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1.
Methods Mol Biol ; 2792: 97-111, 2024.
Article in English | MEDLINE | ID: mdl-38861081

ABSTRACT

To measure the kinetic properties of photorespiratory enzymes, it is necessary to work with purified proteins. Protocols to purify photorespiratory enzymes from leaves of various plant species require several time-consuming steps. It is now possible to produce large quantities of recombinant proteins in bacterial cells. They can be rapidly purified as histidine-tagged recombinant proteins by immobilized metal affinity chromatography using Ni2+-NTA-agarose. This chapter describes protocols to purify several Arabidopsis thaliana His-tagged recombinant photorespiratory enzymes (phosphoglycolate phosphatase, glycolate oxidase, and hydroxypyruvate reductase) from Escherichia coli cell cultures using two bacterial strain-plasmid systems: BL21(DE3)-pET and LMG194-pBAD.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Escherichia coli , Hydroxypyruvate Reductase , Phosphoric Monoester Hydrolases , Arabidopsis/genetics , Escherichia coli/genetics , Escherichia coli/metabolism , Hydroxypyruvate Reductase/genetics , Hydroxypyruvate Reductase/metabolism , Hydroxypyruvate Reductase/chemistry , Phosphoric Monoester Hydrolases/metabolism , Phosphoric Monoester Hydrolases/genetics , Phosphoric Monoester Hydrolases/isolation & purification , Phosphoric Monoester Hydrolases/chemistry , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Arabidopsis Proteins/isolation & purification , Arabidopsis Proteins/chemistry , Histidine/metabolism , Histidine/genetics , Alcohol Oxidoreductases/genetics , Alcohol Oxidoreductases/metabolism , Alcohol Oxidoreductases/isolation & purification , Alcohol Oxidoreductases/chemistry , Chromatography, Affinity/methods , Recombinant Proteins/metabolism , Recombinant Proteins/isolation & purification , Recombinant Proteins/genetics , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/isolation & purification , Recombinant Fusion Proteins/metabolism
2.
Structure ; 32(6): 647-649, 2024 Jun 06.
Article in English | MEDLINE | ID: mdl-38848680

ABSTRACT

In this issue of Structure, Yin et al.1 present the CryoEM structure of the HisRS-like domain of human GCN2 and demonstrate that it is a pseudoenzyme, which binds uncharged tRNA in a different manner than HisRS and does not bind histidine and ATP.


Subject(s)
Adenosine Triphosphate , Humans , Adenosine Triphosphate/metabolism , Adenosine Triphosphate/chemistry , Cryoelectron Microscopy , RNA, Transfer/metabolism , RNA, Transfer/chemistry , Protein Serine-Threonine Kinases/metabolism , Protein Serine-Threonine Kinases/chemistry , Catalysis , Models, Molecular , Histidine/chemistry , Histidine/metabolism
3.
Nat Commun ; 15(1): 3975, 2024 May 10.
Article in English | MEDLINE | ID: mdl-38729930

ABSTRACT

Oxidoreductases have evolved tyrosine/tryptophan pathways that channel highly oxidizing holes away from the active site to avoid damage. Here we dissect such a pathway in a bacterial LPMO, member of a widespread family of C-H bond activating enzymes with outstanding industrial potential. We show that a strictly conserved tryptophan is critical for radical formation and hole transference and that holes traverse the protein to reach a tyrosine-histidine pair in the protein's surface. Real-time monitoring of radical formation reveals a clear correlation between the efficiency of hole transference and enzyme performance under oxidative stress. Residues involved in this pathway vary considerably between natural LPMOs, which could reflect adaptation to different ecological niches. Importantly, we show that enzyme activity is increased in a variant with slower radical transference, providing experimental evidence for a previously postulated trade-off between activity and redox robustness.


Subject(s)
Bacterial Proteins , Mixed Function Oxygenases , Oxidation-Reduction , Mixed Function Oxygenases/metabolism , Mixed Function Oxygenases/genetics , Mixed Function Oxygenases/chemistry , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/chemistry , Catalytic Domain , Tryptophan/metabolism , Polysaccharides/metabolism , Mutation , Oxidative Stress , Tyrosine/metabolism , Models, Molecular , Histidine/metabolism , Histidine/genetics
4.
Nat Commun ; 15(1): 4204, 2024 May 17.
Article in English | MEDLINE | ID: mdl-38760374

