RNA editing of nuclear transcripts in Arabidopsis thaliana

<p>Abstract</p> <p>Background</p> <p>RNA editing is a transcript-based layer of gene regulation. To date, no systemic study on RNA editing of plant nuclear genes has been reported. Here, a transcriptome-wide search for editing sites in nuclear transcripts of Arabidopsis (<it>Arabidopsis thaliana</it>) was performed.</p> <p>Results</p> <p>MPSS (massively parallel signature sequencing) and PARE (parallel analysis of RNA ends) data retrieved from public databases were utilized, focusing on one-base-conversion editing. Besides cytidine (C)-to-uridine (U) editing in mitochondrial transcripts, many nuclear transcripts were found to be diversely edited. Interestingly, a sizable portion of these nuclear genes are involved in chloroplast- or mitochondrion-related functions, and many editing events are tissue-specific. Some editing sites, such as adenosine (A)-to-U editing loci, were found to be surrounded by peculiar elements. The editing events of some nuclear transcripts are highly enriched surrounding the borders between coding sequences (CDSs) and 3′ untranslated regions (UTRs), suggesting site-specific editing. Furthermore, RNA editing is potentially implicated in new start or stop codon generation, and may affect alternative splicing of certain protein-coding transcripts. RNA editing in the precursor microRNAs (pre-miRNAs) of <it>ath-miR854</it> family, resulting in secondary structure transformation, implies its potential role in microRNA (miRNA) maturation.</p> <p>Conclusions</p> <p>To our knowledge, the results provide the first global view of RNA editing in plant nuclear transcripts.</p

LARGE ROOT ANGLE1, encoding OsPIN2, is involved in root system architecture in rice

Root system architecture is very important for plant growth and crop yield. It is essential for nutrient and water uptake, anchoring, and mechanical support. Root growth angle (RGA) is a vital constituent of root system architecture and is used as a parameter for variety evaluation in plant breeding. However, little is known about the underlying molecular mechanisms that determine root growth angle in rice (Oryza sativa). In this study, a rice mutant large root angle1 (lra1) was isolated and shown to exhibit a large RGA and reduced sensitivity to gravity. Genome resequencing and complementation assays identified OsPIN2 as the gene responsible for the mutant phenotypes. OsPIN2 was mainly expressed in roots and the base of shoots, and showed polar localization in the plasma membrane of root epidermal and cortex cells. OsPIN2 was shown to play an important role in mediating root gravitropic responses in rice and was essential for plants to produce normal RGAs. Taken together, our findings suggest that OsPIN2 plays an important role in root gravitropic responses and determining the root system architecture in rice by affecting polar auxin transport in the root tip

Characterization of the rice NLA family reveals a key role for OsNLA1 in phosphate homeostasis

Abstract Background Phosphate (Pi), an essential mineral nutrient for plant development and reproduction, is one of the main components of fertilizers in modern agriculture. Previous research demonstrated that AtNLA1 mediates ubiquitination of Pi transporters in the plasma membrane and triggers their endocytosis and degradation in Arabidopsis. In this study, we researched the function of NLA homologous proteins in Pi homeostasis in rice. Findings Two OsNLA homologs from rice (Oryza sativa L.) were identified by bioinformatics and phylogenetic analysis and designated OsNLA1 and OsNLA2. The OsNLA1 clustered with Arabidopsis AtNLA1, was expressed higher than OsNLA2 and was transcriptionally repressed under Pi-deficient condition. Loss-of-function of OsNLA1 caused P overaccumulation and growth inhibitions in both root and shoot under Pi-sufficient condition. Furthermore, mutation of OsNLA1 affected expression of Pi tranporters and root hair development under Pi-sufficient and/or Pi-deficient conditions. Conclusions OsNLA1 plays a key role in maintaining phosphate homeostasis in rice

Integrated transcriptomic analysis identifies coordinated responses to nitrogen and phosphate deficiency in rice

Nitrogen (N) and phosphorus (P) are two primary components of fertilizers for crop production. Coordinated acquisition and utilization of N and P are crucial for plants to achieve nutrient balance and optimal growth in a changing rhizospheric nutrient environment. However, little is known about how N and P signaling pathways are integrated. We performed transcriptomic analyses and physiological experiments to explore gene expression profiles and physiological homeostasis in the response of rice (Oryza sativa) to N and P deficiency. We revealed that N and P shortage inhibit rice growth and uptake of other nutrients. Gene Ontology (GO) analysis of differentially expressed genes (DEGs) suggested that N and Pi deficiency stimulate specific different physiological reactions and also some same physiological processes in rice. We established the transcriptional regulatory network between N and P signaling pathways based on all DEGs. We determined that the transcript levels of 763 core genes changed under both N or P starvation conditions. Among these core genes, we focused on the transcription factor gene NITRATE-INDUCIBLE, GARP-TYPE TRANSCRIPTIONAL REPRESSOR 1 (NIGT1) and show that its encoded protein is a positive regulator of P homeostasis and a negative regulator of N acquisition in rice. NIGT1 promoted Pi uptake but inhibited N absorption, induced the expression of Pi responsive genes PT2 and SPX1 and repressed the N responsive genes NLP1 and NRT2.1. These results provide new clues about the mechanisms underlying the interaction between plant N and P starvation responses

Molecular Mechanisms of Root Development in Rice

Abstract Roots are fundamentally important for growth and development, anchoring the plant to its growth substrate, facilitating water and nutrient uptake from the soil, and sensing and responding to environmental signals such as biotic and abiotic stresses. Understanding the molecular mechanisms controlling root architecture is essential for improving nutrient uptake efficiency and crop yields. In this review, we describe the progress being made in the identification of genes and regulatory pathways involved in the development of root systems in rice (Oryza sativa L.), including crown roots, lateral roots, root hairs, and root length. Genes involved in the adaptation of roots to the environmental nutrient status are reviewed, and strategies for further study and agricultural applications are discussed. The growth and development of rice roots are controlled by both genetic factors and environmental cues. Plant hormones, especially auxin and cytokinin, play important roles in root growth and development. Understanding the molecular mechanisms regulating root architecture and response to environmental signals can contribute to the genetic improvement of crop root systems, enhancing their adaptation to stressful environmental conditions

The Predicted Arabidopsis Interactome Resource and Network Topology-Based Systems Biology Analyses[W][OA]

Protein–protein interactions are important mechanisms for genes and gene networks to function. This study demonstrates that, although the PAIR database has limited coverage, representing ~24% of the entire interactome with ~40% precision, it is rich enough to capture many significant functional linkages within and between higher-order biological systems, such as pathways and biological processes

Additional file 1: of Characterization of the rice NLA family reveals a key role for OsNLA1 in phosphate homeostasis

Materials and methods. (DOCX 19 kb

Additional file 2: Figure S1. of Characterization of the rice NLA family reveals a key role for OsNLA1 in phosphate homeostasis

Calculation of PCR efficiencies. Figure S2. Leaf blades of 30-d-old WT and osnla1 grown under Pi-sufficient (300 μM; +P) and Pi-deficient (10 μM; -P) conditions. (PPTX 304 kb