Glutathione-S-transferase(GST,EC2.5.1.18)multifunctional protease is important for detoxification,defense against biotic and abiotic stresses,and secondary metabolic material transport for plant growth and development...Glutathione-S-transferase(GST,EC2.5.1.18)multifunctional protease is important for detoxification,defense against biotic and abiotic stresses,and secondary metabolic material transport for plant growth and development.In this study,71 members of the BpGST family were identified from the entire Betula platyphylla Suk.genome.Most of the members encode proteins with amino acid lengths ranging from 101 to 875 and were localized to the cytoplasm by a prediction.BpGSTs can be divided into seven subfamilies,with a majority of birch U and F subfamily members according to gene structure,conserved motifs and evolutionary analysis.GST family genes showed collinearity with 22 genes in Oryza sativa L.,and three genes in Arabidopsis thaliana;promoter cis-acting elements predicted that the GST gene family is functional in growth,hormone regulation,and abiotic stress response.Most members of the F subfamily of GST(BpGSTFs)were expressed in roots,stems,leaves,and petioles,with the most expression observed in leaves.On the basis of the expression profiles of F subfamily genes(BpGSTF1 to BpGSTF13)during salt,mannitol and ABA stress,BpGSTF proteins seem to have multiple functions depending on the type of abiotic stress;for instance,BpGSTs may function at different times during abiotic stress.This study enhances understanding of the GST gene family and provides a basis for further exploration of their function in birch.展开更多
Auxin plays important roles in various aspects of plant growth and development （Zhao, 2010）. In Arabidopsis, a number of YUCCA （YUC） genes, which are involved in auxin biosyn- thesis, have been identified （Zhao e...Auxin plays important roles in various aspects of plant growth and development （Zhao, 2010）. In Arabidopsis, a number of YUCCA （YUC） genes, which are involved in auxin biosyn- thesis, have been identified （Zhao et al., 2001; Woodward et al., 2005; Cheng et al., 2006, 2007; Kim et al., 2007; Chen et al., 2014）. YUC genes encode flavin monooxygenases （FMOs） that convert indole-3-pyruvate （IPA） to indole-3-acetic acid （IAA） （Zhao, 2012）. The Arabidopsis YUC family is comprised of 11 members （Zhao et al., 2001;展开更多
P1B-type ATPase ion pumps that transport heavy metal ions across cellular membranes are essential for plant growth and development. To date, a genomic comparison overview of the family in rice, maize and sorghum is no...P1B-type ATPase ion pumps that transport heavy metal ions across cellular membranes are essential for plant growth and development. To date, a genomic comparison overview of the family in rice, maize and sorghum is not yet available. In this study, a total of 31 heavy metal P1B-type ATPase （HMA） genes were identified, including 9 in rice, 11 each from maize and sorghum. They were classified into two distinct subfamilies based on their sequence composition and phylogenetic relationship. Four pairs of HMA genes were expanded via gene duplication with tandemly duplicated. Comprehensive analyses were performed to investigate the expression profiles of HMA genes in various tissues by using quantitative real-time PCR. Some HMA members exhibited abundant and tissue-specific expression patterns. Moreover, most of the genes were found to be differentially expressed under the Cu/Cd treatment. This study will facilitate further studies on P1B-type ATPase family and provide valuable hints for the functional validation in rice, maize and sorghum.展开更多
Camptotheca acuminata produces camptothecin(CPT),a monoterpene indole alkaloid(MIA)that is widely used in the treatment of lung,colorectal,cervical,and ovarian cancers.Its biosynthesis pathway has attracted significan...Camptotheca acuminata produces camptothecin(CPT),a monoterpene indole alkaloid(MIA)that is widely used in the treatment of lung,colorectal,cervical,and ovarian cancers.Its biosynthesis pathway has attracted significant attention,but the regulation of CPT biosynthesis by the APETALA2/ethylene-responsive factor(AP2/ERF)transcription factors(TFs)remains unclear.In this study,a systematic analysis of the AP2/ERF TFs family in C.acuminata was performed,including phylogeny,gene structure,conserved