March 2015, Volume 57 Issue 3, Pages 234每324.


Cover Caption: Maize Endosperm Transfer Cells
The transfer cell layer in maize endosperm transports sugars from maternal tissues into the kernel to fuel growth and storage compound accumulation in the embryo and endosperm. Mutation of a mitochondrial PORR protein compromised the development of the transfer cell layer.

 

          Commentary
AUXIN BINDING PROTEIN 1 (ABP1): A matter of fact  
Author: Chun-Ming Liu
Journal of Integrative Plant Biology 2015 57(3): 234每235
Published Online: February 9, 2015
DOI: 10.1111/jipb.12339
Abstract (Browse 942)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Cell and Developmental Biology
A putative plant organelle RNA recognition protein gene is essential for maize kernel development
Author: Antony M. Chettoor, Gibum Yi, Elisa Gomez, Gregorio Hueros, Robert B. Meeley and Philip W. Becraft
Journal of Integrative Plant Biology 2015 57(3): 236每246
Published Online: July 2, 2014
DOI: 10.1111/jipb.12234
      
    
Basal endosperm transfer layer (BETL) cells are responsible for transferring apoplastic solutes from the maternal pedicel into the endosperm, supplying the grain with compounds required for embryo development and storage reserve accumulation. Here, we analyze the maize (Zea mays L.) empty pericarp6 (emp6) mutant, which causes early arrest in grain development. The Emp6+gene function is required independently in both the embryo and endosperm. The emp6 mutant causes a notable effect on the differentiation of BETL cells; the extensive cell wall ingrowths that distinguish BETL cells are diminished and BETL marker gene expression is compromised in mutant kernels. Transposon tagging identified the emp6 locus as encoding a putative plant organelle RNA recognition (PORR) protein, 1 of 15 PORR family members in maize. The emp6 transcript is widely detected in plant tissues with highest levels in embryos and developing kernels. EMP6-green fluorescent protein (GFP) fusion proteins transiently expressed in Nicotiana benthamiana leaves were targeted specifically to mitochondria. These results suggest that BETL cell differentiation might be particularly energy intensive, or alternatively, that mitochondria might confer a developmental function.
 

Chettoor AM, Yi G, Gomez E, Hueros G, Meeley RB, Becraft PW (2015) A putative plant organelle RNA recognition protein gene is essential for maize kernel Development. J Integr Plant Biol 57: 236–246. doi: 10.1111/jipb.12234

Abstract (Browse 831)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
A mutation in a maize gene encoding a mitochondrial protein causes seed lethality showing it is essential for grain development. Defects in transfer cells suggest either that this cell type has a particularly high energy requirement or that mitochondria could provide functions required for specific developmental processes.
Organ-specific effects of brassinosteroids on stomatal production coordinate with the action of TOO MANY MOUTHS
Author: Ming Wang, Kezhen Yang and Jie Le
Journal of Integrative Plant Biology 2015 57(3): 247每255
Published Online: September 18, 2014
DOI: 10.1111/jipb.12285
      
    

In Arabidopsis, stomatal development initiates after protodermal cells acquire stomatal lineage cell fate. Stomata or their precursors communicate with their neighbor epidermal cells to ensure the “one cell spacing” rule. The signals from EPF/EPFL peptide ligands received by TOO MANY MOUTHS (TMM) and ERECTA-family receptors are supposed to be transduced by YODA MAPK cascade. A basic helix-loop-helix transcription factor SPEECHLESS (SPCH) is another key regulator of stomatal cell fate determination and asymmetric entry divisions, and SPCH activity is regulated by YODA MAPK cascade. Brassinosteroid (BR) signaling, one of the most well characterized signal transduction pathways in plants, contributes to the control of stomatal production. But opposite organ-specific effects of BR on stomatal production were reported. Here we confirm that stomatal production in hypocotyls is controlled by BR levels. YODA and CYCD4 are not essential for BR stomata-promoting function. Furthermore, we found that BR could confer tmm hypocotyls clustered stomatal phenotype, indicating that the BR organ-specific effects on stomatal production might coordinate with the TMM organ-specific actions.

