Ching Chun Chang

Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots

BackgroundVarious expansions or contractions of inverted repeats (IRs) in chloroplast genomes led to fluxes in the IR-LSC (large single copy) junctions. Previous studies revealed that some monocot IRs contain a trnH-rps19 gene cluster, and it has been speculated that this may be an evidence of a duplication event prior to the divergence of monocot lineages. Therefore, we compared the organizations of genes flanking two IR-LSC junctions in 123 angiosperm representatives to uncover the evolutionary dynamics of IR-LSC junctions in basal angiosperms and monocots.ResultsThe organizations of genes flanking IR-LSC junctions in angiosperms can be classified into three types. Generally each IR of monocots contains a trnH-rps19 gene cluster near the IR-LSC junctions, which differs from those in non-monocot angiosperms. Moreover, IRs expanded more progressively in monocots than in non-monocot angiosperms. IR-LSC junctions commonly occurred at polyA tract or A-rich regions in angiosperms. Our RT-PCR assays indicate that in monocot IRA the trnH-rps19 gene cluster is regulated by two opposing promoters, S10Aand psbA.ConclusionTwo hypotheses are proposed to account for the evolution of IR expansions in monocots. Based on our observations, the inclusion of a trnH-rps19 cluster in majority of monocot IRs could be reasonably explained by the hypothesis that a DSB event first occurred at IRB and led to the expansion of IRs to trnH, followed by a successive DSB event within IRA and lead to the expansion of IRs to rps19 or to rpl22 so far. This implies that the duplication of trnH-rps19 gene cluster was prior to the diversification of extant monocot lineages. The duplicated trnH genes in the IRB of most monocots and non-monocot angiosperms have distinct fates, which are likely regulated by different expression levels of S10Aand S10Bpromoters. Further study is needed to unravel the evolutionary significance of IR expansion in more recently diverged monocots.

Functional Analysis of Two Maize cDNAs Encoding T7-like RNA Polymerases

We have characterized two maize cDNAs, rpoTm and rpoTp, that encode putative T7-like RNA polymerases. In vivo cellular localization experiments using transient expression of the green fluorescent protein suggest that their encoded proteins are targeted exclusively to mitochondria and plastids, respectively. An antibody raised against the C terminus of the rpoTp gene product identified mitochondrial polypeptides of ~100 kD. Their presence was correlated with RNA polymerase activity, and the antibody inhibited mitochondrial in vitro transcription activity. Together, these results strongly suggest that the product of rpoTm is involved in maize mitochondrial transcription. By contrast, immunoblot analysis and an antibody-linked polymerase assay indicated that rpoTp specifies a plastid RNA polymerase component. A quantitative reverse transcription–polymerase chain reaction assay was used to study the transcription of rpoTp and rpoTm in different tissues and under different environmental conditions. Although both genes were constitutively expressed, rpoTm transcripts were generally more prevalent in nonphotosynthetic tissues, whereas an increase in rpoTp transcripts paralleled chloroplast development. We suggest that these two genes encode constitutive components of the organelle transcription machinery but that their expression is nonetheless subject to modulation during plant development.

Regulation of plastid rDNA transcription by interaction of CDF2 with two different RNA polymerases

The plastid genome is known to be transcribed by a plastid‐encoded prokaryotic‐type RNA polymerase (PEP) and by a nucleus‐encoded phage‐type RNA polymerase (NEP). The spinach plastid rrn operon promoter region harbours three different, overlapping promoters. Two of them are of the prokaryotic type. The third promoter is a non‐consensus‐type NEP promoter. We separated three different transcriptional activities from spinach chloroplasts: PEP, the phage‐type RNA polymerase NEP‐1, and a third, hitherto undescribed transcriptional activity (NEP‐2). NEP‐2 specifically transcribes the rrn operon in the presence of the transcription factor CDF2. CDF2 was previously shown to recruit PEP to the rrn promoter to repress transcription. Together, our results suggest the existence of a third RNA polymerase in plastids and a mechanism of rDNA transcriptional regulation that is based on the interaction of the transcription factor CDF2 with two different transcriptional systems.

Photosynthesis in Salt-Adapted Heterotrophic Tobacco Cells and Regenerated Plants.

