October 2013, Volume 55 Issue 10, Pages 889每993.


Cover Caption: Chromatin Remodeling Complexes
About the cover: Chromatin remodeling complexes play essential roles in plant development. In this issue, Dong et al. (pp. 928每937) show that the SLIDE domain of the ISWI is responsible for interacting with DDT-domain proteins. In Arabidopsis, at least 12 proteins carry a DDT domain, suggesting ISWI may achieve multiple functions via formation of different chromatin remodeling complexes with different DDT-domain proteins.

 

          Commentary
Embracing the Integrative  
Author: Tobias I. Baskin
Journal of Integrative Plant Biology 2013 55(10): 890每891
Published Online: October 4, 2013
DOI: 10.1111/jipb.12107
Abstract (Browse 882)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Invited Expert Reviews
Involvement of Histone Modifications in Plant Abiotic Stress Responses  
Author: Lianyu Yuan, Xuncheng Liu, Ming Luo, Songguang Yang and Keqiang Wu
Journal of Integrative Plant Biology 2013 55(10): 892每901
Published Online: August 26, 2013
DOI: 10.1111/jipb.12060
      
    

As sessile organisms, plants encounter various environmental stimuli including abiotic stresses during their lifecycle. To survive under adverse conditions, plants have evolved intricate mechanisms to perceive external signals and respond accordingly. Responses to various stresses largely depend on the plant capacity to modulate the transcriptome rapidly and specifically. A number of studies have shown that the molecular mechanisms driving the responses of plants to environmental stresses often depend on nucleosome histone post-translational modifications including histone acetylation, methylation, ubiquitination, and phosphorylation. The combined effects of these modifications play an essential role in the regulation of stress responsive gene expression. In this review, we highlight our current understanding of the epigenetic mechanisms of histone modifications and their roles in plant abiotic stress response.

Yuan L, Liu X, Luo M, Yang S,Wu K(2013) Involvement of histone modifications in plant abiotic stress responses. J. Integr. Plant Biol. 55(10), 892–901.

Abstract (Browse 1768)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Cell and Developmental Biology
Cotton AnnGh3 Encoding an Annexin Protein is Preferentially Expressed in Fibers and Promotes Initiation and Elongation of Leaf Trichomes in Transgenic Arabidopsis
Author: Bing Li, Deng-Di Li, Jie Zhang, Hui Xia, Xiu-Lan Wang, Ying Li and Xue-Bao Li
Journal of Integrative Plant Biology 2013 55(10): 902每916
Published Online: July 29, 2013
DOI: 10.1111/jipb.12063
      
    
The annexins are a multifamily of calcium-regulated phospholipid-binding proteins. To investigate the roles of annexins in fiber development, four genes encoding putative annexin proteins were isolated from cotton (Gossypium hirsutum) and designated AnnGh3, AnnGh4, AnnGh5, and AnnGh6. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) results indicated that AnnGh3, AnnGh4, and AnnGh5 were preferentially expressed in fibers, while the transcripts of AnnGh6 were predominantly accumulated in roots. During fiber development, the transcripts of AnnGh3/4/5 genes were mainly accumulated in rapidly elongating fibers. With fiber cells further developed, their expression activity was dramatically declined to a relatively low level. In situ hybridization results indicated that AnnGh3 and AnnGh5 were expressed in initiating fiber cells (0–2 DPA). Additionally, their expression in fibers was also regulated by phytohormones and [Ca2+]. Subcellular localization analysis discovered that AnnGh3 protein was localized in the cytoplasm. Overexpression of AnnGh3 in Arabidopsis resulted in a significant increase in trichome density and length on leaves of the transgenic plants, suggesting that AnnGh3 may be involved in fiber cell initiation and elongation of cotton.

Li B, Li DD, Zhang J, Xia H, Wang XL, Li Y, Li XB (2013) Cotton AnnGh3 encoding an annexin protein is preferentially expressed in fibers and promotes initiation and elongation of leaf trichomes in transgenic Arabidopsis. J. Integr. Plant Biol. 55(10), 902–916.

