Special Issue: Frontiers of Plant Molecular Biology   

January 2007, Volume 49 Issue 1, Pages 1-127.

Cover Caption:
Molecular Model Structure of OsHPL3
Aldehydes are important volatiles implicated in plant-plant and plant-insect interactions. The cover shows the molecular model of OsHPL3, an enzyme responsible for the production of aldehydes in rice. This structure will be used for targeted mutagensis in order to improve the enzyme's activity. Backbone structural image for the P450 domain of OsHPL3: random coil is in green, putative binding domain is in ball representation, and the asterisk denotes the position of the signature residue Ala within the binding domain. The docked substrate 13-HPOT (pink) is in tube representation. See pages 43-51 for more details.


          Original Article
A Note from the Executive Editor  
Author: Chun-Ming Liu
Journal of Integrative Plant Biology 2007 49(1): 1-2
DOI: 10.1111/j.1744-7909.2006.00423.x

When Professor Xing-Guo Han, one of the Chief Editors of Journal of Integrative Plant Biology (JIPB) and President of the Botanical Society of China, and Professor Ke-Ping Ma, the Director General of the Institute of Botany, the Chinese Academy of Sciences (CAS), asked me if I would like to be the Executive Editor for JIPB, it really took me a few days to think about it. The major reason for me to be so reluctant to take such a position was that I felt I really did not have enough time to manage a journal promptly, by hiding away from my daily business. At the moment, I run my own laboratory, and take care of the management job for the Center of Signal Transduction & Metabolomics. In addition, I also did not have any experience in editorial business. However, they managed to convince me to take the challenge, by giving me their full support. Anyway, I agreed in the end. I will do my best to assist the Editors to bring up the quality of the journal. Regardless of whether or not I reach my goal, it will be a valuable experience for me. JIPB was established in 1952, for the first 52 years published under the name of Acta Botanica Sinica, and changed to its current name in 2005. It was a quarterly magazine first, and then published bimonthly from 1981, and monthly since 1989. During its 54-year history, the Journal has always been the leading plant science journal in China. It has also witnessed the dark period of the country, when the Journal was stopped for a period of 7 years (between mid-1966 and mid-1973) due to the cultural revolution? In January 2005, the Journal formally entered into a co-publishing partnership with Blackwell Publishing, and now it appears online in Blackwell Synergy, which is available to over 3 000 universities worldwide. Over the last few weeks, I have spoken to many plant scientists, and Dr. Jin-Zhong Cui, the managing editor, to get their advice. The general idea is that to improve the quality of the journal, we need to rethink the strategy. After these discussions we came to the following conclusions: 1) The general scope: with the aim to bring the Journal to a higher standard, we need to have a clear scope for the Journal. We will publish invited reviews to bring our readers to state-of-the-art scientific developments, and research articles with broad interests to plant scientists, with particular focus on those articles that could answer basic biological questions by using reproducible experimental and statistical analyses. We will not consider those purely descriptive observations or confirmation works. The way of describing and discussing the results must be appropriate for a wide audience of plant biologists. 2) The reviewing process: one major change we made in terms of the peer-review process was to establish a board of enthusiastic scientists (see the list below) to be Area Responsible Editors (ARE). These Editors take full responsibility of an area of his/her expertise, and facilitate the peer-reviewing process and decision-making thereafter. To speed up the publication cycle, we are making several changes to the review process: a) we will use Stanford University Libraryís HighWire Press software (the same publication platform used by Plant Cell and Plant Physiology) for handling the manuscript processing; b) at the time when the corresponding author submits the article, he/she must identify the proper ARE; c) we will eliminate the page restriction for each issue, to allow a fast publication even when too many or too few papers have been accepted; d) we will have a PubExp column for rapid publication of papers with exceptional discoveries whereby the manuscript is submitted directly to the Executive Editor; e) we will hire two or three new editorial staff to support the communication, editing and typesetting. 