title: Nitrite promotes the growth and decreases the lignin content of indica rice calli: a comprehensive transcriptome analysis of nitrite-responsive genes during in vitro culture of rice.
abstract: As both major macronutrients and signal molecules, nitrogen metabolites, such as nitrate and nitrite, play an important role in plant growth and development. In this study, the callus growth of indica rice cv. 9311 was significantly enhanced by nitrite, whereas the soluble protein content remained unchanged. The deep RNA sequencing technology (RNA-seq) showed that the transcriptional profiles of cv. 9311 calli were significantly changed after adding nitrite to the nitrate-free medium, and these nitrite-responsive genes were involved in a wide range of plant processes, particularly in the secondary metabolite pathways. Interestingly, most of the genes involved in phenylpropanoid-related pathways were coordinately down-regulated by nitrite, such as four cinnamoyl-CoA reductase, and these in turn resulted in the decrease of lignin content of indica calli. Furthermore, several candidate genes related to cell growth or stress responses were identified, such as genes coding for expansins, SMALL AUXIN UP RNA (SAUR) and HSP20s, and these suggested that nitrite could probably serve as a transcriptome signal to enhance the indica calli growth by regulation of various downstream genes expression. This study contributes to a better understanding of the function of nitrite during the process of plant tissue culture and could aid in the application of this technology to improved indica genetic transformation efficiency.
authors.affiliation: State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, China; CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Li
authors.affiliation: State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, China.
authors.forename: Gen
authors.initials: G
authors.lastname: Fang
authors.affiliation: State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, China.
authors.forename: Qingchuan
authors.initials: Q
authors.lastname: Zhao
authors.affiliation: State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Zeng
authors.affiliation: State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, China.
authors.forename: Xuemei
authors.initials: X
authors.lastname: Li
authors.affiliation: State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, China.
authors.forename: Hanyu
authors.initials: H
authors.lastname: Gong
authors.affiliation: State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, China.
authors.forename: Yangsheng
authors.initials: Y
authors.lastname: Li
mesh_terms: D000445:Aldehyde Oxidoreductases / Q000235:genetics / Q000378:metabolism; D003470:Culture Media / Q000737:chemistry; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D050886:HSP20 Heat-Shock Proteins / Q000235:genetics / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D007210:Indoleacetic Acids / Q000378:metabolism; D007527:Isoenzymes / Q000235:genetics / Q000378:metabolism; D008031:Lignin / Q000037:antagonists & inhibitors* / Q000096:biosynthesis; D053858:Metabolic Networks and Pathways / Q000235:genetics; D009573:Nitrites / Q000378:metabolism / Q000494:pharmacology*; D012275:Oryza / Q000187:drug effects* / Q000235:genetics / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D003470:Culture Media; D050886:HSP20 Heat-Shock Proteins; D007210:Indoleacetic Acids; D007527:Isoenzymes; D009573:Nitrites; D010940:Plant Proteins; C095825:expansin protein, plant; D008031:Lignin; D000445:Aldehyde Oxidoreductases; C019904:cinnamoyl CoA reductase
references.citation: Curr Opin Plant Biol. 2010 Jun;13(3):266-73
references.pmid: 20093067
references.citation: New Phytol. 2010 Jul;187(2):273-285
references.pmid: 20642725
references.citation: FEBS Lett. 2004 Aug 13;572(1-3):27-32
references.pmid: 15304319
references.citation: Plant Biotechnol J. 2006 Nov;4(6):575-603
references.pmid: 17309731
references.citation: J Exp Bot. 2011 Feb;62(4):1391-7
references.pmid: 21118821
references.citation: Plant Signal Behav. 2009 Nov;4(11):1028-34
references.pmid: 19838072
references.citation: Proc Natl Acad Sci U S A. 2005 Aug 16;102(33):11940-4
references.pmid: 16091467
references.citation: Plant Cell. 2003 Jun;15(6):1386-98
references.pmid: 12782731
references.citation: Curr Opin Plant Biol. 2008 Oct;11(5):521-9
references.pmid: 18775665
references.citation: Plant J. 2012 Aug;71(4):684-97
references.pmid: 22507274
references.citation: Plant J. 2006 May;46(4):533-48
references.pmid: 16640592
references.citation: Plant Physiol. 2004 Sep;136(1):2483-99
references.pmid: 15375205
references.citation: Plant Physiol. 2003 Jun;132(2):556-67
references.pmid: 12805587
references.citation: Plant Mol Biol. 2013 Jan;81(1-2):105-17
references.pmid: 23131896
references.citation: Planta. 2003 Jun;217(2):218-28
references.pmid: 12783329
references.citation: Plant Cell Rep. 2005 Jan;23(8):540-7
references.pmid: 15309499
references.citation: Plant Cell Rep. 2006 May;25(5):392-402
references.pmid: 16432631
references.citation: Mol Plant Pathol. 2010 Nov;11(6):829-46
references.pmid: 21029326
references.citation: Plant Sci. 2012 Mar;184:112-20
references.pmid: 22284715
references.citation: Trends Plant Sci. 2012 Aug;17(8):458-67
references.pmid: 22658680
references.citation: PLoS One. 2012;7(3):e33278
references.pmid: 22479379
references.citation: PLoS One. 2012;7(2):e30646
references.pmid: 22347394
references.citation: Plant Cell Physiol. 2007 Mar;48(3):484-97
references.pmid: 17289796
references.citation: Nat Rev Genet. 2009 Jan;10(1):57-63
references.pmid: 19015660
references.citation: Protoplasma. 2013 Apr;250(2):631-6
references.pmid: 22878598
references.citation: Plant Physiol. 2007 Dec;145(4):1735-45
references.pmid: 17951451
references.citation: Nat Protoc. 2006;1(6):2796-802
references.pmid: 17406537
references.citation: Bioinformatics. 2010 Jan 1;26(1):136-8
references.pmid: 19855105
references.citation: Plant Physiol. 2004 Sep;136(1):2512-22
references.pmid: 15333754
references.citation: Curr Opin Plant Biol. 2008 Jun;11(3):278-85
references.pmid: 18434238
references.citation: Genomics. 2006 Sep;88(3):360-71
references.pmid: 16707243
references.citation: Mol Plant. 2010 Jan;3(1):2-20
references.pmid: 20035037
references.citation: Plant J. 2012 Jun;70(6):978-90
references.pmid: 22348445
references.citation: Plant Sci. 2011 Sep;181(3):258-68
references.pmid: 21763536
references.citation: Nature. 2005 Aug 11;436(7052):793-800
references.pmid: 16100779
references.citation: Plant Cell. 2000 Aug;12(8):1491-509
references.pmid: 10948265