April 2011, Volume 53 Issue 4, Pages 258C334.

Cover Caption: Semi-dominant Dwarfism of Rice
About the cover: The height of rice affects lodging resistance and contributes to yield. So far, only a few dominant dwarfing genes have been identified, and the mechanism behind such dwarfisms remains elusive. The study of Liang et al. (pp 312C323) reports a new dwarf mutant (cover picture) of rice, which is controlled by a semi-dominant gene LB4D located on chromosome 11. Microscopic observations suggest that LB4D may regulate the growths of leaves and stems at later stages and the differentiation of vascular tissues.


          Cell and Developmental Biology
A Point Mutation in the Pentatricopeptide repeat Motif of the AtECB2 Protein Causes Delayed Chloroplast Development  
Author: Zhi-Lin Cao, Qing-Bo Yu, Yue Sun, Yang Lu, Yong-Lan Cui and Zhong-Nan Yang
Journal of Integrative Plant Biology 2011 53(4): 258-269
Published Online: February 7, 2011
DOI: 10.1111/j.1744-7909.2011.01030.x

AtECB2 encodes a pentatricopeptide repeat (PPR) protein that regulates the editing of the plastid genes accD and ndhF. The ecb2-1 knockout shows an albino phenotype and is seedling lethal. In this study, we isolated an allelic mutant of the AtECB2 gene, ecb2-2, which showed delayed greening phenotype but could complete their life cycle. In this mutant, the Thr500 is converted to Ile500 in the 13th PPR motif of the AtECB2 protein. Transmission electron microscopy demonstrated that chloroplast development was delayed in both the cotyledons and leaves of the mutant. An investigation of the chloroplast gene expression profile indicated that PEP (plastid-encoded RNA polymerase) activity in ecb2-2 cotyledons was not obviously affected, whereas it was severely impaired in ecb2-1. This result suggests that the PEP activities cause the different phenotypes of the ecb2-1 and ecb2-2 mutants. The editing efficiency of the three editing sites of accD (C794 and C1568) and ndhF (C290) in the mutant was dynamically altered, which was in agreement with the phenotype. This result indicates that the editing efficiency of accD and ndhF in the ecb2-2 mutant is associated with a delayed greening phenotype. As ecb2-2 can survive and set seeds, this mutant can be used for further investigation of RNA editing and chloroplast development in arabidopsis.

Cao ZL, Yu QB, Sun Y, Lu Y, Cui YL, Yang ZN (2011) A point mutation in the pentatricopeptide repeat motif of the AtECB2 protein causes delayed chloroplast development. J. Integr. Plant Biol. 53(4), 258–269.

Abstract (Browse 2510)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Metabolism and Biochemistry
Increased Drying Rate Lowers the Critical Water Content for Survival in Embryonic Axes of English Oak (Quercus robur L.) Seeds  
Author: Tobias M. Ntuli, William E. Finch-Savage, Patricia Berjak and Norman W. Pammenter
Journal of Integrative Plant Biology 2011 53(4): 270-280
Published Online: December 1, 2010
DOI: 10.1111/j.1744-7909.2010.01016.x

The potential to cryopreserve embryonic axes of desiccation-sensitive (recalcitrant) seeds is limited by damage during the desiccation necessary for low temperature survival, but the basis of this injury and how to reduce it is not well understood. The effects of drying rate on the viability, respiratory metabolism and free radical-mediated processes were therefore investigated during dehydration of Quercus robur L. embryonic axes. Viability, assessed by evidence of germination and tetrazolium staining, showed a sharp decline at 0.27 and 0.8 g/g during rapid (<12 h) or slow (3 d) dehydration, respectively. Rapid dehydration therefore lowered the critical water content for survival. At any given water content rapid dehydration was associated with higher activities of the free radical processing enzymes, superoxide dismutase, catalase and glutathione reductase and lower levels of hydroperoxide and membrane damage. Rapid dehydration was also associated with lower malate dehydrogenase activity, and a reduced decline in phosphofructokinase activity and in levels of the oxidized form of nicotinamide dinucleotide. Ageing may have contributed to increased damage during slow dehydration, since viability declined even in hydrated storage after 3 d. The results presented are consistent with rapid dehydration reducing the accumulation of damage resulting from desiccation induced aqueous-based deleterious reactions.

Ntuli TM, Finch-Savage WE, Berjak P, Pammenter NW (2011) Increased drying rate lowers the critical water content for survival in embryonic axes of English oak (Quercus robur L.) seeds. J. Integr. Plant Biol. 53(4), 270–280.

