Ribosomal RNA Biogenesis and Its Response to Chilling Stress in <i>Oryza sativa</i>

Hang, Runlai; Wang, Zhen; Deng, Xian; Liu, Chun yan; Yan, Bin; Yang, Chao; Song, Xianwei; Mo, Beixin; Cao, Xiaofeng

doi:10.1104/pp.17.01714

Cited by 54 publications

(34 citation statements)

References 155 publications

(299 reference statements)

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“…This preferential ITS1-first processing was first observed in xrn2 plants (Zakrzewska-Placzek et al, 2010), while the accumulation of 59ETS-first transcripts was reported in biogenesis of ribosomes in xenopus1 (brx1) plants (Weis et al, 2015b). These two pathways also coexist in rice plants, with the ITS1-first mode being the major pathway (Hang et al, 2018). Environmental stimuli or stress conditions might prevent the accumulation of pre-rRNA from the ITS1-first pathway (Weis et al, 2015a).…”

Section: Processing Of Pre-rrna: Two Alternative Pathwaysmentioning

confidence: 92%

Ribosome Biogenesis in Plants: From Functional 45S Ribosomal DNA Organization to Ribosome Assembly Factors

2019

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The transcription of 18S, 5.8S, and 18S rRNA genes (45S rDNA), cotranscriptional processing of pre-rRNA, and assembly of mature rRNA with ribosomal proteins are the linchpins of ribosome biogenesis. In yeast (Saccharomyces cerevisiae) and animal cells, hundreds of pre-rRNA processing factors have been identified and their involvement in ribosome assembly determined. These studies, together with structural analyses, have yielded comprehensive models of the pre-40S and pre-60S ribosome subunits as well as the largest cotranscriptionally assembled preribosome particle: the 90S/small subunit processome. Here, we present the current knowledge of the functional organization of 45S rDNA, pre-rRNA transcription, rRNA processing activities, and ribosome assembly factors in plants, focusing on data from Arabidopsis (Arabidopsis thaliana). Based on yeast and mammalian cell studies, we describe the ribonucleoprotein complexes and RNA-associated activities and discuss how they might specifically affect the production of 40S and 60S subunits. Finally, we review recent findings concerning pre-rRNA processing pathways and a novel mechanism involved in a ribosome stress response in plants

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Section: Processing Of Pre-rrna: Two Alternative Pathwaysmentioning

confidence: 92%

Ribosome Biogenesis in Plants: From Functional 45S Ribosomal DNA Organization to Ribosome Assembly Factors

2019

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“…The processing of this pre-rRNA has been described in detail in both yeast and humans, but to date there is no clear outline in plants. However, possible models for A. thaliana (35) and Oryza sativa (43) have been proposed.…”

Section: Introductionmentioning

confidence: 99%

Citrus exocortis viroid causes ribosomal stress in tomato plants

Cottilli

Belda-Palazón

Adkar-Purushothama

et al. 2019

Nucleic Acids Research

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Viroids are naked RNAs that do not code for any known protein and yet are able to infect plants causing severe diseases. Because of their RNA nature, many studies have focused on the involvement of viroids in RNA-mediated gene silencing as being their pathogenesis mechanism. Here, the alterations caused by the Citrus exocortis viroid (CEVd) on the tomato translation machinery were studied as a new aspect of viroid pathogenesis. The presence of viroids in the ribosomal fractions of infected tomato plants was detected. More precisely, CEVd and its derived viroid small RNAs were found to co-sediment with tomato ribosomes in vivo, and to provoke changes in the global polysome profiles, particularly in the 40S ribosomal subunit accumulation. Additionally, the viroid caused alterations in ribosome biogenesis in the infected tomato plants, affecting the 18S rRNA maturation process. A higher expression level of the ribosomal stress mediator NAC082 was also detected in the CEVd-infected tomato leaves. Both the alterations in the rRNA processing and the induction of NAC082 correlate with the degree of viroid symptomatology. Taken together, these results suggest that CEVd is responsible for defective ribosome biogenesis in tomato, thereby interfering with the translation machinery and, therefore, causing ribosomal stress.

