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Pöhl S, Osorio-Valeriano M, Cserti E, Harberding J, Hernandez-Tamayo R, Biboy J, Sobetzko P, Vollmer W, Graumann PL, Thanbichler M. A dynamic bactofilin cytoskeleton cooperates with an M23 endopeptidase to control bacterial morphogenesis. eLife 2024; 12:RP86577. [PMID: 38294932 PMCID: PMC10945521 DOI: 10.7554/elife.86577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024] Open
Abstract
Bactofilins have emerged as a widespread family of cytoskeletal proteins with important roles in bacterial morphogenesis, but their precise mode of action is still incompletely understood. In this study, we identify the bactofilin cytoskeleton as a key regulator of cell growth in the stalked budding alphaproteobacterium Hyphomonas neptunium. We show that, in this species, bactofilin polymers localize dynamically to the stalk base and the bud neck, with their absence leading to unconstrained growth of the stalk and bud compartments, indicating a central role in the spatial regulation of cell wall biosynthesis. Database searches reveal that bactofilin genes are often clustered with genes for cell wall hydrolases of the M23 peptidase family, suggesting a functional connection between these two types of proteins. In support of this notion, we find that the H. neptunium M23 peptidase homolog LmdC interacts directly with bactofilin in vitro and is required for proper cell shape in vivo. Complementary studies in the spiral-shaped alphaproteobacterium Rhodospirillum rubrum again reveal a close association of its bactofilin and LmdC homologs, which co-localize at the inner curve of the cell, modulating the degree of cell curvature. Collectively, these findings demonstrate that bactofilins and M23 peptidases form a conserved functional module that promotes local changes in the mode of cell wall biosynthesis, thereby driving cell shape determination in morphologically complex bacteria.
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Affiliation(s)
- Sebastian Pöhl
- Department of Biology, University of Marburg, Marburg, GermanyMarburgGermany
| | - Manuel Osorio-Valeriano
- Department of Biology, University of Marburg, Marburg, GermanyMarburgGermany
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
| | - Emöke Cserti
- Department of Biology, University of Marburg, Marburg, GermanyMarburgGermany
| | - Jannik Harberding
- Department of Biology, University of Marburg, Marburg, GermanyMarburgGermany
| | - Rogelio Hernandez-Tamayo
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
- Department of Chemistry, University of MarburgMarburgGermany
- Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | - Jacob Biboy
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle UniversityNewcastle upon TyneUnited Kingdom
| | | | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle UniversityNewcastle upon TyneUnited Kingdom
- Institute for Molecular Bioscience, The University of QueenslandBrisbaneAustralia
| | - Peter L Graumann
- Department of Chemistry, University of MarburgMarburgGermany
- Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | - Martin Thanbichler
- Department of Biology, University of Marburg, Marburg, GermanyMarburgGermany
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Shavkunov KS, Markelova NY, Glazunova OA, Kolzhetsov NP, Panyukov VV, Ozoline ON. The Fate and Functionality of Alien tRNA Fragments in Culturing Medium and Cells of Escherichia coli. Int J Mol Sci 2023; 24:12960. [PMID: 37629141 PMCID: PMC10455298 DOI: 10.3390/ijms241612960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Numerous observations have supported the idea that various types of noncoding RNAs, including tRNA fragments (tRFs), are involved in communications between the host and its microbial community. The possibility of using their signaling function has stimulated the study of secreted RNAs, potentially involved in the interspecies interaction of bacteria. This work aimed at identifying such RNAs and characterizing their maturation during transport. We applied an approach that allowed us to detect oligoribonucleotides secreted by Prevotella copri (Segatella copri) or Rhodospirillum rubrum inside Escherichia coli cells. Four tRFs imported by E. coli cells co-cultured with these bacteria were obtained via chemical synthesis, and all of them affected the growth of E. coli. Their successive modifications in the culture medium and recipient cells were studied by high-throughput cDNA sequencing. Instead of the expected accidental exonucleolysis, in the milieu, we observed nonrandom cleavage by endonucleases continued in recipient cells. We also found intramolecular rearrangements of synthetic oligonucleotides, which may be considered traces of intermediate RNA circular isomerization. Using custom software, we estimated the frequency of such events in transcriptomes and secretomes of E. coli and observed surprising reproducibility in positions of such rare events, assuming the functionality of ring isoforms or their permuted derivatives in bacteria.
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Affiliation(s)
- Konstantin S. Shavkunov
- Department of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Natalia Yu. Markelova
- Department of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Olga A. Glazunova
- Department of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Nikolay P. Kolzhetsov
- Department of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Valery V. Panyukov
- Institute of Mathematical Problems of Biology RAS—The Branch of Keldysh Institute of Applied Mathematics of the Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Olga N. Ozoline
- Department of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Russia
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Godoy MS, de Miguel SR, Prieto MA. Aerobic-anaerobic transition boosts poly(3-hydroxybutyrate-co-3-hydroxyvalerate) synthesis in Rhodospirillum rubrum: the key role of carbon dioxide. Microb Cell Fact 2023; 22:47. [PMID: 36899367 PMCID: PMC9999600 DOI: 10.1186/s12934-023-02045-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/16/2023] [Indexed: 03/12/2023] Open
Abstract
BACKGROUND Microbially produced bioplastics are specially promising materials since they can be naturally synthesized and degraded, making its end-of-life management more amenable to the environment. A prominent example of these new materials are polyhydroxyalkanoates. These polyesters serve manly as carbon and energy storage and increase the resistance to stress. Their synthesis can also work as an electron sink for the regeneration of oxidized cofactors. In terms of biotechnological applications, the co-polymer poly(3-hydroxybutyrate-co-3-hydroxyvalerate), or PHBV, has interesting biotechnological properties due to its lower stiffness and fragility compared to the homopolymer poly(3-hydroxybutyrate) (P3HB). In this work, we explored the potentiality of Rhodospirillum rubrum as a producer of this co-polymer, exploiting its metabolic versatility when grown in different aeration conditions and photoheterotrophically. RESULTS When shaken flasks experiments were carried out with limited aeration using fructose as carbon source, PHBV production was triggered reaching 29 ± 2% CDW of polymer accumulation with a 75 ± 1%mol of 3-hydroxyvalerate (3HV) (condition C2). Propionate and acetate were secreted in this condition. The synthesis of PHBV was exclusively carried out by the PHA synthase PhaC2. Interestingly, transcription of cbbM coding RuBisCO, the key enzyme of the Calvin-Benson-Bassham cycle, was similar in aerobic and microaerobic/anaerobic cultures. The maximal PHBV yield (81% CDW with 86%mol 3HV) was achieved when cells were transferred from aerobic to anaerobic conditions and controlling the CO2 concentration by adding bicarbonate to the culture. In these conditions, the cells behaved like resting cells, since polymer accumulation prevailed over residual biomass formation. In the absence of bicarbonate, cells could not adapt to an anaerobic environment in the studied lapse. CONCLUSIONS We found that two-phase growth (aerobic-anaerobic) significantly improved the previous report of PHBV production in purple nonsulfur bacteria, maximizing the polymer accumulation at the expense of other components of the biomass. The presence of CO2 is key in this process demonstrating the involvement of the Calvin-Benson-Bassham in the adaptation to changes in oxygen availability. These results stand R. rubrum as a promising producer of high-3HV-content PHBV co-polymer from fructose, a PHBV unrelated carbon source.
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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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Malykh EA, Golubeva LI, Kovaleva ES, Shupletsov MS, Rodina EV, Mashko SV, Stoynova NV. H(+)-Translocating Membrane-Bound Pyrophosphatase from Rhodospirillum rubrum Fuels Escherichia coli Cells via an Alternative Pathway for Energy Generation. Microorganisms 2023; 11. [PMID: 36838259 DOI: 10.3390/microorganisms11020294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 01/24/2023] Open
Abstract
Inorganic pyrophosphatases (PPases) catalyze an essential reaction, namely, the hydrolysis of PPi, which is formed in large quantities as a side product of numerous cellular reactions. In the majority of living species, PPi hydrolysis is carried out by soluble cytoplasmic PPase (S-PPases) with the released energy dissipated in the form of heat. In Rhodospirillum rubrum, part of this energy can be conserved by proton-pumping pyrophosphatase (H+-PPaseRru) in the form of a proton electrochemical gradient for further ATP synthesis. Here, the codon-harmonized gene hppaRru encoding H+-PPaseRru was expressed in the Escherichia coli chromosome. We demonstrate, for the first time, that H+-PPaseRru complements the essential native S-PPase in E. coli cells. 13C-MFA confirmed that replacing native PPase to H+-PPaseRru leads to the re-distribution of carbon fluxes; a statistically significant 36% decrease in tricarboxylic acid (TCA) cycle fluxes was found compared with wild-type E. coli MG1655. Such a flux re-distribution can indicate the presence of an additional method for energy generation (e.g., ATP), which can be useful for the microbiological production of a number of compounds, the biosynthesis of which requires the consumption of ATP.
