Plant Biotechnology Vol.26 No.1
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Contents
Editorial Overview
An eight-year government supported project investigating the control of industrial plant material production processes via genetic engineering in Japan
Daisuke Shibata, Atsuhiko Shinmyo. . . . . . . 1 [PDF]
Articles
Practical network approaches and biologic interpretations of co-expression analyses in plants
Yoshiyuki Ogata, Daisuke Shibata. . . . . . . 3 [PDF]
Co-expression network analysis using DNA microarray datasets can be used to predict the functions of many plant genes. Here, we introduce recent reports for co-expression network analyses in plants and summarize practical approaches for such analyses.
DAGViz : a directed acyclic graph browser that supports analysis of Gene Ontology annotation
Kentaro Yano, Koh Aoki, Hideyuki Suzuki, Daisuke Shibata. . . . . . . 9 [PDF]
We have constructed a web-tool "DAGViz" for browsing relationships among GO terms based on directed acyclic graphs (DAGs) (http://www.pgb.kazusa.or.jp/dagviz/). By displaying all GO terms assigned to genes of interest within a single screen, DAGViz aids in the systematic grasping of gene function.
Functional genomics of the Dof transcription factor family genes in suspension-cultured cells of Arabidopsis thaliana
Yayoi Tsujimoto-Inui, Yuki Naito, Nozomu Sakurai, Hideyuki Suzuki, Ryosuke Sasaki, Hideyuki Takahashi, Namie Ohtsuki, Toshitsugu Nakano, Shuichi Yanagisawa, Daisuke Shibata, Hirofumi Uchimiya, Hideaki Shinshi, Kaoru Suzuki. . . . . . . 15 [PDF]
We examined transcriptional profiles in the Dof gene-overexpressed calli using an Arabidopsis DNA microarray analysis. Based on the results, possible involvements of the Dof genes in regulation of metabolic pathways were discussed.
Manipulation of plant metabolic pathways by transcription factors
Akira Iwase, Kyoko Matsui, Masaru Ohme-Takagi. . . . . . . 29 [PDF]
This review describes the advantages of transcription factors for metabolic engineering in plants. Transcriptional activators and repressors, including the chimeric repressors, are useful tools for the genetic engineering of metabolic pathways. This report summarizes the strategies for the detection of regulators and enzyme genes involved in metabolic pathways.
Metabolic pathway engineering by plastid transformation is a powerful tool for production of compounds in higher plants
Tomohisa Hasunuma, Akihiko Kondo, Chikahiro Miyake. . . . . . . 39 [PDF]
Metabolic pathway engineering by plastid transformation is a powerful tool for the production of useful compounds in higher plants. Recent reports have shown the functional regulation of transgene expression from the plastid genome. In this review, we have focused on the progress of plastid transformation in material production from the aspect of biosynthetic pathway engineering, discussing the issues for future expansion of plastid transformation.
Profiling of primary metabolite by means of capillary electrophoresis-mass spectrometry and its application for plant science
Kazuo Harada, Eiichiro Fukusaki. . . . . . . 47 [PDF]
Metabolites in primary metabolic pathways, such as glycolysis, the TCA cycle, the Calvin cycle and so on, are ionic compounds. It is difficult to analyze these metabolites simultaneously by established methods for metabolite profiling. This review introduces the comprehensive and quantitative analysis of ionic metabolites by using capillary electrophoresis-mass spectrometry (CE-MS).
Selection of synonymous codons for better expression of recombinant proteins in tobacco chloroplasts
Masayuki Nakamura, Masahiro Sugiura. . . . . . . 53 [PDF]
The codon usage table from the entire 79 mRNAs from tobacco chloroplasts is presented. Translation efficiencies of individual codons in tobacco chloroplasts are not always correlated with codon usage.
Function and evolution of plastid sigma factors
Takashi Shiina, Yoko Ishizaki, Yusuke Yagi, Yoichi Nakahira. . . . . . . 57 [PDF]
Chloroplast sigma factors are key regulators of the chloroplast gene expression and chloroplast differentiation. This review summarized recent findings on roles of chloroplast sigma factors in the regulation of gene expression in chloroplasts.
Production of Natural Rubber from Para rubber tree
Yasuyuki Hayashi. . . . . . . 67 [PDF]
The objective of this review is to provide readers with information on the newest trends and market conditions of natural rubber and also explain the historical background and a global view of Hevea breeding and genetics, together with information about alternative resources.
