scholarly journals Presence of a Mitovirus Is Associated with Alteration of the Mitochondrial Proteome, as Revealed by Protein–Protein Interaction (PPI) and Co-Expression Network Models in Chenopodium quinoa Plants

Biology ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 95
Author(s):  
Dario Di Silvestre ◽  
Giulia Passignani ◽  
Rossana Rossi ◽  
Marina Ciuffo ◽  
Massimo Turina ◽  
...  
Keyword(s):  
Stress Response ◽  
Protein Interaction ◽  
Rna Binding ◽  
Redox Homeostasis ◽  
Mitochondrial Protein ◽  
Chenopodium Quinoa ◽  
Network Models ◽  
System Perspective ◽  
Mitochondrial Proteome ◽  
Protein Protein Interaction

Plant mitoviruses belong to Mitoviridae family and consist of positive single-stranded RNA genomes replicating exclusively in host mitochondria. We previously reported the biological characterization of a replicating plant mitovirus, designated Chenopodium quinoa mitovirus 1 (CqMV1), in some Chenopodium quinoa accessions. In this study, we analyzed the mitochondrial proteome from leaves of quinoa, infected and not infected by CqMV1. Furthermore, by protein–protein interaction and co-expression network models, we provided a system perspective of how CqMV1 affects mitochondrial functionality. We found that CqMV1 is associated with changes in mitochondrial protein expression in a mild but well-defined way. In quinoa-infected plants, we observed up-regulation of functional modules involved in amino acid catabolism, mitochondrial respiratory chain, proteolysis, folding/stress response and redox homeostasis. In this context, some proteins, including BCE2 (lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex), DELTA-OAT (ornithine aminotransferase) and GR-RBP2 (glycine-rich RNA-binding protein 2) were interesting because all up-regulated and network hubs in infected plants; together with other hubs, including CAT (catalase) and APX3 (L-ascorbate peroxidase 3), they play a role in stress response and redox homeostasis. These proteins could be related to the higher tolerance degree to drought we observed in CqMV1-infected plants. Although a specific causative link could not be established by our experimental approach at this stage, the results suggest a new mechanistic hypothesis that demands further in-depth functional studies.

scholarly journals Methods for addressing the protein-protein interaction between histone deacetylase 6 and ubiquitin

2017 ◽  
Author(s):  
Carolina dos S. Passos ◽  
Nathalie Deschamps ◽  
Yun Choi ◽  
Robert E. Cohen ◽  
Remo Perozzo ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Stress Response ◽  
Small Molecules ◽  
Histone Deacetylase ◽  
Protein Interaction ◽  
Potential Role ◽  
Histone Deacetylase 6 ◽  
Protein Protein Interaction ◽  
Binding Function

AbstractHistone deacetylase 6 (HDAC6) is a cytoplasmic HDAC isoform able to remove acetyl groups from cellular substrates such as α-tubulin. In addition to the two deacetylase domains, HDAC6 has a C-terminal zinc-finger ubiquitin (Ub)-binding domain (ZnF-UBP) able to recognize free Ub. HDAC6-Ub interaction is thought to function in regulating the elimination of misfolded proteins during stress response through the aggresome pathway. Small molecules inhibiting deacetylation by HDAC6 were shown to reduce aggresomes, but the interplay between HDAC6 catalytic activity and Ub-binding function is not fully understood. Here we describe two methods to measure the HDAC6-Ub interaction in vitro using full-length HDAC6. Both methods were effective for screening inhibitors of the HDAC6-Ub protein-protein interaction independently of the catalytic activity. Our results suggest a potential role for the HDAC6 deacetylase domains in modulating HDAC6-Ub interaction. This new aspect of HDAC6 regulation can be targeted to address the roles of HDAC6-Ub interaction in normal and disease conditions.

scholarly journals Mutational Definition of RNA-binding and Protein-Protein Interaction Domains of Heterogeneous Nuclear RNP C1