 

Wang M, Yang K, Le J (2015). Organ坼specific effects of brassinosteroids on stomatal production coordinate with the action of TOO MANY MOUTHS. J Integr Plant Biol 57: 247–255. doi: 10.1111/jipb.12285

Abstract (Browse 955)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Brassinosteroid (BR) has been shown organ-specific effects in control stomatal production. Mutation of TOO MANY MOUTHS (TMM) leads stomatal clusters in cotyledons but no stomata in hypocotyls. Here, Wang et al. found that BR induced stomatal clusters in tmm hypocotyls, indicating a crosstalk between BR- and TMM-mediated signaling pathways.
          Functional Omics and Systems Biology
Identification of mRNA-like non-coding RNAs and validation of a mighty one named MAR in Panax ginseng
Author: Meizhen Wang, Bin Wu, Chao Chen and Shanfa Lu
Journal of Integrative Plant Biology 2015 57(3): 256每270
Published Online: July 8, 2014
DOI: 10.1111/jipb.12239
      
    

Increasing evidence suggests that long non-coding RNAs (lncRNAs) play significant roles in plants. However, little is known about lncRNAs in Panax ginseng C. A. Meyer, an economically significant medicinal plant species. A total of 3,688 mRNA-like non-coding RNAs (mlncRNAs), a class of lncRNAs, were identified in P. ginseng. Approximately 40% of the identified mlncRNAs were processed into small RNAs, implying their regulatory roles via small RNA-mediated mechanisms. Eleven miRNA-generating mlncRNAs also produced siRNAs, suggesting the coordinated production of miRNAs and siRNAs in P. ginseng. The mlncRNA-derived small RNAs might be 21-, 22-, or 24-nt phased and could be generated from both or only one strand of mlncRNAs, or from super long hairpin structures. A full-length mlncRNA, termed MAR (multiple-function-associated mlncRNA), was cloned. It generated the most abundant siRNAs. The MAR siRNAs were predominantly 24-nt and some of them were distributed in a phased pattern. A total of 228 targets were predicted for 71 MAR siRNAs. Degradome sequencing validated 68 predicted targets involved in diverse metabolic pathways, suggesting the significance of MAR in P. ginseng. Consistently, MAR was detected in all tissues analyzed and responded to methyl jasmonate (MeJA) treatment. It sheds light on the function of mlncRNAs in plants.

 

Wang M, Wu B, Chen C, Lu S (2015) Identification of mRNA坼like non坼coding RNAs and validation of a mighty one named MAR in Panax ginseng. J Integr Plant Biol 57: 256–270. doi: 10.1111/jipb.12239

Abstract (Browse 987)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
MlncRNAs are a class of lncRNAs playing vital roles in plants. Through an integrative analysis of transcriptome, sRNAome and degradome, 3688 mlncRNAs were identified and characterized in Panax ginseng. One of them, termed MAR, was found to play significant regulatory roles in multiple metabolic pathways in a small RNA-dependent manner.
ZmGns, a maize class I 汕-1,3-glucanase, is induced by biotic stresses and possesses strong antimicrobial activity
Author: Yu-Rong Xie, Yenjit Raruang, Zhi-Yuan Chen, Robert L. Brown and Thomas E. Cleveland
Journal of Integrative Plant Biology 2015 57(3): 271每283
Published Online: September 23, 2014
DOI: 10.1111/jipb.12286
      
