Cultured HEK293T Cells Research Articles

N-terminal domain of polypyrimidine-tract binding protein is a dynamic folding platform for adaptive RNA recognition.

The N-terminal RNA recognition motif domain (RRM1) of polypyrimidine tract binding protein (PTB) forms an additional C-terminal helix α3, which docks to one edge of the β-sheet upon binding to a stem-loop RNA containing a UCUUU pentaloop. Importantly, α3 does not contact the RNA. The α3 helix therefore represents an allosteric means to regulate the conformation of adjacent domains in PTB upon binding structured RNAs. Here we investigate the process of dynamic adaptation by stem-loop RNA and RRM1 using NMR and MD in order to obtain mechanistic insights on how this allostery is achieved. Relaxation data and NMR structure determination of the free protein show that α3 is partially ordered and interacts with the domain transiently. Stem-loop RNA binding quenches fast time scale dynamics and α3 becomes ordered, however microsecond dynamics at the protein-RNA interface is observed. MD shows how RRM1 binding to the stem-loop RNA is coupled to the stabilization of the C-terminal helix and helps to transduce differences in RNA loop sequence into changes in α3 length and order. IRES assays of full length PTB and a mutant with altered dynamics in the α3 region show that this dynamic allostery influences PTB function in cultured HEK293T cells.

Generation and characterization of monoclonal antibodies against pathologically phosphorylated TDP-43.

Inclusions containing TAR DNA binding protein 43 (TDP-43) are a pathological hallmark of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). One of the disease-specific features of TDP-43 inclusions is the aberrant phosphorylation of TDP-43 at serines 409/410 (pS409/410). Here, we developed rabbit monoclonal antibodies (mAbs) that specifically detect pS409/410-TDP-43 in multiple model systems and FTD/ALS patient samples. Specifically, we identified three mAbs (26H10, 2E9 and 23A1) from spleen B cell clones that exhibit high specificity and sensitivity to pS409/410-TDP-43 peptides in an ELISA assay. Biochemical analyses revealed that pS409/410 of recombinant TDP-43 and of exogenous 25 kDa TDP-43 C-terminal fragments in cultured HEK293T cells are detected by all three mAbs. Moreover, the mAbs detect pS409/410-positive TDP-43 inclusions in the brains of FTD/ALS patients and mouse models of TDP-43 proteinopathy by immunohistochemistry. Our findings indicate that these mAbs are a valuable resource for investigating TDP-43 pathology both in vitro and in vivo.

Type 2 diabetes affects arsenic metabolism via transporters in arsenic trioxide treated acute promyelocytic leukemia patients

Our study aimed to explore whether type 2 diabetes (T2DM) can affect arsenic metabolism in acute promyelocytic leukemia (APL) patients treated with arsenic trioxide. We found that compared with non-diabetic APL patients, the concentrations of arsenic metabolites in APL patients with T2DM increased significantly and positively correlated with blood glucose (P < 0.05). Meanwhile, APL patients with T2DM were more prone to liver injury and QTc interval prolongation due to altered arsenic methylation capacity. Then we cultured HEK293T cells at different glucose concentrations, and the results showed that the cells with high glucose had higher concentrations of arsenic metabolites compared to other cells. Meanwhile, the high glucose significantly increased the mRNA and protein expression levels of the arsenic uptake transporter AQP7 in HEK293T cells. Overall, our study demonstrated that T2DM can lead to elevated concentrations of arsenic metabolites in APL patients by increasing AQP7 expression.

Real-Time Visualization of Cytosolic and Mitochondrial ATP Dynamics in Response to Metabolic Stress in Cultured Cells.

