Intron retention and 3'-UTR analysis of Arabidopsis Dicer-like 2 transcripts

Arabidopsis thaliana Dicer-like protein 2 (AtDCL2) plays an essential role in the RNA interference pathway. The function of AtDCL2 and other DCLs has been much studied but little has been done to characterize the DCLs transcripts before they are translated into proteins. Here, we investigated AtDCL2 transcripts and showed that all 21 introns of AtDCL2 except intron 9, 18, 20 and 21 could be retained although spliced sequences usually predominated. Intron 10 was more frequently retained and transient expression assays in Nicotiana benthamiana leaves showed that when AG/C at the 3' splicing site of the intron was changed to AG/G, the intron was more frequently spliced out. Conversely, a high retention of intron 18 was obtained if the AG/G at the 3' splicing site was changed to AG/C. These results suggest that the sequence at the 3' splicing site affects the efficiency of intron splicing. The 3'-UTRs of AtDCL2 had lengths between 54 and 154 nts, and the different 3'-UTRs differentially affected the transcriptional levels of fused GFP expressed transiently in N. benthamiana. Further comparisons and mutation experiments suggested that a putative SBF-1 binding site and an AU-rich element in the 3'-UTR both down-regulated expression of the upstream GFP fused to the 3'-UTR. Conversely, a second poly(A) consensus signal sequence in one 3'-UTR up-regulated gene expression. Our results provide insight into the character of AtDCL2 transcripts and demonstrate the potential complexity of factors that affect the frequency and patterns of alternative splicing.

First Report of Basella rugose mosaic virus Infecting Four O'Clock (Mirabilis jalapa) in China

Four o'clock (Mirabilis jalapa) and M. himalaica var. chinensis are members of the family Nyctaginaceae and are widely distributed weeds in Yunnan Province, China. In 2009, mosaic and malformation symptoms were observed on leaves of the four o'clock on the campus of Yunnan Agricultural University and in the Black Dragon Pool Park in Kunming City, China. More than 30% of the four o'clock plants showed symptoms of the disease. Sap from leaves of symptomatic four o'clock plants caused local chlorotic and necrotic lesions in inoculated Chenopodium amaranticolor after 7 to 10 days and systemic mosaic symptoms in C. quinoa and Nicotiana benthamiana after 10 to 12 days. No symptoms were observed following inoculation of sap from asymptomatic plants. A pure virus isolate (MJ) was obtained after three successive single-lesion transfers from C. amaranticolor. Following mechanical inoculation of the MJ isolate, seedlings of indicator plants, N. benthamiana, displayed mosaic symptoms. Moreover, back transmission to healthy four o'clock seedlings by leaf extracts from systemically infected N. benthamiana plants caused similar mosaic and malformation symptoms. Flexuous, filamentous particles (650 to 700 nm long and 13 nm wide) and cytoplasmic laminar aggregates and pinwheel inclusions typical of members of the genus Potyvirus were observed in infected four o'clock leaves by electron microscopy. No other virus particles were observed. Serological testing of 10 symptomatic and healthy plants using a monoclonal antibody specific for Potyvirus group members in an indirect ELISA (Agdia Inc., Elkhart, IN) also resulted in positive reactions in infected leaves, however, all healthy seedlings tested were negative. Total RNAs were extracted from infected four o'clock leaves with the RNeasy Plant Mini Kit (QIAGEN, Hilden, Germany) and the 3'-terminal portion of the viral genome (including part of the NIb polymerase, the entire coat protein (CP), and 3'-UTR) was then amplified by reverse transcription-PCR with a universal Potyviridae primer Sprimer/M4 and an M4T as the initial primer (2). A fragment of 1,720 nucleotides long were separated, purified, and cloned and three independent clones were sequenced (GenBank Accession No. JN250997). Nucleotide and amino acid sequence analysis of the putative CP gene, respectively, revealed 75.1 to 76.3% and 80.3 to 82.1% identity with the Basella rugose mosaic virus (BaRMV) (GenBank Accession Nos. DQ821938, DQ394891, and DQ821939), 77.4 and 81.0% identity with Peace lily mosaic virus (GenBank Accession No. DQ851494), and 76.0 and 81.7% identity with the Phalaenopsis chlorotic spot virus (GenBank Accession No. HM021142). However, on the basis of the CP gene sequence analyses, these three viruses shared high (>88.5 and >94.3%) CP nucleotide and amino acid identity and should be classified as the same Potyvirus species. According to the species demarcation criteria for the Potyviridae (1), the pathogen causing mosaic and malformation symptoms on four o'clock was BaRMV (3). To our knowledge, this is the first report of BaRMV in four o'clock. References: (1) M. J. Adams et al. Arch. Virol. 150:459, 2005. (2) J. Chen et al. Arch. Virol. 146:757, 2001. (3) C. H. Hung and Y. C. Chang. Plant Pathol. 55:819, 2006.