    
Plant β-1,3-glucanases are members of the pathogenesis-related protein 2 (PR-2) family, which is one of the 17 PR protein families and plays important roles in biotic and abiotic stress responses. One of the differentially expressed proteins (spot 842) identified in a recent proteomic comparison between five pairs of closely related maize (Zea mays L.) lines differing in aflatoxin resistance was further investigated in the present study. Here, the corresponding cDNA was cloned from maize and designated as ZmGns. ZmGns encodes a protein of 338 amino acids containing a potential signal peptide. The expression of ZmGns was detectible in all tissues studied with the highest level in silks. ZmGns was significantly induced by biotic stresses including three bacteria and the fungus Aspergillus flavus. ZmGns was also induced by most abiotic stresses tested and growth hormones including salicylic acid. In vivo, ZmGns showed a significant inhibitory activity against the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 and fungal pathogen Botrytis cinerea when it overexpressed in Arabidopsis. Its high level of expression in the silk tissue and its induced expression by phytohormone treatment, as well as by bacterial and fungal infections, suggest it plays a complex role in maize growth, development, and defense.

 

Xie YR, Raruang Y, Chen ZY, Brown RL, Cleveland TE (2015). ZmGns, a maize class Ib坼1,3坼glucanase, is induced by biotic stresses and possesses strong antimicrobial activity. J Integr Plant Biol 57: 271–283. doi: 10.1111/jipb.12286

Abstract (Browse 963)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
ZmGns, a maize glucanase, shows strong antifungal and antibacterial activity in vivo and in vitro. ZmGns also plays great roles in maize growth and development by response to growth hormones such as salicylic acid. In addition, ZmGns was up-regulated when exposed to abiotic stresses including salinity, wound and copper.
          Molecular Ecology and Evolution
Population transcriptomics reveals a potentially positive role of expression diversity in adaptation  
Author: Qin Xu, Shilai Xing, Caiyun Zhu, Wei Liu, Yangyang Fan, Qian Wang, Zhihong Song, Wenhui Yang, Fan Luo, Fei Shang, Lifang Kang, Wenli Chen, Juan Yan, Jianqiang Li and Tao Sang
Journal of Integrative Plant Biology 2015 57(3): 284每299
Published Online: September 23, 2014
DOI: 10.1111/jipb.12287
      
    

While it is widely accepted that genetic diversity determines the potential of adaptation, the role that gene expression variation plays in adaptation remains poorly known. Here we show that gene expression diversity could have played a positive role in the adaptation of Miscanthus lutarioriparius. RNA-seq was conducted for 80 individuals of the species, with half planted in the energy crop domestication site and the other half planted in the control site near native habitats. A leaf reference transcriptome consisting of 18,503 high-quality transcripts was obtained using a pipeline developed for de novo assembling with population RNA-seq data. The population structure and genetic diversity of M. lutarioriparius were estimated based on 30,609 genic single nucleotide polymorphisms. Population expression (Ep) and expression diversity (Ed) were defined to measure the average level and the magnitude of variation of a gene expression in the population, respectively. It was found that expression diversity increased while genetic diversity decreased after the species was transplanted from the native habitats to the harsh domestication site, especially for genes involved in abiotic stress resistance, histone methylation, and biomass synthesis under water limitation. The increased expression diversity could have enriched phenotypic variation directly subject to selections in the new environment.

 

Xu Q, Xing S, Zhu C, Liu W, Fan Y, Wang Q, Song Z, Yang W, Luo F, Shang F, Kang L, Chen W, Yan J, Li J, Sang T (2015) Population transcriptomics reveals a potentially positive role of expression diversity in adaptation. J Integr Plant Biol 57: 284–299. doi: 10.1111/jipb.12287

Abstract (Browse 1416)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
This study shows that the increase in variation of gene expression, while a population being exposed to a new stressful environment, may enhance its adaptability, when has implications in the domestication of new energy crops, control of invasive species, and conservation of biodiversity during climate change.
          Plant-environmental Interactions
The regulatory network mediated by circadian clock genes is related to heterosis in rice
Author: Guojing Shen, Wei Hu, Bo Zhang and Yongzhong Xing
Journal of Integrative Plant Biology 2015 57(3): 300每312
Published Online: July 8, 2014
DOI: 10.1111/jipb.12240
      
