Bioinformatic Evidence for a Widely Distributed, Ribosomally Produced
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Redalyc.Microorganisms Screening for Limonene Oxidation
Ciência e Tecnologia de Alimentos ISSN: 0101-2061 [email protected] Sociedade Brasileira de Ciência e Tecnologia de Alimentos Brasil LERIN, Lindomar; TONIAZZO, Geciane; de OLIVEIRA, Débora; ROTTAVA, Leda; DARIVA, Cláudio; CANSIAN, Rogério Luis; TREICHEL, Helen; PADILHA, Francine; Ceva ANTUNES, Octávio Augusto Microorganisms screening for limonene oxidation Ciência e Tecnologia de Alimentos, vol. 30, núm. 2, abril-junio, 2010, pp. 399-405 Sociedade Brasileira de Ciência e Tecnologia de Alimentos Campinas, Brasil Available in: http://www.redalyc.org/articulo.oa?id=395940100017 How to cite Complete issue Scientific Information System More information about this article Network of Scientific Journals from Latin America, the Caribbean, Spain and Portugal Journal's homepage in redalyc.org Non-profit academic project, developed under the open access initiative Ciência e Tecnologia de Alimentos ISSN 0101-2061 Microorganisms screening for limonene oxidation Seleção de microrganismos para oxidação de limoneno Original Lindomar LERIN1, Geciane TONIAZZO2, Débora de OLIVEIRA2*, Leda ROTTAVA1, Cláudio DARIVA3, Rogério Luis CANSIAN2, Helen TREICHEL2, Francine PADILHA3, Octávio Augusto Ceva ANTUNES1 Abstract Limonene is a monoterpene obtained in large amounts from essential oils and is used as a raw material for the synthesis of flavors and fine chemicals. Several pathways or routes for the microbial degradation of limonene making use of the cytochrome P450-dependent monooxygenases have been described. In this study, we present a fermentative screening of microorganisms in order to verify their ability to perform the desirable conversion. In parallel, the PCR technique was used to select the microorganisms that contain the limC gene, which is responsible for the conversion of carveol to carvone. -
Auxiliary Iron–Sulfur Cofactors in Radical SAM Enzymes☆
Biochimica et Biophysica Acta 1853 (2015) 1316–1334 Contents lists available at ScienceDirect Biochimica et Biophysica Acta journal homepage: www.elsevier.com/locate/bbamcr Review Auxiliary iron–sulfur cofactors in radical SAM enzymes☆ Nicholas D. Lanz a, Squire J. Booker a,b,⁎ a Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States b Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States article info abstract Article history: A vast number of enzymes are now known to belong to a superfamily known as radical SAM, which all contain a Received 19 September 2014 [4Fe–4S] cluster ligated by three cysteine residues. The remaining, unligated, iron ion of the cluster binds in Received in revised form 15 December 2014 contact with the α-amino and α-carboxylate groups of S-adenosyl-L-methionine (SAM). This binding mode Accepted 6 January 2015 facilitates inner-sphere electron transfer from the reduced form of the cluster into the sulfur atom of SAM, Available online 15 January 2015 resulting in a reductive cleavage of SAM to methionine and a 5′-deoxyadenosyl radical. The 5′-deoxyadenosyl Keywords: radical then abstracts a target substrate hydrogen atom, initiating a wide variety of radical-based transforma- – Radical SAM tions. A subset of radical SAM enzymes contains one or more additional iron sulfur clusters that are required Iron–sulfur cluster for the reactions they catalyze. However, outside of a subset of sulfur insertion reactions, very little is known S-adenosylmethionine about the roles of these additional clusters. This review will highlight the most recent advances in the identifica- Cofactor maturation tion and characterization of radical SAM enzymes that harbor auxiliary iron–sulfur clusters. -
From Sporulation to Intracellular Offspring Production: Evolution
