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Cell Feb 2024Chloroplasts are green plastids in the cytoplasm of eukaryotic algae and plants responsible for photosynthesis. The plastid-encoded RNA polymerase (PEP) plays an...
Chloroplasts are green plastids in the cytoplasm of eukaryotic algae and plants responsible for photosynthesis. The plastid-encoded RNA polymerase (PEP) plays an essential role during chloroplast biogenesis from proplastids and functions as the predominant RNA polymerase in mature chloroplasts. The PEP-centered transcription apparatus comprises a bacterial-origin PEP core and more than a dozen eukaryotic-origin PEP-associated proteins (PAPs) encoded in the nucleus. Here, we determined the cryo-EM structures of Nicotiana tabacum (tobacco) PEP-PAP apoenzyme and PEP-PAP transcription elongation complexes at near-atomic resolutions. Our data show the PEP core adopts a typical fold as bacterial RNAP. Fifteen PAPs bind at the periphery of the PEP core, facilitate assembling the PEP-PAP supercomplex, protect the complex from oxidation damage, and likely couple gene transcription with RNA processing. Our results report the high-resolution architecture of the chloroplast transcription apparatus and provide the structural basis for the mechanistic and functional study of transcription regulation in chloroplasts.
Topics: Chloroplasts; Cryoelectron Microscopy; DNA-Directed RNA Polymerases; Nicotiana; Photosynthesis; Plastids
PubMed: 38428393
DOI: 10.1016/j.cell.2024.01.026 -
Journal of Immunology (Baltimore, Md. :... Nov 2023Lipid accumulation in macrophages (Mφs) is a hallmark of atherosclerosis, yet how lipid accumulation affects inflammatory responses through rewiring of Mφ metabolism...
Oxidized Low-Density Lipoprotein Accumulation Suppresses Glycolysis and Attenuates the Macrophage Inflammatory Response by Diverting Transcription from the HIF-1α to the Nrf2 Pathway.
Lipid accumulation in macrophages (Mφs) is a hallmark of atherosclerosis, yet how lipid accumulation affects inflammatory responses through rewiring of Mφ metabolism is poorly understood. We modeled lipid accumulation in cultured wild-type mouse thioglycolate-elicited peritoneal Mφs and bone marrow-derived Mφs with conditional (Lyz2-Cre) or complete genetic deficiency of Vhl, Hif1a, Nos2, and Nfe2l2. Transfection studies employed RAW264.7 cells. Mφs were cultured for 24 h with oxidized low-density lipoprotein (oxLDL) or cholesterol and then were stimulated with LPS. Transcriptomics revealed that oxLDL accumulation in Mφs downregulated inflammatory, hypoxia, and cholesterol metabolism pathways, whereas the antioxidant pathway, fatty acid oxidation, and ABC family proteins were upregulated. Metabolomics and extracellular metabolic flux assays showed that oxLDL accumulation suppressed LPS-induced glycolysis. Intracellular lipid accumulation in Mφs impaired LPS-induced inflammation by reducing both hypoxia-inducible factor 1-α (HIF-1α) stability and transactivation capacity; thus, the phenotype was not rescued in Vhl-/- Mφs. Intracellular lipid accumulation in Mφs also enhanced LPS-induced NF erythroid 2-related factor 2 (Nrf2)-mediated antioxidative defense that destabilizes HIF-1α, and Nrf2-deficient Mφs resisted the inhibitory effects of lipid accumulation on glycolysis and inflammatory gene expression. Furthermore, oxLDL shifted NADPH consumption from HIF-1α- to Nrf2-regulated apoenzymes. Thus, we postulate that repurposing NADPH consumption from HIF-1α to Nrf2 transcriptional pathways is critical in modulating inflammatory responses in Mφs with accumulated intracellular lipid. The relevance of our in vitro models was established by comparative transcriptomic analyses, which revealed that Mφs cultured with oxLDL and stimulated with LPS shared similar inflammatory and metabolic profiles with foamy Mφs derived from the atherosclerotic mouse and human aorta.
Topics: Humans; Mice; Animals; NF-E2-Related Factor 2; Lipopolysaccharides; NADP; Macrophages; Lipoproteins, LDL; Glycolysis; Atherosclerosis; Hypercholesterolemia; Cholesterol; Antioxidants; Hypoxia-Inducible Factor 1, alpha Subunit
PubMed: 37756544
DOI: 10.4049/jimmunol.2300293 -
Journal of Medical Virology Feb 2024Cap RNA methylations play important roles in the replication, evasion of host RNA sensor recognition, and pathogenesis. Coronaviruses possess both guanine N7- and...
