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Hou J, Li XX, Sun Y, Li Y, Yang XY, Sun YP, Cui HL. Novel Archaeal Histamine Oxidase from Natronobeatus ordinarius: Insights into Histamine Degradation for Enhancing Food Safety. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:6519-6525. [PMID: 38497614 DOI: 10.1021/acs.jafc.4c00695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Histamine, found abundantly in salt-fermented foods, poses a risk of food poisoning. Natronobeatus ordinarius, a halophilic archaeon isolated from a salt lake, displayed a strong histamine degradation ability. Its histamine oxidase (HOD) gene was identified (hodNbs). This is the first report of an archaeal HOD. The HODNbs protein was determined to be a tetramer with a molecular weight of 307 kDa. HODNbs displayed optimum activity at 60-65 °C, 1.5-2.0 M NaCl, and pH 6.5. Notably, within the broad NaCl range between 0.5 and 2.5 M, HODNbs retained above 50% of its maximum activity. HODNbs exhibited good thermal stability, pH stability, and salinity tolerance. HODNbs was able to degrade various biogenic amines. The Vmax of HODNbs for histamine was 0.29 μmol/min/mg, and the Km was 0.56 mM. HODNbs exhibited high efficiency in histamine removal from fish sauce, namely, 100 μg of HODNbs degraded 5.63 mg of histamine (37.9%) in 10 g of fish sauce within 24 h at 50 °C. This study showed that HODNbs with excellent enzymatic properties has promising application potentials to degrade histamine in high-salt foods.
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Affiliation(s)
- Jing Hou
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang 212013, Jiangsu, People's Republic of China
| | - Xin-Xin Li
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang 212013, Jiangsu, People's Republic of China
| | - Yu Sun
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang 212013, Jiangsu, People's Republic of China
| | - Yang Li
- School of Oceanography, Zhejiang University, 1 Zheda Road, Dinghai District, Zhoushan 316021, Zhejiang, People's Republic of China
| | - Xiao-Yan Yang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang 212013, Jiangsu, People's Republic of China
| | - Ya-Ping Sun
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang 212013, Jiangsu, People's Republic of China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang 212013, Jiangsu, People's Republic of China
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Madru C, Martínez-Carranza M, Laurent S, Alberti AC, Chevreuil M, Raynal B, Haouz A, Le Meur RA, Delarue M, Henneke G, Flament D, Krupovic M, Legrand P, Sauguet L. DNA-binding mechanism and evolution of replication protein A. Nat Commun 2023; 14:2326. [PMID: 37087464 PMCID: PMC10122647 DOI: 10.1038/s41467-023-38048-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/13/2023] [Indexed: 04/24/2023] Open
Abstract
Replication Protein A (RPA) is a heterotrimeric single stranded DNA-binding protein with essential roles in DNA replication, recombination and repair. Little is known about the structure of RPA in Archaea, the third domain of life. By using an integrative structural, biochemical and biophysical approach, we extensively characterize RPA from Pyrococcus abyssi in the presence and absence of DNA. The obtained X-ray and cryo-EM structures reveal that the trimerization core and interactions promoting RPA clustering on ssDNA are shared between archaea and eukaryotes. However, we also identified a helical domain named AROD (Acidic Rpa1 OB-binding Domain), and showed that, in Archaea, RPA forms an unanticipated tetrameric supercomplex in the absence of DNA. The four RPA molecules clustered within the tetramer could efficiently coat and protect stretches of ssDNA created by the advancing replisome. Finally, our results provide insights into the evolution of this primordial replication factor in eukaryotes.
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Affiliation(s)
- Clément Madru
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Markel Martínez-Carranza
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Sébastien Laurent
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), F-29280, Plouzané, France
| | - Alessandra C Alberti
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Maelenn Chevreuil
- Molecular Biophysics Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Bertrand Raynal
- Molecular Biophysics Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Ahmed Haouz
- Crystallography Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Rémy A Le Meur
- Biological NMR Platform & HDX, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Marc Delarue
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Ghislaine Henneke
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), F-29280, Plouzané, France
| | - Didier Flament
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), F-29280, Plouzané, France
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université Paris Cité, CNRS, UMR 6047, Paris, France
| | - Pierre Legrand
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
- Synchrotron SOLEIL, HelioBio group, L'Orme des Merisiers, 91190, Saint-Aubin, France
| | - Ludovic Sauguet
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France.
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Kropp C, Lipp J, Schmidt AL, Seisenberger C, Linde M, Hinrichs KU, Babinger P. Identification of acetylated diether lipids in halophilic Archaea. Microbiologyopen 2022; 11:e1299. [PMID: 35765181 PMCID: PMC9179154 DOI: 10.1002/mbo3.1299] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 05/20/2022] [Accepted: 05/20/2022] [Indexed: 11/10/2022] Open
Abstract
As a hallmark of Archaea, their cell membranes are comprised of ether lipids. However, Archaea-type ether lipids have recently been identified in Bacteria as well, with a somewhat different composition: In Bacillales, sn-glycerol 1-phosphate is etherified with one C35 isoprenoid chain, which is longer than the typical C20 chain in Archaea, and instead of a second isoprenoid chain, the product heptaprenylglyceryl phosphate becomes dephosphorylated and afterward diacetylated by the O-acetyltransferase YvoF. Interestingly, database searches have revealed YvoF homologs in Halobacteria (Archaea), too. Here, we demonstrate that YvoF from Haloferax volcanii can acetylate geranylgeranylglycerol in vitro. Additionally, we present the first-time identification of acetylated diether lipids in H. volcanii and Halobacterium salinarum by mass spectrometry. A variety of different acetylated lipids, namely acetylated archaeol, and acetylated archaetidylglycerol, were found, suggesting that halobacterial YvoF has a broad substrate range. We suppose that the acetyl group might serve to modify the polarity of the lipid headgroup, with still unknown biological effects.
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Affiliation(s)
- Cosimo Kropp
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Julius Lipp
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Anna Lena Schmidt
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Christina Seisenberger
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Mona Linde
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Patrick Babinger
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
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Hou J, Li SY, Zhao YJ, Cui HL. A novel halolysin without C-terminal extension from an extremely halophilic archaeon. Appl Microbiol Biotechnol 2022; 106:3009-3019. [PMID: 35435453 DOI: 10.1007/s00253-022-11903-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 11/29/2022]
Abstract
Halolysins are extracellular proteases secreted by halophilic archaea for nutritional purposes. They bear great application potentials in various industries. Yet the diversity of halolysins remains underexplored. In this study, a halolysin from the extremely halophilic archaeon Haladaptatus sp. DYF46 (HlyHap) was identified to be a novel type of halolysin without C-terminal extension (CTE). Addition of the CTE of a halolysin from Halococcus salifodinae to HlyHap did not significantly affect its extracellular proteolytic activity. Mature HlyHap was generated from recombinant HlyHap precursor by high-affinity column refolding. HlyHap displayed optimal activity at 0.25-0.50 M NaCl, 45 °C and pH 8.5-9.0. Interestingly, HlyHap preferred a low salinity and was stable in a broad range of salinity, albeit from an extremely halophilic archaeon. Ca2+ and Mg2+ significantly promoted HlyHap activity. HlyHap activity was stable with organic solvents and detergents. The Km and Vmax values of HlyHap against azocasein were 0.018 mM and 7,179 U/mg, and those against succinyl-Ala-Ala-Pro-Phe-pNA were 0.32 mM and 3×106 μmol/min/μg, respectively. The unusual traits of HlyHap, a novel type of halolysin without CTE, may endow it with strong potential for various industrial uses, such as biocatalysis in fluctuating salinities and aqueous-organic solvent. KEY POINTS: • This is the first report of a novel type of halolysin without C-terminal extension • HlyHap was obtained by heterologous expression and high-affinity column refolding • HlyHap exhibited good salinity tolerance.
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Affiliation(s)
- Jing Hou
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, Jiangsu, People's Republic of China
| | - Si-Ya Li
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, Jiangsu, People's Republic of China
| | - Yang-Jie Zhao
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, Jiangsu, People's Republic of China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, Jiangsu, People's Republic of China.
