scholarly journals An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism

2020 ◽  
Author(s):  
Mitchell G. Thompson ◽  
Jacquelyn M. Blake-Hedges ◽  
Jose Henrique Pereira ◽  
John A. Hangasky ◽  
Michael S. Belcher ◽  
...  
Keyword(s):  
Physiological Function ◽  
Germination Rate ◽  
Structural Similarity ◽  
Free Form ◽  
Dependent Manner ◽  
Bacterial Fermentation ◽  
Sequence Identity ◽  
Domains Of Life ◽  
Multiple Domains ◽  
Lysine Catabolism

AbstractDue to low abundance in many staple food crops, the essential amino acid lysine must be produced industrially to meet global food supply needs. Despite intensive study, manipulation, and agricultural importance, the steps of plant lysine catabolism beyond the 2-oxoadipate (2OA) intermediate remain undescribed. Recently we described a missing step in the D-lysine catabolic pathway of the bacterium Pseudomonas putida in which 2OA is converted to D-2-hydroxyglutarate (D2HG) via hydroxyglutarate synthase (HglS), an enzyme belonging to the previously uncharacterized DUF1338 protein family. Here we solve the structure of HglS to 1.1Å resolution in the substrate-free form and in complex with 2OA. Structural similarity to hydroxymandelate synthase suggested a successive decarboxylation and intramolecular hydroxylation mechanism forming 2HG in a Fe(II)- and O2-dependent manner, which is validated experimentally. 2OA specificity was mediated by a single arginine (R74), highly conserved across nearly all DUF1338 family proteins, including in 76% of plant enzymes. In Arabidopsis thaliana, a DUF1338 homolog is coexpressed with known lysine catabolism enzymes, and mutants show significant germination rate defects consistent with disrupted lysine catabolism. Structural and biochemical analysis of the Oryza sativa homolog FLO7 revealed identical activity to HglS despite low sequence identity. Our results suggest that nearly all DUF1338 containing enzymes likely catalyze the same biochemical reaction, exerting the same physiological function across bacteria and eukaryotes.SignificanceTo meet human demands, millions of tons of lysine are produced by bacterial fermentation annually due to its low abundance in staple crops. Here, we show the last missing step of lysine catabolism in nearly all plant endosperms is likely catalyzed by an iron-dependant DUF1338-containing enzyme homologous to the bacterial hydroxyglutarate synthase. Structural and bioninformatic analyses of DUF1338-containing enzymes showed high conservation of critical catalytic and specificity-conferring residues across multiple domains of life despite low sequence identity. These results suggest that the DUF1338 family evolved a specific physiological function within lysine catabolism across multiple domains of life.

scholarly journals Captivating Perplexities of Spinareovirinae 5′ RNA Caps

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 294
Author(s):  
Justine Kniert ◽  
Qi Feng Lin ◽  
Maya Shmulevitz
Keyword(s):  
Immune Recognition ◽  
Domains Of Life ◽  
The Many ◽  
Rna Capping ◽  
Multiple Domains ◽  
Rna Caps

RNAs with methylated cap structures are present throughout multiple domains of life. Given that cap structures play a myriad of important roles beyond translation, such as stability and immune recognition, it is not surprising that viruses have adopted RNA capping processes for their own benefit throughout co-evolution with their hosts. In fact, that RNAs are capped was first discovered in a member of the Spinareovirinae family, Cypovirus, before these findings were translated to other domains of life. This review revisits long-past knowledge and recent studies on RNA capping among members of Spinareovirinae to help elucidate the perplex processes of RNA capping and functions of RNA cap structures during Spinareovirinae infection. The review brings to light the many uncertainties that remain about the precise capping status, enzymes that facilitate specific steps of capping, and the functions of RNA caps during Spinareovirinae replication.

scholarly journals The Demethoxy Derivatives of Curcumin Exhibit Greater Differentiation Suppression in 3T3-L1 Adipocytes Than Curcumin: A Mechanistic Study of Adipogenesis and Molecular Docking

