Genome, transcriptome and proteome in evolution. Xuhua Xia firstname.lastname@example.org http://dambe.bio.uottawa.ca. Transcription and Translation. Gene 1 Gene 2 Gene 3. Polycistronic mRNA. RNA polymerase. GCC~ tRNA Gly. Ribosome. UCC~ tRNA Gly. Protein.
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Genome, transcriptome and proteome in evolution
Gene 1 Gene 2 Gene 3
Elongation: Mn + M Mn+1
Measured in the exponentially proliferating chick embryo fibroblasts, 2hrs, in moles 10-12 per 106 cells. The difference is expected to be more extreme in mitochondria.
NNA would seem to be a more efficient codon than NNC
XIA, X., 1996. Genetics 144: 1309-1320.
EVOLUTIONARY INFORMATION FROM DNA SEQUENCES
- sequence of DNA (or RNA) that is
essential for a specific function
1. Protein-coding genes
U.S. Dept of Energy Human Genome Program,
2. RNA-specifying genes
3. Functional DNA elements
Do not use term in text (p.9): “Untranscribed genes” for #3
- untranscribed, but potentially functional at DNA level
How can pseudogenes arise during evolution?
- descendants of an ancestral gene that was present
in the last common ancestor of two or more species
- arose by gene duplication within a lineage
Where is the promoter?
What regions will be present in the mRNA?
Is there an error in this figure?
How many promoters in this region?
How many proteins encoded?
Operon = cluster of co-transcribed genes
Evolutionary advantages of operon organization?
5’ …. ATG GGA TTG CCC GCC …. 3’
3’ .… TAC CCT AAC GGG CGG …. 5’
5’ …. AUG GGA UUG CCC GCC …. 3’
… so genetic code table can be used directly
polypeptide (Hb-A): Val-His-Leu-Thr-Pro-Glu-Glu……GAA
polypeptide (Hb-S): Val-His-Leu-Thr-Pro-Val-Glu……GUA
Hiroshi Akashi and Takashi Gojobori, PNAS 99:3695–3700
have 1 – 6 members
Synonymous and nonsynonymous substitutions
0-fold, 2-fold, 3-fold, 4-fold degenerate sites
0-fold degenerate = non-degenerate
5’ …. AUG GGA UUG CCC CAC …. 3’
Some mitochondria, a few bacteria, a few protists
use a non-standard code
Table 1.4 Vertebrate mitochondrial code
UGA = Trp (instead of stop codon)
AUA, AUG = Met
AGA, AGG = stop codons
Possible implications of different codes in nature?
Grantham’s distance: F(V, P, C)
Miyata’s distance: F(V, P)
10 20 30 40 50 60
BLOSUM = BLOcks Substitution Matrixa substitution matrix used for sequence alignment of proteins (to score alignments between evolutionarily divergent protein sequences).