DOCSLIB.ORG

1Hro Lichtarge Lab 2006

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
1Hro Lichtarge Lab 2006 Pages 1–6 1hro Evolutionary trace report by report maker September 28, 2008 4.3.1 Alistat 5 4.3.2 CE 6 4.3.3 DSSP 6 4.3.4 HSSP 6 4.3.5 LaTex 6 4.3.6 Muscle 6 4.3.7 Pymol 6 4.4 Note about ET Viewer 6 4.5 Citing this work 6 4.6 About report maker 6 4.7 Attachments 6 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1hro): Title: Molecular structure of a high potential cytochrome c2 isolated from rhodopila globiformis Compound: Mol id: 1; molecule: cytochrome c2; chain: a, b Organism, scientific name: Rhodopila Globiformis 1hro contains a single unique chain 1hroA (105 residues long) and its homologue 1hroB. CONTENTS 1 Introduction 1 2 CHAIN 1HROA 2.1 P00080 overview 2 Chain 1hroA 1 From SwissProt, id P00080, 98% identical to 1hroA: 2.1 P00080 overview 1 Description: Cytochrome c2. 2.2 Multiple sequence alignment for 1hroA 1 Organism, scientific name: Rhodopila globiformis (Rhodopseudo- 2.3 Residue ranking in 1hroA 1 monas globiformis). 2.4 Top ranking residues in 1hroA and their position on Taxonomy: Bacteria; Proteobacteria; Alphaproteobacteria; Rhodo- the structure 1 spirillales; Acetobacteraceae; Rhodopila. 2.4.1 Clustering of residues at 25% coverage. 2 Biophysicochemical properties: 2.4.2 Overlap with known functional surfaces at Redox potential: E(0) is +450 mV; 25% coverage. 2 Ptm: Binds 1 heme group per subunit. 2.4.3 Possible novel functional surfaces at 25% Similarity: Belongs to the cytochrome c family. coverage. 3 About: This Swiss-Prot entry is copyright. It is produced through a 3 Notes on using trace results 4 collaboration between the Swiss Institute of Bioinformatics and the EMBL outstation - the European Bioinformatics Institute. There are 3.1 Coverage 4 no restrictions on its use as long as its content is in no way modified 3.2 Known substitutions 4 and this statement is not removed. 3.3 Surface 5 3.4 Number of contacts 5 2.2 Multiple sequence alignment for 1hroA 3.5 Annotation 5 3.6 Mutation suggestions 5 For the chain 1hroA, the alignment 1hroA.msf (attached) with 31 sequences was used. The alignment was assembled through combi- 4 Appendix 5 nation of BLAST searching on the UniProt database and alignment 4.1 File formats 5 using Muscle program. It can be found in the attachment to this 4.2 Color schemes used 5 report, under the name of 1hroA.msf. Its statistics, from the alistat 4.3 Credits 5 program are the following: 1 Lichtarge lab 2006 Fig. 1. Residues 2-106 in 1hroA colored by their relative importance. (See Appendix, Fig.7, for the coloring scheme.) Format: MSF Number of sequences: 31 Total number of residues: 3204 Smallest: 101 Largest: 105 Average length: 103.4 Alignment length: 105 Average identity: 48% Most related pair: 98% Most unrelated pair: 30% Most distant seq: 51% Fig. 2. Residues in 1hroA, colored by their relative importance. Clockwise: front, back, top and bottom views. Furthermore, 11% of residues show as conserved in this alignment. The alignment consists of 41% eukaryotic ( 22% vertebrata, 12% plantae), and 54% prokaryotic sequences. (Descriptions of some sequences were not readily available.) The file containing the sequence descriptions can be found in the attachment, under the name 1hroA.descr. 