Biomolecules ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1025
Author(s):  
Ahmed Alalaiwe ◽  
Jia-You Fang ◽  
Hsien-Ju Lee ◽  
Chun-Hui Chiu ◽  
Ching-Yun Hsu
Keyword(s):  
Molecular Docking ◽  
Fatty Acid Synthase ◽  
Structural Similarity ◽  
Mechanistic Study ◽  
Peroxisome Proliferator ◽  
Dependent Manner ◽  
Peroxisome Proliferator Activated Receptor ◽  
Enhancer Binding Protein ◽  
Underlying Mechanisms ◽  
Amp Activated Protein Kinase

Curcumin is a known anti-adipogenic agent for alleviating obesity and related disorders. Comprehensive comparisons of the anti-adipogenic activity of curcumin with other curcuminoids is minimal. This study compared adipogenesis inhibition with curcumin, demethoxycurcumin (DMC), and bisdemethoxycurcumin (BDMC), and their underlying mechanisms. We differentiated 3T3-L1 cells in the presence of curcuminoids, to determine lipid accumulation and triglyceride (TG) production. The expression of adipogenic transcription factors and lipogenic proteins was analyzed by Western blot. A significant reduction in Oil red O (ORO) staining was observed in the cells treated with curcuminoids at 20 μM. Inhibition was increased in the order of curcumin < DMC < BDMC. A similar trend was observed in the detection of intracellular TG. Curcuminoids suppressed differentiation by downregulating the expression of peroxisome proliferator-activated receptor γ (PPARγ) and CCAAT/enhancer-binding protein α (C/EBPα), leading to the downregulation of the lipogenic enzymes acetyl-CoA carboxylase (ACC) and fatty acid synthase (FAS). AMP-activated protein kinase α (AMPKα) phosphorylation was also activated by BDMC. Curcuminoids reduced the release of proinflammatory cytokines and leptin in 3T3-L1 cells in a dose-dependent manner, with BDMC showing the greatest potency. BDMC at 20 μM significantly decreased leptin by 72% compared with differentiated controls. Molecular docking computation indicated that curcuminoids, despite having structural similarity, had different interaction positions to PPARγ, C/EBPα, and ACC. The docking profiles suggested a possible interaction of curcuminoids with C/EBPα and ACC, to directly inhibit their expression.

scholarly journals Potentiating Effect of Mandelate and Lactate on Chemically Induced Germination in Members of Bacillus cereus Sensu Lato

2017 ◽  
Vol 83 (24) ◽  
Author(s):  
Alistair H. Bishop
Keyword(s):  
Bacillus Cereus ◽  
Large Scale ◽  
Germination Rate ◽  
Dependent Manner ◽  
Clostridium Sporogenes ◽  
Specific Chemical ◽  
Content Type ◽  
Ph Range ◽  
Significant Discovery ◽  
The Impact

ABSTRACT Endospores of the genus Bacillus can be triggered to germinate by a limited number of chemicals. Mandelate had powerful additive effects on the levels and rates of germination produced in non-heat-shocked spores of Bacillus anthracis strain Sterne, Bacillus cereus, and Bacillus thuringiensis when combined with l-alanine and inosine. Mandelate had no germinant effect on its own but was active with these germinants in a dose-dependent manner at concentrations higher than 0.5 mM. The maximum rate and extent of germination were produced in B. anthracis by 100 mM l-alanine with 10 mM inosine; this was equaled by just 25% of these germinants when supplemented with 10 mM mandelate. Half the maximal germination rate was produced by 40% of the optimum germinant concentrations or 15% of them when supplemented with 0.8 mM mandelate. Germination rates in B. thuringiensis were highest around neutrality, but the potentiating effect of mandelate was maintained over a wider pH range than was germination with l-alanine and inosine alone. For all species, lactate also promoted germination in the presence of l-alanine and inosine; this was further increased by mandelate. Ammonium ions also enhanced l-alanine- and inosine-induced germination but only when mandelate was present. In spite of the structural similarities, mandelate did not compete with phenylalanine as a germinant. Mandelate appeared to bind to spores while enhancing germination. There was no effect when mandelate was used in conjunction with nonnutrient germinants. No effect was produced with spores of Bacillus subtilis, Clostridium sporogenes, or C. difficile. IMPORTANCE The number of chemicals that can induce germination in the species related to Bacillus cereus has been defined for many years, and they conform to specific chemical types. Although not a germinant itself, mandelate has a structure that is different from these germination-active compounds, and its addition to this list represents a significant discovery in the fundamental biology of spore germination. This novel activity may also have important applied relevance given the impact of spores of B. cereus in foodborne disease and B. anthracis as a threat agent. The destruction of spores of B. anthracis, for example, particularly over large outdoor areas, poses significant scientific and logistical problems. The addition of mandelate and lactate to the established mixtures of l-alanine and inosine would decrease the amount of the established germinants required and increase the speed and level of germination achieved. The large-scale application of “germinate to decontaminate” strategy may thus become more practicable.

