Plastid-mediated feedback regulation of Arabidopsis LYCOPENE EPSILON CYCLASE is modulated by the promoter and a 5′UTR structural variant harbouring a conserved IRES | BMC Biology

  • Li Y, Grotewold E, Dudareva N. Enough is enough: feedback control of specialized metabolism. Trends Plant Sci. 2024;29(5):514–23.

    Article 
    PubMed 

    Google Scholar 

  • Li C, Jiang R, Wang X, Lv Z, Li W, Chen W. Feedback regulation of plant secondary metabolism: applications and challenges. Plant Sci. 2024;340:111983.

    Article 
    PubMed 

    Google Scholar 

  • Baranski R, Cazzonelli C. Carotenoid biosynthesis and regulation in plants. In: Kaczor A, Baranska M, editors. Carotenoids: nutrition. Analysis and technology. Wiley-Blackwell. 2016:161–89.

  • Sun T, Rao S, Zhou X, Li L. Plant carotenoids: recent advances and future perspectives. Mol Hortic. 2022;2(1):3.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Cazzonelli CI, Pogson BJ. Source to sink: regulation of carotenoid biosynthesis in plants. Trends Plant Sci. 2010;15(5):266–74.

    Article 
    PubMed 

    Google Scholar 

  • Sun T, Yuan H, Cao H, Yazdani M, Tadmor Y, Li L. Carotenoid metabolism in plants: the role of plastids. Mol Plant. 2018;11(1):58–74.

    Article 
    PubMed 

    Google Scholar 

  • Llorente B, Martinez-Garcia JF, Stange C, Rodriguez-Concepcion M. Illuminating colors: regulation of carotenoid biosynthesis and accumulation by light. Curr Opin Plant Biol. 2017;37:49–55.

    Article 
    PubMed 

    Google Scholar 

  • Zheng X, Yang Y, Al-Babili S. Exploring the diversity and regulation of apocarotenoid metabolic pathways in plants. Front Plant Sci. 2021;12:787049.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Moreno JC, Mi J, Alagoz Y, Al-Babili S. Plant apocarotenoids: from retrograde signaling to interspecific communication. Plant J. 2021;105(2):351.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Cazzonelli CI, Hou X, Alagoz Y, Rivers J, Dhami N, Lee J, et al. A cis-carotene derived apocarotenoid regulates etioplast and chloroplast development. Elife. 2020;9:e45310.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Escobar-Tovar L, Sierra J, Hernandez-Munoz A, McQuinn RP, Mathioni S, Cordoba E, et al. Deconvoluting apocarotenoid-mediated retrograde signaling networks regulating plastid translation and leaf development. Plant J. 2021;105(6):1582–99.

    Article 
    PubMed 

    Google Scholar 

  • Hou X, Alagoz Y, Welsch R, Mortimer MD, Pogson BJ, Cazzonelli CI. Reducing PHYTOENE SYNTHASE activity fine-tunes the abundance of a cis-carotene-derived signal that regulates the PIF3/HY5 module and plastid biogenesis. J Exp Bot. 2024;75(4):1187–204.

    Article 
    PubMed 

    Google Scholar 

  • Van Norman JM, Zhang J, Cazzonelli CI, Pogson BJ, Harrison PJ, Bugg TD, et al. Periodic root branching in Arabidopsis requires synthesis of an uncharacterized carotenoid derivative. Proc Natl Acad Sci U S A. 2014;111(13):E1300–9.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Dickinson AJ, Lehner K, Mi J, Jia KP, Mijar M, Dinneny J, et al. β-Cyclocitral is a conserved root growth regulator. Proc Natl Acad Sci. 2019;116(21):10563–7.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Nayak JJ, Anwar S, Krishna P, Chen ZH, Plett JM, Foo E, et al. Tangerine tomato roots show increased accumulation of acyclic carotenoids, less abscisic acid, drought sensitivity, and impaired endomycorrhizal colonization. Plant Sci. 2022;321:111308.

