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  1 / 120 MEDLINE  
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PMID:29458494
Autor:Hwang WM; Kim SM; Kang K; Ahn TY
Endereço:Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea.
Título:Uliginosibacterium sediminicola sp. nov., isolated from freshwater sediment.
Fonte:Int J Syst Evol Microbiol; 68(3):924-929, 2018 Mar.
ISSN:1466-5034
País de publicação:England
Idioma:eng
Resumo:Strain M1-21 is a Gram-stain-negative, strictly aerobic and short-rod-shaped bacterium, motile by means of a single polar flagellum; it was isolated from freshwater sediment in Korea. It grew at 10-40 °C (optimum 25 °C), pH 6.0-8.0 (optimum pH 7.0) and with 0-0.75 % (w/v) NaCl (optimal growth occurred in the absence of NaCl) on R2A agar, and it accumulated poly-ß-hydroxybutyrate granules inside the cells. According to 16S rRNA gene sequence analysis, strain M1-21 showed highest sequence similarity with Uliginosibacterium gangwonense (94.7 %) and Uliginosibacterium paludis (94.4 %). Phylogenetic analysis of the 16S rRNA gene sequences revealed that strain M1-21 belongs to the genus Uliginosibacterium. The DNA G+C content of strain M1-21 was 61.9 mol%. The predominant respiratory quinone was ubiquinone-8. The major fatty acids (>10 % of the total) were C16 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Strain M1-21 showed distinct phenotypic characteristics that differentiated it from species of the genus Uliginosibacterium. Based on these results, strain M1-21 represents a novel species of the genus Uliginosibacterium, for which the name Uliginosibacterium sediminicola sp. nov. is proposed. The type strain is M1-21 (=KACC 19271 =JCM 32000 ).
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (DNA, Bacterial); 0 (Fatty Acids); 0 (Hydroxybutyrates); 0 (Phospholipids); 0 (Polyesters); 0 (RNA, Ribosomal, 16S); 1339-63-5 (Ubiquinone); 26063-00-3 (poly-beta-hydroxybutyrate); CQA993F7P8 (ubiquinone 8)


  2 / 120 MEDLINE  
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PMID:28550607
Autor:Stawoska I; Dudzik A; Wasylewski M; Jemiola-Rzeminska M; Skoczowski A; Strzalka K; Szaleniec M
Endereço:Institute of Biology, Pedagogical University of Cracow, Podchorazych 2, 30-084, Kraków, Poland.
Título:DFT-based prediction of reactivity of short-chain alcohol dehydrogenase.
Fonte:J Comput Aided Mol Des; 31(6):587-602, 2017 Jun.
ISSN:1573-4951
País de publicação:Netherlands
Idioma:eng
Resumo:The reaction mechanism of ketone reduction by short chain dehydrogenase/reductase, (S)-1-phenylethanol dehydrogenase from Aromatoleum aromaticum, was studied with DFT methods using cluster model approach. The characteristics of the hydride transfer process were investigated based on reaction of acetophenone and its eight structural analogues. The results confirmed previously suggested concomitant transfer of hydride from NADH to carbonyl C atom of the substrate with proton transfer from Tyr to carbonyl O atom. However, additional coupled motion of the next proton in the proton-relay system, between O2' ribose hydroxyl and Tyr154 was observed. The protonation of Lys158 seems not to affect the pKa of Tyr154, as the stable tyrosyl anion was observed only for a neutral Lys158 in the high pH model. The calculated reaction energies and reaction barriers were calibrated by calorimetric and kinetic methods. This allowed an excellent prediction of the reaction enthalpies (R = 0.93) and a good prediction of the reaction kinetics (R = 0.89). The observed relations were validated in prediction of log K obtained for real whole-cell reactor systems that modelled industrial synthesis of S-alcohols.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Alcohols); 0 (Ketones); 0U46U6E8UK (NAD); 42HK56048U (Tyrosine); EC 1.- (Oxidoreductases); EC 1.3.- (1-phenylethanol dehydrogenase); K3Z4F929H6 (Lysine)


