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The Journal of Cell Biology Oct 2023Mitochondria are highly dynamic double membrane-bound organelles that maintain their shape in part through fission and fusion. Mitochondrial fission is performed by a...
Mitochondria are highly dynamic double membrane-bound organelles that maintain their shape in part through fission and fusion. Mitochondrial fission is performed by a dynamin-related protein, Dnm1 (Drp1 in humans), that constricts and divides the mitochondria in a GTP hydrolysis-dependent manner. However, it is unclear whether factors inside mitochondria help coordinate the process and if Dnm1/Drp1 activity is sufficient to complete the fission of both mitochondrial membranes. Here, we identify an intermembrane space protein required for mitochondrial fission in yeast, which we propose to name Mdi1 (also named Atg44). Loss of Mdi1 causes mitochondrial hyperfusion due to defects in fission, but not the lack of Dnm1 recruitment to mitochondria. Mdi1 is conserved in fungal species, and its homologs contain an amphipathic α-helix, mutations of which disrupt mitochondrial morphology. One model is that Mdi1 distorts mitochondrial membranes to enable Dnm1 to robustly complete fission. Our work reveals that Dnm1 cannot efficiently divide mitochondria without the coordinated function of Mdi1 inside mitochondria.
Topics: Dynamins; Mitochondria; Mitochondrial Dynamics; Mitochondrial Membranes; Mitochondrial Proteins; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; GTP Phosphohydrolases
PubMed: 37540145
DOI: 10.1083/jcb.202303147 -
Journal of Pharmacological Sciences Mar 2024Upregulation of nitric oxide (NO) production contributes to the pathogenesis of numerous diseases via S-nitrosylation, a post-translational modification of proteins....
Upregulation of nitric oxide (NO) production contributes to the pathogenesis of numerous diseases via S-nitrosylation, a post-translational modification of proteins. This process occurs due to the oxidative reaction between NO and a cysteine thiol group; however, the extent of this reaction remains unknown. S-Nitrosylation of PRMT1, a major asymmetric arginine methyltransferase of histones and numerous RNA metabolic proteins, was induced by NO donor treatment. We found that nitrosative stress leads to S-nitrosylation of cysteine 119, located near the active site, and attenuates the enzymatic activity of PRMT1. Interestingly, RNA sequencing analysis revealed similarities in the changes in expression elicited by NO and PRMT1 inhibitors or knockdown. A comprehensive search for PRMT1 substrates using the proximity-dependent biotin identification method highlighted many known and new substrates, including RNA-metabolizing enzymes. To validate this result, we selected the RNA helicase DDX3 and demonstrated that arginine methylation of DDX3 is induced by PRMT1 and attenuated by NO treatment. Our results suggest the existence of a novel regulatory system associated with transcription and RNA metabolism via protein S-nitrosylation.
Topics: Protein-Arginine N-Methyltransferases; Arginine; Cysteine; Histones; RNA
PubMed: 38395522
DOI: 10.1016/j.jphs.2023.12.012 -
Saudi Journal of Biological Sciences Oct 2023The "A" protein plays an essential role in the pathogenicity and virulence of this bacterial species. To gain deeper insights into the protein's characteristics, we...
BACKGROUND
The "A" protein plays an essential role in the pathogenicity and virulence of this bacterial species. To gain deeper insights into the protein's characteristics, we conducted an in-depth analysis of its sequence and structure.
OBJECTIVE
This study aimed to unravel the underlying genetic and structural components that contribute to the protein's functional properties.
RESULTS
Utilizing various bioinformatics tools and techniques, we first examined the protein's primary sequence, identifying key amino acid residues and potential functional domains. Additionally, we employed computational modeling and simulation approaches to determine the tertiary structure of the "A" protein. Through this comprehensive analysis, we discovered novel features and interactions within the protein's structure, shedding light on its potential mechanisms of action. Furthermore, we investigated the protein's evolutionary conservation and compared it with related proteins from other bacterial species.
