User:Danlee28/Deep sea fish

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Hydrostatic pressure adaptations for Deep sea Fish
Hydrostatic pressure is the pressure that is exerted by a fluid at equilibrium at a given point within the fluid, due to the force of gravity. For many deep sea fish in the bathypelagic and beyond, the hydrostatic pressure that these organisms experience increases by one atmosphere for every 10 meters deeper in depth. For a fish at the bottom of the bathypelagic zone, this equates to the fish withstanding around 400 atmospheres of hydrostatic pressure. There a variety of adaptations that deep sea fauna possess, on a cellular level and physiological level, that allow them to thrive in an environment of great pressure. These physiological adaptations act as a boundary that limits the depth that shallow-species can penetrate. High levels of external pressure have a great effect on metabolic processes and biochemical reactions. The equilibrium of many chemical reactions can be disturbed by pressure, and thus reactions inducing volume changes are susceptible to pressure. When a volume increase takes place during the process, pressure will inhibit the process. Water, a key proponent in many biological processes, is very susceptible to volume changes. Thus, enzymatic reactions that induce changes in water organization effectively change the system's volume. Proteins that are responsible for catalyzing many reactions are typically held together by a culmination of weak bonds and usually involve an increase in volume during formation. To adapt to this change, the protein structure and reaction criteria of deep sea fish have been adapted to withstand pressure in order to perform reactions in these conditions. In high pressure environments, cellular bilayer membranes experience a loss of fluidity. Therefore, deep-sea cellular membranes favor phospholipid bilayers with a higher proportion of unsaturated fatty acids, which induce a higher fluidity than their sea-level counterparts.

Deep sea species exhibit a lower change of entropy and enthalpy, since a high pressure and low temperature environment seem to favor negative enthalpy changes and a reduced dependence on entropy-driven reactions, compared to that of surface level organisms. From a structural standpoint, globular proteins of deep sea fish the tertiary structure of G-actin is relatively rigid compared to that of surface level fauna. Proteins of deep sea fish are structurally modified is apparent from the observation that actin from the muscle fibers of deep sea fishes are extremely heat resistant; a similar characteristic to those of desert lizards. These proteins are structurally strengthened by modification of the bonds in the tertiary structure of the protein which also happen to induce high levels of thermal stability. Proteins are structurally strengthened to resist pressure by modification of bonds in the tertiary structure. Therefore, high levels of hydrostatic pressure, similar to high body temperatures of thermophilic desert reptiles, favor rigid protein structures.

Na+/K+ -ATPase is an lipoprotein enzyme that plays a prominent role in osmoregulation and is heavily influenced by hydrostatic pressure. The inhibition of Na+/K+ -ATPase is due to increased compression due to pressure. The rate-limiting step of the Na+/K+ -ATPase reaction induces an expansion in the bilayer surrounding the protein, and therefore an increase in volume. An increase in volume makes Na+/K+ -ATPase reactivity susceptible to higher pressures. Even though the Na+/K+ -ATPase activity per gram of gill tissue is lower for deep sea fishes, the Na+/K+ -ATPases of deep sea fishes exhibit a much higher tolerance of hydrostatic pressure compared to their shallow-water counterparts. This is exemplified between the species of the genus Coryphaenoides (around 2000m deep) and its hadalpelagic counterpart C. armatus (around 4000m deep), where the Na+/K+ -ATPases of C. armatus are much less sensitive to pressure. This resistance to pressure can be explained by adaptations in the protein and lipid moieties of Na+/K+ -ATPase.



Some sources That I can add to the article with
'''HOCHACHKA, P., & SOMERO, G. (1984). Adaptations to the Deep Sea. In Biochemical Adaptation (pp. 450-495). Princeton, New Jersey: Princeton University Press. doi:10.2307/j.ctt7zv9d4.18'''

Link to article: https://www.jstor.org/stable/pdf/j.ctt7zv9d4.18.pdf?refreqid=excelsior%3Aef73d097261217f5d90a94ed995863f8 


