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We report on the proof-of-concept of a low-mass, low-power method for collecting micron-sized sulfuric acid aerosols in bulk from the atmosphere of Venus. The collection method uses four wired meshes in a sandwich structure with a deposition area of 225 cm 2 . It operates in two modes: passive and electrostatic. During passive operation, aerosols are gathered on the deposition surface by aerodynamic force. During electrostatic operation, a tungsten needle discharges a high voltage of - 10 kV at the front of the grounded mesh structure. The discharge ionizes aerosols and attracts them to the mesh by Coulomb forces, resulting in improved efficiency and tentative attraction of submicron aerosols. We describe the instrument construction and testing in the laboratory under controlled conditions with aerosols composed of 25%, 50%, 70%, 80%, 90% and 98%* concentration by volume of sulfuric acid, the rest water. We demonstrated the following: (i) both modes of operation can collect the entire range of sulfuric acid solutions; (ii) the collection efficiency increases steadily (from a few percent for water to over 40% for concentrated sulfuric acid) with the increased concentration of sulfuric acid solution in water in both modes; (iii) the relative improvement in the collection of the electrostatic mode decreases as the sulfuric acid concentration increases. We also demonstrated the operation of the instrument in the field, cloud particle collection on Mt. Washington, NH, and crater-rim fumaroles' particle collection on Kīlauea volcano, HI. The collection rate in the field is wind-speed dependent, and we observed collection rates around 0.1 ml[Formula: see text] in low wind environments (1-2 m[Formula: see text]), and around 1 ml[Formula: see text] in stronger wind (7-9 m[Formula: see text])., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Life is a complex, dynamic chemical system that requires a dense fluid solvent in which to take place. A common assumption is that the most likely solvent for life is liquid water, and some researchers argue that water is the only plausible solvent. However, a persistent theme in astrobiological research postulates that other liquids might be cosmically common and could be solvents for the chemistry of life. In this article, we present a new framework for the analysis of candidate solvents for life, and we deploy this framework to review substances that have been suggested as solvent candidates. We categorize each solvent candidate through the following four criteria: occurrence, solvation, solute stability, and solvent chemical functionality. Our semiquantitative approach addresses all the requirements for a solvent not only from the point of view of its chemical properties but also from the standpoint of its biochemical function. Only the protonating solvents fulfill all the chemical requirements to be a solvent for life, and of those only water and concentrated sulfuric acid are also likely to be abundant in a rocky planetary context. Among the nonprotonating solvents, liquid CO 2 stands out as a planetary solvent, and its potential as a solvent for life should be explored. We conclude with a discussion of whether it is possible for a biochemistry to change solvents as an adaptation to radical changes in a planet's environment. Our analysis provides the basis for prioritizing future experimental work to explore potential complex chemistry on other planets. Key Words: Habitability-Alternative solvents for life-Alternative biochemistry. Astrobiology 24, 1231-1256.

Recent renewed interest in the possibility of life in the acidic clouds of Venus has led to new studies on organic chemistry in concentrated sulfuric acid. We have previously found that the majority of amino acids are stable in the range of Venus' cloud sulfuric acid concentrations (81% and 98% w/w, the rest being water). The natural next question is whether dipeptides, as precursors to larger peptides and proteins, could be stable in this environment. We investigated the reactivity of the peptide bond using 20 homodipeptides and find that the majority of them undergo solvolysis within a few weeks, at both sulfuric acid concentrations. Notably, a few exceptions exist. HH and GG dipeptides are stable in 98% w/w sulfuric acid for at least 4 months, while II, LL, VV, PP, RR and KK resist hydrolysis in 81% w/w sulfuric acid for at least 5 weeks. Moreover, the breakdown process of the dipeptides studied in 98% w/w concentrated sulfuric acid is different from the standard acid-catalyzed hydrolysis that releases monomeric amino acids. Despite a few exceptions at a single concentration, no homodipeptides have demonstrated stability across both acid concentrations studied. This indicates that any hypothetical life on Venus would likely require a functional substitute for the peptide bond that can maintain stability throughout the range of sulfuric acid concentrations present., (© 2024. The Author(s).)

Life on Earth is known to rarely make fluorinated carbon compounds, as compared to other halocarbons. We quantify this rarity, based on our exhaustive natural products database curated from available literature. We build on explanations for the scarcity of fluorine chemistry in life on Earth, namely that the exclusion of the C-F bond stems from the unique physico-chemical properties of fluorine, predominantly its extreme electronegativity and strong hydration shell. We further show that the C-F bond is very hard to synthesize and when it is made by life its potential biological functions can be readily provided by alternative functional groups that are much less costly to incorporate into existing biochemistry. As a result, the overall evolutionary cost-to-benefit balance of incorporation of the C-F bond into the chemical repertoire of life is not favorable. We argue that the limitations of organofluorine chemistry are likely universal in that they do not exclusively apply to specifics of Earth's biochemistry. C-F bonds, therefore, will be rare in life beyond Earth no matter its chemical makeup., (© 2024. The Author(s).)

Exoplanet atmospheres are expected to vary significantly in thickness and chemical composition, leading to a continuum of differences in surface pressure and atmospheric density. This variability is exemplified within our Solar System, where the four rocky planets exhibit surface pressures ranging from 1 nPa on Mercury to 9.2 MPa on Venus. The direct effects and potential challenges of atmospheric pressure and density on life have rarely been discussed. For instance, atmospheric density directly affects the possibility of active flight in organisms, a critical factor since without it, dispersing across extensive and inhospitable terrains becomes a major limitation for the expansion of complex life. In this paper, we propose the existence of a critical atmospheric density threshold below which active flight is unfeasible, significantly impacting biosphere development. To qualitatively assess this threshold and differentiate it from energy availability constraints, we analyze the limits of active flight on Earth, using the common fruit fly, Drosophila melanogaster, as a model organism. We subjected Drosophila melanogaster to various atmospheric density scenarios and reviewed previous data on flight limitations. Our observations show that flies in an N 2 -enriched environment recover active flying abilities more efficiently than those in a helium-enriched environment, highlighting behavioral differences attributable to atmospheric density vs. oxygen deprivation., (© 2024. The Author(s).)

