PLANT SIGNALING & BEHAVIOR 2016, VOL. 11, NO. 6, e1184808 (4 pages) http://dx.doi.org/10.1080/15592324.2016.1184808
ARTICLE ADDENDUM
Light-specific transcriptional regulation of the accumulation of carotenoids and phenolic compounds in rice leaves Bijayalaxmi Mohantya, Meiyappan Lakshmananb, Sun-Hyung Limc, Jae Kwang Kimd, Sun-Hwa Hae, and Dong-Yup Leea,b a Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore; bBioprocessing Technology Institute, Agency for Science, Technology and Research (ASTAR), Centros, Singapore; cMetabolic Engineering Division, National Academy of Agricultural Science, Rural Development Administration, Nongsaengmyeong-ro, Wansan-gu, Jeonju-si, Jeollabuk-do, Republic of Korea; dDivision of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Yeonsu-gu, Incheon, Republic of Korea; eDepartment of Genetic Engineering, College of Life Sciences, Kyung Hee University, Giheung gu, Yongin-si, Gyeonggi-do, Republic of Korea
ABSTRACT
ARTICLE HISTORY
Carotenoids and phenolic compounds are important subgroups of secondary metabolites having an array of functional roles in the growth and development of plants. They are also major sources for health and pharmaceutical benefits, and industrially relevant biochemicals. The control of the biosynthesis of these compounds depends mainly on the quality and quantity of different light sources. Thus, to unravel their light-specific transcriptional regulation in rice leaves, we performed promoter analysis of genes upregulated in response to blue and red lights. The analysis results suggested a crosstalk between different phytohormones and the involvement of key transcription factors such as bHLH, bZIP, MYB, WRKY, ZnF and ERF [jasmonic acid inducible], in the regulation of higher accumulation of carotenoids and phenolic compounds upon blue light. Overall, the current analysis could improve our understanding of the light-specific regulatory mechanism involved in the biosynthesis of secondary metabolites via possible critical links between different TFs in rice leaves.
Received 13 April 2016 Accepted 26 April 2016 KEYWORDS
Carotenoids; light; phenolic compounds; rice; transcription factor
Abbreviations: ABA, abscisic acid; GA, gibberellic acid; JA, jasmonic acid; LHCB, light-harvesting chlorophyll a/b-
binding; TF, transcription factor
Plant carotenoids are involved in both photosynthesis and photoprotection, providing substrates for the biosynthesis of hormones.1 They act as accessory pigments in the “Light Harvesting Complex” and then transfer the absorbed energy to chlorophyll a during photosynthesis.2 Similarly, plant phenolic compounds are highly diverse group of secondary natural metabolites with an extremely large structural diversity.3 Their biological functions include phytoalexins, ultraviolet light protectants, pigments, signaling molecules, and mechanical strength (cell wall components). They can modulate essential physiological processes such as transcriptional regulation, membrane permeability, signal transduction, and vesicle trafficking. Hence, both carotenoids and phenolic compounds play multiple roles at different stages and aspects of plant life cycle mainly under biotic and abiotic stress conditions, plant reproduction, and diversity in flowers. Although the biosynthesis of these compounds has been extensively studied, the information on the light-driven regulatory mechanism is relatively limited. In our recently published paper,4 we have already discussed that in rice leaves, the highest and lowest accumulation of carotenoids and total phenolic in rice leaves, under blue light and dark conditions, respectively, following the order of blue>white>green>red>dark (carotenoids) and blue>white>red>green>dark (total phenolics). We also found a very
divergent gene expression pattern in leaves grown in blue and red lights, which was consistent with the observed phenotypes. Since we hypothesized that the relative amount of blue and red lights are the major signaling factors to enhance the metabolic efficiency of rice plants, we aimed to study the transcriptional regulatory mechanism involved in the biosynthesis of carotenoids (a- and b-carotene, lutein) and phenolic compounds in rice leaves in response to these lights. To do so, we performed an ab initio analysis of cis-regulatory information content of the genes associated with the reporter metabolites.
