Browse dbCAN-PUL Entries
| PULID | Characterization Method(s) | Substrate | Organism | Publication | Publish Date | Type | Num Genes | Num CAZymes | CazyFamily |
|---|---|---|---|---|---|---|---|---|---|
| PUL0018 | rapid plate method growth assay, gene deletion mutant and growth assay, RT-PCR, enzyme activity assay | glycosaminoglycan | Streptococcus pneumoniae | 22311922 Streptococcus pneumoniae can utilize multiple sources of hyaluronic acid for growth. Infect Immun. 2012 Apr;80(4):1390-8. doi: 10.1128/IAI.05756-11. Epub 2012 Feb 6. |
2012 Apr | degradation | 13 | 3 | CBM70, PL8_1, GH88, PL12_1 |
| PUL0022 | RT-PCR, gene deletion mutant and growth assay, enzyme activity assay | cellobiose | Bacillus coagulans | 30519284 Simultaneous consumption of cellobiose and xylose by Bacillus coagulans to circumvent glucose repression and identification of its cellobiose-assimilating operons. Biotechnol Biofuels. 2018 Dec 1;11:320. doi: 10.1186/s13068-018-1323-5. eCollection 2018. |
2018 | degradation | 6 | 1 | GH1 |
| PUL0023 | RT-PCR, gene deletion mutant and growth assay, enzyme activity assay | cellobiose | Bacillus coagulans | 30519284 Simultaneous consumption of cellobiose and xylose by Bacillus coagulans to circumvent glucose repression and identification of its cellobiose-assimilating operons. Biotechnol Biofuels. 2018 Dec 1;11:320. doi: 10.1186/s13068-018-1323-5. eCollection 2018. |
2018 | degradation | 5 | 1 | GH1 |
| PUL0027 | Northern Blot, gene deletion mutant and growth assay | alginate | Azotobacter vinelandii | 10352233 Transcriptional organization of the Azotobacter vinelandii algGXLVIFA genes: characterization of algF mutants. Gene. 1999 May 31;232(2):217-22. doi: 10.1016/s0378-1119(99)00119-5. |
1999 May 31 | biosynthesis | 5 | 1 | PL5_1 |
| PUL0030 | isothermal calorimetric titration, gene deletion mutant and growth assay, enzyme activity assay | galactomannan | Bacillus sp. N16-5 | 26978267 A Novel Manno-Oligosaccharide Binding Protein Identified in Alkaliphilic Bacillus sp. N16-5 Is Involved in Mannan Utilization. Galactomannan Degrading Enzymes from the Mannan Utilization Gene Cluster of Alkaliphilic Bacillus sp. N16-5 and Their Synergy on Galactomannan Degradation. Transcriptional regulation of the mannan utilization genes in the alkaliphilic Bacillus sp. N16-5. PLoS One. 2016 Mar 15;11(3):e0150059. doi: 10.1371/journal.pone.0150059. eCollection 2016. J Agric Food Chem. 2018 Oct 24;66(42):11055-11063. doi: 10.1021/acs.jafc.8b03878. Epub 2018 Oct 15. FEMS Microbiol Lett. 2018 Feb 1;365(4). doi: 10.1093/femsle/fnx280. |
2016,2018 Oct 24,2018 Feb 1 | degradation | 12 | 6 | CE7, GH130_1, GH130_2, GH27 |
| PUL0151 | sequence homology analysis, Northern Blot, RT-qPCR, electrophoretic mobility shift assay, clone and expression, gene deletion mutant and growth assay | alginate | Zobellia galactanivorans | 30524390 Evolutionary Evidence of Algal Polysaccharide Degradation Acquisition by Pseudoalteromonas carrageenovora 9(T) to Adapt to Macroalgal Niches. Regulation of alginate catabolism involves a GntR family repressor in the marine flavobacterium Zobellia galactanivorans DsijT. Front Microbiol. 2018 Nov 22;9:2740. doi: 10.3389/fmicb.2018.02740. eCollection 2018. Nucleic Acids Res. 2020 Aug 20;48(14):7786-7800. doi: 10.1093/nar/gkaa533. |
2018,2020 Aug 20 | degradation | 12 | 2 | PL17_2, PL17, PL7 |
