著者

Takeshi Ara Nozomu Sakurai Hideyuki Suzuki Koh Aoki Kazuki Saito Daisuke Shibata

出版者

Japanese Society for Plant Biotechnology

雑誌

Plant Biotechnology (ISSN:13424580)

巻号頁・発行日

vol.38, no.1, pp.167-171, 2021-03-25 (Released:2021-03-25)

参考文献数

15

被引用文献数

4

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Depository of low-molecular-weight compounds or metabolites detected in various organisms in a non-targeted manner is indispensable for metabolomics research. Due to the diverse chemical compounds, various mass spectrometry (MS) setups with state-of-the-art technologies have been used. Over the past two decades, we have analyzed various biological samples by using gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry, or capillary electrophoresis-mass spectrometry, and archived the datasets in the depository MassBase (http://webs2.kazusa.or.jp/massbase/). As the format of MS datasets depends on the MS setup used, we converted each raw binary dataset of the mass chromatogram to text file format, and thereafter, information of the chromatograph peak was extracted in the text file from the converted file. In total, the depository comprises 46,493 datasets, of which 38,750 belong to the plant species and 7,743 are authentic or mixed chemicals as well as other sources (microorganisms, animals, and foods), as on August 1, 2020. All files in the depository can be downloaded in bulk from the website. Mass chromatograms of 90 plant species obtained by LC-Fourier transform ion cyclotron resonance MS or Orbitrap MS, which detect the ionized molecules with high accuracy allowing speculation of chemical compositions, were converted to text files by the software PowerGet, and the chemical annotation of each peak was added. The processed datasets were deposited in the annotation database KomicMarket2 (http://webs2.kazusa.or.jp/km2/). The archives provide fundamental resources for comparative metabolomics and functional genomics, which may result in deeper understanding of living organisms.

著者

Nozomu Sakurai

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

vol.72, no.1, pp.56-65, 2022 (Released:2022-03-08)

参考文献数

90

被引用文献数

11

---

Metabolites play a central role in maintaining organismal life and in defining crop phenotypes, such as nutritional value, fragrance, color, and stress resistance. Among the ‘omes’ in biology, the metabolome is the closest to the phenotype. Consequently, metabolomics has been applied to crop improvement as method for monitoring changes in chemical compositions, clarifying the mechanisms underlying cellular functions, discovering markers and diagnostics, and phenotyping for mQTL, mGWAS, and metabolite-genome predictions. In this review, 359 reports of the most recent applications of metabolomics to plant breeding-related studies were examined. In addition to the major crops, more than 160 other crops including rare medicinal plants were considered. One bottleneck associated with using metabolomics is the wide array of instruments that are used to obtain data and the ambiguity associated with metabolite identification and quantification. To further the application of metabolomics to plant breeding, the features and perspectives of the technology are discussed.

著者

Yasuhide Hiraga Takeshi Ara Yoshiki Nagashima Norimoto Shimada Nozomu Sakurai Hideyuki Suzuki Kota Kera

出版者

Japanese Society for Plant Biotechnology

雑誌

Plant Biotechnology (ISSN:13424580)

巻号頁・発行日

vol.37, no.3, pp.377-381, 2020-09-25 (Released:2020-09-25)

参考文献数

26

被引用文献数

3

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The model land plant Physcomitrella patens synthesizes flavonoids which may act as protectant of ultraviolet-B radiation. We aimed to uncover its flavonoid profile, for which metabolome analysis using liquid chromatography coupled with Ion trap/Orbitrap mass spectrometry was performed. From the 80% methanol extracts, 661 valid peaks were detected. Prediction of the elemental compositions within a mass accuracy of 2 ppm indicated that 217 peaks had single elemental composition. A compound database search revealed 47 peaks to be annotated as secondary metabolites based on the compound database search. Comprehensive substituent search by ShiftedIonsFinder showed there were 13 peaks of potential flavonoid derivatives. Interestingly, a peak having m/z 287.0551, corresponding to that of luteolin, was detected, even though flavone synthase has never been identified in P. patens. Using P. patens labeled with stable isotopes (13C-, 15N-, 18O-, and 34S), we confirmed the elemental composition of the peak as C15H10O6. By a comparison of MS/MS spectra with that of authentic standard, the peak was identified as luteolin or related flavone isomers. This is the first report of luteolin or related flavones synthesis and the possibility of the existence of an unknown enzyme with flavone synthase activity in P. patens.

著者

Takeshi Ara Nozomu Sakurai Hideyuki Suzuki Koh Aoki Kazuki Saito Daisuke Shibata

出版者

Japanese Society for Plant Biotechnology

雑誌

Plant Biotechnology (ISSN:13424580)

巻号頁・発行日

pp.20.0911a, (Released:2021-03-11)

参考文献数

15

被引用文献数

4

---

Depository of low-molecular-weight compounds or metabolites detected in various organisms in a non-targeted manner is indispensable for metabolomics research. Due to the diverse chemical compounds, various mass spectrometry (MS) setups with state-of-the-art technologies have been used. Over the past two decades, we have analyzed various biological samples by using gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry, or capillary electrophoresis-mass spectrometry, and archived the datasets in the depository MassBase (http://webs2.kazusa.or.jp/massbase/). As the format of MS datasets depends on the MS setup used, we converted each raw binary dataset of the mass chromatogram to text file format, and thereafter, information of the chromatograph peak was extracted in the text file from the converted file. In total, the depository comprises 46,493 datasets, of which 38,750 belong to the plant species and 7,743 are authentic or mixed chemicals as well as other sources (microorganisms, animals, and foods), as on August 1, 2020. All files in the depository can be downloaded in bulk from the website. Mass chromatograms of 90 plant species obtained by LC-Fourier transform ion cyclotron resonance MS or Orbitrap MS, which detect the ionized molecules with high accuracy allowing speculation of chemical compositions, were converted to text files by the software PowerGet, and the chemical annotation of each peak was added. The processed datasets were deposited in the annotation database KomicMarket2 (http://webs2.kazusa.or.jp/km2/). The archives provide fundamental resources for comparative metabolomics and functional genomics, which may result in deeper understanding of living organisms.

著者

Takeshi Ara Kunihiro Suda Masayuki Amagai Kiyoshi Namai Hideyuki Suzuki Nozomu Sakurai Daisuke Shibata

出版者

Japanese Society for Plant Biotechnology

雑誌

Plant Biotechnology (ISSN:13424580)

巻号頁・発行日

vol.37, no.3, pp.383-387, 2020-09-25 (Released:2020-09-25)

参考文献数

11

---

Metabolome analysis of flavored vegetables, green spring onion (Allium fistulosum), Chinese chive (A. tuberosum), and their interspecies hybrid Negi-Nira chive, was conducted using liquid chromatography-Fourier transform ion cyclotron resonance-mass spectrometry, with ca. 2 ppm mass accuracy. Ion peaks in the chromatograms of four biological replicates of the vegetable leaves were processed using the alignment software PowerGet for metabolite comparison, from which we obtained the potential chemical formulae. In total, 860 ion peaks were reproducibly detected; of these, 506, 525, and 336 peaks were found in the hybrid, A. tuberosum, and A. fistulosum, respectively. There were 130 peaks specific to the hybrid; from these, 31 metabolites were annotated by searching compound databases. The sulfur-containing compounds and flavonoids were further analyzed using bioinformatics, to examine the sulfur metabolism of Allium volatiles and the flavonoid pathways in these species. In conclusion, our metabolome analysis of this interspecies hybrid and its parents provides a unique opportunity to elucidate their metabolic background.