2.3 Residue ranking in 1hroA The 1hroA sequence is shown in Fig. 1, with each residue colored according to its estimated importance. The full listing of residues in 1hroA can be found in the file called 1hroA.ranks sorted in the attachment. 2.4 Top ranking residues in 1hroA and their position on the structure In the following we consider residues ranking among top 25% of resi- dues in the protein . Figure 2 shows residues in 1hroA colored by their importance: bright red and yellow indicate more conserved/important residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment. 2.4.1 Clustering of residues at 25% coverage. Fig. 3 shows the top 25% of all residues, this time colored according to clusters they belong to. The clusters in Fig.3 are composed of the residues listed in Table 1. Fig. 3. Residues in 1hroA, colored according to the cluster they belong to: Table 1. red, followed by blue and yellow are the largest clusters (see Appendix for cluster size member the coloring scheme). Clockwise: front, back, top and bottom views. The corresponding Pymol script is attached. color residues red 16 6,7,11,15,19,22,23,33,34,36 52,53,96,97,100,101 blue 10 63,68,71,72,75,81,82,84,86 Table 1. continued 88 cluster size member continued in next column color residues Table 1. Clusters of top ranking residues in 1hroA. 2 2.4.2 Overlap with known functional surfaces at 25% coverage. Table 3. continued The name of the ligand is composed of the source PDB identifier res type disruptive and the heteroatom name used in that file. mutations HEM binding site. Table 2 lists the top 25% of residues at the 68 L (YR)(TH)(SKECG)(FQWD) interface with 1hroAHEM1 (hem). The following table (Table 3) sug- 71 Y (K)(Q)(EM)(NR) gests possible disruptive replacements for these residues (see Section 72 I (YR)(TH)(SKECG)(FQWD) 3.6). 36 L (Y)(T)(R)(H) 53 S (KR)(FQMWH)(NELPI)(Y) Table 2. 86 Y (K)(Q)(EM)(NR) res type subst’s cvg noc/ dist (%) bb (A˚ ) Table 3. List of disruptive mutations for the top 25% of residues in 22 C C(100) 0.11 29/10 1.76 1hroA, that are at the interface with HEM. 23 H H(100) 0.11 84/0 1.97 33 G G(100) 0.11 12/12 3.87 34 P P(100) 0.11 19/1 3.77 52 Y Y(100) 0.11 27/6 2.52 63 W W(100) 0.11 36/0 2.93 82 T T(100) 0.11 16/7 2.75 84 M M(100) 0.11 96/24 2.24 19 C C(96) 0.12 35/19 1.83 A(3) 68 L L(96) 0.13 3/0 3.46 I(3) 71 Y Y(67) 0.16 32/0 3.59 F(32) 72 I L(90) 0.20 5/0 3.65 I(9) 36 L L(87) 0.22 22/0 3.57 M(3) H(6) Q(3) 53 S T(29) 0.23 16/9 2.65 S(70) 86 Y F(83) 0.24 26/6 4.05 Y(16) Table 2. The top 25% of residues in 1hroA at the interface with HEM.(Field names: res: residue number in the PDB entry; type: amino acid Fig. 4. Residues in 1hroA, at the interface with HEM, colored by their relative type; substs: substitutions seen in the alignment; with the percentage of each importance. The ligand (HEM) is colored green. Atoms further than 30A˚ type in the bracket; noc/bb: number of contacts with the ligand, with the num- away from the geometric center of the ligand, as well as on the line of sight ber of contacts realized through backbone atoms given in the bracket; dist: to the ligand were removed. (See Appendix for the coloring scheme for the distance of closest apporach to the ligand. ) protein chain 1hroA.) Table 3. Figure 4 shows residues in 1hroA colored by their importance, at the res type disruptive interface with 1hroAHEM1. mutations 2.4.3 Possible novel functional surfaces at 25% coverage. One 