Yeast Cell-free Extracts Research Articles

Extracellular synthesis of silver nanoparticle using yeast extracts: antibacterial and seed priming applicationss.

The evolution and rapid spread of multidrug-resistant (MDR) bacterial pathogens have become a major concern for human health and demand the development of alternative antimicrobial agents to combat this emergent threat. Conventional intracellular methods for producing metal nanoparticles (NPs) using whole-cell microorganisms have limitations, including binding of NPs to cellular components, potential product loss, and environmental contamination. In contrast, this study introduces a green, extracellular, and sustainable methodology for the bio-materialization of silver NPs (AgNPs) using renewable resource cell-free yeast extract. These extracts serve as a sustainable, biogenic route for both reducing the metal precursor and stabilizing the surface of AgNPs. This method offers several advantages such as cost-effectiveness, environment-friendliness, ease of synthesis, and scalability. HR-TEM imaging of the biosynthesized AgNPs revealed an isotropic growth route, resulting in an average size of about ~ 18nm and shapes ranging from spherical to oval. Further characterization by FTIR and XPS results revealed various functional groups, including carboxyl, hydroxyl, and amide contribute to enhanced colloidal stability. AgNPs exhibited potent antibacterial activity against tested MDR strains, showing particularly high efficacy against Gram-negative bacteria. These findings suggest their potential role in developing alternative treatments to address the growing threat of antimicrobial resistance. Additionally, seed priming experiments demonstrated that pre-sowing treatment with AgNPs improves both the germination rate and survival of Sorghum jowar and Zea mays seedlings. KEY POINTS: •Yeast extract enables efficient, cost-effective, and eco-friendly AgNP synthesis. •Biosynthesized AgNPs showed strong antibacterial activity against MDR bacteria. •AgNPs boost seed germination and protect against seed-borne diseases.

In vitro translation in yeast extract to study interactions with cytosolic chaperones.

Saccharomyces cerevisiae, a well-established model organism, serves as a valuable tool for unraveling various eukaryotic cellular processes. Its utility extends to studying protein folding and interactions with chaperones, as it demonstrates a capability to produce and process proteins in a manner closely resembling that of higher eukaryotes. To gain insights into the events taking place following protein synthesis in the cytosol, an in vitro translation system is essential-one that mirrors in vivo processes yet allows for easy manipulation. To address this need, multiple protocols for preparation of cell-free translation lysates from S. cerevisiae have been documented. This chapter introduces an optimized and modified in vitro pull-down approach following protein translation in yeast cell-free extract. The advantages of this system in investigating the interactions of newly synthesized mitochondrial proteins with cytosolic chaperones are described. This procedure exploits the dual advantages of yeast cell-free lysates, serving as both a protein synthesis tool, and a reservoir for cytosolic factors and chaperones. In summary, the depicted approach provides a versatile platform that deepens our understanding of the early cytosolic events in the biogenesis of nascent proteins before reaching their ultimate organelle.

A translation enhancer element from black beetle virus engages yeast eIF4G1 to drive cap-independent translation initiation

Cap-independent translation initiation plays crucial roles in fine-tuning gene expression under global translation shutdown conditions. Translation of uncapped or de-capped transcripts can be stimulated by Cap-independent translation enhancer (CITE) elements, but the mechanisms of CITE-mediated translation initiation remain understudied. Here, we characterized a short 5ʹ-UTR RNA sequence from black beetle virus, BBV-seq. Mutational analysis indicates that the entire BBV-seq is required for efficient translation initiation, but this sequence does not operate as an IRES-type module. In yeast cell-free translation extracts, BBV-seq promoted efficient initiation on cap-free mRNA using a scanning mechanism. Moreover, BBV-seq can increase translation efficiency resulting from conventional cap-dependent translation initiation. Using genetic approaches, we found that BBV-seq exploits RNA-binding properties of eIF4G1 to promote initiation. Thus, BBV-seq constitutes a previously uncharacterized short, linear CITE that influences eIF4G1 to initiate 5′ end-dependent, cap-independent translation. These findings bring new insights into CITE-mediated translational control of gene expression.

Characterization of biogenic selenium nanoparticles derived from cell-free extracts of a novel yeast Magnusiomyces ingens.

