DOCSLIB.ORG

Rnomics and Modomics in the Halophilic Archaea Haloferax Volcanii: Identification of RNA Modification Genes

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Rnomics and Modomics in the Halophilic Archaea Haloferax Volcanii: Identification of RNA Modification Genes RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes. Henri Grosjean, Christine Gaspin, Christian Marck, Wayne A Decatur, Valérie de Crécy-Lagard To cite this version: Henri Grosjean, Christine Gaspin, Christian Marck, Wayne A Decatur, Valérie de Crécy-Lagard. RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modifi- cation genes.. BMC Genomics, BioMed Central, 2008, 9, pp.470. 10.1186/1471-2164-9-470. hal- 00354522 HAL Id: hal-00354522 https://hal.archives-ouvertes.fr/hal-00354522 Submitted on 31 May 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. BMC Genomics BioMed Central Research article Open Access RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes Henri Grosjean1,2,3, Christine Gaspin4, Christian Marck5, Wayne A Decatur6 and Valérie de Crécy-Lagard*1 Address: 1Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainsville, FL-32611, Florida, USA, 2IGM, Université de Paris-sud, UMR 8621, Orsay, F 91405, France, 3CNRS, IGM, Orsay, F-91405, France, 4National Institute of Agronomical Research, Biometrics and Artificial Intelligence Department, Chemin de Borde-Rouge, Auzeville BP 27, 31326 Castanet-Tolosan, France, 5Institut de Biologie et de Technologies de Saclay (iBiTecS), Commissariat à l'Energie Atomique (CEA), Gif sur Yvette, F-91191, France and 6Department of Biochemistry and Molecular Biology, University of Massachussets, Amerherst, MA 01003, Massachusetts, USA Email: Henri Grosjean - [email protected]; Christine Gaspin - [email protected]; Christian Marck - [email protected]; Wayne A Decatur - [email protected]; Valérie de Crécy-Lagard* - [email protected] * Corresponding author Published: 9 October 2008 Received: 1 July 2008 Accepted: 9 October 2008 BMC Genomics 2008, 9:470 doi:10.1186/1471-2164-9-470 This article is available from: http://www.biomedcentral.com/1471-2164/9/470 © 2008 Grosjean et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Naturally occurring RNAs contain numerous enzymatically altered nucleosides. Differences in RNA populations (RNomics) and pattern of RNA modifications (Modomics) depends on the organism analyzed and are two of the criteria that distinguish the three kingdoms of life. If the genomic sequences of the RNA molecules can be derived from whole genome sequence information, the modification profile cannot and requires or direct sequencing of the RNAs or predictive methods base on the presence or absence of the modifications genes. Results: By employing a comparative genomics approach, we predicted almost all of the genes coding for the t+rRNA modification enzymes in the mesophilic moderate halophile Haloferax volcanii. These encode both guide RNAs and enzymes. Some are orthologous to previously identified genes in Archaea, Bacteria or in Saccharomyces cerevisiae, but several are original predictions. Conclusion: The number of modifications in t+rRNAs in the halophilic archaeon is surprisingly low when compared with other Archaea or Bacteria, particularly the hyperthermophilic organisms. This may result from the specific lifestyle of halophiles that require high intracellular salt concentration for survival. This salt content could allow RNA to maintain its functional structural integrity with fewer modifications. We predict that the few modifications present must be particularly important for decoding, accuracy of translation or are modifications that cannot be functionally replaced by the electrostatic interactions provided by the surrounding salt-ions. This analysis also guides future experimental validation work aiming to complete the understanding of the function of RNA modifications in Archaeal translation. Page 1 of 26 (page number not for citation purposes) BMC Genomics 2008, 9:470 http://www.biomedcentral.com/1471-2164/9/470 Background etry techniques [25] (for more recent development of the Post-transcriptional modification of transfer and ribos- technique, see [26] and references therein). However, to