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Evolution of mitochondrial genomes
mediated by DNA replication,
transcription and translation
Xuhua Xia
[email protected]
http://aix1.uottawa.ca/~xxia
Vertebrate mitochondria
• Endosymbiotic origin (Lang et al. 1997. Nature:493)
– Amitochondriate retortamonads
– Jakobid assemblage
– Reclinomonas americana: a heterotrophic flagellate, with a
mitochondrial genome:
• 69034 bp
• 97 genes
• 4 genes specifying a multisubunit, eubacterial-type RNA polymerase
• Vertebrate mitochondria:
–
–
–
–
~16500 bp
13 protein-coding genes
2 rRNA genes
~22 tRNA genes
• Genomes change. What factors govern genomic evolution?
– Mutation
– Selection
Xuhua Xia
Slide 2
Transcription, translation and DNA replication
Gene 1
Polycistronic mRNA
Ribosome
Gene 2
Gene 3
RNA polymerase
GCC~tRNA~Gly
UCC~tRNA~Gly
Protein
UCC~tRNA~Gly
UCC~tRNA~Gly
Xuhua Xia
Slide 3
DNA Replication in VertMT
Parental H
OH
Parental L
Daughter H
OL Daughter L
The parental Hstrand is left singlestranded for an
extended period of
time during mtDNA
duplication
(D.A. Clayton and colleagues, but see Holt et al.
2000 and Yang et al. 2003)
Xuhua Xia
Slide 4
Spontaneous deamination
• Sancar and Sancar 1988; Frederico et al. 1990; Lindahl 1993:
– Deamination of A leads to hypoxanthine that forms stronger base pair
with C than with T, generating an A.TG.C mutation.
– Deamination of C leads to U, generating C.GU.A mutations.
– Among these two types of spontaneous deamination, the CU
mutation occurs more frequently than the AG mutation.
– The spontaneous deamination rate is about 100 times greater in the
single-stranded DNA than in double-stranded DNA.
• Tanaka and Ozawa 1994; Jermiin et al. 1995; Perna and
Kocher 1995; Reyes at al. 1998:
– H-strand rich in G and T.
– L-strand rich in A and C.
Xuhua Xia
Slide 5
Spontaneous Deamination
NH 2
NH2
NH2
O
CH3
N
N
N
N
H
N
H
N
Adenine
N
NH2
Guanine
N
H
N
H
O
Cytosine
O
Methylcytosine
H2O
H2O
H2O
H2 O
O
NH3
NH3
NH3
NH3
O
N
N
NH
O
O
CH3
N
N
NH
N
H
N
Hypoxanthine
(Pair with C)
Xuhua Xia
N
NH
H
N
H
N
Xanthine
(Pair with C)
O
N
H
Uracil
(Pair with A)
N
O
N
H
Thymine
(Pair with A)
Slide 6
O
Effect of Spontaneous Deamination
L: 5’ATG CAA CCG AAT AGC …… TAA 3’
H: 3’TAC GTT GGC TTA TCG …… ATT 5’
L: 5’ATG CAA CCA AAC AAC …… TAA 3’
H: 3’TAC GTT GGU TTG TUG …… ATT 5’
Hb-A: Val-His-Leu-Thr-Pro-Glu-Glu……
Hb-S: Val-His-Leu-Thr-Pro-Val-Glu……
H-strand rich in G and T.
L-strand rich in A and C.