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5
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Halorubrum pleomorphic virus-6 Membrane Fusion Is Triggered by an S-Layer Component of Its Haloarchaeal Host. Viruses 2022; 14:v14020254. [PMID: 35215847 PMCID: PMC8875312 DOI: 10.3390/v14020254] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/21/2022] [Accepted: 01/21/2022] [Indexed: 01/27/2023] Open
Abstract
(1) Background: Haloarchaea comprise extremely halophilic organisms of the Archaea domain. They are single-cell organisms with distinctive membrane lipids and a protein-based cell wall or surface layer (S-layer) formed by a glycoprotein array. Pleolipoviruses, which infect haloarchaeal cells, have an envelope analogous to eukaryotic enveloped viruses. One such member, Halorubrum pleomorphic virus 6 (HRPV-6), has been shown to enter host cells through virus-cell membrane fusion. The HRPV-6 fusion activity was attributed to its VP4-like spike protein, but the physiological trigger required to induce membrane fusion remains yet unknown. (2) Methods: We used SDS-PAGE mass spectroscopy to characterize the S-layer extract, established a proteoliposome system, and used R18-fluorescence dequenching to measure membrane fusion. (3) Results: We show that the S-layer extraction by Mg2+ chelating from the HRPV-6 host, Halorubrum sp. SS7-4, abrogates HRPV-6 membrane fusion. When we in turn reconstituted the S-layer extract from Hrr. sp. SS7-4 onto liposomes in the presence of Mg2+, HRPV-6 membrane fusion with the proteoliposomes could be readily observed. This was not the case with liposomes alone or with proteoliposomes carrying the S-layer extract from other haloarchaea, such as Haloferax volcanii. (4) Conclusions: The S-layer extract from the host, Hrr. sp. SS7-4, corresponds to the physiological fusion trigger of HRPV-6.
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Abstract
In this chapter, we describe the reverse genetics methodology behind generating a targeted gene deletion or replacement in archaeal species of the genus Haloferax, which are renowned for their ease of manipulation. Individual steps in the method include the design of a gene-targeting vector, its use in transforming Haloferax to yield "pop-in" and "pop-out" clones, and techniques for validating the genetically manipulated strain. The vector carries DNA fragments of 500-1000 bp that flank the gene of interest (or a mutant allele), in addition to the pyrE2 gene for uracil biosynthesis (Bitan-Banin et al. J Bacteriol 185:772-778, 2003). The latter is used as a selectable marker for the transformation of Haloferax, wherein the vector integrates by homologous recombination at the genomic locus to generate the "pop-in" strain; this is also known as allele-coupled exchange. Culturing of these transformants in nonselective broth and subsequent plating on 5-fluoroorotic acid (5-FOA)-containing media selects for excision of the vector, yielding either wild type or mutant "pop-out" clones. These 5-FOA-resistant clones are screened to confirm the desired mutation, using a combination of phenotypic assays, colony hybridization and Southern blotting. The pop-in/pop-out method allows for the recycling of the pyrE2 marker to enable multiple gene deletions to be carried out in a single strain, thereby providing insights into the function of multiple proteins and how they interact in their respective cellular pathways.
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Affiliation(s)
- Ambika Dattani
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Catherine Harrison
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK.
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7
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MacNeill SA. Remote Homology Detection Identifies a Eukaryotic RPA DBD-C-like DNA Binding Domain as a Conserved Feature of Archaeal Rpa1-Like Proteins. Front Mol Biosci 2021; 8:675229. [PMID: 34355021 PMCID: PMC8329085 DOI: 10.3389/fmolb.2021.675229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/21/2021] [Indexed: 11/24/2022] Open
Abstract
The eukaryotic single-stranded DNA binding factor replication protein A (RPA) is essential for DNA replication, repair and recombination. RPA is a heterotrimer containing six related OB folds and a winged helix-turn-helix (wH) domain. The OB folds are designated DBD-A through DBD-F, with DBD-A through DBD-D being directly involved in ssDNA binding. DBD-C is located at the C-terminus of the RPA1 protein and has a distinctive structure that includes an integral C4 zinc finger, while the wH domain is found at the C-terminus of the RPA2 protein. Previously characterised archaeal RPA proteins fall into a number of classes with varying numbers of OB folds, but one widespread class includes proteins that contain a C4 or C3H zinc finger followed by a 100–120 amino acid C-terminal region reported to lack detectable sequence or structural similarity. Here, the sequences spanning this zinc finger and including the C-terminal region are shown to comprise a previously unrecognised DBD-C-like OB fold, confirming the evolutionary relatedness of this group of archaeal RPA proteins to eukaryotic RPA1. The evolutionary relationship between eukaryotic and archaeal RPA is further underscored by the presence of RPA2-like proteins comprising an OB fold and C-terminal winged helix (wH) domain in multiple species and crucially, suggests that several biochemically characterised archaeal RPA proteins previously thought to exist as monomers are likely to be RPA1-RPA2 heterodimers.
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Affiliation(s)
- Stuart A MacNeill
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, United Kingdom
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8
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Abstract
Single-stranded (ss) DNA-binding proteins are found in all three domains of life where they play vital roles in nearly all aspects of DNA metabolism by binding to and stabilizing exposed ssDNA and acting as platforms onto which DNA-processing activities can assemble. The ssDNA-binding factors SSB and RPA are extremely well conserved across bacteria and eukaryotes, respectively, and comprise one or more OB-fold ssDNA-binding domains. In the third domain of life, the archaea, multiple types of ssDNA-binding protein are found with a variety of domain architectures and subunit compositions, with OB-fold ssDNA-binding domains being a characteristic of most, but not all. This chapter summarizes current knowledge of the distribution, structure, and biological function of the archaeal ssDNA-binding factors, highlighting key features shared between clades and those that distinguish the proteins of different clades from one another. The likely cellular functions of the proteins are discussed and gaps in current knowledge identified.
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Affiliation(s)
- Najwa Taib
- Unit Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, Paris, France
- Hub Bioinformatics and Biostatistics, Department of Computational Biology, Institut Pasteur, Paris, France
| | - Simonetta Gribaldo
- Unit Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, Paris, France
| | - Stuart A MacNeill
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, UK.
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Pérez-Arnaiz P, Dattani A, Smith V, Allers T. Haloferax volcanii-a model archaeon for studying DNA replication and repair. Open Biol 2020; 10:200293. [PMID: 33259746 PMCID: PMC7776575 DOI: 10.1098/rsob.200293] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/09/2020] [Indexed: 12/16/2022] Open
Abstract
The tree of life shows the relationship between all organisms based on their common ancestry. Until 1977, it comprised two major branches: prokaryotes and eukaryotes. Work by Carl Woese and other microbiologists led to the recategorization of prokaryotes and the proposal of three primary domains: Eukarya, Bacteria and Archaea. Microbiological, genetic and biochemical techniques were then needed to study the third domain of life. Haloferax volcanii, a halophilic species belonging to the phylum Euryarchaeota, has provided many useful tools to study Archaea, including easy culturing methods, genetic manipulation and phenotypic screening. This review will focus on DNA replication and DNA repair pathways in H. volcanii, how this work has advanced our knowledge of archaeal cellular biology, and how it may deepen our understanding of bacterial and eukaryotic processes.
