Lysine crotonylation has attracted widespread attention in recent years. However, little is known about bacterial crotonylation, particularly crotonyltransferase and decrotonylase, and its effects on ...antibiotic resistance. Our study demonstrates the ubiquitous presence of crotonylation in E. coli, which promotes bacterial resistance to polymyxin. We identify the crotonyltransferase YjgM and its regulatory pathways in E. coli with a focus on crotonylation. Further studies show that YjgM upregulates the crotonylation of the substrate protein PmrA, thereby boosting PmrA’s affinity for binding to the promoter of eptA, which, in turn, promotes EptA expression and confers polymyxin resistance in E. coli. Additionally, we discover that PmrA’s crucial crotonylation site and functional site is Lys 164. These significant discoveries highlight the role of crotonylation in bacterial drug resistance and offer a fresh perspective on creating antibacterial compounds.
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•YjgM functions as a crotonyltransferase in Escherichia coli•Crotonylation proteomics reveals differentially crotonylated proteins in PMB-R•YjgM promotes bacterial polymyxin resistance via the crotonylation of PmrA•Crotonylation promotes PmrA’s binding ability to the eptA promoter
Zhuang et al. find that YjgM is a crotonyltransferase in Escherichia coli. YjgM improves the binding affinity between the polymyxin-resistant protein PmrA and the eptA promoter by increasing the crotonoylation level of PmrA, thereby encouraging the expression of eptA, resulting in the development of polymyxin resistance in E. coli.
Infections caused by drug-resistant bacteria are a serious threat to public health worldwide, and the discovery of novel antibacterial compounds is urgently needed. Here, we screened an FDA-approved ...small-molecule library and found that crizotinib possesses good antimicrobial efficacy against Gram-positive bacteria. Crizotinib was found to increase the survival rate of mice infected with bacteria and decrease pulmonary inflammation activity in an animal model. Furthermore, it showed synergy with clindamycin and gentamicin. Importantly, the Gram-positive bacteria showed a low tendency to develop resistance to crizotinib. Mechanistically, quantitative proteomics and biochemical validation experiments indicated that crizotinib exerted its antibacterial effects by reducing ATP production and pyrimidine metabolism. A drug affinity responsive target stability study suggested crizotinib targets the CTP synthase PyrG, which subsequently disturbs pyrimidine metabolism and eventually reduces DNA synthesis. Subsequent molecular dynamics analysis showed that crizotinib binding occurs in close proximity to the ATP binding pocket of PyrG and causes loss of function of this CTP synthase. Crizotinib is a promising antimicrobial agent and provides a novel choice for the development of treatment for Gram-positive infections.
Infections caused by drug-resistant bacteria are a serious problem worldwide. Therefore, there is an urgent need to find novel drugs with good antibacterial activity against multidrug-resistant bacteria. In this study, we found that a repurposed drug, crizotinib, exhibits excellent antibacterial activity against drug-resistant bacteria both
and
via suppressing ATP production and pyrimidine metabolism. Crizotinib was found to disturb pyrimidine metabolism by targeting the CTP synthase PyrG, thus reducing DNA synthesis. This unique mechanism of action may explain the decreased development of resistance by Staphylococcus aureus to crizotinib. This study provides a potential option for the treatment of drug-resistant bacterial infections in the future.
Abstract
Background
CpxR is a critical regulator in bacterial adaptation to various harmful stresses, and is known to regulate bacterial resistance to commonly used antibiotics, such as ...aminoglycosides, β-lactams and polypeptides. However, the detailed study of functional residues of CpxR remains insufficient.
Objectives
To investigate the contribution of Lys219 to CpxR’s function in regulating antibiotic resistance of Escherichia coli.
Methods
We performed sequence alignment and conservative analysis of the CpxR protein and constructed mutant strains. We then performed electrophoretic mobility shift assay, real-time quantitative PCR assay, determination of reactive oxygen species (ROS) levels, molecular dynamics simulation, conformational analysis and circular dichroism.
