DOCSLIB.ORG

Characterizing Restriction-Modification Systems

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Characterizing Restriction-Modification Systems University of Connecticut OpenCommons@UConn Doctoral Dissertations University of Connecticut Graduate School 8-5-2019 Characterizing Restriction-Modification Systems and DNA Methyltransferases in the Halobacteria Matthew Ouellette University of Connecticut - Storrs, [email protected] Follow this and additional works at: https://opencommons.uconn.edu/dissertations Recommended Citation Ouellette, Matthew, "Characterizing Restriction-Modification Systems and DNA Methyltransferases in the Halobacteria" (2019). Doctoral Dissertations. 2280. https://opencommons.uconn.edu/dissertations/2280 Characterizing Restriction-Modification Systems and DNA Methyltransferases in the Halobacteria Matthew Ouellette, Ph.D. University of Connecticut, 2019 Abstract The Halobacteria are a class of archaeal organisms which are obligate halophiles. Several studies have described the Halobacteria as highly recombinogenic, yet members even within the same geographic location cluster into distinct phylogroups, suggesting that barriers exist which limit recombination. Barriers to recombination in the Halobacteria include CRISPRs, glycosylation, and archaeosortases. Another possible barrier which could limit gene transfer might be restriction-modification (RM) systems, which consist of restriction endonucleases (REases) and DNA methyltransferases (MTases) that both target the same sequence of DNA. The REase cleaves the target sequence, whereas the MTase methylates the site and protects it from cleavage. This dissertation examines the role of DNA methylation and RM systems in the Halobacteria and their impact on halobacterial speciation and genetic recombination. Using the model haloarchaeon, Haloferax volcanii, the genomic DNA methylation patterns (methylome) of an archaeal organism was characterized for the first time. Further investigations via gene deletion were used to identify the DNA methyltransferases responsible for the detected methylation patterns in H. volcanii, and experiments were conducted to determine the impact of RM systems on recombination via cell-to-cell mating. The distribution of MTase and RM system genes throughout the Halobacteria was also examined using a bioinformatics approach. The results indicated that the methylome of H. volcanii consists of two methylated motifs: GCAm6BNNNNNNVTGC, methylated by the Type I RM system RmeRMS, and Cm4TAG, methylated by the orphan MTase HVO_0794. Three other putative MTase genes (HVO_C0040, HVO_A0079, and HVO_A0237) were also identified, but were not observed to contribute to the Matthew Ouellette, University of Connecticut, 2019 methylome. Results from mating experiments indicated that RM systems could potentially limit recombination via cell-to-cell mating in H. volcanii. Furthermore, RM system genes were observed to be patchily distributed among the Halobacteria, whereas orphan MTase gene families were more widespread and well-conserved. The results of these studies provide insight into the life cycle of RM systems in the Halobacteria and how they might contribute to halobacterial diversification and speciation. The RM deletion mutants of H. volcanii also have the potential to be useful in future work examining the role of RM systems and DNA methylation in the Halobacteria. Characterizing Restriction-Modification Systems and DNA Methyltransferases in the Halobacteria Matthew Ouellette B.S., Post University, 2011 A Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy at the University of Connecticut i Copyright by: Matthew Ouellette 2019 ii APPROVAL PAGE Doctor of Philosophy Dissertation Characterizing Restriction-Modification Systems and DNA Methyltransferases in the Halobacteria Presented by: Matthew Ouellette, B.S. Major Advisor _______________________________________________________________________ R. Thane Papke, Ph.D. Associate Advisor _______________________________________________________________________ Johann Peter Gogarten, Ph.D. Associate Advisor _______________________________________________________________________ Daniel Gage, Ph.D. Associate Advisor _______________________________________________________________________ Kenneth Noll, Ph.D. Associate Advisor _______________________________________________________________________ Michael O’Neill, Ph.D. University of Connecticut 2019 iii This dissertation is dedicated to my father, Michael Ouellette, whose support and encouragement was the greatest thing a son could ask for. iv Acknowledgements I would like to thank my parents, Melanie and Michael Ouellette, and my brother Eric Ouellette. My family has been the greatest blessing in my life, and this work would not have been possible without their love and support. I would also like to thank my major advisor, Thane Papke, whose guidance and creative ideas were essential to shaping my dissertation work and helping me to grow as a researcher. Thank you, also, to Andrea Makkay, Sean Pearson, Jess Lajoie, Scott Chimileski, Nikhil Ram Mohan, and all current and former Papke Lab members, who provided a wonderful, friendly, and supportive work environment. I am also grateful to Artemis Louyakis and Matt Fullmer of the Gogarten Lab for their support, friendship, and bioinformatics expertise. I am also thankful for the support of my associate advisors: Peter Gogarten, Dan Gage, Ken Noll, and Mike O’Neill. v Table of Contents Chapter 1. Introduction.................................................................................................................1 1. Halobacteria .............................................................................................................................1 