Engineering disease-resistant plants can be a powerful solution to the issue of food security.However,it requires addressing two fundamental questions:what genes to express and how to control their expressions.To find...Engineering disease-resistant plants can be a powerful solution to the issue of food security.However,it requires addressing two fundamental questions:what genes to express and how to control their expressions.To find a solution,we screen CRISPR-edited upstream open reading frame(uORF)variants in rice,aiming to optimize translational control of disease-related genes.By switching uORF types of the 5′-leader from Arabidopsis TBF1,we modulate the ribosome accessibility to the downstream firefly luciferase.We assume that by switching uORF types using CRISPR,we could generate uORF variants with alternative translation efficiency(CRISPR-aTrE-uORF).These variants,capable of boosting translation for resistance-associated genes and dampening it for susceptible ones,can help pinpoint previously unidentified genes with optimal expression levels.To test the assumption,we screened edited uORF variants and found that enhanced translational suppression of the plastic glutamine synthetase 2 can provide broad-spectrum disease resistance in rice with minimal fitness costs.This strategy,which involves modifying uORFs from none to some,or from some to none or different ones,demonstrates how translational agriculture can speed up the development of disease-resistant crops.This is vital for tackling the food security challenges we face due to growing populations and changing climates.展开更多
上游开放阅读框(upstream open reading frame, uORF)是一类能够精确控制蛋白质翻译的mRNA元件,位于mRNA的5'端前导区,主要通过抑制翻译起始来调节下游主体开放阅读框(main open reading frame, mORF)的翻译。目前对植物uORF的预测...上游开放阅读框(upstream open reading frame, uORF)是一类能够精确控制蛋白质翻译的mRNA元件,位于mRNA的5'端前导区,主要通过抑制翻译起始来调节下游主体开放阅读框(main open reading frame, mORF)的翻译。目前对植物uORF的预测和鉴定主要集中于生物信息学和翻译组学鉴定技术。植物uORF广泛参与调节生长发育、营养代谢、抗病免疫等多个生命活动过程。本文对植物uORF的分类、功能机制、预测和鉴定方法、植物规避uORF的方式以及植物uORF的工程应用等进行综述归纳,旨在更系统和深入地理解植物uORF的功能与机制,并为uORF应用于作物分子育种工作提供参考。展开更多
Messenger RNA(mRNA)translation consists of initiation,elongation,termination,and ribosome recycling,carried out by the translation machinery,primarily including tRNAs,ribosomes,and translation factors(TrFs).Translatio...Messenger RNA(mRNA)translation consists of initiation,elongation,termination,and ribosome recycling,carried out by the translation machinery,primarily including tRNAs,ribosomes,and translation factors(TrFs).Translational regulators transduce signals of growth and development,as well as biotic and abiotic stresses,to the translation machinery,where global or selective translational control occurs to modulate mRNA translation efficiency(TrE).As the basis of translational control,the translation machinery directly determines the quality and quantity of newly synthesized peptides and,ultimately,the cellular adaption.Thus,regulating the availability of diverse machinery components is reviewed as the central strategy of translational control.We provide classical signaling pathways(e.g.,integrated stress responses)and cellular behaviors(e.g.,liquideliquid phase separation)to exemplify this strategy within different physiological contexts,particularly during hostemicrobe interactions.With new technologies developed,further understanding this strategy will speed up translational medicine and translational agriculture.展开更多
A 5'-leader,known initially as the 5'-untranslated region,contains multiple isoforms due to alternative splicing(aS)and alternative transcription start site(aTSS).Therefore,a representative 5'-leader is de...A 5'-leader,known initially as the 5'-untranslated region,contains multiple isoforms due to alternative splicing(aS)and alternative transcription start site(aTSS).Therefore,a representative 5'-leader is demanded to examine the embedded RNA regulatory elements in controlling translation efficiency.Here,we develop a ranking algorithm and a deep-learning model to annotate representative 5'-leaders for five plant species.We rank the intra-sample and inter-sample frequency of