Phenolic compounds are a group of secondary metabolites responsible for several processes in plants-these compounds are involved in plant-environment interactions (attraction of pollinators, repelling of herbivores, or chemotaxis of microbiota in soil), but also have antioxidative properties and are capable of binding heavy metals or screening ultraviolet radiation. Therefore, the accumulation of these compounds has to be precisely driven, which is ensured on several levels, but the most important aspect seems to be the control of the gene expression. Such transcriptional control requires the presence and activity of transcription factors (TFs) that are driven based on the current requirements of the plant. Two environmental factors mainly affect the accumulation of phenolic compounds-light and temperature. Because it is known that light perception occurs via the specialized sensors (photoreceptors) we decided to combine the biophysical knowledge about light perception in plants with the molecular biology-based knowledge about the transcription control of specific genes to bridge the gap between them. Our review offers insights into the regulation of genes related to phenolic compound production, strengthens understanding of plant responses to environmental cues, and opens avenues for manipulation of the total content and profile of phenolic compounds with potential applications in horticulture and food production.

Department of Biology and Ecology University of Ostrava 710 00 Ostrava Czech Republic

Department of Physics University of Ostrava 710 00 Ostrava Czech Republic

Global Change Research Institute Czech Academy of Sciences 603 00 Brno Czech Republic

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Csepregi K., Hideg É. Phenolic Compound Diversity Explored in the Context of Photo-Oxidative Stress Protection. Phytochem. Anal. 2018;29:129–136. doi: 10.1002/pca.2720. PubMed DOI

Sarker U., Oba S. Drought stress enhances nutritional and bioactive compounds, phenolic acids and antioxidant capacity of Amaranthus leafy vegetable. BMC Plant Biol. 2018;18:258. doi: 10.1186/s12870-018-1484-1. PubMed DOI PMC

Younis M.E.-B., Hasaneen M.N.A.-G., Abdel-Aziz H.M.M. An enhancing effect of visible light and UV radiation on phenolic compounds and various antioxidants in broad bean seedlings. Plant Signal Behav. 2010;5:1197–1203. doi: 10.4161/psb.5.10.11978. PubMed DOI PMC

Christie P.J., Alfenito M.R., Walbot V. Impact of low-temperature stress on general phenylpropanoid and anthocyanin pathways: Enhancement of transcript abundance and anthocyanin pigmentation in maize seedlings. Planta. 1994;194:541–549. doi: 10.1007/BF00714468. DOI

Catalá R., Medina J., Salinas J. Integration of low temperature and light signaling during cold acclimation response in Arabidopsis. Proc. Natl. Acad. Sci. USA. 2011;108:16475–16480. doi: 10.1073/pnas.1107161108. PubMed DOI PMC

Michalak A. Phenolic Compounds and Their Antioxidant Activity in Plants Growing under Heavy Metal Stress. Pol. J. Environ. Stud. 2006;15:523–530.

Hunt L., Klem K., Lhotáková Z., Vosolsobě S., Oravec M., Urban O., Špunda V., Albrechtová J. Light and CO2 Modulate the Accumulation and Localization of Phenolic Compounds in Barley Leaves. Antioxidants. 2021;10:385. doi: 10.3390/antiox10030385. PubMed DOI PMC

Saile J., Wießner-Kroh T., Erbstein K., Obermüller D.M., Pfeiffer A., Janocha D., Lohmann J., Wachter A. SNF1-RELATED KINASE 1 and TARGET OF RAPAMYCIN control light-responsive splicing events and developmental characteristics in etiolated Arabidopsis seedlings. Plant Cell. 2023;35:3413–3428. doi: 10.1093/plcell/koad168. PubMed DOI PMC

Wu R., Lin X., He J., Min A., Pang L., Wang Y., Lin Y., Zhang Y., He W., Li M., et al. Hexokinase1: A glucose sensor involved in drought stress response and sugar metabolism depending on its kinase activity in strawberry. Front. Plant Sci. 2023;14:1069830. doi: 10.3389/fpls.2023.1069830. PubMed DOI PMC

Moore B., Zhou L., Rolland F., Hall Q., Cheng W.-H., Liu Y.-X., Hwang I., Jones T., Sheen J. Role of the Arabidopsis Glucose Sensor HXK1 in Nutrient, Light, and Hormonal Signaling. Science. 2003;300:332–336. doi: 10.1126/science.1080585. PubMed DOI

