DOCSLIB.ORG

2E7z Lichtarge Lab 2006

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
2E7z Lichtarge Lab 2006 Pages 1–13 2e7z Evolutionary trace report by report maker February 13, 2010 4.3.1 Alistat 13 4.3.2 CE 13 4.3.3 DSSP 13 4.3.4 HSSP 13 4.3.5 LaTex 13 4.3.6 Muscle 13 4.3.7 Pymol 13 4.4 Note about ET Viewer 13 4.5 Citing this work 13 4.6 About report maker 13 4.7 Attachments 13 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 2e7z): Title: Acetylene hydratase from pelobacter acetylenicus CONTENTS Compound: Mol id: 1; molecule: acetylene hydratase ahy; chain: a; ec: 4.2.1.71 1 Introduction 1 Organism, scientific name: Pelobacter Acetylenicus; 2e7z contains a single unique chain 2e7zA (727 residues long). 2 Chain 2e7zA 1 2.1 Q71EW5 overview 1 2.2 Multiple sequence alignment for 2e7zA 1 2.3 Residue ranking in 2e7zA 1 2.4 Top ranking residues in 2e7zA and their position on the structure 1 2 CHAIN 2E7ZA 2.4.1 Clustering of residues at 25% coverage. 2 2.4.2 Overlap with known functional surfaces at 2.1 Q71EW5 overview 25% coverage. 3 From SwissProt, id Q71EW5, 98% identical to 2e7zA: 2.4.3 Possible novel functional surfaces at 25% Description: Acetylene hydratase Ahy. coverage. 7 Organism, scientific name: Pelobacter acetylenicus. Taxonomy: Bacteria; Proteobacteria; Deltaproteobacteria; Desulfu- 3 Notes on using trace results 11 romonadales; Pelobacteraceae; Pelobacter. 3.1 Coverage 11 3.2 Known substitutions 12 3.3 Surface 12 3.4 Number of contacts 12 3.5 Annotation 12 2.2 Multiple sequence alignment for 2e7zA 3.6 Mutation suggestions 12 For the chain 2e7zA, the alignment 2e7zA.msf (attached) with 44 sequences was used. The alignment was downloaded from the HSSP 4 Appendix 12 database, and fragments shorter than 75% of the query as well as 4.1 File formats 12 duplicate sequences were removed. It can be found in the attachment 4.2 Color schemes used 12 to this report, under the name of 2e7zA.msf. Its statistics, from the 4.3 Credits 13 alistat program are the following: 1 Lichtarge lab 2006 Fig. 1. Residues 4-245 in 2e7zA colored by their relative importance. (See Fig. 3. Residues 488-730 in 2e7zA colored by their relative importance. (See Appendix, Fig.15, for the coloring scheme.) Appendix, Fig.15, for the coloring scheme.) 2.4 Top ranking residues in 2e7zA and their position on the structure In the following we consider residues ranking among top 25% of residues in the protein . Figure 4 shows residues in 2e7zA colored by their importance: bright red and yellow indicate more conser- ved/important residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment. Fig. 2. Residues 246-487 in 2e7zA colored by their relative importance. (See Appendix, Fig.15, for the coloring scheme.) Format: MSF Number of sequences: 44 Total number of residues: 30237 Smallest: 648 Largest: 727 Average length: 687.2 Alignment length: 727 Average identity: 32% Most related pair: 98% Most unrelated pair: 21% Most distant seq: 34% Furthermore, 1% of residues show as conserved in this alignment. The alignment consists of 2% archaean sequences. (Descriptions of some sequences were not readily available.) The file containing Fig. 4. Residues in 2e7zA, colored by their relative importance. Clockwise: front, back, top and bottom views. the sequence descriptions can be found in the attachment, under the name 2e7zA.descr. 