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Segura PC, Wattiez R, Vande Wouwer A, Leroy B, Dewasme L. Dynamic modeling of Rhodospirillum rubrum PHA production triggered by redox stress during VFA photoheterotrophic assimilations. J Biotechnol 2022; 360:45-54. [PMID: 36273668 DOI: 10.1016/j.jbiotec.2022.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/29/2022] [Accepted: 10/18/2022] [Indexed: 11/05/2022]
Abstract
Polyhydroxyalkanoates (PHA) represent an environmentally friendly alternative to petroleum based plastics for a broad range of applications from packaging to biomedical devices. In the prospect of an industrial PHA production, it is highly valuable to accurately control the incorporation of different repeating units into the polymer, to produce a polyester with specific material characteristics. In this study, we develop macroscopic dynamic models predicting the polymer production and composition when mixtures containing up to four volatile fatty acids (VFA) are used as substrates. These models successfully reproduce the sequential (and preferential) substrate consumption and polymer production/reconsumption patterns, experimentally observed during biomass growth, thanks to simple kinetic structures based on Monod and inhibition factors. These models can serve as a basis for numerical simulation and process analysis, as well as process intensification through model-based optimization and control.
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Affiliation(s)
| | - Ruddy Wattiez
- Laboratory of Proteomics and Microbiology, University of Mons, 7000 Mons, Belgium
| | - Alain Vande Wouwer
- Systems, Estimation, Control and Optimization Group (SECO), University of Mons, 7000 Mons, Belgium
| | - Baptiste Leroy
- Laboratory of Proteomics and Microbiology, University of Mons, 7000 Mons, Belgium
| | - Laurent Dewasme
- Systems, Estimation, Control and Optimization Group (SECO), University of Mons, 7000 Mons, Belgium.
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Knox PP, Lukashev EP, Korvatovskiy BN, Strakhovskaya MG, Makhneva ZK, Bol'shakov MA, Paschenko VZ. Disproportionate effect of cationic antiseptics on the quantum yield and fluorescence lifetime of bacteriochlorophyll molecules in the LH1-RC complex of R. rubrum chromatophores. Photosynth Res 2022; 153:103-112. [PMID: 35277801 DOI: 10.1007/s11120-022-00909-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 02/26/2022] [Indexed: 06/14/2023]
Abstract
Photosynthetic membrane complexes of purple bacteria are convenient and informative macromolecular systems for studying the mechanisms of action of various physicochemical factors on the functioning of catalytic proteins both in an isolated state and as part of functional membranes. In this work, we studied the effect of cationic antiseptics (chlorhexidine, picloxydine, miramistin, and octenidine) on the fluorescence intensity and the efficiency of energy transfer from the light-harvesting LH1 complex to the reaction center (RC) of Rhodospirillum rubrum chromatophores. The effect of antiseptics on the fluorescence intensity and the energy transfer increased in the following order: chlorhexidine, picloxydine, miramistin, octenidine. The most pronounced changes in the intensity and lifetime of fluorescence were observed with the addition of miramistin and octenidine. At the same concentration of antiseptics, the increase in fluorescence intensity was 2-3 times higher than the increase in its lifetime. It is concluded that the addition of antiseptics decreases the efficiency of the energy migration LH1 → RC and increases the fluorescence rate constant kfl. We associate the latter with a change in the polarization of the microenvironment of bacteriochlorophyll molecules upon the addition of charged antiseptic molecules. A possible mechanism of antiseptic action on R. rubrum chromatophores is considered. This work is a continuation of the study of the effect of antiseptics on the energy transfer and fluorescence intensity in chromatophores of purple bacteria published earlier in Photosynthesis Research (Strakhovskaya et al. in Photosyn Res 147:197-209, 2021).
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Affiliation(s)
- Peter P Knox
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russian Federation, 119234
| | - Eugene P Lukashev
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russian Federation, 119234
| | - Boris N Korvatovskiy
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russian Federation, 119234
| | - Marina G Strakhovskaya
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russian Federation, 119234.
| | - Zoja K Makhneva
- Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Sciences", Pushchino, Russian Federation, 142290
| | - Maxim A Bol'shakov
- Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Sciences", Pushchino, Russian Federation, 142290
| | - Vladimir Z Paschenko
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russian Federation, 119234
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8
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Cavazza C, Collin-Faure V, Pérard J, Diemer H, Cianférani S, Rabilloud T, Darrouzet E. Proteomic analysis of Rhodospirillum rubrum after carbon monoxide exposure reveals an important effect on metallic cofactor biosynthesis. J Proteomics 2022; 250:104389. [PMID: 34601154 DOI: 10.1016/j.jprot.2021.104389] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 12/14/2022]
Abstract
Some carboxydotrophs like Rhodospirillum rubrum are able to grow with CO as their sole source of energy using a Carbone monoxide dehydrogenase (CODH) and an Energy conserving hydrogenase (ECH) to perform anaerobically the so called water-gas shift reaction (WGSR) (CO + H2O → CO2 + H2). Several studies have focused at the biochemical and biophysical level on this enzymatic system and a few OMICS studies on CO metabolism. Knowing that CO is toxic in particular due to its binding to heme iron atoms, and is even considered as a potential antibacterial agent, we decided to use a proteomic approach in order to analyze R. rubrum adaptation in term of metabolism and management of the toxic effect. In particular, this study allowed highlighting a set of proteins likely implicated in ECH maturation, and important perturbations in term of cofactor biosynthesis, especially metallic cofactors. This shows that even this CO tolerant microorganism cannot avoid completely CO toxic effects associated with its interaction with metallic ions. SIGNIFICANCE: This proteomic study highlights the fact that even in a microorganism able to handle carbon monoxide and in some way detoxifying it via the intrinsic action of the carbon monoxide dehydrogenase (CODH), CO has important effects on metal homeostasis, metal cofactors and metalloproteins. These effects are direct or indirect via transcription regulation, and amplified by the high interdependency of cofactors biosynthesis.
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Affiliation(s)
- Christine Cavazza
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France.
| | | | - Julien Pérard
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France.
| | - Hélène Diemer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France; Infrastructure Nationale de Protéomique ProFI - FR2048 (CNRS-CEA), 67087 Strasbourg, France.
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France; Infrastructure Nationale de Protéomique ProFI - FR2048 (CNRS-CEA), 67087 Strasbourg, France.
| | - Thierry Rabilloud
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France.
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Autenrieth C, Shaw S, Ghosh R. New Approach for the Construction and Calibration of Gas-Tight Setups for Biohydrogen Production at the Small Laboratory Scale. Metabolites 2021; 11:metabo11100667. [PMID: 34677382 PMCID: PMC8541310 DOI: 10.3390/metabo11100667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/21/2021] [Accepted: 09/25/2021] [Indexed: 11/25/2022] Open
Abstract
Biohydrogen production in small laboratory scale culture vessels is often difficult to perform and quantitate. One problem is that commonly used silicon tubing and improvised plastic connections used for constructing apparatus are cheap and easy to connect but are generally not robust for gases such as hydrogen. In addition, this type of apparatus presents significant safety concerns. Here, we demonstrate the construction of hydrogen-tight apparatus using a commercially available modular system, where plastic tubing and connections are made of explosion-proof dissipative plastic material. Using this system, we introduce a gas chromatograph calibration procedure, which can be easily performed without necessarily resorting to expensive commercial gas standards for the calibration of hydrogen gas concentrations. In this procedure, the amount of hydrogen produced by the reaction of sodium borohydride with water in a closed air-filled bottle is deduced from the observed decrease of the oxygen partial pressure, using the ideal gas law. Finally, the determined calibration coefficients and the gas-tight apparatus are used for the analysis of simultaneous oxygen consumption and hydrogen production of the purple photosynthetic bacterium, Rhodospirillum rubrum, during semi-aerobic growth in the dark.
