Special Issue: Plant Metabolic Biology   

October 2010, Volume 52 Issue 10, Pages 854C942.

Cover Caption: Plant Metabolic Biology
About the cover: The edible curd of Cauliflower (Brassica oleracea var. botrytis L.) comes in different colors. In addition to the nutrients in white cauliflower, the orange one accumulates carotene, the green one accumulates chlorophylls, and the purple one accumulates anthocyanins. It is of high interest to figure out how different pigments are synthesized, and how these metabolic pathways are regulated in the floral meristematic tissues.


Plant Specialized Metabolism: the Easy and the Hard  
Author: Shan Lu
Journal of Integrative Plant Biology 2010 52(10): 854-855
Published Online: September 29, 2010
DOI: 10.1111/j.1744-7909.2010.00997.x
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          Research Articles
Comprehensive Analysis of Expressed Sequence Tags from the Pulp of the Red Mutant 'Cara Cara' Navel Orange (Citrus sinensis Osbeck)  
Author: Jun-Li Ye, An-Dan Zhu, Neng-Guo Tao, Qiang Xu, Juan Xu and Xiu-Xin Deng
Journal of Integrative Plant Biology 2010 52(10): 856-867
Published Online: May 13, 2010
DOI: 10.1111/j.1744-7909.2010.00952.x

Expressed sequence tag (EST) analysis of the pulp of the red-fleshed mutant ‘Cara Cara’ navel orange provided a starting point for gene discovery and transcriptome survey during citrus fruit maturation. Interpretation of the EST datasets revealed that the mutant pulp transcriptome held a high section of stress responses related genes, such as the type III metallothionein-like gene (6.0%), heat shock protein (2.8%), Cu/Zn superoxide dismutase (0.8%), late embryogenesis abundant protein 5 (0.8%), etc. 133 transcripts were detected to be differentially expressed between the red mutant and its orange-color wild genotype ‘Washington’ via digital expression analysis. Among them, genes involved in metabolism, defense/stress and signal transduction were statistical overrepresented. Fifteen transcription factors, composed of NAM, ATAF, and CUC transcription factor (NAC); myeloblastosis (MYB); myelocytomatosis (MYC); basic helix-loop-helix (bHLH); basic leucine zipper (bZIP) domain members, were also included. The data reflected the distinct expression profile and the unique regulatory module associated with these two genotypes. Eight differently expressed genes analyzed in digital were validated by quantitative real-time polymerase chain reaction. For structural polymorphism, both simple sequence repeats and single nucleotide polymorphisms (SNP) loci were surveyed; dinucleotide presentation revealed a bias toward AG/GA/TC/CT repeats (52.5%), against GC/CG repeats (0%). SNPs analysis found that transitions (73%) outnumbered transversions (27%). Seventeen potential cultivar-specific and 387 heterozygous SNP loci were detected from ‘Cara Cara’ and ‘Washington’ EST pool.


Ye JL, Zhu AD, Tao NG, Xu Q, Xu J, Deng XX (2010) Comprehensive analysis of expressed sequence tags from the pulp of the red mutant ‘Cara Cara’ navel orange (Citrus sinensis Osbeck). J. Integr. Plant Biol. 52(10), 856–867

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Coordinated Regulation of Gene Expression for Carotenoid Metabolism in Chlamydomonas reinhardtii  
Author: Tian-Hu Sun, Cheng-Qian Liu, Yuan-Yuan Hui, Wen-Kai Wu, Zhi-Gang Zhou and Shan Lu
Journal of Integrative Plant Biology 2010 52(10): 868-878
Published Online: August 26, 2010
DOI: 10.1111/j.1744-7909.2010.00993.x

