DOCSLIB.ORG

The Structural Protein E of the Archaeal Virus ␾Ch1: Evidence for Processing in Natrialba Magadii During Virus Maturation

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Structural Protein E of the Archaeal Virus ␾Ch1: Evidence for Processing in Natrialba Magadii During Virus Maturation Virology 276, 376–387 (2000) doi:10.1006/viro.2000.0565, available online at http://www.idealibrary.com on View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector The Structural Protein E of the Archaeal Virus ␾Ch1: Evidence for Processing in Natrialba magadii during Virus Maturation Reinhard Klein,1 Barbara Greineder, Ulrike Baranyi,2 and Angela Witte3 Institute of Microbiology and Genetics, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria Received March 1, 2000; accepted July 31, 2000 ␾Ch1 is a lysogenic virus for the haloalkalophilic archaeon Natrialba magadii. The virus morphology resembles other members of Myoviridae infecting Halobacterium species. The gene of the major capsid protein E of virus ␾Ch1 was cloned and the DNA sequence was determined. Gene E was mapped to a 3.2-kbp ClaI fragment, localized to the 5Ј-end of the ␾Ch1 genome. The complete nucleotide sequence of this region was determined and the identity of gene E was confirmed by comparing the experimentally determined N-terminal amino acid sequence of the purified protein to the translated DNA sequence of its open reading frame. We present evidence that the gene E product is proteolytically cleaved between Lys16 and Asn17 to yield the 305 residue polypeptides found in the mature viral capsid. Processing of the protein itself during virus development was determined by 2D gel electrophoresis using protein E-specific antibodies. Sequence similarity studies revealed an 80% identity to capsid protein Hp32 of ␾H, infecting Halobacterium salinarum. RT-PCR analysis as well as Western blot studies revealed gene E as a late gene. Transcripts and proteins could be detected shortly before onset of lysis of the lysogenic strain N. magadii L11. © 2000 Academic Press Key Words: virus; protein processing; Natrialba; capsid; Archaea; halophilic. INTRODUCTION of virus-encoded insertion sequences (Schnabel et al., 1982; Schnabel, 1984), mapping of early and late tran- Besides Bacteria and Eukarya, Archaea have been scripts (Gropp et al., 1989, 1992; Stolt and Zillig, 1992), suggested to form the third domain of life (Woese and analysis of lytic control by the action of a transcriptional Fox, 1977). Viruses which infect members of each of the repressor as well as antisense RNA control (Ken and three major phenotypic groups of Archaea, the extreme Hackett, 1991; Stolt and Zillig, 1993a,b,c, 1994), and the thermophiles, the methanogens, and the halophiles, identification of genes for structural proteins and putative have been isolated (for reviews see Zillig et al., 1986, methyltransferases (Stolt et al., 1994). 1988; Reiter et al., 1988). Virus ␾Ch1 was the first one isolated from a member Most archaeal viruses known so far have been iso- of the haloalkalophilic branch of Archaea (Witte et al., lated during the last years from the group of extreme 1997). Haloalkalophilic Archaea require not only high salt halophilic Archaea. These viruses include Hs1 (Torsvik concentrations but also high pH for growth and therefore ␾ and Dundas, 1974, 1980), Ja1 (Wais et al., 1975), H differ from the other genera of the Halobacteriales, living (Schnabel et al., 1982), Hh-1 and Hh-3 (Pauling, 1982; at a neutral pH. ␾Ch1 is a head–tail virus belonging to ␾ Rohrmann et al., 1983), and N (Vogelsang-Wenke and the family of Myoviridae and infecting Archaea of the Oesterhelt, 1988), all of them infecting the genus species Natrialba magadii, thereby resulting in lysis of Halobacterium. HF1 and HF2 (Nuttall and Dyall-Smith, the cells. Two strains of N. magadii are available: the 1993) were found to infect Halorubrum and Haloferax. lysogenic strain L11 and strain L13 which has been His1, the first lemon-shaped virus within this group of cured