CONCLUSIONS
Overall, our findings provide valuable insights into the sequence and structure of the Staphylococcus aureus "A" protein, which may have implications for understanding its role in pathogenicity and guiding the development of novel therapeutic strategies.
PubMed: 37766889
DOI: 10.1016/j.sjbs.2023.103812 -
The Journal of Cell Biology Aug 2023In macroautophagy, cellular components are sequestered within autophagosomes and transported to lysosomes/vacuoles for degradation. Although phosphatidylinositol...
In macroautophagy, cellular components are sequestered within autophagosomes and transported to lysosomes/vacuoles for degradation. Although phosphatidylinositol 3-kinase complex I (PI3KCI) plays a pivotal role in the regulation of autophagosome biogenesis, little is known about how this complex localizes to the pre-autophagosomal structure (PAS). In Saccharomyces cerevisiae, PI3KCI is composed of PI3K Vps34 and conserved subunits Vps15, Vps30, Atg14, and Atg38. In this study, we discover that PI3KCI interacts with the vacuolar membrane anchor Vac8, the PAS scaffold Atg1 complex, and the pre-autophagosomal vesicle component Atg9 via the Atg14 C-terminal region, the Atg38 C-terminal region, and the Vps30 BARA domain, respectively. While the Atg14-Vac8 interaction is constitutive, the Atg38-Atg1 complex interaction and the Vps30-Atg9 interaction are enhanced upon macroautophagy induction depending on Atg1 kinase activity. These interactions cooperate to target PI3KCI to the PAS. These findings provide a molecular basis for PAS targeting of PI3KCI during autophagosome biogenesis.
Topics: Autophagosomes; Autophagy; Autophagy-Related Proteins; Membrane Proteins; Phosphatidylinositol 3-Kinases; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Vesicular Transport Proteins
PubMed: 37436710
DOI: 10.1083/jcb.202210017 -
The Journal of Cell Biology Aug 2023As eukaryotic cells progress through cell division, the nuclear envelope (NE) membrane must expand to accommodate the formation of progeny nuclei. In Saccharomyces...
As eukaryotic cells progress through cell division, the nuclear envelope (NE) membrane must expand to accommodate the formation of progeny nuclei. In Saccharomyces cerevisiae, closed mitosis allows visualization of NE biogenesis during mitosis. During this period, the SUMO E3 ligase Siz2 binds the inner nuclear membrane (INM) and initiates a wave of INM protein SUMOylation. Here, we show these events increase INM levels of phosphatidic acid (PA), an intermediate of phospholipid biogenesis, and are necessary for normal mitotic NE membrane expansion. The increase in INM PA is driven by the Siz2-mediated inhibition of the PA phosphatase Pah1. During mitosis, this results from the binding of Siz2 to the INM and dissociation of Spo7 and Nem1, a complex required for the activation of Pah1. As cells enter interphase, the process is then reversed by the deSUMOylase Ulp1. This work further establishes a central role for temporally controlled INM SUMOylation in coordinating processes, including membrane expansion, that regulate NE biogenesis during mitosis.
Topics: Cell Nucleus; Mitosis; Nuclear Envelope; Nuclear Proteins; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Sumoylation; Organelle Biogenesis
PubMed: 37398994
DOI: 10.1083/jcb.202208137 -
European Review For Medical and... Dec 2023Lipedema is an autosomal dominant genetic disease that mainly affects women. It is characterized by excess deposition of subcutaneous adipose tissue, pain, and anxiety....
OBJECTIVE
Lipedema is an autosomal dominant genetic disease that mainly affects women. It is characterized by excess deposition of subcutaneous adipose tissue, pain, and anxiety. The genetic and environmental etiology of lipedema is still largely unknown. Although considered a rare disease, this pathology has been suggested to be underdiagnosed or misdiagnosed as obesity or lymphedema. Steroid hormones seem to be involved in the pathogenesis of lipedema. Indeed, aldo-keto reductase family 1 member C1 (AKR1C1), a gene coding for a protein involved in steroid hormones metabolism, was the first proposed to be correlated with lipedema.
