Cross-species network analysis uncovers conserved nitrogen-regulated network modules in rice

Plant Physiology

Volumn 168, Issue 4, 2015, Pages 1830-1843

  Obertello, Mariana ^a,b   Shrivastava, Stuti ^a   Katari, Manpreet S ^a   Coruzzi, Gloria M ^a  

^a NEW YORK UNIVERSITY   (United States)

^b INSTITUTO DE INVESTIGACIONES EN INGENIERÍA GENÉTICA Y BIOLOGÍA MOLECULAR   (Argentina)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA; ORYZA SATIVA;

ARABIDOPSIS PROTEIN; BASIC LEUCINE ZIPPER TRANSCRIPTION FACTOR; HRS1 PROTEIN, ARABIDOPSIS; NITROGEN; PLANT PROTEIN; PROTEIN BINDING; TRANSCRIPTION FACTOR;

ARABIDOPSIS; BIOLOGICAL MODEL; CLASSIFICATION; DRUG EFFECTS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; METABOLISM; MUTATION; ORYZA; PHYLOGENY; PLANT ROOT; SHOOT; SPECIES DIFFERENCE; TRANSGENIC PLANT;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; BASIC-LEUCINE ZIPPER TRANSCRIPTION FACTORS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE REGULATORY NETWORKS; MODELS, GENETIC; MUTATION; NITROGEN; ORYZA; PHYLOGENY; PLANT PROTEINS; PLANT ROOTS; PLANT SHOOTS; PLANTS, GENETICALLY MODIFIED; PROTEIN BINDING; SPECIES SPECIFICITY; TRANSCRIPTION FACTORS;

EID: 84939125493     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.114.255877     Document Type: Article

References (55)