Transcriptional regulation of carotenoids accumulation The integration of the cis-element enrichment analysis with the gene expression data suggests the involvement of a number of transcription factors (TFs) for the transcriptional regulation of the higher accumulation of carotenoids in rice leaves in response to blue light. G-box-like elements ‘CACGTG’ associated with bZIP TFs and bHLH TFs were identified in the promoters of upregulated genes. In addition, the upregulation of several bZIP and bHLH TF genes such as, Os12g0156200 (DNA-binding factor of bZIP class), Os03g0741100 (basic helix-loop-helix dimerization region bHLH domain-containing
CONTACT Dong-Yup Lee [email protected] Addendum to: Lakshmanan M, Lim S-H, Mohanty B, Kim JK, Ha S-H, Lee D-Y. Unraveling the light-specific metabolic and regulatory signatures of rice through combined in silico modeling and multiomics analysis. Plant Physiol 2015; 169:3002–3020, DOI: 10.1104/pp.15.01379. © 2016 Taylor & Francis Group, LLC
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B. MOHANTY ET AL.
protein) and Os01g0286100 (basic helix-loop-helix dimerization region bHLH domain-containing protein) further associates the regulatory roles of these TFs in the accumulation of carotenoids with the potential involvement in plant hormone signaling as suggested earlier (Fig. 1).4-6 The promoter analysis results also suggest the role of bZIP TF as a positive regulator, and bHLH TFs particularly PIFs as negative regulators of chlorophyll and carotenoid accumulation.7 Among the bZIP TFs, HY5 is a strong antagonist of PIF and functions as an activator of genes for chlorophyll and carotenoid accumulation upon blue light signaling. Hence, in rice leaves both PIFs and HY5 seem to regulate an activation-suppression transcriptional control.8 HY5 has also been shown to regulate plant hormones such as gibberellic acid (GA) and abscisic acid (ABA) signal transduction. Overall, HY5 TF not only acts as a regulator in biosynthesis of carotenoids but also as a crosstalk between ABA and GA, and interaction between light and phytochrome signaling (Fig. 1).9,10 The accumulation of carotenoids is also closely linked to the intracellular levels of GA and ABA. Biosynthesis of carotenoids and GA share a common biosynthetic precursor, i.e.
geranylgeranyl diphosphate, and later carotenoids provide precursor for ABA biosynthesis.11 Hence, the significant enrichment of ABRE-like, G-box-like, MYB-box-like, Pyrimidinebox-like, GARE-like elements in the upregulated genes and the upregulation of MYB and bZIP TF genes such as Os02g0685200 (Myb, DNA-binding domain containing protein), Os02g0706400 (Myb, DNA-binding domain containing protein) and Os12g0156200 (DNA-binding factor of bZIP class) in blue light indicates higher biosynthesis of ABA as well as GA. These results explain the positive feedback inhibition mediated by ABA to control stomatal conductance for chloroplast movement and photosynthesis. Since ABA is synthesized downstream of carotenoids, induction of carotenoid biosynthetic genes are also linked to the increased level of ABA. Moreover, the enrichment of PIF specific cis-elements supports the view that these TFs can also elevate the intracellular ABA levels by precisely promoting the expression of the ABA biosynthetic genes, and repressing the expression of the ABA catabolic genes.12,13 Taken together, our results provide a link between the accumulation of higher carotenoids with higher concentration of both chlorophyll and ABA,14 and possible
Figure 1. The proposed model of rice showing transcriptional regulation of biosynthesis of carotenoids and phenolic compounds in response to blue and red lights. The solid lines represent the findings which are supported by previous studies while the dotted lines are the hypothetical links proposed based on our analysis results.
PLANT SIGNALING & BEHAVIOR
transcriptional regulation by TFs such as MYBs, bZIPs and bHLHs (PIFs) (Fig. 1). Additionally, the presence of W-boxlike elements associated with a number of WRKY family TFs and the upregulation of Os02g0462800 (WRKY TF42 [TF WRKY02]) in blue light appear in balancing the positive function of the light-harvesting chlorophyll a/b-binding (LHCB). ABA is normally required in high level for the full expression of different LHCB proteins and then ABA-responsive WRKYdomain TF which represses LHCB expression acts to balance the positive function of the LHCBs.15 Therefore, in blue light treatment, ABA could act as an inducer to fine-tune LHCB expression in rice leaves and high level of carotenoids supports in activating photosynthesis and photoprotection. Higher biosynthesis of GA in both blue and red light treatment agrees with our identification of a number of GA response elements associated with MYB TF which are involved in the regulation of the biosynthesis of a- and b-carotene, and lutein. On the other hand, occurrence of ERE-like elements associated with a number of AP2/ERF TFs in both blue and red light possibly be acting as negative regulators in carotenoid accumulation which needs further experimental validation.16
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upregulation of ERF TF genes provide support in favor of the involvement of JA-mediated biosynthesis of phenolic compounds. However, experimental validation is required to support our hypothesis. Overall, our results suggest the potential involvement of a number of TFs and a cross talk between different phytohormones such as GA, ABA and JA for the regulation of carotenoids and phenolic compounds in rice leaves in response to blue and red lights.