Results
All mutant proteins (K219Q, K219A and K219R) lost the cpxP DNA-binding ability. Additionally, the three complemented strains eK219A, eK219Q, and eK219R exhibited lower resistance to copper toxicity and alkaline pH toxicity than eWT. Molecular dynamics analysis revealed that mutation of Lys219 leads to looser and more unstable conformation of CpxR, leading to its decreased binding affinity with downstream genes. Moreover, the Lys219 mutation resulted in the down-regulation of efflux pump genes (acrD, tolC, mdtB and mdtA), leading to the accumulation of antibiotics inside the cells and an increase in ROS production, which significantly reduces antibiotic resistance.
Conclusions
The mutation of the key residue Lys219 causes a conformational change that results in the loss of regulatory ability of CpxR, which may potentially reduce to antibiotic resistance. Therefore, this study suggests that targeting the highly conserved sequence of CpxR could be a promising strategy for the development of new antibacterial drugs.
Single-nucleotide polymorphism (SNP) is one of the core mechanisms that respond to antibiotic resistance of Escherichia coli (E. coli), which is a major issue in environmental pollution. A specific ...type of SNPs, synonymous SNPs, have been generally considered as the “silent” SNPs since they do not change the encoded amino acid. However, the impact of synonymous SNPs on mRNA splicing, nucleo-cytoplasmic export, stability, and translation was gradually discovered in the last decades. Figuring out the mechanism of synonymous SNPs in regulating antibiotic resistance is critical to improve antimicrobial therapy strategies in clinics and biological treatment strategies of antibiotic-resistant E. coli-polluted materials. With our newly designed antibiotic resistant SNPs prediction algorithm, Multilocus Sequence Type based Identification for Phenotype-single nucleotide polymorphism Analysis (MIPHA), and in vivo validation, we identified 2 important synonymous SNPs 522 G>A and 972 C>T, located at hisD gene, which was previously predicted as a fluoroquinolone resistance-related gene without a detailed mechanism in the E. coli samples with environmental backgrounds. We first discovered that hisD causes gyrA mutation via the upregulation of sbmC and its downstream gene umuD. Moreover, those 2 synonymous SNPs of hisD cause its own translational slowdown and further reduce the expression levels of sbmC and its downstream gene umuD, making the fluoroquinolone resistance determining region of gyrA remains unmutated, ultimately causing the bacteria to lose their ability to resist drugs. This study provided valuable insight into the role of synonymous SNPs in mediating antibiotic resistance of bacteria and a new perspective for the treatment of environmental pollution caused by drug-resistant bacteria.
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•4598 samples of E. coli WGS and phenotype data, including 3533 samples with environmental background were analyzed.•Two synonymous Single-Nucleotide Polymorphisms that disable hisD functionality were screened by a new developed algorithm.•hisD promotes E. coli fluoroquinolone resistantce by increasing the expression of sbmC and umuD.•The synonymous SNPs cause translational slowdown of HisD and disturb its antibiotic resistant function.
Protein lysine acetylation is a critical post-translational modification involved in a wide range of biological processes. To date, about 20,000 acetylation sites of Homo sapiens were identified ...through mass spectrometry–based proteomic technology, but more than 95% of them have unclear functional annotations because of the lack of existing prioritization strategy to assess the functional importance of the acetylation sites on large scale. Hence, we established a lysine acetylation functional evaluating model (LAFEM) by considering eight critical features surrounding lysine acetylation site to high-throughput estimate the functional importance of given acetylation sites. This was achieved by selecting one of the random forest models with the best performance in 10-fold cross-validation on undersampled training dataset. The global analysis demonstrated that the molecular environment of acetylation sites with high acetylation functional scores (AFSs) mainly had the features of larger solvent-accessible surface area, stronger hydrogen bonding–donating abilities, near motif and domain, higher homology, and disordered degree. Importantly, LAFEM performed well in validation dataset and acetylome, showing good accuracy to screen out fitness directly relevant acetylation sites and assisting to explain the core reason for the difference between biological models from the perspective of acetylome. We further used cellular experiments to confirm that, in nuclear casein kinase and cyclin-dependent kinase substrate 1, acetyl-K35 with higher AFS was more important than acetyl-K9 with lower AFS in the proliferation of A549 cells. LAFEM provides a prioritization strategy to large scale discover the fitness directly relevant acetylation sites, which constitutes an unprecedented resource for better understanding of functional acetylome.
