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Label-free quantitative proteomics of maize roots from different root zones provides insight into proteins associated with enhance water uptake
BACKGROUND: Maize is one of the most important food crops worldwide. Roots play important role in maize productivity through water and nutrient uptake from the soil. Improving maize root traits for efficient water uptake will help to optimize irrigation and contribute to sustainable maize production...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8898408/ https://www.ncbi.nlm.nih.gov/pubmed/35247985 http://dx.doi.org/10.1186/s12864-022-08394-y |
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author | Song, Junqiao Lu, Daowen Niu, Yongfeng Sun, Haichao Zhang, Pan Dong, Wenheng Li, Yongjiang Zhang, Yingying Lu, Lianyong Men, Qi Zhang, Xiaohui Ren, Pengxun Chen, Chuankui |
author_facet | Song, Junqiao Lu, Daowen Niu, Yongfeng Sun, Haichao Zhang, Pan Dong, Wenheng Li, Yongjiang Zhang, Yingying Lu, Lianyong Men, Qi Zhang, Xiaohui Ren, Pengxun Chen, Chuankui |
author_sort | Song, Junqiao |
collection | PubMed |
description | BACKGROUND: Maize is one of the most important food crops worldwide. Roots play important role in maize productivity through water and nutrient uptake from the soil. Improving maize root traits for efficient water uptake will help to optimize irrigation and contribute to sustainable maize production. Therefore, we investigated the protein profiles of maize cv. Anyu308 root system divided into Upper root zone (UR), Middle root (MR), and Lower root (LR), by label free quantitative shotgun proteomic approach (LFQ). The aim of our study was to identify proteins and mechanisms associated with enhanced water uptake in different maize root zones under automatic irrigation system. RESULTS: At field capacity, MR had the highest water uptake than the UR and LR. We identified a total of 489 differentially abundant proteins (DAPs) by pairwise comparison of MR, LR, and UR. Cluster analysis of DAPs revealed MR and UR had similar protein abundance patterns different from LR. More proteins were differentially abundant in MR/UR compared to LR/MR and LR/UR. Comparisons of protein profiles indicate that the DAPs in MR increased in abundance, compared to UR and LR which had more downregulated DAPs. The abundance patterns, functional category, and pathway enrichment analyses highlight chromatin structure and dynamics, ribosomal structures, polysaccharide metabolism, energy metabolism and transport, induction of water channels, inorganic ion transport, intracellular trafficking, and vesicular transport, and posttranslational modification as primary biological processes related to enhanced root water uptake in maize. Specifically, the abundance of histones, ribosomal proteins, and aquaporins, including mitochondrion electron transport proteins and the TCA cycle, underpinned MR’s enhanced water uptake. Furthermore, proteins involved in folding and vascular transport supported the radial transport of solute across cell membranes in UR and MR. Parallel reaction monitoring analysis was used to confirmed profile of the DAPs obtained by LFQ-based proteomics. CONCLUSION: The list of differentially abundant proteins identified in MR are interesting candidates for further elucidation of their role in enhanced water uptake in maize root. Overall, the current results provided an insight into the mechanisms of maize root water uptake. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08394-y. |
format | Online Article Text |
id | pubmed-8898408 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-88984082022-03-16 Label-free quantitative proteomics of maize roots from different root zones provides insight into proteins associated with enhance water uptake Song, Junqiao Lu, Daowen Niu, Yongfeng Sun, Haichao Zhang, Pan Dong, Wenheng Li, Yongjiang Zhang, Yingying Lu, Lianyong Men, Qi Zhang, Xiaohui Ren, Pengxun Chen, Chuankui BMC Genomics Research BACKGROUND: Maize is one of the most important food crops worldwide. Roots play important role in maize productivity through water and nutrient uptake from the soil. Improving maize root traits for efficient water uptake will help to optimize irrigation and contribute to sustainable maize production. Therefore, we investigated the protein profiles of maize cv. Anyu308 root system divided into Upper root zone (UR), Middle root (MR), and Lower root (LR), by label free quantitative shotgun proteomic approach (LFQ). The aim of our study was to identify proteins and mechanisms associated with enhanced water uptake in different maize root zones under automatic irrigation system. RESULTS: At field capacity, MR had the highest water uptake than the UR and LR. We identified a total of 489 differentially abundant proteins (DAPs) by pairwise comparison of MR, LR, and UR. Cluster analysis of DAPs revealed MR and UR had similar protein abundance patterns different from LR. More proteins were differentially abundant in MR/UR compared to LR/MR and LR/UR. Comparisons of protein profiles indicate that the DAPs in MR increased in abundance, compared to UR and LR which had more downregulated DAPs. The abundance patterns, functional category, and pathway enrichment analyses highlight chromatin structure and dynamics, ribosomal structures, polysaccharide metabolism, energy metabolism and transport, induction of water channels, inorganic ion transport, intracellular trafficking, and vesicular transport, and posttranslational modification as primary biological processes related to enhanced root water uptake in maize. Specifically, the abundance of histones, ribosomal proteins, and aquaporins, including mitochondrion electron transport proteins and the TCA cycle, underpinned MR’s enhanced water uptake. Furthermore, proteins involved in folding and vascular transport supported the radial transport of solute across cell membranes in UR and MR. Parallel reaction monitoring analysis was used to confirmed profile of the DAPs obtained by LFQ-based proteomics. CONCLUSION: The list of differentially abundant proteins identified in MR are interesting candidates for further elucidation of their role in enhanced water uptake in maize root. Overall, the current results provided an insight into the mechanisms of maize root water uptake. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08394-y. BioMed Central 2022-03-06 /pmc/articles/PMC8898408/ /pubmed/35247985 http://dx.doi.org/10.1186/s12864-022-08394-y Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Song, Junqiao Lu, Daowen Niu, Yongfeng Sun, Haichao Zhang, Pan Dong, Wenheng Li, Yongjiang Zhang, Yingying Lu, Lianyong Men, Qi Zhang, Xiaohui Ren, Pengxun Chen, Chuankui Label-free quantitative proteomics of maize roots from different root zones provides insight into proteins associated with enhance water uptake |
title | Label-free quantitative proteomics of maize roots from different root zones provides insight into proteins associated with enhance water uptake |
title_full | Label-free quantitative proteomics of maize roots from different root zones provides insight into proteins associated with enhance water uptake |
title_fullStr | Label-free quantitative proteomics of maize roots from different root zones provides insight into proteins associated with enhance water uptake |
title_full_unstemmed | Label-free quantitative proteomics of maize roots from different root zones provides insight into proteins associated with enhance water uptake |
title_short | Label-free quantitative proteomics of maize roots from different root zones provides insight into proteins associated with enhance water uptake |
title_sort | label-free quantitative proteomics of maize roots from different root zones provides insight into proteins associated with enhance water uptake |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8898408/ https://www.ncbi.nlm.nih.gov/pubmed/35247985 http://dx.doi.org/10.1186/s12864-022-08394-y |
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