Production of Eucommia-rubber from Eucommia ulmoides Oliv (Hardy Rubber Tree)
Yoshihisa Nakazawa, Takeshi Bamba, Tuyoshi Takeda, Hirotaka Uefuji, Yoko Harada, Xuehong Li, Ren Chen, Sumihiro Inoue, Masafumi Tutumi, Toru Shimizu, Yin-Quan Su, Koichiro Gyokusen, Eiichiro Fukusaki, Akio Kobayashi. . . . . . . 71 [PDF]
The authors have conducted continuous research on Eucommia-searching for genetic resources, analyzing the biosynthesis pathway and accumulation mechanism or EU-rubber, identifying functions through gene analysis, and evaluating functionality using recombinants. This paper discusses Eucommia as a plant with the potential to produce industrial raw materials, and the production of Eucommia rubber.
Simple functional analysis of key genes involved in astaxanthin biosynthesis using Arabidopsis cultured cells
Hisashi Harada, Masaki Fujisawa, Maki Teramoto, Nozomu Sakurai, Hideyuki Suzuki, Daisuke Shibata, Norihiko Misawa. . . . . . . 81 [PDF]
A plasmid for the expression of six key-gene candidates for astaxanthin production was constructed and introduced into Arabidopsis thaliana T87 cultured cells. Transgenic cell lines were shown to accumulate ketocarotenoids including astaxanthin, which was estimated to be 36% to 53% of the total carotenoids. Microarray analysis of endogenous genes suggests that transgenic cells adjust their whole cellular isoprenoid-metabolic system to direct the high-level production of the carotenoids including the ketocarotenoids in the plastids.
Pathway engineering of plants toward astaxanthin production
Norihiko Misawa. . . . . . . 93 [PDF]
Pathway engineering approaches of plants including staple crops toward astaxanthin production have been undertaken by introducing and expressing in the plants a ketolase gene and sometimes a hydroxylase gene involved in astaxanthin synthesis from β-carotene.
Economic importance of licorice
Hiroaki Hayashi, Hiroshi Sudo. . . . . . . 101 [PDF]
A review of the market of licorice root, licorice extract, glycyrrhizin, and its derivatives. The licorice resources and future technological prospects also discussed.
Expressed sequence tags from rhizomes of Glycyrrhiza uralensis
Hiroshi Sudo, Hikaru Sek, Nozomu Sakurai, Hideyuki Suzuki, Daisuke Shibata, Atsushi Toyoda, Yasushi Totoki, Yoshiyuki Sakaki, Osamu Iida, Toshiro Shibata, Mareshige Kojoma, Toshiya Muranaka, Kazuki Saito. . . . . . . 105 [PDF]
We report the generation of 56,857 expressed sequence tags derived from the cDNA libraries produced from licorice roots. After clustering, a total of 10,474 nonredundant sequences were generated. The gene functions of these sequences were classified on the basis of Gene Ontology.
"Post-genomics" research in Eucalyptus in the near future
Takashi Hibino. . . . . . . 109 [PDF]
Forest produces the most abundant biomass resource on earth, and its ecological and commercial importance in maintaining the global environment and human society is irreplaceable. In this review, the current status and "post-genomics" research directions in Eucalyptus biotechnology are outlined.
Increasing fiber length and growth in transgenic tobacco plants overexpressing a gene encoding the Eucalyptus camaldulensis HD-Zip class II transcription factor
Tetsuya Sonoda, Hisako Koita, Shiho Nakamoto-Ohta, Keiko Kondo, Tazuko Suezaki, Tomohiko Kato, Yoko Ishizaki, Kana Nagai, Nanae Iida, Shigeru Sato, Toshiaki Umezawa, Takashi Hibino. . . . . . . 115 [PDF]
We isolated the Eucalyptus xylem TF gene EcHB1, which encodes a HD-Zip class II. EcHB1 expression was driven by the CaMV35S promoter in transgenic tobacco plants, which showed greater fiber length (≤20%) and plant height (≤50%) than wild-type plants.
Isolation and expression analysis of AGAMOUS-like genes from Eucalyptus grandis
Tomohiko Kato, Takashi Hibino. . . . . . . 121 [PDF]
In this study, we focused on the AGAMOUS-like genes which are especially involved in stamen formation. Three new distinct cDNA fragments (EgAGL1, EgAGL2 and EgAGL3) and two distinct genomic DNA fragments (EgAGL1 and EgAGL2) encoding MADS-box proteins were isolated from Eucalyptus grandis.
