iTRAQ-Based Quantitative Proteomics Analysis of Black Rice Grain Development Reveals Metabolic Pathways Associated with Anthocyanin Biosynthesis

Abstract Little has been established on the relationship between the mevalonate (MVA) pathway and other metabolic pathways except for the sterol and glucosinolate biosynthesis pathways. In the MVA pathway, 3-hydroxy-3-methylglutaryl-CoA synthase (HMGS) catalyses the condensation of acetoacetyl-CoA and acetyl-CoA to form HMG-CoA. Our previous studies had shown that while the recombinant Brassica juncea HMGS1 (BjHMGS1) mutant S359A displayed 10-fold higher enzyme activity than wild-type (wt) BjHMGS1, transgenic tobacco overexpressing S359A (OE-S359A) exhibited higher sterol content, growth rate and seed yield than OE-wtBjHMGS1. Herein, untargeted proteomics and targeted metabolomics were employed to understand the phenotypic effects of HMGS overexpression in tobacco by examining which other metabolic pathways were affected. SWATH-MS quantitative proteomics analysis on OE-wtBjHMGS1 and OE-S359A identified the misregulation of proteins in primary metabolism and cell wall modification, while some proteins related to photosynthesis and the tricarboxylic acid cycle were upregulated in OE-S359A. Metabolomic analysis indicated corresponding changes in carbohydrate, amino acid and fatty acid contents in HMGS-OEs, and F-244, a specific inhibitor of HMGS, was applied successfully on tobacco to confirm these observations. Finally, the crystal structure of acetyl-CoA-liganded S359A revealed that improved activity of S359A likely resulted from a loss in hydrogen bonding between Ser359 and acyl-CoA which is evident in wtBjHMGS1. This work suggests that regulation of plant growth by HMGS can influence the central metabolic pathways. Furthermore, this study demonstrates that the application of the HMGS-specific inhibitor (F-244) in tobacco represents an effective approach for studying the HMGS/MVA pathway.

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A label-free quantitative shotgun proteomics analysis of rice grain development

Proteome Science ◽

10.1186/1477-5956-9-61 ◽

2011 ◽

Vol 9 (1) ◽

pp. 61 ◽

Cited By ~ 31

Author(s):

Joohyun Lee ◽

Hee-Jong Koh

Keyword(s):

Shotgun Proteomics ◽

Rice Grain ◽

Label Free ◽

Grain Development ◽

Proteomics Analysis

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Quantitative Proteomics Analysis Reveals Unique But Overlapping Protein Signatures in HIV Infection

SSRN Electronic Journal ◽

10.2139/ssrn.3424191 ◽

2019 ◽

Author(s):

Maha Al-Mozaini ◽

Ibtihag S. Alsharif ◽

Al-Hussain J. Alzahrani ◽

Zakia Shinwari ◽

Magid Halim ◽

...

Keyword(s):

Hiv Infection ◽

Quantitative Proteomics ◽

Proteomics Analysis ◽

Protein Signatures

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Quantitative Proteomics Analysis Reveals Unique but Overlapping Protein Signatures in HIV Infections

Journal of Infection and Public Health ◽

10.1016/j.jiph.2021.03.009 ◽

2021 ◽

Author(s):

Maha Al-Mozaini ◽

Ibtihag Alsharif ◽

Alhusain Alzahrani ◽

Zakia Shinwari ◽

Magid Halim ◽

...

Keyword(s):

Quantitative Proteomics ◽

Hiv Infections ◽

Proteomics Analysis ◽

Protein Signatures

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OsMYB3 is a R2R3-MYB gene responsible for anthocyanin biosynthesis in black rice

Molecular Breeding ◽

10.1007/s11032-021-01244-x ◽

2021 ◽

Vol 41 (8) ◽

Author(s):

Jie Zheng ◽

Hao Wu ◽

Mingchao Zhao ◽

Zenan Yang ◽

Zaihui Zhou ◽

...

