Proteome profile of the developing maize (Zea mays L.) rachis

In this study, we performed the first high‐throughput proteomic analysis of developing rachis (cob) from maize genotype Mp313E. Using two proteomic approaches, 2‐DE and 2‐D LC, we identified 967 proteins. A 2‐D proteome reference map was established. Functional classification of identified proteins revealed that proteins involved in various cellular metabolisms, response to stimulus and transport, were the most abundant.     

Genetic variation within maize population GT-MAS:gk and the relationship with resistance to Aspergillus flavus and aflatoxin production

Aspergillus flavus (Link:Fr.) infection and aflatoxin contamination of maize (Zea mays L.) grain are an extremely serious problem. Maize genotypes resistant to A. flavus attack are needed. Maize breeders and plant pathologists must identify resistance sources and incorporate resistance into adapted breeding material. Maize population GT-MAS:gk has been released for use as a resistance source. In this study, we surveyed the genetic variation in this population and made the breeders/plant pathologists aware of the heterogeneous nature in this maize population by using RAPD analysis and correlated the RAPD marker association with the resistance to A. flavus and aflatoxin production. Of 40 RAPD primers, only 15 gave sufficient numbers of reproducible and readily scored polymorphic bands suggesting that this population was highly homogeneous. However, genetic distances, ranging from 0.08 to 0.28 and averaging 0.17, suggest that there is variation within the population. Cluster analysis distinguished three major polymorphic groups. Laboratory bioassay revealed that group I contained the most resistant individuals, i.e., those with less aflatoxin production. Group II had the least resistance, and group III was intermediate. This study showed that the maize population GT-MAS:gk is heterogeneous and individuals are different in resistance to A. flavus and aflatoxin production. Resistance should be confirmed through progeny testing before further development. The RAPD marker OPX-04, which may be associated with the resistance trait, has been cloned and further characterization will be pursued. Received: 10 May 2000 / Accepted: 12 January 2001     

Biocontrol of aflatoxin in corn by inoculation with non-aflatoxigenic Aspergillus flavus isolates

The ability of two non-aflatoxigenic Aspergillus flavus Link isolates (CT3 and K49) to reduce aflatoxin contamination of corn was assessed in a 4-year field study (2001–2004). Soil was treated with six wheat inoculant treatments: aflatoxigenic isolate F3W4; two non-aflatoxigenic isolates (CT3 and K49); two mixtures of CT3 or K49 with F3W4; and an autoclaved wheat control, applied at 20 kg ha^?1. In 2001, inoculation with the aflatoxigenic isolate increased corn grain aflatoxin levels by 188% compared to the non-inoculated control, while CT3 and K49 inoculation reduced aflatoxin levels in corn grain by 86 and 60%, respectively. In 2002, the non-toxigenic CT3 and K49 reduced aflatoxin levels by 61 and 76% compared to non-inoculated controls, respectively. In 2001, mixtures of aflatoxigenic and non-aflatoxigenic isolates had little effect on aflatoxin levels, but in 2002, inoculation with mixtures of K49 and CT3 reduced aflatoxin levels 68 and 37% compared to non-inoculated controls, respectively. In 2003 and 2004, a low level of natural aflatoxin contamination was observed (8 ng g^?1). However, inoculation with mixtures of K49?+?F3W4 and CT3?+?F3W4, reduced levels of aflatoxin 65–94% compared to the aflatoxigenic strain alone. Compared to the non-sclerotia producing CT3, strain K49 produces large sclerotia, has more rapid in vitro radial growth, and a greater ability to colonize corn when artificially inoculated, perhaps indicating greater ecological competence. Results indicate that non-aflatoxigenic, indigenous A. flavus isolates, such as strain K49, have potential use for biocontrol of aflatoxin contamination in southern US corn.     

