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Changes of alternative splicing in Arabidopsis thaliana grown under different CO2 concentrations

Huang W, Chen X, Guan Q, Zhong Z, Ma J, Yang B, et al.

Gene, 2019 Mar 20;689:43-50.
PMID: 30528270 DOI: 10.1016/j.gene.2018.11.083

Atmospheric CO2 level is one of the most important factors which affect plant growth and crop production. Although many crucial genes and pathways have been identified in response to atmospheric CO2 changes, the integrated and precise mechanisms of plant CO2 response are not well understood. Alternative splicing (AS) is an important gene regulation process that affects many biological processes in plants. However, the AS pattern changes in plants in response to elevated CO2 levels have not yet been investigated. Here, we used RNA-Seq data of Arabidopsis thaliana grown under different CO2 concentration to analyze the global changes in AS. We found that AS increased with the rise in CO2 concentration. Additionally, we identified 345 differentially expressed (DE) genes and 251 differentially alternative splicing (DAS) genes under the elevated CO2 condition. Moreover, the results showed that the expression of most of the DAS genes did not change significantly, indicating that AS can serve as an independent mechanism for gene regulation in response to elevated CO2. Furthermore, our analysis of function categories revealed that the DAS genes were associated mainly with the stimulus response. Overall, this the first study to explore the changes of AS in plants in response to elevated CO2.
Fulltext Organ-Specific Analysis of Morus alba Using a Gel-Free/Label-Free Proteomic Technique

Zhu W, Zhong Z, Liu S, Yang B, Komatsu S, Ge Z, et al.

Int J Mol Sci, 2019 Jan 16;20(2).
PMID: 30654535 DOI: 10.3390/ijms20020365

Morus alba is an important medicinal plant that is used to treat human diseases. The leaf, branch, and root of Morus can be applied as antidiabetic, antioxidant, and anti-inflammatory medicines, respectively. To explore the molecular mechanisms underlying the various pharmacological functions within different parts of Morus, organ-specific proteomics were performed. Protein profiles of the Morus leaf, branch, and root were determined using a gel-free/label-free proteomic technique. In the Morus leaf, branch, and root, a total of 492, 414, and 355 proteins were identified, respectively, including 84 common proteins. In leaf, the main function was related to protein degradation, photosynthesis, and redox ascorbate/glutathione metabolism. In branch, the main function was related to protein synthesis/degradation, stress, and redox ascorbate/glutathione metabolism. In root, the main function was related to protein synthesis/degradation, stress, and cell wall. Additionally, organ-specific metabolites and antioxidant activities were analyzed. These results revealed that flavonoids were highly accumulated in Morus root compared with the branch and leaf. Accordingly, two root-specific proteins named chalcone flavanone isomerase and flavonoid 3,5-hydroxylase were accumulated in the flavonoid pathway. Consistent with this finding, the content of the total flavonoids was higher in root compared to those detected in branch and leaf. These results suggest that the flavonoids in Morus root might be responsible for its biological activity and the root is the main part for flavonoid biosynthesis in Morus.
Fulltext Transcriptional regulation of Lonicera japonica Thunb. during flower development as revealed by comprehensive analysis of transcription factors

Wang T, Yang B, Guan Q, Chen X, Zhong Z, Huang W, et al.

BMC Plant Biol, 2019 May 14;19(1):198.
PMID: 31088368 DOI: 10.1186/s12870-019-1803-1

