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Ma ZX, Feng CX, Song YZ, Sun J, Shao Y, Song SZ, Wan B, Zhang C, Fan H, Bao K, Yang S. Engineering photo-methylotrophic Methylobacterium for enhanced 3-hydroxypropionic acid production during non-growth stage fermentation. BIORESOURCE TECHNOLOGY 2024; 393:130104. [PMID: 38008225 DOI: 10.1016/j.biortech.2023.130104] [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: 10/18/2023] [Revised: 11/23/2023] [Accepted: 11/23/2023] [Indexed: 11/28/2023]
Abstract
This study explored the potential of methanol as a sustainable feedstock for biomanufacturing, focusing on Methylobacterium extorquens, a well-established representative of methylotrophic cell factories. Despite this bacterium's long history, its untapped photosynthetic capabilities for production enhancement have remained unreported. Using genome-scale flux balance analysis, it was hypothesized that introducing photon fluxes could boost the yield of 3-hydroxypropionic acid (3-HP), an energy- and reducing equivalent-consuming chemicals. To realize this, M. extorquens was genetically modified by eliminating the negative regulator of photosynthesis, leading to improved ATP levels and metabolic activity in non-growth cells during a two-stage fermentation process. This modification resulted in a remarkable 3.0-fold increase in 3-HP titer and a 2.1-fold increase in its yield during stage (II). Transcriptomics revealed that enhanced light-driven methanol oxidation, NADH transhydrogenation, ATP generation, and fatty acid degradation were key factors. This development of photo-methylotrophy as a platform technology introduced novel opportunities for future production enhancements.
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Affiliation(s)
- Zeng-Xin Ma
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China
| | - Chen-Xi Feng
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China
| | - Ya-Zhen Song
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China
| | - Jing Sun
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China
| | - Yi Shao
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China
| | - Shu-Zhen Song
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China
| | - Bin Wan
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China
| | - Cong Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China
| | - Huan Fan
- Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Tianjin Engineering Research Center of Animal Healthy Farming, Institute of Animal Science and Veterinary, Tianjin Academy of Agricultural Sciences, Tianjin 300381, People's Republic of China
| | - Kai Bao
- School of Life Sciences, Hubei University, Wuhan 430062, Hubei, People's Republic of China
| | - Song Yang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, People's Republic of China.
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Zhu L, Song Y, Ma S, Yang S. Heterologous production of 3-hydroxypropionic acid in Methylorubrum extorquens by introducing the mcr gene via a multi-round chromosomal integration system based on cre-lox71/lox66 and transposon. Microb Cell Fact 2024; 23:5. [PMID: 38172868 PMCID: PMC10763676 DOI: 10.1186/s12934-023-02275-z] [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: 04/12/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND AND AIM Reprogramming microorganisms to enhance the production of metabolites is a part of contemporary synthetic biology, which relies on the availability of genetic tools to successfully manipulate the bacteria. Methylorubrum extorquens AM1 is a platform microorganism used to convert C1 compounds into various value-added products. However, the repertoire of available plasmids to conveniently and quickly fine-tune the expression of multiple genes in this strain is extremely limited compared with other model microorganisms such as Escherichia coli. Thus, this study aimed to integrate existing technologies, such as transposon-mediated chromosomal integration and cre-lox-mediated recombination, to achieve the diversified expression of target genes through multiple chromosomal insertions in M. extorquens AM1. RESULTS A single plasmid toolkit, pSL-TP-cre-km, containing a miniHimar1 transposon and an inducible cre-lox71/lox66 system, was constructed and characterized for its multiple chromosomal integration capacity. A co-transcribed mcr-egfp cassette [for the production of 3-hydroxypropionic acid (3-HP) and a reporting green fluorescent protein] was added to construct pTP-cre-mcr-egfp for evaluating its utility in mediating the expression of heterologous genes, resulting in the production of 3-HP with a titer of 34.7-55.2 mg/L by two chromosomal integration copies. Furthermore, in association with the expression of plasmid-based mcr, 3-HP production increased to 65.5-92.4 mg/L. CONCLUSIONS This study used a multi-round chromosomal integration system based on cre-lox71/lox66 and a transposon to construct a single constructed vector. A heterologous mcr gene was introduced through this vector, and high expression of 3-hydroxypropionic acid was achieved in M. extorquens. This study provided an efficient genetic tool for manipulating M. extorquens, which not only help increase the expression of heterologous genes in M. extorquens but also provide a reference for strains lacking genetic manipulation vectors.
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Affiliation(s)
- Liping Zhu
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China.
| | - Yazhen Song
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Shunan Ma
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Song Yang
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China.
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, People's Republic of China.
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Cre/ lox-Mediated CRISPRi Library Reveals Core Genome of a Type I Methanotroph Methylotuvimicrobium buryatense 5GB1C. Appl Environ Microbiol 2023; 89:e0188322. [PMID: 36622175 PMCID: PMC9888281 DOI: 10.1128/aem.01883-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Methanotrophs play key roles in global methane cycling and are promising platforms for methane bioconversion. However, major gaps existing in fundamental knowledge undermines understanding of these methane-consuming microorganisms. To associate genes with a phenotype at the genome-wide level, we developed a Cre/lox-mediated method for constructing a large-scale CRISPRi library in a model methanotroph Methylotuvimicrobium buryatense 5GB1C. The efficiency of this Cre mediated integration method was up to a level of 105 CFU/μg DNA. Targeting 4,100 predicted protein-coding genes, our CRISPRi pooled screening uncovered 788 core genes for the growth of strain 5GB1C using methane. The core genes are highly consistent with the gene knockout results, indicating the reliability of the CRISPRi screen. Insights from the core genes include that annotated isozymes generally exist in metabolic pathways and many core genes are hypothetical genes. This work not only provides functional genomic data for both fundamental research and metabolic engineering of methanotrophs, but also offers a method for CRISPRi library construction. IMPORTANCE Due to their key role in methane cycling and their industrial potential, methanotrophs have drawn increasing attention. Genome-wide experimental approaches for gene-phenotype mapping accelerate our understanding and engineering of a bacterium. However, these approaches are still unavailable in methanotrophs. This work has two significant implications. First, the core genes identified here provide functional genetic basics for complete reconstruction of the metabolic network and afford more clues for knowledge gaps. Second, the Cre-mediated knock-in method developed in this work enables large-scale DNA library construction in methanotrophs; the CRISPRi library can be used to screen the genes associated with special culture conditions.