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Affiliation(s)
| | | | | | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
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Hou J, Han D, Zhou Y, Li Y, Cui HL. Identification and characterization of the gene encoding an extracellular protease from haloarchaeon Halococcus salifodinae. Microbiol Res 2020; 236:126468. [DOI: 10.1016/j.micres.2020.126468] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/10/2020] [Accepted: 03/15/2020] [Indexed: 10/24/2022]
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Characterization of a novel Cu-containing dissimilatory nitrite reductase from the haloarchaeon Halorussus sp. YCN54. Extremophiles 2020; 24:403-411. [DOI: 10.1007/s00792-020-01164-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 03/09/2020] [Indexed: 11/26/2022]
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Haque RU, Paradisi F, Allers T. Haloferax volcanii for biotechnology applications: challenges, current state and perspectives. Appl Microbiol Biotechnol 2019; 104:1371-1382. [PMID: 31863144 PMCID: PMC6985049 DOI: 10.1007/s00253-019-10314-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/05/2019] [Accepted: 12/10/2019] [Indexed: 01/08/2023]
Abstract
Haloferax volcanii is an obligate halophilic archaeon with its origin in the Dead Sea. Simple laboratory culture conditions and a wide range of genetic tools have made it a model organism for studying haloarchaeal cell biology. Halophilic enzymes of potential interest to biotechnology have opened up the application of this organism in biocatalysis, bioremediation, nanobiotechnology, bioplastics and the biofuel industry. Functionally active halophilic proteins can be easily expressed in a halophilic environment, and an extensive genetic toolkit with options for regulated protein overexpression has allowed the purification of biotechnologically important enzymes from different halophiles in H. volcanii. However, corrosion mediated damage caused to stainless-steel bioreactors by high salt concentrations and a tendency to form biofilms when cultured in high volume are some of the challenges of applying H. volcanii in biotechnology. The ability to employ expressed active proteins in immobilized cells within a porous biocompatible matrix offers new avenues for exploiting H. volcanii in biotechnology. This review critically evaluates the various application potentials, challenges and toolkits available for using this extreme halophilic organism in biotechnology.
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Affiliation(s)
- R U Haque
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK.,School of Chemistry, University Park, University of Nottingham, Nottingham, NG7 2RD, UK.,Warwick Integrative Synthetic Biology Centre, School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
| | - F Paradisi
- School of Chemistry, University Park, University of Nottingham, Nottingham, NG7 2RD, UK.,Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - T Allers
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK.
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Unusual Phosphoenolpyruvate (PEP) Synthetase-Like Protein Crucial to Enhancement of Polyhydroxyalkanoate Accumulation in Haloferax mediterranei Revealed by Dissection of PEP-Pyruvate Interconversion Mechanism. Appl Environ Microbiol 2019; 85:AEM.00984-19. [PMID: 31350314 DOI: 10.1128/aem.00984-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/08/2019] [Indexed: 12/21/2022] Open
Abstract
Phosphoenolpyruvate (PEP)/pyruvate interconversion is a major metabolic point in glycolysis and gluconeogenesis and is catalyzed by various sets of enzymes in different Archaea groups. In this study, we report the key enzymes that catalyze the anabolic and catabolic directions of the PEP/pyruvate interconversion in Haloferax mediterranei The in silico analysis showed the presence of a potassium-dependent pyruvate kinase (PYKHm [HFX_0773]) and two phosphoenol pyruvate synthetase (PPS) candidates (PPSHm [HFX_0782] and a PPS homolog protein named PPS-like [HFX_2676]) in this strain. Expression of the pyk Hm gene and pps Hm was induced by glycerol and pyruvate, respectively; whereas the pps-like gene was not induced at all. Similarly, genetic analysis and enzyme activities of purified proteins showed that PYKHm catalyzed the conversion from PEP to pyruvate and that PPSHm catalyzed the reverse reaction, while PPS-like protein displayed no function in PEP/pyruvate interconversion. Interestingly, knockout of the pps-like gene led to a 70.46% increase in poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) production. The transcriptome sequencing (RNA-Seq) and quantitative reverse transcription-PCR (qRT-PCR) results showed that many genes responsible for PHBV monomer supply and for PHBV synthesis were upregulated in a pps-like gene deletion strain and thereby improved PHBV accumulation. Additionally, our phylogenetic evidence suggested that PPS-like protein diverged from PPS enzyme and evolved as a distinct protein with novel function in haloarchaea. Our findings attempt to fill the gaps in central metabolism of Archaea by providing comprehensive information about key enzymes involved in the haloarchaeal PEP/pyruvate interconversion, and we also report a high-yielding PHBV strain with great future potentials.IMPORTANCE Archaea, the third domain of life, have evolved diversified metabolic pathways to cope with their extreme habitats. Phosphoenol pyruvate (PEP)/pyruvate interconversion during carbohydrate metabolism is one such important metabolic process that is highly differentiated among Archaea However, this process is still uncharacterized in the haloarchaeal group. Haloferax mediterranei is a well-studied haloarchaeon that has the ability to produce polyhydroxyalkanoates (PHAs) under unbalanced nutritional conditions. In this study, we identified the key enzymes involved in this interconversion and discussed their differences with their counterparts from other members of the Archaea and Bacteria domains. Notably, we found a novel protein, phosphoenolpyruvate synthetase-like (PPS-like), which exhibited high homology to PPS enzyme. However, PPS-like protein has evolved some distinct sequence features and functions, and strikingly the corresponding gene deletion helped to enhance poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) synthesis significantly. Overall, we have filled the gap in knowledge about PEP/pyruvate interconversion in haloarchaea and reported an efficient strategy for improving PHBV production in H. mediterranei.
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14
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Born J, Pfeifer F. Improved GFP Variants to Study Gene Expression in Haloarchaea. Front Microbiol 2019; 10:1200. [PMID: 31191505 PMCID: PMC6550001 DOI: 10.3389/fmicb.2019.01200] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/13/2019] [Indexed: 12/04/2022] Open
Abstract
The study of promoter activities in haloarchaea is carried out exclusively using enzymes as reporters. An alternative reporter is the gene encoding the Green Fluorescent Protein (GFP), a simple and fast tool for investigating promoter strengths. However, the GFP variant smRS-GFP, used to analyze protein stabilities in haloarchaea, is not suitable to quantify weak promoter activities, since the fluorescence signal is too low. We enhanced the fluorescence of smRS-GFP 3.3-fold by introducing ten amino acid substitutions, resulting in mGFP6. Using mGFP6 as reporter, we studied six haloarchaeal promoters exhibiting different promoter strengths. The strongest activity was observed with the housekeeping promoters Pfdx of the ferredoxin gene and P2 of the ribosomal 16S rRNA gene. Much lower activities were determined for the promoters of the p-vac region driving the expression of gas vesicle protein (gvp) genes in Halobacterium salinarum PHH1. The basal promoter strength dropped in the order PpA, PpO > PpF, PpD. All promoters showed a growth-dependent activity pattern. The GvpE-induced activities of PpA and PpD were high, but lower compared to the Pfdx or P2 promoter activities. The mGFP6 reporter was also used to investigate the regulatory effects of 5′-untranslated regions (5′-UTRs) of three different gvp mRNAs. A deletion of the 5′-UTR always resulted in an increased expression, implying a negative effect of the 5′-UTRs on translation. Our experiments confirmed mGFP6 as simple, fast and sensitive reporter to study gene expression in haloarchaea.
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Affiliation(s)
- Johannes Born
- Microbiology and Archaea, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Felicitas Pfeifer
- Microbiology and Archaea, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
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15
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Kelly SA, Magill DJ, Megaw J, Skvortsov T, Allers T, McGrath JW, Allen CCR, Moody TS, Gilmore BF. Characterisation of a solvent-tolerant haloarchaeal (R)-selective transaminase isolated from a Triassic period salt mine. Appl Microbiol Biotechnol 2019; 103:5727-5737. [PMID: 31123770 PMCID: PMC6597733 DOI: 10.1007/s00253-019-09806-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 03/26/2019] [Accepted: 03/29/2019] [Indexed: 12/11/2022]
Abstract
Transaminase enzymes (TAms) are becoming increasingly valuable in the chemist’s toolbox as a biocatalytic route to chiral amines. Despite high profile successes, the lack of (R)-selective TAms and robustness under harsh industrial conditions continue to prove problematic. Herein, we report the isolation of the first haloarchaeal TAm (BC61-TAm) to be characterised for the purposes of pharmaceutical biocatalysis. BC61-TAm is an (R)-selective enzyme, cloned from an extremely halophilic archaeon, isolated from a Triassic period salt mine. Produced using a Haloferax volcanii–based expression model, the resulting protein displays a classic halophilic activity profile, as well as thermotolerance (optimum 50 °C) and organic solvent tolerance. Molecular modelling predicts the putative active site residues of haloarchaeal TAms, with molecular dynamics simulations providing insights on the basis of BC61-TAm’s organic solvent tolerance. These results represent an exciting advance in the study of transaminases from extremophiles, providing a possible scaffold for future discovery of biocatalytic enzymes with robust properties.
