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Macroautophagy involves the encapsulation of cellular components within double‐membrane autophagosomes for subsequent degradation in vacuoles or lysosomes. Coat protein complex II (COPII) vesicles serve as a membrane source for autophagosome formation. However, the specific role of SEC24D, an isoform of the COPII coat protein SEC24, in the macroautophagy pathway remains unclear. In this study, we demonstrate that SEC24D is indispensable for macroautophagy and important for autophagosome closure. Depletion of SEC24D leads to the accumulation of unsealed isolation membranes. Furthermore, under conditions of starvation, SEC24D interacts with casein kinase1 delta (CK1δ), a member of the casein kinase 1 family, and autophagy‐related 9A (ATG9A). Collectively, our findings unveil the indispensable role of SEC24D in starvation‐induced autophagy in mammalian cells. [ABSTRACT FROM AUTHOR]

Aerobic glycolysis is critical for the energy metabolism of cancer cells. This study focuses on the regulation of forkhead box A2 (FOXA2) on pyruvate kinase M2 (PKM2) and their effects on the glycolytic activity and malignant phenotype of thyroid carcinoma (THCA) cells. By analysing four Gene Expression Omnibus datasets and querying bioinformatics systems, we obtained FOXA2 as a poorly expressed transcription factor in THCA. Later, we validated decreased mRNA and protein levels of FOXA2 in THCA cells by quantitative polymerase chain reaction and western blot assays. FOXA2 upregulation in THCA cells suppressed the glucose uptake and lactate production, and it reduced the extracellular acidification rate, but increased the oxygen consumption rate of cells. Meanwhile, the FOXA2 overexpression blocked the proliferation and mobility, and the tumourigenic activity of cancer cells. The chromatin immunoprecipitation and luciferase assays showed that FOXA2 bound to PKM2 promoter and suppressed the transcription of PKM2, which was highly expressed in THCA cells. Further upregulation of PKM2 elevated the β‐catenin, c‐Myc and cyclin D1 levels and restored the glycolytic activity as well as the malignant properties of cancer cells. Collectively, this work reveals that FOXA2 suppresses aerobic glycolysis and progression of THCA by blocking PKM2 transcription and inactivating the Wnt/β‐catenin pathway. [ABSTRACT FROM AUTHOR]

Optimal project portfolio planning is a typical nonconvex, multiobjective, highly constrained, multitemporal coupling, and combinatorial optimization problem. This paper proposes a novel multistep iterative ranking learning method (MIRL) to solve this complex combinatorial optimization problem from massive infrastructure projects of smart grid. The optimal project portfolio planning problem of power grid is formulated as the optimization process of massive project priority sorting with an improved knapsack model. The proposed method dynamically optimizes the best infrastructure project combination for each round to maximize the economic, social, and security benefits without exceeding the annual investment limit. A pairwise-based ranking learning algorithm is used to mine the priority sorting law from massive historical combination data of power grid to initialize candidate project portfolio. In order to approach the optimal portfolio planning solution with the constraint satisfactions of project construction duration and electric load supplies, a heuristic greedy strategy is designed to search the solution dynamically for selecting the project having highest construction benefits iteratively. The effectiveness of the proposed method is proved by experiments with real-world project data of Hunan power grid in China, and experimental results show that the proposed MIRL can outperform other methods on investment efficiency, calculation time, and rationality of project construction period schedule. [ABSTRACT FROM AUTHOR]

SUMMARY: Heterosis refers to the superior performance of hybrids over their parents, which is a general phenomenon occurring in diverse organisms. Many commercial hybrids produce high yield without delayed flowering, which we refer to as optimal heterosis and is desired in hybrid breeding. Here, we attempted to illustrate the genomic basis of optimal heterosis by reinvestigating the single‐locus quantitative trait loci and digenic interactions of two traits, the number of spikelets per panicle (SP) and heading date (HD), using recombinant inbred lines and 'immortalized F2s' derived from the elite rice (Oryza sativa) hybrid Shanyou 63. Our analysis revealed a regulatory network that may provide an approximation to the genetic constitution of the optimal heterosis observed in this hybrid. In this network, Ghd7 works as the core element, and three other genes, Ghd7.1, Hd1, and Hd3a/RFT1, also have major roles. The effects of positive dominance by Ghd7 and Ghd7.1 and negative dominance by Hd1 and Hd3a/RFT1 in the hybrid background contribute the major part to the high SP without delaying HD; numerous epistatic interactions, most of which involve Ghd7, also play important roles collectively. The results expand our understanding of the genic interaction networks underlying hybrid rice breeding programs, which may be very useful in future crop genetic improvement. Significance Statement: Strong heterosis in the number of spikelets per panicle without delaying flowering is one of the most attractive features of commercial hybrids that is highly desired in breeding. A Ghd7‐centered regulatory network involving Ghd7.1, Hd1, Hd3a/RFT1, and a large number of other loci explains such optimal heterosis, and negative dominance (rather than positive dominance) effects of Hd1 and Hd3a/RFT1 on heading date in complex interactions in the network resulted in optimal heterosis in the hybrid. [ABSTRACT FROM AUTHOR]

