DOCSLIB.ORG

Antioxidants Used by Deinococcus Radiodurans and Implications for Antioxidant Drug Discovery

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Antioxidants Used by Deinococcus Radiodurans and Implications for Antioxidant Drug Discovery CORRESPONDENCE LINK TO ORIGINAL ARTICLE LINK TO AUTHOR’s REPLY In summary, it seems that the antioxi- dant defence system of D. radiodurans Antioxidants used by Deinococcus consists of several lines of antioxidants, including enzymes and non-enzymatic radiodurans and implications for small molecules, which is directly relevant to antioxidant drug discovery. Lipoic antioxidant drug discovery acid has been approved as an antioxidant drug, and therefore the other antioxidants used by D. radiodurans (that is, Mn(II) Hong-Yu Zhang, Xue-Juan Li, Na Gao and Ling-Ling Chen complexes and folates) are good start- ing points for finding novel antioxidant In his recent Opinion article (A new fact, the development of Mn(II)-containing drugs. perspective on radiation resistance based catalytic antioxidant drugs has attracted Hong-Yu Zhang is at the Institute of Bioinformatics and 5 on Deinococcus radiodurans. Nature Rev. much attention in recent years . However, National Key Laboratory of Crop Genetic Improvement, Microbiol. 7, 237–245 (2009))1, Michael as D. radiodurans contains a large number College of Life Science and Technology, Huazhong Daly proposes that high levels of manganese of metabolites, we speculate that other Agricultural University, Wuhan 430070, P. R. China. can protect proteins from the reactive compounds might also be responsible for the Xue-Juan Li, Na Gao and Ling-Ling Chen are at the oxygen species (ROS) that are produced antioxidant defence of D. radiodurans. Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, during irradiation. Owing to the close link Through searching the Kyoto Shandong University of Technology, between reactive oxygen species and various Encyclopedia of Genes and Genomes Zibo 255049, P. R. China. diseases, there is continuing interest in find- (KEGG)6 and analysing the genome of Correspondence to H.Y.Z. 7 ing antioxidants as preventive or therapeutic D. radiodurans , the biosynthetic pathways e-mail: [email protected] drugs. According to the MDL Drug Data for some common antioxidant metabolites Report (MDDR)2, to date, seven antioxidant (for example, carotenoids, lipoic acid and 1. Daly, M. J. A new perspective on radiation resistance based on Deinococcus radiodurans. Nature Rev. drugs have been launched, most of which folates) could be identified. It is interesting Microbiol. 7, 237–245 (2009). (lipoic acid, policosanol, acetylcysteine, ide- to note that the mutant of D. radiodurans 2. MDL Drug Data Report (MDDR) (MDL Information Systems, San Leandro, 2004). benone and probucol) are directly or indi- that fails to synthesize carotenoids was more 3. Wang, P. & Schellhorn, H. E. Induction of resistance to rectly derived from natural antioxidants. sensitive to ionizing radiation and hydrogen hydrogen peroxide and radiation in Deinococcus radiodurans. Can. J. Microbiol. 41, 170–176 (1995). Exploring how organisms use antioxidants peroxide, and therefore that carotenoids, such 4. Makarova, K. S. et al. Genome of the extremely to combat ROS is therefore of great impor- as beta-carotene, lycopene and phytoene, radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. tance for antioxidant drug discovery. indeed play an important part in the radiation Microbiol. Mol. Biol. Rev. 65, 44–79 (2001). It is well known that radiation-resistant resistance of D. radiodurans8. The antioxidant 5. Day, B. J. Catalytic antioxidants: a radical approach to new therapeutics. Drug Discov. Today 9, 557–566 bacteria have evolved strong antioxidant sys- and radioprotective powers of lipoic acid (2004). tems to survive ROS-mediated damage3. have been widely recognized9, which strongly 6. Kanehisa, M. & Goto, S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27–30 For example, various antioxidant enzymes, suggests that lipoic acid is also valuable in (2000). such as Mn- or Fe-superoxide dismutase, protecting D. radiodurans from oxidative 7. White, O. et al. