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Shaik, Md Munan (2011) Pathogenesis-related Proteins From Helicobacter pylori: Structural and Functional Studies. [Ph.D. thesis]

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Abstract (english)

The bacterium Helicobacter pylori is recognized as one of the most successful bacterial pathogens. It colonizes the stomach of more than half of the world’s population and it presents a very high infection rate in developing countries. Most infected people are asymptomatic, however an important minority of them (15–20%) develops during their life severe gastroduodenal pathologies, including stomach and duodenal ulcers, adenocarcinomas and stomach lymphomas. Until now nine H. pylori strains have been completely sequenced and this pathogen presents high genetic variability, not only in the gene sequences but also in genes content. Many of the genes functions are annotated based on sequence similarity and there are around 45% genes with unknown function. The most remarkable differences in H. pylori virulent strains with that of non virulent is the presence or absence of the so-called cag-PAI (a 40-kb DNA sequence named cag Pathogenicity Island), that encodes a Type IV Secretion System, responsible for the translocation of the CagA toxin into host epithelial cells. Although H. pylori can be successfully eradicated by antibiotics in many patients, rising antibiotic resistance in the bacterium left overs a serious problem. New therapies are required to eradicate H. pylori infection and looking for new targets could be useful for the development of new treatment strategies. Recently, new factors important for colonization and establishment of infection have been proposed, using multiple approaches. A pull of these H. pylori proteins have been cloned, expressed in E. coli and purified for structural and functional studies.

The aim of this thesis was to determine the three dimensional structural and characterize the function of H. pylori proteins important for stomach colonization and pathogenesis. In particular, we concentrate our efforts on cell wall modification enzymes (peptidoglycan deacetylase), LPS biosynthesis (ADP-L-glycero-D-manno-heptose-6-epimerase, rfaD), periplasmic substrate binding protein of ABC transporter (ceuE), key enzymes in nitrogen assimilation pathway (Glutamine synthetase), secreted immunogenic disulfide isomerase (DsbG).

The strategy employed are bioinformatic analyses, molecular cloning of the gene starting from PCR amplification, construction of vectors for cloning, expression of the protein in E. coli. After expression analysis and optimization of conditions, the solubility of the recombinant proteins was checked. The soluble recombinant protein was then purified using different chromatography techniques, and eventually characterized by analytical gel filtration, mass spectrometry, UV spectroscopy. Techniques to make the protein samples more suitable for crystallization, as DLS (Dynamic light scattering), and to investigate the secondary structure, as CD (Circular dichroism), were used. The proteins were concentrated for crystallization trials. X-ray diffraction data of the crystals were measured at the ESRF synchrotron (Grenoble, France). Functional characterizations of the proteins were accomplished using fluorescence spectroscopy, CD, ITC, UV spectroscopy and ELISA.

After a general introduction about the bacterium (Chapter 1), in the chapter 2 the three dimensional structure and the enzymatic activity of a putative peptidoglycan deacetylase is described. Peptidoglycan deacetlyase (HP0310, HpPgdA) from H. pylori has been indicated as the enzyme responsible for a modification of peptidoglycan that counteracts the host immune response. The enzyme, which belongs to the polysaccharide deacetylases protein family, is a homo-tetramer. The four polypeptide chains, each folded into a single domain characterized by a non-canonical TIM-barrel fold, are arranged around a four-fold symmetry axis. The active site, one per monomer, contains a heavy ion coordinated in a way similar to other deacetylases. However, the enzyme showed no in vitro activity on the typical polysaccharide substrates of peptidoglycan deacetylases. In striking contrast with the known peptidoglycan deacetylases, HpPgdA does not exhibit a solvent-accessible polysaccharide binding groove, suggesting that the enzyme binds a small substrate at the active site.

