1887

Abstract

The human gut microbiome plays an essential role in maintaining human health including in degradation of dietary fibres and carbohydrates further used as nutrients by both the host and the gut bacteria. Previously, we identified a polysaccharide utilization loci (PUL) involved in sucrose and raffinose family oligosaccharide (RFO) metabolism from one of the most common Firmicutes present in individuals, Ruminococcus gnavus E1. One of the enzymes encoded by this PUL was annotated as a putative sucrose phosphate phosphorylase (RgSPP). In the present study, we have in-depth characterized the heterologously expressed RgSPP as sucrose 6-phosphate phosphorylase (SPP), expanding our knowledge of the glycoside hydrolase GH13_18 subfamily. Specifically, the enzymatic characterization showed a selective activity on sucrose 6-phosphate (S6P) acting both in phosphorolysis releasing alpha-d-glucose-1-phosphate (G1P) and alpha-d-fructose-6-phosphate (F6P), and in reverse phosphorolysis from G1P and F6P to S6P. Interestingly, such a SPP activity had never been observed in gut bacteria before. In addition, a phylogenetic and synteny analysis showed a clustering and a strictly conserved PUL organization specific to gut bacteria. However, a wide prevalence and abundance study with a human metagenomic library showed a correlation between SPP activity and the geographical origin of the individuals and, thus, most likely linked to diet. Rgspp gene overexpression has been observed in mice fed with a high-fat diet suggesting, as observed for humans, that intestine lipid and carbohydrate microbial metabolisms are intertwined. Finally, based on the genomic environment analysis, in vitro and in vivo studies, results provide new insights into the gut microbiota catabolism of sucrose, RFOs and S6P.

  • This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000253
2019-03-26
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/mgen/5/4/mgen000253.html?itemId=/content/journal/mgen/10.1099/mgen.0.000253&mimeType=html&fmt=ahah

References

  1. Sekirov I, Russell SL, Antunes LC, Finlay BB. Gut microbiota in health and disease. Physiol Rev 2010; 90:859–904 [View Article][PubMed]
    [Google Scholar]
  2. Boulangé CL, Neves AL, Chilloux J, Nicholson JK, Dumas ME. Impact of the gut microbiota on inflammation, obesity and metabolic disease. Genome Med 2016; 8: [View Article][PubMed]
    [Google Scholar]
  3. Gericke B, Amiri M, Naim HY. The multiple roles of sucrase-isomaltase in the intestinal physiology. Mol Cell Pediatr 2016; 3: [View Article][PubMed]
    [Google Scholar]
  4. van den Ende W. Multifunctional fructans and raffinose family oligosaccharides. Front Plant Sci 2013247 [View Article][PubMed]
    [Google Scholar]
  5. Collins S, Reid G. Distant site effects of ingested prebiotics. Nutrients 2016; 8:523 [View Article][PubMed]
    [Google Scholar]
  6. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 2014; 42:D490–D495 [View Article][PubMed]
    [Google Scholar]
  7. Janeček Š, Svensson B, MacGregor EA. α-Amylase: an enzyme specificity found in various families of glycoside hydrolases. Cell Mol Life Sci 2014; 71:1149–1170 [View Article][PubMed]
    [Google Scholar]
  8. MacGregor EA, Janeček Š, Svensson B. Relationship of sequence and structure to specificity in the α-amylase family of enzymes. Biochim Biophys Acta 2001; 1546:1–20 [View Article]
    [Google Scholar]
  9. Stam MR, Danchin EG, Rancurel C, Coutinho PM, Henrissat B. Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of alpha-amylase-related proteins. Protein Eng Des Sel 2006; 19:555–562 [View Article][PubMed]
    [Google Scholar]
  10. Aerts D, Verhaeghe TF, Roman BI, Stevens CV, Desmet T et al. Transglucosylation potential of six sucrose phosphorylases toward different classes of acceptors. Carbohydr Res 2011; 346:1860–1867 [View Article][PubMed]
    [Google Scholar]
  11. Goedl C, Schwarz A, Mueller M, Brecker L, Nidetzky B. Mechanistic differences among retaining disaccharide phosphorylases: insights from kinetic analysis of active site mutants of sucrose phosphorylase and alpha,alpha-trehalose phosphorylase. Carbohydr Res 2008; 343:2032–2040 [View Article][PubMed]
