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Godoy MS, Verdú I, de Miguel SR, Jiménez JD, Prieto MA. Exploring Rhodospirillum rubrum response to high doses of carbon monoxide under light and dark conditions. Appl Microbiol Biotechnol 2024; 108:258. [PMID: 38466440 DOI: 10.1007/s00253-024-13079-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/14/2024] [Accepted: 02/16/2024] [Indexed: 03/13/2024]
Abstract
Environmental concerns about residues and the traditional disposal methods are driving the search for more environmentally conscious processes, such as pyrolysis and gasification. Their main final product is synthesis gas (syngas) composed of CO, CO2, H2, and methane. Syngas can be converted into various products using CO-tolerant microorganisms. Among them, Rhodospirillum rubrum is highlighted for its biotechnological potential. However, the extent to which high doses of CO affect its physiology is still opaque. For this reason, we have studied R. rubrum behavior under high levels of this gas (up to 2.5 bar), revealing a profound dependence on the presence or absence of light. In darkness, the key variable affected was the lag phase, where the highest levels of CO retarded growth to more than 20 days. Under light, R. rubrum ability to convert CO into CO2 and H2 depended on the presence of an additional carbon source, such as acetate. In those conditions where CO was completely exhausted, CO2 fixation was unblocked, leading to a diauxic growth. To enhance R. rubrum tolerance to CO in darkness, a UV-accelerated adaptive laboratory evolution (UVa-ALE) trial was conducted to isolate clones with shorter lag phases, resulting in the isolation of clones 1.4-2B and 1.7-2A. The adaptation of 1.4-2B was mainly based on mutated enzymes with a metabolic function, while 1.7-3A was mostly affected at regulatory genes, including the anti-repressor PpaA/AerR. Despite these mutations having slight effects on biomass and pigment levels, they successfully provoked a significant reduction in the lag phase (-50%). KEYPOINTS: • CO affects principally R. rubrum lag phase (darkness) and growth rate (light) • CO is converted to CO2/H2 during acetate uptake and inhibits CO2 fixation (light) • UVa-ALE clones showed a 50% reduction in the lag phase (darkness).
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Affiliation(s)
- Manuel S Godoy
- Polymer Biotechnology Lab, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain.
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-CSIC (SusPlast-CSIC), Madrid, Spain.
| | - Irene Verdú
- Polymer Biotechnology Lab, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain
- Present address: Drexel University, Philadelphia, Pennsylvania, USA
| | - Santiago R de Miguel
- Polymer Biotechnology Lab, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-CSIC (SusPlast-CSIC), Madrid, Spain
| | - José D Jiménez
- Polymer Biotechnology Lab, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-CSIC (SusPlast-CSIC), Madrid, Spain
| | - M Auxiliadora Prieto
- Polymer Biotechnology Lab, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain.
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-CSIC (SusPlast-CSIC), Madrid, Spain.
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Godoy MS, de Miguel SR, Prieto MA. A singular PpaA/AerR-like protein in Rhodospirillum rubrum rules beyond the boundaries of photosynthesis in response to the intracellular redox state. mSystems 2023; 8:e0070223. [PMID: 38054698 PMCID: PMC10734443 DOI: 10.1128/msystems.00702-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/18/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Rhodospirillum rubrum vast metabolic versatility places it as a remarkable model bacterium and an excellent biotechnological chassis. The key component of photosynthesis (PS) studied in this work (HP1) stands out among the other members of PpaA/AerR anti-repressor family since it lacks the motif they all share: the cobalamin B-12 binding motif. Despite being reduced and poorly conserved, HP1 stills controls PS as the other members of the family, allowing a fast response to changes in the redox state of the cell. This work also shows that HP1 absence affects genes from relevant biological processes other than PS, including nitrogen fixation and stress response. From a biotechnological perspective, HP1 could be manipulated in approaches where PS is not necessary, such as hydrogen or polyhydroxyalkanoates production, to save energy.
