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Table 2 Codon data

From: Differences in codon bias cannot explain differences in translational power among microbes

Codon

AA

Codon frequency

tRNA abund.c (%)

Empirical rel. trans. ratesd

Predicted rel. translation rates

  

E. colia (× 10-3)

Low biasb (× 10-3)

  

Sc. 2e

Sc. 3e

Sc. 4e

Sc. 5f

UUU

Phe

8.0

9.6

1.5

8.5

(7.6)

(6.3)

(3.2)

3.7

UUC

Phe

23.4

21.8

1.5

12.0

(12.0)

(10.8)

(10.8)

6.4

UUA

Leu

2.8

6.6

2.7

4.3

(5.1)

(5.2)

(1.9)

7.1

UUG

Leu

4.3

17.1

3.8

8.7

(6.0)

(6.5)

(6.5)

8.9

UCU

Ser

16.5

10.7

3.4

11.6

(10.3)

(9.5)

(9.5)

7.1

UCC

Ser

11.8

7.2

1.2

14.7

(9.0)

(8.0)

(7.3)

6.0

UCA

Ser

2.0

5.4

2.1

7.0

(4.6)

(3.3)

(4.6)

2.5

UCG

Ser

2.5

7.1

2.6

9.0

(5.0)

(3.7)

(0.4)

2.8

UAU

Tyr

6.8

11.3

2.7

4.3

(7.2)

(6.1)

(2.8)

7.3

UAC

Tyr

16.6

12.1

2.7

8.4

(10.4)

(9.5)

(9.5)

11.5

UGU

Cys

2.8

3.1

2.1

4.0

(5.2)

(5.4)

(1.9)

7.6

UGC

Cys

3.8

3.6

2.1

7.0

(5.8)

(6.3)

(6.3)

8.9

UGG

Trp

7.1

7.1

1.5

5.0

(7.3)

(7.3)

(7.3)

6.4

CUU

Leu

3.9

15.2

2.6

8.4

(5.8)

(3.9)

(9.8)

6.3

CUC

Leu

4.1

16.0

1.7

11.0

(5.9)

(4.1)

(12.0)

6.5

CUA

Leu

0.8

4.4

0.9

0.6

(3.6)

(0.6)

(0.6)

2.9

CUG

Leu

61.2

17.9

7.3

14.4

(18.6)

(15.7)

(15.7)

24.9

CCU

Pro

4.4

9.0

1.8

8.4

(6.1)

(4.5)

(7.3)

2.7

CCC

Pro

1.1

6.2

1.1

9.6

(3.9)

(2.3)

(0.5)

1.3

CCA

Pro

5.2

12.1

0.8

1.6

(6.5)

(4.9)

(9.0)

2.9

CCG

Pro

29.0

12.4

1.5

2.5

(13.2)

(11.6)

(11.6)

6.8

CAU

His

6.8

9.0

1.2

4.0

(7.2)

(6.3)

(2.7)

3.5

CAC

His

14.3

12.1

1.2

8.0

(9.7)

(9.1)

(9.1)

5.1

CAA

Gln

7.1

10.7

1.2

5.6

(7.3)

(5.8)

(3.4)

3.3

CAG

Gln

27.5

23.9

2.3

10.0

(12.9)

(11.4)

(11.4)

6.4

CGU

Arg

44.2

21.4

7.5

14.0

(16.0)

(13.7)

(13.7)

31.3

CGC

Arg

20.8

19.1

7.5

11.5

(11.4)

(9.4)

(10.5)

21.4

CGA

Arg

0.7

11.3

7.5

3.0

(3.5)

(1.7)

(0.6)

3.9

CGG

Arg

0.6

5.1

0.6

0.8

(3.4)

(1.6)

(0.6)

2.6

AUU

Ile

15.9

21.5

6.8

 

10.2

8.2

4.1

17.1

AUC

Ile

44.2

28.0

6.8

 

16.0

13.7

13.7

28.6

AUA

Ile

0.5

11.2

0.3

 

3.3

1.5

0.6

1.4

AUG

Met

21.8

21.8

1.4

 