  3 / 120 MEDLINE  
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PMID:28375743
Autor:Hallberg ZF; Su Y; Kitto RZ; Hammond MC
Endereço:Department of Chemistry, University of California, Berkeley, California 94720; email: mingch@berkeley.edu.
Título:Engineering and In Vivo Applications of Riboswitches.
Fonte:Annu Rev Biochem; 86:515-539, 2017 Jun 20.
ISSN:1545-4509
País de publicação:United States
Idioma:eng
Resumo:Riboswitches are common gene regulatory units mostly found in bacteria that are capable of altering gene expression in response to a small molecule. These structured RNA elements consist of two modular subunits: an aptamer domain that binds with high specificity and affinity to a target ligand and an expression platform that transduces ligand binding to a gene expression output. Significant progress has been made in engineering novel aptamer domains for new small molecule inducers of gene expression. Modified expression platforms have also been optimized to function when fused with both natural and synthetic aptamer domains. As this field expands, the use of these privileged scaffolds has permitted the development of tools such as RNA-based fluorescent biosensors. In this review, we summarize the methods that have been developed to engineer new riboswitches and highlight applications of natural and synthetic riboswitches in enzyme and strain engineering, in controlling gene expression and cellular physiology, and in real-time imaging of cellular metabolites and signals.
Tipo de publicação: JOURNAL ARTICLE; REVIEW
Nome de substância:0 (Aptamers, Nucleotide); 0 (Ligands); 0 (Riboswitch)


  4 / 120 MEDLINE  
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PMID:28223460
Autor:Mehta-Kolte MG; Loutey D; Wang O; Youngblut MD; Hubbard CG; Wetmore KM; Conrad ME; Coates JD
Endereço:Energy Biosciences Institute, University of California Berkeley, Berkeley, California, USA.
Título:Mechanism of H S Oxidation by the Dissimilatory Perchlorate-Reducing Microorganism PS.
Fonte:MBio; 8(1), 2017 Feb 21.
ISSN:2150-7511
País de publicação:United States
Idioma:eng
Resumo:The genetic and biochemical basis of perchlorate-dependent H S oxidation (PSOX) was investigated in the dissimilatory perchlorate-reducing microorganism (DPRM) PS (PS). Previously, it was shown that all known DPRMs innately oxidize H S, producing elemental sulfur (S ). Although the process involving PSOX is thermodynamically favorable ( °' = -206 kJ â‹… mol H S), the underlying biochemical and genetic mechanisms are currently unknown. Interestingly, H S is preferentially utilized over physiological electron donors such as lactate or acetate although no growth benefit is obtained from the metabolism. Here, we determined that PSOX is due to a combination of enzymatic and abiotic interactions involving reactive intermediates of perchlorate respiration. Using various approaches, including barcode analysis by sequencing (Bar-seq), transcriptome sequencing (RNA-seq), and proteomics, along with targeted mutagenesis and biochemical characterization, we identified all facets of PSOX in PS. In support of our proposed model, deletion of identified upregulated PS genes traditionally known to be involved in sulfur redox cycling (e.g., Sox, sulfide:quinone reductase [SQR]) showed no defect in PSOX activity. Proteomic analysis revealed differential abundances of a variety of stress response metal efflux pumps and divalent heavy-metal transporter proteins, suggesting a general toxicity response. Furthermore, biochemical studies demonstrated direct PSOX mediated by purified perchlorate reductase (PcrAB) in the absence of other electron transfer proteins. The results of these studies support a model in which H S oxidation is mediated by electron transport chain short-circuiting in the periplasmic space where the PcrAB directly oxidizes H S to S The biogenically formed reactive intermediates (ClO and O ) subsequently react with additional H S, producing polysulfide and S as end products. Inorganic sulfur compounds are widespread in nature, and microorganisms are central to their transformation, thereby playing a key role in the global sulfur cycle. Sulfur oxidation is mediated by a broad phylogenetic diversity of microorganisms, including anoxygenic phototrophs and either aerobic or anaerobic chemotrophs coupled to oxygen or nitrate respiration, respectively. Recently, perchlorate-respiring microorganisms were demonstrated to be innately capable of sulfur oxidation regardless of their phylogenetic affiliation. As recognition of the prevalence of these organisms intensifies, their role in global geochemical cycles is being queried. This is further highlighted by the recently recognized environmental pervasiveness of perchlorate not only across Earth but also throughout our solar system. The inferred importance of this metabolism not only is that it is a novel and previously unrecognized component of the global sulfur redox cycle but also is because of the recently demonstrated applicability of perchlorate respiration in the control of biogenic sulfide production in engineered environments such as oil reservoirs and wastewater treatment facilities, where excess H S represents a significant environmental, process, and health risk, with associated costs approximating $90 billion annually.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Perchlorates); 0 (Proteome); VLA4NZX2P4 (perchlorate); YY9FVM7NSN (Hydrogen Sulfide)


