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Zhang Q, Zhang C, Zhong H, He Q, Xia ZY, Hu Y, Liao YX, Yi L, Lu ZJ, Yu HZ. A Combinatorial Single-Molecule Real-Time and Illumina Sequencing Analysis of Postembryonic Gene Expression in the Asian Citrus Psyllid Diaphorina citri. INSECTS 2024; 15:391. [PMID: 38921106 PMCID: PMC11203772 DOI: 10.3390/insects15060391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/23/2024] [Accepted: 05/23/2024] [Indexed: 06/27/2024]
Abstract
Huanglongbing (HLB) is a systemic plant disease caused by 'Candidatus Liberibacter asiaticus (CLas)' and transmitted by Diaphorina citri. D. citri acquires the CLas bacteria in the nymph stage and transmits it in the adult stage, indicating that molting from the nymph to adult stages is crucial for HLB transmission. However, the available D. citri reference genomes are incomplete, and gene function studies have been limited to date. In the current research, PacBio single-molecule real-time (SMRT) and Illumina sequencing were performed to investigate the transcriptome of D. citri nymphs and adults. In total, 10,641 full-length, non-redundant transcripts (FLNRTs), 594 alternative splicing (AS) events, 4522 simple sequence repeats (SSRs), 1086 long-coding RNAs (lncRNAs), 281 transcription factors (TFs), and 4459 APA sites were identified. Furthermore, 3746 differentially expressed genes (DEGs) between nymphs and adults were identified, among which 30 DEGs involved in the Hippo signaling pathway were found. Reverse transcription-quantitative PCR (RT-qPCR) further validated the expression levels of 12 DEGs and showed a positive correlation with transcriptome data. Finally, the spatiotemporal expression pattern of genes involved in the Hippo signaling pathway exhibited high expression in the D. citri testis, ovary, and egg. Silencing of the D. citri transcriptional co-activator (DcYki) gene significantly increased D. citri mortality and decreased the cumulative molting. Our results provide useful information and a reliable data resource for gene function research of D. citri.
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Affiliation(s)
- Qin Zhang
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (Q.Z.); (C.Z.); (H.Z.); (Q.H.); (Z.-Y.X.); (Y.H.); (Y.-X.L.); (L.Y.); (Z.-J.L.)
| | - Can Zhang
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (Q.Z.); (C.Z.); (H.Z.); (Q.H.); (Z.-Y.X.); (Y.H.); (Y.-X.L.); (L.Y.); (Z.-J.L.)
| | - Hong Zhong
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (Q.Z.); (C.Z.); (H.Z.); (Q.H.); (Z.-Y.X.); (Y.H.); (Y.-X.L.); (L.Y.); (Z.-J.L.)
| | - Qing He
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (Q.Z.); (C.Z.); (H.Z.); (Q.H.); (Z.-Y.X.); (Y.H.); (Y.-X.L.); (L.Y.); (Z.-J.L.)
| | - Zhao-Ying Xia
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (Q.Z.); (C.Z.); (H.Z.); (Q.H.); (Z.-Y.X.); (Y.H.); (Y.-X.L.); (L.Y.); (Z.-J.L.)
| | - Yu Hu
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (Q.Z.); (C.Z.); (H.Z.); (Q.H.); (Z.-Y.X.); (Y.H.); (Y.-X.L.); (L.Y.); (Z.-J.L.)
| | - Yu-Xin Liao
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (Q.Z.); (C.Z.); (H.Z.); (Q.H.); (Z.-Y.X.); (Y.H.); (Y.-X.L.); (L.Y.); (Z.-J.L.)
| | - Long Yi
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (Q.Z.); (C.Z.); (H.Z.); (Q.H.); (Z.-Y.X.); (Y.H.); (Y.-X.L.); (L.Y.); (Z.-J.L.)
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou 341000, China
| | - Zhan-Jun Lu
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (Q.Z.); (C.Z.); (H.Z.); (Q.H.); (Z.-Y.X.); (Y.H.); (Y.-X.L.); (L.Y.); (Z.-J.L.)