Disclosure of potential conflicts of interest No potential conflicts of interest were disclosed.
Funding This work was supported by the Synthetic Biology Initiative of the National University of Singapore (DPRT/943/09/14) and the Next-Generation BioGreen 21 Program of the Rural Development Administration, Republic of Korea (Systems and Synthetic Agrobiotech Center; grant no. PJ01109405).
Transcriptional regulation of phenolic compounds accumulation
References
We have identified several types of TFs that regulate the biosynthesis of different phenolic compounds. Of them, the roles of R1 MYB, R2-MYB, R2R3-MYB TFs in regulation of the synthesis of different phenylpropanoid-derived compounds have been extensively studied in many plants such as Arabidopsis, maize, rice, soybean and other plants.17 In the current analysis, the metabolic genes associated with the reporter metabolites were significantly enriched with putative cis-elements such as MYB-box-like, MYB-box related-like, GARE-like and pyrimidine-box-like associated with the different types of R1MYB, R2MYB and R2R3 MYB in response to both blue and red lights. The enrichment of these elements is supported by the upregulation of Os02g0685200 and Os02g0706400 in blue light, signifying their role in the regulation of the synthesis of different phenolic compounds. Moreover, presence of G-box-like elements associated with bHLH TF provides evidence to support the view that in blue light, there is possible interaction of MYB with bHLH TFs to accumulate more phenolic compounds. Higher accumulation of ABA, high enrichment of W-box-likeelements associated with WRKY TFs together with the upregulation of Os02g0462800 (WRKY transcription factor 42 [Transcription factor WRKY02]) in blue light supports the role of ABA-responsive WRKYs in the regulation of the biosynthesis of phenolic compounds (Fig. 1).18-22 Our analysis also shows the involvement of ZnF TFs (ZCT1, ZCT2 and ZCT3) in the regulation of the biosynthesis of phenolic compounds which needs further validation. In addition to the high enrichment of putative cis-elements associated with TFs such as, bHLH, bZIP, MYB, WRKY and ZnF, genes encoding members of these TF families also showed an upregulation. These genes are known for their roles against abiotic and biotic stresses, so it is possible that these TFs have a general ability to regulate production of phenolic compounds. Presence of JARE-like the motifs associated with ERF TF family [jasmonic acid (JA) induced] and
1. Telfer A. Too much light? How beta-carotene protects the photosystem II reaction centre. Photochem Photobiol Sci 2005; 4:950-6; PMID:16307107; http://dx.doi.org/10.1039/b507888c 2. Schmid VH. Light-harvesting complexes of vascular plants. Cell Mol Life Sci 2008; 65:3619-39; PMID:18791846; http://dx.doi.org/10.1007/ s00018-008-8333-6 3. Quideau S, Deffieux D, Douat-Casassus C, Pouysegu L. Plant polyphenols: chemical properties, biological activities, and synthesis. Angew Chem Int Ed 2011; 50:586-621; PMID:21226137; http://dx.doi.org/ 10.1002/anie.201000044 4. Lakshmanan M, Lim S-H, Mohanty B, Kim JK, Ha S-H, Lee D-Y. Unraveling the light-specific metabolic and regulatory signatures of rice through combined in silico modeling and multiomics analysis. Plant Physiol 2015; 169:3002-20; PMID:26453433; http://dx.doi.org/ 10.1104/pp.15.01379 5. Shin