Avidan O., Moraes T.A., Mengin V., Feil R., Rolland F., Stitt M., Lunn J.E. In vivo protein kinase activity of SnRK1 fluctuates in Arabidopsis rosettes during light-dark cycles. Plant Physiol. 2023;192:387–408. doi: 10.1093/plphys/kiad066. PubMed DOI PMC

Riegler S., Servi L., Scarpin M.R., Godoy Herz M.A., Kubaczka M.G., Venhuizen P., Meyer C., Brunkard J.O., Kalyna M., Barta A., et al. Light regulates alternative splicing outcomes via the TOR kinase pathway. Cell Rep. 2021;36:109676. doi: 10.1016/j.celrep.2021.109676. PubMed DOI PMC

Apel K., Hirt H. Reactive oxygen species: Metabolism, oxidative stress, and signal transduction. Annu. Rev. Plant Biol. 2004;55:373–399. doi: 10.1146/annurev.arplant.55.031903.141701. PubMed DOI

El-Esawi M., Arthaut L.-D., Jourdan N., d’Harlingue A., Link J., Martino C.F., Ahmad M. Blue-light induced biosynthesis of ROS contributes to the signaling mechanism of Arabidopsis cryptochrome. Sci. Rep. 2017;7:13875. doi: 10.1038/s41598-017-13832-z. PubMed DOI PMC

Zandalinas S.I., Sengupta S., Burks D., Azad R.K., Mittler R. Identification and characterization of a core set of ROS wave-associated transcripts involved in the systemic acquired acclimation response of Arabidopsis to excess light. Plant J. 2019;98:126–141. doi: 10.1111/tpj.14205. PubMed DOI PMC

Möglich A., Yang X., Ayers R.A., Moffat K. Structure and Function of Plant Photoreceptors. Annu. Rev. Plant Biol. 2010;61:21–47. doi: 10.1146/annurev-arplant-042809-112259. PubMed DOI

Ponnu J., Hoecker U. Illuminating the COP1/SPA Ubiquitin Ligase: Fresh Insights Into Its Structure and Functions during Plant Photomorphogenesis. Front. Plant Sci. 2021;12:662793. doi: 10.3389/fpls.2021.662793. PubMed DOI PMC

Zvi M.M.B., Shklarman E., Masci T., Kalev H., Debener T., Shafir S., Ovadis M., Vainstein A. PAP1 transcription factor enhances production of phenylpropanoid and terpenoid scent compounds in rose flowers. New Phytol. 2012;195:335–345. doi: 10.1111/j.1469-8137.2012.04161.x. PubMed DOI

Xu W., Dubos C., Lepiniec L. Transcriptional control of flavonoid biosynthesis by MYB–bHLH–WDR complexes. Trends Plant Sci. 2015;20:176–185. doi: 10.1016/j.tplants.2014.12.001. PubMed DOI

Pennisi G., Sanyé-Mengual E., Orsini F., Crepaldi A., Nicola S., Ochoa J., Fernandez J.A., Gianquinto G. Modelling Environmental Burdens of Indoor-Grown Vegetables and Herbs as Affected by Red and Blue LED Lighting. Sustainability. 2019;11:4063. doi: 10.3390/su11154063. DOI

Zhang S., Ma J., Zou H., Zhang L., Li S., Wang Y. The combination of blue and red LED light improves growth and phenolic acid contents in Salvia miltiorrhiza Bunge. Ind. Crops Prod. 2020;158:112959. doi: 10.1016/j.indcrop.2020.112959. DOI

Gupta S.K., Sharma M., Deeba F., Pandey V. UV-B Radiation. John Wiley & Sons, Ltd.; Hoboken, NJ, USA: 2017. Plant Response; pp. 217–258.

Kong S.-G., Okajima K. Diverse photoreceptors and light responses in plants. J. Plant Res. 2016;129:111–114. doi: 10.1007/s10265-016-0792-5. PubMed DOI

Legris M., Ince Y.Ç., Fankhauser C. Molecular mechanisms underlying phytochrome-controlled morphogenesis in plants. Nat. Commun. 2019;10:5219. doi: 10.1038/s41467-019-13045-0. PubMed DOI PMC

Paik I., Huq E. Plant photoreceptors: Multi-functional sensory proteins and their signaling networks. Semin. Cell Dev. Biol. 2019;92:114–121. doi: 10.1016/j.semcdb.2019.03.007. PubMed DOI PMC

