Heterogeneous flow environments mediate defector exclusion during yeast floc formation

<p>Flocculation of Saccharomyces cerevisiae is cooperative phenotype that offers protection against various external stresses. It is modulated by cell-surface proteins, called flocculins, that bind with sugar residues of neighboring cells, effectively increasing cell-cell adhesion. These flocculins are predominantly encoded by the FLO1, which is considered as a &#8216;green beard&#8217; gene as it governs both the cooperative phenotype and kin recognition of other cooperators. Conversely, defecting cells, lacking FLO1 expression, can still be incorporated in the flocs and &#8216;cheat&#8217; on the cooperative benefits.</p> <p>In this work, we investigate various pathways involved in floc formation and specifically their effect on the exclusion of defecting cells. Initially, we experimentally confirmed the heterophilic binding mode of FLO1 and consequently the potential to &#8216;cheat&#8217;. These measured cell mechanical properties were adopted to calibrate the parameters of an individual cell-based model of interacting yeast cells. Using this model, we investigate exclusion of defecting cells for the two mechanisms of group formation; clonal development (staying together) and shear-driven aggregation (coming together). Our results indicate the need for a multi-stage mechanism and selection for the macroscopic flocs with high degree of defector exclusion, as observed experimentally. The stages in this process are (i) nucleation of clusters with FLO1+ rich cores, either due to aggregation or growth, (ii) high shear flow conditions causing erosion of flo1- cells from clusters and exclusion of aggregates due to remodeling, (iii) fast clustering of small but dense flocs of FLO1+ cells in low shear conditions or due to gravitational sedimentation.</p>

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Stoichiometry and compositional plasticity of the yeast nuclear pore complex revealed by quantitative fluorescence microscopy

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1719398115 ◽

2018 ◽

Vol 115 (17) ◽

pp. E3969-E3977 ◽

Cited By ~ 36

Author(s):

Sasikumar Rajoo ◽

Pascal Vallotton ◽

Evgeny Onischenko ◽

Karsten Weis

Keyword(s):

Nuclear Pore Complex ◽

Yeast Cells ◽

Nuclear Pore ◽

Altered Expression ◽

Copy Numbers ◽

Quantitative Image ◽

Multiple Copies ◽

Almost All ◽

High Degree

The nuclear pore complex (NPC) is an eightfold symmetrical channel providing selective transport of biomolecules across the nuclear envelope. Each NPC consists of ∼30 different nuclear pore proteins (Nups) all present in multiple copies per NPC. Significant progress has recently been made in the characterization of the vertebrate NPC structure. However, because of the estimated size differences between the vertebrate and yeast NPC, it has been unclear whether the NPC architecture is conserved between species. Here, we have developed a quantitative image analysis pipeline, termed nuclear rim intensity measurement (NuRIM), to precisely determine copy numbers for almost all Nups within native NPCs of budding yeast cells. Our analysis demonstrates that the majority of yeast Nups are present at most in 16 copies per NPC. This reveals a dramatic difference to the stoichiometry determined for the human NPC, suggesting that despite a high degree of individual Nup conservation, the yeast and human NPC architecture is significantly different. Furthermore, using NuRIM, we examined the effects of mutations on NPC stoichiometry. We demonstrate for two paralog pairs of key scaffold Nups, Nup170/Nup157 and Nup192/Nup188, that their altered expression leads to significant changes in the NPC stoichiometry inducing either voids in the NPC structure or substitution of one paralog by the other. Thus, our results not only provide accurate stoichiometry information for the intact yeast NPC but also reveal an intriguing compositional plasticity of the NPC architecture, which may explain how differences in NPC composition could arise in the course of evolution.

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Complex Minisatellite Rearrangements Generated in the Total or Partial Absence of Rad27/hFEN1 Activity Occur in a Single Generation and Are Rad51 and Rad52 Dependent

Molecular and Cellular Biology ◽

10.1128/mcb.00649-06 ◽

2006 ◽

Vol 26 (17) ◽

pp. 6675-6689 ◽

Cited By ~ 24

Author(s):

Judith Lopes ◽

Cyril Ribeyre ◽

Alain Nicolas

Keyword(s):

