Iron–sulfur protein folds,iron–sulfur chemistry,and evolution

An inventory of unique local protein folds around Fe–S clusters has been derived from the analysis of protein structure databases. Nearly 50 such folds have been identified, and over 90% of them harbor low-potential [2Fe–2S]^2+,+ or [4Fe–4S]^2+,+ clusters. In contrast, high-potential Fe–S clusters, notwithstanding their structural diversity, occur in only three different protein folds. These observations suggest that the extant population of Fe–S protein folds has to a large extent been shaped in the reducing iron- and sulfur-rich environment that is believed to have predominated on this planet until approximately two billion years ago. High-potential active sites are then surmised to be rarer because they emerged later, in a more oxidizing biosphere, in conditions where iron and sulfide had become poorly available, Fe–S clusters were less stable, and in addition faced competition from heme iron and copper active sites. Among the low-potential Fe–S active sites, protein folds hosting [4Fe–4S]^2+,+ clusters outnumber those with [2Fe–2S]^2+,+ ones by a factor of 3 at least. This is in keeping with the higher chemical stability and versatility of the tetranuclear clusters, compared with the binuclear ones. It is therefore suggested that, at least while novel Fe–S sites are evolving within proteins, the intrinsic chemical stability of the inorganic moiety may be more important than the stabilizing effect of the polypeptide chain. The discovery rate of novel Fe–S-containing protein folds underwent a sharp increase around 1995, and has remained stable to this day. The current trend suggests that the mapping of the Fe–S fold space is not near completion, in agreement with predictions made for protein folds in general. Altogether, the data collected and analyzed here suggest that the extant structural landscape of Fe–S proteins has been shaped to a large extent by primeval geochemical conditions on one hand, and iron–sulfur chemistry on the other.     

Iron–sulfur cluster biosynthesis in photosynthetic organisms

Iron–sulfur (Fe/S) cluster containing proteins are widely distributed in nature and are involved in numerous processes including electron transfer, metabolic reactions, sensing, signaling, and regulation of gene expression. The knowledge about the biogenesis of Fe/S clusters, and the assembly and maturation of Fe/S cluster containing proteins is still limited, especially in photosynthetic organisms. In most organisms analyzed so far the biogenesis of Fe/S clusters involves more than one machinery. The additional compartment in photoautotrophic organisms, the plastids, presents an additional challenge for the regulation of Fe/S cluster biogenesis. The requirement for Fe/S proteins in multiple chloroplast processes argues that Fe/S cluster assembly is an essential part of plastid functionality. This review focuses on the interesting and unique aspects of Fe/S cluster biogenesis in photosynthetic organisms and compares them to what is known in other organisms.     

Ring cleavage of sulfur heterocycles: how does it happen?

Sulfur heterocycles are common constituents of petroleum and liquids derived from coal, and they are found in some secondary metabolites of microorganisms and plants. They exist primarily as saturated rings and thiophenes. There are two major objectives driving investigations of the microbial metabolism of organosulfur compounds. One is the quest to develop a process for biodesulfurization of fossil fuels, and the other is to understand the fates of organosulfur compounds in petroleum- or creosote-contaminated environments which is important in assessing bioremediation processes. For these processes to be successful, cleavage of different types of sulfur heterocyclic rings is paramount. This paper reviews the evidence for microbial ring cleavage of a variety of organosulfur compounds and discusses the few well-studied cases which have shown that the C-S bond is most susceptible to breakage leading to disruption of the ring. In most cases, the introduction of one or more oxygen atom(s) onto the adjacent C atom and/or onto the S atom weakens the C-S bond, facilitating its cleavage. Although much is known about the thiophene ring cleavage in dibenzothiophene, there is still a great deal to be learned about the cleavage of other sulfur heterocycles.     

