December 2010, Volume 52 Issue 12, Pages 1036ĘC1126.


Cover Caption: 2-D DIGE Protein Profiling
About the cover: Two-dimensional difference gel electrophoresis (2-D DIGE) is a powerful way to identify proteins involved in plant signal transduction. In this issue, Wang et al. (pp.1075ĘC1085) used the 2-D DIGE method to compare the proteomic differences in shoots and roots of the BR-insensitive d61-4 and BR-deficient brd1-3 rice mutants. The authors identified a large number of proteins differentially expressed in mutants as compared to the wild type. On the cover picture, increased proteins appear as red, repressed proteins appear as green, while unaffected proteins appear as yellow.

 

          New Technology
A Cost-effective High-resolution Melting Approach using the EvaGreen Dye for DNA Polymorphism Detection and Genotyping in Plants
Author: Yi-Dan Li, Zhi-Zhan Chu, Xiang-Guo Liu, Hai-Chun Jing, Yao-Guang Liu and Dong-Yun Hao
Journal of Integrative Plant Biology 2010 52(12): 1036-1042
Published Online: October 5, 2010
DOI: 10.1111/j.1744-7909.2010.01001.x
      
    

High-resolution melting (HRM) analysis relies on the use of fluorescent dyes, such as LCGreen, ResoLight, and SYTO9, which bind in a saturated manner to the double-stranded DNAs. These dyes are expensive in use and may not be affordable when dealing with a large quantity of samples. EvaGreen is a much cheaper DNA helix intercalating dye and has been used in quantitative real-time polymerase chain reaction (PCR) and post-PCR DNA melt curve analysis. Here we report on the development of an EvaGreen-based HRM analysis and its performance, in comparison with the popular LCGreen-based HRM analysis, in detection of DNA polymorphism in plants. We found that various polymorphisms ranged from single nucleotide polymorphisms (SNPs) to Indels were equally detected by using EvaGreen- or LCGreen-based HRM. EvaGreen dye was sensitive enough in discovery of SNPs in fivefold pooled samples. Using this economical dye we successfully identified multiple novel mutant alleles of Gln1-3 gene, which produces a cytosolic glutamine synthetase isoenzyme (GS1), in a maize ethyl methanesulfonate (EMS)-mutagenized library, and genotyped rice mapping populations with SNP markers. The current results suggest that EvaGreen is a promising dye for HRM analysis for its ease to use and cost effectiveness.

Li YD, Chu ZZ, Liu XG, Jing HC, Liu YG, Hao DY (2010) A cost-effective high-resolution melting approach using the EvaGreen dye for DNA polymorphism detection and genotyping in plants. J. Integr. Plant Biol. 52(12), 1036–1042.

Abstract (Browse 2493)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Cell and Developmental Biology
Isobaric Tags for Relative and Absolute Quantification- based Comparative Proteomics Reveals the Features of Plasma Membrane-Associated Proteomes of Pollen Grains and Pollen Tubes from Lilium davidii
Author: Bing Han, Sixue Chen, Shaojun Dai, Ning Yang and Tai Wang
Journal of Integrative Plant Biology 2010 52(12): 1043-1058
Published Online: September 22, 2010
DOI: 10.1111/j.1744-7909.2010.00996.x
      
    

Mature pollen grains (PGs) from most plant species are metabolically quiescent. However, once pollinated onto stigma, they quickly hydrate and germinate. A PG can give rise to a vegetative cell-derived polarized pollen tube (PT), which represents a specialized polar cell. The polarized PT grows by the tip and requires interaction of different signaling molecules localized in the apical plasma membrane and active membrane trafficking. The mechanisms underlying the interaction and membrane trafficking are not well understood. In this work, we purified PG and PT plasma-membrane vesicles from Lilium davidii Duch. using the aqueous two-phase partition technique, then enriched plasma membrane proteins by using Brij58 and KCl to remove loosely bound contaminants. We identified 223 integral and membrane-associated proteins in the plasma membrane of PGs and PTs by using isobaric tags for relative and absolute quantification (iTRAQ) and 2-D high-performance liquid chromatography-tandem mass spectrometry. More than 68% of the proteins have putative transmembrane domains and/or lipid-modified motifs. Proteins involved in signal transduction, membrane trafficking and transport are predominant in the plasma-membrane proteome. We revealed most components of the clathrin-dependent endocytosis pathway. Statistical analysis revealed 14 proteins differentially expressed in the two development stages: in PTs, six upregulated and eight downregulated are mainly involved in signaling, transport and membrane trafficking. These results provide novel insights into polarized PT growth.

Han B, Chen S, Dai S, Yang N, Wang T (2010) Isobaric tags for relative and absolute quantification-based comparative proteomics reveals the features of plasma membrane-associated proteomes of pollen grains and pollen tubes from Lilium davidii. J. Integr. Plant Biol. 52(12), 1043–1058.

