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Myers T, Dykstra CM. Teaching old dogs new tricks: genetic engineering methanogens. Appl Environ Microbiol 2024; 90:e0224723. [PMID: 38856201 PMCID: PMC11267900 DOI: 10.1128/aem.02247-23] [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: 06/11/2024] 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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Funkner K, Poehlein A, Jehmlich N, Egelkamp R, Daniel R, von Bergen M, Rother M. Proteomic and transcriptomic analysis of selenium utilization in Methanococcus maripaludis. mSystems 2024; 9:e0133823. [PMID: 38591896 PMCID: PMC11097638 DOI: 10.1128/msystems.01338-23] [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: 12/11/2023] [Accepted: 03/14/2024] [Indexed: 04/10/2024] Open
Abstract
Methanococcus maripaludis utilizes selenocysteine- (Sec-) containing proteins (selenoproteins), mostly active in the organism's primary energy metabolism, methanogenesis. During selenium depletion, M. maripaludis employs a set of enzymes containing cysteine (Cys) instead of Sec. The genes coding for these Sec-/Cys-containing isoforms were the only genes known of which expression is influenced by the selenium status of the cell. Using proteomics and transcriptomics, approx. 7% and 12%, respectively, of all genes/proteins were found differentially expressed/synthesized in response to the selenium supply. Some of the genes identified involve methanogenesis, nitrogenase functions, and putative transporters. An increase of transcript abundance for putative transporters under selenium depletion indicated the organism's effort to tap into alternative sources of selenium. M. maripaludis is known to utilize selenite and dimethylselenide as selenium sources. To expand this list, a selenium-responsive reporter strain was assessed with nine other, environmentally relevant selenium species. While the effect of some was very similar to that of selenite, others were effectively utilized at lower concentrations. Conversely, selenate and seleno-amino acids were only utilized at unphysiologically high concentrations and two compounds were not utilized at all. To address the role of the selenium-regulated putative transporters, M. maripaludis mutant strains lacking one or two of the putative transporters were tested for the capability to utilize the different selenium species. Of the five putative transporters analyzed by loss-of-function mutagenesis, none appeared to be absolutely required for utilizing any of the selenium species tested, indicating they have redundant and/or overlapping specificities or are not dedicated selenium transporters. IMPORTANCE While selenium metabolism in microorganisms has been studied intensively in the past, global gene expression approaches have not been employed so far. Furthermore, the use of different selenium sources, widely environmentally interconvertible via biotic and abiotic processes, was also not extensively studied before. Methanococcus maripaludis JJ is ideally suited for such analyses, thanks to its known selenium usage and available genetic tools. Thus, an overall view on the selenium regulon of M. maripaludis was obtained via transcriptomic and proteomic analyses, which inspired further experimentation. This led to demonstrating the use of selenium sources M. maripaludis was previously not known to employ. Also, an attempt-although so far unsuccessful-was made to pinpoint potential selenium transporter genes, in order to deepen our understanding of trace element utilization in this important model organism.
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Affiliation(s)
- Katrina Funkner
- Faculty of Biology, Technische Universität Dresden, Dresden, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH–UFZ, Leipzig, Germany
| | - Richard Egelkamp
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH–UFZ, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Leipzig, Germany
| | - Michael Rother
- Faculty of Biology, Technische Universität Dresden, Dresden, Germany
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3
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Abstract
Methanogenic archaea are the only organisms that produce CH4 as part of their energy-generating metabolism. They are ubiquitous in oxidant-depleted, anoxic environments such as aquatic sediments, anaerobic digesters, inundated agricultural fields, the rumen of cattle, and the hindgut of termites, where they catalyze the terminal reactions in the degradation of organic matter. Methanogenesis is the only metabolism that is restricted to members of the domain Archaea. Here, we discuss the importance of model organisms in the history of methanogen research, including their role in the discovery of the archaea and in the biochemical and genetic characterization of methanogenesis. We also discuss outstanding questions in the field and newly emerging model systems that will expand our understanding of this uniquely archaeal metabolism.
