# Role of CIA2 and CIL in the Regulation of Chloroplast Development During Photomorphogenesis in Arabidopsis

**Authors:** Roshanak Zarrin Ghalami, Paweł Burdiak, Muhammad Kamran, Maria Duszyn, Anna Rusaczonek, Ewa Muszyńska, Stanisław Karpiński

PMC · DOI: 10.3390/cells15040333 · 2026-02-11

## TL;DR

This study shows that CIA2 and CIL proteins are important for chloroplast development in plants, especially during the transition from dark to light conditions.

## Contribution

The study reveals CIA2 as the dominant factor in regulating chloroplast development and function during photomorphogenesis.

## Key findings

- CIA2 and CIL affect chloroplast ultrastructure, pigment accumulation, and photosynthetic gene expression.
- Complementation with CIA2 restores chloroplast morphology and function in mutant plants.
- CIA2 and CIL contribute to plant responses to light stress and chloroplast biogenesis.

## Abstract

What are the main findings?
CIA2 and CIL participate and optimize chloroplast biogenesis and development, affecting chloroplast ultrastructure, pigment accumulation, PSII function, and expression of key photosynthetic and protein-import genes.Complementation of the double cia2cil mutant with functional CIA2 restores early greening, chloroplast morphology, PSII performance, and gene expression dynamics to near wild-type levels, revealing CIA2 as the dominant factor in this regulatory module.

CIA2 and CIL participate and optimize chloroplast biogenesis and development, affecting chloroplast ultrastructure, pigment accumulation, PSII function, and expression of key photosynthetic and protein-import genes.

Complementation of the double cia2cil mutant with functional CIA2 restores early greening, chloroplast morphology, PSII performance, and gene expression dynamics to near wild-type levels, revealing CIA2 as the dominant factor in this regulatory module.

What is the implication of the main finding?
The results suggest that CIA2 and CIL may contribute not only in the regulation of responses to UV-AB, high light, heat shock and chloroplast translation regulation as it was indicated before, but also play a role in establishment of functional chloroplasts during early development, providing a basis for future studies for amelioration of crops chloroplast performance and photosynthetic capacity and in general plant light stress responses.

The results suggest that CIA2 and CIL may contribute not only in the regulation of responses to UV-AB, high light, heat shock and chloroplast translation regulation as it was indicated before, but also play a role in establishment of functional chloroplasts during early development, providing a basis for future studies for amelioration of crops chloroplast performance and photosynthetic capacity and in general plant light stress responses.

Chloroplast development plays a crucial role in plant de-etiolation, a process in which plants switch from growth in darkness to light-driven development, known as photomorphogenesis. This study provides evidence that CIA2 (Chloroplast Import Apparatus 2) and CIL (CIA2-Like) contribute to chloroplast biogenesis, likely by affecting and regulating PSII activity and related gene expression. Although their precise molecular roles remain unclear, our findings support their possible involvement in chloroplast development. This is indicated by downregulation of foliar chlorophyll content, chlorophyll a fluorescence parameters, chloroplast size, and gene expression of PSII molecular markers in the cia2cil double mutant during de-etiolation. Chlorophyll a fluorescence and quantitative gene expression analysis during de-etiolation revealed a significant reduction in PSII maximal efficiency and non-photochemical quenching, as well as deregulated expression of genes such as LHCB2.1 and psbA. According to the immunoblotting and microscopy imaging results, there is an impaired function of PSII and a compromised ultrastructure of the chloroplast membranes in cia2cil plants. However, in CIA2p::CIA2cia2cil and 35Sp::CIA2cia2cil complementation lines, reversion of this phenotype was observed. These results suggest a supporting role for CIA2 and CIL in the plant de-etiolation process, expanding our understanding of chloroplast biogenesis regulation.

## Linked entities

- **Genes:** Cia2 (collagen induced arthritis QTL 2) [NCBI Gene 112252], CIL (CCT motif family protein) [NCBI Gene 828705], LHCB2.1 (photosystem II light harvesting complex protein 2.1) [NCBI Gene 815058], psbA (photosystem II protein D1) [NCBI Gene 800253]
- **Species:** Arabidopsis (taxon 3701)

