{"title":"The Draft Genome of the Non-Host-Associated <i>Methanobrevibacter arboriphilus</i> Strain DH1 Encodes a Large Repertoire of Adhesin-Like Proteins.","authors":"Anja Poehlein, Rolf Daniel, Henning Seedorf","doi":"10.1155/2017/4097425","DOIUrl":"10.1155/2017/4097425","url":null,"abstract":"<p><p><i>Methanobrevibacter arboriphilus</i> strain DH1 is an autotrophic methanogen that was isolated from the wetwood of methane-emitting trees. This species has been of considerable interest for its unusual oxygen tolerance and has been studied as a model organism for more than four decades. Strain DH1 is closely related to other host-associated <i>Methanobrevibacter</i> species from intestinal tracts of animals and the rumen, making this strain an interesting candidate for comparative analysis to identify factors important for colonizing intestinal environments. Here, the genome sequence of <i>M. arboriphilus</i> strain DH1 is reported. The draft genome is composed of 2.445.031 bp with an average GC content of 25.44% and predicted to harbour 1964 protein-encoding genes. Among the predicted genes, there are also more than 50 putative genes for the so-called adhesin-like proteins (ALPs). The presence of ALP-encoding genes in the genome of this non-host-associated methanogen strongly suggests that target surfaces for ALPs other than host tissues also need to be considered as potential interaction partners. The high abundance of ALPs may also indicate that these types of proteins are more characteristic for specific phylogenetic groups of methanogens rather than being indicative for a particular environment the methanogens thrives in.</p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2017-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5467289/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35105255","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}
Yang Lü, Hua Lu, Shiwei Wang, Jing Han, Hua Xiang, Cheng Jin
{"title":"An Acidic Exopolysaccharide from <i>Haloarcula hispanica</i> ATCC33960 and Two Genes Responsible for Its Synthesis.","authors":"Yang Lü, Hua Lu, Shiwei Wang, Jing Han, Hua Xiang, Cheng Jin","doi":"10.1155/2017/5842958","DOIUrl":"https://doi.org/10.1155/2017/5842958","url":null,"abstract":"<p><p>A 1.1 × 10<sup>6</sup> Da acidic exopolysaccharide (EPS) was purified from an extremely halophilic archaeon <i>Haloarcula hispanica</i> ATCC33960 with a production of 30 mg L<sup>-1</sup> when grown in AS-168 medium, which mainly composed of mannose and galactose with a small amount of glucose in a molar ratio of 55.9 : 43.2 : 0.9. Two glycosyltransferase genes (<i>HAH_1662</i> and <i>HAH_1667</i>) were identified to be responsible for synthesis of the acidic EPS. Deletion of either <i>HAH_1662</i> or <i>HAH_1667</i> led to loss of the acidic EPS. The mutants displayed a different cell surface morphology, retarded growth in low salty environment, an increased adhesion, and swimming ability. Our results suggest that biosynthesis of the acidic EPS might act as an adaptable mechanism to protect the cells against harsh environments.</p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2017-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2017/5842958","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35105256","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}
Thien-Hoang Ho, Kim-Hung Huynh, Diem Quynh Nguyen, Hyunjae Park, Kyoungho Jung, Bookyo Sur, Yeh-Jin Ahn, Sun-Shin Cha, Lin-Woo Kang
{"title":"Catalytic Intermediate Crystal Structures of Cysteine Desulfurase from the Archaeon <i>Thermococcus onnurineus</i> NA1.","authors":"Thien-Hoang Ho, Kim-Hung Huynh, Diem Quynh Nguyen, Hyunjae Park, Kyoungho Jung, Bookyo Sur, Yeh-Jin Ahn, Sun-Shin Cha, Lin-Woo Kang","doi":"10.1155/2017/5395293","DOIUrl":"https://doi.org/10.1155/2017/5395293","url":null,"abstract":"<p><p><i>Thermococcus onnurineus</i> NA1 is an anaerobic archaeon usually found in a deep-sea hydrothermal vent area, which can use elemental sulfur (S<sup>0</sup>) as a terminal electron acceptor for energy. Sulfur, essential to many biomolecules such as sulfur-containing amino acids and cofactors including iron-sulfur cluster, is usually mobilized from cysteine by the pyridoxal 5'-phosphate- (PLP-) dependent enzyme of cysteine desulfurase (CDS). We determined the crystal structures of CDS from <i>Thermococcus onnurineus</i> NA1 (ToCDS), which include native internal aldimine (NAT), gem-diamine (GD) with alanine, internal aldimine structure with existing alanine (IAA), and internal aldimine with persulfide-bound Cys356 (PSF) structures. The catalytic intermediate structures showed the dihedral angle rotation of Schiff-base linkage relative to the PLP pyridine ring. The ToCDS structures were compared with bacterial CDS structures, which will help us to understand the role and catalytic mechanism of ToCDS in the archaeon <i>Thermococcus onnurineus</i> NA1.