VTechWorks Repository :: Browsing by Author "Dean, Dennis R."

Browsing by Author "Dean, Dennis R."

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Activation of acetate in acetate-grown Methanosarcina thermophila: purificationm and characterization of acetate kinase
Aceti, David John (Virginia Tech, 1980-04-05)
Extracts of acetate-grown Methanosarcina thermoghila were assayed for the presence of enzymes which might catalyze a proposed activation of acetate as the initial step in the pathway of methanogenesis from acetate by that organism. Acetate kinase and phosphate acetyltransferase activities of 4.9 and 49 μmoles of product/min/mg protein, respectively, were detected. Acetate kinase was purified 102- fold to a specific activity of 656 μmoles ADP formed/min/mg protein and was essentially homogeneous by denaturing gel electrophoresis. The native enzyme (Mr 94,000) was an α₂ homodimer with a subunit Mr of 53,000. Activity was optimal between pH 7.0 and 7.4 and was stable to heating at 70°C for 15 min. The apparent Km for acetate was 22 mM (Vmax = 668 μmoles ADP/min/mg protein) and 2.8 mM for ATP (Vmax = 777 pmoles ADP/min/ protein). The enzyme phosphorylated propionate at 602 of the rate with acetate but was unable to use formate. TTP, ITP, UTP, GTP, and CTP replaced ATP as the phosphoryl donor to acetate. One of several divalent cations was required for activity; the maximum rate was obtained with Mn2+.
AnfO controls fidelity of nitrogenase FeFe protein maturation by preventing misincorporation of FeV-cofactor
Perez-Gonzalez, Ana; Jimenez-Vicente, Emilio; Salinero-Lanzarote, Alvaro; Harris, Derek F.; Seefeldt, Lance C.; Dean, Dennis R. (Wiley, 2022-05)
Azotobacter vinelandii produces three genetically distinct, but structurally and mechanistically similar nitrogenase isozymes designated as Mo-dependent, V-dependent, or Fe-only based on the heterometal contained within their associated active site cofactors. These catalytic cofactors, which provide the site for N-2 binding and reduction, are, respectively, designated as FeMo-cofactor, FeV-cofactor, and FeFe-cofactor. Fe-only nitrogenase is a poor catalyst for N-2 fixation, when compared to the Mo-dependent and V-dependent nitrogenases and is only produced when neither Mo nor V is available. Under conditions favoring the production of Fe-only nitrogenase a gene product designated AnfO preserves the fidelity of Fe-only nitrogenase by preventing the misincorporation of FeV-cofactor, which results in the accumulation of a hybrid enzyme that cannot reduce N-2. These results are interpreted to indicate that AnfO controls the fidelity of Fe-only nitrogenase maturation during the physiological transition from conditions that favor V-dependent nitrogenase utilization to Fe-only nitrogenase utilization to support diazotrophic growth.
Assembly of Iron-Sulfur Clusters In Vivo
O'Carroll, Ina Puleri (Virginia Tech, 2009-02-03)
Iron-sulfur [Fe-S] clusters are protein cofactors that facilitate various life-sustaining biological processes. Their in vivo assembly is accomplished by three different systems known to date. These are: the NIF system which provides [Fe-S] clusters for nitrogenase and other nitrogen-fixing proteins, the SUF system which is induced during conditions of oxidative stress and iron starvation in E. coli, and the ISC system which serves as the housekeeping assembly apparatus. The latter is the focus of this dissertation and includes the proteins IscR, IscS, IscU, IscA, HscB, HscA, Fdx, and IscX. IscU is purified in its cluster-less (apo) form, but can serve as a scaffold to assemble [Fe-S] clusters in vitro in the presence of excess iron and sulfide. To test the scaffold hypothesis and gain insight into the events that occur during [Fe-S] cluster assembly and delivery, we developed two methods that allow the isolation of IscU and other ISC proteins in vivo. In the first method, Azotobacter vinelandii IscU is isolated from its native host, whereas in the second, it is isolated recombinantly from E. coli using a vector that allows expression of the entire isc operon. We found that IscU exists in vivo in two forms: apo-IscU and [2Fe-2S]2+ cluster-loaded IscU which are believed to be conformationally distinct. Both transient and stable IscU-IscS complexes were identified, indicating that the two proteins interact in vivo in a manner that involves their association and dissociation. The [2Fe-2S]2+-IscU species was present as a single entity, whereas significant amounts of apo-IscU were found associated with IscS, suggesting that IscU-IscS dissociation is triggered by the completion of [2Fe-2S] clusters. Both apo and [2Fe-2S]2+-IscU were predominantly monomeric whereas IscU-IscS complexes were determined to have an Î±2Î²2 composition. IscU was purified in the absence of the chaperones HscA and HscB and was also shown to accommodate a [2Fe-2S]2+ cluster similar to the one bound to IscU isolated from wild type cells. The findings suggest that [2Fe-2S]2+-IscU exists in one conformation in vivo and that any conformational changes on IscU are exerted after [2Fe-2S] cluster formation. In silico studies showed that a flexible loop containing the conserved LPPVK motif, which is responsible for interactions with HscA, may facilitate cluster exposure to either mediate its delivery to acceptor proteins or participation in the construction of [4Fe-4S] clusters. Experiments with NfuA, a protein similar to the C-terminal domain of NifU, demonstrated that NfuA and similar proteins might serve as [Fe-S] cluster carriers to accomplish the efficient delivery of nascent cofactors to the various recipient proteins.
