We present in this paper an ab initio method, named KnotFold, for RNA H-type pseudoknot prediction. Our method employs an ensemble of RNA folding tools and a filtering heuristic to generate a set of pseudoknot-free st...We present in this paper an ab initio method, named KnotFold, for RNA H-type pseudoknot prediction. Our method employs an ensemble of RNA folding tools and a filtering heuristic to generate a set of pseudoknot-free stems, and then predicts pseudoknots by utilizing a search technique with a pseudo-probability scoring scheme. Experimental results show that KnotFold achieves higher sensitivity than existing methods. The KnotFold package with documentation is freely available at http：//bioinformatics.njit.edu/KnotFold.展开更多
Many biological functions of RNA molecules are re- lated to their pseudoknot structures. It is significant for predicting the structure and function of RNA that learning about the stability and the process of RNA pseu...Many biological functions of RNA molecules are re- lated to their pseudoknot structures. It is significant for predicting the structure and function of RNA that learning about the stability and the process of RNA pseudoknot folding and unfolding. The structural features of mouse mammary tumor virus （MMTV） RNA pseudoknot in different ion concentration, the unfolding process of the RNA pseudoknot, and the two hairpin helices that constitute the RNA pseudoknot were studied with all atom molecule dynam- ics simulation method in this paper. We found that the higher cation concentration can cause structure of the RNA molecules more stable, and ions played an indispensable role in keeping the structure of RNA molecules stable; the unfolding process of hair- pin structure was corresponding to the antiprocess of its folding process. The main pathway of pseudoknot unfolding was that the inner base pair opened first, and then, the two helices, which formed the RNA pseudoknot opened decussately, while the folding pathway of the RNA pseudoknot was a helix folding after forma- tion of the other helix. Therefore, the unfolding process of RNA pseudoknot is different from the antiprocess of its folding process, and the unfolding process of each helix in the RNA pseudoknot is similar to the hairpin structure＇s unfolding process, which means that both are the unzipping process.展开更多
PKR, the interferon （IFN）-inducible protein kinase activated by double-stranded RNA, inhibits translation by phosphorylating the initiation factor eIF2α chain. Uniquely, human IFN-γ mRNA uses local activation of P...PKR, the interferon （IFN）-inducible protein kinase activated by double-stranded RNA, inhibits translation by phosphorylating the initiation factor eIF2α chain. Uniquely, human IFN-γ mRNA uses local activation of PKR in the cell to control its own translation yield. IFN-γ mRNA activates PKR through a structure in its 5＇- region harboring a pseudoknot which is critical for PKR activation. Mutations that impair pseudoknot stability reduce the ability of IFN-γ mRNA to activate PKR and strongly increase its translation efficiency. The cis-acting RNA element in IFN-γ mRNA functions as a biological sensor of intracellular PKR levels. During an immune response, as IFN-γ and other inflammatory cytokines build up in the cell＇s microenvironment, they act to induce higher levels of PKR in the cell, resulting in a more extensive activation of PKR by IFN-γ mRNA. With the resulting phosphorylation of eIF2α, a negative feedback loop is created and the production of IFN-γ is progressively attenuated. We propose that the therapeutic effect of IFN-β in multiple sclerosis may rest, at least in part, on its exquisite ability to induce high levels of PKR in the cell and thereby to limit IFN-γ mRNA translation through this negative feedback loop, blocking the excessive IFN-γ gene expression that precedes clinical attacks.展开更多
The pandemic of SARS-CoV-2 worldwide with successive emerging variants urgently calls for small-molecule oral drugs with broad-spectrum antiviral activity.Here,we show that carrimycin,a new macrolide antibiotic in the...The pandemic of SARS-CoV-2 worldwide with successive emerging variants urgently calls for small-molecule oral drugs with broad-spectrum antiviral activity.Here,we show that carrimycin,a new macrolide antibiotic in the clinic and an antiviral candidate for SARS-CoV-2 in phase III trials,decreases the efficiency of programmed–1 ribosomal frameshifting of coronaviruses and thus impedes viral replication in a broad-spectrum fashion.Carrimycin binds directly to the coronaviral frameshift-stimulatory element(FSE)RNA pseudoknot,interrupting the viral protein translation switch from ORF1a to ORF1b and thereby reducing the level of the core components of the viral replication and transcription complexes.Combined carrimycin with known viral replicase inhibitors yielded a synergistic inhibitory effect on coronaviruses.Because the FSE mechanism is essential in all coronaviruses,carrimycin could be a new broad-spectrum antiviral drug for human coronaviruses by directly targeting the conserved coronaviral FSE RNA.This finding may open a new direction in antiviral drug discovery for coronavirus variants.展开更多
Accurate identification of the correct,biologically relevant RNA structures is critical to understanding various aspects of RNA biology since proper folding represents the key to the functionality of all types of RNA ...Accurate identification of the correct,biologically relevant RNA structures is critical to understanding various aspects of RNA biology since proper folding represents the key to the functionality of all types of RNA molecules and plays pivotal roles in many essential biological processes.Thus,a plethora of approaches have been developed to predict,identify,or solve RNA structures based on various computational,molecular,genetic,chemical,or physicochemical strategies.Purely computational approaches hold distinct advantages over all other strategies in terms of the ease of implementation,time,speed,cost,and throughput,but they strongly underperform in terms of accuracy that significantly limits their broader application.Nonetheless,the advantages of these methods led to a steady development of multiple in silico RNA secondary structure prediction approaches including recent deep learning-based programs.Here,we compared the accuracy of predictions of biologically relevant secondary structures of dozens of self-cleaving ribozyme sequences using seven in silico RNA folding prediction tools with tasks of varying complexity.We found that while many programs performed well in relatively simple tasks,their performance varied significantly in more complex RNA folding problems.However,in general,a modern deep learning method outperformed the other programs in the complex tasks in predicting the RNA secondary structures,at least based on the specific class of sequences tested,suggesting that it may represent the future of RNA structure prediction algorithms.展开更多
