Xia Kai, Liu Fang-Mei, Chen Yu-Qing, Chen Shan-Shan, Huang Chun-Ying, Zhao Xue-Qun, Sha Ru-Yi, Huang Jun
Zhejiang Provincial Collaborative Innovation Center of Agricultural Biological Resources Biochemical Manufacturing, Key Laboratory of Chemical and Biological Processing Technology for Farm Products of Zhejiang Province, School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, China.
Yi Chuan. 2023 Oct 20;45(10):904-921. doi: 10.16288/j.yczz.23-139.
Combined mutagenesis is widely applied for the breeding of robust used in the production of erythritol. However, the changes of genome after mutagenesis remains unclear. This study aimed to unravel the mechanism involved in the improved erythritol synthesis of CA20 and the evolutionary relationship between different by comparative genomics analysis. The results showed that the genome size of CA20 was 20,420,510 bp, with a GC content of 48.97%. There were 6330 CDS and 649 ncRNA (non-coding RNA) in CA20 genome. Average nucleotide identity (ANI) analysis showed that CA20 genome possessed high similarity (ANI > 99.50%) with other strains, while phylogenetic analysis displayed that CA20 was classified together with IBT 446 and H222. CA20 shared 5342 core orthologous genes with the 8 strains while harbored 65 specific genes that mainly participated in the substrate and protein transport processes. CA20 contained 166 genes coding for carbohydrate-active enzymes (CAZymes), which was more than that found in other strains (108－137). Notably, 4, 2, and 13 different enzymes belonging to glycoside hydrolases (GHs), glycosyltransferases (GTs), and carbohydrate esterases (CEs), respectively, were only found in CA20. The enzymes involved in the metabolic pathway of erythritol were highly conserved in , except for transaldolase (TAL1). In addition, the titer and productivity of erythritol by CA20 were 190.97 g/L and 1.33 g/L/h, respectively, which were significantly higher than that of WT5 wherein 128.61 g/L and 0.92 g/L/h were obtained (< 0.001). Five frameshift mutation genes and 15 genes harboring nonsynonymous mutation were found in CA20 compared with that of WT5. Most of these genes were involved in the cell division, cell wall synthesis, protein synthesis, and protein homeostasis maintenance. These findings suggested that the genome of is conserved during evolution, and the variance of living environment is one important factor leading to genome divergence. The varied number of CAZymes existed in is one factor that contributes to the performance difference. The increased synthesis of erythritol by CA20 is correlated with the improvement of the stability of cell structure and internal environment. The results of this study provide a basis for the directional breeding of robust strains used in erythritol production.
复合诱变广泛应用于用于生产赤藓糖醇的优良菌株的育种。然而，诱变后基因组的变化仍不清楚。本研究旨在通过比较基因组学分析揭示CA20中赤藓糖醇合成改善所涉及的机制以及不同[菌株名称未给出]之间的进化关系。结果表明，CA20的基因组大小为20,420,510 bp，GC含量为48.97%。CA20基因组中有6330个编码序列（CDS）和649个非编码RNA（ncRNA）。平均核苷酸同一性（ANI）分析表明，CA20基因组与其他[菌株名称未给出]菌株具有高度相似性（ANI > 99.50%），而系统发育分析显示CA20与[菌株名称未给出]IBT 446和[菌株名称未给出]H222归为一类。CA20与8个菌株共有5342个核心直系同源基因，同时含有65个主要参与底物和蛋白质转运过程的特异性基因。CA20包含166个编码碳水化合物活性酶（CAZymes）的基因，比其他菌株（108 - 137个）中的数量更多。值得注意的是，仅在CA20中发现分别属于糖苷水解酶（GHs）、糖基转移酶（GTs）和碳水化合物酯酶（CEs）的4个、2个和13个不同的酶。除转醛醇酶（TAL1）外，赤藓糖醇代谢途径中涉及的酶在[菌株名称未给出]中高度保守。此外，CA20产生的赤藓糖醇的滴度和生产率分别为190.97 g/L和1.33 g/L/h，显著高于WT5（分别为128.61 g/L和0.92 g/L/h，P < 0.001）。与WT5相比，在CA20中发现了5个移码突变基因和15个携带非同义突变的基因。这些基因大多参与细胞分裂、细胞壁合成、蛋白质合成和蛋白质稳态维持。这些发现表明，[菌株名称未给出]的基因组在进化过程中是保守的，生存环境的差异是导致基因组分化的一个重要因素。[菌株名称未给出]中存在的不同数量的CAZymes是导致性能差异的一个因素。CA20中赤藓糖醇合成的增加与细胞结构和内部环境稳定性的提高相关。本研究结果为用于赤藓糖醇生产的优良菌株的定向育种提供了依据。
