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Ribosome Heterogeneity in Plants
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Ribosome Heterogeneity in Plants

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Cell Biology".

Deadline for manuscript submissions: closed (20 March 2023) | Viewed by 6405

Special Issue Editor

Dr. Julio Sáez-Vásquez

E-Mail Website
Guest Editor
Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS-UPVD, Perpignan, France
Interests: nucleolus; ribosome biogenesis and rRNA genes in plants

Special Issue Information

Dear Colleagues,

Ribosome biogenesis and mRNA translation finetuning are keystones in plant growth and development in response to biotic and abiotic stress conditions. Ribosomal proteins (RP) and RNA (rRNAs) are the building blocks of ribosomes. Thus, controlling expression and modifications of particular RPs and rRNAs can impact the assembly and activity of ribosomes.

The concept of ribosome heterogeneity was proposed many years ago after the initial works reporting existence of ribosomal protein gene families in plants. Additional studies indicate that the expression of specific RP paralogs and their assembly at key positions in the ribosome might modulate translation of mRNAs. In addition, the expression of rDNA variants and rRNA modifications at structural and functional sites/domains might also modulate mRNAs’ translation under specific cellular conditions.

In this context, the main purpose is this Special Issue of Plants is to highlight findings indicating ribosome heterogeneity in different plant organisms in response to stress (biotic or abiotic) or across development. This Special Issue invites submissions of all new aspects regarding RP gene expression, RP protein modifications, and assembly into ribosomes. In addition, studies concerning the expression of rRNA gene variants, base and sugar modifications of rRNA, as well as modifying factors and activities, will also be considered. Original research papers, methods, reviews, and perspectives are welcome.

Dr. Julio Sáez-Vásquez
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • ribosome
  • ribosomal proteins (RP) and RNA (rRNA)
  • C/D and H/ACA snoRNAs

Published Papers (3 papers)