Induction of systemic acquired resistance in Zea mays L. by Aspergillus flavus and A. parasiticus derived elicitors

Host defence mechanisms can be elicited by using different elicitors produced from the pathogen/host. In this study, an effort has been made to study the effect of two fungal elicitors derived from Aspergillus flavus and A. parasiticus on induction of various defence-related enzymes in maize (Zea mays L.). Foliar application was done on 20-days-old maize plant with 10% A. flavus fungal culture filtrate (AFFCF) and A. parasiticus fungal culture filtrate (APFCF) as elicitors to trigger systemic acquired resistance (SAR). As a response of SAR, an increase in activities of phenylalanine ammonia lyase (PAL), peroxidase (POX), β-1,3-glucanase, nitrate reductase (NR) and nitrite reductase (NiR), total proteins were found highest on 4th day after treatment (DAT), whereas total carbohydrate and total chlorophyll on 2nd and 6th DAT, respectively, in comparison with the control plants. The SDS PAGE analysis revealed the induction of PR proteins, namely Chitinase (25, 29?kDa) and β-1,3-glucanase (33?kDa), in treated plants in comparison with untreated control plants. The treated plants showed enhanced growth and development as well as increase in yield. About 100% survival rate was found in maize seeds treated with AFFCF and APFCF and grown on respective fungal infested soil than control. The enhanced activities of defence enzymes and elevated protein, carbohydrate, chlorophyll content in treated maize plants suggest the induction of SAR against A. flavus and A. parasiticus by using the same fungal elicitors.     

Evaluation of bacteria and Trichoderma for biocontrol of pre-harvest seed infection by Aspergillus flavus in groundnut

Pre- and post harvest aflatoxin contamination of groundnut caused by Aspergillus flavus is a major problem in the semi-arid tropics. Fluorescent Pseudomonas, Bacillus and Trichoderma spp. potentially antagonistic to A. flavus were isolated from the geocarposphere (pod-zone) of groundnut and used successfully for the control of pre-harvest groundnut seed infection by A. flavus. In greenhouse and field experiments, inoculation of selected antagonistic strains on groundnut resulted in significant reduction of seed infection by A. flavus, and it also reduced >50% of the A. flavus populations (as cfu) in the geocarposphere of groundnut.     

Proteomic characterization of Phragmites communis in ecotypes of swamp and desert dune

Phragmites communis Trin. (common reed) is a recognized model plant for studying its adaptation to contrasting and harsh environments. To understand the inherent molecular basis for its remarkable resistance to combined stresses, we performed a comprehensive proteomic analysis of the leaf proteins from two ecotypes, i.e. swamp and desert dune, naturally growing in the desert region of northwestern China. First, a proteome reference map of Phragmites was established based on the swamp ecotype. Proteins were resolved by 2‐D/SDS‐PAGE and identified by MALDI‐TOF/TOF MS. In total, 177 spots were identified corresponding to 51 proteins. The major proteins identified are proteins involved in photosynthesis, glutathione and ascorbic acid metabolism as well as protein synthesis and quality control. Second, the 2‐DE profiles of the two ecotypes were compared quantitatively via DIGE analysis. Compared with swamp ecotype, 51 proteins spots are higher‐expressed and 58 protein spots are lower‐expressed by twofold or more in desert dune ecotype. Major differences were found for the proteins involved in light reaction of photosynthesis, protein biosynthesis and quality control and antioxidative reactions. The physiological significance of such differences is discussed in the context of a flow of complex events in relation to plant adaptation to combined environmental stresses.     