We show that the nucleic acid bases adenine, cytosine, guanine, thymine, and uracil, as well as 2,6-diaminopurine, and the "core" nucleic acid bases purine and pyrimidine, are stable for more than one year in concentrated sulfuric acid at room temperature and at acid concentrations relevant for Venus clouds (81% w / w to 98% w / w acid, the rest water). This work builds on our initial stability studies and is the first ever to test the reactivity and structural integrity of organic molecules subjected to extended incubation in concentrated sulfuric acid. The one-year-long stability of nucleic acid bases supports the notion that the Venus cloud environment-composed of concentrated sulfuric acid-may be able to support complex organic chemicals for extended periods of time.

Venus is Earth's sister planet, with similar mass and density but an uninhabitably hot surface, an atmosphere with a water activity 50-100 times lower than anywhere on Earths' surface, and clouds believed to be made of concentrated sulfuric acid. These features have been taken to imply that the chances of finding life on Venus are vanishingly small, with several authors describing Venus' clouds as "uninhabitable," and that apparent signs of life there must therefore be abiotic, or artefactual. In this article, we argue that although many features of Venus can rule out the possibility that Earth life could live there, none rule out the possibility of all life based on what we know of the physical principle of life on Earth. Specifically, there is abundant energy, the energy requirements for retaining water and capturing hydrogen atoms to build biomass are not excessive, defenses against sulfuric acid are conceivable and have terrestrial precedent, and the speculative possibility that life uses concentrated sulfuric acid as a solvent instead of water remains. Metals are likely to be available in limited supply, and the radiation environment is benign. The clouds can support a biomass that could readily be detectable by future astrobiology-focused space missions from its impact on the atmosphere. Although we consider the prospects for finding life on Venus to be speculative, they are not absent. The scientific reward from finding life in such an un-Earthlike environment justifies considering how observations and missions should be designed to be capable of detecting life if it is there.

Scientists have long speculated about the potential habitability of Venus, not at the 700K surface, but in the cloud layers located at 48-60 km altitudes, where temperatures match those found on Earth's surface. However, the prevailing belief has been that Venus' clouds cannot support life due to the cloud chemical composition of concentrated sulfuric acid-a highly aggressive solvent. In this work, we study 20 biogenic amino acids at the range of Venus' cloud sulfuric acid concentrations (81% and 98% w/w, the rest water) and temperatures. We find 19 of the biogenic amino acids we tested are either unreactive (13 in 98% w/w and 12 in 81% w/w) or chemically modified in the side chain only, after 4 weeks. Our major finding, therefore, is that the amino acid backbone remains intact in concentrated sulfuric acid. These findings significantly broaden the range of biologically relevant molecules that could be components of a biochemistry based on a concentrated sulfuric acid solvent.

Long-standing unexplained Venus atmosphere observations and chemical anomalies point to unknown chemistry but also leave room for the possibility of life. The unexplained observations include several gases out of thermodynamic equilibrium ( e.g., tens of ppm O 2 , the possible presence of PH 3 and NH 3 , SO 2 and H 2 O vertical abundance profiles), an unknown composition of large, lower cloud particles, and the "unknown absorber(s)." Here we first review relevant properties of the venusian atmosphere and then describe the atmospheric chemical anomalies and how they motivate future astrobiology missions to Venus.

Isotopologue ratios are anticipated to be one of the most promising signs of life that can be observed remotely. On Earth, carbon isotopes have been used for decades as evidence of modern and early metabolic processes. In fact, carbon isotopes may be the oldest evidence for life on Earth, though there are alternative geological processes that can lead to the same magnitude of fractionation. However, using isotopologues as biosignature gases in exoplanet atmospheres presents several challenges. Most significantly, we will only have limited knowledge of the underlying abiotic carbon reservoir of an exoplanet. Atmospheric carbon isotope ratios will thus have to be compared against the local interstellar medium or, better yet, their host star. A further substantial complication is the limited precision of remote atmospheric measurements using spectroscopy. The various metabolic processes that cause isotope fractionation cause less fractionation than anticipated measurement precision (biological fractionation is typically 2 to 7%). While this level of precision is easily reachable in the laboratory or with special in situ instruments, it is out of reach of current telescope technology to measure isotope ratios for terrestrial exoplanet atmospheres. Thus, gas isotopologues are poor biosignatures for exoplanets given our current and foreseeable technological limitations.

Waste gas products from technological civilizations may accumulate in an exoplanet atmosphere to detectable levels. We propose nitrogen trifluoride (NF 3 ) and sulfur hexafluoride (SF 6 ) as ideal technosignature gases. Earth life avoids producing or using any N-F or S-F bond-containing molecules and makes no fully fluorinated molecules with any element. NF 3 and SF 6 may be universal technosignatures owing to their special industrial properties, which unlike biosignature gases, are not species-dependent. Other key relevant qualities of NF 3 and SF 6 are: their extremely low water solubility, unique spectral features, and long atmospheric lifetimes. NF 3 has no non-human sources and was absent from Earth's pre-industrial atmosphere. SF 6 is released in only tiny amounts from fluorine-containing minerals, and is likely produced in only trivial amounts by volcanic eruptions. We propose a strategy to rule out SF 6 's abiotic source by simultaneous observations of SiF 4 , which is released by volcanoes in an order of magnitude higher abundance than SF 6 . Other fully fluorinated human-made molecules are of interest, but their chemical and spectral properties are unavailable. We summarize why life on Earth-and perhaps life elsewhere-avoids using F. We caution, however, that we cannot definitively disentangle an alien biochemistry byproduct from a technosignature gas., (© 2023. Springer Nature Limited.)

What constitutes a habitable planet is a frontier to be explored and requires pushing the boundaries of our terracentric viewpoint for what we deem to be a habitable environment. Despite Venus' 700 K surface temperature being too hot for any plausible solvent and most organic covalent chemistry, Venus' cloud-filled atmosphere layers at 48 to 60 km above the surface hold the main requirements for life: suitable temperatures for covalent bonds; an energy source (sunlight); and a liquid solvent. Yet, the Venus clouds are widely thought to be incapable of supporting life because the droplets are composed of concentrated liquid sulfuric acid-an aggressive solvent that is assumed to rapidly destroy most biochemicals of life on Earth. Recent work, however, demonstrates that a rich organic chemistry can evolve from simple precursor molecules seeded into concentrated sulfuric acid, a result that is corroborated by domain knowledge in industry that such chemistry leads to complex molecules, including aromatics. We aim to expand the set of molecules known to be stable in concentrated sulfuric acid. Here, we show that nucleic acid bases adenine, cytosine, guanine, thymine, and uracil, as well as 2,6-diaminopurine and the "core" nucleic acid bases purine and pyrimidine, are stable in sulfuric acid in the Venus cloud temperature and sulfuric acid concentration range, using UV spectroscopy and combinations of 1D and 2D 1 H 13 C 15 N NMR spectroscopy. The stability of nucleic acid bases in concentrated sulfuric acid advances the idea that chemistry to support life may exist in the Venus cloud particle environment.