Carotenoids are important plant pigments for both light harvesting and photooxidation protection. Using the model system of the unicellular green alga Chlamydomonas reinhardtii, we characterized the regulation of gene expression for carotenoid metabolism by quantifying changes in the transcript abundance of dxs, dxr and ipi in the plastidic methylerythritol phosphate pathway and of ggps, psy, pds, lcyb and bchy, directly involved in carotenoid metabolism, under different photoperiod, light and metabolite treatments. The expression of these genes fluctuated with light/dark shifting. Light treatment also promoted the accumulation of transcripts of all these genes. Of the genes studied, dxs, ggps and lcyb displayed the typical circadian pattern by retaining a rhythmic fluctuation of transcript abundance under both constant light and constant dark entrainments. The expression of these genes could also be regulated by metabolic intermediates. For example, ggps was significantly suppressed by a geranylgeranyl pyrophosphate supplement and ipi was upregulated by isopentenyl pyrophosphate. Furthermore, CrOr, a C. reinhardtii homolog of the recently characterized Or gene that accounts for carotenoid accumulation, also showed co-expression with carotenoid biosynthetic genes such as pds and lcyb. Our data suggest a coordinated regulation on carotenoid metabolism in C. reinhardtii at the transcriptional level.

Sun TH, Liu CQ, Hui YY, Wu WK, Zhou ZG, Lu S (2010) Coordinated regulation of gene expression for carotenoid metabolism in Chlamydomonas reinhardtii. J. Integr. Plant Biol. 52(10), 868–878.

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Characterization of a Novel -thioglucosidase CpTGG1 in Carica papaya and its Substrate-dependent and Ascorbic Acid-independent O--glucosidase Activity  
Author: Han Nong, Jia-Ming Zhang, Ding-Qin Li, Meng Wang, Xue-Piao Sun, Yun Judy Zhu, Johan Meijer and Qin-Huang Wang
Journal of Integrative Plant Biology 2010 52(10): 879-890
Published Online: August 23, 2010
DOI: 10.1111/j.1744-7909.2010.00988.x

Plant thioglucosidases are the only known S-glycosidases in the large superfamily of glycosidases. These enzymes evolved more recently and are distributed mainly in Brassicales. Thioglucosidase research has focused mainly on the cruciferous crops due to their economic importance and cancer preventive benefits. In this study, we cloned a novel myrosinase gene, CpTGG1, from Carica papaya Linnaeus. and showed that it was expressed in the aboveground tissues in planta. The recombinant CpTGG1 expressed in Pichia pastoris catalyzed the hydrolysis of both sinigrin and glucotropaeolin (the only thioglucoside present in papaya), showing that CpTGG1 was indeed a functional myrosinase gene. Sequence alignment analysis indicated that CpTGG1 contained all the motifs conserved in functional myrosinases from crucifers, except for two aglycon-binding motifs, suggesting substrate priority variation of the non-cruciferous myrosinases. Using sinigrin as substrate, the apparent Km and Vmax values of recombinant CpTGG1 were 2.82 mM and 59.9 μmol min−1 mg protein−1, respectively. The Kcat/Km value was 23 s−1 mM−1. O-β-glucosidase activity towards a variety of substrates were tested, CpTGG1 displayed substrate-dependent and ascorbic acid-independent O-β-glucosidase activity towards 2-nitrophenyl-β-D-glucopyranoside and 4-nitrophenyl-β-D-glucopyranoside, but was inactive towards glucovanillin and n-octyl-β-D-glucopyranoside. Phylogenetic analysis indicated CpTGG1 belongs to the MYR II subfamily of myrosinases.

Nong H, Zhang JM, Li DQ, Wang M, Sun XP, Zhu YJ, Meijer J, Wang QH (2010) Characterization of a novel β-thioglucosidase CpTGG1 in Carica papaya and its substrate-dependent and ascorbic acid-independent O-β-glucosidase activity. J. Integr. Plant Biol. 52(10), 879–890.

