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Du Q, Wei Y, Zhang L, Ren D, Gao J, Dong X, Bai L, Li J. An improved CRISPR and CRISPR interference (CRISPRi) toolkit for engineering the model methanogenic archaeon Methanococcus maripaludis. Microb Cell Fact 2024; 23:239. [PMID: 39227830 PMCID: PMC11373211 DOI: 10.1186/s12934-024-02492-0] [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: 05/14/2024] [Accepted: 07/27/2024] [Indexed: 09/05/2024] Open
Abstract
BACKGROUND The type II based CRISPR-Cas system remains restrictedly utilized in archaea, a featured domain of life that ranks parallelly with Bacteria and Eukaryotes. Methanococcus maripaludis, known for rapid growth and genetic tractability, serves as an exemplary model for studying archaeal biology and exploring CO2-based biotechnological applications. However, tools for controlled gene regulation remain deficient and CRISPR-Cas tools still need improved in this archaeon, limiting its application as an archaeal model cellular factory. RESULTS This study not only improved the CRISPR-Cas9 system for optimizing multiplex genome editing and CRISPR plasmid construction efficiencies but also pioneered an effective CRISPR interference (CRISPRi) system for controlled gene regulation in M. maripaludis. We developed two novel strategies for balanced expression of multiple sgRNAs, facilitating efficient multiplex genome editing. We also engineered a strain expressing Cas9 genomically, which simplified the CRISPR plasmid construction and facilitated more efficient genome modifications, including markerless and scarless gene knock-in. Importantly, we established a CRISPRi system using catalytic inactive dCas9, achieving up to 100-fold repression on target gene. Here, sgRNAs targeting near and downstream regions of the transcription start site and the 5'end ORF achieved the highest repression efficacy. Furthermore, we developed an inducible CRISPRi-dCas9 system based on TetR/tetO platform. This facilitated the inducible gene repression, especially for essential genes. CONCLUSIONS Therefore, these advancements not only expand the toolkit for genetic manipulation but also bridge methodological gaps for controlled gene regulation, especially for essential genes, in M. maripaludis. The robust toolkit developed here paves the way for applying M. maripaludis as a vital model archaeal cell factory, facilitating fundamental biological studies and applied biotechnology development of archaea.
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Affiliation(s)
- Qing Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing, 100101, China
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, China
| | - Yufei Wei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing, 100101, China
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, China
| | - Liuyang Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing, 100101, China
| | - Derong Ren
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing, 100101, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Jian Gao
- School of Basic Medical Sciences, School of Biomedical Engineering, Hubei University of Medicine, Shiyan, China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing, 100101, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Liping Bai
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, China.
| | - Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing, 100101, China.
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing, 100049, China.
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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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Wang L, Liu H. Microbial electrosynthesis of single cell protein and methane by coupling fast-growing Methanococcus maripaludis with microbial electrolysis cells. BIORESOURCE TECHNOLOGY 2024; 393:130025. [PMID: 37972904 DOI: 10.1016/j.biortech.2023.130025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Single cell protein (SCP) is a promising alternative protein source, as its production bypasses the disadvantages of animal protein production in industrial agriculture. Coupling a fast-growing hydrogen consuming organism with microbial electrolysis cells (MECs) could be a viable method for SCP production. In this study, a fast-growing and protein-rich methanogen, Methanococcus maripaludis was selected as the primary SCP source. The inoculation of M. maripaludis in MECs triggered cell synthesis with methane production. The doubling time measured was 11.2 h and the specific growth rate was 0.062 1/h. The highest SCP production rate was 13.7 mg/L/h. In the dried biomass, the weight of protein was over 60 %. Amino acid profiling of the harvested biomass demonstrated high abundance of essential amino acids. The electron flux analysis indicated that 31.3 % electrons in the electrochemical systems were directed into SCP synthesis. These results illustrated the potential for SCP production by coupling a fast-growing methanogen with MECs.
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Affiliation(s)
- Luguang Wang
- Department of Biological and Ecological Engineering, Oregon State University, Corvallis, OR 97331, United States; Department of Biological Engineering, Utah State University, Logan, UT 84322, United States
| | - Hong Liu
- Department of Biological and Ecological Engineering, Oregon State University, Corvallis, OR 97331, United States.
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Payne D, Spietz RL, Newell DL, Dijkstra P, Boyd ES. Influence of sulfide on diazotrophic growth of the methanogen Methanococcus maripaludis and its implications for the origin of nitrogenase. Commun Biol 2023; 6:799. [PMID: 37524775 PMCID: PMC10390477 DOI: 10.1038/s42003-023-05163-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 07/21/2023] [Indexed: 08/02/2023] Open
Abstract
Methanogens inhabit euxinic (sulfide-rich) or ferruginous (iron-rich) environments that promote the precipitation of transition metals as metal sulfides, such as pyrite, reducing metal or sulfur availability. Such environments have been common throughout Earth's history raising the question as to how anaerobes obtain(ed) these elements for the synthesis of enzyme cofactors. Here, we show a methanogen can synthesize molybdenum nitrogenase metallocofactors from pyrite as the source of iron and sulfur, enabling nitrogen fixation. Pyrite-grown, nitrogen-fixing cells grow faster and require 25-fold less molybdenum than cells grown under euxinic conditions. Growth yields are 3 to 8 times higher in cultures grown under ferruginous relative to euxinic conditions. Physiological, transcriptomic, and geochemical data indicate these observations are due to sulfide-promoted metal limitation, in particular molybdenum. These findings suggest that molybdenum nitrogenase may have originated in a ferruginous environment that titrated sulfide to form pyrite, facilitating the availability of sufficient iron, sulfur, and molybdenum for cofactor biosynthesis.
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Affiliation(s)
- Devon Payne
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA
| | - Rachel L Spietz
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA
| | - Dennis L Newell
- Department of Geosciences, Utah State University, Logan, UT, 84322, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA.
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Comparative Transcriptomics Sheds Light on Remodeling of Gene Expression during Diazotrophy in the Thermophilic Methanogen Methanothermococcus thermolithotrophicus. mBio 2022; 13:e0244322. [PMID: 36409126 PMCID: PMC9765008 DOI: 10.1128/mbio.02443-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Some marine thermophilic methanogens are able to perform energy-consuming nitrogen fixation despite deriving only little energy from hydrogenotrophic methanogenesis. We studied this process in Methanothermococcus thermolithotrophicus DSM 2095, a methanogenic archaeon of the order Methanococcales that contributes to the nitrogen pool in some marine environments. We successfully grew this archaeon under diazotrophic conditions in both batch and fermenter cultures, reaching the highest cell density reported so far. Diazotrophic growth depended strictly on molybdenum and, in contrast to other diazotrophs, was not inhibited by tungstate or vanadium. This suggests an elaborate control of metal uptake and a specific metal recognition system for the insertion into the nitrogenase cofactor. Differential transcriptomics of M. thermolithotrophicus grown under diazotrophic conditions with ammonium-fed cultures as controls revealed upregulation of the nitrogenase machinery, including chaperones, regulators, and molybdate importers, as well as simultaneous upregulation of an ammonium transporter and a putative pathway for nitrate and nitrite utilization. The organism thus employs multiple synergistic strategies for uptake of nitrogen nutrients during the early exponential growth phase without altering transcription levels for genes involved in methanogenesis. As a counterpart, genes coding for transcription and translation processes were downregulated, highlighting the maintenance of an intricate metabolic balance to deal with energy constraints and nutrient limitations imposed by diazotrophy. This switch in the metabolic balance included unexpected processes, such as upregulation of the CRISPR-Cas system, probably caused by drastic changes in transcription levels of putative mobile and virus-like elements. IMPORTANCE The thermophilic anaerobic archaeon M. thermolithotrophicus is a particularly suitable model organism to study the coupling of methanogenesis to diazotrophy. Likewise, its capability of simultaneously reducing N2 and CO2 into NH3 and CH4 with H2 makes it a viable target for biofuel production. We optimized M. thermolithotrophicus cultivation, resulting in considerably higher cell yields and enabling the successful establishment of N2-fixing bioreactors. Improved understanding of the N2 fixation process would provide novel insights into metabolic adaptations that allow this energy-limited extremophile to thrive under diazotrophy, for instance, by investigating its physiology and uncharacterized nitrogenase. We demonstrated that diazotrophic growth of M. thermolithotrophicus is exclusively dependent on molybdenum, and complementary transcriptomics corroborated the expression of the molybdenum nitrogenase system. Further analyses of differentially expressed genes during diazotrophy across three cultivation time points revealed insights into the response to nitrogen limitation and the coordination of core metabolic processes.