1.1 Classification and Taxonomy of the Halobacteria .............................................................1 1.2 A Brief History of Halobacteria Discoveries .....................................................................3 1.3 Habitats of Halobacteria .....................................................................................................4 1.4 Physiology of Halobacteria ................................................................................................9 1.5 Genetics of Halobacteria ..................................................................................................13 1.6 Gene Transfer and Recombination in the Halobacteria ...................................................16 2. DNA Methylation and Methyltransferases.............................................................................20 2.1 What is DNA Methylation? ..............................................................................................20 2.2 What are DNA Methyltransferases? .................................................................................21 2.3 Strategies for Detecting DNA Methylation Patterns ........................................................22 3. Restriction-Modification Systems ..........................................................................................24 3.1 What are Restriction-Modification Systems? ...................................................................24 3.2 A Brief History of RM System Discoveries in Bacteria ..................................................25 3.3 Classes of RM Systems ....................................................................................................26 4. Orphan Methyltransferases ....................................................................................................28 4.1 What are Orphan Methyltransferases? .............................................................................28 4.2 DNA Adenine Methyltransferase (Dam) In Escherichia coli ..........................................28 4.3 Cell-Cycle-Regulated Methyltransferase (CcrM) in Caulobacter crescentus .................30 4.4 Campylobacter Transformation System Methyltransferase (CtsM) in Campylobacter jejuni .......................................................................................................................................31 5. DNA Methylation and RM Systems in the Archaea .............................................................32 5.1 RM Systems in Thermophilic Archaea ............................................................................32 5.2 RM Systems in Methanogenic Archaea ..........................................................................35 5.3 RM Systems in the Halobacteria ......................................................................................37 5.4 Domain-wide Investigation of Archaeal DNA Methylation and RM Systems ................38 6. Conclusion ..............................................................................................................................39 References ..................................................................................................................................41 Chapter 2. Dihydroxyacetone metabolism in Haloferax volcanii ............................................58 vi Abstract ......................................................................................................................................59 Introduction ................................................................................................................................59 Materials and Methods ...............................................................................................................60 Strains and Growth Conditions ..............................................................................................60 PCR
Load more

Recommended publications
  • Halorubrum Chaoviator Mancinelli Et Al. 2009 Is a Later, Heterotypic Synonym of Halorubrum Ezzemoulense Kharroub Et Al
    TAXONOMIC DESCRIPTION Corral et al., Int J Syst Evol Microbiol 2018;68:3657–3665 DOI 10.1099/ijsem.0.003005 Halorubrum chaoviator Mancinelli et al. 2009 is a later, heterotypic synonym of Halorubrum ezzemoulense Kharroub et al. 2006. Emended description of Halorubrum ezzemoulense Kharroub et al. 2006 Paulina Corral,1 Rafael R. de la Haba,1 Carmen Infante-Domínguez,1 Cristina Sanchez-Porro, 1 Mohammad A. Amoozegar,2 R. Thane Papke3 and Antonio Ventosa1,* Abstract A polyphasic comparative taxonomic study of Halorubrum ezzemoulense Kharroub et al. 2006, Halorubrum chaoviator Mancinelli et al. 2009 and eight new Halorubrum strains related to these haloarchaeal species was carried out. Multilocus sequence analysis using the five concatenated housekeeping genes atpB, EF-2, glnA, ppsA and rpoB¢, and phylogenetic analysis based on the 757 core protein sequences obtained from their genomes showed that Hrr. ezzemoulense DSM 17463T, Hrr. chaoviator Halo-G*T (=DSM 19316T) and the eight Halorubrum strains formed a robust cluster, clearly separated from the remaining species of the genus Halorubrum. The orthoANI value and digital DNA–DNA hybridization value, calculated by the Genome-to-Genome Distance Calculator (GGDC), showed percentages among Hrr. ezzemoulense DSM 17463T, Hrr. chaoviator DSM 19316T and the eight Halorubrum strains ranging from 99.4 to 97.9 %, and from 95.0 to 74.2 %, respectively, while these values for those strains and the type strains of the most closely related species of Halorubrum were 88.7–77.4 % and 36.1– 22.3 %, respectively. Although some differences were observed, the phenotypic and polar lipid profiles were quite similar for all the strains studied.
