Yirong Sun

Foodborne pathogens exploit acid resistance (AR) mechanisms to survive harsh environments, such as the stomach, increasing contamination risk. While the sigma factor RpoS and cyclic AMP receptor protein (Crp) are known mediators of AR, their systemic regulatory networks remain unclear. Here, we integrated transcriptomics and metabolomics to dissect RpoS- and Crp-dependent responses in E. coli under simulated gastrointestinal neutral (pH 7.5) and acidic (pH 5.5) conditions. We identified 78 coregulated genes, with RpoS dominating energy/amino acid metabolism and Crp primarily modulating amino acid pathways. Both regulators upregulate membrane components (fatty acids, chaperones, transporters) essential for AR, with transporters NarU (RpoS-dependent) and AmtB (Crp-dependent) conferring exceptional survival at pH 2.5. Surprisingly, Crp activates flagellar genes, whereas RpoS suppresses them during acid stress. Our work provides a systems-level understanding of AR adaptation, offering translational potential for antimicrobial development and bioremediation strain engineering. IMPORTANCE: Escherichia coli and other gut bacteria colonize or infect the extremely acidic environment of the gastrointestinal tract through the acid resistance mechanism. Therefore, it is necessary to investigate the acid resistance mechanism of intestinal bacteria. Although RpoS and Crp have long been found to regulate the acid resistance of E. coli , there is a lack of systematic research to analyze its regulatory network under the acidic environment. Through an integrated approach combining genomic analysis, we obtained robust research findings. These results establish a novel theoretical framework for understanding microbial adaptation to acidic environments while offering potential applications for developing new antibiotic targets against intestinal pathogens and engineering industrial bacterial strains with enhanced acid tolerance capabilities.

Radiation exposure from environmental sources, medical procedures, or space exploration poses considerable risks to human health, with profound effects on immune function and inflammatory responses. Radiotherapy (RT) is a cornerstone of modern cancer treatment, leveraging ionizing radiation to induce DNA damage and tumor cell death. However, its biological effects extend beyond direct cytotoxicity, exerting complex and context-dependent influences on both innate and adaptive immunity. Ionizing radiation can enhance antitumor immune responses by promoting tumor antigen release, activating dendritic cells, and augmenting cytotoxic T-cell priming. Conversely, it can also induce immunosuppressive mechanisms, including lymphocyte depletion, regulatory T-cell expansion, immune checkpoint upregulation, and chronic inflammatory signaling, which may limit therapeutic efficacy. These immune effects are critical for optimizing RT protocols, particularly in the era of immunotherapy, where immune modulation plays a pivotal role in treatment efficacy. This review summarizes the current knowledge concerning how radiation induces immune and inflammatory responses in cells and tissues; focuses on key molecular pathways such as the DNA damage response, cGAS–STING signaling, and immune checkpoint modulation; and discusses their clinical implications. These findings provide potential therapeutic strategies for cancer treatment by harnessing the immunomodulatory potential of radiation while reducing adverse effects and for the prevention and treatment of radiation-related diseases.

Acute ionizing radiation (IR) causes severe DNA damage, leading to cell cycle arrest, cell death, and activation of the innate immune system. The role and signaling pathway of stimulator of interferon genes (STING) in IR-induced tissue damage and cell death are not well understood. This study revealed that STING is crucial for promoting apoptosis in response to DNA damage caused by acute IR both in vitro and in vivo. STING binds to poly (ADP‒ribose) (PAR) produced by activated poly (ADP‒ribose) polymerase-1 (PARP1) upon IR. Compared with that in WT cells, apoptosis was suppressed in Sting ^gt-/gt- cells. Excessive PAR production by PARP1 due to DNA damage enhances STING phosphorylation, and inhibiting PARP1 reduces cell apoptosis after IR. In vivo, IR-induced crypt cell death was significantly lower in Sting ^gt-/gt- mice or with low-dose PARP1 inhibitor, PJ34, resulting in substantial resistance to abdominal irradiation. STING deficiency or inhibition of PARP1 function can reduce the expression of the proapoptotic gene PUMA, decrease the localization of Bax on the mitochondrial membrane, and thus reduce cell apoptosis. Our findings highlight crucial roles for STING and PAR in the IR-mediated induction of apoptosis, which may have therapeutic implications for controlling radiation-induced apoptosis or acute radiation symptoms.

