Abstract
Plant stress responses involve numerous changes at the molecular and cellular level and are regulated by highly complex signaling pathways. Studying protein-protein interactions (PPIs) and the resulting networks is therefore becoming increasingly important in understanding these responses. Crucial in PPI networks are the so-called hubs or hub proteins, commonly defined as the most highly connected central proteins in scale-free PPI networks. However, despite their importance, a growing amount of confusion and controversy seems to exist regarding hub protein identification, characterization and classification. In order to highlight these inconsistencies and stimulate further clarification, this review critically analyses the current knowledge on hub proteins in the plant interactome field. We focus on current hub protein definitions, including the properties generally seen as hub-defining, and the challenges and approaches associated with hub protein identification. Furthermore, we give an overview of the most important large-scale plant PPI studies of the last decade that identified hub proteins, pointing out the lack of overlap between different studies. As such, it appears that although major advances are being made in the plant interactome field, defining hub proteins is still heavily dependent on the quality, origin and interpretation of the acquired PPI data. Nevertheless, many hub proteins seem to have a reported role in the plant stress response, including transcription factors, protein kinases and phosphatases, ubiquitin proteasome system related proteins, (co-)chaperones and redox signaling proteins. A significant number of identified plant stress hubs are however still functionally uncharacterized, making them interesting targets for future research. This review clearly shows the ongoing improvements in the plant interactome field but also calls attention to the need for a more comprehensive and precise identification of hub proteins, allowing a more efficient systems biology driven unraveling of complex processes, including those involved in stress responses.
Highlights
Plants are continuously exposed to different kinds of environmental stresses
In order to represent this burst of data in a comprehensive way, graphical network presentations are used, with the most highly connected node proteins, being of great importance for network structure, stability and functionality
Authors do not always follow the same definition to characterize these nodes in protein-protein interactions (PPIs) networks as “hubs.”
Summary
Plants are continuously exposed to different kinds of environmental stresses. These can be abiotic, such as drought, salinity, non-optimal light or temperature conditions, or biotic in origin, such as pathogen or herbivore attacks. Extensive knowledge on the properties and issues inherent to each method and the use of proper controls during experiments is essential as the differences between methods, based on the used technology (i.e., tags, reporters, read out), the type of interactions identified
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