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Bakunina IY, Balabanova LA, Pennacchio A, Trincone A. Hooked on α-d-galactosidases: from biomedicine to enzymatic synthesis. Crit Rev Biotechnol 2015; 36:233-45. [PMID: 25394540 DOI: 10.3109/07388551.2014.949618] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
α-d-Galactosidases (EC 3.2.1.22) are enzymes employed in a number of useful bio-based applications. We have depicted a comprehensive general survey of α-d-galactosidases from different origin with special emphasis on marine example(s). The structures of natural α-galactosyl containing compounds are described. In addition to 3D structures and mechanisms of action of α-d-galactosidases, different sources, natural function and genetic regulation are also covered. Finally, hydrolytic and synthetic exploitations as free or immobilized biocatalysts are reviewed. Interest in the synthetic aspects during the next years is anticipated for access to important small molecules by green technology with an emphasis on alternative selectivity of this class of enzymes from different sources.
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Affiliation(s)
- Irina Yu Bakunina
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences , Vladivostok , Russia and
| | - Larissa A Balabanova
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences , Vladivostok , Russia and
| | - Angela Pennacchio
- b Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche , Pozzuoli , Napoli , Italy
| | - Antonio Trincone
- b Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche , Pozzuoli , Napoli , Italy
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Bruno-Barcena JM, Azcarate-Peril MA. Galacto-oligosaccharides and Colorectal Cancer: Feeding our Intestinal Probiome. J Funct Foods 2015; 12:92-108. [PMID: 25584074 PMCID: PMC4288025 DOI: 10.1016/j.jff.2014.10.029] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Prebiotics are ingredients selectively fermented by the intestinal microbiota that promote changes in the microbial community structure and/or their metabolism, conferring health benefits to the host. Studies show that β (1-4) galacto-oligosaccharides [β (1-4) GOS], lactulose and fructo-oligosaccharides increase intestinal concentration of lactate and short chain fatty acids, and stool frequency and weight, and they decrease fecal concentration of secondary bile acids, fecal pH, and nitroreductase and β-glucuronidase activities suggesting a clear role in colorectal cancer (CRC) prevention. This review summarizes research on prebiotics bioassimilation, specifically β (1-4) GOS, and their potential role in CRC. We also evaluate research that show that the impact of prebiotics on host physiology can be direct or through modulation of the gut intestinal microbiome, specifically the probiome (autochtonous beneficial bacteria), we present studies on a potential role in CRC progression to finally describe the current state of β (1-4) GOS generation for industrial production.
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Affiliation(s)
- Jose M. Bruno-Barcena
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina
| | - M. Andrea Azcarate-Peril
- Department of Cell Biology and Physiology, and Microbiome Core Facility, University of North Carolina School of Medicine, Chapel Hill
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O'Connell KJ, O'Connell Motherway M, O'Callaghan J, Fitzgerald GF, Ross RP, Ventura M, Stanton C, van Sinderen D. Metabolism of four α-glycosidic linkage-containing oligosaccharides by Bifidobacterium breve UCC2003. Appl Environ Microbiol 2013; 79:6280-92. [PMID: 23913435 PMCID: PMC3811189 DOI: 10.1128/aem.01775-13] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/01/2013] [Indexed: 11/20/2022] Open
Abstract
Members of the genus Bifidobacterium are common inhabitants of the gastrointestinal tracts of humans and other mammals, where they ferment many diet-derived carbohydrates that cannot be digested by their hosts. To extend our understanding of bifidobacterial carbohydrate utilization, we investigated the molecular mechanisms by which 11 strains of Bifidobacterium breve metabolize four distinct α-glucose- and/or α-galactose-containing oligosaccharides, namely, raffinose, stachyose, melibiose, and melezitose. Here we demonstrate that all B. breve strains examined possess the ability to utilize raffinose, stachyose, and melibiose. However, the ability to metabolize melezitose was not common to all B. breve strains tested. Transcriptomic and functional genomic approaches identified a gene cluster dedicated to the metabolism of α-galactose-containing carbohydrates, while an adjacent gene cluster, dedicated to the metabolism of α-glucose-containing melezitose, was identified in strains that are able to use this carbohydrate.
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Affiliation(s)
- Kerry Joan O'Connell
- Department of Microbiology
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Mary O'Connell Motherway
- Department of Microbiology
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - John O'Callaghan
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Teagasc Research Centre Moorepark, Fermoy, Cork, Ireland
| | - Gerald F. Fitzgerald
- Department of Microbiology
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - R. Paul Ross
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Teagasc Research Centre Moorepark, Fermoy, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Parma, Italy
| | - Catherine Stanton
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Teagasc Research Centre Moorepark, Fermoy, Cork, Ireland
| | - Douwe van Sinderen
- Department of Microbiology
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
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Shimamoto T, Ahmed AM, Shimamoto T. A novel retron of Vibrio parahaemolyticus is closely related to retron-Vc95 of Vibrio cholerae. J Microbiol 2013; 51:323-8. [PMID: 23812812 DOI: 10.1007/s12275-013-2715-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 02/17/2013] [Indexed: 11/27/2022]
Abstract
Some bacteria produce a satellite RNA-DNA complex termed msDNA, multicopy single-stranded DNA. In this report, msDNA from Vibrio parahaemolyticus, a cause of acute gastroenteritis, was identified and named msDNA-Vp96. The retron element containing the ret gene, encoding the reverse transcriptase (RT) that is responsible for msDNA production, was cloned and characterized. Comparison of msDNA-Vp96 and msDNA-Vc95, from Vibrio cholerae, showed a high level of sequence similarity. We exchanged the two ret genes to examine whether msDNA was produced by the RT from different sources. We found that RT-Vp96 of V. parahaemolyticus was able to synthesize msDNA-Vc95 of V. cholerae and vice versa. To the best of our knowledge, this is the first report that RT from different bacterial species can synthesize msDNA.
