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Myers T, Dykstra CM. Teaching old dogs new tricks: genetic engineering methanogens. Appl Environ Microbiol 2024:e0224723. [PMID: 38856201 DOI: 10.1128/aem.02247-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024] Open
Abstract
Methanogenic archaea, which are integral to global carbon and nitrogen cycling, currently face challenges in genetic manipulation due to unique physiology and limited genetic tools. This review provides a survey of current and past developments in the genetic engineering of methanogens, including selection and counterselection markers, reporter systems, shuttle vectors, mutagenesis methods, markerless genetic exchange, and gene expression control. This review discusses genetic tools and emphasizes challenges tied to tool scarcity for specific methanogenic species. Mutagenesis techniques for methanogens, including physicochemical, transposon-mediated, liposome-mediated mutagenesis, and natural transformation, are outlined, along with achievements and challenges. Markerless genetic exchange strategies, such as homologous recombination and CRISPR/Cas-mediated genome editing, are also detailed. Finally, the review concludes by examining the control of gene expression in methanogens. The information presented underscores the urgent need for refined genetic tools in archaeal research. Despite historical challenges, recent advancements, notably CRISPR-based systems, hold promise for overcoming obstacles, with implications for global health, agriculture, climate change, and environmental engineering. This comprehensive review aims to bridge existing gaps in the literature, guiding future research in the expanding field of archaeal genetic engineering.
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Affiliation(s)
- Tyler Myers
- Department of Civil, Construction and Environmental Engineering, San Diego State University, San Diego, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Christy M Dykstra
- Department of Civil, Construction and Environmental Engineering, San Diego State University, San Diego, California, USA
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2
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Habenicht T, Weidenbach K, Velazquez-Campoy A, Buey RM, Balsera M, Schmitz RA. Small protein mediates inhibition of ammonium transport in Methanosarcina mazei-an ancient mechanism? Microbiol Spectr 2023; 11:e0281123. [PMID: 37909787 PMCID: PMC10714827 DOI: 10.1128/spectrum.02811-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Small proteins containing fewer than 70 amino acids, which were previously disregarded due to computational prediction and biochemical detection challenges, have gained increased attention in the scientific community in recent years. However, the number of functionally characterized small proteins, especially in archaea, is still limited. Here, by using biochemical and genetic approaches, we demonstrate a crucial role of the small protein sP36 in the nitrogen metabolism of M. mazei, which modulates the ammonium transporter AmtB1 according to nitrogen availability. This modulation might represent an ancient archaeal mechanism of AmtB1 inhibition, in contrast to the well-studied uridylylation-dependent regulation in bacteria.
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Affiliation(s)
- Tim Habenicht
- Institut für allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Katrin Weidenbach
- Institut für allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Investigaciones Sanitarias de Aragón (IIS Aragón), Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - Ruben M. Buey
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Monica Balsera
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Spanish National Research Council (IRNASA-CSIC), Salamanca, Spain
| | - Ruth A. Schmitz
- Institut für allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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3
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Gehlert FO, Weidenbach K, Barüske B, Hallack D, Repnik U, Schmitz RA. Newly Established Genetic System for Functional Analysis of MetSV. Int J Mol Sci 2023; 24:11163. [PMID: 37446343 DOI: 10.3390/ijms241311163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
The linear chromosome of the Methanosarcina spherical virus with 10,567 bp exhibits 22 ORFs with mostly unknown functions. Annotation using common tools and databases predicted functions for a few genes like the type B DNA polymerase (MetSVORF07) or the small (MetSVORF15) and major (MetSVORF16) capsid proteins. For verification of assigned functions of additional ORFs, biochemical or genetic approaches were found to be essential. Consequently, we established a genetic system for MetSV by cloning its genome into the E. coli plasmid pCR-XL-2. Comparisons of candidate plasmids with the MetSV reference based on Nanopore sequencing revealed several mutations of yet unknown provenance with an impact on protein-coding sequences. Linear MetSV inserts were generated by BamHI restriction, purified and transformed in Methanosarcina mazei by an optimized liposome-mediated transformation protocol. Analysis of resulting MetSV virions by TEM imaging and infection experiments demonstrated no significant differences between plasmid-born viruses and native MetSV particles regarding their morphology or lytic behavior. The functionality of the genetic system was tested by the generation of a ΔMetSVORF09 mutant that was still infectious. Our genetic system of MetSV, the first functional system for a virus of methanoarchaea, now allows us to obtain deeper insights into MetSV protein functions and virus-host interactions.
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Affiliation(s)
- Finn O Gehlert
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | - Katrin Weidenbach
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | - Brian Barüske
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | - Daniela Hallack
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | - Urska Repnik
- Central Microscopy, Christian Albrechts University, 24118 Kiel, Germany
| | - Ruth A Schmitz
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
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4
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Carr S, Buan NR. Insights into the biotechnology potential of Methanosarcina. Front Microbiol 2022; 13:1034674. [PMID: 36590411 PMCID: PMC9797515 DOI: 10.3389/fmicb.2022.1034674] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/28/2022] [Indexed: 12/23/2022] Open
Abstract
Methanogens are anaerobic archaea which conserve energy by producing methane. Found in nearly every anaerobic environment on earth, methanogens serve important roles in ecology as key organisms of the global carbon cycle, and in industry as a source of renewable biofuels. Environmentally, methanogenic archaea play an essential role in the reintroducing unavailable carbon to the carbon cycle by anaerobically converting low-energy, terminal metabolic degradation products such as one and two-carbon molecules into methane which then returns to the aerobic portion of the carbon cycle. In industry, methanogens are commonly used as an inexpensive source of renewable biofuels as well as serving as a vital component in the treatment of wastewater though this is only the tip of the iceberg with respect to their metabolic potential. In this review we will discuss how the efficient central metabolism of methanoarchaea could be harnessed for future biotechnology applications.
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5
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Thomsen J, Schmitz RA. Generating a Small Shuttle Vector for Effective Genetic Engineering of Methanosarcina mazei Allowed First Insights in Plasmid Replication Mechanism in the Methanoarchaeon. Int J Mol Sci 2022; 23:ijms231911910. [PMID: 36233214 PMCID: PMC9569500 DOI: 10.3390/ijms231911910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/16/2022] Open
Abstract
Due to their role in methane production, methanoarchaea are of high ecological relevance and genetic systems have been ever more established in the last two decades. The system for protein expression in Methanosarcina using a comprehensive shuttle vector is established; however, details about its replication mechanism in methanoarchaea remain unknown. Here, we report on a significant optimisation of the rather large shuttle vector pWM321 (8.9 kbp) generated by Metcalf through a decrease in its size by about 35% by means of the deletion of several non-coding regions and the ssrA gene. The resulting plasmid (pRS1595) still stably replicates in M. mazei and—most likely due to its reduced size—shows a significantly higher transformation efficiency compared to pWM321. In addition, we investigate the essential gene repA, coding for a rep type protein. RepA was heterologously expressed in Escherichia coli, purified and characterised, demonstrating the significant binding and nicking activity of supercoiled plasmid DNA. Based on our findings we propose that the optimised shuttle vector replicates via a rolling circle mechanism with RepA as the initial replication protein in Methanosarcina. On the basis of bioinformatic comparisons, we propose the presence and location of a double-strand and a single-strand origin, which need to be further verified.