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Li J, Akinyemi TS, Shao N, Chen C, Dong X, Liu Y, Whitman WB. Genetic and Metabolic Engineering of Methanococcus spp. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Li J, Zhang L, Xu Q, Zhang W, Li Z, Chen L, Dong X. CRISPR-Cas9 Toolkit for Genome Editing in an Autotrophic CO 2-Fixing Methanogenic Archaeon. Microbiol Spectr 2022; 10:e0116522. [PMID: 35766512 PMCID: PMC9430280 DOI: 10.1128/spectrum.01165-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/04/2022] [Indexed: 11/23/2022] Open
Abstract
The CRISPR-Cas9 system is a robust genome editing tool that is widely applied in eukaryotes and bacteria. However, use of this technique has only been developed for one species of Archaea, a domain of life ranking in parallel with Eukarya and Bacteria. In this study, we applied the CRISPR-Cas9 genome editing technique to Methanococcus maripaludis, an autotrophic and hydrogenotrophic methanogenic archaeon with a remarkably polyploid genome comprising up to ~55 chromosomal copies per cell. An editing plasmid was designed that encodes small guide RNA (sgRNA), Cas9 protein and an ~1-kb repair template (donor). Highly efficient (75% to 100%) and precise genome editing was achieved following one-step transformation. Significantly, the Cas9-based system efficiently deleted one or two genes and a large DNA fragment (~9 kb) and even synchronously deleted 13 genes located at three loci in all chromosomal copies of M. maripaludis. Moreover, precise in situ genome modifications, such as gene tagging and multiple- and even single-nucleotide mutagenesis, were also introduced with high efficiency. Further, as a proof of concept, precise mutagenesis at the nucleotide level allowed the engineering of both transcriptional and translational activities. Mutations were introduced into an archaeal promoter BRE (transcription factor B [TFB] recognition element), a terminator U-tract region, and a gene coding region. Stop codon introduction into a gene through single-nucleotide substitution shut down its expression, providing an alternative strategy for gene inactivation. In conclusion, the robust CRISPR-Cas9 genetic toolkit developed in this investigation greatly facilitates the application of M. maripaludis as a model system in the study of archaeal biology and biotechnology development, particularly CO2-based biotechnologies. IMPORTANCE Archaea are prokaryotes with intriguing biological characteristics. They possess bacterial cell structures but eukaryotic homologous information processing machinery and eukaryotic featured proteins. Archaea also display excellent adaptability to extreme environments and play pivotal roles in ecological processes, thus exhibiting valuable biotechnological potential. However, the in-depth understanding and practical application of archaea are much lagging, because only a minority of pure cultures are available, and even worse, very few can be genetically manipulated. This work developed CRISPR-Cas9-based genome editing technology in Methanococcus maripaludis, a CO2-fixing methanogenic archaeon. The CRISPR-Cas9 approach developed in this study provides an elegant and efficient genome editing toolkit that can be applied in the knockout of single or multiple genes, in situ gene tagging, multiple- or single-nucleotide mutagenesis, and inactivation of gene expression by introduction of stop codons. The successful development of the CRISPR-Cas9 toolkit will facilitate the application of M. maripaludis in archaeal biology research and biotechnology development, particularly CO2-derived biotechnologies.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liuyang Zhang
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Qing Xu
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China
| | - Wenting Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhihua Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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8
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Bao J, de Dios Mateos E, Scheller S. Efficient CRISPR/Cas12a-Based Genome-Editing Toolbox for Metabolic Engineering in Methanococcus maripaludis. ACS Synth Biol 2022; 11:2496-2503. [PMID: 35730587 PMCID: PMC9295151 DOI: 10.1021/acssynbio.2c00137] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
The rapid-growing
and genetically tractable methanogen Methanococcus
maripaludis is a promising host organism
for the biotechnological conversion of carbon dioxide and renewable
hydrogen to fuels and value-added products. Expansion of its product
scope through metabolic engineering necessitates reliable and efficient
genetic tools, particularly for genome edits that affect the primary
metabolism and cell growth. Here, we have designed a genome-editing
toolbox by utilizing Cas12a from Lachnospiraceae bacterium ND2006 (LbCas12a) in combination with the homology-directed repair
machinery endogenously present in M. maripaludis. This toolbox can delete target genes with a success rate of up
to 95%, despite the hyperpolyploidy of M. maripaludis. For the purpose of demonstrating a large deletion, the M. maripaludis flagellum operon (∼8.9 kbp)
was replaced by the Escherichia coli β-glucuronidase gene. To facilitate metabolic engineering
and flux balancing in M. maripaludis, the relative strength of 15 different promoters was quantified
in the presence of two common growth substrates, either formate or
carbon dioxide and hydrogen. This CRISPR/LbCas12a toolbox can be regarded
as a reliable and quick method for genome editing in a methanogen.
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Affiliation(s)
- Jichen Bao
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-02150 Espoo, Finland
| | - Enrique de Dios Mateos
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-02150 Espoo, Finland
| | - Silvan Scheller
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-02150 Espoo, Finland
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Abstract
Methanocaldococcus sp. strain FS406-22, a hyperthermophilic methanogen, fixes nitrogen with a minimal set of known nif genes. Only four structural nif genes, nifH, nifD, nifK, and nifE, are present in a cluster, and a nifB homolog is present elsewhere in the genome. nifN, essential for the final synthesis of the iron-molybdenum cofactor of nitrogenase in well-characterized diazotrophs, is absent from FS406-22. In addition, FS406-22 encodes four novel hypothetical proteins, and a ferredoxin, in the nif cluster. Here, we develop a set of genetic tools for FS406-22 and test the functionality of genes in the nif cluster by making markerless in-frame deletion mutations. Deletion of the gene for one hypothetical protein, designated Hp4, delayed the initiation of diazotrophic growth and decreased the growth rate, an effect we confirmed by genetic complementation. NifE also appeared to play a role in diazotrophic growth, and the encoding of Hp4 and NifE in a single operon suggested they may work together in some way in the synthesis of the nitrogenase cofactor. No role could be discerned for any of the other hypothetical proteins, nor for the ferredoxin, despite the presence of these genes in a variety of related organisms. Possible pathways and evolutionary scenarios for the synthesis of the nitrogenase cofactor in an organism that lacks nifN are discussed. IMPORTANCEMethanocaldococcus has been considered a model genus, but genetic tools have not been forthcoming until recently. Here, we develop and illustrate the utility of positive selection with either of two selective agents (simvastatin and neomycin), negative selection, generation of markerless in-frame deletion mutations, and genetic complementation. These genetic tools should be useful for a variety of related species. We address the question of the minimal set of nif genes, which has implications for how nitrogen fixation evolved.
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Akinyemi TS, Shao N, Lyu Z, Drake IJ, Liu Y, Whitman WB. Tuning Gene Expression by Phosphate in the Methanogenic Archaeon Methanococcus maripaludis. ACS Synth Biol 2021; 10:3028-3039. [PMID: 34665610 DOI: 10.1021/acssynbio.1c00322] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methanococcus maripaludis is a rapidly growing, hydrogenotrophic, and genetically tractable methanogen with unique capabilities to convert formate and CO2 to CH4. The existence of genome-scale metabolic models and an established, robust system for both large-scale and continuous cultivation make it amenable for industrial applications. However, the lack of molecular tools for differential gene expression has hindered its application as a microbial cell factory to produce biocatalysts and biochemicals. In this study, a library of differentially regulated promoters was designed and characterized based on the pst promoter, which responds to the inorganic phosphate concentration in the growth medium. Gene expression increases by 4- to 6-fold when the medium phosphate drops to growth-limiting concentrations. Hence, this regulated system decouples growth from heterologous gene expression without the need for adding an inducer. The minimal pst promoter is identified and contains a conserved AT-rich region, a factor B recognition element, and a TATA box for phosphate-dependent regulation. Rational changes to the factor B recognition element and start codon had no significant impact on expression; however, changes to the transcription start site and the 5' untranslated region resulted in the differential protein production with regulation remaining intact. Compared to a previous expression system based upon the histone promoter, this regulated expression system resulted in significant improvements in the expression of a key methanogenic enzyme complex, methyl-coenzyme M reductase, and the potentially toxic arginine methyltransferase MmpX.