Summary: High temperatures cause huge yield losses in rice. Heat‐shock factors (Hsfs) are key transcription factors which regulate the expression of heat stress‐responsive genes, but natural variation in and functional characterization of Hsfs have seldom been reported.A significant heat response locus was detected via a genome‐wide association study (GWAS) using green leaf area as an indicative trait. A miniature inverted‐repeat transposable element (MITE) in the promoter of a candidate gene, HTG3 (heat‐tolerance gene on chromosome 3), was found to be significantly associated with heat‐induced expression of HTG3 and heat tolerance (HT). The MITE‐absent variant has been selected in heat‐prone rice‐growing regions.HTG3a is an alternatively spliced isoform encoding a functional Hsf, and experiments using overexpression and knockout rice lines showed that HTG3a positively regulates HT at both vegetative and reproductive stages. The HTG3‐regulated genes were enriched for heat shock proteins and jasmonic acid signaling. Two heat‐responsive JASMONATE ZIM‐DOMAIN (JAZ) genes were confirmed to be directly upregulated by HTG3a, and one of them, OsJAZ9, positively regulates HT.We conclude that HTG3 plays an important role in HT through the regulation of JAZs and other heat‐responsive genes. The MITE‐absent allele may be valuable for HT breeding in rice. [ABSTRACT FROM AUTHOR]

The association between collagen type I alpha (COL1A) and chemoresistance has been verified in cancers. However, the specific role of COL1A2 in gastric cancer (GC) cell resistance to apatinib, a highly selective small-molecule inhibitor of vascular endothelial growth factor receptor 2, has not been investigated before. The purpose of this study was to explore the potential factors associated with COL1A2 regulation on GC cell apatinib resistance in vitro. With the aid of the Oncomine database and integrated bioinformatics methods, we identified COL1A2 overexpression in GC and its prognostic value. Mechanistically, the COL1A2 promoter has a distinct H3K27ac modification site and that E1A binding protein p300 (EP300) and twist family bHLH transcription factor 1 (TWIST1) can bind to the COL1A2 promoter, which in turn transcriptionally activated COL1A2 expression. In addition, overexpression of COL1A2 significantly promoted resistance to apatinib in GC cells, but knockdown of EP300 or TWIST1 remarkably inhibited COL1A2 expression and promoted sensitivity of GC cells to apatinib. Our findings demonstrated that the combination of EP300 and TWIST1 has a synergistically regulatory effect on COL1A2 expression, thus contributing to apatinib resistance in GC cells. [ABSTRACT FROM AUTHOR]

Mitogen‐activated protein kinase kinase kinase (MAPKKK) are the first components of MAPK cascades, which play pivotal roles in signaling during plant development and physiological processes. The genome of rice encodes 75 MAPKKKs, of which 43 are Raf‐like MAPKKKs. The functions and action modes of most of the Raf‐like MAPKKKs, whether they function as bona fide MAPKKKs and which are their downstream MAPKKs, are largely unknown. Here, we identified the osmapkkk43 mutant, which conferred broad‐spectrum resistance to Xanthomonas oryzae pv. oryzae (Xoo), the destructive bacterial pathogen of rice. Oryza sativa (Os)MAPKKK43 encoding a Raf‐like MAPKKK was previously known as Increased Leaf Angle 1 (OsILA1). Genetic analysis indicated that OsILA1 functioned as a negative regulator and acted upstream of the OsMAPKK4–OsMAPK6 cascade in rice–Xoo interactions. Unlike classical MAPKKKs, OsILA1 mainly phosphorylated the threonine 34 site at the N‐terminal domain of OsMAPKK4, which possibly influenced the stability of OsMAPKK4. The N‐terminal domain of OsILA1 is required for its homodimer formation and its full phosphorylation capacity. Taken together, our findings reveal that OsILA1 acts as a negative regulator of the OsMAPKK4–OsMAPK6 cascade and is involved in rice–Xoo interactions. [ABSTRACT FROM AUTHOR]

Appearance and taste are important factors in rice (Oryza sativa) grain quality. Here, we investigated the taste scores and related eating‐quality traits of 533 diverse cultivars to assess the relationships between—and genetic basis of—rice taste and eating‐quality. A genome‐wide association study highlighted the Wx gene as the major factor underlying variation in taste and eating quality. Notably, a novel waxy (Wx) allele, Wxla, which combined two mutations from Wxb and Wxin, exhibited a unique phenotype. Reduced GBSSI activity conferred Wxla rice with both a transparent appearance and good eating quality. Haplotype analysis revealed that Wxla was derived from intragenic recombination. In fact, the recombination rate at the Wx locus was estimated to be 3.34 kb/cM, which was about 75‐fold higher than the genome‐wide mean, indicating that intragenic recombination is a major force driving diversity at the Wx locus. Based on our results, we propose a new network for Wx evolution, noting that new Wx alleles could easily be generated by crossing genotypes with different Wx alleles. This study thus provides insights into the evolution of the Wx locus and facilitates molecular breeding for quality in rice. [ABSTRACT FROM AUTHOR]

