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The homeostasis of hydrogen peroxide (H

Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense (Foc), is one of the most destructive diseases of banana. Several experimental systems have been used to study banana—Foc interaction, including pot system and hydroponic system. In this study, an in vitro hydroponic system was developed for the growth of rooted banana plantlet. It was characterized by a filter-paper holder, which consisted of a cone cup and a round tube. Besides being used as supporting material and providing nutrients to the banana plantlet, the filter-paper holder was designed to create a humid and aerobic environment for root growth. It was observed that rooted plantlet could grow normally in inoculum-free nutrient solution for at least 8 weeks. In the following rejuvenation experiment, each plantlet was back-inoculated by adding spore suspension of a degenerated strain of Foc tropical race 4 (TR4) into nutrient solution. Three to four weeks after in vitro inoculation, the rejuvenated strain was isolated from the rhizome of the plantlet showing symptoms under sterile conditions. The results of pathogenicity test indicated that the third-generation rejuvenated strain had partially regained virulence, which was characterized by lower radial growth rate and higher level of sporulation compared with the degenerated strain. In contrast to previously reported hydroponic systems which applied to studies in relation to Fusarium wilt of banana, the one described here is a totally closed system. It is demonstrated that the in vitro hydroponic system can be used for studying the interaction between banana plantlet and Foc TR4. A novel in vitro hydroponic system is described, in which a rooted banana plantlet can grow normally for at least 8 weeks without an air pump. In vitro inoculation technique allows banana plantlet—Foc interaction without interference of other microorganisms.

Exposure to ultraviolet B radiation (UV-B) stress can have serious effects on the growth and development of plants. Germin-like proteins (GLPs) may be involved in different abiotic and biotic stress responses in different plants, but little is known about the role of GLPs in UV-B stress response and acclimation in plants. In the present study, knockout of GLP 8–14 (OsGLP1) using the CRISPR/Cas9 system resulted in mutant rice (Oryza sativa L.) plants (herein called glp1) that exhibited UV-B-dependent formation of lesion mimic in leaves. Moreover, glp1 grown under solar radiation (including UV-B) showed decreased plant height and increased leaf angle, but we observed no significant differences in phenotypes between wild-type (WT) plants and glp1 grown under artificial light lacking UV-B. Fv/Fm, Y (II) and the expression of many genes, based on RNA-seq analysis, related to photosynthesis were also only reduced in glp1, but not in WT, after transfer from a growth cabinet illuminated with artificial white light lacking UV-B to growth under natural sunlight. The genes-associated with flavonoid metabolism as well as UV resistance locus 8 (OsUVR8), phytochrome interacting factor-like 15-like (OsPIF3), pyridoxal 5′-phosphate synthase subunit PDX1.2 (OsPDX1.2), deoxyribodipyrimidine photolyase (OsPHR), and deoxyribodipyrimidine photolyase family protein-like (OsPHRL) exhibited lower expression levels, while higher expression levels of mitogen-activated protein kinase 5-like (OsMPK3), mitogen-activated protein kinase 13-like (OsMPK13), and transcription factor MYB4-like (OsMYB4) were observed in glp1 than in WT after transfer from a growth cabinet illuminated with artificial white light to growth under natural sunlight. Therefore, mutations in OsGLP1 resulted in rice plants more sensitive to UV-B and reduced expression of some genes for UV-B protection, suggesting that OsGLP1 is involved in acclimation to UV-B radiation.

Improving the grain yield of rice is a central goal of basic and applied scientific research. Here, we identified an anion transporter, OsAT1, localized in the endoplasmic reticulum and Golgi. OsAT1 is highly expressed in flag, stem, and sheath as monitored using qRT-PCR and pOsAT1::GUS. Thousand-grain weight, grain weight per plant, and content of starch were significantly increased in OsAT1 knock-down mutants (OsAT1-Ri) but significantly decreased in OsAT1 overexpressed lines (OsAT1-OE). In addition, the grain weight per plant increased by 6.17% to 6.78% in OsAT1-RNAi lines, whereas it decreased by 45.93% to 46.76% in OsAT1-OE lines, compared to wild-type. Moreover, the copper content was noticeably reduced in flag leaf of OsAT1-Ri lines and increased in OsAT1-OE lines. RNA-sequencing analysis of OsAT1-OE lines revealed that the genes related to starch biosynthesis and metabolism pathway were enriched in the down-regulated category. Thus, our results suggest that knock-down of OsAT1 in rice possibly reduces copper accumulation and improves the accumulation of storage starch, hence, increasing the grain size and weight. OsAT1 may be a useful gene to consider for cereal breeding programs.

