Download or read book The Methanosarcina Barkeri Genome written by and published by . This book was released on 2006 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: We report here a comparative analysis of the genome sequence of Methanosarcina barkeri with those of Methanosarcina acetivorans and Methanosarcina mazei. All three genomes share a conserved double origin of replication and many gene clusters. M. barkeri is distinguished by having an organization that is well conserved with respect to the other Methanosarcinae in the region proximal to the origin of replication with interspecies gene similarities as high as 95%. However it is disordered and marked by increased transposase frequency and decreased gene synteny and gene density in the proximal semi-genome. Of the 3680 open reading frames in M. barkeri, 678 had paralogs with better than 80% similarity to both M. acetivorans and M. mazei while 128 nonhypothetical orfs were unique (non-paralogous) amongst these species including a complete formate dehydrogenase operon, two genes required for N-acetylmuramic acid synthesis, a 14 gene gas vesicle cluster and a bacterial P450-specific ferredoxin reductase cluster not previously observed or characterized in this genus. A cryptic 36 kbp plasmid sequence was detected in M. barkeri that contains an orc1 gene flanked by a presumptive origin of replication consisting of 38 tandem repeats of a 143 nt motif. Three-way comparison of these genomes reveals differing mechanisms for the accrual of changes. Elongation of the large M. acetivorans is the result of multiple gene-scale insertions and duplications uniformly distributed in that genome, while M. barkeri is characterized by localized inversions associated with the loss of gene content. In contrast, the relatively short M. mazei most closely approximates the ancestral organizational state.
Download or read book An Updated Genome Scale Metabolic Reconstruction of Methanosarcina Barkeri written by Matthew C. Gonnerman and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Methanosarcina barkeri is a methanogen, meaning that methane is the reduced product for energy generation. M. barkeri can grow on several substrates including methanol, acetate, methyl amines and a combination of hydrogen and carbon dioxide. The Methanosarcina barkeri genome was published in 2006 after the metabolic reconstruction of M. barkeri, iAF692, was published. The iAF692 reconstruction preformed the first large scale simulations of an Archaea. Since the publication of iAF692, a deeper understanding of Archaea biology has shed light on previously unclear metabolic pathways. For methanogenesis, proton pumping has been updated to reflect an improved knowledge of the pathway. Cofactor biosynthesis has been updated to reflect a better understanding of methanogen anabolism. Metabolic networks such as pentose phosphate pathway, amino acid biosynthesis, and cell wall composition have also been updated to reflect Archaea specific biosynthesis pathways. This improved insight has led to an increase in predictive accuracy for knockouts and growth yield predictions for the updated M. barkeri reconstruction, iMG750. As with other metabolic reconstructions, iMG750 will be a useful tool in guiding experimental studies and predicting cellular behavior on a genome scale.
Download or read book Nitrogen Fixation and Its Regulation in the Archaeon Methanosarcina Barkeri 227 written by Yueh-tyng Chien and published by . This book was released on 1996 with total page 350 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Electron Transport in Methanosarcina written by Adam M. Guss and published by . This book was released on 2006 with total page 189 pages. Available in PDF, EPUB and Kindle. Book excerpt: Electron transport during methanogenesis in the freshwater methanogen Methanosarcina barkeri is known to utilize hydrogenases to transfer electrons from ferredoxin to methanophenazine. This thesis characterizes electron transport in the marine methanogen Methanosarcina acetivorans. Genomic comparison of hydrogenase gene clusters reveals that M. acetivorans encodes three putative Ni-Fe hydrogenases common to all sequenced Methanosarcina. However, deletion analysis and enzymatic assays indicate M. acetivorans does not produce functional hydrogenase in crude cell extract. This raised the possibility that M. acetivorans contains a unique electron transport chain distinct from that found in M. barkeri. To address the mechanism of M. acetivorans hydrogenase inactivation, reporter gene fusions to the hydrogenase promoters of M. acetivorans and M. barkeri were inserted into the chromosomes of both M. acetivorans and M. barkeri. The M. barkeri promoters were expressed in both organisms, while the M. acetivorans promoters were not expressed in either organism. This suggests that the M. acetivorans hydrogenases have been inactivated via cis-acting mutations in the promoters. Because M. acetivorans cannot use hydrogenases for electron transport, some other pathway must exist. Three putative oxidoreductase gene clusters have been implicated in this electron transport chain in M. acetivorans: rnf, ehr, and MA3739-3743. Deletion analysis of these three gene clusters indicates Rnf is the primary oxidoreductase during growth on acetate. While the Deltaehr and DeltaMA3739-3743 strains have growth phenotypes identical to the parent strains, the Deltarnf strain does not grow on acetate, grows more slowly on methanol, and has a ca. 300 hour lag period before growth on methanol + pyruvate. These data suggest that Rnf is a ferredoxin-dependent oxidoreductase involved in electron transport during methanogenesis in M. acetivorans.