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Affiliation(s)
- Manuel S. Godoy
- Polymer Biotechnology Lab, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐CSIC (SusPlast‐CSIC), Madrid, Spain
| | - Santiago R. de Miguel
- Polymer Biotechnology Lab, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐CSIC (SusPlast‐CSIC), Madrid, Spain
| | - M. Auxiliadora Prieto
- Polymer Biotechnology Lab, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐CSIC (SusPlast‐CSIC), Madrid, Spain
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Tinguely C, Paulméry M, Terrettaz C, Gonzalez D. Diurnal cycles drive rhythmic physiology and promote survival in facultative phototrophic bacteria. ISME COMMUNICATIONS 2023; 3:125. [PMID: 38001234 PMCID: PMC10674011 DOI: 10.1038/s43705-023-00334-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/02/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023]
Abstract
Bacteria have evolved many strategies to spare energy when nutrients become scarce. One widespread such strategy is facultative phototrophy, which helps heterotrophs supplement their energy supply using light. Our knowledge of the impact that such behaviors have on bacterial fitness and physiology is, however, still limited. Here, we study how a representative of the genus Porphyrobacter, in which aerobic anoxygenic phototrophy is ancestral, responds to different light regimes under nutrient limitation. We show that bacterial survival in stationary phase relies on functional reaction centers and varies depending on the light regime. Under dark-light alternance, our bacterial model presents a diphasic life history dependent on phototrophy: during dark phases, the cells inhibit DNA replication and part of the population lyses and releases nutrients, while subsequent light phases allow for the recovery and renewed growth of the surviving cells. We correlate these cyclic variations with a pervasive pattern of rhythmic transcription which reflects global changes in diurnal metabolic activity. Finally, we demonstrate that, compared to either a phototrophy mutant or a bacteriochlorophyll a overproducer, the wild type strain is better adapted to natural environments, where regular dark-light cycles are interspersed with additional accidental dark episodes. Overall, our results highlight the importance of light-induced biological rhythms in a new model of aerobic anoxygenic phototroph representative of an ecologically important group of environmental bacteria.
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Affiliation(s)
- Camille Tinguely
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Mélanie Paulméry
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Céline Terrettaz
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Diego Gonzalez
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
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Dragnea V, Gonzalez-Gutierrez G, Bauer CE. Structural Analyses of CrtJ and Its B 12-Binding Co-Regulators SAerR and LAerR from the Purple Photosynthetic Bacterium Rhodobacter capsulatus. Microorganisms 2022; 10:912. [PMID: 35630357 PMCID: PMC9144470 DOI: 10.3390/microorganisms10050912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 02/01/2023] Open
Abstract
Among purple photosynthetic bacteria, the transcription factor CrtJ is a major regulator of photosystem gene expression. Depending on growing conditions, CrtJ can function as an aerobic repressor or an anaerobic activator of photosystem genes. Recently, CrtJ's activity was shown to be modulated by two size variants of a B12 binding co-regulator called SAerR and LAerR in Rhodobacter capsulatus. The short form, SAerR, promotes CrtJ repression, while the longer variant, LAerR, converts CrtJ into an activator. In this study, we solved the crystal structure of R. capsulatus SAerR at a 2.25 Å resolution. Hydroxycobalamin bound to SAerR is sandwiched between a 4-helix bundle cap, and a Rossman fold. This structure is similar to a AerR-like domain present in CarH from Thermus termophilus, which is a combined photoreceptor/transcription regulator. We also utilized AlphaFold software to predict structures for the LAerR, CrtJ, SAerR-CrtJ and LAerR-CrtJ co-complexes. These structures provide insights into the role of B12 and an LAerR N-terminal extension in regulating the activity of CrtJ.
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Affiliation(s)
| | | | - Carl E. Bauer
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA; (V.D.); (G.G.-G.)
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Izaki K, Haruta S. Aerobic Production of Bacteriochlorophylls in the Filamentous Anoxygenic Photosynthetic Bacterium, Chloroflexus aurantiacus in the Light. Microbes Environ 2020; 35. [PMID: 32418929 PMCID: PMC7308566 DOI: 10.1264/jsme2.me20015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Filamentous anoxygenic photosynthetic bacteria grow by photosynthesis and aerobic respiration. The present study investigated the effects of light and O2 on bacteriochlorophyll contents and the transcription levels of photosynthesis-related genes in Chloroflexus aurantiacus J-10-fl T. Under aerobic conditions, C. aurantiacus produced marked amounts of bacteriochlorophylls in the presence of light, although their production was strongly suppressed in the dark. The transcription levels of genes related to the synthesis of bacteriochlorophylls, photosystems, and chlorosomes: bchM, bchU, pufL, pufBA, and csmM, were markedly increased by illumination. These results suggest that C. aurantiacus continuously synthesizes ATP by photophosphorylation even in the presence of O2.