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Hemmann JL, Keller P, Hemmerle L, Vonderach T, Ochsner AM, Bortfeld-Miller M, Günther D, Vorholt JA. Lanpepsy is a novel lanthanide-binding protein involved in the lanthanide response of the obligate methylotroph Methylobacillus flagellatus. J Biol Chem 2023; 299:102940. [PMID: 36702252 PMCID: PMC9988556 DOI: 10.1016/j.jbc.2023.102940] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
Lanthanides were recently discovered as metals required in the active site of certain methanol dehydrogenases. Since then, the characterization of the lanthanome, that is, proteins involved in sensing, uptake, and utilization of lanthanides, has become an active field of research. Initial exploration of the response to lanthanides in methylotrophs has revealed that the lanthanome is not conserved and that multiple mechanisms for lanthanide utilization must exist. Here, we investigated the lanthanome in the obligate model methylotroph Methylobacillus flagellatus. We used a proteomic approach to analyze differentially regulated proteins in the presence of lanthanum. While multiple known proteins showed induction upon growth in the presence of lanthanum (Xox proteins, TonB-dependent receptor), we also identified several novel proteins not previously associated with lanthanide utilization. Among these was Mfla_0908, a periplasmic 19 kDa protein without functional annotation. The protein comprises two characteristic PepSY domains, which is why we termed the protein lanpepsy (LanP). Based on bioinformatic analysis, we speculated that LanP could be involved in lanthanide binding. Using dye competition assays, quantification of protein-bound lanthanides by inductively coupled plasma mass spectrometry, as well as isothermal titration calorimetry, we demonstrated the presence of multiple lanthanide binding sites that showed selectivity over the chemically similar calcium ion. LanP thus represents the first member of the PepSY family that binds lanthanides. Although the physiological role of LanP is still unclear, its identification is of interest for applications toward the sustainable purification and separation of rare-earth elements.
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Affiliation(s)
- Jethro L Hemmann
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland.
| | - Philipp Keller
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Lucas Hemmerle
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Thomas Vonderach
- Laboratory of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Andrea M Ochsner
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | | | - Detlef Günther
- Laboratory of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Julia A Vorholt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland.
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Harten T, Nimzyk R, Gawlick VEA, Reinhold-Hurek B. Elucidation of Essential Genes and Mutant Fitness during Adaptation toward Nitrogen Fixation Conditions in the Endophyte Azoarcus olearius BH72 Revealed by Tn-Seq. Microbiol Spectr 2022; 10:e0216222. [PMID: 36416558 PMCID: PMC9769520 DOI: 10.1128/spectrum.02162-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/05/2022] [Indexed: 11/24/2022] Open
Abstract
Azoarcus olearius BH72 is a diazotrophic model endophyte that contributes fixed nitrogen to its host plant, Kallar grass, and expresses nitrogenase genes endophytically. Despite extensive studies on biological nitrogen fixation (BNF) of diazotrophic endophytes, little is known about global genetic players involved in survival under respective physiological conditions. Here, we report a global genomic screen for putatively essential genes of A. olearius employing Tn5 transposon mutagenesis with a modified transposon combined with high-throughput sequencing (Tn-Seq). A large Tn5 master library of ~6 × 105 insertion mutants of strain BH72 was obtained. Next-generation sequencing identified 183,437 unique insertion sites into the 4,376,040-bp genome, displaying one insertion every 24 bp on average. Applying stringent criteria, we describe 616 genes as putatively essential for growth on rich medium. COG (Clusters of Orthologous Groups) assignment of the 564 identified protein-coding genes revealed enrichment of genes related to core cellular functions and cell viability. To mimic gradual adaptations toward BNF conditions, the Tn5 mutant library was grown aerobically in synthetic medium or microaerobically on either combined or atmospheric nitrogen. Enrichment and depletion analysis of Tn5 mutants not only demonstrated the role of BNF- and metabolism-related proteins but also revealed that, strikingly, many genes relevant for plant-microbe interactions decrease bacterial competitiveness in pure culture, such type IV pilus- and bacterial envelope-associated genes. IMPORTANCE A constantly growing world population and the daunting challenge of climate change demand new strategies in agricultural crop production. Intensive usage of chemical fertilizers, overloading the world's fields with organic input, threaten terrestrial and marine ecosystems as well as human health. Long overlooked, the beneficial interaction of endophytic bacteria and grasses has attracted ever-growing interest in research in the last decade. Capable of biological nitrogen fixation, diazotrophic endophytes not only provide a valuable source of combined nitrogen but also are known for diverse plant growth-promoting effects, thereby contributing to plant productivity. Elucidation of an essential gene set for a prominent model endophyte such as A. olearius BH72 provides us with powerful insights into its basic lifestyle. Knowledge about genes detrimental or advantageous under defined physiological conditions may point out a way of manipulating key steps in the bacterium's lifestyle and plant interaction toward a more sustainable agriculture.
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Affiliation(s)
- Theresa Harten
- University of Bremen, Faculty of Biology and Chemistry, CBIB Center for Biomolecular Interactions, Department of Microbe-Plant Interactions, Bremen, Germany
| | - Rolf Nimzyk
- University of Bremen, Faculty of Biology and Chemistry, CBIB Center for Biomolecular Interactions, Department of Microbe-Plant Interactions, Bremen, Germany
- University of Bremen, Faculty of Biology and Chemistry, CBIB Center for Biomolecular Interactions, Nucleic Acid Analysis Facility (NAA), Bremen, Germany
| | - Vivian E. A. Gawlick
- University of Bremen, Faculty of Biology and Chemistry, CBIB Center for Biomolecular Interactions, Department of Microbe-Plant Interactions, Bremen, Germany
| | - Barbara Reinhold-Hurek
- University of Bremen, Faculty of Biology and Chemistry, CBIB Center for Biomolecular Interactions, Department of Microbe-Plant Interactions, Bremen, Germany
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Singh HB, Kang MK, Kwon M, Kim SW. Developing methylotrophic microbial platforms for a methanol-based bioindustry. Front Bioeng Biotechnol 2022; 10:1050740. [PMID: 36507257 PMCID: PMC9727194 DOI: 10.3389/fbioe.2022.1050740] [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: 09/22/2022] [Accepted: 11/11/2022] [Indexed: 11/24/2022] Open
Abstract
Methanol, a relatively cheap and renewable single-carbon feedstock, has gained considerable attention as a substrate for the bio-production of commodity chemicals. Conventionally produced from syngas, along with emerging possibilities of generation from methane and CO2, this C1 substrate can serve as a pool for sequestering greenhouse gases while supporting a sustainable bio-economy. Methylotrophic organisms, with the inherent ability to use methanol as the sole carbon and energy source, are competent candidates as platform organisms. Accordingly, methanol bioconversion pathways have been an attractive target for biotechnological and bioengineering interventions in developing microbial cell factories. This review summarizes the recent advances in methanol-based production of various bulk and value-added chemicals exploiting the native and synthetic methylotrophic organisms. Finally, the current challenges and prospects of streamlining these methylotrophic platforms are discussed.
