Cold acclimation of tomato plants is associated with differential expression of genes of the SlLHC family, carotenoid metabolism, and chlorophyll accumulation/degradation

Tomato (Solanum lycopersicum L.) is sensitive to cold stress. The plant’s adaptive response to low temperatures is accompanied by cellular osmoregulation and a decrease in the rate of photosynthesis due to disruption of the antennae of photosystems I and II, including proteins of the light-harvesting complex (LHC) family that bind chlorophylls a/b and carotenoids. In this study, a transcriptome analysis of differential expression of SlLHC family genes, carotenoid and abscisic acid (ABA) biosynthesis genes, as well as ORANGE and STAY-GREEN genes associated with chlorophyll accumulation and degradation, was performed for the first time during two cycles (I and II) of “cold stress (12 h) – recovery (60 h)”. The tomato cultivar Otradnyi was used for the analysis. 12 h before the end of the recovery period of the second cycle (II-48), the content of chlorophylls a/b and carotenoids in plant leaves was shown to be significantly decreased. It was revealed that 12 h of cold exposure in both cycles (I-12, II-12) suppressed the expression of most LHC family genes. At the same time points, a significant increase in the transcript levels of the NSY, CCD-like, LeNCED1 and NCED6 genes associated with ABA synthesis was detected. Genes, expression profile of which differed between the primary and repeated cycles of cold exposure, were identified. Based on these data, a list of candidate genes for cold stress memory markers in plants was compiled: 10 SlLHC family genes (Cab-1A, Cab-1D, CAB12, CAB5LOC101257186, SEP2, OHP2-LOC101259223, OHP1 and LIL3-2-LOC101247899) and five genes associated with ABA synthesis (VDE, CCD4, CCD-like, LeNCED1 and NCED6). The obtained results are important for identifying and understanding the involvement of photosynthesis-related genes in the response to cold stress and determining cold tolerance of tomato plants, and can be used in breeding cold-resistant varieties.

1. Agurla S., Gahir S., Munemasa S., Murata Y., Raghavendra A.S. Mechanism of stomatal closure in plants exposed to drought and cold stress. In: Iwaya-Inoue M., Sakurai M., Uemura M. (Eds) Survival Strategies in Extreme Cold and Desiccation. Advances in Experimental Medicine and Biology. Vol. 1081. Springer, 2018;215-232. doi 10.1007/978-981-13-1244-1_12

2. Aina O., Bakare O.O., Fadaka A.O., Keyster M., Klein A. Plant biomarkers as early detection tools in stress management in food crops: a review. Planta. 2024;259(3):60. doi 10.1007/s00425-024-04333-1

3. Ashraf M., Harris P.J.C. Photosynthesis under stressful environments: an overview. Photosynthetica. 2013;51:163-190. doi 10.1007/s11099-013-0021-6

4. Bäurle I., Trindade I. Chromatin regulation of somatic abiotic stress memory. J Exp Bot. 2020;71(17):5269-5279. doi 10.1093/jxb/eraa098

5. Browse J., Xin Z. Temperature sensing and cold acclimation. Curr Opin Plant Biol. 2001;4:241-246. doi 10.1016/s1369-5266(00)00167-9

6. Chen K., Li G.J., Bressan R.A., Song C.P., Zhu J.K., Zhao Y. Abscisic acid dynamics, signaling, and functions in plants. J Integr Plant Biol. 2020;62(1):25-54. doi 10.1111/jipb.12899

7. Ding Y., Shi Y., Yang S. Regulatory networks underlying plant responses and adaptation to cold stress. Annu Rev Genet. 2024;58(1):43-65. doi 10.1146/annurev-genet-111523-102226

8. Efremov G.I., Slugina M.A., Shchennikova A.V., Kochieva E.Z. Differential regulation of phytoene synthase PSY1 during fruit carotenogenesis in cultivated and wild tomato species (Solanum section Lycopersicon). Plants. 2020;9(9):1169. doi 10.3390/plants9091169

