February 2016, Volume 58 Issue 2, Pages 105每187.


Cover Caption: Nectary Variation vs Pollination Modes
Nectar is an effective reward for pollinators. In this issue, Liu et al. (pp. 178每187) demonstrate that the floral nectary has experienced morphological and functional differentiation among closely related species of Pedicularis, which could have affected nectar production and pollination modes. The results indicate that the gain or loss of nectar, together with variation incorolla form, may have played a key role in driving species diversification in Pedicularis.

 

          Invited Expert Reviews
Plant Mediator complex and its critical functions in transcription regulation
Author: Yan Yang, Ling Li and Li-Jia Qu
Journal of Integrative Plant Biology 2016 58(2): 106每118
Published Online: July 14, 2015
DOI: 10.1111/jipb.12377
      
    

The Mediator complex is an important component of the eukaryotic transcriptional machinery. As an essential link between transcription factors and RNA polymerase II, the Mediator complex transduces diverse signals to genes involved in different pathways. The plant Mediator complex was recently purified and comprises conserved and specific subunits. It functions in concert with transcription factors to modulate various responses. In this review, we summarize the recent advances in understanding the plant Mediator complex and its diverse roles in plant growth, development, defense, non-coding RNA production, response to abiotic stresses, flowering, genomic stability and metabolic homeostasis. In addition, the transcription factors interacting with the Mediator complex are also highlighted.

 

Yang Y, Li L, Qu L-J (2016) Plant Mediator complex and its critical functions in transcription regulation. J Integr Plant Biol 58: 106–118 doi: 10.1111/jipb.12377

Abstract (Browse 834)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Plant Mediator complex is a hub for transcription regulation. It bridges transcription factors and RNA polymerase II to modulate transcription of genes involved in various processes including plant growth, development, defense, production of non-coding RNAs, response to abiotic stresses, flowering regulation and metabolic homeostasis.
Determinants of timing and amplitude in the plant general stress response  
Author: Marta Bjornson, Abhaya Dandekar and Katayoon Dehesh
Journal of Integrative Plant Biology 2016 58(2): 119每126
Published Online: June 25, 2015
DOI: 10.1111/jipb.12373
      
    

Plants have evolved intricate signaling cascades to rapidly and effectively respond to biotic and abiotic challenges. The precise timing of these responses enables optimal resource reallocation to maintain the balance between stress adaptation and growth. Thus, an in-depth understanding of the immediate and long-term mechanisms regulating resource allocation is critical in deciphering how plants withstand environmental challenges. To date however, understanding of this tradeoff has focused on the amplitude of long-term responses, rather than the timing of rapid stress responses. This review presents current knowledge on kinetics of secondary messengers involved in regulation of rapid and general stress responses, followed by rapid stress responsive transduction machinery, and finally the transcriptional response of a functional general stress responsive cis-element. Within this context we discuss the role of timing of initial peak activation and later oscillating peak responses, and explore hormonal and stress signaling crosstalk confounding greater understanding of these cascades.

 

Bjornson M, Dandekar A, Dehesh K (2016) Determinants of timing and amplitude in the plant general stress response. J Integr Plant Biol 58: 119–126 doi: 10.1111/jipb.12373

Abstract (Browse 878)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
The general stress response enables stress-acclimation via rapid and transient reprograming of gene expression. This article reviews fundamental general stress signaling/response pathways, highlights the importance of timing in staging the response, describes determinants of response peak and amplitude, and explores the role of signaling crosstalk in these processes.
          Metabolism and Biochemistry
Role of rice cytosolic hexokinase OsHXK7 in sugar signaling and metabolism
Author: Hyun-Bi Kim, Jung-Il Cho, Nayeon Ryoo, Dong-Ho Shin, Youn-Il Park, Yong-sic Hwang, Sang-Kyu Lee, Gynheung An and Jong-Seong Jeon
Journal of Integrative Plant Biology 2016 58(2): 127每135
Published Online: May 7, 2015
DOI: 10.1111/jipb.12366
      
    
We characterized the function of the rice cytosolic hexokinase OsHXK7 (Oryza sativa Hexokinase7), which is highly upregulated when seeds germinate under O2-deficient conditions. According to transient expression assays that used the promoter:luciferase fusion construct, OsHXK7 enhanced the glucose (Glc)-dependent repression of a rice α-amylase gene (RAmy3D) in the mesophyll protoplasts of maize, but its catalytically inactive mutant alleles did not. Consistently, the expression of OsHXK7, but not its catalytically inactive alleles, complemented the Arabidopsis glucose insensitive2-1 (gin2-1) mutant, thereby resulting in the wild type characteristics of Glc-dependent repression, seedling development, and plant growth. Interestingly, OsHXK7-mediated Glc-dependent repression was abolished in the O2-deficient mesophyll protoplasts of maize. This result provides compelling evidence that OsHXK7 functions in sugar signaling via a glycolysis-dependent manner under normal conditions, but its signaling role is suppressed when O2 is deficient. The germination of two null OsHXK7 mutants, oshxk7-1 and oshxk7-2, was affected by O2 deficiency, but overexpression enhanced germination in rice. This result suggests the distinct role that OsHXK7 plays in sugar metabolism and efficient germination by enforcing glycolysis-mediated fermentation in O2-deficient rice.