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Validation and Characterization of Ghd7.1, a Major Quantitative Trait Locus with Pleiotropic Effects on Spikelets per Panicle, Plant Height, and Heading Date in Rice (Oryza sativa L.)
Author: Touming Liu, Haiyang Liu, Huang Zhang and Yongzhong Xing
Journal of Integrative Plant Biology 2013 55(10): 917每927
Published Online: July 21, 2013
DOI: 10.1111/jipb.12070
      
    

A quantitative trait locus (QTL) that affects heading date (HD) and the number of spikelets per panicle (SPP) was previously identified in a small region on chromosome 7 in rice (Oryza sativa L.). In order to further characterize the QTL region, near isogenic lines (NILs) were quickly obtained by self-crossing recombinant inbred line 189, which is heterozygous in the vicinity of the target region. The pleiotropic effects of QTL Ghd7.1 on plant height (PH), SPP, and HD, were validated using an NIL-F2 population. Ghd7.1 explained 50.2%, 45.3%, and 76.9% of phenotypic variation in PH, SPP, and HD, respectively. Ghd7.1 was precisely mapped to a 357-kb region on the basis of analysis of the progeny of the NIL-F2 population. Day-length treatment confirmed that Ghd7.1 is sensitive to photoperiod, with long days delaying heading up to 12.5 d. Identification of panicle initiation and development for the pair of NILs showed that Ghd7.1 elongated the photoperiod-sensitive phase more than 10 d, but did not change the basic vegetative phase and the reproductive growth phase. These findings indicated that Ghd7.1 regulates SPP by controlling the rate of panicle differentiation rather than the duration of panicle development.

 

Liu T, Liu H, Zhang H, Xing Y (2013) Validation and characterization of Ghd7.1, a major QTL with pleiotropic effects on spikelets per panicle, plant height, and heading date in rice (Oryza sativa L.). J. Integr. Plant Biol. 55(10), 917–927.

Abstract (Browse 1448)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Metabolism and Biochemistry
SLIDE, The Protein Interacting Domain of Imitation Switch Remodelers, Binds DDT-Domain Proteins of Different Subfamilies in Chromatin Remodeling Complexes  
Author: Jiaqiang Dong, Zheng Gao, Shujing Liu, Guang Li, Zhongnan Yang, Hai Huang and Lin Xu
Journal of Integrative Plant Biology 2013 55(10): 928每937
Published Online: September 16, 2013
DOI: 10.1111/jipb.12069
      
    
The Imitation Switch (ISWI) type adenosine triphosphate (ATP)-dependent chromatin remodeling factors are conserved proteins in eukaryotes, and some of them are known to form stable remodeling complexes with members from a family of proteins, termed DDT-domain proteins. Although it is well documented that ISWIs play important roles in different biological processes in many eukaryotic species, the molecular basis for protein interactions in ISWI complexes has not been fully addressed. Here, we report the identification of interaction domains for both ISWI and DDT-domain proteins. By analyzing CHROMATIN REMODELING11 (CHR11) and RINGLET1 (RLT1), an Arabidopsis thaliana ISWI (AtISWI) and AtDDT-domain protein, respectively, we show that the SLIDE domain of CHR11 and the DDT domain together with an adjacent sequence of RLT1 are responsible for their binding. The Arabidopsis genome contains at least 12 genes that encode DDT-domain proteins, which could be grouped into five subfamilies based on the sequence similarity. The SLIDE domain of AtISWI is able to bind members from different AtDDT subfamilies. Moreover, a human ISWI protein SNF2H is capable of binding AtDDT-domain proteins through its SLIDE domain, suggesting that binding to DDT-domain proteins is a conserved biochemical function for the SLIDE domain of ISWIs in eukaryotes.

Dong J, Gao Z, Liu S, Li G, Yang Z, Huang H, Xu L (2013) SLIDE, the protein interacting domain of Imitation Switch remodelers, binds DDT坼domain proteins of different subfamilies in chromatin remodeling complexes. J. Integr. Plant Biol. 55(10), 928–937.

