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Genomic Prospecting for Microbial Biodiesel Production

Description: Biodiesel is defined as fatty acid mono-alkylesters and is produced from triacylglycerols. In the current article we provide an overview of the structure, diversity and regulation of the metabolic pathways leading to intracellular fatty acid and triacylglycerol accumulation in three types of organisms (bacteria, algae and fungi) of potential biotechnological interest and discuss possible intervention points to increase the cellular lipid content. The key steps that regulate carbon allocation and distribution in lipids include the formation of malonyl-CoA, the synthesis of fatty acids and their attachment onto the glycerol backbone, and the formation of triacylglycerols. The lipid biosynthetic genes and pathways are largely known for select model organisms. Comparative genomics allows the examination of these pathways in organisms of biotechnological interest and reveals the evolution of divergent and yet uncharacterized regulatory mechanisms. Utilization of microbial systems for triacylglycerol and fatty acid production is in its infancy; however, genomic information and technologies combined with synthetic biology concepts provide the opportunity to further exploit microbes for the competitive production of biodiesel.
Date: March 20, 2008
Creator: Lykidis, Athanasios; Lykidis, Athanasios & Ivanova, Natalia
Partner: UNT Libraries Government Documents Department

Comparative Genomics and Evolution of Eukaryotic Phospholipid biosynthesis

Description: Phospholipid biosynthetic enzymes produce diverse molecular structures and are often present in multiple forms encoded by different genes. This work utilizes comparative genomics and phylogenetics for exploring the distribution, structure and evolution of phospholipid biosynthetic genes and pathways in 26 eukaryotic genomes. Although the basic structure of the pathways was formed early in eukaryotic evolution, the emerging picture indicates that individual enzyme families followed unique evolutionary courses. For example, choline and ethanolamine kinases and cytidylyltransferases emerged in ancestral eukaryotes, whereas, multiple forms of the corresponding phosphatidyltransferases evolved mainly in a lineage specific manner. Furthermore, several unicellular eukaryotes maintain bacterial-type enzymes and reactions for the synthesis of phosphatidylglycerol and cardiolipin. Also, base-exchange phosphatidylserine synthases are widespread and ancestral enzymes. The multiplicity of phospholipid biosynthetic enzymes has been largely generated by gene expansion in a lineage specific manner. Thus, these observations suggest that phospholipid biosynthesis has been an actively evolving system. Finally, comparative genomic analysis indicates the existence of novel phosphatidyltransferases and provides a candidate for the uncharacterized eukaryotic phosphatidylglycerol phosphate phosphatase.
Date: December 1, 2006
Creator: Lykidis, Athanasios
Partner: UNT Libraries Government Documents Department

GenePRIMP: A GENE PRediction IMprovement Pipeline for Prokaryotic genomes

Description: We present 'gene prediction improvement pipeline' (GenePRIMP; http://geneprimp.jgi-psf.org/), a computational process that performs evidence-based evaluation of gene models in prokaryotic genomes and reports anomalies including inconsistent start sites, missed genes and split genes. We found that manual curation of gene models using the anomaly reports generated by GenePRIMP improved their quality, and demonstrate the applicability of GenePRIMP in improving finishing quality and comparing different genome-sequencing and annotation technologies.
Date: April 1, 2010
Creator: Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia; Ovchinnikova, Galina; Hooper, Sean D.; Lykidis, Athanasios et al.
Partner: UNT Libraries Government Documents Department

Multiple Syntrophic Interactions in a Terephthalate-Degrading Methanogenic Consortium

