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Oehlmann NN, Schmidt FV, Herzog M, Goldman AL, Rebelein JG. The iron nitrogenase reduces carbon dioxide to formate and methane under physiological conditions: A route to feedstock chemicals. SCIENCE ADVANCES 2024; 10:eado7729. [PMID: 39141735 PMCID: PMC11323892 DOI: 10.1126/sciadv.ado7729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 07/09/2024] [Indexed: 08/16/2024]
Abstract
Nitrogenases are the only known enzymes that reduce molecular nitrogen (N2) to ammonia. Recent findings have demonstrated that nitrogenases also reduce the greenhouse gas carbon dioxide (CO2), suggesting CO2 to be a competitor of N2. However, the impact of omnipresent CO2 on N2 fixation has not been investigated to date. Here, we study the competing reduction of CO2 and N2 by the two nitrogenases of Rhodobacter capsulatus, the molybdenum and the iron nitrogenase. The iron nitrogenase is almost threefold more efficient in CO2 reduction and profoundly less selective for N2 than the molybdenum isoform under mixtures of N2 and CO2. Correspondingly, the growth rate of diazotrophically grown R. capsulatus strains relying on the iron nitrogenase notably decreased after adding CO2. The in vivo CO2 activity of the iron nitrogenase facilitates the light-driven extracellular accumulation of formate and methane, one-carbon substrates for other microbes, and feedstock chemicals for a circular economy.
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Affiliation(s)
- Niels N. Oehlmann
- Research Group Microbial Metalloenzymes, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Frederik V. Schmidt
- Research Group Microbial Metalloenzymes, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Marcello Herzog
- Research Group Microbial Metalloenzymes, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Annelise L. Goldman
- Research Group Microbial Metalloenzymes, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Johannes G. Rebelein
- Research Group Microbial Metalloenzymes, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, 35043 Marburg, Germany
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2
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Körner D, Schäfer NM, Lagares Jr. A, Birmes L, Oehlmann NN, Addison H, Pöhl S, Thanbichler M, Rebelein JG, Petersen J, Becker A. Modular Low-Copy-Number Plasmid Vectors for Rhodobacterales with Extended Host Range in Alphaproteobacteria. ACS Synth Biol 2024; 13:1537-1548. [PMID: 38718218 PMCID: PMC11107812 DOI: 10.1021/acssynbio.4c00062] [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: 01/30/2024] [Revised: 03/27/2024] [Accepted: 04/15/2024] [Indexed: 05/18/2024]
Abstract
Members of the alphaproteobacterial order Rhodobacterales are metabolically diverse and highly abundant in the ocean. They are becoming increasingly interesting for marine biotechnology, due to their ecological adaptability, wealth of versatile low-copy-number plasmids, and their ability to produce secondary metabolites. However, molecular tools for engineering strains of this bacterial lineage are limited. Here, we expand the genetic toolbox by establishing standardized, modular repABC-based plasmid vectors of four well-characterized compatibility groups from the Roseobacter group applicable in the Rhodobacterales, and likely in further alphaproteobacterial orders (Hyphomicrobiales, Rhodospirillales, Caulobacterales). We confirmed replication of these newly constructed pABC vectors in two members of Rhodobacterales, namely, Dinoroseobacter shibae DFL 12 and Rhodobacter capsulatus B10S, as well as in two members of the alphaproteobacterial order Hyphomicrobiales (synonym: Rhizobiales; Ensifer meliloti 2011 and "Agrobacterium fabrum" C58). Maintenance of the pABC vectors in the biotechnologically valuable orders Rhodobacterales and Hyphomicrobiales facilitates the shuttling of genetic constructs between alphaproteobacterial genera and orders. Additionally, plasmid replication was verified in one member of Rhodospirillales (Rhodospirillum rubrum S1) as well as in one member of Caulobacterales (Caulobacter vibrioides CB15N). The modular construction of pABC vectors and the usage of four compatible replication systems, which allows their coexistence in a host cell, are advantageous features for future implementations of newly designed synthetic pathways. The vector applicability was demonstrated by functional complementation of a nitrogenase mutant phenotype by two complementary pABC-based plasmids in R. capsulatus.