FROM SPORULATION TO INTRACELLULAR OFFSPRING PRODUCTION: EVOLUTION OF THE DEVELOPMENTAL PROGRAM OF EPULOPISCIUM A Dissertation Presented to the Faculty of the Graduate School of Cornell University In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by David Alan Miller January 2012 © 2012 David Alan Miller FROM SPORULATION TO INTRACELLULAR OFFSPRING PRODUCTION: EVOLUTION OF THE DEVELOPMENTAL PROGRAM OF EPULOPISCIUM David Alan Miller, Ph. D. Cornell University 2012 Epulopiscium sp. type B is an unusually large intestinal symbiont of the surgeonfish Naso tonganus. Unlike most other bacteria, Epulopiscium sp. type B has never been observed to undergo binary fission. Instead, to reproduce, it forms multiple intracellular offspring. We believe this process is related to endospore formation, an ancient and complex developmental process performed by certain members of the Firmicutes. Endospore formation has been studied for over 50 years and is best characterized in Bacillus subtilis. To study the evolution of endospore formation in the Firmicutes and the relatedness of this process to intracellular offspring formation in Epulopiscium, we have searched for sporulation genes from the B. subtilis model in all of the completed genomes of members of the Firmicutes, in addition to Epulopiscium sp. type B and its closest relative, the spore-forming Cellulosilyticum lentocellum. By determining the presence or absence of spore genes, we see the evolution of endospore formation in closely related bacteria within the Firmicutes and begin to predict if 19 previously characterized non-spore-formers have the genetic capacity to form a spore. We can also map out sporulation-specific mechanisms likely being used by Epulopiscium for offspring formation. -
Annotation Guidelines for Experimental Procedures
Annotation Guidelines for Experimental Procedures Developed By Mohammed Alliheedi Robert Mercer Version 1 April 14th, 2018 1- Introduction and background information What is rhetorical move? A rhetorical move can be defined as a text fragment that conveys a distinct communicative goal, in other words, a sentence that implies an author’s specific purpose to readers. What are the types of rhetorical moves? There are several types of rhetorical moves. However, we are interested in 4 rhetorical moves that are common in the method section of a scientific article that follows the Introduction Methods Results and Discussion (IMRaD) structure. 1- Description of a method: It is concerned with a sentence(s) that describes experimental events (e.g., “Beads with bound proteins were washed six times (for 10 min under rotation at 4°C) with pulldown buffer and proteins harvested in SDS-sample buffer, separated by SDS-PAGE, and analyzed by autoradiography.” (Ester & Uetz, 2008)). 2- Appeal to authority: It is concerned with a sentence(s) that discusses the use of standard methods, protocols, and procedures. There are two types of this move: - A reference to a well-established “standard” method (e.g., the use of a method like “PCR” or “electrophoresis”). - A reference to a method that was previously described in the literature (e.g., “Protein was determined using fluorescamine assay [41].” (Larsen, Frandesn and Treiman, 2001)). 3- Source of materials: It is concerned with a sentence(s) that lists the source of biological materials that are used in the experiment (e.g., “All microalgal strains used in this study are available at the Elizabeth Aidar Microalgae Culture Collection, Department of Marine Biology, Federal Fluminense University, Brazil.” (Larsen, Frandesn and Treiman, 2001)). -
Biosynthesis of New Alpha-Bisabolol Derivatives Through a Synthetic Biology Approach Arthur Sarrade-Loucheur
Biosynthesis of new alpha-bisabolol derivatives through a synthetic biology approach Arthur Sarrade-Loucheur To cite this version: Arthur Sarrade-Loucheur. Biosynthesis of new alpha-bisabolol derivatives through a synthetic biology approach. Biochemistry, Molecular Biology. INSA de Toulouse, 2020. English. NNT : 2020ISAT0003. tel-02976811 HAL Id: tel-02976811 https://tel.archives-ouvertes.fr/tel-02976811 Submitted on 23 Oct 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE En vue de l’obtention du DOCTORAT DE L’UNIVERSITÉ DE TOULOUSE Délivré par l'Institut National des Sciences Appliquées de Toulouse Présentée et soutenue par Arthur SARRADE-LOUCHEUR Le 30 juin 2020 Biosynthèse de nouveaux dérivés de l'α-bisabolol par une approche de biologie synthèse Ecole doctorale : SEVAB - Sciences Ecologiques, Vétérinaires, Agronomiques et Bioingenieries Spécialité : Ingénieries microbienne et enzymatique Unité de recherche : TBI - Toulouse Biotechnology Institute, Bio & Chemical Engineering Thèse dirigée par Gilles TRUAN et Magali REMAUD-SIMEON Jury -
Supplemental Methods