9. ElShamey E., Zeng Y., Ding Y., Yang J. Functional phytochemicals in tomatoes: biosynthesis, gene regulation, and human health implications. Front Plant Sci. 2025;16:1662388. doi 10.3389/fpls.2025.1662388

10. Filyushin M.A., Shchennikova A.V., Kochieva E.Z. Differential expression profile of DREB2 subfamily transcription factor genes in the dynamics of salt stress and post-stress recovery in tomato plants. Vavilovskii Zhurnal Genetiki i Selektsii = Vavilov J Genet Breed. 2025;29(8):1213-1220. doi 10.18699/vjgb-25-128

11. Friedrich T., Faivre L., Bäurle I., Schubert D. Chromatin-based mechanisms of temperature memory in plants. Plant Cell Environ. 2019; 42(3):762-770. doi 10.1111/pce.13373

12. Gao Y., Zhou X., Huang H., Wang C., Xiao X., Wen J., Wu J., Zhou S., de Dios V.R., Rodríguez L.G., Yao Y., Liu J., Deng H. ORANGE proteins mediate adaptation to high light and resistance to Pseudomonas syringae in tomato by regulating chlorophylls and carotenoids accumulation. Int J Biol Macromol. 2025;306(Pt.4):141739. doi 10.1016/j.ijbiomac.2025.141739

13. Ikuyinminu E., Goñi O., Łangowski Ł., O’Connell S. Transcriptome, biochemical and phenotypic analysis of the effects of a precision engineered biostimulant for inducing salinity stress tolerance in tomato. Int J Mol Sci. 2023;24(8):6988. doi 10.3390/ijms24086988

14. Jacques C., Salon C., Barnard R.L., Vernoud V., Prudent M. Drought stress memory at the plant cycle level: a review. Plants (Basel). 2021;10(9):1873. doi 10.3390/plants10091873

15. Jansson S. A guide to the Lhc genes and their relatives in Arabidopsis. Trends Plant Sci. 1999;4(6):236-240. doi 10.1016/s1360-1385(99)01419-3

16. Kidokoro S., Shinozaki K., Yamaguchi-Shinozaki K. Transcriptional regulatory network of plant cold-stress responses. Trends Plant Sci. 2022;27(9):922-935. doi 10.1016/j.tplants.2022.01.008

17. Klimmek F., Sjödin A., Noutsos C., Leister D., Jansson S. Abundantly and rarely expressed Lhc protein genes exhibit distinct regulation patterns in plants. Plant Physiol. 2006;140(3):793-804. doi 10.1104/pp.105.073304

18. Lan Y., Song Y., Zhao F., Cao Y., Luo D., Qiao D., Cao Y., Xu H. Phylogenetic, structural and functional evolution of the LHC gene family in plant species. Int J Mol Sci. 2022;24(1):488. doi 10.3390/ijms24010488

19. Li Y., Cao T., Guo Y., Grimm B., Li X., Duanmu D., Lin R. Regulatory and retrograde signaling networks in the chlorophyll biosynthetic pathway. J Integr Plant Biol. 2025;67(4):887-911. doi 10.1111/jipb.13837

20. Love M.I., Huber W., Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014; 15(12):550. doi 10.1186/s13059-014-0550-8

21. Meng F., Ma M., Li S., Liang P., Liang Y., Shi H., Huang S., Su H., Deng Y., Akram M.A., Shen X., Feng R., Zhan X., Ma F. Genomewide identification of light-harvesting chlorophyll a/b-binding (LHC) gene family in tomato and functional analysis of SlLhcb1.11 and SlELIP1 under cold stress. Genomics. 2025;117(2):111022. doi 10.1016/j.ygeno.2025.111022

22. Mesa T., Polo J., Arabia A., Caselles V., Munné-Bosch S. Differential physiological response to heat and cold stress of tomato plants and its implication on fruit quality. J Plant Physiol. 2022;268:153581. doi 10.1016/j.jplph.2021.153581

