Orthologs of the Small RPB8 Subunit of the Eukaryotic RNA Polymerases
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Functional Equivalence and Evolutionary Convergence In
Functional equivalence and evolutionary convergence PNAS PLUS in complex communities of microbial sponge symbionts Lu Fana,b, David Reynoldsa,b, Michael Liua,b, Manuel Starkc,d, Staffan Kjelleberga,b,e, Nicole S. Websterf, and Torsten Thomasa,b,1 aSchool of Biotechnology and Biomolecular Sciences and bCentre for Marine Bio-Innovation, University of New South Wales, Sydney, New South Wales 2052, Australia; cInstitute of Molecular Life Sciences and dSwiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland; eSingapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Republic of Singapore; and fAustralian Institute of Marine Science, Townsville, Queensland 4810, Australia Edited by W. Ford Doolittle, Dalhousie University, Halifax, NS, Canada, and approved May 21, 2012 (received for review February 24, 2012) Microorganisms often form symbiotic relationships with eukar- ties (11, 12). Symbionts also can be transmitted vertically through yotes, and the complexity of these relationships can range from reproductive cells and larvae, as has been demonstrated in those with one single dominant symbiont to associations with sponges (13, 14), insects (15), ascidians (16), bivalves (17), and hundreds of symbiont species. Microbial symbionts occupying various other animals (18). Vertical transmission generally leads equivalent niches in different eukaryotic hosts may share func- to microbial communities with limited variation in taxonomy and tional aspects, and convergent genome evolution has been function among host individuals. reported for simple symbiont systems in insects. However, for Niches with similar selections may exist in phylogenetically complex symbiont communities, it is largely unknown how prev- divergent hosts that lead comparable lifestyles or have similar alent functional equivalence is and whether equivalent functions physiological properties. -
Differences in Lateral Gene Transfer in Hypersaline Versus Thermal Environments Matthew E Rhodes1*, John R Spear2, Aharon Oren3 and Christopher H House1
Rhodes et al. BMC Evolutionary Biology 2011, 11:199 http://www.biomedcentral.com/1471-2148/11/199 RESEARCH ARTICLE Open Access Differences in lateral gene transfer in hypersaline versus thermal environments Matthew E Rhodes1*, John R Spear2, Aharon Oren3 and Christopher H House1 Abstract Background: The role of lateral gene transfer (LGT) in the evolution of microorganisms is only beginning to be understood. While most LGT events occur between closely related individuals, inter-phylum and inter-domain LGT events are not uncommon. These distant transfer events offer potentially greater fitness advantages and it is for this reason that these “long distance” LGT events may have significantly impacted the evolution of microbes. One mechanism driving distant LGT events is microbial transformation. Theoretically, transformative events can occur between any two species provided that the DNA of one enters the habitat of the other. Two categories of microorganisms that are well-known for LGT are the thermophiles and halophiles. Results: We identified potential inter-class LGT events into both a thermophilic class of Archaea (Thermoprotei) and a halophilic class of Archaea (Halobacteria). We then categorized these LGT genes as originating in thermophiles and halophiles respectively. While more than 68% of transfer events into Thermoprotei taxa originated in other thermophiles, less than 11% of transfer events into Halobacteria taxa originated in other halophiles. Conclusions: Our results suggest that there is a fundamental difference between LGT in thermophiles and halophiles. We theorize that the difference lies in the different natures of the environments. While DNA degrades rapidly in thermal environments due to temperature-driven denaturization, hypersaline environments are adept at preserving DNA. -
Insights Into Archaeal Evolution and Symbiosis from the Genomes of a Nanoarchaeon and Its Inferred Crenarchaeal Host from Obsidian Pool, Yellowstone National Park