A facile one-pot and effective green process for biogenic selenium nanoparticles (SeNPs) was obtained using the cell-free extracts of a novel yeast Magnusiomyces ingens LH-F1. The corresponding absorption peak of SeNPs was observed at ~ 560nm by UV-vis spectrophotometer. In the present study, SeO2 2mM, protein 500mgL-1 and pH 7 were preferable to the biosynthesis of SeNPs. The effects of pH, SeO2 concentration and protein concentration on the synthesis process were different. Transmission electron microscopy image exhibited that all the SeNPs were spherical and quasi-spherical with the diameters mainly distributed in 70-90nm (average particles size was 87.82 ± 2.71nm). X-ray diffraction suggested that the nanoparticles were composed of standard hexagonal crystalline Se with high purity. Fourier transform infrared spectroscopy indicated that some biomolecules such as hydroxyl, carboxyl and amino groups in the yeast cell-free extracts might be involved in the formation of SeNPs. Analyses of sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed that two proteins with low molecular weight approximately ~ 16 and ~ 21kDa were detected on the surface of SeNPs and in the extracts, which could play the role of natural stabilizers and confer stability to synthesized SeNPs; whereas, unbound proteins on the SeNPs surface could act as reducing agents. Antibacterial analysis showed that the SeNPs could inhibit Arthrobacter sp. W1 (Gram positive) but not E. coli BL21 (Gram negative), which could provide reference for antimicrobial application of biogenic SeNPs.

Comparative immunogenicity of preparations of yeast-derived dengue oral vaccine candidate

BackgroundDengue is listed as a neglected tropical disease by the Center for Disease Control and Preservation, as there are insufficient integrated surveillance strategies, no effective treatment, and limited licensed vaccines. Consisting of four genetically distinct serotypes, dengue virus (DENV) causes serious life-threatening infections due to its complexity. Antibody-dependent enhancement by pre-existing cross-reactive as well as homotypic antibodies further worsens the clinical symptoms of dengue. Thus, a vaccine conferring simultaneous and durable immunity to each of the four DENV serotypes is essential to restrict its escalation. In deeply affected resource-limited countries, oral vaccination using food-grade organisms is considered to be a beneficial approach in terms of costs, patient comfort, and simple logistics for mass immunization. The current study used a mouse model to explore the immunogenicity of an oral dengue vaccine candidate prepared using whole recombinant yeast cells (WC) and cell-free extracts (CFE) from cells expressing recombinant Escherichia coli heat-labile toxin protein B-subunit (LTB) fused to the consensus dengue envelope domain III (scEDIII). Mice were treated orally with recombinant WC and CFE vaccines in 2-week intervals for 4 weeks and changes in systemic and mucosal immune responses were monitored.ResultsBoth WC and CFE dosage applications of LTB-scEDIII stimulated a systemic humoral immune response in the form of dengue-specific serum IgG as well as mucosal immune response in the form of secretory sIgA. Antigen-specific B cell responses in isolated lymphoid cells from the spleen and Peyer’s patches further indicated an elevated mucosal immune response. Cellular immune response estimated through lymphocyte proliferation assay indicated higher levels in CFE than WC dosage. Furthermore, sera obtained after both oral administrations successfully neutralized DENV-1, whereas CFE formulation only neutralized DENV-2 serotype, two representative serotypes which cause severe dengue infection. Sera from mice that were fed CFE preparations demonstrated markedly higher neutralizing titers compared to those from WC-fed mice. However, WC feeding elicited strong immune responses, which were similar to the levels induced by CFE feeding after intraperitoneal booster with purified scEDIII antigen.ConclusionsCFE preparations of LTB-scEDIII produced strong immunogenicity with low processing requirements, signifying that this fusion protein shows promise as a potent oral vaccine candidate against dengue viral infection.

Identification and characterization of an enzyme involved in the biosynthesis of the 4-hydroxy-2(or 5)-ethyl-5(or 2)-methyl-3(2H)-furanone in yeast