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Affiliation(s)
| | - Damian J Magill
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Julianne Megaw
- School of Pharmacy, Queen's University Belfast, Belfast, UK
| | | | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - John W McGrath
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | | | - Thomas S Moody
- Almac, Department of Biocatalysis & Isotope Chemistry, 20 Seagoe Industrial Estate, Craigavon, UK
- Arran Chemical Company Limited, Unit 1 Monksland Industrial Estate, Athlone, Co. Roscommon, Ireland
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16
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Braun F, Thomalla L, van der Does C, Quax TEF, Allers T, Kaever V, Albers SV. Cyclic nucleotides in archaea: Cyclic di-AMP in the archaeon Haloferax volcanii and its putative role. Microbiologyopen 2019; 8:e00829. [PMID: 30884174 PMCID: PMC6741144 DOI: 10.1002/mbo3.829] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/06/2019] [Accepted: 02/06/2019] [Indexed: 12/27/2022] Open
Abstract
The role of cyclic nucleotides as second messengers for intracellular signal transduction has been well described in bacteria. One recently discovered bacterial second messenger is cyclic di‐adenylate monophosphate (c‐di‐AMP), which has been demonstrated to be essential in bacteria. Compared to bacteria, significantly less is known about second messengers in archaea. This study presents the first evidence of in vivo presence of c‐di‐AMP in an archaeon. The model organism Haloferax volcanii was demonstrated to produce c‐di‐AMP. Its genome encodes one diadenylate cyclase (DacZ) which was shown to produce c‐di‐AMP in vitro. Similar to bacteria, the dacZ gene is essential and homologous overexpression of DacZ leads to cell death, suggesting the need for tight regulation of c‐di‐AMP levels. Such tight regulation often indicates the control of important regulatory processes. A central target of c‐di‐AMP signaling in bacteria is cellular osmohomeostasis. The results presented here suggest a comparable function in H. volcanii. A strain with decreased c‐di‐AMP levels exhibited an increased cell area in hypo‐salt medium, implying impaired osmoregulation. In summary, this study expands the field of research on c‐di‐AMP and its physiological function to archaea and indicates that osmoregulation is likely to be a common function of c‐di‐AMP in bacteria and archaea.
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Affiliation(s)
- Frank Braun
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Freiburg, Germany
| | - Laura Thomalla
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Freiburg, Germany
| | - Chris van der Does
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Freiburg, Germany
| | - Tessa E F Quax
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Freiburg, Germany
| | - Thorsten Allers
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Volkhard Kaever
- Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Freiburg, Germany
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17
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Akal AL, Karan R, Hohl A, Alam I, Vogler M, Grötzinger SW, Eppinger J, Rueping M. A polyextremophilic alcohol dehydrogenase from the Atlantis II Deep Red Sea brine pool. FEBS Open Bio 2018; 9:194-205. [PMID: 30761247 PMCID: PMC6356862 DOI: 10.1002/2211-5463.12557] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 10/06/2018] [Accepted: 10/15/2018] [Indexed: 12/15/2022] Open
Abstract
Enzymes originating from hostile environments offer exceptional stability under industrial conditions and are therefore highly in demand. Using single-cell genome data, we identified the alcohol dehydrogenase (ADH) gene, adh/a1a, from the Atlantis II Deep Red Sea brine pool. ADH/A1a is highly active at elevated temperatures and high salt concentrations (optima at 70 °C and 4 m KCl) and withstands organic solvents. The polyextremophilic ADH/A1a exhibits a broad substrate scope including aliphatic and aromatic alcohols and is able to reduce cinnamyl-methyl-ketone and raspberry ketone in the reverse reaction, making it a possible candidate for the production of chiral compounds. Here, we report the affiliation of ADH/A1a to a rare enzyme family of microbial cinnamyl alcohol dehydrogenases and explain unique structural features for halo- and thermoadaptation.
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Affiliation(s)
- Anastassja L Akal
- KAUST Catalysis Center (KCC) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia.,Center for Integrated Protein Science Munich at the Department of Chemistry Technical University of Munich (TUM) Garching Germany
| | - Ram Karan
- KAUST Catalysis Center (KCC) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Adrian Hohl
- KAUST Catalysis Center (KCC) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia.,Center for Integrated Protein Science Munich at the Department of Chemistry Technical University of Munich (TUM) Garching Germany
| | - Intikhab Alam
- Computational Bioscience Research Center (CBRC) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Malvina Vogler
- KAUST Catalysis Center (KCC) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia.,Center for Integrated Protein Science Munich at the Department of Chemistry Technical University of Munich (TUM) Garching Germany
| | - Stefan W Grötzinger
- Computational Bioscience Research Center (CBRC) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia.,Institute of Biochemical Engineering Technical University of Munich (TUM) Garching Germany
| | - Jörg Eppinger
- KAUST Catalysis Center (KCC) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Magnus Rueping
- KAUST Catalysis Center (KCC) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia.,Institute of Organic Chemistry RWTH Aachen Aachen Germany
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18
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Delpech F, Collien Y, Mahou P, Beaurepaire E, Myllykallio H, Lestini R. Snapshots of archaeal DNA replication and repair in living cells using super-resolution imaging. Nucleic Acids Res 2018; 46:10757-10770. [PMID: 30212908 PMCID: PMC6237752 DOI: 10.1093/nar/gky829] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 09/03/2018] [Accepted: 09/07/2018] [Indexed: 12/17/2022] Open
Abstract
Using the haloarchaeon Haloferax volcanii as a model, we developed nascent DNA labeling and the functional GFP-labeled single-stranded binding protein RPA2 as novel tools to gain new insight into DNA replication and repair in live haloarchaeal cells. Our quantitative fluorescence microscopy data revealed that RPA2 forms distinct replication structures that dynamically responded to replication stress and DNA damaging agents. The number of the RPA2 foci per cell followed a probabilistic Poisson distribution, implying hitherto unnoticed stochastic cell-to-cell variation in haloarchaeal DNA replication and repair processes. The size range of haloarchaeal replication structures is very similar to those observed earlier in eukaryotic cells. The improved lateral resolution of 3D-SIM fluorescence microscopy allowed proposing that inhibition of DNA synthesis results in localized replication foci clustering and facilitated observation of RPA2 complexes brought about by chemical agents creating DNA double-strand breaks. Altogether our in vivo observations are compatible with earlier in vitro studies on archaeal single-stranded DNA binding proteins. Our work thus underlines the great potential of live cell imaging for unraveling the dynamic nature of transient molecular interactions that underpin fundamental molecular processes in the Third domain of life.
