Rozprawy doktorskie na temat „Protein S”

Protein engineering is a young dynamic discipline with great amount of potential practical applications. However, its success is primarily based on perfect knowledge and usage of all existing information about protein function and structure. To achieve that, protein engineering is supported by plenty of bioinformatic tools and analysis. The goal of this project is to create a new tool for protein engineering that would enable researchers to identificate related proteins with modified function in still growing biological databases. The tool is designed as an automated workflow of existing bioinformatic analyses that leads to identification of proteins with the same type of enzymatic function, but with slightly modified properties - primarily in terms of selectivity, reaction speed and stability.

Protein S (PS) is a vitamin K dependent plasma glycoprotein with multiple functions in coagulation, inflammation and apoptosis. The molecular weight of PS is approximately 70 kDa and its concentration in plasma is about 25 mg/L. In human plasma 40% of PS circulates as free form and the remaining 60% is complexes with complement C4b-binding protein, a component of the complement system. PS circulating in plasma is mainly derived from liver synthesis but, in addition, endothelial cells, testicular Leydig cells and a megakaryocytic cell line (MEG 01) can synthesize PS. Platelet contain PS, but whether this is derived from megakaryocytic synthesis or from uptake of plasma PS by megakaryocyte (Mk) is not known. Free PS acts as a cofactor for activated protein C (APC) in the inactivation of procoagulant factors Va and VIIIa. However, PS also has APC-independent anticoagulant functions, probably through direct inhibition of both the prothrombinase and the tenase complexes. It is hypothesized that intra-platelets PS, release upon platelets stimulation, plays a crucial role in regulating thrombin generation and therefore controlling procoagulant activity. PS deficiency is inherited as an autosomal dominant disordered and is classified in three types: I) reduced plasma levels of total and free PS antigen (PSAg); II) normal concentration of total and free PSAg but with low PS activity; III) low free PSAg; and normal total PSAg. Inherited PS deficiency is generally associated with increased risk of deep venous thrombosis, pulmonary embolism and some cases of arterial thrombosis. The risk of venous thrombosis in PS deficiency increased if 2 associated with other genetic or acquired conditions these includes factor V (FV) Leiden, HR2 aplotype of FV and prothrombin mutation. Several factors influence the concentration of plasma PS, pregnancy, oral contraceptive and oral anticoagulant therapy decreased the levels of PS. To clarify the origin of intra-platelets PS, we development an in vitro model of human megakaryocyte cell culture. Hematopoietic stem cells were isolated by the histopaque system from whole blood of healthy and PS deficiency subjects. Mononuclear cells have been grown in a serum free medium in presence of thrombopoietin (TPO) and interleuchin-3 (IL-3) to stimulate the differentiation into megakaryocytes lineage. The morphology of differentiated mononuclear cells was similar to MKs, and their positive stain with anti-CD41 antibody allowed us to conclude that these cells were indeed Mk. Mk was labeled with ??-tubulin and ?-tubulin antibodies and we observed the cytoplasmatic extensions called proplatelets and the release of platelets. In addition, through immunofluorescence techniques, we detected FV in their cytoplasm whereas protein C was not present as expected. As for PS, it was present in the cytoplasm of MKs obtained from healthy and PS deficiency individuals. Our study demonstrated the PS biosynthesis by megakaryocyte. To study the mechanisms that regulate the concentration of plasma and platelets PS we analyzed plasma and platelets PS from normal and PS deficiency subjects. PS contained in platelets have the same immunoblotting pattern respect to plasma PS. Plasma and platelet PS immunoblotting pattern demonstrated different molecular weight of PS in some deficient PS individuals as compared to normal control, suggesting different mutations in PS gene. We analyzed the presence of mutation and the presence of PS Heerlen allele. We investigated platelets PS antigen levels in type I and type III PS deficient patients. In type I subjects total and plasma free PS antigen levels were (PSAg) 62±7% and 37±12% 3 respectively. In carries of type III defect total and free PSAg levels were 85±13% and 41±13% respectively. Platelets PSAg in type I and type III were 66 ±32% and 80±37%.In a subgroup of healthy individuals total, free and platelet PSAg levels were 119±17%, 110±17% and 101±30%, respectively. The results indicate that type I and III subject’s total and plasma free PSAg levels were lower than normal individuals. Intra-platelets PSAg levels in type I and type III were lower than of healthy individuals. Our analysis demonstrates a strict correlation between total and free plasma PS and Plts PS. The reduction of platelet PS mirrors the reduced levels of free and total PSAg present in carries of the defect even though PS levels in Plts appears unexpectedly higher than the free PS counterpart. Moreover, we study the interaction of anticoagulant drugs on PSAg levels on 35 patient treatments with warfarin. The levels of total and free plasma PS decreased during treatment with oral anticoagulant, since PS is a vitamin K-dependent protein. Our study demonstrated significant decreased levels of platelet PS respectively plasma free and total PS. We valuated the effect of anticoagulant drugs (warfarin) and of vitamin K on Mk cells. The Mk were treatment with 1?g/ml of warfarin or 1?g/ml of vitamin K and analyze synthesis of PS. We observed decreased PS synthesis on MKs with warfarin than control MKs; on the contrary, MKs cultured under vitamin K treatment increase PS synthesis.
La proteina S (PS) è una glicoproteina plasmatica, vitamina K-dipendente, con molteplici funzioni nell’ambito della coagulazione, infiammazione e apoptosi. Il suo peso molecolare è di 70 kDa e la sua concentrazione plasmatica di circa 25 mg/L. Nel plasma umano il 40% della PS circola in forma libera, mentre il restante 60% è legato alla C4b-binding-protein, una proteina del sistema del complemento. La PS circolante nel plasma viene sintetizzata principalmente nel fegato ma anche le cellule endoteliali, le cellule di Leydig e una linea cellulare di megacariociti sono in grado di sintetizzarla. Le piastrine contengono PS, anche se la sua origine non è ancora stata chiarita. Si ipotizza che derivi dalla sintesi dei megacariociti o che siano gli stessi megacariociti ad assumerla dal pool plasmatico mediante un meccanismo di endocitosi. La PS libera agisce da cofattore per la proteina C attivata (APC) nell’inattivazione dei fattori procoagulanti Va (FVa ) e VIIIa (FVIIIa). La PS esercita anche un’azione anticoagulante APC-indipendente, probabilmente inibendo direttamente i complessi tenase e protrombinase. Si suppone che la PS rilasciata dalle piastrine in seguito alla loro attivazione regoli la generazione di trombina, controllando perciò l’attività procoagulante. I difetti di PS sono a trasmissione autosomica dominante e vengono classificati in tre tipi: – difetto di tipo I, caratterizzato da ridotti livelli plasmatici di PS totale e libera; – difetto di tipo II, caratterizzato da livelli fisiologici di PS totale e libera associati ad una ridotta attività; 6 – difetto di tipo III, presenta una PS libera ridotta ed una PS totale nella norma. I difetti di PS sono generalmente associati ad un aumentato rischio di trombosi venosa profonda, embolismo polmonare ed, in qualche caso, a trombosi arteriosa. Nei deficit di PS il rischio di trombosi venosa aumenta se associato ad altre condizioni di carattere genetico o acquisito quali il FV Leiden, l’aplotipo HR2 del FV e mutazioni a carico del gene che codifica per la protrombina. Molteplici fattori, tra cui la gravidanza, la terapia anticoncezionale e anticoagulante orale, riducono la concentrazione plasmatica della PS. Al fine di chiarire l’origine della PS piastrinica, abbiamo messo a punto un modello in vitro di colture di megacariociti umani. Le cellule staminali ematopoietiche sono state isolate con histopaque da sangue intero di soggetti sani e con difetto di PS. Le cellule mononucleate sono state coltivate in un terreno privo di siero ed in presenza di trombopoietina (TPO) e interleuchina 3 (IL3) per stimolarne la differenziazione in una linea magacariocitaria. Le cellule mononucleate differenziate presentavano una morfologia simile a quella dei megacariociti e risultavano positive all’anticorpo anti-CD41; questi elementi ci hanno permesso di confermare che si trattasse effettivamente di megacariociti. Inoltre, la marcatura dei megacariociti con anticorpi anti ??-tubulina e ?-tubulina ha evidenziato sia la presenza di estensioni citoplasmatiche denominate “proplatelets” sia il rilascio di piastrine da parte dei megacariociti. In aggiunta, mediante tecniche di immunofluorescenza, abbiamo rilevato la presenza del FV a livello citoplasmatico, mentre la PC era assente. La PS era presente nel citoplasma dei megacariociti isolati da individui sani e con difetto di PS. La nostra ricerca ha così dimostrato la sintesi di PS da parte dei megacariociti. 7 Per studiare il meccanismo che regola i livelli di PS presenti nel plasma e all’interno delle piastrine, abbiamo determinato la concentrazione di PS plasmatica e piastrinica in soggetti sani e portatori di difetto di PS. La PS piastrinica mostrava lo stesso pattern elettroforetico di quella isolata dal plasma. L’analisi immunologica ha inoltre evidenziato, per alcuni soggetti portatori del difetto, una PS plasmatica con differente peso molecolare rispetto ai controlli sani; questo ci ha suggerito la presenza di mutazioni nel gene della PS. Abbiamo quindi testato la presenza di eventuali mutazioni e dell’allele Heerlen. In soggetti portatori di difetto di PS di tipo I i livelli di PS totale plasmatici, e libera erano: 62±7% e 37±12% . In soggetti portatori di difetto di PS di tipo III i livelli di PS totale e libera nel plasma erano di 85±13% e 41±13%. I livelli di PS nelle piastrine nei soggetti portatori di difetto di PS di tipo I e di tipo III erano di 66 ±32% e 80±37%. In un gruppo di persone sane i livelli di PS totale, libera e piastrinica erano di 119±17%, 110±17% e 101±30%, rispettivamente. Dall’analisi dei livelli plasmatici e piastrinici di PS in soggetti portatori del difetto di tipo I e III è emerso che a) nei pazienti con difetto i livelli di PS totale e libera erano più bassi rispetto ai soggetti sani; b) i pazienti con difetto presentavano livelli di PS piastrinica ridotti rispetto agli individui sani utilizzati come controllo. La nostra analisi ha dimostrato una stretta correlazione tra la PS plasmatica (libera e totale) e quella piastrinica. La diminuzione della concentrazione di PS piastrinica, osservata negli individui portatori del difetto, riflette l’abbassamento del livello di PS plasmatica, sebbene la quota di PS all’interno delle piastrine risulti maggiore rispetto a quella della PS presente nel plasma in forma libera. In seguito abbiamo studiato l’effetto di sostanze anticoagulanti sui livelli plasmatici e piastrinici di PS in pazienti 8 sani in trattamento con warfarina. E’ noto che la warfarina abbassa i livelli plasmatici di PS in quanto quest’ultima è una proteina vitamina Kdipendente. Anche i livelli di PS plasmatica, (totale e libera), e piastrinica dei medesimi soggetti in terapia con warfarina risultano ridotti rispetto alla norma ma l’abbassamento della concentrazione di PS appare molto più marcata all’interno delle piastrine piuttosto che nel plasma. Infine abbiamo valutato l’effetto della warfarina e della vitamina K sulla sintesi di PS da parte dei megacariociti. Mediante tecniche di immunofluorescenza abbiamo osservato una ridotta sintesi della PS nei megacariociti trattati con warfarina rispetto alle cellule di controllo; al contrario, i megacariociti coltivati in un terreno supplementato con vitamina K mostravano un incremento della sintesi di PS.

