1
|
Chen H, Wang Y, Wang W, Cao T, Zhang L, Wang Z, Chi X, Shi T, Wang H, He X, Liang M, Yang M, Jiang W, Lv D, Yu J, Zhu G, Xie Y, Gao B, Wang X, Liu X, Li Y, Ouyang L, Zhang J, Liu H, Li Z, Tong Y, Xia X, Tan GY, Zhang L. High-yield porphyrin production through metabolic engineering and biocatalysis. Nat Biotechnol 2024:10.1038/s41587-024-02267-3. [PMID: 38839873 DOI: 10.1038/s41587-024-02267-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 04/26/2024] [Indexed: 06/07/2024]
Abstract
Porphyrins and their derivatives find extensive applications in medicine, food, energy and materials. In this study, we produced porphyrin compounds by combining Rhodobacter sphaeroides as an efficient cell factory with enzymatic catalysis. Genome-wide CRISPRi-based screening in R. sphaeroides identifies hemN as a target for improved coproporphyrin III (CPIII) production, and exploiting phosphorylation of PrrA further improves the production of bioactive CPIII to 16.5 g L-1 by fed-batch fermentation. Subsequent screening and engineering high-activity metal chelatases and coproheme decarboxylase results in the synthesis of various metalloporphyrins, including heme and the anti-tumor agent zincphyrin. After pilot-scale fermentation (200 L) and setting up the purification process for CPIII (purity >95%), we scaled up the production of heme and zincphyrin through enzymatic catalysis in a 5-L bioreactor, with CPIII achieving respective enzyme conversion rates of 63% and 98% and yielding 10.8 g L-1 and 21.3 g L-1, respectively. Our strategy offers a solution for high-yield bioproduction of heme and other valuable porphyrins with substantial industrial and medical applications.
Collapse
Affiliation(s)
- Haihong Chen
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Yaohong Wang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ting Cao
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Lu Zhang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Zhengduo Wang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Xuran Chi
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Tong Shi
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Huangwei Wang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Xinwei He
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Mindong Liang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Mengxue Yang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Wenyi Jiang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Dongyuan Lv
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Jiaming Yu
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Guoliang Zhu
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Yongtao Xie
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Bei Gao
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Xinye Wang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Youyuan Li
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Liming Ouyang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Jingyu Zhang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Huimin Liu
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Zilong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yaojun Tong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xuekui Xia
- Key Biosensor Laboratory of Shandong Province, Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Gao-Yi Tan
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China.
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China.
| |
Collapse
|
2
|
Grützner J, Börner J, Jäger A, Klug G. The Small RNA-Binding Protein CcaF1 Promotes Formation of Photosynthetic Complexes in Rhodobacter sphaeroides. Int J Mol Sci 2023; 24:ijms24119515. [PMID: 37298460 DOI: 10.3390/ijms24119515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
In natural habitats, bacteria frequently need to adapt to changing environmental conditions. Regulation of transcription plays an important role in this process. However, riboregulation also contributes substantially to adaptation. Riboregulation often acts at the level of mRNA stability, which is determined by sRNAs, RNases, and RNA-binding proteins. We previously identified the small RNA-binding protein CcaF1, which is involved in sRNA maturation and RNA turnover in Rhodobacter sphaeroides. Rhodobacter is a facultative phototroph that can perform aerobic and anaerobic respiration, fermentation, and anoxygenic photosynthesis. Oxygen concentration and light conditions decide the pathway for ATP production. Here, we show that CcaF1 promotes the formation of photosynthetic complexes by increasing levels of mRNAs for pigment synthesis and for some pigment-binding proteins. Levels of mRNAs for transcriptional regulators of photosynthesis genes are not affected by CcaF1. RIP-Seq analysis compares the binding of CcaF1 to RNAs during microaerobic and photosynthetic growth. The stability of the pufBA mRNA for proteins of the light-harvesting I complex is increased by CcaF1 during phototrophic growth but decreased during microaerobic growth. This research underlines the importance of RNA-binding proteins in adaptation to different environments and demonstrates that an RNA-binding protein can differentially affect its binding partners in dependence upon growth conditions.
Collapse
Affiliation(s)
- Julian Grützner
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Janek Börner
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Andreas Jäger
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| |
Collapse
|
3
|
Liu J, Hiser C, Li F, Hall R, Garavito RM, Ferguson-Miller S. New TSPO Crystal Structures of Mutant and Heme-Bound Forms with Altered Flexibility, Ligand Binding, and Porphyrin Degradation Activity. Biochemistry 2023; 62:1262-1273. [PMID: 36947867 PMCID: PMC10077581 DOI: 10.1021/acs.biochem.2c00612] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 03/09/2023] [Indexed: 03/24/2023]
Abstract
The ancient protein TSPO (translocator protein 18kD) is found in all kingdoms and was originally identified as a binding site of benzodiazepine drugs. Its physiological function remains unclear, although porphyrins are conserved ligands. Several crystal structures of bacterial TSPO and nuclear magnetic resonance structures of a mouse form have revealed monomer and dimer configurations, but there have been no reports of structures with a physiological ligand. Here, we present the first X-ray structures of Rhodobacter sphaeroides TSPO with a physiological ligand bound. Two different variants (substituting threonine for alanine at position 139 (A139T) and phenylalanine for alanine at position 138 (A138F)) yielded well-diffracting crystals giving structures of both apo- and heme-containing forms. Both variants have wild-type micromolar affinity for heme and protoporphyrin IX, but A139T has very low ability to accelerate the breakdown of porphyrin in the presence of light and oxygen. The binding of heme to one protomer of the dimer of either mutant induces a more rigid structure, both in the heme-binding protomer and the protomer without heme bound, demonstrating an allosteric response. Ensemble refinement of the X-ray data reveals distinct regions of altered flexibility in response to single heme binding to the dimer. The A139T variant shows a more rigid structure overall, which may relate to extra hydrogen bonding of waters captured in the heme crevice. As TSPO has been suggested to have a role in heme delivery from mitochondria to the cytoplasm, the new structures provide potential clues regarding the structural basis of such activity.
Collapse
Affiliation(s)
- Jian Liu
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Carrie Hiser
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
| | - Fei Li
- Amgen
Inc., San Francisco, California 94080, United States
| | - Robert Hall
- Pharmacology
and Chemical Biology, University of Pittsburgh
School of Medicine, Pittsburgh, Pennsylvania 15213, United States
| | - R. Michael Garavito
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
| | - Shelagh Ferguson-Miller
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
| |
Collapse
|
4
|
Adnan F, Jalil A, Ahmed T, Rahman A, Dawood N, Haider G, Siddiqui MF, Rostock L, Guenther S, Schaufler K. TRAP transporter TakP: a key player in the resistance against selenite-induced oxidative stress in Rhodobacter sphaeroides. Microbiol Res 2021; 252:126828. [PMID: 34543948 DOI: 10.1016/j.micres.2021.126828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 03/28/2021] [Accepted: 07/20/2021] [Indexed: 11/24/2022]
Abstract
Almost one-third of all proteins require metal ions as an essential component in key biological processes and approximately half of all enzymes are associated with one or more metal ions. The naturally occurring selenium is very toxic at higher levels, but few bacteria can reduce it into the less toxic insoluble elemental selenium. Selenium is required for the synthesis of selenocysteine, an essential residue involved in the active sites of various enzymes. The purple non-sulphur bacteria, Rhodobacter sphaeroidesis demonstrated for its selenite reduction capacity. The exact mechanism of selenite toxicity is unknown but it reacts with glutathione to form selenodiglutathione, producing the highly toxic compounds namely, H2O2and O2-. A R. sphaeroidesstrain with mutated takP gene, a member of the TRAP (tripartite ATP-independent periplasmic) family of transporter, was reported to be showing more resistance towards selenite in the growth medium but the reason for the resistance is unknown. TRAP transporters are the best-studied family of substrate-binding protein and in our previous study it was confirmed that the gene takP in R. sphaeroides is down-regulated by a small non-coding RNA SorY, providing more resistance to the bacterium against the oxidative stress. By comparative growth analysis and sensitivity assays in the presence of 2 mM selenite, it was observed that the SorY knockout strain is more sensitive to selenite while overexpression of the sRNA conferred more resistance to the bacterium like the takP mutant strain. TakP is involved in the import of malate into the cell, which under oxidative stress needs to be down-regulated to limit malate flux into the cell. Limited malate flux leads to metabolic rearrangements in the cell to avoid excessive generation of prooxidant NADH and facilitate constant generation of antioxidant NADPH. In the presence and absence of selenite, a drastic increase in the NADPH and decrease in the NADH levels are reported respectively. Accumulation of metallic selenium in the cytoplasm was detected via atomic absorption spectrophotometer and our analysis clearly demonstrated the presence of more selenium in the electron micrographs of the SorY knockout strain compared to the takP mutant grown under dark semi-aerobic growth conditions in the presence of selenite. Hence based on our analysis, it is confirmed that lack of TakP transporter led to reduced selenite influx into the cytoplasm, relieving cells with limited generation of ROS, eventually exhibiting more resistance against selenite-induced oxidative stress.
