Iron sulfur [Fe-S] proteins are essential components of many major biological processes including electron transport, respiration, photosynthesis, hormone biosynthesis, and environmental sensing. The process of [Fe-S] cluster assembly in living cells is a controlled mechanism that is highly conserved across all kingdoms. Considerable progress has been made in deciphering this mechanism in bacteria, yeast, and mammals. The key players are the NifS/IscS/SufS proteins, which act as the sulfur donor, and the NifU/IscU/SufU proteins, which serve as a scaffold that binds Fe and upon which the cluster is assembled. Additional proteins are involved in the maturation and transport of the clusters. In eukaryotes there is redundancy in the proteins involved in this mechanism and the process is compartmentalized. Not much is known about the [Fe-S] cluster assembly mechanism in plants. In addition to the redundancy and compartmentalization seen in this machinery in eukaryotes, plants present a further challenge by offering chloroplasts as an additional site for [Fe-S] cluster assembly. The objective of this project has been to characterize Arabidopsis AtNFS1 and AtISU1-3, which show high homology to NifS/IscS and NifU/IscU, respectively, and are hypothesized to be key players in [Fe-S] cluster biogenesis in plants. Subcellular localization results of the AtNFS1 and AtISU1-3 proteins fused to GFP from this study are consistent with the presence of dual machinery in plants, with both mitochondria and chloroplasts as sites for [Fe-S] cluster assembly. Furthermore, observations also showed that AtISU2 mRNA may be unstable. The results of these experiments, together with promoter analysis described in this dissertation using GUS fusions suggested that the genes encoding the AtISU scaffold proteins are regulated at the transcriptional and probably also at the posttranscriptional level. Gene silencing experiments performed in this dissertation research using antisense and RNAi constructs indicated that these genes have the potential to impact respiration, photosynthesis, phytohormone biosynthesis, and environmental sensing, diverse processes that rely on [Fe-S] proteins. These observations, together with previous in vitro evidence that AtNFS1 and AtISU1 can participate in [Fe-S] cluster assembly, provide strong evidence that these proteins are part of two distinct cluster assembly systems that function in different subcellular locations and perhaps under different environmental conditions. Information gathered here has made it possible to begin developing a detailed model of [Fe-S] cluster biogenesis in plants. / Ph. D.

No description available.

Iron-sulfur clusters are simple inorganic cofactors that are ubiquitous in living systems. The assembly of iron sulfur clusters is an essential process and must be carefully controlled in order to limit the release of toxic free iron or sulfide. Thus far there are three known protein systems for iron sulfur cluster assembly including the <i>nif, suf,</i> and <i>isc</i> systems. The <i>nif</i> system makes iron-sulfur clusters for nitrogenase production, while both the <i>suf</i> and <i>isc</i> systems provide iron-sulfur clusters for general cellular use. In <i>Azotobacter vinelandii</i> the isc operon contains eight genes which are transcribed together as a single operon: <i>iscR iscS iscU iscA hscB hscA fdx iscX</i>. The two central <i>isc</i> players include IscS, a cysteine desulfurase, and IscU the proposed site of iron-sulfur cluster assembly. Using <i>A. vinelandii</i> as a model organism, we have sought to better understand the mechanism of <i>in vivo isc</i> cluster assembly. In order test the scaffold hypothesis, we constructed strains that allowed for quick and rapid isolation of IscU. The purification of IscU with a bound [2Fe-2S] cluster strongly supports the model that IscU serves as the site of cluster synthesis <i>in vivo</i>. Additionally, using this same genetic system we isolated an IscU39DA variant with an oxygen stable bound [2Fe-2S] cluster. The IscU39^DA scaffold came in tight α₂β₂ complex with IscS and was not separated by high salt, size exclusion, or reducing conditions. On the other hand, wild-type IscU also associated with IscS in a α₂β₂ complex, but readily dissociated upon increased salt concentration. The tight association of IscU39^DA and IscS was found to occur regardless of the presence of a bound [Fe-S] cluster. We conclude that the IscU Asp-39 residue is essential for mediating the dissociation of IscU and IscS. In addition to studying IscS and IscU, we were interested to further understand how the isc system is regulated in response to external factors. Previous work has demonstrated that IscR controls expression of the isc operon in <i>Escherichia coli</i>. When IscR is holo this protein represses <i>isc</i> expression, while in its apo-form it allows <i>isc</i> expression. In <i>A. vinelandii</i> we found that ∆<i>iscR</i> strains exhibit in a 5 – 7 fold elevation of isc expression. Additionally, ∆<i>iscR</> strains reveal a small growth phenotype on plates, and a tendency to form spontaneous suppressor mutations allowing reversion to wild-type growth. Loss of apo-IscR function was found to cause a more severe effect on growth than the loss of holo-IscR function, suggesting IscR has cellular roles in addition to the regulation of the <i>isc</i> operon. / Ph. D.