Download or read book Methanogenesis written by James G. Ferry and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 541 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the general recognition of the Archaebacteria, research into the evolution, metabolism, molecular biology and ecological roles of these fastidious anaerobes has proceeded at an ever-increasing pace. All possess a very novel biochemistry and many exploit unique ecological niches. Methanogens, which convert one-and-two carbon compounds into the important atmospheric gas methane, are the largest group among the Archaebacteria. Of all microbial groups, methanogens provide perhaps the best opportunity to study evolution because of their phyologenetic diversity and unique biochemistry. Today, the analysis of methanogens is at a threshold. Molecular-biological studies of these microorganisms are revealing more and more processes unique to this group, and in turn, studies of methanogens are providing new perspectives to the broader fields of biochemistry and molecular biology. This volume is the first book to be published on methanogenesis, and it will provide the reader with a comprehensive view of the field and point to future trends.
Download or read book The methane moment Cross boundary significance of methanogens written by Zhe Lyu and published by Frontiers Media SA. This book was released on 2024-07-30 with total page 271 pages. Available in PDF, EPUB and Kindle. Book excerpt: Methane is a potent greenhouse gas, a relatively clean burning fossil fuel, but also a renewable biofuel when biologically produced from waste treatment plants. Most (~70%) of the global methane emission comes from methanogenic archaea, namely methanogens that produce methane from simple substrates such as H2/CO2, formate, acetate, methanol, and other methylated compounds. Methanogens are found across all corners of the earth, including but not limited to wetlands, animals and humans, rice fields, landfills, sewage, ocean, termites, and hydrothermal vents. Their extensive adaptations to such a wide range of habitats predict a cross-boundary significance of methanogens in many areas such as the environment, energy, agriculture, biotechnology, and human and animal health. The goal of this Research Topic is to offer a forum that highlights the cross-boundary significance of methanogens by bringing together methanogen research from diverse settings to one place. This cross-boundary significance is currently underappreciated but imperative to collectively understanding and helping to solve some of the biggest and most urgent challenges humanity is facing such as global warming, food and energy insecurity, pollution, and disease. As a more potent and shorter-lived greenhouse gas than CO2, methane has moved to the center stage in our efforts in rapidly combating climate change. Presumably, methanogens and their associated microbes may have been forced into a positive feedback loop to fuel the sharp rise of methane in recent years. On the other hand, methanogens are considered keystone species in the ecosystem, which are vital to the stability of the natural biome therein. However, the roles of methanogens as keystone species across their habitats are underexplored. Moreover, the role of methanogens in human and animal intestinal microbiomes have been reconsidered with evidence for links to disease and impact on nutrition. Last but not the least, methanogens are emerging as a cell factory model for green manufacturing, because of their abilities to convert CO2 to valuable biochemicals. Further efforts in the bioengineering of methanogens have the potential to expand their commercial application from waste treatment to biomanufacturing. We welcome both basic and translational studies relevant to methanogens from any setting. Studies with a focus on methanogens are highly encouraged, and manuscripts having methanogens as a significant component are also welcome. All studies should emphasize and envisage their implications in understanding and/or solving one or more challenges humanity is facing. To encourage submissions from multiple disciplines, this Research Topic is cross-listed with a number of Frontiers journals and sections. Manuscripts in the forms of Original Research, Review (including systematic and mini review), Methods, Hypothesis and Theory, and Perspectives are all welcome. Manuscript summary submissions are highly encouraged but all manuscripts submitted prior to the manuscript submission deadline will receive full consideration. This Research Topic is dedicated to Dr. William Barny Whitman, Emeritus Professor of Microbiology at the University of Georgia, Athens, GA. His 40+ years (and still counting) of productive research in methanogens, roseobacter, and other prokaryotes have contributed to and will continue to inspire new discoveries in the cross-boundary significance of both archaea and bacteria – the unseen majority. COI Statement: S.K.-M.R.R. is co-founder of Arkeon GmbH. M.P. is a consultant for Bausch Health, Ferring Pharmaceuticals Inc., Salvo Health, and Vivante Health Inc.
