Browsing by Author "Kennelly, Peter J."
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- Activation of SsoPK4, an Archaeal eIF2α Kinase Homolog, by Oxidized CoARay, William K.; Potters, Mark B.; Haile, January D.; Kennelly, Peter J. (MDPI, 2015-05-15)The eukaryotic protein kinase (ePK) paradigm provides integral components for signal transduction cascades throughout nature. However, while so-called typical ePKs permeate the Eucarya and Bacteria, atypical ePKs dominate the kinomes of the Archaea. Intriguingly, the catalytic domains of the handful of deduced typical ePKs from the archaeon Sulfolobus solfataricus P2 exhibit significant resemblance to the protein kinases that phosphorylate translation initiation factor 2α (eIF2α) in response to cellular stresses. We cloned and expressed one of these archaeal eIF2α protein kinases, SsoPK4. SsoPK4 exhibited protein-serine/threonine kinase activity toward several proteins, including the S. solfataricus homolog of eIF2α, aIF2α. The activity of SsoPK4 was inhibited in vitro by 3ʹ,5ʹ-cyclic AMP (Ki of ~23 µM) and was activated by oxidized Coenzyme A, an indicator of oxidative stress in the Archaea. Activation enhanced the apparent affinity for protein substrates, Km, but had little effect on Vmax. Autophosphorylation activated SsoPK4 and rendered it insensitive to oxidized Coenzyme A.
- The "atypical" protein kinase, SsoPK5, an archaeal member of the piD261/Bud32 subfamilyHaile, January Dendi (Virginia Tech, 2009-08-12)Open reading frame (ORF) sso0433 from the archaeon Sulfolobus solfataricus encodes a protein kinase, SsoPK5 that exhibits 33% sequence identity to p53 related protein kinase (PRPK) from Homo sapiens and 26% sequence identity to piD261/Bud32 from Saccharomyces cerevisiae. Given this high degree of similarity, the objectives of this thesis were to (a) clone and purify recombinant SsoPK5, (b) examine its commonalities and differences with its eukaryotic homologues, and (c) determine if it was regulated by nucleotides or related compounds. Substantial progress was achieved on each objective. After successful cloning of ORF sso0433 and purification of its protein product, SsoPK5, it was determined that SsoPK5 was cold labile and incubation at 4ºC for an extended period of time rendered SsoPK5 incapable of phosphotransferase activity. When stored at room temperature, SsoPK5 was capable of transferring the γ-phosphate from ATP to casein, reduced carboxyamidomethylated and maleylated (RCM) lysozyme,and p53. SsoPK5 phosphotransferase activity required a divalent metal cofactor; like pid261/Bud32, SsoPK5 preferred Mn²⁺ over the more commonly preferred Mg²⁺. SsoPK5 was shown to phosphorylate itself on threonine and serine residues; one of the specific amino acid residues modified is threonine-151. Recombinant SsoPK5 is activated by ADP-ribose and 5′-AMP. Activation was observed when SsoPK5 was stabilized by ATP or a nonhydrolytic analogue, such as β,γ- methylene adenosine 5′-triphosphate (AMP-PCP). Activation was not a result of phosphoryl transfer nor hydrolytic breakdown of ATP or 5′-AMP. This was deduced by the lack of ³²P radioactivity incorporated into SsoPK5 during pre-incubation with [γ-³²P] ATP for 60 min at 65ºC, and activation by adenosine 5′-O-thiomonophosphate (AMPS), a hydrolysis-resistant analog of AMP. These results may indicate that ADP-ribose acts as a pseudochaperone for SsoPK5 thereby facilitating maximal activity.
- Baculovirus-directed expression of the phosphorylase kinase catalytic subunit: pseudosubstrate and calmodulin regulationLanciotti, Robert Arthur (Virginia Tech, 1994-08-05)Phosphorylase kinase (EC 2.7.1.38) is a key enzyme involved in the regulation of the glycogenolysis pathway. It catalyzes the Ca²⁺-dependent phosphorylation and activation of the enzyme glycogen phosphorylase to make the active form glycogen phosphorylase. Phosphorylase kinase is composed of 4 subunits with a stoichiometry of (αβγδ)₄. The γ subunit is the catalytic subunit. The regulatory domain (residues 277-387) of γ contains a sequence resembling the sites phosphorylated in known γ substrates with the exception that a valine₃₃₂ occurs at the analogous position of the phosphorylated serine or threonine residue.
- Biochemical Characterization of Self-Sacrificing P-Aminobenzoate Synthases from Chlamydia Trachomatis and Nitrosomonas EuropaeaStone, Spenser (Virginia Tech, 2023-06-05)Tetrahydrofolate (THF) is an essential cofactor for one-carbon transfer reactions in various biochemical pathways including DNA and amino acid biosynthesis. This cofactor is made up of three distinct moieties: a pteridine ring, p-aminobenzoate (pABA), and glutamate residues. Most bacteria and plants can synthesize folate de novo, unlike animals that obtain folate from their diet. An established pathway for THF biosynthesis exists in most bacteria, but there is evidence of some organisms such as Chlamydia trachomatis and Nitrosomonas europaea which do not contain the canonical THF biosynthesis genes, despite still being able to synthesize THF de novo. Previous studies have shown that these organisms do not contain the pabABC genes, normally required to synthesize the pABA portion of THF, and can circumvent their presence with just a single gene: ct610 and ne1434 from C. trachomatis and N. europaea, respectively. Interestingly, these novel enzymes for pABA synthesis do not use the canonical substrates, chorismate or other shikimate pathway intermediates. The gene product of ct610 was named Chlamydia Protein Associating with Death Domains (CADD) due to its established role in host mediated apoptosis, while the crystal structure showed an architecture similar to know diiron oxygenases. However, we provide evidence of a moonlighting function in pABA synthesis. Isotopic labeling experiments to understand what substrate might be used by CADD found that isotopically labeled tyrosine was incorporated into the final pABA product. Compellingly, CADD was able to produce pABA in the presence of molecular oxygen and a reducing agent alone without the addition of any exogenous substrate, implicating this unusual enzyme as a self-sacrificing pABA synthase from C. trachomatis. Here, we provide strong evidence for Tyr27 being a sacrificial residue that is cleaved from the protein backbone to serve as the pABA scaffold. Furthermore, we also provide evidence that K152 is an internal amino donor for this pABA synthase reaction performed by CADD. In the case of NE1434, we have conducted initial experiments such as site-directed mutagenesis and our findings suggest that these self-sacrificing residues are conserved between two distantly related organisms. Finally, the pABA synthase activity is reliant on an oxygenated dimetal cofactor and despite the crystal structure of CADD depicting a diiron active site, we have demonstrated that CADD's pABA synthase activity is dependent on a heterodinuclear Mn/Fe cofactor. Conversely, NE1434 demonstrates no preference for manganese and likely employs a more traditional Fe/Fe cofactor for catalysis. Our results implicate the CADD and NE1434 as self-sacrificing pABA synthases that have diverging metal requirements for catalysis.
