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Spectroscopic and functional characterization of the [2Fe-2S] scaffold protein Nfu from Synechocystis PCC6803. Biochimie 2022; 192:51-62. [PMID: 34582998 PMCID: PMC8724361 DOI: 10.1016/j.biochi.2021.09.013] [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: 06/02/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 01/03/2023]
Abstract
Iron-sulfur clusters are ubiquitous cofactors required for various essential metabolic processes. Conservation of proteins required for their biosynthesis and trafficking allows for simple bacteria to be used as models to aid in exploring these complex pathways in higher organisms. Cyanobacteria are among the most investigated organisms for these processes, as they are unicellular and can survive under photoautotrophic and heterotrophic conditions. Herein, we report the potential role of Synechocystis PCC6803 NifU (now named SyNfu) as the principal scaffold protein required for iron-sulfur cluster biosynthesis in that organism. SyNfu is a well-folded protein with distinct secondary structural elements, as evidenced by circular dichroism and a well-dispersed pattern of 1H-15N HSQC NMR peaks, and readily reconstitutes as a [2Fe-2S] dimeric protein complex. Cluster exchange experiments show that glutathione can extract the cluster from holo-SyNfu, but the transfer is unidirectional. We also confirm the ability of SyNfu to transfer cluster to both human ferredoxin 1 and ferredoxin 2, while also demonstrating the capacity to deliver cluster to both monothiol glutaredoxin 3 and dithiol glutaredoxin 2. This evidence supports the hypothesis that SyNfu indeed serves as the main scaffold protein in Synechocystis, as it has been shown to be the only protein required for viability in the absence of photoautotrophic conditions. Similar to other NFU-type cluster donors and other scaffold and carrier proteins, such as ISCU, SyNfu is shown by DSC to be structurally less stable than regular protein donors, while retaining a relatively well-defined tertiary structure as represented by 1H-15N HSQC NMR experiments.
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2
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Biochemical elucidation of citrate accumulation in Synechocystis sp. PCC 6803 via kinetic analysis of aconitase. Sci Rep 2021; 11:17131. [PMID: 34429477 PMCID: PMC8385029 DOI: 10.1038/s41598-021-96432-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 08/04/2021] [Indexed: 12/03/2022] Open
Abstract
A unicellular cyanobacterium Synechocystis sp. PCC 6803 possesses a unique tricarboxylic acid (TCA) cycle, wherein the intracellular citrate levels are approximately 1.5–10 times higher than the levels of other TCA cycle metabolite. Aconitase catalyses the reversible isomerisation of citrate and isocitrate. Herein, we biochemically analysed Synechocystis sp. PCC 6803 aconitase (SyAcnB), using citrate and isocitrate as the substrates. We observed that the activity of SyAcnB for citrate was highest at pH 7.7 and 45 °C and for isocitrate at pH 8.0 and 53 °C. The Km value of SyAcnB for citrate was higher than that for isocitrate under the same conditions. The Km value of SyAcnB for isocitrate was 3.6-fold higher than the reported Km values of isocitrate dehydrogenase for isocitrate. Therefore, we suggest that citrate accumulation depends on the enzyme kinetics of SyAcnB, and 2-oxoglutarate production depends on the chemical equilibrium in this cyanobacterium.
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Liu LM, Li DL, Deng B, Wang XW, Jiang HB. Special roles for efflux systems in iron homeostasis of non-siderophore-producing cyanobacteria. Environ Microbiol 2021; 24:551-565. [PMID: 33817959 DOI: 10.1111/1462-2920.15506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 04/03/2021] [Indexed: 11/28/2022]
Abstract
In oligotrophic oceans, low bioavailability of Fe is a key factor limiting primary productivity. However, excessive Fe in cells leads to the Fenton reaction, which is toxic to cells. Cyanobacteria must strictly maintain intracellular Fe homeostasis. Here, we knocked out a series of genes encoding efflux systems in Synechocystis sp. PCC 6803, and found eight genes that are required for high Fe detoxification. Unexpectedly, the HlyBD-TolC efflux system plays an important role in the adaptation of Synechocystis under Fe-deficient conditions. Mutants of HlyD and TolC grew worse than the wild-type strain under low-Fe conditions and showed significantly lower intracellular Fe contents than the wild-type strain. We excluded the possibility that the low Fe sensitivity of the HlyBD-TolC mutants was caused by a loss of the S-layer, the main extracellular protein secreted via this efflux system. Inactivation of the HlyD protein influenced type IV pili formation and direct inactivation of type IV pili related genes affected the adaptation to low-Fe conditions. HlyBD-TolC system is likely involved in the formation of type IV pili and indirectly influenced Fe acquisition. Our findings suggest that efflux system in non-siderophore-producing cyanobacteria can facilitate Fe uptake and help cells adapt to Fe-deficient conditions via novel pathways.