motifs,and gene expression profiles in different tissues and organs(immature bark,cotyledons,young flower,immature fruit,mature fruit,mature leaf,roots,upper stem,and lower stem)of C.acuminata.A total of 198 AP2/ERF genes were identified and divided into five relatively conserved subfamilies,including AP2(26 genes),DREB(61 genes),ERF(92 genes),RAV(18 genes),and Soloist(one gene).The combination of gene expression patterns in different C.acuminata tissues and organs,the phylogenetic tree,the co-expression analysis with biosynthetic genes,and the analysis of promoter sequences of key enzymes genes involved in CPT biosynthesis pathways revealed that eight AP2/ERF TFs in C.acuminata might be involved in CPT synthesis regulation,which exhibit relatively high expression levels in the upper stem or immature bark.Among these,four genes(Cac AP2/ERF123,Cac AP2/ERF125,Cac AP2/ERF126,and Cac AP2/ERF127)belong to the ERF–B2 subgroup;two genes(Cac AP2/ERF149 and Cac AP2/ERF152)belong to the ERF–B3 subgroup;and two more genes(Cac AP2/ERF095 and Cac AP2/ERF096)belong to the DREB–A6 subgroup.These results provide a foundation for future functional characterization of the AP2/ERF genes to enhance the biosynthesis of CPT compounds of C.acuminata.展开更多
Objectives:The basic helix-loop-helix(bHLH)transcription factors(TFs)regulate fruit growth in many plants.However,there is no available study on the bHLH gene family in the haplotype-resolved genome of cultivated stra...Objectives:The basic helix-loop-helix(bHLH)transcription factors(TFs)regulate fruit growth in many plants.However,there is no available study on the bHLH gene family in the haplotype-resolved genome of cultivated strawberry(Fragaria×ananassa).Materials and Methods:The 131 FabHLH genes identifed in the strawberry cultivar‘Yanli’haplotype-resolved genome were classifed into 24 subfamilies according to their phylogenetic relationships.Gene structure,conserved motifs,and chromosomal locations were investigated using bioinformatics.Results:In total,15 FabHLH genes potentially involved in fruit development were screened based on transcriptome analysis of different stages of fruit development.We also identifed the cis-regulatory elements of these 15 FabHLH genes,predicted upstream transcription factors,and identifed protein-protein interactions.Conclusions:The fndings of this study improve our understanding of the regulation mediated by bHLH TFs during strawberry fruit growth and maturation.展开更多
Tanshinones are a class of bioactive components in the traditional Chinese medicine Salvia miltiorrhiza, and their biosynthesis and regulation have been widely studied. Current studies show that basic leucine zipper(b...Tanshinones are a class of bioactive components in the traditional Chinese medicine Salvia miltiorrhiza, and their biosynthesis and regulation have been widely studied. Current studies show that basic leucine zipper(bZIP) proteins regulate plant secondary metabolism, growth and developmental processes. However, the b ZIP transcription factors involved in tanshinone biosynthesis are unknown.Here, we conducted the first genome-wide survey of the b ZIP gene family and analyzed the phylogeny,gene structure, additional conserved motifs and alternative splicing events in S. miltiorrhiza. A total of 70 Smb ZIP transcription factors were identified and categorized into 11 subgroups based on their phylogenetic relationships with those in Arabidopsis. Moreover, seventeen Smb ZIP genes underwent alternative splicing events. According to the transcriptomic data, the Smb ZIP genes that were highly expressed in the Danshen root and periderm were selected. Based on the prediction of b ZIP binding sites in the promoters and the co-expression analysis and co-induction patterns in response to Ag^+ treatment via quantitative real-time polymerase chain reaction(qRT-PCR), we concluded that Smb ZIP7 and Smb ZIP20 potentially participate in the regulation of tanshinone biosynthesis. These results provide a foundation for further functional characterization of the candidate Smb ZIP genes, which have the potential to increase tanshinone production.展开更多
基金supported by the National Key Research and Development Program of China(No.2021YFD2200304)FundamentalResearch Funds for the Central Universities(2572022DQ08)the National Natural Science Foundation of China(No32171738).