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Affiliation(s)
- Kyle C. Costa
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
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4
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Application of the Fluorescence-Activating and Absorption-Shifting Tag (FAST) for Flow Cytometry in Methanogenic Archaea. Appl Environ Microbiol 2023; 89:e0178622. [PMID: 36920214 PMCID: PMC10132111 DOI: 10.1128/aem.01786-22] [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: 03/16/2023] Open
Abstract
Methane-producing archaea play a crucial role in the global carbon cycle and are used for biotechnological fuel production. Methanogenic model organisms such as Methanococcus maripaludis and Methanosarcina acetivorans have been biochemically characterized and can be genetically engineered by using a variety of existing molecular tools. The anaerobic lifestyle and autofluorescence of methanogens, however, restrict the use of common fluorescent reporter proteins (e.g., GFP and derivatives), which require oxygen for chromophore maturation. Recently, the use of a novel oxygen-independent fluorescent activation and absorption-shifting tag (FAST) was demonstrated with M. maripaludis. Similarly, we now describe the use of the tandem activation and absorption-shifting tag protein 2 (tdFAST2), which fluoresces when the cell-permeable fluorescent ligand (fluorogen) 4-hydroxy-3,5-dimethoxybenzylidene rhodanine (HBR-3,5DOM) is present. Expression of tdFAST2 in M. acetivorans and M. maripaludis is noncytotoxic and tdFAST2:HBR-3,5DOM fluorescence is clearly distinguishable from the autofluorescence. In flow cytometry experiments, mixed methanogen cultures can be distinguished, thereby allowing for the possibility of high-throughput investigations of the characteristic dynamics within single and mixed cultures. IMPORTANCE Methane-producing archaea play an essential role in the global carbon cycle and demonstrate great potential for various biotechnological applications, e.g., biofuel production, carbon dioxide capture, and electrochemical systems. Oxygen sensitivity and high autofluorescence hinder the use of common fluorescent proteins for studying methanogens. By using tdFAST2:HBR-3,5DOM fluorescence, which functions under anaerobic conditions and is distinguishable from the autofluorescence, real-time reporter studies and high-throughput investigation of the mixed culture dynamics of methanogens via flow cytometry were made possible. This will further help accelerate the sustainable exploitation of methanogens.
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Kelvin D, Suess B. Tapping the potential of synthetic riboswitches: reviewing the versatility of the tetracycline aptamer. RNA Biol 2023; 20:457-468. [PMID: 37459466 DOI: 10.1080/15476286.2023.2234732] [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] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 07/20/2023] Open
Abstract
Synthetic riboswitches are a versatile class of regulatory elements that are becoming increasingly established in synthetic biology applications. They are characterized by their compact size and independence from auxiliary protein factors. While naturally occurring riboswitches were mostly discovered in bacteria, synthetic riboswitches have been designed for all domains of life. Published design strategies far exceed the number of riboswitches found in nature. A core element of any riboswitch is a binding domain, called an aptamer, which is characterized by high specificity and affinity for its ligand. Aptamers can be selected de novo, allowing the design of synthetic riboswitches against a broad spectrum of targets. The tetracycline aptamer has proven to be well suited for riboswitch engineering. Since its selection, it has been used in a variety of applications and is considered to be well established and characterized. Using the tetracycline aptamer as an example, we aim to discuss a large variety of design approaches for synthetic riboswitch engineering and their application. We aim to demonstrate the versatility of riboswitches in general and the high potential of synthetic RNA devices for creating new solutions in both the scientific and medical fields.
