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1.
mBio ; 12(5): e0205721, 2021 10 26.
Article in English | MEDLINE | ID: mdl-34607461

ABSTRACT

Toxoplasma gondii extracellular signal-regulated kinase 7 (ERK7) is known to contribute to the integrity of the apical complex and to participate in the final step of conoid biogenesis. In the absence of ERK7, mature parasites lose their conoid complex and are unable to glide, invade, or egress from host cells. In contrast to a previous report, we show here that the depletion of ERK7 phenocopies the depletion of the apical cap protein AC9 or AC10. The absence of ERK7 leads to the loss of the apical polar ring (APR), the disorganization of the basket of subpellicular microtubules (SPMTs), and a severe impairment in microneme secretion. Ultrastructure expansion microscopy (U-ExM), coupled to N-hydroxysuccinimide ester (NHS-ester) staining on intracellular parasites, offers an unprecedented level of resolution and highlights the disorganization of the rhoptries as well as the dilated plasma membrane at the apical pole in the absence of ERK7. Comparative proteomics analysis of wild-type and ERK7-depleted parasites confirmed the disappearance of known apical complex proteins, including markers of the apical polar ring and a new apical cap named AC11. Concomitantly, the absence of ERK7 led to an accumulation of microneme proteins, resulting from the defect in the exocytosis of the organelles. AC9-depleted parasites were included as controls and exhibited an increase in inner membrane complex proteins, with two new proteins assigned to this compartment, namely, IMC33 and IMC34. IMPORTANCE The conoid is an enigmatic, dynamic organelle positioned at the apical tip of the coccidian subgroup of the Apicomplexa, close to the apical polar ring (APR) from which the subpellicular microtubules (SPMTs) emerge and through which the secretory organelles (micronemes and rhoptries) reach the plasma membrane for exocytosis. In Toxoplasma gondii, the conoid protrudes concomitantly with microneme secretion, during egress, motility, and invasion. The conditional depletion of the apical cap structural protein AC9 or AC10 leads to a disorganization of SPMTs as well as the loss of the APR and conoid, resulting in a microneme secretion defect and a block in motility, invasion, and egress. We show here that the depletion of the kinase ERK7 phenocopies AC9 and AC10 mutants. The combination of ultrastructure expansion microscopy and NHS-ester staining revealed that ERK7-depleted parasites exhibit a dilated apical plasma membrane and an altered positioning of the rhoptries, while electron microscopy images unambiguously highlight the loss of the APR.


Subject(s)
Extracellular Signal-Regulated MAP Kinases/metabolism , Organelles/enzymology , Protozoan Proteins/metabolism , Toxoplasma/enzymology , Exocytosis , Extracellular Signal-Regulated MAP Kinases/genetics , Microtubules/genetics , Microtubules/metabolism , Organelles/genetics , Protozoan Proteins/genetics , Toxoplasma/genetics
2.
Genes (Basel) ; 11(11)2020 11 19.
Article in English | MEDLINE | ID: mdl-33228188

ABSTRACT

The majority of DNA polymerases (DNAPs) are specialized enzymes with specific roles in DNA replication, translesion DNA synthesis (TLS), or DNA repair. The enzymatic characteristics to perform accurate DNA replication are in apparent contradiction with TLS or DNA repair abilities. For instance, replicative DNAPs incorporate nucleotides with high fidelity and processivity, whereas TLS DNAPs are low-fidelity polymerases with distributive nucleotide incorporation. Plant organelles (mitochondria and chloroplast) are replicated by family-A DNA polymerases that are both replicative and TLS DNAPs. Furthermore, plant organellar DNA polymerases from the plant model Arabidopsis thaliana (AtPOLIs) execute repair of double-stranded breaks by microhomology-mediated end-joining and perform Base Excision Repair (BER) using lyase and strand-displacement activities. AtPOLIs harbor three unique insertions in their polymerization domain that are associated with TLS, microhomology-mediated end-joining (MMEJ), strand-displacement, and lyase activities. We postulate that AtPOLIs are able to execute those different functions through the acquisition of these novel amino acid insertions, making them multifunctional enzymes able to participate in DNA replication and DNA repair.