文摘Glutathione-S-transferase(GST,EC2.5.1.18)multifunctional protease is important for detoxification,defense against biotic and abiotic stresses,and secondary metabolic material transport for plant growth and development.In this study,71 members of the BpGST family were identified from the entire Betula platyphylla Suk.genome.Most of the members encode proteins with amino acid lengths ranging from 101 to 875 and were localized to the cytoplasm by a prediction.BpGSTs can be divided into seven subfamilies,with a majority of birch U and F subfamily members according to gene structure,conserved motifs and evolutionary analysis.GST family genes showed collinearity with 22 genes in Oryza sativa L.,and three genes in Arabidopsis thaliana;promoter cis-acting elements predicted that the GST gene family is functional in growth,hormone regulation,and abiotic stress response.Most members of the F subfamily of GST(BpGSTFs)were expressed in roots,stems,leaves,and petioles,with the most expression observed in leaves.On the basis of the expression profiles of F subfamily genes(BpGSTF1 to BpGSTF13)during salt,mannitol and ABA stress,BpGSTF proteins seem to have multiple functions depending on the type of abiotic stress;for instance,BpGSTs may function at different times during abiotic stress.This study enhances understanding of the GST gene family and provides a basis for further exploration of their function in birch.
基金financially supported by the grant from the National Plant Transgenic Program(No.2013ZX08003-003)from Ministry of Agriculture of the People’s Republic of China
文摘Auxin plays important roles in various aspects of plant growth and development （Zhao, 2010）. In Arabidopsis, a number of YUCCA （YUC） genes, which are involved in auxin biosyn- thesis, have been identified （Zhao et al., 2001; Woodward et al., 2005; Cheng et al., 2006, 2007; Kim et al., 2007; Chen et al., 2014）. YUC genes encode flavin monooxygenases （FMOs） that convert indole-3-pyruvate （IPA） to indole-3-acetic acid （IAA） （Zhao, 2012）. The Arabidopsis YUC family is comprised of 11 members （Zhao et al., 2001;
基金supported by the Special Fund for Agro-Scientific Research in the Public Interest of China(Grant No.201403015)
文摘P1B-type ATPase ion pumps that transport heavy metal ions across cellular membranes are essential for plant growth and development. To date, a genomic comparison overview of the family in rice, maize and sorghum is not yet available. In this study, a total of 31 heavy metal P1B-type ATPase （HMA） genes were identified, including 9 in rice, 11 each from maize and sorghum. They were classified into two distinct subfamilies based on their sequence composition and phylogenetic relationship. Four pairs of HMA genes were expanded via gene duplication with tandemly duplicated. Comprehensive analyses were performed to investigate the expression profiles of HMA genes in various tissues by using quantitative real-time PCR. Some HMA members exhibited abundant and tissue-specific expression patterns. Moreover, most of the genes were found to be differentially expressed under the Cu/Cd treatment. This study will facilitate further studies on P1B-type ATPase family and provide valuable hints for the functional validation in rice, maize and sorghum.
