Abstract
Auxin response factor (ARF) and Auxin/INDOLE-3-ACETIC ACID (Aux/IAA) proteins are the foremost regulators of auxin action and play an essential role in the coordination of many aspects of plant growth and development. Though many members of both ARF and Aux/IAA gene families have been identified and characterized in tomato, they are less studied in other Solanaceae species. In the present study, we focused on gaining insights into their functional conservation as well as diversification during auxin-mediated responses in Solanaceae. First, we identified their full complement in tomato, potato, pepper, Nicotiana benthamiana, eggplant, and petunia and found that both the gene families have expanded in N. benthamiana. We also looked into the structural variations associated with all the members of these two classes of genes in tomato and showed that huge natural variation exists in their sequence in wild relatives. The comprehensive gene expression analysis provided evidence of high conservation in the expression of orthologous ARFs and Aux/IAAs during fruit development and ripening in tomato and pepper. Furthermore, the molecular changes caused by exogenous plant hormones and abiotic stress conditions on their transcript levels were investigated which showed that many members of both the gene families may participate in various hormone- and stress-mediated responses in tomato and potato. Some of these genes may play a role in linking the hormone-controlled plant growth and stress-related signaling pathways. Finally, we demonstrate that single tomato ARF can interact with multiple Aux/IAA proteins and vice versa. Overall, our study will be very helpful in establishing both conserved as well as non-conserved functions of these genes in Solanaceae.
Similar content being viewed by others
References
Abel S, Theologis A (1996) Early genes and auxin action. Plant Physiol 111:9–17
Abel S, Oeller PW, Theologis A (1994) Early auxin-induced genes encode short-lived nuclear proteins. Proc Natl Acad Sci U S A 91:326–330
Abel S, Nguyen MD, Chow W, Theologis A (1995) ACS4, a primary indoleacetic acid-responsive gene encoding 1-aminocyclopropane-1-carboxylate synthase in Arabidopsis thaliana. Structural characterization, expression in Escherichia coli, and expression characteristics in response to auxin. J Biol Chem 270:19093–19099
Audran-Delalande C, Bassa C, Mila I, Regad F, Zouine M, Bouzayen M (2012) Genome-wide identification, functional analysis and expression profiling of the Aux/IAA gene family in tomato. Plant Cell Physiol 53:659–672
Bari R, Jones JD (2009) Role of plant hormones in plant defence responses. Plant Mol Biol 69:473–488. doi:10.1007/s11103-008-9435-0
Bassa C, Mila I, Bouzayen M, Audran-Delalande C (2012) Phenotypes associated with down-regulation of Sl-IAA27 support functional diversity among Aux/IAA family members in tomato. Plant Cell Physiol 53:1583–1595. doi:10.1093/pcp/pcs101
Bhalerao RP, Eklof J, Ljung K, Marchant A, Bennett M, Sandberg G (2002) Shoot-derived auxin is essential for early lateral root emergence in Arabidopsis seedlings. Plant J 29:325–332
Bombarely A, Rosli HG, Vrebalov J, Moffett P, Mueller LA, Martin GB (2012) A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research. Mol Plant Microbe Interact 25:1523–1530. doi:10.1094/MPMI-06-12-0148-TA
Chaabouni S, Jones B, Delalande C, Wang H, Li Z, Mila I, Frasse P, Latche A, Pech JC, Bouzayen M (2009) Sl-IAA3, a tomato Aux/IAA at the crossroads of auxin and ethylene signalling involved in differential growth. J Exp Bot 60:1349–1362. doi:10.1093/jxb/erp009
Chapman EJ, Estelle M (2009) Mechanism of auxin-regulated gene expression in plants. Annu Rev Genet 43:265–285. doi:10.1146/annurev-genet-102108-134148
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. doi:10.1007/s00239-003-2564-9
Chitwood DH, Maloof JN, Sinha NR (2013) Dynamic transcriptomic profiles between tomato and a wild relative reflect distinct developmental architectures. Plant Physiol 162:537–552. doi:10.1104/pp. 112.213546