J, Kim K, Kang H, Zulfugarov IS, Bae G, Lee CH, Lee D, Choi G. Phytochromes promote seedling light responses by inhibiting four negatively-acting phytochrome-interacting factors. Proc Natl Acad Sci USA 2009; 106:7660-5; PMID:19380720; http://dx.doi.org/10.1073/ pnas.0812219106 6. Leivar P, Tepperman JM, Monte E, Calderon RH, Liu TL, Quail PH. Definition of early transcriptional circuitry involved in light-induced reversal of PIF-imposed repression of photomorphogenesis in young Arabidopsis seedlings. Plant Cell 2009; 21:3535-53; PMID:19920208; http://dx.doi.org/10.1105/tpc.109.070672 7. Toledo-Ortiz G, Johansson H, Lee KP, Bou-Torrent J, Stewart K, Steel G, Rodrıguez-Concepci on M, Halliday KJ. The HY5-PIF regulatory module coordinates light and temperature control of photosynthetic gene transcription. PLoS Genet 2014; 10:e1004416; PMID:24922306; http://dx.doi.org/10.1371/journal.pgen.1004416 8. Toledo-Ortiz G, Huq E, Rodriguez-Concepcion M. Direct regulation of phytoene synthase gene expression and carotenoid biosynthesis by phytochrome interacting factors. Proc Natl Acad Sci USA 2010; 107:11626-31; PMID:20534526; http://dx.doi.org/10.1073/ pnas.0914428107 9. Hong GJ, Xue XY, Mao YB, Wang LJ, Chen XY. Arabidopsis MYC2 interacts with DELLA proteins in regulating sesquiterpene synthase gene expression. Plant Cell 2012; 24:2635-48; PMID:22669881; http:// dx.doi.org/10.1105/tpc.112.098749 10. Kazan K, Manners JM. MYC2: The master in action. Mol Plant 2013; 6:686-703; PMID:23142764; http://dx.doi.org/10.1093/mp/sss128
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11. Nambara E, Marion-Poll A. Abscisic acid biosynthesis and catabolism. Ann Rev Plant Biol 2005; 56:165-85; PMID:15862093; http://dx.doi. org/10.1146/annurev.arplant.56.032604.144046 12. Shin J, Kim K, Kang H, Zulfugarov IS, Bae G, Lee CH, Lee D, Choi G. Phytochromes promote seedling light responses by inhibiting four negatively-acting phytochrome-interacting factors. Proc Natl Acad Sci USA 2009; 106:7660-5; PMID:19380720; http://dx.doi.org/10.1073/ pnas.0812219106 13. Leivar P, Tepperman JM, Monte E, Calderon RH, Liu TL, Quail PH. Definition of early transcriptional circuitry involved in light-induced reversal of PIF-imposed repression of photomorphogenesis in young Arabidopsis seedlings. Plant Cell 2009; 21:3535-53; PMID:19920208; http://dx.doi.org/10.1105/tpc.109.070672 14. Barickman TS, Kopsell DA, Sams CE. Abscisic acid increases carotenoid and chlorophyll concentrations in leaves and fruit of two tomato genotypes. J Amer Soc Hort Sci 2014; 139:261-6 15. Liu R, Xu YH, Jiang SC, Lu K, Lu YF, Feng XJ, Wu Z, Liang S, Yu YT, Wang XF, Zhang DP. Lightharvesting chlorophyll a/bbinding proteins, positively involved in abscisic acid signaling, require a transcription repressor, WRKY40, to balance their fucntion. J Exp Bot 2013; 64:5443-56; PMID:24078667; http://dx.doi. org/10.1093/jxb/ert307 16. Lee JM, Joung J-G, McQuinn R, Chung M-Y, Fei Z, Tieman D, Klee H, Giovannoni J. Combined transcriptome, genetic diversity and metabolite profiling in tomato fruit reveals that the ethylene response factor SlERF6 plays an important role in ripening and carotenoid