22 C (KER)(FQMWHD)(NYLPI)(SVA) group of residues is conserved on the 1hroA surface, away from (or 23 H (E)(TQMD)(SNKVCLAPIG)(YR) susbtantially larger than) other functional sites and interfaces reco- 33 G (KER)(FQMWHD)(NYLPI)(SVA) gnizable in PDB entry 1hro. It is shown in Fig. 5. The right panel 34 P (YR)(TH)(SKECG)(FQWD) shows (in blue) the rest of the larger cluster this surface belongs to. 52 Y (K)(QM)(NEVLAPIR)(D) The residues belonging to this surface ”patch” are listed in Table 63 W (KE)(TQD)(SNCRG)(M) 4, while Table 5 suggests possible disruptive replacements for these 82 T (KR)(FQMWH)(NELPI)(D) residues (see Section 3.6). 84 M (Y)(TH)(SCRG)(FWD) 19 C (KER)(QHD)(FYMW)(N) continued in next column 3 Fig. 5. A possible active surface on the chain 1hroA. The larger cluster it belongs to is shown in blue. Table 4. res type substitutions(%) cvg 101 Y Y(96)F(3) 0.14 97 D D(90)N(9) 0.15 7 D D(77)S(9)N(12) 0.17 6 G G(80)A(9)P(6) 0.18 Q(3) 100 A A(90)S(6)E(3) 0.21 Fig. 6. Another possible active surface on the chain 1hroA. 96 A A(90)E(6)G(3) 0.25 Table 6. continued Table 4. Residues forming surface ”patch” in 1hroA. res type substitutions(%) cvg 84 M M(100) 0.11 88 G G(100) 0.11 Table 5. 19 C C(96)A(3) 0.12 res type disruptive 68 L L(96)I(3) 0.13 mutations 71 Y Y(67)F(32) 0.16 101 Y (K)(Q)(EM)(NR) 72 I L(90)I(9) 0.20 97 D (R)(FWH)(Y)(VCAG) 36 L L(87)M(3)H(6) 0.22 7 D (R)(FWH)(Y)(K) Q(3) 6 G (R)(E)(KH)(Y) 53 S T(29)S(70) 0.23 100 A (R)(Y)(K)(H) 86 Y F(83)Y(16) 0.24 96 A (R)(KY)(H)(E) Table 6.
Load more

Recommended publications
  • J. Gen. Appl. Microbiol., 55(1)
    J. Gen. Appl. Microbiol., 55, 43‒50 (2009) Full Paper Rhodovastum atsumiense gen. nov., sp. nov., a phototrophic alphaproteobacterium isolated from paddy soil Keiko Okamura,1 Takayoshi Hisada,1 Toshio Kanbe,2 and Akira Hiraishi1,* 1 Department of Ecological Engineering, Toyohashi University of Technology, Toyohashi 441‒8580, Japan 2 Laboratory of Medical Mycology, Research Institute for Disease Mechanism and Control, Nagoya University Graduate School of Medicine, Nagoya 466‒8550, Japan (Received September 10, 2008; Accepted November 13, 2008) A photoorganotrophic alphaproteobacterium designated strain G2-11T was isolated from sub- merged paddy soil. This bacterium had relatively large, oval to rod-shaped cells (2.0‒3.0×3.0‒10 μm). Cells were motile by means of single polar fl agella. The color of phototrophically growing cultures was reddish-brown. The cell extract had absorption maxima at 375, 465, 492, 529, 592, 804, and 844 nm, indicating the presence of bacteriochlorophyll a and carotenoides of the spiril- loxanthin series. Vesicular intracytoplasmic membranes were present. The main component of cellular fatty acids was C18:1ω7c. Ubiquinone-10 and rhodoquinone-10 were the major quinones. A 16S rRNA gene sequence analysis revealed that the isolate is closest to the acidophilic aerobic photosynthetic bacterium Acidisphaera rubrifaciens strain HS-AP3T (93.3% similarity). The G+C content of genomic DNA is 67.8 mol%. The name Rhodovastum atsumiense gen. nov., sp. nov. is proposed for the novel isolate. The type strain is strain G2-11T (=NBRC 104268T=KCTC 5708T). Key Words—phototrophic bacteria; purple nonsulfurbacteria; Rhodovastum atsumiense Introduction order Rhizobiales. The cell size of PPNS bacteria is less than 2 μm in diameter in most cases.
