January 2016, Volume 58 Issue 1, Pages 1每103.


Cover Caption: Vascular Bundles in Maize Stem
Vascular bundles in plants transport sugars, minerals and water, which is a limiting factor for yield realization. Huang et al. (pp. 81-90) report highresolution genetic analyses of the number of vascular bundles in maize stem using a large maize-teosinte population. Results showed that the vascular bundle number is controlled by a large number of small-effect QTLs that might not be under directional selection during domestication.

 

          Functional Omics and Systems Biology
Multi-scale modeling of Arabidopsis thaliana response to different CO2 conditions: From gene expression to metabolic flux  
Author: Lin Liu, Fangzhou Shen, Changpeng Xin and Zhuo Wang
Journal of Integrative Plant Biology 2016 58(1): 2每11
Published Online: May 23, 2015
DOI: 10.1111/jipb.12370
      
    

Multi-scale investigation from gene transcript level to metabolic activity is important to uncover plant response to environment perturbation. Here we integrated a genome-scale constraint-based metabolic model with transcriptome data to explore Arabidopsis thaliana response to both elevated and low CO2 conditions. The four condition-specific models from low to high CO2 concentrations show differences in active reaction sets, enriched pathways for increased/decreased fluxes, and putative post-transcriptional regulation, which indicates that condition-specific models are necessary to reflect physiological metabolic states. The simulated CO2 fixation flux at different CO2 concentrations is consistent with the measured Assimilation-CO2intercellular curve. Interestingly, we found that reactions in primary metabolism are affected most significantly by CO2 perturbation, whereas secondary metabolic reactions are not influenced a lot. The changes predicted in key pathways are consistent with existing knowledge. Another interesting point is that Arabidopsis is required to make stronger adjustment on metabolism to adapt to the more severe low CO2 stress than elevated CO2. The challenges of identifying post-transcriptional regulation could also be addressed by the integrative model. In conclusion, this innovative application of multi-scale modeling in plants demonstrates potential to uncover the mechanisms of metabolic response to different conditions.

 

Liu L, Shen F, Xin C, Wang Z (2016) Multi-scale modeling of Arabidopsis thaliana response to different CO2 conditions: From gene expression to metabolic flux. J Integr Plant Biol 58: 2–11 doi: 10.1111/jipb.12370

Abstract (Browse 1291)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Studies on plant response to different CO2 conditions in the levels of both gene transcript and metabolic activity are still very limited so far. Here, by integrating metabolic model with transcriptome data, we construct specific models for Arabidopsis under elevated and low CO2, which uncovered differences in active reactions, increased/decreased fluxes, and post-transcriptional regulation.
Single base substitution in OsCDC48 is responsible for premature senescence and death phenotype in rice  
Author: Qi-Na Huang, Yong-Feng Shi, Xiao-Bo Zhang, Li-Xin Song, Bao-Hua Feng, Hui-Mei Wang, Xia Xu, Xiao-Hong Li, Dan Guo and Jian-Li Wu
Journal of Integrative Plant Biology 2016 58(1): 12每28
Published Online: June 4, 2015
DOI: 10.1111/jipb.12372
      
    

A premature senescence and death 128 (psd128) mutant was isolated from an ethyl methane sulfonate-induced rice IR64 mutant bank. The premature senescence phenotype appeared at the six-leaf stage and the plant died at the early heading stage. psd128 exhibited impaired chloroplast development with significantly reduced photosynthetic ability, chlorophyll and carotenoid contents, root vigor, soluble protein content and increased malonaldehyde content. Furthermore, the expression of senescence-related genes was significantly altered in psd128. The mutant trait was controlled by a single recessive nuclear gene. Using map-based strategy, the mutation Oryza sativa cell division cycle 48 (OsCDC48) was isolated and predicted to encode a putative AAA-type ATPase with 809 amino-acid residuals. A single base substitution at position C2347T in psd128 resulted in a premature stop codon. Functional complementation could rescue the mutant phenotype. In addition, RNA interference resulted in the premature senescence and death phenotype. OsCDC48 was expressed constitutively in the root, stem, leaf and panicle. Subcellular analysis indicated that OsCDC48:YFP fusion proteins were located both in the cytoplasm and nucleus. OsCDC48 was highly conserved with more than 90% identity in the protein levels among plant species. Our results indicated that the impaired function of OsCDC48 was responsible for the premature senescence and death phenotype.