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accumulation. Plant J 2012; 70:191-204; PMID:22111515; http://dx. doi.org/10.1111/j.1365-313X.2011.04863.x Liu J, Osbourn A, Ma P. MYB transcription factors as regulators of phenylpropanoid metabolism in plants. Mol Plant 2015; 8:689-708; PMID:25840349; http://dx.doi.org/10.1016/j.molp.2015.03.012 Naoumkina MA, He X, Dixon RA. Elicitor-induced transcription factors for metabolic reprogramming of secondary metabolism in Medicago truncatula. BMC Plant Biol 2008; 8:132; PMID:19102779; http:// dx.doi.org/10.1186/1471-2229-8-132 Wang H, Avci U, Nakashima J, Hahn MG, Chen F, Dixon RA. Mutation of WRKY transcription factors initiates pith secondary wall formation and increases stem biomass in dicotyledonous plants. Proc Natl Acad Sci USA 2010; 107:22338-43; PMID:21135241; http://dx. doi.org/10.1073/pnas.1016436107 Guillaumie S, Mzid R, Mechin V, Leon C, Hichri I, Destrac-Irvine A, Trossat-Magnin C, Delrot S, Lauvergeat V. The grapevine transcription factor WRKY2 influences the lignin pathway and xylem development in tobacco. Plant Mol Biol 2010; 72:215-34; PMID:19902151; http://dx.doi.org/10.1007/s11103-009-9563-1 Schluttenhofer C, Yuan L. Regulation of specialized metabolism by WRKY transcription factors. Plant Physiol 2015; 167:295-306; PMID:25501946; http://dx.doi.org/10.1104/pp.114.251769 Yang L, Zhao X, Yang F, Fan D, Jiang Y, Luo K. PtrWRKY19, a novel WRKY transcription factor, contributes to the regulation of pith secondary wall formation in Populus trichocarpa. Sci Rep 2016; 6:18643; PMID:26819184; http://dx.doi.org/10.1038/srep18643
ARTICLE ADDENDUM
Light-specific transcriptional regulation of the accumulation of carotenoids and phenolic compounds in rice leaves Bijayalaxmi Mohantya, Meiyappan Lakshmananb, Sun-Hyung Limc, Jae Kwang Kimd, Sun-Hwa Hae, and Dong-Yup Leea,b a Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore; bBioprocessing Technology Institute, Agency for Science, Technology and Research (ASTAR), Centros, Singapore; cMetabolic Engineering Division, National Academy of Agricultural Science, Rural Development Administration, Nongsaengmyeong-ro, Wansan-gu, Jeonju-si, Jeollabuk-do, Republic of Korea; dDivision of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Yeonsu-gu, Incheon, Republic of Korea; eDepartment of Genetic Engineering, College of Life Sciences, Kyung Hee University, Giheung gu, Yongin-si, Gyeonggi-do, Republic of Korea
ABSTRACT
ARTICLE HISTORY
Carotenoids and phenolic compounds are important subgroups of secondary metabolites having an array of functional roles in the growth and development of plants. They are also major sources for health and pharmaceutical benefits, and industrially relevant biochemicals. The control of the biosynthesis of these compounds depends mainly on the quality and quantity of different light sources. Thus, to unravel their light-specific transcriptional regulation in rice leaves, we performed promoter analysis of genes upregulated in response to blue and red lights. The analysis results suggested a crosstalk between different phytohormones and the involvement of key transcription factors such as bHLH, bZIP, MYB, WRKY, ZnF and ERF [jasmonic acid inducible], in the regulation of higher accumulation of carotenoids and phenolic compounds upon blue light. Overall, the current analysis could improve our understanding of the light-specific regulatory mechanism involved in the biosynthesis of secondary metabolites via possible critical links between different TFs in rice leaves.