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Affiliation(s)
- Désirée Körner
- Center
for Synthetic Microbiology (SYNMIKRO) and Department of Biology, Philipps-Universität Marburg, Marburg 35043, Germany
| | - Niklas M. Schäfer
- Center
for Synthetic Microbiology (SYNMIKRO) and Department of Biology, Philipps-Universität Marburg, Marburg 35043, Germany
| | - Antonio Lagares Jr.
- Center
for Synthetic Microbiology (SYNMIKRO) and Department of Biology, Philipps-Universität Marburg, Marburg 35043, Germany
| | - Lukas Birmes
- Leibniz-Institut
DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig 38124, Germany
| | - Niels N. Oehlmann
- Max
Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Holly Addison
- Max
Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Sebastian Pöhl
- Center
for Synthetic Microbiology (SYNMIKRO) and Department of Biology, Philipps-Universität Marburg, Marburg 35043, Germany
| | - Martin Thanbichler
- Center
for Synthetic Microbiology (SYNMIKRO) and Department of Biology, Philipps-Universität Marburg, Marburg 35043, Germany
- Max
Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Johannes G. Rebelein
- Center
for Synthetic Microbiology (SYNMIKRO) and Department of Biology, Philipps-Universität Marburg, Marburg 35043, Germany
- Max
Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Jörn Petersen
- Leibniz-Institut
DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig 38124, Germany
| | - Anke Becker
- Center
for Synthetic Microbiology (SYNMIKRO) and Department of Biology, Philipps-Universität Marburg, Marburg 35043, Germany
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Addison H, Glatter T, K. A. Hochberg G, Rebelein JG. Two distinct ferredoxins are essential for nitrogen fixation by the iron nitrogenase in Rhodobacter capsulatus. mBio 2024; 15:e0331423. [PMID: 38377621 PMCID: PMC10936413 DOI: 10.1128/mbio.03314-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
Nitrogenases are the only enzymes able to fix gaseous nitrogen into bioavailable ammonia and hence are essential for sustaining life. Catalysis by nitrogenases requires both a large amount of ATP and electrons donated by strongly reducing ferredoxins or flavodoxins. Our knowledge about the mechanisms of electron transfer to nitrogenase enzymes is limited: The electron transport to the iron (Fe)-nitrogenase has hardly been investigated. Here, we characterized the electron transfer pathway to the Fe-nitrogenase in Rhodobacter capsulatus via proteome analyses, genetic deletions, complementation studies, and phylogenetics. Proteome analyses revealed an upregulation of four ferredoxins under nitrogen-fixing conditions reliant on the Fe-nitrogenase in a molybdenum nitrogenase knockout strain, compared to non-nitrogen-fixing conditions. Based on these findings, R. capsulatus strains with deletions of ferredoxin (fdx) and flavodoxin (fld, nifF) genes were constructed to investigate their roles in nitrogen fixation by the Fe-nitrogenase. R. capsulatus deletion strains were characterized by monitoring diazotrophic growth and Fe-nitrogenase activity in vivo. Only deletions of fdxC or fdxN resulted in slower growth and reduced Fe-nitrogenase activity, whereas the double deletion of both fdxC and fdxN abolished diazotrophic growth. Differences in the proteomes of ∆fdxC and ∆fdxN strains, in conjunction with differing plasmid complementation behaviors of fdxC and fdxN, indicate that the two Fds likely possess different roles and functions. These findings will guide future engineering of the electron transport systems to nitrogenase enzymes, with the aim of increased electron flux and product formation.IMPORTANCENitrogenases are essential for biological nitrogen fixation, converting atmospheric nitrogen gas to bioavailable ammonia. The production of ammonia by diazotrophic organisms, harboring nitrogenases, is essential for sustaining plant growth. Hence, there is a large scientific interest in understanding the cellular mechanisms for nitrogen fixation via nitrogenases. Nitrogenases rely on highly reduced electrons to power catalysis, although we lack knowledge as to which proteins shuttle the electrons to nitrogenases within cells. Here, we characterized the electron transport to the iron (Fe)-nitrogenase in the model diazotroph Rhodobacter capsulatus, showing that two distinct ferredoxins are very important for nitrogen fixation despite having different redox centers. In addition, our research expands upon the debate on whether ferredoxins have functional redundancy or perform distinct roles within cells. Here, we observe that both essential ferredoxins likely have distinct roles based on differential proteome shifts of deletion strains and different complementation behaviors.
