iTRAQ-based quantitative proteomics analysis of Brassica napus leaves reveals pathways associated with chlorophyll deficiency

Integration of proteomic and transcriptomic profiles reveals multiple levels of genetic regulation of salt tolerance in cotton

BACKGROUND

Salinity is a major abiotic stress that limits upland cotton growth and reduces fibre production worldwide. To reveal genetic regulation via transcript and protein levels after salt stress, we comprehensively analysed the global changes in mRNA, miRNA, and protein profiles in response to salt stress in two contrasting salt-tolerant cotton genotypes.

RESULTS

In the current study, proteomic and mRNA-seq data were combined to reveal that some genes are differentially expressed at both the proteomic and mRNA levels. However, we observed no significant change in mRNA corresponding to most of the strongly differentially abundant proteins. This finding may have resulted from global changes in alternative splicing events and miRNA levels under salt stress conditions. Evidence was provided indicating that several salt stress-responsive proteins can alter miRNAs and modulate alternative splicing events in upland cotton. The results of the stringent screening of the mRNA-seq and proteomic data between the salt-tolerant and salt-sensitive genotypes identified 63 and 85 candidate genes/proteins related to salt tolerance after 4 and 24 h of salt stress, respectively, between the tolerant and sensitive genotype. Finally, we predicted an interaction network comprising 158 genes/proteins and then discovered that two main clusters in the network were composed of ATP synthase (CotAD_74681) and cytochrome oxidase (CotAD_46197) in mitochondria. The results revealed that mitochondria, as important organelles involved in energy metabolism, play an essential role in the synthesis of resistance proteins during the process of salt exposure.

CONCLUSION

We provided a plausible schematic for the systematic salt tolerance model; this schematic reveals multiple levels of gene regulation in response to salt stress in cotton and provides a list of salt tolerance-related genes/proteins. The information here will facilitate candidate gene discovery and molecular marker development for salt tolerance breeding in cotton.

Distinct sperm nucleus behaviors between genotypic and temperature-dependent sex determination males are associated with replication and expression-related pathways in a gynogenetic fish

BACKGROUND

Coexistence and transition of diverse sex determination strategies have been revealed in some ectothermic species, but the variation between males caused by different sex determination strategies and the underlying mechanism remain unclear. Here, we used the gynogenetic gibel carp (Carassius gibelio) with both genotypic sex determination (GSD) and temperature-dependent sex determination (TSD) strategies to illustrate this issue.

RESULTS

We found out that males of GSD and TSD in gibel carp had similar morphology, testicular histology, sperm structure and sperm vitality. However, when maternal individuals were mated with males of GSD, sperm nucleus swelling and fusing with the female pronucleus were observed in the fertilized eggs. On the contrary, when maternal individuals were mated with males of TSD, sperm nucleus remained in the condensed status throughout the whole process. Subsequently, semen proteomics analysis unveiled that DNA replication and gene expression-related pathways were inhibited in the sperm from males of TSD compared to males of GSD, and most differentially expressed proteins associated with DNA replication, transcription and translation were down-regulated. Moreover, via BrdU incorporation and immunofluorescence detection, male nucleus replication was revealed to be present in the fertilized eggs by the sperm from males of GSD, but absent in the fertilized eggs by the sperm from males of TSD.

CONCLUSIONS

These findings indicate that DNA replication and gene expression-related pathways are associated with the distinct sperm nucleus development behaviors in fertilized eggs in response to the sperm from males of GSD and TSD. And this study is the first attempt to screen the differences between males determined via GSD and TSD in gynogenetic species, which might give a hint for understanding evolutionary adaption of diverse sex determination mechanisms in unisexual vertebrates.

Candidate Genes for Yellow Leaf Color in Common Wheat (Triticum aestivum L.) and Major Related Metabolic Pathways according to Transcriptome Profiling

The photosynthetic capacity and efficiency of a crop depends on the biosynthesis of photosynthetic pigments and chloroplast development. However, little is known about the molecular mechanisms of chloroplast development and chlorophyll (Chl) biosynthesis in common wheat because of its huge and complex genome. Ygm, a spontaneous yellow-green leaf color mutant of winter wheat, exhibits reduced Chl contents and abnormal chloroplast development. Thus, we searched for candidate genes associated with this phenotype. Comparative transcriptome profiling was performed using leaves from the yellow leaf color type (Y) and normal green color type (G) of the Ygm mutant progeny. We identified 1227 differentially expressed genes (DEGs) in Y compared with G (i.e., 689 upregulated genes and 538 downregulated genes). Gene ontology and pathway enrichment analyses indicated that the DEGs were involved in Chl biosynthesis (i.e., magnesium chelatase subunit H (CHLH) and protochlorophyllide oxidoreductase (POR) genes), carotenoid biosynthesis (i.e., β-carotene hydroxylase (BCH) genes), photosynthesis, and carbon fixation in photosynthetic organisms. We also identified heat shock protein (HSP) genes (sHSP, HSP70, HSP90, and DnaJ) and heat shock transcription factor genes that might have vital roles in chloroplast development. Quantitative RT-PCR analysis of the relevant DEGs confirmed the RNA-Seq results. Moreover, measurements of seven intermediate products involved in Chl biosynthesis and five carotenoid compounds involved in carotenoid-xanthophyll biosynthesis confirmed that CHLH and BCH are vital enzymes for the unusual leaf color phenotype in Y type. These results provide insights into leaf color variation in wheat at the transcriptional level.