Azotobacter vinelandii nitrogenase: role of the MoFe protein α-subunit histidine-195 residue in catalysis
Kim, ChulHwan (Virginia Tech, 1994-06-05)
Site-directed mutagenesis and gene replacement procedures were used to isolate mutant strains of Azotobacter vinelandii that produce altered MoFe proteins where the α-subunit residue-195 position, normally occupied by a histidine residue, was individually substituted by a variety of other amino acids. Structural studies have revealed that this histidine residue is associated with the FeMo-cofactor binding domain and probably provides an NH→S hydrogen bond to a central bridging sulfide located within FeMo-cofactor. The present study investigates the role of the α-histidine-195 residue in nitrogenase catalysis by examining the altered MoFe proteins. Comparisons of the catalytic and spectroscopic properties of altered MoFe proteins produced by the Azotobacter vinelandii mutant strains suggest that the α-histidine-195 residue has a structural role which serves to keep the FeMo-cofactor attached to the MoFe protein and to correctly position the FeMo-cofactor within the polypeptide matrix such that N₂ binding is accommodated. Substitution of the α-His-195 residue by a glutamine residue results in an altered MoFe protein that binds but does not reduce N₂, the physiological substrate. Stopped-flow spectroscopic analyses indicate that the α-195^gln MoFe protein is unable to reduce N₂ even though the altered MoFe protein can reach the redox state necessary for N₂ reduction. Although, N₂ is not a substrate for the altered MoFe protein, it is an inhibitor of both acetylene and proton reduction, both of which are otherwise effectively reduced by the altered MoFe protein. This result provides evidence that N₂ inhibits proton and acetylene reduction by simple occupancy of the active site. The α-195^gln MoFe protein catalyzes HD formation in the presence of N₂ and D₂. Moreover, N₂ binding at the active site of the altered MoFe protein is inhibited by the addition of D₂. These observations indicate that binding of nitrogen to the enzyme is necessary but its reduction is not required for the formation of HD. N₂ uncouples MgATP from proton reduction catalyzed by the α-195gln MoFe protein, but does so without lowering the overall rate of MgA TP hydrolysis. Thus, the quasi-unidirectional flow of electrons from the Fe protein to the MoFe protein that occurs during nitrogenase turnover is controlled, in part, by the substrate serving as an effective electron sink. N₂-induced uncoupling of ATP hydrolysis from substrate reduction by the α-195^gln MoFe protein is reversed by the addition of H₂ (D₂) in the assay atmosphere. This observation can successfully be explained if it-is assumed that the altered MoFe protein has a much greater binding affinity for H₂ (D₂) than for N₂. Substitution of the α-histidie-195 residue by glutamine also imparts hypersensitivity of acetylene reduction and N2 binding to inhibition by CO, indicating that the imidazole group of the α-histidine- 195 residue might protect an Fe contained within FeMo-cofactor from attack by CO.
Biochemical and genetic characterization of mercaptopyruvate sulfurtransferase and paralogous putative sulfurtransferases of Escherichia coli
Jutabha, Promjit (Virginia Tech, 2001-06-11)
Sulfurtransferases, including mercaptopyruvate sulfurtransferase and rhodanese, are widely distributed in living organisms. Mercaptopyruvate sulfurtransferase and rhodanese catalyze the transfer of sulfur from mercaptopyruvate and thiosulfate, respectively, to sulfur acceptors such as thiols or cyanide. There is evidence to suggest that rhodanese can mobilize sulfur from thiosulfate for in vitro formation of iron-sulfur clusters. Additionally, primary sequence analysis reveals that MoeB from some organisms, as well as ThiI of Escherichia coli, contain a C-terminal sulfurtransferase domain. MoeB is required for molybdopterin biosynthesis, whereas ThiI is necessary for biosynthesis of thiamin and 4-thiouridine in transfer ribonucleic acid. These observations led to the hypothesis that sulfurtransferases might be involved in sulfur transfer for biosynthesis of some sulfur-containing cofactors (e.g., biotin, lipoic acid, thiamin and molybdopterin). Results of a BLAST search revealed that E. coli has at least eight potential sulfurtransferases, besides ThiI. Previously, a glpE-encoded rhodanese of E. coli was characterized in our laboratory. In this dissertation, a mercaptopyruvate sulfurtransferase and corresponding gene (sseA) of E. coli were identified. In addition, the possibility that mercaptopyruvate sulfurtransferase could participate or work in concert with a cysteine desulfurase, IscS, in the biosynthesis of cofactors was examined. Cloning of the sseA gene and biochemical characterization of the corresponding protein were used to show that SseA is a mercaptopyruvate sulfurtransferase of E. coli. A strain with a chromosomal insertion mutation in sseA was constructed in order to characterize the physiological function of mercaptopyruvate sulfurtransferase. However, the lack of SseA did not result in a discernable phenotypic change. Redundancy of sulfurtransferases in E. coli may prevent the appearance of a phenotypic change due to the loss of a single sulfurtransferase. Subsequently, other paralogous genes for putative sulfurtransferases, including ynjE and yceA, were cloned. Strains with individual deletions of the chromosomal ynjE and yceA genes were also constructed. Finally, strains with multiple deficiency in potential sulfurtransferase genes, including sseA, ynjE and glpE, as well as iscS, were created. However, no phenotype associated with combinations of sseA, glpE and/or ynjE deficiency was identified. Therefore, the physiological functions of mercaptopyruvate sulfurtransferase and related sulfurtransferases remain unknown.
