July 2018, Volume 60 Issue 7, Pages 529-622.


Cover Caption: Histone methylation and rice growth
Trimethylation of histone H3 at lysine 4 (H3K4me3) plays important roles in growth and development. In this issue, Jiang et al. (530¨C535) report that SDG721 and SDG705 encode TRITHORAX©\like proteins and modulate H3K4 methylation in rice. The sdg721/sdg705 double mutants display semi©\dwarf, reduced cell length, reduced numbers of panicle branching and pollen grain.

 

          Letters to the Editor
SDG721 and SDG705 are required for rice growth  
Author: Pengfei Jiang, Shiliang Wang, Aziz Ul Ikram, Zuntao Xu, Haiyang Jiang, Beijiu Cheng and Yong Ding
Journal of Integrative Plant Biology 2018 60(7): 530-535
Published Online: February 23, 2018
DOI: 10.1111/jipb.12644
      
    

H3K4me3 plays important roles in development, transcription, and environmental responses. Here, we report that SDG721 (SET©\domain group protein 721) and SDG705 are involved in regulating rice development. SDG721 and SDG705 encode TRITHORAX©\like proteins, which appear to modulate H3K4 methylation levels. Loss of SDG721 and SDG705 function resulted in GA©\deficient phenotypes, including semi©\dwarfism, reduced cell length, and reduced panicle branching. The transcripts levels and H3K4me3 levels of GA biosynthesis genes and GA signaling pathway genes were downregulated in the sdg721 sdg705 plants. Together, these results suggest that SDG721 and SDG705 regulate H3K4 methylation, which is crucial for plant development in rice.

Abstract (Browse 269)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Height and grain number are critical for rice yield. Here, we report that SDG721 (SET©\domain group protein 721) and SDG705 are involved in gibberellins (GAs) singling pathway to promote rice height and increase panicle branches and grain number.
Efficient allelic replacement in rice by gene editing: A case study of the NRT1.1B gene  
Author: Jingying Li, Xin Zhang, Yongwei Sun, Jiahui Zhang, Wenming Du, Xiuping Guo, Shaoya Li, Yunde Zhao, Lanqin Xia
Journal of Integrative Plant Biology 2018 60(7): 536-540
Published Online: March 23, 2018
DOI: 10.1111/jipb.12650
      
    

Precise replacement of an existing allele in commercial cultivars with an elite allele is a major goal in crop breeding. A single nucleotide polymorphism in the NRT1.1B gene between japonica and indica rice is responsible for the improved nitrogen use efficiency in indica rice. Herein, we precisely replaced the japonica NRT1.1B allele with the indica allele, in just one generation, using CRISPR/Cas9 gene©\editing technology. No additional selective pressure was needed to enrich the precise replacement events. This work demonstrates the feasibility of replacing any genes with elite alleles within one generation, greatly expanding our ability to improve agriculturally important traits.

Abstract (Browse 229)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Precise replacement of an existing allele in commercial cultivars with an elite allele is a major goal in crop breeding. Herein, we established a CRISPR/Cas9©\mediated targeted gene replacement system in rice without additional selective pressure by using the NRT1.1B gene as an example. This system will greatly expand our ability in crop improvement.
          Cell and Developmental Biology
Plant G proteins interact with endoplasmic reticulum luminal protein receptors to regulate endoplasmic reticulum retrieval  
Author: Shanshan Wang, Ke Xie, Guoyong Xu, Huarui Zhou, Qiang Guo, Jingyi Wu, Zengwei Liao, Na Liu, Yan Wang and Yule Liu
Journal of Integrative Plant Biology 2018 60(7): 541-561
Published Online: March 20, 2018
DOI: 10.1111/jipb.12648
      
    

Maintaining endoplasmic reticulum (ER) homeostasis is essential for the production of biomolecules. ER retrieval, i.e., the retrograde transport of compounds from the Golgi to the ER, is one of the pathways that ensures ER homeostasis. However, the mechanisms underlying the regulation of ER retrieval in plants remain largely unknown. Plant ERD2©\like proteins (ERD2s) were recently suggested to function as ER luminal protein receptors that mediate ER retrieval. Here, we demonstrate that heterotrimeric G protein signaling is involved in ERD2©\mediated ER retrieval. We show that ERD2s interact with the heterotrimeric G protein Gα and Gγ subunits at the Golgi. Silencing of , , or increased the retention of ER luminal proteins. Furthermore, overexpression of Gα, Gβ, or Gγ caused ER luminal proteins to escape from the ER, as did the co©\silencing of ERD2a and ERD2b. These results suggest that G proteins interact with ER luminal protein receptors to regulate ER retrieval.