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Affiliation(s)
- Ling-Mei Liu
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, 519080, China
| | - Ding-Lan Li
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Bin Deng
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Xin-Wei Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, 519080, China.,School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Hai-Bo Jiang
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, 519080, China.,School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
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4
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Identification of Genes Involved in Fe-S Cluster Biosynthesis of Nitrogenase in Paenibacillus polymyxa WLY78. Int J Mol Sci 2021; 22:ijms22073771. [PMID: 33916504 PMCID: PMC8038749 DOI: 10.3390/ijms22073771] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/26/2021] [Accepted: 04/01/2021] [Indexed: 11/17/2022] Open
Abstract
NifS and NifU (encoded by nifS and nifU) are generally dedicated to biogenesis of the nitrogenase Fe–S cluster in diazotrophs. However, nifS and nifU are not found in N2-fixing Paenibacillus strains, and the mechanisms involved in Fe–S cluster biosynthesis of nitrogenase is not clear. Here, we found that the genome of Paenibacillus polymyxa WLY78 contains the complete sufCDSUB operon, a partial sufC2D2B2 operon, a nifS-like gene, two nifU-like genes (nfuA-like and yutI), and two iscS genes. Deletion and complementation studies showed that the sufC, sufD, and sufB genes of the sufCDSUB operon, and nifS-like and yutI genes were involved in the Fe–S cluster biosynthesis of nitrogenase. Heterologous complementation studies demonstrated that the nifS-like gene of P. polymyxa WLY78 is interchangeable with Klebsiella oxytoca nifS, but P. polymyxa WLY78 SufCDB cannot be functionally replaced by K. oxytoca NifU. In addition, K. oxytoca nifU and Escherichia coli nfuA are able to complement the P. polymyxa WLY78 yutI mutant. Our findings thus indicate that the NifS-like and SufCDB proteins are the specific sulfur donor and the molecular scaffold, respectively, for the Fe–S cluster formation of nitrogenase in P. polymyxa WLY78. YutI can be an Fe–S cluster carrier involved in nitrogenase maturation in P. polymyxa WLY78.
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Nie X, Jäger A, Börner J, Klug G. Interplay between formation of photosynthetic complexes and expression of genes for iron-sulfur cluster assembly in Rhodobacter sphaeroides? PHOTOSYNTHESIS RESEARCH 2021; 147:39-48. [PMID: 33064275 PMCID: PMC7728643 DOI: 10.1007/s11120-020-00789-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/04/2020] [Indexed: 06/11/2023]
Abstract
Formation of photosynthetic complexes leads to a higher demand for Fe-S clusters. We hypothesized that in the facultative phototrophic alpha-proteobacterium Rhodobacter sphaeroides expression of the isc-suf operon for Fe-S cluster formation may be increased under conditions that promote formation of photosynthetic complexes and that, vice versa, lack of the IscR regulator may also affect photosynthesis gene expression. To test this hypothesis, we monitored the activities of the isc-suf sense and anti-sense promoters under different growth conditions and in mutants which are impaired in formation of photosynthetic complexes. We also tested expression of photosynthesis genes in a mutant lacking the IscR regulator. Our results are not in agreement with a co-regulation of the Isc-Suf system and the photosynthetic apparatus at level of transcription. We provide evidence that, coordination of the systems occurs at post-transcriptional levels. Increased levels of isc-suf mRNAs under conditions promoting formation of photosynthetic complexes are due to higher RNA stability.
