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PlantCAZyme
Cite: NAR/gkaa742 2020

Because CGCFinder predicted no CGC for this PUL, the gene cluster depicted below contains dbCAN2 and CGC signature predictions for all genes in the PUL, instead of a predicted CGC.


PUL General Information

Literature Information

PUL ID

PUL0322

PubMed

29475869, Appl Environ Microbiol. 2018 Apr 16;84(9):e02694-17. doi: 10.1128/AEM.02694-17. Print 2018 May 1.

Characterization method

liquid chromatography and mass spectrometry

Genomic accession number

LACM01000001.1

Nucelotide position range

2094992-2154688

Substrate

glucan

Loci

Wai35_2039-Wai35_2061

Species

Caldicellulosiruptor danielii/1387557

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- - LACM01000001_1 1 - 2544 (-) LACM01000001.1:2094993-2097536 -
- - LACM01000001_2 2719 - 4074 (-) LACM01000001.1:2097711-2099066 -
- - LACM01000001_3 4174 - 6147 (-) LACM01000001.1:2099166-2101139 -
- - LACM01000001_4 6247 - 8220 (-) LACM01000001.1:2101239-2103212 -
- - LACM01000001_5 8320 - 10293 (-) LACM01000001.1:2103312-2105285 -
- - LACM01000001_6 10457 - 11332 (+) LACM01000001.1:2105449-2106324 -
- - LACM01000001_7 12512 - 14881 (-) LACM01000001.1:2107504-2109873 -
- - LACM01000001_8 15268 - 20862 (-) LACM01000001.1:2110260-2115854 -
- - LACM01000001_9 21135 - 22157 (-) LACM01000001.1:2116127-2117149 -
- - LACM01000001_10 22223 - 23749 (-) LACM01000001.1:2117215-2118741 -
- - LACM01000001_11 23805 - 25250 (-) LACM01000001.1:2118797-2120242 -
- - LACM01000001_12 25290 - 26987 (-) LACM01000001.1:2120282-2121979 -
- - LACM01000001_13 27244 - 31419 (-) LACM01000001.1:2122236-2126411 -
- - LACM01000001_14 31662 - 36446 (-) LACM01000001.1:2126654-2131438 -
- - LACM01000001_15 36630 - 41165 (-) LACM01000001.1:2131622-2136157 -
- - LACM01000001_16 41751 - 45662 (-) LACM01000001.1:2136743-2140654 -
- - LACM01000001_17 45817 - 51048 (-) LACM01000001.1:2140809-2146040 -
- - LACM01000001_18 52767 - 53690 (-) LACM01000001.1:2147759-2148682 -
- - LACM01000001_19 55379 - 57325 (-) LACM01000001.1:2150371-2152317 -
- - LACM01000001_20 57769 - 59754 (-) LACM01000001.1:2152761-2154746 -

Cluster number

0

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2544 (-) CAZyme: CBM3|PL11|CE12 No
- 2719 - 4074 (-) CAZyme: PL3_1|CBM66|PL3 No
- 4174 - 6147 (-) CAZyme: CBM66|PL9|PL9_1 No
- 6247 - 8220 (-) CAZyme: CBM66|PL9|PL9_1 No
- 8320 - 10293 (-) CAZyme: CBM66|PL9|PL9_1 No
- 10457 - 11332 (+) CDS No
- 12512 - 14881 (-) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607,DBD-SUPERFAMILY|0035607 No
- 15268 - 20862 (-) CAZyme: CBM3|GH74|GH48 No
- 21135 - 22157 (-) CDS No
- 22223 - 23749 (-) CDS No
- 23805 - 25250 (-) CDS No
- 25290 - 26987 (-) CAZyme: GT39 No
- 27244 - 31419 (-) CAZyme: CBM3|GH9|GH5|GH5_8 No
- 31662 - 36446 (-) CAZyme: GH5_1|GH10|GH5|CBM22|CBM3 No
- 36630 - 41165 (-) CAZyme: GH48|GH10|GH12|CBM22|CBM3 No
- 41751 - 45662 (-) CAZyme: CBM3|GH5|GH44|GH5_8 No
- 45817 - 51048 (-) CAZyme: CBM3|GH9|GH48 No
- 52767 - 53690 (-) CDS No
- 55379 - 57325 (-) CDS No
- 57769 - 59754 (-) CDS No

PUL ID

PUL0322

PubMed

29475869, Appl Environ Microbiol. 2018 Apr 16;84(9):e02694-17. doi: 10.1128/AEM.02694-17. Print 2018 May 1.

Title

Genus-Wide Assessment of Lignocellulose Utilization in the Extremely Thermophilic Genus Caldicellulosiruptor by Genomic, Pangenomic, and Metagenomic Analyses.

Author

Lee LL, Blumer-Schuette SE, Izquierdo JA, Zurawski JV, Loder AJ, Conway JM, Elkins JG, Podar M, Clum A, Jones PC, Piatek MJ, Weighill DA, Jacobson DA, Adams MWW, Kelly RM

Abstract

Metagenomic data from Obsidian Pool (Yellowstone National Park, USA) and 13 genome sequences were used to reassess genus-wide biodiversity for the extremely thermophilic Caldicellulosiruptor The updated core genome contains 1,401 ortholog groups (average genome size for 13 species = 2,516 genes). The pangenome, which remains open with a revised total of 3,493 ortholog groups, encodes a variety of multidomain glycoside hydrolases (GHs). These include three cellulases with GH48 domains that are colocated in the glucan degradation locus (GDL) and are specific determinants for microcrystalline cellulose utilization. Three recently sequenced species, Caldicellulosiruptor sp. strain Rt8.B8 (renamed here Caldicellulosiruptor morganii), Thermoanaerobacter cellulolyticus strain NA10 (renamed here Caldicellulosiruptor naganoensis), and Caldicellulosiruptor sp. strain Wai35.B1 (renamed here Caldicellulosiruptor danielii), degraded Avicel and lignocellulose (switchgrass). C. morganii was more efficient than Caldicellulosiruptor bescii in this regard and differed from the other 12 species examined, both based on genome content and organization and in the specific domain features of conserved GHs. Metagenomic analysis of lignocellulose-enriched samples from Obsidian Pool revealed limited new information on genus biodiversity. Enrichments yielded genomic signatures closely related to that of Caldicellulosiruptor obsidiansis, but there was also evidence for other thermophilic fermentative anaerobes (Caldanaerobacter, Fervidobacterium, Caloramator, and Clostridium). One enrichment, containing 89.8% Caldicellulosiruptor and 9.7% Caloramator, had a capacity for switchgrass solubilization comparable to that of C. bescii These results refine the known biodiversity of Caldicellulosiruptor and indicate that microcrystalline cellulose degradation at temperatures above 70 degrees C, based on current information, is limited to certain members of this genus that produce GH48 domain-containing enzymes.IMPORTANCE The genus Caldicellulosiruptor contains the most thermophilic bacteria capable of lignocellulose deconstruction, which are promising candidates for consolidated bioprocessing for the production of biofuels and bio-based chemicals. The focus here is on the extant capability of this genus for plant biomass degradation and the extent to which this can be inferred from the core and pangenomes, based on analysis of 13 species and metagenomic sequence information from environmental samples. Key to microcrystalline hydrolysis is the content of the glucan degradation locus (GDL), a set of genes encoding glycoside hydrolases (GHs), several of which have GH48 and family 3 carbohydrate binding module domains, that function as primary cellulases. Resolving the relationship between the GDL and lignocellulose degradation will inform efforts to identify more prolific members of the genus and to develop metabolic engineering strategies to improve this characteristic.