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Affiliation(s)
- Daniel Kelvin
- Fachbereich Biologie, TU Darmstadt, Darmstadt, Germany
| | - Beatrix Suess
- Fachbereich Biologie, TU Darmstadt, Darmstadt, Germany
- Centre for Synthetic Biology, TU Darmstadt, Darmstadt, Germany
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6
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Contreras G, Thomsen J, Pfitzer M, Hafenbradl D, Kostner D, Holtmann D, Schmitz R, Rother M, Molitor B. New perspectives for biotechnological applications of methanogens. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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Finke M, Brecht D, Stifel J, Gense K, Gamerdinger M, Hartig JS. Efficient splicing-based RNA regulators for tetracycline-inducible gene expression in human cell culture and C. elegans. Nucleic Acids Res 2021; 49:e71. [PMID: 33893804 PMCID: PMC8266659 DOI: 10.1093/nar/gkab233] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/17/2021] [Accepted: 04/23/2021] [Indexed: 01/07/2023] Open
Abstract
Synthetic riboswitches gain increasing interest for controlling transgene expression in diverse applications ranging from synthetic biology, functional genomics, and pharmaceutical target validation to potential therapeutic approaches. However, existing systems often lack the pharmaceutically suited ligands and dynamic responses needed for advanced applications. Here we present a series of synthetic riboswitches for controlling gene expression through the regulation of alternative splicing. Placing the 5′-splice site into a stem structure of a tetracycline-sensing aptamer allows us to regulate the accessibility of the splice site. In the presence of tetracycline, an exon with a premature termination codon is skipped and gene expression can occur, whereas in its absence the exon is included into the coding sequence, repressing functional protein expression. We were able to identify RNA switches controlling protein expression in human cells with high dynamic ranges and different levels of protein expression. We present minimalistic versions of this system that circumvent the need to insert an additional exon. Further, we demonstrate the robustness of our approach by transferring the devices into the important research model organism Caenorhabditis elegans, where high levels of functional protein with very low background expression could be achieved.
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Affiliation(s)
- Monika Finke
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Dominik Brecht
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Julia Stifel
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Karina Gense
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.,Department of Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Martin Gamerdinger
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.,Department of Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Jörg S Hartig
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
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8
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Born J, Weitzel K, Suess B, Pfeifer F. A Synthetic Riboswitch to Regulate Haloarchaeal Gene Expression. Front Microbiol 2021; 12:696181. [PMID: 34211452 PMCID: PMC8241225 DOI: 10.3389/fmicb.2021.696181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 05/21/2021] [Indexed: 11/13/2022] Open
Abstract
In recent years, synthetic riboswitches have become increasingly important to construct genetic circuits in all three domains of life. In bacteria, synthetic translational riboswitches are often employed that modulate gene expression by masking the Shine-Dalgarno (SD) sequence in the absence or presence of a cognate ligand. For (halo-)archaeal translation, a SD sequence is not strictly required. The application of synthetic riboswitches in haloarchaea is therefore limited so far, also because of the molar intracellular salt concentrations found in these microbes. In this study, we applied synthetic theophylline-dependent translational riboswitches in the archaeon Haloferax volcanii. The riboswitch variants A through E and E∗ were chosen since they not only mask the SD sequence but also the AUG start codon by forming a secondary structure in the absence of the ligand theophylline. Upon addition of the ligand, the ribosomal binding site and start codon become accessible for translation initiation. Riboswitch E mediated a dose-dependent, up to threefold activation of the bgaH reporter gene expression. Raising the salt concentration of the culture media from 3 to 4 M NaCl resulted in a 12-fold increase in the switching capacity of riboswitch E, and switching activity increased up to 26-fold when the cultivating temperature was reduced from 45 to 30°C. To construct a genetic circuit, riboswitch E was applied to regulate the synthesis of the transcriptional activator GvpE allowing a dose-dependent activation of the mgfp6 reporter gene under P pA promoter control.
