Evolution of orphan and atypical histidine kinases and response regulators for microbial signaling diversity.

Two-component signaling systems (TCS) are the predominant means of microbes for sensing and responding to environmental stimuli. Typically, TCS is comprised of a sensor histidine kinase (HK) and a cognate response regulator (RR), which might have coevolved together. They usually involve the phosphoryl transfer signaling mechanism. However, there are also some orphan and atypical HK and RR homologs, and their evolutionary origins are still not very clear. They are not associated with cognate pairs or lack the conserved residues for phosphoryl transfer, but they could receive or respond to signals from other regulators. The objective of this study is to reveal the evolutionary history of these orphan and atypical HK and RR homologs. Structural, domain, sequence, and phylogenetic analyses indicated that their evolution process might undergo gene duplication, divergence, and domain shuffling. Meanwhile, lateral gene transfer might also be involved for their gene distribution. Evolution of orphan and atypical HK and RR homologs have increased their signaling diversity, which could be helpful for microbial adaption in complex environments.

Diverse evolutionary origins of microbial [4 + 2]-cyclases in natural product biosynthesis.

Natural [4 + 2]-cyclases catalyze concerted cycloaddition during biosynthesis of over 400 natural products reported. Microbial [4 + 2]-cyclases are structurally diverse with a broad range of substrates. Thus far, about 52 putative microbial [4 + 2]-cyclases of 13 different types have been characterized, with over 20 crystal structures. However, how these cyclases have evolved during natural product biosynthesis remains elusive. Structural and phylogenetic analyses suggest that these different types of [4 + 2]-cyclases might have diverse evolutionary origins, such as reductases, dehydratases, methyltransferases, oxidases, etc. Divergent evolution of enzyme function might have occurred in these different families. Understanding the independent evolutionary history of these cyclases would provide new insights into their catalysis mechanisms and the biocatalyst design.

Inhibition of inflammation by SP600125 in cholestatic liver injury is dependent on the administration­based exposure profile.

SP600125 is a classic inhibitor of c­Jun­N­terminal kinase (JNK) that is widely used in numerous medicinal studies, but its administration regimen has yet to be optimized. In the present study, intraperitoneal (i.p.) and intragastric (i.g.) injections of 15 mg/kg SP600125 was performed in mice to compare the inhibitory effect against JNK signalling in cholestasis induced by α­naphthylisothiocyanate (ANIT). SP600125 at a dose of 15 mg/kg administered by i.p. substantially decreased ANIT­induced liver injury as observed by biochemical and histopathological examinations. The adaptation of bile acid synthesis was inhibited in the A­SP­i.p. group compared with that in the A­SP­i.g. group, as indicated by the expression analysis of CYP7A1 and CYP8B1. The transcription of the pro­inflammatory factors IL­6, IL­1ß, ICAM­1 and IL­10 supported the differential toxic responses. Western blot analysis revealed that JNK signalling activated by ANIT was inhibited more markedly in the A­SP­i.p. group than in the A­SP­i.g. group. The peak concentration and the AUC0­24 of SP600125 in the A­SP­i.p. group were 5­fold and 1.56­fold higher, respectively, compared with those in the A­SP­i.g. group. These data indicated that i.p. administration of SP600125 produced a high plasma exposure profile, which directly determined its efficacy of blocking the JNK signalling. This effect of SP600125 on the JNK pathway may provide an optimized design for future in vivo investigations.

[The cholestatic fibrosis induced by α-naphthylisothiocyanate in mice and the inflammation pathway].

