Complex Evolutionary History of Translation Elongation Factor 2 and Diphthamide
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Diversity of Understudied Archaeal and Bacterial Populations of Yellowstone National Park: from Genes to Genomes Daniel Colman
University of New Mexico UNM Digital Repository Biology ETDs Electronic Theses and Dissertations 7-1-2015 Diversity of understudied archaeal and bacterial populations of Yellowstone National Park: from genes to genomes Daniel Colman Follow this and additional works at: https://digitalrepository.unm.edu/biol_etds Recommended Citation Colman, Daniel. "Diversity of understudied archaeal and bacterial populations of Yellowstone National Park: from genes to genomes." (2015). https://digitalrepository.unm.edu/biol_etds/18 This Dissertation is brought to you for free and open access by the Electronic Theses and Dissertations at UNM Digital Repository. It has been accepted for inclusion in Biology ETDs by an authorized administrator of UNM Digital Repository. For more information, please contact [email protected]. Daniel Robert Colman Candidate Biology Department This dissertation is approved, and it is acceptable in quality and form for publication: Approved by the Dissertation Committee: Cristina Takacs-Vesbach , Chairperson Robert Sinsabaugh Laura Crossey Diana Northup i Diversity of understudied archaeal and bacterial populations from Yellowstone National Park: from genes to genomes by Daniel Robert Colman B.S. Biology, University of New Mexico, 2009 DISSERTATION Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Biology The University of New Mexico Albuquerque, New Mexico July 2015 ii DEDICATION I would like to dedicate this dissertation to my late grandfather, Kenneth Leo Colman, associate professor of Animal Science in the Wool laboratory at Montana State University, who even very near the end of his earthly tenure, thought it pertinent to quiz my knowledge of oxidized nitrogen compounds. He was a man of great curiosity about the natural world, and to whom I owe an acknowledgement for his legacy of intellectual (and actual) wanderlust. -
Marsarchaeota Are an Aerobic Archaeal Lineage Abundant in Geothermal Iron Oxide Microbial Mats
Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats Authors: Zackary J. Jay, Jacob P. Beam, Mansur Dlakic, Douglas B. Rusch, Mark A. Kozubal, and William P. Inskeep This is a postprint of an article that originally appeared in Nature Microbiology on May 14, 2018. The final version can be found at https://dx.doi.org/10.1038/s41564-018-0163-1. Jay, Zackary J. , Jacob P. Beam, Mensur Dlakic, Douglas B. Rusch, Mark A. Kozubal, and William P. Inskeep. "Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats." Nature Microbiology 3, no. 6 (May 2018): 732-740. DOI: 10.1038/ s41564-018-0163-1. Made available through Montana State University’s ScholarWorks scholarworks.montana.edu Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats Zackary J. Jay1,4,7, Jacob P. Beam1,5,7, Mensur Dlakić2, Douglas B. Rusch3, Mark A. Kozubal1,6 and William P. Inskeep 1* The discovery of archaeal lineages is critical to our understanding of the universal tree of life and evolutionary history of the Earth. Geochemically diverse thermal environments in Yellowstone National Park provide unprecedented opportunities for studying archaea in habitats that may represent analogues of early Earth. Here, we report the discovery and character- ization of a phylum-level archaeal lineage proposed and herein referred to as the ‘Marsarchaeota’, after the red planet. The Marsarchaeota contains at least two major subgroups prevalent in acidic, microaerobic geothermal Fe(III) oxide microbial mats across a temperature range from ~50–80 °C. Metagenomics, single-cell sequencing, enrichment culturing and in situ transcrip- tional analyses reveal their biogeochemical role as facultative aerobic chemoorganotrophs that may also mediate the reduction of Fe(III). -
Phylogenetics of Archaeal Lipids Amy Kelly 9/27/2006 Outline
