# The circadian clock of Populus affects physiological, transcriptional and metabolomic responses to osmotic and ionic components of salt stress

**Authors:** Cristian Ibáñez, Alexander Vergara, David Castro, Luisa Bascunan-Godoy, Johan Sjölander, Manuela Jurca, Pierre A. Pin, Ove Nilsson, Maria E. Eriksson

PMC · DOI: 10.1038/s44323-025-00052-2 · npj Biological Timing and Sleep · 2025-10-01

## TL;DR

This study shows that the circadian clock in Populus trees helps them adapt to salt stress by regulating growth and metabolism.

## Contribution

The study reveals how specific circadian clock components influence physiological and metabolic responses to salt stress in trees.

## Key findings

- Reduced PttLHY1,2 levels affect growth adaptation under salt stress by controlling PttCyclin D3.
- PttPRR7a,b and PttGI1,2 help maintain root growth through metabolome adaptation.
- Prolonged stress alters root metabolome with changes in carbohydrates, amino acids, and fatty acids.

## Abstract

The circadian oscillator is an innate timing mechanism present in most organisms, including plants. In this study, Populus tremula × P. tremuloides (Populus) trees with reduced expression of circadian clock components were exposed to gradually increases in the osmotic and ionic components of salt stress. Reduced levels of the morning components PttLATE ELONGATED HYPOCOTYL 1 and 2 (PttLHY1,2) or of the evening components PttPSEUDO-RESPONSE REGULATOR 7a and b (PttPRR7a,b) and PttGIGANTEA1,2 (PttGI1,2) affected growth adaptation under stress conditions. PttLHY1,2 regulated growth under NaCl treatment via the control of PttCyclin D3 expression. PttPRR7a,b and PttGI1,2 were instrumental in maintaining growth in roots by enabling effective adaptation of the metabolome. Major changes in the root metabolome under prolonged stress included alterations in carbohydrate, amino acids, and fatty acids. This study places the circadian clock at the centre of adaptation to adverse conditions in trees and will help the development of stress-resistant trees.

## Linked entities

- **Chemicals:** NaCl (PubChem CID 5234)

