Infectious and Inflammatory Diseases Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA.
Graduate School of Biostudies, Kyoto University, Kyoto, Japan.
mSystems. 2022 Oct 26;7(5):e0034322. doi: 10.1128/msystems.00343-22. Epub 2022 Sep 12.
Bifidobacterium longum subsp. is a prevalent beneficial bacterium that colonizes the human neonatal gut and is uniquely adapted to efficiently use human milk oligosaccharides (HMOs) as a carbon and energy source. Multiple studies have focused on characterizing the elements of HMO utilization machinery in B. longum subsp. ; however, the regulatory mechanisms governing the expression of these catabolic pathways remain poorly understood. A bioinformatic regulon reconstruction approach used in this study implicated NagR, a transcription factor from the ROK family, as a negative global regulator of gene clusters encoding lacto--biose/galacto--biose (LNB/GNB), lacto--tetraose (LNT), and lacto--neotetraose (LNnT) utilization pathways in B. longum subsp. This conjecture was corroborated by transcriptome profiling upon genetic inactivation and experimental assessment of binding of recombinant NagR to predicted DNA operators. The latter approach also implicated acetylglucosamine (GlcNAc), a universal intermediate of LNT and LNnT catabolism, and its phosphorylated derivatives as plausible NagR transcriptional effectors. Reconstruction of NagR regulons in various lineages revealed multiple potential regulon expansion events, suggesting evolution from a local regulator of GlcNAc catabolism in ancestral bifidobacteria to a global regulator controlling the utilization of mixtures of GlcNAc-containing host glycans in B. longum subsp. and Bifidobacterium bifidum. The predominance of bifidobacteria in the gut of breastfed infants is attributed to the ability of these bacteria to metabolize human milk oligosaccharides (HMOs). Thus, individual HMOs such as lacto--tetraose (LNT) and lacto--neotetraose (LNnT) are considered promising prebiotics that would stimulate the growth of bifidobacteria and confer multiple health benefits to preterm and malnourished children suffering from impaired (stunted) gut microbiota development. However, the rational selection of HMO-based prebiotics is hampered by the incomplete knowledge of regulatory mechanisms governing HMO utilization in target bifidobacteria. This study describes NagR-mediated transcriptional regulation of LNT and LNnT utilization in Bifidobacterium longum subsp. . The elucidated regulatory network appears optimally adapted to simultaneous utilization of multiple HMOs, providing a rationale to add HMO mixtures (rather than individual components) to infant formulas. The study also provides insights into the evolutionary trajectories of complex regulatory networks controlling carbohydrate metabolism in bifidobacteria.
长双歧杆菌亚种是一种普遍存在的有益细菌，它定植于人类新生儿肠道，能够有效地利用人乳寡糖（HMO）作为碳源和能源。多项研究集中于鉴定长双歧杆菌亚种中 HMO 利用机制的元件；然而，调控这些分解代谢途径表达的机制仍知之甚少。本研究采用生物信息学调控子重建方法，发现 ROK 家族的转录因子 NagR 是编码乳糖-β-半乳糖/乳糖-β-葡萄糖（LNB/GNB）、乳糖-四糖（LNT）和乳糖-新四糖（LNnT）利用途径的基因簇的负全局调控因子。这一推测得到了遗传失活后的转录组分析和重组 NagR 与预测 DNA 操作子结合的实验评估的证实。后一种方法还表明，N-乙酰氨基葡萄糖（GlcNAc），LNT 和 LNnT 分解代谢的普遍中间产物及其磷酸化衍生物可能是 NagR 的转录效应物。在不同谱系中重建 NagR 调控子揭示了多个潜在的调控子扩展事件，表明它是从古老双歧杆菌中 GlcNAc 分解代谢的局部调控因子进化而来，成为控制长双歧杆菌亚种和双歧双歧杆菌中 GlcNAc 含量宿主糖混合物利用的全局调控因子。母乳喂养婴儿肠道中双歧杆菌的优势归因于这些细菌代谢人乳寡糖（HMO）的能力。因此，个别 HMO 如乳糖-四糖（LNT）和乳糖-新四糖（LNnT）被认为是有前途的益生元，它们可以刺激双歧杆菌的生长，并为患有受损（发育迟缓）肠道微生物群发育的早产儿和营养不良儿童带来多种健康益处。然而，由于对目标双歧杆菌中 HMO 利用的调控机制了解不完整，基于 HMO 的益生元的合理选择受到阻碍。本研究描述了 NagR 介导的长双歧杆菌亚种中 LNT 和 LNnT 利用的转录调控。阐明的调控网络似乎最适合同时利用多种 HMO，为在婴儿配方中添加 HMO 混合物（而不是单个成分）提供了依据。该研究还为控制双歧杆菌碳水化合物代谢的复杂调控网络的进化轨迹提供了见解。