Histological, Physiological, and Comparative Proteomic Analyses Provide Insights into Leaf Rolling in Brassica napus

Moderate leaf rolling is important in ideotype breeding, as it improves photosynthetic efficiency and therefore increases crop yields. To understand the regulatory network of leaf rolling in Brassica napus, a down-curved leaf mutant ( Bndcl1) has been investigated. Physiological analyses indicated that the chlorophyll contents and antioxidant enzyme activities were remarkably increased and the photosynthetic performance was significantly improved in Bndcl1. Consistent with these findings, 943 differentially accumulated proteins (DAPs) were identified in the Bndcl1 mutant and its wild-type plants using iTRAQ-based comparative proteomic analyses. Enrichment analysis of proteins with higher abundance in Bndcl1 revealed that the functional category "photosynthesis" was significantly overrepresented. Moreover, proteins associated with oxidative stress response and photosystem II repairing were also up-accumulated in Bndcl1, which might help the mutant to sustain the photosynthetic efficiency under unfavorable conditions. Histological observation showed that the mutant displayed defects in adaxial-abaxial patterning. Important DAPs associated with leaf polarity establishment were detected in Bndcl1, including ribosomal proteins, proteins involved in post-transcriptional gene silencing, and proteins related to brassinosteroid. Together, our findings may help clarify the mechanisms underlying leaf rolling and its physiological effects on plants and may facilitate ideotype breeding in Brassica napus.

Comparative proteomic analysis provides insight into a complex regulatory network of taproot formation in radish (Raphanus sativus L.)

The fleshy taproot of radish is an important storage organ determining its yield and quality. Taproot thickening is a complex developmental process in radish. However, the molecular mechanisms governing this process remain unclear at the proteome level. In this study, a comparative proteomic analysis was performed to analyze the proteome changes at three developmental stages of taproot thickening using iTRAQ approach. In total, 1862 differentially expressed proteins (DEPs) were identified from 6342 high-confidence proteins, among which 256 up-regulated proteins displayed overlapped accumulation in S1 (pre-cortex splitting stage) vs. S2 (cortex splitting stage) and S1 vs. S3 (expanding stage) pairs, whereas 122 up-regulated proteins displayed overlapped accumulation in S1 vs. S3 and S2 vs. S3 pairs. Gene Ontology (GO) and pathway enrichment analysis showed that these DEPs were mainly involved in several processes such as "starch and sucrose metabolism", "plant hormone signal transduction", and "biosynthesis of secondary metabolites". A high concordance existed between iTRAQ and RT-qPCR at the mRNA expression levels. Furthermore, association analysis showed that 187, 181, and 96 DEPs were matched with their corresponding differentially expressed genes (DEGs) in S1 vs. S2, S1 vs. S3, and S2 vs. S3 comparison, respectively. Notably, several functional proteins including cell division cycle 5-like protein (CDC5), expansin B1 (EXPB1), and xyloglucan endotransglucosylase/hydrolase protein 24 (XTH24) were responsible for cell division and expansion during radish taproot thickening process. These results could facilitate a better understanding of the molecular mechanism underlying taproot thickening, and provide valuable information for the identification of critical genes/proteins responsible for taproot thickening in root vegetable crops.

Dissecting Root Proteome Changes Reveals New Insight into Cadmium Stress Response in Radish (Raphanus sativus L.)

Cadmium (Cd) is a widespread heavy metal of particular concern with respect to the environment and human health. Although intensive studies have been conducted on Cd-exposed transcriptome profiling, little systematic proteome information is available on the molecular mechanism of Cd stress response in radish. In this study, the radish root proteome under Cd stress was investigated using a quantitative multiplexed proteomics approach. Seedlings were grown in nutrient solution without Cd (control) or with 10 or 50 μM CdCl2 for 12 h (Cd10 and Cd50, respectively). In total, 91 up- and 66 down-regulated proteins were identified in the control vs Cd10 comparison, while 340 up- and 286 down-regulated proteins were identified in the control vs Cd50 comparison. Functional annotation indicated that these differentially expressed proteins (DEPs) were mainly involved in carbohydrate and energy metabolism, stress and defense and signal transduction processes. Correlation analysis showed that 33 DEPs matched with their transcripts, indicating a relatively low correlation between transcript and protein levels under Cd stress. Quantitative real-time PCR evidenced the expression patterns of 12 genes encoding their corresponding DEPs. In particular, several pivotal proteins associated with carbohydrate metabolism, ROS scavenging, cell transport and signal transduction were involved in the coordinated regulatory network of the Cd stress response in radish. Root exposure to Cd2+ activated several key signaling molecules and metal-containing transcription factors, and subsequently some Cd-responsive functional genes were mediated to reduce Cd toxicity and re-establish redox homeostasis in radish. This is a first report on comprehensive proteomic characterization of Cd-exposed root proteomes in radish. These findings could facilitate unraveling of the molecular mechanism underlying the Cd stress response in radish and provide fundamental insights into the development of genetically engineered low-Cd-content radish cultivars.