omal RNAs is essential for their cellular activities as core date Haloferax volcanii, a Halobacteriaceae that lives opti- molecules of the translation apparatus. To date, the chem- mally at 42°C in the presence of 1.5–2.5 M NaCl [27], is ical structure of more than one hundred RNA modifica- the only Archaea for which both the chemical identities tions have been identified in all domains of life [1-3]. In and positions of almost all modified ribonucleosides have transfer RNAs, modified nucleotides are found predomi- been mapped for nearly the whole set of the 52 sequenced nantly within the 3D-core of molecules and in the antico- tRNAs with distinct anticodons [28,29]. In addition, 13 don arm, especially at the wobble position 34 and at tRNA sequences of two closely related mesophilic halo- position 37, 3' adjacent to the anticodon (conventional philes are available, Halobacterium cutirubrum (12 numbering of tRNA positions is as defined in [4], http:// sequences) and Halococcus morrhuae (one sequence) [4]. www.tRNA.uni-bayreuth.de). These particular modifica- For H. volcanii ribosomal RNAs, the type and position of tions allow the molecules to adopt the canonical L-shaped modifications are available in the case of the 16S RNA conformation and modulate interactions with various [30,31], but not for the 23S nor the 5S RNAs. These can be interacting macromolecules such as aminoacyl:tRNA-syn- inferred from studies on another closely phylogenetically thetases, initiation, elongation and termination factors, related halophilic Archaea Haloarcula marismortui [32,33]. mRNA and/or elements of the decoding and peptidyl- However, while the RNA modifications have been centers of the ribosome (reviewed in [5-10]). In ribos- mapped in RNAs of halophiles, including H. volcanii, the omal RNAs, modified nucleotides are located mostly in identity of the genes that code for the corresponding RNA regions corresponding to the functional centers of the modification enzymes remains largely ignored. ribosome [11-14]. Their location suggests a role in accu- racy and efficiency of translation, however the specific Using a comparative genomic analysis method, that we function of each modified nucleoside is still largely have recently applied to the only other organism with an unknown. This lack of knowledge stems from peculiarities almost complete set of sequenced tRNAs, the pathogenic of the rRNA molecule itself: it is a large molecule (molec- bacteria Mycoplasma capricolum [34], we set out to predict ular mass between 1.5 to 3.9 MDa); some nucleotides are all the RNA modification genes in the halophilic archae- only partially modified and their function(s) are most cer- aon H. volcanii. Some were easily predicted by homology tainly dependent on a network of synergistic interactions with experimentally validated RNA modification genes with different elements of the ribosome, including other from other organisms, while a few are original predictions modified nucleosides that may act cooperatively. Never- based on comparative genomic analysis [35] (not based theless, function has been attributed to modified nucleo- on homology). This computation work provides predic- sides in rRNA in a few cases [13,15-22]. tions that can now guide the experimental validation work with the goals of elucidating the role of RNA modi- Difference in profile and type of RNA modifications fications in Archaeal translation, and ultimately obtaining (Modomics) is one of the criteria that distinguish the a better understanding of the emergence of this extraordi- three kingdoms of life. While universal modifications nary complex enzymatic machinery during evolution. such as Ψ, m5U, t6A or m1G are found in a large numbers of archaeal, bacterial and eukaryal tRNAs, each kingdom Results and Discussion has a set of signature modifications. For examples mimG, Post-transcriptional modification of RNA + 2 6 1 G , m 2Gm, ac A or m Ψ are typical of archaeal tRNAs, Modification pattern of tRNAs while yW, mcm5U and manQ, or k2C, mo5U and m6t6A Thanks to the "tour de force" of Gupta [28,29], a list of are typical of tRNAs from Eukarya or Bacteria respectively almost all of the modified nucleosides present in the dif- (for review see Figure 8.1 in [23]). The same conclusion ferent tRNAs of Haloferax volcanii, a typical mesophilic applies for modified nucleotides in rRNAs (see [24]; http:/ halophile, is available. Figure 1A shows their distribution /people.biochem.umass.edu/fournierlab/snornadb/ (identity and location) in the general 2D-cloverleaf struc- main.php). ture of tRNA, while Figure 1B shows their positions in a schematic 3D-architecture