</p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2017-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2017/5395293","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35020714","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":"Construction of Expression Shuttle Vectors for the Haloarchaeon <i>Natrinema</i> sp. J7 Based on Its Chromosomal Origins of Replication.","authors":"Yuchen Wang, Beibei Chen, Linshan Sima, Mengzhuo Cao, Xiangdong Chen","doi":"10.1155/2017/4237079","DOIUrl":"https://doi.org/10.1155/2017/4237079","url":null,"abstract":"<p><p>Haloarchaeon <i>Natrinema</i> sp. J7, the first reported archaeon harboring both plasmid and chromosome-based temperate viruses, is a useful model for investigating archaeal virus-host and virus-virus interactions. However, the lack of genetic tools has limited such studies. On the basis of the automatically replicating sequences of the J7 chromosome and the <i>pyrF</i> marker, we constructed seven vectors, six of which were confirmed to possess replication ability in a <i>pyrF-</i>deletion derivative of J7 (J7-F). Among these vectors, pFJ1, pFJ4, and pFJ6 could be transformed into the host strain with relatively high efficiency (approximately 10<sup>3</sup> colony-forming units/<i>μ</i>g DNA) and were present at about one copy per chromosome. These three vectors could be stably maintained in J7-F without selection and were used for heterologous protein expression. Only pFJ6 was found to be present in the transformed cells in an exclusively episomal, nonintegrated state (one copy per chromosome). In contrast, some pFJ1 and pFJ4 DNA was probably integrated into the J7-F chromosome. In addition, pFJ6 was found to be compatible with pYCJ in J7 cells, suggesting that these two vectors could be used for further studies of virus-virus and virus-host interactions.</p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2017-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2017/4237079","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34860345","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}
Konrad H Engelhardt, Shashank Reddy Pinnapireddy, Elias Baghdan, Jarmila Jedelská, Udo Bakowsky
{"title":"Transfection Studies with Colloidal Systems Containing Highly Purified Bipolar Tetraether Lipids from <i>Sulfolobus acidocaldarius</i>.","authors":"Konrad H Engelhardt, Shashank Reddy Pinnapireddy, Elias Baghdan, Jarmila Jedelská, Udo Bakowsky","doi":"10.1155/2017/8047149","DOIUrl":"https://doi.org/10.1155/2017/8047149","url":null,"abstract":"<p><p>Lipid vectors are commonly used to facilitate the transfer of nucleic acids into mammalian cells. In this study, two fractions of tetraether lipids from the archaea <i>Sulfolobus acidocaldarius</i> were extracted and purified using different methods. The purified lipid fractions polar lipid fraction E (PLFE) and hydrolysed glycerol-dialkyl-nonitol tetraether (hGDNT) differ in their structures, charge, size, and miscibility from conventional lipids. Liposomes were prepared by mixing tetraether lipids with cholesterol (CH) and 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) resulting in stable vectors for gene delivery. Lipoplexes were prepared by complexation of liposomes with a luciferase expressing plasmid (pCMV-luc) at certain nitrogen-to-phosphorus (N/P) ratios and optimised for the transient transfection of ovarian adenocarcinoma cells (SK-OV-3). Complexation efficacy was investigated by gel-red fluorescence assay. Biophysical properties, like size, surface charge, and morphology, were investigated by differential light scattering (DLS), atomic force microscopy (AFM), and scanning electron microscopy (Cryo-SEM), respectively, revealing structural differences between liposomes and lipoplexes. A range of stable transfecting agents containing tetraether lipids were obtained by incorporating 5 mol% of tetraether lipids. Lipoplexes showed a decrease in free gel-red with increasing N/P ratios indicating efficient incorporation of plasmid DNA (pDNA) and remarkable stability. Transfection experiments of the lipoplexes revealed successful and superior transfection of SK-OV-3 cell line compared to the commercially available DOTAP and branched polyethyleneimine (25 kDa bPEI).</p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2017-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2017/8047149","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34766494","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}
P. Timmers, C. Welte, J. Koehorst, C. Plugge, M. Jetten, A. Stams