Abstract (Browse 2101)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Plant-environmental Interactions
Monitoring the Expression of Maize Genes in Developing Kernels under Drought Stress using Oligo-microarray
Author: Meng Luo, Jia Liu, R. Dewey Lee, Brian T. Scully and Baozhu Guo
Journal of Integrative Plant Biology 2010 52(12): 1059-1074
Published Online: October 5, 2010
DOI: 10.1111/j.1744-7909.2010.01000.x
      
    

Preharvest aflatoxin contamination of grain grown on the US southeastern Coast Plain is provoked and aggravated by abiotic stress. The primary abiotic stress is drought along with high temperatures. The objectives of the present study were to monitor gene expression in developing kernels in response to drought stress and to identify drought-responsive genes for possible use in germplasm assessment. The maize breeding line Tex6 was used, and gene expression profiles were analyzed in developing kernels under drought stress verses well-watered conditions at the stages of 25, 30, 35, 40, 45 d after pollination (DAP) using the 70 mer maize oligo-arrays. A total of 9 573 positive array spots were detected with unique gene IDs, and 7 988 were common in both stressed and well-watered samples. Expression patterns of some genes in several stress response-associated pathways, including abscisic acid, jasmonic acid and phenylalanine ammonia-lyase, were examined, and these specific genes were responsive to drought stress positively. Real-time quantitative polymerase chain reaction validated microarray expression data. The comparison between Tex6 and B73 revealed that there were significant differences in specific gene expression, patterns and levels. Several defense-related genes had been downregulated, even though some defense-related or drought responsive genes were upregulated at the later stages.

Luo M, Liu J, Lee RD, Scully BT, Guo BZ (2010) Monitoring the expression of maize genes in developing kernels under drought stress using oligo-microarray. J. Integr. Plant Biol. 52(12), 1059–1074

Abstract (Browse 2625)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Proteomic Study Identifies Proteins Involved in Brassinosteroid Regulation of Rice Growth  
Author: Fengru Wang, Ming-Yi Bai, Zhiping Deng, Juan A. Oses-Prieto, Alma L. Burlingame, Tiegang Lu, Kang Chong and Zhi-Yong Wang
Journal of Integrative Plant Biology 2010 52(12): 1075-1085
Published Online: August 26, 2010
DOI: 10.1111/j.1744-7909.2010.00992.x
      
    

Brassinosteroids (BRs) are essential hormones for growth and development of plant. In rice, BRs regulate multiple developmental processes and affect many important traits such as height, leaf angle, fertility and seed filling. We identified brassinosteroid-regulated proteins in rice using proteomic approaches and performed functional analysis of some BR-regulated proteins by overexpression experiments. Using two-dimensional difference gel electrophoresis (2-D DIGE) followed by protein identification by mass spectrometry, we compared proteomic differences in the shoots and roots of the BR-insensitive mutant d61-4 and BR-deficient mutant brd1-3. We identified a large number of proteins differentially expressed in the mutants compared with wild type control. These include a glycine-rich RNA-binding protein (OsGRP1) and a DREPP2 protein, which showed reduced levels in the BR mutants. Overexpression of these two proteins partially suppressed the dwarf phenotype of the Arabidopsis BR-insensitive mutant bri1-5. In contrast to the reduced protein level, the RNA level of OsGRP1 was not significantly affected in the BR mutants or by BR treatment, suggesting BR regulation of OsGRP1 at the posttranslational level. This study identifies many BR-regulated proteins and demonstrates that OsGRP1 functions downstream in the BR signal transduction pathway to promote cell expansion.

Wang F, Bai MY, Deng Z, Oses-Prieto JA, Burlingame AL, Lu T, Chong K, Wang ZY (2010) Proteomic study identifies proteins involved in brassinosteroid regulation of rice growth. J. Integr. Plant Biol. 52(12), 1075–1085.

Abstract (Browse 2913)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Molecular Ecology and Evolution
How do Plant Morphological Characteristics, Species Composition and Richness Regulate Eco-hydrological Function?  
Author: Zhen-Hong Wang and Chang-Qun Duan
Journal of Integrative Plant Biology 2010 52(12): 1086-1099
Published Online: June 17, 2010
DOI: 10.1111/j.1744-7909.2010.00964.x
      
    

