The pathogenesis-related protein 1 (PR-1) gene in rice ( Oryza sativa )

Identification of a cluster of PR4-like genes involved in stress responses in rice

In this study, we characterized the semi-dominant mutant nls1-1D (necrotic leaf sheath 1) of rice, which displays spontaneous lesions, specifically on leaf sheaths, with a developmental pattern. nls1-1D plants also exhibited constitutively activated defense responses, including extensive cell death, excess hydrogen peroxide and salicylic acid (SA) accumulation, up-regulated expressions of pathogenesis-related genes, and enhanced resistance to bacterial pathogens. Map-based cloning revealed that NLS1 encodes a typical CC-NB-LRR-type protein in rice. The nls1-1D mutation causes a S367N substitution in the non-conserved region close to the GLPL motif of the NB domain. An adjacent S366T substitution was found in another semi-dominant mutant, nls1-2D, which exhibited the same phenotypes as nls1-1D. Combined analyses of wild-type plants transformed with the mutant NLS1 gene (nls1-1D), NLS1 RNAi and over-expression transgenic lines showed that nls1-2D is allelic to nls1-1D, and both mutations may cause constitutive auto-activation of the NLS1 R protein. Further real-time PCR analysis revealed that NLS1 is expressed constitutively in an age-dependent manner. In addition, because the morphology and constitutive defense responses of nls1-1D were not suppressed by blocking SA or NPR1 transcript accumulation, we suggest that NLS1 mediates both SA and NPR1-independent defense signaling pathways in rice.

C2 domain-containing proteins (C2DPs) have been identified in different genomes that contain single or multiple C2 domains in their C- or N-terminal. It possesses higher functional activity in the transmembrane regions. The identification of C2 domains were reported in a previous study, such as multiple C2 domains and transmembrane-region proteins (MCTPs) and N-terminal-TM-C2 domain proteins (NTMC2s) of rice, Arabidopsis thaliana, and cotton, whereas the C2DP gene family in rice has not been comprehensively studied, and the role of the C2DP gene in rice in response to abiotic stress is not yet fully understood. In this study, we identified 82 C2DPs in the rice genome and divided them into seven groups through phylogenetic analysis. The synteny analysis revealed that duplication events were either exhibited within the genome of rice or between the genomes of rice and other species. Through the analysis of cis-acting elements in promoters, expression profiles, and qRT-PCR results, the functions of OsC2DPs were found to be widely distributed in diverse tissues and were extensively involved in phytohormones-related and abiotic stresses response in rice. The prediction of the microRNA (miRNA) targets of OsC2DPs revealed the possibility of regulation by consistent miRNAs. Notably, OsC2DP50/51/52 as a co-tandem duplication exhibited similar expression variations and involved the coincident miRNA-regulation pathway. Moreover, the results of the genotypic variation and haplotype analysis revealed that OsC2DP17, OsC2DP29, and OsC2DP49 were associated with cold stress responses. These findings provided comprehensive insights for characterizations of OsC2DPs in rice as well as for their roles for abiotic stress.