Silencing of NbXrn4 facilitates the systemic infection of Tobacco mosaic virus in Nicotiana benthamiana

The 5'-3' exoribonucleases (Xrns) play key roles in degradation and processing pathways of several classes of RNAs including mRNA, rRNA, miRNA and other small RNAs. Recent work revealed that the cytoplasmic Xrn (Xrn1p in yeast and Xrn4 in plants) affected the stability of the viral RNA of tombusviruses in yeast and plants, which indicates that the cytoplasmic Xrn might be involved in plant defense against virus by degrading viral RNA. Here, we demonstrated that silencing of Nicotiana benthamiana cytoplasmic Xrn4 facilitated both local and systemic infection of Tobacco mosaic virus (TMV) in N. benthamiana. The results support the suggestion that cytoplasmic Xrn4 participates in the viral defense system of plants.

Mechanisms of transcriptional regulation and prognostic significance of activated leukocyte cell adhesion molecule in cancer

Background

Activated leukocyte cell adhesion molecule (ALCAM) is implicated in the prognosis of multiple cancers with low level expression associated with metastasis and early death in breast cancer. Despite this significance, mechanisms that regulate ALCAM gene expression and ALCAM's role in adhesion of pre-metastatic circulating tumor cells have not been defined. We studied ALCAM expression in 20 tumor cell lines by real-time PCR, western blot and immunochemistry. Epigenetic alterations of the ALCAM promoter were assessed using methylation-specific PCR and bisulfite sequencing. ALCAM's role in adhesion of tumor cells to the vascular wall was studied in isolated perfused lungs.

Results

A common site for transcription initiation of the ALCAM gene was identified and the ALCAM promoter sequenced. The promoter contains multiple cis-active elements including a functional p65 NF-κB motif, and it harbors an extensive array of CpG residues highly methylated exclusively in ALCAM-negative tumor cells. These CpG residues were modestly demethylated after 5-aza-2-deoxycytidine treatment. Restoration of high-level ALCAM expression using an ALCAM cDNA increased clustering of MDA-MB-435 tumor cells perfused through the pulmonary vasculature of ventilated rat lungs. Anti-ALCAM antibodies reduced the number of intravascular tumor cell clusters.

Conclusion

Our data suggests that loss of ALCAM expression, due in part to DNA methylation of extensive segments of the promoter, significantly impairs the ability of circulating tumor cells to adhere to each other, and may therefore promote metastasis. These findings offer insight into the mechanisms for down-regulation of ALCAM gene expression in tumor cells, and for the positive prognostic value of high-level ALCAM in breast cancer.