 

Kim HB, Cho JI, Ryoo N, Shin DH, Park YI, Hwang Ys, Lee SK, An G, Jeon JS (2016) Role of rice cytosolic hexokinase OsHXK7 in sugar signaling and metabolism. J Integr Plant Biol 58: 127–135 doi: 10.1111/jipb.12366

Abstract (Browse 1124)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Rice successfully germinates under O2-deficient conditions utilizing fermentation-produced ATP. OsHXK7, a cytosolic hexokinase, is upregulated in germinating seedlings under O2-deficient conditions. We found that overexpressing OsHXK7 promotes germination and its null mutations suppress germination under O2-deficient conditions. This suggests that OsHXK7 is necessary for efficient seed germination under O2-deficient conditions.
Characterization of novel Brown midrib 6 mutations affecting lignin biosynthesis in sorghum
Author: Erin D. Scully, Tammy Gries, Deanna L. Funnell-Harris, Zhanguo Xin, Frank A. Kovacs, Wilfred Vermerris and Scott E. Sattler
Journal of Integrative Plant Biology 2016 58(2): 136每149
Published Online: July 14, 2015
DOI: 10.1111/jipb.12375
      
    

The presence of lignin reduces the quality of lignocellulosic biomass for forage materials and feedstock for biofuels. In C4 grasses, the brown midrib phenotype has been linked to mutations to genes in the monolignol biosynthesis pathway. For example, the Bmr6 gene in sorghum (Sorghum bicolor) has been previously shown to encode cinnamyl alcohol dehydrogenase (CAD), which catalyzes the final step of the monolignol biosynthesis pathway. Mutations in this gene have been shown to reduce the abundance of lignin, enhance digestibility, and improve saccharification efficiencies and ethanol yields. Nine sorghum lines harboring five different bmr6 alleles were identified in an EMS-mutagenized TILLING population. DNA sequencing of Bmr6 revealed that the majority of the mutations impacted evolutionarily conserved amino acids while three-dimensional structural modeling predicted that all of these alleles interfered with the enzyme's ability to bind with its NADPH cofactor. All of the new alleles reduced in vitro CAD activity levels and enhanced glucose yields following saccharification. Further, many of these lines were associated with higher reductions in acid detergent lignin compared to lines harboring the previously characterized bmr6-ref allele. These bmr6 lines represent new breeding tools for manipulating biomass composition to enhance forage and feedstock quality.

 

Scully ED, Gries T, Funnell-Harris DL, Xin Z, Kovacs FA, Vermerris W, Sattler SE (2016) Characterization of novel Brown midrib 6 mutations affecting lignin biosynthesis in sorghum. J Integr Plant Biol 58: 136–149 doi: 10.1111/jipb.12375

Abstract (Browse 758)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Lignin reduces digestibility and impedes biofuel production. The Bmr6 gene in sorghum encodes an enzyme that catalyzes the last step in lignin synthesis. Several new Bmr6 mutations were identified, which disrupted its protein structure, reduced enzyme activity, significantly reduced lignin content, and improved recovery of fermentable sugars from sorghum biomass.
          Molecular Ecology and Evolution
Transcriptome shock in an interspecific F1 triploid hybrid of Oryza revealed by RNA sequencing  
Author: Ying Wu, Yue Sun, Xutong Wang, Xiuyun Lin, Shuai Sun, Kun Shen, Jie Wang, Tingting Jiang, Silin Zhong, Chunming Xu and Bao Liu
Journal of Integrative Plant Biology 2016 58(2): 150每164
Published Online: April 1, 2015
DOI: 10.1111/jipb.12357
      
    

Interspecific hybridization is a driving force in evolution and speciation of higher plants. Interspecific hybridization often induces immediate and saltational changes in gene expression, a phenomenon collectively termed “transcriptome shock”. Although transcriptome shock has been reported in various plant and animal taxa, the extent and pattern of shock-induced expression changes are often highly idiosyncratic, and hence entails additional investigations. Here, we produced a set of interspecific F1 triploid hybrid plants between Oryza sativa, ssp. japonica (2n = 2x = 24, genome AA) and the tetraploid form of O. punctata (2n = 4x  = 48, genome, BBCC), and conducted RNA-seq transcriptome profiling of the hybrids and their exact parental plants. We analyzed both homeolog expression bias and overall gene expression level difference in the hybrids relative to the in silico “hybrids” (parental mixtures). We found that approximately 16% (2,541) of the 16,112 expressed genes in leaf tissue of the F1 hybrids showed nonadditive expression, which were specifically enriched in photosynthesis-related pathways. Interestingly, changes in the maternal homeolog expression, including non-stochastic silencing, were the major causes for altered homeolog expression partitioning in the F1 hybrids. Our findings have provided further insights into the transcriptome response to interspecific hybridization and heterosis.