Christie J.M., Arvai A.S., Baxter K.J., Heilmann M., Pratt A.J., O’Hara A., Kelly S.M., Hothorn M., Smith B.O., Hitomi K., et al. Plant UVR8 Photoreceptor Senses UV-B by Tryptophan-Mediated Disruption of Cross-Dimer Salt Bridges. Science. 2012;335:1492–1496. doi: 10.1126/science.1218091. PubMed DOI PMC

Mathes T., Heilmann M., Pandit A., Zhu J., Ravensbergen J., Kloz M., Fu Y., Smith B.O., Christie J.M., Jenkins G.I., et al. Proton-Coupled Electron Transfer Constitutes the Photoactivation Mechanism of the Plant Photoreceptor UVR8. J. Am. Chem. Soc. 2015;137:8113–8120. doi: 10.1021/jacs.5b01177. PubMed DOI

Li X., Ren H., Kundu M., Liu Z., Zhong F.W., Wang L., Gao J., Zhong D. A leap in quantum efficiency through light harvesting in photoreceptor UVR8. Nat. Commun. 2020;11:4316. doi: 10.1038/s41467-020-17838-6. PubMed DOI PMC

Tossi V.E., Regalado J.J., Iannicelli J., Laino L.E., Burrieza H.P., Escandón A.S., Pitta-Álvarez S.I. Beyond Arabidopsis: Differential UV-B Response Mediated by UVR8 in Diverse Species. Front. Plant Sci. 2019;10:780. doi: 10.3389/fpls.2019.00780. PubMed DOI PMC

Findlay K.M.W., Jenkins G.I. Regulation of UVR8 photoreceptor dimer/monomer photo-equilibrium in Arabidopsis plants grown under photoperiodic conditions. Plant Cell Environ. 2016;39:1706–1714. doi: 10.1111/pce.12724. PubMed DOI PMC

Gruber H., Heijde M., Heller W., Albert A., Seidlitz H.K., Ulm R. Negative feedback regulation of UV-B–induced photomorphogenesis and stress acclimation in Arabidopsis. Proc. Natl. Acad. Sci. USA. 2010;107:20132–20137. doi: 10.1073/pnas.0914532107. PubMed DOI PMC

Wang L., Wang Y., Chang H., Ren H., Wu X., Wen J., Guan Z., Ma L., Qiu L., Yan J., et al. RUP2 facilitates UVR8 redimerization via two interfaces. Plant Commun. 2022;4:100428. doi: 10.1016/j.xplc.2022.100428. PubMed DOI PMC

Orth C., Niemann N., Hennig L., Essen L.-O., Batschauer A. Hyperactivity of the Arabidopsis cryptochrome (cry1) L407F mutant is caused by a structural alteration close to the cry1 ATP-binding site. J. Biol. Chem. 2017;292:12906–12920. doi: 10.1074/jbc.M117.788869. PubMed DOI PMC

Lopez L., Fasano C., Perrella G., Facella P. Cryptochromes and the Circadian Clock: The Story of a Very Complex Relationship in a Spinning World. Genes. 2021;12:672. doi: 10.3390/genes12050672. PubMed DOI PMC

Lin C., Todo T. The cryptochromes. Genome Biol. 2005;6:220. doi: 10.1186/gb-2005-6-5-220. PubMed DOI PMC

Barrero J.M., Downie A.B., Xu Q., Gubler F. A Role for Barley CRYPTOCHROME1 in Light Regulation of Grain Dormancy and Germination. Plant Cell. 2014;26:1094–1104. doi: 10.1105/tpc.113.121830. PubMed DOI PMC

Klar T., Pokorny R., Moldt J., Batschauer A., Essen L.-O. Cryptochrome 3 from Arabidopsis thaliana: Structural and Functional Analysis of its Complex with a Folate Light Antenna. J. Mol. Biol. 2007;366:954–964. doi: 10.1016/j.jmb.2006.11.066. PubMed DOI

Tissot N., Ulm R. Cryptochrome-mediated blue-light signalling modulates UVR8 photoreceptor activity and contributes to UV-B tolerance in Arabidopsis. Nat. Commun. 2020;11:1323. doi: 10.1038/s41467-020-15133-y. PubMed DOI PMC

Ma L., Guan Z., Wang Q., Yan X., Wang J., Wang Z., Cao J., Zhang D., Gong X., Yin P. Structural insights into the photoactivation of Arabidopsis CRY2. Nat. Plants. 2020;6:1432–1438. doi: 10.1038/s41477-020-00800-1. PubMed DOI