It is not known whether biosynthesis of [Fe-S] clusters occurs through a spontaneous self-assembly process or an enzymatic process. However, in the <I>Azotobacter</I> <I>vinelandii</I> nitrogenase system, it has been proposed that NifS and NifU are involved in the mobilization of sulfur and iron necessary for nitrogenase-specific [Fe-S] cluster assembly. The NifS protein has been shown to have cysteine desulfurase activity and can be used to supply sulfur for the <I>in</I> <I>vitro</I> catalytic formation of [Fe-S] clusters. The activity of the NifU protein has not yet been established, but NifU could have functions complementary to NifS by mobilizing iron or serving as an intermediate site necessary for nitrogenase-specific [Fe-S] cluster assembly. A second iron-binding site within NifU was predicted to serve these functions because two identical [2Fe-2S] clusters that had previously been identified within the homodimeric NifU are tightly bound, and the NifU primary sequence is rich in cysteine residues. In this dissertation, I examined the possibility that NifU might mobilize iron or serve as an intermediate site for [Fe-S] cluster assembly, as well as the possibility that NifU could work in concert with NifS. Primary sequence comparisons, amino acid substitution experiments, and biophysical characterization of recombinantly-produced NifU fragments were used to show that NifU has a modular structure. One module is contained in approximately the C-terminal half of NifU and provides the binding site for the [2Fe-2S] cluster previously identified (the permanent [2Fe-2S] cluster). Cysteine residues Cys¹³⁷, Cys¹³⁹, Cys¹⁷⁵, and Cys¹⁷⁵ serve as ligands to the [2Fe-2S] cluster. Another module (referred to as NifU-1) is contained in approximately the N-terminal third of NifU and provides a second iron-binding site (rubredoxin-like Fe(III)-binding site). Cysteine residues Cys³⁵, Cys⁶², Cys¹⁰⁶>, and a putative non-cysteine ligand of unknown origin provide coordination to the iron at this site. The significance of these iron-binding sites was also accessed by showing that cysteine residues involved in providing the rubredoxin-like Fe(III)-binding site and those that provide the [2Fe-2S] cluster binding site are all required for the full physiological function of NifU. The two other cysteine residues contained within NifU, Cys²⁷² and Cys²⁷⁵, are neither necessary for binding iron at either site nor are they required for the full physiological function of NifU. These results provide the basis for a model where iron bound at the rubredoxin-like sites within NifU-1 (one iron per monomer) is proposed to be destined for [Fe-S] cluster formation. It was possible to find in vitro evidence supporting this idea. First, it was demonstrated that NifU and NifS are able to form a transient complex. Second, in the presence of NifS as well as L-cysteine and a reducing agent, the Fe(III) contained at the rubredoxin-like sites within the NifU-1 or NifU homodimer can rearrange to form a transient [2Fe-2S] cluster between the two subunits. Finally, a mutant form of NifU-1 was isolated that appears to be trapped in the [2Fe-2S] cluster-containing form, and this [2Fe-2S] cluster (the transient [2Fe-2S] cluster) can be released from the polypeptide matrix upon reduction with dithionite. Previous work has shown that the permanent [2Fe-2S] clusters of as-isolated NifU are in the oxidized form but can be reduced chemically. The transient [2Fe-2S] cluster formed between rubredoxin-like sites, in contrast, is reductively labile. If the transient cluster serves as an intermediate [Fe-S] cluster to be destined for [Fe-S] cluster assembly, I propose that the permanent [2Fe-2S] clusters could have redox roles participating in either one or all of the following events. The permanent [2Fe-2S] clusters could have a redox function in the acquisition of iron for initial binding at the mononuclear sites. They could also provide reducing equivalents for releasing the transient [2Fe-2S] cluster. In addition, upon releasing the transient [2Fe-2S] cluster, the permanent [2Fe-2S] clusters could provide the appropriate oxidation state of the irons to be destined to nitrogenase metallocluster core formation. Finally, because proteins homologous to NifU and NifS are widely distributed in nature, it is suggested that the mechanism for NifU and NifS in the formation of nitrogenase-specific [Fe-S] clusters could represent a general mechanism for [Fe-S] cluster synthesis in other systems. / Ph. D.

