-
Cells Dec 2020The biogenesis and function of eukaryotic cytochrome oxidase or mitochondrial respiratory chain complex IV (CIV) undergo several levels of regulation to adapt to... (Review)
Review
The biogenesis and function of eukaryotic cytochrome oxidase or mitochondrial respiratory chain complex IV (CIV) undergo several levels of regulation to adapt to changing environmental conditions. Adaptation to hypoxia and oxidative stress involves CIV subunit isoform switch, changes in phosphorylation status, and modulation of CIV assembly and enzymatic activity by interacting factors. The latter include the Hypoxia Inducible Gene Domain (HIGD) family yeast respiratory supercomplex factors 1 and 2 (Rcf1 and Rcf2) and two mammalian homologs of Rcf1, the proteins HIGD1A and HIGD2A. Whereas Rcf1 and Rcf2 are expressed constitutively, expression of HIGD1A and HIGD2A is induced under stress conditions, such as hypoxia and/or low glucose levels. In both systems, the HIGD proteins localize in the mitochondrial inner membrane and play a role in the biogenesis of CIV as a free unit or as part as respiratory supercomplexes. Notably, they remain bound to assembled CIV and, by modulating its activity, regulate cellular respiration. Here, we will describe the current knowledge regarding the specific and overlapping roles of the several HIGD proteins in physiological and stress conditions.
Topics: Animals; Cell Survival; Cytochromes c; Electron Transport Complex IV; Gene Expression Regulation, Enzymologic; Glucose; Humans; Hypoxia; Intracellular Signaling Peptides and Proteins; Mice; Mitochondrial Membranes; Mitochondrial Proteins; Oxidative Stress; Phosphorylation; Phylogeny; Protein Domains; Protein Isoforms; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
PubMed: 33291261
DOI: 10.3390/cells9122620 -
The Plant Journal : For Cell and... Feb 2022Plants have a diurnal separation of metabolic fluxes and a need for differential maintenance of protein machinery in the day and night. To directly assess the output of...
Plants have a diurnal separation of metabolic fluxes and a need for differential maintenance of protein machinery in the day and night. To directly assess the output of the translation process and to estimate the ATP investment involved, the individual rates of protein synthesis and degradation of hundreds of different proteins need to be measured simultaneously. We quantified protein synthesis and degradation through pulse labelling with heavy hydrogen in Arabidopsis thaliana rosettes to allow such an assessment of ATP investment in leaf proteome homeostasis on a gene-by-gene basis. Light-harvesting complex proteins were synthesised and degraded much faster in the day (approximately 10:1), while carbon metabolism and vesicle trafficking components were translated at similar rates day or night. Few leaf proteins changed in abundance between the day and the night despite reduced protein synthesis rates at night, indicating that protein degradation rates are tightly coordinated. The data reveal how the pausing of photosystem synthesis and degradation at night allows the redirection of a decreased energy budget to a selective night-time maintenance schedule.
Topics: Arabidopsis; Arabidopsis Proteins; Carbon; Carbon Dioxide; Gene Expression Regulation, Plant; Isotope Labeling; Metabolic Networks and Pathways; Plant Leaves; Protein Biosynthesis; Proteolysis
PubMed: 34997626
DOI: 10.1111/tpj.15661 -
Current Opinion in Structural Biology Aug 2022Tail-anchored (TA) proteins are a biologically significant class of membrane proteins, which require specialised cellular pathways to insert their single C-terminal... (Review)
Review
Tail-anchored (TA) proteins are a biologically significant class of membrane proteins, which require specialised cellular pathways to insert their single C-terminal transmembrane domain into the correct membrane. Cryo-electron microscopy has recently provided new insights into the organelle-specific machineries for TA protein biogenesis. Structures of targeting and insertase complexes within the canonical guided entry of TA proteins (GET) pathway indicate how substrates are faithfully chaperoned into the endoplasmic reticulum (ER) membrane in metazoans. The core of the GET insertase is conserved within structures of the ER membrane protein complex (EMC), which acts in parallel to insert a different subset of TA proteins. Furthermore, structures of the dislocases Spf1 and Msp1 show how they remove mislocalised TA proteins from the ER and outer mitochondrial membranes respectively.
