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1. pLMSNOSite: an ensemble-based approach for predicting protein S-nitrosylation sites by integrating supervised word embedding and embedding from pre-trained protein language model

   https://doi.org/10.1186/s12859-023-05164-9  

   Pratyush, Pawel; Pokharel, Suresh; Saigo, Hiroto; KC, Dukka B. (February 2023, BMC Bioinformatics)

   Abstract BackgroundProtein S-nitrosylation (SNO) plays a key role in transferring nitric oxide-mediated signals in both animals and plants and has emerged as an important mechanism for regulating protein functions and cell signaling of all main classes of protein. It is involved in several biological processes including immune response, protein stability, transcription regulation, post translational regulation, DNA damage repair, redox regulation, and is an emerging paradigm of redox signaling for protection against oxidative stress. The development of robust computational tools to predict protein SNO sites would contribute to further interpretation of the pathological and physiological mechanisms of SNO. ResultsUsing an intermediate fusion-based stacked generalization approach, we integrated embeddings from supervised embedding layer and contextualized protein language model (ProtT5) and developed a tool called pLMSNOSite (protein language model-based SNO site predictor). On an independent test set of experimentally identified SNO sites, pLMSNOSite achieved values of 0.340, 0.735 and 0.773 for MCC, sensitivity and specificity respectively. These results show that pLMSNOSite performs better than the compared approaches for the prediction of S-nitrosylation sites. ConclusionTogether, the experimental results suggest that pLMSNOSite achieves significant improvement in the prediction performance of S-nitrosylation sites and represents a robust computational approach for predicting protein S-nitrosylation sites. pLMSNOSite could be a useful resource for further elucidation of SNO and is publicly available athttps://github.com/KCLabMTU/pLMSNOSite. 

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2. S-Nitrosothiols: chemistry and reactions

   https://doi.org/10.1039/c7cc06574d  

   Zhang, Caihong; Biggs, Tyler D.; Devarie-Baez, Nelmi O.; Shuang, Shaomin; Dong, Chuan; Xian, Ming (January 2017, Chem. Commun.)

   The formation of S -nitrosothiols (SNO) in protein cysteine residues is an important post-translational modification elicited by nitric oxide (NO). This process is involved in virtually every class of cell signaling and has attracted considerable attention in redox biology. On the other hand, their unique structural characters make SNO potentially useful synthons. In this review, we summarized the fundamental chemical/physical properties of SNO. We also highlighted the reported chemical reactions of SNO, including the reactions with phosphine reagents, sulfinic acids, various nucleophiles, SNO-mediated radical additions, and the reactions of acyl SNO species. 

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3. Abscisic acid‐controlled redox proteome of Arabidopsis and its regulation by heterotrimeric Gβ protein

   https://doi.org/10.1111/nph.18348  

   Smythers, Amanda L.; Bhatnagar, Nikita; Ha, Chien; Majumdar, Parinita; McConnell, Evan W.; Mohanasundaram, Boominathan; Hicks, Leslie M.; Pandey, Sona (July 2022, New Phytologist)

   Summary The plant hormone abscisic acid (ABA) plays crucial roles in regulation of stress responses and growth modulation. Heterotrimeric G‐proteins are key mediators of ABA responses. Both ABA and G‐proteins have also been implicated in intracellular redox regulation; however, the extent to which reversible protein oxidation manipulates ABA and/or G‐protein signaling remains uncharacterized.To probe the role of reversible protein oxidation in plant stress response and its dependence on G‐proteins, we determined the ABA‐dependent reversible redoxome of wild‐type and Gβ‐protein null mutantagb1of Arabidopsis.We quantified 6891 uniquely oxidized cysteine‐containing peptides, 923 of which show significant changes in oxidation following ABA treatment. The majority of these changes required the presence of G‐proteins. Divergent pathways including primary metabolism, reactive oxygen species response, translation and photosynthesis exhibited both ABA‐ and G‐protein‐dependent redox changes, many of which occurred on proteins not previously linked to them.We report the most comprehensive ABA‐dependent plant redoxome and uncover a complex network of reversible oxidations that allow ABA and G‐proteins to rapidly adjust cellular signaling to adapt to changing environments. Physiological validation of a subset of these observations suggests that functional G‐proteins are required to maintain intracellular redox homeostasis and fully execute plant stress responses. 

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4. Moving beyond the arabidopsis-centric view of G-protein signaling in plants

   https://doi.org/10.1016/j.tplants.2023.07.014  

   Mohanasundaram, Boominathan; Pandey, Sona (December 2023, Trends in Plant Science)

   Heterotrimeric G-protein-mediated signaling is a key mechanism to transduce a multitude of endogenous and environmental signals in diverse organisms. The scope and expectations of plant G-protein research were set by pioneering work in metazoans. Given the similarity of the core constituents, G-protein-signaling mechanisms were presumed to be universally conserved. However, because of the enormous diversity of survival strategies and endless forms among eukaryotes, the signal, its interpretation, and responses vary even among different plant groups. Earlier G-protein research in arabidopsis (Arabidopsis thaliana) has emphasized its divergence from Metazoa. Here, we compare recent evidence from diverse plant lineages with the available arabidopsis G-protein model and discuss the conserved and novel protein components, signaling mechanisms, and response regulation. 

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5. Quantitative Proteome Profiling of a S-Nitrosoglutathione Reductase (GSNOR) Null Mutant Reveals a New Class of Enzymes Involved in Nitric Oxide Homeostasis in Plants

   https://doi.org/10.3389/fpls.2021.787435  

   Treffon, Patrick; Rossi, Jacopo; Gabellini, Giuseppe; Trost, Paolo; Zaffagnini, Mirko; Vierling, Elizabeth (December 2021, Frontiers in Plant Science)

   Nitric oxide (NO) is a short-lived radical gas that acts as a signaling molecule in all higher organisms, and that is involved in multiple plant processes, including germination, root growth, and fertility. Regulation of NO-levels is predominantly achieved by reaction of oxidation products of NO with glutathione to form S -nitrosoglutathione (GSNO), the principal bioactive form of NO. The enzyme S -nitrosoglutathione reductase (GSNOR) is a major route of NADH-dependent GSNO catabolism and is critical to NO homeostasis. Here, we performed a proteomic analysis examining changes in the total leaf proteome of an Arabidopsis thaliana GSNOR null mutant ( hot5-2/gsnor1-3 ). Significant increases or decreases in proteins associated with chlorophyll metabolism and with redox and stress metabolism provide insight into phenotypes observed in hot5-2/gsnor1-3 plants. Importantly, we identified a significant increase in proteins that belong to the aldo-keto reductase (AKR) protein superfamily, AKR4C8 and 9. Because specific AKRs have been linked to NO metabolism in mammals, we expressed and purified A. thaliana AKR4C8 and 9 and close homologs AKR4C10 and 11 and determined that they have NADPH-dependent activity in GSNO and S -nitroso-coenzyme A (SNO-CoA) reduction. Further, we found an increase of NADPH-dependent GSNO reduction activity in hot5-2/gsnor1-3 mutant plants. These data uncover a new, NADPH-dependent component of NO metabolism that may be integrated with NADH-dependent GSNOR activity to control NO homeostasis in plants. 

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