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Affiliation(s)
- Holly Addison
- Microbial Metalloenzymes Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Timo Glatter
- Core Facility for Mass Spectrometry & Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Georg K. A. Hochberg
- Evolutionary Biochemistry Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
| | - Johannes G. Rebelein
- Microbial Metalloenzymes Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
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Schmidt FV, Schulz L, Zarzycki J, Prinz S, Oehlmann NN, Erb TJ, Rebelein JG. Structural insights into the iron nitrogenase complex. Nat Struct Mol Biol 2024; 31:150-158. [PMID: 38062208 PMCID: PMC10803253 DOI: 10.1038/s41594-023-01124-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 09/12/2023] [Indexed: 01/24/2024]
Abstract
Nitrogenases are best known for catalyzing the reduction of dinitrogen to ammonia at a complex metallic cofactor. Recently, nitrogenases were shown to reduce carbon dioxide (CO2) and carbon monoxide to hydrocarbons, offering a pathway to recycle carbon waste into hydrocarbon products. Among the three nitrogenase isozymes, the iron nitrogenase has the highest wild-type activity for the reduction of CO2, but the molecular architecture facilitating these activities has remained unknown. Here, we report a 2.35-Å cryogenic electron microscopy structure of the ADP·AlF3-stabilized iron nitrogenase complex from Rhodobacter capsulatus, revealing an [Fe8S9C-(R)-homocitrate] cluster in the active site. The enzyme complex suggests that the iron nitrogenase G subunit is involved in cluster stabilization and substrate channeling and confers specificity between nitrogenase reductase and catalytic component proteins. Moreover, the structure highlights a different interface between the two catalytic halves of the iron and the molybdenum nitrogenase, potentially influencing the intrasubunit 'communication' and thus the nitrogenase mechanism.
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Affiliation(s)
- Frederik V Schmidt
- Microbial Metalloenzymes Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Luca Schulz
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jan Zarzycki
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Simone Prinz
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Niels N Oehlmann
- Microbial Metalloenzymes Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Johannes G Rebelein
- Microbial Metalloenzymes Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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5
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Zubova SV, Kosyakova NI, Grachev SV, Prokhorenko IR. Rhodobacter capsulatus PG Lipopolysaccharide Blocks the Effects of a Lipoteichoic Acid, a Toll-Like Receptor 2 Agonist. Acta Naturae 2022; 14:69-74. [PMID: 36694898 PMCID: PMC9844088 DOI: 10.32607/actanaturae.11747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/02/2022] [Indexed: 01/22/2023] Open
Abstract
Lipopolysaccharides (LPS) and lipoteichoic acids (LTA) are the major inducers of the inflammatory response of blood cells caused by Gram-negative and some Gram-positive bacteria. CD14 is a common receptor for LPS and LTA that transfers the ligands to TLR4 and TLR2, respectively. In this work, we have demonstrated that the non-toxic LPS from Rhodobacter capsulatus PG blocks the synthesis of pro-inflammatory cytokines during the activation of blood cells by Streptococcus pyogenes LTA through binding to the CD14 receptor, resulting in the signal transduction to TLR2/TLR6 being blocked. The LPS from Rhodobacter capsulatus PG can be considered a prototype for developing preparations to protect blood cells against the LTA of gram-positive bacteria.
