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Hocq R, Bottone S, Gautier A, Pflügl S. A fluorescent reporter system for anaerobic thermophiles. Front Bioeng Biotechnol 2023; 11:1226889. [PMID: 37476481 PMCID: PMC10355840 DOI: 10.3389/fbioe.2023.1226889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/23/2023] [Indexed: 07/22/2023] Open
Abstract
Owing to their inherent capacity to make invisible biological processes visible and quantifiable, fluorescent reporter systems have numerous applications in biotechnology. For classical fluorescent protein systems (i.e., GFP and derivatives), chromophore maturation is O2-dependent, restricting their applications to aerobic organisms. In this work, we pioneered the use of the oxygen-independent system FAST (Fluorescence Activating and absorption Shifting tag) in the thermophilic anaerobe Thermoanaerobacter kivui. We developed a modular cloning system that was used to easily clone a library of FAST expression cassettes in an E. coli-Thermoanaerobacter shuttle plasmid. FAST-mediated fluorescence was then assessed in vivo in T. kivui, and we observed bright green and red fluorescence for cells grown at 55°C. Next, we took advantage of this functional reporter system to characterize a set of homologous and heterologous promoters by quantifying gene expression, expanding the T. kivui genetic toolbox. Low fluorescence at 66°C (Topt for T. kivui) was subsequently investigated at the single-cell level using flow cytometry and attributed to plasmid instability at higher temperatures. Adaptive laboratory evolution circumvented this issue and drastically enhanced fluorescence at 66°C. Whole plasmid sequencing revealed the evolved strain carried functional plasmids truncated at the Gram-positive origin of replication, that could however not be linked to the increased fluorescence displayed by the evolved strain. Collectively, our work demonstrates the applicability of the FAST fluorescent reporter systems to T. kivui, paving the way for further applications in thermophilic anaerobes.
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Affiliation(s)
- Rémi Hocq
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
| | - Sara Bottone
- Laboratoire des Biomolécules (LBM), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, École Normale Supérieure, Université PSL, Paris, France
- Institut Universitaire de France, Paris, France
| | - Arnaud Gautier
- Laboratoire des Biomolécules (LBM), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, École Normale Supérieure, Université PSL, Paris, France
- Institut Universitaire de France, Paris, France
| | - Stefan Pflügl
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
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2
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Yin Y, Zhang L. Archaeal DNA alkylation repair conducted by DNA glycosylase and methyltransferase. Appl Microbiol Biotechnol 2023; 107:3131-3142. [PMID: 37036526 DOI: 10.1007/s00253-023-12506-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/25/2023] [Accepted: 03/28/2023] [Indexed: 04/11/2023]
Abstract
Alkylated bases in DNA created in the presence of endogenous and exogenous alkylating agents are either cytotoxic or mutagenic, or both to a cell. Currently, cells have evolved several strategies for repairing alkylated base. One strategy is a base excision repair process triggered by a specific DNA glycosylase that is used for the repair of the cytotoxic 3-methyladenine. Additionally, the cytotoxic and mutagenic O6-methylguanine (O6-meG) is corrected by O6-methylguanine methyltransferase (MGMT) via directly transferring the methyl group in the lesion to a specific cysteine in this protein. Furthermore, oxidative DNA demethylation catalyzed by DNA dioxygenase is utilized for repairing the cytotoxic 3-methylcytosine (3-meC) and 1-methyladenine (1-meA) in a direct reversal manner. As the third domain of life, Archaea possess 3-methyladenine DNA glycosylase II (AlkA) and MGMT, but no DNA dioxygenase homologue responsible for oxidative demethylation. Herein, we summarize recent progress in structural and biochemical properties of archaeal AlkA and MGMT to gain a better understanding of archaeal DNA alkylation repair, focusing on similarities and differences between the proteins from different archaeal species and between these archaeal proteins and their bacterial and eukaryotic relatives. To our knowledge, it is the first review on archaeal DNA alkylation repair conducted by DNA glycosylase and methyltransferase. KEY POINTS: • Archaeal MGMT plays an essential role in the repair of O 6 -meG • Archaeal AlkA can repair 3-meC and 1-meA.