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Affiliation(s)
| | | | - Beatrix Suess
- Synthetic RNA Biology, Department of Biology, Technical University Darmstadt, Darmstadt, Germany.,Centre of Synthetic Biology, Technical University Darmstadt, Darmstadt, Germany
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Dobrzanski T, Pobre V, Moreno LF, Barbosa HCDS, Monteiro RA, de Oliveira Pedrosa F, de Souza EM, Arraiano CM, Steffens MBR. In silico prediction and expression profile analysis of small non-coding RNAs in Herbaspirillum seropedicae SmR1. BMC Genomics 2020; 21:134. [PMID: 32039705 PMCID: PMC7011215 DOI: 10.1186/s12864-019-6402-x] [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: 06/25/2019] [Accepted: 12/15/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Herbaspirillum seropedicae is a diazotrophic bacterium from the β-proteobacteria class that colonizes endophytically important gramineous species, promotes their growth through phytohormone-dependent stimulation and can express nif genes and fix nitrogen inside plant tissues. Due to these properties this bacterium has great potential as a commercial inoculant for agriculture. The H. seropedicae SmR1 genome is completely sequenced and annotated but despite the availability of diverse structural and functional analysis of this genome, studies involving small non-coding RNAs (sRNAs) has not yet been done. We have conducted computational prediction and RNA-seq analysis to select and confirm the expression of sRNA genes in the H. seropedicae SmR1 genome, in the presence of two nitrogen independent sources and in presence of naringenin, a flavonoid secreted by some plants. RESULTS This approach resulted in a set of 117 sRNAs distributed in riboswitch, cis-encoded and trans-encoded categories and among them 20 have Rfam homologs. The housekeeping sRNAs tmRNA, ssrS and 4.5S were found and we observed that a large number of sRNAs are more expressed in the nitrate condition rather than the control condition and in the presence of naringenin. Some sRNAs expression were confirmed in vitro and this work contributes to better understand the post transcriptional regulation in this bacterium. CONCLUSIONS H. seropedicae SmR1 express sRNAs in the presence of two nitrogen sources and/or in the presence of naringenin. The functions of most of these sRNAs remains unknown but their existence in this bacterium confirms the evidence that sRNAs are involved in many different cellular activities to adapt to nutritional and environmental changes.
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Affiliation(s)
- Tatiane Dobrzanski
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná (UFPR), Av. Coronel. Francisco H. dos Santos, 210, PoBox 19046, Curitiba, 81.531-980, Paraná, Brazil
| | - Vânia Pobre
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
| | - Leandro Ferreira Moreno
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná (UFPR), Av. Coronel. Francisco H. dos Santos, 210, PoBox 19046, Curitiba, 81.531-980, Paraná, Brazil
| | - Helba Cirino de Souza Barbosa
- Graduate Program in Bioinformatics, Universidade Federal do Paraná (UFPR), Rua Alcides Vieira Arcoverde, 1225, Curitiba, 81520-260, Brazil
| | - Rose Adele Monteiro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná (UFPR), Av. Coronel. Francisco H. dos Santos, 210, PoBox 19046, Curitiba, 81.531-980, Paraná, Brazil.,Graduate Program in Bioinformatics, Universidade Federal do Paraná (UFPR), Rua Alcides Vieira Arcoverde, 1225, Curitiba, 81520-260, Brazil
| | - Fábio de Oliveira Pedrosa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná (UFPR), Av. Coronel. Francisco H. dos Santos, 210, PoBox 19046, Curitiba, 81.531-980, Paraná, Brazil
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná (UFPR), Av. Coronel. Francisco H. dos Santos, 210, PoBox 19046, Curitiba, 81.531-980, Paraná, Brazil
| | - Cecília Maria Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Maria Berenice Reynaud Steffens
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná (UFPR), Av. Coronel. Francisco H. dos Santos, 210, PoBox 19046, Curitiba, 81.531-980, Paraná, Brazil.
