Examining the drought stress transcriptome in cotton leaf and root tissue.

Growth, yield, and yield quality of cotton are greatly affected by water-deficit stress. We have identified the genes and associated metabolic pathways involved in the water-deficit stress response in leaf and root. Gene expression profiles were developed for leaf and root tissues subjected to slow-onset water deficit under controlled, glasshouse conditions. The water-deficit stress was characterized by leaf water potential of -23.1 bars for stressed tissue compared to -8.7 bars for fully-irrigated control plants and a corresponding decrease in net carbon assimilation to approximately 60% of the rates seen in the irrigated controls (30.3 ± 4.7 µmol CO(2) m(-2) s(-1) compared to 17.8 ± 5.9 µmol CO(2) m(-2) s(-1)). Profiling experiments revealed 2,106 stress-responsive transcripts, 879 classified as stress-induced, 1,163 stress-repressed, and 64 showed reciprocal expression patterns in root and leaf. The majority of stress-responsive transcripts had tissue-specific expression patterns and only 173 genes showed similar patterns of stress responsive expression in both tissues. A variety of putative metabolic and regulatory pathways were identified using MapMan software and the potential targets for candidate gene selection and ectopic expression to alter these pathways and responses are discussed.

Thermal dependence of enzyme function and inhibition; implications for, herbicide efficacy and tolerance.

Environmental temperature is a critical factor in the lives of almost all organisms. Plants experience periods of thermal stress related to seasonal patterns of temperature and periodic water deficits. Within the range of non-lethal temperatures, there are a number of thermal effects on metabolism that are a result of the thermal dependence of enzymes. The thermal dependence of enzyme kinetic parameters was used to predict that the efficacy of the herbicide pyrithiobac on Palmer amaranth would be reduced at temperatures outside a 20-34 degrees C thermal application range. This prediction is validated in a controlled environment study described in this paper. Palmer amaranth was grown for 16 days in growth chambers with 34/18 degrees C day/night temperature regime. Pyrithiobac was applied to plants at 18, 27 or 40 degrees C. After 1 h at the application temperatures the plants were returned to the 34/18 degrees C regime for 14 days and post-application biomass accumulation (efficacy) was determined. Dry weight accumulation, as a percentage of untreated controls, was 25, 2.5 and 70% for 18, 27 and 40 degrees C application temperatures. Pyrithiobac efficacy was highest for the application within the thermal application range and significantly reduced at temperatures above and below. The validation of the earlier prediction suggests that temperature-related kinetic limitations on herbicide efficacy may also occur in plants with bioengineered herbicide resistance based on herbicide metabolism. The theoretical aspects of such thermal limitations on herbicide resistance mechanisms are discussed.

Vapour pressure deficit aids the interpretation of cotton canopy temperature response to water deficit.

Crop canopy temperature (Tc) is coupled with transpiration, which is a function of soil and atmospheric conditions and plant water status. Thus, Tc has been identified as a real-time, plant-based tool for crop water stress detection. Such plant-based methods theoretically integrate the water status of both the plant and its environment. However, previous studies have highlighted the limitations and difficulty of interpreting the Tc response to plant and soil water stress. This study investigates the links between cotton Tc, established measures of plant water relations and atmospheric vapour pressure deficit (VPDa). Concurrent measures of carbon assimilation (A), stomatal conductance (gs), leaf water potential (Ψl), soil water (fraction of transpirable soil water (FTSW)) and Tc were conducted in surface drip irrigated cotton over two growing seasons. Associations between A, gs, Ψl, FTSW and Tc are presented, which are significantly improved with the inclusion of VPDa. It was concluded that utilising the strong associations between Ψl, VPDa and Tc, an adjustment of 1.8°C for each unit of VPDa should be made to the critical Tc for irrigation. This will improve the precision of irrigation in Tc based irrigation scheduling protocols. Improved accuracy in water stress detection with Tc, and an understanding of the interaction the environment plays in this response, can potentially improve the efficiency of irrigation.

Physiology and transcriptomics of water-deficit stress responses in wheat cultivars TAM 111 and TAM 112.

