Plant multiscale networks: charting plant connectivity by multi-level analysis and imaging techniques

Abstract

In multicellular and even single-celled organisms, individual components are interconnected at multiscale levels to produce enormously complex biological networks that help these systems maintain homeostasis for development and environmental adaptation. Systems biology studies initially adopted network analysis to explore how relationships between individual components give rise to complex biological processes. Network analysis has been applied to dissect the complex connectivity of mammalian brains across different scales in time and space in The Human Brain Project. In plant science, network analysis has similarly been applied to study the connectivity of plant components at the molecular, subcellular, cellular, organic, and organism levels. Analysis of these multiscale networks contributes to our understanding of how genotype determines phenotype. In this review, we summarized the theoretical framework of plant multiscale networks and introduced studies investigating plant networks by various experimental and computational modalities. We next discussed the currently available analytic methodologies and multi-level imaging techniques used to map multiscale networks in plants. Finally, we highlighted some of the technical challenges and key questions remaining to be addressed in this emerging field.

The Cytoskeleton in Plant Immunity: Dynamics, Regulation, and Function

“…(6) As a complex dynamic filamentous network throughout the whole cell, it would be interesting to reveal the real-time dynamic changes in the cytoskeleton and the ultrastructural characterization of pathogen and host responses during the interaction. The recent application of high-spatiotemporal-resolution imaging techniques and volume imaging systems [ 114 , 115 , 116 ] will help us better understand the cytoskeleton remodeling and function during the plant defense response. Recently, Vernet et al successfully observed the nematode–root interactions in tomato using light sheet fluorescence microscopy (LSFM) and optical projection tomography (OPT) [ 117 ].…”

Arabidopsis ORP2A mediates ER–autophagosomal membrane contact sites and regulates PI3P in plant autophagy

“…Lipid transport is one of the functions of a membrane contact site (MCS), which provides a fast and nonvesicular way for material exchange. MCSs have a functional proteomic and/or lipidomic composition which is required for maintenance and function of the architecture ( 19 , 20 ). In mammalian cells, the ER-localized proteins VAMP-associated protein (VAP) A and B have been shown to establish MCSs with multiple organelles including the Golgi, endosomes, and peroxisomes ( 21 ).…”

Membrane Dynamics Regulated by Cytoskeleton in Plant Immunity

“…Due to its close ties to the PM and CW, the cytoskeleton can also take part in the dynamics of CW-involved responses to biotic and abiotic stress [ 80 ]. Targeting of the PM-CW-localized defensive regulator (cellulose or callose) to the plasma membrane also requires the cytoskeleton.…”