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1. Structural Conservation of the Two Phosphoinositide-Binding Sites in WIPI Proteins

Author:
Liang, Ruobing; Ren, Jinqi; Zhang, Yong; Feng, Wei
Source:
Journal of molecular biology 2019 v.431 no.7 pp. 1494-1505
ISSN:
0022-2836
Subject:
yeasts,   etc   ; biogenesis; blades; humans; proteins;     Show all 5 Subjects
Abstract:
... WIPI proteins are mammalian PROPPIN family members that bind to phosphoinositides and play prominent roles in autophagosome biogenesis. Two phosphoinositide-binding sites were previously described in yeast PROPPIN Hsv2 but remain to be determined in mammalian WIPI proteins. Here, we characterized four human WIPI proteins (WIPI1–4) and solved the structure of WIPI3. WIPI proteins can bind to PI(3)P ...
DOI:
10.1016/j.jmb.2019.02.019

2. RSC-Associated Subnucleosomes Define MNase-Sensitive Promoters in Yeast

Author:
Brahma, Sandipan; Henikoff, Steven
Source:
Molecular cell 2019 v.73 no.2 pp. 238-249.e3
ISSN:
1097-2765
Subject:
yeasts,   etc   ; enzymes; nucleosomes; precipitin tests;     Show all 4 Subjects
Abstract:
... The classic view of nucleosome organization at active promoters is that two well-positioned nucleosomes flank a nucleosome-depleted region (NDR). However, this view has been recently disputed by contradictory reports as to whether wider (≳150 bp) NDRs instead contain unstable, micrococcal nuclease-sensitive (“fragile”) nucleosomal particles. To determine the composition of fragile particles, we in ...
DOI:
10.1016/j.molcel.2018.10.046

3. Correction to: Gene overexpression screen for chromosome instability in yeast primarily identifies cell cycle progression genes

Author:
Tutaj, Hanna; Pogoda, Elzbieta; Tomala, Katarzyna; Korona, Ryszard
Source:
Current genetics 2019 v.65 no.2 pp. 493
ISSN:
0172-8083
Subject:
yeasts,   etc   ; cell cycle; chromosomes; gene overexpression; genes;     Show all 5 Subjects
Abstract:
... In the original publication, ‘Frumkin JP et al.’ reference was missed to include in the reference list. The complete reference should read as below. ...
DOI:
10.1007/s00294-018-0893-x

4. Interactions in the ESCRT-III network of the yeast Saccharomyces cerevisiae

Author:
Brune, Thomas; Kunze-Schumacher, Heike; Kölling, Ralf
Source:
Current genetics 2019 v.65 no.2 pp. 607-619
ISSN:
0172-8083
Subject:
yeasts,   etc   ; Saccharomyces cerevisiae; mutation; phenotype; prediction; proteins;     Show all 6 Subjects
Abstract:
... Here, we examine the genetic interactions between ESCRT-III mutations in the yeast Saccharomyces cerevisiae. From the obtained interaction network, we make predictions about alternative ESCRT-III complexes. By the successful generation of an octuple deletion strain using the CRISPR/Cas9 technique, we demonstrate for the first time that ESCRT-III activity as a whole is not essential for the life of ...
DOI:
10.1007/s00294-018-0915-8

5. Proteomic profiling of yeast heterochromatin connects direct physical and genetic interactions

Author:
Zukowski, Alexis; Phillips, Juliana; Park, Soyeon; Wu, Ronghu; Gygi, Steven P.; Johnson, Aaron M.
Source:
Current genetics 2019 v.65 no.2 pp. 495-505
ISSN:
0172-8083
Subject:
yeasts,   etc   ; eukaryotic cells; heterochromatin; nucleosomes; proteomics;     Show all 5 Subjects
Abstract:
... Heterochromatin domains are stably repressed chromatin structures composed of a core assembly of silencing proteins that condense adjacent nucleosomes. The minimal heterochromatin structure can serve as a platform for recruitment of complementary regulatory factors. We find that a reconstituted budding yeast heterochromatin domain can act as a platform to recruit multiple factors that play a role ...
DOI:
10.1007/s00294-018-0889-6

