De novo formation of citrate-based fluorophores on N-termini of peptides and proteins in cells and tissues

2020 ◽  
Vol 56 (1) ◽  
pp. 74-77 ◽  
Author(s):  
Dongwook Jung ◽  
Dongkil Choi ◽  
Changgon Sim ◽  
Yumin Kim ◽  
Sunyoung Kang ◽  
...  

Citrate-based fluorophores are generated in de novo manner on proteins in biological samples under mild conditions.

2021 ◽  
Author(s):  
Maren T. Kuchenbrod ◽  
Ulrich S. Schubert ◽  
Rainer Heintzmann ◽  
Stephanie Hoeppener

This review revisits staining protocols for electron microscopy focussing on the visualization of active sites, i.e. enzymes, metabolites or proteins, in cells and tissues, which were never established as standard protocols in electron microscopy.


Synthesis ◽  
2021 ◽  
Author(s):  
Henry P. Caldora ◽  
Sebastian Govaerts ◽  
Shashikant U. Dighe ◽  
Oliver J. Turner ◽  
Daniele Leonori

Here we report a desaturative approach for oxindole synthesis. This method uses simple γ-ester-containing cyclohexanones and primary amine building blocks as coupling partners. A dual photoredox–cobalt manifold is used to generate a secondary aniline that, upon heating, cyclizes with the pendent ester functionality. The process operates under mild conditions and was applied to the modification of several amino acids, the blockbuster drug mexiletine, as well as the formation of dihydroquinolinones.


2019 ◽  
Vol 20 (16) ◽  
pp. 4023 ◽  
Author(s):  
Justyna P. Wróblewska ◽  
Ida J. van der Klei

There is an ongoing debate on how peroxisomes form: by growth and fission of pre-existing peroxisomes or de novo from another membrane. It has been proposed that, in wild type yeast cells, peroxisome fission and careful segregation of the organelles over mother cells and buds is essential for organelle maintenance. Using live cell imaging we observed that cells of the yeast Hansenula polymorpha, lacking the peroxisome fission protein Pex11, still show peroxisome fission and inheritance. Also, in cells of mutants without the peroxisome inheritance protein Inp2 peroxisome segregation can still occur. In contrast, peroxisome fission and inheritance were not observed in cells of a pex11 inp2 double deletion strain. In buds of cells of this double mutant, new organelles likely appear de novo. Growth of pex11 inp2 cells on methanol, a growth substrate that requires functional peroxisomes, is retarded relative to the wild type control. Based on these observations we conclude that in H. polymorpha de novo peroxisome formation is a rescue mechanism, which is less efficient than organelle fission and inheritance to maintain functional peroxisomes.


Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 2445-2445 ◽  
Author(s):  
Swapna Panuganti ◽  
Lisa M. Giammona ◽  
Jan M. Kemper ◽  
Pani Apostolidis ◽  
Stephan Lindsey ◽  
...  

Abstract Introduction: Megakaryocytic cells (Mks), the precursors to platelets, are among the least understood blood cell types. A primary aspect of Mk differentiation is endomitosis, whereby Mks duplicate their DNA content without undergoing cytokinesis and form cells with 4N, 8N, 16N, etc. Mk ploidy strongly correlates with platelet production. Thrombocytopenia accompanies several hematologic malignancies including myelodysplastic syndromes and is often associated with low in vivo Mk ploidy. Elucidation of the factors that regulate Mk endomitosis will aid in developing treatments for Mk-related disorders. We have previously shown that the B3 vitamin nicotinamide (NIC) causes a dose-dependent increase in Mk size and the fraction of high-ploidy (≥ 8N) Mks and leads to more complex proplatelet formation without affecting Mk commitment, ultrastructure, apoptosis, or viability in cultures of CD34+ cells (Giammona LM, et al. Br J Haem 135 (2006): 554). We examined whether NIC’s roles as an inhibitor of the sirtuin family of histone/protein deacetylases (SIRTs) and as a precursor for NAD+ were responsible for its effects on Mk ploidy. Methods: CD34+ cells, isolated from healthy G-CSF-mobilized peripheral blood donors, were maintained in serum-free X-VIVO 20 media supplemented with 100 ng/mL thrombopoietin (Tpo). On day 5, cells were treated with 6.25 mM NIC, 10 μM cambinol (SIRT1/2 inhibitor), or 10 μM AGK2 (SIRT2 inhibitor) or maintained with Tpo alone. Flow cytometry was used to determine Mk commitment (CD41+), viability, apoptosis, ploidy, and intracellular levels of total and acetylated p53. The intracellular concentration of NAD(H) (NAD+ plus NADH) was determined using an enzymatic assay. Immunoblots were used to detect acetylated and total nucleosomes, as well as the NAD processing enzyme Nmnat1. p53 DNA-binding activity was determined using EMSA analysis. Results: Adding NIC to CD34+ cell cultures increased the percentage of high-ploidy Mks by 3-fold. The SIRT1/2 inhibitor cambinol increased Mk ploidy to a similar extent as NIC, while the SIRT2 inhibitor AGK2 was only 30% as effective. NIC and cambinol more than tripled the fractions of 16N and 32N Mks (Figure). None of the additives affected Mk commitment, viability, or apoptosis. Functional inhibition of SIRT1/2 by NIC was confirmed by increased acetylation of several SIRT1/2 target proteins. Both SIRTs deacetylate histones and we observed up to 3-fold greater nucleosome acetylation in cells treated with NIC. Flow cytometry showed that the ratio of AcK382p53 to total p53 was 3-fold higher in cells treated with NIC as compared to Tpo alone. Consistent with reports that acetylation increases p53 DNA-binding activity, EMSA analysis showed that p53 binding to the p53 consensus sequence was 50% greater in NIC-treated Mks. We have previously shown that p53 knockdown increases Mk ploidy in culture (Fuhrken PG, et al. J Biol Chem 283 (2008): 15589). These results suggest that increased p53 acetylation differentially affects different p53 target genes. NIC increased intracellular levels of NAD(H) by 5-fold. In contrast, an NAD+de novo pathway precursor had minimal impact on ploidy. NIC is incorporated into NAD+ via the salvage pathway, which is localized to the nucleus in yeast, whereas the de novo pathway is distributed throughout the cell. This suggests that NAD+ production in the nucleus may also play a role in NIC-mediated increases in Mk ploidy, and is consistent with higher nuclear levels of the NAD+ salvage pathway enzyme Nmnat1 detected in cells treated with NIC. Conclusions: Inhibition of SIRT1 and SIRT2 appears to be the primary mechanism for NIC-mediated increases in Mk ploidy, and increased p53 acetylation is likely to play an important role in this process. Further study of SIRT targets associated with DNA repair, apoptosis, and cell cycle regulation may provide additional insight into Mk polyploidization. Figure Figure