Proteomic analysis of papaya (Carica papaya L.) displaying typical sticky disease symptoms

Papaya (Carica papaya L.) hosts the only described laticifer-infecting virus (Papaya meleira virus, PMeV), which is the causal agent of papaya sticky disease. To understand the systemic effects of PMeV in papaya, we conducted a comprehensive proteomic analysis of leaf samples from healthy and diseased plants grown under field conditions. First, a reference 2-DE map was established for proteins from healthy samples. A total of 486 reproducible spots were identified, and MALDI-TOF-MS/MS data identified 275 proteins accounting for 159 distinct proteins from 231 spots that were annotated. Second, the differential expression of proteins from healthy and diseased leaves was determined through parallel experiments, using 2-DE and DIGE followed by MALDI-TOF-MS/MS and LC-IonTrap-MS/MS, respectively. Conventional 2-DE analysis revealed 75 differentially expressed proteins. Of those, 48 proteins were identified, with 26 being upregulated (U) and 22 downregulated (D). In general, metabolism-related proteins were downregulated, and stress-responsive proteins were upregulated. This expression pattern was corroborated by the results of the DIGE analysis, which identified 79 differentially expressed proteins, with 23 identified (17 U and 6 D). Calreticulin and the proteasome subunits 20S and RPT5a were shown to be upregulated during infection by both 2-DE and DIGE analyses. These data may help shed light on plant responses against stresses and viral infections.     

Microbe‐mediated control of Aspergillus flavus in stored rice grains with a focus on aflatoxin inhibition and biodegradation

Biological control of mycotoxigenic fungi using antagonistic microbes is a promising alternative to agricultural chemicals for postharvest storage. In this study, we evaluated rice‐derived bacterial strains to identify biocontrol agents to inhibit Aspergillus flavus in stored rice grains. Consequently, we obtained three potential biocontrol strains (Microbacterium testaceum KU313, Bacillus megaterium KU143 and Pseudomonas protegens AS15) from 26 tested strains that were prescreened from the 460 strains isolated from rice grains. The three selected strains proved to be effective biocontrol agents showing antifungal activity against A. flavus and good colonisation ability on rice grains, along with inhibition of the fungal growth and aflatoxin production. In particular, P. protegens AS15 greatly inhibited the aflatoxins produced by A. flavus on rice grains to 8.68 (percent aflatoxin reduction relative to control = 82.9%) and 18.05 (68.3 %) ng g^?1 dry weight of rice grains, compared with the 50.89 and 56.97 ng g^?1 dry weight of rice grains of the MgSO₄ control at 1 and 2 weeks after inoculation, respectively. In addition, strain AS15 had a significant ability to not only degrade aflatoxin B₁ (the most harmful aflatoxin), but also utilise the toxin for bacterial growth in a nutrient‐deficient medium. Therefore, the selected bacterial strains could be environmentally sound alternatives for the management of A. flavus and aflatoxin production by reducing the fungal damage to stored rice grains. This would also reduce the human and animal health hazards associated with the consumption of fungus‐contaminated rice grains. To our knowledge, this is the first report of the potential of the bacterial species M. testaceum and P. protegens as biocontrol agents for controlling aflatoxigenic A. flavus on stored rice grains.     

Use of microsatellite markers to assess the competitive ability of nontoxigenic Aspergillus flavus strains in studies on biocontrol of aflatoxins in maize in Thailand

Many nontoxigenic strains of Aspergillus flavus have been used in studies on biocontrol by competitive exclusion, but assessing their competitive ability is difficult. This paper reports on the use of a microsatellite marker technique for assessing competitiveness. The chosen microsatellite markers were able to differentiate, at an individual level, between the four biocontrol strains used in a study on the biocontrol of aflatoxins in maize in Thailand. The microsatellite markers were then used to determine which of the four biocontrol strains used were identical with 86 nontoxigenic strains of A. flavus taken from dried maize samples produced in that study. Fifty-one of the 86 strains (59%) were identified as one of the four biocontrol strains, with another four likely to be so. Analysis of microsatellites in A. flavus strains taken from dried samples at the conclusion of a field trial was shown to be of value in understanding the competitive ability of the specific strains used for biocontrol. This method provides an objective assessment of the competitiveness of biocontrol strains.     

