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Life Under Extreme Conditions: A Molecular Science View

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: closed (31 May 2022) | Viewed by 7898

Special Issue Editor

Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, 3420 North Broad Street, Philadelphia, PA 19140, USA
Interests: liposomes; fluorescence; drug delivery; membrane biophysics; archaea; high pressure biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Many organisms can inhabit or survive in extreme physical and chemical environments, such as volcanic areas, hot springs, the Antarctic sheet, and deep-sea hydrothermal vents. In these conditions, organisms experience exceedingly high or low temperatures, high pressures, high salinity, a lack of oxygen and/or extreme acidity. In addition to the natural extreme environments on this planet, we are also concerned about how living organisms are adapted to environments outside Earth, and whether extraterrestrial life exists. This Special Issue is intended to serve as a platform to share recent findings in this area from different research disciplines such as biophysics, biochemistry, geochemistry, microbiology, astrobiology, marine science, and evolutionary biology. We are looking for manuscripts that will focus on understanding biochemical, biophysical, and cellular mechanisms at the molecular level that influence the biological behaviors of organisms living in extreme environments. The topics to be covered in this Special Issue entitled “Life Under Extreme Conditions: A Molecular Science View” include, but are not limited to, the following:

  • The effects of extreme temperatures, elevated pressures, and chemical stressors (e.g., high salt concentrations) on the physicochemical properties of biomolecules and bio-assemblies;
  • The effects of extreme temperatures, elevated pressures, and chemical stressors on the genomics, lipidomics, proteomics, and metabolomics of organisms;
  • Biochemical reactions and pathways under extreme physical conditions;
  • New methodologies to study biomolecules or bio-assemblies, or cellular behaviors, under extreme environmental conditions;
  • Molecular characterizations of new species detected in extraordinary environments;
  • Adaptation and evolution theories and experimental findings;
  • Molecular understanding of cellular functions of organisms in extreme environments

Prof. Dr. Parkson Lee-Gau Chong
Guest Editor

Manuscript Submission Information

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Keywords

  • Astrobiology
  • Extraterrestrial life
  • Archaea
  • Extremophiles
  • High-pressure biology
  • Cryobiology
  • Life in microgravity

Published Papers (4 papers)