    [Show full text]
  • Descriptive Bacterial and Fungal Characterization of Propolis Using Ultra-High-Throughput Marker Gene Sequencing
    insects Communication Descriptive Bacterial and Fungal Characterization of Propolis Using Ultra-High-Throughput Marker Gene Sequencing Jose F. Garcia-Mazcorro 1 , Jorge R. Kawas 2 and Alicia G. Marroquin-Cardona 3,* 1 MNA de Mexico, Research and Development, San Nicolas de los Garza, Nuevo Leon 66477, Mexico; [email protected] 2 Faculty of Agronomy, Universidad Autonoma de Nuevo Leon, General Escobedo, Nuevo Leon 66050, Mexico; [email protected] 3 Faculty of Veterinary Medicine, Universidad Autonoma de Nuevo Leon, General Escobedo, Nuevo Leon 66050, Mexico * Correspondence: [email protected]; Tel.: +52-81-1340-4390 Received: 5 October 2019; Accepted: 8 November 2019; Published: 12 November 2019 Abstract: Bees harbor microorganisms that are important for host health, physiology, and survival. Propolis helps modulate the immune system and health of the colony, but little information is available about its microbial constituents. Total genomic DNA from samples of natural propolis from Apis mellifera production hives from four locations in Mexico were used to amplify a region of the 16S rRNA gene (bacteria) and the internal transcriber spacer (fungi), using PCR. The Illumina MiSeq platform was used to sequence PCR amplicons. Extensive variation in microbial composition was observed between the propolis samples. The most abundant bacterial group was Rhodopila spp. (median: 14%; range: 0.1%–27%), a group with one of the highest redox potential in the microbial world. Other high abundant groups include Corynebacterium spp. (median: 8.4%; 1.6%–19.5%) and Sphingomonas spp. (median: 5.9%; 0.03%–14.3%), a group that has been used for numerous biotechnological applications because of its biodegradative capabilities.
    [Show full text]
  • Geography, Not Host Identity, Shapes Bacterial Community in Reindeer Lichens
    bioRxiv preprint doi: https://doi.org/10.1101/2021.01.30.428927; this version posted January 31, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Geography, not host identity, shapes bacterial community in reindeer lichens 2 Marta Alonso-García1,2, * and Juan Carlos Villarreal A.1,2,3 3 1 Département de Biologie, Université Laval, Québec, G1V 0A6, Canada. 4 2 Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 5 0A6, Canada. 6 3 Royal Botanic Garden, 20A Inverleith Row, Edinburgh EH3 5LR. 7 * For correspondence. E-mail [email protected] 8 Factors driving bacteria in the boreal forest 9 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.01.30.428927; this version posted January 31, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Background and Aims Tremendous progress have been recently achieved in host- 2 microbe research, however, there is still a surprising lack of knowledge in many taxa. 3 Despite its dominance and crucial role in boreal forest, reindeer lichens have until now 4 received little attention. We characterize, for the first time, the bacterial community of 5 four species of reindeer lichens from Eastern North America’s boreal forests. We 6 analysed the effect of two factors (host-identity and geography) in the bacterial 7 community composition, we verified the presence of a common core bacteriota and 8 identified the most abundant core taxa.
