Genomic clustering of non-homologous genes for the biosynthesis of plant defensive compounds is an emerging theme, but insights into their formation and physiological function remain limited. Here we report the identi...Genomic clustering of non-homologous genes for the biosynthesis of plant defensive compounds is an emerging theme, but insights into their formation and physiological function remain limited. Here we report the identification of a newly discovered hydroxycinnamoyl tyramine(HT) gene cluster in rice.This cluster contains a pyridoxamine 50-phosphate oxidase(Os PDX3) producing the cofactor pyridoxal50-phosphate(PLP), a PLP-dependent tyrosine decarboxylase(Os Ty DC1), and two duplicated hydroxycinnamoyl transferases(Os THT1 and Os THT2). These members were combined to represent an enzymological innovation gene cluster. Natural variation analysis showed that the abundance of the toxic tyramine intermediate of the gene cluster among different rice accessions is mainly determined by the coordinated transcription of Os Ty DC1 and Os THT1. Further pathogen incubation assays demonstrated that the end products of the HT gene cluster displayed enhanced resistance to the bacterial pathogen Xanthomonas oryzae pv. Oryzae(Xoo) and fungal pathogen Magnaporthe oryzae(M. oryzae), and the enhanced resistance is associated with the boost of phytoalexins and the activation of defense response. The unique presence of the HT gene cluster in Oryza AA genome, together with the enrichment of transposon elements within this gene cluster region, provides an evolutionary background to accelerate cluster member combinations. Our study not only discovered a gene cluster involved in the phenylpropanoid metabolism but also addressed the key aspects of gene cluster formation. In addition, our results provide a new metabolic pool for plant defense against pathogens.展开更多
As one of the most important crops in the world,rice(Oryza sativa)is a model plant for metabolome research.Although many studies have focused on the analysis of specific tissues,the changes in metab-olite abundance ac...As one of the most important crops in the world,rice(Oryza sativa)is a model plant for metabolome research.Although many studies have focused on the analysis of specific tissues,the changes in metab-olite abundance across the entire life cycle have not yet been determined.In this study,combining both tar-geted and nontargeted metabolite profiling methods,a total of 825 annotated metabolites were quantified in rice samples from different tissues covering the entire life cycle.The contents of metabolites in different tissues of rice were significantly different,with various metabolites accumulating in the plumule and radicle during seed germination.Combining these data with transcriptome data obtained from the same time period,we constructed the Rice Metabolic Regulation Network.The metabolites and co-expressed genes were further divided into 12 clusters according to their accumulation patterns,with members within each cluster displaying a uniform and clear pattern of abundance across development.Using this dataset,we established a comprehensive metabolic profile of the rice life cycle and used two independent strategies to identify novel transcription factors-namely the use of known regulatory genes as bait to screen for new networks underlying lignin metabolism and the unbiased identification of new glycerophospholipid metabolism regulators on the basis of tissue specificity.This study thus demonstrates how guilt-by-association analysis of metabolome and transcriptome data spanning the entire life cycle in cereal crops provides novel resources and tools to aid in understanding the mechanisms underlying important agro-nomic traits.展开更多
Dear Editor,Branched-chain amino acids(BCAAs)are essential amino acids that must be obtained from the diet for humans and animals.Branched-chain amino acid transaminases(BCATs)catalyze a key step in the BCAA synthesis...Dear Editor,Branched-chain amino acids(BCAAs)are essential amino acids that must be obtained from the diet for humans and animals.Branched-chain amino acid transaminases(BCATs)catalyze a key step in the BCAA synthesis pathway,however,little is known about their biological roles in planta.In this study,we functionally characterized two BCATs,OsBCAT4 and OsBCAT5,in rice and showed that they regulate the development of rice roots by affecting the levels of mineral elements.展开更多
