Biphasic regulation of transcriptional surge generated by the gene feedback loop in a two-component system

Parachlorometaxylenol stress caused multidrug-type antibiotic resistance genes proliferation via simultaneously reshaping microbial community and interfering metabolic traits during wastewater treatment process

Despite biological wastewater treatment processes (e.g., sequencing batch reactors (SBR)) being able to reduce the dissemination of antibiotic resistance genes (ARGs), the variation of ARGs under exogenous pollutant stress is an open question. This work investigated the impacts of para-chloro-meta-xylenol (PCMX, typical antibacterial contaminants) on ARGs spread in long-term SBR operation. Although the SBR process inherently decreased ARGs abundance, the presence of PCMX substantially amplified both the prevalence (mainly multidrug) and abundance of total ARGs (1.17-fold of the control). Further analysis demonstrated that PCMX disintegrated sludge structures as well as increased membrane permeability, facilitating the release of mobile genetic elements and subsequent horizontal transfer of ARGs. In addition, PCMX selectively enriched potential ARG hosts, notably Nitrospira and Candidatus Accumulibacter, which predominantly served as multidrug ARG hosts. Concurrently, the self-adaptive functions of ARGs hosts in the PCMX-exposed SBR system were activated via quorum sensing, two-component regulatory system, ATP-binding cassette transporters, and bacterial secretion system. The upregulation of these metabolic pathways also contributed to the dissemination of ARGs.

scGIR: deciphering cellular heterogeneity via gene ranking in single-cell weighted gene correlation networks

Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for investigating cellular heterogeneity through high-throughput analysis of individual cells. Nevertheless, challenges arise from prevalent sequencing dropout events and noise effects, impacting subsequent analyses. Here, we introduce a novel algorithm, Single-cell Gene Importance Ranking (scGIR), which utilizes a single-cell gene correlation network to evaluate gene importance. The algorithm transforms single-cell sequencing data into a robust gene correlation network through statistical independence, with correlation edges weighted by gene expression levels. We then constructed a random walk model on the resulting weighted gene correlation network to rank the importance of genes. Our analysis of gene importance using PageRank algorithm across nine authentic scRNA-seq datasets indicates that scGIR can effectively surmount technical noise, enabling the identification of cell types and inference of developmental trajectories. We demonstrated that the edges of gene correlation, weighted by expression, play a critical role in enhancing the algorithm's performance. Our findings emphasize that scGIR outperforms in enhancing the clustering of cell subtypes, reverse identifying differentially expressed marker genes, and uncovering genes with potential differential importance. Overall, we proposed a promising method capable of extracting more information from single-cell RNA sequencing datasets, potentially shedding new lights on cellular processes and disease mechanisms.

A unified approach to dissecting biphasic responses in cell signaling

Biphasic responses are encountered at all levels in biological systems. At the cellular level, biphasic dose-responses are widely encountered in cell signaling and post-translational modification systems and represent safeguards against overactivation or overexpression of species. In this paper, we provide a unified theoretical synthesis of biphasic responses in cell signaling systems, by assessing signaling systems ranging from basic biochemical building blocks to canonical network structures to well-characterized exemplars on one hand, and examining different types of doses on the other. By using analytical and computational approaches applied to a range of systems across levels (described by broadly employed models), we reveal (i) design principles enabling the presence of biphasic responses, including in almost all instances, an explicit characterization of the parameter space (ii) structural factors which preclude the possibility of biphasic responses (iii) different combinations of the presence or absence of enzyme-biphasic and substrate-biphasic responses, representing safeguards against overactivation and overexpression, respectively (iv) the possibility of broadly robust biphasic responses (v) the complete alteration of signaling behavior in a network due to biphasic interactions between species (biphasic regulation) (vi) the propensity of different co-existing biphasic responses in the Erk signaling network. These results both individually and in totality have a number of important consequences for systems and synthetic biology.

Biphasic amplitude oscillator characterized by distinct dynamics of trough and crest

Biphasic amplitude dynamics (BAD) of oscillation have been observed in many biological systems. However, the specific topology structure and regulatory mechanisms underlying these biphasic amplitude dynamics remain elusive. Here, we searched all possible two-node circuit topologies and identified the core oscillator that enables robust oscillation. This core oscillator consists of a negative feedback loop between two nodes and a self-positive feedback loop of the input node, which result in the fast and slow dynamics of the two nodes, thereby achieving relaxation oscillation. Landscape theory was employed to study the stochastic dynamics and global stability of the system, allowing us to quantitatively describe the diverse positions and sizes of the Mexican hat. With increasing input strength, the size of the Mexican hat exhibits a gradual increase followed by a subsequent decrease. The self-activation of input node and the negative feedback on input node, which dominate the fast dynamics of the input node, were observed to regulate BAD in a bell-shaped manner. Both deterministic and statistical analysis results reveal that BAD is characterized by the linear and nonlinear dependence of the oscillation trough and crest on the input strength. In addition, combining with computational and theoretical analysis, we addressed that the linear response of trough to input is predominantly governed by the negative feedback, while the nonlinear response of crest is jointly regulated by the negative feedback loop and the self-positive feedback loop within the oscillator. Overall, this study provides a natural and physical basis for comprehending the occurrence of BAD in oscillatory systems, yielding guidance for the design of BAD in synthetic biology applications.

