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1.
Commun Biol ; 7(1): 693, 2024 Jun 06.
Article En | MEDLINE | ID: mdl-38844781

Pericyte dysfunction, with excessive migration, hyperproliferation, and differentiation into smooth muscle-like cells contributes to vascular remodeling in Pulmonary Arterial Hypertension (PAH). Augmented expression and action of growth factors trigger these pathological changes. Endogenous factors opposing such alterations are barely known. Here, we examine whether and how the endothelial hormone C-type natriuretic peptide (CNP), signaling through the cyclic guanosine monophosphate (cGMP) -producing guanylyl cyclase B (GC-B) receptor, attenuates the pericyte dysfunction observed in PAH. The results demonstrate that CNP/GC-B/cGMP signaling is preserved in lung pericytes from patients with PAH and prevents their growth factor-induced proliferation, migration, and transdifferentiation. The anti-proliferative effect of CNP is mediated by cGMP-dependent protein kinase I and inhibition of the Phosphoinositide 3-kinase (PI3K)/AKT pathway, ultimately leading to the nuclear stabilization and activation of the Forkhead Box O 3 (FoxO3) transcription factor. Augmentation of the CNP/GC-B/cGMP/FoxO3 signaling pathway might be a target for novel therapeutics in the field of PAH.


Cell Proliferation , Cyclic GMP , Forkhead Box Protein O3 , Natriuretic Peptide, C-Type , Pericytes , Signal Transduction , Humans , Pericytes/metabolism , Pericytes/pathology , Natriuretic Peptide, C-Type/metabolism , Cyclic GMP/metabolism , Forkhead Box Protein O3/metabolism , Forkhead Box Protein O3/genetics , Male , Female , Pulmonary Arterial Hypertension/metabolism , Pulmonary Arterial Hypertension/pathology , Middle Aged , Hypertension, Pulmonary/metabolism , Hypertension, Pulmonary/pathology , Adult , Receptors, Atrial Natriuretic Factor/metabolism , Receptors, Atrial Natriuretic Factor/genetics , Cells, Cultured
2.
Nat Commun ; 15(1): 3920, 2024 May 09.
Article En | MEDLINE | ID: mdl-38724508

Monitoring changes of signaling molecules and metabolites with high temporal resolution is key to understanding dynamic biological systems. Here, we use directed evolution to develop a genetically encoded ratiometric biosensor for c-di-GMP, a ubiquitous bacterial second messenger regulating important biological processes like motility, surface attachment, virulence and persistence. The resulting biosensor, cdGreen2, faithfully tracks c-di-GMP in single cells and with high temporal resolution over extended imaging times, making it possible to resolve regulatory networks driving bimodal developmental programs in different bacterial model organisms. We further adopt cdGreen2 as a simple tool for in vitro studies, facilitating high-throughput screens for compounds interfering with c-di-GMP signaling and biofilm formation. The sensitivity and versatility of cdGreen2 could help reveal c-di-GMP dynamics in a broad range of microorganisms with high temporal resolution. Its design principles could also serve as a blueprint for the development of similar, orthogonal biosensors for other signaling molecules, metabolites and antibiotics.


Biofilms , Biosensing Techniques , Cyclic GMP , Biosensing Techniques/methods , Cyclic GMP/analogs & derivatives , Cyclic GMP/metabolism , Biofilms/growth & development , Signal Transduction , Escherichia coli/metabolism , Escherichia coli/genetics , Second Messenger Systems
3.
Sci Rep ; 14(1): 10777, 2024 05 11.
Article En | MEDLINE | ID: mdl-38734687

Emerging evidence has documented that circadian rhythm disorders could be related to cardiovascular diseases. However, there is limited knowledge on the direct adverse effects of circadian misalignment on the heart. This study aimed to investigate the effect of chronic circadian rhythm disorder on heart homeostasis in a mouse model of consistent jetlag. The jetlag model was induced in mice by a serial 8-h phase advance of the light cycle using a light-controlled isolation box every 4 days for up to 3 months. Herein, we demonstrated for the first time that chronic circadian rhythm disorder established in the mouse jetlag model could lead to HFpEF-like phenotype such as cardiac hypertrophy, cardiac fibrosis, and cardiac diastolic dysfunction, following the attenuation of the Clock-sGC-cGMP-PKG1 signaling. In addition, clock gene knock down in cardiomyocytes induced hypertrophy via decreased sGC-cGMP-PKG signaling pathway. Furthermore, treatment with an sGC-activator riociguat directly attenuated the adverse effects of jetlag model-induced cardiac hypertrophy, cardiac fibrosis, and cardiac diastolic dysfunction. Our data suggest that circadian rhythm disruption could induce HFpEF-like phenotype through downregulation of the clock-sGC-cGMP-PKG1 signaling pathway. sGC could be one of the molecular targets against circadian rhythm disorder-related heart disease.


