| PULID | Characterization Method(s) | Substrate | Organism | Publication | Publish Date | Type | Num Genes | Num CAZymes | CazyFamily |
|---|---|---|---|---|---|---|---|---|---|
| PUL0002 | enzyme activity assay, Northern Blot | lichenan | Bacillus subtilis | 8606172 LicT, a Bacillus subtilis transcriptional antiterminator protein of the BglG family. J Bacteriol. 1996 Apr;178(7):1971-9. doi: 10.1128/jb.178.7.1971-1979.1996. |
1996 Apr | degradation | 2 | 1 | GH16 |
| PUL0003 | RT-PCR | xylan | Bacillus subtilis | 26559526 Metabolic potential of Bacillus subtilis 168 for the direct conversion of xylans to fermentation products. Appl Microbiol Biotechnol. 2016 Feb;100(3):1501-1510. doi: 10.1007/s00253-015-7124-x. Epub 2015 Nov 12. |
2016 Feb | degradation | 2 | 2 | GH30, GH30_8, GH43_16, CBM6 |
| PUL0013 | Northern Blot, RT-PCR, isothermal titration calorimetry, electrophoretic mobility shift assay | arabinan | Geobacillus stearothermophilus | 21460081 The L-Arabinan utilization system of Geobacillus stearothermophilus. J Bacteriol. 2011 Jun;193(11):2838-50. doi: 10.1128/JB.00222-11. Epub 2011 Apr 1. |
2011 Jun | degradation | 56 | 11 | GH43_5, GH43, GH43, GH43_4, GH51, GH51, GH127, CE4, GH52, GH10, GH67, GH39, GH43_11 |
| PUL0017 | qRT-PCR, Western Blot, isothermal titration calorimetry | cellobiose | Ruminiclostridium cellulolyticum | 29093754 A seven-gene cluster in Ruminiclostridium cellulolyticum is essential for signalization, uptake and catabolism of the degradation products of cellulose hydrolysis. Biotechnol Biofuels. 2017 Oct 30;10:250. doi: 10.1186/s13068-017-0933-7. eCollection 2017. |
2017 | degradation | 9 | 1 | GH94 |
| 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 | 12 | 3 | CBM70, PL8_1, PL8, GH88, PL12_1 |
| PUL0019 | enzyme activity assay, Northern Blot | lichenan, cellobiose, beta-glucoside | Bacillus subtilis | 8990303 Identification and characterization of a new beta-glucoside utilization system in Bacillus subtilis. J Bacteriol. 1997 Jan;179(2):496-506. doi: 10.1128/jb.179.2.496-506.1997. |
1997 Jan | degradation | 6 | 1 | GH4 |
| 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 |
| PUL0033 | RT-PCR, yeast two hybrid assay, Southern Blot | trehalose | Spiroplasma citri | 12949193 Glucose and trehalose PTS permeases of Spiroplasma citri probably share a single IIA domain, enabling the spiroplasma to adapt quickly to carbohydrate changes in its environment. Microbiology (Reading). 2003 Sep;149(Pt 9):2687-2696. doi: 10.1099/mic.0.26336-0. |
2003 Sep | degradation | 6 | 1 | GH13_29, GH13 |
| PUL0040 | Northern Blot, enzyme activity assay | cellulose | Ruminiclostridium cellulolyticum | 12896991, 1398087, 11844767 A rhamnogalacturonan lyase in the Clostridium cellulolyticum cellulosome. Sequence analysis of a gene cluster encoding cellulases from Clostridium cellulolyticum. Cel9M, a new family 9 cellulase of the Clostridium cellulolyticum cellulosome. J Bacteriol. 2003 Aug;185(16):4727-33. doi: 10.1128/JB.185.16.4727-4733.2003. Gene. 1992 Sep 21;119(1):17-28. doi: 10.1016/0378-1119(92)90062-t. J Bacteriol. 2002 Mar;184(5):1378-84. doi: 10.1128/JB.184.5.1378-1384.2002. |
2003 Aug,1992 Sep 21,2002 Mar | degradation | 6 | 6 | GH9, CBM3, GH9, CBM3, GH5_17, GH9, PL11_1, PL11, GH5_1, GH5 |
| PUL0042 | RT-PCR | sucrose | Caulobacter vibrioides | 30054816 SucA-dependent uptake of sucrose across the outer membrane of Caulobacter crescentus. J Microbiol. 2018 Sep;56(9):648-655. doi: 10.1007/s12275-018-8225-x. Epub 2018 Jul 27. |