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Expression Analysis of Proline Metabolism-related Genes From Halophyte Arabis stelleri under Osmotic Stress Conditions  
Author: Yuchul Jung, Jungan Park, Yunjung Choi, Jin-Gweon Yang, Donggiun Kim, Beom-Gi Kim, Kyunghee Roh, Dong-Hee Lee, Chung-Kyoon Auh and Sukchan Lee
Journal of Integrative Plant Biology 2010 52(10): 891-903
Published Online: August 16, 2010
DOI: 10.1111/j.1744-7909.2010.00990.x

Arabis stelleri var. japonica evidenced stronger osmotic stress tolerance than Arabidopsis thaliana. Using an A. thaliana microarray chip, we determined changes in the expression of approximately 2 800 genes between A. stelleri plants treated with 0.2 M mannitol versus mock-treated plants. The most significant changes in the gene expression patterns were in genes defining cellular components or in genes associated with the endomembrane system, stimulus response, stress response, chemical stimulus response, and defense response. The expression patterns of three de novo proline biosynthesis enzymes were evaluated in A. stelleri var. japonica seedlings treated with 0.2 M mannitol, 0.2 M sorbitol, and 0.2 M NaCl. The expression of Δ1-pyrroline-5-carboxylate synthetase was not affected by NaCl stress but was similarly induced by mannitol and sorbitol. The proline dehydrogenase gene, which is known to be repressed by dehydration stress and induced by free L-proline, was induced at an early stage by mannitol treatment, but the level of proline dehydrogenase was increased later by treatment with both mannitol and NaCl. The level of free L-proline accumulation increased progressively in response to treatments with mannitol, sorbitol, and NaCl. Mannitol induced L-proline accumulation more rapidly than NaCl or sorbitol. These findings demonstrate that the osmotic tolerance of the novel halophyte, Arabis stelleri, is associated with the accumulation of L-proline.

Jung Y, Park J, Choi Y, Yang JG, Kim D, Kim BG, Roh K, Lee DH, Auh CK, Lee S (2010) Expression analysis of proline metabolism-related genes from halophyte Arabis stelleri under osmotic stress conditions. J. Integr. Plant Biol. 52(10), 891–903.

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Effects of CO2 Enrichment on Photosynthesis, Growth, and Biochemical Composition of Seagrass Thalassia hemprichii (Ehrenb.) Aschers  
Author: Zhi-Jian Jiang, Xiao-Ping Huang and Jing-Ping Zhang
Journal of Integrative Plant Biology 2010 52(10): 904-913
Published Online: August 16, 2010
DOI: 10.1111/j.1744-7909.2010.00991.x

The effects of CO2 enrichment on various ecophysiological parameters of tropical seagrass Thalassia hemprichii (Ehrenb.) Aschers were tested. T. hemprichii, collected from a seagrass bed in Xincun Bay, Hainan island of Southern China, was cultured at 4 CO2(aq) concentrations in flow-through seawater aquaria bubbled with CO2. CO2 enrichment considerably enhanced the relative maximum electron transport rate (RETRmax) and minimum saturating irradiance (Ek) of T. hemprichii. Leaf growth rate of CO2-enriched plants was significantly higher than that in unenriched treatment. Nonstructural carbohydrates (NSC) of T. hemprichii, especially in belowground tissues, increased strongly with elevated CO2(aq), suggesting a translocation of photosynthate from aboveground to belowground tissues. Carbon content in belowground tissues showed a similar response with NSC, while in aboveground tissues, carbon content was not affected by CO2 treatments. In contrast, with increasing CO2(aq), nitrogen content in aboveground tissues markedly decreased, but nitrogen content in belowground was nearly constant. Carbon: nitrogen ratio in both tissues were obviously enhanced by increasing CO2(aq). Thus, these results indicate that T. hemprichii may respond positively to CO2-induced acidification of the coastal ocean. Moreover, the CO2-stimulated improvement of photosynthesis and NSC content may partially offset negative effects of severe environmental disturbance such as underwater light reduction.