    

Exploitation of heterosis in rice (Oryza sativa L.) has contributed greatly to global food security. In this study, we generated three sets of reciprocal F1 hybrids of indica and japonica subspecies to evaluate the relationship between yield heterosis and the circadian clock. There were no differences in trait performance or heterosis between the reciprocal hybrids, indicating no maternal effects on heterosis. The indica-indica and indica-japonica reciprocal F1 hybrids exhibited pronounced heterosis for chlorophyll and starch content in leaves and for grain yield/biomass. In contrast, the japonica-japonica F1 hybrids showed low heterosis. The three circadian clock genes investigated expressed in an above-high-parent pattern (AHP) at seedling stage in all the hybrids. The five genes downstream of the circadian clock, and involved in chlorophyll and starch metabolic pathways, were expressed in AHP in hybrids with strong better-parent heterosis (BPH). Similarly, three of these five genes in the japonica-japonica F1 hybrids showing low BPH were expressed in positive overdominance, but the other two genes were expressed in additive or negative overdominance. These results indicated that the expression patterns of circadian clock genes and their downstream genes are associated with heterosis, which suggests that the circadian rhythm pathway may be related to heterosis in rice.

 

Shen G, Hu W, Zhang B, Xing Y (2015) The regulatory network mediated by circadian clock genes is related to heterosis in rice. J Integr Plant Biol 57: 300–312. doi: 10.1111/jipb.12240

Abstract (Browse 1042)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Heterosis is a common phenomenon in plants, which greatly contributes to global food security. Circadian clock is a biochemical mechanism in organisms that coordinates their biology and behavior with daily and seasonal changes. We found the circadian rhythm is highly associated with the magnitude of heterosis.
The CONSTANS-like 4 transcription factor, AtCOL4, positively regulates abiotic stress tolerance through an abscisic acid-dependent manner in Arabidopsis  
Author: Ji-Hee Min, Jung-Sung Chung, Kyeong-Hwan Lee and Cheol Soo Kim
Journal of Integrative Plant Biology 2015 57(3): 313每324
Published Online: July 29, 2014
DOI: 10.1111/jipb.12246
      
    

The precise roles of the B-box zinc finger family of transcription factors in plant stress are poorly understood. Functional analysis was performed on AtCOL4, an Arabidopsis thaliana L. CONSTANS-like 4 protein that is a putative novel transcription factor, and which contains a predicted transcriptional activation domain. Analyses of an AtCOL4 promoter-β-glucuronidase (GUS) construct revealed substantial GUS activity in whole seedlings. The expression of AtCOL4 was strongly induced by abscisic acid (ABA), salt, and osmotic stress. Mutation in atcol4 resulted in increased sensitivity to ABA and salt stress during seed germination and the cotyledon greening process. In contrast, AtCOL4-overexpressing plants were less sensitive to ABA and salt stress compared to the wild type. Interestingly, in the presence of ABA or salt stress, the transcript levels of other ABA biosynthesis and stress-related genes were enhanced induction in AtCOL4-overexpressing and WT plants, rather than in the atcol4 mutant. Thus, AtCOL4 is involved in ABA and salt stress response through the ABA-dependent signaling pathway. Taken together, these findings provide compelling evidence that AtCOL4 is an important regulator for plant tolerance to abiotic stress.

 

Min JH, Chung JS, Lee KH, Kim CS (2015) The CONSTANS坼like 4 transcription factor, AtCOL4, positively regulates abiotic stress tolerance through an abscisic acid坼dependent manner in Arabidopsis. J Integr Plant Biol 57: 313–324. doi: 10.1111/jipb.12246

Abstract (Browse 1406)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
The overexpression of AtCOL4 in Arabidopsis plants conferred increased insensitivity to ABA and salt stress, while atcol4 mutant gained sensitivity to ABA and high salinity condition during seed germination and the cotyledon greening process.
 

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