Transposons - somatic recombination (lecture 12) Flashcards
(23 cards)
what is a transposon?
= transposable element
A DNA sequence able to insert itself (or a copy of itself) at a new location in the genome without having any
sequence relationship with the target locus.
Retrovirus
An RNA virus with the ability to convert its sequence into DNA by reverse transcription and integrate into the host
genome.
in which contexts exist transposable elements?
bacterial, eukaryotic, viral, non-viral retrotransposons
IS
Insertion Sequences (IS) are Simple Transposition Modules
Composite transposons – Transposable elements consisting of two IS elements (which can be the same or
different) and the DNA sequences between the IS elements; the non-IS sequences often include gene(s)
conferring antibiotic resistance
codes for the enzyme(s) needed for
transposition flanked by
short inverted terminal
repeats.
The target site at which an insertion sequence is inserted is duplicated during the insertion process to form two repeats in direct orientation at the ends of the transposon (direct repeats)..
Transposition Occurs by Both Replicative and Non-replicative Mechanisms
nvcvbv
how can host DNA be inverted?
Homologous recombination between multiple copies of a transposon causes rearrangement
of host DNA.
cut and paste
non-replicative mechanism
Transposon moves to new site
“Cut-and-paste” requires only transposase
e.g. IS
single strand cuts in both donor and recipient DNA generate staggered ends
binding of the transposon to the protuding ends of recipient -> crossover structure
the crossover structure is nicked on the unbroken pair of donor strands and the target strands on either side of the
transposon are ligated.
-> non -replicative
(for replicative transposition: no nicking in the crossover structure but replication of the second strands of transposon -> cointegrate is formed)
replicative mechanism
Transposon is copied to new site, rare!
Requires two types of enzymatic activity:
Transposase: acts on the end of the original transposon
Resolvase: acts on the duplicated copy
crossover structure is not nicked but replication forms a cointegrate (single molecule conains two copies of transposon)
-> transposons are at the junctions between replicons
discovery of P Elements?
what is it?
Hybrid dysgenesis –
the hybrids are sterile if male progenitor was P strain
P elements are transposons that are carried in P strains of Drosophila, but not in
M strains.
The insertion of P elements at new sites
in these crosses inactivates many genes
and makes the cross infertile.
mechanism of P elements?
in male somatic mRNA and all female cells, the P element RNA is generated with a certain intron remaining
-> expression of repressor
in male germline, however, tissue specific splicing removes that intron
-> expression of transposase
if the mother is P strain, the maternally inherited cytoplasm of the zygote contains repressor -> no transposase activity
if there’s no maternal repressor, but paternal inherited transposase activity
-> dysgenesis: mutations and
chromosomal break in germ line genes of the offspring
Retrotransposon vs Retrovirus
Retroviruses are retrotransposons
that have
acquired envelope proteins
genes of a typical retrovirus?
how are proteins made?
gag, pol, and env.
each gene generates several protein products:
genome is read in 3 different ways:
1) without frameshift
2) without frameshift and spliced afterwards (->env)
2) with frameshift at end of gag
after translation each product is processed by protease into mutiple proteins
features of retroviruses?
A retrovirus has two copies of its genome of singlestranded
RNA.
A retrovirus generates a provirus by
reverse transcription of the retroviral
genome.
An integrated provirus is a doublestranded
DNA sequence.
synthesis of ds DNA out of ss RNA?
problem: you need primers for the DNA synthesis and you don’t want to loose sequence
solution: usage of DNA repeat sequences instead of RNA as primers
but still you need to start with a tRNA primer to synthesize the first DNA primer for the plus strand
and this needs to jump to the beginning of the sequence (first jump)
-> plus strand is completed
now you need a primer for the minus strand: you degradate the RNA but leave random fragments -> you can synthesize a repeat DNA sequence as primer for the minus strand -> second jump required
-> complete minus strand
Adaptive (acquired) immunity
Adaptive (acquired) immunity – The response mediated by lymphocytes that
are activated by their specific interaction with antigen.
The response develops over several days as lymphocytes with antigenspecific
receptors are stimulated to proliferate and become effector cells.
It is responsible for immunological memory.
T B cells
B cell – A lymphocyte that produces antibodies. Development occurs primarily
in bone marrow.
B cells emerging from the marrow undergo further differentiation in the
bloodstream and peripheral lymphoid organs.
T cells – Lymphocytes of the T (thymic) lineage. T cells differentiate in the
thymus from stem cells of bone marrow origin.
They are grouped in several functional types (subsets) according to their
phenotype, mainly expression of surface proteins CD4 and CD8.
Different T cell subsets are involved in different cell-mediated immune
responses.
TCR BCR bind to
BCR The receptor for antigen expressed on the surface of B
lymphocytes.
The BCR has the same structure and specificity of the antibody that will be
produced by the same B cell after its activation by antigen.
T cell receptor (TCR) – The antigen receptor on T lymphocytes.
It is clonally expressed and binds to a complex of MHC class I or class II
protein and antigen-derived peptide.
BCR - V(D)J Recombination
1) D-to-J recombination
2) V-to-DJ recombination
by RAG1-RAG 2 (recombination activating gene 1)
VDJ build the variable region
the other segments and the signal sequences (RSS) are cut out forming the signal joint
RSS
Recombination Signal Sequence (RSS) in VDJ recombination
lies immediately adjacent to each antigen receptor gene segment and contains two well-conserved DNA elements (the
heptamer and the nonamer) separated by a spacer region
structure:
5’ heptamer - spacer - nonamer 3’
spacer: either 12 or 23 bp (highly conserved length. 12/23 rule)
steps of VDJ recombination
- RAG1 and RAG2 bind to 12RSS or 23RSS -> 12 signal complex / 23 signal complex
- capture of the second RSS -> paired complex/synapsis: RAGs introduce ds breaks between the gene segments and the RSSs (nicking)
- RAGs cooperate with NHEJ -> rejoining of the DNA ends
- RSS are joined to form the signal joint -> discarded
why is the 12/23 rule?
V gene segments lie next to 23
J gene segments next to 12
only two different types (12 and 23) of RSS can recombinate –> only appropiate segments recombine (not two of the same kind)
principle of variety of VDJ recombination?
junctional diversification during recombination of the many gene segments
imprecise NHEJ -> increases diversity
Control of V(D)J rearrangements
Lymphocytes after somatic recombination undergo “selections”.
positive selection in cortex: only lymphocytes with intermediate affinity to cortex specific peptide are allowed
negative selection in medulla: lymphocytes with high affinity to medulla specific peptide undergo apoptosis