TMV(24A+UPD)is a mutant virus that a 24 nt internal poly(A)tract was introduced downstream of the coat protein(CP)gene in TMV genome.TMV(24A+UPD)induced more severe necrosis in Nicotiana benthamiana and its RNA level ...TMV(24A+UPD)is a mutant virus that a 24 nt internal poly(A)tract was introduced downstream of the coat protein(CP)gene in TMV genome.TMV(24A+UPD)induced more severe necrosis in Nicotiana benthamiana and its RNA level accumulated at higher level than that of TMV,indicating that the introduced 24 nt poly(A)tract enhanced virus replication and virulence.In this study,TMV(24A+UPD)was serially passaged 10 times in N.benthamiana to analyze the predominant sequence changes of the introduced internal poly(A)tract and the upstream pseudoknot domain(UPD)in its genome.Results showed that the introduced 24 nt of the poly(A)tract was extended from first to seventh rounds of serial passaging,but shortened from the eighth passage,and reduced to only three adenines at the tenth passage.Also,the nucleotide sequences downstream of the introduced poly(A)tract were deleted gradually during the 10 cycles of passaging.There were mutant viruses generated with partial deletion of CP gene during serial passaging,indicating that extension of the introduced internal poly(A)tract also led to deletion of coding gene sequence of TMV(24A+UPD).These results provided valuable information for our understanding of the dynamics in viral sequence changes to reach a tipping point in its host plants in order to maintain a co-existence relationship during virus evolution.In addition,the introduction of an internal poly(A)tract may be applied to other viruses to study virus evolution and natural selection in host plants.展开更多
文摘We present in this paper an ab initio method, named KnotFold, for RNA H-type pseudoknot prediction. Our method employs an ensemble of RNA folding tools and a filtering heuristic to generate a set of pseudoknot-free stems, and then predicts pseudoknots by utilizing a search technique with a pseudo-probability scoring scheme. Experimental results show that KnotFold achieves higher sensitivity than existing methods. The KnotFold package with documentation is freely available at http：//bioinformatics.njit.edu/KnotFold.
基金Supported by the National Natural Science Foundation of China(10774115)the Doctoral Fund of Ministry of Education of China(20110141110009)
文摘Many biological functions of RNA molecules are re- lated to their pseudoknot structures. It is significant for predicting the structure and function of RNA that learning about the stability and the process of RNA pseudoknot folding and unfolding. The structural features of mouse mammary tumor virus （MMTV） RNA pseudoknot in different ion concentration, the unfolding process of the RNA pseudoknot, and the two hairpin helices that constitute the RNA pseudoknot were studied with all atom molecule dynam- ics simulation method in this paper. We found that the higher cation concentration can cause structure of the RNA molecules more stable, and ions played an indispensable role in keeping the structure of RNA molecules stable; the unfolding process of hair- pin structure was corresponding to the antiprocess of its folding process. The main pathway of pseudoknot unfolding was that the inner base pair opened first, and then, the two helices, which formed the RNA pseudoknot opened decussately, while the folding pathway of the RNA pseudoknot was a helix folding after forma- tion of the other helix. Therefore, the unfolding process of RNA pseudoknot is different from the antiprocess of its folding process, and the unfolding process of each helix in the RNA pseudoknot is similar to the hairpin structure＇s unfolding process, which means that both are the unzipping process.
基金Acknowledgements Research in the author＇s laboratory was supported by grants from the Israel Science Foundation （537/03） and the Deutsche Forschungsgemeinschaft （H0- 1116）,
文摘PKR, the interferon （IFN）-inducible protein kinase activated by double-stranded RNA, inhibits translation by phosphorylating the initiation factor eIF2α chain. Uniquely, human IFN-γ mRNA uses local activation of PKR in the cell to control its own translation yield. IFN-γ mRNA activates PKR through a structure in its 5＇- region harboring a pseudoknot which is critical for PKR activation. Mutations that impair pseudoknot stability reduce the ability of IFN-γ mRNA to activate PKR and strongly increase its translation efficiency. The cis-acting RNA element in IFN-γ mRNA functions as a biological sensor of intracellular PKR levels. During an immune response, as IFN-γ and other inflammatory cytokines build up in the cell＇s microenvironment, they act to induce higher levels of PKR in the cell, resulting in a more extensive activation of PKR by IFN-γ mRNA. With the resulting phosphorylation of eIF2α, a negative feedback loop is created and the production of IFN-γ is progressively attenuated. We propose that the therapeutic effect of IFN-β in multiple sclerosis may rest, at least in part, on its exquisite ability to induce high levels of PKR in the cell and thereby to limit IFN-γ mRNA translation through this negative feedback loop, blocking the excessive IFN-γ gene expression that precedes clinical attacks.