Jiang ZJ, Huang XP, Zhang JP (2010) Effects of CO2 enrichment on photosynthesis, growth, and biochemical composition of seagrass Thalassia hemprichii (Ehrenb.) Aschers. J. Integr. Plant Biol. 52(10), 904–913.

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Characterization of a Novel Rice Metallothionein Gene Promoter: Its Tissue Specificity and Heavy Metal Responsiveness  
Author: Chun-Juan Dong, Yun Wang, Shi-Shi Yu and Jin-Yuan Liu
Journal of Integrative Plant Biology 2010 52(10): 914-924
Published Online: July 7, 2010
DOI: 10.1111/j.1744-7909.2010.00966.x

The rice (Oryza sativa L.) metallothionein gene OsMT-I-4b has previously been identified as a type I MT gene. To elucidate the regulatory mechanism involved in its tissue specificity and abiotic induction, we isolated a 1 730 bp fragment of the OsMT-I-4b promoter region. Histochemical β-glucuronidase (GUS) staining indicated a precise spacial and temporal expression pattern in transgenic Arabidopsis. Higher GUS activity was detected in the roots and the buds of flower stigmas, and relatively lower GUS staining in the shoots was restricted to the trichomes and hydathodes of leaves. No activity was observed in the stems and seeds. Additionally, in the root of transgenic plants, the promoter activity was highly upregulated by various environmental signals, such as abscisic acid, drought, dark, and heavy metals including Cu2+, Zn2+, Pb2+ and Al3+. Slight induction was observed in transgenic seedlings under salinity stress, or when treated with Co2+ and Cd2+. Promoter analysis of 5′-deletions revealed that the region −583/−1 was sufficient to drive strong GUS expression in the roots but not in the shoots. Furthermore, deletion analysis indicated important promoter regions containing different metal-responsive cis-elements that were responsible for responding to different heavy metals. Collectively, these findings provided important insight into the transcriptional regulation mechanisms of the OsMT-I-4b promoter, and the results also gave us some implications for the potential application of this promoter in plant genetic engineering.

Dong CJ, Wang Y, Yu SS, Liu JY (2010) Characterization of a novel rice metallothionein gene promoter: its tissue specificity and heavy metal responsiveness. J. Integr. Plant Biol. 52(10), 914–924.

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Quantitative Analysis of Cytokinins in Plants by High Performance Liquid Chromatography: Electronspray Ionization Ion Trap Mass Spectrometry  
Author: Weiqi Chen, Ying Gai, Shichang Liu, Renxiao Wang and Xiangning Jiang
Journal of Integrative Plant Biology 2010 52(10): 925-932
Published Online: August 6, 2010
DOI: 10.1111/j.1744-7909.2010.00989.x

The present paper introduces a highly sensitive and selective method for simultaneous quantification of 12 cytokinins (free form and their conjugates). The method includes a protocol of extraction with methanol/water/formic acid (15/4/1, v/v/v) to the micro-scale samples, pre-purification with solid phase extraction (SPE) cartridges of the extracts, separation with a high performance liquid chromatography (HPLC) and detection by an electrospray ionization ion trap mass spectrometry (ESI-Ion trap-MS) system in a consecutive ion monitoring (CRM) mode at the three stage fragmentation of mass spectrometry (MS3). The lowest detection level of the cytokinins of the method reaches 0.1–2.0 pg with a very wide range of linear regression from 1–512 pg, at the coefficient factors of 0.98–0.99. The feasibility of this method has been proven in the application of the method to the analysis of the trace-amount contents of cytokinins in the micro-scale samples of various types of plant materials, such as aerial parts of rice and poplar leaves etc. 12 endogenous cytokinins had been identified and quantified in the plant tissues, with an acceptable relatively higher recovery rate from 40% to 70%.

