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1.
iScience ; 27(6): 110123, 2024 Jun 21.
Article in English | MEDLINE | ID: mdl-38966572

ABSTRACT

Metabotropic glutamate receptors (mGlu) regulate multiple functions in the nervous systems and are involved in several neurological disorders. However, selectively targeting individual mGlu subtypes with spatiotemporal precision is still an unmet need. Photopharmacology can address this concern through the utilization of photoswitchable compounds such as optogluram, which is a positive allosteric modulator (PAM) of mGlu4 that enables the precise control of physiological responses using light but does not have an optimal selectivity profile. Optogluram analogs were developed to obtain photoswitchable PAMs of mGlu4 receptor with an improved selectivity. Among them, optogluram-2 emerged as a photoswitchable ligand for mGlu4 receptor with activity as both PAM and allosteric agonists. It presents a higher selectivity and offers improved photoswitching of mGlu4 activity. These improved properties make optogluram-2 an excellent candidate to study the role of mGlu4 with a high spatiotemporal precision in systems where mGlu4 can be co-expressed with other mGlu receptors.

2.
iScience ; 27(6): 110121, 2024 Jun 21.
Article in English | MEDLINE | ID: mdl-38957793

ABSTRACT

Aerobic exercise training (AET) has emerged as a strategy to reduce cancer mortality, however, the mechanisms explaining AET on tumor development remain unclear. Tumors escape immune detection by generating immunosuppressive microenvironments and impaired T cell function, which is associated with T cell mitochondrial loss. AET improves mitochondrial content and function, thus we tested whether AET would modulate mitochondrial metabolism in tumor-infiltrating lymphocytes (TIL). Balb/c mice were subjected to a treadmill AET protocol prior to CT26 colon carcinoma cells injection and until tumor harvest. Tissue hypoxia, TIL infiltration and effector function, and mitochondrial content, morphology and function were evaluated. AET reduced tumor growth, improved survival, and decreased tumor hypoxia. An increased CD8+ TIL infiltration, IFN-γ and ATP production promoted by AET was correlated with reduced mitochondrial loss in these cells. Collectively, AET decreases tumor growth partially by increasing CD8+ TIL effector function through an improvement in their mitochondrial content and function.

3.
Elife ; 132024 Jul 03.
Article in English | MEDLINE | ID: mdl-38959062

ABSTRACT

Bacterial exonuclease III (ExoIII), widely acknowledged for specifically targeting double-stranded DNA (dsDNA), has been documented as a DNA repair-associated nuclease with apurinic/apyrimidinic (AP)-endonuclease and 3'→5' exonuclease activities. Due to these enzymatic properties, ExoIII has been broadly applied in molecular biosensors. Here, we demonstrate that ExoIII (Escherichia coli) possesses highly active enzymatic activities on ssDNA. By using a range of ssDNA fluorescence-quenching reporters and fluorophore-labeled probes coupled with mass spectrometry analysis, we found ExoIII cleaved the ssDNA at 5'-bond of phosphodiester from 3' to 5' end by both exonuclease and endonuclease activities. Additional point mutation analysis identified the critical residues for the ssDNase action of ExoIII and suggested the activity shared the same active center with the dsDNA-targeted activities of ExoIII. Notably, ExoIII could also digest the dsDNA structures containing 3'-end ssDNA. Considering most ExoIII-assisted molecular biosensors require the involvement of single-stranded DNA (ssDNA) or nucleic acid aptamer containing ssDNA, the activity will lead to low efficiency or false positive outcome. Our study revealed the multi-enzymatic activity and the underlying molecular mechanism of ExoIII on ssDNA, illuminating novel insights for understanding its biological roles in DNA repair and the rational design of ExoIII-ssDNA involved diagnostics.