  5 / 120 MEDLINE  
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PMID:27902243
Autor:Corteselli EM; Aitken MD; Singleton DR
Endereço:Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, NC 27599-7431, USA.
Título:Rugosibacter aromaticivorans gen. nov., sp. nov., a bacterium within the family Rhodocyclaceae, isolated from contaminated soil, capable of degrading aromatic compounds.
Fonte:Int J Syst Evol Microbiol; 67(2):311-318, 2017 Feb.
ISSN:1466-5034
País de publicação:England
Idioma:eng
Resumo:A bacterial strain designated Ca6T was isolated from polycyclic aromatic hydrocarbon (PAH)-contaminated soil from the site of a former manufactured gas plant in Charlotte, NC, USA, and linked phylogenetically to the family Rhodocyclaceae of the class Betaproteobacteria. Its 16S rRNA gene sequence was highly similar to globally distributed environmental sequences, including those previously designated 'Pyrene Group 1' demonstrated to grow on the PAHs phenanthrene and pyrene by stable-isotope probing. The most closely related described relative was Sulfuritalea hydrogenivorans strain sk43HT (93.6 % 16S rRNA gene sequence identity). In addition to a limited number of organic acids, Ca6T was capable of growth on the monoaromatic compounds benzene and toluene, and the azaarene carbazole, as sole sources of carbon and energy. Growth on the PAHs phenanthrene and pyrene was also confirmed. Optimal growth was observed aerobically under mesophilic temperature, neutral pH and low salinity conditions. Major fatty acids present included summed feature 3 (C16 : 1ω7c or C16 : 1ω6c) and C16 : 0. The DNA G+C content of the single chromosome was 55.14  mol% as determined by complete genome sequencing. Due to its distinct genetic and physiological properties, strain Ca6T is proposed as a member of a novel genus and species within the family Rhodocyclaceae, for which the name Rugosibacter aromaticivorans gen. nov., sp. nov. is proposed. The type strain of the species is Ca6T (=ATCC TSD-59T=DSM 103039T).
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (DNA, Bacterial); 0 (Fatty Acids); 0 (Polycyclic Aromatic Hydrocarbons); 0 (RNA, Ribosomal, 16S); 0 (Soil Pollutants)


  6 / 120 MEDLINE  
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PMID:27902185
Autor:Liu CT; Lin SY; Hameed A; Liu YC; Hsu YH; Wong WT; Tseng CH; Lur HS; Young CC
Endereço:1​Institute of Biotechnology, National Taiwan University, Taiwan, ROC 2​Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan, ROC.
Título:Oryzomicrobium terrae gen. nov., sp. nov., of the family Rhodocyclaceae isolated from paddy soil.
Fonte:Int J Syst Evol Microbiol; 67(2):183-189, 2017 Feb.
ISSN:1466-5034
País de publicação:England
Idioma:eng
Resumo:A polyphasic approach was used to characterize a novel bacterium, designated strain TPP412T, isolated from a paddy soil in Taiwan. Strain TPP412T was Gram-stain-negative, facultatively anaerobic, rod-shaped, motile with a single polar flagellum and lacked bacteriochlorophyll. Growth was observed at 24-45 °C (optimal 25 °C), at pH 5.0-10.0 (optimal pH 7.0) and with 0-0.75 % (w/v) NaCl. Strain TPP412T showed highest 16S rRNA gene sequence similarity to members of the genera Rhodocyclus (94.1-94.5 %), Azospira (93.9-94.5 %) and Propionivibrio (93.4-94.4 %) and established a discrete taxonomic lineage in phylogenetic analysis. The major fatty acids found in strain TPP412T were C12 : 0, C12 : 0 3-OH, iso-C15 : 0 3-OH, C16 : 0, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. The major polar lipids consisted of phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unidentified lipid. The polyamine pattern showed a predominance of putrescine and a minor amount of spermidine. The DNA G+C content was 58.4 mol% and the predominant quinone system was ubiquinone-8 (Q-8). The low 16S rRNA gene sequence similarity values (≤94.5%) and distinct phylogenetic clustering clearly distinguished strain TPP412T from other representatives of the family Rhodocyclaceae. Based on the discrete phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence analysis, strain TPP412T is considered to represent a novel species of a new genus in the family Rhodocyclaceae, for which the name Oryzomicrobium terrae gen. nov., sp. nov. is proposed. The type strain of Oryzomicrobium terrae is TPP412T (=BCRC 80905T=JCM 30814T).
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (DNA, Bacterial); 0 (Fatty Acids); 0 (Phospholipids); 0 (Polyamines); 0 (RNA, Ribosomal, 16S); 1339-63-5 (Ubiquinone); CQA993F7P8 (ubiquinone 8)