of the virus (Witte et al., 1997). The latter one was halophilic Archaea, was isolated from Haloarcula his- used for infection with ␾Ch1. Nucleic acid preparations panica (Bath and Dyall-Smith, 1998). of purified ␾Ch1 particles have been found to contain Halovirus ␾H is the most intensively studied virus DNA as well as RNA, which is a highly unusual feature of within this group. Studies included the characterization viruses (Witte et al., 1997). The only comparable situation has been found for Bacillus subtilis bacteriophage ␾29 (Guo et al., 1987a,b), as well as for other B. subtilis 1 Present address: Department of Biology, University of Pennsylvania, phages (Wichitwechkarn et al., 1989), in which a certain 415 South University Avenue, Philadelphia, PA 19103. RNA is associated with phage proheads. For phage ␾29 2 Present address: Department of Vascular Biology and Thrombosis Research, VIRCC, University of Vienna, A-1235 Vienna, Austria. it was shown that this RNA is necessary for the DNA 3 ␾ To whom correspondence should be addressed. E-mail: emily@ packaging process (Guo et al., 1987a,b). 29 RNA is gem.univie.ac.at. thought to form a circular, hexameric structure which is 0042-6822/00 $35.00 Copyright © 2000 by Academic Press 376 All rights of reproduction in any form reserved. CAPSID PROTEIN OF ␾Ch1 377 associated with the phage proheads and is not found in mature phage particles contrary to the ␾Ch1 RNA. Fur- thermore, the RNA fraction isolated from ␾Ch1 virus particle preparations is a mixture of primarily host-en- coded but also virus-encoded RNAs varying in length from 100 to 800 nucleotides. Since ␾Ch1 was the first virus detected in haloalkalo- philic Archaea and due to the fact that DNA as well as RNA was found in purified virus particles, ␾Ch1 was FIG. 1. Schematically presentation of the localization of gene E. Part analyzed in more detail. Here we describe studies of the of the restriction map of ␾Ch1 DNA is given with different restriction major capsid protein E of virus ␾Ch1. We have mapped fragments named by their size. Gene E is indicated on the top by a box. and sequenced gene E and expression has been moni- tored on the RNA as well as on the protein level. Two- dimensional protein gel electrophoresis was used to ferred onto PVDF membranes by semidry electroblotting show that protein E is processed in vivo during virus and stained with Coomassie Brilliant Blue. The band maturation. We present evidence that protein E might be containing protein E was excised and subjected to N- associated with the cell envelope of N. magadii during terminal amino acid sequencing using standard Edman virus development. degradation techniques. The N-terminal amino acid se- quence determined for protein E was NALTVDDL, lack- RESULTS AND DISCUSSION ing at least the first methionine. To localize the corre- sponding gene on the ␾Ch1 genome, a degenerate oli- Identification of the gene encoding the major capsid gonucleotide deduced from this sequence was designed protein E of virus ␾Ch1 (oligonucleotide E-deg, Table 1). ␾Ch1 DNA was cut with Purified virus particles were precipitated with 10% TCA restriction enzymes ClaI, PstI, and EcoRV, separated on and separated by 12% SDS-PAGE. Proteins were trans- 0.8% agarose gels, blotted onto nylon membranes, and hybridized with the 32P-labeled oligonucleotide. Hybrid- ization with oligonucleotide E-deg revealed a signal cor- TABLE 1 responding to a 3.2-kbp ClaI fragment (fragment D), a 13-kbp PstI fragment (fragment B), and a 2-kbp EcoRV Strains, Plasmids, and Primers fragment (fragment G). The localization of the gene de- scribed within this study is shown in a partial restriction Strain Relevant marker Source/reference map of the virus genome (Fig. 1). N. magadii L11 wt, ␾Ch1 prophage Witte et al., 1997 Sequence analysis L13 cured for ␾Ch1 Witte et al., 1997 E. coli The ClaI fragment D was isolated and cloned into Ϫ ϩ ϩ XL1-Blue endA1, gyrA96, hsdR17 (r k m K ), Stratagene pBlueskript II KS , resulting in clone pC-E. The fragment