June 2014, Volume 56 Issue 6, Pages 518每605.


Cover Caption: AGO1 Shuts TOO MANY MOUTHS
About the cover: TOO MANY MOUTH (TMM) plays an important role in ligand-receptor signaling modules to regulate the number and pattern of stomata in epidermis. In this issue, Yang et al. (pp. 539每549) report that ARGONAUTE1 (AGO1) acts downstream of TMM and negatively regulates SPEECHLESS expression to control the division of stomatal lineage ground cells. The picture shows the expression pattern of stomatal lineage marker pTMM::TMM-GFP in ago1 mutant.

 

          Minireview
Homeodomain leucine-zipper proteins and their role in synchronizing growth and development with the environment
Author: Ronny Brandt, Marc Cabedo, Yakun Xie and Stephan Wenkel
Journal of Integrative Plant Biology 2014 56(6): 518每526
Published Online: February 15, 2014
DOI: 10.1111/jipb.12185
      
    

The Arabidopsis (Arabidopsis thaliana L.) genome encodes for four distinct classes of homeodomain leucine-zipper (HD-ZIP) transcription factors (HD-ZIPI to HD-ZIPIV), which are all organized in multi-gene families. HD-ZIP transcription factors act as sequence-specific DNA-binding proteins that are able to control the expression level of target genes. While HD-ZIPI and HD-ZIPII proteins are mainly associated with environmental responses, HD-ZIPIII and HD-ZIPIV are primarily known to act as patterning factors. Recent studies have challenged this view. It appears that several of the different HD-ZIP families interact genetically to align both morphogenesis and environmental responses, most likely by modulating phytohormone-signaling networks.

 

Brandt R, Cabedo M, Xie Y, Wenkel S (2014) Homeodomain leucine坼zipper proteins and their role in synchronizing growth and development with the environment. J Integr Plant Biol 56: 518–526. doi: 10.1111/jipb.12185

Abstract (Browse 846)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          New Technology
A step-by-step protocol for formaldehyde-assisted isolation of regulatory elements from Arabidopsis thaliana
Author: Mohammad Amin Omidbakhshfard, Flavia Vischi Wink, Samuel Arvidsson, Diego M. Riaño-Pachón and Bernd Mueller-Roeber
Journal of Integrative Plant Biology 2014 56(6): 527每538
Published Online: December 20, 2013
DOI: 10.1111/jipb.12151
      
    

The control of gene expression by transcriptional regulators and other types of functionally relevant DNA transactions such as chromatin remodeling and replication underlie a vast spectrum of biological processes in all organisms. DNA transactions require the controlled interaction of proteins with DNA sequence motifs which are often located in nucleosome-depleted regions (NDRs) of the chromatin. Formaldehyde-assisted isolation of regulatory elements (FAIRE) has been established as an easy-to-implement method for the isolation of NDRs from a number of eukaryotic organisms, and it has been successfully employed for the discovery of new regulatory segments in genomic DNA from, for example, yeast, Drosophila, and humans. Until today, however, FAIRE has only rarely been employed in plant research and currently no detailed FAIRE protocol for plants has been published. Here, we provide a step-by-step FAIRE protocol for NDR discovery in Arabidopsis thaliana. We demonstrate that NDRs isolated from plant chromatin are readily amenable to quantitative polymerase chain reaction and next-generation sequencing. Only minor modification of the FAIRE protocol will be needed to adapt it to other plants, thus facilitating the global inventory of regulatory regions across species.