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Affiliation(s)
- Caroline Autenrieth
- Institute of Biomaterials and Biomolecular Systems, Department of Bioenergetics, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany; (S.S.); (R.G.)
- Correspondence: ; Tel.: +49-711-685-65048
| | - Shreya Shaw
- Institute of Biomaterials and Biomolecular Systems, Department of Bioenergetics, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany; (S.S.); (R.G.)
- School of Molecular Sciences, Tempe Campus, Mailcode 1604, Arizona State University, Tempe, AZ 85281, USA
| | - Robin Ghosh
- Institute of Biomaterials and Biomolecular Systems, Department of Bioenergetics, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany; (S.S.); (R.G.)
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10
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Rodríguez A, Hernández-Herreros N, García JL, Auxiliadora Prieto M. Enhancement of biohydrogen production rate in Rhodospirillum rubrum by a dynamic CO-feeding strategy using dark fermentation. Biotechnol Biofuels 2021; 14:168. [PMID: 34362414 PMCID: PMC8343937 DOI: 10.1186/s13068-021-02017-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 07/24/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Rhodospirillum rubrum is a purple non-sulphur bacterium that produces H2 by photofermentation of several organic compounds or by water gas-shift reaction during CO fermentation. Successful strategies for both processes have been developed in light-dependent systems. This work explores a dark fermentation bioprocess for H2 production from water using CO as the electron donor. RESULTS The study of the influence of the stirring and the initial CO partial pressure (pCO) demonstrated that the process was inhibited at pCO of 1.00 atm. Optimal pCO value was established in 0.60 atm. CO dose adaptation to bacterial growth in fed-batch fermentations increased the global rate of H2 production, yielding 27.2 mmol H2 l-1 h-1 and reduced by 50% the operation time. A kinetic model was proposed to describe the evolution of the molecular species involved in gas and liquid phases in a wide range of pCO conditions from 0.10 to 1.00 atm. CONCLUSIONS Dark fermentation in R. rubrum expands the ways to produce biohydrogen from CO. This work optimizes this bioprocess at lab-bioreactor scale studying the influence of the stirring speed, the initial CO partial pressure and the operation in batch and fed-batch regimes. Dynamic CO supply adapted to the biomass growth enhances the productivity reached in darkness by other strategies described in the literature, being similar to that obtained under light continuous syngas fermentations. The kinetic model proposed describes all the conditions tested.
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Affiliation(s)
- Alberto Rodríguez
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐of the Spanish National Research Council (SusPlast‐CSIC), Madrid, Spain
- Polymer Biotechnology Group, Department of Plant and Microbial Biotechnology, Biological Research Center, Margarita Salas”-CSIC, 28040 Madrid, Spain
| | - Natalia Hernández-Herreros
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐of the Spanish National Research Council (SusPlast‐CSIC), Madrid, Spain
- Polymer Biotechnology Group, Department of Plant and Microbial Biotechnology, Biological Research Center, Margarita Salas”-CSIC, 28040 Madrid, Spain
| | - José L. García
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐of the Spanish National Research Council (SusPlast‐CSIC), Madrid, Spain
- Environmental Biotechnology Group, Department of Plant and Microbial Biotechnology, Biological Research Center, Margarita Salas”-CSIC 28040, Madrid, Spain
| | - M. Auxiliadora Prieto
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐of the Spanish National Research Council (SusPlast‐CSIC), Madrid, Spain
- Polymer Biotechnology Group, Department of Plant and Microbial Biotechnology, Biological Research Center, Margarita Salas”-CSIC, 28040 Madrid, Spain
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Mickoleit F, Rosenfeldt S, Toro-Nahuelpan M, Schaffer M, Schenk AS, Plitzko JM, Schüler D. High-Yield Production, Characterization, and Functionalization of Recombinant Magnetosomes in the Synthetic Bacterium Rhodospirillum rubrum "magneticum". Adv Biol (Weinh) 2021; 5:e2101017. [PMID: 34296829 DOI: 10.1002/adbi.202101017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/10/2021] [Indexed: 01/02/2023]
Abstract
Recently, the photosynthetic Rhodospirillum rubrum has been endowed with the ability of magnetosome biosynthesis by transfer and expression of biosynthetic gene clusters from the magnetotactic bacterium Magnetospirillum gryphiswaldense. However, the growth conditions for efficient magnetite biomineralization in the synthetic R. rubrum "magneticum", as well as the particles themselves (i.e., structure and composition), have so far not been fully characterized. In this study, different cultivation strategies, particularly the influence of temperature and light intensity, are systematically investigated to achieve optimal magnetosome biosynthesis. Reduced temperatures ≤16 °C and gradual increase in light intensities favor magnetite biomineralization at high rates, suggesting that magnetosome formation might utilize cellular processes, cofactors, and/or pathways that are linked to photosynthetic growth. Magnetosome yields of up to 13.6 mg magnetite per liter cell culture are obtained upon photoheterotrophic large-scale cultivation. Furthermore, it is shown that even more complex, i.e., oligomeric, catalytically active functional moieties like enzyme proteins can be efficiently expressed on the magnetosome surface, thereby enabling the in vivo functionalization by genetic engineering. In summary, it is demonstrated that the synthetic R. rubrum "magneticum" is a suitable host for high-yield magnetosome biosynthesis and the sustainable production of genetically engineered, bioconjugated magnetosomes.
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Affiliation(s)
- Frank Mickoleit
- Dept. Microbiology, University of Bayreuth, D-95447, Bayreuth, Germany
| | - Sabine Rosenfeldt
- Bavarian Polymer Institute (BPI)/Physical Chemistry 1, University of Bayreuth, D-95447, Bayreuth, Germany
| | - Mauricio Toro-Nahuelpan
- Dept. Microbiology, University of Bayreuth, D-95447, Bayreuth, Germany.,Dept. Molecular Structural Biology, Max Planck Institute of Biochemistry, D-82152, Martinsried, Germany
| | - Miroslava Schaffer
- Dept. Molecular Structural Biology, Max Planck Institute of Biochemistry, D-82152, Martinsried, Germany
| | - Anna S Schenk
- Bavarian Polymer Institute (BPI)/Physical Chemistry - Colloidal Systems, University of Bayreuth, D-95447, Bayreuth, Germany
| | - Jürgen M Plitzko
- Dept. Molecular Structural Biology, Max Planck Institute of Biochemistry, D-82152, Martinsried, Germany
| | - Dirk Schüler
- Dept. Microbiology, University of Bayreuth, D-95447, Bayreuth, Germany
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12
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Jaime-Pérez N, Bína D, Kaftan D, Bokhari SNH, Küpper H. Naturally zinc-containing bacteriochlorophyll a ([Zn]-BChl a) protects the photosynthetic apparatus of Acidiphilium rubrum from copper toxicity damage. Biochim Biophys Acta Bioenerg 2021; 1862:148472. [PMID: 34217700 DOI: 10.1016/j.bbabio.2021.148472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 11/21/2022]
Abstract
In almost all photosynthetic organisms the photosynthetic pigments chlorophyll and bacteriochlorophyll (BChl) are Mg2+ containing complexes, but Mg2+ may be exchanged against other metal ions when these are present in toxic concentrations, leading to inactivation of photosynthesis. In this report we studied mechanisms of copper toxicity to the photosynthetic apparatus of Acidiphilium rubrum, an acidophilic purple bacterium that uses Zn2+ instead of Mg2+ as the central metal in the BChl molecules ([Zn]-BChl) of its reaction centres (RCs) and light harvesting proteins (LH1). We used a combination of in vivo measurements of photosynthetic activity (fast fluorescence and absorption kinetics) together with analysis of metal binding to pigments and pigment-protein complexes by HPLC-ICP-sfMS to monitor the effect of Cu2+ on photosynthesis of A. rubrum. Further, we found that its cytoplasmic pH is neutral. We compared these results with those obtained from Rhodospirillum rubrum, a purple bacterium for which we previously reported that the central Mg2+ of BChl can be replaced in vivo in the RCs by Cu2+ under environmentally realistic Cu2+ concentrations, leading to a strong inhibition of photosynthesis. Thus, we observed that A. rubrum is much more resistant to copper toxicity than R. rubrum. Only slight changes of photosynthetic parameters were observed in A. rubrum at copper concentrations that were severely inhibitory in R. rubrum and in A. rubrum no copper complexes of BChl were found. Altogether, the data suggest that [Zn]-BChl protects the photosynthetic apparatus of A. rubrum from detrimental insertion of Cu2+ (trans-metallation) into BChl molecules of its RCs.