| PUL0161 | mass spectrometry, sequence homology analysis, gene deletion mutant and growth assay, microarray, qPCR | alpha-mannan | Bacteroides thetaiotaomicron | 30246424 Alpha- and beta-mannan utilization by marine Bacteroidetes. Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism. Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Environ Microbiol. 2018 Nov;20(11):4127-4140. doi: 10.1111/1462-2920.14414. Epub 2018 Oct 16. Nature. 2015 Jan 8;517(7533):165-169. doi: 10.1038/nature13995. Cell Host Microbe. 2008 Nov 13;4(5):447-57. doi: 10.1016/j.chom.2008.09.007. |
2018 Nov,2015 Jan 8,2008 Nov 13 | degradation | 26 | 6 | GH125, GH67, GH76, GH92, GH97 |
| PUL0168 | gene deletion mutant and growth assay | galactose | Lactococcus lactis subsp. lactis | 30099846 GlaR (YugA)-a novel RpiR-family transcription activator of the Leloir pathway of galactose utilization in Lactococcus lactis IL1403. Microbiologyopen. 2019 May;8(5):e00714. doi: 10.1002/mbo3.714. Epub 2018 Aug 11. |
2019 May | degradation | 9 | 1 | GH2 |
| PUL0186 | gene deletion mutant and growth assay | cellobiose | Streptococcus pneumoniae | 17028271 The two-component regulatory system TCS08 is involved in cellobiose metabolism of Streptococcus pneumoniae R6. J Bacteriol. 2007 Feb;189(4):1342-50. doi: 10.1128/JB.01170-06. Epub 2006 Oct 6. |
2007 Feb | degradation | 7 | 1 | GH1 |
| PUL0194 | enzyme activity assay, gene deletion mutant and growth assay | host glycan | Streptococcus pneumoniae | 28056108 Molecular Characterization of N-glycan Degradation and Transport in Streptococcus pneumoniae and Its Contribution to Virulence. PLoS Pathog. 2017 Jan 5;13(1):e1006090. doi: 10.1371/journal.ppat.1006090. eCollection 2017 Jan. |
2017 Jan | degradation | 6 | 5 | GH125, GH20, GH29, GH38, GH92 |
| PUL0197 | gene deletion mutant and growth assay | starch | Streptococcus mutans | 17233733 Overlapping substrate specificity for sucrose and maltose of two binding protein-dependent sugar uptake systems in Streptococcus mutans. FEMS Microbiol Lett. 2007 Jan;266(2):218-23. doi: 10.1111/j.1574-6968.2006.00522.x. |
2007 Jan | degradation | 7 | 2 | GH77, GT35 |
| PUL0209 | enzyme activity assay, gene deletion mutant and growth assay | galactan | Dickeya dadantii | 17644603 Characterization of the Erwinia chrysanthemi Gan locus, involved in galactan catabolism. J Bacteriol. 2007 Oct;189(19):7053-61. doi: 10.1128/JB.00845-07. Epub 2007 Jul 20. |
2007 Oct | degradation | 9 | 2 | GH42, GH53 |
| PUL0211 | enzyme activity assay, gene deletion mutant and growth assay, thin-layer chromatography | host glycan | Xanthomonas campestris pv. campestris | 25586188 The N-Glycan cluster from Xanthomonas campestris pv. campestris: a toolbox for sequential plant N-glycan processing. The plant pathogen Xanthomonas campestris pv. campestris exploits N-acetylglucosamine during infection. J Biol Chem. 2015 Mar 6;290(10):6022-36. doi: 10.1074/jbc.M114.624593. Epub 2015 Jan 13. mBio. 2014 Sep 9;5(5):e01527-14. doi: 10.1128/mBio.01527-14. |
2015 Mar 6,2014 Sep 9 | degradation | 9 | 8 | GH125, GH18, GH2, GH20, GH29, GH3, GH35, GH92 |
| PUL0244 | gene deletion mutant and growth assay, complementation study, carbohydrate binding assay | host glycan | Tannerella forsythia | 24351045 Structural and functional characterization of NanU, a novel high-affinity sialic acid-inducible binding protein of oral and gut-dwelling Bacteroidetes species. Biochem J. 2014 Mar 15;458(3):499-511. doi: 10.1042/BJ20131415. |