Immune regulation effect of lienal polypeptides extract in Lewis lung carcinoma-bearing mice treated with cyclophosphamide

Polypeptides extracted from animal immune organs have been proved to exert immunomodulatory activities in previous reports. However, relative experimental data regarding the influence of a polypeptide mixture extracted from healthy calf spleen (lienal polypeptide [LP]) on the immune function in tumor therapy are limited, and the components in LP remain unclear. In the present study, the immune regulatory effect of LP was investigated in normal mice and Lewis lung carcinoma (LLC)-bearing mice treated with cyclophosphamide (CTX). The components of LP were identified by liquid chromatography-electrospray ionization-coupled with tandem mass spectrometry (LC-MS/MS) analysis and bioinformatic analysis. In LLC-bearing mice, LP showed a synergic antitumor effect with CTX, whereas LP alone did not present direct antitumor activity. Further, LP was found to enhance immune organ indexes, splenocyte number, and T lymphocyte subsets in normal mice and LLC-bearing mice treated with CTX. The decline of white blood cell and platelet counts, splenocyte proliferation activity, and peritoneal macrophage phagocytic function caused by CTX were also significantly suppressed by LP treatment in LLC-bearing mice. Notably, LP treatment significantly decreased the expression of phagocytosis-related proteins including CD47/signal regulatory protein α/Src homology phosphatase-1 in the tumor tissue of LLC-bearing mice treated with CTX. LC-MS/MS-based peptidomics unraveled the main polypeptides in LP with a length from 8 to 25 amino acids. Bioinformatics analysis further confirmed the possibility of LP to regulate immunity, especially in phagocytosis-related pathway. Our above findings indicated that LP can relieve the immunosuppression induced by chemotherapy and is a beneficial supplement in cancer therapy. Impact statement The immunomodulatory activities of polypeptides extracted from animal immune organs have incurred people's interests since a long time ago. In this study, we investigated the immune regulation effects of a polypeptide mixture extracted from health calf spleen (lienal polypeptide [LP]) in Lewis lung carcinoma-bearing mice treated with cyclophosphamide (CTX). Liquid chromatography-electrospray ionization-coupled with tandem mass spectrometry-based peptidomics and bioinformatics analysis unraveled the main polypeptides in LP and further confirmed that LP is mainly associated with immune regulating pathway, especially in tumor cell phagocytosis-related pathway. Our study for the first time revealed that polypeptides from spleen can relieve the immunosuppression induced by CTX and is a beneficial supplement in cancer therapy.

Respiration disruption and detoxification at the protein expression levels in the Pacific oyster (Crassostrea gigas) under zinc exposure

The Pacific oyster (Crassostrea gigas) can accumulate high levels of zinc (Zn) without obvious toxicity, but the related molecular mechanisms are largely unknown. In the present study, C. gigas were exposed to excess Zn for 9days and the differentially expressed proteins (DEPs) were examined using the isobaric tags for relative and absolute quantitation (iTRAQ) method. In total, 2667 proteins containing at least two peptides and detected in both replicates were used for proteomic analysis. Among these DEPs, 332 were up-regulated and 282 were down-regulated. KEGG enrichment analysis of DEPs revealed that Zn exposure mainly distrubed 'tricarboxylic acid (TCA) cycle', 'electron transport chain (ETC)' and 'glutathione (GSH) metabolism' processes in oysters. Further key protein expressions enriched in these metabolism pathways were analyzed. In TCA cycle, Zn inhibited the Fe-containing protein expressions, which may lead to the accumulation of succinate and induce anaerobiosis. In ETC metabolism process, Zn inhibited ETC complex protein expressions, including complex I-IV, which may affect the electron transport process. Furthermore, Zn induced phytochelatin (PC) and glutathione peroxidase (GPX) expression in GSH catabolism. The proteins play important roles in Zn detoxification and ROS elimination process. The transcriptional expressions of genes encoding these proteins were observed using real-time PCR analysis, and there was good consistency between these two datasets. Overall, we provide direct evidence for Zn toxicity and detoxification mechanisms at protein level.

iTRAQ-Based Quantitative Proteomic Analysis Reveals Cold Responsive Proteins Involved in Leaf Senescence in Upland Cotton (Gossypium hirsutum L.)

Premature leaf senescence occurs in the ultimate phase of the plant, and it occurs through a complex series of actions regulated by stress, hormones and genes. In this study, a proteomic analysis was performed to analyze the factors that could induce premature leaf senescence in two cotton cultivars. We successfully identified 443 differential abundant proteins (DAPs) from 7388 high-confidence proteins at four stages between non-premature senescence (NS) and premature senescence (PS), among which 158 proteins were over-accumulated, 238 proteins were down-accumulated at four stages, and 47 proteins displayed overlapped accumulation. All the DAPs were mapped onto 21 different categories on the basis of a Clusters of Orthologous Groups (COG) analysis, and 9 clusters were based on accumulation. Gene Ontology (GO) enrichment results show that processes related to stress responses, including responses to cold temperatures and responses to hormones, are significantly differentially accumulated. More importantly, the enriched proteins were mapped in The Arabidopsis Information Resource (TAIR), showing that 58 proteins play an active role in abiotic stress, hormone signaling and leaf senescence. Among these proteins, 26 cold-responsive proteins (CRPs) are significantly differentially accumulated. The meteorological data showed that the median temperatures declined at approximately 15 days before the onset of aging, suggesting that a decrease in temperature is tightly linked to an onset of cotton leaf senescence. Because accumulations of H₂O₂ and increased jasmonic acid (JA) were detected during PS, we speculate that two pathways associated with JA and H₂O₂ are closely related to premature leaf senescence in cotton.

