July 2015, Volume 57 Issue 7, Pages 606每660.


Cover Caption: JA Conjugation in Grapes
The hormone jasmonic acid (JA) is activated by conjugation to isoleucine. In this issue, Bötcher et al. (pp. 618每627) analyze two grapevine JAamido synthetases, VvGH3-7 and VvGH3-9, for their roles in JA-Ile conjugate biosynthesis, berry development and stress responses. In leaves, VvGH3-9 is wounding- and JA-responsive, while VvGH3-7 seems to be induced by a mobile wounding signal.

 

          Minireview
Getting started in mapping-by-sequencing  
Author: Héctor Candela, Rubén Casanova-Sáez and José Luis Micol
Journal of Integrative Plant Biology 2015 57(7): 606每612
Published Online: October 31, 2014
DOI: 10.1111/jipb.12305
      
    

Next-generation sequencing (NGS) technologies allow the cost-effective sequencing of whole genomes and have expanded the scope of genomics to novel applications, such as the genome-wide characterization of intraspecific polymorphisms and the rapid mapping and identification of point mutations. Next-generation sequencing platforms, such as the Illumina HiSeq2000 platform, are now commercially available at affordable prices and routinely produce an enormous amount of sequence data, but their wide use is often hindered by a lack of knowledge on how to manipulate and process the information produced. In this review, we focus on the strategies that are available to geneticists who wish to incorporate these novel approaches into their research but who are not familiar with the necessary bioinformatic concepts and computational tools. In particular, we comprehensively summarize case studies where the use of NGS technologies has led to the identification of point mutations, a strategy that has been dubbed “mapping-by-sequencing”, and review examples from plants and other model species such as Caenorhabditis elegans, Saccharomyces cerevisiae, and Drosophila melanogaster. As these technologies are becoming cheaper and more powerful, their use is also expanding to allow mutation identification in species with larger genomes, such as many crop plants.

 

Candela H, Casanova-Sáez R, Micol JL (2015) Getting started in mapping-by-sequencing. J Integr Plant Biol 57: 606–612. doi: 10.1111/jipb.12305

Abstract (Browse 1664)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Next-generation sequencing technologies allow the rapid mapping and identification of point mutations, a strategy that has been dubbed ※mapping-by-sequencing§. We review examples where these technologies have led to the identification of mutations in Arabidopsis and other model species, such as yeast or Drosophila. Mapping-by-sequencing will also help to understand the molecular basis of many traits in species with larger genomes, such as many crops.
          New Technology
CRISPR Primer Designer: Design primers for knockout and chromosome imaging CRISPR-Cas system  
Author: Meng Yan, Shi-Rong Zhou and Hong-Wei Xue
Journal of Integrative Plant Biology 2015 57(7): 613每617
Published Online: October 16, 2014
DOI: 10.1111/jipb.12295
      
    

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated system enables biologists to edit genomes precisely and provides a powerful tool for perturbing endogenous gene regulation, modulation of epigenetic markers, and genome architecture. However, there are concerns about the specificity of the system, especially the usages of knocking out a gene. Previous designing tools either were mostly built-in websites or ran as command-line programs, and none of them ran locally and acquired a user-friendly interface. In addition, with the development of CRISPR-derived systems, such as chromosome imaging, there were still no tools helping users to generate specific end-user spacers. We herein present CRISPR Primer Designer for researchers to design primers for CRISPR applications. The program has a user-friendly interface, can analyze the BLAST results by using multiple parameters, score for each candidate spacer, and generate the primers when using a certain plasmid. In addition, CRISPR Primer Designer runs locally and can be used to search spacer clusters, and exports primers for the CRISPR-Cas system-based chromosome imaging system.

 

Yan M, Zhou SR, Xue HW (2015) CRISPR Primer Designer: Design primers for knockout and chromosome imaging CRISPR-Cas system. J Integr Plant Biol 57: 613–617. doi: 10.1111/jipb.12295

Abstract (Browse 1990)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
CRISPR Primer Designer helps CRISPR-Cas system users to choose specific spacer sequences for genomes editing and chromosome imaging. Not only for plants, but for all organisms that support Whole Genome BLAST in NCBI, local BLAST or other sites. We will update the program continually.
          Molecular Physiology
Jasmonic acid-isoleucine formation in grapevine (Vitis vinifera L.) by two enzymes with distinct transcription profiles
Author: Christine Böttcher, Crista A. Burbidge, Valentina di Rienzo, Paul K. Boss and Christopher Davies
Journal of Integrative Plant Biology 2015 57(7): 618每627
Published Online: December 10, 2014
DOI: 10.1111/jipb.12321
      
    

