Archaea-An International Microbiological Journal最新文献

{"title":"Characterization of Fatty Acids in Crenarchaeota by GC-MS and NMR","authors":"Timothy Hamerly, B. Tripet, Louie Wurch, R. Hettich, M. Podar, B. Bothner, V. Copié","doi":"10.1155/2015/472726","DOIUrl":"https://doi.org/10.1155/2015/472726","url":null,"abstract":"Lipids composed of condensed isoprenyl units connected to glycerol backbones by ether linkages are a distinguishing feature of Archaea. Data suggesting that fatty acids with linear hydrocarbon chains are present in some Archaea have been available for decades. However, lack of genomic and biochemical evidence for the metabolic machinery required to synthesize and degrade fatty acids has left the field unclear on this potentially significant biochemical aspect. Because lipids are energy currency and cell signaling molecules, their presence in Archaea is significant for understanding archaeal biology. A recent large-scale bioinformatics analysis reignited the debate as to the importance of fatty acids in Archaea by presenting genetic evidence for the presence of enzymes required for anabolic and catabolic fatty acid metabolism across the archaeal domain. Here, we present direct biochemical evidence from gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR) spectroscopy for the presence of fatty acids in two members of the Crenarchaeota, Sulfolobus solfataricus and Ignicoccus hospitalis. This is the first report providing biochemical data for the existence of fatty acids in these Crenarchaeota, opening new discussions on energy balance and the potential for the discovery of new thermostable enzymes for industry.","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2015 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2015-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2015/472726","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64985341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sequence, Structure, and Binding Analysis of Cyclodextrinase (TK1770) from T. kodakarensis (KOD1) Using an In Silico Approach","authors":"Ramzan Ali, Muhammad Imtiaz Shafiq","doi":"10.1155/2015/179196","DOIUrl":"https://doi.org/10.1155/2015/179196","url":null,"abstract":"Thermostable cyclodextrinase (Tk1770 CDase) from hyperthermophilic archaeon Thermococcus kodakarensis (KOD1) hydrolyzes cyclodextrins into linear dextrins. The sequence of Tk1770 CDase retrieved from UniProt was aligned with sequences of sixteen CD hydrolyzing enzymes and a phylogenetic tree was constructed using Bayesian inference. The homology model of Tk1770 CDase was constructed and optimized with Modeller v9.14 program. The model was validated with ProSA server and PROCHECK analysis. Four conserved regions and the catalytic triad consisting of Asp411, Glu437, and Asp502 of GH13 family were identified in catalytic site. Also an additional fifth conserved region downstream to the fourth region was also identified. The structure of Tk1770 CDase consists of an additional N′-domain and a helix-loop-helix motif that is conserved in all archaeal CD hydrolyzing enzymes. The N′-domain contains an extended loop region that forms a part of catalytic domain and plays an important role in stability and substrate binding. The docking of substrate into catalytic site revealed the interactions with different conserved residues involved in substrate binding and formation of enzyme-substrate complex.","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"18 1 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2015-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2015/179196","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64826993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular Analysis of Methanogen Richness in Landfill and Marshland Targeting 16S rDNA Sequences","authors":"S. Yadav, Sharbadeb Kundu, S. Ghosh, S. S. Maitra","doi":"10.1155/2015/563414","DOIUrl":"https://doi.org/10.1155/2015/563414","url":null,"abstract":"Methanogens, a key contributor in global carbon cycling, methane emission, and alternative energy production, generate methane gas via anaerobic digestion of organic matter. The methane emission potential depends upon methanogenic diversity and activity. Since they are anaerobes and difficult to isolate and culture, their diversity present in the landfill sites of Delhi and marshlands of Southern Assam, India, was analyzed using molecular techniques like 16S rDNA sequencing, DGGE, and qPCR. The sequencing results indicated the presence of methanogens belonging to the seventh order and also the order Methanomicrobiales in the Ghazipur and Bhalsawa landfill sites of Delhi. Sequences, related to the phyla Crenarchaeota (thermophilic) and Thaumarchaeota (mesophilic), were detected from marshland sites of Southern Assam, India. Jaccard analysis of DGGE gel using Gel2K showed three main clusters depending on the number and similarity of band patterns. The copy number analysis of hydrogenotrophic methanogens using qPCR indicates higher abundance in landfill sites of Delhi as compared to the marshlands of Southern Assam. The knowledge about “methanogenic archaea composition” and “abundance” in the contrasting ecosystems like “landfill” and “marshland” may reorient our understanding of the Archaea inhabitants. This study could shed light on the relationship between methane-dynamics and the global warming process.","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2015 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2015-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2015/563414","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65031390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biotechnological Uses of Archaeal Proteins","authors":"F. Pecorari, V. Arcus, J. Wiegel","doi":"10.1155/2015/809758","DOIUrl":"https://doi.org/10.1155/2015/809758","url":null,"abstract":"Many industrial/biotechnological processes take place under extreme conditions of temperature, pH, salinity, or pressure which are not suitable for activities of proteins from model eukaryotic or common neutrophilic, mesophilic, and prokaryotic microorganisms. In contrast, Archaea offer a large panel of extremophile organisms that express proteins that are able to remain properly folded and functional under the harshest biophysical conditions. \u0000 \u0000The study of this group of organisms has uncovered archaeal enzymes and proteins with unusual properties compared to their traditional homologues. In addition, with their ease of production and better-behaved samples for X-ray crystallography, for example, archaeal proteins are often more convenient for structural biology studies than their eukaryotic equivalents. The knowledge thus gained can open routes to commercial biotechnological applications. These last years, with the emergence of next generation sequencing techniques to decode whole genomes and metagenomes and the pressure to develop “greener” industrial processes, the rate of new archaeal proteins reported has significantly increased, thereby widening again their potential of applications. In this special issue of Archaea, we present selected papers dealing with the uses of archaeal proteins as tools for various fields of biotechnologies and research. \u0000 \u0000DNA and RNA ligases are essential enzymes in living cells and have applications in molecular biology. A review by M. Tanabe et al. discusses the uses of DNA ligases and recent progress in deciphering their catalytic mechanisms via structural studies, and they describe how protein engineering can improve ligation efficiency of an archaeal DNA ligase over a broad temperature range. In another paper on ligases, C. R. Chambers and W. M. Patrick present the current state of knowledge on archaeal nucleic acid ligases including RNA ligases, highlighting their remarkable properties relevant to biotechnologists, and they discuss the modifications of the activities of archaeal RNA ligases by directed mutagenesis to develop more efficient molecular biology protocols. \u0000 \u0000J. A. Littlechild reviews research regarding the discovery and potential applications of a range of thermophilic archaeal proteins, illustrating the power of archaeal enzymes for various industrial biocatalysis. Then, an article by V. M. Gumerov et al. describes the characterization of a novel thermostable and multifunctional β-glycosidase from Acidilobus saccharovorans that displays a high tolerance to glucose, a desired property for such enzymes used to process lignocellulose biomass. C.-H. Wu et al. present a review summarizing the strategies used in engineering and characterizing three different forms of soluble hydrogenase I from the hyperthermophile Pyrococcus furiosus, an enzyme which has been used in vitro for hydrogen production. \u0000 \u0000Archaea are not only interesting for catalysis applications. J. C. Charlesworth and B. P. Burns giv","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2015 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2015-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2015/809758","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65160805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Novel Highly Thermostable Multifunctional Beta-Glycosidase from Crenarchaeon Acidilobus saccharovorans","authors":"V. Gumerov, A. Rakitin, A. Mardanov, N. Ravin","doi":"10.1155/2015/978632","DOIUrl":"https://doi.org/10.1155/2015/978632","url":null,"abstract":"We