CLOCK Proteins , Cyclic GMP , Heart Failure , Signal Transduction , Soluble Guanylyl Cyclase , Animals , Mice , Heart Failure/metabolism , Heart Failure/etiology , Heart Failure/physiopathology , Cyclic GMP/metabolism , Soluble Guanylyl Cyclase/metabolism , CLOCK Proteins/metabolism , CLOCK Proteins/genetics , Male , Disease Models, Animal , Phenotype , Cyclic GMP-Dependent Protein Kinase Type I/metabolism , Cyclic GMP-Dependent Protein Kinase Type I/genetics , Myocytes, Cardiac/metabolism , Circadian Rhythm/physiology , Mice, Inbred C57BL , Chronobiology Disorders/metabolism , Stroke Volume
4.
Biosensors (Basel) ; 14(5)2024 May 16.
Article En | MEDLINE | ID: mdl-38785726

Phosphodiesterases (PDEs), a superfamily of enzymes that hydrolyze cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP), are recognized as a therapeutic target for various diseases. However, the current screening methods for PDE inhibitors usually experience problems due to complex operations and/or high costs, which are not conducive to drug development in respect of this target. In this study, a new method for screening PDE inhibitors based on GloSensor technology was successfully established and applied, resulting in the discovery of several novel compounds of different structural types with PDE inhibitory activity. Compared with traditional screening methods, this method is low-cost, capable of dynamically detecting changes in substrate concentration in live cells, and can be used to preliminarily determine the type of PDEs affected by the detected active compounds, making it more suitable for high-throughput screening for PDE inhibitors.


Phosphodiesterase Inhibitors , Phosphodiesterase Inhibitors/pharmacology , Humans , Cyclic AMP/metabolism , Phosphoric Diester Hydrolases/metabolism , High-Throughput Screening Assays , Biosensing Techniques , Cyclic GMP/metabolism , Drug Evaluation, Preclinical
5.
World J Urol ; 42(1): 333, 2024 May 18.
Article En | MEDLINE | ID: mdl-38761255

PURPOSE: Benign prostatic hyperplasia (BPH) is one of the most prevalent diseases affecting aging males. However, approximately, 8% of the BPH patients under 50-year-old experience remarkably early progression, for reasons that remain elusive. Among the various factors implicated in promoting BPH advancement, the activation of fibroblasts and autophagy hold particular importance. Our research endeavors to explore the mechanisms behind the accelerated progression in these patients. METHODS: Immunohistochemistry and immunofluorescence were performed to detect the expression levels of LC3, p62, PDE5, and α-SMA in diverse BPH tissues and prostate stromal cells. The autophagy activator rapamycin, the autophagy suppressor chloroquine, and siRNA transfection were used to identify the impact of autophagy on fibroblast activation. RESULTS: Prostatic stromal fibroblasts in early progressive BPH tissues displayed activation of autophagy with an upregulation of LC3 and a concurrent downregulation of p62. After starvation or rapamycin treatment to a heightened level of autophagy, fibroblasts exhibited activation. Conversely, chloroquine treatment and ATG-7-knockdown effectively suppressed the level of autophagy and fibroblast activation. High expression of PDE5 was found in early progressive BPH stromal cells. The administration of PDE5 inhibitors (PDE5Is) hindered fibroblast activation through suppressing autophagy by inhibiting the ERK signaling pathway. CONCLUSION: Our findings suggest that autophagy plays a pivotal role in promoting BPH progression through fibroblast activation, while PDE5Is effectively suppress autophagy and fibroblast activation via the ERK signaling pathway. Nevertheless, further investigations are warranted to comprehensively elucidate the role of autophagy in BPH progression.


Autophagy , Disease Progression , Down-Regulation , Fibroblasts , MAP Kinase Signaling System , Phosphodiesterase 5 Inhibitors , Prostatic Hyperplasia , Male , Humans , Autophagy/physiology , Prostatic Hyperplasia/metabolism , Prostatic Hyperplasia/pathology , Fibroblasts/metabolism , Phosphodiesterase 5 Inhibitors/pharmacology , MAP Kinase Signaling System/physiology , Middle Aged , Cyclic GMP/metabolism , Aged , Signal Transduction
6.
Int J Mol Sci ; 25(10)2024 May 10.
Article En | MEDLINE | ID: mdl-38791239