DNA damage can lead to the accumulation of mutations and diseases such as cancer. It is therefore integral for cells to identify this damaged DNA and promote its repair. To carry out this function eukaryotic cells have evolved signal transduction pathways known as the DNA structure checkpoints. Much of the molecular mechanism underlying these pathways is still far from understood. The work in this thesis uses the model organism Schizosaccharomyces pombe to investigate these mechanisms, with a particular focus on the TopBP1 homolog Rad4. TopBP1 plays an essential scaffolding role in the initiation of DNA replication, but is also a key protein in the DNA structure checkpoints. It has previously been shown in metazoans and budding yeast to stimulate the kinase activity of ATR, via its ATR Activation Domain (AAD), an early event in checkpoint activation. The work presented in here, along with initial work carried by previous members of the Carr Laboratory; Su-Jiun Lin and Valerie Garcia, shows that the Rad4TopBP1 AAD acts in a chromatin dependent pathway to amplify the checkpoint signal in G1/S-phase, where DNA resection is limited. A second AAD is also identified in the checkpoint clamp protein Rad9, which acts redundantly with the Rad4 AAD. As well as its AAD function, Rad4 also plays a scaffolding role in the DNA structure checkpoint pathways. The work in this thesis, in collaboration with the Laurence Pearl and Li Lin Du laboratories, identifies the molecular mechanism of the interaction between Rad4 and the mediator protein Crb253BP1. It is shown that sequential phosphorylation of Crb2 by Cdc2CDK is required for the interaction with BRCT domains 1 and 2 of Rad4 and checkpoint activation. It is also shown that Rad4 most likely does not interact with Mrc1 or Slx4 in the S. pombe checkpoint pathways.

Palmitoylation refers to the covalent attachment of fatty acids, such as palmitate, onto the cysteine residues of proteins. This process may subsequently alter their localization and function. Nearly all of the enzymes that catalyze palmitoylation, zDHHC protein acyl transferases (PATs), are implicated in neurological disorders, infectious diseases, and cancer in humans. Of particular interest to those who study palmitoylation are Ras family GTPas and zDHHC9-GCP16, the zDHHC PAT that palmitoylates Ras proteins. Erf2-Erf4 is the zDHHC PAT that palmitoylates Ras proteins in Saccharomyces cerevisiae. Currently, there are no methods to therapeutically target palmitoylation for the treatment of disease. One of the barriers to identifying a modulator of palmitoylation is the lack of a reliable high-throughput screening system. To date, few assay systems have been developed to examine the kinetics and mechanism of that palmitoylation reaction. This lab has developed a fluorescence-based coupled assay to gain insight into the enzymology, biochemical mechanism, and kinetics of the palmitoylation reaction. This assay may be used to identify specific inhibitors of autopalmitoylation. In the first step of this reaction, the palmitoyl-moiety from palmitoyl-CoA is transferred to the zDHHC9 PAT cysteine side chain to form a palmitoyl:enzyme intermediate. The second step of palmitoylation is the subsequent transfer of the palmitoyl-moiety from the palmitoyl:enzyme intermediate to the cysteine residue of the substrate protein. This fluorescence-based coupled assay was utilized to screen a natural products library and a unique synthetic compound library for inhibitors of Erf2 autopalmitoylation. These screens led to the identification of fungal metabolite extracts and ten bis-cyclic piperazine compounds that inhibit Erf2 autopalmitoylation in the low micromolar range. This effect is similar to known inhibitors of palmitoylation that lack specificity for the palmitoylation reaction itself.

[Truncated abstract] Every year thousands of individuals suffer from thrombotic related complications that in some cases can be fatal and every year millions of women take some form of hormonal contraceptive. In some cases, there is a cause and effect relationship between the two as users of the combined oral contraceptive pill have an increased risk of developing a thrombotic event. Increased circulating levels of oestrogen cause a prothrombotic shift in the coagulation cascade resulting from upregulation of several procoagulant proteins and a decrease of key anticoagulant proteins. One of the most oestrogen sensitive anticoagulants is Protein S (PS), a product of the PROS1 gene. PS acts as a cofactor to activated protein C (aPC) and the PS-aPC complex serves to downregulate clot formation by deactivating the tenase and prothrombinase complexes via proteolytic cleavage of activated factors VIII and V, respectively. As such, low PS levels are associated with an increased risk of developing thrombotic disorders such as pulmonary embolism, stroke or coronary thrombosis and deep vein thrombosis. During pregnancy when oestrogen levels increase, a steady decline in PS is evident in the early weeks of gestation and continues to decrease to below the normal range in the 2nd trimester, remaining there until post-partum. In addition, reduced free and total PS levels are observed in users of the combined oral contraceptive (COC) pill that contains an oestrogen and a progestin. Interestingly, users of 3rd generation COCs have significantly greater reductions of PS than do 2nd generation COC users. The difference between the two forms is the type of progestin, not the oestrogen, which is predominantly ethinyl oestradiol in the majority of commercially available preparations. At present, a mechanism to describe the relationship between oestrogen and/or progesterone associated with the observed in vivo changes in the levels of PS has not been identified. The aim of this thesis was to define the molecular mechanisms involved in the regulation of PS expression by oestrogen and progesterone. In this study, a Combined Single-stranded conformational analysis and Heteroduplex Analysis (CSHA) iv methodology was optimised for screening both PROS1 DNA and mRNA for the detection of mutations. '...' This may explain why users of 3rd generation COCs display a greater reduction in circulating PS levels compared to 2nd generation users. To investigate potential PS interactions with other proteins that could be hormonally regulated, a yeast-2-hybrid (Y-2-H) screen was performed using the PS molecule as a 'bait' against molecules derived from liver and bone marrow cDNA libraries. A clone that contained a portion of another haemostatic protein, Protein Z (PZ) was isolated and confirmed via sequencing. As no full length PZ clones were identified, a second Y-2-H screen was performed once again using the PS molecule as bait and the PZ molecule as the fish. Interaction between the two proteins was shown to be possible via the successful growth of colonies on triple knock out selective media and by positive ß-galactosidase activity.

