Dynamic proteomic characteristics and network integration revealing key proteins for two kernel tissue developments in popcorn

Yongbin Dong, Qilei Wang, Long Zhang, Chunguang Du, Wenwei Xiong, Xinjian Chen, Fei Deng, Zhiyan Ma, Dahe Qiao, Chunhui Hu, Yangliu Ren, Yuling Li

Research output: Contribution to journalArticleResearchpeer-review

4 Citations (Scopus)

Abstract

The formation and development of maize kernel is a complex dynamic physiological and biochemical process that involves the temporal and spatial expression of many proteins and the regulation of metabolic pathways. In this study, the protein profiles of the endosperm and pericarp at three important developmental stages were analyzed by isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with LC-MS/MS in popcorn inbred N04. Comparative quantitative proteomic analyses among developmental stages and between tissues were performed, and the protein networks were integrated. A total of 6,876 proteins were identified, of which 1,396 were nonredundant. Specific proteins and different expression patterns were observed across developmental stages and tissues. The functional annotation of the identified proteins revealed the importance of metabolic and cellular processes, and binding and catalytic activities for the development of the tissues. The whole, endosperm-specific and pericarp-specific protein networks integrated 125, 9 and 77 proteins, respectively, which were involved in 54 KEGG pathways and reflected their complex metabolic interactions. Confirmation for the iTRAQ endosperm proteins by two-dimensional gel electrophoresis showed that 44.44% proteins were commonly found. However, the concordance between mRNA level and the protein abundance varied across different proteins, stages, tissues and inbred lines, according to the gene cloning and expression analyses of four relevant proteins with important functions and different expression levels. But the result by western blot showed their same expression tendency for the four proteins as by iTRAQ. These results could provide new insights into the developmental mechanisms of endosperm and pericarp, and grain formation in maize.

Original languageEnglish
Article numbere0143181
JournalPLoS ONE
Volume10
Issue number11
DOIs
StatePublished - 1 Nov 2015

Fingerprint

popcorn
Proteomics
proteomics
Tissue
seeds
Proteins
proteins
Endosperm
endosperm
pericarp
developmental stages
tissues
Zea mays
Biochemical Phenomena
Physiological Phenomena
Molecular Sequence Annotation
Electrophoresis, Gel, Two-Dimensional
corn
Cloning
two-dimensional gel electrophoresis

Cite this

Dong, Yongbin ; Wang, Qilei ; Zhang, Long ; Du, Chunguang ; Xiong, Wenwei ; Chen, Xinjian ; Deng, Fei ; Ma, Zhiyan ; Qiao, Dahe ; Hu, Chunhui ; Ren, Yangliu ; Li, Yuling. / Dynamic proteomic characteristics and network integration revealing key proteins for two kernel tissue developments in popcorn. In: PLoS ONE. 2015 ; Vol. 10, No. 11.
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title = "Dynamic proteomic characteristics and network integration revealing key proteins for two kernel tissue developments in popcorn",
abstract = "The formation and development of maize kernel is a complex dynamic physiological and biochemical process that involves the temporal and spatial expression of many proteins and the regulation of metabolic pathways. In this study, the protein profiles of the endosperm and pericarp at three important developmental stages were analyzed by isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with LC-MS/MS in popcorn inbred N04. Comparative quantitative proteomic analyses among developmental stages and between tissues were performed, and the protein networks were integrated. A total of 6,876 proteins were identified, of which 1,396 were nonredundant. Specific proteins and different expression patterns were observed across developmental stages and tissues. The functional annotation of the identified proteins revealed the importance of metabolic and cellular processes, and binding and catalytic activities for the development of the tissues. The whole, endosperm-specific and pericarp-specific protein networks integrated 125, 9 and 77 proteins, respectively, which were involved in 54 KEGG pathways and reflected their complex metabolic interactions. Confirmation for the iTRAQ endosperm proteins by two-dimensional gel electrophoresis showed that 44.44{\%} proteins were commonly found. However, the concordance between mRNA level and the protein abundance varied across different proteins, stages, tissues and inbred lines, according to the gene cloning and expression analyses of four relevant proteins with important functions and different expression levels. But the result by western blot showed their same expression tendency for the four proteins as by iTRAQ. These results could provide new insights into the developmental mechanisms of endosperm and pericarp, and grain formation in maize.",
author = "Yongbin Dong and Qilei Wang and Long Zhang and Chunguang Du and Wenwei Xiong and Xinjian Chen and Fei Deng and Zhiyan Ma and Dahe Qiao and Chunhui Hu and Yangliu Ren and Yuling Li",
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Dong, Y, Wang, Q, Zhang, L, Du, C, Xiong, W, Chen, X, Deng, F, Ma, Z, Qiao, D, Hu, C, Ren, Y & Li, Y 2015, 'Dynamic proteomic characteristics and network integration revealing key proteins for two kernel tissue developments in popcorn', PLoS ONE, vol. 10, no. 11, e0143181. https://doi.org/10.1371/journal.pone.0143181

