Plant cytoplasmic ribosomal proteins: an update on classification, nomenclature, evolution and resources

Abstract

Standardized naming systems are essential to integrate and unify distinct research fields, and to link multispecies data within and across kingdoms. We conducted a comprehensive survey of cytoplasmic ribosomal proteins (CRPs) in the dicot model Arabidopsis thaliana and the monocot model rice, noting that the standardized naming system has not been widely adopted in the plant community. We generated a database linking the old classical names to their updated and compliant names. We also explored the sequences, molecular evolution, and structural and functional characteristics of all plant CRP families, emphasizing evolutionarily conserved and plant-specific features through cross-kingdom comparisons. Unlike fungal CRP paralogs that were mainly created by whole-genome duplication (WGD) or retroposition under a concerted evolution mode, plant CRP genes evolved primarily through both WGD and tandem duplications in a rapid birth-and-death process. We also provide a web-based resource (http://www.plantcrp.cn/) with the aim of sharing the latest knowledge on plant CRPs and facilitating the continued development of a standardized framework across the entire community.

An updated nomenclature for plant ribosomal protein genes

“…A more detailed comparison highlighting how this naming system builds on the Ban et al . (2014) and Lan et al . (2022) nomenclatures is offered below. At this time, we request community feedback on this proposed nomenclature so that the naming system ultimately chosen represents a broad consensus.…”

“…Here, we propose compatible upgrades to the homology-guided nomenclature proposed by Ban et al (2014) so that this naming system can be adopted for widespread use in the plant biology community. We note that Lan et al (2022) recently proposed updated nomenclature for plant cytosolic ribosomal proteins, focused on Arabidopsis and rice.…”

“…The nomenclature outlined here is an extension of that proposed by Lan et al (2022), expanding to include organellar ribosomes and additional species, with the intent that this nomenclature can serve as a template to guide future plant genome annotations. A more detailed comparison highlighting how this naming system builds on the Ban et al…”

“…We have provided a provisional table of r-protein names for Arabidopsis, tomato, maize, and rice for the plant biology community to consider, alongside their historical names in Arabidopsis and their names as recently proposed by Lan et al (2022) (Supplemental Dataset 1). Note that the Lan et al (2022) nomenclature differs primarily in how paralogues are named, which is a result of the exclusive focus of that nomenclature on cytosolic ribosomes. The new nomenclature will be added to public databases, including TAIR, MaizeGDB, the Plant Cytoplasmic Ribosomal Proteins database (PlantCRP.cn), and any other databases recommended by the community.…”

“…(2022) recently proposed updated nomenclature for plant cytosolic ribosomal proteins, focused on Arabidopsis and rice. The nomenclature outlined here is an extension of that proposed by Lan et al . (2022), expanding to include organellar ribosomes and additional species, with the intent that this nomenclature can serve as a template to guide future plant genome annotations.…”