- Carbohydrate-Interacting Proteins from Two Nostoc (Cyanobacteria) SpeciesJordan, Brian Robert (Virginia Tech, 2004-05-05)Cyanobacteria of the Nostoc genus are known for the thick, mucilaginous carbohydrate coatings that they produce. In this work, two examples of cyanobacterial glycobiology are considered, each of which involves a cyanobacterium of the Nostoc genus. The first portion of this work details attempts to obtain amino acid sequence information from the enzymes (glycosyltransferases) that are responsible for producing the extracellular polysaccharide (EPS) of Nostoc commune DRH1, ultimately to allow the transfer of this capacity to another organism. Two artificial substrates were synthesized for use in a capillary electrophoresis-based enzyme assay, which was used to look for glycosyltransferase activity in Nostoc commune DRH1 cell extracts. Glucuronosyltransferase activity was detected in association with Nostoc commune membrane material. The active enzyme displayed a divalent cation metal dependence (Mg+2) that is typical of glycosyltransferase enzymes purified from other organisms. Because the enzyme responsible for this activity held the potential to be EPS-related, its purification was attempted. The capillary electrophoresis-based enzyme assay and a 32P-labeled affinity tag were utilized to follow the glucuronosyltransferase enzyme through successive purification steps. The active enzyme was extracted from Nostoc commune membrane material using Triton X-100, and then purified by anion exchange chromatography. The active detergent extract was extremely unstable, and consequently, other purification techniques tested were unsuccessful in enriching activity. Affinity-labeling experiments indicated that the active enzyme was forming protein aggregates during these procedures, which were not amenable to in-gel protease digestion and peptide analysis by tandem mass spectrometry. The second portion of this work describes an investigation of an Anabaena (Nostoc) PCC 7120 soluble cell extract. Upon separation by sodium dodecyl sulfate ¡V polyacrylamide gel electrophoresis (SDS-PAGE) and subsequent periodic acid-Schiff (PAS) staining of the resulting gel, the components of this cellular fraction produce a ladder-like pattern, which suggests that the extract may contain glycosylated protein. Analyses of several samples that were taken from within the PAS-staining region of such a gel revealed surface layer homology (SLH) domain-containing proteins, likely candidates to be covalently attached to or non-covalently interacting with carbohydrate. Various protein sequence analyses indicated that the detected SLH domain containing proteins belong to a family of (putative) cyanobacterial porins. Proteins in this family possess features that include a N-terminal signal sequence, a single SLH domain motif, followed by a coiled-coil region, and a C-terminal region that is homologous to the b-barrel-forming region of bacterial porins. All of these features were identified in the detected Anabaena (Nostoc) PCC 7120 SLH domain-containing proteins. Smith degradation was performed on a sample that was electroeluted from the PAS-staining region of a preparative-scale SDS-PAGE gel of the soluble cell extract. Subsequent analyses of the resulting sample by SDS-PAGE and mass spectrometry indicated that at least two SLH domain-containing proteins, encoded by all4499 and alr4550, were non-covalently interacting with the PAS-staining material. Following degradation, the PAS-staining material was still of sufficient size to detected by gel electrophoresis, and it continued to migrate in the absence of an interacting protein component. Protease digestion of a similarly prepared sample, and then subsequent analysis by SDS-PAGE and mass spectrometry, revealed that the region between amino acid residues #504 and #536, in the protein encoded by the alr4550 open reading frame, was interacting with the PAS-staining material. Monosaccharide composition analyses of this material revealed more carbohydrate constituents than are found in cyanobacterial primary (peptidoglycan) cell wall polymer alone, indicating that it contained a significant secondary cell wall polymer component as well.
- Characterization of IphP from Nostoc commune UTEX 584 and a Dual Specificity Protein Phosphatase from Anabaena PCC 7120Howell, Larry Daniel II (Virginia Tech, 1997-09-17)Protein phosphorylation is utilized universally as a mechanism of signal transduction. However, the use of tyrosine phosphorylation by bacteria has been a matter of dispute. Conventional wisdom dictated that "prokaryotic phosphorylation" was typified by phosphorylation of histidine and aspartate residues of proteins, while "eukaryotic phosphorylation" was characterized by modification of serine, threonine, or tyrosine residues. Increasing numbers of reports have emerged challenging the traditional view of "prokaryotic" and "eukaryotic" phosphorlyation. One of the strongest links unifying prokaryotic and eukaryotic protein phosphorylation to date is IphP, a genomically-encoded dual-specificity protein phosphatase from the cyanobacterium Nostoc commune UTEX 584 bearing the active-site signature sequence of eukaryotic tyrosine-specific and dual-specificity protein phosphatases. The catalytic properties and substrate specificity of IphP were examined in detail. The enzyme was able to discriminate among a variety of exogenous peptides and proteins. Kinetic studies revealed that IphP favors protein / peptide substrates over low molecular weight compounds. Heparin effected IphP activity in a substrate-dependent manner. Enzyme activity toward casein (P-Ser) and MAP kinase (P-Thr/P-Tyr) was stimulated in the presence of the polyanion, whereas activity was inhibited by heparin toward other protein substrates. Both stimulation and inhibition by heparin were dose-dependent. The ability to stimulate IphP activity toward select substrates was attributed to the ability of heparin to recruit the enzyme and substrate to the same microenvironment. To facilitate future genetic studies examining the role of tyrosine phosphorylation in cyanobacteria, we searched for evidence of protein tyrosine phosphorylation in Anabaena PCC 7120. In a collaborative effort with the laboratory of Dr. Potts, tyrosine phosphorylated proteins were identified in Anabaena utilizing several approaches, including comparative labelling with alpha- vs gamma-32P-ATP, phosphoamino acid analysis, and selective hydrolysis with a tyrosine specific protein phosphatase. Together, these data unequivocally demonstrate the presence of tyrosine-phosphorylated proteins in Anabaena PCC 7120. Extracts of Anabaena PCC 7120 were examined for protein tyrosine phosphatase activity. An apparent PTP activity was detected, partially purified, and characterized. The protein phosphatase was ~38kDa by SDS-PAGE and sucrose density gradient centrifugation and displayed dual-specificity protein phosphatase (DSP) activity in vitro. The enzyme was localized to the periplasm and was thus assigned the title PAD, for Periplasmic Anabaena DSP. Periplasmic phosphoproteins of ~120 and 55 kDa that had been radiolabelled in vitro were dephosphorylated by partially purified PAD. PAD activity varied in vivo ~5-fold in a rhthymic, seemingly diurnal manner. Periplasmic proteins, including the 55kDa protein, were labelled in vivo and the degree of radiolabel incorporated into these proteins varied inversely with PAD activity.