Chen W, Gai Y, Liu S, Wang R, Jiang X (2010) Quantitative analysis of cytokinins in plants by high performance liquid chromatography: electronspray ionization ion trap mass spectrometry. J. Integr. Plant Biol. 52(10), 925–932.

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Evaluation of Protein Extraction Methods for Vitis vinifera Leaf and Root Proteome Analysis by Two-Dimensional Electrophoresis  
Author: Neila Jellouli, Asma Ben Salem, Abdelwahed Ghorbel and Hatem Ben Jouira
Journal of Integrative Plant Biology 2010 52(10): 933-940
Published Online: June 16, 2010
DOI: 10.1111/j.1744-7909.2010.00973.x

An efficient protein extraction method is crucial to ensure successful separation by two-dimensional electrophoresis (2-DE) for recalcitrant plant species, in particular for grapevine (Vitis vinifera L.). Trichloroacetic acid-acetone (TCA-acetone) and phenol extraction methods were evaluated for proteome analysis of leaves and roots from the Tunisian cultivar ‘Razegui’. The phenol-based protocol proved to give a higher protein yield, a greater spot resolution, and a minimal streaking on 2-DE gels for both leaf and root tissues compared with the TCA-based protocol. Furthermore, the highest numbers of detected proteins on 2-DE gels were observed using the phenol extraction from leaves and roots as compared with TCA-acetone extraction.

Jellouli N, Ben Salem A, Ghorbel A, Ben Jouira H (2010) Evaluation of protein extraction methods for Vitis vinifera leaf and root proteome analysis by two-dimensional electrophoresis. J. Integr. Plant Biol. 52(10), 933–940.

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In Remembrance: Professor Qian Ying-Qian (1932C2010)  
Author: Jitao Zou, Wei Wei and Keping Ma
Journal of Integrative Plant Biology 2010 52(10): 941-942
Published Online: September 29, 2010
DOI: 10.1111/j.1744-7909.2010.00994.x

Professor Qian Ying-Qian, a renowned Chinese plant biologist and a member of the editorial board of Acta Botanica Sinica (predecessor of JIPB) 1989–1993, passed away in Beijing on April 20, 2010 at the age of 78. Professor Qian was a former Secretary-General (1978–1988), and Vice President of the Chinese Botanical Society (1988–1999). During his long and distinguished career, Professor Qian served as Director-General of the Institute of Botany, Chinese Academy of Sciences (CAS), Director-General of the Bureau of Life Sciences and Biotechnology, CAS, President of Guangxi Academy of Sciences, Chief Editor of Chinese Biodiversity (currently Biodiversity Science), Deputy Director of the Biodiversity Committee of CAS, Vice Chair of The State Review Committee on Nature Reserves, Deputy Director of the Endangered Species Scientific Commission, PRC, and Chair of the Chinese Committee of the International Union of Biological Sciences. For more than half a century, Professor Qian dedicated his life and career to the development of the plant science research community in China.

Born on December 28, 1932 in Cixi, Zhejiang Province, Professor Qian received his undergraduate degree in 1954 from the Biology Department, Fudan University. His outstanding academic performance earned him the right to pursue graduate studies, which at the time was extremely difficult to attain in China. He completed his graduate studies in 1957 from Nanjing University, and assumed an assistant professor position there immediately after receiving his graduate degree. In 1959, he joined the Institute of Botany, CAS. He had remained with CAS for the rest of his career.