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Affiliation(s)
- Kazaha Izaki
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University
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The Vitamin B 12-Dependent Photoreceptor AerR Relieves Photosystem Gene Repression by Extending the Interaction of CrtJ with Photosystem Promoters. mBio 2017; 8:mBio.00261-17. [PMID: 28325764 PMCID: PMC5362033 DOI: 10.1128/mbio.00261-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Purple nonsulfur bacteria adapt their physiology to a wide variety of environmental conditions often through the control of transcription. One of the main transcription factors involved in controlling expression of the Rhodobacter capsulatus photosystem is CrtJ, which functions as an aerobic repressor of photosystem genes. Recently, we reported that a vitamin B12 binding antirepressor of CrtJ called AerR is required for anaerobic expression of the photosystem. However, the mechanism whereby AerR regulates CrtJ activity is unclear. In this study, we used a combination of next-generation sequencing and biochemical methods to globally identify genes under control of CrtJ and the role of AerR in controlling this regulation. Our results indicate that CrtJ has a much larger regulon than previously known, with a surprising regulatory function under both aerobic and anaerobic photosynthetic growth conditions. A combination of in vivo chromatin immunoprecipitation-DNA sequencing (ChIP-seq) and ChIP-seq and exonuclease digestion (ChIP-exo) studies and in vitro biochemical studies demonstrate that AerR forms a 1:2 complex with CrtJ (AerR-CrtJ2) and that this complex binds to many promoters under photosynthetic conditions. The results of in vitro and in vivo DNA binding studies indicate that AerR-CrtJ2 anaerobically forms an extended interaction with the bacteriochlorophyll bchC promoter to relieve repression by CrtJ. This is contrasted by aerobic growth conditions where CrtJ alone functions as an aerobic repressor of bchC expression. These results indicate that the DNA binding activity of CrtJ is modified by interacting with AerR in a redox-regulated manner and that this interaction alters CrtJ’s function. Photoreceptors control a wide range of physiology often by regulating downstream gene expression in response to light absorption via a bound chromophore. Different photoreceptors are known to utilize a number of different compounds for light absorption, including the use of such compounds as flavins, linearized tetrapyrroles (bilins), and carotenoids. Recently, a novel class of photoreceptors that use vitamin B12 (cobalamin) as a blue-light-absorbing chromophore have been described. In this study, we analyzed the mechanism by which the vitamin B12 binding photoreceptor AerR controls the DNA binding activity of the photosystem regulator CrtJ. This study shows that a direct interaction between the vitamin B12 binding photoreceptor AerR with CrtJ modulates CrtJ binding to DNA and importantly, the regulatory outcome of gene expression, as shown here with photosystem promoters.
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Fixen KR, Harwood CS. A polymorphism in the oxygen-responsive repressor PpsR2 confers a growth advantage to Rhodopseudomonas palustris under low light. PHOTOSYNTHESIS RESEARCH 2016; 129:199-204. [PMID: 27344652 DOI: 10.1007/s11120-016-0288-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/15/2016] [Indexed: 06/06/2023]
Abstract
The purple nonsulfur bacterium Rhodopseudomonas palustris grows aerobically using oxidative phosphorylation or anaerobically using photophosphorylation. The oxygen-responsive transcription regulator, PpsR2, regulates the transition to a phototrophic lifestyle by repressing transcription of photosynthesis genes during aerobic growth. Whereas most R. palustris strains have an arginine (Arg) at position 439 in the helix-turn-helix DNA-binding domain of this protein, some strains, including the well-studied strain CGA009, have a cysteine (Cys) at this position. Using allelic exchange, we found that the Cys439 in PpsR2 resulted in increased pigmentation and photosynthetic gene expression under both aerobic and anaerobic conditions. The Cys439 substitution also conferred a growth advantage to R. palustris at low light intensities. This indicates that variation in the PpsR2 protein results in R. palustris strains that have two different thresholds for derepressing photosynthesis genes in response to oxygen and light.
