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Correction to: Synthetic biology, genome mining, and combinatorial biosynthesis of NRPS‑derived antibiotics: a perspective

  • Richard H. Baltz
Correction
  • 292 Downloads

Correction to: Journal of Industrial Microbiology & Biotechnology  https://doi.org/10.1007/s10295-017-1999-8

In the original article, Tables 1, 2 and 3 were published incorrectly. The correct Tables 1, 2 and 3 are given below. The ​original ​article ​has ​been ​corrected.
Table 1

Amino acid binding codes for NRPS subunits related to those of daptomycin

Strain

NRPS subunita

Module

Binding codeb

Amino acidc

Streptomyces roseosporus

DptA

1

DVSSIGAVEK

Trp

Saccharomonospora sp. CNQ-490

DptA (Tar8)

1

DVSNVGAVEK

Trp

Saccharomonospora viridis

DptA-sv

1

DVSTVGAVEK

(Trp)

  

2

DLTKLGDVNK

Asn

2

DLT_MGDVHK

Asn

2

DLT_MGDVHK

(Asn)

3

DLTKLGAVNK

Asp

3

DLTKVGAVNK

Asp

3

DLTKVGAVNK

(Asp)

4

DFWSVGMVHK

Thr

4

DFWNIGMVHK

Thr

4

DFWNIGMVHK

(Thr)

5

DILQLGVIWK

Gly

5

DILQLGLIWK

Gly

5

DILQLGLIWK

(Gly)

Streptomyces roseosporus

DptBC

6

DTEDMGYVDK

Orn

Saccharomonospora sp. CNQ-490

DptBC (Tar9)

6

DTEDMGYVDK

Orn

Saccharomonospora viridis

DptBC-sv

6

DTEDMGYVDK

(Orn)

  

7

DLTKLGAVNK

Asp

7

DLTKVGAVNK

Asp

7

DLTKVGAVNK

(Asp)

8

DVVSAAFVYK

Ala

8

DVFSVAVVYK

Ala

8

DVFSVAAVYK

(Ala)

9

DLTKLGAVNK

Asp

9

DLTKVGAVNK

Asp

9

DLTKVGAVNK

(Asp)

10

DILQVGMIWK

Gly

10

DILQLGVIWK

Gly

10

DILQLGVIWK

(Gly)

11

DVWHISLVDK

Ser

11

DVFSVALVYK

Ala

11

DVFSVALVYK

(Ala)

Streptomyces roseosporus

DptD

12

DLGKTGVINK

3mGlu

Saccharomonospora sp. CNQ-490

DptD (Tar10)

12

DLGKTGVVNK

3mGlu

Saccharomonospora viridis

DptD-sv

12

DLGKTGVVNK

(3mGlu)

  

13

DAWTTTGVGK

Kyn

13

DAWTTTGVAK

Kyn

13

DAWTTTGVGK

(Kyn)

aNRPS homologs to DptA, DptBC, and DptD [9, 55, 85]

bAmino acid binding codes were identified by NRPS predictor2 (http://nrps.informatik.uni-tuebingen.de/Controller?cmd=SubmitJob) [72]. Underscores indicate no amino acids assigned

c(), predicted amino acids binding codes. The other amino acid assignments have been confirmed by structural analysis [55, 85]

Table 2

Lipopeptide biosynthetic enzyme BLASTp % identity scores in select actinomycetesa