Biochemical characterization of a novel iron-sulfur flavoprotein from Methanosarcina thermophila strain TM-1
Leartsakulpanich, Ubolsree (Virginia Tech, 1999-06-11)
The iron-sulfur flavoprotein (Isf) from the acetate utilizing methanoarchaeon Methanosarcina thermophila was heterologously produced in Escherichia coli, purified to homogeneity, and characterized to determine the properties of the iron-sulfur cluster and FMN. Chemical and spectroscopic analyses indicated that Isf contained one 4Fe-4S cluster and one FMN per monomer. The midpoint potentials of the [4Fe-4S]2+/1+ center and FMN/FMNH2 redox couple were -394 and -277 mV respectively. The deduced amino acid sequence of Isf revealed high identity with Isf homologues from the CO2 reducing methanoarchaea Methanococcus jannaschii and Methanobacterium thermoautotrophicum. Extracts of H2-CO2-grown M. thermoautotrophicum cells were able to reduce Isf from M. thermophila using either H2 or CO as the reductant. Addition of ferredoxin A to the reaction further stimulated the rate of Isf reduction. These results suggest that Isf homologues are coupled to ferredoxin in electron transfer chains in methanoarchaea with diverse metabolic pathways. Reconstituted systems containing carbon monoxide dehydrogenase/acetyl-CoA synthase complex (CODH/ACS), ferredoxin A, Isf, and the designated electron carriers (NAD, NADP, F420, and 2-hydroxyphenazine) were used in an attempt to determine the electron acceptor for Isf. Isf was unable to reduce any of these compounds. Furthermore, 2-hydroxyphenazine competed with Isf to accept electrons from ferredoxin A indicating that ferredoxin A is a more favorable electron partner for 2-hydroxyphenazine. Thus, the physiological electron acceptor for Isf is unknown. Amino acid sequence alignment of Isf sequences revealed a conserved atypical cysteine motif with the potential to ligate the 4Fe-4S cluster. Site-directed mutagenesis of the cysteine residues in this motif, and the two additional cysteines in the sequence, was used to investigate these cysteine residue as ligands for coordinating the 4Fe-4S center of Isf. Spectroscopic and biochemical analyses were consistent with the conserved cysteine motif functioning as ligating the 4Fe-4S center. Redox properties of the 4Fe-4S and FMN centers revealed a role for the 4Fe-4S center in the transfer of electrons from ferredoxin A to FMN.
Biochemical characterization of Aspergillus fumigatus SidA: a flavin-dependent N-hydroxylating enzyme
Chocklett, Samuel Wyatt (Virginia Tech, 2009-12-09)
Ferrichrome is a hydroxamate-containing siderophore produced by the pathogenic fungus Aspergillus fumigatus during infection. This siderophore includes N5-hydroxylated L-ornithine in the peptide backbone that serve as iron chelators. Af SidA is the L-ornithine N5-hydroxylase, which performs the first enzymatic step in the biosynthesis of ferrichrome. In this study, Af SidA was recombinantly expressed and purified as a soluble tetramer with a bound FAD cofactor. The enzyme demonstrated typical Michaelis-Menten kinetics in a product formation assay with respect to L-ornithine, but similar experiments as a function NADH and NADPH indicated inhibition at high coenzyme concentrations. Af SidA is highly specific for its substrate; however, it is promiscuous with respect to its coenzyme requirement. A multi-functional role of NADPH is observed since NADP+ is a competitive inhibitor with respect to NADPH and steady-state kinetic experiments indicate that Af SidA forms a ternary complex with NADP+ and L-ornithine for catalysis. Furthermore, in the absence of substrate, Af SidA forms a stable C4a-(hydro)peroxyflavin intermediate that is stable on the second time scale. Af SidA is also inhibited by several halides and the arginine-reactive reagent, phenylglyoxal. Biochemical comparison of Af SidA to other flavin-containing monooxygenases reveal that Af SidA likely proceeds by a sequential-ordered mechanism.