Friedreich's ataxia is a neurodegenerative disorder caused by the low expression of a mitochondrial protein called frataxin. Studies in the yeast Saccharomyces cerevisiae have unraveled a role for the frataxin homologue (Yfh1p) in iron-sulfur cluster (Fe/S) biosynthesis, probably by interacting with the scaffold protein, Isu1p, and providing iron to the machinery. Yfh1p possesses a large â-sheet platform that may be involved in the interaction with other proteins through conserved residues at its surface. We have used directed mutagenesis associated with polymerase chain reaction (PCR) to study conserved residues localizing either at the surface of the protein, Thr110, Thr118, Val120, Asn122, Gln124, Gln129, Trp131, Ser137 and Arg141, or buried in the core of the protein, Ile130 and Leu132. Mutants T110A, T118A, V120A, N122A, Q124A, Q129A, I130A, W131A, L132A, S137A and R141A were generated in yeast. Growth on iron- or copper-containing medium was severely impaired for mutants Q129A, I130A, W131A and R141A. Others were roughly growing as well as the wild-type strain. We assessed the efficiency of Fe/S biosynthesis by measuring aconitase activity. The results confirmed those obtained on metal-containing medium: mutants Q129A, I130A, W131A and R141A showed a high decrease in their aconitase activity that dropped to the deleted strain level. Moreover, S137A showed also a decreased aconitase activity. We monitored the interaction between Yfh1p and Isu1p by co-immunoprecipitation and it turned out that only the W131A mutation affects directly this interaction. Even if the amount of Yfh1p determined by western blot analysis was highly decreased for several mutants, it is not sufficient to explain the phenotypes as they were poorly restored by overexpression of the mutant proteins to wild-type levels, except for W131F. We have concluded that Gln129, Trp131, and Arg141 are important for Yfh1p function, while Ile130 and Ser137 are required for the folding of the protein. All these residues cluster to the 4th and 5th â-strand of the protein. Our work has demonstrated for the first time the importance of this area for Yfh1p function and shows that Trp131 is involved in the interaction with Isu1p.