Download or read book A Genetic and Bioinformatic Study Into the Transcriptional Regulation of Nitrogen Fixation in Methanosarcina written by Linda Diane Rankin and published by . This book was released on 2006 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book 23 European Symposium on Computer Aided Process Engineering written by Nishu Goyal and published by Elsevier Inc. Chapters. This book was released on 2013-06-10 with total page 17 pages. Available in PDF, EPUB and Kindle. Book excerpt: Methane (Natural gas) is an important energy source for heating and electricity. Its production by methanogenic bacteria using different carbon substrates is widely known in nature. Methanococcus maripaludis S2, a methanogen is an excellent laboratory strain for which robust genetic tools are available, but a systems biology model to complement these tools is absent in the literature. To understand methanogenesis and to maximize the yield of methane by using carbon dioxide captured from a flue gas, a constraint-based genome-scale metabolic model of fully sequenced hydrogenotrophic methanogenic strain M. maripaludis S2 has been developed. This model serves to predict the effects of any perturbations and/or gene knockouts on different metabolic processes, which can guide or expedite experimental efforts. Genome-scale metabolic model of M. maripaludis S2 was reconstructed using pathway databases such as KEGG, METACYC and SEED to identify gene-protein-reaction (GPR) associations. Gap filling was done by reviewing published experimental literature and using basic biological understanding of the intracellular functions in methanogenic species. The model was validated using biomass growth data, and metabolic phenotypes predicted by our model are consistent with experimental observations.
Download or read book In silico Modeling and Experimental Validation for Improving Methanogenesis from CO2 via M maripaludis written by Nishu Goyal and published by Springer. This book was released on 2016-09-28 with total page 140 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis explores the ability of M. maripaludis to capture and convert CO2 to methane in the presence of free nitrogen, and offers a consolidated review of the metabolic processes and applications of M. maripaludis. Further, it develops, validates and analyzes the first genome-scale metabolic model (iMM518) of M. maripaludis. Readers will discover, for the first time, the impact of nitrogen fixation on methane production. As such, the thesis will be of interest to researchers working on M. maripaludis, biofuels and bioenergy, systems biology modeling and its experimental validation, estimation of maintenance energy parameters, nitrogen fixing microbes, and bioremediation.
Download or read book Biogenesis of Hydrocarbons written by Alfons J. M. Stams and published by Springer. This book was released on 2019-08-14 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book covers the microbiological, environmental and biotechnological aspects of alkane production. Alkanes are important energy-rich compounds on earth. Microbial synthesis of methane and other alkanes is an essential part of the geochemical cycling of carbon and offers perspectives for our biobased economy. This book discusses different aspects of current knowledge of microbial alkane production. Chapters with state of the art information are written by renowned scientists in the field. The chapters are organised into four themed parts:1. Biochemistry of Biogenesis - Hydrocarbons2. Taxonomy, Ecophysiology and Genomics of Biogenesis - Hydrocarbons3. Biogenic Communities: Members, Functional Roles4. Global Consequences of Methane Production
Download or read book Biology of the Nitrogen Cycle written by Hermann Bothe and published by Elsevier. This book was released on 2007 with total page 451 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Prokaryotes written by Edward F. DeLong and published by Springer. This book was released on 2014-10-13 with total page 567 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Prokaryotes is a comprehensive, multi-authored, peer reviewed reference work on Bacteria and Achaea. This fourth edition of The Prokaryotes is organized to cover all taxonomic diversity, using the family level to delineate chapters. Different from other resources, this new Springer product includes not only taxonomy, but also prokaryotic biology and technology of taxa in a broad context. Technological aspects highlight the usefulness of prokaryotes in processes and products, including biocontrol agents and as genetics tools. The content of the expanded fourth edition is divided into two parts: Part 1 contains review chapters dealing with the most important general concepts in molecular, applied and general prokaryote biology; Part 2 describes the known properties of specific taxonomic groups. Two completely new sections have been added to Part 1: bacterial communities and human bacteriology. The bacterial communities section reflects the growing realization that studies on pure cultures of bacteria have led to an incomplete picture of the microbial world for two fundamental reasons: the vast majority of bacteria in soil, water and associated with biological tissues are currently not culturable, and that an understanding of microbial ecology requires knowledge on how different bacterial species interact with each other in their natural environment. The new section on human microbiology deals with bacteria associated with healthy humans and bacterial pathogenesis. Each of the major human diseases caused by bacteria is reviewed, from identifying the pathogens by classical clinical and non-culturing techniques to the biochemical mechanisms of the disease process. The 4th edition of The Prokaryotes is the most complete resource on the biology of prokaryotes. The following volumes are published consecutively within the 4th Edition: Prokaryotic Biology and Symbiotic Associations Prokaryotic Communities and Ecophysiology Prokaryotic Physiology and Biochemistry Applied Bacteriology and Biotechnology Human Microbiology Actinobacteria Firmicutes Alphaproteobacteria and Betaproteobacteria Gammaproteobacteria Deltaproteobacteria and Epsilonproteobacteria Other Major Lineages of Bacteria and the Archaea
