Research article
Pleiotropic functions of catabolite control protein CcpA in Butanol-producing Clostridium acetobutylicum
1 Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
2 School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
3 Shanghai Research and Development Center of Industrial Biotechnology, Shanghai, 201201, China
BMC Genomics 2012, 13:349 doi:10.1186/1471-2164-13-349
Published: 30 July 2012Additional files
Additional file 1:
Figure S1. Comparison of the expression levels of the CcpA-repressed genes involved in carbohydrates metabolism in C. acetobutylicum ATCC 824 (824WT) in the presence and absence of D-glucose. Most of the CcpA-repressed genes exhibited significant upregulation when d-glucose was depleted (S2 and S3) in wild-type strain 824WT.
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Additional file 2::
Table S1. Microarray data. The file lists the complete set of data from microarray experiment and the genes exhibiting 2-fold changes in the ccpA mutant (824ccpA) compared to its parental strain (824WT) at each time point.
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Additional file 3:
Table S2. Identified putative CcpA-binding sites in Clostridium acetobutylicum. The table lists all of predicted catabolite repression elements (CREs) in Clostridium acetobutylicum. HMM method was used for the prediction. The training set for HMM search was obtained from microarray expression data. The genes up-regulated or down-regulated in transcript levels were indicated.
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Additional file 4:
Table S3. List of the up-regulated genes involved in carbohydrates metabolism after ccpA inactivation and their putative CcpA binding sites (CREs).
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Additional file 5:
Table S4. List of the down-regulated genes involved in carbohydrates metabolism after ccpA inactivation and their putative CcpA binding sites (CREs).
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Additional file 6:
Figure S2. Genomic organization of the genes involved in pentose utilization and the corresponding binding loci of CcpA. Genes from the same operon are marked in the same color.
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Additional file 7:
Figure S3. Quantitative RT-PCR analysis of gene araR, gene araD and gene ptk to assess the impact of L-arabinose on transcription of the gene cluster araR-araD-araA1-ptk. The fold difference in gene expression is calculated as the gene expression level in the cultures (grown in D-glucose-L-arabinose mixture) divided by that of the wild-type strain grown in L-arabinose.
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Additional file 8:
Figure S4. Quantitative RT-PCR analysis to assess the impact of D-glucose on the expression of bukII (CAC1660) and bukI (CAC3075) in C. acetobutylicum ATCC 824. Cells were harvested from SMP2 medium with 20 g/L D-glucose (M + G) or without D-glucose (M) at late exponential phase (A600 = 2.0).
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Additional file 9:
Table S5. primers used in this study. The file lists all of the primers used in this study.
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