Topics: ATP-Binding Cassette Transporters; Adenosine Triphosphatases; Cryoelectron Microscopy; Endoplasmic Reticulum; Membrane Proteins; Protein Transport; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
PubMed: 35850079
DOI: 10.1016/j.sbi.2022.102428 -
Cells Oct 2021Neuronal precursor cell-expressed developmentally down-regulated protein 8 (NEDD8) is a ubiquitin-like protein (UBL) whose canonical function involves binding to, and... (Review)
Review
Neuronal precursor cell-expressed developmentally down-regulated protein 8 (NEDD8) is a ubiquitin-like protein (UBL) whose canonical function involves binding to, and thus, activating Cullin-Ring finger Ligases (CRLs), one of the largest family of ubiquitin ligases in the eukaryotic cell. However, in recent years, several non-canonical protein substrates of NEDD8 have been identified. Here we attempt to review the recent literature regarding non-canonical NEDDylation of substrates with a particular focus on how the covalent modification of NEDD8 alters the protein substrate. Like much in the study of ubiquitin and UBLs, there are no clear and all-encompassing explanations to satisfy the textbooks. In some instances, NEDD8 modification appears to alter the substrates localization, particularly during times of stress. NEDDylation may also have conflicting impacts upon a protein's stability: some reports indicate NEDDylation may protect against degradation whereas others show NEDDylation can promote degradation. We also examine how many of the in vitro studies measuring non-canonical NEDDylation were conducted and compare those conditions to those which may occur in vivo, such as cancer progression. It is likely that the conditions used to study non-canonical NEDDylation are similar to some types of cancers, such as glioblastoma, colon and rectal cancers, and lung adenocarcinomas. Although the full outcomes of non-canonical NEDDylation remain unknown, our review of the literature suggests that researchers keep an open mind to the situations where this modification occurs and determine the functional impacts of NEDD8-modification to the specific substrates which they study.
Topics: Animals; Humans; NEDD8 Protein; Protein Stability; Proteolysis; Proteomics; Ribosomal Proteins; Substrate Specificity
PubMed: 34685640
DOI: 10.3390/cells10102660 -
Comptes Rendus Biologies Apr 2023Detection of cytosolic pathological nucleic acids is a key step for the initiation of innate immune responses. In the past decade, the stimulator of interferon genes... (Review)
Review
Detection of cytosolic pathological nucleic acids is a key step for the initiation of innate immune responses. In the past decade, the stimulator of interferon genes (STING) adaptor protein has emerged as a central platform enabling the activation of inflammatory responses in the presence of cytosolic DNAs. This has prompted a plethora of approaches aiming at modulating STING activation in order to boost or inhibit inflammatory responses. However, recent work has revealed that STING is also a direct regulator of metabolic homeostasis. In particular, STING regulates lipid metabolism directly, a function that is conserved throughout evolution. This indicates that STING targeting strategies must take into consideration potential metabolic side effects that may alter disease course, but also suggests that targeting STING may open the route to novel treatments for metabolic disorders. Here we discuss recent work describing the metabolic function of STING and the implications of these findings.
Topics: Lipid Metabolism; Membrane Proteins; Immunity, Innate; DNA
PubMed: 37254782
DOI: 10.5802/crbiol.110 -
ACS Chemical Biology Jan 2023The proteolysis targeting chimera (PROTAC) strategy results in the down-regulation of unwanted protein(s) for disease treatment. In the PROTAC process, a...
The proteolysis targeting chimera (PROTAC) strategy results in the down-regulation of unwanted protein(s) for disease treatment. In the PROTAC process, a heterobifunctional degrader forms a ternary complex with a target protein of interest (POI) and an E3 ligase, which results in ubiquitination and proteasomal degradation of the POI. While ternary complex formation is a key attribute of PROTAC degraders, modification of the PROTAC molecule to optimize ternary complex formation and protein degradation can be a labor-intensive and tedious process. In this study, we take advantage of DNA-encoded library (DEL) technology to efficiently synthesize a vast number of possible PROTAC molecules and describe a parallel screening approach that utilizes DNA barcodes as reporters of ternary complex formation and cooperative binding. We use a designed PROTAC DEL against BRD4 and CRBN to describe a dual protein affinity selection method and the direct discovery of novel, potent BRD4 PROTACs that importantly demonstrate clear SAR. Such an approach evaluates all the potential PROTACs simultaneously, avoids the interference of PROTAC solubility and permeability, and uses POI and E3 ligase proteins in an efficient manner.
Topics: Nuclear Proteins; Transcription Factors; Ubiquitin-Protein Ligases; Ubiquitination; Proteolysis
PubMed: 36606710
DOI: 10.1021/acschembio.2c00797 -
Proteins Nov 2019The growing body of experimental and computational data describing how proteins interact with each other has emphasized the multiplicity of protein interactions and the...
The growing body of experimental and computational data describing how proteins interact with each other has emphasized the multiplicity of protein interactions and the complexity underlying protein surface usage and deformability. In this work, we propose new concepts and methods toward deciphering such complexity. We introduce the notion of interacting region to account for the multiple usage of a protein's surface residues by several partners and for the variability of protein interfaces coming from molecular flexibility. We predict interacting patches by crossing evolutionary, physicochemical and geometrical properties of the protein surface with information coming from complete cross-docking (CC-D) simulations. We show that our predictions match well interacting regions and that the different sources of information are complementary. We further propose an indicator of whether a protein has a few or many partners. Our prediction strategies are implemented in the dynJET algorithm and assessed on a new dataset of 262 protein on which we performed CC-D. The code and the data are available at: http://www.lcqb.upmc.fr/dynJET2/.
