An official website of the United States government
Deep sea biology is known to thrive at pressures up to ≈1 kbar, which motivates fundamental biophysical studies of biomolecules under such extreme environments. In this work, the conformational equilibrium of the lysine riboswitch has been systematically investigated by single molecule FRET (smFRET) microscopy at pressures up to 1500 bar. The lysine riboswitch preferentially unfolds with increasing pressure, which signals an increase in free volume (Δ V 0 > 0) upon folding of the biopolymer. Indeed, the effective lysine binding constant increases quasi-exponentially with pressure rise, which implies a significant weakening of the riboswitch–ligand interaction in a high-pressure environment. The effects of monovalent/divalent cations and osmolytes on folding are also explored to acquire additional insights into cellular mechanisms for adapting to high pressures. For example, we find that although Mg 2+ greatly stabilizes folding of the lysine riboswitch (ΔΔ G 0 < 0), there is negligible impact on changes in free volume (ΔΔ V 0 ≈ 0) and thus any pressure induced denaturation effects. Conversely, osmolytes (commonly at high concentrations in deep sea marine species) such as the trimethylamine N -oxide (TMAO) significantly reduce free volumes (ΔΔ V 0 < 0) and thereby diminish pressure-induced denaturation. We speculate that, besides stabilizing RNA structure, enhanced levels of TMAO in cells might increase the dynamic range for competent riboswitch folding by suppressing the pressure-induced denaturation response. This in turn could offer biological advantage for vertical migration of deep-sea species, with impacts on food searching in a resource limited environment.
more »
« less
Enzymes feel the squeeze: biochemical adaptation to pressure in the deep sea
To the human observer, the deep sea is as extreme an environment as Earth has to offer. Below about 200 metres, there is no light from the surface, the water can be frigid (-2 to 5 ̊C), oxygen and food are scarce, and the pressure is staggering. Of course, to the countless species that inhabit the deep sea, these conditions are not so extreme, and in a statistical sense, they fall fairly close to average, since the deep comprises the planet’s largest habitat by volume. Despite its expanse, we know little about how life persists in an environment so different from our own. Only in the last half-century has technology emerged that allows us to collect and study live deep-sea animals. Diversity, Evolution and EcoPhysiology of Ctenophores (DEEPC, deepc.org, a US NSF-supported research effort) is opening a window on biochemistry in the deep, and specifically on its relationship to high pressure. By determining structural constraints on enzyme function under pressure, we aim to inform models focusing on deep-sea animal colonization, and to find general patterns of protein adaptation with possible applications in protein engineering and biocatalysis.
more »
« less
- Award ID(s):
- 1542679
- PAR ID:
- 10059604
- Date Published:
- Journal Name:
- Biochemist
- Volume:
- 39
- Issue:
- 6
- ISSN:
- 0954-982X
- Page Range / eLocation ID:
- 26-29
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
NA (Ed.)The extreme conditions of the deep-sea environment, including limited light, low oxygen levels, high pressure, and nutrient scarcity, create a natural habitat for deep-sea bacteria. These remarkable microorganisms have developed unique strategies to survive and adapt to their surroundings. However, research on the diversity of deep-sea bacteria, both culture-dependent and culture-independent, in Indonesian waters remains insufficient. This study focused on exploring the biodiversity of deep-sea bacteria, specifically in the Makassar and Lombok Strait, the main Indonesian throughflow pathway characterized by relatively fertile water, which serves as an important deep-sea region. High-throughput DNA sequencing of full-length 16S rRNA was employed to construct a genomic database. The results of the bioinformatic analysis revealed that two stations, 48 and 50 (Makassar Strait), exhibited a more similar community structure of deep-sea bacteria than did station 33 (Lombok Strait). Among the predominant phyla found at a depth of 1000 m, the top ten were Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Planctomycetes, Acidobacteria, Nitrospinae, Verrucomicrobia, Candidatus Melainabacteria, and Cyanobacteria. Furthermore, the genera Colwellia, Moritella, Candidatus Pelagibacter, Alteromonas, and Psychrobacter consistently appeared at all three stations, albeit with varying relative abundance values. These bacterial genera share common characteristics, such as psychrophilic, halophilic, and piezophilic tendencies, and are commonly found in deep-sea ecosystem. The environmental conditions at a depth of 1000 m were relatively stable, with an average pressure 10 MPa, temperature 4.68 °C, salinity 34.58 PSU, pH 8.06, chlorophyll-a 0.29 µg/L, nitrate 3.19 µmol/L, phosphate 6.32 µmol/L and dissolved oxygen (DO) 2.90 mg/L. The bacterial community structures at the three sampling stations located at the same depth (1000 m) exhibited similarities, as indicated by the closely aligned similarity index values.more » « less
-
Abstract Wildfires pose a significant threat to human society as severe natural disasters. The western United States (US) is one hotspot that has experienced dramatic influences from autumn wildfires especially after 2000, but what has caused its year‐to‐year variations remains poorly understood. By analyzing observational and atmospheric reanalysis datasets, we found that the West Pacific (WP) pattern centered in the western North Pacific acted as a major climatic factor to the post‐2000 autumn wildfire activity by inducing anomalous high pressure over the western US via teleconnections with increased surface temperature, decreased precipitation, and reduced relative humidity. The WP pattern explains about one‐third of the post‐2000 years‐to‐year variance of the western US autumn wildfires. These effects were found to be much weaker in the 1980–1990s, as the active region of WP‐associated high pressure was confined to the eastern North Pacific. Such eastward shift of the WP teleconnection pattern and its resultant, enhanced influence on the weather conditions of western US autumn wildfire after 2000 are also captured by the sea surface temperature (SST)‐forced atmospheric model simulations with the Community Atmosphere Model version 6 (CAM6). The CAM6 ensemble‐mean changes in the WP teleconnection pattern at 2000 is about half of the observed changes, which implies that external radiative forcing and/or SST changes have played an important role in the WP pattern shift. Our results highlight a pressing need to consider the joint impacts of atmospheric internal variability and externally forced climate changes when studying the interannual variations of wildfire activity.more » « less
-
null (Ed.)Our laboratory studies putative transcription regulatory proteins from the extreme thermophile, Thermus thermophilus HB8. To do so, these proteins are often expressed in the mesothermic organism Escherichia coli and purified from whole-cell extracts. Here we describe our standard expression and purification scheme and its analysis using the thermostable protein His6-GFP-TEV. His6-GFP-TEV is usually used as an N-terminus tag for the bacterial expression of recombinant proteins. However, this surrogate provides a facile visual indicator of thermostable protein expression and purification and is especially amenable for laboratory instruction in a primarily undergraduate educational environment.more » « less
-
Abstract Close-in lava planets represent an extreme example of terrestrial worlds, but their high temperatures may allow us to probe a diversity of crustal compositions. The brightest and most well-studied of these objects is 55 Cancri e, a nearby super-Earth with a remarkably short 17 hr orbit. However, despite numerous studies, debate remains about the existence and composition of its atmosphere. We present upper limits on the atmospheric pressure of 55 Cnc e derived from high-resolution time-series spectra taken with Gemini-N/MAROON-X. Our results are consistent with current crustal evaporation models for this planet which predict a thin ∼100 mbar atmosphere. We conclude that, if a mineral atmosphere is present on 55 Cnc e, the atmospheric pressure is below 100 mbar.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- The DOI is not currently available.