Collapse
Affiliation(s)
- Fazal Adnan
- Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, Pakistan.
| | - Amna Jalil
- Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, Pakistan.
| | - Tahir Ahmed
- Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, Pakistan.
| | - Afra Rahman
- Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, Pakistan.
| | - Nawal Dawood
- Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, Pakistan.
| | - Ghulam Haider
- Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, Pakistan.
| | | | - Leon Rostock
- Institute of Pharmacy, Pharmaceutical Biology, University of Greifswald, Germany.
| | - Sebastian Guenther
- Institute of Pharmacy, Pharmaceutical Biology, University of Greifswald, Germany.
| | - Katharina Schaufler
- Institute of Pharmacy, Pharmaceutical Microbiology, University of Greifswald, Germany; Institute of infection medicine, Kiel University, Germany.
| |
Collapse
|
5
|
Hiser C, Montgomery BL, Ferguson-Miller S. TSPO protein binding partners in bacteria, animals, and plants. J Bioenerg Biomembr 2021; 53:463-487. [PMID: 34191248 PMCID: PMC8243069 DOI: 10.1007/s10863-021-09905-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 06/12/2021] [Indexed: 12/11/2022]
Abstract
The ancient membrane protein TSPO is phylogenetically widespread from archaea and bacteria to insects, vertebrates, plants, and fungi. TSPO’s primary amino acid sequence is only modestly conserved between diverse species, although its five transmembrane helical structure appears mainly conserved. Its cellular location and orientation in membranes have been reported to vary between species and tissues, with implications for potential diverse binding partners and function. Most TSPO functions relate to stress-induced changes in metabolism, but in many cases it is unclear how TSPO itself functions—whether as a receptor, a sensor, a transporter, or a translocator. Much evidence suggests that TSPO acts indirectly by association with various protein binding partners or with endogenous or exogenous ligands. In this review, we focus on proteins that have most commonly been invoked as TSPO binding partners. We suggest that TSPO was originally a bacterial receptor/stress sensor associated with porphyrin binding as its most ancestral function and that it later developed additional stress-related roles in eukaryotes as its ability to bind new partners evolved.
Collapse
Affiliation(s)
- Carrie Hiser
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA. .,Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA.
| | - Beronda L Montgomery
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.,Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - Shelagh Ferguson-Miller
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| |
Collapse
|
6
|
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.
Collapse
Affiliation(s)
- Kazaha Izaki
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University
| |
Collapse
|
7
|
Pandey R, Armitage JP, Wadhams GH. Use of transcriptomic data for extending a model of the AppA/PpsR system in Rhodobacter sphaeroides. BMC SYSTEMS BIOLOGY 2017; 11:146. [PMID: 29284486 PMCID: PMC5747161 DOI: 10.1186/s12918-017-0489-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 11/10/2017] [Indexed: 12/22/2022]
Abstract
Background Photosynthetic (PS) gene expression in Rhodobacter sphaeroides is regulated in response to changes in light and redox conditions mainly by PrrB/A, FnrL and AppA/PpsR systems. The PrrB/A and FnrL systems activate the expression of them under anaerobic conditions while the AppA/PpsR system represses them under aerobic conditions. Recently, two mathematical models have been developed for the AppA/PpsR system and demonstrated how the interaction between AppA and PpsR could lead to a phenotype in which PS genes are repressed under semi-aerobic conditions. These models have also predicted that the transition from aerobic to anaerobic growth mode could occur via a bistable regime. However, they lack experimentally quantifiable inputs and outputs. Here, we extend one of them to include such quantities and combine all relevant micro-array data publically available for a PS gene of this bacterium and use that to parameterise the model. In addition, we hypothesise that the AppA/PpsR system alone might account for the observed trend of PS gene expression under semi-aerobic conditions. Results Our extended model of the AppA/PpsR system includes the biological input of atmospheric oxygen concentration and an output of photosynthetic gene expression. Following our hypothesis that the AppA/PpsR system alone is sufficient to describe the overall trend of PS gene expression we parameterise the model and suggest that the rate of AppA reduction in vivo should be faster than its oxidation. Also, we show that despite both the reduced and oxidised forms of PpsR binding to the PS gene promoters in vitro, binding of the oxidised form as a repressor alone is sufficient to reproduce the observed PS gene expression pattern. Finally, the combination of model parameters which fit the biological data well are broadly consistent with those which were previously determined to be required for the system to show (i) the repression of PS genes under semi-aerobic conditions, and (ii) bistability. Conclusion We found that despite at least three pathways being involved in the regulation of photosynthetic genes, the AppA/PpsR system alone is capable of accounting for the observed trends in photosynthetic gene expression seen at different oxygen levels. Electronic supplementary material The online version of this article (10.1186/s12918-017-0489-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Rakesh Pandey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK. .,Present Address: National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India.
| | - Judith P Armitage
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | - George H Wadhams
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK.
| |
Collapse
|
8
|
Absence of the cbb3 Terminal Oxidase Reveals an Active Oxygen-Dependent Cyclase Involved in Bacteriochlorophyll Biosynthesis in Rhodobacter sphaeroides. J Bacteriol 2016; 198:2056-63. [PMID: 27215788 PMCID: PMC4944227 DOI: 10.1128/jb.00121-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/13/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The characteristic green color associated with chlorophyll pigments results from the formation of an isocyclic fifth ring on the tetrapyrrole macrocycle during the biosynthesis of these important molecules. This reaction is catalyzed by two unrelated cyclase enzymes employing different chemistries. Oxygenic phototrophs such as plants and cyanobacteria utilize an oxygen-dependent enzyme, the major component of which is a diiron protein named AcsF, while BchE, an oxygen-sensitive [4Fe-4S] cluster protein, dominates in phototrophs inhabiting anoxic environments, such as the purple phototrophic bacterium Rhodobacter sphaeroides We identify a potential acsF in this organism and assay for activity of the encoded protein in a strain lacking bchE under various aeration regimes. Initially, cells lacking bchE did not demonstrate AcsF activity under any condition tested. However, on removal of a gene encoding a subunit of the cbb3-type respiratory terminal oxidase, cells cultured under regimes ranging from oxic to micro-oxic exhibited cyclase activity, confirming the activity of the oxygen-dependent enzyme in this model organism. Potential reasons for the utilization of an oxygen-dependent enzyme in anoxygenic phototrophs are discussed. IMPORTANCE The formation of the E ring of bacteriochlorophyll pigments is the least well characterized step in their biosynthesis, remaining enigmatic for over 60 years. Two unrelated enzymes catalyze this cyclization step; O2-dependent and O2-independent forms dominate in oxygenic and anoxygenic phototrophs, respectively. We uncover the activity of an O2-dependent enzyme in the anoxygenic purple phototrophic bacterium Rhodobacter sphaeroides, initially by inactivation of the high-affinity terminal respiratory oxidase, cytochrome cbb3 We propose that the O2-dependent form allows for the biosynthesis of a low level of bacteriochlorophyll under oxic conditions, so that a rapid initiation of photosynthetic processes is possible for this bacterium upon a reduction of oxygen tension.
Collapse
|
9
|
Kis M, Sipka G, Asztalos E, Rázga Z, Maróti P. Purple non-sulfur photosynthetic bacteria monitor environmental stresses. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 151:110-7. [PMID: 26232748 DOI: 10.1016/j.jphotobiol.2015.07.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/21/2015] [Accepted: 07/23/2015] [Indexed: 11/19/2022]
Abstract
Heavy metal ion pollution and oxygen deficiency are major environmental risks for microorganisms in aqueous habitat. The potential of purple non-sulfur photosynthetic bacteria for biomonitoring and bioremediation was assessed by investigating the photosynthetic capacity in heavy metal contaminated environments. Cultures of bacterial strains Rhodobacter sphaeroides, Rhodospirillum rubrum and Rubrivivax gelatinosus were treated with heavy metal ions in micromolar (Hg(2+)), submillimolar (Cr(6+)) and millimolar (Pb(2+)) concentration ranges. Functional assays (flash-induced absorption changes and bacteriochlorophyll fluorescence induction) and electron micrographs were taken to specify the harmful effects of pollution and to correlate to morphological changes of the membrane. The bacterial strains and functional tests showed differentiated responses to environmental stresses, revealing that diverse mechanisms of tolerance and/or resistance are involved. The microorganisms were vulnerable to the prompt effect of Pb(2+), showed weak tolerance to Hg(2+) and proved to be tolerant to Cr(6+). The reaction center controlled electron transfer in Rvx. gelatinosus demonstrated the highest degree of resistance against heavy metal exposure.
Collapse
Affiliation(s)
- Mariann Kis
- Department of Medical Physics, University of Szeged, Hungary
| | - Gábor Sipka
- Department of Medical Physics, University of Szeged, Hungary
| | - Emese Asztalos
- Department of Medical Physics, University of Szeged, Hungary
| | - Zsolt Rázga
- Department of Pathology, University of Szeged, Hungary
| | - Péter Maróti
- Department of Medical Physics, University of Szeged, Hungary.
| |
Collapse
|
10
|
Leneveu-Jenvrin C, Connil N, Bouffartigues E, Papadopoulos V, Feuilloley MGJ, Chevalier S. Structure-to-function relationships of bacterial translocator protein (TSPO): a focus on Pseudomonas. Front Microbiol 2014; 5:631. [PMID: 25477872 PMCID: PMC4237140 DOI: 10.3389/fmicb.2014.00631] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 11/04/2014] [Indexed: 12/21/2022] Open
Abstract
The translocator protein (TSPO), which was previously designated as the peripheral-type benzodiazepine receptor, is a 3.5 billion year-old evolutionarily conserved protein expressed by most Eukarya, Archae and Bacteria, but its organization and functions differ remarkably. By taking advantage of the genomic data available on TSPO, we focused on bacterial TSPO and attempted to define functions of TSPO in Pseudomonas via in silico approaches. A tspo ortholog has been identified in several fluorescent Pseudomonas. This protein presents putative binding motifs for cholesterol and PK 11195, which is a specific drug ligand of mitochondrial TSPO. While it is a common surface distribution, the sense of insertion and membrane localization differ between α- and γ-proteobacteria. Experimental published data and STRING analysis of common TSPO partners in fluorescent Pseudomonas indicate a potential role of TSPO in the oxidative stress response, iron homeostasis and virulence expression. In these bacteria, TSPO could also take part in signal transduction and in the preservation of membrane integrity.
