Wesley M. Garrett

CTR1 phosphorylates the central regulator EIN2 to control ethylene hormone signaling from the ER membrane to the nucleus in Arabidopsis

The gaseous phytohormone ethylene C2H4 mediates numerous aspects of growth and development. Genetic analysis has identified a number of critical elements in ethylene signaling, but how these elements interact biochemically to transduce the signal from the ethylene receptor complex at the endoplasmic reticulum (ER) membrane to transcription factors in the nucleus is unknown. To close this gap in our understanding of the ethylene signaling pathway, the challenge has been to identify the target of the CONSTITUTIVE TRIPLE RESPONSE1 (CTR1) Raf-like protein kinase, as well as the molecular events surrounding ETHYLENE-INSENSITIVE2 (EIN2), an ER membrane-localized Nramp homolog that positively regulates ethylene responses. Here we demonstrate that CTR1 interacts with and directly phosphorylates the cytosolic C-terminal domain of EIN2. Mutations that block the EIN2 phosphorylation sites result in constitutive nuclear localization of the EIN2 C terminus, concomitant with constitutive activation of ethylene responses in Arabidopsis. Our results suggest that phosphorylation of EIN2 by CTR1 prevents EIN2 from signaling in the absence of ethylene, whereas inhibition of CTR1 upon ethylene perception is a signal for cleavage and nuclear localization of the EIN2 C terminus, allowing the ethylene signal to reach the downstream transcription factors. These findings significantly advance our understanding of the mechanisms underlying ethylene signal transduction.

Quantitative Proteomic Analysis of Bean Plants Infected by a Virulent and Avirulent Obligate Rust Fungus

Plants appear to have two types of active defenses, a broad-spectrum basal system and a system controlled by R-genes providing stronger resistance to some pathogens that break the basal defense. However, it is unknown if the systems are separate entities. Therefore, we analyzed proteins from leaves of the dry bean crop plant Phaseolus vulgaris using a high-throughput liquid chromatography tandem mass spectrometry method. By statistically comparing the amounts of proteins detected in a single plant variety that is susceptible or resistant to infection, depending on the strains of a rust fungus introduced, we defined basal and R-gene-mediated plant defenses at the proteomic level. The data reveal that some basal defense proteins are potential regulators of a strong defense weakened by the fungus and that the R-gene modulates proteins similar to those in the basal system. The results satisfy a new model whereby R-genes are part of the basal system and repair disabled defenses to reinstate strong resistance.

Dual labeling of the cytoskeleton and DNA strand breaks in porcine embryos produced in vivo and in vitro.

In vitro‐produced embryos exhibit decreased cell numbers, small inner cell masses and reduced pregnancy rates after transfer. Evaluation of intracellular components of in vitro‐produced or ‐manipulated embryos will lead to improved methodology for embryo production. Whole mount techniques were developed to utilize terminal deoxynucleotidyl‐transferase 3′ nick end labeling (TUNEL) to detect broken DNA. Subsequent labeling of either tubulin or actin filaments provides further evidence of cytological damage. Porcine embryos produced in vitro or in vivo were evaluated throughout the cleavage and preimplantation stages of development. Early cleavage stages up to the 8‐cell stage never contained TUNEL‐labeled nuclei. However, TUNEL labeling of in vitro‐produced morula revealed some blastomeres with broken DNA. Nearly all in vitro‐produced blastocysts displayed some TUNEL positive cells, whereas in vivo‐collected embryos at a similar stage displayed few, if any, TUNEL‐labeled nuclei. The ratio of TUNEL‐labeled DNA to total DNA area of in vitro‐derived blastocysts was significantly greater than their in vivo counterparts (P < 0.05). Microtubule and microfilament labeling identified blastomeres of unequal size and shape that were losing cellular integrity. These data suggest that the combination of these labeling techniques may be useful in evaluating cellular damage in embryos produced under in vitro conditions. Mol. Reprod. Dev. 51:59–65, 1998. Published 1998 Wiley‐Liss, Inc. This article is a US Government work and, as such, is in the public domain in the United States of America.

An efficient extraction method to enhance analysis of low abundant proteins from soybean seed.