4-Hydroxy-2(or 5)-ethyl-5(or 2)-methyl-3(2H)-furanone (HEMF) is considered a key flavor compound in soy sauce. The compound has a caramel-like aroma and several important physiological activities, such as strong antioxidant activity. Here, we report the identification and characterization of an enzyme involved in the biosynthesis of HEMF in yeast. We fractionated yeast cell-free extract from Saccharomyces cerevisiae using column chromatography and partially purified a fraction with HEMF-forming activity. Peptide mass fingerprinting analysis showed that the partially purified fraction contains aldehyde reductase encoded by YNL134C. This reductase shares low sequence identity with enone oxidoreductase, which is responsible for the formation of 4-hydroxy-2,5-dimethyl-3(2H)-furanone (HDMF) and HEMF in plants. YNL134C was expressed heterologously in Escherichia coli, and the purified protein catalyzed the formation of HEMF from the mixture of Maillard reaction products, acetaldehydes, and NADPH. Multicopy expression in S.cerevisiae resulted in increased HEMF productivity, and gene knockout of YNL134C in S.cerevisiae resulted in decreased HEMF productivity. These data suggest that the translation product of YNL134C is the HEMF-producing enzyme in yeast. Detailed analyses of an intermediate in the enzymatic reaction mixture revealed that HEMF is synthesized from (2E)-2-ethylidene-4-hydroxy-5-methyl-3(2H)-furanone, which formed via Knoevenagel condensation between the acetaldehyde and 4-hydroxy-5-methyl-3(2H)-furanone derived from the Maillard reaction based on ribose and glycine, by YNL134Cp in an NADPH dependent manner. Overall, this study shed light on the molecular basis for the improvement of soy sauce flavor and the biotechnological production of HEMF.

우리나라 야생화에서 분리한 효모의 항산화 활성과 Xanthine Oxidase 및 Tyrosinase 저해활성

We prepared supernatants and cell-free extracts of yeasts isolated from wild flowers in Korea, and their antioxidant activity and inhibitory activities of xanthine oxidase and tyrosinase were investigated. Among them, cell-free extracts of Kuraishia capsulata UL40-2 and Sporobolomyces ruberrimus 121-Z-3 showed significantly high xanthine oxidase inhibitory activity of 46.4% and 48.3%, respectively. Starmerella bombicola 80-J-1 also showed tyrosinase inhibitory activity of 36.2% in the cell-free extract. Other antioxidant activities and tyrosinase inhibitory activities were not detected or were below 20%. Maximal production of the xanthine oxidase inhibitors were observed when Kuraishia capsulate UL40-2 and Sporobolomyces ruberrimus 121-Z-3 were cultured in the yeast extract-peptone-dextrose media at for 24 hour, respectively.

Salicylic Acid Inhibits the Replication of Tomato bushy stunt virus by Directly Targeting a Host Component in the Replication Complex

Although the plant hormone salicylic acid (SA) plays a central role in signaling resistance to viral infection, the underlying mechanisms are only partially understood. Identification and characterization of SA's direct targets have been shown to be an effective strategy for dissecting the complex SA-mediated defense signaling network. In search of additional SA targets, we previously developed two sensitive approaches that utilize SA analogs in conjunction with either a photoaffinity labeling technique or surface plasmon resonance-based technology to identify and evaluate candidate SA-binding proteins (SABPs) from Arabidopsis. Using these approaches, we have now identified several members of the Arabidopsis glyceraldehyde 3-phosphate dehydrogenase (GAPDH) protein family, including two chloroplast-localized and two cytosolic isoforms, as SABPs. Cytosolic GAPDH is a well-known glycolytic enzyme; it also is an important host factor involved in the replication of Tomato bushy stunt virus (TBSV), a single-stranded RNA virus. Using a yeast cell-free extract, an in vivo yeast replication system, and plant protoplasts, we demonstrate that SA inhibits TBSV replication. SA does so by inhibiting the binding of cytosolic GAPDH to the negative (-)RNA strand of TBSV. Thus, this study reveals a novel molecular mechanism through which SA regulates virus replication.