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6
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Gendron A, Allen KD. Overview of Diverse Methyl/Alkyl-Coenzyme M Reductases and Considerations for Their Potential Heterologous Expression. Front Microbiol 2022; 13:867342. [PMID: 35547147 PMCID: PMC9081873 DOI: 10.3389/fmicb.2022.867342] [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: 02/01/2022] [Accepted: 04/01/2022] [Indexed: 12/02/2022] Open
Abstract
Methyl-coenzyme M reductase (MCR) is an archaeal enzyme that catalyzes the final step of methanogenesis and the first step in the anaerobic oxidation of methane, the energy metabolisms of methanogens and anaerobic methanotrophs (ANME), respectively. Variants of MCR, known as alkyl-coenzyme M reductases, are involved in the anaerobic oxidation of short-chain alkanes including ethane, propane, and butane as well as the catabolism of long-chain alkanes from oil reservoirs. MCR is a dimer of heterotrimers (encoded by mcrABG) and requires the nickel-containing tetrapyrrole prosthetic group known as coenzyme F430. MCR houses a series of unusual post-translational modifications within its active site whose identities vary depending on the organism and whose functions remain unclear. Methanogenic MCRs are encoded in a highly conserved mcrBDCGA gene cluster, which encodes two accessory proteins, McrD and McrC, that are believed to be involved in the assembly and activation of MCR, respectively. The requirement of a unique and complex coenzyme, various unusual post-translational modifications, and many remaining questions surrounding assembly and activation of MCR largely limit in vitro experiments to native enzymes with recombinant methods only recently appearing. Production of MCRs in a heterologous host is an important step toward developing optimized biocatalytic systems for methane production as well as for bioconversion of methane and other alkanes into value-added compounds. This review will first summarize MCR catalysis and structure, followed by a discussion of advances and challenges related to the production of diverse MCRs in a heterologous host.
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Affiliation(s)
- Aleksei Gendron
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Kylie D Allen
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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7
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Thomsen J, Weidenbach K, Metcalf WW, Schmitz RA. Genetic Methods and Construction of Chromosomal Mutations in Methanogenic Archaea. Methods Mol Biol 2022; 2522:105-117. [PMID: 36125745 DOI: 10.1007/978-1-0716-2445-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Genetic manipulation through markerless exchange enables the modification of several genomic regions without leaving a selection marker in the genome. Here, a method using hpt coding for hypoxanthine phosphoribosyltransferase as a counter selectable marker is described. For Methanosarcina species a chromosomal deletion of the hpt gene is firstly generated, which confers resistance to the purine analogue 8-aza-2,6-diaminopurine (8-ADP). In a second step, the reintroduction of the hpt gene on a plasmid leads to a selectable loss of 8-ADP resistance after a homologous recombination event (pop-in). A subsequent pop-out event restores the 8-ADP resistance and can generate chromosomal mutants with frequencies of about 50%.
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Affiliation(s)
- Johanna Thomsen
- Institute For General Microbiology, Christian-Albrechts-University, Kiel, Germany
| | - Katrin Weidenbach
- Institute For General Microbiology, Christian-Albrechts-University, Kiel, Germany
| | | | - Ruth A Schmitz
- Institute For General Microbiology, Christian-Albrechts-University, Kiel, Germany.
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8
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Gutt M, Jordan B, Weidenbach K, Gudzuhn M, Kiessling C, Cassidy L, Helbig A, Tholey A, Pyper DJ, Kubatova N, Schwalbe H, Schmitz RA. High complexity of Glutamine synthetase regulation in
Methanosarcina mazei
: Small protein 26 interacts and enhances glutamine synthetase activity. FEBS J 2021; 288:5350-5373. [DOI: 10.1111/febs.15799] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 01/05/2021] [Accepted: 03/02/2021] [Indexed: 12/13/2022]
Affiliation(s)
- Miriam Gutt
- Institute for General Microbiology Christian‐Albrechts‐University Kiel Germany
| | - Britta Jordan
- Institute for General Microbiology Christian‐Albrechts‐University Kiel Germany
| | - Katrin Weidenbach
- Institute for General Microbiology Christian‐Albrechts‐University Kiel Germany
| | - Mirja Gudzuhn
- Institute for General Microbiology Christian‐Albrechts‐University Kiel Germany
| | - Claudia Kiessling
- Institute for General Microbiology Christian‐Albrechts‐University Kiel Germany
| | - Liam Cassidy
- AG Proteomics & Bioanalytics Institute for Experimental Medicine Christian‐Albrechts‐University Kiel Germany
| | - Andreas Helbig
- AG Proteomics & Bioanalytics Institute for Experimental Medicine Christian‐Albrechts‐University Kiel Germany
| | - Andreas Tholey
- AG Proteomics & Bioanalytics Institute for Experimental Medicine Christian‐Albrechts‐University Kiel Germany
| | - Dennis Joshua Pyper
- Institute of Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Johann Wolfgang Goethe University Frankfurt am Main Germany
| | - Nina Kubatova
- Institute of Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Johann Wolfgang Goethe University Frankfurt am Main Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Johann Wolfgang Goethe University Frankfurt am Main Germany
| | - Ruth Anne Schmitz
- Institute for General Microbiology Christian‐Albrechts‐University Kiel Germany
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9
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The CARF Protein MM_0565 Affects Transcription of the Casposon-Encoded cas1-solo Gene in Methanosarcina mazei Gö1. Biomolecules 2020; 10:biom10081161. [PMID: 32784796 PMCID: PMC7465815 DOI: 10.3390/biom10081161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 12/25/2022] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) loci are found in bacterial and archaeal genomes where they provide the molecular machinery for acquisition of immunity against foreign DNA. In addition to the cas genes fundamentally required for CRISPR activity, a second class of genes is associated with the CRISPR loci, of which many have no reported function in CRISPR-mediated immunity. Here, we characterize MM_0565 associated to the type I-B CRISPR-locus of Methanosarcina mazei Gö1. We show that purified MM_0565 composed of a CRISPR-Cas Associated Rossmann Fold (CARF) and a winged helix-turn-helix domain forms a dimer in solution; in vivo, the dimeric MM_0565 is strongly stabilized under high salt stress. While direct effects on CRISPR-Cas transcription were not detected by genetic approaches, specific binding of MM_0565 to the leader region of both CRISPR-Cas systems was observed by microscale thermophoresis and electromobility shift assays. Moreover, overexpression of MM_0565 strongly induced transcription of the cas1-solo gene located in the recently reported casposon, the gene product of which shows high similarity to classical Cas1 proteins. Based on our findings, and taking the absence of the expressed CRISPR locus-encoded Cas1 protein into account, we hypothesize that MM_0565 might modulate the activity of the CRISPR systems on different levels.