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“…These two pre-rRNA processing activities require additional accessory proteins, such as RNA exosome components, Pumilio proteins, and many RNA-binding proteins. It has been reported that Arabidopsis and rice show similar pre-rRNA processing pathways, probably due to the similar anking sequences around the endocleavage sites of A2 and A3 in ITS1 [20], suggesting that RNA binding speci city is essential for the selection of cleavage sites. Recently, APUM23…”

Section: Typical Pumilio Proteins Have Tandem Repeats Of 8 Puf Domainmentioning

confidence: 99%

Structural and functional similarities and differences in nucleolar Pumilio RNA-binding proteins between Arabidopsis and the charophyte Chara corallina

Park

Kim

Kalita

et al. 2020

Preprint

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Background: Pumilio RNA-binding proteins are evolutionarily conserved throughout eukaryotes and are involved in RNA decay, transport, and translation repression in the cytoplasm. Although a majority of Pumilio proteins function in the cytoplasm, two nucleolar forms have been reported to have a function in rRNA processing in Arabidopsis. The species of the genus Chara have been known to be most closely related to land plants, as they share several characteristics with modern Embryophyta. Results: In this study, we identified two putative nucleolar Pumilio protein genes, namely, ChPUM2 and ChPUM3, from the transcriptome of Chara corallina. Of the two ChPUM proteins, ChPUM2 was most similar in amino acid sequence (27% identity and 45% homology) and predicted protein structure to Arabidopsis APUM23, while ChPUM3 was similar to APUM24 (35% identity and 54% homology). The transient expression of 35S:ChPUM2-RFP and 35S:ChPUM3-RFP showed nucleolar localization of fusion proteins in tobacco leaf cells, similar to the expression of 35S:APUM23-GFP and 35S:APUM24-GFP. Moreover, 35S:ChPUM2 complemented the morphological defects of the apum23 phenotypes but not those of apum24, while 35S:ChPUM3 could not complement the apum23 and apum24 mutants. Similarly, the 35S:ChPUM2/apum23 plants rescued the pre-rRNA processing defect of apum23, but 35S:ChPUM3/apum24+/- plants did not rescue that of apum24. Consistent with these complementation results, a known target RNA-binding sequence at the end of the 18S rRNA (5'-GGAAUUGACGG) for APUM23 was conserved in Arabidopsis and C. corallina, whereas a target region of ITS2 pre-rRNA for APUM24 was 156 nt longer in C. corallina than in A. thaliana. Moreover, ChPUM2 and APUM23 were predicted to have nearly identical structures, but ChPUM3 and APUM24 have different structures in the 5th C-terminal Puf RNA-binding domain, which had a longer random coil in ChPUM3 than in APUM24. Conclusions: ChPUM2 of C. corallina was functional in Arabidopsis, similar to APUM23, but ChPUM3 did not substitute for APUM24 in Arabidopsis. Protein homology modeling showed high coverage between APUM23 and ChPUM2, but displayed structural differences between APUM24 and ChPUM3. Together with the protein structure of ChPUM3 itself, a short ITS2 of Arabidopsis pre-rRNA may interrupt the binding of ChPUM3 to 3’-extended 5.8S pre-rRNA.

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Ribosomal RNA Biogenesis and Its Response to Chilling Stress in Oryza sativa

Cited by 54 publications

References 155 publications

Ribosome Biogenesis in Plants: From Functional 45S Ribosomal DNA Organization to Ribosome Assembly Factors

Ribosome Biogenesis in Plants: From Functional 45S Ribosomal DNA Organization to Ribosome Assembly Factors

Citrus exocortis viroid causes ribosomal stress in tomato plants

Structural and functional similarities and differences in nucleolar Pumilio RNA-binding proteins between Arabidopsis and the charophyte Chara corallina

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