Template Role of Double-Stranded RNA in Tombusvirus Replication

Replication of plus-strand RNA [(+)RNA] viruses of plants is a relatively simple process that involves complementary minus-strand RNA [(-)RNA] synthesis and subsequent (+)RNA synthesis. However, the actual replicative form of the (-)RNA template in the case of plant (+)RNA viruses is not yet established unambiguously. In this paper, using a cell-free replication assay supporting a full cycle of viral replication, we show that replication of Tomato bushy stunt virus (TBSV) leads to the formation of double-stranded RNA (dsRNA). Using RNase digestion, DNAzyme, and RNA mobility shift assays, we demonstrate the absence of naked (-)RNA templates during replication. Time course experiments showed the rapid appearance of dsRNA earlier than the bulk production of new (+)RNAs, suggesting an active role for dsRNA in replication. Radioactive nucleotide chase experiments showed that the mechanism of TBSV replication involves the use of dsRNA templates in strand displacement reactions, where the newly synthesized plus strand replaces the original (+)RNA in the dsRNA. We propose that the use of dsRNA as a template for (+)RNA synthesis by the viral replicase is facilitated by recruited host DEAD box helicases and the viral p33 RNA chaperone protein. Altogether, this replication strategy allows TBSV to separate minus- and plus-strand syntheses in time and regulate asymmetrical RNA replication that leads to abundant (+)RNA progeny. Positive-stranded RNA viruses of plants use their RNAs as the templates for replication. First, the minus strand is synthesized by the viral replicase complex (VRC), which then serves as a template for new plus-strand synthesis. To characterize the nature of the (-)RNA in the membrane-bound viral replicase, we performed complete RNA replication of Tomato bushy stunt virus (TBSV) in yeast cell-free extracts and in plant extracts. The experiments demonstrated that the TBSV (-)RNA is present as a double-stranded RNA that serves as the template for TBSV replication. During the production of new plus strands, the viral replicase displaces the old plus strand in the dsRNA template, leading to asymmetrical RNA synthesis. The presented data are in agreement with the model that the dsRNA is present in nuclease-resistant membranous VRCs. This strategy likely allows TBSV to protect the replicating viral RNA from degradation as well as to evade the early detection of viral dsRNAs by the host surveillance system.

Characterization of dominant-negative and temperature-sensitive mutants of tombusvirus replication proteins affecting replicase assembly

The assembly of the viral replicase complex (VRC) on subcellular membranes is a key step in the replication process of plus-stranded RNA viruses. In this work, we have identified lethal and temperature sensitive (ts) point mutations within the essential p33:p33/p92 interaction domain of p33 and p92 replication proteins of Cucumber necrosis virus, a tombusvirus. Mutations within the p33:p33/p92 interaction domain also affected viral RNA recombination in yeast model host. An in vitro approach based on yeast cell free extract demonstrated that several p33 and p92 mutants behaved as dominant-negative during VRC assembly, and they showed reduced binding to the viral (+)RNA and affected activation of the p92 RdRp protein, while they did not directly influence (−) or (+)-strand synthesis. Overall, the presented data provide direct evidence that the p33:p33/p92 interaction domains in p33 and p92 are needed for the early stage of virus replication and also influence viral recombination.

P33-Independent Activation of a Truncated p92 RNA-Dependent RNA Polymerase of Tomato Bushy Stunt Virus in Yeast Cell-Free Extract

Plus-stranded RNA viruses replicate in membrane-bound structures containing the viral replicase complex (VRC). A key component of the VRC is the virally encoded RNA-dependent RNA polymerase (RdRp), which should be activated and incorporated into the VRC after its translation. To study the activation of the RdRp of Tomato bushy stunt virus (TBSV), a small tombusvirus of plants, we used N-terminal truncated recombinant RdRp, which supported RNA synthesis in a cell-free yeast extract-based assay. The truncated RdRp required a cis-acting RNA replication element and soluble host factors, while unlike the full-length TBSV RdRp, the truncated RdRp did not need the viral p33 replication cofactor or cellular membranes for RNA synthesis. Interestingly, the truncated RdRp used 3'-terminal extension for initiation and terminated prematurely at an internal cis-acting element. However, the truncated RdRp could perform de novo initiation on a TBSV plus-strand RNA template in the presence of the p33 replication cofactor, cellular membranes, and soluble host proteins. Altogether, the data obtained with the truncated RdRp indicate that this RdRp still requires activation, but with the participation of fewer components than with the full-length RdRp, making it suitable for future studies on dissection of the RdRp activation mechanism.