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science 286, Cu/Zn-superoxide dismutase, catalase, per- damage. The radioprotective effect of folates 1571–1577 (1999). oxidase, thiol-alkyl hydroperoxide reductases, was also observed10, which was linked, at least 8. Tian, B., Xu, Z., Sun, Z., Lin, J. & Hua, Y. Evaluation of 10 the antioxidant effects of carotenoids from Deinococcus thioredoxin reductase, alkyl hydroperoxide in part, to the antioxidant activity of folates . radiodurans through targeted mutagenesis, reductase, peptide methionine sulphoxide Accumulating evidence indicates that folates chemiluminescence, and DNA damage analyses. Biochim. Biophys. Acta 1770, 902–911 (2007). reductase and glutaredoxin, have been are strong hydrogen and electron donors 9. Manda, K., Ueno, M., Moritake, T. & Anzai, K. α-Lipoic identified from Deinococcus radiodurans, one (when the proton is dissociated)11, especially acid attenuates X-irradiation-induced oxidative stress 3,4 in mice. Cell Biol. Toxicol. 23, 129–137 (2007). of the most radiation-resistant bacteria . in their reduced forms (for example, tetrahy- 10. Pote, M. S., Gandhi, N. M. & Mishra, K. P. Interestingly, Michael Daly revealed that non- drofolates), which endows them with sub- Antiatherogenic and radioprotective role of folic acid in whole body gamma-irradiated mice. Mol. Cell enzymic Mn(II) complexes also have a crucial stantial antioxidant potential that is similar Biochem. 292, 19–25 (2006). role in the antioxidant defence of D. radio- to that of α-tocopherol and ascorbic acid12. 11. Shen, L., Zhang, H.-Y. & Ji, H.-F. A thermodynamic 1 investigation of DPPH radical-scavenging mechanisms durans , which highlights the importance Moreover, the in vivo antioxidant effects of of folates. J. Mol. Struct. (Theochem) 856, 119–123 of small-molecule antioxidants in radiation folates have been preliminarily recognized, (2008). 12. Gliszczyńska-ńwigło, A. Folates as antioxidants. Food resistance. This finding not only sheds new which is independent of their well-known Chem. 101, 1480–1483 (2007). light on the radiation-resistant mechanisms benefits to reduce homocysteine13. Thus, it is 13. Doshi, S. N. et al. Folate improves endothelial function in coronary artery disease: an effect mediated by of D. radiodurans but also has direct implica- reasonable to infer that folates are involved in reduction of intracellular superoxide? Arterioscler. tions for antioxidant drug discovery. In the antioxidant defence of D. radiodurans. Thromb. Vasc. Biol. 21, 1196–1202 (2001). NATURE REVIEWS | MICROBIOLOGY www.nature.com/reviews/micro © 2009 Macmillan Publishers Limited. All rights reserved.
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]
  • 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]
  • The First Recorded Incidence of Deinococcus Radiodurans R1 Biofilm
    bioRxiv preprint doi: https://doi.org/10.1101/234781; this version posted December 15, 2017. 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. 1 The first recorded incidence of Deinococcus radiodurans R1 biofilm 2 formation and its implications in heavy metals bioremediation 3 4 Sudhir K. Shukla1,2, T. Subba Rao1,2,* 5 6 Running title : Deinococcus radiodurans R1 biofilm formation 7 8 1Biofouling & Thermal Ecology Section, Water & Steam Chemistry Division, 9 BARC Facilities, Kalpakkam, 603 102 India 10 11 2Homi Bhabha National Institute, Mumbai 400094, India 12 13 *Corresponding Author: T. Subba Rao 14 Address: Biofouling & Thermal Ecology Section, Water & Steam Chemistry Division, 15 BARC Facilities, Kalpakkam, 603 102 India 16 E-mail: [email protected] 17 Phone: +91 44 2748 0203, Fax: +91 44 2748 0097 18 1 bioRxiv preprint doi: https://doi.org/10.1101/234781; this version posted December 15, 2017. 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. 19 Significance and Impact of this Study 20 This is the first ever recorded study on the Deinococcus radiodurans R1 biofilm. This 21 organism, being the most radioresistant micro-organism ever known, has always been 22 speculated as a potential bacterium to develop a bioremediation process for radioactive heavy 23 metal contaminants. However, the lack of biofilm forming capability proved to be a bottleneck 24 in developing such technology. This study records the first incidence of biofilm formation in a 25 recombinant D.
