What does %GC means?
Is it always the same in different species?
percent of G and C nucleotides in genome
%GC varies among species
particularly bacteria, plants, ..
little variation among vertebrates
What are Isochores?
long stretches (100s of kb) of DNA with uniform %GC
—> isochores could span > 10 Mb
When are isochores heavy / light?
Where are they found?
High %GC = heavy isochores (H)
Low %GC = light isochores (L)
—> heavy only found in warm-blooded vertebrates, not in cold-blooded (fish)
Traditional isochore classification of human genome.
L1 (<37% GC)
L2 (37-42%)
H1 (42-47%)
H2 (47-52%)
H3 (>52%)
What are the two hypotheses for the existance of isochores?
Selectional hypothesis
GC-pairing is stronger than AT-pairing —> stabilize DNA at high temperatures
Support: heavy isochores found in warm-blooded
Mutationist hypothesis
Nucleotide pool changes during replication (GC earlier)
Support: GC-regions replicate early —> bias towards G or C over time
What is the variability (typical order) and correlation pf %GC content among different regions?
Typical Order:
Coding regions > Introns > 5’ flanking regions > 3’ flanking regions
Correlation:
strong correlation in %GC content among all regions
What is the phenomen ‘codon bias’?
Give an example
all synonymous codons for a particular amino acid not used with equal frequency
—> certain codons are preferred e.g. Leucine
encoded by: CTG, CTA, CTC, CTT, TTG, TTA
expected: each codon 1/6 % of time, BUT
E.col CTG —> 90%
yeast TTG —> 90%
—> preferred codon differes from species to species
What are the measures used to quantify codon bias in genes?
ENC (Effective Number of Codons)
average number of codons (20-61) used to encode 20 amino acids
—>Low ENC = high codon bias
Fop (frequency of optimal codons)
frequency with which ‘optimal’ codon (highest frequency in highly expressed genes) user for each amino acid
—> High Fop = high codon bias
Fop species-specific, has to know optimal codons
ENC used with any species, without prior knowledge
What are some observed patterns of codon bias?
higher in highly-expressed genes
higher in short genes than long
higher in female-expressed than male
Why is there codon bias? short
Natural Selection: favors use of optimal codons
—> faster translation, more accurate
Mutation: reverse bias lead to synonymous sites being AT-rich
—> non-random codon usage
Is there evidence for the Selection-explanation for codon bias?
Yes, highly expressed genes have higher codon bias
Explain the Experiment: Changing optimal codons to non-optimal codons reduces protein level
Drosophila Alcohol dehydrogenase (ADH)
Wa-F: wild-type, optimal leucine codons
1 leu: 1 leucine codon changed from optimal to non-optimal
6 leu: 6 codons changed
10 leu: 10 codons changed
Protein Concentration Comparison: Wa-F > 1 leu > 6 leu > 10 leu
Ethanol Tolerance (LD50):
Wa-F: 9%
10 leu: 7.5%
How do most optimal codons end in?
G or C
—> mutational hypothesis requires mutational bias towards G or C
Zuletzt geändertvor 2 Monaten