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Affiliation(s)
- Floriane Delpech
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645 – INSERM U1182, 91128 Palaiseau Cedex, France
| | - Yoann Collien
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645 – INSERM U1182, 91128 Palaiseau Cedex, France
| | - Pierre Mahou
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645 – INSERM U1182, 91128 Palaiseau Cedex, France
| | - Emmanuel Beaurepaire
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645 – INSERM U1182, 91128 Palaiseau Cedex, France
| | - Hannu Myllykallio
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645 – INSERM U1182, 91128 Palaiseau Cedex, France
| | - Roxane Lestini
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645 – INSERM U1182, 91128 Palaiseau Cedex, France
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19
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Transcriptional Landscape and Regulatory Roles of Small Noncoding RNAs in the Oxidative Stress Response of the Haloarchaeon Haloferax volcanii. J Bacteriol 2018; 200:JB.00779-17. [PMID: 29463600 PMCID: PMC5892119 DOI: 10.1128/jb.00779-17] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 02/02/2018] [Indexed: 01/08/2023] Open
Abstract
Haloarchaea in their natural environment are exposed to hypersalinity, intense solar radiation, and desiccation, all of which generate high levels of oxidative stress. Previous work has shown that haloarchaea are an order of magnitude more resistant to oxidative stress than most mesophilic organisms. Despite this resistance, the pathways haloarchaea use to respond to oxidative stress damage are similar to those of nonresistant organisms, suggesting that regulatory processes might be key to their robustness. Recently, small regulatory noncoding RNAs (sRNAs) were discovered in Archaea under a variety of environmental conditions. We report here the transcriptional landscape and functional roles of sRNAs in the regulation of the oxidative stress response of the model haloarchaeon Haloferax volcanii. Thousands of sRNAs, both intergenic and antisense, were discovered using strand-specific sRNA sequencing (sRNA-seq), comprising 25 to 30% of the total transcriptome under no-challenge and oxidative stress conditions, respectively. We identified hundreds of differentially expressed sRNAs in response to hydrogen peroxide-induced oxidative stress in H. volcanii. The targets of a group of antisense sRNAs decreased in expression when these sRNAs were upregulated, suggesting that sRNAs are potentially playing a negative regulatory role on mRNA targets at the transcript level. Target enrichment of these antisense sRNAs included mRNAs involved in transposon mobility, chemotaxis signaling, peptidase activity, and transcription factors. IMPORTANCE While a substantial body of experimental work has been done to uncover the functions of small regulatory noncoding RNAs (sRNAs) in gene regulation in Bacteria and Eukarya, the functional roles of sRNAs in Archaea are still poorly understood. This study is the first to establish the regulatory effects of sRNAs on mRNAs during the oxidative stress response in the haloarchaeon Haloferax volcanii. Our work demonstrates that common principles for the response to a major cellular stress exist across the 3 domains of life while uncovering pathways that might be specific to the Archaea. This work also underscores the relevance of sRNAs in adaptation to extreme environmental conditions.
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20
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Grötzinger SW, Karan R, Strillinger E, Bader S, Frank A, Al Rowaihi IS, Akal A, Wackerow W, Archer JA, Rueping M, Weuster-Botz D, Groll M, Eppinger J, Arold ST. Identification and Experimental Characterization of an Extremophilic Brine Pool Alcohol Dehydrogenase from Single Amplified Genomes. ACS Chem Biol 2018; 13:161-170. [PMID: 29188989 DOI: 10.1021/acschembio.7b00792] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Because only 0.01% of prokaryotic genospecies can be cultured and in situ observations are often impracticable, culture-independent methods are required to understand microbial life and harness potential applications of microbes. Here, we report a methodology for the production of proteins with desired functions based on single amplified genomes (SAGs) from unculturable species. We use this method to resurrect an alcohol dehydrogenase (ADH/D1) from an uncharacterized halo-thermophilic archaeon collected from a brine pool at the bottom of the Red Sea. Our crystal structure of 5,6-dihydroxy NADPH-bound ADH/D1 combined with biochemical analyses reveal the molecular features of its halo-thermophily, its unique habitat adaptations, and its possible reaction mechanism for atypical oxygen activation. Our strategy offers a general guide for using SAGs as a source for scientific and industrial investigations of "microbial dark matter."
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Affiliation(s)
- Stefan W. Grötzinger
- King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering
Division, Computational Bioscience Research Center, Thuwal, Kingdom of Saudi Arabia
- Technical University of Munich, Department of Mechanical
Engineering, Institute of Biochemical Engineering, Garching, Germany
| | - Ram Karan
- King Abdullah University of Science and Technology, Physical Science and Engineering Division, KAUST Catalysis Center, Thuwal, Kingdom of Saudi Arabia
| | - Eva Strillinger
- Technical University of Munich, Department of Mechanical
Engineering, Institute of Biochemical Engineering, Garching, Germany
- King Abdullah University of Science and Technology, Physical Science and Engineering Division, KAUST Catalysis Center, Thuwal, Kingdom of Saudi Arabia
| | - Stefan Bader
- King Abdullah University of Science and Technology, Physical Science and Engineering Division, KAUST Catalysis Center, Thuwal, Kingdom of Saudi Arabia
| | - Annika Frank
- Technical University of Munich, Center for Integrated
Protein Science Munich in the Department Chemistry, Garching, Germany
| | - Israa S. Al Rowaihi
- King Abdullah University of Science and Technology, Physical Science and Engineering Division, KAUST Catalysis Center, Thuwal, Kingdom of Saudi Arabia
| | - Anastassja Akal
- King Abdullah University of Science and Technology, Physical Science and Engineering Division, KAUST Catalysis Center, Thuwal, Kingdom of Saudi Arabia
- Technical University of Munich, Center for Integrated
Protein Science Munich in the Department Chemistry, Garching, Germany
| | - Wiebke Wackerow
- King Abdullah University of Science and Technology, Physical Science and Engineering Division, KAUST Catalysis Center, Thuwal, Kingdom of Saudi Arabia
| | - John A. Archer
- King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering
Division, Computational Bioscience Research Center, Thuwal, Kingdom of Saudi Arabia
| | - Magnus Rueping
- King Abdullah University of Science and Technology, Physical Science and Engineering Division, KAUST Catalysis Center, Thuwal, Kingdom of Saudi Arabia
| | - Dirk Weuster-Botz
- Technical University of Munich, Department of Mechanical
Engineering, Institute of Biochemical Engineering, Garching, Germany
| | - Michael Groll
- Technical University of Munich, Center for Integrated
Protein Science Munich in the Department Chemistry, Garching, Germany
| | - Jörg Eppinger
- King Abdullah University of Science and Technology, Physical Science and Engineering Division, KAUST Catalysis Center, Thuwal, Kingdom of Saudi Arabia
| | - Stefan T. Arold
- King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering
Division, Computational Bioscience Research Center, Thuwal, Kingdom of Saudi Arabia
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21
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Abstract
The study of allele-specific expression (ASE) in interspecific hybrids has played a central role in our understanding of a wide range of phenomena, including genomic imprinting, X-chromosome inactivation, and cis-regulatory evolution. However across the hundreds of studies of hybrid ASE, all have been restricted to sexually reproducing eukaryotes, leaving a major gap in our understanding of the genomic patterns of cis-regulatory evolution in prokaryotes. Here we introduce a method to generate stable hybrids between two species of halophilic archaea, and measure genome-wide ASE in these hybrids with RNA-seq. We found that over half of all genes have significant ASE, and that genes encoding kinases show evidence of lineage-specific selection on their cis-regulation. This pattern of polygenic selection suggested species-specific adaptation to low phosphate conditions, which we confirmed with growth experiments. Altogether, our work extends the study of ASE to archaea, and suggests that cis-regulation can evolve under polygenic lineage-specific selection in prokaryotes.
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22
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Wardell K, Haldenby S, Jones N, Liddell S, Ngo GHP, Allers T. RadB acts in homologous recombination in the archaeon Haloferax volcanii, consistent with a role as recombination mediator. DNA Repair (Amst) 2017; 55:7-16. [PMID: 28501701 PMCID: PMC5480776 DOI: 10.1016/j.dnarep.2017.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 03/23/2017] [Accepted: 04/25/2017] [Indexed: 11/20/2022]
Abstract
Homologous recombination plays a central role in the repair of double-strand DNA breaks, the restart of stalled replication forks and the generation of genetic diversity. Regulation of recombination is essential since defects can lead to genome instability and chromosomal rearrangements. Strand exchange is a key step of recombination - it is catalysed by RecA in bacteria, Rad51/Dmc1 in eukaryotes and RadA in archaea. RadB, a paralogue of RadA, is present in many archaeal species. RadB has previously been proposed to function as a recombination mediator, assisting in RadA-mediated strand exchange. In this study, we use the archaeon Haloferax volcanii to provide evidence to support this hypothesis. We show that RadB is required for efficient recombination and survival following treatment with DNA-damaging agents, and we identify two point mutations in radA that suppress the ΔradB phenotype. Analysis of these point mutations leads us to propose that the role of RadB is to act as a recombination mediator, which it does by inducing a conformational change in RadA and thereby promoting its polymerisation on DNA.
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Affiliation(s)
- Kayleigh Wardell
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Sam Haldenby
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Nathan Jones
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Susan Liddell
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Greg H P Ngo
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK.