The cytosolic iron sulfur cluster assembly (CIA) pathway is responsible for the maturation of >40 cytosolic and nuclear iron sulfur (FeS) proteins critical for fundamental processes such as DNA replication, transcription, and translation. The final stages of the pathway require the CIA targeting complex, which is composed of Cia1, Cia2, and Met18. This large multiprotein complex is proposed to recognize apo-enzyme substrates and insert their FeS clusters. However, it is unclear how these substrates are identified and how the CIA targeting complex mediates cofactor insertion. In this thesis, I mapped the protein-protein interaction sites critical for formation of the CIA targeting complex and discovered the first peptide motif that is both necessary and sufficient for recognition of a subset of FeS proteins by the CIA system. Cia1’s seventh beta-propeller blade was found to bind to Cia2, while Cia2’s fifth conserved region mainly interacts with Cia1, via an in vitro affinity co-purification assay. A quantitative MicroScale Thermophoresis assay supported these findings, in addition this approach affirmed that Cia2’s N-terminal intrinsically disordered domain and hyperreactive cysteine are dispensable for CIA targeting complex assembly. In collaboration with the Drennan Lab at MIT, Met18 was discovered to form a hexamer via cryo-EM. Met18 is proposed to arrange into a hexamer before its CIA-related function. Hexamer formation and Cia2 binding depend on Met18’s C-terminus, whereas Leu1 recognition relies on Met18’s N-terminus. A C-terminal W motif was demonstrated as both necessary and sufficient for identification of a subset of FeS proteins by the CIA targeting complex. A bioinformatics analysis revealed roughly 20% of CIA client proteins, including substrates, factors, and adaptors, terminate in a conserved [LTQ]-[DE]-[W]-COO- motif. CIA recognition depends on the C-terminal aromatic side chain and the carboxy terminus. This tripeptide motif is also sufficient for identification by the CIA system when attached to SUMO. Moreover, a series of competition experiments showed that the CIA targeting complex contains distinct, non-overlapping binding sites for client proteins where Cia1 serves as the docking site for the C-terminal W motif. Altogether, the first recognition motif is defined for one in five of CIA client proteins. / 2024-11-03T00:00:00Z

Les centres FeS sont un des cofacteurs protéiques majeurs, ils se trouvent aussi bien chez les bactéries que chez les eucaryotes. Ils ont des rôles essentiels de transfert d'électron, liaison de substrat et son activation, régulation d'expression de gènes, donneur de soufre etc. Leur agencement est très varié, allant du centre [2Fe-2S] à l'agrégat plus complexe MoFe7S9X (X = C, N ou O) de la nitrogénase. L'assemblage de ces centres se fait par des machineries protéiques. Nous avons étudié le système ISC (Iron-Sulfur Cluster) chez les bactéries, qui fabrique des centres [2Fe-2S] et [4Fe-4S]. Il est composé des protéines IscS, IscU, IscA, HscA, HscB et d'une ferrédoxine. Deux de ces protéines, IscS, qui est une cystéine désulfurase et IscU, protéine dite échafaudage, sont le cœur de la machinerie puisque IscS apporte le soufre sur la protéine IscU, qui, avec le fer qu'elle aura obtenu d'une autre protéine (non clairement identifiée à ce jour), fabriquera le centre fer-soufre et le transfèrera à une apoprotéine. Nous avons isolé un complexe stable (IscS-D35A-IscU)2 contenant un centre [2Fe-2S] dans des conditions anaérobie. Différentes formes du complexe ont été obtenues et cristallisées afin d'obtenir leurs structures, résolues par remplacement moléculaire. Ces structures nous ont permis de proposer un mécanisme d'assemblage des centres [2Fe-2S] à l'échelle atomique et électronique. Nous avons d'autre part étudié la protéine HmdB probablement impliquée dans la maturation de l'hydrogénase à fer. HmdB fait partie de la superfamille des protéines à radical SAM. Des cristaux de l'apoprotéine ont été obtenus et sa structure a été résolue par remplacement moléculaire. Même si une partie de la structure n'est pas visible du fait de l'absence de centre [4Fe-4S], elle donne une première vue du site actif de la protéine. / FeS clusters are widely used protein cofactors, found both in bacteria and eukaryotes. They play key roles such as electron transfer, substrate binding and activation, regulation of gene expression, sulfur donor etc. They are really various, ranging from the [2Fe-2S] cluster to the more complex MoFe7S9X (X = C, N or O) agregate of nitrogenase. Clusters assembly is carried out by protein machineries. We studied the ISC (Iron-Sulfur Cluster) in bacteria, who assembles [2Fe-2S] and [4Fe-4S] clusters. It is composed of IscS, IscU, IscA, HscA, HscB proteins and a ferredoxin. Two of these proteins: the cysteine desulfurase IscS, and the scaffold protein IscU, represent the core of the machinery as IscS provides sulfur protein on IscU, which, with iron obtained from another protein (not clearly identified to date), assemble the iron-sulfur center. The latter transfers it to an apoprotein. We isolated under anaerobic conditions a stable (IscS-D35A-IscU)2 complex containing a [2Fe-2S] cluster. Different forms of the complex were obtained and their structures were solved by molecular replacement. These structures allowed us to propose a mechanism for the assembly of the [2Fe-2S] clusters at the atomic and electronic levels. We have also studied the HmdB protein, which is proposed to maturate the [Fe]-hydrogenase. HmdB is a member of the radical SAM proteins superfamily. Crystals of the apoprotein were obtained and its structure was solved by molecular replacement. Although part of the structure is not visible due to the absence of the [4Fe-4S] cluster, this structure gives a first view of the active site of the protein.