  7 / 120 MEDLINE  
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PMID:27814897
Autor:Coats ER; Brinkman CK; Lee S
Endereço:Department of Civil Engineering, University of Idaho, Moscow, ID 83844-1022, USA. Electronic address: ecoats@uidaho.edu.
Título:Characterizing and contrasting the microbial ecology of laboratory and full-scale EBPR systems cultured on synthetic and real wastewaters.
Fonte:Water Res; 108:124-136, 2017 Jan 01.
ISSN:1879-2448
País de publicação:England
Idioma:eng
Resumo:The anthropogenic discharge of phosphorus (P) into surface waters can induce the proliferation of cyanobacteria and algae, which can negatively impact water quality. Enhanced biological P removal (EBPR) is an engineered process that can be employed to efficiently remove significant quantities of P from wastewater. Within this engineered system, the mixed microbial consortium (MMC) becomes enriched with polyphosphate accumulating organisms (PAOs). To date much knowledge has been developed on PAOs, and the EBPR process is generally well understood; nonetheless, the engineered process remains underutilized. In this study, investigations were conducted using qPCR and Illumina MiSeq to assess the impacts of wastewater (synthetic vs. real) on EBPR microbial ecology. While a strong relationship was demonstrated between EBPR metrics (P:C; influent VFA:P) and excellent P removal across diverse EBPR systems and MMCs, no such correlations existed with the specific MMCs. Moreover, MMCs exhibited distinct clusters based on substrate, and qPCR results based on the putative PAO Accumulibacter did not correlate with BLASTN eubacterial results for either Accumulibacter or Rhodocyclaceae. More critically, PAO-based sequences aligned poorly with Accumulibacter for both eubacterial and PAO primer sets, which strongly suggests that the conventional PAO primers applied in FISH and qPCR analysis do not sufficiently target the putative PAO Accumulibacter. In particular, negligible alignment was observed for PAO amplicons obtained from a MMC performing excellent EBPR on crude glycerol (an atypical substrate). A synthetic wastewater-based MMC exhibited the best observed BLASTN match of the PAO amplicons, raising concerns about the potential relevance in using synthetic substrates in the study of EBPR.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Polyphosphates); 0 (Waste Water); 27YLU75U4W (Phosphorus); PDC6A3C0OX (Glycerol)


  8 / 120 MEDLINE  
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PMID:27867159
Autor:Terashima M; Yama A; Sato M; Yumoto I; Kamagata Y; Kato S
Endereço:Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST).
Título:Culture-Dependent and -Independent Identification of Polyphosphate-Accumulating Dechloromonas spp. Predominating in a Full-Scale Oxidation Ditch Wastewater Treatment Plant.
Fonte:Microbes Environ; 31(4):449-455, 2016 Dec 23.
ISSN:1347-4405
País de publicação:Japan
Idioma:eng
Resumo:The oxidation ditch process is one of the most economical approaches currently used to simultaneously remove organic carbon, nitrogen, and also phosphorus (P) from wastewater. However, limited information is available on biological P removal in this process. In the present study, microorganisms contributing to P removal in a full-scale oxidation ditch reactor were investigated using culture-dependent and -independent approaches. A microbial community analysis based on 16S rRNA gene sequencing revealed that a phylotype closely related to Dechloromonas spp. in the family Rhodocyclaceae dominated in the oxidation ditch reactor. This dominant Dechloromonas sp. was successfully isolated and subjected to fluorescent staining for polyphosphate, followed by microscopic observations and a spectrofluorometric analysis, which clearly demonstrated that the Dechloromonas isolate exhibited a strong ability to accumulate polyphosphate within its cells. These results indicate the potential key role of Dechloromonas spp. in efficient P removal in the oxidation ditch wastewater treatment process.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (DNA, Bacterial); 0 (DNA, Ribosomal); 0 (Polyphosphates); 0 (RNA, Ribosomal, 16S); 0 (Waste Water)