Biochemical Characterization of Two Aminopeptidases Involved in Hemoglobin Catabolism in the Food Vacuole of Plasmodium falciparum
Ragheb, Daniel Raafat Tadros (Virginia Tech, 2011-03-31)
The parasite Plasmodium falciparum is the causative agent of the most severe form of human malaria. During its intraerythocytic life cycle, P. falciparum transports red blood cell contents to its acidic organelle, known as the food vacuole, where a series of proteases degrade a majority of the host hemoglobin. Two metalloaminopeptidases, PfAPP and PfA-M1, have been previously localized to the food vacuole (in addition to distinct secondary locations for each), implicating them in the final stages of hemoglobin catabolism. Prior genetic work has determined these enzymes are necessary for efficient parasite proliferation, highlighting them as potential anti-malarial drug targets. This study presents the biochemical basis for the catalytic roles of these two enzymes in the hemoglobin degradation pathway. PfAPP, an aminopeptidase P homolog, is specific for hydrolyzing the N-termini of peptides containing penultimate prolines. PfA-M1 is a member of the expansive M1 family of proteases and exhibits a broad specificity towards substrates. The two enzymes are ubiquitous, found in organisms across all kingdoms of life. Their presence in an acidic environment is unique for aminopeptidase P proteins and rare for M1 homologs. Our immunolocalization results have confirmed the dual distribution of these two enzymes in the parasite. Vacuolar targeting was found to be associated with the Plasmodium specific N-terminal extension found in the PfA-M1 sequence by yellow fluorescent protein fusion studies. Kinetic analysis of recombinant forms of PfAPP and PfA-M1 revealed both enzymes are stable and catalytically efficient in the substrate rich, acidic environment of the parasite food vacuole. In addition, mutagenic exploration of the PfA-M1 active site has determined a residue important in dictating substrate specificity among homologs of the same family. These results provide insight into the parasite's functional recruitment of these enzymes to deal with the final stages of hemoglobin catabolism and necessary considerations for inhibitor design.
Biochemistry and genetics of the pathway for the anaerobic degradation of aromatic compounds by Eubacterium oxidoreducens
Haddock, John David (Virginia Tech, 1990-08-05)
The biochemical pathway for the anaerobic degradation of gallate, pyrogallol and phloroglucinol by Eubacterium oxidoreducens was investigated. Phloroglucinol reductase was purified 90-fold, from the soluble fraction of cell extract, to electrophoretic homogeneity. The enzyme was an Î±₂ homodimer with a native M_r of 78,000, did not contain metals or cofactors and was specific for phloroglucinol and NADPH with a K_m of 800 μM and 6.7 μM respectively at pH 6.8. The Km for phloroglucinol decreased with increasing pH. The enzyme catalyzed reaction was reversible and the equilibrium constant was 9.6. Dihydroresorcinol was a competitive inhibitor of the reverse reaction (K_i = 756 μM). Dihydrophloroglucinol produced in cell extract with H₂ as the reductant was identical to the compound produced by sodium borohydride reduction of phloroglucinol as shown by ¹H NMR spectroscopy. The ¹³C NMR spectrum was consistent with the structural assignment of dihydrophloroglucinol. The mechanism of the proposed enzymatically catalyzed reaction is proposed to involve transfer of a hydride equivalent from NADPH to the carbonyl carbon of the phloroglucinol dianion. Mutant strains of E. oxidoreducens that showed no gallate decarboxylase or dihydrophloroglucinol hydrolase activity were isolated after mutagenesis with ethylmethane sulfonate and emichment with ampicillin. The decarboxylase deficient mutants were unable to grow on gallate while pyrogallol and phloroglucinol supported growth. The hydrolase deficient mutants were unable to grow on any aromatic substrates and converted gallate to pyrogallol and dihydrophloroglucinol. The conversion of gallate to non-aromatic intermediates by cell extract of the wild-type stain was dependent on the presence of 1,2,3,5-benzenetetrol for the conversion of pyrogallol to phloroglucinol and on formate for the reduction of phloroglucinol to dihydrophloroglucinol. Transhydroxylase activity involved in the conversion of pyrogallol to phloroglucinol was induced by growth on aromatic substrates. The formate dehydrogenase was located in the soluble fraction of cell extract, and activity was protected from oxygen inactivation by sodium azide. The Km for formate and NADP was 290 μM and 140 μM respectively at pH 7.5. The pH optimum for activity was 7.5 and maximum activity was observed at a temperature of 50°C.