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Affiliation(s)
- Youcheng Yin
- Marine Science & Technology Institute, College of Environmental Science and Engineering, Yangzhou University, Yangzhou City, China
| | - Likui Zhang
- Marine Science & Technology Institute, College of Environmental Science and Engineering, Yangzhou University, Yangzhou City, China.
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3
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Merlo R, Mattossovich R, Genta M, Valenti A, Di Mauro G, Minassi A, Miggiano R, Perugino G. First thermostable CLIP-tag by rational design applied to an archaeal O-alkyl-guanine-DNA-alkyl-transferase. Comput Struct Biotechnol J 2022; 20:5275-5286. [PMID: 36212535 PMCID: PMC9519396 DOI: 10.1016/j.csbj.2022.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/08/2022] [Accepted: 09/08/2022] [Indexed: 11/30/2022] Open
Abstract
Self-labelling protein tags (SLPs) are resourceful tools that revolutionized sensor imaging, having the versatile ability of being genetically fused with any protein of interest and undergoing activation with alternative probes specifically designed for each variant (namely, SNAP-tag, CLIP-tag and Halo-tag). Commercially available SLPs are highly useful in studying molecular aspects of mesophilic organisms, while they fail in characterizing model organisms that thrive in harsh conditions. By applying an integrated computational and structural approach, we designed a engineered variant of the alkylguanine-DNA-alkyl-transferase (OGT) from the hyper-thermophilic archaeon Saccharolobus solfataricus (SsOGT), with no DNA-binding activity, able to covalently react with O6-benzyl-cytosine (BC-) derivatives, obtaining the first thermostable CLIP-tag, named SsOGT-MC8. The presented construct is able to recognize and to covalently bind BC- substrates with a marked specificity, displaying a very low activity on orthogonal benzyl-guanine (BG-) substrate and showing a remarkable thermal stability that broadens the applicability of SLPs. The rational mutagenesis that, starting from SsOGT, led to the production of SsOGT-MC8 was first evaluated by structural predictions to precisely design the chimeric construct, by mutating specific residues involved in protein stability and substrate recognition. The final construct was further validated by biochemical characterization and X-ray crystallography, allowing us to present here the first structural model of a CLIP-tag establishing the molecular determinants of its activity, as well as proposing a general approach for the rational engineering of any O6-alkylguanine-DNA-alkyl-transferase turning it into a SNAP- and a CLIP-tag variant.
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Merlo R, Caprioglio D, Cillo M, Valenti A, Mattossovich R, Morrone C, Massarotti A, Rossi F, Miggiano R, Leonardi A, Minassi A, Perugino G. The SNAP- tag technology revised: an effective chemo-enzymatic approach by using a universal azide-based substrate. J Enzyme Inhib Med Chem 2021; 36:85-97. [PMID: 33121288 PMCID: PMC7599001 DOI: 10.1080/14756366.2020.1841182] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
SNAP-tag ® is a powerful technology for the labelling of protein/enzymes by using benzyl-guanine (BG) derivatives as substrates. Although commercially available or ad hoc produced, their synthesis and purification are necessary, increasing time and costs. To address this limitation, here we suggest a revision of this methodology, by performing a chemo-enzymatic approach, by using a BG-substrate containing an azide group appropriately distanced by a spacer from the benzyl ring. The SNAP-tag ® and its relative thermostable version (SsOGT-H5 ) proved to be very active on this substrate. The stability of these tags upon enzymatic reaction makes possible the exposition to the solvent of the azide-moiety linked to the catalytic cysteine, compatible for the subsequent conjugation with DBCO-derivatives by azide-alkyne Huisgen cycloaddition. Our studies propose a strengthening and an improvement in terms of biotechnological applications for this self-labelling protein-tag.