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23
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Enoyl-CoA hydratase mediates polyhydroxyalkanoate mobilization in Haloferax mediterranei. Sci Rep 2016; 6:24015. [PMID: 27052994 PMCID: PMC4823750 DOI: 10.1038/srep24015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 03/17/2016] [Indexed: 02/08/2023] Open
Abstract
Although polyhydroxyalkanoate (PHA) accumulation and mobilization are one of the most general mechanisms for haloarchaea to adapt to the hypersaline environments with changeable carbon sources, the PHA mobilization pathways are still not clear for any haloarchaea. In this study, the functions of five putative (R)-specific enoyl-CoA hydratases (R-ECHs) in Haloferax mediterranei, named PhaJ1 to PhaJ5, respectively, were thoroughly investigated. Through gene deletion and complementation, we demonstrated that only certain of these ECHs had a slight contribution to poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) biosynthesis. But significantly, PhaJ1, the only R-ECH that is associated with PHA granules, was shown to be involved in PHA mobilization in this haloarchaeon. PhaJ1 catalyzes the dehydration of (R)-3-hydroxyacyl-CoA, the common product of PHA degradation, to enoyl-CoA, the intermediate of the β-oxidation cycle, thus could link PHA mobilization to β-oxidation pathway in H. mediterranei. This linkage was further indicated from the up-regulation of the key genes of β-oxidation under the PHA mobilization condition, as well as the obvious inhibition of PHA degradation upon inhibition of the β-oxidation pathway. Interestingly, 96% of phaJ-containing haloarchaeal species possess both phaC (encoding PHA synthase) and the full set genes of β-oxidation, implying that the mobilization of carbon storage in PHA through the β-oxidation cycle would be general in haloarchaea.
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24
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Giroux X, MacNeill SA. A novel archaeal DNA repair factor that acts with the UvrABC system to repair mitomycin C-induced DNA damage in a PCNA-dependent manner. Mol Microbiol 2015; 99:1-14. [PMID: 26337406 DOI: 10.1111/mmi.13210] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2015] [Indexed: 01/11/2023]
Abstract
The sliding clamp proliferating cell nuclear antigen (PCNA) plays a vital role in a number of DNA repair pathways in eukaryotes and archaea by acting as a stable platform onto which other essential protein factors assemble. Many of these proteins interact with PCNA via a short peptide sequence known as a PIP (PCNA interacting protein) motif. Here we describe the identification and functional analysis of a novel PCNA interacting protein NreA that is conserved in the archaea and that has a PIP motif at its C-terminus. Using the genetically tractable euryarchaeon Haloferax volcanii as a model system, we show that the NreA protein is not required for cell viability but that loss of NreA (or replacement of the wild-type protein with a truncated version lacking the C-terminal PIP motif) results in an increased sensitivity to the DNA damaging agent mitomycin C (MMC) that correlates with delayed repair of MMC-induced chromosomal DNA damage monitored by pulsed-field gel electrophoresis. Genetic epistasis analysis in Hfx. volcanii suggests that NreA works together with the UvrABC proteins in repairing DNA damage resulting from exposure to MMC. The wide distribution of NreA family members implies an important role for the protein in DNA damage repair in all archaeal lineages.
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Affiliation(s)
- Xavier Giroux
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Stuart A MacNeill
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
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25
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Production of halophilic proteins using Haloferax volcanii H1895 in a stirred-tank bioreactor. Appl Microbiol Biotechnol 2015; 100:1183-1195. [PMID: 26428236 DOI: 10.1007/s00253-015-7007-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/02/2015] [Accepted: 09/12/2015] [Indexed: 10/23/2022]
Abstract
The success of biotechnological processes is based on the availability of efficient and highly specific biocatalysts, which can satisfy industrial demands. Extreme and remote environments like the deep brine pools of the Red Sea represent highly interesting habitats for the discovery of novel halophilic and thermophilic enzymes. Haloferax volcanii constitutes a suitable expression system for halophilic enzymes obtained from such brine pools. We developed a batch process for the cultivation of H. volcanii H1895 in controlled stirred-tank bioreactors utilising knockouts of components of the flagella assembly system. The standard medium Hv-YPC was supplemented to reach a higher cell density. Without protein expression, cell dry weight reaches 10 g L(-1). Two halophilic alcohol dehydrogenases were expressed under the control of the tryptophanase promoter p.tna with 16.8 and 3.2 mg gCDW (-1), respectively, at a maximum cell dry weight of 6.5 g L(-1). Protein expression was induced by the addition of L-tryptophan. Investigation of various expression strategies leads to an optimised two-step induction protocol introducing 6 mM L-tryptophan at an OD650 of 0.4 followed by incubation for 16 h and a second induction step with 3 mM L-tryptophan followed by a final incubation time of 4 h. Compared with the uncontrolled shaker-flask cultivations used until date, dry cell mass concentrations were improved by a factor of more than 5 and cell-specific enzyme activities showed an up to 28-fold increased yield of the heterologous proteins.
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26
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Giroux X, MacNeill SA. Inhibiting NAD+-dependent DNA ligase activity with 2-(cyclopentyloxy)-5'-deoxyadenosine (CPOdA) offers a new tool for DNA replication and repair studies in the model archaeon Haloferax volcanii. FEMS Microbiol Lett 2015; 362:fnv181. [PMID: 26420852 DOI: 10.1093/femsle/fnv181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2015] [Indexed: 01/16/2023] Open
Abstract
DNA ligases play an essential role in many aspects of DNA metabolism in all three domains of life. The haloarchaeal organism Haloferax volcanii encodes both ATP- and NAD(+)-dependent DNA ligase enzymes designated LigA and LigN, respectively. Neither LigA nor LigN alone is required for cell viability but they share an essential function, most likely the ligation of Okazaki fragments during chromosome replication. Here we show that 2-(cyclopentyloxy)-5'-deoxyadenosine (referred to as CPOdA), originally developed as a inhibitor of bacterial NAD(+)-dependent DNA ligases, is a potent inhibitor of the growth of Hfx. volcanii cells expressing LigN alone, causing chromosome fragmentation and cell death, while cells expressing LigA are unaffected. Growth inhibition occurs at significantly lower CPOdA concentrations (MIC ≤ 50 ng ml(-1)) than those required for inhibition of bacterial growth (≥2 μg ml(-1)). CPOdA has the potential to become a vital tool in DNA replication and repair studies in this important model organism.
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Affiliation(s)
- Xavier Giroux
- School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Stuart A MacNeill
- School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
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Abstract
Bacterial strains carrying nonsense suppressor tRNA genes played a crucial role in early work on bacterial and bacterial viral genetics. In eukaryotes as well, suppressor tRNAs have played important roles in the genetic analysis of yeast and worms. Surprisingly, little is known about genetic suppression in archaea, and there has been no characterization of suppressor tRNAs or identification of nonsense mutations in any of the archaeal genes. Here, we show, using the β-gal gene as a reporter, that amber, ochre, and opal suppressors derived from the serine and tyrosine tRNAs of the archaeon Haloferax volcanii are active in suppression of their corresponding stop codons. Using a promoter for tRNA expression regulated by tryptophan, we also show inducible and regulatable suppression of all three stop codons in H. volcanii. Additionally, transformation of a ΔpyrE2 H. volcanii strain with plasmids carrying the genes for a pyrE2 amber mutant and the serine amber suppressor tRNA yielded transformants that grow on agar plates lacking uracil. Thus, an auxotrophic amber mutation in the pyrE2 gene can be complemented by expression of the amber suppressor tRNA. These results pave the way for generating archaeal strains carrying inducible suppressor tRNA genes on the chromosome and their use in archaeal and archaeviral genetics. We also provide possible explanations for why suppressor tRNAs have not been identified in archaea.
