BMC PLANT BIOLOGY
·
2025
·Vol. 25
·期 1
·1-20
·
IF 4.8
Sun Meiyu,Han Baocai,Xiao Jianhua,Yu Haiyan,Jia Yinli,Yuan Shuhai,Yao Juan,Xing Quan,Wu Dongqi,Sun Guofeng,Zhang Jinzheng
Background Hemerocallis middendorffii is a kind of high quality ornamental plant with strong cold resistance, pleasant aroma, and gorgeous floral color. Hemerocallis is one of the three internationally recognized perennial flowers that has huge demand in the flower market. However, little is known about the floral scent and color biosynthesis in daylily due to the large genome size. Results We reported here a high-quality chromosome-scale genome of H. middendorffii which was a native daylily in China. Using PacBio HiFi and Hi-C sequencing technologies, we assembled a chromosome-level genome of 4.10 Gb with a contig N50 of 12.81 Mb. We identified 65,536 protein-coding genes across the 11 chromosomes. We employed a combination of genomic, transcriptomic, and metabolomic approaches to investigate mechanisms behind the floral scent and color biosynthesis in daylily. The main terpenoids contributing to floral fragrance were linalool, 3-carene, nerolidol, and α-farnesene, while carotenoids and anthocyanidins were the main components of floral color. These traits could be stably inherited by their hybrid progenies, and some of them exhibited heterosis. Through Weighted Gene Co-expression Network Analysis (WGCNA) analysis, we identified two modules MEblueviolet and MEgreenyellow related to terpenoids (floral scents) and carotenoids (floral colors) biosynthesis. The 10 hub genes including DXS , MVD , MVK , DXR , LCYBs , Z-ISO , CYPs , and JAS were screened by network construction. The results of qRT-PCR analysis showed that these hub genes were significant differentially expressed in daylily samples, and these results were basically consistent with the relative transcript levels of RNA-seq. Conclusions This study not only provides new insights into the molecular mechanisms of floral scent and color, but also lays a foundation for subsequent research on key gene functions and molecular breeding in Hemerocallis .
研究领域:
植物学
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遗传学
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生物化学
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产品关联
DOI
PubMed
高影响因子
CHEMOSPHERE
·
2021
·
IF 7.086
Xiaoning Li,Hailong Liu,Weiben Yang,Hongjie Sheng,Fang Wang,Jean Damascene Harindintwali,H.M.S.K. Herath,Yinping Zhang
The search for nature-based tools to enhance bioremediation is essential for the sustainable restoration of contaminated ecosystems. Humic acid (HA) is an important component of organic matter in soil and water, but its effect on the microbial degradation of organic pollutants remains unclear. In this study, the biodegradation of pyrene by Mycobacterium sp. NJS-1 with and without HA was investigated. Only around 10.5% of pyrene was biodegraded in the pyrene treatment alone, whereas the addition of HA significantly enhanced biodegradation to the point where over 90% of pyrene was biodegraded. The production of 4,5-dihydropyrene-4,5-diol and phenanthrene-3,4-diol indicated the metabolic pathway via attacking of 4,5-positions of pyrene. Interestingly, 1,2-dimethoxypyrene was detected with the addition of HA, suggesting that HA induced a new ring-opening pathway involving the attack on the 1,2-positions of pyrene. The addition of HA first induced protein self-cleavage behavior with a significant increase in phenylalanine , tyrosine, and tryptophan containing large numbers of COO − groups. Furthermore, it altered the intracellular and extracellular ultrastructure of bacterial cells, promoting their growth in size and number as well as reducing the space between them. Overall, HA increased the ring-opening positions of pyrene and facilitated its interaction with bacterial cells, thus improving its biodegradability . Building upon the findings of this study to further research is conducive to the sustainable solution of environmental pollution .
