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Glycoside hydrolase family 32 is present in Bacillus subtilis phages.

Maaroufi H, Levesque RC - Virol. J. (2015)

Bottom Line: Glycoside hydrolase family 32 (GH32) enzymes cleave the glycosidic bond between two monosaccharides or between a carbohydrate and an aglycone moiety.This is the first analysis of GH32 enzymes in Bacillus subtilis phage SP10, ϕNIT1 and SPG24.Phylogenetic analysis, molecular docking and secretability predictions suggest that phage GH32 enzymes function as levan (fructose homopolysaccharide) fructotransferase.

View Article: PubMed Central - PubMed

Affiliation: Institut de biologie intégrative et des systèmes (IBIS), Plate-Forme de Bio-Informatique, Université Laval, Pavillon Charles-Eugène Marchand, 1030 Avenue de la médecine, Québec, Québec, G1V 0A6, Canada. halim.maaroufi@ibis.ulaval.ca.

ABSTRACT

Background: Glycoside hydrolase family 32 (GH32) enzymes cleave the glycosidic bond between two monosaccharides or between a carbohydrate and an aglycone moiety. GH32 enzymes have been studied in prokaryotes and in eukaryotes but not in viruses.

Findings: This is the first analysis of GH32 enzymes in Bacillus subtilis phage SP10, ϕNIT1 and SPG24. Phylogenetic analysis, molecular docking and secretability predictions suggest that phage GH32 enzymes function as levan (fructose homopolysaccharide) fructotransferase.

Conclusions: We showed that viruses also contain GH32 enzymes and that our analyses in silico strongly suggest that these enzymes function as levan fructotransferase.

No MeSH data available.


Related in: MedlinePlus

Sequence alignment of enzymes of the GH32 family from Bacillus phages. Accession numbers of sequence are in {} after species name. Highly conserved amino acid residues are shown in red and boxed in blue. Red asterisks represent residues of the proposed catalytic triad. Secondary structures indicated above are assigned according to the crystal structure of A. ureafaciens (pdb: 4FFG). The figure was prepared with ESPript (http://espript.ibcp.fr)
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Fig1: Sequence alignment of enzymes of the GH32 family from Bacillus phages. Accession numbers of sequence are in {} after species name. Highly conserved amino acid residues are shown in red and boxed in blue. Red asterisks represent residues of the proposed catalytic triad. Secondary structures indicated above are assigned according to the crystal structure of A. ureafaciens (pdb: 4FFG). The figure was prepared with ESPript (http://espript.ibcp.fr)

Mentions: During our study of β-fructofuranosidase proteins of budworm (unpublished results), we noticed during the blast search that some bacillus phages also contain homolog to β-fructofuranosidase. The search in the CAZy database (http://www.cazy.org/) showed the presence of one Bacillus phage phiNIT1 sequence (accession AP013029.1) in the section of GH32 family. To determine if other homolog sequences exist in other viruses, we searched for the presence of GH32 enzyme homologs in the complete sequenced genomes of viruses in GenBank using BLASTp, tBLASTn and HMM profiles. Among 4602 (1449 phages) complete viral genomes available at NCBI (as of June 5th, 2015); only three Bacillus phage (SP10, ϕNIT1 and SPG24) genomes contain GH32 homologs. The amino acid sequence of SPG24 and ϕNIT1 shows 98 % of identity and SP10 presents 76 % of identity with SPG24 and ϕNIT1. We used the amino acid sequence of Bacillus phage SP10 GH32 to search by BlastP for close homologues in bacteria, fungi, plants and animals. The sequences extracted from databases were aligned with Mafft [18] (Fig. 1 and Additional file 1: Figure S1). Analysis of sequences alignment showed that in contrast to other enzymes of the GH32 family, the three enzymes from phages did not possess a signal peptide. However, using Secretome 2.0 Server (http://www.cbs.dtu.dk/services/SecretomeP/) that predicts non-classically secreted proteins in Gram-positive and Gram-negative bacteria, we obtained high scores of secretion, 0.90, 0.86 and 0.84 for enzymes from phages SP10, ϕNIT1 and SPG24 and is in accordance with secreted enzymes. Moreover, the GH32 enzymes from the three phages possess the catalytic triad, D19, D150 and E198 (Figs. 1 and 3a). We noted that in these three phage enzymes, the last three amino acid residues in the catalytic nucleophile WMNDPNG motifs are changed to IQR residues (Fig. 1 and Additional file 1: Figure S1).Fig. 1


Glycoside hydrolase family 32 is present in Bacillus subtilis phages.

