Adaptations for Pressure and Temperature in Dihydrofolate Reductases

Enzymes from extremophilic microbes that live in extreme conditions are generally adapted so that they function under those conditions, although adaptations for extreme temperatures and pressures can be difficult to unravel. Previous studies have shown mutation of Asp27 in Escherichia coli dihydrofolate reductase (DHFR) to Glu27 in Moritella profunda (Mp). DHFR enhances activity at higher pressures, although this may be an adaptation for cold. Interestingly, MpDHFR unfolds at ~70 MPa, while Moritella yayanosii (My) was isolated at depths corresponding to ~110 MPa, indicating that MyDHFR might be adapted for higher pressures. Here, these adaptations are examined using molecular dynamics simulations of DHFR from different microbes in the context of not only experimental studies of activity and stability of the protein but also the evolutionary history of the microbe. Results suggest Tyr103 of MyDHFR may be an adaptation for high pressure since Cys103 in helix F of MpDHFR forms an intra-helix hydrogen bond with Ile99 while Tyr103 in helix F of MyDHFR forms a hydrogen bond with Leu78 in helix E. This suggests the hydrogen bond between helices F and E in MyDHFR might prevent distortion at higher pressures.

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Pressure Adaptations in Deep-Sea Moritella Dihydrofolate Reductases: Compressibility versus Stability

Biology ◽

10.3390/biology10111211 ◽

2021 ◽

Vol 10 (11) ◽

pp. 1211

Author(s):

Ryan W. Penhallurick ◽

Toshiko Ichiye

Keyword(s):

Molecular Dynamics ◽

Hydrogen Bond ◽

Dihydrofolate Reductase ◽

Deep Sea ◽

Water Entry ◽

Internal Cavity ◽

Cavity Volume ◽

Dihydrofolate Reductases ◽

Moritella Profunda ◽

Dynamics Simulations

Proteins from “pressure-loving” piezophiles appear to adapt by greater compressibility via larger total cavity volume. However, larger cavities in proteins have been associated with lower unfolding pressures. Here, dihydrofolate reductase (DHFR) from a moderate piezophile Moritella profunda (Mp) isolated at ~2.9 km in depth and from a hyperpiezophile Moritella yayanosii (My) isolated at ~11 km in depth were compared using molecular dynamics simulations. Although previous simulations indicate that MpDHFR is more compressible than a mesophile DHFR, here the average properties and a quasiharmonic analysis indicate that MpDHFR and MyDHFR have similar compressibilities. A cavity analysis also indicates that the three unique mutations in MyDHFR are near cavities, although the cavities are generally similar in size in both. However, while a cleft overlaps an internal cavity, thus forming a pathway from the surface to the interior in MpDHFR, the unique residue Tyr103 found in MyDHFR forms a hydrogen bond with Leu78, and the sidechain separates the cleft from the cavity. Thus, while Moritella DHFR may generally be well suited to high-pressure environments because of their greater compressibility, adaptation for greater depths may be to prevent water entry into the interior cavities.

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Effects of Pressure and Temperature on the Atomic Fluctuations of Dihydrofolate Reductase from a Psychropiezophile and a Mesophile

International Journal of Molecular Sciences ◽

10.3390/ijms20061452 ◽

2019 ◽

Vol 20 (6) ◽

pp. 1452 ◽

Cited By ~ 3

Author(s):

Qi Huang ◽

Jocelyn Rodgers ◽

Russell Hemley ◽

Toshiko Ichiye

Keyword(s):

Hydrogen Bonds ◽

Dihydrofolate Reductase ◽

Thermal Energy ◽

Food Preservation ◽

Enzyme Function ◽

Extreme Conditions ◽

Loop Regions ◽

Temperature And Pressure ◽

Moritella Profunda ◽

Dynamics Simulations

Determining the effects of extreme conditions on proteins from “extremophilic” and mesophilic microbes is important for understanding how life adapts to living at extremes as well as how extreme conditions can be used for sterilization and food preservation. Previous molecular dynamics simulations of dihydrofolate reductase (DHFR) from a psychropiezophile (cold- and pressure-loving), Moritella profunda (Mp), and a mesophile, Escherichia coli (Ec), at various pressures and temperatures indicate that atomic fluctuations, which are important for enzyme function, increase with both temperature and pressure. Here, the factors that cause increases in atomic fluctuations in the simulations are examined. The fluctuations increase with temperature not only because of greater thermal energy and thermal expansion of the protein but also because hydrogen bonds between protein atoms are weakened. However, the increase in fluctuations with pressure cannot be due to thermal energy, which remains constant, nor the compressive effects of pressure, but instead, the hydrogen bonds are also weakened. In addition, increased temperature causes larger increases in fluctuations of the loop regions of MpDHFR than EcDHFR, and increased pressure causes both increases and decreases in fluctuations of the loops, which differ between the two.