The tripeptides glutathione (GSH; γglutamyl-cysteinyl-glycine) and homoglutathione (hGSH; γglutamyl-cysteinyl-β-alanine) are abundant cytosolic tripeptides in legumes. The reactive cysteinyl sulphydryl group enables GSH or hGSH to act as the major cellular redox buffer through the formation of disulphides with other GSH/hGSH molecules. GSH can also form disulphides with cysteinyl groups within proteins, which is termed 5-thiolation, a reversible modification, protecting proteins from irreversible inactivation of thiol residues, as well as being important in regulating protein activity. Following treatment with fungal cell wall elicitors, plant cells produce reactive oxygen species (ROS) which results in cellular oxidative stress. In animal cells ROS generation induces antioxidant defences which include the accumulation of glutathione (GSH) and the formation of mixed disulphides between proteins and GSH. It was hypothesised that following treatment with a fringal elicitor, plant cells also thiolate proteins. It was of interest to determine how protein thiolation changed in response to changes in thiol metabolism known to occur during elicitation, as well as identifying proteins which underwent this modification. Using cell cultures of alfalfa (Medicago saliva L.), a leguminous plant containing both GSH and hGSH, changes in thiol content upon treatment with a fungal cell wall preparation elicitor were determined. By inhibiting protein synthesis and labelling the thiol pools with L-[(^35)S]cysteine, the degree and rate of protein mixed disulphide formation could be monitored in-vivo. To induce the elicitation response, alfalfa cell cultures were treated with a fungal cell-wall elicitor. Following elicitor treatment GSH, but not hGSH, was found to accumulate, with an associated increase in GSH, but not hGSH, forming mixed disulphide with protein. In order to use proteomic tools to identify thiolated proteins, the oxidative stress response in cell cultures of Arabidopsis, a GSH containing species, was then characterised. The level of protein-bound GSH was found to increase following treatment of cell cultures with the oxidant tert-hutyl hydroperoxide and this was associated with changes in cellular thiols. When proteins S-thiolated either in-vivo, or in-vitro, with [(^35)S]-GSH were resolved by SDS-PAGE under non-reducing conditions, a large number of radiolabelled polypeptides were identified in oxidatively stressed preparations. Testing the hypothesis that GSH-dependent enzymes may undergo S-thiolation, proteins which bound GSH were isolated from Arabidopsis using GSH-afFinity chromatography. A number of 30 kDa polypeptides were isolated and found to be S-thiolated under oxidative conditions in-vitro. Several of these were subsequently identified, notably members of the glutathione transferase (GST) superfamily. Representative recombinant GSTs from Arabidopsis, maize and soybean were expressed, Violated in-vitro and the effect on activity determined. Several thiolatable GSTs were identified from Arabidopsis, notably the members of the family of dehydroascorbate reductases (DHAR I, 11, III) and lambda GSTs. Further analysis by elecfrospray mass-spectroscopy confirmed the covalent binding of GSH to DHAR isoenzymes during in-vitro thiolation. It was concluded that S-thiolation of proteins is a commonly observed reversible modification of proteins in plants exposed to oxidative stress with potentially important consequences in cytoprotection and regulation.

This dissertation is a study in how heme facilitates biology using two heme proteins as examples. I write about my mechanistic studies on Cimex nitrophorin and preliminary studies on Ecdysone inducible protein 75, respectively. Nitrophorins are salivary heme proteins used by bloodfeeding insects to deliver NO to the victim, leading to vasodilation and antihemostasis. The bedbug nitrophorin cNP, a thiolate heme protein accomplishes this via an unusual heme-assisted S-nitrosation reaction, requiring proximal ligand cleavage. This dissertation explores this mechanism through mutational, crystallographic and transient kinetic approaches. I present the detailed investigation of the two NO binding events, one at the heme and the other at the proximal cysteine. The heme nitrosyl shows marked pH dependence arising out of the apparent protonation of the proximal cysteine ligand, a feature crucial to cNP function. The structures and spectroscopy of cNP mutant proteins reveal the SNO modification to be regulatory in nature. Laser flash photolysis measurements and the structures of mutant proteins reveal the negative influence of steric hindrance on SNO stability.Studies of insect embryogenesis and metamorphosis reveal the regulatory role of the hormone ecdysone via its target, the ecdysone receptor. Ecdysone triggers expression of several nuclear receptors in a time and tissue dependant fashion, which in turn carry out gene regulation. Ecdysone inducible protein 75 (E75), a nuclear receptor and an early ecdysone responsive gene product, regulates a subset of the developmental activities attributed to ecdysone. We are investigating E75 from Aedes aegypti to uncover its role in ecdysone signaling in mosquitoes. I have expressed and partially purified the full length protein using the baculovirus driven expression in SF9 cells, and purified to homogeneity the heme binding domain resolubilized from inclusion bodies obtained by expression in E. coli. Preliminary characterization of the proteins using UV-visible spectroscopy indicates that E75 has a b type heme with a low spin six-coordinate ferric iron. In the E75 heme binding domain, the heme exhibits an unstable ferrous state and only binds NO and CO at high non-physiological levels. These data place into doubt the suggested roles for E75 as a gas regulated transcription regulator.

The protein SiaA (Streptococcal iron acquisition) is involved in heme uptake in the bacterium Streptococcus pyogenes. It is difficult to obtain this protein in its fully holo form (completely loaded with heme). To increase the concentration of heme in the growing cell, we added ä-aminolevulinic acid (ALA) and ferrous sulfate (FeSO4), precursors of heme, to the growth media. Neither increasing the concentration of heme in vivo, nor growth at lower temperature for longer times, increased the production of holoprotein. The classical method of measuring the concentration of heme in a newly discovered heme protein is cumbersome. We have developed an improved method, which gives a solution that is more stable and has a cleaner spectrum. With further development, this new technique may replace the classical assay. Background information on S. pyogenes, SiaA, ABC transporters, heme biosynthesis, and the pyridine hemochrome assay are described.

Several cell cycle events require specific forms of the cyclin-CDK complexes. It has been known for some time that cyclins not only contribute by activating the CDK but also by choosing substrates and/or specifying the location of the CDK holoenzyme. There are several examples of B-type cyclins identifying certain peptide motifs in their specific substrates through a conserved region in their structure. Such interactions were not known for the G1 class of cyclins, which are instrumental in helping the cell decide whether or not to commit to a new cell cycle, a function that is non-redundant with B-type cylins in budding yeast. In this dissertation, I have presented evidence that some G1 cyclins in budding yeast, Cln1/2, specifically identify substrates by interacting with a leucine-proline rich sequence different from the ones used by B-type cyclins. These “LP” type docking motifs determine cyclin specificity, promote phosphorylation of suboptimal CDK sites and multi-site phosphorylation of substrates both in vivo and in vitro. Subsequently, we have discovered the substrate-binding region in Cln2 and further showed that this region is highly conserved amongst a variety of fungal G1 cyclins from budding yeasts to molds and mushrooms, thus suggesting a conserved function across fungal evolution. Interestingly, this region is close to but not same as the one implicated in B-type cyclins to binding substrates. We discovered that the main effect of obliterating this interaction is to delay cell cycle entry in budding yeast, such that cells begin DNA replication and budding only at a larger than normal cell size, possibly resulting from incomplete multi-site phosphorylation of several key substrates. The docking-deficient Cln2 was also defective in promoting polarized bud morphogenesis. Quite interestingly, we found that a CDK inhibitor, Far1, could regulate the Cln2-CDK1 activity partly by inhibiting the Cln2-substrate interaction, thus demonstrating that docking interactions can be targets of regulation. Finally, by studying many fungal cyclins exogenously expressed in budding yeast, we discovered that some have the ability to make the CDK hyper-potent, which suggests that these cyclins confer special properties to the CDK. My work provides mechanistic clues for cyclinspecific events during the cell cycle, demonstrates the usefulness of synthetic strategies in problem solving and also possibly resolves long-standing uncertainties regarding functions of some cell cycle proteins.

