Abstract
Alginate is an important polysaccharide that is abundant in the marine environments, including the Polar Regions, and bacterial alginate lyases play key roles in its degradation. Many reported alginate lyases show characteristics of cold-adapted enzymes, including relatively low temperature optimum of activities (Topt) and low thermal stabilities. However, the cold-adaption mechanisms of alginate lyases remain unclear. Here, we studied the cold-adaptation mechanisms of alginate lyases by comparing four members of the PL7 family from different environments: AlyC3 from the Arctic ocean (Psychromonas sp. C-3), AlyA1 from the temperate ocean (Zobellia galactanivorans), PA1167 from the human pathogen (Pseudomonas aeruginosa PAO1), and AlyQ from the tropic ocean (Persicobacter sp. CCB-QB2). Sequence comparison and comparative molecular dynamics (MD) simulations revealed two main strategies of cold adaptation. First, the Arctic AlyC3 and temperate AlyA1 increased the flexibility of the loops close to the catalytic center by introducing insertions at these loops. Second, the Arctic AlyC3 increased the electrostatic attractions with the negatively charged substrate by introducing a high portion of positively charged lysine at three of the insertions mentioned above. Furthermore, our study also revealed that the root mean square fluctuation (RMSF) increased greatly when the temperature was increased to Topt or higher, suggesting the RMSF increase temperature as a potential indicator of the cold adaptation level of the PL7 family. This study provided new insights into the cold-adaptation mechanisms of bacterial alginate lyases and the marine carbon cycling at low temperatures.
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Data availability
The structure coordinates and amino acid sequences analyzed in this study are available at the Worldwide Protein Data Bank (wwPDB, http://www.wwpdb.org/) under accessions 7C8G, 3ZPY, 1VAV, and 5XNR.
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Funding
This research was funded by the Youth Interdisciplinary Science and Innovative Research Groups of Shandong University (2020QNQT006), the State Key Laboratory of Microbial Technology Open Projects Fund (Project NO. M2022-04).
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Conceptualization, FB and BBX; methodology, BBX, XYL; formal analysis, BBX, XYL and FB; investigation, BBX; writing—original draft preparation, FB and BBX; writing—review and editing, MW, ZZS; funding acquisition, BBX. All authors have read and agreed to the published version of the manuscript.
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Bian, F., Liang, XY., Wang, M. et al. Comparative molecular dynamics simulations provided insights into the mechanisms of cold-adaption of alginate lyases from the PL7 family. Extremophiles 28, 24 (2024). https://doi.org/10.1007/s00792-024-01340-8
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DOI: https://doi.org/10.1007/s00792-024-01340-8