The effect of elevated hydrostatic pressure on the spectral absorption of deep-sea fish visual pigments

Partridge, Julian C.; White, Elizabeth M.; Douglas, R. H.

doi:10.1242/jeb.01984

Cited by 7 publications

(3 citation statements)

References 30 publications

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“…This is likely in part because of the caveat that investigating rhodopsin cold adaptation in natural systems may be confounded by differences in environment. Naturally occurring habitat transitions may also be accompanied by other, concurrent, selective pressures on rhodopsin function, such as changes in light spectra (12,13,28), pressure (39,40), and temperature (34). To disentangle such effects from other aspects of rhodopsin function, we selected a system that maximized consistency across ambient spectral environments.…”

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confidence: 99%

Evolution of nonspectral rhodopsin function at high altitudes

Castiglione

Hauser

Liao

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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High-altitude environments present a range of biochemical and physiological challenges for organisms through decreases in oxygen, pressure, and temperature relative to lowland habitats. Proteinlevel adaptations to hypoxic high-altitude conditions have been identified in multiple terrestrial endotherms; however, comparable adaptations in aquatic ectotherms, such as fishes, have not been as extensively characterized. In enzyme proteins, cold adaptation is attained through functional trade-offs between stability and activity, often mediated by substitutions outside the active site. Little is known whether signaling proteins [e.g., G protein-coupled receptors (GPCRs)] exhibit natural variation in response to cold temperatures. Rhodopsin (RH1), the temperature-sensitive visual pigment mediating dim-light vision, offers an opportunity to enhance our understanding of thermal adaptation in a model GPCR. Here, we investigate the evolution of rhodopsin function in an Andean mountain catfish system spanning a range of elevations. Using molecular evolutionary analyses and site-directed mutagenesis experiments, we provide evidence for cold adaptation in RH1. We find that unique amino acid substitutions occur at sites under positive selection in high-altitude catfishes, located at opposite ends of the RH1 intramolecular hydrogen-bonding network. Natural high-altitude variants introduced into these sites via mutagenesis have limited effects on spectral tuning, yet decrease the stability of dark-state and light-activated rhodopsin, accelerating the decay of ligand-bound forms. As found in cold-adapted enzymes, this phenotype likely compensates for a cold-induced decrease in kinetic rates-properties of rhodopsin that mediate rod sensitivity and visual performance. Our results support a role for natural variation in enhancing the performance of GPCRs in response to cold temperatures.H igh-altitude environments impose a suite of biochemical and physiological constraints on organisms, such as hypoxia, low atmospheric pressure, and decreasing temperatures (1-3). At the biochemical level, proteins adapted to such conditions are of particular interest to evolutionary biologists (1, 4). Studies of high-altitude-adapted organisms, especially endotherms, have focused primarily on adaptation to hypoxia, including modification of proteins involved in oxygen metabolism (2, 5), and hemoglobin structure and function (6). In contrast, our understanding of biochemical adaptations for high altitude in ectothermic organisms, for which cold temperatures impose unique constraints (7-9), remains limited. Studies in prokaryotes have highlighted how cold adaptation in enzymes is attained by functional trade-offs between protein stability and activity (10), a trade-off also characterized in enzymes from ectothermic vertebrates, such as teleost fishes, where single mutations altering intramolecular hydrogen bonding networks (HBNs) decrease protein stability and ligand binding affinity to optimize kinetic rates for cold environments (11). It is currently...

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confidence: 99%

Evolution of nonspectral rhodopsin function at high altitudes

Castiglione

Hauser

Liao

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…Similar considerations for all these assumptions will apply when using ML to infer other functions from other genes. In fact, many genes are more susceptible than opsins (but see [80]] showing the pressure of ocean depth may slightly affect λ max phenotypes) to changes in pH, temperature, and other environmental factors [81], such that databases compiling these gene functions should also record these parameters for use in training ML models.…”

Section: The Important Relationship Between Data Availability and Pre...mentioning

confidence: 99%

Discovering genotype-phenotype relationships with machine learning and the Visual Physiology Opsin Database (VPOD)