## Full-text entities

- **Genes:** ENT1 (equilibrative nucleotide transporter 1) [NCBI Gene 843369] {aka AT, equilibrative nucleotide transporter 1}, CBF1 (C-repeat/DRE binding factor 1) [NCBI Gene 828653] {aka ATCBF1, C-repeat/DRE binding factor 1, DRE BINDING PROTEIN 1B, DREB1B, T30C3.11, TRANSCRIPTIONAL ACTIVATOR CBF1}, CCA1 (circadian clock associated 1) [NCBI Gene 819296] {aka AtCCA1, F19D11.11, MYB-RELATED DNA BINDING PROTEIN, circadian clock associated 1}, PRR7 (pseudo-response regulator 7) [NCBI Gene 831793] {aka APRR7, F9G14.120, F9G14_120, pseudo-response regulator 7}, TOC1 (CCT motif -containing response regulator protein) [NCBI Gene 836259] {aka APRR1, AtTOC1, MFB13.13, MFB13_13, PRR1, PSEUDO-RESPONSE REGULATOR 1}, CCR2 (CRINKLY4 related 2) [NCBI Gene 818503] {aka ATCRR2, CRINKLY4 related 2, T16B24.18, T16B24_18}, ZTL (Galactose oxidase/kelch repeat superfamily protein) [NCBI Gene 835842] {aka ADAGIO 1, ADO1, FKF1-LIKE PROTEIN 2, FKL2, LKP1, LOV KELCH PROTEIN 1}, LHY (Homeodomain-like superfamily protein) [NCBI Gene 839341] {aka LATE ELONGATED HYPOCOTYL, LATE ELONGATED HYPOCOTYL 1, LHY1, T25K16.6, T25K16_6}, PRR1 (pinoresinol reductase 1) [NCBI Gene 840102] {aka ATPRR1, F3C3.10, F3C3_10, PSEUDO-RESPONSE REGULATOR 1, pinoresinol reductase 1}, FUM2 (FUMARASE 2) [NCBI Gene 835168] {aka FUMARASE 2, K3K7.11, K3K7_11}, APX1 (ascorbate peroxidase 1) [NCBI Gene 837304] {aka ASCORBATE PEROXIDASE, ATAPX01, ATAPX1, CS1, F24B9.2, F24B9_2}, ELF3 (hydroxyproline-rich glycoprotein family protein) [NCBI Gene 817134] {aka EARLY FLOWERING 3, F17H15.25, PYK20}, ELF4 (EARLY FLOWERING-like protein (DUF1313)) [NCBI Gene 818596] {aka EARLY FLOWERING 4, T28M21.24, T28M21_24}, PC1 (pollen calcium-binding protein 1) [NCBI Gene 28721170] {aka APC1, K3M16.50, K3M16_50, pollen calcium-binding protein 1}, PCL1 (Homeodomain-like superfamily protein) [NCBI Gene 823817] {aka LUX, LUX ARRHYTHMO, PHYTOCLOCK 1}, PRR9 (pseudo-response regulator 9) [NCBI Gene 819292] {aka APRR9, Arabidopsis pseudo-response regulator 9, F19D11.7, TL1, TOC1-LIKE PROTEIN 1, pseudo-response regulator 9}
- **Diseases:** arrhythmic (OMIM:212500), arrhythmia (MESH:D001145), energy (MESH:D011502), DF (MESH:D006968), dehydration (MESH:D003681), C (OMIM:211750), water deficiency (MESH:D007174)
- **Chemicals:** benzoic acid (MESH:D019817), iso-citric acid (MESH:C034219), beta-sitostanol (MESH:C021255), uracil (MESH:D014498), beta-sitosterol (MESH:C025473), N (MESH:D009584), Fumaric acid (MESH:C032005), glucose-6-phosphate (MESH:D019298), 3-hydroxy-3-methylglutaric acid (MESH:D015093), histidine (MESH:D006639), DHA (MESH:D003683), agar (MESH:D000362), chlorophyll (MESH:D002734), alanine (MESH:D000409), thymine (MESH:D013941), 5,6 dihydrouracil (MESH:C007419), C (MESH:D002244), TCA (MESH:D014233), succinate (MESH:D019802), NaCl (MESH:D012965), proline (MESH:D011392), salt (MESH:D012492), sugar (MESH:D000073893), NH3 (MESH:D000641), GABA (MESH:D005680), pyroglutamic acid (MESH:D011761), glutamic acid (MESH:D018698), citrulline (MESH:D002956), AsA (MESH:D001205), malate (MESH:C030298), pyrimidine (MESH:C030986), Gly (MESH:D005998), valine (MESH:D014633), C18:0 (MESH:C031183), galactinol (MESH:C013536), saccharic acid (MESH:D005937), aspartic acid (MESH:D001224), amino acid (MESH:D000596), starch (MESH:D013213), octadecadienoic acid (MESH:C027369), fatty acid (MESH:D005227), arginine (MESH:D001120), carbohydrate (MESH:D002241), MS0 (-), raffinose (MESH:D011887), ornithine (MESH:D009952), K+ (MESH:D011188), oligosaccharides (MESH:D009844), 2-oxoglutarate (MESH:D007656), fructose-6-phosphate (MESH:C027618), glycine betaine (MESH:D001622), D-xylopyranose (MESH:C431715), Na (MESH:D012964), H+ (MESH:D006859), caffeic acid (MESH:C040048), Fumarate (MESH:D005650), ribose (MESH:D012266), paraquat (MESH:D010269), ROS (MESH:D017382), threonine (MESH:D013912)
- **Species:** Populus glandulosa (species) [taxon 266768], Populus tremula (European aspen, species) [taxon 113636], Brassica rapa (field mustard, species) [taxon 3711], Populus tremuloides (quaking aspen, species) [taxon 3693], Cauliflower mosaic virus (no rank) [taxon 10641], Homo sapiens (human, species) [taxon 9606], Populus alba (abele, species) [taxon 43335], Arabidopsis thaliana (mouse-ear cress, species) [taxon 3702], Populus tremula x Populus tremuloides (species) [taxon 47664], Hordeum vulgare (barley, species) [taxon 4513], Agrobacterium tumefaciens (species) [taxon 358], Medicago truncatula (barrel medic, species) [taxon 3880], Oryza sativa (Asian cultivated rice, species) [taxon 4530]
- **Cell lines:** -5 — Mus musculus (Mouse), Transformed cell line (CVCL_5U93), gi-13 — Homo sapiens (Human), Melanoma, Cancer cell line (CVCL_B6KN), prr7-5 — Mus musculus (Mouse), Hybridoma (CVCL_A0HR), -13 — Homo sapiens (Human), Childhood T acute lymphoblastic leukemia, Cancer cell line (CVCL_1081), -10 — Mus musculus (Mouse), Hybridoma (CVCL_C4R4), PC3 — Homo sapiens (Human), Prostate carcinoma, Cancer cell line (CVCL_0035)

## Full text

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## Figures

6 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12912307/full.md

## References

2 references — full list in the complete paper: https://tomesphere.com/paper/PMC12912307/full.md

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Source: https://tomesphere.com/paper/PMC12912307