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Affiliation(s)
- Rosa Merlo
- Institute of Biosciences and BioResources, National Research Council of Italy, Naples, Italy
| | - Diego Caprioglio
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Novara, Italy
| | - Michele Cillo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Anna Valenti
- Institute of Biosciences and BioResources, National Research Council of Italy, Naples, Italy
| | - Rosanna Mattossovich
- Institute of Biosciences and BioResources, National Research Council of Italy, Naples, Italy
| | - Castrese Morrone
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Novara, Italy
| | - Alberto Massarotti
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Novara, Italy.,IXTAL srl, Novara, Italy
| | - Franca Rossi
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Novara, Italy
| | - Riccardo Miggiano
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Novara, Italy.,IXTAL srl, Novara, Italy
| | - Antonio Leonardi
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Alberto Minassi
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Novara, Italy
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources, National Research Council of Italy, Naples, Italy
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5
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Turkowyd B, Schreiber S, Wörtz J, Segal ES, Mevarech M, Duggin IG, Marchfelder A, Endesfelder U. Establishing Live-Cell Single-Molecule Localization Microscopy Imaging and Single-Particle Tracking in the Archaeon Haloferax volcanii. Front Microbiol 2020; 11:583010. [PMID: 33329447 PMCID: PMC7714787 DOI: 10.3389/fmicb.2020.583010] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/16/2020] [Indexed: 01/30/2023] Open
Abstract
In recent years, fluorescence microscopy techniques for the localization and tracking of single molecules in living cells have become well-established and are indispensable tools for the investigation of cellular biology and in vivo biochemistry of many bacterial and eukaryotic organisms. Nevertheless, these techniques are still not established for imaging archaea. Their establishment as a standard tool for the study of archaea will be a decisive milestone for the exploration of this branch of life and its unique biology. Here, we have developed a reliable protocol for the study of the archaeon Haloferax volcanii. We have generated an autofluorescence-free H. volcanii strain, evaluated several fluorescent proteins for their suitability to serve as single-molecule fluorescence markers and codon-optimized them to work under optimal H. volcanii cultivation conditions. We found that two of them, Dendra2Hfx and PAmCherry1Hfx, provide state-of-the-art single-molecule imaging. Our strategy is quantitative and allows dual-color imaging of two targets in the same field of view (FOV) as well as DNA co-staining. We present the first single-molecule localization microscopy (SMLM) images of the subcellular organization and dynamics of two crucial intracellular proteins in living H. volcanii cells, FtsZ1, which shows complex structures in the cell division ring, and RNA polymerase, which localizes around the periphery of the cellular DNA. This work should provide incentive to develop SMLM strategies for other archaeal organisms in the near future.
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Affiliation(s)
- Bartosz Turkowyd
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | | | - Julia Wörtz
- Department of Biology II, Ulm University, Ulm, Germany
| | - Ella Shtifman Segal
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Moshe Mevarech
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Iain G. Duggin
- The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | | | - Ulrike Endesfelder
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Physics, Mellon College of Science, Carnegie-Mellon University, Pittsburgh, PA, United States
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6
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Pulschen AA, Mutavchiev DR, Culley S, Sebastian KN, Roubinet J, Roubinet M, Risa GT, van Wolferen M, Roubinet C, Schmidt U, Dey G, Albers SV, Henriques R, Baum B. Live Imaging of a Hyperthermophilic Archaeon Reveals Distinct Roles for Two ESCRT-III Homologs in Ensuring a Robust and Symmetric Division. Curr Biol 2020; 30:2852-2859.e4. [PMID: 32502411 PMCID: PMC7372223 DOI: 10.1016/j.cub.2020.05.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/15/2020] [Accepted: 05/06/2020] [Indexed: 12/14/2022]
Abstract
Live-cell imaging has revolutionized our understanding of dynamic cellular processes in bacteria and eukaryotes. Although similar techniques have been applied to the study of halophilic archaea [1-5], our ability to explore the cell biology of thermophilic archaea has been limited by the technical challenges of imaging at high temperatures. Sulfolobus are the most intensively studied members of TACK archaea and have well-established molecular genetics [6-9]. Additionally, studies using Sulfolobus were among the first to reveal striking similarities between the cell biology of eukaryotes and archaea [10-15]. However, to date, it has not been possible to image Sulfolobus cells as they grow and divide. Here, we report the construction of the Sulfoscope, a heated chamber on an inverted fluorescent microscope that enables live-cell imaging of thermophiles. By using thermostable fluorescent probes together with this system, we were able to image Sulfolobus acidocaldarius cells live to reveal tight coupling between changes in DNA condensation, segregation, and cell division. Furthermore, by imaging deletion mutants, we observed functional differences between the two ESCRT-III proteins implicated in cytokinesis, CdvB1 and CdvB2. The deletion of cdvB1 compromised cell division, causing occasional division failures, whereas the ΔcdvB2 exhibited a profound loss of division symmetry, generating daughter cells that vary widely in size and eventually generating ghost cells. These data indicate that DNA separation and cytokinesis are coordinated in Sulfolobus, as is the case in eukaryotes, and that two contractile ESCRT-III polymers perform distinct roles to ensure that Sulfolobus cells undergo a robust and symmetrical division.
