microRNA-dependent gene regulatory networks in maize leaf senescence

BMC Plant Biology

Volumn 16, Issue 1, 2016, Pages

  Wu, Xiangyuan ^a   Ding, Dong ^a   Shi, Chaonan ^a   Xue, Yadong ^a   Zhang, Zhanhui ^a   Tang, Guiliang ^a,c   Tang, Jihua ^a,b  

^a HENAN AGRICULTURAL UNIVERSITY   (China)

^b YANGTZE UNIVERSITY   (China)

^c MICHIGAN TECHNOLOGICAL UNIVERSITY   (United States)

Author keywords

Deep sequencing; Leaf senescence; Maize; MicroRNAs; Regulatory mechanism

Indexed keywords

MICRORNA; PLANT RNA;

GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; MAIZE; METABOLISM; PHYSIOLOGY; PLANT LEAF; TIME FACTOR;

GENE EXPRESSION REGULATION, PLANT; GENE REGULATORY NETWORKS; MICRORNAS; PLANT LEAVES; RNA, PLANT; TIME FACTORS; ZEA MAYS;

EID: 84962090296     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/s12870-016-0755-y     Document Type: Article

References (50)

1. Khan M, Rozhon W, Poppenberger B. The role of hormones in the aging of plants -Amini-review. Gerontology. 2014;60:49-55.
2. Masclaux-Daubresse C, Reisdorf-Cren M, Orsel M. Leaf nitrogen remobilisation for plant development and grain filling. Plant Biol. 2008;10 Suppl 1:23-36.
3. Zhang Z, Li G, Gao H, Zhang L, Yang C, Liu P, Meng Q. Characterization of photosynthetic performance during senescence in Stay-Green and Quick-Leaf Senescence Zea mays L. inbred lines. PLoS ONE. 2012;7:e42936.
4. Li Z, Zhao Y, Liu X, Peng J, Guo H, Luo J. LSD 2.0: an update of the leaf senescence database. Nucleic Acids Res. 2013;42:D1200-5.
5. Balazadeh S, Riaño-Pachón DM, Mueller-Roeber B. Transcription factors regulating leaf senescence in Arabidopsis thaliana. Plant Biol. 2008;10:63-75.
6. Buchanan-Wollaston V, Page T, Harrison E, Breeze E, Lim PO, Nam HG, Lin JF, Wu SH, Swidzinski J, Ishizaki K. Comparative transcriptome analysis reveals significant differences in gene expression and signaling pathways between developmental and dark/starvation-induced senescence in Arabidopsis. Plant J. 2005;42:567-85.
7. Guo Y, Cai Z, Gan S. Transcriptome of Arabidopsis leaf senescence. Plant Cell Environ. 2004;27:521-49.
8. Li Z, Peng J, Wen X, Guo H. Gene network analysis and functional studies of senescence-associated genes reveal novel regulators of Arabidopsis leaf senescence. J Integr Plant Biol. 2012;54:526-39.
9. Li Z, Peng J, Wen X, Guo H. ETHYLENE-INSENSITIVE3 is a senescence-associated gene that accelerates age-dependent leaf senescence by directly repressing miR164 transcription in Arabidopsis. Plant Cell. 2013;25:3311-28.
10. Tiwari SB. The roles of Auxin response factor domains in Auxin-responsive transcription. Plant Cell. 2003;15:533-43.
11. Choi DS, Hwang BK. Proteomics and functional analyses of pepper abscisic acid-responsive 1 (ABR1), which is involved in cell death and defense signaling. Plant Cell. 2011;23:823-42.
12. Shan X, Wang J, Chua L, Jiang D, Peng W, Xie D. The role of Arabidopsis rubisco activase in jasmonate-induced leaf senescence. Plant Physiol. 2011;155:2751-64.
13. van Verk MC, Bol JF, Linthorst HJ. WRKY transcription factors involved in activation of SA biosynthesis genes. BMC Plant Biol. 2011;11:89.
14. Yang SD, Seo PJ, Yoon HK, Park CM. The Arabidopsis NAC transcription factor VNI2 integrates abscisic acid signals into leaf senescence via the COR/RD genes. Plant Cell. 2011;23:2155-68.
