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Computational and Structural... 2020Puromycin is a naturally occurring aminonucleoside antibiotic that inhibits protein synthesis by ribosome-catalyzed incorporation into the C-terminus of elongating... (Review)
Review
Puromycin is a naturally occurring aminonucleoside antibiotic that inhibits protein synthesis by ribosome-catalyzed incorporation into the C-terminus of elongating nascent chains, blocking further extension and resulting in premature termination of translation. It is most commonly known as a selection marker for cell lines genetically engineered to express a resistance transgene, but its additional uses as a probe for protein synthesis have proven invaluable across a wide variety of model systems, ranging from purified ribosomes and cell-free translation to intact cultured cells and whole animals. Puromycin is comprised of a nucleoside covalently bound to an amino acid, mimicking the 3' end of aminoacylated tRNAs that participate in delivery of amino acids to elongating ribosomes. Both moieties can tolerate some chemical substitutions and modifications without significant loss of activity, generating a diverse toolbox of puromycin-based reagents with added functionality, such as biotin for affinity purification or fluorophores for fluorescent microscopy detection. These reagents, as well as anti-puromycin antibodies, have played a pivotal role in advancing our understanding of the regulation and dysregulation of protein synthesis in normal and pathological processes, including immune response and neurological function. This manuscript reviews the current state of puromycin-based research, including structure and mechanism of action, relevant derivatives, use in advanced methodologies and some of the major insights generated using such techniques both in the lab and the clinic.
PubMed: 32435426
DOI: 10.1016/j.csbj.2020.04.014 -
PloS One 2023Puromycin-sensitive aminopeptidase (E.C. 3.4.11.14, UniProt P55786), a zinc metallopeptidase belonging to the M1 family, degrades a number of bioactive peptides as well...
Puromycin-sensitive aminopeptidase (E.C. 3.4.11.14, UniProt P55786), a zinc metallopeptidase belonging to the M1 family, degrades a number of bioactive peptides as well as peptides released from the proteasome, including polyglutamine. We report the crystal structure of PSA at 2.3 Ǻ. Overall, the enzyme adopts a V-shaped architecture with four domains characteristic of the M1 family aminopeptidases, but it is in a less compact conformation compared to most M1 enzymes of known structure. A microtubule binding sequence is present in a C-terminal HEAT repeat domain of the enzyme in a position where it might serve to mediate interaction with tubulin. In the catalytic metallopeptidase domain, an elongated active site groove lined with aromatic and hydrophobic residues and a large S1 subsite may play a role in broad substrate recognition. The structure with bound polyglutamine shows a possible interacting mode of this peptide, which is supported by mutation.
Topics: Aminopeptidases; Peptides; Metalloproteases; Binding Sites; Substrate Specificity
PubMed: 37440518
DOI: 10.1371/journal.pone.0287086 -
Brain Research Bulletin Apr 2021Memory formation is a fundamental function of the nervous system that enables the experience-based adaptation of behaviour. The formation, recall and updating of... (Review)
Review
Memory formation is a fundamental function of the nervous system that enables the experience-based adaptation of behaviour. The formation, recall and updating of long-term memory (LTM) requires new protein synthesis through its direct involvement in neuronal processes, such as long-term potentiation (LTP), long-term depression (LTD) and synaptic scaling. We discuss the advantages and limitations of several emerging techniques which enable the tagging of newly synthesised proteins, including stable isotope labelling with amino acids in cell culture (SILAC), puromycin labelling, and non-canonical amino acid (NCAA) labelling. We further present how these methods allow for the identification and visualisation of proteins which are newly synthesised during different stages of memory formation. These emerging techniques will continue to expand our understanding of how memories are formed, consolidated and retrieved.
Topics: Animals; Brain; Hippocampus; Memory, Long-Term; Neuronal Plasticity; Proteomics; Synapses
PubMed: 33465403
DOI: 10.1016/j.brainresbull.2020.12.015 -
Animal Cells and Systems 2023Puromycin treatment can cause glomerular injury to the kidney, leading to proteinuria. However, the pathogenesis of acute kidney injury and subsequent regeneration after...