Dynamic proteomic characteristics and network integration revealing key proteins for two kernel tissue developments in popcorn. / Dong, Yongbin; Wang, Qilei; Zhang, Long; Du, Chunguang; Xiong, Wenwei; Chen, Xinjian; Deng, Fei; Ma, Zhiyan; Qiao, Dahe; Hu, Chunhui; Ren, Yangliu; Li, Yuling.

In: PLoS ONE, Vol. 10, No. 11, e0143181, 01.11.2015.

Research output: Contribution to journalArticleResearchpeer-review

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AU - Dong, Yongbin

AU - Wang, Qilei

AU - Zhang, Long

AU - Du, Chunguang

AU - Xiong, Wenwei

AU - Chen, Xinjian

AU - Deng, Fei

AU - Ma, Zhiyan

AU - Qiao, Dahe

AU - Hu, Chunhui

AU - Ren, Yangliu

AU - Li, Yuling

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N2 - The formation and development of maize kernel is a complex dynamic physiological and biochemical process that involves the temporal and spatial expression of many proteins and the regulation of metabolic pathways. In this study, the protein profiles of the endosperm and pericarp at three important developmental stages were analyzed by isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with LC-MS/MS in popcorn inbred N04. Comparative quantitative proteomic analyses among developmental stages and between tissues were performed, and the protein networks were integrated. A total of 6,876 proteins were identified, of which 1,396 were nonredundant. Specific proteins and different expression patterns were observed across developmental stages and tissues. The functional annotation of the identified proteins revealed the importance of metabolic and cellular processes, and binding and catalytic activities for the development of the tissues. The whole, endosperm-specific and pericarp-specific protein networks integrated 125, 9 and 77 proteins, respectively, which were involved in 54 KEGG pathways and reflected their complex metabolic interactions. Confirmation for the iTRAQ endosperm proteins by two-dimensional gel electrophoresis showed that 44.44% proteins were commonly found. However, the concordance between mRNA level and the protein abundance varied across different proteins, stages, tissues and inbred lines, according to the gene cloning and expression analyses of four relevant proteins with important functions and different expression levels. But the result by western blot showed their same expression tendency for the four proteins as by iTRAQ. These results could provide new insights into the developmental mechanisms of endosperm and pericarp, and grain formation in maize.

AB - The formation and development of maize kernel is a complex dynamic physiological and biochemical process that involves the temporal and spatial expression of many proteins and the regulation of metabolic pathways. In this study, the protein profiles of the endosperm and pericarp at three important developmental stages were analyzed by isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with LC-MS/MS in popcorn inbred N04. Comparative quantitative proteomic analyses among developmental stages and between tissues were performed, and the protein networks were integrated. A total of 6,876 proteins were identified, of which 1,396 were nonredundant. Specific proteins and different expression patterns were observed across developmental stages and tissues. The functional annotation of the identified proteins revealed the importance of metabolic and cellular processes, and binding and catalytic activities for the development of the tissues. The whole, endosperm-specific and pericarp-specific protein networks integrated 125, 9 and 77 proteins, respectively, which were involved in 54 KEGG pathways and reflected their complex metabolic interactions. Confirmation for the iTRAQ endosperm proteins by two-dimensional gel electrophoresis showed that 44.44% proteins were commonly found. However, the concordance between mRNA level and the protein abundance varied across different proteins, stages, tissues and inbred lines, according to the gene cloning and expression analyses of four relevant proteins with important functions and different expression levels. But the result by western blot showed their same expression tendency for the four proteins as by iTRAQ. These results could provide new insights into the developmental mechanisms of endosperm and pericarp, and grain formation in maize.

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