Rice(Oryza sativa L)is one of the most important crops world-wide,providing much of the calorific needs for half of the global population[1].Due to the development of the global economy and the improvement of living s...Rice(Oryza sativa L)is one of the most important crops world-wide,providing much of the calorific needs for half of the global population[1].Due to the development of the global economy and the improvement of living standards,people's demand for rice has gradually changed from"being fll"to"eating well",with tasty and nutritious varieties being essential for the latter.In the past few decades,lots of studies have focused on improving the eating and cooking quality(ECQ)of rice to meet the demand for taste[2].Although metabolic engineering has been applied in rice biofortif-cation in recent years[3.4],efforts on improving comprehensive nutrition in rice remain fragmented[5-7].Thus,characterizing QTLs and genes underlying nutrient abundance will provide new guidance for breeding varieties with health benefits.展开更多
Grain essential amino acid(EAA)levels contribute to rice nutritional quality.However,the molecular mechanisms underlying EAA accumulation and natural variation in rice grains remain unclear.Here we report the identifi...Grain essential amino acid(EAA)levels contribute to rice nutritional quality.However,the molecular mechanisms underlying EAA accumulation and natural variation in rice grains remain unclear.Here we report the identification of a previously unrecognized auxin influx carrier subfamily gene,OsAUX5,which encodes an amino acid transporter that functions in uptake of multiple amino acids.We identified an elite haplotype of Pro::OsAUX5^(Hap2) that enhances grain EAA accumulation without an apparent negative effect on agronomic traits.Natural variations of OsAUX5 occur in the cis elements of its promoter,which are differentially activated because of the different binding affinity between OsWRKY78 and the W-box,contributing to grain EAA variation among rice varieties.The two distinct haplotypes were shown to have originated from different Oryza rufipogon progenitors,which contributed to the divergence between japonica and indica.Introduction of the indica-type Pro::OsAUX5^(Hap2) genotype into japonica could significantly increase EAA levels,indicating that indica-type Pro::OsAUX5^(Hap2) can be utilized to increase grain EAAs of japonica varieties.Collectively,our study uncovers an WRKY78–OsAUX5-based regulatory mechanism controlling grain EAA accumulation and provides a potential target for breeding EAA-rich rice.展开更多
Various aspects of the organisms adapt to cyclically changing environmental conditions via transcriptional regulation.However,the role of rhythmicity in altering the global aspects of metabolism is poorly characterize...Various aspects of the organisms adapt to cyclically changing environmental conditions via transcriptional regulation.However,the role of rhythmicity in altering the global aspects of metabolism is poorly characterized.Here,we subjected four rice(Oryza sativa)varieties to a range of metabolic profiles and RNA-seq to investigate the temporal relationships of rhythm between transcription and metabolism.More than 40%of the rhythmic genes and a quarter of metabolites conservatively oscillated across four rice accessions.Compared with the metabolome,the transcriptome was more strongly regulated by rhythm;however,the rhythm of metabolites had an obvious opposite trend between day and night.Through association analysis,the time delay of rhythmic transmission from the transcript to the metabolite level was~4 h under long-day conditions,although the transmission was nearly synchronous for carbohydrate and nucleotide metabolism.The rhythmic accumulation of metabolites maintained highly coordinated temporal relationships in the metabolic network,whereas the correlation of some rhythmic metabolites,such as branched-chain amino acids(BCAAs),was significantly different intervariety.We further demonstrated that the cumulative diversity of BCAAs was due to the differential expression of branched-chain aminotransferase 2 at dawn.Our research reveals the flexible pattern of rice metabolic rhythm existing with conservation and diversity.展开更多
基金supported by the National Science Fund for Distinguished Young Scholars of China (31625021)the Foundation for Innovative Research Groups of the National Natural Science Foundation of China (31821005)+1 种基金the State Key Program of National Natural Science Foundation of China (31530052)the Hainan University Startup Fund (KYQD(ZR)1866)。