Endogenous elemental sulfur production froml-cysteine in dormant α-spores ofPhomopsis viticola

The enzymatic production of sulfur froml-cysteine was studied in young dormant -spores ofPhomopsis viticola. Cysteine aminotransferase (CAT) and mercaptopyruvate sulfurtransferase (MST) activities could be responsible for the production of endogenous elemental sulfur (S⁰) in -spores.l-Cysteine was first deaminated, with production of -mercaptopyruvate, by the CAT. The -mercaptopyruvate produced is successively desulfurated by the MST with production of sulfur and pyruvate. Deaminase activity was recovered principally in the cytoplasmic fraction, whereas desulfurase activity was recovered mainly in the mitochondrial fraction.l-Cysteine and S⁰ sharply affected the respiratory activity, the ATP content, and suppressed germination of -spores. In contrast, reduced glutathione did not affect these metabolic parameters. Production of S⁰ by enzymatic degradation ofl-cysteine could be responsible for the inhibitory action of this amino acid. We suggest that CAT and MST, by their capacity to produce sulfur or S⁰, plays a key role in regulation of morphogenetic processes ofPhomopsis viticola.     

The bound iron–sulfur clusters of Type-I homodimeric reaction centers

The hallmark of a Type-I photosynthetic reaction center (RC) is the presence of three [4Fe–4S]^2+/1+ clusters, named F_X, F_A, and F_B that act as terminal electron acceptors. Their function is to increase the distance, and hence the lifetime, of the initial charge-separated state so that diffusion-mediated processes, such as the reduction of ferredoxin, can occur. Type-I homodimeric RCs, such as those found in heliobacteria, green-sulfur bacteria, and Candidatus Chloracidobacterium thermophilum, are less well understood than Photosystem I, the prototypical Type-I heterodimeric RC found in cyanobacteria and plants. Here, we review recent progress that has been made in elucidating the spectroscopic and biochemical properties of the bound Fe/S clusters and their cognate proteins in homodimeric Type-I RCs. In Heliobacterium modesticaldum, the identification and characterization of two loosely bound polypeptides, PshBI and PshBII that harbor the F_A and F_B clusters threatens to break the long-accepted assumption that Type-I RCs harbor one tightly bound F_A/F_B-containing protein. Additionally, the detection of the F_X cluster in S = 1/2 and S = 3/2 ground spin states has resolved the long-standing issue of its missing EPR spectrum. In Chlorobaculum tepidum, the focus is on the biochemical properties of the unusual extrinsic Fe/S protein, PscB, which is readily dissociable from the RC core. The C-terminal domain of PscB is constructed as a bacterial ferredoxin, harboring the F_A and F_B clusters, but the N-terminal domain contains a number of PxxP motifs and is rich in Lys, Pro, and Ala residues, features characteristic of proteins that interact with SH3 domains. Little is known about Candidatus Chloracidobacterium thermophilum except that the photosynthetic RC is predicted to be a Type-I homodimer with an F_X-binding site. These findings are placed in a context that promises to unify the acceptor side of homodimeric Type-I RCs in prokaryotic phototrophs.     

The enzymology of sulfur metabolism in phototrophic bacteria — A review

Summary The two functions of sulfur metabolism in phototrophic bacteria are to supply electrons for photosynthesis and to supply sulfur for biosynthetic purposes. The pathways for both functions may be partly identical. For the electron-supplying pathway the following enzymes are needed: a sulfide-oxidizing enzyme, a sulfur-oxidizing enzyme system, APS reductase, ADP sulfurylase and — in the case of thiosulfate utilization — thiosulfate reductase. Assimilatory reactions are catalyzed by ATP sulfurylase, APS kinase, sulfotransferases, PAPS reductase, sulfite reductase and o-acetylserine sulfhydrylase. Paper read at the Symposium on the Sulphur Cycle, Wageningen, May 1974.     

Iron–sulfur cluster exchange reactions mediated by the human Nfu protein

Human Nfu is an iron–sulfur cluster protein that has recently been implicated in multiple mitochondrial dysfunctional syndrome (MMDS1). The Nfu family of proteins shares a highly homologous domain that contains a conserved active site consisting of a CXXC motif. There is less functional conservation between bacterial and human Nfu proteins, particularly concerning their Iron–sulfur cluster binding and transfer roles. Herein, we characterize the cluster exchange chemistry of human Nfu and its capacity to bind and transfer a [2Fe–2S] cluster. The mechanism of cluster uptake from a physiologically relevant [2Fe–2S](GS)₄ cluster complex, and extraction of the Nfu-bound iron–sulfur cluster by glutathione are described. Human holo Nfu shows a dimer-tetramer equilibrium with a protein to cluster ratio of 2:1, reflecting the Nfu-bridging [2Fe–2S] cluster. This cluster can be transferred to apo human ferredoxins at relatively fast rates, demonstrating a direct role for human Nfu in the process of [2Fe–2S] cluster trafficking and delivery.     