- Charaterization of the glpEGR operon of Escherichia coli K-12Zeng, Gang (Virginia Tech, 1996)In E. coli, three open reading frames (ORF) are present in the glpEGR operon. The glpR-encoded repressor governs the universal negative regulation of the glp regulon. The glpE and glpG genes are located upstream of glpR. The initiation codons as well as the translational reading frames used by these two genes were determined. Both proteins were successfully overexpressed and GlpE was purified in one step using immobilized metal affinity chromatography. The translational reading frame of glpR in its C-terminal coding region was verified, and confirms the nucleotide sequence reported by other workers. The subcellular locations of GlpE and GlpG were determined, GIpE was in the cytoplasmic fraction and is predicted to be an acidic protein with a molecular weight of 12,082; GlpG was in the cytoplasmic membrane fraction and is predicted to be a basic, hydrophobic protein with a molecular weight of 31,278. glp repressor was also overexpressed and purified. The apparent dissociation constant of the glp repressor-operator complex was estimated to be 50 nM, which indicates that GlpR has a relatively low affinity for a single glp operator site. Isoelectric focusing gel electrophoresis suggested that GlpR exists as three differentially-charged forms in vitro. The major form of GlpR had an isoelectric point of 5.99, and the two minor forms had pl’s of 5.92 and 6.05, respectively. The presence and relative amounts of these forms, however, was not dependent on GlpE/GlpG. The effect of GlpE/GlpG together with GlpR on the regulation of glp operons was studied using an in vivo system that employed compatible expression vectors for GlpE/GlpG and GlpR. Comparison of the patterns of regulation of glpK, glpD and glpT by the glp repressor agreed well with results previously reported on differential repression of these operons. Under the conditions employed, the glp repressor conferred more than 90-fold repression on glpK. Interestingly, in the presence of GlpE and GlpG, the repression ratio for glpK increased to near 170-fold. In contrast, glpD was subject to 23- fold repression by GlpR. The presence of GlpE and GlpG, however, decreased this ratio to 12-fold. The glpTQ operon was subject to relatively weak repression, about 9- to 12- fold, and repression was independent of the glpE/glpG gene products. This is the first time that the effect of the GlpE/GlpG proteins on the regulation of individual glp operons has been examined. The results suggest that GlpE/GlpG exert effects that bring about differential regulation of glpK, glpD, and glpT. Since the precise biochemical functions of GlpE and GlpG remain undetermined, the molecular basis for this effect is still unknown.
- Crosstalk Signaling Between Circadian Clock Components and Iron MetabolismSchiffhauer, Samuel Peter (Virginia Tech, 2017-04-25)Circadian rhythms are daily molecular oscillations within cells ranging from prokaryotes to humans. This rhythm is self sustaining, and receives external cues in order to synchronize an organism's behavior and physiology with the environment. Many metabolites utilized in metabolic processes seem to follow a pattern of circadian oscillation. Iron, an essential component in cellular processes such as respiration and DNA synthesis, is obtained almost exclusively through diet, yet little is known about how the clock governs iron metabolism. The regulation of iron within the cell is very tightly controlled, as iron is highly reactive in the generation of oxidative stress and the excretion of excess iron is very limited. There are limited findings indicating that there are molecular ties between the circadian clock and the regulation of iron metabolism. The first half of my dissertation focuses on the role of the circadian clock in modulating expression of iron metabolic components. We found that key components of iron import, in TFRC, and export, in SLC40A1, show altered expression in response to changes in the expression of clock transcription components. Furthermore, in circadian synchronized HepG2 hepatocytes TFRC and SLC40A1 showed rhythms in their mRNA expression, although expression of these genes was highly altered in conditions of high iron availability. We also examined IREB2, which expresses a master regulator of iron concentration in IRP2. IRP2 showed rhythms in phase with circadian component PER2, and IRP2's rhythmicity was lost under iron overload conditions. We observed that the ability of these three critical iron metabolic components to respond to sudden increases in available iron was mitigated in cells with clock impairment. Whole cistrome and transcriptome analysis was used to determine that rhythmicity in TFRC and SLC40A1 are not equal in their recruitment of circadian protein binding or in the stage of transcription in which circadian rhythms are generated. The cumulative effect of all of this regulation is that rhythmic variation in intracellular hepatic ferrous iron is clock controlled. The second half of my dissertation focuses on understanding how iron uptake influences clock resetting. Initially, iron was added to the cells in the form of ferrous sulfate, or chelated out of the cells using 2-2'-dipyridyl and clock gene expression was monitored. Altered rhythmicity of these components was seen at both the mRNA and protein level in cells with disrupted iron homeostasis. Then, we measured changes in period, phase, and amplitude of these rhythms, ultimately using a luciferase reporter cell line to demonstrate that even slight changes in cellular iron produce an effect on rhythmic period. We find that the circadian clock and iron metabolism pathway are intimately related, and that the intracellular iron concentration plays a role in circadian clock behavior. Overall, our research illustrates the importance of the circadian clock in liver metabolism and physiology. Improper iron metabolism due to genetic or dietary shortcomings is common in humans, and our work builds on the importance of chronotherapy in treatment of these conditions. Conversely, our research into the effect intracellular iron has on the clock contributes to the growing body of research into how circadian clocks, especially the peripheral clock of the liver, receive input from a range of metabolites in conjunction with signals from the master oscillator of the suprachiasmatic nucleus.