Luminogens are molecules that emit light upon exposure to high-energy light, and fluorophores are one class of luminogens. Applications of fluorophores range from microviscosity sensors to light emitting diodes (LEDs), as well as biosensors, just to name a few. Many of these applications require the fluorophore to be in the aggregate or solid state. Some fluorophores become highly emissive in the aggregate state; these fluorophores are aggregation-induced emission (AIE) luminogens. Currently, very few quantum mechanical mechanisms have been proposed to describe the unique AIE behavior of luminogens. Boron difluorohydrazone (BODIHY) dyes are a new type of AIE fluorophore. The bright emission is from the S>1 excited state (“anomalous” emission) contrary to Kasha’s Rule. Thus, the mechanism Suppression of Kasha’s Rule (SOKR) was proposed to be responsible for the family of BODIHY dyes. We hypothesize that the SOKR mechanism can explain AIE as well as the anomalous emission of other fluorophores. New BODIHY derivatives (para-CO2H BODIHY, aluminum difluorohydrazone (ALDIHY), and paranitro ALDIHY) were predicted to be bright anomalous fluorophores through density functional theory (DFT) and time-dependent DFT (TDDFT) investigations. In addition, a series of anomalous fluorophores were investigated to determine if their photophysical properties could be explained by the SOKR mechanism (azulene, 1,6-diphenyl-1,3,5hexatriene, and zinc tetraphenylporphyrin). Finally, several triazolopyridinium and triazoloquinolinium dyes were computationally investigated by DFT and TDDFT calculations, and an accurate computational model for the large Stokes shifts of these dyes was developed. In conclusion, a better understanding of the photophysical properties through DFT and TDDFT modeling and spectroscopic investigation of hydrazone-based fluorophores has been achieved. In addition, the metal active sites and cofactors of metalloproteins were probed by optical spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, and DFT modeling. In conjunction, these techniques can be used to elucidate the electronic structure responsible for the unique function of these metalloproteins. Specifically, a novel ironsulfur cluster of a metalloprotein that may be involved in endospore formation of Clostridium difficile, CotA, was characterized by magnetic circular dichroism (MCD) spectroscopy. We propose that CotA contains a high-spin [4Fe-4S] cluster and a Rieske [2Fe-2S] cluster. It appears that the multimerization of the protein is related to the cluster conversion at the interface of monomeric subunits where two [2Fe-2S] clusters combine to form the [4Fe-4S] cluster. In addition, a putative cobalamin acquisition protein from Phaeodactylum tricornutum, CBA1, was not expressed at sufficient concentrations in Escherichia coli for spectroscopic investigation. Finally, a new technique was developed using cobalt-59 NMR spectroscopy to better understand the nucleophilic character of cobalt tetrapyrroles, such as cobalamin (vitamin B12), as biological cofactors as well as synthetic catalysts. New insight into the electronic structure provides valuable information related to the mechanism of these metalloproteins.