Supplemental Methods: Sample Collection Duplicate surface samples were collected from the Amazon River plume aboard the R/V Knorr in June 2010 (4 52.71’N, 51 21.59’W) during a period of high river discharge. The collection site (Station 10, 4° 52.71’N, 51° 21.59’W; S = 21.0; T = 29.6°C), located ~ 500 Km to the north of the Amazon River mouth, was characterized by the presence of coastal diatoms in the top 8 m of the water column. Sampling was conducted between 0700 and 0900 local time by gently impeller pumping (modified Rule 1800 submersible sump pump) surface water through 10 m of tygon tubing (3 cm) to the ship's deck where it then flowed through a 156 µm mesh into 20 L carboys. In the lab, cells were partitioned into two size fractions by sequential filtration (using a Masterflex peristaltic pump) of the pre-filtered seawater through a 2.0 µm pore-size, 142 mm diameter polycarbonate (PCTE) membrane filter (Sterlitech Corporation, Kent, CWA) and a 0.22 µm pore-size, 142 mm diameter Supor membrane filter (Pall, Port Washington, NY). Metagenomic and non-selective metatranscriptomic analyses were conducted on both pore-size filters; poly(A)-selected (eukaryote-dominated) metatranscriptomic analyses were conducted only on the larger pore-size filter (2.0 µm pore-size). All filters were immediately submerged in RNAlater (Applied Biosystems, Austin, TX) in sterile 50 mL conical tubes, incubated at room temperature overnight and then stored at -80oC until extraction. Filtration and stabilization of each sample was completed within 30 min of water collection. -
Hydrogenases of Methanogens
ANRV413-BI79-18 ARI 27 April 2010 21:0 Hydrogenases from Methanogenic Archaea, Nickel, a Novel Cofactor, and H2 Storage Rudolf K. Thauer, Anne-Kristin Kaster, Meike Goenrich, Michael Schick, Takeshi Hiromoto, and Seigo Shima Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany; email: [email protected] Annu. Rev. Biochem. 2010. 79:507–36 Key Words First published online as a Review in Advance on H2 activation, energy-converting hydrogenase, complex I of the March 17, 2010 respiratory chain, chemiosmotic coupling, electron bifurcation, The Annual Review of Biochemistry is online at reversed electron transfer biochem.annualreviews.org This article’s doi: Abstract 10.1146/annurev.biochem.030508.152103 Most methanogenic archaea reduce CO2 with H2 to CH4. For the Copyright c 2010 by Annual Reviews. activation of H2, they use different [NiFe]-hydrogenases, namely All rights reserved energy-converting [NiFe]-hydrogenases, heterodisulfide reductase- 0066-4154/10/0707-0507$20.00 associated [NiFe]-hydrogenase or methanophenazine-reducing by University of Texas - Austin on 06/10/13. For personal use only. [NiFe]-hydrogenase, and F420-reducing [NiFe]-hydrogenase. The energy-converting [NiFe]-hydrogenases are phylogenetically related Annu. Rev. Biochem. 2010.79:507-536. Downloaded from www.annualreviews.org to complex I of the respiratory chain. Under conditions of nickel limitation, some methanogens synthesize a nickel-independent [Fe]- hydrogenase (instead of F420-reducing [NiFe]-hydrogenase) and by that reduce their nickel requirement. The [Fe]-hydrogenase harbors a unique iron-guanylylpyridinol cofactor (FeGP cofactor), in which a low-spin iron is ligated by two CO, one C(O)CH2-, one S-CH2-, and a sp2-hybridized pyridinol nitrogen. -
Changes in Soil Microbial Communities After Long-Term Warming Exposure" (2019)
University of Massachusetts Amherst ScholarWorks@UMass Amherst Doctoral Dissertations Dissertations and Theses October 2019 CHANGES IN SOIL MICROBIAL COMMUNITIES AFTER LONG- TERM WARMING EXPOSURE William G. Rodríguez-Reillo University of Massachusetts Amherst Follow this and additional works at: https://scholarworks.umass.edu/dissertations_2 Part of the Environmental Microbiology and Microbial Ecology Commons Recommended Citation Rodríguez-Reillo, William G., "CHANGES IN SOIL MICROBIAL COMMUNITIES AFTER LONG-TERM WARMING EXPOSURE" (2019). Doctoral Dissertations. 1757. https://doi.org/10.7275/15007293 https://scholarworks.umass.edu/dissertations_2/1757 This Open Access Dissertation is brought to you for free and open access by the Dissertations and Theses at ScholarWorks@UMass Amherst. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of ScholarWorks@UMass Amherst. For more information, please contact [email protected]. CHANGES IN SOIL MICROBIAL COMMUNITIES AFTER LONG-TERM WARMING EXPOSURE A Dissertation Presented by WILLIAM GABRIEL RODRÍGUEZ-REILLO Submitted to the Graduate School of the University of Massachusetts Amherst in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY SEPTEMBER 2019 Organismic and Evolutionary Biology © Copyright by William Gabriel Rodríguez-Reillo 2019 All Rights Reserved CHANGES IN SOIL MICROBIAL COMMUNITIES AFTER LONG-TERM WARMING EXPOSURE A Dissertation Presented by WILLIAM GABRIEL RODRÍGUEZ-REILLO Approved as to style and content by: _________________________________________ Jeffrey L. Blanchard, Chair _________________________________________ Courtney Babbitt, Member _________________________________________ David Sela, Member _________________________________________ Kristina Stinson, Member ______________________________________ Paige Warren, Graduate Program Director Organismic and Evolutionary Biology DEDICATION To my parents, William Rodriguez Arce and Carmen L. Reillo Batista. A quienes aún en la distancia me mantuvieron en sus oraciones. -
Metabolic Functions of the Human Gut Microbiota: the Role of Metalloenzymes Cite This: DOI: 10.1039/C8np00074c Lauren J
Natural Product Reports View Article Online REVIEW View Journal Metabolic functions of the human gut microbiota: the role of metalloenzymes Cite this: DOI: 10.1039/c8np00074c Lauren J. Rajakovich and Emily P. Balskus * Covering: up to the end of 2017 The human body is composed of an equal number of human and microbial cells. While the microbial community inhabiting the human gastrointestinal tract plays an essential role in host health, these organisms have also been connected to various diseases. Yet, the gut microbial functions that modulate host biology are not well established. In this review, we describe metabolic functions of the human gut microbiota that involve metalloenzymes. These activities enable gut microbial colonization, mediate interactions with the host, and impact human health and disease. We highlight cases in which enzyme characterization has advanced our understanding of the gut microbiota and examples that illustrate the diverse ways in which Received 14th August 2018 Creative Commons Attribution 3.0 Unported Licence. metalloenzymes facilitate both essential and unique functions of this community. Finally, we analyze Human DOI: 10.1039/c8np00074c Microbiome Project sequencing datasets to assess the distribution of a prominent family of metalloenzymes rsc.li/npr in human-associated microbial communities, guiding future enzyme characterization efforts. 1 Introduction our gut from infancy and plays a critical role in the development 2 Commensal colonization of the human gut: tness and and maintenance of healthy human physiology. It aids in adaptation developing the innate and adaptive immune systems,1,2 2.1 Glycan sulfation provides nutrients and vitamins,3 and protects against path- 4 This article is licensed under a 2.2 Glycan fucosylation ogen invasion. -
Gene Conservation Among Endospore-Forming Bacteria Reveals Additional Sporulation Genes in Bacillus Subtilis
Gene Conservation among Endospore-Forming Bacteria Reveals Additional Sporulation Genes in Bacillus subtilis Bjorn A. Traag,a Antonia Pugliese,a Jonathan A. Eisen,b Richard Losicka Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USAa; Department of Evolution and Ecology, University of California Davis Genome Center, Davis, California, USAb The capacity to form endospores is unique to certain members of the low-G؉C group of Gram-positive bacteria (Firmicutes) and requires signature sporulation genes that are highly conserved across members of distantly related genera, such as Clostridium and Bacillus. Using gene conservation among endospore-forming bacteria, we identified eight previously uncharacterized genes that are enriched among endospore-forming species. The expression of five of these genes was dependent on sporulation-specific transcription factors. Mutants of none of the genes exhibited a conspicuous defect in sporulation, but mutants of two, ylxY and ylyA, were outcompeted by a wild-type strain under sporulation-inducing conditions, but not during growth. In contrast, a ylmC mutant displayed a slight competitive advantage over the wild type specific to sporulation-inducing conditions. The phenotype of a ylyA mutant was ascribed to a defect in spore germination efficiency. This work demonstrates the power of combining phy- logenetic profiling with reverse genetics and gene-regulatory studies to identify unrecognized genes that contribute to a con- served developmental process. he formation of endospores is a distinctive developmental the successive actions of four compartment-specific sigma factors Tprocess wherein a dormant cell type (the endospore) is formed (appearing in the order F, E, G, and K), whose activities are inside another cell (the mother cell) and ultimately released into confined to the forespore (F and G) or the mother cell (E and the environment by lysis of the mother cell (1, 2). -