lac, recA1, relA1, supE44, was subjected to DNA sequencing using the dideoxy thi, (FЈ, lacIq, lacZ⌬M15, ϩ method of Sanger et al. (1977). An open reading frame of proAB , tet) 966 nt coding for a 321 aa protein, which included the KT950 placUV5-T7 gene 1-kan::l`acZ Tedin et al., 1995 (FЈ, lacIq, lacZ⌬M15, proABϩ, sequence NALTVDDL as determined by Edman degra- tet) dation, could be identified on ClaI fragment D. This open reading frame was therefore termed gene E (Fig. 2). As Plasmids Relevant marker Source/reference shown in Fig. 2, the N-terminal aa sequence NALTVDDL is in a distance of 16 codons from the first methionine ϩ pKS-II mcs, bla, ColE1 Stratagene start codon of the open reading frame. This indicates pC-E ClaI-E-fragment cloned into pKS-IIϩ This study pET-KH His-tag, mcs, bla, ColE1 Novagen (modified) posttranslational processing of protein E. The size of the pET-E E cloned into pET-KH This study mature protein was calculated to be 34.0 kDa, which is lower than inferred from SDS-PAGE (Table 2). Protein E is Primers Sequence an acidic protein as reflected by a calculated isoelectric point of 3.74. A surplus of acidic over basic residues has E-deg 5Ј-AAYGCXYTXACXGTXGAYGAYYTX-3Ј E-HIS-5 5Ј-GAGATTTCAATGAGATCTCGAACCATCAAC-3Ј also been observed for several H. salinarum proteins E-HIS-3 5Ј-GATGGTGCGGCTAGCCATCGTTCACCG-3Ј (Zaccai et al., 1989; Eisenberg and Wachtel, 1987), as CD-2 5Ј-TCGACTGACAACCAACACACCC-3Ј well as for capsid proteins of virus ␾H infecting H. CD-4 5Ј-GCGTTCAGCCATCGTTCACC-3Ј salinarum (Stolt et al., 1994), a characteristic feature of Ј Ј Nb16F 5 -GGAGACCATTCCGG-3 halophilic proteins in general (Lanyi, 1974; Eisenberg et Nb16R 5Ј-GGATCCGTCTTCCAG-3Ј al., 1992; Frolow et al., 1996). In contrast to the low 378 KLEIN ET AL. FIG. 2. Sequence of gene E encoding the major capsid protein of ␾Ch1.
Load more

Recommended publications
  • Diversity of Halophilic Archaea in Fermented Foods and Human Intestines and Their Application Han-Seung Lee1,2*
    J. Microbiol. Biotechnol. (2013), 23(12), 1645–1653 http://dx.doi.org/10.4014/jmb.1308.08015 Research Article Minireview jmb Diversity of Halophilic Archaea in Fermented Foods and Human Intestines and Their Application Han-Seung Lee1,2* 1Department of Bio-Food Materials, College of Medical and Life Sciences, Silla University, Busan 617-736, Republic of Korea 2Research Center for Extremophiles, Silla University, Busan 617-736, Republic of Korea Received: August 8, 2013 Revised: September 6, 2013 Archaea are prokaryotic organisms distinct from bacteria in the structural and molecular Accepted: September 9, 2013 biological sense, and these microorganisms are known to thrive mostly at extreme environments. In particular, most studies on halophilic archaea have been focused on environmental and ecological researches. However, new species of halophilic archaea are First published online being isolated and identified from high salt-fermented foods consumed by humans, and it has September 10, 2013 been found that various types of halophilic archaea exist in food products by culture- *Corresponding author independent molecular biological methods. In addition, even if the numbers are not quite Phone: +82-51-999-6308; high, DNAs of various halophilic archaea are being detected in human intestines and much Fax: +82-51-999-5458; interest is given to their possible roles. This review aims to summarize the types and E-mail: [email protected] characteristics of halophilic archaea reported to be present in foods and human intestines and pISSN 1017-7825, eISSN 1738-8872 to discuss their application as well. Copyright© 2013 by The Korean Society for Microbiology Keywords: Halophilic archaea, fermented foods, microbiome, human intestine, Halorubrum and Biotechnology Introduction Depending on the optimal salt concentration needed for the growth of strains, halophilic microorganisms can be Archaea refer to prokaryotes that used to be categorized classified as halotolerant (~0.3 M), halophilic (0.2~2.0 M), as archaeabacteria, a type of bacteria, in the past.