Antigen-specific T cell receptor-engineered T cell (TCR-T) based immunotherapy has proven to be an effective method to combat cancer. In recent years, cross-talk between the innate and adaptive immune systems may be requisite to optimize sustained antigen-specific immunity, and the stimulator of interferon genes (STING) is a promising therapeutic target for cancer immunotherapy. The level of expression or presentation of antigen in tumor cells affects the recognition and killing of tumor cells by TCR-T. This study aimed at investigating the potential of innate immune stimulation of T cells and engineered T cells to enhance immunotherapy for low-expression antigen cancer cells. We systematically investigated the function and mechanism of cross-talk between STING agonist diABZI and adaptive immune systems. We established NY-ESO-1 full knockout Mel526 cells for this research and found that diABZI activated STING media and TCR signaling pathways. In addition, the results of flow cytometry showed that antigens presentation from cancer cells induced by STING agonist diABZI also improved the affinity of TCR-T cells function against tumor cells in vitro and in vivo. Our findings revealed that diABZI enhanced the immunotherapy efficacy of TCR-T by activating STING media and TCR signaling pathways, improving interferon-γ expression, and increasing antigens presentation of tumor cells. This indicates that STING agonist could be used as a strategy to promote TCR-T cancer immunotherapy.

Uncoupling protein-1 (UCP1), located at the inner membrane of mitochondria, is expressed primarily in brown adipose tissue and mediates the permeability of protons through the inner mitochondrial membrane. This research examines whether human UCP1 can uncouple oxidative phosphorylation in E. coli. Recombinant human UCP1 that includes an N terminus signal peptide for the bacterial inner membrane was expressed in E. coli. Our testing showed that UCP1 functions as a proton transporter in the bacterial membrane, increasing its permeability, decrease ATP synthesis at neutral pH and reducing the viability of E. coli in markedly acidic environments. These results suggest that UCP1 can uncouple oxidative phosphorylation in E. coli. The decreased acid resistance (AR) of E. coli with UCP1 expressed in the membranes confirmed that oxidative phosphorylation plays a role in AR through the pumping of protons to regulate the intracellular pH, and demonstrate that UCP1 can be used as an uncoupler protein for bacterial metabolic research.

Sulforaphane (SFN) is an organic isothiocyanate and an NF-E2-related factor-2 (Nrf2) inducer that exerts prophylactic effects on depression-like behavior in mice. However, the underlying mechanisms remain poorly understood. Brain-derived neurotrophic factor (BDNF), a neurotrophin, is widely accepted for its antidepressant effects and role in stress resilience. Here, we show that SFN confers stress resilience via BDNF upregulation and changes in abnormal dendritic spine morphology in stressed mice, which is accompanied by rectifying the irregular levels of inflammatory cytokines. Mechanistic studies demonstrated that SFN activated Nrf2 to promote BDNF transcription by binding to the exon I promoter, which is associated with increased Nrf2, and decreased methyl-CpG binding protein-2 (MeCP2), a transcriptional suppressor of BDNF, in BV2 microglial cells. Furthermore, SFN inhibited the pro-inflammatory phenotype and activated the anti-inflammatory phenotype of microglia, which was associated with increased Nrf2 and decreased MeCP2 expression in microglia of stressed mice. Hence, our findings support that Nrf2 induces BDNF transcription via upregulation of Nrf2 and downregulation of MeCP2 in microglia, which is associated with changes in the morphology of damaged dendritic spines in stressed mice. Meanwhile, the data presented here provide evidence for the application of SFN as a candidate for the prevention and intervention of depression.

Objective. This study aims to evaluate the efficacy and safety of traditional Chinese medicine (TCM) therapy of tonifying kidney and activating blood circulation (TKABC) based on the theory of kidney deficiency and blood stasis for the treatment of immune infertility. Methods. Six electronic databases, including the Cochrane Library, PubMed, EMBASE, the China National Knowledge Infrastructure, Wanfang Data, and VIP information database, were searched from inception to January 2021 to identify eligible studies of randomized controlled trials (RCTs). The primary outcome measurements were the total effective rate and pregnancy rate, and the secondary outcome measurements included the negative conversion rate of serum antibodies and the incidence of adverse effects. The quantitative synthesis was performed using the Review Manager 5.3 software. The chi-square statistic and I² statistic were employed to investigate statistical heterogeneity. The fixed-effects model was used for a low heterogeneity (I²I²Results. Thirteen RCTs involving 1298 patients with immune infertility of kidney deficiency and blood stasis were included. Compared with conventional group, TCM TKABC therapy showed a significant improvement on the total effective rate (RR: 1.38; 95 CI: 1.30,1.47; and I²=0), pregnancy rate (RR: 2.04; 95 CI: 1.73, 2.40; and I²=30), negative conversion rates of AsAb (RR: 1.42; 95 CI: 1.12,1.79; and I²=62), AEmAb rates (RR: 1.21; 95 CI: 1.04,1.41; and I²=0), and AhCGAb with less adverse effects (RR: 0.24; 95 CI: 1.73, 2.40; and I²=55). However, the negative conversion rate of AoAb and ACAb showed no significant statistical difference. Conclusions. Our review suggests that TCM TKABC therapy based on the theory of kidney deficiency and blood stasis appears to be an effective and safe approach for patients with immune infertility. However, the methodological quality of included RCTs was unsatisfactory, and it is necessary to verify its effectiveness with more well-designed and high-quality multicenter RCTs.