Collapse
Affiliation(s)
- Charlène Leneveu-Jenvrin
- Laboratory of Microbiology Signals and Microenvironment EA 4312, University of Rouen Evreux, France
| | - Nathalie Connil
- Laboratory of Microbiology Signals and Microenvironment EA 4312, University of Rouen Evreux, France
| | - Emeline Bouffartigues
- Laboratory of Microbiology Signals and Microenvironment EA 4312, University of Rouen Evreux, France
| | - Vassilios Papadopoulos
- Department of Medicine, Research Institute of the McGill University Health Centre, McGill University Montreal, QC, Canada
| | - Marc G J Feuilloley
- Laboratory of Microbiology Signals and Microenvironment EA 4312, University of Rouen Evreux, France
| | - Sylvie Chevalier
- Laboratory of Microbiology Signals and Microenvironment EA 4312, University of Rouen Evreux, France
| |
Collapse
|
11
|
The terminal oxidase cbb3 functions in redox control of magnetite biomineralization in Magnetospirillum gryphiswaldense. J Bacteriol 2014; 196:2552-62. [PMID: 24794567 DOI: 10.1128/jb.01652-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The biomineralization of magnetosomes in Magnetospirillum gryphiswaldense and other magnetotactic bacteria occurs only under suboxic conditions. However, the mechanism of oxygen regulation and redox control of biosynthesis of the mixed-valence iron oxide magnetite [FeII(FeIII)2O4] is still unclear. Here, we set out to investigate the role of aerobic respiration in both energy metabolism and magnetite biomineralization of M. gryphiswaldense. Although three operons encoding putative terminal cbb3-type, aa3-type, and bd-type oxidases were identified in the genome assembly of M. gryphiswaldense, genetic and biochemical analyses revealed that only cbb3 and bd are required for oxygen respiration, whereas aa3 had no physiological significance under the tested conditions. While the loss of bd had no effects on growth and magnetosome synthesis, inactivation of cbb3 caused pleiotropic effects under microaerobic conditions in the presence of nitrate. In addition to their incapability of simultaneous nitrate and oxygen reduction, cbb3-deficient cells had complex magnetosome phenotypes and aberrant morphologies, probably by disturbing the redox balance required for proper growth and magnetite biomineralization. Altogether, besides being the primary terminal oxidase for aerobic respiration, cbb3 oxidase may serve as an oxygen sensor and have a further role in poising proper redox conditions required for magnetite biomineralization.
Collapse
|
12
|
Sevilla E, Silva-Jiménez H, Duque E, Krell T, Rojo F. The Pseudomonas putida HskA hybrid sensor kinase controls the composition of the electron transport chain. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:291-300. [PMID: 23584971 DOI: 10.1111/1758-2229.12017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 11/13/2012] [Indexed: 06/02/2023]
Abstract
Sensor kinases play a key role in sensing and responding to environmental and physiological signals in bacteria. In this study we characterized a previously unknown orphan hybrid sensor kinase from Pseudomonas putida, which is conserved in several Pseudomonads. Inactivation of the gene coding for this sensor kinase, which we have named HskA, modified the expression of at least 85 genes in cells growing in a complete medium. HskA showed a strong influence on the composition of the electron transport chain. In cells growing exponentially in a complete medium, the absence of HskA led to a significant reduction in the expression of the genes coding for the bc1 complex and for the CIO and Cbb3-1 terminal oxidases. In stationary phase cells, however, lack of HskA caused a higher expression of the Cyo terminal oxidase and a lower expression of the Aa3 terminal oxidase. The HskA polypeptide shows two PAS (signal-sensing) domains, a transmitter domain containing the invariant phosphorylatable histidine and an ATP binding site, and a receiver domain containing the conserved aspartate capable of transphosphorylation, but lacks an Hpt module. It is therefore a hybrid sensor kinase. Phosphorylation assays showed that purified HskA undergoes autophosphorylation in the presence of ATP.
Collapse
Affiliation(s)
- Emma Sevilla
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Campus UAM, Cantoblanco, 28049 Madrid, Spain
| | | | | | | | | |
Collapse
|
13
|
Carius L, Hädicke O, Grammel H. Stepwise reduction of the culture redox potential allows the analysis of microaerobic metabolism and photosynthetic membrane synthesis inRhodospirillum rubrum. Biotechnol Bioeng 2012; 110:573-85. [DOI: 10.1002/bit.24734] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 08/29/2012] [Accepted: 09/21/2012] [Indexed: 11/09/2022]
|
14
|
|
15
|
Abstract
Denitrification is generally considered to occur under micro-oxic or anoxic conditions. With this in mind, the physiological function and regulation of several steps in the denitrification of model α-proteobacteria are compared in the present review. Expression of the periplasmic nitrate reductase is quite variable, with this enzyme being maximally expressed under oxic conditions in some bacteria, but under micro-oxic conditions in others. Expression of nitrite and NO reductases in most denitrifiers is more tightly controlled, with expression only occurring under micro-oxic conditions. A possible exception to this may be Roseobacter denitrificans, but the physiological role of these enzymes under oxic conditions is uncertain.
Collapse
|
16
|
Hassani BK, Steunou AS, Liotenberg S, Reiss-Husson F, Astier C, Ouchane S. Adaptation to oxygen: role of terminal oxidases in photosynthesis initiation in the purple photosynthetic bacterium, Rubrivivax gelatinosus. J Biol Chem 2010; 285:19891-9. [PMID: 20335164 DOI: 10.1074/jbc.m109.086066] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The appearance of oxygen in the Earth's atmosphere via oxygenic photosynthesis required strict anaerobes and obligate phototrophs to cope with the presence of this toxic molecule. Here we show that in the anoxygenic phototroph Rubrivivax gelatinosus, the terminal oxidases (cbb(3), bd, and caa(3)) expand the range of ambient oxygen tensions under which the organism can initiate photosynthesis. Unlike the wild type, the cbb(3)(-)/bd(-) double mutant can start photosynthesis only in deoxygenated medium or when oxygen is removed, either by sparging cultures with nitrogen or by co-inoculation with strict aerobes bacteria. In oxygenated environments, this mutant survives nonphotosynthetically until the O(2) tension is reduced. The cbb(3) and bd oxidases are therefore required not only for respiration but also for reduction of the environmental O(2) pressure prior to anaerobic photosynthesis. Suppressor mutations that restore respiration simultaneously restore photosynthesis in nondeoxygenated medium. Furthermore, induction of photosystem in the cbb(3)(-) mutant led to a highly unstable strain. These results demonstrate that photosynthetic metabolism in environments exposed to oxygen is critically dependent on the O(2)-detoxifying action of terminal oxidases.
Collapse
Affiliation(s)
- Bahia Khalfaoui Hassani
- CNRS, Centre de Génétique Moléculaire, F-91198 Gif-sur-Yvette, the Université Paris-Sud, F-91405 Orsay, France
| | | | | | | | | | | |
Collapse
|
17
|
Rojo F. Carbon catabolite repression in Pseudomonas : optimizing metabolic versatility and interactions with the environment. FEMS Microbiol Rev 2010; 34:658-84. [PMID: 20412307 DOI: 10.1111/j.1574-6976.2010.00218.x] [Citation(s) in RCA: 332] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Metabolically versatile free-living bacteria have global regulation systems that allow cells to selectively assimilate a preferred compound among a mixture of several potential carbon sources. This process is known as carbon catabolite repression (CCR). CCR optimizes metabolism, improving the ability of bacteria to compete in their natural habitats. This review summarizes the regulatory mechanisms responsible for CCR in the bacteria of the genus Pseudomonas, which can live in many different habitats. Although the information available is still limited, the molecular mechanisms responsible for CCR in Pseudomonas are clearly different from those of Enterobacteriaceae or Firmicutes. An understanding of the molecular mechanisms underlying CCR is important to know how metabolism is regulated and how bacteria degrade compounds in the environment. This is particularly relevant for compounds that are degraded slowly and accumulate, creating environmental problems. CCR has a major impact on the genes involved in the transport and metabolism of nonpreferred carbon sources, but also affects the expression of virulence factors in several bacterial species, genes that are frequently directed to allow the bacterium to gain access to new sources of nutrients. Finally, CCR has implications in the optimization of biotechnological processes such as biotransformations or bioremediation strategies.
Collapse
Affiliation(s)
- Fernando Rojo
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Madrid, Spain.
| |
Collapse
|
18
|
Todorovic S, Verissimo A, Wisitruangsakul N, Zebger I, Hildebrandt P, Pereira MM, Teixeira M, Murgida DH. SERR-spectroelectrochemical study of a cbb3 oxygen reductase in a biomimetic construct. J Phys Chem B 2009; 112:16952-9. [PMID: 19053671 DOI: 10.1021/jp807862m] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cbb3 oxygen reductase from Bradyrhizobium japonicum was immobilized on nanostructured silver electrodes by anchoring the enzyme via a His-tag to a Ni-NTA coating, followed by reconstitution of a lipid bilayer. The immobilized enzyme retains the native structure and catalytic activity as judged by in situ surface-enhanced vibrational spectroscopy and cyclic voltammetry, respectively. Spectroelectrochemical titrations followed by SERR spectroscopy of the integral enzyme and its monohemic (fixO) and dihemic subunits (fixP), allowed the determination of the reduction potentials for the different heme c groups. Both in the isolated subunits and in the integral enzyme the Met/His-coordinated hemes from the two subunits present identical reduction potentials of 180 mV, whereas for the bis-His heme from fixP the value is ca. 400 mV. The determination of reduction potentials of the individual hemes c reported in this work provides the basis for further exploring the mechanism of electroprotonic energy transduction of this complex enzyme.