PATIENTS AND METHODS
In this study, we employed a molecular dynamics approach to assess the pathogenicity of AKR1C1 genetic variants found in patients with lipedema. Moreover, we combined information theory and structural bioinformatics to identify AKR1C1 polymorphisms from the gnomAD database that could predispose to the development of lipedema.
RESULTS
Three genetic variants in AKR1C1 found in patients with lipedema were disruptive to the protein's function. Furthermore, eight AKR1C1 variants found in the general population could predispose to the development of lipedema.
CONCLUSIONS
The results of this study provide evidence that AKR1C1 may be a key gene in lipedema pathogenesis, and that common polymorphisms could predispose to lipedema development.
Topics: Female; Humans; Hormones; Lipedema; Lymphedema; Steroids; Subcutaneous Fat
PubMed: 38112954
DOI: 10.26355/eurrev_202312_34698 -
Biomolecules Nov 2023mRNA-based therapeutics have been found to be a promising treatment strategy in immunotherapy, gene therapy, and cancer treatments. Effectiveness of mRNA therapeutics...
mRNA-based therapeutics have been found to be a promising treatment strategy in immunotherapy, gene therapy, and cancer treatments. Effectiveness of mRNA therapeutics depends on the level and duration of a desired protein's expression, which is determined by various - and -regulatory elements of the mRNA. Sequences of 5' and 3' untranslated regions (UTRs) are responsible for translational efficiency and stability of mRNA. An optimal combination of the regulatory sequences allows researchers to significantly increase the target protein's expression. Using both literature data and previously obtained experimental data, we chose six sequences of 5'UTRs (adenoviral tripartite leader [TPL], HBB, rabbit β-globin [Rabb], H4C2, Moderna, and Neo2) and five sequences of 3'UTRs (mtRNR-EMCV, mtRNR-AES, mtRNR-mtRNR, BioNTech, and Moderna). By combining them, we constructed 30 in vitro transcribed RNAs encoding firefly luciferase with various combinations of 5'- and 3'UTRs, and the resultant bioluminescence was assessed in the DC2.4 cell line at 4, 8, 24, and 72 h after transfection. The cellular data enabled us to identify the best seven combinations of 5'- and 3'UTRs, whose translational efficiency was then assessed in BALB/c mice. Two combinations of 5'- and 3'UTRs (5'Rabb-3'mtRNR-EMCV and 5'TPL-3'Biontech) led to the most pronounced increase in the luciferase amount in the in vivo experiment in mice. Subsequent analysis of the stability of the mRNA indicated that the increase in luciferase expression is explained primarily by the efficiency of translation, not by the number of RNA molecules. Altogether, these findings suggest that 5'UTR-and-3'UTR combinations 5'Rabb-3'mtRNR- EMCV and 5'TPL-3'Biontech lead to high expression of target proteins and may be considered for use in preventive and therapeutic modalities based on mRNA.
Topics: Mice; Animals; Rabbits; RNA, Messenger; 3' Untranslated Regions; Protein Biosynthesis; Transfection; 5' Untranslated Regions; Luciferases
PubMed: 38002359
DOI: 10.3390/biom13111677 -
NAR Genomics and Bioinformatics Mar 2024Molecular dynamics simulations generate trajectories that depict system's evolution in time and are analyzed visually and quantitatively. Commonly conducted analyses...
Molecular dynamics simulations generate trajectories that depict system's evolution in time and are analyzed visually and quantitatively. Commonly conducted analyses include RMSD, , RMSF, and more. However, those methods are all limited by their strictly statistical nature. Here we present trajectory maps, a novel method to analyze and visualize protein simulation courses intuitively and conclusively. By plotting protein's backbone movements during the simulation as a heatmap, trajectory maps provide new tools to directly visualize protein behavior over time, compare multiple simulations, and complement established methods. A user-friendly Python application developed for this purpose is presented, alongside detailed documentation for easy usage and implementation. The method's validation is demonstrated on three case studies. Considering its benefits, trajectory maps are expected to adopt broad application in obtaining and communicating meaningful results of protein molecular dynamics simulations in many associated fields such as biochemistry, structural biology, pharmaceutical research .