Position-dependence: The effect most visible at the 3rd codon position
Xuhua Xia
Slide 7
Mitochondrial Genetic Code
Xuhua Xia
Codon
Amino
acid
UUU
UUC
UUA
UUG
Codon
Amino
acid
Phe
Phe
Leu
Leu
UCU
UCC
UCA
UCG
CUU
CUC
CUA
CUG
Leu
Leu
Leu
Leu
AUU
AUC
AUA
AUG
GUU
GUC
GUA
GUG
Codon
Amino
acid
Codon
Amino
acid
Ser
Ser
Ser
Ser
UAU
UAC
UAA
UAG
Tyr
Tyr
Stop
Stop
UGU
UGC
UGA
UGG
Cys
Cys
Trp
Trp
CCU
CCC
CCA
CCG
Pro
Pro
Pro
Pro
CAU
CAC
CAA
CAG
His
His
Gln
Gln
CGU
CGC
CGA
CGG
Arg
Arg
Arg
Arg
lle
Ile
Met
Met
ACU
ACC
ACA
ACG
Thr
Thr
Thr
Thr
AAU
AAC
AAA
AAG
Asn
Asn
Lys
Lys
AGU
AGC
AGA
AGG
Ser
Ser
Stop
Stop
Val
Val
Val
Val
GCU
GCC
GCA
GCG
Ala
Ala
Ala
Ala
GAU
GAC
GAA
GAG
Asp
Asp
Glu
Glu
GGU
GGC
GGA
GGG
Gly
Gly
Gly
Gly
Slide 8
Mitochondrial Codon Usage
• The H-strand is the template strand for 12 of the 13 proteincoding genes in mammalian mitochondrial genome
• The RNA transcripts from the H-strand is co-linear with the
L-strand and should be rich in A and C at the third codon
position.
• Codon families and predictions
– Two-fold degenerate:
• Ending with A or G: e.g., AUA and AUG for methionine. Should end with
A
• Ending with C or U: e.g., AUC and AUU for isoleucine. Should end with
C
– Four-fold degenerate: e.g., GGN for glycine. Should end with either A
or C
Xuhua Xia
Slide 9
Two-fold A- or G-ending codons
Codon AA ObsFreq RSCU
AGA *
1 0.444
AGG *
0
0
Codon AA ObsFreq RSCU
UUA L
100 1.038
UUG L
10 0.104
UAA
UAG
*
*
7 3.111
1 0.444
AUA
AUG
M
M
214 1.705
37 0.295
GAA
GAG
E
E
73 1.698
13 0.302
CAA
CAG
Q
Q
79 1.837
7 0.163
AAA
AAG
K
K
88 1.814
9 0.186
UGA
UGG
W
W
91
9
1.82
0.18
12 CDS sequences (excluding ND6), Cow mtDNA.
RSCU: Relative Synonymous Codon Usage
Xuhua Xia
Slide 10
Two-fold C- or U-ending codons
Codon AA ObsFreq RSCU
UGC C
16 1.524
UGU C
5 0.476
Codon AA ObsFreq RSCU
AUC I
160 1.029
AUU I
151 0.971
GAC
GAU
D
D
46 1.438
18 0.563
AAC
AAU
N
N
102 1.291
56 0.709
UUC
UUU
F
F
130 1.156
95 0.844
AGC
AGU
S
S
42 0.955
9 0.205
CAC
CAU
H
H
63 1.355
30 0.645
UAC
UAU
Y
Y
72 1.125
56 0.875
12 CDS sequences (excluding ND6), Cow mtDNA.
RSCU: Relative Synonymous Codon Usage
Xuhua Xia
Slide 11
Four-fold codons
Codon
GCA
GCC
GCG
GCU
AA ObsFreq
A
102
A
90
A
1
A
48
GGA
GGC
GGG
GGU
G
G
G
G
93
60
19
21
CUA
CUC
CUG
CUU
L
L
L
L
283
95
29
61
RSCU
1.693
1.494
0.017
0.797
Codon
CGA
CGC
CGG
CGU
AA ObsFreq RSCU
R
42 2.71
R
11 0.71
R
3 0.194
R
6 0.387
1.927
1.244
0.394
0.435
UCA
UCC
UCG
UCU
S
S
S
S
2.938
0.986
0.301
0.633
ACA
ACC
ACG
ACU
T
T
T
T
98
64
4
47
2.227
1.455
0.091
1.068
150
2
95 1.267
14 0.187
41 0.547
CCA P
85 1.789
GUA V
82 1.964
CCC P
63 1.326
GUC V
46 1.102
CCG P
3 0.063
GUG V
9 0.216
CCU P
39 0.821
GUU V
30 0.719
12 CDS sequences (excluding ND6), Cow mtDNA. RSCU: Relative Synonymous Codon Usage
Xuhua Xia
Slide 12
Ribonucleotide concentration
rATP
1890
rCTP
53
rGTP
190
rUTP
130
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.