2014 Mar 15 | degradation | 9 | 3 | CBM93, GH33, CE20, GH20 |
| PUL0245 | enzyme activity assay, gene deletion mutant and growth assay, Western Blot | fucose | Streptococcus pneumoniae | 24333485 Structural and functional analysis of fucose-processing enzymes from Streptococcus pneumoniae. J Mol Biol. 2014 Apr 3;426(7):1469-82. doi: 10.1016/j.jmb.2013.12.006. Epub 2013 Dec 12. |
2014 Apr 3 | degradation | 11 | 2 | GH95, GH98, CBM47, CBM47, CBM47 |
| PUL0246 | enzyme activity assay, gene deletion mutant and growth assay, Western Blot | fucose | Streptococcus pneumoniae | 24333485 Structural and functional analysis of fucose-processing enzymes from Streptococcus pneumoniae. J Mol Biol. 2014 Apr 3;426(7):1469-82. doi: 10.1016/j.jmb.2013.12.006. Epub 2013 Dec 12. |
2014 Apr 3 | degradation | 11 | 4 | CBM51, CBM51, GH98, GH29, GH36 |
| PUL0265 | enzyme activity assay, gene deletion mutant and growth assay | starch | Staphylococcus xylosus | 7730272 Characterization of a genetic locus essential for maltose-maltotriose utilization in Staphylococcus xylosus. J Bacteriol. 1995 May;177(9):2408-15. doi: 10.1128/jb.177.9.2408-2415.1995. |
1995 May | degradation | 2 | 1 | GH13_31 |
| PUL0277 | gene deletion mutant and growth assay, qRT-PCR | fructan | Streptococcus pneumoniae | 23264576 The ABC transporter encoded at the pneumococcal fructooligosaccharide utilization locus determines the ability to utilize long- and short-chain fructooligosaccharides. J Bacteriol. 2013 Mar;195(5):1031-41. doi: 10.1128/JB.01560-12. Epub 2012 Dec 21. |
2013 Mar | degradation | 5 | 1 | GH32 |
| PUL0278 | gene deletion mutant and growth assay, qRT-PCR | fructan | Streptococcus pneumoniae | 23264576 The ABC transporter encoded at the pneumococcal fructooligosaccharide utilization locus determines the ability to utilize long- and short-chain fructooligosaccharides. J Bacteriol. 2013 Mar;195(5):1031-41. doi: 10.1128/JB.01560-12. Epub 2012 Dec 21. |
2013 Mar | degradation | 6 | 1 | GH32 |
| PUL0279 | gene deletion mutant and growth assay, qRT-PCR | fructan | Streptococcus pneumoniae | 23264576 The ABC transporter encoded at the pneumococcal fructooligosaccharide utilization locus determines the ability to utilize long- and short-chain fructooligosaccharides. J Bacteriol. 2013 Mar;195(5):1031-41. doi: 10.1128/JB.01560-12. Epub 2012 Dec 21. |
2013 Mar | degradation | 6 | 1 | GH32 |
| PUL0302 | RT-qPCR, isothermal titration calorimetry (ITC), enzyme activity assay, gene deletion mutant and growth assay, high-performance anion-exchange chromatography | arabinan | Bacteroides thetaiotaomicron | 29255254 Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides. Prioritization of a plant polysaccharide over a mucus carbohydrate is enforced by a Bacteroides hybrid two-component system. The structure and function of an arabinan-specific alpha-1,2-arabinofuranosidase identified from screening the activities of bacterial GH43 glycoside hydrolases. Nat Microbiol. 2018 Feb;3(2):210-219. doi: 10.1038/s41564-017-0079-1. Epub 2017 Dec 18. Mol Microbiol. 2012 Aug;85(3):478-91. doi: 10.1111/j.1365-2958.2012.08123.x. Epub 2012 Jul 5. J Biol Chem. 2011 Apr 29;286(17):15483-95. doi: 10.1074/jbc.M110.215962. Epub 2011 Feb 21. |
