Archaea-An International Microbiological Journal最新文献_第8页

Archaeal DNA Polymerase-B as a DNA Template Guardian: Links between Polymerases and Base/Alternative Excision Repair Enzymes in Handling the Deaminated Bases Uracil and Hypoxanthine 古细菌DNA聚合酶- b作为DNA模板守护者:聚合酶和碱基/替代切除修复酶在处理脱胺碱基尿嘧啶和次黄嘌呤中的联系

IF 2.4 4区生物学

Archaea-An International Microbiological Journal Pub Date : 2016-09-19 DOI: 10.1155/2016/1510938

J. Abellón-Ruiz, S. Ishino, Y. Ishino, B. Connolly

{"title":"Archaeal DNA Polymerase-B as a DNA Template Guardian: Links between Polymerases and Base/Alternative Excision Repair Enzymes in Handling the Deaminated Bases Uracil and Hypoxanthine","authors":"J. Abellón-Ruiz, S. Ishino, Y. Ishino, B. Connolly","doi":"10.1155/2016/1510938","DOIUrl":"https://doi.org/10.1155/2016/1510938","url":null,"abstract":"In Archaea repair of uracil and hypoxanthine, which arise by deamination of cytosine and adenine, respectively, is initiated by three enzymes: Uracil-DNA-glycosylase (UDG, which recognises uracil); Endonuclease V (EndoV, which recognises hypoxanthine); and Endonuclease Q (EndoQ), (which recognises both uracil and hypoxanthine). Two archaeal DNA polymerases, Pol-B and Pol-D, are inhibited by deaminated bases in template strands, a feature unique to this domain. Thus the three repair enzymes and the two polymerases show overlapping specificity for uracil and hypoxanthine. Here it is demonstrated that binding of Pol-D to primer-templates containing deaminated bases inhibits the activity of UDG, EndoV, and EndoQ. Similarly Pol-B almost completely turns off EndoQ, extending earlier work that demonstrated that Pol-B reduces catalysis by UDG and EndoV. Pol-B was observed to be a more potent inhibitor of the enzymes compared to Pol-D. Although Pol-D is directly inhibited by template strand uracil, the presence of Pol-B further suppresses any residual activity of Pol-D, to near-zero levels. The results are compatible with Pol-D acting as the replicative polymerase and Pol-B functioning primarily as a guardian preventing deaminated base-induced DNA mutations.","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2016 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2016-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2016/1510938","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64226884","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}

引用次数: 4

Fundamental Characteristics of AAA+ Protein Family Structure and Function AAA+蛋白家族结构与功能的基本特征

IF 2.4 4区生物学

Archaea-An International Microbiological Journal Pub Date : 2016-09-14 DOI: 10.1155/2016/9294307

Justin M. Miller, E. J. Enemark

引用次数: 75

The Proteome and Lipidome of Thermococcus kodakarensis across the Stationary Phase. 柯达热球菌静止期蛋白质组和脂质组的研究。

IF 2.4 4区生物学

Archaea-An International Microbiological Journal Pub Date : 2016-05-04 eCollection Date: 2016-01-01 DOI: 10.1155/2016/5938289

Emma J Gagen, Marcos Y Yoshinaga, Franka Garcia Prado, Kai-Uwe Hinrichs, Michael Thomm

{"title":"The Proteome and Lipidome of Thermococcus kodakarensis across the Stationary Phase.","authors":"Emma J Gagen, Marcos Y Yoshinaga, Franka Garcia Prado, Kai-Uwe Hinrichs, Michael Thomm","doi":"10.1155/2016/5938289","DOIUrl":"https://doi.org/10.1155/2016/5938289","url":null,"abstract":"The majority of cells in nature probably exist in a stationary-phase-like state, due to nutrient limitation in most environments. Studies on bacteria and yeast reveal morphological and physiological changes throughout the stationary phase, which lead to an increased ability to survive prolonged nutrient limitation. However, there is little information on archaeal stationary phase responses. We investigated protein- and lipid-level changes in Thermococcus kodakarensis with extended time in the stationary phase. Adaptations to time in stationary phase included increased proportion of membrane lipids with a tetraether backbone, synthesis of proteins that ensure translational fidelity, specific regulation of ABC transporters (upregulation of some, downregulation of others), and upregulation of proteins involved in coenzyme production. Given that the biological mechanism of tetraether synthesis is unknown, we also considered whether any of the protein-level changes in T. kodakarensis might shed light on the production of tetraether lipids across the same period. A putative carbon-nitrogen hydrolase, a TldE (a protease in Escherichia coli) homologue, and a membrane bound hydrogenase complex subunit were candidates for possible involvement in tetraether-related reactions, while upregulation of adenosylcobalamin synthesis proteins might lend support to a possible radical mechanism as a trigger for tetraether synthesis. ","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2016 ","pages":"5938289"},"PeriodicalIF":2.4,"publicationDate":"2016-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2016/5938289","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34556244","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}

引用次数: 6

Methanogen Diversity in Indigenous and Introduced Ruminant Species on the Tibetan Plateau. 青藏高原本地和引进反刍动物甲烷菌多样性研究。