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13
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Markelova N, Glazunova O, Alikina O, Panyukov V, Shavkunov K, Ozoline O. Suppression of Escherichia coli Growth Dynamics via RNAs Secreted by Competing Bacteria. Front Mol Biosci 2021; 8:609979. [PMID: 33937321 PMCID: PMC8082180 DOI: 10.3389/fmolb.2021.609979] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 03/11/2021] [Indexed: 11/13/2022] Open
Abstract
With the discovery of secreted RNAs, it has become apparent that the biological role of regulatory oligonucleotides likely goes beyond the borders of individual cells. However, the mechanisms of their action are still comprehended only in general terms and mainly for eukaryotic microRNAs, which can interfere with mRNAs even in distant recipient cells. It has recently become clear that bacterial cells lacking interference systems can also respond to eukaryotic microRNAs that have targets in their genomes. However, the question of whether bacteria can perceive information transmitted by oligonucleotides secreted by other prokaryotes remained open. Here we evaluated the fraction of short RNAs secreted by Escherichia coli during individual and mixed growth with Rhodospirillum rubrum or Prevotella copri, and found that in the presence of other bacteria E. coli tends to excrete oligonucleotides homologous to alien genomes. Based on this observation, we selected four RNAs secreted by either R. rubrum or P. copri, together with one E. coli-specific oligonucleotide. Both fragments of R. rubrum 23S-RNA suppressed the growth of E. coli. Of the two fragments secreted by P. copri, one abolished the stimulatory effect of E. coli RNA derived from the 3'-UTR of ProA mRNA, while the other inhibited bacterial growth only in the double-stranded state with complementary RNA. The ability of two RNAs secreted by cohabiting bacteria to enter E. coli cells was demonstrated using confocal microscopy. Since selected E. coli-specific RNA also affected the growth of this bacterium, we conclude that bacterial RNAs can participate in inter- and intraspecies signaling.
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Affiliation(s)
- Natalia Markelova
- Laboratory of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia
| | - Olga Glazunova
- Laboratory of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia
| | - Olga Alikina
- Laboratory of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia
| | - Valeriy Panyukov
- Department of Structural and Functional Genomics, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia.,Laboratory of Bioinformatics, Institute of Mathematical Problems of Biology, Pushchino, Russia
| | - Konstantin Shavkunov
- Laboratory of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia.,Department of Structural and Functional Genomics, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia
| | - Olga Ozoline
- Laboratory of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia.,Department of Structural and Functional Genomics, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia
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14
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McCully AL, Onyeziri MC, LaSarre B, Gliessman JR, McKinlay JB. Reductive tricarboxylic acid cycle enzymes and reductive amino acid synthesis pathways contribute to electron balance in a Rhodospirillum rubrum Calvin-cycle mutant. Microbiology (Reading) 2020; 166:199-211. [PMID: 31774392 DOI: 10.1099/mic.0.000877] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Purple non-sulfur bacteria (PNSB) use light for energy and organic substrates for carbon and electrons when growing photoheterotrophically. This lifestyle generates more reduced electron carriers than are required for biosynthesis, even during consumption of some of the most oxidized organic substrates like malate and fumarate. Reduced electron carriers not used in biosynthesis must still be oxidized for photoheterotrophic growth to occur. Diverse PNSB commonly rely on the CO2-fixing Calvin cycle to oxidize reduced electron carriers. Some PNSB also produce H2 or reduce terminal electron acceptors as alternatives to the Calvin cycle. Rhodospirillum rubrum Calvin-cycle mutants defy this trend by growing phototrophically on malate or fumarate without H2 production or access to terminal electron acceptors. We used 13C-tracer experiments to examine how a Rs. rubrum Calvin-cycle mutant maintains electron balance under such conditions. We detected the reversal of some tricarboxylic acid cycle enzymes, carrying reductive flux from malate or fumarate to αKG. This pathway and the reductive synthesis of αKG-derived amino acids are likely important for electron balance, as supplementing the growth medium with αKG-derived amino acids prevented Rs. rubrum Calvin-cycle-mutant growth unless a terminal electron acceptor was provided. Flux estimates also suggested that the Calvin-cycle mutant preferentially synthesized isoleucine using the reductive threonine-dependent pathway instead of the less-reductive citramalate-dependent pathway. Collectively, our results suggest that alternative biosynthetic pathways can contribute to electron balance within the constraints of a relatively constant biomass composition.
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Affiliation(s)
- Alexandra L McCully
- Present address: Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, USA.,Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | | | - Breah LaSarre
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | | | - James B McKinlay
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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15
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Razjivin AP, Kozlovsky VS. Unique features of the 'photo-energetics' of purple bacteria: a critical survey by the late Aleksandr Yuryevich Borisov (1930-2019). Photosynth Res 2020; 146:17-24. [PMID: 31655967 DOI: 10.1007/s11120-019-00683-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 10/04/2019] [Indexed: 06/10/2023]
Abstract
We provide here an edited version of the "Farewell discussion" by the late Aleksandr (Alex) Yuryevich (Yu) Borisov (1930-2019) on several aspects related to the excitation energy transfer in photosynthetic bacteria. It is preceded by a prolog giving the events that led to our decision to publish it. Further, we include here a few photographs to give a personal glimpse of this unique biophysicist of our time. In addition, we provide here a reminiscence, by Andrei B. Rubin, on the scientific beginnings of Borisov. This article follows a Tribute to Borisov by Semenov et al. (2019, Photosynthesis Research, this issue).
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Affiliation(s)
- Andrei P Razjivin
- Department of Photosynthesis, A.N.Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Vladimir S Kozlovsky
- Department of Photosynthesis, A.N.Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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16
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Vredenberg WJ, Govindjee G. Christiaan Sybesma (August 31, 1928-January 31, 2018), an extraordinary biophysicist of our time. Photosynth Res 2020; 144:297-300. [PMID: 32240497 PMCID: PMC7239804 DOI: 10.1007/s11120-020-00734-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/06/2020] [Indexed: 06/11/2023]
Abstract
We provide here a brief Tribute to Christiaan Sybesma (1928-2018), a highly respected biophysicist of our time. We remember him by giving a brief highlight of his life and a glimpse of his outstanding contributions in photosynthesis. He was a charming and highly respected scientist of our time.
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Affiliation(s)
- Wim J. Vredenberg
- Department of Plant Physiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Govindjee Govindjee
- Department of Plant Biology, Department of Biochemistry and Center of Biophysics and Quantitative Biology, University of Illinois at Urbana, Champaign, IL 61801 USA
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17
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North JA, Wildenthal JA, Erb TJ, Evans BS, Byerly KM, Gerlt JA, Tabita FR. A bifunctional salvage pathway for two distinct S-adenosylmethionine by-products that is widespread in bacteria, including pathogenic Escherichia coli. Mol Microbiol 2020; 113:923-937. [PMID: 31950558 DOI: 10.1111/mmi.14459] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 01/08/2020] [Accepted: 01/12/2020] [Indexed: 01/19/2023]
Abstract
S-adenosyl-l-methionine (SAM) is a necessary cosubstrate for numerous essential enzymatic reactions including protein and nucleotide methylations, secondary metabolite synthesis and radical-mediated processes. Radical SAM enzymes produce 5'-deoxyadenosine, and SAM-dependent enzymes for polyamine, neurotransmitter and quorum sensing compound synthesis produce 5'-methylthioadenosine as by-products. Both are inhibitory and must be addressed by all cells. This work establishes a bifunctional oxygen-independent salvage pathway for 5'-deoxyadenosine and 5'-methylthioadenosine in both Rhodospirillum rubrum and Extraintestinal Pathogenic Escherichia coli. Homologous genes for this pathway are widespread in bacteria, notably pathogenic strains within several families. A phosphorylase (Rhodospirillum rubrum) or separate nucleoside and kinase (Escherichia coli) followed by an isomerase and aldolase sequentially function to salvage these two wasteful and inhibitory compounds into adenine, dihydroxyacetone phosphate and acetaldehyde or (2-methylthio)acetaldehyde during both aerobic and anaerobic growth. Both SAM by-products are metabolized with equal affinity during aerobic and anaerobic growth conditions, suggesting that the dual-purpose salvage pathway plays a central role in numerous environments, notably the human body during infection. Our newly discovered bifunctional oxygen-independent pathway, widespread in bacteria, salvages at least two by-products of SAM-dependent enzymes for carbon and sulfur salvage, contributing to cell growth.
