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Construction of a Rhodobacter sphaeroides Strain That Efficiently Produces Hydrogen Gas from Acetate without Poly(β-Hydroxybutyrate) Accumulation: Insight into the Role of PhaR in Acetate Metabolism. Appl Environ Microbiol 2022; 88:e0050722. [PMID: 35670584 DOI: 10.1128/aem.00507-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The purple nonsulfur phototrophic bacterium Rhodobacter sphaeroides produces hydrogen gas (H2) from acetate. An approach to improve the H2 production is preventing accumulation of an intracellular energy storage molecule known as poly(β-hydroxybutyrate) (PHB), which competes with H2 production for reducing power. However, disruption of PHB biosynthesis has been reported to severely impair the acetate assimilation depending on the genetic backgrounds and/or culture conditions. To solve this problem, we analyzed the relationship between PHB accumulation and acetate metabolism in R. sphaeroides. Gene deletion analyses based on the wild-type strain revealed that among the two polyhydroxyalkanoate synthase genes in the genome, phaC1, but not phaC2, is essential for PHB accumulation, and the phaC1 deletion mutant exhibited slow growth with acetate. On the other hand, a strain with the deletion of phaC1 together with phaR, which encodes a transcriptional regulator capable of sensing PHB accumulation, exhibited growth comparable to that of the wild-type strain despite no accumulation of PHB. These results suggest that PHB accumulation is required for normal growth with acetate by altering the expression of genes under the control of phaR. This hypothesis was supported by a transcriptome sequencing (RNA-seq) analysis revealing that phaR is involved in the regulation of the ethylmalonyl coenzyme A pathway for acetate assimilation. Consistent with these findings, deletion of phaC1 in a genetically engineered H2-producing strain resulted in lower H2 production from acetate due to growth defects, whereas deletion of phaR together with phaC1 restored growth with acetate and increased H2 production from acetate without PHB accumulation. IMPORTANCE This study provides a novel approach for increasing the yield of photofermentative H2 production from acetate by purple nonsulfur phototrophic bacteria. This study further suggests that polyhydroxyalkanoate is not only a storage substance for carbon and energy in bacteria, but may also act as a signaling molecule that mediates bacterial metabolic adaptations to specific environments. This notion will be helpful for understanding the physiology of polyhydroxyalkanoate-producing bacteria, as well as for their metabolic engineering via synthetic biology.
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Orsi E, Beekwilder J, Eggink G, Kengen SWM, Weusthuis RA. The transition of Rhodobacter sphaeroides into a microbial cell factory. Biotechnol Bioeng 2020; 118:531-541. [PMID: 33038009 PMCID: PMC7894463 DOI: 10.1002/bit.27593] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/29/2020] [Accepted: 10/09/2020] [Indexed: 12/11/2022]
Abstract
Microbial cell factories are the workhorses of industrial biotechnology and improving their performances can significantly optimize industrial bioprocesses. Microbial strain engineering is often employed for increasing the competitiveness of bio‐based product synthesis over more classical petroleum‐based synthesis. Recently, efforts for strain optimization have been standardized within the iterative concept of “design‐build‐test‐learn” (DBTL). This approach has been successfully employed for the improvement of traditional cell factories like Escherichia coli and Saccharomyces cerevisiae. Within the past decade, several new‐to‐industry microorganisms have been investigated as novel cell factories, including the versatile α‐proteobacterium Rhodobacter sphaeroides. Despite its history as a laboratory strain for fundamental studies, there is a growing interest in this bacterium for its ability to synthesize relevant compounds for the bioeconomy, such as isoprenoids, poly‐β‐hydroxybutyrate, and hydrogen. In this study, we reflect on the reasons for establishing R. sphaeroides as a cell factory from the perspective of the DBTL concept. Moreover, we discuss current and future opportunities for extending the use of this microorganism for the bio‐based economy. We believe that applying the DBTL pipeline for R. sphaeroides will further strengthen its relevance as a microbial cell factory. Moreover, the proposed use of strain engineering via the DBTL approach may be extended to other microorganisms that have not been critically investigated yet for industrial applications.
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Affiliation(s)
- Enrico Orsi
- Bioprocess Engineering, Wageningen University, Wageningen, The Netherlands.,Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Gerrit Eggink
- Bioprocess Engineering, Wageningen University, Wageningen, The Netherlands.,Wageningen Food and Biobased Research, Wageningen, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Ruud A Weusthuis
- Bioprocess Engineering, Wageningen University, Wageningen, The Netherlands
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3
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Policastro G, Luongo V, Fabbricino M. Biohydrogen and poly-β-hydroxybutyrate production by winery wastewater photofermentation: Effect of substrate concentration and nitrogen source. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 271:111006. [PMID: 32778291 DOI: 10.1016/j.jenvman.2020.111006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/07/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
The applicability and convenience of biohydrogen and poly-β-hydroxybutyrate production through single-stage photofermentation of winery wastewater is demonstrated in the present study. Experiments are conducted using a purple non-sulfur bacteria mixed consortium, subject to variable nutrient conditions, to analyze the effect of initial chemical oxygen demand and the available nitrogen source on the metabolic response. Results show that winery wastewater is a promising substrate for photofermentation processes, despite the presence of inhibiting compounds such as phenolics. Nonetheless, the initial chemical oxygen demand must be carefully controlled to maximize hydrogen production. Up to 468 mL L-1 of hydrogen and 203 mg L-1 of poly-β-hydroxybutyrate can be produced starting from an initial chemical oxygen demand of 1500 mg L-1. The used nitrogen source may direct substrate transformation through different metabolic pathways. Interestingly, the maximum production of both hydrogen and poly-β-hydroxybutyrate occurred when glutamate was used as the nitrogen source.
