Genome analysis of cellulose and hemicellulose degrading Micromonospora sp. CP22

Abstract

In this study, a bacterial strain CP22 with ability to produce cellulase, xylanase and mannanase was isolated from the oil palm compost. Based on the 16S rRNA gene analysis, the strain was affiliated to genus Micromonospora. To further investigate genes that are related to cellulose and hemicellulose degradation, the genome of strain CP22 was sequenced, annotated and analyzed. The de novo assembled genome of strain CP22 featured a size of 5,856,203 bp with G + C content of 70.84%. Detailed genome analysis on lignocellulose degradation revealed a total of 60 genes consisting of 47 glycoside hydrolase domains and 16 carbohydrate esterase domains predicted to be involved in cellulolytic and hemicellulolytic deconstruction. Particularly, 20 genes encode for cellulases (8 endoglucanases, 3 exoglucanases and 9 β-glucosidases) and 40 genes encode for hemicellulases (15 endo-1,4-β-xylanase, 3 β-xylosidase, 3 α-arabinofuranosidase, 10 acetyl xylan esterase, 6 polysaccharide deacetylase, 1 β-mannanase, 1 β-mannosidase and 1 α-galactosidase). Thirty-two genes encoding carbohydrate-binding modules (CBM) from six different families (CBM2, CBM4, CBM6, CBM9, CBM13 and CBM22) were present in the genome of strain CP22. These CBMs were found in 27 cellulolytic and hemicellulolytic genes, indicating their potential role in enhancing the substrate-binding capability of the enzymes. CBM2 and CBM13 are the major CBMs present in cellulases and hemicellulases (xylanases and mannanases), respectively. Moreover, a GH10 xylanase was found to contain 3 CBMs (1 CBM9 and 2 CBM22) and these CBMs were reported to bind specifically to xylan. This genome-based analysis could facilitate the exploration of this strain for lignocellulosic biomass degradation.

Keywords: Genome; Glycosyl hydrolase; Lignocellulose; Micromonospora.

Fig. 1

Cellulolytic, xylanolytic and mannanolytic enzyme activities in cell-free supernatant of strain CP22. The experiment was performed in triplicate and standard deviations are indicated as error bar

Fig. 2

COG functional categories of Micromonospora sp. CP22

Fig. 3

a Neighbor-joining tree derived from 16S rRNA gene sequence data of Micromonospora sp. CP22 and its relatives. b The neighbor-joining phylogenomic tree derived from genome data of Micromonospora sp. CP22 and other strains which are publicly available online. Streptomyces coelicolor A3(2) was used as the outgroup. Filled circles indicate the corresponding nodes were recovered in the trees generated with all three methods (neighbor joining, maximum likelihood and maximum parsimony). Open circles indicate that the corresponding nodes were recovered in the trees generated with either two methods. Bar, 0.01 nucleotide substitutions per site

Fig. 4

The number of CAZyme domains containing enzymes involved in the cellulose and hemicellulose deconstruction in the genome of strain CP22 and Micromonospora sediminimaris CGMCC 4.3550 ^T

Fig. 5

The domain organization of GH8 protein sequence (Protein ID: FF096_26150) from the genome of strain CP22. From left to right: SP signal peptide; CBM6 carbohydrate-binding module family 6; GH8 glycoside hydrolase family 8; FN3 fibronectin type 3