## Full-text entities

- **Genes:** GPRI1 (GBF's pro-rich region-interacting factor 1) [NCBI Gene 816579] {aka ARABIDOPSIS GOLDEN2-LIKE 1, ATGLK1, GBF's pro-rich region-interacting factor 1, GLK1, GOLDEN2-LIKE 1, T13C7.1}, rbcL (ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit) [NCBI Gene 844754], CIA2 (chloroplast import apparatus 2) [NCBI Gene 835824] {aka MUL3.13, MUL3_13, chloroplast import apparatus 2}, PP2AA3 (protein phosphatase 2A subunit A3) [NCBI Gene 837892] {aka 65 KDA REGULATORY SUBUNIT OF PROTEIN PHOSPHATASE 2A, PR65, T6J4.8, T6J4_8, protein phosphatase 2A  subunit A3, protein phosphatase 2A subunit A3}, GLK2 (GOLDEN2-like 2) [NCBI Gene 834442] {aka ATGLK2, GBF'S PRO-RICH REGION-INTERACTING FACTOR 2, GOLDEN2-like 2, GPRI2, MLN1.11, MLN1_11}, psbA (photosystem II protein D1) [NCBI Gene 844802], RPL18 (ribosomal protein L18) [NCBI Gene 819725] {aka CYTOPLASMIC RIBOSOMAL PROTEIN L18, F18C1.14, F18C1_14, ribosomal protein L18}, PIL5 (phytochrome interacting factor 3-like 5) [NCBI Gene 816538] {aka PHY-INTERACTING FACTOR 1, PIF1, T2G17.2, T2G17_2, phytochrome interacting factor 3-like 5}, TOC159 (translocon at the outer envelope membrane of chloroplasts 159) [NCBI Gene 827934] {aka ATTOC159, PLASTID PROTEIN IMPORT 2, PPI2, T10P11.19, TOC160, TOC86}, ELIP1 (Chlorophyll A-B binding family protein) [NCBI Gene 821855] {aka EARLY LIGHT-INDUCABLE PROTEIN, ELIP}, PIF4 (phytochrome interacting factor 4) [NCBI Gene 818903] {aka AtPIF4, MFL8.13, MFL8_13, SRL2, phytochrome interacting factor 4}, TIC110 (translocon at the inner envelope membrane of chloroplasts 110) [NCBI Gene 837205] {aka ARABIDOPSIS THALIANA TRANSLOCON AT THE INNER ENVELOPE MEMBRANE OF CHLOROPLASTS 110, ATTIC110, translocon at the inner envelope membrane of chloroplasts 110}, CGA1 (cytokinin-responsive gata factor 1) [NCBI Gene 828721] {aka F20B18.260, F20B18_260, GATA TRANSCRIPTION FACTOR 22, GATA22, GNC-LIKE, GNL}, CIL (CCT motif family protein) [NCBI Gene 828705] {aka F20B18.100, F20B18_100}, PAD4 (alpha/beta-Hydrolases superfamily protein) [NCBI Gene 824408] {aka ARABIDOPSIS PHYTOALEXIN DEFICIENT 4, ATPAD4, PHYTOALEXIN DEFICIENT 4}, UPL7 (ubiquitin-protein ligase 7) [NCBI Gene 824475] {aka ubiquitin-protein ligase 7}, TIC (time for coffee) [NCBI Gene 821807] {aka TIME FOR COFFEE}, LHCB2.1 (photosystem II light harvesting complex protein 2.1) [NCBI Gene 815058] {aka F15L11.2, F15L11_2, LHCB2, LIGHT-HARVESTING CHLOROPHYLL B-BINDING 2, photosystem II light harvesting complex gene 2.1}, HY5 (Basic-leucine zipper (bZIP) transcription factor family protein) [NCBI Gene 830996] {aka BZIP TRANSCRIPTION FACTOR HY5, ELONGATED HYPOCOTYL 5, F2I11.150, F2I11_150, REVERSAL OF THE DET PHENOTYPE 5, TED 5}, NPQ4 (Chlorophyll A-B binding family protein) [NCBI Gene 841033] {aka CP22, NONPHOTOCHEMICAL QUENCHING 4, PHOTOSYSTEM II SUBUNIT S, PSBS, PSII-S, T18F15.3}, LSD1 (LSD1 zinc finger family protein) [NCBI Gene 827786] {aka F9F13.30, F9F13_30, LESION SIMULATING DISEASE, LESION SIMULATING DISEASE 1}, RPS6 (disease resistance protein (TIR-NBS-LRR class) family) [NCBI Gene 834690] {aka K11I1.6, K11I1_6, RESISTANT TO P. SYRINGAE 6}, EDS1 (alpha/beta-Hydrolases superfamily protein) [NCBI Gene 823964] {aka ATEDS1, EDS1 PROTEIN, enhanced disease susceptibility 1}
- **Diseases:** Pigment (MESH:D010859), impaired photosynthetic (MESH:D060825), injury to (MESH:D014947), retardation (MESH:D008607), chlorophyll deficiencies (MESH:D007153), impaired function of PSII (MESH:D003072)
- **Chemicals:** acetonitrile (MESH:C032159), agar (MESH:D000362), Chlorophyll (MESH:D002734), polyacrylamide (MESH:C016679), bromophenol blue (MESH:D001978), nitrogen (MESH:D009584), salts (MESH:D012492), osmium tetroxide (MESH:D009993), GTP (MESH:D006160), methanol (MESH:D000432), ethanol (MESH:D000431), b (MESH:D001895), dithiothreitol (MESH:D004229), SDS (MESH:D012967), HCl (MESH:D006851), gibberellin (MESH:D005875), carotenoid (MESH:D002338), cacodylate (MESH:D002101), uranyl acetate (MESH:C005460), chlorine (MESH:D002713), sodium hypochlorite (MESH:D012973), lutein (MESH:D014975), acetone (MESH:D000096), CTAB (MESH:D000077286), glycerol (MESH:D005990), Chlorophyll a (-), ethyl acetate (MESH:C007650), glutaraldehyde (MESH:D005976), xanthophylls (MESH:D024341), PVDF (MESH:C024865), Coomassie blue (MESH:C048139), paraformaldehyde (MESH:C003043), sucrose (MESH:D013395), propylene oxide (MESH:C009068), cytokinin (MESH:D003583), luciferin (MESH:D000090562)
- **Species:** Homo sapiens (human, species) [taxon 9606], Arabidopsis thaliana (mouse-ear cress, species) [taxon 3702], Agrobacterium tumefaciens (species) [taxon 358]
- **Cell lines:** Col- — Homo sapiens (Human), Plasma cell myeloma, Cancer cell line (CVCL_A6IS), 35Sp::CIA2cia2cil — Mus musculus (Mouse), Hybridoma (CVCL_H155)

## Figures

6 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12940039/full.md

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Source: https://tomesphere.com/paper/PMC12940039