Received 13 April 2016 Accepted 26 April 2016 KEYWORDS
Carotenoids; light; phenolic compounds; rice; transcription factor
Abbreviations: ABA, abscisic acid; GA, gibberellic acid; JA, jasmonic acid; LHCB, light-harvesting chlorophyll a/b-
binding; TF, transcription factor
Plant carotenoids are involved in both photosynthesis and photoprotection, providing substrates for the biosynthesis of hormones.1 They act as accessory pigments in the “Light Harvesting Complex” and then transfer the absorbed energy to chlorophyll a during photosynthesis.2 Similarly, plant phenolic compounds are highly diverse group of secondary natural metabolites with an extremely large structural diversity.3 Their biological functions include phytoalexins, ultraviolet light protectants, pigments, signaling molecules, and mechanical strength (cell wall components). They can modulate essential physiological processes such as transcriptional regulation, membrane permeability, signal transduction, and vesicle trafficking. Hence, both carotenoids and phenolic compounds play multiple roles at different stages and aspects of plant life cycle mainly under biotic and abiotic stress conditions, plant reproduction, and diversity in flowers. Although the biosynthesis of these compounds has been extensively studied, the information on the light-driven regulatory mechanism is relatively limited. In our recently published paper,4 we have already discussed that in rice leaves, the highest and lowest accumulation of carotenoids and total phenolic in rice leaves, under blue light and dark conditions, respectively, following the order of blue>white>green>red>dark (carotenoids) and blue>white>red>green>dark (total phenolics). We also found a very
divergent gene expression pattern in leaves grown in blue and red lights, which was consistent with the observed phenotypes. Since we hypothesized that the relative amount of blue and red lights are the major signaling factors to enhance the metabolic efficiency of rice plants, we aimed to study the transcriptional regulatory mechanism involved in the biosynthesis of carotenoids (a- and b-carotene, lutein) and phenolic compounds in rice leaves in response to these lights. To do so, we performed an ab initio analysis of cis-regulatory information content of the genes associated with the reporter metabolites.
Transcriptional regulation of carotenoids accumulation The integration of the cis-element enrichment analysis with the gene expression data suggests the involvement of a number of transcription factors (TFs) for the transcriptional regulation of the higher accumulation of carotenoids in rice leaves in response to blue light. G-box-like elements ‘CACGTG’ associated with bZIP TFs and bHLH TFs were identified in the promoters of upregulated genes. In addition, the upregulation of several bZIP and bHLH TF genes such as, Os12g0156200 (DNA-binding factor of bZIP class), Os03g0741100 (basic helix-loop-helix dimerization region bHLH domain-containing
CONTACT Dong-Yup Lee [email protected] Addendum to: Lakshmanan M, Lim S-H, Mohanty B, Kim JK, Ha S-H, Lee D-Y. Unraveling the light-specific metabolic and regulatory signatures of rice through combined in silico modeling and multiomics analysis. Plant Physiol 2015; 169:3002–3020, DOI: 10.1104/pp.15.01379. © 2016 Taylor & Francis Group, LLC
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B. MOHANTY ET AL.
protein) and Os01g0286100 (basic helix-loop-helix dimerization region bHLH domain-containing protein) further associates the regulatory roles of these TFs in the accumulation of carotenoids with the potential involvement in plant hormone signaling as suggested earlier (Fig. 1).4-6 The promoter analysis results also suggest the role of bZIP TF as a positive regulator, and bHLH TFs particularly PIFs as negative regulators of chlorophyll and carotenoid accumulation.7 Among the bZIP TFs, HY5 is a strong antagonist of PIF and functions as an activator of genes for chlorophyll and carotenoid accumulation upon blue light signaling. Hence, in rice leaves both PIFs and HY5 seem to regulate an activation-suppression transcriptional control.8 HY5 has also been shown to regulate plant hormones such as gibberellic acid (GA) and abscisic acid (ABA) signal transduction. Overall, HY5 TF not only acts as a regulator in biosynthesis of carotenoids but also as a crosstalk between ABA and GA, and interaction between light and phytochrome signaling (Fig. 1).9,10 The accumulation of carotenoids is also closely linked to the intracellular levels of GA and ABA. Biosynthesis of carotenoids and GA share a common biosynthetic precursor, i.e.
geranylgeranyl diphosphate, and later carotenoids provide precursor for ABA biosynthesis.11 Hence, the significant enrichment of ABRE-like, G-box-like, MYB-box-like, Pyrimidinebox-like, GARE-like elements in the upregulated genes and the upregulation of MYB and bZIP TF genes such as Os02g0685200 (Myb, DNA-binding domain containing protein), Os02g0706400 (Myb, DNA-binding domain containing protein) and Os12g0156200 (DNA-binding factor of bZIP class) in blue light indicates higher biosynthesis of ABA as well as GA. These results explain the positive feedback inhibition mediated by ABA to control stomatal conductance for chloroplast movement and photosynthesis. Since ABA is synthesized downstream of carotenoids, induction of carotenoid biosynthetic genes are also linked to the increased level of ABA. Moreover, the enrichment of PIF specific cis-elements supports the view that these TFs can also elevate the intracellular ABA levels by precisely promoting the expression of the ABA biosynthetic genes, and repressing the expression of the ABA catabolic genes.12,13 Taken together, our results provide a link between the accumulation of higher carotenoids with higher concentration of both chlorophyll and ABA,14 and possible
Figure 1. The proposed model of rice showing transcriptional regulation of biosynthesis of carotenoids and phenolic compounds in response to blue and red lights. The solid lines represent the findings which are supported by previous studies while the dotted lines are the hypothetical links proposed based on our analysis results.