BACKGROUND: Lonicera japonica Thunb. flower has been used for the treatment of various diseases for a long time and attracted many studies on its potential effects. Transcription factors (TFs) regulate extensive biological processes during plant development. As the restricted reports of L. japonica on TFs, our work was carried out to better understand the TFs' regulatory roles under different developmental stages in L. japonica.
RESULTS: In this study, 1316 TFs belonging to 52 families were identified from the transcriptomic data, and corresponding expression profiles during the L. japonica flower development were comprehensively analyzed. 917 (69.68%) TFs were differentially expressed. TFs in bHLH, ERF, MYB, bZIP, and NAC families exhibited obviously altered expression during flower growth. Based on the analysis of differentially expressed TFs (DETFs), TFs in MYB, WRKY, NAC and LSD families that involved in phenylpropanoids biosynthesis, senescence processes and antioxidant activity were detected. The expression of MYB114 exhibited a positive correlation with the contents of luteoloside; Positive correlation was observed among the expression of MYC12, chalcone synthase (CHS) and flavonol synthase (FLS), while negative correlation was observed between the expression of MYB44 and the synthases; The expression of LSD1 was highly correlated with the expression of SOD and the total antioxidant capacity, while the expression of LOL1 and LOL2 exhibited a negative correlation with them; Many TFs in NAC and WRKY families may be potentially involved in the senescence process regulated by hormones and reactive oxygen species (ROS). The expression of NAC19, NAC29, and NAC53 exhibited a positive correlation with the contents of ABA and H2O2, while the expression of WRKY53, WRKY54, and WRKY70 exhibited a negative correlation with the contents of JA, SA and ABA.
CONCLUSIONS: Our study provided a comprehensive characterization of the expression profiles of TFs during the developmental stages of L. japonica. In addition, we detected the key TFs that may play significant roles in controlling active components biosynthesis, antioxidant activity and flower senescence in L. japonica, thereby providing valuable insights into the molecular networks underlying L. japonica flower development.
Molecular Characterization of a Geranyl Diphosphate-Specific Prenyltransferase Catalyzing Stilbenoid Prenylation from Morus alba

Zhong Z, Zhu W, Liu S, Guan Q, Chen X, Huang W, et al.

Plant Cell Physiol, 2018 Nov 01;59(11):2214-2227.
PMID: 30020500 DOI: 10.1093/pcp/pcy138

Pharmaceutically active compounds from medical plants are attractive as a major source for new drug development. Prenylated stilbenoids with increased lipophilicity are valuable secondary metabolites which possess a wide range of biological activities. So far, many prenylated stilbenoids have been isolated from Morus alba but the enzyme responsible for the crucial prenyl modification remains unknown. In the present study, a stilbenoid-specific prenyltransferase (PT), termed Morus alba oxyresveratrol geranyltransferase (MaOGT), was identified and functionally characterized in vitro. MaOGT recognized oxyresveratrol and geranyl diphosphate (GPP) as natural substrates, and catalyzed oxyresveratrol prenylation. Our results indicated that MaOGT shared common features with other aromatic PTs, e.g. multiple transmembrane regions, conserved functional domains and targeting to plant plastids. This distinct PT represents the first stilbenoid-specific PT accepting GPP as a natural prenyl donor, and could help identify additional functionally varied PTs in moraceous plants. Furthermore, MaOGT might be applied for high-efficiency and large-scale prenylation of oxyresveratrol to produce bioactive compounds for potential therapeutic applications.
Sodium butyrate reduces ammonia emissions through glutamate metabolic pathways in cecal microorganisms of laying hens

Zhong Z, Wang C, Zhang H, Mi J, Liang JB, Liao X, et al.

Ecotoxicol Environ Saf, 2022 Feb 14;233:113299.
PMID: 35176673 DOI: 10.1016/j.ecoenv.2022.113299

Ammonia emission is an important problem that needs to be solved in laying hen industries. Sodium butyrate (SB) is considered to have potential for reducing ammonia production because of its ability to improve nitrogen metabolism. In this in vitro fermentation study, we presented a correlation analysis of the metatranscriptome and metaproteome of lay hen cecal microorganisms, in order to identify important proteins and pathways involved in ammonia production reduction due to sodium butyrate supplementation. The results showed that sodium butyrate supplement decreased the production of ammonia by 26.22% as compared with the non-sodium butyrate supplementation (CK) group. The SB group exhibited a lower concentration of ammonium nitrogen (NH4+-N) and a decreased pH. Sodium butyrate promoted the uric acid concentration and lowered the uricase activity in the fermentation broth of laying hens cecal content. Notably, the 'alanine, aspartate and glutamate metabolism' category was more abundant in the SB group. The addition of sodium butyrate increased the expression of glutamate dehydrogenase (GDH) gene in cecal microbiota (e.g., Ruminococcus sp. and Bacteroides sp.) in vitro. The metaproteome analysis results showed that the expression of GDH with NADPH as coenzyme (NADPH-GDH) was up-regulated in cecal microbiota by sodium butyrate supplement. Our results indicate that sodium butyrate can affect glutamate metabolism through regulating the expression of glutamate dehydrogenase in cecal microorganisms, thereby reducing ammonia production. This study reveals that glutamate dehydrogenase-mediated glutamate metabolism play a key role in ammonia emission reduction in laying hen and provide theoretical basis for further developing ammonia production reduction approach.
The Effect of Cyclosporin A on Aspergillus niger and the Possible Mechanisms Involved

Li F, Lv Z, Zhong Z, Mao L, Chua LS, Xu L, et al.