Adenosine 5' triphosphate (ATP) is the energy currency of life, which is produced in mitochondria (~90%) and cytosol (less than 10%). Real-time effects of metabolic changes on cellular ATP dynamics remain indeterminate. Here we report the design and validation of a genetically encoded fluorescent ATP indicator that allows for real-time, simultaneous visualization of cytosolic and mitochondrial ATP in cultured cells. This dual-ATP indicator, called smacATPi (simultaneous mitochondrial and cytosolic ATP indicator), combines previously described individual cytosolic and mitochondrial ATP indicators. The use of smacATPi can help answer biological questions regarding ATP contents and dynamics in living cells. As expected, 2-deoxyglucose (2-DG, a glycolytic inhibitor) led to substantially decreased cytosolic ATP, and oligomycin (a complex V inhibitor) markedly decreased mitochondrial ATP in cultured HEK293T cells transfected with smacATPi. With the use of smacATPi, we can also observe that 2-DG treatment modestly attenuates mitochondrial ATP and oligomycin reduces cytosolic ATP, indicating the subsequent changes of compartmental ATP. To evaluate the role of ATP/ADP carrier (AAC) in ATP trafficking, we treated HEK293T cells with an AAC inhibitor, Atractyloside (ATR). ATR treatment attenuated cytosolic and mitochondrial ATP in normoxia, suggesting AAC inhibition reduces ADP import from the cytosol to mitochondria and ATP export from mitochondria to cytosol. In HEK293T cells subjected to hypoxia, ATR treatment increased mitochondrial ATP along with decreased cytosolic ATP, implicating that ACC inhibition during hypoxia sustains mitochondrial ATP but may not inhibit the reversed ATP import from the cytosol. Furthermore, both mitochondrial and cytosolic signals decrease when ATR is given in conjunction with 2-DG in hypoxia. Thus, real-time visualization of spatiotemporal ATP dynamics using smacATPi provides novel insights into how cytosolic and mitochondrial ATP signals respond to metabolic changes, providing a better understanding of cellular metabolism in health and disease.

Enhancement of Vivid-based photo-activatable Gal4 transcription factor in mammalian cells.

The Gal4/UAS system is a versatile tool to manipulate exogenous gene expression of cells spatially and temporally in many model organisms. Many variations of light-controllable Gal4/UAS system are now available, following the development of photo-activatable (PA) molecular switches and integration of these tools. However, many PA-Gal4 transcription factors have undesired background transcription activities even in dark conditions, and this severely attenuates reliable light-controlled gene expression. Therefore, it is important to develop reliable PA-Gal4 transcription factors with robust light-induced gene expression and limited background activity. By optimization of synthetic PA-Gal4 transcription factors, we have validated configurations of Gal4 DNA biding domain, transcription activation domain and blue light-dependent dimer formation molecule Vivid (VVD), and applied types of transcription activation domains to develop a new PA-Gal4 transcription factor we have named eGAV (enhanced Gal4-VVD transcription factor). Background activity of eGAV in dark conditions was significantly lower than that of hGAVPO, a commonly used PA-Gal4 transcription factor, and maximum light-induced gene expression levels were also improved. Light-controlled gene expression was verified in cultured HEK293T cells with plasmid-transient transfections, and in mouse EpH4 cells with lentivirus vector-mediated transduction. Furthermore, light-controlled eGAV-mediated transcription was confirmed in transfected neural stem cells and progenitors in developing and adult mouse brain and chick spinal cord, and in adult mouse hepatocytes, demonstrating that eGAV can be applied to a wide range of experimental systems and model organisms.Key words: optogenetics, Gal4/UAS system, transcription, gene expression, Vivid.

Aryl Fluorosulfate Based Inhibitors That Covalently Target the SIRT5 Lysine Deacylase**

AbstractThe sirtuin enzymes are a family of lysine deacylases that regulate gene transcription and metabolism. Sirtuin 5 (SIRT5) hydrolyzes malonyl, succinyl, and glutaryl ϵ‐N‐carboxyacyllysine posttranslational modifications and has recently emerged as a vulnerability in certain cancers. However, chemical probes to illuminate its potential as a pharmacological target have been lacking. Here we report the harnessing of aryl fluorosulfate‐based electrophiles as an avenue to furnish covalent inhibitors that target SIRT5. Alkyne‐tagged affinity‐labeling agents recognize and capture overexpressed SIRT5 in cultured HEK293T cells and can label SIRT5 in the hearts of mice upon intravenous injection of the compound. This work demonstrates the utility of aryl fluorosulfate electrophiles for targeting of SIRT5 and suggests this as a means for the development of potential covalent drug candidates. It is our hope that these results will serve as inspiration for future studies investigating SIRT5 and general sirtuin biology in the mitochondria.