PLANT SIGNALING & BEHAVIOR
transcriptional regulation by TFs such as MYBs, bZIPs and bHLHs (PIFs) (Fig. 1). Additionally, the presence of W-boxlike elements associated with a number of WRKY family TFs and the upregulation of Os02g0462800 (WRKY TF42 [TF WRKY02]) in blue light appear in balancing the positive function of the light-harvesting chlorophyll a/b-binding (LHCB). ABA is normally required in high level for the full expression of different LHCB proteins and then ABA-responsive WRKYdomain TF which represses LHCB expression acts to balance the positive function of the LHCBs.15 Therefore, in blue light treatment, ABA could act as an inducer to fine-tune LHCB expression in rice leaves and high level of carotenoids supports in activating photosynthesis and photoprotection. Higher biosynthesis of GA in both blue and red light treatment agrees with our identification of a number of GA response elements associated with MYB TF which are involved in the regulation of the biosynthesis of a- and b-carotene, and lutein. On the other hand, occurrence of ERE-like elements associated with a number of AP2/ERF TFs in both blue and red light possibly be acting as negative regulators in carotenoid accumulation which needs further experimental validation.16
e1184808-3
upregulation of ERF TF genes provide support in favor of the involvement of JA-mediated biosynthesis of phenolic compounds. However, experimental validation is required to support our hypothesis. Overall, our results suggest the potential involvement of a number of TFs and a cross talk between different phytohormones such as GA, ABA and JA for the regulation of carotenoids and phenolic compounds in rice leaves in response to blue and red lights.
Disclosure of potential conflicts of interest No potential conflicts of interest were disclosed.
Funding This work was supported by the Synthetic Biology Initiative of the National University of Singapore (DPRT/943/09/14) and the Next-Generation BioGreen 21 Program of the Rural Development Administration, Republic of Korea (Systems and Synthetic Agrobiotech Center; grant no. PJ01109405).
Transcriptional regulation of phenolic compounds accumulation
References
We have identified several types of TFs that regulate the biosynthesis of different phenolic compounds. Of them, the roles of R1 MYB, R2-MYB, R2R3-MYB TFs in regulation of the synthesis of different phenylpropanoid-derived compounds have been extensively studied in many plants such as Arabidopsis, maize, rice, soybean and other plants.17 In the current analysis, the metabolic genes associated with the reporter metabolites were significantly enriched with putative cis-elements such as MYB-box-like, MYB-box related-like, GARE-like and pyrimidine-box-like associated with the different types of R1MYB, R2MYB and R2R3 MYB in response to both blue and red lights. The enrichment of these elements is supported by the upregulation of Os02g0685200 and Os02g0706400 in blue light, signifying their role in the regulation of the synthesis of different phenolic compounds. Moreover, presence of G-box-like elements associated with bHLH TF provides evidence to support the view that in blue light, there is possible interaction of MYB with bHLH TFs to accumulate more phenolic compounds. Higher accumulation of ABA, high enrichment of W-box-likeelements associated with WRKY TFs together with the upregulation of Os02g0462800 (WRKY transcription factor 42 [Transcription factor WRKY02]) in blue light supports the role of ABA-responsive WRKYs in the regulation of the biosynthesis of phenolic compounds (Fig. 1).18-22 Our analysis also shows the involvement of ZnF TFs (ZCT1, ZCT2 and ZCT3) in the regulation of the biosynthesis of phenolic compounds which needs further validation. In addition to the high enrichment of putative cis-elements associated with TFs such as, bHLH, bZIP, MYB, WRKY and ZnF, genes encoding members of these TF families also showed an upregulation. These genes are known for their roles against abiotic and biotic stresses, so it is possible that these TFs have a general ability to regulate production of phenolic compounds. Presence of JARE-like the motifs associated with ERF TF family [jasmonic acid (JA) induced] and
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