2018 Sep | degradation | 4 | 1 | GH13_4 |
| PUL0063 | bicinchoninic acid (BCA) reducing-sugar assay, enzymatic product analysis, affinity gel electrophoresis, isothermal titration calorimetry | xyloglucan | Bacteroides ovatus | 31420336 Adaptation of Syntenic Xyloglucan Utilization Loci of Human Gut Bacteroidetes to Polysaccharide Side Chain Diversity. Appl Environ Microbiol. 2019 Oct 1;85(20):e01491-19. doi: 10.1128/AEM.01491-19. Print 2019 Oct 15. |
2019 Oct 15 | degradation | 16 | 8 | GH3, GH2, GH31, GH9, GH5_4, GH43, GH43_12, GH43_12, GH3 |
| PUL0064 | bicinchoninic acid (BCA) reducing-sugar assay, enzymatic product analysis, affinity gel electrophoresis, isothermal titration calorimetry | xyloglucan | Bacteroides cellulosilyticus | 31420336 Adaptation of Syntenic Xyloglucan Utilization Loci of Human Gut Bacteroidetes to Polysaccharide Side Chain Diversity. Appl Environ Microbiol. 2019 Oct 1;85(20):e01491-19. doi: 10.1128/AEM.01491-19. Print 2019 Oct 15. |
2019 Oct 15 | degradation | 12 | 4 | GH5, GH5_4, GH31, GH2, GH3 |
| PUL0065 | bicinchoninic acid (BCA) reducing-sugar assay, enzymatic product analysis, affinity gel electrophoresis, isothermal titration calorimetry | xyloglucan | Bacteroides uniformis | 31420336 Adaptation of Syntenic Xyloglucan Utilization Loci of Human Gut Bacteroidetes to Polysaccharide Side Chain Diversity. Appl Environ Microbiol. 2019 Oct 1;85(20):e01491-19. doi: 10.1128/AEM.01491-19. Print 2019 Oct 15. |
2019 Oct 15 | degradation | 13 | 6 | GH43_12, GH43, GH5_4, GH5, GH31, GH2, GH3, GH95 |
| PUL0066 | bicinchoninic acid (BCA) reducing-sugar assay, enzymatic product analysis, affinity gel electrophoresis, isothermal titration calorimetry | xyloglucan | Bacteroides fluxus | 31420336 Adaptation of Syntenic Xyloglucan Utilization Loci of Human Gut Bacteroidetes to Polysaccharide Side Chain Diversity. Appl Environ Microbiol. 2019 Oct 1;85(20):e01491-19. doi: 10.1128/AEM.01491-19. Print 2019 Oct 15. |
2019 Oct 15 | degradation | 13 | 6 | GH43_12, GH43, GH5, GH5_4, GH31, GH2, GH3, GH95 |
| PUL0067 | bicinchoninic acid (BCA) reducing-sugar assay, enzymatic product analysis, affinity gel electrophoresis, isothermal titration calorimetry | xyloglucan | Dysgonomonas gadei | 31420336 Adaptation of Syntenic Xyloglucan Utilization Loci of Human Gut Bacteroidetes to Polysaccharide Side Chain Diversity. Appl Environ Microbiol. 2019 Oct 1;85(20):e01491-19. doi: 10.1128/AEM.01491-19. Print 2019 Oct 15. |
2019 Oct 15 | degradation | 11 | 6 | GH2, GH5_4, GH5, GH31, GH95, GH3, GH43_12 |
| PUL0068 | enzyme activity assay, electrophoretic mobility shift assay | raffinose | Escherichia coli | 8277949 Role of two operators in regulating the plasmid-borne raf operon of Escherichia coli. Mol Gen Genet. 1994 Jan;242(1):90-9. doi: 10.1007/BF00277352. |
1994 Jan | degradation | 4 | 2 | GH36, GH32 |
| PUL0082 | electrophoretic mobility shift assay, enzyme activity assay | melibiose, raffinose-oligosaccharide, stachyose | Bacillus subtilis | 31138628 The melREDCA Operon Encodes a Utilization System for the Raffinose Family of Oligosaccharides in Bacillus subtilis. J Bacteriol. 2019 Jul 10;201(15):e00109-19. doi: 10.1128/JB.00109-19. Print 2019 Aug 1. |
2019 Aug 1 | degradation | 6 | 2 | GH4 |
| PUL0111 | enzyme activity assay, Northern Blot, transport assay | melibiose | Escherichia coli | 9642246 Conversion of temperature-sensitive to -resistant gene expression due to mutations in the promoter region of the melibiose operon in Escherichia coli. J Biol Chem. 1998 Jul 3;273(27):16860-4. doi: 10.1074/jbc.273.27.16860. |