Aryl Fluorosulfate Based Inhibitors That Covalently Target the SIRT5 Lysine Deacylase.

The sirtuin enzymes are a family of lysine deacylases that regulate gene transcription and metabolism. Sirtuin 5 (SIRT5) hydrolyzes malonyl, succinyl, and glutaryl ϵ-N-carboxyacyllysine posttranslational modifications and has recently emerged as a vulnerability in certain cancers. However, chemical probes to illuminate its potential as a pharmacological target have been lacking. Here we report the harnessing of aryl fluorosulfate-based electrophiles as an avenue to furnish covalent inhibitors that target SIRT5. Alkyne-tagged affinity-labeling agents recognize and capture overexpressed SIRT5 in cultured HEK293T cells and can label SIRT5 in the hearts of mice upon intravenous injection of the compound. This work demonstrates the utility of aryl fluorosulfate electrophiles for targeting of SIRT5 and suggests this as a means for the development of potential covalent drug candidates. It is our hope that these results will serve as inspiration for future studies investigating SIRT5 and general sirtuin biology in the mitochondria.

Lipophilic poly(glycolide) blocks in morpholin-2-one-based CARTs for plasmid DNA delivery: Polymer regioregularity, sequence of lipophilic/polyamine blocks, and nanoparticle stability as factors of transfection efficiency

In the present work, monosubstituted glycolides (G2–G4) derived from the (L)-tyrosine-based glycolide G1 and containing –CH2C6H4OR substituents (R = decanoyl, oleoyl, C(O)CH(n-C6H13)(n-C8H17)) have been used to design biodegradable and biocompatible lipophilic blocks in N-BOC-morpholin-2-one (M1)-based Charge-Altering Releasable Transporters (CARTs). Copolymers of dodecyl carbonate C1 (the ‘benchmark’ lipophilic comonomer) and M1, having direct (P1) or inverse (P2) block sequences; copolymers of G2–G4 and M1, having inverse block sequences and irregular, head-to-head in places, microstructures of the poly(glycolide) blocks (P3–P7); and copolymers of G2 and M1, having solely alternating head-to-tail microstructures of the poly(glycolide) blocks and direct (P8) or inverse (P9) block sequences, have been synthesized. DLS studies have shown that, after deprotection, the copolymers P1′–P9′ form liposomal particles in aqueous medium, differing considerably in their colloidal behavior, which depended on the length of the polyamine fragment and the nature of the lipophilic block. The ability of P1′–P9′ to deliver the plasmid pEGFP-N1 into cultured HEK293T cells (transfection efficiency) has been assessed at N/P ratios of the corresponding polyplexes in the range 1:1–50:1 by flow cytometry and further confirmed by fluorescence microscopy. Transfection experiments have demonstrated that the CARTs P1′, P4′, and P6′, containing ten (2-oxyethyl)glycine fragments, are about four times more efficient in delivering pDNA than commercial agents (Lipofectamine™ 3000, PEI MAX, X-tremeGENE™ 9, and GenJet™ In Vitro DNA Transfection Reagent). A correlation between the results of those studies and DLS / ζ-potential measurements has been established for P1′ and P4′: the transfection is efficient, if N/P ratios are equal to those favoring ζ-potential inversion at physiological pH. We conclude that glycolide-based CARTs show significant promise for further development as non-viral NA delivery vehicles and that DLS should be regarded as an efficient method of primary screening of amphiphilic copolymers, as well as copolymer-NA complexes and formulations thereof.

