Paleoproterozic Icehouses and the Evolution of Oxygen Mediating Enzymes: The Case for a Late Origin of Photosystem -- II

Two major geological problems regarding the origin of oxygenic photosynthesis are: (1) identifying a source of oxygen predating biological oxygen production and capable of driving the evolution of oxygen tolerance, and (2) determining when oxygenic photosynthesis evolved. One solution to the first problem is the accumulation of photochemically-produced H2O2 at the surface of glaciers and its subsequent incorporation into ice. Melting at the glacier base would release H2O2, which interacts with seawater to produce O2 in an environment shielded from the lethal levels of ultraviolet radiation needed to produce H2O2. Answers to the second problem are controversial and range from 3.8 to 2.2 Ga. A skeptical view, based on metals that have redox potentials close to oxygen, argues for the late end of the range. The preponderance of geological evidence suggests little or no oxygen in the late Archaean atmosphere (< 1 ppm). The main piece of evidence for an earlier evolution of oxygenic photosynthesis comes from lipid biomarkers. Recent work, however, has shown that 2-methylhopanes, once thought to be unique biomarkers for cyanobacteria, are also produced anaerobically in significant quantities by at least two strains of anoxygenic phototrophs. Sterane biomarkers provide the strongest evidence for a date ≥2.7 Ga but could also be explained by the common evolutionary pattern of replacing anaerobic enzymes with oxygen-dependent ones. Although no anaerobic sterol synthesis pathway has been identified in the modern biosphere, enzymes that perform the necessary chemistry do exist. This analysis suggests that oxygenic photosynthesis could have evolved close in geological time to the Makganyene Snowball Earth Event and argues for a causal link between the two

An expanding range of targets for kynurenine metabolites of tryptophan

The kynurenine pathway of tryptophan metabolism accounts for most of the tryptophan that is not committed to protein synthesis and includes compounds active in the nervous and immune systems. Kynurenine acts on the aryl hydrocarbon receptor, affecting the metabolism of xenobiotics and promoting carcinogenesis. Quinolinic acid is an agonist at N-methyl-D-aspartate receptors (NMDARs), but is also pro-oxidant, has immunomodulatory actions, and promotes the formation of hyperphosphorylated tau proteins. Kynurenic acid blocks NMDARs and α7-homomeric nicotinic cholinoceptors and is also an agonist at the orphan G-protein-coupled receptor GPR35. 3-Hydroxykynurenine and 3-hydroxyanthranilic acid have pronounced redox activity and regulate T cell function. Cinnabarinic acid can activate metabotropic glutamate receptors. This review highlights the increasing range of molecular targets for components of the kynurenine pathway in both the nervous and immune systems in relation to their relevance to disease and drug development

The "Oil-Spill Snorkel": an innovative bioelectrochemical approach to accelerate hydrocarbons biodegradation in marine sediments

This study presents the proof-of-concept of the "Oil-Spill Snorkel": a novel bioelectrochemical approach to stimulate the oxidative biodegradation of petroleum hydrocarbons in sediments. The "Oil-Spill Snorkel" consists of a single conductive material (the snorkel) positioned suitably to create an electrochemical connection between the anoxic zone (the contaminated sediment) and the oxic zone (the overlying O-2-containing water). The segment of the electrode buried within the sediment plays a role of anode, accepting electrons deriving from the oxidation of contaminants. Electrons flow through the snorkel up to the part exposed to the aerobic environment (the cathode), where they reduce oxygen to form water. Here we report the results of lab-scale microcosms setup with marine sediments and spiked with crude oil. Microcosms containing one or three graphite snorkels and controls (snorkel-free and autoclaved) were monitored for over 400 days. Collectively, the results of this study confirmed that the snorkels accelerate oxidative reactions taking place within the sediment, as documented by a significant 1.7-fold increase (p = 0.023, two-tailed t-test) in the cumulative oxygen uptake and 1.4-fold increase (p = 0.040) in the cumulative CO2 evolution in the microcosms containing three snorkels compared to snorkel-free controls. Accordingly, the initial rate of total petroleum hydrocarbons (TPH) degradation was also substantially enhanced. Indeed, while after 200 days of incubation a negligible degradation of TPH was noticed in snorkel-free controls, a significant reduction of 12 1% (p = 0.004) and 21 1% (p = 0.001) was observed in microcosms containing one and three snorkels, respectively. Although, the "Oil-Spill Snorkel" potentially represents a groundbreaking alternative to more expensive remediation options, further research efforts are needed to clarify factors and conditions affecting the snorkel-driven biodegradation processes and to identify suitable configurations for field applications