研究领域:
环境科学
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微生物学
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产品关联
DOI
PubMed
高影响因子
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
·
2018
·
IF 2.831
Chuqi Hou,Wenqin Liu,Zhi Liang,Weichao Han,Jinqing Li,Ling Ye,Menghua Liu,Zheng Cai,Jie Zhao,Yi Chen,Shuwen Liu,Lan Tang
Morusin is a prenylated flavone isolated from mulberry, the branch and root bark of various Morus species, which possesses diverse pharmacological activities. However, it lacks extensive studies about its absorption and disposition. This study investigated the pharmacokinetic behavior of morusin in rat, and its first-pass metabolism in situ . The metabolic pathway of morusin was further investigated by 12 human recombinant UDP-glucuronosyltransferases (UGTs), 9 CYP450s, as well as liver and intestinal microsomes. Four mono-glucuronide metabolites (M-5-G, M-4′-G, M-2′-G, and M II-2 ) were identified in rat intestine and bile by LC–MS/MS, while three of them were also detected in plasma (M-5-G, M-4′-G, and M II-2 ). M-4′-G was the principal conjugate. However, few CYP450 metabolites were found in rat intestine and bile. Only a small amount of M I-1 could be detected in rat plasma. UGT1A1, 1A3, 1A7, and 2B7 were the major contributors to morusin glucuronidation. Morusin exhibited substrate inhibition kinetic characteristics in all UGTs. Clearance rates of M-4′-G in HLM, RLM, UGT1A1, UGT1A3, and UGT2B7 were 137.02, 127.55, 32.54, 41.18, and 35.07 ml/min/mg, respectively. Besides, CYP3A5, 3A4, and 2C19 primarily contributed to the oxidative metabolism of morusin. The pharmacokinetic curves of morusin and its conjugates presented double peaks, showing that an enterohepatic recycling may exist. In conclusion, glucuronidation was confirmed to be the crucial metabolic pathway for morusin in vivo , and M-4′-G was the main metabolite.
研究领域:
药理学
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生物化学
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药物代谢
✓ 已验证
DOI
高影响因子
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
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2015
·
IF 3.082
Rui Cai,Yahong Yuan,Zhouli Wang,Chunfeng Guo,Bin Liu,Laping Liu,Yutang Wang,Tianli Yue
Alicyclobacillus acidoterrestris has recently received much attention due to its implication in the spoilage of pasteurized fruit juices, which was manifested by the production of guaiacol. Vanillic acid and vanillin have been accepted as the biochemical precursors of guaiacol in fruit juices. The purpose of this study was to try to find other precursors and elucidate details about the conversion of vanillic acid and vanillin to guaiacol by A . acidoterrestris . Four potential substrates including ferulic acid, catechol, phenylalanine and tyrosine were analyzed, but they could not be metabolized to guaiacol by all the thirty A . acidoterrestris strains tested. Resting cell studies and enzyme assays demonstrated that vanillin was reduced to vanillyl alcohol by NADPH-dependent vanillin reductase and oxidized to vanillic acid by NAD(P) + -dependent vanillin dehydrogenases in A . acidoterrestris DSM 3923. Vanillic acid underwent a nonoxidative decarboxylation to guaiacol. The reversible vanillic acid decarboxylase involved was oxygen insensitive and pyridine nucleotide-independent.
研究领域:
微生物学
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食品科学
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产品关联
DOI
PubMed
高影响因子
BIORESOURCE TECHNOLOGY
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2015
·
IF 4.494
Shengnan Shi,Yuanyuan Qu,Hao Zhou,Qiao Ma,Fang Ma
Arthrobacter sp. W1 was used to characterize the pathways involved in cometabolic degradation of carbazole (CA) with phenol as the primary substrate. To clarify the upper pathway of cometabolic degradation CA, Escherichia coli strain BL21 expressing phenol hydroxylase from strain W1 (PH IND ) was investigated to degrade CA. Firstly, CA was initially monohydroxylated at C-2 and C-4 positions to produce 2- and 4-hydroxycarbazole, followed by successively hydroxylated to the corresponding 1,2- and 3,4-dihydroxycarbazole, of which 3,4-dihydroxycarbazole was unequivocally identified for the first time. To characterize the downstream cometabolic degradation CA pathway, purified 3,4-dihydroxycarbazole was used as the substrate for phenol-grown W1, and a series of novel indole derivatives were identified. These results suggested that a novel pathway of CA catabolism was employed by strain W1 via a successive hydroxylation and meta -cleavage pathway. These findings provide new insights into the cometabolic degradation CA process and have potential applications in biotechnology and bioremediation.