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Affiliation(s)
- Taiwo S. Akinyemi
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, United States
| | - Nana Shao
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, United States
| | - Zhe Lyu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Ian J. Drake
- Corporate Strategic Research, ExxonMobil Research & Engineering Company, Annandale, New Jersey 08801, United States
| | - Yuchen Liu
- Corporate Strategic Research, ExxonMobil Research & Engineering Company, Annandale, New Jersey 08801, United States
| | - William B. Whitman
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, United States
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Pastor-Soler S, Camacho M, Bautista V, Bonete MJ, Esclapez J. Towards the Elucidation of Assimilative nasABC Operon Transcriptional Regulation in Haloferax mediterranei. Genes (Basel) 2021; 12:genes12050619. [PMID: 33921943 PMCID: PMC8143581 DOI: 10.3390/genes12050619] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/14/2021] [Accepted: 04/20/2021] [Indexed: 11/22/2022] Open
Abstract
The assimilatory pathway of the nitrogen cycle in the haloarchaeon Haloferax mediterranei has been well described and characterized in previous studies. However, the regulatory mechanisms involved in the gene expression of this pathway remain unknown in haloarchaea. This work focuses on elucidating the regulation at the transcriptional level of the assimilative nasABC operon (HFX_2002 to HFX_2004) through different approaches. Characterization of its promoter region using β-galactosidase as a reporter gene and site-directed mutagenesis has allowed us to identify possible candidate binding regions for a transcriptional factor. The identification of a potential transcriptional regulator related to nitrogen metabolism has become a real challenge due to the lack of information on haloarchaea. The investigation of protein–DNA binding by streptavidin bead pull-down analysis combined with mass spectrometry resulted in the in vitro identification of a transcriptional regulator belonging to the Lrp/AsnC family, which binds to the nasABC operon promoter (p.nasABC). To our knowledge, this study is the first report to suggest the AsnC transcriptional regulator as a powerful candidate to play a regulatory role in nasABC gene expression in Hfx. mediterranei and, in general, in the assimilatory nitrogen pathway.
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Li Q, Chen S. Transfer of Nitrogen Fixation (nif) Genes to Non-diazotrophic Hosts. Chembiochem 2020; 21:1717-1722. [PMID: 32009294 DOI: 10.1002/cbic.201900784] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Indexed: 12/20/2022]
Abstract
Nitrogen is one of the most important nutrients for plant growth. To enhance crop productivity, chemical nitrogen fertilizer is commonly applied in agriculture. Biological nitrogen fixation, the conversion of atmospheric N2 to NH3 , is an important source of nitrogen input in agriculture and represents a promising substitute for chemical nitrogen fertilizers. However, nitrogen fixation is only sporadically distributed within bacteria and archaea (diazotrophs). Thus, many biologists hope to reconstitute a nitrogenase biosynthetic pathway in a eukaryotic host, with the final aim of developing N2 -fixing cereal crops. With the advent of synthetic biology and a deep understanding of the fundamental genetic determinants necessary to sustain nitrogen fixation in bacteria, much progress has been made toward this goal. Transfer of native and refactored nif (nitrogen fixation) genes to non-diazotrophs has been attempted in model bacteria, yeast, and plants. Specifically, nif genes from Klebsiella oxytoca, Azotobacter vinelandii, and Paenibacillus polymyxa have been successfully transferred and expressed in Escherichia coli, Saccharomyces cerevisiae, and even in the tobacco plant. These advances have laid the groundwork to enable cereal crops to "fix" nitrogen themselves to sustain their growth and yield.
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Affiliation(s)
- Qin Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology of Agriculture Ministry and, College of Biological Sciences, China Agricultural University, Haidian District Yuanmingyuan West Road No.2, Beijing, P. R. China
| | - Sanfeng Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology of Agriculture Ministry and, College of Biological Sciences, China Agricultural University, Haidian District Yuanmingyuan West Road No.2, Beijing, P. R. China
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Evolution and Functional Analysis of orf1 Within nif Gene Cluster from Paenibacillus graminis RSA19. Int J Mol Sci 2019; 20:ijms20051145. [PMID: 30845717 PMCID: PMC6429469 DOI: 10.3390/ijms20051145] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 02/27/2019] [Accepted: 03/01/2019] [Indexed: 12/21/2022] Open
Abstract
Paenibacillus is a genus of Gram-positive, facultative anaerobic and endospore-forming bacteria. Genomic sequence analysis has revealed that a compact nif (nitrogen fixation) gene cluster comprising 9–10 genes nifBHDKENX(orf1)hesAnifV is conserved in diazotrophic Paenibacillus species. The evolution and function of the orf1 gene within the nif gene cluster of Paenibacillus species is unknown. In this study, a careful comparison analysis of the compositions of the nif gene clusters from various diazotrophs revealed that orf1 located downstream of nifENX was identified in anaerobic Clostridium ultunense, the facultative anaerobic Paenibacillus species and aerobic diazotrophs (e.g., Azotobacter vinelandii and Azospirillum brasilense). The predicted amino acid sequences encoded by the orf1 gene, part of the nif gene cluster nifBHDKENXorf1hesAnifV in Paenibacillus graminis RSA19, showed 60–90% identity with those of the orf1 genes located downstream of nifENX from different diazotrophic Paenibacillus species, but shared no significant identity with those of the orf1 genes from different taxa of diazotrophic organisms. Transcriptional analysis showed that the orf1 gene was expressed under nitrogen fixation conditions from the promoter located upstream from nifB. Mutational analysis suggested that the orf1 gene functions in nitrogen fixation in the presence of a high concentration of O2.
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Abstract
Global (metabolic) regulatory networks allow microorganisms to survive periods of nitrogen starvation or general nutrient stress. Uptake and utilization of various nitrogen sources are thus commonly tightly regulated in Prokarya (Bacteria and Archaea) in response to available nitrogen sources. Those well-studied regulations occur mainly at the transcriptional and posttranslational level. Surprisingly, and in contrast to their involvement in most other stress responses, small RNAs (sRNAs) involved in the response to environmental nitrogen fluctuations are only rarely reported. In addition to sRNAs indirectly affecting nitrogen metabolism, only recently it was demonstrated that three sRNAs were directly involved in regulation of nitrogen metabolism in response to changes in available nitrogen sources. All three trans-acting sRNAs are under direct transcriptional control of global nitrogen regulators and affect expression of components of nitrogen metabolism (glutamine synthetase, nitrogenase, and PII-like proteins) by either masking the ribosome binding site and thus inhibiting translation initiation or stabilizing the respective target mRNAs. Most likely, there are many more sRNAs and other types of noncoding RNAs, e.g., riboswitches, involved in the regulation of nitrogen metabolism in Prokarya that remain to be uncovered. The present review summarizes the current knowledge on sRNAs involved in nitrogen metabolism and their biological functions and targets.
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Biosensors-Based In Vivo Quantification of 2-Oxoglutarate in Cyanobacteria and Proteobacteria. Life (Basel) 2018; 8:life8040051. [PMID: 30373229 PMCID: PMC6315671 DOI: 10.3390/life8040051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 10/24/2018] [Accepted: 10/25/2018] [Indexed: 01/12/2023] Open
Abstract
2-oxoglutarate (α-ketoglutarate; 2-OG) is an intermediate of the Krebs cycle, and constitutes the carbon skeleton for nitrogen assimilation and the synthesis of a variety of compounds. In addition to being an important metabolite, 2-OG is a signaling molecule with a broad regulatory repertoire in a variety of organisms, including plants, animals, and bacteria. Although challenging, measuring the levels and variations of metabolic signals in vivo is critical to better understand how cells control specific processes. To measure cellular 2-OG concentrations and dynamics, we designed a set of biosensors based on the fluorescence resonance energy transfer (FRET) technology that can be used in vivo in different organisms. For this purpose, we took advantage of the conformational changes of two cyanobacterial proteins induced by 2-OG binding. We show that these biosensors responded immediately and specifically to different 2-OG levels, and hence allowed to measure 2-OG variations in function of environmental modifications in the proteobacterium Escherichia coli and in the cyanobacterium Anabaena sp. PCC 7120. Our results pave the way to study 2-OG dynamics at the cellular level in uni- and multi-cellular organisms.
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16
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Clauß K, Popp AP, Schulze L, Hettich J, Reisser M, Escoter Torres L, Uhlenhaut NH, Gebhardt JCM. DNA residence time is a regulatory factor of transcription repression. Nucleic Acids Res 2017; 45:11121-11130. [PMID: 28977492 PMCID: PMC5737411 DOI: 10.1093/nar/gkx728] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 08/08/2017] [Indexed: 12/21/2022] Open
Abstract
Transcription comprises a highly regulated sequence of intrinsically stochastic processes, resulting in bursts of transcription intermitted by quiescence. In transcription activation or repression, a transcription factor binds dynamically to DNA, with a residence time unique to each factor. Whether the DNA residence time is important in the transcription process is unclear. Here, we designed a series of transcription repressors differing in their DNA residence time by utilizing the modular DNA binding domain of transcription activator-like effectors (TALEs) and varying the number of nucleotide-recognizing repeat domains. We characterized the DNA residence times of our repressors in living cells using single molecule tracking. The residence times depended non-linearly on the number of repeat domains and differed by more than a factor of six. The factors provoked a residence time-dependent decrease in transcript level of the glucocorticoid receptor-activated gene SGK1. Down regulation of transcription was due to a lower burst frequency in the presence of long binding repressors and is in accordance with a model of competitive inhibition of endogenous activator binding. Our single molecule experiments reveal transcription factor DNA residence time as a regulatory factor controlling transcription repression and establish TALE-DNA binding domains as tools for the temporal dissection of transcription regulation.
