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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

Phylogenetic relationships between the GH32 enzymes from Bacillus phages, bacteria, fungi, plants and animals. Sequence alignment of Additional file 1: Figure S1 was used to construct a maximum likelihood phylogenetic tree, rooted with Cichorium GH32. The analysis used a WAG substitution model, and the statistical confidence of the nodes was calculated using the aLRT test. GH32 enzymes from phages, bacteria, fungi, plants and animals are in blue, black, orange, green and red, respectively
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Fig2: Phylogenetic relationships between the GH32 enzymes from Bacillus phages, bacteria, fungi, plants and animals. Sequence alignment of Additional file 1: Figure S1 was used to construct a maximum likelihood phylogenetic tree, rooted with Cichorium GH32. The analysis used a WAG substitution model, and the statistical confidence of the nodes was calculated using the aLRT test. GH32 enzymes from phages, bacteria, fungi, plants and animals are in blue, black, orange, green and red, respectively

Mentions: To establish the phylogenetic relationships between GH32 of phages and those of prokaryotes and eukaryotes, the sequences were aligned with Mafft (Additional file 1: Figure S1) and a phylogenetic tree was constructed using PhyML [19] and BioNJ [20]. The three phage GH32 enzymes are phylogenetically closer to enzyme GH32 of Sporolactobacillus laevolacticus than B. subtilis (Fig. 2). Interestingly, S. laevolacticus was first isolated and described as Bacillus laevolacticus by Nakayama and Yanoshi [21] and confirmed by Andersch et al. [22]. In 2006, Hatayama et al. [23] phylogenetically reclassified Bacillus laevolacticus as Sporolactobacillus laevolacticus supported by chemotaxonomic and physiological characterizations. In addition to phylogeny, among 67 complete Bacillus phage genomes, only three contain the GH32 enzymes. Therefore, we can speculate that the Bacillus phages SP10, ϕNIT1 and SPG24 acquired the GH32 gene by lateral gene transfer (LGT) from S. laevolacticus. In metazoans, enzymes of the GH32 family are present only in arthropoda that acquired this gene from bacteria by LGT [24]. Bacillus phage GH32 enzymes are also close to the Clostridium genus. The cluster (Clostridium and Sporolactobacillus) closest to GH32 phage enzymes (Fig. 2) has the canonical catalytic nucleophile WMXDI/VQR-motif instead of the classic WMNDPNG motif (Additional file 1: Figure S1).Fig. 2


Glycoside hydrolase family 32 is present in Bacillus subtilis phages.

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

Phylogenetic relationships between the GH32 enzymes from Bacillus phages, bacteria, fungi, plants and animals. Sequence alignment of Additional file 1: Figure S1 was used to construct a maximum likelihood phylogenetic tree, rooted with Cichorium GH32. The analysis used a WAG substitution model, and the statistical confidence of the nodes was calculated using the aLRT test. GH32 enzymes from phages, bacteria, fungi, plants and animals are in blue, black, orange, green and red, respectively
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: Phylogenetic relationships between the GH32 enzymes from Bacillus phages, bacteria, fungi, plants and animals. Sequence alignment of Additional file 1: Figure S1 was used to construct a maximum likelihood phylogenetic tree, rooted with Cichorium GH32. The analysis used a WAG substitution model, and the statistical confidence of the nodes was calculated using the aLRT test. GH32 enzymes from phages, bacteria, fungi, plants and animals are in blue, black, orange, green and red, respectively
Mentions: To establish the phylogenetic relationships between GH32 of phages and those of prokaryotes and eukaryotes, the sequences were aligned with Mafft (Additional file 1: Figure S1) and a phylogenetic tree was constructed using PhyML [19] and BioNJ [20]. The three phage GH32 enzymes are phylogenetically closer to enzyme GH32 of Sporolactobacillus laevolacticus than B. subtilis (Fig. 2). Interestingly, S. laevolacticus was first isolated and described as Bacillus laevolacticus by Nakayama and Yanoshi [21] and confirmed by Andersch et al. [22]. In 2006, Hatayama et al. [23] phylogenetically reclassified Bacillus laevolacticus as Sporolactobacillus laevolacticus supported by chemotaxonomic and physiological characterizations. In addition to phylogeny, among 67 complete Bacillus phage genomes, only three contain the GH32 enzymes. Therefore, we can speculate that the Bacillus phages SP10, ϕNIT1 and SPG24 acquired the GH32 gene by lateral gene transfer (LGT) from S. laevolacticus. In metazoans, enzymes of the GH32 family are present only in arthropoda that acquired this gene from bacteria by LGT [24]. Bacillus phage GH32 enzymes are also close to the Clostridium genus. The cluster (Clostridium and Sporolactobacillus) closest to GH32 phage enzymes (Fig. 2) has the canonical catalytic nucleophile WMXDI/VQR-motif instead of the classic WMNDPNG motif (Additional file 1: Figure S1).Fig. 2

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