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Genome analysis of cellulose and hemicellulose degrading Micromonospora sp. CP22

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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.

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Acknowledgements

This work was financially sponsored by Universiti Teknologi Malaysia under Research University Grant (GUP 2018 Tier 1) with project number 20H43. The authors would like to acknowledge palm oil mill, Johor for the permission for sample collection. Sye Jinn Chen acknowledges UTM Zamalah Scholarship from Universiti Teknologi Malaysia. Ming Quan Lam acknowledges Khazanah Watan Postgraduate (PhD) scholarship (scholar ID: 40852) from Yayasan Khazanah.

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Authors and Affiliations

  1. Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81300, Skudai, Johor, Malaysia

    Sye Jinn Chen, Ming Quan Lam, Suganthi Thevarajoo, Fazilah Abd Manan, Adibah Yahya & Chun Shiong Chong

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  1. Sye Jinn Chen
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  2. Ming Quan Lam
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  3. Suganthi Thevarajoo
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  4. Fazilah Abd Manan
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  5. Adibah Yahya
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  6. Chun Shiong Chong
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Contributions

SJC: carried out the experiment, analyzed the data and drafted the manuscript. MQL: designed the experiment, assisted in bioinformatics analyses and edited the manuscript. CSC: conceived of the presented idea, designed the experiment and provided expertise. AY, FAM and ST: provided expertise and edited the manuscript. All authors read, edited and approved the final manuscript.

Corresponding author

Correspondence to Chun Shiong Chong.

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Additional information

Genome sequence accession number: The whole-genome shotgun project of strain CP22 has been deposited at DDBJ/ENA/GenBank under the accession number VCJO00000000. The 16S rRNA gene of the strain CP22 is available at DDBJ/ENA/GenBank under accession MK934350.

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Chen, S.J., Lam, M.Q., Thevarajoo, S. et al. Genome analysis of cellulose and hemicellulose degrading Micromonospora sp. CP22. 3 Biotech 10, 160 (2020). https://doi.org/10.1007/s13205-020-2148-z

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