In this study, the first complete mitochondrial genome（mitogenome） of lepidopteran family Drepanidae（superfamily Drepanoidea） was reported with the notes about its phylogenetic implications. The Oreta fuscopurpure...In this study, the first complete mitochondrial genome（mitogenome） of lepidopteran family Drepanidae（superfamily Drepanoidea） was reported with the notes about its phylogenetic implications. The Oreta fuscopurpurea mitogenome is 15,564 bp in length, including 13 protein-coding genes, two ribosomal RNAs（lrRNA and srRNA）, 22 transfer RNAs and a non-coding control region（AT-rich region）, with a 79.6% A＋T content. The gene orientation and arrangement of the mitogenome are the same as other sequenced lepidopterans. All protein-coding genes usually start with the common ATN codon except for COI gene, which used CGA as the initial codon; eight PCGs use a typical stop codon of TAA, whereas the remaining PCGs use incomplete stop codon of T or TA. All tRNAs have the typical clover-leaf structure with the exception of t RNA^（Ser）（AGN）. The lrRNA and sr RNA genes are 1,409 bp and 778 bp in size respectively, with the former harboring one（TA）_（13） microsatellite-like repeat and an 17 bp insertion. The 20 intergenic spacers totaling of 184 bp and 8 overlapping sequences totaling of 25 bp are scattered throughout the whole mitogenome. The 526 bp AT-rich region contains some structures characteristic of lepidopterans, such as the motif ATAGA preceded by an 19 bp poly-T stretch, a tRNA-like and a sterm-loop structures. Phylogenetic analysis of the Oreta fuscopurpurea with other 47 insect species covering 20 lepidopteran families were conducted based on the sequence data of the 13 mitogenomic protein coding genes with maximum likelihood（ML） and Bayesian inference（BI） methods, and the results showed distinctly that the superfamily Drepanoidea was sister to the clade of（Bombycoidea, Lasiocampoidea） ＋（Noctuoidea, Geometroidea）.展开更多
为了解拟南芥中Dicer-like蛋白对tRNA衍生的小RNA(tRNA-derived small RNAs,tsRNAs)的产生有何影响,对拟南芥野生型和不同Dicer-like(DCL)基因突变体进行tRNA-seq测序,并分析tsRNA和tRNA的表达量.结果显示,DCL4基因突变后tsRNA的表达量...为了解拟南芥中Dicer-like蛋白对tRNA衍生的小RNA(tRNA-derived small RNAs,tsRNAs)的产生有何影响,对拟南芥野生型和不同Dicer-like(DCL)基因突变体进行tRNA-seq测序,并分析tsRNA和tRNA的表达量.结果显示,DCL4基因突变后tsRNA的表达量明显降低,说明DCL4可能参与tsRNA的产生.拟南芥tRC1位点(Chr1:21268000-21310000)具有大量串联分布的tRNA序列,通过对RNA介导的甲基化(RdDM)途径相关基因CLSY1突变体中tRC1位点的24 nt siRNA和tsRNA进行分析,推断tRC1位点的tsRNA受RdDM途径负调控.综上,本研究鉴定到DCL4在tsRNA生成中的潜在作用,部分tsRNA的生成与RdDM途径有关.展开更多
Mutations in the small genome present in mitochondria often result in severe pathologies.Different genetic strategies have been explored,aiming to rescue such mutations.A number of these strategies were based on the c...Mutations in the small genome present in mitochondria often result in severe pathologies.Different genetic strategies have been explored,aiming to rescue such mutations.A number of these strategies were based on the capacity of human mitochondria to import RNAs from the cytosol and designed to repress the replication of the mutated genomes or to provide the organelles with wild-type versions of mutant transcripts.However,the mutant RNAs present in mitochondria turned out to be an obstacle to therapy and little attention has been devoted so far to their elimination.Here,we present the development of a strategy to knockdown mitochondrial RNAs in human cells using the transfer RNA-like structure of Brome mosaic virus or Tobacco mosaic virus as a shuttle to drive trans-cleaving ribozymes into the organelles in human cell lines.We obtained a specific knockdown of the targeted mitochondrial ATP6 mRNA,followed by a deep drop in ATP6 protein and a functional impairment of the oxidative phosphorylation chain.Our strategy provides a powerful approach to eliminate mutant organellar transcripts and to analyse the control and communication of the human organellar genetic system.展开更多