In our previous paper we have modelled a dielectrophoretic force (DEP) and cell particle behavior in a microfluidic channel (Weber MU et al 2023 Chip for dielectrophoretic microbial capture, separation and detection I: theoretical basis of electrode design Nanotechnology this issue). Here we test and confirm the results of our modeling work by experimentally validating the theoretical design constraints of the ring electrode architecture. We have compared and tested the geometry and particle capture and separation performance of the two separate electrode designs (the ring and dot electrode structures) by investigating bacterial motion in response to the applied electric field. We have quantitatively evaluated the electroosmosis (EO) to positive DEP (PDEP) transition in both electrode designs and explained the differences in capture efficiency of the ring and dot electrode systems. The ring structure shows 99% efficiency of bacterial capture both for PDEP and for EO. Moreover, the ring structure shows an over 200 faster bacterial response to the electric field. We have also established that the ring electrode architecture, with appropriate structure periodicity and spacing, results in efficient capture and separation of microbial cells. We have identified several critical design constraints that are required to achieve high efficiency bacterial capture. We have established that the spacing between consecutive DEP traps smaller than the length of the depletion zone will ensure that the DEP force dominates bacterial motion over motility and Brownian motion., (© 2023 IOP Publishing Ltd.)

We model the dielectrophoretic response of E. coli bacterial cells and red blood cells, upon exposure to an electric field. We model the separation, capture, and release mechanisms under flow conditions in a microfluidic channel and show under which conditions efficient separation of different cell types occurs. The modelling work is aimed to guide the separation electrode architecture and design for experimental validation of the model. The dielectrophoretic force is affected both by the geometry of the electrodes (the gradient of the electric field), the Re{CM( ω )} factor, and the permittivity of the medium ϵ m . Our modelling makes testable predictions and shows that designing the electrode structure to ensure structure periodicity with spacing between consecutive traps smaller than the length of the depletion zone ensures efficient capture and separation. Such electrode system has higher capture and separation efficiency than systems with the established circular electrode architecture. The simulated, modelled microfluidic design allows for the separated bacteria, concentrated by dedicated dielectrophoretic regions, to be subsequently detected using label-free functionalized nanowire sensors. The experimental validation of the modelling work presented here and the validation of the theoretical design constraints of the chip electrode architecture is presented in the companion paper in the same issue (Weber MU et al 2022 Chip for dielectrophoretic Microbial Capture, Separation and Detection II: Experimental Study)., (© 2023 IOP Publishing Ltd.)

Ammonia (NH 3 ) in a terrestrial planet atmosphere is generally a good biosignature gas, primarily because terrestrial planets have no significant known abiotic NH 3 source. The conditions required for NH 3 to accumulate in the atmosphere are, however, stringent. NH 3 's high water solubility and high biousability likely prevent NH 3 from accumulating in the atmosphere to detectable levels unless life is a net source of NH 3 and produces enough NH 3 to saturate the surface sinks. Only then can NH 3 accumulate in the atmosphere with a reasonable surface production flux. For the highly favorable planetary scenario of terrestrial planets with hydrogen (H 2 )-dominated atmospheres orbiting M dwarf stars (M5V), we find that a minimum of about 5 ppm column-averaged mixing ratio is needed for NH 3 to be detectable with JWST, considering a 10 ppm JWST systematic noise floor. When the surface is saturated with NH 3 ( i.e ., there are no NH 3 -removal reactions on the surface), the required biological surface flux to reach 5 ppm is on the order of 10 10 molecules/(cm 2 ·s), comparable with the terrestrial biological production of methane (CH 4 ). However, when the surface is unsaturated with NH 3 , due to additional sinks present on the surface, life would have to produce NH 3 at surface flux levels on the order of 10 15 molecules/(cm 2 ·s) (∼4.5 × 10 6 Tg/year). This value is roughly 20,000 times greater than the biological production of NH 3 on the Earth and about 10,000 times greater than Earth's CH 4 biological production. Volatile amines have similar solubilities and reactivities to NH 3 and hence share NH 3 's weaknesses and strengths as a biosignature. Finally, to establish NH 3 as a biosignature gas, we must rule out mini-Neptunes with deep atmospheres, where temperatures and pressures are high enough for NH 3 's atmospheric production.

The atmosphere of Venus remains mysterious, with many outstanding chemical connundra. These include the unexpected presence of ∼10 ppm O 2 in the cloud layers, an unknown composition of large particles in the lower cloud layers, and hard to explain measured vertical abundance profiles of SO 2 and H 2 O. We propose a hypothesis for the chemistry in the clouds that largely addresses all of the above anomalies. We include ammonia (NH 3 ), a key component that has been tentatively detected both by the Venera 8 and Pioneer Venus probes. NH 3 dissolves in some of the sulfuric acid cloud droplets, effectively neutralizing the acid and trapping dissolved SO 2 as ammonium sulfite salts. This trapping of SO 2 in the clouds, together with the release of SO 2 below the clouds as the droplets settle out to higher temperatures, explains the vertical SO 2 abundance anomaly. A consequence of the presence of NH 3 is that some Venus cloud droplets must be semisolid ammonium salt slurries, with a pH of ∼1, which matches Earth acidophile environments, rather than concentrated sulfuric acid. The source of NH 3 is unknown but could involve biological production; if so, then the most energy-efficient NH 3 -producing reaction also creates O 2, explaining the detection of O 2 in the cloud layers. Our model therefore predicts that the clouds are more habitable than previously thought, and may be inhabited. Unlike prior atmospheric models, ours does not require forced chemical constraints to match the data. Our hypothesis, guided by existing observations, can be tested by new Venus in situ measurements., Competing Interests: The authors declare no competing interest., (Copyright © 2021 the Author(s). Published by PNAS.)