aS-mediated transcript isoforms using the Kruskal-Wallis test-based algorithm and identify the representative aS-5'-leader.To further assign a representative 5'-end,we train the deep-learning model 5'leaderP to learn aTsS-mediated 5'-end distribution patterns from cap-analysis gene expression data.The model accurately predicts the 5'-end,confirmed experimentally in Arabidopsis and rice.The representative 5'-leader-contained gene models and 5'leaderP can be accessed at RNAirport(http:/www.rnairport.com/leader5P/).The Stage 1 annotation of 5'-leader records 5'-leader diversity and will pave the way to Ribo-Seq open-reading frame annotation,identical to the project recently initiated by human GENCODE.展开更多
Research Aims: Obesity and type 2 diabetes are known to be associated with increased risk of various types of cancer. However, the molecular biological mechanism of how the risk of cancer is increased in obesity or ty...Research Aims: Obesity and type 2 diabetes are known to be associated with increased risk of various types of cancer. However, the molecular biological mechanism of how the risk of cancer is increased in obesity or type 2 diabetes is not known. The aim this research is to investigate if the decreased expression of p27Kip1, a cell cycle repressor protein, plays a central role in this mechanism. Research Methods, Previous Studies and Theoretical Backgrounds: It is well known that the expression of p27Kip1 is increased by numerous nutritional or chemopreventive anti-cancer agents. But it has never been known that the expression of p27Kip1 could be decreased, rather than increased, and the risk of cancer could be increased, rather than decreased. This problem was solved recently and this new analytical method was used in this study. Results: 1) The expression of p27Kip1 was indeed significantly decreased in human obese type 2 diabetic individuals relative to the lean normal controls. 2) The expression of p27Kip1 was also significantly decreased in genetically obese rodents relative to the lean normal controls. Additionally, in obese rodents, the concentrations of glucose or insulin were significantly increased relative to the lean normal controls. 3) Using human cells cultured in vitro it was found that the increased concentrations of glucose or insulin decrease the expression of p27Kip1. Conclusions: These results suggest that higher concentrations of glucose or insulin increase the risk of various types of cancer in obesity or type 2 diabetes by decreasing the expression of p27Kip1.展开更多
基因组中约有20%的基因具有上游开放阅读框(upstream open reading frame,uORF),它位于成熟mRNA 5'端非编码区(5'-UTR)。本文简介了uORF同源群的挖掘方法、分类和进化,以及调控下游mORF翻译的研究进展。植物(拟南芥和水稻等)和...基因组中约有20%的基因具有上游开放阅读框(upstream open reading frame,uORF),它位于成熟mRNA 5'端非编码区(5'-UTR)。本文简介了uORF同源群的挖掘方法、分类和进化,以及调控下游mORF翻译的研究进展。植物(拟南芥和水稻等)和昆虫(果蝇等)基因组中普遍存在保守肽uORFs,并且在序列多样性方面有相似之处。但它们在平均长度、基因组聚类、与甲基转移酶的关联性上有所不同。植物uORF的长度通常短于昆虫uORF。借助拟南芥和水稻全长cDNA序列比较,不同的uORF同源群对其下游如转录因子,信号转导因子、发育信号分子和翻译起始因子eIF5等编码基因的mORF具有调控功能。对于真核生物基因组中包含CHCH域的uORF进行贝叶斯系统发育分析,结果表明,同源群8-like分属5个物种(绿藻、节肢动物、线虫、无脊椎动物和真菌)。在真核生物生长、发育和生理过程中,uORF通常作为反式因子对mORF表达起调节器作用,例如,在植物蔗糖、多胺、磷脂酰胆碱,以及甲基转移酶反应中,相当大比例的uORF参与介导mORF的翻译调控。展开更多
小开放阅读框(small open reading frame,sORF)广泛存在于不同生物基因组中,由于其序列短,以及编码的产物小蛋白(small protein,或称微蛋白;microprotein或迷你蛋白miniprotein)检测困难等原因,小开放阅读框长期未得到充分注释和研究。...小开放阅读框(small open reading frame,sORF)广泛存在于不同生物基因组中,由于其序列短,以及编码的产物小蛋白(small protein,或称微蛋白;microprotein或迷你蛋白miniprotein)检测困难等原因,小开放阅读框长期未得到充分注释和研究。近年来,随着高通量测序、翻译组和质谱分析等技术的不断发展,在不同生物中发现大量新的小开放阅读框,其编码的小蛋白及介导的翻译调控已应用于药物开发及植物抗病机理等研究。但是,目前对微生物的小开放阅读框相关研究和应用还相对有限。本文综述了小开放阅读框编码产物小蛋白的发现和鉴定,以及上游开放阅读框(upstream open reading frame,uORF)对mRNA翻译调控等最新研究进展,重点介绍了微生物基因组中小开放阅读框的鉴定和功能研究进展,为深入认识微生物中小开放阅读框的功能和作用机制,以及植物和动物等高等其他生物的小蛋白和翻译调控相关研究提供参考。展开更多
基金supported by the National Key Research and Development Program of China(2023ZD04073)the Major Project of Hubei Hongshan Laboratory(2022hszd016)+2 种基金the National Natural Science Foundation of China(32070284,32172421)the Key Research and Development Program of Hubei Province(2022BFE003)the Fundamental Research Funds for the Central Universities(2662023PY006).
