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Michieli, Francesca (2013) Analisi bioinformatica e molecolare di cheratine e proteine associate nell'epidermide di cheloni e lucertole. [Tesi di dottorato]

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Abstract (inglese)


The integument of Reptiles is different with respect to that of other Vertebrates because it is composed of scales, which are horny thickenings of the epidermis with shape, extension and different overlapping degrees in many groups of Reptiles depending on the habitat and adaptation (Lillywhite and Maderson, 1982; Price, 1982; Irish et al., 1988).
The protein component of this peculiar epithelium consists mainly of alpha-keratins and keratin-associated beta-proteins (KabetaPs), formerly indicated as beta-keratins, so called because the presence of beta-pleated sheets and filamentous aggregation.
The alpha-keratins or cytokeratins are present in all Vertebrates and they are fibrous structural proteins belonging to the intermediate filaments family. They form the framework and therefore determine the shape of keratinocytes and are responsible for the resilience in epithelia against mechanical forces and tensile strength. They have a molecular weight of 40-70 kDa and contain a conserved central alpha-helical structure for the assembly of the filaments and of globular variable N- and C- regions (Steinert and Freedberg, 1991; Fuchs and Weber, 1994). The KAbetaPs proteins are exclusive of epidermis and skin appendages of Reptiles and Birds and they are responsible for the formation of a thick and hard stratum corneum as they are associated with alpha-keratins in the pre-horny layers and progressively mask and replace them in the outermost horny layers of the epidermis. Beta-proteins are little extensible, non-pliable proteins. The characteristic rigidity is most likely due to their cysteine content that allows the formation of intra- and inter-molecular crosslinks (disulfide bridges) which confer compactness and resistance. The mechanism of aggregation of beta-proteins is not known in detail but the prediction models indicate that a 34 amino acid long central part of the molecule, including the highly homologous core-box presents a beta-sheet conformation (Fraser and Parry, 1996, 2011). Strong intermolecular bonds formed between these regions in numerous beta-protein monomers are believed to be responsible for the possible formation of polymers and of filaments. Monomer beta-proteins have low molecular weight (10-25 kDa), and a low solubility likely due to a high amount of glycine, and a basic isoelectric point (Werlang and Brandelli, 2005).
The present work is focused on the study of the role played by some types of keratins and beta-associated proteins in influencing the process of epidermal cornification in some species of turtles and lizards. The research has been divided into three main lines.
In the first line two species of freshwater turtles were considered (A. spinifera, also known as soft-shelled turtle, and P. nelsonii, hard-shelled turtle) in order to examine the role of cytokeratins and keratin-associated beta-proteins in the process of differentiation and hardnening of the epidermis. In particular, since A. spinifera does not possess a scaled integument, it was hypothesized that the soft consistency of its epidermis was due to absence of KAbetaPs or that these proteins were missing of the core-box region. Through the construction of a cDNA library from the soft-shelled turtle carapace exctracted-mRNA some sequences encoding alpha-keratins and beta-proteins were isolated and further characterized. Subsequent bioinformatic analyzes have shown the presence of a well conserved core-box region in all identified KAbetaPs. Even though these analyzes have refuted the initial assumptions, it remains still unclear why these proteins are not able to aggregate and form the classic dense corneous material present in the beta-layer of the other reptiles. The comparison by absolute Real-Time PCR of alpha-keratins and beta-proteins expression in A. spinifera with their orthologous genes in the hard-shelled turtle P. nelsonii, has shown a higher expression of all genes in the soft-shelled turtle than in hard-shelled turtle. These results are most likely due not only to the quantity and variety of keratins and associated proteins in the two species, but also to a different structure and dynamics of epidermis renewal: a faster cell turnover that occurs by continues exfoliation in A. spinifera versus a greater accumulation ability over time of specific proteins due to a periodic wearing that takes place once a year in P. nelsonii.
Since the regenerating lizard tail is a good experimental model to study the formation and differentiation of the horny layers in reptilian epidermis, the second line of research has been addressed to the comparative study of the expression of some cytokeratins (type I, acid, and type II, basic) and some particular beta-proteins, using absolute Real Time PCR, in normal and regenerating tail of the American green lizard Anolis carolinensis.
The results obtained have showed that transcripts encoding these proteins are mainly expressed in the regenerating than in normal tail. This is likely due to the high rate of cell differentiation present in regenerating scales. Interestingly, each transcript has a peculiar difference of expression between normal and regenerating tail. These results are indicative of a different transcription regulation.
Finally, the third line of research has been focused on the initial attempt to study the gene promoter that triggers the rapid synthesis of beta-proteins during the renewal cycle that determines shedding. This has been done by analyzing by bioinformatic analysis the promoter region in all 40 KAbetaPs isolated from the A. carolinensis genome (Dalla Valle et al., 2010) in order to identify possible patterns of transcription factors binding site. The study has identified some general factors normally present and some others frequently occurring, including specific factors. Futher experimental analysis is need to identify the transcription factors that regulate the tissue-specific gene expression of these proteins.