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Affiliation(s)
- Karen Clauß
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Achim P Popp
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Lena Schulze
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Johannes Hettich
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Matthias Reisser
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Laura Escoter Torres
- Helmholtz Diabetes Center (HMGU) and German Center for Diabetes Research (DZD), IDO, Parkring 13, 85748 Garching, Munich, Germany
| | - N Henriette Uhlenhaut
- Helmholtz Diabetes Center (HMGU) and German Center for Diabetes Research (DZD), IDO, Parkring 13, 85748 Garching, Munich, Germany
| | - J Christof M Gebhardt
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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Ding Y, Berezuk A, Khursigara CM, Jarrell KF. Bypassing the Need for the Transcriptional Activator EarA through a Spontaneous Deletion in the BRE Portion of the fla Operon Promoter in Methanococcus maripaludis. Front Microbiol 2017; 8:1329. [PMID: 28769898 PMCID: PMC5512572 DOI: 10.3389/fmicb.2017.01329] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 06/30/2017] [Indexed: 11/13/2022] Open
Abstract
In Methanococcus maripaludis, the euryarchaeal archaellum regulator A (EarA) is required for the transcription of the fla operon, which is comprised of a series of genes which encode most of the proteins needed for the formation of the archaeal swimming organelle, the archaellum. In mutants deleted for earA (ΔearA), there is almost undetectable transcription of the fla operon, Fla proteins are not synthesized and the cells are non-archaellated. In this study, we have isolated a spontaneous mutant of a ΔearA mutant in which the restoration of the transcription and translation of the fla operon (using flaB2, the second gene of the operon, as a reporter), archaella formation and swarming motility were all restored even in the absence of EarA. Analysis of the DNA sequence from the fla promoter of this spontaneous mutant revealed a deletion of three adenines within a string of seven adenines in the transcription factor B recognition element (BRE). When the three adenine deletion in the BRE was regenerated in a stock culture of the ΔearA mutant, very similar phenotypes to that of the spontaneous mutant were observed. Deletion of the three adenines in the fla promoter BRE resulted in the mutant BRE having high sequence identity to BREs from promoters that have strong basal transcription level in Mc. maripaludis and Methanocaldococcus jannaschii. These data suggest that EarA may help recruit transcription factor B to a weak BRE in the fla promoter of wild-type cells but is not required for transcription from the fla promoter with a strong BRE, as in the three adenine deletion version in the spontaneous mutant.
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Affiliation(s)
- Yan Ding
- Department of Biomedical and Molecular Sciences, Queen's University, KingstonON, Canada
| | - Alison Berezuk
- Department of Molecular and Cellular Biology, University of Guelph, GuelphON, Canada
| | - Cezar M Khursigara
- Department of Molecular and Cellular Biology, University of Guelph, GuelphON, Canada
| | - Ken F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, KingstonON, Canada
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Phylogenomic proximity and metabolic discrepancy of Methanosarcina mazei Go1 across methanosarcinal genomes. Biosystems 2017; 155:20-28. [DOI: 10.1016/j.biosystems.2017.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 03/15/2017] [Accepted: 03/20/2017] [Indexed: 02/04/2023]
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19
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Phylogenetic distribution of the euryarchaeal archaellum regulator EarA and complementation of a Methanococcus maripaludis ∆earA mutant with heterologous earA homologues. Microbiology (Reading) 2017; 163:804-815. [DOI: 10.1099/mic.0.000464] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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20
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Fernandes GDC, Hauf K, Sant'Anna FH, Forchhammer K, Passaglia LMP. Glutamine synthetase stabilizes the binding of GlnR to nitrogen fixation gene operators. FEBS J 2017; 284:903-918. [DOI: 10.1111/febs.14021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/22/2016] [Accepted: 01/18/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Gabriela de C. Fernandes
- Departamento de Genética Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre RS Brazil
- Interfaculty Institute for Microbiology and Infection Medicine University of Tuebingen Germany
| | - Ksenia Hauf
- Interfaculty Institute for Microbiology and Infection Medicine University of Tuebingen Germany
| | - Fernando H. Sant'Anna
- Departamento de Genética Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre RS Brazil
| | - Karl Forchhammer
- Interfaculty Institute for Microbiology and Infection Medicine University of Tuebingen Germany
| | - Luciane M. P. Passaglia
- Departamento de Genética Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre RS Brazil
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21
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Complementation of an aglB Mutant of Methanococcus maripaludis with Heterologous Oligosaccharyltransferases. PLoS One 2016; 11:e0167611. [PMID: 27907170 PMCID: PMC5131992 DOI: 10.1371/journal.pone.0167611] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 11/17/2016] [Indexed: 01/04/2023] Open
Abstract
The oligosaccharyltransferase is the signature enzyme for N-linked glycosylation in all domains of life. In Archaea, this enzyme termed AglB, is responsible for transferring lipid carrier-linked glycans to select asparagine residues in a variety of target proteins including archaellins, S-layer proteins and pilins. This study investigated the ability of a variety of AglBs to compensate for the oligosaccharyltransferase activity in Methanococcus maripaludis deleted for aglB, using archaellin FlaB2 as the reporter protein since all archaellins in Mc. maripaludis are modified at multiple sites by an N-linked tetrasaccharide and this modification is required for archaellation. In the Mc. maripaludis ΔaglB strain FlaB2 runs as at a smaller apparent molecular weight in western blots and is nonarchaellated. We demonstrate that AglBs from Methanococcus voltae and Methanothermococcus thermolithotrophicus functionally replaced the oligosaccharyltransferase activity missing in the Mc. maripaludis ΔaglB strain, both returning the apparent molecular weight of FlaB2 to wildtype size and restoring archaellation. This demonstrates that AglB from Mc. voltae has a relaxed specificity for the linking sugar of the transferred glycan since while the N-linked glycan present in Mc. voltae is similar to that of Mc. maripaludis, the Mc. voltae glycan uses N-acetylglucosamine as the linking sugar. In Mc. maripaludis that role is held by N-acetylgalactosamine. This study also identifies aglB from Mtc. thermolithotrophicus for the first time by its activity. Attempts to use AglB from Methanocaldococcus jannaschii, Haloferax volcanii or Sulfolobus acidocaldarius to functionally replace the oligosaccharyltransferase activity missing in the Mc. maripaludis ΔaglB strain were unsuccessful.
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22
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Ding Y, Nash J, Berezuk A, Khursigara CM, Langelaan DN, Smith SP, Jarrell KF. Identification of the first transcriptional activator of an archaellum operon in a euryarchaeon. Mol Microbiol 2016; 102:54-70. [PMID: 27314758 DOI: 10.1111/mmi.13444] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2016] [Indexed: 12/21/2022]
Abstract
The archaellum is the swimming organelle of the third domain, the Archaea. In the euryarchaeon Methanococcus maripaludis, genes involved in archaella formation, including the three archaellins flaB1, flaB2 and flaB3, are mainly located in the fla operon. Previous studies have shown that transcription of fla genes and expression of Fla proteins are regulated under different growth conditions. In this study, we identify MMP1718 as the first transcriptional activator that directly regulates the fla operon in M. maripaludis. Mutants carrying an in-frame deletion in mmp1718 did not express FlaB2 detected by western blotting. Quantitative reverse transcription PCR analysis of purified RNA from the Δmmp1718 mutant showed that transcription of flaB2 was negligible compared to wildtype cells. In addition, no archaella were observed on the cell surface of the Δmmp1718 mutant. FlaB2 expression and archaellation were restored when the Δmmp1718 mutant was complemented with mmp1718 in trans. Electrophoretic motility shift assay and isothermal titration calorimetry results demonstrated the specific binding of purified MMP1718 to DNA fragments upstream of the fla promoter. Four 6 bp consensus sequences were found immediately upstream of the fla promoter and are considered the putative MMP1718-binding sites. Herein, we designate MMP1718 as EarA, the first euryarchaeal archaellum regulator.
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Affiliation(s)
- Yan Ding
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - John Nash
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, Ontario, N1G 3W4, Canada
| | - Alison Berezuk
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Cezar M Khursigara
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - David N Langelaan
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Steven P Smith
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Ken F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada.