    Article 
    PubMed 

    Google Scholar 

  • van Veen E, Küpers JJ, Gommers CMM. Plastids in a Pinch: Coordinating Stress and Developmental Responses Through Retrograde Signalling. Plant Cell Environ. 2025;48(9):6897-6911. https://doi.org/10.1111/pce.15664. Epub 2025 Jun 5. PMID: 40474490; PMCID: PMC12319301.

  • Agrawal S, Karcher D, Ruf S, Erban A, Hertle AP, Kopka J, et al. Riboswitch-mediated inducible expression of an astaxanthin biosynthetic operon in plastids. Plant Physiol. 2022;188(1):637–52.

    Article 
    PubMed 

    Google Scholar 

  • Alagoz Y, Nayak P, Dhami N, Cazzonelli CI. Cis-carotene biosynthesis, evolution and regulation in plants: the emergence of novel signaling metabolites. Arch Biochem Biophys. 2018;654:172–84. https://doi.org/10.1016/j.abb.2018.07.014.

    Article 
    PubMed 

    Google Scholar 

  • Alagoz Y, Nayak P, Dhami N, Cazzonelli CI. cis-carotene biosynthesis, evolution and regulation in plants: The emergence of novel signaling metabolites. Arch Biochem Biophys. 2018;654:172-184. https://doi.org/10.1016/j.abb.2018.07.014. Epub 2018 Jul 18. PMID: 30030998.

  • Álvarez D, Voß B, Maass D, Wüst F, Schaub P, Beyer P, et al. Carotenogenesis is regulated by 5′ UTR-mediated translation of phytoene synthase splice variants. Plant Physiol. 2016;172(4):2314–26.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Mitra S, Estrada-Tejedor R, Volke DC, Phillips MA, Gershenzon J, Wright LP. Negative regulation of plastidial isoprenoid pathway by herbivore-induced β-cyclocitral in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2021;118(10):e2008747118.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Sun J, Narayanasamy S, Curley RW Jr, Harrison EH. B;-Apo-13-carotenone regulates retinoid X receptor transcriptional activity through tetramerization of the receptor *. J Biol Chem. 2014;289(48):33118–24.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Cunningham FX Jr, Pogson B, Sun Z, McDonald KA, DellaPenna D, Gantt E. Functional analysis of the beta and epsilon lycopene cyclase enzymes of Arabidopsis reveals a mechanism for control of cyclic carotenoid formation. Plant Cell. 1996;8(9):1613–26.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Pogson B, McDonald KA, Truong M, Britton G, DellaPenna D. Arabidopsis carotenoid mutants demonstrate that lutein is not essential for photosynthesis in higher plants. Plant Cell. 1996;8(9):1627–39.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Enfissi EM, Nogueira M, Bramley PM, Fraser PD. The regulation of carotenoid formation in tomato fruit. Plant J. 2017;89(4):774–88.

    Article 
    PubMed 

    Google Scholar 

  • Park H, Kreunen SS, Cuttriss AJ, DellaPenna D, Pogson BJ. Identification of the carotenoid isomerase provides insight into carotenoid biosynthesis, prolamellar body formation, and photomorphogenesis. Plant Cell. 2002;14(2):321–32.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Cuttriss AJ, Chubb AC, Alawady A, Grimm B, Pogson BJ. Regulation of lutein biosynthesis and prolamellar body formation in Arabidopsis. Funct Plant Biol. 2007;34(8):663–72.

    Article 
    PubMed 

    Google Scholar 

  • Cazzonelli CI, Cuttriss AJ, Cossetto SB, Pye W, Crisp P, Whelan J, et al. Regulation of carotenoid composition and shoot branching in Arabidopsis by a chromatin modifying histone methyltransferase, SDG8. Plant Cell. 2009;21(1):39–53.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Shi Y, Wang R, Luo Z, Jin L, Liu P, Chen Q, et al. Molecular cloning and functional characterization of the lycopene ε-cyclase gene via virus-induced gene silencing and its expression pattern in Nicotiana tabacum. Int J Mol Sci. 2014;15(8):14766–85.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Yu B, Lydiate DJ, Young LW, Schäfer UA, Hannoufa A. Enhancing the carotenoid content of Brassica napus seeds by downregulating lycopene epsilon cyclase. Transgenic Res. 2008;17(4):573–85.