The spring-like effect of microRNA-31 in balancing inflammatory and regenerative responses in colitis

Inflammatory bowel diseases (IBDs) are chronic inflammatory disorders caused by the disruption of immune tolerance to the gut microbiota. MicroRNA-31 (MIR31) has been proven to be up-regulated in intestinal tissues from patients with IBDs and colitis-associated neoplasias. While the functional role of MIR31 in colitis and related diseases remain elusive. Combining mathematical modeling and experimental analysis, we systematically explored the regulatory mechanism of MIR31 in inflammatory and epithelial regeneration responses in colitis. Level of MIR31 presents an "adaptation" behavior in dextran sulfate sodium (DSS)-induced colitis, and the similar behavior is also observed for the key cytokines of p65 and STAT3. Simulation analysis predicts MIR31 suppresses the activation of p65 and STAT3 but accelerates the recovery of epithelia in colitis, which are validated by our experimental observations. Further analysis reveals that the number of proliferative epithelial cells, which characterizes the inflammatory process and the recovery of epithelia in colitis, is mainly determined by the inhibition of MIR31 on IL17RA. MIR31 promotes epithelial regeneration in low levels of DSS-induced colitis but inhibits inflammation with high DSS levels, which is dominated by the competition for MIR31 to either inhibit inflammation or promote epithelial regeneration by binding to different targets. The binding probability determines the functional transformation of MIR31, but the functional strength is determined by MIR31 levels. Thus, the role of MIR31 in the inflammatory response can be described as the "spring-like effect," where DSS, MIR31 action strength, and proliferative epithelial cell number are regarded as external force, intrinsic spring force, and spring length, respectively. Overall, our study uncovers the vital roles of MIR31 in balancing inflammation and the recovery of epithelia in colitis, providing potential clues for the development of therapeutic targets in drug design.

Para-chloro-meta-xylenol reshaped the fates of antibiotic resistance genes during sludge fermentation: Insights of cell membrane permeability, bacterial structure and biological pathways

The occurrence of para-chloro-meta-xylenol (PCMX, as largely consumed antimicrobial chemicals) in waste activated sludge (WAS) would pose environmental risks for WAS utilization. This study revealed that PCMX principally prompted the abundances and diversity of antibiotic resistance genes (ARGs), particularly for the multidrug- genes (i.e., acrB and mexW), and reshaped the resistance mechanism categories during WAS fermentation process. The genotype and phenotype results indicated that PCMX upregulated abundances of transposase and increased cell permeability via disrupting WAS structure, which further facilitated the horizontal transfer of ARGs. The network and correlation analysis among ARGs, mobile genetic elements (MGEs) and genera (i.e., Sphingopyxis and Pseudoxanthomonas) verified that PCMX enriched the potential ARGs hosts associated with multidrug resistance mechanism. Also, PCMX upregulated the genes involved in ARGs-associated metabolic pathways, such as two-component (i.e., phoP and vcaM) and quorum sensing systems (i.e., lasR and cciR), which determined the ARGs proliferation via multidrug efflux pump and outer membrane proteins, and facilitated the recognition between ARGs hosts. Variance partitioning analysis (VPA) implied that the shift of microbial community contributed predominantly to the dissemination of ARGs. These findings unveiled the environmental behaviors and risks of exogenous pollutants in WAS with insightful understanding, which could guide the WAS utilization for resource recovery.

Network modeling-based identification of the switching targets between pyroptosis and secondary pyroptosis

The newly identified cell death type, pyroptosis plays crucial roles in various diseases. Most recently, mounting evidence accumulates that pyroptotic signaling is highly correlated with coronavirus disease 2019 (COVID-19). Thus, understanding the induction of the pyroptotic signaling and dissecting the detail molecular control mechanisms are urgently needed. Based on recent experimental studies, a core regulatory model of the pyroptotic signaling is constructed to investigate the intricate crosstalk dynamics between the two cell death types, i.e., pyroptosis and secondary pyroptosis. The model well reproduces the experimental observations under different conditions. Sensitivity analysis determines that only the expression level of caspase-1 or GSDMD has the potential to individually change death modes. The decrease of caspase-1 or GSDMD level switches cell death from pyroptosis to secondary pyroptosis. Besides, eight biochemical reactions are identified that can efficiently switch death modes. While from the viewpoint of bifurcation analysis, the expression level of caspase-3 is further identified and twelve biochemical reactions are obtained. The coexistence of pyroptosis and secondary pyroptosis is predicted to be observed not only within the bistable range, but also within proper monostable range, presenting two potential different control mechanisms. Combined with the landscape theory, we further explore the stochastic dynamic and global stability of the pyroptotic system, accurately quantifying how each component mediates the individual occurrence probability of pyroptosis and secondary pyroptosis. Overall, this study sheds new light on the intricate crosstalk of the pyroptotic signaling and uncovers the regulatory mechanisms of various stable state transitions, providing potential clues to guide the development for prevention and treatment of pyroptosis-related diseases.

How the PhoP/PhoQ System Controls Virulence and Mg2+ Homeostasis: Lessons in Signal Transduction, Pathogenesis, Physiology, and Evolution

The PhoP/PhoQ two-component system governs virulence, Mg2+ homeostasis, and resistance to a variety of antimicrobial agents, including acidic pH and cationic antimicrobial peptides, in several Gram-negative bacterial species. Best understood in Salmonella enterica serovar Typhimurium, the PhoP/PhoQ system consists o-regulated gene products alter PhoP-P amounts, even under constant inducing conditions. PhoP-P controls the abundance of hundreds of proteins both directly, by having transcriptional effects on the corresponding genes, and indirectly, by modifying the abundance, activity, or stability of other transcription factors, regulatory RNAs, protease regulators, and metabolites. The investigation of PhoP/PhoQ has uncovered novel forms of signal transduction and the physiological consequences of regulon evolution.