Systems Analysis of Plant Functional, Transcriptional, Physical Interaction, and Metabolic Networks

Abstract

Physiological responses, developmental programs, and cellular functions rely on complex networks of interactions at different levels and scales. Systems biology brings together high-throughput biochemical, genetic, and molecular approaches to generate omics data that can be analyzed and used in mathematical and computational models toward uncovering these networks on a global scale. Various approaches, including transcriptomics, proteomics, interactomics, and metabolomics, have been employed to obtain these data on the cellular, tissue, organ, and whole-plant level. We summarize progress on gene regulatory, cofunction, protein interaction, and metabolic networks. We also illustrate the main approaches that have been used to obtain these networks, with specific examples from Arabidopsis thaliana, and describe the pros and cons of each approach.

SND1 Transcription Factor-Directed Quantitative Functional Hierarchical Genetic Regulatory Network in Wood Formation in Populus trichocarpa

“…However, ChIP does not reveal the regulatory effects of the TF on its bound targets (Solomon et al, 1988;Farnham, 2009;Bassel et al, 2012). A combination of ChIP sequencing or ChIP-PCR and the TF-induced differential gene expression is needed to reveal the functional network and its regulatory effects.…”

“…The regulatory effects of some of these interactions were demonstrated through perturbation or induction of the specific TF in transgenics or mutants (Pruneda-Paz et al, 2009;Zheng et al, 2009;Bassel et al, 2012;Huang et al, 2012;Kumar et al, 2012). Knowledge of the TF-DNA interactions in species other than Arabidopsis is limited.…”

Are We There Yet? Reliably Estimating the Completeness of Plant Genome Sequences

“…In addition, a complete set of annotated genes offers a starting point for a detailed characterization of gene functions, biochemical and regulatory pathways, or quantitative trait loci. Genes are the nodes in a biological network, which offers valuable insights into protein complexes, regulatory interactions, and metabolic processes that determine the physiological and biochemical properties of a cell, an organ or an organism (Bassel et al, 2012).…”

PP2A-3 interacts with ACR4 and regulates formative cell division in the Arabidopsis root

“…Although membrane proteins play a crucial role in many biological processes, knowledge of the in planta membrane interactome is limited (21). Notwithstanding the recent progress with respect to global analyses of membrane protein interactions, so far ACR4 has not been represented in a membrane-linked Arabidopsis interactome (22).…”

“…In addition to posttranslational modifications such as phosphorylation, developmental programs and cellular functions largely rely on interactions between proteins, forming complex networks to control biological processes (21). Although membrane proteins play a crucial role in many biological processes, knowledge of the in planta membrane interactome is limited (21).…”