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23
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Goyal N, Zhou Z, Karimi IA. Metabolic processes of Methanococcus maripaludis and potential applications. Microb Cell Fact 2016; 15:107. [PMID: 27286964 PMCID: PMC4902934 DOI: 10.1186/s12934-016-0500-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 05/31/2016] [Indexed: 12/30/2022] Open
Abstract
Methanococcus maripaludis is a rapidly growing, fully sequenced, genetically tractable model organism among hydrogenotrophic methanogens. It has the ability to convert CO2 and H2 into a useful cleaner energy fuel (CH4). In fact, this conversion enhances in the presence of free nitrogen as the sole nitrogen source due to prolonged cell growth. Given the global importance of GHG emissions and climate change, diazotrophy can be attractive for carbon capture and utilization applications from appropriately treated flue gases, where surplus hydrogen is available from renewable electricity sources. In addition, M. maripaludis can be engineered to produce other useful products such as terpenoids, hydrogen, methanol, etc. M. maripaludis with its unique abilities has the potential to be a workhorse like Escherichia coli and S. cerevisiae for fundamental and experimental biotechnology studies. More than 100 experimental studies have explored different specific aspects of the biochemistry and genetics of CO2 and N2 fixation by M. maripaludis. Its genome-scale metabolic model (iMM518) also exists to study genetic perturbations and complex biological interactions. However, a comprehensive review describing its cell structure, metabolic processes, and methanogenesis is still lacking in the literature. This review fills this crucial gap. Specifically, it integrates distributed information from the literature to provide a complete and detailed view for metabolic processes such as acetyl-CoA synthesis, pyruvate synthesis, glycolysis/gluconeogenesis, reductive tricarboxylic acid (RTCA) cycle, non-oxidative pentose phosphate pathway (NOPPP), nitrogen metabolism, amino acid metabolism, and nucleotide biosynthesis. It discusses energy production via methanogenesis and its relation to metabolism. Furthermore, it reviews taxonomy, cell structure, culture/storage conditions, molecular biology tools, genome-scale models, and potential industrial and environmental applications. Through the discussion, it develops new insights and hypotheses from experimental and modeling observations, and identifies opportunities for further research and applications.
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Affiliation(s)
- Nishu Goyal
- />Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585 Singapore
| | - Zhi Zhou
- />School of Civil Engineering and Division of Environmental and Ecological Engineering, Purdue University, 550 Stadium Mall Drive, West Lafayette, IN 47907 USA
| | - Iftekhar A. Karimi
- />Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585 Singapore
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24
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Abstract
The metabolite 2-oxoglutarate (also known as α-ketoglutarate, 2-ketoglutaric acid, or oxoglutaric acid) lies at the intersection between the carbon and nitrogen metabolic pathways. This compound is a key intermediate of one of the most fundamental biochemical pathways in carbon metabolism, the tricarboxylic acid (TCA) cycle. In addition, 2-oxoglutarate also acts as the major carbon skeleton for nitrogen-assimilatory reactions. Experimental data support the conclusion that intracellular levels of 2-oxoglutarate fluctuate according to nitrogen and carbon availability. This review summarizes how nature has capitalized on the ability of 2-oxoglutarate to reflect cellular nutritional status through evolution of a variety of 2-oxoglutarate-sensing regulatory proteins. The number of metabolic pathways known to be regulated by 2-oxoglutarate levels has increased significantly in recent years. The signaling properties of 2-oxoglutarate are highlighted by the fact that this metabolite regulates the synthesis of the well-established master signaling molecule, cyclic AMP (cAMP), in Escherichia coli.
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25
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Ding Y, Jones GM, Brimacombe C, Uchida K, Aizawa SI, Logan SM, Kelly JF, Jarrell KF. Identification of a gene involved in the biosynthesis pathway of the terminal sugar of the archaellin N-linked tetrasaccharide in Methanococcus maripaludis. Antonie van Leeuwenhoek 2015; 109:131-48. [PMID: 26590834 DOI: 10.1007/s10482-015-0615-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/28/2015] [Indexed: 10/22/2022]
Abstract
In Methanococcus maripaludis, the three archaellins which comprise the archaellum are modified at multiple sites with an N-linked tetrasaccharide with the structure of Sug-4-β-ManNAc3NAmA6Thr-4-β-GlcNAc3NAcA-3-β-GalNAc, where Sug is a unique sugar (5S)-2-acetamido-2,4-dideoxy-5-O-methyl-L-erythro-hexos-5-ulo-1,5-pyranose, so far found exclusively in this species. In this study, a six-gene cluster mmp1089-1094, neighboring one of the genomic regions already known to contain genes involved with the archaellin N-glycosylation pathway, was examined for its potential involvement in the archaellin N-glycosylation or sugar biosynthesis pathway. The co-transcription of these six genes was demonstrated by RT-PCR. Mutants carrying an in-frame deletion in mmp1090, mmp1091 or mmp1092 were successfully generated. The Δmmp1090 deletion mutant was archaellated when examined by electron microscopy and mass spectrometry analysis of purified archaella showed that the archaellins were modified with a truncated N-glycan in which the terminal sugar residue and the threonine linked to the third sugar residue were missing. Both gene annotation and bioinformatic analyses indicate that MMP1090 is a UDP-glucose 4-epimerase, suggesting that the unique terminal sugar of the archaellin N-glycan might be synthesised from UDP-glucose or UDP-N-acetylglucosamine with an essential early step in synthesis catalysed by MMP1090. In contrast, no detectable phenotype related to archaellin glycosylation was observed in mutants deleted for either mmp1091 or mmp1092 while attempts to delete mmp1089, mmp1093 and mmp1094 were unsuccessful. Based on its demonstrated involvement in the archaellin N-glycosylation pathway, we designated mmp1090 as aglW.
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Affiliation(s)
- Yan Ding
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L 3N6, Canada
| | - Gareth M Jones
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L 3N6, Canada
| | - Cedric Brimacombe
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L 3N6, Canada
| | - Kaoru Uchida
- Department of Life Sciences, Prefectural University of Hiroshima, Shobara, Hiroshima, 727-0023, Japan
| | - Shin-Ichi Aizawa
- Department of Life Sciences, Prefectural University of Hiroshima, Shobara, Hiroshima, 727-0023, Japan
| | - Susan M Logan
- Human Health Therapeutics Portfolio, National Research Council, Ottawa, K1A 0R6, Canada
| | - John F Kelly
- Human Health Therapeutics Portfolio, National Research Council, Ottawa, K1A 0R6, Canada.
| | - Ken F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L 3N6, Canada.
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26
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Lyu Z, Lu Y. Comparative genomics of three Methanocellales strains reveal novel taxonomic and metabolic features. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:526-537. [PMID: 25727385 DOI: 10.1111/1758-2229.12283] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 02/22/2015] [Indexed: 06/04/2023]
Abstract
Methanocellales represents a new order of methanogens, which is widespread in environments and plays specifically the important role in methane emissions from paddy fields. To gain more insights into Methanocellales, comparative genomic studies were performed among three Methanocellales strains through the same annotation pipeline. Genetic relationships among strains revealed by genome alignment, pan-genome reconstruction and comparison of amino average identity suggest that they should be classified in different genera. In addition, multiple copies of cell cycle regulator proteins were identified for the first time in Archaea. Core metabolisms were reconstructed, predicting certain unique and novel features for Methanocellales, including a set of methanogenesis genes potentially organized toward specialization in utilizing low concentrations of H2, a new route of disulfide reduction catalysed by a disulfide-reducing hydrogenase (Drh) complex phylogenetically related to sulfate-reducing prokaryotes, an oxidative tricarboxylic acid (TCA) cycle, a sophisticated nitrogen uptake and regulation system as well as a versatile sulfur utilization system. These core metabolisms are largely conserved among the three strains, but differences in gene copy number and metabolic diversity are evident. The present study thus adds new dimensions to the unique ecophysiology of Methanocellales and offers a road map for further experimental characterization of this methanogen lineage.