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Affiliation(s)
- Toshi Shimamoto
- Laboratory of Food Microbiology and Hygiene, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima 739-8528, Japan
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Aga1, the first alpha-Galactosidase from the human bacteria Ruminococcus gnavus E1, efficiently transcribed in gut conditions. Res Microbiol 2011; 163:14-21. [PMID: 22036918 DOI: 10.1016/j.resmic.2011.10.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 09/14/2011] [Indexed: 11/23/2022]
Abstract
Differential gene expression analysis was performed in monoxenic mice colonized with Ruminococcus gnavus strain E1, a major endogenous member of the gut microbiota. RNA arbitrarily primed-PCR fingerprinting assays allowed to specifically detect the in vivo expression of the aga1 gene, which was further confirmed by RT-PCR. The aga1 gene encoded a protein of 744 residues with calculated molecular mass of 85,207 Da. Aga1 exhibited significant similarity with previously characterized α-Galactosidases of the GH 36 family. Purified recombinant protein demonstrated high catalytic activity (104 ± 7 U mg(-1)) and efficient p-nitrophenyl-α-d-galactopyranoside hydrolysis [k(cat)/K(m) = 35.115 ± 8.82 s(-1) mM(-1) at 55 °C and k(cat)/K(m) = 17.48 ± 4.25 s(-1) mM(-1) at 37 °C].
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Glasner ME, Gerlt JA, Babbitt PC. Mechanisms of protein evolution and their application to protein engineering. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2010; 75:193-239, xii-xiii. [PMID: 17124868 DOI: 10.1002/9780471224464.ch3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein engineering holds great promise for the development of new biosensors, diagnostics, therapeutics, and agents for bioremediation. Despite some remarkable successes in experimental and computational protein design, engineered proteins rarely achieve the efficiency or specificity of natural enzymes. Current protein design methods utilize evolutionary concepts, including mutation, recombination, and selection, but the inability to fully recapitulate the success of natural evolution suggests that some evolutionary principles have not been fully exploited. One aspect of protein engineering that has received little attention is how to select the most promising proteins to serve as templates, or scaffolds, for engineering. Two evolutionary concepts that could provide a rational basis for template selection are the conservation of catalytic mechanisms and functional promiscuity. Knowledge of the catalytic motifs responsible for conserved aspects of catalysis in mechanistically diverse superfamilies could be used to identify promising templates for protein engineering. Second, protein evolution often proceeds through promiscuous intermediates, suggesting that templates which are naturally promiscuous for a target reaction could enhance protein engineering strategies. This review explores these ideas and alternative hypotheses concerning protein evolution and engineering. Future research will determine if application of these principles will lead to a protein engineering methodology governed by predictable rules for designing efficient, novel catalysts.
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Affiliation(s)
- Margaret E Glasner
- Department of Biopharmaceutical Sciences, University of California-San Francisco, San Francisco, CA 94143, USA
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Silvestroni A, Connes C, Sesma F, De Giori GS, Piard JC. Characterization of the melA locus for alpha-galactosidase in Lactobacillus plantarum. Appl Environ Microbiol 2002; 68:5464-71. [PMID: 12406739 PMCID: PMC129937 DOI: 10.1128/aem.68.11.5464-5471.2002] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2002] [Accepted: 08/29/2002] [Indexed: 11/20/2022] Open
Abstract
Alpha-galactosides are abundant sugars in legumes such as soy. Because of the lack of alpha-galactosidase (alpha-Gal) in the digestive tract, humans are unable to digest these sugars, which consequently induce flatulence. To develop the consumption of the otherwise highly nutritional soy products, the use of exogenous alpha-Gal is promising. In this framework, we characterized the melA gene for alpha-Gal in Lactobacillus plantarum. The melA gene encodes a cytoplasmic 84-kDa protein whose enzymatically active form occurs as oligomers. The melA gene was cloned and expressed in Escherichia coli, yielding an active alpha-Gal. We show that melA is transcribed from its own promoter, yielding a monocistronic mRNA, and that it is regulated at the transcriptional level, i.e., it is induced by melibiose but is not totally repressed by glucose. Posttranscriptional regulation by the carbon source could also occur. Upstream of melA, a putative galactoside transporter, designated RafP, was identified that shows high homology to LacS, the unique transporter for both alpha- and beta-galactosides in Streptococcus thermophilus. rafP is also expressed as a monocistronic mRNA. Downstream of melA, the lacL and lacM genes were identified that encode a heterodimeric beta-galactosidase. A putative galM gene identified in the same cluster suggests the presence of a galactose operon. These results indicate that the genes involved in galactoside catabolism are clustered in L. plantarum ATCC 8014. This first genetic characterization of melA and of its putative associated transporter, rafP, in a lactobacillus opens doors to various applications both in the manufacture of soy-derived products and in probiotic and nutraceutical issues.
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Affiliation(s)
- Aurelio Silvestroni
- Centro de Referencia para Lactobacillos (CERELA-CONICET), Chacabuco 145, 4000 Tucumán, Argentina. INRA-URLGA, Useful Bacterial Surface Proteins, 78352 Jouy-en-Josas, France
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