Subject(s)
DNA Repair/physiology , DNA-Directed DNA Polymerase/genetics , Organelles/enzymology , Plant Proteins/genetics , Amino Acids/genetics , Amino Acids/metabolism , Arabidopsis/genetics , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , DNA End-Joining Repair/physiology , DNA-Directed DNA Polymerase/metabolism , Evolution, Molecular , Plant Proteins/metabolism
3.
Lett Appl Microbiol ; 71(4): 413-419, 2020 Oct.
Article in English | MEDLINE | ID: mdl-32623751

ABSTRACT

As a result of electron microscopic studies of morphogenesis in yeast Candida guilliermondii NP-4, the formation of new structures of volutin acidocalcisomes has been established within the cell cytoplasm. Under influence of X-irradiation, the changes in morphometric and electron-dense properties of yeast cells were identified: in yeast cytoplasm, the electron-dense volutin granules were increased up to 400 nm in size. After 24-h post-irradiation incubation of yeasts, the large volutin pellets are fragmented into smaller number particles in size up to 25-150 nm. The ATPase activity in yeast mitochondria was changed under X-irradiation. In latent phase of growth, ATPase activity was decreased 1·35-fold in comparison with non-irradiated yeasts. In logarithmic phase of growth, ATPase activity was three times higher than in latent phase, and in stationary phase of growth it has a value similar to the latent phase. Probably, the cells receive the necessary energy from alternative energy sources, such as volutin. Electron microscopy of volutin granule changes might serve as convenient method for evaluation of damages and repair processes in cells under influence of different environmental stress-factors.


Subject(s)
Adenosine Triphosphatases/metabolism , Candida/radiation effects , Candida/ultrastructure , Fungal Proteins/metabolism , Organelles/enzymology , Adenosine Triphosphatases/genetics , Adenosine Triphosphatases/ultrastructure , Adenosine Triphosphate/metabolism , Candida/enzymology , Candida/genetics , Fungal Proteins/chemistry , Fungal Proteins/genetics , Organelles/genetics , Organelles/radiation effects , Organelles/ultrastructure , X-Rays
4.
Nucleic Acids Res ; 48(11): 6353-6366, 2020 06 19.
Article in English | MEDLINE | ID: mdl-32396195

ABSTRACT

Most eukaryotic mRNAs harbor a characteristic 5' m7GpppN cap that promotes pre-mRNA splicing, mRNA nucleocytoplasmic transport and translation while also protecting mRNAs from exonucleolytic attacks. mRNA caps are eliminated by Dcp2 during mRNA decay, allowing 5'-3' exonucleases to degrade mRNA bodies. However, the Dcp2 decapping enzyme is poorly active on its own and requires binding to stable or transient protein partners to sever the cap of target mRNAs. Here, we analyse the role of one of these partners, the yeast Pby1 factor, which is known to co-localize into P-bodies together with decapping factors. We report that Pby1 uses its C-terminal domain to directly bind to the decapping enzyme. We solved the structure of this Pby1 domain alone and bound to the Dcp1-Dcp2-Edc3 decapping complex. Structure-based mutant analyses reveal that Pby1 binding to the decapping enzyme is required for its recruitment into P-bodies. Moreover, Pby1 binding to the decapping enzyme stimulates growth in conditions in which decapping activation is compromised. Our results point towards a direct connection of Pby1 with decapping and P-body formation, both stemming from its interaction with the Dcp1-Dcp2 holoenzyme.


Subject(s)
DNA-Binding Proteins/metabolism , Endoribonucleases/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Transcription Factors/metabolism , Adenosine Triphosphate/metabolism , Catalytic Domain , DNA-Binding Proteins/chemistry , Endopeptidases/chemistry , Endopeptidases/metabolism , Endoribonucleases/chemistry , Holoenzymes/chemistry , Holoenzymes/metabolism , Ligases/metabolism , Models, Molecular , Organelles/enzymology , Organelles/metabolism , Protein Binding , Protein Domains , Saccharomyces cerevisiae/cytology , Saccharomyces cerevisiae/enzymology , Saccharomyces cerevisiae Proteins/chemistry , Transcription Factors/chemistry
5.
Crit Rev Biochem Mol Biol ; 55(1): 17-32, 2020 02.
Article in English | MEDLINE | ID: mdl-32069425

ABSTRACT

AMP-activated protein kinase (AMPK) is a master regulator of energy homeostasis that functions to restore the energy balance by phosphorylating its substrates during altered metabolic conditions. AMPK activity is tightly controlled by diverse regulators including its upstream kinases LKB1 and CaMKK2. Recent studies have also identified the localization of AMPK at different intracellular compartments as another key mechanism for regulating AMPK signaling in response to specific stimuli. This review discusses the AMPK signaling associated with different subcellular compartments, including lysosomes, endoplasmic reticulum, mitochondria, Golgi apparatus, nucleus, and cell junctions. Because altered AMPK signaling is associated with various pathologic conditions including cancer, targeting AMPK signaling in different subcellular compartments may present attractive therapeutic approaches for treatment of disease.


