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Phung DK, Etienne C, Batista M, Langendijk-Genevaux P, Moalic Y, Laurent S, Liuu S, Morales V, Jebbar M, Fichant G, Bouvier M, Flament D, Clouet-d’Orval B. RNA processing machineries in Archaea: the 5'-3' exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3'-5' exoribonucleolytic RNA exosome machinery. Nucleic Acids Res 2020; 48:3832-3847. [PMID: 32030412 PMCID: PMC7144898 DOI: 10.1093/nar/gkaa052] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/14/2020] [Accepted: 01/23/2020] [Indexed: 01/22/2023] Open
Abstract
A network of RNA helicases, endoribonucleases and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focussed on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5'-3' exoribonuclease of the β-CASP family conserved in Euryarchaeota, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, at the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses, strengthened by comprehensive phylogenomic studies demonstrated that aRNase J interplay with ASH-Ski2 and a cap exosome subunit. Finally, Thermococcus barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome that is emphasised in absence of ASH-Ski2. Whilst aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism.
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Affiliation(s)
- Duy Khanh Phung
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Clarisse Etienne
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Manon Batista
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Petra Langendijk-Genevaux
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Yann Moalic
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Sébastien Laurent
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Sophie Liuu
- Micalis Institute, PAPPSO, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Violette Morales
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Mohamed Jebbar
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Gwennaele Fichant
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Marie Bouvier
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Didier Flament
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Béatrice Clouet-d’Orval
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
- To whom correspondence should be addressed. Tel: +33 561 335 875; Fax: +33 561 335 886;
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2
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Killelea T, Palud A, Akcha F, Lemor M, L'haridon S, Godfroy A, Henneke G. The interplay at the replisome mitigates the impact of oxidative damage on the genetic integrity of hyperthermophilic Archaea. eLife 2019; 8:45320. [PMID: 31184586 PMCID: PMC6559790 DOI: 10.7554/elife.45320] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/28/2019] [Indexed: 12/12/2022] Open
Abstract
8-oxodeoxyguanosine (8-oxodG), a major oxidised base modification, has been investigated to study its impact on DNA replication in hyperthermophilic Archaea. Here we show that 8-oxodG is formed in the genome of growing cells, with elevated levels following exposure to oxidative stress. Functional characterisation of cell-free extracts and the DNA polymerisation enzymes, PolB, PolD, and the p41/p46 complex, alone or in the presence of accessory factors (PCNA and RPA) indicates that translesion synthesis occurs under replicative conditions. One of the major polymerisation effects was stalling, but each of the individual proteins could insert and extend past 8-oxodG with differing efficiencies. The introduction of RPA and PCNA influenced PolB and PolD in similar ways, yet provided a cumulative enhancement to the polymerisation performance of p41/p46. Overall, 8-oxodG translesion synthesis was seen to be potentially mutagenic leading to errors that are reminiscent of dA:8-oxodG base pairing.
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Affiliation(s)
- Tom Killelea
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Adeline Palud
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Farida Akcha
- Laboratoire d'Ecotoxicologie, Ifremer, Nantes, France
| | - Mélanie Lemor
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Stephane L'haridon
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Anne Godfroy
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Ghislaine Henneke
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
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3
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Lemor M, Kong Z, Henry E, Brizard R, Laurent S, Bossé A, Henneke G. Differential Activities of DNA Polymerases in Processing Ribonucleotides during DNA Synthesis in Archaea. J Mol Biol 2018; 430:4908-4924. [PMID: 30342933 DOI: 10.1016/j.jmb.2018.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/09/2018] [Accepted: 10/12/2018] [Indexed: 12/11/2022]
Abstract
Consistent with the fact that ribonucleotides (rNTPs) are in excess over deoxyribonucleotides (dNTPs) in vivo, recent findings indicate that replicative DNA polymerases (DNA Pols) are able to insert ribonucleotides (rNMPs) during DNA synthesis, raising crucial questions about the fidelity of DNA replication in both Bacteria and Eukarya. Here, we report that the level of rNTPs is 20-fold higher than that of dNTPs in Pyrococcus abyssi cells. Using dNTP and rNTP concentrations present in vivo, we recorded rNMP incorporation in a template-specific manner during in vitro synthesis, with the family-D DNA Pol (PolD) having the highest propensity compared with the family-B DNA Pol and the p41/p46 complex. We also showed that ribonucleotides accumulate at a relatively high frequency in the genome of wild-type Thermococcales cells, and this frequency significantly increases upon deletion of RNase HII, the major enzyme responsible for the removal of RNA from DNA. Because ribonucleotides remain in genomic DNA, we then analyzed the effects on polymerization activities by the three DNA Pols. Depending on the identity of the base and the sequence context, all three DNA Pols bypass rNMP-containing DNA templates with variable efficiency and nucleotide (mis)incorporation ability. Unexpectedly, we found that PolD correctly base-paired a single ribonucleotide opposite rNMP-containing DNA templates. An evolutionary scenario is discussed concerning rNMP incorporation into DNA and genome stability.