Polygoni multiflori radix extracts inhibit SARS-CoV-2 pseudovirus entry in HEK293T cells and zebrafish larvae

BackgroundGlobally, COVID-19 has caused millions of deaths and led to unprecedented socioeconomic damage. There is therefore, in addition to vaccination, an urgent need to develop complementary effective treatments and/or protective and preventative therapies against this deadly disease. MethodsHere, a multi-component testing platform was established to screen a library of herbal extracts from traditional Chinese medicine (TCM), to identify potent herbal extracts/phytochemicals as possible therapeutics for COVID-19. We utilized assays for spike protein (S-protein) binding to angiotensin-converting enzyme II (ACE2); the enzymatic inhibition of 3CL protease; and entry of the SARS-CoV-2 pseudovirus into cultured HEK293T cells and zebrafish larvae. ResultsOver a thousand herbal extracts were screened and approximately 20 positive hits were identified. Among these, we found that the water and ethanol extracts of Polygoni Multiflori Radix (PMR) significantly inhibited S-protein binding to ACE2, 3CL protease activity, and viral entry into the cell and fish models. The water extract was more effective than the ethanol extract, with IC50 values of 25 to 500 µg/ml. In addition, the polysaccharide-depleted fraction of the former, and epigallocatechin gallate (EGCG) which was found in both extracts, displayed significant antiviral activity. ConclusionsOur results indicate that the water and ethanol extracts of PMR have an inhibitory effect on SARS-CoV-2 pseudovirus host-cell entry. Furthermore, EGCG might be an active component of PMR, which blocks SARS-CoV-2 entry to cells. Taken together, our findings suggest that PMR might be considered as a potential treatment for COVID-19.

Cyclosporine as a novel treatment for amatoxin-containing mushroom poisoning: a case series

Ingestion of amatoxin-containing mushrooms can lead to fulminant hepatotoxicity and death. Despite recent interest in therapeutic options for amatoxin-exposed patients, there is no single, recommended treatment for amatoxin poisoning. Alpha-amanitin, the principal toxin in amatoxin-containing mushrooms, requires entry into hepatocytes via organic anion transporting polypeptide (OATP) 1B3 before the cascade of cellular events occurs leading to hepatocyte necrosis, liver failure, and in severe cases liver transplantation or death. Three patients managed through a single poison centre with confirmed amatoxin-containing mushrooms ingestions were treated with intravenous cyclosporine, a known potent OATP1B3 inhibitor, along with supportive care. All patients presented with classic delayed symptoms of nausea, vomiting and diarrhea. No patient progressed to fulminant hepatic failure, although two patients developed a transient rise in liver transaminases. All recovered and were discharged from hospital. No patient had an adverse effect from cyclosporine. In addition, we performed an in-vitro study of the role of cyclosporine in cultured HEK293T cells and human hepatoma Huh7 cells. Cyclosporine effectively inhibited OATP1B3-mediated uptake of alpha-amanitin, and improved cell viability of alpha-amanitin exposed cultured Huh7 cells. We conclude that IV cyclosporine, a drug readily available in most hospitals, may be useful to reduce hepatotoxicity from amatoxin poisoning.

Mulberry fruit extract alleviates the intracellular amyloid-β oligomer-induced cognitive disturbance and oxidative stress in Alzheimer's disease model mice.

Intracellular amyloid-β (Aβ) oligomers are key therapeutic targets because they are strongly cytotoxic and play crucial roles in the cognitive function in Alzheimer's disease (AD). Anthocyanins, polyphenolic flavonoids with antioxidant and neuroprotective properties, are potential therapeutic candidates for AD. Here, we investigated the effects of anthocyanin-enriched extracts from fruits of mulberry (Morus alba Linn.) in Thailand against the neurotoxicity of Aβ oligomers. Using the monitoring system for Aβ aggregation, we showed that the extract induced the dissociation of Aβ in cultured HEK293T cells. To investigate the effects on cognitive function, we orally administered the extract to Aβ-GFP transgenic mice (Aβ-GFP Tg), a mouse model that expresses Aβ oligomers inside neurons, and performed the novel object recognition test and passive avoidance test. Aβ-GFP Tg usually showed deficits in novel object recognition memory and reference memory compared with non-Tg, but administration of the extract improved both compared with vehicle-treated Aβ-GFP Tg. Aβ-GFP Tg exhibited lower superoxide dismutase (SOD) activity than non-Tg. However, after the administration of the extract, the SOD activity was restored. These results suggest that Thai mulberry fruit extract ameliorates cytotoxicity induced by the intracellular Aβ oligomers and may be an effective therapeutic or preventive candidate for AD.