Subject(s)
AMP-Activated Protein Kinases/metabolism , Neoplasm Proteins/metabolism , Neoplasms/enzymology , Organelles/enzymology , Signal Transduction , AMP-Activated Protein Kinase Kinases , Animals , Calcium-Calmodulin-Dependent Protein Kinase Kinase/metabolism , Humans , Neoplasms/pathology , Organelles/pathology , Phosphorylation , Protein Serine-Threonine Kinases/metabolism
6.
Microbiologyopen ; 9(5): e1010, 2020 05.
Article in English | MEDLINE | ID: mdl-32053746

ABSTRACT

Metabolosomes, catabolic bacterial microcompartments (BMCs), are proteinaceous organelles that are associated with the breakdown of metabolites such as propanediol and ethanolamine. They are composed of an outer multicomponent protein shell that encases a specific metabolic pathway. Protein cargo found within BMCs is directed by the presence of an encapsulation peptide that appears to trigger aggregation before the formation of the outer shell. We investigated the effect of three distinct encapsulation peptides on foreign cargo in a recombinant BMC system. Our data demonstrate that these peptides cause variations in enzyme activity and protein aggregation. We observed that the level of protein aggregation generally correlates with the size of metabolosomes, while in the absence of cargo BMCs self-assemble into smaller compartments. The results agree with a flexible model for BMC formation based around the ability of the BMC shell to associate with an aggregate formed due to the interaction of encapsulation peptides.


Subject(s)
Bacteria/metabolism , Bacterial Proteins/metabolism , Metallothionein/metabolism , Organelles/enzymology , Peptides/metabolism , Bacteria/genetics , Bacteria/ultrastructure , Bacterial Proteins/genetics , Genes, Bacterial , Metabolic Networks and Pathways , Organelles/ultrastructure , Peptides/genetics , Protein Transport , Pyruvate Decarboxylase/metabolism , Recombinant Proteins/genetics , Recombinant Proteins/metabolism
7.
Nat Commun ; 11(1): 388, 2020 01 20.
Article in English | MEDLINE | ID: mdl-31959751

ABSTRACT

Bacterial microcompartments (BMCs) are prokaryotic organelles consisting of a protein shell and an encapsulated enzymatic core. BMCs are involved in several biochemical processes, such as choline, glycerol and ethanolamine degradation and carbon fixation. Since non-native enzymes can also be encapsulated in BMCs, an improved understanding of BMC shell assembly and encapsulation processes could be useful for synthetic biology applications. Here we report the isolation and recombinant expression of BMC structural genes from the Klebsiella pneumoniae GRM2 locus, the investigation of mechanisms behind encapsulation of the core enzymes, and the characterization of shell particles by cryo-EM. We conclude that the enzymatic core is encapsulated in a hierarchical manner and that the CutC choline lyase may play a secondary role as an adaptor protein. We also present a cryo-EM structure of a pT = 4 quasi-symmetric icosahedral shell particle at 3.3 Å resolution, and demonstrate variability among the minor shell forms.


Subject(s)
Bacterial Proteins/metabolism , Klebsiella pneumoniae/cytology , Lyases/metabolism , Organelles/ultrastructure , Bacterial Proteins/genetics , Choline/metabolism , Cryoelectron Microscopy , Genetic Loci , Klebsiella pneumoniae/enzymology , Klebsiella pneumoniae/genetics , Klebsiella pneumoniae/ultrastructure , Lyases/genetics , Organelles/enzymology , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Synthetic Biology
8.
J Diabetes Res ; 2020: 8872639, 2020.
Article in English | MEDLINE | ID: mdl-33457426

ABSTRACT

The purpose of this review is to integrate the role of nutrient-sensing pathways into ß-cell organelle dysfunction prompted by nutrient excess during type 2 diabetes (T2D). T2D encompasses chronic hyperglycemia, hyperlipidemia, and inflammation, which each contribute to ß-cell failure. These factors can disrupt the function of critical ß-cell organelles, namely, the ER, mitochondria, lysosomes, and autophagosomes. Dysfunctional organelles cause defects in insulin synthesis and secretion and activate apoptotic pathways if homeostasis is not restored. In this review, we will focus on mTORC1 and OGT, two major anabolic nutrient sensors with important roles in ß-cell physiology. Though acute stimulation of these sensors frequently improves ß-cell function and promotes adaptation to cell stress, chronic and sustained activity disturbs organelle homeostasis. mTORC1 and OGT regulate organelle function by influencing the expression and activities of key proteins, enzymes, and transcription factors, as well as by modulating autophagy to influence clearance of defective organelles. In addition, mTORC1 and OGT activity influence islet inflammation during T2D, which can further disrupt organelle and ß-cell function. Therapies for T2D that fine-tune the activity of these nutrient sensors have yet to be developed, but the important role of mTORC1 and OGT in organelle homeostasis makes them promising targets to improve ß-cell function and survival.