    [Show full text]
  • Microbiological Analysis and Control of the Fruit Vinegar Production Process
    MICROBIOLOGICAL ANALYSIS AND CONTROL OF THE FRUIT VINEGAR PRODUCTION PROCESS Claudio Esteban Hidalgo Albornoz Dipòsit Legal: T.1422-2012 ADVERTIMENT. L'accés als continguts d'aquesta tesi doctoral i la seva utilització ha de respectar els drets de la persona autora. Pot ser utilitzada per a consulta o estudi personal, així com en activitats o materials d'investigació i docència en els termes establerts a l'art. 32 del Text Refós de la Llei de Propietat Intel·lectual (RDL 1/1996). Per altres utilitzacions es requereix l'autorització prèvia i expressa de la persona autora. En qualsevol cas, en la utilització dels seus continguts caldrà indicar de forma clara el nom i cognoms de la persona autora i el títol de la tesi doctoral. No s'autoritza la seva reproducció o altres formes d'explotació efectuades amb finalitats de lucre ni la seva comunicació pública des d'un lloc aliè al servei TDX. Tampoc s'autoritza la presentació del seu contingut en una finestra o marc aliè a TDX (framing). Aquesta reserva de drets afecta tant als continguts de la tesi com als seus resums i índexs. ADVERTENCIA. El acceso a los contenidos de esta tesis doctoral y su utilización debe respetar los derechos de la persona autora. Puede ser utilizada para consulta o estudio personal, así como en actividades o materiales de investigación y docencia en los términos establecidos en el art. 32 del Texto Refundido de la Ley de Propiedad Intelectual (RDL 1/1996). Para otros usos se requiere la autorización previa y expresa de la persona autora.
    [Show full text]
  • Oecophyllibacter Saccharovorans Gen. Nov. Sp. Nov., a Bacterial Symbiont of the Weaver Ant Oecophylla Smaragdina with a Plasmid-Borne Sole Rrn Operon
    bioRxiv preprint doi: https://doi.org/10.1101/2020.02.15.950782; this version posted March 26, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Oecophyllibacter saccharovorans gen. nov. sp. nov., a bacterial symbiont of the weaver ant Oecophylla smaragdina with a plasmid-borne sole rrn operon Kah-Ooi Chuaa, Wah-Seng See-Tooa, Jia-Yi Tana, Sze-Looi Songb, c, Hoi-Sen Yonga, Wai-Fong Yina, Kok-Gan Chana,d* a Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia b Institute of Ocean and Earth Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia c China-ASEAN College of Marine Sciences, Xiamen University Malaysia, 43900 Sepang, Selangor, Malaysia d International Genome Centre, Jiangsu University, Zhenjiang, China * Corresponding author at: Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia Email address: [email protected] Keywords: Acetobacteraceae, Insect, Whole genome sequencing, Phylogenomics, Plasmid-borne rrn operon Abstract In this study, acetic acid bacteria (AAB) strains Ha5T, Ta1 and Jb2 that constitute the core microbiota of weaver ant Oecophylla smaragdina were isolated from multiple ant colonies and were distinguished as different strains by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry and distinctive random-amplified polymorphic DNA (RAPD) fingerprints. These strains showed similar phenotypic characteristics and were considered a single species by multiple delineation indexes. 16S rRNA gene sequence-based phylogenetic analysis and phylogenomic analysis based on 96 core genes placed the strains in a distinct lineage in family Acetobacteraceae.
    [Show full text]
  • Oecophyllibacter Saccharovorans Gen. Nov. Sp. Nov., A
    bioRxiv preprint doi: https://doi.org/10.1101/2020.02.15.950782; this version posted February 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Oecophyllibacter saccharovorans gen. nov. sp. nov., a 2 bacterial symbiont of the weaver ant Oecophylla smaragdina 3 with a plasmid-borne sole rrn operon 4 Kah-Ooi Chuaa, Wah-Seng See-Tooa, Jia-Yi Tana, Sze-Looi Songb, c, Hoi-Sen Yonga, Wai-Fong 5 Yina, Kok-Gan Chana,d* a Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia b Institute of Ocean and Earth Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia c China-ASEAN College of Marine Sciences, Xiamen University Malaysia, 43900 Sepang, Selangor, Malaysia d International Genome Centre, Jiangsu University, Zhenjiang, China * Corresponding author Email address: [email protected] 6 Keywords: 7 Acetobacteraceae, Insect, Whole genome sequencing, Phylogenomics, Plasmid-borne rrn operon 8 9 Abstract 10 In this study, acetic acid bacteria (AAB) strains Ha5T, Ta1 and Jb2 that constitute the core microbiota 11 of weaver ant Oecophylla smaragdina were isolated from multiple ant colonies and were distinguished 12 as different strains by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass 13 spectrometry and distinctive random-amplified polymorphic DNA (RAPD) fingerprints. These strains 14 showed similar phenotypic characteristics and were considered a single species by multiple delineation 15 indexes. 16S rRNA gene sequence-based phylogenetic analysis and phylogenomic analysis based on 16 96 core genes placed the strains in a distinct lineage in family Acetobacteraceae.
