General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany.
Department Microbial Ecology and Diversity, Leibniz Institute German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Microb Physiol. 2020;30(1-6):9-24. doi: 10.1159/000508591. Epub 2020 Jul 24.
The marine alphaproteobacterium Phaeobacter inhibens DSM 17395, a member of the Roseobacter group, was recently shown to markedly enhance growth upon deletion of its 262-kb chromid encoding biosynthesis of tropodithietic acid (TDA). To scrutinize the metabolic/regulatory adaptations that underlie enhanced growth of the Δ262 mutant, its transcriptome and proteome compared to the wild type were investigated in process-controlled bioreactors with Casamino Acids as growth substrate. Genome resequencing revealed only few additional genetic changes (a heterogenic insertion, prophage activation, and several point mutations) between wild type and Δ262 mutant, albeit with no conceivable effect on the studied growth physiology. The abundances of the vast majority of transcripts and proteins involved in the catabolic network for complete substrate oxidation to CO2 were found to be unchanged, suggesting that the enhanced amino acid utilization of the Δ262 mutant did not require elevated synthesis of most enzymes of the catabolic network. Similarly, constituents of genetic information processing and cellular processes remained mostly unchanged. In contrast, 426 genes displayed differential expression, of which 410 were localized on the 3.2-Mb chromosome, 5 on the 65-kb chromid, and 11 on the 78-kb chromid. Notably, the branched-chain amino transferase IlvE acting on rapidly utilized Val, Ile, and Leu was upregulated. Moreover, the transportome was reconfigured, as evidenced from increased abundances of transcripts and proteins of several uptake systems for amino acids and inorganic nutrients (e.g., phosphate). Some components of the respiratory chain were also upregulated, which correlates with the higher respiration rates of the Δ262 mutant. Furthermore, chromosomally encoded transcripts and proteins that are peripherally related to TDA biosynthesis (e.g., the serine acyl transferase CysE) were strongly downregulated in the Δ262 mutant. Taken together, these observations reflect adaptations to enhanced growth as well as the functional interconnectivity of the replicons of P. inhibens DSM 17395.
海洋 α-变形菌 Phaeobacter inhibens DSM 17395 是 Roseobacter 群的成员，最近的研究表明，该菌缺失 262kb 大小的染色体后，其生长明显加快，该染色体编码 Tropodithietic Acid (TDA) 的生物合成。为了深入研究增强生长的代谢/调控适应机制，我们在以 Casamino Acids 为生长基质的过程控制生物反应器中，比较了野生型和Δ262 突变株的转录组和蛋白质组。基因组重测序结果表明，尽管在研究的生长生理学方面没有任何可想象的影响，但在野生型和Δ262 突变株之间仅发现了少数额外的遗传变化（杂合插入、噬菌体激活和几个点突变）。参与完全底物氧化为 CO2 的分解代谢网络的绝大多数转录物和蛋白质的丰度保持不变，这表明Δ262 突变株增强的氨基酸利用并不需要大多数分解代谢网络酶的合成增加。同样，遗传信息处理和细胞过程的组成部分也基本不变。相反，426 个基因显示出差异表达，其中 410 个位于 3.2Mb 染色体上，5 个位于 65kb 染色体上，11 个位于 78kb 染色体上。值得注意的是，作用于快速利用 Val、Ile 和 Leu 的支链氨基酸转移酶 IlvE 上调。此外，转运体也被重新配置，这可以从氨基酸和无机营养物（如磷酸盐）的几个摄取系统的转录物和蛋白质的增加得到证明。呼吸链的一些组成部分也上调，这与Δ262 突变株更高的呼吸速率相关。此外，与 TDA 生物合成相关的染色体编码转录物和蛋白质（例如丝氨酸酰基转移酶 CysE）在Δ262 突变株中强烈下调。总之，这些观察结果反映了对增强生长的适应以及 P. inhibens DSM 17395 复制子的功能相互连接。
