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Oligopeptides with functional activities are of current interest in the nutraceutical and medical sectors. The development of the biosynthetic process of oligopeptides through a nonribosomal peptide synthetase (NRPS) system has become more challenging. To develop a production platform for nonribosomal peptides (NRPs), reprogramming of transcriptional regulation of the acv gene encoded ACV synthetase (ACVS) was implemented in Aspergillus oryzae using the CRISPR-Cas9 system. Awakening silent acv expression was successfully achieved by promoter substitution. Among the three exchanged promoters, AoPgpdA, AoPtef1, and PtPtoxA, the replacement of the native promoter with AoPgpdA led to the highest ACV production in A. oryzae. However, the ACV production of the AoPGpdA strain was also dependent on the medium composition, in which urea was the best nitrogen source, and a C:N ratio of 20:1 was optimal for tripeptide production. In addition to cell growth, magnesium ions are an essential element for ACV production and might participate in ACVS activity. It was also found that ACV was the growth-associated product of the engineered strain that might be a result of constitutive transcriptional control by the AoPgpdA promoter. This study offers a potential strategy for nonribosomal ACV production using the fungal system, which is applicable for redesigning bioactive oligopeptides with industrial relevance.

Background Flowers of Chrysanthemum × morifolium Ramat. are used as tea in traditional Chinese cuisine. However, with increasing population and urbanization, water and land availability have become limiting for chrysanthemum tea production. Hydroponic culture enables effective, rapid nutrient exchange, while requiring no soil and less water than soil cultivation. Hydroponic culture can reduce pesticide residues in food and improve the quantity or size of fruits, flowers, and leaves, and the levels of active compounds important for nutrition and health. To date, studies to improve the yield and active compounds of chrysanthemum have focused on soil culture. Moreover, the molecular effects of hydroponic and soil culture on chrysanthemum tea development remain understudied. Results Here, we studied the effects of soil and hydroponic culture on yield and total flavonoid and chlorogenic acid contents in chrysanthemum flowers (C. morifolium ‘wuyuanhuang’). Yield and the total flavonoids and chlorogenic acid contents of chrysanthemum flowers were higher in the hydroponic culture system than in the soil system. Transcriptome profiling using RNA-seq revealed 3858 differentially expressed genes (DEGs) between chrysanthemum flowers grown in soil and hydroponic conditions. Gene Ontology (GO) enrichment annotation revealed that these differentially transcribed genes are mainly involved in “cytoplasmic part”, “biosynthetic process”, “organic substance biosynthetic process”, “cell wall organization or biogenesis” and other processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed enrichment in “metabolic pathways”, “biosynthesis of secondary metabolites”, “ribosome”, “carbon metabolism”, “plant hormone signal transduction” and other metabolic processes. In functional annotations, pathways related to yield and formation of the main active compounds included phytohormone signaling, secondary metabolism, and cell wall metabolism. Enrichment analysis of transcription factors also showed that under the hydroponic system, bHLH, MYB, NAC, and ERF protein families were involved in metabolic pathways, biosynthesis of secondary metabolites, and plant hormone signal transduction. Conclusions Hydroponic culture is a simple and effective way to cultivate chrysanthemum for tea production. A transcriptome analysis of chrysanthemum flowers grown in soil and hydroponic conditions. The large number of DEGs identified confirmed the difference of the regulatory machinery under two culture system.

Subterranean rodents could maintain their normal activities in hypoxic environments underground. Eospalax fontanierii, as one kind of subterranean rodent found in China can survive very low oxygen concentration in labs. It has been demonstrated that long non-coding RNAs (lncRNAs) have important roles in gene expression regulations at different levels and some lncRNAs were found as hypoxia-regulated lncRNAs in cancers. We predicted thousands of lncRNAs in the liver and heart tissues by analyzing RNA-Seq data in Eospalax fontanierii. Those lncRNAs often have shorter lengths, lower expression levels, and lower GC contents than mRNAs. Majors of lncRNAs have expression peaks in hypoxia conditions. We found 1128 DE-lncRNAs (differential expressed lncRNAs) responding to hypoxia. To search the miRNA regulation network for lncRNAs, we predicted 471 and 92 DE-lncRNAs acting as potential miRNA target and target mimics, respectively. We also predicted the functions of DE-lncRNAs based on the co-expression networks of lncRNA-mRNA. The DE-lncRNAs participated in the functions of biological regulation, signaling, development, oxoacid metabolic process, lipid metabolic/biosynthetic process, and catalytic activity. As the first study of lncRNAs in Eospalax fontanierii, our results show that lncRNAs are popular in transcriptome widely and can participate in multiple biological processes in hypoxia responses.

Excessive mucus secretion is the most prominent feature of pseudomyxoma peritonei (PMP), which often leads to significant increase in abdominal circumference, intractable abdominal pain, progressive intestinal obstruction, abdominal organ adhesions, and cachexia. Excessive mucus secretion is also the main cause of death. Cytoreductive surgery (CRS) combined with hyperthermic intraperitoneal chemotherapy (HIPEC) is the recommended treatment for PMP. However, recurrence is frequently observed even after CRS and HIPEC, presenting similar clinical manifestations. Mucin 2 (MUC2) is the main type of mucin in PMP and plays a key role in the progressive sclerosis of mucus. To comprehensively demonstrate the biosynthetic process and molecular features of MUC2 and to provide new directions for the development of PMP mucolytic strategies, this review systematically summarizes the molecular biology of MUC2, including MUC2 gene structure, transcription, translation, post-translational modification, tertiary structure, and factors regulating mucus viscoelasticity. The results show that MUC2 is a highly glycosylated protein, with glycan accounts for 80% to 90% of the dry weight. The assembly pattern of MUC2 is highly complicated, presenting a bead-like filament. Salt concentration, pH, mucin concentration and trefoil factor family may contribute to the increase in mucus viscoelasticity and sclerosis, which could be used to develop drugs to soften or even dissolve mucus in the future.

Photosynthesis is a fundamental biosynthetic process in plants that can enhance carbon absorption and increase crop productivity. Heat stress severely inhibits photosynthetic efficiency. Melatonin is a bio-stimulator capable of regulating diverse abiotic stress tolerances. However, the underlying mechanisms of melatonin-mediated photosynthesis in plants exposed to heat stress largely remain elucidated. Our results revealed that melatonin treatment (100 μM) in tomato seedlings increased the endogenous melatonin levels and photosynthetic pigment content along with upregulated of their biosynthesis gene expression under high-temperature stress (42 °C for 24 h), whereas heat stress significantly decreased the values of gas exchange parameters. Under heat stress, melatonin boosted CO2 assimilation, i.e., Vc,max (maximum rate of ribulose-1,5-bisphosphate carboxylase, Rubisco), and Jmax (electron transport of Rubisco generation) and also enhanced the Rubisco and FBPase activities, which resulted in upregulated photosynthetic related gene expression. In addition, heat stress greatly reduced the photochemical chemistry of photosystem II (PSII) and photosystem I (PSI), particularly the maximum quantum efficiency of PSII (Fv/Fm) and PSI (Pm). Conversely, melatonin supplementation increased the chlorophyll a fluorescence parameters led to amplifying the electron transport efficiency. Moreover, heat stress decreased the actual PSII efficiency (ΦPSII), electron transport rate (ETR) and photochemical quenching coefficient (qP), while increasing nonphotochemical quenching (NPQ); however, melatonin reversed these values, which helps to fostering the dissipation of excess excitation energy. Taken together, our results provide a concrete insight into the efficacy of melatonin-mediated photosynthesis performance in a high-temperature regime.