  9 / 120 MEDLINE  
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PMID:27624617
Autor:Chen WM; Li YS; Chen ZH; Young CC; Sheu SY
Endereço:1​Department of Seafood Science, Laboratory of Microbiology, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan ROC.
Título:Uliginosibacterium paludis sp. nov., isolated from a marsh.
Fonte:Int J Syst Evol Microbiol; 66(12):5118-5123, 2016 Dec.
ISSN:1466-5034
País de publicação:England
Idioma:eng
Resumo:A novel bacterial strain, designated KBP-13T, was isolated from a water sample taken from the Banping Lake Wetland Park in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain KBP-13T were Gram-stain-negative, aerobic, poly-ß-hydroxybutyrate-accumulating, motile rods that formed light yellow colonies. Growth occurred at 15-40 °C (optimum, 30-40 °C), at pH 6.0-8.0 (optimum, pH 6.0) and with 0-2 % (w/v) NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KBP-13T belonged to the genus Uliginosibacterium within the family Rhodocyclaceae of the class Betaproteobacteria and its most closely related neighbour was Uliginosibacterium gangwonense 5YN10-9T with sequence similarity of 96.0 %. Strain KBP-13T contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C14 : 0 as predominant fatty acids. The major respiratory quinone was Q-8. The DNA G+C content of the genomic DNA was 65.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one uncharacterized aminophospholipid, one uncharacterized aminolipid, two uncharacterized phospholipids and three uncharacterized glycolipids. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain KBP-13T represents a novel species in the genus Uliginosibacterium, for which the name Uliginosibacterium paludis sp. nov. is proposed. The type strain is KBP-13T (=BCRC 80903T=LMG 28837T=KCTC 42655T).
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (DNA, Bacterial); 0 (Fatty Acids); 0 (Hydroxybutyrates); 0 (Phospholipids); 0 (Polyesters); 0 (RNA, Ribosomal, 16S); 1339-63-5 (Ubiquinone); 26063-00-3 (poly-beta-hydroxybutyrate); CQA993F7P8 (ubiquinone 8)


  10 / 120 MEDLINE  
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PMID:27274029
Autor:Curtis PD
Endereço:Department of Biology, University of Mississippi, University, Mississippi, USA pdcurtis@olemiss.edu.
Título:Essential Genes Predicted in the Genome of Rubrivivax gelatinosus.
Fonte:J Bacteriol; 198(16):2244-50, 2016 Aug 15.
ISSN:1098-5530
País de publicação:United States
Idioma:eng
Resumo:UNLABELLED: Rubrivivax gelatinosus is a betaproteobacterium with impressive metabolic diversity. It is capable of phototrophy, chemotrophy, two different mechanisms of sugar metabolism, fermentation, and H2 gas production. To identify core essential genes, R. gelatinosus was subjected to saturating transposon mutagenesis and high-throughput sequencing (TnSeq) analysis using nutrient-rich, aerobic conditions. Results revealed that virtually no primary metabolic genes are essential to the organism and that genomic redundancy only explains a portion of the nonessentiality, but some biosynthetic pathways are still essential under nutrient-rich conditions. Different essentialities of different portions of the Pho regulatory pathway suggest that overexpression of the regulon is toxic and hint at a larger connection between phosphate regulation and cellular health. Lastly, various essentialities of different tRNAs hint at a more complex situation than would be expected for such a core process. These results expand upon research regarding cross-organism gene essentiality and further enrich the study of purple nonsulfur bacteria. IMPORTANCE: Microbial genomic data are increasing at a tremendous rate, but physiological characterization of those data lags far behind. One mechanism of high-throughput physiological characterization is TnSeq, which uses high-volume transposon mutagenesis and high-throughput sequencing to identify all of the essential genes in a given organism's genome. Here TnSeq was used to identify essential genes in the metabolically versatile betaproteobacterium Rubrivivax gelatinosus The results presented here add to the growing TnSeq field and also reveal important aspects of R. gelatinosus physiology, which are applicable to researchers working on metabolically flexible organisms.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Bacterial Proteins); 0 (Cell Cycle Proteins)



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