Production of lotion using neem (Azadirachta Indica A. Juss) extract

Nowadays, the most emerging disease which is arthropod borne disease cannot be prevented from vaccines and become a potential threat especially in tropical world such as America, Africa and Asia and has become a trend (Al-Hashemi et al., 2016; Biswas et al., 2002; Brian et al., 2011). One of the preventive measures is by using extracted neem oil blended into lotions for daily usage. According to Ayurveda medicine, neem (AzadirachtinIndica A. Juss) oil is widely used as a pesticide agent in India which reduce insect feeding and acts a repellent (Costa et al., 2017; Dubey et al., 2014). World Health Organization (WHO) and United Nation Environment Programme (UNEP) 1989 identified neem as an environmentally powerful natural pesticide, considered to be one of the most promising tress of the 21st Century for its great potential in pest management, environment protection and medicine (Costa et al., 2017)

The thermodynamic landscape of carbon redox biochemistry

Redox biochemistry plays a key role in the transduction of chemical energy in all living systems. Observed redox reactions in metabolic networks represent only a minuscule fraction of the space of all possible redox reactions. Here we ask what distinguishes observed, natural redox biochemistry from the space of all possible redox reactions between natural and non-natural compounds. We generate the set of all possible biochemical redox reactions involving linear chain molecules with a fixed numbers of carbon atoms. Using cheminformatics and quantum chemistry tools we analyze the physicochemical and thermodynamic properties of natural and non-natural compounds and reactions. We find that among all compounds, aldose sugars are the ones with the highest possible number of connections (reductions and oxidations) to other molecules. Natural metabolites are significantly enriched in carboxylic acid functional groups and depleted in carbonyls, and have significantly higher solubilities than non-natural compounds. Upon constructing a thermodynamic landscape for the full set of reactions as a function of pH and of steady-state redox cofactor potential, we find that, over this whole range of conditions, natural metabolites have significantly lower energies than the non-natural compounds. For the set of 4-carbon compounds, we generate a Pourbaix phase diagram to determine which metabolites are local energetic minima in the landscape as a function of pH and redox potential. Our results suggest that, across a set of conditions, succinate and butyrate are local minima and would thus tend to accumulate at equilibrium. Our work suggests that metabolic compounds could have been selected for thermodynamic stability, and yields insight into thermodynamic and design principles governing nature’s metabolic redox reactions.https://www.biorxiv.org/content/10.1101/245811v1Othe

Role of the PAS2 domain of the NifL regulatory protein in redox signal transduction

EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Ring-hydroxylating dioxygenases involved in PAH biodegradation : structure, function, biodiversity

International audienceThe first step in the biodegradation of PAHs by aerobic bacteria is catalyzed by metalloenzymes known as ring-hydroxylating dioxygenases (RHDs). Because of the hydrophobic nature and chemical resistance of PAHs, their initial attack by RHDs is a difficult reaction, which is critical to the whole degradation process. This chapter gives an overview of the current knowledge on the genetics, structure, catalytic mechanism and diversity of RHDs involved in PAH degradation. In the past decade, the crystal structures of 10 RHDs have been determined, giving insights into the mechanism of substrate recognition and regioselectivity of dioxygenation. The reaction catalyzed by the archetypal naphthalene dioxygenase has been investigated in detail, thus providing a better understanding of the RHD catalytic mechanism. Studies on the catabolic genes responsible for PAH degradation in several bacterial taxa have highlighted the great phylogenetic diversity of RHDs. The implementation of culture-independent methods has afforded means to further explore the environmental diversity of PAH-degrading bacteria and RHDs. Recent advances in this field now allow the in situ identification of bacteria responsible for pollutant removal. Further biotechnological developments based on microarrays and functional metagenomics should lead to the conception of molecular tools useful for the bioremediation of PAH-contaminated ecosystems

Non-conventional gas phase remediation of volatile halogenated compounds by dehydrated bacteria

Traditional biological removal processes are limited by the low solubility of halogenated compounds in aqueous media. A new technology appears very suitable for the remediation of these volatile organic compounds (VOCs). Solid/gas bio-catalysis applied in VOC remediation can transform halogenated compounds directly in the gas phase using dehydrated cells as a bio-catalyst. The hydrolysis of volatile halogenated substrates into the corresponding alcohol was studied in a solid/gas biofilter where lyophilised bacterial cultures were used as the catalyst. Four strains containing dehalogenase enzymes were tested for the hydrolysis of 1-chlorobutane. The highest removal yield was obtained using the dhaA-containing strains, the maximal reaction rate of 0.8 micromol min(-1)g(-1) being observed with Escherichia coli BL21(DE3)(dhaA). Various treatments such as cell disruption by lysozyme or alkaline gas addition in the bio-filter could stabilise the dehalogenase activity of the bacteria. A pre-treatment of the dehydrated bacterial cells by ammonia vapour improved the stability of the catalyst and a removal activity of 0.9 micromol min(-1)g(-1) was then obtained for 60h. Finally, the process was extended to a range of halogenated substrates including bromo- and chloro-substrates. It was shown that the removal capacity for long halogenated compounds (C(5)-C(6)) was greatly increased relative to traditional biological processes