Organization and nucleotide sequence of genes at both junctions between the two inverted repeats and the large single-copy region in the rice chloroplast genome

Effect of microRNA-455-5p (miR-455-5p) on the Expression of the Cytokine Signaling-3 (SOCS3) Gene During Myocardial Infarction

To explore the effect of microRNA-455-5p (miR-455-5p) and Cytokine Signaling-3 (SOCS3) expression, a model of the cell damage induced during myocardial infarction was established using H2O2. The cell counting Kit-8 (CCK-8) and quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) assays were used to detect the cell viability and the expression of miR-455-5p and SOCS3 in cells cultured with different concentrations of H2O2. After the selection of the optimum culture concentration, a dual-luciferase reporter gene assay was used to detect the binding between and miR-455-5p and its potential target SOCS3. SOCS3 siRNA was transfected into cardiomyocytes using chitosan nanoparticles as a gene carrier, which led to the knockdown of SOCS3 expression, and the cells were transfected with miR-455-5p mimics and inhibitors. The expression of cardiac protective proteins was detected by western blotting, cell viability was detected by CCK8, and cell apoptosis was detected by flow cytometry. The aim of this study was to investigate the effect of miR-455-5p and SOCS3 expression on the activity and apoptosis of damaged cardiomyocytes, and to identify any protective effect on cardiomyocytes. Finally, after the simultaneous overexpression of SOCS3 and miR-455-5p, and the expression of cardiac protective proteins, cell activity, and apoptosis rate were detected. The results showed that the expression of miR-455-5p decreased in a concentration-dependent manner and that the expression of SOCS3 increased in a concentration-dependent manner when the cells were cultured in different concentrations of H2O2. The knockdown of SOCS3 expression promoted an increase in cell activity, an increase in cardiac protective proteins, and a decrease in apoptosis. The upregulation of miR-455-5p significantly inhibited the expression of SOCS3, increased cell activity, inhibited apoptosis, and exerted protective effects in myocardial cells. The overexpression of SOCS3 reversed the inhibition of SOCS3 by miR-455-5p and reduced the protective effect of miR-455-5p on myocardial cells. Therefore, this study showed that the upregulation of miR-455-5p significantly inhibited the expression of SOCS3 and resulted in the increased protection of cells damaged by H2O2, which was used as a model of myocardial infarction. These results indicate the potential of miR-455-5p in myocardial protection, suggesting that miRNA may be a resource for myocardial therapy.

SIX INDEPENDENT LOSSES OF THE CHLOROPLAST DNA rpl2 INTRON IN DICOTYLEDONS: MOLECULAR AND PHYLOGENETIC IMPLICATIONS

Previous studies have shown that in several angiosperms and the liverwort Marchantia the chloroplast gene rpl2, encoding ribosomal protein L2, is interrupted by an intron, but that in spinach (Spinacia oleracea, Caryophyllales) this intron has been lost. We have determined the distribution of the rpl2 intron for 390 species representing 116 angiosperm families. Filter hybridizations reveal that the intron is absent from the chloroplast genomes of all examined families of the Caryophyllales, suggesting that the intron was lost in the common ancestor of the order. Sequencing of the rpl2 gene in five genera of the Caryophyllales and in Rumex (Polygonales) not only confirms the filter hybridization results, but also shows that for all taxa lacking the intron, the rpl2 gene has undergone a precise deletion of the intron. In all cases, it is the original rpl2 gene that has sustained loss of its intron. This implies that in chloroplast DNA, integration of exogenous genes (e.g., a reverse transcript of a spliced mRNA) occurs mainly by homologous, replacement recombination, rather than by illegitimate recombination elsewhere in the genome. Filter hybridizations also reveal that the rpl2 intron was lost independently in the common ancestors of at least five other lineages of dicotyledons: Saxifragaceae (s.s.), Convolvulaceae (including Cuscuta), Menyanthaceae, two genera of Geraniaceae, and one genus of Droseraceae. The molecular and phylogenetic implications of these independent intron losses are discussed.

Poly(ADP-ribose) polymerase interacts with novel Drosophila ribosomal proteins, L22 and l23a, with unique histone-like amino-terminal extensions

Poly(ADP-ribose) polymerase (PARP) is a nuclear enzyme that recognizes and binds to the nicks and ends of DNA, and catalyses successive ADP-ribosylation reactions. To clarify the function of PARP at the molecular level, we searched proteins which interact with PARP. In the auto-modification domain of PARP in Drosophila, there is a putative leucine-zipper motif which can interact with other protein molecules. To find interacting proteins we examined the auto-modification domain of Drosophila PARP, using the Far-Western screening method. From six independent cDNA clones isolated, we characterized two clones, PBP-3 and PBP-12. The predicted amino acid sequences from 109 to 269 of PBP-3 and from 184 to 312 of PBP-12 had more than 62% identities to mammalian L23a (rpl23a) and L22 (rpl22), the ribosomal proteins of the large subunit. This indicated that PBP-3 and PBP-12 are Drosophila homologues of L23a and L22, respectively. These Drosophila ribosomal protein L22 and L23a have additional Ala-, Lys- and Pro-rich sequences at the amino terminus, which have a resemblance to the carboxy-terminal portion of histone H1. Thus, Drosophila L22 and L23a might have two functions, namely the role of DNA-binding similar to histone H1 and the role of organizing the ribosome.