Bacterial culture methods, e.g. Plate Counting Method (PCM), are a gold standard in the assessment of microbial contamination in multitude of human industries. They are however slow, labor intensive, and prone to manual errors. Dielectrophoresis (DEP) has shown great promise for particle separation for decades; however, it has not yet been widely applied in routine laboratory setting. This paper provides an overview of a new DEP microbial capture and separation method called Fluid-Screen (FS), that achieves very fast, efficient, reliable and repeatable capture and separation of microbial cells. Method verification experiments demonstrated that the FS system captured 100% of bacteria in test samples, a capture efficiency much higher than previously reported for similar technology. Data generated supports the superiority of the FS method as compared to the established Plate Counting Method (PCM), that is routinely used to detect bacterial contamination in healthcare, pharmacological and food industries. We demonstrate that the FS method is universal and can capture and separate different species of bacteria and fungi to viruses, from various sample matrices (i.e. human red blood cells, mammalian cells)., (© 2021. The Author(s).)

We revisit the hypothesis that there is life in the venusian clouds to propose a life cycle that resolves the conundrum of how life can persist aloft for hundreds of millions to billions of years. Most discussions of an aerial biosphere in the venusian atmosphere temperate layers never address whether the life-small microbial-type particles-is free floating or confined to the liquid environment inside cloud droplets. We argue that life must reside inside liquid droplets such that it will be protected from a fatal net loss of liquid to the atmosphere, an unavoidable problem for any free-floating microbial life forms. However, the droplet habitat poses a lifetime limitation: Droplets inexorably grow (over a few months) to large enough sizes that are forced by gravity to settle downward to hotter, uninhabitable layers of the venusian atmosphere. (Droplet fragmentation-which would reduce particle size-does not occur in venusian atmosphere conditions.) We propose for the first time that the only way life can survive indefinitely is with a life cycle that involves microbial life drying out as liquid droplets evaporate during settling, with the small desiccated "spores" halting at, and partially populating, the venusian atmosphere stagnant lower haze layer (33-48 km altitude). We, thus, call the venusian lower haze layer a "depot" for desiccated microbial life. The spores eventually return to the cloud layer by upward diffusion caused by mixing induced by gravity waves, act as cloud condensation nuclei, and rehydrate for a continued life cycle. We also review the challenges for life in the extremely harsh conditions of the venusian atmosphere, refuting the notion that the "habitable" cloud layer has an analogy in any terrestrial environment.

The recent candidate detection of ∼1 ppb of phosphine in the middle atmosphere of Venus is so unexpected that it requires an exhaustive search for explanations of its origin. Phosphorus-containing species have not been modeled for Venus' atmosphere before, and our work represents the first attempt to model phosphorus species in the venusian atmosphere. We thoroughly explore the potential pathways of formation of phosphine in a venusian environment, including in the planet's atmosphere, cloud and haze layers, surface, and subsurface. We investigate gas reactions, geochemical reactions, photochemistry, and other nonequilibrium processes. None of these potential phosphine production pathways is sufficient to explain the presence of ppb phosphine levels on Venus. If PH 3 's presence in Venus' atmosphere is confirmed, it therefore is highly likely to be the result of a process not previously considered plausible for venusian conditions. The process could be unknown geochemistry, photochemistry, or even aerial microbial life, given that on Earth phosphine is exclusively associated with anthropogenic and biological sources. The detection of phosphine adds to the complexity of chemical processes in the venusian environment and motivates in situ follow-up sampling missions to Venus. Our analysis provides a template for investigation of phosphine as a biosignature on other worlds.

Productive ribosomal RNA (rRNA) compaction during ribosome assembly necessitates establishing correct tertiary contacts between distant secondary structure elements. Here, we quantify the response of the yeast proteome to low temperature (LT), a condition where aberrant mis-paired RNA folding intermediates accumulate. We show that, at LT, yeast cells globally boost production of their ribosome assembly machinery. We find that the LT-induced assembly factor, Puf6, binds to the nascent catalytic RNA-rich subunit interface within the 60S pre-ribosome, at a site that eventually loads the nuclear export apparatus. Ensemble Förster resonance energy transfer studies show that Puf6 mimics the role of Mg 2+ to usher a unique long-range tertiary contact to compact rRNA. At LT, puf6 mutants accumulate 60S pre-ribosomes in the nucleus, thus unveiling Puf6-mediated rRNA compaction as a critical temperature-regulated rescue mechanism that counters rRNA misfolding to prime export competence., (© 2021. The Author(s).)

The search for possible biosignature gases in habitable exoplanet atmospheres is accelerating, although actual observations are likely years away. This work adds isoprene, C 5 H 8 , to the roster of biosignature gases. We found that isoprene geochemical formation is highly thermodynamically disfavored and has no known abiotic false positives. The isoprene production rate on Earth rivals that of methane (CH 4 ; ∼500 Tg/year). Unlike methane, on Earth isoprene is rapidly destroyed by oxygen-containing radicals. Although isoprene is predominantly produced by deciduous trees, isoprene production is ubiquitous to a diverse array of evolutionary distant organisms, from bacteria to plants and animals-few, if any, volatile secondary metabolites have a larger evolutionary reach. Although non-photochemical sinks of isoprene may exist, such as degradation of isoprene by life or other high deposition rates, destruction of isoprene in an anoxic atmosphere is mainly driven by photochemistry. Motivated by the concept that isoprene might accumulate in anoxic environments, we model the photochemistry and spectroscopic detection of isoprene in habitable temperature, rocky exoplanet anoxic atmospheres with a variety of atmosphere compositions under different host star ultraviolet fluxes. Limited by an assumed 10 ppm instrument noise floor, habitable atmosphere characterization when using James Webb Space Telescope (JWST) is only achievable with a transit signal similar or larger than that for a super-Earth-sized exoplanet transiting an M dwarf star with an H 2 -dominated atmosphere. Unfortunately, isoprene cannot accumulate to detectable abundance without entering a run-away phase, which occurs at a very high production rate, ∼100 times the Earth's production rate. In this run-away scenario, isoprene will accumulate to >100 ppm, and its spectral features are detectable with ∼20 JWST transits. One caveat is that some isoprene spectral features are hard to distinguish from those of methane and also from other hydrocarbons containing the isoprene substructure. Despite these challenges, isoprene is worth adding to the menu of potential biosignature gases.