Description: Terephthalate (TA) is one of the top 50 chemicals produced worldwide. Its production results in a TA-containing wastewater that is treated by anaerobic processes through a poorly understood methanogenic syntrophy. Using metagenomics, we characterized the methanogenic consortium tinside a hyper-mesophilic (i.e., between mesophilic and thermophilic), TA-degrading bioreactor. We identified genes belonging to dominant Pelotomaculum species presumably involved in TA degradation through decarboxylation, dearomatization, and modified ?-oxidation to H{sub 2}/CO{sub 2} and acetate. These intermediates are converted to CH{sub 4}/CO{sub 2} by three novel hyper-mesophilic methanogens. Additional secondary syntrophic interactions were predicted in Thermotogae, Syntrophus and candidate phyla OP5 and WWE1 populations. The OP5 encodes genes capable of anaerobic autotrophic butyrate production and Thermotogae, Syntrophus and WWE1 have the genetic potential to oxidize butyrate to COsub 2}/H{sub 2} and acetate. These observations suggest that the TA-degrading consortium consists of additional syntrophic interactions beyond the standard H{sub 2}-producing syntroph ? methanogen partnership that may serve to improve community stability.
Date: August 5, 2010
Creator: Lykidis, Athanasios; Chen, Chia-Lung; Tringe, Susannah G.; McHardy, Alice C.; Copeland, Alex 5; Kyrpides, Nikos C. et al.
Partner: UNT Libraries Government Documents Department

Genome analysis of the Anerobic Thermohalophilic bacterium Halothermothrix orenii

Description: Halothermothirx orenii is a strictly anaerobic thermohalophilic bacterium isolated from sediment of a Tunisian salt lake. It belongs to the order Halanaerobiales in the phylum Firmicutes. The complete sequence revealed that the genome consists of one circular chromosome of 2578146 bps encoding 2451 predicted genes. This is the first genome sequence of an organism belonging to the Haloanaerobiales. Features of both Gram positive and Gram negative bacteria were identified with the presence of both a sporulating mechanism typical of Firmicutes and a characteristic Gram negative lipopolysaccharide being the most prominent. Protein sequence analyses and metabolic reconstruction reveal a unique combination of strategies for thermophilic and halophilic adaptation. H. orenii can serve as a model organism for the study of the evolution of the Gram negative phenotype as well as the adaptation under thermohalophilic conditions and the development of biotechnological applications under conditions that require high temperatures and high salt concentrations.
Date: November 3, 2008
Creator: Mavromatis, Konstantinos; Ivanova, Natalia; Anderson, Iain; Lykidis, Athanasios; Hooper, Sean D.; Sun, Hui et al.
Partner: UNT Libraries Government Documents Department

The Complete Multipartite Genome Sequence of Cupriavidus necator JMP134, a Versatile Pollutant Degrader

Description: Cupriavidus necator JMP134 (formerly Ralstonia eutropha JMP134) is a Gram-negative {beta}-proteobacterium able to degrade a variety of chloroaromatic compounds and chemically-related pollutants. It was originally isolated based on its ability to use 2,4 dichlorophenoxyacetic acid (2,4-D) as a sole carbon and energy source [1]. In addition to 2,4-D, this strain can also grow on a variety of aromatic substrates, such as 4-chloro-2-methylphenoxyacetate (MCPA), 3-chlorobenzoic acid (3-CB) [2], 2,4,6-trichlorophenol [3], and 4-fluorobenzoate [4]. The genes necessary for 2,4-D utilization have been identified. They are located in two clusters on plasmid pPJ4: tfd{sub I} and tfd{sub II} [5,6,7,8]. The sequence and analysis of plasmid pJP4 was reported and a congruent model for bacterial adaptation to chloroaromatic pollutants was proposed [9]. According to this model, catabolic gene clusters assemble in a modular manner into broad-host-range plasmid backbones by means of repeated chromosomal capture events. Cupriavidus and related Burkholderia genomes are typically multipartite, composed of two large replicons (chromosomes) accompanied by classical plasmids. Previous work with Burkholderia xenovorans LB400 revealed a differential gene distribution with core functions preferentially encoded by the larger chromosome and secondary functions by the smaller [10]. It has been proposed that the secondary chromosomes in many bacteria originated from ancestral plasmids which, in turn, had been the recipient of genes transferred earlier from ancestral primary chromosomes [11]. The existence of multiple Cupriavidus and Burkholderia genomes provides the opportunity for comparative studies that will lead to a better understanding of the evolutionary mechanisms for the formation of multipartite genomes and the relation with biodegradation abilities.
Date: February 1, 2010
Creator: Lykidis, Athanasios; Perez-Pantoja, Danilo; Ledger, Thomas; Mavromatis, Kostantinos; Anderson, Iain J.; Ivanova, Natalia N. et al.
Partner: UNT Libraries Government Documents Department