Palayam M., Ganapathy J., Guercio A.M., Tal L., Deck S.L., Shabek N. Structural insights into photoactivation of plant Cryptochrome-2. Commun. Biol. 2021;4:1–11. doi: 10.1038/s42003-020-01531-x. PubMed DOI PMC

Shao K., Zhang X., Li X., Hao Y., Huang X., Ma M., Zhang M., Yu F., Liu H., Zhang P. The oligomeric structures of plant cryptochromes. Nat. Struct. Mol. Biol. 2020;27:480–488. doi: 10.1038/s41594-020-0420-x. PubMed DOI

The UniProt Consortium UniProt: A worldwide hub of protein knowledge. Nucleic Acids Res. 2019;47:D506–D515. doi: 10.1093/nar/gky1049. PubMed DOI PMC

Christie J.M. Phototropin Blue-Light Receptors. Annu. Rev. Plant Biol. 2007;58:21–45. doi: 10.1146/annurev.arplant.58.032806.103951. PubMed DOI

Christie J.M., Swartz T.E., Bogomolni R.A., Briggs W.R. Phototropin LOV domains exhibit distinct roles in regulating photoreceptor function. Plant J. 2002;32:205–219. doi: 10.1046/j.1365-313X.2002.01415.x. PubMed DOI

Inoue S., Takemiya A., Shimazaki K. Phototropin signaling and stomatal opening as a model case. Curr. Opin. Plant Biol. 2010;13:587–593. doi: 10.1016/j.pbi.2010.09.002. PubMed DOI

Nakasone Y., Ohshima M., Okajima K., Tokutomi S., Terazima M. Photoreaction Dynamics of Full-Length Phototropin from Chlamydomonas reinhardtii. J. Phys. Chem. B. 2019;123:10939–10950. doi: 10.1021/acs.jpcb.9b09685. PubMed DOI

Motchoulski A., Liscum E. Arabidopsis NPH3: A NPH1 Photoreceptor-Interacting Protein Essential for Phototropism. Science. 1999;286:961–964. doi: 10.1126/science.286.5441.961. PubMed DOI

Inada S., Ohgishi M., Mayama T., Okada K., Sakai T. RPT2 Is a Signal Transducer Involved in Phototropic Response and Stomatal Opening by Association with Phototropin 1 in Arabidopsis thaliana. Plant Cell. 2004;16:887–896. doi: 10.1105/tpc.019901. PubMed DOI PMC

Sakai T., Wada T., Ishiguro S., Okada K. RPT2: A Signal Transducer of the Phototropic Response in Arabidopsis. Plant Cell. 2000;12:225–236. doi: 10.1105/tpc.12.2.225. PubMed DOI PMC

Pudasaini A., Zoltowski B.D. Zeitlupe Senses Blue-Light Fluence to Mediate Circadian Timing in Arabidopsis thaliana. Biochemistry. 2013;52:7150–7158. doi: 10.1021/bi401027n. PubMed DOI

Pudasaini A., Shim J.S., Song Y.H., Shi H., Kiba T., Somers D.E., Imaizumi T., Zoltowski B.D. Kinetics of the LOV domain of ZEITLUPE determine its circadian function in Arabidopsis. eLife. 2017;6:e21646. doi: 10.7554/eLife.21646. PubMed DOI PMC

Ito S., Song Y.H., Imaizumi T. LOV Domain-Containing F-Box Proteins: Light-Dependent Protein Degradation Modules in Arabidopsis. Mol. Plant. 2012;5:573–582. doi: 10.1093/mp/sss013. PubMed DOI PMC

Rockwell N.C., Su Y.-S., Lagarias J.C. Phytochrome Structure and Signaling Mechanisms. Annu. Rev. Plant Biol. 2006;57:837–858. doi: 10.1146/annurev.arplant.56.032604.144208. PubMed DOI PMC

Li J., Li G., Wang H., Deng X.W. Phytochrome Signaling Mechanisms. Arab. Book. 2011;9:e0148. doi: 10.1199/tab.0148. PubMed DOI PMC

Franklin K.A., Allen T., Whitelam G.C. Phytochrome A is an irradiance-dependent red light sensor. Plant J. 2007;50:108–117. doi: 10.1111/j.1365-313X.2007.03036.x. PubMed DOI