    [Show full text]
  • Protection of Chemolithoautotrophic Bacteria Exposed to Simulated
    Protection Of Chemolithoautotrophic Bacteria Exposed To Simulated Mars Environmental Conditions Felipe Gómez, Eva Mateo-Martí, Olga Prieto-Ballesteros, Jose Martín-Gago, Ricardo Amils To cite this version: Felipe Gómez, Eva Mateo-Martí, Olga Prieto-Ballesteros, Jose Martín-Gago, Ricardo Amils. Pro- tection Of Chemolithoautotrophic Bacteria Exposed To Simulated Mars Environmental Conditions. Icarus, Elsevier, 2010, 209 (2), pp.482. 10.1016/j.icarus.2010.05.027. hal-00676214 HAL Id: hal-00676214 https://hal.archives-ouvertes.fr/hal-00676214 Submitted on 4 Mar 2012 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. Accepted Manuscript Protection Of Chemolithoautotrophic Bacteria Exposed To Simulated Mars En‐ vironmental Conditions Felipe Gómez, Eva Mateo-Martí, Olga Prieto-Ballesteros, Jose Martín-Gago, Ricardo Amils PII: S0019-1035(10)00220-4 DOI: 10.1016/j.icarus.2010.05.027 Reference: YICAR 9450 To appear in: Icarus Received Date: 11 August 2009 Revised Date: 14 May 2010 Accepted Date: 28 May 2010 Please cite this article as: Gómez, F., Mateo-Martí, E., Prieto-Ballesteros, O., Martín-Gago, J., Amils, R., Protection Of Chemolithoautotrophic Bacteria Exposed To Simulated Mars Environmental Conditions, Icarus (2010), doi: 10.1016/j.icarus.2010.05.027 This is a PDF file of an unedited manuscript that has been accepted for publication.
    [Show full text]
  • DNA Gyrase of Deinococcus Radiodurans Is Characterized As Type II Bacterial Topoisomerase and Its Activity Is Differentially Regulated by Ppra in Vitro
    Extremophiles (2016) 20:195–205 DOI 10.1007/s00792-016-0814-1 ORIGINAL PAPER DNA Gyrase of Deinococcus radiodurans is characterized as Type II bacterial topoisomerase and its activity is differentially regulated by PprA in vitro Swathi Kota1 · Yogendra S. Rajpurohit1 · Vijaya K. Charaka1,4 · Katsuya Satoh2 · Issay Narumi3 · Hari S. Misra1 Received: 8 October 2015 / Accepted: 20 January 2016 / Published online: 5 February 2016 © Springer Japan 2016 Abstract The multipartite genome of Deinococcus radio- W183R, which formed relatively short oligomers did not durans forms toroidal structure. It encodes topoisomerase interact with GyrA. The size of nucleoid in PprA mutant IB and both the subunits of DNA gyrase (DrGyr) while (1.9564 0.324 µm) was significantly bigger than the wild ± lacks other bacterial topoisomerases. Recently, PprA a plei- type (1.6437 0.345 µm). Thus, we showed that DrGyr ± otropic protein involved in radiation resistance in D. radio- confers all three activities of bacterial type IIA family DNA durans has been suggested for having roles in cell division topoisomerases, which are differentially regulated by PprA, and genome maintenance. In vivo interaction of PprA with highlighting the significant role of PprA in DrGyr activity topoisomerases has also been shown. DrGyr constituted regulation and genome maintenance in D. radiodurans. from recombinant gyrase A and gyrase B subunits showed decatenation, relaxation and supercoiling activities. Wild Keywords Deinococcus · DNA gyrase · Genome type PprA stimulated DNA relaxation activity while inhib- maintenance · PprA · Radioresistance ited supercoiling activity of DrGyr. Lysine133 to glutamic acid (K133E) and tryptophane183 to arginine (W183R) replacements resulted loss of DNA binding activity in Introduction PprA and that showed very little effect on DrGyr activi- ties in vitro.
    [Show full text]
  • Ionizing Radiation Resistance in Deinococcus Radiodurans
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by CSCanada.net: E-Journals (Canadian Academy of Oriental and Occidental Culture,... ISSN 1715-7862 [PRINT] Advances in Natural Science ISSN 1715-7870 [ONLINE] Vol. 7, No. 2, 2014, pp. 6-14 www.cscanada.net DOI: 10.3968/5058 www.cscanada.org Ionizing Radiation Resistance in Deinococcus Radiodurans LI Wei[a]; MA Yun[a]; XIAO Fangzhu[a]; HE Shuya[a],* [a]Institute of Biochemistry and Molecular Biology, University of South Treatment of D. radiodurans with an acute dose of 5,000 China, Hengyang, China. Gy of ionizing radiation with almost no loss of viability, *Corresponding author. and an acute dose of 15,000 Gy with 37% viability (Daly, Supported by the National Natural Science Foundation of China 2009; Ito, Watanabe, Takeshia, & Iizuka, 1983; Moseley (81272993). & Mattingly, 1971). In contrast, 5 Gy of ionizing radiation can kill a human, 200-800 Gy of ionizing radiation will Received 12 March 2014; accepted 2 June 2014 Published online 26 June 2014 kill E. coli, and more than 4,000 Gy of ionizing radiation will kill the radiation-resistant tardigrade. D. radiodurans can survive 5,000 to 30,000 Gy of ionizing radiation, Abstract which breaks its genome into hundreds of fragments (Daly Deinococcus radiodurans is unmatched among all known & Minton, 1995; Minton, 1994; Slade & Radman, 2011). species in its ability to resist ionizing radiation and other Surprisingly, the genome is reassembled accurately before DNA-damaging factors. It is considered a model organism beginning of the next cycle of cell division.
