Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Apr;110(1):292-318.
doi: 10.1111/tpj.15667. Epub 2022 Mar 5.

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

Ting Lan #  1   2 , Wei Xiong #  1 , Xuemei Chen  3 , Beixin Mo  1 , Guiliang Tang  4
Affiliations
Free article

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

Ting Lan et al. Plant J. 2022 Apr.
Free article

Abstract

Standardized naming systems are essential to integrate and unify distinct research fields, and to link multi-species 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.

Keywords: Arabidopsis thaliana; Oryza sativa; evolution; function; new naming system; plant cytoplasmic ribosomal proteins; structure.

PubMed Disclaimer

References

REFERENCES

    1. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25, 3389-3402.
    1. Anger, A.M., Armache, J.P., Berninghausen, O., Habeck, M., Subklewe, M., Wilson, D.N. et al. (2013) Structures of the human and drosophila 80S ribosome. Nature, 497, 80-85.
    1. Armache, J.P., Jarasch, A., Anger, A.M., Villa, E., Becker, T., Bhushan, S. et al. (2010) Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-a resolution. Proceedings of the National Academy of Sciences of the United States of America, 107, 19748-19753.
    1. Armache, J.P., Jarasch, A., Anger, A.M., Villa, E., Becker, T., Bhushan, S. et al. (2010) Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome. Proceedings of the National Academy of Sciences of the United States of America, 107, 19754-19759.
    1. Balasubramanian, S., Zheng, D., Liu, Y.J., Fang, G., Frankish, A., Carriero, N. et al. (2009) Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes. Genome Biology, 10, R2.

Publication types

LinkOut - more resources