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•LAFEM is the first prioritization strategy to evaluate functional acetylome.•LAFEM enriches functional annotations of 15,410 acetylation sites.•Eight molecular features in LAFEM are related to the function of acetylation site.•Assessment of acetylation sites by LAFEM provide support for quantitative acetylomics.
Not all acetylation sites contribute equally to fitness, which disturbs us to find out the core reason between different biological models. In fact, it is insufficient to evaluate functional acetylation sites only relying on quantification acetylome. Therefore, we developed LAFEM to comprehensively consider the molecular environment of individual acetylation sites. The LAFEM score of acetylation site is beneficial to the following experimental validation and the discover of core biological regularity.
Previous studies have shown increased aberrant expression of immune checkpoint (IC) proteins, such as programmed cell death receptor-1 (PD-1) and T cell immunoglobulin mucin-domain-containing-3 ...(Tim-3) on T cells from patients with multiple myeloma (MM), which result in T cell exhaustion and dysfunction. However, little is known about the mechanism regulating aberrant IC protein expression. In this study, we analyzed the expression of TOX (thymocyte selection-associated HMG BOX), a crucial transcription factor involved in T cell exhaustion, and its co-expression with PD-1, Tim-3, and CD244 in T cell subsets by multi-color fluorescent flow cytometry in peripheral blood (PB) and bone marrow (BM) samples from patients with MM. Significantly, the percentage of TOX + CD3 +/CD4 +/CD8 + T cells was increased, and similarly, higher numbers of TOX co-expression with PD-1, Tim-3, and CD244 on CD3 +/CD4 +/CD8 + T cells were found. Interestingly, the numbers of TOX +, TOX + PD-1 +, and TOX + Tim-3 + regulatory T (Treg) cells also significantly increased in both the PB and BM of MM patients. In summary, we for the first time observed increased TOX expression concurrent with PD-1, Tim-3, and CD244 on T cells, which may contribute to T cell exhaustion and impair their function in MM. Thus, TOX may be considered a potential target for reversing T cell exhaustion and improving T cell function in MM.
Compressive strength of concrete structures is a crucial quality parameter that determines their performance throughout lifespan. This study introduces an innovative approach of utilizing ...electromagnetic nondestructive testing to assess the compressive strength of mature concrete. The dielectric constant and compressive strength of standard specimens were tested by open coaxial probe and pressure testing machine, respectively, using ordinary Portland cement concrete with various water-cement ratios (0.4, 0.45, 0.5, 0.55, 0.6 and 0.65) as the research object. It has been discovered that increasing porosity reduces the number of polarized particles per unit volume of concrete, resulting in a decrease in polarization intensity. This decrease is manifested as a reduction in the dielectric constant in macro parameters. The relationship between porosity and dielectric constant was characterized using a series-parallel composite concrete dielectric model. Additionally, as porosity increases, the compressive strength of concrete decreases exponentially. By considering porosity as an intermediate variable, a concrete compressive strength model based on the dielectric constant was established. The model exhibits an average error of 3.62%, indicating the precise characterization of concrete's compressive strength using the dielectric constant. This model can serve as a theoretical basis for the implementation of electromagnetic nondestructive testing techniques in strength evaluation.
•The compressive strength and dielectric constant of mature concrete are inextricably linked.•Series parallel composite dielectric model of concrete based on Abstraction concept of structure.•Concrete compressive strength and porosity have an exponential function connection.•Create a concrete compressive strength model based on dielectric properties using porosity as an intermediate variable.