1998 Jul 3 | degradation | 3 | 1 | GH4 |
| PUL0118 | qRT-PCR, affinity gel electrophoresis, isothermal titration calorimetry | laminarin, beta-glucan | Bacteroides uniformis | 32265336 Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human Gut Bacteroides. mBio. 2020 Apr 7;11(2):e00095-20. doi: 10.1128/mBio.00095-20. |
2020 Apr 7 | degradation | 7 | 3 | CBM6, GH3, GH158, GH16 |
| PUL0128 | RT-PCR, enzyme activity assay | hemicellulose | Bifidobacterium longum subsp. longum JCM 1217 | 30635377 Two Novel alpha-l-Arabinofuranosidases from Bifidobacterium longum subsp. longum Belonging to Glycoside Hydrolase Family 43 Cooperatively Degrade Arabinan. Appl Environ Microbiol. 2019 Mar 6;85(6):e02582-18. doi: 10.1128/AEM.02582-18. Print 2019 Mar 15. |
2019 Mar 15 | degradation | 24 | 8 | GH43, GH43_24, GH30_5, GH30, CBM13, GH146, GH43, GH43_34, GH43_22, GH43, GH43_22, GH43_26, GH43_27, GH43, GH43_22, GH43_22 |
| 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, 32585009 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 | PL7, PL17_2, PL17 |
| PUL0166 | enzyme activity assay, RT-PCR | starch | Bacteroides fragilis | 16788175 Characterization of the primary starch utilization operon in the obligate anaerobe Bacteroides fragilis: Regulation by carbon source and oxygen. J Bacteriol. 2006 Jul;188(13):4663-72. doi: 10.1128/JB.00125-06. |
2006 Jul | degradation | 5 | 1 | GH13_10, GH13 |
| PUL0174 | RT-PCR, enzyme activity assay, enzymatic product analysis | starch | Kribbella flavida | 27302067 Two Novel Glycoside Hydrolases Responsible for the Catabolism of Cyclobis-(1-->6)-alpha-nigerosyl. J Biol Chem. 2016 Aug 5;291(32):16438-47. doi: 10.1074/jbc.M116.727305. Epub 2016 Jun 14. |
2016 Aug 5 | degradation | 3 | 2 | CBM20, GH31, CBM35, GH31 |
| PUL0176 | RT-PCR, enzyme activity assay, enzymatic product analysis | isomaltose | Kribbella flavida | 27302067 Two Novel Glycoside Hydrolases Responsible for the Catabolism of Cyclobis-(1-->6)-alpha-nigerosyl. J Biol Chem. 2016 Aug 5;291(32):16438-47. doi: 10.1074/jbc.M116.727305. Epub 2016 Jun 14. |
2016 Aug 5 | degradation | 6 | 2 | GH31, GH15 |
| PUL0189 | RNA-Seq, RT-PCR, qPCR | pectin | Bacteroides xylanisolvens | 26920945 Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis. BMC Genomics. 2016 Feb 27;17:147. doi: 10.1186/s12864-016-2472-1. |
2016 Feb 27 | degradation | 17 | 7 | GH95, GH140, CBM67, GH78, GH33, GH28, GH78, CBM67, GH43_18, GH43, PL1, CE8, PL1_2, GH92 |
| PUL0190 | RNA-Seq, RT-PCR, qPCR | pectin | Bacteroides xylanisolvens | 26920945 Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis. BMC Genomics. 2016 Feb 27;17:147. doi: 10.1186/s12864-016-2472-1. |
2016 Feb 27 | degradation | 15 | 5 | GH51, GH146, GH43, GH43_4, GH43_4, GH51, GH43_29 |
| PUL0191 | RNA-Seq, RT-PCR, qPCR | pectin | Bacteroides xylanisolvens | 26920945 Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis. BMC Genomics. 2016 Feb 27;17:147. doi: 10.1186/s12864-016-2472-1. |
2016 Feb 27 | degradation | 11 | 5 | GH105, CE8, CE8, CE12, CE4, PL1_2, PL1_2 |
| PUL0192 | RNA-Seq, RT-PCR, qPCR | pectin | Bacteroides xylanisolvens | 26920945 Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis. BMC Genomics. 2016 Feb 27;17:147. doi: 10.1186/s12864-016-2472-1. |
2016 Feb 27 | degradation | 27 | 12 | GH106, GH28, GH28, CE12, GH2, GH43_18, GH43_34, GH43, CBM32, GH42, GH28, PL11, PL11_1, PL26, CE12, GH105, PL11_1, GH105 |
