Enzymatic Activity Assays in Yeast Cell Extracts

BIO-PROTOCOL ◽  
2014 ◽  
Vol 4 (23) ◽  
Author(s):  
Melike Çağlayan ◽  
Samuel Wilson
2014 ◽  
Vol 80 (14) ◽  
pp. 4184-4188 ◽  
Author(s):  
Jumpei Washio ◽  
Yuko Shimada ◽  
Masakazu Yamada ◽  
Ryouichi Sakamaki ◽  
Nobuhiro Takahashi

ABSTRACTIndigenous oral bacteria in the tongue coating such asVeillonellahave been identified as the main producers of hydrogen sulfide (H2S), one of the major components of oral malodor. However, there is little information on the physiological properties of H2S production by oralVeillonellasuch as metabolic activity and oral environmental factors which may affect H2S production. Thus, in the present study, the H2S-producing activity of growing cells, resting cells, and cell extracts of oralVeillonellaspecies and the effects of oral environmental factors, including pH and lactate, were investigated. Type strains ofVeillonella atypica,Veillonella dispar, andVeillonella parvulawere used. TheseVeillonellaspecies produced H2S during growth in the presence ofl-cysteine. Resting cells of these bacteria produced H2S froml-cysteine, and the cell extracts showed enzymatic activity to convertl-cysteine to H2S. H2S production by resting cells was higher at pH 6 to 7 and lower at pH 5. The presence of lactate markedly increased H2S production by resting cells (4.5- to 23.7-fold), while lactate had no effect on enzymatic activity in cell extracts. In addition to H2S, ammonia was produced in cell extracts of all the strains, indicating that H2S was produced by the catalysis of cystathionine γ-lyase (EC 4.4.1.1). Serine was also produced in cell extracts ofV. atypicaandV. parvula, suggesting the involvement of cystathionine β-synthase lyase (EC 4.2.1.22) in these strains. This study indicates thatVeillonellaproduce H2S froml-cysteine and that their H2S production can be regulated by oral environmental factors, namely, pH and lactate.


2020 ◽  
Vol 21 (21) ◽  
pp. 8304
Author(s):  
Valentina V. Rekstina ◽  
Tatyana A. Sabirzyanova ◽  
Fanis A. Sabirzyanov ◽  
Alexei A. Adzhubei ◽  
Yaroslav V. Tkachev ◽  
...  

Glucan linked to proteins is a natural mega-glycoconjugate (mGC) playing the central role as a structural component of a yeast cell wall (CW). Regulation of functioning of non-covalently bound glucanosyltransglycosylases (ncGTGs) that have to remodel mGC to provide CW extension is poorly understood. We demonstrate that the main ncGTGs Bgl2 and Scw4 have phosphorylated and glutathionylated residues and are represented in CW as different pools of molecules having various firmness of attachment. Identified pools contain Bgl2 molecules with unmodified peptides, but differ from each other in the presence and combination of modified ones, as well as in the presence or absence of other CW proteins. Correlation of Bgl2 distribution among pools and its N-glycosylation was not found. Glutathione affects Bgl2 conformation, probably resulting in the mode of its attachment and enzymatic activity. Bgl2 from the pool of unmodified and monophosphorylated molecules demonstrates the ability to fibrillate after isolation from CW. Revealing of Bgl2 microcompartments and their mosaic arrangement summarized with the results obtained give the evidence that the functioning of ncGTGs in CW can be controlled by reversible post-translational modifications and facilitated due to their compact localization. The hypothetical scheme of distribution of Bgl2 inside CW is represented.


2018 ◽  
Vol 3 (1) ◽  
Author(s):  
David C Garcia ◽  
Benjamin P Mohr ◽  
Jakob T Dovgan ◽  
Gregory B Hurst ◽  
Robert F Standaert ◽  
...  

Abstract Living systems possess a rich biochemistry that can be harnessed through metabolic engineering to produce valuable therapeutics, fuels and fine chemicals. In spite of the tools created for this purpose, many organisms tend to be recalcitrant to modification or difficult to optimize. Crude cellular extracts, made by lysis of cells, possess much of the same biochemical capability, but in an easier to manipulate context. Metabolic engineering in crude extracts, or cell-free metabolic engineering, can harness these capabilities to feed heterologous pathways for metabolite production and serve as a platform for pathway optimization. However, the inherent biochemical potential of a crude extract remains ill-defined, and consequently, the use of such extracts can result in inefficient processes and unintended side products. Herein, we show that changes in cell growth conditions lead to changes in the enzymatic activity of crude cell extracts and result in different abilities to produce the central biochemical precursor pyruvate when fed glucose. Proteomic analyses coupled with metabolite measurements uncover the diverse biochemical capabilities of these different crude extract preparations and provide a framework for how analytical measurements can be used to inform and improve crude extract performance. Such informed developments can allow enrichment of crude extracts with pathways that promote or deplete particular metabolic processes and aid in the metabolic engineering of defined products.


1995 ◽  
Vol 15 (12) ◽  
pp. 6895-6900 ◽  
Author(s):  
K McKune ◽  
P A Moore ◽  
M W Hull ◽  
N A Woychik

To assess functional relatedness of individual components of the eukaryotic transcription apparatus, three human subunits (hsRPB5, hsRPB8, and hsRPB10) were tested for their ability to support yeast cell growth in the absence of their essential yeast homologs. Two of the three subunits, hsRPB8 and hsRPB10, supported normal yeast cell growth at moderate temperatures. A fourth human subunit, hsRPB9, is a homolog of the nonessential yeast subunit RPB9. Yeast cells lacking RPB9 are unable to grow at high and low temperatures and are defective in mRNA start site selection. We tested the ability of hsRPB9 to correct the growth and start site selection defect seen in the absence of RPB9. Expression of hsRPB9 on a high-copy-number plasmid, but not a low-copy-number plasmid, restored growth at high temperatures. Recombinant human hsRPB9 was also able to completely correct the start site selection defect seen at the CYC1 promoter in vitro as effectively as the yeast RPB9 subunit. Immunoprecipitation of the cell extracts from yeast cells containing either of the human subunits that function in place of their yeast counterparts in vivo suggested that they assemble with the complete set of yeast RNA polymerase II subunits. Overall, a total of six of the seven human subunits tested previously or in this study are able to substitute for their yeast counterparts in vivo, underscoring the remarkable similarities between the transcriptional machineries of lower and higher eukaryotes.