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Research

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12 pages, 1012 KiB  
Article
Certain, but Not All, Tetraether Lipids from the Thermoacidophilic Archaeon Sulfolobus acidocaldarius Can Form Black Lipid Membranes with Remarkable Stability and Exhibiting Mthk Channel Activity with Unusually High Ca2+ Sensitivity
by Alexander Bonanno and Parkson Lee-Gau Chong
Int. J. Mol. Sci. 2021, 22(23), 12941; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222312941 - 30 Nov 2021
Cited by 5 | Viewed by 1558
Abstract
Bipolar tetraether lipids (BTL) have been long thought to play a critical role in allowing thermoacidophiles to thrive under extreme conditions. In the present study, we demonstrated that not all BTLs from the thermoacidophilic archaeon Sulfolobus acidocaldarius exhibit the same membrane behaviors. We [...] Read more.
Bipolar tetraether lipids (BTL) have been long thought to play a critical role in allowing thermoacidophiles to thrive under extreme conditions. In the present study, we demonstrated that not all BTLs from the thermoacidophilic archaeon Sulfolobus acidocaldarius exhibit the same membrane behaviors. We found that free-standing planar membranes (i.e., black lipid membranes, BLM) made of the polar lipid fraction E (PLFE) isolated from S. acidocaldarius formed over a pinhole on a cellulose acetate partition in a dual-chamber Teflon device exhibited remarkable stability showing a virtually constant capacitance (~28 pF) for at least 11 days. PLFE contains exclusively tetraethers. The dominating hydrophobic core of PLFE lipids is glycerol dialky calditol tetraether (GDNT, ~90%), whereas glycerol dialkyl glycerol tetraether (GDGT) is a minor component (~10%). In sharp contrast, BLM made of BTL extracted from microvesicles (Sa-MVs) released from the same cells exhibited a capacitance between 36 and 39 pF lasting for only 8 h before membrane dielectric breakdown. Lipids in Sa-MVs are also exclusively tetraethers; however, the dominating lipid species in Sa-MVs is GDGT (>99%), not GDNT. The remarkable stability of BLMPLFE can be attributed to strong PLFE–PLFE and PLFE–substrate interactions. In addition, we compare voltage-dependent channel activity of calcium-gated potassium channels (MthK) in BLMPLFE to values recorded in BLMSa-MV. MthK is an ion channel isolated from a methanogenic that has been extensively characterized in diester lipid membranes and has been used as a model for calcium-gated potassium channels. We found that MthK can insert into BLMPLFE and exhibit channel activity, but not in BLMSa-MV. Additionally, the opening/closing of the MthK in BLMPLFE is detectable at calcium concentrations as low as 0.1 mM; conversely, in diester lipid membranes at such a low calcium concentration, no MthK channel activity is detectable. The differential effect of membrane stability and MthK channel activity between BLMPLFE and BLMSa-MV may be attributed to their lipid structural differences and thus their abilities to interact with the substrate and membrane protein. Since Sa-MVs that bud off from the plasma membrane are exclusively tetraether lipids but do not contain the main tetraether lipid component GDNT of the plasma membrane, domain segregation must occur in S. acidocaldarius. The implication of this study is that lipid domain formation is existent and functionally essential in all kinds of cells, but domain formation may be even more prevalent and pronounced in hyperthermophiles, as strong domain formation with distinct membrane behaviors is necessary to counteract randomization due to high growth temperatures while BTL in general make archaea cell membranes stable in high temperature and low pH environments whereas different BTL domains play different functional roles. Full article
(This article belongs to the Special Issue Life Under Extreme Conditions: A Molecular Science View)
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15 pages, 1839 KiB  
Article
Ions in the Deep Subsurface of Earth, Mars, and Icy Moons: Their Effects in Combination with Temperature and Pressure on tRNA–Ligand Binding
by Nisrine Jahmidi-Azizi, Stewart Gault, Charles S. Cockell, Rosario Oliva and Roland Winter
Int. J. Mol. Sci. 2021, 22(19), 10861; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms221910861 - 08 Oct 2021
Cited by 3 | Viewed by 1649
Abstract
The interactions of ligands with nucleic acids are central to numerous reactions in the biological cell. How such reactions are affected by harsh environmental conditions such as low temperatures, high pressures, and high concentrations of destructive ions is still largely unknown. To elucidate [...] Read more.
The interactions of ligands with nucleic acids are central to numerous reactions in the biological cell. How such reactions are affected by harsh environmental conditions such as low temperatures, high pressures, and high concentrations of destructive ions is still largely unknown. To elucidate the ions’ role in shaping habitability in extraterrestrial environments and the deep subsurface of Earth with respect to fundamental biochemical processes, we investigated the effect of selected salts (MgCl2, MgSO4, and Mg(ClO4)2) and high hydrostatic pressure (relevant for the subsurface of that planet) on the complex formation between tRNA and the ligand ThT. The results show that Mg2+ salts reduce the binding tendency of ThT to tRNA. This effect is largely due to the interaction of ThT with the salt anions, which leads to a strong decrease in the activity of the ligand. However, at mM concentrations, binding is still favored. The ions alter the thermodynamics of binding, rendering complex formation that is more entropy driven. Remarkably, the pressure favors ligand binding regardless of the type of salt. Although the binding constant is reduced, the harsh conditions in the subsurface of Earth, Mars, and icy moons do not necessarily preclude nucleic acid–ligand interactions of the type studied here. Full article
(This article belongs to the Special Issue Life Under Extreme Conditions: A Molecular Science View)
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17 pages, 3925 KiB  
Article
Structure and Function of Piezophilic Hyperthermophilic Pyrococcus yayanosii pApase
by Zheng Jin, Weiwei Wang, Xuegong Li, Huan Zhou, Gangshun Yi, Qisheng Wang, Feng Yu, Xiang Xiao and Xipeng Liu
Int. J. Mol. Sci. 2021, 22(13), 7159; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22137159 - 02 Jul 2021
Cited by 3 | Viewed by 2075
Abstract
3’-Phosphoadenosine 5’-monophosphate (pAp) is a byproduct of sulfate assimilation and coenzyme A metabolism. pAp can inhibit the activity of 3′-phosphoadenosine 5′-phosphosulfate (PAPS) reductase and sulfotransferase and regulate gene expression under stress conditions by inhibiting XRN family of exoribonucleases. In metazoans, plants, yeast, and [...] Read more.
3’-Phosphoadenosine 5’-monophosphate (pAp) is a byproduct of sulfate assimilation and coenzyme A metabolism. pAp can inhibit the activity of 3′-phosphoadenosine 5′-phosphosulfate (PAPS) reductase and sulfotransferase and regulate gene expression under stress conditions by inhibiting XRN family of exoribonucleases. In metazoans, plants, yeast, and some bacteria, pAp can be converted into 5’-adenosine monophosphate (AMP) and inorganic phosphate by CysQ. In some bacteria and archaea, nanoRNases (Nrn) from the Asp-His-His (DHH) phosphoesterase superfamily are responsible for recycling pAp. In addition, histidinol phosphatase from the amidohydrolase superfamily can hydrolyze pAp. The bacterial enzymes for pAp turnover and their catalysis mechanism have been well studied, but these processes remain unclear in archaea. Pyrococcus yayanosii, an obligate piezophilic hyperthermophilic archaea, encodes a DHH family pApase homolog (PyapApase). Biochemical characterization showed that PyapApase can efficiently convert pAp into AMP and phosphate. The resolved crystal structure of apo-PyapApase is similar to that of bacterial nanoRNaseA (NrnA), but they are slightly different in the α-helix linker connecting the DHH and Asp-His-His associated 1 (DHHA1) domains. The longer α-helix of PyapApase leads to a narrower substrate-binding cleft between the DHH and DHHA1 domains than what is observed in bacterial NrnA. Through mutation analysis of conserved amino acid residues involved in coordinating metal ion and binding substrate pAp, it was confirmed that PyapApase has an ion coordination pattern similar to that of NrnA and slightly different substrate binding patterns. The results provide combined structural and functional insight into the enzymatic turnover of pAp, implying the potential function of sulfate assimilation in hyperthermophilic cells. Full article
(This article belongs to the Special Issue Life Under Extreme Conditions: A Molecular Science View)
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Review