Abstract (Browse 2021)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Plant-environmental Interactions
Identification of Target Ligands of CORYNE in Arabidopsis by Phage Display Library
Author: Heng Zhao, Shuzhen Li, Jiping Sheng, Lin Shen, Yuhui Yang and Bin Yao
Journal of Integrative Plant Biology 2011 53(4): 281-288
Published Online: January 10, 2011
DOI: 10.1111/j.1744-7909.2010.01028.x

CORYNE (CRN) plays important roles in stem cell division and differentiation of shoot apical meristem (SAM) in Arabidopsis thaliana. The cytoplasmic kinase domain of CRN has been cloned and expressed in Escherichia coli, and further purified by two consecutive steps of affinity chromatography. By using this purified CRN as a ligand, a 12-mer random-peptide library was used to determine the specific amino acid sequences binding with the recombinant CRN molecule. After four rounds of biopanning, positive phage clones were isolated and sequenced, and further tested by enzyme linked immunosorbent assay for their binding ability and specificity. Two positive clones that specifically bind to the intracellular protein kinase domain of CRN have been identified. Alignment of these peptides and the kinase-associated protein phosphatase (KAPP) shows high similarity, indicating that KAPP might interact with the cytoplasmic kinase domain of CRN and negatively regulate the CLV signal. Our current study would be helpful to better understand the CLV3 signal pathway.

Zhao H, Li S, Sheng J, Shen L, Yang Y, Yao B (2011) Identification of target ligands of CORYNE in Arabidopsis by phage display library. J. Integr. Plant Biol. 53(4), 281–288.

Abstract (Browse 1890)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Rice Phospholipase D is Involved in Salt Tolerance by the Mediation of H+-ATPase Activity and Transcription
Author: Peng Shen, Rong Wang, Wen Jing and Wenhua Zhang
Journal of Integrative Plant Biology 2011 53(4): 289-299
Published Online: December 16, 2010
DOI: 10.1111/j.1744-7909.2010.01021.x

Phospholipase Dα (PLDα) is involved in plant response to salt stress, but the mechanisms remain unclear. We investigated rice PLDα (OsPLDα) localization and its effect on tonoplast (TP) and plasma membrane (PM) H+-ATPase activity and transcription in response to NaCl. When rice suspension-cultured cells were treated with 100 mM NaCl, PLDα activity in cell extracts showed a transient activation with a threefold increase at 1 h. The amount of OsPLDα protein decreased slightly in the cytosolic fractions, whereas it increased significantly in the TP after NaCl treatment. OsPLDα1 knockdown cells were developed using RNA interference (RNAi) methods. The increase in TP and PM H+-ATPase activity induced by NaCl was significantly inhibited in OsPLDα1-RNAi cells. Knockdown of OsPLDα1 prevented the NaCl-induced increase in the transcript level of OsVHA-A (encodes TP H+-ATPase) and OSA2 (encodes PM H+-ATPase), as well as OsNHX1 (encodes TP Na+/H+ antiporter). The cells died more in OsPLDα1-RNAi mutant than in wild type when they were treated with NaCl. These results suggest that OsPLDα is involved in salt tolerance in rice through the mediation of H+-ATPase activity and transcription.

Shen P, Wang R, Jing W, Zhang W (2011) Rice phospholipase Dα is involved in salt tolerance by the mediation of H+-ATPase activity and transcription. J. Integr. Plant Biol. 53(4), 289–299.

Abstract (Browse 2112)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Transcriptional Characteristics of Xa21-mediated Defense Responses in Rice
Author: Qiang Gan, Hui Bai, Xianfeng Zhao, Yong Tao, Haipan Zeng, Yuning Han, Wenyuan Song, Lihuang Zhu and Guozhen Liu
Journal of Integrative Plant Biology 2011 53(4): 300-311
Published Online: February 17, 2011
DOI: 10.1111/j.1744-7909.2011.01032.x

Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is the most destructive bacterial disease of rice. The cloned rice gene Xa21 confers resistance to a broad spectrum of Xoo races. To identify genes involved in Xa21-mediated immunity, a whole-genome oligonucleotide microarray of rice was used to profile the expression of rice genes between incompatible interactions and mock treatments at 0, 4, 8, 24, 72 and 120 h post inoculation (hpi) or between incompatible and compatible interactions at 4 hpi, respectively. A total of 441 differentially expressed genes, designated as XDGs (Xa21 mediated differentially expressed genes), were identified. Based on their functional annotations, the XDGs were assigned to 14 categories, including defense-related, signaling, transcriptional regulators. Most of the defense-related genes belonged to the pathogenesis-related gene family, which was induced dramatically at 72 and 120 hpi. Interestingly, most signaling and transcriptional regulator genes were downregulated at 4 and 8 hpi, suggesting that negative regulation of cellular signaling may play a role in the Xa21-mediated defense response. Comparison of expression profiles between Xa21- and other R gene-mediated defense systems revealed interesting common responses. Representative XDGs with supporting evidences were also discussed.

Gan Q, Bai H, Zhao X, Tao Y, Zeng H, Han Y, Song W, Zhu L, Liu G (2011) Transcriptional characteristics of Xa21-mediated defense responses in rice. J. Integr. Plant Biol. 53(4), 300–311.

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          Molecular Physiology
Genetic Analysis and Fine Mapping of a Novel Semidominant Dwarfing Gene LB4D in Rice
Author: Fei Liang, Xiaoyun Xin, Zejun Hu, Jiandi Xu, Gang Wei, Xiaoyin Qian, Jinshui Yang, Haohua He and Xiaojin Luo
Journal of Integrative Plant Biology 2011 53(4): 312-323
Published Online: February 7, 2011
DOI: 10.1111/j.1744-7909.2011.01031.x

A dwarf mutant, designated LB4D, was obtained among the progeny of backcrosses to a wild rice introgression line. Genetic analysis of LB4D indicated that the dwarf phenotype was controlled by a single semidominant dwarfing gene, which was named LB4D. The mutants were categorized as dn-type dwarf mutants according to the pattern of internode reduction. In addition, gibberellin (GA) response tests showed that LB4D plants were neither deficient nor insensitive to GA. This study found that tiller formation by LB4D plants was decreased by 40% compared with the wild type, in contrast to other dominant dwarf mutants that have been identified, indicating that a different dwarfing mechanism might be involved in the LB4D dominant mutant. The reduction of plant height in F1 plants ranged from 27.9% to 38.1% in different genetic backgrounds, showing that LB4D exerted a stronger dominant dwarfing effect. Using large F2 and F3 populations derived from a cross between heterozygous LB4D and the japonica cultivar Nipponbare, the LB4D gene was localized to a 46 kb region between the markers Indel 4 and Indel G on the short arm of chromosome 11, and four predicted genes were identified as candidates in the target region.

Liang F, Xin X, Hu Z, Xu J,Wei G, Qian X, Yang J, He H, Luo X (2011) Genetic analysis and fine mapping of a novel semidominant dwarfing gene LB4D in rice. J. Integr. Plant Biol. 53(4), 312–323.

Abstract (Browse 2435)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Molecular Ecology and Evolution
Codon Usage Bias and Determining Forces in Green Plant Mitochondrial Genomes
Author: Bin Wang, Jing Yuan, Jing Liu, Liang Jin and Jian-Qun Chen
Journal of Integrative Plant Biology 2011 53(4): 324-334
Published Online: February 18, 2011
DOI: 10.1111/j.1744-7909.2011.01033.x

The phenomenon of codon usage bias has been observed in a wide range of organisms. As organisms evolve, how their codon usage pattern change is still an intriguing question. In this article, we focused on the green plant mitochondrial genomes to analyze the codon usage patterns in different lineages, and more importantly, to investigate the possible change of determining forces during the plant evolution. Two patterns were observed between the separate lineages of green plants: Chlorophyta and Streptophyta. In Chlorophyta lineages, their codon usages showed substantial variation (from strongly A, T-biased to strongly G, C-biased); while in Streptophyta lineages, especially in the land plants, the overall codon usages are interestingly stable. Further, based on the Nc-GC3s plots and Akashi's scaled χ2-tests, we found that lineages within Chlorophyta exhibit much stronger evidence of deviating from neutrality; while lineages within Streptophyta rarely do so. Such differences, together with previous reports based on the chloroplast data, suggests that after plants colonized the land, their codon usages in organellar genomes are more reluctant to be shaped by selection force.

Wang B, Yuan J, Liu J, Jin L, Chen JQ (2011) Codon usage bias and determining forces in green plant mitochondrial genomes. J. Integr. Plant Biol. 53(4), 324–334.

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