG—3' sequences.
Chromosomal preference: TRIM elements in
Drosophila miranda exhibit a preference for the Y
chromosome.
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Hotspots for P element insertion in the X
chromosome of Drosophila melanogaster
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Genomic locations of target sites for
transposition:
The DIRS-1 transposable element in the
slime mold Dictyostelium discoideum
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Genomic locations of target sites for
transposition:
Self affinity: DIRS-1 preferentially inserts itself into
other DIRS-1 sequences. D. discoideum contains, on
average, ~40 intact copies of DIRS-1 and ~300 fragments.
oldest
newest
Active DIRS
oldest
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Species specificity:
DIRS in Dictyostelium discoideum
only.
mariner moves from species to
species, even if the species belong to
different taxonomic kingdoms.
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Retroelements are sequences that contain a
gene for reverse transcriptase, which
catalyzes the synthesis of cDNA from an
RNA template.
Not all retroelements possess the intrinsic
capability to transpose. Therefore, not all
retroelements are transposable elements.
Retroelements that transpose do so by
retroposition.
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Central Dogma
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Modified Central Dogma
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Not the Central Dogma
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That would have been nice…
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That would have been nice…
Joanna Masel
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Retroelements
Retroelements are DNA or RNA sequences that contain a gene
encoding the enzyme reverse transcriptase, which catalyzes the
synthesis of DNA from an RNA template. The resulting DNA
molecule is called complementary DNA (cDNA). Not all
retroelements are transposable or mobile.
Retroelements can be divided into three categories:
(1) transposable elements that move within a genome by replicative
RNA-mediated transposition (but may also move
intergenomically)
(2) mobile nontransposable elements that only move
intergenomically
(3) non-mobile elements
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Masayori Inouye
Rutgers University
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Retrons are widely distributed among bacterial
species.
Within each bacterial species retrons tend to be
rare.
Natural populations of retron-carrying genomes
possess a single retron copy, either in the intergenic
part of the genome or inside a prophage (a viral
genome that had became integrated into the
bacterial chromosome).
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multicopy single-stranded DNA (msDNA)
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TERT genes
Human telomeres consist of the sequence TTAGGG tandemly
repeated many thousand times. Because of asymmetrical DNA
replication, a few of these repeats are lost from the tips of the
chromosomes each replication cycle.
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TERT genes
Telomerases are nucleoproteins whose function is to add DNAsequence repeats to the 3' end of the DNA strands in the telomeres at
the ends of linear eukaryotic chromosomes.
The de novo addition of TTAGGG repeats by the enzyme telomerase
partially or wholly compensates for telomere shortening.
Telomerases in all eukaryotic species share at least two components
essential for catalytic activity: a telomerase reverse transcriptase
protein (TERT) and a telomerase RNA.
The TERT encoding gene is a retroelement. In humans, this
retroelement is located on chromosome 5.
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Retroplasmids
Extragenomic DNA and RNA molecules (plasmids) are
frequently detected in fungal mitochondria. They can be
divided into:
- Genomically derived plasmids (similar in sequence to
the mitochondrial sequence)
- Autonomously-replicating true plasmids that exhibit no
sequence similarity with the host mitochondrial genome.
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Group-II introns
Group-II introns are a subclass of self-splicing introns.
Some group II introns contain protein-coding genes for
endonuclease and reverse transcriptase. The latter may act
as retrotransposable genetic elements.
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Group-II introns
Group-II introns can integrate into the homologous
position of an intronless allele of the same gene (homing),
and at much lower frequencies into other sites
(retroposition).
Retroposition
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Twintrons are introns-within-introns excised by
sequential splicing reactions.
Group II twintrons have presumably been formed by the
insertion of a group II intron into an existing group II
intron.
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Group-III introns are short ORF-less introns found in a
small number of protist eukaryotes, such as Euglena
gracilis. They appear to be group-II introns from which
the central ORF-containing portion has been removed.
Thus, group-III introns are essentially nonautonomous
group-II introns.
Group III twintrons are known.
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Retrotransposons are transposable elements that use RNAmediated transposition, but do not construct virion particles,
i.e., they lack the env (envelope) gene, and so, unlike retroviruses,
cannot independently transport themselves across cells.
Initially, the retrotransposons were divided into LTR
retrotransposons and non-LTR retrotransposons (or
retroposons) according to whether or not their coding sequences
were flanked by long terminal repeats (LTRs).
Subsequent evolutionary studies indicated that while most nonLTR retrotransposons constitute a monophyletic group, the
LTR-retrotransposons are paraphyletic.
