6(5) 2013 issue
September 2013 issue
Southern Cross Publishing Group©2013

Plant Omics | September 2013
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Proteomic profiling of rice roots from a super-hybrid rice cultivar and its parental lines

Xiaoliang Xiang1,3, Shuju Ning2, Daozhi Wei1*

1School of life sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
2School of Crop sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
3JNU-HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, Jinan University, Guangzhou, 510632, P. R. China

Heterosis is a common phenomenon in which the hybrids exhibit superior agronomic performance than both parents such as biomass production, grain yield, and stress tolerance. Although heterosis breeding is one of the main techniques in rice breeding, the molecular mechanisms responsible for this basic biological phenomenon are not well understood. To further get an insight into the molecular mechanisms of rice heterosis, comparative root proteomic analysis between a super-hybrid rice LYP9 and its parental cultivars 9311 and PA64S at seedling stage were performed. Total proteins were extracted and subjected to two-dimensional gel electrophoresis. The scatter plots analysis results showed that the LYP9’s expression profiles were more similar to 9311 than PA64S. A total of 11 differentially expressed protein spots were detected and identified by matrix-assisted laser desorption/ionization-time of flight/time of flight mass spectrometry, corresponding to 10 unique proteins. These proteins were identified to be involved in several cellular processes, including metabolism, secondary metabolism, Transcription regulation, energy metabolism, signal transduction, disease and defense. Moreover, based on our present data, the differentially expressed proteins could work together to play a major role in the induced defense response. In addition, we observed that phenylalanine ammonia-lyase, Os12g0440200 and putative PrMC3 proteins had higher expression in LYP9 than its parents. These proteins can be strongest candidates for further functional research.

Pages 318-324 | Full Text PDF

Applying DNA barcoding to identify Nervilia fordii and six congeneric species

Qionglin HUANG, Lingling LIANG, Rui HE*, Xinye MA, Ruoting ZHAN, Weiwen CHEN*

Research Center of Chinese Medicinal Resource Science and Engineering, Guangzhou University of Chinese Medicine (GZUCM), Guangzhou 510006, P.R. China
Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, Guangzhou 510006, P.R. China

DNA barcoding is a novel technique which enables species identification and taxonomic classification using a short and standard DNA sequence. In this study, traditional herbal medicine Nervilia fordii and its congeneric species included all three distributed in mainland China and three acquired from Genbank were sampled. Four popular candidate DNA barcodes, ITS2, rbcL, matK, and LSU D1-D3, were amplified and sequenced with corresponding pairs of universal primers. The PCR amplification and sequencing efficiency, intra- and interspecific variation and barcoding gap were used to evaluate each locus, and the success rate of correct identification was assessed by the BLAST 1 method. The sequencing efficiency of rbcL and LSU D1-D3 was 100%, while that of matK and ITS2 was 95.8% and 91.4%, respectively. Although relatively lower contribution in sequencing efficiency and interspecific divergence, matK exhibited significant barcoding gap and discriminated all the given species in our study. ITS2 had the largest variation in both intra- and interspecific level, which enabled classification at the genus level. Our findings showed that DNA barcoding is an efficient biomarker for identification of N. fordii and its congeners and that matK gene is a potential DNA barcode for Nervilia.

Pages 325-332 | Full Text PDF

Comparative proteomic identification of embryo proteins associated with hydropriming induced rapid-germination of maize seeds

Fangping Gong, Xiaolin Wu, Wei Wang*

Synergetic Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural University, Zhengzhou, China

Maize (Zea mays) is one of the most important crops and widely planted in the world. In the arid and semi-arid maize production regions, hydropriming is a simple technique to improve seed germination and seedling establishment. However, the mechanism underlying hydropriming is largely unclear at the molecular level. This study aimed to analyze the priming-induced changes in maize embryo proteome and to identify priming-associated proteins. Mature maize seeds of Zhengdan 958, the most sown cultivar in China currently, were used for hydropriming. Hydropriming was performed by soaking seeds in water for 12 h (25°C) and air-drying them to original moisture contents. Primed and unprimed seeds were subjected to germination test  and comparative proteomic analysis. The results showed that hydropriming significantly improved seed germination and overwhelming embryo proteins were unchanged in abundance after priming. At least 8 protein spots changed greatly, of which 5 increased and 3 decreased in the primed seeds. These proteins were identified as peroxiredoxin-5, 1-Cys peroxiredoxin, embryonic protein DC-8, cupin, globulin-1 and late embryogenesis abundant protein. DC-8 and globulin-1 may be used for the molecular markers of priming effect and seed vigor. Our results would contribute to the understanding of hydropriming mechanism at the proteome level.