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou 341000, China
| | - Hai-Zhong Yu
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (Q.Z.); (C.Z.); (H.Z.); (Q.H.); (Z.-Y.X.); (Y.H.); (Y.-X.L.); (L.Y.); (Z.-J.L.)
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou 341000, China
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Deng Y, Wang R, Zhang Y, Li J, Gooneratne R. Effect of Amino Acids on Fusarium oxysporum Growth and Pathogenicity Regulated by TORC1- Tap42 Gene and Related Interaction Protein Analysis. Foods 2023; 12:foods12091829. [PMID: 37174368 PMCID: PMC10177761 DOI: 10.3390/foods12091829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Free amino acids (AAs) formed in fermented meat products are important nitrogen sources for the survival and metabolism of contaminating fungi. These AAs are mainly regulated by the TORC1-Tap42 signaling pathway. Fusarium spp., a common contaminant of fermented products, is a potential threat to food safety. Therefore, there is an urgent need to clarify the effect of different AAs on Fusarium spp. growth and metabolism. This study investigated the effect of 18 AAs on Fusarium oxysporum (Fo17) growth, sporulation, T-2 toxin (T-2) synthesis and Tri5 expression through Tap42 gene regulation. Co-immunoprecipitation and Q Exactive LC-MS/MS methods were used to detect the interacting protein of Tap42 during specific AA treatment. Tap42 positively regulated L-His, L-Ile and L-Tyr absorption for Fo17 colony growth. Acidic (L-Asp, L-Glu) and sulfur-containing (L-Cys, L-Met) AAs significantly inhibited the Fo17 growth which was not regulated by Tap42. The L-Ile and L-Pro addition significantly activated the sporulation of ΔFoTap42. L-His and L-Ser inhibited the sporulation of ΔFoTap42. In T-2 synthesis, ΔFoTap42 was increased in GYM medium, but was markedly inhibited in L-Asp and L-Glu addition groups. Dose-response experiments showed that 10-70 mg/mL of neutral AA (L-Thr) and alkaline AA (L-His) significantly increased the T-2 production and Tri5 expression of Fo17, but Tri5 expression was not activated in ΔFoTap42. Inhibition of T-2 synthesis and Tri5 expression were observed in Fo17 following the addition of 30-70 mg/mL L-Asp. KEGG enrichment pathway analysis demonstrated that interacting proteins of Tap42 were from glycerophospholipid metabolism, pentose phosphate pathway, glyoxylate and dicarboxylate metabolism, glycolysis and gluconeogenesis, and were related to the MAPK and Hippo signaling pathways. This study enhanced our understanding of AA regulation in fermented foods and its effect on Fusarium growth and metabolism, and provided insight into potential ways to control fungal contamination in high-protein fermented foods.
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Affiliation(s)
- Yijia Deng
- College of Food Science, Southwest University, Chongqing 400715, China
- College of Food Science and Engineering, Bohai University, Jinzhou 121013, China
| | - Rundong Wang
- College of Food Science, Southwest University, Chongqing 400715, China
- College of Food Science and Engineering, Bohai University, Jinzhou 121013, China
| | - Yuhao Zhang
- College of Food Science, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing 400715, China
| | - Jianrong Li
- College of Food Science and Engineering, Bohai University, Jinzhou 121013, China
| | - Ravi Gooneratne
- Department of Wine, Food and Molecular Biosciences, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
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Wei Y, Zhou X, Chen P, Jiang X, Jiang Z, Dong Z, Pan M, Lu C. BmCDK5 Affects Cell Proliferation and Cytoskeleton Morphology by Interacting with BmCNN in Bombyx mori. INSECTS 2022; 13:insects13070609. [PMID: 35886785 PMCID: PMC9323621 DOI: 10.3390/insects13070609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 02/04/2023]
Abstract
The ordered cell cycle is important to the proliferation and differentiation of living organisms. Cyclin-dependent kinases (CDKs) perform regulatory functions in different phases of the cell cycle process to ensure order. We identified a homologous gene of the Cyclin-dependent kinase family, BmCDK5, in Bombyx mori. BmCDK5 contains the STKc_CDK5 domain. The BmCDK5 gene was highly expressed in S phase. Overexpression of the BmCDK5 gene accelerates the process of the cell cycle's mitotic period (M) and promotes cell proliferation; knocking out the BmCDK5 gene inhibited cell proliferation. Furthermore, we identified a protein, BmCNN, which can interact with BmCDK5 and represents the same express patterns as the BmCDK5 gene in the cell cycle phase and the spatial-temporal expression of B. mori. This study revealed that BmCDK5 and BmCNN play roles in promoting cell proliferation and regulating cytoskeleton morphology, but do not induce expression changes in microtubule protein. Therefore, our findings provide a new insight; the BmCDK5 gene has a regulatory effect on the cell cycle and proliferation of B. mori, which is presumably due to the interaction between BmCDK5 and BmCNN regulating changes in the cytoskeleton.