Cadmium effects on DNA and protein metabolism in oyster (Crassostrea gigas) revealed by proteomic analyses

Marine molluscs, including oysters, can concentrate high levels of cadmium (Cd) in their soft tissues, but the molecular mechanisms of Cd toxicity remain speculative. In this study, Pacific oysters (Crassostrea gigas) were exposed to Cd for 9 days and their gills were subjected to proteomic analysis, which were further confirmed with transcriptomic analysis. A total of 4,964 proteins was quantified and 515 differentially expressed proteins were identified in response to Cd exposure. Gene Ontology enrichment analysis revealed that excess Cd affected the DNA and protein metabolism. Specifically, Cd toxicity resulted in the inhibition of DNA glycosylase and gap-filling and ligation enzymes expressions in base excision repair pathway, which may have decreased DNA repair capacity. At the protein level, Cd induced the heat shock protein response, initiation of protein refolding as well as degradation by ubiquitin proteasome pathway, among other effects. Excess Cd also induced antioxidant responses, particularly glutathione metabolism, which play important roles in Cd chelation and anti-oxidation. This study provided the first molecular mechanisms of Cd toxicity on DNA and protein metabolism at protein levels, and identified molecular biomarkers for Cd toxicity in oysters.

Unraveling the Root Proteome Changes and Its Relationship to Molecular Mechanism Underlying Salt Stress Response in Radish (Raphanus sativus L.)

To understand the molecular mechanism underlying salt stress response in radish, iTRAQ-based proteomic analysis was conducted to investigate the differences in protein species abundance under different salt treatments. In total, 851, 706, and 685 differential abundance protein species (DAPS) were identified between CK vs. Na100, CK vs. Na200, and Na100 vs. Na200, respectively. Functional annotation analysis revealed that salt stress elicited complex proteomic alterations in radish roots involved in carbohydrate and energy metabolism, protein metabolism, signal transduction, transcription regulation, stress and defense and transport. Additionally, the expression levels of nine genes encoding DAPS were further verified using RT-qPCR. The integrative analysis of transcriptomic and proteomic data in conjunction with miRNAs was further performed to strengthen the understanding of radish response to salinity. The genes responsible for signal transduction, ROS scavenging and transport activities as well as several key miRNAs including miR171, miR395, and miR398 played crucial roles in salt stress response in radish. Based on these findings, a schematic genetic regulatory network of salt stress response was proposed. This study provided valuable insights into the molecular mechanism underlying salt stress response in radish roots and would facilitate developing effective strategies toward genetically engineered salt-tolerant radish and other root vegetable crops.

Quantitative proteome-level analysis of paulownia witches' broom disease with methyl methane sulfonate assistance reveals diverse metabolic changes during the infection and recovery processes

Paulownia witches' broom (PaWB) disease caused by phytoplasma is a fatal disease that leads to considerable economic losses. Although there are a few reports describing studies of PaWB pathogenesis, the molecular mechanisms underlying phytoplasma pathogenicity in Paulownia trees remain uncharacterized. In this study, after building a transcriptome database containing 67,177 sequences, we used isobaric tags for relative and absolute quantification (iTRAQ) to quantify and analyze the proteome-level changes among healthy P. fortunei (PF), PaWB-infected P. fortunei (PFI), and PaWB-infected P. fortunei treated with 20 mg L^-1 or 60 mg L^-1 methyl methane sulfonate (MMS) (PFI-20 and PFI-60, respectively). A total of 2,358 proteins were identified. We investigated the proteins profiles in PF vs. PFI (infected process) and PFI-20 vs. PFI-60 (recovered process), and further found that many of the MMS-response proteins mapped to "photosynthesis" and "ribosome" pathways. Based on our comparison scheme, 36 PaWB-related proteins were revealed. Among them, 32 proteins were classified into three functional groups: (1) carbohydrate and energy metabolism, (2) protein synthesis and degradation, and (3) stress resistance. We then investigated the PaWB-related proteins involved in the infected and recovered processes, and discovered that carbohydrate and energy metabolism was inhibited, and protein synthesis and degradation decreased, as the plant responded to PaWB. Our observations may be useful for characterizing the proteome-level changes that occur at different stages of PaWB disease. The data generated in this study may serve as a valuable resource for elucidating the pathogenesis of PaWB disease during phytoplasma infection and recovery stages.

