• Proceedings of the Botanical Society of Korea Conference
• /
• 1987.07a
• /
• pp.391-401
• /
• 1987

Plant chloroplast DNA exists as an unique circular structure in which large single copy(LSC) region and small single copy (SSC) region are separated by large inverted repeat sequences (IRS). It has been known that the unique existence of inverted repeat sequences in chloroplast DNA has no relation with the stability of the chloroplast DNA, but causes the inversion between inverted repeat its biological significance has not been understood so far. In rice, several gene clusters have been cloned and sequenced which contain ribulose-5-biophosphate car-boxylase large subunit (rbcL). Especially, one rbcL gene is linked with rp12 gene which is located in the IRS region in one of the gene clusters. By comparison of nucleotide sequence, the two genes are found to be linked through 151 bp repeat sequence which is homologous to the rp123 gene in IRS region. The repeat sequence is found to be located 3' downstream of rfcL gene and near psbA gene in LSC region. The existence of these repeat sequences and the presence of gene clusters caused by the gene rearrangement thorough the repeat sequence provide a possible which is found to be dispersed chloroplast DNA provide the model system to explaine the heterogeneity of the chloroplast DNA in rice in term of gene rearrangement.

• Journal of Microbiology
• /
• v.37 no.4
• /
• pp.229-233
• /
• 1999

The mitochondrial plasmid pMLP1 from a white-rot fungus, Pleurotus ostreatus, is a double-stranded DNA containing 381 bp terminal inverted repeat (TIR) whose 5'-ends are covalently bound by terminal proteins. The plasmid contains two major open reading frames (ORFs), encoding putative DNA and RNA polymerases, and a minor ORF encoding a small, highly basic protein. To identify the DNA binding activity that recognizes the TIR region of pMLP1, gel retardation assays were performed with mitochondrial extracts. A specific protein binding to a region between 123 and 248 nt within TIR was observed. We examined whether the gene product of mORF1 bindes to this region specifically. E. coli cell extract which contains an overproduced mORF1 protein formed a complex specific to the region between 123 and 248 nt. Inclusion of mORF1 protein in the specific complex formed between P. ostreatus mitochondrial extract and TIR was confirmed by a supershift assay using polyclonal antibodies against the mORF1 protein. Our result suggest that the product of mORF1 may function as a terminal region recognition factor (TRF), recognizing an internal region in TIR.

• Journal of Plant Biotechnology
• /
• v.46 no.4
• /
• pp.323-330
• /
• 2019

The high expression level of industrial and metabolically important proteins in plants can be achieved by plastid transformation. The CaIA vector, a Capsicum-specific vector harboring aadA (spectinomycin resistance), is a selectable marker controlled by the PsbA promoter, and the terminator is flanked by the trnA and trnI regions of the inverted repeat (IR) region of the plastid. The CaIA vector can introduce foreign genes into the IR region of the plastid genome. The biolistic method was used for chloroplast transformation in Scoparia dulcis with leaf explants followed by antibiotic selection on regeneration medium. Transplastomes were successfully screened, and the transformation efficiency of 3 transgenic lines from 25 bombarded leaf explants was determined. Transplastomic lines were evaluated by PCR and Southern blotting for the confirmation of aadA insertion and its integration into the chloroplast genome. Seeds collected from transplastomes were analyzed on spectinomycin medium with wild types to determine genetic stability. The increased chloroplast transformation efficiency (3 transplastomic lines from 25 bombarded explants) would be useful for expressing therapeutically and industrially important genes in Scoparia dulcis L.

• Korean Journal of Plant Taxonomy
• /
• v.53 no.3
• /
• pp.230-236
• /
• 2023

Rhododendron caucasicum Pall. is a shrub distributed in the mountainous areas of the Caucasus from northeastern Türkiye towards the Caspian Sea. This study reports the first complete chloroplast genome sequence of R. caucasicum. The plastome is 199,487 base pairs (bp) long and exhibits a typical quadripartite structure comprising a large single-copy region of 107,645 bp, a small single-copy region of 2,598 bp, and a pair of identical inverted repeat regions of 44,622 bp each. It contains 143 genes, comprising 93 protein-coding genes, 42 tRNA genes, and eight rRNA genes. The large chloroplast genome size is likely due to the expansion of inverted repeats. A phylogenetic analysis of chloroplast genomes with other Rhododendron species supports previously recognized infrageneric relationship.

