Long inverted repeats(LIRs) are evolutionarily and functionally important structures in genomes because of their involvement in RNA interference, DNA recombination, and gene duplication. Identification of LIRs is high...Long inverted repeats(LIRs) are evolutionarily and functionally important structures in genomes because of their involvement in RNA interference, DNA recombination, and gene duplication. Identification of LIRs is highly complicated when mismatches and indels between the repeats are permitted. Long inverted repeat explorer(Lirex) was developed and introduced in this report. Written in Java, Lirex provides a user-friendly interface and allows users to specify LIR searching criteria, such as length of the region, as well as pattern and size of the repeats. Recombinogenic LIRs can be selected on the basis of mismatch rate and internal spacer size from identified LIRs. Lirex, as a cross-platform tool to identify LIRs in a genome, may assist in designing following experiments to explore the function of LIRs. Our tool can identify more LIRs than other LIR searching tools. Lirex is publicly available at http://124.16.219.129/Lirex.展开更多
The leader sequence of the 16S rDNA gene from the Vicia faba chloroplast is reported in this paper. In this sequence, F1 and the X-protein gene are absent which can be explained by the genome rearrangement. Comparison...The leader sequence of the 16S rDNA gene from the Vicia faba chloroplast is reported in this paper. In this sequence, F1 and the X-protein gene are absent which can be explained by the genome rearrangement. Comparison of F3 of V. faba and those of other plant indicates that: (ⅰ) the conservative regions in F3 of V. faba are more consistent with the consensus sequences, (ⅱ) in F3 of V. faba, the region between --10 and the start point is richer in A-T, and (ⅲ) a stable stem-loop structure can form upstream the 5’ end of the 16S rRNA gene in Brassica napus, tobacco, maize and spinach, however, no such structure could form in V. faba. We conclude that the rDNA promoter of V. faba is more efficient and the single rDNA copy fulfils the role of the double rDNA copies by enhancing the rDNA transcription.展开更多
Unicellular micro-alga Chlamydomonas reinhardtii has been recognized as a promising host for expressing recombinant proteins albeit its limited utility due to low levels of heterologous protein expression. Here, trans...Unicellular micro-alga Chlamydomonas reinhardtii has been recognized as a promising host for expressing recombinant proteins albeit its limited utility due to low levels of heterologous protein expression. Here, transcription of the 3.4-kb mosquito-larvicidal cry4Ba gene from Bacillus thuringiensis in transgenic C. reinhardtii chloroplasts under control of the promoter and 5’-untranslated region of photosynthetic psbA gene was accomplished. Inverted repeats in chloroplast genomes of the host strain with deleted endogenous psbA genes were selected as recombination targets. Two transformant lines were obtained by dual-phenotypic screening via exhibition of resistance to spectinomycin and restoration of photosynthetic activity. Stable and site-specific integration of intact cry4Ba and psbA genes into chloroplast genomes found in both transgenic lines implied homoplasmy of organelle populations. Achievement in cotranscription of cry4Ba and psbA transgenes revealed by RT-PCR and Northern blot analyses demonstrates the sufficiency of this system’s transcription machinery, offering the further innovation for insecticidal protein production.展开更多
Results from a previous rice transcription mapping and the GeSTer algorithm analysis used in this in-vestigation for rice plastid genome suggest that an inverted repeat, IRs18, in 3′ region of the plastid rps18 gene ...Results from a previous rice transcription mapping and the GeSTer algorithm analysis used in this in-vestigation for rice plastid genome suggest that an inverted repeat, IRs18, in 3′ region of the plastid rps18 gene may serve as a transcription terminator. The in vitro transcription assay showed that the transcript ending at the IRs18 was not proc-essed by ribonucleases but terminated intrinsically in an rNTP substrate-dependent manner as demonstrated for the first time in plant gene regulation. For the poly-T tract (TTCTTTTTT) 3′-proximal to the IRs18, the C base conver-sion to T resulting in a perfect 9 Ts can dramatically increase termination efficiency, which is a common feature of bacte-rial intrinsic termination. This study is the first case to indi-cate that a conserved inverted repeat with a poly-T tract from higher plant chloroplast contributes to transcription termination of the translation-associated rps18 gene in a manner with the intrinsic termination, probably resulting from a heritage of endosymbiosis.展开更多