The plant hormone jasmonic acid (JA) is essential for stress responses and the formation of reproductive organs, but its role in fruit development and ripening is unclear. Conjugation of JA to isoleucine is a crucial step in the JA signaling pathway since only JA-Ile is recognized by the jasmonate receptor. The conjugation reaction is catalyzed by JA-amido synthetases, belonging to the family of Gretchen Hagen3 (GH3) proteins. Here, in vitro studies of two grapevine (Vitis vinifera L. cv Shiraz) GH3 enzymes, VvGH3-7 and VvGH3-9, demonstrated JA-conjugating activities with an overlapping range of amino acid substrates, including isoleucine. Expression studies of the corresponding genes in grape berries combined with JA and JA-Ile measurements suggested a primary role for JA signaling in fruit set and cell division and did not support an involvement of JA in the ripening process. In response to methyl JA (MeJA) treatment, and in wounded and unwounded (distal) leaves, VvGH3-9 transcripts accumulated, indicating a participation in the JA response. In contrast, VvGH3-7 was unresponsive to MeJA and local wounding, demonstrating a differential transcriptional regulation of VvGH3-7 and VvGH3-9. The transient induction of VvGH3-7 in unwounded, distal leaves was suggestive of the involvement of an unknown mobile wound signal.

 

Böttcher C, Burbidge CA, di Rienzo V, Boss PK, Davies C (2015) Jasmonic acid-isoleucine formation in grapevine (Vitis vinifera L.) by two enzymes with distinct transcription profiles. J Integr Plant Biol 57: 618–627 doi: 10.1111/jipb.12321

Abstract (Browse 737)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
In grapevine, the hormone JA-Ile was shown to be produced by two enzymes, VvGH3-7 and VvGH3-9. Studies of gene expression and hormone measurements revealed that the above two GH3 proteins are likely to be involved in early berry development, but play different roles in the leaf wound response.
          Plant-environmental Interactions
Hydrogen sulfide regulates abiotic stress tolerance and biotic stress resistance in Arabidopsis
Author: Haitao Shi, Tiantian Ye, Ning Han, Hongwu Bian, Xiaodong Liu and Zhulong Chan
Journal of Integrative Plant Biology 2015 57(7): 628每640
Published Online: October 20, 2014
DOI: 10.1111/jipb.12302
      
    

Hydrogen sulfide (H2S) is an important gaseous molecule in various plant developmental processes and plant stress responses. In this study, the transgenic Arabidopsis thaliana plants with modulated expressions of two cysteine desulfhydrases, and exogenous H2S donor (sodium hydrosulfide, NaHS) and H2S scavenger (hypotaurine, HT) pre-treated plants were used to dissect the involvement of H2S in plant stress responses. The cysteine desulfhydrases overexpressing plants and NaHS pre-treated plants exhibited higher endogenous H2S level and improved abiotic stress tolerance and biotic stress resistance, while cysteine desulfhydrases knockdown plants and HT pre-treated plants displayed lower endogenous H2S level and decreased stress resistance. Moreover, H2S upregulated the transcripts of multiple abiotic and biotic stress-related genes, and inhibited reactive oxygen species (ROS) accumulation. Interestingly, MIR393-mediated auxin signaling including MIR393a/b and their target genes (TIR1, AFB1, AFB2, and AFB3) was transcriptionally regulated by H2S, and was related with H2S-induced antibacterial resistance. Moreover, H2S regulated 50 carbon metabolites including amino acids, organic acids, sugars, sugar alcohols, and aromatic amines. Taken together, these results indicated that cysteine desulfhydrase and H2S conferred abiotic stress tolerance and biotic stress resistance, via affecting the stress-related gene expressions, ROS metabolism, metabolic homeostasis, and MIR393-targeted auxin receptors.

 

Shi H, Ye T, Han N, Bian H, Liu X, Chan Z (2015) Hydrogen sulfide regulates abiotic stress tolerance and biotic stress resistance in Arabidopsis. J Integr Plant Biol 57: 628–640. doi: 10.1111/jipb.12302

Abstract (Browse 913)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
H2S is an important gaseous molecule in various plant developmental processes and plant stress responses. Herein, this study shows that cysteine desulfhydrase and H2S confer abiotic stress tolerance and biotic stress resistance in Arabidopsis, via affecting the stress-related gene expressions, ROS metabolism, metabolic homeostasis, and MIR393-targeted auxin receptors.
Enhancement of innate immune system in monocot rice by transferring the dicotyledonous elongation factor Tu receptor EFR
Author: Fen Lu, Huiqin Wang, Shanzhi Wang, Wendi Jiang, Changlin Shan, Bin Li, Jun Yang, Shiyong Zhang and Wenxian Sun
Journal of Integrative Plant Biology 2015 57(7): 641每652
Published Online: October 31, 2014
DOI: 10.1111/jipb.12306
      