Load more

Recommended publications
  • Detection of a Bacterial Group Within the Phylum Chloroflexi And
    Microbes Environ. Vol. 21, No. 3, 154–162, 2006 http://wwwsoc.nii.ac.jp/jsme2/ Detection of a Bacterial Group within the Phylum Chloroflexi and Reductive-Dehalogenase-Homologous Genes in Pentachlorobenzene- Dechlorinating Estuarine Sediment from the Arakawa River, Japan KYOSUKE SANTOH1, ATSUSHI KOUZUMA1, RYOKO ISHIZEKI2, KENICHI IWATA1, MINORU SHIMURA3, TOSHIO HAYAKAWA3, TOSHIHIRO HOAKI4, HIDEAKI NOJIRI1, TOSHIO OMORI2, HISAKAZU YAMANE1 and HIROSHI HABE1*† 1 Biotechnology Research Center, The University of Tokyo, 1–1–1 Yayoi, Bunkyo-ku, Tokyo 113–8657, Japan 2 Department of Industrial Chemistry, Faculty of Engineering, Shibaura Institute of Technology, Minato-ku, Tokyo 108–8548, Japan 3 Environmental Biotechnology Laboratory, Railway Technical Research Institute, 2–8–38 Hikari-cho, Kokubunji-shi, Tokyo 185–8540, Japan 4 Technology Research Center, Taisei Corporation, 344–1 Nase, Totsuka-ku, Yokohama 245–0051, Japan (Received April 21, 2006—Accepted June 12, 2006) We enriched a pentachlorobenzene (pentaCB)-dechlorinating microbial consortium from an estuarine-sedi- ment sample obtained from the mouth of the Arakawa River. The sediment was incubated together with a mix- ture of four electron donors and pentaCB, and after five months of incubation, the microbial community structure was analyzed. Both DGGE and clone library analyses showed that the most expansive phylogenetic group within the consortium was affiliated with the phylum Chloroflexi, which includes Dehalococcoides-like bacteria. PCR using a degenerate primer set targeting conserved regions in reductive-dehalogenase-homologous (rdh) genes from Dehalococcoides species revealed that DNA fragments (approximately 1.5–1.7 kb) of rdh genes were am- plified from genomic DNA of the consortium. The deduced amino acid sequences of the rdh genes shared sever- al characteristics of reductive dehalogenases.
    [Show full text]
  • Genome Sequence and Description of Haloferax Massiliense Sp. Nov., a New Halophilic Archaeon Isolated from the Human Gut
    Extremophiles (2018) 22:485–498 https://doi.org/10.1007/s00792-018-1011-1 ORIGINAL PAPER Genome sequence and description of Haloferax massiliense sp. nov., a new halophilic archaeon isolated from the human gut Saber Khelaifa1 · Aurelia Caputo1 · Claudia Andrieu1 · Frederique Cadoret1 · Nicholas Armstrong1 · Caroline Michelle1 · Jean‑Christophe Lagier1 · Felix Djossou2 · Pierre‑Edouard Fournier1 · Didier Raoult1,3 Received: 14 November 2017 / Accepted: 5 February 2018 / Published online: 12 February 2018 © The Author(s) 2018. This article is an open access publication Abstract By applying the culturomics concept and using culture conditions containing a high salt concentration, we herein isolated the frst known halophilic archaeon colonizing the human gut. Here we described its phenotypic and biochemical characteriza- tion as well as its genome annotation. Strain Arc-HrT (= CSUR P0974 = CECT 9307) was mesophile and grew optimally at 37 °C and pH 7. Strain Arc-HrT was also extremely halophilic with an optimal growth observed at 15% NaCl. It showed gram-negative cocci, was strictly aerobic, non-motile and non-spore-forming, and exhibited catalase and oxidase activities. The 4,015,175 bp long genome exhibits a G + C% content of 65.36% and contains 3911 protein-coding and 64 predicted RNA genes. PCR-amplifed 16S rRNA gene of strain Arc-HrT yielded a 99.2% sequence similarity with Haloferax prahovense, the phylogenetically closest validly published species in the Haloferax genus. The DDH was of 50.70 ± 5.2% with H. prahovense, 53.70 ± 2.69% with H. volcanii, 50.90 ± 2.64% with H. alexandrinus, 52.90 ± 2.67% with H.
