Jun Ji-Su, Jeong Hyang-Eun, Moon Su-Yeong, Shin Se-Hee, Hong Kwang-Won
Department of Food Science and Biotechnology, College of Life Science and Biotechnology, Dongguk University, Goyang-si 10326, Republic of Korea.
Microorganisms. 2023 Jul 28;11(8):1928. doi: 10.3390/microorganisms11081928.
DB104, an extracellular protease-deficient derivative of 168, is widely used for recombinant protein expression. An understanding of the changes in gene expression during growth is essential for the commercial use of bacterial strains. Transcriptome and proteome analyses are ideal methods to study the genomic response of microorganisms. In this study, transcriptome analysis was performed to monitor changes in the gene expression level of DB104 while growing on a complete medium. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, K-mean cluster analysis, gene ontology (GO) enrichment analysis, and the function of sigma factors were used to divide 2122 differentially expressed genes (DEGs) into 10 clusters and identified gene functions according to expression patterns. The results of KEGG pathway analysis indicated that ABC transporter is down-regulated during exponential growth and metabolic changes occur at the transition point where sporulation starts. At this point, several stress response genes were also turned on. The genes involved in the lipid catabolic process were up-regulated briefly at 15 h as an outcome of the programmed cell death that postpones sporulation. The results suggest that changes in the gene expression of DB104 were dependent on the initiation of sporulation. However, the expression timing of the spore coat gene was only affected by the relevant sigma factor. This study can help to understand gene expression and regulatory mechanisms in species by providing an overall view of transcriptional changes during the growth of DB104.
DB104是168的一种细胞外蛋白酶缺陷衍生物，被广泛用于重组蛋白表达。了解生长过程中基因表达的变化对于细菌菌株的商业应用至关重要。转录组和蛋白质组分析是研究微生物基因组反应的理想方法。在本研究中，进行了转录组分析以监测DB104在完全培养基上生长时基因表达水平的变化。利用京都基因与基因组百科全书（KEGG）分析、K均值聚类分析、基因本体（GO）富集分析以及σ因子的功能，将2122个差异表达基因（DEG）分为10个簇，并根据表达模式确定基因功能。KEGG通路分析结果表明，ABC转运蛋白在指数生长期间下调，并且在孢子形成开始的过渡点发生代谢变化。此时，几个应激反应基因也被开启。参与脂质分解代谢过程的基因在15小时时短暂上调，这是推迟孢子形成的程序性细胞死亡的结果。结果表明，DB104的基因表达变化取决于孢子形成的起始。然而，孢子壁基因的表达时间仅受相关σ因子的影响。本研究通过提供DB104生长过程中转录变化的整体视图，有助于了解该物种的基因表达和调控机制。