| PUL0193 | RNA-Seq, RT-PCR, qPCR | pectin | Bacteroides xylanisolvens | 26920945 Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis. BMC Genomics. 2016 Feb 27;17:147. doi: 10.1186/s12864-016-2472-1. |
2016 Feb 27 | degradation | 30 | 10 | GH2, PL11_1, PL11, GH28, GH117, PL11_1, PL11, GH28, GH105, GH28 |
| PUL0195 | RT-PCR | cellobiose | Clostridium acetobutylicum | 26691835 PTS regulation domain-containing transcriptional activator CelR and sigma factor sigma(54) control cellobiose utilization in Clostridium acetobutylicum. Mol Microbiol. 2016 Apr;100(2):289-302. doi: 10.1111/mmi.13316. Epub 2016 Feb 9. |
2016 Apr | degradation | 5 | 1 | GH1 |
| PUL0216 | Western Blot, enzyme activity assay, RT-PCR, microarray | alginate | Sphingomonas sp. | 24816607 Alginate-dependent gene expression mechanism in Sphingomonas sp. strain A1. J Bacteriol. 2014 Jul;196(14):2691-700. doi: 10.1128/JB.01666-14. Epub 2014 May 9. |
2014 Jul | degradation | 10 | 1 | PL7, PL5, PL15_1 |
| PUL0224 | RT-PCR, qRT-PCR | cellulose | Ruminiclostridium cellulolyticum | 23418511 A two-component system (XydS/R) controls the expression of genes encoding CBM6-containing proteins in response to straw in Clostridium cellulolyticum. PLoS One. 2013;8(2):e56063. doi: 10.1371/journal.pone.0056063. Epub 2013 Feb 13. |
2013 | degradation | 16 | 14 | GH43_16, GH43, CBM6, GH10, CBM6, GH43, GH43_29, CBM6, CBM6, CE1, GH43_10, CBM6, GH62, CBM6, GH43, GH43_29, CBM6, GH146, CBM22, GH27, CBM6, GH59, CBM6, GH2, CBM6, GH62, CBM6, CE6, CBM32, GH95, CBM6, GH30_8, CBM6 |
| PUL0225 | RT-PCR | porphyran | Bacteroides plebeius | 23150581 Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes. Proc Natl Acad Sci U S A. 2012 Nov 27;109(48):19786-91. doi: 10.1073/pnas.1211002109. Epub 2012 Nov 12. |
2012 Nov 27 | degradation | 36 | 12 | GH16, GH117, GH2, GH2, GH50, GH154, GH105, GH16, GH86, GH86, GH29, GH16, GH2 |
| PUL0229 | RT-PCR | aldouronate | Paenibacillus sp. JDR-2 | 17921311 Structure, function, and regulation of the aldouronate utilization gene cluster from Paenibacillus sp. strain JDR-2. J Bacteriol. 2007 Dec;189(24):8863-70. doi: 10.1128/JB.01141-07. Epub 2007 Oct 5. |
2007 Dec | degradation | 8 | 3 | GH67, CBM22, GH10, GH43_12, GH43 |
| PUL0230 | RT-PCR, enzyme activity assay, clone, enzyme kinetic analysis, thin layer chromatography, crystallization | maltooligosaccharide | Lactobacillus acidophilus | 22685275, 32444471 Enzymology and structure of the GH13_31 glucan 1,6-alpha-glucosidase that confers isomaltooligosaccharide utilization in the probiotic Lactobacillus acidophilus NCFM. An 1,4-alpha-Glucosyltransferase Defines a New Maltodextrin Catabolism Scheme in Lactobacillus acidophilus. J Bacteriol. 2012 Aug;194(16):4249-59. doi: 10.1128/JB.00622-12. Epub 2012 Jun 8. Appl Environ Microbiol. 2020 Jul 20;86(15):e00661-20. doi: 10.1128/AEM.00661-20. Print 2020 Jul 20. |
2012 Aug,2020 Jul 20 | degradation | 12 | 4 | GH65, CBM34, GH13, GH13_20 |
| PUL0232 | microarray, electrophoretic mobility shift assay | raffinose | Bifidobacterium breve | 24705323 Transcription of two adjacent carbohydrate utilization gene clusters in Bifidobacterium breve UCC2003 is controlled by LacI- and repressor open reading frame kinase (ROK)-type regulators. Appl Environ Microbiol. 2014 Jun;80(12):3604-14. doi: 10.1128/AEM.00130-14. |
2014 Jun | degradation | 6 | 1 | GH36 |
