Differential proteomic analysis during the vegetative phase change and the floral transition in Malus domestica

Proteomic Identification of Differentially Expressed Proteins during Alfalfa (Medicago sativa L.) Flower Development

Flower development, pollination, and fertilization are important stages in the sexual reproduction process of plants; they are also critical steps in the control of seed formation and development. During alfalfa (Medicago sativa L.) seed production, some distinct phenomena such as a low seed setting ratio, serious flower falling, and seed abortion commonly occur. However, the causes of these phenomena are complicated and largely unknown. An understanding of the mechanisms that regulate alfalfa flowering is important in order to increase seed yield. Hence, proteomic technology was used to analyze changes in protein expression during the stages of alfalfa flower development. Flower samples were collected at pre-pollination (S1), pollination (S2), and the post-pollination senescence period (S3). Twenty-four differentially expressed proteins were successfully identified, including 17 down-regulated in pollinated flowers, one up-regulated in pollinated and senesced flowers, and six up-regulated in senesced flowers. The largest proportions of the identified proteins were involved in metabolism, signal transduction, defense response, oxidation reduction, cell death, and programmed cell death (PCD). Their expression profiles demonstrated that energy metabolism, carbohydrate metabolism, and amino acid metabolism provided the nutrient foundation for pollination in alfalfa. Furthermore, there were three proteins involved in multiple metabolic pathways: dual specificity kinase splA-like protein (kinase splALs), carbonic anhydrase, and NADPH: quinone oxidoreductase-like protein. Expression patterns of these proteins indicated that MAPK cascades regulated multiple processes, such as signal transduction, stress response, and cell death. PCD also played an important role in the alfalfa flower developmental process, and regulated both pollination and flower senescence. The current study sheds some light on protein expression profiles during alfalfa flower development and contributes to the understanding of the basic molecular mechanisms during the alfalfa flowering process. These results may offer insight into potential strategies for improving seed yield, quality, and stress tolerance in alfalfa.

Omics studies of citrus, grape and rosaceae fruit trees

Recent advance of bioinformatics and analytical apparatuses such as next generation DNA sequencer (NGS) and mass spectrometer (MS) has brought a big wave of comprehensive study to biology. Comprehensive study targeting all genes, transcripts (RNAs), proteins, metabolites, hormones, ions or phenotypes is called genomics, transcriptomics, proteomics, metabolomics, hormonomics, ionomics or phenomics, respectively. These omics are powerful approaches to identify key genes for important traits, to clarify events of physiological mechanisms and to reveal unknown metabolic pathways in crops. Recently, the use of omics approach has increased dramatically in fruit tree research. Although the most reported omics studies on fruit trees are transcriptomics, proteomics and metabolomics, and a few is reported on hormonomics and ionomics. In this article, we reviewed recent omics studies of major fruit trees, i.e. citrus, grapevine and rosaceae fruit trees. The effectiveness and prospects of omics in fruit tree research will as well be highlighted.

Redox homeostasis and reactive oxygen species scavengers shift during ontogenetic phase changes in apple

The change from juvenile to adult phase is a universal phenomenon in perennial plants such as apple. To validate the changes in hydrogen peroxide (H2O2) levels and scavenging during ontogenesis in apple seedlings, the H2O2 contents, its scavenging capacity, and the expression of related genes, as well as miR156 levels, were measured in leaf samples from different nodes in seedlings of 'Zisai Pearl' (Malus asiatica)×'Red Fuji' (M. domestica). Then in vitro shoots were treated with redox modulating chemicals to verify the response of miR156 to redox alteration. The expression of miR156 decreased gradually during ontogenesis, indicating a progressive loss of juvenility. During the phase changes, H2O2 and ascorbate contents, the ratio of ascorbate to dehydroascorbate, the ascorbate peroxidase, catalase and glutathione reductase activities, and the expressions of some MdGR and MdAPX gene family members increased remarkably. However, the glutathione content and glutathione to glutathione disulfide ratio declined. In chemicals treated in vitro shoots, the changes in miR156 levels were coordinated with GSH contents and GSH/GSSG ratio but not H2O2 contents. Conclusively, the relative reductive thiol redox status is critical for the maintenance of juvenility and the reductive ascorbate redox environment was elevated and sustained during the reproductive phase.