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Affiliation(s)
- Mélanie Lemor
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Ziqing Kong
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Etienne Henry
- CNRS, Ifremer, Univ Brest, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280, Plouzané, France
| | - Raphaël Brizard
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Sébastien Laurent
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Audrey Bossé
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Ghislaine Henneke
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France.
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Appolaire A, Rosenbaum E, Durá MA, Colombo M, Marty V, Savoye MN, Godfroy A, Schoehn G, Girard E, Gabel F, Franzetti B. Pyrococcus horikoshii TET2 peptidase assembling process and associated functional regulation. J Biol Chem 2013; 288:22542-54. [PMID: 23696647 PMCID: PMC3829341 DOI: 10.1074/jbc.m113.450189] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 05/13/2013] [Indexed: 11/06/2022] Open
Abstract
Tetrahedral (TET) aminopeptidases are large polypeptide destruction machines present in prokaryotes and eukaryotes. Here, the rules governing their assembly into hollow 12-subunit tetrahedrons are addressed by using TET2 from Pyrococcus horikoshii (PhTET2) as a model. Point mutations allowed the capture of a stable, catalytically active precursor. Small angle x-ray scattering revealed that it is a dimer whose architecture in solution is identical to that determined by x-ray crystallography within the fully assembled TET particle. Small angle x-ray scattering also showed that the reconstituted PhTET2 dodecameric particle displayed the same quaternary structure and thermal stability as the wild-type complex. The PhTET2 assembly intermediates were characterized by analytical ultracentrifugation, native gel electrophoresis, and electron microscopy. They revealed that PhTET2 assembling is a highly ordered process in which hexamers represent the main intermediate. Peptide degradation assays demonstrated that oligomerization triggers the activity of the TET enzyme toward large polypeptidic substrates. Fractionation experiments in Pyrococcus and Halobacterium cells revealed that, in vivo, the dimeric precursor co-exists together with assembled TET complexes. Taken together, our observations explain the biological significance of TET oligomerization and suggest the existence of a functional regulation of the dimer-dodecamer equilibrium in vivo.
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Affiliation(s)
- Alexandre Appolaire
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - Eva Rosenbaum
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - M. Asunción Durá
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - Matteo Colombo
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - Vincent Marty
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - Marjolaine Noirclerc Savoye
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - Anne Godfroy
- the Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Guy Schoehn
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - Eric Girard
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - Frank Gabel
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - Bruno Franzetti
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
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Deive FJ, López E, Rodríguez A, Longo MA, Sanromán MÁ. Targeting the Production of Biomolecules by Extremophiles at Bioreactor Scale. Chem Eng Technol 2012. [DOI: 10.1002/ceat.201100528] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Konn C, Testemale D, Querellou J, Holm NG, Charlou JL. New insight into the contributions of thermogenic processes and biogenic sources to the generation of organic compounds in hydrothermal fluids. GEOBIOLOGY 2011; 9:79-93. [PMID: 21062404 DOI: 10.1111/j.1472-4669.2010.00260.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Experiments on hydrothermal degradation of Pyrococcus abyssi biomass were conducted at elevated pressure (40 MPa) over a 200-450 °C temperature range in sapphire reaction cells. Few organic compounds could be detected in the 200 °C experiment. This lack was attributed to an incomplete degradation of P. abyssi cells. On the contrary, a wide range of soluble organic molecules were generated at temperatures ≥ 350 °C including toluene, styrene, C₈-C₁₆ alkyl-benzenes, naphthalene, C₁₁-C₁₆ alkyl-naphthalenes, even carbon number C₁₂-C₁₈ polycyclic aromatic hydrocarbons, C₁₅-C₁₈ alkyl-phenanthrenes and C₈:₀-C₁₆:₀ n-carboxylic acids. The effect of time on the final organic composition of the degraded P. abyssi solutions at 350 °C was also investigated. For that purpose the biomass was exposed for 10, 20, 60, 90, 270 and 720 min at 350 °C. We observed a similar effect of temperature and time on the chemical diversity obtained. In addition, temperature and time increased the degree of alkylation of alkyl-benzenes. This study offers additional evidence that a portion of the aliphatic hydrocarbons present in the fluids from the Rainbow ultramafic-hosted hydrothermal field may be abiogenic whereas a portion of the aromatic hydrocarbons and n-carboxylic acids may have a biogenic origin. We suggest that aromatic hydrocarbons and linear fatty acids at the Rainbow site may be derived directly from thermogenic alteration of material from the sub-seafloor biosphere. Yet we infer that the formation and dissolution of carboxylic acids in hydrothermal fluids may be controlled by other processes than in our experiments.
