title: γ-PGA Hydrolases of Phage Origin in Bacillus subtilis and Other Microbial Genomes.
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.
authors.affiliation: Dept. of Biology and Biotechnology, Università degli Studi di Pavia, Pavia 27100 (I), Italy.
authors.forename: Stefania
authors.initials: S
authors.lastname: Mamberti
authors.affiliation: Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Sezione Diagnostica di Pavia, Pavia 27100 (I), Italy.
authors.forename: Paola
authors.initials: P
authors.lastname: Prati
authors.affiliation: Institute of Molecular Genetics, National Research Council of Italy, Pavia 27100 (I), Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Cremaschi
authors.affiliation: Dept. of Biology and Biotechnology, Università degli Studi di Pavia, Pavia 27100 (I), Italy.
authors.forename: Claudio
authors.initials: C
authors.lastname: Seppi
authors.affiliation: Department of Chemistry, Università degli Studi di Milano, Milan 20133 (I), Italy.
authors.forename: Carlo F
authors.initials: CF
authors.lastname: Morelli
authors.affiliation: Dept. of Biology and Biotechnology, Università degli Studi di Pavia, Pavia 27100 (I), Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Galizzi
authors.affiliation: Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Sezione Diagnostica di Pavia, Pavia 27100 (I), Italy.
authors.forename: Massimo
authors.initials: M
authors.lastname: Fabbi
authors.affiliation: Dept. of Biology and Biotechnology, Università degli Studi di Pavia, Pavia 27100 (I), Italy; Italian Interuniversity Consortium on Materials, Science, and Technology (INSTM), Pavia Research Unit, Pavia 27100 (I), Italy.
authors.forename: Cinzia
authors.initials: C
authors.lastname: Calvio
mesh_terms: D000595:Amino Acid Sequence; D017103:Bacillus Phages / Q000145:classification / Q000201:enzymology* / Q000235:genetics; D001412:Bacillus subtilis / Q000235:genetics / Q000378:metabolism / Q000821:virology*; D004587:Electrophoresis, Agar Gel; D016680:Genome, Bacterial / Q000235:genetics; D064349:Genome, Microbial; D008969:Molecular Sequence Data; D011099:Polyglutamic Acid / Q000031:analogs & derivatives / Q000378:metabolism; D039002:Prophages / Q000201:enzymology / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity; D014764:Viral Proteins / Q000235:genetics / Q000378:metabolism*; D011623:gamma-Glutamyl Hydrolase / Q000235:genetics / Q000378:metabolism*
chemical_list: D014764:Viral Proteins; C511775:poly(gamma-glutamic acid); D011099:Polyglutamic Acid; D011623:gamma-Glutamyl Hydrolase