Subject(s)
DNA, Single-Stranded , Escherichia coli , Exodeoxyribonucleases , Exodeoxyribonucleases/metabolism , Exodeoxyribonucleases/genetics , DNA, Single-Stranded/metabolism , DNA, Single-Stranded/genetics , Escherichia coli/genetics , Escherichia coli/metabolism , Escherichia coli/enzymology , Escherichia coli Proteins/metabolism , Escherichia coli Proteins/genetics
4.
Elife ; 132024 Jul 08.
Article in English | MEDLINE | ID: mdl-38976500

ABSTRACT

New antimalarial drug candidates that act via novel mechanisms are urgently needed to combat malaria drug resistance. Here, we describe the multi-omic chemical validation of Plasmodium M1 alanyl metalloaminopeptidase as an attractive drug target using the selective inhibitor, MIPS2673. MIPS2673 demonstrated potent inhibition of recombinant Plasmodium falciparum (PfA-M1) and Plasmodium vivax (PvA-M1) M1 metalloaminopeptidases, with selectivity over other Plasmodium and human aminopeptidases, and displayed excellent in vitro antimalarial activity with no significant host cytotoxicity. Orthogonal label-free chemoproteomic methods based on thermal stability and limited proteolysis of whole parasite lysates revealed that MIPS2673 solely targets PfA-M1 in parasites, with limited proteolysis also enabling estimation of the binding site on PfA-M1 to within ~5 Å of that determined by X-ray crystallography. Finally, functional investigation by untargeted metabolomics demonstrated that MIPS2673 inhibits the key role of PfA-M1 in haemoglobin digestion. Combined, our unbiased multi-omic target deconvolution methods confirmed the on-target activity of MIPS2673, and validated selective inhibition of M1 alanyl metalloaminopeptidase as a promising antimalarial strategy.


Subject(s)
Antimalarials , Plasmodium falciparum , Plasmodium vivax , Proteomics , Protozoan Proteins , Antimalarials/pharmacology , Antimalarials/chemistry , Plasmodium falciparum/enzymology , Plasmodium falciparum/drug effects , Plasmodium vivax/enzymology , Plasmodium vivax/drug effects , Humans , Protozoan Proteins/metabolism , Protozoan Proteins/antagonists & inhibitors , Protozoan Proteins/chemistry , Proteomics/methods , Aminopeptidases/metabolism , Aminopeptidases/antagonists & inhibitors , Aminopeptidases/chemistry
5.
iScience ; 27(6): 110109, 2024 Jun 21.
Article in English | MEDLINE | ID: mdl-38989321

ABSTRACT

TDP-43 nuclear clearance and cytoplasmic aggregation are hallmarks of TDP-43 proteinopathies. We recently demonstrated that binding to endogenous nuclear GU-rich RNAs sequesters TDP-43 in the nucleus by restricting its passive nuclear export. Here, we tested the feasibility of synthetic RNA oligonucleotide-mediated augmentation of TDP-43 nuclear localization. Using biochemical assays, we compared the ability of GU-rich oligonucleotides to engage in multivalent, RRM-dependent binding with TDP-43. When transfected into cells, (GU)16 attenuated TDP-43 mislocalization induced by transcriptional blockade or RanGAP1 ablation. Clip34nt and (GU)16 accelerated TDP-43 nuclear re-import after cytoplasmic mislocalization. RNA pulldowns confirmed that multivalent GU-oligonucleotides induced high molecular weight RNP complexes, incorporating TDP-43 and possibly other GU-binding proteins. Transfected GU-repeat oligos disrupted TDP-43 cryptic exon repression, likely by diverting TDP-43 from endogenous RNAs, except for Clip34nt that contains interspersed A and C. Thus, exogenous multivalent GU-RNAs can promote TDP-43 nuclear localization, though pure GU-repeat motifs impair TDP-43 function.

