The iron-sulfur cluster assembly machineries in plants: current knowledge and open questions

Abstract

Many metabolic pathways and cellular processes occurring in most sub-cellular compartments depend on the functioning of iron-sulfur (Fe-S) proteins, whose cofactors are assembled through dedicated protein machineries. Recent advances have been made in the knowledge of the functions of individual components through a combination of genetic, biochemical and structural approaches, primarily in prokaryotes and non-plant eukaryotes. Whereas most of the components of these machineries are conserved between kingdoms, their complexity is likely increased in plants owing to the presence of additional assembly proteins and to the existence of expanded families for several assembly proteins. This review focuses on the new actors discovered in the past few years, such as glutaredoxin, BOLA and NEET proteins as well as MIP18, MMS19, TAH18, DRE2 for the cytosolic machinery, which are integrated into a model for the plant Fe-S cluster biogenesis systems. It also discusses a few issues currently subjected to an intense debate such as the role of the mitochondrial frataxin and of glutaredoxins, the functional separation between scaffold, carrier and iron-delivery proteins and the crosstalk existing between different organelles.

Keywords: assembly machineries; carrier Proteins; iron donor; iron-sulfur; repair; scaffold proteins.

Figure 1

Different types of Fe-S clusters found in proteins from photosynthetic organisms. Schematic representation of Fe-S clusters and their ligands with sulfur, iron and nitrogen atoms colored in yellow, green and blue, respectively. (A). classical [Fe₂S₂] ligated by four cysteines as in ferredoxin from Cyanidioschyzon merolae, (B). NEET-type [Fe₂S₂] ligated by three cysteines and one histidine as in Arabidopsis thaliana NEET, (C). Rieske-type [Fe₂S₂] ligated by two cysteines and two histidines as in the Rieske protein subunit of the b₆/f complex from Spinacia oleracea, (D). [Fe₃S₄] ligated by three cysteines as in Synechocystis sp. PCC 6803 glutamate synthase, (E). [Fe₄S₄] ligated by four cysteines as in the ferredoxin-thioredoxin reductase from Synechocystis sp. PCC 6803, and (F). [Fe₄S₄] ligated by four cysteines but with one thiolate ligand serving also for siroheme as in Nicotiana tabacum nitrite reductase. PDB codes used for drawing these clusters using Pymol are 3AB5, 3S2Q, 1RFS, 1OFD, 2PU9, and 3B0G, respectively.

Figure 2

The two-steps of de novo assembly of Fe-S clusters. An Fe-S cluster is assembled on scaffold proteins (S) from iron and sulfur sulfane generated as a persulfide on cysteine desulfurase whose activity is regulated by specific proteins (R). For this step, two electrons are required to reduce sulfur sulfane (S⁰) into sulfide (S²⁻). This cluster is subsequently transferred to acceptor apoproteins via the action of carrier proteins (C). The cysteine desulfurase is colored in yellow and the regulators in orange. Putative scaffold and carrier proteins are colored in purple and green, respectively.

Figure 3

Model for the Fe-S cluster assembly machinery in mitochondria. This scheme has been drawn essentially based on the current models of Fe-S cluster assembly for the bacterial and the mitochondrial yeast ISC machineries. The color code is the same as in Figure 2. The complex between the cysteine desulfurase NFS1 and ISD11 mobilizes sulfur from cysteine and frataxin (FH) promotes the interaction with the scaffold protein ISUs and favor sulfur transfer reaction. In addition to iron whose origin is yet unidentified, the Fe-S cluster synthesis on ISUs also requires electrons probably coming from the ferredoxin/ferredoxin reductase system. According to the yeast model, HSCA, HSCB, MGE1 and GRXS15 may be involved in Fe-S cluster release from ISU and subsequent transfer to carrier proteins such as IND1, ISCA2-4/IBA57 couple and NFU4-5 that finally transfer the Fe-S cluster to specific target proteins. Due to its localization in mitochondria and its ability to stimulate in vitro the activity of NFS1, SUFE1 may also be involved in sulfur mobilization.

Figure 4

Model for the Fe-S cluster assembly machinery in chloroplasts. This scheme has been drawn essentially based on the current models of Fe-S cluster assembly for the plant plastidial and bacterial SUF assembly machineries. The color code is the same as in Figure 2. SUFE1/2 stimulate the cysteine desulfurase activity of NFS2 and transfer the sulfur to SUFB that fulfills scaffold protein function by forming a complex with SUFC and SUFD. The iron source is unknown and electrons may be channeled from NADPH to a SUFB-bound FAD via an as yet unidentified flavin reductase. Fe-S cluster transfer to specific proteins is then accomplished by carrier proteins. Hence, NFU2 and HCF101 are involved in the maturation of one or several proteins belonging to PSI and some other stromal proteins. Up to now, target proteins of SUFA1, NFU1 and 3 are not identified. Finally, some plants possess a plastidial isoform of IBA57. By analogy with the mitochondrial isoform, plastidial IBA57 might act as carrier protein in conjunction with SUFA1 but this assumption awaits confirmation. Finally, the role of GRXS14 and GRXS16 is uncertain but they may be involved in Fe-S cluster release from scaffold protein as in mitochondria and/or they could be carrier proteins for the delivery of Fe-S clusters to specific target proteins.

Figure 5

Model for the Fe-S cluster assembly machinery in the cytosol. Both the CIA machinery and the connected ISC export machinery have been represented. The color code is the same as in Figure 2. A sulfide compound originating from NFS1 activity and preferentially transported by the ATM3 transporter may represent the sulfur source for Fe-S cluster biogenesis in the cytosol. ERV1, another mitochondrial protein and glutathione are also important for this process although their specific roles are not elucidated. As for organellar assembly machineries, the iron source is also unclear. Based on yeast and human models of the CIA machinery assembly, TAH18 transfers electrons from NADPH to DRE2. In plants, NBP35 constitutes the sole scaffold protein. Then, the Fe-S cluster is transferred to target apoproteins via a NAR1-CIA1-AE7-MET18 complex. The involvement of GRXS17 and of ISU1, HSCA and HSCB in the cytosolic Fe-S cluster biogenesis is not yet elucidated.

Figure 6

Evolution of selected Fe-S biogenesis components in photosynthetic organisms. Proteins belonging to the SUFE, AE7 and NFU families have been retrieved in 17 other genomes from microphytes, bryophytes, monocots and dicots available in the Phytozome (version 9.1) database (http://www.phytozome.net/) by BLASTP or TBLASTN using Arabidopsis amino acid sequences. The amino acid sequence alignments were done using CLUSTALW and imported into the Molecular Evolutionary Genetics Analysis (MEGA) package version 4.1 for the phylogenetic analysis. Phylogenetic analyses were conducted using the neighbor-joining (NJ) method implemented in MEGA, with the pairwise deletion option for handling alignment gaps, and with the Poisson correction model for distance computation. Bootstrap tests were conducted using 1000 replicates. Branch lengths are proportional to phylogenetic distances. For more clarity, protein names have been removed and replaced by colored circles corresponding to specific organisms.