    Article 
    PubMed 

    Google Scholar 

  • Kim SH, Kim YH, Ahn YO, Ahn MJ, Jeong JC, Lee HS, et al. Downregulation of the lycopene ϵ-cyclase gene increases carotenoid synthesis via the β-branch-specific pathway and enhances salt-stress tolerance in sweetpotato transgenic calli. Physiol Plant. 2013;147(4):432–42.

    Article 
    PubMed 

    Google Scholar 

  • Ke Q, Kang L, Kim HS, Xie T, Liu C, Ji CY, et al. Down-regulation of lycopene ε-cyclase expression in transgenic sweetpotato plants increases the carotenoid content and tolerance to abiotic stress. Plant Sci. 2019;281:52–60.

    Article 
    PubMed 

    Google Scholar 

  • Diretto G, Tavazza R, Welsch R, Pizzichini D, Mourgues F, Papacchioli V, et al. Metabolic engineering of potato tuber carotenoids through tuber-specific silencing of lycopene epsilon cyclase. BMC Plant Biol. 2006;6(1):1–11.

    Article 

    Google Scholar 

  • Kaur N, Alok A, Kumar P, Kaur N, Awasthi P, Chaturvedi S, et al. CRISPR/Cas9 directed editing of lycopene epsilon-cyclase modulates metabolic flux for β-carotene biosynthesis in banana fruit. Metab Eng. 2020;59:76–86.

    Article 
    PubMed 

    Google Scholar 

  • Livneh Y, Leor-Librach E, Agmon D, Makov-Bouaniche T, Tiwari V, Shor E, et al. Combined enhancement of ascorbic acid, β-carotene and zeaxanthin in gene-edited lettuce. Plant Biotechnol J. 2025;23(6):1954–67.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Richaud D, Stange C, Gadaleta A, Colasuonno P, Parada R, Schwember AR. Identification of Lycopene epsilon cyclase (LCYE) gene mutants to potentially increase β-carotene content in durum wheat (Triticum turgidum L. ssp. durum) through TILLING. PLoS ONE. 2018;13(12):e0208948.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Harjes CE, Rocheford TR, Bai L, Brutnell TP, Kandianis CB, Sowinski SG, et al. Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification. Science. 2008;319(5861):330–3.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Muthusamy V, Hossain F, Thirunavukkarasu N, Saha S, Gupta HS. Allelic variations for lycopene-ε-cyclase and β-carotene hydroxylase genes in maize inbreds and their utilization in β-carotene enrichment programme. Cogent Food Agric. 2015;1(1):1033141.

    Article 

    Google Scholar 

  • Thatcher LF, Carrie C, Andersson CR, Sivasithamparam K, Whelan J, Singh KB. Differential gene expression and subcellular targeting of Arabidopsis glutathione S-transferase F8 is achieved through alternative transcription start sites. J Biol Chem. 2007;282(39):28915–28.