    [Show full text]
  • Novel Molecular Signatures in the PIP4K/PIP5K Family of Proteins Specific for Different Isozymes and Subfamilies Provide Importa
    G C A T T A C G G C A T genes Article Novel Molecular Signatures in the PIP4K/PIP5K Family of Proteins Specific for Different Isozymes and Subfamilies Provide Important Insights into the Evolutionary Divergence of this Protein Family Bijendra Khadka and Radhey S. Gupta * Department of Biochemistry and Biomedical Sciences McMaster University, Hamilton, ON L8N 3Z5, Canada; [email protected] * Correspondence: [email protected]; Tel.: +1-905-525-9140 Received: 22 February 2019; Accepted: 15 April 2019; Published: 21 April 2019 Abstract: Members of the PIP4K/PIP5K family of proteins, which generate the highly important secondary messenger phosphatidylinositol-4,5-bisphosphate, play central roles in regulating diverse signaling pathways. In eukaryotic organisms, multiple isozymes and subfamilies of PIP4K/PIP5K proteins are found and it is of much interest to understand their evolution and species distribution and what unique molecular and biochemical characteristics distinguish specific isozymes and subfamilies of proteins. We report here the species distribution of different PIP4K/PIP5K family of proteins in eukaryotic organisms and phylogenetic analysis based on their protein sequences. Our results indicate that the distinct homologs of both PIP4K and PIP5K are found in different organisms belonging to the Holozoa clade of eukaryotes, which comprises of various metazoan phyla as well as their close unicellular relatives Choanoflagellates and Filasterea. In contrast, the deeper-branching eukaryotic lineages, as well as plants and fungi, contain only a single homolog of the PIP4K/PIP5K proteins. In parallel, our comparative analyses of PIP4K/PIP5K protein sequences have identified six highly-specific molecular markers consisting of conserved signature indels (CSIs) that are uniquely shared by either the PIP4K or PIP5K proteins, or both, or specific subfamilies of these proteins.
    [Show full text]
  • Haloarcula Quadrata Sp. Nov., a Square, Motile Archaeon Isolated from a Brine Pool in Sinai (Egypt)
    International Journal of Systematic Bacteriology (1999), 49, 1 149-1 155 Printed in Great Britain Haloarcula quadrata sp. nov., a square, motile archaeon isolated from a brine pool in Sinai (Egypt) Aharon Oren,’ Antonio Ventosa,2 M. Carmen Gutierrez* and Masahiro Kamekura3 Author for correspondence: Aharon Oren. Tel: +972 2 6584951. Fax: +972 2 6528008. e-mail : orena @ shum.cc. huji. ac.il 1 Division of Microbial and The motile, predominantly square-shaped, red archaeon strain 80103O/lT, Molecular Ecology, isolated from a brine pool in the Sinai peninsula (Egypt), was characterized Institute of Life Sciences and the Moshe Shilo taxonomically. On the basis of its polar lipid composition, the nucleotide Center for Marine sequences of its two 16s rRNA genes, the DNA G+C content (60-1 molo/o) and its Biogeochemistry, The growth characteristics, the isolate could be assigned to the genus Haloarcula. Hebrew University of Jerusalem, Jerusalem However, phylogenetic analysis of the two 165 rRNA genes detected in this 91904, Israel organism and low DNA-DNA hybridization values with related Haloarcula 2 Department of species showed that strain 801030/ITis sufficiently different from the Microbiology and recognized Haloarcula species to warrant its designation as a new species. A Parasitology, Faculty of new species, Haloarcula quadrata, is therefore proposed, with strain 801030/IT Pharmacy, University of SeviIIe, SeviIIe 41012, Spain (= DSM 119273 as the type strain. 3 Noda Institute for Scientific Research, 399 Noda, Noda-shi, Chiba-ken Keywords : Haloarcula quadrata, square bacteria, archaea, halophile 278-0037, Japan INTRODUCTION this type of bacterium from a Spanish saltern was published by Torrella (1986).