SUMMARY: Spontaneous mutants are mainly obtained from tissue culture or natural occurrences in plants. The traditional strategy for identifying spontaneously mutated genes is to continuously backcross these mutants to another variety and develop a near‐isogenic F2 population for map‐based cloning or bulked segregant analysis. However, this strategy is time‐consuming. Here, we have developed a new method to efficiently accelerate the identification process. The chemical mutagen ethyl methanesulfonate was first used to treat the wild type of the spontaneous mutants to induce thousands of neutral mutations. An induced individual without any statistically significant phenotypic changes which was compared with the wild type was chosen as the neutral mutant. The spontaneous mutant was then crossed with the neutral mutant to develop a pseudo‐near‐isogenic F2 population in which only the induced neutral mutations and the causal mutation were segregated in the genome. This population ensures that the variation of the mutated trait is controlled only by the spontaneously mutated gene. Finally, after sequencing the neutral mutant and the mutant‐type DNA pool of the F2 population the spontaneous mutation will be identified quickly by bioinformatics analysis. Using this method, two spontaneously mutated genes were identified successfully. Therefore, the neutral mutant‐bridging method efficiently identifies spontaneously mutated genes in rice, and its value in other plants is discussed. Significance Statement: Ethyl methanesulfonate (EMS) can induce thousands of single nucleotide polymorphisms as molecular markers in plants. By crossing a spontaneous mutant with the neutral mutant induced by EMS, a pseudo‐near‐isogenic F2 population is developed and only the induced neutral mutations and causal mutation are segregated in the genome. After sequencing the neutral mutant and the mutant type DNA pool of the F2 population, spontaneous mutation will be identified quickly by bioinformatics analysis. [ABSTRACT FROM AUTHOR]

Summary: Plant cell wall composition and structure can be modified as plants adapt to environmental stresses; however, the underlying regulatory mechanisms remain elusive.Here, we report that OsTMF, a homologue of the human TATA modulatory factor (TMF) in rice (Oryza sativa) and highly conserved in plants, negatively regulates cold tolerance through modification of cell wall properties.Cold stress increased the expression of OsTMF and accumulation of OsTMF in the nucleus, where OsTMF acts as a transcription activator and modulates the expression of genes involved in pectin degradation (OsBURP16), cellulose biosynthesis (OsCesA4 and OsCesA9), and cell wall structural maintenance (genes encoding proline‐rich proteins and peroxidases). OsTMF directly activated the expression of OsBURP16, OsCesA4, and OsCesA9 through binding to the TATA cis‐elements in their promoters. Under cold stress conditions, OsTMF negatively regulated pectin content and peroxidase activity and positively regulated cellulose content, causing corresponding alterations to cell wall properties, all of which collectively contribute to the negative effect of OsTMF on cold tolerance.Our findings unravel a previously unreported molecular mechanism of a conserved plant TMF protein in the regulation of cell wall changes under cold stress. [ABSTRACT FROM AUTHOR]

Summary: Lamin proteins in animals are implicated in important nuclear functions, including chromatin organization, signalling transduction, gene regulation and cell differentiation. Nuclear Matrix Constituent Proteins (NMCPs) are lamin analogues in plants, but their regulatory functions remain largely unknown.We report that OsNMCP1 is localized at the nuclear periphery in rice (Oryza sativa) and induced by drought stress. OsNMCP1 overexpression resulted in a deeper and thicker root system, and enhanced drought resistance compared to the wild‐type control. An assay for transposase accessible chromatin with sequencing (ATAC‐seq) analysis revealed that OsNMCP1‐overexpression altered chromatin accessibility in hundreds of genes related to drought resistance and root growth, including OsNAC10, OsERF48, OsSGL, SNAC1 and OsbZIP23.OsNMCP1 can interact with SWITCH/SUCROSE NONFERMENTING (SWI/SNF) chromatin remodelling complex subunit OsSWI3C. The reported drought resistance or root growth‐related genes that were positively regulated by OsNMCP1 were negatively regulated by OsSWI3C under drought stress conditions, and OsSWI3C overexpression led to decreased drought resistance.We propose that the interaction between OsNMCP1 and OsSWI3C under drought stress conditions may lead to the release of OsSWI3C from the SWI/SNF gene silencing complex, thus changing chromatin accessibility in the genes related to root growth and drought resistance. [ABSTRACT FROM AUTHOR]