The chemistry of life requires a solvent, which for life on Earth is water. Several alternative solvents have been suggested, but there is little quantitative analysis of their suitability as solvents for life. To support a novel (non-terrestrial) biochemistry, a solvent must be able to form a stable solution of a diverse set of small molecules and polymers, but must not dissolve all molecules. Here, we analyze the potential of concentrated sulfuric acid (CSA) as a solvent for biochemistry. As CSA is a highly effective solvent but a reactive substance, we focused our analysis on the stability of chemicals in sulfuric acid, using a model built from a database of kinetics of reaction of molecules with CSA. We consider the sulfuric acid clouds of Venus as a test case for this approach. The large majority of terrestrial biochemicals have half-lives of less than a second at any altitude in Venus's clouds, but three sets of human-synthesized chemicals are more stable, with average half-lives of days to weeks at the conditions around 60 km altitude on Venus. We show that sufficient chemical structural and functional diversity may be available among those stable chemicals for life that uses concentrated sulfuric acid as a solvent to be plausible. However, analysis of meteoritic chemicals and possible abiotic synthetic paths suggests that postulated paths to the origin of life on Earth are unlikely to operate in CSA. We conclude that, contrary to expectation, sulfuric acid is an interesting candidate solvent for life, but further work is needed to identify a plausible route for life to originate in it.

Despite more than one hundred years of work on organosilicon chemistry, the basis for the plausibility of silicon-based life has never been systematically addressed nor objectively reviewed. We provide a comprehensive assessment of the possibility of silicon-based biochemistry, based on a review of what is known and what has been modeled, even including speculative work. We assess whether or not silicon chemistry meets the requirements for chemical diversity and reactivity as compared to carbon. To expand the possibility of plausible silicon biochemistry, we explore silicon's chemical complexity in diverse solvents found in planetary environments, including water, cryosolvents, and sulfuric acid. In no environment is a life based primarily around silicon chemistry a plausible option. We find that in a water-rich environment silicon's chemical capacity is highly limited due to ubiquitous silica formation; silicon can likely only be used as a rare and specialized heteroatom. Cryosolvents (e.g., liquid N 2 ) provide extremely low solubility of all molecules, including organosilicons. Sulfuric acid, surprisingly, appears to be able to support a much larger diversity of organosilicon chemistry than water.

A long-term goal of exoplanet studies is the identification and detection of biosignature gases. Beyond the most discussed biosignature gas O 2 , only a handful of gases have been considered in detail. In this study, we evaluate phosphine (PH 3 ). On Earth, PH 3 is associated with anaerobic ecosystems, and as such, it is a potential biosignature gas in anoxic exoplanets. We simulate the atmospheres of habitable terrestrial planets with CO 2 - and H 2 -dominated atmospheres and find that PH 3 can accumulate to detectable concentrations on planets with surface production fluxes of 10 10 to 10 14 cm -2 s -1 (corresponding to surface concentrations of 10s of ppb to 100s of ppm), depending on atmospheric composition and ultraviolet (UV) irradiation. While high, the surface flux values are comparable to the global terrestrial production rate of methane or CH 4 (10 11 cm -2 s -1 ) and below the maximum local terrestrial PH 3 production rate (10 14 cm -2 s -1 ). As with other gases, PH 3 can more readily accumulate on low-UV planets, for example, planets orbiting quiet M dwarfs or with a photochemically generated UV shield. PH 3 has three strong spectral features such that in any atmosphere scenario one of the three will be unique compared with other dominant spectroscopic molecules. Phosphine's weakness as a biosignature gas is its high reactivity, requiring high outgassing rates for detectability. We calculate that tens of hours of JWST (James Webb Space Telescope) time are required for a potential detection of PH 3 . Yet, because PH 3 is spectrally active in the same wavelength regions as other atmospherically important molecules (such as H 2 O and CH 4 ), searches for PH 3 can be carried out at no additional observational cost to searches for other molecular species relevant to characterizing exoplanet habitability. Phosphine is a promising biosignature gas, as it has no known abiotic false positives on terrestrial planets from any source that could generate the high fluxes required for detection.

Unambiguously identifying molecules in spectra is of fundamental importance for a variety of scientific and industrial uses. Interpreting atmospheric spectra for the remote detection of volatile compounds requires information about the spectrum of each relevant molecule. However, spectral data currently exist for a few hundred molecules and only a fraction of those have complete spectra (e.g. H2O, NH3). Consequently, molecular detections in atmospheric spectra remain vulnerable to false positives, false negatives, and missassignments. There is a key need for spectral data for a broad range of molecules. Given how challenging it is to obtain high-resolution molecular spectra, there is great value in creating intermediate approximate spectra that can provide a starting point for the analysis of atmospheric spectra. Using a combination of experimental measurements, organic chemistry, and quantum mechanics, RASCALL (Rapid Approximate Spectral Calculations for ALL) is a computational approach that provides approximate spectral data for any given molecule, including thousands of potential atmospheric gases. RASCALL is a new theoretical chemistry method for the simulation of spectral data. RASCALL 1.0, presented here, is capable of simulating molecular spectral data, in a few seconds, by interpreting functional group data from experimental and theoretical sources to estimate the position and strength of molecular bands. The RASCALL 1.0 spectra consist of approximate band centers and qualitative intensities. RASCALL 1.0 is also able to assess hundreds of molecules simultaneously, which will inform prioritization protocols for future, computationally and experimentally costly, high-accuracy physical chemistry studies. Finally, RASCALL can be used to study spectral patterns between molecules, highlighting ambiguities in molecular detections and also directing observations towards spectral regions that reduce the degeneracy in molecular identification. The RASCALL catalogue, and its preliminary version RASCALL 1.0, contains spectral data for more molecules than any other publicly available database, with applications in all fields interested in the detection of molecules in the gas phase (e.g., medical imaging, petroleum industry, pollution monitoring, astrochemistry). The preliminary catalogue of molecular data and associated documentation are freely available online and will be routinely updated.