ABSTRACT

Life continuously transduces energy to perform critical functions using energy stored in reactive molecules like ATP or NADH. ATP dynamically phosphorylates active sites on proteins and thereby regulates their function. Inspired by such machinery, regulating supramolecular functions using energy stored in reactive molecules has gained traction. Enzyme-free, synthetic systems that use dynamic phosphorylation to regulate supramolecular processes have not yet been reported, to our knowledge. Here, we show an enzyme-free reaction cycle that consumes the phosphorylating agent monoamidophosphate by transiently phosphorylating histidine and histidine-containing peptides. The phosphorylated species are labile and deactivate through hydrolysis. The cycle exhibits versatility and tunability, allowing for the dynamic phosphorylation of multiple precursors with a tunable half-life. Notably, we show the resulting phosphorylated products can regulate the peptide's phase separation, leading to active droplets that require the continuous conversion of fuel to sustain. The reaction cycle will be valuable as a model for biological phosphorylation but can also offer insights into protocell formation.


Subject(s)
Peptides , Phosphorylation , Peptides/metabolism , Peptides/chemistry , Histidine/metabolism , Histidine/chemistry , Adenosine Triphosphate/metabolism , Hydrolysis
5.
Int J Biol Macromol ; 270(Pt 2): 132393, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38761898

ABSTRACT

Light chain amyloidosis is a conformational disease caused by the abnormal proliferation and deposition of antibody light chains as amyloid fibers in organs and tissues. The effect of Cu(II) binding to the model recombinant protein 6aJL2-R24G was previously characterized in our group, and we found an acceleration of the aggregation kinetics of the protein. In this study, in order to confirm the Cu(II) binding sites, histidine variants of 6aJL2-R24G were prepared and the effects of their interaction with Cu(II) were analyzed by circular dichroism, fluorescence spectroscopy, isothermal calorimetry titrations, and molecular dynamics simulations. Confirming our earlier work, we found that His8 and His99 are the highest affinity Cu(II) binding sites, and that Cu(II) binding to both sites is a cooperative event.


Subject(s)
Copper , Histidine , Protein Binding , Copper/metabolism , Copper/chemistry , Histidine/chemistry , Histidine/metabolism , Humans , Binding Sites , Molecular Dynamics Simulation , Immunoglobulin Light Chains/metabolism , Immunoglobulin Light Chains/genetics , Immunoglobulin Light Chains/chemistry , Immunoglobulin Light-chain Amyloidosis/metabolism , Immunoglobulin Light-chain Amyloidosis/genetics , Amyloidosis/metabolism , Amyloidosis/genetics , Kinetics
6.
Photochem Photobiol Sci ; 23(5): 997-1010, 2024 May.
Article in English | MEDLINE | ID: mdl-38693447

ABSTRACT

Firefly luciferases emit yellow-green light and are pH-sensitive, changing the bioluminescence color to red in the presence of heavy metals, acidic pH and high temperatures. These pH and metal-sensitivities have been recently harnessed for intracellular pH indication and toxic metal biosensing. However, whereas the structure of the pH sensor and the metal binding site, which consists mainly of two salt bridges that close the active site (E311/R337 and H310/E354), has been identified, the specific role of residue H310 in pH and metal sensing is still under debate. The Amydetes vivianii firefly luciferase has one of the lowest pH sensitivities among the group of pH-sensitive firefly luciferases, displaying high bioluminescent activity and special spectral selectivity for cadmium and mercury, which makes it a promising analytical reagent. Using site-directed mutagenesis, we have investigated in detail the role of residue H310 on pH and metal sensitivity in this luciferase. Negatively charged residues at position 310 increase the pH sensitivity and metal sensitivity; H310G considerably increases the size of the cavity, severely impacting the activity, H310R closes the cavity, and H310F considerably decreases both pH and metal sensitivities. However, no substitution completely abolished pH and metal sensitivities. The results indicate that the presence of negatively charged and basic side chains at position 310 is important for pH sensitivity and metals coordination, but not essential, indicating that the remaining side chains of E311 and E354 may still coordinate some metals in this site. Furthermore, a metal binding site search predicted that H310 mutations decrease the affinity mainly for Zn, Ni and Hg but less for Cd, and revealed the possible existence of additional binding sites for Zn, Ni and Hg.


