Arabidopsis REI-LIKE proteins activate ribosome biogenesis during cold acclimation

Abstract

29 30 WORD COUNT 31 18,932 32 2 TITLE 33 Arabidopsis REIL proteins activate ribosome biogenesis during cold acclimation 34 Running Title 35 REIL proteins activate ribosome biogenesis 36 Highlight of this study (summarizing sentence) (27 words) 37 REIL proteins affect paralog composition of eukaryotic ribosomes and suppress accumulation of 38 43S-preinitiation and pre-60S-maturation complexes, suggesting functions of ribosome 39 heterogeneity and biogenesis in plant cold acclimation. 40 Abstract (150 words) 41 Arabidopsis REIL proteins are cytosolic ribosomal 60S-biogenesis factors. After shift to 10°C, reil 42 mutants deplete and slowly replenish non-translating eukaryotic ribosome complexes of root 43 tissue, while tightly controlling the balance of non-translating 40S-and 60S-subunits. Reil 44 mutations compensate by hyper-accumulation of non-translating subunits at steady-state 45 temperature; after cold-shift, a KCl-sensitive 80S sub-fraction remains depleted. We infer that 46 Arabidopsis buffers fluctuating translation by pre-existing non-translating ribosomes before de 47 novo synthesis meets temperature-induced demands. Reil1 reil2 double mutants accumulate 43S-48 preinitiation and pre-60S-maturation complexes and have altered paralog composition of 49 ribosomal proteins in non-translating complexes. With few exceptions, e.g. RPL3B and RPL24C, 50 these changes are not under transcriptional control. Our study suggests requirement of de novo 51 synthesis of eukaryotic ribosomes for long-term cold acclimation, feedback control of NUC2 and 52 eIF3C2 transcription and links new proteins, AT1G03250, AT5G60530, to plant ribosome 53 biogenesis. We propose that Arabidopsis requires biosynthesis of specialized ribosomes for cold 54 acclimation. 55 Key words (6-10, in alphabetical order) 56 abiotic stress, Arabidopsis, cold acclimation, proteomics, REI-LIKE proteins, ribosome 57 biogenesis, roots, system analysis, transcriptomics 58 59 60 61The Arabidopsis thaliana Col-0 (Arabidopsis) REI1-LIKE (REIL) proteins, REIL1 62 (At4g31420) and REIL2 (At2g24500) are homologs of the yeast Rei1 (YBR267W) and the paralog 63 Reh1 (YLR387C) proteins. In yeast, both the Rei1 and Reh1 proteins function as ribosome 64 biogenesis factors that participate either in parallel or sequentially in the late ribosome biogenesis 65 step of cytoplasmic 60S ribosomal subunit maturation (Greber et al., 2012; Greber et al., 2016). 66 Aside from this function, these proteins are required to maintain growth at suboptimal or cold 67 temperatures. The ∆rei1 mutant is cold sensitive already at moderately suboptimal temperatures 68 of yeast. The ∆rei1 ∆reh1 double mutant is even more cold sensitive, while the yeast ∆reh1 69 mutation alone has no effect on growth in the cold (Iwase and Toh-e, 2004; Lebreton et al., 2006; 70 Parnell and Bass, 2009). Heterologous expression of Arabidopsis REIL1, but not of REIL2 partly 71 complements the cold sensitivity of the yeast ∆rei1 mutant (Schmidt et al., 2013). The Arabidopsis 72 REIL paralogs differ in st...

Separation and Paired Proteome Profiling of Plant Chloroplast and Cytoplasmic Ribosomes

“…Our current study did not allow a further analysis of mitochondrial RPs from leaf material. Low abundance of small and large subunit mitochondrial RPs was reported by Cheong and co-workers, too [ 34 ]. In this study of root material plastid and mitochondrial ribosomes co-purified and both prokaryote-type ribosome complexes were on average more than 100-fold less abundant than eukaryote ribosome complexes [ 34 ].…”

“…This tissue contained both chloroplast and cytoplasmic ribosomes and was expected to have a highly complex composition of eukaryote- and prokaryote-type ribosome complexes. As a tissue with lower expected complexity, we chose root tissue [ 34 ] that we obtained from axenic cultures of hydroponically grown plants. This cultivation method was standardized and delivered whole root material from pooled samples of up to four co-cultivated plants ( Figure S1 ).…”

Systematic Review of Plant Ribosome Heterogeneity and Specialization

“…Absence of both paralogs, however, enhances the defect and halts Arabidopsis development and growth at low temperature ( Schmidt et al., 2013 ; Beine-Golovchuk et al, 2018 ). REIL proteins affect accumulation of non-translational ribosomal complexes ( Cheong et al., 2020 ), that is, free pools of 60S LSUs and single 80S monosomes. and in the case of REIL2 are linked to the cold induced C-repeat-binding factor (CBF) regulon ( Yu et al., 2020 ), which is a compendium of more than 100 genes with altered expressions due to the action of CBF transcription factors and enhances freezing tolerance.…”

“…This process is modulated by CKB1, i.e., the regulatory subunit of plastid Casein kinase2 ( Zhang et al., 2020 ). Mutants of the cold-specific Arabidopsis RBF, REIL, indicated that ribosome biogenesis can alter RP paralog accumulation in non-translational ribosome complexes ( Cheong et al., 2020 ). The abundance of specific paralogs, namely, eL28 (AtRPL28A) and eS7 (AtRPS7C), changed upon sucrose feeding ( Hummel et al., 2012 ), and importantly, this effect of sucrose is concomitant to selective mRNA translation ( Gamm et al., 2014 ).…”

“…RP transcript levels of Arabidopsis roots are, however, not necessarily associated with compositional changes of the non-translating ribo-proteome ( Cheong et al., 2020 ). Ribosomes are stable complexes and have a longer half-life as compared to average protein half-lives.…”