Iron-sulfur cluster biosynthesis in photosynthetic organisms

Parameterization of a Fluctuating Charge Model for Complexes Containing 3d Transition Metals

Metalloproteins widely exist in biology, playing pivotal roles in diverse life processes. Meanwhile, molecular dynamics (MD) simulations based on classical force fields has emerged as an important tool in scientific research. Partial charges are critical parameters within classical force fields and usually derived from quantum mechanical (QM) calculations. However, QM calculations are often time-consuming and prone to basis set dependence. Alternatively, fluctuating charge (FQ) models offer another avenue for partial charge derivation, which has significant speed advantages and can be used for large-scale screening. Building upon our previous work, which introduced an FQ model for zinc-containing complexes, herein we extend this model to include additional 3d transition metals which are important to the life sciences, namely chromium, manganese, iron, cobalt, and nickel. Employing CM5 charges as target for parametrization, our FQ model accurately reproduces partial charges for 3d metal complexes featuring biologically relevant ligands. Furthermore, by using atomic charges derived by our FQ model, MD simulations have been performed. These charges showed excellent performance in simulating proteomic metal sites housing multiple metal ions, specifically, a metalloprotein containing an iron-sulfur cluster and another containing a dimanganese metal site, showcasing comparable performance to those of RESP charges. We anticipate that our study can accelerate the parametrization of atomic charges for metalloproteins featuring 3d transition metals, thereby facilitating simulations of relevant systems.

The Effect of Geometry, Spin, and Orbital Optimization in Achieving Accurate, Correlated Results for Iron-Sulfur Cubanes

Iron-sulfur clusters comprise an important functional motif in the catalytic centers of biological systems, capable of enabling important chemical transformations at ambient conditions. This remarkable capability derives from a notoriously complex electronic structure that is characterized by a high density of states that is sensitive to geometric changes. The spectral sensitivity to subtle geometric changes has received little attention from correlated, large active space calculations, owing partly to the exceptional computational complexity for treating these large and correlated systems accurately. To provide insight into this aspect, we report the first Complete Active Space Self Consistent Field (CASSCF) calculations for different geometries of the [Fe(II/III)₄S₄(SMe)₄]^-2 clusters using two complementary, correlated solvers: spin-pure Adaptive Sampling Configuration Interaction (ASCI) and Density Matrix Renormalization Group (DMRG). We find that the previously established picture of a double-exchange driven magnetic structure, with minute energy gaps (<1 mHa) between consecutive spin states, has a weak dependence on the underlying geometry. However, the spin gap between the singlet and the spin state 2S + 1 = 19, corresponding to a maximal number of Fe-d electrons being unpaired and of parallel spin, is strongly geometry dependent, changing by a factor of 3 upon slight deformations that are still within biologically relevant parameters. The CASSCF orbital optimization procedure, using active spaces as large as 86 electrons in 52 orbitals, was found to reduce this gap compared to typical mean-field orbital approaches. Our results show the need for performing large active space calculations to unveil the challenging electronic structure of these complex catalytic centers and should serve as accurate starting points for fully correlated treatments upon inclusion of dynamical correlation outside the active space.

Transcript profiling of stress-responsive genes and metabolic changes during salinity in indica and japonica rice exhibit distinct varietal difference

In the present study, we carried out comprehensive transcript profiling of diverse genes under salinity (200 mM NaCl) at different time points, accompanied by certain biochemical alterations of the indica (IR-64 and Pokkali) and japonica (Nipponbare and M-202) rice. The higher susceptibility of Nipponbare and IR-64 was reflected by lower relative water content, chlorophyll loss, higher malondialdehyde content, and accumulation of H₂ O₂ , and reduced nitrate reductase activity, compared to M-202 and Pokkali, where such changes were less pronounced. Enhanced levels of anthocyanins and reduced glutathione, together with elevated phenylalanine ammonia lyase activity, mainly conferred protection to Nipponbare and IR-64, while metabolites like phenolics, flavonoids, proline, and polyamines were more induced in M-202 and Pokkali. Varietal differences in the expression pattern of diverse groups of genes during different durations (6, 24, and 48 h) of stress were striking. A gene showing early induction for a particular variety exhibited a delayed induction in another variety or a gradually decreased expression with treatment time. Pokkali was clearly identified as the salt-tolerant genotype among the examined varieties based on increased antioxidant potential and enhanced expression of genes encoding for PAL, CHS, and membrane transporters like SOS3, NHX-1, and HKT-1. The results presented in this work provide insight into the complex varying regulation patterns for different genes across the investigated rice varieties in providing salt tolerance and highlights distinct differences in expression patterns between susceptible and tolerant indica and japonica rice.

