Label-free quantitative proteomics of maize roots from different root zones provides insight into proteins associated with enhance water uptake

Abstract

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.

Proteomics Analysis Reveals Hormone Metabolic Process Involved in the Regulation of Kernel Water Content Induced by Exogenous Abscisic Acid in Maize

“…Differentially expressed proteins (DAPs) were classified as upregulated (fold change > 1.2) or downregulated (fold change > 0.8) based on a t-test (p < 0.05) [38]. Annotation information was obtained for GO terms (second, third, and fourth layers of biological process, cellular component, and molecular function, respectively), KEGG pathways, and COG (cluster of orthologous groups) categories corresponding to the submitted protein sequences [46]. Functional enrichment analysis was performed using the hypergeometric test to identify significant functional categories.…”

Effects of exogenous abscisic acid on kernel water content of Different Maize Varieties during grain filling

“…GO terms (annotation information of the second, third and fourth layers of Biological Process, Cellular Component and Molecular Function, respectively), KEGG pathway and COG (Cluster of Orthologous Groups) categories corresponding to the submitted protein sequences were obtained for annotation (Song et al 2022). Differentially expressed proteins were subsequently identi ed then functional enrichment analysis was carried out based on the hypergeometric test to screen for signi cant functional categories.…”