Improved annotation of conjugated bile acid hydrolase superfamily members in Gram-positive bacteria

Lambert, Jolanda; Siezen, Roland J.; Vos, Willem M. de; Kleerebezem, Michiel

doi:10.1099/mic.0.2008/016808-0

Cited by 40 publications

(34 citation statements)

References 37 publications

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“…Similarly, the known BSH archaeal enzymes from Methanosphaera stadtmanae and Methanobrevibacter smithii were also predicted correctly as Cluster1-BSH enzymes. The BSS scoring system was further validated against the Grampositive CGH enzymes annotated previously as BSH/PVA by Lambert et al (2008). The BSS-based functional assignment was found to be in agreement with the earlier annotations (Table S3).…”

Section: Substrate Specificity Annotation Of Family Memberssupporting

confidence: 69%

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An improved method for specificity annotation shows a distinct evolutionary divergence among the microbial enzymes of the cholylglycine hydrolase family

et al. 2014

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Bile salt hydrolases (BSHs) are gut microbial enzymes that play a significant role in the bile acid modification pathway. Penicillin V acylases (PVAs) are enzymes produced by environmental microbes, having a possible role in pathogenesis or scavenging of phenolic compounds in their microbial habitats. The correct annotation of such physiologically and industrially important enzymes is thus vital. The current methods relying solely on sequence homology do not always provide accurate annotations for these two members of the cholylglycine hydrolase (CGH) family as BSH/PVA enzymes. Here, we present an improved method [binding site similarity (BSS)-based scoring system] for the correct annotation of the CGH family members as BSH/PVA enzymes, which along with the phylogenetic information incorporates the substrate specificity as well as the binding site information. The BSS scoring system was developed through the analysis of the binding sites and binding modes of the available BSH/PVA structures with substrates glycocholic acid and penicillin V. The 198 sequences in the dataset were then annotated accurately using BSS scores as BSH/PVA enzymes. The dataset presented contained sequences from Grampositive bacteria, Gram-negative bacteria and archaea. The clustering obtained for the dataset using the method described above showed a clear distinction in annotation of Gram-positive bacteria and Gram-negative bacteria. Based on this clustering and a detailed analysis of the sequences of the CGH family in the dataset, we could infer that the CGH genes might have evolved in accordance with the hypothesis stating the evolution of diderms and archaea from the monoderms.

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Section: Substrate Specificity Annotation Of Family Memberssupporting

confidence: 69%

“…Based on the BSS scores obtained, the 198 sequences in the dataset were annotated as BSH/PVA enzymes. The BSS scoring system was tested on experimentally characterized BSH and PVA enzymes annotated previously by Lambert et al (2008) and Jones et al (2008).…”

Section: Methodsmentioning

confidence: 99%

An improved method for specificity annotation shows a distinct evolutionary divergence among the microbial enzymes of the cholylglycine hydrolase family

et al. 2014

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“…The genome of L. salivarius UCC118 contains two genes that were originally annotated as encoding choloylglycine hydrolases: the chromosomally located LSL_0518 and the megaplasmid-located LSL_1801 (11). Based upon sequence alignment, phylogenetic clustering, and protein homology modeling, the product of LSL_0518 has recently been identified unequivocally as a PVA (30), along with many other misannotated genes for presumptive Bsh enzymes. The sequence of the LSL_1801 product, whose annotation as a Bsh is supported, is 53% identical to that of functionally characterized CBA hydrolase (CAD00145) from L. monocytogenes EGDe (3).…”

Section: Resultsmentioning

confidence: 99%

“…In addition to presence in a single copy in some species, multiple copies of bsh were annotated in Lactobacillus acidophilus NCFM (bshA and bshB), Lactobacillus johnsonii NCC533 (three genes), and Lactobacillus gasseri ATCC 33323 (two genes) (30). In some Lactobacillus strains, bsh was part of an operon (20).…”

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confidence: 99%

Allelic Variation of Bile Salt Hydrolase Genes in Lactobacillus salivarius Does Not Determine Bile Resistance Levels

Fang

Bumann³

et al. 2009

J Bacteriol

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Commensal lactobacilli frequently produce bile salt hydrolase (Bsh) enzymes whose roles in intestinal survival are unclear. Twenty-six Lactobacillus salivarius strains from different sources all harbored a bsh1 allele on their respective megaplasmids. This allele was related to the plasmid-borne bsh1 gene of the probiotic strain UCC118. A second locus (bsh2) was found in the chromosomes of two strains that had higher bile resistance levels. Four Bsh1-encoding allele groups were identified, defined by truncations or deletions involving a conserved residue. In vitro analyses showed that this allelic variation was correlated with widely varying bile deconjugation phenotypes. Despite very low activity of the UCC118 Bsh1 enzyme, a mutant lacking this protein had significantly lower bile resistance, both in vitro and during intestinal transit in mice. However, the overall bile resistance phenotype of this and other strains was independent of the bsh1 allele type. Analysis of the L. salivarius transcriptome upon exposure to bile and cholate identified a multiplicity of stress response proteins and putative efflux proteins that appear to broadly compensate for, or mask, the effects of allelic variation of bsh genes. Bsh enzymes with different bile-degrading kinetics, though apparently not the primary determinants of bile resistance in L. salivarius, may have additional biological importance because of varying effects upon bile as a signaling molecule in the host.

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“…43,44 In addition, specific adaptation to the human intestine is also evident from the existence of a bile salt hydrolase (BSH) encoded by all sequenced intestinal lactobacilli. 45 Gut-adaptation functions are not only encoded by chromosomal DNA but also by large extrachromosomal replicons such as megaplasmids. The first megaplasmid described in lactic acid bacteria was that of L. salivarius UCC118, representing almost 11% of the overall coding capacity of the L. salivarius genome.…”

Section: Probiogenomics Of Lactobacillimentioning

confidence: 99%

Probiogenomics as a tool to obtain genetic insights into adaptation of probiotic bacteria to the human gut

2012

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Improved annotation of conjugated bile acid hydrolase superfamily members in Gram-positive bacteria

Cited by 40 publications

References 37 publications

An improved method for specificity annotation shows a distinct evolutionary divergence among the microbial enzymes of the cholylglycine hydrolase family

An improved method for specificity annotation shows a distinct evolutionary divergence among the microbial enzymes of the cholylglycine hydrolase family

Allelic Variation of Bile Salt Hydrolase Genes in Lactobacillus salivarius Does Not Determine Bile Resistance Levels

Probiogenomics as a tool to obtain genetic insights into adaptation of probiotic bacteria to the human gut

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