11.7

10.5

10.5

5.7

ACU

Thr

20.8

15.0

3.8

 

11.4

9.9

8.7

7.6

ACC

Thr

26.9

18.7

1.8

 

12.8

11.3

11.3

8.7

ACA

Thr

2.6

10.0

2.0

 

5.1

3.5

0.5

2.7

ACG

Thr

4.2

10.8

2.9

 

6.0

4.5

7.1

3.4

AAU

Asn

5.7

16.7

2.1

 

6.7

5.1

3.5

3.9

AAC

Asn

29.4

18.4

2.1

 

13.3

11.7

11.7

8.9

AAA

Lys

55.4

39.6

3.1

 

17.8

15.0

15.0

12.8

AAG

Lys

17.4

33.2

1.2

 

10.6

8.4

4.5

2.9

AGU

Ser

2.2

6.8

1.7

 

4.8

3.8

2.3

3.4

AGC

Ser

9.4

7.2

1.7

 

8.2

7.9

7.9

7.0

AGA

Arg

0.6

5.4

1.1

 

3.4

4.9

0.6

3.7

AGG

Arg

0.0

4.5

1.7

 

2.6

1.1

0.6

0.8

GUU

Val

43.5

38.8

7.9

 

15.9

13.6

13.6

23.3

GUC

Val

7.7

13.2

2.0

 

7.5

5.7

0.6

9.8

GUA

Val

22.5

20.1

6.0

 

11.8

9.8

10.5

16.8

GUG

Val

15.1

16.8

6.0

 

9.9

8.0

8.5

13.7

GCU

Ala

39.8

38.6

7.2

 

15.3

13.2

13.2

19.4

GCC

Ala

11.9

15.7

1.1

 

9.0

7.2

0.5

10.6

GCA

Ala

25.1

30.6

6.1

 

12.4

10.4

10.1

15.4

GCG

Ala

24.3

16.2

6.1

 

12.2

10.3

8.2

15.1

GAU

Asp

19.4

22.3

4.4

 

11.1

9.3

3.7

14.0

GAC

Asp

34.0

31.1

4.4

 

14.2

12.4

12.4

18.5

GAA

Glu

58.3

39.8

8.5

 

18.2

15.3

15.3

35.7

GAG

Glu

17.1

35.6

3.4

 

10.5

8.3

4.5

7.7

GGU

Gly

45.9

23.7

9.3

 

16.3

13.9

13.9

21.0

GGC

Gly

34.4

23.0

7.3

 

14.3

12.1

10.7

18.2

GGA

Gly

1.3

17.8

1.9

 

4.1

2.3

0.6

3.5

GGG

Gly

2.4

19.5

3.2

 

4.9

3.2

8.7

4.8

  1. a Proteome codon frequencies from reference [70] for E. coli growing at a specific growth rate of 1.73 hr-1, modified slightly as described in Methods.
  2. b Low bias codon frequencies representing the degree of codon bias present in the genome of T. pallidum, generated as described in Methods.
  3. c Summed abundance of all tRNA species cognate to the listed codon, expressed as a percentage of total tRNA, based on tRNA abundance data of references [70] and [69] and cognate specificity of reference [85], modified slightly as described in Methods. Values for all codons sum to >100%, a result of the partially overlapping codon specificity of many tRNA species.
  4. d Empirically determined relative rates of ternary complex selection at the listed codon from reference [45], expressed relative to the rate of a uniform competing frameshift event. Rate for codons CGC and CGA modified as described in Methods. Estimates of s bias were made using the rates as listed or with a correction for the duration of translocation, as described in Methods.
  5. e Predicted relative translation rates based on the empirical rates of column 6 and scenarios as described in Methods. Estimates of s bias were made using empirical rates of column 6 for YNN codons in preference to the predicted rates shown in parentheses; predicted rates are shown for comparison only.
  6. f Predicted relative translation rates from theory of reference [62], modified slightly as described in Methods, using the codon frequency data of column 3 and the cognate tRNA abundance data of column 5.
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