S-acylation, commonly known as S-palmitoylation, is a reversible posttranslational lipid modification in which fatty acid, usually palmitic acid, covalently attaches to specific cysteine residues of proteins via thioester bonds. Palmitoylation enhances the hydrophobicity of proteins and contributes to their membrane association. It plays roles in protein trafficking, signalling, protein-protein interaction, protein stability and other important cellular functions. A family of Protein S-acyl Transferases (PATs) is responsible for this reaction. PATs are multi-pass transmembrane proteins that possess a catalytic Asp- His-His-Cys cysteine rich domain (DHHC-CRD) of ~50 amino acids. In Arabidopsis there are at least 24 such DHHC-CRD containing PAT proteins and they are named as AtPAT01 to AtPAT24. The function of only 2 AtPATs, AtPAT10 and AtPAT24 were studied in some detail, and a recent survey showed the ubiquitous expression pattern and different membrane localization habit of all 24 AtPATs. However, the biological function of the remaining 22 AtPATs in Arabidopsis was not reported when I started my project. Therefore, we carried out an initial screen of all the available T-DNA insertion lines of the 22 Arabidopsis PATs and identified transcriptional null mutants of 18 of the AtPATs. Among them, the k/o mutant plants of only 3 genes showed significantly altered phenotypes compared to wild-type Arabidopsis, and the mutants are named as atpat14, atpat21 and plp1(PAT-like Protein 1). This project aims to characterize these three putative PATs in details in terms of their PAT activities, catalytic domains, expression patterns, subcellular localizations and biological functions. AtPAT14 was proved as a PAT by yeast complementary and in vitro auto-acylation assays. Mutagenesis studies clearly demonstrated that the cysteine residue in the DHHCmotif is essential for the enzyme activity of AtPAT14. Transgenic Arabidopsis plants expressing AtPAT14-GFP were observed and it was shown that AtPAT14 is predominantly localized at the Trans-Golgi. The phenotype was observed in both atpat14-1 and atpat14-2 mutant lines and this showed that the leaves of both lines were aging much faster than the WT. Analysis of the levels of different phytohormones revealed that the mutant leaves contained much higher salicylic acid (SA) than the WT. This coincided with the increased transcript levels of genes involved in SA biosynthesis and signalling. Therefore, AtPAT14 mediated protein S-acylation plays important roles in leaf senescence via the regulation of SA biosynthesis and signalling pathways. AtPAT21 was also confirmed as a PAT and the DHHC its functional domain by similar approaches as for AtPAT14. The plasma membrane (PM) localized AtPAT21 plays essential roles in both male and female gametogenesis. As such, loss-of-function by TDNA insertion in AtPAT21 leads to the plant being completely sterile. Therefore, AtPAT21-mediated S-acylation of proteins(s) plays important roles in the reproduction of Arabidopsis. AtPLP1 (PAT-like Protein 1) contains the signature DHHC-CRD. However, it does not rescue the growth defects of akr1, pfa3 and swf1, the 3 yeast PAT mutants used in enzyme activity assays of other known PATs from plant and animals. Further, the cysteine residue in the DHHC motif was not essential for the function of AtPLP1 as mutated variant containing serine in place of cysteine of the DHHC motif can still rescue the growth defects of atplp1-1. Seedling establishment of atplp1-1 was impaired without external carbon source. This is because the efficiency in converting the seed storage lipid to sugar in the mutant is much lower than WT due to the defective β-oxidation process involved in the degradation of free fatty acids released from lipid during post-germinative growth. In addition, atplp1-1 seedlings are also de-etiolated in the dark, and this was coincided with more cytokinin (CK) and less active gibberellin (GA) related pathway in the mutant. Other defects were also found in atplp1-1, such as hypersensitive to abscisic acid (ABA) and sugar during seed germination and abnormal shoot apical meristem (SAM) in older plants. Therefore, protein S-acyltransferases play distinct and diverse roles throughout the life cycle, from seed germination, seedling growth to seed production in Arabidopsis. This is most likely through the palmitoylation of an array of proteins they modify. Hence, our results provide vital clues for future studies on the molecular mechanism as to how AtPATs operate in plant.

S-nitrosylation (or S-nitrosation) has emerged as an important pathway of non-classical nitric oxide signaling. This post-translational modification involves the transfer of a nitroso group onto a cysteine residue and has been shown to regulate protein function. However, very little is known about the mechanism and structure-dependent factors of the modification. Understanding of S-nitrosothiol chemistry has lagged behind that for the classical nitric oxide signaling pathway due to challenges and limitations of current detection methods of S-nitrosothiols. The S-N bond is typically labile and indirect detection by traditional biotin switch method has low sensitivity and is prone to false positives. In this work, I have explored phosphine derivatization as a new direct approach to labeling protein S-nitrosothiols. Syntheses of aza-ylide derivatives of small organic S-nitrosothiols were successful and the termolecularity of the reaction was overcome by using a bisphosphine. Similarly, S-nitrosated cysteines of thioredoxin were successfully derivatized with the phosphine TCEP and identified by tandem mass spectrometry of the digested protein. Surprisingly, derivatization of S-nitrosoglutathione was found to be unsuccessful and ¹⁸O-labeling of the reaction indicated hydrolysis of the aza-ylide product. We hypothesize that solvent effects are the source of this discrepancy. In addition, x-ray crystallography studies were undertaken to investigate structural rearrangement of a thioredoxin helix to expose residue Cys 62 to S-nitrosation. A new structure of thioredoxin Q63A/C69S/C73S mutant was found to exhibit a highly dynamic N-terminal loop surrounding the pocket of Cys 62 which could have an effect on S-nitrosation of this residue.

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Objective: To evaluate the association of maternal serum uric acid (UA) and proteinuria with clinical and demographic data of pregnant women with preeclampsia syndrome (PES) complicated by HELLP syndrome. Methods: One hundred and nine pregnant women were divided into two groups: group 1 - HELLP pregnant women with PES complicated by HELLP syndrome (n=64); group 2 PES pregnant women with PES but no HELLP syndrome (n=105). Results: Age, ethnicity, parity, delivery mode and perinatal mortality were not statistically different between groups. Systolic and diastolic blood pressure, protein to creatinine (P/C) ratio, uric acid, creatinine and maternal complications were statistically different between groups; values were higher and events, more frequent among pregnant women with HELLP syndrome. The newborns of pregnant women with HELLP syndrome were more premature, had a lower birth weight and a lower APGAR score. Conclusion: Uric acid equal to or higher than 6.0 gm/dL and P/C ratio equal to or higher than 5 were more frequent in gestations with HELLP syndrome, which suggests that elevated proteinuria and uric acid levels in pregnant women with PES may increase the chances of developing HELLP syndrome
Objetivo: Avaliar a associa??o dos n?veis maternos de ?cido ?rico s?rico (AU) e protein?ria e os dados cl?nicos e demogr?ficos em gesta??es complicadas por s?ndrome de pr?-ecl?mpsia (SPE), com s?ndrome de HELLP. M?todos: Cento e sessenta e nove gestantes foram divididas em dois grupos: Grupo 1 - HELLP gestantes com SPE complicada pela s?ndrome de HELLP (n=64); Grupo 2 SPE gestantes com SPE sem s?ndrome de HELLP (n=105). Resultados: N?o ocorreram diferen?as estatisticamente significativas quanto ?s vari?veis idade, cor, paridade, via de parto e mortalidade perinatal entre os grupos. Press?o arterial sist?lica, press?o arterial diast?lica, ?ndice protein?ria/creatinin?ria (P/C), ?cido ?rico, creatinina e complica??es maternas apresentaram diferen?a estatisticamente significativa entre os dois grupos, sendo mais elevados e mais frequentes nas gestantes com s?ndrome de HELLP. Observou-se que os RN de gestantes com s?ndrome de HELLP foram mais prematuros, apresentaram menor peso ao nascimento e menor ?ndice de APGAR. Conclus?o: ?cido ?rico igual ou maior do que 6,0 mg/dL e ?ndice P/C igual ou maior do que 5 foram mais frequentes nas gesta??es com s?ndrome de HELLP, o que permite supor que maiores valores de ?cido ?rico e de protein?ria em gestantes com SPE aumentam a chance de desenvolvimento de s?ndrome de HELLP.

