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Schluchter WM, Babin CH, Liu X, Bieller A, Shen G, Alvey RM, Bryant DA. Loss of Biliverdin Reductase Increases Oxidative Stress in the Cyanobacterium Synechococcus sp. PCC 7002. Microorganisms 2023; 11:2593. [PMID: 37894251 PMCID: PMC10608806 DOI: 10.3390/microorganisms11102593] [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: 09/24/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Oxygenic photosynthesis requires metal-rich cofactors and electron-transfer components that can produce reactive oxygen species (ROS) that are highly toxic to cyanobacterial cells. Biliverdin reductase (BvdR) reduces biliverdin IXα to bilirubin, which is a potent scavenger of radicals and ROS. The enzyme is widespread in mammals but is also found in many cyanobacteria. We show that a previously described bvdR mutant of Synechocystis sp. PCC 6803 contained a secondary deletion mutation in the cpcB gene. The bvdR gene from Synechococcus sp. PCC 7002 was expressed in Escherichia coli, and recombinant BvdR was purified and shown to reduce biliverdin to bilirubin. The bvdR gene was successfully inactivated in Synechococcus sp. PCC 7002, a strain that is naturally much more tolerant of high light and ROS than Synechocystis sp. PCC 6803. The bvdR mutant strain, BR2, had lower total phycobiliprotein and chlorophyll levels than wild-type cells. As determined using whole-cell fluorescence at 77 K, the photosystem I levels were also lower than those in wild-type cells. The BR2 mutant had significantly higher ROS levels compared to wild-type cells after exposure to high light for 30 min. Together, these results suggest that bilirubin plays an important role as a scavenger for ROS in Synechococcus sp. PCC 7002. The oxidation of bilirubin by ROS could convert bilirubin to biliverdin IXα, and thus BvdR might be important for regenerating bilirubin. These results further suggest that BvdR is a key component of a scavenging cycle by which cyanobacteria protect themselves from the toxic ROS byproducts generated during oxygenic photosynthesis.
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Affiliation(s)
- Wendy M. Schluchter
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA; (C.H.B.); (X.L.); (A.B.)
| | - Courtney H. Babin
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA; (C.H.B.); (X.L.); (A.B.)
| | - Xindi Liu
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA; (C.H.B.); (X.L.); (A.B.)
| | - Amori Bieller
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA; (C.H.B.); (X.L.); (A.B.)
| | - Gaozhong Shen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA (R.M.A.); (D.A.B.)
| | - Richard M. Alvey
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA (R.M.A.); (D.A.B.)
- Biology Department, Bloomington, Illinois Wesleyan University, Bloomington, IL 61702, USA
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA (R.M.A.); (D.A.B.)
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Jackson PJ, Hitchcock A, Brindley AA, Dickman MJ, Hunter CN. Absolute quantification of cellular levels of photosynthesis-related proteins in Synechocystis sp. PCC 6803. PHOTOSYNTHESIS RESEARCH 2023; 155:219-245. [PMID: 36542271 PMCID: PMC9958174 DOI: 10.1007/s11120-022-00990-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Quantifying cellular components is a basic and important step for understanding how a cell works, how it responds to environmental changes, and for re-engineering cells to produce valuable metabolites and increased biomass. We quantified proteins in the model cyanobacterium Synechocystis sp. PCC 6803 given the general importance of cyanobacteria for global photosynthesis, for synthetic biology and biotechnology research, and their ancestral relationship to the chloroplasts of plants. Four mass spectrometry methods were used to quantify cellular components involved in the biosynthesis of chlorophyll, carotenoid and bilin pigments, membrane assembly, the light reactions of photosynthesis, fixation of carbon dioxide and nitrogen, and hydrogen and sulfur metabolism. Components of biosynthetic pathways, such as those for chlorophyll or for photosystem II assembly, range between 1000 and 10,000 copies per cell, but can be tenfold higher for CO2 fixation enzymes. The most abundant subunits are those for photosystem I, with around 100,000 copies per cell, approximately 2 to fivefold higher than for photosystem II and ATP synthase, and 5-20 fold more than for the cytochrome b6f complex. Disparities between numbers of pathway enzymes, between components of electron transfer chains, and between subunits within complexes indicate possible control points for biosynthetic processes, bioenergetic reactions and for the assembly of multisubunit complexes.
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Affiliation(s)
- Philip J Jackson
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK.
