Abstract
Plants are constantly exposed to environmental stresses and in part due to their sessile nature, they have evolved signal perception and adaptive strategies that are distinct from those of other eukaryotes. This is reflected at the cellular level where receptors and signalling molecules cannot be identified using standard homology-based searches querying with proteins from prokaryotes and other eukaryotes. One of the reasons for this is the complex domain architecture of receptor molecules. In order to discover hidden plant signalling molecules, we have developed a motif-based approach designed specifically for the identification of functional centers in plant molecules. This has made possible the discovery of novel components involved in signalling and stimulus-response pathways; the molecules include cyclic nucleotide cyclases, a nitric oxide sensor and a novel target for the hormone abscisic acid. Here, we describe the major steps of the method and illustrate it with recent and experimentally confirmed molecules as examples. We foresee that carefully curated search motifs supported by structural and bioinformatic assessments will uncover many more structural and functional aspects, particularly of signalling molecules.
Highlights
Plant biotechnological innovations and genetic engineering require an understanding of the signalling pathways in plant cells including their constituent molecular components which are often complex in nature [1,2,3]
Plants are constantly exposed to fluctuations in environmental conditions and stresses including high salinity, temperature, light and pathogens that challenge their growth, development and reproductive capabilities [4,5,6]. In response to these stresses they have evolved adaptive strategies including rapid and effective molecular signal perception and processing that in many instances are distinct from those in animals [7,8,9,10,11,12]. They make use of signalling molecules that exist in many prokaryotic and lower eukaryotic cells leveraging on the ubiquitous second messengers such as calcium ions [13], cyclic nucleotide monophosphates i.e., cyclic guanosine 3′,5′‐monophosphate and cyclic adenosine 3′,5′‐monophosphate [14,15,16,17], and the gaseous nitric oxide (NO) [18,19,20,21,22] in addition to generating their own set of plant specific hormones [3] to perceive environmental cues, transduce external signals into the cell and orchestrate appropriate responses
As motif searches continue to identify novel functional centers in other systems, the strength of this method relies on its ability to reduce misidentifications or false positives; an issue that is commonly associated to many high-throughout computational predictions [117,118,119]
Summary
Plant biotechnological innovations and genetic engineering require an understanding of the signalling pathways in plant cells including their constituent molecular components which are often complex in nature [1,2,3]. Regular homologybased approaches did not yield a comprehensive coverage of the signalling pathways as many molecules known to perform key signalling roles in other eukaryotic cells, are seemingly elusive in the plant cell [15,27,28] This is because rather than a stand-alone molecule, many plant proteins have evolved complex domain organizations [29,30] consisting for instance of an extracellular ligand recognition receptor region, a single or multi-pass transmembrane region and a cytosolic region that may accommodate one or several functional domains with protein-protein interaction or catalytic roles [31,32]. We discuss how systematically curated search motifs can be generated for the discovery of hitherto elusive functional centers
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