Acinetobacter baumannii is an important opportunistic pathogeq in hospital, and tile multidrug-resistant isolates of A. haumannii have been increasingly reported i,a recent years. A num- ber of different mechanisms of...Acinetobacter baumannii is an important opportunistic pathogeq in hospital, and tile multidrug-resistant isolates of A. haumannii have been increasingly reported i,a recent years. A num- ber of different mechanisms of resistance have been reported, some of which are associated with plasmid-mediated acquisition of genes. Therefore, studies on plasmids in A. haumannii have been a hot issue lately. We have performed complete genome sequencing of A. haumannii MDR-TJ, which is a multidrug-resistant isolate. Finalizing the remaining large scaffold of the previous assem- bly, we found a new plasmid pABTJ2, which carries many phage-like elements. The plasmid pAB- TJ2 is a circular double-stranded DNA molecule, which is 110,967 bp in length. We annotated 125 CDSs from pABTJ2 using IMG ER and ZCURVE_V, accounting lbr 88.28% of the whole plasmid sequence. Many phage-like elements and a tRNA-coding gene were detected in pABTJ2, which is rarely reported among A. haumannii. The tRNA gene is specific for asparagine codon GTT, which may be a small chromosomal sequence picked up through incorrect excision during plasmid forma- tion. The phage-like elements may have been acquired during the integration process, as the GC content of the region carrying phage-like elements was higher than that of the adjacent regions. The finding of phage-like elements and tRNA-coding gene in pABTJ2 may provide a novel insight into the study of A. haumannii pan-plasmidome.展开更多
基金supported by the Special Funds for Cultivation of Preponderant Disciplines of Anhui Normal Universityfunds from the State Key Laboratory of Palaeobiology and Stratigraphy(Nanjing Institute of Geology and Palaeontology,CAS)(Y626040108)
文摘In this study, the first complete mitochondrial genome（mitogenome） of lepidopteran family Drepanidae（superfamily Drepanoidea） was reported with the notes about its phylogenetic implications. The Oreta fuscopurpurea mitogenome is 15,564 bp in length, including 13 protein-coding genes, two ribosomal RNAs（lrRNA and srRNA）, 22 transfer RNAs and a non-coding control region（AT-rich region）, with a 79.6% A＋T content. The gene orientation and arrangement of the mitogenome are the same as other sequenced lepidopterans. All protein-coding genes usually start with the common ATN codon except for COI gene, which used CGA as the initial codon; eight PCGs use a typical stop codon of TAA, whereas the remaining PCGs use incomplete stop codon of T or TA. All tRNAs have the typical clover-leaf structure with the exception of t RNA^（Ser）（AGN）. The lrRNA and sr RNA genes are 1,409 bp and 778 bp in size respectively, with the former harboring one（TA）_（13） microsatellite-like repeat and an 17 bp insertion. The 20 intergenic spacers totaling of 184 bp and 8 overlapping sequences totaling of 25 bp are scattered throughout the whole mitogenome. The 526 bp AT-rich region contains some structures characteristic of lepidopterans, such as the motif ATAGA preceded by an 19 bp poly-T stretch, a tRNA-like and a sterm-loop structures. Phylogenetic analysis of the Oreta fuscopurpurea with other 47 insect species covering 20 lepidopteran families were conducted based on the sequence data of the 13 mitogenomic protein coding genes with maximum likelihood（ML） and Bayesian inference（BI） methods, and the results showed distinctly that the superfamily Drepanoidea was sister to the clade of（Bombycoidea, Lasiocampoidea） ＋（Noctuoidea, Geometroidea）.