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Affiliation(s)
- Kathryn R Fixen
- Department of Microbiology, University of Washington, Box 375573, HSB K-340B, 1705 NE Pacific Street, Seattle, WA, 98195, USA
| | - Caroline S Harwood
- Department of Microbiology, University of Washington, Box 375573, HSB K-340B, 1705 NE Pacific Street, Seattle, WA, 98195, USA.
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Shimizu T, Cheng Z, Matsuura K, Masuda S, Bauer CE. Evidence that Altered Cis Element Spacing Affects PpsR Mediated Redox Control of Photosynthesis Gene Expression in Rubrivivax gelatinosus. PLoS One 2015; 10:e0128446. [PMID: 26030916 PMCID: PMC4452267 DOI: 10.1371/journal.pone.0128446] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/27/2015] [Indexed: 11/18/2022] Open
Abstract
PpsR is a major regulator of photosynthesis gene expression among all characterized purple photosynthetic bacteria. This transcription regulator has been extensively characterized in Rhodobacter (Rba.) capsulatus and Rba. sphaeroides which are members of the α-proteobacteria lineage. In this study, we have investigated the biochemical properties and mutational effects of a ppsR deletion strain in the β-proteobacterium Rubrivivax (Rvi.) gelatinosus in order to reveal phylogenetically conserved mechanisms and species-specific characteristics. A deletion of the ppsR gene resulted in de-repression of photosystem synthesis showing that PpsR functions as a repressor of photosynthesis genes in this species. We also constructed a Rvi. gelatinosus PpsR mutant in which a conserved cysteine at position 436 was changed to an alanine to examine whether or not this residue is important for sensing redox, as reported in Rhodobacter species. Surprisingly, the Cys436 Ala mutant retained the ability to repress photosynthesis gene expression under aerobic conditions, suggesting that PpsR from Rvi. gelatinosus has different redox-responding characteristics. Furthermore, biochemical analyses demonstrated that Rvi. gelatinosus PpsR only shows redox-dependent binding to promoters with 9-bp spacing, but not 8-bp spacing, between two PpsR-recognition sequences. These results indicate that redox-dependent binding of PpsR requires appropriate cis configuration of PpsR target sequences in Rvi. gelatinosus. These results also indicate that PpsR homologs from different species regulate photosynthesis genes with altered biochemical properties.
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Affiliation(s)
- Takayuki Shimizu
- Department of Biological Sciences, Tokyo Institute of Technology, Kanagawa 226–8501, Japan
| | - Zhuo Cheng
- Department of Molecular and Cellar Biochemistry, Indiana University, Bloomington, Indiana 47405, United States of America
| | - Katsumi Matsuura
- Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo 192–0397, Japan
| | - Shinji Masuda
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Kanagawa 226–8501, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152–8551, Japan
| | - Carl E. Bauer
- Department of Molecular and Cellar Biochemistry, Indiana University, Bloomington, Indiana 47405, United States of America
- * E-mail:
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Heintz U, Meinhart A, Winkler A. Multi-PAS domain-mediated protein oligomerization of PpsR from Rhodobacter sphaeroides. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:863-76. [PMID: 24598755 PMCID: PMC3949515 DOI: 10.1107/s1399004713033634] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 12/12/2013] [Indexed: 01/04/2023]
Abstract
Per-ARNT-Sim (PAS) domains are essential modules of many multi-domain signalling proteins that mediate protein interaction and/or sense environmental stimuli. Frequently, multiple PAS domains are present within single polypeptide chains, where their interplay is required for protein function. Although many isolated PAS domain structures have been reported over the last decades, only a few structures of multi-PAS proteins are known. Therefore, the molecular mechanism of multi-PAS domain-mediated protein oligomerization and function is poorly understood. The transcription factor PpsR from Rhodobacter sphaeroides is such a multi-PAS domain protein that, in addition to its three PAS domains, contains a glutamine-rich linker and a C-terminal helix-turn-helix DNA-binding motif. Here, crystal structures of two N-terminally and C-terminally truncated PpsR variants that comprise a single (PpsRQ-PAS1) and two (PpsRN-Q-PAS1) PAS domains, respectively, are presented and the multi-step strategy required for the phasing of a triple PAS domain construct (PpsRΔHTH) is illustrated. While parts of the biologically relevant dimerization interface can already be observed in the two shorter constructs, the PpsRΔHTH structure reveals how three PAS domains enable the formation of multiple oligomeric states (dimer, tetramer and octamer), highlighting that not only the PAS cores but also their α-helical extensions are essential for protein oligomerization. The results demonstrate that the long helical glutamine-rich linker of PpsR results from a direct fusion of the N-cap of the PAS1 domain with the C-terminal extension of the N-domain that plays an important role in signal transduction.