Xuhua Xia
Slide 13
Transcription and Translation
Gene 1
Gene 2
Polycistronic mRNA
Ribosome
Gene 3
RNA polymerase
GCC~tRNA~Gly
UCC~tRNA~Gly
Protein
UCC~tRNA~Gly
Initiation: Met-Gly-...
UCC~tRNA~Gly
Elongation: Mn + M  Mn+1
Xuhua Xia
Slide 14
Translational Hypothesis: Illustration
Protein:
Gly-Gly-Gly-Gly-...
mRNA 1:
GGA GGA GGA GGA GGA GGA GGA
mRNA 2:
GCC~tRNA~Gly
UCC~tRNA~Gly
UCC~tRNA~Gly
UCC~tRNA~Gly
UCC~tRNA~Gly
UCC~tRNA~Gly
UCC~tRNA~Gly
UCC~tRNA~Gly
UCC~tRNA~Gly
GGC GGC GGC GGC GGC GGC GGC
• There are two kinds of tRNA molecules, one with the
anticodon GCC and the other with the anticodon UCC. The
former is rare and the latter abundant.
• Which mRNA will be translated faster?
• (We have assumed no depletion of UCC-tRNA-Gly)
Xuhua Xia
Slide 15
E. Coli Data (highly expressed genes)
AA
Gly
Ala
Arg
Ile
Thr
Gln
IDtRNA Codon
3 GGU,GGC
2 GGA,GGG
1 GGG
1 GCU,GCA,GCG
2 GCC
2(1) CGU,CGC,CGA
CGG CGG
1 AUU,AUC
2 AUA
1+3 ACU,ACC
2 ACG
4 ACA,ACG
2 CAG
1 CAA
NtRNA tRNA p M
QM
4
1.1 0.82 0.995
1 0.15
1
0.1
3
1 0.77 0.964
2
0.3
4
0.9 0.97
1
1 0.025*
3
1 0.95
1
1 0.05
2
0.8 0.8 0.992
1
0.1
1
0.1
2
0.4 0.57 0.954
2
0.3
PM – proportion of the most abundant tRNA
QM – proportion of the codon(s) recognized by the most abundant tRNA.
Xuhua Xia
Ikemura 1981; Mouy and Gautier 1982; Kimura, M. 1983.
Xia, X. 1998. Genetics 149: 37-44
Slide 16
tRNA Anticodon and Codon Usage
• Classical view: tRNA concentration is fixed and codon usage
evolves to adapt to relative tRNA availability
• In vertebrate mtDNA, the evolution of codon usage is
constrained by the AC-biased mutation on the L-strand, with
most codons ending with either A or C.
• tRNA anticodons need to evolve to accommodate the
mutation-mediated codon usage bias.
• Predictions based on this selection hypothesis:
– For two-fold degenerate NNY and NNR codons which end mainly in
C and A, respectively, the wobble site of the tRNA anticodon should
be G and U, respectively.
– For four-fold degenerate NNN codons which end mainly in A, the
wobble site of the anticodon should be U.
Xuhua Xia
Slide 17
Alternative mutation hypothesis
• Given the wobble-paring, the
wobble site is perhaps neutral
and may be shaped by ACbiased mutation on the Lstrand and GT-biased mutation
on the H-strand.