The crystal structure of the last enzyme of the biosynthesis pathway of core oligosaccharides (L, D-heptose) of the LPS is discussed in details in the chapter 3. H. pylori owes much of the integrity of its outer membrane on lipopolysaccharides (LPSs). Together with their essential structural role, LPSs contribute to the bacterial adherence properties, as well as they are well characterized for the capability to modulate the immune response. In H. pylori the core oligosaccharide, one of the three main domains of LPSs, shows a peculiar structure in the branching organization of the repeating units, which displayed further variability when different strains have been compared. We present here the crystal structure of ADP-L-glycero-D-manno-heptose-6-epimerase (HP0859, rfaD), the last enzyme in the pathway that produces L-glycero-D-manno-heptose starting from sedoheptulose-7-phosphate, a crucial compound in the synthesis of the core oligosaccharide. In a recent study, a HP0859 knockout mutant has been characterized, demonstrating a severe loss of lipopolysaccharide structure and a significant reduction of adhesion levels in an infection model to AGS cells, if compared with the wild type strain, in good agreement with its enzymatic role. The crystal structure reveals that the enzyme is a homo-pentamer, and NAD is bound as a cofactor in a highly conserved pocket. The substrate-binding site of the enzyme is very similar to that of its orthologue in E. coli, suggesting also a similar catalytic mechanism. The other enzymes of the pathway are also discussed in terms of their three-dimensional structure.

The crystal structure of the periplasmic ABC transporter substrate-binding protein is discussed in chapter 4. Host-derived iron sources, including heme compounds released from damaged tissues, utilized by H. pylori have been identified. H. pylori can use heme as a sole iron source. Heme transport across the periplasmic space and into the cytoplasm is affected by an active transport system comprising a soluble periplasmic binding protein, a cytoplasmic permease, and an ATPase (ABC transporter). Periplasmic heme binding protein have been identified and characterized in several different pathogenic bacteria, but until now no protein was recognized as heme binding in H. pylori. HP15161 (ceuE) was annotated as ABC transporter periplasmic iron-binding protein but the homologous gene from H. mustalae was reported to be involved in nickel transport. To elucidate the structural features of this putative periplasmic ABC transporter binding protein the protein was cloned, expressed and purified in good yield in E. coli, crystallized, its structure determined in apo form and in complex with nickel. The structure was solved by means of single anomalous dispersion experiments on crystals of a selenomethionine variant of the protein. The overall structure is folded in two main domain connected by a long alpha helix It shares the common features of other bacterial periplasmic ABC transporter heme or vitamin B12 binding protein. The substrate binding site is generated in between these two domain. The crystal structure revels that nickel is not the right substrate for this protein and that the substrate-binding cavity is more similar to a heme-binding groove. In vitro binding activity with heme was performed with different techniques (Fluorescence and ITC), which confirms that ceuE in H. pylori is a periplasmic heme binding protein responsible for heme uptake in conjunction with other members of the ABC transporters family.

The crystal structure of the key enzyme in the unique nitrogen assimilation pathway glutamine synthetase is discussed in chapter 5. Glutamine synthetase catalyzes the synthesis of glutamine, a central intermediate in nitrogen metabolism, from ATP, glutamate, and ammonia in a divalent metal ion dependent reaction. Ammonia, which is also a preferred nitrogen source for H. pylori, is available in plentiful quantity owing to urease activity. It is assimilated into proteins and other nitrogenous compounds through one single nitrogen incorporation pathway, mediated by GS, an enzyme encoded by gene Hp0512. The absence of an allosteric regulation site (adenylation site) and other key enzymes in the single nitrogen assimilation pathways makes HpGS a potential target for structural studies. In order to elucidate the structural features of the synthetase and to establish a possible regulatory mechanism of the enzyme, glutamine synthetase (HpGS) from H. pylori was cloned, expressed and purified in good yield in E. coli, crystallized and its structure determined. The enzyme is dodecamer, held together mainly by hydrophobic and hydrogen bonding interactions between the two hexameric rings. The N-terminal helix assembles above the hexameric ring and is exposed to solvent. The C-terminal helix, called the `helical thong,' is inserted into a hydrophobic hole in the eclipsed subunit on the opposite hexameric ring. In addition, the central channel of the dodecamer is lined by six four-stranded L-sheets, each built from an antiparallel loop contributed by subunits in opposite rings. The structure of one monomer consists of a smaller N-terminal domain and a larger C-terminal domain. The dodecameric enzyme contains 12 active sites, which can be described as a 'bifunnel' in which ATP and glutamate bind at opposite ends. The ATP binding site is located at the top of the bifunnel, because it opens to the external 6-fold surface of GS. At the junction of the bifunnel there are two divalent cation binding sites. The adenylation site that in all the most similar homologs of HpGS contains the consensus sequence NLYDLP, is replaced in H. pylori by NLFKLT (residues 405 to 410). Since the Tyr407 residue is the well-conserved target of adenylation and H. pylori glutamine synthetase apparently lacks that residue, no adenylation occurs for this enzyme within this motif and no significant structural changes are observed in the loop of adenylation comparing with other structure of GS.