文摘Genomic clustering of non-homologous genes for the biosynthesis of plant defensive compounds is an emerging theme, but insights into their formation and physiological function remain limited. Here we report the identification of a newly discovered hydroxycinnamoyl tyramine(HT) gene cluster in rice.This cluster contains a pyridoxamine 50-phosphate oxidase(Os PDX3) producing the cofactor pyridoxal50-phosphate(PLP), a PLP-dependent tyrosine decarboxylase(Os Ty DC1), and two duplicated hydroxycinnamoyl transferases(Os THT1 and Os THT2). These members were combined to represent an enzymological innovation gene cluster. Natural variation analysis showed that the abundance of the toxic tyramine intermediate of the gene cluster among different rice accessions is mainly determined by the coordinated transcription of Os Ty DC1 and Os THT1. Further pathogen incubation assays demonstrated that the end products of the HT gene cluster displayed enhanced resistance to the bacterial pathogen Xanthomonas oryzae pv. Oryzae(Xoo) and fungal pathogen Magnaporthe oryzae(M. oryzae), and the enhanced resistance is associated with the boost of phytoalexins and the activation of defense response. The unique presence of the HT gene cluster in Oryza AA genome, together with the enrichment of transposon elements within this gene cluster region, provides an evolutionary background to accelerate cluster member combinations. Our study not only discovered a gene cluster involved in the phenylpropanoid metabolism but also addressed the key aspects of gene cluster formation. In addition, our results provide a new metabolic pool for plant defense against pathogens.
基金supported by the Hainan Province Major Research Project(modern agricuture,ZDYF2020066)the Foundation for Innovative Research Groups of the National Natural Science Foundation of China 01821005)+1 种基金the Hainan Major Science and Technolgy Project(No,ZDKJ202002).the Hainan Academician Innovaton Platform(HD-YSZX-202003)and the Hainan University Startup Fund(KYQD(ZR)1866).
文摘As one of the most important crops in the world,rice(Oryza sativa)is a model plant for metabolome research.Although many studies have focused on the analysis of specific tissues,the changes in metab-olite abundance across the entire life cycle have not yet been determined.In this study,combining both tar-geted and nontargeted metabolite profiling methods,a total of 825 annotated metabolites were quantified in rice samples from different tissues covering the entire life cycle.The contents of metabolites in different tissues of rice were significantly different,with various metabolites accumulating in the plumule and radicle during seed germination.Combining these data with transcriptome data obtained from the same time period,we constructed the Rice Metabolic Regulation Network.The metabolites and co-expressed genes were further divided into 12 clusters according to their accumulation patterns,with members within each cluster displaying a uniform and clear pattern of abundance across development.Using this dataset,we established a comprehensive metabolic profile of the rice life cycle and used two independent strategies to identify novel transcription factors-namely the use of known regulatory genes as bait to screen for new networks underlying lignin metabolism and the unbiased identification of new glycerophospholipid metabolism regulators on the basis of tissue specificity.This study thus demonstrates how guilt-by-association analysis of metabolome and transcriptome data spanning the entire life cycle in cereal crops provides novel resources and tools to aid in understanding the mechanisms underlying important agro-nomic traits.
基金supported by the National Science Fund for Distinguished Young Scholars (31625021)the State Key Program of National Natural Science Foundation of China (31530052)+2 种基金the Ministry of Science and Technology of China (2016YFD0100500) to J.L.the China Postdoctoral Science Foundation (2017M610480)the National Natural Science Foundation of China (31800203) to C.J.
文摘Dear Editor,Branched-chain amino acids(BCAAs)are essential amino acids that must be obtained from the diet for humans and animals.Branched-chain amino acid transaminases(BCATs)catalyze a key step in the BCAA synthesis pathway,however,little is known about their biological roles in planta.In this study,we functionally characterized two BCATs,OsBCAT4 and OsBCAT5,in rice and showed that they regulate the development of rice roots by affecting the levels of mineral elements.
