Rice is a crucial food source for millions of people worldwide, and its endosperm plays a vital role in seed germination and determining grain yield. The endosperm is the part of the seed that provides the necessary nutrients for the growing plant. One important process that happens during the development of rice endosperm is RNA editing, a modification that changes RNA molecules after they are made from DNA. However, scientists have not fully understood how this process works during the development of rice endosperm—until now.
Recent work by researchers at the Beijing Institute of Genomics has focused on characterizing the RNA editing process in rice endosperm. This study found that most editing occurs in a specific type of RNA known as coding sequence (CDS) RNA, which contains instructions for making proteins. More specifically, the research revealed that RNA editing mostly involves changing cytosine (C) bases to uracil (U) bases in the mitochondria, the energy-producing parts of the cell. These changes lead to the production of proteins with more hydrophobic amino acids—amino acids that do not mix well with water. This alteration can change the structure and function of mitochondrial proteins, which are crucial for energy production in the plant.
Characteristics of RNA editome during rice endosperm development
A RNA editing sites in rice mitochondria and plastids. 369 RNA editing sites in mitochondria (364) and plastids (5) are categorized by editing types, which are color-coded, with pink for C-to-U (mitochondria), blue for C-to-U (plastids), green for G-to-A (mitochondria) and purple for U-to-C (mitochondria), respectively. B Distribution of 369 RNA editing sites at 3, 6, 9, 12, and 15 DAF (n = 5). Bars with pink, green, blue, and purple denote C-to-U (mitochondria), G-to-A (mitochondria), C-to-U (plastids), and U-to-C (mitochondria) RNA editing types, respectively. C Distribution of RNA editing events and their corresponding RNA-seq coverage in rice mitochondria. The outer circle denotes rice mitochondrial genes; genes outside the circle are on the positive strand and oriented clockwise, while genes inside the circle are on the negative strand and oriented anticlockwise. The gray circles, from outer to inner denote RNA-seq coverage (Bar plot, C: Coverage) and frequency (Heatmap, E: Editing) of RNA editing sites at 3, 6, 9, 12, and 15 DAF. D Distribution of editing frequency of 298 C-to-U editing sites. Components of the box plot are: center line, median value; box limits, upper and lower quartiles; whiskers, 1.5x interquartile range; error bars, the highest and lowest values excluding outliers. E Distribution of 298 C-to-U editing sites in different sequence regions. Mit mitochondria, Plt plastids.
The researchers also discovered that RNA editing occurs more frequently at certain sites, especially in the coding regions of mitochondrial genes. These highly edited sites tend to be more stable and are less variable, suggesting they play a crucial role in the plant’s evolution and adaptation. By comparing the RNA editing patterns across different plants, the study found that these edited amino acids are often conserved, meaning they remain unchanged throughout evolution in many land plants. This suggests that these changes are beneficial and critical for survival.
Additionally, the researchers identified and categorized mitochondrial genes into three groups based on their RNA editing patterns. This classification helps to highlight different roles and functions of these genes in the rice endosperm. The team also conducted a genome-wide screening to identify a group of proteins called pentatricopeptide repeat (PPR) proteins. These proteins are believed to help in the RNA editing process, and the researchers created profiles to understand how these PPR proteins bind to RNA.
In summary, this research sheds light on the important role of RNA editing in rice endosperm development. By understanding how RNA editing works, scientists can gain valuable insights into the fundamental mechanisms that support rice growth and grain production. This knowledge can ultimately help improve rice yield and quality, which is essential for feeding the growing global population.