Objective: To explore the development of cholestatic fibrosis induced by α-naphthylisothiocyanate (ANIT) and the inflammation pathways. Methods: Fifteen 129/Sv mice weighing (23±2) g were randomly divided into 2 groups: control group (n=5) and experiment group (n=10). The control group was fed commercial chow diet and the experiment group was fed the same diet supplemented with 0. 05% ANIT. Five mice in the experiment group were sacrificed on day 14 and 28 respectively. The gallbladder, serum and liver samples were collected. Biochemical indicators of cholestasis were detected following the procedures in the kit. Liver injury was evaluated by histopathological. Hepatic fibrosis and inflammatory response were analyzed by Q-PCR and WB. Results: Compared with the control group, total bile acid (TBA), the main cholestasis biomarker, was increased from (3. 2±0. 9) µmol/L to (31. 6±4. 3) µmol/L in A-D14 group. AST and ALT, the biomarkers of liver injury, were also increased significantly (P＜0. 05). The expression levels of fibrotic factor tissue inhibitors of metalloproteinases 1 (TIMP-1), monocyte chemoattractant protein 1 (MCP-1) and collagen protein I (Collagen I) were higher than those of control group (P＜0. 05). The expressions of fibrosis protein Collagen I and α-SMA were also up-regulated. The collagen fibers of the liver were largely deposited and the liver fibrosis occurred (P＜0. 05). The expression of inflammatory factors was higher than the control group, JNK, c-Jun and STAT3 were activated (P＜0. 05). In A-D28 group, except AST, matrix metalloproteinases 2 (MMP-2) and Collagen I indicators were slightly decreased, other indicators of cholestasis, liver injury, liver fibrosis and inflammation continued to be up-regulated or stable (P＜0. 05). Conclusion: After 14-day treatment with 0. 05% ANIT diet, significant cholestatic liver fibrosis occurred in mice. After 28 days of treatment, cholestasis liver fibrosis kept stable. The JNK inflammatory pathway played a crucial role in the development of liver fibrosis.

Cholestatic models induced by lithocholic acid and α­naphthylisothiocyanate: Different etiological mechanisms for liver injury but shared JNK/STAT3 signaling.

α­naphthylisothiocyanate (ANIT) is used to induce intrahepatic cholestasis and it is frequently used for investigations into the disease mechanism. The lithocholic acid (LCA) cholestatic model has also been extensively used in various studies; however, to the best of our knowledge, a comparative study determining the hepatotoxic mechanisms induced by these two models has not been previously conducted. In the present study, ICR mice were treated with ANIT or LCA to induce cholestatic liver injury. Biochemical analysis was used to determine the serum. Alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP) and total bile acid (TBA) levels, and histopathological assessment was used to examine the liver tissue. Metabolomic analysis was used for the serum biomarker identification. Reverse transcription­quantitative PCR analysis and western blotting were used to analyze the inflammation biomarkers. The serum metabolome of the ANIT group clustered away from of the LCA group, which was demonstrated by the different modifications of the BA components. ALP level was found to be preferentially increased in the ANIT group from 24 to 48 h. Total BA levels was only increased in the ANIT group at 24 h. In contrast, AST and ALT activity levels were preferentially increased in the LCA group. The bile ducts in the hepatic tissues of the ANIT group were observed to be severely dilated, whereas the presence of edematous hepatocytes around the necrotic lesions and neutrophil infiltration were identified in the LCA group. The expression levels of cholesterol 7α­hydroxylase and sterol 12α­hydroxylase genes were significantly downregulated in the ANIT group compared with the LCA group, where a stronger adaptation of BA metabolism was supported by major differences in the concentration of the BA components. Despite the aforementioned etiological differences in the cholestasis induced by each treatment, the activation of the JNK/STAT3 signaling pathway was similar between the two cholestatic models. In conclusion, these data suggested that the liver injury induced by ANIT may be cholestatic, while the liver injury caused in the LCA model may be hepatocellular. Moreover, the downstream cholestatic liver injury in both models was indicated to be mediated by the JNK/STAT3 signaling pathway.

Therapeutic action against chronic cholestatic liver injury by low-dose fenofibrate involves anti-chemotaxis via JNK-AP1-CCL2/CXCL2 signaling.