3) New protocols: we will publish methodology papers to describe procedures that could be used reproducibly in other laboratories for studies in plant sciences. Of course, the most important thing to make a good journal is to get the support from you, the readers, the authors, the reviewers and the editors. I hope we can work together with you to allow JIPB to be an internationally recognized journal. To reach this goal, we need good manuscripts, critical reviewers, speedy publication and the best services. If you have suggestions and comments, please do not hesitate to contact me. Sincerely, Chun-Ming Liu, PhD The ARE members 1) Ecology Prof. Jianguo (Jingle) Wu (landscape & urban ecology) Arizona State University, USA Prof. Jianxin Sun (ecosystems & modeling) Institute of Botany, CAS, China Prof. Jiquan Chen (forest ecology, conservation biology) The University of Toledo, USA Prof. Weixin Cheng (ecosystem) University of California, USA 2) Stress & Phytochemistry Prof. Wei-Hua Wu (membrane channel) China Agricultural University, China Prof. Zhi-Zhong Gong (abiotic stress) China Agricultural University, Beijing Prof. Daoxin Xie (viral and bacterium diseases) Tsinghua University, China Prof. Ninghua Tan (phytochemistry & functional products) Kunming Institute of Botany, CAS, China Prof. Xiao-Quan Qi (metabolites/fungal diseases) Institute of Botany, CAS, China 3) Omics & Epigenetics Prof. Jun Yu (transcriptome, bioinformatics) Beijing Institute of Genomics, CAS, China Prof. Dabing Zhang (rice functional genomics) Shanghai Jiao Tong University, China Prof. Bin Han (genomics; genome evolution) National Center for Gene Research, CAS, China Prof. Tai Wang (proteomics) Institute of Botany, CAS, China Prof. Xiaofeng Cao (epigenetics) Institute of Genetics & Developmental Biology, CAS, China 4) Development & Photosynthesis Prof. Da Luo (flower development) Institute of Plant Physiology & Ecology, CAS, China Prof. Yuxin Hu (vegetative organ development & architecture) Institute of Botany, CAS, China Prof. Wei-Cai Yang (pollen, embryo sac and embryo development) Institute of Genetics & Developmental Biology, CAS, China Prof. Yong-Biao Xue (fertilization and self-incomparability) Institute of Genetics & Developmental Biology, CAS, China Prof. Jin-Xing Lin (cell biology) Institute of Botany, CAS, China Prof. Cong-Ming Lu (photosynthesis) Institute of Botany, CAS, China 5) Signal Transduction Prof. Hongwei Xue (auxin and BR signaling) Institute of Plant Physiology & Ecology, CAS, China Prof. Xiangdong Fu (GA signaling) Institute of Genetics & Developmental Biology, CAS, China Prof. Hongwei Guo (ethylene signaling) Peking University, China Prof. Jianru Zuo (cytokinin/regeneration/programmed cell death) Institute of Genetics & Developmental Biology, CAS, China Prof. Qi Xie (ABA & protein degradation) Institute of Genetics & Developmental Biology, CAS, China Prof. Chentao Lin (light signal transduction) University of California, Los Angeles, USA 6) Evolution Prof. Yang Zhong (molecular evolution, bioinformatics, statistics) Fudan University, China Prof. Shuang-Quan Huang (reproductive ecology) Wuhan University, China Prof. Song Ge (conservation genetics, molecular systematics) Institute of Botany, CAS, China Prof. Xiao-Quan Wang (biogeography, molecular ecology) Institute of Botany, CAS, China About Professor Chun-Ming Liu Professor Chun-Ming Liu received his BSc degree in 1984 from Shandong Normal University (Jinan), MSc degree in 1987 from Shanghai Institute of Plant Physiology (Shanghai), the Chinese Academy of Sciences, and his PhD degree in 1996 from John Innes Center/University of East Anglia (Norwich, UK). Thereafter, he went to Professor David Meinkeís laboratory (Stillwater, USA) for his 3-year post-doctoral training. Between 1999 and 2005 he worked as a senior scientist and group leader at Plant Research International (Wageningen, The Netherlands). From the beginning of the year, he became a Professor and Director of the Center for Signal Transduction & Metabolomics, Institute of Botany, the Chinese Academy of Sciences, Beijing. His research is always associated with seed development, in particular in embryogenesis, endosperm development and meristem formation. Selected publications Liu CM, Xu ZH and Chua NH (1993). Auxin polar transport is essential for the establishment of bilateral symmetry during early plant embryogenesis. Plant Cell 5: 621-630. Liu CM, Xu ZH and Chua NH (1993). Proembryo culture: in vitro development of early globular-staged zygotic embryos of Brassica juncea. Plant J 3: 291-300. Liu CM and Meinke DW (1998). The titan mutants of Arabidopsis are disrupted in mitosis and cell cycle control during seed development. Plant J 16: 21-31. Liu CM, McElver J, Tzafrir I, Joosen R, Wittich P, Patton D, van Lammeren AAM and Meinke D (2002). Condensin and cohesin knockouts in Arabidopsis exhibit a titan seed phenotype. Plant J 29: 405-415. Fiers M, Hause G, Boutilier K, Casamitjana-Marinez E, Weijers D, Offringa R, van der Geest L, van Lookeren Campagne M and Liu CM (2004). Mis-expression of the CLV3/ESR-like gene CLE19 in Arabidopsis leads to a consumption of root meristem. Gene 327: 37-49. Xu J, Zhang HY, Xie CH, Xue HW, Dijkhuis P and Liu CM (2005). EMBRYONIC FACTOR 1 encodes an AMP deaminase and is essential for the zygote to embryo transition in Arabidopsis. Plant J 42: 743-756. Fiers M, Golemiec E, Xu J, van der Geest L, Heidstra R, Stiekema W and Liu CM (2005). The 14-amino acid CLV3, CLE19 and CLE40 peptides trigger consumption of the root meristem in Arabidopsis through a CLAVATA2-dependent pathway. Plant Cell 17: 2542-2553. Fiers M, Golemiec E, van der Schors R, van der Geest L, Li KW, Stiekema WJ and Liu CM (2006). The CLV3/ESR motif of CLV3 is functionally independent from the non-conserved flanking sequences. Plant Physiol 141: 1284-1294. Fiers M, Ku KL and Liu CM (2007). CLE peptide ligands and their roles in establishing meristems. Curr Opin Plant Biol (in press).

