Zheng Huajun, Liu Enuo, Shi Tao, Ye Luyi, Konno Tomonobu, Oda Munehiro, Ji Zai-Si
Laboratory of Medical Foods, Shanghai Institute of Planned Parenthood Research, 2140 Xie-Tu Road, Shanghai 200032, China.
Division of Research and Development, Meiji Co., Ltd, 540 Naruda, Odawara, Kanagawa 250-0862, Japan.
Mol Biosyst. 2016 Feb;12(2):508-19. doi: 10.1039/c5mb00547g.
Lactobacillus delbrueckii subsp. bulgaricus 2038 (Lb. bulgaricus 2038) is an industrial bacterium that is used as a starter for dairy products. We proposed several hypotheses concerning its industrial features previously. Here, we utilized RNA-seq to explore the transcriptome of Lb. bulgaricus 2038 from four different growth phases under whey conditions. The most abundantly expressed genes in the four stages were mainly involved in translation (for the logarithmic stage), glycolysis (for control/lag stages), lactic acid production (all the four stages), and 10-formyl tetrahydrofolate production (for the stationary stage). The high expression of genes like d-lactate dehydrogenase was thought as a result of energy production, and consistent expression of EPS synthesis genes, the restriction-modification (RM) system and the CRISPR/Cas system were validated for explaining the advantage of this strain in yoghurt production. Several postulations, like NADPH production through GapN bypass, converting aspartate into carbon-skeleton intermediates, and formate production through degrading GTP, were proved not working under these culture conditions. The high expression of helicase genes and co-expressed amino acids/oligopeptides transporting proteins indicated that the helicase might mediate the strain obtaining nitrogen source from the environment. The transport system of Lb. bulgaricus 2038 was found to be regulated by antisense RNA, hinting the potential application of non-coding RNA in regulating lactic acid bacteria (LAB) gene expression. Our study has primarily uncovered Lb. bulgaricus 2038 transcriptome, which could gain a better understanding of the regulation system in Lb. bulgaricus and promote its industrial application.
德氏乳杆菌保加利亚亚种2038（保加利亚乳杆菌2038）是一种工业用细菌，用作乳制品发酵剂。我们之前提出了几个关于其工业特性的假设。在此，我们利用RNA测序技术探究了保加利亚乳杆菌2038在乳清条件下四个不同生长阶段的转录组。四个阶段中表达量最高的基因主要参与翻译（对数期）、糖酵解（对照/延滞期）、乳酸生成（所有四个阶段）以及10-甲酰四氢叶酸生成（稳定期）。d-乳酸脱氢酶等基因的高表达被认为是能量产生的结果，并且验证了胞外多糖合成基因、限制修饰（RM）系统和CRISPR/Cas系统的持续表达，以解释该菌株在酸奶生产中的优势。一些假设，如通过GapN旁路产生NADPH、将天冬氨酸转化为碳骨架中间体以及通过降解GTP产生甲酸，在这些培养条件下被证明不成立。解旋酶基因的高表达以及共表达的氨基酸/寡肽转运蛋白表明，解旋酶可能介导该菌株从环境中获取氮源。发现保加利亚乳杆菌2038的转运系统受反义RNA调控，这暗示了非编码RNA在调控乳酸菌（LAB）基因表达方面的潜在应用。我们的研究初步揭示了保加利亚乳杆菌2038的转录组，这有助于更好地理解保加利亚乳杆菌的调控系统并促进其工业应用。
