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A Plastoglobuli-Localized Enzyme Links Phenylalanine Biosynthesis to Translational Homeostasis in Maize

ABSTRACT:

Aromatic amino acids are essential precursors for numerous plant metabolites, with phenylalanine (Phe) forming the basis of the phenylpropanoid pathway. Here, we reveal a critical mechanism for Phe biosynthesis in maize, demonstrating that all seven arogenate dehydratases (ADTs) are specifically localized to plastoglobuli (PGs) in chloroplasts, and ADT2.2 shows high catalytic activity towards arogenate and prephenate. This discovery establishes PGs as a site for Phe synthesis. Genetic analysis confirms that only ADT2.2 is indispensable for plant and seed development, with its loss causing a severe Phe deficiency in seeds. This metabolic blockage directly reduced the tRNAPhe-GAA charging, thereby repressing protein translation. Crucially, we uncover that Phe starvation disproportionately affects the decoding efficiency of wobble-paired codons, increasing ribosome pausing. Our work provides biochemical and genetic evidence that PGs-localized ADT2.2 catalyzes Phe synthesis and reveals a link between amino acid availability and codon-specific translation dynamics.

INSTRUMENT(S): Liquid Chromatography MS - negative - reverse-phase, Liquid Chromatography MS - positive - reverse-phase

PROVIDER: MTBLS14848 | MetaboLights | 2026-06-25

REPOSITORIES: MetaboLights

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			Action	DRS
	a_MTBLS14848_LC-MS_negative_reverse-phase.txt	Txt
	a_MTBLS14848_LC-MS_positive_reverse-phase.txt	Txt
	i_Investigation.txt	Txt
	m_MTBLS14848_LC-MS_negative_reverse-phase_v2_maf.tsv	Tabular
	m_MTBLS14848_LC-MS_positive_reverse-phase_v2_maf.tsv	Tabular

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A Plastoglobuli-Localized Enzyme Links Phenylalanine Biosynthesis to Translational Homeostasis in Maize

Project description:Aromatic amino acids are essential precursors for numerous plant metabolites, with phenylalanine (Phe) forming the basis of the phenylpropanoid pathway. Here, we reveal a critical mechanism for Phe biosynthesis in maize, demonstrating that all seven arogenate dehydratases (ADTs) are specifically localized to plastoglobuli (PGs) in chloroplasts, and ADT2.2 shows high catalytic activity towards arogenate and prephenate. This discovery establishes PGs as a site for Phe synthesis. Genetic analysis confirms that only ADT2.2 is indispensable for plant and seed development, with its loss causing a severe Phe deficiency in seeds. This metabolic blockage directly reduced the tRNAPhe-GAA charging, thereby repressing protein translation. Crucially, we uncover that Phe starvation disproportionately affects the decoding efficiency of wobble-paired codons, increasing ribosome pausing. Our work provides biochemical and genetic evidence that PGs-localized ADT2.2 catalyzes Phe synthesis and reveals a link between amino acid availability and codon-specific translation dynamics.

2026-06-25 | MTBLS14849 | MetaboLights

A Plastoglobuli-Localized Enzyme Links Phenylalanine Biosynthesis to Translational Homeostasis in Maize

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A Plastoglobuli-Localized Enzyme Links Phenylalanine Biosynthesis to Translational Homeostasis in Maize

2026-06-25 | MTBLS14852 | MetaboLights

m6A is decoded by modified tRNAs to coordinate mRNA decay [ribosome profiling]

Project description:In eukaryotes, the genetic code is transcribed into messenger RNA (mRNA) in the nucleus and decoded by transfer RNA (tRNA) in the cytosol. Nuclear mRNA processing events that do not affect the nucleotide sequence of an mRNA are thought to be invisible to tRNAs during protein translation in the cytosol. Here, we report a mechanism by which the modified mRNA nucleotide N6‑methyladenosine (m6A) connects nuclear mRNA processing to tRNA decoding. m6A is deposited in the protein coding sequence (CDS) of mRNAs with long exons, where it slows the decoding of a subset of m6A-modified codons in vivo. Translation of codons with m6A at the wobble position is facilitated by 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U), a modified nucleotide of the tRNA anticodon loop that juxtaposes the wobble-m6A. This unanticipated link between the mRNA and tRNA epitranscriptomes controls mRNA half-life in a translation-dependent manner and connects the exon-intron architecture of mRNAs to their turnover. The pathways for m6A and mcm5s2U biogenesis are tightly co-regulated in human tissues but deregulated in cancer cells. In breast cancer, a shift towards more mcm5s2U is associated with tumor aggressiveness and poor prognosis. Thus, the m6A/mcm5s2U-balance has evolved as a pan-epitranscriptomic mechanism that coordinates gene expression changes and curtails tumorigenesis.