研究领域:
微生物学
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环境科学
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生物技术
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DOI
高影响因子
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
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2015
·
IF 2.729
Xiaolan Zeng,Xuesheng Zhang,Li Qin,Zunyao Wang
The tissue distribution, excretion, and metabolic pathway of 2,2′,4,4′,5-penta-chlorinated diphenylsulfide (CDPS-99) in ICR mice were investigated after oral perfusion at 10 mg/kg body weight (b.w.). Biological samples were extracted and separated and, for the first time, were determined by a novel, sensitive, and specific GC–MS method under the full scan and selected ion monitoring (SIM) modes. The results showed that the concentrations of CDPS-99 in the liver, kidneys, and serum reached a maximum after a one-day exposure and that the CDPS-99 concentration in the liver was the highest (3.43 μg/g). The increase in the concentration of CDPS-99 in muscle, skin, and adipose tissue was slower, and the concentrations of CDPS-99 achieved their highest levels after 3 days of exposure. It was observed that the CDPS-99 concentration in adipose tissue was still very high (0.71 μg/g) after 21 days of exposure, which suggested that CDPS-99 was able to accumulate in adipose tissue. In addition, mouse feces accounted for approximately 75% of the total gavage dose, indicating that CDPS-99 was mainly excreted via mouse feces. Metabolism analysis demonstrated that there were three possible metabolic pathways of CDPS-99 in mice: dechlorination reactions with the formation of tetra-CDPS and hydroxylation and oxidation reactions with the formation of OH-CDPS-99 and chlorinated diphenylsulfone. The present study will help to develop a better understanding of mammalian metabolism of CDPS-99.
研究领域:
环境科学
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毒理学
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分析化学
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产品关联
DOI
PubMed
高影响因子
PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY
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2024
·
IF 4.2
Zhengsheng Mao,Youjia Yu,Gen Ba,Hongmei Zhao,Qifang Shi,Yue Cao,Weiran Xie,Jinsong Zhang,Hao Sun,Feng Chen
Diquat (DQ) poisoning has garnered attention in recent years, primarily due to the rising incidence of cases worldwide, coupled with the absence of a viable antidote for its treatment. Despite the fact that diquat monopyridone (DQ-M) has been identified as a significant metabolite of DQ, the enzyme responsible for its formation remains unknown. In this study, we have identified aldehyde oxidase (AOX) as a vital enzyme involved in DQ oxidative metabolism . The metabolism of DQ to DQ-M was significantly inhibited by AOX inhibitors including raloxifene and hydralazine . The source of oxygen incorporated into DQ-M was proved to be from water through a H2 18 O incubation experiment which further corroborated DQ-M formation via AOX metabolism. The product of DQ-M in vitro generated by fresh rat tissues co-incubation was consistent with its AOX expression. The result of the molecular docking analysis of DQ and AOX protein showed that DQ is capable of binding to AOX. Furthermore, the cytotoxicity of DQ was significantly higher than DQ-M at the same concentration tested in six cell types. This work is the first to uncover the involvement of aldehyde oxidase, a non-cytochrome P450 enzyme, in the oxidative metabolic pathway of diquat, thus providing a potential target for the development of detoxification treatment.