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Affiliation(s)
| | - Delyan R Mutavchiev
- MRC-Laboratory for Molecular Cell Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Siân Culley
- MRC-Laboratory for Molecular Cell Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Kim Nadine Sebastian
- Molecular Biology of Archaea, Institute of Biology II - Microbiology, University of Freiburg, 79104 Freiburg, Germany
| | | | | | | | - Marleen van Wolferen
- Molecular Biology of Archaea, Institute of Biology II - Microbiology, University of Freiburg, 79104 Freiburg, Germany
| | - Chantal Roubinet
- MRC-Laboratory for Molecular Cell Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Uwe Schmidt
- Center for System Biology Dresden (CSBD), 01307 Dresden, Germany; Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), 01307 Dresden, Germany
| | - Gautam Dey
- MRC-Laboratory for Molecular Cell Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II - Microbiology, University of Freiburg, 79104 Freiburg, Germany
| | - Ricardo Henriques
- MRC-Laboratory for Molecular Cell Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Buzz Baum
- MRC-Laboratory for Molecular Cell Biology, UCL, Gower Street, London WC1E 6BT, UK; Institute for the Physics of Living Systems, UCL, London WC1E 6BT, UK.
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7
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Mattossovich R, Merlo R, Miggiano R, Valenti A, Perugino G. O6-alkylguanine-DNA Alkyltransferases in Microbes Living on the Edge: From Stability to Applicability. Int J Mol Sci 2020; 21:E2878. [PMID: 32326075 DOI: 10.3390/ijms21082878] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/09/2020] [Accepted: 04/16/2020] [Indexed: 02/06/2023] Open
Abstract
The genome of living cells is continuously exposed to endogenous and exogenous attacks, and this is particularly amplified at high temperatures. Alkylating agents cause DNA damage, leading to mutations and cell death; for this reason, they also play a central role in chemotherapy treatments. A class of enzymes known as AGTs (alkylguanine-DNA-alkyltransferases) protects the DNA from mutations caused by alkylating agents, in particular in the recognition and repair of alkylated guanines in O6-position. The peculiar irreversible self-alkylation reaction of these enzymes triggered numerous studies, especially on the human homologue, in order to identify effective inhibitors in the fight against cancer. In modern biotechnology, engineered variants of AGTs are developed to be used as protein tags for the attachment of chemical ligands. In the last decade, research on AGTs from (hyper)thermophilic sources proved useful as a model system to clarify numerous phenomena, also common for mesophilic enzymes. This review traces recent progress in this class of thermozymes, emphasizing their usefulness in basic research and their consequent advantages for in vivo and in vitro biotechnological applications.
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Abstract
Replicative DNA helicases are essential cellular enzymes that unwind duplex DNA in front of the replication fork during chromosomal DNA replication. Replicative helicases were discovered, beginning in the 1970s, in bacteria, bacteriophages, viruses, and eukarya, and, in the mid-1990s, in archaea. This year marks the 20th anniversary of the first report on the archaeal replicative helicase, the minichromosome maintenance (MCM) protein. This minireview summarizes 2 decades of work on the archaeal MCM.