2018 Feb,2012 Aug,2011 Apr 29 | degradation | 22 | 6 | GH146, GH43_29, GH43_4, GH51_1, GH51_2 |
| PUL0304 | RT-qPCR, isothermal titration calorimetry (ITC), enzyme activity assay, gene deletion mutant and growth assay | galactan | Bacteroides thetaiotaomicron | 29255254 Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides. Nat Microbiol. 2018 Feb;3(2):210-219. doi: 10.1038/s41564-017-0079-1. Epub 2017 Dec 18. |
2018 Feb | degradation | 7 | 2 | GH2, GH53 |
| PUL0305 | RT-qPCR, isothermal titration calorimetry (ITC), enzyme activity assay, gene deletion mutant and growth assay | pectin | Bacteroides thetaiotaomicron | 29255254 Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides. Nat Microbiol. 2018 Feb;3(2):210-219. doi: 10.1038/s41564-017-0079-1. Epub 2017 Dec 18. |
2018 Feb | degradation | 17 | 7 | CE12, CE8, CE8, GH105, GH28, PL1_2 |
| PUL0306 | RT-qPCR, isothermal titration calorimetry (ITC), enzyme activity assay, gene deletion mutant and growth assay | pectin | Bacteroides ovatus | 29255254 Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides. Nat Microbiol. 2018 Feb;3(2):210-219. doi: 10.1038/s41564-017-0079-1. Epub 2017 Dec 18. |
2018 Feb | degradation | 7 | 3 | GH147, GH2, GH53 |
| PUL0313 | microarray, Northern Blot, RT-qPCR, electrophoretic mobility shift assay, clone and expression, gene deletion mutant and growth assay | alginate | Zobellia galactanivorans | 28983288 Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses. Regulation of alginate catabolism involves a GntR family repressor in the marine flavobacterium Zobellia galactanivorans DsijT. Front Microbiol. 2017 Sep 21;8:1808. doi: 10.3389/fmicb.2017.01808. eCollection 2017. Nucleic Acids Res. 2020 Aug 20;48(14):7786-7800. doi: 10.1093/nar/gkaa533. |
2017,2020 Aug 20 | degradation | 3 | 3 | PL6, PL6_1, PL7_5 |
| PUL0326 | gene deletion mutant and growth assay, enzyme activity assay, thin-layer chromatography | beta-glucan | Bacteroides ovatus | 28461332 A Bacteroidetes locus dedicated to fungal 1,6-beta-glucan degradation: Unique substrate conformation drives specificity of the key endo-1,6-beta-glucanase. J Biol Chem. 2017 Jun 23;292(25):10639-10650. doi: 10.1074/jbc.M117.787606. Epub 2017 May 1. |
2017 Jun 23 | degradation | 13 | 1 | GH73 |
| PUL0327 | microarray, gas chromatography, mass spectrometry, gene deletion mutant and growth assay, complementation study | starch | Enterococcus faecalis | 28455338 Enzymes Required for Maltodextrin Catabolism in Enterococcus faecalis Exhibit Novel Activities. Enterococcus faecalis Maltodextrin Gene Regulation by Combined Action of Maltose Gene Regulator MalR and Pleiotropic Regulator CcpA. Appl Environ Microbiol. 2017 Jun 16;83(13):e00038-17. doi: 10.1128/AEM.00038-17. Print 2017 Jul 1. Appl Environ Microbiol. 2020 Sep 1;86(18):e01147-20. doi: 10.1128/AEM.01147-20. Print 2020 Sep 1. |
2017 Jul 1,2020 Sep 1 | degradation | 6 | 2 | CBM34, GH13_20, GH13_31 |
| PUL0342 | enzyme activity assay, gene deletion mutant and growth assay | xylan | Prevotella ruminicola | 19304844 Biochemical analysis of a beta-D-xylosidase and a bifunctional xylanase-ferulic acid esterase from a xylanolytic gene cluster in Prevotella ruminicola 23. J Bacteriol. 2009 May;191(10):3328-38. doi: 10.1128/JB.01628-08. Epub 2009 Mar 20. |
2009 May | degradation | 5 | 3 | GH10, CE1, GH3, GH95 |