15. Jones-Rhoades MW, Bartel DP, Bartel B. MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol. 2006;57:19-53.
16. Brodersen P, Sakvarelidze AL, Bruun RM, Dunoyer P, Yamamoto YY, Sieburth L, Voinnet O. Widespread translational inhibition by plant miRNAs and siRNAs. Sci Signal. 2008;320:1185-90.
17. Kim JH, Woo HR, Kim J, Lim PO, Lee IC, Choi SH, Hwang D, Nam HG. Trifurcate feed-forward regulation of age-dependent cell death involving miR164 in Arabidopsis. Science. 2009;323:1053-7.
18. Qiu K, Li Z, Yang Z, Chen J, Wu S, Zhu X, Gao S, Gao J, Ren G, Kuai B, Zhou X. EIN3 and ORE1accelerate degreeningduring ethylene-mediated leaf senescence by directly activating Chlorophyll catabolic genes in Arabidopsis. PLoS Genet. 2015;11, e1005399.
19. Koyama T, Furutani M, Tasaka M, Ohme-Takagi M. TCP transcription factors control the morphology of shoot lateral organs via negative regulation of the expression of boundary-specific genes in Arabidopsis. Plant Cell. 2007;19:473-84.
20. Kosugi S, Ohashi Y. DNA binding and dimerization specificity and potential targets for the TCP protein family. The Plant journal. 2002;30:337-48.
21. Palatnik JF, Allen E, Wu X, Schommer C, Schwab R, Carrington JC, Weigel D. Control of leaf morphogenesis by microRNAs. Nature. 2003;425:257-63.
22. Schommer C, Palatnik JF, Aggarwal P, Chetelat A, Cubas P, Farmer EE, Nath U, Weigel D. Control of jasmonate biosynthesis and senescence by miR319 targets. PLoS Biol. 2008;6, e230.
23. Xu X, Bai H, Liu C, Chen E, Chen Q, Zhuang J, Shen B. Genome-wide analysis of microRNAs and their target genes related to leaf senescence of rice. PLoS ONE. 2014;9, e114313.
24. Noode'n LD. Whole plant senescence. In: Noode'n LD, Leopold AC, editors. Senescence and aging in plants. San Diego: AcadPress; 1988a. p. 392-439.
25. Gregersen PL, Holm PB, Krupinska K. Leaf senescence and nutrient remobilisation in barley and wheat. Plant Biol. 2008;10 Suppl 1:37-49.
26. Gregersen PL, Culetic A, Boschian L, Krupinska K. Plant senescence and crop productivity. Plant Mol Biol. 2013;82:603-22.
27. Gut H, Ruts C, Matile P, Thomas H. Leaf senescence in a non-yellowing mutant of Festucapratensis: Degradation of carotenoids. Plant Physiol. 1987;70:659-63.
28. Sekhon RS, Childs KL, Santoro N, Foster CE, Buell CR, de Leon N, Kaeppler SM. Transcriptional and metabolic analysis of senescence induced by preventing pollination in maize. Plant Physiol. 2012;159:1730-44.
29. Stone JM, Walker JC. Plant protein kinase families and signal transduction. Plant Physiol. 1995;108:451-7.
30. Giranton JL, Dumas C, Cock JM, Gaude T. The integral membrane S-locus receptor kinase of Brassica has seringe/threonine kinase activity in a membranous environment and spontaneously forms oligomers in planta. Proc Natl Acad Sci U S A. 2000;97:3759-64.
31. Song WY, Wang GL, Chen LL, Kim HS, Pi LY, Holsten T, Gardner J, Wang B, Zhai WX, Zhu LH, Fauquet C, Ronald P. Areceptor kinase-like protein encoded by the rice disease resistance gene Xa21. Science. 1995;270:1804-6.
32. Hajouj T, Michelis R, Gepstein S. Cloning and characterization of a receptor-like protein kinase gene associated with senescence. Plant Physiol. 2000;124:1305-14.
