Riboswitches are highly conserved RNA elements that located in the 5’-UTR of m RNAs,which undergo real-time structure conformational change to achieve the regulation of downstream gene expression by sensing their cog...Riboswitches are highly conserved RNA elements that located in the 5’-UTR of m RNAs,which undergo real-time structure conformational change to achieve the regulation of downstream gene expression by sensing their cognate ligands.S-adenosylmethionine(SAM)is a ubiquitous methyl donor for transmethylation reactions in all living organisms.SAM riboswitch is one of the most abundant riboswitches that bind to SAM with high affinity and selectivity,serving as regulatory modules in multiple metabolic pathways.To date,seven SAM-specific riboswitch classes that belong to four families,one SAM/SAH riboswitch and one SAH riboswitch have been identified.Each SAM riboswitch family has a well-organized tertiary core scaffold to support their unique ligand-specific binding pocket.In this review,we summarize the current research progress on the distribution,structure,ligand recognition and gene regulation mechanism of these SAM-related riboswitch families,and further discuss their evolutionary prospects and potential applications.展开更多
Riboswitches are functional RNA elements that regulate gene expression by directly detecting metabolites.Twenty years have passed since it was first discovered,researches on riboswitches are becoming increasingly stan...Riboswitches are functional RNA elements that regulate gene expression by directly detecting metabolites.Twenty years have passed since it was first discovered,researches on riboswitches are becoming increasingly standardized and refined,which could significantly promote people’s cognition of RNA function as well.Here,we focus on some representative orphan riboswitches,enumerate the structural and functional transformation and artificial design of riboswitches including the coupling with ribozymes,hoping to attain a comprehensive understanding of riboswitch research.展开更多
Transcription attenuation in response to the availability of a specific amino acid is believed to be controlled by alternative configurations of RNA secondary structures that lead to the arrest of translation or the r...Transcription attenuation in response to the availability of a specific amino acid is believed to be controlled by alternative configurations of RNA secondary structures that lead to the arrest of translation or the release of the arrested ribosome from the leader mRNA molecule.In this study,we first report a possible example of the DnaA‐dependent riboswitch for transcription attenuation in Escherichia coli.We show that(i)DnaA regulates the transcription of the structural genes but not that of the leader hisL gene;(ii)DnaA might bind to rDnaA boxes present in the HisL‐SL RNA,and subsequently attenuate the transcription of the operon;(iii)the HisL‐SL RNA and rDnaA boxes are phylogenetically conserved and evolutionarily important;and(iv)the translating ribosome is required for deattenuation of the his operon,whereas tRNA^(His) strengthens attenuation.This mechanism seems to be phylogenetically conserved in Gram‐negative bacteria and evolutionarily important.展开更多
Most riboswitches are characterized by two components, an aptamer domain that folds into a unique ligand binding pocket to interact with the ligand, and an expression platform that converts folding changes in the apta...Most riboswitches are characterized by two components, an aptamer domain that folds into a unique ligand binding pocket to interact with the ligand, and an expression platform that converts folding changes in the aptamer into changes in gene expression. Using the recently developed systematic helix-based computational method, we theoretically studied the refolding and co-transcriptional folding behaviors of the purine riboswitch aptamers from Bacillus subtilis xpt-pbu X guanine riboswitch and Vibrio vulnificus add adenine riboswitch. Despite several intermediate structures persisting a short time during the transcription, helices P2, P3 and P1 fold in turn for both aptamers. Although some misfolded structures are observed during the refolding process, the RNAs can fold into the ligand binding pocket structure containing helices P2, P3 and P1 within a few seconds, suggesting the aptamer domains are highly evolved. The purine riboswitch aptamers can quickly fold into the ligand binding pocket structure even at a high transcription speed, possibly because formation of this structure is the necessary prerequisite for the riboswitch to bind its ligand and then regulate relevant gene expression.展开更多
With the support by the National Natural Science Foundation of China,the research team led by Dr.Liu Yuchen(刘宇辰)at the State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology,Shenz...With the support by the National Natural Science Foundation of China,the research team led by Dr.Liu Yuchen(刘宇辰)at the State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology,Shenzhen Second People’s Hospital,the First Affiliated Hospital of Shenzhen University,developed a type of CRISPR-based riboswitch,which was published in Nature Methods(2016,doi:10.展开更多
