School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China.
Institute for Genome Sciences, University of Maryland, School of Medicine, Baltimore, Maryland, USA.
Sci Rep. 2016 Dec 14;6:38818. doi: 10.1038/srep38818.
Degenerate Clostridium beijerinckii strain (DG-8052) can be partially recovered by supplementing CaCO to fermentation media. Genome resequencing of DG-8052 showed no general regulator mutated. This study focused on transcriptional analysis of DG-8052 and its response to CaCO treatment via microarray. The expressions of 5168 genes capturing 98.6% of C. beijerinckii NCIMB 8052 genome were examed. The results revealed that with addition of CaCO 565 and 916 genes were significantly up-regulated, and 704 and 1044 genes significantly down-regulated at acidogenic and solventogenic phase of DG-8052, respectively. These genes are primarily responsible for glycolysis to solvent/acid production (poR, pfo), solventogensis (buk, ctf, aldh, adh, bcd) and sporulation (spo0A, sigE, sigma-70, bofA), cell motility and division (ftsA, ftsK, ftsY, ftsH, ftsE, mreB, mreC, mreD, rodA), and molecular chaperones (grpE, dnaK, dnaJ, hsp20, hsp90), etc. The functions of some altered genes in DG-8052, totalling 5.7% at acidogenisis and 8.0% at sovlentogenisis, remain unknown. The response of the degenerate strain to CaCO was suggested significantly pleiotropic. This study reveals the multitude of regulatory function that CaCO has in clostridia and provides detailed insights into degeneration mechanisms at gene regulation level. It also enables us to develop effective strategies to prevent strain degeneration in future.
退化梭菌（Clostridium beijerinckii）菌株（DG-8052）可以通过在发酵培养基中添加碳酸钙部分恢复。DG-8052 的基因组重测序表明没有普遍的调控因子发生突变。本研究通过微阵列重点研究了 DG-8052 的转录分析及其对碳酸钙处理的反应。共检测到 5168 个基因的表达，占 C. beijerinckii NCIMB 8052 基因组的 98.6%。结果表明，在添加碳酸钙后，酸生成和溶剂生成期 DG-8052 的分别有 565 个和 916 个基因显著上调，704 个和 1044 个基因显著下调。这些基因主要负责糖酵解至溶剂/酸生成（poR、pfo）、溶剂生成（buk、ctf、aldh、adh、bcd）和孢子形成（spo0A、sigE、sigma-70、bofA）、细胞运动和分裂（ftsA、ftsK、ftsY、ftsH、ftsE、mreB、mreC、mreD、rodA）和分子伴侣（grpE、dnaK、dnaJ、hsp20、hsp90）等。DG-8052 中一些改变基因的功能仍未知，酸生成期有 5.7%，溶剂生成期有 8.0%。退化菌株对碳酸钙的反应提示其具有显著的多效性。本研究揭示了碳酸钙在梭菌中具有多种调节功能，并提供了在基因调控水平上对退化机制的详细了解。它还使我们能够制定未来防止菌株退化的有效策略。