Diet-induced fatty liver is a considerable threaten to fish aquaculture due to the popularity of the high-fat diet (HFD) feeding. Our study aims to investigate the effects of flavanones from Sedum sarmentosum Bunge (FSSB) on the liver function to identify a potential treatment for HFD-induced fatty liver disease. Physiological and pathological indicators were tested in the liver of Nile tilapia (Oreochromis niloticus) and results showed parameters including lipid metabolites, redox parameters, and inflammatory factors could be adequately restored to normal level by addition of 150 mg/kg FSSB to HFD. Proteomics analysis was performed in liver tissues from tilapia with normal diet (ND), HFD, and HFD+FSSB. Totally, 51 upregulated proteins and 77 downregulated proteins were identified in HFD groups and 67 proteins of them were restored after treated with FSSB. Bioinformatics analysis showed that differentially expressed proteins (DEPs) in HFD+FSSB150 group compared with HFD group are mainly enriched in acety-CoA metabolic process, adenosine-triphosphate (ATP) biosynthetic process, lipid metabolic process, and phospholipid metabolic process. The dysregulated proteins were involved in peroxidosome proliferators-activated receptor (PPAR) signaling pathway, fat digestion and absorption, and immune system. The quantitative real-time PCR (qRT-PCR) assay further revealed that the expression of GST, PPARα, PPARγ, and multiple-inflammatory cytokines could be also reversed in HFD group under the treatment of 150 mg/kg FSSB. Our findings demonstrated FSSB is efficient for the treatment of fatty liver disease through regulation of lipid metabolism and antioxidation in Nile tilapia, providing a new treatment of non-alcoholic fatty liver disease (NAFLD) in fish aquaculture.

Biobased processes to minimize environmental pollutants have attracted much attention. l-Carnosine has been produced by chemical synthesis, and as an alternative to this method, we newly developed engineered Corynebacterium glutamicum synthesizing l-carnosine. To develop the strain, the pentose phosphate pathway (PPP) was enhanced by attenuating flux to nonoxidative PPP. Enhanced PPP strengthened the histidine pathway and produced 5.0 g/L l-histidine and 3.9 mg/L l-carnosine. Then, the histidine synthetic pathway was reinforced by overexpressing HisG and Rel. This pathway reduced feedback inhibition by l-histidine and strengthened the flux of the histidine pathway; thus, it produced 552.20 mg/g DCW l-histidine. As a result, enhancement of the PPP accumulates more l-histidine than the histidine pathway; thus, the PPP was further enhanced by pgi gene alteration. For sufficient β-alanine products, PanD was overexpressed and produced 99.17 mg/L l-carnosine. The final strain, Car15, which consolidated all three pathways, produced 323.26 mg/L l-carnosine via fed-batch fermentation. Finally, we confirmed the antioxidant and antiglycation effects of biologically synthesized l-carnosine, and the biologically synthesized l-carnosine showed inhibitory activity similar to that of commercial l-carnosine. Consequently, this study suggested a new biosynthetic process for l-carnosine and showed potential as a treatment for metabolic disorders through the assessment of its functions.

We provided a study on homeologous gene evolution of homeologous genes by comparing Brassica genomes. Polyploidy has played fundamental roles during the evolution of plants. Following polyploidization, many duplicated genes are diversified or lost in a process termed diploidization. Understanding the retention and diversification of homeologs after polyploidization will help elucidate the process of diploidization. Here, we investigated the evolution of homeologous genes in Brassica genomes and observed similarly asymmetrical gene retention among different functional groups and consistent retention after recurrent polyploidizations. In the comparative analysis of Brassica diploid genomes, we found that preferentially retained genes show different patterns on sequence and expression divergence: genes with the function of 'biosynthetic process' and 'transport' were under much stronger purifying selection, while transcriptional regulatory genes diverged much faster than other genes. Duplicate pairs of the former two functional groups show conserved high expression patterns, while most of transcriptional regulatory genes are simultaneously lowly expressed. Furthermore, homeologs in diploids and allotetraploids showed similar loss and retention patterns: duplicates in progenitor genomes were more likely to be retained and accumulated fewer substitutions. However, transcriptional regulation is also enriched in the genes that do not have any non-synonymous mutations in the Brassica allotetraploids, indicating that some of these genes were under strong purifying selection. Overall, our study provided insight into the evolution of homeologs genes during diploidization process.

Microbial production of l-tryptophan (l-trp) has received considerable attention because of its diverse applications in food additives and pharmaceuticals. Overexpression of rate-limiting enzymes and blockage of competing pathways can effectively promote microbial production of l-trp. However, the biosynthetic process remains suboptimal due to imbalanced flux distribution between central carbon and tryptophan metabolism, presenting a major challenge to further improvement of l-trp yield. In this study, we redistributed central carbon metabolism to improve phosphoenolpyruvate (PEP) and erythrose-4-phosphate (E4P) pools in an l-trp producing strain of Escherichia coli for efficient l-trp synthesis. To do this, a phosphoketolase from Bifidobacterium adolescentis was introduced to strengthen E4P formation, and the l-trp titer and yield increased to 10.8 g/L and 0.148 g/g glucose, respectively. Next, the phosphotransferase system was substituted with PEP-independent glucose transport, meditated by a glucose facilitator from Zymomonas mobilis and native glucokinase. This modification improved l-trp yield to 0.164 g/g glucose, concomitant with 58% and 40% decreases of acetate and lactate accumulation, respectively. Then, to channel more central carbon flux to the tryptophan biosynthetic pathway, several metabolic engineering strategies were applied to rewire the PEP-pyruvate-oxaloacetate node. Finally, the constructed strain SX11 produced 41.7 g/L l-trp with an overall yield of 0.227 g/g glucose after 40 h fed-batch fermentation in 5-L bioreactor. This is the highest overall yield of l-trp ever reported from a rationally engineered strain. Our results suggest the flux redistribution of central carbon metabolism to maintain sufficient supply of PEP and E4P is a promising strategy for efficient l-trp biosynthesis, and this strategy would likely also increase the production of other aromatic amino acids and derivatives.

Transcription factor Broad Complex (BR-C) is an ecdysone primary response gene in insects and participates in the regulation of insect growth and development. In this study, we performed a genome-wide identification of BR-C target genes in silkworm (Bombyx mori) using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq). As a result, a total of 1006 BR-C ChIP peaks were identified, and 15% of peaks were located in the promoter regions of 133 protein-coding genes. Functional annotation revealed that these ChIP peak-associated genes, as potential BR-C targets, were enriched in pathways related to biosynthetic process, metabolic process, and development. Transcriptome analysis and quantitative real-time polymerase chain reaction (PCR) examination revealed that developmental changes in expression patterns of a portion of potential BR-C targets, including HR96 and GC-α1, were similar to those of BR-C. ChIP-PCR examination confirmed that BR-C could directly bind to the promoters of potential targets. Further, dual luciferase assays demonstrated that HR96 promoter activity was significantly upregulated following BR-C overexpression, and this upregulation was abolished when the binding motif in the promoter was truncated. This study will be helpful for deciphering the regulatory roles of BR-C during insect growth and development.

© 2020 Informa UK Limited, trading as Taylor & Francis Group.NADPH-dependent oxidoreductases are crucial biocatalysts for the industrial production of chiral compounds. For in situ recycling of required expensive cofactors in this biosynthetic process, NAD(P)+-dependent formate dehydrogenases (FDHs) are wanted to be employed as redox biocatalysts due to their greener and process friendly nature. However, their utilization is limited by their undesired cofactor preference that strongly prone to NAD+ more than NADP+ and catalytic efficiency. To mine NADP+-dependent FDHs in nature by the guidance of bioinformatic tools or re-engineering of their NAD+-dependent equivalents to get an applicable recycler are attractive topics in bioengineering. It can be said that, up to now, the attempts to switch the cofactor preference of the FDHs generally have resulted in NADP+-dependent enzymes that have not to catch the desired catalytic efficiencies or stability. In this review, all studies about the native NADP+-dependent FDHs and also engineered equivalents that reconstructed with different protein engineering approaches for altering the coenzyme specificity are outlined. To switch the coenzyme preference of FDHs or to find the native NADP+-dependent FDHs will be the hot topics in bioengineering until finding a feasible regenerator. Therefore, this study will be a useful guide to get a pathway for designing or discovering novel NADP+-dependent FDHs.

Cadmium selenide (CdSe) quantum dots (QDs) were biosynthesized rapidly in 18 h in Bacillus licheniformis ATCC 11946 (B. licheniformis); this process benefited from the cellular machinery of bacteria metal metabolism, in which inorganic Na2 SeO3 and CdCl2 were chosen as raw materials to produce high quality CdSe QDs by a designed two-step protocol. Research outcomes demonstrated that the purified CdSe QDs possessed maximum fluorescence intensities at weak alkalinity solutions and had good fluorescence stabilities at 4°C as well as at room temperature after standing for 1 week. Glutathione (GSH) concentration and superoxide dismutase (SOD) content, both of which were reported to be greatly related to biosynthetic activities in some bacterial matrices, were monitored during the biosynthetic process in B. licheniformis. Bacterial resistance research further showed that the change in rates in bacterial inhibition zone diameter to seven different antibiotics was less than 9% after B. licheniformis was used to manufacture CdSe QDs, showing a relative lower environmental risk in short-term heavy metal exposure.