In the chapter 6 the cloning, expression and characterization of secreted immunogenic protein DsbG is discussed. Proteins were identified that are involved in disulfide isomerization. They are located in the membranes or in the periplasm and are called Dsb’s for disulfide bond formation. These proteins catalyze the introduction of disulfide bridges, isomerization (shuffling) of incorrectly introduced disulfide bonds and reduction (removal) of inappropriate disulfide bonds. Secreting proteins is a way to interact with hosts by many pathogenic bacteria. In H. pylori, type IV secretion pathways have been identified. Among the secreted proteins, many of them, either residing in or transiting through the periplasmic space, form disulfide bonds after translocation. HP0231 has a sequence similarity with E. coli DsbG and contains the CXXC motif. HP0231 have been already identified as an immunogenic protein recognized by patient sera. The recombinant protein, expressed in E. coli, did not bind strongly to the affinity IMAC-Ni2+ resin, probably because of the degradation of the N-terminal His-tag. To solve the purification problems, two approaches were adopted: the cloning of a new HP0231 construct with a C-terminal His-tag and the purification and the refolding of the HP0421 protein from the inclusion bodies. Finally, refolding procedure was optimized and the protein was purified to high homogeneity. HP0231 was characterized employing immunological techniques and blot with patient blood sera. HP0231 was also further characterized using bioinformatics tools.

Abstract (italian)

Il batterio Helicobacter pylori è riconosciuto essere uno dei più diffusi patogeni umani: esso colonizza circa la metà della popolazione umana, con una elevata velocità di propagazione nei paesi in via di sviluppo. Benché molti soggetti infetti siano asintomatici, una significativa minoranza di questi (15-20%) sviluppano durante la loro vita patologie duodenali gravi, che includono ulcera gastrica e duodenale, adeno-carcinoma e linfoma dello stomaco. Fino ad oggi sono stati completamente sequenziati nove diversi ceppi di H. pylori, in quanto esso presenta una alta variabilità genetica, non solo nelle sequenze geniche, ma anche nel contenuto di geni. Molti dei geni del batterio sono annotati solo sulla base dell’omologia di sequenza e per circa il 45% di essi la funzione è incerta o addirittura ignota. La differenza più significativa tra i ceppi virulenti del batterio rispetto ai ceppi non virulenti è la presenza o assenza della cosiddetta cag-PAI (una sequenza del DNA di 40-kb definita “isola di patogenicità cag”), un inserto genico che codifica per un sistema di secrezione di tipo IV, responsabile della trasloscazione della tossina CagA nelle cellule epiteliali. Benché H. pylori in molti pazienti possa essere sradicato mediante antibiotici, l’aumento della resistenza in alcuni ceppi rappresenta un problema emergente. Nuove terapie sono richieste per combattere il batterio e l’individuazione di nuovi bersagli farmacologici può essere utile per sviluppare nuove strategie di trattamento. Recentemente, nuovi fattori importanti per la colonizzazione e per lo stabilirsi dell’infezione sono stati identificati. In questo lavoro di tesi, un gruppo di queste proteine sono state clonate, espresse in E. coli e purificate allo scopo di effettuare studi strutturali.
Obiettivo della tesi era quello di determinare la struttura tridimensionale e caratterizzare la funzione di proteine importanti per la colonizzazione dello stomaco e per la patogenesi. In particolare, gli sforzi sono stati concentrati sugli enzimi coinvolti nella modifica della parete cellulare (peptidoglicano deacetilasi), nella biosintesi di LPS (ADP-L-glycero-D-manno-eptoso-6-epimerasi, rfaD), su una periplasmic-substrate binding protein di un trasportatore ABC (ceuE), su enzimi chiave nel ciclo di assimilazione dell’azoto (glutamina sintasi) e sulla disolfuro ìsomerasi (DsbG), una proteina immunogenica secreta.