Protein phosphorylation differs significantly among ontogenetic phases in Malus seedlings

BACKGROUND

Although protein phosphorylation is an important post-translational modification affecting protein function and metabolism, dynamic changes in this process during ontogenesis remain unexplored in woody angiosperms.

METHODS

Phosphorylated proteins from leaves of three apple seedlings at juvenile, adult vegetative and reproductive stages were extracted and subjected to alkaline phosphatase pre-treatment. After separating the proteins by two-dimensional gel electrophoresis and phosphoprotein-specific Pro-Q Diamond staining, differentially expressed phosphoproteins were identified by MALDI-TOF-TOF mass spectrometry.

RESULTS

A total of 107 phosphorylated protein spots on nine gels (three ontogenetic phases × three seedlings) were identified by MALDI-TOF-TOF mass spectrometry. The 55 spots of ribulose-1, 5-bisphosphate carboxylase/oxygenase (Rubisco) large-chain fragments varied significantly in protein abundance and degree of phosphorylation among ontogenetic phases. Abundances of the 27 spots corresponding to Rubisco activase declined between juvenile and reproductive phases. More extensively, phosphorylated β-tubulin chain spots with lower isoelectric points were most abundant during juvenile and adult vegetative phases.

CONCLUSIONS

Protein phosphorylation varied significantly during vegetative phase change and floral transition in apple seedlings. Most of the observed changes were consistent among seedlings and between hybrid populations.

Proteomic changes in different growth periods of ginseng roots

For the first time, proteomics and biochemical variables have been employed to unravel the growth strategies for the different root growth periods of ginseng (Panax ginseng CA May., Araliaceae). Enzymatic activities and cellular contents, except for starch, related to defence and metabolism were significantly increased in the slow-growth period but decreased in the fast-growth period. Proteomic characterisation by two-dimensional gel electrophoresis (2DE) showed 83 differentially expressed spots; 62 spots were up-regulated and 21 spots were down-regulated in the slow-growth period when compared to the fast-growth period. The identification of these spots indicated that the major groups of differential proteins were associated with energy metabolism (37%) and defence (17%), which was consistent with the changes observed in the biochemical measurements. These results clearly demonstrate that ginseng stores energy during its fast-growth period to promote root elongation, whereas it expends energy to improve the synthesis of secondary metabolites and stress resistance during its slow-growth period. The levels of many proteins were changed during the conversion period from fast to slow growth, providing new insights into ginseng proteome evolution. The proposed hypothetical model explains the interaction of metabolic proteins associated with the growth strategies of ginseng.

Differential expression and modification of proteins during ontogenesis in Malus domestica

Many morphological and physiological changes have been widely reported during ontogeny in higher plants. In order for the better understanding of the proteomic differences between ontogenetic phases, protein compositions between leaves of juvenile, adult vegetative and reproductive phases were compared in an apple (Malus domestica Borkh., Jonathan × Golden Delicious) seedling. Totally, 122 differentially expressed or modified protein spots were separated by DIGE. Of the 122 protein spots, 44, 17 and 29 were abundant in the leaf samples from the juvenile, adult vegetative and reproductive phases, respectively, two spots showed a lower level in the adult vegetative tissue, while the amount of protein increased in 21 spots during ontogeny and declined in nine spots. One hundred and fifteen spots were successfully picked and 95 spots were identified by MALDI-TOF-TOF high-resolution tandem mass spectrometry. Twenty-three juvenile phase abundant or down-regulated spots were photosynthesis-associated proteins, implying a juvenile phase-related photosynthesis enhancement. The expression of 10 enzymes and coenzymes involved in protein synthesis and catabolism was elevated in the adult reproductive phase or up-regulated during ontogeny, contributing a phase change-related activation in protein metabolism. Six proteins generated 30 differential gel spots via post-translational modifications. The differential expression of NADP-dependent D-sorbitol-6-phosphate dehydrogenase was confirmed by Western blotting in six seedlings derived from two hybrid populations. The results of semi-quantitative PCR indicate that some but not all of these proteomic changes were transcriptionally regulated.