Summary Nucleolar GTP-binding protein 1 (NOG1) is a highly conserved GTPase first reported in Trypanosoma as required for ribosome biogenesis. We characterized NbNOG1, a Nicotiana benthamiana NOG1 ortholog sharing mor...Summary Nucleolar GTP-binding protein 1 (NOG1) is a highly conserved GTPase first reported in Trypanosoma as required for ribosome biogenesis. We characterized NbNOG1, a Nicotiana benthamiana NOG1 ortholog sharing more than 4570 amino acid identity with Trypanosoma, yeast, and human NOG1. N. benthamiana plants silenced for NbNO0 were stunted and produced sterile flowers.展开更多
Mitochondria are double-membrane organelles within the cytoplasm,primarily responsible for the efficient production of ATP through oxidative phosphorylation(OXPHOS).These organelles harbor an autonomous genetic system...Mitochondria are double-membrane organelles within the cytoplasm,primarily responsible for the efficient production of ATP through oxidative phosphorylation(OXPHOS).These organelles harbor an autonomous genetic system independent of the nuclear genome,encoded by mitochondrial DNA(mtDNA).Human mitochondria contain a compact 16.6-kilobase circular genome(37 genes,13 protein-coding)that relies on over 1000 nuclear-encoded proteins for its functionality.The mtDNA forms a double-stranded structure where both the sense and antisense strands are transcribed into polycistronic precursors.The heavy(H)strand encodes 12 mRNAs,2 rRNAs,and 14 tRNAs,whereas the light(L)strand produces 1 mRNA and 8 tRNAs.These primary transcripts undergo extensive processing and maturation,including cleavage,RNA modifications,and polyadenylation,yielding functional tRNAs,rRNAs,and mRNAs.Characteristically,most mRNAs and rRNAs are interspersed with tRNA genes,which serve as recognition sites for endonucleases that process the primary transcripts into individual RNA units through site-specific cleavage at tRNA boundaries.展开更多
Basal endosperm transfer layer（BETL） cells are responsible for transferring apoplastic solutes from the maternal pedicel into the endosperm,supplying the grain with compounds required for embryo development and stor...Basal endosperm transfer layer（BETL） cells are responsible for transferring apoplastic solutes from the maternal pedicel into the endosperm,supplying the grain with compounds required for embryo development and storage reserve accumulation.Here,we analyze the maize（Zea mays L.） empty pericarp6（emp6） mutant,which causes early arrest in grain development.The Emp6 tgene function is required independently in both the embryo and endosperm.The emp6 mutant causes a notable effect on the differentiation of BETL cells;the extensive cell wall ingrowths that distinguish BETL cells are diminished and BETL marker gene expression is compromised in mutant kernels.Transposon tagging identified the emp6 locus as encoding a putative plant organelle RNA recognition（PORR） protein,1 of 15 PORR family members in maize.The emp6 transcript is widely detected in plant tissues with highest Researclevels in embryos and developing kernels.EMP6-green fluorescent protein（GFP） fusion proteins transiently expressed in Nicotiana benthamiana leaves were targeted specifically to mitochondria.These results suggest that BETL cell differentiation might be particularly energy intensive,or alternatively,that mitochondria might confer a developmental function.展开更多
The formation of eukaryotic mRNAs involves the cleavage and polyadenylation of pre-mRNAs.To investigate the sequence requirement of putative polyadenylation signals(PASs),poly(A)sites and downstream elements(DUEs)in 3...The formation of eukaryotic mRNAs involves the cleavage and polyadenylation of pre-mRNAs.To investigate the sequence requirement of putative polyadenylation signals(PASs),poly(A)sites and downstream elements(DUEs)in 3'-end-processing in rice,we compared expressed sequences tags(ESTs)with poly(A)extremity to full-length cDNA sequences and constructed a database of 12969 pre-mRNA sequences in-40--+40 nt surrounding the poly(A)sites,which were from 9953 genes.The alternative poly(A)sites were revealed in approximately 25%of mRNAs.Nearly 80%of pre-mRNAs showed stringent requirement of the YA(CA or UA)at poly(A)sites for