Background Glycolate oxidase (GLO) is not only a key enzyme in photorespiration but also a major engine for H2O2 production in plants. Catalase (CAT)-dependent H2O2 decomposition has been previously reported to be involved in the regulation of IAA biosynthesis. However, it is still not known which mechanism contributed to the H2O2 production in IAA regulation. Results In this study, we found that in glo mutants of rice, as H2O2 levels decreased IAA contents significantly increased, whereas high CO2 abolished the difference in H2O2 and IAA contents between glo mutants and WT. Further analyses showed that tryptophan (Trp, the precursor for IAA biosynthesis in the Trp-dependent biosynthetic pathway) also accumulated due to increased tryptophan synthetase β (TSB) activity. Moreover, expression of the genes involved in Trp-dependent IAA biosynthesis and IBA to IAA conversion were correspondingly up-regulated, further implicating that both pathways contribute to IAA biosynthesis as mediated by the GLO-dependent production of H2O2. Conclusion We investigated the function of GLO in IAA signaling in different levels from transcription, enzyme activities to metabolic levels. The results suggest that GLO-dependent H2O2 signaling, essentially via photorespiration, confers regulation over IAA biosynthesis in rice plants.

Over the past few years, three photorespiratory bypasses have been introduced into plants, two of which led to observable increases in photosynthesis and biomass yield. However, most of the experiments were carried out using Arabidopsis under controlled environmental conditions, and the increases were only observed under low-light and short-day conditions. In this study, we designed a new photorespiratory bypass (called GOC bypass), characterized by no reducing equivalents being produced during a complete oxidation of glycolate into CO2 catalyzed by three rice-self-originating enzymes, i.e., glycolate oxidase, oxalate oxidase, and catalase. We successfully established this bypass in rice chloroplasts using a multi-gene assembly and transformation system. Transgenic rice plants carrying GOC bypass (GOC plants) showed significant increases in photosynthesis efficiency, biomass yield, and nitrogen content, as well as several other CO2-enriched phenotypes under both greenhouse and field conditions. Grain yield of GOC plants varied depending on seeding season and was increased significantly in the spring. We further demonstrated that GOC plants had significant advantages under high-light conditions and that the improvements in GOC plants resulted primarily from a photosynthetic CO2-concentrating effect rather than from improved energy balance. Taken together, our results reveal that engineering a newly designed chloroplastic photorespiratory bypass could increase photosynthetic efficiency and yield of rice plants grown in field conditions, particularly under high light.

Background The glyoxylate reductase (GR) multigene family has been described in various plant species, their isoforms show different biochemical features in plants. However, few studies have addressed the biological roles of GR isozymes, especially for rice. Results Here, we report a detailed analysis of the enzymatic properties and physiological roles of OsGR1 and OsGR2 in rice. The results showed that both enzymes prefer NADPH to NADH as cofactor, and the NADPH-dependent glyoxylate reducing activity represents the major GR activity in various tissues and at different growth stages; and OsGR1 proteins were more abundant than OsGR2, which is also a major contributor to total GR activities. By generating and characterizing various OsGR-genetically modified rice lines, including overexpression, single and double-knockout lines, we found that no phenotypic differences occur among the various transgenic lines under normal growth conditions, while a dwarfish growth phenotype was noticed under photorespiration-promoted conditions. Conclusion Our results suggest that OsGR1 and OsGR2, with distinct enzymatic characteristics, function redundantly in detoxifying glyoxylate in rice plants under normal growth conditions, whereas both are simultaneously required under high photorespiration conditions.

Several photorespiratory bypasses have been introduced into plants and shown to improve photosynthesis by increasing chloroplastic CO2 concentrations or optimizing energy balance. We recently reported that an engineered GOC bypass could increase photosynthesis and productivity in rice. However, the grain yield of GOC plants was unstable, fluctuating in different cultivation seasons because of varying seed setting rates. In this study, we designed a synthetic photorespiratory shortcut (the GCGT bypass) consisting of genes encoding Oryza sativa glycolate oxidase and Escherichia coli catalase, glyoxylate carboligase, and tartronic semialdehyde reductase. The GCGT bypass was guided by an optimized chloroplast transit peptide that targeted rice chloroplasts and redirected 75% of carbon from glycolate metabolism to the Calvin cycle, identical to the native photorespiration pathway. GCGT transgenic plants exhibited significantly increased biomass production and grain yield, which were mainly attributed to enhanced photosynthesis due to increased chloroplastic CO2 concentrations. Despite the increases in biomass production and grain yield, GCGT transgenic plants showed a reduced seed setting rate, a phenotype previously reported for the GOC plants. Integrative transcriptomic, physiological, and biochemical assays revealed that photosynthetic carbohydrates were not transported to grains in an efficient manner, thereby reducing the seed setting rate. Taken together, our results demonstrate that the GCGT photorespiratory shortcut confers higher yield by promoting photosynthesis in rice, mainly through increasing chloroplastic CO2 concentrations.

