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The Journal of Biological Chemistry Sep 2023Ferredoxins are a family of iron-sulfur (Fe-S) cluster proteins that serve as essential electron donors in numerous cellular processes that are conserved through...
Ferredoxins are a family of iron-sulfur (Fe-S) cluster proteins that serve as essential electron donors in numerous cellular processes that are conserved through evolution. The promiscuous nature of ferredoxins as electron donors enables them to participate in many metabolic processes including steroid, heme, vitamin D, and Fe-S cluster biosynthesis in different organisms. However, the unique natural function(s) of each of the two human ferredoxins (FDX1 and FDX2) are still poorly characterized. We recently reported that FDX1 is both a crucial regulator of copper ionophore-induced cell death and serves as an upstream regulator of cellular protein lipoylation, a mitochondrial lipid-based post-translational modification naturally occurring on four mitochondrial enzymes that are crucial for TCA cycle function. Here we show that FDX1 directly regulates protein lipoylation by binding the lipoyl synthase (LIAS) enzyme promoting its functional binding to the lipoyl carrier protein GCSH and not through indirect regulation of cellular Fe-S cluster biosynthesis. Metabolite profiling revealed that the predominant cellular metabolic outcome of FDX1 loss of function is manifested through the regulation of the four lipoylation-dependent enzymes ultimately resulting in loss of cellular respiration and sensitivity to mild glucose starvation. Transcriptional profiling established that FDX1 loss-of-function results in the induction of both compensatory metabolism-related genes and the integrated stress response, consistent with our findings that FDX1 loss-of-function is conditionally lethal. Together, our findings establish that FDX1 directly engages with LIAS, promoting its role in cellular protein lipoylation, a process essential in maintaining cell viability under low glucose conditions.
Topics: Humans; Ferredoxins; Lipoylation; Protein Binding; Cell Respiration; Cell Proliferation; Metabolome; Sulfurtransferases
PubMed: 37453661
DOI: 10.1016/j.jbc.2023.105046 -
The Journal of Biological Chemistry Sep 2023Iron-sulfur clusters (ISC) are essential cofactors that participate in electron transfer, environmental sensing, and catalysis. Amongst the most ancient ISC-containing...
Iron-sulfur clusters (ISC) are essential cofactors that participate in electron transfer, environmental sensing, and catalysis. Amongst the most ancient ISC-containing proteins are the ferredoxin (FDX) family of electron carriers. Humans have two FDXs- FDX1 and FDX2, both of which are localized to mitochondria, and the latter of which is itself important for ISC synthesis. We have previously shown that hypoxia can eliminate the requirement for some components of the ISC biosynthetic pathway, but FDXs were not included in that study. Here, we report that FDX1, but not FDX2, is dispensable under 1% O in cultured human cells. We find that FDX1 is essential for production of the lipoic acid cofactor, which is synthesized by the ISC-containing enzyme lipoyl synthase. While hypoxia can rescue the growth phenotype of either FDX1 or lipoyl synthase KO cells, lipoylation in these same cells is not rescued, arguing against an alternative biosynthetic route or salvage pathway for lipoate in hypoxia. Our work reveals the divergent roles of FDX1 and FDX2 in mitochondria, identifies a role for FDX1 in lipoate synthesis, and suggests that loss of lipoic acid can be tolerated under low oxygen tensions in cell culture.
Topics: Humans; Ferredoxins; Lipoylation; Thioctic Acid; Cell Hypoxia; Gene Knockout Techniques; Oxygen; Proteome; Sulfurtransferases; Binding Sites; Protein Stability; Protein Biosynthesis
PubMed: 37481209
DOI: 10.1016/j.jbc.2023.105075 -
ELife Jan 2024Mammalian ferredoxin 1 and 2 (FDX1/2) belong to an evolutionary conserved family of iron-sulfur cluster containing proteins and act as electron shutters between...
