High-pressure adaptation of extremophiles and biotechnological applications

Salvador-Castell, Marta; Oger, Philippe; Peters, Judith

doi:10.1016/b978-0-12-818322-9.00008-3

Cited by 2 publications

(6 citation statements)

References 171 publications

(170 reference statements)

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“…The names of microorganisms found in the deep sea were collected from literature 17,34–36 . The literature for each organism was reviewed manually.…”

Section: Methodsmentioning

confidence: 99%

“…The names of microorganisms found in the deep sea were collected from literature. 17,[34][35][36] The literature for each organism was reviewed manually. The resulting list of organism names was matched to the source organism annotation in the PDB to retrieve protein structures (using the binomial nomenclature and manual review).…”

Section: Collection Of Deep-sea Protein Structuresmentioning

confidence: 99%

“…16 The average pressure at the ocean floor is 38 MPa 8 and reaches a maximum of approximately 110 MPa at the Challenger Deep of Mariana Trench. 17 In addition, other stressors like an extreme salt range can be found in the deep-sea sediment and at hydrothermal vents. 18 Within this study we aim to disentangle the multifactorial aspects of several adaptations in proteins from deep-sea organisms.…”

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confidence: 99%

“…The organisms that live under elevated pressure or even need high pressure to grow are called piezophiles (or barophiles). 9,15,19,20 Protein adaptations to high pressure are not well-described 9,16,17 and the identification of a molecular signature for high pressure is complicated through other prevailing extremes, for example, the temperature differences of most high pressure environments. 4,15 Different studies also suggest that pressure adaptations might be challenging to detect, because they might be rather subtle and pronounced differently in different protein classes.…”

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confidence: 99%

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Analyzing structural features of proteins from deep‐sea organisms

et al. 2022

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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.

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“…The names of microorganisms found in the deep sea were collected from literature 17,34–36 . The literature for each organism was reviewed manually.…”

Section: Methodsmentioning

confidence: 99%

Section: Collection Of Deep-sea Protein Structuresmentioning

confidence: 99%

mentioning

confidence: 99%

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confidence: 99%

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Analyzing structural features of proteins from deep‐sea organisms

et al. 2022

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“…There is still limited knowledge about how LAB responds to the HHP, and its molecular mechanisms are not fully understood. HHP can negatively affect all molecular mechanisms in bacteria where DNA is involved, such as replication, transcription, and recombination (Salvador-Castell et al, 2020). The interaction between DNA and proteins may be disturbed due to the changes in the electrostatic and hydrophobic interactions.…”

Section: Impact Of High Hydrostatic Pressurementioning

confidence: 99%

Impact of high hydrostatic pressure on the single nucleotide polymorphism of stress-related dnaK, hrcA, and ctsR in the Lactobacillus strains

Bucka-Kolendo

Sokołowska

2022

Qual. Assur. Saf. Crops Foods

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Lactic acid bacteria (LAB) are widespread in environments and can either have a positive impact because their ability to survive in harsh conditions and influence the product (probiotic properties, change of structure-EPS [exopolysaccharides], etc.), or a negative impact, (so not needed) because of their spoilage ability (beer, juices). High hydrostatic pressure (HHP), one of the non-thermal preservation methods used in the food industry, can force the LAB to activate the adaptative mechanisms. Under pressurization, the changes in the bacteria cells can occur at the transcriptional or translational level. This study evaluated the HHP on the single nucleotide polymorphism (SNP) changes in three genes, dnaK, ctsR, and hrcA, related to the stress-response mechanism in LAB. The correlation between the DNA polymorphism and the gene expression under HHP stress was assessed. The applied pressure of 300 MPa resulted in a low ratio of nonsynonymous substitutions to the synonymous substitutions (0 to 1.12), and a lower number of mutations was observed for pressurized strains (from 6 in hrcA to 11 in dnaK) than in controlled (from 3 in ctsR to 92 in hrcA). In all pressurized strains, the expression of genes was observed, whereas, in control strains, the gene expression was detected in three out of five strains. Although there was a noticeable change in stress-related gene expression after HHP, there was no correlation with SNPs. At the same time, with a high frequency of synonymous changes in nucleotide and high diversity for hrcA and dnaK, a very low diversity was found in ctsR sequences. The LAB strains stress response mechanisms are much more complex. The study requires information on the general mechanism and changes in the membranes’ composition, proteome changes, and gene expression patterns. The mutations in genes related to stress can have important implications for the strains’ fitness effect and adaptive ability of LAB strains, especially considering their food industry implication where the HHP techniques are used.

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High-pressure adaptation of extremophiles and biotechnological applications

Cited by 2 publications

References 171 publications

Analyzing structural features of proteins from deep‐sea organisms

Analyzing structural features of proteins from deep‐sea organisms

Impact of high hydrostatic pressure on the single nucleotide polymorphism of stress-related dnaK, hrcA, and ctsR in the Lactobacillus strains

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