2.4.1 Clustering of residues at 25% coverage. Fig. 5 shows the 2.3 Residue ranking in 2e7zA top 25% of all residues, this time colored according to clusters they The 2e7zA sequence is shown in Figs. 1–3, with each residue colored belong to. The clusters in Fig.5 are composed of the residues listed according to its estimated importance. The full listing of residues in Table 1. in 2e7zA can be found in the file called 2e7zA.ranks sorted in the attachment. 2 Table 1. continued cluster size member color residues 641,642,645,648,652,655,661 672 green 6 9,12,16,46,48,49 Table 1. Clusters of top ranking residues in 2e7zA. 2.4.2 Overlap with known functional surfaces at 25% coverage. The name of the ligand is composed of the source PDB identifier and the heteroatom name used in that file. MGD binding site. Table 2 lists the top 25% of residues at the interface with 2e7zAMGD801 (mgd). The following table (Table 3) suggests possible disruptive replacements for these residues (see Section 3.6). Table 2. res type subst’s cvg noc/ dist (%) bb (A˚ ) 418 N N(95) 0.02 30/17 3.01 D(2) Fig. 5. Residues in 2e7zA, colored according to the cluster they belong to: red, followed by blue and yellow are the largest clusters (see Appendix for E(2) the coloring scheme). Clockwise: front, back, top and bottom views. The 141 C C(88) 0.08 23/2 2.50 corresponding Pymol script is attached. S(4) I(4) T(2) Table 1. 604 G G(88) 0.08 1/1 4.67 cluster size member .(2) color residues T(4) red 79 141,154,170,171,197,199,200 P(2) 201,202,204,207,210,211,213 A(2) 214,217,218,219,220,221,223 445 F F(79) 0.11 3/1 4.31 224,225,226,227,231,232,233 W(9) 235,237,238,239,242,243,246 Y(9) 249,250,253,256,257,260,262 M(2) 265,268,269,270,276,279,280 443 D D(77) 0.12 48/13 2.65 281,283,284,288,289,294,298 E(22) 308,313,315,317,318,319,324 447 T T(77) 0.12 5/0 3.34 554,555,557,558,559,560,561 S(9) 562,563,566,573,575,576,577 N(13) 578,580 613 S S(79) 0.12 19/8 2.60 blue 71 61,62,65,66,68,70,73,74,78 A(4) 81,82,83,84,85,86,87,90,93 L(2) 94,102,104,111,114,124,125 Q(6) 129,130,131,132,133,406,407 T(6) 408,411,416,418,432,433,437 606 R R(72) 0.14 22/0 2.90 438,440,443,445,447,448,449 G(9) 453,454,456,457,458,464,465 S(2) 487,490,494,497,501,502,505 H(9) 606,613,616,622,628,676,677 K(4) 678,679,681,682 P(2) yellow 15 597,598,599,601,634,636,637 676 H H(65) 0.16 57/2 3.01 continued in next column continued in next column 3 Table 2. continued Table 3. res type subst’s cvg noc/ dist res type disruptive (%) bb (A˚ ) mutations R(11) 418 N (Y)(FWH)(T)(R) S(4) 141 C (R)(K)(E)(H) A(2) 604 G (R)(K)(E)(H) Y(11) 445 F (K)(E)(TQD)(R) V(2) 443 D (R)(FWH)(YVCAG)(K) G(2) 447 T (R)(K)(FWH)(M) 416 A G(43) 0.17 47/34 3.14 613 S (R)(K)(H)(FW) A(29) 606 R (D)(T)(YE)(SVCLAPIG) N(6) 676 H (E)(Q)(D)(M) S(18) 416 A (R)(K)(E)(Y) T(2) 111 T (KR)(Q)(H)(M) 111 T G(63) 0.22 12/1 2.64 465 R (TD)(Y)(EVA)(CLPIG) S(11) 114 N (Y)(FW)(H)(T) A(2) 424 A (R)(K)(Y)(EH) V(9) E(2) Table 3. List of disruptive mutations for the top 25% of residues in Y(2) 2e7zA, that are at the interface with MGD. H(2) T(4) L(2) 465 R E(2) 0.22 8/0 2.86 R(65) H(15) T(4) Q(4) K(2) Y(2) V(2) 114 N R(29) 0.24 39/13 2.93 N(11) K(11) .(18) M(2) S(6) G(13) H(2) T(4) 424 A S(9) 0.24 1/1 4.94 P(25) G(18) A(40) E(2) T(2) Fig. 6. Residues in 2e7zA, at the interface with MGD, colored by their rela- V(2) tive importance. The ligand (MGD) is colored green. Atoms further than 30A˚ away from the geometric center of the ligand, as well as on the line of sight to the ligand were removed. (See Appendix for the coloring scheme for the Table 2. The top 25% of residues in 2e7zA at the interface with protein chain 2e7zA.) MGD.