Current knowledge and recent advances in understanding metabolism of the model cyanobacterium Synechocystis sp. PCC 6803

Cyanobacteria are key organisms in the global ecosystem, useful models for studying metabolic and physiological processes conserved in photosynthetic organisms, and potential renewable platforms for production of chemicals. Characterizing cyanobacterial metabolism and physiology is key to understanding their role in the environment and unlocking their potential for biotechnology applications. Many aspects of cyanobacterial biology differ from heterotrophic bacteria. For example, most cyanobacteria incorporate a series of internal thylakoid membranes where both oxygenic photosynthesis and respiration occur, while CO2 fixation takes place in specialized compartments termed carboxysomes. In this review, we provide a comprehensive summary of our knowledge on cyanobacterial physiology and the pathways in Synechocystis sp. PCC 6803 (Synechocystis) involved in biosynthesis of sugar-based metabolites, amino acids, nucleotides, lipids, cofactors, vitamins, isoprenoids, pigments and cell wall components, in addition to the proteins involved in metabolite transport. While some pathways are conserved between model cyanobacteria, such as Synechocystis, and model heterotrophic bacteria like Escherichia coli, many enzymes and/or pathways involved in the biosynthesis of key metabolites in cyanobacteria have not been completely characterized. These include pathways required for biosynthesis of chorismate and membrane lipids, nucleotides, several amino acids, vitamins and cofactors, and isoprenoids such as plastoquinone, carotenoids, and tocopherols. Moreover, our understanding of photorespiration, lipopolysaccharide assembly and transport, and degradation of lipids, sucrose, most vitamins and amino acids, and haem, is incomplete. We discuss tools that may aid our understanding of cyanobacterial metabolism, notably CyanoSource, a barcoded library of targeted Synechocystis mutants, which will significantly accelerate characterization of individual proteins.

Interplay between formation of photosynthetic complexes and expression of genes for iron-sulfur cluster assembly in Rhodobacter sphaeroides?

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.

Compartmentalisation of [FeFe]-hydrogenase maturation in Chlamydomonas reinhardtii

Molecular hydrogen (H₂ ) can be produced in green microalgae by [FeFe]-hydrogenases as a direct product of photosynthesis. The Chlamydomonas reinhardtii hydrogenase HYDA1 contains a catalytic site comprising a classic [4Fe4S] cluster linked to a unique 2Fe sub-cluster. From in vitro studies it appears that the [4Fe4S] cluster is incorporated first by the housekeeping FeS cluster assembly machinery, followed by the 2Fe sub-cluster, whose biosynthesis requires the specific maturases HYDEF and HYDG. To investigate the maturation process in vivo, we expressed HYDA1 from the C. reinhardtii chloroplast and nuclear genomes (with and without a chloroplast transit peptide) in a hydrogenase-deficient mutant strain, and examined the cellular enzymatic hydrogenase activity, as well as in vivo H₂ production. The transformants expressing HYDA1 from the chloroplast genome displayed levels of H₂ production comparable to the wild type, as did the transformants expressing full-length HYDA1 from the nuclear genome. In contrast, cells equipped with cytoplasm-targeted HYDA1 produced inactive enzyme, which could only be activated in vitro after reconstitution of the [4Fe4S] cluster. This indicates that the HYDA1 FeS cluster can only be built by the chloroplastic FeS cluster assembly machinery. Further, the expression of a bacterial hydrogenase gene, CPI, from the C. reinhardtii chloroplast genome resulted in H₂ -producing strains, demonstrating that a hydrogenase with a very different structure can fulfil the role of HYDA1 in vivo and that overexpression of foreign hydrogenases in C. reinhardtii is possible. All chloroplast transformants were stable and no toxic effects were seen from HYDA1 or CPI expression.