Hard red winter wheat crops on the U.S. Southern Great Plains often experience moderate to severe drought stress, especially during the grain filling stage, resulting in significant yield losses. Cultivars TAM 111 and TAM 112 are widely cultivated in the region, share parentage and showed superior but distinct adaption mechanisms under water-deficit (WD) conditions. Nevertheless, the physiological and molecular basis of their adaptation remains unknown. A greenhouse study was conducted to understand the differences in the physiological and transcriptomic responses of TAM 111 and TAM 112 to WD stress. Whole-plant data indicated that TAM 112 used more water, produced more biomass and grain yield under WD compared to TAM 111. Leaf-level data at the grain filling stage indicated that TAM 112 had elevated abscisic acid (ABA) content and reduced stomatal conductance and photosynthesis as compared to TAM 111. Sustained WD during the grain filling stage also resulted in greater flag leaf transcriptome changes in TAM 112 than TAM 111. Transcripts associated with photosynthesis, carbohydrate metabolism, phytohormone metabolism, and other dehydration responses were uniquely regulated between cultivars. These results suggested a differential role for ABA in regulating physiological and transcriptomic changes associated with WD stress and potential involvement in the superior adaptation and yield of TAM 112.

Artificial neural network method for solution of boundary value problems with exact satisfaction of arbitrary boundary conditions.

A method for solving boundary value problems (BVPs) is introduced using artificial neural networks (ANNs) for irregular domain boundaries with mixed Dirichlet/Neumann boundary conditions (BCs). The approximate ANN solution automatically satisfies BCs at all stages of training, including before training commences. This method is simpler than other ANN methods for solving BVPs due to its unconstrained nature and because automatic satisfaction of Dirichlet BCs provides a good starting approximate solution for significant portions of the domain. Automatic satisfaction of BCs is accomplished by the introduction of an innovative length factor. Several examples of BVP solution are presented for both linear and nonlinear differential equations in two and three dimensions. Error norms in the approximate solution on the order of 10(-4) to 10(-5) are reported for all example problems.

Liver fatty acid-binding protein initiates budding of pre-chylomicron transport vesicles from intestinal endoplasmic reticulum.

The rate-limiting step in the transit of absorbed dietary fat across the enterocyte is the generation of the pre-chylomicron transport vesicle (PCTV) from the endoplasmic reticulum (ER). This vesicle does not require coatomer-II (COPII) proteins for budding from the ER membrane and contains vesicle-associated membrane protein 7, found in intestinal ER, which is a unique intracellular location for this SNARE protein. We wished to identify the protein(s) responsible for budding this vesicle from ER membranes in the absence of the requirement for COPII proteins. We chromatographed rat intestinal cytosol on Sephacryl S-100 and found that PCTV budding activity appeared in the low molecular weight fractions. Additional chromatographic steps produced a single major and several minor bands on SDS-PAGE. By tandem mass spectroscopy, the bands contained both liver and intestinal fatty acid-binding proteins (L- and I-FABP) as well as four other proteins. Recombinant proteins for each of the six proteins identified were tested for PCTV budding activity; only L-FABP and I-FABP (23% the activity of L-FABP) were active. The vesicles generated by L-FABP were sealed, contained apolipoproteins B48 and AIV, were of the same size as PCTV on Sepharose CL-6B, and by electron microscopy, excluded calnexin and calreticulin but did not fuse with cis-Golgi nor did L-FABP generate COPII-dependent vesicles. Gene-disrupted L-FABP mouse cytosol had 60% the activity of wild type mouse cytosol. We conclude that L-FABP can select cargo for and bud PCTV from intestinal ER membranes.

The identification of a novel endoplasmic reticulum to Golgi SNARE complex used by the prechylomicron transport vesicle.