    [Show full text]
  • Biology of Extreme Radiation Resistance: the Way of Deinococcus Radiodurans
    Biology of Extreme Radiation Resistance: The Way of Deinococcus radiodurans Anita Krisko1 and Miroslav Radman1,2 1Mediterranean Institute for Life Sciences, 21000 Split, Croatia 2Faculte´ de Me´decine, Universite´ Rene´ Descartes—Paris V, INSERM U1001, 75015 Paris, France Correspondence: [email protected] The bacterium Deinococcus radiodurans is a champion of extreme radiation resistance that is accounted for by a highly efficient protection against proteome, but not genome, damage. A well-protected functional proteome ensures cell recovery from extensive radiation damage to other cellular constituents by molecular repair and turnover processes, including an efficient repair of disintegrated DNA. Therefore, cell death correlates with radiation- induced protein damage, rather than DNA damage, in both robust and standard species. From the reviewed biology of resistance to radiation and other sources of oxidative damage, we conclude that the impact of protein damage on the maintenance of life has been largely underestimated in biology and medicine. everal recent reviews comprehensively pres- rather than the genome. A cell that instantly Sent the extraordinary bacterium Deinococ- loses its genome can function for some time, cus radiodurans, best known for its biological unlike one that loses its proteome. In other robustness involving an extremely efficient words, the proteome sustains and maintains DNA repair system (Cox and Battista 2005; Bla- life, whereas the genome ensures the perpetua- sius et al. 2008; Daly 2009; Slade and Radman tion of life by renewing the proteome, a process 2011). The aim of this short review of the biol- contingent on a preexisting proteome that re- ogy of D. radiodurans is to single out a general pairs, replicates, and expresses the genome.
    [Show full text]
  • Conserved Signature Indels (Csis) Are an Important Category of Shared Derived Molecular Markers
    Defending Darwin: Do Microbial Genomes Support or Challenge the Darwinian Mode of Evolution? Radhey S. Gupta McMaster University, Canada © by author ECCMID 2013, ESCMID Online Lecture LibraryBerlin, April 28, 2013 Current State of Microbiology 16S rRNA tree • 16S rRNA trees provide the current framework for understanding microbiology. • About 30 main groups/phyla within Bacteria have been identified. These groups are also seen in most other phylogenetic trees. • Interrelationships among different groups are not resolved. • Most higher taxa are distinguished only in phylogenetic (or statistical) terms. In most cases, no biochemical or molecular markers are known that are specific for these groups. © by author Ludwig and Klenk, Bergey’s Manual of Systematic Bacteriology (2005) Some Important Issues in Microbiology Requiring Understanding • ESCMIDAbility to distinguish different Online groups of microorganisms Lecture in more definitive Library molecular terms • Development of a reliable classification system reflecting their evolutionary relationships. • Understanding what unique molecular, biochemical or other properties distinguish different groups of microbes from each other. Are Genome Sequences helpful in Understanding Microbial Evolution? Widely held view Doolittle, W.F. (1999) Science 284,2124 Koonin and Wolf (2012) Front. Cell. Infect. Microbiol. 284,2124 © by author Prokaryotic genomes have acquired extensive information from sources other than through vertical descent. Only a vague outline of the main domains/phyla (STOL) can be inferred. ESCMID OnlineA treeLecture-like evolutionary relationship Library (i.e. Darwinian mode of evolution) is very weakly supported or not at all supported. Are any of the Critical Issues Related to Microbial Phylogeny/Taxonomy better understood? Merhej and Raoult (2012) Front. Cell. Infect. Microbiol.
    [Show full text]
  • 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.