The functions of cardiolipin in cellular metabolism-potential modifiers of the Barth syndrome phenotype

The phospholipid cardiolipin (CL) plays a role in many cellular functions and signaling pathways both inside and outside of mitochondria. This review focuses on the role of CL in energy metabolism. Many reactions of electron transport and oxidative phosphorylation, the transport of metabolites required for these processes, and the stabilization of electron transport chain supercomplexes require CL. Recent studies indicate that CL is required for the synthesis of iron-sulfur (Fe-S) co-factors, which are essential for numerous metabolic pathways. Activation of carnitine shuttle enzymes that are required for fatty acid metabolism is CL dependent. The presence of substantial amounts of CL in the peroxisomal membrane suggests that CL may be required for peroxisomal functions. Understanding the role of CL in energy metabolism may identify physiological modifiers that exacerbate the loss of CL and underlie the variation in symptoms observed in Barth syndrome, a genetic disorder of CL metabolism.

Iron cofactor assembly in plants

Iron is an essential element for all photosynthetic organisms. The biological use of this transition metal is as an enzyme cofactor, predominantly in electron transfer and catalysis. The main forms of iron cofactor are, in order of decreasing abundance, iron-sulfur clusters, heme, and di-iron or mononuclear iron, with a wide functional range. In plants and algae, iron-sulfur cluster assembly pathways of bacterial origin are localized in the mitochondria and plastids, where there is a high demand for these cofactors. A third iron-sulfur cluster assembly pathway is present in the cytosol that depends on the mitochondria but not on plastid assembly proteins. The biosynthesis of heme takes place mainly in the plastids. The importance of iron-sulfur cofactors beyond photosynthesis and respiration has become evident with recent discoveries of novel iron-sulfur proteins involved in epigenetics and DNA metabolism. In addition, increased understanding of intracellular iron trafficking is opening up research into how iron is distributed between iron cofactor assembly pathways and how this distribution is regulated.

Iron-sulfur clusters: biogenesis, molecular mechanisms, and their functional significance

Iron-sulfur clusters [Fe-S] are small, ubiquitous inorganic cofactors representing one of the earliest catalysts during biomolecule evolution and are involved in fundamental biological reactions, including regulation of enzyme activity, mitochondrial respiration, ribosome biogenesis, cofactor biogenesis, gene expression regulation, and nucleotide metabolism. Although simple in structure, [Fe-S] biogenesis requires complex protein machineries and pathways for assembly. [Fe-S] are assembled from cysteine-derived sulfur and iron onto scaffold proteins followed by transfer to recipient apoproteins. Several predominant iron-sulfur biogenesis systems have been identified, including nitrogen fixation (NIF), sulfur utilization factor (SUF), iron-sulfur cluster (ISC), and cytosolic iron-sulfur protein assembly (CIA), and many protein components have been identified and characterized. In eukaryotes ISC is mainly localized to mitochondria, cytosolic iron-sulfur protein assembly to the cytosol, whereas plant sulfur utilization factor is localized mainly to plastids. Because of this spatial separation, evidence suggests cross-talk mediated by organelle export machineries and dual targeting mechanisms. Although research efforts in understanding iron-sulfur biogenesis has been centered on bacteria, yeast, and plants, recent efforts have implicated inappropriate [Fe-S] biogenesis to underlie many human diseases. In this review we detail our current understanding of [Fe-S] biogenesis across species boundaries highlighting evolutionary conservation and divergence and assembling our knowledge into a cellular context.

Building Fe-S proteins: bacterial strategies

The broad range of cellular activities carried out by Fe-S proteins means that they have a central role in the life of most organisms. At the interface between biology and chemistry, studies of bacterial Fe-S protein biogenesis have taken advantage of the specific approaches of each field and have begun to reveal the molecular mechanisms involved. The multiprotein systems that are required to build Fe-S proteins have been identified, but the in vivo roles of some of the components remain to be clarified. The way in which cellular Fe-S cluster trafficking pathways are organized remains a key issue for future studies.