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10
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Vogel M, Weigand JE, Kluge B, Grez M, Suess B. A small, portable RNA device for the control of exon skipping in mammalian cells. Nucleic Acids Res 2019; 46:e48. [PMID: 29420816 PMCID: PMC5934650 DOI: 10.1093/nar/gky062] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 01/29/2018] [Indexed: 12/17/2022] Open
Abstract
Splicing is an essential and highly regulated process in mammalian cells. We developed a synthetic riboswitch that efficiently controls alternative splicing of a cassette exon in response to the small molecule ligand tetracycline. The riboswitch was designed to control the accessibility of the 3' splice site by placing the latter inside the closing stem of a conformationally controlled tetracycline aptamer. In the presence of tetracycline, the cassette exon is skipped, whereas it is included in the ligand's absence. The design allows for an easy, context-independent integration of the regulatory device into any gene of interest. Portability of the device was shown through its functionality in four different systems: a synthetic minigene, a reporter gene and two endogenous genes. Furthermore, riboswitch functionality to control cellular signaling cascades was demonstrated by using it to specifically induce cell death through the conditionally controlled expression of CD20, which is a target in cancer therapy.
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Affiliation(s)
- Marc Vogel
- Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Julia E Weigand
- Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Britta Kluge
- Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Manuel Grez
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Paul-Ehrlich-Str. 42-44, 60596 Frankfurt/M, Germany
| | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
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Abstract
Advances in genome-wide sequence technologies allow for detailed insights into the complexity of RNA landscapes of organisms from all three domains of life. Recent analyses of archaeal transcriptomes identified interaction and regulation networks of noncoding RNAs in this understudied domain. Here, we review current knowledge of small, noncoding RNAs with important functions for the archaeal lifestyle, which often requires adaptation to extreme environments. One focus is RNA metabolism at elevated temperatures in hyperthermophilic archaea, which reveals elevated amounts of RNA-guided RNA modification and virus defense strategies. Genome rearrangement events result in unique fragmentation patterns of noncoding RNA genes that require elaborate maturation pathways to yield functional transcripts. RNA-binding proteins, e.g., L7Ae and LSm, are important for many posttranscriptional control functions of RNA molecules in archaeal cells. We also discuss recent insights into the regulatory potential of their noncoding RNA partners.
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Affiliation(s)
- José Vicente Gomes-Filho
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany;, ,
| | - Michael Daume
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany;, ,
| | - Lennart Randau
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany;, ,
- LOEWE Center for Synthetic Microbiology (Synmikro), 35032 Marburg, Germany
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12
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Sinumvayo JP, Zhao C, Tuyishime P. Recent advances and future trends of riboswitches: attractive regulatory tools. World J Microbiol Biotechnol 2018; 34:171. [PMID: 30413889 DOI: 10.1007/s11274-018-2554-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/02/2018] [Indexed: 01/06/2023]
Abstract
Bacterial genomes contain a huge amount of different genes. These genes are spatiotemporally expressed to accomplish some required functions within the organism. Inside the cell, any step of gene expression may be modulated at four possible places such as transcription initiation, translation regulation, mRNA stability and protein stability. To achieve this, there is a necessity of strong regulators either natural or synthetic which can fine-tune gene expression regarding the required function. In recent years, riboswitches as metabolite responsive control elements residing in the untranslated regions of certain messenger RNAs, have been known to control gene expression at transcription or translation level. Importantly, these control elements do not prescribe the involvement of protein factors for metabolite binding. However, they own their particular properties to sense intramolecular metabolites (ligands). Herein, we highlighted current important bacterial riboswitches, their applications to support genetic control, ligand-binding domain mechanisms and current progress in synthetic riboswitches.