Tobacco (Nicotiana tabacum L.) cells growing heterotrophically in the light on supplied sucrose (S0) have previously been adapted to grow in 428 mM NaCl (S25). Among the changes occurring in salinity-adapted cell cultures are (a) elevated levels of chlorophyll compared to unadapted cells; (b) decreased levels of starch; (c) alterations in chloroplast ultrastructure, including loss of starch grains, increased thylakoid membrane structure, and the presence of plastoglobules; and (d) increased rates of O2 evolution, CO2 fixation, and photophosphorylation relative to S0 cells. These latter changes apparently derive from the fact that thylakoid membranes in S25 cells contain higher levels of photosystem I- and II-associated proteins as well as thylakoid ATPase components. S25 chloroplasts contain immunologically detectable levels of ribulose-1,5-bisphosphate carboxylase/oxygenase, whereas S0 completely lack the enzyme. These changes taken together suggest that even in the presence of sucrose, S25 cells have acquired a significant degree of salt-tolerant photosynthetic competence. This salt-tolerant photoysynthetic capability manifests itself in plants backcrossed with normal plants for three generations. These plants contain chloroplasts that demonstrate in vitro more salt-tolerant CO2 fixation, O2 evolution, and photophosphorylation than do backcross progeny of plants regenerated from S0 cultures.

The comparative chloroplast genomic analysis of photosynthetic orchids and developing DNA markers to distinguish Phalaenopsis orchids

The chloroplast genome of Phalaenopsis equestris was determined and compared to those of Phalaenopsis aphrodite and Oncidium Gower Ramsey in Orchidaceae. The chloroplast genome of P. equestris is 148,959 bp, and a pair of inverted repeats (25,846 bp) separates the genome into large single-copy (85,967 bp) and small single-copy (11,300 bp) regions. The genome encodes 109 genes, including 4 rRNA, 30 tRNA and 75 protein-coding genes, but loses four ndh genes (ndhA, E, F and H) and seven other ndh genes are pseudogenes. The rate of inter-species variation between the two moth orchids was 0.74% (1107 sites) for single nucleotide substitution and 0.24% for insertions (161 sites; 1388 bp) and deletions (189 sites; 1393 bp). The IR regions have a lower rate of nucleotide substitution (3.5-5.8-fold) and indels (4.3-7.1-fold) than single-copy regions. The intergenic spacers are the most divergent, and based on the length variation of the three intergenic spacers, 11 native Phalaenopsis orchids could be successfully distinguished. The coding genes, IR junction and RNA editing sites are relatively more conserved between the two moth orchids than between those of Phalaenopsis and Oncidium spp.

Sesamin Inhibits Macrophage-Induced Vascular Endothelial Growth Factor and Matrix Metalloproteinase-9 Expression and Proangiogenic Activity in Breast Cancer Cells

Sesamin is a sesame component with antihypertensive and antioxidative activities and has recently aroused much interest in studying its potential anticancer application. Macrophage is one of the infiltrating inflammatory cells in solid tumor and may promote tumor progression via enhancement of tumor angiogenesis. In this study, we investigated whether sesamin inhibited macrophage-enhanced proangiogenic activity of breast cancer cell lines MCF-7 and MDA-MB-231. Using vascular endothelial cell capillary tube and network formation assays, both breast cancer cell lines exhibited elevated proangiogenic activities after coculture with macrophages or pretreatment with macrophage-conditioned medium. This elevation of proangiogenic activity was drastically suppressed by sesamin. Vascular endothelial growth factor (VEGF) and matrix metalloproteinase-9 (MMP-9) induced by macrophages in both cell lines were also inhibited by sesamin. Nuclear levels of HIF-1α and NF-κB, important transcription factors for VEGF and MMP-9 expression, respectively, were obviously reduced by sesamin. VEGF induction by macrophage in MCF-7 cells was shown to be via ERK, JNK, phosphatidylinositol 3-kinase, and NF-κB-mediated pathways. These signaling molecules and additional p38MAPK were also involved in macrophage-induced MMP-9 expression. Despite such diverse pathways were induced by macrophage, only Akt and p38MAPK activities were potently inhibited by sesamin. Expression of interleukin (IL)-6, IL-8, and tumor necrosis factor-α were substantially increased and involved in macrophage-induced VEGF and MMP-9 mRNA expression in MCF-7 cells. Sesamin effectively inhibited the expression of these cytokines to avoid the reinforced induction of VEGF and MMP-9. In conclusion, sesamin potently inhibited macrophage-enhanced proangiogenic activity of breast cancer cells via inhibition of VEGF and MMP-9 induction.

Early signalling pathways in rice roots under vanadate stress.