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Affiliation(s)
- Zhe Lyu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Yahai Lu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
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27
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Evidence that biosynthesis of the second and third sugars of the archaellin Tetrasaccharide in the archaeon Methanococcus maripaludis occurs by the same pathway used by Pseudomonas aeruginosa to make a di-N-acetylated sugar. J Bacteriol 2015; 197:1668-80. [PMID: 25733616 DOI: 10.1128/jb.00040-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 02/24/2015] [Indexed: 01/09/2023] Open
Abstract
UNLABELLED Methanococcus maripaludis has two surface appendages, archaella and type IV pili, which are composed of glycoprotein subunits. Archaellins are modified with an N-linked tetrasaccharide with the structure Sug-1,4-β-ManNAc3NAmA6Thr-1,4-β-GlcNAc3NAcA-1,3-β-GalNAc, where Sug is (5S)-2-acetamido-2,4-dideoxy-5-O-methyl-α-L-erythro-hexos-5-ulo-1,5-pyranose. The pilin glycan has an additional hexose attached to GalNAc. In this study, genes located in two adjacent, divergently transcribed operons (mmp0350-mmp0354 and mmp0359-mmp0355) were targeted for study based on annotations suggesting their involvement in biosynthesis of N-glycan sugars. Mutants carrying deletions in mmp0350, mmp0351, mmp0352, or mmp0353 were nonarchaellated and synthesized archaellins modified with a 1-sugar glycan, as estimated from Western blots. Mass spectroscopy analysis of pili purified from the Δmmp0352 strain confirmed a glycan with only GalNAc, suggesting mmp0350 to mmp0353 were all involved in biosynthesis of the second sugar (GlcNAc3NAcA). The Δmmp0357 mutant was archaellated and had archaellins with a 2-sugar glycan, as confirmed by mass spectroscopy of purified archaella, indicating a role for MMP0357 in biosynthesis of the third sugar (ManNAc3NAmA6Thr). M. maripaludis mmp0350, mmp0351, mmp0352, mmp0353, and mmp0357 are proposed to be functionally equivalent to Pseudomonas aeruginosa wbpABEDI, involved in converting UDP-N-acetylglucosamine to UDP-2,3-diacetamido-2,3-dideoxy-d-mannuronic acid, an O5-specific antigen sugar. Cross-domain complementation of the final step of the P. aeruginosa pathway with mmp0357 supports this hypothesis. IMPORTANCE This work identifies a series of genes in adjacent operons that are shown to encode the enzymes that complete the entire pathway for generation of the second and third sugars of the N-linked tetrasaccharide that modifies archaellins of Methanococcus maripaludis. This posttranslational modification of archaellins is important, as it is necessary for archaellum assembly. Pilins are modified with a different N-glycan consisting of the archaellin tetrasaccharide but with an additional hexose attached to the linking sugar. Mass spectrometry analysis of the pili of one mutant strain provided insight into how this different glycan might ultimately be assembled. This study includes a rare example of an archaeal gene functionally replacing a bacterial gene in a complex sugar biosynthesis pathway.
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28
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Nair DB, Jarrell KF. Pilin Processing Follows a Different Temporal Route than That of Archaellins in Methanococcus maripaludis. Life (Basel) 2015; 5:85-101. [PMID: 25569238 PMCID: PMC4390842 DOI: 10.3390/life5010085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 12/26/2014] [Indexed: 11/16/2022] Open
Abstract
Methanococcus maripaludis has two different surface appendages: type IV-like pili and archaella. Both structures are believed to be assembled using a bacterial type IV pilus mechanism. Each structure is composed of multiple subunits, either pilins or archaellins. Both pilins and archaellins are made initially as preproteins with type IV pilin-like signal peptides, which must be removed by a prepilin peptidase-like enzyme. This enzyme is FlaK for archaellins and EppA for pilins. In addition, both pilins and archaellins are modified with N-linked glycans. The archaellins possess an N-linked tetrasaccharide while the pilins have a pentasaccharide which consists of the archaellin tetrasaccharide but with an additional sugar, an unidentified hexose, attached to the linking sugar. In this report, we show that archaellins can be processed by FlaK in the absence of N-glycosylation and N-glycosylation can occur on archaellins that still retain their signal peptides. In contrast, pilins are not glycosylated unless they have been acted on by EppA to have the signal peptide removed. However, EppA can still remove signal peptides from non-glycosylated pilins. These findings indicate that there is a difference in the order of the posttranslational modifications of pilins and archaellins even though both are type IV pilin-like proteins.
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Affiliation(s)
- Divya B Nair
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Ken F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
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Goyal N, Widiastuti H, Karimi IA, Zhou Z. A genome-scale metabolic model of Methanococcus maripaludis S2 for CO2 capture and conversion to methane. MOLECULAR BIOSYSTEMS 2014; 10:1043-54. [PMID: 24553424 DOI: 10.1039/c3mb70421a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Methane is a major energy source for heating and electricity. Its production by methanogenic bacteria is widely known in nature. M. maripaludis S2 is a fully sequenced hydrogenotrophic methanogen and an excellent laboratory strain with robust genetic tools. However, a quantitative systems biology model to complement these tools is absent in the literature. To understand and enhance its methanogenesis from CO2, this work presents the first constraint-based genome-scale metabolic model (iMM518). It comprises 570 reactions, 556 distinct metabolites, and 518 genes along with gene-protein-reaction (GPR) associations, and covers 30% of open reading frames (ORFs). The model was validated using biomass growth data and experimental phenotypic studies from the literature. Its comparison with the in silico models of Methanosarcina barkeri, Methanosarcina acetivorans, and Sulfolobus solfataricus P2 shows M. maripaludis S2 to be a better organism for producing methane. Using the model, genes essential for growth were identified, and the efficacies of alternative carbon, hydrogen and nitrogen sources were studied. The model can predict the effects of reengineering M. maripaludis S2 to guide or expedite experimental efforts.
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Affiliation(s)
- Nishu Goyal
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117576.
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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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Nair DB, Uchida K, Aizawa SI, Jarrell KF. Genetic analysis of a type IV pili-like locus in the archaeon Methanococcus maripaludis. Arch Microbiol 2014; 196:179-91. [PMID: 24493292 DOI: 10.1007/s00203-014-0956-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 12/28/2013] [Accepted: 01/24/2014] [Indexed: 12/29/2022]
Abstract
Methanococcus maripaludis is a stringently anaerobic archaeon with two studied surface structures, archaella and type IV pili. Previously, it was shown that three pilin genes (mmp0233 [epdA], mmp0236 [epdB] and mmp0237 [epdC]) located within an 11 gene cluster in the genome were necessary for normal piliation. This study focused on analysis of the remaining genes to determine their potential involvement in piliation. Reverse transcriptase PCR experiments demonstrated the 11 genes formed a single transcriptional unit. Deletions were made in all the non-pilin genes except mmp0231. Electron microscopy revealed that all the genes in the locus except mmp0235 and mmp0238 were essential for piliation. Complementation with a plasmid-borne wild-type copy of the deleted gene restored at least some piliation. We identified genes for an assembly ATPase and two versions of the conserved pilin platform forming protein necessary for pili assembly at a separate genetic locus.
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Affiliation(s)
- Divya B Nair
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada
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Development of β -lactamase as a tool for monitoring conditional gene expression by a tetracycline-riboswitch in Methanosarcina acetivorans. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014; 2014:725610. [PMID: 24678266 PMCID: PMC3942078 DOI: 10.1155/2014/725610] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 12/02/2013] [Indexed: 11/17/2022]
Abstract
The use of reporter gene fusions to assess cellular processes such as protein targeting and regulation of transcription or translation is established technology in archaeal, bacterial, and eukaryal genetics. Fluorescent proteins or enzymes resulting in chromogenic substrate turnover, like β-galactosidase, have been particularly useful for microscopic and screening purposes. However, application of such methodology is of limited use for strictly anaerobic organisms due to the requirement of molecular oxygen for chromophore formation or color development. We have developed β-lactamase from Escherichia coli (encoded by bla) in conjunction with the chromogenic substrate nitrocefin into a reporter system usable under anaerobic conditions for the methanogenic archaeon Methanosarcina acetivorans. By using a signal peptide of a putative flagellin from M. acetivorans and different catabolic promoters, we could demonstrate growth substrate-dependent secretion of β-lactamase, facilitating its use in colony screening on agar plates. Furthermore, a series of fusions comprised of a constitutive promoter and sequences encoding variants of the synthetic tetracycline-responsive riboswitch (tc-RS) was created to characterize its influence on translation initiation in M. acetivorans. One tc-RS variant resulted in more than 11-fold tetracycline-dependent regulation of bla expression, which is in the range of regulation by naturally occurring riboswitches. Thus, tc-RS fusions represent the first solely cis-active, that is, factor-independent system for controlled gene expression in Archaea.
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Abstract
The ability of organisms to sense and respond to their environment is essential to their survival. This is no different for members of the third domain of life, the Archaea. Archaea are found in diverse and often extreme habitats. However, their ability to sense and respond to their environment at the level of gene expression has been understudied when compared to bacteria and eukaryotes. Over the last decade, the field has expanded, and a variety of unique and interesting regulatory schemes have been unraveled. In this review, the current state of knowledge of archaeal transcription regulation is explored.
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Nair DB, Chung DKC, Schneider J, Uchida K, Aizawa SI, Jarrell KF. Identification of an additional minor pilin essential for piliation in the archaeon Methanococcus maripaludis. PLoS One 2013; 8:e83961. [PMID: 24386316 PMCID: PMC3875500 DOI: 10.1371/journal.pone.0083961] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 11/11/2013] [Indexed: 11/19/2022] Open
Abstract
Methanococcus maripaludis is an archaeon with two studied surface appendages, archaella and type IV-like pili. Previously, the major structural pilin was identified as MMP1685 and three additional proteins were designated as minor pilins (EpdA, EpdB and EpdC). All of the proteins are likely processed by the pilin-specific prepilin peptidase EppA. Six other genes were identified earlier as likely encoding pilin proteins processed also by EppA. In this study, each of the six genes (mmp0528, mmp0600, mmp0601, mmp0709, mmp0903 and mmp1283) was deleted and the mutants examined by electron microscopy to determine their essentiality for pili formation. While mRNA transcripts of all genes were detected by RT-PCR, only the deletion of mmp1283 led to nonpiliated cells. This strain could be complemented back to a piliated state by supplying a wildtype copy of the mmp1283 gene in trans. This study adds to the complexity of the type IV pili system in M. maripaludis and raises questions about the functions of the remaining five pilin-like genes and whether M. maripaludis under other growth conditions may be able to assemble additional pili-like structures.