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Affiliation(s)
- Hawaibam Birla Singh
- Division of Applied Life Science (BK21 Four), ABC-RLRC, PMBBRC, Gyeongsang National University, Jinju, South Korea
| | - Min-Kyoung Kang
- Division of Applied Life Science (BK21 Four), ABC-RLRC, PMBBRC, Gyeongsang National University, Jinju, South Korea
| | - Moonhyuk Kwon
- Division of Life Science, ABC-RLRC, PMBBRC, Gyeongsang National University, Jinju, South Korea,*Correspondence: Moonhyuk Kwon, ; Seon-Won Kim,
| | - Seon-Won Kim
- Division of Applied Life Science (BK21 Four), ABC-RLRC, PMBBRC, Gyeongsang National University, Jinju, South Korea,*Correspondence: Moonhyuk Kwon, ; Seon-Won Kim,
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7
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Pan-genome Analysis Reveals Comparative Genomic Features of Central Metabolic Pathways in Methylorubrum extorquens. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0154-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (RubisCO) Is Essential for Growth of the Methanotroph Methylococcus capsulatus Strain Bath. Appl Environ Microbiol 2021; 87:e0088121. [PMID: 34288705 PMCID: PMC8388818 DOI: 10.1128/aem.00881-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) enzyme found in plants, algae, and an array of autotrophic bacteria is also encoded by a subset of methanotrophs, but its role in these microbes has largely remained elusive. In this study, we showed that CO2 was requisite for RubisCO-encoding Methylococcus capsulatus strain Bath growth in a bioreactor with continuous influent and effluent gas flow. RNA sequencing identified active transcription of several carboxylating enzymes, including key enzymes of the Calvin and serine cycles, that could mediate CO2 assimilation during cultivation with both CH4 and CO2 as carbon sources. Marker exchange mutagenesis of M. capsulatus Bath genes encoding key enzymes of potential CO2-assimilating metabolic pathways indicated that a complete serine cycle is not required, whereas RubisCO is essential for growth of this bacterium. 13CO2 tracer analysis showed that CH4 and CO2 enter overlapping anaplerotic pathways and implicated RubisCO as the primary enzyme mediating CO2 assimilation in M. capsulatus Bath. Notably, we quantified the relative abundance of 3-phosphoglycerate and ribulose-1,5-bisphosphate 13C isotopes, which supported that RubisCO-produced 3-phosphoglycerate is primarily converted to ribulose-1-5-bisphosphate via the oxidative pentose phosphate pathway in M. capsulatus Bath. Collectively, our data establish that RubisCO and CO2 play essential roles in M. capsulatus Bath metabolism. This study expands the known capacity of methanotrophs to fix CO2 via RubisCO, which may play a more pivotal role in the Earth's biogeochemical carbon cycling and greenhouse gas regulation than previously recognized. Further, M. capsulatus Bath and other CO2-assimilating methanotrophs represent excellent candidates for use in the bioconversion of biogas waste streams that consist of both CH4 and CO2. IMPORTANCE The importance of RubisCO and CO2 in M. capsulatus Bath metabolism is unclear. In this study, we demonstrated that both CO2 and RubisCO are essential for M. capsulatus Bath growth. 13CO2 tracing experiments supported that RubisCO mediates CO2 fixation and that a noncanonical Calvin cycle is active in this organism. Our study provides insights into the expanding knowledge of methanotroph metabolism and implicates dually CH4/CO2-utilizing bacteria as more important players in the biogeochemical carbon cycle than previously appreciated. In addition, M. capsulatus and other methanotrophs with CO2 assimilation capacity represent candidate organisms for the development of biotechnologies to mitigate the two most abundant greenhouse gases, CH4 and CO2.
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9
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Zhu LP, Song SZ, Yang S. Gene repression using synthetic small regulatory RNA in Methylorubrum extorquens. J Appl Microbiol 2021; 131:2861-2875. [PMID: 34021964 DOI: 10.1111/jam.15159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/07/2021] [Accepted: 05/18/2021] [Indexed: 12/11/2022]
Abstract
AIM Genetic tools are a prerequisite for engineering cell factories for synthetic biology and biotechnology. Methylorubrum extorquens is an important platform for a future one-carbon (C1) bioeconomy, but its application is currently limited by the availability of genetic tools. Small regulatory RNA (sRNA) is an important regulatory factor in bacteria and has been applied for gene repression in several strains. This study aimed to construct a synthetic sRNA system based on the MicC scaffold and the chaperone Hfq to control gene expression in M. extorquens. METHODS AND RESULTS Initially, the exogenous lacZ gene was transposed into the M. extorquens chromosome as a reporter, and corresponding β-galactosidase was measured to assess the knockdown efficiency of lacZ. A synthetic sRNA containing a 24-nt antisense RNA targeting lacZ and an Escherichia coli MicC scaffold were constructed, and different Hfqs from E. coli, M. extorquens AM1 and PA1 were further identified. The results showed that the expression of endogenous hfqs from the chromosome in M. extorquens strains was inadequate, and only when it was overexpressed via the plasmid did the colonies show a colour change and a corresponding decrease in β-galactosidase expression. More specifically, M. extorquens strains with overexpressing their own Hfq showed the best gene repression efficiency. Furthermore, this E. coli MicC scaffold and AM1 Hfq system were combined to knock down crtI gene expression in AM1, leading to an 86% decrease in carotenoid production (0·09 mg g-1 ) compared to that (0·65 mg g-1 ) in the wild-type strain. CONCLUSION A functional synthetic sRNA system combined with E. coli MicC and endogenous Hfq was constructed in M. extorquens strains, which was able to interfere with the target crtI gene and reduce carotenoid production. SIGNIFICANCE AND IMPACT OF THE STUDY The synthetic sRNA system reported in this study provides a genetic tool for the manipulation of M. extorquens. The present findings might be helpful for achieving high-throughput gene knockdown expression.