Towards a phylogeny of phototrophic purple sulfur bacteria — the genus Ectothiorhodospira

While most strains of heterofermentative lactobacilli and strains of Leuconostoc species contained only traces of a dehydratase reacting with glycerol or propanediol-1,2, three strains of Lactobacillus brevis and one strain of L. buchneri that metabolized glycerol readily in the presence of glucose, contained propanediol-1,2 dehydratase (EC 4.2.1.28). This cobamide requiring enzyme from L. brevis B 18 was partially purified. It reacts with the substrates propanediol-1,2, glycerol and ethanediol-1,2 with the relative activities of about 3:2:1. This ratio remained unchanged throughout the purification procedure. The substrate affinities were measured: propanediol-1,2 K _m=0.6 mM, glycerol K _m=4 mM, ethanediol-1,2 K _m=5.3 mM coenzyme B₁₂ (substrate glycerol) K _m=0.007 mM. The activity of the dehydratase was promoted by potassium or ammonium ions and inhibited by sodium, lithium, magnesium or specially manganese. The apparent molecular weight of propanediol-1,2 dehydratase was determined as M_r=180,000.Dedicated to Prof. Dr. H. G. Schlegel on behalf of his 60th birthday     

Magnetic circular dichroism studies on monomeric and dimeric iron—sulfur complexes

Magnetic Circular dichroism (MCD) spectra were obtained for bis(o-xylyl-dithiolato)ferrate(III) ([Fe(S₂-o-xylyl)₂]⁻) and bis[o-xylyl-dithiolato-μ₂-sulfidoferrate(III)] ([Fe₂S^*₂(S₂-o-xylyl)₂]²⁻) ions. The MCD magnitude of the dimeric [Fe₂S^*₂(S₂-o-xylyl)₂]²⁻ ion was found to be only one half of that for the monomeric [Fe(S₂-o-xylyl)₂]⁻ ion. The difference in MCD magnitudes was attributed to the change in the thermal populations of ground state sublevels derived from the magnetic exchange interaction.     

Novel sulfur and selenium containing bis-α-amino acids from 4-hydroxyproline

The synthesis of new substituted prolines carrying at C-4 a second α-amino acid residue is reported. The amino acid, l-cysteine or l-selenocysteine, is linked to the proline ring through the sulfur or the selenium atom, respectively. The products were prepared with different stereochemistry at C-4, in few and clean high-yielding steps, with suitable protections for solid phase applications. The introduction of both sulfur and selenium atoms at C-4 of the proline ring seems to enhance significantly the cis geometry at the prolyl amide bond.     

Requirements of the cytosolic iron–sulfur cluster assembly pathway in Arabidopsis

The assembly of iron–sulfur (Fe–S) clusters requires dedicated protein factors inside the living cell. Striking similarities between prokaryotic and eukaryotic assembly proteins suggest that plant cells inherited two different pathways through endosymbiosis: the ISC pathway in mitochondria and the SUF pathway in plastids. Fe–S proteins are also found in the cytosol and nucleus, but little is known about how they are assembled in plant cells. Here, we show that neither plastid assembly proteins nor the cytosolic cysteine desulfurase ABA3 are required for the activity of cytosolic aconitase, which depends on a [4Fe–4S] cluster. In contrast, cytosolic aconitase activity depended on the mitochondrial cysteine desulfurase NFS1 and the mitochondrial transporter ATM3. In addition, we were able to complement a yeast mutant in the cytosolic Fe–S cluster assembly pathway, dre2, with the Arabidopsis homologue AtDRE2, but only when expressed together with the diflavin reductase AtTAH18. Spectroscopic characterization showed that purified AtDRE2 could bind up to two Fe–S clusters. Purified AtTAH18 bound one flavin per molecule and was able to accept electrons from NAD(P)H. These results suggest that the proteins involved in cytosolic Fe–S cluster assembly are highly conserved, and that dependence on the mitochondria arose before the second endosymbiosis event leading to plastids.     