| PUL0233 | microarray, electrophoretic mobility shift assay | melezitose | Bifidobacterium breve | 24705323 Transcription of two adjacent carbohydrate utilization gene clusters in Bifidobacterium breve UCC2003 is controlled by LacI- and repressor open reading frame kinase (ROK)-type regulators. Appl Environ Microbiol. 2014 Jun;80(12):3604-14. doi: 10.1128/AEM.00130-14. |
2014 Jun | degradation | 5 | 2 | GH36 |
| PUL0238 | Northern Blot | glucomannan | Bacillus subtilis | 18177310 Glucomannan utilization operon of Bacillus subtilis. FEMS Microbiol Lett. 2008 Feb;279(1):103-9. doi: 10.1111/j.1574-6968.2007.01018.x. |
2008 Feb | degradation | 8 | 1 | GH26 |
| PUL0268 | Northern Blot, promoter assay | starch | Geobacillus kaustophilus | 23793634 Polysaccharide-degrading thermophiles generated by heterologous gene expression in Geobacillus kaustophilus HTA426. Appl Environ Microbiol. 2013 Sep;79(17):5151-8. doi: 10.1128/AEM.01506-13. Epub 2013 Jun 21. |
2013 Sep | degradation | 5 | 1 | GH13_1, GH13 |
| PUL0269 | RT-PCR | chitin | Haloferax mediterranei | 23674154 Characterization of genes for chitin catabolism in Haloferax mediterranei. Appl Microbiol Biotechnol. 2014 Feb;98(3):1185-94. doi: 10.1007/s00253-013-4969-8. Epub 2013 May 15. |
2014 Feb | degradation | 16 | 4 | GH3, CBM5, CBM5, GH18, CBM5, GH18 |
| PUL0287 | RT-PCR | unknown polysaccharide | Streptococcus pneumoniae | 23082033 Characterization of the ROK-family transcriptional regulator RokA of Streptococcus pneumoniae D39. Microbiology (Reading). 2012 Dec;158(Pt 12):2917-2926. doi: 10.1099/mic.0.062919-0. Epub 2012 Oct 18. |
2012 Dec | degradation | 6 | 1 | GH1 |
| PUL0291 | electrophoretic mobility shift assay, qPCR | lactose | Escherichia coli | 29453395 The genes of the sulphoquinovose catabolism in Escherichia coli are also associated with a previously unknown pathway of lactose degradation. Sci Rep. 2018 Feb 16;8(1):3177. doi: 10.1038/s41598-018-21534-3. |
2018 Feb 16 | degradation | 10 | 1 | GH31 |
| PUL0302 | RT-qPCR, isothermal titration calorimetry, enzyme activity assay, gene deletion mutant and growth assay | arabinan | 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 | 22 | 6 | GH51, GH146, GH43_4, GH43, GH43_4, GH51, GH43_29 |
| PUL0304 | RT-qPCR, isothermal titration calorimetry, 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, enzyme activity assay, gene deletion mutant and growth assay | homogalacturonan | 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 | GH105, CE8, CE4, CE8, CE12, PL1_2, PL1, CE8, PL1_2, PL1, CE8, PL1_2, GH28 |
| PUL0306 | RT-qPCR, isothermal titration calorimetry, enzyme activity assay, gene deletion mutant and growth assay | galactan | 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 | GH2, GH53, GH147 |
| PUL0309 | enzyme activity assay, substrate binding assay, isothermal titration calorimetry | arabinan | Caldanaerobius polysaccharolyticus | 28710263 Enzymatic Mechanism for Arabinan Degradation and Transport in the Thermophilic Bacterium Caldanaerobius polysaccharolyticus. Appl Environ Microbiol. 2017 Aug 31;83(18):e00794-17. doi: 10.1128/AEM.00794-17. Print 2017 Sep 15. |
2017 Sep 15 | degradation | 12 | 6 | GH43_4, GH43, GH127, GH51, GH27, GH51, GH146 |
| PUL0312 | RT-PCR | sucrose | Gluconacetobacter diazotrophicus | 19139238 Transcriptional regulation and signal-peptide-dependent secretion of exolevanase (LsdB) in the endophyte Gluconacetobacter diazotrophicus. Appl Environ Microbiol. 2009 Mar;75(6):1782-5. doi: 10.1128/AEM.01887-08. Epub 2009 Jan 9. |