    [Show full text]
  • Natrialba Hulunbeirensis Sp. Nov. and Natrialba Chahannaoensis Sp. Nov., Novel Haloalkaliphilic Archaea from Soda Lakes in Inner Mongolia Autonomous Region, China
    International Journal of Systematic and Evolutionary Microbiology (2001), 51, 1693–1698 Printed in Great Britain Natrialba hulunbeirensis sp. nov. and Natrialba chahannaoensis sp. nov., novel haloalkaliphilic archaea from soda lakes in Inner Mongolia Autonomous Region, China 1 Institute of Microbiology, Yi Xu,1 Zhenxiong Wang,1 Yanfen Xue,1 Peijin Zhou,1 Yanhe Ma,1 Chinese Academy of 2 3 Sciences, Zhongguancun Antonio Ventosa and William D. Grant district, Beijing 100080, China Author for correspondence: Yanhe Ma. Tel: 86 10 62553628. Fax: 86 10 62560912. 2 j j Department of e-mail: mayh!sun.im.ac.cn Microbiology and Parasitology, Faculty of Pharmacy, University of T T Sevilla, 41012 Sevilla, Spain Two haloalkaliphilic archaeal strains, X21 and C112 , were isolated from soda lakes in Inner Mongolia Autonomous Region, China. Their morphology, 3 Department of Microbiology and physiology, biochemical features, polar lipid composition and 16S rRNA genes Immunology, University of were characterized in order to elucidate their taxonomy. According to these Leicester, Leicester data, strains X21T and C112T belong to the genus Natrialba, although there are LE1 9HN, UK clear differences with respect to their physiology and polar lipid composition between the two strains and the type species, Natrialba asiatica. On the basis of low DNA–DNA hybridizations, these two strains should be considered as new species of genus Natrialba. The names Natrialba hulunbeirensis sp. nov. (type strain X21T l AS 1.1986T l JCM 10989T ) and Natrialba chahannaoensis sp. nov. (type strain C112T l AS 1.1977T l JCM 10990T ) are proposed. Keywords: Natrialba hulunbeirensis, Natrialba chahannaoensis, archaea, haloalkaliphiles INTRODUCTION Smith, 1995; Kamekura et al., 1997; Montalvo- Rodrı!guez et al., 1998; McGenity et al., 1998; Ventosa The family Halobacteriaceae was proposed by et al., 1999; Xu et al., 1999; Wainø et al., 2000).
    [Show full text]
  • Nucleoside Diphosphate Kinase of Halobacteria - Amino Acid Sequence and Salt-Response Pattern
    գ؈೰ি൝ԙӔࠠ Vol.3, 2004ۙئ Journal of Japanese Society for Extremophiles (2004), Vol. 3, 18-27 ଙཉ൫ۍ Mizuki T1, Kamekura M2, Ishibashi M3, Usami R1, Yoshida Y1, Tokunaga M3, Horikoshi K1 Nucleoside diphosphate kinase of halobacteria - Amino acid sequence and salt-response pattern - 1 Department of Applied Chemistry, Faculty of Engineering, Toyo University, Kawagoe, Saitama 350-8585, Japan 2 Noda Institute for Scientific Research, Noda, Chiba 278-0037, Japan 3 Department of Agricultural Chemistry, Kagoshima University, Kagoshima 890-0065, Japan Corresponding author: Kamekura M, [email protected] Phone: +81-4-7123-5573. Fax: +81-4-7123-5953. Received: Oct. 15, 2003 / Accepted: Nov. 27, 2003 Abstract Nucleotide diphosphate kinase (NDK) was purified exchange g-phosphates between nucleoside triphosphates and from 12 strains of halobacteria using ATP-agarose diphosphates, thus playing a key role in maintaining cellular chromatography and their N-terminal amino acid sequences pools of all nucleoside triphosphates 1). NDK of halobacteria were determined. The electrophoretic mobilities of these was first studied as a major cytosolic protein of Natrialba enzymes differed significantly on the native-PAGE or the SDS- magadii (formerly Natronobacterium magadii) that bound to PAGE when the samples were not heat treated. Comparison of ATP-agarose and eluted with 5 mM ATP (adenosine seven complete amino acid sequences from seven species of triphosphate) in the presence of 3.5 M NaCl 16). This enzyme Haloarcula and those from Har. californiae and Har. japonica, was active over a wide range of NaCl concentrations; from whose N-terminal 3 amino acids have not been determined yet, 0.09 M to 3.5 M.
