Enzyme activity profiling for physiological phenotyping within functional phenomics: plant growth and stress responses

Abstract

High-throughput profiling of key enzyme activities of carbon, nitrogen, and antioxidant metabolism is emerging as a valuable approach to integrate cell physiological phenotyping into a holistic functional phenomics approach. However, the analyses of the large datasets generated by this method represent a bottleneck, often keeping researchers from exploiting the full potential of their studies. We address these limitations through the exemplary application of a set of data evaluation and visualization tools within a case study. This includes the introduction of multivariate statistical analyses that can easily be implemented in similar studies, allowing researchers to extract more valuable information to identify enzymatic biosignatures. Through a literature meta-analysis, we demonstrate how enzyme activity profiling has already provided functional information on the mechanisms regulating plant development and response mechanisms to abiotic stress and pathogen attack. The high robustness of the distinct enzymatic biosignatures observed during developmental processes and under stress conditions underpins the enormous potential of enzyme activity profiling for future applications in both basic and applied research. Enzyme activity profiling will complement molecular -omics approaches to contribute to the mechanistic understanding required to narrow the genotype-to-phenotype knowledge gap and to identify predictive biomarkers for plant breeding to develop climate-resilient crops.

Early leaf responses of cell physiological and sensor‐based signatures reflect susceptibility of wheat seedlings to infection by leaf rust

“…The profound physiological phenotyping (Grosskinsky et al, 2015) using enzyme activity profiling (Jammer et al, 2022) was applied to assess the impact on the plant's primary carbohydrate metabolism. Stabilization of the central carbohydrate metabolism is crucial in the plant stress response.…”

Crop/Plant Modeling Supports Plant Breeding: II. Guidance of Functional Plant Phenotyping for Trait Discovery

“…Although experimental methods can test the expression of a trait by modifying it in assessing its effect on crop yield, they may be expensive, impractical, and even impossible to realize in traditional multisite, multiseason cultivation trials [ 28 ]. Performance at the whole plant level results from accumulated responses at the cellular, tissue, and organ levels to various abiotic factors [ 14 , 23 , 40 ]. This requires an effective tool in assisting to systematically dissect plant growth and development into secondary functional traits [ 15 , 33 ], such as early vigor, Rubisco carboxylation rate, electron transport rate, specific leaf nitrogen, assimilate allocation, etc.…”

“…Advanced multi-omics and plant phenomics technologies offer an unprecedented capacity for parameterization and validation of model. At the molecular scale, transcriptomes, proteomes, and metabolomes make it possible for parameterizing mechanistic models down to the actual molecular components involved [ 23 , 85 ]. At the leaf or even the whole plant scale, progress in plant phenomics has been achieved in high-throughput monitoring functional traits such as photosynthetic status, water, and pigment content (Table 1 ).…”

“…Constrained by phenotyping techniques, noninvasive and high-throughput analyses of underlying functional traits are far behind the morphological features since the latter is easier to be caught by imaging systems [ 23 , 26 , 27 , 29 ]. Thus, there is a great demand for tools to identify fundamentally functional traits.…”

Functional phenomics for improved climate resilience in Nordic agriculture

“…A high dimensional physiological phenotyping across scales is needed that integrates the precise characterization of the internal phenotype into HTP of whole plants and canopies ( Großkinsky et al, 2015 , 2018 ). The determination of enzyme activity signatures is emerging as a robust, semi-high-throughput tool to bridge the genotype–phenotype gap to assess the impact of pedoclimatic condition and the integration of environmental variables and crop management in the genetic programmes ( Gibon et al , 2004 ; Jammer et al , 2015 ; Fimognari et al , 2020 ), and is also reviewed in this special issue ( Jammer et al , 2022 ). By this means, complex traits can be broken down into individual components of physiological traits.…”