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10
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Archaeosine Modification of Archaeal tRNA: Role in Structural Stabilization. J Bacteriol 2020; 202:JB.00748-19. [PMID: 32041795 DOI: 10.1128/jb.00748-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 01/29/2020] [Indexed: 12/20/2022] Open
Abstract
Archaeosine (G+) is a structurally complex modified nucleoside found quasi-universally in the tRNA of Archaea and located at position 15 in the dihydrouridine loop, a site not modified in any tRNA outside the Archaea G+ is characterized by an unusual 7-deazaguanosine core structure with a formamidine group at the 7-position. The location of G+ at position 15, coupled with its novel molecular structure, led to a hypothesis that G+ stabilizes tRNA tertiary structure through several distinct mechanisms. To test whether G+ contributes to tRNA stability and define the biological role of G+, we investigated the consequences of introducing targeted mutations that disrupt the biosynthesis of G+ into the genome of the hyperthermophilic archaeon Thermococcus kodakarensis and the mesophilic archaeon Methanosarcina mazei, resulting in modification of the tRNA with the G+ precursor 7-cyano-7-deazaguansine (preQ0) (deletion of arcS) or no modification at position 15 (deletion of tgtA). Assays of tRNA stability from in vitro-prepared and enzymatically modified tRNA transcripts, as well as tRNA isolated from the T. kodakarensis mutant strains, demonstrate that G+ at position 15 imparts stability to tRNAs that varies depending on the overall modification state of the tRNA and the concentration of magnesium chloride and that when absent results in profound deficiencies in the thermophily of T. kodakarensis IMPORTANCE Archaeosine is ubiquitous in archaeal tRNA, where it is located at position 15. Based on its molecular structure, it was proposed to stabilize tRNA, and we show that loss of archaeosine in Thermococcus kodakarensis results in a strong temperature-sensitive phenotype, while there is no detectable phenotype when it is lost in Methanosarcina mazei Measurements of tRNA stability show that archaeosine stabilizes the tRNA structure but that this effect is much greater when it is present in otherwise unmodified tRNA transcripts than in the context of fully modified tRNA, suggesting that it may be especially important during the early stages of tRNA processing and maturation in thermophiles. Our results demonstrate how small changes in the stability of structural RNAs can be manifested in significant biological-fitness changes.
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11
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Schwarz TS, Wäber NB, Feyh R, Weidenbach K, Schmitz RA, Marchfelder A, Hartmann RK. Homologs of aquifex aeolicus protein-only RNase P are not the major RNase P activities in the archaea haloferax volcanii and methanosarcina mazei. IUBMB Life 2019; 71:1109-1116. [PMID: 31283101 DOI: 10.1002/iub.2122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/07/2019] [Accepted: 06/09/2019] [Indexed: 01/20/2023]
Abstract
The mature 5'-ends of tRNAs are generated by RNase P in all domains of life. The ancient form of the enzyme is a ribonucleoprotein consisting of a catalytic RNA and one or more protein subunits. However, in the hyperthermophilic bacterium Aquifex aeolicus and close relatives, RNase P is a protein-only enzyme consisting of a single type of polypeptide (Aq_880, ~23 kDa). In many archaea, homologs of Aq_880 were identified (termed HARPs for Homologs of Aquifex RNase P) in addition to the RNA-based RNase P, raising the question about the functions of HARP and the classical RNase P in these archaea. Here we investigated HARPs from two euryarchaeotes, Haloferax volcanii and Methanosarcina mazei. Archaeal strains with HARP gene knockouts showed no growth phenotypes under standard conditions, temperature and salt stress (H. volcanii) or nitrogen deficiency (M. mazei). Recombinant H. volcanii and M. mazei HARPs were basically able to catalyse specific tRNA 5'-end maturation in vitro. Furthermore, M. mazei HARP was able to rescue growth of an Escherichia coli RNase P depletion strain with comparable efficiency as Aq_880, while H. volcanii HARP was unable to do so. In conclusion, both archaeal HARPs showed the capacity (in at least one functional assay) to act as RNases P. However, the ease to obtain knockouts of the singular HARP genes and the lack of growth phenotypes upon HARP gene deletion contrasts with the findings that the canonical RNase P RNA gene cannot be deleted in H. volcanii, and a knockdown of RNase P RNA in H. volcanii results in severe tRNA processing defects. We conclude that archaeal HARPs do not make a major contribution to global tRNA 5'-end maturation in archaea, but may well exert a specialised, yet unknown function in (t)RNA metabolism. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1109-1116, 2019.
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Affiliation(s)
| | - Nadine B Wäber
- Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany
| | - Rebecca Feyh
- Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany
| | - Katrin Weidenbach
- Institute of General Microbiology, Christian-Albrechts-Universität, Kiel, Germany
| | - Ruth A Schmitz
- Institute of General Microbiology, Christian-Albrechts-Universität, Kiel, Germany
| | | | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany
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12
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Nickel L, Ulbricht A, Alkhnbashi OS, Förstner KU, Cassidy L, Weidenbach K, Backofen R, Schmitz RA. Cross-cleavage activity of Cas6b in crRNA processing of two different CRISPR-Cas systems in Methanosarcina mazei Gö1. RNA Biol 2018; 16:492-503. [PMID: 30153081 DOI: 10.1080/15476286.2018.1514234] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR) system is a prokaryotic adaptive defense system against foreign nucleic acids. In the methanoarchaeon Methanosarcina mazei Gö1, two types of CRISPR-Cas systems are present (type I-B and type III-C). Both loci encode a Cas6 endonuclease, Cas6b-IB and Cas6b-IIIC, typically responsible for maturation of functional short CRISPR RNAs (crRNAs). To evaluate potential cross cleavage activity, we biochemically characterized both Cas6b proteins regarding their crRNA binding behavior and their ability to process pre-crRNA from the respective CRISPR array in vivo. Maturation of crRNA was studied in the respective single deletion mutants by northern blot and RNA-Seq analysis demonstrating that in vivo primarily Cas6b-IB is responsible for crRNA processing of both CRISPR arrays. Tentative protein level evidence for the translation of both Cas6b proteins under standard growth conditions was detected, arguing for different activities or a potential non-redundant role of Cas6b-IIIC within the cell. Conservation of both Cas6 endonucleases was observed in several other M. mazei isolates, though a wide variety was displayed. In general, repeat and leader sequence conservation revealed a close correlation in the M. mazei strains. The repeat sequences from both CRISPR arrays from M. mazei Gö1 contain the same sequence motif with differences only in two nucleotides. These data stand in contrast to all other analyzed M. mazei isolates, which have at least one additional CRISPR array with repeats belonging to another sequence motif. This conforms to the finding that Cas6b-IB is the crucial and functional endonuclease in M. mazei Gö1. Abbreviations: sRNA: small RNA; crRNA: CRISPR RNA; pre-crRNAs: Precursor CRISPR RNA; CRISPR: clustered regularly interspaced short palindromic repeats; Cas: CRISPR associated; nt: nucleotide; RNP: ribonucleoprotein; RBS: ribosome binding site.