Collapse
Affiliation(s)
- Smilja Todorovic
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, EAN, 2780-157 Oeiras, Portugal.
| | | | | | | | | | | | | | | |
Collapse
|
19
|
RegB/RegA, A Global Redox-Responding Two-Component System. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008; 631:131-48. [DOI: 10.1007/978-0-387-78885-2_9] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
20
|
The use of chromatin immunoprecipitation to define PpsR binding activity in Rhodobacter sphaeroides 2.4.1. J Bacteriol 2008; 190:6817-28. [PMID: 18689484 DOI: 10.1128/jb.00719-08] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The expression of genes involved in photosystem development in Rhodobacter sphaeroides is dependent upon three major regulatory networks: FnrL, the PrrBA (RegBA) two-component system, and the transcriptional repressor/antirepressor PpsR/AppA. Of the three regulators, PpsR appears to have the narrowest range of physiological effects, which are limited to effects on the structural and pigment biosynthetic activities involved in photosynthetic membrane function. Although a PrrA(-) mutant is unable to grow under photosynthetic conditions, when a ppsR mutation was present, photosynthetic growth occurred. An examination of the double mutant under anaerobic-dark-dimethyl sulfoxide conditions using microarray analysis revealed the existence of an "extended" PpsR regulon and new physiological roles. To characterize the PpsR regulon and to better ascertain the significance of degeneracy within the PpsR binding sequence in vivo, we adapted the chromatin immunoprecipitation technique to R. sphaeroides. We demonstrated that in vivo there was direct and significant binding by PpsR to newly identified genes involved in microaerobic respiration and periplasmic stress resistance, as well as to photosynthesis genes. The new members of the PpsR regulon are located outside the photosynthesis gene cluster and have degenerate PpsR binding sequences. The possible interaction under physiologic conditions with degenerate binding sequences in the presence of other biologically relevant molecules is discussed with respect to its importance in physiological processes and to the existence of complex phenotypes associated with regulatory mutants. This study further defines the DNA structure necessary for PpsR binding in situ.
Collapse
|
21
|
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.
Collapse
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
| | | |
Collapse
|
22
|
Stability of the cbb3-type cytochrome oxidase requires specific CcoQ-CcoP interactions. J Bacteriol 2008; 190:5576-86. [PMID: 18556791 DOI: 10.1128/jb.00534-08] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cytochrome cbb(3)-type oxidases are members of the heme copper oxidase superfamily and are composed of four subunits. CcoN contains the heme b-Cu(B) binuclear center where oxygen is reduced, while CcoP and CcoO are membrane-bound c-type cytochromes thought to channel electrons from the donor cytochrome into the binuclear center. Like many other bacterial members of this superfamily, the cytochrome cbb(3)-type oxidase contains a fourth, non-cofactor-containing subunit, which is termed CcoQ. In the present study, we analyzed the role of CcoQ on the stability and activity of Rhodobacter capsulatus cbb(3)-type oxidase. Our data showed that CcoQ is a single-spanning membrane protein with a N(out)-C(in) topology. In the absence of CcoQ, cbb(3)-type oxidase activity is significantly reduced, irrespective of the growth conditions. Blue native polyacrylamide gel electrophoresis analyses revealed that the lack of CcoQ specifically impaired the stable recruitment of CcoP into the cbb(3)-type oxidase complex. This suggested a specific CcoQ-CcoP interaction, which was confirmed by chemical cross-linking. Collectively, our data demonstrated that in R. capsulatus CcoQ was required for optimal cbb(3)-type oxidase activity because it stabilized the interaction of CcoP with the CcoNO core complex, leading subsequently to the formation of the active 230-kDa cbb(3)-type oxidase complex.
Collapse
|
23
|
Role of the global transcriptional regulator PrrA in Rhodobacter sphaeroides 2.4.1: combined transcriptome and proteome analysis. J Bacteriol 2008; 190:4831-48. [PMID: 18487335 DOI: 10.1128/jb.00301-08] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The PrrBA two-component regulatory system is a major global regulator in Rhodobacter sphaeroides 2.4.1. Here we have compared the transcriptome and proteome profiles of the wild-type (WT) and mutant PrrA2 cells grown anaerobically in the dark with dimethyl sulfoxide as an electron acceptor. Approximately 25% of the genes present in the PrrA2 genome are regulated by PrrA at the transcriptional level, either directly or indirectly, by twofold or more relative to the WT. The genes affected are widespread throughout all COG (cluster of orthologous group) functional categories, with previously unsuspected "metabolic" genes affected in PrrA2 cells. PrrA was found to act as both an activator and a repressor of transcription, with more genes being repressed in the presence of PrrA (9:5 ratio). An analysis of the genes encoding the 1,536 peptides detected through our chromatographic study, which corresponds to 36% coverage of the genome, revealed that approximately 20% of the genes encoding these proteins were positively regulated, whereas approximately 32% were negatively regulated by PrrA, which is in excellent agreement with the percentages obtained for the whole-genome transcriptome profile. In addition, comparison of the transcriptome and proteome mean parameter values for WT and PrrA2 cells showed good qualitative agreement, indicating that transcript regulation paralleled the corresponding protein abundance, although not one for one. The microarray analysis was validated by direct mRNA measurement of randomly selected genes that were both positively and negatively regulated. lacZ transcriptional and kan translational fusions enabled us to map putative PrrA binding sites and revealed potential gene targets for indirect regulation by PrrA.
Collapse
|
24
|
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.
Collapse
Affiliation(s)
- Steffen Klamt
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.
| | | | | | | | | |
Collapse
|
25
|
Mackenzie C, Eraso JM, Choudhary M, Roh JH, Zeng X, Bruscella P, Puskás A, Kaplan S. Postgenomic adventures with Rhodobacter sphaeroides. Annu Rev Microbiol 2007; 61:283-307. [PMID: 17506668 DOI: 10.1146/annurev.micro.61.080706.093402] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This review describes some of the recent highlights taken from the studies of Rhodobacter sphaeroides 2.4.1. The review is not intended to be comprehensive, but to reflect the bias of the authors as to how the availability of a sequenced and annotated genome, a gene-chip, and proteomic profile as well as comparative genomic analyses can direct the progress of future research in this system.
Collapse
Affiliation(s)
- Chris Mackenzie
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas 77030, USA.
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Kim EJ, Kim JS, Lee IH, Rhee HJ, Lee JK. Superoxide generation by chlorophyllide a reductase of Rhodobacter sphaeroides. J Biol Chem 2007; 283:3718-30. [PMID: 18079120 DOI: 10.1074/jbc.m707774200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Chlorophyllide a reductase of Rhodobacter sphaeroides, which were reconstituted with the purified subunits of BchX, BchY, and BchZ, reduced ring B of chlorophyllide a using NADH under anaerobic conditions. Interestingly, suppressor mutations rescuing the inability of R. sphaeroides Fe-SOD mutant to grow in succinate-based minimal medium were predominantly mapped to BchZ subunit of chlorophyllide a reductase. The enzyme is labile in the presence of O(2). However, it generates superoxide at low O(2). The enzymes reconstituted with BchX, BchY, and the mutein subunit of BchZ from suppressor mutants showed less activity not only for chlorophyllide a reduction but also for superoxide generation compared with the enzyme reconstituted with the wild-type subunits. BchX, which contains FMN, and BchY are iron-sulfur proteins, whereas BchZ is a hemoprotein containing b-type heme. Neither chlorophyllide a reduction nor superoxide generation was observed with the enzyme reconstituted with the wild-type subunits of BchX and BchY, and the apo-subunit of BchZ that had been refolded without heme, in which FMN of BchX was fully reduced. Thus, superoxide is generated not from FMN of BchX but from heme of BchZ. Consistently, the heme of BchZ muteins was half-reduced in its redox state compared with that of wild-type BchZ.
Collapse
Affiliation(s)
- Eui-Jin Kim
- Department of Life Science and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul 121-742, Korea
| | | | | | | | | |
Collapse
|
27
|
Han Y, Meyer MHF, Keusgen M, Klug G. A haem cofactor is required for redox and light signalling by the AppA protein of Rhodobacter sphaeroides. Mol Microbiol 2007; 64:1090-104. [PMID: 17501930 DOI: 10.1111/j.1365-2958.2007.05724.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The AppA protein of Rhodobacter sphaeroides is unique in its ability to sense and transmit redox signals as well as light signals. By functioning as antagonist to the PpsR transcriptional repressor, it regulates the expression of photosynthesis genes in response to these environmental stimuli. Here we show binding of the cofactor haem to a domain in the C-terminal part of AppA and redox activity of bound haem. This is supported by the findings that: (i) the C-terminal domain of AppA (AppADeltaN) binds to haemin agarose, (ii) AppADeltaN isolated from Escherichia coli shows absorbance at 411 nm and absorbances at 424 nm and 556 nm after reduction with dithionite and (iii) AppADeltaN can be reconstituted with haem in vitro. Expression of AppA variants in R. sphaeroides reveals that the haem binding domain is important for normal expression levels of photosynthesis genes and for normal light regulation in the presence of oxygen. The haem cofactor affects the interaction of the C-terminal part of AppA to PpsR but also its interaction to the N-terminal light sensing AppA-BLUF domain. Based on this we present a model for the transmission of light and redox signals by AppA.
Collapse
Affiliation(s)
- Yuchen Han
- Institut für Mikrobiologie und Molekularbiologie, University of Giessen, D-35392 Giessen, Germany
| | | | | | | |
Collapse
|
28
|
Transcriptome dynamics during the transition from anaerobic photosynthesis to aerobic respiration in Rhodobacter sphaeroides 2.4.1. J Bacteriol 2007; 190:286-99. [PMID: 17965166 DOI: 10.1128/jb.01375-07] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhodobacter sphaeroides 2.4.1 is a facultative photosynthetic anaerobe that grows by anoxygenic photosynthesis under anaerobic-light conditions. Changes in energy generation pathways under photosynthetic and aerobic respiratory conditions are primarily controlled by oxygen tensions. In this study, we performed time series microarray analyses to investigate transcriptome dynamics during the transition from anaerobic photosynthesis to aerobic respiration. Major changes in gene expression profiles occurred in the initial 15 min after the shift from anaerobic-light to aerobic-dark conditions, with changes continuing to occur up to 4 hours postshift. Those genes whose expression levels changed significantly during the time series were grouped into three major classes by clustering analysis. Class I contained genes, such as that for the aa3 cytochrome oxidase, whose expression levels increased after the shift. Class II contained genes, such as those for the photosynthetic apparatus and Calvin cycle enzymes, whose expression levels decreased after the shift. Class III contained genes whose expression levels temporarily increased during the time series. Many genes for metabolism and transport of carbohydrates or lipids were significantly induced early during the transition, suggesting that those endogenous compounds were initially utilized as carbon sources. Oxidation of those compounds might also be required for maintenance of redox homeostasis after exposure to oxygen. Genes for the repair of protein and sulfur groups and uptake of ferric iron were temporarily upregulated soon after the shift, suggesting they were involved in a response to oxidative stress. The flagellar-biosynthesis genes were expressed in a hierarchical manner at 15 to 60 min after the shift. Numerous transporters were induced at various time points, suggesting that the cellular composition went through significant changes during the transition from anaerobic photosynthesis to aerobic respiration. Analyses of these data make it clear that numerous regulatory activities come into play during the transition from one homeostatic state to another.