    [Show full text]
  • Construction of an ORF34 Deletion Φch1 Strain and Secretion of Putative Tail Fibre Proteins“
    DIPLOMARBEIT Titel der Diplomarbeit „Construction of an ORF34 deletion φCh1 strain and secretion of putative tail fibre proteins“ Verfasserin Dimmel Katharina angestrebter akademischer Grad Magistra der Naturwissenschaften (Mag.rer.nat.) Wien, 2013 Studienkennzahl lt. Studienblatt: A 441 Studienrichtung lt. Studienblatt: Diplomstudium Genetik – Mikrobiologie (Stzw) UniStG Betreut von: Ao. Univ.-Prof. Dipl.-Biol. Dr. Angela Witte 2 3 4 Table of the contents 1. INTRODUCTION ........................................................................................................................... 10 1.1 ARCHAEA – THE THIRD DOMAIN OF LIFE ....................................................................................................10 1.1.1 Diversity and abundance ................................................................................................................. 11 1.1.2 Archaea a mosaic of Bacteria and Eukarya ..................................................................................... 13 1.1.3 Archaea, Bacteria and Eukarya in contrast ..................................................................................... 13 1.1.3.1 Structural aspect .....................................................................................................................................13 1.1.3.2 Genetic aspect .........................................................................................................................................14 1.1.3.3 Replication process .................................................................................................................................14
    [Show full text]
  • Quorum Sensing in Extreme Environments
    Life 2013, 3, 131-148; doi:10.3390/life3010131 OPEN ACCESS life ISSN 2075-1729 www.mdpi.com/journal/life Review Quorum Sensing in Extreme Environments Kate Montgomery 1, James C. Charlesworth 1, Rebecca LeBard 1, Pieter T. Visscher 2, 3 and Brendan P. Burns 1,3,* 1 School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; E-Mails: [email protected] (K.M.); [email protected] (J.C.C.); [email protected] (R.L.) 2 Center for Integrative Geosciences, University of Connecticut 354 Mansfield Road, Storrs, CT 06269-2045, USA; E-Mail: [email protected] 3 Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW 2052, Australia * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +61-2-9385-3659; Fax: +61-2-9385-1591. Received: 10 December 2012; in revised form: 21 January 2013 / Accepted: 22 January 2013 / Published: 29 January 2013 Abstract: Microbial communication, particularly that of quorum sensing, plays an important role in regulating gene expression in a range of organisms. Although this phenomenon has been well studied in relation to, for example, virulence gene regulation, the focus of this article is to review our understanding of the role of microbial communication in extreme environments. Cell signaling regulates many important microbial processes and may play a pivotal role in driving microbial functional diversity and ultimately ecosystem function in extreme environments. Several recent studies have characterized cell signaling in modern analogs to early Earth communities (microbial mats), and characterization of cell signaling systems in these communities may provide unique insights in understanding the microbial interactions involved in function and survival in extreme environments.
    [Show full text]
  • Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes
    GBE Different Ways of Doing the Same: Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes Dennifier Costa Brandao~ Cruz1, Lenon Lima Santana1, Alexandre Siqueira Guedes2, Jorge Teodoro de Souza3,*, and Phellippe Arthur Santos Marbach1,* 1CCAAB, Biological Sciences, Recoˆ ncavo da Bahia Federal University, Cruz das Almas, Bahia, Brazil 2Agronomy School, Federal University of Goias, Goiania,^ Goias, Brazil 3 Department of Phytopathology, Federal University of Lavras, Minas Gerais, Brazil Downloaded from https://academic.oup.com/gbe/article/11/4/1235/5345563 by guest on 27 September 2021 *Corresponding authors: E-mails: [email protected]fla.br; [email protected]. Accepted: February 16, 2019 Abstract The last two steps of the purine biosynthetic pathway may be catalyzed by different enzymes in prokaryotes. The genes that encode these enzymes include homologs of purH, purP, purO and those encoding the AICARFT and IMPCH domains of PurH, here named purV and purJ, respectively. In Bacteria, these reactions are mainly catalyzed by the domains AICARFT and IMPCH of PurH. In Archaea, these reactions may be carried out by PurH and also by PurP and PurO, both considered signatures of this domain and analogous to the AICARFT and IMPCH domains of PurH, respectively. These genes were searched for in 1,403 completely sequenced prokaryotic genomes publicly available. Our analyses revealed taxonomic patterns for the distribution of these genes and anticorrelations in their occurrence. The analyses of bacterial genomes revealed the existence of genes coding for PurV, PurJ, and PurO, which may no longer be considered signatures of the domain Archaea. Although highly divergent, the PurOs of Archaea and Bacteria show a high level of conservation in the amino acids of the active sites of the protein, allowing us to infer that these enzymes are analogs.