Bacillus velezensis FZB42 is a plant growth-promoting rhizobacterium (PGPR) and a model microorganism for biofilm studies. Biofilms are required for the colonization and promotion of plant growth in the rhizosphere. However, little is known about how the final stage of the biofilm life cycle is regulated, when cells regain their motility and escape the mature biofilm to spread and colonize new niches. In this study, the non-annotated gene ccdC was found to be involved in the process of biofilm dispersion. We found that the ccdC-deficient strain maintained a wrinkled state at the late stage of biofilm formation in the liquid-gas interface culture, and the bottom solution showed a clear state, indicating that no bacterial cells actively escaped, which was further evidenced by the formation of a cellular ring (biofilm pellicle) located on top of the preformed biofilm. It can be concluded that dispersal, a biofilm property that relies on motility proficiency, is also positively affected by the unannotated gene ccdC. Furthermore, we found that the level of cyclic diguanylate (c-di-GMP) in the ccdC-deficient strain was significantly greater than that in the wild-type strain, suggesting that B. velezensis exhibits a similar mechanism by regulating the level of c-di-GMP, the master regulator of biofilm formation, dispersal, and cell motility, which controls the fitness of biofilms in Pseudomonas aeruginosain. In this study, we investigated the mechanism regulating biofilm dispersion in PGPR.


Bacillus , Bacterial Proteins , Biofilms , Biofilms/growth & development , Bacillus/physiology , Bacillus/genetics , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Cyclic GMP/metabolism , Cyclic GMP/analogs & derivatives , Gene Expression Regulation, Bacterial , Rhizosphere
7.
Int J Mol Sci ; 25(10)2024 May 14.
Article En | MEDLINE | ID: mdl-38791377

Phosphodiesterases (PDEs) are ubiquitous enzymes that hydrolyse cAMP and cGMP second messengers temporally, spatially, and integratedly according to their expression and compartmentalization inside the cell [...].


Phosphoric Diester Hydrolases , Phosphoric Diester Hydrolases/metabolism , Humans , Animals , Cyclic AMP/metabolism , Cyclic GMP/metabolism
8.
Physiol Rep ; 12(9): e16033, 2024 May.
Article En | MEDLINE | ID: mdl-38740564

The pathophysiology behind sodium retention in heart failure with preserved ejection fraction (HFpEF) remains poorly understood. We hypothesized that patients with HFpEF have impaired natriuresis and diuresis in response to volume expansion and diuretic challenge, which is associated with renal hypo-responsiveness to endogenous natriuretic peptides. Nine HFpEF patients and five controls received saline infusion (0.25 mL/kg/min for 60 min) followed by intravenous furosemide (20 mg or home dose) 2 h after the infusion. Blood and urine samples were collected at baseline, 2 h after saline infusion, and 2 h after furosemide administration; urinary volumes were recorded. The urinary cyclic guanosine monophosphate (ucGMP)/plasma B-type NP (BNP) ratio was calculated as a measure of renal response to endogenous BNP. Wilcoxon rank-sum test was used to compare the groups. Compared to controls, HFpEF patients had reduced urine output (2480 vs.3541 mL; p = 0.028), lower urinary sodium excretion over 2 h after saline infusion (the percentage of infused sodium excreted 12% vs. 47%; p = 0.003), and a lower baseline ucGMP/plasma BNP ratio (0.7 vs. 7.3 (pmol/mL)/(mg/dL)/(pg/mL); p = 0.014). Patients with HFpEF had impaired natriuretic response to intravenous saline and furosemide administration and lower baseline ucGMP/plasma BNP ratios indicating renal hypo-responsiveness to NPs.


Furosemide , Heart Failure , Kidney , Natriuretic Peptide, Brain , Sodium , Stroke Volume , Humans , Heart Failure/physiopathology , Heart Failure/metabolism , Male , Female , Aged , Pilot Projects , Furosemide/pharmacology , Furosemide/administration & dosage , Sodium/metabolism , Sodium/urine , Natriuretic Peptide, Brain/blood , Natriuretic Peptide, Brain/metabolism , Kidney/metabolism , Kidney/physiopathology , Kidney/drug effects , Middle Aged , Natriuresis/drug effects , Diuretics/pharmacology , Diuretics/administration & dosage , Cyclic GMP/metabolism , Cyclic GMP/urine , Aged, 80 and over
9.
Anal Chem ; 96(21): 8308-8316, 2024 May 28.
Article En | MEDLINE | ID: mdl-38752543

Microbial biofilms represent an important lifestyle for bacteria and are dynamic three-dimensional structures. Cyclic dimeric guanosine monophosphate (c-di-GMP) is a ubiquitous signaling molecule that is known to be tightly regulated with biofilm processes. While measurements of global levels of c-di-GMP have proven valuable toward understanding the genetic control of c-di-GMP production, there is a need for tools to observe the local changes of c-di-GMP production in biofilm processes. We have developed a label-free method for the direct detection of c-di-GMP in microbial colony biofilms using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). We applied this method to the enteric pathogen Vibrio cholerae, the marine symbiont V. fischeri, and the opportunistic pathogen Pseudomonas aeruginosa PA14 and detected spatial and temporal changes in c-di-GMP signal that accompanied genetic alterations in factors that synthesize and degrade the compound. We further demonstrated how this method can be simultaneously applied to detect additional metabolites of interest from a single sample.