BackgroundModification of nucleosides on transfer RNA (tRNA) is important either for correct mRNA decoding process or for tRNA structural stabilization. Nucleoside methylations catalyzed by MTase (methyltransferase) are the most common type among all tRNA nucleoside modifications. Although tRNA modified nucleosides and modification enzymes have been extensively studied in prokaryotic systems, similar research remains preliminary in higher plants, especially in crop species, such as rice (Oryza sativa). Rice is a monocot model plant as well as an important cereal crop, and stress tolerance and yield are of great importance for rice breeding.ResultsIn this study, we investigated how the composition and abundance of tRNA modified nucleosides could change in response to drought, salt and cold stress, as well as in different tissues during the whole growth season in two model plants–O. sativa and Arabidopsis thaliana. Twenty two and 20 MTase candidate genes were identified in rice and Arabidopsis, respectively, by protein sequence homology and conserved domain analysis. Four methylated nucleosides, Am, Cm, m1A and m7G, were found to be very important in stress response both in rice and Arabidopsis. Additionally, three nucleosides,Gm, m5U and m5C, were involved in plant development. Hierarchical clustering analysis revealed consistency on Am, Cm, m1A and m7G MTase candidate genes, and the abundance of the corresponding nucleoside under stress conditions. The same is true for Gm, m5U and m5C modifications and corresponding methylation genes in different tissues during different developmental stages.ConclusionsWe identified candidate genes for various tRNA modified nucleosides in rice and Arabidopsis, especially on MTases for methylated nucleosides. Based on bioinformatics analysis, nucleoside abundance assessments and gene expression profiling, we propose four methylated nucleosides (Am, Cm, m1A and m7G) that are critical for stress response in rice and Arabidopsis, and three methylated nucleosides (Gm, m5U and m5C) that might be important during development.

Novel insight into kinetin-inducible stress responses in rice seedlings

The Calcineurin B-like (CBL) and CBL-interacting protein kinase (CIPK) system constitute critical signaling modules mediating plant responses to abiotic stress. Although these families have been studied across various species, their evolutionary dynamics across grasses and the functional plasticity of specific isoforms remain elusive. A genome-wide analysis of CBL and CIPK families was conducted across five major Poaceae species (Oryza sativa, Triticum aestivum, Zea mays, Sorghum bicolor, and Saccharum spontaneum). Phylogenetic and synteny analyses were analyzed to family expansion and evolution. Cis-regulatory elements analysis in gene promoter regions were examined to predict potential stress-responsive features. Expression profiles of OsCBL and OsCIPK gene families were examined by qRT-PCR under conditions involving PEG-induced osmotic stress, pathogen strain P6 inoculation, and exogenous application of the phytohormones abscisic acid (ABA) and methyl jasmonate (MeJA). Protein-protein interactions between selected CBL (OsCBL4) and CIPK pairs were assessed via Yeast Two-Hybrid (Y2H) and Luciferase Complementation Imaging assays (LCI). Phylogenetic and synteny analyses indicated that segmental duplications have contributed substantially to the expansion of these gene families. Promoter analysis revealed that the majority of CBL and CIPK family members, exemplified by OsCBL4, traditionally characterized as a salt sensor, possesses a cis-element architecture (rich in ABREs and MBS) heavily biased towards dehydration responsiveness. Expression profiling showed that OsCBL4 is significantly hyper-induced by direct osmotic stress (PEG) but exhibits almost no response to exogenous ABA. A subset of kinases genes (e.g., OsCIPK2, 9, 18) displayed PEG-induced expression patterns resembling those of OsCBL4, whereas OsCIPK30 remained transcriptionally unresponsive under the same conditions. Protein interaction assays demonstrated that OsCBL4 physically interacts exclusively with PEG-responsive transcriptionally activated kinases such as OsCIPK9, but failed to interact with the non-responsive OsCIPK30. Our study provides a genomic characterization of CBL and CIPK families across five major Poaceae species. The combined expression and interaction data reveal that OsCBL4-assembles with specific CIPKs into signaling modules during osmotic stress responses in rice, pointing to roles that go beyond salt stress responses. The findings establish a foundation for further functional dissection of CBL-CIPK pathway diversification in abiotic stress adaptation.

Understanding the cross-talk of major abiotic-stress-responsive genes in rice: A computational biology approach

Conditions within the endoplasmic reticulum (ER) influence most secretory proteins that pass through the ER. Therefore, eukaryotic cells must strike a balance between the ER stress response, which changes the conditions in the ER, and other considerations associated with protein secretion. Here, an interaction between the ER stress and defence responses in rice is described. Expression of OsWRKY45, which encodes a transcription factor that plays a central role in defence mediated by salicylic acid (SA), is induced by ER stress. Additionally, expression of some genes encoding pathogenesis-related (PR) secretory proteins is reduced by the ER stress response mediated by the stress sensor IRE1. Concomitant activation of the SA and ER stress responses suppresses the induction of ER stress-responsive genes, with the exception of OsWRKY45, and the reduction of PR gene expression. These findings demonstrate a functional integration between the defence and ER stress responses in plants.