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Microbiology Publications and Other Works Microbiology 4-22-2013 Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar University of Tennessee - Knoxville, [email protected] Kira S. Makarova National Institutes of Health David E. Graham University of Tennessee - Knoxville, [email protected] Yuri I. Wolf National Institutes of Health Eugene V. Koonin National Institutes of Health See next page for additional authors Follow this and additional works at: https://trace.tennessee.edu/utk_micrpubs Part of the Microbiology Commons Recommended Citation Biology Direct 2013, 8:9 doi:10.1186/1745-6150-8-9 This Article is brought to you for free and open access by the Microbiology at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Microbiology Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Authors Mircea Podar, Kira S. Makarova, David E. Graham, Yuri I. Wolf, Eugene V. Koonin, and Anna-Louise Reysenbach This article is available at TRACE: Tennessee Research and Creative Exchange: https://trace.tennessee.edu/ utk_micrpubs/44 Podar et al. Biology Direct 2013, 8:9 http://www.biology-direct.com/content/8/1/9 RESEARCH Open Access Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar1,2*, Kira S Makarova3, David E Graham1,2, Yuri I Wolf3, Eugene V Koonin3 and Anna-Louise Reysenbach4 Abstract Background: A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes. -
Oceans of Archaea Abundant Oceanic Crenarchaeota Appear to Derive from Thermophilic Ancestors That Invaded Low-Temperature Marine Environments
Oceans of Archaea Abundant oceanic Crenarchaeota appear to derive from thermophilic ancestors that invaded low-temperature marine environments Edward F. DeLong arth’s microbiota is remarkably per- karyotes), Archaea, and Bacteria. Although al- vasive, thriving at extremely high ternative taxonomic schemes have been recently temperature, low and high pH, high proposed, whole-genome and other analyses E salinity, and low water availability. tend to support Woese’s three-domain concept. One lineage of microbial life in par- Well-known and cultivated archaea generally ticular, the Archaea, is especially adept at ex- fall into several major phenotypic groupings: ploiting environmental extremes. Despite their these include extreme halophiles, methanogens, success in these challenging habitats, the Ar- and extreme thermophiles and thermoacido- chaea may now also be viewed as a philes. Early on, extremely halo- cosmopolitan lot. These microbes philic archaea (haloarchaea) were exist in a wide variety of terres- first noticed as bright-red colonies trial, freshwater, and marine habi- Archaea exist in growing on salted fish or hides. tats, sometimes in very high abun- a wide variety For many years, halophilic isolates dance. The oceanic Marine Group of terrestrial, from salterns, salt deposits, and I Crenarchaeota, for example, ri- freshwater, and landlocked seas provided excellent val total bacterial biomass in wa- marine habitats, model systems for studying adap- ters below 100 m. These wide- tations to high salinity. It was only spread Archaea appear to derive sometimes in much later, however, that it was from thermophilic ancestors that very high realized that these salt-loving invaded diverse low-temperature abundance “bacteria” are actually members environments. -
Novel Insights Into the Thaumarchaeota in the Deepest Oceans: Their Metabolism and Potential Adaptation Mechanisms
Zhong et al. Microbiome (2020) 8:78 https://doi.org/10.1186/s40168-020-00849-2 RESEARCH Open Access Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms Haohui Zhong1,2, Laura Lehtovirta-Morley3, Jiwen Liu1,2, Yanfen Zheng1, Heyu Lin1, Delei Song1, Jonathan D. Todd3, Jiwei Tian4 and Xiao-Hua Zhang1,2,5* Abstract Background: Marine Group I (MGI) Thaumarchaeota, which play key roles in the global biogeochemical cycling of nitrogen and carbon (ammonia oxidizers), thrive in the aphotic deep sea with massive populations. Recent studies have revealed that MGI Thaumarchaeota were present in the deepest part of oceans—the hadal zone (depth > 6000 m, consisting almost entirely of trenches), with the predominant phylotype being distinct from that in the “shallower” deep sea. However, little