Mammalian ferredoxin 1 and 2 (FDX1/2) belong to an evolutionary conserved family of iron-sulfur cluster containing proteins and act as electron shutters between ferredoxin reductase (FDXR) and numerous proteins involved in critical biological pathways. FDX1 is involved in biogenesis of steroids and bile acids, Vitamin A/D metabolism, and lipoylation of tricarboxylic acid (TCA) cycle enzymes. FDX1 has been extensively characterized biochemically but its role in physiology and lipid metabolism has not been explored. In this study, we generated -deficient mice and showed that knockout of both alleles of the gene led to embryonic lethality. We also showed that like +/-, +/- had a shorter life span and were prone to steatohepatitis. However, unlike +/-, +/- were not prone to spontaneous tumors. Additionally, we showed that FDX1 deficiency led to lipid droplet accumulation possibly via the ABCA1-SREBP1/2 pathway. Specifically, untargeted lipidomic analysis showed that FDX1 deficiency led to alterations in several classes of lipids, including cholesterol, triacylglycerides, acylcarnitines, ceramides, phospholipids and lysophospholipids. Taken together, our data indicate that FDX1 is essential for mammalian embryonic development and lipid homeostasis at both cellular and organismal levels.
Topics: Animals; Mice; Embryonic Development; Ferredoxins; Homeostasis; Iron-Sulfur Proteins; Lipids; Mammals
PubMed: 38251655
DOI: 10.7554/eLife.91656 -
Photosynthesis Research Dec 2017Ferredoxin-NADP reductase (FNR) catalyzes the last step of linear electron transfer in photosynthetic light reactions. The FAD cofactor of FNR accepts two electrons from... (Review)
Review
Ferredoxin-NADP reductase (FNR) catalyzes the last step of linear electron transfer in photosynthetic light reactions. The FAD cofactor of FNR accepts two electrons from two independent reduced ferredoxin molecules (Fd) in two sequential steps, first producing neutral semiquinone and then the fully anionic reduced, or hydroquinone, form of the enzyme (FNR). FNR transfers then both electrons in a single hydride transfer step to NADP. We are presenting the recent progress in studies focusing on Fd:FNR interaction and subsequent electron transfer processes as well as on interaction of FNR with NADP/H followed by hydride transfer, both from the structural and functional point of views. We also present the current knowledge about the physiological role(s) of various FNR isoforms present in the chloroplasts of higher plants and the functional impact of subchloroplastic location of FNR. Moreover, open questions and current challenges about the structure, function, and physiology of FNR are discussed.
Topics: Electron Transport; Ferredoxin-NADP Reductase; Ferredoxins; NADP; Photosynthesis
PubMed: 28361449
DOI: 10.1007/s11120-017-0372-0 -
Plant, Cell & Environment Jun 2013Ferredoxin (Fd) is a small [2Fe-2S] cluster-containing protein found in all organisms performing oxygenic photosynthesis. Fd is the first soluble acceptor of electrons... (Review)
Review
Ferredoxin (Fd) is a small [2Fe-2S] cluster-containing protein found in all organisms performing oxygenic photosynthesis. Fd is the first soluble acceptor of electrons on the stromal side of the chloroplast electron transport chain, and as such is pivotal to determining the distribution of these electrons to different metabolic reactions. In chloroplasts, the principle sink for electrons is in the production of NADPH, which is mostly consumed during the assimilation of CO2 . In addition to this primary function in photosynthesis, Fds are also involved in a number of other essential metabolic reactions, including biosynthesis of chlorophyll, phytochrome and fatty acids, several steps in the assimilation of sulphur and nitrogen, as well as redox signalling and maintenance of redox balance via the thioredoxin system and Halliwell-Asada cycle. This makes Fds crucial determinants of the electron transfer between the thylakoid membrane and a variety of soluble enzymes dependent on these electrons. In this article, we will first describe the current knowledge on the structure and function of the various Fd isoforms present in chloroplasts of higher plants and then discuss the processes involved in oxidation of Fd, introducing the corresponding enzymes and discussing what is known about their relative interaction with Fd.
Topics: Chloroplasts; Electron Transport; Ferredoxins; Photosynthesis; Plants
PubMed: 23190083
DOI: 10.1111/pce.12046 -
Molecules (Basel, Switzerland) May 2022Superfolds are folds commonly observed among evolutionarily unrelated multiple superfamilies of proteins. Since discovering superfolds almost two decades ago, structural...