RNAs carry out diverse biological functions, partly because different conformations of the same RNA sequence can play different roles in cellular activities. To fully understand the biological functions of RNAs requir...RNAs carry out diverse biological functions, partly because different conformations of the same RNA sequence can play different roles in cellular activities. To fully understand the biological functions of RNAs requires a conceptual framework to investigate the folding kinetics of RNA molecules, instead of native structures alone. Over the past several decades, many experimental and theoretical methods have been developed to address RNA folding. The helix-based RNA folding theory is the one which uses helices as building blocks, to calculate folding kinetics of secondary structures with pseudoknots of long RNA in two different folding scenarios. Here, we will briefly review the helix-based RNA folding theory and its application in exploring regulation mechanisms of several riboswitches and self-cleavage activities of the hepatitis delta virus (HDV) ribozyme.展开更多
T box sequences have been identified upstream of a large number of uncharacterized genes such as transporters in bacterial genomes. Expression of each T box family gene is induced by limitation for a specific amino ac...T box sequences have been identified upstream of a large number of uncharacterized genes such as transporters in bacterial genomes. Expression of each T box family gene is induced by limitation for a specific amino acid. T box family genes contain an untranslated leader region containing a factor-independent transcriptional terminator upstream of the structural genes. The anticodon of uncharged tRNA base-pairs with the leader mRNA at a codon referred to as the specifier sequence, inducing formation of an alternative antiterminator structure, allowing expression of the structural genes. There are several additional conserved primary sequence and secondary structural elements. Analysis of these elements can be used to predict the identity of the specifier codon and the amino acid signal.?Bacillus subtilis hypothetical amino acid permease, yvbW, was analyzed as an example of this type of transcriptional regulatory prediction suggesting expression in response to leucine limitation. Expression was induced up to 130-fold in response to leucine limitation, utilizing a yvbW-lacZ transcriptional fusion. These data suggest that hypothetical amino acid permease YvbW may participate in leucine metabolism. A yvbW knockout strain was generated, although the substrate specificity for the putative amino acid permease was not identified.展开更多
采用常压室温等离子体(atmospheric and room temperature plasma,ARTP)诱变脱氮假单胞菌(Pseudomonas denitrificans)并从中筛选高产维生素B12突变株,确定等离子诱变最优处理时间75,s、输出功率100,W.通过流式细胞仪并结合核糖开关(rib...采用常压室温等离子体(atmospheric and room temperature plasma,ARTP)诱变脱氮假单胞菌(Pseudomonas denitrificans)并从中筛选高产维生素B12突变株,确定等离子诱变最优处理时间75,s、输出功率100,W.通过流式细胞仪并结合核糖开关(riboswitch)感应元件检测其荧光值以初筛诱变后高产菌株,并利用48孔板高通量培养发酵,酶标仪快速检测维生素B_(12)产量,建立完整的诱变后高通量筛选体系.通过4轮ARTP诱变,筛选得到的突变株PA320-M4-1B1在250,mL摇瓶发酵6,d的条件下,维生素B_(12)产量达到(103.2±2.1)mg/L,较初始菌株PA320的(71.9±1.8)mg/L提高了43.8%,且遗传性状稳定.展开更多
基金supported by the National Natural Science Foundation of China(32022039,31870810,91940302,91640104)the National Key Research and Development Project of China(2021YFC2300300)+2 种基金the China Postdoctoral Science Foundation(2022M713637)the Outstanding Youth Fund of Zhejiang Province(LR19C050003)the Fundamental Research Funds for the Central Universities(2017QN81010)。
文摘Riboswitches are highly conserved RNA elements that located in the 5’-UTR of m RNAs,which undergo real-time structure conformational change to achieve the regulation of downstream gene expression by sensing their cognate ligands.S-adenosylmethionine(SAM)is a ubiquitous methyl donor for transmethylation reactions in all living organisms.SAM riboswitch is one of the most abundant riboswitches that bind to SAM with high affinity and selectivity,serving as regulatory modules in multiple metabolic pathways.To date,seven SAM-specific riboswitch classes that belong to four families,one SAM/SAH riboswitch and one SAH riboswitch have been identified.Each SAM riboswitch family has a well-organized tertiary core scaffold to support their unique ligand-specific binding pocket.In this review,we summarize the current research progress on the distribution,structure,ligand recognition and gene regulation mechanism of these SAM-related riboswitch families,and further discuss their evolutionary prospects and potential applications.
基金the National Key Research and Development Program of China(2021YFC2100700)the National Natural Science Foundation of China(Grant NSFC-22278313).
文摘Riboswitches are functional RNA elements that regulate gene expression by directly detecting metabolites.Twenty years have passed since it was first discovered,researches on riboswitches are becoming increasingly standardized and refined,which could significantly promote people’s cognition of RNA function as well.Here,we focus on some representative orphan riboswitches,enumerate the structural and functional transformation and artificial design of riboswitches including the coupling with ribozymes,hoping to attain a comprehensive understanding of riboswitch research.
基金supported by grants from the National Natural Science Foundation of China(Grant no.32260233 to Morigen)the Science and Technology Foundation of Inner Mongolia(Inner Mongolia Key Laboratory for Molecular Regulation of the Cell,Grant no.2021PT0002).