 * This article is from 1984, but features a very general overview of adapting to the deep sea environment. It features adaptations to temperature, light and pressure
 * There are a few pages relating pressure to metabolism and therefore, volume.
 * “Most metabolic intermediates and protein amino acid side chains are surrounded by a layer or several water molecules in thickness of ordered water”
 * Therefore, metabolic processes induce volume changes and thus the intense hydrostatic pressure is a great influencer of metabolic rate in the deep sea.
 * The article brings up the point, do the volume changes of these chemical processes actually necessitate a pressure adaptive change to these enzymes? And they go on to say yes, pressure adaptive changes are needed.
 * Adapting enzymes to high pressure means sacrificing competitive abilities in the shallower depths.
 * The enzyme they studied was M4 isozyme of lactate dehydrogenase (LDH), and how this enzyme differs between shallow and deep water fishes. Maintenance of KM values within a range optimal for catalysis and regulation
 * Enzymes of shallow depth fish would be handicapped at deeper depths due to abnormally high Km values for the substrate and cofactor
 * Distinguishing the two types of LDH pressure sensitive/pressure insensitive- only a slight change in primary protein structure, with a single amino acid substitution difference
 * Pressure effects on protein structure
 * Tertiary structure of G-actin is rigid, pressure favors selection for rigid protein structures
 * The first figure (12-1) depicts the classification of marine environments and includes the area of the ocean floor in each environment.
 * Figure (12-3) The effects of hydrostatic pressure on the apparent Kn, of NADH (upper panel) and pyruvate (lower panel) for purified M4 -lactate dehydrogenases of several deep- and shallow-living marine teleost fishes.
 * Figure (12-4) - depth distributions for different species of fish

'''Priede, I. G. (2017). Adaptations to the Deep Sea. In Deep-Sea Fishes: Biology, Diversity, Ecology and Fisheries (pp. 87–138). chapter, Cambridge: Cambridge University Press.DOI: https://doi.org/10.1017/9781316018330.004 '''

Link to article : https://www.cambridge.org/core/books/deepsea-fishes/adaptations-to-the-deep-sea/594899C502F534259535DE1745CFD96B/core-reader 


 * There is a section dedicated to the effects of pressure on biochemical reactions of deep sea organisms
 * Biochemical reactions that involve an increase of volume of reactants are inhibited by hydrostatic pressure.
 * In deeper-living species there appears to be natural selection for phospholipids with high inherent fluidity
 * Sodium potassium pump activity is also less sensitive to pressure for deep sea fish due to gill membrane fluidity protecting the enzyme function
 * Pressure tolerance found in enzymes involved with muscle anaerobic metabolic pathways, LDH, MDH, GAPDH,
 * Sacrifice of reaction rate for pressure resistance, kreb cycle enzyme citrate synthase~⅕ the rate of surface
 * pressure has multiple effects on metabolism
 * compensated for by changes in membrane phospholipid composition,
 * intrinsic modifications of proteins
 * extrinsic conservation of protein function by accumulation of protective osmolytes such as TMAO
 * Important evidence that proteins of deep-sea fishes are structurally modified arose from the observation that actin extracted from muscle fibres of deep-sea fishes is extremely heat resistant with properties equivalent to actins from heat-loving desert lizards.
 * proteins are structurally strengthened to resist pressure by modification of bonds in the tertiary structure shaping the molecule. This has the side effect of conferring high thermal stability.
 * While air can be expelled through the pneumatic duct in physostomes, inflation of the swim bladder in deep-sea fishes must occur through the bloodstream.
 * Physostomous fish have a pneumatic duct connecting esophagus and gas bladder
 * Figure 3.8 describes the adaptations of the gas bladder to depth.
 * Rete capillary length increases with depth (in a sqrt(x) graphical pattern)
 * Guanine crystal content increases with depth. (guanine crystals act as barrier for gas diffusion)
 * Allows fish to maintain near-neutral buoyancy at deep levels.