Collapse
|
29
|
Zeng X, Roh JH, Callister SJ, Tavano CL, Donohue TJ, Lipton MS, Kaplan S. Proteomic characterization of the Rhodobacter sphaeroides 2.4.1 photosynthetic membrane: identification of new proteins. J Bacteriol 2007; 189:7464-74. [PMID: 17704227 PMCID: PMC2168454 DOI: 10.1128/jb.00946-07] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Rhodobacter sphaeroides intracytoplasmic membrane (ICM) is an inducible membrane that is dedicated to the major events of bacterial photosynthesis, including harvesting light energy, separating primary charges, and transporting electrons. In this study, multichromatographic methods coupled with Fourier transform ion cyclotron resonance mass spectrometry, combined with subcellular fractionation, was used to test the hypothesis that the photosynthetic membrane of R. sphaeroides 2.4.1 contains a significant number of heretofore unidentified proteins in addition to the integral membrane pigment-protein complexes, including light-harvesting complexes 1 and 2, the photochemical reaction center, and the cytochrome bc(1) complex described previously. Purified ICM vesicles are shown to be enriched in several abundant, newly identified membrane proteins, including a protein of unknown function (AffyChip designation RSP1760) and a possible alkane hydroxylase (RSP1467). When the genes encoding these proteins are mutated, specific photosynthetic phenotypes are noted, illustrating the potential new insights into solar energy utilization to be gained by this proteomic blueprint of the ICM. In addition, proteins necessary for other cellular functions, such as ATP synthesis, respiration, solute transport, protein translocation, and other physiological processes, were also identified to be in association with the ICM. This study is the first to provide a more global view of the protein composition of a photosynthetic membrane from any source. This protein blueprint also provides insights into potential mechanisms for the assembly of the pigment-protein complexes of the photosynthetic apparatus, the formation of the lipid bilayer that houses these integral membrane proteins, and the possible functional interactions of ICM proteins with activities that reside in domains outside this specialized bioenergetic membrane.
Collapse
Affiliation(s)
- Xiaohua Zeng
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston TX, 77030, USA
| | | | | | | | | | | | | |
Collapse
|
30
|
Kim YJ, Ko IJ, Lee JM, Kang HY, Kim YM, Kaplan S, Oh JI. Dominant role of the cbb3 oxidase in regulation of photosynthesis gene expression through the PrrBA system in Rhodobacter sphaeroides 2.4.1. J Bacteriol 2007; 189:5617-25. [PMID: 17557830 PMCID: PMC1951837 DOI: 10.1128/jb.00443-07] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, the H303A mutant form of the cbb(3) oxidase (H303A oxidase), which has the H303A mutation in its catalytic subunit (CcoN), was purified from Rhodobacter sphaeroides. The H303A oxidase showed the same catalytic activity as did the wild-type form of the oxidase (WT oxidase). The heme contents of the mutant and WT forms of the cbb(3) oxidase were also comparable. However, the puf and puc operons, which are under the control of the PrrBA two-component system, were shown to be derepressed aerobically in the R. sphaeroides strain expressing the H303A oxidase. Since the strain harboring the H303A oxidase exhibited the same cytochrome c oxidase activity as the stain harboring the WT oxidase did, the aerobic derepression of photosynthesis gene expression observed in the H303A mutant appears to be the result of a defective signaling function of the H303A oxidase rather than reflecting any redox changes in the ubiquinone/ubiquinol pool. It was also demonstrated that ubiquinone inhibits not only the autokinase activity of full-length PrrB but also that of the truncated form of PrrB lacking its transmembrane domain, including the proposed quinone binding sequence. These results imply that the suggested ubiquinone binding site within the PrrB transmembrane domain is not necessary for the inhibition of PrrB kinase activity by ubiquinone. Instead, it is probable that signaling through H303 of the CcoN subunit of the cbb(3) oxidase is part of the pathway through which the cbb(3) oxidase affects the relative kinase/phosphatase activity of the membrane-bound PrrB.
Collapse
Affiliation(s)
- Yong-Jin Kim
- Department of Microbiology, Pusan National University, 30 Jangjeon-dong, Geumjeong-gu, 609-735 Busan, Korea
| | | | | | | | | | | | | |
Collapse
|
31
|
Laan W, Horst MA, Van Stokkum IH, Hellingwerf KJ. Initial Characterization of the Primary Photochemistry of AppA, a Blue-light-using Flavin Adenine Dinucleotide-domain Containing Transcriptional Antirepressor Protein from Rhodobacter sphaeroides: A Key Role for Reversible Intramolecular Proton Transfer f. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2003)0780290icotpp2.0.co2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
32
|
Jäger A, Braatsch S, Haberzettl K, Metz S, Osterloh L, Han Y, Klug G. The AppA and PpsR proteins from Rhodobacter sphaeroides can establish a redox-dependent signal chain but fail to transmit blue-light signals in other bacteria. J Bacteriol 2007; 189:2274-82. [PMID: 17209035 PMCID: PMC1899404 DOI: 10.1128/jb.01699-06] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The AppA protein of Rhodobacter sphaeroides has the unique ability to sense and transmit redox and light signals. In response to decreasing oxygen tension, AppA antagonizes the transcriptional regulator PpsR, which represses the expression of photosynthesis genes, including the puc operon. This mechanism, which is based on direct protein-protein interaction, is prevented by blue-light absorption of the BLUF domain located in the N-terminal part of AppA. In order to test whether AppA and PpsR are sufficient to transmit redox and light signals, we expressed these proteins in three different bacterial species and monitored oxygen- and blue-light-dependent puc expression either directly or by using a luciferase-based reporter construct. The AppA/PpsR system could mediate redox-dependent gene expression in the alphaproteobacteria Rhodobacter capsulatus and Paracoccus denitrificans but not in the gammaproteobacterium Escherichia coli. Analysis of a prrA mutant strain of R. sphaeroides strongly suggests that light-dependent gene expression requires a balanced interplay of the AppA/PpsR system with the PrrA response regulator. Therefore, the AppA/PpsR system was unable to establish light signaling in other bacteria. Based on our data, we present a model for the interdependence of AppA/PpsR signaling and the PrrA transcriptional activator.
Collapse
Affiliation(s)
- Andreas Jäger
- Institut für Mikrobiologie und Molekularbiologie, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | | | | | | | | | | | | |
Collapse
|
33
|
Williams HD, Zlosnik JEA, Ryall B. Oxygen, cyanide and energy generation in the cystic fibrosis pathogen Pseudomonas aeruginosa. Adv Microb Physiol 2006; 52:1-71. [PMID: 17027370 DOI: 10.1016/s0065-2911(06)52001-6] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pseudomonas aeruginosa is a gram-negative, rod-shaped bacterium that belongs to the gamma-proteobacteria. This clinically challenging, opportunistic pathogen occupies a wide range of niches from an almost ubiquitous environmental presence to causing infections in a wide range of animals and plants. P. aeruginosa is the single most important pathogen of the cystic fibrosis (CF) lung. It causes serious chronic infections following its colonisation of the dehydrated mucus of the CF lung, leading to it being the most important cause of morbidity and mortality in CF sufferers. The recent finding that steep O2 gradients exist across the mucus of the CF-lung indicates that P. aeruginosa will have to show metabolic adaptability to modify its energy metabolism as it moves from a high O2 to low O2 and on to anaerobic environments within the CF lung. Therefore, the starting point of this review is that an understanding of the diverse modes of energy metabolism available to P. aeruginosa and their regulation is important to understanding both its fundamental physiology and the factors significant in its pathogenicity. The main aim of this review is to appraise the current state of knowledge of the energy generating pathways of P. aeruginosa. We first look at the organisation of the aerobic respiratory chains of P. aeruginosa, focusing on the multiple primary dehydrogenases and terminal oxidases that make up the highly branched pathways. Next, we will discuss the denitrification pathways used during anaerobic respiration as well as considering the ability of P. aeruginosa to carry out aerobic denitrification. Attention is then directed to the limited fermentative capacity of P. aeruginosa with discussion of the arginine deiminase pathway and the role of pyruvate fermentation. In the final part of the review, we consider other aspects of the biology of P. aeruginosa that are linked to energy metabolism or affected by oxygen availability. These include cyanide synthesis, which is oxygen-regulated and can affect the operation of aerobic respiratory pathways, and alginate production leading to a mucoid phenotype, which is regulated by oxygen and energy availability, as well as having a role in the protection of P. aeruginosa against reactive oxygen species. Finally, we consider a possible link between cyanide synthesis and the mucoid switch that operates in P. aeruginosa during chronic CF lung infection.
Collapse
Affiliation(s)
- Huw D Williams
- Division of Biology, Faculty of Natural Sciences, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, UK
| | | | | |
Collapse
|
34
|
Ouchane S, Picaud M, Therizols P, Reiss-Husson F, Astier C. Global regulation of photosynthesis and respiration by FnrL: the first two targets in the tetrapyrrole pathway. J Biol Chem 2006; 282:7690-9. [PMID: 17178720 DOI: 10.1074/jbc.m605985200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Fnr is a regulator that controls the expression of a variety of genes in response to oxygen limitation in bacteria. To assess the role of Fnr in photosynthesis in Rubrivivax gelatinosus, a strain carrying a null mutation in fnrL was constructed. It was unable to grow anaerobically in the light, but, intriguingly, it was able to produce photosynthetic complexes under high oxygenation conditions. The mutant lacked all c-type cytochromes normally detectable in microaerobically-grown wild type cells and accumulated coproporphyrin III. These data suggested that the pleiotropic phenotype observed in FNR is primarily due to the control at the level of the HemN oxygen-independent coproporphyrinogen III dehydrogenase. hemN expression in trans partially suppressed the FNR phenotype, as it rescued heme and cytochrome syntheses. Nevertheless, these cells were photosynthetically deficient, and pigment analyses showed that they were blocked at the level of Mg(2+)-protoporphyrin monomethyl ester. Expression of both hemN and bchE in the FNR mutant restored synthesis of Mg(2+)-protochlorophyllide. We, therefore, conclude that FnrL controls respiration by regulating hemN expression and controls photosynthesis by regulating both hemN and bchE expression. A comprehensive picture of the control points of microaerobic respiration and photosynthesis by FnrL is provided, and the prominent role of this factor in activating alternative gene programs after reduction of oxygen tension in facultative aerobes is discussed.