| PUL0343 | gene deletion mutant and growth assay, enzyme activity assay, Western Blot, isothermal titration calorimetry (ITC) | beta-glucan | uncultured bacterium | 28091525 A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic. Sci Rep. 2017 Jan 16;7:40248. doi: 10.1038/srep40248. |
2017 Jan 16 | degradation | 39 | 1 | GH5_2 |
| PUL0344 | gene deletion mutant and growth assay, protein structure characterization | chitin | Flavobacterium johnsoniae | 27933102 A polysaccharide utilization locus from Flavobacterium johnsoniae enables conversion of recalcitrant chitin. Structural insights of the enzymes from the chitin utilization locus of Flavobacterium johnsoniae. Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis. Biotechnol Biofuels. 2016 Nov 28;9:260. doi: 10.1186/s13068-016-0674-z. eCollection 2016. Sci Rep. 2020 Aug 13;10(1):13775. doi: 10.1038/s41598-020-70749-w. Appl Environ Microbiol. 2009 Nov;75(21):6864-75. doi: 10.1128/AEM.01495-09. Epub 2009 Aug 28. |
2016,2020 Aug 13,2009 Nov | degradation | 11 | 3 | GH18, GH18, GH18, GH20 |
| PUL0346 | gene deletion mutant and growth assay | xylan | uncultured bacterium | 24066026 Functional metagenomics reveals novel pathways of prebiotic breakdown by human gut bacteria. Functional characterization of a gene locus from an uncultured gut Bacteroides conferring xylo-oligosaccharides utilization to Escherichia coli. PLoS One. 2013 Sep 16;8(9):e72766. doi: 10.1371/journal.pone.0072766. eCollection 2013. Mol Microbiol. 2016 Nov;102(4):579-592. doi: 10.1111/mmi.13480. Epub 2016 Sep 14. |
2013,2016 Nov | degradation | 13 | 5 | GH10, GH16_3, GH43_1, GH43_12, CBM91, GH43_29 |
| PUL0347 | gene deletion mutant and growth assay, RT-PCR | starch | Bifidobacterium breve | 24581150 Comparative genomics of the Bifidobacterium breve taxon. BMC Genomics. 2014 Mar 1;15(1):170. doi: 10.1186/1471-2164-15-170. |
2014 Mar 1 | degradation | 13 | 1 | GH13_11 |
| PUL0381 | microarray, gene deletion mutant and growth assay | chitin | Vibrio cholerae | 14983042 The Vibrio cholerae chitin utilization program. Proc Natl Acad Sci U S A. 2004 Feb 24;101(8):2524-9. doi: 10.1073/pnas.0308707101. |
2004 Feb 24 | degradation | 6 | 2 | CE4, GH4 |
| PUL0387 | gene deletion mutant and growth assay, qRT-PCR, GlcNAc phosphorylation assays | glycosaminoglycan | Xanthomonas campestris pv. campestris | 20081036 Identification and regulation of the N-acetylglucosamine utilization pathway of the plant pathogenic bacterium Xanthomonas campestris pv. campestris. J Bacteriol. 2010 Mar;192(6):1487-97. doi: 10.1128/JB.01418-09. Epub 2010 Jan 15. |
2010 Mar | degradation | 7 | 1 | CE9 |
| PUL0396 | gene deletion mutant and growth assay | glycosaminoglycan | Cupriavidus necator | 21478317 Effects of homologous phosphoenolpyruvate-carbohydrate phosphotransferase system proteins on carbohydrate uptake and poly(3-Hydroxybutyrate) accumulation in Ralstonia eutropha H16. Appl Environ Microbiol. 2011 Jun;77(11):3582-90. doi: 10.1128/AEM.00218-11. Epub 2011 Apr 8. |
2011 Jun | degradation | 7 | 1 | CE9 |
| PUL0397 | gene deletion mutant and growth assay | glycosaminoglycan | Capnocytophaga canimorsus | 21762219 The genome and surface proteome of Capnocytophaga canimorsus reveal a key role of glycan foraging systems in host glycoproteins deglycosylation. Mol Microbiol. 2011 Aug;81(4):1050-60. doi: 10.1111/j.1365-2958.2011.07750.x. Epub 2011 Jul 18. |
2011 Aug | degradation | 5 | 1 | GH18 |