Additional file 3. Molecular evalution of the Crispr-Cas9 generated OsGR1 and OsGR2 single and double mutants.

Additional file 2. OsGR1 and OsGR2 transcript abundances in the leaves of different OsGR-genetically modified plants were determined by qRT-PCR. Relative mRNA levels in various rice lines were graphed based on the OsGR1 mRNA level in WT as 1.

Additional file 1. Multiple sequence alignment (MSA) of OsGR and AtGR isoforms at the level of protein and nucleotide.

Additional file 5. The primers used for real-time quantitative PCR.

Oxalic acid is widely distributed in biological systems and known to play functional roles in plants. The gene AAE3 was recently identified to encode an oxalyl-CoA synthetase (OCS) in Arabidopsis that catalyzes the conversion of oxalate and CoA into oxalyl-CoA. It will be even particularly significant to characterize the homologous gene in rice since rice is not only a monocotyledonous model plant, but also a staple food crop. Our current study firstly defined that AAE3 in the rice genome (OsAAE3) also encodes an OCS enzyme. Its Km for oxalate is 1.73±0.12 mM, and the Vm was 6824.9±410.29 units/min/mg protein. Chemical modification and site-directed mutagenesis analyses identified thiols as the active site residues for rice OCS catalysis, implicating that the enzyme may be regulated by redox state. Subcellular localization assay showed that the enzyme is located in the cytosol and predominantly distributed in leaf epidermis cells. As expected, oxalate levels were increased when OCS was suppressed in the RNAi transgenic plants. More interestingly, the OCS-suppressed plants were shown to be more susceptible to bacterial blight but more resistant to Al toxicity. The results demonstrate that the OsAAE3-encoded protein also acts as an OCS in rice, and it may play differential roles in coping with stresses. These molecular, enzymatic and functional data provide firsthand information for us to further clarify the function and mechanism of OCS in rice plants. This article is protected by copyright. All rights reserved.

Table S1. Similarities of Arabidopsis and rice GLO genes at the level of mRNA and protein. (DOCX 58 kb)

Figure S1. Phylogenetic relationships among NCA and orthologous proteins from other species. (DOCX 18 kb)

Table S2. Primers used in this study. (DOCX 20 kb)

WD40 repeat-containing proteins (WD40 proteins) serve as versatile scaffolds for protein–protein interactions, modulating a variety of cellular processes such as plant stress and hormone responses. Here we report the identification of a WD40 protein, XIW1 (for XPO1-interacting WD40 protein 1), which positively regulates the abscisic acid (ABA) response in Arabidopsis. XIW1 is located in the cytoplasm and nucleus. We found that it interacts with the nuclear transport receptor XPO1 and is exported by XPO1 from the nucleus. Mutation of XIW1 reduces the induction of ABA-responsive genes and the accumulation of ABA Insensitive 5 (ABI5), causing mutant plants with ABA-insensitive phenotypes during seed germination and seedling growth, and decreased drought stress resistance. ABA treatment upregulates the expression of XIW1, and both ABA and abiotic stresses promote XIW1 accumulation in the nucleus, where it interacts with ABI5. Loss of XIW1 function results in rapid proteasomal degradation of ABI5. Taken together, these findings suggest that XIW1 is a nucleocytoplasmic shuttling protein and plays a positive role in ABA responses by interacting with and maintaining the stability of ABI5 in the nucleus.