Maaroufi H, Levesque RC - Virol. J. (2015)

Sequence alignment of enzymes of the GH32 family from Bacillus phages. Accession numbers of sequence are in {} after species name. Highly conserved amino acid residues are shown in red and boxed in blue. Red asterisks represent residues of the proposed catalytic triad. Secondary structures indicated above are assigned according to the crystal structure of A. ureafaciens (pdb: 4FFG). The figure was prepared with ESPript (http://espript.ibcp.fr)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4595243&req=5

Fig1: Sequence alignment of enzymes of the GH32 family from Bacillus phages. Accession numbers of sequence are in {} after species name. Highly conserved amino acid residues are shown in red and boxed in blue. Red asterisks represent residues of the proposed catalytic triad. Secondary structures indicated above are assigned according to the crystal structure of A. ureafaciens (pdb: 4FFG). The figure was prepared with ESPript (http://espript.ibcp.fr)
Mentions: During our study of β-fructofuranosidase proteins of budworm (unpublished results), we noticed during the blast search that some bacillus phages also contain homolog to β-fructofuranosidase. The search in the CAZy database (http://www.cazy.org/) showed the presence of one Bacillus phage phiNIT1 sequence (accession AP013029.1) in the section of GH32 family. To determine if other homolog sequences exist in other viruses, we searched for the presence of GH32 enzyme homologs in the complete sequenced genomes of viruses in GenBank using BLASTp, tBLASTn and HMM profiles. Among 4602 (1449 phages) complete viral genomes available at NCBI (as of June 5th, 2015); only three Bacillus phage (SP10, ϕNIT1 and SPG24) genomes contain GH32 homologs. The amino acid sequence of SPG24 and ϕNIT1 shows 98 % of identity and SP10 presents 76 % of identity with SPG24 and ϕNIT1. We used the amino acid sequence of Bacillus phage SP10 GH32 to search by BlastP for close homologues in bacteria, fungi, plants and animals. The sequences extracted from databases were aligned with Mafft [18] (Fig. 1 and Additional file 1: Figure S1). Analysis of sequences alignment showed that in contrast to other enzymes of the GH32 family, the three enzymes from phages did not possess a signal peptide. However, using Secretome 2.0 Server (http://www.cbs.dtu.dk/services/SecretomeP/) that predicts non-classically secreted proteins in Gram-positive and Gram-negative bacteria, we obtained high scores of secretion, 0.90, 0.86 and 0.84 for enzymes from phages SP10, ϕNIT1 and SPG24 and is in accordance with secreted enzymes. Moreover, the GH32 enzymes from the three phages possess the catalytic triad, D19, D150 and E198 (Figs. 1 and 3a). We noted that in these three phage enzymes, the last three amino acid residues in the catalytic nucleophile WMNDPNG motifs are changed to IQR residues (Fig. 1 and Additional file 1: Figure S1).Fig. 1

Bottom Line: Glycoside hydrolase family 32 (GH32) enzymes cleave the glycosidic bond between two monosaccharides or between a carbohydrate and an aglycone moiety.This is the first analysis of GH32 enzymes in Bacillus subtilis phage SP10, ϕNIT1 and SPG24.Phylogenetic analysis, molecular docking and secretability predictions suggest that phage GH32 enzymes function as levan (fructose homopolysaccharide) fructotransferase.

View Article: PubMed Central - PubMed

Affiliation: Institut de biologie intégrative et des systèmes (IBIS), Plate-Forme de Bio-Informatique, Université Laval, Pavillon Charles-Eugène Marchand, 1030 Avenue de la médecine, Québec, Québec, G1V 0A6, Canada. halim.maaroufi@ibis.ulaval.ca.

ABSTRACT

Background: Glycoside hydrolase family 32 (GH32) enzymes cleave the glycosidic bond between two monosaccharides or between a carbohydrate and an aglycone moiety. GH32 enzymes have been studied in prokaryotes and in eukaryotes but not in viruses.

Findings: This is the first analysis of GH32 enzymes in Bacillus subtilis phage SP10, ϕNIT1 and SPG24. Phylogenetic analysis, molecular docking and secretability predictions suggest that phage GH32 enzymes function as levan (fructose homopolysaccharide) fructotransferase.

Conclusions: We showed that viruses also contain GH32 enzymes and that our analyses in silico strongly suggest that these enzymes function as levan fructotransferase.

No MeSH data available.


Related in: MedlinePlus