 

Omidbakhshfard MA, Winck FV, Arvidsson S, Riaño坼Pachón DM, Mueller坼Roeber B (2014) A step坼by坼step protocol for formaldehyde坼assisted isolation of regulatory elements from Arabidopsis thaliana. J Integr Plant Biol 56: 527–538. doi: 10.1111/jipb.12151

Abstract (Browse 1074)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Cell and Developmental Biology
A new loss-of-function allele 28y reveals a role of ARGONAUTE1 in limiting asymmetric division of stomatal lineage ground cell
Author: Kezhen Yang, Min Jiang and Jie Le
Journal of Integrative Plant Biology 2014 56(6): 539每549
Published Online: January 4, 2014
DOI: 10.1111/jipb.12154
      
    

In Arabidopsis thaliana L., stomata are produced through a series of divisions including asymmetric and symmetric divisions. Asymmetric entry division of meristemoid mother cell produces two daughter cells, the smaller meristemoid and the larger sister cell, a stomatal lineage ground cell (SLGC). Stomatal lineage ground cells can differentiate into epidermal pavement cells but have the potential to divide asymmetrically, spacing divisions, to create satellite meristemoids. Peptide ligands and TOO MANY MOUTHS (TMM) and ERECTA family receptors regulate the initiation of stomatal lineages, activity, and orientation of spacing divisions. Here, we reported that a natural mutant 28y displayed an increased stomatal density and index. Using map-based cloning, we identified mutation in ARGONAUTE1 (AGO1) as the cause of 28y phenotypes. Time-lapse tracing of stomatal lineage cells reveals that stomatal overproduction in 28y is caused by the excessive asymmetric spacing division of SLGCs. Further genetic results demonstrated that AGO1 acts downstream of TMM and negatively regulates the SPCH transcripts, but in a brassinosteroid-independent manner. Upregulation of AGAMOUS-LIKE16 (AGL16) in 28y mutants suggests that AGO1 is required to restrict AGL16-mediated stomatal spacing divisions, an miRNA pathway in addition to ligand-receptor signaling modules.

 

Yang K, Jiang M, Le J (2014) A new loss坼of坼function allele 28y reveals a role of ARGONAUTE1 in limiting asymmetric division of stomatal lineage ground cell. J Integr Plant Biol 56: 539–549. doi: 10.1111/jipb.12154

Abstract (Browse 1082)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Polycomb-group histone methyltransferase CLF is required for proper somatic recombination in Arabidopsis  
Author: Na Chen, Wang-Bin Zhou, Ying-Xiang Wang, Ai-Wu Dong and Yu Yu
Journal of Integrative Plant Biology 2014 56(6): 550每558
Published Online: January 7, 2014
DOI: 10.1111/jipb.12157
      
    

Homologous recombination (HR) is a key process during meiosis in reproductive cells and the DNA damage repair process in somatic cells. Although chromatin structure is thought to be crucial for HR, only a small number of chromatin modifiers have been studied in HR regulation so far. Here, we investigated the function of CURLY LEAF (CLF), a Polycomb-group (PcG) gene responsible for histone3 lysine 27 trimethylation (H3K27me3), in somatic and meiotic HR in Arabidopsis thaliana. Although fluorescent protein reporter assays in pollen and seeds showed that the frequency of meiotic cross-over in the loss-of-function mutant clf-29 was not significantly different from that in wild type, there was a lower frequency of HR in clf-29 than in wild type under normal conditions and under bleomycin treatment. The DNA damage levels were comparable between clf-29 and wild type, even though several DNA damage repair genes (e.g. ATM, BRCA2a, RAD50, RAD51, RAD54, and PARP2) were expressed at lower levels in clf-29. Under bleomycin treatment, the expression levels of DNA repair genes were similar in clf-29 and wild type, thus CLF may also regulate HR via other mechanisms. These findings expand the current knowledge of PcG function and contribute to general interests of epigenetic regulation in genome stability regulation.

