The Conserved Endoribonuclease YbeY Is Required for Chloroplast Ribosomal RNA Processing in Arabidopsis

Liu, Jinwen; Zhou, Wen; Liu, Guifeng; Yang, Chuanping; Sun, Yuena; Wu, Wenjuan; Cao, Shenquan; Wang, Chong; Hai, Guanghui; Wang, Zhifeng; Bock, Ralph; Huang, Jirong; Cheng, Yuxiang

doi:10.1104/pp.114.255000

Cited by 57 publications

(75 citation statements)

References 68 publications

(105 reference statements)

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“…The atrsgA‐i intron mutant showed a typical chloroplast deficiency phenotype, such as chlorotic leaves with a reduced rosette area (Figure ), depleted photosynthetic pigments and reduced photosynthesis (Figure ). These phenotypes have been described for numerous mutants with disturbed chloroplast biogenesis, chlorophyll production (Motohashi et al ., ; Liu et al ., ; Maekawa et al ., ) and chloroplast ribosome assembly (Komatsu et al ., ; Liu et al ., ; Fristedt et al ., ). These defects ultimately resulted in massive growth retardation and a decrease in the rosette area of the mutant (Figure S3).…”

Section: Discussionmentioning

confidence: 98%

AtRsgA from Arabidopsis thaliana is important for maturation of the small subunit of the chloroplast ribosome

et al. 2018

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Plastid ribosomes are very similar in structure and function to the ribosomes of their bacterial ancestors. Since ribosome biogenesis is not thermodynamically favorable under biological conditions it requires the activity of many assembly factors. Here we have characterized a homolog of bacterial RsgA in Arabidopsis thaliana and show that it can complement the bacterial homolog. Functional characterization of a strong mutant in Arabidopsis revealed that the protein is essential for plant viability, while a weak mutant produced dwarf, chlorotic plants that incorporated immature pre-16S ribosomal RNA into translating ribosomes. Physiological analysis of the mutant plants revealed smaller, but more numerous, chloroplasts in the mesophyll cells, reduction of chlorophyll a and b, depletion of proplastids from the rib meristem and decreased photosynthetic electron transport rate and efficiency. Comparative RNA sequencing and proteomic analysis of the weak mutant and wild-type plants revealed that various biotic stress-related, transcriptional regulation and post-transcriptional modification pathways were repressed in the mutant. Intriguingly, while nuclear- and chloroplast-encoded photosynthesis-related proteins were less abundant in the mutant, the corresponding transcripts were increased, suggesting an elaborate compensatory mechanism, potentially via differentially active retrograde signaling pathways. To conclude, this study reveals a chloroplast ribosome assembly factor and outlines the transcriptomic and proteomic responses of the compensatory mechanism activated during decreased chloroplast function.

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Section: Discussionmentioning

confidence: 98%

AtRsgA from Arabidopsis thaliana is important for maturation of the small subunit of the chloroplast ribosome

et al. 2018

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“…2E). In this regard, SOT1 is similar to the conserved endoribonuclease YbeY, which is able to cleave Arabidopsis total rRNA (38). The expression of the SMR domain of SOT1 in sot1-3 plants resulted in a lethal phenotype (Fig.…”

Section: Discussionmentioning

confidence: 98%

“…RNA nuclease activity was performed as described previously (38). The total RNA (3 μg) extracted from wild-type plants was incubated with MBP, SOT1 SMR , SOT1 SMR variants, Gm-SOT1 SMR , Gm-SOT1 SMR variants, or Gm-SOT1 in buffer [20 mM phosphate, pH 7.5, 160 mM NaCl, 40 mM KCl, and 4% (vol/vol) glycerol] at 25°C for 30 min.…”