Subject(s)
Fireflies , Histidine , Luciferases, Firefly , Mutagenesis, Site-Directed , Hydrogen-Ion Concentration , Animals , Luciferases, Firefly/metabolism , Luciferases, Firefly/chemistry , Luciferases, Firefly/genetics , Fireflies/enzymology , Histidine/chemistry , Histidine/metabolism , Color , Metals, Heavy/chemistry , Metals, Heavy/metabolism , Mercury/chemistry , Mercury/metabolism , Cadmium/chemistry , Cadmium/metabolism
7.
Chem Biol Interact ; 394: 110992, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38579923

ABSTRACT

Histidine residues 44 and 48 in yeast alcohol dehydrogenase (ADH) bind to the coenzymes NAD(H) and contribute to catalysis. The individual H44R and H48Q substitutions alter the kinetics and pH dependencies, and now the roles of other ionizable groups in the enzyme were studied in the doubly substituted H44R/H48Q ADH. The substitutions make the enzyme more resistant to inactivation by diethyl pyrocarbonate, modestly improve affinity for coenzymes, and substantially decrease catalytic efficiencies for ethanol oxidation and acetaldehyde reduction. The pH dependencies for several kinetic parameters are shifted from pK values for wild-type ADH of 7.3-8.1 to values for H44R/H48Q ADH of 8.0-9.6, and are assigned to the water or alcohol bound to the catalytic zinc. It appears that the rate of binding of NAD+ is electrostatically favored with zinc-hydroxide whereas binding of NADH is faster with neutral zinc-water. The pH dependencies of catalytic efficiencies (V/EtKm) for ethanol oxidation and acetaldehyde reduction are similarly controlled by deprotonation and protonation, respectively. The substitutions make an enzyme that resembles the homologous horse liver H51Q ADH, which has Arg-47 and Gln-51 and exhibits similar pK values. In the wild-type ADHs, it appears that His-48 (or His-51) in the proton relay systems linked to the catalytic zinc ligands modulate catalytic efficiencies.


Subject(s)
Alcohol Dehydrogenase , Catalytic Domain , Histidine , Saccharomyces cerevisiae , Acetaldehyde/metabolism , Acetaldehyde/chemistry , Alcohol Dehydrogenase/metabolism , Alcohol Dehydrogenase/genetics , Alcohol Dehydrogenase/chemistry , Amino Acid Substitution , Diethyl Pyrocarbonate/chemistry , Diethyl Pyrocarbonate/pharmacology , Ethanol/metabolism , Histidine/metabolism , Histidine/chemistry , Hydrogen-Ion Concentration , Kinetics , NAD/metabolism , Oxidation-Reduction , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae/enzymology , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/genetics , Zinc/metabolism , Zinc/chemistry
8.
PLoS One ; 19(4): e0299701, 2024.
Article in English | MEDLINE | ID: mdl-38683788

ABSTRACT

Recombinant Francisella tularensis universal stress protein with a C-terminal histidine-tag (rUsp/His6) was expressed in Escherichia coli. Endogenous F. tularensis Usp has a predicted molecular mass of 30 kDa, but rUsp/His6 had an apparent molecular weight of 33 kDa based on Western blot analyses. To determine the source of the higher molecular weight for rUsp/His6, post translational modifications were examined. Tryptic peptides of purified rUsp/His6 were subjected to liquid chromatography tandem mass spectrometry (LC-MS/MS) and fragmentation spectra were searched for acetylated lysines and polyaminated glutamines. Of the 24 lysines in rUsp/His6, 10 were acetylated (K63, K68, K72, K129, K175, K201, K208, K212, K233, and K238) and three of the four glutamines had putrescine, spermidine and spermine adducts (Q55, Q60 and Q267). The level of post-translational modification was substoichiometric, eliminating the possibility that these modifications were the sole contributor to the 3 kDa extra mass of rUsp/His6. LC-MS/MS revealed that stop codon readthrough had occurred resulting in the unexpected addition of 20 extra amino acids at the C-terminus of rUsp/His6, after the histidine tag. Further, the finding of polyaminated glutamines in rUsp/His6 indicated that E. coli is capable of transglutaminase activity.


Subject(s)
Bacterial Proteins , Codon, Terminator , Escherichia coli , Francisella tularensis , Protein Processing, Post-Translational , Recombinant Proteins , Escherichia coli/genetics , Escherichia coli/metabolism , Acetylation , Codon, Terminator/genetics , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Francisella tularensis/genetics , Francisella tularensis/metabolism , Tandem Mass Spectrometry , Histidine/metabolism , Amino Acid Sequence
9.
Nat Commun ; 15(1): 3301, 2024 Apr 26.
Article in English | MEDLINE | ID: mdl-38671004