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Affiliation(s)
- C Konn
- Département Geosciences Marines, Ifremer C/Brest, Plouzané, France.
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Gunbin KV, Afonnikov DA, Kolchanov NA. Molecular evolution of the hyperthermophilic archaea of the Pyrococcus genus: analysis of adaptation to different environmental conditions. BMC Genomics 2009; 10:639. [PMID: 20042074 PMCID: PMC2816203 DOI: 10.1186/1471-2164-10-639] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Accepted: 12/30/2009] [Indexed: 05/14/2023] Open
Abstract
Background Prokaryotic microorganisms are able to survive and proliferate in severe environmental conditions. The increasing number of complete sequences of prokaryotic genomes has provided the basis for studying the molecular mechanisms of their adaptation at the genomic level. We apply here a computer-based approach to compare the genomes and proteomes from P. furiosus, P. horikoshii, and P. abyssi to identify features of their molecular evolution related to adaptation strategy to diverse environmental conditions. Results Phylogenetic analysis of rRNA genes from 26 Pyrococcus strains suggested that the divergence of P. furiosus, P. horikoshii and P. abyssi might have occurred from ancestral deep-sea organisms. It was demonstrated that the function of genes that have been subject to positive Darwinian selection is closely related to abiotic and biotic conditions to which archaea managed to become adapted. Divergence of the P. furiosus archaea might have been due to loss of some genes involved in cell motility or signal transduction, and/or to evolution under positive selection of the genes for translation machinery. In the course of P. horikoshii divergence, positive selection was found to operate mainly on the transcription machinery; divergence of P. abyssi was related with positive selection for the genes mainly involved in inorganic ion transport. Analysis of radical amino acid replacement rate in evolving P. furiosus, P. horikoshii and P. abyssi showed that the fixation rate was higher for radical substitutions relative to the volume of amino acid side-chain. Conclusions The current results give due credit to the important role of hydrostatic pressure as a cause of variability in the P. furiosus, P. horikoshii and P. abyssi genomes evolving in different habitats. Nevertheless, adaptation to pressure does not appear to be the sole factor ensuring adaptation to environment. For example, at the stage of the divergence of P. horikoshii and P. abyssi, an essential evolutionary role may be assigned to changes in the trophic chain, namely, acquisition of a consumer status at a high (P. horikoshii) or low level (P. abyssi).