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Affiliation(s)
- Lisa Nickel
- a Institute of General Microbiology , Christian-Albrechts-University of Kiel , Kiel , Germany
| | - Andrea Ulbricht
- a Institute of General Microbiology , Christian-Albrechts-University of Kiel , Kiel , Germany
| | - Omer S Alkhnbashi
- b Bioinformatics Group, Department of Computer Science , University of Freiburg , Freiburg , Germany
| | - Konrad U Förstner
- c Core Unit Systems Medicine , Institute of Molecular Infection Biology, University of Würzburg , Würzburg , Germany
| | - Liam Cassidy
- d Institute for Experimental Medicine , Christian-Albrechts-University of Kiel , Kiel , Germany
| | - Katrin Weidenbach
- a Institute of General Microbiology , Christian-Albrechts-University of Kiel , Kiel , Germany
| | - Rolf Backofen
- b Bioinformatics Group, Department of Computer Science , University of Freiburg , Freiburg , Germany.,e BIOSS Centre for Biological Signaling Studies , University of Freiburg , Freiburg , Germany
| | - Ruth A Schmitz
- a Institute of General Microbiology , Christian-Albrechts-University of Kiel , Kiel , Germany
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13
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Buddeweg A, Sharma K, Urlaub H, Schmitz RA. sRNA 41 affects ribosome binding sites within polycistronic mRNAs in Methanosarcina mazei Gö1. Mol Microbiol 2018; 107:595-609. [PMID: 29271512 DOI: 10.1111/mmi.13900] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 12/15/2017] [Accepted: 12/15/2017] [Indexed: 11/26/2022]
Abstract
Several noncoding RNAs potentially involved in nitrogen (N)-regulation have been detected in Methanosarcina mazei, however, targets have been identified only for one of them. Here, we report on the function of sRNA41 , highly expressed under N-sufficiency. Comprising 120 nucleotides, sRNA41 shows high sequence and structural conservation within draft genomes of numerous Methanosarcina species. In silico target prediction revealed several potential targets, including genes of two homologous operons encoding for acetyl-CoA-decarbonylase/synthase complexes (ACDS) representing highly probable target candidates. A highly conserved single stranded region of sRNA41 was predicted to mask six independent ribosome binding sites of these two polycistronic mRNAs and was verified in vitro by microscale thermophoresis. Proteome analysis of the respective sRNA41 -deletion mutant showed increased protein expression of both ACDS complexes in the absence of sRNA41 , whereas no effect on transcript levels was detected, arguing for sRNA41 -mediated post-transcriptional fine-tuning of ACDS expression. We hypothesize that the physiological advantage of downregulating sRNA41 under N-limiting conditions is the resulting increase of ACDS protein levels. This provides sufficient amounts of amino acids for nitrogenase synthesis as well as reducing equivalents and energy for N2 -fixation, thus linking the carbon and N-metabolism.
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Affiliation(s)
- Anne Buddeweg
- Christian-Albrechts-University Kiel, Institute for General Microbiology, Kiel, Germany
| | - Kundan Sharma
- Department of Clinical Chemistry, Bioanalytics Research Group, University Medical Centre, Göttingen, Germany.,Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Henning Urlaub
- Department of Clinical Chemistry, Bioanalytics Research Group, University Medical Centre, Göttingen, Germany.,Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ruth A Schmitz
- Christian-Albrechts-University Kiel, Institute for General Microbiology, Kiel, Germany
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14
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Prasse D, Förstner KU, Jäger D, Backofen R, Schmitz RA. sRNA 154 a newly identified regulator of nitrogen fixation in Methanosarcina mazei strain Gö1. RNA Biol 2017; 14:1544-1558. [PMID: 28296572 DOI: 10.1080/15476286.2017.1306170] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Trans-encoded sRNA154 is exclusively expressed under nitrogen (N)-deficiency in Methanosarcina mazei strain Gö1. The sRNA154 deletion strain showed a significant decrease in growth under N-limitation, pointing toward a regulatory role of sRNA154 in N-metabolism. Aiming to elucidate its regulatory function we characterized sRNA154 by means of biochemical and genetic approaches. 24 homologs of sRNA154 were identified in recently reported draft genomes of Methanosarcina strains, demonstrating high conservation in sequence and predicted secondary structure with two highly conserved single stranded loops. Transcriptome studies of sRNA154 deletion mutants by an RNA-seq approach uncovered nifH- and nrpA-mRNA, encoding the α-subunit of nitrogenase and the transcriptional activator of the nitrogen fixation (nif)-operon, as potential targets besides other components of the N-metabolism. Furthermore, results obtained from stability, complementation and western blot analysis, as well as in silico target predictions combined with electrophoretic mobility shift-assays, argue for a stabilizing effect of sRNA154 on the polycistronic nif-mRNA and nrpA-mRNA by binding with both loops. Further identified N-related targets were studied, which demonstrates that translation initiation of glnA2-mRNA, encoding glutamine synthetase2, appears to be affected by sRNA154 masking the ribosome binding site, whereas glnA1-mRNA appears to be stabilized by sRNA154. Overall, we propose that sRNA154 has a crucial regulatory role in N-metabolism in M. mazei by stabilizing the polycistronic mRNA encoding nitrogenase and glnA1-mRNA, as well as allowing a feed forward regulation of nif-gene expression by stabilizing nrpA-mRNA. Consequently, sRNA154 represents the first archaeal sRNA, for which a positive posttranscriptional regulation is demonstrated as well as inhibition of translation initiation.
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Affiliation(s)
- Daniela Prasse
- a Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel , Am Botanischen Garten 1-9, Kiel , Germany
| | - Konrad U Förstner
- b Zentrum für Infektionsforschung , Universität Würzburg , Josef Schneider-Str. 2/ Bau D15, Würzburg
| | - Dominik Jäger
- a Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel , Am Botanischen Garten 1-9, Kiel , Germany
| | - Rolf Backofen
- c Institut für Informatik, Albert-Ludwigs-Universität zu Freiburg , Georges-Koehler-Allee, Freiburg , Germany
| | - Ruth A Schmitz
- a Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel , Am Botanischen Garten 1-9, Kiel , Germany
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Prasse D, Thomsen J, De Santis R, Muntel J, Becher D, Schmitz RA. First description of small proteins encoded by spRNAs in Methanosarcina mazei strain Gö1. Biochimie 2015; 117:138-48. [DOI: 10.1016/j.biochi.2015.04.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 04/08/2015] [Indexed: 01/06/2023]
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Welte C, Kröninger L, Deppenmeier U. Experimental evidence of an acetate transporter protein and characterization of acetate activation in aceticlastic methanogenesis of Methanosarcina mazei. FEMS Microbiol Lett 2014; 359:147-53. [PMID: 25088360 DOI: 10.1111/1574-6968.12550] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 06/12/2014] [Accepted: 07/28/2014] [Indexed: 11/29/2022] Open
Abstract
Aceticlastic methanogens metabolize acetate to methane and carbon dioxide. The central metabolism and the electron transport chains of these organisms have already been investigated. However, no particular attention has been paid to the mechanism by which acetate enters the archaeal cell. In our study we investigated Methanosarcina mazei acetate kinase (Ack) and the acetate uptake reaction. At a concentration of 2 mM acetate, the Ack activity in cell extract of M. mazei was not limiting for the methane formation rate. Instead, the methanogenesis rate was controlled by the substrate concentration and increased 10-fold at 10 mM acetate. Subsequently, we analyzed the involvement of the putative acetate permease MM_0903 using a corresponding deletion mutant. At 2 mM acetate, only 25% of the wild-type methane formation rate was measured in the mutant. This indicated that the supply of acetate to Ack was limiting the rate of methane formation. Moreover, the mutant revealed an increased acetate kinase activity compared with the wild type. These results show for the first time that an acetate transporter is involved in aceticlastic methanogenesis and may be an important factor in the acetate threshold concentration for methanogenesis of Methanosarcina spp.