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A patatin-like protein associated with the polyhydroxyalkanoate (PHA) granules of Haloferax mediterranei acts as an efficient depolymerase in the degradation of native PHA. Appl Environ Microbiol 2015; 81:3029-38. [PMID: 25710370 DOI: 10.1128/aem.04269-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 02/15/2015] [Indexed: 01/14/2023] Open
Abstract
The key enzymes and pathways involved in polyhydroxyalkanoate (PHA) biosynthesis in haloarchaea have been identified in recent years, but the haloarchaeal enzymes for PHA degradation remain unknown. In this study, a patatin-like PHA depolymerase, PhaZh1, was determined to be located on the PHA granules in the haloarchaeon Haloferax mediterranei. PhaZh1 hydrolyzed the native PHA (nPHA) [including native polyhydroxybutyrate (nPHB) and native poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (nPHBV) in this study] granules in vitro with 3-hydroxybutyrate (3HB) monomer as the primary product. The site-directed mutagenesis of PhaZh1 indicated that Gly16, Ser47 (in a classical lipase box, G-X-S47-X-G), and Asp195 of this depolymerase were essential for its activity in nPHA granule hydrolysis. Notably, phaZh1 and bdhA (encoding putative 3HB dehydrogenase) form a gene cluster (HFX_6463 to _6464) in H. mediterranei. The 3HB monomer generated from nPHA degradation by PhaZh1 could be further converted into acetoacetate by BdhA, indicating that PhaZh1-BdhA may constitute the first part of a PHA degradation pathway in vivo. Interestingly, although PhaZh1 showed efficient activity and was most likely the key enzyme in nPHA granule hydrolysis in vitro, the knockout of phaZh1 had no significant effect on the intracellular PHA mobilization, implying the existence of an alternative PHA mobilization pathway(s) that functions effectively within the cells of H. mediterranei. Therefore, identification of this patatin-like depolymerase of haloarchaea may provide a new strategy for producing the high-value-added chiral compound (R)-3HB and may also shed light on the PHA mobilization in haloarchaea.
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Molecular Genetic Methods to Study DNA Replication Protein Function in Haloferax volcanii, A Model Archaeal Organism. Methods Mol Biol 2015; 1300:187-218. [PMID: 25916714 DOI: 10.1007/978-1-4939-2596-4_13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Successful high-fidelity chromosomal DNA replication is fundamental to all forms of cellular life and requires the complex interplay of a variety of essential and nonessential protein factors in a spatially and temporally coordinated manner. Much of what is known about the enzymes and mechanisms of chromosome replication has come from analysis of simple microbial model systems, such as yeast and archaea. Archaea possess a highly simplified eukaryotic-like replication apparatus, making them an excellent model for gaining novel insights into conserved aspects of protein function at the heart of the replisome. Amongst the thermophilic archaea, a number of species have proved useful for biochemical analysis of protein function, but few of these organisms are suited to genetic analysis. One archaeal organism that is genetically tractable is the mesophilic euryarchaeon Haloferax volcanii, a halophile that grows aerobically in high salt medium at an optimum temperature of 40-45 °C and with a doubling time of 2-3 h. The Hfx. volcanii genome has been sequenced and a range of methods have been developed to allow reverse genetic analysis of protein function in vivo, including techniques for gene replacement and gene deletion, transcriptional regulation, point mutation and gene tagging. Here we briefly summarize current knowledge of the chromosomal DNA replication machinery in the haloarchaea before describing in detail the molecular methods available to probe protein structure and function within the Hfx. volcanii replication apparatus.
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Raymann K, Forterre P, Brochier-Armanet C, Gribaldo S. Global phylogenomic analysis disentangles the complex evolutionary history of DNA replication in archaea. Genome Biol Evol 2014; 6:192-212. [PMID: 24398374 PMCID: PMC3914693 DOI: 10.1093/gbe/evu004] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The archaeal machinery responsible for DNA replication is largely homologous to that of eukaryotes and is clearly distinct from its bacterial counterpart. Moreover, it shows high diversity in the various archaeal lineages, including different sets of components, heterogeneous taxonomic distribution, and a large number of additional copies that are sometimes highly divergent. This has made the evolutionary history of this cellular system particularly challenging to dissect. Here, we have carried out an exhaustive identification of homologs of all major replication components in over 140 complete archaeal genomes. Phylogenomic analysis allowed assigning them to either a conserved and probably essential core of replication components that were mainly vertically inherited, or to a variable and highly divergent shell of extra copies that have likely arisen from integrative elements. This suggests that replication proteins are frequently exchanged between extrachromosomal elements and cellular genomes. Our study allowed clarifying the history that shaped this key cellular process (ancestral components, horizontal gene transfers, and gene losses), providing important evolutionary and functional information. Finally, our precise identification of core components permitted to show that the phylogenetic signal carried by DNA replication is highly consistent with that harbored by two other key informational machineries (translation and transcription), strengthening the existence of a robust organismal tree for the Archaea.
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Affiliation(s)
- Kasie Raymann
- Département de Microbiologie, Institut Pasteur, Unité Biologie Moléculaire du Gene chez les Extrêmophiles, Paris, France
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31
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Kristensen TP, Maria Cherian R, Gray FC, MacNeill SA. The haloarchaeal MCM proteins: bioinformatic analysis and targeted mutagenesis of the β7-β8 and β9-β10 hairpin loops and conserved zinc binding domain cysteines. Front Microbiol 2014; 5:123. [PMID: 24723920 PMCID: PMC3972481 DOI: 10.3389/fmicb.2014.00123] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 03/10/2014] [Indexed: 11/13/2022] Open
Abstract
The hexameric MCM complex is the catalytic core of the replicative helicase in eukaryotic and archaeal cells. Here we describe the first in vivo analysis of archaeal MCM protein structure and function relationships using the genetically tractable haloarchaeon Haloferax volcanii as a model system. Hfx. volcanii encodes a single MCM protein that is part of the previously identified core group of haloarchaeal MCM proteins. Three structural features of the N-terminal domain of the Hfx. volcanii MCM protein were targeted for mutagenesis: the β7-β8 and β9-β10 β-hairpin loops and putative zinc binding domain. Five strains carrying single point mutations in the β7-β8 β-hairpin loop were constructed, none of which displayed impaired cell growth under normal conditions or when treated with the DNA damaging agent mitomycin C. However, short sequence deletions within the β7-β8 β-hairpin were not tolerated and neither was replacement of the highly conserved residue glutamate 187 with alanine. Six strains carrying paired alanine substitutions within the β9-β10 β-hairpin loop were constructed, leading to the conclusion that no individual amino acid within that hairpin loop is absolutely required for MCM function, although one of the mutant strains displays greatly enhanced sensitivity to mitomycin C. Deletions of two or four amino acids from the β9-β10 β-hairpin were tolerated but mutants carrying larger deletions were inviable. Similarly, it was not possible to construct mutants in which any of the conserved zinc binding cysteines was replaced with alanine, underlining the likely importance of zinc binding for MCM function. The results of these studies demonstrate the feasibility of using Hfx. volcanii as a model system for reverse genetic analysis of archaeal MCM protein function and provide important confirmation of the in vivo importance of conserved structural features identified by previous bioinformatic, biochemical and structural studies.
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Affiliation(s)
- Tatjana P Kristensen
- Department of Biology, University of Copenhagen, Københavns Biocenter Copenhagen N, Denmark
| | - Reeja Maria Cherian
- Department of Biology, University of Copenhagen, Københavns Biocenter Copenhagen N, Denmark
| | - Fiona C Gray
- Department of Biology, University of Copenhagen, Københavns Biocenter Copenhagen N, Denmark
| | - Stuart A MacNeill
- Department of Biology, University of Copenhagen, Københavns Biocenter Copenhagen N, Denmark ; School of Biology, University of St. Andrews North Haugh, St. Andrews, Fife, UK
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Adaptation of the Halobacterium salinarum ssp. NRC-1 gene deletion system for modification of chromosomal loci. J Microbiol Methods 2014; 99:22-6. [PMID: 24491836 DOI: 10.1016/j.mimet.2014.01.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 01/22/2014] [Accepted: 01/23/2014] [Indexed: 11/23/2022]
Abstract
The model archaeon Halobacterium salinarum ssp. NRC-1 is an excellent system for the study of archaeal molecular biology. Unlike many other archaea, its only special growth requirement is high levels of sodium chloride and other salts; it requires neither high-temperature incubation nor anaerobic environments. Additionally, there are a number of well-developed post-genomic tools available, including whole-genome microarrays and a ura3-based gene deletion system. While some tools are available for protein expression, a system for measurement and purification of protein expressed from native promoters is lacking. We have adapted the established H. salinarum gene deletion system for this purpose, and have used this to place 8×-histidine tags on either the carboxyl or amino terminus of the protein encoded by the chromosomal rfa3 gene. To demonstrate the utility of this approach, we used Western blot analysis to determine levels of the Rfa3 protein under different conditions. This system provides another powerful molecular tool for studies of native protein expression and for simple protein purification in H. salinarum.