- DD34E DNA Transposable Elements of Mosquitoes: Whole-Genome Survey, Evolution, and TranspositionCoy, Monique Royer (Virginia Tech, 2007-06-13)Transposable elements (TEs) are mobile genetic elements capable of replicating and spreading within, and in some cases, between genomes. I describe a whole-genome analysis of DD34E TEs, which belong to the IS630-Tc1-mariner superfamily of DNA transposable elements, in the African malaria mosquito, Anopheles gambiae. Twenty-six new transposons as well as a new family, gambol, were identified. The gambol family shares the DD34E catalytic motif with Tc1-DD34E transposons, but is distinct from these elements in their phylogenetic relationships. Although gambol appears to be related to a few DD34E transposons from cyanobacteria and fungi, no gambol elements have been reported in any other insects or animals thus far. This discovery expands the already expansive diversity of the IS630-Tc1-mariner TEs, and raises interesting questions as to the origin of gambol elements and their apparent diversity in An. gambiae. Several DD34E transposons discovered in An. gambiae possess characteristics that are associated with recent transposition, such as high sequence identity between copies, and intact terminal-inverted repeats and open reading frames. One such element, AgTango, was also found in a distantly related mosquito species, Aedes aegypti, at high amino acid sequence identity (79.9%). It was discovered that Tango transposons have patchy distribution among twelve mosquito species surveyed using PCR as well as genomic searches, suggesting a possible case for horizontal transfer. Additionally, it was discovered that in some mosquito genomes, there are several Tango transposons. These observations suggest differential evolutionary scenarios and/or TE-host interaction of Tango elements between mosquito species. This strengthened the case that AgTango may be a functional transposase, and I sought to test its potential activity in a cell culture-based inter-plasmid transposition assay using the Herves plasmids as a positive control (Arensburger et al., 2005). AgTango constructs were successfully constructed; however, no transposition events were detected for Tango or Herves. Because the positive control failed to work, no assessment can be made concerning Tango's transposase. Possible causes and solutions for these results, alternative means to detect transposition, as well as future directions with Tango are discussed.
- Defining Novel Clusters of PPAR gamma Partial Agonists for Virtual ScreeningCollins, Erin Taylor (Virginia Tech, 2022-06-03)Peroxisome proliferator-activated receptor γ (PPARγ) is associated with a wide range of diseases, including type 2 diabetes mellitus (T2D). Thiazolidinediones (TZDs) are agonists of PPARγ which have an insulin sensitizing effect, and are therefore used as a treatment for T2D. However, TZDs cause negative side effects in patients, such as weight gain, edema, and increased risk of bone fracture. Partial agonists could be an alternative to TZD-based drugs with fewer side effects. However, there is a lack of understanding of the types of PPARγ partial agonists and how they differ from full agonists. In silico techniques, like virtual screening, molecular docking, and pharmacophore modeling, allow us to determine and characterize markers of varying levels of agonism. An extensive search of the RCSB Protein Data Bank found 62 structures of PPARγ resolved with partial agonists. Cross-docking was performed and found that two PDB structures, 3TY0 and 5TWO, would be effective as receptor structures for virtual screening. By clustering known partial agonists by common pharmacophore features, we found several distinct groups of partial agonists. Interaction and pharmacophore models were created for each group of partial agonists. Virtual screening of FDA-approved compounds showed that the models were able to predict potential partial agonists of PPARγ. This study provides additional insight into the different binding modes of partial agonists of PPARγ and their characteristics. These models can be used to assist drug discovery efforts for intelligently designing novel therapeutics for T2D which have fewer negative side effects.
- Development of a Certification Exam to Assess Undergraduate Students' Proficiency in Biochemistry and Molecular Biology Core ConceptsZeidan, Quira; Loertscher, Jennifer; Wolfson, Adele J.; Tansey, John T.; Offerdahl, Erika G.; Kennelly, Peter J.; Dries, Daniel R.; Moore, Victoria Del Gaizo; Dean, Diane M.; Carastro, L. Michael; Villafane, Sachel M.; Tyler, Ludmila (2021-06-01)With support from the American Society for Biochemistry and Molecular Biology (ASBMB), a community of biochemistry and molecular biology (BMB) scientist-educators has developed and administered an assessment instrument designed to evaluate student competence across four core concept and skill areas fundamental to BMB. The four areas encompass energy and metabolism; information storage and transfer; macromolecular structure, function, and assembly; and skills including analytical and quantitative reasoning. First offered in 2014, the exam has now been administered to nearly 4000 students in ASBMB-accredited programs at more than 70 colleges and universities. Here, we describe the development and continued maturation of the exam program, including the organic role of faculty volunteers as drivers and stewards of all facets: content and format selection, question development, and scoring.