Actinomycete

Query protein sequences

DptI

GlmT

LptI

LptJ

LptK

LptL

AsnO

GlmB

DptD

LptD

Cda-PS3

PstD

LpmD

DptE

LptEF

LipA

S. roseosporus

100

37

38

39b

37b

100

53

52

49

48

100

52

48

S. Sp. CNQ490

55

38

38

32b

35b

56

50

50

47

47

46

48

41

S. viridis

54

40

39

35b

56

50

51

48

48

48

47

43

S. fradiae

38

32

100

100

100

100

47c

53

100

50

49

49

52

100

48

S. exfoliates

38

34

87

93

93

93

48c

61

53

93

50

49

49

51

90

48

S. griseoluteus

37

35

87

93

93

91

47c

53

93

50

49

49

51

89

48

S. pini

41

39

75

86

80

81

47c

52

81

50

48

48

51

79

47

S. coelicolor

37

100

32

47d,e

100

52

50

100

49

50

S. lividans

37

99

32

47d,e

100

52

50

99

49

50

S. sp. MBT28

38

89

36

45

90

58

52

50

90

49

50

S. sp. NRRL WC-3795

38

90

35

45

90

58

49

48

90

49

50

S. gilvosporeus

35

52

34

34

52

63

57

39

40

40

S. natalensis

35

52

35

33

51

66

S. kanamyceticus

41

70

32

37

38

33

35

60

49

49

53

48

48

47

44

48

S. aureofaciens

42

36

40

40

52

51

67

50

50

52

62

72

46

49

62

A. friuliensis

100

49

49

49

100

64

48

48

100

S. viridochromogenes

36

41

31

49

49

50

64

100

47

47

59

S. olivaceus

37

41

67

49

50

52

67

72

49

49

62

S. canus

67

51

50

52

67

74

47

48

61

aLipopeptide biosynthetic enzyme homologs were identified by BLASTp analysis (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins) [4]

bNot in daptomycin-like pathways

cIn A54145-like pathways (LptL paralog)

dIn CDA pathway (AsnO paralog)

eS. coelicolor and S. lividans have a second LptL paralog with 49% sequence identities

Table 3

Amino acid binding codes for NRPS subunits related to those of A54145

Strain

NRPS subunita

Module

Binding codeb

Amino acid

Streptomyces fradiae A54145

LptA

1

DVALVGVVQK

Trp

Streptomyces griseoluteus ISP-5360

LptA

1

DVALVGVVQK

Streptomyces exfoliatus DSM41693

LptA

1

DVALVGVVQK

Streptomyces pini PL19

LptA

1

DVALVGVVQK

  

2

DLVKVASVNK

Glu

2

DLVKVASVNK

2

DLVKVASVNK

2

DLAKVASVNK

3

DLTKVGDVNK

hAsn

3

DLTKVGDVNK

3

DLTKVGDVNK

3

DLTKVGDVNK

4

DFWSVGMVHK

Thr

4

DFWSVGMVHK

4

DFWSVGMVHK

4

DFVSVGMVHK

5

DILQLGVIWK

Sar

5

DILQLGVIWK

5

DILQLGVIWK

5

DILQLGVIWK

Streptomyces fradiae

LptB

6

DVFNLALVFK

Ala

Streptomyces griseoluteus

LptB

6

DVFNLALVFK

Streptomyces exfoliatus

LptB

6

DVFNLALVFK

Streptomyces pini

LptB

6

DVFNLALVFK

  

7

DLTKVGAVNK

Asp

7

DLTKVGAVNK

7

DLTKVGAVNK

7

DLTKVGAVNK

Streptomyces fradiae

LptC

8

DADDAGTVDK

Lys

Streptomyces griseoluteus

LptC

8

Streptomyces exfoliatus

LptC

8

Streptomyces pini

LptC

8

DADDAGTVDKc

  

9

DLTKIGAVNK

moAsp

9

9

9

10

DILQLGLVWK

Gly

10

10

10

DILQLGLVW

11

DLTKVGDVSK

Asn

11

DLTKVGDVSK

11

DLTKVGDVSK

11

DLTKVGDVSKc

Streptomyces fradiae

LptD

12

DLGKTGVVNK

3mGlu/Glu

Streptomyces griseoluteus

LptD

12

DLGKTGVVNK

Streptomyces exfoliatus

LptD

12

DLGKTGVVNK

Streptomyces pini

LptD

12

DLGKTGVVNK

  

13

DGLFVGIAVK

Ile/Val

13

DGLFVGIAVK

13

DGLFVGIAVK

13

DGLFVGIAVK

aNRPS homologs to LptA, LptB, LptC, and LptD were identified by BLASTp analysis (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins) [4]

bAmino acid binding codes were identified by NRPS predictor2 (http://nrps.informatik.uni-tuebingen.de/Controller?cmd=SubmitJob) [72]

cThese three modules are located on three separate contigs of the S. pini genome sequence. Module ten is missing the conserved K in position 10 of the binding code

Copyright information

© Society for Industrial Microbiology and Biotechnology 2018

Authors and Affiliations

  1. 1.CognoGen Biotechnology ConsultingSarasotaUSA

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