expressed a putative β-galactosidase Asac_1390 from hyperthermophilic crenarchaeon Acidilobus saccharovorans in Escherichia coli and purified the recombinant enzyme. Asac_1390 is composed of 490 amino acid residues and showed high sequence similarity to family 1 glycoside hydrolases from various thermophilic Crenarchaeota. The maximum activity was observed at pH 6.0 and 93°C. The half-life of the enzyme at 90°C was about 7 hours. Asac_1390 displayed high tolerance to glucose and exhibits hydrolytic activity towards cellobiose and various aryl glucosides. The hydrolytic activity with p-nitrophenyl (pNP) substrates followed the order pNP-β-D-galactopyranoside (328 U mg−1), pNP-β-D-glucopyranoside (246 U mg−1), pNP-β-D-xylopyranoside (72 U mg−1), and pNP-β-D-mannopyranoside (28 U mg−1). Thus the enzyme was actually a multifunctional β-glycosidase. Therefore, the utilization of Asac_1390 may contribute to facilitating the efficient degradation of lignocellulosic biomass and help enhance bioconversion processes.","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2015 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2015-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2015/978632","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64192733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Archaeal MCM Proteins as an Analog for the Eukaryotic Mcm2–7 Helicase to Reveal Essential Features of Structure and Function","authors":"Justin M. Miller, E. J. Enemark","doi":"10.1155/2015/305497","DOIUrl":"https://doi.org/10.1155/2015/305497","url":null,"abstract":"In eukaryotes, the replicative helicase is the large multisubunit CMG complex consisting of the Mcm2–7 hexameric ring, Cdc45, and the tetrameric GINS complex. The Mcm2–7 ring assembles from six different, related proteins and forms the core of this complex. In archaea, a homologous MCM hexameric ring functions as the replicative helicase at the replication fork. Archaeal MCM proteins form thermostable homohexamers, facilitating their use as models of the eukaryotic Mcm2–7 helicase. Here we review archaeal MCM helicase structure and function and how the archaeal findings relate to the eukaryotic Mcm2–7 ring.","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2015 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2015-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2015/305497","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64895641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From Structure-Function Analyses to Protein Engineering for Practical Applications of DNA Ligase.","authors":"Maiko Tanabe,&nbsp;Yoshizumi Ishino,&nbsp;Hirokazu Nishida","doi":"10.1155/2015/267570","DOIUrl":"https://doi.org/10.1155/2015/267570","url":null,"abstract":"<p><p>DNA ligases are indispensable in all living cells and ubiquitous in all organs. DNA ligases are broadly utilized in molecular biology research fields, such as genetic engineering and DNA sequencing technologies. Here we review the utilization of DNA ligases in a variety of in vitro gene manipulations, developed over the past several decades. During this period, fewer protein engineering attempts for DNA ligases have been made, as compared to those for DNA polymerases. We summarize the recent progress in the elucidation of the DNA ligation mechanisms obtained from the tertiary structures solved thus far, in each step of the ligation reaction scheme. We also present some examples of engineered DNA ligases, developed from the viewpoint of their three-dimensional structures. </p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":" ","pages":"267570"},"PeriodicalIF":2.4,"publicationDate":"2015-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2015/267570","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34124246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Archaeal Nucleic Acid Ligases and Their Potential in Biotechnology.","authors":"Cecilia R Chambers,&nbsp;Wayne M Patrick","doi":"10.1155/2015/170571","DOIUrl":"https://doi.org/10.1155/2015/170571","url":null,"abstract":"<p><p>With their ability to catalyse the formation of phosphodiester linkages, DNA ligases and RNA ligases are essential tools for many protocols in molecular biology and biotechnology. Currently, the nucleic acid ligases from bacteriophage T4 are used extensively in these protocols. In this review, we argue that the nucleic acid ligases from Archaea represent a largely untapped pool of enzymes with diverse and potentially favourable properties for new and emerging biotechnological applications. We summarise the current state of knowledge on