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Affiliation(s)
- Xin Nie
- Institute of Microbiology and Molecular Biology, University of Giessen, IFZ, Heinrich-Buff-Ring, 26-32, Germany
- School of Basic Medical Sciences, Chengdu Medical College, Chengdu, 610500, China
| | - Andreas Jäger
- Institute of Microbiology and Molecular Biology, University of Giessen, IFZ, Heinrich-Buff-Ring, 26-32, Germany
| | - Janek Börner
- Institute of Microbiology and Molecular Biology, University of Giessen, IFZ, Heinrich-Buff-Ring, 26-32, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, University of Giessen, IFZ, Heinrich-Buff-Ring, 26-32, Germany.
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Gao F. Iron-Sulfur Cluster Biogenesis and Iron Homeostasis in Cyanobacteria. Front Microbiol 2020; 11:165. [PMID: 32184761 PMCID: PMC7058544 DOI: 10.3389/fmicb.2020.00165] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 01/23/2020] [Indexed: 01/23/2023] Open
Abstract
Iron–sulfur (Fe–S) clusters are ancient and ubiquitous cofactors and are involved in many important biological processes. Unlike the non-photosynthetic bacteria, cyanobacteria have developed the sulfur utilization factor (SUF) mechanism as their main assembly pathway for Fe–S clusters, supplemented by the iron–sulfur cluster and nitrogen-fixing mechanisms. The SUF system consists of cysteine desulfurase SufS, SufE that can enhance SufS activity, SufBC2D scaffold complex, carrier protein SufA, and regulatory repressor SufR. The S source for the Fe–S cluster assembly mainly originates from L-cysteine, but the Fe donor remains elusive. This minireview mainly focuses on the biogenesis pathway of the Fe–S clusters in cyanobacteria and its relationship with iron homeostasis. Future challenges of studying Fe–S clusters in cyanobacteria are also discussed.
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Affiliation(s)
- Fudan Gao
- College of Life Sciences, Shanghai Normal University, Shanghai, China
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7
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Thiel V, Garcia Costas AM, Fortney NW, Martinez JN, Tank M, Roden EE, Boyd ES, Ward DM, Hanada S, Bryant DA. " Candidatus Thermonerobacter thiotrophicus," A Non-phototrophic Member of the Bacteroidetes/Chlorobi With Dissimilatory Sulfur Metabolism in Hot Spring Mat Communities. Front Microbiol 2019; 9:3159. [PMID: 30687241 PMCID: PMC6338057 DOI: 10.3389/fmicb.2018.03159] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/05/2018] [Indexed: 12/31/2022] Open
Abstract
In this study we present evidence for a novel, thermophilic bacterium with dissimilatory sulfur metabolism, tentatively named “Candidatus Thermonerobacter thiotrophicus,” which is affiliated with the Bacteroides/Ignavibacteria/Chlorobi and which we predict to be a sulfate reducer. Dissimilatory sulfate reduction (DSR) is an important and ancient metabolic process for energy conservation with global importance for geochemical sulfur and carbon cycling. Characterized sulfate-reducing microorganisms (SRM) are found in a limited number of bacterial and archaeal phyla. However, based on highly diverse environmental dsrAB sequences, a variety of uncultivated and unidentified SRM must exist. The recent development of high-throughput sequencing methods allows the phylogenetic identification of some of these uncultured SRM. In this study, we identified a novel putative SRM inhabiting hot spring microbial mats that is a member of the OPB56 clade (“Ca. Kapabacteria”) within the Bacteroidetes/Chlorobi superphylum. Partial genomes for this new organism were retrieved from metagenomes from three different hot springs in Yellowstone National Park, United States, and Japan. Supporting the prediction of a sulfate-reducing metabolism for this organism during period of anoxia, diel metatranscriptomic analyses indicate highest relative transcript levels in situ for all DSR-related genes at night. The presence of terminal oxidases, which are transcribed during the day, further suggests that these organisms might also perform aerobic respiration. The relative phylogenetic proximity to the sulfur-oxidizing, chlorophototrophic Chlorobi further raises new questions about the evolution of dissimilatory sulfur metabolism.
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Affiliation(s)
- Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Amaya M Garcia Costas
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States.,Department of Biology, Colorado State University-Pueblo, Pueblo, CO, United States
| | - Nathaniel W Fortney
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI, United States
| | - Joval N Martinez
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.,Department of Natural Sciences, University of St. La Salle, Bacolod, Philippines
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Eric E Roden
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI, United States
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - David M Ward
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, United States
| | - Satoshi Hanada
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States.,Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
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