Abstract (Browse 1425)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Molecular Ecology and Evolution
GS6, A Member of the GRAS Gene Family, Negatively Regulates Grain Size in Rice
Author: Lianjun Sun, Xiaojiao Li, Yongcai Fu, Zuofeng Zhu, Lubin Tan, Fengxia Liu, Xianyou Sun, Xuewen Sun and Chuanqing Sun
Journal of Integrative Plant Biology 2013 55(10): 938每949
Published Online: August 2, 2013
DOI: 10.1111/jipb.12062
      
    
Grain size is an important yield坼related trait in rice. Intensive artificial selection for grain size during domestication is evidenced by the larger grains of most of today’s cultivars compared with their wild relatives. However, the molecular genetic control of rice grain size is still not well characterized. Here, we report the identification and cloning of Grain Size 6 (GS6), which plays an important role in reducing grain size in rice. A premature stop at the þ348 position in the coding sequence (CDS) of GS6 increased grain width and weight significantly. Alignment of the CDS regions of GS6 in 90 rice materials revealed three GS6 alleles. Most japonica varieties (95%) harbor the Type I haplotype, and 62.9% of indica varieties harbor the Type II haplotype. Association analysis revealed that the Type I haplotype tends to increase the width and weight of grains more than either of the Type II or Type III haplotypes. Further investigation of genetic diversity and the evolutionary mechanisms of GS6 showed that the GS6 gene was strongly selected in japonica cultivars. In addition, a “ggc” repeat region identified in the region that encodes the GRAS domain of GS6 played an important historic role in the domestication of grain size in rice. Knowledge of the function of GS6 might aid efforts to elucidate the molecular mechanisms that control grain development and evolution in rice plants, and could facilitate the genetic improvement of rice yield.

Sun L, Li X, Fu Y, Zhu Z, Tan L, Liu F, Sun X, Sun X, Sun C(2013) GS6, a member of the GRAS gene family, negatively regulates grain size in rice. J. Integr. Plant Biol. 55(10), 938–949.

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Out of Africa: Miocene Dispersal, Vicariance, and Extinction within Hyacinthaceae Subfamily Urgineoideae
Author: Syed Shujait Ali, Martin Pfosser, Wolfgang Wetschnig, Mario Martínez-Azorín, Manuel B. Crespo and Yan Yu
Journal of Integrative Plant Biology 2013 55(10): 950每964
Published Online: August 30, 2013
DOI: 10.1111/jipb.12065
      
    
Disjunct distribution patterns in plant lineages are usually explained according to three hypotheses: vicariance, geodispersal, and long-distance dispersal. The role of these hypotheses is tested in Urgineoideae (Hyacinthaceae), a subfamily disjunctly distributed in Africa, Madagascar, India, and the Mediterranean region. The potential ancestral range, dispersal routes, and factors responsible for the current distribution in Urgineoideae are investigated using divergence time estimations. Urgineoideae originated in Southern Africa approximately 48.9 Mya. Two independent dispersal events in the Western Mediterranean region possibly occurred during Early Oligocene and Miocene (29.9–8.5 Mya) via Eastern and Northwestern Africa. A dispersal from Northwestern Africa to India could have occurred between 16.3 and 7.6 Mya. Vicariance and extinction events occurred approximately 21.6 Mya. Colonization of Madagascar occurred between 30.6 and 16.6 Mya, after a single transoceanic dispersal event from Southern Africa. The current disjunct distributions of Urgineoideae are not satisfactorily explained by Gondwana fragmentation or dispersal via boreotropical forests, due to the younger divergence time estimates. The flattened winged seeds of Urgineoideae could have played an important role in long-distance dispersal by strong winds and big storms, whereas geodispersal could have also occurred from Southern Africa to Asia and the Mediterranean region via the so-called arid and high-altitude corridors.