基金supported by the National Key R&D Program of China(No.2019YFC1711100)the CAMS Innovation Fund for Medical Sciences(CIFMS,No.2016-I2M-3-016)。
文摘Camptotheca acuminata produces camptothecin(CPT),a monoterpene indole alkaloid(MIA)that is widely used in the treatment of lung,colorectal,cervical,and ovarian cancers.Its biosynthesis pathway has attracted significant attention,but the regulation of CPT biosynthesis by the APETALA2/ethylene-responsive factor(AP2/ERF)transcription factors(TFs)remains unclear.In this study,a systematic analysis of the AP2/ERF TFs family in C.acuminata was performed,including phylogeny,gene structure,conserved motifs,and gene expression profiles in different tissues and organs(immature bark,cotyledons,young flower,immature fruit,mature fruit,mature leaf,roots,upper stem,and lower stem)of C.acuminata.A total of 198 AP2/ERF genes were identified and divided into five relatively conserved subfamilies,including AP2(26 genes),DREB(61 genes),ERF(92 genes),RAV(18 genes),and Soloist(one gene).The combination of gene expression patterns in different C.acuminata tissues and organs,the phylogenetic tree,the co-expression analysis with biosynthetic genes,and the analysis of promoter sequences of key enzymes genes involved in CPT biosynthesis pathways revealed that eight AP2/ERF TFs in C.acuminata might be involved in CPT synthesis regulation,which exhibit relatively high expression levels in the upper stem or immature bark.Among these,four genes(Cac AP2/ERF123,Cac AP2/ERF125,Cac AP2/ERF126,and Cac AP2/ERF127)belong to the ERF–B2 subgroup;two genes(Cac AP2/ERF149 and Cac AP2/ERF152)belong to the ERF–B3 subgroup;and two more genes(Cac AP2/ERF095 and Cac AP2/ERF096)belong to the DREB–A6 subgroup.These results provide a foundation for future functional characterization of the AP2/ERF genes to enhance the biosynthesis of CPT compounds of C.acuminata.
基金supported by the National Natural Science Foundation of China(Nos.32130092,31872072,and 32102350)the Liaoning Provincial Department of Education Scientifc Research Funding Project(No.LJKZ0635),China.
文摘Objectives:The basic helix-loop-helix(bHLH)transcription factors(TFs)regulate fruit growth in many plants.However,there is no available study on the bHLH gene family in the haplotype-resolved genome of cultivated strawberry(Fragaria×ananassa).Materials and Methods:The 131 FabHLH genes identifed in the strawberry cultivar‘Yanli’haplotype-resolved genome were classifed into 24 subfamilies according to their phylogenetic relationships.Gene structure,conserved motifs,and chromosomal locations were investigated using bioinformatics.Results:In total,15 FabHLH genes potentially involved in fruit development were screened based on transcriptome analysis of different stages of fruit development.We also identifed the cis-regulatory elements of these 15 FabHLH genes,predicted upstream transcription factors,and identifed protein-protein interactions.Conclusions:The fndings of this study improve our understanding of the regulation mediated by bHLH TFs during strawberry fruit growth and maturation.
基金supported by the National Natural Science Foundation (Grant No.81573398)Chinese Academy of Medical Sciences(CAMS)Innovation Fund for Medical Sciences (CIFMS,2016-I2M-3–016)
文摘Tanshinones are a class of bioactive components in the traditional Chinese medicine Salvia miltiorrhiza, and their biosynthesis and regulation have been widely studied. Current studies show that basic leucine zipper(bZIP) proteins regulate plant secondary metabolism, growth and developmental processes. However, the b ZIP transcription factors involved in tanshinone biosynthesis are unknown.Here, we conducted the first genome-wide survey of the b ZIP gene family and analyzed the phylogeny,gene structure, additional conserved motifs and alternative splicing events in S. miltiorrhiza. A total of 70 Smb ZIP transcription factors were identified and categorized into 11 subgroups based on their phylogenetic relationships with those in Arabidopsis. Moreover, seventeen Smb ZIP genes underwent alternative splicing events. According to the transcriptomic data, the Smb ZIP genes that were highly expressed in the Danshen root and periderm were selected. Based on the prediction of b ZIP binding sites in the promoters and the co-expression analysis and co-induction patterns in response to Ag^+ treatment via quantitative real-time polymerase chain reaction(qRT-PCR), we concluded that Smb ZIP7 and Smb ZIP20 potentially participate in the regulation of tanshinone biosynthesis. These results provide a foundation for further functional characterization of the candidate Smb ZIP genes, which have the potential to increase tanshinone production.