- Dual-specific protein phosphatases in the ArchaeaDahche, Hanan Mohamad (Virginia Tech, 2010-04-02)Three distinct families of PTPs, the conventional (cPTPs), low molecular weight (LMW PTPs), and Cdc25 PTPs, have converged upon a common catalytic mechanism and active site sequence, mainly, the phosphate-binding loop encompassing the PTP signature motif (H/V)C(X)₅R(S/T) and an essential Asp residue on a surface loop. There is little sequence similarity among the three families of phosphatases. All known LMW PTP remove phosphoryl groups esterified to the hydroxyl amino acid: tyrosine, whereas all members of the Cdc25 family are dual-specificity protein phosphatases that dephosphorylate all the hydroxyl amino acids: tyrosine, serine and threonine. The cPTP family primarily functions as tyrosine phosphatases, but it also includes dual-specific members. ORFs encoding potential cPTPs have been identified in five archaeal species: Methanobacterium thermoautotrophicum, Methanococcus jannaschii, Thermococcus kodakaraensis, Pyrococcus horikoshii, and S. solfataricus. Only one has been partially characterized, Tk-PTP from T. kodakaraensis. Hence, our current body of knowledge concerning the functional properties and physiological roles of these enzymes remains fragmented. The genome of S. solfataricus encodes a single conventional protein tyrosine phosphatase, SsoPTP. SsoPTP is the smallest known archaeal PTP (18.3 kDa) with a primary amino acid sequence that conforms to the cPTP protein tyrosine phosphatase paradigm, HCX₅R(S/T). Relatively little is known about its mode of action " whether it follows the conventional PTP mechanism or employs a different route for catalysis " or its physiological role. ORF sso2453 from the genome of Sulfolobus solfataricus, encoding a protein tyrosine phosphatase, was cloned and its recombinant protein product, SsoPTP, was expressed in E. coli and purified by immobilized metal affinity chromatography. SsoPTP displayed the ability to dephosphorylate protein-bound phosphotyrosine as well as protein-bound phosphoserine/phosphothreonine. SsoPTP hydrolyzed both isomers of naphthyl phosphate, an indication of dual specificity. The four conserved residues within the presumed active site sequence: Asp⁶⁹, His⁹⁵, and Arg¹⁰², and the invariant Gln¹³⁹ residue were essential for catalysis, as it was predicted for the established members of the PTP family in both bacteria and eukaryotes. A substrate trapping protein variant, SsoPTP-C96S/D69A, was constructed to isolate possible SsoPTP substrates present in S. solfataricus cell lysates. Several potential substrates were isolated and identified by mass spectroscopy.
- Enzymology and Physiology of a New Type of Phosphoenolpyruvate Carboxylase and the Development of a Pyruvate Carboxylase Expression SystemKraszewski, Jessica (Virginia Tech, 2007-01-29)Our laboratory is interested in studying the junction of glycolysis and the tricarboxylic acid (TCA) cycle, specifically the enzymes phosphoenolpyruvate carboxykinase, pyruvate carboxylase and phosphoenolpyruvate carboxylase. All produce oxaloacetate (OAA) for the cell. OAA production is critical for cell carbon synthesis in the methanogenic archaea. Therefore OAA-generating enzymes are essential for the survival of methanogens. In part of this study we investigated archaeal-type phosphoenolpyruvate carboxylase (PpcA), a new type of phosphoenolpyruvate carboxylase, which is widespread in the archaea and is found in three bacterial species. The form of phosphoenolpyruvate carboxylase (Ppc) that is prevalent in bacteria and plants is not found in the archaea. Due to complications expressing PpcA in the soluble form and difficulty purifying this enzyme from methanogens, an in-depth investigation of this enzyme's biochemical properties has yet to occur. In this study we demonstrate the successful expression of a PpcA homolog in the soluble fraction of Escherichia coli. We purified the recombinant protein to homogeneity. This development provides the means to study the enzyme's biochemical properties and manipulate the primary sequence in order to identify residues critical to the enzyme's function. We also show that this PpcA homolog does have the postulated activity and investigate its biochemical properties. The data show that PpcA has unique properties in regard to the enzyme's substrate and its regulation by metabolites. Our data also reveal that PpcA is a membrane associated protein, unlike Ppc, which is a soluble protein. We also show that pyruvate carboxylase (Pyc) can be expressed recombinantly in Pseudomonas aeruginosa at levels sufficient for structure-function studies. This is a major step forward in the expression in Pyc because it cannot be expressed at high levels in Escherichia coli. These are important developments in studying the enzymes that connect glycolysis and the TCA cycle.
- Experimental evidnece for hysteresis in the cell cycles of Xenopus Laevis egg extractsSha, Wei (Virginia Tech, 2002-08-05)In 1993, Novak and Tyson published a comprehensive mathematical model of the regulation of M-phase promoting factor (MPF) activity in Xenopus laevis eggs and egg extracts. Although this model was in agreement with existing and subsequent experimental data, fundamental predictions that the cell cycle is driven by a hysteresis loop have never been validated experimentally. The model's predictions of bifurcations that create and destroy MPF activity, indicative of hysteresis, were tested in this study. Prediction 1: The threshold concentration of cyclin B required to activate MPF is measurably higher than the threshold concentration required to inactivate MPF. The difference in thresholds implies that the MPF control system is hysteretic and bistable. To measure these thresholds, extracts in interphase or M-phase were supplemented with varying concentrations of non-degradable human cyclin B1 protein. MPF activity was determined by the morphology of sperm nuclei and by assays of histone H1 kinase activity. Consistent with the model, the activation threshold was determined to be 40 nM, which is two-fold higher than the inactivation threshold, 20 nM. Prediction 2: For cyclin levels marginally above the activation threshold concentration of cyclin B, there is a dramatic "slowing-down" in the rate of MPF activation. Supra-threshold concentrations of nondegradable cyclin B1 were added to cycloheximide-treated CSF-released extracts, and samples taken at various time-points were analyzed for MPF activity. At 40 nM cyclin B1, just above the activation threshold, the lag time for MPF activation was 45 - 60 minutes; at 50 nM cyclin B1, the lag time was between 30 - 45 minutes; and at 60 nM or higher concentrations of cyclin B1, the lag time was 20 - 30 minutes, thus confirming the prediction of the Novak-Tyson model. Prediction 3: DNA replication checkpoint increases the activation threshold concentration of cyclin B by increasing the hysteresis loop. Cycloheximide-treated, CSF-released extracts containing 1200 sperm nuclei/μl were treated with aphidicolin, then supplemented with varying concentrations of nondegradable cyclin B1. The activation threshold was 100 nM, 2.5 fold higher than in extracts lacking aphidicolin. Conclusions: These studies confirm three predictions of the Novak-Tyson model and indicate that hysteresis underlies cell cycle control in Xenopus egg extracts. These experiments validate use of mathematical models to study complex biological control systems such as the eukayotic cell cycle.