PubMed: 38226394
DOI: 10.1093/nargab/lqad114 -
The Journal of Biological Chemistry Aug 2023Transcription-coupled repair (TCR) is a subpathway of nucleotide excision repair (NER) that is regulated by multiple facilitators, such as Rad26, and repressors, such as...
Transcription-coupled repair (TCR) is a subpathway of nucleotide excision repair (NER) that is regulated by multiple facilitators, such as Rad26, and repressors, such as Rpb4 and Spt4/Spt5. How these factors interplay with each other and with core RNA polymerase II (RNAPII) remains largely unknown. In this study, we identified Rpb7, an essential RNAPII subunit, as another TCR repressor and characterized its repression of TCR in the AGP2, RPB2, and YEF3 genes, which are transcribed at low, moderate, and high rates, respectively. The Rpb7 region that interacts with the KOW3 domain of Spt5 represses TCR largely through the same common mechanism as Spt4/Spt5, as mutations in this region mildly enhance the derepression of TCR by spt4Δ only in the YEF3 gene but not in the AGP2 or RPB2 gene. The Rpb7 regions that interact with Rpb4 and/or the core RNAPII repress TCR largely independently of Spt4/Spt5, as mutations in these regions synergistically enhance the derepression of TCR by spt4Δ in all the genes analyzed. The Rpb7 regions that interact with Rpb4 and/or the core RNAPII may also play positive roles in other (non-NER) DNA damage repair and/or tolerance mechanisms, as mutations in these regions can cause UV sensitivity that cannot be attributed to derepression of TCR. Our study reveals a novel function of Rpb7 in TCR regulation and suggests that this RNAPII subunit may have broader roles in DNA damage response beyond its known function in transcription.
Topics: DNA Repair; Peptide Elongation Factors; Receptors, Antigen, T-Cell; RNA Polymerase II; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Transcription, Genetic
PubMed: 37380080
DOI: 10.1016/j.jbc.2023.104969 -
Hematology Reports Dec 2023Platelet "Microvesicles" (MVs) are studied for their role in blood coagulation and inflammation. The study aimed to establish if MVs are related to age, plasma levels of...
BACKGROUND
Platelet "Microvesicles" (MVs) are studied for their role in blood coagulation and inflammation. The study aimed to establish if MVs are related to age, plasma levels of inflammation, coagulation, and fibrinolysis markers in healthy individuals.
METHODS
We prospectively enrolled volunteers aged over 18 years. MVs, plasma levels of C-reactive protein (CRP), Interleukin 6 (IL-6), Interleukin 10 (IL-10), Interleukin 17 (IL-17), and transforming growth factor β (TGF-β), fibrinogen, plasminogen activator inhibitor-1 (PAI-1), von Willebrand factor (VWF), homocysteine, factor VII (FVII), thrombin activatable fibrinolysis inhibitor (TAFI), and Protein S were tested.
RESULTS
A total of 246 individuals (median age 65 years ("IQR"54-72)) were evaluated. Both univariate analysis and logistic regression models showed that MVs positively correlate with age, CRP, IL-6, IL-10, IL-17, TGF-β, fibrinogen, PAI-1, VWF, FVII, and homocysteine, while inversely correlating with TAFI and Protein S. The ROC curve analysis performed to identify a cut off for MV values (700 kMP) showed a good accuracy with over-range cytokines fibrinolysis factor and coagulation markers.
CONCLUSIONS
To the best of our knowledge, this study is the first to correlate MVs with an entire panel of cardiovascular risk factors in healthy individuals. A future possible role of MVs in screening exams is suggested.
PubMed: 38132277
DOI: 10.3390/hematolrep15040069