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Affiliation(s)
- L-P Zhu
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, and School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - S-Z Song
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, and School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - S Yang
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, and School of Life Sciences, Qingdao Agricultural University, Qingdao, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
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10
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Inferring Active Metabolic Pathways from Proteomics and Essentiality Data. Cell Rep 2021; 31:107722. [PMID: 32492430 PMCID: PMC7273199 DOI: 10.1016/j.celrep.2020.107722] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 03/04/2020] [Accepted: 05/12/2020] [Indexed: 12/11/2022] Open
Abstract
Here, we propose an approach to identify active metabolic pathways by integrating gene essentiality analysis and protein abundance. We use two bacterial species (Mycoplasma pneumoniae and Mycoplasma agalactiae) that share a high gene content similarity yet show significant metabolic differences. First, we build detailed metabolic maps of their carbon metabolism, the most striking difference being the absence of two key enzymes for glucose metabolism in M. agalactiae. We then determine carbon sources that allow growth in M. agalactiae, and we introduce glucose-dependent growth to show the functionality of its remaining glycolytic enzymes. By analyzing gene essentiality and performing quantitative proteomics, we can predict the active metabolic pathways connected to carbon metabolism and show significant differences in use and direction of key pathways despite sharing the large majority of genes. Gene essentiality combined with quantitative proteomics and metabolic maps can be used to determine activity and directionality of metabolic pathways. Active metabolic bacterial pathways are identified Integration of gene essentiality and proteomics allow prediction of active pathways Glucose-dependent growth is restored in Mycoplasma agalactiae Two Mycoplasma species show different usage of metabolic pathways
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Feng H, Yuan Y, Yang Z, Xing XH, Zhang C. Genome-wide genotype-phenotype associations in microbes. J Biosci Bioeng 2021; 132:1-8. [PMID: 33895083 DOI: 10.1016/j.jbiosc.2021.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 03/17/2021] [Accepted: 03/23/2021] [Indexed: 12/24/2022]
Abstract
The concept of a gene has been developed a lot since the Mendelian era owing to the rapid progress in molecular biology and informatics. To explore the nature of life, varieties of biological tools have been continuously established. Many achievements have been made to clarify the relationships between genotypes and phenotypes. However, it is still not completely clear that how traits of an organism are encoded by its genome. In this review, we will summarize and discuss representative works in systematical functional genomic studies in microbes. By analyzing their developmental progressions and limitations, we may have chances to design more powerful means to decipher the code of life.
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Affiliation(s)
- Huibao Feng
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yaomeng Yuan
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Zheng Yang
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Xin-Hui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Chong Zhang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.
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12
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Ma ZX, Zhang M, Zhang CT, Zhang H, Mo XH, Xing XH, Yang S. Metabolomic analysis improves bioconversion of methanol to isobutanol in Methylorubrum extorquens AM1. Biotechnol J 2021; 16:e2000413. [PMID: 33595188 DOI: 10.1002/biot.202000413] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/09/2021] [Accepted: 02/15/2021] [Indexed: 11/12/2022]
Abstract
BACKGROUND Methylorubrum extorquens AM1 can be engineered to convert methanol to value-added chemicals. Most of these chemicals derive from acetyl-CoA involved in the serine cycle. However, recent studies on methylotrophic metabolism have suggested that C3 pyruvate is a good potential precursor for broadening the types of synthesized products. METHODS AND RESULTS In the present study, we found that isobutanol was a model chemical that could be generated from pyruvate through a 2-keto acid pathway. Initially, the engineered M. extorquens AM1 could only produce a trace amount of isobutanol at 0.62 mgL-1 after introducing the heterologous 2-ketoisovalerate decarboxylase and alcohol dehydrogenase. Furthermore, the metabolomic analysis revealed that insufficient carbon fluxes through 2-ketoisovalerate and pyruvate were the key limitation steps for efficient biosynthesis of isobutanol. Based on this analysis, the titer of isobutanol was improved by over 20-fold after overexpressing alsS gene encoding acetolactate synthase and deleting ldhA gene for lactate dehydrogenase. Moreover, substituting the cell chassis with the isobutanol-tolerant strain isolated from adaptive evolution of M. extorquens AM1 further increased the production of isobutanol by 1.7-fold, resulting in the final titer of 19 mgL-1 in flask cultivation. CONCLUSION Our current findings provided promising insights into engineering methylotrophic cell factories capable of converting methanol to isobutanol or value-added chemicals using pyruvate as the precursor.
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Affiliation(s)
- Zeng-Xin Ma
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Min Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China.,Shandong Longkete Enzyme Co., Ltd., Linyi, Shandong, People's Republic of China
| | - Chang-Tai Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Hui Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Xu-Hua Mo
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Xin-Hui Xing
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, People's Republic of China.,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, and Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, People's Republic of China
| | - Song Yang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, People's Republic of China
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13
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Mass spectrometry-based approaches to study lanthanides and lanthanide-dependent proteins in the phyllosphere. Methods Enzymol 2021; 650:215-236. [PMID: 33867023 DOI: 10.1016/bs.mie.2021.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Rare-earth elements (REEs) were recently discovered to be biologically significant. The finding was originally made with the methanol dehydrogenase XoxF, which depends on REEs for its activity, and reports of lanthanide-utilizing bacteria have since expanded. Environmental proteomics allows the identification of proteins specifically induced by the presence of lanthanides or can provide insights into the preferred use of lanthanide-dependent and -independent isoenzymes, for example. Here we describe protocols for the growth and subsequent mass spectrometry-based proteome analysis of bacteria obtained from controlled artificial media and from the phyllosphere of the model plant Arabidopsis thaliana. In addition, the use of inductively coupled plasma mass spectrometry (ICP-MS) is described for the quantification of REEs in biological samples.
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Yuan XJ, Chen WJ, Ma ZX, Yuan QQ, Zhang M, He L, Mo XH, Zhang C, Zhang CT, Wang MY, Xing XH, Yang S. Rewiring the native methanol assimilation metabolism by incorporating the heterologous ribulose monophosphate cycle into Methylorubrum extorquens. Metab Eng 2021; 64:95-110. [PMID: 33493644 DOI: 10.1016/j.ymben.2021.01.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 01/05/2021] [Accepted: 01/18/2021] [Indexed: 10/22/2022]
Abstract
Methanol is assimilated through the serine cycle to generate acetyl-CoA without carbon loss. However, a highly active serine cycle requires high consumption of reducing equivalents and ATP, thereby leading to the impaired efficiency of methanol conversion to reduced chemicals. In the present study, a genome-scale flux balance analysis (FBA) predicted that the introduction of the heterologous ribulose monophosphate (RuMP) cycle, a more energy-efficient pathway for methanol assimilation, could theoretically increase growth rate by 31.3% for the model alphaproteobacterial methylotroph Methylorubrum extorquens AM1. Based on this analysis, we constructed a novel synergistic assimilation pathway in vivo by incorporating the RuMP cycle into M. extroquens metabolism with the intrinsic serine cycle. We demonstrated that the operation of the synergistic pathway could increase cell growth rate by 16.5% and methanol consumption rate by 13.1%. This strategy rewired the central methylotrophic metabolism through adjusting core gene transcription, leading to a pool size increase of C2 to C5 central intermediates by 1.2- to 3.6-fold and an NADPH cofactor improvement by 1.3-fold. The titer of 3-hydroxypropionic acid (3-HP), a model product in the newly engineered chassis of M. extorquens AM1, was increased to 91.2 mg/L in shake-flask culture, representing a 3.1-fold increase compared with the control strain with only the serine cycle. The final titer of 3-HP was significantly improved to 0.857 g/L in the fed-batch bioreactor, which was more competitive compared with the other 3-HP producers using methane and CO2 as C1 sources. Collectively, our current study demonstrated that engineering the synergistic methanol assimilation pathway was a promising strategy to increase the carbon assimilation and the yields of reduced chemicals in diverse host strains for C1 microbial cell factories.