Chloroplast DnaJ-like proteins 3 and 4 (CDJ3/4) from Chlamydomonas reinhardtii contain redox-active Fe–S clusters and interact with stromal HSP70B

In the present study we report on the identification and characterization of three novel chloroplast-targeted DnaJ-like proteins CDJ3–5, which in addition to their J-domains contain bacterial-type ferredoxin domains. In sequence databases we could identify homologues of CDJ3–5 in green algae, moss and higher plants, but not in cyanobacteria. Phylogenetic analyses allowed us to distinguish two clades containing CDJ3/4 and CDJ5 that must have diverged early in the ancestor of the ‘green lineage’ and have further diversified later on. Molecular and biochemical analysis of CDJ3 and CDJ4 from Chlamydomonas reinhardtii revealed that both proteins are weakly expressed and appear to be localized to the stroma and to thylakoid membranes respectively. The low transcript levels of the CDJ3 and CDJ4 genes declined even further in the initial phase of heat shock, but CDJ3 transcript levels strongly increased after a dark-to-light shift. Accordingly, the Arabidopsis orthologue of CDJ5 was also found to be light-inducible and to be under strong circadian control. CDJ3 and CDJ4 proteins could both be expressed in Escherichia coli and had redox-active Fe–S clusters. In vitro cross-linking studies demonstrated that CDJ3 and CDJ4 interact with chloroplast ATP-bound HSP70B (heat-shock protein 70B), presumably as dimers, and immunoprecipitation studies showed that CDJ3/4 were also in a complex with HSP70B in Chlamydomonas cell extracts. Finally, CDJ3 was found in complexes with apparent molecular masses of approx. 550–2800 kDa, which appeared to contain RNA. We speculate that the CDJ3–5 proteins might represent redox switches that act by recruiting HSP70B for the reorganization of regulatory protein complexes.

SufU is an essential iron-sulfur cluster scaffold protein in Bacillus subtilis

Bacteria use three distinct systems for iron-sulfur (Fe/S) cluster biogenesis: the ISC, SUF, and NIF machineries. The ISC and SUF systems are widely distributed, and many bacteria possess both of them. In Escherichia coli, ISC is the major and constitutive system, whereas SUF is induced under iron starvation and/or oxidative stress. Genomic analysis of the Fe/S cluster biosynthesis genes in Bacillus subtilis suggests that this bacterium's genome encodes only a SUF system consisting of a sufCDSUB gene cluster and a distant sufA gene. Mutant analysis of the putative Fe/S scaffold genes sufU and sufA revealed that sufU is essential for growth under minimal standard conditions, but not sufA. The drastic growth retardation of a conditional mutant depleted of SufU was coupled with a severe reduction of aconitase and succinate dehydrogenase activities in total-cell lysates, suggesting a crucial function of SufU in Fe/S protein biogenesis. Recombinant SufU was devoid of Fe/S clusters after aerobic purification. Upon in vitro reconstitution, SufU bound an Fe/S cluster with up to approximately 1.5 Fe and S per monomer. The assembled Fe/S cluster could be transferred from SufU to the apo form of isopropylmalate isomerase Leu1, rapidly forming catalytically active [4Fe-4S]-containing holo-enzyme. In contrast to native SufU, its D43A variant carried a Fe/S cluster after aerobic purification, indicating that the cluster is stabilized by this mutation. Further, we show that apo-SufU is an activator of the cysteine desulfurase SufS by enhancing its activity about 40-fold in vitro. SufS-dependent formation of holo-SufU suggests that SufU functions as an Fe/S cluster scaffold protein tightly cooperating with the SufS cysteine desulfurase.

Chloroplast HCF101 is a scaffold protein for [4Fe-4S] cluster assembly

Oxygen-evolving chloroplasts possess their own iron-sulfur cluster assembly proteins including members of the SUF (sulfur mobilization) and the NFU family. Recently, the chloroplast protein HCF101 (high chlorophyll fluorescence 101) has been shown to be essential for the accumulation of the membrane complex Photosystem I and the soluble ferredoxin-thioredoxin reductases, both containing [4Fe-4S] clusters. The protein belongs to the FSC-NTPase ([4Fe-4S]-cluster-containing P-loop NTPase) superfamily, several members of which play a crucial role in Fe/S cluster biosynthesis. Although the C-terminal ISC-binding site, conserved in other members of the FSC-NTPase family, is not present in chloroplast HCF101 homologues using Mössbauer and EPR spectroscopy, we provide evidence that HCF101 binds a [4Fe-4S] cluster. 55Fe incorporation studies of mitochondrially targeted HCF101 in Saccharomyces cerevisiae confirmed the assembly of an Fe/S cluster in HCF101 in an Nfs1-dependent manner. Site-directed mutagenesis identified three HCF101-specific cysteine residues required for assembly and/or stability of the cluster. We further demonstrate that the reconstituted cluster is transiently bound and can be transferred from HCF101 to a [4Fe-4S] apoprotein. Together, our findings suggest that HCF101 may serve as a chloroplast scaffold protein that specifically assembles [4Fe-4S] clusters and transfers them to the chloroplast membrane and soluble target proteins.