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Affiliation(s)
- Udo Heintz
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Anton Meinhart
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Andreas Winkler
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
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Cheng Z, Wu J, Setterdahl A, Reddie K, Carroll K, Hammad LA, Karty JA, Bauer CE. Activity of the tetrapyrrole regulator CrtJ is controlled by oxidation of a redox active cysteine located in the DNA binding domain. Mol Microbiol 2012; 85:734-46. [PMID: 22715852 DOI: 10.1111/j.1365-2958.2012.08135.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
CrtJ from Rhodobacter capsulatus is a regulator of genes involved in the biosynthesis of haem, bacteriochlorophyll, carotenoids as well as structural proteins of the light harvesting-II complex. Fluorescence anisotropy-based DNA-binding analysis demonstrates that oxidized CrtJ exhibits ~20-fold increase in binding affinity over that of reduced CrtJ. Liquid chromatography electrospray tandem ionization mass spectrometric analysis using DAz-2, a sulfenic acid (-SOH)-specific probe, demonstrates that exposure of CrtJ to oxygen or to hydrogen peroxide leads to significant accumulation of a sulfenic acid derivative of Cys420 which is located in the helix-turn-helix (HTH) motif. In vivo labelling with 4-(3-azidopropyl)cyclohexane-1,3-dione (DAz-2) shows that Cys420 also forms a sulfenic acid modification in vivo when cells are exposed to oxygen. Moreover, a Cys420 to Ala mutation leads to a ~60-fold reduction of DNA binding activity while a Cys to Ser substitution at position 420 that mimics a cysteine sulfenic acid results in a ~4-fold increase in DNA binding activity. These results provide the first example where sulfenic acid oxidation of a cysteine in a HTH-motif leads to differential effects on gene expression.
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Affiliation(s)
- Zhuo Cheng
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
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Abstract
Phytochromes are environmental sensors, historically thought of as red/far-red photoreceptors in plants. Their photoperception occurs through a covalently linked tetrapyrrole chromophore, which undergoes a light-dependent conformational change propagated through the protein to a variable output domain. The phytochrome composition is modular, typically consisting of a PAS-GAF-PHY architecture for the N-terminal photosensory core. A collection of three-dimensional structures has uncovered key features, including an unusual figure-of-eight knot, an extension reaching from the PHY domain to the chromophore-binding GAF domain, and a centrally located, long α-helix hypothesized to be crucial for intramolecular signaling. Continuing identification of phytochromes in microbial systems has expanded the assigned sensory abilities of this family out of the red and into the yellow, green, blue, and violet portions of the spectrum. Furthermore, phytochromes acting not as photoreceptors but as redox sensors have been recognized. In addition, architectures other than PAS-GAF-PHY are known, thus revealing phytochromes to be a varied group of sensory receptors evolved to utilize their modular design to perceive a signal and respond accordingly. This review focuses on the structures of bacterial phytochromes and implications for signal transmission. We also discuss the small but growing set of bacterial phytochromes for which a physiological function has been ascertained.
