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PubMed2026

Multi-Omics Analysis Reveals Molecular Networks and Key Pathways Associated with Cysteine- and Methionine-Mediated Biosynthesis of Sulfur-Containing Flavor Metabolites in Lentinula edodes.

Lentinula edodes is renowned for its unique aroma, which is characterized by various volatile sulfur-containing flavor metabolites (SCFMs). Cysteine and methionine could enhance the SCFMs biosynthesis in L. edodes; however, the underlying metabolic pathways remain unclear. To bridge this gap, integrated proteomic and metabolomic analysis were performed to decipher pathways through which cysteine and methionine regulate SCFM biosynthesis. Results showed that exogenous cysteine and methionine supplementation significantly increased the content of lenthionine, the key aroma compound of shiitake mushrooms. Both treatments induced substantial changes in the proteomic and metabolomic profiles. Proteomic analysis revealed that differentially expressed proteins were predominantly enriched in cysteine and methionine metabolism and sulfur metabolism following cysteine treatment, whereas methionine treatment mainly affected proteins associated with tryptophan metabolism and sulfur metabolism. Metabolomic analysis showed that differentially accumulated metabolites were significantly enriched in D-amino acid metabolism and cysteine and methionine metabolism, with glutathione metabolism specifically enriched under cysteine treatment. Integrated omics analysis further uncovered distinct sulfur metabolite-protein regulatory networks under different sulfur nutrition and identified treatment-specific hub proteins. These findings establish a molecular regulatory framework linking SCFM biosynthesis with broader primary metabolic pathways involved in sulfur intermediate generation and regulation, providing new insights into the potential regulatory networks underlying SCFM formation in L. edodes.

Methionine↗
PubMed2026

Desmoplakin loss in alveolar epithelium drives Wnt/β-Catenin-mediated extracellular matrix remodeling and fibrotic signaling in vitro.

BACKGROUND: Idiopathic pulmonary fibrosis (IPF) is a progressive fibrotic interstitial lung disease characterized by aberrant extracellular matrix (ECM) remodeling, epithelial dysfunction, and limited therapeutic options. Genetic studies implicate Desmoplakin (DSP), a desmosomal adhesion protein, in IPF susceptibility; however, its mechanistic role remains unclear. This study aimed to investigate the role of DSP in regulating fibrotic and ECM remodeling pathways in alveolar epithelial cells. METHODS AND RESULTS: DSP was silenced using siRNA in adenocarcinoma-derived human alveolar epithelial A549 cells. DSP loss induced epithelial-to-mesenchymal transition, enhanced cell migration, and increased epithelial permeability, along with upregulation of fibrotic and ECM-associated genes. Pathway enrichment analysis of DSP interactors (STRING database) identified the Wnt/β-catenin signaling as a potential key pathway. Mechanistic validation using cycloheximide chase assays, qPCR, western blotting, immunofluorescence, and luciferase-reporter assays suggested that DSP loss destabilizes desmosomal complexes, promoting plakoglobin (γ-catenin) degradation while reducing β-catenin turnover. This was associated with increased nuclear accumulation of β-catenin and enhanced TCF/LEF-dependent transcription, leading to elevated expression of ECM-related genes, including COL1A1 and MMP9. DSP overexpression suppressed Wnt/β-catenin signaling and fibrotic gene expression, while pharmacological inhibition of this pathway attenuated DSP-dependent increases in ECM-associated gene expression. CONCLUSION: These findings suggest that DSP may function as a regulator of alveolar epithelial homeostasis and extracellular matrix remodeling in an in vitro epithelial model. Loss of DSP is associated with activation of Wnt/β-catenin-mediated fibrotic signaling, correlating with reduced plakoglobin stability. This study provides mechanistic insight into epithelial-matrix crosstalk in vitro and identifies a candidate pathway that may contribute to ECM dysregulation in IPF, the disease relevance of which will require validation in primary human alveolar epithelial cells and in vivo models.

Humans↗
PubMed1993

Cloning and characterisation of the Schizosaccharomyces pombe rad8 gene, a member of the SNF2 helicase family.