Summary: Grain size is a major determinant of grain weight, a key component of grain yield of rice. Here, we identified the grain size gene WIDE GRAIN 7 (WG7) from a T‐DNA insertion mutant. The grain size of WG7 knockout mutants and WG7 overexpression lines indicated that WG7 is a positive regulator of grain size. WG7 encodes a cysteine‐tryptophan (CW) domain‐containing transcriptional activator. EMSAs and ChIP‐qPCR assay confirmed that WG7 directly bound to the promoter of OsMADS1, a grain size gene, and thereby significantly activated its expression. Point mutations showed that the cis‐element CATTTC motif in the promoter was the binding site of WG7. Compared with the wild‐type, deletion mutants of the cis‐element motif exhibited lower expression of OsMADS1 and produced narrower grains, implicating the requirement of this motif for WG7 function. ChIP‐qPCR assays showed that WG7 enhanced histone H3K4me3 enrichment in the promoter of OsMADS1. WG7 underwent directional selection due to the poor fertility of the non‐functional mutant. These findings demonstrated that WG7 upregulated OsMADS1 expression by directly binding to its promoter, enhanced histone H3K4me3 enrichment in the promoter and ultimately increased grain width. This study will enrich the knowledge concerning the regulatory network of grain size formation in rice. Significance Statement: WG7 encoding a CW domain‐containing transcriptional activator is a positive regulator of grain size, which directly binds to the promoter of OsMADS1 and thereby significantly activates OsMADS1 expression. This paper demonstrates the role of rice CW domain‐containing protein in the regulation of grain size, which enriches our knowledge of the regulatory network of grain size in rice. [ABSTRACT FROM AUTHOR]

Mitogen-activated protein kinase ( MAPK) cascades, with each cascade consisting of a MAPK kinase kinase ( MAPKKK), a MAPK kinase ( MAPKK) and a MAPK, have important roles in different biological processes. However, the signal transduction in rice MAPK cascades remains to be elucidated. We show that the structural non-canonical MAPKK, MPKK10.2, enhances rice resistance to Xanthomonas oryzae pv. oryzicola ( Xoc), which causes bacterial streak disease, and increases rice tolerance to drought stress by phosphorylating and activating two MAPKs, MPK6 and MPK3, respectively. MPKK10.2-overexpressing (oe) plants showed enhanced resistance to both Xoc and drought, whereas MPKK10.2- RNA interference ( RNAi) plants had increased sensitivity to both Xoc and drought. MPKK10.2 physically interacted with MPK6 and MPK3, and phosphorylated the two MAPKs in vivo. Transcriptionally modulating MPKK10.2 influenced MPK6 phosphorylation during rice- Xoc interaction, and MPKK10.2-oe/ MPK6- RNAi double mutants showed increased sensitivity to Xoc. MPKK10.2-oe/ MPK3- RNAi double mutants showed survival rates similar to those of control plants, although the survival rates of MPKK10.2 transgenic plants changed after drought stress. These results suggest that MPKK10.2 is a node involved in rice response to biotic and abiotic responses by functioning in the cross-point of two MAPK cascades leading to Xoc resistance and drought tolerance. [ABSTRACT FROM AUTHOR]

Systematic characterization of genetic and molecular mechanisms in the formation of hybrid sterility is of fundamental importance in understanding reproductive isolation and speciation. Using ultra-high-density genetic maps, 43 single-locus quantitative trait loci ( QTLs) and 223 digenic interactions for embryo-sac, pollen, and spikelet fertility are depicted from three crosses between representative varieties of japonica and two varietal groups of indica, which provide an extensive archive for investigating the genetic basis of reproductive isolation in rice. Ten newly detected single-locus QTLs for inter- and intra-subspecific fertility are identified. Three loci for embryo-sac fertility are detected in both Nip × ZS97 and Nip × MH63 crosses, whereas QTLs for pollen fertility are not in common between the two crosses thus leading to fertility variation. Five loci responsible for fertility and segregation distortion are observed in the ZS97 × MH63 cross. The importance of two-locus interactions on fertility are quantified in the whole genome, which identify that three types of interaction contribute to fertility reduction in the hybrid. These results construct the genetic architecture with respect to various forms of reproductive barriers in rice, which have significant implications in utilization of inter-subspecific heterosis along with improvement in the fertility of indica-indica hybrids at single- and multi-locus level. [ABSTRACT FROM AUTHOR]

