| PULID | Characterization Method(s) | Substrate | Organism | Publication | Publish Date | Type | Num Genes | Num CAZymes | CazyFamily |
|---|---|---|---|---|---|---|---|---|---|
| PUL0040 | Northern Blot, enzyme activity assay | cellulose | Ruminiclostridium cellulolyticum | <a href=https://pubmed.ncbi.nlm.nih.gov/12896991/>12896991</a>, <a href=https://pubmed.ncbi.nlm.nih.gov/1398087/>1398087</a>, <a href=https://pubmed.ncbi.nlm.nih.gov/11844767 />11844767 </a> 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 | GH5_1, GH5_17, GH9, GH9, CBM3, PL11 |
| PUL0086 | label-free quantitative proteomics, functional enrichment analysis, enzyme activity assay | pectin | Ruminiclostridium papyrosolvens | <a href=https://pubmed.ncbi.nlm.nih.gov/31338125/>31338125</a> Secretomic analyses of Ruminiclostridium papyrosolvens reveal its enzymatic basis for lignocellulose degradation. Biotechnol Biofuels. 2019 Jul 15;12:183. doi: 10.1186/s13068-019-1522-8. eCollection 2019. |
2019 | degradation | 3 | 3 | CE8, PL10_1, PL11 |
| PUL0192 | RNA-seq, RT-PCR, qPCR | pectin | Bacteroides xylanisolvens | <a href=https://pubmed.ncbi.nlm.nih.gov/26920945/>26920945</a> 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 | 14 | CE12, CE12, CE12, GH105, GH106, GH2, GH28, GH42, GH43_18, GH43_34, CBM32, PL11, PL11_1, PL26 |
| PUL0193 | RNA-seq, RT-PCR, qPCR | pectin | Bacteroides xylanisolvens | <a href=https://pubmed.ncbi.nlm.nih.gov/26920945/>26920945</a> 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 | 8 | CE20, GH105, GH117, GH117, GH2, GH28, PL11 |
| PUL0249 | microarray | pectin | Bacillus subtilis | <a href=https://pubmed.ncbi.nlm.nih.gov/17449691/>17449691</a> Plant cell wall degradation by saprophytic Bacillus subtilis strains: gene clusters responsible for rhamnogalacturonan depolymerization. Appl Environ Microbiol. 2007 Jun;73(12):3803-13. doi: 10.1128/AEM.00147-07. Epub 2007 Apr 20. |
2007 Jun | degradation | 12 | 6 | CE12, GH105, GH42, PL11 |
| PUL0320 | liquid chromatography and mass spectrometry, mass spectrometry, target decoy database analysis | cellulose | Caldicellulosiruptor bescii | <a href=https://pubmed.ncbi.nlm.nih.gov/29475869/>29475869</a>, <a href=https://pubmed.ncbi.nlm.nih.gov/29588665/>29588665</a>, <a href=https://pubmed.ncbi.nlm.nih.gov/21227922/>21227922</a> Genus-Wide Assessment of Lignocellulose Utilization in the Extremely Thermophilic Genus Caldicellulosiruptor by Genomic, Pangenomic, and Metagenomic Analyses. The diversity and specificity of the extracellular proteome in the cellulolytic bacterium Caldicellulosiruptor bescii is driven by the nature of the cellulosic growth substrate. Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725. Appl Environ Microbiol. 2018 Apr 16;84(9):e02694-17. doi: 10.1128/AEM.02694-17. Print 2018 May 1. Biotechnol Biofuels. 2018 Mar 23;11:80. doi: 10.1186/s13068-018-1076-1. eCollection 2018. Nucleic Acids Res. 2011 Apr;39(8):3240-54. doi: 10.1093/nar/gkq1281. Epub 2011 Jan 11. |
2018 May 1,2018,2011 Apr | degradation | 19 | 10 | CBM66, PL3_1, CBM66, PL9_1, GH10, CBM3, CBM3, GH48, GH5_8, CBM3, CBM3, CBM3, GH5_1, GH5_8, CBM3, CBM3, GH44, GH74, GH74, GH74, GH74, CBM3, CBM3, GH48, GH9, CBM3, CBM3, CBM3, GH48, GH9, CBM3, CBM3, CBM3, GH5_8, GT39, PL11, CBM3 |