A Metagenomic Window Into the 2-Km-Deep Terrestrial Subsurface Aquifer Revealed Multiple Pathways of Organic Matter Decomposition Vitaly V
FEMS Microbiology Ecology, 94, 2018, fiy152 doi: 10.1093/femsec/fiy152 Advance Access Publication Date: 7 August 2018 Research Article RESEARCH ARTICLE A metagenomic window into the 2-km-deep terrestrial subsurface aquifer revealed multiple pathways of organic matter decomposition Vitaly V. Kadnikov1, Andrey V. Mardanov1, Alexey V. Beletsky1, David Banks3, Nikolay V. Pimenov4, Yulia A. Frank2,OlgaV.Karnachuk2 and Nikolai V. Ravin1,* 1Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prosp. 33-2, Moscow, 119071, Russia, 2Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Lenina prosp. 35, Tomsk, 634050, Russia, 3School of Engineering, Systems Power & Energy, Glasgow University, Glasgow G12 8QQ, and Holymoor Consultancy Ltd., 360 Ashgate Road, Chesterfield, Derbyshire S40 4BW, UK and 4Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prosp 33-2, Moscow, 119071, Russia ∗Corresponding author: Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prosp. 33-2, Moscow, 119071, Russia. Tel: +74997833264; Fax: +74991353051; E-mail: [email protected] One sentence summary: metagenome-assembled genomes of microorganisms from the deep subsurface thermal aquifer revealed functional diversity of the community and novel uncultured bacterial lineages Editor: Tillmann Lueders ABSTRACT We have sequenced metagenome of the microbial community of a deep subsurface thermal aquifer in the Tomsk Region of the Western Siberia, Russia. Our goal was the recovery of near-complete genomes of the community members to enable accurate reconstruction of metabolism and ecological roles of the microbial majority, including previously unstudied lineages. The water, obtained via a 2.6 km deep borehole 1-R, was anoxic, with a slightly alkaline pH, and a temperature around 45◦C. -
2018 Summer Symposium Program
Ofce of UNDERGRADUATE RESEARCH ® THE UNIVERSITY OF UTAH 2018 Summer Symposium THURSDAY, AUGUST 2, 2018 9:00AM - 12:00PM CROCKER SCIENCE CENTER UNIVERSITY OF UTAH 2018 SUMMER SYMPOSIUM Thursday, August 2, 2018 9:00 AM – 12:00 PM Crocker Science Center University of Utah The Office of Undergraduate Research is grateful for the generous support of the Office of the Vice President for Research. We are also thankful for the development of the Summer Research Program Partnership, which is a new collaboration among the Chemistry Research Experience for Undergraduates (REU), the Huntsman Cancer Institute’s PathMaker Cancer Research Program, the Native American Summer Research Internship (NARI), the Physics & Astronomy REU and Summer Undergraduate Research Program, and the Summer Program for Undergraduate Research (SPUR). Together, these programs are serving more than 90 undergraduate researchers in Summer 2018. Finally, we would like to express our utmost pride and congratulations to the students, graduate students, and faculty mentors without whose efforts and dedication this event would not be possible. PROGRAM SCHEDULE NOTE: All student presenters MUST check-in Snacks available at 10:15 AM in Room 205/206 8:30 – 9:00 AM CHECK-IN & POSTER SET-UP 9:00 – 10:30 AM POSTER SESSION I (ODD POSTERS) 10:30 AM – 12:00 PM POSTER SESSION II (EVEN POSTERS) 12:00 – 12:15 PM POSTER TAKE-DOWN 2 SCHEDULE OF PRESENTATIONS POSTER SESSION I 9:00 – 10:30 AM Poster 1 Presenter: Sara Alektiar (University of Michigan) Mentor: Matthew Sigman (Chemistry) Electrocatalytic Bis(bipyidine)ruthenium Hydroxylation of Tertiary and Benzylic C-H Bonds The Sigman and Du Bois labs recently reported a methodology that employs a bis(bipyridine)Ru catalyst operating in acidic water to achieve oxidation of tertiary and benzylic C-H bonds in the presence of basic amines.