is known about the metabolism and distribution of these ammonia oxidizers in the hadal water. Results: In this study, metagenomic data were obtained from 0–10,500 m deep seawater samples from the Mariana Trench. The distribution patterns of Thaumarchaeota derived from metagenomics and 16S rRNA gene sequencing were in line with that reported in previous studies: abundance of Thaumarchaeota peaked in bathypelagic zone (depth 1000–4000 m) and the predominant clade shifted in the hadal zone. Several metagenome-assembled thaumarchaeotal genomes were recovered, including a near-complete one representing the dominant hadal phylotype of MGI. Using comparative genomics, we predict that unexpected genes involved in bioenergetics, including two distinct ATP synthase genes (predicted to be coupled with H+ and Na+ respectively), and genes horizontally transferred from other extremophiles, such as those encoding putative di-myo-inositol-phosphate (DIP) synthases, might significantly contribute to the success of this hadal clade under the extreme condition. -
Sulfolobus As a Model Organism for the Study of Diverse
SULFOLOBUS AS A MODEL ORGANISM FOR THE STUDY OF DIVERSE BIOLOGICAL INTERESTS; FORAYS INTO THERMAL VIROLOGY AND OXIDATIVE STRESS by Blake Alan Wiedenheft A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Microbiology MONTANA STATE UNIVERSITY Bozeman, Montana November 2006 © COPYRIGHT by Blake Alan Wiedenheft 2006 All Rights Reserved ii APPROVAL of a dissertation submitted by Blake Alan Wiedenheft This dissertation has been read by each member of the dissertation committee and has been found to be satisfactory regarding content, English usage, format, citations, bibliographic style, and consistency, and is ready for submission to the Division of Graduate Education. Dr. Mark Young and Dr. Trevor Douglas Approved for the Department of Microbiology Dr.Tim Ford Approved for the Division of Graduate Education Dr. Carl A. Fox iii STATEMENT OF PERMISSION TO USE In presenting this dissertation in partial fulfillment of the requirements for a doctoral degree at Montana State University – Bozeman, I agree that the Library shall make it available to borrowers under rules of the Library. I further agree that copying of this dissertation is allowable only for scholarly purposes, consistent with “fair use” as prescribed in the U.S. Copyright Law. Requests for extensive copying or reproduction of this dissertation should be referred to ProQuest Information and Learning, 300 North Zeeb Road, Ann Arbor, Michigan 48106, to whom I have granted “the exclusive right to reproduce and distribute my dissertation in and from microfilm along with the non-exclusive right to reproduce and distribute my abstract in any format in whole or in part.” Blake Alan Wiedenheft November, 2006 iv DEDICATION This work was funded in part through grants from the National Aeronautics and Space Administration Program (NAG5-8807) in support of Montana State University’s Center for Life in Extreme Environments (MCB-0132156), and the National Institutes of Health (R01 EB00432 and DK57776). -
Alternative Strategies of Nutrient Acquisition and Energy Conservation Map to the Biogeography of Marine Ammonia- Oxidizing Archaea
The ISME Journal (2020) 14:2595–2609 https://doi.org/10.1038/s41396-020-0710-7 ARTICLE Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia- oxidizing archaea 1 2,3 2,3 4 5 6 Wei Qin ● Yue Zheng ● Feng Zhao ● Yulin Wang ● Hidetoshi Urakawa ● Willm Martens-Habbena ● 7 8 9 10 11 12 Haodong Liu ● Xiaowu Huang ● Xinxu Zhang ● Tatsunori Nakagawa ● Daniel R. Mende ● Annette Bollmann ● 13 14 15 16 17 10 Baozhan Wang ● Yao Zhang ● Shady A. Amin ● Jeppe L. Nielsen ● Koji Mori ● Reiji Takahashi ● 1 18 11 9 19,8 E. Virginia Armbrust ● Mari-K.H. Winkler ● Edward F. DeLong ● Meng Li ● Po-Heng Lee ● 20,21,22 7 4 18 1 Jizhong Zhou ● Chuanlun Zhang ● Tong Zhang ● David A. Stahl ● Anitra E. Ingalls Received: 15 February 2020 / Revised: 16 June 2020 / Accepted: 25 June 2020 / Published online: 7 July 2020 © The Author(s) 2020. This article is published with open access Abstract Ammonia-oxidizing archaea (AOA) are among the most abundant and ubiquitous microorganisms in the ocean, exerting primary control on nitrification and nitrogen oxides emission. Although united by a common physiology of 1234567890();,: 1234567890();,: chemoautotrophic growth on ammonia, a corresponding high genomic and habitat variability suggests tremendous adaptive capacity. Here, we compared 44 diverse AOA genomes, 37 from species cultivated from samples collected across diverse geographic locations and seven assembled from metagenomic sequences from the mesopelagic to hadopelagic zones of the deep ocean. Comparative analysis identified seven major marine AOA genotypic groups having gene content correlated with their distinctive biogeographies. -