La strategia applicata è consistita in una analisi bioinformatica preliminare, nell’ottenimento del gene a partire da amplificazione mediante PCR, nella costruzione di un vettore per la clonazione e nell’espressione della proteina in E. coli. Dopo analisi dell’espressione e ottimizzazione delle condizioni, è stata analizzata la solubilità della proteina ricombinante. Quest’ultima è stata quindi purificata mediante diverse tecniche cromatografiche, ed eventualmente caratterizzata per gel-filtrazione analitica, spettrometria di massa, spettroscopia UV. Sono state usate tecniche per rendere i campioni di proteina più adatti per la cristallizzazione, quali DLS (dynamic light scattering) e per investigarne la struttura secondaria, quali CD (dicroismo circolare). La proteina è stata quindi concentrata prima di essere sottoposta ai test di cristallizzazione. I dati di diffrazione sono stati misurati ai sincrotroni ESRF (Grenoble, Francia). La caratterizzazione funzionale delle proteine è stata eseguita usando spettroscopia di fluorescenza, CD, ITC, UV ed ELISA.

Dopo una introduzione generale sul batterio (Capitolo 1), nel capitolo 2 viene descritta la struttura tridimensionale e l’attività enzimatica di una putativa peptidoglicano deacetilasi. HP0310 (HpPdgA) da H. pylori è stato indicato come l’enzima responsabile della modifica del peptidoglicano che serve a minimizzare la risposta immunitaria da parte dell’ospite. L’enzima, che appartiene alla famiglia delle polisaccaride deacetilasi, è un omo-tetramero. Le quattro catene polipeptidiche, ciascuna avvolta in un dominio singolo caratterizzato da un TIM-barrel non canonico, sono arrangiate attorno ad un asse di rotazione quaternario. Il sito attivo, uno per monomero, contiene uno ione coordinato in modo simile ad altre deacetilasi. L’enzima non presenta però in vitro attività sui tipici substrati delle peptidoglicano deaetilasi. In netto contrasto con altre peptidoglicano deacetilasi conosciute, HpPdgA non ha un sito di legame accessibile ad una molecola ingombrante quale un polisaccaride, suggerendo che l’enzima leghi nel proprio sito attivo un substrato di piccole dimensioni.

Nel capitolo 3 viene discussa in dettaglio la struttura cristallina dell’ultimo degli enzimi del ciclo della biosintesi dell’oligosaccaride (L,D-eptoso) del core di LPS. H. pylori deve molta dell’integrità della sua membrana esterna ai lipopolisaccaridi (LPS). Insieme al loro esenziale ruolo strutturale, gli LPS contribuiscono alle proprietà di aderenze del batterio, come anche alla modulazione della risposta immunitaria. L’oligosaccaride del core del batterio, uno dei tre principali domini dell’LPS, presenta una struttura peculiare nell’organizzazione della ramificazione delle unità che si ripetono. Queste mostrano ulteriore variabilità quando si confrontano ceppi diversi. In questo capitolo viene presentata la struttura cristallina della ADP-L-glicero-D-manno-eptoso-6-epimerasi (HP0859, rfaD), l’ultimo enzima del ciclo che produce L-glicero-D-manno-eptoso partendo da sedoeptuloso-7-fosfato, un composto cruciale nella sintesi dell’oligosaccaride del core. In uno studio recente è stato caratterizzato un mutante knok-out di HP0859 che mostra, in un modello di infezione in cellule AGS, una seria perdita di struttura del lipopolisaccaride e una significativa riduzione dei livelli di adesione, se paragonato ai ceppi wild-type. La struttura cristallina rivela che l’enzima è un omo-pentamero e che NAD è legato come cofattore in una cavità altamente conservata. Il sito di legame del substrato è molto simile a quello del suo ortologo in E. coli, suggerendo anche un simile meccanismo catalitico. Altri enzimi del ciclo sono discussi nei termini della loro struttura tridimensionale.