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Affiliation(s)
- Michele E Auldridge
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
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Bauer CE, Setterdahl A, Wu J, Robinson BR. Regulation of Gene Expression in Response to Oxygen Tension. THE PURPLE PHOTOTROPHIC BACTERIA 2009. [DOI: 10.1007/978-1-4020-8815-5_35] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Masuda S, Berleman J, Hasselbring BM, Bauer CE. Regulation of aerobic photosystem synthesis in the purple bacterium Rhodospirillum centenum by CrtJ and AerR. Photochem Photobiol Sci 2008; 7:1267-72. [PMID: 18846293 DOI: 10.1039/b802365b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Genes coding for putative CrtJ and AerR homologs were identified and characterized in the purple photosynthetic bacterium Rhodospirillum centenum (also known as Rhodocista centenaria), an organism that synthesizes photopigments even under highly aerated conditions. Mutational analysis indicated that in Rsp. centenum, gene crtJ codes for a repressor for photosynthesis gene expression as in Rhodobacter capsulatus, which exhibits a high level of oxygen repression of photosystem synthesis. In contrast to Rba. capsulatus, AerR in Rsp. centenum appears to be an aerobic activator; an aerR mutation resulted in significantly reduced levels of photopigment synthesis. Both aerR and crtJ mutants retained essentially normal levels of photosystem synthesis under anaerobic conditions, indicating that their activities are specific for aerobic photosystem synthesis. The readthrough transcript from crtE promoter, which is regulated by AerR and CrtJ, seems to be significant in maintaining the expression levels of the light harvesting I (puf) genes in Rsp. centenum. We suggest that AerR and CrtJ regulate aerobic photosystem synthesis primarily through controlling activity of the transcriptional readthrough.
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Affiliation(s)
- Shinji Masuda
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan.
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Giraud E, Verméglio A. Bacteriophytochromes in anoxygenic photosynthetic bacteria. PHOTOSYNTHESIS RESEARCH 2008; 97:141-153. [PMID: 18612842 DOI: 10.1007/s11120-008-9323-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Accepted: 06/16/2008] [Indexed: 05/26/2023]
Abstract
Since the first discovery of a bacteriophytochrome in Rhodospirillum centenum, numerous bacteriophytochromes have been identified and characterized in other anoxygenic photosynthetic bacteria. This review is focused on the biochemical and biophysical properties of bacteriophytochromes with a special emphasis on their roles in the synthesis of the photosynthetic apparatus.
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Affiliation(s)
- Eric Giraud
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, CIRAD, AGRO-M, INRA, UM2, TA A-82/J, Campus de Baillarguet, 34398, Montpellier Cedex 5, France
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15
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Yamazaki Y, Fukusumi H, Kamikubo H, Kataoka M. Role of the N-terminal region in the function of the photosynthetic bacterium transcription regulator PpsR. Photochem Photobiol 2008; 84:839-44. [PMID: 18282179 DOI: 10.1111/j.1751-1097.2008.00306.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PpsR is a transcription repressor for the gene cluster encoding photosystem genes in Rhodobacter sphaeroides. Repression activity is accomplished by DNA binding on the promoter regions of the photosystem gene clusters, and depends on both the redox potential and the presence of antirepressor protein AppA. To understand DNA repression regulation by PpsR, we investigated the function of PpsR domains in self-association for DNA binding. We constructed domain-deletion mutants and verified DNA-binding activity and dimer formation. Gel shift assay for measuring the DNA-binding activity of three sequential N-terminal deletion mutants revealed that N-terminal deletions (of minimum 121 residues) caused loss of binding activity. Size-exclusion gel chromatography revealed that deletion mutant which lacks the N-terminal 121-amino acid deletion mutant to exist as a dimer, although it was less stable than the intact PpsR. The mutants lacking the adjacent regions, Q-linker region and the first Per-Ant-Sim domain, did not form dimers, suggesting the involvement of the N-terminal region in dimer formation. This region is thus considered to be a functional domain in self-association, although not yet identified as a structural domain. Circular dichroism spectrum of the N-terminal region fragment exhibited a alpha/beta structure. We conclude that this region is a structural and functional domain, contributing to PpsR repression through dimer stabilization.
