Phylogenetic analysis and substrate specificity of GH2 β‐mannosidases from <i>Aspergillus</i> species

Reddy, Sumitha K.; Rosengren, Anna; Klaubauf, Sylvia; Kulkarni, Tejas S.; Karlsson, Eva Nordberg; Vries, Ronald P. de; Stålbrand, Henrik

doi:10.1016/j.febslet.2013.08.029

Cited by 15 publications

(6 citation statements)

References 27 publications

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“…Thus, different substrate specificities of UbiA and its Mqn co-occurring homologs could correlate with distinguishable differences on the amino acid sequence level. Correlations between phylogeny and substrate specificity have been reported for various enzymes (Lee et al, 2007 ; Olivares-Hernández et al, 2010 ; Reddy et al, 2013 ; Ratnikov et al, 2014 ). Consequently, we proposed that UbiA and its Mqn co-occurring homolog form a clearly distinguished branches in their phylogenetical tree.…”

Section: Resultsmentioning

confidence: 97%

Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis

Ravcheev

Thiele

2016

Front. Microbiol.

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Ubiquinone and menaquinone are membrane lipid-soluble carriers of electrons that are essential for cellular respiration. Eukaryotic cells can synthesize ubiquinone but not menaquinone, whereas prokaryotes can synthesize both quinones. So far, most of the human gut microbiome (HGM) studies have been based on metagenomic analysis. Here, we applied an analysis of individual HGM genomes to the identification of ubiquinone and menaquinone biosynthetic pathways. In our opinion, the shift from metagenomics to analysis of individual genomes is a pivotal milestone in investigation of bacterial communities, including the HGM. The key results of this study are as follows. (i) The distribution of the canonical pathways in the HGM genomes was consistent with previous reports and with the distribution of the quinone-dependent reductases for electron acceptors. (ii) The comparative genomics analysis identified four alternative forms of the previously known enzymes for quinone biosynthesis. (iii) Genes for the previously unknown part of the futalosine pathway were identified, and the corresponding biochemical reactions were proposed. We discuss the remaining gaps in the menaquinone and ubiquinone pathways in some of the microbes, which indicate the existence of further alternate genes or routes. Together, these findings provide further insight into the biosynthesis of quinones in bacteria and the physiology of the HGM.

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Section: Resultsmentioning

confidence: 97%

Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis

Ravcheev

Thiele

2016

Front. Microbiol.

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“…The peak areas were analyzed using a standard curve to determine the concentration decrease of the relevant oligosaccharide. The ln[S 0 ]/[S t ] over time was plotted, and the trend line was divided with the enzyme concentration to give k cat / K m values for each oligosaccharide (54, 55). …”

Section: Methodsmentioning

confidence: 99%

Galactomannan Catabolism Conferred by a Polysaccharide Utilization Locus of Bacteroides ovatus

Bågenholm

Reddy

Bouraoui

et al. 2017

Journal of Biological Chemistry

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156

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A recently identified polysaccharide utilization locus (PUL) from Bacteroides ovatus ATCC 8483 is transcriptionally up-regulated during growth on galacto- and glucomannans. It encodes two glycoside hydrolase family 26 (GH26) β-mannanases, BoMan26A and BoMan26B, and a GH36 α-galactosidase, BoGal36A. The PUL also includes two glycan-binding proteins, confirmed by β-mannan affinity electrophoresis. When this PUL was deleted, B. ovatus was no longer able to grow on locust bean galactomannan. BoMan26A primarily formed mannobiose from mannan polysaccharides. BoMan26B had higher activity on galactomannan with a high degree of galactosyl substitution and was shown to be endo-acting generating a more diverse mixture of oligosaccharides, including mannobiose. Of the two β-mannanases, only BoMan26B hydrolyzed galactoglucomannan. A crystal structure of BoMan26A revealed a similar structure to the exo-mannobiohydrolase CjMan26C from Cellvibrio japonicus, with a conserved glycone region (−1 and −2 subsites), including a conserved loop closing the active site beyond subsite −2. Analysis of cellular location by immunolabeling and fluorescence microscopy suggests that BoMan26B is surface-exposed and associated with the outer membrane, although BoMan26A and BoGal36A are likely periplasmic. In light of the cellular location and the biochemical properties of the two characterized β-mannanases, we propose a scheme of sequential action by the glycoside hydrolases encoded by the β-mannan PUL and involved in the β-mannan utilization pathway in B. ovatus. The outer membrane-associated BoMan26B initially acts on the polysaccharide galactomannan, producing comparably large oligosaccharide fragments. Galactomanno-oligosaccharides are further processed in the periplasm, degalactosylated by BoGal36A, and subsequently hydrolyzed into mainly mannobiose by the β-mannanase BoMan26A.

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“…Around 500 n m of enzyme was incubated with 5 m m of each oligosaccharide in a total volume of 500 μL for maximum of 12 h. Polysaccharides (0.5% Locust bean gum, guar gum or acetylated GGM) were also incubated with 1 μ m of enzyme in a total volume of 500 μL. Aliquots of 150 μL were taken at 1 h, 3 h and 12 h and the samples were analysed for galactose release by high‐performance anion exchange chromatography with pulsed amperometric detection (HPAEC‐PAD) (Dionex, Sunnyvale, CA, USA) on a PA10 column with 1% NaOH isocratic elution . Specific activity and extent of galactose released from polysaccharides were calculated based on the galactose release after 1 h and 12 h respectively.…”

Section: Methodsmentioning

confidence: 99%

A β‐mannan utilization locus in Bacteroides ovatus involves a GH36 α‐galactosidase active on galactomannans

et al. 2016

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The Bacova_02091 gene in the β‐mannan utilization locus of Bacteroides ovatus encodes a family GH36 α‐galactosidase (BoGal36A), transcriptionally upregulated during growth on galactomannan. Characterization of recombinant BoGal36A reveals unique properties compared to other GH36 α‐galactosidases, which preferentially hydrolyse terminal α‐galactose in raffinose family oligosaccharides. BoGal36A prefers hydrolysing internal galactose substitutions from intact and depolymerized galactomannan. BoGal36A efficiently releases (> 90%) galactose from guar and locust bean galactomannans, resulting in precipitation of the polysaccharides. As compared to other GH36 structures, the BoGal36A 3D model displays a loop deletion, resulting in a wider active site cleft which likely can accommodate a galactose‐substituted polymannose backbone.

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Phylogenetic analysis and substrate specificity of GH2 β‐mannosidases from Aspergillus species

Abstract: Edited by Takashi Gojobori

Cited by 15 publications

References 27 publications

Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis

Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis

Galactomannan Catabolism Conferred by a Polysaccharide Utilization Locus of Bacteroides ovatus

A β‐mannan utilization locus in Bacteroides ovatus involves a GH36 α‐galactosidase active on galactomannans

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