 

Huang QN, Shi YF, Zhang XB, Song LX, Feng BH, Wang HM, Xu X, Li XH, Guo D, Wu JL (2016) Single base substitution in OsCDC48 is responsible for premature senescence and death phenotype in rice. J Integr Plant Biol 58: 12–28 doi: 10.1111/jipb.12372

Abstract (Browse 1599)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Plant senescence and death can be caused by various factors. One of them is an enzyme termed AAA-ATPase showing multiple biological functions and mainly servicing as the energy provider. OsCDC48 is the corresponding enzyme in rice and its defect cause early senescence and death in rice.
          Molecular Physiology
Decreased glutathione reductase2 leads to early leaf senescence in Arabidopsis  
Author: Shunhua Ding, Liang Wang, Zhipan Yang, Qingtao Lu, Xiaogang Wen and Congming Lu
Journal of Integrative Plant Biology 2016 58(1): 29每47
Published Online: June 1, 2015
DOI: 10.1111/jipb.12371
      
    

Glutathione reductase (GR) catalyzes the reduction of glutathione disulfide (GSSG) to reduced glutathione (GSH) and participates in the ascorbate-glutathione cycle, which scavenges H2O2. Here, we report that chloroplastic/mitochondrial GR2 is an important regulator of leaf senescence. Seed development of the homozygous gr2 knockout mutant was blocked at the globular stage. Therefore, to investigate the function of GR2 in leaf senescence, we generated transgenic Arabidopsis plants with decreased GR2 using RNAi. The GR2 RNAi plants displayed early onset of age-dependent and dark- and H2O2-induced leaf senescence, which was accompanied by the induction of the senescence-related marker genes SAG12 and SAG13. Furthermore, transcriptome analysis revealed that genes related to leaf senescence, oxidative stress, and phytohormone pathways were upregulated directly before senescence in RNAi plants. In addition, H2O2 accumulated to higher levels in RNAi plants than in wild-type plants and the levels of H2O2 peaked in RNAi plants directly before the early onset of leaf senescence. RNAi plants showed a greater decrease in GSH/GSSG levels than wild-type plants during leaf development. Our results suggest that GR2 plays an important role in leaf senescence by modulating H2O2 and glutathione signaling in Arabidopsis.

 

Ding S, Wang L, Yang Z, Lu Q, Wen X, Lu C (2016) Decreased glutathione reductase2 leads to early leaf senescence in Arabidopsis. J Integr Plant Biol 58: 29–47 doi: 10.1111/jipb.12371

Abstract (Browse 888)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Glutathione reductase (GR) functions in the ascorbate-glutathione cycle, which scavenges H2O2. Here, we report that GR2 regulates leaf senescence by modulating H2O2 and glutathione signaling in Arabidopsis.
Gene expression and physiological responses to salinity and water stress of contrasting durum wheat genotypes  
Author: Salima Yousfi, Antonio J. Márquez, Marco Betti, José Luis Araus and Maria Dolores Serret
Journal of Integrative Plant Biology 2016 58(1): 48每66
Published Online: April 13, 2015
DOI: 10.1111/jipb.12359
      