The Biosynthesis and Function of Nitrogenase Metalloclusters
Dos Santos, Patricia C. (Virginia Tech, 2004-11-29)
Nitrogenase catalyzes the biological reduction of N2 to ammonia (nitrogen fixation). The metalloclusters associated with the nitrogenase components include the [4Fe-4S] cluster of the Fe protein, and the P-cluster [8Fe7S] and FeMo-cofactor [7Fe-9S-Mo-X-homocitrate], both contained within the MoFe protein. These metal-complexes play a vital role in enzyme activity during electron transport and substrate reduction. It is known that the FeMo-cofactor provides the site of substrate reduction, but the exact site of substrate binding remains a topic of intense debate. Some models for the substrate binding location favor the molybdenum atom, while other models favor one or more iron atoms within FeMo-cofactor. We have shown that the a-70 residue of the MoFe protein plays a significant role in defining substrate access to the active site: a-70 approaches one 4Fe-4S face of the FeMo-cofactor. Substitutions at this position alter enzyme specificity for reduction of alternative alkyne substrates. These altered MoFe proteins and alternative alkyne substrates, such as propargyl alcohol, were used to trap an intermediate during substrate reduction. Further studies involving the effect of pH on substrate reduction of these altered MoFe proteins pinpointed the location of the bound substrate-derived intermediate on the FeMo-cofactor to a specific Fe atom, designated Fe6. In addition to understanding how substrates are bound and reduced at the active site, understanding how these clusters are biologically assembled is a second point of interest. Inactivation of NifU or NifS has been shown to affect the activity of both nitrogenase components. NifS is a cysteine desulfurase that provides the sulfur for cluster formation and NifU serves as a molecular scaffold during [Fe-S] cluster assembly. Genetic and biochemical experiments involving amino acid substitutions within the N-terminal and C-terminal domains of NifU indicate that both domains can separately participate in nitrogenase-specific [Fe-S] cluster formation. Furthermore, the NifU and NifS protein appear to have specialized functions in the maturation of metalloclusters of nitrogenase and cannot functionally replace the isc [Fe-S] cluster system used for the maturation of other [Fe-S] proteins. These results indicate that, in certain cases, [Fe-S] cluster biosynthetic machineries have evolved to perform only specialized functions.
Biosynthesis of Iron-Sulfur Clusters
Yuvaniyama, Pramvadee (Virginia Tech, 1999-11-17)
It is not known whether biosynthesis of [Fe-S] clusters occurs through a spontaneous self-assembly process or an enzymatic process. However, in the Azotobacter vinelandii 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 in vitro 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.
Biosynthesis of the nitrogenase active-site cofactor precursor NifB-co in Saccharomyces cerevisiae
Buren, Stefan; Pratt, Katelin; Jiang, Xi; Guo, Yisong; Jimenez-Vicente, Emilio; Echavarri-Erasun, Carlos; Dean, Dennis R.; Saaem, Ishtiaq; Gordon, D. Benjamin; Voigt, Christopher A.; Rubio, Luis M. (National Academy of Sciences, 2019-12-10)
The radical S-adenosylmethionine (SAM) enzyme NifB occupies a central and essential position in nitrogenase biogenesis. NifB catalyzes the formation of an [8Fe-9S-C] cluster, called NifB-co, which constitutes the core of the active-site cofactors for all 3 nitrogenase types. Here, we produce functional NifB in aerobically cultured Saccharomyces cerevisiae. Combinatorial pathway design was employed to construct 62 strains in which transcription units driving different expression levels of mitochondria-targeted nif genes (nifUSXB and fdxN) were integrated into the chromosome. Two combinatorial libraries totaling 0.7 Mb were constructed: An expression library of 6 partial clusters, including nifUSX and fdxN, and a library consisting of 28 different nifB genes mined from the Structure–Function Linkage Database and expressed at different levels according to a factorial design. We show that coexpression in yeast of the nitrogenase maturation proteins NifU, NifS, and FdxN from Azotobacter vinelandii with NifB from the archaea Methanocaldococcus infernus or Methanothermobacter thermautotrophicus yields NifB proteins equipped with [Fe-S] clusters that, as purified, support in vitro formation of NifB-co. Proof of in vivo NifB-co formation was additionally obtained. NifX as purified from aerobically cultured S. cerevisiae coexpressing M. thermautotrophicus NifB with A. vinelandii NifU, NifS, and FdxN, and engineered yeast SAM synthase supported FeMo-co synthesis, indicative of NifX carrying in vivo-formed NifB-co. This study defines the minimal genetic determinants for the formation of the key precursor in the nitrogenase cofactor biosynthetic pathway in a eukaryotic organism.
Biosynthesis of the Nitrogenase FeMo-cofactor from Azotobacter vinelandii: Involvement of the NifEN complex, NifX and the Fe protein
Goodwin, Paul Joshua (Virginia Tech, 1999-10-25)
The iron-molybdenum cofactor (FeMo-cofactor) of nitrogenase is the subject of one the most intensive biochemical/genetic detective cases of modern science. At the active site of nitrogenase, the FeMo-cofactor not only represents the heart of biological nitrogen fixation, but its synthesis also serves as a model for complex metallocluster biosynthesis. Research in the Dean Lab is focused on furthering the understanding of Fe-S cluster biosynthesis in the nitrogenase enzyme system. Throughout the years, scientists from a broad range of disciplines have focused their intellectual might on deciphering not only the chemistry of the FeMo-cofactor, but also the biosynthesis of this unique metallocluster. Recent advances in the study of FeMo-cofactor biosynthesis have produced considerable insight regarding the complex series of biological reactions necessary for the synthesis of this metallocluster. The work contained within this dissertation represents my efforts to further the understanding of FeMo-cofactor biosynthesis. The concept of a molecular scaffold in FeMo-cofactor biosynthesis is generally accepted in the field of nitrogenase. Previous work has implicated the products of nifE and nifN as providing the assembly site for FeMo-cofactor synthesis. Researchers were able to purify this molecular scaffold, commonly referred to as the NifEN