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK.
| | - Andrew Hitchcock
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Amanda A Brindley
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK
| | - C Neil Hunter
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
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Production of bilirubin by biotransformation of biliverdin using recombinant Escherichia coli cells. Bioprocess Biosyst Eng 2022; 45:563-571. [DOI: 10.1007/s00449-021-02679-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/07/2021] [Indexed: 11/02/2022]
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Takao H, Hirabayashi K, Nishigaya Y, Kouriki H, Nakaniwa T, Hagiwara Y, Harada J, Sato H, Yamazaki T, Sakakibara Y, Suiko M, Asada Y, Takahashi Y, Yamamoto K, Fukuyama K, Sugishima M, Wada K. A substrate-bound structure of cyanobacterial biliverdin reductase identifies stacked substrates as critical for activity. Nat Commun 2017; 8:14397. [PMID: 28169272 PMCID: PMC5309722 DOI: 10.1038/ncomms14397] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 12/23/2016] [Indexed: 01/20/2023] Open
Abstract
Biliverdin reductase catalyses the last step in haem degradation and produces the major lipophilic antioxidant bilirubin via reduction of biliverdin, using NAD(P)H as a cofactor. Despite the importance of biliverdin reductase in maintaining the redox balance, the molecular details of the reaction it catalyses remain unknown. Here we present the crystal structure of biliverdin reductase in complex with biliverdin and NADP+. Unexpectedly, two biliverdin molecules, which we designated the proximal and distal biliverdins, bind with stacked geometry in the active site. The nicotinamide ring of the NADP+ is located close to the reaction site on the proximal biliverdin, supporting that the hydride directly attacks this position of the proximal biliverdin. The results of mutagenesis studies suggest that a conserved Arg185 is essential for the catalysis. The distal biliverdin probably acts as a conduit to deliver the proton from Arg185 to the proximal biliverdin, thus yielding bilirubin.
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Affiliation(s)
- Haruna Takao
- Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki 889-1692, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Kei Hirabayashi
- Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Yuki Nishigaya
- Advanced Analysis Center, National Agriculture and Food Research Organization, Ibaraki 305-8602, Japan
| | - Haruna Kouriki
- Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Tetsuko Nakaniwa
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | - Yoshinori Hagiwara
- Department of Biochemistry and Applied Chemistry, National Institute of Technology, Kurume College, Fukuoka 830-8555, Japan
| | - Jiro Harada
- Department of Medical Biochemistry, Kurume University School of Medicine, Fukuoka 830-0011, Japan
| | - Hideaki Sato
- Department of Medical Biochemistry, Kurume University School of Medicine, Fukuoka 830-0011, Japan
| | - Toshimasa Yamazaki
- Advanced Analysis Center, National Agriculture and Food Research Organization, Ibaraki 305-8602, Japan
| | - Yoichi Sakakibara
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Masahito Suiko
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Yujiro Asada
- Department of Pathology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Yasuhiro Takahashi
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Ken Yamamoto
- Department of Medical Biochemistry, Kurume University School of Medicine, Fukuoka 830-0011, Japan
| | - Keiichi Fukuyama
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan
| | - Masakazu Sugishima
- Department of Medical Biochemistry, Kurume University School of Medicine, Fukuoka 830-0011, Japan
| | - Kei Wada
- Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki 889-1692, Japan
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Ahmed FH, Mohamed AE, Carr PD, Lee BM, Condic-Jurkic K, O'Mara ML, Jackson CJ. Rv2074 is a novel F420 H2 -dependent biliverdin reductase in Mycobacterium tuberculosis. Protein Sci 2016; 25:1692-709. [PMID: 27364382 DOI: 10.1002/pro.2975] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/29/2016] [Indexed: 12/12/2022]
Abstract
Bilirubin is a potent antioxidant that is produced from the reduction of the heme degradation product biliverdin. In mammalian cells and Cyanobacteria, NADH/NADPH-dependent biliverdin reductases (BVRs) of the Rossmann-fold have been shown to catalyze this reaction. Here, we describe the characterization of Rv2074 from Mycobacterium tuberculosis, which belongs to a structurally and mechanistically distinct family of F420 H2 -dependent BVRs (F-BVRs) that are exclusively found in Actinobacteria. We have solved the crystal structure of Rv2074 bound to its cofactor, F420 , and used this alongside molecular dynamics simulations, site-directed mutagenesis and NMR spectroscopy to elucidate its catalytic mechanism. The production of bilirubin by Rv2074 could exploit the anti-oxidative properties of bilirubin and contribute to the range of immuno-evasive mechanisms that have evolved in M. tuberculosis to allow persistent infection.