Pedigree Analysis ◽

Model System ◽

Yeast Cells ◽

Single Generation ◽

Daughter Cells ◽

Double Deletion ◽

Mother And Daughter ◽

Complex Events ◽

High Degree ◽

Insight Into

ABSTRACT Genomes contain tandem repeat blocks that are at risk of expansion or contraction. The mechanisms of destabilization of the human minisatellite CEB1 (arrays of 36- to 43-bp repeats) were investigated in a previously developed model system, in which CEB1-0.6 (14 repeats) and CEB1-1.8 (42 repeats) alleles were inserted into the genome of Saccharomyces cerevisiae. As in human cells, CEB1 is stable in mitotically growing yeast cells but is frequently rearranged in the absence of the Rad27/hFEN1 protein involved in Okazaki fragments maturation. To gain insight into this mode of destabilization, the CEB1-1.8 and CEB1-0.6 human alleles and 47 rearrangements derived from a CEB1-1.8 progenitor in rad27Δ cells were sequenced. A high degree of polymorphism of CEB1 internal repeats was observed, attesting to a large variety of homology-driven rearrangements. Simple deletion, double deletion, and highly complex events were observed. Pedigree analysis showed that all rearrangements, even the most complex, occurred in a single generation and were inherited equally by mother and daughter cells. Finally, the rearrangement frequency was found to increase with array size, and partial complementation of the rad27Δ mutation by hFEN1 demonstrated that the production of novel CEB1 alleles is Rad52 and Rad51 dependent. Instability can be explained by an accumulation of unresolved flap structures during replication, leading to the formation of recombinogenic lesions and faulty repair, best understood by homology-dependent synthesis-strand displacement and annealing.

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Effects of Low-Shear Modeled Microgravity on Cell Function, Gene Expression, and Phenotype in Saccharomyces cerevisiae

Applied and Environmental Microbiology ◽

10.1128/aem.03050-05 ◽

2006 ◽

Vol 72 (7) ◽

pp. 4569-4575 ◽

Cited By ~ 58

Author(s):

B. Purevdorj-Gage ◽

K. B. Sheehan ◽

L. E. Hyman

Keyword(s):

Gene Expression ◽

Saccharomyces Cerevisiae ◽

Cell Function ◽

Yeast Cells ◽

Lag Phase ◽

Limited Information ◽

Cellular Functions ◽

Modeled Microgravity ◽

Expression Of Genes ◽

Low Shear

ABSTRACT Only limited information is available concerning the effects of low-shear modeled microgravity (LSMMG) on cell function and morphology. We examined the behavior of Saccharomyces cerevisiae grown in a high-aspect-ratio vessel, which simulates the low-shear and microgravity conditions encountered in spaceflight. With the exception of a shortened lag phase (90 min less than controls; P < 0.05), yeast cells grown under LSMMG conditions did not differ in growth rate, size, shape, or viability from the controls but did differ in the establishment of polarity as exhibited by aberrant (random) budding compared to the usual bipolar pattern of controls. The aberrant budding was accompanied by an increased tendency of cells to clump, as indicated by aggregates containing five or more cells. We also found significant changes (greater than or equal to twofold) in the expression of genes associated with the establishment of polarity (BUD5), bipolar budding (RAX1, RAX2, and BUD25), and cell separation (DSE1, DSE2, and EGT2). Thus, low-shear environments may significantly alter yeast gene expression and phenotype as well as evolutionary conserved cellular functions such as polarization. The results provide a paradigm for understanding polarity-dependent cell responses to microgravity ranging from pathogenesis in fungi to the immune response in mammals.

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The population’s potential for subjectness in regards to national projects

VESTNIK INSTITUTA SOTZIOLOGII ◽

10.19181/vis.2020.11.4.683 ◽

2020 ◽

Vol 11 (4) ◽

pp. 143-166

Author(s):

Andrey A. Merzlykov

Keyword(s):