complex, however, detailed characterization was precluded by the inability to obtain sufficient quantities of NifEN. In an effort to fully characterize the NifEN complex, we initiated a gene fusion approach for the high level production NifEN. In addition to gene fusion, a poly-histidine tag was incorporated into NifEN, allowing purification through the application of immobilized metal-affinity chromatography (IMAC). NifEN obtained in this way was characterized using a variety of biophysical techniques and found to contain two [4Fe-4S] clusters in each NifEN tetramer. These clusters were also shown to be completely ligated by cysteine residues. With the information obtained from this study, it is concluded that the [4Fe-4S] clusters of the NifEN complex are likely to play either a structural or a redox role rather than being transferred and becoming incorporated into the FeMo-cofactor. In addition to the biophysical characterization of the NifEN complex, a separate study was started to characterize the apo-MoFe protein. In this study we used IMAC to purify a poly-histidine-tagged apo-MoFe protein produced by a nifB-deletion mutant of A. vinelandii. Using the poly-histidine fusion approach, apo-MoFe protein was obtained in sufficient quantities for detailed catalytic, kinetic and spectroscopic analyses. This multidisciplinary approach confirmed that apo-MoFe protein contained intact P clusters and P cluster environments, as well as the ability to interact with the Fe protein. It was also shown for the first time that this tetrameric form of purified apo-MoFe protein could be activated by the addition of preformed FeMo-cofactor. The NifEN complex was further characterized to investigate the presence of bound FeMo-cofactor intermediates. NifEN purified by IMAC is produced in the absence of the nitrogenase structural genes (nifHDK). In this genetic background, it is believed that the FeMo-cofactor biosynthetic machinery will become obstructed with unprocessed FeMo-cofactor intermediates, such as the Fe-S precursors of FeMo-cofactor, NifB-cofactor. Previous work indicated that NifEN can exist in either a charged or discharged form, based on the presence or absence of the FeMo-cofactor precursor, NifB-cofactor. EPR and VTMCD spectroscopies showed the presence of a new paramagnetic signal associated with NifEN that is believed to be in the charged or precursor bound state. This represents the first spectroscopic evidence for a precursor to the FeMo-cofactor. Furthermore, an interaction of NifEN and NifX was examined by size exclusion chromatography. From this study, NifX exhibited the capacity to bind a chromophore, presumably an FeMo-cofactor precursor, from the NifEN complex. NifX was also capable of binding to isolated FeMo-cofactor and the FeMo-cofactor precursor, NifB-cofactor. Finally, preliminary investigations involving interaction between the Fe protein and NifEN were initiated. Recent findings indicate that NifEN and the Fe protein have the capacity to interact specifically with one another. The interaction of NifEN and Fe protein appears to be dependent on the association of FeMo-cofactor precursor with NifEN. The NifEN complex also has the capacity to accept electrons from the Fe protein in a MgATP dependent manner. The ability of NifEN to accept electrons from the Fe protein may be involved in the role of Fe protein in FeMo-cofactor biosynthesis.
The capsular polysaccharide of Actinobacillus pleuropneumoniae serotype 5A: role in serum resistance and characterization of the genetic basis for expression
Ward, Christine K. (Virginia Tech, 1995)
Actinobacillus pleuropneumoniae synthesizes a serotype-specific capsular polysaccharide (CP) that protects this bacterium from host defenses. In the presence of anti-CP IgG, encapsulated A. pleuropneumoniae K17 was killed in precolostral calf serum (PCS) but not in normal serum used as a complement source. In contrast, two capsule-deficient mutants were killed in normal serum. The CP of A. pleuropneumoniae contributed to serum-resistance by limiting the amount of C9, a component of the membrane attack complex, but not C3, that bound to the bacteria in PCS. A second mechanism of serum resistance was due to a lipopolysaccharide (LPS)-specific antibody present in the IgG fractions of normal swine serum, swine anti-K17 serum, and guinea pig anti-K17 LPS serum that blocked anti-CP IgG complement-mediated killing of A. pleuropneumoniae. This LPS-specific antibody prevented complement-mediated killing of K17 in the presence of potentially bactericidal anti-CP IgG by reducing the deposition of C9 onto A. pleuropneumoniae, and by directing the deposition of C9 to sites on the bacteria where the bound C9 was easily eluted. Thus, CP and anti-LPS antibody may act synergistically or at different stages of infection to limit the ability of complement to eliminate A. pleuropneumoniae. Two overlapping regions of the A. pleuropneumoniae J45 capsulation locus were cloned and partially sequenced. One region was conserved among A. pleuropneumoniae serotypes and contained four open reading frames, cpxDCBA, that were highly homologous at both the nucleotide and amino acid levels to genes involved in the export of the CP of H. influenzae type b (bexDCBA), Neisseria meningitidis group B (ctrABCD), and to a lesser extent Escherichia coli K1 and K5 (kpsED, kpsMT). The J45 cpxDCBA gene cluster was able to partially complement kpsM::TnphoA or kpsT::TnphoA mutations within a plasmid-encoded E. coli K5 kps locus and restored sensitivity to a K5-specific bacteriophage, indicating that cpxDCBA functioned in capsular polysaccharide export. A DNA region adjacent to A. pleuropneumoniae J45 cpxDCBA was identified that was serotype-specific. This region contained two complete open reading frames (cpsA and cpsB), and a third partial open reading frame, cpsC. These genes may encode proteins involved in A. pleuropneumoniae J45 CP biosynthesis. A recombinant A. pleuropneumoniae J45 mutant in which the three serotype-specific genes, cpsABC, were partially or completely deleted was generated by allelic exchange. This mutant did not produce intracellular or extracellular CP, was serum-sensitive, and was attenuated in pigs. These studies demonstrated that CP contributed to the serum-resistance and virulence of A. pleuropneumoniae. This noncapsulated mutant will be evaluated as a potential live vaccine strain for the control of swine pleuropneumonia.