    [Show full text]
  • In Vitro Dual (Anticancer and Antiviral) Activity of the Carotenoids Produced by Haloalkaliphilic Archaeon Natrialba Sp. M6 Ghada E
    www.nature.com/scientificreports OPEN In vitro dual (anticancer and antiviral) activity of the carotenoids produced by haloalkaliphilic archaeon Natrialba sp. M6 Ghada E. Hegazy1, Marwa M. Abu-Serie2, Gehan M. Abo-Elela1, Hanan Ghozlan3, Soraya A. Sabry3, Nadia A. Soliman4* & Yasser R. Abdel-Fattah4* Halophilic archaea are a promising natural source of carotenoids. However, little information is available about the biological impacts of these archaeal metabolites. Here, carotenoids of Natrialba sp. M6, which was isolated from Wadi El-Natrun, were produced, purifed and identifed by Raman spectroscopy, GC-mass spectrometry, and Fourier transform infrared spectroscopy, LC–mass spectrometry and Nuclear magnetic resonance spectroscopy. The C50 carotenoid bacterioruberin was found to be the predominant compound. Because cancer and viral hepatitis are serious diseases, the anticancer, anti-HCV and anti-HBV potentials of these extracted carotenoids (pigments) were examined for the frst time. In vitro results indicated that the caspase-mediated apoptotic anticancer efect of this pigment and its inhibitory efcacy against matrix metalloprotease 9 were signifcantly higher than those of 5-fuorouracil. Furthermore, the extracted pigment exhibited signifcantly stronger activity for eliminating HCV and HBV in infected human blood mononuclear cells than currently used drugs. This antiviral activity may be attributed to its inhibitory potential against HCV RNA and HBV DNA polymerases, which thereby suppresses HCV and HBV replication, as indicated by a high viral clearance % in the treated cells. These novel fndings suggest that the C50 carotenoid of Natrialba sp. M6 can be used as an alternative source of natural metabolites that confer potent anticancer and antiviral activities. Halophilic archaea (haloarchaea) belong to the family Halobacteriaceae.
    [Show full text]
  • Isolation and Identification of Haloalkaliphilic Archaeal Isolates from a Soda Lake in India
    ISSN(Online) : 2319-8753 ISSN (Print) : 2347-6710 International Journal of Innovative Research in Science, Engineering and Technology (An ISO 3297: 2007 Certified Organization) Website: www.ijirset.com Vol. 6, Issue 6, June 2017 Isolation and Identification of Haloalkaliphilic Archaeal Isolates from a Soda Lake in India Gopal N. Kalambe 1, Vivek N. Upasani 2 Research Student, Department of Microbiology, JJTU, Vidyanagari, Jhunjhunu, Rajasthan, India Associate Professor, Department of Microbiology, M. G. Science Institute, Ahmedabad, Gujarat, India2 ABSTRACT: Although an extreme environment, the hypersaline ecosystems are rich in microbial diversity for biotechnological applications. The aerobic, gram-negative, pleomorphic rods and cocci, chemoorganotrophic archaea belonging to the family Halobacteriaceae within the Phylum Euryarchaeota have been extensively studied in the last few decades. They have provided new insights for survival under high salinity and/or alkalinity. They occur in both marine as well as inland saline regions mainly in solar salterns. The soda lakes are intermittent saline lakes that contain sodium carbonate / bicarbonate (soda) alongwith sodium chloride that are found in desert regions of the world for example, Lake Magadii (Kenya), Wadi Natrun lakes (Egypt), Sambhar Salt Lake (India), etc. Several halobacterial strains were isolated from the hypersaline brines collected from Sambhar Lake, Rajasthan. Three of the isolates were selected based on differences in colony/cultural characteristics and identified phylogenetically based on 16S rRNA sequence homology studies. Two isolates were identified as strains identical to Natronobacterium sp. and one as Natrialba sp. KEYWORDS: Natronobacterium, Natrialba, Haloarchaea, Sambhar Lake. I. INTRODUCTION The extremely halophilic archaea belonging to the family Halobacteriaceae (Phylum Euryarchaeota) are commonly found in the hypersaline environments such as salt lakes, salt ponds, marine salterns and soda lakes.
