【目的】克隆家蚕精氨酸激酶基因,分析其基因结构与表达特性,为揭示无脊椎动物体内能量代谢调节规律提供重要基础。【方法】通过分析家蚕EST、利用RACE法和基因组文库筛选法克隆了家蚕精氨酸激酶(BmAK,Bombyx mori arginine kinase)基因...【目的】克隆家蚕精氨酸激酶基因,分析其基因结构与表达特性,为揭示无脊椎动物体内能量代谢调节规律提供重要基础。【方法】通过分析家蚕EST、利用RACE法和基因组文库筛选法克隆了家蚕精氨酸激酶(BmAK,Bombyx mori arginine kinase)基因,并对其基因结构和表达特性进行了分析。【结果】克隆了BmAK基因,cDNA全长为1 268bp,编码355个氨基酸,具有精氨酸激酶典型的酶活性部位氨基酸序列,酶活性中心位点氨基酸和能形成离子偶结构氨基酸;该基因由2个外显子和1个内含子组成;5′调控序列存在BRCZ、E74A、FTZ等多个潜在转录因子结合位点,但没有TATA盒启动子序列;该基因的表达在不同组织和不同发育时期存在明显差异。【结论】BmAK具有精氨酸激酶的典型特征,BmAK基因表达随发育时期不同而发生变化,基因的表达可能受蜕皮激素调控。展开更多
The past two decades revealed a plethora of Ca^2＋-responsive proteins and downstream targets in plants, of which several are unique to plants. More recent high-throughput ＇omics＂ approaches and bioinformatics are e...The past two decades revealed a plethora of Ca^2＋-responsive proteins and downstream targets in plants, of which several are unique to plants. More recent high-throughput ＇omics＂ approaches and bioinformatics are exposing Ca^2＋-responsive cis-elements and the corresponding Ca^2＋-responsive genes. Here, we review the current knowledge on Ca^2＋-signaling pathways that regulate gene expression in plants, and we link these to mechanisms by which plants respond to biotic and abiotic stresses.展开更多
Flavonoid biosynthetic genes are often coordinately regulated in a temporal manner during flower or fruit development, resulting in specific accumulation profiles of flavonoid compounds. R2R3-MYB-type transcription fa...Flavonoid biosynthetic genes are often coordinately regulated in a temporal manner during flower or fruit development, resulting in specific accumulation profiles of flavonoid compounds. R2R3-MYB-type transcription factors （TFs） ＂recruit＂ a set of biosynthetic genes to produce flavonoids, and, therefore, R2R3-MYBs are responsible for the coordinated expression of structural genes. Although a wealth of information regarding the identified and functionally characterized R2R3-MYBs that are involved in flavonoid accumulation is available to date, this is the first review on the global regulation of MYB factors in the flavonoid pathway. The data presented in this review demonstrate that anthocyanin, flavone/flavonol/3-deoxyflavonoid （FFD）, proanthocyanidin （PA）, and isoflavonoid are independently regulated by different subgroups of R2R3-MYBs. Furthermore, FFD-specific R2R3-MYBs have a preference for early biosynthetic genes （EBGs） as their target genes; anthocyanin-specific R2R3-MYBs from dicot species essentially regulate late biosynthetic genes （LBGs）; the remaining R2R3-MYBs have a wider range of target gene specificity. To elucidate the nature of the differential target gene specificity between R2R3-MYBs, we analyzed the DNA binding domain （also termed the MYB-domain） of R2R3-MYBs and the distribution of the recognition cis-elements. We identified four conserved amino acid residues located in or just before helix-3 of dicot anthocyanin R2R3-MYBs that might account for the different recognition DNA sequence and subsequently the different target gene specificity to the remaining R2R3-MYB TFs.展开更多
Genomic clustering of non-homologous genes for the biosynthesis of plant defensive compounds is an emerging theme, but insights into their formation and physiological function remain limited. Here we report the identi...Genomic clustering of non-homologous genes for the biosynthesis of plant defensive compounds is an emerging theme, but insights into their formation and physiological function remain limited. Here we report the identification of a newly discovered hydroxycinnamoyl tyramine(HT) gene cluster in rice.This cluster contains a pyridoxamine 50-phosphate oxidase(Os PDX3) producing the cofactor pyridoxal50-phosphate(PLP), a PLP-dependent tyrosine decarboxylase(Os Ty DC1), and two duplicated hydroxycinnamoyl transferases(Os THT1 and Os THT2). These members were combined to represent an enzymological innovation gene cluster. Natural variation analysis showed that the abundance of the toxic tyramine intermediate of the gene cluster among different rice accessions is mainly determined by the coordinated transcription of Os Ty DC1 and Os THT1. Further pathogen incubation assays demonstrated that the end products of the HT gene cluster displayed enhanced resistance to the bacterial pathogen Xanthomonas oryzae pv. Oryzae(Xoo) and fungal pathogen Magnaporthe oryzae(M. oryzae), and the enhanced resistance is associated with the boost of phytoalexins and the activation of defense response. The unique presence of the HT gene cluster in Oryza AA genome, together with the enrichment of transposon elements within this gene cluster region, provides an evolutionary background to accelerate cluster member combinations. Our study not only discovered a gene cluster involved in the phenylpropanoid metabolism but also addressed the key aspects of gene cluster formation. In addition, our results provide a new metabolic pool for plant defense against pathogens.展开更多