• Predictions:
– The wobble site of the 8 tRNA
genes collinear with the H strand
should be mostly G or U
– The wobble site of the 14 tRNA
genes collinear with the L strand
should be mostly A or C
Xuhua Xia
Slide 18
AC% in tRNA
tRNA
Pro
Gln
Glu
Ala
Ser1
Asn
Cys
Tyr
Ile
Arg
Asp
Thr
Leu1
Met
Gly
Leu2
His
Ser2
Lys
Val
Trp
Phe
Xuhua Xia
Bos
0.379
0.347
0.406
0.377
0.394
0.397
0.463
0.500
0.522
0.507
0.507
0.565
0.547
0.522
0.507
0.521
0.571
0.500
0.522
0.582
0.582
0.612
Erpetoichthys
0.429
0.380
0.420
0.391
0.394
0.466
0.470
0.451
0.493
0.486
0.536
0.521
0.533
0.529
0.557
0.548
0.493
0.591
0.562
0.549
0.571
0.620
Masturus
0.414
0.437
0.377
0.420
0.437
0.397
0.448
0.423
0.514
0.551
0.507
0.514
0.541
0.536
0.521
0.548
0.536
0.529
0.573
0.556
0.583
0.603
Mus
0.373
0.380
0.377
0.449
0.435
0.437
0.455
0.522
0.493
0.485
0.557
0.507
0.533
0.551
0.574
0.563
0.612
0.525
0.538
0.580
0.582
0.574
Slide 19
Transfer RNA (tRNA)
Note that the 3’-end CCA is posttranscriptionally added by tRNA nucleotidyltransferase (tNtase).
Xuhua Xia
Slide 20
Standard and Non-standard Base Pairing
A/T
G/U
G/C
Xuhua Xia
Slide 21
Anticodon Loop
5’ 3’
A-U
G-C
C-G
U-A
G-C
A-U
A
C
A
U
UCC
3-AGG-5
Xuhua Xia
Anticodon
Codon (Gly)
Slide 22
Find tRNA Anticodon
>MYPU_TRNA_HIS
GTGAATATGGCGAAGGGGTCAACGCATCGGGTTGTGGTTCCGACATTCGCGGGTTCGAATCCCGTTATTCACCCCA
>MYPU_TRNA_LEU_1
CCCGAGTGGTGAAATGGCAGACACAGTTGACTCAAAATCAACCGCTTCACGGCGTGCTGGTTCAAGTCCAGTCTCGG
GCACCA
>MYPU_TRNA_CYS
GGCACCATAGCCAAATGGGCAAGGCATGGGTCTGCAACACCCTGATTACCGGTTCGAGTCCGGTTGGTGCCTCCA
5’---UCGGG
|||||
3’---AGCCU
Xuhua Xia
UU
UG
Slide 23
tRNA anticodons (AG-ending codons)
tRNA
tRNA-Cys
tRNA-Asp
tRNA-Phe
tRNA-His
tRNA-Ile
tRNA-Asn
tRNA-Tyr
Anticodon
GCA (C)
GUC
GAA
GUG
GAU
GUU (C)
GUA (C)
WC Cod
UGC
GAC
UUC
CAC
AUC
AAC
UAC
AA
Cys
Asp
Phe
His
Ile
Asn
Tyr
Anticodon Stem-Loop
23UUGAAUUGCAAAUUCAG39
24UAAUUUUGUCAAAGUUA40
25AGGCACUGAAAAUGCCU41
24UUAGAUUGUGAAUCUAA40
23UUACUUUGAUAGAGUAA39
27UUUAGCUGUUAACUAAA43
23UUAGACUGUAAAUCUAA39
tRNA-Gln
tRNA-Glu
tRNA-Lys
tRNA-Leu
tRNA-Met
tRNA-Trp
UUG (C)
UUC (C)
UUU
UAA
CAU
UCA
CAA
GAA
AAA
UUA
AUG
UGA
Gln
Glu
Lys
Leu
Met
Trp
26AAGAGTTTTGGATTCTT43
23GAUGGUUUUUCAUAUCAUU41
21CUAACCUUUUAAGUUAG37
28AUAAAACUUAAACUUUUAU46
24UCGGGCCCAUACCCCGA40
24AGAGCCUUCAAAGCCCU40*
tRNA-Pro
tRNA-Ala
tRNA-Gly
tRNA-Leu
tRNA-Arg
tRNA-Ser
tRNA-Thr
tRNA-Val
UCC (C)
UGC (C)
UCC
UAG
UCG
UGA (C)
UGU
UAC
GGA
GCA
GGA
CUA
CGA
UCA
ACA
GUA
Pro
Ala
Gly
Leu
Arg
Ser
Thr
Val
24TCAGCTTTGGGGGTTGA40
22UGGUUGAUUUGCAUUCAAUUG42
24AGCUGACUUCCAAUCAGCU42
27UUGGUCUUAGGAACCAA43
25AAUGAUUUCGACUCAUU41
25UGUUGGCUUGAAACCAAUA43
23CUGGUCUUGUAAACCAG39
24UCCAGUUUACACCUAGA40*
Xuhua Xia
Alternative
hypothesis:
Wobble
Capacity
Hypothesis.
