Enzyme phylogenies as markers for the oxidation state of the environment: The case of respiratory arsenate reductase and related enzymes

<p>Abstract</p> <p>Background</p> <p>Phylogenies of certain bioenergetic enzymes have proved to be useful tools for deducing evolutionary ancestry of bioenergetic pathways and their relationship to geochemical parameters of the environment. Our previous phylogenetic analysis of arsenite oxidase, the molybdopterin enzyme responsible for the biological oxidation of arsenite to arsenate, indicated its probable emergence prior to the Archaea/Bacteria split more than 3 billion years ago, in line with the geochemical fact that arsenite was present in biological habitats on the early Earth. Respiratory arsenate reductase (Arr), another molybdopterin enzyme involved in microbial arsenic metabolism, serves as terminal oxidase, and is thus situated at the opposite end of bioenergetic electron transfer chains as compared to arsenite oxidase. The evolutionary history of the Arr-enzyme has not been studied in detail so far.</p> <p>Results</p> <p>We performed a genomic search of genes related to <it>arrA </it>coding for the molybdopterin subunit. The multiple alignment of the retrieved sequences served to reconstruct a neighbor-joining phylogeny of Arr and closely related enzymes. Our analysis confirmed the previously proposed proximity of Arr to the cluster of polysulfide/thiosulfate reductases but also unravels a hitherto unrecognized clade even more closely related to Arr. The obtained phylogeny strongly suggests that Arr originated after the Bacteria/Archaea divergence in the domain Bacteria, and was subsequently laterally distributed within this domain. It further more indicates that, as a result of accumulation of arsenate in the environment, an enzyme related to polysulfide reductase and not to arsenite oxidase has evolved into Arr.</p> <p>Conclusion</p> <p>These findings are paleogeochemically rationalized by the fact that the accumulation of arsenate over arsenite required the increase in oxidation state of the environment brought about by oxygenic photosynthesis.</p

Phylloquinone (vitamin K 1 ) biosynthesis in plants: two peroxisomal thioesterases of lactobacillales origin hydrolyze 1,4‐dihydroxy‐2‐naphthoyl‐coa

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/92396/1/TPJ_4972_sm_FigS3.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/92396/2/TPJ_4972_sm_TableS1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/92396/3/TPJ_4972_sm_FigS2.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/92396/4/TPJ_4972_sm_TableS4.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/92396/5/TPJ_4972_sm_FigS6.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/92396/6/j.1365-313X.2012.04972.x.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/92396/7/TPJ_4972_sm_FigS1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/92396/8/TPJ_4972_sm_TableS3.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/92396/9/TPJ_4972_sm_FigS5.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/92396/10/TPJ_4972_sm_TableS2.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/92396/11/TPJ_4972_sm_FigS4.pd

Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function

Background Riverine ecosystems are biogeochemical powerhouses driven largely by microbial communities that inhabit water columns and sediments. Because rivers are used extensively for anthropogenic purposes (drinking water, recreation, agriculture, and industry), it is essential to understand how these activities affect the composition of river microbial consortia. Recent studies have shown that river metagenomes vary considerably, suggesting that microbial community data should be included in broad-scale river ecosystem models. But such ecogenomic studies have not been applied on a broad “aquascape” scale, and few if any have applied the newest nanopore technology. Results We investigated the metagenomes of 11 rivers across 3 continents using MinION nanopore sequencing, a portable platform that could be useful for future global river monitoring. Up to 10 Gb of data per run were generated with average read lengths of 3.4 kb. Diversity and diagnosis of river function potential was accomplished with 0.5–1.0 ⋅ 106 long reads. Our observations for 7 of the 11 rivers conformed to other river-omic findings, and we exposed previously unrecognized microbial biodiversity in the other 4 rivers. Conclusions Deeper understanding that emerged is that river microbial consortia and the ecological functions they fulfil did not align with geographic location but instead implicated ecological responses of microbes to urban and other anthropogenic effects, and that changes in taxa manifested over a very short geographic space

The ocean sampling day consortium

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits

The Ocean Sampling Day Consortium

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits

Origine enzymatique de la respiration aérobie (étude évolutive des HCOs et caractérisation d'un modèle choisi : l'oxydase cbb3 de Sulfurihydrogenibium azorense)