Section: Discussionmentioning

confidence: 99%

PPR-SMR protein SOT1 has RNA endonuclease activity

Zhou

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Numerous attempts have been made to identify and engineer sequence-specific RNA endonucleases, as these would allow for efficient RNA manipulation. However, no natural RNA endonuclease that recognizes RNA in a sequence-specific manner has been described to date. Here, we report that SUPPRESSOR OF THYLAKOID FORMATION 1 (SOT1), an Arabidopsis pentatricopeptide repeat (PPR) protein with a small MutS-related (SMR) domain, has RNA endonuclease activity. We show that the SMR moiety of SOT1 performs the endonucleolytic maturation of 23S and 4.5S rRNA through the PPR domain, specifically recognizing a 13-nucleotide RNA sequence in the 5′ end of the chloroplast 23S-4.5S rRNA precursor. In addition, we successfully engineered the SOT1 protein with altered PPR motifs to recognize and cleave a predicted RNA substrate. Our findings point to SOT1 as an exciting tool for RNA manipulation.photosynthesis | PPR-SMR protein | RNA endonuclease | rRNA biogenesis S equence-specific RNA endonucleases are crucial to establishing RNA manipulation technology (1). Compared with DNA editing, RNA manipulation could be more useful and reversible because it does not result in permanent changes to the genome. In addition, sequence-specific RNA endonucleases could potentially be used as an RNA silencing tool to complement RNAi, because RNAi is sometimes ineffective in certain organisms and RNAi machinery is not present in cellular compartments such as chloroplasts and mitochondria. Despite extensive investigations, a natural RNA endonuclease that recognizes RNA in an intrinsic sequence-specific manner has not yet been identified.Pentatricopeptide repeat (PPR) proteins exist in eukaryotes, have greatly expanded in terrestrial plants, and take part in most RNA metabolic processes in organelles (2-5). The PPR domain can specifically recognize RNAs in an intrinsic sequence-specific manner (5-8). The 2nd, 5th, and 35th (or 1st, 4th, and 34th or 3rd, 6th, and 1st in other numbering systems) residues at each repeat are considered to be RNA selection "codes" (9-11). Based on these codes, several PPR proteins have been successfully modified to recognize predictable RNA targets (9,(12)(13)(14)(15)(16)(17).The small MutS-related (SMR) domain was originally identified at the C terminus of MutS2 in the cyanobacterium Synechocystis (18). SMR proteins are widely distributed in almost all organisms (19). Recent studies demonstrated the SMR domain exhibits DNA nicking nuclease activity in vitro (20-25). Furthermore, a C-terminal SMR domain in Leishmania donovani S-phase mRNA cycling sequence binding protein (CSBP) has RNA cleavage activity in vitro (26). These findings suggest that the SMR domain has nuclease activity.Interestingly, a small protein family containing both PPR and SMR domains was recently described (27). PPR-SMR proteins are found mainly in land plants. Arabidopsis thaliana contains eight PPR-SMR proteins localized to the organelles, including mitochondria and chloroplasts (27). Currently, four PPR-SMR proteins have been characterized. They play ...

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“…However, to date, detailed characterizations of YbeY function in eukaryotes have been limited to a single study of a plant [26]. The Arabidopsis thaliana homologue of YbeY (AtYbeY) has been shown to be an RNase that localizes to chloroplasts [26], where it is involved in processing of chloroplast 23S, 16S, and 4.5S rRNAs in the plant. In the absence of YbeY, plants show a defect in seed germination and growth, and leaves become pale-green [26].…”

Section: Introductionmentioning

confidence: 99%

“…The Arabidopsis thaliana homologue of YbeY (AtYbeY) has been shown to be an RNase that localizes to chloroplasts [26], where it is involved in processing of chloroplast 23S, 16S, and 4.5S rRNAs in the plant. In the absence of YbeY, plants show a defect in seed germination and growth, and leaves become pale-green [26]. In contrast HuYbeY and its mouse ortholog have been reported to be part of the proteome of a different organelle, the mitochondrion [27].…”

Section: Introductionmentioning

confidence: 99%

C21orf57 is a human homologue of bacterial YbeY proteins

Ghosal

Köhrer

Babu

et al. 2017

Biochemical and Biophysical Research Communications

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The product of the human C21orf57 (huYBEY) gene is predicted to be a homologue of the highly conserved YbeY proteins found in nearly all bacteria. We show that, like its bacterial and chloroplast counterparts, the HuYbeY protein is an RNase and that it retains sufficient function in common with bacterial YbeY proteins to partially suppress numerous aspects of the complex phenotype of an Escherichia coli ΔybeY mutant. Expression of HuYbeY in Saccharomyces cerevisiae, which lacks a YbeY homologue, results in a severe growth phenotype. This observation suggests that the function of HuYbeY in human cells is likely regulated through specific interactions with partner proteins similarly to the way YbeY is regulated in bacteria.

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The Conserved Endoribonuclease YbeY Is Required for Chloroplast Ribosomal RNA Processing in Arabidopsis

Cited by 57 publications

References 68 publications

AtRsgA from Arabidopsis thaliana is important for maturation of the small subunit of the chloroplast ribosome

AtRsgA from Arabidopsis thaliana is important for maturation of the small subunit of the chloroplast ribosome

PPR-SMR protein SOT1 has RNA endonuclease activity

C21orf57 is a human homologue of bacterial YbeY proteins

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