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Affiliation(s)
- S. V. Zubova
- Institute of Basic Biological Problems of RAS FRC PSCBR RAS, Pushchino, 142290 Russia
| | - N. I. Kosyakova
- Clinical Hospital at the Pushchino Research Center, Pushchino, 142290 Russia
| | - S. V. Grachev
- Institute of Basic Biological Problems of RAS FRC PSCBR RAS, Pushchino, 142290 Russia
- First Moscow State Medical University named I.M. Sechenov of Russia Health Ministry (Sechenov University), Moscow, 119991 Russia
| | - I. R. Prokhorenko
- Institute of Basic Biological Problems of RAS FRC PSCBR RAS, Pushchino, 142290 Russia
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6
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Heterologous Production of Plant Terpenes in the Photosynthetic Bacterium Rhodobacter capsulatus. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2379:125-154. [PMID: 35188660 DOI: 10.1007/978-1-0716-1791-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Terpenes are one of the largest classes of secondary metabolites that occur in all kingdoms of life and offer diverse valuable properties for food and pharma industry including pleasant odor or taste as well as antimicrobial or anticancer activities. A multitude of terpene biosynthesis pathways are known, but their efficient biotechnological exploitation requires an adequate microorganism as host which can ideally provide an optimal supply with biosynthetic isoprene precursors. Rhodobacter capsulatus, a Gram-negative, facultative anaerobic, photosynthetic non-sulfur purple bacterium belonging to the α-proteobacteria represents such a host particularly suitable for terpene production. Here, we describe methods for the expression of terpene biosynthetic enzymes in R. capsulatus and the extraction of products for analysis. At the same time, we summarize the current strategies to adjust the biosynthetic precursor supply via isoprenoid biosynthetic pathways.
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7
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Troost K, Loeschcke A, Hilgers F, Özgür AY, Weber TM, Santiago-Schübel B, Svensson V, Hage-Hülsmann J, Habash SS, Grundler FMW, Schleker ASS, Jaeger KE, Drepper T. Engineered Rhodobacter capsulatus as a Phototrophic Platform Organism for the Synthesis of Plant Sesquiterpenoids. Front Microbiol 2019; 10:1998. [PMID: 31555236 PMCID: PMC6742980 DOI: 10.3389/fmicb.2019.01998] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/15/2019] [Indexed: 12/11/2022] Open
Abstract
Sesquiterpenoids are a large class of natural compounds offering manifold properties valuable for food, cosmetics, agriculture, and pharma industry. Production in microorganisms is a sustainable approach to provide sesquiterpenoids for research and industrial use independent of their natural sources. This requires the functional transfer of the respective biocatalytic pathways in an adequate host microorganism offering a sufficient supply of precursors that is ideally adjusted to the individual demand of the recombinant biosynthesis route. The phototrophic purple bacterium Rhodobacter capsulatus offers unique physiological properties that are favorable for biosynthesis of hydrophobic terpenes. Under phototrophic conditions, it develops a large intracytoplasmic membrane suitable for hosting membrane-bound enzymes and metabolites of respective biosynthetic pathways. In addition, Rhodobacter harbors an intrinsic carotenoid biosynthesis that can be engineered toward the production of foreign terpenes. Here, we evaluate R. capsulatus as host for the production of plant sesquiterpenoids under phototrophic conditions using patchoulol and valencene as a proof of concept. The heterologous expression of patchoulol synthase PcPS from Pogostemon cablin as well as the valencene synthases CsVS from Citrus sinensis and CnVS from Callitropsis nootkatensis led to the production of the respective sesquiterpenoids in R. capsulatus. To analyze, if gradually adjustable formation of the key precursor farnesylpyrophosphate (FPP) is beneficial for sesquiterpene synthesis under phototrophic conditions, the intrinsic 1-deoxy-D-xylulose 5-phosphate (DXP) pathway genes as well as the heterologous mevalonate pathway genes were modularly expressed in various combinations. To this end, different plasmids and chromosomally integrated expression tools were developed harboring the strong and tightly controlled Pnif promoter for heterologous gene expression. Notably, comparative studies identified a distinct combination of precursor biosynthetic genes as best-performing setup for each of the tested sesquiterpene synthases. In summary, we could demonstrate that R. capsulatus is a promising alternative platform organism that is suited for sustainable sesquiterpenoid formation under phototrophic cultivation conditions. A modular engineering of R. capsulatus strains via tailored co-expression of FPP biosynthetic genes further allowed adaptation of sesquiterpene precursor formation to its catalytic conversion by different plant terpene synthases.