2-D DIGE analysis of UV-C radiation-responsive proteins in globe artichoke leaves

Plants respond to ultraviolet stress inducing a self-defence through the regulation of specific gene family members. The UV acclimation is the result of biochemical and physiological processes, such as enhancement of the antioxidant enzymatic system and accumulation of UV-absorbing phenolic compounds (e.g. flavonoids). Globe artichoke is an attractive species for studying the protein network involved in UV stress response, being characterized by remarkable levels of inducible antioxidants. Proteomic tools can assist the evaluation of the expression patterns of UV-responsive proteins and we applied the difference in-gel electrophoresis (DIGE) technology for monitoring the globe artichoke proteome variation at four time points following an acute UV-C exposure. A total of 145 UV-C-modulated proteins were observed and 119 were identified by LC-MS/MS using a ～144,000 customized Compositae protein database, which included about 19,000 globe artichoke unigenes. Proteins were Gene Ontology (GO) categorized, visualized on their pathways and their behaviour was discussed. A predicted protein interaction network was produced and highly connected hub-like proteins were highlighted. Most of the proteins differentially modulated were chloroplast located, involved in photosynthesis, sugar metabolisms, protein folding and abiotic stress. The identification of UV-C-responsive proteins may contribute to shed light on the molecular mechanisms underlying plant responses to UV stress.     

Comparative proteomic analysis of the Arabidopsis cbl1 mutant in response to salt stress

Many environmental stimuli, including light, biotic and abiotic stress factors, induce changes in cellular Ca(2+) concentrations in plants. Such Ca(2+) signatures are perceived by sensor molecules such as calcineurin B-like (CBL) proteins. AtCBL1, a member of the CBL family which is highly inducible by multiple stress signals, is known to function in the salt stress signal transduction pathway and to positively regulate the plant tolerance to salt. To shed light into the molecular mechanisms of the salt stress response mediated by AtCBL1, a two-dimensional DIGE proteomic approach was applied to identify the differentially expressed proteins in Arabidopsis wild-type and cbl1 null mutant plants in response to salt stress. Seventy-three spots were found altered in expression by least 1.2-fold and 50 proteins were identified by MALDI-TOF/TOF-MS, including some well-known and novel salt-responsive proteins. These proteins function in various processes, such as signal transduction, ROS scavenging, energy production, carbon fixation, metabolism, mRNA processing, protein processing and structural stability. Receptor for activated C kinase 1C (RACK1C, spot 715), a WD40 repeat protein, was up-regulated in the cbl1 null mutant, and two rack1c mutant lines showed decreased tolerance to salt stress, suggesting that RACK1C plays a role in salt stress resistance. In conclusion, our work demonstrated the advantages of the proteomic approach in studies of plant biology and identified candidate proteins in CBL1-mediated salt stress signaling network.     

Proteomic identification of rainbow trout blood plasma proteins and their relationship to seminal plasma proteins

The characterisation of fish blood proteomes is important for comparative studies of seminal and blood proteins as well as for the analysis of fish immune mechanisms and pathways. In this study, LC‐MS/MS and 2D‐DIGE were applied to compare rainbow trout seminal (SP) and blood plasma (BP) proteomes. The 54 differentially abundant proteins identified in SP are involved in a variety of signalling pathways, including protein ubiquitination, liver X receptor/retinoid X receptor (LXR/RXR) and farnesoid X receptor activation, cell cycle and acute phase signalling. These findings may indicate the prevalence of acute phase signalling pathways in trout SP, and its essential role in protecting spermatozoa and reproductive tissues. Our study provides the first in‐depth analysis of the trout BP proteome, with a total of 119 proteins identified. The major proteins of rainbow trout BP were recognised as acute phase proteins. Analysis of BP proteins indicated that acute phase response signalling, the complement system, liver X receptor/retinoid X receptor and farnesoid X receptor activation and the coagulation system are the top canonical pathways. This study enhances knowledge of the blood origin of trout SP proteins and understanding of fish reproductive biology. Our results provide new insight into blood proteins specifically important for fish physiology and innate immunity. The mass spectrometry data are available via ProteomeXchange with the identifier PXD005988 and https://doi.org/10.6019/PXD005988 .     