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Affiliation(s)
- Justin A North
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - John A Wildenthal
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Bradley S Evans
- The Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Kathryn M Byerly
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - John A Gerlt
- Department of Biochemistry, The Institute for Genomic Biology, Champaign, IL, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Fred R Tabita
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
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18
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Kulakovskaya T, Zvonarev A, Laurinavichius K, Khokhlova G, Vainshtein M. Effect of Fe on inorganic polyphosphate level in autotrophic and heterotrophic cells of Rhodospirillum rubrum. Arch Microbiol 2019; 201:1307-1312. [PMID: 31273403 DOI: 10.1007/s00203-019-01697-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/11/2019] [Accepted: 06/30/2019] [Indexed: 12/27/2022]
Abstract
Inorganic polyphosphate is involved in metal homeostasis in microorganisms. The aim of the study was to reveal differences in polyphosphate metabolism of Rhodospirillum rubrum under autotrophic and heterotrophic cultivation in the presence of Fe (2.3 mg Fe3+ L-1) and without Fe (traces). Heterotrophic conditions without Fe resulted in cell lysis and low biomass yield. High polyphosphate content and low exopolyphosphatase activity were observed in the cells cultivated autotrophically in the presence of Fe. The cells grown heterotrophically in the presence of Fe contained more phosphate and low-molecular polyphosphate; on the contrary, the content of the high molecular polyphosphate decreased in parallel with the increase in exopolyphosphatase activity. The possible involvement of Pi and polyphosphate to the formation of Fe-containing inclusions is discussed.
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Affiliation(s)
- Tatiana Kulakovskaya
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Prospect Nauki 5, Pushchino, 142290, Russia.
| | - Anton Zvonarev
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Prospect Nauki 5, Pushchino, 142290, Russia
| | - Kestutis Laurinavichius
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Prospect Nauki 5, Pushchino, 142290, Russia
| | - Galina Khokhlova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Prospect Nauki 5, Pushchino, 142290, Russia
| | - Mikhail Vainshtein
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Prospect Nauki 5, Pushchino, 142290, Russia
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19
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Razjivin A, Solov'ev A, Kompanets V, Chekalin S, Moskalenko A, Lokstein H. The origin of the "dark" absorption band near 675 nm in the purple bacterial core light-harvesting complex LH1: two-photon measurements of LH1 and its subunit B820. Photosynth Res 2019; 140:207-213. [PMID: 30411209 DOI: 10.1007/s11120-018-0602-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/27/2018] [Indexed: 06/08/2023]
Abstract
A comparative two-photon excitation spectroscopic study of the exciton structure of the core antenna complex (LH1) and its subunit B820 was carried out. LH1 and its subunit B820 were isolated from cells of the carotenoid-less mutant G9 of Rhodospirillum rubrum. The measurements were performed by two-photon pump-probe spectroscopy. Samples were excited by 70 fs pulses at 1390 nm at a frequency of 1 kHz. Photoinduced absorption changes were recorded in the spectral range from 780 to 1020 nm for time delays of the probe pulse relative to the pump pulse in the - 1.5 to 11 ps range. All measurements were performed at room temperature. Two-photon excitation caused bleaching of exciton bands (k = 0, k = ± 1) of the circular bacteriochlorophyll aggregate of LH1. In the case of the B820 subunit, two-photon excitation did not cause absorption changes in this spectral range. It is proposed that in LH1 upper exciton branch states are mixed with charge-transfer (CT) states. In B820 such mixing is absent, precluding two-photon excitation in this spectral region. Usually, CT states are optically "dark", i.e., one photon-excitation forbidden. Thus, their investigation is rather complicated by conventional spectroscopic methods. Thus, our study provides a novel approach to investigate CT states and their interaction(s) with other excited states in photosynthetic light-harvesting complexes and other molecular aggregates.
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Affiliation(s)
- Andrei Razjivin
- Belozersky Research Institute of Physico-Chemical Biology, MSU, Moscow, Russia.
| | - Alexander Solov'ev
- Institute of Basic Biological Problems, RAS, Pushchino, Moscow Region, Russia
| | | | | | - Andrey Moskalenko
- Institute of Basic Biological Problems, RAS, Pushchino, Moscow Region, Russia
| | - Heiko Lokstein
- Department of Chemical Physics and Optics, Charles University, Ke Karlovu 3, 121 16, Prague, Czech Republic
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20
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Karmann S, Panke S, Zinn M. Fed-Batch Cultivations of Rhodospirillum rubrum Under Multiple Nutrient-Limited Growth Conditions on Syngas as a Novel Option to Produce Poly(3-Hydroxybutyrate) (PHB). Front Bioeng Biotechnol 2019; 7:59. [PMID: 31001525 PMCID: PMC6454858 DOI: 10.3389/fbioe.2019.00059] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 03/05/2019] [Indexed: 11/13/2022] Open
Abstract
Syngas from gasified organic waste materials is a promising feedstock for the biotechnological synthesis of the bioplastic poly([R]-3-hydroxybutyrate) (PHB) with Rhodospirillum rubrum. In a first approach, growth studies were carried out with this strain in gas-tight serum vials. When syngas (40% CO, 40% H2, 10% CO2, and 10% N2 v/v) was diluted with N2 to 60%, a 4-fold higher biomass production was detected compared to samples grown on 100% syngas, thus indicating a growth inhibitory effect. The best performing syngas-mixture was then used for C-, C,N-, and C,P-limited fed-batch fermentations in a bioreactor with continuous syngas and acetate supply. It was found that C,P-limited PHB productivity was 5 times higher than for only C-limited growth and reached a maximal PHB content of 30% w/w. Surprisingly, growth and PHB production stopped when N, as a second nutrient, became growth-limiting. Finally, it was concluded that a minimal supply of 0.2 g CO g-1 biomass h-1 has to be guaranteed in order to cover the cellular maintenance energy.
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Affiliation(s)
- Stephanie Karmann
- Institute of Life Technologies, University of Applied Sciences and Arts Western Switzerland (HES-SO Valais-Wallis), Sion, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Manfred Zinn
- Institute of Life Technologies, University of Applied Sciences and Arts Western Switzerland (HES-SO Valais-Wallis), Sion, Switzerland
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21
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Autenrieth C, Ghosh R. The Methoxylated, Highly Conjugated C 40 Carotenoids, Spirilloxanthin and Anhydrorhodovibrin, Can Be Separated Using High Performance Liquid Chromatography with Safe and Environmentally Friendly Solvents. Metabolites 2019; 9:metabo9020020. [PMID: 30682824 PMCID: PMC6410002 DOI: 10.3390/metabo9020020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/11/2019] [Accepted: 01/19/2019] [Indexed: 11/21/2022] Open
Abstract
High performance liquid chromatography (HPLC) is a frequently used technique in carotenoid research. So far, however, little attention has been paid to the fact that many of the organic solvents used in HPLC separation of highly apolar C40 carotenoids impose a significant threat to both health (especially for women) and the general laboratory environment. Here, we developed a solvent combination capable of allowing high-resolution HPLC separation of the C40 carotenoid, spirilloxanthin, and all of its biosynthetic precursors beginning with phytoene, using relatively safe, environmentally friendly solvents. We show that separation of spirilloxanthin and its precursors anhydrorhodovibrin and lycopene using modern ultra-high performance chromatography (UHPLC) poses particular problems for apolar carotenoid separation, due to the long residence times in the sample delivery system, which facilitates carotenoid aggregation. We resolved these problems by developing the solvent delivery combination acetone/acetonitrile/isopropanol/methanol (65/30/5/2 (v/v/v/v)), which allows excellent column separation using the safe isocratic solvent system methanol/tetrahydrofuran (98/2 (v/v)). We also demonstrate that the development strategy for optimizing a solvent system for carotenoid separation can be well-described by the use of the average dielectric constant of the total sample delivery solvent, and present a formal method for analysis of the efficiency of separation.