    Article 
    PubMed 

    Google Scholar 

  • Chung BY, Balcerowicz M, Di Antonio M, Jaeger KE, Geng F, Franaszek K, et al. An RNA thermoswitch regulates daytime growth in Arabidopsis. Nat Plants. 2020;6(5):522–32.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Assmann SM, Chou HL, Bevilacqua PC. Rock, scissors, paper: how RNA structure informs function. Plant Cell. 2023;35(6):1671–707.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bocobza S, Adato A, Mandel T, Shapira M, Nudler E, Aharoni A. Riboswitch-dependent gene regulation and its evolution in the plant kingdom. Genes Dev. 2007;21(22):2874–9.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wachter A, Tunc-Ozdemir M, Grove BC, Green PJ, Shintani DK, Breaker RR. Riboswitch control of gene expression in plants by splicing and alternative 3′ end processing of mrnas. Plant Cell. 2007;19(11):3437–50.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li S, Breaker RR. Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing. Nucleic Acids Res. 2013;41(5):3022–31.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Martinez-Salas E, Francisco-Velilla R, Fernandez-Chamorro J, Embarek AM. Insights into structural and mechanistic features of viral IRES elements. Front Microbiol. 2018;8:2629.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Cui Y, Rao S, Chang B, Wang X, Zhang K, Hou X, et al. Atla1 protein initiates IRES-dependent translation of WUSCHEL mRNA and regulates the stem cell homeostasis of Arabidopsis in response to environmental hazards. Plant, Cell Environ. 2015;38(10):2098–114.

    Article 
    PubMed 

    Google Scholar 

  • Dinkova TD, Zepeda H, Martínez-Salas E, Martínez LM, Nieto-Sotelo J, de Jiménez ES. Cap-independent translation of maize Hsp101. Plant J. 2005;41(5):722–31.

    Article 
    PubMed 

    Google Scholar 

  • Jiménez-González AS, Fernández N, Martínez-Salas E, Sánchez de Jiménez E. Functional and structural analysis of maize hsp101 IRES. PLoS One. 2014;9(9):e107459.

  • Urwin P, Yi L, Martin H, Atkinson H, Gilmartin PM. Functional characterization of the EMCV IRES in plants. Plant J. 2000;24(5):583–9.

    Article 
    PubMed 

    Google Scholar 

  • Fernandez J, Yaman I, Huang C, Liu H, Lopez AB, Komar AA, et al. Ribosome stalling regulates IRES-mediated translation in eukaryotes, a parallel to prokaryotic attenuation. Mol Cell. 2005;17(3):405–16.

    Article 
    PubMed 

    Google Scholar 

  • Kawaguchi R, Bailey-Serres J. mRNA sequence features that contribute to translational regulation in Arabidopsis. Nucleic Acids Res. 2005;33(3):955–65.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Isaacson T, Ronen G, Zamir D, Hirschberg J. Cloning of tangerine from tomato reveals a carotenoid isomerase essential for the production of beta-carotene and xanthophylls in plants. Plant Cell. 2002;14(2):333–42.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Romer S, Fraser PD, Kiano JW, Shipton CA, Misawa N, Schuch W, et al. Elevation of the provitamin A content of transgenic tomato plants. Nat Biotechnol. 2000;18(6):666–9.

    Article 
    PubMed 

    Google Scholar 

  • Yoon SH, Kim JE, Lee SH, Park HM, Choi MS, Kim JY, et al. Engineering the lycopene synthetic pathway in E. coli by comparison of the carotenoid genes of Pantoea agglomerans and Pantoea ananatis. Appl Microbiol Biotechnol. 2007;74(1):131–9.

    Article 
    PubMed 

    Google Scholar 

  • Wong EY, Hironaka CM, Fischhoff DA. Arabidopsis thaliana small subunit leader and transit peptide enhance the expression of Bacillus thuringiensis proteins in transgenic plants. Plant Mol Biol. 1992;20(1):81–93.

    Article 
    PubMed 

    Google Scholar 

  • Næsted H, Holm A, Jenkins T, Nielsen HB, Harris CA, Beale MH, et al. Arabidopsis VARIEGATED 3 encodes a chloroplast-targeted, zinc-finger protein required for chloroplast and palisade cell development. J Cell Sci. 2004;117(20):4807–18.