Recently, the rarely reported tet(31) tetracycline resistance determinant was commonly found in Aeromonas salmonicida, Gallibacterium anatis, and Oblitimonas alkaliphila isolated from farming animals and related envir...Recently, the rarely reported tet(31) tetracycline resistance determinant was commonly found in Aeromonas salmonicida, Gallibacterium anatis, and Oblitimonas alkaliphila isolated from farming animals and related environment. However, its distribution in other bacteria and potential molecular dissemination mechanism in environment are still unknown. The purpose of this study was to investigate the potential mechanism underlying dissemination of tet(31) by analysing the tet(31)-carrying fragments in A. caviae strains isolated from an aerobic biofilm reactor treating oxytetracycline bearing wastewater. Twenty-three A. caviae strains were screened for the tet(31) gene by polymerase chain reaction(PCR). Three strains(two harbouring tet(31), one not) were subjected to whole genome sequencing using the PacBio RSII platform. Seventeen A. caviae strains carried the tet(31) gene and exhibited high resistance levels to oxytetracycline with minimum inhibitory concentrations(MICs)ranging from 256 to 512 mg/L. tet(31) was comprised of the transposon Tn6432 on the chromosome of A. caviae, and Tn6432 was also found in 15 additional tet(31)-positive A. caviae isolates by PCR. More important, Tn6432 was located on an integrative conjugative element(ICE)-like element, which could mediate the dissemination of the tet(31)-carrying transposon Tn6432 between bacteria. Comparative analysis demonstrated that Tn6432 homologs with the structure ISCR2-ΔphzF-tetR(31)-tet(31)-ΔglmM-sul2 were also carried by A. salmonicida, G. anatis, and O. alkaliphila, suggesting that this transposon can be transferred between species and even genera. This work provides the first report on the identification of the tet(31) gene in A. caviae, and will be helpful in exploring the dissemination mechanisms of tet(31) in water environment.展开更多
Auxin response factors(ARFs) are transcription factors that activate or repress the expression of primary/early auxin response genes by binding to auxin-responsive elements(Aux REs) in their promoter regions. The ARFs...Auxin response factors(ARFs) are transcription factors that activate or repress the expression of primary/early auxin response genes by binding to auxin-responsive elements(Aux REs) in their promoter regions. The ARFs play important roles in diverse developmental processes.To explore the ARF gene family in hot pepper(Capsicum annuum L.), we performed a genome-wide identification and expression analysis. In this study, 19 pepper ARF genes(Ca ARFs) clustered into three phylogenetic groups(I, II, and III) were comprehensively analyzed. Conserved domain analysis showed that all Ca ARFs contained a B3 DNA-binding domain and a middle domain, but two members lacked the carboxyterminal dimerization(CTD) domain. The number of introns in Ca ARF genes ranged from 1 to 13 and the gene structure was similar among genes in the same phylogenetic group. Additionally, prediction of Ca ARFs promoter elements and putative targets for micro RNAs suggested that the regulation of Ca ARFs may occur at both transcriptional and posttranscriptional levels. Most Ca ARFs were expressed in more than one tested tissue, and most Ca ARFs were identified as being responsive to exogenous auxin. Moreover, time-course transcription profiles of Ca ARFs revealed their roles in adventitious rooting of hypocotyl cuttings from pepper seedlings. Therefore, our results will provide a foundation for better understanding the regulatory mechanisms and molecular functions of Ca ARFs in hot pepper.展开更多
