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Gardin, Chiara (2009) Interaction between fatz and myotilin families and enigma family proteins at the sarcomeric Z-DISC. [Tesi di dottorato]

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Abstract (inglese)

The Z-disc of striated muscle cells is a highly specialized three-dimensional structure which delineates the boundary of the individual sarcomeres. It accomplishes a unique role by anchoring actin filaments and acts as a molecular trigger for contraction. Beyond a well-defined structural role, in recent years it is emerging the hypothesis that Z-disc may be directly involved in the perception and transmission of muscular stress signals. To achieve these complex functions, many Z-disc proteins are involved in multiple protein interactions. The importance of these interactions is indicated by the fact that mutations in several Z-disc proteins can result in muscular dystrophies and/or cardiomyopathies in human and mice. The knowledge of Z-disc interactome and its regulation would improve by far the comprehension of the Z-disc biology and the onset of muscular disorders.
The main goal of my project was to understand the complex network of protein-protein interactions occurring at the Z-disc of skeletal and cardiac muscle. In particular, my work was focused on two groups of Z-disc proteins: the FATZ and myotilin protein families on one hand, and some proteins belonging to the enigma family on the other hand. This work led to the identification of a specific interaction between the PDZ domains of enigma family members and the C-terminal five amino acids of the FATZ and myotilin families.
The work of this thesis is part of a wider project involving the groups of Dr. G. Faulkner at ICGEB, Trieste, and Prof. O. Carpen at University of Turku, Finland. Together with our collaborators we noted that the C-terminal five amino acids of FATZ-1 (ETEEL), FATZ-2 (ESEDL), FATZ-3 (ESEEL), myotilin (ESEEL), palladin (ESEDL) and myopalladin (ESDEL) are highly similar. Searches in protein sequence database revealed that this E-[S/T]-[D/E]-[D/E]-L motif is restricted in Vertebrates to the FATZ and myotilin families of proteins, and it is evolutionary conserved from zebrafish to humans, indicating its importance for their biological function. The ELM program (a source for predicting functional sites in eukaryotic proteins) predicted that the terminal four amino acids of the FATZ family, myotilin, palladin and myopalladin constitute a binding motif for class III PDZ domain proteins (X-[D/E]-X-[V/I/L]). The first object of my work was to determine if the proteins with this new type of class III PDZ binding motif at their C-terminal could effectively bind PDZ domains. We knew from the literature that ZASP binds to all the three members of the FATZ family by means of its N-terminal PDZ domain, and that the C-terminal region of myotilin interacts with ZASP. In addition to ZASP, other two members of the enigma family of PDZ proteins, ALP and CLP-36, were included in this study. Both the full-length and the truncated (lacking the last five amino acids) version of the FATZ and myotilin families were produced as native proteins and tested for PDZ binding using the AlphaScreen (Amplified Luminescence Proximity Homogeneous Assay) technique. Biotinylated phosphorylated and non-phosphorylated peptides corresponding to the C-terminal five amino acids of the FATZ family, myotilin, palladin and myopalladin were also used in AlphaScreen interaction experiments, as well as a control peptide having E instead of L as its last amino acid (ESEEE). The results presented in this thesis show that the final five amino acids of the FATZ and myotilin families of proteins are responsible for the binding to the PDZ domains of ZASP, ALP and CLP-36, and that the nature of the last amino acid of the motif is crucial for the interaction. We also show that phosphorylation of the ligand sequence modulates the ability of the peptides to bind to the PDZ domains of the enigma family. ?-actinin-2 was included in this study as its C-terminus (GESDL) is classified as a class I PDZ binding motif that is able to bind to ZASP and ALP PDZ domains. AlphaScreen experiments confirm the binding of both the full-length and the C-terminal phosphorylated and non-phosphorylated peptides of ?-actinin-2 to the PDZ domains of ZASP and ALP, and they also reveal an interaction with the PDZ domain of CLP-36.
These interactions were verified using another in vitro binding technique, the TranSignal PDZ Domain Array. Based on the results of the PDZ arrays, RIL was found to be another member of the enigma family capable to bind to the E-[S/T]-[D/E]-[D/E]-L motif. Therefore, these final five amino acids can be considered a novel type of class III PDZ binding motif specific for the PDZ domains of enigma proteins.
To better quantify the strength of the noted interactions, SPR (Surface Plasmon Resonance) experiments were performed in the laboratory of Dr. A. Baines at University of Kent, UK. The affinities of the interactions between the PDZ domain of ZASP and some of the phosphorylated and non-phosphorylated peptides of the FATZ and myotilin families result to be in the nM range. The SPR results also demonstrate a new interaction between the PDZ domain of ZASP and ANKRD2. This protein is a member of the MARP family and it is thought to be involved in muscle stress response pathways. ANKRD2 localizes both in the sarcomeric I-band and the nucleus, and it is able to bind to several transcription factors, including YB-1, PML and p53. This interaction strengthens the hypothesis that, besides a structural function, Z-disc could have a role in cell signalling.
The fact that at the Z-disc many proteins can interact with the same partners, it would be helpful to define the pattern and level of expression of the individual proteins in different muscle tissues. Another aim of my work was to measure the abundance of mRNAs of some Z-disc proteins using the Real-Time PCR technique. Four different muscles from adult mice were considered: tibialis (a fast-twitch skeletal muscle), soleus (a slow-twitch skeletal muscle), gastrocnemius (a skeletal muscle with mixed fibers) and heart (cardiac muscle). The different distribution of the FATZ proteins, myotilin and the alternatively spliced variants of ZASP suggest that, at least in mouse, the interactions between these proteins could be compartmentalized in distinct fiber types.