23. Nakashima K., Yamaguchi-Shinozaki K. ABA signaling in stress-response and seed development. Plant Cell Rep. 2013;32(7):959-970. doi 10.1007/s00299-013-1418-1

24. Neilson K.A., Mariani M., Haynes P.A. Quantitative proteomic analysis of cold-responsive proteins in rice. Proteomics. 2011;11(9):1696- 1706. doi 10.1002/pmic.201000727

25. Piechulla B., Merforth N., Rudolph B. Identification of tomato Lhc promoter regions necessary for circadian expression. Plant Mol Biol. 1998;38(4):655-662. doi 10.1023/a:1006094015513

26. Pietrzykowska M., Suorsa M., Semchonok D.A., Tikkanen M., Boekema E.J., Aro E.-M., Jansson S. The light-harvesting chlorophyll a/b binding proteins Lhcb1 and Lhcb2 play complementary roles during state transitions in Arabidopsis. Plant Cell. 2014;26(9):3646-3660. doi 10.1105/tpc.114.127373

27. Soualiou S., Duan F., Li X., Zhou W. Nitrogen supply alleviates cold stress by increasing photosynthesis and nitrogen assimilation in maize seedlings. J Exp Bot. 2023;74(10):3142-3162. doi 10.1093/jxb/erad073

28. Sreenivasulu N., Harshavardhan V.T., Govind G., Seiler C., Kohli A. Contrapuntal role of ABA: does it mediate stress tolerance or plant growth retardation under long-term drought stress? Gene. 2012; 506(2):265-273. doi 10.1016/j.gene.2012.06.076

29. Tee E.E. Orange is the new green: Arabidopsis ORANGE represses chloroplast biogenesis. Plant Cell. 2019;31(12):2824-2825. doi 10.1105/tpc.19.00670

30. Villagómez-Aranda A.L., Feregrino-Pérez A.A., García-Ortega L.F., González-Chavira M.M., Torres-Pacheco I., Guevara-González R.G. Activating stress memory: eustressors as potential tools for plant breeding. Plant Cell Rep. 2022;41(7):1481-1498. doi 10.1007/s00299-022-02858-x

31. Xu C., Wang Y., Yang H., Tang Y., Liu B., Hu X., Hu Z. Cold acclimation alleviates photosynthetic inhibition and oxidative damage induced by cold stress in citrus seedlings. Plant Signal Behav. 2023; 18(1):2285169. doi 10.1080/15592324.2023.2285169

32. Yamori W., Hikosaka K., Way D.A. Temperature response of photosynthesis in C3, C4, and CAM plants: temperature acclimation and temperature adaptation. Photosynth Res. 2014;119(1-2):101-117. doi 10.1007/s11120-013-9874-6

33. Yan J., Liu J., Yang S., Jiang C., Liu Y., Zhang N., Sun X., … Liu Y., Sun Z., Qi M., Wang F., Li T. Light quality regulates plant biomass and fruit quality through a photoreceptor-dependent HY5-LHC/ CYCB module in tomato. Hortic Res. 2023;10(12):uhad219. doi 10.1093/hr/uhad219

34. Zhang Q., Ma C., Wang X., Ma Q., Fan S., Zhang C. Genome-wide identification of the light-harvesting chlorophyll a/b binding (Lhc) family in Gossypium hirsutum reveals the influence of GhLhcb2.3 on chlorophyll a synthesis. Plant Biol (Stuttg). 2021;23(5):831-842. doi 10.1111/plb.13294

35. Zhao S., Gao H., Luo J., Wang H., Dong Q., Wang Y., Yang K., Mao K., Ma F. Genome-wide analysis of the light-harvesting chlorophyll a/b-binding gene family in apple (Malus domestica) and functional characterization of MdLhcb4.3, which confers tolerance to drought and osmotic stress. Plant Physiol Biochem. 2020;154:517-529. doi 10.1016/j.plaphy.2020.06.022