Ali SS, Pfosser M, Wetschnig W, Martínez坼Azorín M, Crespo MB, Yu Y (2013) Out of Africa: Miocene dispersal, vicariance, and extinction within Hyacinthaceae subfamily Urgineoideae. J. Integr. Plant Biol. 55(10), 950–964.

Abstract (Browse 1068)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Molecular Physiology
Comparative Proteomic Analysis of Rice Shoots Exposed to High Arsenate
Author: Yanli Liu, Ming Li, Chao Han, Fengxia Wu, Bingkun Tu and Pingfang Yang
Journal of Integrative Plant Biology 2013 55(10): 965每978
Published Online: June 17, 2013
DOI: 10.1111/jipb.12058
      
    
Consumption of arsenic contaminated water and cereals is a serious threat to humans all over the world. Rice (Oryza sativa “Nipponbare”), as a main cereal crop, can accumulate arsenic more than 10-fold that of in other cereals. To gain a comprehensive understanding of the response of rice subjected to 100 µM arsenate stress, a comparative proteomic analysis of rice shoots in combination with morphological and biochemical investigations have been performed in this study. The results demonstrated that arsenate suppressed the growth of rice seedlings, destroyed the cellular ultra-structure and changed the homeostasis of reactive oxygen species. Moreover, a total of 38 differentially displayed proteins, which were mainly involved in metabolism, redox and protein-metabolism, were identified. The data suggest the arsenic can inhibit rice growth through negatively affecting chloroplast structure and photosynthesis. In addition, upregulation of the proteins involved in redox and protein metabolism might help the rice to be resistant or tolerant to arsenic toxicity. In general, this study improves our understanding about the rice arsenic responsive mechanism.

Liu Y, Li M, Han C, Wu F, Tu B, Yang P (2013) Comparative proteomic analysis of rice shoots exposed to high arsenate. J. Integr. Plant Biol. 55(10), 965–978.

Abstract (Browse 1220)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Genetic Interactions Reveal that Specific Defects of Chloroplast Translation are Associated with the Suppression of var2-Mediated Leaf Variegation
Author: Xiayan Liu, Mengdi Zheng, Rui Wang, Ruijuan Wang, Lijun An, Steve R. Rodermel and Fei Yu
Journal of Integrative Plant Biology 2013 55(10): 979每993
Published Online: September 10, 2013
DOI: 10.1111/jipb.12078
      
    
Arabidopsis thaliana L. yellow variegated (var2) mutant is defective in a chloroplast FtsH family metalloprotease, AtFtsH2/VAR2, and displays an intriguing green and white leaf variegation. This unique var2-mediated leaf variegation offers a simple yet powerful tool for dissecting the genetic regulation of chloroplast development. Here, we report the isolation and characterization of a new var2 suppressor gene, SUPPRESSOR OF VARIEGATION8 (SVR8), which encodes a putative chloroplast ribosomal large subunit protein, L24. Mutations in SVR8 suppress var2 leaf variegation at ambient temperature and partially suppress the cold-induced chlorosis phenotype of var2. Loss of SVR8 causes unique chloroplast rRNA processing defects, particularly the 23S–4.5S dicistronic precursor. The recovery of the major abnormal processing site in svr8 23S–4.5S precursor indicate that it does not lie in the same position where SVR8/L24 binds on the ribosome. Surprisingly, we found that the loss of a chloroplast ribosomal small subunit protein, S21, results in aberrant chloroplast rRNA processing but not suppression of var2 variegation. These findings suggest that the disruption of specific aspects of chloroplast translation, rather than a general impairment in chloroplast translation, suppress var2 variegation and the existence of complex genetic interactions in chloroplast development.
 

Liu X, Zheng M, Wang R, Wang R, An L, Rodermel SR, Yu F (2013) Genetic interactions reveal that specific defects of chloroplast translation are associated with the suppression of var2坼mediated leaf variegation. J. Integr. Plant Biol. 55(10), 979–993.

Abstract (Browse 1128)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
 

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