Structural Similarity between the Prion Domain of HET-s and a Homologue Can Explain Amyloid Cross-Seeding in Spite of Limited Sequence Identity

2010 ◽  
Vol 402 (2) ◽  
pp. 311-325 ◽  
Author(s):  
Christian Wasmer ◽  
Agnes Zimmer ◽  
Raimon Sabaté ◽  
Alice Soragni ◽  
Sven J. Saupe ◽  
...  
Keyword(s):  
Structural Similarity ◽  
Sequence Identity ◽  
Limited Sequence

scholarly journals Novel Galectin-3 Roles in Neurogenesis, Inflammation and Neurological Diseases

Cells ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 3047
Author(s):  
Luana C. Soares ◽  
Osama Al-Dalahmah ◽  
James Hillis ◽  
Christopher C. Young ◽  
Isaiah Asbed ◽  
...  
Keyword(s):  
Brain Injuries ◽  
Neurological Diseases ◽  
Structural Similarity ◽  
Bmp Signaling ◽  
Brain Inflammation ◽  
Molecular Pathways ◽  
Dependent Manner ◽  
Multifunctional Protein ◽  
Natural Ligand ◽  
Galectin 3

Galectin-3 (Gal-3) is an evolutionarily conserved and multifunctional protein that drives inflammation in disease. Gal-3′s role in the central nervous system has been less studied than in the immune system. However, recent studies show it exacerbates Alzheimer’s disease and is upregulated in a large variety of brain injuries, while loss of Gal-3 function can diminish symptoms of neurodegenerative diseases such as Alzheimer’s. Several novel molecular pathways for Gal-3 were recently uncovered. It is a natural ligand for TREM2 (triggering receptor expressed on myeloid cells), TLR4 (Toll-like receptor 4), and IR (insulin receptor). Gal-3 regulates a number of pathways including stimulation of bone morphogenetic protein (BMP) signaling and modulating Wnt signalling in a context-dependent manner. Gal-3 typically acts in pathology but is now known to affect subventricular zone (SVZ) neurogenesis and gliogenesis in the healthy brain. Despite its myriad interactors, Gal-3 has surprisingly specific and important functions in regulating SVZ neurogenesis in disease. Gal-1, a similar lectin often co-expressed with Gal-3, also has profound effects on brain pathology and adult neurogenesis. Remarkably, Gal-3′s carbohydrate recognition domain bears structural similarity to the SARS-CoV-2 virus spike protein necessary for cell entry. Gal-3 can be targeted pharmacologically and is a valid target for several diseases involving brain inflammation. The wealth of molecular pathways now known further suggest its modulation could be therapeutically useful.

scholarly journals Effect of Ammonia and Indole-3-acetic Acid Producing Endophytic Klebsiella pneumoniae YNA12 as a Bio-Herbicide for Weed Inhibition: Special Reference with Evening Primroses

Plants ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 761
Author(s):  
Sang-Mo Kang ◽  
Saqib Bilal ◽  
Raheem Shahzad ◽  
Yu-Na Kim ◽  
Chang-Wook Park ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Klebsiella Pneumoniae ◽  
Culture Filtrate ◽  
Catalase Activity ◽  
Endophytic Bacteria ◽  
Germination Rate ◽  
Herbicidal Activity ◽  
Dependent Manner ◽  
Evening Primrose ◽  
Indole 3 Acetic Acid