(Field names: res: residue number in the PDB entry; type: amino acid type; substs: substitutions seen in the alignment; with the percentage of each type in the bracket; noc/bb: number of contacts with the ligand, with the num- Figure 6 shows residues in 2e7zA colored by their importance, at the ber of contacts realized through backbone atoms given in the bracket; dist: interface with 2e7zAMGD801. distance of closest apporach to the ligand. ) MGD binding site. Table 4 lists the top 25% of residues at the interface with 2e7zAMGD802 (mgd). The following table (Table 5) suggests possible disruptive replacements for these residues (see Section 3.6). 4 Table 4. Table 4. continued res type subst’s cvg noc/ dist res type subst’s cvg noc/ dist (%) bb (A˚ ) (%) bb (A˚ ) 200 D D(100) 0.01 164/31 1.80 S(2) 221 D D(100) 0.01 81/5 1.46 H(9) 219 G G(97) 0.02 29/29 2.88 K(4) R(2) P(2) 201 P P(97) 0.03 88/14 3.01 171 G G(84) 0.17 88/88 2.79 S(2) W(4) 12 C .(15) 0.06 5/0 4.65 S(2) C(81) A(6) H(2) N(2) 220 T T(86) 0.06 5/5 4.10 199 L V(52) 0.18 34/27 2.68 S(13) L(11) 48 K R(43) 0.07 23/0 2.94 I(36) K(50) 204 T N(9) 0.23 11/0 3.31 G(4) S(20) S(2) T(65) 218 Y S(6) 0.07 145/19 2.69 I(4) A(4) P(86) Table 4.
Load more

Recommended publications
  • Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
    Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg
    [Show full text]
  • Development of UASB-DHS System for Treating Industrial Wastewater Containing Ethylene Glycol
    Journal of Water and Environment Technology, Vol.13, No.2, 2015 Development of UASB-DHS System for Treating Industrial Wastewater Containing Ethylene Glycol Takahiro WATARI 1), Daisuke TANIKAWA2), Kyohei KURODA1), Akinobu NAKAMURA1), Nanako FUJII3), Fuminori YONEYAMA3), Osamu WAKISAKA3), Masashi HATAMOTO1), Takashi YAMAGUCHI 1) 1) Department of Environmental Systems Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan 2) Department of Civil and Environmental Engineering, National Institute of Technology, Kure College, 2-1-11 Agaminami, Kure, Hiroshima 737-8506, Japan 3) Fundamental Material Laboratory Office, Material Technology Research and Development Laboratory, Research and Development Headquarters, Sumitomo Riko Company Limited, 3-1 Higashi, Komaki, Aichi 485-8550, Japan ABSTRACT This study evaluated the performance of a novel treatment system consisting of an upflow anaerobic sludge blanket (UASB) and a downflow hanging sponge (DHS) for the treatment of industrial wastewater containing 8% ethylene glycol and 2% propylene glycol discharged from a rubber production unit. The system achieved high COD removal (91 ± 4.3%) and methane recovery (82 ± 20%) at an organic loading rate of 8.5 kg-COD/(m3·day). The UASB allowed an organic loading rate of 14 kg-COD/(m3·day) with a constant hydraulic retention time of 24 h. The COD of DHS effluent was 370 ± 250 mg-COD/L during the entire experimental period. Thus, the proposed system could be applicable for treating industrial wastewater containing ethylene glycol. Massively parallel 16S rRNA gene sequencing elucidated the microbial community structure of the UASB. The dominant family Pelobacteriaceae could mainly degrade the organic compounds of ethylene glycol and decomposed products of ethanol.