Differential expression of the partially duplicated chloroplast S10 ribosomal protein operon

The chloroplast S10 ribosomal protein operon is partially duplicated in many plants because it initiates within the inverted repeat of the circular chloroplast genome. In spinach, the complete S10 operon (S10B) spans the junction between inverted repeat B (IRB) and the large single-copy (LSC) region. The S10 operon is partially duplicated in the inverted repeat A (IRA), but the sequence of S10A completely diverges from S10B at the junction of S10A and the LSC region. The DNA sequence shared by S10A and S10B includes trnI1, the rpl23 pseudogene (rpl23 psi), the intron-containing rpl2 and rps19, which is truncated in S10A at the S10A/LSC junction (rps19'). Transcription of rps19' from the promoter region of S10A could result in the synthesis of a mutant S19 protein. Analysis of RNA accumulation and run-on transcription from S10A and S10B using unique probes from the S10A/LSC and S10B/LSC junctions reveals that expression of S10A is reduced. The difference in S10A and S10B expression appears to be the result of reduced transcription from S10A, rather than differences in RNA stability. Transcription of S10B can initiate at three distinct promoter regions, P1, P2 and P3, which map closely to transcripts detected by S1 nuclease analysis. P1 is located upstream of trnI1 and has the highest transcription initiation frequency in vitro of the three promoter regions. The DNA sequence of P1 is most similar to the chloroplast promoter consensus DNA sequence. Interference by the highly and convergently transcribed psbA-trnH1 operon is considered as a mechanism to explain the reduced activity of the S10A promoters.

RNA editing in plant mitochondria and chloroplasts

In the mitochondria and chloroplasts of flowering plants (angiosperms), transcripts of protein-coding genes are altered after synthesis so that their final primary nucleotide sequence differs from that of the corresponding DNA sequence. This posttranscriptional mRNA editing consists almost exclusively of C-to-U substitutions. Editing occurs predominantly within coding regions, mostly at isolated C residues, and usually at first or second positions of codons, thereby almost always changing the amino acid from that specified by the unedited codon. Editing may also create initiation and termination codons. The net effect of C-to-U RNA editing in plants is to make proteins encoded by plant organelles more similar in sequence to their nonplant homologs. In a few cases, a strong argument can be made that specific C-to-U editing events are essential for the production of functional plant mitochondrial proteins. Although the phenomenon of RNA editing in plants is now well documented, fundamental questions remain to be answered: What determines the specificity of editing? What is the biochemical mechanism (deamination, base exchange, or nucleotide replacement)? How did the system evolve? RNA editing in plants, as in other organisms, challenges our traditional notions of genetic information transfer.

Rice mitochondrial genome contains a rearranged chloroplast gene cluster

We have previously reported the isolation and partial sequence analysis of a rice mitochondrial DNA fragment (6.9 kb) which contains a transferred copy of a chloroplast gene cluster coding for the large subunit of ribulose-1,5-bisphosphate carboxylase (rbcL), beta and epsilon subunits of ATPase (atpB and atpE), methionine tRNA (trnM) and valine tRNA (trnV). We have now completely sequenced this 6.9 kb fragment and found it to also contain a sequence homologous to the chloroplast gene coding for the ribosomal protein L2 (rpl2), beginning at a site 430 bp downstream from the termination codon of rbcL. In the chloroplast genome, two copies of rpl2 are located at distances of 20 kb and 40 kb, respectively, from rbcL. We have sequenced these two copies of rice chloroplast rpl2 and found their sequences to be identical. In addition, a 151 bp sequence located upstream of the chloroplast rpl2 coding region is also found in the 3' noncoding region of chloroplast rbcL and other as yet undefined locations in the rice chloroplast genome. Hybridization analysis revealed that this 151 bp repeat sequence identified in rice is also present in several copies in 11 other plant species we have examined. Findings from these studies suggest that the translocation of rpl2 to the rbcL gene cluster found in the rice mitochondrial genome might have occurred through homologous recombination between the 151 bp repeat sequence present in both rpl2 and rbcL.