- Fatty acid synthase is a major polypeptide constituent of cytosolic lipoprotein and is associated with components of the milk lipid secretory pathwayKeon, Brigitte H. (Virginia Tech, 1993-05-15)Most of the lipid present in lactating mammary gland cytosol was associated with a high molecular weight aggregate isolated from cytosol by gel exclusion chromatography or by density gradient centrifugation. The major polypeptide constituent of this lipoprotein aggregate was the monomer of fatty acid synthase (FAS). The major milk lipid globule proteins, butyrophilin (8u) and xanthine oxidase (XO), as well as the small GTP-binding protein ARF, also were present. This lipoprotein complex was abundant in cytosol from lactating but not from involuting mammary glands. HPTLC analysis of lipids extracted from the low density FAS (LDFAS) complex demonstrated the presence of the five major milk phospholipids as well as triacylglycerols, cholesterol, unesterified fatty acids, and diacylglycerols. ³²P-labeled phospholipids present in cytosol could be transferred to microlipid droplets (MLD) and endoplasmic reticulum (ER), in vitro, and could be precipitated along with FAS, and other polypeptide constituents of the LDFAS complex. Complexed FAS could be separated from noncorrlplexed FAS by density gradient centrifugation, native PAGE, and gel exclusion chromatography. A large amount of phospholipid consistently was retained with the complexed form of FAS. These results suggest that FAS migrates to a low density fraction by virtue of its association to other proteins and lipids. FAS was found to be associated with ER, intracellular lipid droplets, and the milk lipid globule membrane (MLGM). A similar complex to LDFAS was isolated from ER from liver and mammary gland homogenates following incubation in buffer containing ATP. Polypeptide constituents of this complex had similar electrophoretic patterns to LDFAS, but behaved differently from LDFAS constituents when fractionated with the detergent TX-114. While most of the polypeptides in LDFAS partitioned equally into the detergent and aqueous phases, a constituent with an approximate molecular weight of 70 kDa was enriched in the detergent phase. For the ER-derived FAS complex, most of the polypeptides remained in the aqueous phase but the detergent phase also was enriched with a polypeptide similar in size to the LDFAS detergent enriched constituent. Western blot analysis failed to detect Bu in the ER-derived complex. However, protein disulfide isomerase (PDI) was detected in this complex as well as a polypeptide with approximate molecular weight 50 kDa that cross-reacted with PDI antibody. Extraction of lipids from this ER-derived complex demonstrated the presence of large quantities of unesterified fatty acids, with relatively low amounts of complex lipids. In studies using ¹²⁵I labeled LDFAS, labeled polypeptides were shown to associate with ER and intracellular lipid droplets and their dissociation was stimulated by ATP. Immunocytochemistry using antibody to rat liver FAS revealed distribution of FAS at localized regions of the cytoplasmic surface of rough endoplasmic reticulum and on surfaces of intracellular lipid droplets. Electron micrographs of the LDFAS complex showed a homogeneous morphology of granular, symmetrical particles ranging in size from 40 nm to 170 nm in diameter. These particles resembled low density lipoprotein (LDL) in morphology. From the available data, the following model was proposed for a possible involvement of FAS in lipid droplet secretion in the mammary gland. During active lipogenesis, FAS is targeted to ER membrane by association with a signal or targeting peptide(s) in the cytosol. The signal peptide then binds to selected regions of ER where signal receptors reside. Binding of FAS may initiate synthesis and accumulation of triacylglycerol between ER membrane bilayers. Upon the achievement of a "critical mass", the lipid core may be released into the cytoplasm in an ATP-dependent manner, surrounded by the membrane components that provided the hydrophobic pocket for lipid accumulation. Butyrophilin and the 70 kDa detergent-extractable constituent released from the ER and present in LDFAS are possible sources of such a function. Polypeptides from the cytosolic leaflet of the ER, and proteins peripherally associated with the leaflet then would comprise the polypeptide constituents of the lipid particle.
- Flavin-dependent Enzymes in Natural Product BiosynthesisValentino, Hannah Rachel (Virginia Tech, 2021-03-31)Natural products are biologically active metabolites produced by fungi, bacteria, and plants that have an extended application in pharmaceutical and chemical industries. Because of their chemical versatility, flavoenzymes are commonly involved in natural product biosynthetic pathways. This has given rise to the identification of flavoenzymes that are promising candidates for biomedical and biotechnical applications. This dissertation discusses the characterization of three flavoenzymes involved in natural product biosynthesis. The class B flavin-dependent monooxygenases S-monoooxygenase from Allium sativum (AsFMO) and N-hydroxylating monooxygenase from Streptomyces sp. XY332 (FzmM) were studied. Both enzymes perform heteroatom oxidation as part of allicin or fosfazinomycin biosynthesis respectively. AsFMO was predicted to oxidize S-allyl-L-cysteine (SAC) to alliin in allicin biosynthesis. Surprisingly, AsFMO exhibited negligible activity with SAC, and instead was highly active with allyl mercaptan and NADPH. This contradicted the initial proposal and suggested that AsFMO is involved in an alternative path producing allicin directly from allyl mercaptan. FzmM was identified to perform multiple N-oxidations which lead to the formation of a nitro group. FzmM performed a highly coupled and specific reaction with L-aspartate and NADPH to produce nitrosuccinate. Both AsFMO and FzmM followed a kinetic mechanism representative of class B flavin-dependent monooxygenases with a rapid pro-R stereospecific reduction and the formation of a C(4a)-hydroperoxyflavin intermediate during oxidation. In addition, the AsFMO structure was obtained and consisted of two domains for FAD and NADPH binding signature of class B monooxygenases. The biochemical and structural study of the Acinetobacter baumannii siderophore interacting protein (BauF) was also accomplished. This enzyme is essential in acinetobactin mediated iron assimilation and is important for virulence. The characterization of the binding and reduction of acinetobactin-ferric iron complex revealed that BauF is specific for this substrate and does not utilize NAD(P)H as an electron donor. The unique activity and structure of BauF can aid future drug design.
