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Comparative analysis of genome-based CAZyme cassette in Antarctic Microbacterium sp. PAMC28756 with 31 other Microbacterium species

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Abstract

Background

The genus Microbacterium belongs to the family Microbacteriaceae and phylum Actinobacteria. A detailed study on the complete genome and systematic comparative analysis of carbohydrate-active enzyme (CAZyme) among the Microbacterium species would add knowledge on metabolic and environmental adaptation. Here we present the comparative genomic analysis of CAZyme using the complete genome of Antarctic Microbacterium sp. PAMC28756 with other complete genomes of 31 Microbacterium species available.

Objective

The genomic and CAZyme comparison of Microbacterium species and to rule out the specific features of CAZyme for the environmental and metabolic adaptation.

Methods

Bacterial source were collected from NCBI database, CAZyme annotation of Microbacterium species was analyzed using dbCAN2 Meta server. Cluster of orthologous groups (COGs) analysis was performed using the eggNOG4.5 database. Whereas, KEGG database was used to compare and obtained the functional genome annotation information in carbohydrate metabolism and glyoxylate cycle.

Results

Out of 32 complete genomes of Microbacterium species, strain No. 7 isolated from Activated Sludge showed the largest genomic size at 4.83 Mb. The genomic size of PAMC28756 isolated from Antarctic lichen species Stereocaulons was 3.54 Mb, the G + C content was 70.4% with 3,407 predicted genes, of which 3.36% were predicted CAZyme. In addition, while comparing the Glyoxylate cycle among 32 bacteria, except 10 strains, all other, including our strain have Glyoxylate pathway. PAMC28756 contained the genes that degrade cellulose, hemicellulose, amylase, pectinase, chitins and other exo-and endo glycosidases. Utilizing these polysaccharides can provides source of energy in an extreme environment. In addition, PAMC28756 assigned the (10.15%) genes in the carbohydrate transport and metabolism functional group closely related to the CAZyme for polysaccharides degradation.

Conclusions

The genomic content and CAZymes distribution was varied in Microbacterium species. There was the presence of more than 10% genes in the carbohydrate transport and metabolism functional group closely related to the CAZyme for polysaccharides degradation. In addition, occurrence of glyoxylate cycle for alternative utilization of carbon sources suggest the adaptation of PAMC28756 in the harsh microenvironment.

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Acknowledgements

This research was a part of the project titled “Development of potential antibiotic compounds using polar organism resources (15250103, KOPRI Grant PM21030)”, funded by the Ministry of Oceans and Fisheries, Korea.

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Authors and Affiliations

  1. Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, 31460, South Korea

    Sushma Gupta, So-Ra Han, Byeollee Kim & Tae-Jin Oh

  2. Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 55365, South Korea

    Chang-Muk Lee

  3. Genome-Based BioIT Convergence Institute, Asan, 31460, South Korea

    Tae-Jin Oh

  4. Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, 31460, South Korea

    Tae-Jin Oh

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13258_2022_1254_MOESM1_ESM.xlsx

Table S1: list of bacterial Gene Bank accession number and strains deposited in National Center for Biotechnology Information (NCBI). Table S2: Comparison of genomic characteristic between the complete genomes of Microbacterium species. Table S3: The functional classification of COG genes. Table S4: Prediction of carbohydrate metabolism genes and pathways in 32 complete genome of Microbacterium species by using Kyoto Encyclopedia of Genes and Genomes (KEGG) web service. Table S5: Predicated amount of carbohydrate-active enzymes in the complete genomes of Microbacterium species. Table S6: Predicated number of genes of the GH family involved in cellulose and starch degradation in 32 complete genome of Microbacterium species. Table S7: Predicated number of Glycoside hydrolase family (GHs). Table S8: Predicated number of Glycosyl transferase family (GTs). Table S9: Predicated number of Polysaccharide lyases family (PLs). Table S10: Predicated number of Carbohydrate esterase family (CEs). Table S11: Predicated number of Auxiliary activities family (AAs). Table S12: Predicated number of Carbohydrate-binding module family (CBMs). Table S13: Predicated GH families involved in hemicellulose degradation in 32 complete genomes of Microbacterium species. (Supplementary Materials). (XLSX 56 KB)

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Gupta, S., Han, SR., Kim, B. et al. Comparative analysis of genome-based CAZyme cassette in Antarctic Microbacterium sp. PAMC28756 with 31 other Microbacterium species. Genes Genom 44, 733–746 (2022). https://doi.org/10.1007/s13258-022-01254-9

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