Biofilms , Cyclic GMP , Pseudomonas aeruginosa , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Vibrio cholerae , Cyclic GMP/analogs & derivatives , Cyclic GMP/metabolism , Cyclic GMP/analysis , Pseudomonas aeruginosa/metabolism , Vibrio cholerae/metabolism , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Aliivibrio fischeri/metabolism
10.
Sci Rep ; 14(1): 11898, 2024 05 24.
Article En | MEDLINE | ID: mdl-38789479

We have previously reported the transcriptomic and lipidomic profile of the first-generation, hygromycin-resistant (HygR) version of the BCGΔBCG1419c vaccine candidate, under biofilm conditions. We recently constructed and characterized the efficacy, safety, whole genome sequence, and proteomic profile of a second-generation version of BCGΔBCG1419c, a strain lacking the BCG1419c gene and devoid of antibiotic markers. Here, we compared the antibiotic-less BCGΔBCG1419c with BCG. We assessed their colonial and ultrastructural morphology, biofilm, c-di-GMP production in vitro, as well as their transcriptomic and lipidomic profiles, including their capacity to activate macrophages via Mincle and Myd88. Our results show that BCGΔBCG1419c colonial and ultrastructural morphology, c-di-GMP, and biofilm production differed from parental BCG, whereas we found no significant changes in its lipidomic profile either in biofilm or planktonic growth conditions. Transcriptomic profiling suggests changes in BCGΔBCG1419c cell wall and showed reduced transcription of some members of the DosR, MtrA, and ArgR regulons. Finally, induction of TNF-α, IL-6 or G-CSF by bone-marrow derived macrophages infected with either BCGΔBCG1419c or BCG required Mincle and Myd88. Our results confirm that some differences already found to occur in HygR BCGΔBCG1419c compared with BCG are maintained in the antibiotic-less version of this vaccine candidate except changes in production of PDIM. Comparison with previous characterizations conducted by OMICs show that some differences observed in BCGΔBCG1419c compared with BCG are maintained whereas others are dependent on the growth condition employed to culture them.


BCG Vaccine , Biofilms , Cyclic GMP , Lipidomics , Macrophages , Mycobacterium bovis , Myeloid Differentiation Factor 88 , Transcriptome , Animals , Myeloid Differentiation Factor 88/metabolism , Myeloid Differentiation Factor 88/genetics , Mice , Macrophages/metabolism , Macrophages/immunology , BCG Vaccine/immunology , Cyclic GMP/metabolism , Cyclic GMP/analogs & derivatives , Mycobacterium bovis/genetics , Mycobacterium bovis/immunology , Biofilms/growth & development , Cytokines/metabolism , Membrane Proteins/metabolism , Membrane Proteins/genetics , Gene Expression Profiling , Lectins, C-Type
11.
ACS Chem Neurosci ; 15(8): 1652-1668, 2024 Apr 17.
Article En | MEDLINE | ID: mdl-38579109

In treating retinitis pigmentosa, a genetic disorder causing progressive vision loss, selective inhibition of rod cyclic nucleotide-gated (CNG) channels holds promise. Blocking the increased Ca2+-influx in rod photoreceptors through CNG channels can potentially delay disease progression and improve the quality of life for patients. To find inhibitors for rod CNG channels, we investigated the impact of 16 cGMP analogues on both rod and cone CNG channels using the patch-clamp technique. Although modifications at the C8 position of the guanine ring did not change the ligand efficacy, modifications at the N1 and N2 positions rendered cGMP largely ineffective in activating retinal CNG channels. Notably, PET-cGMP displayed selective potential, favoring rod over cone, whereas Rp-cGMPS showed greater efficiency in activating cone over rod CNG channels. Ligand docking and molecular dynamics simulations on cyclic nucleotide-binding domains showed comparable binding energies and binding modes for cGMP and its analogues in both rod and cone CNG channels (CNGA1 vs CNGA3 subunits). Computational experiments on CNGB1a vs CNGB3 subunits showed similar binding modes albeit with fewer amino acid interactions with cGMP due to an inactivated conformation of their C-helix. In addition, no clear correlation could be observed between the computational scores and the CNG channel efficacy values, suggesting additional factors beyond binding strength determining ligand selectivity and potency. This study highlights the importance of looking beyond the cyclic nucleotide-binding domain and toward the gating mechanism when searching for selective modulators. Future efforts in developing selective modulators for CNG channels should prioritize targeting alternative channel domains.