基金supported by grants from the National Natural Science Foundation,China(82151525)the National key research and development program,China(2022YFC0869000)the CAMS Innovation Fund for Medical Sciences(2022-I2M-JB-013,2021-I2M-1-028 and 2022-I2M-2-002,China).
文摘The pandemic of SARS-CoV-2 worldwide with successive emerging variants urgently calls for small-molecule oral drugs with broad-spectrum antiviral activity.Here,we show that carrimycin,a new macrolide antibiotic in the clinic and an antiviral candidate for SARS-CoV-2 in phase III trials,decreases the efficiency of programmed–1 ribosomal frameshifting of coronaviruses and thus impedes viral replication in a broad-spectrum fashion.Carrimycin binds directly to the coronaviral frameshift-stimulatory element(FSE)RNA pseudoknot,interrupting the viral protein translation switch from ORF1a to ORF1b and thereby reducing the level of the core components of the viral replication and transcription complexes.Combined carrimycin with known viral replicase inhibitors yielded a synergistic inhibitory effect on coronaviruses.Because the FSE mechanism is essential in all coronaviruses,carrimycin could be a new broad-spectrum antiviral drug for human coronaviruses by directly targeting the conserved coronaviral FSE RNA.This finding may open a new direction in antiviral drug discovery for coronavirus variants.
基金supported by the National Natural Science Foundation of China(Grant No.32000462 to Fei Qi,Grant No.32170619 to Philipp Kapranovand Grant No.32201055 to Yue Chen)+2 种基金the Research Fund for International Senior Scientists from the National Natural Science Foundation of China(Grant No.32150710525 to Philipp Kapranov)the Natural Science Foundation of Fujian Province,China(Grant No.2020J02006 to Philipp Kapranov)the Scientific Research Funds of Huaqiao University,China(Grant No.22BS114 to Fei Qi,Grant No.21BS127 to Yue Chen,and Grant No.15BS101 to Philipp Kapranov).
文摘Accurate identification of the correct,biologically relevant RNA structures is critical to understanding various aspects of RNA biology since proper folding represents the key to the functionality of all types of RNA molecules and plays pivotal roles in many essential biological processes.Thus,a plethora of approaches have been developed to predict,identify,or solve RNA structures based on various computational,molecular,genetic,chemical,or physicochemical strategies.Purely computational approaches hold distinct advantages over all other strategies in terms of the ease of implementation,time,speed,cost,and throughput,but they strongly underperform in terms of accuracy that significantly limits their broader application.Nonetheless,the advantages of these methods led to a steady development of multiple in silico RNA secondary structure prediction approaches including recent deep learning-based programs.Here,we compared the accuracy of predictions of biologically relevant secondary structures of dozens of self-cleaving ribozyme sequences using seven in silico RNA folding prediction tools with tasks of varying complexity.We found that while many programs performed well in relatively simple tasks,their performance varied significantly in more complex RNA folding problems.However,in general,a modern deep learning method outperformed the other programs in the complex tasks in predicting the RNA secondary structures,at least based on the specific class of sequences tested,suggesting that it may represent the future of RNA structure prediction algorithms.
基金Singapore Ministry of Education Tier 1 Academic Research grant R-154-000-B23–114 through National University of Singapore,Suzhou Science&Technology Bureau grant SNG2018039National Natural Science Foundation of China grant 31872639.
文摘TMV(24A+UPD)is a mutant virus that a 24 nt internal poly(A)tract was introduced downstream of the coat protein(CP)gene in TMV genome.TMV(24A+UPD)induced more severe necrosis in Nicotiana benthamiana and its RNA level accumulated at higher level than that of TMV,indicating that the introduced 24 nt poly(A)tract enhanced virus replication and virulence.In this study,TMV(24A+UPD)was serially passaged 10 times in N.benthamiana to analyze the predominant sequence changes of the introduced internal poly(A)tract and the upstream pseudoknot domain(UPD)in its genome.Results showed that the introduced 24 nt of the poly(A)tract was extended from first to seventh rounds of serial passaging,but shortened from the eighth passage,and reduced to only three adenines at the tenth passage.Also,the nucleotide sequences downstream of the introduced poly(A)tract were deleted gradually during the 10 cycles of passaging.There were mutant viruses generated with partial deletion of CP gene during serial passaging,indicating that extension of the introduced internal poly(A)tract also led to deletion of coding gene sequence of TMV(24A+UPD).These results provided valuable information for our understanding of the dynamics in viral sequence changes to reach a tipping point in its host plants in order to maintain a co-existence relationship during virus evolution.In addition,the introduction of an internal poly(A)tract may be applied to other viruses to study virus evolution and natural selection in host plants.
