Special Issue: Frontiers of Integrative Plant Biology   

April 2010, Volume 52 Issue 4, Pages 350¨C430.

Cover Caption: Frontiers of Integrative Plant Biology
Integrative biology is to use multidisciplinary approaches to elucidating complex biological processes. This special issue of ˇ°Frontiers of Integrative Plant Biologyˇ± focuses on the latest developments in this area, targeted at unraveling the mechanisms by which plants respond to environmental and developmental cues. The cover picture (provided by Katie Dehesh, see pages 354¨C359 for details) displays an Arabidopsis seedling expressing the firefly luciferase gene under the control of a novel cis-regulatory element which responds rapidly (within 5 min) and transiently to a wide range of biotic and abiotic stimuli. The seedling is challenged by a fungal pathogen Botrytis cinerea.


Understanding Plant Development and Stress Responses through Integrative Approaches  
Author: Katie Dehesh and Chun-Ming Liu
Journal of Integrative Plant Biology 2010 52(4): 350-353
Published Online: March 30, 2010
DOI: 10.1111/j.1744-7909.2010.00950.x
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          Invited Expert Reviews
Molecular Mechanisms Regulating Rapid Stress Signaling Networks in Arabidopsis  
Author: Justin W Walley, and Katayoon Dehesh
Journal of Integrative Plant Biology 2010 52(4): 354-359
Published Online: March 30, 2010
DOI: 10.1111/j.1744-7909.2010.00940.x

As sessile organisms plants must cope with ever changing environmental conditions. To survive plants have evolved elaborate mechanisms to perceive and rapidly respond to a diverse range of abiotic and biotic stresses. Central to this response is the ability to modulate gene expression at both the transcriptional and post-transcriptional levels. This review will focus on recent progress that has been made towards understanding the rapid reprogramming of the transcriptome that occurs in response to stress as well as emerging mechanisms underpinning the reprogramming of gene expression in response to stress.

Walley JW, Dehesh K (2010) Molecular mechanisms regulating rapid stress signaling networks in Arabidopsis. J. Integr. Plant Biol. 52(4), 354–359.

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Abiotic and Biotic Stresses and Changes in the Lignin Content and Composition in Plants  
Author: Jullyana Cristina Magalhães Silva Moura, Cesar Augusto Valencise Bonine, Juliana de Oliveira Fernandes Viana, Marcelo Carnier Dornelas and Paulo Mazzafera
Journal of Integrative Plant Biology 2010 52(4): 360-376
Published Online: March 12, 2010
DOI: 10.1111/j.1744-7909.2010.00892.x

Lignin is a polymer of phenylpropanoid compounds formed through a complex biosynthesis route, represented by a metabolic grid for which most of the genes involved have been sequenced in several plants, mainly in the model-plants Arabidopsis thaliana and Populus. Plants are exposed to different stresses, which may change lignin content and composition. In many cases, particularly for plant-microbe interactions, this has been suggested as defence responses of plants to the stress. Thus, understanding how a stressor modulates expression of the genes related with lignin biosynthesis may allow us to develop study-models to increase our knowledge on the metabolic control of lignin deposition in the cell wall. This review focuses on recent literature reporting on the main types of abiotic and biotic stresses that alter the biosynthesis of lignin in plants.

Moura JCMS, Bonine CAV, Viana JOF, Dornelas MC, Mazzafera P (2010) Abiotic and biotic stresses and changes in the lignin content and composition in plants. J. Integr. Plant Biol. 52(4), 360–376.

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Reviewing the Technical Designs for Experiments with Ultraviolet-B Radiation and Impact on Photosynthesis, DNA and Secondary Metabolism  
Author: Chenping Xu and Joe H. Sullivan
Journal of Integrative Plant Biology 2010 52(4): 377-387
Published Online: March 30, 2010
DOI: 10.1111/j.1744-7909.2010.00939.x

The ultraviolet-B (UV-B) portion of sunlight has received much attention in the last three decades, because radiation from this spectral region increases due to the stratospheric ozone depletion, which results from increases of chlorofluorocarbons in the atmosphere. Plant responses to UV-B exposure vary greatly and the interpretation of and comparison between studies is hindered, mainly by the contrasting experimental conditions used and interactive factors such as low light levels and possible artifacts due to the artificial experimental conditions. It seems likely that increases in solar UV-B radiation of the magnitude anticipated under current stratospheric ozone projections will not significantly inhibit photosynthesis and cause DNA damage in plants. This is in part due to the well-evolved protection mechanisms present in most plant species. One of the significant plant responses to UV-B is changes in foliar secondary chemistry, which could be translated into significant effects at higher trophic levels through plant-herbivore interactions and decomposition. Enhanced UV-B radiation due to stratospheric ozone depletion could also cause morphological changes that would affect competitive interactions, especially if contrasting UV-B sensitivity exists among the competitors.