Subject(s)
Blood Glucose/metabolism , Diabetes Mellitus, Type 2/enzymology , Insulin-Secreting Cells/enzymology , Organelles/enzymology , TOR Serine-Threonine Kinases/metabolism , Animals , Autophagy , Biomarkers/blood , Diabetes Mellitus, Type 2/blood , Diabetes Mellitus, Type 2/pathology , Glucose Tolerance Test , Homeostasis , Humans , Insulin-Secreting Cells/pathology , Mechanistic Target of Rapamycin Complex 1/metabolism
9.
Nature ; 573(7772): 144-148, 2019 09.
Article in English | MEDLINE | ID: mdl-31435012

ABSTRACT

The ability of proteins and nucleic acids to undergo liquid-liquid phase separation has recently emerged as an important molecular principle of how cells rapidly and reversibly compartmentalize their components into membrane-less organelles such as the nucleolus, processing bodies or stress granules1,2. How the assembly and turnover of these organelles are controlled, and how these biological condensates selectively recruit or release components are poorly understood. Here we show that members of the large and highly abundant family of RNA-dependent DEAD-box ATPases (DDXs)3 are regulators of RNA-containing phase-separated organelles in prokaryotes and eukaryotes. Using in vitro reconstitution and in vivo experiments, we demonstrate that DDXs promote phase separation in their ATP-bound form, whereas ATP hydrolysis induces compartment turnover and release of RNA. This mechanism of membrane-less organelle regulation reveals a principle of cellular organization that is conserved from bacteria to humans. Furthermore, we show that DDXs control RNA flux into and out of phase-separated organelles, and thus propose that a cellular network of dynamic, DDX-controlled compartments establishes biochemical reaction centres that provide cells with spatial and temporal control of various RNA-processing steps, which could regulate the composition and fate of ribonucleoprotein particles.


Subject(s)
Adenosine Triphosphatases/metabolism , Cell Compartmentation , DEAD-box RNA Helicases/metabolism , Eukaryotic Cells/enzymology , Organelles/enzymology , Organelles/metabolism , Prokaryotic Cells/enzymology , Biocatalysis , Cell Line , Conserved Sequence , Cytoplasmic Granules/metabolism , Eukaryotic Cells/cytology , Evolution, Molecular , Humans , Prokaryotic Cells/cytology , RNA/metabolism , RNA Transport , Saccharomyces cerevisiae/cytology , Saccharomyces cerevisiae/enzymology , Saccharomyces cerevisiae Proteins/metabolism
10.
Sci Rep ; 9(1): 8607, 2019 06 13.
Article in English | MEDLINE | ID: mdl-31197208

ABSTRACT

Cell membrane phospholipids regulate various biological functions. We previously reported enzymatic fluorometric methods for quantifying phosphatidic acid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, sphingomyelin, phosphatidylglycerol and cardiolipin. In the present report, a new enzymatic fluorometric assay was developed for quantifying phosphatidylinositol. These simple, sensitive and high-throughput methods enabled us to quantify all major phospholipid classes in cultured cells and intracellular organelles. By conducting comprehensive quantitative analyses of major phospholipid classes, we demonstrated that the contents of phospholipid classes in HEK293 cells changed with cell density and that overexpression of phosphatidylinositol synthase or CDP-diacylglycerol synthase significantly affected the phospholipid compositions of microsomal and mitochondrial membranes. These enzymatic fluorometric assays for measuring all major phospholipid classes may be applicable to tissues, fluids, lipoproteins, extracellular vesicles and intracellular organelles of many organisms and will further our understanding of cellular, physiological and pathological processes.