Plants always adjust the opening of stomatal pores to adapt to the environment, for example CO2 concentration ([CO2]), humidity and temperature. Low [CO2] will trigger the opening of stomatal pores to absorb extra CO2. However, little is known about how CO2 supply affects the carbon fixation and opening of stomatal pores in rice. Here, a chloroplast-located gene coding for β-carbonic anhydrase (βCA) was found to be involved in carbon assimilation and the CO2-mediated stomatal pore response in rice. Osβ CA1 was constitutively expressed in all tissues and its transcripts were induced by high [CO2] in leaves. Both T-DNA mutant and RNA interference lines showed phenotypes of lower biomass and CA activities. Knockout of Osβ CA1 obviously decreased photosynthetic capacity, as demonstrated by the increased CO2 compensation point and decreased light saturation point in the mutant, while knockout increased the opening ratio of stomatal pores and the rate of water loss. Moreover, the mutant showed a delayed response to low [CO2], and stomatal pores could not be closed to the same degree as those of wild type even though the stomatal pores could rapidly respond to high [CO2]. Genome-wide gene expression analysis via RNA sequencing demonstrated that the transcript abundance of genes related to Rubisco, photosystem compounds and the opening of stomatal pores was globally upregulated in the mutant. Taken together, the inadequate CO2 supply caused by the absence of Osβ CA1 reduces photosynthetic efficiency, triggers the opening of stomatal pores and finally decreases their sensitivity to CO2 fluctuation. [ABSTRACT FROM AUTHOR]

Background The prognostic value of the telomerase reverse transcriptase (TERT) promoter mutation, resulting in poor clinical outcomes of papillary thyroid carcinoma (PTC), has been generally confirmed. To data, there is no high-level evidence approving the association of TERT promoter mutation and aggressive clinical behaviours in PTC. To systematically evaluate it, a systematic review and meta-analysis of the published literatures were carried out. Methods We conducted a systematic search in PubMed, EMBASE, OVID and Web of Science databases for relevant studies. We selected all the studies that reported clinicopathological features of PTC patients with information available on TERT promoter mutation status. Individual study-specific odds ratios (ORs) and 95% confidence intervals (CIs) were calculated, as were Mantel-Haenszel pooled odds ratios for the combined studies. Results Eight eligible trials involved 2035 patients were included in the analysis. The average prevalence of the TERT promoter mutation was 10·32%. Compared with the wild-type TERT promoter gene, the TERT promoter mutation was associated with male gender, lymph node metastasis, extrathyroidal extension, distant metastasis, advanced TNM stage III/IV, poor clinical outcome (persistence or recurrence) and mortality. The associations were generally consistent across the different study populations. Conclusions Thus, our findings from this large meta-analysis definitively demonstrate that TERT promoter mutation-positive PTC is more likely to manifest with aggressive clinicopathological characteristics. In appropriate clinical settings, testing for the TERT promoter mutation is likely to be useful in assisting the risk stratification and management of PTC. [ABSTRACT FROM AUTHOR]

In order to understand cold adaptability and explore additional genetic resources for the cold tolerance improvement of rice, we investigated the genetic variation of 529 rice accessions under natural chilling and cold shock stress conditions at the seedling stage using genome-wide association studies; a total of 132 loci were identified. Among them, 12 loci were common for both chilling and cold shock tolerance, suggesting that rice has a distinct and overlapping genetic response and adaptation to the two stresses. Haplotype analysis of a known gene OsMYB2, which is involved in cold tolerance, revealed indica-japonica differentiation and latitude tendency for the haplotypes of this gene. By checking the subpopulation and geographical distribution of accessions with tolerance or sensitivity under these two stress conditions, we found that the chilling tolerance group, which mainly consisted of japonica accessions, has a wider latitudinal distribution than the chilling sensitivity group. We conclude that the genetic basis of natural chilling stress tolerance in rice is distinct from that of cold shock stress frequently used for low-temperature treatment in the laboratory and the cold adaptability of rice is associated with the subpopulation and latitudinal distribution. [ABSTRACT FROM AUTHOR]

The shoot apical meristem ( SAM) produces all of the plant's aerial organs. The SAM is established either during embryogenesis or experimentally in in vitro tissue culture. Although several factors including the Class I KNOTTED1- LIKE HOMEOBOX ( KNOXI) proteins, auxin, and cytokinin are known to play essential roles in SAM development, the underlying mechanisms of SAM formation and maintenance are still largely not understood. Herein we demonstrate that Os ARID3, a member of the rice ( Oryza sativa) AT-rich Interaction Domain ( ARID) family, is required for SAM development. Disruption of Os ARID3 leads to a defective SAM, early seedling lethality, and impaired capacity of in vitro shoot regeneration. We show that the expression levels of several KNOXI genes and the biosynthetic genes for auxin and cytokinin are significantly altered in the Osarid3 mutant calli. Moreover, we determine that auxin concentrations are increased, whereas cytokinin levels are decreased, in Osarid3 calli. Furthermore, chromatin immunoprecipitation results demonstrate that Os ARID3 binds directly to the KNOXI gene OSH71, the auxin biosynthetic genes Os YUC1 and Os YUC6, and the cytokinin biosynthetic genes Os IPT2 and Os IPT7. We also show through electrophoretic mobility shift assays that Os ARID3 specifically binds to the AT-rich DNA sequences of the identified target genes. We conclude that Os ARID3 is an AT-rich specific DNA-binding protein and that it plays a major role in SAM development in rice. [ABSTRACT FROM AUTHOR]