Methane is a greenhouse gas and a major contributor to climate change. Methanogenic Archaea produce more than 1 billion tons of this gas each year through methanogenesis, the anaerobic reduction of CO₂ to methane. Coenzyme B (CoB) is one of eight coenzymes required for methanogenesis and it is unique to methanogens. Therefore, this coenzyme is a potential target for inhibiting methanogenesis. To further elucidate the CoB biosynthetic pathway, genes from Methanocaldococcus jannaschii were cloned and expressed in an effort to identify the CoB homoaconitase. From this study, the MJ0499-MJ1277 pair of proteins was identified as the methanogen isopropylmalate isomerase involved in leucine and isoleucine biosynthesis. The MJ1003-MJ1271 pair of proteins was characterized as the homoaconitase required for CoB biosynthesis. This enzyme exhibited broad substrate specificity, catalyzing the isomerization of cis-unsaturated tri-carboxylates with [gamma]-chains of 1-5 methylenes in length. Previously characterized homoaconitases only catalyzed half of the predicted reactions in the isomerization of homocitrate. The MJ1003-MJ1271 proteins function as the first homoaconitase described to catalyze the full isomerization of homocitrate to homoisocitrate. Also, the CoB homoaconitase was identified as specific for (R)-homocitrate and cis-unsaturated intermediates, contrary to a previous study that suggested the substrate specificity of this enzyme included (S)-homocitrate and trans-homoaconitate. The M. jannaschii isopropylmalate isomerase and homoaconitase share more than 50% sequence identity and catalyze analogous reactions. Site directed mutagenesis of the MJ1271 protein was used to identify residues involved in substrate specificity. Arg26 of MJ1271 was critical for the specificity of the CoB homoaconitase. Mutation of this residue to the analogous residue in the M. jannaschii isopropylmalate isomerase, Val28, altered the substrate specificity of the homoaconitase to include the substrates of isopropylmalate isomerase. These homologs of aconitase require a [4Fe-4S] cluster for coordinating their respective substrates at the enzyme active site. However, methanogens lack most of the proteins required for iron-sulfur cluster assembly. Therefore, genes homologous to the Salmonella enterica ApbC iron-sulfur scaffold protein were characterized from methanogens. The MMP0704, MJ0283, and SSO0460 proteins from Methanococcus maripaludis, M. jannaschii, and Solfolobus solfataricus, respectively, were identified as scaffold proteins involved in methanogen iron-sulfur cluster biosynthesis. / text

abstract: One of the greatest problems facing society today is the development of a sustainable, carbon neutral energy source to curb the reliance on fossil fuel combustion as the primary source of energy. To overcome this challenge, research efforts have turned to biology for inspiration, as nature is adept at inter-converting low molecular weight precursors into complex molecules. A number of inorganic catalysts have been reported that mimic the active sites of energy-relevant enzymes such as hydrogenases and carbon monoxide dehydrogenase. However, these inorganic models fail to achieve the high activity of the enzymes, which function in aqueous systems, as they lack the critical secondary-shell interactions that enable the active site of enzymes to outperform their organometallic counterparts. To address these challenges, my work utilizes bio-hybrid systems in which artificial proteins are used to modulate the properties of organometallic catalysts. This approach couples the diversity of organometallic function with the robust nature of protein biochemistry, aiming to utilize the protein scaffold to not only enhance rates of reaction, but also to control catalytic cycles and reaction outcomes. To this end, I have used chemical biology techniques to modify natural protein structures and augment the H2 producing ability of a cobalt-catalyst by a factor of five through simple mutagenesis. Concurrently I have designed and characterized a de novo peptide that incorporates various iron sulfur clusters at discrete distances from one another, facilitating electron transfer between the two. Finally, using computational methodologies I have engineered proteins to alter the specificity of a CO2 reduction reaction. The proteins systems developed herein allow for study of protein secondary-shell interactions during catalysis, and enable structure-function relationships to be built. The complete system will be interfaced with a solar fuel cell, accepting electrons from a photosensitized dye and storing energy in chemical bonds, such as H2 or methanol. / Dissertation/Thesis / Doctoral Dissertation Biochemistry 2016