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Hernández-Herreros N, Rodríguez A, Galán B, Auxiliadora Prieto M. Boosting hydrogen production in Rhodospirillum rubrum by syngas-driven photoheterotrophic adaptive evolution. BIORESOURCE TECHNOLOGY 2024; 406:130972. [PMID: 38876276 DOI: 10.1016/j.biortech.2024.130972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 05/07/2024] [Accepted: 06/12/2024] [Indexed: 06/16/2024]
Abstract
Rhodospirillum rubrum is a photosynthetic purple non-sulphur bacterium with great potential to be used for complex waste valorisation in biotechnological applications due to its metabolic versatility. This study investigates the production of hydrogen (H2) and polyhydroxyalkanoates (PHA) by R. rubrum from syngas under photoheterotrophic conditions. An adaptive laboratory evolution strategy (ALE) has been carried out to improve the yield of the process. After 200 generations, two evolved strains were selected that showed reduced lag phase and enhanced PHB and H2 synthesis compared to the parental strain. Genomic analysis of the photo-adapted (PA) variants showed four genes with single point mutations, including the photosynthesis gene expression regulator PpsR. The proteome of the variants suggested that the adapted variants overproduced H2 due to a more efficient CO oxidation through the CO-dehydrogenase enzyme complex and confirmed that energy acquisition was enhanced through overexpression of the photosynthetic system and metal cofactors essential for pigment biosynthesis.
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Affiliation(s)
- Natalia Hernández-Herreros
- Microbial & Plant Biotechnology Department, Polymer Biotechnology Group, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Alberto Rodríguez
- Microbial & Plant Biotechnology Department, Polymer Biotechnology Group, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Beatriz Galán
- Microbial & Plant Biotechnology Department, Environmental Biotechnology Group, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain
| | - M Auxiliadora Prieto
- Microbial & Plant Biotechnology Department, Polymer Biotechnology Group, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain.
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Godoy MS, Verdú I, de Miguel SR, Jiménez JD, Prieto MA. Exploring Rhodospirillum rubrum response to high doses of carbon monoxide under light and dark conditions. Appl Microbiol Biotechnol 2024; 108:258. [PMID: 38466440 DOI: 10.1007/s00253-024-13079-5] [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: 11/28/2023] [Revised: 01/14/2024] [Accepted: 02/16/2024] [Indexed: 03/13/2024]
Abstract
Environmental concerns about residues and the traditional disposal methods are driving the search for more environmentally conscious processes, such as pyrolysis and gasification. Their main final product is synthesis gas (syngas) composed of CO, CO2, H2, and methane. Syngas can be converted into various products using CO-tolerant microorganisms. Among them, Rhodospirillum rubrum is highlighted for its biotechnological potential. However, the extent to which high doses of CO affect its physiology is still opaque. For this reason, we have studied R. rubrum behavior under high levels of this gas (up to 2.5 bar), revealing a profound dependence on the presence or absence of light. In darkness, the key variable affected was the lag phase, where the highest levels of CO retarded growth to more than 20 days. Under light, R. rubrum ability to convert CO into CO2 and H2 depended on the presence of an additional carbon source, such as acetate. In those conditions where CO was completely exhausted, CO2 fixation was unblocked, leading to a diauxic growth. To enhance R. rubrum tolerance to CO in darkness, a UV-accelerated adaptive laboratory evolution (UVa-ALE) trial was conducted to isolate clones with shorter lag phases, resulting in the isolation of clones 1.4-2B and 1.7-2A. The adaptation of 1.4-2B was mainly based on mutated enzymes with a metabolic function, while 1.7-3A was mostly affected at regulatory genes, including the anti-repressor PpaA/AerR. Despite these mutations having slight effects on biomass and pigment levels, they successfully provoked a significant reduction in the lag phase (-50%). KEYPOINTS: • CO affects principally R. rubrum lag phase (darkness) and growth rate (light) • CO is converted to CO2/H2 during acetate uptake and inhibits CO2 fixation (light) • UVa-ALE clones showed a 50% reduction in the lag phase (darkness).
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Affiliation(s)
- Manuel S Godoy
- Polymer Biotechnology Lab, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain.
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-CSIC (SusPlast-CSIC), Madrid, Spain.
| | - Irene Verdú
- Polymer Biotechnology Lab, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain
- Present address: Drexel University, Philadelphia, Pennsylvania, USA
| | - Santiago R de Miguel
- Polymer Biotechnology Lab, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-CSIC (SusPlast-CSIC), Madrid, Spain
| | - José D Jiménez
- Polymer Biotechnology Lab, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-CSIC (SusPlast-CSIC), Madrid, Spain
| | - M Auxiliadora Prieto
- Polymer Biotechnology Lab, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain.
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-CSIC (SusPlast-CSIC), Madrid, Spain.
