Patakova Petra, Branska Barbora, Vasylkivska Maryna, Jureckova Katerina, Musilova Jana, Provaznik Ivo, Sedlar Karel
University of Chemistry and Technology Prague, Technicka 5, 16628 Prague 6, Czech Republic.
University of Chemistry and Technology Prague, Technicka 5, 16628 Prague 6, Czech Republic.
Biotechnol Adv. 2022 Sep;58:107889. doi: 10.1016/j.biotechadv.2021.107889. Epub 2021 Dec 17.
Solventogenic clostridia are not a strictly defined group within the genus Clostridium but its representatives share some common features, i.e. they are anaerobic, non-pathogenic, non-toxinogenic and endospore forming bacteria. Their main metabolite is typically 1-butanol but depending on species and culture conditions, they can form other metabolites such as acetone, isopropanol, ethanol, butyric, lactic and acetic acids, and hydrogen. Although these organisms were previously used for the industrial production of solvents, they later fell into disuse, being replaced by more efficient chemical production. A return to a more biological production of solvents therefore requires a thorough understanding of clostridial metabolism. Transcriptome analysis, which reflects the involvement of individual genes in all cellular processes within a population, at any given (sampling) moment, is a valuable tool for gaining a deeper insight into clostridial life. In this review, we describe techniques to study transcription, summarize the evolution of these techniques and compare methods for data processing and visualization of solventogenic clostridia, particularly the species Clostridium acetobutylicum and Clostridium beijerinckii. Individual approaches for evaluating transcriptomic data are compared and their contributions to advancements in the field are assessed. Moreover, utilization of transcriptomic data for reconstruction of computational clostridial metabolic models is considered and particular models are described. Transcriptional changes in glucose transport, central carbon metabolism, the sporulation cycle, butanol and butyrate stress responses, the influence of lignocellulose-derived inhibitors on growth and solvent production, and other respective topics, are addressed and common trends are highlighted.
产溶剂梭菌并非梭菌属中严格定义的一个类群，但其代表菌株具有一些共同特征，即它们是厌氧、非致病性、不产毒素且能形成芽孢的细菌。它们的主要代谢产物通常是1-丁醇，但根据菌种和培养条件的不同，它们还能形成其他代谢产物，如丙酮、异丙醇、乙醇、丁酸、乳酸、乙酸以及氢气。尽管这些微生物曾被用于工业溶剂生产，但后来逐渐被淘汰，取而代之的是更高效的化学合成方法。因此，要恢复到更多基于生物途径的溶剂生产，就需要深入了解梭菌的代谢过程。转录组分析能够反映在任何给定（采样）时刻群体中各个基因在所有细胞过程中的参与情况，是深入了解梭菌生命过程的一个有价值的工具。在这篇综述中，我们描述了研究转录的技术，总结了这些技术的发展历程，并比较了产溶剂梭菌，特别是丙酮丁醇梭菌和拜氏梭菌的数据处理和可视化方法。我们比较了评估转录组数据的各种方法，并评估了它们对该领域进展的贡献。此外，还考虑了利用转录组数据重建梭菌计算代谢模型的情况，并描述了具体的模型。文中还探讨了葡萄糖转运、中心碳代谢、芽孢形成周期、丁醇和丁酸盐应激反应、木质纤维素衍生抑制剂对生长和溶剂生产的影响等方面的转录变化，并突出了共同趋势。