Novel series of Farnesylthiosalicylic acid-diamine/phenylpropenoic acid hybrids were designed and synthesized. Their in vitro growth inhibitory assays showed that most compounds displayed strong antiproliferation activity against seven cancer cells. Especially, the new hybrid 12f, by the conjugation of 10a with ferulic acid, could selectively suppress the proliferation of tumor cells and display significantly lower toxicities to normal cells than its intermediate 10a. Furthermore, 12f dose-dependently induced SMMC-7721 cell apoptosis. Additionally, our observations demonstrated that 12f inhibited both Ras-related signaling and phosphorylated NF- κB synergistically, which may be advantageous to the strong antitumor activities of 12f. Our findings suggest that these novel hybrids may hold a great promise as therapeutic agents for the intervention of human cancers. [ABSTRACT FROM AUTHOR]

The rice MtN3/saliva/SWEET gene family consists of 21 paralogs. However, their functions in physiological processes are largely unknown, although at least three of the 21 paralogs are used by pathogenic bacteria to infect rice. Here, we report the evolutionary features, transcriptional characteristics, and putative functions in sugar transport of this gene family. The wild rice accessions in this study included those with AA, BB, CC, BBCC, CCDD, EE, and GG genomes, which appeared approximately 0.58-14.6 million years ago. The structures, chromosomal locations, phylogenetic relationships, and homologous distribution among the accessions suggest that the number of rice MtN3/saliva/SWEET paralogs gradually increased as the Oryza genus evolved, and one third of the paralogs may have originated recently. These paralogs are differentially expressed in vegetative and reproductive tissues, in the leaf senescence process, and in signaling dependent on gibberellic acid, cytokinin, or 1-naphthalene acetic acid (an analog of auxin), suggesting that they may be associated with multiple physiological processes. Four paralogs could transport galactose in yeast, which suggests that they may have a similar function in rice. These results will help to elucidate their roles and biochemical functions in rice development, adaptation to environment, host-pathogen interaction, and so forth. [ABSTRACT FROM AUTHOR]

Submergence and drought are major limiting factors for crop production. However, very limited studies have been reported on the distinct or overlapping mechanisms of plants in response to the two water extremes. Here we report an ETHYLENE OVERPRODUCER 1-like gene ( Os ETOL1) that modulates differentially drought and submergence tolerance in rice ( Oryza sativa L.). Two allelic mutants of Os ETOL1 showed increased resistance to drought stress at the panicle development stage. Interestingly, the mutants exhibited a significantly slower growth rate under submergence stress at both the seedling and panicle development stages. Over-expression ( OE) of Os ETOL1 in rice resulted in reverse phenotypes when compared with the mutants. The Os ETOL1 transcript was differentially responsive to abiotic stresses. Os ETOL1 was found to interact with Os ACS2, a homolog of 1-amino-cyclopropane-1-carboxylate ( ACC) synthase ( ACS), which acts as a rate-limiting enzyme for ethylene biosynthesis. In the osacs2 mutant and Os ETOL1- OE plants, ACC and ethylene content were decreased significantly, and exogenous ACC restored the phenotype of osetol1 and Os ETOL1- OE to wild-type under submergence stress, implying a negative role for Os ETOL1 in ethylene biosynthesis. The expression of several genes related to carbohydrate catabolism and fermentation showed significant changes in the osetol1 and Os ETOL1- OE plants, implying that Os ETOL1 may affect energy metabolism. These results together suggest that Os ETOL1 plays distinct roles in drought and submergence tolerance by modulating ethylene production and energy metabolism. Findings from the expression and functional comparison of three ethylene overproducer ( ETOL) family members in rice further supported the specific role of Os ETOL1 in the responses to the two water stresses. [ABSTRACT FROM AUTHOR]

The extensively studied Arabidopsis phytoalexin deficient 4 ( At PAD4) gene plays an important role in Arabidopsis disease resistance; however, the function of its sequence ortholog in rice is unknown. Here, we show that rice Os PAD4 appears not to be the functional ortholog of At PAD4 in host-pathogen interactions, and that the Os PAD4 encodes a plasma membrane protein but that At PAD4 encodes a cytoplasmic and nuclear protein. Suppression of Os PAD4 by RNA interference ( RNAi) increased rice susceptibility to the biotrophic pathogen Xanthomonas oryzae pv. oryzae ( Xoo), which causes bacteria blight disease in local tissue. Os PAD4- RNAi plants also show compromised wound-induced systemic resistance to Xoo. The increased susceptibility to Xoo was associated with reduced accumulation of jasmonic acid ( JA) and phytoalexin momilactone A ( MOA). Exogenous application of JA complemented the phenotype of Os PAD4- RNAi plants in response to Xoo. The following results suggest that Os PAD4 functions differently than At PAD4 in response to pathogen infection. First, Os PAD4 plays an important role in wound-induced systemic resistance, whereas At PAD4 mediates systemic acquired resistance. Second, Os PAD4-involved defense signaling against Xoo is JA-dependent, but At PAD4-involved defense signaling against biotrophic pathogens is salicylic acid-dependent. Finally, Os PAD4 is required for the accumulation of terpenoid-type phytoalexin MOA in rice-bacterium interactions, but At PAD4-mediated resistance is associated with the accumulation of indole-type phytoalexin camalexin. [ABSTRACT FROM AUTHOR]