Effect of hypernatremia on injury caused by energy deficiency: role of T-type Ca2+ channel

Hypernatremia exerts multiple cellular effects, many of which could influence the outcome of an ischemic event. To further evaluate these effects of hypernatremia, isolated neonatal cardiomyocytes were chronically incubated with medium containing either normal (142 mM) or elevated sodium (167 mM) and then transferred to medium containing deoxyglucose and the electron transport chain inhibitor amobarbital. Chronic hypernatremia diminished the degree of calcium accumulation and reactive oxygen species generation during the period of metabolic inhibition. The improvement in calcium homeostasis was traced in part to the downregulation of the Ca(V)3.1 T-type calcium channel, as deficiency in the Ca(V)3.1 subtype using short hairpin RNA or treatment with an inhibitor of the Ca(V)3.1 variant of the T-type calcium channel (i.e., diphenylhydantoin) attenuated energy deficiency-mediated calcium accumulation and cell death. Although hyperosmotically stressed cells (exposed to 50 mM mannitol) had no effect on T-type calcium channel activity, they were also resistant to death during metabolic inhibition. Both hyperosmotic stress and hypernatremia activated Akt, suggesting that they initiate the phosphatidylinositol 3-kinase/Akt cytoprotective pathway, which protects the cell against calcium overload and oxidative stress. Thus hypernatremia appears to protect the cell against metabolic inhibition by promoting the downregulation of the T-type calcium channel and stimulating cytoprotective protein kinase pathways.

Alpha1G T-type calcium channel selectively regulates P-selectin surface expression in pulmonary capillary endothelium

Regulated P-selectin surface expression provides a rapid measure for endothelial transition to a proinflammatory phenotype. In general, P-selectin surface expression results from Weibel-Palade body (WPb) exocytosis. Yet, it is unclear whether pulmonary capillary endothelium possesses WPbs or regulated P-selectin surface expression and, if so, how inflammatory stimuli initiate exocytosis. We used immunohistochemistry, immunofluorescence labeling, ultrastructural assessment, and an isolated perfused lung model to demonstrate that capillary endothelium lacks WPbs but possesses P-selectin. Thrombin stimulated P-selectin surface expression in both extra-alveolar vessel and alveolar capillary endothelium. Only in capillaries was the thrombin-stimulated P-selectin surface expression considerably mitigated by pharmacologic blockade of the T-type channel or genetic knockout of the T-type channel alpha(1G)-subunit. Depolarization of endothelial plasma membrane via high K(+) perfusion capable of eliciting cytosolic Ca(2+) transients also provoked P-selectin surface expression in alveolar capillaries that was abolished by T-type channel blockade or alpha(1G) knockout. Our findings reveal an intracellular WPb-independent P-selectin pool in pulmonary capillary endothelium, where the regulated P-selectin surface expression is triggered by Ca(2+) transients evoked through activation of the alpha(1G) T-type channel.

A role of functional T-type Ca2+ channel in hepatocellular carcinoma cell proliferation

The role of T-type Ca2+ channels in hepatocellular carcinoma cell proliferation was investigated in vitro. Eleven hepatocellular carcinoma cell lines and one immortalized liver cell line (LO2) were examined for the status of T-type Ca2+ channels with RT-PCR and voltage-clamp recordings. Except HBxF344, other cell lines tested had one, two or all three of alpha1-subunits (alpha1G, alpha1H and alpha1I) mRNA expression. Obvious T-type current was recorded in SNU449 cells, while others exhibited a minimal or no T-type current. SNU449, PLC/PRF5, Hep3B and LO2 cell lines were subjected to growth assay in the presence of Mibefradil, a T-type Ca2+ channel blocker, only the proliferation of SNU449 cell which had functional T-type Ca2+ channel was reduced by Mibefradil treatment. Furthermore, the persistent increase of phosphorylated ERK1/2 in SNU449 cells was found when treated with Mibefradil. A microarray assay also demonstrated some down-regulated genes were mainly associated with cell cycle and cell proliferation in Mibefradil treated SNU449 cells. In conclusion, this study showed that the functional T-type Ca2+ channels probably participate in modulating the proliferation of some hepatocellular carcinoma cells. The cell proliferation reduction of SNU449 with Mibefradil treatment is possibly associated with the persistent increase of phosphorylated ERK1/2.

