Wnt5a Signaling in Normal and Cancer Stem Cells.

Wnt5a is involved in activating several noncanonical Wnt signaling pathways, which can inhibit or activate canonical Wnt/β-catenin signaling pathway in a receptor context-dependent manner. Wnt5a signaling is critical for regulating normal developmental processes, including stem cell self-renewal, proliferation, differentiation, migration, adhesion, and polarity. Moreover, the aberrant activation or inhibition of Wnt5a signaling is emerging as an important event in cancer progression, exerting both oncogenic and tumor suppressive effects. Recent studies show the involvement of Wnt5a signaling in regulating normal and cancer stem cell self-renewal, cancer cell proliferation, migration, and invasion. In this article, we review recent findings regarding the molecular mechanisms and roles of Wnt5a signaling in stem cells in embryogenesis and in the normal or neoplastic breast or ovary, highlighting that Wnt5a may have different effects on target cells depending on the surface receptors expressed by the target cell

Structure and Temperature Regulated Expression of a Cysteine Proteinase Gene in Pachysandra terminalis Sieb. & Zucc.

A cysteine proteinase gene (DQ403257) with an open reading frame of 1125 base pairs was isolated from Pachysdandra terminalis. The primary translated peptide has a predicted length of 374 amino acids, pI (isoelectric point) of 5.70, and molecular mass of 40.9 kDa. The Peptidase_C1 domain is between residue 141 and 367. The proteinase has a conserved motif Gly-Xaa-Thy-Xaa-Phe-Xaa-Asn in the pro region. Sequence comparison shows that the deduced peptide shares 82% identity with the cysteine proteinase RD19a precursor (RD19) (accession P43296) from Arabidopsis thaliana (L.) Heynh. Real-time quantitative reverse-transcriptase–polymerase chain reaction revealed that the gene is induced by treatments of 1 to 7 days of darkness, 2 hours and 3 to 7 days at 5 °C, and 3 days at 38 °C

Microarray analysis of genes affected by salt stress in tomato

Large-scale gene expression affected by salt stress was analyzed with tomato seedlings (Lycoperson esculentum Mill cv. Money Maker) by a cDNA microarray (Tom1). The significantly differentially expressed genes (5% Benjamini-Hochberg false discovery rate) consisted of 1757 sequences in the analyzed tissues (cotyledons + shoot tip). Genes with over 2 fold difference were selected from the list and further categorized into different function and cellular processes. Tomato homologous genes for the chaperone proteins, antioxidant enzymes (catalase and peroxidase), and ion transporters (Na+- driven multidrug efflux pump, vacuolar ATPase, and others) were induced. The ACC oxidase and ethylene-responsive gene tomato homologs had higher transcript level after salt treatment. Multiple members with different expression patterns were identified for the bZIP, WRKY, and MADS-box transcription regulator. Different genes in the signal transduction pathway, such as the protein kinases (Shaggy kinase, mitogen-activated protein kinase, ethylene receptor neverripe, and others), protein phosphatases, calmodulin, G-protein, and the N- myristoyltransferase were regulated by salt stress. Most of the protease and the inhibitor homologs were suppressed by salt stress. In addition, different isoforms of cytochrome P450, genes for polyamine biosynthesis (putrescine and proline) and detoxification compounds (glutathione and thioredoxin), several key enzyme genes in the metabolic pathways of carbohydrates, amino acids, and fatty acids, were also affected by salt treatment. This study has provided a set of candidate genes, especially those in the regulatory machinery that can be further investigated to define salt stress in tomato and other plant species.Keywords: Antioxidants, cellular metabolism, cell wall, chaperonine, ethylene, protein kinase, tomato, transcription regulator, translation regulator, salt stres

Salt-induced and Salt-suppressed Proteins in Tomato Leaves

Tomato (Solanum lycopersicum cv. Money Maker) seedlings at the two-leaf stage were grown in one-half strength Hoagland solution supplemented with 50 mm NaCl for 4 days, with 100 mm NaCl for 4 days, with 150 mm NaCl for 4 days, and with a final concentration 200 mm NaCl for 2 days. Solutions were refreshed every 2 days for treated and untreated seedlings. Non-treated plants were grown in nonamended one-half strength Hoagland solution. Three biological replicates (BR) were included for treated and control experiments. At the end of treatments, the uppermost three newly expanded leaves from all 12 plants in each BR were collected and bulked to extract total protein. Proteomic analysis resulted in the identification of several salt-induced and salt-suppressed proteins. Salt-induced proteins were: vacuolar H+-ATPase A1 subunit isoform (1.6-fold), germin-like protein (1.5-fold), ferredoxin-NADP (+) reductase (1.2-fold), quinone oxidoreductase-like protein (4.4-fold), heat-shock protein (4.9-fold), and pyrophosphorylase (1.7-fold). Salt-suppressed proteins were: ATPase alpha subunit (−1.5-fold) and rubisco activase (−1.4-fold). Proteins identified in this study affect cellular activities for antioxidant, stress protection, carbon fixation, and carbohydrate partitioning in young tomato leaves under salt stress

Identification of T-DNA structure and insertion site in transgenic crops using targeted capture sequencing