Xu C, Sullivan JH (2010) Reviewing the technical designs for experiments with UV-B radiation and UV-B impact on photosynthesis, DNA and secondary metabolism. J. Integr. Plant Biol. 52(4), 377–387.

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Short RNAs in Tomato  
Author: Tamas Dalmay
Journal of Integrative Plant Biology 2010 52(4): 388-392
Published Online: February 10, 2010
DOI: 10.1111/j.1744-7909.2009.00871.x

Short RNAs are 20–24 nucleotide long non-coding RNA molecules generated by one of the Dicer-like enzymes. They recognize specific RNA or DNA sequences and guide the RNA silencing complex to their targets leading to post-transcriptional or transcriptional gene silencing of the target. Most of our knowledge about short RNAs comes from studying the model species Arabidopsis. Recently, however, several reports emerged about short RNAs in tomato, which is a model plant for fleshy fruit development and ripening. Tomato short RNAs have been sequenced and a database was established. Novel non-conserved microRNAs were found that showed differential expression between fruit and other tissues, even during fruit development, suggesting that they may play a role in fruit formation. Several target genes were predicted and validated for both conserved and non-conserved miRNAs and some of these targets are key players in fruit ripening, such as Colourless non-ripening. The present study reviews the current state of tomato short RNAs research and suggests future directions.

Dalmay T (2010) Short RNAs in tomato. J. Integr. Plant Biol. 52(4), 388–392.

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Novel Insights from Live-imaging in Shoot Meristem Development  
Author: Paja Sijacic and Zhongchi Liu
Journal of Integrative Plant Biology 2010 52(4): 393-399
Published Online: March 30, 2010
DOI: 10.1111/j.1744-7909.2010.00941.x

Microscopic imaging of fluorescent reporters for key meristem regulators in live tissues is emerging as a powerful technique, enabling researchers to observe dynamic spatial and temporal distribution of hormonal and developmental regulators in living cells. Aided by time-lapse microphotography, new types of imaging acquisition and analysis software, and computational modeling, we are gaining significant insights into shoot apical meristem (SAM) behavior and function. This review is focused on summarizing recent advances in the understanding of SAM organization, development, and behavior derived from live-imaging techniques. This includes the revelation of mechanical forces in microtubule-controlled anisotropic growth, the role of the CLV-WUS network in the specification of peripheral zone and central zone cells, the multiple feedback loops involving cytokinin in controlling WUS expression, auxin dynamics in determining the position of new primordia, and, finally, sequence of regulatory events leading to de novo assembly of shoots from callus in culture. Future studies toward formulating "digital SAM" that incorporates multi-dimensional data ranging from images of SAM morphogenesis to a genome-scale expression map of SAM will greatly enhance our ability to understand, predict, and manipulate SAM, containing the stem cells that give rise to all above ground parts of a plant.

Sijacic P, Liu Z (2010) Novel insights from live-imaging in shoot meristem development. J. Integr. Plant Biol. 52(4), 393–399.

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          Research Articles
Increased Vitamin C Content Accompanied by an Enhanced Recycling Pathway Confers Oxidative Stress Tolerance in Arabidopsis  
Author: Zinan Wang, Ying Xiao, Wansheng Chen, Kexuan Tang and Lei Zhang
Journal of Integrative Plant Biology 2010 52(4): 400-409
Published Online: February 25, 2010
DOI: 10.1111/j.1744-7909.2010.00921.x