'''Somero, G. (1990). Life at Low Volume Change: Hydrostatic Pressure as a Selective Factor in the Aquatic Environment. American Zoologist, 30(1), 123-135. Retrieved October 2, 2020, from http://www.jstor.org/stable/3883429 '''


 * Adaptations below a certain depth are required to reduce volume changes and minimize effect of pressure on biochemical structures and their functions
 * Reduced sensitivity of pressure linked to reduced enzymatic performance
 * Changes in water structure that accompany catalysis, ligand binding and protein assembly
 * Dehydrogenase enzymes - at deeper depths these enzymes show no perturbation of Km of cofactor → evidence of adaptation
 * Fishes capable of effective cofactor binding at high pressures
 * Large increases in Km with increasing pressure found for dehydrogenases of shallow species are not observed for species of the deep sea.
 * Pressure also affects maximal velocity of reaction
 * This article has a lot of graphs illustrating the enzymatic performance at various pressures.
 * Figure 1: the effects of hydrostatic pressure on homologues of four dehydrogenase enzymes purified from fishes living at different depths
 * Adaptations of proteins to pressure: structural stability
 * Skeletal muscle actins from different depths showed volume change accompanying actin self-assembly is not a fixed property of the actin assembly reaction
 * LDH’s (lactate dehydrogenase) of deep fish are more resistant to denaturation by high pressures
 * Adaptations limited by reductions in volume?

'''Porter, M. & Roberts, N. & Partridge, J. (2016) Evolution under pressure and the adaptation of visual pigment compressibility in deep-sea environments. Molecular Phylogenetics and Evolution, Volume (105), 160-165. DOI: https://doi.org/10.1016/j.ympev.2016.08.007 '''

Link: https://www.sciencedirect.com/science/article/pii/S1055790316302007 


 * Opsins - group of proteins that are important for light-sensing systems, circadian rhythms,  and photosyntesis
 * The selection of specific amino acid properties may play a role in protein evolution in the deep-sea
 * In marine animals two types of changes that maintain protein function at high hydrostatic pressures:
 * extrinsic (changes in cellular and/or membrane composition)
 * intrinsic (amino acid substitutions leading to modifications of protein structure).
 * Opsin proteins of deep fish are less compressible, due to positive destabilizing selection of amino acid properties that relate to compressibility. This study links specific amino acid properties to protein compressibility in high hydrostatic pressure
 * Middle of transmembrane helices - more stable helix structure under higher pressures (helix III and helix VI via Amino acid substitutions- open G-protein binding sites upon visual pigment activation (sight)
 * Materials/methods
 * Opsin sequence were taken from GenBank
 * Rh1 sequences from 128 species of fish from taxon Teleostei
 * Rhodopsin sequences from 65 species of cephalopods
 * DNA dataset -> Amino acid sequence and aligned
 * Amino acid alignments were used to create phylogenies
 * For each species, median depth was calculated using capture depth records (OBIS)
 * Adiabatic compressibility (βs) is the relative change in the volume of the system per unit adiabatic change in its pressure, and can be estimated for proteins based solely on amino acid sequences

'''Somero, Somero N. (1992) Adaptations to High Hydrostatic Pressure. Annual Review of Physiology Volume 54, pp 557-577. Doi: Https://doi.org/10.1146/annurev.ph.54.030192.003013 '''

Link: https://www.annualreviews.org/doi/pdf/10.1146/annurev.ph.54.030192.003013 


 * This article goes into pressure adaptations of various biochemical systems


 * At 11000m below sea level, pressures near 1100 atm
 * Effects of hydrostatic pressure - change in system volume
 * Enzymatic catalysis, assembly of multisubunit proteins, membrane-based transport, ligand binding- all affected by pressure
 * Adaptations of membrane-based systems
 * Homeoviscous adaptation - keeping membrane fluidity via lipids
 * Rich in mono-unsaturated fatty acids and low in saturated fatty acids
 * Unsaturated fatty acids contribute to membrane fluidity
 * Pressure adaptation of the Na+ K+ ATPase
 * This enzyme plays key role in osmoregulation, strongly inhibited by pressure
 * Adaptations in subunit assembly and stability of proteins
 * Multisubunit proteins are usually disassociated in high pressures
 * Actins of deep sea fishes - enthalpy, entropy and volume changes accompanying actin subunit polymerization are much lower for deep sea fishes
 * High thermal stability of pressure-adapted proteins
 * Adaptations of enzymatic function
 * Strong conservation of michaelis-menten constants (Km values)
 * Mentioned in other articles too
 * Pressure resistant Km values correlated with loss of catalytic performance
 * Pressure effects on transcription and translation
 * These two processes highly sensitive to pressure, inhibitory