This thesis describes an immunochemical and immunocytochemical study of the bovine brain S-lOOb protein. The two major forms of the S-100 isoproteins (S-lOOa and S-lOOb) were purified to apparent homogeneity from bovine brain. A polyclonal rabbit antiserum to the S-lOOb protein was prepared. The antiserum was characterized by solid phase immunochemical methods. The S-lOOb derived antiserum displayed a high degree of specificity for S-lOOb, but also crossreacted with the purified S-lOOa protein. The characteristics of the immunochemical reactivity of the antiserum towards these two isoproteins suggests the antiserum has specificity for the 6-subunit of the S-100 proteins. An immunohistochemical analysis of the cellular localization of S-lOOb immunoreactivity was undertaken. In the adult rat brain only the astrocytes were S-lOOb immunoreactive. This conclusion is supported by the morphological characteristics of the immunolabelled cells, as well as the observed co-localization of the immunoreactivities for S-lOOb and the Glial Fibrillary Acidic protein (GFAP), the major protein of the astrocyte intermediate filaments. These two antigens were always found to coexist. The immunolabelling of rat brain astrocytes by the S-lOOb derived antiserum stained the entire cell, yielding more complete morphological detail than is possible with the GFAP immunohistochemistry, which only labels the filamentous glial processes. It is concluded that S-lOOb immunohistochemistry could be of general utility in the investigation of astrocyte morphology. The present results also determine that the as yet unknown biological function(s) of the S-100 proteins must be related to a property of astrocytes.
Medicine, Faculty of
Graduate

Surface layer (S-layer) proteins form 2-dimensional crystalline structures at the cell surface of most eubacteria and all archaea. S-layers are generally composed of a single self-assembling (glyco)protein species and can fulfil a number of roles including shape maintenance, exo-enzyme adhesion, and virulence promotion. Engineered S-layers carrying functional inserts at high density also show potential in nanotechnology. However, there is currently no complete structure at atomic resolution available for any S-layer protein. This work is engaged in the (i) structural elucidation of the SbsB S-layer protein of Geobacillus stearothermophilus by determining the surface location of individual residues. A cross-linking screen was used to analyse 23 cysteine residues, known to be surface accessible in the monomer, with respect to their position within the assembled S-layer. The study was able to distinguish between eight residues that are positioned close to the subunit-subunit interface and 10 residues located at the cell-wall facing inner surface. The assay also confirmed the previous assignment of four residues to the outer ambient-exposed surface. The tolerance of the individual sites to insertion of a short peptide sequence was investigated to (ii) create chimeric S-layer proteins for nanobiotechnological applications and (iii) advance the structural elucidation of SbsB. Insertion mutagenesis at nine of the surface sites led to mutants of conserved tertiary structure, of which six were assembly-positive. The six proteins provide model constructs for the incorporation of functional tags into S-layer arrays for nanobiotechnology application as high-density vaccine carriers. The mutagenesis screen also revealed three mutants of conserved tertiary structure but of assembly-negative phenotype. The potential of forming 3D crystals for X-ray crystallography was tested with one mutant yielding small crystals. In conclusion, my work has advanced the understanding of the molecular structure of S-layer proteins and provided the basis for future structural investigations.

Protein S has an established role in the protein C anticoagulant pathway as a cofactor for anticoagulant protein C (APC) and has also recently been shown to serve as a cofactor enhancing the anticoagulant activity of tissue factor pathway inhibitor (TFPI). Despite its physiological role and clinical importance, the molecular bases of its functions are not fully understood. The aim of my thesis was to clarify the molecular mechanisms involved in the protein S interaction with APC and TFPI. More than 30 point or composite protein S variants were constructed and analysed during this project. These variants spanned the Gla, thrombin sensitive region (TSR), epidermal growth-factor1 (EGF1) and EGF2 domains of protein S. Protein S was expressed in mammalian cells and was purified by chromatography, as required. Protein S was characterised by size, cleavage, multimerisation, γ-carboxylation of the Gla domain, binding to phospholipids and to domain specific monoclonal antibodies. Variants were evaluated for their APC and TFPI cofactor activities both by calibrated automated thrombography and in purified FVa inactivation or FXa inhibition assays, respectively. The protein S variant, protein S D95A, with substitution in EGF1 was found to be largely devoid of functional APC cofactor activity and I believe that this residue plays an important role in protein S anticoagulant function. It was γ- carboxylated and bound phospholipids and domain specific monoclonal antibodies with an apparent dissociation constant similar to that of wild type protein S. Importantly, protein S D95A enhanced the anticoagulant activity of TFPI, suggesting that distinct residues in protein S mediate its APC and TFPI cofactor activity. Two composite mutants in the protein S EGF1 domain had partially reduced TFPI cofactor activity in plasma. However, none of the more than 30 variants spanning the Gla-TSR-EGF1-EGF2 domain of protein S completely disrupted the protein S cofactor activity towards TFPI. Collectively, these results shed light on the molecular basis of protein S cofactor function and suggest distinct residues in protein S are involved in the binding to APC and to TFPI.

Die Fusionsreaktion des Coronavirus MHV wird vom S-Protein vermittelt. In der vorliegenden Arbeit wurde der Eintrittsweg von MHV-A59 in Mauszellen untersucht. Die Infektivität kann durch lysosomotrope Substanzen und Inhibitoren der Clathrin-abhängigen Endozytose gehemmt werden. Der Eintritt von MHV-A59 in Mauszellen erfolgt über die Clathrin-abhängige Endozytose und setzt die anschließende Fusion der viralen und zellulären Membran bei niedrigem pH-Wert voraus. Fluoreszenzmikroskopische Studien zur Interaktion fluoreszenzmarkierter MHV-A59 Partikel mit Mauszellen bestätigen, dass MHV-A59 über Endozytose aufgenommen wird. Nach Bindung der Viren an die Zellen und anschließende Erniedrigung des pH-Wertes kommt es zur Färbung der Plasmamembran. Die Erniedrigung des pH-Wertes in Abwesenheit des Rezeptors führt zu einer irreversiblen Konformationsumwandlung im viralen Fusionsprotein, die die Inaktivierung der Fusionsaktivität und den Verlust der Infektivität zur Folge hat. Die Ergebnisse deuten auf die Beteiligung des endozytotischen Weges für den viralen Eintritt von MHV-A59 hin. Ein niedriger pH-Wert eines zellulären endosomalen Kompartiments induziert vermutlich die Konformationsänderung im S-Protein und löst die Fusionsreaktion aus. Ein vorläufiges 3D-Modell des S-Proteins von MHV-A59 konnte erstellt werden. Darüber hinaus wurde die Struktur und Fusionsfähigkeit des S-Proteins von SARS-CoV analysiert. Ein Zell-Zell-Fusionsassay konnte nachweisen, dass die Fusion zwischen S-Protein und ACE2-exprimierenden Zellen sowohl abhängig vom pH-Wert als auch von der proteolytischen Spaltung in S1- und S2-Untereinheit ist und durch Erniedrigung des pH-Wertes zusätzlich verstärkt werden kann. Im abschließenden Teil der Arbeit wurde auf Basis theoretischer Untersuchungen eine Vorhersage des mutmaßlichen Fusionspeptids des S-Proteins von MHV-A59, welches alle wesentlichen Merkmale eines internen Fusionspeptids aufweist, vorgenommen. Es liegt nahe der "Heptad-Repeat" (HR) Domäne HR1.
Fusion of the Coronavirus MHV-A59 is mediated by the viral S-protein. The entry pathway of MHV-A59 into murine cells was studied in this work. Infection was strongly inhibited by lysosomotropic compounds and substances interfering with clathrin-dependent endocytosis, suggesting that MHV-A59 is taken up via endocytosis and delivered to acidic compartments. Fluorescence microscopy of labeled MHV-A59 confirmed that the virus is taken up via endocytosis. When the virus was bound to cells and the pH was lowered to 5.0, we observed a strong labeling of the plasma membrane. Electron microscopy revealed low pH triggered conformational alterations of the S-ectodomain. These alterations are likely to be irreversible because low pH-treatment of viruses caused an irreversible loss of fusion activity. The results imply that endocytosis plays a major role in MHV-A59 infection and that the acidic pH of the endosomal compartment triggers a conformational change of the S-protein mediating fusion. Furthermore the conformation of the trimeric spike protein of the murine hepatitis virus A59 was characterized by cryoelectron microscopy. A preliminary 3D-reconsruction of the native structure could be accomplished. Besides we studied the structure and fusion capability of the spike protein expressed by SARS-CoV. The cell-based fusion assay revealed that fusion of spike protein and ACE2-receptor expressing cells was strongly dependent on low pH and on proteolytic cleavage of the S-protein into S1 and S2 subunit. Additionally fusion could be significantly increased by lowering of the pH. The theoretical part of the thesis allowed the identification of the putative fusion peptide, which showed main characteristics of internal fusion peptides. It allows the heptad regions of the spike protein to assemble in the six-helix bundle structure (6HB). This structure is of great importance to initiate the approximation of viral and cellular membrane and thus to induce fusion.