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Affiliation(s)
- Xiao-Jie Yuan
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, And Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China; Department of Molecular Biology, Qingdao Vland Biotech Inc., Qingdao, Shandong Province, People's Republic of China
| | - Wen-Jing Chen
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, And Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Zeng-Xin Ma
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, And Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Qian-Qian Yuan
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Min Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, And Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Lian He
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Xu-Hua Mo
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, And Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Chong Zhang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, People's Republic of China
| | - Chang-Tai Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, And Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Meng-Ying Wang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, And Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Xin-Hui Xing
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, People's Republic of China; Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, And Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, China
| | - Song Yang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, And Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, People's Republic of China.
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Genome-Wide Identification of Essential and Auxiliary Gene Sets for Magnetosome Biosynthesis in Magnetospirillum gryphiswaldense. mSystems 2020; 5:5/6/e00565-20. [PMID: 33203687 PMCID: PMC7676999 DOI: 10.1128/msystems.00565-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Magnetospirillum gryphiswaldense is one of the few tractable model magnetotactic bacteria (MTB) for studying magnetosome biomineralization. So far, knowledge on the genetic determinants of this complex process has been mainly gathered using reverse genetics and candidate approaches. In contrast, nontargeted forward genetics studies are lacking, since application of such techniques in MTB has been complicated for a number of technical reasons. Here, we report on the first comprehensive transposon mutagenesis study in MTB, aiming at systematic identification of auxiliary genes necessary to support magnetosome formation in addition to key genes harbored in the magnetosome island (MAI). Our work considerably extends the candidate set of novel subsidiary determinants and shows that the full gene complement underlying magnetosome biosynthesis is larger than assumed. In particular, we were able to define certain cellular pathways as specifically important for magnetosome formation that have not been implicated in this process so far. Magnetotactic bacteria (MTB) stand out by their ability to manufacture membrane-enclosed magnetic organelles, so-called magnetosomes. Previously, it has been assumed that a genomic region of approximately 100 kbp, the magnetosome island (MAI), harbors all genetic determinants required for this intricate biosynthesis process. Recent evidence, however, argues for the involvement of additional auxiliary genes that have not been identified yet. In the present study, we set out to delineate the full gene complement required for magnetosome production in the alphaproteobacterium Magnetospirillum gryphiswaldense using a systematic genome-wide transposon mutagenesis approach. By an optimized procedure, a Tn5 insertion library of 80,000 clones was generated and screened, yielding close to 200 insertants with mild to severe impairment of magnetosome biosynthesis. Approximately 50% of all Tn5 insertion sites mapped within the MAI, mostly leading to a nonmagnetic phenotype. In contrast, in the majority of weakly magnetic Tn5 insertion mutants, genes outside the MAI were affected, which typically caused lower numbers of magnetite crystals with partly aberrant morphology, occasionally combined with deviant intracellular localization. While some of the Tn5-struck genes outside the MAI belong to pathways that have been linked to magnetosome formation before (e.g., aerobic and anaerobic respiration), the majority of affected genes are involved in so far unsuspected cellular processes, such as sulfate assimilation, oxidative protein folding, and cytochrome c maturation, or are altogether of unknown function. We also found that signal transduction and redox functions are enriched in the set of Tn5 hits outside the MAI, suggesting that such processes are particularly important in support of magnetosome biosynthesis. IMPORTANCEMagnetospirillum gryphiswaldense is one of the few tractable model magnetotactic bacteria (MTB) for studying magnetosome biomineralization. So far, knowledge on the genetic determinants of this complex process has been mainly gathered using reverse genetics and candidate approaches. In contrast, nontargeted forward genetics studies are lacking, since application of such techniques in MTB has been complicated for a number of technical reasons. Here, we report on the first comprehensive transposon mutagenesis study in MTB, aiming at systematic identification of auxiliary genes necessary to support magnetosome formation in addition to key genes harbored in the magnetosome island (MAI). Our work considerably extends the candidate set of novel subsidiary determinants and shows that the full gene complement underlying magnetosome biosynthesis is larger than assumed. In particular, we were able to define certain cellular pathways as specifically important for magnetosome formation that have not been implicated in this process so far.
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Abstract
The goal of genomics and systems biology is to understand how complex systems of factors assemble into pathways and structures that combine to form living organisms. Great advances in understanding biological processes result from determining the function of individual genes, a process that has classically relied on characterizing single mutations. Advances in DNA sequencing has made available the complete set of genetic instructions for an astonishing and growing number of species. To understand the function of this ever-increasing number of genes, a high-throughput method was developed that in a single experiment can measure the function of genes across the genome of an organism. This occurred approximately 10 years ago, when high-throughput DNA sequencing was combined with advances in transposon-mediated mutagenesis in a method termed transposon insertion sequencing (TIS). In the subsequent years, TIS succeeded in addressing fundamental questions regarding the genes of bacteria, many of which have been shown to play central roles in bacterial infections that result in major human diseases. The field of TIS has matured and resulted in studies of hundreds of species that include significant innovations with a number of transposons. Here, we summarize a number of TIS experiments to provide an understanding of the method and explanation of approaches that are instructive when designing a study. Importantly, we emphasize critical aspects of a TIS experiment and highlight the extension and applicability of TIS into nonbacterial species such as yeast.
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Affiliation(s)
- Tim van Opijnen
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, USA;
| | - Henry L Levin
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA;
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Flores-Tinoco CE, Tschan F, Fuhrer T, Margot C, Sauer U, Christen M, Christen B. Co-catabolism of arginine and succinate drives symbiotic nitrogen fixation. Mol Syst Biol 2020; 16:e9419. [PMID: 32490601 PMCID: PMC7268258 DOI: 10.15252/msb.20199419] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/13/2020] [Accepted: 04/21/2020] [Indexed: 12/22/2022] Open
Abstract
Biological nitrogen fixation emerging from the symbiosis between bacteria and crop plants holds promise to increase the sustainability of agriculture. One of the biggest hurdles for the engineering of nitrogen-fixing organisms is an incomplete knowledge of metabolic interactions between microbe and plant. In contrast to the previously assumed supply of only succinate, we describe here the CATCH-N cycle as a novel metabolic pathway that co-catabolizes plant-provided arginine and succinate to drive the energy-demanding process of symbiotic nitrogen fixation in endosymbiotic rhizobia. Using systems biology, isotope labeling studies and transposon sequencing in conjunction with biochemical characterization, we uncovered highly redundant network components of the CATCH-N cycle including transaminases that interlink the co-catabolism of arginine and succinate. The CATCH-N cycle uses N2 as an additional sink for reductant and therefore delivers up to 25% higher yields of nitrogen than classical arginine catabolism-two alanines and three ammonium ions are secreted for each input of arginine and succinate. We argue that the CATCH-N cycle has evolved as part of a synergistic interaction to sustain bacterial metabolism in the microoxic and highly acid environment of symbiosomes. Thus, the CATCH-N cycle entangles the metabolism of both partners to promote symbiosis. Our results provide a theoretical framework and metabolic blueprint for the rational design of plants and plant-associated organisms with new properties to improve nitrogen fixation.