Puromycin treatment can cause glomerular injury to the kidney, leading to proteinuria. However, the pathogenesis of acute kidney injury and subsequent regeneration after puromycin administration in animal models remain unclear. In this work, we examined the characteristics of kidney injury and subsequent regeneration following puromycin treatment in adult zebrafish. We intraperitoneally injected 100 μg of puromycin into zebrafish; sacrificed them at 1, 3, 5, 7, or 14 days post-injection (dpi); and examined the morphological, functional, and molecular changes in the kidney. Puromycin-treated zebrafish presented more rapid clearance of rhodamine dextran than control animals. Morphological changes were observed immediately after the puromycin injection (1-7 dpi) and had recovered by 14 dpi. The mRNA production of , a renal progenitor marker, increased during recovery from kidney injury. Levels of NFκB, TNFα, Nampt, and p-ERK increased significantly during nephron injury and regeneration, and Sirt1, FOXO1, pax2, and wt1b showed an increasing tendency. However, TGF-β1 and smad5 production did not show any changes after puromycin treatment. This study provides evidence that puromycin-induced injury in adult zebrafish kidneys is a potential tool for evaluating the mechanism of nephron injury and subsequent regeneration.
PubMed: 37089626
DOI: 10.1080/19768354.2023.2203211 -
Current Opinion in Chemical Biology Feb 2022Tight regulation of protein translation drives the proteome to undergo changes under influence of extracellular or intracellular signals. Despite mass spectrometry-based... (Review)
Review
Tight regulation of protein translation drives the proteome to undergo changes under influence of extracellular or intracellular signals. Despite mass spectrometry-based proteomics being an excellent method to study differences in protein abundance in complex proteomes, analyzing minute or rapid changes in protein synthesis and abundance remains challenging. Therefore, several dedicated techniques to directly detect and quantify newly synthesized proteins have been developed, notably puromycin-based, bio-orthogonal noncanonical amino acid tagging-based, and stable isotope labeling by amino acids in cell culture-based methods, combined with mass spectrometry. These techniques have enabled the investigation of perturbations, stress, or stimuli on protein synthesis. Improvements of these methods are still necessary to overcome various remaining limitations. Recent improvements include enhanced enrichment approaches and combinations with various stable isotope labeling techniques, which allow for more accurate analysis and comparison between conditions on shorter timeframes and in more challenging systems. Here, we aim to review the current state in this field.
Topics: Amino Acids; Isotope Labeling; Mass Spectrometry; Proteome; Proteomics
PubMed: 34364788
DOI: 10.1016/j.cbpa.2021.07.001 -
Nephrology, Dialysis, Transplantation :... Jun 2024Glucocorticoids are the treatment of choice for proteinuric patients with minimal change disease (MCD) and primary focal segmental glomerulosclerosis (FSGS)....
BACKGROUND
Glucocorticoids are the treatment of choice for proteinuric patients with minimal change disease (MCD) and primary focal segmental glomerulosclerosis (FSGS). Immunosuppressive as well as direct effects on podocytes are believed to mediate their actions. In this study, we analyzed the anti-proteinuric effects of inhibition of the glucocorticoid receptor (GR) in glomerular epithelial cells, including podocytes.
METHODS
We employed genetic and pharmacological approaches to inhibit the GR. Genetically, we used Pax8-Cre/GRfl/fl mice to specifically inactivate the GR in kidney epithelial cells. Pharmacologically, we utilized a glucocorticoid antagonist called mifepristone.
RESULTS
Genetic inactivation of GR, specifically in kidney epithelial cells, using Pax8-Cre/GRfl/fl mice, ameliorated proteinuria following protein overload. We further tested the effects of pharmacological GR inhibition in three models and species: the puromycin aminonucleoside-induced nephrosis model in rats, the protein overload model in mice and the inducible transgenic NTR/MTZ zebrafish larvae with specific and reversible podocyte injury. In all three models, both pharmacological GR activation and inhibition consistently and significantly ameliorated proteinuria. Additionally, we translated our findings to humans, where three nephrotic adult patients with MCD or primary FSGS with contraindications or insufficient responses to corticosteroids were treated with mifepristone. This treatment resulted in a clinically relevant reduction of proteinuria.