文摘Engineering disease-resistant plants can be a powerful solution to the issue of food security.However,it requires addressing two fundamental questions:what genes to express and how to control their expressions.To find a solution,we screen CRISPR-edited upstream open reading frame(uORF)variants in rice,aiming to optimize translational control of disease-related genes.By switching uORF types of the 5′-leader from Arabidopsis TBF1,we modulate the ribosome accessibility to the downstream firefly luciferase.We assume that by switching uORF types using CRISPR,we could generate uORF variants with alternative translation efficiency(CRISPR-aTrE-uORF).These variants,capable of boosting translation for resistance-associated genes and dampening it for susceptible ones,can help pinpoint previously unidentified genes with optimal expression levels.To test the assumption,we screened edited uORF variants and found that enhanced translational suppression of the plastic glutamine synthetase 2 can provide broad-spectrum disease resistance in rice with minimal fitness costs.This strategy,which involves modifying uORFs from none to some,or from some to none or different ones,demonstrates how translational agriculture can speed up the development of disease-resistant crops.This is vital for tackling the food security challenges we face due to growing populations and changing climates.
文摘上游开放阅读框(upstream open reading frame, uORF)是一类能够精确控制蛋白质翻译的mRNA元件,位于mRNA的5'端前导区,主要通过抑制翻译起始来调节下游主体开放阅读框(main open reading frame, mORF)的翻译。目前对植物uORF的预测和鉴定主要集中于生物信息学和翻译组学鉴定技术。植物uORF广泛参与调节生长发育、营养代谢、抗病免疫等多个生命活动过程。本文对植物uORF的分类、功能机制、预测和鉴定方法、植物规避uORF的方式以及植物uORF的工程应用等进行综述归纳,旨在更系统和深入地理解植物uORF的功能与机制,并为uORF应用于作物分子育种工作提供参考。
基金supported by grants from the National Natural Science Foundation of China(32070284)the Major Project of Hubei Hongshan Laboratory(2022hszd016)the Key Research and Development Program of Hubei Province(2022BFE003)to G.Xu.We apologize to colleagues whose excellent work was not cited in this review due to the space limit.
文摘Messenger RNA(mRNA)translation consists of initiation,elongation,termination,and ribosome recycling,carried out by the translation machinery,primarily including tRNAs,ribosomes,and translation factors(TrFs).Translational regulators transduce signals of growth and development,as well as biotic and abiotic stresses,to the translation machinery,where global or selective translational control occurs to modulate mRNA translation efficiency(TrE).As the basis of translational control,the translation machinery directly determines the quality and quantity of newly synthesized peptides and,ultimately,the cellular adaption.Thus,regulating the availability of diverse machinery components is reviewed as the central strategy of translational control.We provide classical signaling pathways(e.g.,integrated stress responses)and cellular behaviors(e.g.,liquideliquid phase separation)to exemplify this strategy within different physiological contexts,particularly during hostemicrobe interactions.With new technologies developed,further understanding this strategy will speed up translational medicine and translational agriculture.
基金supported by grants from the National Key R&D Program of China(2023ZD04073)the Major Project of Hubei Hongshan Laboratory(2022hszd016)+1 种基金the Key Research and Development Program of Hubei Province(2022BFE003)the National Natural Science Foundation of China(32070284)to G.Xu.
