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

PUL0598

PubMed

26020016, AMB Express. 2015 May 23;5:29. doi: 10.1186/s13568-015-0115-6. eCollection 2015.

Characterization method

liquid chromatography and mass spectrometry, differential gene expression

Genomic accession number

CP002160.1

Nucelotide position range

731364-737408

Substrate

xylose

Loci

Clocel_0589-0592

Species

Clostridium cellulovorans 743B/573061

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- Clocel_0589 ADL50360.1 0 - 2310 (+) CP002160.1:731364-733674 3.2.1.51
- Clocel_0590 ADL50361.1 2412 - 3732 (+) CP002160.1:733776-735096 5.3.1.5
- Clocel_0591 ADL50362.1 3891 - 4539 (+) CP002160.1:735255-735903 -
- Clocel_0592 ADL50363.1 4554 - 6045 (+) CP002160.1:735918-737409 -

Cluster number

0

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2310 (+) CAZyme: GH95 No
- 2413 - 3732 (+) CDS No
- 3892 - 4539 (+) CDS No
- 4555 - 6045 (+) CDS No

PUL ID

PUL0598

PubMed

26020016, AMB Express. 2015 May 23;5:29. doi: 10.1186/s13568-015-0115-6. eCollection 2015.

Title

Elucidation of the recognition mechanisms for hemicellulose and pectin in Clostridium cellulovorans using intracellular quantitative proteome analysis.

Author

Aburaya S, Esaka K, Morisaka H, Kuroda K, Ueda M

Abstract

Clostridium cellulovorans is an anaerobic, cellulolytic bacterium, capable of effectively degrading and metabolizing various types of substrates, including cellulose, hemicellulose (xylan and galactomannan), and pectin. Among Clostridia, this ability to degrade and metabolize a wide range of hemicellulose and pectin substrates is a unique feature; however, the mechanisms are currently unknown. To clarify the mechanisms of hemicelluloses and pectin recognition and metabolism, we carried out a quantitative proteome analysis of C. cellulovorans cultured with these substrates. C. cellulovorans was cultured in the medium of glucose (control), xylan, galactomannan (Locus bean gum, LBG), or pectin for 36 h. Xylan and galactomannan were used to search for the common recognition mechanisms of hemicellulose, and pectin was used to search for unique recognition systems in C. cellulovorans. Using an isobaric tag method and liquid chromatograph/mass spectrometer equipped with a long monolithic silica capillary column, we identified 734 intracellular proteins from all substrates. We performed KEGG analyses and cluster analyses of the resulting proteins. In the KEGG analyses, we found common degradation mechanisms for hemicellulose and pectin. In the cluster analysis corresponding to the genome analysis, we detected substrate-specific clusters that include genes involved in substrate recognition, substrate degradation, and metabolism. Combining the results of the KEGG analyses and cluster analyses, we propose the mechanisms involved in the recognition and metabolism of hemicellulose and pectin in C. cellulovorans.