Small kernel 1 encodes a pentatricopeptide repeat protein required for mitochondrial nad7 transcript editing and seed development in maize (Zea mays) and rice (Oryza sativa)

Abstract

SUMMARYRNA editing modifies cytidines (C) to uridines (U) at specific sites in the transcripts of mitochondria and plastids, altering the amino acid specified by the DNA sequence. Here we report the identification of a critical editing factor of mitochondrial nad7 transcript via molecular characterization of a small kernel 1 (smk1) mutant in Zea mays (maize). Mutations in Smk1 arrest both the embryo and endosperm development. Cloning of Smk1 indicates that it encodes an E-subclass pentatricopeptide repeat (PPR) protein that is targeted to mitochondria. Loss of SMK1 function abolishes the C ? U editing at the nad7-836 site, leading to the retention of a proline codon that is edited to encode leucine in the wild type. The smk1 mutant showed dramatically reduced complex-I assembly and NADH dehydrogenase activity, and abnormal biogenesis of the mitochondria. Analysis of the ortholog in Oryza sativa (rice) reveals that rice SMK1 has a conserved function in C ? U editing of the mitochondrial nad7-836 site. T-DNA knock-out mutants showed abnormal embryo and endosperm development, resulting in embryo or seedling lethality. The leucine at NAD7-279 is highly conserved from bacteria to flowering plants, and analysis of genome sequences from many plants revealed a molecular coevolution between the requirement for C ? U editing at this site and the existence of an SMK1 homolog. These results demonstrate that Smk1 encodes a PPR-E protein that is required for nad7-836 editing, and this editing is critical to NAD7 function in complex-I assembly in mitochondria, and hence to embryo and endosperm development in maize and rice.

E+ subgroup PPR protein defective kernel 36 is required for multiple mitochondrial transcripts editing and seed development in maize and Arabidopsis

“…This functional divergence is likely common to PPR ortholog pairs between monocot maize and dicot Arabidopsis, such as PPR2263 and MEF29 (Sosso et al ., ). However, between maize and rice, the function of the PPR othologs is highly conserved in editing mitochondrial transcripts (Liu et al ., ; Li et al ., ). The driving pressure behind these changes may be due to the coevolution of PPR proteins and organelle genomes during plant speciation.…”

“…a–c). Likely, SMK1 is required for nad7‐ 836 editing and complex I assembly (Li et al ., ). Jointly, these data indicate that the accurate editing of nad7 is essential for its function in mitochondrial oxidative phosphorylation (Pineau et al ., ; Zhu et al ., ).…”

“…EMP4 and EMP16 regulate the expression and splicing of mitochondrial transcripts, respectively (Gutierrez‐Marcos et al ., ; Xiu et al ., ). By contrast, SMK1, PPR2263, EMP5 and EMP7 are required for editing of mitochondrial RNAs (Sosso et al ., ; Liu et al ., ; Li et al ., ; Sun et al ., ). We revealed that DEK36 encodes an E+ subgroup PPR protein that is required for mitochondrial transcripts editing and seed development in both maize and Arabidopsis.…”

The Conserved and Unique Genetic Architecture of Kernel Size and Weight in Maize and Rice

“…On the other hand, many genes controlling maize kernel development have been cloned using kernel mutants identified from Robertson's Mutator stocks, including emp2 (empty pericarp2), emp4, emp5, emp16, dek1 (defective kernel1), dek35, maize pentatricopeptide repeat6, small kernel1, embryo defective14, U6 biogenesis-like1, and many others (Fu et al, 2002;Lid et al, 2002;Gutiérrez-Marcos et al, 2007;Manavski et al, 2012;Liu et al, 2013;Li et al, 2014Li et al, , 2015Chen et al, 2016;Xiu et al, 2016). Mutations in these genes usually have severe phenotypes in kernels, such as empty pericarp, where both embryo and endosperm cannot develop properly.…”

The retromer protein ZmVPS29 regulates maize kernel morphology likely through an auxin‐dependent process(es)

“…However, none of the identified QTLs have been molecularly cloned or functionally characterized. In contrast, recent mutational studies have identified a number of genes that regulate kernel development, such as SMALL KERNEL 1 (encoding a PPR‐E protein; Li et al ., ), Supernumerary Aleurone Layers 1 (encoding a vacuolar sorting protein; Shen et al ., ), U6 Biogenesis‐Like 1 (encoding an RNA exonuclease; Li et al ., ) and Unhealthy Ribosome Biogenesis 2 (encoding an Urb2 domain‐containing protein; Wang et al ., ). Of particular interest, numerous studies have shown that maize mutants defective in auxin biosynthesis, transport or response display a wide range of abnormalities in the development of the embryo , endosperm, spikelet‐pair meristem or branch meristem, kernel number and kernel weight (Barazesh and McSteen, ; Bernardi et al ., ; Chen et al ., ; Forestan et al ., , ; Galli et al ., ; Scanlon et al ., ).…”