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Matallana-Surget S, Geron A, Decroo C, Wattiez R. Diel Cycle Proteomics: Illuminating Molecular Dynamics in Purple Bacteria for Optimized Biotechnological Applications. Int J Mol Sci 2024; 25:2934. [PMID: 38474181 DOI: 10.3390/ijms25052934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Circadian rhythms, characterized by approximately 24 h cycles, play a pivotal role in enabling various organisms to synchronize their biological activities with daily variations. While ubiquitous in Eukaryotes, circadian clocks remain exclusively characterized in Cyanobacteria among Prokaryotes. These rhythms are regulated by a core oscillator, which is controlled by a cluster of three genes: kaiA, kaiB, and kaiC. Interestingly, recent studies revealed rhythmic activities, potentially tied to a circadian clock, in other Prokaryotes, including purple bacteria such as Rhodospirillum rubrum, known for its applications in fuel and plastic bioproduction. However, the pivotal question of how light and dark cycles influence protein dynamics and the expression of putative circadian clock genes remains unexplored in purple non-sulfur bacteria. Unraveling the regulation of these molecular clocks holds the key to unlocking optimal conditions for harnessing the biotechnological potential of R. rubrum. Understanding how its proteome responds to different light regimes-whether under continuous light or alternating light and dark cycles-could pave the way for precisely fine-tuning bioproduction processes. Here, we report for the first time the expressed proteome of R. rubrum grown under continuous light versus light and dark cycle conditions using a shotgun proteomic analysis. In addition, we measured the impact of light regimes on the expression of four putative circadian clock genes (kaiB1, kaiB2, kaiC1, kaiC2) at the transcriptional and translational levels using RT-qPCR and targeted proteomic (MRM-MS), respectively. The data revealed significant effects of light conditions on the overall differential regulation of the proteome, particularly during the early growth stages. Notably, several proteins were found to be differentially regulated during the light or dark period, thus impacting crucial biological processes such as energy conversion pathways and the general stress response. Furthermore, our study unveiled distinct regulation of the four kai genes at both the mRNA and protein levels in response to varying light conditions. Deciphering the impact of the diel cycle on purple bacteria not only enhances our understanding of their ecology but also holds promise for optimizing their applications in biotechnology, providing valuable insights into the origin and evolution of prokaryotic clock mechanisms.
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Affiliation(s)
- Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - Augustin Geron
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
- Proteomic and Microbiology Department, University of Mons, B-7000 Mons, Belgium
| | - Corentin Decroo
- Proteomic and Microbiology Department, University of Mons, B-7000 Mons, Belgium
| | - Ruddy Wattiez
- Proteomic and Microbiology Department, University of Mons, B-7000 Mons, Belgium
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Godoy MS, de Miguel SR, Prieto MA. A singular PpaA/AerR-like protein in Rhodospirillum rubrum rules beyond the boundaries of photosynthesis in response to the intracellular redox state. mSystems 2023; 8:e0070223. [PMID: 38054698 PMCID: PMC10734443 DOI: 10.1128/msystems.00702-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/18/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Rhodospirillum rubrum vast metabolic versatility places it as a remarkable model bacterium and an excellent biotechnological chassis. The key component of photosynthesis (PS) studied in this work (HP1) stands out among the other members of PpaA/AerR anti-repressor family since it lacks the motif they all share: the cobalamin B-12 binding motif. Despite being reduced and poorly conserved, HP1 stills controls PS as the other members of the family, allowing a fast response to changes in the redox state of the cell. This work also shows that HP1 absence affects genes from relevant biological processes other than PS, including nitrogen fixation and stress response. From a biotechnological perspective, HP1 could be manipulated in approaches where PS is not necessary, such as hydrogen or polyhydroxyalkanoates production, to save energy.
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Affiliation(s)
- Manuel S. Godoy
- Polymer Biotechnology Lab, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐CSIC (SusPlast‐CSIC), Madrid, Spain
| | - Santiago R. de Miguel
- Polymer Biotechnology Lab, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐CSIC (SusPlast‐CSIC), Madrid, Spain
| | - M. Auxiliadora Prieto
- Polymer Biotechnology Lab, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐CSIC (SusPlast‐CSIC), Madrid, Spain
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Padhan B, Ray M, Patel M, Patel R. Production and Bioconversion Efficiency of Enzyme Membrane Bioreactors in the Synthesis of Valuable Products. MEMBRANES 2023; 13:673. [PMID: 37505039 PMCID: PMC10384387 DOI: 10.3390/membranes13070673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/06/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023]
Abstract
The demand for bioactive molecules with nutritional benefits and pharmaceutically important properties is increasing, leading researchers to develop modified production strategies with low-cost purification processes. Recent developments in bioreactor technology can aid in the production of valuable products. Enzyme membrane bioreactors (EMRs) are emerging as sustainable synthesis processes in various agro-food industries, biofuel applications, and waste management processes. EMRs are modified reactors used for chemical reactions and product separation, particularly large-molecule hydrolysis and the conversion of macromolecules. EMRs generally produce low-molecular-weight carbohydrates, such as oligosaccharides, fructooligosaccharides, and gentiooligosaccharides. In this review, we provide a comprehensive overview of the use of EMRs for the production of valuable products, such as oligosaccharides and oligodextrans, and we discuss their application in the bioconversion of inulin, lignin, and sugars. Furthermore, we critically summarize the application and limitations of EMRs. This review provides important insights that can aid in the production of valuable products by food and pharmaceutical industries, and it is intended to assist scientists in developing improved quality and environmentally friendly prebiotics using EMRs.
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Affiliation(s)
- Bandana Padhan
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata 700126, West Bengal, India
| | - Madhubanti Ray
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata 700126, West Bengal, India
| | - Madhumita Patel
- Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
| | - Rajkumar Patel
- Energy & Environmental Science and Engineering (EESE), Integrated Science and Engineering Division (ISED), Underwood International College, Yonsei University, 85 Songdogwahak-ro, Yeonsugu, Incheon 21938, Republic of Korea
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García JL, Galán B. Integrating greenhouse gas capture and C1 biotechnology: a key challenge for circular economy. Microb Biotechnol 2021; 15:228-239. [PMID: 34905295 PMCID: PMC8719819 DOI: 10.1111/1751-7915.13991] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 11/27/2021] [Indexed: 12/02/2022] Open
Affiliation(s)
- José L García
- Environmental Biotechnology Laboratory, Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas (CIB-MS, CSIC), Madrid, Spain
| | - Beatriz Galán
- Environmental Biotechnology Laboratory, Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas (CIB-MS, CSIC), Madrid, Spain
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