• BMB Reports
• /
• v.40 no.3
• /
• pp.404-411
• /
• 2007

Transformation of cantaloupes with the coat protein (cp) gene of papaya ringspot virus type W (PRSV-W), Thai isolate, was used to introduce virus resistance. Binary vectors containing either the full length coat protein coding region under control of the 35S CaMV promoter(pSA1175), or the inverted-repeat of a coat protein coding region (pSA1304), were constructed and used for Agrobacteriummediated transformation of cotyledonary explants of the cantaloupe cultivar Sun Lady. Four independent transgenic lines were obtained using pSA1304 and one using pSA1175. Integration of the PRSV-W cp gene into the genome of these transgenic lines was verified by PCR amplification, GUS assays and Southern blot hybridization. In vitro inoculation of these lines with PRSV-W revealed that whereas the line containing pSA1175 remained sensitive, the four lines containing pSA1304 were resistant. The presence of small RNA species, presumably siRNA, corresponding to regions of the viral cp gene in transgenic lines resistant to PRSV-W supports the involvement of post-transcriptional gene silencing in the establishment of resistance.

• Molecules and Cells
• /
• v.26 no.4
• /
• pp.387-395
• /
• 2008

A novel Tc1-like transposable element has been identified as a new DNA transposon in the mud loach, Misgurnus mizolepis. The M. mizolepis Tc1-like transposon (MMTS) is comprised of inverted terminal repeats and a single gene that codes Tc1-like transposase. The deduced amino acid sequence of the transposase-encoding region of MMTS transposon contains motifs including DDE motif, which was previously recognized in other Tc1-like transposons. However, putative MMTS transposase has only 34-37% identity with well-known Tc1, PPTN, and S elements at the amino acid level. In dot-hybridization analysis used to measure the copy numbers of the MMTS transposon in genomes of the mud loach, it was shown that the MMTS transposon is present at about $3.36{\times}10^4$ copies per $2{\times}10^9$ bp, and accounts for approximately 0.027% of the mud loach genome. Here, we also describe novel MMTS-like transposons from the genomes of carp-like fishes, flatfish species, and cichlid fishes, which bear conserved inverted repeats flanking an apparently intact transposase gene. Additionally, BLAST searches and phylogenetic analysis indicated that MMTS-like transposons evolved uniquely in fishes, and comprise a new subfamily of Tc1-like transposons, with only modest similarity to Drosophila melanogaster (foldback element FB4, HB2, HB1), Xenopus laevis, Xenopus tropicalis, and Anopheles gambiae (Frisky).

• Genomics & Informatics
• /
• v.1 no.1
• /
• pp.55-60
• /
• 2003

The nucleotide sequence of pZMO1, a small cryptic plasmid of Zymomonas mobilis ATCC10988 was determined. Analysis of 1,680 bp of sequence revealed $69\%$ identity with Shigella sonnei plasmid, pKYM and $61\%$ identity with Nostoc sp. ss DNA replicating plasmid. Analysis of a deduced amino acid sequence of an orf of pZMO1 revealed $75\%$ identity and $90\%$ similarity with the repA gene of Synechocystis sp. plasmid pCA2.4. The upstream region of the repA gene of pZMO1 possesses six directed repeat sequences and two inverted repeat sequences at downstream of the IR consensus sequence of nick region of rolling circle replication (RCR) plasmid. A typical terminator hairpin structure was found at the downstream region of repA gene. Degradation of single-stranded plasmid DNA by S1 nuclease was detected by Southern hybridization. It suggests that pZMO1 replicates by a rolling circle mechanism in Z. mobilis ATCC10988 cells.