BACKGROUND: Fenofibrate was reported to be beneficial for cholestasis in combination with ursodeoxycholic acid. However, its therapeutic action as single therapy for chronic cholestasis and the underlying mechanism are not known. METHODS: In the present study, wild-type (WT) mice were administered a 0.05% ANIT diet to mimic chronic cholestatic liver injury. Mice were dosed fenofibrate 25 mg/kg twice every day for 10 days to investigate the therapeutic action of fenofibrate on chronic cholestatic liver injury. Ppara-null (KO) mice were used to explore PPARα's role in the therapeutic outcome. RESULTS: Fenofibrate, administered at 25 mg/kg twice daily, substantially reversed ANIT-induced chronic cholestatic liver injury shown by biochemical and pathological end points. The modifications of bile acid metabolism were found to be adaptive responses. The JNK-AP1-CCL2/CXCL2 axis was activated in all the mice administered ANIT which developed chronic cholestatic liver injury. But it was substantially decreased by fenofibrate in WT mice rather than that in KO mice. CONCLUSIONS: Low-dose fenofibrate reversed chronic cholestatic liver injury in mice. The therapeutic action was dependent on PPARα activation and occurred by inhibiting chemotaxis via the JNK-AP1-CCL2/CXCL2 signaling. These data provided an exciting basis for optimization of therapeutic fenofibrate regimen in the clinic. Additionally, they suggested anti-chemotaxis of low-dose fenofibrate in single therapy to treat cholestatic liver diseases.

Evolution of LuxR solos in bacterial communication: receptors and signals.

Cell-cell communication in bacteria needs chemical signals and cognate receptors. Many Gram-negative bacteria use acyl-homoserine lactones (AHLs) and cognate LuxR-type receptors to regulate their quorum sensing (QS) systems. The signal synthase-receptor (LuxI-LuxR) pairs may have co-evolved together. However, many LuxR solo (orphan LuxR) regulators sense more signals than just AHLs, and expand the regulatory networks for inter-species and inter-kingdom communication. Moreover, there are also some QS regulators from the TetR family. LuxR solo regulators might have evolved by gene duplication and horizontal gene transfer. An increased understanding of the evolutionary roles of QS regulators would be helpful for engineering of cell-cell communication circuits in bacteria.

Regulatory and evolutionary roles of pseudo γ-butyrolactone receptors in antibiotic biosynthesis and resistance.

Bacteria modulate their physiological behavior by responding to various signal molecules. The signals are received by cognate receptors, which usually mediate transcriptional regulation. Streptomyces employ γ-butyrolactones (GBLs) and cognate GBL receptors (GblRs) to regulate secondary metabolism and morphological development. However, there are additional transcriptional regulators called pseudo GblR regulators, which cannot bind GBLs and are not directly associated with GBL synthase. The pseudo GblR regulators may act as transcriptional repressors and respond to antibiotic signals. They play regulatory roles in coordination of antibiotic biosynthesis by connecting the hormone feed-forward loops and the antibiotic feedback loops. As the TetR family members, they might also have evolutionary roles between the transcriptional regulators of quorum sensing and antibiotic resistance. Understanding the regulatory and evolutionary roles of the pseudo GblR family would be helpful for fine-tuning regulation of antibiotic biosynthesis and resistance.

Basal PPARα inhibits bile acid metabolism adaptation in chronic cholestatic model induced by α-naphthylisothiocyanate.

Cholestasis is one of the most challenging diseases to be treated in current hepatology. However little is known about the adaptation difference and the underlying mechanism between acute and chronic cholestasis. In this study, wild-type and Pparα-null mice were orally administered diet containing 0.05% ANIT to induce chronic cholestasis. Biochemistry, histopathology and serum metabolome analysis exhibited the similar toxic phenotype between wild-type and Pparα-null mice. Bile acid metabolism was strongly adapted in Pparα-null mice but not in wild-type mice. The Shp and Fxr mRNA was found to be doubled in cholestatic Pparα-null mice compared with the control group. Western blot confirmed the up-regulated expression of FXR in Pparα-null mice treated with ANIT. Inflammation was found to be stronger in Pparα-null mice than those in wild-type mice in chronic cholestasis. These data chain indicated that bile acid metabolism and inflammation signaling were different between wild-type and Pparα-null mice developing chronic cholestasis, although their toxic phenotypes could not be discriminated. So basal PPARα cross-talked with FXR and inhibited bile acid metabolism adaptation in chronic cholestasis.

20-Nor-Isopimarane Epimers Produced by Aspergillus wentii SD-310, a Fungal Strain Obtained from Deep Sea Sediment.