    [Google Scholar]
  12. de Winter K, Verlinden K, Křen V, Weignerová L, Soetaert W et al. Ionic liquids as cosolvents for glycosylation by sucrose phosphorylase: balancing acceptor solubility and enzyme stability. Green Chem 2013; 15:1949–1955 [View Article]
    [Google Scholar]
  13. de Bruyn F, van Brempt M, Maertens J, van Bellegem W, Duchi D et al. Metabolic engineering of Escherichia coli into a versatile glycosylation platform: production of bio-active quercetin glycosides. Microb Cell Fact 2015; 14:138 [View Article][PubMed]
    [Google Scholar]
  14. Verhaeghe T, de Winter K, Berland M, de Vreese R, D'Hooghe M et al. Converting bulk sugars into prebiotics: semi-rational design of a transglucosylase with controlled selectivity. Chem Commun 2016; 52:3687–3689 [View Article][PubMed]
    [Google Scholar]
  15. Kraus M, Görl J, Timm M, Seibel J. Synthesis of the rare disaccharide nigerose by structure-based design of a phosphorylase mutant with altered regioselectivity. Chem Commun 2016; 52:4625–4627 [View Article][PubMed]
    [Google Scholar]
  16. Russell RR, Mukasa H, Shimamura A, Ferretti JJ. Streptococcus mutans gtfA gene specifies sucrose phosphorylase. Infect Immun 1988; 56:2763–2765[PubMed]
    [Google Scholar]
  17. Koga T, Nakamura K, Shirokane Y, Mizusawa K, Kitao S et al. Purification and some properties of sucrose phosphorylase from Leuconostoc mesenteroides. Agric Biol Chem 1991; 55:1805–1810 [View Article][PubMed]
    [Google Scholar]
  18. Trethewey RN, Fernie AR, Bachmann A, Fleischer-Notter H, Geigenberger P et al. Expression of a bacterial sucrose phosphorylase in potato tubers results in a glucose-independent induction of glycolysis. Plant Cell Environ 2001; 24:357–365 [View Article]
    [Google Scholar]
  19. Kim M, Kwon T, Lee HJ, Kim KH, Chung DK et al. Cloning and expression of sucrose phosphorylase gene from Bifidobacterium longum in E. coli and characterization of the recombinant enzyme. Biotechnol Lett 2003; 25:1211–1217 [View Article][PubMed]
    [Google Scholar]
  20. Sprogøe D, van den Broek LA, Mirza O, Kastrup JS, Voragen AG et al. Crystal structure of sucrose phosphorylase from Bifidobacterium adolescentis. Biochemistry 2004; 43:1156–1162 [View Article][PubMed]
    [Google Scholar]
  21. Lee J-H, Yoon S-H, Nam S-H, Moon Y-H, Moon Y-Y et al. Molecular cloning of a gene encoding the sucrose phosphorylase from Leuconostoc mesenteroides B-1149 and the expression in Escherichia coli. Enzyme Microb Technol 2006; 39:612–620 [View Article]
    [Google Scholar]
  22. Nishimoto M, Kitaoka M. Identification of the putative proton donor residue of lacto-N-biose phosphorylase (EC 2.4.1.211). Biosci Biotechnol Biochem 2007; 71:1587–1591 [View Article][PubMed]
    [Google Scholar]
  23. Lee J-H, Moon Y-H, Kim N, Kim Y-M, Kang H-K et al. Cloning and expression of the sucrose phosphorylase gene from Leuconostoc mesenteroides in Escherichia coli. Biotechnol Lett 2008; 30:749–754 [View Article][PubMed]
    [Google Scholar]
  24. Teixeira JS, Abdi R, Su MS, Schwab C, Gänzle MG. Functional characterization of sucrose phosphorylase and scrR, a regulator of sucrose metabolism in Lactobacillus reuteri. Food Microbiol 2013; 36:432–439 [View Article][PubMed]
    [Google Scholar]
  25. Verhaeghe T, Aerts D, Diricks M, Soetaert W, Desmet T. The quest for a thermostable sucrose phosphorylase reveals sucrose 6'-phosphate phosphorylase as a novel specificity. Appl Microbiol Biotechnol 2014; 98:7027–7037 [View Article][PubMed]
    [Google Scholar]
  26. Franceus J, Pinel D, Desmet T. Glucosylglycerate phosphorylase, an enzyme with novel specificity involved in compatible solute metabolism. Appl Environ Microbiol 2017; 83::e01434-17 [View Article][PubMed]
    [Google Scholar]
  27. Franceus J, Decuyper L, D'Hooghe M, Desmet T. Exploring the sequence diversity in glycoside hydrolase family 13_18 reveals a novel glucosylglycerol phosphorylase. Appl Microbiol Biotechnol 2018; 102:3183–3191 [View Article][PubMed]
    [Google Scholar]