| PUL0398 | gene deletion mutant and growth assay | mucin | Capnocytophaga canimorsus | 21762219 The genome and surface proteome of Capnocytophaga canimorsus reveal a key role of glycan foraging systems in host glycoproteins deglycosylation. Glycan-foraging systems reveal the adaptation of Capnocytophaga canimorsus to the dog mouth. Mol Microbiol. 2011 Aug;81(4):1050-60. doi: 10.1111/j.1365-2958.2011.07750.x. Epub 2011 Jul 18. mBio. 2015 Mar 3;6(2):e02507. doi: 10.1128/mBio.02507-14. |
2011 Aug,2015 Mar 3 | degradation | 9 | 3 | CBM32, GH2 |
| PUL0475 | clone and expression, gene deletion mutant and growth assay | beta-glucan | Streptomyces reticuli | 10347054 Characterization of the binding protein-dependent cellobiose and cellotriose transport system of the cellulose degrader Streptomyces reticuli. Appl Environ Microbiol. 1999 Jun;65(6):2636-43. doi: 10.1128/AEM.65.6.2636-2643.1999. |
1999 Jun | degradation | 7 | 2 | CBM2, GH18, GH1 |
| PUL0519 | gene deletion mutant and growth assay | starch | Streptococcus pneumoniae | 8244973 Characterization of the Streptococcus pneumoniae maltosaccharide regulator MalR, a member of the LacI-GalR family of repressors displaying distinctive genetic features. J Biol Chem. 1993 Dec 5;268(34):25402-8. |
1993 Dec 5 | degradation | 7 | 2 | GH77, GT35 |
| PUL0555 | gene deletion mutant and growth assay, qRT-PCR, microarray, enzyme activity assay | host glycan | Bacteroides fragilis | 25139987 Efficient utilization of complex N-linked glycans is a selective advantage for Bacteroides fragilis in extraintestinal infections. Proc Natl Acad Sci U S A. 2014 Sep 2;111(35):12901-6. doi: 10.1073/pnas.1407344111. Epub 2014 Aug 19. |
2014 Sep 2 | degradation | 9 | 5 | GH154, GH2, GH20, GH88, PL33_1 |
| PUL0556 | gene deletion mutant and growth assay, qRT-PCR, microarray, enzyme activity assay | host glycan | Bacteroides fragilis | 25139987 Efficient utilization of complex N-linked glycans is a selective advantage for Bacteroides fragilis in extraintestinal infections. Proc Natl Acad Sci U S A. 2014 Sep 2;111(35):12901-6. doi: 10.1073/pnas.1407344111. Epub 2014 Aug 19. |
2014 Sep 2 | degradation | 8 | 2 | GH18, GH97 |
| PUL0558 | gene deletion mutant and growth assay, growth assay, enzyme activity assay | pectin | Bacteroides thetaiotaomicron | 28329766 Complex pectin metabolism by gut bacteria reveals novel catalytic functions. Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. Nature. 2017 Apr 6;544(7648):65-70. doi: 10.1038/nature21725. Epub 2017 Mar 22. PLoS Biol. 2011 Dec;9(12):e1001221. doi: 10.1371/journal.pbio.1001221. Epub 2011 Dec 20. |
2017 Apr 6,2011 Dec | degradation | 50 | 21 | CBM67, GH78, CBM67, GH78, GH33, CE19, CE20, GH105, GH106, GH127, GH137, GH2, CBM57, CBM97, GH138, GH139, GH140, GH141, GH143, GH142, GH2, GH28, GH43_18, GH78, GH95, PL1_2 |
| PUL0559 | gene deletion mutant and growth assay, growth assay, enzyme activity assay, microarray, qPCR | pectin | Bacteroides thetaiotaomicron | 28329766 Complex pectin metabolism by gut bacteria reveals novel catalytic functions. Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period. Nature. 2017 Apr 6;544(7648):65-70. doi: 10.1038/nature21725. Epub 2017 Mar 22. Cell Host Microbe. 2008 Nov 13;4(5):447-57. doi: 10.1016/j.chom.2008.09.007. PLoS Biol. 2011 Dec;9(12):e1001221. doi: 10.1371/journal.pbio.1001221. Epub 2011 Dec 20. J Biol Chem. 2006 Nov 24;281(47):36269-79. doi: 10.1074/jbc.M606509200. Epub 2006 Sep 12. |