The Schizosaccharomyces pombe rad8 mutant is sensitive to both UV and gamma irradiation. We have cloned the rad8 gene by complementation of the UV sensitivity of a rad8.190 mutant strain. The gene comprises an open reading frame of 3.4 kb which does not contain any introns and is capable of encoding a 1133 amino acid protein of 129 kDa. Deletion of the gene indicates that it is not essential for cell viability. Recognisable motifs are present for a nuclear localisation signal, a RING finger and helicase domains. The predicted protein is a member of the SNF2 subfamily of proteins and shows particular homology to the Saccharomyces cerevisiae RAD5 protein. Double mutant analysis demonstrated that the rad8 mutant is not epistatic to mutants in the excision repair pathway (rad13) or checkpoint pathway (rad9). Analysis of radiation sensitivity though the cell cycle indicates that, unlike most other rad mutants, rad8 is most sensitive to irradiation during the G1/S period.

Amino Acid Sequence↗
PubMed2004

Ethylene response factor 1 mediates Arabidopsis resistance to the soilborne fungus Fusarium oxysporum.

Ethylene response factor 1 (ERF1) is a transcriptional factor from Arabidopsis thaliana that regulates plant resistance to the necrotrophic fungi Botrytis cinerea and Plectosphaerella cucumerina and whose overexpression enhances resistance to these fungi. Here, we show that ERF1 also mediates Arabidopsis resistance to the soilborne fungi Fusarium oxysporum sp. conglutinans and F. oxysporum f. sp. lycopersici, because its constitutive expression in Arabidopsis confers enhanced resistance to these pathogens. Expression of ERF1 was upregulated after inoculation with F. oxysporum f. sp. conglutinans, and this response was blocked in ein2-5 and coi1-1 mutants, impaired in the ethylene (ET) and jasmonic acid (JA) signal pathways, respectively, which further indicates that ERF1 is a downstream component of ET and JA defense responses. The signal transduction network controlling resistance to F. oxysporum fungi was explored using signaling-defective mutants in ET (ein2-5), JA (jar1-1), and salicylic acid (SA) (NahG, sid2-1, eds5-1, npr1-1, pad4-1, eds1-1, and pad2-1) transduction pathways. This analysis revealed that Arabidopsis resistance to F. oxysporum requires the ET, JA, and SA signaling pathways and the NPR1 gene, although it is independent of the PAD4 and EDS1 functions.

Arabidopsis↗
PubMed2004

Acylic sugar derivatives for GC/MS analysis of 13C-enrichment during carbohydrate metabolism.

Metabolic profiling with stable-isotope tracers in combination with gas chromatography/mass spectrometry (GC/MS) is a well-established technique for measuring substrate redistribution within metabolic pathways. This analysis relies on the ability to localize and quantify the fractional incorporation of 13C isotope into each carbon atom of precursor-derived metabolites. In this paper, several carbohydrate derivatization procedures (peracetylation, deuterioalditol acetates, and aldononitrile acetates) are evaluated for the positional isotopic information obtained by gas chromatography/electron impact mass spectrometry (GC/EI-MS). These derivatives have been compared for the quantitative evaluation of 13C distribution into isotopomers of 13C-labeled aldoses and ketoses, and the fragmentation pathways for 15 hexoses, pentoses, and amino sugars of biological origin have been assessed. In addition, a new type of carbohydrate derivative (dialkyldithioacetal acetates) has been developed for GC/MS that retains the charge on the anomeric carbon of the original monosaccharide. Electron impact ionization of these derivatives generates well-resolved base peaks arising from C1-C2 bond cleavage with charge retention at the C1 thiol groups. The dialkyldithioacetal acetates are uniquely well suited for measuring isotopic enrichment into the characteristic anomeric carbon of aldose sugars and will facilitate the global analysis of metabolic flux in carbohydrate pathways.

Carbohydrate Metabolism↗
PubMed2006

Boolean network analysis of a neurotransmitter signaling pathway.