研究领域:
药理学
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毒理学
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产品关联
DOI
PubMed
高影响因子
RSC Advances
·
2019
·Vol. 9
·期 26
·15004-15012
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IF 3.049
Shihan Zhang,Zanyun Ying,Juping You,Jiexu Ye,Zhuowei Cheng,Dongzhi Chen,Jianmeng Chen
A newly isolated strain was identified as Ochrobactrum sp. by 16S rRNA sequence analysis and named as ZJUTCB-1. The strain was able to degrade mono-chlorobenzene (CB) as the sole carbon and energy source under aerobic conditions. This study is the first to report the degradation of CB by the genus Ochrobactrum. The degradation rate of CB reached 170.9 μmol L−1 h−1, which is at least 6 times higher than the previously reported data. The strain can efficiently degrade CB under a rang of temperatures (30–40 °C) and pH (6.0–7.0) with optimum at 40 °C and pH 7.0. Salt concentration higher than 0.05 mol L−1 remarkably reduced the biodegradation capability. Moreover, true oxic condition was not an essential element for biodegradation given that the CB degradation rate of 210.4 μmol L−1 h−1 was obtained under microaerobic condition. Based on the Haldane kinetic model, the maximum specific growth rate was 0.895 h−1, which is the highest in ever described CB-degrading strains. According to GC-MS analysis and enzymatic assay, CB was degraded via the meta-cleavage pathway by using 2,3-dioxygenase and 2-chlorophenol as the main intermediates, producing CO2 and Cl− as the final products. The great performance of CB degradation by Ochrobactrum sp. ZJUTCB-1 provided an alternative for development of more effective and reliable biotreatment process.
研究领域:
环境微生物学
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生物化学
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DOI
PubMed
高影响因子
PEDOSPHERE
·
2024
·
IF 5.2
Yang LIU,Lihua ZHU,Junyuan ZHANG,Zhuo WEI,Xuhan HUANG,Christian E.W. STEINBERG,Hao QIU,Martina G. VIJVER,Jing ZHAO,Willie J.G.M. PEIJNENBURG
Due to the complex composition of biochar and the potential interactions between the components that jointly make up biochar, previous studies have always shown controversial results regarding impacts of biochar on soil phosphorus (P) solubilization. Using a nested experimental design, this study investigated the effects of different components of biochar, i.e. whole biochar (BC), dissolved biochar (DBC) and washed biochar (WBC) on the microbial-mediated P solubilizing process. The growth of Bacillus megaterium , acid/alkaline phosphatase activity, differential metabolites of bacteria and metabolic pathways were measured in treatments with biochar pyrolyzed at 200, 300, 400, 500 and 600 °C. Results showed that BC, DBC and WBC all negatively affected the growth and alkaline phosphatase activity of B. megaterium , and BC500/WBC500 and BC400/WBC400 had the greatest impacts. The negative effects of high-temperature biochar on cell proliferation were caused by persistent free radicals and included down-regulation of histidine metabolism by BC400 and interference in nucleotide metabolism by BC600. The impacts of low-temperature biochar on cell proliferation and alkaline phosphatase activity were highly related to the metal content. Using the independent action model, antagonistic effects were found between DBC and WBC on inhibiting B. megaterium growth, while these biochars had synergistic effects on inhibition of alkaline phosphatase activity. Overall, this study provides insights on how biochar adversely modulates microbial-mediated P solubilization.
研究领域:
环境科学
·
微生物学
✓ 已验证
DOI
高影响因子
Frontiers in Nutrition
·
2025
·
IF 5.1
Xi Che,Yifei Zhao,Yuxiao Wang,Xin Sun,Hongxun Tao,Rentang Zhang
Introduction: Obesity, a growing public health issue, is closely associated with excessive energy intake and gut microbiota imbalances. Despite the increasing attention given to black jujube as a blackened fermented food in recent years, the role of its melanoidins (MLD) in obesity-related biological mechanisms has yet to be thoroughly investigated.Methods: This study investigated the effects of black jujube MLD on obesity induced by a high-fat diet in C57BL/6J mice. We hypothesize that MLD exerts an anti-obesity effect, potentially mediated by alterations in gut microbiota composition and the modulation of metabolic responses.Results: The results demonstrate that MLD administration mitigated HFD-induced weight gain, improved insulin resistance, and enhanced glucose metabolism by reducing blood glucose and insulin levels (p < 0.05). MLD also protected the liver, as evidenced by a 16.4% decrease in alanine aminotransferase (ALT) levels and a 29.6% decrease in aspartate aminotransferase (AST) levels (p < 0.05). Furthermore, MLD treatment restored the compromised intestinal microbiota to a healthier state at the genus level by lowering the Firmicutes/Bacteroidetes ratio (38.9%), suppressing the abundance of pathogenic bacteria, such as Erysipelatoclostridium and Bacteroides descendants, and promoting the growth of beneficial bacteria, including Bifidobacterium and norank_f_Muribaculaceae. Metabolomic profiling revealed that MLD can alleviate metabolic disorders by downregulating arginine metabolism and sphingolipid metabolism. Its metabolites are significantly correlated with several bacterial genera, including Bacteroides, Roseburia, Erysipelatoclostridium, Bacteroides, norank_f_Muribaculaceae, and Lachnospiraceae NK4A136 group.Discussion: Based on these findings, MLD may mitigate obesity and other associated metabolic disorders by modulating the gut microbiome–metabolism axis.