 

Wu Y, Sun Y, Wang X, Lin X, Sun S, Shen K, Wang J, Jiang T, Zhong S, Xu C, Liu B (2016) Transcriptome shock in an interspecific F1 triploid hybrid of Oryza revealed by RNA sequencing. J Integr Plant Biol 58: 150–164 doi: 10.1111/jipb.12357

Abstract (Browse 1197)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Wide hybrids of Oryza can be accompanied with rapid genome-wide changes in gene expression, especially homeolog (alleles from parental species) expression partitioning. These changes may provide a basis for rapid adaptation of the hybrids, and which, if proven heritable, could be introduced to rice cultivars to enrich its genetic diversity.
Uncovering the dynamic evolution of nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes in Brassicaceae
Author: Yan-Mei Zhang, Zhu-Qing Shao, Qiang Wang, Yue-Yu Hang, Jia-Yu Xue, Bin Wang and Jian-Qun Chen
Journal of Integrative Plant Biology 2016 58(2): 165每177
Published Online: April 29, 2015
DOI: 10.1111/jipb.12365
      
    

Plant genomes harbor dozens to hundreds of nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes; however, the long-term evolutionary history of these resistance genes has not been fully understood. This study focuses on five Brassicaceae genomes and the Carica papaya genome to explore changes in NBS-LRR genes that have taken place in this Rosid II lineage during the past 72 million years. Various numbers of NBS-LRR genes were identified from Arabidopsis lyrata (198), A. thaliana (165), Brassica rapa (204), Capsella rubella (127), Thellungiella salsuginea (88), and C. papaya (51). In each genome, the identified NBS-LRR genes were found to be unevenly distributed among chromosomes and most of them were clustered together. Phylogenetic analysis revealed that, before and after Brassicaceae speciation events, both toll/interleukin-1 receptor-NBS-LRR (TNL) genes and non-toll/interleukin-1 receptor-NBS-LRR (nTNL) genes exhibited a pattern of first expansion and then contraction, suggesting that both subclasses of NBS-LRR genes were responding to pathogen pressures synchronically. Further, by examining the gain/loss of TNL and nTNL genes at different evolutionary nodes, this study revealed that both events often occurred more drastically in TNL genes. Finally, the phylogeny of nTNL genes suggested that this NBS-LRR subclass is composed of two separate ancient gene types: RPW8-NBS-LRR and Coiled-coil-NBS-LRR.

 

Zhang YM, Shao ZQ, Wang Q, Hang YY, Xue JY, Wang B, Chen JQ (2016) Uncovering the dynamic evolution of nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes in Brassicaceae. J Integr Plant Biol 58: 165–177 doi: 10.1111/jipb.12365

Abstract (Browse 812)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Plant genomes harbor dozens to hundreds of nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes. However, the long-term evolutionary history of these resistance genes has not been fully understood. This study reveals that before and after Brassicaceae speciation, NBS-LRR genes exhibit a dynamic evolutionary pattern of first expansion and then contraction.
Floral nectary, nectar production dynamics, and floral reproductive isolation among closely related species of Pedicularis
Author: Ya-Nan Liu, Yan Li, Fu-Sheng Yang and Xiao-Quan Wang
Journal of Integrative Plant Biology 2016 58(2): 178每187
Published Online: July 14, 2015
DOI: 10.1111/jipb.12374
      
    

Floral nectar is thought to be one of the most important rewards that attract pollinators in Pedicularis; however, few studies have examined variation of nectary structure and/or nectar secretion in the genus, particularly among closely related species. Here we investigated nectary morphology, nectar quality, and nectar production dynamics in flowers of Pedicularis section Cyathophora. We found a conical floral nectary at the base of the ovary in species of the rex-thamnophila clade. Stomata were found on the surface of the nectary, and copious starch grains were detected in the nectary tissues. In contrast, a semi-annular nectary was found in flowers of the species of the superba clade. Only a few starch grains were observed in tissues of the semi-annular nectary, and the nectar sugar concentration in these flowers was much lower than that in the flowers of the rex-thamnophila clade. Our results indicate that the floral nectary has experienced considerable morphological, structural, and functional differentiation among closely related species of Pedicularis. This could have affected nectar production, leading to a shift of the pollination mode. Our results also imply that variation of the nectary morphology and nectar production may have played an important role in the speciation of sect. Cyathophora.

 

Liu YN, Li Y, Yang FS, Wang XQ (2016) Floral nectary, nectar production dynamics, and floral reproductive isolation among closely related species of Pedicularis. J Integr Plant Biol 58: 178–187 doi: 10.1111/jipb.12374

Abstract (Browse 814)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Floral nectar is an effective reward for pollinators. We detected considerable morphological, structural, and functional differentiation among closely related species of Pedicularis. This could affect nectar production, leading to a shift of pollination patterns rather than pollinators.
 

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