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Affiliation(s)
- Yi Wei
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; (Y.W.); (X.Z.); (P.C.); (X.J.); (Z.J.); (Z.D.)
| | - Xiaolin Zhou
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; (Y.W.); (X.Z.); (P.C.); (X.J.); (Z.J.); (Z.D.)
| | - Peng Chen
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; (Y.W.); (X.Z.); (P.C.); (X.J.); (Z.J.); (Z.D.)
- Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing 400716, China
| | - Xia Jiang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; (Y.W.); (X.Z.); (P.C.); (X.J.); (Z.J.); (Z.D.)
| | - Ziyi Jiang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; (Y.W.); (X.Z.); (P.C.); (X.J.); (Z.J.); (Z.D.)
| | - Zhanqi Dong
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; (Y.W.); (X.Z.); (P.C.); (X.J.); (Z.J.); (Z.D.)
- Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing 400716, China
| | - Minhui Pan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; (Y.W.); (X.Z.); (P.C.); (X.J.); (Z.J.); (Z.D.)
- Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing 400716, China
- Correspondence: (M.P.); (C.L.); Tel.: +86-23-6825-0076 (M.P.); Fax: 86-23-6825-1128 (M.P.)
| | - Cheng Lu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; (Y.W.); (X.Z.); (P.C.); (X.J.); (Z.J.); (Z.D.)
- Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing 400716, China
- Correspondence: (M.P.); (C.L.); Tel.: +86-23-6825-0076 (M.P.); Fax: 86-23-6825-1128 (M.P.)
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Zhang Z, Ji M, Li J, Wu Q, Huang Y, He G, Xu J. Molecular Classification Based on Prognostic and Cell Cycle-Associated Genes in Patients With Colon Cancer. Front Oncol 2021; 11:636591. [PMID: 33898311 PMCID: PMC8059408 DOI: 10.3389/fonc.2021.636591] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/11/2021] [Indexed: 01/27/2023] Open
Abstract
The molecular classification of patients with colon cancer is inconclusive. The gene set enrichment analysis (GSEA) of dysregulated genes among normal and tumor tissues indicated that the cell cycle played a crucial role in colon cancer. We performed univariate Cox regression analysis to find out the prognostic-related genes, and these genes were then intersected with cell cycle-associated genes and were further recognized as prognostic and cell cycle-associated genes. Unsupervised non-negative matrix factorization (NMF) clustering was performed based on cell cycle-associated genes. Two subgroups were identified with different overall survival, clinical features, cell cycle enrichment profile, and mutation profile. Through nearest template prediction (NTP), the molecular classification could be effectively repeated in the original data set and validated in several independent data sets indicating that the classification is highly repeatable. Furthermore, we constructed two prognostic signatures in two subgroups, respectively. Our molecular classification based on cell cycle may provide novel insight into the treatment and the prognosis of colon cancer.
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Affiliation(s)
- Zhiyuan Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Meiling Ji
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jie Li
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qi Wu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuanjian Huang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Guodong He
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jianmin Xu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
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