6.
Trop Anim Health Prod ; 56(6): 202, 2024 Jul 12.
Article in English | MEDLINE | ID: mdl-38992295

ABSTRACT

The objective of the study was to determine whether adding grape seed oil (GSO) to the diet of primiparous Jersey breeds during the transition period would improve animal health by measuring effects on the rumen environment, serum biochemistry, oxidative response, and the composition and quality of milk. We used 14 Jersey heifers, weighing an average of 430 kg and 240 days of gestation. The animals were divided into two groups and offered a basal diet, including GSO in the concentrate for the GSO group (dose of 25 mL per animal day) and the same dose of soybean oil (SO) for the control group. The animals were allocated and maintained in a compost barn system, receiving an anionic diet (pre-partum) and a diet for postpartum lactating animals. Dry matter intake (DMI), milk production, serum biochemistry, serum and milk oxidative stability, ruminal fluid and milk fatty acid profile, milk qualitative aspects, and ruminal parameters such as pH, bacterial activity, and protozoan count were evaluated. The addition of GSO had a positive effect on the health of the cows, especially on the oxidative stability of the cows, by increasing total thiols (P = 0.03), higher plasma ferric reducing capacity (FRAP) (P = 0.01), and total antioxidant capacity (TAC) (P = 0.01). In the oxidative stability of the milk produced by the treated animals, there was also an increase in TAC (P = 0.05) and FRAP (P = 0.03). Discreet changes were observed in the ruminal environment with a decreasing trend in pH (P = 0.04) but an increase in bacterial activity (P = 0.05) and protozoa counts (P = 0.07) in cows that consumed the additive. GSO consumption affected the fatty acid profile in milk, increasing saturated fatty acids (SFA) (P = 0.05) and reducing unsaturated fatty acids (UFA) (P = 0.03). The oil did not affect milk production or efficiency in the postpartum period. Based on this information, it is concluded that the addition of GSO positively affects the cow's antioxidant system.


Subject(s)
Animal Feed , Diet , Lactation , Milk , Rumen , Animals , Milk/chemistry , Female , Cattle , Rumen/parasitology , Rumen/metabolism , Diet/veterinary , Animal Feed/analysis , Pregnancy , Animal Nutritional Physiological Phenomena
7.
Front Vet Sci ; 11: 1379980, 2024.
Article in English | MEDLINE | ID: mdl-38983768

ABSTRACT

Clinical metrics of baseline health in sentinel seabird species can offer insight into marine ecosystem dynamics, individual and population health, and assist in wildlife rehabilitation and conservation efforts. Protein electrophoresis is useful for detecting changes in acute phase proteins and immunoglobulin levels that may indicate subtle inflammatory responses and/or infectious disease. Serum biochemistry can highlight nutritional status, metabolic derangements, and organ injury and function. However, baseline values for such health parameters are largely unknown for many seabird species. Therefore, the objective of this study is to establish baseline clinical health reference intervals for serum protein electrophoresis, acute phase proteins including serum amyloid A and haptoglobin, and biochemistry parameters in the rhinoceros auklet (Cerorhinca monocerata), a key sentinel species in the North Pacific. From 2013 to 2019, 178 wild, apparently healthy breeding adult rhinoceros auklets were captured across four breeding colonies in British Columbia, Canada (Lucy Island, Pine Island, Triangle Islands, and SGang Gwaay) and from one colony in Washington, United States (Protection Island). Reference intervals were calculated for protein electrophoresis fractions and acute phase proteins (n = 163), and serum biochemistry (n = 35) following established guidelines by the American Society of Veterinary Clinical Pathology. Animals were also assessed for the presence of antibodies to the influenza A virus. Approximately 48% (70/147) of sampled birds were seropositive for influenza A virus, with a prevalence of 50% (6/12) in 2013, 75% (47/63) in 2014, and 24% (17/72) in 2019. This work provides clinical baseline health metrics of a key North Pacific sentinel species to help inform marine ecosystem monitoring, recovery, and rehabilitation efforts in the Pacific Northwest.