polyadenylation.About 7.9%had the AAUAAA signals on-40---1 nt upstream of the poly(A)sites.Over 60%of mRNAs probably used the oneor two-base variants of AAUAAA hexamers as their PASs in 3'fragments.The single-base variants of AAUGAA revealed the high frequency in 11.5%of 3'fragments.The DUEs were detected in 90%of pre-mRNAs,especially more than half of the pre-mRNAs with multi-base variants of AAUAAA had the DUEs surrounding the poly(A)site.The location of DUE is also important for defining the cleavage site.Although most of the rice pre-mRNAs did not contain AAUAAA signal,the existence of downstream elements ensured the efficiency of cleavage-polyade-nylation.展开更多
The sessile nature of plants confines their responsiveness to changing environmental conditions.Gene expression regulation becomes a paramount mechanism for plants to adjust their physiological and morphological behav...The sessile nature of plants confines their responsiveness to changing environmental conditions.Gene expression regulation becomes a paramount mechanism for plants to adjust their physiological and morphological behaviors.Alternative polyadenylation(APA)is known for its capacity to augment transcriptome diversity and plasticity,thereby furnishing an additional set of tools for modulating gene expression.APA has also been demonstrated to exhibit intimate associations with plant stress responses.In this study,we review APA dynamic features and consequences in plants subjected to both biotic and abiotic stresses.These stresses include adverse environmental stresses,and pathogenic attacks,such as cadmium toxicity,high salt,hypoxia,oxidative stress,cold,heat shock,along with bacterial,fungal,and viral infections.We analyzed the overarching research framework employed to elucidate plant APA response and the alignment of polyadenylation site transitions with the modulation of gene expression levels within the ambit of each stress condition.We also proposed a general APA model where transacting factors,including poly(A)factors,epigenetic regulators,RNA m6A modification factors,and phase separation proteins,assume pivotal roles in APA related transcriptome plasticity during stress response in plants.展开更多
Dear Editor,Nuclear speckles,hubs for gene expression and storage sites for RNA processing factors in typical mammalian nuclei(Chen and Belmont,2019),concentrate numerous functional components(Gordon et al.,2021).Rece...Dear Editor,Nuclear speckles,hubs for gene expression and storage sites for RNA processing factors in typical mammalian nuclei(Chen and Belmont,2019),concentrate numerous functional components(Gordon et al.,2021).Recent evidence suggests that genomic nuclear speckle-associated domains(SPADs)are transcriptionally active,whereas those nuclear lamina-associated domain(LADs)are inactive(Payne et al.,2021;Quinodoz et al.,2018).展开更多
Pentatricopeptide repeat(PPR)proteins are involved in nearly all aspects of post-transcriptional process-ing in plant mitochondria and plastids,playing vital roles in plant growth,development,cytoplasmic male sterilit...Pentatricopeptide repeat(PPR)proteins are involved in nearly all aspects of post-transcriptional process-ing in plant mitochondria and plastids,playing vital roles in plant growth,development,cytoplasmic male sterility restoration,and responses to biotic and abiotic stresses.Over the last three decades,significant advances have been made in understanding the functions of PPR proteins and the primary mechanisms through which they mediate post-transcriptional processing.This review aims to summarize these ad-vancements,highlighting the mechanisms by which PPR proteins facilitate RNA editing,intron splicing,and RNA maturation in the context of organellar gene expression.We also present the latest progress in PPR engineering and discuss its potential as a biotechnological tool.Additionally,we discuss key chal-lenges and questions that remain in PPR research.展开更多