Four new uncommon 20-nor-isopimarane diterpenoid epimers, aspewentins I-L (1⁻4), together with a new methylated derivative of 3, aspewentin M (5), were isolated from the deep sea sediment-derived fungus Aspergillus wentii SD-310. The very similar structures of these epimers made the separation and purification procedures difficult. The structures of compounds 1⁻5 were illustrated based on spectroscopic analysis, and the absolute configurations of compounds 1⁻5 were unambiguously determined by the combination of NOESY, time-dependent density functional (TDDFT)-ECD calculations, and X-ray crystallographic analysis. These metabolites represented the rare examples of 20-nor-isopimarane analogues possessing a cyclohexa-2,5-dien-1-one moiety. These compounds were tested for antimicrobial activities against human and aquatic pathogenic bacteria, as well as plant-pathogenic fungi. While compounds 1 and 2 exhibited inhibitory activities against zoonotic pathogenic bacteria such as Escherichia coli, Edwardsiella tarda, Vibrio harveyi, and V. parahaemolyticus, compound 5 showed potent activity against the plant pathogen Fusarium graminearum.

PPARα-independent action against metabolic syndrome development by fibrates is mediated by inhibition of STAT3 signalling.

OBJECTIVES: Metabolic syndrome (MS) is the concurrence of at least three of five medical conditions: obesity, high blood pressure, insulin resistance, high serum triglyceride (TG) and low serum high-density lipoprotein levels. While fibrates are used to treat disorders other than the lowering serum TG, the mechanism by which fibrates decrease MS has not been established. METHODS: In this study, wild-type and Ppara-null mice fed a medium-fat diet (MFD) were administered gemfibrozil and fenofibrate for 3 months respectively, to explore the effect and action mechanism. KEY FINDINGS: In Ppara-null mice, MFD treatment increased body weight, adipose tissue, serum TG and impaired glucose tolerance. These phenotypes were attenuated in two groups treated with gemfibrozil and fenofibrate. The STAT3 pathway was activated in adipose and hepatic tissues in positive control, and inhibited in groups treated with gemfibrozil and fenofibrate. The above phenotypes and inflammation were not observed in any wild-type group. In 3T3-L1 adipogenic stem cells treated with high glucose, STAT3 knockdown greatly decreased the number of lipid droplets. CONCLUSIONS: Low dose of clinical fibrates was effective against MS development independent of PPARα, and this action was mediated by STAT3 signalling inhibition in adipose tissue and, to a lesser extent, in hepatic tissues.

Antibacterial anthraquinone derivatives isolated from a mangrove-derived endophytic fungus Aspergillus nidulans by ethanol stress strategy.

Three new natural products, including a new anthraquinone derivative isoversicolorin C (1), a new xanthone analog isosecosterigmatocystin (2), and a new amino acid derivative, glulisine A (3), along with six related metabolites (4-9) were isolated from the culture broth and mycelia extracts of the mangrove-derived endophytic fungus Aspergillus nidulans MA-143 under 0.1% ethanol stress. Their structures were elucidated by detailed analysis of their NMR spectra, ECD spectrum, and X-ray crystallographic experiments. Compounds 1 and 4 showed potent antibacterial activity against some of the tested microbes.

The plant hormone abscisic acid regulates the growth and metabolism of endophytic fungus Aspergillus nidulans.

Plant hormones are well known chemical signals that regulate plant growth, development, and adaptation. However, after comparative transcriptome and metabolite analysis, we found that the plant hormone abscisic acid (ABA) also affect the growth and metabolism of endophytic fungus Aspergillus nidulans. There were 3148 up-regulated and 3160 down-regulated genes identified during 100 nM ABA induction. These differentially expressed genes (DEGs) were mainly involved in: RNA polymerase and basal transcription factors; ribosome biogenesis, protein processing, proteasome, and ubiquitin mediated proteolysis; nucleotide metabolism and tri-carboxylic acid (TCA) cycle; cell cycle and biosynthesis of secondary metabolites. Production of mycotoxins, which have insect-resistance or anti-pathogen activity, was also changed with ABA induction. This study provides the first global view of ABA induced transcription and metabolite changes in endophytic fungus, which might suggest a potential fungus-plant cross-talk via ABA.

Targeted Metabolomics Reveals a Protective Role for Basal PPARα in Cholestasis Induced by α-Naphthylisothiocyanate.