    [Show full text]
  • Syntrophics Bridging the Gap of Methanogenesis in the Jharia Coal
    g in Geno nin m i ic M s ta & a P Jha et al., J Data Mining Genomics Proteomics 2015, 6:3 D r f o Journal of o t e l DOI: 10.4172/2153-0602.1000177 o a m n r i c u s o J ISSN: 2153-0602 Data Mining in Genomics & Proteomics Short Communication Open Access Syntrophics Bridging the Gap of Methanogenesis in the Jharia Coal Bed Basin Priyanka Jha1,5*, Sujit Ghosh1,2 $, Kunal Mukhopadhyay1, Ashish Sachan1 and Ambarish S Vidyarthi 3,4 1Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India– 835215 2Department of Botany, J.K. College, Purulia, West Bengal, India– 723101 3Department of Biotechnology, Birla Institute of Technology, Mesra, Patna Extension, Bihar, India– 800014 4Institute of Engineering and Technology, Sitapur Road, Lucknow, India– 226021 5Discipline of Microbiology, School of Life Sciences, University of KwaZulu Natal, Pietermaritzburg Campus, Pietermaritzburg– 3201, South Africa $ - Authors contributed equally Abstract The bituminous and sub-bituminous rank of coals is being produced from the Jharia basin of Jharkhand which is the largest producer of CBM in India. Although there have been many reports on methanogenesis from Jharia, the present study deals with the special emphasis on the syntrophic microbes which can act as catalyst for the hydrogenotrophic methanogenesis. Using the metagenomic approach followed by 454 pyro sequencing, the presence of syntrophic community has been deciphered for the first time from the formation water samples of Jharia coal bed basin. The taxonomic assignment of unassembled clean metagenomic sequences was performed using BLASTX against the GenBank database through MG-RAST server.
    [Show full text]
  • Th Annual Argonne National Laboratory Soil Metagenomics
    th Annual 7Argonne National Laboratory Soil Metagenomics Meeting OCTOBER 21st- 23rd, 2015 Lisle/Naperville Hilton Hotel Lisle, IL Acknowledgements We would like to thank our sponsors for their generous support ArgonneSoilMetagenomicsMeeting2015 October 21, 2015 Welcome to the 7th Annual Argonne Soil Metagenomics Meeting! The aim of this series of meetings has been to incite discussion on the challenges and opportunities afforded by next-generation DNA sequencing and associated ‘omics approaches to understand the complex nature of soil microbial communities. This meeting aims to serve the research community by providing a venue for interaction among ecologists, microbiologists, bioinformaticists, and ‘omics enthusiasts — all focused on the wonders of life in soil. Through oral presentations, posters, discussion sessions, and participation by industry sponsors, the meeting will cover any aspect of soil metagenomics research, from technical development to data analysis to science breakthroughs. We hope you share your research, meet some new folks, learn something new, and enjoy the meeting! Sincerely, The Organizing Committee Sarah O’Brien, Chair Sarah Owens Darlyn Mishur Dionysios Antonopoulos Folker Meyer Will Trimble David Myrold 1 AGENDA Wednesday, October 21 7:30 Registration Continental breakfast 8:15 Introduction & announcements Session I: The Underexplored Biosphere 8:30 Ecological and evolutionary insight into the persistence of soil bacteria Jay T. Lennon, Stuart E. Jones 8:50 Phylogenetic distribution of resuscitation genes in soil microbes Fan Yang, Stuart E. Jones, Jay T. Lennon, Adina Howe 9:10 Moleculo hybrid synthetic long reads reconstruct full genomes from the rare biosphere with functional potential elucidated by high resolution mass spectrometry Richard Allen White III, Eric M.