While triboelectric nanogenerated knitted fabrics are regarded as a state-of-the-art and reliable energy source for wearable electronics, there are two bottlenecks in their widespread applications: ...few mass-manufacturing strategies and low power output. Here, by mature weft-knitted technologies, a 3D single-faced jacquard pile fabric TENG (SJPF-TENG) with the merits of high surface pile density, excellent comfort and breathability, good thermal insulation property, and superior durability, is mass-produced. Based on the high-density pile structure (about 16128 piles per cm2), the surface area of pile fabrics is 42.2 times that of the plain structure, which endows the SJPF-TENG with higher electrical outputs and good detection precision. With a peak power density of 1.4 W m−2 (dozens of times that of conventional textile-based TENGs), the SJPF-TENG is capable of lighting up 1392 light-emitting diodes, powering miniature electronics, and charging various capacitors. Furthermore, a self-powered remote control, an intelligent alphabet writing pad, a smart fluff carpet, and a proof-of-concept fluff keyboard array with 3×3 sensing pixels are demonstrated to verify its outstanding sensing performance. Our results provide a massive prospect for high-power textile-based TENGs in large-area energy harvesting, smart-home control systems, entertainment, elder healthcare, and security warnings.
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•The mechanism of pile fabric with enhanced outputs is simulated and calculated from the contact area of nano/microfibers.•The surface area of pile fabrics with high-density structure is 42.2 times as that of the plain structure.•With a maximum peak power density of 1.4 W m-2, the 3D SJPF-TENG is capable of lighting up 1392 LEDs.•About 928.8-1115.6 m2 of SJPF-TENG can be mass-manufactured on a high-speed weft machine in one day.•This theoretical study has an enlightening effect on the research of biomimetic fur materials (whether micro or macro).
► Influences of roughness and oxidation on total emissivity are investigated. ► Increase roughness will increase total emissivity of iron-based alloy. ► Emissivities of alloy samples oxidized at ...400°C for various times are similar. ► Emissivities of alloy samples oxidized at 600°C increase with oxidation time. ► Oxide layer formed at high-temperature enhances radiation performance of sample.
The influences of surface conditions, including surface roughness and oxidation state, on the total hemispherical emissivity were experimentally investigated using an improved steady-state calorimetric technique for iron-based alloy samples. The investigated samples were prepared using rough polishing grits and high-temperature oxidization. The surface micrograph, roughness and composition of the oxide layer were analyzed using scanning electron microscope (SEM) and auger electron spectroscope (AES) to quantitatively describe the surface characteristics. Results of two iron-based alloy samples with different surface roughnesses showed that the measured total hemispherical emissivity increased with the roughness. However, the effect of surface roughness on total hemispherical emissivity gradually became smaller at high temperatures above 1200K for the investigated roughness conditions of iron-based alloys. Another six iron-based alloy samples were pre-oxidized in a high-temperature air muffle furnace with three oxidized at 400°C and the other three oxidized at 600°C for various times. The results showed that the emissivities of samples oxidized at 400°C for various times were similar to each other and the un-oxidized substrate, while the emissivities of samples oxidized at 600°C increased with oxidation time. This distinction arose from the different oxide layer thickness as the oxidation time increased at 600°C, while the thickness was almost constant at 400°C. The characteristics of the oxide layer grown in different oxidation temperatures were different as well. For the same oxidation time, the emissivities of samples oxidized at the higher oxidation temperature were larger than the values of samples oxidized at lower oxidation temperature. At high temperature (600°C) oxidation process of iron-based alloys, the oxide layer might be compact and its density was large which would strength the capacity of radiation heat transfer of iron-based alloy, comparing with the oxide layer grown in low temperature (400°C) oxidation process at the same oxidation time.
Urban Emergency Response System (UERS) is a modernization symbol of a city. With acceleration of urbanization process and constant expansion of city size in China, China cities must respond to ...various emergencies timely and effectively to satisfy urban residents’ needs for public security. In recent years, many China cities made trials and efforts in setting up and improving the UERS. At the same time, the China government began to build Emergency Response Systems (ERS) in some cities to deal with various possible emergencies. In this paper, using Petri net (PN), we study the performance of China typical UERS and establish its PN model for performance analysis. Based on the Markov chain (MC) of the model, the performance of China typical UERS is analyzed. Results from our simulation are in conformity with practical operation of China current UERS.
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