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Table 1 Summary of pectinolytic enzymes in three metagenomes

From: Metagenomic mining pectinolytic microbes and enzymes from an apple pomace-adapted compost microbial community

Pectinolytic enzymes

CAZy family

Predominant activity

This study

RSAa

EMSD5b

Depolymerizing enzymes

Glycoside hydrolases (GHs)

GH4

Exo-polygalacturonase (EC 3.2.1.67)

14

21

24

GH28

Polygalacturonase (EC 3.2.1.15); exo-polygalacturonase (EC 3.2.1.67); exo-polygalacturonosidase (EC 3.2.1.82); rhamnogalacturonase (EC 3.2.1.171); rhamnogalacturonan α-1,2-galacturonohydrolase (EC 3.2.1.173); rhamnogalacturonan α-l-rhamnopyranohydrolase (EC 3.2.1.174)

32

11

3

Polysaccharide lyases (PLs)

PL1

Pectate lyase (EC 4.2.2.2); exo-pectate lyase (EC 4.2.2.9); pectin lyase (EC 4.2.2.10)

30

8

4

PL3

Pectate lyase (EC 4.2.2.2)

2

4

0

PL4

Rhamnogalacturonan lyase (EC 4.2.2.-)

0

0

1

PL9

Pectate lyase (EC 4.2.2.2); exopolygalacturonate lyase (EC 4.2.2.9)

12

15

4

PL10

pectate lyase (EC 4.2.2.2)

13

8

0

PL11

Rhamnogalacturonan endolyase (EC 4.2.2.23); rhamnogalacturonan exolyase (EC 4.2.2.24)

18

10

1

PL22

Oligogalacturonate lyase/oligogalacturonide lyase (EC 4.2.2.6, 9)

30

21

12

Pectinesterases

Carbohydrate esterases (CEs)

CE1

Feruloyl esterase (EC 3.1.1.73)

482

223

82

CE8

Pectin methylesterase (EC 3.1.1.11)

17

8

6

CE12

Pectin acetylesterase (EC 3.1.1.6); rhamnogalacturonan acetylesterase (EC 3.1.1.86)

34

4

8

CE13

Pectin acetylesterase (EC 3.1.1.6)

2

0

0

CE16

Pectin acetylesterase (EC 3.1.1.6)

4

0

0

De-branching enzymes

Glycoside hydrolases (GHs)

GH1

β-Glucosidase (EC 3.2.1.23)

60

63

44

GH2

β-Glucosidase (EC 3.2.1.23); α-L-arabinofuranosidase (EC 3.2.1.55)

76

27

19

GH3

β-Glucosidase (EC 3.2.1.23); α-l-arabinofuranosidase (EC 3.2.1.55)

143

83

32

GH10

Endo-1,4-β-xylanase (EC 3.2.1.8); endo-1,3-β-xylanase (EC 3.2.1.32)

50

37

6

GH35

β-Glucosidase (EC 3.2.1.23)

9

7

1

GH42

β-Glucosidase (EC 3.2.1.23)

33

14

9

GH43

α-l-Arabinofuranosidase (EC 3.2.1.55); arabinanase (EC 3.2.1.99)

205

51

33

GH51

α-l-Arabinofuranosidase (EC 3.2.1.55)

40

24

4

GH53

Arabinogalactanase (EC 3.2.1.89)

8

6

6

GH59

β-Glucosidases (EC 3.2.1.23)

2

2

0

GH62

α-l-Arabinofuranosidase (EC 3.2.1.55)

2

6

0

GH78

α-l-Rhamnosidase (EC 3.2.1.40)

92

39

8

GH105

Unsaturated rhamnogalacturonyl hydrolase (EC 3.2.1.172)

35

4

5

GH106

α-l-Rhamnosidase (EC 3.2.1.40)

30

6

3

GH127

β-l-Arabinofuranosidase (EC 3.2.1.185)

51

17

11

 

Carbohydrate-binding modules (CBMs)

CBM13

Arabinanase (GH43D;RUM_09280); feruloyl esterase I (FaeI;CGSCsYakCAS_18248); pectate lyase B (PelB)

25

14

24

CBM32

Binding to galactose, lactose, polygalacturonic acid and LacNAc

137

63

23

CBM35

Arabinanase; feruloyl esterase D (Fae1;XylD;XynD;CJA_3282); pectate lyase (PelA;CJA_3104)

27

17

10

CBM61

Modules of approx. 150 residues found appended to GH43, GH53 catalytic domains

3

3

2

CBM66

Pectate lyase (PecB;Athe_1854;Cbes_1854;Cbes1854)

63

27

13

Total

Families

33

31

28

ORFs

1756

843

398

  1. aRSA (Rice Straw-Adapted) microbial consortia adapted to rice straw from Ref. [44]
  2. bEMSD5 microbial consortia adapted to corn stover from reference of [52]