2009 Mar | degradation | 2 | 2 | GH68, GH32 |
| PUL0313 | microarray, Northern Blot, RT-qPCR, electrophoretic mobility shift assay, clone and expression, gene deletion mutant and growth assay | alginate | Zobellia galactanivorans | 28983288, 32585009 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, PL7, PL6, PL6_1 |
| PUL0324 | RT-PCR, enzyme activity assay | capsule polysaccharide | Serratia marcescens | 28536292 Capsule Production and Glucose Metabolism Dictate Fitness during Serratia marcescens Bacteremia. mBio. 2017 May 23;8(3):e00740-17. doi: 10.1128/mBio.00740-17. |
2017 May 23 | biosynthesis | 17 | 2 | GT4, GT4 |
| PUL0325 | RT-PCR, enzyme activity assay | beta-glucan | Bacteroides thetaiotaomicron | 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 | 6 | 2 | GH30, GH30_3, GH3 |
| PUL0343 | gene deletion mutant and growth assay, enzyme activity assay, Western Blot, isothermal titration calorimetry | carboxymethylcellulose, xylan, beta-glucan, lichenan | 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, GH5_2 |
| PUL0347 | gene deletion mutant and growth assay, RT-PCR | sorbitol | 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 | CBM48, GH13_11 |
| PUL0365 | RT-PCR | maltodextrin | Xanthomonas campestris pv. campestris | 17311090 Plant carbohydrate scavenging through tonB-dependent receptors: a feature shared by phytopathogenic and aquatic bacteria. PLoS One. 2007 Feb 21;2(2):e224. doi: 10.1371/journal.pone.0000224. |
2007 Feb 21 | degradation | 8 | 4 | GH13, GH13_2, GH97 |
| PUL0366 | RT-PCR | N-acetyl-D-galactosamine, d-galactosamine | Escherichia coli | 10931310 Pathways for the utilization of N-acetyl-galactosamine and galactosamine in Escherichia coli. Mol Microbiol. 2000 Jul;37(1):125-35. doi: 10.1046/j.1365-2958.2000.01969.x. |
2000 Jul | degradation | 13 | 1 | CE9 |
| PUL0369 | RT-PCR | unsaturated hyaluronate disaccharide, chondroitin disaccharide | Streptococcus agalactiae NEM316 | 19416976 Substrate specificity of streptococcal unsaturated glucuronyl hydrolases for sulfated glycosaminoglycan. J Biol Chem. 2009 Jul 3;284(27):18059-69. doi: 10.1074/jbc.M109.005660. Epub 2009 May 5. |
2009 Jul 3 | degradation | 11 | 1 | GH88 |
| PUL0370 | RT-PCR | beta-glucoside | Corynebacterium glutamicum | 19628558 Identification of a second beta-glucoside phosphoenolpyruvate: carbohydrate phosphotransferase system in Corynebacterium glutamicum R. Microbiology (Reading). 2009 Nov;155(Pt 11):3652-3660. doi: 10.1099/mic.0.029496-0. Epub 2009 Jul 23. |
2009 Nov | degradation | 3 | 1 | GH1 |
| PUL0392 | RT-PCR, qPCR | xylan | Bacteroides xylanisolvens | 27142817 Xylan degradation by the human gut Bacteroides xylanisolvens XB1A(T) involves two distinct gene clusters that are linked at the transcriptional level. BMC Genomics. 2016 May 4;17:326. doi: 10.1186/s12864-016-2680-8. |
2016 May 4 | degradation | 8 | 3 | GH67, GH13_14 |
| PUL0395 | isothermal calorimetric titration, electrophoretic mobility shift assay, Northern Blot | arabinose, arabinan | Geobacillus stearothermophilus | 21460081 The L-Arabinan utilization system of Geobacillus stearothermophilus. J Bacteriol. 2011 Jun;193(11):2838-50. doi: 10.1128/JB.00222-11. Epub 2011 Apr 1. |
2011 Jun | degradation | 25 | 5 | GH43, GH43_5, GH43, GH43_4, CBM54, GH51, GH51, GH127 |