Abstract (italiano)

Il disco-Z del muscolo striato è una struttura molecolare altamente specializzata a livello della quale si instaurano numerose interazioni proteina-proteina. Il disco-Z delinea il confine dei singoli sarcomeri, fornendo un punto di ancoraggio per i filamenti sottili di actina; il loro scorrimento sui filamenti spessi di miosina produce la forza meccanica responsabile della contrazione. Uno dei ruoli chiave del disco-Z, dunque, è quello di trasmettere la tensione generata dalla struttura seriale dei sarcomeri lungo le miofibrille e, di conseguenza, lungo tutto il muscolo. Al di là di un evidente significato strutturale, negli ultimi anni sta diventando sempre più consistente l’ipotesi di un suo coinvolgimento anche nella percezione e nella trasmissione di segnali. L’importanza delle interazioni tra le proteine del disco-Z è indicata dal fatto che mutazioni in molte di queste proteine possono risultare in distrofie muscolari e/o cardiomiopatie sia in uomo sia in topo. Una più ampia conoscenza delle interazioni che si articolano a livello del disco-Z e, in generale, degli eventi che le regolano, aiuterebbe a chiarire la biologia del disco-Z e l’insorgenza di eventuali patologie associate. Il mio progetto di Dottorato è stato incentrato su due gruppi di proteine sarcomeriche e sulle loro interazioni: le proteine delle famiglie FATZ e miotilina da un lato, e alcune proteine appartenenti alla famiglia enigma dall’altro. Questo lavoro ha portato all’identificazione di un’interazione specifica tra i domini PDZ delle proteine della famiglia enigma e gli ultimi cinque residui aminoacidici presenti nelle proteine delle famiglie FATZ e miotilina.
Il lavoro di questa tesi fa parte di un progetto più ampio che coinvolge i gruppi coordinati dalla Dr.ssa G. Faulkner dell’ICGEB, Trieste, e il Prof. O. Carpen dell’Università di Turku, Finlandia. Grazie alla loro collaborazione, è stato possibile notare che i cinque residui C-terminali delle proteine FATZ-1 (ETEEL), FATZ-2 (ESEDL), FATZ-3 (ESEEL), miotilina (ESEEL), palladina (ESEDL) e miopalladina (ESDEL) sono molto simili. Una ricerca effettuata in database di sequenze proteiche ha rivelato che questo motivo, E-[S/T]-[D/E]-[D/E]-L, è quasi esclusivamente ristretto nei Vertebrati alle proteine delle famiglie FATZ e miotilina; inoltre, esso sembra essere conservato da zebrafish ad uomo, suggerendo la sua importanza per le proteine che lo contengono. Il programma ELM (che predice siti funzionali in proteine eucariotiche) ha predetto che gli ultimi quattro amino acidi delle proteine FATZ, miotilina, palladina e miopalladina costituiscono un motivo di legame per le proteine con domini PDZ di classe III (X-[D/E]-X-[V/I/L]). Il mio primo obiettivo è stato quello di verificare se le proteine caratterizzate da questo nuovo motivo C-terminale potessero effettivamente legare domini PDZ. E’ noto dalla letteratura che tutti e tre i componenti della famiglia FATZ legano il PDZ di ZASP, e che l’interazione tra ZASP e miotilina è mediata dalla regione C-terminale di quest’ultima. Oltre a ZASP, altri due membri della famiglia enigma, ALP e CLP-36, sono stati inclusi nello studio. Le proteine della famiglia FATZ e miotilina sono state prodotte sia in versione full-length sia priva degli ultimi cinque amino acidi per essere utilizzate in saggi di interazione AlphaScreen (Amplified Luminescence Proximity Homogeneous Assay). Peptidi biotinilati, fosforilati e non, corrispondenti ai cinque amino acidi finali delle FATZ, miotilina, palladina e miopalladina sono stati inoltre impiegati nei saggi AlphaScreen, così come un peptide di controllo avente in ultima posizione un acido glutammico (E) invece che una leucina (L). I risultati riportati in questa tesi dimostrano che gli ultimi cinque amino acidi delle proteine delle famiglie FATZ e miotilina sono responsabili del legame ai domini PDZ di ZASP, ALP e CLP-36, e che la natura dell’ultimo residuo aminoacidico è cruciale per questa interazione. Inoltre, la fosforilazione del residuo di serina o treonina del ligando C-terminale può influenzare il legame dei peptidi nei confronti dei domini PDZ della famiglia enigma. La proteina ?