8.
Front Microbiol ; 15: 1368293, 2024.
Article in English | MEDLINE | ID: mdl-38946897

ABSTRACT

Introduction: The drawbacks of using antibiotics as feed additives for blue foxes have gradually become apparent; moreover, thymol has wide-spectrum antimicrobial activity and has the potential to replace antibiotics in various animals. However, there are few reports on the effects of thymol on blue foxes. Methods: This study aimed to investigate the effects of different concentrations of thymol on the growth performance, apparent nutrient digestibility, serum biochemical indicators, intestinal morphology, and gut microbiota of blue foxes. Twenty-four male blue foxes (120 ± 5 d) of similar weight (6.05 ± 0.16 kg) were randomly divided into 4 groups. 0, 100, 200, and 300 mg/kg thymol were added to the basal diets of groups C, L, M, and H, respectively. Results: Compared with those in the C group, the addition of 100 mg/kg thymol to the diet significantly increased organic matter (OM) digestibility, crude protein (CP) digestibility, immunoglobulin (Ig) A, IgM, the VH of the duodenum, the CD of the jejunum, the VH of the ileum, and the VH/CD of the ileum (P < 0.05) and strongly significantly increased IgG (P < 0.01). The addition of 200 mg/kg thymol to the diet increased the VH/CD of the duodenum (P < 0.05). The addition of 300 mg/kg thymol to the diet significantly increased the VH and CD of the jejunum (P < 0.05). The addition of 200 mg/kg and 300 mg/kg thymol to the diets increased the final weight (FW) (P < 0.05). Adding 100 mg/kg thymol significantly increased the levels of interleukin-4 (IL-4) and catalase (CAT) compared with those in the other groups (P < 0.05). 16S rRNA gene detection revealed that thymol can change the abundances of Bifidobacterium, Fusobacterium, Allobaculum, Streptococcus, Megasphaera, and Lactobacillus in the gut. Conclusion: The addition of thymol to diets can increase the abundance of Bifidobacterium, Fusobacterium, and Allobaculum, which may contribute to improving the growth performance of blue foxes.

9.
iScience ; 27(6): 110014, 2024 Jun 21.
Article in English | MEDLINE | ID: mdl-38947512

ABSTRACT

The NAD+-dependent deacetylase SIRT7 is a pivotal regulator of DNA damage response (DDR) and a promising drug target for developing cancer therapeutics. However, limited progress has been made in SIRT7 modulator discovery. Here, we applied peptide-based deacetylase platforms for SIRT7 enzymatic evaluation and successfully identified a potent SIRT7 inhibitor YZL-51N. We initially isolated bioactive YZL-51N from cockroach (Periplaneta americana) extracts and then developed the de novo synthesis of this compound. Further investigation revealed that YZL-51N impaired SIRT7 enzymatic activities through occupation of the NAD+ binding pocket. YZL-51N attenuated DNA damage repair induced by ionizing radiation (IR) in colorectal cancer cells and exhibited a synergistic anticancer effect when used in combination with etoposide. Overall, our study not only identified YZL-51N as a selective SIRT7 inhibitor from insect resources, but also confirmed its potential use in combined chemo-radiotherapy by interfering in the DNA damage repair process.

10.
iScience ; 27(6): 110059, 2024 Jun 21.
Article in English | MEDLINE | ID: mdl-38947513

ABSTRACT

This study characterized the effect of calorie restriction (CR) on elemental content and stable isotope ratio measurements of bone "collagen" and hair keratin. Adult mice on graded CR (10-40%; 84 days) showed decreased hair δ 15N, δ 13C, and δ 34S values (significantly for δ 15N) with increasing CR, alongside a significant increase in bone "collagen" δ 15N values and a decrease in "collagen" δ 13C values. We propose this was likely due to the intensified mobilization of endogenous proteins, as well as lipids in newly synthesized "collagen". Elemental analysis of bone "collagen" revealed decreased carbon, nitrogen, and sulfur % content with increasing CR which is attributed to a change in the in vivo bone "collagen" structure with extent of CR. This complexity challenges the use of elemental indicators in the assessment of collagen quality in archaeological studies where nutritional stress may be a factor.

11.
iScience ; 27(6): 110045, 2024 Jun 21.
Article in English | MEDLINE | ID: mdl-38947529

ABSTRACT

Aging is closely associated with inflammation, which affects renal function reserve (RFR) in the kidneys. This study aims to investigate the impact of reduced RFR reduction on kidney aging and the influence of renal inflammation and RFR reduction on this process. Natural aging rats and those subjected to unilateral nephrectomy (UNX), 1/6 nephrectomy (1/6NX), and unilateral ureteral obstruction (UUO) were observed at 6, 12, 18, and 21 months. Our findings suggest that RFR reduction and renal inflammation can accelerate kidney aging, and inflammation contributes more. Metabolomics analysis revealed alterations in amino acid metabolism contribute to RFR decline. Furthermore, experiments in vitro confirmed the involvement of pentose phosphate pathway (PPP) in promoting aging though inflammation. Our research provides novel insights into for the mechanism of kidney aging and provides indirect support for clinical treatment decisions, such as addressing kidney inflammation, stones, or tumors that may necessitate partial or complete nephrectomy.