BACKGROUND: A Boolean network is a simple computational model that may provide insight into the overall behavior of genetic networks and is represented by variables with two possible states (on/off), of the individual nodes/genes of the network. In this study, a Boolean network model has been used to simulate a molecular pathway between two neurotransmitter receptor, dopamine and glutamate receptor, systems in order to understand the consequence of using logic gate rules between nodes, which have two possible states (active and inactive). RESULTS: The dynamical properties of this Boolean network model of the biochemical pathway shows that, the pathway is stable and that, deletion/knockout of certain biologically important nodes cause significant perturbation to this network. The analysis clearly shows that in addition to the expected components dopamine and dopamine receptor 2 (DRD2), Ca(2+) ions play a critical role in maintaining stability of the pathway. CONCLUSION: So this method may be useful for the identification of potential genetic targets, whose loss of function in biochemical pathways may be responsible for disease onset. The molecular pathway considered in this study has been implicated with a complex disorder like schizophrenia, which has a complex multifactorial etiology.

Animals↗
PubMed1998

Impact of clinical pathways for total hip replacement: a community-based analysis.

The implementation of clinical pathways for total hip replacement was carried out by five hospitals in the metropolitan area of Syracuse, New York. This process occurred under the leadership of clinical nurse specialists and nurse managers. It was supported by preadmission patient education programs and active physician involvement. The participating hospitals shared utilization quality assurance data and benchmarked with respect to the experience of Sacramento, California, and each others' progress. The effort produced substantial reductions in hospital stays without adverse impacts on quality of care.

Arthroplasty, Replacement, Hip↗
PubMed1994

[Analysis of electrically evoked response in relation to the central pathway of the cat (3). Current source density analysis in area 17 of cats].

We analyzed current source density and multiple unit activity of area 17 of cats in response to transcorneal electrical stimuli to clarify the localization of the transmembrane current flows contributing to the generation of the electrically evoked response. The results of the current source density analysis were as follows. 1. Current sinks within 20 ms were observed in layers 4 and 6. 2. Current sinks corresponding to N3 (latency 35 ms) were detected in layers 4 and lower 3 and current sources were in the supragranular layers. 3. Current sinks with a latency of more than 40 ms were observed in the supragranular layers. Simultaneous multiple unit activity was present in cases 1 and 2. With increased stimulus frequency or double electrical stimuli, the current sinks corresponding to N3 were decreased. These findings indicate that N1 (latency 9 ms) and N2 (latency 20 ms) reflect near-field potentials generated by geniculocortical afferents in layers 4 and 6, and that N3 is a post-and polysynaptic component. In addition, it appears that dipoles consisting of cell bodies and apical dendrites of pyramidal cells in layer 3 generated by satellite cell in layer 4, play a major role in generating N3.

Animals↗
PubMed2005

Flexibility of prolyl oligopeptidase: molecular dynamics and molecular framework analysis of the potential substrate pathways.

The flexibility of prolyl oligopeptidase has been investigated using molecular dynamics (MD) and molecular framework approaches to delineate the route of the substrate to the active site. The selectivity of the enzyme is mediated by a seven-bladed beta-propeller that in the crystal structure does not indicate the possible passage for the substrate to the catalytic center. Its open topology however, could allow the blades to move apart and let the substrate into the large central cavity. Flexibility analysis of prolyl oligopeptidase structure using the FIRST (Floppy Inclusion and Rigid Substructure Topology) approach and the atomic fluctuations derived from MD simulations demonstrated the rigidity of the propeller domain, which does not permit the substrate to approach the active site through this domain. Instead, a smaller tunnel at the inter-domain region comprising the highly flexible N-terminal segment of the peptidase domain and a facing hydrophilic loop from the propeller (residues 192-205) was identified by cross-correlation analysis and essential dynamics as the only potential pathway for the substrate. The functional importance of the flexible loop has been also verified by kinetic analysis of the enzyme with a split loop. Catalytic effect of engineered disulfide bridges was rationalized by characterizing the concerted motions of the two domains.

Animals↗
PubMed2006

The vtc4 gene influences polyphosphate storage, morphogenesis, and virulence in the maize pathogen Ustilago maydis.