2000 ◽  
Vol 276 (10) ◽  
pp. 7681-7688 ◽  
Author(s):  
Lili Wan ◽  
Jeong-Kook Kim ◽  
Victoria W. Pollard ◽  
Gideon Dreyfuss
Keyword(s):  
Protein Interaction ◽  
Rna Binding ◽  
Protein Protein Interaction ◽  
Interaction Domains ◽  
Definition Of

scholarly journals CLUH regulates mitochondrial metabolism by controlling translation and decay of target mRNAs

2017 ◽  
Vol 216 (3) ◽  
pp. 675-693 ◽  
Author(s):  
Désirée Schatton ◽  
David Pla-Martin ◽  
Marie-Charlotte Marx ◽  
Henriette Hansen ◽  
Arnaud Mourier ◽  
...  
Keyword(s):  
Mitochondrial Function ◽  
Rna Binding ◽  
Metabolic Response ◽  
Mitochondrial Protein ◽  
Messenger Rnas ◽  
Mitochondrial Proteome ◽  
Metabolic Conditions ◽  
The Stability ◽  
Neonatal Transition ◽  
Energy Converting

Mitochondria are essential organelles that host crucial metabolic pathways and produce adenosine triphosphate. The mitochondrial proteome is heterogeneous among tissues and can dynamically change in response to different metabolic conditions. Although the transcriptional programs that govern mitochondrial biogenesis and respiratory function are well known, posttranscriptional regulatory mechanisms remain unclear. In this study, we show that the cytosolic RNA-binding protein clustered mitochondria homologue (CLUH) regulates the expression of a mitochondrial protein network supporting key metabolic programs required under nutrient deprivation. CLUH exerts its function by controlling the stability and translation of target messenger RNAs. In the absence of Cluh, mitochondria are severely depleted of crucial enzymes involved in catabolic energy-converting pathways. CLUH preserves oxidative mitochondrial function and glucose homeostasis, thus preventing death at the fetal–neonatal transition. In the adult liver, CLUH ensures maximal respiration capacity and the metabolic response to starvation. Our results shed new light on the posttranscriptional mechanisms controlling the expression of mitochondrial proteins and suggest novel strategies to tailor mitochondrial function to physiological and pathological conditions.

Molecular Genetic Analysis of Glucocorticoid Signaling Using the Cre/loxP System

2000 ◽  
Vol 381 (9-10) ◽  
pp. 961-964 ◽  
Author(s):  
Holger M. Reichardt ◽  
François Tronche ◽  
Anton Bauer ◽  
Günther Schütz
Keyword(s):  
Stress Response ◽  
Dna Binding ◽  
Gene Targeting ◽  
Protein Interaction ◽  
Molecular Genetic ◽  
Molecular Genetic Analysis ◽  
Emotional Behavior ◽  
Protein Protein Interaction ◽  
Stress Erythropoiesis ◽  
Physiological Processes

Abstract Glucocorticoids (GC) are involved in a plethora of physiological processes that range from the regulation of the stress response and the control of the immune system to modulation of behavior. Most GC effects are mediated by the glucocorticoid receptor (GR) via activation and repression of gene expression. Whereas in most cases activation requires DNA binding of the receptor, repression is usually mediated by protein-protein interaction with other transcription factors. To decipher the molecular mode of action of GR, mice were generated by gene targeting carrying a point mutation in one of the dimerization domains, thus abrogating DNA binding by GR. Analysis of these mice demonstrated that thymocyte apoptosis and stress erythropoiesis require the DNA binding-dependent function of GR, whereas lung development and the anti-inflammatory activity of GR are mediated by protein-protein interaction. Furthermore, to study the role of GC in the brain, mice were generated specifically lacking GR function in the nervous system. Using these mice we demonstrated that GR is essential for the regulation of the HPA-axis and the stress response, as well as for the control of emotional behavior. Taken together, gene targeting using the Cre/loxP system proved to be highly valuable for the analysis of both molecular mechanism and tissue-specific functions of the GR.

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