研究领域:
营养学
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微生物学
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代谢组学
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产品关联
DOI
PubMed
高影响因子
PLoS Genetics
·
2025
·Vol. 21
·期 5
·e1011704
·
IF 3.7
Zhiming Liu,Gang Du,Yi Chen,Haiyang Chen
The decline in adult stem cell performance is closely linked to tissue malfunction and the rising incidence of age-related diseases. To investigate the molecular basis of these impairments, our screening strategy identified reduced activity in the pantothenate/coenzyme A (CoA) pathway within aged ISCs. Furthermore, exogenous CoA supplementation restructured ISC metabolic pathways, reversing age-induced hyperproliferation and intestinal dysfunction, and thus extending Drosophila lifespan by curbing excessive iron accumulation in ISCs. These findings uncover a new mechanism of stem cell aging and propose that pantothenate and CoA could be potential therapeutic targets for treating age-related diseases and enhancing healthy aging in humans.
In our study, we explored the connection between the aging of adult stem cells and the rise of age-related diseases, uncovering a significant metabolic link. As stem cells age, a key metabolic pathway involving pantothenate and CoA becomes less active, leading to an accumulation of excess iron, which disrupts cellular function and contributes to the aging process. To counteract this decline, we added pantothenate and CoA to the aging stem cells, restoring their normal function, reducing iron buildup, and ultimately improving the health and lifespan of old fruit flies. This simple intervention not only highlights the potential of pantothenate and CoA as powerful tools to combat the effects of aging but also suggests broader implications for treating age-related diseases and promoting healthy aging in humans. Our findings provide a new perspective on the biology of aging and open up exciting new avenues for therapeutic interventions that could improve the quality of life for older individuals.
研究领域:
细胞生物学
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分子生物学
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衰老研究
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营养学
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产品关联
DOI
PubMed
高影响因子
CHEMOSPHERE
·
2020
·
IF 5.778
Tianli Tong,Ruili Li,Jianfei Chen,Yanchu Ke,Shuguang Xie
Bisphenol A (BPA) is one of the widely detected endocrine disrupting chemicals in coastal sediment . Biodegradation is a vital pathway of BPA elimination in sediment. However, the impact of vegetation on BPA degradation in coastal sediment is still unclear. In this study, the differences of BPA biodegradation and the functional microbial community and metabolic pathway were explored between mangrove forest and mudflat sediments. A nearly complete BPA attenuation was detected in 4 days in mudflat sediment but 8 days in forest sediment. Bacterial abundance varied greatly in different sediment types. Bacterial community structure changed with BPA biodegradation, dependent on sediment type. During the degradation, the proportions of Alphaproteobacteria and Gammaproteobacteria were higher in BPA amended microcosms than in un-amended microcosms. With BPA biodegradation, a substantial increase in Novosphingobium and Croceicoccus occurred in forest sediment and mudflat sediment, respectively. Additionally, two divergent BPA biodegradation pathways were proposed based on functional annotation and KEGG pathway database. The abundance of functional genes also varied with BPA biodegradation, dependent on sediment type. Gene pcaGH decreased, while genes ligK and pcaD increased in both sediment types. Gene pcaB showed a remarkable increase in forest sediment but a decrease in mudflat sediment. Therefore, BPA degradation and the associated microbial community and metabolic pathway differed between mudflat and mangrove forest sediments.
研究领域:
环境科学
·
微生物学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
危险品化学品经营许可证（带存储）