'''Gerringer, M.E., Yancey, P.H., Tikhonova, O.V., Vavilov, N.E., Zgoda, V.G. and Davydov, D.R. (2020), Pressure tolerance of Deep‐sea Enzymes can be evolved through increasing volume changes in protein transitions: a study with lactate dehydrogenases from abyssal and hadal fishes. FEBS Journal. doi:10.1111/febs.15317'''

 https://febs.onlinelibrary.wiley.com/doi/full/10.1111/febs.15317 

'''COAD, B. (2018). Family 28. Myctophidae: Lanternfishes, Poissons-lanternes (8). In MØLLER P., RENAUD C., ALFONSO N., DUNMALL K., POWER M., SAWATZKY C., et al. (Authors) & COAD B. & REIST J. (Eds.), Marine Fishes of Arctic Canada (pp. 322-332). TORONTO; BUFFALO; LONDON: University of Toronto Press. Retrieved October 18, 2020, from http://www.jstor.org/stable/10.3138/j.ctt1x76h0b.51 '''
 * Case study of LDH and its pressure tolerance in deep sea fishes
 * Comparing effects of pressure on LDH activity between deep and shallow fishes
 * Quantified LDH content in muscle homogenates
 * Increased hydrostatic pressure impacts biological systems by affecting all transitions that involve changes in the system volume
 * nonlinear relationship of Kp due to pressure‐induced conformational transitions or a change in the rate‐limiting step of enzymatic reaction
 * the effect of pressure on the enzyme may be considered as a pressure‐induced reshaping of the protein conformational landscape.
 * A new aspect of high-pressure adaptation in proteins - substantial increase in volume changes associated with the protein’s transition to a pressure-promoted conformational state
 * Though enzymatic performance is lowered, this is countered by having a higher enzyme content
 * intriguing finding in this study is a prominent increase in the absolute value of VPP of LDH observed with increasing habitat depth of the host species
 * VPP  is short for  pressure-promoted conformational state

'''Martin, R., & Davis, M. (2016). Patterns of Phenotypic Variation in the Mouth Size of Lanternfishes (Teleostei: Myctophiformes). Copeia, 104(4), 795-807. Retrieved October 18, 2020, from http://www.jstor.org/stable/45163970 '''

'''Weisberger, M. (2016, June 28). Invasive Lionfish Arrive in the Mediterranean. Retrieved October 18, 2020, from https://www.scientificamerican.com/article/invasive-lionfish-arrive-in-the-mediterranean/ '''

'''Hixon, M., Green, S., Albins, M., Akins, J., & Morris, J. (2016). INTRODUCTION: Lionfish: A major marine invasion. Marine Ecology Progress Series, 558, 161-166. doi:10.2307/24897425'''

'''Sutton, T.T. (2013), Vertical ecology of the pelagic ocean: classical patterns and new perspectives. J Fish Biol, 83: 1508-1527. doi:10.1111/jfb.12263'''

'''Peake, J., Bogdanoff, A. K., Layman, C. A., Castillo, B., Reale-Munroe, K., Chapman, J.,. . . Morris,James A.,,Jr. (2018). Feeding ecology of invasive lionfish (0RW1S34RfeSDcfkexd09rT2pterois volitans1RW1S34RfeSDcfkexd09rT2 and 0RW1S34RfeSDcfkexd09rT2pterois miles1RW1S34RfeSDcfkexd09rT2) in the temperate and tropical western atlantic. Biological Invasions, 20(9), 2567-2597. doi: http://dx.doi.org/10.1007/s10530-018-1720-5 '''

'''SCOTT, T., & POWELL, J. (2018). OCEANS. In The Universe as It Really Is: Earth, Space, Matter, and Time (pp. 186-209). NEW YORK: Columbia University Press. doi:10.7312/scot18494.15'''

'''Denny, M. (2008). Ocean Basins. In How the Ocean Works: An Introduction to Oceanography (pp. 33-53). Princeton; Oxford: Princeton University Press. doi:10.2307/j.ctvcm4g2r.7'''

'''M. (Ed.). (2020, May 03). The Open Ocean ~ MarineBio Conservation Society. Retrieved October 18, 2020, from https://marinebio.org/oceans/open-ocean/ '''