Keyword(s):

Anthocyanin Biosynthesis ◽

Black Rice ◽

Myb Gene ◽

R2r3 Myb

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Genome Wide Analysis of the Transcriptional Profiles in Different Regions of the Developing Rice Grains

Rice ◽

10.1186/s12284-020-00421-4 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Ting-Ying Wu ◽

Marlen Müller ◽

Wilhelm Gruissem ◽

Navreet K. Bhullar

Keyword(s):

Gene Expression ◽

Dna Sequence ◽

Expression Patterns ◽

Grain Filling ◽

Aleurone Layer ◽

Rice Grain ◽

Sequence Motifs ◽

Grain Development ◽

Spatio Temporal ◽

Dna Sequence Motifs

Abstract Background Rice is an important food source for humans worldwide. Because of its nutritional and agricultural significance, a number of studies addressed various aspects of rice grain development and grain filling. Nevertheless, the molecular processes underlying grain filling and development, and in particular the contributions of different grain tissues to these processes, are not understood. Main Text Using RNA-sequencing, we profiled gene expression activity in grain tissues comprised of cross cells (CC), the nucellar epidermis (NE), ovular vascular trace (OVT), endosperm (EN) and the aleurone layer (AL). These tissues were dissected using laser capture microdissection (LCM) at three distinct grain development stages. The mRNA expression datasets offer comprehensive and new insights into the gene expression patterns in different rice grain tissues and their contributions to grain development. Comparative analysis of the different tissues revealed their similar and/or unique functions, as well as the spatio-temporal regulation of common and tissue-specific genes. The expression patterns of genes encoding hormones and transporters indicate an important role of the OVT tissue in metabolite transport during grain development. Gene co-expression network prediction on OVT-specific genes identified several distinct and common development-specific transcription factors. Further analysis of enriched DNA sequence motifs proximal to OVT-specific genes revealed known and novel DNA sequence motifs relevant to rice grain development. Conclusion Together, the dataset of gene expression in rice grain tissues is a novel and useful resource for further work to dissect the molecular and metabolic processes during rice grain development.

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To Stretch the Boundary of Secondary Metabolite Production in Plant Cell-Based Bioprocessing: Anthocyanin as a Case Study

Journal of Biomedicine and Biotechnology ◽

10.1155/s1110724304404148 ◽

2004 ◽

Vol 2004 (5) ◽

pp. 264-271 ◽

Cited By ~ 18

Author(s):

Wei Zhang ◽

Chris Franco ◽

Chris Curtin ◽

Simon Conn

Keyword(s):

Secondary Metabolites ◽

Plant Cell ◽

Metabolic Pathways ◽

Anthocyanin Biosynthesis ◽

Rational Approach ◽

Great Promise ◽

Primary Metabolism ◽

Global Correlation ◽

Empirical Level

Plant cells and tissue cultures hold great promise for controlled production of a myriad of useful secondary metabolites on demand. The current yield and productivity cannot fulfill the commercial goal of a plant cell-based bioprocess for the production of most secondary metabolites. In order to stretch the boundary, recent advances, new directions and opportunities in plant cell-based bioprocessing, have been critically examined for the 10 years from 1992 to 2002. A review of the literature indicated that most of the R&D work was devoted predominantly to studies at an empirical level. A rational approach to molecular plant cell bioprocessing based on the fundamental understanding of metabolic pathways and their regulations is urgently required to stimulate further advances; however, the strategies and technical framework are still being developed. It is the aim of this review to take a step forward in framing workable strategies and technologies for molecular plant cell-based bioprocessing. Using anthocyanin biosynthesis as a case study, an integrated postgenomic approach has been proposed. This combines the functional analysis of metabolic pathways for biosynthesis of a particular metabolite from profiling of gene expression and protein expression to metabolic profiling. A global correlation not only can thus be established at the three molecular levels, but also places emphasis on the interactions between primary metabolism and secondary metabolism; between competing and/or complimentary pathways; and between biosynthetic and post-biosynthetic events.

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