ABSTRACT

Diphthamide is a modified histidine residue unique for eukaryotic translation elongation factor 2 (eEF2), a key ribosomal protein. Loss of this evolutionarily conserved modification causes developmental defects through unknown mechanisms. In a patient with compound heterozygous mutations in Diphthamide Biosynthesis 1 (DPH1) and impaired eEF2 diphthamide modification, we observe multiple defects in neural crest (NC)-derived tissues. Knockin mice harboring the patient's mutations and Xenopus embryos with Dph1 depleted also display NC defects, which can be attributed to reduced proliferation in the neuroepithelium. DPH1 depletion facilitates dissociation of eEF2 from ribosomes and association with p53 to promote transcription of the cell cycle inhibitor p21, resulting in inhibited proliferation. Knockout of one p21 allele rescues the NC phenotypes in the knockin mice carrying the patient's mutations. These findings uncover an unexpected role for eEF2 as a transcriptional coactivator for p53 to induce p21 expression and NC defects, which is regulated by diphthamide modification.


Subject(s)
Cyclin-Dependent Kinase Inhibitor p21 , Histidine , Histidine/analogs & derivatives , Minor Histocompatibility Antigens , Neural Crest , Peptide Elongation Factor 2 , Tumor Suppressor Protein p53 , Tumor Suppressor Proteins , Animals , Neural Crest/metabolism , Tumor Suppressor Protein p53/metabolism , Tumor Suppressor Protein p53/genetics , Humans , Cyclin-Dependent Kinase Inhibitor p21/metabolism , Cyclin-Dependent Kinase Inhibitor p21/genetics , Mice , Peptide Elongation Factor 2/metabolism , Peptide Elongation Factor 2/genetics , Histidine/metabolism , Ribosomes/metabolism , Mutation , Cell Proliferation , Xenopus laevis , Female , Gene Knock-In Techniques , Xenopus , Male , Mice, Knockout
10.
Nat Plants ; 10(5): 743-748, 2024 May.
Article in English | MEDLINE | ID: mdl-38600265

ABSTRACT

NARROW LEAF1 (NAL1) exerts a multifaceted influence on leaf morphology and crop yield. Recent crystal study proposed that histidine 233 (H233) is part of the catalytic triad. Here we report that unlike suggested previously, H234 instead of H233 is a component of the catalytic triad alongside residues D291 and S385 in NAL1. Remarkably, residue 233 unexpectedly plays a pivotal role in regulating NAL1's proteolytic activity. These findings establish a strong foundation for utilizing NAL1 in breeding programs aimed at improving crop yield.


Subject(s)
Oryza , Plant Proteins , Oryza/genetics , Oryza/metabolism , Plant Proteins/metabolism , Plant Proteins/genetics , Plant Leaves/metabolism , Plant Leaves/genetics , Histidine/metabolism
11.
J Microbiol Biotechnol ; 34(5): 1178-1187, 2024 May 28.
Article in English | MEDLINE | ID: mdl-38563100

ABSTRACT

Cordyceps militaris is a significant edible fungus that produces a variety of bioactive compounds. We have previously established a uridine/uracil auxotrophic mutant and a corresponding Agrobacterium tumefaciens-mediated transformation (ATMT) system for genetic characterization in C. militaris using pyrG as a screening marker. In this study, we constructed an ATMT system based on a dual pyrG and hisB auxotrophic mutant of C. militaris. Using the uridine/uracil auxotrophic mutant as the background and pyrG as a selection marker, the hisB gene encoding imidazole glycerophosphate dehydratase, required for histidine biosynthesis, was knocked out by homologous recombination to construct a histidine auxotrophic C. militaris mutant. Then, pyrG in the histidine auxotrophic mutant was deleted to construct a ΔpyrG ΔhisB dual auxotrophic mutant. Further, we established an ATMT transformation system based on the dual auxotrophic C. militaris by using GFP and DsRed as reporter genes. Finally, to demonstrate the application of this dual transformation system for studies of gene function, knock out and complementation of the photoreceptor gene CmWC-1 in the dual auxotrophic C. militaris were performed. The newly constructed ATMT system with histidine and uridine/uracil auxotrophic markers provides a promising tool for genetic modifications in the medicinal fungus C. militaris.