Pages 333-339 | Full Text PDF | Supplementary data

In vitro and in silico screening for Andrographis paniculata quorum sensing mimics: new therapeutic leads for cystic fibrosis Pseudomonas aeruginosa biofilms

Murugan K1*, Sangeetha S2, Kalyanasundaram V.B3 and Saleh Al-Sohaibani1

1Department of Botany & Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
2Bioinformatics Laboratory, AU-KBC Research Centre, MIT campus of Anna  University Chennai, Chromepet, Chennai, India
3Post Graduate and Research Department of Microbiology, K.S.R. College of Arts and Science, Tiruchengodu, India

The clinical management and definitive treatment of cystic fibrosis (CF) biofilm-mediated chronic Pseudomonas aeruginosa lung infection remains a challenge. The methanol extract of the popular ethanomedicinal herb Andrographis paniculata L., which is traditionally used to treat respiratory illnesses, was shown to have growth and biofilm inhibitory activities against clinical isolates of P. aeruginosa from CF patients. Here, we report the antibiofilm activity of A. paniculata methanol extract on quorum sensing (QS) inhibition using both in vitro and molecular docking studies. The inhibitory activity of the extracts on exopolysaccharide and pigment production by the CF isolate and the QS indicator organism Chromobacterium violaceum ATCC 12472 and the interaction between the phytoconstituent, biofilm and QS proteins were determined. GC-MS analysis detected 32 plant phytochemicals of diverse nature that may account for its antibiofilm activity and its traditional use in the treatment of many illnesses, including respiratory infections. A number of compounds such as carbamic acid, N-phenyl-, 2-methylphenyl ester, and 2-methoxy-4-[(1-phenylpropan-2-ylamino)methyl]phenol, were found to possess better binding affinity (= -5) to no less than two P. aeruginosa QS proteins without violation of Lipinski’s rule. Furthermore, several compounds exhibited high drug-like molecular activity scores indicating their bioavailability and possible activity. These results indicate a significant affinity between the antibiofilm and quorum quenching activities and a probable use for the development of novel CF biofilm specific therapeutic strategies using A. paniculata extracts in the future. Moreover, the results also support the use of A. paniculata in traditional medicine.

Pages 340-346 | Full Text PDF

Overexpression of the chloride channel gene (GmCLC1) from soybean increases salt tolerance in transgenic Populus deltoides × P. euramericana ‘Nanlin895’

Weibo Sun, Daxia Deng, Liheng Yang, Xiaojiao Zheng, Juan Yu, Huixin Pan and Qiang Zhuge*

Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education,  Nanjing Forestry University, Nanjing 210037, China

The GmCLC1 encodes a vacuolar Cl- transporter protein that sequesters ions from the cytoplasm to the vacuole, thereby reducing the toxic effects of salt stress. We constructed a GmCLC1 overexpression vector, pGWB402O, and introduced it into poplar hybrid, Populus deltoides × P. euramericana ‘Nanlin895’, by Agrobacterium tumefaciens-mediated transformation. PCR and Southern blot analyses showed that GmCLC1 was integrated into the genome of the hybrid poplar line. When transgenic plants overexpressing GmCLC1 were subjected to salt stress, the contents of soluble protein and photosynthetic pigments and the activity of antioxidant enzymes (POD and SOD) were increased, and the MDA concentrations were significantly decreased in transgenic lines compared with the control lines. Also, the defoliation rates of the transgenic plants were signi?cantly lower than that of the control plants. These results suggest that overexpression of GmCLC1 plays a significant role in improving salt tolerance of poplars, reducing damage to membrane structures, and enhancing osmotic adjustment and antioxidative enzyme regulation during salt stress.