12.
Elife ; 132024 Jul 01.
Article in English | MEDLINE | ID: mdl-38949655

ABSTRACT

Secreted chemokines form concentration gradients in target tissues to control migratory directions and patterns of immune cells in response to inflammatory stimulation; however, how the gradients are formed is much debated. Heparan sulfate (HS) binds to chemokines and modulates their activities. In this study, we investigated the roles of HS in the gradient formation and chemoattractant activity of CCL5 that is known to bind to HS. CCL5 and heparin underwent liquid-liquid phase separation and formed gradient, which was confirmed using CCL5 immobilized on heparin-beads. The biological implication of HS in CCL5 gradient formation was established in CHO-K1 (wild-type) and CHO-677 (lacking HS) cells by Transwell assay. The effect of HS on CCL5 chemoattractant activity was further proved by Transwell assay of human peripheral blood cells. Finally, peritoneal injection of the chemokines into mice showed reduced recruitment of inflammatory cells either by mutant CCL5 (lacking heparin-binding sequence) or by addition of heparin to wild-type CCL5. Our experimental data propose that co-phase separation of CCL5 with HS establishes a specific chemokine concentration gradient to trigger directional cell migration. The results warrant further investigation on other heparin-binding chemokines and allows for a more elaborate insight into disease process and new treatment strategies.


Subject(s)
Chemokine CCL5 , Chemotaxis , Cricetulus , Heparitin Sulfate , Chemokine CCL5/metabolism , Chemokine CCL5/genetics , Animals , Heparitin Sulfate/metabolism , Humans , CHO Cells , Mice , Heparin/metabolism , Heparin/pharmacology , Phase Separation
13.
iScience ; 27(7): 110191, 2024 Jul 19.
Article in English | MEDLINE | ID: mdl-38974968

ABSTRACT

Significant progress has been recently made in our understanding of the evolution of jasmonates biosynthesis and signaling. The bioactive jasmonate activating COI1-JAZ co-receptor differs in bryophytes and vascular plants. Dinor-iso-12-oxo-phytodienoic acid (dn-iso-OPDA) is the bioactive hormone in bryophytes and lycophytes. However, further studies showed that the full activation of hormone signaling in Marchantia polymorpha requires additional unidentified hormones. Δ4-dn-OPDAs were previously identified as novel bioactive jasmonates in M. polymorpha. In this paper, we describe the major bioactive isomer of Δ4-dn-OPDAs as Δ4-dn-iso-OPDA through chemical synthesis, receptor binding assay, and biological activity in M. polymorpha. In addition, we disclosed that Δ4-dn-cis-OPDA is a biosynthetic precursor of Δ4-dn-iso-OPDA. We demonstrated that in planta cis-to-iso conversion of Δ4-dn-cis-OPDA occurs in the biosynthesis of Δ4-dn-iso-OPDA, defining a key biosynthetic step in the chemical evolution of hormone structure. We predict that these findings will facilitate further understanding of the molecular evolution of plant hormone signaling.