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Affiliation(s)
- Konstantin V Gunbin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
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Byrne N, Lesongeur F, Bienvenu N, Geslin C, Alain K, Prieur D, Godfroy A. Effect of variation of environmental conditions on the microbial communities of deep-sea vent chimneys, cultured in a bioreactor. Extremophiles 2009; 13:595-608. [DOI: 10.1007/s00792-009-0242-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Accepted: 03/30/2009] [Indexed: 10/20/2022]
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9
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Durá MA, Rosenbaum E, Larabi A, Gabel F, Vellieux FMD, Franzetti B. The structural and biochemical characterizations of a novel TET peptidase complex from Pyrococcus horikoshii reveal an integrated peptide degradation system in hyperthermophilic Archaea. Mol Microbiol 2009; 72:26-40. [DOI: 10.1111/j.1365-2958.2009.06600.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Le Breton M, Henneke G, Norais C, Flament D, Myllykallio H, Querellou J, Raffin JP. The heterodimeric primase from the euryarchaeon Pyrococcus abyssi: a multifunctional enzyme for initiation and repair? J Mol Biol 2007; 374:1172-85. [PMID: 17991487 DOI: 10.1016/j.jmb.2007.10.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Revised: 10/02/2007] [Accepted: 10/05/2007] [Indexed: 11/27/2022]
Abstract
We report on the characterization of the DNA primase complex of the hyperthermophilic archaeon Pyrococcus abyssi (Pab). The Pab DNA primase complex is composed of the proteins Pabp41 and Pabp46, which show sequence similarities to the p49 and p58 subunits, respectively, of the eukaryotic polymerase alpha-primase complex. Both subunits were expressed, purified, and characterized. The Pabp41 subunit alone had no RNA synthesis activity but could synthesize long (up to 3 kb) DNA strands. Addition of the Pabp46 subunit increased the rate of DNA synthesis but decreased the length of the DNA fragments synthesized and conferred RNA synthesis capability. Moreover, in our experimental conditions, Pab DNA primase had comparable affinities for ribonucleotides and deoxyribonucleotides, and its activity was dependent on the presence of Mg2+ and Mn2+. Interestingly, Pab DNA primase also displayed DNA polymerase, gap-filling, and strand-displacement activities. Genetic analyses undertaken in Haloferax volcanii suggested that the eukaryotic-type heterodimeric primase is essential for survival in archaeal cells. Our results are in favor of a multifunctional archaeal primase involved in priming and repair.
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Affiliation(s)
- Magali Le Breton
- Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, Ifremer, BP 70, F-29280 Plouzané, France
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Postec A, Lesongeur F, Pignet P, Ollivier B, Querellou J, Godfroy A. Continuous enrichment cultures: insights into prokaryotic diversity and metabolic interactions in deep-sea vent chimneys. Extremophiles 2007; 11:747-57. [PMID: 17576518 DOI: 10.1007/s00792-007-0092-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2007] [Accepted: 05/15/2007] [Indexed: 10/23/2022]
Abstract
The prokaryotic diversity of culturable thermophilic communities of deep-sea hydrothermal chimneys was analysed using a continuous enrichment culture performed in a gas-lift bioreactor, and compared to classical batch enrichment cultures in vials. Cultures were conducted at 60 degrees C and pH 6.5 using a complex medium containing carbohydrates, peptides and sulphur, and inoculated with a sample of a hydrothermal black chimney collected at the Rainbow field, Mid-Atlantic Ridge, at 2,275 m depth. To assess the relevance of both culture methods, bacterial and archaeal diversity was studied using cloning and sequencing, DGGE, and whole-cell hybridisation of 16S rRNA genes. Sequences of heterotrophic microorganisms belonging to the genera Marinitoga, Thermosipho, Caminicella (Bacteria) and Thermococcus (Archaea) were obtained from both batch and continuous enrichment cultures while sequences of the autotrophic bacterial genera Deferribacter and Thermodesulfatator were only detected in the continuous bioreactor culture. It is presumed that over time constant metabolite exchanges will have occurred in the continuous enrichment culture enabling the development of a more diverse prokaryotic community. In particular, CO(2) and H(2) produced by the heterotrophic population would support the growth of autotrophic populations. Therefore, continuous enrichment culture is a useful technique to grow over time environmentally representative microbial communities and obtain insights into prokaryotic species interactions that play a crucial role in deep hydrothermal environments.
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Affiliation(s)
- Anne Postec
- Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197, IFREMER, Centre de Brest, BP 70, 29280, Plouzané, France.