Simultaneous Evaluation of Mitochondrial and Cytosolic ATP Dynamics in Cultured HEK293T Cells

Adenosine triphosphate (ATP) is the “energy currency” of all living organisms. It is crucial for cells to maintain consistent ATP levels, especially when supply is limited and demand is high. ATP is vital for organs with high ATP demands, such as the heart and the brain. In mammalian cells, oxidative phosphorylation in mitochondria produces most ATP, whereas glycolysis in cytosol yields the remaining portion of ATP. When the supply/demand of ATP alters, cells undergo drastic metabolic remodeling, which often maintains cellular function and links to mitochondrial dysfunction and even cell death. However, the mechanisms underlying the regulation of cellular ATP remain incompletely understood, mainly due to the lack of a tool to monitor spatiotemporal ATP changes in cells. In the present study, we designed a dual-ATP probe that allows for visualization of ATP dynamics in mitochondria and cytosol of an individual cell. This probe was based on two previously described single probes containing fusion proteins of GFP- and mApple-FoF1-ATP synthase e subunit (B. subtilis). The latter contains a mitochondrial singling sequence for mitochondrial localization. As such, cytosol ATP shows green and mitochondrial ATP shows red. We generated a plasmid for the dual-ATP probe containing a polycistronic arrangement of sequences coding for the two fusion proteins, rendering spatiotemporal recording of ATP dynamics simultaneously in mitochondria and cytosol of cultured cells. We first validated the dual-ATP probe did display red in mitochondria and green in the cytosol in cultured HEK293T cells upon feeding with glucose. Seahorse analysis indicated that the probe does not change cellular respiration. HEK293T cells were cultured for 24 hours after the transfection of the dual-ATP probe vector. We then tested several compounds known to target specific regions of the electron transport chain. When treated with oligomycin, a Complex V inhibitor, mitochondrial ATP declined within 20 min, but cytosolic ATP remained relatively constant. When we added Antimycin A, a Complex III inhibitor, ATP levels declined from time of injection until fluorescence plateaued at 20 minutes. Likewise, we saw similar responses occur after adding FCCP, a mitochondrial uncoupler, and rotenone, a Complex I inhibitor. When we added drugs such as 2-DG and KCN, a glycolysis inhibitor and a Complex IV inhibitor, respectively, both cytosolic and mitochondrial fluorescence plummeted, suggesting dramatic inhibition of ATP production from glycolysis and OXPHOS. Under hypoxic conditions, the mitochondrial ATP declined over the course of 6 hours while the cytosolic ATP remained stable. In summary, our results support the feasibility of our dual-ATP probe for spatiotemporal evaluation of cellular ATP level, distribution, and inter-compartmental trafficking. This innovative technology will provide unprecedented research opportunities for in-depth insight into the regulatory mechanisms of cellular energy metabolism in physiological and pathological states.

Generation and proliferation assessment of HEK293T cells stably expressing Kv1.5 channel with and without regulatory subunits β1.1 or β1.2