Subject(s)
Agrobacterium tumefaciens , Cordyceps , Transformation, Genetic , Uracil , Agrobacterium tumefaciens/genetics , Agrobacterium tumefaciens/metabolism , Cordyceps/genetics , Cordyceps/metabolism , Cordyceps/growth & development , Uracil/metabolism , Histidine/metabolism , Uridine/metabolism , Fungal Proteins/genetics , Fungal Proteins/metabolism , Gene Knockout Techniques , Hydro-Lyases/genetics , Hydro-Lyases/metabolism , Genes, Reporter , Mutation , Homologous Recombination
12.
Biophys J ; 123(9): 1139-1151, 2024 May 07.
Article in English | MEDLINE | ID: mdl-38571309

ABSTRACT

Lytic polysaccharide monooxygenases (LPMOs) catalyze a reaction that is crucial for the biological decomposition of various biopolymers and for the industrial conversion of plant biomass. Despite the importance of LPMOs, the exact molecular-level nature of the reaction mechanism is still debated today. Here, we investigated the pH-dependent conformation of a second-sphere histidine (His) that we call the stacking histidine, which is conserved in fungal AA9 LPMOs and is speculated to assist catalysis in several of the LPMO reaction pathways. Using constant-pH and accelerated molecular dynamics simulations, we monitored the dynamics of the stacking His in different protonation states for both the resting Cu(II) and active Cu(I) forms of two fungal LPMOs. Consistent with experimental crystallographic and neutron diffraction data, our calculations suggest that the side chain of the protonated and positively charged form is rotated out of the active site toward the solvent. Importantly, only one of the possible neutral states of histidine (HIE state) is observed in the stacking orientation at neutral pH or when bound to cellulose. Our data predict that, in solution, the stacking His may act as a stabilizer (via hydrogen bonding) of the Cu(II)-superoxo complex after the LPMO-Cu(I) has reacted with O2 in solution, which, in fine, leads to H2O2 formation. Also, our data indicate that the HIE-stacking His is a poor acid/base catalyst when bound to the substrate and, in agreement with the literature, may play an important stabilizing role (via hydrogen bonding) during the peroxygenase catalysis. Our study reveals the pH titration midpoint values of the pH-dependent orientation of the stacking His should be considered when modeling and interpreting LPMO reactions, whether it be for classical LPMO kinetics or in industry-oriented enzymatic cocktails, and for understanding LPMO behavior in slightly acidic natural processes such as fungal wood decay.


Subject(s)
Histidine , Mixed Function Oxygenases , Molecular Dynamics Simulation , Histidine/chemistry , Histidine/metabolism , Hydrogen-Ion Concentration , Mixed Function Oxygenases/metabolism , Mixed Function Oxygenases/chemistry , Fungal Proteins/chemistry , Fungal Proteins/metabolism , Catalytic Domain , Polysaccharides/metabolism , Polysaccharides/chemistry , Copper/chemistry , Copper/metabolism , Cellulose/metabolism , Cellulose/chemistry
13.
Arch Microbiol ; 206(4): 148, 2024 Mar 11.
Article in English | MEDLINE | ID: mdl-38462558

ABSTRACT

Pseudomonas aeruginosa is an opportunistic gram-negative pathogenic microorganism that poses a significant challenge in clinical treatment. Antibiotics exhibit limited efficacy against mature biofilm, culminating in an increase in the number of antibiotic-resistant strains. Therefore, novel strategies are essential to enhance the effectiveness of antibiotics against Pseudomonas aeruginosa biofilms. D-histidine has been previously identified as a prospective anti-biofilm agent. However, limited attention has been directed towards its impact on Pseudomonas aeruginosa. Therefore, this study was undertaken to explore the effect of D-histidine on Pseudomonas aeruginosa in vitro. Our results demonstrated that D-histidine downregulated the mRNA expression of virulence and quorum sensing (QS)-associated genes in Pseudomonas aeruginosa PAO1 without affecting bacterial growth. Swarming and swimming motility tests revealed that D-histidine significantly reduced the motility and pathogenicity of PAO1. Moreover, crystal violet staining and confocal laser scanning microscopy demonstrated that D-histidine inhibited biofilm formation and triggered the disassembly of mature biofilms. Notably, D-histidine increased the susceptibility of PAO1 to amikacin compared to that in the amikacin-alone group. These findings underscore the efficacy of D-histidine in combating Pseudomonas aeruginosa by reducing biofilm formation and increasing biofilm disassembly. Moreover, the combination of amikacin and D-histidine induced a synergistic effect against Pseudomonas aeruginosa biofilms, suggesting the potential utility of D-histidine as a preventive strategy against biofilm-associated infections caused by Pseudomonas aeruginosa.