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9
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Affiliation(s)
- Yoann G. Santin
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la MéditerranéeAix‐Marseille Université – CNRS UMR7255 31 Chemin Joseph Aiguier, CS70071, 13402 Marseille Cedex 09 France
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10
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Mattossovich R, Merlo R, Fontana A, d'Ippolito G, Terns MP, Watts EA, Valenti A, Perugino G. A journey down to hell: new thermostable protein-tags for biotechnology at high temperatures. Extremophiles 2019; 24:81-91. [PMID: 31555904 DOI: 10.1007/s00792-019-01134-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/13/2019] [Indexed: 12/14/2022]
Abstract
The specific labelling of proteins in recent years has made use of self-labelling proteins, such as the SNAP-tag® and the Halotag®. These enzymes, by their nature or suitably engineered, have the ability to specifically react with their respective substrates, but covalently retaining a part of them in the catalytic site upon reaction. This led to the synthesis of substrates conjugated with, e.g., fluorophores (proposing them as alternatives to fluorescent proteins), but also with others chemical groups, for numerous biotechnological applications. Recently, a mutant of the OGT from Saccharolobus solfataricus (H5) very stable to high temperatures and in the presence of physical and chemical denaturing agents has been proposed as a thermostable SNAP-tag® for in vivo and in vitro harsh reaction conditions. Here, we show two new thermostable OGTs from Thermotoga neapolitana and Pyrococcus furiosus, which, respectively, display a higher catalytic activity and thermostability respect to H5, proposing them as alternatives for in vivo studies in these extreme model organisms.
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Affiliation(s)
- Rosanna Mattossovich
- Institute of Biosciences and BioResources, National Council of Research of Italy, Via P. Castellino 111, 80131, Naples, Italy
| | - Rosa Merlo
- Institute of Biosciences and BioResources, National Council of Research of Italy, Via P. Castellino 111, 80131, Naples, Italy
| | - Angelo Fontana
- Institute of Biomolecular Chemistry, National Council of Research of Italy, Via Campi Flegrei, 34, 80078, Pozzuoli, NA, Italy
| | - Giuliana d'Ippolito
- Institute of Biomolecular Chemistry, National Council of Research of Italy, Via Campi Flegrei, 34, 80078, Pozzuoli, NA, Italy
| | - Michael P Terns
- Departments of Biochemistry and Molecular Biology, Genetics, and Microbiology, University of Georgia, Athens, GA, USA
| | - Elizabeth A Watts
- Departments of Biochemistry and Molecular Biology, Genetics, and Microbiology, University of Georgia, Athens, GA, USA
| | - Anna Valenti
- Institute of Biosciences and BioResources, National Council of Research of Italy, Via P. Castellino 111, 80131, Naples, Italy
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources, National Council of Research of Italy, Via P. Castellino 111, 80131, Naples, Italy.
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11
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Kramm K, Endesfelder U, Grohmann D. A Single-Molecule View of Archaeal Transcription. J Mol Biol 2019; 431:4116-4131. [PMID: 31207238 DOI: 10.1016/j.jmb.2019.06.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/27/2019] [Accepted: 06/06/2019] [Indexed: 01/03/2023]
Abstract
The discovery of the archaeal domain of life is tightly connected to an in-depth analysis of the prokaryotic RNA world. In addition to Carl Woese's approach to use the sequence of the 16S rRNA gene as phylogenetic marker, the finding of Karl Stetter and Wolfram Zillig that archaeal RNA polymerases (RNAPs) were nothing like the bacterial RNAP but are more complex enzymes that resemble the eukaryotic RNAPII was one of the key findings supporting the idea that archaea constitute the third major branch on the tree of life. This breakthrough in transcriptional research 40years ago paved the way for in-depth studies of the transcription machinery in archaea. However, although the archaeal RNAP and the basal transcription factors that fine-tune the activity of the RNAP during the transcription cycle are long known, we still lack information concerning the architecture and dynamics of archaeal transcription complexes. In this context, single-molecule measurements were instrumental as they provided crucial insights into the process of transcription initiation, the architecture of the initiation complex and the dynamics of mobile elements of the RNAP. In this review, we discuss single-molecule approaches suitable to examine molecular mechanisms of transcription and highlight findings that shaped our understanding of the archaeal transcription apparatus. We furthermore explore the possibilities and challenges of next-generation single-molecule techniques, for example, super-resolution microscopy and single-molecule tracking, and ask whether these approaches will ultimately allow us to investigate archaeal transcription in vivo.
