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Deciphering the Cold Adaptive Mechanisms in Pseudomonas psychrophila MTCC12324 Isolated from the Arctic at 79° N

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Abstract

Psychrophiles, host of cold environments, have been successfully undergoing the process of evolution by which they have acquired innate adaptations to withstand the unfavorable effects of low temperature. Psychrophiles renders immense opportunity to explore the underlying mechanisms of cold adaptation. The present study focused to explore the cold adaptive mechanisms of Pseudomonas psychrophila MTCC12324, a facultative psychrophilic bacterium isolated from the Ny-Alesund, an island in the Svalbard Archipelago (79°55′ N, 11°56′ E) in the Arctic. Whole genome sequencing of P. psychrophila MTCC12324 and its analysis revealed the redundant nature of genome and identified several cold acclimation genes including cold shock proteins, and chaperones involved in the adaptive mechanism to thrive in the cold environment. Comparative proteome analysis of P. psychrophila MTCC12324 at 4 °C and 25 °C has thrown lights on the metabolic pathways and cellular processes adopted to withstand the cold environment. Basic survival pathways and factors involved in energy metabolism were found to be unaltered whereas stress response factors, enzymes involved in fatty acid elongation and cold-adapted chaperones were found to be enhanced towards cold stress. The present study facilitates recognition of crucial factors including polyunsaturated fatty acid biosynthesis, mRNA chaperones, and other cold-inducible proteins which favors the bacteria in conferring cold adaptation.

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Data Availability

The whole-genome shotgun sequence has been deposited in GenBank under the accession no. LBHT00000000. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD012212.

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Acknowledgements

ST acknowledges Ministry of Earth Sciences, Govt. of India for all the financial and logistic support during Indian Arctic Expedition 2009, Dr. Rasik Ravindra, former Director of The National Centre for Polar and Ocean Research (NCPOR), Goa and Dr. K.P. Krishnan, other scientists and staff of NCPOR for the necessary help during Indian Arctic Expedition. We also acknowledge Dr. Abdul Jaleel K.A, Aneesh Kumar A and Arun Surendran at the Proteomics Core Facility for LC–MS/MS analysis. The authors thank Sivakumar K.C for the timely help in pan-genome analysis. The authors would like to thank Prof. M. Radhakrishna Pillai, Director, Rajiv Gandhi Centre for Biotechnology for providing the necessary facilities.

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Authors and Affiliations

  1. Cholera & Biofilm Research Laboratory, Pathogen Biology Division, Rajiv Gandhi Centre for Biotechnology, Thycaud P.O., Thiruvananthapuram, Kerala, 695014, India

    Wilson Peter Abraham, Karthika Suryaletha & Sabu Thomas

  2. Mycobacterium Research Laboratory, Pathogen Biology Division, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India

    Sajith Raghunandanan

  3. Department of Clinical Laboratory Services and Translational Research, Malabar Cancer Centre, Thalassery, Kannur, 670 103, India

    Vipin Gopinath

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  1. Wilson Peter Abraham
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  5. Sabu Thomas
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Contributions

Conceptualization-WPA and ST; Methodology- WPA, SR, VG, and ST; Data analysis-WPA, SR, and ST; Manuscript drafting and editing-WPA, SR, KS and ST.

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Correspondence to Sabu Thomas.

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Electronic Supplementary Material

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284_2020_2006_MOESM1_ESM.xls

Table S1. List of genes common among the test strain (P. psychrophila MTCC 12,324) and either of the reference strains (P. psychrophila HA-4/ P. psychrophila JSM 10,889). Supplementary file1 (XLS 239 kb)

284_2020_2006_MOESM2_ESM.doc

Table S2: Genome to Genome comparison between Pseudomonas psychrophila MTCC12324 & Psychrobacter arcticus 273-4. Supplementary file2 (DOC 157 kb)

284_2020_2006_MOESM3_ESM.docx

Table S3: List of total proteins of P. psychrophila MTCC12324 and their expression at 4 °C which fall in biological processes such as (A) DNA replication, repair, recombination & cell division (B) Transcription and RNA processing (C) Translation (D) Protein folding and processing (E) Carbohydrate and energy metabolism (F) Amino acid metabolism (G) Nucleotide metabolism (H) Fatty acid metabolism (I) Transport. A fold change higher than 70% (ratio of either < 0.70 for downregulation or > 1.3 for upregulation) was considered to be indicative of significantly altered levels of expression.4 °C & 25 °C indicates the unique representation of corresponding proteins in their respective conditions. Supplementary file3 (DOCX 123 kb)

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Abraham, W.P., Raghunandanan, S., Gopinath, V. et al. Deciphering the Cold Adaptive Mechanisms in Pseudomonas psychrophila MTCC12324 Isolated from the Arctic at 79° N. Curr Microbiol 77, 2345–2355 (2020). https://doi.org/10.1007/s00284-020-02006-2

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