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About the Special Issue  
Author: Chen-Tao Lin and Hong Ma
Journal of Integrative Plant Biology 2007 49(1): 3-3
DOI: 10.1111/j.1744-7909.2006.00425.x

In May of 2006, over three hundred plant researchers attended the conference Frontiers of Plant Molecular Biology, 2006?in Changsha, China. This was the fifth time that the Frontiers of Plant Molecular Biology?conference had been held. Each time, plant biologists from China, the United States, and other countries have gathered and discussed the latest advances in plant molecular biology. During the conference this year, topics covered included light signaling, hormonal responses, plant pathogen interactions, and development. Among the meeting participants were also many graduate students, postdoctoral researchers, and teachers from local institutions of higher education and plant research. This international meeting provided an excellent opportunity for young students to gain valuable exposure to the most recent developments in plant molecular biology. The meeting was co-organized and sponsored primarily by the Hunan University, Hunan Normal University, and Hunan Agricultural University. Although several hundred participants benefited directly from the conference in Changsha, many more researchers working in plant biology fields were unable to attend. To promote further scientific exchange with a larger number of readers, Journal of Integrative Plant Biology (JIPB) extended an invitation to the speakers of the Changsha Conference to contribute to a special issue of JIPB. A total of seventeen speakers kindly accepted the invitation and contributed to this special issue. Their articles should give our readers a glimpse of the scientific progress discussed at the Changsha Conference. Most of the articles are short reviews discussing recent developments in various fields of plant biology: from plant-bacterium warfare to anther and pollen development, from regulation of ubiquitination to chromatin remodeling, and from the function of light receptors to the regulation of flowering time, as well as others. We would like to thank all of the authors of this special issue for their hard work and generous contribution. We hope that our readers find these articles as informative and stimulating as we did during the Changsha Conference. In particular, we hope that this special issue will benefit one of the most important groups of readers of this journal ?the undergraduate and graduate students who are interested in plant biology. Chentao Lin, University of California, Los Angeles, USA Hong Ma, Pennsylvania State University, University Park, USA

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          Invited Expert Reviews
Phototropins and Their LOV Domains: Versatile Plant Blue-Light Receptors  
Author: Winslow R. Briggs, Tong-Seung Tseng, Hae-Young Cho, Trevor E. Swartz, Stuart Sullivan, Roberto A. Bogomolni, Eirini Kaiserli and John M. Christie
Journal of Integrative Plant Biology 2007 49(1): 4-10
DOI: 10.1111/j.1744-7909.2006.00406.x

The phototropins phot1 and phot2 are plant blue-light receptors that mediate phototropism, chloroplast movements, stomatal opening, leaf expansion, the rapid inhibition of hypocotyl growth in etiolated seedlings, and possibly solar tracking by leaves in those species in which it occurs. The phototropins are plasma membrane-associated hydrophilic proteins with two chromophore domains (designated LOV1 and LOV2 for their resemblance to domains in other signaling proteins that detect light, oxygen, or voltage) in their N-terminal half and a classic serine/threonine kinase domain in their C-terminal half. Both chromophore domains bind flavin mononucleotide (FMN) and both undergo light-activated formation of a covalent bond between a nearby cysteine and the C(4a) carbon of the FMN to form the signaling state. LOV2-cysteinyl adduct formation leads to the release downstream of a tightly bound amphipathic É—-helix, a step required for activation of the kinase function. This cysteinyl adduct then slowly decays over a matter of seconds or minutes to return the photoreceptor chromophore modules to their ground state. Functional LOV2 is required for light-activated phosphorylation and for various blue-light responses mediated by the phototropins. The function of LOV1 is still unknown, although it may serve to modulate the signal generated by LOV2. The LOV domain is an ancient chromophore module found in a wide range of otherwise unrelated proteins in fungi and prokaryotes, the latter including cyanobacteria, eubacteria, and archaea. Further general reviews on the phototropins are those by Celaya and Liscum (2005) and Christie and Briggs (2005).Author for correspondence. Tel: +1 650 325 1521 (extension 207); Fax: +1 650 325 06857; E-mail: briggs@stanford.edu

