RNA-Seq reveals the key pathways and genes involved in the light-regulated flavonoids biosynthesis in mango (Mangifera indica L.) peel

IntroductionFlavonoids are important water soluble secondary metabolites in plants, and light is one of the most essential environmental factors regulating flavonoids biosynthesis. In the previous study, we found bagging treatment significantly inhibited the accumulation of flavonols and anthocyanins but promoted the proanthocyanidins accumulation in the fruit peel of mango (Mangifera indica L.) cultivar ‘Sensation’, while the relevant molecular mechanism is still unknown.MethodsIn this study, RNA-seq was conducted to identify the key pathways and genes involved in the light-regulated flavonoids biosynthesis in mango peel.ResultsBy weighted gene co-expression network analysis (WGCNA), 16 flavonoids biosynthetic genes were crucial for different flavonoids compositions biosynthesis under bagging treatment in mango. The higher expression level of LAR (mango026327) in bagged samples might be the reason why light inhibits proanthocyanidins accumulation in mango peel. The reported MYB positively regulating anthocyanins biosynthesis in mango, MiMYB1, has also been identified by WGCNA in this study. Apart from MYB and bHLH, ERF, WRKY and bZIP were the three most important transcription factors (TFs) involved in the light-regulated flavonoids biosynthesis in mango, with both activators and repressors. Surprisingly, two HY5 transcripts, which are usually induced by light, showed higher expression level in bagged samples.DiscussionOur results provide new insights of the regulatory effect of light on the flavonoids biosynthesis in mango fruit peel

Nicotinamide Mononucleotide Administration Amends Protein Acetylome of Aged Mouse Liver

It is known that the activities of nicotine adenine dinucleotide (NAD+)-dependent deacetylase decline in the aging mouse liver, and nicotinamide mononucleotide (NMN)-mediated activation of deacetylase has been shown to increase healthspans. However, age-induced changes of the acetylomic landscape and effects of NMN treatment on protein acetylation have not been reported. Here, we performed immunoprecipitation coupled with label-free quantitative LC-MS/MS (IPMS) to identify the acetylome and investigate the effects of aging and NMN on liver protein acetylation. In total, 7773 acetylated peptides assigned to 1997 proteins were commonly identified from young and aged livers treated with vehicle or NMN. The major biological processes associated with proteins exhibiting increased acetylation from aged livers were oxidation-reduction and metabolic processes. Proteins with decreased acetylation from aged livers mostly participated in transport and translation processes. Furthermore, NMN treatment inhibited the aging-related increase of acetylation on proteins regulating fatty acid β oxidation, the tricarboxylic acid (TCA) cycle and valine degradation. In particular, NAD (P) transhydrogenase (NNT) was markedly hyperacetylated at K70 in aged livers, and NMN treatment decreased acetylation intensity without altering protein levels. Acetylation at cytochrome 3a25 (Cyp3a25) at K141 was also greatly increased in aged livers, and NMN treatment totally arrested this increase. Our extensive identification and analysis provide novel insight and potential targets to combat aging and aging-related functional decline

Genome-Wide Identification and Expression Analysis of <i>WRKY</i> Genes during Anthocyanin Biosynthesis in the Mango (<i>Mangifera indica</i> L.)