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19 pages, 4878 KiB  
Article
Arabidopsis ASYMMETRIC LEAVES2 and Nucleolar Factors Are Coordinately Involved in the Perinucleolar Patterning of AS2 Bodies and Leaf Development
by Sayuri Ando, Mika Nomoto, Hidekazu Iwakawa, Simon Vial-Pradel, Lilan Luo, Michiko Sasabe, Iwai Ohbayashi, Kotaro T. Yamamoto, Yasuomi Tada, Munetaka Sugiyama, Yasunori Machida, Shoko Kojima and Chiyoko Machida
Plants 2023, 12(20), 3621; https://doi.org/10.3390/plants12203621 - 19 Oct 2023
Viewed by 1323
Abstract
Arabidopsis ASYMMETRIC LEAVES2 (AS2) plays a key role in the formation of flat symmetric leaves. AS2 represses the expression of the abaxial gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3). AS2 interacts in vitro with the CGCCGC sequence in ETT [...] Read more.
Arabidopsis ASYMMETRIC LEAVES2 (AS2) plays a key role in the formation of flat symmetric leaves. AS2 represses the expression of the abaxial gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3). AS2 interacts in vitro with the CGCCGC sequence in ETT/ARF3 exon 1. In cells of leaf primordia, AS2 localizes at peripheral regions of the nucleolus as two AS2 bodies, which are partially overlapped with chromocenters that contain condensed 45S ribosomal DNA repeats. AS2 contains the AS2/LOB domain, which consists of three sequences conserved in the AS2/LOB family: the zinc finger (ZF) motif, the ICG sequence including the conserved glycine residue, and the LZL motif. AS2 and the genes NUCLEOLIN1 (NUC1), RNA HELICASE10 (RH10), and ROOT INITIATION DEFECTIVE2 (RID2) that encode nucleolar proteins coordinately act as repressors against the expression of ETT/ARF3. Here, we examined the formation and patterning of AS2 bodies made from as2 mutants with amino acid substitutions in the ZF motif and the ICG sequence in cells of cotyledons and leaf primordia. Our results showed that the amino acid residues next to the cysteine residues in the ZF motif were essential for both the formation of AS2 bodies and the interaction with ETT/ARF3 DNA. The conserved glycine residue in the ICG sequence was required for the formation of AS2 bodies, but not for the DNA interaction. We also examined the effects of nuc1, rh10, and rid2 mutations, which alter the metabolism of rRNA intermediates and the morphology of the nucleolus, and showed that more than two AS2 bodies were observed in the nucleolus and at its periphery. These results suggested that the patterning of AS2 bodies is tightly linked to the morphology and functions of the nucleolus and the development of flat symmetric leaves in plants. Full article
(This article belongs to the Special Issue Ribosome Heterogeneity in Plants)
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21 pages, 6638 KiB  
Article
45S rDNA Diversity In Natura as One Step towards Ribosomal Heterogeneity in Arabidopsis thaliana
by Valérie Delorme-Hinoux, Assane Mbodj, Sophie Brando, Anne De Bures, Christel Llauro, Fabrice Covato, Joseph Garrigue, Claude Guisset, Jacques Borrut, Marie Mirouze, Jean-Philippe Reichheld and Julio Sáez-Vásquez
Plants 2023, 12(14), 2722; https://doi.org/10.3390/plants12142722 - 21 Jul 2023
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Abstract
The keystone of ribosome biogenesis is the transcription of 45S rDNA. The Arabidopsis thaliana genome contains hundreds of 45S rDNA units; however, they are not all transcribed. Notably, 45S rDNA units contain insertions/deletions revealing the existence of heterogeneous rRNA genes and, likely, heterogeneous [...] Read more.
The keystone of ribosome biogenesis is the transcription of 45S rDNA. The Arabidopsis thaliana genome contains hundreds of 45S rDNA units; however, they are not all transcribed. Notably, 45S rDNA units contain insertions/deletions revealing the existence of heterogeneous rRNA genes and, likely, heterogeneous ribosomes for rRNAs. In order to obtain an overall picture of 45S rDNA diversity sustaining the synthesis of rRNAs and, subsequently, of ribosomes in natura, we took advantage of 320 new occurrences of Arabidopsis thaliana as a metapopulation named At66, sampled from 0 to 1900 m of altitude in the eastern Pyrenees in France. We found that the 45S rDNA copy number is very dynamic in natura and identified new genotypes for both 5′ and 3′ External Transcribed Spacers (ETS). Interestingly, the highest 5′ETS genotype diversity is found in altitude while the highest 3′ETS genotype diversity is found at sea level. Structural analysis of 45S rDNA also shows conservation in natura of specific 5′ETS and 3′ETS sequences/features required to control rDNA expression and the processing of rRNAs. In conclusion, At66 is a worthwhile natural laboratory, and unraveled 45S rDNA diversity represents an interesting starting material to select subsets for rDNA transcription and alter the rRNA composition of ribosomes both intra- and inter-site. Full article
(This article belongs to the Special Issue Ribosome Heterogeneity in Plants)
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15 pages, 694 KiB  
Perspective
Engineering Ribosomes to Alleviate Abiotic Stress in Plants: A Perspective
by Leticia Dias-Fields and Katarzyna P. Adamala
Plants 2022, 11(16), 2097; https://doi.org/10.3390/plants11162097 - 12 Aug 2022
Cited by 4 | Viewed by 2959
Abstract
As the centerpiece of the biomass production process, ribosome activity is highly coordinated with environmental cues. Findings revealing ribosome subgroups responsive to adverse conditions suggest this tight coordination may be grounded in the induction of variant ribosome compositions and the differential translation outcomes [...] Read more.
As the centerpiece of the biomass production process, ribosome activity is highly coordinated with environmental cues. Findings revealing ribosome subgroups responsive to adverse conditions suggest this tight coordination may be grounded in the induction of variant ribosome compositions and the differential translation outcomes they might produce. In this perspective, we go through the literature linking ribosome heterogeneity to plants’ abiotic stress response. Once unraveled, this crosstalk may serve as the foundation of novel strategies to custom cultivars tolerant to challenging environments without the yield penalty. Full article
(This article belongs to the Special Issue Ribosome Heterogeneity in Plants)
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