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Phytochrome-regulated Gene Expression  
Author: Peter H. Quail
Journal of Integrative Plant Biology 2007 49(1): 11-20
DOI: 10.1111/j.1744-7909.2006.00422.x

Identification of all genes involved in the phytochrome (phy)-mediated responses of plants to their light environment is an important goal in providing an overall understanding of light-regulated growth and development. This article highlights and integrates the central findings of two recent comprehensive studies in Arabidopsis that have identified the genome-wide set of phy-regulated genes that respond rapidly to red-light signals upon first exposure of dark-grown seedlings, and have tested the functional relevance to normal seedling photomorphogenesis of an initial subset of these genes. The data: (a) reveal considerable complexity in the channeling of the light signals through the different phy-family members (phyA to phyE) to responsive genes; (b) identify a diversity of transcription-factor-encoding genes as major early, if not primary, targets of phy signaling, and, therefore, as potentially important regulators in the transcriptional-network hierarchy; and (c) identify auxin-related genes as the dominant class among rapidly-regulated, hormone-related genes. However, reverse-genetic functional profiling of a selected subset of these genes reveals that only a limited fraction are necessary for optimal phy-induced seedling deetiolation.Author for correspondence. E-mail: quail@nature.berkeley.edu

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Light Regulation of Gibberellins Metabolism in Seedling Development  
Author: Xiao-Ying Zhao, Xu-Hong Yu, Xuan-Ming Liu and Chen-Tao Lin
Journal of Integrative Plant Biology 2007 49(1): 21-27
DOI: 10.1111/j.1744-7909.2006.00407.x

Light affects many aspects of plant development, including seed germination, stem elongation, and floral initiation. How photoreceptors control photomorphogenic processes is not yet fully understood. Because phytohormones are chemical regulators of plant development, it may not be surprising that light affects, directly or indirectly, cellular levels and signaling processes of various phytohormones, such as auxin, gibberellins (GA), cytokinin, ethylene, abscisic acid (ABA), and brassinosteroids (BR). Among those phytohormones, light regulation of GA metabolism has probably attracted more attention among photobiologists and it is arguably the most extensively studied plant hormone at present with respect to its role in photomorphogenesis. It has become increasingly clear that phytochromes and cryptochromes are the major photoreceptors mediating light regulation of GA homeostasis. This short article attempts to examine some recent developments in our understanding of how light and photoreceptors regulate GA biosynthesis and catabolism during seedling development. It is not our intention to carry out a comprehensive review of the field, and readers are referred to recent review articles for a more complete view of this area of study (Kamiya and Garcia-Martinez 1999; Hedden and Phillips 2000; Garcia-Martinez and Gil 2001; Olszewski et al. 2002; Halliday and Fankhauser 2003; Sun and Gubler 2004).Author for correspondence. Tel: +1 310 206 9576; Fax: +1 310 206 3987; E-mail: clin@mcdb.ucla.edu

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Timing of Photoperiodic Flowering: Light Perception and Circadian Clock  
Author: Yun Zhou, Xiao-Dong Sun and Min Ni
Journal of Integrative Plant Biology 2007 49(1): 28-34
DOI: 10.1111/j.1744-7909.2006.00411.x

Flowering symbolizes the transition of a plant from vegetative phase to reproductive phase and is controlled by fairly complex and highly coordinated regulatory pathways. Over the last decade, genetic studies in Arabidopsis have aided the discovery of many signaling components involved in these pathways. In this review, we discuss how the timing of flowering is regulated by photoperiod and the involvement of light perception and the circadian clock in this process. The specific regulatory mechanisms on CONSTANS expression and CONSTANS stability by the circadian clock and photoreceptors are described in detail. In addition, the roles of CONSTANS, FLOWERING LOCUS T, and several other light signaling and circadian-dependent components in photoperiodic flowering are also highlighted.Author for correspondence. Tel: +1 612 625 3702; Fax: +1 612 625 1738; E-mail: nixxx008@tc.umn.edu

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Targeting Proteins for Degradation by Arabidopsis COP1: Teamwork Is What Matters  
Author: Rong-Cheng Lin and Hai-Yang Wang
Journal of Integrative Plant Biology 2007 49(1): 35-42
DOI: 10.1111/j.1744-7909.2006.00414.x