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Affiliation(s)
- Caroline Autenrieth
- Department of Bioenergetics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany.
| | - Robin Ghosh
- Department of Bioenergetics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany.
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22
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Akentieva N. Posttranslational modification of dinitrogenase reductase in Rhodospirillum rubrum treated with fluoroacetate. World J Microbiol Biotechnol 2018; 34:184. [PMID: 30488133 DOI: 10.1007/s11274-018-2564-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 11/20/2018] [Indexed: 10/27/2022]
Abstract
Nitrogen fixation is one of the major biogeochemical contributions carried out by diazotrophic microorganisms. The goal of this research is study of posttranslational modification of dinitrogenase reductase (Fe protein), the involvement of malate and pyruvate in generation of reductant in Rhodospirillum rubrum. A procedure for the isolation of the Fe protein from cell extracts was developed and used to monitor the modification of the Fe protein in vivo. The subunit pattern of the isolated the Fe protein after sodium dodecyl sulfate-polyacrylamide gel electrophoresis was assayed by Western blot analysis. Whole-cell nitrogenase activity was also monitored during the Fe protein modification by gas chromatograpy, using the acetylene reduction assay. It has been shown, that the addition of fluoroacetate, ammonia and darkness resulted in the loss of whole-cell nitrogenase activity and the in vivo modification of the Fe protein. For fluoroacetate, ammonia and darkness, the rate of loss of nitrogenase activity was similar to that for the Fe protein modification. The addition of NADH and reillumination of a culture incubated in the dark resulted in the rapid restoration of nitrogenase activity and the demodification of the Fe protein. Fluoroacetate inhibited the nitrogenase activity of R. rubrum and resulted in the modification of the Fe protein in cells, grown on pyruvate or malate as the endogeneous electron source. The nitrogenase activity in draTG mutant (lacking DRAT/DRAG system) decreased after the addition of fluoroacetate, but the Fe protein remained completely unmodified. The results showed that the reduced state of cell, posttranslational modifications of the Fe protein and the DRAT/DRAG system are important for nitrogenase activity and the regulation of nitrogen fixation.
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Affiliation(s)
- Natalia Akentieva
- Department of Kinetics of Chemical and Biological Processes, Institute of Problems of Chemical Physics, Russian Academy of Sciences, Street Academician Semenov, 1., Chernogolovka, 142432, Moscow Region, Russia.
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23
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Ghosh R, Roth E, Abou-Aisha K, Saegesser R, Autenrieth C. The monofunctional cobalamin biosynthesis enzyme precorrin-3B synthase (CobZRR) is essential for anaerobic photosynthesis in Rhodospirillum rubrum but not for aerobic dark metabolism. Microbiology (Reading) 2018; 164:1416-1431. [PMID: 30222098 DOI: 10.1099/mic.0.000718] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The in vivo physiological role of the gene cobZ, which encodes precorrin-3B synthase, which catalyzes the initial porphyrin ring contraction step of cobalamin biosynthesis via the cob pathway, has been demonstrated here for the first time. Cobalamin is known to be essential for an early step of bacteriochlorophyll biosynthesis in anoxygenic purple bacteria. The cobZ (cobZRR) gene of the purple bacterium Rhodospirillum rubrum was localized to a 23.5 kb insert of chromosomal DNA contained on the cosmid pSC4. pSC4 complemented several mutants of bacteriochlorophyll and carotenoid biosynthesis, due to the presence of the bchCX and crtCDEF genes at one end of the cosmid insert, flanking cobZRR. A second gene, citB/tcuB, immediately downstream of cobZRR, shows homologies to both a tricarballylate oxidoreductase (tcuB) and a gene (citB) involved in signal transduction during citrate uptake. CobZRR shows extensive homology to the N-terminal domain of the bifunctional CobZ from Rhodobacter capsulatus, and the R. rubrum citB/tcuB gene is homologous to the CobZ C-terminal domain. A mutant, SERGK25, containing a terminatorless kanamycin interposon inserted into cobZRR, could not grow by anaerobic photosynthesis, but grew normally under dark, aerobic and microaerophilic conditions with succinate and fructose as carbon sources. The anaerobic in vivo activity of CobZ indicates that it does not require oxygen as a substrate. The mutant excreted large amounts of protoporphyrin IX-monomethylester, a brown precursor of bacteriochlorophyll biosynthesis. The mutant was complemented either by the cobZRR gene in trans, or when exogenous cobalamin was added to the medium. A deletion mutant of tcuB/citB did not exhibit the cob phenotype. Thus, a role for tcuB/citB in cobalamin biosynthesis could not be confirmed.
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Affiliation(s)
- Robin Ghosh
- Department of Bioenergetics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Erik Roth
- Department of Bioenergetics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Khaled Abou-Aisha
- Department of Bioenergetics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
- †Present address: Department of Microbiology and Biotechnology, German University in Cairo, Egypt
| | - Rudolf Saegesser
- Department of Bioenergetics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Caroline Autenrieth
- Department of Bioenergetics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
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Abstract
Lycopene plays an important role as an antioxidative and anticancer agent, and is an increasingly valuable commodity in the global market. Rhodobacter sphaeroides, a carotenogenic and phototrophic bacterium, is an efficient and practical host for carotenoid production. Herein, we explored the potential of metabolically engineered Rb. sphaeroides as a novel platform to produce lycopene. The basal lycopene-producing strain was generated by introducing an exogenous crtI4 from Rhodospirillum rubrum to replace the native crtI3 and deleting crtC in Rb. sphaeroides. Furthermore, knocking out zwf blocked the competitive pentose phosphate pathway and improved the lycopene content by 88%. Finally, the methylerythritol phosphate pathway was reinforced by integration of dxs combined with zwf deletion, which further increased the lycopene content. The final engineered strain produced lycopene to 10.32 mg/g dry cell weight. This study describes a new lycopene producer and provides insight into a photosynthetic bacterium as a host for lycopene biosynthesis.
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Affiliation(s)
- Anping Su
- Shaanxi Engineering Lab for Food Green Processing and Security Control, College of Food Engineering and Nutritional Science , Shaanxi Normal University , 620 West Chang'an Avenue , Chang'an, Xi'an 710119 , P.R. China
| | - Shuang Chi
- State Key Laboratory of Agrobiotechnology , China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District , Beijing 100193 , P.R. China
| | - Ying Li
- State Key Laboratory of Agrobiotechnology , China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District , Beijing 100193 , P.R. China
| | - Siyuan Tan
- Shaanxi Engineering Lab for Food Green Processing and Security Control, College of Food Engineering and Nutritional Science , Shaanxi Normal University , 620 West Chang'an Avenue , Chang'an, Xi'an 710119 , P.R. China
| | - Shan Qiang
- Xi'an Healthful Biotechnology Co., Ltd., HangTuo Road , Chang'an, Xi'an 710100 , P.R. China
| | - Zhi Chen
- State Key Laboratory of Agrobiotechnology , China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District , Beijing 100193 , P.R. China
| | - Yonghong Meng
- Shaanxi Engineering Lab for Food Green Processing and Security Control, College of Food Engineering and Nutritional Science , Shaanxi Normal University , 620 West Chang'an Avenue , Chang'an, Xi'an 710119 , P.R. China
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Narancic T, Scollica E, Cagney G, O'Connor KE. Three novel proteins co-localise with polyhydroxybutyrate (PHB) granules in Rhodospirillum rubrum S1. Microbiology (Reading) 2018; 164:625-634. [PMID: 29493489 DOI: 10.1099/mic.0.000642] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Polyhydroxybutyrate (PHB), a biodegradable polymer accumulated by bacteria is deposited intracellularly in the form of inclusion bodies often called granules. The granules are supramolecular complexes harbouring a varied number of proteins on their surface, which have specific but incompletely characterised functions. By comparison with other organisms that produce biodegradable polymers, only two phasins have been described to date for Rhodosprillum rubrum, raising the possibility that more await discovery. Using a comparative proteomics strategy to compare the granules of wild-type R. rubrum with a PHB-negative mutant housing artificial PHB granules, we identified four potential PHB granules' associated proteins. These were: Q2RSI4, an uncharacterised protein; Q2RWU9, annotated as an extracellular solute-binding protein; Q2RQL4, annotated as basic membrane lipoprotein; and Q2RQ51, annotated as glucose-6-phosphate isomerase. In silico analysis revealed that Q2RSI4 harbours a Phasin_2 family domain and shares low identity with a single-strand DNA-binding protein from Sphaerochaeta coccoides. Fluorescence microscopy found that three proteins Q2RSI4, Q2EWU9 and Q2RQL4 co-localised with PHB granules. This work adds three potential new granule associated proteins to the repertoire of factors involved in bacterial storage granule formation, and confirms that proteomics screens are an effective strategy for discovery of novel granule associated proteins.