Subject(s)
Enzyme Assays , Fluorometry/methods , Intracellular Space/metabolism , Organelles/enzymology , Phospholipids/metabolism , Cell Count , HEK293 Cells , Humans , Microsomes/enzymology , Phosphatidylinositols/metabolism , Phospholipase D/metabolism
11.
Nat Nanotechnol ; 14(3): 252-259, 2019 03.
Article in English | MEDLINE | ID: mdl-30742135

ABSTRACT

Cellular reporters of enzyme activity are based on either fluorescent proteins or small molecules. Such reporters provide information corresponding to wherever inside cells the enzyme is maximally active and preclude minor populations present in subcellular compartments. Here we describe a chemical imaging strategy to selectively interrogate minor, subcellular pools of enzymatic activity. This new technology confines the detection chemistry to a designated organelle, enabling imaging of enzymatic cleavage exclusively within the organelle. We have thus quantitatively mapped disulfide reduction exclusively in endosomes in Caenorhabditis elegans and identified that exchange is mediated by minor populations of the enzymes PDI-3 and TRX-1 resident in endosomes. Impeding intra-endosomal disulfide reduction by knocking down TRX-1 protects nematodes from infection by Corynebacterium diphtheriae, revealing the importance of this minor pool of endosomal TRX-1. TRX-1 also mediates endosomal disulfide reduction in human cells. A range of enzymatic cleavage reactions in organelles are amenable to analysis by this new reporter strategy.


Subject(s)
DNA/chemistry , Nanoparticles/chemistry , Organelles/enzymology , Animals , Caenorhabditis elegans/metabolism , Diphtheria Toxin/metabolism , Disulfides/metabolism , Endosomes/metabolism , Genes, Reporter , HeLa Cells , Humans , Thioredoxins/metabolism
12.
FEBS J ; 285(21): 4005-4018, 2018 11.
Article in English | MEDLINE | ID: mdl-30152200

ABSTRACT

The coding sequences of plant mitochondrial and chloroplast genomes present a lower mutation rate than the coding sequences of animal mitochondria. However, plant mitochondrial genomes frequently rearrange and present high mutation rates in their noncoding sequences. DNA replication in plant organelles is carried out by two DNA polymerases (DNAP) paralogs. In Arabidopsis thaliana at least one DNAP paralog (AtPolIA or AtPolIB) is necessary for plant viability, suggesting that both genes are partially redundant. To understand how AtPolIs replicate genomes that present low and high mutation rates, we measured their nucleotide incorporation for all 16-base pair combinations in vitro. AtPolIA presents an error rate of 7.26 × 10-5 , whereas AtPolIB has an error rate of 5.45 × 10-4 . Thus, AtPolIA and AtPolIB are 3.5 and 26-times less accurate than human mitochondrial DNAP γ. The 8-fold difference in fidelity between both AtPolIs results from a higher catalytic efficiency in AtPolIA. Both AtPolIs extend from mismatches and the fidelity of AtPolIs ranks between high fidelity and lesion bypass DNAPs. The different nucleotide incorporation fidelity between AtPolIs predicts a prevalent role of AtPolIA in DNA replication and AtPolIB in DNA repair. We hypothesize that in plant organelles, DNA mismatches generated during DNA replication are repaired via recombination-mediated or DNA mismatch repair mechanisms that selectively target the coding region and that the mismatches generated by AtPolIs may result in the frequent expansion and rearrangements present in plant mitochondrial genomes.


Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/enzymology , DNA Replication , DNA, Plant/genetics , DNA-Directed DNA Polymerase/metabolism , Nucleotides/genetics , Organelles/enzymology , Arabidopsis/genetics , Arabidopsis Proteins/chemistry , Arabidopsis Proteins/genetics , Base Sequence , DNA Damage , DNA Repair , DNA-Directed DNA Polymerase/chemistry , DNA-Directed DNA Polymerase/genetics , Organelles/genetics , Protein Conformation
13.
Nat Commun ; 9(1): 1127, 2018 03 19.
Article in English | MEDLINE | ID: mdl-29555899

ABSTRACT

Despite tremendous efforts to develop stimuli-responsive enzyme delivery systems, their efficacy has been mostly limited to in vitro applications. Here we introduce, by using an approach of combining biomolecules with artificial compartments, a biomimetic strategy to create artificial organelles (AOs) as cellular implants, with endogenous stimuli-triggered enzymatic activity. AOs are produced by inserting protein gates in the membrane of polymersomes containing horseradish peroxidase enzymes selected as a model for natures own enzymes involved in the redox homoeostasis. The inserted protein gates are engineered by attaching molecular caps to genetically modified channel porins in order to induce redox-responsive control of the molecular flow through the membrane. AOs preserve their structure and are activated by intracellular glutathione levels in vitro. Importantly, our biomimetic AOs are functional in vivo in zebrafish embryos, which demonstrates the feasibility of using AOs as cellular implants in living organisms. This opens new perspectives for patient-oriented protein therapy.