Subject(s)
Amikacin , Pseudomonas Infections , Humans , Amikacin/pharmacology , Amikacin/metabolism , Amikacin/therapeutic use , Pseudomonas aeruginosa , Histidine/pharmacology , Histidine/metabolism , Histidine/therapeutic use , Biofilms , Quorum Sensing , Anti-Bacterial Agents/chemistry , Pseudomonas Infections/microbiology , Virulence Factors/metabolism
14.
Biochem Biophys Res Commun ; 707: 149785, 2024 May 07.
Article in English | MEDLINE | ID: mdl-38503150

ABSTRACT

Melanoma, originating from melanocytes, is a highly aggressive tumor. Tyrosinase is involved in melanin production in melanocytes, and its overexpression is noted in malignant melanomas. However, the role of tyrosinase in melanomas remains unclear. Therefore, this study aimed to evaluate the potential functions of tyrosinase in the human melanoma cell line A375. The expression level of tyrosinase in A375 cells was undetectable. However, markedly increased expression level was observed in the mouse melanoma cell line B16F10 and the human melanoma cell line WM266-4. Subsequently, we investigated the effect of ectopic tyrosinase expression on A375 cell motility using wound-healing assay. The overexpression of tyrosinase resulted in enhanced cell migration in both stable and transient tyrosinase expression cells. The levels of filamentous actin were decreased in tyrosinase-expressing A375 cells, suggesting that tyrosinase regulates cell motility by modulating actin polymerization. Histidine residues in tyrosinase are important for its enzymatic activity for synthesizing melanin. Substitution of these histidine residues to alanine residues mitigated the promotion of tyrosinase-induced A375 cell metastasis. Furthermore, melanin treatment enhanced A375 cell metastasis and phosphorylation of Cofilin. Thus, our findings suggest that tyrosinase increases the migration of A375 cells by regulating actin polymerization through its enzymatic activity.


Subject(s)
Melanins , Melanoma, Experimental , Animals , Mice , Humans , Melanins/metabolism , Monophenol Monooxygenase/genetics , Monophenol Monooxygenase/metabolism , Mixed Function Oxygenases/metabolism , Actins/metabolism , Histidine/metabolism , Melanoma, Experimental/pathology , Cell Line, Tumor , Melanocytes/metabolism
15.
Biochem Biophys Res Commun ; 709: 149824, 2024 May 21.
Article in English | MEDLINE | ID: mdl-38537598

ABSTRACT

Heat shock factor 1 (HSF1) primarily regulates various cellular stress responses. Previous studies have shown that low pH within the physiological range directly activates HSF1 function in vitro. However, the detailed molecular mechanisms remain unclear. This study proposes a molecular mechanism based on the trimerization behavior of HSF1 at different pH values. Extensive mutagenesis of human and goldfish HSF1 revealed that the optimal pH for trimerization depended on the identity of residue 103. In particular, when residue 103 was occupied by tyrosine, a significant increase in the optimal pH was observed, regardless of the rest of the sequence. This behavior can be explained by the protonation state of the neighboring histidine residues, His101 and His110. Residue 103 plays a key role in trimerization by forming disulfide or non-covalent bonds with Cys36. If tyrosine resides at residue 103 in an acidic environment, its electrostatic interactions with positively charged histidine residues prevent effective trimerization. His101 and His110 are neutralized at a higher pH, which releases Tyr103 to interact with Cys36 and drives the effective trimerization of HSF1. This study showed that the protonation state of a histidine residue can regulate the intramolecular interactions, which consequently leads to a drastic change in the oligomerization behavior of the entire protein.


Subject(s)
DNA-Binding Proteins , Transcription Factors , Humans , DNA-Binding Proteins/metabolism , Heat Shock Transcription Factors/genetics , Histidine/genetics , Histidine/metabolism , Hydrogen-Ion Concentration , Transcription Factors/metabolism , Tyrosine
16.
Structure ; 32(6): 795-811.e6, 2024 Jun 06.
Article in English | MEDLINE | ID: mdl-38531363

ABSTRACT

GCN2 is a stress response kinase that phosphorylates the translation initiation factor eIF2α to inhibit general protein synthesis when activated by uncharged tRNA and stalled ribosomes. The presence of a HisRS-like domain in GCN2, normally associated with tRNA aminoacylation, led to the hypothesis that eIF2α kinase activity is regulated by the direct binding of this domain to uncharged tRNA. Here we solved the structure of the HisRS-like domain in the context of full-length GCN2 by cryoEM. Structure and function analysis shows the HisRS-like domain of GCN2 has lost histidine and ATP binding but retains tRNA binding abilities. Hydrogen deuterium exchange mass spectrometry, site-directed mutagenesis and computational docking experiments support a tRNA binding model that is partially shifted from that employed by bona fide HisRS enzymes. These results demonstrate that the HisRS-like domain of GCN2 is a pseudoenzyme and advance our understanding of GCN2 regulation and function.