Legris M., Klose C., Burgie E.S., Rojas C.C.R., Neme M., Hiltbrunner A., Wigge P.A., Schäfer E., Vierstra R.D., Casal J.J. Phytochrome B integrates light and temperature signals in Arabidopsis. Science. 2016;354:897–900. doi: 10.1126/science.aaf5656. PubMed DOI

Qiu Y., Li M., Kim R.J.-A., Moore C.M., Chen M. Daytime temperature is sensed by phytochrome B in Arabidopsis through a transcriptional activator HEMERA. Nat. Commun. 2019;10:140. doi: 10.1038/s41467-018-08059-z. PubMed DOI PMC

Bianchetti R., De Luca B., de Haro L.A., Rosado D., Demarco D., Conte M., Bermudez L., Freschi L., Fernie A.R., Michaelson L.V., et al. Phytochrome-Dependent Temperature Perception Modulates Isoprenoid Metabolism. Plant Physiol. 2020;183:869–882. doi: 10.1104/pp.20.00019. PubMed DOI PMC

Pham V.N., Kathare P.K., Huq E. Phytochromes and Phytochrome Interacting Factors. Plant Physiol. 2018;176:1025–1038. doi: 10.1104/pp.17.01384. PubMed DOI PMC

Sakamoto T., Kimura S. Plant Temperature Sensors. Sensors. 2018;18:4365. doi: 10.3390/s18124365. PubMed DOI PMC

Chung B.Y.W., Balcerowicz M., Di Antonio M., Jaeger K.E., Geng F., Franaszek K., Marriott P., Brierley I., Firth A.E., Wigge P.A. An RNA thermoswitch regulates daytime growth in Arabidopsis. Nat. Plants. 2020;6:522–532. doi: 10.1038/s41477-020-0633-3. PubMed DOI PMC

Hayes S., Schachtschabel J., Mishkind M., Munnik T., Arisz S.A. Hot topic: Thermosensing in plants. Plant Cell Environ. 2021;44:2018–2033. doi: 10.1111/pce.13979. PubMed DOI PMC

Fujii Y., Tanaka H., Konno N., Ogasawara Y., Hamashima N., Tamura S., Hasegawa S., Hayasaki Y., Okajima K., Kodama Y. Phototropin perceives temperature based on the lifetime of its photoactivated state. Proc. Natl. Acad. Sci. USA. 2017;114:9206–9211. doi: 10.1073/pnas.1704462114. PubMed DOI PMC

Pooam M., Dixon N., Hilvert M., Misko P., Waters K., Jourdan N., Drahy S., Mills S., Engle D., Link J., et al. Effect of temperature on the Arabidopsis cryptochrome photocycle. Physiol. Plant. 2021;172:1653–1661. doi: 10.1111/ppl.13365. PubMed DOI

Salomé P.A. In the Heat of the Moment: ZTL-Mediated Protein Quality Control at High Temperatures. Plant Cell. 2017;29:2685–2686. doi: 10.1105/tpc.17.00871. PubMed DOI PMC

Noguchi M., Kodama Y. Temperature Sensing in Plants: On the Dawn of Molecular Thermosensor Research. Plant Cell Physiol. 2022;63:737–743. doi: 10.1093/pcp/pcac033. PubMed DOI

Pires N., Dolan L. Origin and Diversification of Basic-Helix-Loop-Helix Proteins in Plants. Mol. Biol. Evol. 2010;27:862–874. doi: 10.1093/molbev/msp288. PubMed DOI PMC

Hao Y., Zong X., Ren P., Qian Y., Fu A. Basic Helix-Loop-Helix (bHLH) Transcription Factors Regulate a Wide Range of Functions in Arabidopsis. Int. J. Mol. Sci. 2021;22:7152. doi: 10.3390/ijms22137152. PubMed DOI PMC

Qian Y., Zhang T., Yu Y., Gou L., Yang J., Xu J., Pi E. Regulatory Mechanisms of bHLH Transcription Factors in Plant Adaptive Responses to Various Abiotic Stresses. Front. Plant Sci. 2021;12:677611. doi: 10.3389/fpls.2021.677611. PubMed DOI PMC

Nesi N., Debeaujon I., Jond C., Pelletier G., Caboche M., Lepiniec L. The TT8 Gene Encodes a Basic Helix-Loop-Helix Domain Protein Required for Expression of DFR and BAN Genes in Arabidopsis Siliques. Plant Cell. 2000;12:1863–1878. doi: 10.1105/tpc.12.10.1863. PubMed DOI PMC