Large amounts of the major storage proteins, beta-conglycinin and glycinin, in soybean (Glycine max) seeds hinder the isolation and characterization of less abundant seed proteins. We investigated whether isopropanol extraction could facilitate resolution of the low abundant proteins, different from the main storage protein fractions, in one-dimensional polyacrylamide gel electrophoresis (1D-PAGE) and two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). 1D-PAGE of proteins extracted by different concentrations (10%, 20%, 30%, 40%, 50%, 60%, 70% and 80%) of isopropanol showed that greater than 30% isopropanol was suitable for preferential enrichment of low abundant proteins. Analysis of 2D-PAGE showed that proteins which were less abundant or absent by the conventional extraction procedure were clearly seen in the 40% isopropanol extracts. Increasing isopropanol concentration above 40% resulted in a decrease in the number of less abundant protein spots. We have identified a total of 107 protein spots using matrix-assisted laser desorption/ionization time of flight mass spectrophotometry (MALDI-TOF-MS) and liquid chromatography-mass spectrometry (LC-MS/MS). Our results suggest that extraction of soybean seed powder with 40% isopropanol enriches lower abundance proteins and is a suitable method for 2D-PAGE separation and identification. This methodology could potentially allow the extraction and characterization of low abundant proteins of other legume seeds containing highly abundant storage proteins.

Relative, Label-free Protein Quantitation: Spectral Counting Error Statistics from Nine Replicate MudPIT Samples

Nine replicate samples of peptides from soybean leaves, each spiked with a different concentration of bovine apotransferrin peptides, were analyzed on a mass spectrometer using multidimensional protein identification technology (MudPIT). Proteins were detected from the peptide tandem mass spectra, and the numbers of spectra were statistically evaluated for variation between samples. The results corroborate prior knowledge that combining spectra from replicate samples increases the number of identifiable proteins and that a summed spectral count for a protein increases linearly with increasing molar amounts of protein. Furthermore, statistical analysis of spectral counts for proteins in two- and three-way comparisons between replicates and combined replicates revealed little significant variation arising from run-to-run differences or data-dependent instrument ion sampling that might falsely suggest differential protein accumulation. In these experiments, spectral counting was enabled by PANORAMICS, probability-based software that predicts proteins detected by sets of observed peptides. Three alternative approaches to counting spectra were also evaluated by comparison. As the counting thresholds were changed from weaker to more stringent, the accuracy of ratio determination also changed. These results suggest that thresholds for counting can be empirically set to improve relative quantitation. All together, the data confirm the accuracy and reliability of label-free spectral counting in the relative, quantitative analysis of proteins between samples.

Protein Accumulation in the Germinating Uromyces appendiculatus Uredospore

Uromyces appendiculatus is a rust fungus that causes disease on beans. To understand more about the biology of U. appendiculatus, we have used multidimensional protein identification technology to survey proteins in germinating asexual uredospores and have compared this data with proteins discovered in an inactive spore. The relative concentrations of proteins were estimated by counting the numbers of tandem mass spectra assigned to peptides for each detected protein. After germination, there were few changes in amounts of accumulated proteins involved in glycolysis, acetyl Co-A metabolism, citric acid cycle, ATP-coupled proton transport, or gluconeogenesis. Moreover, the total amount of translation elongation factors remained high, supporting a prior model that suggests that germlings acquire protein translation machinery from uredospores. However, germlings contained a higher amount of proteins involved in mitochondrial ADP:ATP translocation, which is indicative of increased energy production. Also, there were more accumulating histone proteins, pointing to the reorganization of the nuclei that occurs after germination prior to appressorium formation. Generally, these changes are indicative of metabolic transition from dormancy to germination and are supported by cytological and developmental models of germling growth.

Spontaneous differentiation of porcine and bovine embryonic stem cells (Epiblast) into astrocytes or neurons

SummaryThe culture of porcine or bovine epiblasts, i.e., embryonic stem cells, on STO feeder cells resulted in their spontaneous differentiation into multiple cell types that were subsequently isolated as separate cell lines. Some of these cell lines were “neuron-like” in morphology. Immunofluorescent analysis of two porcine epiblast-derived cell lines demonstrated that the cells were positive for the expression of vimentin and the glial fibrillary acidic protein (GFAP). Because of their stellate morphology and lack of neurofilament expression, it is possible that the cells are type 2 astrocytes. Similar analysis of a bovine epiblast-derived cell line showed that the cells were positive for vimentin but that they did not express GFAP. However, a few cells within the population expressed neurofilaments and alpha-internexin. It is possible that the bovine cells are neural precursor cells. The results confirm and extend the demonstrated in vitro pluripotency of porcine and bovine epiblast cultures and provide evidence for an in vitro model of embryonic neuroectoderm development.