Subject(s)
Protein Binding , Protein Serine-Threonine Kinases , RNA, Transfer , Protein Serine-Threonine Kinases/metabolism , Protein Serine-Threonine Kinases/chemistry , Protein Serine-Threonine Kinases/genetics , RNA, Transfer/metabolism , RNA, Transfer/chemistry , Binding Sites , Protein Domains , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/genetics , Cryoelectron Microscopy , Molecular Docking Simulation , Models, Molecular , Adenosine Triphosphate/metabolism , Saccharomyces cerevisiae/metabolism , Humans , Histidine/metabolism , Histidine/chemistry , Phosphorylation
17.
mBio ; 15(4): e0224823, 2024 Apr 10.
Article in English | MEDLINE | ID: mdl-38477571

ABSTRACT

Sporulation is an important feature of the clostridial life cycle, facilitating survival of these bacteria in harsh environments, contributing to disease transmission for pathogenic species, and sharing common early steps that are also involved in regulating industrially important solvent production by some non-pathogenic species. Initial genomics studies suggested that Clostridia lack the classical phosphorelay that phosphorylates Spo0A and initiates sporulation in Bacillus, leading to the hypothesis that sporulation in Clostridia universally begins when Spo0A is phosphorylated by orphan histidine kinases (OHKs). However, components of the classical Bacillus phosphorelay were recently identified in some Clostridia. Similar Bacillus phosphorelay components have not yet been found in the pathogenic Clostridia or the solventogenic Clostridia of industrial importance. For some of those Clostridia lacking a classical phosphorelay, the involvement of OHKs in sporulation initiation has received support from genetic studies demonstrating the involvement of several apparent OHKs in their sporulation. In addition, several clostridial OHKs directly phosphorylate Spo0A in vitro. Interestingly, there is considerable protein domain diversity among the sporulation-associated OHKs in Clostridia. Further adding to the emergent complexity of sporulation initiation in Clostridia, several candidate OHK phosphotransfer proteins that were OHK candidates were shown to function as phosphatases that reduce sporulation in some Clostridia. The mounting evidence indicates that no single pathway explains sporulation initiation in all Clostridia and supports the need for further study to fully understand the unexpected and biologically fascinating mechanistic diversity of this important process among these medically and industrially important bacteria.


Subject(s)
Bacillus , Histidine , Histidine Kinase/genetics , Histidine Kinase/metabolism , Histidine/metabolism , Phosphorylation , Transcription Factors/metabolism , Bacillus/metabolism , Clostridium/genetics , Clostridium/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Spores, Bacterial/metabolism , Bacillus subtilis/genetics , Gene Expression Regulation, Bacterial
18.
Nat Commun ; 15(1): 2264, 2024 Mar 13.
Article in English | MEDLINE | ID: mdl-38480688

ABSTRACT

NME3 is a member of the nucleoside diphosphate kinase (NDPK) family localized on the mitochondrial outer membrane (MOM). Here, we report a role of NME3 in hypoxia-induced mitophagy dependent on its active site phosphohistidine but not the NDPK function. Mice carrying a knock-in mutation in the Nme3 gene disrupting NME3 active site histidine phosphorylation are vulnerable to ischemia/reperfusion-induced infarction and develop abnormalities in cerebellar function. Our mechanistic analysis reveals that hypoxia-induced phosphatidic acid (PA) on mitochondria is essential for mitophagy and the interaction of DRP1 with NME3. The PA binding function of MOM-localized NME3 is required for hypoxia-induced mitophagy. Further investigation demonstrates that the interaction with active NME3 prevents DRP1 susceptibility to MUL1-mediated ubiquitination, thereby allowing a sufficient amount of active DRP1 to mediate mitophagy. Furthermore, MUL1 overexpression suppresses hypoxia-induced mitophagy, which is reversed by co-expression of ubiquitin-resistant DRP1 mutant or histidine phosphorylatable NME3. Thus, the site-specific interaction with active NME3 provides DRP1 a microenvironment for stabilization to proceed the segregation process in mitophagy.