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Affiliation(s)
- Kevin Kramm
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Ulrike Endesfelder
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Str. 16, 35043 Marburg, Germany
| | - Dina Grohmann
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.
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12
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Merlo R, Del Prete S, Valenti A, Mattossovich R, Carginale V, Supuran CT, Capasso C, Perugino G. An AGT-based protein-tag system for the labelling and surface immobilization of enzymes on E. coli outer membrane. J Enzyme Inhib Med Chem 2019; 34:490-499. [PMID: 30724623 PMCID: PMC6366409 DOI: 10.1080/14756366.2018.1559161] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The use of natural systems, such as outer membrane protein A (OmpA), phosphoporin E (PhoE), ice nucleation protein (INP), etc., has been proved very useful for the surface exposure of proteins on the outer membrane of Gram-negative bacteria. These strategies have the clear advantage of unifying in a one-step the production, the purification and the in vivo immobilisation of proteins/biocatalysts onto a specific biological support. Here, we introduce the novel Anchoring-and-Self-Labelling-protein-tag (ASLtag), which allows the in vivo immobilisation of enzymes on E. coli surface and the labelling of the neosynthesised proteins with the engineered alkylguanine-DNA-alkyl-transferase (H5) from Sulfolobus solfataricus. Our results demonstrated that this tag enhanced the overexpression of thermostable enzymes, such as the carbonic anhydrase (SspCA) from Sulfurihydrogenibium yellowstonense and the β-glycoside hydrolase (SsβGly) from S. solfataricus, without affecting their folding and catalytic activity, proposing a new tool for the improvement in the utilisation of biocatalysts of biotechnological interest.
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Affiliation(s)
- Rosa Merlo
- a Department of Biology Agriculture and Food Sciences , Institute of Bioscience and BioResources - National Research Council of Italy , Naples , Italy
| | - Sonia Del Prete
- a Department of Biology Agriculture and Food Sciences , Institute of Bioscience and BioResources - National Research Council of Italy , Naples , Italy
| | - Anna Valenti
- a Department of Biology Agriculture and Food Sciences , Institute of Bioscience and BioResources - National Research Council of Italy , Naples , Italy
| | - Rosanna Mattossovich
- a Department of Biology Agriculture and Food Sciences , Institute of Bioscience and BioResources - National Research Council of Italy , Naples , Italy
| | - Vincenzo Carginale
- a Department of Biology Agriculture and Food Sciences , Institute of Bioscience and BioResources - National Research Council of Italy , Naples , Italy
| | - Claudiu T Supuran
- b Neurofarba Department , University of Florence, Polo Scientifico , Sesto Fiorentino Firenze , Italy
| | - Clemente Capasso
- a Department of Biology Agriculture and Food Sciences , Institute of Bioscience and BioResources - National Research Council of Italy , Naples , Italy
| | - Giuseppe Perugino
- a Department of Biology Agriculture and Food Sciences , Institute of Bioscience and BioResources - National Research Council of Italy , Naples , Italy
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13
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Lo Gullo G, Mattossovich R, Perugino G, La Teana A, Londei P, Benelli D. Optimization of an In Vitro Transcription/Translation System Based on Sulfolobus solfataricus Cell Lysate. Archaea 2019; 2019:9848253. [PMID: 30886540 DOI: 10.1155/2019/9848253] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 11/05/2018] [Indexed: 11/18/2022]
Abstract
A system is described which permits the efficient synthesis of proteins in vitro at high temperature. It is based on the use of an unfractionated cell lysate (S30) from Sulfolobus solfataricus previously well characterized in our laboratory for translation of pretranscribed mRNAs, and now adapted to perform coupled transcription and translation. The essential element in this expression system is a strong promoter derived from the S. solfataricus 16S/23S rRNA-encoding gene, from which specific mRNAs may be transcribed with high efficiency. The synthesis of two different proteins is reported, including the S. solfataricus DNA-alkylguanine-DNA-alkyl-transferase protein (SsOGT), which is shown to be successfully labeled with appropriate fluorescent substrates and visualized in cell extracts. The simplicity of the experimental procedure and specific activity of the proteins offer a number of possibilities for the study of structure-function relationships of proteins.