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Affiliation(s)
- Cornelia Welte
- Institute for Microbiology & Biotechnology, University of Bonn, Bonn, Germany; Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
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Weidenbach K, Ehlers C, Schmitz RA. The transcriptional activator NrpA is crucial for inducing nitrogen fixation in Methanosarcina mazei Gö1 under nitrogen-limited conditions. FEBS J 2014; 281:3507-22. [PMID: 24930989 DOI: 10.1111/febs.12876] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 06/05/2014] [Accepted: 06/11/2014] [Indexed: 11/29/2022]
Abstract
With the aim of unraveling their potential involvement in the regulation of nitrogen metabolism in Methanosarcina mazei strain Gö1, we characterized five genes that are differentially transcribed in response to changing nitrogen availability and encoding putative transcriptional regulators. Study of the respective mutant strains under nitrogen-limited conditions revealed a growth delay for M. mazei MM0444::pac and MM1708::pac, and strongly reduced diazotrophic growth for MM0872::pac, whereas the absence of MM2441 or MM2525 did not affect growth behaviour. Transcriptome analyses further demonstrated that only MM1708 - encoding a CxxCG zinc finger protein - plays a regulatory role in nitrogen metabolism, most likely by specifically enhancing transcription of the N2 fixation (nif) operon under nitrogen-limited conditions. In agreement with this, a palindromic binding motif was predicted in silico in the nifH promoter region, nine nucleotides upstream of the BRE box, and confirmed to bind purified maltose-binding protein-MM1708 by electromobility shift assays. As MM1708 itself is under the control of the global nitrogen repressor NrpR, this adds a secondary level to the transcriptional regulation of the nif genes, and is most likely crucial for maximal nif induction under nitrogen-limited conditions. This is in accordance with the finding that protein expression of NifH is highly reduced in the absence of MM1708 under nitrogen-limited conditions. On the basis of our findings, we hypothesize that, in M. mazei, nitrogen fixation is controlled by a hierarchical network of two transcriptional regulators, the global nitrogen repressor NrpR, and the newly identified activator NrpA (MM1708), thereby providing tight control of N2 fixation.
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Babski J, Maier LK, Heyer R, Jaschinski K, Prasse D, Jäger D, Randau L, Schmitz RA, Marchfelder A, Soppa J. Small regulatory RNAs in Archaea. RNA Biol 2014; 11:484-93. [PMID: 24755959 PMCID: PMC4152357 DOI: 10.4161/rna.28452] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Small regulatory RNAs (sRNAs) are universally distributed in all three domains of life, Archaea, Bacteria, and Eukaryotes. In bacteria, sRNAs typically function by binding near the translation start site of their target mRNAs and thereby inhibit or activate translation. In eukaryotes, miRNAs and siRNAs typically bind to the 3′-untranslated region (3′-UTR) of their target mRNAs and influence translation efficiency and/or mRNA stability. In archaea, sRNAs have been identified in all species investigated using bioinformatic approaches, RNomics, and RNA-Seq. Their size can vary significantly between less than 50 to more than 500 nucleotides. Differential expression of sRNA genes has been studied using northern blot analysis, microarrays, and RNA-Seq. In addition, biological functions have been unraveled by genetic approaches, i.e., by characterization of designed mutants. As in bacteria, it was revealed that archaeal sRNAs are involved in many biological processes, including metabolic regulation, adaptation to extreme conditions, stress responses, and even in regulation of morphology and cellular behavior. Recently, the first target mRNAs were identified in archaea, including one sRNA that binds to the 5′-region of two mRNAs in Methanosarcina mazei Gö1 and a few sRNAs that bind to 3′-UTRs in Sulfolobus solfataricus, three Pyrobaculum species, and Haloferax volcanii, indicating that archaeal sRNAs appear to be able to target both the 5′-UTR or the 3′-UTRs of their respective target mRNAs. In addition, archaea contain tRNA-derived fragments (tRFs), and one tRF has been identified as a major ribosome-binding sRNA in H. volcanii, which downregulates translation in response to stress. Besides regulatory sRNAs, archaea contain further classes of sRNAs, e.g., CRISPR RNAs (crRNAs) and snoRNAs.
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Affiliation(s)
- Julia Babski
- Institute for Molecular Biosciences; Biocentre; Goethe University; Frankfurt, Germany
| | | | - Ruth Heyer
- Biology II; Ulm University; Ulm, Germany
| | - Katharina Jaschinski
- Institute for Molecular Biosciences; Biocentre; Goethe University; Frankfurt, Germany
| | - Daniela Prasse
- Institute for Microbiology; Christian-Albrechts-University; Kiel, Germany
| | - Dominik Jäger
- Institute for Microbiology; Christian-Albrechts-University; Kiel, Germany
| | - Lennart Randau
- Prokaryotic Small RNA Biology Group; Max Planck Institute for Terrestrial Microbiology; Marburg, Germany
| | - Ruth A Schmitz
- Institute for Microbiology; Christian-Albrechts-University; Kiel, Germany
| | | | - Jörg Soppa
- Institute for Molecular Biosciences; Biocentre; Goethe University; Frankfurt, Germany
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Nickel L, Weidenbach K, Jäger D, Backofen R, Lange SJ, Heidrich N, Schmitz RA. Two CRISPR-Cas systems in Methanosarcina mazei strain Gö1 display common processing features despite belonging to different types I and III. RNA Biol 2013; 10:779-91. [PMID: 23619576 DOI: 10.4161/rna.23928] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) system represents a highly adaptive and heritable defense system against foreign nucleic acids in bacteria and archaea. We analyzed the two CRISPR-Cas systems in Methanosarcina mazei strain Gö1. Although belonging to different subtypes (I-B and III-B), the leaders and repeats of both loci are nearly identical. Also, despite many point mutations in each array, a common hairpin motif was identified in the repeats by a bioinformatics analysis and in vitro structural probing. The expression and maturation of CRISPR-derived RNAs (crRNAs) were studied in vitro and in vivo. Both respective potential Cas6b-type endonucleases were purified and their activity tested in vitro. Each protein showed significant activity and could cleave both repeats at the same processing site. Cas6b of subtype III-B, however, was significantly more efficient in its cleavage activity compared with Cas6b of subtype I-B. Northern blot and differential RNAseq analyses were performed to investigate in vivo transcription and maturation of crRNAs, revealing generally very low expression of both systems, whereas significant induction at high NaCl concentrations was observed. crRNAs derived proximal to the leader were generally more abundant than distal ones and in vivo processing sites were clarified for both loci, confirming the previously well-established 8 nt 5' repeat tags. The 3'-ends were more diverse, but generally ended in a prefix of the following repeat sequence (3'-tag). The analysis further revealed a 5'-hydroxy and 3'-phosphate termini architecture of small crRNAs specific for cleavage products of Cas6 endonucleases from type I-E and I-F and type III-B.