Most environmental perturbations have a direct or indirect deleterious impact on photosynthesis, and, in consequence, the overall energy status of the cell. Despite our increased understanding of convergent energy and stress signals, the connections between photosynthesis, energy and stress signals through putative common nodes are still unclear. Here we identified an endoplasmic reticulum (ER)-localized adenine nucleotide transporter1 (ER-ANT1), whose deficiency causes seedling lethality in air but viable under high CO2, exhibiting the typical photorespiratory phenotype. Metabolic analysis suggested that depletion of ER-ANT1 resulted in circadian rhythm disorders in sucrose synthesis and induced sucrose signaling pathways, indicating that the ER is involved in the regulation of vital energy metabolism in plants. In addition, the defect of ER-ANT1 triggers ER stress and activates the unfolded protein response in plant cells, suggesting ER stress and photorespiration are closely linked. These findings provide an important evidence for a key role of ER-localized ER-ANT1 in convergent energy and stress signals in rice. Our findings support the idea that ATP is a central signal involved in the plant response to a variety of stresses.

Banana (Musa acuminata, AAA group) is a representative climacteric fruit with essential nutrients and pleasant flavors. Control of its ripening determines both the fruit quality and the shelf life. NAC (NAM, ATAF, CUC2) proteins, as one of the largest superfamilies of transcription factors, play crucial roles in various functions, especially developmental processes. Thus, it is important to conduct a comprehensive identification and characterization of the NAC transcription factor family at the genomic level in M. acuminata. In this article, a total of 181 banana NAC genes were identified. Phylogenetic analysis indicated that NAC genes in M. acuminata, Arabidopsis, and rice were clustered into 18 groups (S1&ndash, S18), and MCScanX analysis disclosed that the evolution of MaNAC genes was promoted by segmental duplication events. Expression patterns of NAC genes during banana fruit ripening induced by ethylene were investigated using RNA-Seq data, and 10 MaNAC genes were identified as related to fruit ripening. A subcellular localization assay of selected MaNACs revealed that they were all localized to the nucleus. These results lay a good foundation for the investigation of NAC genes in banana toward the biological functions and evolution.

Although dozens of stress inducible promoters have been identified in rice, detailed and comparative investigations under uniform condition are still limited. In this study, we selected eight previously reported drought-inducible genes [Oshox24, hypothetical protein (hp), OsLEA3-1, OsNAC5, OsNCED3, Rab21, RRJ1 and Wsi18] and analyzed their transcriptional responses to drought and osmotic stresses in rice. Based on their transcription patterns and the required standards for inducible promoters, Oshox24, Rab21 and OsLEA3-1 were chosen for cloning of their promoters for detailed analyses at both the RNA and protein/activity levels, with rice oxalate oxidase gene (OsOxO3) as a reporter gene. By generating transgenic plants and determining oxalate oxidase activity that is activated under different stresses, we defined more quantitatively that the promoters of Oshox24, OsLEA3-1 and Rab21 are ideally applicable to transgene expression for inducibly controlling drought resistance genes or other functional genes in rice. The results provided a quantitative assessment of the strength, sensitivity, stress specificity and time course of the three promoters. Such detailed information is essential for the selection of promoters for use in improving stress resistance.

Photorespiration is an essential process for plant photosynthesis, development and growth in aerobic conditions. Recent studies have shown that photorespiration is an open system integrated with the plant primary metabolism network and intracellular redox systems, though the mechanisms of regulating photorespiration are far from clear. Through a forward genetic method, we identified a photorespiratory mutant pr1 (photorespiratory related 1), which produced a chlorotic and smaller photorespiratory growth phenotype with decreased chlorophyll content and accumulation of glycine and serine in ambient air. Morphological and physiological defects in pr1 plants can be largely abolished under elevated CO2 conditions. Genetic mapping and complementation confirmed that PR1 encodes an FtsH (Filamentation temperature-sensitive H)-like protein, FtsHi5. Reduced FtsHi5 expression in DEX-induced RNAi transgenic plants produced a similar growth phenotype with pr1 (ftsHi5-1). Transcriptome analysis suggested a changed expression pattern of redox-related genes and an increased expression of senescence-related genes in DEX: RNAi-FtsHi5 seedlings. Together with the observation that decreased accumulation of D1 and D2 proteins of photosystem II (PSII) and over-accumulation of reactive oxygen species (ROS) in ftsHi5 mutants, we hypothesize that FtsHi5 functions in maintaining the cellular redox balance and thus regulates photorespiratory metabolism.