Vanadate is beneficial to plant growth at low concentration. However, plant exposure to high concentrations of vanadate has been shown to arrest cell growth and lead to cell death. We are interested in understanding the signalling pathways of rice roots in response to vanadate stress. In this study, we demonstrated that vanadate induced rice root cell death and suppressed root growth. In addition, we found that vanadate induced ROS accumulation, increased lipid peroxidation and elicited a remarkable increase of MAPKs and CDPKs activities in rice roots. In contrast, pre-treatment of rice roots with ROS scavenger (sodium benzoate), serine/threonine protein phosphatase inhibitor (endothall), and CDPK antagonist (W7), reduced the vanadate-induced MAPKs activation. Furthermore, the expression of a MAPK gene (OsMPK3) and four tyrosine phosphatase genes (OsDSP3, OsDSP5, OsDSP6, and OsDSP10) were regulated by vanadate in rice roots. Collectively, these results strongly suggest that ROS, protein phosphatase, and CDPK may function in the vanadate-triggered MAPK signalling pathway cause cell death and retarded growth in rice roots.

Biochemical Characterization of an Acid Phosphatase from Thermus thermophilus

A recombinant putative acid phosphatase from Thermus thermophilus was expressed and purified from Escherichia coli. The recombinant phosphatase displayed activities in a broad range of temperature, from 40 to 90 °C, with optimal temperature at 70 °C. In addition, the recombinant enzyme had activities in a wide range of pH, from 3.6 to 9.1, with optimal pH at 6 in acetate buffer and with optimal pH at 6.5 in Hepes buffer. Furthermore, it showed significant thermal stability and still possessed 44% residual activity after 70 °C treatment for 15 min. Moreover, the recombinant phosphatase showed broad substrates specificities for monophosphate esters, p-nitrophenyl phosphate (pNPP) being the most preferred substrate, and it was able to resist inhibition by sodium tartrate. Additionally, the recombinant protein formed stable oligomer under partially denatured conditions and required calcium ions for enzymic activity.

The mitochondrial DNA markers for distinguishing Phalaenopsis species and revealing maternal phylogeny

Moth orchids (Phalaenopsis) are among the top-traded blooming potted plants in the world. To explore mitochondrial DNA (mtDNA) markers for species identification, we located simple sequence repeats in the mtDNA of Phalaenopsis aphrodite subsp. formosana and then pre-screened them for polymorphic markers by their comparison with corresponding mtDNA regions of P. equestris. The combination of 13 selected markers located in intergenic spacers could unambiguously distinguish 15 endemic moth orchids. Five most variable markers with polymorphic information content (PIC) ≥ 0.7 could be combined to classify 18 of 19 endemic moth orchids including parental strains most commonly used in breeding programs. The sequences of four selected mtDNA regions were highly variable, and one region (MT2) could be used to completely distinguish 19 endemic moth orchids. Though mitochondrial introns were highly conserved among moth orchids, evolutionary hotspots, such as variable simple sequence repeats and minisatellite repeats, were identified as useful markers. Furthermore, a marker technology was applied to reveal the maternal inheritance mode of mtDNA in the moth orchids. Moreover, phylogenetic analysis indicates that the mtDNA was nonmonophyletic below the Phalaenopsis genus. In summary, we have revealed a set of mtDNA markers that could be used for identification and phylogenetic study of Phalaenopsis orchids.

Expression of avian reovirus minor capsid protein in plants

The minor coat protein of the avian reovirus (ARV), σC, encoded by the S1 genome segment, is one of the major candidates for the development of a subunit vaccine against ARV infection. To develop a plant-based vaccine to immunize poultry against ARV infection, we constructed 4 plant nuclear expression vectors with or without codon modification of the S1 gene, and their expression was driven by a CaMV 35S promoter or rice actin1 promoter. In addition, the expressed σC proteins were targeted subcellularly to cytosol or chloroplasts, respectively. Agrobacterium containing the S1 expression constructs was used to transform tobacco leaf disks, and transformants were selected with kanamycin (100 μg/ml). The integration of the S1 transgene into the tobacco chromosome was confirmed by PCR and Southern blot analysis. Western blot analysis with antiserum against σC was performed to determine the expression of σC protein in transgenic tobacco plants. The highest expression levels of σC protein in the cellular extracts of selected p35S1, pActS1 and p35UmS1 transgenic lines were 0.013%, 0.021% and 0.0013% of the total soluble protein, respectively, but the protein was barely detectable in p35TmS1 transgenic lines. However, the level of σC protein expression was not associated with the level of corresponding RNA transcripts in selected transgenic lines. Taken together, the results suggest that the major limiting factor for the expression of σC protein in plants might be at the post-transcriptional level.