To clarify crucial key micro-RNAs and mRNAs associated with hand, foot, and mouth disease (HFMD) virus infection, we conducted this bioinformatics analysis from four GEO datasets. The following datasets were used for the analysis: GSE85829, GSE94551, GSE52780, and GSE45589. Differentially expressed genes (DEGs) were acquired, and the analysis of functional and pathway enrichment and the relative regulatory network were conducted. After screening common differentially expressed miRNAs (DE-miRNAs), five key miRNAs were acquired: miR-100-3p, miR-125a-3p, miR-1273g-3p, miR-5585-3p, and miR-671-5p. There were three common enriched GO terms between miRNA-derived prediction and mRNA-derived analysis: biosynthetic process, cytosol, and nucleoplasm. There was one common KEGG pathway, i.e., cell cycle shared between miRNA-based and mRNA-based enrichment. Using TarBase V8 in DIANA tools, we acquired 1,520 potential targets (mRNA) from the five key DE-miRNAs, among which the159 DE-mRNAs also included 11 DEGs. These common DEGs showed a PPI network mainly connected by SMC1A, SMARCC1, SF3B3, LIG1, and BRMS1L. Together, changes in five key miRNAs and 11 key mRNAs may play crucial roles in HFMD progression. A combination of these roles may benefit the early diagnosis and treatment of HFMD.

Purpose. To investigate the expression profiles of long noncoding RNAs (lncRNAs) in patients with atrial fibrillation (AF). Methods. The peripheral blood monocytes of a total of 20 patients with AF and 20 healthy subjects were collected for gene chip technology to detect differentially expressed lncRNAs from 2017.01 to 2017.08. Reverse transcription polymerase chain reaction (RT-PCR) was applied for further verification. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to identify the functions of differentially expressed genes and related pathways. Results. There were 19 lncRNAs differentially expressed ( FC ≥ 2 , P < 0.05 ), of which 6 were upregulated and 13 were downregulated. Two of three upregulated lncRNAs ( P = 0.014 and 0.006 for HNRNPU-AS1 and LINC00861, respectively) and two of three downregulated lncRNAs ( P = 0.028 and 0.032 for RP11-443B7.3 and CTD-2616J11.14, respectively) were randomly confirmed by RT-PCR and showed a significantly different expression with the RNA-seq results. GO analysis showed that differentially expressed genes enriched in differentially expressed transcripts in biological process were mainly involved in metabolic process, catabolic process, and biosynthetic process. Differentially expressed transcripts in cellular component were mainly involved in nuclear lumen, organelle lumen, and cytoplasm. Differentially expressed transcripts in molecular function were mainly involved in protein binding, RNA binding, and molecular function. KEGG enrichment pathway analysis showed that some of the enrichment pathways associated with differentially expressed lncRNAs include calcium signaling pathway, NF-kappa B signaling pathway, cytokine-cytokine receptor interaction, and Toll-like receptor signaling pathway. HNRNPU-AS1 was the highest positive correlated lncRNA in the networks. Conclusions. The expression of lncRNA in peripheral blood of AF patients is different from that of normal people. The physiological functions of these differentially expressed lncRNAs may be related to the pathogenesis of AF, which provide experimental basis and new therapeutic target for prognosis and treatment of patients with AF. HNRNPU-AS1 may play an important role in the pathophysiology and mechanisms of AF.

Aging is a very complicated biological process that can change gene expressions. The Chinese rhesus macaque (Macaca mulatta lasiota; CR) is closely related to humans. We explored gene expression with increasing age and DNA methylation changes in young and old CRs. Results showed blood transcriptome and DNA methylome significantly changed from young to old CRs. The age-associated differentially expressed genes (DEGs) and differentially methylated regions (DMRs) were associated with age-related biological features, such as immunity, blood coagulation, and biosynthetic process. The measurements of coagulation indicators confirmed old CRs had shorter coagulation time than young CRs, and the activities of coagulation factor II (FII) and factor VIII (FVIII) were enhanced in old CRs. Humans and CRs exhibited the same enhanced blood coagulation with age phenotype. Our study found aging is a critical factor affecting gene expression in CRs, and also provided new insights into the blood coagulation changes in non-human primates.

Objective Myricetin 3-O-galactoside is an active compound with pharmaceutical potential. The insufficient supply of this compound becomes a bottleneck in the druggability study of myricetin 3-O-galactoside. Thus, it is necessary to develop a biosynthetic process for myricetin 3-O-galactoside through metabolic engineering. Methods Two genes OcSUS1 and OcUGE1 encoding sucrose synthase and UDP-glucose 4-epimerase were introduced into BL21(DE3) to reconstruct a UDP-D-galactose (UDP-Gal) biosynthetic pathway in Escherichia coli. The resultant chassis strain was able to produce UDP-Gal. Subsequently, a flavonol 3-O-galactosyltransferase DkFGT gene was transformed into the chassis strain producing UDP-Gal. An artificial pathway for myricetin 3-O-galactoside biosynthesis was thus constructed in E. coli. Results The obtained engineered strain was demonstrated to be capable of producing myricetin 3-O-galactoside, reaching 29.7 mg/L. Conclusion Biosynthesis of myricetin 3-O-galactoside through engineered E. coli could be achieved. This result lays the foundation for the large-scale preparation of myricetin 3-O-galactoside.

The indolizidine alkaloid swainsonine (SW) is a deadly mycotoxin to livestock that can be produced by different plant-associated fungi, including the endophytic entomopathogenic fungi Metarhizium species. The SW biosynthetic gene cluster has been identified but the genetic mechanism of SW biosynthesis remains obscure. To unveil the SW biosynthetic pathway, we performed gene deletions in M. robertsii, heterologous expression of a core biosynthetic gene, substrate feedings, mass spectrometry, and bioassay analyses in this study. It was unveiled that SW is produced via a multibranched pathway by the hybrid nonribosomal peptide-polyketide synthase (NRPS-PKS) gene cluster in M. robertsii. The precursor pipecolic acid can be converted from lysine by both the SW biosynthetic cluster and the unclustered genes such as lysine cyclodeaminase. The hybrid NRPS-PKS enzyme produces three intermediates with and without domain skipping. Intriguingly, the biosynthetic process is coupled with the cis to trans nonenzymatic epimerization of C1-OH for both hydroxyl- and dihydroxyl-indolizidine intermediates. We also found that SW production was dispensable for fungal colonization of plants and infection of insect hosts. Functional characterization of the SW biosynthetic genes in this study may benefit the safe use of Metarhizium fungi as insect biocontrol agents and the management of livestock pastures from SW contamination by genetic manipulation of the toxin-producing fungi.

Calcitonin gene-related peptide (CGRP) is a mediator of microglial activation at the transcriptional level. The involvement of the epigenetic mechanism in this process is largely undefined. Histone deacetylase (HDAC)1/2 are considered important epigenetic regulators of gene expression in activated microglia. In this study, we examined the effect of CGRP on HDAC2-mediated gene transcription in microglial cells through the chromatin immunoprecipitation sequencing (ChIP-seq) method. Immunofluorescence analysis showed that mouse microglial cells (BV2) expressed CGRP receptor components. Treatment of microglia with CGRP increased HDAC2 protein expression. ChIP-seq data indicated that CGRP remarkably altered promoter enrichments of HDAC2 in microglial cells. We identified 1271 gene promoters, whose HDAC2 enrichments are significantly altered in microglia after CGRP treatment, including 1181 upregulating genes and 90 downregulating genes. Bioinformatics analyses showed that HDAC2-enriched genes were mainly associated with immune- and inflammation-related pathways, such as nitric oxide synthase (NOS) biosynthetic process, retinoic acid-inducible gene- (RIG-) like receptor signaling pathway, and nuclear factor kappa B (NF-κB) signaling pathway. The expression of these key pathways (NOS, RIG-I, and NF-κB) were further verified by Western blot. Taken together, our findings suggest that genes with differential HDAC2 enrichments induced by CGRP function in diverse cellular pathways and many are involved in immune and inflammatory responses.