  28. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010; 464:59–65 [View Article][PubMed]
    [Google Scholar]
  29. Ramare F, Nicoli J, Dabard J, Corring T, Ladire M et al. Trypsin-dependent production of an antibacterial substance by a human Peptostreptococcus strain in gnotobiotic rats and in vitro. Appl Environ Microbiol 1993; 59:2876–2883[PubMed]
    [Google Scholar]
  30. Dabard J, Bridonneau C, Phillipe C, Anglade P, Molle D et al. Ruminococcin A, a new lantibiotic produced by a Ruminococcus gnavus strain isolated from human feces. Appl Environ Microbiol 2001; 67:4111–4118 [View Article][PubMed]
    [Google Scholar]
  31. Pujol A, Crost EH, Simon G, Barbe V, Vallenet D et al. Characterization and distribution of the gene cluster encoding RumC, an anti-Clostridium perfringens bacteriocin produced in the gut. FEMS Microbiol Ecol 2011; 78:405–415 [View Article][PubMed]
    [Google Scholar]
  32. Crost EH, Ajandouz EH, Villard C, Geraert PA, Puigserver A et al. Ruminococcin C, a new anti-Clostridium perfringens bacteriocin produced in the gut by the commensal bacterium Ruminococcus gnavus E1. Biochimie 2011; 93:1487–1494 [View Article][PubMed]
    [Google Scholar]
  33. Bruel L, Sulzenbacher G, Cervera Tison M, Pujol A, Nicoletti C et al. α-Galactosidase/sucrose kinase (AgaSK), a novel bifunctional enzyme from the human microbiome coupling galactosidase and kinase activities. J Biol Chem 2011; 286:40814–40823 [View Article][PubMed]
    [Google Scholar]
  34. Aguilera M, Rakotoarivonina H, Brutus A, Giardina T, Simon G et al. Aga1, the first alpha-galactosidase from the human bacteria Ruminococcus gnavus E1, efficiently transcribed in gut conditions. Res Microbiol 2012; 163:14–21 [View Article][PubMed]
    [Google Scholar]
  35. Cervera-Tison M, Tailford LE, Fuell C, Bruel L, Sulzenbacher G et al. Functional analysis of family GH36 α-galactosidases from Ruminococcus gnavus E1: insights into the metabolism of a plant oligosaccharide by a human gut symbiont. Appl Environ Microbiol 2012; 78:7720–7732 [View Article][PubMed]
    [Google Scholar]
  36. Crost EH, Tailford LE, Le Gall G, Fons M, Henrissat B et al. Utilisation of mucin glycans by the human gut symbiont Ruminococcus gnavus is strain-dependent. PLoS One 2013; 8:e76341 [View Article][PubMed]
    [Google Scholar]
  37. Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 1970; 227:680–685 [View Article][PubMed]
    [Google Scholar]
  38. Lafond M, Tauzin A, Desseaux V, Bonnin E, Ajandouz E-H et al. GH10 xylanase D from Penicillium funiculosum: biochemical studies and xylooligosaccharide production. Microb Cell Fact 2011; 10:20 [View Article][PubMed]
    [Google Scholar]
  39. West DB, Boozer CN, Moody DL, Atkinson RL. Dietary obesity in nine inbred mouse strains. Am J Physiol 1992; 262:R1025–R1032 [View Article][PubMed]
    [Google Scholar]
  40. Graziani F, Pujol A, Nicoletti C, Dou S, Maresca M et al. Ruminococcus gnavus E1 modulates mucin expression and intestinal glycosylation. J Appl Microbiol 2016; 120:1403–1417 [View Article][PubMed]
    [Google Scholar]
  41. Rossmeisl M, Rim JS, Koza RA, Kozak LP. Variation in type 2 diabetes-related traits in mouse strains susceptible to diet-induced obesity. Diabetes 2003; 52:1958–1966 [View Article][PubMed]
    [Google Scholar]
  42. Rabot S, Membrez M, Bruneau A, Gérard P, Harach T et al. Germ-free C57BL/6J mice are resistant to high-fat-diet-induced insulin resistance and have altered cholesterol metabolism. Faseb J 2010; 24:4948–4959 [View Article][PubMed]
    [Google Scholar]
  43. Faith JJ, McNulty NP, Rey FE, Gordon JI. Predicting a human gut microbiota's response to diet in gnotobiotic mice. Science 2011; 333:101–104 [View Article][PubMed]
    [Google Scholar]
  44. Doré J, Sghir A, Hannequart-Gramet G, Corthier G, Pochart P. Design and evaluation of a 16S rRNA-targeted oligonucleotide probe for specific detection and quantitation of human faecal Bacteroides populations. Syst Appl Microbiol 1998; 21:65–71 [View Article][PubMed]
    [Google Scholar]
  45. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001; 25:402–408 [View Article][PubMed]
    [Google Scholar]