Cap RNA methylations play important roles in the replication, evasion of host RNA sensor recognition, and pathogenesis. Coronaviruses possess both guanine N7- and 2'-O-ribose methyltransferases (N7-MTase and 2'-O-MTase) encoded by nonstructural protein (nsp) 14 and nsp16/10 complex, respectively. In this study, we reconstituted the two-step RNA methylations of N7-MTase and 2'-O-MTase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in vitro and demonstrated its common and different features in comparison with that of SARS-CoV. We revealed that the nsp16/10 2'-O-MTase of SARS-CoV-2 has a broader substrate selectivity than the counterpart of SARS-CoV and can accommodate both unmethylated and uncapped RNA substrates in a sequence-independent manner. Most intriguingly, the substrate selectivity of nsp16/10 complex is not determined by the apoenzyme of nsp16 MTase but by its cofactor nsp10. These results provide insight into the unique features of SARS-CoV-2 MTases and may help develop strategies to precisely intervene in the methylation pathway and pathogenesis of SARS-CoV-2.
Topics: Humans; Methyltransferases; SARS-CoV-2; COVID-19; RNA Methylation; RNA Caps
PubMed: 38285434
DOI: 10.1002/jmv.29411 -
International Journal of Molecular... Mar 2024Enzymes reliant on pyridoxal 5'-phosphate (PLP), the metabolically active form of vitamin B, hold significant importance in both biology and medicine. They facilitate... (Review)
Review
Enzymes reliant on pyridoxal 5'-phosphate (PLP), the metabolically active form of vitamin B, hold significant importance in both biology and medicine. They facilitate various biochemical reactions, particularly in amino acid and neurotransmitter metabolisms. Vitamin B is absorbed by organisms in its non-phosphorylated form and phosphorylated within cells via pyridoxal kinase (PLK) and pyridox-(am)-ine 5'-phosphate oxidase (PNPOx). The flavin mononucleotide-dependent PNPOx enzyme converts pyridoxine 5'-phosphate and pyridoxamine 5'-phosphate into PLP. PNPOx is vital for both biosynthesis and salvage pathways in organisms producing B vitamers. However, for those depending on vitamin B as a nutrient, PNPOx participates only in the salvage pathway. Transferring the PLP produced via PNPOx to client apo-enzymes is indispensable for their catalytic function, proper folding and targeting of specific organelles. PNPOx activity deficiencies due to inborn errors lead to severe neurological pathologies, particularly neonatal epileptic encephalopathy. PNPOx maintains PLP homeostasis through highly regulated mechanisms, including structural alterations throughout the catalytic cycle and allosteric PLP binding, influencing substrate transformation at the active site. Elucidation at the molecular level of the mechanisms underlying PNPOx activity deficiencies is a requirement to develop personalized approaches to treat related disorders. Finally, despite shared features, the few PNPOx enzymes molecularly and functionally studied show species-specific regulatory properties that open the possibility of targeting it in pathogenic organisms.
Topics: Humans; Infant, Newborn; Oxidoreductases; Phosphates; Pyridoxaminephosphate Oxidase; Pyridoxal Phosphate; Vitamin B 6; Pyridoxine; Metabolic Diseases; Vitamins
PubMed: 38542149
DOI: 10.3390/ijms25063174 -
Frontiers in Cellular and Infection... 2024Monkeypox or mpox virus (mpox) is a double-stranded DNA virus that poses a significant threat to global public health security. The F3 protein, encoded by mpox, is an...
BACKGROUND
Monkeypox or mpox virus (mpox) is a double-stranded DNA virus that poses a significant threat to global public health security. The F3 protein, encoded by mpox, is an apoenzyme believed to possess a double-stranded RNA-binding domain (dsRBD). However, limited research has been conducted on its function. In this study, we present data on the transcriptomics and proteomics of F3L-transfected HEK293T cells, aiming to enhance our comprehension of F3L.
METHODS
The gene expression profiles of pCAGGS-HA-F3L transfected HEK293T cells were analyzed using RNA-seq. Proteomics was used to identify and study proteins that interact with F3L. Real-time PCR was used to detect mRNA levels of several differentially expressed genes (DEGs) in HEK293T cells (or Vero cells) after the expression of F3 protein.
RESULTS
A total of 14,822 genes were obtained in cells by RNA-Seq and 1,672 DEGs were identified, including 1,156 up-regulated genes and 516 down-regulated genes. A total of 27 cellular proteins interacting with F3 proteins were identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS), and 19 cellular proteins with large differences in abundance ratios were considered to be candidate cellular proteins. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that the DEGs were significantly enriched in immune-related pathways, including type I interferon signaling pathway, response to virus, RIG-I-like receptor signaling pathway, NOD-like receptor signaling pathway, etc. Moreover, some selected DEGs were further confirmed by real-time PCR and the results were consistent with the transcriptome data. Proteomics data show that cellular proteins interacting with F3 proteins are mainly related to RNA splicing and protein translation.
