Iron-sulfur (Fe-S) clusters are critical protein cofactors found in all life forms. In eukaryotes, a well-conserved biosynthetic pathway located in the mitochondria is used to assemble Fe-S clusters. Although proteins required for Fe-S cluster biosynthesis have been identified, their precise function and mechanism remain elusive. In this study, biochemical and biophysical methods are applied to understand molecular details for the core components of the human Fe-S cluster biosynthesis: Nfs1, Isd11, Isu2, and frataxin (Fxn). Nfs1 is a cysteine desulfurase that converts cysteine into alanine and transfers the sulfur to a scaffold protein Isu2 for Fe-S clusters. Fxn depletion is associated with the neurodegenerative disease Friedreich’s ataxia (FRDA), and results in a complicated phenotype that includes loss of Fe-S clusters. The results presented here provide the first in vitro evidence for a stable protein complex that exists in at least two forms: an inactive complex with Nfs1, Isd11, and Isu2 (SDU) components and an active form that also includes Fxn (SDUF). Fxn binding dramatically changes the catalytic efficiency (kcat/KM) of Nfs1 from 25 to 10,100 M-1s-1 and enhances the rate of Fe-S cluster biosynthesis 25 fold. Oxidizing conditions diminish the levels of both complex formation and Fxn-based activation, whereas Fe2 further stimulates Nfs1 activity. Mutagenesis coupled to enzyme kinetics indicate that one of the three conserved cysteines (C104) on Isu2 accepts the sulfane sulfur from Nfs1 and that this transfer event likely requires prior binding of Fxn. In vitro interrogation of FRDA I154F and W155R and related Fxn variants revealed the binding affinity to SDU followed the trend Fxn ~ I154F > W155F > W155A ~ W155R. The Fxn variants also have diminished ability to facilitate both sulfur transfer and Fe-S cluster assembly. Fxn crystallographic structures reveal specific rearrangements associated with the loss of function. Importantly, the weaker binding and lower activity of the W155R variant compared to I154F explains the earlier onset and more severe disease progression. Finally, these experimental results coupled with computational docking studies suggest a model for how human Fxn functions as an allosteric activator and triggers sulfur transfer and Fe-S cluster assembly.

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

Thesis (Ph. D. in Biochemistry)--Vanderbilt University, Dec. 2005. / Title from title screen. Includes bibliographical references.

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

Congenital sideroblastic anemias (CSA) are inherited diseases resulting from defects in heme biosynthesis, mitochondrial iron-sulfur cluster (ISC) assembly, or mitochondrial translation. CSAs are characterized by pathological iron deposits in the mitochondria of bone marrow erythroblasts. Recently the Fleming Lab at Boston Children’s Hospital has reported mutations in HSPA9, a chaperone involved in ISC assembly, as a cause of nonsyndromic CSA. Here we identified a CSA patient harboring two variants in HSCB, encoding a binding partner of HSPA9: a paternally inherited promoter variant (c-134C>A) and a maternally inherited frameshift variant (T87fs) predicted to result in a truncated protein. To better understand the pathophysiology of these variants, we investigated HSCB protein expression and function in patient-derived skin fibroblasts. Patient fibroblasts show evidence of decreased HSCB protein levels. shRNA targeting HSCB was employed to specifically suppress HSCB expression in the K562 erythroid-like cell line model. shRNA-infected K562 cells presented with perturbed iron homeostasis, a shift to glycolytic energy production, and diminished hemoglobinization. Targeted deletion of murine Hscb is embryonic lethal prior day E7.0. Tissue-specific lox-Cre transgenic lines, including Vav-, EpoR- and Mx-Cre demonstrate that Hscb is essential for hematopoiesis and erythropoiesis. Mutant mice present with hematopoietic defects similar to the index patient. Vav-Cre animals die prior to post-natal day 9 with decreased red cell counts, white cell counts, and decreased hemoglobin compared to wild-type animals. Floxed-null EpoR-Cre animals die before embryonic day 13. To excise Hscb specifically in the hematopoietic compartment of adult animals, conditional Mx-Cre animals were generated through bone marrow transplantation and temporally induced with polyinosinic-polycytidylic acid treatment. The animals died 22 days post-injection with decreased red blood cells, white blood cells, hemoglobin, and an overall decline in hematopoiesis of the bone marrow. These data demonstrate that HSCB is required for erythropoiesis and hematopoiesis and that the patient mutations are a pathogenic cause of CSA.

abstract: Redox enzymes represent a big group of proteins and they serve as catalysts for biological processes that involve electron transfer. These proteins contain a redox center that determines their functional properties, and hence, altering this center or incorporating non-biological redox cofactor to proteins has been used as a means to generate redox proteins with desirable activities for biological and chemical applications. Porphyrins and Fe-S clusters are among the most common cofactors that biology employs for electron transfer processes and there have been many studies on potential activities that they offer in redox reactions. In this dissertation, redox activity of Fe-S clusters and catalytic activity of porphyrins have been explored with regard to protein scaffolds. In the first part, modular property of repeat proteins along with previously established protein design principles have been used to incorporate multiple Fe-S clusters within the repeat protein scaffold. This study is the first example of exploiting a single scaffold to assemble a determined number of clusters. In exploring the catalytic activity of transmetallated porphyrins, a cobalt-porphyrin binding protein known as cytochrome c was employed in a water oxidation photoelectrochemical cell. This system can be further coupled to a hydrogen production electrode to achieve a full water splitting tandem cell. Finally, a cobalt-porphyrin binding protein known as cytochrome b562 was employed to design a whole cell catalysis system, and the activity of the surface-displayed protein for hydrogen production was explored photochemically. This system can further be expanded for directed evolution studies and high-throughput screening. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2019

京都大学 / 新制・課程博士 / 博士(工学) / 甲第24638号 / 工博第5144号 / 新制||工||1982(附属図書館) / 京都大学大学院工学研究科合成・生物化学専攻 / (主査)教授 跡見 晴幸, 教授 森 泰生, 教授 浜地 格 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

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