基金supported by the National Natural Science Foundation of China (Grant Nos. 41476104 and 31460001)the Strategic Priority Research Program of the Chinese Academy of Sciences (Grant No. XDB06010201)+1 种基金the International Science and Technology Cooperation Project of Hainan Province, China (Grant No. KJHZ2015-22)the support from the Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences (Grant Nos. SIDSSE-BR-201303 and SIDSSE-201305)
文摘Long inverted repeats(LIRs) are evolutionarily and functionally important structures in genomes because of their involvement in RNA interference, DNA recombination, and gene duplication. Identification of LIRs is highly complicated when mismatches and indels between the repeats are permitted. Long inverted repeat explorer(Lirex) was developed and introduced in this report. Written in Java, Lirex provides a user-friendly interface and allows users to specify LIR searching criteria, such as length of the region, as well as pattern and size of the repeats. Recombinogenic LIRs can be selected on the basis of mismatch rate and internal spacer size from identified LIRs. Lirex, as a cross-platform tool to identify LIRs in a genome, may assist in designing following experiments to explore the function of LIRs. Our tool can identify more LIRs than other LIR searching tools. Lirex is publicly available at http://124.16.219.129/Lirex.
文摘The leader sequence of the 16S rDNA gene from the Vicia faba chloroplast is reported in this paper. In this sequence, F1 and the X-protein gene are absent which can be explained by the genome rearrangement. Comparison of F3 of V. faba and those of other plant indicates that: (ⅰ) the conservative regions in F3 of V. faba are more consistent with the consensus sequences, (ⅱ) in F3 of V. faba, the region between --10 and the start point is richer in A-T, and (ⅲ) a stable stem-loop structure can form upstream the 5’ end of the 16S rRNA gene in Brassica napus, tobacco, maize and spinach, however, no such structure could form in V. faba. We conclude that the rDNA promoter of V. faba is more efficient and the single rDNA copy fulfils the role of the double rDNA copies by enhancing the rDNA transcription.
文摘Unicellular micro-alga Chlamydomonas reinhardtii has been recognized as a promising host for expressing recombinant proteins albeit its limited utility due to low levels of heterologous protein expression. Here, transcription of the 3.4-kb mosquito-larvicidal cry4Ba gene from Bacillus thuringiensis in transgenic C. reinhardtii chloroplasts under control of the promoter and 5’-untranslated region of photosynthetic psbA gene was accomplished. Inverted repeats in chloroplast genomes of the host strain with deleted endogenous psbA genes were selected as recombination targets. Two transformant lines were obtained by dual-phenotypic screening via exhibition of resistance to spectinomycin and restoration of photosynthetic activity. Stable and site-specific integration of intact cry4Ba and psbA genes into chloroplast genomes found in both transgenic lines implied homoplasmy of organelle populations. Achievement in cotranscription of cry4Ba and psbA transgenes revealed by RT-PCR and Northern blot analyses demonstrates the sufficiency of this system’s transcription machinery, offering the further innovation for insecticidal protein production.
文摘Results from a previous rice transcription mapping and the GeSTer algorithm analysis used in this in-vestigation for rice plastid genome suggest that an inverted repeat, IRs18, in 3′ region of the plastid rps18 gene may serve as a transcription terminator. The in vitro transcription assay showed that the transcript ending at the IRs18 was not proc-essed by ribonucleases but terminated intrinsically in an rNTP substrate-dependent manner as demonstrated for the first time in plant gene regulation. For the poly-T tract (TTCTTTTTT) 3′-proximal to the IRs18, the C base conver-sion to T resulting in a perfect 9 Ts can dramatically increase termination efficiency, which is a common feature of bacte-rial intrinsic termination. This study is the first case to indi-cate that a conserved inverted repeat with a poly-T tract from higher plant chloroplast contributes to transcription termination of the translation-associated rps18 gene in a manner with the intrinsic termination, probably resulting from a heritage of endosymbiosis.
