Integrative Analyses of Biochemical Properties and Transcriptome Reveal the Dynamic Changes in Leaf Senescence of Tobacco ( L.)

Overview

Journal Front Genet

Date 2022 Jan 10

PMID 35003224

Authors

Binghui Zhang

Jiahan Yang

Gang Gu

Liao Jin

Chengliang Chen

Zhiqiang Lin

Jiangyu Song

Xiaofang Xie

Affiliations

Soon will be listed here.

Abstract

Leaf senescence is an important process of growth and development in plant, and it is a programmed decline controlled by a series of genes. In this study, the biochemical properties and transcriptome at five maturity stages (M1∼M5) of tobacco leaves were analyzed to reveal the dynamic changes in leaf senescence of tobacco. A total of 722, 1,534, 3,723, and 6,933 genes were differentially expressed (DEG) between M1 and M2, M1 and M3, M1 and M4, and M1 and M5, respectively. Significant changes of nitrogen, sugars, and the DEGs related to metabolite accumulation were identified, suggesting the importance of energy metabolism during leaf senescence. Gene Ontology (GO) analysis found that DEGs were enriched in biosynthetic, metabolic, photosynthesis, and redox processes, and especially, the nitrogen metabolic pathways were closely related to the whole leaf senescence process (M1∼M5). All the DEGs were grouped into 12 expression profiles according to their distinct expression patterns based on Short Time-series Expression Miner (STEM) software analysis. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis found that these DEGs were enriched in pathways of carbon metabolism, starch and sucrose metabolism, nitrogen metabolism, and photosynthesis among these expression profiles. A total of 30 core genes were examined by Weight Gene Co-expression Network Analysis (WGCNA), and they appeared to play a crucial role in the regulatory of tobacco senescence. Our results provided valuable information for further functional investigation of leaf senescence in plants.

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References

Chen W, Provart N, Glazebrook J, Katagiri F, Chang H, Eulgem T . Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses. Plant Cell. 2002; 14(3):559-74. PMC: 150579. DOI: 10.1105/tpc.010410. View

Trapnell C, Williams B, Pertea G, Mortazavi A, Kwan G, van Baren M . Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010; 28(5):511-5. PMC: 3146043. DOI: 10.1038/nbt.1621. View

Gan S, Amasino R . Making Sense of Senescence (Molecular Genetic Regulation and Manipulation of Leaf Senescence). Plant Physiol. 1997; 113(2):313-319. PMC: 158144. DOI: 10.1104/pp.113.2.313. View

Kong X, Luo Z, Dong H, Eneji A, Li W, Lu H . Gene expression profiles deciphering leaf senescence variation between early- and late-senescence cotton lines. PLoS One. 2013; 8(7):e69847. PMC: 3726770. DOI: 10.1371/journal.pone.0069847. View

Moriya Y, Itoh M, Okuda S, Yoshizawa A, Kanehisa M . KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 2007; 35(Web Server issue):W182-5. PMC: 1933193. DOI: 10.1093/nar/gkm321. View

Pourtau N, Jennings R, Pelzer E, Pallas J, Wingler A . Effect of sugar-induced senescence on gene expression and implications for the regulation of senescence in Arabidopsis. Planta. 2006; 224(3):556-68. DOI: 10.1007/s00425-006-0243-y. View

Rogers H . Is there an important role for reactive oxygen species and redox regulation during floral senescence?. Plant Cell Environ. 2011; 35(2):217-33. DOI: 10.1111/j.1365-3040.2011.02373.x. View

Conesa A, Gotz S, Garcia-Gomez J, Terol J, Talon M, Robles M . Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005; 21(18):3674-6. DOI: 10.1093/bioinformatics/bti610. View

Ougham H, Hortensteiner S, Armstead I, Donnison I, King I, Thomas H . The control of chlorophyll catabolism and the status of yellowing as a biomarker of leaf senescence. Plant Biol (Stuttg). 2008; 10 Suppl 1:4-14. DOI: 10.1111/j.1438-8677.2008.00081.x. View

10.

Liu Y, Wang L, Liu H, Zhao R, Liu B, Fu Q . The antioxidative defense system is involved in the premature senescence in transgenic tobacco (Nicotiana tabacum NC89). Biol Res. 2016; 49(1):30. PMC: 4930573. DOI: 10.1186/s40659-016-0088-1. View

11.

Li W, Guo Y . RNA-Seq Analysis of the Transcriptome of Leaf Senescence in Tobacco. Methods Mol Biol. 2018; 1744:331-337. DOI: 10.1007/978-1-4939-7672-0_27. View

12.

Qi T, Wang J, Huang H, Liu B, Gao H, Liu Y . Regulation of Jasmonate-Induced Leaf Senescence by Antagonism between bHLH Subgroup IIIe and IIId Factors in Arabidopsis. Plant Cell. 2015; 27(6):1634-49. PMC: 4498205. DOI: 10.1105/tpc.15.00110. View

13.

Jibran R, Hunter D, Dijkwel P . Hormonal regulation of leaf senescence through integration of developmental and stress signals. Plant Mol Biol. 2013; 82(6):547-61. DOI: 10.1007/s11103-013-0043-2. View

14.

He Y, Gan S . A gene encoding an acyl hydrolase is involved in leaf senescence in Arabidopsis. Plant Cell. 2002; 14(4):805-15. PMC: 150683. DOI: 10.1105/tpc.010422. View

15.

Fujiki Y, Yoshikawa Y, Sato T, Inada N, Ito M, Nishida I . Dark-inducible genes from Arabidopsis thaliana are associated with leaf senescence and repressed by sugars. Physiol Plant. 2001; 111(3):345-352. DOI: 10.1034/j.1399-3054.2001.1110312.x. View

16.

Lim P, Woo H, Nam H . Molecular genetics of leaf senescence in Arabidopsis. Trends Plant Sci. 2003; 8(6):272-8. DOI: 10.1016/S1360-1385(03)00103-1. View

17.

Lim P, Kim H, Nam H . Leaf senescence. Annu Rev Plant Biol. 2006; 58:115-36. DOI: 10.1146/annurev.arplant.57.032905.105316. View

18.

Masclaux C, Valadier M, Brugiere N, Morot-Gaudry J, Hirel B . Characterization of the sink/source transition in tobacco ( Nicotiana tabacum L.) shoots in relation to nitrogen management and leaf senescence. Planta. 2000; 211(4):510-8. DOI: 10.1007/s004250000310. View

19.

Gregersen P, Holm P . Transcriptome analysis of senescence in the flag leaf of wheat (Triticum aestivum L.). Plant Biotechnol J. 2007; 5(1):192-206. DOI: 10.1111/j.1467-7652.2006.00232.x. View

20.

Gregersen P, Holm P, Krupinska K . Leaf senescence and nutrient remobilisation in barley and wheat. Plant Biol (Stuttg). 2008; 10 Suppl 1:37-49. DOI: 10.1111/j.1438-8677.2008.00114.x. View