Although considerable research has focused on the relationship between ecosystem structure and function, interactions of plant morphological characteristics, species composition and richness with eco-hydrological functions remain unclear. We measured water adherence (i.e. the capacity of a plant species to retain water), documented plant surface morphology and observed surface runoff at three sites in China. The adhering water ratios for each plant species differed, ranging from 17.1% to 151.5% in leaves, and from 14.4% to 41.1% in branches. Small, light-weight, soft, non-cuticularized leaves that were densely situated on small branches showed good water adherence. The next best adherence was found by branches with intermediately coarse surfaces. The plant species with high standing biomass also showed good water adherence, and the contribution of a species to total adherence was dependent upon its aboveground standing biomass. Vegetation parameters strongly affected water adherence, whereas the effect of species richness was not significant. Conversely, species richness showed a significant influence on surface runoff. The effect of plant morphological characteristics and composition constitutes a basic process in the regulation of eco-hydrological function, and vegetation parameters play somewhat different roles in that regulation. The key roles must therefore be considered from a management perspective.

Wang ZH, Duan CQ (2010) How do plant morphological characteristics, species composition and richness regulate eco-hydrological function? J. Integr. Plant Biol. 52(12), 1086–1099.

Abstract (Browse 1902)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Complex Mutation and Weak Selection together Determined the Codon Usage Bias in Bryophyte Mitochondrial Genomes
Author: Bin Wang, Jing Liu, Liang Jin, Xue-Ying Feng and Jian-Qun Chen
Journal of Integrative Plant Biology 2010 52(12): 1100-1108
Published Online: September 27, 2010
DOI: 10.1111/j.1744-7909.2010.00998.x
      
    

Mutation and selection are two major forces causing codon usage biases. How these two forces influence the codon usages in green plant mitochondrial genomes has not been well investigated. In the present study, we surveyed five bryophyte mitochondrial genomes to reveal their codon usage patterns as well as the determining forces. Three interesting findings were made. First, comparing to Chara vulgaris, an algal species sister to all extant land plants, bryophytes have more G, C-ending codon usages in their mitochondrial genes. This is consistent with the generally higher genomic GC content in bryophyte mitochondria, suggesting an increased mutational pressure toward GC. Second, as indicated by Wright's Nc-GC3s plot, mutation, not selection, is the major force affecting codon usages of bryophyte mitochondrial genes. However, the real mutational dynamics seem very complex. Context-dependent analysis indicated that nucleotide at the 2nd codon position would slightly affect synonymous codon choices. Finally, in bryophyte mitochondria, tRNA genes would apply a weak selection force to fine-tune the synonymous codon frequencies, as revealed by data of Ser4-Pro-Thr-Val families. In summary, complex mutation and weak selection together determined the codon usages in bryophyte mitochondrial genomes.

Wang B, Liu J, Jin L, Feng XY, Chen JQ (2010) Complex mutation and weak selection together determined the codon usage bias in bryophyte mitochondrial genomes. J. Integr. Plant Biol. 52(12), 1100–1108.

Abstract (Browse 1940)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
A Test of Seven Candidate Barcode Regions from the Plastome in Picea (Pinaceae)
Author: Jin-Hua Ran, Pei-Pei Wang, Hui-Juan Zhao and Xiao-Quan Wang
Journal of Integrative Plant Biology 2010 52(12): 1109-1126
Published Online: September 11, 2010
DOI: 10.1111/j.1744-7909.2010.00995.x
      
    

DNA barcoding, as a tool for species discrimination, has been used efficiently in animals, algae and fungi, but there are still debates on which DNA region(s) can be used as the standard barcode(s) for land plants. Gymnosperms, especially conifers, are important components of forests, and there is an urgent need for them to be identified through DNA barcoding because of their high frequency of collection in the field. However, the feasibility of DNA barcoding in gymnosperms has not been examined based on a dense species sampling. Here we selected seven candidate DNA barcodes from the plastome (matK, rbcL, rpoB, rpoC1, atpF-atpH, psbA-trnH, and psbK-psbI) to evaluate their suitability in Picea (spruce). The results showed that none of them or their different combinations has sufficient resolution for spruce species, although matK+rbcL might be used as a two-locus barcode. The low efficiency of these candidate barcodes in Picea might be caused by the paternal inheritance of the chloroplast genome, long generation time, recent radiation, and frequent inter-specific hybridization aided by wind pollination. Some of these factors could also be responsible for the difficulties in barcoding other plant groups. Furthermore, the potential of the nuclear LEAFY gene as a land plant barcode was discussed.

Ran JH, Wang PP, Zhao HJ, Wang XQ (2010) A test of seven candidate barcode regions from the plastome in Picea (Pinaceae). J. Integr. Plant Biol. 52(12), 1109–1126.

Abstract (Browse 1883)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Acknowledgements
Acknowledgements
Author:
Journal of Integrative Plant Biology 2010 52(12): i-ii
Published Online: November 24, 2010
DOI: 10.1111/j.1744-7909.2010.01013.x
Abstract (Browse 836)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
 

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