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Godfroy A, Postec A, Raven N. 4 Growth of Hyperthermophilic Microorganisms for Physiological and Nutritional Studies. METHODS IN MICROBIOLOGY 2006. [DOI: 10.1016/s0580-9517(08)70007-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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13
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Postec A, Breton CL, Fardeau ML, Lesongeur F, Pignet P, Querellou J, Ollivier B, Godfroy A. Marinitoga hydrogenitolerans sp. nov., a novel member of the order Thermotogales isolated from a black smoker chimney on the Mid-Atlantic Ridge. Int J Syst Evol Microbiol 2005; 55:1217-1221. [PMID: 15879258 DOI: 10.1099/ijs.0.63550-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, thermophilic, anaerobic bacterium that is able to tolerate hydrogen was isolated from a deep-sea hydrothermal chimney collected at the Rainbow field on the Mid-Atlantic Ridge. Cells were rod-shaped and surrounded by a sheath-like outer structure (toga); they were weakly motile by means of a polar flagellum. They appeared singly, in pairs or in short chains. They grew at 35-65 degrees C (optimum 60 degrees C), pH 4.5-8.5 (optimum pH 6.0) and 10-65 g sea salts l(-1) (optimum 30-40 g l(-1)). The isolate was organotrophic, and able to grow on various carbohydrates or complex proteinaceous substrates. Growth was not inhibited under 100 % hydrogen or in the presence of 2 % oxygen in the gas phase. The isolate reduces sulfur, although sulfur reduction is not required for growth. The fermentation products identified on glucose were acetate, ethanol, formate, hydrogen and CO(2). The G + C content of the genomic DNA was 28 +/- 1 mol%. Phylogenetic analysis of the 16S rRNA gene placed the strain within the genus Marinitoga, order Thermotogales, in the bacterial domain. On the basis of the 16S rRNA gene sequence comparisons and physiological characteristics, the isolate is considered to represent a novel species, for which the name Marinitoga hydrogenitolerans sp. nov. is proposed. The type strain is AT1271(T) (=DSM 16785(T) = JCM 12826(T)).
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MESH Headings
- Acetic Acid/metabolism
- Atlantic Ocean
- Base Composition
- Carbohydrate Metabolism
- Carbon Dioxide/metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Ethanol/metabolism
- Flagella/physiology
- Formates/metabolism
- Genes, rRNA
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/classification
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/cytology
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/isolation & purification
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/physiology
- Hot Temperature
- Hydrogen/metabolism
- Hydrogen/toxicity
- Hydrogen-Ion Concentration
- Molecular Sequence Data
- Movement
- Oxidation-Reduction
- Oxygen/toxicity
- Phylogeny
- Proteins/metabolism
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Seawater/microbiology
- Sequence Analysis, DNA
- Sulfur/metabolism
- Water Microbiology
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Affiliation(s)
- Anne Postec
- Laboratoire de Microbiologie et de Biotechnologie des Extrêmophiles, IFREMER, Centre de Brest, BP 70, 29280 Plouzané, France
| | - Claire Le Breton
- Laboratoire de Microbiologie et de Biotechnologie des Extrêmophiles, IFREMER, Centre de Brest, BP 70, 29280 Plouzané, France
| | - Marie-Laure Fardeau
- Laboratoire IRD de Microbiologie des Anaérobies, UR 101, Universités de Provence et de la Méditerranée, CESB-ESIL, case 925, 163 avenue de Luminy, 13288 Marseille, France
| | - Françoise Lesongeur
- Laboratoire de Microbiologie et de Biotechnologie des Extrêmophiles, IFREMER, Centre de Brest, BP 70, 29280 Plouzané, France
| | - Patricia Pignet
- Laboratoire de Microbiologie et de Biotechnologie des Extrêmophiles, IFREMER, Centre de Brest, BP 70, 29280 Plouzané, France
| | - Joël Querellou
- Laboratoire de Microbiologie et de Biotechnologie des Extrêmophiles, IFREMER, Centre de Brest, BP 70, 29280 Plouzané, France
| | - Bernard Ollivier
- Laboratoire IRD de Microbiologie des Anaérobies, UR 101, Universités de Provence et de la Méditerranée, CESB-ESIL, case 925, 163 avenue de Luminy, 13288 Marseille, France
| | - Anne Godfroy
- Laboratoire de Microbiologie et de Biotechnologie des Extrêmophiles, IFREMER, Centre de Brest, BP 70, 29280 Plouzané, France
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14
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Postec A, Pignet P, Cueff-Gauchard V, Schmitt A, Querellou J, Godfroy A. Optimisation of growth conditions for continuous culture of the hyperthermophilic archaeon Thermococcus hydrothermalis and development of sulphur-free defined and minimal media. Res Microbiol 2005; 156:82-7. [PMID: 15636751 DOI: 10.1016/j.resmic.2004.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2004] [Accepted: 08/02/2004] [Indexed: 11/21/2022]
Abstract
The hyperthermophilic archaeon Thermococcus hydrothermalis was cultivated in continuous culture in a gas-lift bioreactor in the absence of elemental sulphur on both proteinaceous and maltose-containing media. Optimal conditions (pH, temperature and gas flow rate), determined on complex media that yielded maximal growth rate and maximal steady state cell density, were obtained at 80 degrees C, pH 6 and gas sparging at 0.2 v v(-1) min(-1). Higher steady state cell densities were obtained on a medium containing maltose and yeast extract. In order to design a defined and minimal media, the nutritional requirements of T. hydrothermalis were then investigated using continuous culture in the absence of elemental sulphur in the gas-lift bioreactor. First, the complex nutriments were replaced and a defined medium containing maltose, 19 amino acids and the two nitrogenous bases adenine and thymine, was determined. Secondly, selective feedings and withdrawal of amino acids showed requirements for 14 amino acids.