6. Craving for Introns

Author:
Zaffagni, Michela; Kadener, Sebastian
Source:
Molecular cell 2019 v.73 no.6 pp. 1095-1096
ISSN:
1097-2765
Subject:
yeasts,   etc   ; craving; introns; non-coding RNA; spliceosomes;     Show all 5 Subjects
Abstract:
... Parenteau et al. (2019) and Morgan et al. (2019) showed that a subset of introns can work as non-coding RNAs that trap the spliceosome and decrease global splicing upon nutrient depletion in yeast, providing a new example of the functionality of introns, molecules that were previously assumed to be useless. ...
DOI:
10.1016/j.molcel.2019.03.008

7. The Yeast Voltage-Dependent Anion Channel Porin: More IMPORTant than Just Metabolite Transport

Author:
Edwards, Ruairidh; Tokatlidis, Kostas
Source:
Molecular cell 2019 v.73 no.5 pp. 861-862
ISSN:
1097-2765
Subject:
yeasts,   etc   ; metabolites; mitochondria; porins; protein transport;     Show all 5 Subjects
Abstract:
... Porin is crucial for metabolite flux in mitochondria. In this issue of Molecular Cell, Sakaue et al. (2019) and Ellenrieder et al. (2019) describe an unexpected role for Porin in mitochondrial protein import by regulating the oligomeric state of the major protein import gate, the TOM complex, and the inner membrane insertion of metabolite carriers. ...
DOI:
10.1016/j.molcel.2019.02.028

8. Development and comparative analysis of yeast protein extraction protocols for mass spectrometry

Author:
Almeida, Lauana Fogaça de; Moraes, Leonardo Nazário de; Santos, Lucilene Delazari dos; Valente, Guilherme Targino
Source:
Analytical biochemistry 2019 v.567 pp. 90-95
ISSN:
0003-2697
Subject:
yeasts,   etc   ; mass spectrometry; proteinase inhibitors; proteins;     Show all 4 Subjects
Abstract:
... Mass spectrometry is the most used method for protein identification and quantification. Here we developed four protein extraction protocols precisely for mass spectrometry, and we compared with other ones already published. The best protocol developed by us consists on a simple extraction solution, a heat-shock step, and does not use protease inhibitor; moreover, it is the most efficient and unif ...
DOI:
10.1016/j.ab.2018.10.028

9. Chromatin mobility upon DNA damage: state of the art and remaining questions

Author:
Zimmer, Christophe; Fabre, Emmanuelle
Source:
Current genetics 2019 v.65 no.1 pp. 1-9
ISSN:
0172-8083
Subject:
yeasts,   etc   ; DNA; DNA damage; chromatin; genome; metabolism;     Show all 6 Subjects
Abstract:
... Chromosome organization and chromatin mobility are central to DNA metabolism. In particular, it has been recently shown by several labs that double strand breaks (DSBs) in yeast induce a change in chromatin mobility at the site of the damage. Intriguingly, DSB also induces a global mobility of the genome, at others, potentially undamaged positions. How mobility is regulated and what are the functi ...
DOI:
10.1007/s00294-018-0852-6

10. Nucleosome Orientation Map Finds Two New Chromatin Folding Motifs

Author:
Risca, Viviana I.
Source:
Cell 2019 v.176 no.3 pp. 412-413
ISSN:
0092-8674
Subject:
yeasts,   etc   ; Saccharomyces cerevisiae; genome; molecular conformation; nucleosomes;     Show all 5 Subjects
Abstract:
... A method for mapping nucleosome contacts and relative nucleosome orientations reveals new detail about the folding of the S. cerevisiae genome. Two new chromatin folding patterns emerge, with one enriched and the other depleted at transcription start and end sites. ...
DOI:
10.1016/j.cell.2019.01.011

11. Synthesis of a biotinylated probe from biotechnologically derived β-d-mannopyranosyl-(1 → 2)-d-mannopyranose for assessment of carbohydrate specificity of antibodies

