Genome-wide identification and characterization of CKIN/SnRK gene family in Chlamydomonas reinhardtii

Abstract

The SnRK (Snf1-Related protein Kinase) gene family plays an important role in energy sensing and stress-adaptive responses in plant systems. In this study, Chlamydomonas CKIN family (SnRK in Arabidopsis) was defined after a genome-wide analysis of all sequenced Chlorophytes. Twenty-two sequences were defined as plant SnRK orthologs in Chlamydomonas and classified into two subfamilies: CKIN1 and CKIN2. While CKIN1 subfamily is reduced to one conserved member and a close protein (CKIN1L), a large CKIN2 subfamily clusters both plant-like and algae specific CKIN2s. The responsiveness of these genes to abiotic stress situations was tested by RT-qPCR. Results showed that almost all elements were sensitive to osmotic stress while showing different degrees of sensibility to other abiotic stresses, as occurs in land plants, revealing their specialization and the family pleiotropy for some elements. The regulatory pathway of this family may differ from land plants since these sequences shows unique regulatory features and some of them are sensitive to ABA, despite conserved ABA receptors (PYR/PYL/RCAR) and regulatory domains are not present in this species. Core Chlorophytes and land plant showed divergent stress signalling, but SnRKs/CKINs share the same role in cell survival and stress response and adaption including the accumulation of specific biomolecules. This fact places the CKIN family as well-suited target for bioengineering-based studies in microalgae (accumulation of sugars, lipids, secondary metabolites), while promising new findings in stress biology and specially in the evolution of ABA-signalling mechanisms.

Low UV-C stress modulates Chlamydomonas reinhardtii biomass composition and oxidative stress response through proteomic and metabolomic changes involving novel signalers and effectors

“…1b). Chlamydomonas cultures irradiated with low UV-C dosages show no reduction in their biomass yield (FW) compared to unstressed [22]. Although applied UV-C stress did not change yields, it modi ed Chlamydomonas biomass composition with the accumulation of starch and the fall of soluble sugars upon stress imposition (ANOVA 0.05) (Fig.…”

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

“…Non-SnRK sequences were filtered out from homology results through the analysis of their domain composition using the version 75.0 of the Inter Pro Scan database [27]. Only P. pinaster sequences with the Arabidopsis SnRKs canonical domain composition-including Ser/Thr kinase domains (PTHR24343, PTHR43895), UBA (IPR015940), KA1/ αCTD (IPR001772), Immunoglobulin E-set (IPR014756), AMPK glycogen binding subunit (IPR032640), ASC (IPR006828), Immunoglobulin E-set (IPR014756), CBS (IPR000644) and NAF/FISL (IPR018451) domains (Table S1)-were maintained for further analyses as previously specified [28]. Pinus pinaster PpiSNRK transcript sequences were used for the identification of possible PpiSNRK isoforms.…”

“…PpiSnRK sequences were aligned with other SnRK sequences belonging to Arabidopsis and different microalgae species [28] (Table S2) using the M-Coffee consensus alignment method with default parameters [29]. Alignment was filter-curated through the Transitive Consistency Score algorithm (TCS) using default parameters [30].…”

“…P. pinaster PpiSnRK2 sequences were all included into the SnRK2A group along Arabidopsis SnRK2s. The third cluster, PpiSnRK2 sequences (Ser/Thr kinase (PTHR24343) domain), was divided into SnRK2(A) and (B) clusters as previously described [28] with all the P. pinaster PpiSnRK2 and Arabidopsis SnRK2 sequences falling into the SnRK2(A) cluster (Figure 1, Table S1). SnRK2(A) also included a small group of plant-like microalgae SnRK2s conforming the Group 2 of SnRK2(A) ( Figure 1).…”

Engineering the metabolic pathways of lipid biosynthesis to develop robust microalgal strains for biodiesel production

“…Similarly, the presence and role of CKIN (protein kinase family) have been studied in C. reinhardtii through genome‐wide identification. The role of this gene family in stress tolerance, adaptation, cell survival, and biomolecule accumulation was elucidated . In short, genomics provides a basic overview of the overall functionality and relatedness between different algal species.…”