Life and the evolution of Earth's atmosphere

Animal models of complex diseases: An initial strategy

We speculated that the rise in atmospheric oxygen from 2 billion years ago was so integral for the evolution of biocomplexity that it must also associate strongly with complex diseases. As a remote test of this idea, we hypothesized that lines contrasting for disease and health would emerge from artificial selection for low and high aerobic treadmill running capacity. Eleven generations of selection in rats produced lines that differed by 347% in running capacity. The low line demonstrated health risk factors including higher visceral adiposity, blood pressure, insulin, and triglycerides. The high line was superior for VO2max, economy of running, heart function, and nitric oxide-induced vascular dilation.

An obligately photosynthetic bacterial anaerobe from a deep-sea hydrothermal vent

The abundance of life on Earth is almost entirely due to biological photosynthesis, which depends on light energy. The source of light in natural habitats has heretofore been thought to be the sun, thus restricting photosynthesis to solar photic environments on the surface of the Earth. If photosynthesis could take place in geothermally illuminated environments, it would increase the diversity of photosynthetic habitats both on Earth and on other worlds that have been proposed to possibly harbor life. Green sulfur bacteria are anaerobes that require light for growth by the oxidation of sulfur compounds to reduce CO2 to organic carbon, and are capable of photosynthetic growth at extremely low light intensities. We describe the isolation and cultivation of a previously unknown green sulfur bacterial species from a deep-sea hydrothermal vent, where the only source of light is geothermal radiation that includes wavelengths absorbed by photosynthetic pigments of this organism.

Post-traumatic inflammatory response: perhaps a succession of phases with a nutritional purpose

Post-traumatic inflammatory response, whether this be local or systemic, is considered to be the succession of three functional phases called nervous, immune and endocrine, that could have a nutritional significance. In the nervous phase, ischemia-reperfusion, which causes interstitial and cellular edema, is produced. Both types of edema could represent an ancestral mechanism to feed the cells by diffusion. During the immune phase, the tissues are infiltrated by inflammatory cells and bacteria. Then, extracellular digestion, by enzyme release (fermentation), and intracellular digestion by phagocytosis could be associated with a hypothetical trophic capacity for the neighbouring cells. Finally, in the late or endocrine phase nutrition mediated by the blood capillaries is established. In these three successive phases the inflammatory response goes on from an anaerobic metabolism (ischemia) through a metabolism characterized by a defective oxygen use (reperfusion, oxidative burst and heat hyperproduction) to an oxidative metabolism (oxidative phosphorilation) with a correct use of oxygen to produce usable energy. This type of metabolism is characterized by a large production of ATP, which is used to drive specialized multiple cellular processes. Since the nervous, immune and endocrine phases of the inflammatory response go from ischemia to the development of an oxidative metabolism, It is also tempting to speculate on whether the body reproduces the successive stages by which life passes from its origin without oxygen until it develops an effective, although costly, system for the use of oxygen every time we suffer post-traumatic acute inflammation.

Methanoarchaeal sulfolactate dehydrogenase: prototype of a new family of NADH-dependent enzymes

The crystal structure of the sulfolactate dehydrogenase from the hyperthermophilic and methanogenic archaeon Methanocaldococcus jannaschii was solved at 2.5 A resolution (PDB id. 1RFM). The asymmetric unit contains a tetramer of tight dimers. This structure, complexed with NADH, does not contain a cofactor-binding domain with 'Rossmann-fold' topology. Instead, the tertiary and quaternary structures indicate a novel fold. The NADH is bound in an extended conformation in each active site, in a manner that explains the pro-S specificity. Cofactor binding involves residues belonging to both subunits within the tight dimers, which are therefore the smallest enzymatically active units. The protein was found to be a homodimer in solution by size-exclusion chromatography, analytical ultracentrifugation and small-angle neutron scattering. Various compounds were tested as putative substrates. The results indicate the existence of a substrate discrimination mechanism, which involves electrostatic interactions. Based on sequence homology and phylogenetic analyses, several other enzymes were classified as belonging to this novel family of homologous (S)-2-hydroxyacid dehydrogenases.

The Natural History of Nitrogen Fixation

In recent years, our understanding of biological nitrogen fixation has been bolstered by a diverse array of scientific techniques. Still, the origin and extant distribution of nitrogen fixation has been perplexing from a phylogenetic perspective, largely because of factors that confound molecular phylogeny such as sequence divergence, paralogy, and horizontal gene transfer. Here, we make use of 110 publicly available complete genome sequences to understand how the core components of nitrogenase, including NifH, NifD, NifK, NifE, and NifN proteins, have evolved. These genes are universal in nitrogen fixing organisms-typically found within highly conserved operons-and, overall, have remarkably congruent phylogenetic histories. Additional clues to the early origins of this system are available from two distinct clades of nitrogenase paralogs: a group composed of genes essential to photosynthetic pigment biosynthesis and a group of uncharacterized genes present in methanogens and in some photosynthetic bacteria. We explore the complex genetic history of the nitrogenase family, which is replete with gene duplication, recruitment, fusion, and horizontal gene transfer and discuss these events in light of the hypothesized presence of nitrogenase in the last common ancestor of modern organisms, as well as the additional possibility that nitrogen fixation might have evolved later, perhaps in methanogenic archaea, and was subsequently transferred into the bacterial domain.