Phosphorus is an essential element for all life on Earth, yet trivalent phosphorus ( e.g. , in phosphines) appears to be almost completely absent from biology. Instead phosphorus is utilized by life almost exclusively as phosphate, apart from a small contingent of other pentavalent phosphorus compounds containing structurally similar chemical groups. In this work, we address four previously stated arguments as to why life does not explore trivalent phosphorus: (1) precedent (lack of confirmed instances of trivalent phosphorus in biochemicals suggests that life does not have the means to exploit this chemistry), (2) thermodynamic limitations (synthesizing trivalent phosphorus compounds is too energetically costly), (3) stability (phosphines are too reactive and readily oxidize in an oxygen (O 2 )-rich atmosphere), and (4) toxicity (the trivalent phosphorus compounds are broadly toxic). We argue that the first two of these arguments are invalid, and the third and fourth arguments only apply to the O 2 -rich environment of modern Earth. Specifically, both the reactivity and toxicity of phosphines are specific to aerobic life and strictly dependent on O 2 -rich environment. We postulate that anaerobic life persisting in anoxic (O 2 -free) environments may exploit trivalent phosphorus chemistry much more extensively. We review the production of trivalent phosphorus compounds by anaerobic organisms, including phosphine gas and an alkyl phosphine, phospholane. We suggest that the failure to find more such compounds in modern terrestrial life may be a result of the strong bias of the search for natural products toward aerobic organisms. We postulate that a more thorough identification of metabolites of the anaerobic biosphere could reveal many more trivalent phosphorus compounds. We conclude with a discussion of the implications of our work for the origin and early evolution of life, and suggest that trivalent phosphorus compounds could be valuable markers for both extraterrestrial life and the Shadow Biosphere on Earth.

A fundamental goal of biology is to understand the rules behind life's use of chemical space. Established work focuses on why life uses the chemistry that it does. Given the enormous scope of possible chemical space, we postulate that it is equally important to ask why life largely avoids certain areas of chemical space. The nitrogen-sulfur bond is a prime example, as it rarely appears in natural molecules, despite the very rich N-S bond chemistry applied in various branches of industry (e.g., industrial materials, agrochemicals, pharmaceuticals). We find that, out of more than 200,000 known, unique compounds made by life, only about 100 contain N-S bonds. Furthermore, the limited number of N-S bond-containing molecules that life produces appears to fall into a few very distinctive structural groups. One may think that industrial processes are unrelated to biochemistry because of a greater possibility of solvents, catalysts, and temperatures available to industry than to the cellular environment. However, the fact that life does rarely make N-S bonds, from the plentiful precursors available, and has evolved the ability to do so independently several times, suggests that the restriction on life's use of N-S chemistry is not in its synthesis. We present a hypothesis to explain life's extremely limited usage of the N-S bond: that the N-S bond chemistry is incompatible with essential segments of biochemistry, specifically with thiols. We support our hypothesis by (1) a quantitative analysis of the occurrence of N-S bond-containing natural products and (2) reactivity experiments between selected N-S compounds and key biological molecules. This work provides an example of a reason why life nearly excludes a distinct region of chemical space. Combined with future examples, this potentially new field of research may provide fresh insight into life's evolution through chemical space and its origin and early evolution.

We present a new model for the biological production of phosphine (PH 3 ). Phosphine is found globally, in trace amounts, in the Earth's atmosphere. It has been suggested as a key molecule in the phosphorus cycle, linking atmospheric, lithospheric and biological phosphorus chemistry. Phosphine's production is strongly associated with marshes, swamps and other sites of anaerobic biology. However the mechanism of phosphine's biological production has remained controversial, because it has been believed that reduction of phosphate to phosphine is endergonic. In this paper we show through thermodynamic calculations that, in specific environments, the combined action of phosphate reducing and phosphite disproportionating bacteria can produce phosphine. Phosphate-reducing bacteria can capture energy from the reduction of phosphate to phosphite through coupling phosphate reduction to NADH oxidation. Our hypothesis describes how the phosphate chemistry in an environmental niche is coupled to phosphite generation in ground water, which in turn is coupled to the phosphine production in water and atmosphere, driven by a specific microbial ecology. Our hypothesis provides clear predictions on specific complex environments where biological phosphine production could be widespread. We propose tests of our hypothesis in fieldwork., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Phosphorous-containing molecules are essential constituents of all living cells. While the phosphate functional group is very common in small molecule natural products, nucleic acids, and as chemical modification in protein and peptides, phosphorous can form P⁻N (phosphoramidate), P⁻S (phosphorothioate), and P⁻C (e.g., phosphonate and phosphinate) linkages. While rare, these moieties play critical roles in many processes and in all forms of life. In this review we thoroughly categorize P⁻N, P⁻S, and P⁻C natural organophosphorus compounds. Information on biological source, biological activity, and biosynthesis is included, if known. This review also summarizes the role of phosphorylation on unusual amino acids in proteins ( N - and S -phosphorylation) and reviews the natural phosphorothioate (P⁻S) and phosphoramidate (P⁻N) modifications of DNA and nucleotides with an emphasis on their role in the metabolism of the cell. We challenge the commonly held notion that nonphosphate organophosphorus functional groups are an oddity of biochemistry, with no central role in the metabolism of the cell. We postulate that the extent of utilization of some phosphorus groups by life, especially those containing P⁻N bonds, is likely severely underestimated and has been largely overlooked, mainly due to the technological limitations in their detection and analysis.

Only about 100 natural products are known to contain a nitrogen-sulfur (N-S) bond. This review thoroughly categorizes N-S bond-containing compounds by structural class. Information on biological source, biological activity, and biosynthesis is included, if known. We also review the role of N-S bond functional groups as post-translational modifications of amino acids in proteins and peptides, emphasizing their role in the metabolism of the cell.

A subset of B-cell lymphoma patients have dominant mutations in the histone H3 lysine 27 (H3K27) methyltransferase EZH2, which change it from a monomethylase to a trimethylase. These mutations occur in aromatic resides surrounding the active site and increase growth and alter transcription. We study the N-terminal trimethylase NRMT1 and the N-terminal monomethylase NRMT2. They are 50% identical, but differ in key aromatic residues in their active site. Given how these residues affect EZH2 activity, we tested whether they are responsible for the distinct catalytic activities of NRMT1/2. Additionally, NRMT1 acts as a tumor suppressor in breast cancer cells. Its loss promotes oncogenic phenotypes but sensitizes cells to DNA damage. Mutations of NRMT1 naturally occur in human cancers, and we tested a select group for altered activity. While directed mutation of the aromatic residues had minimal catalytic effect, NRMT1 mutants N209I (endometrial cancer) and P211S (lung cancer) displayed decreased trimethylase and increased monomethylase/dimethylase activity. Both mutations are located in the peptide-binding channel and indicate a second structural region impacting enzyme specificity. The NRMT1 mutants demonstrated a slower rate of trimethylation and a requirement for higher substrate concentration. Expression of the mutants in wild type NRMT backgrounds showed no change in N-terminal methylation levels or growth rates, demonstrating they are not acting as dominant negatives. Expression of the mutants in cells lacking endogenous NRMT1 resulted in minimal accumulation of N-terminal trimethylation, indicating homozygosity could help drive oncogenesis or serve as a marker for sensitivity to DNA damaging chemotherapeutics or γ-irradiation., (© 2017 The Protein Society.)