Topics: Algorithms; Animals; Binding Sites; Humans; Molecular Docking Simulation; Protein Binding; Protein Conformation; Protein Interaction Domains and Motifs; Protein Interaction Mapping; Protein Interaction Maps; Proteins; Software
PubMed: 31199528
DOI: 10.1002/prot.25757 -
Mitochondrion Jul 2020The biological function of plant mitochondrial uncoupling proteins (pUCPs) has been a matter of considerable controversy. For example, the pUCP capacity to uncouple... (Review)
Review
The biological function of plant mitochondrial uncoupling proteins (pUCPs) has been a matter of considerable controversy. For example, the pUCP capacity to uncouple respiration from ATP synthesis in vivo has never been fully acknowledged, in contrast to the mammalian UCP1 (mUCP1) role in uncoupling respiration-mediated thermogenesis. Interestingly, both pUCPs and mUCPs have been associated with stress response and metabolic perturbations. Some central questions that remain are how pUCPs and mUCPs compare in biochemical properties, molecular structure and cell biology under physiological and metabolically perturbed conditions. This review takes advantage of the large amount of data available for mUCPs to review the biochemical properties, 3D structure models and potential physiological roles of pUCPs during plant development and response to stress. The biochemical properties and structure of pUCPs are revisited in light of the recent findings that pUCPs catalyse the transport of metabolites across the mitochondrial inner membrane and the resolved mUCP2 protein structure. Additionally, transcriptional regulation and co-expression networks of UCP orthologues across species are analysed, taking advantage of publicly available curated experimental datasets. Taking these together, the biological roles of pUCPs are analysed in the context of their potential roles in thermogenesis, ROS production, cell signalling and the regulation of plant cellular bioenergetics. Finally, pUCPs biological function is discussed in the context of their potential role in protecting against environmental stresses.
Topics: Energy Metabolism; Gene Expression Regulation, Plant; Mitochondrial Uncoupling Proteins; Models, Molecular; Plant Development; Plant Proteins; Plants; Protein Conformation; Stress, Physiological
PubMed: 32439620
DOI: 10.1016/j.mito.2020.05.001 -
Biochemical Society Transactions Feb 2020The post-translational modification protein S-acylation (commonly known as palmitoylation) plays a critical role in regulating a wide range of biological processes... (Review)
Review
The post-translational modification protein S-acylation (commonly known as palmitoylation) plays a critical role in regulating a wide range of biological processes including cell growth, cardiac contractility, synaptic plasticity, endocytosis, vesicle trafficking, membrane transport and biased-receptor signalling. As a consequence, zDHHC-protein acyl transferases (zDHHC-PATs), enzymes that catalyse the addition of fatty acid groups to specific cysteine residues on target proteins, and acyl proteins thioesterases, proteins that hydrolyse thioester linkages, are important pharmaceutical targets. At present, no therapeutic drugs have been developed that act by changing the palmitoylation status of specific target proteins. Here, we consider the role that palmitoylation plays in the development of diseases such as cancer and detail possible strategies for selectively manipulating the palmitoylation status of specific target proteins, a necessary first step towards developing clinically useful molecules for the treatment of disease.
Topics: Acyltransferases; Animals; B7-H1 Antigen; Cysteine; Drug Discovery; Humans; Lipoylation; Mice; Neoplasms; Palmitoyl-CoA Hydrolase; Protein Processing, Post-Translational; Receptor, Melanocortin, Type 1; ras Proteins
PubMed: 31872231
DOI: 10.1042/BST20190707 -
The Journal of Biological Chemistry Jan 2024Intermediary metabolites and flux through various pathways have emerged as key determinants of post-translational modifications. Independently, dynamic fluctuations in...
Intermediary metabolites and flux through various pathways have emerged as key determinants of post-translational modifications. Independently, dynamic fluctuations in their concentrations are known to drive cellular energetics in a bi-directional manner. Notably, intracellular fatty acid pools that drastically change during fed and fasted states act as precursors for both ATP production and fatty acylation of proteins. Protein fatty acylation is well regarded for its role in regulating structure and functions of diverse proteins; however, the effect of intracellular concentrations of fatty acids on protein modification is less understood. In this regard, we unequivocally demonstrate that metabolic contexts, viz. fed and fasted states, dictate the extent of global fatty acylation. Moreover, we show that presence or absence of glucose that influences cellular and mitochondrial uptake/utilization of fatty acids and affects palmitoylation and oleoylation, which is consistent with their intracellular abundance in fed and fasted states. Employing complementary approaches including click-chemistry, lipidomics, and imaging, we show the top-down control of cellular metabolic state. Importantly, our results establish the crucial role of mitochondria and retrograde signaling components like SIRT4, AMPK, and mTOR in orchestrating protein fatty acylation at a whole cell level. Specifically, pharmacogenetic perturbations that alter either mitochondrial functions and/or retrograde signaling affect protein fatty acylation. Besides illustrating the cross-talk between carbohydrate and lipid metabolism in mediating bulk post-translational modification, our findings also highlight the involvement of mitochondrial energetics.
Topics: Acylation; Adenosine Triphosphate; AMP-Activated Protein Kinases; Click Chemistry; Fasting; Fatty Acids; Glucose; Lipid Metabolism; Lipidomics; Lipoylation; Mitochondria; Mitochondrial Proteins; Protein Processing, Post-Translational; Proteins; Sirtuins; TOR Serine-Threonine Kinases
PubMed: 38101568
DOI: 10.1016/j.jbc.2023.105563