Phylogeny and Taxonomy of Archaea: a Comparison of the Whole-Genome-Based Cvtree Approach with 16S Rrna Sequence Analysis
Life 2015, 5, 949-968; doi:10.3390/life5010949 OPEN ACCESS life ISSN 2075-1729 www.mdpi.com/journal/life Article Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis Guanghong Zuo 1, Zhao Xu 2 and Bailin Hao 1;* 1 T-Life Research Center and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China; E-Mail: [email protected] 2 Thermo Fisher Scientific, 200 Oyster Point Blvd, South San Francisco, CA 94080, USA; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +86-21-6565-2305. Academic Editors: Roger A. Garrett, Hans-Peter Klenk and Michael W. W. Adams Received: 9 December 2014 / Accepted: 9 March 2015 / Published: 17 March 2015 Abstract: A tripartite comparison of Archaea phylogeny and taxonomy at and above the rank order is reported: (1) the whole-genome-based and alignment-free CVTree using 179 genomes; (2) the 16S rRNA analysis exemplified by the All-Species Living Tree with 366 archaeal sequences; and (3) the Second Edition of Bergey’s Manual of Systematic Bacteriology complemented by some current literature. A high degree of agreement is reached at these ranks. From the newly proposed archaeal phyla, Korarchaeota, Thaumarchaeota, Nanoarchaeota and Aigarchaeota, to the recent suggestion to divide the class Halobacteria into three orders, all gain substantial support from CVTree. In addition, the CVTree helped to determine the taxonomic position of some newly sequenced genomes without proper lineage information. A few discrepancies between the CVTree and the 16S rRNA approaches call for further investigation. -
Downloaded from Mage and Compared
bioRxiv preprint doi: https://doi.org/10.1101/527234; this version posted January 23, 2019. 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. Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta Florian U. Moeller1, Nicole S. Webster2,3, Craig W. Herbold1, Faris Behnam1, Daryl Domman1, 5 Mads Albertsen4, Maria Mooshammer1, Stephanie Markert5,8, Dmitrij Turaev6, Dörte Becher7, Thomas Rattei6, Thomas Schweder5,8, Andreas Richter9, Margarete Watzka9, Per Halkjaer Nielsen4, and Michael Wagner1,* 1Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, 10 Austria. 2Australian Institute of Marine Science, Townsville, Queensland, Australia. 3 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of 15 Queensland, St Lucia, QLD, Australia 4Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark. 20 5Institute of Marine Biotechnology e.V., Greifswald, Germany 6Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Austria. 25 7Institute of Microbiology, Microbial Proteomics, University of Greifswald, Greifswald, Germany 8Institute of Pharmacy, Pharmaceutical Biotechnology, University of Greifswald, Greifswald, Germany 9Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, 30 University of Vienna, Austria. *Corresponding author: Michael Wagner, Department of Microbiology and Ecosystem Science, Althanstrasse 14, University of Vienna, 1090 Vienna, Austria. Email: wagner@microbial- ecology.net 1 bioRxiv preprint doi: https://doi.org/10.1101/527234; this version posted January 23, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. -
(Gid ) Genes Coding for Putative Trna:M5u-54 Methyltransferases in 355 Bacterial and Archaeal Complete Genomes