    [Show full text]
  • Delft University of Technology Halococcoides Cellulosivorans Gen
    Delft University of Technology Halococcoides cellulosivorans gen. nov., sp. nov., an extremely halophilic cellulose- utilizing haloarchaeon from hypersaline lakes Sorokin, Dimitry Y.; Khijniak, Tatiana V.; Elcheninov, Alexander G.; Toshchakov, Stepan V.; Kostrikina, Nadezhda A.; Bale, Nicole J.; Sinninghe Damsté, Jaap S.; Kublanov, Ilya V. DOI 10.1099/ijsem.0.003312 Publication date 2019 Document Version Accepted author manuscript Published in International Journal of Systematic and Evolutionary Microbiology Citation (APA) Sorokin, D. Y., Khijniak, T. V., Elcheninov, A. G., Toshchakov, S. V., Kostrikina, N. A., Bale, N. J., Sinninghe Damsté, J. S., & Kublanov, I. V. (2019). Halococcoides cellulosivorans gen. nov., sp. nov., an extremely halophilic cellulose-utilizing haloarchaeon from hypersaline lakes. International Journal of Systematic and Evolutionary Microbiology, 69(5), 1327-1335. [003312]. https://doi.org/10.1099/ijsem.0.003312 Important note To cite this publication, please use the final published version (if applicable). Please check the document version above. Copyright Other than for strictly personal use, it is not permitted to download, forward or distribute the text or part of it, without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license such as Creative Commons. Takedown policy Please contact us and provide details if you believe this document breaches copyrights. We will remove access to the work immediately and investigate your claim. This work is downloaded from Delft University of Technology. For technical reasons the number of authors shown on this cover page is limited to a maximum of 10. International Journal of Systematic and Evolutionary Microbiology Halococcoides cellulosivorans gen.
    [Show full text]
  • Diversity of Halophilic Archaea in Fermented Foods and Human Intestines and Their Application Han-Seung Lee1,2*
    J. Microbiol. Biotechnol. (2013), 23(12), 1645–1653 http://dx.doi.org/10.4014/jmb.1308.08015 Research Article Minireview jmb Diversity of Halophilic Archaea in Fermented Foods and Human Intestines and Their Application Han-Seung Lee1,2* 1Department of Bio-Food Materials, College of Medical and Life Sciences, Silla University, Busan 617-736, Republic of Korea 2Research Center for Extremophiles, Silla University, Busan 617-736, Republic of Korea Received: August 8, 2013 Revised: September 6, 2013 Archaea are prokaryotic organisms distinct from bacteria in the structural and molecular Accepted: September 9, 2013 biological sense, and these microorganisms are known to thrive mostly at extreme environments. In particular, most studies on halophilic archaea have been focused on environmental and ecological researches. However, new species of halophilic archaea are First published online being isolated and identified from high salt-fermented foods consumed by humans, and it has September 10, 2013 been found that various types of halophilic archaea exist in food products by culture- *Corresponding author independent molecular biological methods. In addition, even if the numbers are not quite Phone: +82-51-999-6308; high, DNAs of various halophilic archaea are being detected in human intestines and much Fax: +82-51-999-5458; interest is given to their possible roles. This review aims to summarize the types and E-mail: [email protected] characteristics of halophilic archaea reported to be present in foods and human intestines and pISSN 1017-7825, eISSN 1738-8872 to discuss their application as well. Copyright© 2013 by The Korean Society for Microbiology Keywords: Halophilic archaea, fermented foods, microbiome, human intestine, Halorubrum and Biotechnology Introduction Depending on the optimal salt concentration needed for the growth of strains, halophilic microorganisms can be Archaea refer to prokaryotes that used to be categorized classified as halotolerant (~0.3 M), halophilic (0.2~2.0 M), as archaeabacteria, a type of bacteria, in the past.