Information on the use of endophytic bacteria as a bio-herbicide for the management of weed control in agricultural fields is limited. The current study aimed to isolate endophytic bacteria from evening primroses and to screen them for their bio-herbicidal activity. Two isolated endophytic bacteria (Pantoea dispersa YNA11 and Klebsiella pneumoniae YNA12) were initially screened for citrate utilization and for indole-3-acetic acid (IAA) and catalase production. The preliminary biochemical assessment showed YNA12 as a positive strain. Ammonia, catalase, and IAA in its culture filtrate were quantified. Gas Chromatography/Mass Spectroscopy- Selective Ion Monitoring (GC/MS-SIM) analysis revealed the production of IAA by YNA12 in a time-dependent manner. YNA12 also exhibited significant ammonia-producing potential and catalase activity against hydrogen peroxide. The YNA12 culture filtrate significantly inhibited the germination rate of evening primrose seeds, resulting in a marked reduction in seedling length and biomass compared with those of the control seeds. Moreover, the culture filtrate of YNA12 significantly accelerated the endogenous abscisic acid (ABA) production and catalase activity of evening primrose seedlings. Macronutrient regulation was adversely affected in the seedlings exposed to the culture filtrate of YNA12, leading to inhibition of seed germination. The current results suggest that endophytic YNA12 may be used as a potent bio-herbicidal agent for controlling weed growth and development.

scholarly journals Progression from remodeling to hibernation of ribosomes in zinc-starved mycobacteria

2020 ◽  
Vol 117 (32) ◽  
pp. 19528-19537
Author(s):  
Yunlong Li ◽  
Jamie H. Corro ◽  
Christopher D. Palmer ◽  
Anil K. Ojha
Keyword(s):  
Zinc Concentration ◽  
Specific Protein ◽  
Zinc Binding ◽  
Free Form ◽  
Dependent Manner ◽  
Drug Resistant ◽  
Zinc Depletion ◽  
Cellular Zinc ◽  
Mouse Lungs ◽  
Insight Into

Zinc starvation in mycobacteria leads to remodeling of ribosomes, in which multiple ribosomal (r-) proteins containing the zinc-binding CXXC motif are replaced by their motif-free paralogues, collectively called C− r-proteins. We previously reported that the 70S C− ribosome is exclusively targeted for hibernation by mycobacterial-specific protein Y (Mpy), which binds to the decoding center and stabilizes the ribosome in an inactive and drug-resistant state. In this study, we delineate the conditions for ribosome remodeling and hibernation and provide further insight into how zinc depletion induces Mpy recruitment to C− ribosomes. Specifically, we show that ribosome hibernation in a batch culture is induced at an approximately two-fold lower cellular zinc concentration than remodeling. We further identify a growth phase in which the C− ribosome remains active, while its hibernation is inhibited by the caseinolytic protease (Clp) system in a zinc-dependent manner. The Clp protease system destabilizes a zinc-bound form of Mpy recruitment factor (Mrf), which is stabilized upon further depletion of zinc, presumably in a zinc-free form. Stabilized Mrf binds to the 30S subunit and recruits Mpy to the ribosome. Replenishment of zinc to cells harboring hibernating ribosomes restores Mrf instability and dissociates Mpy from the ribosome. Finally, we demonstrate zinc-responsive binding of Mpy to ribosomes inMycobacterium tuberculosis(Mtb) and show Mpy-dependent antibiotic tolerance of Mtb in mouse lungs. Together, we propose that ribosome hibernation is a specific and conserved response to zinc depletion in both environmental and pathogenic mycobacteria.

Data Integration Through Protein Ontology

2011 ◽  
pp. 106-122
Author(s):  
Amandeep S. Sidhu ◽  
Tharam S. Dillon ◽  
Elizabeth Chang
Keyword(s):  
Hierarchical Classification ◽  
Structural Similarity ◽  
Protein Annotation ◽  
Functional Identification ◽  
Sequence Identity ◽  
Alternative Protein ◽  
Traditional Approaches ◽  
High Degree ◽  
Keyword Searches

Traditional approaches to integrate protein data generally involved keyword searches, which immediately excludes unannotated or poorly annotated data. An alternative protein annotation approach is to rely on sequence identity, or structural similarity, or functional identification. Some proteins have high degree of sequence identity, or structural similarity, or similarity in functions that are unique to members of that family alone. Consequently, this approach can’t be generalized to integrate the protein data. Clearly, these traditional approaches have limitations in capturing and integrating data for Protein Annotation. For these reasons, we have adopted an alternative method that does not rely on keywords or similarity metrics, but instead uses ontology. In this chapter we discuss conceptual framework of Protein Ontology that has a hierarchical classification of concepts represented as classes, from general to specific; a list of attributes related to each concept, for each class; a set of relations between classes to link concepts in ontology in more complicated ways then implied by the hierarchy, to promote reuse of concepts in the ontology; and a set of algebraic operators for querying protein ontology instances.