    [Show full text]
  • Supplementary Material
    Supplementary Material 1 Supplementary Figures and Tables 1.1 Supplementary Figures Deltaproteobacterium PSCGC (2) Deltaproteobacteria Gammaproteobacteria bacterium isolate NP949 Gammaproteobacteria Deltaproteobacteria bacterium spp. (4) Deltaproteobacteria Streptomyces sp. CNQ-509 Actinobacteria candidate division KSB1 bacterium RBG_16_48_16 candidate division KSB1 Dethiobacter alkaliphilus AHT-1 Firmicutes-Clostridia Desulfuromonas sp. DDH-964 Deltaproteobacteria Desulfuromonas spp. (2) Deltaproteobacteria OTU-487 (Deltaproteobacteria bacterium 37-65-8) Spirochaetes bacterium (2) Spirochaetes Methanocella sp. RC-I Methanomicrobia Methanoregula boonei 6A8 Methanomicrobia candidate division OP9 bacterium SCGC AAA255-N14 Atribacteria Methanoregulace aearchaeon JGI M3C4D3-001-G22 Methanomicrobia Methanomicrobia (5) Methanofollis liminatans GKZPZ Methanomicrobia OTU-267 (uncultured microorganism) Candidatus Aminicenantes bacterium RBG_13_59_9 Aminicenantes Methanomassiliicoccus luminyensis B10 Thermoplasmata Anaerolineae bacterium CG_4_9_14_0_8 Chloroflexi Elusimicrobia bacterium GW (2) Elusimicrobia candidate division WOR-3 bacterium SM23_42 Methanomassiliicoccales archaeon RumEn M1 Thermoplasmata OTU-858 (uncultured microorganism) OTU-544 (uncultured bacterium) Theionarchaea archaeon DG-70-1 Theionarchaea Chloroflexi bacterium RIFOXYD12_FULL_57_15 Chloroflexi OTU-201 (uncultured bacterium) OTU-481 (uncultured bacterium) Methanomicrobia (6) Lentisphaerae bacterium (2) Lentisphaerae Fimicutes (5) Bdellovibrionales bacterium GWB1_55_8 Deltaproteobacteria
    [Show full text]
  • Fabrício César Heleno Santos a Relação Evolutiva Dos
    FABRÍCIO CÉSAR HELENO SANTOS A RELAÇÃO EVOLUTIVA DOS GENES ASSOCIADOS À FIXAÇÃO DE NITROGÊNIO MOGI DAS CRUZES 2007 2 UNIVERSIDADE DE MOGI DAS CRUZES FABRÍCIO CÉSAR HELENO SANTOS A RELAÇÃO EVOLUTIVA DOS GENES ASSOCIADOS À FIXAÇÃO DE NITROGÊNIO Dissertação apresentada ao Curso de Pós-graduação em Biotecnologia da Universidade de Mogi das Cruzes como requerimento parcial para a obtenção do grau de Mestre em Biotecnologia. ORIENTADOR: Prof. Dr. Welington Luiz de Araújo ÁREA DE CONCENTRAÇÃO: Biotecnologia aplicada a Recursos Naturais e Agronegócios MOGI DAS CRUZES 2007 3 4 “Dedico este trabalho primeiramente a Deus, que nos deu a vida e permite que façamos dela nossas grandes obras. Dedico também a meus pais que juntamente com Deus, me deram a vida e a razão de viver. “A Luana, minha esposa, que mesmo nos piores momentos, sempre esteve do meu lado” 5 “Nada em biologia faz sentido a não ser a luz da evolução” Theodosius Dobzhansky 6 7 AGRADECIMENTOS Ao orientador Prof. Dr. Welington Luis de Araújo pela confiança depositada em mim, pela oportunidade de realizar esse trabalho e principalmente pela orientação e amizade, que vem desde 2006 quando sem orientador, este me acolheu. Ao Prof. Dr. Vitor Miranda pelas significativas contribuições na realização deste. Ao Colegiado do curso de Pós-Graduação em Biotecnologia da Universidade de Mogi das Cruzes. À Secretária de Estado da Educação de São Paulo pelo auxílio financeiro através do Projeto Bolsa Mestrado. Ao meu pai Geraldo Medeiros Santos, à minha mãe Elizete Terzinha Heleno Santos e à minha irmã Adria Cristina Heleno Santos pelo incentivo, amor e atenção dedicados em todos os momentos.