Rad4TopBP1, a multiple BRCT domain protein, is essential for initiation of replication and participates in checkpoint responses following genotoxic treatment during the S and G2 phases of the cell cycle. Rad4 interacts with several proteins that are involved in initiation of DNA replication (i.e. Sld2) or activation of Chk1 and/or Cds1 checkpoint kinases (i.e. Rad9, Crb2, and Rad3). However, it remained unclear how Rad4 and its homologues are regulated to coordinate these diverse functions. This PhD project presents a comprehensive structure/function analysis of the fission yeast Rad4TopBP1. In order to obtain separation of function mutants of Rad4, a hydroxylamine random mutagenesis genetic screen was performed. However, we were not able to separate a checkpoint activation function from replicative function. Rad4 being phosphorylated in a Cdc2-dependent manner, the role of Rad4 phosphorylation by Cdc2 was investigated. A mutant strain containing multiple mutations at Rad4 Cdc2 consensus phosphorylation sites does not exhibit significant sensitivity to DNA damage or HU. In addition, Rad4 Cdc2 phosphorylation sites do not play a role in DNA re-replication. There is no significant phenotypic effect observed after DNA damage in S. pombe strains expressing a Rad4 protein deleted for a putative domain (RXL motif) interaction with cyclin, or harboring mutations in putative sumoylation motifs, or C-terminus truncation. In higher eukaryotes, TopBP1 binds and activates the ATR-ATRIP complex via an ATR-activating domain (AAD) in order to activate a checkpoint function. We identified a potential AAD in C-terminal of Rad4 in S. pombe. I show that Rad4 physically associates with Rad3 in vitro in an AAD-dependent manner. S. pombe strains mutated in the AAD show a slight sensitivity to DNA damage and HU. The rad4 AAD mutants do not completely prevent Rad3-mediated G2/M checkpoint activation after DNA damage. The sensitivity in a rad4 AAD mutant increases when damage occurs in S-phase, when histone H2A phosphorylation is defective. I established an artificial checkpoint induction system in the absence of exogenous lesions by targeting checkpoint proteins onto chromatin in S. pombe. Interestingly, Rad4 AAD is essential for checkpoint activation in this system. Because this checkpoint activation is independent of ssDNA-RPA formation, the data suggest that the AAD plays a role in chromatin-mediated checkpoint maintenance/amplification. Altogether, this pathway seems to play an important role in S-phase when DSBs resection is limited.

本文データは平成22年度国立国会図書館の学位論文(博士)のデジタル化実施により作成された画像ファイルを基にpdf変換したものである
Kyoto University (京都大学)
0048
新制・論文博士
博士(農学)
乙第8019号
論農博第1796号
新制||農||640(附属図書館)
学位論文||H4||N2518(農学部図書室)
UT51-92-U255
(主査)教授 左右田 健次, 教授 駒野 徹, 教授 清水 昌
学位規則第4条第2項該当

Cancer is of paramount medical concern as an increasingly major contributor of disease-related fatalities of significant prevalence - particularly in the context of current statisticaLlstochastical epidemiological studies which predict that one in three people will contract cancer at some stage of their lives, whilst one in four of these patients will die as a consequence of their particular neoplastic-associated condition. The human Rad9 protein exists in two full-length isoforms (termed Rad9A and Rad9B) whose respective differentially-elevated levels and related expression profiles are distinctive for specific tumour cell tissue types. Most known functions of the DNA damage response protein Rad9 are executed via the well- characterised Rad9-Rad l-Hus 1 ("9-1-1") protein complex, which is loaded onto chromatin in close vicinity to DNA lesion sites. The chromatin-loaded "9-1-1" complex functions as both a DNA damage "sliding-clamp" sensor and a recruitment platform which modulates and co-ordinates the activities of a wide variety of different proteins implicated in cell cycle checkpoint signalling, steroidal nuclear receptor signalling, protein chaperoning and DNA repair - via associative protein-protein interactions with the C-terminal tail domain of the Rad9 sub-unit. This toroidal, heterotrimeric "9-1-1" DNA sliding-clamp complex is highly conserved and its recently resolved crystal structure shows a functional similarity to the homotrimeric PCNA DNA sliding-clamp complex.

Due to the increasing resistance against the currently used antimalarial drugs, novel chemotherapeutic agents that target new metabolic pathways for the treatment of malarial infections are urgently needed. One approach to the drug discovery process is to use interaction analysis to find proteins that are involved in a specific metabolic pathway that has been identified as a drug target. Protein-protein interactions in such a pathway can be preferential targets since a) there is often greater structural variability in protein-protein interfaces, which can lead to more effective differentiation between the parasite and host proteins; and b) the important amino acids in a protein-protein interface are often conserved and even one amino acid mutation can lead to the dissociation of the complex, implying that resistance should be slower to appear. Since polyamines and their biosynthetic enzymes occur in increased concentrations in rapidly proliferating cells, the inhibition of polyamine metabolism is a rational approach for the development of antiparasitic drugs. Polyamine synthesis in P. falciparum is uniquely facilitated by a single open reading frame that encodes both rate-limiting enzymes in the pathway, namely ornithine decarboxylase (ODC) and S-adenosylmethionine decarboxylase (AdoMetDC). The AdoMetDC/ODC domains are assembled in a heterotetrameric bifunctional protein complex of ~330 kDa. Inhibition of both decarboxylase activities is curative of murine malaria and indicates the viability of such strategies in malaria control. It was hypothesized that protein ligands to this enzyme can be utilized in targeting the polyamine biosynthetic pathway in a novel approach. The bifunctional PfAdoMetDC/ODC was recombinantly expressed with a C-terminal Strep-tag-II to allow affinity purification. Subsequent gel electrophoresis analysis showed the presence of 3 contaminating proteins (~60 kDa, ~70 kDa and ~112 kDa) that co-elute with the ~330 kDa AdoMetDC/ODC. Efforts to purify the bifunctional protein to homogeneity included subcloning into a double-tagged vector for tandem affinity purification as well as size-exclusion HPLC. SDS-PAGE analysis of these indicated that separation of the four proteins was not successful, implicating the presence of strong protein-protein interactions. Western blot analysis showed that the ~112 kDa and ~70 kDa peptides were recombinantly produced with a C-terminal Strep-tag, indicating their heterologous origin. The ~60 kDa fragment was however not recognised by the tag-specific antibodies. This implies that this fragment is of E. coli origin. MS-analysis of the contaminating bands showed that the ~112 kDa peptide is an N-terminally truncated form of the full-length protein, the ~70 kDa peptide is a mixture of N-terminally truncated recombinant protein and E. coli DnaK and the ~60 kDa peptide is E. coli GroEL. A P. falciparum cDNA phage display library was used to identify peptide ligands to PfAdoMetDC/ODC. Of the peptides isolated through the biopanning process, only one was shown to occur in vivo. It could however not be conclusively shown that the isolated peptides bind to PfAdoMetDC/ODC and not to the co-eluting E. coli proteins. It is thought that while it is extremely likely that interacting protein partners to PfAdoMetDC/DOC exist, the available technologies are not sufficient to lead to the identification of such partners.
Dissertation (MSc (Biochemistry))--University of Pretoria, 2008.
Biochemistry
unrestricted

Metronidazole is an essential component of the triple therapy regimen against Helicobacter pylori infection. The development of resistance towards metronidazole results in failure to eradicate H. pylori completely. The main aim of the investigation was to understand further the mechanism(s) of resistance in H. pylori. The investigation focussed upon studying the role and function of NADH oxidase in metronidazole resistance. The NADH oxidase levels were shown to be significantly higher in metronidazole susceptible strains than in resistant strains. The purification and characterisation of the enzyme responsible for the oxidation of NADH resulted in isolation of a protein shown to be catalase. The results suggest that NADH oxidase activity in susceptible strains is a function of a bifunctional catalase rather than that of a distinct enzyme. This was confirmed by isolation of catalase from E. coli cells containing cloned H. pylori catalase and demonstration that catalase and NADH activities co-purified. The catalase activity of the purified protein from the bacterial strains used was retained but the oxidation of NADH was not significant in the resistant strain. The base sequence of the catalase gene from the susceptible strain was determined and shown to be 99% identical to that from the cloned gene. The comparison of the derived amino acid sequence of catalase from H. pylori and Proteus mirabilis showed that the heme-binding site is highly conserved. The amino acids in the NAD(P)H binding site are conserved in both strain NCTC 11639 (Mtz s ) and the genomic strain ATCC 26695 (Mtz s) of H. pylori but show significant differences compared with P. mirabilis. A three-dimensional model of catalase from a metronidazole-susceptible H. pylori strain showed stearic hindrance around the NAD(P)H binding site and a substitution of an acidic for a basic residue within the phosphate binding site. Both effects could result in NAD(P)H being less tightly bound and, hence able to leave the catalase in exchange for NADH. Other substitutions may account for the ability of the modified binding site to oxidise NADH. The oxidation of NADH aids in the activation of metronidazole, which damages DNA. The absence of NADH oxidase activity in resistant strains results in the inability of the enzyme to activate metronidazole leading to resistance. The finding that this NADH oxidase activity is a function of a modified catalase in susceptible strains suggests a novel mechanism of metronidazole resistance in H. pylori.