Proteomics in commercial crops: An overview

Proteomics is a rapidly growing area of biological research that is positively affecting plant science. Recent advances in proteomic technology, such as mass spectrometry, can now identify a broad range of proteins and monitor their modulation during plant growth and development, as well as during responses to abiotic and biotic stresses. In this review, we highlight recent proteomic studies of commercial crops and discuss the advances in understanding of the proteomes of these crops. We anticipate that proteomic-based research will continue to expand and contribute to crop improvement.

SIGNIFICANCE

Plant proteomics study is a rapidly growing area of biological research that is positively impacting plant science. With the recent advances in new technologies, proteomics not only allows us to comprehensively analyses crop proteins, but also help us to understand the functions of the genes. In this review, we highlighted recent proteomic studies in commercial crops and updated the advances in our understanding of the proteomes of these crops. We believe that proteomic-based research will continue to grow and contribute to the improvement of crops.

Heme oxygenase 1 defects lead to reduced chlorophyll in Brassica napus

We previously described a Brassica napus chlorophyll-deficient mutant (ygl) with yellow-green seedling leaves and mapped the related gene, BnaC.YGL, to a 0.35 cM region. However, the molecular mechanisms involved in this chlorophyll defect are still unknown. In this study, the BnaC07.HO1 gene (equivalent to BnaC.YGL) was isolated by the candidate gene approach, and its function was confirmed by genetic complementation. Comparative sequencing analysis suggested that BnaC07.HO1 was lost in the mutant, while a long noncoding-RNA was inserted into the promoter of the homologous gene BnaA07.HO1. This insert was widely present in B. napus cultivars and down-regulated BnaA07.HO1 expression. BnaC07.HO1 was highly expressed in the seedling leaves and encoded heme oxygenase 1, which was localized in the chloroplast. Biochemical analysis showed that BnaC07.HO1 can catalyze heme conversion to form biliverdin IXα. RNA-seq analysis revealed that the loss of BnaC07.HO1 impaired tetrapyrrole metabolism, especially chlorophyll biosynthesis. According, the levels of chlorophyll intermediates were reduced in the ygl mutant. In addition, gene expression in multiple pathways was affected in ygl. These findings provide molecular evidences for the basis of the yellow-green leaf phenotype and further insights into the crucial role of HO1 in B. napus.

Proteomic analysis of stress-related proteins and metabolic pathways in Picea asperata somatic embryos during partial desiccation

Partial desiccation treatment (PDT) stimulates germination and enhances the conversion of conifer somatic embryos. To better understand the mechanisms underlying the responses of somatic embryos to PDT, we used proteomic and physiological analyses to investigate these responses during PDT in Picea asperata. Comparative proteomic analysis revealed that, during PDT, stress-related proteins were mainly involved in osmosis, endogenous hormones, antioxidative proteins, molecular chaperones and defence-related proteins. Compared with those in cotyledonary embryos before PDT, these stress-related proteins remained at high levels on days 7 (D7) and 14 (D14) of PDT. The proteins that differentially accumulated in the somatic embryos on D7 were mapped to stress and/or stimuli. They may also be involved in the glyoxylate cycle and the chitin metabolic process. The most significant difference in the differentially accumulated proteins occurred in the metabolic pathways of photosynthesis on D14. Furthermore, in accordance with the changes in stress-related proteins, analyses of changes in water content, abscisic acid, indoleacetic acid and H₂ O₂ levels in the embryos indicated that PDT is involved in water-deficit tolerance and affects endogenous hormones. Our results provide insight into the mechanisms responsible for the transition from morphologically mature to physiologically mature somatic embryos during the PDT process in P. asperata.

Proteomic and physiological approach reveals drought-induced changes in rapeseeds: Water-saver and water-spender strategy

The cultivar-dependent differences in Brassica napus L. seed yield are significantly affected by drought stress. Here, the response of leaf proteome to long-term drought (28days) was studied in cultivars (cvs): Californium (C), Cadeli (D), Navajo (N), and Viking (V). Analysis of twenty-four 2-D DIGE gels revealed 134 spots quantitatively changed at least 2-fold; from these, 79 proteins were significantly identified by MALDI-TOF/TOF. According to the differences in water use, the cultivars may be assigned to two categories: water-savers or water-spenders. In the water-savers group (cvs C+D), proteins related to nitrogen assimilation, ATP and redox homeostasis were increased under stress, while in the water-spenders category (cvs N+V), carbohydrate/energy, photosynthesis, stress related and rRNA processing proteins were increased upon stress. Taking all data together, we indicated cv C as a drought-adaptable water-saver, cv D as a medium-adaptable water-saver, cv N as a drought-adaptable water-spender, and cv V as a low-adaptable drought sensitive water-spender rapeseed. Proteomic data help to evaluate the impact of drought and the extent of genotype-based adaptability and contribute to the understanding of their plasticity. These results provide new insights into the provenience-based drought acclimation/adaptation strategy of contrasting winter rapeseeds and link data at gasometric, biochemical, and proteome level.

SIGNIFICANCE

Soil moisture deficit is a real problem for every crop. The data in this study demonstrates for the first time that in stem-prolongation phase cultivars respond to progressive drought in different ways and at different levels. Analysis of physiological and proteomic data showed two different water regime-related strategies: water-savers and spenders. However, not only water uptake rate itself, but also individual protein abundances, gasometric and biochemical parameters together with final biomass accumulation after stress explained genotype-based responses. Interestingly, under a mixed climate profile, both water-use patterns (savers or spenders) can be appropriate for drought adaptation. These data suggest, than complete "acclimation image" of rapeseeds in stem-prolongation phase under drought could be reached only if these characteristics are taken, explained and understood together.