Clarkson JJ, Lim KY, Kovarik A, Chase MW, Knapp S, Leitch AR (2005) Long-term genome diploidization in allopolyploid Nicotiana section Repandae (Solanaceae). New Phytol 168:241–252. doi:10.1111/j.1469-8137.2005.01480.x
de Jong M, Wolters-Arts M, Feron R, Mariani C, Vriezen WH (2009) The Solanum lycopersicum auxin response factor 7 (SlARF7) regulates auxin signaling during tomato fruit set and development. Plant J 57:160–170. doi:10.1111/j.1365-313X.2008.03671.x
Deng W, Yang Y, Ren Z, Audran-Delalande C, Mila I, Wang X, Song H, Hu Y, Bouzayen M, Li Z (2012) The tomato SlIAA15 is involved in trichome formation and axillary shoot development. New Phytol 194:379–390. doi:10.1111/j.1469-8137.2012.04053.x
Dharmasiri N, Dharmasiri S, Estelle M (2005a) The F-box protein TIR1 is an auxin receptor. Nature 435:441–445. doi:10.1038/nature03543
Dharmasiri N, Dharmasiri S, Weijers D, Lechner E, Yamada M, Hobbie L, Ehrismann JS, Jurgens G, Estelle M (2005b) Plant development is regulated by a family of auxin receptor F box proteins. Dev Cell 9:109–119. doi:10.1016/j.devcel.2005.05.014
Ghanashyam C, Jain M (2009) Role of auxin-responsive genes in biotic stress responses. Plant Signal Behav 4:846–848
Gray WM, Kepinski S, Rouse D, Leyser O, Estelle M (2001) Auxin regulates SCF(TIR1)-dependent degradation of AUX/IAA proteins. Nature 414:271–276. doi:10.1038/3510450035104500
Guillon F, Philippe S, Bouchet B, Devaux M-F, Frasse P, Jones B, Bouzayen M, Lahaye M (2008) Down-regulation of an Auxin Response Factor in the tomato induces modification of fine pectin structure and tissue architecture. J Exp Bot 59:273–288
Hagen G, Guilfoyle T (2002) Auxin-responsive gene expression: genes, promoters and regulatory factors. Plant Mol Biol 49:373–385
Halliday KJ, Martinez-Garcia JF, Josse EM (2009) Integration of light and auxin signaling. Cold Spring Harbor Perspect Biol 1:a001586. doi:10.1101/cshperspect.a001586
Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 27:297–300
Jain M, Kaur N, Garg R, Thakur JK, Tyagi AK, Khurana JP (2006) Structure and expression analysis of early auxin-responsive Aux/IAA gene family in rice (Oryza sativa). Funct Integr Genomics 6:47–59. doi:10.1007/s10142-005-0005-0
Jones B, Frasse P, Olmos E, Zegzouti H, Li ZG, Latche A, Pech JC, Bouzayen M (2002) Down-regulation of DR12, an auxin-response-factor homolog, in the tomato results in a pleiotropic phenotype including dark green and blotchy ripening fruit. Plant J 32:603–613
Kalluri UC, Difazio SP, Brunner AM, Tuskan GA (2007) Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa. BMC Plant Biol 7:59
Kenworthy AK (2001) Imaging protein-protein interactions using fluorescence resonance energy transfer microscopy. Methods 24:289–296. doi:10.1006/meth.2001.1189
Kepinski S, Leyser O (2005) The Arabidopsis F-box protein TIR1 is an auxin receptor. Nature 435:446–451
Kim S, Park M, Yeom SI et al (2014) Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat Genet 46:270–278. doi:10.1038/ng.2877
Kloosterman B, Visser RG, Bachem CW (2006) Isolation and characterization of a novel potato Auxin/Indole-3-Acetic Acid family member (StIAA2) that is involved in petiole hyponasty and shoot morphogenesis. Plant Physiol Biochem 44:766–775. doi:10.1016/j.plaphy.2006.10.026
Koenig D, Jimenez-Gomez JM, Kimura S, Fulop D, Chitwood DH, Headland LR, Kumar R, Covington MF, Devisetty UK, Tat AV, Tohge T, Bolger A, Schneeberger K, Ossowski S, Lanz C, Xiong G, Taylor-Teeples M, Brady SM, Pauly M, Weigel D, Usadel B, Fernie AR, Peng J, Sinha NR, Maloof JN (2013) Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. Proc Natl Acad Sci U S A 110:2655–2662. doi:10.1073/pnas.1309606110
Kumar R, Tyagi AK, Sharma AK (2011) Genome-wide analysis of auxin response factor (ARF) gene family from tomato and analysis of their role in flower and fruit development. Mol Genet Genomics 285:245–260. doi:10.1007/s00438-011-0602-7
Kumar R, Agarwal P, Tyagi AK, Sharma AK (2012a) Genome-wide investigation and expression analysis suggest diverse roles of auxin-responsive GH3 genes during development and response to different stimuli in tomato (Solanum lycopersicum). Mol Genet Genomics 287:221–235
