To analyze the mechanism of the
acid tolerance response (ATR) in Bifidobacterium longum subsp.
longum BBMN68, we optimized the
acid-adaptation condition to stimulate ATR effectively and analyzed the change of gene expression profile after
acid-adaptation using high-throughput
RNA-Seq. After
acid-adaptation at pH 4.5 for 2 hours, the survival rate of BBMN68 at lethal pH 3.5 for 120 min was increased by 70 fold and the expression of 293 genes were upregulated by more than 2 fold, and 245 genes were downregulated by more than 2 fold. Gene expression profiling of ATR in BBMN68 suggested that, when the bacteria faced
acid stress, the cells strengthened the integrity of cell wall and changed the permeability of membrane to keep the H(+) from entering. Once the H(+) entered the cytoplasm, the cells showed four main responses: First, the F(0)F(1)-ATPase system was initiated to discharge H(+). Second, the ability to produce NH(3) by
cysteine-
cystathionine-cycle was strengthened to neutralize excess H(+). Third, the cells started NER-UVR and NER-VSR systems to minimize the damage to
DNA and upregulated HtpX, IbpA, and γ-glutamylcysteine production to protect
proteins against damage. Fourth, the cells initiated global response signals ((
p)ppGpp,
polyP, and Sec-SRP) to bring the whole cell into a state of response to the stress. The cells also secreted the quorum sensing signal (AI-2) to communicate between intraspecies cells by the cellular signal system, such as two-component systems, to improve the overall survival rate. Besides, the cells varied the pathways of producing energy by shifting to BCAA metabolism and enhanced the ability to utilize
sugar to supply sufficient energy for the operation of the mechanism mentioned above. Based on these reults, it was inferred that, during industrial applications, the
acid resistance of bifidobacteria could be improved by adding BCAA, γ-glutamylcysteine,
cysteine, and
cystathionine into the
acid-stress environment.