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Affiliation(s)
- Grazia Policastro
- Department of Civil, Architectural and Environmental Engineering, University of Naples Federico II, via Claudio 21, 80125, Naples, Italy.
| | - Vincenzo Luongo
- Department of Mathematics and Applications Renato Caccioppoli, University of Naples Federico II, via Cintia, Monte S. Angelo, I-80126 Naples, Italy.
| | - Massimiliano Fabbricino
- Department of Civil, Architectural and Environmental Engineering, University of Naples Federico II, via Claudio 21, 80125, Naples, Italy.
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Production of polyhydroxybutyrate by pure and mixed cultures of purple non-sulfur bacteria: A review. J Biotechnol 2020; 317:39-47. [DOI: 10.1016/j.jbiotec.2020.04.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 04/20/2020] [Accepted: 04/20/2020] [Indexed: 11/24/2022]
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Mougiakos I, Orsi E, Ghiffary MR, Post W, de Maria A, Adiego-Perez B, Kengen SWM, Weusthuis RA, van der Oost J. Efficient Cas9-based genome editing of Rhodobacter sphaeroides for metabolic engineering. Microb Cell Fact 2019; 18:204. [PMID: 31767004 PMCID: PMC6876111 DOI: 10.1186/s12934-019-1255-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 11/13/2019] [Indexed: 12/18/2022] Open
Abstract
Background Rhodobacter sphaeroides is a metabolically versatile bacterium that serves as a model for analysis of photosynthesis, hydrogen production and terpene biosynthesis. The elimination of by-products formation, such as poly-β-hydroxybutyrate (PHB), has been an important metabolic engineering target for R. sphaeroides. However, the lack of efficient markerless genome editing tools for R. sphaeroides is a bottleneck for fundamental studies and biotechnological exploitation. The Cas9 RNA-guided DNA-endonuclease from the type II CRISPR-Cas system of Streptococcus pyogenes (SpCas9) has been extensively employed for the development of genome engineering tools for prokaryotes and eukaryotes, but not for R. sphaeroides. Results Here we describe the development of a highly efficient SpCas9-based genomic DNA targeting system for R. sphaeroides, which we combine with plasmid-borne homologous recombination (HR) templates developing a Cas9-based markerless and time-effective genome editing tool. We further employ the tool for knocking-out the uracil phosphoribosyltransferase (upp) gene from the genome of R. sphaeroides, as well as knocking it back in while altering its start codon. These proof-of-principle processes resulted in editing efficiencies of up to 100% for the knock-out yet less than 15% for the knock-in. We subsequently employed the developed genome editing tool for the consecutive deletion of the two predicted acetoacetyl-CoA reductase genes phaB and phbB in the genome of R. sphaeroides. The culturing of the constructed knock-out strains under PHB producing conditions showed that PHB biosynthesis is supported only by PhaB, while the growth of the R. sphaeroides ΔphbB strains under the same conditions is only slightly affected. Conclusions In this study, we combine the SpCas9 targeting activity with the native homologous recombination (HR) mechanism of R. sphaeroides for the development of a genome editing tool. We further employ the developed tool for the elucidation of the PHB production pathway of R. sphaeroides. We anticipate that the presented work will accelerate molecular research with R. sphaeroides.
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Affiliation(s)
- Ioannis Mougiakos
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Enrico Orsi
- Bioprocess Engineering, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Mohammad Rifqi Ghiffary
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.,Bioprocess Engineering, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.,Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Wilbert Post
- Bioprocess Engineering, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Alberto de Maria
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.,Bioprocess Engineering, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.,Systems and Synthetic Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Belén Adiego-Perez
- Bioprocess Engineering, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Ruud A Weusthuis
- Bioprocess Engineering, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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Orsi E, Folch PL, Monje-López VT, Fernhout BM, Turcato A, Kengen SWM, Eggink G, Weusthuis RA. Characterization of heterotrophic growth and sesquiterpene production by Rhodobacter sphaeroides on a defined medium. J Ind Microbiol Biotechnol 2019; 46:1179-1190. [PMID: 31187318 PMCID: PMC6697705 DOI: 10.1007/s10295-019-02201-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/29/2019] [Indexed: 11/30/2022]
Abstract
Rhodobacter sphaeroides is a metabolically versatile bacterium capable of producing terpenes natively. Surprisingly, terpene biosynthesis in this species has always been investigated in complex media, with unknown compounds possibly acting as carbon and nitrogen sources. Here, a defined medium was adapted for R. sphaeroides dark heterotrophic growth, and was used to investigate the conversion of different organic substrates into the reporter terpene amorphadiene. The amorphadiene synthase was cloned in R. sphaeroides, allowing its biosynthesis via the native 2-methyl-d-erythritol-4-phosphate (MEP) pathway and, additionally, via a heterologous mevalonate one. The latter condition increased titers up to eightfold. Consequently, better yields and productivities to previously reported complex media cultivations were achieved. Productivity was further investigated under different cultivation conditions, including nitrogen and oxygen availability. This novel cultivation setup provided useful insight into the understanding of terpene biosynthesis in R. sphaeroides, allowing to better comprehend its dynamics and regulation during chemoheterotrophic cultivation.