    [Show full text]
  • Seasonal Fluctuations in Ionic Concentrations Drive Microbial Succession in a Hypersaline Lake Community
    The ISME Journal (2014) 8, 979–990 & 2014 International Society for Microbial Ecology All rights reserved 1751-7362/14 www.nature.com/ismej ORIGINAL ARTICLE Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community Sheila Podell1, Joanne B Emerson2,3, Claudia M Jones2, Juan A Ugalde1, Sue Welch4, Karla B Heidelberg5, Jillian F Banfield2,6 and Eric E Allen1,7 1Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA; 2Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA; 3Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA; 4School of Earth Sciences, Byrd Polar Research Center, Ohio State University, Columbus, OH, USA; 5Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA; 6Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA and 7Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA Microbial community succession was examined over a two-year period using spatially and temporally coordinated water chemistry measurements, metagenomic sequencing, phylogenetic binning and de novo metagenomic assembly in the extreme hypersaline habitat of Lake Tyrrell, Victoria, Australia. Relative abundances of Haloquadratum-related sequences were positively correlated with co-varying concentrations of potassium, magnesium and sulfate,
    [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]
  • Draft Genome of Haloarcula Rubripromontorii Strain SL3, a Novel Halophilic Archaeon Isolated from the Solar Salterns of Cabo Rojo, Puerto Rico
    UC Davis UC Davis Previously Published Works Title Draft genome of Haloarcula rubripromontorii strain SL3, a novel halophilic archaeon isolated from the solar salterns of Cabo Rojo, Puerto Rico. Permalink https://escholarship.org/uc/item/61m6b8d8 Authors Sánchez-Nieves, Rubén Facciotti, Marc Saavedra-Collado, Sofía et al. Publication Date 2016-03-01 DOI 10.1016/j.gdata.2016.02.005 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Genomics Data 7 (2016) 287–289 Contents lists available at ScienceDirect Genomics Data journal homepage: www.elsevier.com/locate/gdata Data in Brief Draft genome of Haloarcula rubripromontorii strain SL3, a novel halophilic archaeon isolated from the solar salterns of Cabo Rojo, Puerto Rico Rubén Sánchez-Nieves a,MarcFacciottib, Sofía Saavedra-Collado a, Lizbeth Dávila-Santiago a, Roy Rodríguez-Carrero a, Rafael Montalvo-Rodríguez a,⁎ a Biology Department, University of Puerto Rico, Mayaguez, Box 9000, 00681-9000, Puerto Rico b Biomedical Engineering and Genome Center, 451 Health Sciences Drive, Davis, CA, 95618, United States article info abstract Article history: The genus Haloarcula belongs to the family Halobacteriaceae which currently has 10 valid species. Here we report Received 1 February 2016 the draft genome sequence of strain SL3, a new species within this genus, isolated from the Solar Salterns of Cabo Accepted 5 February 2016 Rojo, Puerto Rico. Genome assembly performed using NGEN Assembler resulted in 18 contigs (N50 = Available online 6 February 2016 601,911 bp), the largest of which contains 1,023,775 bp. The genome consists of 3.97 MB and has a GC content of 61.97%.
