User:Danlee28/Deep sea fish/Bibliography

Bibliography (Danlee28)
This is where you will compile the bibliography for your Wikipedia assignment. Please refer to the following resources for help:

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


 * 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

Bibliography (Danielk1m1005)
Mechanism of Deep-Sea Fish α-Actin Pressure Tolerance Investigated by Molecular Dynamics Simulations

Citation:

'''Wakai N, Takemura K, Morita T, Kitao A (2014). Mechanism of Deep-Sea Fish α-Actin Pressure Tolerance Investigated by Molecular Dynamics Simulations. PLOS ONE 9(1): e85852. https://doi.org/10.1371/journal.pone.0085852                                                        '''

Information summary:


 * Actin is a protein responsible for numerous cellular functions, and a-actin is the main component of muscle fiber, highly conserved across a variety  of species.
 * In these species, which are pressure tolerant to depths of at least 5000 and 6000m respectively, C. armatus and C. yaquinae have actins with specific substitutions.
 * Q137K and V54A (C. armatus) or I67P (C. yaquinae)
 * Q137K substitution is observed in the active site and is predicted to be important for pressure tolerance.  
 * At high pressure, significant changes in the salt bridge patterns in deep-sea fish actins were observed, and they are expected to stabilize ATP binding and subdomain arrangement.
 * Deep-sea fish actins formed a great total number of salt bridges than non deep-sea fish actins.
 * Salt bridge pattern of Arm and Yaq showed notable differences compared to the others studied in this work. The salt bridges between ATP and K137, which were only formed in deep-sea fish actins, are expected to stabilize ATP binding even under high pressure.
 * It was concluded that two amino acid differences are sufficient to significantly stabilize ATP binding and subunit arrangement through the salt bridges.
 * Free energy analysis suggests that deep-sea fish actins are stabilized to a greater degree by the conformational energy decrease associated with pressure effect.
 * Free energy differences between 60 and 0.1 MPa (ΔG values) of Arm and Yaq were the lowest and second lowest, respectively, and were significantly lower than the others. This is consistent to the fact that Arm and Yaq are stable at high pressure.

Molecular dynamics simulation of proteins under high pressure: Structure, function and thermodynamics

Citation:

'''Hiroaki Hata, Masayoshi Nishiyama, & Akio Kitao (2019). Molecular dynamics simulation of proteins under high pressure: Structure, function and thermodynamics. Biochimica et Biophysica Acta (BBA) - General Subjects 1864(2), https://doi.org/10.1016/j.bbagen.2019.07.004 '''

Information summary:


 * Molecular  dynamics simulation is used to investigate the property differences of proteins and  water between ambient and high pressure conditions.
 * Pressure increases the density of water around proteins and changes the structure of hydrogen bonding networks between proteins and water molecules.
 * It showed that the ATP–binding and post–ATP–binding steps are pressure–sensitive reactions, and the others are insensitive.
 * MD reveals that two amino acid differences between deep-sea and non-deep-sea fish actins are sufficient to induce significant changes in the salt bridging pattern, and showed that these salt bridges in deep-sea actions play a significant role in stabilizing ATP binding and actin subdomain arrangement at high pressure.

Osmolyte Adjustments as a Pressure Adaptation in Deep-Sea Chondrichthyan Fishes: An Intraspecific Test in Arctic Skates (Amblyraja hyperborea) along a depth Gradient

Citation:

'''Paul H. Yancey, Ben Speers-Roesch, Sheila Atchinson, James D. Reist, Andrew R. Majewski, and Jason R. Treberg (2017). Osmolyte Adjustments as a Pressure Adaptation in Deep-Sea Chondrichthyan Fishes: An Intraspecific Test in Arctic Skates (Amblyraja hyperborea) along a Depth Gradient. Physiological and Biochemical Zoology 2018 91:2, 788-796'''

 https://www.journals.uchicago.edu/doi/full/10.1086/696157# 

Information summary:


 * Accumulation of trimethylamine N-oxide (TMAO) by deep-sea animals is proposed to protect proteins against the destabilizing effects of high hydrostatic pressure (the piezolyte hypothesis).
 * Flexible adjustments of osmolyte combinations are a key response for deep-sea living in individual chondrichthyans, supporting the piezolyte hypothesis.
 * It was found that the urea-to-TMAO ratio decreased linearly with depth, with tighter correlation than that seen in interspecific studies.
 * Minor osmolytes, including betaine, sarcosine, and some α-amino acids, also declined with depth, apparently replaced by TMAO (a stronger piezolyte than those solutes).
 * For chondrichthyans, the ability to increase TMAO with depth while simultaneously reducing urea and other osmolytes is probably important for living in deep waters to cope with hydrostatic pressure.