Collapse
Affiliation(s)
- Soufian Ouchane
- Centre de Génétique Moléculaire CNRS (UPR-2167) Associéà l'Université Pierre et Marie Curie et Paris XI, Bâtiment 26, Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France.
| | | | | | | | | |
Collapse
|
35
|
Montecchia MS, Pucheu NL, Kerber NL, García AF. Oxygen and light effects on the expression of the photosynthetic apparatus in Bradyrhizobium sp. C7T1 strain. PHOTOSYNTHESIS RESEARCH 2006; 90:215-22. [PMID: 17279441 DOI: 10.1007/s11120-007-9129-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Accepted: 12/29/2006] [Indexed: 05/13/2023]
Abstract
Photosynthetic bradyrhizobia are nitrogen-fixing symbionts colonizing the stem and roots of some leguminous plants like Aeschynomene. The effect of oxygen and light on the formation of the photosynthetic apparatus of Bradyrhizobium sp. C7T1 strain is described here. Oxygen is required for growth, but at high concentration inhibits the synthesis of bacteriochlorophyll (BChl) and of the photosynthetic apparatus. However, we show that in vitro, aerobic photosynthetic electron transport occurred leading to ADP photophosphorylation. The expression of the photosynthetic apparatus was regulated by oxygen in a manner which did not agree with earlier results in other photosynthetic bradyrhizobia since BChl accumulation was the highest under microaerobic conditions. This strain produces photosynthetic pigments when grown under cyclic illumination or darkness. However, under continuous white light illumination, a Northern blot analysis of the puf operon showed that, the expression of the photosynthetic genes of the antenna was considerable. Under latter conditions BChl accumulation in the cells was dependent on the oxygen concentration. It was not detectable at high oxygen tensions but became accumulated under low oxygen (microaerobiosis). It is known that in photosynthetic bradyrhizobia bacteriophytochrome photoreceptor (BphP) partially controls the synthesis of the photosystem in response to light. In C7T1 strain far-red light illumination did not stimulate the synthesis of the photosynthetic apparatus suggesting the presence of a non-functional BphP-mediated light regulatory mechanism.
Collapse
Affiliation(s)
- M S Montecchia
- Instituto de Investigaciones Bioquímicas y Fisiológicas (IBYF-CONICET) and Cátedra de Microbiología Agrícola, Facultad de Agronomía, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
| | | | | | | |
Collapse
|
36
|
Seok JS, Kaplan S, Oh JI. Interacting specificity of a histidine kinase and its cognate response regulator: the PrrBA system of Rhodobacter sphaeroides. MICROBIOLOGY-SGM 2006; 152:2479-2490. [PMID: 16849810 DOI: 10.1099/mic.0.28961-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Using a yeast two-hybrid assay system, it was demonstrated that the four-helix bundle of the Rhodobacter sphaeroides PrrB histidine kinase both serves as the interaction site for the regulatory domain of its cognate response regulator PrrA and is the primary determinant of the interaction specificity. The alpha-helix 1 and its flanking turn region within the dimerization domain (DD) of the PrrB histidine kinase appear to play an important role in conferring the recognition specificity for the PrrA response regulator on the DD. The catalytic ATP-binding domain of the histidine kinase, which functions as the catalytic unit for the phosphotransfer reaction from ATP to the conserved histidine residue in the DD, also appears to contribute to the enhancement of the recognition specificity conferred by the DD. It was also revealed that replacement of Asp-63 and Lys-113 of the PrrA response regulator by alanine abolished protein-protein interactions between PrrA and its cognate histidine kinase PrrB, whereas mutations of Asp-19, Asp-20 and Thr-87 to alanine did not affect protein-protein interactions, indicating that among the active site residues of PrrA, Asp-63 and Lys-113 are important not only in the function of PrrA but also for protein-protein interactions between PrrA and PrrB.
Collapse
Affiliation(s)
- Jin-Sook Seok
- Department of Microbiology, Pusan National University, 609-735 Busan, South Korea
| | - Samuel Kaplan
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center Medical School, 6431 Fannin, Houston, TX 77030, USA
| | - Jeong-Il Oh
- Department of Microbiology, Pusan National University, 609-735 Busan, South Korea
| |
Collapse
|
37
|
Wilson KE, Ivanov AG, Öquist G, Grodzinski B, Sarhan F, Huner NP. Energy balance, organellar redox status, and acclimation to environmental stress. ACTA ACUST UNITED AC 2006. [DOI: 10.1139/b06-098] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In plants and algal cells, changes in light intensity can induce intrachloroplastic and retrograde regulation of gene expression in response to changes in the plastoquinone redox status. We review the evidence in support of the thesis that the chloroplast acts as a general sensor of cellular energy imbalance sensed through the plastoquinone pool. Alteration in cellular energy balance caused by chloroplast or mitochondrial metabolism can induce intracellular signalling to affect chloroplastic and nuclear gene expression in response, not only to light intensity, but to a myriad of abiotic stresses. In addition, this chloroplastic redox sensing also appears to have a broader impact, affecting long-distance systemic signalling related to plant growth and development. The organization of the respiratory electron transport chains of mitochondria and heterotrophic prokaryotes is comparable to that of chloroplast thylakoid membranes, and the redox state of the respiratory ubiquinone pool is a well-documented cellular energy sensor. Thus, modulation of electron transport component redox status by abiotic stress regulates organellar as well as nuclear gene expression. From the evidence presented, we suggest that the photosynthetic and respiratory machinery in prokaryotic and eukaryotic organisms have a dual function: primary cellular energy transformation, and global environmental sensing.
Collapse
Affiliation(s)
- Kenneth E. Wilson
- Department of Biology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada
- Department of Biology and The Biotron, University of Western Ontario, London, ON N6A 5B7, Canada
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, S-901 87, Sweden
- Departments of Plant Agriculture and Environmental Biology, Bovey Complex, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Département des Sciences biologiques, Université du Québec à Montréal, C.P. 8888 Succursale Centre-ville, Montréal, QC H3C 3P8, Canada
| | - Alexander G. Ivanov
- Department of Biology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada
- Department of Biology and The Biotron, University of Western Ontario, London, ON N6A 5B7, Canada
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, S-901 87, Sweden
- Departments of Plant Agriculture and Environmental Biology, Bovey Complex, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Département des Sciences biologiques, Université du Québec à Montréal, C.P. 8888 Succursale Centre-ville, Montréal, QC H3C 3P8, Canada
| | - Gunnar Öquist
- Department of Biology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada
- Department of Biology and The Biotron, University of Western Ontario, London, ON N6A 5B7, Canada
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, S-901 87, Sweden
- Departments of Plant Agriculture and Environmental Biology, Bovey Complex, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Département des Sciences biologiques, Université du Québec à Montréal, C.P. 8888 Succursale Centre-ville, Montréal, QC H3C 3P8, Canada
| | - Bernard Grodzinski
- Department of Biology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada
- Department of Biology and The Biotron, University of Western Ontario, London, ON N6A 5B7, Canada
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, S-901 87, Sweden
- Departments of Plant Agriculture and Environmental Biology, Bovey Complex, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Département des Sciences biologiques, Université du Québec à Montréal, C.P. 8888 Succursale Centre-ville, Montréal, QC H3C 3P8, Canada
| | - Fathey Sarhan
- Department of Biology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada
- Department of Biology and The Biotron, University of Western Ontario, London, ON N6A 5B7, Canada
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, S-901 87, Sweden
- Departments of Plant Agriculture and Environmental Biology, Bovey Complex, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Département des Sciences biologiques, Université du Québec à Montréal, C.P. 8888 Succursale Centre-ville, Montréal, QC H3C 3P8, Canada
| | - Norman P.A. Huner
- Department of Biology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada
- Department of Biology and The Biotron, University of Western Ontario, London, ON N6A 5B7, Canada
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, S-901 87, Sweden
- Departments of Plant Agriculture and Environmental Biology, Bovey Complex, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Département des Sciences biologiques, Université du Québec à Montréal, C.P. 8888 Succursale Centre-ville, Montréal, QC H3C 3P8, Canada
| |
Collapse
|
38
|
Laratta WP, Nanaszko MJ, Shapleigh JP. Electron transfer to nitrite reductase of Rhodobacter sphaeroides 2.4.3: examination of cytochromes c 2 and c Y. Microbiology (Reading) 2006; 152:1479-1488. [PMID: 16622064 DOI: 10.1099/mic.0.28524-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The role of cytochromec2, encoded bycycA, and cytochromecY, encoded bycycY, in electron transfer to the nitrite reductase ofRhodobacter sphaeroides2.4.3 was investigated using bothin vivoandin vitroapproaches. BothcycAandcycYwere isolated, sequenced and insertionally inactivated in strain 2.4.3. Deletion of either gene alone had no apparent effect on the ability ofR. sphaeroidesto reduce nitrite. In acycA–cycYdouble mutant, nitrite reduction was largely inhibited. However, the expression of the nitrite reductase genenirKfrom a heterologous promoter substantially restored nitrite reductase activity in the double mutant. Using purified protein, a turnover number of 5 s−1was observed for the oxidation of cytochromec2by nitrite reductase. In contrast, oxidation ofcYonly resulted in a turnover of ∼0·1 s−1. The turnover experiments indicate thatc2is a major electron donor to nitrite reductase butcYis probably not. Taken together, these results suggest that there is likely an unidentified electron donor, in addition toc2, that transfers electrons to nitrite reductase, and that the decreased nitrite reductase activity observed in thecycA–cycYdouble mutant probably results from a change innirKexpression.