Dual localized AtHscB involved in iron sulfur protein biogenesis in Arabidopsis

Background

Iron-sulfur clusters are ubiquitous structures which act as prosthetic groups for numerous proteins involved in several fundamental biological processes including respiration and photosynthesis. Although simple in structure both the assembly and insertion of clusters into apoproteins requires complex biochemical pathways involving a diverse set of proteins. In yeast, the J-type chaperone Jac1 plays a key role in the biogenesis of iron sulfur clusters in mitochondria.

Methodology/Principal Findings

In this study we demonstrate that AtHscB from Arabidopsis can rescue the Jac1 yeast knockout mutant suggesting a role for AtHscB in iron sulfur protein biogenesis in plants. In contrast to mitochondrial Jac1, AtHscB localizes to both mitochondria and the cytosol. AtHscB interacts with AtIscU1, an Isu-like scaffold protein involved in iron-sulfur cluster biogenesis, and through this interaction AtIscU1 is most probably retained in the cytosol. The chaperone AtHscA can functionally complement the yeast Ssq1knockout mutant and its ATPase activity is enhanced by AtHscB and AtIscU1. Interestingly, AtHscA is also localized in both mitochondria and the cytosol. Furthermore, AtHscB is highly expressed in anthers and trichomes and an AtHscB T-DNA insertion mutant shows reduced seed set, a waxless phenotype and inappropriate trichome development as well as dramatically reduced activities of the iron-sulfur enzymes aconitase and succinate dehydrogenase.

Conclusions

Our data suggest that AtHscB together with AtHscA and AtIscU1 plays an important role in the biogenesis of iron-sulfur proteins in both mitochondria and the cytosol.

An allelic mutant series of ATM3 reveals its key role in the biogenesis of cytosolic iron-sulfur proteins in Arabidopsis

The ATP-binding cassette transporters of mitochondria (ATMs) are highly conserved proteins, but their function in plants is poorly defined. Arabidopsis (Arabidopsis thaliana) has three ATM genes, namely ATM1, ATM2, and ATM3. Using a collection of insertional mutants, we show that only ATM3 has an important function for plant growth. Additional atm3 alleles were identified among sirtinol-resistant lines, correlating with decreased activities of aldehyde oxidases, cytosolic enzymes that convert sirtinol into an auxin analog, and depend on iron-sulfur (Fe-S) and molybdenum cofactor (Moco) as prosthetic groups. In the sirtinol-resistant atm3-3 allele, the highly conserved arginine-612 is replaced by a lysine residue, the negative effect of which could be mimicked in the yeast Atm1p ortholog. Arabidopsis atm3 mutants displayed defects in root growth, chlorophyll content, and seedling establishment. Analyses of selected metal enzymes showed that the activity of cytosolic aconitase (Fe-S) was strongly decreased across the range of atm3 alleles, whereas mitochondrial and plastid Fe-S enzymes were unaffected. Nitrate reductase activity (Moco, heme) was decreased by 50% in the strong atm3 alleles, but catalase activity (heme) was similar to that of the wild type. Strikingly, in contrast to mutants in the yeast and mammalian orthologs, Arabidopsis atm3 mutants did not display a dramatic iron homeostasis defect and did not accumulate iron in mitochondria. Our data suggest that Arabidopsis ATM3 may transport (1) at least two distinct compounds or (2) a single compound required for both Fe-S and Moco assembly machineries in the cytosol, but not iron.

Iron-sulfur cluster biogenesis systems and their crosstalk

The biogenesis of iron-sulfur clusters ([Fe-S]) plays a very important role in many essential functions of life. Several [Fe-S] biogenesis systems have been discovered, such as the NIF (nitrogen fixation), SUF (mobilisation of sulfur) and ISC (iron-sulfur cluster) systems in bacteria, and the ISC-like and CIA (cytosolic iron-sulfur protein assembly) systems in yeast. Experimental evidence has revealed that SUF and ISC in bacteria communicate with each other partly through IscR to coordinate the utilisation of iron and cysteine. The ISC-like system in yeast is localised to the mitochondria, while the ISC-dependent CIA system is localised to the cytosol; this suggests a possible role for the ISC mitochondrial export machinery in mediating crosstalk between the two systems. Based on genetic analysis, the model plant Arabidopsis thaliana contains three [Fe-S] biogenesis systems similar to SUF, ISC and CIA named AtSUF, AtISC and AtCIA. Possible communication between these three systems has been proposed.