    
Elucidating the relationships between gene expression and the physiological mechanisms remains a bottleneck in breeding for resistance to salinity and drought. This study related the expression of key target genes with the physiological performance of durum wheat under different combinations of salinity and irrigation. The candidate genes assayed included two encoding for the DREB (dehydration responsive element binding) transcription factors TaDREB1A and TaDREB2B, another two for the cytosolic and plastidic glutamine synthetase (TaGS1 and TaGS2), and one for the specific Na+/H+ vacuolar antiporter (TaNHX1). Expression of these genes was related to growth and different trait indicators of nitrogen metabolism (nitrogen content, stable nitrogen isotope composition, and glutamine synthetase and nitrate reductase activities), photosynthetic carbon metabolism (stable carbon isotope composition and different gas exchange traits) and ion accumulation. Significant interaction between genotype and growing conditions occurred for growth, nitrogen content, and the expression of most genes. In general terms, higher expression of TaGS1, TaGS2, TaDREB2B, and to a lesser extent of TaNHX1 were associated with a better genotypic performance in growth, nitrogen, and carbon photosynthetic metabolism under salinity and water stress. However, TaDREB1A was increased in expression under stress compared with control conditions, with tolerant genotypes exhibiting lower expression than susceptible ones.

 

Yousfi S, Marquez AJ, Betti M, Araus JL, Serret MD (2016) Gene expression and physiological responses to salinity and water stress of contrasting durum wheat genotypes. J Integr Plant Biol 58: 48–66 doi: 10.1111/jipb.12359

Abstract (Browse 1018)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Durum wheat is a major crop in Mediterranean arid environments, where salinity driven by irrigation is an increasing problem, and breeding is a way for mitigation. Our study shows that genotypes more resilient to salinity exhibit increased expression of key genes involved in the photosynthetic metabolism of carbon and nitrogen.
Arabidopsis C3HC4-RING finger E3 ubiquitin ligase AtAIRP4 positively regulates stress-responsive abscisic acid signaling  
Author: Liang Yang, Qiaohong Liu, Zhibin Liu, Hao Yang, Jianmei Wang, Xufeng Li and Yi Yang
Journal of Integrative Plant Biology 2016 58(1): 67每80
Published Online: April 24, 2015
DOI: 10.1111/jipb.12364
      
    

Degradation of proteins via the ubiquitin system is an important step in many stress signaling pathways in plants. E3 ligases recognize ligand proteins and dictate the high specificity of protein degradation, and thus, play a pivotal role in ubiquitination. Here, we identified a gene, named Arabidopsis thaliana abscisic acid (ABA)-insensitive RING protein 4 (AtAIRP4), which is induced by ABA and other stress treatments. AtAIRP4 encodes a cellular protein with a C3HC4-RING finger domain in its C-terminal side, which has in vitro E3 ligase activity. Loss of AtAIRP4 leads to a decrease in sensitivity of root elongation and stomatal closure to ABA, whereas overexpression of this gene in the T-DNA insertion mutant atairp4 effectively recovered the ABA-associated phenotypes. AtAIRP4 overexpression plants were hypersensitive to salt and osmotic stresses during seed germination, and showed drought avoidance compared with the wild-type and atairp4 mutant plants. In addition, the expression levels of ABA- and drought-induced marker genes in AtAIRP4 overexpression plants were markedly higher than those in the wild-type and atairp4 mutant plants. Hence, these results indicate that AtAIRP4 may act as a positive regulator of ABA-mediated drought avoidance and a negative regulator of salt tolerance in Arabidopsis.

 

Yang L, Liu Q, Liu Z, Yang H, Wang J, Li X, Yang Y (2016) Arabidopsis C3HC4-RING finger E3 ubiquitin ligase AtAIRP4 positively regulates stress-responsive abscisic acid signaling. J Integr Plant Biol 58: 67–80 doi: 10.1111/jipb.12364

Abstract (Browse 1105)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Protein degradation mediated by ubiquitin plays a primary role in plant stress signaling transduction. E3 ligases recognize the acceptor protein and play a pivotal role in ubiquitination. Here, we identified that AtAIRP4, a C3HC4-RING finger E3 ligase, is a positive regulator of ABA-mediated drought and salt tolerance in Arabidopsis.
          Plant-environmental Interactions
Identification and fine mapping of quantitative trait loci for the number of vascular bundle in maize stem  
Author: Cheng Huang, Qiuyue Chen, Guanghui Xu, Dingyi Xu, Jinge Tian and Feng Tian
Journal of Integrative Plant Biology 2016 58(1): 81每90
Published Online: April 3, 2015
DOI: 10.1111/jipb.12358
      