    [Show full text]
  • Tratamiento Biológico Aerobio Para Aguas Residuales Con Elevada Conductividad Y Concentración De Fenoles
    PROGRAMA DE DOCTORADO EN INGENIERÍA Y PRODUCCIÓN INDUSTRIAL Tratamiento biológico aerobio para aguas residuales con elevada conductividad y concentración de fenoles TESIS DOCTORAL Presentada por: Eva Ferrer Polonio Dirigida por: Dr. José Antonio Mendoza Roca Dra. Alicia Iborra Clar Valencia Mayo 2017 AGRADECIMIENTOS La sabiduría popular, a la cual recurro muchas veces, dice: “Es de bien nacido ser agradecido”… pues sigamos su consejo, aquí van los míos. En primer lugar quiero agradecer a mis directores la confianza depositada en mí y a Depuración de Aguas del Mediterráneo, especialmente a Laura Pastor y Silvia Doñate, la dedicación e ilusión puestas en el proyecto. Durante el desarrollo de esta Tesis Doctoral he tenido la inmensa suerte de contar con un grupo de personas de las que he aprendido muchísimo y que de forma desinteresada han colaborado en este trabajo, enriqueciéndolo enormemente. Gracias al Dr. Jaime Primo Millo, del Instituto Agroforestal Mediterráneo de la Universitat Politècnica de València, por el asesoramiento recibido y por permitirme utilizar los equipos de cromatografía de sus instalaciones. También quiero dar un agradecimiento especial a una de las personas de su equipo de investigación, ya que sin su ayuda, tiempo y enseñanzas en los primeros análisis realizados con esta técnica, no me hubiera sido posible llevar a cabo esta tarea con tanta facilidad…gracias Dra. Nuria Cabedo Escrig. Otra de las personas con las que he tenido la suerte de colaborar ha sido la Dra. Blanca Pérez Úz, del Departamento de Microbiología III de la Facultad de Ciencias Biológicas de la Universidad Complutense de Madrid. Blanca, aunque no nos conocemos personalmente, tu profesionalidad y dedicación han permitido superar las barreras de la distancia…gracias.
    [Show full text]
  • University of Oklahoma Graduate College
    UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE THE ISOLATION AND CHARACTERIZATION OF NOVEL EXTREME HALOPHILIC ARCHAEA FROM A LOW-SALT, SULFIDE- AND SULFUR-RICH SPRING. A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By KRISTEN NICHOLE SAVAGE Norman, Oklahoma 2009 THE ISOLATION AND CHARACTERIZATION OF NOVEL EXTREME HALOPHILIC ARCHAEA FROM A LOW-SALT, SULFIDE- AND SULFUR-RICH SPRING. A DISSERTATION APPROVED FOR THE DEPARTMENT OF BOTANY AND MICROBIOLOGY BY __________________________ Dr. Lee R. Krumholz, Chair __________________________ Dr. Mostafa S. Elshahed __________________________ Dr. Joseph M. Suflita __________________________ Dr. Michael J. McInerney __________________________ Dr. R. Paul Philp © Copyright by KRISTEN NICHOLE SAVAGE 2009 All Rights Reserved. I dedicate this to my parents, Monty and Debbie Savage. You honestly believed from the day that I was born that I could be anything that I wanted to be. Thank you for believing in me, and I hope that I have become a person that you can be proud of. Acknowledgements I would not be here today without the support of many people. I am grateful to so many in this department, for people in my family and my friends but I feel that there are some that deserve special acknowledgement I would like to thank all members of my committee each of you were integral in my development as a scientist. Each of you contributed to my education in one way or another and for that I am very appreciative. I truly believe you have given me the tools to succeed. I know that now it is up to me to make the most of those as I take the next step in my scientific career.