Author:
Karelin, Alexander A.; Ustyuzhanina, Nadezhda E.; Tsvetkov, Yury E.; Nifantiev, Nikolay E.
Source:
Carbohydrate research 2019 v.471 pp. 39-42
ISSN:
0008-6215
Subject:
yeasts,   etc   ; antibodies; carbohydrates; cell walls; dephosphorylation;     Show all 5 Subjects
Abstract:
... The disaccharide β-d-mannopyranosyl-(1 → 2)-d-mannopyranose obtained by chemical cleavage and enzymatic dephosphorylation of biotechnologically available phosphomannan was transformed over six steps into a biotinylated probe suitable for assessment of carbohydrate specificity of antibodies induced by yeast cell wall preparations. ...
DOI:
10.1016/j.carres.2018.10.013

12. Enrichment of midsized RNAs with manganese chloride precipitation

Author:
Friday, Dillon; Freidhoff, Paul; Baumstark, Tilman; Bruist, Michael F.
Source:
Analytical biochemistry 2018 v.560 pp. 56-59
ISSN:
0003-2697
Subject:
yeasts,   etc   ; RNA; manganese chloride;     Show all 3 Subjects
Abstract:
... Enrichment of specific RNAs is important for RNA analysis. MnCl2 has been used previously to enrich viroid RNA fractions from total RNA from infected plants. We have expanded this method to show that MnCl2 can enrich single-stranded as well as structured RNAs of 450 nt and below from a total RNA preparation. We have applied this method to map the transcription start sites of a PSTVd transcript fro ...
DOI:
10.1016/j.ab.2018.09.003

13. An optimized FAIRE procedure for low cell numbers in yeast

Author:
Segorbe, David; Wilkinson, Derek; Mizeranschi, Alexandru; Hughes, Timothy; Aaløkken, Ragnhild; Váchová, Libuše; Palková, Zdena; Gilfillan, Gregor D.
Source:
Yeast 2018 v.35 no.8 pp. 507-512
ISSN:
0749-503X
Subject:
yeasts,   etc   ; chromatin; epigenetics; liquids;     Show all 4 Subjects
Abstract:
... We report an optimized low‐input FAIRE‐seq (Formaldehyde‐Assisted Isolation of Regulatory Elements‐sequencing) procedure to assay chromatin accessibility from limited amounts of yeast cells. We demonstrate that the method performs well on as little as 4 mg of cells scraped directly from a few colonies. Sensitivity, specificity and reproducibility of the scaled‐down method are comparable with those ...
DOI:
10.1002/yea.3316

14. Three Distinct Types of Microautophagy Based on Membrane Dynamics and Molecular Machineries

Author:
Oku, Masahide; Sakai, Yasuyoshi
Source:
BioEssays 2018 v.40 no.6 pp. e1800008
ISSN:
0265-9247
Subject:
yeasts,   etc   ; models; proteins; vacuoles;     Show all 4 Subjects
Abstract:
... Microautophagy is originally defined as lysosomal (vacuolar) membrane dynamics to directly enwrap and transport cytosolic components into the lumen of the lytic organelle. Molecular details of microautophagy had remained unknown until genetic studies in yeast identified a set of proteins required for the process. Subsequent studies with other experimental model organisms resulted in a series of di ...
DOI:
10.1002/bies.201800008

15. Evaluation of the chitin-binding dye Congo red as a selection agent for the isolation, classification, and enumeration of ascomycete yeasts

Author:
Linder, Tomas
Source:
Archives of microbiology 2018 v.200 no.4 pp. 671-675
ISSN:
0302-8933
Subject:
yeasts,   etc   ; Ascomycota; dyes; phenotype;     Show all 4 Subjects
Abstract:
... Thirty-nine strains of ascomycete yeasts representing 35 species and 33 genera were tested for their ability to grow on solid agar medium containing increasing concentrations of the chitin-binding dye Congo red. Six strains were classified as hypersensitive (weak or no growth at 10 mg/l Congo red), five were moderately sensitive (weak or no growth at 50 mg/l), three were moderately tolerant (weak ...
DOI:
10.1007/s00203-018-1498-y