Arabidopsis COP1 (Constitutive Photomorphogenic 1) defines a key repressor of photomorphogenesis in darkness by acting as an E3 ubiquitin ligase in the nucleus, and is responsible for the targeted degradation of a number of photomorphogenesis-promoting factors, including phyA, HY5, LAF1, and HFR1. Light activation of multiple classes of photoreceptors (including both phytochromes and cryptochromes) inactivates COP1 and reduces its nuclear abundance, allowing the accumulation of these positively acting light signaling intermediates to promote photomorphogenic development. Recent studies suggest that Arabidopsis COP1 teams up with a family of SPA proteins (SPA1-SPA4) to form the physiologically active COP1-SPA E3 ubiquitin ligase complexes. These COP1-SPA complexes play overlapping and distinct functions in regulating seedling photomorphogenesis under different light conditions and adult plant growth. Further, the COP1-SPA complexes act in concert at a biochemical level with the CDD (COP10, DET1, and DDB1) complex and COP9 signalosome (CSN) to orchestrate the repression of photomorphogenesis.Author for correspondence. Tel: +1 607 254 7476; Fax: +1 607 254 1242; E-mail: hw75@cornell.edu

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Oxylipin Pathway in Rice and Arabidopsis  
Author: E. Wassim Chehab, John V. Perea, Banu Gopalan, Steve Theg and Katayoon Dehesh
Journal of Integrative Plant Biology 2007 49(1): 43-51
DOI: 10.1111/j.1744-7909.2006.00405.x

Plants have evolved complex signaling pathways to coordinate responses to developmental and environmental information. The oxylipin pathway is one pivotal lipid-based signaling network, composed of several competing branch pathways, that determines the plant’s ability to adapt to various stimuli. Activation of the oxylipin pathway induces the de novo synthesis of biologically active metabolites called “oxylipins”. The relative levels of these metabolites are a distinct indicator of each plant species and determine the ability of plants to adapt to different stimuli. The two major branches of the oxylipin pathway, allene oxide synthase (AOS) and hydroperoxide lyase (HPL) are responsible for production of the signaling compounds, jasmonates and aldehydes respectively. Here, we compare and contrast the regulation of AOS and HPL branch pathways in rice and Arabidopsis as model monocotyledonous and dicotyledonous systems. These analyses provide new insights into the evolution of JAs and aldehydes signaling pathways, and the complex network of processes responsible for stress adaptations in monocots and dicots.Author for correspondence. Tel: +1 (530) 752 8187; Fax: +1 (530) 752 5410; E-mail: kdehesh@ucdavis.edu

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Polycomb-group (Pc-G) Proteins Control Seed Development in Arabidopsis thaliana L.  
Author: Xiao-Xue Wang and Li-Geng Ma
Journal of Integrative Plant Biology 2007 49(1): 52-59
DOI: 10.1111/j.1744-7909.2006.00415.x

Polycomb-group (Pc-G) proteins repress their target gene expression by assemble complexes in Drosophila and mammals. Three groups of Pc-G genes, controlling seed development, flower development and vernalization response, have been identified in Arabidopsis (Arabidopsis thaliana L.). MEDEA (MEA), FERTILIZATION INDEPENDENT SEED2 (FIS2), and FERTILIZATION INDEPENDENT ENDOSPERM (FIE) are Pc-G genes in Arabidopsis. Their functions in seed development have been extensively explored. The advanced findings of molecular mechanism on how MEA, FIS2 and FIE control seed development in Arabidopsis are reviewed in this paper.

Author for correspondence. Tel: +86 (0)10 8072 7510; Fax: +86 (0)10 8072 7511; E-mail: maligeng@nibs.ac.cn

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Regulation of Arabidopsis Early Anther Development by Putative Cell-Cell Signaling Molecules and Transcriptional Regulators  
Author: Yu-Jin Sun, Carey LH Hord, Chang-Bin Chen and Hong Ma
Journal of Integrative Plant Biology 2007 49(1): 60-68
DOI: 10.1111/j.1744-7909.2006.00408.x