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Affiliation(s)
- Divya B Nair
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Daniel K C Chung
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - James Schneider
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Kaoru Uchida
- Department of Life Sciences, Prefectural University of Hiroshima, 562 Nanatsuka, Shobara, Hiroshima, Japan
| | - Shin-Ichi Aizawa
- Department of Life Sciences, Prefectural University of Hiroshima, 562 Nanatsuka, Shobara, Hiroshima, Japan
| | - Ken F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
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Affiliation(s)
- Joel A. Farkas
- Department of Microbiology and Center for RNA Biology, Ohio State University, Columbus, Ohio 43210
| | - Jonathan W. Picking
- Department of Microbiology and Center for RNA Biology, Ohio State University, Columbus, Ohio 43210
| | - Thomas J. Santangelo
- Department of Microbiology and Center for RNA Biology, Ohio State University, Columbus, Ohio 43210
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523;
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Abstract
For cellular fitness and survival, gene expression levels need to be regulated in response to a wealth of cellular and environmental signals. TFs (transcription factors) execute a large part of this regulation by interacting with the basal transcription machinery at promoter regions. Archaea are characterized by a simplified eukaryote-like basal transcription machinery and bacteria-type TFs, which convert sequence information into a gene expression output according to cis-regulatory rules. In the present review, we discuss the current state of knowledge about these rules in archaeal systems, ranging from DNA-binding specificities and operator architecture to regulatory mechanisms.
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Identification of genes involved in the biosynthesis of the third and fourth sugars of the Methanococcus maripaludis archaellin N-linked tetrasaccharide. J Bacteriol 2013; 195:4094-104. [PMID: 23836872 DOI: 10.1128/jb.00668-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
N-glycosylation is a protein posttranslational modification found in all three domains of life. Many surface proteins in Archaea, including S-layer proteins, pilins, and archaellins (archaeal flagellins) are known to contain N-linked glycans. In Methanococcus maripaludis, the archaellins are modified at multiple sites with an N-linked tetrasaccharide with the structure Sug-1,4-β-ManNAc3NAmA6Thr-1,4-β-GlcNAc3NAcA-1,3-β-GalNAc, where Sug is the unique sugar (5S)-2-acetamido-2,4-dideoxy-5-O-methyl-α-l-erythro-hexos-5-ulo-1,5-pyranose. In this study, four genes--mmp1084, mmp1085, mmp1086, and mmp1087--were targeted to determine their potential involvement of the biosynthesis of the sugar components in the N-glycan, based on bioinformatics analysis and proximity to a number of genes which have been previously demonstrated to be involved in the N-glycosylation pathway. The genes mmp1084 to mmp1087 were shown to be cotranscribed, and in-frame deletions of each gene as well as a Δmmp1086Δmmp1087 double mutant were successfully generated. All mutants were archaellated and motile. Mass spectrometry examination of purified archaella revealed that in Δmmp1084 mutant cells, the threonine linked to the third sugar of the glycan was missing, indicating a putative threonine transferase function of MMP1084. Similar analysis of the archaella of the Δmmp1085 mutant cells demonstrated that the glycan lacked the methyl group at the C-5 position of the terminal sugar, indicating that MMP1085 is a methyltransferase involved in the biosynthesis of this unique sugar. Deletion of the remaining two genes, mmp1086 and mmp1087, either singularly or together, had no effect on the structure of the archaellin N-glycan. Because of their demonstrated involvement in the N-glycosylation pathway, we designated mmp1084 as aglU and mmp1085 as aglV.
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Peeters E, van Oeffelen L, Nadal M, Forterre P, Charlier D. A thermodynamic model of the cooperative interaction between the archaeal transcription factor Ss-LrpB and its tripartite operator DNA. Gene 2013; 524:330-40. [PMID: 23603352 DOI: 10.1016/j.gene.2013.03.118] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 03/07/2013] [Indexed: 10/26/2022]
Abstract
Ss-LrpB is a transcription factor of the archaeon Sulfolobus solfataricus that belongs to the leucine-responsive regulatory protein family. This protein binds to three distinct binding sites in the control region of its own gene, suggestive of autoregulation. Here, we present a detailed study of the thermodynamic and conformational rules that govern the interaction between Ss-LrpB and its tripartite operator DNA. Lane-per-lane partition analysis of macroscopic binding state populations in electrophoretic mobility shift assays, probing binding to full-length, truncated and mutated forms of the operator, allowed determination of equilibrium association constants and cooperativity parameters. The resulting thermodynamic model demonstrates that the Ss-LrpB-operator regulatory complex is formed with a significant positive cooperativity, which is mostly arising from dimer-dimer interactions between pairs of adjacent binding sites. There is a constraint on the spacing between these binding sites, with a preference for a cis-alignment on the DNA helix and with a 16-bp linker yielding maximal pairwise cooperativity. DNase I footprinting assays demonstrated that the extent of Ss-LrpB-induced DNA deformations depends on linker length. The knowledge of the thermodynamic principles underlying the Ss-LrpB-operator interaction, presented here, will contribute to unraveling of the cis-regulatory code of Ss-LrpB autoregulation.
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Affiliation(s)
- Eveline Peeters
- Research group of Microbiology, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
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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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Essential anaplerotic role for the energy-converting hydrogenase Eha in hydrogenotrophic methanogenesis. Proc Natl Acad Sci U S A 2012; 109:15473-8. [PMID: 22872868 DOI: 10.1073/pnas.1208779109] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite decades of study, electron flow and energy conservation in methanogenic Archaea are still not thoroughly understood. For methanogens without cytochromes, flavin-based electron bifurcation has been proposed as an essential energy-conserving mechanism that couples exergonic and endergonic reactions of methanogenesis. However, an alternative hypothesis posits that the energy-converting hydrogenase Eha provides a chemiosmosis-driven electron input to the endergonic reaction. In vivo evidence for both hypotheses is incomplete. By genetically eliminating all nonessential pathways of H(2) metabolism in the model methanogen Methanococcus maripaludis and using formate as an additional electron donor, we isolate electron flow for methanogenesis from flux through Eha. We find that Eha does not function stoichiometrically for methanogenesis, implying that electron bifurcation must operate in vivo. We show that Eha is nevertheless essential, and a substoichiometric requirement for H(2) suggests that its role is anaplerotic. Indeed, H(2) via Eha stimulates methanogenesis from formate when intermediates are not otherwise replenished. These results fit the model for electron bifurcation, which renders the methanogenic pathway cyclic, and as such requires the replenishment of intermediates. Defining a role for Eha and verifying electron bifurcation provide a complete model of methanogenesis where all necessary electron inputs are accounted for.
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Sharma K, Gillum N, Boyd JL, Schmid A. The RosR transcription factor is required for gene expression dynamics in response to extreme oxidative stress in a hypersaline-adapted archaeon. BMC Genomics 2012; 13:351. [PMID: 22846541 PMCID: PMC3443676 DOI: 10.1186/1471-2164-13-351] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 07/05/2012] [Indexed: 11/10/2022] Open
Abstract
Background Previous work has shown that the hypersaline-adapted archaeon, Halobacterium salinarum NRC-1, is highly resistant to oxidative stress caused by exposure to hydrogen peroxide, UV, and gamma radiation. Dynamic alteration of the gene regulatory network (GRN) has been implicated in such resistance. However, the molecular functions of transcription regulatory proteins involved in this response remain unknown. Results Here we have reanalyzed several existing GRN and systems biology datasets for H. salinarum to identify and characterize a novel winged helix-turn-helix transcription factor, VNG0258H, as a regulator required for reactive oxygen species resistance in this organism. This protein appears to be unique to the haloarchaea at the primary sequence level. High throughput quantitative growth assays in a deletion mutant strain implicate VNG0258H in extreme oxidative stress resistance. According to time course gene expression analyses, this transcription factor is required for the appropriate dynamic response of nearly 300 genes to reactive oxygen species damage from paraquat and hydrogen peroxide. These genes are predicted to function in repair of oxidative damage to proteins and DNA. In vivo DNA binding assays demonstrate that VNG0258H binds DNA to mediate gene regulation. Conclusions Together these results suggest that VNG0258H is a novel archaeal transcription factor that regulates gene expression to enable adaptation to the extremely oxidative, hypersaline niche of H. salinarum. We have therefore renamed VNG0258H as RosR, for reactive oxygen species regulator.