Carbonic anhydrase from Methanosarcina thermophila: proposal of a new class of carbonic anhydrases and putative roles for the enzyme in anaerobic acetate catabolism
Alber, Birgit E. (Virginia Tech, 1995-06-09)
Carbonic anhydrase (CA) from acetate-grown Methanosarcina thermophila strain TM-1 was purified> 10,OOO-fold (22% recovery) to apparent homogeneity and a specific activity of 4,900 units mg⁻¹.The gene encoding this CA was isolated fronl a partial genomic library on a 12-kb fragment and sequenced. Comparison of the deduced anlino acid sequence with the N-terminaI sequence of the purified protein shows that the gene encodes an additional 34 N-terminal residues with properties characteristic of signal peptides in secretory proteins. The deduced amino acid sequence has no significant identity to any known CAs, but has, among others, 35% sequence identity to the first 197 deduced N-terminal amino acids of a proposed CO₂-concentrating-mechanism protein from Synechococcus sp. strain PCC7942.
Characterization and Molecular Analysis of Fragilysin: The Bacteroides fragilis Toxin
Obiso, Richard J. Jr. (Virginia Tech, 1997-05-06)
Bacteroides fragilis is a gram negative, anaerobic rod, that is a member of the normal colonic microflora of most mammals, and it is the anaerobe most commonly isolated from human soft tissue infections. During the past decade, strains of B. fragilis that produce an enterotoxin have been implicated as the cause of diarrhea in a number of animals, including humans. The extracellular enterotoxin has been purified and characterized as a single polypeptide (Mr~ 20,600) that causes rapid morphological changes in human colon carcinoma cell lines, particularly, HT-29. This dissertation research began in 1993 with the purpose of determining how this enterotoxin, termed fragilysin, causes diarrhea. The deduced amino acid sequence revealed a signature zinc binding consensus motif (His-Glu-Xx-Xxx-His-Xxx-Xxx-Gly-Xxx-Xxx-His/Met) characteristic of metalloproteinases. Sequence analysis showed close identity with metalloproteinases within the zinc-binding and Met-turn regions. Purified fragilysin contained 1 gram atom of zinc per molecule, and it hydrolyzed a number of proteins, including gelatin. Optimal proteolytic activity occurred at 37° C and pH 6.5. Activity was inhibited by metal chelators but not by inhibitors of other classes of proteinases. When fragilysin is injected into ligated ileal and colonic loops of animals, there is significant tissue damage and a subsequent dose dependent fluid response. Histological examination revealed mild necrosis of epithelial cells, crypt elongation, villus attenuation, and hyperplasia. There was extensive detachment and rounding of surface epithelial cells and an infiltration of neutrophils. Enterotoxic activity was inhibited by the metal chelators EDTA and 1,10-phenanthroline; and, to some degree, the enterotoxic activity could be reconstituted by the addition of zinc to chelated toxin. Fragilysin rapidly increased the permeability of the paracellular barrier of epithelial cells to ions (decrease in electrical resistance across monolayers) and to larger molecules (increase in mannitol flux across monolayers). Furthermore, there is a direct effect on the tight junction proteins. Fragilysin appears to cause diarrhea by proteolytically degrading the paracellular barrier of epithelial cells. Fragilysin is a recently discovered virulence factor that could contribute to the pathogenesis of B. fragilis in both intestinal and soft tissue infections. This research was supported by a Public Health Service grants AI 322940 and AI 32940-03 from the National Institute of Allergy and Infectious Diseases, and by the Commonwealth of Virginia project 6127250
Characterization and regulation of the speA gene in Escherichia coli
Moore, Robert C. (Virginia Tech, 1990)
In Escherichia coli, the speA gene encodes biosynthetic arginine decarboxylase (ADC), the first enzyme in a putrescine biosynthetic pathway. ADC converts arginine to agmatine, which is hydrolyzed by agmatine ureohydrolase, encoded by the speB gene, to putrescine and urea. ADC is negatively regulated by mechanisms requiring either cAMP and cAMP receptor protein (CRP) or putrescine. A 3,236 base pair (bp) BalI-AccI restriction fragment derived from plasmid pKA5, which contains a 7.5 kilobase (kb) E. coli genomic fragment in pBR322, was subcloned into pGEM-3Z to produce plasmids pRM15 and pRM59. Both pRM15 and pRM59 overexpress ADC and the DNA sequence of the BalI-AccI fragment in each plasmid was determined. A 2,119 bp restriction fragment containing 730 bp 5’ to speA, the speA promoter, and 1,389 bp (463 amino acids) of the 5’-end of speA was used to construct transcriptional (pRM161 and pRM162) and translational (pRM65) speA-lacZ fusion plasmids. The presence of the predicted 160,000 and 157,000 dalton ADC
Characterization and site-directed mutagenesis of NifU from Azotobacter vinelandii
Jack, Richard F. (Virginia Tech, 1995-10-05)
In order to elucidate the function of the nifU gene product in nitrogenase maturation in Azotobacter vinelandii. the gene product has been hyperexpressed in Escherichia coli and characterized by various biophysical techniques. Following the initial characterization, site-directed mutagenesis of conserved cysteinyl residues was performed in order to gain further insight into the structure/function relationship of NifU. Both the Fe protein and the MoFe protein of nitrogenase require processing by additional nif genes including nifM (Fe protein), and nifE, N, B, H, V, and Q (MoFe protein). Two additional genes, nifU and nifS, are required for the maturation of both nitrogenase component proteins. It has been proposed that they may somehow be involved in metallocluster biosynthesis (Jacobson et al., 1989b). Our laboratory has determined that the nifS gene product (Nifs) is a pyridoxal-phosphate containing enzyme capable of catalyzing the desulfurization of L-cysteine and can provide the inorganic sulfide necessary for in vitro metallocluster biosynthesis of the Fe protein (Zheng, et al., 1993: Zheng, et al., 1994).