Potassium channels, including voltage-gated potassium (Kv) channels, play an important role in regulation of vascular smooth muscle cell (VSMC) contraction and proliferation. Our previous studies indicate that KV1.5 is a major type of shaker-family KV1 channels expressed in human coronary and adipose arterioles. The function of KV1.5 channels is impaired in disease, contributing to reduced KV1.5-dependent VSMC relaxation and leading to vascular dysfunction in subjects with coronary artery disease (CAD). However, it remains largely unknown whether KV1.5, alone and with its regulatory subunits (β1.1 and β1.2), also regulates VSMC proliferation in CAD. This study was designed to examine if expression of KV1.5 with and without β1.1 or β1.2) modulates cell proliferation in cultured HEK293T cells. We created a Kv1.5 cell line with lentiviral transduction at a multiplicity of infection (MOI) of 20. We used this cell line to introduce β1.1 subunit with the same protocol (MOI=20). However, when we attempted to introduce β1.2 subunit to Kv1.5 cell line, transduction efficiency was only 40% prompting us to repeat the experiment with MOI of 40 to obtain transduction efficiency of over 90%. These results suggest that the β1.2 subunit may be responsible for inhibiting cell proliferation. To test our hypothesis, we took images of transduced cultured cells every 24 hours from 24 to 96 hours and analyzed them with ImageJ software. Each cell was outlined to indicate the surface area taken up by the cells as compared to total surface area of the image for estimation of the overall cell density/confluency. ImageJ analysis revealed that the lowest density was observed in Kv1.5+ β1.2 cell line (25±3% at 48 hours, n=15 images from 6 independent experiments P<0.001) as compared with densities of Kv1.5 (72±3%, n=18); Kv1.5+ β1.1 (75±1%, n=15); and GFP (65±2%, n=9). Kv1.5+ β1.2 consistently exhibited the lowest confluency at all time points (24, 72, and 96 hours). Next, we performed cell counting with a trypan blue solution using a hemocytometer to assess the cell density of the entire sample at 48 hours. After we converted the number of cells into percentages relative to GFP control, our data indicated that Kv1.5 was at 97±1%, n=6; Kv1.5+ β1.1 at 96±1%, n=6; and Kv1.5+ β1.2 was at 41±0.5%, n=6 (P<0.001). In conclusion, our results indicate that, expression of Kv1.5 channel + β1.2 regulatory subunit, but not KV1.5 alone or with β1.1 subunit, inhibits cell proliferation in heterologous expression cell systems. Future studies will identify the role and mechanism of KV1.5 and its β1.2 subunit in VSMC proliferation in CAD or other vascular diseases.

Exploring GPCR-arrestin interfaces with genetically encoded crosslinkers.

β‐arrestins (βarr1 and βarr2) are ubiquitous regulators of G protein‐coupled receptor (GPCR) signaling. Available data suggest that β‐arrestins dock to different receptors in different ways. However, the structural characterization of GPCR‐arrestin complexes is challenging and alternative approaches to study GPCR‐arrestin complexes are needed. Here, starting from the finger loop as a major site for the interaction of arrestins with GPCRs, we genetically incorporate non‐canonical amino acids for photo‐ and chemical crosslinking into βarr1 and βarr2 and explore binding topologies to GPCRs forming either stable or transient complexes with arrestins: the vasopressin receptor 2 (rhodopsin‐like), the corticotropin‐releasing factor receptor 1, and the parathyroid hormone receptor 1 (both secretin‐like). We show that each receptor leaves a unique footprint on arrestins, whereas the two β‐arrestins yield quite similar crosslinking patterns. Furthermore, we show that the method allows defining the orientation of arrestin with respect to the GPCR. Finally, we provide direct evidence for the formation of arrestin oligomers in the cell.

Angiotensin Ⅱ induces apoptosis of HEK293T cells by up-regulating Cyr61 expression

To investigate the role of Cyr61 in angiotensin Ⅱ (AngⅡ)-induced functional changes in HEK293 cells and explore the mechanism. Cyr61 knockdown in cultured HEK293T cells was achieved by transfection of the cells with CRISPR/Cas9 KO plasmid. The changes in apoptosis and expression levels of Cyr61 and Bcl-2 in the cells with or without Cyr61 knockdown in response to treatment with 10-7 mol/L AngⅡ for 48 h were analyzed using flow cytometry, qRT-PCR and Western blotting. The cells with Cyr61 knockdown showed significantly decreased expression of Cyr61 protein as compared with the control cells (P &lt; 0.05). AngⅡ treatment for 48 h significantly increased the expression of Cyr61 and lowers the expression of Bcl-2 at both the protein and mRNA levels in HEK293T cells. In HEK293T cells with Cyr61 knockdown, AngⅡ treatment resulted in significantly increased expression of Bcl-2 in HEK293T cells as compared with that of the control group (P &lt; 0.05). AngⅡ treatment caused significantly increased apoptotic rate in HEK293T cells as compared with the cells with Cyr61 knockdown [(26.94 ± 3.73)% vs (3.87 ± 0.83)%, P &lt; 0.05), and the apoptosis rate was significantly lowered to (15.76 ± 1.31)% in HEK293T cells with Cyr61 knockdown following AngⅡ treatment (P &lt; 0.05). The up-regulation of Cyr61 expression is related with AngⅡ-induced injury in HEK293T cells, and down-regulating Cyr61 expression can effectively protect HEK293T cells against AngⅡ-induced injury.

