Mobile Genetic Elements
What are several possible mutations caused by transposons?
Duplications, Deletions, Insertions, Inversions, Translocations, Activation/Deactivation of gene, & initiates genome rearrangement. [This is because transposable elements can insert into other genes & disrupt their function]
How could SINES arise if they do not contain RTase?
RTase (Reverse Transcriptase) has to be there for SINES to arise.
Why is Resolvase needed in replication transposition?
Resolvase resolves pseudo-replication forks (cointegrate).
What is the difference between a Retrotransposons & a retrovirus?
Retrotransposons: Not infectious & do not move from organism to organism or cell to cell. Retrovirus: Is infectious & does move from cell to cell.
What is the difference between a retrovirus and other DNA or RNA viruses?
Retrovirus uses reverse transcriptase (to synthesize RNA from DNA) & other DNA/RNA can replicate on its own.
What are Alu elements?
SINES
Are sequences for new transposition insertion random?
Sometimes. Insertion is random at the level of the gene, but there are hotspots that sometimes occur.
What is one difference between c-onc & v-onc sequence?
C-onc: normal gene V-onc: gene present in cancer cells moved by retrovirus (mutated, overactive)
What serves as a primer for reverse transcriptase during Retroviral infection?
tRNA
What is a difference between (+) and (-) strand of viral DNA?
(+): Message strand [coding] (-): Template strand [noncoding]
What are the activities of RTase?
-DNA synthesis (-) strand of DNA -Reverse Transcriptase to degrade RNA
3 Examples of Retrotransposons
-LTR Retrotransposons -Non-LTR Retrotransposons -SINES
Overview of Retroviral Integration
1. Virus attaches to host receptors via the membrane. 2. Reverse transcriptase synthesizes 1st strand of DNA 3. Reverse transcriptase degrades RNA 4. Reverse transcriptase synthesizes 2nd strand of DNA 5. Viral DNA is integrated into host DNA 6. Viral DNA is transcribed 7. Viral DNA is exported 8. Viral DNA is translated. 9. Viral DNA & proteins are packed into the new virus [Note: Retrotransposons are not able to escape from the cell]
What RNA are the Alu elements related to?
7S RNA
How did Alu elements becomes so widespread in the genome?
7S RNA was reverse transcriptased to another enzyme
What is the difference between autonomous & incomplete (nonautonomous) elements?
Autonomous: can move by itself Nonautonomous: needs enzymes expressed by another autonomous element to be able to move (ex. RTase, Transposase)
Why is the DNA stage necessary in the retrovirus life cycle?
Because of the integration into the host genome
Where is the gene for Transposase located?
Between the Inverted Repeats.
Are transposons found in Prokaryotes or in Eukaryotes?
Both. 4% in yeast genome, 70% of amphibians & plant genome, 45% human genome
How are SINES converted back to DNA?
By RTase
Genes inside of a virus
Gag---(Packaging includes matrix, capsid, & nucleocapsid) Pol----(Enzymes that transform nucleic acid including protease, reverse transcriptase, & integrase) *env---(Signaling proteins such as surface & transmembrane proteins) Other---(Virus may "pick up" host genes & integrate these genes into itself) *Most important for DNA to remain infectious
Composite Transposons (Tn element)
Has insertion sequences (identical or closely related), with a transposable gene & can also carry additional genes
Insertion Sequences (IS)
Have inverted terminal repeats (itr), with a transposase gene & are autonomous with a simple transposon
Why are they called Alu?
Have restriction sites for the Alu restriction enzyme
How are the ends of IS elements different from the target sequence?
IS element: Inverted Repeats Target sequence: Direct Repeat
How can TyB be expressed in Ty elements?
If Frameshift occurs
Where is reverse transcriptase encoded in LTR (Long Terminal Repeats) Retrotransposons?
In TyB between the Long Terminal Repeats (LTR)
What enzyme is required for the integration of a dsDNA Retroviral genome into the host genome?
Integrase
What does it mean to be "autonomous"?
It means it does not need other enzymes. It has what it needs to regulate, synthesize, and function.
How can an organism deal with transposons?
It will silence the DNA with that transposon (RNAi)
Structure of a Retrovirus
LIPID BILAYER Membrane (RT) REVERSE TRANSCRIPTASE synthesizes RNA from DNA (SU) SURFACE PROTEIN proteins interacting with host (CA) CAPSID structural component (PR) PROTEASE. Cleaves Gag-Pol & Env VIRAL RNA Gag, Pol, Env & others (can be directly translated by host polymerase) (NC) NUCLEOCAPSID packaging dimer for RNA (MA) MATRIX between nucleocapsid & envelope) (IN) INTEGRASE integrates provirus into genome (TM) TRANSMEMBRANE mediates virus-host fusion
Can transposons make copies of themselves?
Yes.
Can transposons move from one location to another within the same genome?
Yes.
What are Retrotransposons?
Move by Copy & Paste but copy is made of RNA which is then transcribed to DNA (using reverse transcriptase) & these are then inserted into new places within the genome.
Replicative Transposition (Copy & Paste)
Needs a Transposase & Resolvase, the initial break is ss & cointegrate is formed. [The original element stays put & the copy goes to the new location]
Nonreplicative Transposition (Cut & Paste)
Needs a Transposase but no Resolvase, the initiate break can be ss or ds & no cointegrate is formed. [This is a "conservative model", the element moves from old to new site]
Can transposons infect other hosts than a host in which they are found?
No. Transposons do not have the genes necessary for conjugation.
When a transposon is removed from one location and transposed to another, is the "cutting out" precise?
Not always because it can tend to leave genes (information) behind
When a retrovirus integrates into DNA, does it generate extra direct repeats as transposons do?
Yes.
If supplemented with extra genes can a retrotransposon become a functional retrovirus?
Yes. If it acquires the necessary genes.
What is the result of the target sequence after transposition?
The target sequence gets duplicated.
Why can genes in a viral genome be mutated quicker?
There is no proofreading since they just go through transcription.
Why are composite transposons called "composite"?
They carry additional genes & have Transposase genes.
In most cases what protein is responsible for choosing the target sequence for a transposon?
Transposase.
What is the difference between transposons and defective elements?
Transposons have a Transposase (functional & codes for tranposase) & defective elements are missing Transposase (nonfunctional & do not code for anything).
What is an additional gene that could by carried by a retrovirus?
V-Oncogenes (for Cancer)
What is VLP?
Virus Like Particle [It looks like a virus but is not because it cannot infect]
Are transposable elements common in many organisms?
Yes.
Can one organism have more than one type of transposon?
Yes.
Can transposons exist in genomic DNA and plasmids?
Yes.