Cyclic Nucleotide-Gated Cation Channels , Quality of Life , Humans , Cyclic Nucleotide-Gated Cation Channels/metabolism , Ligands , Retina/metabolism , Nucleotides, Cyclic , Cyclic GMP/metabolism
12.
Mol Biol Rep ; 51(1): 510, 2024 Apr 15.
Article En | MEDLINE | ID: mdl-38622307

Phosphodiesterases (PDEs) have become a promising therapeutic target for various disorders. PDEs are a vast and diversified family of enzymes that degrade cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP), which have several biochemical and physiological functions. Phosphodiesterase 4 (PDE4) is the most abundant PDE in the central nervous system (CNS) and is extensively expressed in the mammalian brain, where it catalyzes the hydrolysis of intracellular cAMP. An alteration in the balance of PDE4 and cAMP results in the dysregulation of different biological mechanisms involved in neurodegenerative diseases. By inhibiting PDE4 with drugs, the levels of cAMP inside the cells could be stabilized, which may improve the symptoms of mental and neurological disorders such as memory loss, depression, and Parkinson's disease (PD). Though numerous studies have shown that phosphodiesterase 4 inhibitors (PDE4Is) are beneficial in PD, there are presently no approved PDE4I drugs for PD. This review presents an overview of PDE4Is and their effects on PD, their possible underlying mechanism in the restoration/protection of dopaminergic cell death, which holds promise for developing PDE4Is as a treatment strategy for PD. Methods on how these drugs could be effectively delivered to develop as a promising treatment for PD have been suggested.


Diethylstilbestrol/analogs & derivatives , Neurodegenerative Diseases , Parkinson Disease , Phosphodiesterase 4 Inhibitors , Animals , Humans , Cyclic Nucleotide Phosphodiesterases, Type 4/metabolism , Parkinson Disease/drug therapy , Phosphodiesterase 4 Inhibitors/pharmacology , Phosphodiesterase 4 Inhibitors/therapeutic use , Cyclic AMP/metabolism , Neurodegenerative Diseases/metabolism , Cyclic GMP/metabolism , Mammals/metabolism
13.
Cell Mol Biol (Noisy-le-grand) ; 70(3): 48-53, 2024 Mar 31.
Article En | MEDLINE | ID: mdl-38650154

Plentiful studies have clarified miRNAs take on a key role in the sexual dysfunction of diabetic rats. This study aimed to figure out microRNA (miR)-503-5p/SYDE2 axis' latent mechanisms in streptozotocin-induced diabetic rat sexual dysfunction. A model of erectile dysfunction (ED) in diabetic rats was established by injecting streptozotocin. MiR-503-5p and SYDE2 in ED rats were altered by injection of miR-503-5p mimic or si/oe-SYDE2. The targeting link between miR-503-5p and SYDE2 was testified. ICP/MAP value was tested by pressure sensor; Penile capillary abundance was assessed; Penile cGMP and AGEs were detected; penile smooth muscle cell apoptosis was assessed; MiR-503-5p and SYDE2 were tested. In streptozotocin-induced ED rats, miR-503-5p was reduced and SYDE2 was elevated. Elevating miR-503-5p or silencing of SYDE2 can enhance penile erection rate, ICP/MAP value, capillary abundance, and cGMP but reduce AGEs and penile smooth muscle cell apoptosis rate in ED rats. Strengthening SYDE2 with elevating miR-503-5p turned around the accelerating effect of elevated miR-503-5p on penile erection in ED rats. SYDE2 was a downstream target gene of miR-503-5p. MiR-503-5p protects streptozotocin-induced sexual dysfunction in diabetic rats by targeting SYDE2.