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Affiliation(s)
- Kriti Sharma
- Center for Systems Biology, Institute for Genome Sciences and Policy, Durham, NC 27710, USA
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Identification of genes involved in the acetamidino group modification of the flagellin N-linked glycan of Methanococcus maripaludis. J Bacteriol 2012; 194:2693-702. [PMID: 22408155 DOI: 10.1128/jb.06686-11] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
N-linked glycosylation of protein is a posttranslational modification found in all three domains of life. The flagellin proteins of the archaeon Methanococcus maripaludis are known to be modified with an N-linked tetrasaccharide consisting of N-acetylgalactosamine (GalNAc), a diacetylated glucuronic acid (GlcNAc3NAc), an acetylated and acetamidino-modified mannuronic acid with a substituted threonine group (ManNAc3NAmA6Thr), and a novel terminal sugar residue [(5S)-2-acetamido-2,4-dideoxy-5-O-methyl-α-L-erythro-hexos-5-ulo-1,5-pyranose]. To identify genes involved in biosynthesis of the component sugars of this glycan, three genes, mmp1081, mmp1082, and mmp1083, were targeted for in-frame deletion, based on their annotation and proximity to glycosyltransferase genes known to be involved in assembly of the glycan. Mutants carrying a deletion in any of these three genes remained flagellated and motile. A strain with a deletion of mmp1081 had lower-molecular-mass flagellins in Western blots. Mass spectrometry of purified flagella revealed a truncated glycan with the terminal sugar absent and the threonine residue and the acetamidino group missing from the third sugar. No glycan modification was seen in either the Δmmp1082 or Δmmp1083 mutant grown in complex Balch III medium. However, a glycan identical to the Δmmp1081 glycan was observed when the Δmmp1082 or Δmmp1083 mutant was grown under ammonia-limited conditions. We hypothesize that MMP1082 generates ammonia and tunnels it through MMP1083 to MMP1081, which acts as the amidotransferase, modifying the third sugar residue of the M. maripaludis glycan with the acetamidino group.
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Overcoming fluctuation and leakage problems in the quantification of intracellular 2-oxoglutarate levels in Escherichia coli. Appl Environ Microbiol 2011; 77:6763-71. [PMID: 21821754 DOI: 10.1128/aem.05257-11] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2-Oxoglutarate is located at the junction between central carbon and nitrogen metabolism, serving as an intermediate for both. In nitrogen metabolism, 2-oxoglutarate acts as both a carbon skeletal carrier and an effector molecule. There have been only sporadic reports of its internal concentrations. Here we describe a sensitive and accurate method for determination of the 2-oxoglutarate pool concentration in Escherichia coli. The detection was based on fluorescence derivatization followed by reversed-phase high-pressure liquid chromatography separation. Two alternative cell sampling strategies, both of which were based on a fast filtration protocol, were sequentially developed to overcome both its fast metabolism and contamination from 2-oxoglutarate that leaks into the medium. We observed rapid changes in the 2-oxoglutarate pool concentration upon sudden depletion of nutrients: decreasing upon carbon depletion and increasing upon nitrogen depletion. The latter was studied in mutants lacking either of the two enzymes using 2-oxoglutarate as the carbon substrate for glutamate biosynthesis. The results suggest that flux restriction on either reaction greatly influences the internal 2-oxoglutarate level. Additional study indicates that KgtP, a 2-oxoglutarate proton symporter, functions to recover the leakage loss of 2-oxoglutarate. This recovery mechanism benefits the measurement of cellular 2-oxoglutarate level in practice by limiting contamination from 2-oxoglutarate leakage.
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Leigh JA, Albers SV, Atomi H, Allers T. Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales. FEMS Microbiol Rev 2011; 35:577-608. [PMID: 21265868 DOI: 10.1111/j.1574-6976.2011.00265.x] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The tree of life is split into three main branches: eukaryotes, bacteria, and archaea. Our knowledge of eukaryotic and bacteria cell biology has been built on a foundation of studies in model organisms, using the complementary approaches of genetics and biochemistry. Archaea have led to some exciting discoveries in the field of biochemistry, but archaeal genetics has been slow to get off the ground, not least because these organisms inhabit some of the more inhospitable places on earth and are therefore believed to be difficult to culture. In fact, many species can be cultivated with relative ease and there has been tremendous progress in the development of genetic tools for both major archaeal phyla, the Euryarchaeota and the Crenarchaeota. There are several model organisms available for methanogens, halophiles, and thermophiles; in the latter group, there are genetic systems for Sulfolobales and Thermococcales. In this review, we present the advantages and disadvantages of working with each archaeal group, give an overview of their different genetic systems, and direct the neophyte archaeologist to the most appropriate model organism.
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Affiliation(s)
- John A Leigh
- Department of Microbiology, University of Washington, Seattle, WA, USA
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Structural underpinnings of nitrogen regulation by the prototypical nitrogen-responsive transcriptional factor NrpR. Structure 2011; 18:1512-21. [PMID: 21070950 PMCID: PMC2996049 DOI: 10.1016/j.str.2010.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 08/02/2010] [Accepted: 08/13/2010] [Indexed: 10/18/2022]
Abstract
Plants and microorganisms reduce environmental inorganic nitrogen to ammonium, which then enters various metabolic pathways solely via conversion of 2-oxoglutarate (2OG) to glutamate and glutamine. Cellular 2OG concentrations increase during nitrogen starvation. We recently identified a family of 2OG-sensing proteins--the nitrogen regulatory protein NrpR--that bind DNA and repress transcription of nitrogen assimilation genes. We used X-ray crystallography to determine the structure of NrpR regulatory domain. We identified the NrpR 2OG-binding cleft and show that residues predicted to interact directly with 2OG are conserved among diverse classes of 2OG-binding proteins. We show that high levels of 2OG inhibit NrpRs ability to bind DNA. Electron microscopy analyses document that NrpR adopts different quaternary structures in its inhibited 2OG-bound state compared with its active apo state. Our results indicate that upon 2OG release, NrpR repositions its DNA-binding domains correctly for optimal interaction with DNA thereby enabling gene repression.
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Payankaulam S, Li LM, Arnosti DN. Transcriptional repression: conserved and evolved features. Curr Biol 2011; 20:R764-71. [PMID: 20833321 DOI: 10.1016/j.cub.2010.06.037] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The regulation of gene expression by transcriptional repression is an ancient and conserved mechanism that manifests itself in diverse ways. Here we summarize conserved pathways for transcriptional repression prevalent throughout all forms of life, as well as indirect mechanisms that appear to have originated in eukaryotes, consistent with the unique chromatin environment of eukaryotic genes. The direct interactions between transcriptional repressors and the core transcriptional machinery in bacteria and archaea are sufficient to generate a sophisticated suite of mechanisms that provide flexible control. These direct interactions contrast with the activity of corepressors, which provide an additional regulatory control in eukaryotes. Their modulation of chromatin structure represents an indirect pathway to downregulate transcription, and their diversity and modulation provide additional complexity suited to the requirements of elaborate eukaryotic repression patterns. New findings indicate that corepressors are not necessarily restricted to generating a single stereotypic output, but can rather exhibit diverse functional responses depending on the context in which they are recruited, providing a hitherto unsuspected additional source of diversity in transcriptional control. Mechanisms within eukaryotes appear to be highly conserved, with novel aspects chiefly represented by addition of lineage-specific corepressor scaffolds that provide additional opportunities for recruiting the same core machinery.
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Affiliation(s)
- Sandhya Payankaulam
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48910, USA
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50
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Abstract
Methanogenic archaea are a unique group of strictly anaerobic microorganisms characterized by their ability, and dependence, to convert simple C1 and C2 compounds to methane for growth. The major models for studying the biology of methanogens are members of the Methanococcus and Methanosarcina species. Recent development of sophisticated tools for molecular analysis and for genetic manipulation allows investigating not only their metabolism but also their cell cycle, and their interaction with the environment in great detail. One aspect of such analyses is assessment and dissection of methanoarchaeal gene regulation, for which, at present, only a handful of cases have been investigated thoroughly, partly due to the great methodological effort required. However, it becomes more and more evident that many new regulatory paradigms can be unraveled in this unique archaeal group. Here, we report both molecular and physiological/genetic methods to assess gene regulation in Methanococcus maripaludis and Methanosarcina acetivorans, which should, however, be applicable for other methanogens as well.
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Affiliation(s)
- Michael Rother
- Institut fu¨ r Molekulare Biowissenschaften, Molekulare Mikrobiologie & Bioenergetik, Johann Wolfgang Goethe-Universita¨t, Frankfurt am Main, Germany
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