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Affiliation(s)
- Tanja Narancic
- UCD Earth Institute and School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Elisa Scollica
- UCD Earth Institute and School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Gerard Cagney
- School of Biomolecular and Biomedical Sciences, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kevin E O'Connor
- UCD Earth Institute and School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland.,BEACON - Bioeconomy Research Centre, University College Dublin, Belfield, Dublin 4, Ireland
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26
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Zhang J, Yuan J, Zhang WX, Tu F, Jiang Y, Sun CZ. Anaerobic detoxification fermentation by Rhodospirillum rubrum for rice straw as feed with moderate pretreatment. Prep Biochem Biotechnol 2018; 48:75-83. [PMID: 29194020 DOI: 10.1080/10826068.2017.1405023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A novel and effective process was put forward for converting rice straw into feed by combining diluted acid hydrolysis and ammonization with Rhodospirillum rubrum fermentation. After pretreatment with dilute sulfuric or phosphoric acid (1%, w/w) at 100°C, materials were subjected to fermentation under several gases (N2, CO2, and air) and different light intensities in a 2-L fermentor. The key indexes of feed for fermented materials were estimated and several toxic substances were investigated during the fermentation. Following sulfuric acid treatment, the true protein of rice straw increased from 29 to 143 g kg-1 and the crude fiber decreased from 359 to 136 g kg-1 after fermentation at 0.3 L min-1 L-1 of N2 flow and a light intensity of 3400 lux; and following phosphoric acid treatment, the true protein increased by 286% and the crude fiber decreased by 52% after fermentation at 0.4 L min-1 L-1 of N2 flow and a light intensity of 3000 lux. Other key contents were also improved for use as feed, and some toxic substances (i.e., furfural, hydroxymethylfurfural, acetic acid, phenol, cresol) produced by the pretreatments could be removed at low levels during the fermentations.
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Affiliation(s)
- Jian Zhang
- a Department of Life Science and Food Engineering/Key Laboratory of Fermentation Resource and Application in Sichuan/Department of Library , Yibin University , Yibin , Sichuan , China
| | - Jie Yuan
- a Department of Life Science and Food Engineering/Key Laboratory of Fermentation Resource and Application in Sichuan/Department of Library , Yibin University , Yibin , Sichuan , China
| | - Wen-Xue Zhang
- b Food microbiology laboratory, College of Light Industry, Textile and Food Engineering , Sichuan University , Chengdu , Sichuan , China
| | - Fang Tu
- a Department of Life Science and Food Engineering/Key Laboratory of Fermentation Resource and Application in Sichuan/Department of Library , Yibin University , Yibin , Sichuan , China
| | - Ya Jiang
- a Department of Life Science and Food Engineering/Key Laboratory of Fermentation Resource and Application in Sichuan/Department of Library , Yibin University , Yibin , Sichuan , China
| | - Chuan-Ze Sun
- c Production Department , Xu Fu Liquor Company , Yibin , Sichuan , China
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27
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Khokhlova G, Vainshtein M. Application of static and impulse magnetic fields to bacteria Rhodospirillum rubrum VKM B-1621. AMB Express 2017; 7:60. [PMID: 28284003 PMCID: PMC5346098 DOI: 10.1186/s13568-017-0362-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/03/2017] [Indexed: 01/08/2023] Open
Abstract
The paper presents effects of different magnetic fields (MFs) (static—SMF and impulse—IMF) on bacteria Rhodospirillum rubrum VKM B-1621. The MFs had different magnetic strength: SMF—up to 173 mT; IMF—25 mT. The studied object was amylase activity which was measured by decrease in the starch concentration during incubation in the MFs. The term of incubation in the MFs was limited with 2 h. The SMF affected neither amylase activity of R. rubrum nor standard deviation in distribution of the residual starch concentration along the plate but the IMF did. The IMS effects varied along the plate which could be related with distance from the magnetic center of the applied device. In whole, application of impulse MFs can regulate bacterial activity and thus could be used for biotechnological application.
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28
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North JA, Miller AR, Wildenthal JA, Young SJ, Tabita FR. Microbial pathway for anaerobic 5'-methylthioadenosine metabolism coupled to ethylene formation. Proc Natl Acad Sci U S A 2017; 114:E10455-E10464. [PMID: 29133429 PMCID: PMC5715764 DOI: 10.1073/pnas.1711625114] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Numerous cellular processes involving S-adenosyl-l-methionine result in the formation of the toxic by-product, 5'-methylthioadenosine (MTA). To prevent inhibitory MTA accumulation and retain biologically available sulfur, most organisms possess the "universal" methionine salvage pathway (MSP). However, the universal MSP is inherently aerobic due to a requirement of molecular oxygen for one of the key enzymes. Here, we report the presence of an exclusively anaerobic MSP that couples MTA metabolism to ethylene formation in the phototrophic bacteria Rhodospirillum rubrum and Rhodopseudomonas palustris In vivo metabolite analysis of gene deletion strains demonstrated that this anaerobic MSP functions via sequential action of MTA phosphorylase (MtnP), 5-(methylthio)ribose-1-phosphate isomerase (MtnA), and an annotated class II aldolase-like protein (Ald2) to form 2-(methylthio)acetaldehyde as an intermediate. 2-(Methylthio)acetaldehyde is reduced to 2-(methylthio)ethanol, which is further metabolized as a usable organic sulfur source, generating stoichiometric amounts of ethylene in the process. Ethylene induction experiments using 2-(methylthio)ethanol versus sulfate as sulfur sources further indicate anaerobic ethylene production from 2-(methylthio)ethanol requires protein synthesis and that this process is regulated. Finally, phylogenetic analysis reveals that the genes corresponding to these enzymes, and presumably the pathway, are widespread among anaerobic and facultatively anaerobic bacteria from soil and freshwater environments. These results not only establish the existence of a functional, exclusively anaerobic MSP, but they also suggest a possible route by which ethylene is produced by microbes in anoxic environments.
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Affiliation(s)
- Justin A North
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
| | - Anthony R Miller
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
| | - John A Wildenthal
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
| | - Sarah J Young
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
| | - F Robert Tabita
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
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29
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Karmann S, Follonier S, Bassas-Galia M, Panke S, Zinn M. Robust at-line quantification of poly(3-hydroxyalkanoate) biosynthesis by flow cytometry using a BODIPY 493/503-SYTO 62 double-staining. J Microbiol Methods 2016; 131:166-171. [PMID: 27720900 DOI: 10.1016/j.mimet.2016.10.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/04/2016] [Accepted: 10/04/2016] [Indexed: 12/22/2022]
Abstract
Poly(3-hydroxyalkanoates) (PHAs) are bio-based and biodegradable polyesters which have been considered as a promising alternative to petrol-based plastics. Their bacterial production is a dynamic process in which intracellular polymerization and depolymerization are closely linked and depend on the availability of carbon substrates and other nutrients. These dynamics require a fast and quantitative method to determine the optimal harvest-time of PHA containing cells or to adjust carbon supply. In principle, flow cytometry (FCM) is an ideal tool that suits these requirements and, in addition, provides data on the PHA content of different cell populations. However, FCM-based PHA quantification methods have often relied on laborious sample preparation including washing steps and long incubation times. Here, we introduce a fast method based on double-staining using BODIPY 493/503 for PHA staining and SYTO 62 for DNA that allows acquiring reliable fluorescence and cell count data in <10min. Finally, fed-batch experiments with Pseudomonas putida KT2440 and Rhodospirillum rubrum S1 revealed that the method was robust and independent of the strain and type of PHA (medium-chain-length [mcl-] and short-chain-length [scl-] PHA, respectively). Interestingly, the specific PHA fluorescence was in case of mcl-PHA larger than for scl-PHA, probably reflecting the different material properties (e.g., specific density, hydrophilicity and crystallinity).
