Regulation of Cell Wall Formation by Membrane Traffic

Sánchez‐Rodríguez, Clara; Persson, Staffan

doi:10.1002/9781118647363.ch2

Cited by 2 publications

(1 citation statement)

References 147 publications

(199 reference statements)

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“…The results of our network-based analysis reveal new insight on spatially related strategies, commonly or specifically activated in the different bent root sectors (ABS, BS, and BBS) and sides (cx and cv). In particular, ABS-cx was characterized by factors (GO terms grouped in cluster-related subnetwork I) strictly linked to and essential for plant development and responses to mechanical stimuli [42], primarily related to the nucleotides metabolism (GO-BP) and pectate lyase and thioredoxin activities (GO-MF). Furthermore, here, the 60S ribosomal protein L5 (POPTR_0013s13220, POPTR_0014s17230, and POPTR_0019s13040) resulted as the top three hub genes.…”

Section: Discussionmentioning

confidence: 99%

Network-Based Analysis to Identify Hub Genes Involved in Spatial Root Response to Mechanical Constrains

Dimitrova

Sferra

Scippa

et al. 2022

Cells

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Previous studies report that the asymmetric response, observed along the main poplar woody bent root axis, was strongly related to both the type of mechanical forces (compression or tension) and the intensity of force displacement. Despite a large number of targets that have been proposed to trigger this asymmetry, an understanding of the comprehensive and synergistic effect of the antistress spatially related pathways is still lacking. Recent progress in the bioinformatics area has the potential to fill these gaps through the use of in silico studies, able to investigate biological functions and pathway overlaps, and to identify promising targets in plant responses. Presently, for the first time, a comprehensive network-based analysis of proteomic signatures was used to identify functions and pivotal genes involved in the coordinated signalling pathways and molecular activities that asymmetrically modulate the response of different bent poplar root sectors and sides. To accomplish this aim, 66 candidate proteins, differentially represented across the poplar bent root sides and sectors, were grouped according to their abundance profile patterns and mapped, together with their first neighbours, on a high-confidence set of interactions from STRING to compose specific cluster-related subnetworks (I–VI). Successively, all subnetworks were explored by a functional gene set enrichment analysis to identify enriched gene ontology terms. Subnetworks were then analysed to identify the genes that are strongly interconnected with other genes (hub gene) and, thus, those that have a pivotal role in the bent root asymmetric response. The analysis revealed novel information regarding the response coordination, communication, and potential signalling pathways asymmetrically activated along the main root axis, delegated mainly to Ca2+ (for new lateral root formation) and ROS (for gravitropic response and lignin accumulation) signatures. Furthermore, some of the data indicate that the concave side of the bent sector, where the mechanical forces are most intense, communicates to the other (neighbour and distant) sectors, inducing spatially related strategies to ensure water uptake and accompanying cell modification. This information could be critical for understanding how plants maintain and improve their structural integrity—whenever and wherever it is necessary—in natural mechanical stress conditions.

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Section: Discussionmentioning

confidence: 99%