Increasing the integration density of electron device components will necessitate the use of new nanofabrication paradigms that complement and extend existing technologies. One potential approach to overcome the current limitations of electron-beam lithography may involve the use of hybrid systems, in which existing lithographic techniques are coupled with “bottom up” approaches such as supramolecular self-assembly. In this respect, biological systems offer some unique possibilities as they combine both self-organization and spatial patterning at the nanometer length scale. In particular, Surface Layer Proteins (S-layers) can facilitate high order organization and specific orientation of inorganic structures as they are two-dimensional porous crystalline membranes with regular structure at the nanometer scale. In this framework, the aim of the present work was the characterization of the S-layer of Sporosarcina ureae ATCC 13881 (SslA) with respect to its self-assembling properties and modification that would allow it to be employed as a patterning element and a new building block for nanobiotechnology. In vitro recrystallization experiments have shown that wild type SslA self-assembles into monolayers, multilayers or tubes. Factors such as initial monomer concentration, Ca2+ ions, pH of the recrystallization buffer and the presence of a silicon substrate have a strong influence on the recrystallization process. SslA monolayers proved to be an excellent biotemplate for ordered assembly of gold nanoparticle arrays. The recombinant SslA after expression and purification formed micrometer sized, crystalline monolayers exhibiting the same lattice structure as the wild type protein (p4 symmetry). This remarkable property of self-assembling has been preserved even when SslA was truncated. The deletion of both, N- and C-terminal SslA domains does not hinder self-assembly; the resulting protein is able to form extended monolayers that exhibit the p4 lattice symmetry. The central SslA-domain is self sufficient for the self-assembly. The possibility to change the natural properties of S-layers by genetic engineering techniques opens a new horizon for the tuning of their structural and functional features. The SslA-streptavidin fusion protein combines the remarkable property of self-assembling with the ligand i.e. biotin binding function. On silicon wafers, this chimeric protein recrystallized into coherent protein layers and exposes streptavidin, fact demonstrated by binding studies using biotinylated quantum dots. In this way, it can serve as a functional surface for controlled immobilization of biologically active molecules but also as a platform for the synthesis of planar arrays of quantum dots. Furthermore, the results open up exciting possibilities for construction of hybrid S-layers, structures that may ultimately promote the fabrication of miniaturized, nanosized electronic devices.

S-layer proteins of S. ureae ATCC 13881 form on the cell surface an S-layer lattice with p4 square type symmetry and a period of about 13.5 nm. These lattices were shown to be the excellent nanotemplates for deposition of regular metal clusters. The synthesis of the S. ureae S-layer protein is highly efficient, the protein accounts for approximately 10-15 % of the total cell protein content, judged by the SDS-PAGE results. Besides, the S-layer protein production is tightly regulated, since only negligible amounts of S-layer proteins are observed in the medium at different cell growth phases. At the same time, mechanisms of the regulation of S-layer protein synthesis are poorly understood. As several hundreds of S-layer proteins are produced per second during the cell growth, the S-layer gene promoters are among the strongest prokaryotic promoters at all. However, little is known about factors regulating the expression of S-layer genes, furthermore, no experimental identification of other upstream regulatory sequences except for -35/-10 and RBS sequences was presented to our knowledge to date. A sequence of the S-layer gene of S. ureae ATCC 13881, encoding the previously described S-layer protein, was identified in this work by combination of different approaches. The largest part of the gene, excluding its upstream regulatory and ORF 5’ regions, was isolated from a genomic library by hybridization. The sequence of the isolated fragment proved to contain additionally an 1.9 kb non-coding region and an incomplete 0.8 kb ORF region in its 3’-part. No RBS sequence and apparent promoter regions could be identified in front of the latter sequence, suggesting that it might represent a pseudogene sequence. The sequences of the 5’ and upstream regions of the S. ureae ATCC 13881 S-layer gene were identified by combination of PCR-sequencing and chromosome walking. Totally, a sequence of the 6.4 kb long region of S. ureae genomic DNA was established. The sequence of the S. ureae S-layer protein was deduced from the respective gene sequence and agreed with the peptide sequences, obtained after N-terminal sequencing of tryptic peptides of the S. ureae ATCC 13881 S-layer protein. For the protein the name SslA was proposed, which is an abbreviation for “Sporosarcina ureae S-layer protein A”. Several specific features were observed in gene organisation of sslA, which are also characteristic for other S-layer genes. The distance between the -35/-10 region and the ATG initiation codon is unusually long and a 41 bp palindromic sequence is present in the immediate vicinity of the -35/-10 region. Besides, a distant location of the rho-independent transcription terminator, which is 647 bp remote from the stop codon, will result in the mRNA transcripts with unusually long trailer region. Both the long 5’ UTR and the long 3’ trailer may have a regulatory function, either by conferring increased mRNA stability and/or by affecting translation efficiency. Potentially these sequences may define the binding sites of regulatory proteins. For example, palindromic sequences constitute the regulatory sites in several bacterial operons and may act as the binding sites of regulatory dimeric proteins. In respect to the conservation of the sslA sequence high similarity to the sequences of other functional S-layer genes, especially the slfA and slfB genes of B. sphaericus, was observed, whereas the results of phylogenetic analysis support the hypothesis that S-layer genes may have evolved via the lateral gene transfer. Based on the sslA sequence, several recombinant proteins with truncations of the terminal protein parts or C-terminal fusion of either EGFP or histidine tags were constructed. For all the truncated or EGFP-fusion SslA derivatives high level overexpression in E. coli was possible. For native SslA a moderate level of expression was observed suggesting that its high intracellular concentration may downregulate the protein synthesis. Interestingly, fluorescence microscopy indicates the same intracellular localization for heterologously produced recombinant proteins with fusions of EGFP either to the precursor or to the native SslA protein, suggesting that SslA secretion signal is not functional in E. coli. Heterologously produced SslA derivatives with truncations of N-, C- or both N- and C-terminal parts were shown to self- assemble in vitro, although the size of self-assembly structures was different from that observed upon the self-assembly of the native SslA. In the latter case extended self-assembly layers with the size up to 5x10 µm were observed, with a surface area of up to two orders of magnitude higher than that of S-layer patches, routinely isolated from S. ureae surface. Dependent on the applied recrystallization conditions preferential formation of single- or multilayer self-assembly structures was observed.

This work describes the characterization of the CAN1 gene, thought to encode the arginine permease of yeast. I have identified the RNA transcript of this gene and obtained the DNA sequence, which specifies a highly hydrophobic protein with multiple potential membrane-spanning domains. I use a gene fusion approach to identify sequences within the CAN1 protein that can translocate adjacent sequences across the E.R. membrane in vitro and extend these observations by finding that the topology of E.R. insertion is conserved up to the plasma membrane in vivo. Using a series of CAN1 gene fusions to the secreted yeast killer toxin, I find that the pathway of membrane protein export to the cell surface need not be functionally distinct from that of secreted proteins. Finally, I describe a mutation in the CAN1 gene that leads to altered rates of lysine uptake and results in growth inhibition and rapid plasmid loss in the presence of lysine.

Bien que l'initiation de la traduction soit un processus conservé entre les bactéries, nous avons montré que le mécanisme par lequel les ARNm structurés sont reconnus et adaptés sur le ribosome diffère chez Staphylococcus aureus, un micro-organisme avec un bas taux de G+C et chez Escherichia coli. Une particularité du ribosome de S. aureus est l'absence de la protéine ribosomale S1, qui non seulement est plus courte que celle de E. coli mais qui possède également une organisation distincte des domaines. Mes expériences suggèrent que la protéine S1 (SauS1) favorise spécifiquement l'initiation de la traduction de l'opéron α-psm 1-4 en liant son ARNm hautement structuré. En outre, il influence aussi l'expression et la production de facteurs de virulence comme les exotoxines (α-haemolysine, δ-hémolysine et γ- hémolysine) et les exoenzymes (protéases et lipases). En plus de son rôle dans la traduction, SauS1 pourrait être impliquée dans d'autres processus cellulaires tels que le métabolisme de l'ARN et la régulation par des ARN non-codants (ARNnc). Elle forme des complexes in vivo avec plusieurs ARNnc dont la stabilité serait affectée dans la souche délétée du gène rpsA codant S1. SauS1 a donc une activité chaperonne favorisant la cinétique d’appariement entre deux molécules d'ARN et au moins dans un cas, elle stimule la reconnaissance entre un ARNnc et son ARN cible. Ainsi, SauS1 appartient à une nouvelle classe de chaperons d'ARN qui jouent un rôle clé dans la régulation du virulon de S. aureus
Even if translation initiation is a conserved process among bacteria, we have recently shown that low G+C content Gram-positive, such as Staphylococcus aureus, differ from E. coli on the mechanism by which structured mRNAs are recognized and adapted on the ribosome. One peculiarity of the S. aureus ribosome is the absence of ribosomal protein S1, which is shorter than E. coli S1 and has different domains organization. My work could demonstrate that S. aureus S1 (SauS1) specifically promotes translation initiation of the α-psm 1-4 operon by binding its highly structured mRNA. Moreover, it influences the expression and production of other exotoxins (α-haemolysin, δ-haemolysin and γ-haemolysins) and exoenzymes (proteases and lipases). Besides its role in translation, SauS1 could be implicated in other cellular processes such as RNA maturation/degradation and sRNA-mediated regulation. It forms in vivo complexes with several sRNAs whose level is affected in a strain deleted of rpsA gene, coding for S1. Preliminary results show that SauS1 has a chaperone activity promoting the kinetic of annealing of two model RNA molecules and at least in one case, we could demonstrate that it stimulates the recognition between a sRNA and its target RNA. Taken together, SauS1 belongs to a new class of RNA chaperones that play key roles in the regulation of S.aureus virulon