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Affiliation(s)
- Stephanie Karmann
- University of Applied Sciences and Arts Western Switzerland (HES-SO Valais), Institute of Life Technologies, Route du Rawyl 47, 1950 Sion, Switzerland; ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Stéphanie Follonier
- University of Applied Sciences and Arts Western Switzerland (HES-SO Valais), Institute of Life Technologies, Route du Rawyl 47, 1950 Sion, Switzerland
| | - Monica Bassas-Galia
- University of Applied Sciences and Arts Western Switzerland (HES-SO Valais), Institute of Life Technologies, Route du Rawyl 47, 1950 Sion, Switzerland
| | - Sven Panke
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Manfred Zinn
- University of Applied Sciences and Arts Western Switzerland (HES-SO Valais), Institute of Life Technologies, Route du Rawyl 47, 1950 Sion, Switzerland.
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30
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He D, Hughes S, Vanden-Hehir S, Georgiev A, Altenbach K, Tarrant E, Mackay CL, Waldron KJ, Clarke DJ, Marles-Wright J. Structural characterization of encapsulated ferritin provides insight into iron storage in bacterial nanocompartments. eLife 2016; 5. [PMID: 27529188 PMCID: PMC5012862 DOI: 10.7554/elife.18972] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/14/2016] [Indexed: 12/17/2022] Open
Abstract
Ferritins are ubiquitous proteins that oxidise and store iron within a protein shell to protect cells from oxidative damage. We have characterized the structure and function of a new member of the ferritin superfamily that is sequestered within an encapsulin capsid. We show that this encapsulated ferritin (EncFtn) has two main alpha helices, which assemble in a metal dependent manner to form a ferroxidase center at a dimer interface. EncFtn adopts an open decameric structure that is topologically distinct from other ferritins. While EncFtn acts as a ferroxidase, it cannot mineralize iron. Conversely, the encapsulin shell associates with iron, but is not enzymatically active, and we demonstrate that EncFtn must be housed within the encapsulin for iron storage. This encapsulin nanocompartment is widely distributed in bacteria and archaea and represents a distinct class of iron storage system, where the oxidation and mineralization of iron are distributed between two proteins. DOI:http://dx.doi.org/10.7554/eLife.18972.001 Iron is essential for life as it is a key component of many different enzymes that participate in processes such as energy production and metabolism. However, iron can also be highly toxic to cells because it readily reacts with oxygen. This reaction can damage DNA, proteins and the membranes that surround cells. To balance the cell’s need for iron against its potential damaging effects, organisms have evolved iron storage proteins known as ferritins that form cage-like structures. The ferritins convert iron into a less reactive form that is mineralised and safely stored in the central cavity of the ferritin cage and is available for cells when they need it. Recently, a new family of ferritins known as encapsulated ferritins have been found in some microorganisms. These ferritins are found in bacterial genomes with a gene that codes for a protein cage called an encapsulin. Although the structure of the encapsulin cage is known to look like the shell of a virus, the structure that the encapsulated ferritin itself forms is not known. It is also not clear how encapsulin and the encapsulated ferritin work together to store iron. He et al. have now used the techniques of X-ray crystallography and mass spectrometry to determine the structure of the encapsulated ferritin found in some bacteria. The encapsulated ferritin forms a ring-shaped doughnut in which ten subunits of ferritin are arranged in a ring; this is totally different from the enclosed cages that other ferritins form. Biochemical studies revealed that the encapsulated ferritin is able to convert iron into a less reactive form, but it cannot store iron on its own since it does not form a cage. Thus, the encapsulated ferritin needs to be housed within the encapsulin cage to store iron. Further work is needed to investigate how iron moves into the encapsulin cage to reach the ferritin proteins. Some organisms have both standard ferritin cages and encapsulated ferritins; why this is the case also remains to be discovered. DOI:http://dx.doi.org/10.7554/eLife.18972.002
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Affiliation(s)
- Didi He
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Sam Hughes
- The School of Chemistry, The University of Edinburgh, Edinburgh, United Kingdom
| | - Sally Vanden-Hehir
- The School of Chemistry, The University of Edinburgh, Edinburgh, United Kingdom
| | - Atanas Georgiev
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Kirsten Altenbach
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Emma Tarrant
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcasle upon Tyne, United Kingdom
| | - C Logan Mackay
- The School of Chemistry, The University of Edinburgh, Edinburgh, United Kingdom
| | - Kevin J Waldron
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcasle upon Tyne, United Kingdom
| | - David J Clarke
- The School of Chemistry, The University of Edinburgh, Edinburgh, United Kingdom
| | - Jon Marles-Wright
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom.,School of Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
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31
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Heinrich D, Raberg M, Steinbüchel A. Synthesis of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) from unrelated carbon sources in engineered Rhodospirillum rubrum. FEMS Microbiol Lett 2015; 362:fnv038. [PMID: 25761750 DOI: 10.1093/femsle/fnv038] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2015] [Indexed: 11/12/2022] Open
Abstract
Different genes encoding pyridine nucleotide transhydrogenases (pntAB, udhA) and acetoacetyl-CoA reductases (phaB) were heterologously overexpressed in Rhodospirillum rubrum S1. A recombinant strain, which harbored the gene encoding the membrane-bound transhydrogenase PntAB from Escherichia coli MG1655 and the phaB1 gene coding for an NADPH-dependent acetoacetyl-CoA reductase from Ralstonia eutropha H16, accumulated poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [Poly(3HB-co-3HV)] with a 3HV fraction of up to 13 mol% from fructose. This was a 13-fold increase of the 3HV content when compared to the wild-type strain. Higher contents of 3HV are known to reduce the brittleness of this polymer, which is advantageous for most applications. The engineered R. rubrum strain was also able to synthesize this industrially relevant copolymer from CO2 and CO from artificial synthesis gas (syngas) with a 3HV content of 56 mol%. The increased incorporation of 3HV was attributed to an excess of propionyl-CoA, which was generated from threonine and related amino acids to compensate for the intracellular redox imbalance resulting from the transhydrogenase reaction. Thereby, our study presents a novel, molecular approach to alter the composition of bacterial PHAs independently from external precursor supply. Moreover, this study also provides a promising production strain for syngas-derived second-generation biopolymers.
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Affiliation(s)
- Daniel Heinrich
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, D-48149 Münster, Germany
| | - Matthias Raberg
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, D-48149 Münster, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, D-48149 Münster, Germany; Environmental Sciences Department, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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32
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Nordlund S, Högbom M. ADP-ribosylation, a mechanism regulating nitrogenase activity. FEBS J 2013; 280:3484-90. [PMID: 23574616 DOI: 10.1111/febs.12279] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 03/26/2013] [Accepted: 04/08/2013] [Indexed: 11/29/2022]
Abstract
Nitrogen fixation is the vital biochemical process in which atmospheric molecular nitrogen is made available to the biosphere. The process is highly energetically costly and thus tightly regulated. The activity of the key enzyme, nitrogenase, is controlled by reversible mono-ADP-ribosylation of one of its components, the Fe protein. This protein provides the other component, the MoFe protein, with the electrons required for the reduction of molecular nitrogen. The Fe-protein is ADP-ribosylated and de-ADP-ribosylated by dinitrogenase reductase ADP-ribosyl transferase and dinitrogenase reductase activating glycohydrolase, respectively. Here we review the current biochemical and structural knowledge of this central regulatory reaction.
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Affiliation(s)
- Stefan Nordlund
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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