Kumar R, Sharma MK, Kapoor S, Tyagi AK, Sharma AK (2012b) Transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes provides insight into LeMADS-RIN-regulated ethylene-dependent as well as ethylene-independent aspects of ripening in tomato. Mol Genet Genomics 287:189–203. doi:10.1007/s00438-011-0671-7
Kumar R, Khurana A, Sharma AK (2014) Role of plant hormones and their interplay in development and ripening of fleshy fruits. J Exp Bot 65(16):4561–4575
Lescot M, Dehais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouze P, Rombauts S (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 30:325–327
Liscum E, Reed JW (2002) Genetics of Aux/IAA and ARF action in plant growth and development. Plant Mol Biol 49:387–400
Liu N, Wu S, Van Houten J, Wang Y, Ding B, Fei Z, Clarke TH, Reed JW, van der Knaap E (2014) Down-regulation of AUXIN RESPONSE FACTORS 6 and 8 by microRNA 167 leads to floral development defects and female sterility in tomato. J Exp Bot 65(9):2507–2520
Lleres D, Swift S, Lamond AI (2007) Detecting protein-protein interactions in vivo with FRET using multiphoton fluorescence lifetime imaging microscopy (FLIM). Current protocols in cytometry / editorial board, J Paul Robinson, managing editor Chapter 12:Unit12 10. doi:10.1002/0471142956.cy1210s42
Nagpal P, Ellis CM, Weber H, Ploense SE, Barkawi LS, Guilfoyle TJ, Hagen G, Alonso JM, Cohen JD, Farmer EE, Ecker JR, Reed JW (2005) Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation. Development 132:4107–4118
Nickrent DL, Parkinson CL, Palmer JD, Duff RJ (2000) Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants. Mol Biol Evol 17:1885–1895
Nuez F, Prohens J, Blanca JM (2004) Relationships, origin, and diversity of Galapagos tomatoes: implications for the conservation of natural populations. Am J Bot 91:86–99. doi:10.3732/ajb.91.1.86
Okushima Y, Overvoorde PJ, Arima K, Alonso JM, Chan A, Chang C, Ecker JR, Hughes B, Lui A, Nguyen D, Onodera C, Quach H, Smith A, Yu G, Theologis A (2005) Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19. Plant Cell 17:444–463
Paponov IA, Teale W, Lang D, Paponov M, Reski R, Rensing SA, Palme K (2009) The evolution of nuclear auxin signalling. BMC Evol Biol 9:126. doi:10.1186/1471-2148-9-126
Peralta IE, Knapp S, Spooner DM (2005) New species of wild tomatoes (Solanum Section Lycopersicon: Solanaceae) from Northern Peru. Syst Bot 30:424–434
Piya S, Shrestha SK, Binder B, Stewart CN Jr, Hewezi T (2014) Protein-protein interaction and gene co-expression maps of ARFs and Aux/IAAs in Arabidopsis. Front Plant Sci 5:744
Rahman A (2013) Auxin: a regulator of cold stress response. Physiol Plant 147:28–35. doi:10.1111/j.1399-3054.2012.01617.x
Sagar M, Chervin C, Mila I, Hao Y, Roustan JP, Benichou M, Gibon Y, Biais B, Maury P, Latche A, Pech JC, Bouzayen M, Zouine M (2013) SlARF4, an auxin response factor involved in the control of sugar metabolism during tomato fruit development. Plant Physiol 161:1362–1374. doi:10.1104/pp. 113.213843
Salinas M, Xing S, Hohmann S, Berndtgen R, Huijser P (2012) Genomic organization, phylogenetic comparison and differential expression of the SBP-box family of transcription factors in tomato. Planta 235:1171–1184. doi:10.1007/s00425-011-1565-y
Sharma MK, Kumar R, Solanke AU, Sharma R, Tyagi AK, Sharma AK (2010) Identification, phylogeny, and transcript profiling of ERF family genes during development and abiotic stress treatments in tomato. Mol Genet Genomics 284:455–475. doi:10.1007/s00438-010-0580-1
Shen C, Bai Y, Wang S, Zhang S, Wu Y, Chen M, Jiang D, Qi Y (2010) Expression profile of PIN, AUX/LAX and PGP auxin transporter gene families in Sorghum bicolor under phytohormone and abiotic stress. FEBS J 277:2954–2969. doi:10.1111/j.1742-4658.2010.07706.x
Song Y, Wang L, Xiong L (2009) Comprehensive expression profiling analysis of OsIAA gene family in developmental processes and in response to phytohormone and stress treatments. Planta 229:577–591. doi:10.1007/s00425-008-0853-7
Szemenyei H, Hannon M, Long JA (2008) TOPLESS mediates auxin-dependent transcriptional repression during Arabidopsis embryogenesis. Science 319:1384–1386. doi:10.1126/science.1151461