First Report of Botryosphaeria dothidea Causing Canker and Shoot Blight of Eucalyptus in China

Eucalyptus spp. are grown on approximately 2 million ha in China and is the most important genus in forest plantations worldwide. An outbreak of cankers and shoot blight was observed for the first time on Eucalyptus grandis in China during May of 2008. Symptoms included dieback of shoots and branches, lesions and canker formation on the stems, and clear or yellow-to-red exudates on stems and branches. Isolations were made from affected trees in Shilin County from May to July of 2008. Diseased samples were plated on potato dextrose agar (PDA) and incubated at 26°C. Fungal isolates developed copious, white, aerial mycelium that became dark gray after 5 to 6 days and formed black pycnidia after 14 days. Conidia were hyaline, aseptate, thin walled, fusiform, and measured 19 to 28 × 4 to 6 μm. Ascospores were hyaline, aseptate, and widest from the middle to upper third (17 to 28 × 6 to 13 μm). Identity was confirmed by analysis of the rDNA internal transcribed spacer region (ITSI-5.8S-ITS2) with primers ITS1 and ITS4. BLAST searches showed 99 to 100% identity with Botryosphaeria dothidea isolates from GenBank (Accession Nos. FJ358703 and EU080916). Representative sequences of B. dothidea from eucalyptus from China were deposited into GenBank (Accession Nos. FJ517657 and FJ517658). On the basis of morphological and molecular results, the fungus isolated from diseased eucalyptus wood was confirmed to be B. dothidea. Pathogenicity tests were conducted by stem inoculation of 10-month-old E. grandis seedlings. Two experiments were conducted using two inoculation techniques. In the first experiment, 2-mm-diameter actively growing mycelium plugs of B. dothidea were applied to 2-mm-long bark wounds on the middle point of the stems, and control seedlings were inoculated with sterile PDA plugs in a similar fashion as above. Inoculated and control seedlings were inoculated in a greenhouse and watered as needed. In the second experiment, segments of branches (averaging 18 mm in diameter and 30 cm long) were inoculated with 5-mm-diameter plugs of actively growing mycelium. Control segments of branches were inoculated as previously described. The branches were incubated at 26°C in moist chambers. There were five replicate seedlings per inoculation technique. After 20 days, all E. grandis seedlings showed leaf wilting, Dark, vascular stem tissue was observed. Symptoms were more abundant on the segment of branches. After 6 days, vascular necroses that developed on the inoculated plants were 5.2 ± 1.2 cm. B. dothidea was reisolated from all inoculated symptomatic tissue; no symptoms were visible in the control seedlings and no fungus was isolated from them. These results confirm previous reports of B. dothidea causing canker and dieback symptoms of Eucalyptus species in Australia (2), the United States (1), and South Africa (3). To our knowledge, this is the first report of B. dothidea causing canker disease on eucalyptus in China. References: (1) E. L. Barnard et al. Plant Dis. 71:358, 1987. (2) E. M. Davison and C. S. Tay. Plant Dis. 67:1285, 1983. (3) H. Smith et al. Plant Pathol. 43:1031, 1994.

Identification of novel splice variants of the Arabidopsis DCL2 gene

In Arabidopsis thaliana, Dicer-like protein 2 (DCL2) cleaves double-stranded virus RNA, playing an essential role in the RNA interference pathway. Here, we describe three alternative splicing (AS) forms of AtDCL2: in one, both intron 8 and intron 10 are retained in the mRNA, in second only intron 8 is retained and in the third no intron is retained, but there is a deletion of 56 nucleotides at the end of exon 10. These splicing forms are present in stems and leaves at different development stages. AS was also detected in DCL2 of Brassica rapa, where intron 9, but not intron 8 or intron 10, was retained suggesting that AS may be a common phenomenon in cruciferous plant DCL2s. The retained introns and sequence deletions detected in AtDCL2 changed the reading frame and produced premature terminal codons. The AS forms appeared to be substrates of nonsense-mediated decay of mRNA.