{"title":"Reverse Methanogenesis and Respiration in Methanotrophic Archaea","authors":"P. Timmers, C. Welte, J. Koehorst, C. Plugge, M. Jetten, A. Stams","doi":"10.1155/2017/1654237","DOIUrl":"https://doi.org/10.1155/2017/1654237","url":null,"abstract":"Anaerobic oxidation of methane (AOM) is catalyzed by anaerobic methane-oxidizing archaea (ANME) via a reverse and modified methanogenesis pathway. Methanogens can also reverse the methanogenesis pathway to oxidize methane, but only during net methane production (i.e., “trace methane oxidation”). In turn, ANME can produce methane, but only during net methane oxidation (i.e., enzymatic back flux). Net AOM is exergonic when coupled to an external electron acceptor such as sulfate (ANME-1, ANME-2abc, and ANME-3), nitrate (ANME-2d), or metal (oxides). In this review, the reversibility of the methanogenesis pathway and essential differences between ANME and methanogens are described by combining published information with domain based (meta)genome comparison of archaeal methanotrophs and selected archaea. These differences include abundances and special structure of methyl coenzyme M reductase and of multiheme cytochromes and the presence of menaquinones or methanophenazines. ANME-2a and ANME-2d can use electron acceptors other than sulfate or nitrate for AOM, respectively. Environmental studies suggest that ANME-2d are also involved in sulfate-dependent AOM. ANME-1 seem to use a different mechanism for disposal of electrons and possibly are less versatile in electron acceptors use than ANME-2. Future research will shed light on the molecular basis of reversal of the methanogenic pathway and electron transfer in different ANME types.","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2017-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2017/1654237","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47046452","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}
ShengShee Thor, Joseph R. Peterson, Z. Luthey-Schulten
{"title":"Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function","authors":"ShengShee Thor, Joseph R. Peterson, Z. Luthey-Schulten","doi":"10.1155/2017/9763848","DOIUrl":"https://doi.org/10.1155/2017/9763848","url":null,"abstract":"Decades of biochemical, bioinformatic, and sequencing data are currently being systematically compiled into genome-scale metabolic reconstructions (GEMs). Such reconstructions are knowledge-bases useful for engineering, modeling, and comparative analysis. Here we review the fifteen GEMs of archaeal species that have been constructed to date. They represent primarily members of the Euryarchaeota with three-quarters comprising representative of methanogens. Unlike other reviews on GEMs, we specially focus on archaea. We briefly review the GEM construction process and the genealogy of the archaeal models. The major insights gained during the construction of these models are then reviewed with specific focus on novel metabolic pathway predictions and growth characteristics. Metabolic pathway usage is discussed in the context of the composition of each organism's biomass and their specific energy and growth requirements. We show how the metabolic models can be used to study the evolution of metabolism in archaea. Conservation of particular metabolic pathways can be studied by comparing reactions using the genes associated with their enzymes. This demonstrates the utility of GEMs to evolutionary studies, far beyond their original purpose of metabolic modeling; however, much needs to be done before archaeal models are as extensively complete as those for bacteria.","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2017-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2017/9763848","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47288725","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":"Marine Subsurface Microbial Community Shifts Across a Hydrothermal Gradient in Okinawa Trough Sediments","authors":"L. Brandt, C. House","doi":"10.1155/2016/2690329","DOIUrl":"https://doi.org/10.1155/2016/2690329","url":null,"abstract":"Sediments within the Okinawa back-arc basin overlay a subsurface hydrothermal network, creating intense temperature gradients with sediment depth and potential limits for microbial diversity. We investigated taxonomic changes across 45 m of recovered core with a temperature gradient of 3°C/m from the dynamic Iheya North Hydrothermal System. The interval transitions sharply from low-temperature marine mud to hydrothermally altered clay at 10 meters below seafloor (mbsf). Here, we present taxonomic results from an analysis of the 16S rRNA gene that support a conceptual model in which common marine subsurface taxa persist into the subsurface, while high temperature adapted archaeal taxa show localized peaks