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Affiliation(s)
- F Hafna Ahmed
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - A Elaaf Mohamed
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Paul D Carr
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Brendon M Lee
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Karmen Condic-Jurkic
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Megan L O'Mara
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
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Watanabe A, Hirata K, Hagiwara Y, Yutani Y, Sugishima M, Yamamoto M, Fukuyama K, Wada K. Expression, purification and preliminary X-ray crystallographic analysis of cyanobacterial biliverdin reductase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:313-7. [PMID: 21393834 DOI: 10.1107/s1744309110053431] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Accepted: 12/20/2010] [Indexed: 01/24/2023]
Abstract
Biliverdin reductase (BVR) catalyzes the conversion of biliverdin IX α to bilirubin IX α with concomitant oxidation of an NADH or NADPH cofactor. This enzyme also binds DNA and enhances the transcription of specific genes. Recombinant cyanobacterial BVR was overexpressed in Escherichia coli, purified and crystallized. A native data set was collected to 2.34 Å resolution on beamline BL38B1 at SPring-8. An SeMet data set was collected from a microcrystal (300×10×10 µm) on the RIKEN targeted protein beamline BL32XU and diffraction spots were obtained to 3.0 Å resolution. The native BVR crystal belonged to space group P2(1)2(1)2(1), with unit-cell parameters a=58.8, b=88.4, c=132.6 Å. Assuming that two molecules are present in the asymmetric unit, VM (the Matthews coefficient) was calculated to be 2.37 Å3 Da(-1) and the solvent content was estimated to be 48.1%. The structure of cyanobacterial BVR may provide insights into the mechanisms of its enzymatic and physiological functions.
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Affiliation(s)
- Aya Watanabe
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
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Shang L, Rockwell NC, Martin SS, Lagarias JC. Biliverdin amides reveal roles for propionate side chains in bilin reductase recognition and in holophytochrome assembly and photoconversion. Biochemistry 2010; 49:6070-82. [PMID: 20565135 DOI: 10.1021/bi100756x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Linear tetrapyrroles (bilins) perform important antioxidant and light-harvesting functions in cells from bacteria to humans. To explore the role of the propionate moieties in bilin metabolism, we report the semisynthesis of mono- and diamides of biliverdin IXalpha and those of its non-natural XIIIalpha isomer. Initially, these were examined as substrates of two types of NADPH-dependent biliverdin reductase, BVR and BvdR, and of the representative ferredoxin-dependent bilin reductase, phycocyanobilin:ferredoxin oxidoreductase (PcyA). Our studies indicate that the NADPH-dependent biliverdin reductases are less accommodating to amidation of the propionic acid side chains of biliverdin IXalpha than PcyA, which does not require free carboxylic acid side chains to yield its phytobilin product, phycocyanobilin. Bilin amides were also assembled with BV-type and phytobilin-type apophytochromes, demonstrating a role for the 8-propionate in the formation of the spectroscopically native P(r) dark states of these biliprotein photosensors. Neither ionizable propionate side chain proved to be essential to primary photoisomerization for both classes of phytochromes, but an unsubstituted 12-propionate was required for full photointerconversion of phytobilin-type phytochrome Cph1. Taken together, these studies provide insight into the roles of the ionizable propionate side chains in substrate discrimination by two bilin reductase families while further underscoring the mechanistic differences between the photoconversions of BV-type and phytobilin-type phytochromes.
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Affiliation(s)
- Lixia Shang
- Department of Molecular and Cellular Biology, University of California, One Shields Avenue, Davis, California 95616, USA
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Franklin EM, Browne S, Horan AM, Inomata K, Hammam MAS, Kinoshita H, Lamparter T, Golfis G, Mantle TJ. The use of synthetic linear tetrapyrroles to probe the verdin sites of human biliverdin-IXalpha reductase and human biliverdin-IXbeta reductase. FEBS J 2009; 276:4405-13. [PMID: 19614742 DOI: 10.1111/j.1742-4658.2009.07148.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many vertebrate species express two enzymes that are capable of catalysing the reduction of various isomers of biliverdin. Biliverdin-IXalpha reductase (BVR-A) is most active with its physiological substrate biliverdin-IXalpha, but can also reduce the three other biliverdin isomers IXbeta, IXdelta and IXgamma. Biliverdin-IXbeta reductase (BVR-B) catalyses the reduction of only the IXbeta, IXdelta and IXgamma isomers of biliverdin. Therefore, the activity of BVR-A can be measured using biliverdin-IXalpha as a specific substrate. We now show that the dimethyl esters of biliverdin-IXbeta and biliverdin-IXdelta are substrates for BVR-B, but not for BVR-A. This provides a useful method for specifically assaying the activity of both BVR-A and BVR-B in crude mixtures, using biliverdin-IXalpha for BVR-A and the dimethyl ester of either biliverdin-IXbeta or biliverdin-IXdelta for BVR-B. Human BVR-A has been suggested as a pharmacological target for neonatal jaundice. Because of the absence of a crystal structure with biliverdin bound to BVR-A, we have investigated indirect ways of examining tetrapyrrole binding. In the present study, we report that a number of sterically locked conformers of 18-ethylbiliverdin-IXalpha are substrates for human BVR-A, and discuss the implications for the biliverdin binding site. The oxidation of bilirubin-IXalpha ditaurate to biliverdin-IXalpha ditaurate is also described. We show that biliverdin-IXalpha ditaurate is a substrate for human BVR-A and discuss the possibility of using a competing substrate, which is reduced to a water soluble and excretable rubin, as a prototypic inhibitor of BVR-A.
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Affiliation(s)
- Edward M Franklin
- School of Biochemistry and Immunology, Trinity College, Dublin, Ireland.
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