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Affiliation(s)
- Enrico Orsi
- Bioprocess Engineering, Department of Agrotechnology and Food, Wageningen University and Research, Wageningen, The Netherlands
| | - Pauline L Folch
- Bioprocess Engineering, Department of Agrotechnology and Food, Wageningen University and Research, Wageningen, The Netherlands
| | - Vicente T Monje-López
- Bioprocess Engineering, Department of Agrotechnology and Food, Wageningen University and Research, Wageningen, The Netherlands
| | - Bas M Fernhout
- Bioprocess Engineering, Department of Agrotechnology and Food, Wageningen University and Research, Wageningen, The Netherlands
| | - Alessandro Turcato
- Bioprocess Engineering, Department of Agrotechnology and Food, Wageningen University and Research, Wageningen, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Department of Agrotechnology and Food, Wageningen University and Research, Wageningen, The Netherlands
| | - Gerrit Eggink
- Bioprocess Engineering, Department of Agrotechnology and Food, Wageningen University and Research, Wageningen, The Netherlands.,Biobased Products Food and Biobased Research, Wageningen University and Research, Wageningen, The Netherlands
| | - Ruud A Weusthuis
- Bioprocess Engineering, Department of Agrotechnology and Food, Wageningen University and Research, Wageningen, The Netherlands.
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Ghimire A, Valentino S, Frunzo L, Pirozzi F, Lens PNL, Esposito G. Concomitant biohydrogen and poly-β-hydroxybutyrate production from dark fermentation effluents by adapted Rhodobacter sphaeroides and mixed photofermentative cultures. BIORESOURCE TECHNOLOGY 2016; 217:157-164. [PMID: 27005789 DOI: 10.1016/j.biortech.2016.03.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 02/27/2016] [Accepted: 03/01/2016] [Indexed: 06/05/2023]
Abstract
This work aimed at investigating concomitant production of biohydrogen and poly-β-hydroxybutyrate (PHB) by photofermentation (PF) using dark fermentation effluents (DFE). An adapted culture of Rhodobacter sphaeroides AV1b (pH 6.5, 24±2°C) achieved H2 and PHB yields of 256 (±2) NmLH2/g Chemical Oxygen Demand (COD) and 273.8mgPHB/gCOD (32.5±3% of the dry cells weight (DCW)), respectively. When a diluted (1:2) DFE medium was applied to the adapted pure and mixed photofermentative culture, the respective H2 yields were 164.0 (±12) and 71.3 (±6) NmLH2/gCOD and the PHB yields were 212.1 (±105.2) and 50.7 (±2.7) mgPHB/gCOD added, corresponding to 24 (±0.7) and 6.3 (±0) % DCW, respectively. The concomitant H2 and PHB production from the PF process gave a good DFE post treatment achieving up to 80% COD removal from the initial DFE.
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Affiliation(s)
- Anish Ghimire
- Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, via Di Biasio 43, 03043 Cassino (FR), Italy; Department of Civil, Architectural and Environmental Engineering, University of Naples Federico II, via Claudio 21, 80125 Naples, Italy.
| | - Serena Valentino
- Department of Civil, Architectural and Environmental Engineering, University of Naples Federico II, via Claudio 21, 80125 Naples, Italy
| | - Luigi Frunzo
- Department of Mathematics and Applications Renato Caccioppoli, University of Naples Federico II, via Cintia, Monte S. Angelo, I-80126 Naples, Italy
| | - Francesco Pirozzi
- Department of Civil, Architectural and Environmental Engineering, University of Naples Federico II, via Claudio 21, 80125 Naples, Italy
| | - Piet N L Lens
- UNESCO-IHE Institute for Water Education, Westvest 7, 2611 AX Delft, The Netherlands
| | - Giovanni Esposito
- Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, via Di Biasio 43, 03043 Cassino (FR), Italy
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Golomysova AN, Ivanov PS. Investigation of the anaerobic metabolism of Rhodobacter capsulatus by means of a flux model. Biophysics (Nagoya-shi) 2011. [DOI: 10.1134/s000635091101009x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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