A screen for potential ferredoxin electron transfer partners uncovers new, redox dependent interactions

Laboratory for the Regulation of Biological Reactions, Institute for Protein Research, Osaka University, Suita, Osaka, Japan.
Biochimica et Biophysica Acta (Impact Factor: 4.66). 02/2011; 1814(2):366-74. DOI: 10.1016/j.bbapap.2010.09.011
Source: PubMed


Ferredoxin (Fd) is the primary soluble acceptor at the end of the photosynthetic electron transport chain, and is known to directly transfer electrons to a wide range of proteins for use in metabolism and regulatory processes. We have conducted a screen to identify new putative Fd interaction partners in the cyanobacteria Synechocystis sp. PCC 6803 using Fd-chromatography in combination with MALDI-TOF mass spectrometry. Many novel interactions were detected, including several redox enzymes, which are now candidates for further experiments to investigate electron transfer with Fd. In addition, some proteins with regulatory activity related to photosynthesis were identified. We cloned and expressed one such protein, known as RpaA, which is a specific regulator of energy transfer between phycobilisomes and PSI. Using the recombinant protein we confirmed direct interaction with Fd, and discovered that this was dependent on redox state. The screen for putative Fd-binding proteins was repeated, comparing oxidizing and reducing conditions, identifying many proteins whose interaction with Fd is redox dependent. These include several additional signaling molecules, among them the LexA repressor, Ycf53 and NII, which are all involved in interpreting the redox state of the cell.