Dietary long chain fatty acids are absorbed in the intestine, esterified to triacylglycerol, and packaged in the unique lipoprotein of the intestine, the chylomicron. The rate-limiting step in the transit of chylomicrons through the enterocyte is the exit of chylomicrons from the endoplasmic reticulum in prechylomicron transport vesicles (PCTV) that transport chylomicrons to the cis-Golgi. Because chylomicrons are 250 nm in average diameter and lipid absorption is intermittent, we postulated that a unique SNARE pairing would be utilized to fuse PCTV with their target membrane, cis-Golgi. PCTV loaded with [(3)H]triacylglycerol were incubated with cis-Golgi and were separated from the Golgi by a sucrose step gradient. PCTV-chylomicrons acquire apolipoprotein-AI (apoAI) only after fusion with the Golgi. PCTV became isodense with Golgi upon incubation and were considered fused when their cargo chylomicrons acquired apoAI but docked when they did not. PCTV, docked with cis-Golgi, were solubilized in 2% Triton X-100, and proteins were immunoprecipitated using VAMP7 or rBet1 antibodies. In both cases, a 112-kDa complex was identified in nonboiled samples that dissociated upon boiling. The constituents of the complex were VAMP7, syntaxin 5, vti1a, and rBet1. Antibodies to each SNARE component significantly inhibited fusion of PCTV with cis-Golgi. Membrin, Sec22b, and Ykt6 were not found in the 112-kDa complex. We conclude that the PCTV-cis-Golgi SNARE complex is composed of VAMP7, syntaxin 5, Bet1, and vti1a.

Vesicle-associated membrane protein 7 is expressed in intestinal ER.

Intestinal dietary triacylglycerol absorption is a multi-step process. Triacylglycerol exit from the endoplasmic reticulum (ER) is the rate-limiting step in the progress of the lipid from its apical absorption to its basolateral membrane export. Triacylglycerol is transported from the ER to the cis Golgi in a specialized vesicle, the pre-chylomicron transport vesicle (PCTV). The vesicle-associated membrane protein 7 (VAMP7) was found to be more concentrated on PCTVs compared with ER membranes. VAMP7 has been previously identified associated with post-Golgi sites in eukaryotes. To examine the potential role of VAMP7 in PCTV trafficking, antibodies were generated that identified a 25 kDa band consistent with VAMP7 but did not crossreact with VAMP1,2. VAMP7 was concentrated on intestinal ER by immunofluorescence microscopy. Immunoelectron microscopy showed that the ER proteins Sar1 and rBet1 were present on PCTVs and colocalized with VAMP7. Iodixanol gradient centrifugation showed VAMP7 to be isodense with ER and endosomes. Although VAMP7 localized to intestinal ER, it was not present in the ER of liver and kidney. Anti-VAMP7 antibodies reduced the transfer of triacylglycerol, but not newly synthesized proteins, from the ER to the Golgi by 85%. We conclude that VAMP7 is enriched in intestinal ER and that it plays a functional role in the delivery of triacylglycerol from the ER to the Golgi.

Overexpression of apolipoprotein A-IV enhances lipid secretion in IPEC-1 cells by increasing chylomicron size.

Intestinal apolipoprotein A-IV expression is highly regulated by dietary lipid in newborn swine, suggesting a role in lipid absorption. Constitutive overexpression of apoA-IV in newborn swine enterocytes enhances basolateral secretion of triacylglycerol (TG) in TG-rich lipoproteins 4.9-fold (Lu, S., Yao, Y., Meng, S., Cheng, X., and Black, D. D. (2002) J. Biol. Chem. 277, 31929-31937). To investigate the mechanism of this enhancement, IPEC-1 cells were transfected with a tetracycline-regulatable expression system (Tet-On). In cells incubated with oleic acid, a dose response relationship was observed between medium doxycycline concentration and basolateral apoA-IV and TG secretion. Similarly regulated expression of apoA-I did not enhance lipid secretion. The mean diameter of TG-rich lipoproteins secreted from doxycycline-treated cells was larger than from untreated cells (87.0 nm versus 53.4 nm). Basolateral apoB secretion decreased. Using the same expression system, full-length human apoA-IV (376 amino acids); a "pig-like" human apoA-IV, lacking the C-terminal EQQQ repeats (361 amino acids); and a "chicken-like" apoA-IV, further truncated to 343 amino acids, were expressed in IPEC-1 cells. With increasing protein secretion, cells expressing the full-length human apoA-IV displayed a 2-fold increase in TG secretion; in sharp contrast, cells expressing the pig-like human apoA-IV displayed a 25-fold increase in TG secretion and a 27-fold increase in lipoprotein diameter. When human apoA-IV was further truncated to yield a chicken-like protein, TG secretion was inhibited. We conclude that overexpression of swine apoA-IV enhances basolateral TG secretion in a dose-dependent manner by increasing the size of secreted lipoproteins. These data suggest that the region in the human apoA-IV protein from residues 344 to 354 is critical to its ability to enhance lipid secretion, perhaps by enabling the packaging of additional core TG into chylomicron particles. The EQQQ-rich region may play an inhibitory or modulatory role in chylomicron packaging in humans.