14.
Interact J Med Res ; 13: e46570, 2024 Jul 08.
Article in English | MEDLINE | ID: mdl-38976326

ABSTRACT

BACKGROUND: Gaming has become an integrated part of life for children and adults worldwide. Previous studies on the impact of gaming on biochemical parameters have primarily addressed the acute effects of gaming. The literature is limited, and the study designs are very diverse. The parameters that have been investigated most thoroughly are blood glucose and cortisol. OBJECTIVE: This exploratory study is the first to investigate the effects of long gaming sessions on the biochemical parameters of healthy male adults. The extensive testing allowed us to observe short-term changes (within 6 hours), long-term changes during the duration of the gaming sessions, and follow-up after 1 week to determine whether any changes were longer lasting. METHODS: In total, 9 experienced gamers completed 2 back-to-back 18-hour gaming sessions interspersed with a 6-hour rest period. All participants adhered to a structured sleep pattern due to daytime employment or attending university. Blood, saliva, and urine samples were collected from the participants every 6 hours. Linear mixed-effect models were used to analyze the repeated-measures data accumulated during the study. A total of 51 biochemical parameters were investigated. RESULTS: In total, 12 of the 51 biochemical parameters significantly changed during the study: alkaline phosphatase, aspartate aminotransferase, bilirubin, chloride, creatinine, glucose, hemoglobin, immature reticulocyte fraction, lactate, methemoglobin, sodium, and thrombocytes. All changes were within the normal range. The mean glucose level of the participants was 4.39 (SD 0.07) mmol/L at baseline, which increased significantly by 0.24 (SD 0.07) mmol/L per 6 hours during the first period and by 0.38 (SD 0.07) mmol/L per 6 hours in the second period (P<.001). The glucose levels during the second session increased even though the participants had little energy intake. Cortisol levels did not change significantly, although the cortisol pattern deviated from the typical circadian rhythm. During both gaming sessions, we observed increasing cortisol levels from 6 AM until noon. The participants were relatively dehydrated at the start of the study. The patients were asked to fast before the first blood sampling. Within the first 6 hours of the study, the participants rehydrated, followed by relative dehydration during the remainder of the study. This pattern was identified using the following parameters: albumin, creatinine, hemoglobin, erythrocytes, potassium, and platelets. CONCLUSIONS: This study is the first of its kind, and many of the analyses in the study yielded novel results. The study was designed to emulate the behavior of gamers during the weekend and other long gaming sessions. At this point, we are not able to determine the difference between the effects of gaming and behavior during gaming. Regardless, the results of this study suggest that healthy gamers can partake in long gaming sessions, with ample amounts of unhealthy foods and little rest, without acute impacts on health.

15.
Plant J ; 2024 Jul 08.
Article in English | MEDLINE | ID: mdl-38976445

ABSTRACT

Plants synthesize an array of volatile compounds, many of which serve ecological roles in attracting pollinators, deterring herbivores, and communicating with their surroundings. Methyl anthranilate (MeAA) is an anti-herbivory defensive volatile responsible for grape aroma that is emitted by several agriculturally relevant plants, including citrus, grapes, and maize. Unlike maize, which uses a one-step anthranilate methyltransferase (AAMT), grapes have been thought to use a two-step pathway for MeAA biosynthesis. By mining available transcriptomics data, we identified two AAMTs in Vitis vinifera (wine grape), as well as one ortholog in "Concord" grape. Many angiosperms methylate the plant hormone salicylic acid (SA) to produce methyl salicylate, which acts as a plant-to-plant communication molecule. Because the Citrus sinensis (sweet orange) SA methyltransferase can methylate both anthranilate (AA) and SA, we used this enzyme to examine the molecular basis of AA activity by introducing rational mutations, which identified several active site residues that increase activity with AA. Reversing this approach, we introduced mutations that imparted activity with SA in the maize AAMT, which uncovered different active site residues from those in the citrus enzyme. Sequence and phylogenetic analysis revealed that one of the Vitis AAMTs shares an ancestor with jasmonic acid methyltransferases, similar to the AAMT from strawberry (Frageria sp.). Collectively, these data demonstrate the molecular mechanisms underpinning AA activity across methyltransferases and identify one-step enzymes by which grapes synthesize MeAA.

