Translatomics for chloroplast, rice, and uORF
Recent Publications Harnessing the Power of Translatomics
Every week we provide a digest of a small number of recent interesting papers in the field of translatomics.
In this week’s Sunday papers,
- Hong et al. demonstrated that chloroplast precursor accumulation triggers heat shock-like responses, translational reprogramming, and proteostasis mechanisms.
- Luo et al. showed that FLR2 phosphorylates CPR5 to regulate mRNA poly(A) tail processing, controlling translation and enhancing rice immunity against Magnaporthe oryzae.
- Zhang et al. indicated that a uORF represses OsHsfA1a translation to fine-tune WOX11 expression, balancing crown root development with optimal rice growth and yield.
Chloroplast precursor protein preClpD overaccumulation triggers multilevel reprogramming of gene expression and a heat shock-like response
Nature Communications, 2025.
Hong, Z.H., Zhu, L., Gao, L.L., Zhu, Z., Su, T., Krall, L., Wu, X.N., Bock, R. and Wu, G.Z.
The study investigates how plant cells respond when chloroplast precursor proteins accumulate in the cytosol due to impaired chloroplast protein import. Ribosome profiling and polysome profiling were used to study selective translational reprogramming and translation of stress-responsive transcripts. Using inducible and constitutive overexpression of the chloroplast precursor preClpD, the authors demonstrate that precursor overaccumulation stress (cPOS) triggers extensive transcriptional, translational, and proteomic reprogramming.
Chloroplast development is impaired, leading to reduced photosystem assembly, defective ribosome biogenesis, altered RNA editing, and increased chloroplast-derived reactive oxygen species (ROS). These ROS act as retrograde signals to activate small heat-shock protein (sHSP) genes. Simultaneously, translational activation enhances the production of cytosolic chaperones, including HSPs, while the chaperone HOT1/ClpB1 promotes precursor granule formation and maintains cytosolic proteostasis.
The study also shows increased ribosome biogenesis and ubiquitin–proteasome system activity to manage protein quality control. Together, these findings reveal that chloroplast protein import stress elicits a coordinated heat shock-like response integrating chloroplast-to-nucleus signaling, translational regulation, and proteostasis to protect plant cells from precursor protein toxicity.
Learn more about EIRNABio’s ribosome profiling and polysome profiling services here.
Phosphorylation of CPR5 by the receptor kinase FLR2 promotes mRNA poly (A) tail processing and immunity in rice against Magnaporthe oryzae
Plant Communications, 2025.
Luo, X., Xing, J., Peng, Z., Zhang, M., Wei, Z., Xu, J., Yu, F. and Deng, H.
The study demonstrates that the receptor-like kinase FLR2 regulates rice immunity against Magnaporthe oryzae by controlling post-transcriptional gene expression through CPR5. FLR2 phosphorylates CPR5, which modulates the poly(A) tail length of OsEIL1 mRNA, thereby regulating its translation. Loss of FLR2 or CPR5 results in longer OsEIL1 poly(A) tails, increased OsEIL1 translation, elevated ROS production, and enhanced resistance to the rice blast fungus. Phospho-dead and phospho-mimic CPR5 mutants confirmed that FLR2-dependent phosphorylation is essential for proper poly(A) tail processing and immune regulation.
Polysome profiling showed that OsEIL1 mRNA was enriched in heavy polysome fractions in flr2 and cpr5 mutants, demonstrating that altered poly(A) tail length directly enhances translational efficiency. These findings reveal a previously unknown mechanism linking plasma membrane receptor signaling to mRNA processing and translation during plant immunity.
Learn more about EIRNABio’s polysome profiling services here.
The uORF-HsfA1a-WOX11 module controls crown root development in rice
New Phytologist, 2025.
Zhang, T., Xiang, Y., Ye, M., Yuan, M., Xu, G., Zhou, D.X. and Zhao, Y.
The study identifies a uORF–HsfA1a–WOX11 regulatory module that fine-tunes crown root development in rice. The transcription factor OsHsfA1a directly activates OsWOX11, a key regulator of crown root formation, while an upstream open reading frame (uORF) in the 5′-UTR of OsHsfA1a represses its translation to maintain optimal WOX11 expression. Disrupting this uORF increases HsfA1a translation, causing excessive crown root growth, dwarfism, and reduced yield.
Polysome profiling demonstrated that the uORF limits OsHsfA1a translational efficiency by reducing its association with actively translating ribosomes, providing direct evidence that uORF-mediated translational control balances root and shoot development. These findings highlight translational regulation as a promising strategy for engineering improved rice root architecture without compromising crop productivity.
Learn more about EIRNABio’s polysome profiling services here.