<scp>SOT</scp>1, a pentatricopeptide repeat protein with a small MutS‐related domain, is required for correct processing of plastid 23S–4.5S <scp>rRNA</scp> precursors in <i>Arabidopsis thaliana</i>

Wu, Wenjuan; Liu, Sheng; Ruwe, Hannes; Zhang, Delin; Melonek, Joanna; Zhu, Yajuan; Hu, Xupeng; Gusewski, Sandra; Yin, Ping; Small, Ian; Howell, Katharine A.; Huang, Jirong

doi:10.1111/tpj.13126

Cited by 73 publications

(85 citation statements)

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“…4). A similar loss of processed ndhA transcripts has been observed in other plastid development mutants, including otp70, clb19 (Chateigner-Boutin et al, 2011), and sot1 (Wu et al, 2016), so it is probably an indirect effect.…”

Section: Emb2654 Is Involved In Trans-splicing Of Rps12 Transcriptssupporting

confidence: 66%

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The Pentatricopeptide Repeat Protein EMB2654 Is Essential for Trans-Splicing of a Chloroplast Small Ribosomal Subunit Transcript

et al. 2016

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We report the partial complementation and subsequent comparative molecular analysis of two nonviable mutants impaired in chloroplast translation, one (emb2394) lacking the RPL6 protein, and the other (emb2654) carrying a mutation in a gene encoding a P-class pentatricopeptide repeat protein. We show that EMB2654 is required for the trans-splicing of the plastid rps12 transcript and that therefore the emb2654 mutant lacks Rps12 protein and fails to assemble the small subunit of the plastid ribosome, explaining the loss of plastid translation and consequent embryo-lethal phenotype. Predictions of the EMB2654 binding site match a small RNA "footprint" located on the 59 half of the trans-spliced intron that is almost absent in the partially complemented mutant. EMB2654 binds sequence specifically to this target sequence in vitro. Altered patterns in nucleaseprotected small RNA fragments in emb2654 show that EMB2654 binding must be an early step in, or prior to, the formation of a large protein-RNA complex covering the free ends of the two rps12 intron halves.

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Section: Emb2654 Is Involved In Trans-splicing Of Rps12 Transcriptssupporting

confidence: 66%

“…Gel purification, sequencing of small RNAs, and sequence analysis was done as described in Wu et al (2016).…”

Section: Sequencingmentioning

confidence: 99%

The Pentatricopeptide Repeat Protein EMB2654 Is Essential for Trans-Splicing of a Chloroplast Small Ribosomal Subunit Transcript

et al. 2016

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“…SOT1 and its maize ortholog PPR53 encode proteins with 11 PPR motifs in the N-terminal region and a SMR domain in the C-terminal region and both are involved in the maturation of 23S and 4.5S rRNA (33,34). Our results with sot1-3 show that the loss of SOT1 resulted in less mature 23S and 4.5S rRNA as well as staggered 23S rRNA 5′ ends (SI Appendix, Fig.…”

Section: Significancementioning

confidence: 73%

“…S2D). AT5G46580 was previously assigned the name SOT1 because the corresponding mutants sot1-1 and sot1-2 (suppressor of thf1 1/2) were identified in a suppressor screen for the leaf variegation phenotype of thylakoid formation 1 (thf1) (34). Accordingly, we designated the mutant identified in our screen as sot1-3.…”

Section: Significancementioning

confidence: 99%

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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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The Enigmatic Roles of PPR‐SMR Proteins in Plants

Zhang

2019

Advanced Science

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The pentatricopeptide repeat (PPR) protein family, with more than 400 members, is one of the largest and most diverse protein families in land plants. A small subset of PPR proteins contain a C‐terminal small MutS‐related (SMR) domain. Although there are relatively few PPR‐SMR proteins, they play essential roles in embryo development, chloroplast biogenesis and gene expression, and plastid‐to‐nucleus retrograde signaling. Here, recent advances in understanding the roles of PPR‐SMR proteins and the SMR domain based on a combination of genetic, biochemical, and physiological analyses are described. In addition, the potential of the PPR‐SMR protein SOT1 to serve as a tool for RNA manipulation is highlighted.

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SOT1, a pentatricopeptide repeat protein with a small MutS‐related domain, is required for correct processing of plastid 23S–4.5S rRNA precursors in Arabidopsis thaliana

Cited by 73 publications

References 79 publications

The Pentatricopeptide Repeat Protein EMB2654 Is Essential for Trans-Splicing of a Chloroplast Small Ribosomal Subunit Transcript

The Pentatricopeptide Repeat Protein EMB2654 Is Essential for Trans-Splicing of a Chloroplast Small Ribosomal Subunit Transcript

PPR-SMR protein SOT1 has RNA endonuclease activity

The Enigmatic Roles of PPR‐SMR Proteins in Plants

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