Spatially Enriched Paralog Rearrangements Argue Functionally Diverse Ribosomes Arise during Cold Acclimation in Arabidopsis.

Ribosome biogenesis is essential for plants to successfully acclimate to low temperature. Without dedicated steps supervising the 60S large subunits (LSUs) maturation in the cytosol, e.g., Rei-like (REIL) factors, plants fail to accumulate dry weight and fail to grow at suboptimal low temperatures. Around REIL, the final 60S cytosolic maturation steps include proofreading and assembly of functional ribosomal centers such as the polypeptide exit tunnel and the P-Stalk, respectively. In consequence, these ribosomal substructures and their assembly, especially during low temperatures, might be changed and provoke the need for dedicated quality controls. To test this, we blocked ribosome maturation during cold acclimation using two independent reil double mutant genotypes and tested changes in their ribosomal proteomes. Additionally, we normalized our mutant datasets using as a blank the cold responsiveness of a wild-type Arabidopsis genotype. This allowed us to neglect any reil-specific effects that may happen due to the presence or absence of the factor during LSU cytosolic maturation, thus allowing us to test for cold-induced changes that happen in the early nucleolar biogenesis. As a result, we report that cold acclimation triggers a reprogramming in the structural ribosomal proteome. The reprogramming alters the abundance of specific RP families and/or paralogs in non-translational LSU and translational polysome fractions, a phenomenon known as substoichiometry. Next, we tested whether the cold-substoichiometry was spatially confined to specific regions of the complex. In terms of RP proteoforms, we report that remodeling of ribosomes after a cold stimulus is significantly constrained to the polypeptide exit tunnel (PET), i.e., REIL factor binding and functional site. In terms of RP transcripts, cold acclimation induces changes in RP families or paralogs that are significantly constrained to the P-Stalk and the ribosomal head. The three modulated substructures represent possible targets of mechanisms that may constrain translation by controlled ribosome heterogeneity. We propose that non-random ribosome heterogeneity controlled by specialized biogenesis mechanisms may contribute to a preferential or ultimately even rigorous selection of transcripts needed for rapid proteome shifts and successful acclimation.

Duplicated paralog of sulfide: quinone oxidoreductase contributes to the adaptation to hydrogen sulfide-rich environment in the hydrothermal vent crab, Xenograpsus testudinatus.

The hydrothermal crab, Xenograpsus testudinatus (xtcrab) inhabits shallow-water, hydrogen sulfide (H2S)-rich hydrothermal vent regions. Until now, the adaptative strategy of xtcrab to this toxic environment was unknown. Herein, we investigated the sulfide tolerance and detoxification mechanisms of xtcrabs collected in their high-sulfide hydrothermal vent habitat. Experimental immersion of xtcrab in various sulfide concentrations in the field or in aquaria assessed its high sulfide tolerance. HPLC measurement of hemolymph sulfur compounds highlighted xtcrab detoxification capacity via catabolism of sulfide into much less toxic thiosulfate. We focused on a key enzyme for H2S detoxification, sulfide: quinone oxidoreductase (SQR). Cloning and phylogenetic analysis revealed two SQR paralogs in xtcrab, that we named xtSQR1 and xtSQR2. As shown by qPCR, xtSQR2 and xtSQR1 were expressed in the digestive gland, suggesting the involvement of both paralogs in the detoxification of food-related H2S. In contrast, xtSQR1 transcript was highly expressed in the gill, while xtSQR2 was not detectable, suggesting a specific role of SQR1 in gill detoxification of H2S of environmental origin. Comparison between xtcrabs in their hydrogen sulfide-rich hydrothermal habitat, and xtcrabs maintained for one month in sulfide-free seawater aquarium, showed higher transcript levels of gill xtSQR1 in sulfide-rich habitat, further supporting the specific role of xtSQR1 paralog in environmental H2S detoxification in the gill. Gill SQR protein level as measured by Western blot, and gill SQR enzyme activity were also higher in sulfide-rich habitat. Immunohistochemical staining further showed that SQR expression was co-localized with Na+/K+-ATPase-positive epithelial and pillar cells of the gill filament. This is the first evidence of duplicate SQR genes in crustaceans. Overall, our study suggests that the subfunctionalization of duplicate xtSQR genes may play an important role in sulfide detoxification to maintain the sulfide homeostasis in X. testudinatus, providing an ecophysiological basis for its adaptation to the high-sulfide hydrothermal vent environment.