文摘为了解拟南芥中Dicer-like蛋白对tRNA衍生的小RNA(tRNA-derived small RNAs,tsRNAs)的产生有何影响,对拟南芥野生型和不同Dicer-like(DCL)基因突变体进行tRNA-seq测序,并分析tsRNA和tRNA的表达量.结果显示,DCL4基因突变后tsRNA的表达量明显降低,说明DCL4可能参与tsRNA的产生.拟南芥tRC1位点(Chr1:21268000-21310000)具有大量串联分布的tRNA序列,通过对RNA介导的甲基化(RdDM)途径相关基因CLSY1突变体中tRC1位点的24 nt siRNA和tsRNA进行分析,推断tRC1位点的tsRNA受RdDM途径负调控.综上,本研究鉴定到DCL4在tsRNA生成中的潜在作用,部分tsRNA的生成与RdDM途径有关.
基金supported by a grant from the Polish Medical Research Agency(2021/ABM/05/00004)The research was further funded by grants from the Polish National Science Centre(2016/21/N/NZ1/00564)+2 种基金the French State Program‘Investments for the future’(LABEX ANR-11-LABX-0057_MITOCROSS and ANR-10-LABX-0040-SPS)the French National Research Agency(ANR-06-MRAR-037-02 and ANR-09-BLAN-0240-01)R.V.was supported by a fellowship from CNRS and the French Région Alsace.
文摘Mutations in the small genome present in mitochondria often result in severe pathologies.Different genetic strategies have been explored,aiming to rescue such mutations.A number of these strategies were based on the capacity of human mitochondria to import RNAs from the cytosol and designed to repress the replication of the mutated genomes or to provide the organelles with wild-type versions of mutant transcripts.However,the mutant RNAs present in mitochondria turned out to be an obstacle to therapy and little attention has been devoted so far to their elimination.Here,we present the development of a strategy to knockdown mitochondrial RNAs in human cells using the transfer RNA-like structure of Brome mosaic virus or Tobacco mosaic virus as a shuttle to drive trans-cleaving ribozymes into the organelles in human cell lines.We obtained a specific knockdown of the targeted mitochondrial ATP6 mRNA,followed by a deep drop in ATP6 protein and a functional impairment of the oxidative phosphorylation chain.Our strategy provides a powerful approach to eliminate mutant organellar transcripts and to analyse the control and communication of the human organellar genetic system.
基金partially supported by the National Natural Science Foundation of China (Grant Nos. 90408028, 31171238, 30800642 and 10747150)the Program for New Century Excellent Talents in University of China (Grant No. NCET-120396) Tianjin Municipal Natural Science Foundation of China (Grant No. 09JCZDJC17100)
文摘Acinetobacter baumannii is an important opportunistic pathogeq in hospital, and tile multidrug-resistant isolates of A. haumannii have been increasingly reported i,a recent years. A num- ber of different mechanisms of resistance have been reported, some of which are associated with plasmid-mediated acquisition of genes. Therefore, studies on plasmids in A. haumannii have been a hot issue lately. We have performed complete genome sequencing of A. haumannii MDR-TJ, which is a multidrug-resistant isolate. Finalizing the remaining large scaffold of the previous assem- bly, we found a new plasmid pABTJ2, which carries many phage-like elements. The plasmid pAB- TJ2 is a circular double-stranded DNA molecule, which is 110,967 bp in length. We annotated 125 CDSs from pABTJ2 using IMG ER and ZCURVE_V, accounting lbr 88.28% of the whole plasmid sequence. Many phage-like elements and a tRNA-coding gene were detected in pABTJ2, which is rarely reported among A. haumannii. The tRNA gene is specific for asparagine codon GTT, which may be a small chromosomal sequence picked up through incorrect excision during plasmid forma- tion. The phage-like elements may have been acquired during the integration process, as the GC content of the region carrying phage-like elements was higher than that of the adjacent regions. The finding of phage-like elements and tRNA-coding gene in pABTJ2 may provide a novel insight into the study of A. haumannii pan-plasmidome.