1. Alvarez JM, Riveras E, Vidal EA, Gras DE, Contreras-López O, Tamayo KP, Aceituno F, Gómez I, Ruffel S, Lejay L, et al (2014) Systems approach identifies TGA1 and TGA4 transcription factors as important regulatory components of the nitrate response of Arabidopsis thaliana roots. Plant J 80: 1-13
2. Baena-González E, Rolland F, Thevelein JM, Sheen J (2007) A central integrator of transcription networks in plant stress and energy signalling. Nature 448: 938-942
3. Bargmann BO, Marshall-Colon A, Efroni I, Ruffel S, Birnbaum KD, Coruzzi GM, Krouk G (2013) TARGET: a transient transformation system for genome-wide transcription factor target discovery. Mol Plant 6: 978-980
4. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser A Stat Soc 57: 289-300
5. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinformatics 10: 421
6. Canales J, Moyano TC, Villarroel E, Gutiérrez RA (2014) Systems analysis of transcriptome data provides new hypotheses about Arabidopsis root response to nitrate treatments. Front Plant Sci 5: 22
7. Castaings L, Marchive C, Meyer C, Krapp A (2011) Nitrogen signalling in Arabidopsis: how to obtain insights into a complex signalling network. J Exp Bot 62: 1391-1397
8. Chaw SM, Chang CC, Chen HL, Li WH (2004) Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes. J Mol Evol 58: 424-441
9. Cramer M, Lewis OA (1993) The influence of nitrate and ammonium nutrition on the growth of wheat (Triticum aestivum) and maize (Zea mays) plants. Ann Bot (Lond) 72: 359-365
10. Devaiah BN, Karthikeyan AS, Raghothama KG (2007) WRKY75 transcription factor is a modulator of phosphate acquisition and root development in Arabidopsis. Plant Physiol 143: 1789-1801
11. Dharmawardhana P, Ren L, Amarasinghe V, Monaco M, Thomason J, Ravenscroft D, McCouch S, Ware D, Jaiswal P (2013) A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress. Rice (N Y) 6: 15
12. Ding X, Richter T, Chen M, Fujii H, Seo YS, Xie M, Zheng X, Kanrar S, Stevenson RA, Dardick C, et al (2009) A rice kinase-protein interaction map. Plant Physiol 149: 1478-1492
13. Fischer S, Brunk BP, Chen F, Gao X, Harb OS, Iodice JB, Shanmugam D, Roos DS, Stoeckert CJ Jr (2011) Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups. Curr Protoc Bioinformatics Chapter 6: 1-19
14. Forde BG (2014) Glutamate signalling in roots. J Exp Bot 65: 779-787
15. Fried M, Zsoldos F, Vose PB, Shatokhin IL (1965) Characterizing the NO3 and NH4 uptake process of rice roots by use of 15N labelled NH4NO3. Physiol Plant 18: 313-321
16. Gale MD, Devos KM (1998) Plant comparative genetics after 10 years. Science 282: 656-659
17. Gifford ML, Dean A, Gutierrez R, Coruzzi GM, Birnbaum KD (2008) Cell-specific nitrogen responses mediate developmental plasticity. Proc Natl Acad Sci USA 105: 803-808
18. Gu H, Zhu P, Jiao Y, Meng Y, Chen M (2011) PRIN: a predicted rice interactome network. BMC Bioinformatics 12: 161
19. Gutiérrez R, Stokes TL, Thum K, Xu X, Obertello M, Katari MS, Tanurdzic M, Dean A, Nero DC, McClung CR, et al (2008) Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1. Proc Natl Acad Sci USA 105: 4939-4944
20. Hanke GUYT, Okutani S, Satomi Y, Takao T, Suzuki A, Hase T (2005) Multiple iso-proteins of FNR in Arabidopsis: evidence for different contributions to chloroplast function and nitrogen assimilation. Plant Cell Environ 28: 1146-1157
21. Hanson J, Hanssen M, Wiese A, Hendriks MM, Smeekens S (2008) The sucrose regulated transcription factor bZIP11 affects amino acid metabolism by regulating the expression of ASPARAGINE SYNTHETASE1 and PROLINE DEHYDROGENASE2. Plant J 53: 935-949
22. Hiei Y, Komari T (2008) Agrobacterium-mediated transformation of rice using immature embryos or calli induced from mature seed. Nat Protoc 3: 824-834
23. Ho CL, Wu Y, Shen HB, Provart NJ, Geisler M (2012) A predicted protein interactome for rice. Rice (N Y) 5: 15
24. Hollander M, Wolfe D (2014) Nonparametric Statistical Methods. Wiley, New York
25. Hu HC, Wang YY, Tsay YF (2009) AtCIPK8, a CBL-interacting protein kinase, regulates the low-affinity phase of the primary nitrate response. Plant J 57: 264-278
26. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436: 793-800
27. Jin J, Zhang H, Kong L, Gao G, Luo J (2014) PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Res 42: D1182-D1187
28. Jonassen EM, Sévin DC, Lillo C (2009) The bZIP transcription factors HY5 and HYH are positive regulators of the main nitrate reductase gene in Arabidopsis leaves, NIA2, but negative regulators of the nitrate uptake gene NRT1.1. J Plant Physiol 166: 2071-2076