Subject(s)
Artificial Cells/metabolism , Biomimetic Materials , Cellular Microenvironment/physiology , Amino Acid Substitution , Animals , Biocatalysis , Bioengineering , Biomimetics , HeLa Cells , Humans , Organelles/enzymology , Porins/chemistry , Porins/genetics , Porins/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Zebrafish/embryology
14.
PLoS One ; 13(3): e0194451, 2018.
Article in English | MEDLINE | ID: mdl-29547664

ABSTRACT

P5B ATPases are present in the genomes of diverse unicellular and multicellular eukaryotes, indicating that they have an ancient origin, and that they are important for cellular fitness. Inactivation of ATP13A2, one of the four human P5B ATPases, leads to early-onset Parkinson's disease (Kufor-Rakeb Syndrome). The presence of an invariant PPALP motif within the putative substrate interaction pocket of transmembrane segment M4 suggests that all P5B ATPases might have similar transport specificity; however, the identity of the transport substrate(s) remains unknown. Nematodes of the genus Caenorhabditis possess three paralogous P5B ATPase genes, catp-5, catp-6 and catp-7, which probably originated from a single ancestral gene around the time of origin of the Caenorhabditid clade. By using CRISPR/Cas9, we have systematically investigated the expression patterns, subcellular localization and biological functions of each of the P5B ATPases of C. elegans. We find that each gene has a unique expression pattern, and that some tissues express more than one P5B. In some tissues where their expression patterns overlap, different P5Bs are targeted to different subcellular compartments (e.g., early endosomes vs. plasma membrane), whereas in other tissues they localize to the same compartment (plasma membrane). We observed lysosomal co-localization between CATP-6::GFP and LMP-1::RFP in transgenic animals; however, this was an artifact of the tagged LMP-1 protein, since anti-LMP-1 antibody staining of native protein revealed that LMP-1 and CATP-6::GFP occupy different compartments. The nematode P5Bs are at least partially redundant, since we observed synthetic sterility in catp-5(0); catp-6(0) and catp-6(0) catp-7(0) double mutants. The double mutants exhibit defects in distal tip cell migration that resemble those of ina-1 (alpha integrin ortholog) and vab-3 (Pax6 ortholog) mutants, suggesting that the nematode P5Bs are required for ina-1and/or vab-3 function. This is potentially a conserved regulatory interaction, since mammalian ATP13A2, alpha integrin and Pax6 are all required for proper dopaminergic neuron function.


Subject(s)
Adenosine Triphosphatases/genetics , Caenorhabditis elegans Proteins/genetics , Caenorhabditis elegans/genetics , Gene Expression Profiling , Gene Expression Regulation, Enzymologic , Adenosine Triphosphatases/classification , Adenosine Triphosphatases/metabolism , Amino Acid Sequence , Animals , Animals, Genetically Modified , Caenorhabditis elegans/cytology , Caenorhabditis elegans/enzymology , Caenorhabditis elegans Proteins/metabolism , Cell Movement/genetics , Luminescent Proteins/genetics , Luminescent Proteins/metabolism , Membrane Proteins/genetics , Membrane Proteins/metabolism , Mutation , Organelles/enzymology , Phylogeny , Sequence Homology, Amino Acid
15.
PLoS One ; 13(3): e0193538, 2018.
Article in English | MEDLINE | ID: mdl-29509772

ABSTRACT

The ability of Plasmodium parasites to egress from their host red blood cell is critical for the amplification of these parasites in the blood. Previous forward chemical genetic approaches have implicated the subtilisin-like protease (SUB1) and the cysteine protease dipeptidyl aminopeptidase 3 (DPAP3) as key players in egress, with the final step of SUB1 maturation thought to be due to the activity of DPAP3. In this study, we have utilized a reverse genetics approach to engineer transgenic Plasmodium falciparum parasites in which dpap3 expression can be conditionally regulated using the glmS ribozyme based RNA-degrading system. We show that DPAP3, which is expressed in schizont stages and merozoites and localizes to organelles distinct from the micronemes, rhoptries and dense granules, is not required for the trafficking of apical proteins or processing of SUB1 substrates, nor for parasite maturation and egress from red blood cells. Thus, our findings argue against a role for DPAP3 in parasite egress and indicate that the phenotypes observed with DPAP3 inhibitors are due to off-target effects.