tRNase Z (TRZ) is a ubiquitous endonuclease that removes the 3′-trailer from precursor tRNAs during maturation. In yeast and animals, TRZ regulates the cell cycle via its (t)RNA processing activity; however, its physiological function in higher plants has not been well characterized. This study describes the identification of a rice ( Oryza sativa) TRZ2 mutant; plants homozygous for the osatrz2 mutation were albinos with deficient chlorophyll content. A microscopic analysis of the mutant plants revealed that the transition of proplastids to chloroplasts was arrested at an early stage, and the number and size of the plastids in callus cells was substantially decreased. A genetic complementation test and an RNA interference analysis confirmed that disruption of OsaTRZ2 was responsible for the mutant phenotype. OsaTRZ2 is expressed in all rice tissues, but is preferentially expressed in leaves, sheathes, and calli. OsaTRZ2 was subcellularly localized in chloroplasts, and displayed tRNA 3′-end processing activity in both in vitro and in vivo assays. In the osatrz2 mutants, transcription of plastid-encoded and nucleus-encoded RNA polymerases was severely reduced and moderately increased, respectively. These results suggest that the tRNA 3′ processing activity of OsaTRZ2 contributes to chloroplast biogenesis. [ABSTRACT FROM AUTHOR]

Organ size is determined by cell number and size, and involves two fundamental processes: cell proliferation and cell expansion. Although several plant hormones are known to play critical roles in shaping organ size by regulating the cell cycle, it is not known whether brassinosteroids (BRs) are also involved in regulating cell division. Here we identified a rice T-DNA insertion mutant for organ size, referred to as xiao, that displays dwarfism and erect leaves, typical BR-related phenotypes, together with reduced seed setting. XIAO is predicted to encode an LRR kinase. The small stature of the xiao mutant resulted from reduced organ sizes due to decreased cell numbers resulting from reduced cell division rate, as supported by the observed co-expression of XIAO with a number of genes involved in cell cycling. The xiao mutant displayed a tissue-specific enhanced BR response and greatly reduced BR contents at the whole-plant level. These results indicated that XIAO is a regulator of BR signaling and cell division. Thus, XIAO may provide a possible connection between BRs and cell-cycle regulation in controlling organ growth. [ABSTRACT FROM AUTHOR]

ABSTRACT Approximately one third of the identified 34 rice major disease resistance ( R) genes conferring race-specific resistance to different strains of Xanthomonas oryzae pv. oryzae ( Xoo), which causes rice bacterial blight disease, are recessive genes. However, only two of the recessive resistance genes have been characterized thus far. Here we report the characterization of another recessive resistance gene, xa25, for Xoo resistance. The xa25, localized in the centromeric region of chromosome 12, mediates race-specific resistance to Xoo strain PXO339 at both seedling and adult stages by inhibiting Xoo growth. It encodes a protein of the MtN3/saliva family, which is prevalent in eukaryotes, including mammals. Transformation of the dominant Xa25 into a resistant rice line carrying the recessive xa25 abolished its resistance to PXO339. The encoding proteins of recessive xa25 and its dominant allele Xa25 have eight amino acid differences. The expression of dominant Xa25 but not recessive xa25 was rapidly induced by PXO339 but not other Xoo strain infections. The nature of xa25-encoding protein and its expression pattern in comparison with its susceptible allele in rice- Xoo interaction indicate that the mechanism of xa25-mediated resistance appears to be different from that conferred by most of the characterized R proteins. [ABSTRACT FROM AUTHOR]

Rice OsEDR1 is a sequence ortholog of Arabidopsis EDR1. However, its molecular function is unknown. We show here that OsEDR1-suppressing/knockout (KO) plants, which developed spontaneous lesions on the leaves, have enhanced resistance to Xanthomonas oryzae pv. oryzae ( Xoo) causing bacterial blight disease. This resistance was associated with increased accumulation of salicylic acid (SA) and jasmonic acid (JA), induced expression of SA- and JA-related genes and suppressed accumulation of 1-aminocyclopropane-1-carboxylic acid (ACC), the direct precursor of ethylene, and expression of ethylene-related genes. OsEDR1-KO plants also showed suppressed production of ethylene. Knockout of OsEDR1 suppressed the ACC synthase (ACS) gene family, which encodes the rate-limiting enzymes of ethylene biosynthesis by catalysing the formation of ACC. The lesion phenotype and enhanced bacterial resistance of the OsEDR1-KO plants was partly complemented by the treatment with ACC. ACC treatment was associated with decreased SA and JA biosynthesis in OsEDR1-KO plants. In contrast, aminoethoxyvinylglycine, the inhibitor of ethylene biosynthesis, promoted expression of SA and JA synthesis-related genes in OsEDR1-KO plants. These results suggest that ethylene is a negative signalling molecule in rice bacterial resistance. In the rice- Xoo interaction, OsEDR1 transcriptionally promotes the synthesis of ethylene that, in turn, suppresses SA- and JA-associated defence signalling. [ABSTRACT FROM AUTHOR]