Morphology and genome of a snailfish from the Mariana Trench provide insights into deep-sea adaptation

Citation:

'''Wang, K., Shen, Y., Yang, Y. et al. (2019). Morphology and genome of a snailfish from the Mariana Trench provide insights into deep-sea adaptation. Nat Ecol Evol 3, 823–833. https://doi.org/10.1038/s41559-019-0864-8 '''

Information summary:


 * Genomic analyses of Pseudoliparis swirei, a Mariana hadal snailfish (MHS), revealed molecular adaptations consistent with pressure-tolerant cartilage, loss of visual function and skin colour, enhanced cell membrane fluidity and transport protein activity, and increased protein stability.
 * The numerous genetic changes identified in this study shed light on how vertebrate species can survive and thrive in the deep oceans.
 * Vertebrates living on the surface of the Earth have closed skull spaces surrounded by hard bone, to protect the brain and maintain an appropriate intracranial pressure, but closed skulls cannot maintain their structural integrity under the very high pressures of the hadal environment, necessitating an open system. It was found that the premature termination of bglap in the MHS may be associated with this species’ unusual skull structure and reduced bone hardness.
 * It was found that the skull of the MHS is not completely closed, allowing internal and external pressure equalization.
 * Most of the bones consist of cartilage rather than being ossified.
 * (which can be seen as a structural adaptation).
 * The osteocalcin gene, also known as the bone Gla protein (bglap) gene, which regulates tissue mineralization and skeletal development has a frameshift mutation that may cause premature termination of cartilage calcification in the MHS, which might cause its pseudogenization or severe modification
 * High hydrostatic pressures reduce the fluidity of lipid bilayers and the reversibility of their phase transitions, ultimately leading to the denaturation and functional disorder of membrane-associated proteins. Pressure also rigidifies membranes, impairing their transport functions.
 * Biochemical studies have suggested that the membranes of deep-sea-adapted organisms contain a higher weight percentage of unsaturated fatty acids than the equivalent membranes of shallow-sea species.
 * These changes may increase the abundance of fluid membrane lipids, enabling survival in the world’s deepest ocean trench. Other significantly expanded categories include genes belonging to families with ion and solute transport-related functions, such as tfa and slc29a3. This is consistent with a need to resist high-pressure-induced inhibition of fluid transport in hadal organisms.
 * Hydrostatic pressure strongly inhibits protein function, affecting both folding and enzyme activity. Consequently, species living at great depths must maintain an intracellular milieu that preserves the intrinsic properties of proteins and confers pressure resistance.
 * Mechanisms based on physiological and structural adaptations have been proposed to explain the preservation of protein functionality in deep-sea organisms.

Adaptations to the Deep Sea

Citation:

'''Hochachka, P., Somero, G. (1984). “Adaptations to the Deep Sea.” Biochemical Adaptation. Princeton, New Jersey: Princeton University Press. doi:10.2307/j.ctt7zv9d4'''

Information summary:


 * Without the capacity to maintain an adequate rate of closely regulated metabolic flow in the face of high pressures, it would be pointless to be concerned with the food abundance in the depth.
 * A consequence of the water-structuring abilities of metabolites, allosteric effectors, and amino acid side chains is that whenever an enzymatic reaction takes place, some change in water organization and, hence, in system volume is likely to occur.
 * The reversible hydration/dehydration of these groups during binding events is likely to occur with substantial changes in system (water-protein-ligand) volume.
 * Why?: Because  enzyme-ligand interactions typically are mediated through charge-charge interactions or through polar, but noncharged interactions, and so it will change water organization in organisms’ bodies.
 * It should also be noted that pressure-sensitivity can arise during assembly events involving proteins.
 * Even without changes in the inherent volumes of the subunits during polymerization, subunit assembly equilibria may be perturbed by increases in pressure.
 * Similar to high body temperature, elevated hydrostatic pressure might favor selection for rigid protein structures.

Direct Links:


 * https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0085852#pone-0085852-t003
 * https://www.sciencedirect.com/science/article/pii/S0304416519301758
 * https://www.journals.uchicago.edu/doi/full/10.1086/696157#
 * https://www.nature.com/articles/s41559-019-0864-8#citeas
 * https://www.jstor.org/stable/pdf/j.ctt7zv9d4.18.pdf?refreqid=excelsior%3A9a2268dbc93945911c52bca4c76830c2

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