Subject(s)
Dipeptidyl-Peptidases and Tripeptidyl-Peptidases/metabolism , Erythrocytes/parasitology , Plasmodium falciparum/enzymology , Blotting, Western , Dipeptidyl-Peptidases and Tripeptidyl-Peptidases/genetics , Fluorescent Antibody Technique, Indirect , Gene Expression , Gene Knockdown Techniques , Humans , Microscopy, Immunoelectron , Organelles/enzymology , Organisms, Genetically Modified , Plasmodium falciparum/genetics , Plasmodium falciparum/growth & development , Protein Transport/physiology , Protozoan Proteins/metabolism , Real-Time Polymerase Chain Reaction , Subtilisins/metabolism
16.
Angew Chem Int Ed Engl ; 56(51): 16233-16238, 2017 12 18.
Article in English | MEDLINE | ID: mdl-28967234

ABSTRACT

Next-generation therapeutic approaches are expected to rely on the engineering of biomimetic cellular systems that can mimic specific cellular functions. Herein, we demonstrate a highly effective route for constructing structural and functional eukaryotic cell mimics by loading pH-sensitive polymersomes as membrane-associated and free-floating organelle mimics inside the multifunctional cell membrane. Metabolism mimicry has been validated by performing successive enzymatic cascade reactions spatially separated at specific sites of cell mimics in the presence and absence of extracellular organelle mimics. These enzymatic reactions take place in a highly controllable, reproducible, efficient, and successive manner. Our biomimetic approach to material design for establishing functional principles brings considerable enrichment to the fields of biomedicine, biocatalysis, biotechnology, and systems biology.


Subject(s)
Biocatalysis , Biomimetic Materials/metabolism , Enzymes/metabolism , Eukaryotic Cells/metabolism , Organelles/metabolism , Biomimetic Materials/chemistry , Cell Membrane/enzymology , Cell Membrane/metabolism , Enzymes/chemistry , Eukaryotic Cells/enzymology , Hydrogen-Ion Concentration , Organelles/enzymology , Particle Size , Surface Properties , Temperature
17.
Nanoscale ; 9(30): 10662-10673, 2017 Aug 03.
Article in English | MEDLINE | ID: mdl-28616951

ABSTRACT

Carboxysomes are proteinaceous organelles that play essential roles in enhancing carbon fixation in cyanobacteria and some proteobacteria. These self-assembling organelles encapsulate Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase using a protein shell structurally resembling an icosahedral viral capsid. The protein shell serves as a physical barrier to protect enzymes from the cytosol and a selectively permeable membrane to mediate transport of enzyme substrates and products. The structural and mechanical nature of native carboxysomes remain unclear. Here, we isolate functional ß-carboxysomes from the cyanobacterium Synechococcus elongatus PCC7942 and perform the first characterization of the macromolecular architecture and inherent physical mechanics of single ß-carboxysomes using electron microscopy, atomic force microscopy (AFM) and proteomics. Our results illustrate that the intact ß-carboxysome comprises three structural domains, a single-layered icosahedral shell, an inner layer and paracrystalline arrays of interior Rubisco. We also observe the protein organization of the shell and partial ß-carboxysomes that likely serve as the ß-carboxysome assembly intermediates. Furthermore, the topography and intrinsic mechanics of functional ß-carboxysomes are determined in native conditions using AFM and AFM-based nanoindentation, revealing the flexible organization and soft mechanical properties of ß-carboxysomes compared to rigid viruses. Our study provides new insights into the natural characteristics of ß-carboxysome organization and nanomechanics, which can be extended to diverse bacterial microcompartments and are important considerations for the design and engineering of functional carboxysomes in other organisms to supercharge photosynthesis. It offers an approach for inspecting the structural and mechanical features of synthetic metabolic organelles and protein scaffolds in bioengineering.


Subject(s)
Carbon Cycle , Organelles/ultrastructure , Synechococcus/cytology , Bacterial Proteins/metabolism , Carbonic Anhydrases/metabolism , Organelles/enzymology , Photosynthesis , Ribulose-Bisphosphate Carboxylase/metabolism
18.
Proc Natl Acad Sci U S A ; 114(12): E2460-E2465, 2017 03 21.
Article in English | MEDLINE | ID: mdl-28193863

ABSTRACT

A large number of genes are necessary for the biosynthesis and activity of the enzyme nitrogenase to carry out the process of biological nitrogen fixation (BNF), which requires large amounts of ATP and reducing power. The multiplicity of the genes involved, the oxygen sensitivity of nitrogenase, plus the demand for energy and reducing power, are thought to be major obstacles to engineering BNF into cereal crops. Genes required for nitrogen fixation can be considered as three functional modules encoding electron-transport components (ETCs), proteins required for metal cluster biosynthesis, and the "core" nitrogenase apoenzyme, respectively. Among these modules, the ETC is important for the supply of reducing power. In this work, we have used Escherichia coli as a chassis to study the compatibility between molybdenum and the iron-only nitrogenases with ETC modules from target plant organelles, including chloroplasts, root plastids, and mitochondria. We have replaced an ETC module present in diazotrophic bacteria with genes encoding ferredoxin-NADPH oxidoreductases (FNRs) and their cognate ferredoxin counterparts from plant organelles. We observe that the FNR-ferredoxin module from chloroplasts and root plastids can support the activities of both types of nitrogenase. In contrast, an analogous ETC module from mitochondria could not function in electron transfer to nitrogenase. However, this incompatibility could be overcome with hybrid modules comprising mitochondrial NADPH-dependent adrenodoxin oxidoreductase and the Anabaena ferredoxins FdxH or FdxB. We pinpoint endogenous ETCs from plant organelles as power supplies to support nitrogenase for future engineering of diazotrophy in cereal crops.