Apoptosis , Diabetes Mellitus, Experimental , Down-Regulation , Erectile Dysfunction , MicroRNAs , Penis , Rats, Sprague-Dawley , Animals , Male , MicroRNAs/genetics , MicroRNAs/metabolism , Erectile Dysfunction/genetics , Erectile Dysfunction/etiology , Diabetes Mellitus, Experimental/complications , Diabetes Mellitus, Experimental/genetics , Apoptosis/genetics , Down-Regulation/genetics , Penis/pathology , Streptozocin , Penile Erection , Rats , Cyclic GMP/metabolism , Intracellular Signaling Peptides and Proteins/genetics , Intracellular Signaling Peptides and Proteins/metabolism , Myocytes, Smooth Muscle/metabolism , Glycation End Products, Advanced/metabolism
14.
Sci Rep ; 14(1): 9919, 2024 04 30.
Article En | MEDLINE | ID: mdl-38689031

Natriuretic peptides (NP) have multiple actions benefitting cardiovascular and metabolic health. Although many of these are mediated by Guanylyl Cyclase (GC) receptors NPR1 and NPR2, their role and relative importance in vivo is unclear. The intracellular mediator of NPR1 and NPR2, cGMP, circulates in plasma and can be used to examine relationships between receptor activity and tissue responses targeted by NPs. Plasma cGMP was measured in 348 participants previously recruited in a multidisciplinary community study (CHALICE) at age 50 years at a single centre. Associations between bio-active NPs and bio-inactive aminoterminal products with cGMP, and of cGMP with tissue response, were analysed using linear regression. Mediation of associations by NPs was assessed by Causal Mediation Analysis (CMA). ANP's contribution to cGMP far exceed those of other NPs. Modelling across three components (demographics, NPs and cardiovascular function) shows that ANP and CNP are independent and positive predictors of cGMP. Counter intuitively, findings from CMA imply that in specific tissues, NPR1 responds more to BNP stimulation than ANP. Collectively these findings align with longer tissue half-life of BNP, and direct further therapeutic interventions towards extending tissue activity of ANP and CNP.


Cyclic GMP , Receptors, Atrial Natriuretic Factor , Humans , Receptors, Atrial Natriuretic Factor/metabolism , Middle Aged , Male , Female , Cyclic GMP/metabolism , Natriuretic Peptides/metabolism , Atrial Natriuretic Factor/metabolism , Atrial Natriuretic Factor/blood
15.
Proc Natl Acad Sci U S A ; 121(18): e2313107121, 2024 Apr 30.
Article En | MEDLINE | ID: mdl-38652742

Full understanding of proteostasis and energy utilization in cells will require knowledge of the fraction of cell proteins being degraded with different half-lives and their rates of synthesis. We therefore developed a method to determine such information that combines mathematical analysis of protein degradation kinetics obtained in pulse-chase experiments with Bayesian data fitting using the maximum entropy principle. This approach will enable rapid analyses of whole-cell protein dynamics in different cell types, physiological states, and neurodegenerative disease. Using it, we obtained surprising insights about protein stabilities in cultured cells normally and upon activation of proteolysis by mTOR inhibition and increasing cAMP or cGMP. It revealed that >90% of protein content in dividing mammalian cell lines is long-lived, with half-lives of 24 to 200 h, and therefore comprises much of the proteins in daughter cells. The well-studied short-lived proteins (half-lives < 10 h) together comprise <2% of cell protein mass, but surprisingly account for 10 to 20% of measurable newly synthesized protein mass. Evolution thus appears to have minimized intracellular proteolysis except to rapidly eliminate misfolded and regulatory proteins.


Entropy , Proteolysis , Proteome , Proteome/metabolism , Humans , Animals , Bayes Theorem , Proteostasis , Kinetics , Cyclic AMP/metabolism , TOR Serine-Threonine Kinases/metabolism , Cyclic GMP/metabolism
16.
Drug Dev Res ; 85(3): e22192, 2024 May.
Article En | MEDLINE | ID: mdl-38678552

Non-small cell lung cancer (NSCLC) is a malignant tumor with low overall cure and survival rates. Uncovering abnormally expressed genes is significantly important for developing novel targeted therapies in NSCLC. This study aimed to discover new differentially expressed genes (DEGs) of NSCLC. The DEGs of NSCLC were identified in eight data sets from Gene Expression Omnibus (GEO) database. The expression profiles and the prognostic significance of SCN4B in LUAD and LUSC were analyzed using GEPIA database. LinkedOmics was used to identify co-expressed genes with SCN4B, which were further subjected to KEGG pathway enrichment analysis. SCN4B-overexpressing plasmid (pcDNA/SCN4B) was transfected into A549 and NCI-H2170 cells to elevate the expression of SCN4B. MTT and TUNEL assays were performed to evaluate cell viability and apoptosis. Relying on the screened DEGs from GEO database, we identified that SCN4B was significantly downregulated in LUAD and LUSC. We confirmed the downregulation of SCN4B in NSCLC tissues using GEPIA database. SCN4B has a prognostic value in LUAD, but not LUSC. KEGG pathway enrichment analysis of SCN4B-related genes showed that cGMP-PKG signaling pathway might be involved in the role of SCN4B in NSCLC. Overexpression of SCN4B in A549 and NCI-H2170 cells inhibited the cell viability. Besides, SCN4B overexpression induced apoptosis of A549 and NCI-H2170 cells. SCN4B inhibited the expression of PKG1 and p-CREB in NSCLC cells. Moreover, the inhibitory effects of SCN4B on tumor malignancy were attenuated by the activator of PKG. In conclusion, integrated bioinformatical analysis proved that SCN4B was downregulated and had a prognostic significance in NSCLC. In vitro experimental studies demonstrated that SCN4B regulated NSCLC cells viability and apoptosis via inhibiting cGMP-PKG signaling pathway.