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Cooperation in primates

Interaction Studies ◽

10.1075/is.16.3.02alb ◽

2015 ◽

Vol 16 (3) ◽

pp. 361-382 ◽

Cited By ~ 8

Author(s):

Anna Albiach-Serrano

Keyword(s):

Observational Studies ◽

Evolutionary History ◽

Nonhuman Primates ◽

Cooperative Behavior ◽

Experimental Studies ◽

Primate Species ◽

Future Studies ◽

History Of ◽

Methodological Difficulties

Observational studies have suggested that some nonhuman primates’ cooperative behavior may rely on their capacity to share goals and understand the role of their partners. Experimental studies have tried to find evidence for this under controlled conditions, investigating aspects like the degree of organization in different primate species and the individuals’ capacity to recognize and choose good partners, switch roles with them, and care about their outcomes. Often, the results have been mixed. Partly, this is because of the methodological difficulties inherent to empirical research. In this paper, I offer a critical, methodological review of the experimental studies done in the last years on nonhuman primates’ cooperation, I discuss their findings, and suggest possible solutions to some of the procedural problems. Hopefully, this will contribute to improve the design of future studies and therefore our knowledge about the evolutionary history of cooperation.

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Urbilaterian origin and evolution of sNPF-type neuropeptide signalling

10.1101/712687 ◽

2019 ◽

Cited By ~ 1

Author(s):

Luis Alfonso Yañez-Guerra ◽

Xingxing Zhong ◽

Ismail Moghul ◽

Thomas Butts ◽

Cleidiane G. Zampronio ◽

...

Keyword(s):

Evolutionary History ◽

Molecular Phylogenetics ◽

Common Ancestor ◽

Sequence Data ◽

Experimental Studies ◽

Peptide Ligands ◽

Origin And Evolution ◽

History Of ◽

Type Receptor ◽

Signalling Systems

AbstractPhysiology and behaviour are controlled by neuropeptide signalling systems comprising peptide ligands and cognate receptors. Molecular phylogenetics combined with experimental identification of neuropeptide-receptor pairs has revealed that many neuropeptide signalling systems originated in the urbilaterian common ancestor of protostomes and deuterostomes. Neuropeptide-Y/neuropeptide-F (NPY/NPF)-type signalling is one such example, whereas NPY/NPF-related short-NPF (sNPF)-type signalling has hitherto only been identified in protostomes. Here we report the discovery of a neuropeptide (pQDRSKAMQAERTGQLRRLNPRF-NH2) that is the ligand for an sNPF-type receptor in a deuterostome, the starfish Asterias rubens (Phylum Echinodermata). Informed by phylogenetic analysis of sequence data, we conclude that the paralogous NPY/NPF-type and sNPF-type signalling systems originated in Urbilateria but NPY/NPF-type signalling was lost in echinoderms. Furthermore, we present evidence that sNPF-type peptides are orthologs of vertebrate prolactin-releasing peptides. Our findings demonstrate the importance of experimental studies on echinoderms for reconstructing the evolutionary history of neuropeptide signalling systems.

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Is embryonic hypothermia tolerance common in birds?

Biology Letters ◽

10.1098/rsbl.2016.0967 ◽

2017 ◽

Vol 13 (4) ◽

pp. 20160967 ◽

Cited By ~ 4

Author(s):

Jin-Ming Zhao ◽

Zhi-Ming Han ◽

Yue-Hua Sun

Keyword(s):

Evolutionary History ◽

Experimental Studies ◽

Columba Livia ◽

Avian Species ◽

Coturnix Japonica ◽

Future Research ◽

Domestic Species ◽

Avian Incubation ◽

History Of ◽

Incubation Temperatures

Avian incubation temperatures oscillate within narrow limits to ensure proper embryonic development. However, field observations and experimental studies have found that some species can tolerate very low incubation temperatures, either regularly or occasionally. We artificially incubated eggs from five domestic species, which represent a range of egg sizes, to examine whether a diversity of avian species could exhibit an unusual hypothermia tolerance, as observed in the field. We found that eggs of the chicken ( Gallus gallus domesticus ), pigeon ( Columba livia domestica ), Japanese quail ( Coturnix japonica ) and budgerigar ( Melopsittacus undulatus ) survived the incubation period and hatched after experiencing 10°C hypothermia for 6 h each day. However, embryos of white-rumped munia ( Lonchura striata ) died after 10 days of hypothermia. Our results showed that unusual hypothermia tolerance occurs in several avian species. This phenomenon might have been selected through the evolutionary history of birds. Future research should identify the importance of phylogeny, egg size and embryonic stage in tolerance to hypothermia.

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Elaborating the role of reflection and individual differences in the study of folk-economic beliefs

Behavioral and Brain Sciences ◽

10.1017/s0140525x18000274 ◽

2018 ◽

Vol 41 ◽

Author(s):

Kevin Arceneaux

Keyword(s):

Decision Making ◽

Individual Differences ◽

Cognitive Processes ◽

Evolutionary History ◽

Behavioral Responses ◽

History Of ◽

Economic Beliefs

AbstractIntuitions guide decision-making, and looking to the evolutionary history of humans illuminates why some behavioral responses are more intuitive than others. Yet a place remains for cognitive processes to second-guess intuitive responses – that is, to be reflective – and individual differences abound in automatic, intuitive processing as well.

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