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. doi:10.1093/molbev/msr121
TGC (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641. doi:10.1038/nature11119
Thompson JD, Gibson TJ, Higgins DG (2002) Multiple sequence alignment using ClustalW and ClustalX. Current protocols in bioinformatics/editoral board, Andreas D Baxevanis Chapter 2:Unit 2 3. doi:10.1002/0471250953.bi0203s00
Tiwari SB, Hagen G, Guilfoyle T (2003) The roles of auxin response factor domains in auxin-responsive transcription. Plant Cell 15:533–543
Ulmasov T, Hagen G, Guilfoyle TJ (1997) ARF1, a transcription factor that binds to auxin response elements. Science 276:1865–1868
Vriezen WH, Feron R, Maretto F, Keijman J, Mariani C (2008) Changes in tomato ovary transcriptome demonstrate complex hormonal regulation of fruit set. New Phytol 177:60–76
Wang H, Jones B, Li Z, Frasse P, Delalande C, Regad F, Chaabouni S, Latche A, Pech JC, Bouzayen M (2005) The tomato Aux/IAA transcription factor IAA9 is involved in fruit development and leaf morphogenesis. Plant Cell 17:2676–2692
Wang D, Pajerowska-Mukhtar K, Culler AH, Dong X (2007) Salicylic acid inhibits pathogen growth in plants through repression of the auxin signaling pathway. Curr Biol 17:1784–1790. doi:10.1016/j.cub.2007.09.025
Wang Y, Diehl A, Wu F, Vrebalov J, Giovannoni J, Siepel A, Tanksley SD (2008) Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae. Genetics 180:391–408
Wang H, Schauer N, Usadel B, Frasse P, Zouine M, Hernould M, Latche A, Pech JC, Fernie AR, Bouzayen M (2009) Regulatory features underlying pollination-dependent and -independent tomato fruit set revealed by transcript and primary metabolite profiling. Plant Cell 21:1428–1452
Wilmoth JC, Wang S, Tiwari SB, Joshi AD, Hagen G, Guilfoyle TJ, Alonso JM, Ecker JR, Reed JW (2005) NPH4/ARF7 and ARF19 promote leaf expansion and auxin-induced lateral root formation. Plant J 43:118–130. doi:10.1111/j.1365-313X.2005.02432.x
Wu F, Tanksley SD (2010) Chromosomal evolution in the plant family Solanaceae. BMC Genomics 11:182
Wu J, Wang F, Cheng L, Kong F, Peng Z, Liu S, Yu X, Lu G (2011) Identification, isolation and expression analysis of auxin response factor (ARF) genes in Solanum lycopersicum. Plant Cell Rep 30:2059–2073. doi:10.1007/s00299-011-1113-z
Wu J, Peng Z, Liu S, He Y, Cheng L, Kong F, Wang J, Lu G (2012) Genome-wide analysis of Aux/IAA gene family in Solanaceae species using tomato as a model. Mol Genet Genomics 287:295–211
Xu X, Pan S, Cheng S et al (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–195. doi:10.1038/nature10158
Yuan H, Zhao K, Lei H, Shen X, Liu Y, Liao X, Li T (2013) Genome-wide analysis of the GH3 family in apple (Malus x domestica). BMC Genomics 14:297. doi:10.1186/1471-2164-14-297
Zouine M, Fu Y, Chateigner-Boutin AL, Mila I, Frasse P, Wang H, Audran C, Roustan JP, Bouzayen M (2014) Characterization of the tomato ARF gene family uncovers a multi-levels post-transcriptional regulation including alternative splicing. PLoS One 9:e84203. doi:10.1371/journal.pone.0084203
Acknowledgments
This work was financially supported by grants received from the Department of Biotechnology, Government of India. RK, AP, and PA acknowledge DST, CSIR, and UGC, respectively, for the fellowship granted during their tenure as research fellows. RK is grateful to DST for INSPIRE-Faculty Award (grant number IFA-LSPA-15) and to CSIR for Travel Grant (TG/8137/HRD). Authors also acknowledge the Solanaceae Genomics Network for the use of Tomato BAC Sequence Database to retrieve putative promoter sequences. We are grateful to 150 tomato genome consortium for sequence data of wild relatives.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Kumar, R., Agarwal, P., Pareek, A. et al. Genomic Survey, Gene Expression, and Interaction Analysis Suggest Diverse Roles of ARF and Aux/IAA Proteins in Solanaceae. Plant Mol Biol Rep 33, 1552–1572 (2015). https://doi.org/10.1007/s11105-015-0856-z
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11105-015-0856-z