The WRKY family is one of the largest transcription factor (TF) families in plants and is involved in the regulation of plant physiological processes, such as anthocyanin accumulation. However, little information is known regarding the WRKY genes in the mango. In this study, a total of 87 mango WRKY genes were identified and named MiWRKY1 to MiWRKY87. Phylogenetic results showed that the 87 MiWRKYs could be divided into three groups (I, II, III) and five subgroups of group II (II-a, II-b, II-c, II-d, II-e), with high similarity in exon–intron structures and WRKY domain and motif compositions within the same group and subgroup. One tandem duplication (MiWRKY76 and MiWRKY82) and 97 pairs of segmental duplicates were identified in the mango genome. Syntenic analysis showed that mango MiWRKY genes had 52 and 69 orthologous pairs with Arabidopsis and citrus, respectively. Promoter cis-acting element analysis revealed that MiWRKYs contain a large number of elements associated with light signaling, hormonal response, environmental stress, and plant development. Tissue specific expression profiles showed that the expression of MiWRKY genes displayed tissue preference. Quantitative-PCR analysis showed that high expression levels of MiWRKY1, MiWRKY3, MiWRKY5, MiWRKY81, and MiWRKY84 were detected in the skin of red mango cultivar, and the expressions of MiWRKY1 and MiWRKY81 were up-regulated during light-induced anthocyanin accumulation in the mango, indicating these genes might regulate anthocyanin biosynthesis in the mango. This study provides comprehensive genetic information on the MiWRKYs in mango fruit

High VHL Expression Reverses Warburg Phenotype and Enhances Immunogenicity in Kidney Tumor Cells

Clear cell renal cell carcinoma (ccRCC) is a frequently occurring renal cancer. The Von Hippel-Lindau disease tumor suppressor VHL, a known tumor suppressor gene, is frequently mutated in about 50% of patients with ccRCC. However, it is unclear whether VHL influences the progression of ccRCC tumors expressing wild-type VHL. In the present study, we found that higher expression of VHL was correlated with the better disease-free survival (DFS) in ccRCC patients using The Cancer Genome Atlas (TCGA) datasets. We revealed that VHL overexpression in ccRCC cells inhibited epithelial-mesenchymal transition (EMT), sterol regulatory element-binding protein 1 (SREBP1)-regulated triglyceride synthesis, and cell proliferation. Proteomic analysis provided us a global view that VHL regulated four biological processes, including metabolism, immune regulation, apoptosis, and cell movement. Importantly, we found that VHL overexpression led to up-regulated expression of proteins associated with antigen processing and interferon-responsive proteins, thus rendering ccRCC cells more sensitive to interferon treatment. We defined an interferon-responsive signature (IRS) composed of ten interferon-responsive proteins, whose mRNA expression levels were positively correlated with DFS in ccRCC patients. Taken together, our results propose that the subset of ccRCC patients with high VHL expression benefit from immunotherapy

Data from: Ancient DNA provides new insight into the maternal lineages and domestication of Chinese donkeys

Background: The donkey (Equus asinus) is an important domestic animal that provides a reliable source of protein and method of transportation for many human populations. However, the process of domestication and the dispersal routes of the Chinese donkey are still unclear, as donkey remains are sparse in the archaeological record and often confused with horse remains. To explore the maternal origins and dispersal route of Chinese donkeys, both mitochondrial DNA D-loop and cytochrome b gene fragments of 21 suspected donkey remains from four archaeological sites in China were amplified and sequenced.Results: Molecular methods of species identification show that 17 specimens were donkeys and three samples had the maternal genetic signature of horses. One sample that dates to about 20,000 years before present failed to amplify. In this study, the phylogenetic analysis reveals that ancient Chinese donkeys have high mitochondrial DNA diversity and two distinct mitochondrial maternal lineages, known as the Somali and Nubian lineages. These results indicate that the maternal origin of Chinese domestic donkeys was probably related to the African wild ass, which includes the Nubian wild ass (Equus africanus africanus) and the Somali wild ass (Equus africanus somaliensis). Combined with historical records, the results of this study implied that domestic donkeys spread into west and north China before the emergence of the Han dynasty. The number of Chinese domestic donkeys had increased primarily to meet demand for the expansion of trade, and they were likely used as commodities or for shipping goods along the Silk Road during the Tang Dynasty, when the Silk Road reached its golden age. Conclusions: This study is the first to provide valuable ancient animal DNA evidence for early trade between African and Asian populations. The ancient DNA analysis of Chinese donkeys also sheds light on the dynamic process of the maternal origin, domestication, and dispersal route of ancient Chinese donkeys

Halo- and Thiocarbazomycins from Coral- and Coral Reef Sands-Derived Actinomycetes

