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.

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.

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.

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.

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.

Citrifelins A and B, Citrinin Adducts with a Tetracyclic Framework from Cocultures of Marine-Derived Isolates of Penicillium citrinum and Beauveria felina.

Citrifelins A (1) and B (2), two citrinin adducts possessing a unique tetracyclic framework, were characterized from a coculture of marine-derived fungal isolates of Penicillium citrinum and Beauveria felina. Neither fungus produced these compounds when cultured alone under the same conditions. The structures of these adducts were elucidated on the basis of spectroscopic analysis, and the absolute configurations were assigned on the basis of TDDFT-ECD calculations. A hypothesis that adducts 1 and 2 might be derived from a citrinin derivative through a non-pericyclic Michael reaction is proposed. Compounds 1, 2, and 5 showed inhibitory activities against several human and aquatic pathogens.

Rubrumazines A-C, Indolediketopiperazines of the Isoechinulin Class from Eurotium rubrum MA-150, a Fungus Obtained from Marine Mangrove-Derived Rhizospheric Soil.

Three new indolediketopiperazine alkaloids of the isoechinulin type, rubrumazines A-C (1-3), each possessing an oxygenated prenyl group either at C-7 (1 and 2) or at C-5 (3), along with 13 related analogues (4-16), were isolated and identified from a culture extract of Eurotium rubrum MA-150, a fungus obtained from mangrove-derived rhizospheric soil collected from the Andaman Sea coastline, Thailand. Their structures were established by detailed interpretation of NMR spectroscopic and mass spectrometry data analysis. The structure and absolute configuration of compound 1 were confirmed by X-ray crystallographic analysis, thus providing the first characterized crystal structure of an isoechinulin-type alkaloid. All isolated compounds were evaluated for brine shrimp lethality and antibacterial activity.

Antimicrobial Phenolic Bisabolanes and Related Derivatives from Penicillium aculeatum SD-321, a Deep Sea Sediment-Derived Fungus.

Three new phenolic bisabolane sesquiterpenes, peniciaculins A (1) and B (2) and (7S)-(-)-10-hydroxysydonic acid (3), together with a new nor-bisabolane derivative, 1-hydroxyboivinianin A (4), as well as six known bisabolanes (5-10), were identified from the culture of Penicillium aculeatum SD-321, a fungus isolated from deep-sea sediments. The structures of these compounds were mainly determined by analysis of spectroscopic data, and the absolute configurations of compounds 1-4 were established by comparing their ECD spectra with those of known analogues or by TDDFT-ECD calculations. Compound 1 represents the first example of a bisabolane analogue linked to a diphenyl ether moiety via an ether bond, while compound 2 appears to be the first dimeric bisabolane analogue where the two monomers are coupled to each other via an ester bond. The isolated compounds were evaluated for antimicrobial activity against 10 human and aquatic pathogenic bacteria and three plant-pathogenic fungi.

Bisthiodiketopiperazines and Acorane Sesquiterpenes Produced by the Marine-Derived Fungus Penicillium adametzioides AS-53 on Different Culture Media.

Chemical investigation of the marine-sponge-derived fungus Penicillium adametzioides AS-53 resulted in the identification of two new bisthiodiketopiperazine derivatives, adametizines A (1) and B (2), from cultivation in a liquid potato-dextrose broth (PDB) culture medium, whereas two new acorane sesquiterpenes, adametacorenols A (3) and B (4), were isolated from a rice solid culture medium. The structures of these compounds were elucidated on the basis of spectroscopic analysis. The absolute configuration of compound 1 was determined by X-ray crystallographic analysis, and that of 3 was determined by modified Mosher's method. Compound 1 exhibited lethality against brine shrimp (Artemia salina) with an LD50 value of 4.8 µM and inhibitory activities against Staphyloccocus aureus, Aeromonas hydrophilia, Vibrio spp. V. harveyi and V. parahaemolyticus, and Gaeumannomyces graminis with minimum inhibitory concentration values of 8, 8, 32, 8, and 16 µg/mL, respectively. Chlorination at C-7 significantly increased the brine shrimp lethality and antimicrobial activity of the bisthiodiketopiperazines.

Characterization of a Newly Isolated Marine Fungus Aspergillus dimorphicus for Optimized Production of the Anti-Tumor Agent Wentilactones.

The potential anti-tumor agent wentilactones were produced by a newly isolated marine fungus Aspergillus dimorphicus. This fungus was derived from deep-sea sediment and identified by polyphasic approach, combining phenotypic, molecular, and extrolite profiles. However, wentilactone production was detected only under static cultures with very low yields. In order to improve wentilactone production, culture conditions were optimized using the response surface methodology. Under the optimal static fermentation conditions, the experimental values were closely consistent with the prediction model. The yields of wentilactone A and B were increased about 11-fold to 13.4 and 6.5 mg/L, respectively. The result was further verified by fermentation scale-up for wentilactone production. Moreover, some small-molecule elicitors were found to have capacity of stimulating wentilactone production. To our knowledge, this is first report of optimized production of tetranorlabdane diterpenoids by a deep-sea derived marine fungus. The present study might be valuable for efficient production of wentilactones and fundamental investigation of the anti-tumor mechanism of norditerpenoids.

Prenylated indolediketopiperazine peroxides and related homologues from the marine sediment-derived fungus Penicillium brefeldianum SD-273.