Public Attitudes ◽

Group Formation ◽

Self Organization ◽

Administrative Authority ◽

Resource Base ◽

Building Relationships ◽

The Russian Federation ◽

High Degree ◽

Empirical Material ◽

Considerable Experience

This article is devoted to evaluating the population’s potential for subjectness in regards to implementing national projects, in other words – the people’s willingness to act in the name of contributing to their implementation: so this is not just a matter of agreeing with any goals and tasks that are laid out, but actively participating in achieving them. The empirical material for this study is based on the results of the first (pilot) stage of an RSF research project titled “Academic project: handling processes associated with social group formation in regions with varying levels of socio-cultural modernization, support from the population of development strategies for the Russian Federation up to 2024”. This article presents a scientific interpretation of the population’s subjectness from the position of sociology of management. According to the author, the main point of studying subjectness was to determine and examine means of building relationships between subjects, with the intention to collaborate in resolving those issues which bear significance to said subjects. The population’s subjectness is characterized by the interactions between society and authorities, where for society it is vital to have the ability to self-organize as a full-fledged social subject, while for authorities the important component would be to create the conditions for a constructive dialog. The results of the study indicate that society does possess a certain potential for subjectness, and the willingness to actively support national projects. Certain group formational indicators for developing subjectness within the population were identified, of the socio-mental, socio-structural and behavioral variety. Its resource base is assessed, with it being characterized by a high degree of self-organization, an active civic stance, considerable experience in management and sufficient administrative authority. The study analyzes the established public attitudes when it comes to collaborating with authorities in discussing national projects. It is noted that the attitudes of active groups of the population mostly tend to be functional (constructive) in nature, as opposed to dysfunctional (destructive), with them being oriented towards cooperating with authorities in the name of successfully implementing any planned national projects.

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Deoxynucleotide Triphosphate Binding Mode Conserved in Y Family DNA Polymerases

Molecular and Cellular Biology ◽

10.1128/mcb.23.8.3008-3012.2003 ◽

2003 ◽

Vol 23 (8) ◽

pp. 3008-3012 ◽

Cited By ~ 17

Author(s):

Robert E. Johnson ◽

José Trincao ◽

Aneel K. Aggarwal ◽

Satya Prakash ◽

Louise Prakash

Keyword(s):

Dna Polymerase ◽

Close Contact ◽

Dna Polymerases ◽

Binding Mode ◽

Nucleotide Incorporation ◽

The Family ◽

And Function ◽

High Degree ◽

Y Family ◽

Deoxynucleotide Triphosphate

ABSTRACT Although DNA polymerase η (Polη) and other Y family polymerases differ in sequence and function from classical DNA polymerases, they all share a similar right-handed architecture with the palm, fingers, and thumb domains. Here, we examine the role in Saccharomyces cerevisiae Polη of three conserved residues, tyrosine 64, arginine 67, and lysine 279, which come into close contact with the triphosphate moiety of the incoming nucleotide, in nucleotide incorporation. We find that mutational alteration of these residues reduces the efficiency of correct nucleotide incorporation very considerably. The high degree of conservation of these residues among the various Y family DNA polymerases suggests that these residues are also crucial for nucleotide incorporation in the other members of the family. Furthermore, we note that tyrosine 64 and arginine 67 are functionally equivalent to the deoxynucleotide triphosphate binding residues arginine 518 and histidine 506 in T7 DNA polymerase, respectively.

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Cyclic peptides can engage a single binding pocket through highly divergent modes

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2003086117 ◽

2020 ◽

Vol 117 (43) ◽

pp. 26728-26738

Author(s):

Karishma Patel ◽

Louise J. Walport ◽

James L. Walshe ◽

Paul D. Solomon ◽

Jason K. K. Low ◽

...

Keyword(s):

Cyclic Peptides ◽

Cyclic Peptide ◽

Binding Pocket ◽

Binding Mode ◽

Structural Features ◽

Binding Modes ◽

Single Target ◽

Bromodomain Proteins ◽

High Degree ◽

Drug Leads

Cyclic peptide library screening technologies show immense promise for identifying drug leads and chemical probes for challenging targets. However, the structural and functional diversity encoded within such libraries is largely undefined. We have systematically profiled the affinity, selectivity, and structural features of library-derived cyclic peptides selected to recognize three closely related targets: the acetyllysine-binding bromodomain proteins BRD2, -3, and -4. We report affinities as low as 100 pM and specificities of up to 106-fold. Crystal structures of 13 peptide–bromodomain complexes reveal remarkable diversity in both structure and binding mode, including both α-helical and β-sheet structures as well as bivalent binding modes. The peptides can also exhibit a high degree of structural preorganization. Our data demonstrate the enormous potential within these libraries to provide diverse binding modes against a single target, which underpins their capacity to yield highly potent and selective ligands.

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Permissive aggregative group formation favors coexistence in yeast

10.1101/2021.12.03.471114 ◽

2021 ◽

Author(s):

Tom E. R. Belpaire ◽

Jiří Pešek ◽

Bram Lories ◽

Kevin J. Verstrepen ◽

Hans P. Steenackers ◽

...