Seed germination is the first stage in wheat growth and development, directly affecting grain yield and quality. As an important post-translation modification, lysine acetylation participates in diverse biological functions. However, little is known regarding the quantitative acetylproteome characterization during wheat seed germination. In this study, we generated the first comparative proteomes and lysine acetylomes during wheat seed germination. In total, 5,639 proteins and 1,301 acetylated sites on 722 proteins were identified at 0, 12 and 24 h after imbibitions. Several particularly preferred amino acids were found near acetylation sites, including KacS, KacT, KacK, KacR, KacH, KacF, KacN, Kac*E, FKac and Kac*D, in the embryos during seed germination. Among them, KacH, KacF, FKac and KacK were conserved in wheat. Biosynthetic process, transcriptional regulation, ribosome and proteasome pathway related proteins were significantly enriched in both differentially expressed proteins and differentially acetylated proteins through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. We also revealed that histone acetylation was differentially involved in epigenetic regulation during seed germination. Meanwhile, abscisic acid and stress related proteins were found with acetylation changes. In addition, we focused on 8 enzymes involved in carbohydrate metabolism, and found they were differentially acetylated during seed germination. Finally, a putative metabolic pathway was proposed to dissect the roles of protein acetylation during wheat seed germination. These results not only demonstrate that lysine acetylation may play key roles in seed germination of wheat but also reveal insights into the molecular mechanism of seed germination in this crop.

Aromatic polyketides have attractive biological activities and pharmacological properties. Different from other polyketides, aromatic polyketides are characterized by their polycyclic aromatic structure. The biosynthesis of aromatic polyketides is usually accomplished by the type II polyketide synthases (PKSs), which produce highly diverse polyketide chains by sequential condensation of the starter units with extender units, followed by reduction, cyclization, aromatization and tailoring reactions. Recently, significant progress has been made in characterization and engineering of type II PKSs to produce novel products and improve product titers. In this review, we briefly summarize the architectural organizations and genetic contributions of PKS genes to provide insight into the biosynthetic process. We then review the most recent progress in engineered biosynthesis of aromatic polyketides, with emphasis on generating novel molecular structures. We also discuss the current challenges and future perspectives in the rational engineering of type II PKSs for large scale production of aromatic polyketides.

Background Lipid infiltration and inflammatory response run through the occurrence of atherosclerosis. Differentiation into macrophages and foam cell formation are the key steps of AS. Aim of this study was that the differential gene expression between foam cells and macrophages was analyzed to search the key links of foam cell generation, so as to explore the pathogenesis of atherosclerosis and provide targets for the early screening and prevention of coronary artery disease (CAD). Methods The gene expression profiles of GSE9874 were downloaded from Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9874) on GPL96 [HG-U133A] Affymetrix Human Genome U133. A total of 22,383 genes were analyzed for differentially expression genes (DEGs) by Bayes package. GO enrichment analysis and KEGG pathway analysis for DEGs were performed using KOBAS 3.0 software (Peking University, Beijing, China). STRING software (STRING 10.0; European Molecular Biology Laboratory, Heidelberg, Germany) was used to analyze the protein-protein interaction (PPI) of DEGs. Results A total of 167 DEGs between macrophages and foam cells were identified. Compared with macrophages, 102 genes were significantly upregulated and 65 genes were significantly downregulated (P 1) in foam cells. DEGs were mainly enrich in ‘sterol biosynthetic and metabolic process’, ‘cholesterol metabolic and biosynthetic process’ by GO enrichment analysis. The results of KEGG pathway analysis showed all differential genes are involved in biological processes through 143 KEGG pathways. A PPI network of the DEGs was constructed and 10 outstanding genes of the PPI network was identified by using Cytoscape, which include HMGCR, SREBF2, LDLR, HMGCS1, FDFT1, LPL, DHCR24, SQLE, ABCA1 and FDPS. Conclusion: Lipid metabolism related genes and molecular pathways were the key to the transformation of macrophages into foam cells. Therefore, lipid metabolism disorder is the key to turn macrophages into foam cells, which plays a major role in CAD.

Black pepper (Piper nigrum) is a vital spice crop with uses ranging from culinary to pharmacological applications. However, limited genetic information has constrained the understanding of the molecular regulation of flower and fruit development in black pepper. In this study, a comparison among three different black pepper varieties, Semengok Aman (SA), Kuching (KC), and Semengok 1 (S1), with varying fruit characteristics was used to provide insight on the genetic regulation of flower and fruit development. Next-generation sequencing (NGS) technology was used to determine the flower and fruit transcriptomes by sequencing on an Illumina HiSeq 2500 platform followed byde novoassembly using SOAPdenovo-Trans. The high-quality assembly of 66,906 of unigenes included 64.4% of gene sequences (43,115) with similarity to one or more protein sequences from the GenBank database. Annotation with Blast2Go assigned 37,377 genes to one or more Gene Ontology terms. Of these genes, 5,874 genes were further associated with the biological pathways recorded in the KEGG database. Comparison of flower and fruit transcriptome data from the three different black pepper varieties revealed a large number of DEGs between flower and fruit of the SA variety. Gene Ontology (GO) enrichment analysis further supports functions of DEGs between flower and fruit in the categories of carbohydrate metabolic processes, embryo development, and DNA metabolic processes while the DEGs in fruit relate to biosynthetic process, secondary metabolic process, and catabolic process. The enrichment of DEGs in KEGG pathways was also investigated, and a large number of genes were found to belong to the nucleotide metabolism and carbohydrate metabolism categories. Gene expression profiling of flower formation-related genes reveals that other than regulating the flowering in black pepper, the flowering genes might also be implicated in the fruit development process. Transcriptional analysis of sugar transporter and carbohydrate metabolism genes in different fruit varieties suggested that the carbohydrate metabolism in black pepper fruit is developmentally regulated, and some genes might serve as potential genes for future crop quality improvement. Study on the piperine-related gene expression analysis suggested that lysine-derived products might present in all stages of fruit development, but the transportation was only active at the early stage of fruit development. These results indicate several candidate genes related to the development of flower and fruit in black pepper and provide a resource for future functional analysis and potentially for future crop improvement.

The effects of six metal oxide nanoparticles (MO-NPs) on the activity and biosynthesis of an enzyme (β-galactosidase) were examined using a mutant strain of E. coli. Different sensitivities were observed according to the type of NP and metabolic process. The toxic effects on enzyme activity were significantly greater than on biosynthesis (p < 0.011), except in the presence of NiO. In both cases, ZnO NP caused the greatest inhibition among the tested NPs, followed by CuO. The EC50s for ZnO were 0.19 and 3.68 mg/L for enzyme activity and biosynthesis, respectively. Similar orders of toxicity were observed as follows: ZnO > CuO > NiO > Co3O4 > TiO2, Al2O3 for enzyme activity; and ZnO > CuO > NiO ≫ Al2O3, TiO2, Co3O4 for the biosynthetic process. More systematic research, including in-depth studies like investigation of the molecular mechanisms, is necessary to elucidate the detailed mechanisms of inhibition involved in both metabolic processes.

Aluminum compounds have been observed in various brain regions, and their accumulation has been associated with many neurodegenerative disorders. Neurotoxic effects of aluminum are attributed to reactive oxygen species generation, induction of apoptosis and inflammatory reactions activation. Metalloestrogen activity of aluminum has also been linked to breast cancer progression and metastasis. In this study, taking into account the anti-apoptotic and anti-oxidant activities of estrogens in neuronal cells, which are mediated by estrogen receptors, the possible estrogenic activity of aluminum in SH-SY5Y neuroblastoma cells was studied. Our results showed that aluminum in the form of aluminum chlorohydrate (ACH) exhibited no effect on estrogen receptors transcriptional activation, and differential effect on estrogen receptor alpha (ERα) and estrogen receptor beta (ERβ) protein levels. ACH caused reduction in ERβ protein levels, and increase in its mitochondrial localization. ACH-induced reduction in ERβ protein level may be linked, at least in part, to the ACH-induced increase in ERα protein level. This statement is based on our observations showing aluminum-induced reduction in the E2-induced increase in ERα S118 phosphorylation, in MCF-7 and SH-SH5Y cells. Phosphorylation at S118 residue is known to be associated with inhibition of the ubiquitin-induced proteolytic degradation of ERα, leading to its accumulation. Since it is known that ERα negatively regulate ERβ expression, increase in ERα, may contribute to reduction in ERβ levels and subsequent weakening of its anti-apoptotic and anti-oxidant activity, justified by the observed reduction in procaspase 9, mitochondrial cytochrome c, Bcl-2, Bcl-xL and mitochondrial thioredoxin protein level, as well as by the increase in proapoptotic BAX level, in ACH treated SH-SY5Y cells. In addition, increase in mitochondrial ERβ localization may also trigger mitochondrial metabolism, suppress biosynthetic process of gluconeogenesis, as indicated by the observed reduction in the phosphoenolpyruvate carboxykinase protein level, and eventually lead to increase in reactive oxygen species (ROS) generation, known to be implicated in aluminum induced neurodegeneration. This statement was verified by the observed ACH-induced increase in ERβ mitochondrial localization, induction of the mitochondrial membrane depolarization and increase in ROS production, in neuronal-like differentiated SH-SY5Y cells.

