Integrated Transcriptomic and Proteomic Analysis of the Bile Stress Response in a Centenarian-originated Probiotic Bifidobacterium longum BBMN68

Abstract

Bifidobacteria are natural inhabitants of the human gastrointestinal tract and well known for their health-promoting effects. Tolerance to bile stress is crucial for bifidobacteria to survive in the colon and to exert their beneficial actions. In this work, RNA-Seq transcriptomic analysis complemented with proteomic analysis was used to investigate the cellular response to bile in Bifidobacterium longum BBMN68. The transcript levels of 236 genes were significantly changed (> threefold, p < 0.001) and 44 proteins were differentially abundant (>1.6-fold, p < 0.01) in B. longum BBMN68 when exposed to 0.75 g l ؊1 ox-bile. The hemolysin-like protein and bile efflux systems were significantly over produced, which might prevent bile adsorption and exclude bile, respectively. The cell membrane composition was modified probably by an increase of cyclopropane fatty acid and a decrease of transmembrane proteins, resulting in a cell membrane more impermeable to bile salts. Our hypothesis was later confirmed by surface hydrophobicity assay. The transcription of genes related to xylose utilization and bifid shunt were up-regulated, which increased the production of ATP and reducing equivalents to cope with bile-induced damages in a xylan-rich colon environment. Bile salts signal the B. longum BBMN68 to gut entrance and enhance the expression of esterase and sortase associated with adhesion and colonization in intestinal tract, which was supported by a fivefold increased adhesion ability to HT-29 cells by BBMN68 upon bile exposure. Notably, bacterial one-hybrid and EMSA assay revealed that the two-component system senX3-regX3 controlled the expression of pstS in bifidobacteria and the role of this target gene in bile resistance was further verified by heterologous expression in Lactococcus lactis. Taken altogether, this study established a model for global response mechanisms in B. longum to bile. Molecular & Cellular

Quantitative proteomics of Lactococcus lactis F44 under cross-stress of low pH and lactate

“…Furthermore, the GroEL/ES complex is responsible for appropriate protein folding and frequently participates in response to diverse stresses. The transcription of groES is also increased with exposure to bile salts or acidic environments (Wu et al, 2012;An et al, 2014). Analogously, chaperone GroEL upregulation preserves protein function under acid stress in Strep.…”

Tools to map target genes of bacterial two‐component system response regulators

“…A binding site motif can be determined from the sequences obtained and then the bacterial genome can be scanned for the motif to identify target promoters (Meng et al ., ; Meng and Wolfe, ). The bacterial one‐hybrid screen has been successfully used to determine the regulon for a few RRs (Tomljenovic‐Berube et al ., ; An et al ., ; Svensson et al ., ; Hebdon et al ., ). This screen can also be used to determine the TFs that bind to a particular promoter of interest, as was done for M .…”

Functional role oftlyC1encoding a hemolysin-like protein fromBifidobacterium longumBBMN68 in bile tolerance

“…longum BBMN68 (CGMCC 2265) was isolated from healthy centenarians in Bama longevity villages of Guangxi province in China (Yang et al ., ). In previous work from our research group, RNA‐Seq transcriptomic analysis showed that the tlyC1 gene from B. longum BBMN68 was 10‐fold upregulated upon ox‐bile exposure (An et al ., ). TlyC1 is a hemolysin‐like protein (HLP), belonging to the large YGGT protein family (EMBL InterPro accession no.…”