    

The elongation factor Tu (EF-Tu) receptor (EFR) in cruciferous plants specifically recognizes the N-terminal acetylated elf18 region of bacterial EF-Tu and thereby activates plant immunity. It has been demonstrated that Arabidopsis EFR confers broad-spectrum bacterial resistance in the EFR transgenic solanaceous plants. Here, the transgenic rice plants (Oryza sativa L. ssp. japonica cv. Zhonghua 17) and cell cultures with constitutive expression of AtEFR were developed to investigate whether AtEFR senses EF-Tu and thus enhances bacterial resistance in the monocot plants. We demonstrated that the Xanthomonas oryzae-derived elf18 peptide induced oxidative burst and mitogen-activated protein kinase activation in the AtEFR transgenic rice cells and plants, respectively. Pathogenesis-related genes, such as OsPBZ1, were upregulated dramatically in transgenic rice plant and cell lines in response to elf18 stimulation. Importantly, pretreatment with elf18 triggered strong resistance to X. oryzae pv. oryzae in the transgenic plants, which was largely dependent on the AtEFR expression level. These plants also exhibited enhanced resistance to rice bacterial brown stripe, but not to rice fungal blast. Collectively, the results indicate that the rice plants with heterologous expression of AtEFR recognize bacterial EF-Tu and exhibit enhanced broad-spectrum bacterial disease resistance and that pattern recognition receptor-mediated immunity may be manipulated across the two plant classes, dicots and monocots.

 

Lu F, Wang H, Wang S, Jiang W, Shan C, Li B, Yang J, Zhang S, Sun W (2015) Enhancement of innate immune system in monocot rice by transferring the dicotyledonous elongation factor Tu receptor EFR. J Integr Plant Biol 57: 641–652. doi: 10.1111/jipb.12306

Abstract (Browse 1160)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Heterologous expression of EFR, a Brassicaceae-specific pattern recognition receptor, in rice was demonstrated to be functional to sense bacterial EF-Tu and confer broad-spectrum bacterial disease resistance. The study opens new avenues for genetic engineering of broad-spectrum disease resistance in rice by transfer of pattern recognition receptor genes across plant classes.
Effect of elevated CO2 concentration on photosynthetic characteristics of hyperaccumulator Sedum alfredii under cadmium stress
Author: Tingqiang Li, Qi Tao, Zhenzhen Di, Fan Lu and Xiaoe Yang
Journal of Integrative Plant Biology 2015 57(7): 653每660
Published Online: November 4, 2014
DOI: 10.1111/jipb.12307
      
    

The combined effects of elevated CO2 and cadmium (Cd) on photosynthetic rate, chlorophyll fluorescence and Cd accumulation in hyperaccumulator Sedum alfredii Hance were investigated to predict plant growth under Cd stress with rising atmospheric CO2 concentration. Both pot and hydroponic experiments were conducted and the plants were grown under ambient (350 µL L−1) or elevated (800 µL L−1) CO2. Elevated CO2 significantly (P < 0.05) increased Pn (105%–149%), Pnmax (38.8%–63.0%) and AQY (20.0%–34.8%) of S. alfredii in all the Cd treatments, but reduced chlorophyll concentration, dark respiration and photorespiration. After 10 days growth in medium with 50 µM Cd under elevated CO2, PSII activities were significantly enhanced (P < 0.05) with Pm, Fv/Fm, Φ(II) and qP increased by 66.1%, 7.5%, 19.5% and 16.4%, respectively, as compared with ambient-grown plants. Total Cd uptake in shoot of S. alfredii grown under elevated CO2 was increased by 44.1%–48.5%, which was positively correlated with the increase in Pn. These results indicate that elevated CO2 promoted the growth of S. alfredii due to increased photosynthetic carbon uptake rate and photosynthetic light-use efficiency, and showed great potential to improve the phytoextraction of Cd by S. alfredii.

 

Li TQ, Tao Q, Di ZZ, Lu F, Yang XE (2015) Effect of elevated CO2 concentration on photosynthetic characteristics of hyperaccumulator Sedum alfredii under cadmium stress. J Integr Plant Biol 57: 653–660. doi: 10.1111/jipb.12307

Abstract (Browse 915)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
An increase in atmospheric CO2 concentration has profound influences on plant growth. In this study, we found that elevated CO2 promoted the growth of Sedum alfredii, a Cd hyperaccumulator native to China, due to increased photosynthetic carbon uptake rate and photosynthetic light-use efficiency, and significantly increased Cd uptake by S. alfredii.
 

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