Cold stress is an upcoming challenge for rice (Oryza sativa L.) cultivation, especially at the seedling establishment stage. It causes serious constraints in its production and productivity as it is a thermophilic cereal crop. North-western Himalayan region has a rich repository of temperate rice genotypes, and there is a need to identify cold-tolerant rice varieties from these available genetic resources. The present study screened 90 rice accessions (indica and japonica) grown in the high-altitude regions at 2200mamsl for cold tolerance (5°C) at the seedling stage, and found 14 highly cold-tolerant accessions. Almost eighty per cent of the indica types clustered into cold-sensitive class. One cold-tolerant japonica (GS-74) accession and one cold-susceptible (SR-4) accession were used to compare their biochemical and gene expression response during cold stress and after recovery. A wide range of differences was noticed at different time points in the accumulation of ROS scavengers, osmo-protectants and antioxidant enzymes, with significant differences between the contrasting genotypes. Similarly, gene expression of five transcription factors OsMYB4, OsAP37, OsDREB1A, OsDREB1B and OsDREB1D revealed their role in cold responsiveness at the seedling stage, critically modulating the cold-induced osmoprotectant-mediated tolerance mechanism. This is the first study that explored the high-altitude Himalayan rice germplasm for cold tolerance at the critical S3 seedling stage under controlled conditions. It demonstrated that the upregulation of OsDREB1A, OsDREB1B, OsMYB4 and OsAP37 transcription factors modulates cold stress response in rice via a complex mechanism involving ROS scavengers and osmoprotectants.

Bacterial blight of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most critical diseases in rice. In order to study rice responsive genes to bacterial stress, microarray data were retrieved from GEO dataset. To identify the responsive genes to biotic stress (bacteria) bioinformatic tools were employed and the data presented in the forms of heatmap, gene ontology, gene network, and cis-element prediction were used. Almost all responsive genes were down-regulated at around 3 h time point and up-regulated 24 h time point in response to bacterial stress in rice varieties (Oryza sativa subs. japonica ‘IR64’, ‘IRBB5’, ‘IRBB7’ and ‘Y73’). Gene ontology showed that genes are involved in different biological processes including translation and cellular protein metabolic processes. Network analysis showed that genes expressed in response to pathogen infection (Xoo) included protein translation, eukaryotic initiation factors (eIFs), ribosomal proteins, protein ubiquitin, and MAPK genes. The genes expressed in response to bacterial stress can enable plant balance between synthesis and degradation of proteins which in turn allows plants for further growth and development. TATA-box and CAAT box had the highest number of cis elements involved in bacterial stress. These genes can provide novel insights into regulatory mechanisms in biotic stress responses in rice. Identification of bacterial stress response/tolerance genes of rice can assist the molecular breeding of new rice varieties tolerant to bacterial stress.

Calcineurin B-like interacting protein kinase OsCIPK23 functions in pollination and drought stress responses in rice (Oryza sativa L.)

As a well-known animal hormone, melatonin (N-acetyl-5-methoxytryptamine) is also involved in multiple plant biological processes, especially in various stress responses. Rice is one of the most important crops, and melatonin is taken in by many people everyday from rice. However, the transcriptional profiling of melatonin-related genes in rice is largely unknown. In this study, the expression patterns of 11 melatonin related genes in rice in different periods, tissues, in response to different treatments were synthetically analyzed using published microarray data. These results suggest that the melatonin-related genes may play important and dual roles in rice developmental stages. We highlight the commonly regulation of rice melatonin-related genes by abscisic acid (ABA), jasmonic acid (JA), various abiotic stresses and pathogen infection, indicating the possible role of these genes in multiple stress responses and underlying crosstalks of plant hormones, especially ABA and JA. Taken together, this study may provide insight into the association among melatonin biosynthesis and catabolic pathway, plant development and stress responses in rice. The profile analysis identified candidate genes for further functional characterization in circadian rhythm and specific stress responses.