Keyword(s):

Kin Recognition ◽

Group Formation ◽

Cluster Formation ◽

Dual Function ◽

Bond Stability ◽

Selective Pressures ◽

Formation And Evolution ◽

The Impact ◽

Selection Of

ABSTRACTIn Saccharomyces cerevisiae, the FLO1 gene encodes flocculins that lead to formation of multicellular flocs, that offer protection to the constituent cells. Flo1p was found to preferentially bind to fellow cooperators compared to defectors lacking FLO1 expression, resulting in enrichment of cooperators within the flocs. Given this dual function in cooperation and kin recognition, FLO1 has been termed a ‘green beard gene’. Because of the heterophilic nature of Flo1p binding however, we hypothesize that kin recognition is permissive and depends on the relative stability of FLO1+/flo1− versus FLO1+/FLO1+ bonds, which itself can be dependent on environmental conditions and intrinsic cell properties. We combine single cell measurements of adhesion strengths, individual cell-based simulations of cluster formation and evolution, and in vitro flocculation experiments to study the impact of relative bond stability on defector exclusion as well as benefit and stability of cooperation. We hereto vary the relative bond stability by changing the shear flow rate and the inherent bond strength. We identify a marked trade-off between both aspects of the green beard mechanism, with reduced relative bond stability leading to increased kin recognition, but at the expense of decreased cluster sizes and benefit of cooperation. Most notably, we show that the selection of FLO1 cooperators is negative-frequency dependent, which we directly attribute to the permissive character of the Flo1p bond. Taking into account the costs associated to FLO1 expression, this asymmetric selection results in a broad range of ecological conditions where coexistence between cooperators and defectors is stable. Although the kin recognition aspect of the FLO1 ‘green beard gene’ is thus limited and condition dependent, the negative-frequency dependency of selection can conserve the diversity of flocculent and non-flocculent phenotypes ensuring flexibility towards variable selective pressures.

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ProXs drive the formation of membraneless organelles in plants

10.1101/2021.07.04.451080 ◽

2021 ◽

Author(s):

Honghong Zhang ◽

Fangyu Peng ◽

Yan Liu ◽

Haiteng Deng ◽

Xiaofeng Fang

Keyword(s):

Phase Separation ◽

Higher Plants ◽

Research Community ◽

Yeast Cells ◽

Cellular Functions ◽

Crop Species ◽

Cellular Space ◽

High Degree ◽

Heterologous Expression In Yeast ◽

Liquid Liquid Phase Separation

Membraneless organelles (MLOs) are non-membranous structures inside cells that organize cellular space and processes. The recent discovery that MLOs can be assembled via liquid-liquid phase separation (LLPS) advanced our understanding of these structures. However, the proteins that are capable of forming MLOs are largely unknown, especially in plants. In this study, we developed a method to identify proteins that we referred as ProXs (Proteins enriched by b-isoX) in Arabidopsis. Heterologous expression in yeast cells showed that most ProXs were capable of forming MLOs autonomously. We applied this method to several model and crop species including early and higher plants. This allowed us to generate an atlas of ProXs for studying plant MLOs. Analysis of ProXs from different species revealed high degree of conservation, supporting that they play important roles in cellular functions and are positively selected during evolution. Our method will be a valuable tool to characterize novel MLOs from desired cells and the data generated in present study will be instrumental for the plant research community to investigate MLO biology.

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Effect of. Oxygen and Carbon Dioxide on the Mitochondria of Sclerotium Rolfsh

Australian Journal of Biological Sciences ◽

10.1071/bi9691061 ◽

1969 ◽

Vol 22 (4) ◽

pp. 1061

Author(s):

NG Nair ◽

NH White ◽

DM Griffin ◽

Suzanne Blair§

Keyword(s):

Carbon Dioxide ◽

Sclerotium Rolfsii ◽

Yeast Cells ◽

Low Oxygen ◽

High Carbon ◽

Anaerobic Conditions ◽

External Stresses ◽

Carbon Dioxide Levels ◽

Effect Of Oxygen ◽

High Carbon Dioxide

The number of mitochondria apparently vary with the energy requirements of the cell (see Rouiller 1960). Although swelling and multiplication of mitochondria have been observed to occur in cells, a quantitative analysis of these changes has not been recorded. Matile and Bahr (1968) have recently provided electron micro-scopic evidence of the heterogeneity of density, mass, and volume of the mitochon-drial population in respiring baker's yeast. There are reports in the literature of the complete absence of mitochondria in yeast cells growing under anaerobic conditions (see Marchant and Smith 1968). Griffin and Nair (1968) demonstrated that the growth of Sclerotium rolfsii was inhibited by concentrations of oxygen below 4% and by concentrations of carbon dioxide above 0�03 %. It was, therefore, thought worthwhile to study the changes in mitochondria of this fungus when the cells are subjected to external stresses of low oxygen and high carbon dioxide levels.

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