33. Robatzek S, Somssich E. Targetsof AtWRKY6 regulation during plant senescence and pathogen defense. Genes Dev. 2002;16:1139-49.
34. Li XP, Gan R, Li PL, Ma YY, Zhang LW, Zhang R, Wang Y, Wang NN. Identification and functional characterization of a leucine-rich repeat receptor-like kinase gene that is involved in regulation of soybean leaf senescence. Plant Mol Bio. 2006;l61:829-44.
35. Karlova R, Rosin FM, Busscher-Lange J, Parapunova V, Do PT, Fernie AR, Fraser PD, Baxter C, Angenent GC, de Maagd RA. Transcriptome and metabolite profiling show that APETALA2a is a major regulator of tomato fruit ripening. Plant Cell. 2011;23:923-41.
36. Morcillo F, Gallard A, Pillot M, Jouannic S, Aberlenc-Bertossi F, Collin M, VerdeilJL, TregearJW. EgAP2-1, an AINTEGUMENTA-like (AIL) gene expressed in meristematic and proliferating tissues of embryos in oil palm. Planta. 2007;226:1353-62.
37. Klempnauer KH, Gonda JJ, Bishop JM. Nucleotide sequence of the retroviral leukemia gene v-myb and its cellular progenitor c-myb: the architecture of a transduced oncogene. Cell. 1982;31:453-63.
38. Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C, Lepiniec L. MYB transcription factors in Arabidopsis. Trends Plant Sci. 2010;15:573-81.
39. Huang CK, Lo PC, Huang LF, Wu SJ, Yeh CH, Lu CA. A single-repeat MYB transcription repressor, MYBH, participates in regulation of leaf senescence in Arabidopsis. Plant Mol Biol. 2015;88:269-86.
40. Guo Y, Gan S. AtMYB2 regulates whole plant senescence by inhibiting cytokinin-mediated branching at late stages of development in Arabidopsis. Plant Physiol. 2011;156:1612-9.
41. Khan MS, Hameed W, Nozoe M, Shiina T. Disruption of the psbA gene by the copy correction mechanism reveals that the expression of plastid-encoded genes is regulated by photosynthesis activity. J Plant Res. 2007;120:421-30.
42. Naora H. Involvement of ribosomal proteins in regulating cell growth andapoptosis: translational modulation or recruitment for extraribosomal activity? Immunol Cell Biol. 1999;77:197-205.
43. Wei S, Wang X, Zhang J, Liu P, Zhao B, Li G, Dong S. The role of nitrogen in leaf senescence of summer maize and analysis of underlying mechanisms using comparative proteomics. Plant Sci. 2015;233:72-81.
44. 2 population. Thero Appl Genet. 2010;120:333-40.
45. Shen WQ. Extraction of mixed solution for determination of chlorophyll content in rice leaf blade. Plant Physlology Communication. 1988;3:62-4.
46. Ding D, Li W, Han M, Wang Y, Fu Z, Wang B, Tang J. Identification and characterization of maize microRNAs involved in developing ears. Plant Biol. 2013;16:9-15.
47. Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ. Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr Biol. 2008;8:758-62.
48. Addo-Quaye C, Snyder JA, Park YB, Li YF, Sunkar R, Axtell MJ. Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome. RNA. 2009;15:2112-21.
49. Ma Z, Coruh C, Axtell MJ. Arabidopsis lyrata Small RNAs: Transient MIRNA and Small Interfering RNA Loci within the Arabidopsis Genus. Plant Cell. 2010;22:1090-103.
50. Varkonyi-Gasic E, Wu R, Wood M, Walton EF, Hellens RP. Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs. Plant Methods. 2007;3:12.