archaeal DNA and RNA ligases, which makes apparent the relative scarcity of information on in vitro activities that are of most relevance to biotechnologists (such as the ability to join blunt- or cohesive-ended, double-stranded DNA fragments). We highlight the existing biotechnological applications of archaeal DNA ligases and RNA ligases. Finally, we draw attention to recent experiments in which protein engineering was used to modify the activities of the DNA ligase from Pyrococcus furiosus and the RNA ligase from Methanothermobacter thermautotrophicus, thus demonstrating the potential for further work in this area. </p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":" ","pages":"170571"},"PeriodicalIF":2.4,"publicationDate":"2015-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2015/170571","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34281263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ecology and Distribution of Thaumarchaea in the Deep Hypolimnion of Lake Maggiore.","authors":"Manuela Coci,&nbsp;Nina Odermatt,&nbsp;Michaela M Salcher,&nbsp;Jakob Pernthaler,&nbsp;Gianluca Corno","doi":"10.1155/2015/590434","DOIUrl":"https://doi.org/10.1155/2015/590434","url":null,"abstract":"<p><p>Ammonia-oxidizing Archaea (AOA) play an important role in the oxidation of ammonia in terrestrial, marine, and geothermal habitats, as confirmed by a number of studies specifically focused on those environments. Much less is known about the ecological role of AOA in freshwaters. In order to reach a high resolution at the Thaumarchaea community level, the probe MGI-535 was specifically designed for this study and applied to fluorescence in situ hybridization and catalyzed reporter deposition (CARD-FISH) analysis. We then applied it to a fine analysis of diversity and relative abundance of AOA in the deepest layers of the oligotrophic Lake Maggiore, confirming previous published results of AOA presence, but showing differences in abundance and distribution within the water column without significant seasonal trends with respect to Bacteria. Furthermore, phylogenetic analysis of AOA clone libraries from deep lake water and from a lake tributary, River Maggia, suggested the riverine origin of AOA of the deep hypolimnion of the lake. </p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":" ","pages":"590434"},"PeriodicalIF":2.4,"publicationDate":"2015-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2015/590434","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34013407","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessment of the Carbon Monoxide Metabolism of the Hyperthermophilic Sulfate-Reducing Archaeon Archaeoglobus fulgidus VC-16 by Comparative Transcriptome Analyses.","authors":"William P Hocking,&nbsp;Irene Roalkvam,&nbsp;Carina Magnussen,&nbsp;Runar Stokke,&nbsp;Ida H Steen","doi":"10.1155/2015/235384","DOIUrl":"https://doi.org/10.1155/2015/235384","url":null,"abstract":"<p><p>The hyperthermophilic, sulfate-reducing archaeon, Archaeoglobus fulgidus, utilizes CO as an energy source and it is resistant to the toxic effects of high CO concentrations. Herein, transcription profiles were obtained from A. fulgidus during growth with CO and sulfate or thiosulfate, or without an electron acceptor. This provided a basis for a model of the CO metabolism of A. fulgidus. The model suggests proton translocation by \"Mitchell-type\" loops facilitated by Fqo catalyzing a Fd(red):menaquinone oxidoreductase reaction, as the major mode of energy conservation, rather than formate or H2 cycling during respiratory growth. The bifunctional CODH (cdhAB-2) is predicted to play an ubiquitous role in the metabolism of CO, and a novel nitrate reductase-associated respiratory complex was induced specifically in the presence of sulfate. A potential role of this complex in relation to Fd(red) and APS reduction is discussed. Multiple membrane-bound heterodisulfide reductase (DsrMK) could promote both energy-conserving and non-energy-conserving menaquinol oxidation. Finally, the FqoF subunit may catalyze a Fd(red):F420 oxidoreductase reaction. In the absence of electron acceptor, downregulation of F420H2 dependent steps of the acetyl-CoA pathway is linked to transient formate generation. Overall, carboxidotrophic growth seems as an intrinsic capacity of A. fulgidus with little need for novel resistance or respiratory complexes.</p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":" ","pages":"235384"},"PeriodicalIF":2.4,"publicationDate":"2015-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2015/235384","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33983927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}