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Affiliation(s)
- Jean Paul Sinumvayo
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
| | - Chunhua Zhao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Philibert Tuyishime
- University of Chinese Academy of Sciences, Beijing, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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13
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Quitzke V, Fersch J, Seyhan D, Rother M. Selenium-dependent gene expression in Methanococcus maripaludis: Involvement of the transcriptional regulator HrsM. Biochim Biophys Acta Gen Subj 2018; 1862:2441-2450. [DOI: 10.1016/j.bbagen.2018.03.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/28/2018] [Accepted: 03/29/2018] [Indexed: 01/23/2023]
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14
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Denis A, Martínez-Núñez MA, Tenorio-Salgado S, Perez-Rueda E. Dissecting the Repertoire of DNA-Binding Transcription Factors of the Archaeon Pyrococcus furiosus DSM 3638. Life (Basel) 2018; 8:life8040040. [PMID: 30248960 PMCID: PMC6316755 DOI: 10.3390/life8040040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/11/2018] [Accepted: 09/19/2018] [Indexed: 01/06/2023] Open
Abstract
In recent years, there has been a large increase in the amount of experimental evidence for diverse archaeal organisms, and these findings allow for a comprehensive analysis of archaeal genetic organization. However, studies about regulatory mechanisms in this cellular domain are still limited. In this context, we identified a repertoire of 86 DNA-binding transcription factors (TFs) in the archaeon Pyrococcus furiosus DSM 3638, that are clustered into 32 evolutionary families. In structural terms, 45% of these proteins are composed of one structural domain, 41% have two domains, and 14% have three structural domains. The most abundant DNA-binding domain corresponds to the winged helix-turn-helix domain; with few alternative DNA-binding domains. We also identified seven regulons, which represent 13.5% (279 genes) of the total genes in this archaeon. These analyses increase our knowledge about gene regulation in P. furiosus DSM 3638 and provide additional clues for comprehensive modeling of transcriptional regulatory networks in the Archaea cellular domain.
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Affiliation(s)
- Antonia Denis
- Facultad de Medicina, Universidad Juárez Autónoma de Tabasco, C.P. 86100, Tabasco, Mexico.
| | - Mario Alberto Martínez-Núñez
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Unidad Académica de Ciencias y Tecnología de la UNAM en Yucatán, Carretera Sierra Papacal-Chuburna Km. 5, C.P. 97302, Mérida, Yucatán, Mexico.
| | - Silvia Tenorio-Salgado
- Tecnológico Nacional de México, Instituto Tecnológico de Mérida, C.P. 97000, Mérida, Yucatán, Mexico.
| | - Ernesto Perez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, C.P. 97302, Mérida, Yucatán, Mexico.
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Karim AA, Gestaut DR, Fincker M, Ruth JC, Holmes EC, Sheu W, Spormann AM. Fine-Tuned Protein Production in Methanosarcina acetivorans C2A. ACS Synth Biol 2018; 7:1874-1885. [PMID: 29920209 DOI: 10.1021/acssynbio.8b00062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Methanogenic archaea can be integrated into a sustainable, carbon-neutral cycle for producing organic chemicals from C1 compounds if the rate, yield, and titer of product synthesis can be improved using metabolic engineering. However, metabolic engineering techniques are limited in methanogens by insufficient methods for controlling cellular protein levels. We conducted a systematic approach to tune protein levels in Methanosarcina acetivorans C2A, a model methanogen, by regulating transcription and translation initiation. Rationally designed core promoter and ribosome binding site mutations in M. acetivorans C2A resulted in a predicable change in protein levels over a 60 fold range. The overall range of protein levels was increased an additional 3 fold by introducing the 5' untranslated region of the mcrB transcript. This work demonstrates a wide range of precisely controlled protein levels in M. acetivorans C2A, which will help facilitate systematic metabolic engineering efforts in methanogens.