Phylogenetics of Archaeal Lipids Amy Kelly 9/27/2006 Outline • Phlogenetics of Archaea • Phlogenetics of archaeal lipids • Papers Phyla • Two? main phyla – Euryarchaeota • Methanogens • Extreme halophiles • Extreme thermophiles • Sulfate-reducing – Crenarchaeota • Extreme thermophiles – Korarchaeota? • Hyperthermophiles • indicated only by environmental DNA sequences – Nanoarchaeum? • N. equitans a fast evolving euryarchaeal lineage, not novel, early diverging archaeal phylum – Ancient archael group? • In deepest brances of Crenarchaea? Euryarchaea? Archaeal Lipids • Methanogens – Di- and tetra-ethers of glycerol and isoprenoid alcohols – Core mostly archaeol or caldarchaeol – Core sometimes sn-2- or Images removed due to sn-3-hydroxyarchaeol or copyright considerations. macrocyclic archaeol –PMI • Halophiles – Similar to methanogens – Exclusively synthesize bacterioruberin • Marine Crenarchaea Depositional Archaeal Lipids Biological Origin Environment Crocetane methanotrophs? methane seeps? methanogens, PMI (2,6,10,15,19-pentamethylicosane) methanotrophs hypersaline, anoxic Squalane hypersaline? C31-C40 head-to-head isoprenoids Smit & Mushegian • “Lost” enzymes of MVA pathway must exist – Phosphomevalonate kinase (PMK) – Diphosphomevalonate decarboxylase – Isopentenyl diphosphate isomerase (IPPI) Kaneda et al. 2001 Rohdich et al. 2001 Boucher et al. • Isoprenoid biosynthesis of archaea evolved through a combination of processes – Co-option of ancestral enzymes – Modification of enzymatic specificity – Orthologous and non-orthologous gene -
A Survey of Carbon Fixation Pathways Through a Quantitative Lens
Journal of Experimental Botany, Vol. 63, No. 6, pp. 2325–2342, 2012 doi:10.1093/jxb/err417 Advance Access publication 26 December, 2011 REVIEW PAPER A survey of carbon fixation pathways through a quantitative lens Arren Bar-Even, Elad Noor and Ron Milo* Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel * To whom correspondence should be addressed. E-mail: [email protected] Received 15 August 2011; Revised 4 November 2011; Accepted 8 November 2011 Downloaded from Abstract While the reductive pentose phosphate cycle is responsible for the fixation of most of the carbon in the biosphere, it http://jxb.oxfordjournals.org/ has several natural substitutes. In fact, due to the characterization of three new carbon fixation pathways in the last decade, the diversity of known metabolic solutions for autotrophic growth has doubled. In this review, the different pathways are analysed and compared according to various criteria, trying to connect each of the different metabolic alternatives to suitable environments or metabolic goals. The different roles of carbon fixation are discussed; in addition to sustaining autotrophic growth it can also be used for energy conservation and as an electron sink for the recycling of reduced electron carriers. Our main focus in this review is on thermodynamic and kinetic aspects, including thermodynamically challenging reactions, the ATP requirement of each pathway, energetic constraints on carbon fixation, and factors that are expected to limit the rate of the pathways. Finally, possible metabolic structures at Weizmann Institute of Science on July 3, 2016 of yet unknown carbon fixation pathways are suggested and discussed. -
Title Genomic Analysis of the Marine Hyperthermophilic Archaeon
Genomic analysis of the marine hyperthermophilic archaeon Title Aeropyrum( Dissertation_全文 ) Author(s) Daifuku, Takashi Citation 京都大学 Issue Date 2015-03-23 URL https://doi.org/10.14989/doctor.k19034 学位規則第9条第2項により要約公開; 許諾条件により本文 Right は2019-08-01に公開 Type Thesis or Dissertation Textversion ETD Kyoto University 1. General introduction Chapter 1 General introduction Gene repertoires and genome organizations differ between closely related microbial organisms depending on the ecological characteristics of each habitat (Cohan and Koeppel 2008). The cyanobacterial Prochlorococcus spp. account for a significant fraction of primary production in the ocean (Goericke and Welschmeyer 1993) and show physiological features relevant to the different ecological niches within a stratified oceanic water column (Moore et al. 1998; West et al. 2001). The whole-genomic comparisons of the Prochlorococcus spp. strains show gross signatures according to this niche differentiation (Rocap et al. 2003). Alpha-proteobacterium Pelagibacter ubique which belongs to the SAR11 clade in the phylogenetic tree based on the 16S rRNA gene is the most abundant microorganism in the ocean (Morris et al. 2002). The genomes of the SAR11 isolates are highly conserved in the core genes that are common to all strains (Medini et al. 2005) and show synteny (the conservation of DNA sequence and gene order) (Bentley and Parkhill 2004). However, variations exist among genes for phosphorus metabolism, glycolysis, and C1 metabolism, suggesting that adaptive specialization in nutrient resource utilization is important for niche partitioning (Grote et al. 2012). This adaptation at the genomic level was also observed in archaea. The members of the genus Pyrococcus are anaerobic and hyperthermophilic archaea (Fiala and Stetter 1 1. -
The Archaeal Ced System Imports DNA