2003 ◽  
Vol 161 (4) ◽  
pp. 697-705 ◽  
Author(s):  
James G. Evans ◽  
Ivan Correia ◽  
Olga Krasavina ◽  
Nicki Watson ◽  
Paul Matsudaira

Podosomes are actin- and fimbrin-containing adhesions at the leading edge of macrophages. In cells transfected with β-actin–ECFP and L-fimbrin–EYFP, quantitative four-dimensional microscopy of podosome assembly shows that new adhesions arise at the cell periphery by one of two mechanisms; de novo podosome assembly, or fission of a precursor podosome into daughter podosomes. The large podosome cluster precursor also appears to be an adhesion structure; it contains actin, fimbrin, integrin, and is in close apposition to the substratum. Microtubule inhibitors paclitaxel and demecolcine inhibit the turnover and polarized formation of podosomes, but not the turnover rate of actin in these structures. Because daughter podosomes and podosome cluster precursors are preferentially located at the leading edge, they may play a critical role in continually generating new sites of cell adhesion.


2000 ◽  
Vol 74 (24) ◽  
pp. 11782-11791 ◽  
Author(s):  
Guoying Zhou ◽  
Veronica Galvan ◽  
Gabriella Campadelli-Fiume ◽  
Bernard Roizman

ABSTRACT We have made two stocks of a herpes simplex virus 1 mutant lacking intact US5 and US6 open reading frames encoding glycoproteins J (gJ) and D (gD), respectively. The stock designated gD−/+, made in cells carrying US6 and expressing gD, was capable of productively infecting cells, whereas the stock designated gD−/−, made in cells lacking viral DNA sequences, was known to attach but not initiate infection. We report the following. (i) Both stocks of virus induced apoptosis in SK-N-SH cells. Thus, annexin V binding to cell surfaces was detected as early as 8 h after infection. (ii) US5 or US6 cloned into the baculovirus under the human cytomegalovirus immediate-early promoter was expressed in SK-N-SH cells and blocked apoptosis in cells infected with either gD−/+ or gD−/− virus, whereas glycoprotein B, infected cell protein 22, or the wild-type baculovirus did not block apoptosis. (iii) In SK-N-SH cells, internalized, partially degraded virus particles were detected at 30 min after exposure to gD−/− virus but not at later intervals. (iv) Concurrent infection of cells with baculoviruses did not alter the failure of gD−/− virus from expressing its genes or, conversely, the expression of viral genes by gD−/+ virus. These results underscore the capacity of herpes simplex virus to initiate the apoptotic cascade in the absence of de novo protein synthesis and indicate that both gD and gJ independently, and most likely at different stages in the reproductive cycle, play a key role in blocking the apoptotic cascade leading to cell death.