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Affiliation(s)
- Ann A. Karim
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Daniel R. Gestaut
- Department of Biology, Stanford University, Stanford, California 94305, United States
| | - Maeva Fincker
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - John C. Ruth
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Eric C. Holmes
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Wayne Sheu
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Alfred M. Spormann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
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An Archaeal Fluoride-Responsive Riboswitch Provides an Inducible Expression System for Hyperthermophiles. Appl Environ Microbiol 2018; 84:AEM.02306-17. [PMID: 29352088 DOI: 10.1128/aem.02306-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/07/2018] [Indexed: 12/12/2022] Open
Abstract
Robust genetic systems for the hyperthermophilic Thermococcales have facilitated the overexpression of native genes, enabled the addition of sequences encoding secretion signals, epitope, and affinity tags to coding regions, and aided the introduction of sequences encoding new proteins in these fast-growing fermentative heterotrophs. However, tightly controlled and easily manipulated systems facilitating regulated gene expression are limited for these hosts. Here, we describe an alternative method for regulatory control reliant on a cis-encoded functional riboswitch in the model archaeon Thermococcus kodakarensis Despite the hyperthermophilic growth temperatures, the proposed structure of the riboswitch conforms to a fluoride-responsive riboswitch encoded in many bacteria and similarly functions to regulate a component-conserved fluoride export pathway. Deleting components of the fluoride export pathway generates T. kodakarensis strains with increased fluoride sensitivity. The mechanism underlying regulated expression suggested that the riboswitch-encoding sequences could be utilized as a tunable expression cassette. When appended to a reporter gene, the riboswitch-mediated control system provides fluoride-dependent tunable regulatory potential, offering an alternative system for regulating gene expression. Riboswitch-regulated expression is thus ubiquitous in extant life and can be exploited to generate regulated expression systems for hyperthermophiles.IMPORTANCE Gene expression is controlled by a myriad of interconnected mechanisms that interpret metabolic states and environmental cues to balance cell physiology. Transcription regulation in Archaea is known to employ both typical repressors-operators and transcription activators to regulate transcription initiation in addition to the regulation afforded by chromatin structure. It was perhaps surprising that the presumed ancient mechanism of riboswitch-mediated regulation is found in Bacteria and Eukarya, but seemingly absent in Archaea We demonstrate here that a fluoride-responsive riboswitch functions to regulate a detoxification pathway in the hyperthermophilic archaeon Thermococcus kodakarensis The results obtained define a universal role for riboswitch-mediated regulation, adumbrate the presence of several riboswitch-regulated genes in Thermococcus kodakarensis, demonstrate the utility of RNA-based regulation at high temperatures, and provide a novel riboswitch-regulated expression system to employ in hyperthermophiles.
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17
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Enzmann F, Mayer F, Rother M, Holtmann D. Methanogens: biochemical background and biotechnological applications. AMB Express 2018; 8:1. [PMID: 29302756 PMCID: PMC5754280 DOI: 10.1186/s13568-017-0531-x] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 12/19/2017] [Indexed: 02/05/2023] Open
Abstract
Since fossil sources for fuel and platform chemicals will become limited in the near future, it is important to develop new concepts for energy supply and production of basic reagents for chemical industry. One alternative to crude oil and fossil natural gas could be the biological conversion of CO2 or small organic molecules to methane via methanogenic archaea. This process has been known from biogas plants, but recently, new insights into the methanogenic metabolism, technical optimizations and new technology combinations were gained, which would allow moving beyond the mere conversion of biomass. In biogas plants, steps have been undertaken to increase yield and purity of the biogas, such as addition of hydrogen or metal granulate. Furthermore, the integration of electrodes led to the development of microbial electrosynthesis (MES). The idea behind this technique is to use CO2 and electrical power to generate methane via the microbial metabolism. This review summarizes the biochemical and metabolic background of methanogenesis as well as the latest technical applications of methanogens. As a result, it shall give a sufficient overview over the topic to both, biologists and engineers handling biological or bioelectrochemical methanogenesis.