The present study aimed to identify potentially important biomarkers associated with polycystic ovary syndrome (PCOS) by integrating DNA methylation with transcriptome profiling. The transcription (E‑MTAB‑3768) and methylation (E‑MTAB‑3777) datasets were retrieved from ArrayExpress. Paired transcription and methylation profiling data of 10 cases of PCOS and 10 healthy controls were available for screening differentially expressed genes (DEGs) and differentially methylated genes (DMGs). Genes with a negative correlation between expression levels and methylation levels were retained by correlation analysis to construct a protein‑protein interaction (PPI) network. Subsequently, functional and pathway enrichment analyses were performed to identify genes in the PPI network. Additionally, a disease‑associated pathway network was also established. A total of 491 overlapping genes, and the expression levels of 237 genes, were negatively correlated with their methylation levels. Functional enrichment analysis revealed that genes in the PPI network were mainly involved with biological processes of cellular response to stress, negative regulation of the biosynthetic process, and regulation of cell proliferation. The constructed pathway network associated with PCOS led to the identification of four important genes (SPP1, F2R, IL12B and RBP4) and two important pathways (Jak‑STAT signaling pathway and neuroactive ligand‑receptor interaction). Taken, together, the results from the present study have revealed numerous important genes with abnormal DNA methylation levels and altered mRNA expression levels, along with their associated functions and pathways. These findings may contribute to an improved understanding of the possible pathophysiology of PCOS.

Recently the B6.CBA-D13Mit76C (B6-M76C) and B6.CBA-D13Mit76B (B6-M76B) recombinant mouse lines have been created, which differ in the sensitivity of the 5-HT1A-receptor to chronic activation by an 8-OH-DPAT (8-hydroxy-2- (di-n-propylamino) tetralin). 5-HT1A-receptor is the key regulator of the brain serotonin (5-HT) system that is implicated in the regulation of stress response. In this work, it was found that acute emotional stress (immobilization of 40 min) increases the expression of the c-fos gene, which is a marker of the response to stress, in the brain of both lines. The stress-induced increase c-fos expression in the striatum, hypothalamus, and cortex of B6-M76C mice was more pronounced. The reaction to emotional stress led to an increase in the ratio of the serotonin metabolite - 5-HIAA (5-hydroxyinodolacetic acid) to 5-HT in the midbrain and hippocampus in both lines. An increased 5-HIAA/5-HT ratio was detected in the hypothalamus B6-M76C and cortex B6-M76B of mice after stress. Moreover, the reaction to stress led to decrease in the level of norepinephrine in the hippocampus and hypothalamus in B6-M76C mice. The levels of dopamine, norepinephrine, epinephrine and the dopamine/norepinephrine ratio in the adrenal glands increased in response to the stress effect only in B6-M76C. The present study showed that the sympathoadrenal system is more sensitive to acute stress in the B6-M76C mice. Reaction to stress in B6-M76C mice leads to an increase in the content of norepinephrine and epinephrine in adrenal tissue. An increase in the adrenal dopamine/norepinephrine ratio may indicate a more rapid transition of catecholamine biosynthesis intermediates (dopamine) to norepinephrine and further epinephrine due to the acceleration of the biosynthetic process in response to stress in B6-M76C mice. In addition, an increased sensitivity of the hypothalamic neurons to the action of stress in B6-M76C was shown. Thus, B6-M76C mice are of significant interest for the study of the hypothalamic-pituitary-adrenal system with an overactive response to stress, and can contribute to the identification of new biomarkers for clinical studies

Thiopeptides, which are a class of sulfur-rich, ribosomally synthesized and post-translationally modified peptides (RiPPs), have great potential in the treatment of diseases caused by oral pathogens. Nocathiacin I (NOC-I) and nosiheptide (NOS) are two structurally similar thiopeptide members that feature an indolic side ring. In the structure of NOC-I, this side ring is further rigidified through the formation of an ether linkage; however, the related biosynthetic process remains poorly understood. Here, we report that NocV, a cytochrome P450 protein found to be unique in the biosynthetic pathway of NOC-I, is responsible for the establishment of the intramolecular ether linkage through two oxidation steps. This observation benefited from the heterologous overexpression of the gene nocV in an engineered Streptomyces strain producing the bicyclic NOS intermediate NOS1260, and subsequent isolation and structure characterization of two functionalized products. The product NOS-V1 contains a new hydroxyl group at Cα of the residue Glu6, in contrast with the other product NOS-V2, in which this hydroxyl group is further coupled with the C4 methyl group of the indolic moiety to form an ether linkage. These findings provide insights into the catalytic logic of NocV in the biosynthesis of NOC-I, during which this cytochrome P450 protein appears to act in tandem on two positions in NOS1260 by selectively hydroxylating Glu6 and then oxidatively coupling the indolic moiety. Rigidifying the side ring via ether bond formation has a positive impact on the antibacterial properties of NOS-type thiopeptides, evidenced by the improved activity of NOC-V2 against various tested oral pathogens compared with NOS1260.

Membrane-spanning lipids are present in a wide variety of archaea but they are rarely in bacteria. Nevertheless, the (hyper)thermophilic members of the order Thermotogales harbor tetraester, tetraether, and mixed ether/ester membrane-spanning lipids mostly composed of core lipids derived from diabolic acids, C30, C32 and C34 dicarboxylic acids with two adjacent mid-chain methyl substituents. Lipid analysis of Thermotoga maritima across growth phases revealed a decrease of the relative abundance of fatty acids together with an increase of diabolic acids with independence of growth temperature. We also identified isomers of C30 and C32 diabolic acids, i.e. dicarboxylic acids with only one methyl group at C-15. Their distribution suggests they are products of the condensation reaction but preferably produced when the length of the acyl chains is not optimal. In comparison with growth at the optimal temperature of 80°C, an increase of glycerol ether-derived lipids was observed at 55°C. Besides, our analysis only detected diabolic acid-containing intact polar lipids with phosphoglycerol (PG) headgroups. Considering these findings, we hypothesize a biosynthetic pathway for the synthesis of membrane-spanning lipids based on PG polar lipid formation, suggesting that the protein catalyzing this process could be a membrane protein. We also identified, by genomic and protein domain analyses, a gene coding for a putative plasmalogen synthase homologue in T. maritima, which is also present in other bacteria producing sn1-alkyl ether lipids but not plasmalogens, suggesting it could be involved in the conversion of the ester to ether bond in the diabolic acids bound in membrane-spanning lipids. Importance Membrane-spanning lipids are unique compounds found in most archaeal membranes, but they are also present in specific bacterial groups like the Thermotogales. The synthesis and physiological role of membrane-spanning lipids in bacteria represent an evolutionary and biochemical open question that points to the differentiation of the membrane lipids composition. Understanding the formation of membrane-spanning lipids is crucial to solving this question and identifying the enzymatic and biochemical mechanism performing this procedure. In the present work, we found changes at the core lipid level, and we propose that the growth phase drives the biosynthesis of these lipids rather than temperature. Our results identified physiological conditions influencing the membrane-spanning lipids biosynthetic process which can further clarify the pathway leading to the biosynthesis of these compounds.