文摘【目的】克隆家蚕精氨酸激酶基因,分析其基因结构与表达特性,为揭示无脊椎动物体内能量代谢调节规律提供重要基础。【方法】通过分析家蚕EST、利用RACE法和基因组文库筛选法克隆了家蚕精氨酸激酶(BmAK,Bombyx mori arginine kinase)基因,并对其基因结构和表达特性进行了分析。【结果】克隆了BmAK基因,cDNA全长为1 268bp,编码355个氨基酸,具有精氨酸激酶典型的酶活性部位氨基酸序列,酶活性中心位点氨基酸和能形成离子偶结构氨基酸;该基因由2个外显子和1个内含子组成;5′调控序列存在BRCZ、E74A、FTZ等多个潜在转录因子结合位点,但没有TATA盒启动子序列;该基因的表达在不同组织和不同发育时期存在明显差异。【结论】BmAK具有精氨酸激酶的典型特征,BmAK基因表达随发育时期不同而发生变化,基因的表达可能受蜕皮激素调控。
文摘The past two decades revealed a plethora of Ca^2＋-responsive proteins and downstream targets in plants, of which several are unique to plants. More recent high-throughput ＇omics＂ approaches and bioinformatics are exposing Ca^2＋-responsive cis-elements and the corresponding Ca^2＋-responsive genes. Here, we review the current knowledge on Ca^2＋-signaling pathways that regulate gene expression in plants, and we link these to mechanisms by which plants respond to biotic and abiotic stresses.
文摘Flavonoid biosynthetic genes are often coordinately regulated in a temporal manner during flower or fruit development, resulting in specific accumulation profiles of flavonoid compounds. R2R3-MYB-type transcription factors （TFs） ＂recruit＂ a set of biosynthetic genes to produce flavonoids, and, therefore, R2R3-MYBs are responsible for the coordinated expression of structural genes. Although a wealth of information regarding the identified and functionally characterized R2R3-MYBs that are involved in flavonoid accumulation is available to date, this is the first review on the global regulation of MYB factors in the flavonoid pathway. The data presented in this review demonstrate that anthocyanin, flavone/flavonol/3-deoxyflavonoid （FFD）, proanthocyanidin （PA）, and isoflavonoid are independently regulated by different subgroups of R2R3-MYBs. Furthermore, FFD-specific R2R3-MYBs have a preference for early biosynthetic genes （EBGs） as their target genes; anthocyanin-specific R2R3-MYBs from dicot species essentially regulate late biosynthetic genes （LBGs）; the remaining R2R3-MYBs have a wider range of target gene specificity. To elucidate the nature of the differential target gene specificity between R2R3-MYBs, we analyzed the DNA binding domain （also termed the MYB-domain） of R2R3-MYBs and the distribution of the recognition cis-elements. We identified four conserved amino acid residues located in or just before helix-3 of dicot anthocyanin R2R3-MYBs that might account for the different recognition DNA sequence and subsequently the different target gene specificity to the remaining R2R3-MYB TFs.
基金supported by the National Science Fund for Distinguished Young Scholars of China (31625021)the Foundation for Innovative Research Groups of the National Natural Science Foundation of China (31821005)+1 种基金the State Key Program of National Natural Science Foundation of China (31530052)the Hainan University Startup Fund (KYQD(ZR)1866)。
文摘Genomic clustering of non-homologous genes for the biosynthesis of plant defensive compounds is an emerging theme, but insights into their formation and physiological function remain limited. Here we report the identification of a newly discovered hydroxycinnamoyl tyramine(HT) gene cluster in rice.This cluster contains a pyridoxamine 50-phosphate oxidase(Os PDX3) producing the cofactor pyridoxal50-phosphate(PLP), a PLP-dependent tyrosine decarboxylase(Os Ty DC1), and two duplicated hydroxycinnamoyl transferases(Os THT1 and Os THT2). These members were combined to represent an enzymological innovation gene cluster. Natural variation analysis showed that the abundance of the toxic tyramine intermediate of the gene cluster among different rice accessions is mainly determined by the coordinated transcription of Os Ty DC1 and Os THT1. Further pathogen incubation assays demonstrated that the end products of the HT gene cluster displayed enhanced resistance to the bacterial pathogen Xanthomonas oryzae pv. Oryzae(Xoo) and fungal pathogen Magnaporthe oryzae(M. oryzae), and the enhanced resistance is associated with the boost of phytoalexins and the activation of defense response. The unique presence of the HT gene cluster in Oryza AA genome, together with the enrichment of transposon elements within this gene cluster region, provides an evolutionary background to accelerate cluster member combinations. Our study not only discovered a gene cluster involved in the phenylpropanoid metabolism but also addressed the key aspects of gene cluster formation. In addition, our results provide a new metabolic pool for plant defense against pathogens.
