Jones Shawn W, Paredes Carlos J, Tracy Bryan, Cheng Nathan, Sillers Ryan, Senger Ryan S, Papoutsakis Eleftherios T
Department of Chemical and Biological Engineering, Northwestern University, Sheridan Road, Evanston, IL 60208-3120, USA.
Genome Biol. 2008;9(7):R114. doi: 10.1186/gb-2008-9-7-r114. Epub 2008 Jul 16.
Clostridia are ancient soil organisms of major importance to human and animal health and physiology, cellulose degradation, and the production of biofuels from renewable resources. Elucidation of their sporulation program is critical for understanding important clostridial programs pertaining to their physiology and their industrial or environmental applications.
Using a sensitive DNA-microarray platform and 25 sampling timepoints, we reveal the genome-scale transcriptional basis of the Clostridium acetobutylicum sporulation program carried deep into stationary phase. A significant fraction of the genes displayed temporal expression in six distinct clusters of expression, which were analyzed with assistance from ontological classifications in order to illuminate all known physiological observations and differentiation stages of this industrial organism. The dynamic orchestration of all known sporulation sigma factors was investigated, whereby in addition to their transcriptional profiles, both in terms of intensity and differential expression, their activity was assessed by the average transcriptional patterns of putative canonical genes of their regulon. All sigma factors of unknown function were investigated by combining transcriptional data with predicted promoter binding motifs and antisense-RNA downregulation to provide a preliminary assessment of their roles in sporulation. Downregulation of two of these sigma factors, CAC1766 and CAP0167, affected the developmental process of sporulation and are apparently novel sporulation-related sigma factors.
This is the first detailed roadmap of clostridial sporulation, the most detailed transcriptional study ever reported for a strict anaerobe and endospore former, and the first reported holistic effort to illuminate cellular physiology and differentiation of a lesser known organism.
梭菌是古老的土壤微生物，对人类和动物健康与生理学、纤维素降解以及从可再生资源生产生物燃料具有重要意义。阐明其芽孢形成程序对于理解与梭菌生理学及其工业或环境应用相关的重要程序至关重要。
我们使用灵敏的DNA微阵列平台和25个采样时间点，揭示了丙酮丁醇梭菌芽孢形成程序深入到稳定期的全基因组规模转录基础。很大一部分基因在六个不同的表达簇中呈现出时间依赖性表达，借助本体分类法对这些表达簇进行了分析，以阐明这种工业微生物所有已知的生理学观察结果和分化阶段。我们研究了所有已知芽孢形成σ因子的动态调控，除了它们的转录谱，包括强度和差异表达方面，还通过其调控子假定的典型基因的平均转录模式评估了它们的活性。通过将转录数据与预测的启动子结合基序和反义RNA下调相结合，对所有功能未知的σ因子进行了研究，以初步评估它们在芽孢形成中的作用。下调其中两个σ因子，即CAC1766和CAP0167，影响了芽孢形成的发育过程，它们显然是与芽孢形成相关的新型σ因子。
这是梭菌芽孢形成的首张详细路线图，是有史以来针对严格厌氧菌和内生孢子形成菌报道的最详细的转录研究，也是首次报道的全面阐释一种鲜为人知的生物体细胞生理学和分化的研究。
