Genome-wide dynamic transcriptional profiling in clostridium beijerinckii NCIMB 8052 using single-nucleotide resolution RNA-Seq

被引:63
作者
Wang, Yi [1 ,2 ]
Li, Xiangzhen [3 ,4 ]
Mao, Yuejian [3 ]
Blaschek, Hans P. [1 ,5 ,6 ]
机构
[1] Univ Illinois, Inst Genom Biol, Urbana, IL 61801 USA
[2] Univ Illinois, Dept Agr & Biol Engn, Urbana, IL 61801 USA
[3] Univ Illinois, Dept Anim Sci, Urbana, IL 61801 USA
[4] Chinese Acad Sci, Chengdu Inst Biol, Chengdu 610041, Sichuan, Peoples R China
[5] Univ Illinois, Dept Food Sci & Human Nutr, Urbana, IL 61801 USA
[6] Univ Illinois, Ctr Adv Bioenergy Res CABER, Urbana, IL 61801 USA
来源
BMC GENOMICS | 2012年 / 13卷
关键词
FORESPORE-SPECIFIC TRANSCRIPTION; DIFFERENTIAL EXPRESSION ANALYSIS; GENE-EXPRESSION; HISTIDINE KINASES; BUTANOL DEHYDROGENASE; ENDOSPORE FORMATION; EARLY SPORULATION; STATIONARY-PHASE; SIGMA-FACTOR; ACETOBUTYLICUM;
D O I
10.1186/1471-2164-13-102
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Background: Clostridium beijerinckii is a prominent solvent-producing microbe that has great potential for biofuel and chemical industries. Although transcriptional analysis is essential to understand gene functions and regulation and thus elucidate proper strategies for further strain improvement, limited information is available on the genome-wide transcriptional analysis for C. beijerinckii. Results: The genome-wide transcriptional dynamics of C. beijerinckii NCIMB 8052 over a batch fermentation process was investigated using high-throughput RNA-Seq technology. The gene expression profiles indicated that the glycolysis genes were highly expressed throughout the fermentation, with comparatively more active expression during acidogenesis phase. The expression of acid formation genes was down-regulated at the onset of solvent formation, in accordance with the metabolic pathway shift from acidogenesis to solventogenesis. The acetone formation gene (adc), as a part of the sol operon, exhibited highly-coordinated expression with the other sol genes. Out of the > 20 genes encoding alcohol dehydrogenase in C. beijerinckii, Cbei_1722 and Cbei_2181 were highly up-regulated at the onset of solventogenesis, corresponding to their key roles in primary alcohol production. Most sporulation genes in C. beijerinckii 8052 demonstrated similar temporal expression patterns to those observed in B. subtilis and C. acetobutylicum, while sporulation sigma factor genes sigE and sigG exhibited accelerated and stronger expression in C. beijerinckii 8052, which is consistent with the more rapid forespore and endspore development in this strain. Global expression patterns for specific gene functional classes were examined using self-organizing map analysis. The genes associated with specific functional classes demonstrated global expression profiles corresponding to the cell physiological variation and metabolic pathway switch. Conclusions: The results from this work provided insights for further C. beijerinckii strain improvement employing system biology-based strategies and metabolic engineering approaches.
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页数:15
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