-actinina-2 è stata introdotta nello studio, poiché la sua sequenza C-terminale (GESDL) è classificata come motivo di legame per i domini PDZ di classe I (X-[S/T]-X-[V/I/L]). Gli esperimenti AlphaScreen hanno confermato l’interazione di ?-actinina-2 (sia della forma full-length sia dei peptidi C-terminali, fosforilati e non) con i PDZ di ZASP e ALP, e hanno fatto emergere una nuova interazione con il PDZ di CLP-36.
Molte di queste interazioni sono state verificate con un altro metodo di interazione proteina-proteina in vitro, il TranSignal PDZ Domain Array. Sulla base dei risultati di PDZ array è stato possibile identificare un altro membro della famiglia di proteine enigma, RIL, in grado di legare il motivo E-[S/T]-[D/E]-[D/E]-L. Possiamo considerare questi cinque amino acidi C-terminali come un nuovo motivo di legame per le proteine con domini PDZ di classe III, specifico per i domini PDZ delle proteine enigma.
Per poter meglio quantificare la forza delle interazioni studiate, alcuni esperimenti di SPR (Surface Plasmon Resonance) sono stati eseguiti nel laboratorio del Dr. A. Baines all’Università di Kent, UK. Le affinità delle interazioni tra il dominio PDZ di ZASP e alcuni dei peptidi fosforilati e non-fosforilati delle famiglie di proteine FATZ e miotilina risultano essere nell’ordine del nM. Gli esperimenti di SPR hanno portato anche all’identificazione di un’interazione tra il PDZ di ZASP e ANKRD2. Si pensa che questa proteina, membro della famiglia MARP, sia coinvolta nelle vie di risposta a stress muscolari. ANKRD2 può trovarsi sia nella banda-I del sarcomero sia nel nucleo ed è in grado di legare diversi fattori di trascrizione, come YB-1, PML e p53. La scoperta di questa interazione rafforza l’ipotesi che il disco-Z, oltre ad un ruolo specificamente strutturale, potrebbe essere coinvolto in vie di segnalazione.
Dal momento che a livello del disco-Z molte proteine hanno più di un partner proteico, sarebbe utile cercare di definire il livello e il profilo di espressione delle singole proteine in tessuti muscolari con diverse caratteristiche. Un altro obiettivo del mio lavoro è stato quindi quello di valutare l’abbondanza degli mRNA di alcune delle proteine del disco-Z da me studiate con la Real-Time PCR. Allo scopo sono stati presi in considerazione quattro tessuti muscolari di topo adulto: il tibiale (un muscolo scheletrico a contrazione rapida), il soleo (un muscolo scheletrico a contrazione lenta), il gastrocnemio (un muscolo scheletrico con fibre miste) e il muscolo cardiaco. La differente distribuzione delle FATZ, miotilina e ZASP (con le sue varianti di splicing) suggerisce che, almeno in topo, le interazioni tra queste proteine potrebbero essere compartimentalizzate in distinte fibre muscolari.

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Tipo di EPrint:Tesi di dottorato
Relatore:Valle, Giorgio
Dottorato (corsi e scuole):Ciclo 21 > Scuole per il 21simo ciclo > BIOCHIMICA E BIOTECNOLOGIE > BIOTECNOLOGIE
Data di deposito della tesi:01 Febbraio 2009
Anno di Pubblicazione:01 Febbraio 2009
Parole chiave (italiano / inglese):sarcomere, protein-protein interactions, PDZ domain
Settori scientifico-disciplinari MIUR:Area 05 - Scienze biologiche > BIO/11 Biologia molecolare
Struttura di riferimento:Dipartimenti > Dipartimento di Biologia
Codice ID:1859
Depositato il:01 Feb 2009
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