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Rekadwad B, Gonzalez JM. Multidisciplinary involvement and potential of thermophiles. Folia Microbiol (Praha) 2019; 64:389-406. [PMID: 30386965 DOI: 10.1007/s12223-018-0662-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/25/2018] [Indexed: 12/15/2022]
Abstract
The full biotechnological exploitation of thermostable enzymes in industrial processes is necessary for their commercial interest and industrious value. The heat-tolerant and heat-resistant enzymes are a key for efficient and cost-effective translation of substrates into useful products for commercial applications. The thermophilic, hyperthermophilic, and microorganisms adapted to extreme temperatures (i.e., low-temperature lovers or psychrophiles) are a rich source of thermostable enzymes with broad-ranging thermal properties, which have structural and functional stability to underpin a variety of technologies. These enzymes are under scrutiny for their great biotechnological potential. Temperature is one of the most critical parameters that shape microorganisms and their biomolecules for stability under harsh environmental conditions. This review describes in detail the sources of thermophiles and thermostable enzymes from prokaryotes and eukaryotes (microbial cell factories). Furthermore, the review critically examines perspectives to improve modern biocatalysts, its production and performance aiming to increase their value for biotechnology through higher standards, specificity, resistance, lowing costs, etc. These thermostable and thermally adapted extremophilic enzymes have been used in a wide range of industries that span all six enzyme classes. Thus, in particular, target of this review paper is to show the possibility of both high-value-low-volume (e.g., fine-chemical synthesis) and low-value-high-volume by-products (e.g., fuels) by minimizing changes to current industrial processes.
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Tusk SE, Delalez NJ, Berry RM. Subunit Exchange in Protein Complexes. J Mol Biol 2018; 430:4557-4579. [DOI: 10.1016/j.jmb.2018.06.039] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/21/2018] [Accepted: 06/21/2018] [Indexed: 01/09/2023]
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Miggiano R, Valenti A, Rossi F, Rizzi M, Perugino G, Ciaramella M. Every OGT Is Illuminated … by Fluorescent and Synchrotron Lights. Int J Mol Sci 2017; 18:ijms18122613. [PMID: 29206193 PMCID: PMC5751216 DOI: 10.3390/ijms18122613] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 11/28/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022] Open
Abstract
O6-DNA-alkyl-guanine-DNA-alkyl-transferases (OGTs) are evolutionarily conserved, unique proteins that repair alkylation lesions in DNA in a single step reaction. Alkylating agents are environmental pollutants as well as by-products of cellular reactions, but are also very effective chemotherapeutic drugs. OGTs are major players in counteracting the effects of such agents, thus their action in turn affects genome integrity, survival of organisms under challenging conditions and response to chemotherapy. Numerous studies on OGTs from eukaryotes, bacteria and archaea have been reported, highlighting amazing features that make OGTs unique proteins in their reaction mechanism as well as post-reaction fate. This review reports recent functional and structural data on two prokaryotic OGTs, from the pathogenic bacterium Mycobacterium tuberculosis and the hyperthermophilic archaeon Sulfolobus solfataricus, respectively. These studies provided insight in the role of OGTs in the biology of these microorganisms, but also important hints useful to understand the general properties of this class of proteins.
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Affiliation(s)
- Riccardo Miggiano
- DSF-Dipartimento di Scienze del Farmaco, University of Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy.
| | - Anna Valenti
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy.
| | - Franca Rossi
- DSF-Dipartimento di Scienze del Farmaco, University of Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy.
| | - Menico Rizzi
- DSF-Dipartimento di Scienze del Farmaco, University of Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy.
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy.
| | - Maria Ciaramella
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy.
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