29. Katari MS, Nowicki SD, Aceituno FF, Nero D, Kelfer J, Thompson LP, Cabello JM, Davidson RS, Goldberg AP, Shasha DE, et al (2010) VirtualPlant: a software platform to support systems biology research. Plant Physiol 152: 500-515
30. Kronzucker HJ, Glass AD, Yaeesh Siddiqi M (1999a) Inhibition of nitrate uptake by ammonium in barley: analysis of component fluxes. Plant Physiol 120: 283-292
31. Kronzucker HJ, Siddiqi MY, Glass AD, Kirk GJ (1999b) Nitrate-ammonium synergism in rice: a subcellular flux analysis. Plant Physiol 119: 1041- 1046
32. Krouk G, Mirowski P, LeCun Y, Shasha DE, Coruzzi GM (2010) Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate. Genome Biol 11: R123
33. Krouk G, Tranchina D, Lejay L, Cruikshank AA, Shasha D, Coruzzi GM, Gutiérrez RA (2009) A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis. PLoS Comput Biol 5: e1000326
34. Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, et al (2012) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 40: D1202-D1210
35. Medici A, Marshall-Colon A, Ronzier E, Szponarski W, Wang R, Gojon A, Crawford NM, Ruffel S, Coruzzi GM, Krouk G (2015) AtNIGT1/ HRS1 integrates nitrate and phosphate signals at the Arabidopsis root tip. Nat Commun 6: 6274
36. Murashige T, Skoog F (1962) A revised medium for rapid growth and bio assays with tobacco tissue cultures. Physiol Plant 15: 473-497
37. Obertello M, Krouk G, Katari MS, Runko SJ, Coruzzi GM (2010) Modeling the global effect of the basic-leucine zipper transcription factor 1 (bZIP1) on nitrogen and light regulation in Arabidopsis. BMC Syst Biol 4: 111
38. Palaniswamy SK, James S, Sun H, Lamb RS, Davuluri RV, Grotewold E (2006) AGRIS and AtRegNet: a platform to link cis-regulatory elements and transcription factors into regulatory networks. Plant Physiol 140: 818-829
39. Para A, Li Y, Marshall-Colón A, Varala K, Francoeur NJ, Moran TM, Edwards MB, Hackley C, Bargmann BO, Birnbaum KD, et al (2014) Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis. Proc Natl Acad Sci USA 111: 10371-10376
40. Plant Metabolic Network (2013) Plant Metabolic Network (PMN). http:// pmn.plantcyc.org/ORYZA/class-tree?object=Pathways, on www.plantcyc.org (July 2013)
41. Rohila JS, Chen M, Chen S, Chen J, Cerny R, Dardick C, Canlas P, Fujii H, Gribskov M, Kanrar S, et al (2009) Protein-protein interactions of tandem affinity purified protein kinases from rice. PLoS ONE 4: e6685
42. Rohila JS, Chen M, Chen S, Chen J, Cerny R, Dardick C, Canlas P, Xu X, Gribskov M, Kanrar S, et al (2006) Protein-protein interactions of tandem affinity purification-tagged protein kinases in rice. Plant J 46: 1-13
43. Rubin G, Tohge T, Matsuda F, Saito K, Scheible WR (2009) Members of the LBD family of transcription factors repress anthocyanin synthesis and affect additional nitrogen responses in Arabidopsis. Plant Cell 21: 3567-3584
44. Santi C, Bogusz D, Franche C (2013) Biological nitrogen fixation in nonlegume plants. Ann Bot (Lond) 111: 743-767
45. Sasaki T, Sederoff RR (2003) Genome studies and molecular genetics: the rice genome and comparative genomics of higher plants. Curr Opin Plant Biol 6: 97-100
46. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504
47. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739
48. van Helden J (2003) Regulatory sequence analysis tools. Nucleic Acids Res 31: 3593-3596
49. van Verk MC, Bol JF, Linthorst HJ (2011) WRKY transcription factors involved in activation of SA biosynthesis genes. BMC Plant Biol 11: 89
50. Vidal EA, Tamayo KP, Gutierrez RA (2010) Gene networks for nitrogen sensing, signaling, and response in Arabidopsis thaliana. Wiley Interdiscip Rev Syst Biol Med 2: 683-693
51. Wang R, Guegler K, LaBrie ST, Crawford NM (2000) Genomic analysis of a nutrient response in Arabidopsis reveals diverse expression patterns and novel metabolic and potential regulatory genes induced by nitrate. Plant Cell 12: 1491-1509
52. Wang R, OkamotoM, Xing X, Crawford NM(2003) Microarray analysis of the nitrate response in Arabidopsis roots and shoots reveals over 1,000 rapidly responding genes and new linkages to glucose, trehalose-6- phosphate, iron, and sulfate metabolism. Plant Physiol 132: 556-567
53. Wang R, Tischner R, Gutiérrez RA, Hoffman M, Xing X, Chen M, Coruzzi G, Crawford NM (2004) Genomic analysis of the nitrate response using a nitrate reductase-null mutant of Arabidopsis. Plant Physiol 136: 2512- 2522
54. Yilmaz A, Nishiyama MY Jr, Fuentes BG, Souza GM, Janies D, Gray J, Grotewold E (2009) GRASSIUS: a platform for comparative regulatory genomics across the grasses. Plant Physiol 149: 171-180
55. Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W,Hu S, Zeng C, et al (2005) The genomes of Oryza sativa: a history of duplications. PLoS Biol 3: e38