User talk:Bhavana G Krishnan

1. Overview

The study by Smirnova et al. reports a near-atomic (2.2 Å) cryo-EM structure of the Nicotiana tabacum 80S ribosome, captured in the midst of active translation. The structure includes mRNA, two hybrid-state tRNAs, and a nascent polypeptide, offering a realistic representation of an elongating ribosome rather than a static, isolated particle.

This contribution fills a critical gap in plant structural biology. Although high-resolution cytosolic ribosomes from yeast, mammals, and multiple protists have been described, equivalent plant structures have remained limited. By presenting the architecture of an actively translating plant ribosome, the work highlights how plants retain the conserved eukaryotic catalytic core while evolving lineage-specific regulatory features that support their unique physiological demands.

2. Active Translational State

The ribosome is visualized in a rotated-2 (hybrid) state, where tRNAs occupy the A/P and P/E positions. This state reflects the dynamic phase of the elongation cycle in which the small and large subunits undergo relative rotation. The clear density for the nascent chain and mRNA enables the entire path of ligand engagement to be followed with precision.

This representation aligns with elongation intermediates described in diverse eukaryotic lineages, reinforcing the conservation of the fundamental translation mechanism. At the same time, peripheral structural features distinguish the plant ribosome from fungal and metazoan systems.

3. rRNA Modifications

More than 200 rRNA modifications are mapped within the structure, including 2'-O-methylations, pseudouridines, and additional base modifications. These modifications cluster in regions associated with:codon–anticodon recognition, the peptidyl-transferase center, the mRNA channel, and tRNA transit sites.

Their distribution reflects the importance of epitranscriptomic tuning in plant translation. Given the wide environmental fluctuations encountered by plants, such modifications likely stabilize ribosomal performance under varying physiological conditions.

4. Ion Coordination and Microenvironment

The structural analysis reveals a dense network of K⁺ ions, particularly concentrated near the decoding center. Three monovalent ions reinforce interactions at the codon–anticodon interface and are coordinated by plant-specific residues in protein uS12.

This ion arrangement differs from that observed in bacterial and some eukaryotic systems, suggesting a specialized ionic microenvironment that supports stable decoding in plants. Such adaptations may provide resilience to osmotic or ionic fluctuations linked to plant environmental responses.

5. Expansion Segments and Ribosomal Extensions

Plant rRNA contains distinctive expansion segments (ESs), with ES7L being a prominent example. The plant-specific subdivisions ES7Ld and ES7Le contribute to a uniquely elaborate architecture not present in fungal or animal ribosomes.

A plant-conserved N-terminal extension of eL6 stabilizes ES7L, indicating co-evolution between rRNA and ribosomal proteins. Expansion segments of this scale likely serve as docking or regulatory platforms for translation factors, particularly those involved in initiation and reinitiation.

6. Intersubunit Bridges

The ribosome exhibits conformational adjustments within several intersubunit bridges. The eB13 bridge, typically stabilized by eL24 in other eukaryotes, displays reduced density in this structure. In plants, this appears to be compensated by the Reinitiation Supporting Protein (RISP), a factor not required in mammalian or fungal systems.

This structural dependency offers a biochemical explanation for the plant-specific requirement of RISP and highlights how intersubunit connectivity evolves in response to regulatory needs associated with complex mRNA landscapes, including uORFs and polycistronic transcripts.

7. Structural and Evolutionary Significance

The actively translating plant 80S ribosome presents a combination of: a deeply conserved catalytic core, extensive lineage-specific expansion, a diverse modification landscape, and unique patterns of ion coordination.

These features underscore the ribosome’s role as a dynamic molecular platform shaped by the ecological and physiological demands of each lineage. In the context of plants, the structure provides essential insights into how translational regulation supports environmental adaptation, metabolic flexibility, and rapid proteome remodeling.

The work establishes a foundational reference for future comparative studies and for understanding translational control mechanisms that are unique to plant systems.