    [Show full text]
  • Uncovering Multi-Faceted Taxonomic and Functional Diversity of Soil
    www.nature.com/scientificreports OPEN Uncovering multi‑faceted taxonomic and functional diversity of soil bacteriomes in tropical Southeast Asian countries Somsak Likhitrattanapisal, Paopit Siriarchawatana, Mintra Seesang, Suwanee Chunhametha, Worawongsin Boonsin, Chitwadee Phithakrotchanakoon, Supattra Kitikhun, Lily Eurwilaichitr* & Supawadee Ingsriswang* Environmental microbiomes encompass massive biodiversity and genetic information with a wide‑ranging potential for industrial and agricultural applications. Knowledge of the relationship between microbiomes and environmental factors is crucial for translating that information into practical uses. In this study, the integrated data of Southeast Asian soil bacteriomes were used as models to assess the variation in taxonomic and functional diversity of bacterial communities. Our results demonstrated that there were diferences in soil bacteriomes across diferent geographic locality with diferent soil characteristics: soil class and pH level. Such diferences were observed in taxonomic diversity, interspecifc association patterns, and functional diversity of soil bacteriomes. The bacterial‑mediated biogeochemical cycles of nitrogen, sulfur, carbon, and phosphorus illustrated the functional relationship of soil bacteriome and soil characteristics, as well as an infuence from bacterial interspecifc interaction. The insights from this study reveal the importance of microbiome data integration for future microbiome research. Recent advancements in high-throughput sequencing and metagenomic technologies
    [Show full text]
  • Insights Into Autotrophic Activities and Carbon Flow in Iron-Rich Pelagic Aggregates (Iron Snow)
    microorganisms Article Insights into Autotrophic Activities and Carbon Flow in Iron-Rich Pelagic Aggregates (Iron Snow) Qianqian Li 1 , Rebecca E. Cooper 1 , Carl-Eric Wegner 1 , Martin Taubert 1, Nico Jehmlich 2 , Martin von Bergen 2,3 and Kirsten Küsel 1,4,* 1 Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743 Jena, Germany; [email protected] (Q.L.); [email protected] (R.E.C.); [email protected] (C.-E.W.); [email protected] (M.T.) 2 Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research—UFZ, Permoserstrasse 15, 04318 Leipzig, Germany; [email protected] (N.J.); [email protected] (M.v.B.) 3 Pharmacy and Psychology, Faculty of Biosciences, Institute of Biochemistry, University of Leipzig, Brüderstraße 32, 04103 Leipzig, Germany 4 The German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany * Correspondence: [email protected]; Tel.: +49-3641-949461 Abstract: Pelagic aggregates function as biological carbon pumps for transporting fixed organic carbon to sediments. In iron-rich (ferruginous) lakes, photoferrotrophic and chemolithoautotrophic bacteria contribute to CO2 fixation by oxidizing reduced iron, leading to the formation of iron-rich pelagic aggregates (iron snow). The significance of iron oxidizers in carbon fixation, their general role in iron snow functioning and the flow of carbon within iron snow is still unclear. Here, we combined a two-year metatranscriptome analysis of iron snow collected from an acidic lake with protein-based Citation: Li, Q.; Cooper, R.E.; 13 stable isotope probing to determine general metabolic activities and to trace CO2 incorporation Wegner, C.-E.; Taubert, M.; Jehmlich, in iron snow over time under oxic and anoxic conditions.