The archaeal Ced system imports DNA Marleen van Wolferena,1, Alexander Wagnera,1, Chris van der Doesa, and Sonja-Verena Albersa,2 aMolecular Biology of Archaea, Institute of Biology II – Microbiology, University of Freiburg, 79104 Freiburg, Germany Edited by Norman R. Pace, University of Colorado at Boulder, Boulder, CO, and approved January 12, 2016 (received for review July 13, 2015) The intercellular transfer of DNA is a phenomenon that occurs species exchange chromosomal DNA between cells connected by in all domains of life and is a major driving force of evolution. bridges (11). This transfer is thought to occur in a bidirectional Upon UV-light treatment, cells of the crenarchaeal genus Sulfo- manner via cell fusion leading to the formation of diploid cells with lobus express Ups pili, which initiate cell aggregate formation. mixed chromosomes (12). Interestingly, this type of DNA transfer Within these aggregates, chromosomal DNA, which is used for was shown to occur between different Haloferax species and in- the repair of DNA double-strand breaks, is exchanged. Because volved DNA fragments of up to 500 kbp DNA (13). Nevertheless, so far no clear homologs of bacterial DNA transporters have the mechanism of DNA transfer is so far not understood. Other been identified among the genomes of Archaea, the mechanisms described archaeal conjugative systems include self-transmissible of archaeal DNA transport have remained a puzzling and under- plasmids, which have so far only been studied for Sulfolobus spe- saci_0568 saci_0748, investigated topic. Here we identify and cies. These plasmids are grouped into the so-called pKEF and Sulfolobus acidocaldarius two genes from that are highly in- pARN plasmids (14, 15) and only a few of their genes encode duced upon UV treatment, encoding a transmembrane protein homologs of bacterial conjugation proteins, including the so-far- and a membrane-bound VirB4/HerA homolog, respectively. -
(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; -
Pyrolobus Fumarii Type Strain (1A)
Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A). Permalink https://escholarship.org/uc/item/89r1s0xt Journal Standards in genomic sciences, 4(3) ISSN 1944-3277 Authors Anderson, Iain Göker, Markus Nolan, Matt et al. Publication Date 2011-07-01 DOI 10.4056/sigs.2014648 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2011) 4:381-392 DOI:10.4056/sigs.2014648 Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1AT) Iain Anderson1, Markus Göker2, Matt Nolan1, Susan Lucas1, Nancy Hammon1, Shweta Deshpande1, Jan-Fang Cheng1, Roxanne Tapia1,3, Cliff Han1,3, Lynne Goodwin1,3, Sam Pitluck1, Marcel Huntemann1, Konstantinos Liolios1, Natalia Ivanova1, Ioanna Pagani1, Konstantinos Mavromatis1, Galina Ovchinikova1, Amrita Pati1, Amy Chen4, Krishna Pala- niappan4, Miriam Land1,5, Loren Hauser1,5, Evelyne-Marie Brambilla2, Harald Huber6, Montri Yasawong7, Manfred Rohde7, Stefan Spring2, Birte Abt2, Johannes Sikorski2, Reinhard Wirth6, John C. Detter1,3, Tanja Woyke1, James Bristow1, Jonathan A. Eisen1,8, Victor Markowitz4, Philip Hugenholtz1,9, Nikos C. Kyrpides1, Hans-Peter Klenk2, and Alla Lapidus1* 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, -
A Meta-Analysis of the Publicly Available Bacterial and Archaeal Sequence Diversity in Saline Soils
World J Microbiol Biotechnol (2013) 29:2325–2334 DOI 10.1007/s11274-013-1399-9 ORIGINAL PAPER A meta-analysis of the publicly available bacterial and archaeal sequence diversity in saline soils Bin Ma • Jun Gong Received: 19 April 2013 / Accepted: 3 June 2013 / Published online: 12 June 2013 Ó Springer Science+Business Media Dordrecht 2013 Abstract An integrated view of bacterial and archaeal Halorubrum and Thermofilum were the dominant archaeal diversity in saline soil habitats is essential for understanding genera in saline soils. Rarefaction analysis indicated that less the biological and ecological processes and exploiting than 25 % of bacterial diversity, and approximately 50 % of potential of microbial resources from such environments. archaeal diversity, in saline soil habitats has been sampled. This study examined the collective bacterial and archaeal This analysis of the global bacterial and archaeal diversity in diversity in saline soils using a meta-analysis approach. All saline soil habitats can guide future studies to further available 16S rDNA sequences recovered from saline soils examine the microbial diversity of saline soils. were retrieved from publicly available databases and sub- jected to phylogenetic and statistical analyses. A total of Keywords Archaea Á Bacteria Á Halophilic Á Microbial 9,043 bacterial and 1,039 archaeal sequences, each longer diversity Á Saline soil than 250 bp, were examined. The bacterial sequences were assigned into 5,784 operational taxonomic units (OTUs, based on C97 % sequence identity), representing 24 known Introduction bacterial phyla, with Proteobacteria (44.9 %), Actinobacte- ria (12.3 %), Firmicutes (10.4 %), Acidobacteria (9.0 %), Saline soils are increasingly abundant as a consequence of Bacteroidetes (6.8 %), and Chloroflexi (5.9 %) being pre- irrigation and desertification processes (Rengasamy 2006). -