Foods, 2023 Jan 28;12(3).
PMID: 36766095 DOI: 10.3390/foods12030567

Aspergillus niger is one of the major pathogenic fungi causing postharvest grape decay. The development of antifungal agents is beneficial to reduce the loss of grapes during storage. The aim of this study was to investigate the antifungal mechanism of cyclosporin A (CsA). It was indicated that the rot development on grapes caused by A. niger was almost completely inhibited with CsA in vivo at a concentration of 200 mg/L. The transcriptomic analysis revealed that the expression levels of genes involved in rRNA processing and ribosome biogenesis were down-regulated, whereas those related to β-glucosidases and chitinases were up-regulated. The results implied that CsA may disturb rRNA and ribosome formation to obstruct protein synthesis, accelerate chitin and glucan degradation to destruct cell walls, and ultimately reduce postharvest decay caused by A. niger in grapes. This study evaluated the potential of CsA as a grape preservative and provided new insights into the mechanisms underlying the molecular response in A. niger with the treatment of CsA.
Fulltext Comparative Proteomic Analysis Reveals Elevated Capacity for Photosynthesis in Polyphenol Oxidase Expression-Silenced Clematis terniflora DC. Leaves

Chen X, Yang B, Huang W, Wang T, Li Y, Zhong Z, et al.

Int J Mol Sci, 2018 Dec 05;19(12).
PMID: 30563128 DOI: 10.3390/ijms19123897

Polyphenol oxidase (PPO) catalyzes the o-hydroxylation of monophenols and oxidation of o-diphenols to quinones. Although the effects of PPO on plant physiology were recently proposed, little has been done to explore the inherent molecular mechanisms. To explore the in vivo physiological functions of PPO, a model with decreased PPO expression and enzymatic activity was constructed on Clematis terniflora DC. using virus-induced gene silencing (VIGS) technology. Proteomics was performed to identify the differentially expressed proteins (DEPs) in the model (VC) and empty vector-carrying plants (VV) untreated or exposed to high levels of UV-B and dark (HUV-B+D). Following integration, it was concluded that the DEPs mainly functioned in photosynthesis, glycolysis, and redox in the PPO silence plants. Mapman analysis showed that the DEPs were mainly involved in light reaction and Calvin cycle in photosynthesis. Further analysis illustrated that the expression level of adenosine triphosphate (ATP) synthase, the content of chlorophyll, and the photosynthesis rate were increased in VC plants compared to VV plants pre- and post HUV-B+D. These results indicate that the silence of PPO elevated the plant photosynthesis by activating the glycolysis process, regulating Calvin cycle and providing ATP for energy metabolism. This study provides a prospective approach for increasing crop yield in agricultural production.
Fulltext Draft Genomes of Anopheles cracens and Anopheles maculatus: Comparison of Simian Malaria and Human Malaria Vectors in Peninsular Malaysia

Lau YL, Lee WC, Chen J, Zhong Z, Jian J, Amir A, et al.

PLoS One, 2016;11(6):e0157893.
PMID: 27347683 DOI: 10.1371/journal.pone.0157893

Anopheles cracens has been incriminated as the vector of human knowlesi malaria in peninsular Malaysia. Besides, it is a good laboratory vector of Plasmodium falciparum and P. vivax. The distribution of An. cracens overlaps with that of An. maculatus, the human malaria vector in peninsular Malaysia that seems to be refractory to P. knowlesi infection in natural settings. Whole genome sequencing was performed on An. cracens and An. maculatus collected here. The draft genome of An. cracens was 395 Mb in size whereas the size of An. maculatus draft genome was 499 Mb. Comparison with the published Malaysian An. maculatus genome suggested the An. maculatus specimen used in this study as a different geographical race. Comparative analyses highlighted the similarities and differences between An. cracens and An. maculatus, providing new insights into their biological behavior and characteristics.
Fulltext Platanosides, a Potential Botanical Drug Combination, Decrease Liver Injury Caused by Acetaminophen Overdose in Mice

Samuvel DJ, Nguyen NT, Jaeschke H, Lemasters JJ, Wang X, Choo YM, et al.