Vitamin C (L-ascorbic acid, AsA) has important antioxidant and metabolic functions in both plants and animals. Once used, ascorbic acid can be regenerated from its oxidized form in a reaction catalyzed by dehydroascorbate reductase (DHAR, EC To analyze the physiological role of DHAR catalyzing the reduction of DHA to ascorbate in environmental stress adaptation, we examined whether increasing the level of AsA through enhanced AsA recycling would limit the deleterious effects of oxidative stress. A chimeric construct consisting of the double CaMV35S promoter fused to the Myc-dhar gene was introduced into Arabidopsis thaliana. Transgenic plants were biochemically characterized and tested for responses to oxidative stress. Western blot indicated that the dhar-transgene was successfully expressed. In homozygous T4 transgenic seedlings, DHAR overexpression was increased up to 1.5 to 5.4 fold, which enhanced foliar ascorbic acid levels 2- to 4.25-fold and ratio of AsA/DHA about 3- to 16-fold relative to wild type. In addition, the level of glutathione, the reductant used by DHAR, also increased as did its redox state. When whole plants were treated with high light and high temperature stress or in vitro leaf discs were subjected to 10 μM paraquat, transgenic plants showed a larger AsA pool size, lower membrane damage, and a higher level of chlorophyll compared with controls. These data suggested that increasing the plant vitamin C content through enhanced ascorbate recycling could limit the deleterious effects of environmental oxidative stress.

Wang Z, Xiao Y, Chen W, Tang K, Zhang L (2010) Increased vitamin C content accompanied by an enhanced recycling pathway confers oxidative stress tolerance in Arabidopsis. J. Integr. Plant Biol. 52(4), 400–409.

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Proteomics Study of COI1-regulated Proteins in Arabidopsis Flower  
Author: Lingling Chua, Xiaoyi Shan, Junxia Wang, Wen Peng and Daoxin Xie
Journal of Integrative Plant Biology 2010 52(4): 410-419
Published Online: March 30, 2010
DOI: 10.1111/j.1744-7909.2010.00938.x

Jasmonates (JAs) are a new class of plant hormone that regulate expression of diverse genes to mediate various plant responses. The Arabidopsis F-box protein COI1 is required for plant defense and male fertility in JA signal pathway. To further investigate the regulatory role of COI1 in male fertility, we compared the proteomics profiles of Arabidopsis wild type (WT) flowers with coi1-1 mutant male-sterile flowers using two-dimensional difference gel electrophoresis coupled with matrix-assisted laser desoption/ionization-time-of-flight mass spectrometry. Sixteen proteins with potential function in specific biological processes such as metabolism processes and defense/stress responses were differentially expressed in WT and coi1-1 mutant flowers. Verification on a phi class glutathione transferase AtGSTF9, one out of these 16 identified proteins, revealed that the expression of AtGSTF9 was severely downregulated in flowers of coi1-1 mutant compared with that of WT. Further function analyses of these genes would provide new insights into the molecular basis of COI1-regulated male fertility.

Chua L, Shan X, Wang J, Peng W, Zhang G, Xie D (2010) Proteomics study of COI1-regulated proteins in Arabidopsis flower. J. Integr. Plant Biol. 52(4), 410–419.

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SDG714 Regulates Specific Gene Expression and Consequently Affects Plant Growth via H3K9 Dimethylation  
Author: Bo Ding, Yan Zhu, Zhong-Yuan Bu, Wen-Hui Shen, Yu Yu and Ai-Wu Dong
Journal of Integrative Plant Biology 2010 52(4): 420-430
Published Online: March 19, 2010
DOI: 10.1111/j.1744-7909.2010.00927.x

Histone lysine methylation is known to be involved in the epigenetic regulation of gene expression in all eukaryotes including plants. Here we show that the rice SDG714 is primarily responsible for dimethylation but not trimethylation on histone H3K9 in vivo. Overexpression of YFP-SDG714 in Arabidopsis significantly inhibits plant growth and this inhibition is associated with an enhanced level of H3K9 dimethylation. Our microarray results show that many genes essential for the plant growth and development were downregulated in transgenic Arabidopsis plants overexpressing YFP-SDG714. By chromatin immunoprecipitation analysis, we show that YFP-SDG714 is targeted to specific chromatin regions and dimethylate the H3K9, which is linked with heterochromatinization and the downregulation of genes. Most interestingly, when YFP-SDG714 production is stopped, the inhibited plants can partially restore their growth, suggesting that the perturbation of gene expression caused by YFP-SDG714 is revertible. Taken together, our results point to an important role of SDG714 in H3K9 dimethylation, suppression of gene expression and plant growth, and provide a potential method to regulate gene expression and plant development by an on-off switch of SDG714 expression.

Ding B, Zhu Y, Bu ZY, Shen WH, Yu Y, Dong AW (2010) SDG714 regulates specific gene expression and consequently affects plant growth via H3K9 dimethylation. J. Integr. Plant Biol. 52(4), 420–430.

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