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Affiliation(s)
- Katrin Troost
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Fabienne Hilgers
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Armagan Yakup Özgür
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Tim Moritz Weber
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Beatrix Santiago-Schübel
- Central Institute for Engineering, Electronics and Analytics ZEA-3, Analytics, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Vera Svensson
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Jennifer Hage-Hülsmann
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Samer S Habash
- INRES-Molecular Phytomedicine, Rhenish Friedrich-Wilhelm University of Bonn, Bonn, Germany
| | - Florian M W Grundler
- INRES-Molecular Phytomedicine, Rhenish Friedrich-Wilhelm University of Bonn, Bonn, Germany
| | - A Sylvia S Schleker
- INRES-Molecular Phytomedicine, Rhenish Friedrich-Wilhelm University of Bonn, Bonn, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany.,Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany
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Katzke N, Knapp A, Loeschcke A, Drepper T, Jaeger KE. Novel Tools for the Functional Expression of Metagenomic DNA. Methods Mol Biol 2017; 1539:159-196. [PMID: 27900689 DOI: 10.1007/978-1-4939-6691-2_10] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Functional expression of genes from metagenomic libraries is limited by various factors including inefficient transcription and/or translation of target genes as well as improper folding and assembly of the corresponding proteins caused by the lack of appropriate chaperones and cofactors. It is now well accepted that the use of different expression hosts of distinct phylogeny and physiology can dramatically increase the rate of success. In the following chapter, we therefore describe tools and protocols allowing for the comparative heterologous expression of genes in five bacterial expression hosts, namely Escherichia coli, Pseudomonas putida, Bacillus subtilis, Burkholderia glumae, and Rhodobacter capsulatus. Different broad-host-range shuttle vectors are described that allow activity-based screening of metagenomic DNA in these bacteria. Furthermore, we describe the newly developed transfer-and-expression system TREX which comprises genetic elements essential to allow for expression of large clusters of functionally coupled genes in different microbial species.
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Affiliation(s)
- Nadine Katzke
- Institute of Molecular Enzyme Technology, Forschungszentrum Jülich GmbH, Heinrich-Heine-University Düsseldorf, 52426, Jülich, Germany
| | - Andreas Knapp
- Institute of Molecular Enzyme Technology, Forschungszentrum Jülich GmbH, Heinrich-Heine-University Düsseldorf, 52426, Jülich, Germany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology, Forschungszentrum Jülich GmbH, Heinrich-Heine-University Düsseldorf, 52426, Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Forschungszentrum Jülich GmbH, Heinrich-Heine-University Düsseldorf, 52426, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Forschungszentrum Jülich GmbH, Heinrich-Heine-University Düsseldorf, 52426, Jülich, Germany.
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Liebl W, Angelov A, Juergensen J, Chow J, Loeschcke A, Drepper T, Classen T, Pietruszka J, Ehrenreich A, Streit WR, Jaeger KE. Alternative hosts for functional (meta)genome analysis. Appl Microbiol Biotechnol 2014; 98:8099-109. [PMID: 25091044 DOI: 10.1007/s00253-014-5961-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/14/2014] [Accepted: 07/15/2014] [Indexed: 11/25/2022]
Abstract
Microorganisms are ubiquitous on earth, often forming complex microbial communities in numerous different habitats. Most of these organisms cannot be readily cultivated in the laboratory using standard media and growth conditions. However, it is possible to gain access to the vast genetic, enzymatic, and metabolic diversity present in these microbial communities using cultivation-independent approaches such as sequence- or function-based metagenomics. Function-based analysis is dependent on heterologous expression of metagenomic libraries in a genetically amenable cloning and expression host. To date, Escherichia coli is used in most cases; however, this has the drawback that many genes from heterologous genomes and complex metagenomes are expressed in E. coli either at very low levels or not at all. This review emphasizes the importance of establishing alternative microbial expression systems consisting of different genera and species as well as customized strains and vectors optimized for heterologous expression of membrane proteins, multigene clusters encoding protein complexes or entire metabolic pathways. The use of alternative host-vector systems will complement current metagenomic screening efforts and expand the yield of novel biocatalysts, metabolic pathways, and useful metabolites to be identified from environmental samples.
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Affiliation(s)
- Wolfgang Liebl
- Lehrstuhl für Mikrobiologie, Technische Universität München, Emil-Ramann-Str. 4, 85654, Freising, Germany,
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