Three new indolediketopiperazine peroxides, namely, 24-hydroxyverruculogen (1), 26-hydroxyverruculogen (2), and 13-O-prenyl-26-hydroxyverruculogen (3), along with four known homologues (4-7), were isolated and identified from the culture extract of the marine sediment-derived fungus Penicillium brefeldianum SD-273. Their structures were determined based on the extensive spectroscopic analysis and compound 1 was confirmed by X-ray crystallographic analysis. The absolute configuration of compounds 1-3 was determined using chiral HPLC analysis of their acidic hydrolysates. Each of the isolated compounds was evaluated for antibacterial and cytotoxic activity as well as brine shrimp (Artemia salina) lethality.

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.

Sulfur-containing cytotoxic curvularin macrolides from Penicillium sumatrense MA-92, a fungus obtained from the rhizosphere of the mangrove Lumnitzera racemosa.

Sumalarins A-C (1-3), the new and rare examples of sulfur-containing curvularin derivatives, along with three known analogues (4-6), were isolated and identified from the cytotoxic extract of Penicillium sumatrense MA-92, a fungus obtained from the rhizosphere of the mangrove Lumnitzera racemosa . Their structures were established by detailed interpretation of NMR and MS data, and compound 1 was confirmed by X-ray crystallographic analysis. Compounds 1-3 and 5 showed potent cytotoxicity against some of the tested tumor cell lines. Sulfur substitution at C-11 or a double bond at C-10 significantly increased the cytotoxic activities of the curvularin analogues.

4-Phenyl-3,4-dihydroquinolone derivatives from Aspergillus nidulans MA-143, an endophytic fungus isolated from the mangrove plant Rhizophora stylosa.

Six new 4-phenyl-3,4-dihydroquinolone derivatives (1-6) along with the related aflaquinolone A (7) were isolated and identified from the cultures of Aspergillus nidulans MA-143, an endophytic fungus obtained from the fresh leaves of the marine mangrove plant Rhizophora stylosa. Their structures including absolute configurations were determined by spectroscopic analysis and electronic circular dichroism experiments, and the structure of compound 1 was confirmed by single-crystal X-ray crystallographic analysis. In bioscreening experiments, none of the isolated compounds showed potent antibacterial or cytotoxic activity. However, compounds 2, 3, and 7 exhibited lethality against brine shrimp (Artemia salina), with LD50 values of 7.1, 4.5, and 5.5 µM, respectively.

Aniquinazolines A-D, four new quinazolinone alkaloids from marine-derived endophytic fungus Aspergillus nidulans.

Four new quinazolinone alkaloids, namely, aniquinazolines A-D (1-4), were isolated and identified from the culture of Aspergillus nidulans MA-143, an endophytic fungus obtained from the leaves of marine mangrove plant Rhizophora stylosa. The structures of the new compounds were elucidated by spectroscopic analysis, and their absolute configurations were determined on the basis of chiral HPLC analysis of the acidic hydrolysates. The structure for 1 was confirmed by single-crystal X-ray diffraction analysis. All these compounds were examined for antibacterial and cytotoxic activity as well as brine shrimp (Artemia salina) lethality.

Autoregulation of antibiotic biosynthesis by binding of the end product to an atypical response regulator.

In bacteria, many "atypical" response regulators (ARRs) lack the conserved residues important for phosphorylation by which typical response regulators switch their output response, suggesting the existence of alternative regulatory mechanisms. However, such mechanisms have not been established. JadR1, an OmpR-type ARR of Streptomyces venezuelae, appears to activate the transcription of jadomycin B (JdB) biosynthetic genes while repressing its own gene. JadR1 activities were inhibited in cells induced to produce JdB, which was found to bind directly to the N-terminal receiver domain of JadR1, causing JadR1 to dissociate from target promoters. The activity of a NarL-type ARR, RedZ, that regulates production of another antibiotic was likewise modulated by the end product (undecylprodigisines), implying that end-product-mediated control of antibiotic pathway-specific ARRs may be widespread. These results could prove relevant to knowledge-based improvements in yield of commercially important antibiotics.

"Pseudo" gamma-butyrolactone receptors respond to antibiotic signals to coordinate antibiotic biosynthesis.

In actinomycetes, the onset of secondary metabolite biosynthesis is often triggered by the quorum-sensing signal gamma-butyrolactones (GBLs) via specific binding to their cognate receptors. However, the presence of multiple putative GBL receptor homologues in the genome suggests the existence of an alternative regulatory mechanism. Here, in the model streptomycete Streptomyces coelicolor, ScbR2 (SCO6286, a homologue of GBL receptor) is shown not to bind the endogenous GBL molecule SCB1, hence designated "pseudo" GBL receptor. Intriguingly, it could bind the endogenous antibiotics actinorhodin and undecylprodigiosin as ligands, leading to the derepression of KasO, an activator of a cryptic type I polyketide synthase gene cluster. Likewise, JadR2 is also a putative GBL receptor homologue in Streptomyces venezuelae, the producer of chloramphenicol and cryptic antibiotic jadomycin. It is shown to coordinate their biosynthesis via direct repression of JadR1, which activates jadomycin biosynthesis while repressing chloramphenicol biosynthesis directly. Like ScbR2, JadR2 could also bind these two disparate antibiotics, and the interactions lead to the derepression of jadR1. The antibiotic responding activities of these pseudo GBL receptors were further demonstrated in vivo using the lux reporter system. Overall, these results suggest that pseudo GBL receptors play a novel role to coordinate antibiotic biosynthesis by binding and responding to antibiotics signals. Such an antibiotic-mediated regulatory mechanism could be a general strategy to coordinate antibiotic biosynthesis in the producing bacteria.

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.