Phenotypic, histological and proteomic analyses reveal multiple differences associated with chloroplast development in yellow and variegated variants from Camellia sinensis

Leaf colour variation is observed in several plants. We obtained two types of branches with yellow and variegated leaves from Camellia sinensis. To reveal the mechanisms that underlie the leaf colour variations, combined morphological, histological, ionomic and proteomic analyses were performed using leaves from abnormal branches (variants) and normal branches (CKs). The measurement of the CIE-Lab coordinates showed that the brightness and yellowness of the variants were more intense than the CKs. When chloroplast profiles were analysed, HY1 (branch with yellow leaves) and HY2 (branch with variegated leaves) displayed abnormal chloroplast structures and a reduced number and size compared with the CKs, indicating that the abnormal chloroplast development might be tightly linked to the leaf colour variations. Moreover, the concentration of elemental minerals was different between the variants and the CKs. Furthermore, DEPs (differentially expressed proteins) were identified in the variants and the CKs by a quantitative proteomics analysis using the label-free approach. The DEPs were significantly involved in photosynthesis and included PSI, PSII, cytochrome b6/f complex, photosynthetic electron transport, LHC and F-type ATPase. Our results suggested that a decrease in the abundance of photosynthetic proteins might be associated with the changes of leaf colours in tea plants.

Fine mapping of a dominant gene conferring chlorophyll-deficiency in Brassica napus

Leaf colour regulation is important in photosynthesis and dry material production. Most of the reported chlorophyll-deficient loci are recessive. The dominant locus is rarely reported, although it may be more important than the recessive locus in the regulation of photosynthesis efficiency. During the present study, we mapped a chlorophyll-deficient dominant locus (CDE1) from the ethyl methanesulfonate-mutagenized Brassica napus line NJ7982. Using an F₂ population derived from the chlorophyll-deficient mutant (cde1) and the canola variety ‘zhongshuang11’, a high-density linkage map was constructed, consisting of 19 linkage groups with 2,878 bins containing 13,347 SNP markers, with a total linkage map length of 1,968.6 cM. Next, the CDE1 locus was mapped in a 0.9-cM interval of chromosome C08 of B. napus, co-segregating with nine SNP markers. In the following fine-mapping of the gene using the inherited F_2:3 populations of 620 individuals, the locus was identified in an interval with a length of 311 kb. A bioinformatics analysis revealed that the mapping interval contained 22 genes. These results produced a good foundation for continued research on the dominant locus involved in chlorophyll content regulation.

Fine mapping of a major locus controlling plant height using a high-density single-nucleotide polymorphism map in Brassica napus

A saturated map was constructed using SNP markers to fine-map a Brassica napus dominant locus for dwarf mutant onto a 152-kb interval of chromosome A09 containing 14 genes. Major dwarf loci in crops may play important roles in crop improvement and developmental genetics. The present study investigated and fine-mapped a Brassica napus dwarf-dominant locus BnDWF1. Plants carrying the BnDWF1 locus in populations derived from 'zhongshuang11' and Bndwf1 have deep-green leaves and dwarf architecture that differ sharply from tall plants with normal green leaves. BnDWF1, as a major locus controlling plant height, showed a very high heritability (0.91-0.95). To map this locus, a high-density single-nucleotide polymorphism map was constructed, and the BnDWF1 locus was mapped at an interval between single-nucleotide polymorphism markers, M19704 and M19695, on linkage group A09 of B. napus, with five co-segregating single-nucleotide polymorphism markers. Furthermore, fine mapping narrowed the interval harboring BnDWF1 to 152 kb in length in B. napus. This interval contains 14 annotated or predicted genes, seven of which are candidates responsible for the dwarf trait. This study provides an effective foundation for the study of plant height regulation and plant type breeding in B. napus.

iTRAQ-Based Quantitative Proteomics Analysis of Black Rice Grain Development Reveals Metabolic Pathways Associated with Anthocyanin Biosynthesis

BACKGROUND

Black rice (Oryza sativa L.), whose pericarp is rich in anthocyanins (ACNs), is considered as a healthier alternative to white rice. Molecular species of ACNs in black rice have been well documented in previous studies; however, information about the metabolic mechanisms underlying ACN biosynthesis during black rice grain development is unclear.

RESULTS

The aim of the present study was to determine changes in the metabolic pathways that are involved in the dynamic grain proteome during the development of black rice indica cultivar, (Oryza sativa L. indica var. SSP). Isobaric tags for relative and absolute quantification (iTRAQ) MS/MS were employed to identify statistically significant alterations in the grain proteome. Approximately 928 proteins were detected, of which 230 were differentially expressed throughout 5 successive developmental stages, starting from 3 to 20 days after flowering (DAF). The greatest number of differentially expressed proteins was observed on 7 and 10 DAF, including 76 proteins that were upregulated and 39 that were downregulated. The biological process analysis of gene ontology revealed that the 230 differentially expressed proteins could be sorted into 14 functional groups. Proteins in the largest group were related to metabolic process, which could be integrated into multiple biochemical pathways. Specifically, proteins with a role in ACN biosynthesis, sugar synthesis, and the regulation of gene expression were upregulated, particularly from the onset of black rice grain development and during development. In contrast, the expression of proteins related to signal transduction, redox homeostasis, photosynthesis and N-metabolism decreased during grain maturation. Finally, 8 representative genes encoding different metabolic proteins were verified via quantitative real-time polymerase chain reaction (qRT-PCR) analysis, these genes had differed in transcriptional and translational expression during grain development.