Rubisco jest enzymem występującym u organizmów fotosyntetyzujących katalizującym pierwszy etap procesu akumulacji biomasy, przyłączenie dwutlenku węgla do cukru, rybulozo-1,5-bisfosforanu. Skomplikowana, multimeryczna budowa i obecność wielu labilnych elementów strukturalnych w tym białku, powodują że nie jest ono w stanie samodzielnie uzyskać swojej natywnej struktury czwartorzędowej i wymaga do tego celu ściśle zorganizowanego działania szeregu czynników pomocniczych. Wyspecjalizowane białka chaperonowe uczestniczą kolejno w fałdowaniu podjednostek holoenzymu, pośredniczą w ich stopniowej oligomeryzacji, a w niektórych przypadkach dodatkowo kierują do komórkowego miejsca przeznaczenia, takiego jak karboksysomy, czy pyrenoid. Oprócz pełnienia swojej kanonicznej funkcji, polegającej na pośredniczeniu w składaniu Rubisco, chaperony te zaangażowane są w dodatkowe procesy, takie jak kontrola jakości procesu biosyntezy, czy regulacja fizjologii organelli i kompartmentów komórkowych.

The evolution of resistance in Salmonella to fluoroquinolones (FQs) under a broad range of sub-inhibitory concentrations (sub-MICs) has not been systematically studied. This study investigated the mechanism of resistance development in Salmonella enterica serovar Enteritidis (S. Enteritidis) under sub-MICs of 1/128×MIC to 1/2×MIC of enrofloxacin (ENR), a widely used veterinary FQ. It was shown that the resistance rate and resistance level of S. Enteritidis varied with the increase of ENR concentration and duration of selection. qRT-PCR results demonstrated that the expression of outer membrane porin (OMP) genes, ompF, ompC and ompD, were down-regulated first to rapidly adapt and develop resistance of ≤ 4×MIC, and as the resistance level increased (≥8×MIC), the up-regulated expression of efflux pump genes, acrB, emrB amd mdfA, along with mutations in quinolone resistance-determining region (QRDR) gradually played a decisive role. Cytohubba analysis based on transcriptomic profiles demonstrated that purB, purC, purD, purF, purH, purK, purL, purM, purN and purT were the hub genes for the FQs resistance. ‘de novo’ IMP biosynthetic process, purine ribonucleoside monophosphate biosynthetic process and purine ribonucleotide biosynthetic process were the top three biological processes screened by MCODE. This study first described the dynamics of FQ resistance evolution in Salmonella under a long-term selection of sub-MICs of ENR in vitro. In addition, this work offers greater insight into the transcriptome changes of S. Enteritidis under the selection of ENR and provides a framework for FQs resistance of Salmonella for further studies.

Cellulose is the most abundant biological compound on Earth and while it is the predominant building constituent of plants, it is also a key extracellular matrix component in many diverse bacterial species. While bacterial cellulose was first described in the 19th century, it was not until this last decade that a string of structural works provided insights into how the cellulose synthase BcsA, assisted by its inner-membrane partner BcsB, senses c-di-GMP to simultaneously polymerize its substrate and extrude the nascent polysaccharide across the inner bacterial membrane. It is now established that bacterial cellulose can be produced by several distinct types of cellulose secretion systems and that in addition to BcsAB, they can feature multiple accessory subunits, often indispensable for polysaccharide production. Importantly, the last years mark significant progress in our understanding not only of cellulose polymerization per se but also of the bigger picture of bacterial signaling, secretion system assembly, biofilm formation and host tissue colonization, as well as of structural and functional parallels of this dominant biosynthetic process between the bacterial and eukaryotic domains of life. Here, we review current mechanistic knowledge on bacterial cellulose secretion with focus on the structure, assembly and cooperativity of Bcs secretion system components.

Summary The biosynthesis of metal nanoparticles from precious metals has been of wide concern. Their antibacterial activity is a main bottleneck restricting the bacterial activity and reduction performance. Here, bio-electrochemical systems were used to harvest electroactive biofilms (EABs), where bacteria were naturally protected by extracellular polymeric substances to keep activity. The biofilm was further encapsulated with polydopamine (PDA) as additional shield. Silver nanoparticles (AgNPs) were biosynthesized on EABs, whose electroactivity could be fully recovered after Ag+ reduction. The PDA increased bacterial viability by 90%–105%, confirmed as an effective protection against antibacterial activity of Ag+/AgNPs. The biosynthetic process changed the component and function of the microbial community, shifting from bacterial Fe reduction to archaeal methanogenesis. These results demonstrated that the electrochemical acclimation of EABs and encapsulation with PDA were effective protective measures during the biosynthesis of AgNPs. These approaches have a bright future in the green synthesis of nanomaterials, biotoxic wastewater treatment, and sustainable bio-catalysis., Graphical abstract, Highlights • The EABs formed using BESs had an efficient ability to recover Ag+ to AgNPs • The bio-reduction efficiencies of AgNPs reached more than 94% • The PDA increased by 90%–105% of the bacterial viability • The biosynthesis process changed the microbial community, Electrochemistry; Microbiofilms; Nanoparticles

microRNAs (miRNAs) are short noncoding RNA sequences, approximately 20-22 nucleotides, synthesized in the cell nucleus, through a complex multi-step biosynthetic process, starting from RNA polymerase II. miRNAs regulate a wide range of biological processes as cell differentiation, proliferation and development, cell-to-cell communication, cell metabolism and apoptosis. There is evidence that miRNAs may have a role in molecular mechanisms linked to cellular pathways of certain diseases, as viral infections, cancer, diabetes and cardiovascular disease. miRNAs expression was investigated in diabetes mellitus: a lot of altered circulating levels of different miRNAs were found to be linked to type 1 and type 2 diabetes, both at onset and in advanced disease. At least 12 circulating miRNAs were found consistently dysregulated in type 1 diabetes mellitus and, more or less, 40 circulating miRNAs in type 2 diabetic patients. miR-126 seems to be miRNA most linked to pathways and development of type 1 and type 2 diabetes and their complications. Dysregulation of several miRNAs involves different aspects of diabetic disease: glycemic control, residual beta cell function, insulin secretion and sensitivity, micro- and macro-vascular complications, particularly endothelial dysfunction, renal disease and retinopathy. The analysis of circulating miRNAs might be a good source of diagnostic and prognostic biomarkers in diabetic patients. Large and long-term clinical studies should be conducted to evaluate the value of these nucleotides as biomarkers for predicting progression of diabetes, though the high detection costs might be the main limitations on their use in daily clinical practice.

Tetrahydrocurcumin (THC) has been well known for its superior antioxidant properties. Therefore, it is speculated that it might be effective to relieve oxidative stress-induced diseases, such as skin hyperpigmentation. In this work, an in vitro B16F10 melanoma cell model was used to study the impact of THC on the melanogenic process under stressed conditions. It was demonstrated that THC could effectively inhibit the α-MSH (melanocyte-stimulating hormone) induced melanin production in B16F10 melanoma cells and the expressions of three key enzymes involved with the biosynthetic process of melanin, tyrosinase (TYR), tyrosinase-related protein 1 (TRP-1), and tyrosinase-related protein 2 (TRP-2), were all significantly reduced. In addition, an in vitro human keratinocyte cell model was used to investigate the potential protective role of THC on H2O2-induced cytotoxicity. It was found that THC could prevent H2O2-induced oxidative stress based on the results of both the cell viability study and the intracellular ROS (reactive oxygen species) study assessed by the flow cytometry. Last, THC was formulated into a lecithin based nanoemulsion, and an in vitro Franz diffusion cell study using Strat-M® membrane concluded that the nanoemulsion could significantly enhance the membrane permeation compared to the unformatted THC suspension. This research demonstrated the anti-melanogenic benefits of THC on the melanoma and keratinocyte cell models and the topical delivery efficacy could be significantly enhanced using a lecithin based nanoemulsion.