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Optimization of codon translation rates via tRNA modifications maintains proteome integrity

Project description:Proteins begin to fold as they emerge from translating ribosomes. The kinetics of ribosome transit along a given mRNA can influence nascent chain folding, but the extent to which individual codon translation rates impact proteome integrity remains unknown. Here, we show that slower decoding of discrete codons elicits widespread protein aggregation in vivo. Using ribosome profiling, we find that loss of anticodon wobble uridine (U34) modifications in a subset of tRNAs leads to ribosome pausing at their cognate codons in S. cerevisiae and C. elegans. Yeast cells lacking U34 modifications exhibit gene expression hallmarks of proteotoxic stress and accumulate aggregates of endogenous proteins with key cellular functions. Moreover, these cells are severely compromised in clearing stress-induced protein aggregates. Overexpression of hypomodified tRNAs alleviates ribosome pausing, concomitantly restoring protein homeostasis. Our findings demonstrate that modified U34 is an evolutionarily conserved accelerator of decoding and reveal an unanticipated role for tRNA anticodon modifications in maintaining proteome integrity. Ribosome profiling of wild-type and tRNA modification-deficient yeast and nematodes. Yeast samples were generated in various growth conditions (rich medium versus stress induced by treatment with diamide or rapamycin) and paired mRNA-Seq was performed on a subset of samples. Dataset contains three biological replicates for yeast samples and two biological replicates for nematode samples.

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Project description:Recent evidence indicates that codon usage bias regulates gene expression. How viruses, such as the emerging mosquito-borne Chikungunya virus (CHIKV), express their genomes at high levels despite an enrichment in rare codons remains a puzzling question. Using ribosome footprinting, here we analysed translational changes that occur upon CHIKV infection at the ER and the cytosol. We show that CHIKV infection induces codon-specific reprogramming of the host translation machinery to favor the translation of viral RNA genomes over host mRNAs with an otherwise optimal codon usage. This reprogramming was mostly apparent at the ER, where CHIKV RNAs are efficiently translated. Mechanistically, it involves CHIKV-induced overexpression of KIAA1456, an enzyme that modifies the wobble U34 position in the anticodon of tRNAs, which we find is required for proper decoding of codons that are highly enriched in CHIKV RNAs. Our findings demonstrate an unprecedented interplay of viruses with the host tRNA epitranscriptome to adapt the host translation machinery to viral production.

2025-06-16 | MTBLS2443 | MetaboLights

TCR alpha sequencing of CD4+ Tcells infiltrating melanoma B16 control or depleted of Elp3

Project description:The tRNA epitranscriptome is composed of a wide variety of base modifications in tRNAs and is emerging as a potential key vulnerability of cancer. Wobble tRNA modifications are required for specific codon decoding during translation and maintenance of protein homeostasis and support cancer metastasis and resistance to therapy. Here we show that ablation of enzymes catalyzing wobble uridine (U34) tRNA modification (U34 enzymes) remodels the MHC-II-associated antigen repertoire of melanoma by perturbing codon-specific mRNA translation. This perturbation in translation triggers the formation of aggregates that are subsequently degraded through the autophagy-lysosomal pathway and presented on MHC-II. The remodeled MHC-II repertoire in turn induces a CD4+ effector T cell-mediated anti-tumor response displaying specific clonal selection and immunodominance in melanoma. Our results identify a novel, potentially tractable, vulnerability of melanoma, in which codon-specific mRNA translation through wobble uridine tRNA modification, optimizes proteome homeostasis, prevents excessive antigen presentation, and limits T cell activity in melanoma.

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TCR beta sequencing of CD4+ Tcells infiltrating melanoma B16 control or depleted of Elp3

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Deciphering the reading of the genetic code by near-cognate tRNA

Project description:Some codons of the genetic code can be read not only by cognate, but also by near-cognate tRNAs. This flexibility is thought to be conferred mainly by a mismatch between the third base of the codon and the first of the anticodon (the so-called wobble position). However, this simplistic explanation underestimates the importance of nucleotide modifications in the decoding process. Using a system in which only near-cognate tRNAs can decode a specific codon, we investigated the role of six modifications of the anticodon, or adjacent nucleotides, of the tRNAs specific for Tyr, Gln, Lys, Trp, Cys and Arg in Saccharomyces cerevisiae. Modifications almost systematically rendered these tRNAs able to act as near-cognate tRNAs at stop codons, even though they involve non-canonical base-pairs, without markedly affecting their ability to decode cognate or near-cognate sense codons. These findings reveal an important effect of modifications to tRNA decoding with implications for understanding the flexibility of the genetic code.

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Ribosome decoding memory directs translational re-coding of codon repeats

Project description:During mRNA translation, ribosome dynamics at individual codons critically shape the quality and quantity of protein products. Long runs of consecutive codons are generally thought to impede elongation by depleting cognate tRNAs. However, in Huntington’s disease, ribosomes translate hundreds of consecutive CAG codons without catastrophic stalling. Here, we systematically profile ribosome behavior across repeats of all 20 amino acids encoded in the human genome. For proline and lysine repeats – commonly considered difficult to decode – we find that ribosomes accelerate after an initial phase of slow decoding, a phenomenon we term adaptive decoding. Remarkably, codon-specific decoding memory enables iterative translation of arginine repeats, generating internally expanded protein products. In contrast, acidic amino acid repeats trigger ribosomal bypassing and produce internally truncated proteins. Contrary to prevailing assumptions, decoding inertia acquired during repeat translation constraints frameshifting. Disrupting the decoding memory of CAG repeats by inserting proline codons is beneficial in reducing polyglutamine synthesis and aggregation. These findings uncover an adaptive dimension of ribosome decoding that contributes to the synthesis of physiological and pathological amino acid repeats.

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