Dissection, Optimization, and Structural Analysis of a Covalent Irreversible DDAH1 Inhibitor.

Inhibitors of the human enzyme dimethylarginine dimethylaminohydrolase-1 (DDAH1) can control endogenous nitric oxide production. A time-dependent covalent inactivator of DDAH1, N5-(1-imino-2-chloroethyl)-l-ornithine ( KI = 1.3 μM, kinact = 0.34 min-1), was conceptually dissected into two fragments and each characterized separately: l-norvaline ( Ki = 470 μM) and 2-chloroacetamidine ( KI = 310 μM, kinact = 4.0 min-1). This analysis suggested that the two fragments were not linked in a manner that allows either to reach full affinity or reactivity, prompting the synthesis and characterization of three analogues: two that mimic the dimethylation status of the substrate, N5-(1-imino-2-chloroisopropyl)-l-ornithine ( kinact /KI = 208 M-1 s-1) and N5-(1-imino-2-chlorisopropyl)-l-lysine ( kinact /KI = 440 M-1 s-1), and one that lengthens the linker beyond that found in the substrate, N5-(1-imino-2-chloroethyl)-l-lysine (Cl-NIL, KI = 0.19 μM, kinact = 0.22 min-1). Cl-NIL is one of the most potent inhibitors reported for DDAH1, inactivates with a second order rate constant (1.9 × 104 M-1 s-1) larger than the catalytic efficiency of DDAH1 for its endogenous substrate (1.6 × 102 M-1 s-1), and has a partition ratio of 1 with a >100 000-fold selectivity for DDAH1 over arginase. An activity-based protein-profiling probe is used to show inhibition of DDAH1 within cultured HEK293T cells (IC50 = 10 μM) with cytotoxicity appearing only at higher concentrations (ED50 = 118 μM). A 1.91 Å resolution X-ray crystal structure reveals specific interactions made with DDAH1 upon covalent inactivation by Cl-NIL. Dissecting a covalent inactivator and analysis of its constituent fragments proved useful for the design and optimization of this potent and effective DDAH1 inhibitor.

TRNA fragments (tRFs) guide Ago to regulate gene expression post-transcriptionally in a Dicer-independent manner.

tRNA related RNA fragments (tRFs), also known as tRNA-derived RNAs (tdRNAs), are abundant small RNAs reported to be associated with Argonaute proteins, yet their function is unclear. We show that endogenous 18 nucleotide tRFs derived from the 3′ ends of tRNAs (tRF-3) post-transcriptionally repress genes in HEK293T cells in culture. tRF-3 levels increase upon parental tRNA overexpression. This represses target genes with a sequence complementary to the tRF-3 in the 3′ UTR. The tRF-3-mediated repression is Dicer-independent, Argonaute-dependent, and the targets are recognized by sequence complementarity. Furthermore, tRF-3:target mRNA pairs in the RNA induced silencing complex associate with GW182 proteins, known to repress translation and promote the degradation of target mRNAs. RNA-seq demonstrates that endogenous target genes are specifically decreased upon tRF-3 induction. Therefore, Dicer-independent tRF-3s, generated upon tRNA overexpression, repress genes post-transcriptionally through an Argonaute-GW182 containing RISC via sequence matches with target mRNAs.