16. Recent advancements in fungal-derived fuel and chemical production and commercialization

Author:
Ekas, Holly; Deaner, Matthew; Alper, Hal S
Source:
Current opinion in biotechnology 2019 v.57 pp. 1-9
ISSN:
0958-1669
Subject:
yeasts,   etc   ; Escherichia coli; animals; commercialization; fermentation; petroleum; synthetic biology;     Show all 7 Subjects
Abstract:
... Due to unsustainable petroleum supply and poor yields from plant and animal sources, there is an increased effort to engineer microbial hosts for renewable chemical production. When compared to microbes such as Escherichia coli, fungal hosts show advantages due to their natural robust tolerance for industrial fermentation. Synthetic biology has focused on implementing heterologous pathways and man ...
DOI:
10.1016/j.copbio.2018.08.014

17. Aggregation and degradation scales for prion-like domains: sequence features and context weigh in

Author:
Cascarina, Sean M.; Ross, Eric D.
Source:
Current genetics 2019 v.65 no.2 pp. 387-392
ISSN:
0172-8083
Subject:
yeasts,   etc   ; amino acid sequences; amino acids; mutagenesis; proteins; proteome; screening;     Show all 7 Subjects
Abstract:
... Protein aggregation in vivo is generally combated by extensive proteostatic defenses. Many proteostasis factors specifically recognize aggregation-prone features and re-fold or degrade the targeted protein. However, protein aggregation is not uncommon, suggesting that some proteins employ evasive strategies to aggregate in spite of the proteostasis machinery. Therefore, in addition to understandin ...
DOI:
10.1007/s00294-018-0890-0

18. Stressing out or stressing in: intracellular pathways for SAPK activation

Author:
Lee, Jongmin; Liu, Li; Levin, David E.
Source:
Current genetics 2019 v.65 no.2 pp. 417-421
ISSN:
0172-8083
Subject:
yeasts,   etc   ; DNA damage; arsenites; mitogen-activated protein kinase; phosphorylation;     Show all 5 Subjects
Abstract:
... Stress-activated MAP kinases (SAPKs) respond to a wide variety of stressors. In most cases, the pathways through which specific stress signals are transmitted to the SAPKs are not known. Our recent findings have begun to address two important and related questions. First, do various stresses activate a SAPK through common pathways initiated at the cell surface, or through alternative, intracellula ...
DOI:
10.1007/s00294-018-0898-5

19. Application of rotational vibration in a submerged hollow fibre membrane system for bioseparation of high concentration yeast suspensions

Author:
Chai, Milton; Ye, Yun; Chen, Vicki
Source:
Journal of membrane science 2019 v.573 pp. 145-156
ISSN:
0376-7388
Subject:
yeasts,   etc   ; artificial membranes; biomass; carbohydrates; filtration; fouling; fractionation; vibration;     Show all 8 Subjects
Abstract:
... A novel submerged rotational vibration membrane system was investigated using high concentration yeast suspensions to demonstrate the capability of this system for the separation of high concentration biomass. The critical flux and shear rate for this system can be correlated by the expression, Jcritical=1.2γ̅0.55, for the filtration of 200 g/L yeast suspension. Good fouling control performance as ...
DOI:
10.1016/j.memsci.2018.11.069

20. Pulsed electric field effects on inactivation of microorganisms in acid whey

Author:
Simonis, Povilas; Kersulis, Skirmantas; Stankevich, Voitech; Sinkevic, Kamilija; Striguniene, Kristina; Ragoza, Gregoz; Stirke, Arunas
Source:
International journal of food microbiology 2019 v.291 pp. 128-134
ISSN:
0168-1605
Subject:
yeasts,   etc   ; Lactobacillus; Saccharomyces; electric field; pulsed electric fields; whey;     Show all 6 Subjects
Abstract:
... Prospects of pulsed electric field technology application on acid whey concentrate pretreatment were analyzed. Stationary and flow pre-treatment systems were combined with different treatment parameters: electric field strength (E = 39 kV/cm, 95 kV/cm, 92 kV/cm), pulse duration (τ = 60 ns, 90 ns, 1000 ns) and pulse number (pn = up to 100 pulses). Isolates of Saccharomyces sp. and Lactobacillus sp. ...
DOI:
10.1016/j.ijfoodmicro.2018.11.024