Analyzing structural features of proteins from deep‐sea organisms

Abstract

Protein adaptations to extreme environmental conditions are drivers in biotechnological process optimization and essential to unravel the molecular limits of life. Most proteins with such desirable adaptations are found in extremophilic organisms inhabiting extreme environments. The deep sea is such an environment and a promising resource that poses multiple extremes on its inhabitants. Conditions like high hydrostatic pressure and high or low temperature are prevalent and many deep-sea organisms tolerate multiple of these extremes. While molecular adaptations to high temperature are comparatively good described, adaptations to other extremes like high pressure are not well-understood yet. To fully unravel the molecular mechanisms of individual adaptations it is probably necessary to disentangle multifactorial adaptations. In this study, we evaluate differences of protein structures from deepsea organisms and their respective related proteins from nondeep-sea organisms. We created a data collection of 1281 experimental protein structures from 25 deep-sea organisms and paired them with orthologous proteins. We exhaustively evaluate differences between the protein pairs with machine learning and Shapley values to determine characteristic differences in sequence and structure. The results show a reasonable discrimination of deep-sea and nondeep-sea proteins from which we distinguish correlations previously attributed to thermal stability from other signals potentially describing adaptions to high pressure. While some distinct correlations can be observed the overall picture appears intricate.

Biomolecules under Pressure: Phase Diagrams, Volume Changes, and High Pressure Spectroscopic Techniques

“…Morris et al found significant increases in the transcription of genes coding GAPDH and the heat shock protein HSP70 in response to high pressure [ 110 ]. Sieg et al compiled a database comparing protein sequences from deep-sea organisms with their orthologous proteins [ 111 ]. As mentioned previously, the stability and flexibility of the deep-sea proteins should change on the way to allow them to be able to function under pressure.…”

“…As mentioned previously, the stability and flexibility of the deep-sea proteins should change on the way to allow them to be able to function under pressure. A clear pattern or mechanism for high pressure adaptations was, however, not apparent from the database [ 111 ]. Actin is one of the most basic proteins in all living organisms.…”