1991 ◽  
Vol 39 (5) ◽  
pp. 695-700 ◽  
Author(s):  
W Cammer ◽  
M Downing

The CAD multidomain protein, which includes active sites of carbamyl phosphate synthetase II (CPS II, glutamine-dependent), aspartate transcarbamylase, and dihydroorotase, was immunostained in normal rat brains, the gliotic brains of myelin-deficient mutant rats, and brains from normal weanling hamsters. In each of these tissues CAD was observed in cells resembling astrocytes. In hamster brain, CAD immunofluorescence was also found in cells closely related to astrocytes, i.e., the Bergmann glia in cerebellum and the tanycytes surrounding the third ventricle. The astrocytic identity of the CAD-positive cells in rat brain was confirmed by double immunofluorescence staining with antibodies against glial fibrillary acidic protein (GFAP). The two enzymes carbonic anhydrase and glutamine synthetase occur in the cytoplasm of normal astrocytes in gray matter and of reactive astrocytes during gliosis. Products of each enzyme, i.e., bicarbonate and glutamine, are required for the CPS II reaction, which is the first step in the biosynthesis of pyrimidines. Therefore, the present results suggest roles for carbonic anhydrase and glutamine synthetase, as well as CAD, in pyrimidine biosynthesis in brain and a role for the astrocytes in the de novo synthesis of pyrimidines.


2016 ◽  
Vol 82 (8) ◽  
pp. 2270-2279 ◽  
Author(s):  
Kristen Bennett ◽  
Natalie C. Sadler ◽  
Aaron T. Wright ◽  
Chris Yeager ◽  
Michael R. Hyman

ABSTRACTNitrosomonas europaeais an aerobic nitrifying bacterium that oxidizes ammonia (NH3) to nitrite (NO2−) through the sequential activities of ammonia monooxygenase (AMO) and hydroxylamine dehydrogenase (HAO). Many alkynes are mechanism-based inactivators of AMO, and here we describe an activity-based protein profiling method for this enzyme using 1,7-octadiyne (17OD) as a probe. Inactivation of NH4+-dependent O2uptake byN. europaeaby 17OD was time- and concentration-dependent. The effects of 17OD were specific for ammonia-oxidizing activity, andde novoprotein synthesis was required to reestablish this activity after cells were exposed to 17OD. Cells were reacted with Alexa Fluor 647 azide using a copper-catalyzed azide-alkyne cycloaddition (CuAAC) (click) reaction, solubilized, and analyzed by SDS-PAGE and infrared (IR) scanning. A fluorescent 28-kDa polypeptide was observed for cells previously exposed to 17OD but not for cells treated with either allylthiourea or acetylene prior to exposure to 17OD or for cells not previously exposed to 17OD. The fluorescent polypeptide was membrane associated and aggregated when heated with β-mercaptoethanol and SDS. The fluorescent polypeptide was also detected in cells pretreated with other diynes, but not in cells pretreated with structural homologs containing a single ethynyl functional group. The membrane fraction from 17OD-treated cells was conjugated with biotin-azide and solubilized in SDS. Streptavidin affinity-purified polypeptides were on-bead trypsin-digested, and amino acid sequences of the peptide fragments were determined by liquid chromatography-mass spectrometry (LC-MS) analysis. Peptide fragments from AmoA were the predominant peptides detected in 17OD-treated samples. In-gel digestion and matrix-assisted laser desorption ionization–tandem time of flight (MALDI-TOF/TOF) analyses also confirmed that the fluorescent 28-kDa polypeptide was AmoA.


2019 ◽  
Vol 116 (42) ◽  
pp. 21268-21273 ◽  
Author(s):  
Haruhiko Jimbo ◽  
Taichi Izuhara ◽  
Yukako Hihara ◽  
Toru Hisabori ◽  
Yoshitaka Nishiyama

In photosynthetic organisms, the repair of photosystem II (PSII) is enhanced after acclimation to strong light, with the resultant mitigation of photoinhibition of PSII. We previously reported that oxidation of translation elongation factor EF-Tu, which delivers aminoacyl-tRNA to the ribosome, depresses the repair of PSII in the cyanobacterium Synechocystis sp. PCC 6803. In the present study, we investigated the role of EF-Tu in the repair of PSII after acclimation of Synechocystis to strong light. In cells that had been grown under strong light, both the repair of PSII and the synthesis of proteins de novo were enhanced under strong light, with the resultant mitigation of photoinhibition of PSII. Moreover, levels of EF-Tu were elevated, whereas levels of other components of the translation machinery, such as translation factor EF-G and ribosomal proteins L2 and S12, did not change significantly. The expression of the gene for EF-Tu was induced by light, as monitored at the transcriptional level. Elevation of the level of EF-Tu was strongly correlated with the subsequent enhancement of PSII repair in cells that had been grown under light at various intensities. Furthermore, overexpression of EF-Tu in Synechocystis enhanced protein synthesis and PSII repair under strong light, even after cell culture under nonacclimating conditions. These observations suggest that elevation of the level of EF-Tu might be a critical factor in enhancing the capacity for repair of PSII that develops during acclimation to strong light.


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