Abstract (italiano)

Il tegumento dei Rettili è molto particolare rispetto a quello degli altri Vertebrati in quanto è dotato di squame. Queste sono costituite da ispessimenti cornei dell’epidermide con una forma, estensione e grado di sovrapposizione variabile nei numerosi gruppi di Rettili a seconda dell’habitat in cui si sono adattati a vivere (Lillywhite e Maderson, 1982; Price, 1982; Irish et al., 1988).
La componente proteica di questo peculiare epitelio è costituita principalmente da alfa-cheratine e beta-proteine associate alle cheratine o KAbetaPs, un tempo chiamate beta-cheratine a causa della presenza di foglietti beta e della capacità di formare filamenti.
Le alfa-cheratine o citocheratine sono presenti in tutti i Vertebrati e sono proteine strutturali fibrose appartenenti alla famiglia dei filamenti intermedi. Esse costituiscono l’impalcatura e determinano quindi la forma dei cheratinociti, sono responsabili della resistenza degli epiteli contro forze meccaniche e di tensione. Sono dotate di un peso molecolare che si aggira attorno ai 40-70 kDa, presentano un dominio centrale ad alfa-elica conservato per l’assemblaggio dei filamenti stessi, ed estremità globulari variabili (Steinert e Freedberg, 1991; Fuchs e Weber, 1994). Le KAbetaPs sono invece proteine esclusive dell’epidermide e di annessi cutanei di Rettili e Uccelli, sono le responsabili della formazione di uno spesso e robusto strato corneo in quanto si associano alle alfa-cheratine negli strati pre-cornei e progressivamente le mascherano fino a sostituirle completamente negli strati cornei più esterni dell’epidermide. Le beta-proteine sono inestensibili e non pieghevoli. La rigidità è dovuta principalmente al loro contenuto in cisteina, amminoacido che permette la formazione di ponti disolfuro che formano legami crociati intra- ed intermolecolari. Il meccanismo di aggregazione delle beta-proteine non è ancora del tutto noto ma modelli di predizione della loro struttura proteica indicano che la porzione centrale della molecola costituita da 34 amminoacidi ad alta omologia, anche chiamata “core-box”, presenta una conformazione secondaria a foglietto beta (Fraser e Parry, 1996, 2011). Legami di interazione forte tra queste regioni beta sono ritenuti responsabili della formazione dei polimeri a partire dai monomeri di beta-proteina. I monomeri hanno basso peso molecolare, compreso tra i 10 e i 25 kDa, ridotta solubilità, dovuta presumibilmente ad una elevata quantità di glicina e un punto isoelettrico generalmente basico (Werlang e Brandelli, 2005).
Il presente lavoro di tesi si è focalizzato sullo studio del ruolo svolto da alcuni tipi di alfa-cheratine e beta-proteine nell’influenzare il processo di corneificazione dell’epidermide in alcune specie di tartarughe e lucertole. La ricerca è stata suddivisa in tre filoni principali.
Nel primo filone sono state prese in considerazione due specie di tartarughe dulcacquicole (A. spinifera, nota anche come tartaruga a guscio molle, e P. nelsonii, tartaruga a guscio duro) allo scopo di esaminare il ruolo di alcune citocheratine e beta-proteine associate nel conferire robustezza e durezza all’epidermide. In particolare A. spinifera è dotata di un tegumento non squamato che ha portato ad ipotizzare, nel tentativo di spiegare la consistenza soffice della cute, l’assenza di KAbetaPs o una loro modificazione nella regione del “core-box”. Tramite la costruzione di una libreria di cDNA a partire da mRNA estratto dai bordi del carapace della tartaruga a guscio molle sono state isolate e in seguito caratterizzate alcune sequenze codificanti alfa-cheratine e beta-proteine. Successive analisi bioinformatiche hanno evidenziato la presenza di una