  46. Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ. The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 2015; 10:845–858 [View Article][PubMed]
    [Google Scholar]
  47. Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011; 8:785–786 [View Article][PubMed]
    [Google Scholar]
  48. Katoh K, Frith MC. Adding unaligned sequences into an existing alignment using MAFFT and LAST. Bioinformatics 2012; 28:3144–3146 [View Article][PubMed]
    [Google Scholar]
  49. Robert X, Gouet P. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res 2014; 42:W320–W324 [View Article][PubMed]
    [Google Scholar]
  50. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  51. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  52. Zuckerkandl E, Pauling L. Evolutionary divergence and convergence in proteins.. In Bryson V, Vogel HJ. (editors) Evolving Genes and Proteins New York: Academic Press; 1965 pp. 97–166
    [Google Scholar]
  53. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  54. Li J, Jia H, Cai X, Zhong H, Feng Q et al. An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol 2014; 32:834–841 [View Article][PubMed]
    [Google Scholar]
  55. Tasse L, Bercovici J, Pizzut-Serin S, Robe P, Tap J et al. Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res 2010; 20:1605–1612 [View Article][PubMed]
    [Google Scholar]
  56. Goedl C, Nidetzky B. Sucrose phosphorylase harbouring a redesigned, glycosyltransferase-like active site exhibits retaining glucosyl transfer in the absence of a covalent intermediate. Chembiochem 2009; 10:2333–2337 [View Article][PubMed]
    [Google Scholar]
  57. Terrapon N, Lombard V, Gilbert HJ, Henrissat B. Automatic prediction of polysaccharide utilization loci in Bacteroidetes species. Bioinformatics 2015; 31:647–655 [View Article][PubMed]
    [Google Scholar]
  58. Sheridan PO, Martin JC, Lawley TD, Browne HP, Harris HM et al. Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes. Microb Genom 2016; 2:e000043 [View Article][PubMed]
    [Google Scholar]
  59. Ferretti JJ, Huang TT, Russell RR. Sequence analysis of the glucosyltransferase A gene (gtfA) from Streptococcus mutans Ingbritt. Infect Immun 1988; 56:1585–1588[PubMed]
    [Google Scholar]
  60. Altermann E, Russell WM, Azcarate-Peril MA, Barrangou R, Buck BL et al. Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM. Proc Natl Acad Sci USA 2005; 102:3906–3912 [View Article][PubMed]
    [Google Scholar]
  61. Ojala T, Kuparinen V, Koskinen JP, Alatalo E, Holm L et al. Genome sequence of Lactobacillus crispatus ST1. J Bacteriol 2010; 192:3547–3548 [View Article][PubMed]
    [Google Scholar]
  62. Sun Z, Harris HM, McCann A, Guo C, Argimón S et al. Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera. Nat Commun 2015; 6:8322 [View Article][PubMed]
    [Google Scholar]
  63. Hao Y, Huang D, Guo H, Xiao M, An H et al. Complete genome sequence of Bifidobacterium longum subsp. longum BBMN68, a new strain from a healthy Chinese centenarian. J Bacteriol 2011; 193:787–788 [View Article][PubMed]
    [Google Scholar]
  64. Wildt S, Nordgaard I, Hansen U, Brockmann E, Rumessen JJ. A randomised double-blind placebo-controlled trial with Lactobacillus acidophilus La-5 and Bifidobacterium animalis subsp. lactis BB-12 for maintenance of remission in ulcerative colitis. J Crohns Colitis 2011; 5:115–121 [View Article][PubMed]
    [Google Scholar]
  65. Gerritsen J, Hornung B, Renckens B, van Hijum S, Martins dos Santos VAP et al. Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine. PeerJ 2017; 5:e3698 [View Article][PubMed]
    [Google Scholar]
  66. Murphy EA, Velazquez KT, Herbert KM. Influence of high-fat diet on gut microbiota: a driving force for chronic disease risk. Curr Opin Clin Nutr Metab Care 2015; 18:515–520 [View Article][PubMed]
    [Google Scholar]
  67. Daniel H, Gholami AM, Berry D, Desmarchelier C, Hahne H et al. High-fat diet alters gut microbiota physiology in mice. ISME J 2014; 8:295–308 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000253
Loading
/content/journal/mgen/10.1099/mgen.0.000253
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error