2017 Apr 6,2008 Nov 13,2011 Dec,2006 Nov 24 | degradation | 12 | 4 | GH29, GH43_10, CBM91, GH43_34, CBM32, GH97 |
| PUL0575 | microarray, growth assay, gene deletion mutant and growth assay | raffinose | Enterococcus faecium | 20946531 A genetic element present on megaplasmids allows Enterococcus faecium to use raffinose as carbon source. Environ Microbiol. 2011 Feb;13(2):518-28. doi: 10.1111/j.1462-2920.2010.02355.x. Epub 2010 Oct 15. |
2011 Feb | degradation | 11 | 4 | GH13_18, GH13_31, GH36, GH4 |
| PUL0582 | NMR, microarray, enzyme activity assay, gene deletion mutant and growth assay | human milk oligosaccharide | Lactococcus lactis | 22660716 A specific mutation in the promoter region of the silent cel cluster accounts for the appearance of lactose-utilizing Lactococcus lactis MG1363. Appl Environ Microbiol. 2012 Aug;78(16):5612-21. doi: 10.1128/AEM.00455-12. Epub 2012 Jun 1. |
2012 Aug | degradation | 5 | 2 | GH1, GH170 |
| PUL0583 | enzyme activity assay, gene deletion mutant and growth assay | cellobiose | Geobacillus stearothermophilus | 8407820 Cloning and sequencing of a cellobiose phosphotransferase system operon from Bacillus stearothermophilus XL-65-6 and functional expression in Escherichia coli. J Bacteriol. 1993 Oct;175(20):6441-50. doi: 10.1128/jb.175.20.6441-6450.1993. |
1993 Oct | degradation | 5 | 0 | NA |
| PUL0585 | microarray, gene deletion mutant and growth assay, beta-galactosidase assays | cellobiose | Streptococcus pneumoniae | 21778207 CelR-mediated activation of the cellobiose-utilization gene cluster in Streptococcus pneumoniae. Microbiology (Reading). 2011 Oct;157(Pt 10):2854-2861. doi: 10.1099/mic.0.051359-0. Epub 2011 Jul 21. |
2011 Oct | degradation | 7 | 1 | GH1 |
| PUL0590 | qRT-PCR, gene deletion mutant and growth assay, microarray | starch | Enterococcus faecium | 23951303 A LacI-family regulator activates maltodextrin metabolism of Enterococcus faecium. PLoS One. 2013 Aug 7;8(8):e72285. doi: 10.1371/journal.pone.0072285. eCollection 2013. |
2013 | degradation | 5 | 1 | CBM34, GH13_20 |
| PUL0605 | RT-PCR, gene deletion mutant and growth assay | glycogen | Escherichia coli | 33101261 Glycogen Metabolism Impairment via Single Gene Mutation in the glgBXCAP Operon Alters the Survival Rate of Escherichia coli Under Various Environmental Stresses. Escherichia coli glycogen genes are organized in a single glgBXCAP transcriptional unit possessing an alternative suboperonic promoter within glgC that directs glgAP expression. Front Microbiol. 2020 Sep 25;11:588099. doi: 10.3389/fmicb.2020.588099. eCollection 2020. Biochem J. 2011 Jan 1;433(1):107-17. doi: 10.1042/BJ20101186. |
2020,2011 Jan 1 | biosynthesis | 5 | 4 | CBM48, GH13_11, CBM48, GH13_9, GT35, GT5 |
| PUL0650 | enzyme activity assay, high-performance anion-exchange chromatography, recombinant protein expression, NMR, gene deletion mutant and growth assay | arabinogalactan | Bifidobacterium longum JCM 7052 | 33674431 Novel 3-O-alpha-d-Galactosyl-alpha-l-Arabinofuranosidase for the Assimilation of Gum Arabic Arabinogalactan Protein in Bifidobacterium longum subsp. longum. Appl Environ Microbiol. 2021 Apr 27;87(10):e02690-20. doi: 10.1128/AEM.02690-20. Print 2021 Apr 27. |
2021 Apr 27 | degradation | 7 | 2 | GH36, GH39, CBM35 |