Subject(s)
Dynamins , Mitophagy , Animals , Mice , Dynamins/genetics , Dynamins/metabolism , Histidine/metabolism , Hypoxia , Mitophagy/genetics , Ubiquitination
19.
PLoS One ; 19(3): e0301037, 2024.
Article in English | MEDLINE | ID: mdl-38547208

ABSTRACT

BACKGROUND: The favorable health-promoting adaptations to exercise result from cumulative responses to individual bouts of physical activity. Older adults often exhibit anabolic resistance; a phenomenon whereby the anabolic responses to exercise and nutrition are attenuated in skeletal muscle. The mechanisms contributing to age-related anabolic resistance are emerging, but our understanding of how chronological age influences responsiveness to exercise is incomplete. The objective was to determine the effects of healthy aging on peripheral blood metabolomic response to a single bout of resistance exercise and whether any metabolites in circulation are predictive of anabolic response in skeletal muscle. METHODS: Thirty young (20-35 years) and 49 older (65-85 years) men and women were studied in a cross-sectional manner. Participants completed a single bout of resistance exercise consisting of eight sets of 10 repetitions of unilateral knee extension at 70% of one-repetition maximum. Blood samples were collected before exercise, immediately post exercise, and 30-, 90-, and 180-minutes into recovery. Proton nuclear magnetic resonance spectroscopy was used to profile circulating metabolites at all timepoints. Serial muscle biopsies were collected for measuring muscle protein synthesis rates. RESULTS: Our analysis revealed that one bout of resistance exercise elicits significant changes in 26 of 33 measured plasma metabolites, reflecting alterations in several biological processes. Furthermore, 12 metabolites demonstrated significant interactions between exercise and age, including organic acids, amino acids, ketones, and keto-acids, which exhibited distinct responses to exercise in young and older adults. Pre-exercise histidine and sarcosine were negatively associated with muscle protein synthesis, as was the pre/post-exercise fold change in plasma histidine. CONCLUSIONS: This study demonstrates that while many exercise-responsive metabolites change similarly in young and older adults, several demonstrate age-dependent changes even in the absence of evidence of sarcopenia or frailty. TRIAL REGISTRATION: Clinical trial registry: ClinicalTrials.gov NCT03350906.


Subject(s)
Resistance Training , Aged , Aged, 80 and over , Female , Humans , Male , Cross-Sectional Studies , Histidine/metabolism , Muscle Proteins/metabolism , Muscle, Skeletal/physiology , Proton Magnetic Resonance Spectroscopy , Young Adult , Adult
20.
J Nutr ; 154(4): 1165-1174, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38311065

ABSTRACT

BACKGROUND: The recommended transition toward more plant-based diets, particularly containing legumes, requires a wider knowledge of plant protein bioavailability. Faba beans are cultivated at different latitudes and are used increasingly in human nutrition. OBJECTIVES: We aimed to assess the nutritional quality of faba bean protein in healthy volunteers equipped with an intestinal tube to implement the ileal 15N balance method. METHODS: Nine volunteers completed the study (7 males, 2 females, aged 33 ± 10 y, BMI: 24.7 ± 2.6 kg/m2). They were equipped with a nasoileal tube. After fasting overnight, they ingested a test meal consisting of cooked mash of dehulled faba bean seeds (20 g protein per serving of approximately 250 g) intrinsically labeled with 15N. Samples of ileal contents, plasma, and urine were collected over an 8-h postprandial period. Undigested nitrogen (N) and amino acids (AAs) were determined using isotopic MS, and subsequently, ileal digestibility and digestible indispensable amino acid score (DIAAS) were calculated. The measurement of postprandial deamination allowed calculation of the net postprandial protein utilization (NPPU). RESULTS: The ileal N digestibility was 84.1% ± 7.7%. Postprandial deamination represented 19.2% ± 3.6% of ingested N, and the NPPU was 64.7% ± 9.7%. The ileal digestibility of individual AAs varied from 85.1% ± 13.7% for histidine to 94.2% ± 3.6% for glutamine + glutamate. The mean AA digestibility was ∼6 percentage points higher than the digestibility of N, reaching 89.8% ± 5.9%, whereas indispensable AA digestibility was 88.0% ± 7.3%. Histidine and tryptophan were the first limiting AAs [DIAAS = 0.77 (calculated by legume-specific N-to-protein conversion factor 5.4); 0.67 (by default factor 6.25)]. Sulfur AAs were limiting to a lesser extent [DIAA ratio = 0.94 (N × 5.4); 0.81 (N × 6.25)]. CONCLUSIONS: Protein ileal digestibility of cooked, dehulled faba beans in humans was moderate (<85%), but that of AAs was close to 90%. Overall protein quality was restricted by the limited histidine and tryptophan content. This trial was registered at clinicaltrials.gov as NCT05047757.


Subject(s)
Fabaceae , Vicia faba , Female , Humans , Male , Amino Acids/metabolism , Animal Feed , Diet , Dietary Proteins/metabolism , Digestion , Fabaceae/chemistry , Histidine/metabolism , Ileum/metabolism , Tryptophan/metabolism , Vicia faba/metabolism
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