Extended cultivation with multiple removal of BC pellicles is proposed herein as a new biosynthetic process for bacterial cellulose (BC). This method enhances the BC surface area by 5–11 times per unit volume of the growth medium, improving the economic efficiency of biosynthesis. The resultant BC gel-films were thin, transparent, and congruent. The degree of polymerization (DP) and elastic modulus (EM) depended on the number of BC pellicle removals, vessel shape, and volume. The quality of BC from removals II–III to VII was better than from removal I. The process scale-up of 1:40 by volume increased DP by 1.5 times and EM by 5 times. A fact was established that the symbiotic Medusomyces gisevii Sa-12 was adaptable to exhausted growth medium: the medium was able to biosynthesize BC for 60 days, while glucose ran low at 24 days. On extended cultivation, DP and EM were found to decline by 39–64% and 57–65%, respectively. The BC gel-films obtained upon removals I–VI were successfully trialed in experimental tension-free hernioplasty.

SummaryThe morphotype of arbuscular mycorrhizal (AM) roots is distinct mostly depending on AM host species: Arum, Paris, and Intermediate types. We previously reported that gibberellin (GA) promotes the establishment of Paris-type AM symbiosis in Eustoma grandiflorum despite its negative effects on Arum-type AM symbiosis in model plants. However, the molecular mechanisms underlying the differential effects of GA on different morphotypes, including Intermediate-type AM symbiosis, remain elusive.Comparative transcriptomics revealed that several symbiosis-related genes were transcriptionally promoted upon AM fungal colonization in Lotus japonicus (Arum-type), Daucus carota (Intermediate-type), and E. grandiflorum (Paris-type). Interestingly, upon GA treatment, the fungal colonization levels and expression of symbiosis-related genes were suppressed in L. japonicus and D. carota but were promoted in E. grandiflorum.Exogenous GA transcriptionally inhibited the biosynthetic process of a host-derived signal molecule involved in AM symbiosis, strigolactone, in L. japonicus and E. grandiflorum. Additionally, disaccharides mainly metabolized in AM roots would be different between L. japonicus and D. carota/E. grandiflorum.This study uncovered the conserved transcriptional responses during mycorrhization and diverse responses to GA in AM roots with distinct morphotypes among phylogenetically distant host plants.

The gamma-butyrolactone structural motif is commonly found in many natural signaling molecules and other specialized metabolites. A prominent example is the potent aquatic phytotoxin cyanobacterin bearing a highly functionalized gamma-butyrolactone core structure. The enzymatic machinery assembling cyanobacterin and the many structurally related natural products – herein termed furanolides – has remained elusive over decades. Here we discover and characterize the underlying biosynthetic process of furanolide core structure assembly. The cyanobacterin biosynthetic gene cluster (cyb) is identified by targeted bioinformatic screening and validated by heterologous expression in E. coli. Functional evaluation of the recombinant key enzymes provides in-depth mechanistic insights into a streamlined C,C-bond-forming cascade that involves installation of compatible reactivity at seemingly unreactive C-alpha-positions of the amino acid precursors and facilitates development of a one-pot biocatalytic in vitro synthesis. Our work extends the biosynthetic and biocatalytic toolbox for gamma-butyrolactone formation. It thereby provides a general paradigm for the biosynthesis of furanolides and thus sets the stage for their targeted discovery, biosynthetic engineering and enzymatic synthesis.

Background The molecular mechanism of denervated muscle atrophy is very complex and has not been elucidated to date. In this study, we aimed to use transcriptome sequencing technology to systematically analyze the molecular mechanism of denervated muscle atrophy in order to eventually develop effective strategies or drugs to prevent muscle atrophy. Methods Transcriptome sequencing technology was used to analyze the differentially expressed genes (DEGs) in denervated skeletal muscles. Unsupervised hierarchical clustering of DEGs was performed. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was used to analyze the DEGs. Results Results showed that 2,749 transcripts were up-regulated, and 2,941 transcripts were down-regulated in denervated tibialis anterior (TA) muscles after 14 days of denervation. The up-regulated expressed genes were analyzed through GO and the results demonstrated that biological processes of the up-regulated expressed genes included apoptotic process, cellular response to DNA damage stimulus, aging, and protein ubiquitination; the cellular component of the up-regulated expressed genes included cytoplasm, cytoskeleton, and nucleus; and the molecular function of the up-regulated expressed genes included ubiquitin-protein transferase activity and hydrolase activity. The KEGG pathway of the up-regulated expressed genes included ubiquitin mediated proteolysis, Fc gamma R-mediated phagocytosis, and transforming growth factor-beta (TGF-β) signaling pathway. The biological processes of the down-regulated expressed genes included angiogenesis, tricarboxylic acid cycle, adenosine triphosphate (ATP) biosynthetic process, muscle contraction, gluconeogenesis; the cellular component of the down-regulated expressed genes included mitochondrion, cytoskeleton, and myofibril; and the molecular function of the down-regulated expressed genes included nicotinamide adenine dinucleotide plus hydrogen (NADH) dehydrogenase (ubiquinone) activity, proton-transporting ATP synthase activity, ATP binding, electron carrier activity, cytochrome-c oxidase activity, and oxidoreductase activity. The KEGG pathway of the down-regulated expressed genes included oxidative phosphorylation, tricarboxylic acid cycle, glycolysis/gluconeogenesis, and the PI3K-Akt signaling pathway. Conclusions A huge number of DEGs were identified in TA muscles after denervation. The up-regulated expressed genes mainly involve in proteolysis, apoptosis, and ageing. The down-regulated expressed genes mainly involve in energy metabolism, angiogenesis, and protein synthesis. This study further enriched the molecular mechanism of denervation-induced muscle atrophy.

Natural pigments, including carotenoids, flavonoids and anthocyanidins, determine the attractive color of fruits. These natural pigments are essential secondary metabolites, which play multiple roles in the whole life cycle of plants and are characterized by powerful antioxidant activity. After decades of research and development, multiple benefits of these natural pigments to human health have been explored and recognized and have shown bright application prospects in food, medicine, cosmetics and other industries. In this paper, the research progress of natural fruit pigments in recent years was reviewed, including the structural characteristics and classification, distribution in fruits and analysis methods, biosynthetic process, antioxidant capacity and mechanism, bioaccessibility and bioavailability, and health benefits. Overall, this paper summarizes the recent advances in antioxidant activity and other biological functions of natural fruit pigments, which aims to provide guidance for future research.

Enrofloxacin is widely used for the prevention and control of bacterial diseases in aquaculture. The liver is crucial for enrofloxacin metabolism, but enrofloxacin can induce liver damage. Herein, we explored proteomic changes in the liver of grass carp (Ctenopharyngodon idellus) following treatment with enrofloxacin using isobaric tag for relative and absolute quantitation (iTRAQ) technology. All experiments included two biological replicates and blank controls. Among the 3082 proteins identified, 103 were differentially abundant, comprising 49 up- and 54 downregulated proteins. Gene Ontology (GO) annotation identified macromolecular complex (63.60%), intracellular non-membrane-bound organelle (51.50%), and non-membrane-bound organelle (51.50%) as the most enriched cellular component terms. Structural molecule activity (26.80%), structural constituent of ribosome (17.90%), and calcium ion binding (16.10%) were the top three molecular function terms. Organic substance biosynthetic process (37.80%), biosynthetic process (37.80%), and protein metabolic process (37.80%) were the top three biological process terms. The Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis found 17 enriched KEGG pathways, with protein digestion and absorption, extracellular matrix (ECM)–receptor interactions, and ribosome and focal adhesion the most significant (p

Background RNA-binding proteins (RBPs) are well known as key factors in gene expression regulation in eukaryotes. These proteins associate with mRNAs and other proteins to form mRNP complexes that ultimately determine the fate of target transcripts in the cell. This association is usually mediated by an RNA-recognition motif (RRM). In the case of trypanosomatids, these proteins play a paramount role, as gene expression regulation is mostly posttranscriptional. Despite their relevance in the life cycle of Trypanosoma cruzi, the causative agent of Chagas’ disease, to date, few RBPs have been characterized in this parasite. Results We investigated the role of DRBD2 in T. cruzi, an RBP with two RRM domains that is associated with cytoplasmic translational complexes. We show that DRBD2 is an ortholog of the Gbp2 in yeast, an SR-rich protein involved in mRNA quality control and export. We used an immunoprecipitation assay followed by shotgun proteomics and RNA-seq to assess the interaction partners of the DRBD2-mRNP complex in epimastigotes. The analysis identified mostly proteins involved in RNA metabolism and regulation, such as ALBA1, ALBA3, ALBA4, UBP1, UBP2, DRBD3, and PABP2. The RNA-seq results showed that most of the transcripts regulated by the DRBD2 complex mapped to hypothetical proteins related to multiple processes, such as to biosynthetic process, DNA metabolic process, protein modification, and response to stress. Conclusions The identification of regulatory proteins in the DRBD2-mRNP complex corroborates the important role of DRBD2 in gene expression regulation in T. cruzi. We consider these results an important contribution to future studies regarding gene expression regulation in T. cruzi, especially in the field of RNA-binding proteins. Electronic supplementary material The online version of this article (10.1186/s12866-019-1505-8) contains supplementary material, which is available to authorized users.

