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γ-PGA Hydrolases of Phage Origin in Bacillus subtilis and Other Microbial Genomes.

Mamberti S, Prati P, Cremaschi P, Seppi C, Morelli CF, Galizzi A, Fabbi M, Calvio C - PLoS ONE (2015)

Bottom Line: The recombinant products of two of them demonstrate efficient polymer degradation, confirming that sequence similarity reflects functional homology.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.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.

View Article: PubMed Central - PubMed

Affiliation: Dept. of Biology and Biotechnology, Università degli Studi di Pavia, Pavia 27100 (I), Italy.

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.

No MeSH data available.


Related in: MedlinePlus

Clustal alignment of B. subtilis gene products showing similarity to Bacillus phage ΦNIT1 PghP.Black triangles below the sequences point to residues involved in Zn coordination according to the PghP structure [31, 32]. The valine residues enclosed in a rectangle in YoqZ and YndL sequences were transformed in the initial methionine in the recombinant proteins. An * (asterisk) in the clustal consensus line indicates positions which have a single, fully conserved residue. A: (colon) indicates conservation between groups of amino acids with strongly similar properties. A. (period) indicates conservation between groups of amino acids with weakly similar properties.
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pone.0130810.g001: Clustal alignment of B. subtilis gene products showing similarity to Bacillus phage ΦNIT1 PghP.Black triangles below the sequences point to residues involved in Zn coordination according to the PghP structure [31, 32]. The valine residues enclosed in a rectangle in YoqZ and YndL sequences were transformed in the initial methionine in the recombinant proteins. An * (asterisk) in the clustal consensus line indicates positions which have a single, fully conserved residue. A: (colon) indicates conservation between groups of amino acids with strongly similar properties. A. (period) indicates conservation between groups of amino acids with weakly similar properties.

Mentions: In an extension of our efforts to improve -PGA productivity in B. subtilis [24] a BLAST search for PghP homologue enzymes was performed on B. subtilis strain 168 genome ORFs using the phage protein sequence as a query. Four different hits were identified which correspond to the predicted products of yjqB, ymaC, yoqZ and yndL [43]. Sequence alignment confirmed that the four gene products are highly similar amongst themselves and display outstanding similarities to PghP, ranging from 53.8% to 41% (Fig 1 and Table 1) [44]. The four genes are encased in prophages or putative prophage sequence relics present in the B. subtilis chromosome: yjqB is located in the PBSX prophage element at 1,390 kb; yoqZ is in the SPβ prophage region at 2,190 kb [44], ymaC and yndL are in the prophage-like element 5 (numbered in order of appearance according to Kunst et al. [43]) at 1,864 and 1,915 kb, respectively. In all the databases the four genes are currently annotated as coding for phage-related (replication) proteins, although no functional studies for any of them have been conducted to support such a prediction. The encoded proteins share amongst themselves and with phagic PghP the signature of a sequence-based domain of unknown function, namely DUF867, equivalent to the InterPro family IPR008585 or to Pfam PF05908 (S2 File) [45–47]. The DUF867 protein family lacks a functional annotation although it is sometimes connected with the crystal structure of the characterized protein PghP from ΦNIT1 [PDB: 3a9l] [32].


γ-PGA Hydrolases of Phage Origin in Bacillus subtilis and Other Microbial Genomes.

Mamberti S, Prati P, Cremaschi P, Seppi C, Morelli CF, Galizzi A, Fabbi M, Calvio C - PLoS ONE (2015)

Clustal alignment of B. subtilis gene products showing similarity to Bacillus phage ΦNIT1 PghP.Black triangles below the sequences point to residues involved in Zn coordination according to the PghP structure [31, 32]. The valine residues enclosed in a rectangle in YoqZ and YndL sequences were transformed in the initial methionine in the recombinant proteins. An * (asterisk) in the clustal consensus line indicates positions which have a single, fully conserved residue. A: (colon) indicates conservation between groups of amino acids with strongly similar properties. A. (period) indicates conservation between groups of amino acids with weakly similar properties.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4497714&req=5

pone.0130810.g001: Clustal alignment of B. subtilis gene products showing similarity to Bacillus phage ΦNIT1 PghP.Black triangles below the sequences point to residues involved in Zn coordination according to the PghP structure [31, 32]. The valine residues enclosed in a rectangle in YoqZ and YndL sequences were transformed in the initial methionine in the recombinant proteins. An * (asterisk) in the clustal consensus line indicates positions which have a single, fully conserved residue. A: (colon) indicates conservation between groups of amino acids with strongly similar properties. A. (period) indicates conservation between groups of amino acids with weakly similar properties.
Mentions: In an extension of our efforts to improve -PGA productivity in B. subtilis [24] a BLAST search for PghP homologue enzymes was performed on B. subtilis strain 168 genome ORFs using the phage protein sequence as a query. Four different hits were identified which correspond to the predicted products of yjqB, ymaC, yoqZ and yndL [43]. Sequence alignment confirmed that the four gene products are highly similar amongst themselves and display outstanding similarities to PghP, ranging from 53.8% to 41% (Fig 1 and Table 1) [44]. The four genes are encased in prophages or putative prophage sequence relics present in the B. subtilis chromosome: yjqB is located in the PBSX prophage element at 1,390 kb; yoqZ is in the SPβ prophage region at 2,190 kb [44], ymaC and yndL are in the prophage-like element 5 (numbered in order of appearance according to Kunst et al. [43]) at 1,864 and 1,915 kb, respectively. In all the databases the four genes are currently annotated as coding for phage-related (replication) proteins, although no functional studies for any of them have been conducted to support such a prediction. The encoded proteins share amongst themselves and with phagic PghP the signature of a sequence-based domain of unknown function, namely DUF867, equivalent to the InterPro family IPR008585 or to Pfam PF05908 (S2 File) [45–47]. The DUF867 protein family lacks a functional annotation although it is sometimes connected with the crystal structure of the characterized protein PghP from ΦNIT1 [PDB: 3a9l] [32].

Bottom Line: The recombinant products of two of them demonstrate efficient polymer degradation, confirming that sequence similarity reflects functional homology.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.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.

View Article: PubMed Central - PubMed

Affiliation: Dept. of Biology and Biotechnology, Università degli Studi di Pavia, Pavia 27100 (I), Italy.

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.

No MeSH data available.


Related in: MedlinePlus