Genetic engineering of glycine betaine biosynthesis to enhance abiotic stress tolerance in plants
Mohammad Sayyar Khan, Xiang Yu, Akira Kikuchi, Masashi Asahina, Kazuo N. Watanabe. . . . . . . 125 [PDF]
Glycine betaine is an important compatible solute that protects plants against the damaging effects of abiotic stresses. This review focuses on recent progress in studies of abiotic stress tolerance conferred by GB in transgenic plants.
Establishment of the evaluation system of salt tolerance on transgenic woody plants in the special netted-house
Xiang Yu, Akira Kikuchi, Etsuko Matsunaga, Yoshihiko Morishita, Kazuya Nanto, Nozomu Sakurai, Hideyuki Suzuki, Daisuke Shibata, Teruhisa Shimada, Kazuo N. Watanabe. . . . . . . 135 [PDF]
Trait of transgenic plants should be evaluated in semi-confinement conditions before field cultivation. In this paper, new evaluation system of salt tolerance transgenic tree was established through the selection of the transgenic E. globulus with the codA gene. This system is valuable for testing transgenic plants in semi-confinement and will contribute to an increase in the useful applications of transgenic plants.
Establishment of a homogenized method for environmental biosafety assessments of transgenic plants
Takayoshi Shimazaki, Akira Kikuchi, Etsuko Matsunaga, Kazuya Nanto, Teruhisa Shimada, Kazuo N. Watanabe. . . . . . . 143 [PDF]
The transgenic plant should be examined for new compounds that influence plant growth in semi-confinement conditions before field cultivation. Here, we report a new "homogenized method" that relies on homogenizing fleshy leaf samples, instead of drying them. This method may be an effective and useful tool for evaluating differences between non-transgenic and transgenic plants using multiple, concurrent samples.
Genetic engineering of hexsosamine with L-glutamine D-fructose-6-phosphate amidotransferase genes in plants
Shigeo Shibatani, Hiroaki Kitazawa. . . . . . . 149 [PDF]
An Arabidopsis GFAT gene was identified by using a wheat germ in vitro translation system. Transgenic BY-2 cells with a chlorella virus GFAT gene had higher levels of hexosamines than wild type, but no such hexosamine production was observed in transgenic BY-2 cells with the Arabidopsis GFAT gene.
ASN2 is a key enzyme in asparagine biosynthesis under ammonium sufficient conditions
Daisuke Igarashi, Takashi Ishizaki, Kazuhiko Totsuka, Chieko Ohsumi. . . . . . . 153 [PDF]
To identify the key genes that regulate the amino acid contents, we analyzed the profiles of gene expression and amino acid contents diurnally at different growth stages. The correlation of asparagine contents and ASN2 expression was observed. The analysis of ASN2 over- / under-expression plants suggested that ASN2 could be a key factor in asparagine biosynthesis.
ARTRA: a new database of the Arabidopsis transcriptome and gene-specific sequences for microarray probes and RNAi triggers
Toshiharu Ohba, Kensuke Suzuki, Tomonori Oura, Tatsuya Ando, Hideyuki Noda, Nozomu Sakurai, Hideyuki Suzuki, Daisuke Shibata, Kiyozo Asada, Ikunoshin Kato. . . . . . . 161 [PDF]
A new database has been developed that contains Arabidopsis transcriptome sequences and gene-specific sequences for a DNA microarray and RNAi knockdown triggers. Access to the database is available to any researcher on request from the web site of http://artra.kazusa.or.jp/.
An approach to peak detection in GC-MS chromatograms and application of KNApSAcK database in prediction of candidate metabolites
Takashi Oishi, Ken-ichi Tanaka, Takuya Hashimoto, Yoko Shinbo, Kanokwan Jumtee, Takeshi Bamba, Eiichiro Fukusaki, Hideyuki Suzuki, Daisuke Shibata, Hiroki Takahashi, Hiroko Asahi, Ken Kurokawa, Yukiko Nakamura, Aki Hirai, Kensuke Nakamura, Md. Altaf-Ul-Amin, Shigehiko Kanaya. . . . . . . 167 [PDF]
Metabolomics for the characterization of cytochromes P450-dependent fatty acid hydroxylation reactions in Arabidopsis
Kosuke Kai, Hiroko Hashidzume, Kazuya Yoshimura, Hideyuki Suzuki, Nozomu Sakurai, Daisuke Shibata, Daisaku Ohta. . . . . . . 175 [PDF]
An FT-ICR/MS based metabolomics scheme was successfully implemented to clarify the P450 functions at the enzyme level and in a cell-culture system. We demonstrated that rCYP78A5, rCYP78A7, rCYP78A10, and rCYP86C3 proteins catalyze fatty acid hydroxylase reactions in substrates of different chain lengths.