16.
Elife ; 122024 Jul 05.
Article in English | MEDLINE | ID: mdl-38968292

ABSTRACT

A small, nucleotide-binding domain, the ATP-cone, is found at the N-terminus of most ribonucleotide reductase (RNR) catalytic subunits. By binding adenosine triphosphate (ATP) or deoxyadenosine triphosphate (dATP) it regulates the enzyme activity of all classes of RNR. Functional and structural work on aerobic RNRs has revealed a plethora of ways in which dATP inhibits activity by inducing oligomerisation and preventing a productive radical transfer from one subunit to the active site in the other. Anaerobic RNRs, on the other hand, store a stable glycyl radical next to the active site and the basis for their dATP-dependent inhibition is completely unknown. We present biochemical, biophysical, and structural information on the effects of ATP and dATP binding to the anaerobic RNR from Prevotella copri. The enzyme exists in a dimer-tetramer equilibrium biased towards dimers when two ATP molecules are bound to the ATP-cone and tetramers when two dATP molecules are bound. In the presence of ATP, P. copri NrdD is active and has a fully ordered glycyl radical domain (GRD) in one monomer of the dimer. Binding of dATP to the ATP-cone results in loss of activity and increased dynamics of the GRD, such that it cannot be detected in the cryo-EM structures. The glycyl radical is formed even in the dATP-bound form, but the substrate does not bind. The structures implicate a complex network of interactions in activity regulation that involve the GRD more than 30 Å away from the dATP molecules, the allosteric substrate specificity site and a conserved but previously unseen flap over the active site. Taken together, the results suggest that dATP inhibition in anaerobic RNRs acts by increasing the flexibility of the flap and GRD, thereby preventing both substrate binding and radical mobilisation.


Subject(s)
Adenosine Triphosphate , Protein Binding , Ribonucleotide Reductases , Ribonucleotide Reductases/metabolism , Ribonucleotide Reductases/chemistry , Adenosine Triphosphate/metabolism , Allosteric Regulation , Anaerobiosis , Deoxyadenine Nucleotides/metabolism , Catalytic Domain , Protein Conformation , Substrate Specificity , Protein Multimerization , Models, Molecular
17.
STAR Protoc ; 5(3): 103171, 2024 Jul 05.
Article in English | MEDLINE | ID: mdl-38970794

ABSTRACT

Here, we present a protocol to quantify interactions among difficult-to-express proteins from Drosophila cells using the select western blot-free tagged-protein interaction (SWFTI) assay. We describe steps for plasmid design, cell plating, protein expression, and immunoprecipitation preparation. We then detail procedures for protein labeling, gel purification, and protein quantification. This protocol offers a fluorescence-based technique for rapid quantification of ectopically expressed proteins that are fused to SNAP and CLIP tags without the need for membrane transfer. For complete details on the use and execution of this protocol, please refer to Lin et al.1.

18.
bioRxiv ; 2024 Jun 29.
Article in English | MEDLINE | ID: mdl-38979229

ABSTRACT

Over the past 15 years, hundreds of previously undiscovered bacterial small open reading frame (sORF)-encoded polypeptides (SEPs) of fewer than fifty amino acids have been identified, and biological functions have been ascribed to an increasing number of SEPs from intergenic regions and small RNAs. However, despite numbering in the dozens in Escherichia coli, and hundreds to thousands in humans, same-strand nested sORFs that overlap protein coding genes in alternative reading frames remain understudied. In order to provide insight into this enigmatic class of unannotated genes, we characterized GndA, a 36-amino acid, heat shock-regulated SEP encoded within the +2 reading frame of the gnd gene in E. coli K-12 MG1655. We show that GndA pulls down components of respiratory complex I (RCI) and is required for proper localization of a RCI subunit during heat shock. At high temperature GndA deletion (ΔGndA) cells exhibit perturbations in cell growth, NADH+/NAD ratio, and expression of a number of genes including several associated with oxidative stress. These findings suggest that GndA may function in maintenance of homeostasis during heat shock. Characterization of GndA therefore supports the nascent but growing consensus that functional, overlapping genes occur in genomes from viruses to humans.