Dans la chaîne membranaire mitochondriale de transduction de l énergie, le complexe IV est l élément ultime qui permet la réduction de l accepteur final d électrons, le dioxygène (O2). C est l enzyme qui, par excellence, utilise l O2 dans un but bioénergétique. Chez les procaryotes, cette fonction est assumée par de multiples homologues du complexe IV formant la superfamille des HCOs (Heme-Copper Oxydase). Celle-ci regroupe 3 types d O2 réductases (SoxB, SoxM et cbb3) et les NO réductases qui participent à la dénitrification dissimilatrice. L établissement de l histoire évolutive des HCOs chez les procaryotes revient à approcher les origines de la capacité d utilisation de l O2 comme oxydant fort par les organismes vivants. Il s agit d un sujet controversé : les principales études évolutives concernant les HCOs s opposent aux données de la Paléogéochimie qui montrent que l O2 était absent de l atmosphère terrestre jusqu à l avènement de la photosynthèse oxygénique par les Cyanobactéria (-2, 7 milliards d années). Nous avons entrepris de réévaluer l histoire évolutive des HCOs. Notre méthodologie s est basée sur l établissement de phylogénies de divers éléments des complexes HCOs, mises en contact de données structurales et fonctionnelles. Guidés par ces données, nous avons choisi l oxydase cbb3 de Sulfurihydrogenibium azorense comme nouveau modèle enzymatique expérimental. Les résultats obtenus suggèrent que les O2 réductases SoxB/M et cbb3 sont 2 systèmes respiratoires mis en place indépendamment chez les Archaea (SoxB/M) et les Bactéria (cbb3). La NO réductase pourrait avoir fait partie répertoire protéique de LUCA et se positionne ainsi comme ancêtre le plus probable de la superfamille. Nous proposons un mécanisme hypothétique de conversion fonctionnelle de l enzyme NO réductase en O2 réductase pour expliquer les émergences de cette dernière activité chez les familles SoxB/M et cbb3. Ce scénario implique que le NO soit le substrat originel des HCOs et a fortiori l oxydant fort de l atmosphère primordiale. Nous aboutissons ainsi à une unification de l histoire évolutive des HCOs avec les données paléogéochimiques qui donnent le NO, a contrario de l O2, comme une espèce abondante de l atmosphère primordiale.AIX-MARSEILLE1-BU Sci.St Charles (130552104) / SudocSudocFranceF

pNEB193-derived suicide plasmids for gene deletion and protein expression in the methane-producing archaeon, Methanosarcina acetivorans

Gene deletion and protein expression are cornerstone procedures for studying metabolism in any organism, including methane-producing archaea (methanogens). Methanogens produce coenzymes and cofactors not found in most bacteria, therefore it is sometimes necessary to express and purify methanogen proteins from the natural host. Protein expression in the native organism is also useful when studying post-translational modifications and their effect on gene expression or enzyme activity. We have created several new suicide plasmids to complement existing genetic tools for use in the methanogen, Methanosarcina acetivorans. The new plasmids are derived from the commercially available E. coli plasmid, pNEB193, and cannot replicate autonomously in methanogens. The designed plasmids facilitate markerless gene deletion, gene transcription, protein expression, and purification of proteins with cleavable affinity tags from the methanogen, Methanosarcina acetivorans

The evolution of respiratory O\u3csub\u3e2\u3c/sub\u3e/NO reductases: An out-of-the-phylogenetic-box perspective

Complex life on our planet crucially depends on strong redox disequilibria afforded by the almost ubiquitous presence of highly oxidizing molecular oxygen. However, the history of O2-levels in the atmosphere is complex and prior to the Great Oxidation Event some 2.3 billion years ago, the amount of O2 in the biosphere is considered to have been extremely low as compared with present-day values. Therefore the evolutionary histories of life and of O2-levels are likely intricately intertwined. The obvious biological proxy for inferring the impact of changing O2-levels on life is the evolutionary history of the enzyme allowing organisms to tap into the redox power of molecular oxygen, i.e. the bioenergetic O2 reductases, alias the cytochrome and quinol oxidases. Consequently, molecular phylogenies reconstructed for this enzyme superfamily have been exploited over the last two decades in attempts to elucidate the interlocking between O2 levels in the environment and the evolution of respiratory bioenergetic processes. Although based on strictly identical datasets, these phylogenetic approaches have led to diametrically opposite scenarios with respect to the history of both the enzyme superfamily and molecular oxygen on the Earth. In an effort to overcome the deadlock of molecular phylogeny, we here review presently available structural, functional, palaeogeochemical and thermodynamic information pertinent to the evolution of the superfamily (which notably also encompasses the subfamily of nitric oxide reductases). The scenario which, in our eyes, most closely fits the ensemble of these non-phylogenetic data, sees the low O2-affinity SoxM- (or A-) type enzymes as the most recent evolutionary innovation and the high-affinity O2 reductases (SoxB or B and cbb3 or C) as arising independently from NO-reducing precursor enzymes

The nitrogen cycle in the archaean: an intricate interplay of enzymatic and abiotic reactions

On modern planet Earth, a multitude of nitrogen cycle enzymes equilibrate the atmospheric reservoir of dinitrogen with the more oxidized and more reduced nitrogen compounds essential for life. The respective enzymes are elaborate entities and the reactions performed are complicated and in cases energetically challenging. Nitrogen, however, must have been a crucial element already at life's very beginnings which raises the question how the primordial nitrogen cycle of emerging life in the Archaean - necessarily using simpler and likely fewer enzymes - may have evolved into the very complex network of present planet Earth. To address this question, we have analysed molecular phylogenies of the presently known enzymes involved in the present day nitrogen cycle. The results collected and presented in this chapter indicate that in the Archaean, the enzymatic part of this cycle was restricted to a partial segment of the modern energy conserving denitrification pathway and that abiotic redox conversions of nitrogen specific to the geoenvironment of the Archaean were the evolutionary precursors of many reactions now requiring enzyme catalysis. As found in recent years for other core metabolic processes, the biological nitrogen cycle appears to be evolutionarily rooted in inorganic chemistry