Nel capitolo 4 viene descritta la struttura tridimensionale di una binding-protein al trasportatore periplasmico ABC. E’ noto dalla letteratura che il batterio può utilizzare l’eme come sola sorgente di ferro, e sono state identificate sorgenti di ferro, derivanti dall’ospite, utilizzate da H. pylori, inclusi composti provenienti da gruppi eme da tessuti danneggiati. Il trasporto di eme entro il citoplasma è effettuato da un sistema di trasporto attivo che comprende una proteina periplasmica solubile, una permease citoplasmatica e una ATPase (ABC transporter). La proteina periplasmica che lega l’eme è stata identificata e caratterizzata in vari batteri patogeni, ma fino ad ora non era ancora stata identificata una heme-binding protein in H. pylori. Hp1561 (ceuE) era annotata come una “ABC transporter periplasmic binding protein”, ma un gene omologo from H. mustalae era stato riportato essere coinvolto nel trasporto del nichel. Per chiarire le caratteristiche strutturali di questa putativa proteina di trasporto, essa è stata clonata, espressa e purificata con buona resa in E. coli, cristallizzata e la sua struttura determinata nella forma apo- and in complesso con il Ni(II). La struttura è stata risolta per mezzo di esperimenti di dispersione anomala singola (SAD) su cristalli di Se-metionina. Il modello molecolare è costituito da due domini, collegati da una lunga α-elica e presenta le caratteristiche generali di altre “heme-binding periplasmic ABC transporters” o di “B12 binding-proteins”. Il sito di legame del substrato è localizzato tra i due domini. La struttura cristallina suggerisce che il Ni(II) non è il legante naturale della proteina e che la cavità di legame assomiglia di più a quella delle heme-binding proteins. Sono stati effettuati anche studi di legame in vitro con tecniche diverse (fluorescenza e ITC), che hanno confermato che ceuE in H. pylori è una “periplasmic heme-binding protein”, responsabile per l’assunzione dell’eme.

La struttura cristallina di un enzima chiave nell’unico ciclo di assimilazione dell’azoto in H. pylori è discusso nel capitolo 5. La glutamina sintetasi (GS) catalizza la sintesi di glutamina, un intermedio centrale nel metabolismo dell’azoto, da ATP, glutammato e ammoniaca, in una reazione dipendente da un catione bivalente. L’ammoniaca, che è anche una sorgente preferita di azoto per H. pylori, è disponibile in grande quantità, grazie all’attività ureasica del batterio. E’ assimilato in proteine e altri composti contenenti azoto attraverso un singolo ciclo di incorporazione dell’azoto, mediato da GS, un enzima codificato dal gene hp0512. L’assenza di un sito si regolazione allosterico (sito di adenilazione) e di altri enzimi chiave nel ciclo di assimilazione dell’azoto rende HpGS un interessante soggetto per gli studi strutturali, per chiarirne le caratteristiche strutturali e il meccanismo regolatorio. La glutamina sintetasi (HpGS) di H. pylori è stata clonata, espressa, purificata e cristallizzata e la sua struttura determinata. L’enzima è un dodecamero, i cui monomeri sono tenuti assieme soprattutto da interazioni idrofobiche e legami ad idrogeno tra i due anelli esamerici. L’elica N-terminale, chiamata “elica stringa”, è inserita in una cavità idrofobia nella subunità eclissata sull’anello esamerico opposto. In aggiunta, il canale centrale del dodecamero è formato da sei fogli L a quattro fogli beta, ciascuno costituito da un loop antiparallelo cui contribuiscono subunità in anelli opposti. La struttura di un monomero consiste di un piccolo dominio N-terminale e di un dominio C-terminale più grande. L’enzima dodecamerico contiene 12 siti attivi, ciascuno dei quali può essere descritto come un “bifunnel”, in cui ATP e glutammato legano da lati opposti. Il sito di legame dell’ATP è localizzato nella parte alta del bifunnel, alla giunzione del quale ci sono due siti per il legame di cationi bivalenti. Il sito di adenilazione che in tutti gli enzimi omologhi contiene la sequenza consenso NLYDLP è sostituita in H. pylori da NLFKLT (residui da 405 a 410). Poiché la tirosina 407 è il bersaglio conservato dell’adenilazione e H. pylori apparentemente manca di questo residuo, non c’è adenilazione nell’enzima e non si osservano modifiche strutturali significative in questo loop a confronto con altre strutture di GS.