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Affiliation(s)
- Yoichi Yamazaki
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
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Klamt S, Grammel H, Straube R, Ghosh R, Gilles ED. Modeling the electron transport chain of purple non-sulfur bacteria. Mol Syst Biol 2008; 4:156. [PMID: 18197174 PMCID: PMC2238716 DOI: 10.1038/msb4100191] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Accepted: 10/18/2007] [Indexed: 11/09/2022] Open
Abstract
Purple non-sulfur bacteria (Rhodospirillaceae) have been extensively employed for studying principles of photosynthetic and respiratory electron transport phosphorylation and for investigating the regulation of gene expression in response to redox signals. Here, we use mathematical modeling to evaluate the steady-state behavior of the electron transport chain (ETC) in these bacteria under different environmental conditions. Elementary-modes analysis of a stoichiometric ETC model reveals nine operational modes. Most of them represent well-known functional states, however, two modes constitute reverse electron flow under respiratory conditions, which has been barely considered so far. We further present and analyze a kinetic model of the ETC in which rate laws of electron transfer steps are based on redox potential differences. Our model reproduces well-known phenomena of respiratory and photosynthetic operation of the ETC and also provides non-intuitive predictions. As one key result, model simulations demonstrate a stronger reduction of ubiquinone when switching from high-light to low-light conditions. This result is parameter insensitive and supports the hypothesis that the redox state of ubiquinone is a suitable signal for controlling photosynthetic gene expression.
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Affiliation(s)
- Steffen Klamt
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.
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Abstract
The importance of chlorophyll (Chl) to the process of photosynthesis is obvious, and there is clear evidence that the regulation of Chl biosynthesis has a significant role in the regulation of assembly of the photosynthetic apparatus. The understanding of Chl biosynthesis has rapidly advanced in recent years. The identification of genetic loci associated with each of the biochemical steps has been accompanied by a greater appreciation of the role of Chl biosynthesis intermediates in intracellular signaling. The purpose of this review is to provide a source of information for all the steps in Chl and bacteriochlorophyll a biosynthesis, with an emphasis on steps that are believed to be key regulation points.
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Affiliation(s)
- David W Bollivar
- Department of Biology, Illinois Wesleyan University, Bloomington, IL 61702-2900, USA.
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Kim SK, Mason JT, Knaff DB, Bauer CE, Setterdahl AT. Redox properties of the Rhodobacter sphaeroides transcriptional regulatory proteins PpsR and AppA. PHOTOSYNTHESIS RESEARCH 2006; 89:89-98. [PMID: 16915353 PMCID: PMC2774731 DOI: 10.1007/s11120-006-9086-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2006] [Accepted: 07/13/2006] [Indexed: 05/11/2023]
Abstract
Redox properties of the photosynthetic gene repressor PpsR and the blue-light photoreceptor/antirepressor AppA from Rhodobacter sphaeroides have been characterized. Redox titrations of PpsR reveal the presence of a two-electron couple, with an E (m) value of -320 mV at pH 7.0, which is likely to arise from the reversible conversion of two cysteine thiols to a disulfide. This E (m) value is very much more negative than the E (m) = -180 mV value measured previously at pH 7.0 for the disulfide/dithiol couple in CrtJ, the homolog for PpsR in the closely related bacterium Rhodobacter capsulatus. AppA, a flavin-containing blue-light receptor that is also involved in the regulation of gene expression in R. sphaeroides, contains multiple cysteines in its C-terminal region, two of which function as a redox-active dithiol/disulfide couple with an E (m) value of -325 mV at pH 7.0 in the dark. Titrations of this dithiol/disulfide couple in illuminated samples of AppA indicate that the E (m) value of this disulfide/dithiol couple is -315 mV at pH 7.0, identical to the value obtained for AppA in the dark within the combined experimental uncertainties of the two measurements. The E (m) values of AppA and PpsR demonstrate that these proteins are thermodynamically capable of electron transfer for their activity as an anti-repressor/repressor in R. sphaeroides.
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Affiliation(s)
- S. -K. Kim
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - J. T. Mason
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - D. B. Knaff
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
- Institute for Biotechnology and Genomics, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - C. E. Bauer
- Department of Biology, Indiana University, 915 E. 3rd St., Myers Hall, Bloomington, IN 47405, USA
| | - A. T. Setterdahl
- Department of Biology, Indiana University, 915 E. 3rd St., Myers Hall, Bloomington, IN 47405, USA
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