Dear Editor,Nuclear speckles,hubs for gene expression and storage sites for RNA processing factors in typical mammalian nuclei(Chen and Belmont,2019),concentrate numerous functional components(Gordon et al.,2021).Rece...Dear Editor,Nuclear speckles,hubs for gene expression and storage sites for RNA processing factors in typical mammalian nuclei(Chen and Belmont,2019),concentrate numerous functional components(Gordon et al.,2021).Recent evi dence suggests that genomic nuclear speckle-associated domains(SPADs)are transcriptionally active,whereas those nuclear lamina-associated domain(LADs)are inactive(Payne et al.,2021;Quinodoz et al.,2018).Disruptions in chromatin organization lead to aberrant gene expression and altered cell fate decisions(Cuartero et al.,2023;Wang et al.,2022).Notably,LAD formation during mouse embryogenesis has been shown to occur de novo through interactions with the nuclear lamina(Borsos et al.,2019).展开更多
DDX21 belongs to the DEAD-box(DDX)family of helicases but deviates from the characteristic sequence Asp–Glu–Ala–Asp(DEAD)to Asp–Glu–Val–Asp.In addition to the typical helicase activity associated with the DEAD-b...DDX21 belongs to the DEAD-box(DDX)family of helicases but deviates from the characteristic sequence Asp–Glu–Ala–Asp(DEAD)to Asp–Glu–Val–Asp.In addition to the typical helicase activity associated with the DEAD-box family,DDX21 also possesses foldase and adenosine triphosphatase activities.It plays crucial roles in various molecular processes,including the regulation of transcription,ribosomal RNA processing,modification,and unwinding of RNA spatial structures.DDX21 is subject to intricate regulation by multiple upstream factors,including expression control and posttranslational modification.In numerous cancer types,abnormal expression of DDX21 has been observed to influence cancer cell behaviors,such as the cell cycle,proliferation,invasion,migration,and apoptosis.In addition,DDX21 modulates innate immunity following viral infection and plays a dual role in the viral infection process.This review comprehensively explores the protein structure,molecular regulatory mechanisms,and pathophysiological functions of DDX21.Consequently,this study not only offers potential avenues for future research but also sparks novel ideas for targeted treatments for both cancer and viral infections.展开更多
文摘Summary Nucleolar GTP-binding protein 1 (NOG1) is a highly conserved GTPase first reported in Trypanosoma as required for ribosome biogenesis. We characterized NbNOG1, a Nicotiana benthamiana NOG1 ortholog sharing more than 4570 amino acid identity with Trypanosoma, yeast, and human NOG1. N. benthamiana plants silenced for NbNO0 were stunted and produced sterile flowers.
基金supported by the National Key Research and Development Program of China(2022YFC2601800)the National Natural Science Foundation of China(82472761 and 82173833)+6 种基金the Guangdong Basic and Applied Basic Research Foundation(2023B1515040006)the Key-Area Research and Development Program of Guangdong Province(2023B1111020007)the Guangzhou Science and Technology Program(2024A04J6480 and 2025A04J4549)the Guangdong Provincial Key Laboratory of Construction Foundation(2023B1212060022)the Fundamental Research Funds for the Central Universities(Sun Yat-sen University)(24xkjc018)the Basic Scientific Research Fund-Young Faculty Development Program(24qnpy184)the Shenzhen Bay Scholars Program.
文摘Mitochondria are double-membrane organelles within the cytoplasm,primarily responsible for the efficient production of ATP through oxidative phosphorylation(OXPHOS).These organelles harbor an autonomous genetic system independent of the nuclear genome,encoded by mitochondrial DNA(mtDNA).Human mitochondria contain a compact 16.6-kilobase circular genome(37 genes,13 protein-coding)that relies on over 1000 nuclear-encoded proteins for its functionality.The mtDNA forms a double-stranded structure where both the sense and antisense strands are transcribed into polycistronic precursors.The heavy(H)strand encodes 12 mRNAs,2 rRNAs,and 14 tRNAs,whereas the light(L)strand produces 1 mRNA and 8 tRNAs.These primary transcripts undergo extensive processing and maturation,including cleavage,RNA modifications,and polyadenylation,yielding functional tRNAs,rRNAs,and mRNAs.Characteristically,most mRNAs and rRNAs are interspersed with tRNA genes,which serve as recognition sites for endonucleases that process the primary transcripts into individual RNA units through site-specific cleavage at tRNA boundaries.
