A Young Seedling Stripe2 phenotype in rice is caused by mutation of a chloroplast-localized nucleoside diphosphate kinase 2 required for chloroplast biogenesis

Regulation of Chloroplast Development and Function at Adverse Temperatures in Plants

The chloroplast is essential for photosynthesis, plant growth and development. As semiautonomous organelles, the biogenesis and development of chloroplasts need to be well-regulated during plant growth and stress responses. Low or high ambient temperatures are adverse environmental stresses that affect crop growth and productivity. As sessile organisms, plants regulate the development and function of chloroplasts in a fluctuating temperature environment to maintain normal photosynthesis. This review focuses on the molecular mechanisms and regulatory factors required for chloroplast biogenesis and development under cold or heat stress conditions and highlights the importance of chloroplast gene transcription, RNA metabolism, ribosome function and protein homeostasis essential for chloroplast development under adverse temperature conditions.

Temperature differentially modulates the transcriptome response in Oryza sativa to Xanthomonas oryzae pv. oryzae infection

Bacterial blight is caused by the pathogen Xanthomonas oryzae pv. oryzae (Xoo). Genome scale integrative analysis on the interaction of high and low temperatures on the molecular response signature in rice during the Xoo infection has not been conducted yet. We have analysed a unique RNA-Seq dataset generated on the susceptible rice variety IR24 under combined exposure of Xoo with low 29/21 °C (day/night) and high 35/31 °C (day/night) temperatures. Differentially regulated key genes and pathways in rice plants during both the stress conditions were identified. Differential dynamics of the regulatory network topology showed that WRKY and ERF families of transcription factors play a crucial role during signal crosstalk events in rice plants while responding to combined exposure of Xoo with low temperature vs. Xoo with high temperatures. Our study suggests that upon onset of high temperature, rice plants tend to switch its focus from defence response towards growth and reproduction.

Nucleotide Metabolism in Plants

Nucleotide metabolism is an essential function in plants.

Mutagenesis in Rice: The Basis for Breeding a New Super Plant

The high selection pressure applied in rice breeding since its domestication thousands of years ago has caused a narrowing in its genetic variability. Obtaining new rice cultivars therefore becomes a major challenge for breeders and developing strategies to increase the genetic variability has demanded the attention of several research groups. Understanding mutations and their applications have paved the way for advances in the elucidation of a genetic, physiological, and biochemical basis of rice traits. Creating variability through mutations has therefore grown to be among the most important tools to improve rice. The small genome size of rice has enabled a faster release of higher quality sequence drafts as compared to other crops. The move from structural to functional genomics is possible due to an array of mutant databases, highlighting mutagenesis as an important player in this progress. Furthermore, due to the synteny among the Poaceae, other grasses can also benefit from these findings. Successful gene modifications have been obtained by random and targeted mutations. Furthermore, following mutation induction pathways, techniques have been applied to identify mutations and the molecular control of DNA damage repair mechanisms in the rice genome. This review highlights findings in generating rice genome resources showing strategies applied for variability increasing, detection and genetic mechanisms of DNA damage repair.

UMP Kinase Regulates Chloroplast Development and Cold Response in Rice

Pyrimidine nucleotides are important metabolites that are building blocks of nucleic acids, which participate in various aspects of plant development. Only a few genes involved in pyrimidine metabolism have been identified in rice and the majority of their functions remain unclear. In this study, we used a map-based cloning strategy to isolate a UMPK gene in rice, encoding the UMP kinase that phosphorylates UMP to form UDP, from a recessive mutant with pale-green leaves. In the mutant, UDP content always decreased, while UTP content fluctuated with the development of leaves. Mutation of UMPK reduced chlorophyll contents and decreased photosynthetic capacity. In the mutant, transcription of plastid-encoded RNA polymerase-dependent genes, including psaA, psbB, psbC and petB, was significantly reduced, whereas transcription of nuclear-encoded RNA polymerase-dependent genes, including rpoA, rpoB, rpoC1, and rpl23, was elevated. The expression of UMPK was significantly induced by various stresses, including cold, heat, and drought. Increased sensitivity to cold stress was observed in the mutant, based on the survival rate and malondialdehyde content. High accumulation of hydrogen peroxide was found in the mutant, which was enhanced by cold treatment. Our results indicate that the UMP kinase gene plays important roles in regulating chloroplast development and stress response in rice.

PUMPKIN, the Sole Plastid UMP Kinase, Associates with Group II Introns and Alters Their Metabolism

The chloroplast hosts photosynthesis and a variety of metabolic pathways that are essential for plant viability and acclimation processes. In this study, we show that the sole plastid UMP kinase (PUMPKIN) in Arabidopsis (Arabidopsis thaliana) associates specifically with the introns of the plastid transcripts trnG-UCC, trnV-UAC, petB, petD, and ndhA in vivo, as revealed by RNA immunoprecipitation coupled with deep sequencing (RIP-Seq); and that PUMPKIN can bind RNA efficiently in vitro. Analyses of target transcripts showed that PUMPKIN affects their metabolism. Null alleles and knockdowns of pumpkin were viable but clearly affected in growth, plastid translation, and photosynthetic performance. In pumpkin mutants, the levels of many plastid transcripts were reduced, while the amounts of others were increased, as revealed by RNA-Seq analysis. PUMPKIN is a homomultimeric, plastid-localized protein that forms in vivo RNA-containing megadalton-sized complexes and catalyzes the ATP-dependent conversion of UMP to UDP in vitro with properties characteristic of known essential eubacterial UMP kinases. A moonlighting function of PUMPKIN combining RNA and pyrimidine metabolism is discussed.