    [Show full text]
  • Pan-Genome Analysis and Ancestral State Reconstruction Of
    www.nature.com/scientificreports OPEN Pan‑genome analysis and ancestral state reconstruction of class halobacteria: probability of a new super‑order Sonam Gaba1,2, Abha Kumari2, Marnix Medema 3 & Rajeev Kaushik1* Halobacteria, a class of Euryarchaeota are extremely halophilic archaea that can adapt to a wide range of salt concentration generally from 10% NaCl to saturated salt concentration of 32% NaCl. It consists of the orders: Halobacteriales, Haloferaciales and Natriabales. Pan‑genome analysis of class Halobacteria was done to explore the core (300) and variable components (Softcore: 998, Cloud:36531, Shell:11784). The core component revealed genes of replication, transcription, translation and repair, whereas the variable component had a major portion of environmental information processing. The pan‑gene matrix was mapped onto the core‑gene tree to fnd the ancestral (44.8%) and derived genes (55.1%) of the Last Common Ancestor of Halobacteria. A High percentage of derived genes along with presence of transformation and conjugation genes indicate the occurrence of horizontal gene transfer during the evolution of Halobacteria. A Core and pan‑gene tree were also constructed to infer a phylogeny which implicated on the new super‑order comprising of Natrialbales and Halobacteriales. Halobacteria1,2 is a class of phylum Euryarchaeota3 consisting of extremely halophilic archaea found till date and contains three orders namely Halobacteriales4,5 Haloferacales5 and Natrialbales5. Tese microorganisms are able to dwell at wide range of salt concentration generally from 10% NaCl to saturated salt concentration of 32% NaCl6. Halobacteria, as the name suggests were once considered a part of a domain "Bacteria" but with the discovery of the third domain "Archaea" by Carl Woese et al.7, it became part of Archaea.
    [Show full text]
  • The Role of Stress Proteins in Haloarchaea and Their Adaptive Response to Environmental Shifts
    biomolecules Review The Role of Stress Proteins in Haloarchaea and Their Adaptive Response to Environmental Shifts Laura Matarredona ,Mónica Camacho, Basilio Zafrilla , María-José Bonete and Julia Esclapez * Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain; [email protected] (L.M.); [email protected] (M.C.); [email protected] (B.Z.); [email protected] (M.-J.B.) * Correspondence: [email protected]; Tel.: +34-965-903-880 Received: 31 July 2020; Accepted: 24 September 2020; Published: 29 September 2020 Abstract: Over the years, in order to survive in their natural environment, microbial communities have acquired adaptations to nonoptimal growth conditions. These shifts are usually related to stress conditions such as low/high solar radiation, extreme temperatures, oxidative stress, pH variations, changes in salinity, or a high concentration of heavy metals. In addition, climate change is resulting in these stress conditions becoming more significant due to the frequency and intensity of extreme weather events. The most relevant damaging effect of these stressors is protein denaturation. To cope with this effect, organisms have developed different mechanisms, wherein the stress genes play an important role in deciding which of them survive. Each organism has different responses that involve the activation of many genes and molecules as well as downregulation of other genes and pathways. Focused on salinity stress, the archaeal domain encompasses the most significant extremophiles living in high-salinity environments. To have the capacity to withstand this high salinity without losing protein structure and function, the microorganisms have distinct adaptations.
    [Show full text]
  • Thèses Traditionnelles
    UNIVERSITÉ D’AIX-MARSEILLE FACULTÉ DE MÉDECINE DE MARSEILLE ECOLE DOCTORALE DES SCIENCES DE LA VIE ET DE LA SANTÉ THÈSE Présentée et publiquement soutenue devant LA FACULTÉ DE MÉDECINE DE MARSEILLE Le 23 Novembre 2017 Par El Hadji SECK Étude de la diversité des procaryotes halophiles du tube digestif par approche de culture Pour obtenir le grade de DOCTORAT d’AIX-MARSEILLE UNIVERSITÉ Spécialité : Pathologie Humaine Membres du Jury de la Thèse : Mr le Professeur Jean-Christophe Lagier Président du jury Mr le Professeur Antoine Andremont Rapporteur Mr le Professeur Raymond Ruimy Rapporteur Mr le Professeur Didier Raoult Directeur de thèse Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR 7278 Directeur : Pr. Didier Raoult 1 Avant-propos : Le format de présentation de cette thèse correspond à une recommandation de la spécialité Maladies Infectieuses et Microbiologie, à l’intérieur du Master des Sciences de la Vie et de la Santé qui dépend de l’Ecole Doctorale des Sciences de la Vie de Marseille. Le candidat est amené à respecter des règles qui lui sont imposées et qui comportent un format de thèse utilisé dans le Nord de l’Europe et qui permet un meilleur rangement que les thèses traditionnelles. Par ailleurs, la partie introduction et bibliographie est remplacée par une revue envoyée dans un journal afin de permettre une évaluation extérieure de la qualité de la revue et de permettre à l’étudiant de commencer le plus tôt possible une bibliographie exhaustive sur le domaine de cette thèse. Par ailleurs, la thèse est présentée sur article publié, accepté ou soumis associé d’un bref commentaire donnant le sens général du travail.