CONCLUSIONS
Our analysis of transcriptomic and proteomic data showed that (1) F3L up-regulates the transcript levels of key genes in the innate immune signaling pathway, such as , and elicits a broad spectrum of antiviral immune responses in the host. F3L also increases the expression of the FOS and JNK genes while decreasing the expression of TNFR2, these factors may ultimately induce apoptosis. (2) F3 protein interacts with host proteins involved in RNA splicing and protein translation, such as SNRNP70, POLR2H, HNRNPA1, DDX17, etc. The findings of this study shed light on the function of the F3 protein.
Topics: Animals; Chlorocebus aethiops; Humans; Transcriptome; Monkeypox virus; Vero Cells; Chromatography, Liquid; HEK293 Cells; Mpox (monkeypox); Proteomics; Tandem Mass Spectrometry; Gene Expression Profiling; Ribonucleoprotein, U1 Small Nuclear
PubMed: 38415010
DOI: 10.3389/fcimb.2024.1354410 -
Acta Crystallographica. Section D,... Aug 2023Candida auris has emerged as a global health problem with a dramatic spread by nosocomial transmission and a high mortality rate. Antifungal therapy for C. auris...
Candida auris has emerged as a global health problem with a dramatic spread by nosocomial transmission and a high mortality rate. Antifungal therapy for C. auris infections is currently limited due to widespread resistance to fluconazole and amphotericin B and increasing resistance to the front-line drug echinocandin. Therefore, new treatments are urgently required to combat this pathogen. Dihydrofolate reductase (DHFR) has been validated as a potential drug target for Candida species, although no structure of the C. auris enzyme (CauDHFR) has been reported. Here, crystal structures of CauDHFR are reported as an apoenzyme, as a holoenzyme and in two ternary complexes with pyrimethamine and cycloguanil, which are common antifolates, at near-atomic resolution. Preliminary biochemical and biophysical assays and antifungal susceptibility testing with a variety of classical antifolates were also performed, highlighting the enzyme-inhibition rates and the inhibition of yeast growth. These structural and functional data might provide the basis for a novel drug-discovery campaign against this global threat.
Topics: Humans; Antifungal Agents; Candida auris; Tetrahydrofolate Dehydrogenase; Folic Acid Antagonists; Microbial Sensitivity Tests; Candidiasis, Invasive; Saccharomyces cerevisiae
PubMed: 37428844
DOI: 10.1107/S2059798323004709 -
Journal of Molecular Graphics &... Mar 2024Protein Tyrosine Phosphatase 1B (PTP1B), being negative regulator of insulin signaling pathways is considered as potential medicinal target. Selective and targeted...
Protein Tyrosine Phosphatase 1B (PTP1B), being negative regulator of insulin signaling pathways is considered as potential medicinal target. Selective and targeted inhibitors for PTP1B can impact the therapeutic options available to cure chronic illness such as diabetes. Significant research evidence including computational studies on the role of Zn in binding and inhibiting the catalytic pocket have been reported along with experimental exploration of zinc(II) complexes as potent inhibitors of the enzyme. The current study has employed advanced computational methods to explore the binding and conformational orientation of zinc(II) complexes in the active site of apoenzyme, phosphoenzyme, and TSA 2 of PTP1B. Metal ion modeling was performed for zinc metal center (Zn-OOOO) utilizing a Python based Metal Center Parameter Builder (MCPB.py). The findings of the study suggest that zinc(II) complex binds to structurally and functionally important residues in open and closed conformation as well as in the phosphorylated state of the enzyme. It was observed that when the catalytic cysteine is phosphorylated in a closed conformation, the zinc(II) complex forms significant interactions with PHE182, VAL184, GLY183, and PRO180 while pushing away Q-loop GLN262 which is crucial for the hydrolysis of phosphoenzyme. Subsequently, the reported inhibitor has also demonstrated its potential to function as allosteric modulator of the enzyme occupying catalytic WPD loop residues. The study uncovers putative binding sites of zinc-containing drugs and gives insight into the size and design of such compounds which keeps them accessible and anchored in the vicinity of active site residues. Reported inhibitor offers enhanced selectivity and inhibition in all three states of the enzyme in contrast to zinc ions which can only impede enzyme in the phosphorylated state. In addition to this, investigation of ASP265→GLU265 mutation reveals the role of GLU265 in affecting the flexibility of WPD loop residues highlighting it as loss-of-function mutation. Our results hints towards a metallodrug approach that builds on the research evidence of inhibition effects of Zn in the binding pocket of PTP1B. The findings presented are noteworthy, not just due to their significant relevance for clinical application, but also for the design and synthesis of novel zinc(II) complexes.