基金supported by the Key Research and Development Program of Hainan(ZDYF2020066)the Foundation for Innovative Research Groups of the National Natural Science Foundation of China(31821005)+2 种基金“111”Project(D20024)Hainan Academician Innovation Platform(HD-YSZX-202003 and HD-YSZX-202004)the Hainan University Startup Fund(KYQD(ZR)1866)。
文摘Rice(Oryza sativa L)is one of the most important crops world-wide,providing much of the calorific needs for half of the global population[1].Due to the development of the global economy and the improvement of living standards,people's demand for rice has gradually changed from"being fll"to"eating well",with tasty and nutritious varieties being essential for the latter.In the past few decades,lots of studies have focused on improving the eating and cooking quality(ECQ)of rice to meet the demand for taste[2].Although metabolic engineering has been applied in rice biofortif-cation in recent years[3.4],efforts on improving comprehensive nutrition in rice remain fragmented[5-7].Thus,characterizing QTLs and genes underlying nutrient abundance will provide new guidance for breeding varieties with health benefits.
基金supported by grants from the National Natural Science Foundation of China(32170267 and 32001528)the Key Research and Development Program of Hainan(ZDYF2020066)+3 种基金the Hainan Province Science and Technology Special Fund(ZDYF2022XDNY261)the Hainan Major Science and Technology Project(ZDKJ202002 and ZDKJ202001)the Hainan Academician Innovation Platform(HD-YSZX-202003)the Hainan Yazhou Bay Seed Laboratory(B21Y10902).
文摘Grain essential amino acid(EAA)levels contribute to rice nutritional quality.However,the molecular mechanisms underlying EAA accumulation and natural variation in rice grains remain unclear.Here we report the identification of a previously unrecognized auxin influx carrier subfamily gene,OsAUX5,which encodes an amino acid transporter that functions in uptake of multiple amino acids.We identified an elite haplotype of Pro::OsAUX5^(Hap2) that enhances grain EAA accumulation without an apparent negative effect on agronomic traits.Natural variations of OsAUX5 occur in the cis elements of its promoter,which are differentially activated because of the different binding affinity between OsWRKY78 and the W-box,contributing to grain EAA variation among rice varieties.The two distinct haplotypes were shown to have originated from different Oryza rufipogon progenitors,which contributed to the divergence between japonica and indica.Introduction of the indica-type Pro::OsAUX5^(Hap2) genotype into japonica could significantly increase EAA levels,indicating that indica-type Pro::OsAUX5^(Hap2) can be utilized to increase grain EAAs of japonica varieties.Collectively,our study uncovers an WRKY78–OsAUX5-based regulatory mechanism controlling grain EAA accumulation and provides a potential target for breeding EAA-rich rice.
基金This work was supported by the Hainan Major Science and Technology Project(ZDKJ202002)the State Key Program of National Natural Science Foundation of China(31530052)+2 种基金the Key Research and Development Program of Hainan(ZDYF2020066)the Hainan Academician Innovation Platform(HD-YSZX-202003 and HD-YSZX-202004)the Hainan University Startup Fund(KYQD(ZR)1866).
文摘Various aspects of the organisms adapt to cyclically changing environmental conditions via transcriptional regulation.However,the role of rhythmicity in altering the global aspects of metabolism is poorly characterized.Here,we subjected four rice(Oryza sativa)varieties to a range of metabolic profiles and RNA-seq to investigate the temporal relationships of rhythm between transcription and metabolism.More than 40%of the rhythmic genes and a quarter of metabolites conservatively oscillated across four rice accessions.Compared with the metabolome,the transcriptome was more strongly regulated by rhythm;however,the rhythm of metabolites had an obvious opposite trend between day and night.Through association analysis,the time delay of rhythmic transmission from the transcript to the metabolite level was~4 h under long-day conditions,although the transmission was nearly synchronous for carbohydrate and nucleotide metabolism.The rhythmic accumulation of metabolites maintained highly coordinated temporal relationships in the metabolic network,whereas the correlation of some rhythmic metabolites,such as branched-chain amino acids(BCAAs),was significantly different intervariety.We further demonstrated that the cumulative diversity of BCAAs was due to the differential expression of branched-chain aminotransferase 2 at dawn.Our research reveals the flexible pattern of rice metabolic rhythm existing with conservation and diversity.