α-Naphthylisothiocyanate (ANIT) is an experimental agent used to induce intrahepatic cholestasis. The Ppara-null mouse line is widely employed to explore the physiological and pathological roles of PPARα. However, little is known about how PPARα influences the hepatotoxicity of ANIT. In the present study, wild-type and Ppara-null mice were orally treated with ANIT to induce cholestasis. The serum metabolome of wild-type mice segregated from that of the Ppara-null mice, driven by changes of bile acid (BA) metabolites. Alkaline phosphatase and total BAs were elevated preferentially in Ppara-null mice, which correlated with changes in Cyp7a1, Cyp8b1, Mrp3, Cyp3a11, Cyp2b10, Ugt1a2, and Ugt1a5 genes and showed cross-talk between basal PPARα and potentially adaptive pathways. Il6, Tnfa, and target genes in the STAT3 pathway ( Socs3, Fga, Fgb, and Fgg) were up-regulated in Ppara-null mice but not in wild-type mice. The JNK pathway was activated in both mouse lines, while NF-κB and STAT3 were activated only in Ppara-null mice. These data suggest protection against cholestasis by basal PPARα involves regulation of BA metabolism and inhibition of NF-κB/STAT3 signaling. Considering studies on the protective effects of both basal and activated PPARα, caution should be exercised when one attempts to draw conclusions in which the PPARα is modified by genetic manipulation, fasting, or activation in pharmacological and toxicological studies.

Inhibition of JNK signalling mediates PPARα-dependent protection against intrahepatic cholestasis by fenofibrate.

BACKGROUND AND PURPOSE: Fenofibrate, a PPARα agonist, is the most widely prescribed drug for treating hyperlipidaemia. Although fibrate drugs are reported to be beneficial for cholestasis, their underlying mechanism has not been determined. EXPERIMENTAL APPROACH: Wild-type mice and Pparα-null mice were pretreated orally with fenofibrate for 3 days, following which α-naphthylisothiocyanate (ANIT) was administered to induce cholestasis. The PPARα agonist WY14643 and JNK inhibitor SP600125 were used to determine the role of PPARα and the JNK pathway, respectively, in cholestatic liver injury. The same fenofibrate regimen was applied to investigate its beneficial effects on sclerosing cholangitis in a DDC-induced cholestatic model. KEY RESULTS: Fenofibrate, 25 mg·kg-1 twice a day, totally attenuated ANIT-induced cholestasis and liver injury as indicated by biochemical and histological analyses. This protection occurred in wild-type, but not in Pparα-null, mice. Alterations in bile acid synthesis and transport were found to be an adaptive response rather than a direct effect of fenofibrate. WY14643 attenuated ANIT-induced cholestasis and liver injury coincident with inhibition of JNK signalling. Although SP600125 did not affect cholestasis, it inhibited liver injury in the ANIT model when the dose of fenofibrate used was ineffective. Fenofibrate was also revealed to have a beneficial effect in the sclerosing cholangitis model. CONCLUSIONS AND IMPLICATIONS: These data suggest that the protective effects of fenofibrate against cholestasis-induced hepatic injury are dependent on PPARα and fenofibrate dose, and are mediated through inhibition of JNK signalling. This mechanism of fenofibrate protection against intrahepatic cholestasis may offer additional therapeutic opportunities for cholestatic liver diseases.

Peroxisome Proliferator-Activated Receptor α Activation Suppresses Cytochrome P450 Induction Potential in Mice Treated with Gemfibrozil.

Gemfibrozil, a peroxisome proliferator-activated receptor α (PPARα) agonist, is widely used for hypertriglyceridaemia and mixed hyperlipidaemia. Drug-drug interaction of gemfibrozil and other PPARα agonists has been reported. However, the role of PPARα in cytochrome P450 (CYP) induction by fibrates is not well known. In this study, wild-type mice were first fed gemfibrozil-containing diets (0.375%, 0.75% and 1.5%) for 14 days to establish a dose-response relationship for CYP induction. Then, wild-type mice and Pparα-null mice were treated with a 0.75% gemfibrozil-containing diet for 7 days. CYP3a, CYP2b and CYP2c were induced in a dose-dependent manner by gemfibrozil. In Pparα-null mice, their mRNA level, protein level and activity were induced more than those in wild-type mice. So, gemfibrozil induced CYP, and this action was inhibited by activated PPARα. These data suggested that the induction potential of CYPs was suppressed by activated PPARα, showing a potential role of this receptor in drug-drug interactions and metabolic diseases treated with fibrates.