    Article 
    PubMed 

    Google Scholar 

  • Bhuiyan NH, Friso G, Rowland E, Majsec K, van Wijk KJ. The plastoglobule-localized metallopeptidase PGM48 is a positive regulator of senescence in Arabidopsis thaliana. Plant Cell. 2016;28(12):3020–37.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Gonzalez-Jorge S, Ha SH, Magallanes-Lundback M, Gilliland LU, Zhou A, Lipka AE, et al. Carotenoid cleavage dioxygenase4 is a negative regulator of β-carotene content in Arabidopsis seeds. Plant Cell. 2013;25(12):4812–26.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Brausemann A, Gemmecker S, Koschmieder J, Ghisla S, Beyer P, Einsle O. Structure of phytoene desaturase provides insights into herbicide binding and reaction mechanisms involved in carotene desaturation. Structure. 2017;25(8):1222-32.e3.

    Article 
    PubMed 

    Google Scholar 

  • Mayfield SP, Taylor WC. Carotenoid-deficient maize seedlings fail to accumulate light-harvesting chlorophyll a/b binding protein (LHCP) mRNA. Eur J Biochem. 1984;144(1):79–84.

    Article 
    PubMed 

    Google Scholar 

  • Dhami N, Pogson BJ, Tissue DT, Cazzonelli CI. A foliar pigment-based bioassay for interrogating chloroplast signalling revealed that carotenoid isomerisation regulates chlorophyll abundance. Plant Methods. 2022;18(1):18.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Cazzonelli CI, Roberts AC, Carmody ME, Pogson BJ. Transcriptional control of SET DOMAIN GROUP 8 and CAROTENOID ISOMERASE during Arabidopsis development. Mol Plant. 2010;3(1):174–91.

    Article 
    PubMed 

    Google Scholar 

  • Kumari S, Ware D. Genome-wide computational prediction and analysis of core promoter elements across plant monocots and dicots. PLoS ONE. 2013;8(10):e79011.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Shahmuradov IA, Umarov RK, Solovyev VV. TSSPlant: a new tool for prediction of plant Pol II promoters. Nucleic acids Res. 2017;45(8):e65-e.

  • Yamamoto YY, Ichida H, Matsui M, Obokata J, Sakurai T, Satou M, et al. Identification of plant promoter constituents by analysis of local distribution of short sequences. BMC Genomics. 2007;8:67.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Srivastava R, Rai KM, Srivastava M, Kumar V, Pandey B, Singh SP, et al. Distinct role of core promoter architecture in regulation of light-mediated responses in plant genes. Mol Plant. 2014;7(4):626–41.

    Article 
    PubMed 

    Google Scholar 

  • Yamamoto YY, Yoshitsugu T, Sakurai T, Seki M, Shinozaki K, Obokata J. Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis. Plant J. 2009;60(2):350–62.

    Article 
    PubMed 

    Google Scholar 

  • Parra G, Bradnam K, Rose AB, Korf I. Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants. Nucleic Acids Res. 2011;39(13):5328–37.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Gallegos JE, Rose AB. Intron DNA sequences can be more important than the proximal promoter in determining the site of transcript initiation. Plant Cell. 2017;29(4):843–53.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Laxa M, Müller K, Lange N, Doering L, Pruscha JT, Peterhänsel C. The 5′ UTR intron of Arabidopsis GGT1 aminotransferase enhances promoter activity by recruiting RNA polymerase II. Plant Physiol. 2016;172(1):313–27.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Etzel M, Mörl M. Synthetic riboswitches: from plug and pray toward plug and play. Biochemistry. 2017;56(9):1181–98.

    Article 
    PubMed 

    Google Scholar 

  • Boerneke MA, Dibrov SM, Gu J, Wyles DL, Hermann T. Functional conservation despite structural divergence in ligand-responsive RNA switches. Proc Natl Acad Sci. 2014;111(45):15952–7.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Giegerich R, Haase D, Rehmsmeier M. Prediction and visualization of structural switches in RNA. Biocomputing’99: World Scientific. 1999:126–37.

  • Voss B, Meyer C, Giegerich R. Evaluating the predictability of conformational switching in RNA. Bioinformatics. 2004;20(10):1573–82.

