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CAZy
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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

PUL0084

PubMed

31338125, Biotechnol Biofuels. 2019 Jul 15;12:183. doi: 10.1186/s13068-019-1522-8. eCollection 2019.

Characterization method

label-free quantitative proteomics,functional enrichment analysis,enzyme activity assay

Genomic accession number

ACXX02000002.1

Nucelotide position range

36152-61034

Substrate

lignocellulose

Loci

cpap_3302-cpap_3314

Species

Ruminiclostridium papyrosolvens/29362

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- Cpap_3302 EGD48876.1 0 - 1626 (+) ACXX02000002.1:36152-37778 -
- Cpap_3303 EGD48877.1 1674 - 3249 (+) ACXX02000002.1:37826-39401 -
- Cpap_3304 EGD48878.1 3316 - 4750 (+) ACXX02000002.1:39468-40902 -
- Cpap_3305 EGD48879.1 4842 - 7065 (+) ACXX02000002.1:40994-43217 -
- Cpap_3306 EGD48880.1 7109 - 8729 (+) ACXX02000002.1:43261-44881 -
- Cpap_3307 EGD48881.1 8783 - 10313 (+) ACXX02000002.1:44935-46465 3.2.1.55
- Cpap_3309 EGD48882.1 10661 - 12476 (+) ACXX02000002.1:46813-48628 3.2.1.22
- Cpap_3310 EGD48883.1 12497 - 15863 (+) ACXX02000002.1:48649-52015 -
- Cpap_3311 EGD48884.1 15917 - 18260 (+) ACXX02000002.1:52069-54412 -
- Cpap_3312 EGD48885.1 18399 - 21480 (+) ACXX02000002.1:54551-57632 -
- Cpap_3313 EGD48886.1 21517 - 22969 (+) ACXX02000002.1:57669-59121 -
- Cpap_3314 EGD48887.1 22993 - 24883 (+) ACXX02000002.1:59145-61035 -

Cluster number

0

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1626 (+) CAZyme: GH10|CBM6 No
- 1675 - 3249 (+) CAZyme: GH43_29|GH43|CBM6 No
- 3317 - 4750 (+) CAZyme: CE1|CBM6 No
- 4843 - 7065 (+) CAZyme: GH43_10|CBM6 No
- 7110 - 8729 (+) CAZyme: GH62|CBM6 No
- 8784 - 10313 (+) CAZyme: GH43_29|GH43|CBM6 No
- 10662 - 12476 (+) CAZyme: GH27|CBM6 No
- 12498 - 15863 (+) CAZyme: GH59|CBM6 No
- 15918 - 18260 (+) CAZyme: GH62|CE6|CBM6 No
- 18400 - 21480 (+) CAZyme: GH95|CBM32 No
- 21518 - 22969 (+) CAZyme: CE1|CBM6 No
- 22994 - 24883 (+) CAZyme: GH30_8|CBM6 No

PUL ID

PUL0084

PubMed

31338125, Biotechnol Biofuels. 2019 Jul 15;12:183. doi: 10.1186/s13068-019-1522-8. eCollection 2019.

Title

Secretomic analyses of Ruminiclostridium papyrosolvens reveal its enzymatic basis for lignocellulose degradation.

Author

Ren Z, You W, Wu S, Poetsch A, Xu C

Abstract

BACKGROUND: Efficient biotechnological conversion of lignocellulosic biomass to valuable products, such as transportation biofuels, is ecologically attractive, yet requires substantially improved mechanistic understanding and optimization to become economically feasible. Cellulolytic clostridia, such as Ruminiclostridium papyrosolvens (previously Clostridium papyrosolvens), produce a wide variety of carbohydrate-active enzymes (CAZymes) including extracellular multienzyme complexes-cellulosomes with different specificities for enhanced cellulosic biomass degradation. Identification of the secretory components, especially CAZymes, during bacterial growth on lignocellulose and their influence on bacterial catalytic capabilities provide insight into construction of potent cellulase systems of cell factories tuned or optimized for the targeted substrate by matching the type and abundance of enzymes and corresponding transporters. RESULTS: In this study, we firstly predicted a total of 174 putative CAZymes from the genome of R. papyrosolvens, including 74 cellulosomal components. To explore profile of secreted proteins involved in lignocellulose degradation, we compared the secretomes of R. papyrosolvens grown on different substrates using label-free quantitative proteomics. CAZymes, extracellular solute-binding proteins (SBPs) of transport systems and proteins involved in spore formation were enriched in the secretome of corn stover for lignocellulose degradation. Furthermore, compared with free CAZymes, complex CAZymes (cellulosomal components) had larger fluctuations in variety and abundance of enzymes among four carbon sources. In particular, cellulosomal proteins encoded by the cip-cel operon and the xyl-doc gene cluster had the highest abundance with corn stover as substrate. Analysis of differential expression of CAZymes revealed a substrate-dependent secretion pattern of CAZymes, which was consistent with their catalytic activity from each secretome determined on different cellulosic substrates. The results suggest that the expression of CAZymes is regulated by the type of substrate in the growth medium. CONCLUSIONS: In the present study, our results demonstrated the complexity of the lignocellulose degradation systems of R. papyrosolvens and showed the potency of its biomass degradation activity. Differential proteomic analyses and activity assays of CAZymes secreted by R. papyrosolvens suggested a distinct environment-sensing strategy for cellulose utilization in which R. papyrosolvens modulated the composition of the CAZymes, especially cellulosome, according to the degradation state of its natural substrate.