    [Show full text]
  • Gene Identification and Molecular Characterization of Solvent Stable Protease from a Moderately Haloalkaliphilic Bacterium, Geomicrobium Sp
    J. Microbiol. Biotechnol. (2011), 21(2), 129–135 doi: 10.4014/jmb.1007.07064 First published online 22 November 2010 Gene Identification and Molecular Characterization of Solvent Stable Protease from A Moderately Haloalkaliphilic Bacterium, Geomicrobium sp. EMB2 Karan, Ram1, Raj Kumar Mohan Singh2, Sanjay Kapoor2, and S. K. Khare1* 1Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110 016, 2Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110 021, India Received: July 30, 2010 / Revised: October 21, 2010 / Accepted: November 11, 2010 Cloning and characterization of the gene encoding a A few proteases from moderately halophilic bacteria solvent-tolerant protease from the haloalkaliphilic bacterium have been purified and studied; namely, those from Geomicrobium sp. EMB2 are described. Primers designed Bacillus sp. no. 21-1 [13], haloalkaliphilic Bacillus sp. Vel [7], based on the N-terminal amino acid sequence of the Filobacillus sp. RF2-5 [8], Halobacillus sp. SR5-3 [22], purified EMB2 protease helped in the amplification of a Salinivibrio sp. strain AF-2004 [16], haloalkaliphilic 1,505-bp open reading frame that had a coding potential bacterium sp. AH-6 [4], and Halobacillus karajensis [15]. of a 42.7-kDa polypeptide. The deduced EMB2 protein Reports on the protease gene are still less documented; for contained a 35.4-kDa mature protein of 311 residues, with example, halolysin 172P1 from Natrialba asiatica [12], a high proportion of acidic amino acid residues. Phylogenetic halolysin R4 from Haloferax mediterranei [11], Spt A analysis placed the EMB2 gene close to a known serine from Natrinema sp.
    [Show full text]
  • Tracing the Repertoire of Promiscuous Enzymes Along the Metabolic Pathways in Archaeal Organisms
    life Article Tracing the Repertoire of Promiscuous Enzymes along the Metabolic Pathways in Archaeal Organisms Mario Alberto Martínez-Núñez 1,* , Zuemy Rodríguez-Escamilla 2 , Katya Rodríguez-Vázquez 3 and Ernesto Pérez-Rueda 4,5 1 Laboratorio de Estudios Ecogenómicos, Facultad de Ciencias, Unidad Académica de Ciencias y Tecnología de la UNAM en Yucatán, Universidad Nacional Autónoma de México, Carretera Sierra Papacal-Chuburna Km. 5, C.P. 97302, Mérida, Yucatán, Mexico 2 Departamento de Microbiología, Instituto de Biotecnología, Universidad Nacional, Autónoma de México, C.P. 62210, Cuernavaca, Morelos, Mexico; [email protected] 3 Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Ciudad Universitaria, C.P. 04510, Ciudad de México, Mexico; [email protected] 4 Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, C.P. 62210, Cuernavaca, Morelos, Mexico; [email protected] 5 Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Carretera Sierra Papacal-Chuburna Km. 5, C.P. 97302, Mérida, Yucatán, Mexico * Correspondence: [email protected]; Tel.: +52-999-341-0860 (ext. 7630) Received: 12 April 2017; Accepted: 10 July 2017; Published: 13 July 2017 Abstract: The metabolic pathways that carry out the biochemical transformations sustaining life depend on the efficiency of their associated enzymes. In recent years, it has become clear that promiscuous enzymes have played an important role in the function and evolution of metabolism. In this work we analyze the repertoire of promiscuous enzymes in 89 non-redundant genomes of the Archaea cellular domain.