Topics: Hypoglycemic Agents; Zinc; Molecular Dynamics Simulation; Binding Sites; Catalytic Domain; Protein Tyrosine Phosphatase, Non-Receptor Type 1; Enzyme Inhibitors
PubMed: 38029632
DOI: 10.1016/j.jmgm.2023.108665 -
Chemical Communications (Cambridge,... Feb 2024Hydrogenases are enzymes that catalyze the reversible conversion of protons to hydrogen gas, using earth-abundant metals such as nickel and/or iron. This characteristic...
Hydrogenases are enzymes that catalyze the reversible conversion of protons to hydrogen gas, using earth-abundant metals such as nickel and/or iron. This characteristic makes them promising for sustainable energy applications, particularly in clean hydrogen production. However, their widespread use faces challenges, including a limited pH range and susceptibility to oxygen. In response to these issues, SacCoMyo is introduced as an artificial enzyme. SacCoMyo is designed by replacing the native metal in the myoglobin (Myo) scaffold with a hydroxocobalamin (Co) porphyrin core and complemented by a protective heteropolysaccharide-linked (Sac) shell. This engineered protein proves to be resilient, maintaining robust functionality even in acidic environments and preventing denaturation in a pH 1 electrolyte. The cobalt porphyrin core of SacCoMyo reduces the activation overpotential for hydrogen generation. A high turnover frequency of about 2400 H s is demonstrated in the presence of molecular oxygen, showcasing its potential in biohydrogen production and its ability to overcome the limitations associated with natural hydrogenases.
Topics: Hydrogen; Cobalt; Oxygen; Apoenzymes; Hydrogenase; Hydrogen-Ion Concentration; Porphyrins
PubMed: 38333929
DOI: 10.1039/d3cc06185j -
Proceedings of the National Academy of... Jan 2024The emergence of an RNA replicase capable of self-replication is considered an important stage in the origin of life. RNA polymerase ribozymes (PR) - including a variant...
The emergence of an RNA replicase capable of self-replication is considered an important stage in the origin of life. RNA polymerase ribozymes (PR) - including a variant that uses trinucleotide triphosphates (triplets) as substrates - have been created by in vitro evolution and are the closest functional analogues of the replicase, but the structural basis for their function is poorly understood. Here we use single-particle cryogenic electron microscopy (cryo-EM) and high-throughput mutation analysis to obtain the structure of a triplet polymerase ribozyme (TPR) apoenzyme and map its functional landscape. The cryo-EM structure at 5-Å resolution reveals the TPR as an RNA heterodimer comprising a catalytic subunit and a noncatalytic, auxiliary subunit, resembling the shape of a left hand with thumb and fingers at a 70° angle. The two subunits are connected by two distinct kissing-loop (KL) interactions that are essential for polymerase function. Our combined structural and functional data suggest a model for templated RNA synthesis by the TPR holoenzyme, whereby heterodimer formation and KL interactions preorganize the TPR for optimal primer-template duplex binding, triplet substrate discrimination, and templated RNA synthesis. These results provide a better understanding of TPR structure and function and should aid the engineering of more efficient PRs.
Topics: RNA, Catalytic; Cryoelectron Microscopy; RNA; DNA-Directed RNA Polymerases; RNA-Dependent RNA Polymerase
PubMed: 38207080
DOI: 10.1073/pnas.2313332121 -
Antimicrobial Agents and Chemotherapy Jul 2023KPC-2 is one of the most relevant serine-carbapenemases among the carbapenem-resistant We previously isolated from the environmental species Chromobacterium...
KPC-2 is one of the most relevant serine-carbapenemases among the carbapenem-resistant We previously isolated from the environmental species Chromobacterium haemolyticum a class A CRH-1 β-lactamase displaying 69% amino acid sequence identity with KPC-2. The objective of this study was to analyze the kinetic behavior and crystallographic structure of this β-lactamase. Our results showed that CRH-1 can hydrolyze penicillins, cephalosporins (except ceftazidime), and carbapenems with similar efficacy compared to KPC-2. Inhibition kinetics showed that CRH-1 is not well inhibited by clavulanic acid, in contrast to efficient inhibition by avibactam (AVI). The high-resolution crystal of the apoenzyme showed that CRH-1 has a similar folding compared to other class A β-lactamases. The CRH-1/AVI complex showed that AVI adopts a chair conformation, stabilized by hydrogen bonds to Ser70, Ser237, Asn132, and Thr235. Our findings highlight the biochemical and structural similarities of CRH-1 and KPC-2 and the potential clinical impact of this carbapenemase in the event of recruitment by pathogenic bacterial species.
Topics: Escherichia coli; Bacterial Proteins; beta-Lactamases; Ceftazidime; Carbapenems; Microbial Sensitivity Tests; Azabicyclo Compounds; Anti-Bacterial Agents; Klebsiella pneumoniae; Drug Combinations
PubMed: 37272821
DOI: 10.1128/aac.00061-23