- Plasmodium-Induced Nitrosative Stress in Anopheles stephensi: The Cost of Host DefensePeterson, Tina Marie Loane (Virginia Tech, 2005-05-23)Both vertebrates and anopheline mosquitoes inhibit Plasmodium spp. (malaria parasite) development via induction of nitric oxide (·NO) synthase. Expression of Anopheles stephensi ·NO synthase (AsNOS) is induced in the midgut epithelium beginning at 6 h following a Plasmodium berghei-infected blood meal. ·NO reacts readily with other biocompounds forming a variety of reactive nitrogen intermediates (RNIs) that may impose a nitrosative stress. These RNIs are proposed to be responsible for the AsNOS-dependent inhibition of Plasmodium development. In my studies, I identified several RNIs that are induced in the blood-filled midgut in response to Plasmodium infection. Stable end products of ·NO (NO₃⁻ and NO₂⁻), measured using a modified Griess assay, are elevated in infected midguts at 24 h post-blood meal (pBM). Further studies using chemical reduction-chemiluminescence with Hg displacement showed that infected midguts contained elevated levels of potentially toxic higher oxides of nitrogen (NOx), but S-nitrosothiol (SNO) and nitrite levels did not differ between infected and uninfected midguts at 12.5 and 24 h pBM. Thus, nitrates contributed to elevated NOx levels. SNO-biotin switch westerns indicated that S-nitrosated midgut proteins change over the course of blood meal digestion, but not in response to infection. Photolysis-chemiluminescence was used to release and detect bound ·NO from compounds in blood-filled midguts dissected from 0-33 h pBM. Results showed increased ·NO levels in Plasmodium-infected midgut lysates beginning at 8 h, with significant increases at 12.5-13.5 h and 24-25.5 h pBM and peak levels at 20-24 h. Photolyzed ·NO is derived from SNOs and metal nitrosyls. Since SNO concentrations did not change in response to infection, I proposed that metal nitrosyls, specifically Fe nitrosyl hemoglobin (nitrosylHb) based on the concentration of hemoglobin, were elevated in the infected midgut. At 12-24 h pBM, levels of midgut RNIs in infected mosquitoes were typical of levels measured during mammalian septic inflammation. The inverse relationship between AsNOS activity and parasite abundance indicates that nitrosative stress has a detrimental effect on parasite development. However, nitrosative stress may impact mosquito tissues as well in a manner analogous to mammalian tissue damage during inflammation. Elevated levels of nitrotyrosine (NTYR), a marker for nitrosative stress in many mammalian disease states, were detected in tissues of parasite-infected A. stephensi at 24 h pBM. Greater nitration of tyrosine residues was detected in the blood bolus, midgut epithelium, eggs and fat body. In the midgut, Hb remained in an oxygenated state for the duration of blood digestion. The reaction between ·NO and oxyhemoglobin (oxyHb) can result in the formation of nitrate and methemoglobin (metHb). Although nitrate levels were elevated in response to parasite infection, there was little to no metHb present in the mosquito midgut. The simultaneous presence of nitrates, nitrosylHb, oxyHb, and NTYR, together with a lack of elevated nitrites and metHb, suggested that alternative reaction mechanisms involving â ¢NO had occurred in the reducing environment of the midgut. In addition, I proposed that nitroxyl and peroxynitrite participated in reactions that yielded observed midgut RNIs. To cope with the parasite-induced nitrosative stress, cellular defenses in the mosquito may be induced to minimize self damage. I proposed that peroxiredoxins (Prx), enzymes that can detoxify peroxides and peroxynitrite, may protect A. stephensi from nitrosative stress. Six Prx genes were identified in the A. gambiae genome based on homology with known D. melanogaster Prxs. I identified one A. stephensi Prx, AsPrx, that shared 78% amino acid identity with a D. melanogaster 2-Cys Prx known to protect fly cells against various oxidative stresses. AsPrx was expressed in the midgut epithelium and is encoded by a single-copy, intronless gene. Quantitative RT-PCR analyses confirmed that induction of AsPrx expression in the midgut was correlated with malaria parasite infection and nitrosative stress. To determine whether AsPrx could protect against RNI- and ROS-mediated cell death, transient transfection protocols were established for AsPrx overexpression in D. melanogaster (S2) and A. stephensi (MSQ43) cells and for AsPrx gene silencing using RNA interference in MSQ43 cells. Viability assays in MSQ43 cells showed that AsPrx conferred protection against hydrogen peroxide, ·NO, nitroxyl and peroxynitrite. These data suggested that the ·NO-mediated defense response is toxic to both host and parasite. However, AsPrx may shift the balance in favor of the mosquito.
- Identification of a Low Molecular Weight Protein Tyrosine Phosphatase and Its Potential Physiological Substrates in Synechocystis sp. PCC 6803Mukhopadhyay, Archana (Virginia Tech, 2006-02-10)The predicted protein product of open reading frame slr0328 from Synechocystis sp. PCC 6803, SynPTP, possesses significant amino acid sequence similarity with known low molecular weight protein tyrosine phosphatases (PTPs). To determine the gross functional properties of this hypothetical protein, open reading frame slr0328 was cloned, and its predicted protein product was expressed in E. coli. The recombinant protein, SynPTP, was purified by metal ion column chromatography. The catalytic activity of SynPTP was examined toward several exogenous protein substrates that had been phosphorylated on either tyrosine residues or serine residues. SynPTP exhibited phosphatase activity toward tyrosine phosphorylated protein substrates (Vmax toward phosphotyrosyl 32P-casein was 1.5 nmol/min/mg). However, no phosphatase activity was detected toward serine phosphorylated protein substrates. SynPTP displayed phosphohydrolase activity toward several organophosphoesters including para-nitrophenyl phosphate (p-NPP), beta-napthyl phosphate and phosphotyrosine but not toward alpha-napthyl phosphate, phosphoserine, or phosphothreonine. Kinetic analysis indicated that the Km (0.6 mM) and Vmax (3.2 mmole/min/mg) values for SynPTP toward pNPP are similar to those of other known bacterial low molecular weight PTPs. The protein phosphatase activity of SynPTP was inhibited by sodium orthovanadate, a known inhibitor for tyrosine phosphatases, but not by okadaic acid, an inhibitor for many serine/threonine phosphatases. Mutagenic alteration of the predicted catalytic cysteine, Cys7, to serine abolished enzyme activity. Several phosphotyrosine containing proteins were detected from the whole cell extracts of Synechocystis sp. PCC 6803 through immunoreactions using anti-phosphotyrosine antibody. SynPTP was observed to dephosphorylate three of these proteins in vitro. Two of these proteins were identified by peptide-mass fingerprinting analysis, as PsaD (photosystem I subunit II) and CpcD (phycocyanin rod linker protein). In addition, several phosphotyrosine proteins were detected from the soluble and membrane fractions of Synechocystis sp. PCC 6803 cell extracts by in vitro substrate trapping as potential endogenous substrates of SynPTP. Two of these proteins were identified as the alpha and beta subunits of phycocyanin. We therefore speculate that SynPTP might be involved in the regulation of photosynthesis in Synechocystis sp. PCC 6803.