文摘A 5'-leader,known initially as the 5'-untranslated region,contains multiple isoforms due to alternative splicing(aS)and alternative transcription start site(aTSS).Therefore,a representative 5'-leader is demanded to examine the embedded RNA regulatory elements in controlling translation efficiency.Here,we develop a ranking algorithm and a deep-learning model to annotate representative 5'-leaders for five plant species.We rank the intra-sample and inter-sample frequency of aS-mediated transcript isoforms using the Kruskal-Wallis test-based algorithm and identify the representative aS-5'-leader.To further assign a representative 5'-end,we train the deep-learning model 5'leaderP to learn aTsS-mediated 5'-end distribution patterns from cap-analysis gene expression data.The model accurately predicts the 5'-end,confirmed experimentally in Arabidopsis and rice.The representative 5'-leader-contained gene models and 5'leaderP can be accessed at RNAirport(http:/www.rnairport.com/leader5P/).The Stage 1 annotation of 5'-leader records 5'-leader diversity and will pave the way to Ribo-Seq open-reading frame annotation,identical to the project recently initiated by human GENCODE.
文摘Research Aims: Obesity and type 2 diabetes are known to be associated with increased risk of various types of cancer. However, the molecular biological mechanism of how the risk of cancer is increased in obesity or type 2 diabetes is not known. The aim this research is to investigate if the decreased expression of p27Kip1, a cell cycle repressor protein, plays a central role in this mechanism. Research Methods, Previous Studies and Theoretical Backgrounds: It is well known that the expression of p27Kip1 is increased by numerous nutritional or chemopreventive anti-cancer agents. But it has never been known that the expression of p27Kip1 could be decreased, rather than increased, and the risk of cancer could be increased, rather than decreased. This problem was solved recently and this new analytical method was used in this study. Results: 1) The expression of p27Kip1 was indeed significantly decreased in human obese type 2 diabetic individuals relative to the lean normal controls. 2) The expression of p27Kip1 was also significantly decreased in genetically obese rodents relative to the lean normal controls. Additionally, in obese rodents, the concentrations of glucose or insulin were significantly increased relative to the lean normal controls. 3) Using human cells cultured in vitro it was found that the increased concentrations of glucose or insulin decrease the expression of p27Kip1. Conclusions: These results suggest that higher concentrations of glucose or insulin increase the risk of various types of cancer in obesity or type 2 diabetes by decreasing the expression of p27Kip1.
文摘基因组中约有20%的基因具有上游开放阅读框(upstream open reading frame,uORF),它位于成熟mRNA 5'端非编码区(5'-UTR)。本文简介了uORF同源群的挖掘方法、分类和进化,以及调控下游mORF翻译的研究进展。植物(拟南芥和水稻等)和昆虫(果蝇等)基因组中普遍存在保守肽uORFs,并且在序列多样性方面有相似之处。但它们在平均长度、基因组聚类、与甲基转移酶的关联性上有所不同。植物uORF的长度通常短于昆虫uORF。借助拟南芥和水稻全长cDNA序列比较,不同的uORF同源群对其下游如转录因子,信号转导因子、发育信号分子和翻译起始因子eIF5等编码基因的mORF具有调控功能。对于真核生物基因组中包含CHCH域的uORF进行贝叶斯系统发育分析,结果表明,同源群8-like分属5个物种(绿藻、节肢动物、线虫、无脊椎动物和真菌)。在真核生物生长、发育和生理过程中,uORF通常作为反式因子对mORF表达起调节器作用,例如,在植物蔗糖、多胺、磷脂酰胆碱,以及甲基转移酶反应中,相当大比例的uORF参与介导mORF的翻译调控。
文摘小开放阅读框(small open reading frame,sORF)广泛存在于不同生物基因组中,由于其序列短,以及编码的产物小蛋白(small protein,或称微蛋白;microprotein或迷你蛋白miniprotein)检测困难等原因,小开放阅读框长期未得到充分注释和研究。近年来,随着高通量测序、翻译组和质谱分析等技术的不断发展,在不同生物中发现大量新的小开放阅读框,其编码的小蛋白及介导的翻译调控已应用于药物开发及植物抗病机理等研究。但是,目前对微生物的小开放阅读框相关研究和应用还相对有限。本文综述了小开放阅读框编码产物小蛋白的发现和鉴定,以及上游开放阅读框(upstream open reading frame,uORF)对mRNA翻译调控等最新研究进展,重点介绍了微生物基因组中小开放阅读框的鉴定和功能研究进展,为深入认识微生物中小开放阅读框的功能和作用机制,以及植物和动物等高等其他生物的小蛋白和翻译调控相关研究提供参考。