Collapse
Affiliation(s)
- William P Laratta
- Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14850-8101, USA
| | - Michael J Nanaszko
- Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14850-8101, USA
| | - James P Shapleigh
- Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14850-8101, USA
| |
Collapse
|
39
|
Jones DF, Stenzel RA, Donohue TJ. Mutational analysis of the C-terminal domain of the Rhodobacter sphaeroides response regulator PrrA. MICROBIOLOGY-SGM 2006; 151:4103-4110. [PMID: 16339955 PMCID: PMC2800098 DOI: 10.1099/mic.0.28300-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Rhodobacter sphaeroides response regulator PrrA directly activates transcription of genes necessary for energy conservation at low O2 tensions and under anaerobic conditions. It is proposed that PrrA homologues contain a C-terminal DNA-binding domain (PrrA-CTD) that lacks significant amino acid sequence similarity to those found in other response regulators. To test this hypothesis, single amino acid substitutions were created at 12 residues in the PrrA-CTD. These mutant PrrA proteins were purified and tested for the ability to be phosphorylated by the low-molecular-mass phosphate donor acetyl phosphate, to activate transcription and to bind promoter DNA. Each mutant PrrA protein accepted phosphate from 32P-labelled acetyl phosphate. At micromolar concentrations of acetyl phosphate-treated wild-type PrrA, a single 20 bp region in the PrrA-dependent cycA P2 promoter was protected from DNase I digestion. Of the mutant PrrA proteins tested, only acetyl phosphate-treated PrrA-N168A and PrrA-I177A protected cycA P2 from DNase I digestion at similar protein concentrations compared to wild-type PrrA. The use of in vitro transcription assays with the PrrA-dependent cycA P2 and puc promoters showed that acetyl phosphate-treated PrrA-N168A produced transcript levels similar to that of wild-type PrrA at comparable protein concentrations. Using concentrations of acetyl phosphate-treated PrrA that are saturating for the wild-type protein, PrrA-H170A and PrrA-I177A produced <45 % as much transcript as wild-type PrrA. Under identical conditions, the remaining mutant PrrA proteins produced little or no detectable transcripts from either promoter in vitro. Explanations are presented for why these amino acid side chains in the PrrA-CTD are important for its ability to activate transcription.
Collapse
Affiliation(s)
- Denise F Jones
- Department of Bacteriology, University of Wisconsin-Madison, Room 390B, 420 Henry Mall, Madison, WI 53706, USA
| | - Rachelle A Stenzel
- Department of Bacteriology, University of Wisconsin-Madison, Room 390B, 420 Henry Mall, Madison, WI 53706, USA
| | - Timothy J Donohue
- Department of Bacteriology, University of Wisconsin-Madison, Room 390B, 420 Henry Mall, Madison, WI 53706, USA
| |
Collapse
|
40
|
Happ HN, Braatsch S, Broschek V, Osterloh L, Klug G. Light-dependent regulation of photosynthesis genes in Rhodobacter sphaeroides 2.4.1 is coordinately controlled by photosynthetic electron transport via the PrrBA two-component system and the photoreceptor AppA. Mol Microbiol 2006; 58:903-14. [PMID: 16238636 DOI: 10.1111/j.1365-2958.2005.04882.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Formation of the photosynthetic apparatus in Rhodobacter is regulated by oxygen tension and light intensity. Here we show that in anaerobically grown Rhodobacter cells a light-dependent increase in expression of the puc and puf operons encoding structural proteins of the photosynthetic complexes requires an active photosynthetic electron transport. The redox-sensitive CrtJ/PpsR repressor of photosynthesis genes, which was suggested to mediate electron transport-dependent signals, is not involved in this light-dependent signal chain. Our data reveal that the signal initiated in the photosynthetic reaction centre is transmitted via components of the electron transport chain and the PrrB/PrrA two-component system in Rhodobacter sphaeroides. Under blue light illumination in the absence of oxygen this signal leads to activation of photosynthesis genes and interferes with a blue-light repression mediated by the AppA photoreceptor and the PpsR transcriptional repressor in R. sphaeroides. Thus, light either sensed by a photoreceptor or initiating photosynthetic electron transport has opposite effects on the transcription of photosynthesis genes. Both signalling pathways involve redox-dependent steps that finally determine the effect of light on gene expression.
Collapse
Affiliation(s)
- Hendrik N Happ
- Institut für Mikrobiologie und Molekularbiologie, Universität Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | | | | | | | | |
Collapse
|
41
|
Structure, Function and Formation of Bacterial Intracytoplasmic Membranes. MICROBIOLOGY MONOGRAPHS 2006. [DOI: 10.1007/7171_025] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
42
|
Mao L, Mackenzie C, Roh JH, Eraso JM, Kaplan S, Resat H. Combining microarray and genomic data to predict DNA binding motifs. Microbiology (Reading) 2005; 151:3197-3213. [PMID: 16207904 DOI: 10.1099/mic.0.28167-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability to detect regulatory elements within genome sequences is important in understanding how gene expression is controlled in biological systems. In this work, microarray data analysis is combined with genome sequence analysis to predict DNA sequences in the photosynthetic bacterium Rhodobacter sphaeroides that bind the regulators PrrA, PpsR and FnrL. These predictions were made by using hierarchical clustering to detect genes that share similar expression patterns. The DNA sequences upstream of these genes were then searched for possible transcription factor recognition motifs that may be involved in their co-regulation. The approach used promises to be widely applicable for the prediction of cis-acting DNA binding elements. Using this method the authors were independently able to detect and extend the previously described consensus sequences that have been suggested to bind FnrL and PpsR. In addition, sequences that may be recognized by the global regulator PrrA were predicted. The results support the earlier suggestions that the DNA binding sequence of PrrA may have a variable-sized gap between its conserved block elements. Using the predicted DNA binding sequences, a whole-genome-scale analysis was performed to determine the relative importance of the interplay between the three regulators PpsR, FnrL and PrrA. Results of this analysis showed that, compared to the regulation by PpsR and FnrL, a much larger number of genes are candidates to be regulated by PrrA. The study demonstrates by example that integration of multiple data types can be a powerful approach for inferring transcriptional regulatory patterns in microbial systems, and it allowed the detection of photosynthesis-related regulatory patterns in R. sphaeroides.
Collapse
Affiliation(s)
- Linyong Mao
- Pacific Northwest National Laboratory, Computational Biology and Bioinformatics Group, PO Box 999, MS: K7-90, Richland, WA 99352, USA
| | - Chris Mackenzie
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center, Medical School, Houston, TX 77030, USA
| | - Jung H Roh
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center, Medical School, Houston, TX 77030, USA
| | - Jesus M Eraso
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center, Medical School, Houston, TX 77030, USA
| | - Samuel Kaplan
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center, Medical School, Houston, TX 77030, USA
| | - Haluk Resat
- Pacific Northwest National Laboratory, Computational Biology and Bioinformatics Group, PO Box 999, MS: K7-90, Richland, WA 99352, USA
| |
Collapse
|
43
|
Elsen S, Jaubert M, Pignol D, Giraud E. PpsR: a multifaceted regulator of photosynthesis gene expression in purple bacteria. Mol Microbiol 2005; 57:17-26. [PMID: 15948946 DOI: 10.1111/j.1365-2958.2005.04655.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Purple bacteria control the level of expression and the composition of their photosystem according to light and redox conditions. This control involves several regulatory systems that have been now well characterized. Among them, the PpsR regulator plays a central role, because it directly or indirectly controls the synthesis of all of the different components of the photosystem. In this review, we report our knowledge of the PpsR protein, highlighting the diversity of its mode of action and focusing on the proteins identified in four model purple bacteria (Rhodobacter capsulatus, Rhodobacter sphaeroides, Rubrivivax gelatinosus, Bradyrhizobium ORS278). This regulator exhibits unique regulatory features in each bacterium: it can activate and/or repress the expression of photosynthesis genes, its activity can be modulated or not by the redox conditions, it can interact with other specific regulators and therefore be involved differently in light and/or redox regulatory circuits.
Collapse
Affiliation(s)
- Sylvie Elsen
- Laboratoire de Biochimie et Biophysique des Systèmes Intégrés (UMR 5092 CNRS-CEA-UJF), CEA-Grenoble, 38054 Grenoble Cedex 9, France
| | | | | | | |
Collapse
|
44
|
Tavano CL, Podevels AM, Donohue TJ. Identification of genes required for recycling reducing power during photosynthetic growth. J Bacteriol 2005; 187:5249-58. [PMID: 16030219 PMCID: PMC1196016 DOI: 10.1128/jb.187.15.5249-5258.2005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Photosynthetic organisms have the unique ability to transform light energy into reducing power. We study the requirements for photosynthesis in the alpha-proteobacterium Rhodobacter sphaeroides. Global gene expression analysis found that approximately 50 uncharacterized genes were regulated by changes in light intensity and O\2 tension, similar to the expression of genes known to be required for photosynthetic growth of this bacterium. These uncharacterized genes included RSP4157 to -4159, which appeared to be cotranscribed and map to plasmid P004. A mutant containing a polar insertion in RSP4157, CT01, was able to grow via photosynthesis under autotrophic conditions using H2 as an electron donor and CO2 as a carbon source. However, CT01 was unable to grow photoheterotrophically in a succinate-based medium unless compounds that could be used to recycle reducing power (the external electron acceptor dimethyl sulfoxide (DMSO) or CO2 were provided. This suggests that the insertion in RSP4157 caused a defect in recycling reducing power during photosynthetic growth when a fixed carbon source was present. CT01 had decreased levels of RNA for genes encoding putative glycolate degradation functions. We found that exogenous glycolate also rescued photoheterotrophic growth of CT01, leading us to propose that CO2 produced from glycolate metabolism can be used by the Calvin cycle to recycle reducing power generated in the photosynthetic apparatus. The ability of glycolate, CO2, or DMSO to support photoheterotrophic growth of CT01 suggests that one or more products of RSP4157 to -4159 serve a previously unknown role in recycling reducing power under photosynthetic conditions.