    Article 
    PubMed 

    Google Scholar 

  • Steffen P, Voß B, Rehmsmeier M, Reeder J, Giegerich R. RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics. 2006;22(4):500–3.

    Article 
    PubMed 

    Google Scholar 

  • Lorenz R, Bernhart SH, Zu Siederdissen CH, Tafer H, Flamm C, Stadler PF, et al. ViennaRNA Package 2.0. Algorithms Mol Biol. 2011;6(1):1–14.

  • Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL. The Vienna RNA websuite. Nucleic Acids Res. 2008;36(Web Server issue):W70-W4.

  • Wu GZ, Bock R. GUN control in retrograde signaling: how GENOMES UNCOUPLED proteins adjust nuclear gene expression to plastid biogenesis. Plant Cell. 2021;33(3):457–74.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Shi Y, Liu P, Xia Y, Wei P, Li W, Zhang W, et al. Downregulation of the lycopene ε-cyclase gene confers tolerance to salt and drought stress in Nicotiana tabacum. Acta Physiol Plant. 2015;37(10):1–15.

    Article 

    Google Scholar 

  • Hernandez-Verdeja T, Strand A. Retrograde signals navigate the path to chloroplast development. Plant Physiol. 2018;176(2):967–76.

    Article 
    PubMed 

    Google Scholar 

  • Zhong V, Archibald BN, Brophy JAN. Transcriptional and post-transcriptional controls for tuning gene expression in plants. Curr Opin Plant Biol. 2023;71:102315.

    Article 
    PubMed 

    Google Scholar 

  • Yang Y, Wang Z. IRES-mediated cap-independent translation, a path leading to hidden proteome. J Mol Cell Biol. 2019;11(10):911–9.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lozano G, Trapote A, Ramajo J, Elduque X, Grandas A, Robles J, et al. Local RNA flexibility perturbation of the IRES element induced by a novel ligand inhibits viral RNA translation. RNA Biol. 2015;12(5):555–68.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Ebina I, Takemoto-Tsutsumi M, Watanabe S, Koyama H, Endo Y, Kimata K, et al. Identification of novel Arabidopsis thaliana upstream open reading frames that control expression of the main coding sequences in a peptide sequence-dependent manner. Nucleic Acids Res. 2015;43(3):1562–76.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Cazzonelli CI, McCallum EJ, Lee R, Botella JR. Characterization of a strong, constitutive mung bean (Vigna radiata L.) promoter with a complex mode of regulation in planta. Transgenic Res. 2005;14(6):941–67.

    Article 
    PubMed 

    Google Scholar 

  • Fitzgerald KD, Semler BL. Bridging IRES elements in mrnas to the eukaryotic translation apparatus. Biochim Biophys Acta. 2009;1789(9–10):518–28.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Martínez-Salas E, Lozano G, Fernandez-Chamorro J, Francisco-Velilla R, Galan A, Diaz R. RNA-binding proteins impacting on internal initiation of translation. Int J Mol Sci. 2013;14(11):21705–26.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Srivastava AK, Lu Y, Zinta G, Lang Z, Zhu JK. Utr-dependent control of gene expression in plants. Trends Plant Sci. 2018;23(3):248–59.

    Article 
    PubMed 

    Google Scholar 

  • Hardy EC, Balcerowicz M. Untranslated yet indispensable—UTRs act as key regulators in the environmental control of gene expression. J Exp Bot. 2024;75(14):4314–31.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Chen Y, Li F, Wurtzel ET. Isolation and characterization of the Z-ISO gene encoding a missing component of carotenoid biosynthesis in plants. Plant Physiol. 2010;153(1):66–79.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Chory J, Peto C, Feinbaum R, Pratt L, Ausubel F. Arabidopsis thaliana mutant that develops as a light-grown plant in the absence of light. Cell. 1989;58(5):991–9.