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Affiliation(s)
- Franziska Enzmann
- DECHEMA Research Institute, Industrial Biotechnology, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
| | - Florian Mayer
- DECHEMA Research Institute, Industrial Biotechnology, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
| | - Michael Rother
- Technische Universität Dresden, Institut für Mikrobiologie, Zellescher Weg 20b, 01217 Dresden, Germany
| | - Dirk Holtmann
- DECHEMA Research Institute, Industrial Biotechnology, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
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18
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Noncoding RNAs in Archaea: Genome-Wide Identification and Functional Classification. Methods Enzymol 2018; 612:413-442. [DOI: 10.1016/bs.mie.2018.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Shea MT, Walter ME, Duszenko N, Ducluzeau AL, Aldridge J, King SK, Buan NR. pNEB193-derived suicide plasmids for gene deletion and protein expression in the methane-producing archaeon, Methanosarcina acetivorans. Plasmid 2016; 84-85:27-35. [PMID: 26876941 DOI: 10.1016/j.plasmid.2016.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 02/10/2016] [Accepted: 02/10/2016] [Indexed: 10/22/2022]
Abstract
Gene deletion and protein expression are cornerstone procedures for studying metabolism in any organism, including methane-producing archaea (methanogens). Methanogens produce coenzymes and cofactors not found in most bacteria, therefore it is sometimes necessary to express and purify methanogen proteins from the natural host. Protein expression in the native organism is also useful when studying post-translational modifications and their effect on gene expression or enzyme activity. We have created several new suicide plasmids to complement existing genetic tools for use in the methanogen, Methanosarcina acetivorans. The new plasmids are derived from the commercially available Escherichia coli plasmid, pNEB193, and cannot replicate autonomously in methanogens. The designed plasmids facilitate markerless gene deletion, gene transcription, protein expression, and purification of proteins with cleavable affinity tags from the methanogen, M. acetivorans.
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Affiliation(s)
- Mitchell T Shea
- Redox Biology Center, Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Mary E Walter
- Redox Biology Center, Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Nikolas Duszenko
- Redox Biology Center, Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Anne-Lise Ducluzeau
- Redox Biology Center, Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Jared Aldridge
- Redox Biology Center, Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Shannon K King
- Redox Biology Center, Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Nicole R Buan
- Redox Biology Center, Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States.
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Berens C, Groher F, Suess B. RNA aptamers as genetic control devices: the potential of riboswitches as synthetic elements for regulating gene expression. Biotechnol J 2015; 10:246-57. [PMID: 25676052 DOI: 10.1002/biot.201300498] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/23/2014] [Accepted: 01/15/2015] [Indexed: 12/16/2022]
Abstract
RNA utilizes many different mechanisms to control gene expression. Among the regulatory elements that respond to external stimuli, riboswitches are a prominent and elegant example. They consist solely of RNA and couple binding of a small molecule ligand to the so-called "aptamer domain" with a conformational change in the downstream "expression platform" which then determines system output. The modular organization of riboswitches and the relative ease with which ligand-binding RNA aptamers can be selected in vitro against almost any molecule have led to the rapid and widespread adoption of engineered riboswitches as artificial genetic control devices in biotechnology and synthetic biology over the past decade. This review highlights proof-of-principle applications to demonstrate the versatility and robustness of engineered riboswitches in regulating gene expression in pro- and eukaryotes. It then focuses on strategies and parameters to identify aptamers that can be integrated into synthetic riboswitches that are functional in vivo, before finishing with a reflection on how to improve the regulatory properties of engineered riboswitches, so that we can not only further expand riboswitch applicability, but also finally fully exploit their potential as control elements in regulating gene expression.
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Affiliation(s)
- Christian Berens
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Jena, Germany
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Berens C, Suess B. Riboswitch engineering - making the all-important second and third steps. Curr Opin Biotechnol 2014; 31:10-5. [PMID: 25137633 DOI: 10.1016/j.copbio.2014.07.014] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 07/30/2014] [Indexed: 11/20/2022]
Abstract
Synthetic biology uses our understanding of biological systems to develop innovative solutions for challenges in fields as diverse as genetic control and logic devices, bioremediation, materials production or diagnostics and therapy in medicine by designing new biological components. RNA-based elements are key components of these engineered systems. Their structural and functional diversity is ideal for generating regulatory riboswitches that react with many different types of output to molecular and environmental signals. Recent advances have added new sensor and output domains to the existing toolbox, and demonstrated the portability of riboswitches to many different organisms. Improvements in riboswitch design and screens for selecting in vivo active switches provide the means to isolate riboswitches with regulatory properties more like their natural counterparts.
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Affiliation(s)
- Christian Berens
- Fachbereich Biologie, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287 Darmstadt, Germany.
| | - Beatrix Suess
- Fachbereich Biologie, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287 Darmstadt, Germany.
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