Overlapping Genes Flashcards
1
Q
Overlapping Genes
A
- adjacent genes located on either DNA strand sharing one or more nucleotides in the coding sequence
- one gene considered reference gene
- other genes either in or out of phase
2
Q
Same strand overlap
A
- uni directional
- 3’ end of one gene overlaps with 5’ end of another
- regulated by common promoter
- expressed at the same time
3
Q
Different strand overlap
A
- convergent: 3’ end overlap
- divergent: 5’ end overlap
4
Q
In phase overlaps
A
Initiation diff.
- alternative translation start site
- new internal promoter formation
- identical c and different n terminals
Termination diff.
- same initiator codon
- termination at distinct codons
5
Q
Thermus flavus
A
- aspartokinase has A/B genes
- askA: a subunit
- askB contains B subunit at 3’ end of askA
6
Q
Out of Phase Overlaps
A
- non identical reading frames
- hard to get large overlaps due to higher percentage of stop codons
eg. mouse tumor suppressor gene - link4a/Arf locus
- alternative first exons transcribed from different promoters
- spliced to same acceptor site and translated in different frames
- both products key tumor suppressors
7
Q
Partial Overlap
A
- small overlaps of 5’/3’ end
- terminator site of 1 gene overlaps with initiator of another
eg. Tryptophan operon - trpE-D have one base overlap
- proteins synthesize in equimolar ratios
- couples translation
8
Q
Translational Recoding
A
- ribosomes directed to utilise alternative start sites, bypass termination codons, or programmed shift of reading frame
9
Q
Ribosomal Frameshift
A
- ribosome pauses and moves one nucleotide before continuing
- not all ribosomes shift
- depends on mRNA regulatory structure and sequence
10
Q
-1 Frameshift
A
- slippery sequence: 7 nucleotides
- spacer sequence: 12 nucleotides
- downstream stimulatory structure: pseudoknots/stem loops creating an energetic barrier that must be unfolded
- aids positioning over slippery site/pause of ribosome
- ribosome encounters frameshifting signal
- ribosome pauses at pseudoknot
- slips back one base
- unwinds pseudoknot and continues translating in -1 frame
11
Q
+1 Frameshift
A
eg. S. cerevisiae
- OAZ1 gene
- ODC produces polyamines
- OAZ stimulates ubiquitin independent degradation of ODC
- polyamines stabilise pseudoknot causing +1 frameshift
- maintains polyamine levels at suitable levels as OCD increases them, producing OAZ that degrades ODC and stops their production
12
Q
HIV Virus
A
- 1 PRF example
- Gag produced as precursor protein
- GagPol polyprotein contains viral enzymes protease, reverse transcriptase, and integrase in expressed at 1% of the Gag level due to -1 frameshift
- disruption causes inefficient assembly
- drug target to combat HIV
- stem loop stabilise to give more GagPol making it less efficient for virus to assemble
13
Q
Advantages
A
- genome compression
- PRF increases diversity
- coordinated control
- might mitigate detrimental effects of mutation
14
Q
Disadvantages
A
- overlapping genes may be subject to evolutionary constraint
- one gene adaptation is constrained by other overlapping genes
15
Q
Eukaryotes vs Prokaryotes
A
Eukaryotes
- overlap can be in introns
- more abundant overlaps
- less divergent different strand overlaps (5’ end important for regulation/localisation)
Prokaryotes
- exon overlapping common
- unidirectional overlap common