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Affiliation(s)
| | - Flavia Tschan
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Céline Margot
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Matthias Christen
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Beat Christen
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
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Mo XH, Zhang H, Wang TM, Zhang C, Zhang C, Xing XH, Yang S. Establishment of CRISPR interference in Methylorubrum extorquens and application of rapidly mining a new phytoene desaturase involved in carotenoid biosynthesis. Appl Microbiol Biotechnol 2020; 104:4515-4532. [PMID: 32215707 DOI: 10.1007/s00253-020-10543-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/02/2020] [Accepted: 03/11/2020] [Indexed: 02/04/2023]
Abstract
The methylotrophic bacterium Methylorubrum extorquens AM1 holds a great potential of a microbial cell factory in producing high value chemicals with methanol as the sole carbon and energy source. However, many gene functions remain unknown, hampering further rewiring of metabolic networks. Clustered regularly interspaced short palindromic repeat interference (CRISPRi) has been demonstrated to be a robust tool for gene knockdown in diverse organisms. In this study, we developed an efficient CRISPRi system through optimizing the promoter strength of Streptococcus pyogenes-derived deactivated cas9 (dcas9). When the dcas9 and sgRNA were respectively controlled by medium PR/tetO and strong PmxaF-g promoters, dynamic repression efficacy of cell growth through disturbing a central metabolism gene glyA was achieved from 41.9 to 96.6% dependent on the sgRNA targeting sites. Furthermore, the optimized CRISPRi system was shown to effectively decrease the abundance of exogenous fluorescent protein gene mCherry over 50% and to reduce the expression of phytoene desaturase gene crtI by 97.7%. We then used CRISPRi technology combined with 26 sgRNAs pool to rapidly discover a new phytoene desaturase gene META1_3670 from 2470 recombinant mutants. The gene function was further verified through gene deletion and complementation as well as phylogenetic tree analysis. In addition, we applied CRISPRi to repress the transcriptional level of squalene-hopene cyclase gene shc involved in hopanoid biosynthesis by 64.9%, which resulted in enhancing 1.9-fold higher of carotenoid production without defective cell growth. Thus, the CRISPRi system developed here provides a useful tool in mining functional gene of M. extorquens as well as in biotechnology for producing high-valued chemicals from methanol. KEY POINTS: Developing an efficient CRISPRi to knockdown gene expression in C1-utilizing bacteria CRISPRi combined with sgRNAs pool to rapidly discover a new phytoene desaturase gene Improvement of carotenoid production by repressing a competitive pathway.
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Affiliation(s)
- Xu-Hua Mo
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Hui Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Tian-Min Wang
- Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China
| | - Chong Zhang
- Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China
| | - Cong Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Xin-Hui Xing
- Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China
| | - Song Yang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China.
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, People's Republic of China.
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Shao Y, Wang Y, Zhao R, Chen J, Zhang F, Linhardt RJ, Zhong W. Biotechnology progress for removal of indoor gaseous formaldehyde. Appl Microbiol Biotechnol 2020; 104:3715-3727. [PMID: 32172323 DOI: 10.1007/s00253-020-10514-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 02/21/2020] [Accepted: 02/28/2020] [Indexed: 11/25/2022]
Abstract
Formaldehyde is a ubiquitous carcinogenic indoor pollutant. The treatment of formaldehyde has attracted increasing social attention. Over the past few decades, an increasing number of publications have reported approaches for removing indoor formaldehyde. These potential strategies include physical adsorption, chemical catalysis, and biodegradation. Although physical adsorption is widely used, it does not really remove pollution. Chemical catalysis is very efficient but adds the risk of introducing secondary pollutants. Biological removal strategies have attracted more research attention than the first two methods, because it is more efficient, clean, and economical. Plants and bacteria are the common organisms used in formaldehyde removal. However, both have limitations and shortcomings when used alone. This review discusses the mechanisms, applications, and improvements of existing biological methods for the removal of indoor gaseous formaldehyde. A combination strategy relying on plants, bacteria, and physical adsorbents exhibits best ability to remove formaldehyde efficiently, economically, and safely. When this combination system is integrated with a heating, ventilation, air conditioning, and cooling (HVAC) system, a practical combined system can be established in formaldehyde removal. Multivariate interactions of biological and non-biological factors are needed for the future development of indoor formaldehyde removal. KEY POINTS: • Indoor gaseous formaldehyde removal is necessary especially for new residence. • Biological removal strategies have attracted increasing research attentions. • Combined system of plants, bacteria, and physical adsorbents exhibits best efficiency. • Integrated device of biological and non-biological factors will be potential practical.
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Affiliation(s)
- Yunhai Shao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - Yanxin Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - Rui Zhao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - Jianmen Chen
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - Fuming Zhang
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Robert J Linhardt
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Weihong Zhong
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China.