 

Chen N, Zhou WB, Wang YX, Dong AW, Yu Y (2014) Polycomb坼group histone methyltransferase CLF is required for proper somatic recombination in Arabidopsis. J Integr Plant Biol 56: 550–558. doi: 10.1111/jipb.12157

Abstract (Browse 1233)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Rice MtN3/saliva/SWEET gene family: Evolution, expression profiling, and sugar transport
Author: Meng Yuan, Junwei Zhao, Renyan Huang, Xianghua Li, Jinghua Xiao and Shiping Wang
Journal of Integrative Plant Biology 2014 56(6): 559每570
Published Online: January 24, 2014
DOI: 10.1111/jipb.12173
      
    
The rice MtN3/saliva/SWEET gene family consists of 21 paralogs. However, their functions in physiological processes are largely unknown, although at least three of the 21 paralogs are used by pathogenic bacteria to infect rice. Here, we report the evolutionary features, transcriptional characteristics, and putative functions in sugar transport of this gene family. The wild rice accessions in this study included those with AA, BB, CC, BBCC, CCDD, EE, and GG genomes, which appeared approximately 0.58–14.6 million years ago. The structures, chromosomal locations, phylogenetic relationships, and homologous distribution among the accessions suggest that the number of rice MtN3/saliva/SWEET paralogs gradually increased as the Oryza genus evolved, and one third of the paralogs may have originated recently. These paralogs are differentially expressed in vegetative and reproductive tissues, in the leaf senescence process, and in signaling dependent on gibberellic acid, cytokinin, or 1-naphthalene acetic acid (an analog of auxin), suggesting that they may be associated with multiple physiological processes. Four paralogs could transport galactose in yeast, which suggests that they may have a similar function in rice. These results will help to elucidate their roles and biochemical functions in rice development, adaptation to environment, host-pathogen interaction, and so forth.

 

Yuan M, Zhao J, Huang R, Li X, Xiao J, Wang S (2014) Rice MtN3/saliva/SWEET gene family: Evolution, expression profiling, and sugar transport. J Integr Plant Biol 56: 559–570. doi: 10.1111/jipb.12173

Abstract (Browse 1205)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Molecular Physiology
Molecular characterization and expression analysis of Triticum aestivum squamosa-promoter binding protein-box genes involved in ear development  
Author: Bin Zhang, Xia Liu, Guangyao Zhao, Xinguo Mao, Ang Li and Ruilian Jing
Journal of Integrative Plant Biology 2014 56(6): 571每581
Published Online: January 6, 2014
DOI: 10.1111/jipb.12153
      
    

Wheat (Triticum aestivum L.) is one of the most important crops in the world. Squamosa-promoter binding protein (SBP)-box genes play a critical role in regulating flower and fruit development. In this study, 10 novel SBP-box genes (TaSPL genes) were isolated from wheat ((Triticum aestivum L.) cultivar Yanzhan 4110). Phylogenetic analysis classified the TaSPL genes into five groups (G1–G5). The motif combinations and expression patterns of the TaSPL genes varied among the five groups with each having own distinctive characteristics: TaSPL20/21 in G1 and TaSPL17 in G2 mainly expressed in the shoot apical meristem and the young ear, and their expression levels responded to development of the ear; TaSPL6/15 belonging to G3 were upregulated and TaSPL1/23 in G4 were downregulated during grain development; the gene in G5 (TaSPL3) expressed constitutively. Thus, the consistency of the phylogenetic analysis, motif compositions, and expression patterns of the TaSPL genes revealed specific gene structures and functions. On the other hand, the diverse gene structures and different expression patterns suggested that wheat SBP-box genes have a wide range of functions. The results also suggest a potential role for wheat SBP-box genes in ear development. This study provides a significant beginning of functional analysis of SBP-box genes in wheat.