Slide 24
Initiation and Elongation
• Met codon usage from the 12 CDSs:
AUA
214
AUG
37
• Met-tRNA anticodon: CAU favoring the AUG codon
• Two choices for the Met anticodon evolution:
– UAU (matching AUA) to increase the translation elongation rate
– CAU (matching AUG) to increase the translation initiation rate
• Natural selection has chosen CAU.
• Translation initiation is important.
• Alternative explanation: C in anticodon CAU modified to 5formylcytidine which may allow it to pair with both A and G
(Moriya et al., 1994; Matsuyama et al., 1998)
Xuhua Xia
Slide 25
Summary
• mtDNA replication leaves the H-strand single stranded for an
extended period, leading to elevated C  U mutations on the
H-strand and G A mutations on the L-strand.
• This biased mutation spectrum leads to differential codon
usage bias for protein-coding genes residing on the two
strands consistent with the differential mutation pressure.
• The biased codon usage leads to anticodon evolution to
optimize transcription and translation.
• Increasing translation initiation rate is important in genome
evolution
• Mutation and selection to increase the transcription and
translation rates are important determinants of codonanticodon adaptation in vertebrate mitochondrial genomes.
Xuhua Xia
Slide 26
ND6 Gene
Xuhua Xia
Slide 27
Cow MtDNA (AG-ending codons)
Codon AA ObsFreq RSCU
AGA *
0
0
AGG *
0
0
Codon AA ObsFreq RSCU
UUA L
10 3.158
UUG L
6 1.895
UAA
UAG
*
*
1
0
4
0
AUA
AUG
M
M
4 0.727
7 1.273
GAA
GAG
E
E
5 1.111
4 0.889
CAA
CAG
Q
Q
0
1
0
2
AAA
AAG
K
K
2
2
UGA
UGG
W
W
1
3
0.5
1.5
1
1
ND6 sequence
Xuhua Xia
Slide 28
Cow MtDNA (CU-ending codons)
Codon AA ObsFreq RSCU
UGC C
0
0
UGU C
1
2
Codon AA ObsFreq RSCU
AUC I
0
0
AUU I
14
2
GAC
GAU
D
D
0
4
0
2
AAC
AAU
N
N
0
4
UUC
UUU
F
F
3
12
0.4
1.6
AGC
AGU
S
S
1 0.545
3 1.636
CAC
CAU
H
H
0
0
0
0
UAC
UAU
Y
Y
2
8
0
2
0.4
1.6
ND6 sequence
Xuhua Xia
Slide 29
Cow MtDNA (N-ending codons)
Codon
CGA
CGC
CGG
CGU
AA ObsFreq RSCU
0
0
R
0
0
R
0
0
R
4
1
R
0.615
0.308
1.846
1.231
UCA
UCC
UCG
UCU
S
S
S
S
1
1
1
4
0.545
0.545
0.545
2.182
L
L
L
L
2 0.632
0
0
0
0
1 0.316
ACA
ACC
ACG
ACU
T
T
T
T
3
1
1
3
1.5
0.5
0.5
1.5
P
P
P
P
0
0
0
3
0
0
0
4
GUA
GUC
GUG
GUU
V
V
V
V
Codon
GCA
GCC
GCG
GCU
AA ObsFreq
1
A
1
A
1
A
4
A
RSCU
0.571
0.571
0.571
2.286
GGA
GGC
GGG
GGU
G
G
G
G
4
2
12
8
CUA
CUC
CUG
CUU
CCA
CCC
CCG
CCU
5 0.87
2 0.348
6 1.043
10 1.739
ND6 sequence
Xuhua Xia
Slide 30
Wobble Capacity Hypothesis
• Recall predictions based on the selection hypothesis:
– For two-fold degenerate NNY and NNR codons which end mainly in
C and A, respectively, the wobble site of the tRNA anticodon should
be G and U, respectively.