Thesis (Ph. D.)--Massachusetts Institute of Technology, Biological Engineering Division, 2006.
Vita.
Includes bibliographical references.
The continued success of protein therapeutics has put a strain on industry's ability to meet the large demand. Creating a more productive expression host for the manufacture of these proteins is a potential solution. Although heterologous proteins are frequently made in organisms as disparate as E. coli and bovines, the single-celled organism S. cerevisiae has emerged as a well-qualified candidate due to its approachable genetic and fermentation attributes as well as its ability to stably fold disulfide bonded and multi domain proteins. Because S. cerevisiae screens for enhanced protein secretion have traditionally utilized low-throughput and often plate-based methods, a high-throughput, liquid phase assay could offer a real advantage in secretory selection. In this thesis, yeast surface display is investigated as a potential proxy for heterologous protein secretion. Although ultimately unsuitable as a screening proxy, the surface display experiments did show a novel method of improving protein secretion by co-expressing a more stably folded protein with the protein of interest. In these studies the secretion of an scFv-Aga2p fusion was stimulated 1 0-fold by the concomitant surface expression of BPTI.
(cont.) BPTI surface expression also stimulated the secretion of secreted scFv three-fold suggesting a niche for protein coexpression as well as secretion by way of Aga2p fusions. A new screening method was developed that involves the capture of secreted protein on the surface of the cell where it can be labeled and sorted by FACS. This new method was verified to achieve thirty-five fold enrichment per pass for a three-fold enhanced protein secretor making it easily suitable for screening. The new screening methodology, the Cell Surface Secretion Assay (CeSSA), was also modeled and verified with time course data that enabled optimization of sort parameters and predicted sort outcomes based on user-derived selection parameters. The CeSSA was used to screen a library of mutant yeast alpha mating factor leader sequences for improved secretion of the scFv 4m5.3. The improved leaders imparted up to a twenty-fold improvement in scFv secretion per cell and up to thirty-fold improvement after expression tuning. These engineered leader sequences also conferred improved secretion on other scFv's and proteins including whole IgG. Moreover, the leader sequence mutants give indications of where the important residues in secretory leaders lie and the aberrations in protein traffic that result in reduced secretion.
by James A. Rakestraw.
Ph.D.

Thesis advisor: Charles Hoffman
Faithful chromosome segregation is necessary for the successful completion of mitosis and meiosis. The centromere is the site of kinetochore and microtubule attachment during chromosome segregation, and it is critical that the centromere is properly formed and maintained. Many proteins contribute to centromere formation, and this process has been extensively studied during the mitotic cell cycle. However, the roles of the centromere and its associated proteins during meiosis and their contribution to the fidelity of chromosome segregation process are not as well understood. Here, I aim to elucidate a mechanism that may contribute to aneuploidy in gametes, which is a major contributing factor in human infertility. In this study, I investigate the role of Abp1, the most prominent member of the transposase-derived protein family homologous to mammalian CENP-B in the assembly of centromeric chromatin during meiosis in the fission yeast Schizosaccharomyces pombe. I reveal that in contrast to its known role as a major regulator of LTR retrotransposons during the mitotic and meiotic cell cycles, Abp1 has a specialized role at the centromere during meiosis. My results indicate that Abp1 displays dynamic localization to the centromeres during meiosis compared to the vegetative cell cycle. I show that loss of abp1 impairs pericentromeric heterochromatin and the localization of Cnp1, a CENP-A ortholog, to the centromere central cores during meiosis. Moreover, Abp1 appears to suppress formation of meiotic neocentromeres by restricting deposition of Cnp1 at certain heterochromatin loci. Loss of abp1 has a drastic effect on chromosome segregation, resulting in dramatic frequency of aneuploidy. Furthermore, the genome surveillance role for retrotransposons by Abp1 appears to encompass centromeres as the mere insertion of an LTR sequence within the centromere central cores further exacerbates incidence of meiotic aneuploidy in abp1 null cells. This study provides intriguing insights into factors controlling the assembly of centromeric chromatin and its impact on the fidelity of chromosome segregation process during meiosis with important implications for advancing our understanding of the evolutionary forces driving the evolution of eukaryotic centromeres
Thesis (PhD) — Boston College, 2016
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology

Despite a great deal of research, the functional significance of tightly bound DNA-protein complexes is not yet clear, therefore these complexes are perfect object for pioneering research. Very little is known about plant TBP-DNA complexes. In this work we investigated barley TBP-DNA complexes from different organs (first leaves, roots and coleoptiles) at different developmental stages. We characterized individual components of tightly bound DNA-proteins complexes: polypeptides (TBP) and DNA. We isolated and characterized TBP proteins from barley first leaves, roots and coleoptiles of different age and differentiation stage. Also we isolated and characterized the DNA fragments from barley first leaves and water ripe and milky ripe grain TBP-DNA complexes. We demonstrated that in different developmental stages of coleoptiles, first leaves and roots TBP-DNA complexes were identified as a group of 15-160 kDa proteins, most of TBPs are acidic. Some of barley TBPs (10, 25, 38, 40 and 55 kDa) exhibit phosphatase, maybe Ser/Thr activity. We have identified also that some of TBPs tyrosines were phosphorylated, this modification depends on organ and developmental stage. Identified barley TBPs were involved in fundamental genetic processes, as well as in chromatin rearrangement and regulation processes. Nuclear matrix proteins, enzymes, transcription factors, serpins, immunophilins, and transposon polypeptides were identified among TBPs. We demonstrated that expression of TBPs depends... [to full text]
Žinoma, kad pastovi nehistoninių polipetidų frakcija yra išgryninama kartu su eukariotine DNR ir sudaro labai tvirtus (galbūt kovalentinius) kompleksus tarp branduolio baltymų ir DNR. Nustatyta, kad Erlicho ascito tvirtuose DNR-baltymų kompleksuose yra baltymas C1D, baltymai, pasižymintys fosfataziniu ir kinaziniu aktyvumais, kai kurie proteazių slopikliai ir kiti, dar neištirti baltymai. Nepaisant intensyvių tyrinėjimų, eukariotinių ląstelių tvirti DNR-baltymų kompleksai vis dar lieka menkai aprašyti ir yra objektas tolimesniems tyrimams. Augalų TBP-DNR kompleksai kol kas buvo tyrinėti labai mažai. Šiame darbe charakterizuojami miežių Hordeum vulgare tvirti DNR-baltymų kompleksai. Mes tyrėme TBP-DNR kompleksus iš miežių skirtingų ūglių organų ir skirtingų vystymosi stadijų ląstelių: lapų, šaknų, koleoptilės. Norint ištirti tokių nukleoproteidų funkcijas, svarbu charakterizuoti individualius komplekso komponentus: polipeptidus ir DNR. Taigi, išskyrėme tvirtai su DNR sąveikaujančius baltymus iš miežių skirtingos diferenciacijos bei skirtingo amžiaus ląstelių: pirminių lapelių, šaknų, koleoptilės ir juos charakterizavome. Taip pat išskyrėme ir charakterizavome DNR fragmentus iš miežių pirminių lapelių bei vandeninės brandos ir pieninės brandos grūdų TBP-DNR kompleksų. Parodėme, kad miežių TBP baltymai yra 15-160 kDa, dauguma baltymų yra rūgštiniai. Kai kurie iš miežių TBP baltymų (10, 25, 38, 40 ir 55 kDa) pasižymi fosfataziniu, galbūt, Ser/Thr aktyvumu. Nustatėme, kad tam... [toliau žr. visą tekstą]