Transgenic cotton (Gossypium hirsutum L.) seedlings expressing a tobacco glutathione S-transferase fail to provide improved stress tolerance.

Transgenic cotton (Gossypium hirsutum L.) lines expressing the tobacco glutathione S-transferase (GST) Nt107 were evaluated for tolerance to chilling, salinity, and herbicides, antioxidant enzyme activity, antioxidant compound levels, and lipid peroxidation. Although transgenic seedlings exhibited ten-fold and five-fold higher GST activity under normal and salt-stress conditions, respectively, germinating seedlings did not show improved tolerance to salinity, chilling conditions, or herbicides. Glutathione peroxidase (GPX) activity in transgenic seedlings was 30% to 60% higher under normal conditions, but was not different than GPX activity in wild-type seedlings under salt-stress conditions. Glutathione reductase, superoxide dismutase, ascorbate peroxidase, and monodehydroascorbate reductase activities were not increased in transgenic seedlings under salt-stress conditions, while dehydroascorbate reductase activity was decreased in transgenic seedlings under salt-stress conditions. Transgenic seedlings had 50% more oxidized glutathione when exposed to salt stress. Ascorbate levels were not increased in transgenic seedlings under salt-stress conditions. Malondialdehyde content in transgenic seedlings was nearly double that of wild-type seedlings under normal conditions and did not increase under salt-stress conditions. These results show that expression of Nt107 in cotton does not provide adequate protection against oxidative stress and suggests that the endogenous antioxidant system in cotton may be disrupted by the expression of the tobacco GST.

COPII proteins are required for Golgi fusion but not for endoplasmic reticulum budding of the pre-chylomicron transport vesicle.

The budding of vesicles from endoplasmic reticulum (ER) that contains nascent proteins is regulated by COPII proteins. The mechanisms that regulate lipid-carrying pre-chylomicron transport vesicles (PCTVs) budding from the ER are unknown. To study the dependence of PCTV-ER budding on COPII proteins we examined protein and PCTV budding by using ER prepared from rat small intestinal mucosal cells prelabeled with (3)H-oleate or (14)C-oleate and (3)H-leucine. Budded (3)H-oleate-containing PCTVs were separated by sucrose density centrifugation and were revealed by electron microscopy as 142-500 nm vesicles. Our results showed the following: (1) Proteinase K treatment did not degrade the PCTV cargo protein, apolipoprotein B-48, unless Triton X-100 was added. (2) PCTV budding was dependent on cytosol and ATP. (3) The COPII proteins Sar1, Sec24 and Sec13/31 and the membrane proteins syntaxin 5 and rBet1 were associated with PCTVs. (4) Isolated PCTVs were able to fuse with intestinal Golgi. (5) Antibodies to Sar1 completely inhibited protein vesicle budding but increased the generation of PCTV; these changes were reversed by the addition of recombinant Sar1. (6) PCTVs formed in the absence of Sar1 did not contain the COPII proteins Sar1, Sec24 or Sec31 and did not fuse with the Golgi complex. Together, these findings suggest that COPII proteins may not be required for the exit of membrane-bound chylomicrons from the ER but that they or other proteins may be necessary for PCTV fusion with the Golgi.