The maize pathogen Ustilago maydis switches from budding to filamentous, dikaryotic growth in response to environmental signals including nutrient status, growth in the host, and the presence of mating pheromones. The filamentous dikaryon is capable of proliferating within host tissue to cause disease symptoms including tumors. The transition from yeast cells to hyphal filaments is regulated by a mitogen-activated protein kinase cascade and a cyclic-AMP-protein kinase A (PKA) pathway. Serial analysis of gene expression with PKA mutants identified orthologs of components of the PHO phosphate acquisition pathway as transcriptional targets of the PKA pathway, and these included genes for Pho84, an acid phosphatase, and the vacuolar transport chaperones Vtc1 and Vtc4. In Saccharomyces cerevisiae, Vtc4p is required during the fusion of inorganic-phosphate-containing vesicles to the vacuolar membrane and the consequent accumulation of phosphate stored as polyphosphate (polyP) in the vacuole. We found that deletion of vtc4 in U. maydis also reduced polyP stored in vacuoles. Intriguingly, Deltavtc4 mutants possessed a filamentous cellular morphology, in contrast to the budding, yeast-like growth of the wild-type parent. The Deltavtc4 mutants also displayed decreased symptom development and reduced proliferation in planta. The interaction with PKA signaling was further investigated by the generation of Deltavtc4 ubc1 double mutants. Deletion of vtc4 completely suppressed the multiple-budded phenotype of a Deltaubc1 mutant, indicating that polyP stores are essential for this PKA-induced trait. Overall, this study reveals a novel role for PKA-regulated polyP accumulation in the control of fungal morphogenesis and virulence.

Cyclic AMP↗
PubMed1994

Regulation of Sertoli cell differentiation by the testicular paracrine factor PModS: analysis of common signal transduction pathways.

In the testis the mesenchymally derived peritubular cells produce a paracrine factor, PModS, that mediates mesenchymal-epithelial interactions and modulates Sertoli cell functions essential for the process of spermatogenesis. PModS has a more dramatic effect on Sertoli cell differentiated functions in vitro than any regulatory agent previously shown to influence the cells, including FSH. The current study initiates an investigation of the pharmacology of PModS through an analysis of several common signal transduction pathways. PModS was found to stimulate cGMP levels in Sertoli cells and maintain elevated levels for up to 5 days in culture. PModS had no influence on cAMP levels. In contrast, FSH stimulated cAMP, but had no influence on cGMP levels. For comparison, an agent known to influence cGMP levels, atrial naturetic factor (ANF), was used to treat Sertoli cells. ANF caused a dramatic increase in Sertoli cell cGMP levels within minutes of treatment, but did not maintain elevated cGMP levels after a 72-h treatment. Although ANF increased guanylate cyclase in whole Sertoli cell homogenates and particulate fractions, PModS did not directly influence guanylate cyclase activity. As previously shown, PModS stimulates transferrin expression as a marker of Sertoli cell differentiated function. Agents that elevate cellular cGMP, including ANF, sodium nitroprusside, and 8-bromo-cGMP, did not influence Sertoli cell transferrin expression. In addition, these agents did not influence the actions of PModS or FSH. Therefore, cGMP does not appear to directly mediate the actions of PModS. As an alternative signal transduction pathway, calcium mobilization and inositol phosphate (IP) metabolism were examined. PModS did not alter calcium uptake or intracellular calcium mobilization. PModS also did not influence the levels of inositol mono-, bis-, or trisphosphates, whereas calf serum did stimulate levels of all three IP metabolites in Sertoli cells. Therefore, PModS does not appear to act through a mobilization of calcium or increased metabolism of IP. A final signal transduction pathway involving phosphorylation was also examined. PModS treatment was found to increase tyrosine phosphorylation of specific proteins in a crude Sertoli cell cytosol preparation. Genistein is an inhibitor of tyrosine kinases and was found to reduce PModS actions at a 3.7-microM concentration of genistein and inhibit PModS actions at a 37-microM concentration of genistein. Therefore, PModS may act through a tyrosine phosphorylation event that remains to be elucidated. Combined observations indicate that PModS does not use cyclic nucleotides, calcium mobilization, or IP metabolism as a signal transduction pathway.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1989

The matrix method of metabolic control analysis: its validity for complex pathway structures.

The sensitivities of the variables of a metabolic system (such as fluxes and concentrations) to variations in enzyme concentration are expressed in metabolic control analysis as control coefficients. The matrix method is a system of writing matrix equations that generate expressions for the control coefficients in terms of the characteristics of the components (principally the enzymes). Previously, the matrix method has been considered in terms of simple pathway structures; here we justify its applicability to complex pathways, such as those with multiple branches. It is shown that this requires modification of the branch point relationship to take account of changes of flux along the limbs of the branch and of stoichiometric factors. The method of deriving the flux control coefficients with respect to different fluxes in the system is extended to cope with these circumstances.