– For four-fold degenerate NNN codons which end mainly in A, the
wobble site of the anticodon should be U.
• Why the wobble site should be G or U according to the
wobble capacity hypothesis (Agris 2004; Bonitz et al.1980;
Heckman et al. 1980; Martin et al. 1990; Tong and Wong
2004):
– NNY codons should have G at the anticodon wobble site because G
can pair with both C and U; NNR codons should have U at the
anticodon wobble site because U can pair with both A and G.
– NNN codons which have U at the anticodon wobble site because U
appears to be the most versatile in wobble-paring with other
nucleotides (Sibler et al., 1986; Inagaki et al., 1995; Yokoyama and
Nishimura, 1995).
Xuhua Xia
Slide 31
Arginine Codon Usage in 4 Species
The arginine codons are translated by a single tRNA with a wobbling A
Species
Accession
CGA
CGC
CGG
CGU
C. elegans
NC_001328
1
0
1
29
M. polymorpha
NC_001660
260
165
118
286
P. Canadensis
NC_001762
0
1
0
19
S. cerevisiae
NC_001224
0
2
1
18
Xuhua Xia
Slide 32
Illustration of Different predictions
• A lysine (Lys) codon family has 20 AAA and 60 AAG codons.
– WVH: a wobble U in the tRNALys anticodon
– CAAH would predict a wobble C
– If the tRNALys anticodon is found to have a wobble U, then WVH is
supported; if a wobble C is found, then CAAH is supported.
• If we have 60 AAA codons and 20 AAG codons and if tRNALys
anticodon has a wobble U, then both hypotheses are supported.
• If the Lys codon has 40 AAA and 40 AAG codons
– WVH: a wobble U
– CAAH: no prediction
• If we have no AAA codon but 80 AAG codon,
– WVH: a wobble U
– CAAH: a wobble C
• Anticodon wobble nucleotides in vertebrate mtDNA are consistent with
both hypotheses which have the same prediction for every codon family.
Xuhua Xia
Slide 33
Fungal Data
Species
Accession(1)
Allomyces macrogynus
NC_001715
4
1
13
Ashbya gossypii ATCC 10895
NC_005789
3
0
10
•UGA = Trp
Aspergillus niger
NC_007445
4
0
12
•AUA = Met
Aspergillus tubingensis
NC_007597
4
0
12
Candida albicans SC5314
NC_002653
4
1
11
Candida glabrata
NC_004691
3
0
12
Kluyveromyces thermotolerans
NC_006626
3
0
11
Rhizophydium sp.136
NC_003053
16
0
2
Spizellomyces punctatus1
NC_003052
16
0
4
…
…
…
…
…
23
414
Sum
Xuhua Xia
Code(2) NCAAH NWVH
• TT3:
•CUN = Thr
• TT4:
•UGA= Trp
• TT16:
•UAG = Leu
Slide 34
Codon families supporting CAAH
AC(4) RSCU(5)
Codon
Candida metapsilosis
CGU
43
CGG
0
0.00
CGC
0
0.00
CGA
3
0.26
CGU
37
CGG
0
0.00
CGC
0
0.00
CGA
3
0.30
CGU
19
CGG
0
0.00
CGC
1
0.20
CGA
0
0.00
AGU
120
AGC
1
UGG
77
UGA
0
UGG
77
UGA
0
UGG
109
UGA
0
Candida orthopsilosis
Pichia Canadensis
Pichia Canadensis
Harpochytrium sp. JEL94
Harpochytrium sp. JEL105
Hyaloraphidium curvatum
Xuhua Xia
N(1) ECAAH(2) EWVH(3)
Species
A
A
A
A
U
U
U
G
ACG
ACG
ACG
ACU
3.74
3.70
3.80
1.98
0.02
C
U
CCA
2.00
0.00
C
U
CCA
Only CGN (Arg)
and AGY (Ser) and
UGR (Trp) codon
families support
CAAH.
