Journal of Molecular Evolution

, Volume 75, Issue 3, pp 151–153

Erratum to: Transfer RNA Gene Numbers may not be Completely Responsible for the Codon Usage Bias in Asparagine, Isoleucine, Phenylalanine, and Tyrosine in the High Expression Genes in Bacteria

Authors

  • Siddhartha Sankar Satapathy
    • Departments of Computer Science and EngineeringTezpur University
  • Malay Dutta
    • Departments of Computer Science and EngineeringTezpur University
  • Alak Kumar Buragohain
    • Departments of Molecular Biology and BiotechnologyTezpur University
    • Departments of Molecular Biology and BiotechnologyTezpur University
Erratum

DOI: 10.1007/s00239-012-9531-2

Cite this article as:
Satapathy, S.S., Dutta, M., Buragohain, A.K. et al. J Mol Evol (2012) 75: 151. doi:10.1007/s00239-012-9531-2
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Erratum to: J Mol Evol (2012) 75:34–42 DOI 10.1007/s00239-012-9524-1

We regret to inform that the data presented in our published article (Satapathy et al. 2012) for the whole genome with respect to amino acid usage and NNC/NNU ratio is erroneous for the two bacteria Pseudomonas aeruginosa and Streptomyces coelicolor in Tables 1 and 2 of the article. The correct data under the “Whole genome” heading for the two bacteria are as follows:

In Table 1
  1. (i)

    The correct “Whole genome” data for the bacteria P. aeruginosa are 1859569, 3.56, 2.64, 4.17, 2.54.

     
  2. (ii)

    The correct “Whole genome” data for the bacteria S. coelicolor are 2560775, 2.65, 1.70, 2.86, 2.05.

     
In view of the above changes in Table 1, the amino acid usage data of these two bacteria given in the Supplementary Table 1 is no longer required and hence to be ignored.
In Table 2
  1. (i)

    The correct “Whole genome” data for the bacteria P. aeruginosa are 19.62, 6.06, 13.25, 3.82.

     
  2. (ii)

    The correct “Whole genome” data for the bacteria S. coelicolor are 61.99, 23.83, 46.16, 20.5.

     

In view of the above corrections in Table 1, what has been stated in the first paragraph of the result section in the article about the amino acid composition difference between the whole genomes and high expression genes in these two bacteria is no longer valid and hence to be ignored.

In view of the above corrections in Table 2, the NNC/NNU results for the two bacteria are in agreement with the earlier observation of Sharp et al. (2005). Hence what has been stated in the third paragraph in the discussion section of the article is no longer valid and hence to be ignored.

The changes in Tables 1 and 2 have no effect on the main findings of the analyses presented in the article. There is no change in the Title, Abstract, and Reference sections of the article.

Corrected tables with the relevant changes in the footnote are given below.
Table 1

Usage (in %) of phenylalanine (Phe), asparagine (Asn), isoleucine (Ile) and tyrosine (Tyr) amino acids

S. no.

Strain

Group

Genome size

GC (%)

