Poly-γ-glutamate (γ-PGA) is an industrially interesting polymer secreted mainly by members of the class Bacilli which forms a shield able to protect bacteria from phagocytosis and phages. Few enzymes are known to degrade γ-PGA; among them is a phage-encoded γ-PGA hydrolase, PghP. The supposed role of PghP in phages is to ensure access to the surface of bacterial cells by dismantling the γ-PGA barrier. We identified four unannotated B. subtilis genes through similarity of their encoded products to PghP; in fact these genes reside in prophage elements of B. subtilis genome. The recombinant products of two of them demonstrate efficient polymer degradation, confirming that sequence similarity reflects functional homology. Genes encoding similar γ-PGA hydrolases were identified in phages specific for the order Bacillales and in numerous microbial genomes, not only belonging to that order. The distribution of the γ-PGA biosynthesis operon was also investigated with a bioinformatics approach; it was found that the list of organisms endowed with γ-PGA biosynthetic functions is larger than expected and includes several pathogenic species. Moreover in non-Bacillales bacteria the predicted γ-PGA hydrolase genes are preferentially found in species that do not have the genetic asset for polymer production. Our findings suggest that γ-PGA hydrolase genes might have spread across microbial genomes via horizontal exchanges rather than via phage infection.We hypothesize that, in natural habitats rich in γ-PGA supplied by producer organisms, the availability of hydrolases that release glutamate oligomers from γ-PGA might be a beneficial trait under positive selection.
Il poly-γ-glutammato (γ-PGA) è un polimero di interesse industriale secreto principalmente da membri della classe Bacilli, che forma uno scudo capace di proteggere i batteri dalla fagocitosi e dai fagi. Attualmente si conoscono pochi enzimi in grado di degradare il γ-PGA, tra questi vi è una γ-PGA-idrolasi codificata da fago, PghP. Il ruolo di PghP nei fagi è assicurare l'accesso alla superficie delle cellule batteriche tramite la degradazione della barriera di γ-PGA. Abbiamo identificato quattro geni non annotati di B. subtilis tramite similarità dei loro prodotti con PghP; infatti questi geni risiedono in elementi profagici del genoma di B. subtilis. I prodotti ricombinanti di due di loro mostrano efficiente degradazione del polimero, duque la similarità della sequenza riflette omologia funzionale. Geni codificanti simili γ-PGA-idrolasi sono stati identificati in fagi specifici per l'ordine Bacillales e in molti genomi batterici, non appartenti solo a quell'ordine. Anche la distribuzione dell'operone per la biosintesi del γ-PGA è stata analizzata con un approccio bioinformatico; la lista di organisimi con funzioni biosintetiche si è rivelata più estesa di quanto atteso e include molte specie patogene. Inoltre in batteri non-Bacillales i geni predetti per γ-PGA-idrolasi si trovano preferenzialmente in specie che non hanno i geni relativi alla produzione del polimero. I geni relativi a γ-PGA-idrolasi potrebbero quindi esser stati distribuiti tra i genomi batterici tramite scambi orizzontali, piuttosto che tramite infezione fagica. In habitat naturali ricchi in γ-PGA fornito dagli organismi produttori, la disponibilità di idrolasi che rilasciano oligomeri di glutammato dal γ-PGA potrebbe conferire un vantaggio e potrebbe subire quindi una selezione positiva.
γ-PGA idrolasi di origine fagica in Bacillus subtilis ed in altri genomi batterici
MAMBERTI, STEFANIA
2014/2015
Abstract
Poly-γ-glutamate (γ-PGA) is an industrially interesting polymer secreted mainly by members of the class Bacilli which forms a shield able to protect bacteria from phagocytosis and phages. Few enzymes are known to degrade γ-PGA; among them is a phage-encoded γ-PGA hydrolase, PghP. The supposed role of PghP in phages is to ensure access to the surface of bacterial cells by dismantling the γ-PGA barrier. We identified four unannotated B. subtilis genes through similarity of their encoded products to PghP; in fact these genes reside in prophage elements of B. subtilis genome. The recombinant products of two of them demonstrate efficient polymer degradation, confirming that sequence similarity reflects functional homology. Genes encoding similar γ-PGA hydrolases were identified in phages specific for the order Bacillales and in numerous microbial genomes, not only belonging to that order. The distribution of the γ-PGA biosynthesis operon was also investigated with a bioinformatics approach; it was found that the list of organisms endowed with γ-PGA biosynthetic functions is larger than expected and includes several pathogenic species. Moreover in non-Bacillales bacteria the predicted γ-PGA hydrolase genes are preferentially found in species that do not have the genetic asset for polymer production. Our findings suggest that γ-PGA hydrolase genes might have spread across microbial genomes via horizontal exchanges rather than via phage infection.We hypothesize that, in natural habitats rich in γ-PGA supplied by producer organisms, the availability of hydrolases that release glutamate oligomers from γ-PGA might be a beneficial trait under positive selection.È consentito all'utente scaricare e condividere i documenti disponibili a testo pieno in UNITESI UNIPV nel rispetto della licenza Creative Commons del tipo CC BY NC ND.
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https://hdl.handle.net/20.500.14239/18546