    [Show full text]
  • Supplementary Material
    Supplementary Material Figure S1. SEM images of CNT_N after ball milling treatment. Int. J. Mol. Sci. 2021, 22, 2932. https://doi.org/10.3390/ijms22062932 www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2021, 22, 2932 2 of 11 Figure S2. Ethanol conversion in the anaerobic assays: (A) GS+E, (B) GS+CIP+E, (C) GS+E+CNT@2%Fe and (D) GS+CIP+E+CNT@2%Fe, over 3 cycles of CIP removal: ethanol (■), acetate (□) and methane (●) concentrations. Int. J. Mol. Sci. 2021, 22, 2932 3 of 11 Figure S3. Experimental setup of the biological assays in the presence and absence of CNM (GS + CIP + E + CNT, GS + CIP + E + CNT@2%Fe and GS + CIP + E). For blank and abiotic controls, substrate and GS was not added, respectively. Int. J. Mol. Sci. 2021, 22, 2932 4 of 11 Cycle 1, t = 0h Cycle 1, t = 24h Cycle 2, t = 0h Cycle 2, t = 24h Cycle 3, t = 0h Cycle 3, t = 8h Cycle 3, t = 24h Figure S4. HPLC chromatograms of the biological removal of CIP, in the presence of CNT@2%Fe (GS+CIP+E+CNT@2%Fe), at the beginning ( t=0h) and after 24 h of reaction in the three cycles of CIP addition. CIP was detected at the RT= 12.5 min and at 275 nm. Table S1. Removal of CIP (1 mmol L-1) in the absence and presence of the different CNM in the reactional medium without Na2S Removal Sample (%) No CNM 0 CNT 3.84 CNT_N 3.29 CNT_HNO3 3.18 1 Int.
    [Show full text]
  • Rf-076-25 Rf−076 複合微生物解析による環境質評価のための迅速・網羅的微生物検出・定量
    RF-076-25 ＲＦ−０７６ 複合微生物解析による環境質評価のための迅速・網羅的微生物検出・定量技術の開 発 （２）環境質評価のための微生物種検出DNAプローブの設計・評価と検出技術の環境への適用 独立行政法人産業技術総合研究所 生物機能工学研究部門 バイオメジャー研究グループ 野田尚宏 平成19～20年度合計予算額 8,705千円 （うち、平成20年度予算額 4,200千円） ※ 上記の合計予算額は、間接経費2,019千円を含む ［要旨］複合微生物群集中の特定微生物群（例えば好気性細菌、嫌気性細菌、メタン生成古細菌 や硝化菌、脱窒菌等）について、その変遷を定量的に評価する必要がある場合がある。その場合、 各微生物群を検出するためのDNAプローブや、標的とする核酸の国家計量標準および実用標準と 計測のトレーサビリティ体系を整備することが重要である。本サブテーマでは、バイオレメディ エーションや環境質評価に利用可能な微生物検出プローブ（16S rRNAを標的としたオリゴヌクレ オチドプローブ）を整備し、様々な微生物分類群を検出するための基盤を整備すると共に、その 検出と定量のための標準核酸物質となるrRNAライブラリを整備した。また、サブテーマ(1)で整備 した技術を実際の環境質評価に利用し、その有効性を確認することを目標に研究を行うことを目 標とする。本サブテーマでは、各種嫌気性微生物群、好気性微生物群や硝化細菌等のゲノムDNA を調整し、そこから16S rRNA遺伝子を増幅、プラスミドの形で保持する系を構築した。それらの プラスミドは、in vitroでrRNAを転写、合成できるよう作成し、人工的に容易にrRNAを調整するた めのライブラリを作成した（120種類）。また、特に嫌気性微生物群を検出するDNAプローブ群を 68種類整備し、その特異的切断条件を評価した。 ［キーワード］環境質評価、微生物定量技術、DNAプローブ、16S rRNA、核酸標準物質 １．はじめに バイオレメディエーション指針（平成17年3月30日環境省・経済産業省告示）においては、培養 した微生物を土壌等に導入する環境修復技術であるバイオオーグメンテーションの実施において 人・動物等への安全性の評価や生態系への影響評価（すなわち環境質評価）を実施することを求 めている。すなわち、生態系等への影響評価において、「当該土壌等の物質循環に深く関与して いる微生物のうち特定の種を選定して評価し、（中略）微生物の特定の種を選定して評価する場 合は一般細菌、硝化菌、脱窒菌等を選定して当該菌数の増減を測定」することが求められており、 好気性細菌、嫌気性細菌、メタン生成古細菌や硝化菌、脱窒菌等について、その変遷を評価する 必要がある。