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Affiliation(s)
- Lisa Nickel
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, Kiel, Germany
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Atomi H, Imanaka T, Fukui T. Overview of the genetic tools in the Archaea. Front Microbiol 2012; 3:337. [PMID: 23060865 PMCID: PMC3462420 DOI: 10.3389/fmicb.2012.00337] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Accepted: 09/01/2012] [Indexed: 01/17/2023] Open
Abstract
This section provides an overview of the genetic systems developed in the Archaea. Genetic manipulation is possible in many members of the halophiles, methanogens, Sulfolobus, and Thermococcales. We describe the selection/counterselection principles utilized in each of these groups, which consist of antibiotics and their resistance markers, and auxotrophic host strains and complementary markers. The latter strategy utilizes techniques similar to those developed in yeast. However, Archaea are resistant to many of the antibiotics routinely used for selection in the Bacteria, and a number of strategies specific to the Archaea have been developed. In addition, examples utilizing the genetic systems developed for each group will be briefly described.
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Affiliation(s)
- Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku Kyoto, Japan ; JST, CREST, Sanbancho, Chiyoda-ku Tokyo, Japan
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Jäger D, Pernitzsch SR, Richter AS, Backofen R, Sharma CM, Schmitz RA. An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains. Nucleic Acids Res 2012; 40:10964-79. [PMID: 22965121 PMCID: PMC3510493 DOI: 10.1093/nar/gks847] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We report on the characterization and target analysis of the small (s)RNA162 in the methanoarchaeon Methanosarcina mazei. Using a combination of genetic approaches, transcriptome analysis and computational predictions, the bicistronic MM2441-MM2440 mRNA encoding the transcription factor MM2441 and a protein of unknown function was identified as a potential target of this sRNA, which due to processing accumulates as three stabile 5′ fragments in late exponential growth. Mobility shift assays using various mutants verified that the non-structured single-stranded linker region of sRNA162 (SLR) base-pairs with the MM2440-MM2441 mRNA internally, thereby masking the predicted ribosome binding site of MM2441. This most likely leads to translational repression of the second cistron resulting in dis-coordinated operon expression. Analysis of mutant RNAs in vivo confirmed that the SLR of sRNA162 is crucial for target interactions. Furthermore, our results indicate that sRNA162-controlled MM2441 is involved in regulating the metabolic switch between the carbon sources methanol and methylamine. Moreover, biochemical studies demonstrated that the 5′ end of sRNA162 targets the 5′-untranslated region of the cis-encoded MM2442 mRNA. Overall, this first study of archaeal sRNA/mRNA-target interactions unraveled that sRNA162 acts as an antisense (as)RNA on cis- and trans-encoded mRNAs via two distinct domains, indicating that cis-encoded asRNAs can have larger target regulons than previously anticipated.
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Affiliation(s)
- Dominik Jäger
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany
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Kohler PRA, Metcalf WW. Genetic manipulation of Methanosarcina spp. Front Microbiol 2012; 3:259. [PMID: 22837755 PMCID: PMC3403347 DOI: 10.3389/fmicb.2012.00259] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 07/03/2012] [Indexed: 11/13/2022] Open
Abstract
The discovery of the third domain of life, the Archaea, is one of the most exciting findings of the last century. These remarkable prokaryotes are well known for their adaptations to extreme environments; however, Archaea have also conquered moderate environments. Many of the archaeal biochemical processes, such as methane production, are unique in nature and therefore of great scientific interest. Although formerly restricted to biochemical and physiological studies, sophisticated systems for genetic manipulation have been developed during the last two decades for methanogenic archaea, halophilic archaea and thermophilic, sulfur-metabolizing archaea. The availability of these tools has allowed for more complete studies of archaeal physiology and metabolism and most importantly provides the basis for the investigation of gene expression, regulation and function. In this review we provide an overview of methods for genetic manipulation of Methanosarcina spp., a group of methanogenic archaea that are key players in the global carbon cycle and which can be found in a variety of anaerobic environments.
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Affiliation(s)
- Petra R A Kohler
- Department of Microbiology, B103 Chemical and Life Science Laboratory, University of Illinois at Urbana-Champaign Urbana, IL, USA
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A novel inducible protein production system and neomycin resistance as selection marker for Methanosarcina mazei. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2012; 2012:973743. [PMID: 22851906 PMCID: PMC3407599 DOI: 10.1155/2012/973743] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 06/26/2012] [Indexed: 11/17/2022]
Abstract
Methanosarcina mazei is one of the model organisms for the methanogenic order Methanosarcinales whose metabolism has been studied in detail. However, the genetic toolbox is still limited. This study was aimed at widening the scope of utilizable methods in this group of organisms. (i) Proteins specific to methanogens are oftentimes difficult to produce in E. coli. However, a protein production system is not available for methanogens. Here we present an inducible system to produce Strep-tagged proteins in Ms. mazei. The promoter p1687, which directs the transcription of methyl transferases that demethylate methylamines, was cloned into plasmid pWM321 and its activity was determined by monitoring β-glucuronidase production. The promoter was inactive during growth on methanol but was rapidly activated when trimethylamine was added to the medium. The gene encoding the β-glucuronidase from E. coli was fused to a Strep-tag and was cloned downstream of the p1687 promoter. The protein was overproduced in Ms. mazei and was purified in an active form by affinity chromatography. (ii) Puromycin is currently the only antibiotic used as a selectable marker in Ms. mazei and its relatives. We established neomycin resistance as a second selectable marker by designing a plasmid that confers neomycin resistance in Ms. mazei.
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Establishing a markerless genetic exchange system for Methanosarcina mazei strain Gö1 for constructing chromosomal mutants of small RNA genes. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2011; 2011:439608. [PMID: 21941461 PMCID: PMC3177094 DOI: 10.1155/2011/439608] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 07/04/2011] [Accepted: 07/07/2011] [Indexed: 11/17/2022]
Abstract
A markerless genetic exchange system was successfully established in Methanosarcina mazei strain Gö1 using the hpt gene coding for hypoxanthine phosphoribosyltransferase. First, a chromosomal deletion mutant of the hpt gene was generated conferring resistance to the purine analog 8-aza-2,6-diaminopurine (8-ADP). The nonreplicating allelic exchange vector (pRS345) carrying the pac-resistance cassette for direct selection of chromosomal integration, and the hpt gene for counterselection was introduced into this strain. By a pop-in and ultimately pop-out event of the plasmid from the chromosome, allelic exchange is enabled. Using this system, we successfully generated a M. mazei deletion mutant of the gene encoding the regulatory non-coding RNA sRNA154. Characterizing M. mazeiΔsRNA154 under nitrogen limiting conditions demonstrated differential expression of at least three cytoplasmic proteins and reduced growth strongly arguing for a prominent role of sRNA154 in regulation of nitrogen fixation by posttranscriptional regulation.
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Welte C, Deppenmeier U. Re-evaluation of the function of the F420 dehydrogenase in electron transport of Methanosarcina mazei. FEBS J 2011; 278:1277-87. [DOI: 10.1111/j.1742-4658.2011.08048.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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In vitro proof of direct regulation of glutamine synthetase by GlnK proteins in the extreme halophilic archaeon Haloferax mediterranei. Biochem Soc Trans 2011; 39:259-62. [DOI: 10.1042/bst0390259] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Haloferax mediterranei is an extreme halophilic micro-organism belonging to the Archaea domain that was isolated from the Santa Pola solar salterns (Alicante, Spain) in 1983. The biochemistry of the proteins involved in nitrogen metabolism is being studied, but the knowledge of their regulation is very scarce at present. The PII superfamily is constituted by major regulators of nitrogen metabolism, which are widespread in prokaryotic and eukaryotic organisms. These trimeric proteins (12 kDa per subunit) have in Escherichia coli long been known to regulate GS (glutamine synthetase) activity via its adenylyltransferase/adenylyl-removing enzyme and, more recently, to be able to interact directly with this enzyme in methanogenic archaea. We have tested the possible role of PII proteins in the regulation of ammonium assimilation in our model organism and the results clearly indicate that the direct influence of GS by PII proteins can also take place in halophilic archaea, starting with the comprehension of nitrogen regulation in those organisms.