regione “core-box” molto ben conservata in tutte le KAbetaPs identificate. Anche se tali analisi hanno confutato le ipotesi iniziali, rimane però ancora da chiarire come mai queste proteine non riescano ad aggregarsi per formare i tipici filamenti densi presenti negli strati beta degli altri Rettili. Confrontando in seguito mediante Real-Time PCR assoluta l’espressione di alfa-cheratine e beta-proteine isolate in A. spinifera con i rispettivi putativi geni ortologhi presenti nella tartaruga a guscio duro P. nelsonii, si è rilevata una maggiore espressione di tutti i geni presi in considerazione nella tartaruga a guscio molle rispetto a quella a guscio duro. Questi risultati sono molto probabilmente imputabili non solo alla quantità e varietà di cheratine e proteine associate nelle due specie, ma anche a una diversa struttura e dinamica di rinnovo dell’epidermide: una maggiore velocità di ricambio cellulare che avviene per esfoliazione continua in A. spinifera contro una maggiore capacità di accumulo nel tempo di specifiche proteine dovuta a una muta periodica che avviene una volta all’anno in P. nelsonii.
Dal momento che la coda di lucertola in rigenerazione rappresenta un buon modello sperimentale per lo studio della formazione e differenziazione degli strati cornei del tegumento dei Rettili, nel secondo filone di ricerca è stata inoltre analizzata e confrontata tramite Real-Time PCR assoluta l’espressione di alcune citocheratine (tipo I, acido, e II, basico) e di particolari beta-proteine nella coda normale e in rigenerazione della lucertola verde americana Anolis carolinensis.
I risultati ottenuti hanno mostrato che i trascritti codificanti tali proteine sono maggiormente espressi nella coda in rigenerazione rispetto alla coda normale, fatto questo dovuto all’elevato tasso di differenziazione cellulare che si ha nel corso della rigenerazione delle squame, ma l’aspetto interessante è che ogni trascritto presenta un peculiare e diverso livello di espressione tra coda normale e coda in rigenerazione, a dimostrazione che i vari trascritti sono regolati in modo diverso a livello trascrizionale.
Infine, il terzo filone di ricerca ha riguardato un primo approccio di studio del promotore genico che scatena la rapida sintesi di beta-proteine durante il rinnovo epidermico che porta alla muta. Si è svolta l’analisi bioinformatica della regione promotrice di tutte le 40 sequenze che codificano KAbetaPs isolate dal genoma completo dell’A. carolinensis (Dalla Valle et al., 2010), allo scopo di individuare possibili pattern di siti di legame per fattori di trascrizione. Lo studio ha individuato alcuni fattori generali sempre presenti, alcuni molto ricorrenti e numerosi fattori specifici. Restano ancora necessarie ulteriori analisi di tipo sperimentale per identificare i fattori di trascrizione implicati nella regolazione dell’espressione genica tessuto-specifica di queste proteine.

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Tipo di EPrint:Tesi di dottorato
Relatore:Dalla Valle , Luisa
Correlatore:Alibardi, Lorenzo
Dottorato (corsi e scuole):Ciclo 25 > Scuole 25 > BIOLOGIA E MEDICINA DELLA RIGENERAZIONE > BIOLOGIA DELL'INTEGRAZIONE CELLULARE
Data di deposito della tesi:25 Febbraio 2013
Anno di Pubblicazione:25 Febbraio 2013
Parole chiave (italiano / inglese):Alfa-cheratine/alpha-keratins Beta-proteine/beta-proteins Corneificazione epidermica/epidermal cornification Cheratinociti/keratinocytes
Settori scientifico-disciplinari MIUR:Area 05 - Scienze biologiche > BIO/11 Biologia molecolare
Struttura di riferimento:Dipartimenti > Dipartimento di Biologia
Codice ID:6063
Depositato il:15 Ott 2013 15:54
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