Optimized protein extraction methods for proteomic analysis of Rhizoctonia solani

Rhizoctonia solani (Teleomorph: Thanatephorus cucumeris, T. praticola) is a basidiomycetous fungus and a major cause of root diseases of economically important plants. Various isolates of this fungus are also beneficially associated with orchids, may serve as biocontrol agents or remain as saprophytes with roles in decaying and recycling of soil organic matter. R. solani displays several hyphal anastomosis groups (AG) with distinct host and pathogenic specializations. Even though there are reports on the physiological and histological basis of Rhizoctonia-host interactions, very little is known about the molecular biology and control of gene expression early during infection by this pathogen. Proteomic technologies are powerful tools for examining alterations in protein profiles. To aid studies on its biology and host pathogen interactions, a two-dimensional (2-D) gel-based global proteomic study has been initiated. To develop an optimized protein extraction protocol for R. solani, we compared two previously reported protein extraction protocols for 2-D gel analysis of R. solani (AG-4) isolate Rs23. Both TCA-acetone precipitation and phosphate solubilization before TCA-acetone precipitation worked well for R. solani protein extraction, although selective enrichment of some proteins was noted with either method. About 450 spots could be detected with the densitiometric tracing of Coomassie blue-stained 2-D PAGE gels covering pH 4–7 and 6.5–205 kDa. Selected protein spots were subjected to mass spectrometric analysis with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Eleven protein spots were positively identified based on peptide mass fingerprinting match with fungal proteins inPUBLIC databases with the Mascot search engine. These results testify to the suitability of the two optimized protein extraction protocols for 2-D proteomic studies of R. solani.

Ultrastructure of the embryonic stem cells of the 8-day pig blastocyst before and after in vitro manipulation: Development of junctional apparatus and the lethal effects of PBS mediated cell–cell dissociation

Ultrastructural examination of 8‐day hatched pig blastocysts (large and small), their cultured inner cell mass (ICM), and cultured epiblast tissue (embryonic stem cells) was undertaken to assess the development of epiblast cell junctions and cytoskeletal elements. In small blastocysts, epiblast cells had no desmosomes or tight junction (TJ) connections and few organized microfilament bundles, whereas in large blastocysts the epiblast cells were connected by TJ and desmosomes with associated microfilaments. ICM isolation by immunodissection damaged the endoderm cells beneath the trophectoderm cells but did not appear to damage the epiblast cells or their associated endoderm cells. Epiblast cells in cultured ICMs were similar in character to those in the intact large blastocyst except that perinuclear microfilaments were observed. Isolated pig epiblasts, cultured for ∼36 hr on STO feeder layers, formed a monolayer whose cells were connected by TJ, adherens junctions and desmosomes with prominent microfilament bundles running parallel to the apical cytoplasmic membranes. Perinuclear microfilaments were a consistent feature in the ∼36 hr cultured epiblast cells. A feature characteristic of differentiation into notochordal cells, i.e., a solitary cilium, was also observed in the cultured epiblast. Exposure of the cultured epiblast cells to Ca++‐Mg++‐free phosphate buffered saline (PBS) for 5–10 min resulted in extensive cell blebbing and lysis. The results may indicate that pig epiblast cells could be more easily dissociated from early blastocysts (∼400 μm in diameter) if immunodissection damage to the ICM can be avoided. It may be difficult, however, to establish them as embryonic stem cell lines because the cultured pig epiblast cells were easily lysed by standard cell–cell dissociation methods. Anat Rec 264:101–113, 2001.

Changes in porcine oocyte germinal vesicle development as follicles approach preovulatory maturity.

This study was conducted to determine the distribution of oocytes in meiotic arrest as a function of follicle maturation, atresia status, and follicular fluid steroid concentrations. Oocytes (n = 138) from > or = 3 mm follicles were recovered from gilts (n = 3/d) on Days 1, 3, 5, and 7 of the follicular phase initiated by withdrawal of altrenogest treatment. They were fixed in 4% paraformaldehyde, stained with Hoechst 33342, and examined by laser scanning confocal microscopy using combined bright field Nomarski optics and ultraviolet laser illumination. The number of oocytes in complete meiotic arrest increased (P < 0.05) as a function of the stage of maturation from 29% on Day 1 to 79 and 67% on Days 3 and 5, respectively. Oocytes showing complete germinal vesicle breakdown (GVBD) were found only on Day 7 (24 to 36 h after the preovulatory LH surge). The distribution of GV stages on Days 1 to 5 did not differ between atretic (n = 27) and nonatretic follicles (n = 81). In nonatretic follicles, GV stage was inversely related to the concentration of estradiol on Day 7 and to the concentrations of progesterone and androstenedione (P < 0.05) on Days 5 and 7 indicating that meiotically arrested oocytes were likely to be found in follicles with highest levels of steroidogenesis. In conclusion, a large proportion of oocytes present in 3 to 5 mm follicles had begun GVBD. The follicles in the ovulatory cohort may be recruited or selected from preexisting 3 to 5 mm follicles, or younger population with oocytes that are in complete meiotic arrest.