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Methylofuran is a prosthetic group of the formyltransferase/hydrolase complex and shuttles one-carbon units between two active sites. Proc Natl Acad Sci U S A 2019; 116:25583-25590. [PMID: 31776258 PMCID: PMC6926001 DOI: 10.1073/pnas.1911595116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Methylotrophs play a crucial role in the global carbon cycle as they oxidize reduced one-carbon compounds such as methanol or methane to CO2. The step-wise conversion of these substrates generally takes place while the one-carbon units are bound to diffusible carrier molecules. However, our crystal structure of the formyltransferase/hydrolase complex from Methylorubrum extorquens demonstrates that the one-carbon carrier methylofuran tightly binds to the enzyme via its extended and branched polyglutamate chain. A swinging motion of the coenzyme then shuttles one-carbon units between the two active sites of the enzyme complex over a distance of 50 Å. The structure further highlights how the bacterial formate generation system relates to the archaeal CO2 fixation system. Methylotrophy, the ability of microorganisms to grow on reduced one-carbon substrates such as methane or methanol, is a feature of various bacterial species. The prevailing oxidation pathway depends on tetrahydromethanopterin (H4MPT) and methylofuran (MYFR), an analog of methanofuran from methanogenic archaea. Formyltransferase/hydrolase complex (Fhc) generates formate from formyl-H4MPT in two consecutive reactions where MYFR acts as a carrier of one-carbon units. Recently, we chemically characterized MYFR from the model methylotroph Methylorubrum extorquens and identified an unusually long polyglutamate side chain of up to 24 glutamates. Here, we report on the crystal structure of Fhc to investigate the function of the polyglutamate side chain in MYFR and the relatedness of the enzyme complex with the orthologous enzymes in archaea. We identified MYFR as a prosthetic group that is tightly, but noncovalently, bound to Fhc. Surprisingly, the structure of Fhc together with MYFR revealed that the polyglutamate side chain of MYFR is branched and contains glutamates with amide bonds at both their α- and γ-carboxyl groups. This negatively charged and branched polyglutamate side chain interacts with a cluster of conserved positively charged residues of Fhc, allowing for strong interactions. The MYFR binding site is located equidistantly from the active site of the formyltransferase (FhcD) and metallo-hydrolase (FhcA). The polyglutamate serves therefore an additional function as a swinging linker to shuttle the one-carbon carrying amine between the two active sites, thereby likely increasing overall catalysis while decreasing the need for high intracellular MYFR concentrations.
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Shao Y, Li J, Wang Y, Yi F, Zhang Y, Cui P, Zhong W. Comparative genomics and transcriptomics insights into the C1 metabolic model of a formaldehyde-degrading strain Methylobacterium sp. XJLW. Mol Omics 2019; 15:138-149. [PMID: 30785446 DOI: 10.1039/c8mo00198g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A formaldehyde-degrading strain Methylobacterium sp. XJLW was isolated and exhibited a special phenotype for formaldehyde utilization. The accumulation of formic acid in large quantities and lower cell growth was detected when XJLW utilized formaldehyde as the sole carbon source, suggesting XJLW has a potentially novel pathway to transfer formaldehyde to methanol and then enter the serine cycle for C1 metabolism. This mechanism requires exploration via molecular omics. Thus, the complete genome of XJLW was sequenced, and the transcriptome difference was also analyzed based on the RNA-seq data of strain XJLW cultivated with methanol and glucose, respectively. XJLW has a chromosome DNA and a mega-plasmid DNA. Ten percent of genes on chromosome DNA are strain-specific in genus Methylobacterium. Transcriptome analysis results showed that 623 genes were significantly up-regulated and that 207 genes were significantly down-regulated for growth in methanol. Among the up-regulated genes, 90 genes belong to strain-specific regions and are densely distributed in three areas. A specific gene (A3862_27225) annotated as methyltransferase was found ranking in the top 4 of up-regulated genes. This methyltransferase may play a role in the specific C1 metabolism of XJLW. Methylobacterium sp. XJLW should contain a potential methyl transport pathway via the novel methyltransferase, which is different from known pathways. These findings provide the basis for additional possibilities, which improve the formaldehyde-degrading ability of Methylobacterium sp. XJLW.
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Affiliation(s)
- Yunhai Shao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.
| | - Jun Li
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.
| | - Yanxin Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.
| | - Fengmei Yi
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.
| | - Yanan Zhang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.
| | - Peiwu Cui
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.
| | - Weihong Zhong
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.
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Ochsner AM, Hemmerle L, Vonderach T, Nüssli R, Bortfeld-Miller M, Hattendorf B, Vorholt JA. Use of rare-earth elements in the phyllosphere colonizer Methylobacterium extorquens PA1. Mol Microbiol 2019; 111:1152-1166. [PMID: 30653750 PMCID: PMC6850437 DOI: 10.1111/mmi.14208] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2019] [Indexed: 01/03/2023]
Abstract
Until recently, rare‐earth elements (REEs) had been thought to be biologically inactive. This view changed with the discovery of the methanol dehydrogenase XoxF that strictly relies on REEs for its activity. Some methylotrophs only contain xoxF, while others, including the model phyllosphere colonizer Methylobacterium extorquens PA1, harbor this gene in addition to mxaFI encoding a Ca2+‐dependent enzyme. Here we found that REEs induce the expression of xoxF in M. extorquens PA1, while repressing mxaFI, suggesting that XoxF is the preferred methanol dehydrogenase in the presence of sufficient amounts of REE. Using reporter assays and a suppressor screen, we found that lanthanum (La3+) is sensed both in a XoxF‐dependent and independent manner. Furthermore, we investigated the role of REEs during Arabidopsisthaliana colonization. Element analysis of the phyllosphere revealed the presence of several REEs at concentrations up to 10 μg per g dry weight. Complementary proteome analyses of M. extorquens PA1 identified XoxF as a top induced protein in planta and a core set of La3+‐regulated proteins under defined artificial media conditions. Among these was a REE‐binding protein that is encoded next to a gene for a TonB‐dependent transporter. The latter was essential for REE‐dependent growth on methanol indicating chelator‐assisted uptake of REEs.
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Affiliation(s)
- Andrea M Ochsner
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
| | - Lucas Hemmerle
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
| | - Thomas Vonderach
- Laboratory of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
| | - Ralph Nüssli
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
| | - Miriam Bortfeld-Miller
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
| | - Bodo Hattendorf
- Laboratory of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
| | - Julia A Vorholt
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
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Schada von Borzyskowski L, Carrillo M, Leupold S, Glatter T, Kiefer P, Weishaupt R, Heinemann M, Erb TJ. An engineered Calvin-Benson-Bassham cycle for carbon dioxide fixation in Methylobacterium extorquens AM1. Metab Eng 2018; 47:423-433. [DOI: 10.1016/j.ymben.2018.04.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 03/21/2018] [Accepted: 04/02/2018] [Indexed: 10/17/2022]
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N-terminome and proteogenomic analysis of the Methylobacterium extorquens DM4 reference strain for dichloromethane utilization. J Proteomics 2018; 179:131-139. [DOI: 10.1016/j.jprot.2018.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 02/28/2018] [Accepted: 03/16/2018] [Indexed: 12/29/2022]
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25
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Chistoserdova L, Kalyuzhnaya MG. Current Trends in Methylotrophy. Trends Microbiol 2018; 26:703-714. [PMID: 29471983 DOI: 10.1016/j.tim.2018.01.011] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/18/2018] [Accepted: 01/30/2018] [Indexed: 11/26/2022]
Abstract
Methylotrophy is a field of study dealing with microorganisms capable of utilization of compounds devoid of carbon-carbon bonds (C1 compounds). In this review, we highlight several emerging trends in methylotrophy. First, we discuss the significance of the recent discovery of lanthanide-dependent alcohol dehydrogenases for understanding both the occurrence and the distribution of methylotrophy functions among bacteria, and then we discuss the newly appreciated role of lanthanides in biology. Next, we describe the detection of other methylotrophy pathways across novel bacterial taxa and insights into the evolution of methylotrophy. Further, data are presented on the occurrence and activity of aerobic methylotrophs in hypoxic and anoxic environments, questioning the prior assumptions on niche separation of aerobic and anaerobic methylotrophy. The concept of communal function in aerobic methane oxidation is also briefly discussed. Finally, we review recent research in engineering methylotrophs for biotechnological applications as well as recent progress in engineering synthetic methylotrophy.