    [Show full text]
  • Ammonia-Oxidizing Archaea Use the Most Energy Efficient Aerobic Pathway for CO2 Fixation
    Ammonia-oxidizing archaea use the most energy efficient aerobic pathway for CO2 fixation Martin Könneke, Daniel M. Schubert, Philip C. Brown, Michael Hügler, Sonja Standfest, Thomas Schwander, Lennart Schada von Borzyskowski, Tobias J. Erb, David A. Stahl, Ivan A. Berg Supporting Information: Supplementary Appendix SI Text Phylogenetic analysis of the proteins involved in the HP/HB cycle in N. maritimus. The enzymes of the HP/HB cycle with unequivocally identified genes consisting of more than 200 amino acids were used for the phylogenetic analysis (Table 1). The genes for biotin carrier protein (Nmar_0274, 140 amino acids), small subunit of methylmalonyl-CoA mutase (Nmar_0958, 140 amino acids) and methylmalonyl-CoA epimerase (Nmar_0953, 131 amino acids) were not analyzed, because their small size prevents reliable phylogenetic tree construction. The genes for acetyl-CoA/propionyl-CoA carboxylase and methylmalonyl-CoA carboxylase homologues can be found in autotrophic Thaumarchaeota and aerobic Crenarchaeota as well as in some heterotrophic Archaea (SI Appendix, Figs. S7-S9, Table S4). Although these enzymes are usually regarded as characteristic enzymes of the HP/HB cycle, they also participate in various heterotrophic pathways in Archaea, e.g. in the methylaspartate cycle of acetate assimilation in haloarchaea (1), propionate and leucine assimilation (2, 3), oxaloacetate or methylmalonyl-CoA decarboxylation (4, 5), anaplerotic pyruvate carboxylation (6). In all three trees (SI Appendix, Figs. S7-S9) the crenarchaeal enzymes tend to cluster with thaumarchaeal ones, but there appears to be no special connection between aerobic Crenarchaeota (Sulfolobales) and Thaumarchaeota sequences. Thaumarchaeal 4-hydroxybutyryl-CoA dehydratase genes form a separate cluster closely related to bacterial sequences; the bacterial enzymes are probably involved in aminobutyrate fermentation (Fig.
    [Show full text]
  • Reverse Methanogenesis and Respiration in Methanotrophic Archaea
    Hindawi Archaea Volume 2017, Article ID 1654237, 22 pages https://doi.org/10.1155/2017/1654237 Review Article Reverse Methanogenesis and Respiration in Methanotrophic Archaea Peer H. A. Timmers,1,2,3 Cornelia U. Welte,3,4 Jasper J. Koehorst,5 Caroline M. Plugge,1,2 Mike S. M. Jetten,3,4,6 and Alfons J. M. Stams1,3,7 1 Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, Netherlands 2Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, Netherlands 3Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands 4Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands 5Laboratory of Systems and Synthetic Biology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, Netherlands 6TU Delft Biotechnology, Julianalaan 67, 2628 BC Delft, Netherlands 7Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal Correspondence should be addressed to Peer H. A. Timmers; [email protected] Received 3 August 2016; Revised 11 October 2016; Accepted 31 October 2016; Published 5 January 2017 Academic Editor: Michael W. Friedrich Copyright © 2017 Peer H. A. Timmers et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Anaerobic oxidation of methane (AOM) is catalyzed by anaerobic methane-oxidizing archaea (ANME) via a reverse and modified methanogenesis pathway. Methanogens can also reverse the methanogenesis pathway to oxidize methane, but only during net methane production (i.e., “trace methane oxidation”). In turn, ANME can produce methane, but only during net methane oxidation (i.e., enzymatic back flux).