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Affiliation(s)
- Anne Postec
- Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197 Ifremer, Centre de Brest, BP 70, 29280 Plouzané, France
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15
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Postec A, Urios L, Lesongeur F, Ollivier B, Querellou J, Godfroy A. Continuous Enrichment Culture and Molecular Monitoring to Investigate the Microbial Diversity of Thermophiles Inhabiting Deep-Sea Hydrothermal Ecosystems. Curr Microbiol 2005; 50:138-44. [PMID: 15717222 DOI: 10.1007/s00284-004-4443-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2004] [Accepted: 10/05/2004] [Indexed: 10/25/2022]
Abstract
The microflora developing during a continuous enrichment culture from a hydrothermal chimney sample was investigated by molecular methods. The culture was performed in a gas-lift bioreactor under anaerobic conditions, at 90 degrees C and pH 6.5, on a complex medium containing sulfur as the terminal electron acceptor. Archaeal and bacterial diversity was studied. Microorganisms affiliated with the genera Pyrococcus, Marinitoga, and Bacillus were detected through DGGE analysis of 16S rDNA. Additional sequences phylogenetically related to Thermococcus and epsilon-Proteobacteria were detected by cloning and sequencing of 16S rDNA from two samples of the enrichment culture. In comparison, the sequences retrieved from cloning analysis from an enrichment culture performed in a flask (batch condition) using the same culture medium showed that only members of the genus Thermococcus were cultivated. Therefore, continuous enrichment culture using the gas-lift bioreactor can be considered as an efficient and improved method for investigating microbial communities originating from deep-sea hydrothermal vents.
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Affiliation(s)
- Anne Postec
- UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes, IFREMER, Centre de Brest, BP 70, 29280 Plouzané, France.
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16
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Cohen GN, Barbe V, Flament D, Galperin M, Heilig R, Lecompte O, Poch O, Prieur D, Quérellou J, Ripp R, Thierry JC, Van der Oost J, Weissenbach J, Zivanovic Y, Forterre P. An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi. Mol Microbiol 2003; 47:1495-512. [PMID: 12622808 DOI: 10.1046/j.1365-2958.2003.03381.x] [Citation(s) in RCA: 144] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The hyperthermophilic euryarchaeon Pyrococcus abyssi and the related species Pyrococcus furiosus and Pyrococcus horikoshii, whose genomes have been completely sequenced, are presently used as model organisms in different laboratories to study archaeal DNA replication and gene expression and to develop genetic tools for hyperthermophiles. We have performed an extensive re-annotation of the genome of P. abyssi to obtain an integrated view of its phylogeny, molecular biology and physiology. Many new functions are predicted for both informational and operational proteins. Moreover, several candidate genes have been identified that might encode missing links in key metabolic pathways, some of which have unique biochemical features. The great majority of Pyrococcus proteins are typical archaeal proteins and their phylogenetic pattern agrees with its position near the root of the archaeal tree. However, proteins probably from bacterial origin, including some from mesophilic bacteria, are also present in the P. abyssi genome.