Carcinoma, Non-Small-Cell Lung , Computational Biology , Cyclic GMP , Lung Neoplasms , Humans , A549 Cells , Apoptosis , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/metabolism , Carcinoma, Non-Small-Cell Lung/pathology , Cell Line, Tumor , Cell Survival , Cyclic GMP/metabolism , Cyclic GMP-Dependent Protein Kinases/metabolism , Cyclic GMP-Dependent Protein Kinases/genetics , Down-Regulation , Gene Expression Regulation, Neoplastic , Lung Neoplasms/genetics , Lung Neoplasms/metabolism , Lung Neoplasms/pathology , Signal Transduction
17.
Sci Total Environ ; 928: 172408, 2024 Jun 10.
Article En | MEDLINE | ID: mdl-38608880

This study investigated the mechanisms of microbial growth and metabolism during biofilm cultivation in the biofilm sequencing batch reactor (BSBR) process for phosphate (P) enrichment. The results showed that the sludge discharge was key to biofilm growth, as it terminated the competition for carbon (C) source between the nascent biofilm and the activated sludge. For the tested reactor, after the sludge discharge on 18 d, P metabolism and C source utilization improved significantly, and the biofilm grew rapidly. The P concentration of the recovery liquid reached up to 157.08 mg/L, which was sufficient for further P recovery via mineralization. Meta-omics methods were used to analyze metabolic pathways and functional genes in microbial growth during biofilm cultivation. It appeared that the sludge discharge activated the key genes of P metabolism and inhibited the key genes of C metabolism, which strengthened the polyphosphate-accumulating metabolism (PAM) as a result. The sludge discharge not only changed the types of polyphosphate-accumulating organisms (PAOs) but also promoted the growth of dominant PAOs. Before the sludge discharge, the necessary metabolic abilities that were spread among different microorganisms gradually concentrated into a small number of PAOs, and after the sludge discharge, they further concentrated into Candidatus_Contendobacter (P3) and Candidatus_Accumulibacter (P17). The messenger molecule C-di-GMP, produced mostly by P3 and P17, facilitated P enrichment by regulating cellular P and C metabolism. The glycogen-accumulating organism (GAO) Candidatus_Competibacter secreted N-Acyl homoserine lactones (AHLs), which stimulated the secretion of protein in extracellular polymeric substances (EPS), thus promoting the adhesion of microorganisms to biofilm and improving P metabolism via EPS-based P adsorption. Under the combined action of the dominant GAOs and PAOs, AHLs and C-di-GMP mediated QS to promote biofilm development and P enrichment. The research provides theoretical support for the cultivation of biofilm and its wider application.


Acyl-Butyrolactones , Biofilms , Cyclic GMP , Cyclic GMP/analogs & derivatives , Phosphates , Waste Disposal, Fluid , Acyl-Butyrolactones/metabolism , Phosphates/metabolism , Cyclic GMP/metabolism , Waste Disposal, Fluid/methods , Bioreactors/microbiology , Sewage/microbiology
18.
Cell Rep ; 43(5): 114154, 2024 May 28.
Article En | MEDLINE | ID: mdl-38669142

Cyclic di-guanosine monophosphate (c-di-GMP) is a bacterial second messenger that governs the lifestyle switch between planktonic and biofilm states. While substantial investigation has focused on the proteins that produce and degrade c-di-GMP, less attention has been paid to the potential for metabolic control of c-di-GMP signaling. Here, we show that micromolar levels of specific environmental purines unexpectedly decrease c-di-GMP and biofilm formation in Pseudomonas aeruginosa. Using a fluorescent genetic reporter, we show that adenosine and inosine decrease c-di-GMP even when competing purines are present. We confirm genetically that purine salvage is required for c-di-GMP decrease. Furthermore, we find that (p)ppGpp prevents xanthosine and guanosine from producing an opposing c-di-GMP increase, reinforcing a salvage hierarchy that favors c-di-GMP decrease even at the expense of growth. We propose that purines can act as a cue for bacteria to shift their lifestyle away from the recalcitrant biofilm state via upstream metabolic control of c-di-GMP signaling.