    [Show full text]
  • Genome-Wide Metabolic Reconstruction and Flux Balance Analysis Modeling of Haloferax Volcanii by Andrew S
    Genome-wide Metabolic Reconstruction and Flux Balance Analysis Modeling of Haloferax volcanii by Andrew S. Rosko Department of Computational Biology and Bioinformatics Duke University Date:_______________________ Approved: ___________________________ Amy K. Schmid, Supervisor ___________________________ Paul Magwene ___________________________ Timothy Reddy Thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in the Department of Computational Biology and Bioinformatics in the Graduate School of Duke University 2018 ABSTRACT Genome-wide Metabolic Reconstruction and Flux Balance Analysis Modeling of Haloferax volcanii by Andrew S. Rosko Department of Computational Biology and Bioinformatics Duke University Date:_______________________ Approved: ___________________________ Amy K. Schmid, Supervisor ___________________________ Paul Magwene ___________________________ Timothy Reddy An abstract of a thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in the Department of Computational Biology and Bioinformatics in the Graduate School of Duke University 2018 Copyright by Andrew S. Rosko 2018 Abstract The Archaea are an understudied domain of the tree of life and consist of single-celled microorganisms possessing rich metabolic diversity. Archaeal metabolic capabilities are of interest for industry and basic understanding of the early evolution of metabolism. However, archaea possess many unusual pathways that remain unknown or unclear. To address this knowledge gap, here I built a whole-genome metabolic reconstruction of a model archaeal species, Haloferax volcanii, which included several atypical reactions and pathways in this organism. I then used flux balance analysis to predict fluxes through central carbon metabolism during growth on minimal media containing two different sugars. This establishes a foundation for the future study of the regulation of metabolism in Hfx.
    [Show full text]
  • Haloarcula Marismortui (Volcani) Sp
    INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Apr., 1990, p. 209-210 Vol. 40. No. 2 0020-7713/90/020209-02$02.00/0 Copyright 0 1990, International Union of Microbiological Societies Haloarcula marismortui (Volcani) sp. nov. nom. rev. an Extremely Halophilic Bacterium from the Dead Sea A. OREN,l* M. GINZBURG,2 B. Z. GINZBURG,2 L. I. HOCHSTEIN,3 AND B. E. VOLCAN14 Division of Microbial and Molecular Ecology,’ and Plant Biophysical Laboratory,2 Institute of Life Sciences, The Hebrew University of Jerusalem, 91 904 Jerusalem, Israel; National Aeronautics and Space Administration Ames Research Center, Mofett Field, California 9403j3; and Scripps Institution of Oceanography, University of California, Sun Diego, La Jolla, California 920934 An extremely halophilic red archaebacterium isolated from the Dead Sea (Ginzburg et a]., J. Gen. Physiol. 55: 187-207,1970) belongs to the genus Haloarcula and differs sufficiently from the previously described species of the genus to be designated a new species; we propose the name Haloarcula marismortui (Volcani) sp. nov., nom. rev. because of the close resemblance of this organism to “Halobacterium marismortui,” which was first described by Volcani in 1940. The type strain is strain ATCC 43049. During his studies on the microbiology of the Dead Sea in served after electrophoresis of digests of DNA preparations the 1930s and 1940s Elazari-Volcani isolated a novel strain of with different restriction enzymes (ll), and although the the genus Halobacterium. This strain differed from the then DNA-DNA hybridization ratio of these organisms is rather known halobacterial types in its ability to form acid from low, the new isolate and strain ATCC 29715 appeared to be glucose, fructose, mannose, and glycerol and in its produc- related, as shown by the near identity of their 5s and 16s tion of gas from nitrate.
    [Show full text]
  • Mutations Affecting HVO 1357 Or HVO 2248 Cause Hypermotility in Haloferax Volcanii, Suggesting Roles in Motility Regulation
    G C A T T A C G G C A T genes Article Mutations Affecting HVO_1357 or HVO_2248 Cause Hypermotility in Haloferax volcanii, Suggesting Roles in Motility Regulation Michiyah Collins 1 , Simisola Afolayan 1, Aime B. Igiraneza 1, Heather Schiller 1 , Elise Krespan 2, Daniel P. Beiting 2, Mike Dyall-Smith 3,4 , Friedhelm Pfeiffer 4 and Mechthild Pohlschroder 1,* 1 Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA; [email protected] (M.C.); [email protected] (S.A.); [email protected] (A.B.I.); [email protected] (H.S.) 2 Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; [email protected] (E.K.); [email protected] (D.P.B.) 3 Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville 3010, Australia; [email protected] 4 Computational Biology Group, Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany; [email protected] * Correspondence: [email protected]; Tel.: +1-215-573-2283 Abstract: Motility regulation plays a key role in prokaryotic responses to environmental stimuli. Here, we used a motility screen and selection to isolate hypermotile Haloferax volcanii mutants from a transposon insertion library. Whole genome sequencing revealed that hypermotile mutants were predominantly affected in two genes that encode HVO_1357 and HVO_2248. Alterations of these genes comprised not only transposon insertions but also secondary genome alterations. HVO_1357 Citation: Collins, M.; Afolayan, S.; Igiraneza, A.B.; Schiller, H.; contains a domain that was previously identified in the regulation of bacteriorhodopsin transcription, Krespan, E.; Beiting, D.P.; as well as other domains frequently found in two-component regulatory systems.