Top 100 HE genes

Whole genome

Total

Phe

Asn

Ile

Tyr

Total

Phe

Asn

Ile

Tyr

1

S. aureus

Firmicutes

2903636

32.84

33828

3.50

4.70

7.42

2.82

801462

4.48

5.69

8.59

3.93

2

S. mutans

Firmicutes

2030921

36.83

39508

3.60

5.06

6.85

3.26

579702

4.76

4.85

7.74

3.85

3

L. monocytogenes

Firmicutes

2944528

37.98

31671

3.72

4.58

6.96

3.2

870878

4.53

4.62

7.84

3.45

4

H. influenzae

γ Proteobacteria

1830069

38.15

25071

4.38

5.23

6.75

3.28

521077

4.48

4.88

7.11

3.14

5

B. subtilis

Firmicutes

4214630

43.52

32519

3.65

4.06

6.45

3.02

1228408

4.50

3.95

7.37

3.49

6

L. plantarum

Firmicutes

3348625

44.42

32119

3.63

4.58

6.54

3.50

920243

3.97

4.41

6.56

3.52

7

E. coli

γ Proteobacteria

4639675

50.00

22219

3.34

3.94

5.99

2.58

1313473

3.90

3.89

6.01

2.83

8

N. europaea

β Proteobacteria

2812094

50.72

22536

4.05

3.70

6.17

2.95

800071

3.92

3.58

6.39

2.84

9

P. syringae

γ Proteobacteria

6538260

58.34

26326

3.18

3.26

5.10

2.87

1814263

3.63

3.19

4.98

2.55

10

B. longum

Actinobacteria

2260266

60.13

30848

3.55

3.90

6.04

2.91

640513

3.41

3.43

5.37

2.68

11

D. vulgaris

δ Proteobacteria

3773159

63.28

26270

3.49

3.03

5.09

2.55

1020841

3.59

2.41

4.45

2.27

12

B. japonicum

α Proteobacteria

9105828

64.06

23090

3.55

3.61

5.29

2.70

2634346

3.73

2.76

5.26

2.21

13

R. palustris

α Proteobacteria

5467640

65.03

30075

3.91

3.96

5.46

3.20

1580833

3.64

2.58

5.26

2.22

14

P. aeruginosa

γ Proteobacteria

6264404

66.56

21744

3.59

3.68

5.05

2.72

1859569

3.56

2.64

4.17

2.54

15

R. sphaeroides

α Proteobacteria

4603060

68.79

23416

3.74

3.25

5.56

2.72

943868

3.49

2.02

4.52

1.91

16

T. thermophilus

Deinococcus-Thermus

2116056

69.50

23854

3.45

2.84

4.87

3.11

589163

3.77

1.55

2.67

2.87

17

S. coelicolor

Actinobacteria

9054847

72.00

27997

2.68

2.61

4.02

2.33

2560775

2.65

1.70

2.86

2.05

Table presents total number of codons and percentage of codons encoding four amino acids, phenylalanine (Phe), asparagine (Asn), isoleucine (Ile) and tyrosine (Tyr) in top 100 high expression (HE) genes as well as in the whole genome of seventeen bacteria (Bacillus subtilis, Bifidobacterium longum, Bradyrhizobium japonicum, Desulfovibrio vulgarisHildenborough, Escherichia coli, Haemophilus influenzae, Lactobacillus plantarum, Listeria monocytogenes, Nitrosomonas europaea, Pseudomonas aeruginosa, Pseudomonas syringae, Rhodobacter sphaeroides, Rhodopseudomonas palustris, Staphylococcus aureus, Streptococcus mutans, Streptomyces coelicolor, Thermus thermophilus)

Table 2

Transfer RNA gene number and synonymous codon usage in phenylalanine (Phe), asparagine (Asn), isoleucine (Ile) and tyrosine (Tyr) amino acids

S. no.

Name

tRNA Gene number

Top100 HE genesb

Whole genomeb

Phe

Asn

Ile

Tyr

Phe

Asn

Ile

Tyr

Phe

Asn

Ile

Tyr

GAA

GTT

GAT

GTA

UUC/ UUU

AAC/ AAU

AUC/ AUU

UAC/ UAU

UUC/ UUU

AAC/ AAU

AUC/ AUU

UAC/ UAU

1

S. aureus

2

3

2

2

1.02

0.75

0.51

0.51

0.37

0.31

0.28

0.28

2

S. mutans

2

2

2

2

0.38

0.33

0.35

0.35

0.25

0.24

0.30

0.27

3

L. monocytogenes

2

4

3

2

1.11

1.18

0.67

0.79

0.47

0.45

0.36

0.46

4

H. influenzae

1

2

3

1

0.45

0.36

0.36

0.33

0.38

0.33

0.28

0.28

5

B. subtilis

3

4

3

2

0.78

1.36

1.06

0.81

0.46

0.77

0.73

0.53

6

L. plantarum

2

5

3

2

0.59

0.72

0.58

0.73

0.53

0.66

0.52

0.63

7

E. coli

2

4

3

3

2.42

4.54

1.99

1.88

0.74

1.24

0.83

0.76

8

N. europaea

1

1

1

1

0.70

0.72

0.74

0.62

0.98

0.68

1.49

0.68

9

P. syringae

1

2

5

1

1.38

3.03

2.30

0.94

1.81

2.36

2.25

1.80

10

B. longum

1

3

1

1

25.05

9.95

4.85

8.07

6.89

2.81

2.81

2.24

11

D. vulgaris

1

2

5

1

12.10

5.91

7.84

4.32

7.04

4.37

7.49

2.43

12

B. japonicum

2

2

1

1

2.55

1.77

3.12

1.51

4.70

2.21

7.16

1.15

13

R. palustris

1

1

2

1

12.21

4.54

10.27

2.46

6.24

2.40

8.19

1.33

14

P. aeruginosa

1

2

4

1

40.05

10.13

11.66

5.09

19.62

6.06

13.25

3.82

15

R. sphaeroides

1

1

3

0a

37.09

11.06

31.50

1.86

11.96

3.63

18.90

1.12

16

T. thermophilus

1

1

1

1

5.65

134.40

7.30

56.15

4.68

40.06

9.30

23.38

17

S. coelicolor

1

2

1

1

73.90

59.83

64.41

35.22

61.99

23.83

46.16

20.5

aNo tRNA gene according the Genomic tRNA database (http://gtrnadb.ucsc.edu)

bThe ratio between abundance values of the two synonymous codons of an amino acid in the high expression (HE) genes and in the whole genome

Copyright information

© Springer Science+Business Media New York 2012