Unlabelled: Thousands of exoplanets are known to orbit nearby stars. Plans for the next generation of space-based and ground-based telescopes are fueling the anticipation that a precious few habitable planets can be identified in the coming decade. Even more highly anticipated is the chance to find signs of life on these habitable planets by way of biosignature gases. But which gases should we search for? Although a few biosignature gases are prominent in Earth's atmospheric spectrum (O2, CH4, N2O), others have been considered as being produced at or able to accumulate to higher levels on exo-Earths (e.g., dimethyl sulfide and CH3Cl). Life on Earth produces thousands of different gases (although most in very small quantities). Some might be produced and/or accumulate in an exo-Earth atmosphere to high levels, depending on the exo-Earth ecology and surface and atmospheric chemistry. To maximize our chances of recognizing biosignature gases, we promote the concept that all stable and potentially volatile molecules should initially be considered as viable biosignature gases. We present a new approach to the subject of biosignature gases by systematically constructing lists of volatile molecules in different categories. An exhaustive list up to six non-H atoms is presented, totaling about 14,000 molecules. About 2500 of these are CNOPSH compounds. An approach for extending the list to larger molecules is described. We further show that about one-fourth of CNOPSH molecules (again, up to N = 6 non-H atoms) are known to be produced by life on Earth. The list can be used to study classes of chemicals that might be potential biosignature gases, considering their accumulation and possible false positives on exoplanets with atmospheres and surface environments different from Earth's. The list can also be used for terrestrial biochemistry applications, some examples of which are provided. We provide an online community usage database to serve as a registry for volatile molecules including biogenic compounds., Key Words: Astrobiology-Atmospheric gases-Biosignatures-Exoplanets. Astrobiology 16, 465-485.

The ribosome is responsible for the final step of decoding genetic information into proteins. Therefore, correct assembly of ribosomes is a fundamental task for all living cells. In eukaryotes, the construction of the ribosome which begins in the nucleolus requires coordinated efforts of >350 specialized factors that associate with pre-ribosomal particles at distinct stages to perform specific assembly steps. On their way through the nucleus, diverse energy-consuming enzymes are thought to release assembly factors from maturing pre-ribosomal particles after accomplishing their task(s). Subsequently, recruitment of export factors prepares pre-ribosomal particles for transport through nuclear pore complexes. Pre-ribosomes are exported into the cytoplasm in a functionally inactive state, where they undergo final maturation before initiating translation. Accumulating evidence indicates a tight coupling between nuclear export, cytoplasmic maturation, and final proofreading of the ribosome. In this review, we summarize our current understanding of nuclear export of pre-ribosomal subunits and cytoplasmic maturation steps that render pre-ribosomal subunits translation-competent.

NRMT (N-terminal regulator of chromatin condensation 1 methyltransferase) was the first eukaryotic methyltransferase identified to specifically methylate the free α-amino group of proteins. Since the discovery of this N-terminal methyltransferase, many new substrates have been identified and the modification itself has been shown to regulate DNA-protein interactions. Sequence analysis predicts one close human homologue of NRMT, METTL11B (methyltransferase-like protein 11B, now renamed NRMT2). We show in the present paper for the first time that NRMT2 also has N-terminal methylation activity and recognizes the same N-terminal consensus sequences as NRMT (now NRMT1). Both enzymes have similar tissue expression and cellular localization patterns. However, enzyme assays and MS experiments indicate that they differ in their specific catalytic functions. Although NRMT1 is a distributive methyltransferase that can mono-, di- and tri-methylate its substrates, NRMT2 is primarily a monomethylase. Concurrent expression of NRMT1 and NRMT2 accelerates the production of trimethylation, and we propose that NRMT2 activates NRMT1 by priming its substrates for trimethylation.

Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of a myriad of insidious and intractable infections in humans, especially in patients with compromised immune systems and children. Here, we report the apo- and CoA-bound crystal structures of a member of the galactoside acetyltransferase superfamily from methicillin-resistant S. aureus SACOL2570 which was recently shown to be down regulated in S. aureus grown in the presence of fusidic acid, an antibiotic used to treat MRSA infections. SACOL2570 forms a homotrimer in solution, as confirmed by small-angle X-ray scattering and dynamic light scattering. The protein subunit consists of an N-terminal alpha-helical domain connected to a C-terminal LβH domain. CoA binds in the active site formed by the residues from adjacent LβH domains. After determination of CoA-bound structure, molecular dynamics simulations were performed to model the binding of AcCoA. Binding of both AcCoA and CoA to SACOL2570 was verified by isothermal titration calorimetry. SACOL2570 most likely acts as an acetyltransferase, using AcCoA as an acetyl group donor and an as-yet-undetermined chemical moiety as an acceptor. SACOL2570 was recently used as a scaffold for mutations that lead the generation of cage-like assemblies, and has the potential to be used for the generation of more complex nanostructures.