    [Show full text]
  • Investigating Bacterial Ribosomal Sequence Variation in Regards to Future Structural and Antibiotic Research
    bioRxiv preprint doi: https://doi.org/10.1101/2021.06.14.448437; this version posted June 14, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Investigating bacterial ribosomal sequence variation in regards to future structural and antibiotic research. Helena B. Cooper1, Kurt L. Krause1 & Paul P. Gardner1. 1Department of Biochemistry, School of Biomedical Sciences, University of Otago. Author Note Keywords: Bacterial Ribosome, Antibiotic Resistance, Phylogeny Analysis, Genomics. We have no known conflicts of interest to disclose. Correspondence concerning this article should be addressed to: Paul P. Gardner, Department of Biochemistry, University of Otago, P. O. Box 56, Dunedin, 9054. Email: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.06.14.448437; this version posted June 14, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Abstract Ribosome-targeting antibiotics comprise over half of antibiotics used in medicine, but our fundamental knowledge of their binding sites is derived primarily from ribosome structures from non-pathogenic species. These include Thermus thermophilus, Deinococcus radiodurans and Haloarcula marismortui, as well as the commensal or pathogenic Escherichia coli. Advancements in electron cryomicroscopy have allowed for the determination of more ribosome structures from pathogenic bacteria, with each study highlighting species-specific differences that had not been observed in the non-pathogenic structures.
    [Show full text]
  • Isolation and Cultivation of Halophilic Archaea from Solar Salterns Located in Peninsular Coast of India K Asha, D Vinitha, S Kiran, W Manjusha, N Sukumaran, J Selvin
    The Internet Journal of Microbiology ISPUB.COM Volume 1 Number 2 Isolation and Cultivation of Halophilic Archaea from Solar Salterns Located in Peninsular Coast of India K Asha, D Vinitha, S Kiran, W Manjusha, N Sukumaran, J Selvin Citation K Asha, D Vinitha, S Kiran, W Manjusha, N Sukumaran, J Selvin. Isolation and Cultivation of Halophilic Archaea from Solar Salterns Located in Peninsular Coast of India. The Internet Journal of Microbiology. 2004 Volume 1 Number 2. Abstract Two brightly red-pigmented, motile, rod and triangular-shaped, extremely halophilic archaea were isolated from saltern crystallizer ponds located in peninsular coast of India. They grew optimally at salt concentrations between 25 and 35% and did not grow below 20% salts. Thus, these isolates are among the most halophilic organisms known within the domain Bacteria. The isolate HA3 showed optimal growth at 42°C whereas HA9 showed optimal growth at 52°C. These haloversatile microorganisms were presumed as new strains of Haloarcula. H. quadrata (HA3) showed unusual broad spectrum antibiotic resistance pattern. The isolate HA9 was named as H. vallismortis var. cellulolytica due to its peculiar cellulolytic activity, though full taxonomic description is pending. INTRODUCTION 1999; Ventosa et al., 1998). A unique feature of halobacteria Though the oceans are invariably considered as largest saline is the purple membrane, specialized regions of the cell body, hypersaline environments are, particularly, those membrane that contain a two-dimensional crystalline lattice containing salt concentrations in excess of seawater (3.5% of a chromoprotein, bacteriorhodopsin. Bacteriorhodopsin total dissolved salts). Many hypersaline bodies derive from contains a protein moiety (bacteriorhodopsin) and a the evaporation of seawater and are called thalassic covalently bound chromophore (retinal) and acts as a light- (DasSharma and Arora, 2001).
    [Show full text]