Four actinomycete strains isolated from the coral Acropora austera and coral sand samples from the South China Sea, were found to produce a series of halogenated compounds baring similar ultraviolet absorption based on the analysis of HPLC and LC-MS. The production titers of halogenated compounds from Streptomyces diacarni SCSIO 64983 exceeded those of other similar strains leading us to focus on SCSIO 64983. Four new thiocarbazomycins A&ndash;B (1&ndash;2), chlocarbazomycin E (3), and brocarbazomycin A (4), together with three known chlocarbazomycins A&ndash;C (5&ndash;7) containing a carbazole core were identified, and their structures were determined using a combination of spectroscopic analysis including HRESIMS, 1D and 2D NMR. Structurally speaking, compounds 1 and 2 have the rare sulfur-containing carbazole nuclei, and 3 and 4 contain Cl and Br atoms, respectively. Although these compounds have not yet been found to have obvious biological activity, their discovery highlights the role of molecular libraries in subsequent drug discovery campaigns

Data from: Ancient DNA provides new insight into the maternal lineages and domestication of Chinese donkeys

Background: The donkey (Equus asinus) is an important domestic animal that provides a reliable source of protein and method of transportation for many human populations. However, the process of domestication and the dispersal routes of the Chinese donkey are still unclear, as donkey remains are sparse in the archaeological record and often confused with horse remains. To explore the maternal origins and dispersal route of Chinese donkeys, both mitochondrial DNA D-loop and cytochrome b gene fragments of 21 suspected donkey remains from four archaeological sites in China were amplified and sequenced.Results: Molecular methods of species identification show that 17 specimens were donkeys and three samples had the maternal genetic signature of horses. One sample that dates to about 20,000 years before present failed to amplify. In this study, the phylogenetic analysis reveals that ancient Chinese donkeys have high mitochondrial DNA diversity and two distinct mitochondrial maternal lineages, known as the Somali and Nubian lineages. These results indicate that the maternal origin of Chinese domestic donkeys was probably related to the African wild ass, which includes the Nubian wild ass (Equus africanus africanus) and the Somali wild ass (Equus africanus somaliensis). Combined with historical records, the results of this study implied that domestic donkeys spread into west and north China before the emergence of the Han dynasty. The number of Chinese domestic donkeys had increased primarily to meet demand for the expansion of trade, and they were likely used as commodities or for shipping goods along the Silk Road during the Tang Dynasty, when the Silk Road reached its golden age. Conclusions: This study is the first to provide valuable ancient animal DNA evidence for early trade between African and Asian populations. The ancient DNA analysis of Chinese donkeys also sheds light on the dynamic process of the maternal origin, domestication, and dispersal route of ancient Chinese donkeys

Proteomic profiling of IgA nephropathy reveals distinct molecular prognostic subtypes

Summary: IgA nephropathy (IgAN) is a heterogeneous disease, which poses a series of challenges to accurate diagnosis and personalized therapy. Herein, we constructed a systematic quantitative proteome atlas from 59 IgAN and 19 normal control donors. Consensus sub-clustering of proteomic profiles divided IgAN into three subtypes (IgAN-C1, C2, and C3). IgAN-C2 had similar proteome expression patterns with normal control, while IgAN-C1/C3 exhibited higher level of complement activation, more severe mitochondrial injury, and significant extracellular matrix accumulation. Interestingly, the complement mitochondrial extracellular matrix (CME) pathway enrichment score achieved a high diagnostic power to distinguish IgAN-C2 from IgAN-C1/C3 (AUC>0.9). In addition, the proteins related to mesangial cells, endothelial cells, and tubular interstitial fibrosis were highly expressed in IgAN-C1/C3. Most critically, IgAN-C1/C3 had a worse prognosis compared to IgAN-C2 (30% eGFR decline, p = 0.02). Altogether, we proposed a molecular subtyping and prognostic system which could help to understand IgAN heterogeneity and improve the treatment in the clinic