基金supported by grants from the US National Science Foundation (IOS-1121738) to PWBthe Spanish Ministerio de Ciencia e Innovacion (Grant BIO2009-11856) to GH
文摘Basal endosperm transfer layer（BETL） cells are responsible for transferring apoplastic solutes from the maternal pedicel into the endosperm,supplying the grain with compounds required for embryo development and storage reserve accumulation.Here,we analyze the maize（Zea mays L.） empty pericarp6（emp6） mutant,which causes early arrest in grain development.The Emp6 tgene function is required independently in both the embryo and endosperm.The emp6 mutant causes a notable effect on the differentiation of BETL cells;the extensive cell wall ingrowths that distinguish BETL cells are diminished and BETL marker gene expression is compromised in mutant kernels.Transposon tagging identified the emp6 locus as encoding a putative plant organelle RNA recognition（PORR） protein,1 of 15 PORR family members in maize.The emp6 transcript is widely detected in plant tissues with highest Researclevels in embryos and developing kernels.EMP6-green fluorescent protein（GFP） fusion proteins transiently expressed in Nicotiana benthamiana leaves were targeted specifically to mitochondria.These results suggest that BETL cell differentiation might be particularly energy intensive,or alternatively,that mitochondria might confer a developmental function.
基金supported by the Ministry of Science and Technology of China(Grant No.2002AA2Z1003)the Chinese Academy of Sciences,and the Shanghai Municipal Commissionof Sciences and Tech-nology(Grant No.038019315).
文摘The formation of eukaryotic mRNAs involves the cleavage and polyadenylation of pre-mRNAs.To investigate the sequence requirement of putative polyadenylation signals(PASs),poly(A)sites and downstream elements(DUEs)in 3'-end-processing in rice,we compared expressed sequences tags(ESTs)with poly(A)extremity to full-length cDNA sequences and constructed a database of 12969 pre-mRNA sequences in-40--+40 nt surrounding the poly(A)sites,which were from 9953 genes.The alternative poly(A)sites were revealed in approximately 25%of mRNAs.Nearly 80%of pre-mRNAs showed stringent requirement of the YA(CA or UA)at poly(A)sites for polyadenylation.About 7.9%had the AAUAAA signals on-40---1 nt upstream of the poly(A)sites.Over 60%of mRNAs probably used the oneor two-base variants of AAUAAA hexamers as their PASs in 3'fragments.The single-base variants of AAUGAA revealed the high frequency in 11.5%of 3'fragments.The DUEs were detected in 90%of pre-mRNAs,especially more than half of the pre-mRNAs with multi-base variants of AAUAAA had the DUEs surrounding the poly(A)site.The location of DUE is also important for defining the cleavage site.Although most of the rice pre-mRNAs did not contain AAUAAA signal,the existence of downstream elements ensured the efficiency of cleavage-polyade-nylation.
基金Open access funding provided by Shanghai Jiao Tong Universityfunded in part by the National Nature Science Foundation of China(grant#32270344).
文摘The sessile nature of plants confines their responsiveness to changing environmental conditions.Gene expression regulation becomes a paramount mechanism for plants to adjust their physiological and morphological behaviors.Alternative polyadenylation(APA)is known for its capacity to augment transcriptome diversity and plasticity,thereby furnishing an additional set of tools for modulating gene expression.APA has also been demonstrated to exhibit intimate associations with plant stress responses.In this study,we review APA dynamic features and consequences in plants subjected to both biotic and abiotic stresses.These stresses include adverse environmental stresses,and pathogenic attacks,such as cadmium toxicity,high salt,hypoxia,oxidative stress,cold,heat shock,along with bacterial,fungal,and viral infections.We analyzed the overarching research framework employed to elucidate plant APA response and the alignment of polyadenylation site transitions with the modulation of gene expression levels within the ambit of each stress condition.We also proposed a general APA model where transacting factors,including poly(A)factors,epigenetic regulators,RNA m6A modification factors,and phase separation proteins,assume pivotal roles in APA related transcriptome plasticity during stress response in plants.