Summary The pathogen-induced plant defense signaling network consists of multiple components, although only some of them are characterized. Most of the known components function either as activators or repressors in host-pathogen interactions. Here we report that a mitogen-activated protein kinase, OsMPK6, functions both as an activator and a repressor in rice resistance against Xanthomonas oryzae pv. oryzae ( Xoo), the causal organism of bacterial blight disease. Activation of OsMPK6 resulted in the formation of lesion mimics and local resistance to Xoo, accompanied by the accumulation of salicylic acid (SA) and jasmonic acid (JA), and the induced expression of SA- and JA-signaling genes. Nuclear localization of OsMPK6 was essential for local resistance, suggesting that modulating the expression of defense-responsive genes through transcription regulators may be the primary mechanism of OsMPK6-mediated local resistance. The knock-out of OsMPK6 resulted in enhanced Xoo resistance, increased accumulation of SA and enhanced resistance to X. oryzae pv. oryzicola, the causal organism of bacterial streak disease, in systemic tissues. Xoo infection induced the expression of PR1a, the marker gene of systemic acquired resistance (SAR), in systemic health tissues of OsMPK6-knock-out plants. These results suggest that OsMPK6 negatively regulates SAR. Thus OsMPK6 is a two-faced player in the rice- Xoo interaction. [ABSTRACT FROM AUTHOR]

The tissue-specific expression of transgenes is essential in plant breeding programmes to avoid the fitness costs caused by constitutive expression of a target gene. However, knowledge on the molecular mechanisms of tissue-specific gene expression and practicable tissue-specific promoters is limited. In this study, we identified the cis-acting elements of a tissue-specific promoter from rice, PD54O, and tested the application of original and modified PD54O and its cis-elements in the regulation of gene expression. PD54O is a green tissue-specific promoter. Five novel tissue-specific cis-elements (LPSE1, LPSE2, LPSRE1, LPSRE2, PSE1) were characterized from PD54O. LPSE1 activated gene expression in leaf and young panicle. LPSRE2 suppressed gene expression in leaf, root, young panicle and stem, and PSE1 suppressed gene expression in young panicle and stem. LPSRE1 and LPSE2 had dual roles in the regulation of tissue-specific gene expression; both functioned as activators in leaf, but LPSRE1 acted as a repressor in stem and LPSE2 as a repressor in young panicle and root. Transgenic rice plants carrying cry1Ac encoding Bacillus thuringiensis endotoxin, regulated by PD54O, were resistant to leaf-folders, with no Cry1Ac protein found in endosperm or embryo. A reporter gene regulated by a series of truncated PD54O showed various tissue-specific expression patterns. Different fragments of PD54O fused with the constitutive cauliflower mosaic virus 35S promoter suppressed 35S-regulated gene expression in various tissues. PD54O, truncated PD54O and the tissue-specific cis-elements provide useful tools for the regulation of tissue-specific gene expression in rice breeding programmes. [ABSTRACT FROM AUTHOR]

Summary Enhancer trapping has provided a powerful strategy for identifying novel genes and regulatory elements. In this study, we adopted an enhancer trap system, consisting of the GAL4/VP16–UAS elements with GUS as the reporter, to generate a trapping population of rice. Currently, 31 443 independent transformants were obtained from two cultivars using Agrobacterium -mediated T-DNA insertion. PCR tests and DNA blot hybridization showed that about 94% of the transformants contained T-DNA insertions. The transformants carried, on average, two copies of the T-DNA, and 42% of the transformants had single-copy insertions. Histochemical assays of approximately 1000 T0 plants revealed various patterns of the reporter gene expression, including expression in only one tissue, and simultaneously in two or more tissues. The expression pattern of the reporter gene in T1 families corresponded well with the T0 plants and segregated in a 3 : 1 Mendelian ratio in majority of the T1 families tested. The frequency of reporter gene expression in the enhancer trap lines was much higher than that in gene trap lines reported previously. Analysis of flanking sequences of T-DNA insertion sites from about 200 transformants showed that almost all the sequences had homology with the sequences in the rice genome databases. Morphologically conspicuous mutations were observed in about 7.5% of the 2679 T1 families that were field-tested, and segregation in more than one-third of the families fit the 3 : 1 ratio. It was concluded that GAL4/VP16–UAS elements provided a useful system for enhancer trap in rice. [ABSTRACT FROM AUTHOR]