Animals↗
PubMedDate not supplied

Analysis of local electrograms at successful and unsuccessful sites for slow pathway ablation of atrioventricular nodal reentrant tachycardia.

Anatomic and electrogram approaches have been described for ablation of slow pathway in patients with atrioventricular nodal tachycardia. The purpose of this study was to identify parameters to predict successful slow pathway ablation using the anatomic approach. Local electrograms at successful and unsuccessful sites were compared in 36 patients undergoing slow pathway ablation using anatomic approach. A total of 208 local electrograms were studied. Fragmented atrial electrogram was seen in 24/36 (67%) of successful and in 46/172 (26%) of unsuccessful sites (p < 0.001). The sensitivity, specificity and positive and negative predictive values of fragmented atrial electrogram were 67, 73, 34 and 91 percent respectively. A slow pathway potential was noted in three of successful sites. There was no difference in the atrial to ventricular amplitude ratio in these sites. In conclusion, fragmentation of atrial electrogram and presence of possible slow pathway potential are seen more often at successful than at unsuccessful sites. In our opinion, while using an anatomic approach for slow pathway ablation, an analysis of local electrogram may help in identifying the proper site and avoiding unnecessary radiofrequency energy delivery.

Adult↗
PubMed2024

Metagenomic Analysis of Gut Microbiome of Persistent Pulmonary Hypertension of the Newborn.

Persistent pulmonary hypertension of the newborn (PPHN) is one of the most common diseases in the neonatal intensive care unit which severely affects neonatal survival. Gut microbes play an increasingly important role in human health, but there are rarely reported how gut microbiota contribute to PPHN. In our study, the metagenomic sequencing of feces from 12 PPHN's neonates and 8 controls were performed to expose the relation between neonatal gut microbes and PPHN disease. Firstly, we found that the abundance of Actinobacteria, Proteobacteria, Bacteroidetes were significantly increased in PPHN compared with controls, but the Firmicutes components was reduced. And some pathogenic strains (like Vibrio metschnikovii) were significantly enriched in the PPHN compared with controls. Secondly, functional annotation of genes found that PPHN up-regulated transmembrane transport, but down-regulated ribosome and ATP binding. Lastly, microbial metabolic pathway enrichment analysis indicated that some metabolic pathway in PPHN were conflicting and contradictory, showed that an abnormally increased metabolism, disturbed protein synthesis and genomic instability in the PPHN neonate. Our results contribute to understanding the changes in the species and function of gut microbiota in PPHN, thus providing a theoretical basis for the explanation and treatment of PPHN.

Gastrointestinal Microbiome↗
PubMed1993

Activation of serum complement by polysaccharide-containing antigens of Porphyromonas gingivalis.

We previously reported that hot aqueous phenol extraction of Porphyromonas gingivalis yields a preparation containing both lipopolysaccharide (LPS) and an antigenically distinct capsular polysaccharide (PS). In the present study, we examined the capacity of phenol-water extracts from a number of strains of P. gingivalis to activate human serum complement. Anticomplementary activity of extracts from two invasive and two noninvasive strains of P. gingivalis was assessed in a sheep erythrocyte hemolytic assay and in an alternative pathway-selective rabbit erythrocyte hemolytic assay. In the sheep erythrocyte assay, extracts from noninvasive strains were found to exhibit greater anticomplementary activity than extracts derived from invasive strains. A phenol-water extract from invasive strain ATCC 53977 was further resolved into its LPS and PS fractions. Whereas isolated LPS from this strain exhibited strong anticomplementary activity, the PS fraction was only weakly active. Phenol-water extracts from three of four strains were found to be potent activators of the alternative pathway, with extracts from the two noninvasive strains being most active. The extract from the remaining strain (ATCC 53977) was a poor activator of the alternative pathway. Further analysis of this extract revealed, however, that the LPS fraction was a potent activator of the alternative pathway, although the PS fraction exhibited negligible activity. The results of this study indicate that phenol-water extracts of invasive and noninvasive strains of P. gingivalis differ in their respective anticomplementary activities, with invasive strains being less active. Although extracts from both invasive and noninvasive strains activated the alternative pathway, this activity appears to be attributable to the LPS, rather than the PS, component.