IF 2.4 4区生物学

Archaea-An International Microbiological Journal Pub Date : 2016-04-28 eCollection Date: 2016-01-01 DOI: 10.1155/2016/5916067

Xiao Dan Huang, Gonzalo Martinez-Fernandez, Jagadish Padmanabha, Ruijun Long, Stuart E Denman, Christopher S McSweeney

{"title":"Methanogen Diversity in Indigenous and Introduced Ruminant Species on the Tibetan Plateau.","authors":"Xiao Dan Huang, Gonzalo Martinez-Fernandez, Jagadish Padmanabha, Ruijun Long, Stuart E Denman, Christopher S McSweeney","doi":"10.1155/2016/5916067","DOIUrl":"https://doi.org/10.1155/2016/5916067","url":null,"abstract":"Host factors are regarded as important in shaping the archaeal community in the rumen but few controlled studies have been performed to demonstrate this across host species under the same environmental conditions. A study was designed to investigate the structure of the methanogen community in the rumen of two indigenous (yak and Tibetan sheep) and two introduced domestic ruminant (cattle and crossbred sheep) species raised and fed under similar conditions on the high altitude Tibetan Plateau. The methylotrophic Methanomassiliicoccaceae was the predominant archaeal group in all animals even though Methanobrevibacter are usually present in greater abundance in ruminants globally. Furthermore, within the Methanomassiliicoccaceae family members from Mmc. group 10 and Mmc. group 4 were dominant in Tibetan Plateau ruminants compared to Mmc. group 12 found to be highest in other ruminants studied. Small ruminants presented the highest number of sequences that belonged to Methanomassiliicoccaceae compared to the larger ruminants. Although the methanogen community structure was different among the ruminant species, there were striking similarities between the animals in this environment. This indicates that factors such as the extreme environmental conditions and diet on the Tibetan Plateau might have a greater impact on rumen methanogen community compared to host differences. ","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2016 ","pages":"5916067"},"PeriodicalIF":2.4,"publicationDate":"2016-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2016/5916067","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34556243","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}

引用次数: 58

Characterization of the ATP-Dependent Lon-Like Protease in Methanobrevibacter smithii. 史密斯甲烷杆菌atp依赖性长链样蛋白酶的研究。

IF 2.4 4区生物学

Archaea-An International Microbiological Journal Pub Date : 2016-04-28 eCollection Date: 2016-01-01 DOI: 10.1155/2016/5759765

Jihua Pei, Jianfang Yan, Yi Jiang

引用次数: 4

Discovery and Characterization of Iron Sulfide and Polyphosphate Bodies Coexisting in Archaeoglobus fulgidus Cells. 硫化铁和多磷酸体共存于始祖舌藻细胞的发现及特性研究。

IF 2.4 4区生物学

Archaea-An International Microbiological Journal Pub Date : 2016-04-19 eCollection Date: 2016-01-01 DOI: 10.1155/2016/4706532

Daniel B Toso, Muhammad Mohsin Javed, Elizabeth Czornyj, Robert P Gunsalus, Z Hong Zhou

{"title":"Discovery and Characterization of Iron Sulfide and Polyphosphate Bodies Coexisting in Archaeoglobus fulgidus Cells.","authors":"Daniel B Toso, Muhammad Mohsin Javed, Elizabeth Czornyj, Robert P Gunsalus, Z Hong Zhou","doi":"10.1155/2016/4706532","DOIUrl":"https://doi.org/10.1155/2016/4706532","url":null,"abstract":"Inorganic storage granules have long been recognized in bacterial and eukaryotic cells but were only recently identified in archaeal cells. Here, we report the cellular organization and chemical compositions of storage granules in the Euryarchaeon, Archaeoglobus fulgidus strain VC16, a hyperthermophilic, anaerobic, and sulfate-reducing microorganism. Dense granules were apparent in A. fulgidus cells imaged by cryo electron microscopy (cryoEM) but not so by negative stain electron microscopy. Cryo electron tomography (cryoET) revealed that each cell contains one to several dense granules located near the cell membrane. Energy dispersive X-ray (EDX) spectroscopy and scanning transmission electron microscopy (STEM) show that, surprisingly, each cell contains not just one but often two types of granules with different elemental compositions. One type, named iron sulfide body (ISB), is composed mainly of the elements iron and sulfur plus copper; and the other one, called polyphosphate body (PPB), is composed of phosphorus and oxygen plus magnesium, calcium, and aluminum. PPBs are likely used for energy storage and/or metal sequestration/detoxification. ISBs could result from the reduction of sulfate to sulfide via anaerobic energy harvesting pathways and may be associated with energy and/or metal storage or detoxification. The exceptional ability of these archaeal cells to sequester different elements may have novel bioengineering applications. ","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2016 ","pages":"4706532"},"PeriodicalIF":2.4,"publicationDate":"2016-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2016/4706532","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34561829","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}

引用次数: 9

Archaeal Community Changes Associated with Cultivation of Amazon Forest Soil with Oil Palm 油棕种植与亚马逊森林土壤古细菌群落变化