Devic M., Guilleminot J., Debeaujon I., Bechtold N., Bensaude E., Koornneef M., Pelletier G., Delseny M. The BANYULS gene encodes a DFR-like protein and is a marker of early seed coat development. Plant J. 1999;19:387–398. doi: 10.1046/j.1365-313X.1999.00529.x. PubMed DOI

Xie D.-Y., Sharma S.B., Paiva N.L., Ferreira D., Dixon R.A. Role of Anthocyanidin Reductase, Encoded by BANYULS in Plant Flavonoid Biosynthesis. Science. 2003;299:396–399. doi: 10.1126/science.1078540. PubMed DOI

Corrêa L.G.G., Riaño-Pachón D.M., Schrago C.G., dos Santos R.V., Mueller-Roeber B., Vincentz M. The Role of bZIP Transcription Factors in Green Plant Evolution: Adaptive Features Emerging from Four Founder Genes. PLoS ONE. 2008;3:e2944. doi: 10.1371/journal.pone.0002944. PubMed DOI PMC

Yu Y., Qian Y., Jiang M., Xu J., Yang J., Zhang T., Gou L., Pi E. Regulation Mechanisms of Plant Basic Leucine Zippers to Various Abiotic Stresses. Front. Plant Sci. 2020;11:1258. doi: 10.3389/fpls.2020.01258. PubMed DOI PMC

Alves M.S., Dadalto S.P., Gonçalves A.B., De Souza G.B., Barros V.A., Fietto L.G. Plant bZIP Transcription Factors Responsive to Pathogens: A Review. Int. J. Mol. Sci. 2013;14:7815–7828. doi: 10.3390/ijms14047815. PubMed DOI PMC

Gangappa S.N., Botto J.F. The Multifaceted Roles of HY5 in Plant Growth and Development. Mol. Plant. 2016;9:1353–1365. doi: 10.1016/j.molp.2016.07.002. PubMed DOI

Nguyen N.H. HY5, an integrator of light and temperature signals in the regulation of anthocyanins biosynthesis in Arabidopsis. AIMS Mol. Sci. 2020;7:70–81. doi: 10.3934/molsci.2020005. DOI

Xu D., Jiang Y., Li J., Lin F., Holm M., Deng X.W. BBX21, an Arabidopsis B-box protein, directly activates HY5 and is targeted by COP1 for 26S proteasome-mediated degradation. Proc. Natl. Acad. Sci. USA. 2016;113:7655–7660. doi: 10.1073/pnas.1607687113. PubMed DOI PMC

Holm M., Ma L.-G., Qu L.-J., Deng X.-W. Two interacting bZIP proteins are direct targets of COP1-mediated control of light-dependent gene expression in Arabidopsis. Genes Dev. 2002;16:1247–1259. doi: 10.1101/gad.969702. PubMed DOI PMC

Zhang Y., Zheng S., Liu Z., Wang L., Bi Y. Both HY5 and HYH are necessary regulators for low temperature-induced anthocyanin accumulation in Arabidopsis seedlings. J. Plant Physiol. 2011;168:367–374. doi: 10.1016/j.jplph.2010.07.025. PubMed DOI

Dubos C., Stracke R., Grotewold E., Weisshaar B., Martin C., Lepiniec L. MYB transcription factors in Arabidopsis. Trends Plant Sci. 2010;15:573–581. doi: 10.1016/j.tplants.2010.06.005. PubMed DOI

Katiyar A., Smita S., Lenka S.K., Rajwanshi R., Chinnusamy V., Bansal K.C. Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis. BMC Genom. 2012;13:544. doi: 10.1186/1471-2164-13-544. PubMed DOI PMC

Nesi N., Jond C., Debeaujon I., Caboche M., Lepiniec L. The Arabidopsis TT2 Gene Encodes an R2R3 MYB Domain Protein That Acts as a Key Determinant for Proanthocyanidin Accumulation in Developing Seed. Plant Cell. 2001;13:2099–2114. doi: 10.1105/TPC.010098. PubMed DOI PMC

Yang Y., Sulpice R., Himmelbach A., Meinhard M., Christmann A., Grill E. Fibrillin expression is regulated by abscisic acid response regulators and is involved in abscisic acid-mediated photoprotection. Proc. Natl. Acad. Sci. USA. 2006;103:6061–6066. doi: 10.1073/pnas.0501720103. PubMed DOI PMC