Various chloroplast transit peptides (CTP) have been used to successfully target some foreign proteins into chloroplasts, but for other proteins these same CTPs have reduced localization efficiencies or fail completely. The underlying cause of the failures remains an open question, and more effective CTPs are needed. In this study, we initially observed that two E.coli enzymes, EcTSR and EcGCL, failed to be targeted into rice chloroplasts by the commonly-used rice rbcS transit peptide (rCTP) and were subsequently degraded. Further analyses revealed that the N-terminal unfolded region of cargo proteins is critical for their localization capability, and that a length of about 20 amino acids is required to attain the maximum localization efficiency. We considered that the unfolded region may alleviate the steric hindrance produced by the cargo protein, by functioning as a spacer to which cytosolic translocators can bind. Based on this inference, an optimized CTP, named RC2, was constructed. Analyses showed that RC2 can more effectively target diverse proteins, including EcTSR and EcGCL, into rice chloroplasts. Collectively, our results provide further insight into the mechanism of CTP-mediated chloroplastic localization, and more importantly, RC2 can be widely applied in future chloroplastic metabolic engineering, particularly for crop plants.

The primers used for the plasmid construction and real-time quantitative PCR. (DOCX 18 kb)

Similarities of rice GLO gene members at the level of mRNA and protein. (DOCX 16 kb)

GLO activity in root of GLO3 over expression plants. (DOCX 17 kb)

The V max of purified GLO isozymes with various substrates. (DOCX 18 kb)

Although copper (Cu) is an essential micronutrient for plants, a slight excess of Cu in soil can be harmful to plants. Unfortunately, Cu contamination is a growing problem all over the world due to human activities, and poses a soil stress to plant development. As one of the most important biological processes, seed germination is sensitive to Cu stress. However, little is known about the mechanism of Cu-induced inhibition of seed germination. In the present study, we investigated the relationship between Cu and ABA which is the predominant regulator of seed germination. Cu at a concentration of 30 µM effectively inhibited germination of rice caryopsis. ABA content in germinating seeds under copper stress was also higher than that under control conditions. Quantitative real-time PCR (qRT-PCR) revealed that Cu treatment reduced the expression of OsABA8ox2, a key gene of ABA catabolism in rice seeds. In addition, both malondialdehyde (MDA) and H2O2 contents were increased by Cu stress in the germinating seeds. Antioxidant enzyme assays revealed that only catalase activity was reduced by excess Cu, which was consistent with the mRNA profile of OsCATa during seed germination under Cu stress. Together, our results demonstrate that suppression of ABA catabolism and catalase (CAT) activity by excess Cu leads to the inhibition of seed germination of rice.

Mutations in the photorespiration pathway display a lethal phenotype in atmospheric air, which can be fully recovered by elevated CO2 . An exception is that mutants of peroxisomal hydroxypyruvate reductase (HPR1) do not have this phenotype, indicating the presence of cytosolic bypass in the photorespiration pathway. In this study, we constructed overexpression of the OsHPR1 gene and RNA interference plants of OsHPR1 and OsHPR2 genes in rice (Oryza sativa L. cv. Zhonghua 11). Results from reverse transcription-polymerase chain reaction (RT-PCR), Western blot, and enzyme assays showed that HPR1 activity changed significantly in corresponding transgenic lines without any effect on HPR2 activity, which is the same for HPR2. However, metabolite analysis and the serine glyoxylate aminotransferase (SGAT) activity assay showed that the metabolite flux of photorespiration was disturbed in RNAi lines of both HPR genes. Furthermore, HPR1 and HPR2 proteins were located to the peroxisome and cytosol, respectively, by transient expression experiment. Double mutant hpr1 × hpr2 was generated by crossing individual mutant of hpr1 and hpr2. The phenotypes of all transgenic lines were determined in ambient air and CO2 -elevated air. The phenotype typical of photorespiration mutants was observed only where activity of both HPR1 and HPR2 were downregulated in the same line. These findings demonstrate that two hydroxypyruvate reductases encoded by OsHPR1 and OsHPR2 are involved in photorespiratory metabolism in rice.

Modern rice cultivars have large panicle but their yield potential is often not fully achieved due to poor grain-filling of late-flowering inferior spikelets (IS). Our earlier work suggested a broad transcriptional reprogramming during grain filling and showed a difference in gene expression between IS and earlier-flowering superior spikelets (SS). However, the links between the abundances of transcripts and their corresponding proteins are unclear. In this study, a SWATH-MS (sequential window acquisition of all theoretical spectra-mass spectrometry) -based quantitative proteomic analysis has been applied to investigate SS and IS proteomes. A total of 304 proteins of widely differing functionality were observed to be differentially expressed between IS and SS. Detailed gene ontology analysis indicated that several biological processes including photosynthesis, protein metabolism, and energy metabolism are differentially regulated. Further correlation analysis revealed that abundances of most of the differentially expressed proteins are not correlated to the respective transcript levels, indicating that an extra layer of gene regulation which may exist during rice grain filling. Our findings raised an intriguing possibility that these candidate proteins may be crucial in determining the poor grain-filling of IS. Therefore, we hypothesize that the regulation of proteome changes not only occurs at the transcriptional, but also at the post-transcriptional level, during grain filling in rice.