Anther development in flowering plants involves the formation of several cell types, including the tapetal and pollen mother cells. The use of genetic and molecular tools has led to the identification and characterization of genes that are critical for normal cell division and differentiation in Arabidopsis early anther development. We review here several recent studies on these genes, including the demonstration that the putative receptor protein kinases BAM1 and BAM2 together play essential roles in the control of early cell division and differentiation. In addition, we discuss the hypothesis that BAM1/2 may form a positive-negative feedback regulatory loop with a previously identified key regulator, SPOROCYTELESS (also called NOZZLE), to control the balance between sporogenous and somatic cell types in the anther. Furthermore, we summarize the isolation and functional analysis of the DYSFUNCTIONAL TAPETUM1 (DYT1) gene in promoting proper tapetal cell differentiation. Our finding that DYT1 encodes a putative transcription factor of the bHLH family, as well as relevant expression analyses, strongly supports a model that DYT1 serves as a critical link between upstream factors and downstream target genes that are critical for normal tapetum development and function. These studies, together with other recently published works, indicate that cell-cell communication and transcriptional control are key processes essential for cell fate specification in anther development.Author for correspondence. Tel: +1 814 0863 6414; Fax: +1 814 863 1357; E-mail: hxm16@psu.edu

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Molecular Biological and Biochemical Studies Reveal New Pathways Important for Cotton Fiber Development  
Author: Yu Xu, Hong-Bin Li and Yu-Xian Zhu
Journal of Integrative Plant Biology 2007 49(1): 69-74
DOI: 10.1111/j.1744-7909.2006.00420.x

As the longest single-celled seed trichomes, fibers provide an excellent model for studying fundamental biological processes such as cell differentiation, cell expansion, and cell wall biosynthesis. In this review, we summarize recent progress in cotton functional genomic studies that characterize the dynamic changes in the transcriptomes of fiber cells. Extensive expression profilings of cotton fiber transcriptomes have provided comprehensive information, as quite a number of transcription factors and enzyme-coding genes have been shown to express preferentially during the fiber elongation period. Biosynthesis of the plant hormone ethylene is found significantly upregulated during the fiber growth period as revealed by both microarray analysis and by biochemical and physiological studies. It is suggested that genetic engineering of the ethylene pathway may improve the quality and the productivity of cotton lint. Many metabolic pathways, such as biosynthesis of cellulose and matrix polysaccharides are preferentially expressed in actively growing fiber cells. Five gene families, including proline-rich proteins (PRP), arabinogalactan proteins (AGP), expansins, tubulins and lipid transfer proteins (LTP) are activated during early fiber development, indicating that they may also be needed for cell elongation. In conclusion, we identify a few areas of future research for cotton functional genomic studies.Author for correspondence. Tel: +86 (0)10 6275 1193; Fax: +86 (0)10 6275 4427; E-mail: zhuyx@water.pku.edu.cn

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Hormonal Regulation of Leaf Morphogenesis in Arabidopsis  
Author: Lin-Chuan Li, Ding-Ming Kang, Zhang-Liang Chen and Li-Jia Qu
Journal of Integrative Plant Biology 2007 49(1): 75-80
DOI: 10.1111/j.1744-7909.2006.00410.x

Leaf morphogenesis is strictly controlled not only by intrinsic genetic factors, such as transcriptional factors, but also by environmental cues, such as light, water and pathogens. Nevertheless, the molecular mechanism of how leaf morphogenesis is regulated by genetic programs and environmental cues is far from clear. Numerous series of events demonstrate that plant hormones, mostly small and simple molecules, play crucial roles in plant growth and development, and in responses of plants to environmental cues such as light. With more and more genetics and molecular evidence obtained from the model plant Arabidopsis, several fundamental aspects of leaf morphogenesis including the initiation of leaf primordia, the determination of leaf axes, the regulation of cell division and expansion in leaves have been gradually unveiled. Among these phytohormones, auxin is found to be essential in the regulation of leaf morphogenesis.Author for correspondence. Fax: +86 (0)10 6275 3339; E-mail: qulj@pku.edu.cn

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Jasmonate Signal Pathway in Arabidopsis  
Author: Xiao-Yi Shan, Zhi-Long Wang and Daoxin Xie
Journal of Integrative Plant Biology 2007 49(1): 81-86
DOI: 10.1111/j.1744-7909.2006.00416.x

Jasmonates (JAs), which include jasmonic acid and its cyclopentane derivatives are synthesized from the octadecanoid pathway and widely distributed throughout the plant kingdom. JAs modulate the expression of numerous genes and mediate responses to stress, wounding, insect attack, pathogen infection, and UV damage. They also affect a variety of processes in many plant developmental processes. The JA signal pathway involves two important events: the biosynthesis of JA and the transduction of JA signal. Several important Arabidopsis mutants in jasmonate signal pathway were described in this review.Author for correspondence. Tel: +86 (0)10 6279 6679; E-mail: shanxd05@mails.tsinghua.edu.cn

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Ubiquitination in Abscisic Acid-Related Pathway  
Author: Yi-Yue Zhang and Qi Xie
Journal of Integrative Plant Biology 2007 49(1): 87-93
DOI: 10.1111/j.1744-7909.2006.00417.x