| PUL0322 | liquid chromatography and mass spectrometry | cellulose | Caldicellulosiruptor danielii | <a href=https://pubmed.ncbi.nlm.nih.gov/29475869/>29475869</a> Genus-Wide Assessment of Lignocellulose Utilization in the Extremely Thermophilic Genus Caldicellulosiruptor by Genomic, Pangenomic, and Metagenomic Analyses. Appl Environ Microbiol. 2018 Apr 16;84(9):e02694-17. doi: 10.1128/AEM.02694-17. Print 2018 May 1. |
2018 May 1 | degradation | 19 | 12 | CBM22, CBM22, GH10, CBM3, CBM3, GH5_1, CBM66, PL3_1, CBM66, PL9_1, GH10, CBM3, GH12, GH48, GH5_8, CBM3, CBM3, GH44, GH74, GH74, GH74, GH74, CBM3, CBM3, GH48, GH9, CBM3, CBM3, CBM3, GH48, GH9, CBM3, CBM3, CBM3, GH5_8, GT39, PL11, CBM3 |
| PUL0385 | ion trap liquid chromatography, mass spectrometry, target decoy database analysis, high-performance anion-exchange chromatography | cellulose | Ruminiclostridium cellulolyticum | <a href=https://pubmed.ncbi.nlm.nih.gov/20013800/>20013800</a>, <a href=https://pubmed.ncbi.nlm.nih.gov/8936327/>8936327</a> Modulation of cellulosome composition in Clostridium cellulolyticum: adaptation to the polysaccharide environment revealed by proteomic and carbohydrate-active enzyme analyses. Molecular study and overexpression of the Clostridium cellulolyticum celF cellulase gene in Escherichia coli. Proteomics. 2010 Feb;10(3):541-54. doi: 10.1002/pmic.200900311. Microbiology (Reading). 1996 Apr;142 ( Pt 4):1013-1023. doi: 10.1099/00221287-142-4-1013. |
2010 Feb,1996 Apr | degradation | 12 | 10 | CBM4, GH9, GH48, GH5_1, GH5_17, GH8, GH9, GH9, CBM3, PL11 |
| PUL0539 | RNA-seq | pectin | Bacteroides cellulosilyticus | <a href=https://pubmed.ncbi.nlm.nih.gov/23976882/>23976882</a> Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome. PLoS Biol. 2013;11(8):e1001637. doi: 10.1371/journal.pbio.1001637. Epub 2013 Aug 20. |
2013 | degradation | 16 | 7 | CE20, GH105, GH105, GH106, GH28, PL11, PL1_2 |
| PUL0723 | crystallization, high-performance anion-exchange chromatography, enzyme activity assay | pectin | Phocaeicola dorei DSM 17855 | <a href=https://pubmed.ncbi.nlm.nih.gov/38179933/>38179933</a> Polysaccharide utilization loci from Bacteroidota encode CE15 enzymes with possible roles in cleaving pectin-lignin bonds. Appl Environ Microbiol. 2024 Jan 24;90(1):e0176823. doi: 10.1128/aem.01768-23. Epub 2024 Jan 5. |
2024 Jan 24 | degradation | 17 | 12 | CE12, CE15, GH105, GH106, GH106, GH28, GH2, GH28, GH42, GH43_18, GH43_34, CBM32, GH78, PL11 |
| PUL0724 | crystallization, high-performance anion-exchange chromatography, enzyme activity assay | pectin | Phocaeicola vulgatus ATCC 8482 | <a href=https://pubmed.ncbi.nlm.nih.gov/38179933/>38179933</a> Polysaccharide utilization loci from Bacteroidota encode CE15 enzymes with possible roles in cleaving pectin-lignin bonds. Appl Environ Microbiol. 2024 Jan 24;90(1):e0176823. doi: 10.1128/aem.01768-23. Epub 2024 Jan 5. |
2024 Jan 24 | degradation | 16 | 12 | CE12, CE15, GH105, GH106, GH106, GH28, GH2, GH28, GH42, GH43_18, GH43_34, CBM32, GH78, PL11 |
| PUL0788 | RNA-seq, reducing-sugar assay, growth assay | pectic polysaccharide | Bacteroides ovatus strain ATCC 8483 | <a href=https://pubmed.ncbi.nlm.nih.gov/39892338/>39892338</a> In vitro fermentation of a purified fraction of polysaccharides from the root of Brassica rapa L. by human gut microbiota and its interaction with Bacteroides ovatus. Food Chem. 2025 May 1;473:143109. doi: 10.1016/j.foodchem.2025.143109. Epub 2025 Jan 27. |
2025 May 1 | degradation | 26 | 8 | CE20, GH105, GH2, GH28, PL11, PL1_2, PL9_1 |
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