CONCLUSIONS

Expression analyses of metabolism-related protein groups belonging to different functional categories and subcategories indicated that significantly upregulated proteins were related to flavonoid and starch synthesis. On the other hand, the downregulated proteins were determined to be related to nitrogen metabolism, as well as other functional categories and subcategories, including photosynthesis, redox homeostasis, tocopherol biosynthetic, and signal transduction. The results provide valuable new insights into the characterization and understanding of ACN pigment production in black rice.

iTRAQ-Based Quantitative Proteomic Analysis of Cotton Roots and Leaves Reveals Pathways Associated with Salt Stress

Salinity is a major abiotic stress that affects plant growth and development. In this study, we performed a proteomic analysis of cotton roots and leaf tissue following exposure to saline stress. 611 and 1477 proteins were differentially expressed in the roots and leaves, respectively. In the roots, 259 (42%) proteins were up-regulated and 352 (58%) were down-regulated. In the leaves, 748 (51%) proteins were up-regulated and 729 (49%) were down-regulated. On the basis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, we concluded that the phenylalanine metabolism and starch and sucrose metabolism were active for energy homeostasis to cope with salt stress in cotton roots. Moreover, photosynthesis, pyruvate metabolism, glycolysis / gluconeogenesis, carbon fixation in photosynthetic organisms and phenylalanine metabolism were inhabited to reduce energy consumption. Characterization of the signaling pathways will help elucidate the mechanism activated by cotton in response to salt stress.

Isobaric Tag for Relative and Absolute Quantitation (iTRAQ)-Based Protein Profiling in Plants

Isobaric tags for relative and absolute quantitation (iTRAQ) is a technology that utilizes isobaric reagents to label the primary amines of peptides and proteins and is used in proteomics to study quantitative changes in the proteome by tandem mass spectrometry . Here, we present an adaptation of the iTRAQ experimental protocol for plants that allows the identification and quantitation of more than 12,000 plant proteins in Arabidopsis with a false discovery rate of less than 5 %.

Proteome Dynamics and Physiological Responses to Short-Term Salt Stress in Brassica napus Leaves

Salt stress limits plant growth and crop productivity and is an increasing threat to agriculture worldwide. In this study, proteomic and physiological responses of Brassica napus leaves under salt stress were investigated. Seedlings under salt treatment showed growth inhibition and photosynthesis reduction. A comparative proteomic analysis of seedling leaves exposed to 200 mM NaCl for 24 h, 48 h and 72 h was conducted. Forty-four protein spots were differentially accumulated upon NaCl treatment and 42 of them were identified, including several novel salt-responsive proteins. To determine the functional roles of these proteins in salt adaptation, their dynamic changes in abundance were analyzed. The results suggested that the up-accumulated proteins, which were associated with protein metabolism, damage repair and defense response, might contribute to the alleviation of the deleterious effect of salt stress on chlorophyll biosynthesis, photosynthesis, energy synthesis and respiration in Brassica napus leaves. This study will lead to a better understanding of the molecular basis of salt stress adaptation in Brassica napus and provides a basis for genetic engineering of plants with improved salt tolerance in the future.

Maternal N-Carbamylglutamate Supplementation during Early Pregnancy Enhances Embryonic Survival and Development through Modulation of the Endometrial Proteome in Gilts

BACKGROUND

Early pregnancy loss is a major concern in humans and animals. N-carbamylglutamate (NCG) has been found to enhance embryonic survival during early pregnancy in rats. However, little is known about the key factors in the endometrium involved in the improvement of embryonic implantation and development induced by maternal NCG supplementation.

OBJECTIVES

Our objectives were to investigate whether NCG supplementation during early gestation enhanced embryonic survival and development in gilts and to uncover the related factors using the approach of endometrium proteome analysis with isobaric tags for relative and absolute quantification (iTRAQ).

METHODS

Uteruses and embryos/fetuses were obtained on days 14 and 28 of gestation from gilts fed a basal diet that was or was not supplemented with 0.05% NCG. The iTRAQ-based quantitative proteomics approach was performed to explore the endometrium proteome altered by NCG supplementation.

RESULTS

Maternal NCG supplementation significantly increased the number of total fetuses and live fetuses on day 28 of gestation by 1.32 and 1.29, respectively (P < 0.05), with a significant decrease in embryonic mortality (P < 0.05). iTRAQ results indicated that a total of 59 proteins showed at least 2-fold differences (P < 0.05), including 52 proteins that were present at higher abundance and 7 proteins present at lower abundance in NCG-supplemented gilts. The differentially expressed proteins primarily are involved in cell adhesion, energy metabolism, lipid metabolism, protein metabolism, antioxidative stress, and immune response. On day 14 of gestation, several proteins closely related to embryonic implantation and development, such as integrin-αv, integrin-β3, talin, and endothelial nitric oxide synthase, were upregulated (3.7-, 4.1-, 2.4-, and 5.4-fold increases, respectively) by NCG supplementation.