Superfolds are folds commonly observed among evolutionarily unrelated multiple superfamilies of proteins. Since discovering superfolds almost two decades ago, structural rules distinguishing superfolds from the other ordinary folds have been explored but remained elusive. Here, we analyzed a typical superfold, the ferredoxin fold, and the fold which reverses the N to C terminus direction from the ferredoxin fold as a case study to find the rule to distinguish superfolds from the other folds. Though all the known structural characteristics for superfolds apply to both the ferredoxin fold and the reverse ferredoxin fold, the reverse fold has been found only in a single superfamily. The database analyses in the present study revealed the structural preferences of αβ- and βα-units; the preferences separate two α-helices in the ferredoxin fold, preventing their collision and stabilizing the fold. In contrast, in the reverse ferredoxin fold, the preferences bring two helices near each other, inducing structural conflict. The Rosetta folding simulations suggested that the ferredoxin fold is physically much more realizable than the reverse ferredoxin fold. Therefore, we propose that minimal structural conflict or minimal frustration among secondary structures is the rule to distinguish a superfold from ordinary folds. Intriguingly, the database analyses revealed that a most stringent structural rule in proteins, the right-handedness of the βαβ-unit, is broken in a set of structures to prevent the frustration, suggesting the proposed rule of minimum frustration among secondary structural units is comparably strong as the right-handedness rule of the βαβ-unit.
Topics: Ferredoxins; Protein Conformation; Protein Folding; Protein Structure, Secondary; Proteins
PubMed: 35684484
DOI: 10.3390/molecules27113547 -
Journal of Experimental Botany Oct 2014Ferredoxins are electron shuttles harbouring iron-sulfur clusters that connect multiple oxido-reductive pathways in organisms displaying different lifestyles. Some... (Review)
Review
Ferredoxins are electron shuttles harbouring iron-sulfur clusters that connect multiple oxido-reductive pathways in organisms displaying different lifestyles. Some prokaryotes and algae express an isofunctional electron carrier, flavodoxin, which contains flavin mononucleotide as cofactor. Both proteins evolved in the anaerobic environment preceding the appearance of oxygenic photosynthesis. The advent of an oxygen-rich atmosphere proved detrimental to ferredoxin owing to iron limitation and oxidative damage to the iron-sulfur cluster, and many microorganisms induced flavodoxin expression to replace ferredoxin under stress conditions. Paradoxically, ferredoxin was maintained throughout the tree of life, whereas flavodoxin is absent from plants and animals. Of note is that flavodoxin expression in transgenic plants results in increased tolerance to multiple stresses and iron deficit, through mechanisms similar to those operating in microorganisms. Then, the question remains open as to why a trait that still confers plants such obvious adaptive benefits was not retained. We compare herein the properties of ferredoxin and flavodoxin, and their contrasting modes of expression in response to different environmental stimuli. Phylogenetic analyses suggest that the flavodoxin gene was already absent in the algal lineages immediately preceding land plants. Geographical distribution of phototrophs shows a bias against flavodoxin-containing organisms in iron-rich coastal/freshwater habitats. Based on these observations, we propose that plants evolved from freshwater macroalgae that already lacked flavodoxin because they thrived in an iron-rich habitat with no need to back up ferredoxin functions and therefore no selective pressure to keep the flavodoxin gene. Conversely, ferredoxin retention in the plant lineage is probably related to its higher efficiency as an electron carrier, compared with flavodoxin. Several lines of evidence supporting these contentions are presented and discussed.
Topics: Biological Evolution; Electron Transport; Ferredoxins; Flavodoxin; Iron; Phylogeny
PubMed: 25009172
DOI: 10.1093/jxb/eru273 -
Proceedings of the National Academy of... Dec 1996A 16-amino acid residue peptide derived from a consensus motif of natural ferredoxins incorporates a tetranuclear iron sulfur cluster under physiological conditions....