- Identification of a protein kinase substrate in Sulfolobus solfataricus P2Redbird, Ruth Ann (Virginia Tech, 2010-04-01)Living organisms rely on many different mechanisms to adapt to changes within their environment. Protein phosphorylation and dephosphorylation events are one such way cells can communicate to generate a response to environmental changes. In the Kennelly laboratory we hope to gain insight on phosphorylation events in the domain Archaea through the study of the acidothermophilic organism Sulfolobus solfataricus. Such findings may provide answers into evolutionary relationships and facilitate an understanding of phosphate transfer via proteins in more elaborate systems where pathway disturbances can lead to disease processes. A λ-phage expression library was generated from S. solfataricus genomic DNA. The immobilized expression products were probed with a purified protein kinase, SsoPK4, and radiolabeled ATP to identify potential native substrates. A protein fragment of the ORF sso0563, the catalytic A-type ATPase subunit A (AtpA), was phosphorylated by SsoPK4. Full length and truncated forms of AtpA were overexpressed in E. coli. Additional subunits of the ATPase were also overexpressed and ATPase activity reconstituted in vitro. Phosphoamino acid analysis and MS identified the phosphorylation sites on AtpA. Several variants of AtpA were derived via site-directed mutagenesis and assayed for ATPase activity. Chemical cross-linking was employed to determine possible ATPase subunit interactions; tryptic digests of AtpA and its mutant variants were performed to examine protein folding. The phosphorylated-mimic variant of AtpA, T98D, resulted in an inactive ATPase complex as determined by ATPase activity assays and native-PAGE indicating potential phosphoregulation by SsoPK4 on enzyme activity. Ultimately, any findings would need verification with in vivo studies.
- Induction of Anopheles stephensi nitric oxide synthase by Plasmodium-derived factor(s)Lim, Junghwa (Virginia Tech, 2004-11-03)Malaria parasite (Plasmodium spp.) infection in the mosquito Anopheles stephensi induces significant expression of A. stephensi nitric oxide synthase (AsNOS) in the midgut epithelium as early as 6 h post-infection and intermittently thereafter. This induction results in the synthesis of inflammatory levels of nitric oxide (NO) in the blood-filled midgut that limit parasite development. However, the Plasmodium-derived factors that can induce AsNOS expression and the signaling pathways responsible for transduction in A. stephensi have not been identified until completion of the work described herein. In my studies, I have determined that P. falciparum glycosylphosphatidylinositol (PfGPIs) can induce AsNOS expression in A. stephensi cells in vitro and in the midgut epithelium in vivo. Based on related work in mammals, I hypothesized that parasite-derived AsNOS-inducing factors signal through the insulin signaling pathway and the NF-kappaB-dependent Toll and Immune deficiency (Imd) signaling pathways. In support of this hypothesis, I have determined that signaling by P. falciparum merozoites and PfGPIs is mediated through A. stephensi protein kinase B (Akt/PKB) and DSOR1 (mitogen activated protein kinase kinase, MEK)/Extracellular signal-regulated protein kinase (ERK), kinases which are associated with the insulin signaling pathway. However, signaling by P. falciparum and PfGPIs is distinctively different from signaling by insulin and these parasite signals are not insulin-mimetic to A. stephensi cells. In other studies, treatment with pyrrolidine dithiocarbamate (PDTC), an inhibitor of NF-kappaB, reduced AsNOS expression by P. falciparum merozoites in A. stephensi cells. This result suggested the involvement of Toll and Imd pathways in parasite signaling of mosquito cells. Knockout of Pelle, a proximal signaling protein in the Toll pathway, increased AsNOS expression following parasite stimulation, suggesting that the Toll pathway may negatively regulate signaling by Plasmodium-derived AsNOS-inducing factors. In contrast, knockout of TGF-beta-activated kinase 1 (Tak1), a proximal signaling protein in the Imd pathway, reduced AsNOS expression by 20% relative to the control, suggesting that the Imd pathway is required for signaling by Plasmodium-derived AsNOS-inducing factors. Despite the NO-rich environment of the midgut, Plasmodium development is not completely inhibited. This observation suggests that Plasmodium may have efficient detoxification systems during sexual development in A. stephensi. To identify Plasmodium defense genes that may defend parasites against nitrosative stress caused by AsNOS induction, expression of several antioxidant defense genes known to function in nitrosative stress defense in a variety of organisms were examined during sporogonic development. Notably, increased expression levels of P. falciparum peroxiredoxins containing 1 or 2 cysteines (1-cys or 2-cys PfPrx) were associated with periods of parasite development just prior to and during parasite penetration of midgut epithelium, an event associated with significant AsNOS induction in the midgut. The provision of N omega-L-arginine (L-NAME), a known inhibitor of NOS enzyme activity, to A. stephensi with Plasmodium culture by artificial bloodmeal significantly reduced expression of 1-cys and 2-cys PfPrx indicating that these gene products may function to protect parasites against nitrosative stress induced by AsNOS.