    Article 
    PubMed 

    Google Scholar 

  • Kachanovsky DE, Filler S, Isaacson T, Hirschberg J. Epistasis in tomato color mutations involves regulation of phytoene synthase 1 expression by cis-carotenoids. Proc Natl Acad Sci U S A. 2012;109(46):19021–6.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Cazzonelli CI, Velten J. An in vivo, luciferase-based, Agrobacterium-infiltration assay system: implications for post-transcriptional gene silencing. Planta. 2006;224(3):582–97.

    Article 
    PubMed 

    Google Scholar 

  • Cazzonelli CI, Velten J. In vivo characterization of plant promoter element interaction using synthetic promoters. Transgenic Res. 2008;17(3):437–57.

    Article 
    PubMed 

    Google Scholar 

  • Cazzonelli CI, Velten J. Analysis of RNA-mediated gene silencing using a new vector (pKNOCKOUT) and an in planta Agrobacterium transient expression system. Plant Mol Biol Rep. 2004;22(4):347–59.

    Article 

    Google Scholar 

  • Holsters M, De Waele D, Depicker A, Messens E, Van Montagu M, Schell J. Transfection and transformation of Agrobacterium tumefaciens. Mol Gen Genet MGG. 1978;163(2):181–7.

    Article 
    PubMed 

    Google Scholar 

  • Hanahan D. Techniques for transformation of E. coli. DNA Cloning. 1985;1:109–35.

  • Velten J, Pogson B, Cazzonelli CI. Luciferase as a reporter of gene activity in plants. Transgenic Plant J. 2008;2:1–13.

    Google Scholar 

  • Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, et al. Primer3—new capabilities and interfaces. Nucleic Acids Res. 2012;40(15):e115-e.

    Article 

    Google Scholar 

  • Pfaffl MW. A new mathematical model for relative quantification in real-time RT–PCR. Nucleic Acids Res. 2001;29(9):e45-e.

    Article 

    Google Scholar 

  • Czechowski T, Stitt M, Altmann T, Udvardi MK, Scheible W-R. Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant Physiol. 2005;139(1):5–17.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Alagoz Y, Dhami N, Mitchell C, Cazzonelli CI. cis/trans carotenoid extraction, purification, detection, quantification, and profiling in plant tissues. Plant and food carotenoids. Springer. 2020:145–63.

  • Anwar S, Nayak JJ, Alagoz Y, Wojtalewicz D, Cazzonelli CI. Purification and use of carotenoid standards to quantify cis-trans geometrical carotenoid isomers in plant tissues. Methods Enzymol. 2022;670:57-85. https://doi.org/10.1016/bs.mie.2022.01.005. Epub 2022 Jan 31. PMID: 35871846.

  • Janssen S, Giegerich R. The RNA shapes studio. Bioinformatics. 2015;31(3):423–5.

    Article 
    PubMed 

    Google Scholar 

  • Grillo G, Turi A, Licciulli F, Mignone F, Liuni S, Banfi S, et al. UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res. 2010;38(Database issue):D75-D80.

  • Mokrejs M, Masek T, Vopálensky V, Hlubucek P, Delbos P, Pospísek M. IRESite–a tool for the examination of viral and cellular internal ribosome entry sites. Nucleic Acids Res. 2010;38(Database issue):D131–6.

    Article 
    PubMed 

    Google Scholar 

  • Pesole G, Liuni S. Internet resources for the functional analysis of 5′ and 3′ untranslated regions of eukaryotic mRNAs. Trends Genet. 1999;15(9):378.

    Article 
    PubMed 

    Google Scholar 

  • Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, et al. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 2002;30(1):325–7.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, et al. Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. Adv Bioinformatics. 2008;2008:420747.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Winter D, Vinegar B, Nahal H, Ammar R, Wilson GV, Provart NJ. An “Electronic Fluorescent Pictograph” browser for exploring and analyzing large-scale biological data sets. PLoS ONE. 2007;2(8):e718.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Klepikova AV, Kasianov AS, Gerasimov ES, Logacheva MD, Penin AA. A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling. Plant J. 2016;88(6):1058–70.

    Article 
    PubMed 

    Google Scholar 

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