Abstract (Browse 97)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
G proteins have multiple roles inside the cells. In this study, we found a new function of heterotrimeric G proteins. We demonstrated that G protein subunits negatively regulate the ER retrieval by interacting with ER luminal protein receptors, which is responsible for ER retrieval from Golgi to ER.
Phot2©\regulated relocation of NPH3 mediates phototropic response to high©\intensity blue light in Arabidopsis thaliana  
Author: Xiang Zhao, Qingping Zhao, Chunye Xu, Jin Wang, Jindong Zhu, Baoshuan Shang and Xiao Zhang
Journal of Integrative Plant Biology 2018 60(7): 562-577
Published Online: February 2, 2018
DOI: 10.1111/jipb.12639
      
    
Two redundant blue©\light receptors, known as phototropins (phot1 and phot2), influence a variety of physiological responses, including phototropism, chloroplast positioning, and stomatal opening in Arabidopsis thaliana. Whereas phot1 functions in both low©\ and high©\intensity blue light (HBL), phot2 functions primarily in HBL. Here, we aimed to elucidate phot2©\specific functions by screening for HBL©\insensitive mutants among mutagenized Arabidopsis phot1 mutants. One of the resulting phot2 signaling associated (p2sa) double mutants, phot1 p2sa2, exhibited phototropic defects that could be restored by constitutively expressing NON©\PHOTOTROPIC HYPOCOTYL 3 (NPH3), indicating that P2SA2 was allelic to NPH3. It was observed that NPH3©\GFP signal mainly localized to and clustered on the plasma membrane in darkness. This NPH3 clustering on the plasma membrane was not affected by mutations in genes encoding proteins that interact with NPH3, including PHOT1, PHOT2 and ROOT PHOTOTROPISM 2 (RPT2). However, the HBL irradiation©\mediated release of NPH3 proteins into the cytoplasm was inhibited in phot1 mutants and enhanced in phot2 and rpt2©\2 mutants. Furthermore, HBL©\induced hypocotyl phototropism was enhanced in phot1 mutants and inhibited in the phot2 and rpt2©\2 mutants. Our findings indicate that phot1 regulates the dissociation of NPH3 from the plasma membrane, whereas phot2 mediates the stabilization and relocation of NPH3 to the plasma membrane to acclimate to HBL.
Abstract (Browse 237)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Blue light receptor phototropins (phot1 and phot2), redundantly regulate hypocotyl phototropism, which restricts the understanding of the specific roles of phot2. In this study, we showed that phot1 regulates the dissociation of NPH3 from membranes, whereas phot2 mediates the stabilization and relocation of NPH3 to the membrane to acclimate to high blue light.
          Functional Omics and Systems Biology
Transcriptional and temporal response of Populus stems to gravi©\stimulation  
Author: Matthew Zinkgraf, Suzanne Gerttula, Shutang Zhao, Vladimir Filkov and Andrew Groover
Journal of Integrative Plant Biology 2018 60(7): 578-590
Published Online: February 26, 2018
DOI: 10.1111/jipb.12645
      
    

Plants modify development in response to external stimuli, to produce new growth that is appropriate for environmental conditions. For example, gravi©\stimulation of leaning branches in angiosperm trees results in modifications of wood development, to produce tension wood that pulls leaning stems upright. Here, we use gravi©\stimulation and tension wood response to dissect the temporal changes in gene expression underlying wood formation in Populus stems. Using time©\series analysis of seven time points over a 14©\d experiment, we identified 8,919 genes that were differentially expressed between tension wood (upper) and opposite wood (lower) sides of leaning stems. Clustering of differentially expressed genes showed four major transcriptional responses, including gene clusters whose transcript levels were associated with two types of tissue©\specific impulse responses that peaked at about 24–48 h, and gene clusters with sustained changes in transcript levels that persisted until the end of the 14©\d experiment. Functional enrichment analysis of those clusters suggests they reflect temporal changes in pathways associated with hormone regulation, protein localization, cell wall biosynthesis and epigenetic processes. Time©\series analysis of gene expression is an underutilized approach for dissecting complex developmental responses in plants, and can reveal gene clusters and mechanisms influencing development.