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. -
Protein Based Molecular Markers Provide Reliable Means to Understand Prokaryotic Phylogeny and Support Darwinian Mode of Evolution
REVIEW ARTICLE published: 26 July 2012 CELLULAR AND INFECTION MICROBIOLOGY doi: 10.3389/fcimb.2012.00098 Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution Vaibhav Bhandari , Hafiz S. Naushad and Radhey S. Gupta* Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada Edited by: The analyses of genome sequences have led to the proposal that lateral gene transfers Yousef Abu Kwaik, University of (LGTs) among prokaryotes are so widespread that they disguise the interrelationships Louisville School of Medicine, USA among these organisms. This has led to questioning of whether the Darwinian model Reviewed by: of evolution is applicable to prokaryotic organisms. In this review, we discuss the Srinand Sreevastan, University of Minnesota, USA usefulness of taxon-specific molecular markers such as conserved signature indels (CSIs) Andrey P.Anisimov, State Research and conserved signature proteins (CSPs) for understanding the evolutionary relationships Center for Applied Microbiology and among prokaryotes and to assess the influence of LGTs on prokaryotic evolution. The Biotechnology, Russia analyses of genomic sequences have identified large numbers of CSIs and CSPs that are *Correspondence: unique properties of different groups of prokaryotes ranging from phylum to genus levels. Radhey S. Gupta, Department of Biochemistry and Biomedical The species distribution patterns of these molecular signatures strongly support a tree-like Sciences, McMaster University, vertical inheritance of the genes containing these molecular signatures that is consistent 1200 Main Street West, Health with phylogenetic trees. Recent detailed studies in this regard on the Thermotogae and Sciences Center, Hamilton, Archaea, which are reviewed here, have identified large numbers of CSIs and CSPs that ON L8N 3Z5, Canada. -
The Draft Genome of the Hyperthermophilic Archaeon Pyrodictium Delaneyi Strain Hulk, an Iron and Nitrate Reducer, Reveals the Capacity for Sulfate Reduction Lucas M
Demey et al. Standards in Genomic Sciences (2017) 12:47 DOI 10.1186/s40793-017-0260-4 EXTENDED GENOME REPORT Open Access The draft genome of the hyperthermophilic archaeon Pyrodictium delaneyi strain hulk, an iron and nitrate reducer, reveals the capacity for sulfate reduction Lucas M. Demey1, Caitlin R. Miller1, Michael P Manzella1,4, Rachel R. Spurbeck2, Sukhinder K. Sandhu3, Gemma Reguera1 and Kazem Kashefi1* Abstract Pyrodictium delaneyi strain Hulk is a newly sequenced strain isolated from chimney samples collected from the Hulk sulfide mound on the main Endeavour Segment of the Juan de Fuca Ridge (47.9501 latitude, −129.0970 longitude, depth 2200 m) in the Northeast Pacific Ocean. The draft genome of strain Hulk shared 99.77% similarity with the complete genome of the type strain Su06T, which shares with strain Hulk the ability to reduce iron and nitrate for respiration. The annotation of the genome of strain Hulk identified genes for the reduction of several sulfur-containing electron acceptors, an unsuspected respiratory capability in this species that was experimentally confirmed for strain Hulk. This makes P. delaneyi strain Hulk the first hyperthermophilic archaeon known to gain energy for growth by reduction of iron, nitrate, and sulfur-containing electron acceptors. Here we present the most notable features of the genome of P. delaneyi strain Hulk and identify genes encoding proteins critical to its respiratory versatility at high temperatures. The description presented here corresponds to a draft genome sequence containing 2,042,801 bp in 9 contigs, 2019 protein-coding genes, 53 RNA genes, and 1365 hypothetical genes. Keywords: Pyrodictium delaneyi strain Hulk, Pyrodictiaceae, Sulfate reducer, Hyperthermophile, Juan de Fuca ridge Introduction archaeon known to respire iron, nitrate, and sulfur- The unifying metabolic feature of the first five species containing electron acceptors.