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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0224

PubMed

23418511, PLoS One. 2013;8(2):e56063. doi: 10.1371/journal.pone.0056063. Epub 2013 Feb 13.

Characterization method

RT-PCR,qRT-PCR

Genomic accession number

NC_011898.1

Nucelotide position range

1502003-1537237

Substrate

cellulose

Loci

CCEL_RS06150-CCEL_RS06225

Species

Ruminiclostridium cellulolyticum/1521

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- CCEL_RS06150 WP_015924732.1 0 - 1467 (+) NC_011898.1:1502003-1503470 -
- CCEL_RS06155 WP_015924733.1 1488 - 3087 (+) NC_011898.1:1503491-1505090 -
- CCEL_RS06160 WP_015924734.1 3659 - 5267 (+) NC_011898.1:1505662-1507270 -
- CCEL_RS06165 WP_015924735.1 5372 - 6998 (+) NC_011898.1:1507375-1509001 -
- CCEL_RS06170 WP_015924736.1 7065 - 8640 (+) NC_011898.1:1509068-1510643 -
- CCEL_RS06175 WP_015924737.1 8662 - 10135 (+) NC_011898.1:1510665-1512138 -
- CCEL_RS06180 WP_015924738.1 10210 - 12451 (+) NC_011898.1:1512213-1514454 -
- CCEL_RS06185 WP_015924739.1 12534 - 14145 (+) NC_011898.1:1514537-1516148 -
- CCEL_RS06190 WP_015924740.1 14219 - 15749 (+) NC_011898.1:1516222-1517752 -
- CCEL_RS06195 WP_015924741.1 15837 - 18705 (+) NC_011898.1:1517840-1520708 -
- CCEL_RS06200 WP_015924742.1 18813 - 20628 (+) NC_011898.1:1520816-1522631 -
- CCEL_RS06205 WP_015924743.1 20657 - 24026 (+) NC_011898.1:1522660-1526029 -
- CCEL_RS06210 WP_015924744.1 24089 - 27137 (+) NC_011898.1:1526092-1529140 -
- CCEL_RS06215 WP_015924745.1 27197 - 29540 (+) NC_011898.1:1529200-1531543 -
- CCEL_RS06220 WP_015924746.1 29756 - 33251 (+) NC_011898.1:1531759-1535254 -
- CCEL_RS06225 WP_015924747.1 33345 - 35235 (+) NC_011898.1:1535348-1537238 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1467 (+) TC: gnl|TC-DB|Q81JL2|9.B.33.1.1 Yes
- 1489 - 3087 (+) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 Yes
- 3660 - 5267 (+) CAZyme: GH43_16|GH43|CBM6 Yes
- 5373 - 6998 (+) CAZyme: GH10|CBM6 Yes
- 7066 - 8640 (+) CAZyme: GH43|GH43_29|CBM6 Yes
- 8663 - 10135 (+) CAZyme: CBM6|CE1 Yes
- 10211 - 12451 (+) CAZyme: GH43_10|CBM6 Yes
- 12535 - 14145 (+) CAZyme: GH62|CBM6 Yes
- 14220 - 15749 (+) CAZyme: GH43|GH43_29|CBM6 Yes
- 15838 - 18705 (+) CAZyme: GH146|CBM22 Yes
- 18814 - 20628 (+) CAZyme: GH27|CBM6 Yes
- 20658 - 24026 (+) CAZyme: GH59|CBM6 Yes
- 24090 - 27137 (+) CAZyme: GH2|CBM6 Yes
- 27198 - 29540 (+) CAZyme: GH62|CBM6|CE6 Yes
- 29757 - 33251 (+) CAZyme: CBM32|GH95|CBM6 Yes
- 33346 - 35235 (+) CAZyme: GH30_8|CBM6 Yes

PUL ID

PUL0224

PubMed

23418511, PLoS One. 2013;8(2):e56063. doi: 10.1371/journal.pone.0056063. Epub 2013 Feb 13.

Title

A two-component system (XydS/R) controls the expression of genes encoding CBM6-containing proteins in response to straw in Clostridium cellulolyticum.

Author

Celik H, Blouzard JC, Voigt B, Becher D, Trotter V, Fierobe HP, Tardif C, Pages S, de Philip P

Abstract

The composition of the cellulosomes (multi enzymatic complexes involved in the degradation of plant cell wall polysaccharides) produced by Clostridium cellulolyticum differs according to the growth substrate. In particular, the expression of a cluster of 14 hemicellulase-encoding genes (called xyl-doc) seems to be induced by the presence of straw and not of cellulose. Genes encoding a putative two-component regulation system (XydS/R) were found upstream of xyl-doc. First evidence for the involvement of the response regulator, XydR, part of this two-component system, in the expression of xyl-doc genes was given by the analysis of the cellulosomes produced by a regulator overproducing strain when grown on cellulose. Nano-LC MS/MS analysis allowed the detection of the products of all xyl-doc genes and of the product of the gene at locus Ccel_1656 predicted to bear a carbohydrate binding domain targeting hemicellulose. RT-PCR experiments further demonstrated that the regulation occurs at the transcriptional level and that all xyl-doc genes are transcriptionally linked. mRNA quantification in a regulator knock-out strain and in its complemented derivative confirmed the involvement of the regulator in the expression of xyl-doc genes and of the gene at locus Ccel_1656 in response to straw. Electrophoretic mobility shift assays using the purified regulator further demonstrated that the regulator binds to DNA regions located upstream of the first gene of the xyl-doc gene cluster and upstream of the gene at locus Ccel_1656.