| PUL0653 | gene deletion mutant and growth assay, complementation study, enzyme activity assay, RNA-seq, electrophoretic mobility shift assay | agarose | Streptomyces coelicolor A3(2) | 33889146 LacI-Family Transcriptional Regulator DagR Acts as a Repressor of the Agarolytic Pathway Genes in Streptomyces coelicolor A3(2). Front Microbiol. 2021 Apr 6;12:658657. doi: 10.3389/fmicb.2021.658657. eCollection 2021. |
2021 | degradation | 17 | 4 | GH117, GH117, GH16_16, GH2, GH50 |
| PUL0671 | gene deletion mutant and growth assay, enzyme activity assay, Western Blot, qPCR | cellulose | Cytophaga hutchinsonii ATCC 33406 | 34731049 A Type IX Secretion System Substrate Involved in Crystalline Cellulose Degradation by Affecting Crucial Cellulose Binding Proteins in Cytophaga hutchinsonii. Appl Environ Microbiol. 2022 Jan 25;88(2):e0183721. doi: 10.1128/AEM.01837-21. Epub 2021 Nov 3. |
2022 Jan 25 | degradation | 6 | 0 | NA |
| PUL0680 | gene deletion mutant and growth assay, clone and expression, qRT-PCR, high-performance anion-exchange chromatography, crystallization, recombinant protein expression | xyloglucan | Bacteroides uniformis ATCC 8492 | 34995484 Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions. Cell Surface Xyloglucan Recognition and Hydrolysis by the Human Gut Commensal Bacteroides uniformis. Cell Host Microbe. 2022 Feb 9;30(2):200-215.e12. doi: 10.1016/j.chom.2021.12.006. Epub 2022 Jan 6. Appl Environ Microbiol. 2022 Jan 11;88(1):e0156621. doi: 10.1128/AEM.01566-21. Epub 2021 Nov 3. |
2022 Feb 9,2022 Jan 11 | degradation | 15 | 10 | CE20, GH43_16, CBM6, GH2, GH29, GH2, GH2, GH31_4, GH42, GH43_33, GH5_4, GH97 |
| PUL0690 | electrophoretic mobility shift assay, qRT-PCR, gene deletion mutant and growth assay | raffinose family oligosaccharides | Bacteroides thetaiotaomicron VPI-5482 | 34251866 A Novel Family of RNA-Binding Proteins Regulate Polysaccharide Metabolism in Bacteroides thetaiotaomicron. Dynamic genetic adaptation of Bacteroides thetaiotaomicron during murine gut colonization. Determinants of raffinose family oligosaccharide use in Bacteroides species. J Bacteriol. 2021 Oct 12;203(21):e0021721. doi: 10.1128/JB.00217-21. Epub 2021 Jul 12. Cell Rep. 2023 Aug 29;42(8):113009. doi: 10.1016/j.celrep.2023.113009. Epub 2023 Aug 21. J Bacteriol. 2024 Oct 24;206(10):e0023524. doi: 10.1128/jb.00235-24. Epub 2024 Sep 27. |
2021 Oct 12,2023 Aug 29,2024 Oct 24 | degradation | 8 | 4 | GH3, GH43_17, GH92, GH97 |
| PUL0702 | enzyme activity assay, gene deletion mutant and growth assay | xyloglucan | Xanthomonas citri pv. citri str. 306 | 34193873 Xyloglucan processing machinery in Xanthomonas pathogens and its role in the transcriptional activation of virulence factors. Nat Commun. 2021 Jun 30;12(1):4049. doi: 10.1038/s41467-021-24277-4. |
2021 Jun 30 | degradation | 8 | 5 | CE20, CE20, GH31_4, GH35, GH74, GH95 |
| PUL0721 | RNA-seq, RT-qPCR, gene deletion mutant and growth assay | human milk oligosaccharide | Phocaeicola dorei strain DSM 17855 | 38167825 CRISPR-Cas-based identification of a sialylated human milk oligosaccharides utilization cluster in the infant gut commensal Bacteroides dorei. Nat Commun. 2024 Jan 2;15(1):105. doi: 10.1038/s41467-023-44437-y. |
2024 Jan 2 | degradation | 13 | 9 | CBM93, GH33, CE3, CE20, CE9, GH2, GH20, GH92 |
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