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Saum R, Mingote A, Santos H, Müller V. A novel limb in the osmoregulatory network of Methanosarcina mazei Gö1: N(epsilon)-acetyl-beta-lysine can be substituted by glutamate and alanine. Environ Microbiol 2009; 11:1056-65. [PMID: 19452593 DOI: 10.1111/j.1462-2920.2008.01826.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
N(epsilon)-acetyl-beta-lysine is a unique compatible solute found in methanogenic archaea grown at high salinities. Deletion of the genes that encode the lysine-2,3-aminomutase (ablA) and the beta-lysine acetyltransferase (ablB) abolished the production of N(epsilon)-acetyl-beta-lysine in Methanosarcina mazei Gö1. The mutant grew well at low and intermediate salinities. Interestingly, growth at high salt (800 mM NaCl) was only slowed down but not impaired demonstrating that in M. mazei Gö1 N(epsilon)-acetyl-beta-lysine is not essential for growth at high salinities. Nuclear magnetic resonance (NMR) analysis revealed an increased glutamate pool in the mutant. In addition to alpha-glutamate, a novel solute, alanine, was produced. The intracellular alanine concentration was as high as 0.36 +/- 0.05 micromol (mg protein)-1 representing up to 18% of the total solute pool at 800 mM NaCl. The cellular alanine concentration increased with the salinity of the medium and decreased in the presence of glycine betaine in the medium, indicating that alanine is used as compatible solute by M. mazei Gö1.
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Affiliation(s)
- Regina Saum
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt, Frankfurt am Main, Germany
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Saum R, Mingote A, Santos H, Müller V. Genetic analysis of the role of the ABC transporter Ota and Otb in glycine betaine transport in Methanosarcina mazei Gö1. Arch Microbiol 2008; 191:291-301. [DOI: 10.1007/s00203-008-0449-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Revised: 11/13/2008] [Accepted: 11/21/2008] [Indexed: 01/16/2023]
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Hauenstein SI, Perona JJ. Redundant synthesis of cysteinyl-tRNACys in Methanosarcina mazei. J Biol Chem 2008; 283:22007-17. [PMID: 18559341 PMCID: PMC2494925 DOI: 10.1074/jbc.m801839200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Revised: 05/19/2008] [Indexed: 11/06/2022] Open
Abstract
A subset of methanogenic archaea synthesize the cysteinyl-tRNA(Cys) (Cys-tRNA(Cys)) needed for protein synthesis using both a canonical cysteinyl-tRNA synthetase (CysRS) as well as a set of two enzymes that operate via a separate indirect pathway. In the indirect route, phosphoseryl-tRNA(Cys) (Sep-tRNA(Cys)) is first synthesized by phosphoseryl-tRNA synthetase (SepRS), and this misacylated intermediate is then converted to Cys-tRNA(Cys) by Sep-tRNA:Cys-tRNA synthase (SepCysS) via a pyridoxal phosphate-dependent mechanism. Here, we explore the function of all three enzymes in the mesophilic methanogen Methanosarcina mazei. The genome of M. mazei also features three distinct tRNA(Cys) isoacceptors, further indicating the unusual and complex nature of Cys-tRNA(Cys) synthesis in this organism. Comparative aminoacylation kinetics by M. mazei CysRS and SepRS reveals that each enzyme prefers a distinct tRNA(Cys) isoacceptor or pair of isoacceptors. Recognition determinants distinguishing the tRNAs are shown to reside in the globular core of the molecule. Both enzymes also require the S-adenosylmethione-dependent formation of (m1)G37 in the anticodon loop for efficient aminoacylation. We further report a new, highly sensitive assay to measure the activity of SepCysS under anaerobic conditions. With this approach, we demonstrate that SepCysS functions as a multiple-turnover catalyst with kinetic behavior similar to bacterial selenocysteine synthase and the archaeal/eukaryotic SepSecS enzyme. Together, these data suggest that both metabolic routes and all three tRNA(Cys) species in M. mazei play important roles in the cellular physiology of the organism.
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Affiliation(s)
- Scott I Hauenstein
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, USA
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Hauenstein SI, Hou YM, Perona JJ. The homotetrameric phosphoseryl-tRNA synthetase from Methanosarcina mazei exhibits half-of-the-sites activity. J Biol Chem 2008; 283:21997-2006. [PMID: 18559342 DOI: 10.1074/jbc.m801838200] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Synthesis of cysteinyl-tRNA(Cys) in methanogenic archaea proceeds by a two-step pathway in which tRNA(Cys) is first aminoacylated with phosphoserine by phosphoseryl-tRNA synthetase (SepRS). Characterization of SepRS from the mesophile Methanosarcina mazei by gel filtration and nondenaturing mass spectrometry shows that the native enzyme exists as an alpha4 tetramer when expressed at high levels in Escherichia coli. However, active site titrations monitored by ATP/PP(i) burst kinetics, together with analysis of tRNA binding stoichiometry by fluorescence spectroscopy, show that the tetrameric enzyme binds two tRNAs and that only two of the four chemically equivalent subunits catalyze formation of phosphoseryl adenylate. Therefore, the phenomenon of half-of-the-sites activity, previously described for synthesis of 1 mol of tyrosyl adenylate by the dimeric class I tyrosyl-tRNA synthetase, operates as well in this homotetrameric class II tRNA synthetase. Analysis of cognate and noncognate reactions by ATP/PP(i) and aminoacylation kinetics strongly suggests that SepRS is able to discriminate against the noncognate amino acids glutamate, serine, and phosphothreonine without the need for a separate hydrolytic editing site. tRNA(Cys) binding to SepRS also enhances the capacity of the enzyme to discriminate among amino acids, indicating the existence of functional connectivity between the tRNA and amino acid binding sites of the enzyme.
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Affiliation(s)
- Scott I Hauenstein
- Department of Chemistry and Biochemistry and Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, California 93106-9510, USA
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Insights into the NrpR regulon in Methanosarcina mazei Gö1. Arch Microbiol 2008; 190:319-32. [DOI: 10.1007/s00203-008-0369-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Revised: 03/20/2008] [Accepted: 03/25/2008] [Indexed: 10/22/2022]
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The molecular basis of salt adaptation in Methanosarcina mazei Gö1. Arch Microbiol 2008; 190:271-9. [PMID: 18379758 DOI: 10.1007/s00203-008-0363-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Revised: 03/04/2008] [Accepted: 03/06/2008] [Indexed: 12/18/2022]
Abstract
The study on the molecular basis of salt adaptation and its regulation in archaea is still in its infancy, but genomics and functional genome analyses combined with classical biochemistry shed light on the processes conferring salt adaptation in the methanogenic archaeon Methanosarcina mazei Gö1. In this article, we will review discoveries made within the last years that will culminate in the description of the overall cellular response of M. mazei Gö1 to elevated salinities. This response includes accumulation of solutes and export of Na+ as well as potential uptake/export of K+ but also a restructuring of the cell surface.