The integrated microbial genomes (IMG) system in 2007: datacontent and analysis tool extensions

Description: The Integrated Microbial Genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and annotating genomes, genes and functions, individually or in a comparative context. Since its first release in 2005, IMG's data content and analytical capabilities have been constantly expanded through quarterly releases. IMG is provided by the DOE-Joint Genome Institute (JGI) and is available from http://img.jgi.doe.gov.
Date: August 1, 2007
Creator: Markowitz, Victor M.; Szeto, Ernest; Palaniappan, Krishna; Grechkin, Yuri; Chu, Ken; Chen, I-Min A. et al.
Partner: UNT Libraries Government Documents Department

Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction

Description: We report the complete genome of Thermofilum pendens, a deep-branching, hyperthermophilic member of the order Thermoproteales within the archaeal kingdom Crenarchaeota. T. pendens is a sulfur-dependent, anaerobic heterotroph isolated from a solfatara in Iceland. It is an extracellular commensal, requiring an extract of Thermoproteus tenax for growth, and the genome sequence reveals that biosynthetic pathways for purines, most amino acids, and most cofactors are absent. In fact T. pendens has fewer biosynthetic enzymes than obligate intracellular parasites, although it does not display other features common among obligate parasites and thus does not appear to be in the process of becoming a parasite. It appears that T. pendens has adapted to life in an environment rich in nutrients. T. pendens was known to utilize peptides as an energy source, but the genome reveals substantial ability to grow on carbohydrates. T. pendens is the first crenarchaeote and only the second archaeon found to have a transporter of the phosphotransferase system. In addition to fermentation, T. pendens may gain energy from sulfur reduction with hydrogen and formate as electron donors. It may also be capable of sulfur-independent growth on formate with formate hydrogenlyase. Additional novel features are the presence of a monomethylamine:corrinoid methyltransferase, the first time this enzyme has been found outside of Methanosarcinales, and a presenilin-related protein. Predicted highly expressed proteins do not include housekeeping genes, and instead include ABC transporters for carbohydrates and peptides, and CRISPR-associated proteins.
Date: January 1, 2008
Creator: Kyrpides, Nikos; Anderson, Iain; Rodriguez, Jason; Susanti, Dwi; Porat, Iris; Reich, Claudia et al.
Partner: UNT Libraries Government Documents Department

Genome Sequence and Analysis of the Soil Cellulolytic ActinomyceteThermobifida fusca

Description: Thermobifida fusca is a moderately thermophilic soilbacterium that belongs to Actinobacteria. 3 It is a major degrader ofplant cell walls and has been used as a model organism for the study of 4secreted, thermostable cellulases. The complete genome sequence showedthat T. fusca has a 5 single circular chromosome of 3642249 bp predictedto encode 3117 proteins and 65 RNA6 species with a coding densityof 85percent. Genome analysis revealed the existence of 29 putative 7glycoside hydrolases in addition to the previously identified cellulasesand xylanases. The 8 glycosyl hydrolases include enzymes predicted toexhibit mainly dextran/starch and xylan 9 degrading functions. T. fuscapossesses two protein secretion systems: the sec general secretion 10system and the twin-arginine translocation system. Several of thesecreted cellulases have 11 sequence signatures indicating theirsecretion may be mediated by the twin-arginine12 translocation system. T.fusca has extensive transport systems for import of carbohydrates 13coupled to transcriptional regulators controlling the expression of thetransporters and14 glycosylhydrolases. In addition to providing anoverview of the physiology of a soil 15 actinomycete, this study presentsinsights on the transcriptional regulation and secretion of16 cellulaseswhich may facilitate the industrial exploitation of thesesystems.
Date: February 1, 2007
Creator: Lykidis, Athanasios; Mavromatis, Konstantinos; Ivanova, Natalia; Anderson, Iain; Land, Miriam; DiBartolo, Genevieve et al.
Partner: UNT Libraries Government Documents Department