Genome analysis of Chlamydomonas reinhardtii reveals the existence of multiple, compartmentalized iron-sulfur protein assembly machineries of different evolutionary origins

The unicellular green alga Chlamydomonas reinhardtii is used extensively as a model to study eukaryotic photosynthesis, flagellar functions, and more recently the production of hydrogen as biofuel. Two of these processes, photosynthesis and hydrogen production, are highly dependent on iron-sulfur (Fe-S) enzymes. To understand how Fe-S proteins are assembled in Chlamydomonas, we have analyzed its recently sequenced genome for orthologs of genes involved in Fe-S cluster assembly. We found a total of 32 open reading frames, most single copies, that are thought to constitute a mitochondrial assembly pathway, mitochondrial export machinery, a cytosolic assembly pathway, and components for Fe-S cluster assembly in the chloroplast. The chloroplast proteins are also expected to play a role in the assembly of the H-cluster in [FeFe]-hydrogenases, together with the recently identified HydEF and HydG proteins. Comparison with the higher plant model Arabidopsis indicated a strong degree of conservation of Fe-S cofactor assembly pathways in the green lineage, the pathways being derived from different origins during the evolution of the photosynthetic eukaryote. As a haploid, unicellular organism with available forward and reverse genetic tools, Chlamydomonas provides an excellent model system to study Fe-S cluster assembly and its regulation in photosynthetic eukaryotes.

Biogenesis of Fe/S proteins and pathogenicity: IscR plays a key role in allowing Erwinia chrysanthemi to adapt to hostile conditions

The Erwinia chrysanthemi genome is predicted to encode three systems, Nif, Isc and Suf, known to assist Fe/S cluster biogenesis and the CsdAE cysteine desulphurase. Single iscU, hscA and fdx mutants were found sensitive to paraquat and exhibited reduced virulence on both chicory leaves and Arabidopsis thaliana. Depletion of the whole Isc system led to a pleiotropic phenotype, including sensitivity to both paraquat and 2,2'-dipyridyl, auxotrophies for branched-chain amino acids, thiamine, nicotinic acid, and drastic alteration in virulence. IscR was able to suppress all of the phenotypes listed above in a sufC-dependent manner while depletion of the Isc system led to IscR-dependent activation of the suf operon. No virulence defects were found associated with csdA or nifS mutations. Surprisingly, we found that the sufC mutant was virulent against A. thaliana, whereas its virulence had been found altered in Saintpaulia. Collectively, these results lead us to propose that E. chrysanthemi possess the Fe/S biogenesis strategy suited to the physico-chemical conditions encountered in its host upon infection. In this view, the IscR regulator, which controls both Isc and Suf, is predicted to play a major role in the ability of E. chrysanthemi to colonize a wide array of different plants.

A network of genes regulated by light in cyanobacteria

Oxygenic photosynthetic organisms require light for their growth and development. However, exposure to high light is detrimental to them. Using time series microarray data from a model cyanobacterium, Synechocystis 6803 transferred from low to high light, we generated a gene co-expression network. The network has twelve sub-networks connected hierarchically, each consisting of an interconnected hub-and-spoke architecture. Within each sub-network, edges formed between genes that recapitulate known pathways. Analysis of the expression profiles shows that the cells undergo a phase transition 6-hours post-shift to high light, characterized by core sub-network. The core sub-network is enriched in proteins that (putatively) bind Fe-S clusters and proteins that mediate iron and sulfate homeostasis. At the center of this core is a sulfate permease, suggesting sulfate is rate limiting for cells grown in high light. To validate this novel finding, we demonstrate the limited ability of cell growth in sulfate-depleted medium in high light. This study highlights how understanding the organization of the networks can provide insights into the coordination of physiologic responses.