Nel capitolo 6 vengono discussi la clonazione, l’espressione e la caratterizzazione della proteina immunogenica secreta DsbG. Le proteine coinvolte nell’isomerizzazione dei ponti disolfuro sono ben note. Esse sono localizzate nelle membrane o nel periplasma e sono chiamate Dsb (Disulfide bond formation). Questi enzimi catalizzano l’introduzione di ponti disolfuro, la loro isomerizzazione o rimozione. Secernere alcune proteine è un modo attraverso il quale un batterio può interagire con l’ospite e in H. pylori questo avviene attraverso uno dei tre sistemi di secrezione di tipo IV presenti. Molte tra le proteine secrete, alcune delle quali risiedono nello spazio periplasmico, formano ponti a disolfuro dopo la traslocazione. HP0231 ha una sequenza simile a Dsbg di E. coli e contiene un motivo CXXC. Essa è stata già identificata come una proteina immunogenica riconosciuta da sieri di pazienti. La proteina ricombinante, espressa in E. coli, non lega fortemente alla resina di affinità IMAC-Ni2+, probabilmente a causa di degradazione dell’His-tag presente all’N-terminale. Per risolvere il problema della purificazione sono perciò stati adottati due approcci: è stato preparato un nuovo costrutto di HP0231 con His-tag al C-terminale, e in parallelo la proteina è stata purificata dai corpi di inclusione e poi rifoldata. La proteina è infine stata purificata ad alta omogeneità. HP0231 è stata caratterizzata usando tecniche immunologiche e blot con sieri di pazienti.

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EPrint type:Ph.D. thesis
Tutor:Zanotti, Giuseppe
Data di deposito della tesi:16 December 2011
Anno di Pubblicazione:31 December 2011
Key Words:X-ray crystallography, Structural Biology, Helicobacter pylori, Peptidoglycan deacetylase, Lipopolysaccharide, Epimerase, Polysaccharide deacetylase, Biosynthesis, Periplasmic Protein, Substrate binding protein, Heme, ABC transporter, Heme transport, Iron Transport, Glutamine synthetase, Nitrogen assimilation, Regulation, Immunogenic proteins, DsbG, Protein disulfied isomearse.
Settori scientifico-disciplinari MIUR:Area 05 - Scienze biologiche > BIO/13 Biologia applicata
Area 05 - Scienze biologiche > BIO/10 Biochimica
Area 05 - Scienze biologiche > BIO/15 Biologia farmaceutica
Area 05 - Scienze biologiche > BIO/11 Biologia molecolare
Area 05 - Scienze biologiche > BIO/12 Biochimica clinica e biologia molecolare clinica
Area 05 - Scienze biologiche > BIO/19 Microbiologia generale
Struttura di riferimento:Dipartimenti > pre 2012 Dipartimento di Chimica Biologica
Codice ID:4325
Depositato il:07 Nov 2012 11:53
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