Genomic Characterization of Methanomicrobiales Reveals Three Classes of Methanogens

Description: Methanomicrobiales is the least studied order of methanogens. While these organisms appear to be more closely related to the Methanosarcinales in ribosomal-based phylogenetic analyses, they are metabolically more similar to Class I methanogens. In order to improve our understanding of this lineage, we have completely sequenced the genomes of two members of this order, Methanocorpusculum labreanum Z and Methanoculleus marisnigri JR1, and compared them with the genome of a third, Methanospirillum hungatei JF-1. Similar to Class I methanogens, Methanomicrobiales use a partial reductive citric acid cycle for 2-oxoglutarate biosynthesis, and they have the Eha energy-converting hydrogenase. In common with Methanosarcinales, Methanomicrobiales possess the Ech hydrogenase and at least some of them may couple formylmethanofuran formation and heterodisulfide reduction to transmembrane ion gradients. Uniquely, M. labreanum and M. hungatei contain hydrogenases similar to the Pyrococcus furiosus Mbh hydrogenase, and all three Methanomicrobiales have anti-sigma factor and anti-anti-sigma factor regulatory proteins not found in other methanogens. Phylogenetic analysis based on seven core proteins of methanogenesis and cofactor biosynthesis places the Methanomicrobiales equidistant from Class I methanogens and Methanosarcinales. Our results indicate that Methanomicrobiales, rather than being similar to Class I methanogens or Methanomicrobiales, share some features of both and have some unique properties. We find that there are three distinct classes of methanogens: the Class I methanogens, the Methanomicrobiales (Class II), and the Methanosarcinales (Class III).
Date: May 1, 2009
Creator: Anderson, Iain; Ulrich, Luke E.; Lupa, Boguslaw; Susanti, Dwi; Porat, Iris; Hooper, Sean D. et al.
Partner: UNT Libraries Government Documents Department

IMG/M: A data management and analysis system for metagenomes

Description: IMG/M is a data management and analysis system for microbial community genomes (metagenomes) hosted at the Joint Genome Institute (JGI). IMG/M consists of metagenome data integrated with isolate microbial genomes from the Integrated Microbial Genomes (IMG) system. IMG/M provides IMG's comparative data analysis tools extended to handle metagenome data, together with metagenome-specific analysis tools. IMG/M is available at http://img.jgi.doe.gov/m. Studies of the collective genomes (also known as metagenomes) of environmental microbial communities (also known as microbiomes) are expected to lead to advances in environmental cleanup, agriculture, industrial processes, alternative energy production, and human health (1). Metagenomes of specific microbiome samples are sequenced by organizations worldwide, such as the Department of Energy's (DOE) Joint Genome Institute (JGI), the Venter Institute and the Washington University in St. Louis using different sequencing strategies, technology platforms, and annotation procedures. According to the Genomes OnLine Database, about 28 metagenome studies have been published to date, with over 60 other projects ongoing and more in the process of being launched (2). The Department of Energy's (DOE) Joint Genome Institute (JGI) is one of the major contributors of metagenome sequence data, currently sequencing more than 50% of the reported metagenome projects worldwide. Due to the higher complexity, inherent incompleteness, and lower quality of metagenome sequence data, traditional assembly, gene prediction, and annotation methods do not perform on these datasets as well as they do on isolate microbial genome sequences (3, 4). In spite of these limitations, metagenome data are amenable to a variety of analyses, as illustrated by several recent studies (5-10). Metagenome data analysis is usually set up in the context of reference isolate genomes and considers the questions of composition and functional or metabolic potential of individual microbiomes, as well as differences between microbiome samples. Such analysis relies on efficient management of genome and metagenome ...
Date: August 1, 2007
Creator: Markowitz, Victor M.; Ivanova, Natalia N.; Szeto, Ernest; Palaniappan, Krishna; Chu, Ken; Dalevi, Daniel et al.
Partner: UNT Libraries Government Documents Department

Comparison of the complete genome sequences of Pseudomonassyringae pv. syringae B728a and pv. tomato DC3000.