Some LTR-retrotransposons have secondarily acquired env-like
reading frames that may enable them to move from cell to cell (i.e.,
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they are in practice viruses).
LTR retrotransposons
Non-LTR retrotransposons
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Integrase
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Pararetroviruses:
1. HepaDNAviruses, e.g., hepatitis B virus
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Pararetroviruses:
2. Caulimoviruses, e.g., cauliflower mosaic
virus
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Pararetroviruses are not transposable elements
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RETROSEQUENCES
Restrosequences (or retrotranscripts) are
genomic sequences that have been derived
through the reverse transcription of RNA and
subsequent integration of the resulting cDNA
into the genome.
Retrosequences lack the ability to produce reverse
transcriptase, and have been produced through the
use of a reverse transcriptase from a retroelement.
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Diagnostic features of mRNA derived retrosequences
1. lack of introns
2. precise boundaries coinciding with
the transcribed regions
3. stretches of poly(A) at the 3’ end
4. short direct repeats at both ends
5. truncations
6. posttranscriptional modifications
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many
many
few
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Retrosequences:
Retrogenes
Processed genes
Semiprocessed genes
Retropseudogenes
Processed pseudogenes
Semiprocessed pseudogenes
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Number of human retropseudogenes and number of parental functional genes
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Number of
Number of
Gene
genes
retropseudogenes
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argininosuccinate synthetase
1
14
-actin
1
~20
-tubulin
2
15-20
Cu/Zn superoxide dismutase
1
>4
cytochrome c
2
20-30
dihydrofolate reductase
1
~5
G3PD
1
~25
lactate dehydrogenase A
1
10
lactate dehydrogenase B
1
3
lactate dehydrogenase C
1
6
laminin
1
>20
nonmuscle tropomyosin
1
>3
nucleophosmin B23
1
7-9
phosphoglycerate kinase
1
2
prohibitin
1
>4
prothymosin 
1
>5
ribosomal protein L32
1
~20
triosephosphate isomerase
1
5-6
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Genes tend to “bombard”
the genome with dead copies
of themselves.
The “Vesuvian” paradigm
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How do you get reverse
transcribed sequences to
become incorporated into the
germline genome if the gene
itself is not transcribed in the
germline?
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Pseudogenes are affected by two evolutionary
processes:
Compositional assimilation: The accumulation
of mutations which obliterate the similarity
between the pseudogene and its functional
paralogue. The nucleotide composition of the
pseudogene will come to resemble its
surroundings, eventually “blending” into it.
Abridgment: Due to the excess of deletions over
insertions, pseudogenes become increasingly
shorter compared to the functional gene.
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It takes on average 400 million years
for a mammalian retropseudogene to
lose half of its length.
Mammals are ~200 million years old
and, therefore, the mammalian
genome is expected to contain
reptilian pseudogenes. These ancient
pseudogenes have by now become
unrecognizable.
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Mammalian processed
pseudogenes are created at
a much faster rate than the
rate by which they are
obliterated by deletion.
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Processed pseudogenes are
abundant in mammals.
Processed pseudogenes are
rare in amphibians, rarer in
birds, and even rarer in
Drosophila.
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Creation rates
rates
Deletion
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Hypothesis: Retroposition occurs
mainly in the female germline
Spermatogenesis is similar among
animals.
Oogenesis in mammals differs from
that in the other animals by a
prolonged lambrush stage (=
suspended animation) that lasts from
birth to ovulation (up to 40 years in
humans).
Lampbrush chromosome
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Creation rates are determined by
the length of the suspended
animation during oogenesis
20-40 years in humans.
2-4 months in amphibians.
Less than 3 weeks in birds.
Less than 1 day in Drosophila.
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Prediction:
Retrosequences should be found in
high numbers on the X chromosome,
in intermediate numbers on
autosomes, and be rare on the Y
chromosome.
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Prediction:
Retrosequences should be found in
high numbers on the X chromosome,
in intermediate numbers on
autosomes, and be rare on the Y
chromosome.
Density of Processed Pseudogenes in Human Chromosomes
(from Bischof et al. 2006)
Mean Density
in Autosomes
Density in
X-chromosome
Density in
Y-chromosome
2.28 ± 0.40
3.01
0.74
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Differences among organisms in
numbers of retropseudogenes can also
be due to deletion rate.
DNA loss in Drosophila is ~75 times
faster than that in mammals.
This high rate may explain the
dearth of pseudogenes in
Drosophila.
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