Table S1. Taxonomic distribution of the trmA and trmFO (gid ) genes coding for putative tRNA:m5U-54 methyltransferases in 355 bacterial and archaeal complete genomes. Asterisks indicate the presence and the number of putative genes found. Genomes Taxonomic position TrmA Gid Archaea Crenarchaea Aeropyrum pernix_K1 Crenarchaeota; Thermoprotei; Desulfurococcales; Desulfurococcaceae Cenarchaeum symbiosum Crenarchaeota; Thermoprotei; Cenarchaeales; Cenarchaeaceae Pyrobaculum aerophilum_str_IM2 Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae Sulfolobus acidocaldarius_DSM_639 Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Sulfolobus solfataricus Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Sulfolobus tokodaii Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Euryarchaea Archaeoglobus fulgidus Euryarchaeota; Archaeoglobi; Archaeoglobales; Archaeoglobaceae Haloarcula marismortui_ATCC_43049 Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloarcula Halobacterium sp Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloarcula Haloquadratum walsbyi Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloquadra Methanobacterium thermoautotrophicum Euryarchaeota; Methanobacteria; Methanobacteriales; Methanobacteriaceae Methanococcoides burtonii_DSM_6242 Euryarchaeota; Methanomicrobia; Methanosarcinales; Methanosarcinaceae Methanococcus jannaschii Euryarchaeota; Methanococci; Methanococcales; Methanococcaceae Methanococcus maripaludis_S2 Euryarchaeota; Methanococci; -
Codon Usage Bias in Archaea
Codon usage bias in Archaea Laura R. Emery Ph.D. University of Edinburgh 2010 1 2 for Mom 3 ACKNOWLEDGEMENTS P.M. Sharp has provided me with this superb opportunity to pursue an area of research which has thoroughly intrigued me. I thank him for his experience, expertise and unsurpassed attention to detail. I thank the numerous members of I.E.B for their guidance and support throughout my time in Edinburgh. A particular thanks to B.C. and D.C. Charlesworth who have made me feel very welcome at their lab group, where I have learned a lot. The recent computational support from R.H.J. Perry has been invaluable and I thank P.R. Haddrill, J.J. Welsh, K. Zeng and S.J. Lycett for advice and/or discussion. I thank my school teachers for inspiration and C.M. Wade for the advice to embark upon this project in Edinburgh. The encouragement and endurance from my friends, J. Raghwani and M.J. Ward, has been greatly appreciated. I thank my family: B.A. Evans, S.C. Emery and M.W.H. Emery for their infallible support and tolerance. I would thank H.C. Emery if it were possible; she always insisted that I pursue my dreams, and yet ironically, has exemplified the roles of mutation and natural selection in bringing life in and out of existence. I DECLARATION The work of this thesis is my own unless stated otherwise. Laura R. Emery 2010 II PUBLICATIONS SHARP, P. M., L. R. EMERY and K. ZENG, 2010 Forces that influence the evolution of codon bias. -
Post-Genomic Characterization of Metabolic Pathways in Sulfolobus Solfataricus
Post-Genomic Characterization of Metabolic Pathways in Sulfolobus solfataricus Jasper Walther Thesis committee Thesis supervisors Prof. dr. J. van der Oost Personal chair at the laboratory of Microbiology Wageningen University Prof. dr. W. M. de Vos Professor of Microbiology Wageningen University Other members Prof. dr. W.J.H. van Berkel Wageningen University Prof. dr. V.A.F. Martins dos Santos Wageningen University Dr. T.J.G. Ettema Uppsala University, Sweden Dr. S.V. Albers Max Planck Institute for Terrestrial Microbiology, Marburg, Germany This research was conducted under the auspices of the Graduate School VLAG Post-Genomic Characterization of Metabolic Pathways in Sulfolobus solfataricus Jasper Walther Thesis Submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. dr. M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Monday 23 January 2012 at 11 a.m. in the Aula. Jasper Walther Post-Genomic Characterization of Metabolic Pathways in Sulfolobus solfataricus, 164 pages. Thesis, Wageningen University, Wageningen, NL (2012) With references, with summaries in Dutch and English ISBN 978-94-6173-203-3 Table of contents Chapter 1 Introduction 1 Chapter 2 Hot Transcriptomics 17 Chapter 3 Reconstruction of central carbon metabolism in Sulfolobus solfataricus using a two-dimensional gel electrophoresis map, stable isotope labelling and DNA microarray analysis 45 Chapter 4 Identification of the Missing