A Mesoscale Abscisic Acid Hormone Interactome Reveals a Dynamic Signaling Landscape in Arabidopsis

Abstract

The sesquiterpenoid abscisic acid (ABA) mediates an assortment of responses across a variety of kingdoms including both higher plants and animals. In plants, where most is known, a linear core ABA signaling pathway has been identified. However, the complexity of ABA-dependent gene expression suggests that ABA functions through an intricate network. Here, using systems biology approaches that focused on genes transcriptionally regulated by ABA, we defined an ABA signaling network of over 500 interactions among 138 proteins. This map greatly expanded ABA core signaling but was still manageable for systematic analysis. For example, functional analysis was used to identify an ABA module centered on two sucrose nonfermenting (SNF)-like kinases. We also used coexpression analysis of interacting partners within the network to uncover dynamic subnetwork structures in response to different abiotic stresses. This comprehensive ABA resource allows for application of approaches to understanding ABA functions in higher plants.

Revealing Shared and Distinct Gene Network Organization in Arabidopsis Immune Responses by Integrative Analysis

“…Second, mRNA microarray data provide no information of the regulation of immune-related genes by posttranslational modifications. We believe that these problems will be alleviated gradually with the development of more reliable computational algorithms (Lee et al, 2010) and highthroughput experimental methods (Jones et al, 2014;Lumba et al, 2014). Finally, NGF only distinguishes plant immune responses as two conditions (on/off).…”

Group VII Ethylene Response Factors in Arabidopsis: Regulation and Physiological Roles

“…Therefore, RAP2.3 participates in the interplay between ethylene and GA, which regulates apical hook formation (Abbas et al, 2013), by hindering premature hook opening under darkness. C, During germination, RAP2.2 is as a negative regulator of ABA responses (Lumba et al, 2014). This function has been associated with RAP2.2 phosphorylation, following its interaction with an SNRK3 kinase complex that mediates ABA insensitivity.…”

“…RAP2.2 has been revealed to be part of a PP2C-SNRK3 complex that promotes ABA insensitivity (Lumba et al, 2014; Fig. 2C).…”

SOS2-LIKE PROTEIN KINASE5, an SNF1-RELATED PROTEIN KINASE3-Type Protein Kinase, Is Important for Abscisic Acid Responses in Arabidopsis through Phosphorylation of ABSCISIC ACID-INSENSITIVE5

“…After the perception of elevated calcium elicited by various environmental stimuli, SCaBPs interact with and activate a group of protein kinases, SOS2-LIKE PROTEIN KINASEs (PKSs), also known as CALCINEURIN B-LIKE PROTEIN-INTERACTING PROTEIN KINASEs (CIPKs; Luan et al, 2002;Gong et al, 2004). Many PKSs have been shown to be involved in ABA responses, serving as both positive or negative regulators of plant ABA signaling Guo et al, 2002;Kim et al, 2003;Song et al, 2005;D'Angelo et al, 2006;Pandey et al, 2008;Qin et al, 2008;Lyzenga et al, 2013;Lumba et al, 2014). PKS3 (also known as CIPK15 or SnRK3.1; Table I) negatively regulates ABA signaling via the phosphorylation of ETHYLENE RESPONSE FACTOR7 (ERF7), which is an APETALA2/ETHYLENE-RESPONSIVE ELEMENT BINDING PROTEIN-type transcription factor (Guo et al, 2002;Song et al, 2005).…”