This paper is aimed at reviewing the application of biological extracts from plants, fungi and bacteria in the synthesis of metal/metal oxide nanoparticles with reference to Ag and TiO2 nanoparticles as a case study. The procedures for the extraction of the biological extracts as well as the chemical instrumentation analysis of the extracts and metal/metal oxide nanoparticles were explained in this review. It was reported that standard chemical test confirms the presence of tannins, alkanoids, flavonoids and terpenoids in various plant extracts, while FTIR characterization of various biological extracts confirms the presence of organic compounds as a capping and reducing agents in the biosynthetic process for the preparation of the nanoparticles. The use of other instrumental techniques such as FESEM, XRD, SEM, EDX, TEM and UV-Visible spectroscopy in the characterization of biosynthesized metal/metal oxide nanoparticles were also explained in this review.

Background Starch is a complex branched glucose polymer, mainly comprising amylose and amylopectin. The number of individual chains as a function of the number of monomer units they contain, i.e. the chain-length distributions (CLDs), are controlled by the underlying biosynthetic process occurring during plant growth. CLDs are currently commonly related to biosynthetic processes and to functional properties by dividing into arbitrarily chosen regions. However, this empiricism is not completely satisfactory: conclusions can depend on the choice of division. Biosynthesis-based models replacing this arbitrary division by model-based parameterization have been developed, but are presently rarely used, because of the complex underlying mathematics. Scope and approach These models are summarized in non-mathematical language. These give information on the biosynthetic processes producing the starch, and yield a parameterization of CLD data to give a fit that is essentially the same as experiment. Additionally, the models are sufficiently flexible that they can also fit data for modified starches. This enables the whole CLDs for both amylose and amylopectin as a small number of parameters which can be used to find statistically-valid structure-property relations. Key findings and conclusions The underlying theory and data-fitting methodology can be used both to better understand starch biosynthesis, to see what structural features control functional properties and to deduce mechanisms for observed correlations. This enables raw materials to be chosen in non-empirical ways to select and process grains and other starch sources for improved foods and other products.

Nitric oxide (NO) has wide-ranging roles in biology, but less is known about its role in building chemical diversity. Here we report a new route to NO from the biosynthetic pathway to the N-nitroso compound streptozocin. We show that the N-nitroso group of streptozocin comes from the biosynthetic reassembly of l-arginine, with the guanidino nitrogens forming a nitrogen–nitrogen bond. To understand this biosynthetic process, we identify the biosynthetic gene cluster of streptozocin and demonstrate that free l-arginine is N-methylated by StzE to give Nω-monomethyl-l-arginine. We show that this product is then oxidized by StzF, a nonheme iron-dependent enzyme unrelated to known nitric oxide synthases, generating a urea compound and NO. Our work implies that formation and capture of NO is the likely route to N-nitroso formation in vivo. Altogether, our work unveils a new enzyme pair for the production of NO from l-arginine and sets the stage for understanding biosynthetic routes to N-nitroso natural products.

A unique thermostable amylosucrase from Bifidobacterium thermophilum was produced as a recombinant protein with the half-life of 577 h at 50 °C. By adding 1.0 M fructose, turanose yield was improved from 22.7% to 43.3% with 1.0 M sucrose, and from 23.7% to 39.4% with 1.5 M sucrose. Sucrose consumption rate was greatest at 55 °C, but the lowest amount of turanose was produced. Thus, turanose yield from sucrose biomass was inversely proportional to reaction temperature and was highly dependent on [fructose]. Meanwhile, insoluble α-glucan yield was clearly reduced as [fructose] increased. With 1.0 M fructose + 1.0 M sucrose, glucan byproduct yield significantly decreased from 29.4% to 1.1%. Molecular weights of linear glucans were almost identical among various [sucrose]s and were homogenous with very low polydispersity. This unique dual reaction patterns of amylosucrase enzyme would be very useful for massive productions of two different biomaterials simply by changing sucrose biomass concentration.

Paper description: Chrysanthemum morifolium cv. ‘Huaihuang’ is a medicinal plant of China with a huge medicinal and commercial value. Limited genomic and transcriptional information restricts further research on the biosynthesis of active components, its genetic background and evolutionary origin. We performed RNA-Seq, excavated abundant unigenes involved in the biosynthesis of primary active components and developed new EST-SSR markers. This work will contribute to the further clarification of the biosynthetic process of primary active components, it will enrich molecular marker resources and contribute to research of population structure, evolutionary adaptation and genetic breeding in ‘Huaihuang’ and other chrysanthemum species. Abstract : Chrysanthemum morifolium cv. ‘Huaihuang’ has great medicinal and commercial value. However, limited genomic and transcriptional information restricts the further research of ‘Huaihuang’. In this study, using ‘Huaihuang’ leaf as the sample, we performed RNA-Seq and obtained numerous unigene sequences for functional characterization, and developed new EST-SSR markers. The results show that 176 unigenes were assigned to the ‘antioxidant activity’ in GO annotations, 998 unigenes were assigned to ‘Secondary metabolite biosynthesis, transport and catabolism’ in the KOG database, 381 unigenes were assigned to ‘Biosynthesis of other secondary metabolites’, and 377 unigenes were assigned to ‘Metabolism of terpenoids and polyketides’ in the KEGG database. A number of genes involved in the biosynthesis of flavones and terpenes, such as CHS , CHI , FLS , HMGR and MVD , were found in the transcription data of ‘Huaihuang’. Also, 36 new polymorphic EST-SSR markers were developed and validated. Using them, the genetic diversity was analyzed and a dendrogram of six clades was constructed among 15 medicinal chrysanthemum varieties. The excavated unigenes and identified new EST-SSR markers will provide useful resources for the study of biosynthesis of active components, genetic diversity analysis, population structure identification and in molecular breeding research of ‘Huaihuang’ and related species. https://doi.org/10.2298/ABS181226032Z Received: December 26, 2018; Revised: April 19, 2019; Accepted: May 17, 2019; Published online: May 29, 2019 How to cite this article: Zhao X, Song L, Ma M, Liu K, Lv M, Zhu Y, Jiang L. RNA-Seq for excavation of genes involved in the biosynthesis of primary active components and identification of new EST-SSR markers in medicinal chrysanthemum. Arch Biol Sci. 2019;71(3):489-500.

This is the first study to report on the biocompatible and immunogenic properties of one-pot synthesised gold and silver nanoparticles (Au@UI and Ag@UI) using the macroalgae Ulva intestinalis (UI). The UI aqueous extract, Au@UI, and Ag@UI were obtained under sterile conditions and fully characterized by UV-vis spectroscopy, TEM, HRTEM, STEM and FTIR spectroscopy. Moreover, for the first time, the composition of carbohydrates in the UI extract has been reported along with the changes observed after nanoparticle synthesis by size exclusion chromatography, in order to investigate their possible role in the biosynthetic process. This study suggested that the polysaccharide fraction of the extract is involved in the formation and stabilization of the nanoparticles. The potential toxicity of the samples was evaluated using different cell lines and the hemocompatibility was tested in mouse erythrocytes. In addition, ROS production, complement activation and cytokine release were evaluated to determine the immunogenicity. The results showed that Au@UI and Ag@UI exhibit good biocompatibility and hemocompatibility, with the exception of Ag@UI nanoparticles at high concentration, which were hemolytic. The samples induced ROS release and complement activation, two key mechanisms in innate immunity. The samples also induced the release of cytokines from Th1 and Th2 profiles, and other cytokines implicated in the activation of the immune system. Au@UI and Ag@UI were biocompatible and preserved the immunostimulant properties of the UI extract. Hence, Au@UI and Ag@UI could be useful as adjuvants in vaccine development and promote a balanced Th1 and Th2 immune response mediated by ROS production, cytokine release and complement activation.