19.
Elife ; 132024 Jul 12.
Article in English | MEDLINE | ID: mdl-38995680

ABSTRACT

Truncation of the protein-protein interaction SH3 domain of the membrane remodeling Bridging Integrator 1 (BIN1, Amphiphysin 2) protein leads to centronuclear myopathy. Here, we assessed the impact of a set of naturally observed, previously uncharacterized BIN1 SH3 domain variants using conventional in vitro and cell-based assays monitoring the BIN1 interaction with dynamin 2 (DNM2) and identified potentially harmful ones that can be also tentatively connected to neuromuscular disorders. However, SH3 domains are typically promiscuous and it is expected that other, so far unknown partners of BIN1 exist besides DNM2, that also participate in the development of centronuclear myopathy. In order to shed light on these other relevant interaction partners and to get a holistic picture of the pathomechanism behind BIN1 SH3 domain variants, we used affinity interactomics. We identified hundreds of new BIN1 interaction partners proteome-wide, among which many appear to participate in cell division, suggesting a critical role of BIN1 in the regulation of mitosis. Finally, we show that the identified BIN1 mutations indeed cause proteome-wide affinity perturbation, signifying the importance of employing unbiased affinity interactomic approaches.


Subject(s)
Adaptor Proteins, Signal Transducing , Myopathies, Structural, Congenital , Nuclear Proteins , Tumor Suppressor Proteins , src Homology Domains , Myopathies, Structural, Congenital/metabolism , Myopathies, Structural, Congenital/genetics , Humans , Adaptor Proteins, Signal Transducing/metabolism , Adaptor Proteins, Signal Transducing/genetics , Tumor Suppressor Proteins/metabolism , Tumor Suppressor Proteins/genetics , Nuclear Proteins/metabolism , Nuclear Proteins/genetics , Protein Binding , Dynamin II/metabolism , Dynamin II/genetics , Mutation
20.
Sci Rep ; 14(1): 16195, 2024 Jul 13.
Article in English | MEDLINE | ID: mdl-39003295

ABSTRACT

Multiple sclerosis (MS) is a demyelinating and neurodegenerative disease due to an autoimmune chronic inflammatory response, yet the etiology is currently not completely understood. It is already known that physical activity plays an essential role in improving quality of life, especially in neuropathological conditions. The study was aimed to investigate the possible benefits of high-intensity interval training (HIIT) in bone and lipid metabolism markers, and neuromotor abilities in MS patients. 130 participants were recruited; 16 subjects with MS met the inclusion criteria and were included in the data analysis. The patients were randomly assigned to two groups: a Control group (CG) (34.88 ± 4.45 yrs) that didn't perform any physical activity and the Exercise group (EG) (36.20 ± 7.80 yrs) that performed HIIT protocol. The training program was conducted remotely by a kinesiologist. It was performed three times a week for 8 weeks. At the beginning (T0) and the end of the study (T1) physical function tests, bone remodelling markers, and lipid markers analyses were performed. After 8 weeks of training the wall squat (s) (T0 = 27.18 ± 4.21; T1 = 41.68 ± 5.38, p ≤ 0.01) and Time Up and Go test (s) (T0 = 7.65 ± 0.43; T1 = 6.34 ± 0.38 p ≤ 0.01) performances improved; lipid markers analysis showed a decrease in Total (mg/dl) (T0 = 187.22 ± 15.73; T1 = 173.44 ± 13.03, p ≤ 0.05) and LDL (mg/dl) (T0 = 108 ± 21.08; T1 = 95.02 ± 17.99, p < 0.05) cholesterol levels. Additionally, the levels of osteocalcin (µg/L), a marker of bone formation increased (T0 = 20.88 ± 4.22; T1 = 23.66 ± 6.24, p < 0.05), 25-OH Vitamin D (µg/L) improved after 8 weeks (T0 = 21.11 ± 7.11; T1 = 27.66 ± 7.59, p < 0.05). HIIT had an effect on lower limb strength and gait control, improved bone formation, and lipid management, in MS patients.


Subject(s)
Bone Remodeling , High-Intensity Interval Training , Multiple Sclerosis , Humans , High-Intensity Interval Training/methods , Male , Female , Adult , Multiple Sclerosis/physiopathology , Multiple Sclerosis/blood , Multiple Sclerosis/therapy , Lipids/blood , Lipid Metabolism , Biomarkers/blood , Middle Aged , Quality of Life , Exercise Therapy/methods , Exercise/physiology
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