Regulation of the cysteine desulfurase Nfs1 and the scaffold protein IscU in macrophages stimulated with interferon-γ and lipopolysaccharide

Biogenesis of iron-sulfur (Fe-S) clusters in mammals involves a complex mitochondrial machinery that provides inorganic sulfide and iron for their assembly and insertion into apo-proteins. Mechanisms of Fe-S cluster assembly are just being unraveled, and regulation of the genes of this machinery remains unknown. In this study, we report that expression of two essential components of the Fe-S machinery, the cysteine desulfurase Nfs1 and its scaffold protein partner IscU, is down-regulated at both mRNA and protein levels when murine macrophages are physiologically stimulated with IFN-gamma and LPS. Regulation did not rely on cluster disassembly or NO production because exposure of cells to exogenous sources of NO did not alter Nfs1 expression, while it converted cytosolic Fe-S aconitase into its apo-form and because macrophages from NOS2 deficient mice displayed Nfs1 down-regulation. While IFN-gamma alone induced Nfs1 protein instability, LPS triggered a delayed decline of Nfs1, rather involving transcriptional events or mRNA instability. Also, the expression of IscU was down-regulated in IFN-gamma- and/or LPS-stimulated macrophages independently of NO, pointing to a general mechanism for marshalling the regulation of the Fe-S cluster assembly machinery in macrophages exposed to inflammatory stimuli.

Functional analysis of Arabidopsis genes involved in mitochondrial iron-sulfur cluster assembly

Machinery for the assembly of the iron-sulfur ([Fe-S]) clusters that function as cofactors in a wide variety of proteins has been identified in microbes, insects, and animals. Homologs of the genes involved in [Fe-S] cluster biogenesis have recently been found in plants, as well, and point to the existence of two distinct systems in these organisms, one located in plastids and one in mitochondria. Here we present the first biochemical confirmation of the activity of two components of the mitochondrial machinery in Arabidopsis, AtNFS1 and AtISU1. Analysis of the expression patterns of the corresponding genes, as well as AtISU2 and AtISU3, and the phenotypes of plants in which these genes are up or down-regulated are consistent with a role for the mitochondrial [Fe-S] assembly system in the maturation of proteins required for normal plant development.

Iron-sulfur protein biogenesis in eukaryotes: components and mechanisms

Iron-sulfur (Fe/S) clusters require a complex set of proteins to become assembled and incorporated into apoproteins in a living cell. Researchers have described three distinct assembly systems in eukaryotes that are involved in the maturation of cellular Fe/S proteins. Mitochondria are central for biogenesis. They contain the ISC-the iron-sulfur cluster assembly machinery that was inherited from a similar system of eubacteria in evolution and is involved in biogenesis of all cellular Fe/S proteins. The basic principle of mitochondrial (and bacterial) Fe/S protein maturation is the synthesis of the Fe/S cluster on a scaffold protein before the cluster is transferred to apoproteins. Biogenesis of cytosolic and nuclear Fe/S proteins is facilitated by the cytosolic iron-sulfur protein assembly (CIA) apparatus. This process requires the participation of mitochondria that export a still unknown component via the ISC export machinery, including an ABC transporter.

Sulfur Mobilization in Cyanobacteria

Sulfur mobilization represents one of the key steps in ubiquitous Fe-S clusters assembly and is performed by a recently characterized set of proteins encompassing cysteine desulfurases, assembly factors, and shuttle proteins. Despite the evolutionary conservation of these proteins, some degree of variability among organisms was observed, which might reflect functional specialization. L-Cyst(e)ine lyase (C-DES), a pyridoxal 5'-phosphatedependent enzyme identified in the cyanobacterium Synechocystis, was reported to use preferentially cystine over cysteine with production of cysteine persulfide, pyruvate, and ammonia. In this study, we demonstrate that C-DES sequences are present in all cyanobacterial genomes and constitute a new family of sulfur-mobilizing enzymes, distinct from cysteine desulfurases. The functional properties of C-DES from Synechocystis sp. PCC 6714 were investigated under pre-steady-state and steady-state conditions. Single wavelength and rapid scanning stopped-flow kinetic data indicate that the internal aldimine reacts with cystine forming an external aldimine that rapidly decays to a transient quinonoid species and stable tautomers of the alpha-aminoacrylate Schiff base. In the presence of cysteine, the transient formation of a dipolar species precedes the selective and stable accumulation of the enolimine tautomer of the external aldimine, with no formation of the alpha-aminoacrylate Schiff base under reducing conditions. Effective sulfur mobilization from cystine might represent a mechanism that allows adaptation of cyanobacteria to different environmental conditions and to light-dark cycles.