Biofilms , Cyclic GMP , Pseudomonas aeruginosa , Purines , Pseudomonas aeruginosa/metabolism , Pseudomonas aeruginosa/physiology , Biofilms/growth & development , Cyclic GMP/metabolism , Cyclic GMP/analogs & derivatives , Purines/metabolism , Purines/pharmacology , Bacterial Proteins/metabolism
19.
Sci Total Environ ; 927: 172376, 2024 Jun 01.
Article En | MEDLINE | ID: mdl-38604376

Biofilms are widely used and play important roles in biological processes. Low temperature of wastewater inhibits the development of biofilms derived from wastewater activated sludge. However, the specific mechanism of temperature on biofilm development is still unclear. This study explored the mechanism of temperature on biofilm development and found a feasible method to enhance biofilm development at low temperature. The amount of biofilm development decreased by approximately 66 % and 55 % at 4 °C and 15 °C, respectively, as compared to 28 °C. The cyclic dimeric guanosine monophosphate (c-di-GMP) concentration also decreased at low temperature and was positively correlated with extracellular polymeric substance (EPS) content, formation, and adhesion strength. Microbial community results showed that low temperature inhibited the normal survival of most microorganisms, but promoted the growth of some psychrophile bacteria like Sporosarcina, Caldilineaceae, Gemmataceae, Anaerolineaceae and Acidobacteriota. Further analysis of functional genes demonstrated that the abundance of functional genes related to the synthesis of c-di-GMP (K18968, K18967 and K13590) decreased at low temperature. Subsequently, the addition of exogenous spermidine increased the level of intracellular c-di-GMP and alleviated the inhibition effect of low temperature on biofilm development. Therefore, the possible mechanism of low temperature on biofilm development could be the inhibition of the microorganism activity and reduction of the communication level between cells, which is the closely related to the EPS content, formation, and adhesion strength. The enhancement of c-di-GMP level through the exogenous addition of spermidine provides an alternative strategy to enhance biofilm development at low temperatures. The results of this study enhance the understanding of the influence of temperature on biofilm development and provide possible strategies for enhancing biofilm development at low temperatures.


Bacteria , Biofilms , Cyclic GMP , Bacterial Physiological Phenomena , Cold Temperature , Cyclic GMP/analogs & derivatives , Cyclic GMP/metabolism , Extracellular Polymeric Substance Matrix , Wastewater/microbiology
20.
Pharmacol Ther ; 258: 108653, 2024 Jun.
Article En | MEDLINE | ID: mdl-38679204

Cyclic nucleotides are important signaling molecules that play many critical physiological roles including controlling cell fate and development, regulation of metabolic processes, and responding to changes in the environment. Cyclic nucleotides are also pivotal regulators in immune signaling, orchestrating intricate processes that maintain homeostasis and defend against pathogenic threats. This review provides a comprehensive examination of the pharmacological potential of cyclic nucleotide signaling pathways within the realm of immunity. Beginning with an overview of the fundamental roles of cAMP and cGMP as ubiquitous second messengers, this review delves into the complexities of their involvement in immune responses. Special attention is given to the challenges associated with modulating these signaling pathways for therapeutic purposes, emphasizing the necessity for achieving cell-type specificity to avert unintended consequences. A major focus of the review is on the recent paradigm-shifting discoveries regarding specialized cyclic nucleotide signals in the innate immune system, notably the cGAS-STING pathway. The significance of cyclic dinucleotides, exemplified by 2'3'-cGAMP, in controlling immune responses against pathogens and cancer, is explored. The evolutionarily conserved nature of cyclic dinucleotides as antiviral agents, spanning across diverse organisms, underscores their potential as targets for innovative immunotherapies. Findings from the last several years have revealed a striking diversity of novel bacterial cyclic nucleotide second messengers which are involved in antiviral responses. Knowledge of the existence and precise identity of these molecules coupled with accurate descriptions of their associated immune defense pathways will be essential to the future development of novel antibacterial therapeutic strategies. The insights presented herein may help researchers navigate the evolving landscape of immunopharmacology as it pertains to cyclic nucleotides and point toward new avenues or lines of thinking about development of therapeutics against the pathways they regulate.


Nucleotides, Cyclic , Signal Transduction , Humans , Animals , Nucleotides, Cyclic/metabolism , Immunity, Innate , Cyclic AMP/metabolism , Cyclic GMP/metabolism , Neoplasms/drug therapy , Neoplasms/immunology , Nucleotidyltransferases/metabolism , Membrane Proteins/metabolism
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