The Analysis of Pinus pinaster SnRKs Reveals Clues of the Evolution of This Family and a New Set of Abiotic Stress Resistance Biomarkers

Abstract

Climate change is increasing the intensity and incidence of environmental stressors, reducing the biomass yields of forestry species as Pinus pinaster. Selection of new stress-tolerant varieties is thus required. Many genes related to plant stress signaling pathways have proven useful for this purpose with sucrose non-fermenting related kinases (SnRK), conserved across plant evolution and connected to different phosphorylation cascades within ABA- and Ca2+-mediated signaling pathways, as a good example. The modulation of SnRKs and/or the selection of specific SnRK alleles have proven successful strategies to increase plant stress resistance. Despite this, SnRKs have been barely studied in gymnosperms. In this work P. pinaster SnRK sequences (PpiSnRK) were identified through a homology- and domain-based sequence analysis using Arabidopsis SnRK sequences as query. Moreover, PpiSnRKs links to the gymnosperm stress response were modeled out of the known interactions of PpiSnRKs orthologs from other species with different signaling complexity. This approach successfully identified the pine SnRK family and predicted their central role into the gymnosperm stress response, linking them to ABA, Ca2+, sugar/energy and possibly ethylene signaling. These links made the gymnosperm kinases promising candidates into the search for new stress resistance-related biomarkers, which would be useful into future breeding strategies.

Multiomics analyses reveal the central role of nucleolus and nucleoid machinery during heat stress acclimation in Pinus radiata

“…PC1, gathering 40% of the total variance, separated the different samples according to stress time. Transcripts exhibiting positive higher loadings to PC1, and thus explaining stress acclimation, included several RNA interacting and ribonuclear proteins and epigenetics-related proteins, characteristic of processes involved a transcriptome reprogramming, stress-signalers such as SNRK2 (Colina et al, 2020) and other kinases, cell cycle proteins, and solute transporters, which accumulation probably aims to retain water and to avoid a heat-driven drought/hyperosmotic cell stress. On the other hand, the proteins negatively correlated to PC1, and characteristic of control plants, pointed to normal plant metabolism and respiration, with no striking enrichment of transcripts belonging to any pathway.…”

Proteomics research in forest trees: A 2012-2022 update

“…The last decade has witnessed a huge advance in pine proteomics research that has continued the transition from gel-based to gel-free systems based on mass spectrometry thanks to important methodological developments, such as those of databases ( Nystedt et al., 2013 ; Zimin et al., 2014 ; Stevens et al., 2016 ; Zimin et al., 2017 ) and their use ( Romero-Rodríguez et al., 2014 ). In addition, the development of new protein isolation protocols ( Valledor et al., 2014 ; Colina et al., 2020 ) and fractionation methods has allowed studying subcellular proteomes ( Alegre et al., 2016 ; Lamelas et al., 2020a ). Noteworthy, proteomic analysis has been very commonly performed in combination with other omics, like transcriptomics or metabolomics, which has needed new computational strategies and algorithms to allow the integration of different omic layers effectively, and comprehensively ( Escandón et al., 2020 ; Sundararaman et al., 2020 ).…”