Frazer,

Baghbanzadeh,

Rahnavard

et al. 2024

Preprint

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BackgroundPredicting phenotypes from genetic variation is foundational for fields as diverse as bioengineering and global change biology, highlighting the importance of efficient methods to predict gene functions. Linking genetic changes to phenotypic changes has been a goal of decades of experimental work, especially for some model gene families including light-sensitive opsin proteins. Opsins can be expressed in vitro to measure light absorption parameters, including λmax - the wavelength of maximum absorbance - which strongly affects organismal phenotypes like color vision. Despite extensive research on opsins, the data remain dispersed, uncompiled, and often challenging to access, thereby precluding systematic and comprehensive analyses of the intricate relationships between genotype and phenotype.ResultsHere, we report a newly compiled database of all heterologously expressed opsin genes with λmaxphenotypes called the Visual Physiology Opsin Database (VPOD).VPOD_1.0contains 864 unique opsin genotypes and corresponding λmaxphenotypes collected across all animals from 73 separate publications. We useVPODdata anddeepBreaksto show regression-based machine learning (ML) models often reliably predict λmax, account for non-additive effects of mutations on function, and identify functionally critical amino acid sites.ConclusionThe ability to reliably predict functions from gene sequences alone using ML will allow robust exploration of molecular-evolutionary patterns governing phenotype, will inform functional and evolutionary connections to an organism’s ecological niche, and may be used more broadly forde-novoprotein design. Together, our database, phenotype predictions, and model comparisons lay the groundwork for future research applicable to families of genes with quantifiable and comparable phenotypes.Key PointsWe introduce the Visual Physiology Opsin Database (VPOD_1.0), which includes 864 unique animal opsin genotypes and corresponding λmaxphenotypes from 73 separate publications.We demonstrate that regression-based ML models can reliably predict λmax from gene sequence alone, predict non-additive effects of mutations on function, and identify functionally critical amino acid sites.We provide an approach that lays the groundwork for future robust exploration of molecular-evolutionary patterns governing phenotype, with potential broader applications to any family of genes with quantifiable and comparable phenotypes.

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“…Since large numbers of biological communities were first discovered near hydrothermal vents (Lonsdale 1977), much interest has been focused on the effects of hydrostatic pressure on a variety of deep-sea organisms (Sakiyama & Ohwada 1998, Kaye & Baross 2004, Partridge et al 2006, Campanaro et al 2008. Many studies have shown that organisms retrieved from depths of 2000 to 3000 m or more do not survive under normal pressure (Gross & Jaenicke 1994, Pradillon et al 2004, Pradillon & Gaill 2007.…”

Section: Introductionmentioning

confidence: 99%

High-hydrostatic-pressure optical chamber system for cultivation and microscopic observation of deep-sea organisms

Bao¹,

Gai²,

Lou³

et al. 2010

Aquat. Biol.

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We developed and tested a high-pressure optical chamber system for cultivation and microscopic observation of deep-sea organisms. The system is composed of an optical chamber, a highpressure pump, a pressure sensor and a microscope. The chamber has an observation cavity, 2 cultivation cavities and 2 sapphire windows. The pump is employed for perfusion of culture medium and for increasing the pressure. The pressure sensor monitors the pressure in the chamber. The microscope is used for observing samples through the sapphire windows. In the future, the optical chamber system could be used alone for short-term research or be connected to a large high-pressure vessel to create a flow-through system for long-term research. Using the system, the swimming activity of Bosmina longirostris (Branchiopoda: Cladocera) was observed at different pressures. Swimming activity increased with increasing compression up to 30 MPa. During decompression, this activity reappeared when pressure decreased to 45 MPa and increased with further decreasing pressure. KEY WORDS: Optical chamber system · Real-time · Microscopic observation · PlanktonResale or republication not permitted without written consent of the publisher Aquat Biol 11: 157-162, 2010 To overcome these drawbacks, we developed a high-pressure optical chamber system specifically used for cultivation and microscopic observation of organisms ranging from 100 to 1000 µm in size. The high-pressure chamber is made of titanium, which has been proven to be an excellent biocompatible material and can be used under high pressure up to 60 MPa (6000 m depth in the deep sea). The chamber can either be used alone for short-term research or as part of a flow-through system by connection with a large vessel. A flow-through system could maintain water chemistry conditions in the pressure chamber for longterm observation without decreasing the pressure. We examined the stability of the pressure chamber system and successfully made real-time observations of plankton under different pressures. MATERIALS AND METHODSOptical chamber system. The highhydrostatic-pressure optical chamber system is mainly composed of an optical pressure chamber, a microscope, a pressure pump and a pressure sensor. The temperature is controlled by a water bath.High-hydrostatic-pressure optical chamber: The optical chamber (Fig. 1) is made of titanium, an excellent material for highpressure research. The chamber is in the form of a rectangular box (180 × 44 × 38 mm), which has an observation cavity and 2 cultivation cavities. The maximum pressure in the chamber is 60 MPa.The observation cavity (Fig. 2a) is 13 mm in diameter and provides 2 opposite optical windows for real-time microscopic observation. The optical window (Fig. 2b) is made of sapphire, 16 mm in diameter and 8 mm in thickness. It provides clear images with common microscopes and excellent biocompatibility. A fluorine rubber O-ring (16 mm diameter, 1.8 mm thick) is used to seal the window. The sapphire window is tightened by a compression cove...

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The effect of elevated hydrostatic pressure on the spectral absorption of deep-sea fish visual pigments

Cited by 7 publications

References 30 publications

Evolution of nonspectral rhodopsin function at high altitudes

Evolution of nonspectral rhodopsin function at high altitudes

Discovering genotype-phenotype relationships with machine learning and the Visual Physiology Opsin Database (VPOD)

High-hydrostatic-pressure optical chamber system for cultivation and microscopic observation of deep-sea organisms

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