Bacillus pumilus BA06 has great potential for the production of alkaline proteases. To improve the protease yield, classical mutagenesis to combine the physical and chemical mutagens was performed to obtain a protease hyper-productive mutant SCU11. The full genome sequences of BA06 and SCU11 strains were assembled through DNA sequencing using the PacBio sequencing platform. By comparative genomics analysis, 147 SNPs and 15 InDels were found between these two genomes, which lead to alternation of coding sequence in 15 genes. Noticeable, the gene (kinA) encoding sporulation kinase A is interrupted by introducing a stop codon in its coding region in BA06. Interestedly, this gene is reversely corrected in SCU11. Furthermore, comparative transcriptome analysis revealed that kinA and two positive regulatory genes (DegU and Spo0A) were upregulated in transcription in SCU11. In terms of the transcriptional data, upregulation of a phosphorylation cascade starting with KinA may enhance Spo0A phosphorylation, and thus activate expression of the gene aprE (encoding major extracellular protease) through repression of AbrB (a repressor of aprE) and activation of SinI, an antagonist of SinR (a repressor of aprE). In addition, the other genes involved in various metabolic pathways, especially of membrane transport and sporulation, were altered in transcription between these two strains. Conclusively, our transcriptome data suggested that upregulation degU and spo0A, as well as kinA, may at least partially contribute to the high production of alkaline protease in SCU11.

中文翻译：

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通过比较基因组和转录组学分析表征短小芽孢杆菌蛋白酶高产突变体

短小芽孢杆菌 BA06 具有生产碱性蛋白酶的巨大潜力。为了提高蛋白酶产量，进行了结合物理和化学诱变剂的经典诱变，以获得蛋白酶高产突变体 SCU11。BA06 和 SCU11 菌株的全基因组序列是使用 PacBio 测序平台通过 DNA 测序组装的。通过比较基因组学分析，在这两个基因组之间发现了147个SNP和15个InDels，导致15个基因的编码序列发生改变。值得注意的是，编码孢子形成激酶 A 的基因 (kinA) 通过在 BA06 的编码区引入终止密码子而中断。有趣的是，该基因在 SCU11 中被反向校正。此外，比较转录组分析显示 kinA 和两个正调节基因（DegU 和 Spo0A）在 SCU11 中的转录上调。在转录数据方面，从 KinA 开始的磷酸化级联的上调可能会增强 Spo0A 磷酸化，从而通过抑制 AbrB（aprE 的阻遏物）和激活 SinI 来激活基因 aprE（编码主要胞外蛋白酶）的表达。 SinR 的拮抗剂（aprE 的阻遏物）。此外，参与各种代谢途径的其他基因，尤其是膜转运和孢子形成，在这两种菌株之间的转录中发生了改变。最后，我们的转录组数据表明，degU 和 spo0A 以及 kinA 的上调可能至少部分有助于 SCU11 中碱性蛋白酶的高产量。