Involvement of the recoverin C-terminal segment in recognition of the target enzyme rhodopsin kinase

2011 ◽  
Vol 435 (2) ◽  
pp. 441-450 ◽  
Author(s):  
Evgeni Yu. Zernii ◽  
Konstantin E. Komolov ◽  
Sergei E. Permyakov ◽  
Tatiana Kolpakova ◽  
Daniele Dell'orco ◽  
...  
Keyword(s):  
Structural Control ◽  
Target Recognition ◽  
Computational Modelling ◽  
Structural Similarity ◽  
Terminal Segment ◽  
Site Directed Mutagenesis ◽  
Resonance Spectroscopy ◽  
Dependent Manner ◽  
C Terminus ◽  
Rhodopsin Kinase

NCS (neuronal Ca2+ sensor) proteins belong to a family of calmodulin-related EF-hand Ca2+-binding proteins which, in spite of a high degree of structural similarity, are able to selectively recognize and regulate individual effector enzymes in a Ca2+-dependent manner. NCS proteins vary at their C-termini, which could therefore serve as structural control elements providing specific functions such as target recognition or Ca2+ sensitivity. Recoverin, an NCS protein operating in vision, regulates the activity of rhodopsin kinase, GRK1, in a Ca2+-dependent manner. In the present study, we investigated a series of recoverin forms that were mutated at the C-terminus. Using pull-down assays, surface plasmon resonance spectroscopy and rhodopsin phosphorylation assays, we demonstrated that truncation of recoverin at the C-terminus significantly reduced the affinity of recoverin for rhodopsin kinase. Site-directed mutagenesis of single amino acids in combination with structural analysis and computational modelling of the recoverin–kinase complex provided insight into the protein–protein interface between the kinase and the C-terminus of recoverin. Based on these results we suggest that Phe3 from the N-terminal helix of rhodopsin kinase and Lys192 from the C-terminal segment of recoverin form a cation–π interaction pair which is essential for target recognition by recoverin. Taken together, the results of the present study reveal a novel rhodopsin-kinase-binding site within the C-terminal region of recoverin, and highlights its significance for target recognition and regulation.

scholarly journals Crystal Structure of the Dog Allergen Can f 6

2019 ◽  
Author(s):  
Gina M Clayton ◽  
Janice White ◽  
John W Kappler ◽  
Sanny K Chan
Keyword(s):  
Ligand Binding ◽  
Structural Similarity ◽  
Binding Pocket ◽  
Cross Reactivity ◽  
Binding Partner ◽  
Sequence Identity ◽  
Natural Ligand ◽  
Binding Cavity ◽  
Can F 1 ◽  
High Degree

AbstractLipocalins represent the most important protein family of the mammalian respiratory allergens. Four of the seven named dog allergens are lipocalins: Can f 1, Can f 2, Can f 4, and Can f 6. We present the structure of Can f 6 along with data on the biophysical and biological activity of this protein in comparison with other animal lipocalins. The Can f 6 structure displays the classic lipocalin calyx-shaped ligand binding cavity within a central β-barrel similar to other lipocalins. Despite low sequence identity between the different dog lipocalin proteins, there is a high degree of structural similarity. On the other hand, Can f 6 has a similar primary sequence to cat, horse, mouse lipocalins as well as a structure that may underlie their cross reactivity. Interestingly, the entrance to the ligand binding pocket is capped by a His instead of the usually seen Tyr that may help select its natural ligand binding partner. Our highly pure recombinant Can f 6 is able to bind to human IgE (hIgE) demonstrating biological antigenicity.

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