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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0601

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

2667794-2686941

Substrate

pectin

Loci

Clocel_2249-Clocel_2264

Species

Clostridium cellulovorans/1493

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- Clocel_2249 ADL51988.1 0 - 1407 (-) CP002160.1:2667794-2669201 5.3.1.12
- Clocel_2250 ADL51989.1 1420 - 2908 (-) CP002160.1:2669214-2670702 4.2.1.7
- Clocel_2251 ADL51990.1 2900 - 4370 (-) CP002160.1:2670694-2672164 -
- Clocel_2252 ADL51991.1 4425 - 5256 (-) CP002160.1:2672219-2673050 -
- Clocel_2253 ADL51992.1 5890 - 6586 (-) CP002160.1:2673684-2674380 -
- Clocel_2254 ADL51993.1 6681 - 8214 (-) CP002160.1:2674475-2676008 -
- Clocel_2255 ADL51994.1 8461 - 9970 (-) CP002160.1:2676255-2677764 -
- Clocel_2256 ADL51995.1 10053 - 11142 (-) CP002160.1:2677847-2678936 -
- Clocel_2257 ADL51996.1 11735 - 12572 (-) CP002160.1:2679529-2680366 -
- Clocel_2258 ADL51997.1 12667 - 13294 (-) CP002160.1:2680461-2681088 -
- Clocel_2259 ADL51998.1 13366 - 14314 (-) CP002160.1:2681160-2682108 -
- Clocel_2260 ADL51999.1 14470 - 15253 (-) CP002160.1:2682264-2683047 -
- Clocel_2262 ADL52000.1 16046 - 16850 (-) CP002160.1:2683840-2684644 -
- Clocel_2263 ADL52001.1 17120 - 17951 (-) CP002160.1:2684914-2685745 5.3.1.17
- Clocel_2264 ADL52002.1 18386 - 19148 (-) CP002160.1:2686180-2686942 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1407 (-) CDS No
- 1421 - 2908 (-) CDS No
- 2901 - 4370 (-) CDS No
- 4426 - 5256 (-) CDS No
- 5891 - 6586 (-) TF: DBD-Pfam|GntR,DBD-SUPERFAMILY|0039384 No
- 6682 - 8214 (-) CAZyme: GH28 Yes
- 8462 - 9970 (-) TC: gnl|TC-DB|Q93KC2|2.A.2.5.1 Yes
- 10054 - 11142 (-) CAZyme: GH105 Yes
- 11736 - 12572 (-) CDS No
- 12668 - 13294 (-) CDS No
- 13367 - 14314 (-) STP: STP|PfkB No
- 14471 - 15253 (-) CDS No
- 16047 - 16850 (-) CDS No
- 17121 - 17951 (-) CDS No
- 18387 - 19148 (-) TF: DBD-Pfam|TrmB,DBD-SUPERFAMILY|0040266 No

PUL ID

PUL0601

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.