J Nat Prod, 2022 Jul 22;85(7):1779-1788.
PMID: 35815804 DOI: 10.1021/acs.jnatprod.2c00324

Oxidative stress plays an important role in acetaminophen (APAP)-induced hepatotoxicity. Platanosides (PTSs) isolated from the American sycamore tree (Platanus occidentalis) represent a potential new four-molecule botanical drug class of antibiotics active against drug-resistant infectious disease. Preliminary studies have suggested that PTSs are safe and well tolerated and have antioxidant properties. The potential utility of PTSs in decreasing APAP hepatotoxicity in mice in addition to an assessment of their potential with APAP for the control of infectious diseases along with pain and pyrexia associated with a bacterial infection was investigated. On PTS treatment in mice, serum alanine aminotransferase (ALT) release, hepatic centrilobular necrosis, and 4-hydroxynonenal (4-HNE) were markedly decreased. In addition, inducible nitric oxide synthase (iNOS) expression and c-Jun-N-terminal kinase (JNK) activation decreased when mice overdosed with APAP were treated with PTSs. Computational studies suggested that PTSs may act as JNK-1/2 and Keap1-Nrf2 inhibitors and that the isomeric mixture could provide greater efficacy than the individual molecules. Overall, PTSs represent promising botanical drugs for hepatoprotection and drug-resistant bacterial infections and are effective in protecting against APAP-related hepatotoxicity, which decreases liver necrosis and inflammation, iNOS expression, and oxidative and nitrative stresses, possibly by preventing persistent JNK activation.
Fulltext First-line erlotinib versus gemcitabine/cisplatin in patients with advanced EGFR mutation-positive non-small-cell lung cancer: analyses from the phase III, randomized, open-label, ENSURE study

Wu YL, Zhou C, Liam CK, Wu G, Liu X, Zhong Z, et al.

Ann Oncol, 2015 Sep;26(9):1883-1889.
PMID: 26105600 DOI: 10.1093/annonc/mdv270

BACKGROUND: The phase III, randomized, open-label ENSURE study (NCT01342965) evaluated first-line erlotinib versus gemcitabine/cisplatin (GP) in patients from China, Malaysia and the Philippines with epidermal growth factor receptor (EGFR) mutation-positive non-small-cell lung cancer (NSCLC).
PATIENTS AND METHODS: Patients ≥18 years old with histologically/cytologically confirmed stage IIIB/IV EGFR mutation-positive NSCLC and Eastern Cooperative Oncology Group performance status 0-2 were randomized 1:1 to receive erlotinib (oral; 150 mg once daily until progression/unacceptable toxicity) or GP [G 1250 mg/m(2) i.v. days 1 and 8 (3-weekly cycle); P 75 mg/m(2) i.v. day 1, (3-weekly cycle) for up to four cycles]. Primary end point: investigator-assessed progression-free survival (PFS). Other end points include objective response rate (ORR), overall survival (OS), and safety.
RESULTS: A total of 217 patients were randomized: 110 to erlotinib and 107 to GP. Investigator-assessed median PFS was 11.0 months versus 5.5 months, erlotinib versus GP, respectively [hazard ratio (HR), 0.34, 95% confidence interval (CI) 0.22-0.51; log-rank P < 0.0001]. Independent Review Committee-assessed median PFS was consistent (HR, 0.42). Median OS was 26.3 versus 25.5 months, erlotinib versus GP, respectively (HR, 0.91, 95% CI 0.63-1.31; log-rank P = .607). ORR was 62.7% for erlotinib and 33.6% for GP. Treatment-related serious adverse events (AEs) occurred in 2.7% versus 10.6% of erlotinib and GP patients, respectively. The most common grade ≥3 AEs were rash (6.4%) with erlotinib, and neutropenia (25.0%), leukopenia (14.4%), and anemia (12.5%) with GP.
CONCLUSION: These analyses demonstrate that first-line erlotinib provides a statistically significant improvement in PFS versus GP in Asian patients with EGFR mutation-positive NSCLC (NCT01342965).

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