文摘Transcription attenuation in response to the availability of a specific amino acid is believed to be controlled by alternative configurations of RNA secondary structures that lead to the arrest of translation or the release of the arrested ribosome from the leader mRNA molecule.In this study,we first report a possible example of the DnaA‐dependent riboswitch for transcription attenuation in Escherichia coli.We show that(i)DnaA regulates the transcription of the structural genes but not that of the leader hisL gene;(ii)DnaA might bind to rDnaA boxes present in the HisL‐SL RNA,and subsequently attenuate the transcription of the operon;(iii)the HisL‐SL RNA and rDnaA boxes are phylogenetically conserved and evolutionarily important;and(iv)the translating ribosome is required for deattenuation of the his operon,whereas tRNA^(His) strengthens attenuation.This mechanism seems to be phylogenetically conserved in Gram‐negative bacteria and evolutionarily important.
基金Supported by the National Natural Science Foundation of China(31600592)Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization,Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains(2017BX08)
文摘Most riboswitches are characterized by two components, an aptamer domain that folds into a unique ligand binding pocket to interact with the ligand, and an expression platform that converts folding changes in the aptamer into changes in gene expression. Using the recently developed systematic helix-based computational method, we theoretically studied the refolding and co-transcriptional folding behaviors of the purine riboswitch aptamers from Bacillus subtilis xpt-pbu X guanine riboswitch and Vibrio vulnificus add adenine riboswitch. Despite several intermediate structures persisting a short time during the transcription, helices P2, P3 and P1 fold in turn for both aptamers. Although some misfolded structures are observed during the refolding process, the RNAs can fold into the ligand binding pocket structure containing helices P2, P3 and P1 within a few seconds, suggesting the aptamer domains are highly evolved. The purine riboswitch aptamers can quickly fold into the ligand binding pocket structure even at a high transcription speed, possibly because formation of this structure is the necessary prerequisite for the riboswitch to bind its ligand and then regulate relevant gene expression.
文摘With the support by the National Natural Science Foundation of China,the research team led by Dr.Liu Yuchen(刘宇辰)at the State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology,Shenzhen Second People’s Hospital,the First Affiliated Hospital of Shenzhen University,developed a type of CRISPR-based riboswitch,which was published in Nature Methods(2016,doi:10.
基金Project supported by the Science Fund from the Key Laboratory of Hubei Province, China (Grant No. 201932003)the National Natural Science Foundation of China (Grant Nos. 1157324 and 31600592).
文摘RNAs carry out diverse biological functions, partly because different conformations of the same RNA sequence can play different roles in cellular activities. To fully understand the biological functions of RNAs requires a conceptual framework to investigate the folding kinetics of RNA molecules, instead of native structures alone. Over the past several decades, many experimental and theoretical methods have been developed to address RNA folding. The helix-based RNA folding theory is the one which uses helices as building blocks, to calculate folding kinetics of secondary structures with pseudoknots of long RNA in two different folding scenarios. Here, we will briefly review the helix-based RNA folding theory and its application in exploring regulation mechanisms of several riboswitches and self-cleavage activities of the hepatitis delta virus (HDV) ribozyme.
文摘T box sequences have been identified upstream of a large number of uncharacterized genes such as transporters in bacterial genomes. Expression of each T box family gene is induced by limitation for a specific amino acid. T box family genes contain an untranslated leader region containing a factor-independent transcriptional terminator upstream of the structural genes. The anticodon of uncharged tRNA base-pairs with the leader mRNA at a codon referred to as the specifier sequence, inducing formation of an alternative antiterminator structure, allowing expression of the structural genes. There are several additional conserved primary sequence and secondary structural elements. Analysis of these elements can be used to predict the identity of the specifier codon and the amino acid signal.?Bacillus subtilis hypothetical amino acid permease, yvbW, was analyzed as an example of this type of transcriptional regulatory prediction suggesting expression in response to leucine limitation. Expression was induced up to 130-fold in response to leucine limitation, utilizing a yvbW-lacZ transcriptional fusion. These data suggest that hypothetical amino acid permease YvbW may participate in leucine metabolism. A yvbW knockout strain was generated, although the substrate specificity for the putative amino acid permease was not identified.
文摘采用常压室温等离子体(atmospheric and room temperature plasma,ARTP)诱变脱氮假单胞菌(Pseudomonas denitrificans)并从中筛选高产维生素B12突变株,确定等离子诱变最优处理时间75,s、输出功率100,W.通过流式细胞仪并结合核糖开关(riboswitch)感应元件检测其荧光值以初筛诱变后高产菌株,并利用48孔板高通量培养发酵,酶标仪快速检测维生素B_(12)产量,建立完整的诱变后高通量筛选体系.通过4轮ARTP诱变,筛选得到的突变株PA320-M4-1B1在250,mL摇瓶发酵6,d的条件下,维生素B_(12)产量达到(103.2±2.1)mg/L,较初始菌株PA320的(71.9±1.8)mg/L提高了43.8%,且遗传性状稳定.