 

Zhang B, Liu X, Zhao G, Mao X, Li A, Jing R (2014) Molecular characterization and expression analysis of Triticum aestivum squamosa坼promoter binding protein坼box genes involved in ear development. J Integr Plant Biol 56: 571–581. doi: 10.1111/jipb.12153

Abstract (Browse 1064)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
BnWRI1 coordinates fatty acid biosynthesis and photosynthesis pathways during oil accumulation in rapeseed
Author: Xue-Long Wu, Zhi-Hong Liu, Zhang-Hua Hu and Rui-Zhi Huang
Journal of Integrative Plant Biology 2014 56(6): 582每593
Published Online: January 7, 2014
DOI: 10.1111/jipb.12158
      
    

Photosynthesis in “green” seeds, such as rapeseed, soybean, and Arabidopsis, plays a substantial role in the improved efficiency of oil accumulation. However, the molecular mechanism underpinning the coordinated expression of fatty acid (FA) biosynthesis- and photosynthesis-related genes in such developing seeds remains to be elucidated. Here, we found that seed-specific overexpression of BnWRI1, a WRI1 homolog from rapeseed (Brassica napus cv. ZGY2), results in enhanced chlorophyll content in developing seeds and increased oil content and seed mass in matured seeds. BnWRI1 was co-expressed with BnBCCP and BnCAB, two marker genes of FA biosynthesis and photosynthesis during seed development, respectively. Overexpression of BnWRI1 increased expression of both marker genes. Further, the nuclear-localized BnWRI1 protein was found to act as a transcription activator. It could bind to the GT1-element and/or GCC-box, which are widespread in the upstream regions of genes involved in FA biosynthesis and photosynthesis pathways. Accordingly, BnWRI1 could interact with promoters of BCCP2 and LHB1B2 in vivo. These results suggested that BnWRI1 may coordinate FA biosynthesis and photosynthesis pathways in developing seeds via directly stimulating expression of GT1-element and/or GCC-box containing genes.

 

Wu XL, Liu ZH, Hu ZH, Huang RZ (2014) BnWRI1 coordinates fatty acid biosynthesis and photosynthesis pathways during oil accumulation in rapeseed. J Integr Plant Biol 56: 582–593. doi: 10.1111/jipb.12158

Abstract (Browse 825)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Plant-environmental Interactions
Genetic analysis of biomass and photosynthetic parameters in wheat grown in different light intensities  
Author: Hongwei Li, Gui Wang, Qi Zheng, Bin Li, Ruilian Jing and Zhensheng Li
Journal of Integrative Plant Biology 2014 56(6): 594每604
Published Online: January 24, 2014
DOI: 10.1111/jipb.12174
      
    

Growth light intensities largely determine photosynthesis, biomass, and grain yield of cereal crops. To explore the genetic basis of light responses of biomass and photosynthetic parameters in wheat (Triticum aestivum L.), a quantitative trait locus (QTL) analysis was carried out in a doubled haploid (DH) population grown in low light (LL), medium light (ML), and high light (HL), respectively. The results showed that the wheat seedlings grown in HL produced more biomass with lower total chlorophyll content (Chl), carotenoid content, and maximum photochemical efficiency of photosystem II (Fv/Fm) while the wheat seedlings grown in LL produced less biomass with higher Chl compared with those grown in ML. In total, 48 QTLs were identified to be associated with the investigated parameters in relation to growth light intensities. These QTLs were mapped to 15 chromosomes which individually explained 6.3%–36.0% of the phenotypic variance, of which chromosomes 3A, 1D, and 6B were specifically involved in LL response, 5D and 7A specifically involved in ML response, and 4B specifically involved in HL response. Several light-responsive QTLs were co-located with QTLs for photosynthetic parameters, biomass, and grain weight under various conditions which may provide new hints to uncover the genetic control of photosynthesis, biomass, and grain weight.

 

Li H, Wang G, Zheng Q, Li B, Jing R, Li Z (2014) Genetic analysis of biomass and photosynthetic parameters in wheat grown in different light intensities. J Integr Plant Biol 56: 594–604. doi: 10.1111/jipb.12174

Abstract (Browse 1074)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Corrigendum
Author:
Journal of Integrative Plant Biology 2014 56(6): 605每605
Published Online: June 5, 2014
DOI: 10.1111/jipb.12219
Abstract (Browse 397)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
 

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