Direct Inhibition of Tombusvirus Plus-Strand RNA Synthesis by a Dominant Negative Mutant of a Host Metabolic Enzyme, Glyceraldehyde-3-Phosphate Dehydrogenase, in Yeast and Plants

The replication of plus-strand RNA viruses depends on many cellular factors. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an abundant metabolic enzyme that is recruited to the replicase complex of Tomato bushy stunt virus (TBSV) and affects asymmetric viral RNA synthesis. To further our understanding on the role of GAPDH in TBSV replication, we used an in vitro TBSV replication assay based on recombinant p33 and p92(pol) viral replication proteins and cell-free yeast extract. We found that the addition of purified recombinant GAPDH to the cell extract prepared from GAPDH-depleted yeast results in increased plus-strand RNA synthesis and asymmetric production of viral RNAs. Our data also demonstrate that GAPDH interacts with p92(pol) viral replication protein, which may facilitate the recruitment of GAPDH into the viral replicase complex in the yeast model host. In addition, we have identified a dominant negative mutant of GAPDH, which inhibits RNA synthesis and RNA recruitment in vitro. Moreover, this mutant also exhibits strong suppression of tombusvirus accumulation in yeast and in virus-infected Nicotiana benthamiana. Overall, the obtained data support the model that the co-opted GAPDH plays a direct role in TBSV replication by stimulating plus-strand synthesis by the viral replicase.

알코올 대사 효소 alcohol dehydrogenase (ADH) 및 acetaldehyde dehydrogenase (ALDH) 활성에 미치는 아미노산의 영향

본 연구에서는 숙취해소에 좋은 것으로 알려진 식품 소재의 주요 아미노산을 포함하여 효소 활성에 영향을 미치는 것으로 알려진 아미노산을 선택하였고, 효소 활성도가 상대적으로 높은 yeast와 rat liver 유래의 ADH 및 ALDH 효소를 대상으로 알코올 대사에 관련된 효소 활성의 촉진 효과에 대하여 검토하였다. Rat liver 유래의 ADH 활성은 처리한 아미노산 중에서 arginine에서 가장 높았다. Arginine의 첨가 농도를 달리하여 효소 활성을 측정한 결과 <TEX>$10{\sim}50\;mg$</TEX>/ml 농도에서 <TEX>$118{\sim}120.6%$</TEX>로 양성대조구의 90.6% 보다 약간 높은 것으로 나타났다. 또한, yeast 유래의 ADH 활성은 methionine에서 가장 높은 활성을 보였고, methionine의 처리 농도를 달리한 경우에서는 첨가 농도 의존적으로 높은 활성을 보였다. Rat liver 유래의 ALDH 활성은 methionine이 가장 높은 활성을 보였다. Methionine의 첨가 농도별 측정에서는 10 mg/ml에서 30 및 50 mg/ml 첨가 농도에서 보다 높은 활성을 보였으며, 이들 모든 처리 농도에서 양성대조구 보다 상당히 높은 활성을 보였다. 한편 yeast 유래의 ALDH 활성은 각 아미노산별 큰 차이는 없었으나, arginine에서 높은 활성을 보였다. Arginine의 첨가 농도별 측정에서는 처리 농도 의존적으로 활성이 약간씩 증가하는 경향을 보였으며, 양성대조구 보다 높은 활성을 나타내었다. 효모 유래 ALDH 및 rat liver 유래 ADH 효소 활성을 촉진시키는 작용을 가진 arginine을 효모 배양에 첨가시킬 경우 세포 내 ALDH 및 ADH 활성 염색 정도가 증가함으로써 arginine은 ALDH 및 ADH 활성을 촉진시키는 효능이 in vivo 실험계에서도 확인되었다. 이상의 실험 결과에서 아미노산 중에서는 arginie과 methionine이 ADH 및 ALDH 활성을 촉진시키는 작용에 의해 알코올 분해뿐만 아니라 acetaldehyde의 분해도 촉진시킬 가능성이 높아 숙취해소 효과는 물론 간 보호 효과도 동시에 있을 것으로 시사 되어 진다. 따라서 arginine과 methionine과 같은 아미노산을 주류 제품에 첨가하게 될 경우 숙취해소 경감과 간 보호 효능을 어느 정도 나타낼 수 있을 가능성이 제기되었다. The present study examined the comparative effects of various amino acids on the alcohol dehydrogenase (ADH) and acetaldehyde dehydrogenase (ALDH) activities of yeast Saccharomyces cereviciae and rat liver homogenate in vitro. Methionine showed the highest activity in yeast ADH among the amino acids used in this study, but this was not higher than that of the hangover product, Condition-Power (CP) used as positive control. Methionine was also found to be the best amino acid in terms of the ALDH activity in rat liver homogenate among the treatment amino acids, which was comparatively higher than that of positive control CP. It was chosen for further experiments and yeast ADH activity increased in parallel with increased methionine concentration, but not rat liver ALDH activity, and it was comparatively higher than those of the positive control. Arginine showed the highest values in yeast ALDH and rat liver ADH activities among amino acids, and it was chosen for further experiments. Yeast ALDH activity increased in parallel with increased arginine concentration, which was higher than that of positive control CP, and rat liver ADH activity was also comparatively higher in all treatment concentrations of arginine than that of positive control CP. The native electrophoresis of ADH and ALDH from cell-free extracts of yeast Saccharomyces cerevisiae cultured in the growth medium containing various arginine concentrations by <TEX>$0{\sim}0.1%$</TEX> showed two active bands upon zymogram staining analysis, and the straining intensity of ADH and ALDH active bands in arginine treatment yeast was stronger than that of non-yeast or low treatment yeast. These results indicate that alcohol metabolizing enzyme activities can be enhanced by arginine and methionine, suggesting that arginine and methionine have potent ethanol-metabolizing activities.