| PUL0402 | Northern Blot, enzyme activity assay | xylan, xylose | Lactococcus lactis subsp. lactis IO-1 | 11282589 Genetic evidence for a defective xylan degradation pathway in Lactococcus lactis. Appl Environ Microbiol. 2001 Apr;67(4):1445-52. doi: 10.1128/AEM.67.4.1445-1452.2001. |
2001 Apr | degradation | 6 | 1 | GH43_11, GH43 |
| PUL0430 | RT-PCR, microarray, differential gene expression | O-antigen, exopolysaccharide | Clavibacter michiganensis | 22326627 Analysis of the interaction of Clavibacter michiganensis subsp. michiganensis with its host plant tomato by genome-wide expression profiling. J Biotechnol. 2012 Jul 31;160(1-2):42-54. doi: 10.1016/j.jbiotec.2012.01.023. Epub 2012 Feb 1. |
2012 Jul 31 | biosynthesis | 13 | 2 | GT4, GT4, GT94 |
| PUL0460 | recombinant protein expression, RT-PCR, enzyme activity assay | carrageenan, agar | Paraglaciecola hydrolytica | 29774012 A Novel Enzyme Portfolio for Red Algal Polysaccharide Degradation in the Marine Bacterium Paraglaciecola hydrolytica S66(T) Encoded in a Sizeable Polysaccharide Utilization Locus. Front Microbiol. 2018 May 3;9:839. doi: 10.3389/fmicb.2018.00839. eCollection 2018. |
2018 | degradation | 108 | 18 | GH2, GH29, GH63, GH86, CBM6, GH50, GH86, GH50, GH117, GH50, GH16, GH50, CE1, GH16, GH127, GH16, GH82, GH16, GH16, GH16 |
| PUL0466 | clone and expression, enzyme activity assay, Northern Blot | arabinan | Bacillus subtilis | 14973026 Transcriptional regulation of genes encoding arabinan-degrading enzymes in Bacillus subtilis. J Bacteriol. 2004 Mar;186(5):1287-96. doi: 10.1128/JB.186.5.1287-1296.2004. |
2004 Mar | degradation | 9 | 1 | GH51 |
| PUL0486 | RT-PCR, sugar utilization assay | raffinose | Streptococcus pneumoniae | 10613841 Regulation of the alpha-galactosidase activity in Streptococcus pneumoniae: characterization of the raffinose utilization system. Genome Res. 1999 Dec;9(12):1189-97. doi: 10.1101/gr.9.12.1189. |
1999 Dec | degradation | 8 | 2 | GH13, GH13_18, GH36 |
| PUL0553 | RT-PCR, qPCR | xylan | Bacteroides xylanisolvens | 27142817 Xylan degradation by the human gut Bacteroides xylanisolvens XB1A(T) involves two distinct gene clusters that are linked at the transcriptional level. BMC Genomics. 2016 May 4;17:326. doi: 10.1186/s12864-016-2680-8. |
2016 May 4 | degradation | 21 | 13 | GH43_10, GH43, CBM6, GH3, GH43, GH43_12, GH31, GH97, CBM66, CBM6, GH43, GH43_29, GH43, GH43_12, CBM4, CBM0, GH10, GH5_21, CE1, CE6, CBM6, GH43_29, GH95, GH115 |
| PUL0568 | clone and expression, enzyme activity assay, Northern Blot | sucrose | Clostridium beijerinckii | 10411273 The genes controlling sucrose utilization in Clostridium beijerinckii NCIMB 8052 constitute an operon. Microbiology (Reading). 1999 Jun;145 ( Pt 6):1461-1472. doi: 10.1099/13500872-145-6-1461. |
1999 Jun | degradation | 4 | 1 | GH32 |
| PUL0569 | clone and expression, enzyme activity assay, Northern Blot | levan | Bacillus subtilis | 11739774 yveB, Encoding endolevanase LevB, is part of the sacB-yveB-yveA levansucrase tricistronic operon in Bacillus subtilis. Microbiology (Reading). 2001 Dec;147(Pt 12):3413-9. doi: 10.1099/00221287-147-12-3413. |
2001 Dec | degradation | 3 | 1 | GH68, GH32 |
| PUL0571 | Northern Blot | chitooligosaccharide | Salmonella enterica | 19638370 Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target. Genes Dev. 2009 Sep 1;23(17):2004-15. doi: 10.1101/gad.541609. Epub 2009 Jul 28. |
2009 Sep 1 | degradation | 8 | 1 | GH4 |