• BMB Reports
• /
• v.40 no.4
• /
• pp.577-587
• /
• 2007

Single-copy chloroplast loci are used widely to infer phylogenetic relationship at different taxonomic levels among various groups of plants. To test the utility of chloroplast loci and to provide additional data applicable to hybrid evolution in Musa, we sequenced two introns, rpl16 and ndhA, and two intergenic spacers, psaA-ycf3 and petA-psbJ-psbL-psbF and combined these data. Using these four regions, Musa acuminata Cola(A)- and M. balbisiana Colla (B)-containing genomes were clearly distinguished. Some triploid interspecific hybrids contain A-type chloroplasts (the AAB/ABB) while others contain B-type chloroplasts (the BBA/BBB). The chloroplasts of all cultivars in 'Namwa' (BBA) group came from the same wild maternal origin, but the specific parents are still unrevealed. Though, average sequence divergences in each region were little (less than 2%), we propose that petA-psbJ intergenic spacer could be developed for diversity assessment within each genome. This segment contains three single nucleotide polymorphisms (SNPs) and two indels which could distinguish diversity within A genome whereas this same region also contains one SNP and an indel which could categorize B genome. However, an inverted repeat region which could form hairpin structure was detected in this spacer and thus was omitted from the analyses due to their incongruence to other regions. Until thoroughly identified in other members of Musaceae and Zingiberales clade, utility of this inverted repeat as phylogenetic marker in these taxa are cautioned.

• Proceedings of the Plant Resources Society of Korea Conference
• /
• 2018.04a
• /
• pp.40-40
• /
• 2018

Pseudostellaria Pax (Caryophyllaceae) is a small genus distributed in temperate region. It consists of 25 species presenting high diversity in Asia. Pseudostellaria longipedicellata S. Lee, K. Heo & S. C. Kim was first announced as new species in 2012. Morphological characters of P. longipedicellata are closely related to those of Psedusotellaria palibiniana and Psedusotellaria okmotoi. These are distinguished from P. longipedicellata by shorter pedicel and puberulent pedicels, respectively and by being distributed allopatically between P. longipedicellata and rest of species. The complete chloroplast genome of P. longipedicellata was successfully rescued from raw reads generated by HiSeq2000. Its total length is 149,626 bp consisting of four regions: large single copy (LSC) region (81,292 bp), small single copy (SSC) region (16,984bp), and inverted repeats (IRs; 25,765 bp per each). It contained 126 genes (81 coding DNA sequence (CDS), eight rRNAs, and 37 tRNAs); 18 genes (seven CDS, four rRNAs, and seven tRNAs) are duplicated in inverted repeat regions. The overall GC content of P. longipedicellata is 36.5% and in the LSC, SSC, and IR regions were 34.3%, 29.3%, and 42.4%, respectively. Based on phylogenetic analysis of chloroplast genomes of P. longipedicellata and relatives species presents clear phylogenetic positions of Pseudostellaria genus. This chloroplast genome will be an important sequence resources for further researches of Pseudostellaria genus.

• Molecules and Cells
• /
• v.19 no.1
• /
• pp.104-113
• /
• 2005

Large inversions are well characterized in the chloroplast genomes of land plants. In contrast, reports of small inversions are rare and involve limited plant groups. In this study, we report the widespread occurrence of small inversions ranging from 5 to 50 bp in fully and partially sequenced chloroplast genomes of both monocots and dicots. We found that small inversions were much more common than large inversions. The small inversions were scattered over the chloroplast genome including the IR, SSC, and LSC regions. Several small inversions were uncovered in chloroplast genomes even though they shared the same overall gene order. The majority of these small inversions were located within 100 bp downstream of the 3' ends of genes. All had inverted repeat sequences, ranging from 11 to 24 bp, at their ends. Such small inversions form stem-loop hairpin structures that usually have the function of stabilizing the corresponding mRNA molecules. Intra-molecular recombination between the inverted sequences in the stem-forming regions are responsible for generating flip-flop orientations of the loops. The presence of two different orientations of the stem-loop in the trnL-F noncoding region of a single species of Jasminum elegans suggests that a short inversion can be generated within a short period of time. Small inversions of non-coding sequences may influence sequence alignment and character interpretation in phylogeny reconstructions, as shown in nine species of Jasminum. Many small inversions may have been generated by parallel or back mutation events during chloroplast genome evolution. Our data indicate that caution is needed when using chloroplast non-coding sequences for phylogenetic analysis.