また、環境浄化などの目的で各種微生物資材が活用されているが、その性状や有効 性を微生物学的視点から正しく評価する手法と指針の整備が急務である。これらの分野において、 複合微生物群を培養法に依存することなく迅速、簡便かつ網羅的に（遺伝的に多様な微生物群を 同時並列的に）定性・定量するための技術は十分に確立されておらず、その基盤研究と技術の整 RF-076-26 備が急務となっている。また、それらの微生物群を分子生物学的に検出するにあたっては、その 計測標準にあたる核酸標準物質が整備されている必要があるが、その整備はほとんど行われてい ないのが現状である。 ２．研究目的 本サブテーマにおいては、バイオレメディエーションや環境質評価に利用可能な微生物検出プ ローブ（16S rRNAを標的としたオリゴヌクレオチドプローブ）を整備し、様々な微生物分類群を 検出するための基盤を整備すると共に、その検出と定量のための標準核酸物質となるrRNAライブ
    [Show full text]
  • Unravelling the Diversity of Magnetotactic Bacteria Through Analysis of Open Genomic Databases
    www.nature.com/scientificdata OPEN Unravelling the diversity of AnALySiS magnetotactic bacteria through analysis of open genomic databases Maria Uzun 1,2 ✉ , Lolita Alekseeva 1,2, Maria Krutkina1, Veronika Koziaeva 1 & Denis Grouzdev 1 Magnetotactic bacteria (MTB) are prokaryotes that possess genes for the synthesis of membrane- bounded crystals of magnetite or greigite, called magnetosomes. Despite over half a century of studying MTB, only about 60 genomes have been sequenced. Most belong to Proteobacteria, with a minority afliated with the Nitrospirae, Omnitrophica, Planctomycetes, and Latescibacteria. Due to the scanty information available regarding MTB phylogenetic diversity, little is known about their ecology, evolution and about the magnetosome biomineralization process. This study presents a large-scale search of magnetosome biomineralization genes and reveals 38 new MTB genomes. Several of these genomes were detected in the phyla Elusimicrobia, Candidatus Hydrogenedentes, and Nitrospinae, where magnetotactic representatives have not previously been reported. Analysis of the obtained putative magnetosome biomineralization genes revealed a monophyletic origin capable of putative greigite magnetosome synthesis. The ecological distributions of the reconstructed MTB genomes were also analyzed and several patterns were identifed. These data suggest that open databases are an excellent source for obtaining new information of interest. Introduction Te amount of data obtained from genome and metagenome sequencing has been sharply increasing for the last several years1. Tese data are kept in open databases, such as the widely used NCBI2 and IMG3 databases. In the case of IMG, the number of entries for metagenomic data greatly exceeds that for genomic ones3. In most cases, scientists use only a part of the sequencing information uploaded to the databases, leaving large quantities of information essentially unanalyzed.