    [Show full text]
  • The Genome Sequence of Methanohalophilus Mahii SLPT
    Hindawi Publishing Corporation Archaea Volume 2010, Article ID 690737, 16 pages doi:10.1155/2010/690737 Research Article TheGenomeSequenceofMethanohalophilus mahii SLPT Reveals Differences in the Energy Metabolism among Members of the Methanosarcinaceae Inhabiting Freshwater and Saline Environments Stefan Spring,1 Carmen Scheuner,1 Alla Lapidus,2 Susan Lucas,2 Tijana Glavina Del Rio,2 Hope Tice,2 Alex Copeland,2 Jan-Fang Cheng,2 Feng Chen,2 Matt Nolan,2 Elizabeth Saunders,2, 3 Sam Pitluck,2 Konstantinos Liolios,2 Natalia Ivanova,2 Konstantinos Mavromatis,2 Athanasios Lykidis,2 Amrita Pati,2 Amy Chen,4 Krishna Palaniappan,4 Miriam Land,2, 5 Loren Hauser,2, 5 Yun-Juan Chang,2, 5 Cynthia D. Jeffries,2, 5 Lynne Goodwin,2, 3 John C. Detter,3 Thomas Brettin,3 Manfred Rohde,6 Markus Goker,¨ 1 Tanja Woyke, 2 Jim Bristow,2 Jonathan A. Eisen,2, 7 Victor Markowitz,4 Philip Hugenholtz,2 Nikos C. Kyrpides,2 and Hans-Peter Klenk1 1 DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany 2 DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545-001, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA 5 Oak Ridge National Laboratory, Oak Ridge, TN 37830-8026, USA 6 HZI—Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany 7 Davis Genome Center, University of California, Davis, CA 95817, USA Correspondence should be addressed to Stefan Spring, [email protected] and Hans-Peter Klenk, [email protected] Received 24 August 2010; Accepted 9 November 2010 Academic Editor: Valerie´ de Crecy-Lagard´ Copyright © 2010 Stefan Spring et al.
    [Show full text]
  • Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes
    GBE Different Ways of Doing the Same: Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes Dennifier Costa Brandao~ Cruz1, Lenon Lima Santana1, Alexandre Siqueira Guedes2, Jorge Teodoro de Souza3,*, and Phellippe Arthur Santos Marbach1,* 1CCAAB, Biological Sciences, Recoˆ ncavo da Bahia Federal University, Cruz das Almas, Bahia, Brazil 2Agronomy School, Federal University of Goias, Goiania,^ Goias, Brazil 3 Department of Phytopathology, Federal University of Lavras, Minas Gerais, Brazil Downloaded from https://academic.oup.com/gbe/article/11/4/1235/5345563 by guest on 27 September 2021 *Corresponding authors: E-mails: [email protected]fla.br; [email protected]. Accepted: February 16, 2019 Abstract The last two steps of the purine biosynthetic pathway may be catalyzed by different enzymes in prokaryotes. The genes that encode these enzymes include homologs of purH, purP, purO and those encoding the AICARFT and IMPCH domains of PurH, here named purV and purJ, respectively. In Bacteria, these reactions are mainly catalyzed by the domains AICARFT and IMPCH of PurH. In Archaea, these reactions may be carried out by PurH and also by PurP and PurO, both considered signatures of this domain and analogous to the AICARFT and IMPCH domains of PurH, respectively. These genes were searched for in 1,403 completely sequenced prokaryotic genomes publicly available. Our analyses revealed taxonomic patterns for the distribution of these genes and anticorrelations in their occurrence. The analyses of bacterial genomes revealed the existence of genes coding for PurV, PurJ, and PurO, which may no longer be considered signatures of the domain Archaea. Although highly divergent, the PurOs of Archaea and Bacteria show a high level of conservation in the amino acids of the active sites of the protein, allowing us to infer that these enzymes are analogs.
    [Show full text]