| Volcano plots of proteins identified in non-bleached and bleached (A) outer layer (OL) tissue and (B) inner core (IC) intra-skeletal tissue and skeleton of Montipora capitata. Points represent the magnitude of the log 2 fold change and the z-score for each protein. Dashed lines indicate significance thresholds. Select proteins that are discussed in the text are indicated by their abbreviated protein name.

| Volcano plots of proteins identified in non-bleached and bleached (A) outer layer (OL) tissue and (B) inner core (IC) intra-skeletal tissue and skeleton of Montipora capitata. Points represent the magnitude of the log 2 fold change and the z-score for each protein. Dashed lines indicate significance thresholds. Select proteins that are discussed in the text are indicated by their abbreviated protein name.

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Coral bleaching events are increasing with such frequency and intensity that many of the world’s reef-building corals are in peril. Some corals appear to be more resilient after bleaching but the mechanisms underlying their ability to recover from bleaching and persist are not fully understood. We used shotgun proteomics to compare the proteomes of...

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... analysis of differential abundances between the OL of bleached and non-bleached corals revealed 63 significant proteins at higher, and 28 at lower, abundance in bleached corals compared to non-bleached corals (Supplementary File 3). Biological enrichment analysis of GO terms identified that the OL of bleached corals have a higher abundance of proteins involved in carbon metabolism, lipid metabolism, nitrogen metabolism, protein metabolism, response to oxidative stress, RNA processing and cellular signaling and transport than non-bleached corals (Figures 5A, 6). Proteins with the highest log-fold change included calumenin (CALU; m.10914, LFC + 1.8), betainehomocysteine S-methyltransferase (BHMT; m.1453, LFC + 1.6), peroxidasin (PER1; m.28022, LFC + 1.5), urease (URE; m.24102, LFC + 1.4), and catalase (CAT; m.4762, LFC + 1) (Figures 5A, 6). ...
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... enrichment analysis of GO terms identified that the OL of bleached corals have a higher abundance of proteins involved in carbon metabolism, lipid metabolism, nitrogen metabolism, protein metabolism, response to oxidative stress, RNA processing and cellular signaling and transport than non-bleached corals (Figures 5A, 6). Proteins with the highest log-fold change included calumenin (CALU; m.10914, LFC + 1.8), betainehomocysteine S-methyltransferase (BHMT; m.1453, LFC + 1.6), peroxidasin (PER1; m.28022, LFC + 1.5), urease (URE; m.24102, LFC + 1.4), and catalase (CAT; m.4762, LFC + 1) (Figures 5A, 6). Key cellular pathways that increased in the OL of bleached corals include the glyoxylate cycle, fatty acid beta oxidation, beta alanine metabolism, protein degradation and synthesis, betaine degradation and urea degradation. ...
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... cellular pathways that increased in the OL of bleached corals include the glyoxylate cycle, fatty acid beta oxidation, beta alanine metabolism, protein degradation and synthesis, betaine degradation and urea degradation. GO terms associated with less abundant proteins in the OL of bleached corals are associated with biological processes involved in lipid metabolism, amino acid synthesis, protein metabolism, RNA processing, cellular signaling and transport, and cellular structure (Figures 5A, 6). Proteins that were significantly lower in abundance in the OL of bleached corals included cholesterol transporter (CHLT; m.15955, LFC −1.8), glutamine synthetase (GS; m.30399, LFC −1.6), phospholipase B (PLIP; m.27749, LFC −1.1), and mucin protein (MUC; m.29491, LFC −1) (Figures 5A, 6). ...
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... terms associated with less abundant proteins in the OL of bleached corals are associated with biological processes involved in lipid metabolism, amino acid synthesis, protein metabolism, RNA processing, cellular signaling and transport, and cellular structure (Figures 5A, 6). Proteins that were significantly lower in abundance in the OL of bleached corals included cholesterol transporter (CHLT; m.15955, LFC −1.8), glutamine synthetase (GS; m.30399, LFC −1.6), phospholipase B (PLIP; m.27749, LFC −1.1), and mucin protein (MUC; m.29491, LFC −1) (Figures 5A, 6). ...
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... analysis of relative abundances of the proteins detected in the IC revealed 22 proteins at significantly higher abundance and 17 at lower abundance in the IC of bleached corals compared to nonbleached corals. Associated GO terms indicate that proteins at higher abundance in the IC of bleached corals are involved in biological functions including carbon metabolism, protein metabolism, response to oxidative stress and RNA processing (Figures 5B, 6). (Figures 5B, 6). ...
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... GO terms indicate that proteins at higher abundance in the IC of bleached corals are involved in biological functions including carbon metabolism, protein metabolism, response to oxidative stress and RNA processing (Figures 5B, 6). (Figures 5B, 6). Additionally, a protein involved in the pentose phosphate pathway was also represented in this dataset with significantly increased abundance (Figures 5B, 6). ...
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... 5B, 6). Additionally, a protein involved in the pentose phosphate pathway was also represented in this dataset with significantly increased abundance (Figures 5B, 6). Biologically enriched GO terms associated with the IC of nonbleached corals were involved in nitrogen metabolism, cellular signaling and cellular structure (Figures 5B, 6). ...
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... a protein involved in the pentose phosphate pathway was also represented in this dataset with significantly increased abundance (Figures 5B, 6). Biologically enriched GO terms associated with the IC of nonbleached corals were involved in nitrogen metabolism, cellular signaling and cellular structure (Figures 5B, 6). The proteins that were lower in abundance in the IC of bleached corals compared to the IC of non-bleached corals included glutamine synthetase (GS; m.30399, LFC −1.9), peroxidasin (PER3; m.6107, LFC −1.2), and mucin (MUC; m.29491, LFC −0.8) (Figures 5B, 6). ...
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... enriched GO terms associated with the IC of nonbleached corals were involved in nitrogen metabolism, cellular signaling and cellular structure (Figures 5B, 6). The proteins that were lower in abundance in the IC of bleached corals compared to the IC of non-bleached corals included glutamine synthetase (GS; m.30399, LFC −1.9), peroxidasin (PER3; m.6107, LFC −1.2), and mucin (MUC; m.29491, LFC −0.8) (Figures 5B, 6). ...
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... associated with the glyoxylate cycle and fatty acid betaoxidation were higher in the OL of bleached corals than the OL of non-bleached corals. However, ALDH was more abundant in both the OL and IC of bleached corals compared to these compartments in non-bleached corals (Figure 5). ...
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... the coral host and Symbiodiniaceae are able to assimilate ammonia via catalysis by glutamine synthetase (GS) or glutamine dehydrogenase in the host ( Yellowlees et al., 1994;Wang and Douglas, 1998;Su et al., 2018) and via the glutamine synthetase/glutamine:2-oxoglutarate aminotransferase (GS/GOGAT) cycle in Symbiodiniaceae (D'Elia et al., 1983;Roberts et al., 2001). In bleached corals, GS was present at significantly lower abundances in both the OL and the IC compared to non-bleached corals, suggesting an alternate route for N acquisition must be utilized (Figures 5, 6). This result is consistent with recent studies in corals ( Petrou et al., 2021;Rädecker et al., 2021), however, increased GS activity has been reported for other cnidarians ( Wang and Douglas, 1998;Lipschultz and Cook, 2002;Oakley et al., 2016). ...