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    • "Due to the lack of the FMN binding site, the NuoF2 subunit cannot interact with a two-electron carrier such as NAD+/NADH. However, as NADH and ferredoxin binding sites display homology in some proteins (Hanke et al., 2011), the predicted NADH binding site of NUO-2 might interact with the single-electron carrier ferredoxin. Powered by proton motive force and with the help of the four additional Fe-S clusters in NuoG2 and NuoF2, two of which are of the bacterial [4Fe- 4S] ferredoxin type, it might be possible to elevate electrons from the quinol pool not only to the redox potential of NADH, but further to the potential of ferredoxin. "
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    ABSTRACT: In marine systems, nitrate is the major reservoir of inorganic fixed nitrogen. The only known biological nitrate-forming reaction is nitrite oxidation, but despite its importance, our knowledge of the organisms catalyzing this key process in the marine N-cycle is very limited. The most frequently encountered marine NOB are related to Nitrospina gracilis, an aerobic chemolithoautotrophic bacterium isolated from ocean surface waters. To date, limited physiological and genomic data for this organism were available and its phylogenetic affiliation was uncertain. In this study, the draft genome sequence of N. gracilis strain 3/211 was obtained. Unexpectedly for an aerobic organism, N. gracilis lacks classical reactive oxygen defense mechanisms and uses the reductive tricarboxylic acid cycle for carbon fixation. These features indicate microaerophilic ancestry and are consistent with the presence of Nitrospina in marine oxygen minimum zones. Fixed carbon is stored intracellularly as glycogen, but genes for utilizing external organic carbon sources were not identified. N. gracilis also contains a full gene set for oxidative phosphorylation with oxygen as terminal electron acceptor and for reverse electron transport from nitrite to NADH. A novel variation of complex I may catalyze the required reverse electron flow to low-potential ferredoxin. Interestingly, comparative genomics indicated a strong evolutionary link between Nitrospina, the nitrite-oxidizing genus Nitrospira, and anaerobic ammonium oxidizers, apparently including the horizontal transfer of a periplasmically oriented nitrite oxidoreductase and other key genes for nitrite oxidation at an early evolutionary stage. Further, detailed phylogenetic analyses using concatenated marker genes provided evidence that Nitrospina forms a novel bacterial phylum, for which we propose the name Nitrospinae.
    Frontiers in Microbiology 02/2013; 4:27. DOI:10.3389/fmicb.2013.00027 · 3.99 Impact Factor
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    • "We also looked at the expression of rpaA, which codes for a DNA-binding protein acting as the response regulator of the KaiC-interacting kinase SasA, a two-component system that mediates the diel oscillations generated by KaiC phosphorylation to global transcription rhythms (Takai et al., 2006). RpaA is also known to be involved in the regulation of energy transfer from PBS to PSI and to interact with ferredoxin (Ashby and Mullineaux, 1999; Hanke et al., 2011). In both organisms, rpaA was maximally expressed around noontime and UVR had no significant effect on its diel transcription pattern. "
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    ABSTRACT: Prochlorococcus and Synechococcus, which numerically dominate vast oceanic areas, are the two most abundant oxygenic phototrophs on Earth. Although they require solar energy for photosynthesis, excess light and associated high UV radiations can induce high levels of oxidative stress that may have deleterious effects on their growth and productivity. Here, we compared the photophysiologies of the model strains Prochlorococcus marinus PCC 9511 and Synechococcus sp. WH7803 grown under a bell-shaped light/dark cycle of high visible light supplemented or not with UV. Prochlorococcus exhibited a higher sensitivity to photoinactivation than Synechococcus under both conditions, as shown by a larger drop of photosystem II (PSII) quantum yield at noon and different diel patterns of the D1 protein pool. In the presence of UV, the PSII repair rate was significantly depressed at noon in Prochlorococcus compared to Synechococcus. Additionally, Prochlorococcus was more sensitive than Synechococcus to oxidative stress, as shown by the different degrees of PSII photoinactivation after addition of hydrogen peroxide. A transcriptional analysis also revealed dramatic discrepancies between the two organisms in the diel expression patterns of several genes involved notably in the biosynthesis and/or repair of photosystems, light-harvesting complexes, CO(2) fixation as well as protection mechanisms against light, UV, and oxidative stress, which likely translate profound differences in their light-controlled regulation. Altogether our results suggest that while Synechococcus has developed efficient ways to cope with light and UV stress, Prochlorococcus cells seemingly survive stressful hours of the day by launching a minimal set of protection mechanisms and by temporarily bringing down several key metabolic processes. This study provides unprecedented insights into understanding the distinct depth distributions and dynamics of these two picocyanobacteria in the field.
    Frontiers in Microbiology 08/2012; 3:285. DOI:10.3389/fmicb.2012.00285 · 3.99 Impact Factor
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    • "FNR NADP + reduction Photosynthesis Cyanobacteria, plants [1] [83] Nitrite reductase Reduction of NO 2 -to NH4 + Nitrogen assimilation Cyanobacteria, algae, plants [1] [83] Nitrate reductase Reduction of NO 3 -to NO 2 - Nitrogen assimilation Cyanobacteria [1] [83] Nitrogenase and pyruvate:Fd oxidoreductase or FNR N 2 fixation Nitrogen assimilation Cyanobacteria [84] Hydrogenase H 2 formation Hydrogen metabolism Cyanobacteria [84] Glutamate–oxoglutarate amino transferase (GOGAT) Glutamate synthesis Amino acid synthesis Cyanobacteria, algae, plants [1] [83] Sulfite reductase Reduction of SO 3 2À to H 2 S Sulfur assimilation Plants [1] Ferredoxin-thioredoxin reductase Thioredoxin reduction Redox regulation a Cyanobacteria, algae, plants [1] [83] Fatty acid desaturase Double bond formation in fatty acids Lipid metabolism Cyanobacteria, plants [83] [85] Monodehydroascorbate reductase Ascorbate regeneration Antioxidant defense Plants [86] Heme oxigenase and phytochromobilin synthase Phytochromobilin b synthesis Development Plants [87] [88] Heme oxigenase and phycocyanobilin:Fd oxidoreductase Phycocyanobilin c synthesis Development Cyanobacteria [83] [89] [90] PGRL1, PGR5, FNR and PSI Cyclic electron flow Photosynthesis Algae, plants [91] [92] Flavodoxin PSI Photosynthetic electron transport Photosynthesis Cyanobacteria, algae [82] FNR NADP + reduction Photosynthesis Cyanobacteria, algae [22] [93] FNR and PSI Cyclic electron flow Photosynthesis Cyanobacteria [94] Nitrogenase N 2 fixation Nitrogen assimilation Cyanobacteria [95] Hydrogenase H 2 formation Hydrogen metabolism Cyanobacteria [84] a Reduced thioredoxin activates key chloroplast enzymes of the Calvin cycle, the malate valve, etc. b Plant chromophore of the light sensor phytochrome and intermediate in the synthesis of chlorophyll. c Chromophore of the light sensor phytochrome in cyanobacteria and green algae, and precursor of the chromophores of the light-harvesting phycobiliproteins. "
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    ABSTRACT: Ferredoxins are electron shuttles harboring iron-sulfur clusters which participate in oxido-reductive pathways in organisms displaying very different lifestyles. Ferredoxin levels decline in plants and cyanobacteria exposed to environmental stress and iron starvation. Flavodoxin is an isofunctional flavoprotein present in cyanobacteria and algae (not plants) which is induced and replaces ferredoxin under stress. Expression of a chloroplast-targeted flavodoxin in plants confers tolerance to multiple stresses and iron deficit. We discuss herein the bases for functional equivalence between the two proteins, the reasons for ferredoxin conservation despite its susceptibility to aerobic stress and for the loss of flavodoxin as an adaptive trait in higher eukaryotes. We also propose a mechanism to explain the tolerance conferred by flavodoxin when expressed in plants.
    FEBS letters 07/2012; 586(18):2917-24. DOI:10.1016/j.febslet.2012.07.026 · 3.17 Impact Factor
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