The total oxalate contents of various vegetables, legume seeds, cereals, fruits and nuts commonly available in Southern China were determined using an improved enzymatic method. Spinach, xeric water spinach (grows on moist soil), amaranth, bamboo shoot, ginger, Chinese wolfberry, rice bean and black glutinous rice contained more than 100mg oxalate/100gFW, but leaf mustard, white radish, broccoli, cauliflower, cabbage, onion, gourd except bitter melon, tomato, pepper, chufa, kelp, mushroom, soybean sprout and cowpea contained less than 10mg oxalate/100gFW. The oxalate contents of star fruit and dragon fruit were 111.4 and 97.1mg/100gFW, respectively, and those of other fruits except strawberry and black plum were less than 20mg/100gFW. Almond, cashew, hazel, pine nut and abalone fruit contained more than 150mg total oxalate/100gFW, and the oxalate levels in Chinese torreya fruit, peanut, pistachio and walnut ranged from 54.1 to 83.1mg/100gFW. Based on the results obtained, water spinach, Chinese wolfberry, black glutinous rice, dragon fruit, rice bean, abalone fruit and Chinese torreya fruit should also be considered as high oxalate-foods. The enzymatic method used in the present study enabled us to perform a large-scale quantitative investigation of oxalate contents of different foods.

Fusarium wilt of banana is caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (Foc). The fact that there are no economically viable biological, chemical, or cultural measures of controlling the disease in an infected field leads to search for alternative strategies involving activation of the plant's innate defense system. The mechanisms underlying systemic acquired resistance (SAR) are much less understood in monocots than in dicots. Since systemic protection of plants by attenuated or avirulent pathogens is a typical SAR response, the establishment of a biologically induced SAR model in banana is helpful to investigate the mechanism of SAR to Fusarium wilt. This paper described one such model using incompatible Foc race 1 to induce resistance against Foc tropical race 4 in an in vitro pathosystem. Consistent with the observation that the SAR provided the highest level of protection when the time interval between primary infection and challenge inoculation was 10d, the activities of defense-related enzymes such as phenylalanine ammonia lyase (PAL, EC 4.3.1.5), peroxidase (POD, EC 1.11.1.7), polyphenol oxidase (PPO, EC 1.14.18.1), and superoxide dismutase (SOD, EC 1.15.1.1) in systemic tissues also reached the maximum level and were 2.00-2.43 times higher than that of the corresponding controls on the tenth day. The total salicylic acid (SA) content in roots of banana plantlets increased from about 1 to more than 5 μg g⁻¹ FW after the second leaf being inoculated with Foc race 1. The systemic up-regulation of MaNPR1A and MaNPR1B was followed by the second up-regulation of PR-1 and PR-3. Although SA and jasmonic acid (JA)/ethylene (ET) signaling are mostly antagonistic, systemic expression of PR genes regulated by different signaling pathways were simultaneously up-regulated after primary infection, indicating that both pathways are involved in the activation of the SAR.

Background ROOT UV-B SENSITIVE (RUS) genes exist in most eukaryotic organisms, and encode proteins that contain a DUF647 (domain of unknown function 647). Although the RUS genes are known to play essential roles in Arabidopsis seedling development, their precise functions are not well understood in other plants, including rice. Findings In this study, six OsRUS genes were cloned from rice root and leaf cDNA libraries. Our analysis showed that the sequence and open reading frame of cloned OsRUS3 cDNA differs from the predictions reported in the RAP-DB and RGAP databases. Public microarray, MPSS, and EST databases were used to analyze the expression profiles of the six OsRUS genes. Expression profiles for all OsRUS genes at different rice developmental stages were also analyzed by qRT-PCR. The signal peptide, GPI-anchor, transmembrane domain and subcellular localization of OsRUS proteins were predicted by various bioinformatics tools. Furthermore OsRUS1 was determined to be localized to the chloroplast by a protoplast experiment. Conclusions All the characterization of the OsRUS family generated from this study will provide a crucial foundation from which to further dissect how OsRUS genes function in rice development. Electronic supplementary material The online version of this article (doi:10.1186/s12284-016-0127-0) contains supplementary material, which is available to authorized users.