MicroRNP‐mediated translational activation of nonadenylated mRNAs in a mammalian cell‐free system

MicroRNAs are small noncoding RNAs that regulate translation and mRNA stability by binding target mRNAs in complex with Argonaute (AGO) proteins. AGO interacts with a member of the TNRC6 family proteins to form a microRNP complex, which recruits the CCR4-NOT complex to accelerate deadenylation and inhibits translation. MicroRNAs primarily repress translation of target mRNAs but have been shown to enhance translation of a specific type of target reporter mRNAs in various experimental systems: G0 quiescent mammalian cells, Xenopus laevis oocytes, Drosophila embryo extracts, and HeLa cells. In all of the cases mentioned, a common feature of the activated target mRNAs is the lack of a poly(A) tail. Here, we show let-7-microRNP-mediated translational activation of nonadenylated target mRNAs in a mammalian cell-free system, which contains over-expressed AGO2, TNRC6B, and PAPD7 (TUTase5, TRF4-1). Importantly, translation of nonadenylated mRNAs was activated also by tethered TNRC6B silencing domain (SD), in the presence of PAPD7. Deletion of the poly(A)-binding protein (PABP) interacting motif (PAM2) from the TNRC6B-SD abolished the translational activation, suggesting the involvement of PABP in the process. Similar results were also obtained in cultured HEK293T cells. This work may provide novel insights into microRNP-mediated mRNA regulation.

A Chinese herbal decoction, Jian-Pi-Yi-Shen, regulates the expressions of erythropoietin and pro-inflammatory cytokines in cultured cells

BackgroundA Chinese herbal formula, namely Jian-Pi-Yi-Shen (JPYS), has been clinically prescribed for patients with chronic kidney disease associated-anemia, and which can improve the patient’s immunological system. However, the mechanisms of JPYS involved in anemia and immune response have not been investigated. To study the role of JPYS in regulating hematopoietic and immunological functions, we investigated its activities on the expressions of erythropoietin and pro-inflammatory cytokines in cultured cells.MethodsThe standardized herbal extracts of JPYS (0–30 μg/ml) were applied onto cultured cells for 24–48 h. Total RNA was collected from the treated cells and subjected to real-time quantitative PCR analysis. Cultured HEK293T cells, transfected with a construct composed of hypoxia response element tagged with a luciferase gene, i.e. pHRE-Luc, were treated with JPYS extracts (1–30 μg/ml) for 24 h. The cell lysates were subjected to luciferase assay.ResultsThe treatment with JPYS extract onto cultured HEK293T cells induced erythropoietin expression in a dose-dependent manner, having the highest response by ~ 50% of increase. In parallel, application of JPYS extract for 24 h stimulated expressions of interleukin (IL)-1β, IL-6, and tumor necrosis factor (TNF)-α in cultured RAW 264.7 macrophages. In contrast, the pretreatment with JPYS extract suppressed expressions of IL-1β, IL-6, and TNF-α in lipopolysaccharide-induced macrophages.ConclusionsThese results confirmed the hematopoietic function of JPYS in regulating erythropoietin expression, as well as the bidirectional immune-modulatory roles of JPYS by regulating the expression of pro-inflammatory cytokines in cultures.

An acid-compatible co-polymer for the solubilization of membranes and proteins into lipid bilayer-containing nanoparticles.

The fundamental importance of membrane proteins in drug discovery has meant that membrane mimetic systems for studying membrane proteins are of increasing interest. One such system has been the amphipathic, negatively charged poly(styrene-co-maleic acid) (SMA) polymer to form "SMA Lipid Particles" (SMALPs) which have been widely adopted to solubilize membrane proteins directly from the cell membrane. However, SMALPs are only soluble under basic conditions and precipitate in the presence of divalent cations required for many downstream applications. Here, we show that the positively charged poly(styrene-co-maleimide) (SMI) forms similar nanoparticles with comparable efficiency to SMA, whilst remaining functional at acidic pH and compatible with high concentrations of divalent cations. We have performed a detailed characterization of the performance of SMI that enables a direct comparison with similar data published for SMA. We also demonstrate that SMI is capable of extracting proteins directly from the cell membrane and can solubilize functional human G-protein coupled receptors (GPCRs) expressed in cultured HEK 293T cells. "SMILPs" thus provide an alternative membrane solubilization method that successfully overcomes some of the limitations of the SMALP method.