Haze aerosols in the atmosphere of early Earth: manna from heaven

An organic haze layer in the upper atmosphere of Titan plays a crucial role in the atmospheric composition and climate of that moon. Such a haze layer may also have existed on the early Earth, providing an ultraviolet shield for greenhouse gases needed to warm the planet enough for life to arise and evolve. Despite the implications of such a haze layer, little is known about the organic material produced under early Earth conditions when both CO(2) and CH(4) may have been abundant in the atmosphere. For the first time, we experimentally demonstrate that organic haze can be generated in different CH(4)/CO(2) ratios. Here, we show that haze aerosols are able to form at CH(4) mixing ratios of 1,000 ppmv, a level likely to be present on early Earth. In addition, we find that organic hazes will form at C/O ratios as low as 0.6, which is lower than the predicted value of unity. We also show that as the C/O ratio decreases, the organic particles produced are more oxidized and contain biologically labile compounds. After life arose, the haze may thus have provided food for biota.

A Cyanobacterial Circadian Timing Mechanism

Cyanobacteria such as Synechococcus elongatus PCC 7942 exhibit 24-h rhythms of gene expression that are controlled by an endogenous circadian clock that is mechanistically distinct from those described for diverse eukaryotes. Genetic and biochemical experiments over the past decade have identified key components of the circadian oscillator, input pathways that synchronize the clock with the daily environment, and output pathways that relay temporal information to downstream genes. The mechanism of the cyanobacterial circadian clock that is emerging is based principally on the assembly and disassembly of a large complex at whose heart are the proteins KaiA, KaiB, and KaiC. Signal transduction pathways that feed into and out of the clock employ protein domains that are similar to those in two-component regulatory systems of bacteria.

The interface between the biological and inorganic worlds: iron-sulfur metalloclusters

Complex iron-sulfur metalloclusters form the active sites of the enzymes that catalyze redox transformations of N2, CO, and H2, which are likely components of Earth's primordial atmosphere. Although these centers reflect the organizational principles of simpler iron-sulfur clusters, they exhibit extensive elaborations that confer specific ligand-binding and catalytic properties. These changes were probably achieved through evolutionary processes, including the fusion of small clusters, the addition of new metals, and the development of cluster assembly pathways, driven by selective pressures resulting from changes in the chemical composition of the biosphere.

The fundamental processes in ecology: a thought experiment on extraterrestrial biospheres

Ecological science is often organised as a hierarchical series of entities: genes, individuals, populations, species, communities, ecosystems and biosphere. Here, I consider an alternative process-based approach to ecology, and analyse the nature of the fundamental processes in ecology. These fundamental processes are discussed in the context of the following question: 'for any planet with carbon-based life, which persists over geological time scales, what are the minimum set of ecological processes that must be present?' I suggest that the following processes would be present on any such planet: energy flow, multiple guilds, ecological trade-offs leading to within-guild biodiversity, ecological hypercycles, merging of organismal and ecological physiology, carbon sequestration and possibly photosynthesis. Nutrient cycling is described as an emergent property of these fundamental processes. I discuss reasons why a biosphere based on a single species with no nutrient cycling is very unlikely to exist. I also describe the concept of 'Gaian effect'. This suggests that some processes will always tend to extend the lifespan of a biosphere in which they develop (positive Gaian effect) while others could either increase or decrease (negative Gaian effect) such a lifespan. These ideas are discussed in the context of astrobiology, ecosystem services, conservation biology and Gaia theory.

Nitrogen fixation and photosynthetic oxygen evolution in cyanobacteria

The biological reduction of N(2) is catalyzed by nitrogenase, which is irreversibly inhibited by molecular oxygen. Cyanobacteria are the only diazotrophs (nitrogen-fixing organisms) that produce oxygen as a by-product of the photosynthetic process, and which must negotiate the inevitable presence of molecular oxygen with an essentially anaerobic enzyme. In this review, we present an analysis of the geochemical conditions under which nitrogenase evolved and examine how the evolutionary history of the enzyme complex corresponds to the physiological, morphological, and developmental strategies for reducing damage by molecular oxygen. Our review highlights biogeochemical constraints on diazotrophic cyanobacteria in the contemporary world.

Geomicrobiology: how molecular-scale interactions underpin biogeochemical systems

Microorganisms populate every habitable environment on Earth and, through their metabolic activity, affect the chemistry and physical properties of their surroundings. They have done this for billions of years. Over the past decade, genetic, biochemical, and genomic approaches have allowed us to document the diversity of microbial life in geologic systems without cultivation, as well as to begin to elucidate their function. With expansion of culture-independent analyses of microbial communities, it will be possible to quantify gene activity at the species level. Genome-enabled biogeochemical modeling may provide an opportunity to determine how communities function, and how they shape and are shaped by their environments.

Reassessing the possibility of life on venus: proposal for an astrobiology mission

With their similar size, chemical composition, and distance from the Sun, Venus and Earth may have shared a similar early history. Though surface conditions on Venus are now too extreme for life as we know it, it likely had abundant water and favorable conditions for life when the Sun was fainter early in the Solar System. Given the persistence of life under stabilizing selection in static environments, it is possible that life could exist in restricted environmental niches, where it may have retreated after conditions on the surface became untenable. High-pressure subsurface habitats with water in the supercritical liquid state could be a potential refugium, as could be the zone of dense cloud cover where thermoacidophilic life might have retreated. Technology based on the Stardust Mission to collect comet particles could readily be adapted for a pass through the appropriate cloud layer for sample collection and return to Earth.