ZHANG Yue, WANG Kaifang, PAN Long, CHEN Xusheng
ε-Poly-lysine (ε-PL) is a naturally occurring poly(amino acid) consisting of 25-35 L-lysine residues with amide linkages formed between the α-carboxyl group and the ε-amino group of the side chain, which possesses excellent antibacterial activity against bacteria and fungi. As a natural preservative, ε-PL is widely used in the food industry. Streptomyces albulus is one of the major ε-PL producers, which can only secret a large amount of ε-PL under environmental conditions around pH 4.0, so it is often subject to acid stress. However, few studies have focused on the physiological mechanisms of S. albulus in responds to low pH stress. Here, we investigated the effect of different pH on the cell growth and ε-PL synthesis of S. albulus M-Z18. The results showed that S. albulus M-Z18 could grow normally when pH>3.5, while ε-PL can accumulate when pH≤5, and its production gradually increased with the decreased pH level. Subsequently, the physiological mechanisms of S. albulus M-Z18 in response to low pH stress were investigated by comparative transcriptome analysis. The chemostat culture assay was conducted at different pH (5.5, 4.0) by S. albulus M-Z18, and a global transcriptional analysis at pH 5.5 and pH 4.0 were investigated. A total of 3 893 significantly differentially expressed genes (DEGs) were detected at pH 4.0 compared to pH 5.5, with 1 786 significantly up-regulated DEGs and 2 107 down-regulated DEGs, representing 53.97% of the number of genes detected. This result indicated that S. albulus M-Z18 gene expression was significantly altered in response to low pH stress. GO and KEGG analyses of DEGs showed that DEGs were mainly concentrated in biological process (GO analysis) and metabolism (KEGG analysis). Further analysis revealed that genes related to the third stage of the glycolytic pathway, TCA cycle, oxidative phosphorylation pathway and the oxidative stage of the pentose phosphate pathway were significantly upregulated, while genes related to the non-oxidative stage of the pentose phosphate pathway were significantly downregulated. These suggests that the acid tolerance of S. albulus M-Z18 may be enhanced by the improved cell metabolism. The analysis of the cell wall peptidoglycan synthesis pathway showed significant down-regulation of several genes involved in the first phase of cell wall peptidoglycan synthesis, which would lead to an overall limitation of peptidoglycan synthesis. However, some genes involved in peptidoglycan cross-linking and modification were significantly up-regulated at pH 4.0, which would help to increase the rate of cell wall peptidoglycan cross-linking and maintain the integrity of the S. albulus M-Z18 cell wall at low pH. Meanwhile, analysis of the cell membrane fatty acid synthesis pathway showed that genes related to cell membrane unsaturated fatty acid and cyclopropane fatty acid synthesis were significantly up-regulated at pH 4.0, which suggested that the unsaturation of cell membrane fatty acids and the content of cyclopropane fatty acids may be increased. S. albulus M-Z18 may limit the entry of H+ into the cell by altering the fatty acid components of the cell membrane, which is conductive to the maintenance of normal physiological functions of S. albulus M-Z18 in a low pH environment. In addition, the analysis of the amino acid synthesis pathway indicated that the synthesis of most amino acids was reduced, but the synthesis of some basic amino acids (histidine and lysine) and substrates of amino acid tolerant systems (glutamate and glutamine) was enhanced, which is advantageous for S. albulus M-Z18 to maintain the stability of intracellular pH. Finally, the changes in genes related to the protection and repair of the intracellular macromolecules under low pH conditions were analyzed. The results showed that molecular chaperone genes, ATP-dependent protease genes, nucleotide excision repair and non-homologous end-joining repair-related genes were significantly up-regulated, indicating that the protein repair capacity and DNA damage repair of S. albulus M-Z18 were enhanced in at low pH, which helped the strain to repair the damage caused by acid stress. The transcriptome data were further retrieved, and S. albulus M-Z18 genome was found to harbor a glutamate decarboxylase system, a glutamate-glutamine transporter protein system, a lysine decarboxylase system, an agmatine deaminase deiminase system, a urease system and an arginine deiminase system. As a result, the glutamate decarboxylase system, glutamate-glutamine transporter protein system, agmatine deiminase system and urease system were all up-regulated to different degrees at pH 4.0. Interestingly, the urease subunit α (UreC) and nickel transporter protein (NixA) were significantly up-regulated by 84.64-fold and 47.97-fold, respectively, which suggests that the urease system may play an important role in the resistance of S. albulus M-Z18 to acid stress. In conclusion, S. albulus M-Z18 may response to low pH stress by enhancing cell metabolism, alkaline amino acid synthesis, cell membrane fluidity, protein and DNA repair capacity, acid tolerance systems as well as maintaining cell wall integrity. The above results provide guidance for further investigation on the molecular mechanism of S. albulus in response to low pH stress.