Ubiquitination is emerging as a tight regulatory mechanism that is necessary for all aspects of development and survival of all eukaryotes. Recent genomic and genetic analysis in Arabidopsis suggests that ubiquitination may also play important roles in plant response to the phytohormone abscisic acid (ABA). Many components of the ubiquitination pathway, such as ubiquitin-conjugating enzyme E2, ubiquitin ligase E3 and components of the proteasome, have been identified or predicted to be essential in ABA biosynthesis, catabolism and signaling. In addition, the ubiquitination-related pathway, sumoylation, is also involved in ABA signaling. We summarize in this report recent developments to elucidate their roles in the ABA-related pathway.Author for correspondence. Tel (Fax): +86 (0)10 6488 9351; E-mail: qxie@genetics.ac.cn

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Roles of Pectin Methylesterases in Pollen-Tube Growth  
Author: Li-Qun Chen and De Ye
Journal of Integrative Plant Biology 2007 49(1): 94-98
DOI: 10.1111/j.1744-7909.2006.00418.x

Elongation of the pollen tube in pistil is essential for delivering sperms into the female gametophyte in sexual plant reproduction. Recently, a group of cell wall enzymes, pectin methylesterases (PMEs), have been identified as playing an important role in this process. This article reviews the new understanding of the roles of PMEs in regulating pollen tube growth.Author for correspondence. Tel: +86 (0)10 6273 3798; Fax: +86 (0)10 6273 4839; E-mail: yede@cau.edu.cn

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A Role for Auxin in Flower Development  
Author: Youfa Cheng and Yunde Zhao
Journal of Integrative Plant Biology 2007 49(1): 99-104
DOI: 10.1111/j.1744-7909.2006.00412.x

Auxin has long been implicated in many aspects of plant growth and development including flower development. However, the exact roles of auxin in flower development have not been well defined until the recent identification of auxin biosynthesis mutants. Auxin is necessary for the initiation of floral primordia, and the disruption of auxin biosynthesis, polar auxin transport or auxin signaling leads to the failure of flower formation. Auxin also plays an essential role in specifying the number and identity of floral organs. Further analysis of the relationship between the auxin pathways and the known flower development genes will provide critical information regarding mechanisms of organogenesis and pattern formation in plants.

Author for correspondence. Tel: +1 858 822 2670; Fax: +1 858 534 7108; E-mail: yzhao@biomail.ucsd.edu

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Endless Hide-and-Seek: Dynamic Co-evolution in Plant-Bacterium Warfare  
Author: Libo Shan, Ping He and Jen Sheen
Journal of Integrative Plant Biology 2007 49(1): 105-111
DOI: 10.1111/j.1744-7909.2006.00409.x

Plants possess innate immune systems to prevent most potential infections. The ancient and conserved innate immune responses are triggered by microbe-associated molecular patterns (MAMPs) and play important roles in broad-spectrum defenses. However, successful bacterial pathogens evolved type III virulence effectors to suppress MAMP-mediated immunity. To survive, plants further developed highly specific resistance (R) genes to trigger gene-for-gene-mediated immunity and turn the virulent pathogens into avirulent ones. We summarize here the very recent advances in this dynamic coevolution of plant-bacterium interaction.Author for correspondence. Tel: +1 617 643 3314; E-mail: shan@molbio.mgh.harvard.edu

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Recent Advances in Cloning and Characterization of Disease Resistance Genes in Rice  
Author: Liang-Ying Dai, Xiong-Lun Liu, Ying-Hui Xiao and Guo-Liang Wang
Journal of Integrative Plant Biology 2007 49(1): 112-119
DOI: 10.1111/j.1744-7909.2006.00413.x

Rice diseases caused by fungi, bacteria and viruses are one of the major constraints for sustainable rice (Oryza sativa L.) production worldwide. The use of resistant cultivars is considered the most economical and effective method to control rice diseases. In the last decade, a dozen resistance genes against the fungal pathogen Magnaporthe grisea and the bacterial pathogen Xanthomonas oryzae pv. oryzae have been cloned. Approximately half of them encode nuclear binding site (NBS) and leucine rich repeat (LRR)-containing proteins, the most common type of cloned plant resistance genes. Interestingly, four of them encode novel proteins which have not been identified in other plant species, suggesting that unique mechanisms might be involved in rice defense responses. This review summarizes the recent advances in cloning and characterization of disease resistance genes in rice and presents future perspectives for in-depth molecular analysis of the function and evolution of rice resistance genes and their interaction with avirulence genes in pathogens.Author for correspondence. Tel: +1 614 292 9280; E-mail: wang.620@osu.edu