Subject(s)
Escherichia coli/enzymology , Eukaryota/enzymology , Nitrogenase/metabolism , Organelles/enzymology , Anabaena/enzymology , Anabaena/genetics , Electron Transport , Escherichia coli/genetics , Escherichia coli/metabolism , Eukaryota/genetics , Eukaryota/metabolism , Ferredoxin-NADP Reductase/genetics , Ferredoxin-NADP Reductase/metabolism , Molybdenum/metabolism , Nitrogenase/genetics , Organelles/genetics , Oxidation-Reduction
19.
Cell Microbiol ; 19(3)2017 03.
Article in English | MEDLINE | ID: mdl-27649068

ABSTRACT

HSP90 chaperones are essential regulators of cellular function, as they ensure the appropriate conformation of multiple key client proteins. Four HSP90 isoforms were identified in the protozoan parasite Theileria annulata. Partial characterization was undertaken for three and localization confirmed for cytoplasmic (TA12105), endoplasmic reticulum (TA06470), and apicoplast (TA10720) forms. ATPase activity and binding to the HSP90 inhibitor geldanamycin were demonstrated for recombinant TA12105, and all three native forms could be isolated to varying extents by binding to geldanamycin beads. Because it is essential, HSP90 is considered a potential therapeutic drug target. Resistance to the only specific Theileriacidal drug is increasing, and one challenge for design of drugs that target the parasite is to limit the effect on the host. An in vitro cell culture system that allows comparison between uninfected bovine cells and the T. annulata-infected counterpart was utilized to test the effects of geldanamycin and the derivative 17-AAG. T. annulata-infected cells had greater tolerance to geldanamycin than uninfected cells yet exhibited significantly more sensitivity to 17-AAG. These findings suggest that parasite HSP90 isoform(s) can alter the drug sensitivity of infected host cells and that members of the Theileria HSP90 family are potential targets worthy of further investigation.


Subject(s)
HSP90 Heat-Shock Proteins/analysis , Leukocytes/parasitology , Organelles/enzymology , Protein Isoforms/analysis , Theileria annulata/enzymology , Animals , Cattle , Cells, Cultured
20.
Adv Healthc Mater ; 6(4)2017 Feb.
Article in English | MEDLINE | ID: mdl-28004530

ABSTRACT

The creation of artificial organelles is a new paradigm in medical therapy that aims to substitute for missing cellular function by replenishing a specific cellular task. Artificial organelles tackle the challenge of mimicking metabolism, which is the set of chemical reactions that occur within a cell, mainly catalyzed by enzymes. So far, the few reported carriers able to conduct enzymatic reactions intracellularly are based on single-compartment carriers. However, cell organelles outperform by conducting multiple reactions simultaneously within confined sub-compartments. Here, the field of artificial organelles is advanced by reporting the assembly of a microreactor consisting of polymer capsules entrapping gold nanoclusters (AuNCs) and liposomes as sub-compartments. The fluorescence properties of AuNCs are employed to monitor the microreactors uptake by macrophages. Encapsulation is demonstrated and functionality of microreactors with trypsin (TRP) and horseradish peroxidase (HRP)-loaded liposomes is preserved. Multiple enzymatic reactions taking place simultaneously is demonstrated by exposing macrophages with the internalized microreactors to bis-(benzyloxycarbonyl-Ile-Pro-Arg)-Rho-110 and Amplex Red substrates, which are specific for TRP and HRP, respectively. Conversion of the substrates into the respective fluorescent products is observed. This report on the first microreactor conducting multiple enzymatic reactions simultaneously inside a cell is a considerable step in the field of artificial organelles.


Subject(s)
Gold/chemistry , Liposomes/chemistry , Metal Nanoparticles/chemistry , Organelles , Trypsin/chemistry , Animals , Cattle , Horseradish Peroxidase/chemistry , Organelles/chemistry , Organelles/enzymology
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