Collapse
Affiliation(s)
- Christine L Tavano
- University of Wisconsin-Madison Department of Bacteriology, 420 Henry Mall, Madison, WI 53711, USA
| | | | | |
Collapse
|
45
|
Cases I, de Lorenzo V. Promoters in the environment: transcriptional regulation in its natural context. Nat Rev Microbiol 2005; 3:105-18. [PMID: 15685222 DOI: 10.1038/nrmicro1084] [Citation(s) in RCA: 167] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Transcriptional activation of many bacterial promoters in their natural environment is not a simple on/off decision. The expression of cognate genes is integrated in layers of iterative regulatory networks that ensure the performance not only of the whole cell, but also of the bacterial population, and even the microbial community, in a changing environment. Unlike in vitro systems, where transcription initiation can be recreated with a handful of essential components, in vivo, promoters must process various physicochemical and metabolic signals to determine their output. This helps to achieve optimal bacterial fitness in extremely competitive niches. Promoters therefore merge specific responses to distinct signals with inclusive reactions to more general environmental changes.
Collapse
Affiliation(s)
- Ildefonso Cases
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus de Cantoblanco, 28049 Madrid, Spain
| | | |
Collapse
|
46
|
Kaplan S, Eraso J, Roh JH. Interacting regulatory networks in the facultative photosynthetic bacterium, Rhodobacter sphaeroides 2.4.1. Biochem Soc Trans 2005; 33:51-5. [PMID: 15667262 DOI: 10.1042/bst0330051] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Regulation of photosynthetic membrane synthesis in Rhodobacter sphaeroides 2.4.1 is dependent on the interactions of numerous regulatory elements, with two of the most important being the cbb3 terminal oxidase and the PrrBAC two-component regulatory system. Here, we reveal that the cbb3 terminal oxidase possesses extensive, additional regulatory activities under anaerobic conditions, and that the PrrBAC system is further involved in the regulation of the expression of more than 20% of the R. sphaeroides genome under anaerobic conditions, extending well beyond functions related to redox gene expression.
Collapse
Affiliation(s)
- S Kaplan
- Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | | | | |
Collapse
|
47
|
Dubbs JM, Tabita FR. Regulators of nonsulfur purple phototrophic bacteria and the interactive control of CO2 assimilation, nitrogen fixation, hydrogen metabolism and energy generation. FEMS Microbiol Rev 2004; 28:353-76. [PMID: 15449608 DOI: 10.1016/j.femsre.2004.01.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
For the metabolically diverse nonsulfur purple phototrophic bacteria, maintaining redox homeostasis requires balancing the activities of energy supplying and energy-utilizing pathways, often in the face of drastic changes in environmental conditions. These organisms, members of the class Alphaproteobacteria, primarily use CO2 as an electron sink to achieve redox homeostasis. After noting the consequences of inactivating the capacity for CO2 reduction through the Calvin-Benson-Bassham (CBB) pathway, it was shown that the molecular control of many additional important biological processes catalyzed by nonsulfur purple bacteria is linked to expression of the CBB genes. Several regulator proteins are involved, with the two component Reg/Prr regulatory system playing a major role in maintaining redox poise in these organisms. Reg/Prr was shown to be a global regulator involved in the coordinate control of a number of metabolic processes including CO2 assimilation, nitrogen fixation, hydrogen metabolism and energy-generation pathways. Accumulating evidence suggests that the Reg/Prr system senses the oxidation/reduction state of the cell by monitoring a signal associated with electron transport. The response regulator RegA/PrrA activates or represses gene expression through direct interaction with target gene promoters where it often works in concert with other regulators that can be either global or specific. For the key CO2 reduction pathway, which clearly triggers whether other redox balancing mechanisms are employed, the ability to activate or inactivate the specific regulator CbbR is of paramount importance. From these studies, it is apparent that a detailed understanding of how diverse regulatory elements integrate and control metabolism will eventually be achieved.
Collapse
Affiliation(s)
- James M Dubbs
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand
| | | |
Collapse
|
48
|
Jaubert M, Zappa S, Fardoux J, Adriano JM, Hannibal L, Elsen S, Lavergne J, Verméglio A, Giraud E, Pignol D. Light and Redox Control of Photosynthesis Gene Expression in Bradyrhizobium. J Biol Chem 2004; 279:44407-16. [PMID: 15304477 DOI: 10.1074/jbc.m408039200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The two closely related bacteria Bradyrhizobium and Rhodopseudomonas palustris show an unusual mechanism of regulation of photosystem formation by light thanks to a bacteriophytochrome that antirepresses the regulator PpsR. In these two bacteria, we found out, unexpectedly, that two ppsR genes are present. We show that the two Bradyrhizobium PpsR proteins exert antagonistic effects in the regulation of photosystem formation with a classical repressor role for PpsR2 and an unexpected activator role for PpsR1. DNase I footprint analysis show that both PpsR bind to the same DNA TGTN12ACA motif that is present in tandem in the bchC promoter and the crtED intergenic region. Interestingly, the cycA and aerR promoter regions that contain only one conserved palindrome are recognized by PpsR2, but not PpsR1. Further biochemical analyses indicate that PpsR1 only is redox sensitive through the formation of an intermolecular disulfide bond, which changes its oligomerization state from a tetramer to an octamer under oxidizing conditions. Moreover, PpsR1 presents a higher DNA affinity under its reduced form in contrast to what has been previously found for PpsR or its homolog CrtJ from the Rhodobacter species. These results suggest that regulation of photosystem synthesis in Bradyrhizobium involves two PpsR competing for the binding to the same photosynthesis genes and this competition might be modulated by two factors: light via the antagonistic action of a bacteriophytochrome on PpsR2 and redox potential via the switch of PpsR1 oligomerization state.
Collapse
Affiliation(s)
- Marianne Jaubert
- Laboratoire des Symbioses Tropicales et Méditerranéennes (UMR113-IRD-CIRAD-AGRO-M-INRA-UM2), TA 10/J, Campus de Baillarguet, 34398 Montpellier 5, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Pappas CT, Sram J, Moskvin OV, Ivanov PS, Mackenzie RC, Choudhary M, Land ML, Larimer FW, Kaplan S, Gomelsky M. Construction and validation of the Rhodobacter sphaeroides 2.4.1 DNA microarray: transcriptome flexibility at diverse growth modes. J Bacteriol 2004; 186:4748-58. [PMID: 15231807 PMCID: PMC438620 DOI: 10.1128/jb.186.14.4748-4758.2004] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A high-density oligonucleotide DNA microarray, a genechip, representing the 4.6-Mb genome of the facultative phototrophic proteobacterium, Rhodobacter sphaeroides 2.4.1, was custom-designed and manufactured by Affymetrix, Santa Clara, Calif. The genechip contains probe sets for 4,292 open reading frames (ORFs), 47 rRNA and tRNA genes, and 394 intergenic regions. The probe set sequences were derived from the genome annotation generated by Oak Ridge National Laboratory after extensive revision, which was based primarily upon codon usage characteristic of this GC-rich bacterium. As a result of the revision, numerous missing ORFs were uncovered, nonexistent ORFs were deleted, and misidentified start codons were corrected. To evaluate R. sphaeroides transcriptome flexibility, expression profiles for three diverse growth modes--aerobic respiration, anaerobic respiration in the dark, and anaerobic photosynthesis--were generated. Expression levels of one-fifth to one-third of the R. sphaeroides ORFs were significantly different in cells under any two growth modes. Pathways involved in energy generation and redox balance maintenance under three growth modes were reconstructed. Expression patterns of genes involved in these pathways mirrored known functional changes, suggesting that massive changes in gene expression are the major means used by R. sphaeroides in adaptation to diverse conditions. Differential expression was observed for genes encoding putative new participants in these pathways (additional photosystem genes, duplicate NADH dehydrogenase, ATP synthases), whose functionality has yet to be investigated. The DNA microarray data correlated well with data derived from quantitative reverse transcription-PCR, as well as with data from the literature, thus validating the R. sphaeroides genechip as a powerful and reliable tool for studying unprecedented metabolic versatility of this bacterium.
Collapse
Affiliation(s)
- Christopher T Pappas
- Department of Molecular Biology, University of Wyoming, 1000 E. University Ave., Dept. 3944, Laramie, WY 82071, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Elsen S, Swem LR, Swem DL, Bauer CE. RegB/RegA, a highly conserved redox-responding global two-component regulatory system. Microbiol Mol Biol Rev 2004; 68:263-79. [PMID: 15187184 PMCID: PMC419920 DOI: 10.1128/mmbr.68.2.263-279.2004] [Citation(s) in RCA: 154] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Reg regulon from Rhodobacter capsulatus and Rhodobacter sphaeroides encodes proteins involved in numerous energy-generating and energy-utilizing processes such as photosynthesis, carbon fixation, nitrogen fixation, hydrogen utilization, aerobic and anaerobic respiration, denitrification, electron transport, and aerotaxis. The redox signal that is detected by the membrane-bound sensor kinase, RegB, appears to originate from the aerobic respiratory chain, given that mutations in cytochrome c oxidase result in constitutive RegB autophosphorylation. Regulation of RegB autophosphorylation also involves a redox-active cysteine that is present in the cytosolic region of RegB. Both phosphorylated and unphosphorylated forms of the cognate response regulator RegA are capable of activating or repressing a variety of genes in the regulon. Highly conserved homologues of RegB and RegA have been found in a wide number of photosynthetic and nonphotosynthetic bacteria, with evidence suggesting that RegB/RegA plays a fundamental role in the transcription of redox-regulated genes in many bacterial species.
Collapse
Affiliation(s)
- Sylvie Elsen
- Laboratoire de Biochimie et de Biophysique des Systèmes Intégrés (UMR 5092 CNRS-CEA-UJF), Grenoble, France
| | | | | | | |
Collapse
|