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Case Reports
. 2023 Feb;13(2):50.
doi: 10.1007/s13205-023-03472-8. Epub 2023 Jan 17.

Draft genome sequence of Joostella atrarenae M1-2T with cellulolytic and hemicellulolytic ability

Kok Jun Liew  1 , Muhammad Ramziuddin Zakaria  1 , Clarine Wan Ling Hong  1 , Melvin Chun Yun Tan  1 , Chun Shiong Chong  1
Affiliations
Case Reports

Draft genome sequence of Joostella atrarenae M1-2T with cellulolytic and hemicellulolytic ability

Kok Jun Liew et al. 3 Biotech. 2023 Feb.

Abstract

The halophilic genus Joostella is one of the least-studied genera in the family of Flavobacteriaceae. So far, only two species were taxonomically identified with limited genomic analysis in the aspect of application has been reported. Joostella atrarenae M1-2T was previously isolated from a seashore sample and it is the second discovered species of the genus Joostella. In this project, the genome of J. atrarenae M1-2T was sequenced using NovaSeq 6000. The final assembled genome is comprised of 71 contigs, a total of 3,983,942 bp, a GC ratio of 33.2%, and encoded for 3,416 genes. The 16S rRNA gene sequence of J. atrarenae M1-2T shows 97.3% similarity against J. marina DSM 19592T. Genome-genome comparison between the two strains by ANI, dDDH, AAI, and POCP shows values of 80.8%, 23.3%, 83.4%, and 74.1% respectively. Pan-genome analysis shows that strain M1-2T and J. marina DSM 19592T shared a total of 248 core genes. Taken together, strain M-2T and J. marina DSM 19592T belong to the same genus but are two different species. CAZymes analysis revealed that strain M1-2T harbors 109 GHs, 40 GTs, 5 PLs, 9 CEs, and 6 AAs. Among these CAZymes, while 5 genes are related to cellulose degradation, 12 and 24 genes are found to encode for xylanolytic enzymes and other hemicellulases that involve majorly in the side chain removal of the lignocellulose structure, respectively. Furthermore, both the intracellular and extracellular crude extracts of strain M1-2T exhibited enzymatic activities against CMC, xylan, pNPG, and pNPX substrates, which corresponding to endoglucanase, xylanase, β-glucosidase, and β-xylosidase, respectively. Collectively, description of genome coupled with the enzyme assay results demonstrated that J. atrarenae M1-2T has a role in lignocellulosic biomass degradation, and the strain could be useful for lignocellulosic biorefining.

Keywords: Cellulase; Flavobacteriaceae; Halophile; Hemicellulase; Joostella.

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Conflict of interest statement

Conflict of interestOn behalf of all authors, the corresponding author states that there is no conflict of interest.

Figures

Fig. 1
Fig. 1
Prediction of cellulose, xylan, and xyloglucan degradation by J. atrarenae M1-2T based on lignocellulolytic gene mining
Fig. 2
Fig. 2
The ability to utilize different polysaccharides by J. atrarenae M1-2T. a Hydrolytic plate assays and b measurement of reducing sugar released from suspension culture supplemented with different substrates from Day 1 – 5
Fig. 3
Fig. 3
Specific enzyme activities of endoglucanase, beta-glucosidase, xylanase, and beta-xylosidase as tested in the intracellular and extracellular crude extracts of J. atrarenae M1-2.T, which were harvested from Day 1 – 5
See this image and copyright information in PMC

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