Description: The complete genomic sequence of Pseudomonas syringaepathovar syringae B728a (Pss B728a), has been determined and is comparedwith that of Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). Thesetwo pathovars of this economically important species of plant pathogenicbacteria differ in host range and apparent patterns of interaction withplants, with Pss having a more pronounced epiphytic stage of growth andhigher abiotic stress tolerance and Pst DC3000 having a more pronouncedapoplastic growth habitat. The Pss B728a genome (6.1 megabases) containsa circular chromosome and no plasmid, whereas the Pst DC3000 genome is6.5 mbp in size, composed of a circular chromosome and two plasmids.While a high degree of similarity exists between the two sequencedPseudomonads, 976 protein-encoding genes are unique to Pss B728a whencompared to Pst DC3000, including large genomic islands likely tocontribute to virulence and host specificity. Over 375 repetitiveextragenic palindromic sequences (REPs) unique to Pss B728a when comparedto Pst DC3000 are widely distributed throughout the chromosome except in14 genomic islands, which generally had lower GC content than the genomeas a whole. Content of the genomic islands vary, with one containing aprophage and another the plasmid pKLC102 of P. aeruginosa PAO1. Among the976 genes of Pss B728a with no counterpart in Pst DC3000 are thoseencoding for syringopeptin (SP), syringomycin (SR), indole acetic acidbiosynthesis, arginine degradation, and production of ice nuclei. Thegenomic comparison suggests that several unique genes for Pss B728a suchas ectoine synthase, DNA repair, and antibiotic production may contributeto epiphytic fitness and stress tolerance of this organism. Pseudomonassyringae, a member of the gamma subgroup of the Proteobacteria, is awidespread bacterial pathogen of many plant species. The species P.syringae is subdivided into approximately 50 pathovars based onpathogenicity and host range. P. syringae is capable of producing avariety of different symptoms depending on the host species and site ofinfection. For example, it causes leaf spot diseases that ...
Date: April 1, 2005
Creator: Feil, Helene; Feil, William S.; Chain, Patrick; Larimer, Frank; DiBartolo, Genevieve; Copeland, Alex et al.
Partner: UNT Libraries Government Documents Department

A genomic analysis of the archael system Ignicoccus hospitalis-Nanoarchaeum equitans

Description: BACKGROUND: The relationship between the hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans is the only known example of a specific association between two species of Archaea. Little is known about the mechanisms that enable this relationship. RESULTS: We sequenced the complete genome of I. hospitalis and found it to be the smallest among independent, free-living organisms. A comparative genomic reconstruction suggests that the I. hospitalis lineage has lost most of the genes associated with a heterotrophic metabolism that is characteristic of most of the Crenarchaeota. A streamlined genome is also suggested by a low frequency of paralogs and fragmentation of many operons. However, this process appears to be partially balanced by lateral gene transfer from archaeal and bacterial sources. CONCLUSIONS: A combination of genomic and cellular features suggests highly efficient adaptation to the low energy yield of sulfur-hydrogen respiration and efficient inorganic carbon and nitrogen assimilation. Evidence of lateral gene exchange between N. equitans and I. hospitalis indicates that the relationship has impacted both genomes. This association is the simplest symbiotic system known to date and a unique model for studying mechanisms of interspecific relationships at the genomic and metabolic levels.
Date: September 1, 2008
Creator: Sun, Hui; Anderson, Iain; Makarova, Kira S.; Elkins, James G.; Ivanova, Natalia; Wall, Mark A. et al.
Partner: UNT Libraries Government Documents Department