CONCLUSIONS
Thus, across multiple species and proteinuria models, both genetic and pharmacological GR inhibition was at least as effective as pronounced GR activation. While the mechanism remains perplexing, GR inhibition may be a novel and targeted therapeutic approach to treat glomerular proteinuria potentially bypassing adverse actions of steroids.
Topics: Animals; Receptors, Glucocorticoid; Mice; Proteinuria; Humans; Rats; Podocytes; Zebrafish; Male; Mifepristone; Disease Models, Animal; Glomerulosclerosis, Focal Segmental; Female; Kidney Diseases; Puromycin Aminonucleoside; Hormone Antagonists; Nephrosis, Lipoid; Mice, Inbred C57BL; Mice, Transgenic
PubMed: 38037533
DOI: 10.1093/ndt/gfad254 -
Small Methods Jul 2023Viral-mediated delivery of the CRISPR-Cas9 system is one the most commonly used techniques to modify the genome of a cell, with the aim of analyzing the function of the...
Viral-mediated delivery of the CRISPR-Cas9 system is one the most commonly used techniques to modify the genome of a cell, with the aim of analyzing the function of the targeted gene product. While these approaches are rather straightforward for membrane-bound proteins, they can be laborious for intracellular proteins, given that selection of full knockout (KO) cells often requires the amplification of single-cell clones. Moreover, viral-mediated delivery systems, besides the Cas9 and gRNA, lead to the integration of unwanted genetic material, such as antibiotic resistance genes, introducing experimental biases. Here, an alternative non-viral delivery approach is presented for CRISPR/Cas9, allowing efficient and flexible selection of KO polyclonal cells. This all-in-one mammalian CRISPR-Cas9 expression vector, ptARgenOM, encodes the gRNA and the Cas9 linked to a ribosomal skipping peptide sequence followed by the enhanced green fluorescent protein and the puromycin N-acetyltransferase, allowing for transient, expression-dependent selection and enrichment of isogenic KO cells. After evaluation using more than 12 distinct targets in 6 cell lines, ptARgenOM is found to be efficient in producing KO cells, reducing the time required to obtain a polyclonal isogenic cell line by 4-6 folds. Altogether ptARgenOM provides a simple, fast, and cost-effective delivery tool for genome editing.
Topics: Animals; CRISPR-Cas Systems; Gene Editing; Cell Line; Mammals
PubMed: 37156748
DOI: 10.1002/smtd.202300069 -
IScience Jul 2022Cellular global translation is often measured using ribosome profiling or quantitative mass spectrometry, but these methods do not provide direct information at the...
Cellular global translation is often measured using ribosome profiling or quantitative mass spectrometry, but these methods do not provide direct information at the level of elongating nascent polypeptide chains (NPCs) and associated co-translational events. Here, we describe pSNAP, a method for proteome-wide profiling of NPCs by affinity enrichment of puromycin- and stable isotope-labeled polypeptides. pSNAP does not require ribosome purification and/or chemical labeling, and captures NPCs that characteristically exhibit protein N-terminus-biased positions. We applied pSNAP to evaluate the effect of silmitasertib, a potential molecular therapy for cancer, and revealed acute translational repression through casein kinase II and mTOR pathways. We also characterized modifications on NPCs and demonstrated that the combination of different types of modifications, such as acetylation and phosphorylation in the N-terminal region of histone H1.5, can modulate interactions with ribosome-associated factors. Thus, pSNAP provides a framework for dissecting co-translational regulations on a proteome-wide scale.
PubMed: 35754732
DOI: 10.1016/j.isci.2022.104516 -
FEBS Open Bio Jun 2021In this issue of FEBS Open Bio, Shen Li et al., in the laboratory of Hector L. Franco (University of North Carolina), provide a proof-of-principle solution for...
