Abstract
The genomic analysis of industrially important bacteria can help in understanding their capability to withstand extreme environments and shed light on their metabolic capabilities. The whole genome of a previously reported broad temperature active lipase-producing Pseudomonas sp. HS6, isolated from snow-covered soil of the Sikkim Himalayan Region, was analyzed to understand the capability of the bacterium to withstand cold temperatures and study its lipolytic nature. Pseudomonas sp. HS6 was found to be psychrotolerant with an optimal growth temperature ranging between 25 and 30 °C, with the ability to grow at 5 °C. The genome harbours various cold-adaptation genes, such as cold-shock proteins, fatty acid alteration, and cold stress-tolerance genes, supporting the psychrotolerant nature of the organism. The comparative analysis of Pseudomonas sp. HS6 genome showed the presence of amino acid substitutions in genes that favor efficient functioning and flexibility at cold temperatures. Genome mining revealed the presence of four triacylglycerol lipases, among which the putative lipase 3 was highly similar to the broad temperature-active lipase purified and characterized in our previous study. In silico studies of putative lipase 3 revealed broad substrate specificity with partial and no inhibition of the enzyme activity in the presence of PMSF and orlistat. The presence of genes associated with cold adaptations and true lipases with activity at broad temperature and substrate specificity in the genome of Pseudomonas sp. HS6 makes this bacterium a suitable candidate for industrial applications.
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Data availability
The complete genome sequence of Pseudomonas sp. HS6 has been deposited in NCBI Genbank with Genbank accession number CP067412, BioSample accession number SAMN17257339, and BioProject accession number PRJNA690690. The annotated genome can be accessed from JGI IMG/ER portal under the project ID-Gp0545573, and Taxon ID-2926928646.
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Acknowledgements
The authors would like to thank the Department of Biotechnology, Govt. of India, for funding the research work on exploring native microorganisms for the production of industrially important enzymes. We thank Director, IBSD, for the kind support and encouragement. We would also like to thank the Sikkim State Biodiversity Board, Department of Forests, Environment and Wildlife Management, Government of Sikkim for granting permission to collect high-altitude soil samples of Sikkim. The manuscript number corresponds to manuscript ID- IBSD/2020/01/071.
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Research grant from Department of Biotechnology, Govt. of India.
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LCP: methodology, investigation, validation, formal analysis, visualization, writing—original draft. RC: investigation, validation, data curation, writing—original draft. SP: investigation, validation, data curation, visualization. MMA: investigation, validation, data curation, visualization. TKG: investigation, validation, data curation, visualization. SPS: writing—review and editing, supervision. BP: writing—review and editing, supervision. AKR: conceptualization, resources, writing—review and editing, visualization, supervision, project administration, funding acquisition.
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Phukon, L.C., Chourasia, R., Padhi, S. et al. Cold-adaptive traits identified by comparative genomic analysis of a lipase-producing Pseudomonas sp. HS6 isolated from snow-covered soil of Sikkim Himalaya and molecular simulation of lipase for wide substrate specificity. Curr Genet 68, 375–391 (2022). https://doi.org/10.1007/s00294-022-01241-3
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DOI: https://doi.org/10.1007/s00294-022-01241-3