Molecular cloning and characterization of the Dicer-like 2 gene from Brassica rapa

Dicer-like proteins (DCLs) are involved in small RNA-mediated development and viral defense in plants. In model plants, at least four DCLs have been found and a number of studies have helped to understand their function. However, the function of the Dicer or DCLs in other plants is still unclear. Here, we report the full-length cDNA sequence of Brassica rapa ssp. chinensis DCL2 (BrDCL2) gene, which contains a 4,179 bp open reading frame (ORF) encoding a protein of 1,392 amino acids. At the 3' end of BrDCL2, clones with three different lengths of 3' untranslated region were found. An alternative splice variant of BrDCL2, BrDCL2sv, in which one intron was retained between exon9 and exon10, was also cloned. Because of a change in the coding sequence resulting in a premature terminal codon, BrDCL2sv was expected to translate a short peptide containing the whole DEXHc domain.

Microtubule motors regulate ISOC activation necessary to increase endothelial cell permeability

Calcium store depletion activates multiple ion channels, including calcium-selective and nonselective channels. Endothelial cells express TRPC1 and TRPC4 proteins that contribute to a calcium-selective store-operated current, I(SOC). Whereas thapsigargin activates the I(SOC) in pulmonary artery endothelial cells (PAECs), it does not activate I(SOC) in pulmonary microvascular endothelial cells (PMVECs), despite inducing a significant rise in global cytosolic calcium. Endoplasmic reticulum exhibits retrograde distribution in PMVECs when compared with PAECs. We therefore sought to determine whether endoplasmic reticulum-to-plasma membrane coupling represents an important determinant of I(SOC) activation in PAECs and PMVECs. Endoplasmic reticulum organization is controlled by microtubules, because nocodozole induced microtubule disassembly and caused retrograde endoplasmic reticulum collapse in PMVECs. In PMVECs, rolipram treatment produced anterograde endoplasmic reticulum distribution and revealed a thapsigargin-activated I(SOC) that was abolished by nocodozole and taxol. Microtubule motors control organelle distribution along microtubule tracks, with the dynein motor causing retrograde movement and the kinesin motor causing anterograde movement. Dynamitin expression reduces dynein motor function inducing anterograde endoplasmic reticulum transport, which allows for direct activation of I(SOC) by thapsigargin in PMVECs. In contrast, expression of dominant negative kinesin light chain reduces kinesin motor function and induces retrograde endoplasmic reticulum transport; dominant negative kinesin light chain expression prevented the direct activation of I(SOC) by thapsigargin in PAECs. I(SOC) activation is an important step leading to disruption of cell-cell adhesion and increased macromolecular permeability. Thus, microtubule motor function plays an essential role in activating cytosolic calcium transitions through the membrane I(SOC) channel leading to endothelial barrier disruption.

T-type Ca2+ channel expression in human esophageal carcinomas: a functional role in proliferation