The commercialization of GE crops requires a rigorous safety assessment, which includes a precise DNA level characterization of inserted T-DNA. In the past, several strategies have been developed for identifying T-DNA insertion sites including, Southern blot and different PCR-based methods. However, these methods are often challenging to scale up for screening of dozens of transgenic events and for crops with complex genomes, like potato. Here, we report using target capture sequencing (TCS) to characterize the T-DNA structure and insertion sites of 34 transgenic events in potato. This T-DNA is an 18 kb fragment between left and right borders and carries three resistance (R) genes (RB, Rpi-blb2 and Rpi-vnt1.1 genes) that result in complete resistance to late blight disease. Using TCS, we obtained a high sequence read coverage within the T-DNA and junction regions. We identified the T-DNA breakpoints on either ends for 85% of the transgenic events. About 74% of the transgenic events had their T-DNA with 3R gene sequences intact. The flanking sequences of the T-DNA were from the potato genome for half of the transgenic events, and about a third (11) of the transgenic events have a single T-DNA insertion mapped into the potato genome, of which five events do not interrupt an existing potato gene. The TCS results were confirmed using PCR and Sanger sequencing for 6 of the best transgenic events representing 20% of the transgenic events suitable for regulatory approval. These results demonstrate the wide applicability of TCS for the precise T-DNA insertion characterization in transgenic crops

Draft Genome Sequences of Three Cellulolytic Bacillus licheniformis Strains Isolated from Imperial Geyser, Amphitheater Springs, and Whiterock Springs inside Yellowstone National Park

Novel cellulolytic microorganisms are becoming more important for rapidly growing biofuel industries. This paper reports the draft genome sequences of Bacillus licheniformis strains YNP2-TSU, YNP3-TSU, and YNP5-TSU. These cellulolytic isolates were collected from several hydrothermal features inside Yellowstone National Park

Overexpression of Pear (Pyrus pyrifolia) CAD2 in Tomato Affects Lignin Content

PpCAD2 was originally isolated from the ‘Wangkumbae’ pear (Pyrus pyrifolia Nakai), and it encodes for cinnamyl alcohol dehydrogenase (CAD), which is a key enzyme in the lignin biosynthesis pathway. In order to verify the function of PpCAD2, transgenic tomato (Solanum lycopersicum) ‘Micro-Tom’ plants were generated using over-expression constructs via the agrobacterium-mediated transformation method. The results showed that the PpCAD2 over-expression transgenic tomato plant had a strong growth vigor. Furthermore, these PpCAD2 over-expression transgenic tomato plants contained a higher lignin content and CAD enzymatic activity in the stem, leaf and fruit pericarp tissues, and formed a greater number of vessel elements in the stem and leaf vein, compared to wild type tomato plants. This study clearly indicated that overexpressing PpCAD2 increased the lignin deposition of transgenic tomato plants, and thus validated the function of PpCAD2 in lignin biosynthesis

Draft Genome Sequence of Bacillus altitudinis YNP4-TSU, Isolated from Yellowstone National Park

Undisturbed hot springs inside Yellowstone National Park remain a dynamic biome for novel cellulolytic thermophiles. We report here the draft genome sequence of one of these isolates, Bacillus altitudinis YNP4-TSU

Differential Root Proteome Expression in Tomato Genotypes with Contrasting Drought Tolerance Exposed to Dehydration

A comparative proteomics study using isobaric tags for relative and absolute quantitation (iTRAQ) was performed on a mesophytic tomato (Solanum lycopersicum) cultivar and a dehydration-resistant wild species (Solanum chilense) to identify proteins that play key roles in tolerance to water deficit stress. In tomato ‘Walter’ LA3465, 130 proteins were identified, of which 104 (80%) were repressed and 26 (20%) were induced. In S. chilense LA1958, a total of 170 proteins were identified with 106 (62%) repressed and 64 (38%) induced. According to their putative molecular functions, the differentially expressed proteins belong to the following subgroups: stress proteins, gene expression, nascent protein processing, protein folding, protein degradation, carbohydrate metabolism, amino acid and nucleotide metabolism, lipid metabolism, signal transduction, and cell cycle regulation. Based on changes in protein abundance induced by the dehydration treatment, cellular metabolic activities and protein biosynthesis were suppressed by the stress. In S. chilense, dehydration treatment led to elevated accumulation of proteins involved in post-transcriptional gene regulation and fidelity in protein translation including prefoldin, which promotes protein folding without the use of adenosine-5′-triphosphate (ATP), several hydrophilic proteins, and calmodulin in the calcium signal transduction pathway. Those protein changes were not found in the susceptible tomato, ‘Walter’. Within each functional protein group, proteins showing opposite changes (dehydration induced vs. repressed) in the two species were identified and roles of those proteins in conferring tolerance to water deficit stress are discussed. Information provided in this report will be useful for selection of proteins or genes in analyzing or improving dehydration tolerance in tomato cultivars

Draft Genome Sequence of Bacillus licheniformis Strain YNP1-TSU Isolated from Whiterock Springs in Yellowstone National Park

Novel cellulolytic microorganisms can potentially influence second-generation biofuel production. This paper reports the draft genome sequence of Bacillus licheniformis strain YNP1-TSU, isolated from hydrothermal-vegetative microbiomes inside Yellowstone National Park. The assembled sequence contigs predicted 4,230 coding genes, 66 tRNAs, and 10 rRNAs through automated annotation