in abundances in the hydrothermal clay horizons. Specifically, the bacterial phylum Chloroflexi accounts for a major proportion of the total microbial community within the upper 10 mbsf, whereas high temperature archaea (Terrestrial Hot Spring Crenarchaeotic Group and methanotrophic archaea) appear in varying local abundances in deeper, hydrothermal clay horizons with higher in situ temperatures (up to 55°C, 15 mbsf). In addition, geochemical evidence suggests that methanotrophy may be occurring in various horizons. There is also relict DNA (i.e., DNA preserved after cell death) that persists in horizons where the conditions suitable for microbial communities have ceased.","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2016-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2016/2690329","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64291998","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}
A. Ziganshin, E. Ziganshina, S. Kleinsteuber, M. Nikolausz
{"title":"Comparative Analysis of Methanogenic Communities in Different Laboratory-Scale Anaerobic Digesters","authors":"A. Ziganshin, E. Ziganshina, S. Kleinsteuber, M. Nikolausz","doi":"10.1155/2016/3401272","DOIUrl":"https://doi.org/10.1155/2016/3401272","url":null,"abstract":"Comparative analysis of methanogenic archaea compositions and dynamics in 11 laboratory-scale continuous stirred tank reactors fed with different agricultural materials (chicken manure, cattle manure, maize straw, maize silage, distillers grains, and Jatropha press cake) was carried out by analysis of the methyl coenzyme-M reductase α-subunit (mcrA) gene. Various taxa within Methanomicrobiales, Methanobacteriaceae, Methanosarcinaceae, Methanosaetaceae, and Methanomassiliicoccales were detected in the biogas reactors but in different proportions depending on the substrate type utilized as well as various process parameters. Improved coverage and higher taxonomic resolution of methanogens were obtained compared to a previous 16S rRNA gene based study of the same reactors. Some members of the genus Methanoculleus positively correlated with the relative methane content, whereas opposite correlations were found for Methanobacterium. Specific biogas production was found to be significantly correlating with Methanosarcinaceae. Statistical analysis also disclosed that some members of the genus Methanoculleus positively correlated with the ammonia level, whereas the prevalence of Methanocorpusculum, Methanobacterium, and Methanosaeta was negatively correlated with this parameter. These results suggest that the application of methanogenic archaea adapted to specific feedstock might enhance the anaerobic digestion of such waste materials in full-scale biogas reactors.","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2016-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2016/3401272","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64326779","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}
Xue Yang, Xiang Liu, Si Chen, Guangmin Liu, Shuyan Wu, Chunli Wan
{"title":"Volatile Fatty Acids Production from Codigestion of Food Waste and Sewage Sludge Based on β-Cyclodextrins and Alkaline Treatments","authors":"Xue Yang, Xiang Liu, Si Chen, Guangmin Liu, Shuyan Wu, Chunli Wan","doi":"10.1155/2016/1698163","DOIUrl":"https://doi.org/10.1155/2016/1698163","url":null,"abstract":"Volatile fatty acids (VFAs) are preferred valuable resources, which can be produced from anaerobic digestion process. This study presents a novel technology using β-cyclodextrins (β-CD) pretreatment integrated alkaline method to enhance VFAs production from codigestion of food waste and sewage sludge. Experiment results showed that optimized ratio of food waste to sewage sludge was 3 : 2 because it provided adequate organic substance and seed microorganisms. Based on this optimized ratio, the integrated treatment of alkaline pH 10 and β-CD addition (0.2 g/g TS) performed the best enhancement on VFAs production, and the maximum VFAs production was 8631.7 mg/L which was 6.13, 1.38, and 1.57 times higher than that of control, initial pH 10, and 0.2 g β-CD/g TS treatment, respectively. Furthermore, the hydrolysis rate of protein and polysaccharides was greatly improved in integration treatment, which was 1.18–3.45 times higher than that of other tests. Though the VFAs production and hydrolysis of polymeric organics were highly enhanced, the primary bacterial communities with different treatments did not show substantial differences.","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2016-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2016/1698163","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64237932","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}