In this issue of FEBS Open Bio, Shen Li et al., in the laboratory of Hector L. Franco (University of North Carolina), provide a proof-of-principle solution for correcting all copies of a gene in the widely used MCF7 breast cancer cell line. The gene for the FOXA1 pioneer transcription factor is localised on chromosome 14, which is present at least 4-5 times in MCF7 cells. To achieve their goal, the authors used a 'classical' version of the CRISPR/Cas9 system. Both sgRNA and Cas9 components were expressed from a single vector, which also has a puromycin resistance cassette; this is an essential module for the chosen strategy, because it ensures expression of both sgRNA and Cas9 in selected cells. A targeting template in the form of nonlinearised plasmid was shown to have the best efficiency and was used to introduce a substitution at position 295 in the gene encoding FOXA1 to change a codon encoding lysine into a codon encoding glutamine (K295Q). The strategy suggested by Li and co-authors is an important development towards genome editing of multiple copy genes in a polyploid environment like cancer cells. One important application of the technique could be in creating models to study the role of single nucleotide polymorphisms in cancer progression and metastasis. Isogenic cancer lines carrying polymorphic variants of key drug targets could be used to optimise anticancer treatment protocols, laying a foundation for personalised therapy.
Topics: CRISPR-Cas Systems; Gene Editing; Plasmids
PubMed: 34060719
DOI: 10.1002/2211-5463.13195 -
Laboratory Investigation; a Journal of... Jul 2019High-density lipoprotein (HDL) and its main protein, apolipoprotein AI (apoAI), have established benefits in various cells, but whether these cytoprotective effects of...
High-density lipoprotein (HDL) and its main protein, apolipoprotein AI (apoAI), have established benefits in various cells, but whether these cytoprotective effects of HDL pertain to renal cells is unclear. We investigated the in vitro consequences of exposing damaged podocytes to normal apoAI, HDL, and apoAI mimetic (L-4F), and the in vivo effects of L-4F on kidney and atherosclerotic injury in a podocyte-specific injury model of proteinuria. In vitro, primary mouse podocytes were injured by puromycin aminonucleoside (PAN). Cellular viability, migration, production of reactive oxygen species (ROS), apoptosis, and the underlying signaling pathway were assessed. In vivo, we used a proteinuric model, Nphs1-hCD25 transgenic (NEP25) mice, which express human CD25 on podocytes. Podocyte injury was induced by using immunotoxin (LMB2) and generated a proteinuric atherosclerosis model, NEP25:apoE mice, was generated by mating apoE-deficient (apoE) mice with NEP25 mice. Animals received L-4F or control vehicle. Renal function, podocyte injury, and atherosclerosis were assessed. PAN reduced podocyte viability, migration, and increased ROS production, all significantly lessened by apoAI, HDL, and L-4F. L-4F attenuated podocyte apoptosis and diminished PAN-induced inactivation of Janus family protein kinase-2/signal transducers and activators of transcription 3. In NEP25 mice, L-4F significantly lessened overall proteinuria, and preserved podocyte expression of synaptopodin and cell density. Proteinuric NEP25:apoE mice had more atherosclerosis than non-proteinuric apoE mice, and these lesions were significantly decreased by L-4F. Normal human apoAI, HDL, and apoAI mimetic protect against podocyte damage. ApoAI mimetic provides in vivo beneficial effects on podocytes that culminate in reduced albuminuria and atherosclerosis. The results suggest supplemental apoAI/apoAI mimetic may be a novel candidate to lessen podocyte damage and its complications.
Topics: Animals; Apolipoprotein A-I; Cells, Cultured; Humans; Interleukin-2 Receptor alpha Subunit; Kidney Diseases; Kidney Glomerulus; Lipoproteins, HDL; Mice; Mice, Transgenic; Podocytes; Protective Agents; Proteinuria; Puromycin Aminonucleoside
PubMed: 31019291
DOI: 10.1038/s41374-019-0253-6