title: Comparative transcriptomic analysis of Clostridium acetobutylicum biofilm and planktonic cells.
abstract: Biofilm-based immobilization of solventogenic Clostridia has been extensively exploited to overcome traditional bottlenecks in biobutanol production like solvent toxicity and low productivities. However, the molecular basis of solventogenic Clostridia biofilm is rarely explored. Here, for the first time, we report DNA array-based study of Clostridium acetobutylicum biofilm cells to elucidate the transcriptional modulation. Results showed that 16.2% of the C. acetobutylicum genome genes within the biofilm cells were differentially expressed, with most genes being up-regulated. The most dramatic changes occurred with amino acid biosynthesis, with sulfur uptake and cysteine biosynthesis being the most up-regulated and histidine biosynthesis being the most down-regulated in the biofilm cells. It was demonstrated that C. acetobutylicum biofilm cells increased metabolic activities probably by up-regulating iron and sulfur uptake and Fe-S cluster biosynthesis genes as well as glycolysis genes. Furthermore, genes involved in sporulation, granulose formation, extracellular polymer degradation, pentose catabolisms, and various other processes were also notably regulated, indicating that the biofilm mode of growth rendered the cells a distinct phenotype. This study provides valuable insights into the transcriptional regulation in C. acetobutylicum biofilm cells and should be highly useful for understanding and developing the biofilm-based processes.
authors.affiliation: State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China.
authors.forename: Dong
authors.initials: D
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China.
authors.forename: Jiahui
authors.initials: J
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China.
authors.forename: Yanyan
authors.initials: Y
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China.
authors.forename: Xiaoning
authors.initials: X
authors.lastname: Shen
authors.affiliation: State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China.
authors.forename: Huanqing
authors.initials: H
authors.lastname: Niu
authors.affiliation: State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China.
authors.forename: Ting
authors.initials: T
authors.lastname: Guo
authors.affiliation: State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China. Electronic address: yinghanjie@njtech.edu.cn.
authors.forename: Hanjie
authors.initials: H
authors.lastname: Ying
mesh_terms: D000596:Amino Acids / Q000096:biosynthesis; D001426:Bacterial Proteins / Q000096:biosynthesis / Q000378:metabolism; D018441:Biofilms; D046969:Clostridium acetobutylicum / Q000166:cytology* / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D003545:Cysteine / Q000096:biosynthesis; D015536:Down-Regulation; D020869:Gene Expression Profiling; D006019:Glycolysis / Q000235:genetics; D006639:Histidine / Q000096:biosynthesis; D007501:Iron / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D013455:Sulfur / Q000378:metabolism; D015854:Up-Regulation
chemical_list: D000596:Amino Acids; D001426:Bacterial Proteins; D006639:Histidine; D013455:Sulfur; D007501:Iron; D003545:Cysteine
keywords: Biofilm; Clostridium acetobutylicum; Microarray; Transcriptomic analysis