Translatomics for algae, liverwort, and E. coli
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,
- Ghandour et al. used Ribo-Seq and RNA-seq to systematically investigate assembly-dependent translational feedback loops across photosynthetic electron transport chain complexes in land plants.
- Chotewutmontri et al. utilize Ribo-Seq and RNA-seq to examine chloroplast translation in the liverwort Marchantia polymorpha.
- Borovská et al. establish transcriptome-scale mapping of RNA secondary structure ensembles to systematically discover novel, conserved RNA regulatory switches in both prokaryotic and eukaryotic models.
Assembly-dependent translational feedback regulation of photosynthetic proteins in land plants
Nature Plants, 2025
Ghandour, R., Gao, Y., Ruf, S., Bock, R. and Zoschke, R.
In the model green alga Chlamydomonas reinhardtii, the synthesis of chloroplast-encoded photosynthetic subunits is tightly synchronized with their complex assembly state. This feedback mechanism, termed “Control by Epistasy of Synthesis” (CES), coordinates protein production across all major photosynthetic complexes. However, in land plants (embryophytes), CES had only been established for Rubisco. The authors aimed to systematically investigate whether land plants employ similar assembly-dependent translational feedback loops across their photosynthetic electron transport chain complexes. They utilized a combination of RNA-seq and ribosome profiling (Ribo-Seq) across land plant mutants with specific assembly defects in photosystem II (PSII), cytochrome b6f (Cyt b6f) photosystem I (PSI), ATP synthase, the NAD(P)H dehydrogenase-like (NDH) complex, and Rubisco.
Parallel RNA-seq and ribosome profiling confirmed CES in Rubisco and revealed active translational feedback regulation within PSII, specifically altering the translation rates of psbA, psbB, and psbD, as well as within the Cyt b6f complex, where petA and petB translation was affected. The data also highlighted potential feedback networks among ATP synthase subunits and uncovered an unexpected cross-talk regulation linking PSII assembly to PSI translation. In contrast to algae, the translatome data showed no evidence of CES or translational feedback occurring during PSI or NDH complex assembly. Ultimately, the study demonstrates that while assembly-dependent feedback exists in land plants, most specific regulatory connections are evolutionary divergent from those found in green algae.
Learn more about EIRNABio’s ribosome profiling services here.
Effects of light on chloroplast translation in Marchantia polymorpha are similar to those in angiosperms and are not influenced by light‐independent chlorophyll synthesis
The Plant Journal, 2025
Chotewutmontri, P., Williams‐Carrier, R., Belcher, S. and Barkan, A.
In angiosperms, photodamage to the D1 subunit of photosystem II (PSII) triggers a sharp increase in the translation of chloroplast psbA mRNA to supply new D1 for repair. Because angiosperms can only synthesize chlorophyll in the light, and certain regulatory proteins mediate chlorophyll/D1 interactions, it has been hypothesized that chlorophyll synthesis itself drives this light-dependent translational regulation. The authors’ aim was to test this hypothesis by examining chloroplast translation in the liverwort Marchantia polymorpha, a non-vascular plant that naturally synthesizes chlorophyll in both the light and the dark. They utilized RNA-seq and ribosome profiling (Ribo-Seq) to analyze chloroplast gene expression across wild-type Marchantia and a mutant incapable of dark chlorophyll synthesis, comparing light- and dark-treated conditions.
Ribosome profiling revealed that ribosome occupancy on psbA mRNA dropped dramatically in the dark and was rapidly restored upon light exposure, whereas other chloroplast mRNAs showed minimal changes. This pattern was identical in the mutant lacking dark chlorophyll synthesis, proving that constitutive chlorophyll synthesis does not influence light-regulated psbA translation initiation. Integrated data showed that light drives a global, plastome-wide activation of translation elongation alongside the specific increase in psbA initiation. RNA-seq and translatome comparisons showed that while total chloroplast protein outputs are highly similar between Marchantia and angiosperms, they are achieved through differing baseline configurations of mRNA abundance and translational efficiency, underscoring co-evolutionary tuning.
Learn more about EIRNABio’s ribosome profiling services here.
Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis
Nature Biotechnology, 2025
Borovská, I., Zhang, C., Dülk, S.L.J., Morandi, E., Cardoso, M.F., Bourkia, B.M., van den Homberg, D.A., Wolfinger, M.T., Velema, W.A. and Incarnato, D.
RNA molecules dynamically fold into alternative structural conformations that control gene expression. However, comprehensively mapping these complex RNA conformational landscapes and identifying functional, shape-shifting regulatory switches directly within living cells has remained technically elusive. The authors’ aim was to bridge this gap by establishing transcriptome-scale mapping of RNA secondary structure ensembles to systematically discover novel, conserved RNA regulatory switches in both prokaryotic and eukaryotic models. Instead of traditional RNA-seq or ribosome profiling, the authors generated transcriptome-scale secondary structure ensemble maps combined with ensemble deconvolution and covariation analyses in Escherichia coli and human cells (HEK293).
In E. coli, conditional structure mapping during temperature shifts revealed massive restructuring of RNA ensembles. The authors discovered and deconvoluted several novel bacterial “RNA thermometers” in the 5′ untranslated regions (UTRs) of cspG, cspI, cpxP, and lpxP mRNAs, demonstrating how they alter structure during cold shock. They also uncovered an intricate regulation of lpxP mediated by the CspE chaperone. Additionally, they introduced a tailored method for transcriptome-wide 5′ UTR structure mapping in eukaryotes. Applying this to human HEK293 cells, they successfully uncovered functional RNA structural switches that regulate the differential usage of upstream open reading frames (uORFs) in the 5′ UTRs of the CKS2 and TXNL4A mRNAs. Ultimately, this study uncovers the hidden complexity of in vivo RNA structural dynamics and provides a high-throughput framework to accelerate the discovery of regulatory RNA switches across species.
Learn more about EIRNABio’s ribosome profiling services here.