A 16-amino acid residue peptide derived from a consensus motif of natural ferredoxins incorporates a tetranuclear iron sulfur cluster under physiological conditions. Successful assembly of the [4Fe-4S]2+/1+ cluster within a monomeric peptide was demonstrated using size exclusion chromatography, UV-visible, visible CD, and cryogenic EPR spectroscopies. The robustness of [4Fe-4S]2+/1+ formation was tested using peptides with either the ligating cysteine exchanged for alanine or with the intervening amino acids replaced by glycine. The small size of the peptide allows for modular incorporation into more complex protein structures. In one larger structure, we describe a tetra-alpha-helix bundle that self-assembles both iron-sulfur clusters and hemes, thereby demonstrating feasibility for the general synthesis of maquettes containing multiple, juxtaposed redox cofactors. This is a motif common to the catalytic sites of native oxidoreductases.
Topics: Amino Acid Sequence; Circular Dichroism; Electron Spin Resonance Spectroscopy; Ferredoxins; Heme; Models, Molecular; Molecular Sequence Data; Peptide Fragments; Protein Structure, Secondary; Pseudomonas; Spectrophotometry
PubMed: 8986760
DOI: 10.1073/pnas.93.26.15041 -
Trends in Parasitology Oct 2022The apicoplast, a relict plastid found in most species of the phylum Apicomplexa, harbors the ferredoxin redox system which supplies electrons to enzymes of various... (Review)
Review
The apicoplast, a relict plastid found in most species of the phylum Apicomplexa, harbors the ferredoxin redox system which supplies electrons to enzymes of various metabolic pathways in this organelle. Recent reports in Toxoplasma gondii and Plasmodium falciparum have shown that the iron-sulfur cluster (FeS)-containing ferredoxin is essential in tachyzoite and blood-stage parasites, respectively. Here we review ferredoxin's crucial contribution to isoprenoid and lipoate biosynthesis as well as tRNA modification in the apicoplast, highlighting similarities and differences between the two species. We also discuss ferredoxin's potential role in the initial reductive steps required for FeS synthesis as well as recent evidence that offers an explanation for how NADPH required by the redox system might be generated in Plasmodium spp.
Topics: Apicomplexa; Apicoplasts; Electrons; Ferredoxins; Iron; NADP; Oxidation-Reduction; Plasmodium falciparum; RNA, Transfer; Sulfur; Terpenes; Toxoplasma
PubMed: 35999149
DOI: 10.1016/j.pt.2022.08.002 -
Current Issues in Molecular Biology Sep 2021Ferredoxins, iron-sulfur (Fe-S) cluster proteins, play a key role in oxidoreduction reactions. To date, evolutionary analysis of these proteins across the domains of...
Ferredoxins, iron-sulfur (Fe-S) cluster proteins, play a key role in oxidoreduction reactions. To date, evolutionary analysis of these proteins across the domains of life have been confined to observing the abundance of Fe-S cluster types (2Fe-2S, 3Fe-4S, 4Fe-4S, 7Fe-8S (3Fe-4s and 4Fe-4S) and 2[4Fe-4S]) and the diversity of ferredoxins within these cluster types was not studied. To address this research gap, here we propose a subtype classification and nomenclature for ferredoxins based on the characteristic spacing between the cysteine amino acids of the Fe-S binding motif as a subtype signature to assess the diversity of ferredoxins across the living organisms. To test this hypothesis, comparative analysis of ferredoxins between bacterial groups, and and ferredoxins collected from species of different domains of life that are reported in the literature has been carried out. Ferredoxins were found to be highly diverse within their types. Large numbers of alphaproteobacterial species ferredoxin subtypes were found in species and the same ferredoxin subtypes across the species of Bacteria, Archaea, and Eukarya, suggesting shared common ancestral origin of ferredoxins between Archaea and Bacteria and lateral gene transfer of ferredoxins from prokaryotes (Archaea/Bacteria) to eukaryotes. This study opened new vistas for further analysis of diversity of ferredoxins in living organisms.
Topics: Archaea; Bacteria; Computational Biology; Databases, Genetic; Eukaryota; Evolution, Molecular; Ferredoxins; Genetic Variation; Phylogeny; Species Specificity
PubMed: 34698119
DOI: 10.3390/cimb43030098