    

Studies that investigated the genetic basis of source and sink related traits have been widely conducted. However, the vascular system that links source and sink received much less attention. When maize was domesticated from its wild ancestor, teosinte, the external morphology has changed dramatically; however, less is known for the internal anatomy changes. In this study, using a large maize-teosinte experimental population, we performed a high-resolution quantitative trait locus (QTL) mapping for the number of vascular bundle in the uppermost internode of maize stem. The results showed that vascular bundle number is dominated by a large number of small-effect QTLs, in which a total of 16 QTLs that jointly accounts for 52.2% of phenotypic variation were detected, with no single QTL explaining more than 6% of variation. Different from QTLs for typical domestication traits, QTLs for vascular bundle number might not be under directional selection following domestication. Using Near Isogenic Lines (NILs) developed from heterogeneous inbred family (HIF), we further validated the effect of one QTL qVb9-2 on chromosome 9 and fine mapped the QTL to a 1.8-Mb physical region. This study provides important insights for the genetic architecture of vascular bundle number in maize stem and sets basis for cloning of qVb9-2.

 

Huang C, Chen Q, Xu G, Xu D, Tian J, Tian F (2016) Identification and fine mapping of quantitative trait loci for the number of vascular bundle in maize stem. J Integr Plant Biol 58: 81–90 doi: 10.1111/jipb.12358

Abstract (Browse 981)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Vascular bundle is the plant transport system that links source and sink, and acts as an important factor for yield potential realization. We report a high-resolution QTL mapping for vascular bundle number in maize stem using a large maize-teosinte population, and show that vascular bundle number is dominated by a large number of small-effect QTLs.
A pair of light signaling factors FHY3 and FAR1 regulates plant immunity by modulating chlorophyll biosynthesis  
Author: Wanqing Wang, Weijiang Tang, Tingting Ma, De Niu, Jing Bo Jin, Haiyang Wang and Rongcheng Lin
Journal of Integrative Plant Biology 2016 58(1): 91每103
Published Online: May 18, 2015
DOI: 10.1111/jipb.12369
      
    

Light and chloroplast function is known to affect the plant immune response; however, the underlying mechanism remains elusive. We previously demonstrated that two light signaling factors, FAR-RED ELONGATED HYPOCOTYL 3 (FHY3) and FAR-RED IMPAIRED RESPONSE 1 (FAR1), regulate chlorophyll biosynthesis and seedling growth via controlling HEMB1 expression in Arabidopsis thaliana. In this study, we reveal that FHY3 and FAR1 are involved in modulating plant immunity. We showed that the fhy3 far1 double null mutant displayed high levels of reactive oxygen species and salicylic acid (SA) and increased resistance to Pseudomonas syringae pathogen infection. Microarray analysis revealed that a large proportion of pathogen-related genes, particularly genes encoding nucleotide-binding and leucine-rich repeat domain resistant proteins, are highly induced in fhy3 far1. Genetic studies indicated that the defects of fhy3 far1 can be largely rescued by reducing SA signaling or blocking SA accumulation, and by overexpression of HEMB1, which encodes a 5-aminolevulinic acid dehydratase in the chlorophyll biosynthetic pathway. Furthermore, we found that transgenic plants with reduced expression of HEMB1 exhibit a phenotype similar to fhy3 far1. Taken together, this study demonstrates an important role of FHY3 and FAR1 in regulating plant immunity, through integrating chlorophyll biosynthesis and the SA signaling pathway.

 

Wang W, Tang W, Ma T, Niu D, Jin JB, Wang H, Lin R (2016) A pair of light signaling factors FHY3 and FAR1 regulates plant immunity by modulating chlorophyll biosynthesis. J Integr Plant Biol 58: 91–103 doi: 10.1111/jipb.12369

Abstract (Browse 1043)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
This study reveals that two light signaling transcription factors modulate plant immune response through regulating chlorophyll biosynthesis and the salicylic acid biosynthetic and signaling pathways.
 

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