基金supported by grants from the Biological Breeding-National Science and Technology Major Project(2023ZD04075)the National Key Research and Development Program of China(2022YFC2703302)+1 种基金the National Natural Science Foundation of China(32170587)the 2115 Talent Development Program of China Agricultural University.
文摘Dear Editor,Nuclear speckles,hubs for gene expression and storage sites for RNA processing factors in typical mammalian nuclei(Chen and Belmont,2019),concentrate numerous functional components(Gordon et al.,2021).Recent evidence suggests that genomic nuclear speckle-associated domains(SPADs)are transcriptionally active,whereas those nuclear lamina-associated domain(LADs)are inactive(Payne et al.,2021;Quinodoz et al.,2018).
基金supported by the National Natural Science Foundation of China(project no.32101640 and 32230075).
文摘Pentatricopeptide repeat(PPR)proteins are involved in nearly all aspects of post-transcriptional process-ing in plant mitochondria and plastids,playing vital roles in plant growth,development,cytoplasmic male sterility restoration,and responses to biotic and abiotic stresses.Over the last three decades,significant advances have been made in understanding the functions of PPR proteins and the primary mechanisms through which they mediate post-transcriptional processing.This review aims to summarize these ad-vancements,highlighting the mechanisms by which PPR proteins facilitate RNA editing,intron splicing,and RNA maturation in the context of organellar gene expression.We also present the latest progress in PPR engineering and discuss its potential as a biotechnological tool.Additionally,we discuss key chal-lenges and questions that remain in PPR research.
基金supported by grants from the Biological Breeding-National Science and Technology Major Project(2023ZD04075)the National Key Research and Development Program of China(2022YFC2703302)+1 种基金the National Natural Science Foundation of China(32170587)the 2115 Talent Development Program of China Agricultural University.
文摘Dear Editor,Nuclear speckles,hubs for gene expression and storage sites for RNA processing factors in typical mammalian nuclei(Chen and Belmont,2019),concentrate numerous functional components(Gordon et al.,2021).Recent evi dence suggests that genomic nuclear speckle-associated domains(SPADs)are transcriptionally active,whereas those nuclear lamina-associated domain(LADs)are inactive(Payne et al.,2021;Quinodoz et al.,2018).Disruptions in chromatin organization lead to aberrant gene expression and altered cell fate decisions(Cuartero et al.,2023;Wang et al.,2022).Notably,LAD formation during mouse embryogenesis has been shown to occur de novo through interactions with the nuclear lamina(Borsos et al.,2019).
基金supported by the Qiantang Scholars Fund at Hangzhou City University(no.210000-581835).
文摘DDX21 belongs to the DEAD-box(DDX)family of helicases but deviates from the characteristic sequence Asp–Glu–Ala–Asp(DEAD)to Asp–Glu–Val–Asp.In addition to the typical helicase activity associated with the DEAD-box family,DDX21 also possesses foldase and adenosine triphosphatase activities.It plays crucial roles in various molecular processes,including the regulation of transcription,ribosomal RNA processing,modification,and unwinding of RNA spatial structures.DDX21 is subject to intricate regulation by multiple upstream factors,including expression control and posttranslational modification.In numerous cancer types,abnormal expression of DDX21 has been observed to influence cancer cell behaviors,such as the cell cycle,proliferation,invasion,migration,and apoptosis.In addition,DDX21 modulates innate immunity following viral infection and plays a dual role in the viral infection process.This review comprehensively explores the protein structure,molecular regulatory mechanisms,and pathophysiological functions of DDX21.Consequently,this study not only offers potential avenues for future research but also sparks novel ideas for targeted treatments for both cancer and viral infections.
