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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]