Download or read book Methods in Methane Metabolism written by Amy Claire Rosenzweig and published by Academic Press. This book was released on 2011 with total page 421 pages. Available in PDF, EPUB and Kindle. Book excerpt: Produced by microbes on a large scale, methane is an important alternative fuel as well as a potent greenhouse gas. This volume focuses on microbial methane metabolism, which is central to the global carbon cycle. Both methanotrophy and methanogenesis are covered in detail. Topics include isolation and classification of microorganisms, metagenomics approaches, biochemistry of key metabolic enzymes, gene regulation and genetic systems, and field measurements. The state of the art techniques described here will both guide researchers in specific pursuits and educate the wider scientific community about this exciting and rapidly developing field. Topics include isolation and classification of microorganisms, metagenomics approaches, biochemistry of key metabolic enzymes, gene regulation and genetic systems, and field measurements. The state of the art techniques described here will both guide researchers in specific pursuits and educate the wider scientific community about this exciting and rapidly developing field.
Download or read book Epigenetic Technological Applications written by Yujun George Zheng and published by Academic Press. This book was released on 2015-05-30 with total page 516 pages. Available in PDF, EPUB and Kindle. Book excerpt: Epigenetic Technological Applications is a compilation of state-of-the-art technologies involved in epigenetic research. Epigenetics is an exciting new field of biology research, and many technologies are invented and developed specifically for epigenetics study. With chapters covering the latest developments in crystallography, computational modeling, the uses of histones, and more, Epigenetic Technological Applications addresses the question of how these new ideas, procedures, and innovations can be applied to current epigenetics research, and how they can keep pushing discovery forward and beyond the epigenetic realm. Discusses technologies that are critical for epigenetic research and application Includes epigenetic applications for state-of-the-art technologies Contains a global perspective on the future of epigenetics
Download or read book Peptide Protein and Enzyme Design written by and published by Academic Press. This book was released on 2016-08-27 with total page 686 pages. Available in PDF, EPUB and Kindle. Book excerpt: De Novo Enzyme Design, the newest volume in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume includes the design of metal binding maquettes, insertion of non-natural cofactors, Cu metallopeptides, non-covalent interactions in peptide assemblies, peptide binding and bundling, heteronuclear metalloenzymes, florinated peptides, De Novo imaging agents, and protein-protein interaction. Continues the legacy of this premier serial with quality chapters on de novo enzyme design Represents the newest volume in the Methods in Enzymology series, providing premier, quality chapters authored by leaders in the field Ideal reference for those interested in the study of enzyme design that looks at both structure and mechanism
Download or read book Analysis of Methylotrophic Methanogenesis in Methanosarcina Barkeri Fusaro written by and published by . This book was released on 2007 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Genomes and Genomics of Nitrogen fixing Organisms written by Rafael Palacios and published by Springer Science & Business Media. This book was released on 2005-02-15 with total page 268 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genomes and Genomics of Nitrogen-fixing Organisms This is Volume 3 of a seven-volume series on all aspects of Nitrogen Fixation. The series aims to be the definitive authority in the field and to act as a benchmark for some years to come. Rather than attempting to cram the whole field into a single volume, the subject matter is divided among seven volumes to allow authors the luxury of writing in depth with a comprehensive reference base. All authors are recognized practicing scientists in the area of their contribution, which ensures the high quality, relevance, and readability of the chapters. In establishing the rationale for, and the organization of, this book, we realized the need to divide it into two sections. The first section should be organism based and should review our current knowledge of the genomes of nitrogen-fixing organisms and what these nucleotide sequences tell us. The second section should then be technology based. It should review what technologies are available to mine the data inherent in the nucleotide sequences and how they are now being used to produce gene-function data from differential gene expression.