Centromeres are chromosomal loci required for accurate segregation of sister chromatids during mitosis. The location of the centromere on the chromosome is not dependent on DNA sequence, but rather it is epigenetically specified by the histone H3 variant centromere protein A (CENP-A). The N-terminal tail of CENP-A is highly divergent from other H3 variants. Canonical histone N termini are hotspots of conserved posttranslational modification; however, no broadly conserved modifications of the vertebrate CENP-A tail have been previously observed. Here, we report three posttranslational modifications on human CENP-A N termini using high-resolution MS: trimethylation of Gly1 and phosphorylation of Ser16 and Ser18. Our results demonstrate that CENP-A is subjected to constitutive initiating methionine removal, similar to other H3 variants. The nascent N-terminal residue Gly1 becomes trimethylated on the α-amino group. We demonstrate that the N-terminal RCC1 methyltransferase is capable of modifying the CENP-A N terminus. Methylation occurs in the prenucleosomal form and marks the majority of CENP-A nucleosomes. Serine 16 and 18 become phosphorylated in prenucleosomal CENP-A and are phosphorylated on asynchronous and mitotic nucleosomal CENP-A and are important for chromosome segregation during mitosis. The double phosphorylation motif forms a salt-bridged secondary structure and causes CENP-A N-terminal tails to form intramolecular associations. Analytical ultracentrifugation of phospho-mimetic CENP-A nucleosome arrays demonstrates that phosphorylation results in greater intranucleosome associations and counteracts the hyperoligomerized state exhibited by unmodified CENP-A nucleosome arrays. Our studies have revealed that the major modifications on the N-terminal tail of CENP-A alter the physical properties of the chromatin fiber at the centromere.

RutC is the third enzyme in the Escherichia coli rut pathway of uracil degradation. RutC belongs to the highly conserved YjgF family of proteins. The structure of the RutC protein was determined and refined to 1.95 Å resolution. The crystal belonged to space group P2(1)2(1)2 and contained six molecules in the asymmetric unit. The structure was solved by SAD phasing and was refined to an Rwork of 19.3% (Rfree=21.7%). The final model revealed that this protein has a Bacillus chorismate mutase-like fold and forms a homotrimer with a hydrophobic cavity in the center of the structure and ligand-binding clefts between two subunits. A likely function for RutC is the reduction of peroxy-aminoacrylate to aminoacrylate as a part of a detoxification process.

The rut pathway of pyrimidine catabolism is a novel pathway that allows pyrimidine bases to serve as the sole nitrogen source in suboptimal temperatures. The rut operon in E. coli evaded detection until 2006, yet consists of seven proteins named RutA, RutB, etc. through RutG. The operon is comprised of a pyrimidine transporter and six enzymes that cleave and further process the uracil ring. Herein, we report the structure of RutD, a member of the α/β hydrolase superfamily, which is proposed to enhance the rate of hydrolysis of aminoacrylate, a toxic side product of uracil degradation, to malonic semialdehyde. Although this reaction will occur spontaneously in water, the toxicity of aminoacrylate necessitates catalysis by RutD for efficient growth with uracil as a nitrogen source. RutD has a novel and conserved arrangement of residues corresponding to the α/β hydrolase active site, where the nucleophile's spatial position occupied by Ser, Cys, or Asp of the canonical catalytic triad is replaced by histidine. We have used a combination of crystallographic structure determination, modeling and bioinformatics, to propose a novel mechanism for this enzyme. This approach also revealed that RutD represents a previously undescribed family within the α/β hydrolases. We compare and contrast RutD with PcaD, which is the closest structural homolog to RutD. PcaD is a 3-oxoadipate-enol-lactonase with a classic arrangement of residues in the active site. We have modeled a substrate in the PcaD active site and proposed a reaction mechanism., (Copyright © 2012 Wiley Periodicals, Inc.)

N-Terminal methylation of free α-amino groups is a post-translational modification of proteins that was first described 30 years ago but has been studied very little. In this modification, the initiating M residue is cleaved and the exposed α-amino group is mono-, di-, or trimethylated by NRMT, a recently identified N-terminal methyltransferase. Currently, all known eukaryotic α-amino-methylated proteins have a unique N-terminal motif, M-X-P-K, where X is A, P, or S. NRMT can also methylate artificial substrates in vitro in which X is G, F, Y, C, M, K, R, N, Q, or H. Methylation efficiencies of N-terminal amino acids are variable with respect to the identity of X. Here we use in vitro peptide methylation assays and substrate immunoprecipitations to show that the canonical M-X-P-K methylation motif is not the only one recognized by NRMT. We predict that N-terminal methylation is a widespread post-translational modification and that there is interplay between N-terminal acetylation and N-terminal methylation. We also use isothermal calorimetry experiments to demonstrate that NRMT can efficiently recognize and bind to its fully methylated products.

The post-translational methylation of alpha-amino groups was first discovered over 30 years ago on the bacterial ribosomal proteins L16 and L33 (refs 1, 2), but almost nothing is known about the function or enzymology of this modification. Several other bacterial and eukaryotic proteins have since been shown to be alpha-N-methylated. However, the Ran guanine nucleotide-exchange factor, RCC1, is the only protein for which any biological function of alpha-N-methylation has been identified. Methylation-defective mutants of RCC1 have reduced affinity for DNA and cause mitotic defects, but further characterization of this modification has been hindered by ignorance of the responsible methyltransferase. All fungal and animal N-terminally methylated proteins contain a unique N-terminal motif, Met-(Ala/Pro/Ser)-Pro-Lys, indicating that they may be targets of the same, unknown enzyme. The initiating Met is cleaved, and the exposed alpha-amino group is mono-, di- or trimethylated. Here we report the discovery of the first alpha-N-methyltransferase, which we named N-terminal RCC1 methyltransferase (NRMT). Substrate docking and mutational analysis of RCC1 defined the NRMT recognition sequence and enabled the identification of numerous new methylation targets, including SET (also known as TAF-I or PHAPII) and the retinoblastoma protein, RB. Knockdown of NRMT recapitulates the multi-spindle phenotype seen with methylation-defective RCC1 mutants, demonstrating the importance of alpha-N-methylation for normal bipolar spindle formation and chromosome segregation.

Crystal structures of two orthologs of the regulatory subunit of acetohydroxyacid synthase III (AHAS, EC 2.2.1.6) from Thermotoga maritima (TM0549) and Nitrosomonas europea (NE1324) were determined by single-wavelength anomalous diffraction methods with the use of selenomethionine derivatives at 2.3 A and 2.5 A, respectively. TM0549 and NE1324 share the same fold, and in both proteins the polypeptide chain contains two separate domains of a similar size. Each protein contains a C-terminal domain with ferredoxin-type fold and an N-terminal ACT domain, of which the latter is characteristic for several proteins involved in amino acid metabolism. The ferredoxin domain is stabilized by a calcium ion in the crystal structure of NE1324 and by a Mg(H2O)(6)2+ ion in TM0549. Both TM0549 and NE1324 form dimeric assemblies in the crystal lattice.