1999 ◽  
Vol 73 (12) ◽  
pp. 10224-10235 ◽  
Author(s):  
Gregor Meyers ◽  
Armin Saalmüller ◽  
Mathias Büttner

ABSTRACT Classical swine fever (CSF) is a severe hemorrhagic disease of swine caused by the pestivirus CSF virus (CSFV). Amino acid exchanges or deletions introduced by site-directed mutagenesis into the putative active site of the RNase residing in the glycoprotein Ernsof CSFV abolished the enzymatic activity of this protein, as demonstrated with an RNase test suitable for detection of the enzymatic activity in crude cell extracts. Incorporation of the altered sequences into an infectious CSFV clone resulted in recovery of viable viruses upon RNA transfection, except for a variant displaying a deletion of the histidine codon at position 297 of the long open reading frame. These RNase-negative virus mutants displayed growth characteristics in tissue culture that were undistinguishable from wild-type virus and were stable for at least seven passages. In contrast to animals inoculated with an RNase-positive control virus, infection of piglets with an RNase-negative mutant containing a deletion of the histidine codon 346 of the open reading frame did not lead to CSF. Neither fever nor extended viremia could be detected. Animals infected with this mutant did not show decrease of peripheral B cells, a characteristic feature of CSF in swine. Animal experiments with four other mutants with either exchanges of codons 297 or 346 or double exchanges of both codons 297 and 346 showed that all these RNase-negative mutants were attenuated. All viruses with mutations affecting codon 346 were completely apathogenic, whereas those containing only changes of codon 297 consistently induced clinical symptoms for several days, followed by sudden recovery. Analyses of reisolated viruses gave no indication for the presence of revertants in the infected animals.


2017 ◽  
Vol 2017 (2) ◽  
pp. pdb.prot091595 ◽  
Author(s):  
Agnes Grallert ◽  
Iain M. Hagan

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 3523-3523 ◽  
Author(s):  
Constantine S. Mitsiades ◽  
Luba Benimetskaya ◽  
Krishna Menon ◽  
Cinara Echart ◽  
Cecile Rouleau ◽  
...  

Abstract Introduction: Defibrotide (DF), a polydisperse oligonucleotide with anti-thrombotic, thrombolytic, and anti-adhesive properties, but minimal hemorrhagic risk, selectively targets microvasculature and is a promising treatment for stem cell transplant-associated hepatic veno-occlusive disease (VOD), a serious complication characterized by endothelial cell (EC) and stromal injury in liver. We previously reported that DF has minimal activity against multiple myeloma (MM) in vitro, but increases MM cell sensitivity to conventional chemotherapy, including melphalan and dexamethasone in vivo. We hypothesized that DF modulates MM cell interactions with local microenvironment, including stroma and ECs, as well as the bioavailability of cytokine/growth factors for tumor and ECs. Methods/Results: Pharmacokinetics of DF (administered po vs. iv) at clinically-relevant doses (0–48 mg/kg) to 8 week-old male Fisher 344 rats were first evaluated. Peripheral blood plasma was collected (0–8hrs) and HPLC analyses, validated by agarose gel determination (mean and median variability of measurement of 8.1% and 7.9%, respectively), showed that after iv and po administration, peak DF levels (Cmax) were 1253 and 474 μg/mL, and area under the curve (AUC0-240 min) were 14.7 and 17.2 μg*min/Lt. Time to Cmax was 30 min for po administration, with undetectable levels by 240 min after po or iv treatment. In vitro studies at DF concentrations achievable in vivo were next conducted to evaluate effects on growth factors (including VEGF, bFGF, PDGF) critical for tumor neovascularization and pathways regulating bioavailability of extracellular matrix (ECM)-resident growth factors, including expression/enzymatic activity of heparanase, which degrades heparin sulfate (HS), releases HS-bound growth factors and promotes tumor invasion and metastasis. Using a ClRNH32P-OdT18 probe and increasing DF concentrations as a competitor of probe binding to growth factors, we observed high-affinity of DF for certain heparin-binding growth factors, including bFGF and PDGF (calculated Kc values of 30 and 40 nM, respectively), but not others, such as VEGF (Kc1200 nM). Pharmacologically achievable DF levels suppressed in vitro heparanase mRNA (by Real-Time PCR) in U226 MM cells and heparanase enzymatic activity in U266 cell extracts. These data suggest that DF can perturb bioavailability, expression and/or function of diverse positive regulators of neo-angiogenesis. Indeed DF suppressed in vitro formation of vessel-like structures by ECs in corneal matrix assays. Conclusions: DF, a known anti-thrombotic agent, exhibits, at concentrations achievable after oral administration, diverse biological functions that may suppress tumor-associated angiogenesis. These include direct DF binding to pro-angiogenic growth factors, suppression of enzymes responsible for release of these factors, and thus their depletion from tumor ECM. These studies, combined with our data that DF can counteract stroma-derived protection to MM cells against chemotherapy, provide the framework for an ongoing Phase I/II clinical trial of oral melphalan, prednisone, thalidomide and DF in advanced MM.


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