Characterization of a glycerophosphodiester phosphodiesterase in the human malaria parasite Plasmodium falciparum
Denloye, Titilola Ifeoma (Virginia Tech, 2012-04-25)
Active lipid metabolism is a key process required for the intra-erythrocytic development of the malaria parasite, Plasmodium falciparum. Enzymes that hydrolyze host-derived lipids play key roles in parasite growth, virulence, differentiation, cell-signaling and hemozoin formation. Therefore, investigating enzymes involved in lipid degradation could uncover novel drug targets. We have identified in P. falciparum, a glycerophosphodiester phosphodiesterase (PfGDPD), involved in the downstream pathway of phosphatidylcholine degradation. PfGDPD hydrolyzes deacylated phospholipids, glycerophosphodiesters to glycerol-3-phosphate and choline. In this study, we have characterized PfGDPD using bioinformatics, biochemical and genetic approaches. Knockout experiments showed a requirement for PfGDPD for parasite survival. Sequence analysis revealed PfGDPD possesses the unique GDPD insertion domain sharing a cluster of conserved residues present in other GDPD homologues. We generated yellow fluorescent fusion proteins that revealed a complex distribution of PfGDPD within the parasite cytosol, parasitophorous vacuole and food vacuole. To gain insight into the role of PfGDPD, sub-cellular localization was modulated and resulted in a shift in protein distribution, which elicited no growth phenotype. Kinetic analyses suggest PfGDPD activity is Mg₂⁺ dependent and catalytically efficient at the neutral pH environment of the parasitophorous vacuole. Next, our aim was to determine the upstream pathway that provides deacylated glycerophosphodiesters as substrate for PfGDPD. We identified via bioinformatics, a P. falciparum lysophospholipase (PfLPL1) that directly generates the substrate. Knockout clones were generated and genotyped by Southern and PCR analysis. The effects of PfLPL1 knockouts on parasite fitness were studied, and the results showed that PfLPL1was not required for parasite survival and proliferation.
Characterization of an altered MoFe protein from a nifV- strain from Azotobacter vinelandii
Comaratta, Leonard M. (Virginia Tech, 1998-12-03)
The site of substrate binding and reduction for the nitrogenase complex is located on the iron molybdenum cofactor (FeMo-co) which is contained within the a-subunit of the molybdenum iron protein. FeMo co consists of a metal sulfur core composed of an FeS cluster bridged by three inorganic sulfides to a MoFeS cluster. An organic acid, homocitrate, is coordinated to the Mo atom through its 2-carboxy and 2-hydroxy groups. Homocitrate is formed by the condensation of acetyl-CoA and a-ketoglutarate, which is catalyzed by a homocitrate synthase encoded by nifV. By deleting the nifV gene from Azotobacter vinelandii we were able to study the role of homocitrate in nitrogenase catalysis. A poly-histidine tail was incorporated into the C-termini of the a-subunit permitting isolation of the homocitrateless MoFe protein by using metal affinity chromatography. We have found that the addition of a poly-histidine tag does not alter the catalytic behavior of the native enzyme. In NifV- strains of Klebsiella pneumoniae, citrate has been found to replace homocitrate as the organic constituent of FeMo-co. We have found no evidence this is so in A. vinelandii. Gas chromatography mass spectrophotometry studies indicate little or no organic acids are associated with FeMo-co. We examined the catalytic properties of the NifV- MoFe protein In the mutant, H2 evolution is inhibited by the addition of CO, unlike in the wild type. We have found that the NifV- MoFe protein from A. vinelandii is able to catalyze the reduction of acetylene to both ethylene and ethane.

Browsing by Author "Dean, Dennis R."

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