Shi M.-Z., Xie D.-Y. Features of anthocyanin biosynthesis in pap1-D and wild-type Arabidopsis thaliana plants grown in different light intensity and culture media conditions. Planta. 2010;231:1385–1400. doi: 10.1007/s00425-010-1142-9. PubMed DOI

Zhang Y., Yan Y.-P., Wang Z.-Z. The Arabidopsis PAP1 Transcription Factor Plays an Important Role in the Enrichment of Phenolic Acids in Salvia miltiorrhiza. J. Agric. Food Chem. 2010;58:12168–12175. doi: 10.1021/jf103203e. PubMed DOI

Li X., Gao M.-J., Pan H.-Y., Cui D.-J., Gruber M.Y. Purple Canola: Arabidopsis PAP1 Increases Antioxidants and Phenolics in Brassica napus Leaves. J. Agric. Food Chem. 2010;58:1639–1645. doi: 10.1021/jf903527y. PubMed DOI

Mitsunami T., Nishihara M., Galis I., Alamgir K.M., Hojo Y., Fujita K., Sasaki N., Nemoto K., Sawasaki T., Arimura G. Overexpression of the PAP1 Transcription Factor Reveals a Complex Regulation of Flavonoid and Phenylpropanoid Metabolism in Nicotiana tabacum Plants Attacked by Spodoptera litura. PLoS ONE. 2014;9:e108849. doi: 10.1371/journal.pone.0108849. PubMed DOI PMC

Youssef A., Laizet Y., Block M.A., Maréchal E., Alcaraz J.-P., Larson T.R., Pontier D., Gaffé J., Kuntz M. Plant lipid-associated fibrillin proteins condition jasmonate production under photosynthetic stress. Plant J. 2010;61:436–445. doi: 10.1111/j.1365-313X.2009.04067.x. PubMed DOI

Jiang J., Ma S., Ye N., Jiang M., Cao J., Zhang J. WRKY transcription factors in plant responses to stresses. J. Integr. Plant Biol. 2017;59:86–101. doi: 10.1111/jipb.12513. PubMed DOI

Guillaumie S., Mzid R., Méchin V., Léon 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;72:215–234. doi: 10.1007/s11103-009-9563-1. PubMed DOI

Phukan U.J., Jeena G.S., Shukla R.K. WRKY Transcription Factors: Molecular Regulation and Stress Responses in Plants. Front. Plant Sci. 2016;7:760. doi: 10.3389/fpls.2016.00760. PubMed DOI PMC

Grunewald W., De Smet I., Lewis D.R., Löfke C., Jansen L., Goeminne G., Vanden Bossche R., Karimi M., De Rybel B., Vanholme B., et al. Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis. Proc. Natl. Acad. Sci. USA. 2012;109:1554–1559. doi: 10.1073/pnas.1121134109. PubMed DOI PMC

Aamir M., Singh V.K., Meena M., Upadhyay R.S., Gupta V.K., Singh S. Structural and Functional Insights into WRKY3 and WRKY4 Transcription Factors to Unravel the WRKY–DNA (W-Box) Complex Interaction in Tomato (Solanum lycopersicum L.). A Computational Approach. Front. Plant Sci. 2017;8:819. doi: 10.3389/fpls.2017.00819. PubMed DOI PMC

Chen L., Song Y., Li S., Zhang L., Zou C., Yu D. The role of WRKY transcription factors in plant abiotic stresses. Biochim. Biophys. Acta (BBA)-Gene Regul. Mech. 2012;1819:120–128. doi: 10.1016/j.bbagrm.2011.09.002. PubMed DOI

Chi Y., Yang Y., Zhou Y., Zhou J., Fan B., Yu J.-Q., Chen Z. Protein–Protein Interactions in the Regulation of WRKY Transcription Factors. Mol. Plant. 2013;6:287–300. doi: 10.1093/mp/sst026. PubMed DOI

Yang Y., Liang T., Zhang L., Shao K., Gu X., Shang R., Shi N., Li X., Zhang P., Liu H. UVR8 interacts with WRKY36 to regulate HY5 transcription and hypocotyl elongation in Arabidopsis. Nat. Plants. 2018;4:98–107. doi: 10.1038/s41477-017-0099-0. PubMed DOI

van Nocker S., Ludwig P. The WD-repeat protein superfamily in Arabidopsis: Conservation and divergence in structure and function. BMC Genom. 2003;4:50. doi: 10.1186/1471-2164-4-50. PubMed DOI PMC

