Department of Agricultural Biotechnology, Ondokuz Mayıs University, Samsun, 55139, Turkey.
Department of Biological Sciences, Middle East Technical University, Ankara, 06800, Turkey.
Appl Microbiol Biotechnol. 2022 Sep;106(18):6139-6156. doi: 10.1007/s00253-022-12098-4. Epub 2022 Aug 10.
Clavulanic acid (CA) is a clinically important secondary metabolite used to treat infectious diseases. We aimed to decipher complex regulatory mechanisms acting in CA biosynthesis by analyzing transcriptome- and proteome-wide alterations in an industrial CA overproducer Streptomyces clavuligerus strain, namely DEPA and its wild-type counterpart NRRL3585. A total of 924 differentially expressed genes (DEGs) and 271 differentially produced proteins (DPPs) were obtained by RNA-seq and nanoLC-MS/MS analyses, respectively. In particular, CA biosynthetic genes, namely, car (cad), cas2, oat2, pah, bls, ceas2, orf12, and claR, a cluster situated regulatory (CSR) gene, were significantly upregulated as shown by RNA-seq. Enzymes of clavam biosynthesis were downregulated considerably in the DEPA strain, while the genes involved in the arginine biosynthesis, one of the precursors of CA pathway, were overexpressed. However, the biosynthesis of the other CA precursor, glyceraldehyde-3-phosphate (G3P), was not affected. CA overproduction in the DEPA strain was correlated with BldD, BldG, BldM, and BldN (AdsA) overrepresentation. In addition, TetR, WhiB, and Xre family transcriptional regulators were shown to be significantly overrepresented. Several uncharacterized/unknown proteins differentially expressed in the DEPA strain await further studies for functional characterization. Correlation analysis indicated an acceptable degree of consistency between the transcriptome and proteome data. The study represents the first integrative-omics analysis in a CA overproducer S. clavuligerus strain, providing insights into the critical control points and potential rational engineering targets for a purposeful increase of CA yields in strain improvement. KEY POINTS: ∙ Transcriptome and proteome-wide alterations in industrial CA overproducer strain DEPA ∙ An acceptable degree of consistency between the transcriptome and proteome data ∙ New targets to be exploited for rational engineering.
克拉维酸 (CA) 是一种临床重要的次级代谢产物，用于治疗传染病。我们旨在通过分析工业 CA 高产菌株即 DEPA 及其野生型 NRRL3585 的转录组和蛋白质组的广泛变化来破译作用于 CA 生物合成的复杂调控机制。通过 RNA-seq 和 nanoLC-MS/MS 分析，分别获得了 924 个差异表达基因 (DEGs) 和 271 个差异产生蛋白 (DPP)。特别是 CA 生物合成基因，即 car (cad)、cas2、oat2、pah、bls、ceas2、orf12 和 claR，一个位于集群调节 (CSR) 基因的基因，如 RNA-seq 所示，其表达显著上调。在 DEPA 菌株中，克拉维酸生物合成酶被显著下调，而 CA 途径的前体之一精氨酸生物合成的基因则被过度表达。然而，CA 的另一个前体甘油醛-3-磷酸 (G3P) 的生物合成不受影响。DEPA 菌株中 CA 的过度产生与 BldD、BldG、BldM 和 BldN (AdsA) 的过度表达有关。此外，TetR、WhiB 和 Xre 家族转录调节因子被证明过度表达。在 DEPA 菌株中差异表达的几种未鉴定/未知蛋白有待进一步研究以进行功能表征。相关性分析表明，转录组和蛋白质组数据之间具有可接受的一致性程度。该研究代表了在 CA 高产菌株 S. clavuligerus 中首次进行的综合组学分析，为有目的地提高 CA 产量提供了关键控制点和潜在的理性工程目标，以进行菌株改良。要点：·工业 CA 高产菌株 DEPA 的转录组和蛋白质组的广泛变化·转录组和蛋白质组数据之间具有可接受的一致性程度·新的目标可用于理性工程。