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21 pages, 1139 KiB  
Review
Biomolecules under Pressure: Phase Diagrams, Volume Changes, and High Pressure Spectroscopic Techniques
by László Smeller
Int. J. Mol. Sci. 2022, 23(10), 5761; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23105761 - 20 May 2022
Cited by 3 | Viewed by 1897
Abstract
Pressure is an equally important thermodynamical parameter as temperature. However, its importance is often overlooked in the biophysical and biochemical investigations of biomolecules and biological systems. This review focuses on the application of high pressure (>100 MPa = 1 kbar) in biology. Studies [...] Read more.
Pressure is an equally important thermodynamical parameter as temperature. However, its importance is often overlooked in the biophysical and biochemical investigations of biomolecules and biological systems. This review focuses on the application of high pressure (>100 MPa = 1 kbar) in biology. Studies of high pressure can give insight into the volumetric aspects of various biological systems; this information cannot be obtained otherwise. High-pressure treatment is a potentially useful alternative method to heat-treatment in food science. Elevated pressure (up to 120 MPa) is present in the deep sea, which is a considerable part of the biosphere. From a basic scientific point of view, the application of the gamut of modern spectroscopic techniques provides information about the conformational changes of biomolecules, fluctuations, and flexibility. This paper reviews first the thermodynamic aspects of pressure science, the important parameters affecting the volume of a molecule. The technical aspects of high pressure production are briefly mentioned, and the most common high-pressure-compatible spectroscopic techniques are also discussed. The last part of this paper deals with the main biomolecules, lipids, proteins, and nucleic acids: how they are affected by pressure and what information can be gained about them using pressure. I I also briefly mention a few supramolecular structures such as viruses and bacteria. Finally, a subjective view of the most promising directions of high pressure bioscience is outlined. Full article
(This article belongs to the Special Issue Life Under Extreme Conditions: A Molecular Science View)
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