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          Research Articles
Characterization of the Ubiquitin E2 Enzyme Variant Gene Family in Arabidopsis  
Author: Yu Zhang, Pei Wen, On-Sun Lau and Xing Wang Deng
Journal of Integrative Plant Biology 2007 49(1): 120-126
DOI: 10.1111/j.1744-7909.2006.00419.x

Ubiquitin E2 enzyme variant (UEV) proteins are similar to ubiquitin-conjugating enzyme (E2) in both sequence and structure, but the lack of a catalytic cysteine residue renders them incapable of forming a thiol-ester linkage with ubiquitin. While the functional roles of several UEVs have been defined in yeast and animal systems, Arabidopsis COP10, a photomorphogenesis repressor, is the only UEV characterized in plants. Phylogenetic analysis revealed that the eight Arabidopsis UEV genes belong to three subfamilies. The expression of those genes is supported by either the presence of ESTs or RT-PCR analysis. We also characterized the other members of the COP10 subfamily, UEV2. Semi-quantitative RT-PCR analysis indicated that the UEV2 transcripts can be detected in most organs of Arabidopsis. Analysis of UEV2::GUS transgenic lines also showed its ubiquitous expression in nearly all the developmental stages of Arabidopsis. Transient expression analysis indicated that the sGFP-UEV2 fusion protein can localize to both the cytoplasm and nucleus. A T-DNA insertion mutant, uev2-1, which abolished the transcription of UEV2, displays no visible phenotype. Further, the cop10-4 uev2-1 double mutant exhibits the same phenotype as the cop10-4 mutant in darkness. UEV2 is therefore not functionally redundant with COP10.Author for correspondence. Tel: +1 203 432 8908; Fax: +1 203 432 5726; E-mail: xingwang.deng@yale.edu

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Journal of Integrative Plant Biology 2007 49(1): 127-127
DOI: 10.1111/j.1744-7909.2006.00424.x

Shangguan ZP, Lei TW, Shao MA, Xue QW (2005). Effects of Phosphorus Nutrient on the Hydraulic Conductivity of Sorghum (Sorghum vulgare Pers.) Seedling Roots Under Water Deficiency. J Integr Plant Biol 47, 421-427. The first and corresponding author, Zhou-Ping Shangguan, of the above article has requested that its publication be retracted from the Journal of Integrative Plant Biology (JIPB), with the following statement: With the fact that the data published in the above-mentioned article contained plagiarized materials from the article of Shen Y, Wang B, Qu D, Chen R. Effects of phosphorus on root hydraulic conductance of corn under water stress. Journal of Northwest Sci-Tech University of Agriculture and Forestry (JNSTUAF, Natural Science Edition). 2002, 30: 11-15, I have to retract the paper from JIPB. In addition, I admit that the manuscript was prepared and published without the consensus of the other three authors listed, therefore, I myself am solely responsible for the plagiarizm and falsification. I deeply apologize for the damages to JIPB and the authors of the JNSTUAF paper, and for misleading the readers by the publication and citation of the data. Zhou-Ping Shangguan Institute of Soil and Water Conservation, the Chinese Academy of Sciences Yangling, Shannxi, 712100, China Tel: 86-29-87019107 Fax: 86-29-87012210 E-mail: shangguan@ms.iswc.ac.cn July 16, 2006 Editorial It was brought to our attention that the above-mentioned paper co-authored by ZP Shangguan was involved in serious scientific misconduct. We communicated several times with the first and corresponding author (ZP Shangguan), to allow him to clarify the case by himself. We have carefully investigated the case, with help from the author's home institution, the Institute of Soil and Water Conservation (ISWC), the Chinese Academy of Sciences. On December 5, 2006, we received a formal statement from the ISWC, that described the results of an official investigation into the case. Based on these documents, we would like to make the following statements: 1) It is apparent that the above-mentioned paper contains falsified and plagiarized data from the following paper: Shen Y, Wang B, Qu D, Chen R (2002). Effects of phosphorus on root hydraulic conductance of corn under water stress. Journal of Northwest Sci-Tech University of Agriculture and Forestry (Natural Science Edition), 30: 11-15. 2) The first author is fully responsible for the misconduct, although he has stated that an un-authored visiting student was involved in putting the data together. 3) We acknowledge that a formal request was made by ZP Shangguan on April 10, 2006, to the editorial office to retract the paper; however, the Journal has not been able to publish the retraction letter earlier because the investigation was not formally completed. 4) ZP Shangguan has been discharged from administrative duties of the ISWC. This serves as a reminder to all involved with the Journal that scientific integrity requires original research from each published author. Journal of Integrative Plant Biology December 11, 2006

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