The use of 2D‐DIGE to understand the regeneration of somatic embryos in avocado

Avocado embryogenic cell cultures can be classified into two groups based on their morphology when cultured on a medium containing auxin: somatic embryo (SE) and proembryonic masses (PEM) type cultures. The calli of SE‐type cell lines are able to go through the maturation process, whereas the calli of PEM cell lines rarely mature. We have investigated four independent avocado cell cultures (two SE and two PEM). The aim of this study was to link the differential regeneration capacity of the four cell cultures to a proteomic pattern and to gain insight into the regeneration capacity. A 2D‐DIGE analysis followed by a blind multivariate analysis was able to separate the two SE lines from the PEM lines indicating that the protein profiles of SE and PEM calli are different. Based on the variable importance, that is, the differential protein pattern, we hypothesize that the regeneration capacity in avocado is correlated to the ability to overcome the physicochemical stress stimuli associated with the in vitro culture. Our identical culture conditions do not seem to trigger an appropriate response in PEM lines.     

Proteomic analysis of membrane proteins expressed specifically in pluripotent murine embryonic stem cells

Embryonic stem cells (ESCs) are established from the inner cell mass of preimplantation embryos, are capable of self‐renewal, and exhibit pluripotency. Given these unique properties, ESCs are expected to have therapeutic potential in regenerative medicine and as a powerful tool for in vitro differentiation studies of stem cells. Various growth factors and extracellular matrix components regulate the pluripotency and differentiation of ESC progenies. Thus, the cell surface receptors that bind these regulatory factors are crucial for the precise regulation of stem cells. To identify membrane proteins that are involved in the regulation of pluripotent stem cells, the membrane proteins of murine ESCs cultured with or without leukemia inhibitory factor (LIF) were purified and analyzed by quantitative proteomics. 2‐D PAGE‐based analysis using fluorescently labeled proteins and shotgun‐based analysis with isotope‐labeled peptides identified 338 proteins, including transmembrane, membrane‐binding, and extracellular proteins, which were expressed specifically in pluripotent or differentiated murine ESCs. Functions of the identified proteins revealed cell adhesion molecules, channels, and receptors, which are expected to play important roles in the maintenance of murine ESC pluripotency. Membrane proteins that are expressed in pluripotent ESCs but not in differentiated cells such as Slc16a1 and Bsg could be useful for the selection of the stem cells in vitro.     

Proteomic analysis of salicylic acid-induced resistance to Magnaporthe oryzae in susceptible and resistant rice

To probe salicylic acid (SA)-induced sequential events at translational level and factors associated with SA response, we conducted virulence assays and proteomic profiling analysis on rice resistant and susceptible cultivars against Magnaporthe oryzae at various time points after SA treatment. The results showed that SA significantly enhanced rice resistance against M. oryzae. Proteomic analysis of SA-treated leaves unveiled 36 differentially expressed proteins implicated in various functions, including defense, antioxidative enzymes, and signal transduction. Majority of these proteins were induced except three antioxidative enzymes, which were negatively regulated by SA. Consistent with the above findings, SA increased the level of reactive oxygen species (ROS) with resistant cultivar C101LAC showing faster response to SA and producing higher level of ROS than susceptible cultivar CO39. Furthermore, we showed that nucleoside diphosphate kinase 1, which is implicated in regulation of ROS production, was strongly induced in C101LAC but not in CO39. Taken together, the findings suggest that resistant rice cultivar might possess a more sensitive SA signaling system or effective pathway than susceptible cultivar. In addition, our results indicate that SA also coordinates other cellular activities such as photosynthesis and metabolism to facilitate defense response and recovery, highlighting the complexity of SA-induced resistance mechanisms.