Abstract (Browse 148)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Analysis of gene expression data from time series studies can provide novel insights into gene networks and developmental processes. Here, we used a time series approach to understand how poplar trees change wood formation in response to gravistimulation.
          Molecular Physiology
The Arabidopsis catalase triple mutant reveals important roles of catalases and peroxisome©\derived signaling in plant development
Author: Tong Su, Pingping Wang, Huijuan Li, Yiwu Zhao, Yao Lu, Peng Dai, Tianqi Ren, Xiaofeng Wang, Xuezhi Li, Qun Shao, Dazhong Zhao, Yanxiu Zhao and Changle Ma
Journal of Integrative Plant Biology 2018 60(7): 591-607
Published Online: March 23, 2018
DOI: 10.1111/jipb.12649
      
    

Hydrogen peroxide (H2O2) is generated in many metabolic processes. As a signaling molecule, H2O2 plays important roles in plant growth and development, as well as environmental stress response. In Arabidopsis, there are three catalase genes, CAT1, CAT2, and CAT3. The encoded catalases are predominately peroxisomal proteins and are critical for scavenging H2O2. Since CAT1 and CAT3 are linked on chromosome 1, it has been almost impossible to generate cat1/3 and cat1/2/3 mutants by traditional genetic tools. In this study, we constructed cat1/3 double mutants and cat1/2/3 triple mutants by CRISPR/Cas9 to investigate the role of catalases. The cat1/2/3 triple mutants displayed severe redox disturbance and growth defects under physiological conditions compared with wild©\type and the cat2/3 double mutants. Transcriptome analysis showed a more profound transcriptional response in the cat1/2/3 triple mutants compared to the cat2/3 mutants. These differentially expressed genes are involved in plant growth regulation as well as abiotic and biotic stress responses. In addition, expression of OXI1 (OXIDATIVE SIGNAL INDUCIBLE 1) and several MAPK cascade genes were changed dramatically in the catalase triple mutant, suggesting that H2O2 produced in peroxisomes could serve as a peroxisomal retrograde signal.

Abstract (Browse 183)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Catalases, which are predominate peroxisomal proteins, function as antioxidant enzymes to scavenge H2O2. In this study, using the CRISPR/Cas9 technology, we generated the cat1/2/3 triple mutants, which displayed severe redox disturbance and growth defects. Transcriptome analysis showed that H2O2 produced in peroxisomes could serve as a peroxisomal retrograde signal.
Two soybean bHLH factors regulate response to iron deficiency
Author: Lin Li, Wenwen Gao, Qi Peng, Bin Zhou, Qihui Kong, Yinghui Ying, Huixia Shou
Journal of Integrative Plant Biology 2018 60(7): 608-622
Published Online: March 23, 2018
DOI: 10.1111/jipb.12651
      
    

Iron is an indispensable micronutrient for plant growth and development. Limited bioavailability of Fe in the soil leads to iron deficiency chlorosis in plants and yield loss. In this study, two soybean basic helix©\loop©\helix transcription factors, GmbHLH57 and GmbHLH300, were identified in response to Fe©\deficiency. Both transcription factors are expressed in roots and nodules, and are induced by Fe deficiency; these patterns were confirmed in transgenic hairy roots expressing constructs of the endogenous promoters fused to a GUS reporter gene. Bimolecular fluorescence complementation, yeast two©\hybrid and coimmunoprecipitation (co©\IP) assays indicated a physical interaction between GmbHLH57 and GmbHLH300. Studies on transgenic soybeans overexpressing GmbHLH57 and GmbHLH300 revealed that overexpression of each transcription factor, alone, results in no change of the responses to Fe deficiency, whereas overexpression of both transcription factors upregulated the downstream Fe uptake genes and increased the Fe content in these transgenic plants. Compared to wild type, these double overexpression transgenic plants were more tolerant to Fe deficiency. Taken together, our findings establish that GmbHLH57 and GmbHLH300 are important transcription factors involved in Fe homeostasis in soybean.

Abstract (Browse 87)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Iron is an indispensable micronutrient for plant growth and development. Two soybean basic helix©\loop©\helix transcription factors, GmbHLH57 and GmbHLH300, were identified in response to Fe©\deficiency. Overexpression of both transcription factors increased the expression of Fe uptake downstream genes and elevated the Fe deficiency tolerance in soybean.
 
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