Measuring strand discontinuity-directed mismatch repair in yeast Saccharomyces cerevisiae by cell-free nuclear extracts

Mismatch repair corrects biosynthetic errors generated during DNA replication, whose deficiency causes a mutator phenotype and directly underlies hereditary non-polyposis colorectal cancer and sporadic cancers. Because of remarkably high conservation of the mismatch repair machinery between the budding yeast ( Saccharomyces cerevisiae) and humans, the study of mismatch repair in yeast has provided tremendous insights into the mechanisms of this repair pathway in humans. In addition, yeast cells possess an unbeatable advantage over human cells in terms of the easy genetic manipulation, the availability of whole genome deletion strains, and the relatively low cost for setting up the system. Although many components of eukaryotic mismatch repair have been identified, it remains unclear if additional factors, such as DNA helicase(s) and redundant nuclease(s) besides EXO1, participate in eukaryotic mismatch repair. To facilitate the discovery of novel mismatch repair factors, we developed a straightforward in vitro cell-free repair system. Here, we describe the practical protocols for preparation of yeast cell-free nuclear extracts and DNA mismatch substrates, and the in vitro mismatch repair assay. The validity of the cell-free system was confirmed by the mismatch repair deficient yeast strain (Δ msh2) and the complementation assay with purified yeast MSH2-MSH6.

In vitro assembly of the Tomato bushy stunt virus replicase requires the host Heat shock protein 70

To gain insights into the functions of a viral RNA replicase, we have assembled in vitro and entirely from nonplant sources, a fully functional replicase complex of Tomato bushy stunt virus (TBSV). The formation of the TBSV replicase required two purified recombinant TBSV replication proteins, which were obtained from E. coli, the viral RNA replicon, rATP, rGTP, and a yeast cell-free extract. The in vitro assembly of the replicase took place in the membraneous fraction of the yeast extract, in which the viral replicase-RNA complex became RNase- and proteinase-resistant. The assembly of the replicase complex required the heat shock protein 70 (Hsp70 = yeast Ssa1/2p) present in the soluble fraction of the yeast cell-free extract. The assembled TBSV replicase performed a complete replication cycle, synthesizing RNA complementary to the provided RNA replicon and using the complementary RNA as template to synthesize new TBSV replicon RNA.

Translation factors promote the formation of two states of the closed-loop mRNP

Efficient translation initiation and optimal stability of most eukaryotic messenger RNAs depends on the formation of a closed-loop structure and the resulting synergistic interplay between the 5' m(7)G cap and the 3' poly(A) tail. Evidence of eIF4G and Pab1 interaction supports the notion of a closed-loop mRNP, but the mechanistic events that lead to its formation and maintenance are still unknown. Here we use toeprinting and polysome profiling assays to delineate ribosome positioning at initiator AUG codons and ribosome-mRNA association, respectively, and find that two distinct stable (resistant to cap analogue) closed-loop structures are formed during initiation in yeast cell-free extracts. The integrity of both forms requires the mRNA cap and poly(A) tail, as well as eIF4E, eIF4G, Pab1 and eIF3, and is dependent on the length of both the mRNA and the poly(A) tail. Formation of the first structure requires the 48S ribosomal complex, whereas the second requires an 80S ribosome and the termination factors eRF3/Sup35 and eRF1/Sup45. The involvement of the termination factors is independent of a termination event.