| PUL0573 | enzyme activity assay, electrophoretic mobility shift assay, RT-PCR, qRT-PCR | cellobiose, cellulose, cellooligosaccharide | Streptomyces griseus | 19648249 CebR as a master regulator for cellulose/cellooligosaccharide catabolism affects morphological development in Streptomyces griseus. J Bacteriol. 2009 Oct;191(19):5930-40. doi: 10.1128/JB.00703-09. Epub 2009 Jul 31. |
2009 Oct | degradation | 5 | 1 | GH1 |
| PUL0578 | qRT-PCR, enzyme activity assay, electrophoretic mobility shift assay | cellodextrin | Bifidobacterium breve | 21216899 Cellodextrin utilization by bifidobacterium breve UCC2003. Appl Environ Microbiol. 2011 Mar;77(5):1681-90. doi: 10.1128/AEM.01786-10. Epub 2011 Jan 7. |
2011 Mar | degradation | 5 | 1 | GH1 |
| PUL0587 | RT-PCR, enzyme activity assay | levan, inulin, fructan | Prevotella intermedia | 23266804 Identification and functional analysis of the gene cluster for fructan utilization in Prevotella intermedia. Gene. 2013 Feb 25;515(2):291-7. doi: 10.1016/j.gene.2012.12.023. Epub 2012 Dec 22. |
2013 Feb 25 | degradation | 3 | 1 | GH32 |
| PUL0588 | enzyme activity assay, RT-PCR | chitin | Streptomyces coelicolor | 23278377 Enzymatic and genetic characterization of the DasD protein possessing N-acetyl-beta-d-glucosaminidase activity in Streptomyces coelicolor A3(2). FEMS Microbiol Lett. 2013 Mar;340(1):33-40. doi: 10.1111/1574-6968.12069. Epub 2013 Jan 16. |
2013 Mar | degradation | 4 | 1 | GH3 |
| PUL0591 | growth assay, Northern Blot | N-acetylglucosamine | Bacillus subtilis | 23667565 The use of amino sugars by Bacillus subtilis: presence of a unique operon for the catabolism of glucosamine. PLoS One. 2013 May 8;8(5):e63025. doi: 10.1371/journal.pone.0063025. Print 2013. |
2013 | degradation | 4 | 1 | CE9 |
| PUL0593 | Northern Blot | maltose, maltotriose | Thermoanaerobacterium thermosulfurigenes | 8576036 Molecular analysis of the amy gene locus of Thermoanaerobacterium thermosulfurigenes EM1 encoding starch-degrading enzymes and a binding protein-dependent maltose transport system. J Bacteriol. 1996 Feb;178(4):1039-46. doi: 10.1128/jb.178.4.1039-1046.1996. |
1996 Feb | degradation | 6 | 2 | GH13_39, CBM34, GH13, CBM20, GH13_2, CBM20 |
| PUL0605 | RT-PCR, gene deletion mutant and growth assay | glycogen | Escherichia coli | 33101261, 21029047 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 | GT35, GT5, GH13, GH13_11, CBM48, GH77, GH13, GH13_9, CBM48 |
| PUL0646 | recombinant protein expression, crystallization, affinity gel electrophoresis, isothermal titration calorimetry | beta-glucan | Bacteroides fluxus YIT 12057 | 33587952 Distinct protein architectures mediate species-specific beta-glucan binding and metabolism in the human gut microbiota. J Biol Chem. 2021 Jan-Jun;296:100415. doi: 10.1016/j.jbc.2021.100415. Epub 2021 Feb 13. |
2021 Jan-Jun | degradation | 6 | 2 | GH3, CBM6, GH158 |
| PUL0653 | gene deletion mutant and growth assay, complementation study, enzyme activity assay, RNA-Seq, electrophoretic mobility shift assay | agar | 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 | GH16_16, 3.2.1.81, CBM67, GH2, GH117, 3.2.1.81, GH50 |
| PUL0656 | gene deletion mutant and growth assay, complementation study, clone and expression, isothermal titration calorimetry | exopolysaccharide | Bacillus cereus ATCC 10987 | 32236137 Discovery and characterization of a Gram-positive Pel polysaccharide biosynthetic gene cluster. PLoS Pathog. 2020 Apr 1;16(4):e1008281. doi: 10.1371/journal.ppat.1008281. eCollection 2020 Apr. |
2020 Apr | biosynthesis | 6 | 2 | GH0, GH166, GT4 |
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