Simultaneous biological removal of nitrogen–sulfur–carbon: Recent advances and challenges

Biological removal of carbon, nitrogen and sulfur is drawing increasing research interest in search for an efficient and cost-effective wastewater treatment. While extensive work on separate removal of nitrogen and sulfur is well documented, investigation on simultaneous denitrifying sulfide removal has only been reported recently. Most of the work on denitrifying sulfide removal has been focusing on bioreactor performance, loading and operating conditions. Nonetheless, underlying principles elucidating the biochemical reactions and the mechanisms of the microbial degradation are yet to be established. In addition, unstable denitrifying sulfide removal which is a major operating problem that hinders practical application of the process, is yet to be resolved. This paper provides a review on the state-of-the-art development of simultaneous biological removal of sulfur, nitrogen and carbon. Research on bioreactor operation and performance, reactor configurations, mechanisms and modeling work including the use of mass balance analysis and artificial neural networks is delineated. An in-depth discussion on the microbial community and functional consortium is also provided. Challenges and future work on simultaneous biological removal of nitrogen–sulfur–carbon are also outlined.     

Production of methanethiol and volatile sulfur compounds by the archaeon “Ferroplasma acidarmanus”

Acidophiles are typically isolated from sulfate-rich ecological niches yet the role of sulfur metabolism in their growth and survival is poorly defined. Studies of heterotrophically grown “Ferroplasma acidarmanus” showed that its growth requires a minimum of 100 mM of a sulfate-containing salt. Headspace gas analyses by GC/MS determined that the volatile sulfur compound emitted by active “F. acidarmanus” cultures is methanethiol. In “F. acidarmanus” cultures grown either heterotrophically or chemolithotrophically, methanethiol was produced constitutively. Radiotracer studies with ³⁵S-labeled methionine, cysteine, and sulfate showed that all three were used in methanethiol production. Additionally, ³H-labeled methionine was incorporated into methanethiol and was probably used as a methyl-group donor. Methanethiol production in whole cell lysates supplied with SO₃²⁻ indicated that NADPH-dependant sulfite reductase and methyltransferase activities were present. Cell lysates also contained enzymatic activity for methionine-γ-lyase that cleaved the side chain of either methionine to form methanethiol or cysteine to produce H₂S. Since methanethiol was detected from the degradation of cysteine, it is likely that sulfide was methylated by a thiol methyltransferase. Collectively, these data demonstrate that “F. acidarmanus” produces methanethiol through the metabolism of methionine, cysteine, or sulfate. This is the first report of a methanethiol-producing acidophile, thus identifying a new contributor to the global sulfur cycle.     

Can anomalous signal of sulfur become a tool for solving protein crystal structures?

A general method for solving the phase problem from native crystals of macromolecules has long eluded structural biology. For well diffracting crystals this goal can now be achieved, as is shown here, thanks to modern data collection techniques and new statistical phasing algorithms. Using solely a native crystal of tetragonal hen egg-white lysozyme, a protein of 14 kDa molecular mass, it was possible to detect the positions of the ten sulfur and seven chlorine atoms from their anomalous signal, and proceed from there to obtain an electron-density map of very high quality.     

H and poly-β-hydroxybutyrate, two alternative chemicals from purple non sulfur bacteria

The feasibility of a process for the photoproduction of both H 2 and poly-b-hydroxybutyrate (PHB)-containing biomass has been tested utilizing semi-continuous cultures of Rhodopseudomonas palustris growing in a tubular system with limiting amounts of fixed nitrogen. A two-stage batch process, consisting in a first period of nitrogen-limited cell growth followed by a second period of cell cultivation under conditions of phosphorus shortage, showed the possibility to separate the H production phase from the PHB accumulation phase, making possible to carry out processes that otherwise would be in competition.     

Di-iron proteins of the Ric family are involved in iron–sulfur cluster repair

A key element in eukaryotic immune defenses against invading microbes is the production of reactive oxygen and nitrogen species. One of the main targets of these species are the iron–sulfur clusters, which are essential prosthetic groups that confer to proteins the ability to perform crucial roles in biological processes. Microbes have developed sophisticated systems to eliminate nitrosative and oxidative species and promote the repair of the damages inflicted. The Ric (Repair of Iron Centers) proteins constitute a novel family of microbial di-iron proteins with a widespread distribution among microbes, including Gram-positive and Gram-negative bacteria, protozoa and fungi. The Ric proteins are encoded by genes that are up-regulated by nitric oxide and hydrogen peroxide. Recent studies have shown that the active di-iron center is involved in the restoration of Fe–S clusters damaged by exposure to nitric oxide and hydrogen peroxide.