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Weidenbach K, Glöer J, Ehlers C, Sandman K, Reeve JN, Schmitz RA. Deletion of the archaeal histone in Methanosarcina mazei Gö1 results in reduced growth and genomic transcription. Mol Microbiol 2007; 67:662-71. [PMID: 18086209 DOI: 10.1111/j.1365-2958.2007.06076.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
HMm is the only archaeal histone in Methanosarcina mazei Göl and recombinant HMm, synthesized by expression of MM1825 in Escherichia coli, has been purified and confirmed to have the DNA binding and compaction properties characteristic of an archaeal histone. Insertion of a puromycin resistance conferring cassette (pac) into MM1825 was not lethal but resulted in mutants (M. mazei MM1825::pac) that have impaired ability to grow on methanol and trimethylamine. Loss of HMm also resulted in increased sensitivity to UV light and decreased transcript levels for approximately 25% of all M. mazei genes. For most genes, the transcript decrease was 3- to 10-fold, but transcripts of MM483 (small heat-shock protein), MM1688 (trimethylamine:corrinoid methyl transferase) and MM3195 (transcription regulator), were reduced 100-, 100- and 25-fold, respectively, in M. mazei MM1825::pac cells. Transcripts of only five adjacent genes that appear to constitute an aromatic amino acid biosynthetic operon were elevated in M. mazei MM1825::pac cells. Complementary synthesis of HMm from a plasmid transformed into M. mazei MM1825::pac restored wild-type growth and transcript levels.
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Affiliation(s)
- Katrin Weidenbach
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts Universität zu Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany
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Essential and non-essential DNA replication genes in the model halophilic Archaeon, Halobacterium sp. NRC-1. BMC Genet 2007; 8:31. [PMID: 17559652 PMCID: PMC1906834 DOI: 10.1186/1471-2156-8-31] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Accepted: 06/08/2007] [Indexed: 11/22/2022] Open
Abstract
Background Information transfer systems in Archaea, including many components of the DNA replication machinery, are similar to those found in eukaryotes. Functional assignments of archaeal DNA replication genes have been primarily based upon sequence homology and biochemical studies of replisome components, but few genetic studies have been conducted thus far. We have developed a tractable genetic system for knockout analysis of genes in the model halophilic archaeon, Halobacterium sp. NRC-1, and used it to determine which DNA replication genes are essential. Results Using a directed in-frame gene knockout method in Halobacterium sp. NRC-1, we examined nineteen genes predicted to be involved in DNA replication. Preliminary bioinformatic analysis of the large haloarchaeal Orc/Cdc6 family, related to eukaryotic Orc1 and Cdc6, showed five distinct clades of Orc/Cdc6 proteins conserved in all sequenced haloarchaea. Of ten orc/cdc6 genes in Halobacterium sp. NRC-1, only two were found to be essential, orc10, on the large chromosome, and orc2, on the minichromosome, pNRC200. Of the three replicative-type DNA polymerase genes, two were essential: the chromosomally encoded B family, polB1, and the chromosomally encoded euryarchaeal-specific D family, polD1/D2 (formerly called polA1/polA2 in the Halobacterium sp. NRC-1 genome sequence). The pNRC200-encoded B family polymerase, polB2, was non-essential. Accessory genes for DNA replication initiation and elongation factors, including the putative replicative helicase, mcm, the eukaryotic-type DNA primase, pri1/pri2, the DNA polymerase sliding clamp, pcn, and the flap endonuclease, rad2, were all essential. Targeted genes were classified as non-essential if knockouts were obtained and essential based on statistical analysis and/or by demonstrating the inability to isolate chromosomal knockouts except in the presence of a complementing plasmid copy of the gene. Conclusion The results showed that ten out of nineteen eukaryotic-type DNA replication genes are essential for Halobacterium sp. NRC-1, consistent with their requirement for DNA replication. The essential genes code for two of ten Orc/Cdc6 proteins, two out of three DNA polymerases, the MCM helicase, two DNA primase subunits, the DNA polymerase sliding clamp, and the flap endonuclease.
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Veit K, Ehlers C, Ehrenreich A, Salmon K, Hovey R, Gunsalus RP, Deppenmeier U, Schmitz RA. Global transcriptional analysis of Methanosarcina mazei strain Gö1 under different nitrogen availabilities. Mol Genet Genomics 2006; 276:41-55. [PMID: 16625354 DOI: 10.1007/s00438-006-0117-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2005] [Accepted: 02/27/2006] [Indexed: 10/24/2022]
Abstract
Certain archaeal species can fix molecular nitrogen under nitrogen limiting conditions although little is known about this process at either the genetic or molecular level. To address this on a genome-wide scale, transcriptional analysis was performed on the model methanogen Methanosarcina mazei strain Gö1 using DNA-microarrays. The genomic expression patterns for cells grown under nitrogen fixing conditions versus nitrogen sufficiency (10 mM ammonium) revealed that approximately 5% of all genes are differentially expressed. Besides a small set of genes previously known to be up-regulated under nitrogen limitation, 14 additional genes involved in nitrogen metabolism were identified plus 10 genes encoding potential transcriptional regulators, 13 genes involved in carbon metabolism, 3 genes in general stress response, 8 putative transporter genes, and an additional 21 genes with unknown function. Quantitative reverse transcriptase PCR experiments confirmed the differential expression of a subset of these genes. Promoter analysis revealed a palindromic DNA motif centered nearby the transcriptional start point for several genes up-regulated under nitrogen limitation. A bioinformatics study demonstrated the presence of this motif in the up-stream region of 52 genes genome-wide, the majority of which showed nitrogen dependent differential transcription. We therefore hypothesize that this DNA element is involved in nitrogen control in M. mazei where it may act as a binding site for a regulatory protein.
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Affiliation(s)
- Katharina Veit
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany
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Rother M, Metcalf WW. Genetic technologies for Archaea. Curr Opin Microbiol 2005; 8:745-51. [PMID: 16257573 DOI: 10.1016/j.mib.2005.10.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2005] [Accepted: 10/12/2005] [Indexed: 11/25/2022]
Abstract
Members of the third domain of life, the Archaea, possess structural, physiological, biochemical and genetic features distinct from Bacteria and Eukarya and, therefore, have drawn considerable scientific interest. Physiological, biochemical and molecular analyses have revealed many novel biological processes in these important prokaryotes. However, assessment of the function of genes in vivo through genetic analysis has lagged behind because suitable systems for the creation of mutants in most Archaea were established only in the past decade. Among the Archaea, sufficiently sophisticated genetic systems now exist for some thermophilic sulfur-metabolizing Archaea, halophilic Archaea and methanogenic Archaea. Recently, there have been developments in genetic analysis of thermophilic and methanogenic Archaea and in the use of genetics to study the physiology, metabolism and regulatory mechanisms that direct gene expression in response to changes of environmental conditions in these important microorganisms.
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Affiliation(s)
- Michael Rother
- Institut für Mikrobiologie, Johann Wolfgang Goethe-Universität, Marie-Curie-Strasse 9, D-60439 Frankfurt (Main), Germany
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