CONCLUSION

To our knowledge, our results provide the first evidence that altered abundance of the endometrial proteome induced by NCG supplementation is highly associated with the improvement of embryonic survival and development in gilts.

Complementary transcriptomic and proteomic analyses of a chlorophyll-deficient tea plant cultivar reveal multiple metabolic pathway changes

To uncover the mechanisms that underlie the chlorina phenotype of the tea plant, this study employs morphological, biochemical, transcriptomic, and iTRAQ-based proteomic analyses to compare the green tea cultivar LJ43 and the yellow-leaf tea cultivar ZH1. ZH1 exhibited the chlorina phenotype, with significantly decreased chlorophyll content and abnormal chloroplast development compared with LJ43. ZH1 also displayed higher theanine and free amino acid content and lower carotenoid and catechin content. Microarray and iTRAQ analyses indicated that the differentially expressed genes and proteins could be mapped to the following pathways: 'phenylpropanoid biosynthesis,' 'glutathione metabolism,' 'phenylalanine metabolism,' 'photosynthesis,' and 'flavonoid biosynthesis.' Altered gene and protein levels in these pathways may account for the increased amino acid content and reduced chlorophyll and flavonoid content of ZH1. Altogether, this study combines transcriptomic and proteomic approaches to better understand the mechanisms responsible for the chlorina phenotype.

Comparative Proteomic Analysis of Brassica napus in Response to Drought Stress

Drought is one of the most widespread stresses leading to retardation of plant growth and development. We examined proteome changes of an important oil seed crop, canola (Brassica napus L.), under drought stress over a 14-day period. Using iTRAQ LC-MS/MS, we identified 1976 proteins expressed during drought stress. Among them, 417 proteins showed significant changes in abundance, and 136, 244, 286, and 213 proteins were differentially expressed in the third, seventh, 10th, and 14th day of stress, respectively. Functional analysis indicated that the number of proteins associated with metabolism, protein folding and degradation, and signaling decreased, while those related to energy (photosynthesis), protein synthesis, and stress and defense increased in response to drought stress. The seventh and 10th-day profiles were similar to each other but with more post-translational modifications (PTMs) at day 10. Interestingly, 181 proteins underwent PTMs; 49 of them were differentially changed in drought-stressed plants, and 33 were observed at the 10th day. Comparison of protein expression changes with those of gene transcription showed a positive correlation in B. napus, although different patterns between transcripts and proteins were observed at each time point. Under drought stress, most protein abundance changes may be attributed to gene transcription, and PTMs clearly contribute to protein diversity and functions.

Advances in plant proteomics toward improvement of crop productivity and stress resistancex

Abiotic and biotic stresses constrain plant growth and development negatively impacting crop production. Plants have developed stress-specific adaptations as well as simultaneous responses to a combination of various abiotic stresses with pathogen infection. The efficiency of stress-induced adaptive responses is dependent on activation of molecular signaling pathways and intracellular networks by modulating expression, or abundance, and/or post-translational modification (PTM) of proteins primarily associated with defense mechanisms. In this review, we summarize and evaluate the contribution of proteomic studies to our understanding of stress response mechanisms in different plant organs and tissues. Advanced quantitative proteomic techniques have improved the coverage of total proteomes and sub-proteomes from small amounts of starting material, and characterized PTMs as well as protein-protein interactions at the cellular level, providing detailed information on organ- and tissue-specific regulatory mechanisms responding to a variety of individual stresses or stress combinations during plant life cycle. In particular, we address the tissue-specific signaling networks localized to various organelles that participate in stress-related physiological plasticity and adaptive mechanisms, such as photosynthetic efficiency, symbiotic nitrogen fixation, plant growth, tolerance and common responses to environmental stresses. We also provide an update on the progress of proteomics with major crop species and discuss the current challenges and limitations inherent to proteomics techniques and data interpretation for non-model organisms. Future directions in proteomics research toward crop improvement are further discussed.

Data for iTRAQ-based quantitative proteomics analysis of Brassica napus leaves in response to chlorophyll deficiency

The essential pigment chlorophyll (Chl) plays important roles in light harvesting and energy transfer during photosynthesis. Here we present the data from a comparative proteomic analysis of chlorophyll-deficient Brassica napus mutant cde1 and its corresponding wild-type using the iTRAQ approach (Pu Chu et al., 2014 [1]). The distribution of length and number of peptides, mass and sequence coverage of proteins identified was calculated, and the repeatability of the replicates was analyzed. A total of 443 differentially expressed proteins were identified in B. napus leaves, including 228 down-accumulated proteins mainly involved in photosynthesis, porphyrin and chlorophyll metabolism, biosynthesis of secondary metabolites, carbon fixation and 215 up-accumulated proteins that enriched in the spliceosome, mRNA surveillance and RNA degradation.