Temperature dependence and temperature compensation of kinetics of chemical oscillations; Belousov–Zhabotinskii reaction, glycolysis and circadian rhythms

Based on the distribution of activation energies around the experimental mean and averaging of rate constants we propose a theoretical scheme to examine the temperature dependence and temperature compensation of time periods of chemical oscillations. The critical finite width of the distribution is characteristic of endogeneous oscillations for compensating kinetics as observed in circadian oscillations, while the vanishing width corresponds to Arrhenius temperature dependent kinetics of non-endogeneous chemical oscillation in Belousov–Zhabotinskii reaction in a CSTR or glycolysis in cell-free yeast extracts. Our theoretical analysis is corroborated with experimental data.

Regulation of GTP hydrolysis prior to ribosomal AUG selection during eukaryotic translation initiation

Genetic studies in yeast have shown that the translation initiation factor eIF5 plays an important role in the selection of the AUG start codon. In order to ensure translation fidelity, the hydrolysis of GTP bound to the 40S preinitiation complex (40S.Met-tRNA(i).eIF2.GTP), promoted by eIF5, must occur only when the complex has selected the AUG start codon. However, the mechanism that prevents the eIF5-promoted GTP hydrolysis, prior to AUG selection by the ribosomal machinery, is not known. In this work, we show that the presence of initiation factors eIF1, eIF1A and eIF3 in the 40S preinitiation complex (40S.eIF1.eIF1A.eIF3.Met-tRNA(i).eIF2.GTP) and the subsequent binding of the preinitiation complex to eIF4F bound at the 5'-cap structure of mRNA are necessary for preventing eIF5-promoted hydrolysis of GTP in the 40S preinitiation complex. This block in GTP hydrolysis is released upon AUG selection by the 40S preinitiation complex. These results, taken together, demonstrate the biochemical requirements for regulation of GTP hydrolysis and its coupling to the AUG selection process during translation initiation.

In Vitro Assembly of the Characteristic Chromatin Organization at the Yeast PHO5 Promoter by a Replication-independent Extract System

An extensive set of analyses of the yeast PHO5 gene, mostly performed in vivo, has made this gene a model for the role of chromatin structure in gene regulation. In the repressed state, the PHO5 promoter shows a characteristic chromatin organization with four positioned nucleosomes and a short hypersensitive site. So far the basis for this nucleosome positioning has remained unresolved. We have therefore decided to complement the in vivo studies by an in vitro approach. As a first step, we have asked whether the characteristic PHO5 promoter chromatin structure depends on the cellular context including replication or higher order nuclear chromatin organization or whether it can be reconstituted in vitro in a cell-free system. To this end we have established an in vitro chromatin assembly system based on yeast extracts. It is capable of generating extensive regular nucleosomal arrays with physiological spacing. Assembly requires supplementation with exogenous histones and is dependent on energy leading to chromatin with dynamic properties due to ATP-dependent activities of the extract. Using the PHO5 promoter sequence as template in this replication independent system, we obtain a nucleosomal pattern over the PHO5 promoter region that is very similar to the in vivo pattern of the repressed state. This shows that the chromatin structure at the PHO5 promoter represents a self-organizing system in cell-free yeast extracts and provides a promising substrate for in vitro studies with a direct in vivo correlate.

Dynamics and processivity of 40S ribosome scanning on mRNA in yeast.

The eukaryotic 40S ribosomal subunit locates the translation initiation codon on an mRNA via the so-called scanning process that follows 40S binding to the capped 5' end. This key step in translation is required for the expression of almost all eukaryotic genes, yet the mechanism and dynamics of scanning are unknown. We have performed quantitative studies in vivo and in vitro of the movement of yeast 40S ribosomes along 5' untranslated regions (UTRs) of different lengths. 40S subunits perform cap-dependent scanning with high processivity for more than 1700 nucleotides in cells of Saccharomyces cerevisiae. Moreover, the observed rates of expression indicate that scanning is performed by an untethered 40S subunit that has been released from the 5' cap complex. Unexpectedly, the capability to maintain scanning competence on a long 5' UTR is more dependent on the Ded1/Dbp1 type of helicase than on eIF4A or eIF4B. In a yeast cell-free extract, scanning shows reduced processivity, with an estimated net 5'-->3' rate of approximately 10 nucleotides per second at 26 degrees C. We have developed a biased bidirectional walking model of ribosomal scanning that provides a framework for understanding the above observations as well as other known quantitative and qualitative features of this process.