    [Show full text]
  • Complete Genome Sequence of Strain HIMB100, a Cultured Representative of the SAR116 Clade of Marine Alphaproteobacteria
    Complete genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria Jana Grote1,2, Cansu Bayindirli1,3, Kristin Bergauer1,4, Paula Carpintero de Moraes1,5, Huan Chen1,6, Lindsay D’Ambrosio1,7, Bethanie Edwards1,8, Beatriz Fernández-Gómez1,9, Miriam Hamisi1,10, Ramiro Logares1,9, Dan Nguyen1,11, Yoshimi M. Rii1,12, Emily Saeck1,13, Charles Schutte1,14, Brittany Widner1,15, Matthew J. Church1,12, Grieg F. Steward1,12, David M. Karl1,12, Edward F. DeLong1,16, John M. Eppley1,16, Stephan Schuster1,17, Nikos C. Kyrpides1,18, and Michael S. Rappé1,2* 1 Center for Microbial Oceanography: Research and Education, 2010 Summer Course in Microbial Oceanography, SOEST, University of Hawaii, Honolulu, Hawaii, USA 2 Hawaii Institute of Marine Biology, SOEST, University of Hawaii, Kaneohe, Hawaii, USA 3 Plymouth Marine Laboratory, University of East Anglia, Norwich, UK 4 Department of Marine Biology, University of Vienna, Vienna, Austria 5 Instituto Oceanografico, Universidade de Sao Paulo, Sao Paulo, Brazil 6 Environmental Sciences Institute, Florida A&M University, Tallahassee, Florida, USA 7 Department of Marine Sciences, University of North Carolina, Chapel Hill, North Carolina, USA 8 Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA 9 Departament de Biologia Marina i Oceanografia, Institut de Cièncias del Mar, CMIMA, CSIC, Barcelona, Spain 10 School of Natural Sciences and Mathematics, The University of Dodoma, Dodoma, Tanzania 11 Département de
    [Show full text]
  • Thinning Partially Mitigates the Impact of Atlantic Forest Replacement by Pine Monocultures on the Soil Microbiome
    fmicb-11-01491 July 2, 2020 Time: 16:18 # 1 ORIGINAL RESEARCH published: 03 July 2020 doi: 10.3389/fmicb.2020.01491 Thinning Partially Mitigates the Impact of Atlantic Forest Replacement by Pine Monocultures on the Soil Microbiome Carolina Paola Trentini1, Paula Inés Campanello2, Mariana Villagra1, Julian Ferreras3 and Martin Hartmann4* 1 Laboratorio de Ecología Forestal y Ecofisiología, Instituto de Biología Subtropical, CONICET-UNaM, Puerto Iguazú, Misiones, Argentina, 2 Centro de Estudios Ambientales Integrados, Facultad de Ingeniería, Universidad Nacional de la Patagonia San Juan Bosco, CONICET, Esquel, Argentina, 3 Grupo de Investigación en Genética Aplicada, Instituto de Biología Subtropical, CONICET-UNaM, Posadas, Misiones, Argentina, 4 Sustainable Agroecosystems, Department of Environmental Systems Science, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland Forest replacement by exotic plantations drive important changes at the level of the overstory, understory and forest floor. In the Atlantic Forest of northern Argentina, large areas have been replaced by loblolly pine (Pinus taeda L.) monocultures. Plant and litter transformation, together with harvesting operations, change microclimatic Edited by: conditions and edaphic properties. Management practices such as thinning promote Jaak Truu, University of Tartu, Estonia the development of native understory vegetation and could counterbalance negative Reviewed by: effects of forest replacement on soil. Here, the effects of pine plantations and thinning Dima Chen, on physical, chemical and microbiological soil properties were assessed. Bacterial, China Three Gorges University, China archaeal, and fungal community structure were analyzed using a metabarcoding Yu-Te Lin, Academia Sinica, Taiwan approach targeting ribosomal markers. Forest replacement and, to a lesser extent, *Correspondence: thinning practices in the pine plantations induced significant changes in soil physico- Martin Hartmann chemical properties and associated shifts in bacterial and fungal communities.