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26
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Chistoserdova L. Applications of methylotrophs: can single carbon be harnessed for biotechnology? Curr Opin Biotechnol 2018; 50:189-194. [PMID: 29414059 DOI: 10.1016/j.copbio.2018.01.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 12/07/2017] [Accepted: 01/11/2018] [Indexed: 02/06/2023]
Abstract
This review summarizes developments in the field of applied research involving microbial conversion of single carbon compounds (methane, methanol, CO2). The potential of the microorganisms involved in biotechnological applications could be realized via engineering native C1 utilizers toward higher output of value-added compounds, including biofuels, or via production of value chemicals as parts of novel, heterologously expressed biochemical pathways. Alternatively, C1 metabolism could be implemented in traditional industrial platforms (Escherichia coli, yeast), via introduction of specific metabolic modules. Most recent research spanning both approaches is covered. The potential of C1 utilizers in biomining of rare Earth elements, as well as the potential of C1 consuming microbial consortia in industrial applications are discussed.
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Affiliation(s)
- Ludmila Chistoserdova
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States.
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27
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Bringel F, Vuilleumier S. Metabolic Regulation: A Master Role for Ribulose-1,5-Bisphosphate in One-Carbon Assimilation. Curr Biol 2017; 27:R1127-R1129. [PMID: 29065298 DOI: 10.1016/j.cub.2017.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Engineering organisms for biotechnology applications requires knowledge of their essential genes and associated regulatory networks. A new study of methylotrophic metabolism in Methylobacterium reveals essentiality of the unregulated, off-pathway phosphoribulokinase gene and an unexpected key regulatory role for its product ribulose-1,5-bisphosphate.
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Affiliation(s)
- Françoise Bringel
- Université de Strasbourg, CNRS, GMGM UMR 7156, Department of Microbiology, Genomics and the Environment, Strasbourg, France.
| | - Stéphane Vuilleumier
- Université de Strasbourg, CNRS, GMGM UMR 7156, Department of Microbiology, Genomics and the Environment, Strasbourg, France
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28
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Chaignaud P, Maucourt B, Weiman M, Alberti A, Kolb S, Cruveiller S, Vuilleumier S, Bringel F. Genomic and Transcriptomic Analysis of Growth-Supporting Dehalogenation of Chlorinated Methanes in Methylobacterium. Front Microbiol 2017; 8:1600. [PMID: 28919881 PMCID: PMC5585157 DOI: 10.3389/fmicb.2017.01600] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 08/07/2017] [Indexed: 11/13/2022] Open
Abstract
Bacterial adaptation to growth with toxic halogenated chemicals was explored in the context of methylotrophic metabolism of Methylobacterium extorquens, by comparing strains CM4 and DM4, which show robust growth with chloromethane and dichloromethane, respectively. Dehalogenation of chlorinated methanes initiates growth-supporting degradation, with intracellular release of protons and chloride ions in both cases. The core, variable and strain-specific genomes of strains CM4 and DM4 were defined by comparison with genomes of non-dechlorinating strains. In terms of gene content, adaptation toward dehalogenation appears limited, strains CM4 and DM4 sharing between 75 and 85% of their genome with other strains of M. extorquens. Transcript abundance in cultures of strain CM4 grown with chloromethane and of strain DM4 grown with dichloromethane was compared to growth with methanol as a reference C1 growth substrate. Previously identified strain-specific dehalogenase-encoding genes were the most transcribed with chlorinated methanes, alongside other genes encoded by genomic islands (GEIs) and plasmids involved in growth with chlorinated compounds as carbon and energy source. None of the 163 genes shared by strains CM4 and DM4 but not by other strains of M. extorquens showed higher transcript abundance in cells grown with chlorinated methanes. Among the several thousand genes of the M. extorquens core genome, 12 genes were only differentially abundant in either strain CM4 or strain DM4. Of these, 2 genes of known function were detected, for the membrane-bound proton translocating pyrophosphatase HppA and the housekeeping molecular chaperone protein DegP. This indicates that the adaptive response common to chloromethane and dichloromethane is limited at the transcriptional level, and involves aspects of the general stress response as well as of a dehalogenation-specific response to intracellular hydrochloric acid production. Core genes only differentially abundant in either strain CM4 or strain DM4 total 13 and 58 CDS, respectively. Taken together, the obtained results suggest different transcriptional responses of chloromethane- and dichloromethane-degrading M. extorquens strains to dehalogenative metabolism, and substrate- and pathway-specific modes of growth optimization with chlorinated methanes.
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Affiliation(s)
- Pauline Chaignaud
- Department of Molecular Genetics, Genomics, and Microbiology, UMR 7156 Université de Strasbourg (UNISTRA)-Centre National de la Recherche ScientifiqueStrasbourg, France.,Department of Ecological Microbiology, University of BayreuthBayreuth, Germany
| | - Bruno Maucourt
- Department of Molecular Genetics, Genomics, and Microbiology, UMR 7156 Université de Strasbourg (UNISTRA)-Centre National de la Recherche ScientifiqueStrasbourg, France
| | - Marion Weiman
- UMR 8030 Centre National de la Recherche Scientifique-CEA, DSV/IG/Genoscope, LABGeMEvry, France
| | - Adriana Alberti
- UMR 8030 Centre National de la Recherche Scientifique-CEA, DSV/IG/Genoscope, LABGeMEvry, France
| | - Steffen Kolb
- Department of Ecological Microbiology, University of BayreuthBayreuth, Germany.,Institute of Landscape Biogeochemistry-Leibniz Centre for Agricultural Landscape Research (ZALF)Müncheberg, Germany
| | - Stéphane Cruveiller
- UMR 8030 Centre National de la Recherche Scientifique-CEA, DSV/IG/Genoscope, LABGeMEvry, France
| | - Stéphane Vuilleumier
- Department of Molecular Genetics, Genomics, and Microbiology, UMR 7156 Université de Strasbourg (UNISTRA)-Centre National de la Recherche ScientifiqueStrasbourg, France
| | - Françoise Bringel
- Department of Molecular Genetics, Genomics, and Microbiology, UMR 7156 Université de Strasbourg (UNISTRA)-Centre National de la Recherche ScientifiqueStrasbourg, France
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