Antigens, Bacterial↗
PubMed2025

Mechanism of Qigu capsule as a treatment for sarcopenia based on network pharmacology and experimental validation.

OBJECTIVE: To explore the potential molecular mechanism of Qigu capsule (&#xff0c;QGC) in the treatment of sarcopenia through network pharmacology and to verify it experimentally. METHODS: The active compounds of QGC and common targets between QGC and sarcopenia were screened from databases. Then the herbs-compounds-targets network, and protein-protein interaction (PPI) network was constructed. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed by R software. Next, we used a dexamethasone-induced sarcopenia mouse model to evaluate the anti-sarcopenic mechanism of QGC. RESULTS: A total of 57 common targets of QGC and sarcopenia were obtained. Based on the enrichment analysis of GO and KEGG, we took the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt) signaling pathway as a key target to explore the mechanism of QGC on sarcopenia. Animal experiments showed that QGC could increase muscle strength and inhibit muscle fiber atrophy. In the model group, the expression of muscle ring finger-1 and Atrogin-1 were increased, while myosin heavy chain was decreased, QGC treatment reversed these changes. Moreover, compared with the model group, the expressions of p-PI3K, p-Akt, p-mammalian target of rapamycin and p-Forkhead box O3 in the QGC group were all upregulated. CONCLUSION: QGC exerts an anti-sarcopenic effect by activating PI3K/Akt signaling pathway to regulate skeletal muscle protein metabolism.

Sarcopenia↗
PubMed2001

Effect of postoperative atrial fibrillation on length of stay after cardiac surgery (The Postoperative Atrial Fibrillation in Cardiac Surgery study [PACS(2)].

Atrial fibrillation (AF) after cardiac surgery is thought to increase length of stay (LOS). A clinical pathway focused on the management of postoperative AF, including prophylaxis with beta blockers, was implemented to assess the effect of AF on LOS after cardiac surgery. Data were obtained on consecutive cardiac surgery patients in preoperative normal sinus rhythm, no prior history of AF, and no chronic antiarrhythmic therapy from January to May 1995 (control) and November 1996 to June 1997 (pathway). Statistical analysis was performed to assess the effect of postoperative AF on the LOS, clinical outcomes, and cost after cardiac surgery. Despite the clinical pathway, the LOS (7 days for both periods; p = 0.12) and incidence of AF (28.9% vs 28.4%; p = 0.92) remained unchanged. Unadjusted direct costs were 15% higher in the pathway period (p <0.001). Increased rates of beta-blocker therapy had a marginal effect on the incidence of postoperative AF, except in the group who only underwent primary coronary artery bypass graft surgery (31.2% vs 25.3%; p = 0.31). Multivariate analysis revealed that AF contributed only 1 to 1.5 days to the LOS. Thus, this investigation represents the most recent analysis of the effects of postoperative AF on LOS, clinical outcomes, and cost after cardiac surgery. Unlike prior studies, the impact of postoperative AF is less prominent in the current era of cardiac surgical care regardless of the presence of a clinical pathway addressing AF.

Adrenergic beta-Antagonists↗
PubMed2005

Single, context-specific glycans can target misfolded glycoproteins for ER-associated degradation.

The endoplasmic reticulum (ER) maintains an environment essential for secretory protein folding. Consequently, the premature transport of polypeptides would be harmful to the cell. To avert this scenario, mechanisms collectively termed "ER quality control" prevent the transport of nascent polypeptides until they properly fold. Irreversibly misfolded molecules are sorted for disposal by the ER-associated degradation (ERAD) pathway. To better understand the relationship between quality control and ERAD, we studied a new misfolded variant of carboxypeptidase Y (CPY). The molecule was recognized and retained by ER quality control but failed to enter the ERAD pathway. Systematic analysis revealed that a single, specific N-linked glycan of CPY was required for sorting into the pathway. The determinant is dependent on the putative lectin-like receptor Htm1/Mnl1p. The discovery of a similar signal in misfolded proteinase A supported the generality of the mechanism. These studies show that specific signals embedded in glycoproteins can direct their degradation if they fail to fold.

Aspartic Acid Endopeptidases↗