    [Show full text]
  • Antonie Van Leeuwenhoek Genome Analysis Suggests the Bacterial
    Antonie van Leeuwenhoek Genome analysis suggests the bacterial family Acetobacteraceae is a source of undiscovered specialized metabolites Juan Guzman1,*, Andreas Vilcinskas1,2 1 Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, D-35392 Giessen, Germany 2 Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, D-35392, Giessen, Germany Corresponding author: Juan Guzman [email protected] Telefon +49 641 9937761 Fax +49 641 4808581 ORCID: Juan Guzman (0000-0003-4120-9065) Andreas Vilcinskas (0000-0001-8276-4968) Abstract Acetobacteraceae is an economically important family of bacteria that is used for industrial fermentation in the food/feed sector and for the preparation of sorbose and bacterial cellulose. It comprises two major groups: acetous species (acetic acid bacteria) associated with flowers, fruits and insects, and acidophilic species, a phylogenetically basal and physiologically heterogeneous group inhabiting acid or hot springs, sludge, sewage and freshwater environments. Despite the biotechnological importance of the family Acetobacteraceae, the literature does not provide any information about its ability to produce specialized metabolites. We therefore constructed a phylogenomic tree based on concatenated protein sequences from 127 type strains of the family and predicted the presence of small-molecule biosynthetic gene clusters (BGCs) using the antiSMASH tool. This dual approach allowed us to associate certain biosynthetic pathways with particular taxonomic groups. We found that acidophilic and acetous species contain on average ~6 and ~3.4 BGCs per genome, respectively. All the Acetobacteraceae strains encoded proteins associated involved in hopanoid biosynthesis, with many also featuring genes encoding type-1 and type-3 polyketide and non-ribosomal peptide synthases, and enzymes for aryl polyene, lactone and ribosomal peptide biosynthesis.
    [Show full text]
  • Anaerobic 3-Methylhopanoid Production by an Acidophilic Phototrophic Purple Bacterium
    Anaerobic 3-Methylhopanoid Production By An Acidophilic Phototrophic Purple Bacterium Marisa Mayer ( [email protected] ) Stanford University School of Earth Energy and Environmental Sciences https://orcid.org/0000-0002- 0493-0163 Mary N. Parenteau NASA Ames Research Center Megan L. Kempher University of Oklahoma: The University of Oklahoma Michael T. Madigan Southern Illinois University Carbondale Linda L. Jahnke NASA Ames Research Center Paula V. Welander Stanford University School of Earth Energy and Environmental Sciences Research Article Keywords: anoxygenic phototrophs, Rhodopila globiformis, hopanoids, warm thermal springs Posted Date: April 7th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-390249/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/14 Abstract Bacterial lipids are well preserved in ancient rocks and certain ones have been used as indicators of specic bacterial metabolisms or environmental conditions existing at the time of rock deposition. Here we show that an anaerobic bacterium produces 3-methylbacteriohopanepolyols (3-MeBHPs), pentacyclic lipids previously detected only in aerobic bacteria and widely used as biomarkers for methane-oxidizing bacteria. Both Rhodopila globiformis, a phototrophic purple nonsulfur bacterium isolated from an acidic warm spring in Yellowstone, and a newly isolated Rhodopila species from a geochemically similar spring in Lassen Volcanic National Park (USA), synthesized 3-MeBHPs and a suite of related BHPs and contained the genes encoding the necessary biosynthetic enzymes. Our results show that 3-MeBHPs can be produced under anoxic conditions and challenges the use of 3-MeBHPs as biomarkers of oxic conditions in ancient rocks and as prima facie evidence that methanotrophic bacteria were active when the rocks were deposited.
    [Show full text]