Acid resistance is an intrinsic characteristic of intestinal bacteria in order to survive passage through the stomach. Adenosine triphosphate (ATP), the ubiquitous chemical used to power metabolic reactions, activate signaling cascades, and form precursors of nucleic acids, was also found to be associated with the survival of Escherichia coli (E. coli) in acidic environments. The metabolic pathway responsible for elevating the level of ATP inside these bacteria during acid adaptation has been unclear. E. coli uses several mechanisms of ATP production, including oxidative phosphorylation, glycolysis and the oxidation of organic compounds. To uncover which is primarily used during adaptation to acidic conditions, we broadly analyzed the levels of gene transcription of multiple E. coli metabolic pathway components. Our findings confirmed that the primary producers of ATP in E. coli undergoing mild acidic stress are the glycolytic enzymes Glk, PykF and Pgk, which are also essential for survival under markedly acidic conditions. By contrast, the transcription of genes related to oxidative phosphorylation was downregulated, despite it being the major producer of ATP in neutral pH environments.

Alpha-lipoic acid (LA) is an important enzyme cofactor widely used by organisms and is also a natural antioxidant for the treatment of pathologies driven by low levels of endogenous antioxidants. In order to establish a safer and more efficient process for LA production, we developed a new biological method for LA synthesis based on the emerging knowledge of lipoic acid biosynthesis. We first cloned the lipD gene, which encodes the lipoyl domain of the E2 subunit of pyruvate dehydrogenase, allowing high levels of LipD production. Plasmids containing genes for the biosynthesis of LA were subsequently constructed utilizing various vectors and promotors to produce high levels of LA. These plasmids were transformed into the Escherichia coli strain BL21. Octanoic acid (OA) was used as the substrate for LA synthesis. One transformant, YS61, which carried lipD, lplA, and lipA, produced LA at levels over 200-fold greater than the wild-type strain, showing that LA could be produced efficiently in E. coli using genetic engineering methods.

FabG is the only known enzyme that catalyzes reduction of the 3-ketoacyl-ACP intermediates of bacterial fatty acid synthetic pathways. However, there are two Ralstonia solanacearum genes, RSc1052 (fabG1) and RSp0359 (fabG2), annotated as encoding putative 3-ketoacyl-ACP reductases. Both FabG homologues possess the conserved catalytic triad and the N-terminal cofactor binding sequence of the short chain dehydrogenase/reductase (SDR) family. Thus, it seems reasonable to hypothesize that RsfabG1 and RsfabG2 both encode functional 3-ketoacyl-ACP reductases and play important roles in R. solanacearum fatty acid synthesis and growth. Complementation of Escherichia coli fabG temperature-sensitive mutant with R. solanacearum fabGs encoded plasmids was carried out to test the function of RsfabGs in fatty acid biosynthesis. RsFabGs proteins were purified by nickel chelate chromatography and fatty acid biosynthetic reaction was reconstituted to investigate the 3-ketoacyl-ACP reductase activity of RsFabGs in vitro. Disruption of both RsfabG genes was done via DNA homologous recombination to test the function of both RsfabG in vivo. And more we also carried out pathogenicity tests on tomato plants using RsfabG mutant strains. We report that expression of either of the two proteins (RsFabG1 and RsFabG2) restores growth of the E. coli fabG temperature-sensitive mutant CL104 under non-permissive conditions. In vitro assays demonstrate that both proteins restore fatty acid synthetic ability to extracts of the E. coli strain. The RsfabG1 gene carried on the R. solanacearum chromosome is essential for growth of the bacterium, as is the case for fabG in E. coli. In contrast, the null mutant strain with the megaplasmid-encoded RsfabG2 gene is viable but has a fatty acid composition that differs significantly from that of the wild type strain. Our study also shows that RsFabG2 plays a role in adaptation to high salt concentration and low pH, and in pathogenesis of disease in tomato plants. R. solanacearum encodes two 3-ketoacyl-ACP reductases that both have functions in fatty acid synthesis. We supply the first evidence that, like other enzymes in the bacterial fatty acid biosynthetic pathway, one bacterium may simultaneously possess two or more 3-oxoacyl-ACP reductase isozymes.