In the present study the role of T-type Ca(2+) channels in cancer cell proliferation was examined. Seventeen human esophageal cancer cell lines were screened for T-type channels using RT-PCR and voltage-clamp recordings. mRNAs for all three T-type channel alpha(1)-subunits (alpha(1G), alpha(1H), and alpha(1I)) were detected in all 17 cell lines: either alpha(1H) alone, alpha(1H) and alpha(1G), or all three T-type alpha(1)-subunits. Eleven cell lines were further subjected to voltage-clamp recordings: one, i.e. the TE8 cell line, was found to exhibit a typical T-type current while others exhibited a minimal or no T-type current. Cell proliferation assays were performed in the presence or absence of T-type channel blocker mibefradil in KYSE150, KYSE180 and TE1 cells expressing mRNA for T-type channel alpha(1)-subunits but lacking T-type current, and TE8 cells exhibiting T-type current. Only TE8 cell proliferation was reduced by mibefradil. Silencing the alpha(1G)-gene that encodes functional T-type Ca(2+) channels in TE8 cells with type-specific shRNA transduction also significantly decreased TE8 cell proliferation. The reduction of cell proliferation in TE8 cells was found to be associated with an up-regulation of p21(CIP1). Moreover, p53 silencing nearly abolished the up-regulation of p21(CIP1) resulting from mibefradil T-type channel blockade. Together, these findings suggest a functional role of T-type channels in certain esophageal carcinomas, and that inhibition of T-type channels reduces cell proliferation via a p53-dependent p21(CIP1) pathway.

Cav3.1 (alpha1G) controls von Willebrand factor secretion in rat pulmonary microvascular endothelial cells

The T-type Ca2+ channel Cav3.1 subunit is present in pulmonary microvascular endothelial cells (PMVECs), but not in pulmonary artery endothelial cells (PAECs). The present study sought to assess the role of Cav3.1 in thrombin-induced Weibel-Palade body exocytosis and consequent von Willebrand factor (VWF) release. In PMVECs and PAECs transduced with a green fluorescent protein (GFP)-tagged VWF chimera, we examined the real-time dynamics and secretory process of VWF-GFP-containing vesicles in response to thrombin and the cAMP-elevating agent isoproterenol. Whereas thrombin stimulated a progressive decrease in the number of VWF-GFP-containing vesicles in both cell types, isoproterenol only decreased the number of VWF-GFP-containing vesicles in PAECs. In PMVECs, thrombin-induced decrease in the number of VWF-GFP-containing vesicles was nearly abolished by the T-type Ca2+ channel blocker mibefradil as well as by Cav3.1 gene silencing with small hairpin RNA. Expression of recombinant Cav3.1 subunit in PAECs resulted in pronounced increase in thrombin-stimulated Ca2+ entry, which is sensitive to mibefradil. Together, these data indicate that VWF secretion from lung endothelial cells is regulated by two distinct pathways involving Ca2+ or cAMP, and support the hypothesis that activation of Cav3.1 T-type Ca2+ channels in PMVECs provides a unique cytosolic Ca2+ source important for Gq-linked agonist-induced VWF release.

[Current situation and prospect of studies on genus Umbravirus]

Umbraviruses are a group of imperfectly characterized plant viruses, which are distinguished from most other viruses by their genomes lack of a gene for coat protein (CP) , and as a result umbraviruses do not form conventional virus particles. Umbraviruses are mechanically transmissible, and can be aphid transmitted in the persistent manner by an unrelated assistor virus, which is always a member of the family Luteoviridae . In nature, each umbravirus depends for survival on one particular luteovirus. The genus Umbravirus comprises seven distinct virus specieses and three tentative members. Only Tobacco bushy top virus (TBTV) has been reported in China as an umbravirus. Tobacco bushy top disease, caused by TBTV and its helper, Tobacco vein distorting virus(TVDV), which resulted in severe tobacco losses in western of Yunan. Umbraviruses had a restricted host range in nature, and their infectivity and longevity in vitro are not so stable. Plants infected umbraviruses contain abundant double-stranded RNA (dsRNA), and some umbraviruses possess one or more additional dsRNA species associated with the presence of a satellite RNA. The genomes of the umbraviruses consist of one linear segment of positive sense single-stranded RNA(ssRNA), and the nucleotide sequences possess ORFs for four potential non-structural protein products. The umbravirus-encoded ORF3 proteins play essential roles in stabilization of viral RNA and mediation of its long-distance movement. The current research progresses have been reviewed detailly, and the future research tendency and research fields about umbraviruses and umbravirus-caused diseases are put forward.