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Brendel J, Stoll B, Lange SJ, Sharma K, Lenz C, Stachler AE, Maier LK, Richter H, Nickel L, Schmitz RA, Randau L, Allers T, Urlaub H, Backofen R, Marchfelder A. A complex of Cas proteins 5, 6, and 7 is required for the biogenesis and stability of clustered regularly interspaced short palindromic repeats (crispr)-derived rnas (crrnas) in Haloferax volcanii. J Biol Chem 2014; 289:7164-7177. [PMID: 24459147 PMCID: PMC3945376 DOI: 10.1074/jbc.m113.508184] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR-Cas) system is a prokaryotic defense mechanism against foreign genetic elements. A plethora of CRISPR-Cas versions exist, with more than 40 different Cas protein families and several different molecular approaches to fight the invading DNA. One of the key players in the system is the CRISPR-derived RNA (crRNA), which directs the invader-degrading Cas protein complex to the invader. The CRISPR-Cas types I and III use the Cas6 protein to generate mature crRNAs. Here, we show that the Cas6 protein is necessary for crRNA production but that additional Cas proteins that form a CRISPR-associated complex for antiviral defense (Cascade)-like complex are needed for crRNA stability in the CRISPR-Cas type I-B system in Haloferax volcanii in vivo. Deletion of the cas6 gene results in the loss of mature crRNAs and interference. However, cells that have the complete cas gene cluster (cas1–8b) removed and are transformed with the cas6 gene are not able to produce and stably maintain mature crRNAs. crRNA production and stability is rescued only if cas5, -6, and -7 are present. Mutational analysis of the cas6 gene reveals three amino acids (His-41, Gly-256, and Gly-258) that are essential for pre-crRNA cleavage, whereas the mutation of two amino acids (Ser-115 and Ser-224) leads to an increase of crRNA amounts. This is the first systematic in vivo analysis of Cas6 protein variants. In addition, we show that the H. volcanii I-B system contains a Cascade-like complex with a Cas7, Cas5, and Cas6 core that protects the crRNA.
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Affiliation(s)
- Jutta Brendel
- Department of Biology II, Ulm University, 89069 Ulm, Germany
| | - Britta Stoll
- Department of Biology II, Ulm University, 89069 Ulm, Germany
| | - Sita J Lange
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany
| | - Kundan Sharma
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christof Lenz
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Bioanalytics, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany
| | | | | | - Hagen Richter
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Lisa Nickel
- Institute for General Microbiology, Christian-Albrechts-Universität Kiel, 24118 Kiel, Germany
| | - Ruth A Schmitz
- Institute for General Microbiology, Christian-Albrechts-Universität Kiel, 24118 Kiel, Germany
| | - Lennart Randau
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Henning Urlaub
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Bioanalytics, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany; Centre for Biological Signalling Studies (BIOSS), Cluster of Excellence, University of Freiburg, 79110 Freiburg, Germany
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Bioengineering radioresistance by overproduction of RPA, a mammalian-type single-stranded DNA-binding protein, in a halophilic archaeon. Appl Microbiol Biotechnol 2013; 98:1737-47. [PMID: 24292079 PMCID: PMC4096848 DOI: 10.1007/s00253-013-5368-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 10/21/2013] [Accepted: 10/25/2013] [Indexed: 10/26/2022]
Abstract
Halobacterium sp. NRC-1 is a wild-type extremophilic microbe that is naturally tolerant to high levels of ionizing radiation. Mutants of strain NRC-1 with even higher levels of resistance to ionizing radiation, named RAD, were previously isolated after selecting survival to extremely high doses of ionizing radiation. These RAD mutants displayed higher transcription levels for the rfa3 operon, coding two subunits of the RPA-like putative single-stranded binding protein, rfa3 and rfa8, and a third downstream gene, ral. In order to bioengineer cells with increased tolerance to ionizing radiation and further explore the genetic basis of the RAD phenotype, we placed the rfa3 operon under control of the gvpA promoter in a Halobacterium expression plasmid, pDRK1. When pDRK1 was introduced into the wild-type NRC-1 strain, overproduction of the Rfa3 and Rfa8 proteins was observed by Western blotting and proteomic analysis. The Halobacterium strains expressing Rfa3 and Rfa8 also displayed improved survival after exposure to ionizing radiation, similar to the RAD mutants, when compared to wild-type strain NRC-1. The Rfa3 and Rfa8 proteins co-purified by affinity chromatography on single-stranded DNA cellulose columns, confirming the ability of the proteins to bind to single-stranded DNA as well as their relative abundance in the wild-type, RAD mutants, and rfa3 operon overexpression strains. These results clearly establish that overexpression of haloarchaeal RPA promotes ionizing radiation resistance in Halobacterium sp. NRC-1 and that the Rfa3 and Rfa8 subunits bind single-stranded DNA. Bioengineering cells with increased levels of ionizing radiation resistance may have potential value in medical and environmental applications.
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Lockhart JS, DeVeaux LC. The essential role of the Deinococcus radiodurans ssb gene in cell survival and radiation tolerance. PLoS One 2013; 8:e71651. [PMID: 23951213 PMCID: PMC3739723 DOI: 10.1371/journal.pone.0071651] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/02/2013] [Indexed: 11/18/2022] Open
Abstract
Recent evidence has implicated single-stranded DNA-binding protein (SSB) expression level as an important factor in microbial radiation resistance. The genome of the extremely radiation resistant bacterium Deinococcus radiodurans contains genes for two SSB homologs: the homodimeric, canonical Ssb, encoded by the gene ssb, and a novel pentameric protein encoded by the gene ddrB. ddrB is highly induced upon exposure to radiation, and deletions result in decreased radiation-resistance, suggesting an integral role of the protein in the extreme resistance exhibited by this organism. Although expression of ssb is also induced after irradiation, Ssb is thought to be involved primarily in replication. In this study, we demonstrate that Ssb in D. radiodurans is essential for cell survival. The lethality of an ssb deletion cannot be complemented by providing ddrB in trans. In addition, the radiation-sensitive phenotype conferred by a ddrB deletion is not alleviated by providing ssb in trans. By altering expression of the ssb gene, we also show that lower levels of transcription are required for optimal growth than are necessary for high radiation resistance. When expression is reduced to that of E. coli, ionizing radiation resistance is similarly reduced. UV resistance is also decreased under low ssb transcript levels where growth is unimpaired. These results indicate that the expression of ssb is a key component of both normal cellular metabolism as well as pathways responsible for the high radiation tolerance of D. radiodurans.
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Affiliation(s)
- J. Scott Lockhart
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, United States of America
| | - Linda C. DeVeaux
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, United States of America
- * E-mail:
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36
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Effects of intracellular Mn on the radiation resistance of the halophilic archaeon Halobacterium salinarum. Extremophiles 2013; 17:485-97. [DOI: 10.1007/s00792-013-0533-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 03/07/2013] [Indexed: 02/01/2023]
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37
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Radiation Resistance in Extremophiles: Fending Off Multiple Attacks. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2013. [DOI: 10.1007/978-94-007-6488-0_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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38
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Robb FT, Lowe TM, Kelman Z. The modern "3G" age of archaeal molecular biology. Front Microbiol 2012; 3:430. [PMID: 23267357 PMCID: PMC3527003 DOI: 10.3389/fmicb.2012.00430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 12/06/2012] [Indexed: 11/13/2022] Open
Affiliation(s)
- Frank T Robb
- Institute of Marine and Environmental Technology Baltimore, MD, USA ; University of Maryland School of Medicine Baltimore, MD, USA
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