The PPR ‐ SMR protein PPR 53 enhances the stability and translation of specific chloroplast RNA s in maize

• Published in: The Plant journal : for cell and molecular biology 2016-03, Vol.85 (5), p.594-606
• Main Authors: Zoschke, Reimo, Watkins, Kenneth P., Miranda, Rafael G., Barkan, Alice
• Format: Article
• Language: English
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/tpj.13093

Pentatricopeptide repeat ( PPR ) proteins are helical repeat proteins that bind RNA and influence gene expression in mitochondria and chloroplasts. Several PPR proteins in plants harbor a carboxy‐terminal small‐MutS‐related ( SMR ) domain, but the functions of the SMR appendage are unknown. To address this issue, we studied a maize PPR ‐ SMR protein denoted PPR 53 ( GRMZM 2G438524), which is orthologous to the Arabidopsis protein SOT 1 ( AT 5G46580). Null ppr53 alleles condition a chlorotic, seedling‐lethal phenotype and a reduction in plastid ribosome content. Plastome‐wide transcriptome and translatome analyses revealed strong defects in the expression of the ndhA and rrn23 genes, which were superimposed on secondary effects resulting from a decrease in plastid ribosome content. Transcripts with processed 5′‐ends mapping approximately 70 nucleotides upstream of rrn23 and ndhA are absent in ppr53 mutants, and the translational efficiency of the residual ndhA mRNA s is reduced. Recombinant PPR 53 binds with high affinity and specificity to the 5′ proximal region of the PPR 53‐dependent 23S rRNA , suggesting that PPR 53 protects this RNA via a barrier mechanism similar to that described for several PPR proteins lacking SMR motifs. However, recombinant PPR 53 did not bind with high affinity to the ndhA 5′ untranslated region, suggesting that PPR 53's RNA ‐stabilization and translation‐enhancing effects at the ndhA locus involve the participation of other factors. PPR‐SMR proteins are nucleic acid‐binding proteins found in plant chloroplasts and mitochondria. Members of this protein family have diverse effects on plant physiology, but little is known about their direct molecular activities. Here we show that one PPR‐SMR protein is a sequence‐specific RNA binding protein that promotes the expression of two chloroplast genes by influencing the stability, processing, and translation of their RNAs.