Mishra A.K., Puranik S., Prasad M. Structure and regulatory networks of WD40 protein in plants. J. Plant Biochem. Biotechnol. 2012;21:32–39. doi: 10.1007/s13562-012-0134-1. DOI

Pan Y., Shi H. Stabilizing the Transcription Factors by E3 Ligase COP1. Trends Plant Sci. 2017;22:999–1001. doi: 10.1016/j.tplants.2017.09.012. PubMed DOI

Laubinger S., Fittinghoff K., Hoecker U. The SPA Quartet: A Family of WD-Repeat Proteins with a Central Role in Suppression of Photomorphogenesis in Arabidopsis. Plant Cell. 2004;16:2293–2306. doi: 10.1105/tpc.104.024216. PubMed DOI PMC

Lloyd A., Brockman A., Aguirre L., Campbell A., Bean A., Cantero A., Gonzalez A. Advances in the MYB–bHLH–WD Repeat (MBW) Pigment Regulatory Model: Addition of a WRKY Factor and Co-option of an Anthocyanin MYB for Betalain Regulation. Plant Cell Physiol. 2017;58:1431–1441. doi: 10.1093/pcp/pcx075. PubMed DOI PMC

Li S. Transcriptional control of flavonoid biosynthesis. Plant Signal. Behav. 2014;9:e27522. doi: 10.4161/psb.27522. PubMed DOI PMC

Jin J., Tian F., Yang D.-C., Meng Y.-Q., Kong L., Luo J., Gao G. PlantTFDB 4.0: Toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res. 2017;45:D1040–D1045. doi: 10.1093/nar/gkw982. PubMed DOI PMC

Yu L., Sun Y., Zhang X., Chen M., Wu T., Zhang J., Xing Y., Tian J., Yao Y. ROS1 promotes low temperature-induced anthocyanin accumulation in apple by demethylating the promoter of anthocyanin-associated genes. Hortic. Res. 2022;9:uhac007. doi: 10.1093/hr/uhac007. PubMed DOI PMC

Pečinka P., Bohálová N., Volná A., Kundrátová K., Brázda V., Bartas M. Analysis of G-Quadruplex-Forming Sequences in Drought Stress-Responsive Genes, and Synthesis Genes of Phenolic Compounds in Arabidopsis thaliana. Life. 2023;13:199. doi: 10.3390/life13010199. PubMed DOI PMC

Volná A., Bartas M., Pečinka P., Špunda V., Červeň J. What Do We Know about Barley miRNAs? Int. J. Mol. Sci. 2022;23:14755. doi: 10.3390/ijms232314755. PubMed DOI PMC

Sharma D., Tiwari M., Pandey A., Bhatia C., Sharma A., Trivedi P.K. MicroRNA858 Is a Potential Regulator of Phenylpropanoid Pathway and Plant Development. Plant Physiol. 2016;171:944–959. doi: 10.1104/pp.15.01831. PubMed DOI PMC

Yang F., Cai J., Yang Y., Liu Z. Overexpression of microRNA828 reduces anthocyanin accumulation in Arabidopsis. Plant Cell Tiss. Organ Cult. 2013;115:159–167. doi: 10.1007/s11240-013-0349-4. DOI

Jia X., Shen J., Liu H., Li F., Ding N., Gao C., Pattanaik S., Patra B., Li R., Yuan L. Small tandem target mimic-mediated blockage of microRNA858 induces anthocyanin accumulation in tomato. Planta. 2015;242:283–293. doi: 10.1007/s00425-015-2305-5. PubMed DOI

Luo Q.-J., Mittal A., Jia F., Rock C.D. An autoregulatory feedback loop involving PAP1 and TAS4 in response to sugars in Arabidopsis. Plant Mol. Biol. 2012;80:117–129. doi: 10.1007/s11103-011-9778-9. PubMed DOI PMC

Pech R., Volná A., Hunt L., Bartas M., Červeň J., Pečinka P., Špunda V., Nezval J. Regulation of Phenolic Compound Production by Light Varying in Spectral Quality and Total Irradiance. Int. J. Mol. Sci. 2022;23:6533. doi: 10.3390/ijms23126533. PubMed DOI PMC

Abiotic Stresses in Plants: From Molecules to Environment