Studies on Oryza sativa (rice) are crucial for improving agricultural productivity and ensuring global sustenance security, especially considering the increasing drought and heat stress caused by extreme climate change. Currently, the genes and mechanisms underlying drought and heat resistance in rice are not fully understood, and the scope for enhancing the development of new strains remains considerable. To accurately identify the key genes related to drought and heat stress responses in rice, multiple datasets from the Gene Expression Omnibus (GEO) database were integrated in this study. A co-expression network was constructed using a Weighted Correlation Network Analysis (WGCNA) algorithm. We further distinguished the core network and intersected it with differentially expressed genes and multiple expression datasets for screening. Differences in gene expression levels were verified using quantitative real-time polymerase chain reaction (PCR). OsDjC53, MBF1C, BAG6, HSP23.2, and HSP21.9 were found to be associated with the heat stress response, and it is also possible that UGT83A1 and OsCPn60a1, although not directly related, are affected by drought stress. This study offers significant insights into the molecular mechanisms underlying stress responses in rice, which could promote the development of stress-tolerant rice breeds.

Rice (Oryza sativa L.), originating from tropical and subtropical regions, is a cold-sensitive and water-demanding crop whose yield and quality are severely compromised by chilling injury or water deficits during growth and development. In this study, we systematically characterized Cold and Drought Resistance 1 (OsCDR1), a nucleus-localized transcription activator belonging to the bZIP transcription factor family. OsCDR1 overexpression enhances rice tolerance to cold and drought stress, whereas knockout mutants of OsCDR1 exhibit reduced resistance to low temperatures and drought conditions. Furthermore, OsCDR1 positively regulates abscisic acid (ABA) signaling in rice, and mediates ABA-regulated drought tolerance responses in rice. Integrated RNA-seq and CUT&Tag analyses demonstrated that OsCDR1 coordinates with ABA-dependent (PIP2;2) and -independent genes (DREB1J). OsCDR1 specifically binds to the G-box cis-element in the promoters of PIP2;2 and DREB1J, thereby activating their transcription and regulating the abiotic stress responses in rice. Protein interaction analysis revealed that OsCDR1 interacts with the kinase OsMPK9 in vivo and in vitro, and a dual-luciferase reporter assay showed that OsMPK9 and OsCDR1 regulate the transcription of DREB1J and PIP2;2 in the same functional pathway. Overexpression of OsMPK9 inhibits ABA responses in rice and reduces cold and drought tolerance. Our findings establish the OsMPK9-OsCDR1 module as a critical hub connecting ABA signaling to abiotic stress resilience, providing new insights for breeding crops.

Salinity is one of the most common abiotic stress which limits agricultural crop production. Salinity stress tolerance in rice (Oryza sativa L.) is an important trait controlled by various genes. The mechanism of salinity stress response in rice is quite complex. Modelling and construction of genetic regulatory networks is an important tool and can be used for understanding this underlying mechanism. This paper considers the problem of modeling and construction of Gene Regulatory Networks using Multiple Linear Regression and Singular Value Decomposition approach coupled with a number of computational tools. The gene networks constructed by using this approach satisfied the scale free property of biological networks and such networks can be used to extract valuable information on the transcription factors, which are salt responsive. The gene ontology enrichment analysis of selected nodes is performed. The developed model can also be used for predicting the gene responses under stress condition and the result shows that the model fits well for the given gene expression data in rice. In this paper, we have identified ten target genes and a series of potential transcription factors for each target gene in rice which are highly salt responsive.