基金supported by the National Natural Scientific Foundation of China (No.21437005)
文摘Recently, the rarely reported tet(31) tetracycline resistance determinant was commonly found in Aeromonas salmonicida, Gallibacterium anatis, and Oblitimonas alkaliphila isolated from farming animals and related environment. However, its distribution in other bacteria and potential molecular dissemination mechanism in environment are still unknown. The purpose of this study was to investigate the potential mechanism underlying dissemination of tet(31) by analysing the tet(31)-carrying fragments in A. caviae strains isolated from an aerobic biofilm reactor treating oxytetracycline bearing wastewater. Twenty-three A. caviae strains were screened for the tet(31) gene by polymerase chain reaction(PCR). Three strains(two harbouring tet(31), one not) were subjected to whole genome sequencing using the PacBio RSII platform. Seventeen A. caviae strains carried the tet(31) gene and exhibited high resistance levels to oxytetracycline with minimum inhibitory concentrations(MICs)ranging from 256 to 512 mg/L. tet(31) was comprised of the transposon Tn6432 on the chromosome of A. caviae, and Tn6432 was also found in 15 additional tet(31)-positive A. caviae isolates by PCR. More important, Tn6432 was located on an integrative conjugative element(ICE)-like element, which could mediate the dissemination of the tet(31)-carrying transposon Tn6432 between bacteria. Comparative analysis demonstrated that Tn6432 homologs with the structure ISCR2-ΔphzF-tetR(31)-tet(31)-ΔglmM-sul2 were also carried by A. salmonicida, G. anatis, and O. alkaliphila, suggesting that this transposon can be transferred between species and even genera. This work provides the first report on the identification of the tet(31) gene in A. caviae, and will be helpful in exploring the dissemination mechanisms of tet(31) in water environment.
基金supported by the National Natural Science Foundation of China (31172001)the Special Fund for Agro-scientific Research in the Public Interest (201303014)+1 种基金the China Agriculture Research System (CARS-25)the Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences (CAAS-ASTIP-IVFCAAS)
文摘Auxin response factors(ARFs) are transcription factors that activate or repress the expression of primary/early auxin response genes by binding to auxin-responsive elements(Aux REs) in their promoter regions. The ARFs play important roles in diverse developmental processes.To explore the ARF gene family in hot pepper(Capsicum annuum L.), we performed a genome-wide identification and expression analysis. In this study, 19 pepper ARF genes(Ca ARFs) clustered into three phylogenetic groups(I, II, and III) were comprehensively analyzed. Conserved domain analysis showed that all Ca ARFs contained a B3 DNA-binding domain and a middle domain, but two members lacked the carboxyterminal dimerization(CTD) domain. The number of introns in Ca ARF genes ranged from 1 to 13 and the gene structure was similar among genes in the same phylogenetic group. Additionally, prediction of Ca ARFs promoter elements and putative targets for micro RNAs suggested that the regulation of Ca ARFs may occur at both transcriptional and posttranscriptional levels. Most Ca ARFs were expressed in more than one tested tissue, and most Ca ARFs were identified as being responsive to exogenous auxin. Moreover, time-course transcription profiles of Ca ARFs revealed their roles in adventitious rooting of hypocotyl cuttings from pepper seedlings. Therefore, our results will provide a foundation for better understanding the regulatory mechanisms and molecular functions of Ca ARFs in hot pepper.