    [Show full text]
  • Towards a Balanced View of the Bacterial Tree of Life Frederik Schulz*, Emiley A
    Schulz et al. Microbiome (2017) 5:140 DOI 10.1186/s40168-017-0360-9 SHORTREPORT Open Access Towards a balanced view of the bacterial tree of life Frederik Schulz*, Emiley A. Eloe-Fadrosh, Robert M. Bowers, Jessica Jarett, Torben Nielsen, Natalia N. Ivanova, Nikos C. Kyrpides and Tanja Woyke* Abstract The bacterial tree of life has recently undergone significant expansion, chiefly from candidate phyla retrieved through genome-resolved metagenomics. Bypassing the need for genome availability, we present a snapshot of bacterial phylogenetic diversity based on the recovery of high-quality SSU rRNA gene sequences extracted from nearly 7000 metagenomes and all available reference genomes. We illuminate taxonomic richness within established bacterial phyla together with environmental distribution patterns, providing a revised framework for future phylogeny-driven sequencing efforts. Keywords: Bacteria, Bacterial diversity, Tree of life, Small subunit (SSU) rRNA, Candidate Phyla Radiation (CPR), Microbial dark matter (MDM), Metagenomics, Novel bacterial lineages Main text clades [7, 8], as achieved by data de-replication after Bacteria are major drivers of global biogeochemical cycles, clustering. We constructed a robust phylogeny from all impacting the environment, animal and plant health, and SSU rRNA gene sequences extracted from metagenomes theevolutionarytrajectoryoflifeonEarth.Modern and high-quality reference genomes available through molecular approaches have provided a means to construct the Integrated Microbial Genomes with Microbiome
    [Show full text]
  • Community Structure and Influencing Factors of Airborne Microbial
    atmosphere Article Community Structure and Influencing Factors of Airborne Microbial Aerosols over Three Chinese Cities with Contrasting Social-Economic Levels 1,2,3, , 2,4, , 5 1,6,7, 1 1 Ying Rao * y , Heyang Li * y, Mingxia Chen , Kan Huang *, Jia Chen , Jian Xu and Guoshun Zhuang 1,* 1 Center for Atmospheric Chemistry Study, Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China; [email protected] (J.C.); [email protected] (J.X.) 2 Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China 3 Education and Research office of Health Centre, Minnan Normal University, Zhangzhou 363000, China 4 Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration, Xiamen 361005, China 5 Department of Biological Technology and Engineering, HuaQiao University, Xiamen 361021, China; [email protected] 6 Institute of Eco-Chongming (IEC), Shanghai 202162, China 7 Institute of Atmospheric Sciences, Fudan University, Shanghai 200433, China * Correspondence: [email protected] (Y.R.); [email protected] (H.L.); [email protected] (K.H.); [email protected] (G.Z.) Ying Rao and Heyang Li contributed equally to this work. y Received: 6 February 2020; Accepted: 11 March 2020; Published: 25 March 2020 Abstract: As an important part of atmospheric aerosol, airborne bacteria have major impacts on human health. However, variations of airborne community structure due to human-induced activities and their possible impact on human health have not been well understood. In this study, we sampled atmospheric microbial aerosols in three Chinese cities (Shanghai, Xiamen, and Zhangzhou) with contrasting social-economic levels and analyzed the bacterial composition using high-throughput sequencing methods.
    [Show full text]
  • New Insights Into the Activation of Radiation Desiccation Response Regulon in Deinococcus Radiodurans
    J Biosci (2021)46:10 Ó Indian Academy of Sciences DOI: 10.1007/s12038-020-00123-5 (0123456789().,-volV)(0123456789().,-volV) New insights into the activation of Radiation Desiccation Response regulon in Deinococcus radiodurans 1,2 1,2 ANAGANTI NARASIMHA and BHAKTI BASU * 1Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400 085, India 2Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400 094, India *Corresponding author (Email, [email protected]) MS received 3 September 2020; accepted 17 November 2020 The highly radiation-resistant bacterium Deinococcus radiodurans responds to gamma radiation or desiccation through the coordinated expression of genes belonging to Radiation and Desiccation Resistance/Response (RDR) regulon. RDR regulon is operated through cis-acting sequence RDRM (Radiation Desiccation Response Motif), trans-acting repressor DdrO and protease IrrE (also called PprI). The present study evaluated whether RDR regulon controls the response of D. radiodurans to various other DNA damaging stressors, to which it is resistant, such as UV rays, mitomycin C (MMC), methyl methanesulfonate (MMS), ethidium bromide (EtBr), etc. Activation of 3 RDR regulon genes (ddrB, gyrB and DR1143) was studied by tagging their promoter sequences with a highly sensitive GFP reporter. Here we demonstrated that all the DNA damaging stressors elicited activation of RDR regulon of D. radiodurans in a dose-dependent and RDRM-/ IrrE-dependent manner. However, ROS-mediated indirect effects [induced by hydrogen peroxide (H2O2), methyl viologen (MV), heavy metal/metalloid (zinc or tellurite), etc.] did not activate RDR regulon. We also showed that level of activation was inversely proportional to cellular abundance of repressor DdrO.
    [Show full text]