    [Show full text]
  • Sulphate-Reducing Bacterial Diversity in a Calcareous Sandy Sediment Of
    DEPARTAMENTO DE MICROBIOLOGÍA Sulphate‐reducing bacterial diversity in a calcareous sandy sediment of Mallorca and community response to hydrocarbon contamination TESIS DOCTORAL Ana Belén Suárez Suárez Palma de Mallorca, 2012 The study was supported by the ECOSIP project (200530F0182‐200530F0183) funded by the CSIC, the FBBVA project BIOCON05/094, and the Spanish Ministry of Science and Innovation projects Consolider Ingenio 2010 CE‐CSD2007‐0005 and VEM2003‐0075‐C02‐01 (both co‐ financed with FEDER funding); additional funding was provided by the Max‐Planck Society and the Helmholtz Association. 2 Contents Resume ......................................................................................................................5 General Introduction..................................................................................................7 1. Anthropocene ‐ Mankind as a major geological force ............................................. 8 1.1. Fossil fuel consumption .............................................................................................................. 8 1.2. Petroleum composition .............................................................................................................. 9 1.3. Petroleum formation ................................................................................................................ 12 1.4. Environmental consequences of fossil fuel consumption ‐ hydrocarbon pollution in the marine environment ....................................................................................................................................14
    [Show full text]
  • Tochko Colostate 0053N 15136.Pdf (4.934Mb)
    THESIS PROCESSES GOVERNING THE PERFORMANCE OF OLEOPHILIC BIO-BARRIERS (OBBS) – LABORATORY AND FIELD STUDIES Submitted by Laura Tochko Department of Civil and Environmental Engineering In partial fulfillment of the requirements For the Degree of Master of Science Colorado State University Fort Collins, Colorado Fall 2018 Master’s Committee: Advisor: Tom Sale Joe Scalia Sally Sutton Copyright by Laura Elizabeth Tochko 2018 All Rights Reserved ABSTRACT PROCESSES GOVERNING THE PERFORMANCE OF OLEOPHILIC BIO-BARRIERS (OBBS) – LABORATORY AND FIELD STUDIES Petroleum sheens, a potential Clean Water Act violation, can occur at petroleum refining, distribution, and storage facilities located near surface water. In general, sheen remedies can be prone to failure due to the complex processes controlling the flow of light non-aqueous phase liquid (LNAPL) at groundwater/surface water interfaces (GSIs). Even a small gap in a barrier designed to resist the movement of LNAPL can result in a sheen of large areal extent. The cost of sheen remedies, exacerbated by failure, has led to research into processes governing sheens and development of the oleophilic bio-barrier (OBB). OBBs involve 1) an oleophilic (oil-loving) plastic geocomposite which intercepts and retains LNAPL and 2) cyclic delivery of oxygen and nutrients via tidally driven water level fluctuations. The OBB retains LNAPL that escapes the natural attenuation system through oleophilic retention and enhances the natural biodegradation capacity such that LNAPL is retained or degraded instead of discharging to form a sheen. Sand tank experiments were conducted to visualize the movement of LNAPL as a wetting and non-wetting fluid in a water-saturated tank.
    [Show full text]
  • 1Ti2 Lichtarge Lab 2006
    Pages 1–19 1ti2 Evolutionary trace report by report maker September 24, 2008 4 Notes on using trace results 17 4.1 Coverage 17 4.2 Known substitutions 17 4.3 Surface 17 4.4 Number of contacts 17 4.5 Annotation 17 4.6 Mutation suggestions 17 5 Appendix 17 5.1 File formats 17 5.2 Color schemes used 17 5.3 Credits 18 5.3.1 Alistat 18 5.3.2 CE 18 5.3.3 DSSP 18 5.3.4 HSSP 18 5.3.5 LaTex 18 5.3.6 Muscle 18 5.3.7 Pymol 18 5.4 Note about ET Viewer 18 5.5 Citing this work 18 5.6 About report maker 18 CONTENTS 5.7 Attachments 18 1 Introduction 1 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1ti2): 2 Chain 1ti2F 1 Title: Crystal structure of pyrogallol-phloroglucinol transhydro- 2.1 P80564 overview 1 xylase from pelobacter acidigallici 2.2 Multiple sequence alignment for 1ti2F 1 Compound: Mol id: 1; molecule: pyrogallol hydroxytransferase 2.3 Residue ranking in 1ti2F 1 large subunit; chain: a, c, e, g, i, k; synonym: transhydroxylase alpha 2.4 Top ranking residues in 1ti2F and their position on subunit; ec: 1.97.1.2; mol id: 2; molecule: pyrogallol hydroxytrans- the structure 2 ferase small subunit; chain: b, d, f, h, j, l; synonym: transhydroxylase 2.4.1 Clustering of residues at 28% coverage. 2 beta subunit; ec: 1.97.1.2 2.4.2 Overlap with known functional surfaces at Organism, scientific name: Pelobacter Acidigallici; 28% coverage.
    [Show full text]