IF 2.4 4区生物学

Archaea-An International Microbiological Journal Pub Date : 2016-02-24 DOI: 10.1155/2016/3762159

D. D. Tupinambá, M. Cantão, O. Y. Costa, J. Bergmann, R. Kruger, C. Kyaw, C. Barreto, B. Quirino

{"title":"Archaeal Community Changes Associated with Cultivation of Amazon Forest Soil with Oil Palm","authors":"D. D. Tupinambá, M. Cantão, O. Y. Costa, J. Bergmann, R. Kruger, C. Kyaw, C. Barreto, B. Quirino","doi":"10.1155/2016/3762159","DOIUrl":"https://doi.org/10.1155/2016/3762159","url":null,"abstract":"This study compared soil archaeal communities of the Amazon forest with that of an adjacent area under oil palm cultivation by 16S ribosomal RNA gene pyrosequencing. Species richness and diversity were greater in native forest soil than in the oil palm-cultivated area, and 130 OTUs (13.7%) were shared between these areas. Among the classified sequences, Thaumarchaeota were predominant in the native forest, whereas Euryarchaeota were predominant in the oil palm-cultivated area. Archaeal species diversity was 1.7 times higher in the native forest soil, according to the Simpson diversity index, and the Chao1 index showed that richness was five times higher in the native forest soil. A phylogenetic tree of unclassified Thaumarchaeota sequences showed that most of the OTUs belong to Miscellaneous Crenarchaeotic Group. Several archaeal genera involved in nutrient cycling (e.g., methanogens and ammonia oxidizers) were identified in both areas, but significant differences were found in the relative abundances of Candidatus Nitrososphaera and unclassified Soil Crenarchaeotic Group (prevalent in the native forest) and Candidatus Nitrosotalea and unclassified Terrestrial Group (prevalent in the oil palm-cultivated area). More studies are needed to culture some of these Archaea in the laboratory so that their metabolism and physiology can be studied.","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2016 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2016-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2016/3762159","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64347198","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}

引用次数: 11

The Vertical Distribution of Sediment Archaeal Community in the “Black Bloom” Disturbing Zhushan Bay of Lake Taihu 太湖珠山湾“黑水华”沉积物古细菌群落的垂直分布

IF 2.4 4区生物学

Archaea-An International Microbiological Journal Pub Date : 2016-01-17 DOI: 10.1155/2016/8232135

Xianfang Fan, Peng Xing

{"title":"The Vertical Distribution of Sediment Archaeal Community in the “Black Bloom” Disturbing Zhushan Bay of Lake Taihu","authors":"Xianfang Fan, Peng Xing","doi":"10.1155/2016/8232135","DOIUrl":"https://doi.org/10.1155/2016/8232135","url":null,"abstract":"Using the Illumina sequencing technology, we investigated the vertical distribution of archaeal community in the sediment of Zhushan Bay of Lake Taihu, where the black bloom frequently occurred in summer. Overall, the Miscellaneous Crenarchaeotal Group (MCG), Deep Sea Hydrothermal Vent Group 6 (DHVEG-6), and Methanobacterium dominated the archaeal community. However, we observed significant difference in composition of archaeal community among different depths of the sediment. DHVEG-6 dominated in the surface layer (0–3 cm) sediment. Methanobacterium was the dominating archaeal taxa in the L2 (3–6 cm) and L3 (6–10) sediment. MCG was most abundant in the L4 (10–15 cm) and L5 (15–20 cm) sediment. Besides, DHVEG-6 was significantly affected by the concentration of total phosphorus (TP). And loss on ignition (LOI) was an important environmental factor for Methanobacterium. As the typical archaeal taxa in the surface layer sediment, DHVEG-6 and Methanobacterium might be more adapted to abundant substrate supply from cyanobacterial blooms and take active part in the biomass transformation. We propose that DHVEG-6 and Methanobacterium could be the key archaeal taxa correlated with the “black bloom” formation in Zhushan Bay.","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2016 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2016-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2016/8232135","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64555770","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}

引用次数: 32

Characterization of Fatty Acids in Crenarchaeota by GC-MS and NMR 气相色谱-质谱和核磁共振表征绿藻中脂肪酸

IF 2.4 4区生物学

Archaea-An International Microbiological Journal Pub Date : 2015-12-31 DOI: 10.1155/2015/472726

Timothy Hamerly, B. Tripet, Louie Wurch, R. Hettich, M. Podar, B. Bothner, V. Copié

{"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}

引用次数: 19

Sequence, Structure, and Binding Analysis of Cyclodextrinase (TK1770) from T. kodakarensis (KOD1) Using an In Silico Approach 柯达芽孢杆菌(T. kodakarensis, KOD1)环糊精酶(TK1770)的序列、结构和结合分析

IF 2.4 4区生物学

Archaea-An International Microbiological Journal Pub Date : 2015-12-24 DOI: 10.1155/2015/179196

Ramzan Ali, Muhammad Imtiaz Shafiq

{"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}

引用次数: 6