Pages 347-354 | Full Text PDF
Research Note

Mutagenic effects of low energy ions on root tip cells of tomato (Lycopersicum esculentum)

Hongying Duan, Yongang Yu, Yunlong He, Yanqing Zhou and Longdou Lu*

College of Life Sciences, Henan Normal University, Henan Xinxiang 453007, P. R. China

Low energy ion has been successfully applied to crop breeding, but there are few studies on application of ion beam in tomato breeding. In this research, effects of ion beam on root tip cells of tomato were studied. We found that nitrogen ion (N+) or argon ion (Ar+) had obvious influences on cell mitosis and chromosome structure, and lead to various types of chromosome aberration. When dose of ion beam increased within the scope of 1-4×1017 ions cm-2, the index of cell mitosis declined and rate of chromosome aberration increased, and various types of chromosome aberration occurred in the same cell when dose of ion beam was high. In addition, compared to the same dose of Ar+ ion, the index of cell mitosis was lower and rate of chromosome aberration was higher as implanted with N+ ion, suggesting N+ ion had greater influence on cell mitosis and chromosome structure. Taken together, cell aberration could be induced by N+ or Ar+ ion, and genetic material of tomato might be damaged, therefore low energy ion is potential to be as mutagenic agent in breeding and improvement of tomato.

Pages 355-358 | Full Text PDF

Polyclonal antibody preparation and immunolocalization of maize (Zea mays) seed protein EMB564

Xiaolin Wu1, Monica Scali2, Claudia Faleri2, and Wei Wang1,*

1Synergetic Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
2Department of Life Sciences, University of Siena, 53100, Italy

Maize protein EMB564 is a member of group 1 LEA (late embryogenesis abundant) proteins. Currently, there is accumulating information available concerning the biological functions and subcellular localization of group 1 LEA proteins. We recently found that EMB564 protein is associated with maize seed viability. In order to elucidate the function of EMB564, its tissue and subcellular localization in mature seeds was analyzed by immunochemical analysis. A peptide corresponding to a 20-mer consensus (TVVPGGTGGKSVEAQEHLAE) of EMB564 was chemically synthesized and used to immunize rabbits for polyclonal antibody preparation. This antibody reacted strongly with EMB564. Immunoblot analysis revealed that EMB564 existed in highest abundance in the plumule, followed by the radicle and scutellum in the maize embryo. Immunoelectron microscopy demonstrated the preferential nuclear localization of EMB564, associated with chromatin, in the embryonic cells. This subcellular localization is consistent with the previous bioinformatic prediction. This is the first immunoelectron microscopy evidence of subcellular localization of the group 1 LEA proteins. This work would help to understand the mechanism underlying the function of the EMB564 in seed vigor maintenance.

Pages 359-363 | Full Text PDF

Expression analysis of proline metabolism-related genes in salt-tolerant soybean mutant plants

Özge Çelik, Selin Gül Ünsal

Istanbul Kültür University, Faculty of Science and Letters, Department of Molecular Biology and Genetics, 34156, Ataköy, Istanbul, Turkey

Salt stress is one of the important abiotic stress factors. Proline is generally thought to play an important role in the improvement of salt tolerance in plants. In the present study, we discussed the relationship between free proline accumulation and the expression patterns of the genes that play roles in proline metabolism (P5CS, P5CR, PDH, P5CDH) under 90 mM NaCl stress. We used three salt tolerant M3 generation soybean mutant plants (Ataem-7/150-68, S04-05/150-2 and S04-05/150-114). The mutants belonging to M3 generation are determined as tolerant to 90 mM NaCl. The free proline contents of the salt-tolerant mutants were measured at the upper phase of the extract with respect to toluene. We observed 1.96-, 2.43- and 1.14-fold increases in the free proline accumulation of Ataem-7/150-68, S04-05/150-2 and S04-05/150-114 mutant plants after 7 days of salt treatment in accordance with control groups, respectively. The expression analyses were performed using specific primers designed for soybean gene regions. According to the results of the quantitative reverse-transcriptase polymerase chain reaction, all the genes were up-regulated when these mutants were subjected to salt stress. In addition to increased expression levels of these genes in three salt tolerant soybean mutants, the only statistically significant relation was observed between the regulation of P5CR and PDH gene expressions and proline content in S04-05/150-114 mutant. In further studies, the other possible mechanisms that cause proline accumulation should be evaluated for these salt tolerant soybean mutants.

Pages 364-370 | Full Text PDF