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Affiliation(s)
- Georges N Cohen
- Institut Pasteur, 25,28 rue du Docteur Roux, 75724 Paris CEDEX 15, France
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17
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Abstract
The discovery of life in seemingly prohibitive environments continues to challenge conventional concepts of the growth-limiting conditions of many cellular organisms. The diversity of extremophiles has barely been tapped -estimates generally agreeing that <1% of the microorganisms in the environment have been cultivated in pure cultures to date. The production of extremophilic biomass is very important to provide sufficient material for enzyme and biomolecule isolation and characterization, eventually revealing particular features of industrial interest. Hence, special equipment and custom-tailored processes have been developed and are currently under evaluation for the improvement of fermentation productivity. Despite the remarkable opportunities that these uncommon organisms present for biotechnological applications only few instances can be reported for actual exploitation. This lack of progress from the research findings at a laboratory-scale to the actual development of pilot and large-scale production is correlated with the difficulties encountered in extremophile cultivations. Here, we report recent achievements in the production of biomass and related enzymes and biomolecules from extremophile sources, especially focusing on the application of novel fermentation strategies.
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Affiliation(s)
- Chiara Schiraldi
- Biotechnology and Molecular Biology Unit, Dept of Experimental Medicine, Faculty of Medicine, Second University of Naples, Italy
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18
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Schiraldi C, Giuliano M, De Rosa M. Perspectives on biotechnological applications of archaea. ARCHAEA (VANCOUVER, B.C.) 2002; 1:75-86. [PMID: 15803645 PMCID: PMC2685559 DOI: 10.1155/2002/436561] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2001] [Accepted: 05/06/2002] [Indexed: 11/17/2022]
Abstract
Many archaea colonize extreme environments. They include hyperthermophiles, sulfur-metabolizing thermophiles, extreme halophiles and methanogens. Because extremophilic microorganisms have unusual properties, they are a potentially valuable resource in the development of novel biotechnological processes. Despite extensive research, however, there are few existing industrial applications of either archaeal biomass or archaeal enzymes. This review summarizes current knowledge about the biotechnological uses of archaea and archaeal enzymes with special attention to potential applications that are the subject of current experimental evaluation. Topics covered include cultivation methods, recent achievements in genomics, which are of key importance for the development of new biotechnological tools, and the application of wild-type biomasses, engineered microorganisms, enzymes and specific metabolites in particular bioprocesses of industrial interest.
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Affiliation(s)
- Chiara Schiraldi
- Department of Experimental Medicine, Section of Biotechnology and Molecular Biology, Faculty of Medicine, II University of Naples, via Costantinopoli 16, 80138 Naples, Italy
| | - Mariateresa Giuliano
- Department of Experimental Medicine, Section of Biotechnology and Molecular Biology, Faculty of Medicine, II University of Naples, via Costantinopoli 16, 80138 Naples, Italy
| | - Mario De Rosa
- Department of Experimental Medicine, Section of Biotechnology and Molecular Biology, Faculty of Medicine, II University of Naples, via Costantinopoli 16, 80138 Naples, Italy
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19
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Koning SM, Elferink MG, Konings WN, Driessen AJ. Cellobiose uptake in the hyperthermophilic archaeon Pyrococcus furiosus is mediated by an inducible, high-affinity ABC transporter. J Bacteriol 2001; 183:4979-84. [PMID: 11489849 PMCID: PMC95372 DOI: 10.1128/jb.183.17.4979-4984.2001] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The hyperthermophilic archaeon Pyrococcus furiosus can utilize different beta-glucosides, like cellobiose and laminarin. Cellobiose uptake occurs with high affinity (K(m) = 175 nM) and involves an inducible binding protein-dependent transport system. The cellobiose binding protein (CbtA) was purified from P. furiosus membranes to homogeneity as a 70-kDa glycoprotein. CbtA not only binds cellobiose but also cellotriose, cellotetraose, cellopentaose, laminaribiose, laminaritriose, and sophorose. The cbtA gene was cloned and functionally expressed in Escherichia coli. cbtA belongs to a gene cluster that encodes a transporter that belongs to the Opp family of ABC transporters.
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Affiliation(s)
- S M Koning
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 90750 AA Haren, The Netherlands
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