    [Show full text]
  • Diversity of Halophilic Archaea from Six Hypersaline Environments in Turkey
    J. Microbiol. Biotechnol. (2007), 17(5), 745–752 Diversity of Halophilic Archaea From Six Hypersaline Environments in Turkey OZCAN, BIRGUL1, GULAY OZCENGIZ2, ARZU COLERI3, AND CUMHUR COKMUS3* 1Mustafa Kemal University, Sciences and Letters Faculty, Department of Biology, 31024, Hatay, Turkey 2METU, Department of Biological Sciences, 06531, Ankara, Turkey 3Ankara University, Faculty of Science, Department of Biology, 06100, Ankara, Turkey Received: October 17, 2006 Accepted: December 1, 2006 Abstract The diversity of archaeal strains from six environments worldwide. To date, 64 species and 20 hypersaline environments in Turkey was analyzed by comparing genera of Halobacteriaceae have been described [5, 8, 9, their phenotypic characteristics and 16S rDNA sequences. 26, 27], and new taxa in the Halobacteriales are still being Thirty-three isolates were characterized in terms of their described. phenotypic properties including morphological and biochemical Halophilic archaea have been isolated from various characteristics, susceptibility to different antibiotics, and total hypersaline environments such as aquatic environments lipid and plasmid contents, and finally compared by 16S including salt lakes and saltern crystalizer ponds, and saline rDNA gene sequences. The results showed that all isolates soils [9]. Turkey, especially central Anatolia, accommodates belong to the family Halobacteriaceae. Phylogenetic analyses extensive hypersaline environments. To the best of our using approximately 1,388 bp comparisions of 16S rDNA knowledge, there is quite limited information on extremely sequences demonstrated that all isolates clustered closely to halophilic archaea of Turkey origin. Previously, extremely species belonging to 9 genera, namely Halorubrum (8 isolates), halophilic communities of the Salt Lake-Ankara region were Natrinema (5 isolates), Haloarcula (4 isolates), Natronococcus partially characterized by comparing their biochemical and (4 isolates), Natrialba (4 isolates), Haloferax (3 isolates), morphological characteristics [2].
    [Show full text]
  • Draft Genome Sequence of a Haloalkaliphilic Archaeon: Natrialba Sp
    Int.J.Curr.Microbiol.App.Sci (2017) 6(5): 2399-2408 International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 6 Number 5 (2017) pp. 2399-2408 Journal homepage: http://www.ijcmas.com Original Research Article https://doi.org/10.20546/ijcmas.2017.605.268 Draft Genome Sequence of a Haloalkaliphilic archaeon: Natrialba sp. SSL1 (ATCC 43988) Isolated from Sambhar Salt Lake, India G.N. Kalambe1, P.M. Chandarana2, V.M. Tanavade2,3,4 and V.N. Upasani5* 1JJTU, Vidyanagari, Jhunjhunu-333001, Rajasthan, India 2IBioAnalysis Pvt. Ltd., Ahmedabad 380009, Gujarat, India 3Division of Biological & Life Sciences, School of Arts & Sciences, Ahmedabad University, Ahmedabad 380009, Gujarat, India 4Bioinformatics Institute, Agency for Science Technology & Research (A*STAR), 30 Biopolis Street, Singapore 138671 5Department of Microbiology, M. G. Science Institute, Ahmedabad 380009, Gujarat, India *Corresponding author: [email protected] ABSTRACT An extremely haloalkaliphilic archaeon, Natrialba sp. SSL1, gram-negative, rod-shaped, K e yw or ds motile, aerobic, chemoorganotrophic belonging to the family Halobacteriaceae within the Phylum Euryarchaeota was isolated from Sambhar Salt Lake (SSL), Rajasthan, India in Natrialba SSL1, the 1980s. The Whole Genome Sequence (WGS) of this archaeon was deciphered for the haloalkaliphiles, haloarchaea, purpose of comparative genomics with other halobacteria as well as eubacteria. The WGS Whole Genome raw data of the genome was assembled into 61 contigs, showing total sequence length of 4,580,837bp, comprising of 4276 genes, out of which 4126 were found to be coding genes Sequencing (WGS), IlluminaHiseq, soda (exons), while 96 were psuedogenes. It encodes for 4048 proteins, some of which are lakes, Sambhar Lake.
    [Show full text]