Codon families
supporting CAAH
exhibit greater
codon usage bias
than those not
supporting CAAH
2
0
C
U
CCA
2.00
0.00
Only a subset of data is
shown
Slide 35
CGN codon family support CAAH. Why?
• The anticodon for the CGN codon family is ACG to
match the more abundant CGU codon instead of
UCG to wobble pair with all four codons. Possible
alternative explanations:
– UCG can wobble pair with UGA which is a stop codon
– Historical inertia: in most bacterial species, the anticodon
is ACG which undergoes the A-I (inosine) conversion,
with I capable of pairing with A, C, U. Mitochondrial
genome is a highly degenerated bacterial genome and
consequently still have kept the ACG anticodon.
Xuhua Xia
Slide 36
UGR codon family supports CAAH. Why?
• UGG codon is more abundant than UGA codon, and the
anticodon is CCA to match the more abundant UGG instead
of UCA to wobble pair with both codons.
• Historical inertia:
– The standard genetic code has UGA being stop codon and UGG as
tryptophan.
– This has two consequences:
• The anticodon for UGG should naturally be CCA.
• UGG is far more abundant than UGA (stop)
– When UGA was captured as a Trp codon, the anticodon remains CCA
and UGG remains far more abundant than UGA.
– So the support of CAAH is not really due to codon-anticodon
adaptation.
• The mitochondrial genome of K. thermotolerans has 60 UGA
codons and only one UGG codon, its tRNATrp anticodon has
changed from CCA to UCA
Xuhua Xia
Slide 37
Met codon usage (TT 3)
Species
Xuhua Xia
AUA AUG
Ashbya gossypii ATCC 10895
95
34
Candida glabrata
85
78
Kluyveromyces thermotolerans
30
78
Saccharomyces cerevisiae
244
184
Saccharomyces castelli
128
69
Saccharomyces servazzii
181
93
Yarrowia lipolytica
596
232
The anticodon is CAU
matching AUG
Slide 38
Selection against AUA codons
Met
Leu
Glu
Lys
Gln
Arg
Trp
Species
AUA UUA GAA AAA
A. gossypii
1.473 1.993 1.826 1.852 1.917
2
2
C. glabrata
1.043 1.995 2.000 1.938 1.889
2
2
K. thermotolerans
0.556 1.973 1.910 1.948 1.945
2 1.967
S. cerevisiae
1.140 1.969 1.800 1.883 1.794 1.947 1.908
S. castelli
1.299 1.994 1.891 1.981 1.969
S. servazzii
1.321 1.931 1.702 1.824 1.841 1.959
Y. lipolytica
1.440 1.968 1.536 1.859 1.963 1.922 1.882
Xuhua Xia
CAA AGA UGA
2 1.918
2
In species with two
tRNAMet, with one
having a UAU
anticodon, then AUA
codon usage is
significantly increased
(Xia, X. 2007).
Slide 39
Why so little support for CAAH?
• Altering tRNA anticodons (including the wobble nucleotide)
often results in decreased efficiency and specificity of
aminoacylation of altered tRNA (Li et al. 1993; Pallanck et al.
1992; Pallanck and Schulman 1991; Schulman 1991).
• tRNA anticodons may not be flexible to adapt to codon usage
bias and consequently raises difficulties for CAAH.
• CAAH is supported only when codon families
– Exhibit extreme codon usage bias and
– Code for a frequently used amino acid
• Further reading: Xia, X. 2008. The cost of wobble translation
in fungal mitochondrial genomes: integration of two
traditional hypotheses. BMC Evolutionary Biology 8:211.
Xuhua Xia
Slide 40