Relationships between the Regulatory Systems of Quorum Sensing and Multidrug Resistance.

Cell-cell communications, known as quorum sensing (QS) in bacteria, involve the signal molecules as chemical languages and the corresponding receptors as transcriptional regulators. In Gram-negative bacteria, orphan LuxR receptors recognize signals more than just acylhomoserine lactones, and modulate interspecies and interkingdom communications. Whereas, in the Gram-positive Streptomyces, pseudo gamma-butyrolactones (GBLs) receptors bind antibiotics other than GBL signals, and coordinate antibiotics biosynthesis. By interacting with structurally diverse molecules like antibiotics, the TetR family receptors regulate multidrug resistance (MDR) by controlling efflux pumps. Antibiotics at subinhibitory concentration may act as signal molecules; while QS signals also have antimicrobial activity at high concentration. Moreover, the QS and MDR systems may share the same exporters to transport molecules. Among these orphan LuxR, pseudo GBL receptors, and MDR regulators, although only with low sequence homology, they have some structure similarity and function correlation. Therefore, perhaps there might be evolutionary relationship and biological relevance between the regulatory systems of QS and MDR. Since the QS systems become new targets for antimicrobial strategy, it would expand our understanding about the evolutionary history of these regulatory systems.

Tetranorlabdane Diterpenoids from the Deep Sea Sediment-Derived Fungus Aspergillus wentii SD-310.

Two new tetranorlabdane diterpenoids, asperolides D (1) and E (2), along with six related known congeners (3-8), were isolated and identified from the culture extract of the deep sea sediment-derived fungus Aspergillus wentii SD-310. The structures of these compounds were established on the basis of spectroscopic interpretation, and the skeleton and absolute configurations of asperolides D (1) and E (2) were determined by X-ray crystallographic analysis. Compounds 1 and 2 were evaluated for their cytotoxic activity against seven tumor cell lines and antibacterial activity against two human and eight aquatic pathogens.

Aspewentins D-H, 20-Nor-isopimarane Derivatives from the Deep Sea Sediment-Derived Fungus Aspergillus wentii SD-310.

Five new 20-nor-isopimarane diterpenoids, aspewentins D-H (1-5), along with a related known congener, aspewentin A (6), were isolated from the culture extract of Aspergillus wentii SD-310, a fungal strain obtained from a deep-sea sediment sample. The structures of these compounds were established on the basis of spectroscopic interpretation, and the absolute configurations of compounds 1-5 were determined by X-ray crystallographic analysis and TDDFT-ECD calculations. The isolated compounds were evaluated for antimicrobial activity against nine human and aquatic pathogenic bacteria and four plant pathogenic fungi as well as for lethality against brine shrimp (Artemia salina). 20-Nor-isopimarane derivatives rarely occur in fungi, and only three (aspewentins A-C) have previously been reported from a marine-derived fungus.

Independent Evolution of Six Families of Halogenating Enzymes.

Halogenated natural products are widespread in the environment, and the halogen atoms are typically vital to their bioactivities. Thus far, six families of halogenating enzymes have been identified: cofactor-free haloperoxidases (HPO), vanadium-dependent haloperoxidases (V-HPO), heme iron-dependent haloperoxidases (HI-HPO), non-heme iron-dependent halogenases (NI-HG), flavin-dependent halogenases (F-HG), and S-adenosyl-L-methionine (SAM)-dependent halogenases (S-HG). However, these halogenating enzymes with similar biological functions but distinct structures might have evolved independently. Phylogenetic and structural analyses suggest that the HPO, V-HPO, HI-HPO, NI-HG, F-HG, and S-HG enzyme families may have evolutionary relationships to the α/ß hydrolases, acid phosphatases, peroxidases, chemotaxis phosphatases, oxidoreductases, and SAM hydroxide adenosyltransferases, respectively. These halogenating enzymes have established sequence homology, structural conservation, and mechanistic features within each family. Understanding the distinct evolutionary history of these halogenating enzymes will provide further insights into the study of their catalytic mechanisms and halogenation specificity.