Professor Qian was one of the scientists whose research established the foundation of modern plant cell biology research in China. As deputy head of the Cell Biology Laboratory in the early 1960's, Professor Qian established the electron microscopy platform at the Institute of Botany, CAS, which led to the transition of their research from light microscopy to ultrastructural studies. He was among a group of key plant cell biologists led by Professor Wu Su-Xuan that strongly advocated the importance of moving forward from morphological studies of the cell to the dynamic aspects of cell differentiation and development. Illustrating this foresight in scientific leadership was the fact that, despite the challenging environment unimaginable to many researchers nowadays in China, he initiated in the 1960's a “Plant Cellular Biochemistry team” in the Cell Biology Laboratory of the Institute of Botany, emphasizing methodologies employing protein, DNA and RNA analytical tools. Leading a project that made the earliest successful maize anther culture in China, he was one of the pioneers in microspore culture research, a field that inspired a generation of Chinese plant biotechnology researchers. Professor Qian was always keen in the practical application of plant research to crop improvement (Qian et al. 1981). In search of new cell technology for crop improvement, he enthusiastically embarked on protoplast culture and somatic hybridization technology. He reported the successful inter-genus protoplast fusion between tobacco and soybean, and provided chromosomal, isozymes and ultrastructural evidence to demonstrate the hybrid nature of the fusion product (Qian et al. 1982). Under his leadership, the Cell Biology Laboratory at the Institute of Botany, CAS, was in the forefront of protoplast culture technology for many years, achieving plant regeneration from protoplasts of numerous crop species including maize, rice and kiwifruit (Cai et al. 1978; Cai et al. 1987; Qian and Yu 1992).

In the latter part of his career, Professor Qian dedicated his efforts to Biodiversity research in China. With his endeavor, a working group on biodiversity was set up in the CAS in 1990. In 1992, the Biodiversity Committee of the CAS was established with Professor Qian as the first deputy director. This committee had significantly motivated the biodiversity research community in China and strongly supported biodiversity conservation activities. Professor Qian had organized and directly participated in research projects on assessment of biodiversity status and strategies in China. He also studied the principles and methodologies of biodiversity conservation in practice (Qian and Ma 1994). He co-authored several key reports on biodiversity, including the action plan of biodiversity conservation and the report on current situation of biodiversity in China. These documents provided solid scientific basis for achieving regulations on biodiversity conservation and sustainable utilization at the state level. Professor Qian was also the first scientist in China realizing the significant implication of biosafety issues to biodiversity. With the fast development of biotechnology, Professor Qian called attention on biosafety research of genetically modified organisms in China in 1992, and contributed numerous publications introducing biosafety research (e.g. Qian 1994; Qian and Ma 1995, 1998). With his leadership, the Institute of Botany, CAS, established a strong biosafety research platform with dynamic research programs on biodiversity.

Professor Qian was a tireless promoter of academic exchange between China and the international community. He was among the first wave of Chinese scientists going abroad for academic exchange. Many at the National Research Council Canada-Plant Biotechnology Institute where he conducted somatic hybridization research in the early 1980's fondly remember him as an exceedingly hard working scientist and remarkably productive in research. As happened many times in his career, he placed his organizational duty ahead of everything else: he had to cut short his research visit in Canada upon a call of return to lead the Institute of Botany of CAS. As Director-General of the Institute, he opened many channels of academic exchange for researchers and students.

Professor Qian was a scientific management leader, a scholar, scientist, mentor, colleague, and friend. More than his scientific contributions, Professor Qian will be remembered for mentoring more than 20 students. Those of us who had the privilege being his students have myriad tales to tell about his kindness and generosity. Although saddled with management duties, he always made sure to allocate time for discussion and often demonstrated directly to students cell biology techniques. After he took on the position of Director-General of the Bureau of Life Sciences and Biotechnology, the weekly meeting with students proceeded normally in his office at the headquarters of CAS, and the scientific discussion was often followed by a lunch treat. He encouraged independent thinking and was always open to seeking inputs from other scientists to student research projects.

It is important to recognize that the impact of a scientist, as that of any individual, can only be fully appreciated through a prism of his or her specific time and space. Plant science research in China for the last few decades has gone through a tremendous transformation. Entrusted with many challenging management positions during the early transition phase of this period, Professor Qian made incalculable contribution to what the Chinese Plant science research is today. Professor Qian will be sadly missed by countless ones whose career has been made better by his life and career.


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