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 ID

PUL0320

PubMed

29475869, Appl Environ Microbiol. 2018 Apr 16;84(9). pii: AEM.02694-17. doi: 10.1128/AEM.02694-17. Print 2018 May 1.
29588665, Biotechnol Biofuels. 2018 Mar 23;11:80. doi: 10.1186/s13068-018-1076-1. eCollection 2018.

Characterization method

liquid chromatography and mass spectrometry, mass spectrometry, target decoy database analysis

Genomic accession number

CP001393.1

Nucelotide position range

1929397-1982736

Substrate

glucan

Loci

Athe_1853-Athe_1871

Species

Caldicellulosiruptor bescii/31899

Degradation or Biosynthesis

degradation

Cluster number

0

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2502 (-) CAZyme: CE12|PL11|CBM3 No
- 2692 - 4074 (-) CAZyme: PL3_1|CBM66|PL3 No
- 4131 - 6092 (-) CAZyme: PL9_1|PL9|CBM66 No
- 6438 - 8819 (-) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607,DBD-SUPERFAMILY|0035607 No
- 9211 - 13647 (-) CAZyme: CBM22|GH10|GH48|CBM3 No
- 14024 - 14155 (-) CDS No
- 14245 - 18129 (-) CAZyme: GH44|GH5|CBM3|GH5_8 No
- 18285 - 23999 (-) CAZyme: GH48|GH74|CBM3 No
- 24272 - 25294 (-) CDS No
- 25367 - 26905 (-) CDS No
- 26956 - 28416 (-) CDS No
- 28445 - 30145 (-) CAZyme: GT39 No
- 30559 - 34668 (-) CAZyme: GH5|GH9|CBM3|GH5_8 No
- 34925 - 39169 (-) CAZyme: GH5_1|CBM3|GH5_8 No
- 39325 - 44604 (-) CAZyme: GH9|GH48|CBM3 No
- 45387 - 45689 (-) CDS No
- 46856 - 47779 (-) CDS No
- 49032 - 50981 (-) CDS No
- 51412 - 53340 (-) CDS No

PUL ID

PUL0320

PubMed

29475869, Appl Environ Microbiol. 2018 Apr 16;84(9). pii: AEM.02694-17. 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.

PubMed

29588665, Biotechnol Biofuels. 2018 Mar 23;11:80. doi: 10.1186/s13068-018-1076-1. eCollection 2018.

Title

The diversity and specificity of the extracellular proteome in the cellulolytic bacterium Caldicellulosiruptor bescii is driven by the nature of the cellulosic growth substrate.

Author

Poudel S, Giannone RJ, Basen M, Nookaew I, Poole FL 2nd, Kelly RM, Adams MWW, Hettich RL

Abstract

Background: Caldicellulosiruptor bescii is a thermophilic cellulolytic bacterium that efficiently deconstructs lignocellulosic biomass into sugars, which subsequently can be fermented into alcohols, such as ethanol, and other products. Deconstruction of complex substrates by C. bescii involves a myriad of highly abundant, substrate-specific extracellular solute binding proteins (ESBPs) and carbohydrate-active enzymes (CAZymes) containing carbohydrate-binding modules (CBMs). Mass spectrometry-based proteomics was employed to investigate how these substrate recognition proteins and enzymes vary as a function of lignocellulosic substrates. Results: Proteomic analysis revealed several key extracellular proteins that respond specifically to either C5 or C6 mono- and polysaccharides. These include proteins of unknown functions (PUFs), ESBPs, and CAZymes. ESBPs that were previously shown to interact more efficiently with hemicellulose and pectin were detected in high abundance during growth on complex C5 substrates, such as switchgrass and xylan. Some proteins, such as Athe_0614 and Athe_2368, whose functions are not well defined were predicted to be involved in xylan utilization and ABC transport and were significantly more abundant in complex and C5 substrates, respectively. The proteins encoded by the entire glucan degradation locus (GDL; Athe_1857, 1859, 1860, 1865, 1867, and 1866) were highly abundant under all growth conditions, particularly when C. bescii was grown on cellobiose, switchgrass, or xylan. In contrast, the glycoside hydrolases Athe_0609 (Pullulanase) and 0610, which both possess CBM20 and a starch binding domain, appear preferential to C5/complex substrate deconstruction. Some PUFs, such as Athe_2463 and 2464, were detected as highly abundant when grown on C5 substrates (xylan and xylose), also suggesting C5-substrate specificity. Conclusions: This study reveals the protein membership of the C. bescii secretome and demonstrates its plasticity based on the complexity (mono-/disaccharides vs. polysaccharides) and type of carbon (C5 vs. C6) available to the microorganism. The presence or increased abundance of extracellular proteins as a response to specific substrates helps to further elucidate C. bescii's utilization and conversion of lignocellulosic biomass to biofuel and other valuable products. This includes improved characterization of extracellular proteins that lack discrete functional roles and are poorly/not annotated.