The ability of yeast cells to adhere to solid surfaces or even penetrate semi-solid surfaces and form multicellular biofilms are critical factors in infection. This study examines the relationship between cell adhesion capability and the ability to create spatially organized biofilms in selected Saccharomyces cerevisiae strains, including clinical isolates, and five Candida species (C. albicans, C. glabrata, C. krusei, C. parapsilosis, and C. tropicalis). We assessed cell adhesion to polystyrene surface in four media varying in source of carbon and other nutrients. Using microscopy of vertical cell arrangement profiles within yeast populations grown at the solid-liquid interface, we evaluated their internal organization to determine whether the populations exhibit typical biofilm characteristics, such as the spatial organization of distinct cell types. Results indicate that well adherent S. cerevisiae strains form spatial biofilms with typical internal organization, highlighting strain-specific responses to media composition and supporting the use of natural S. cerevisiae strains for biofilm research. Among Candida species, biofilm formation did not consistently align with adhesion efficiency to plastic; while C. albicans and C. krusei formed spatially structured biofilms on media where they adhered well, C. tropicalis and C. glabrata exhibited efficient adhesion without biofilm structuring. Interestingly, C. parapsilosis formed a structured biofilm despite minimal adhesion. These findings emphasize the role of media composition, particularly components of yeast extract and defined medium for mammalian cell growth RPMI, which differentially impacted adhesion and biofilm formation in S. cerevisiae and C. albicans.

• Klíčová slova
• Adhesion, Biofilm, Microscopy, Spatial structure, Yeast,
• Publikační typ
• časopisecké články MeSH

Cell death is a natural part of the development of multicellular organisms and is central to their physiological and pathological states. However, the existence of regulated cell death in unicellular microorganisms, including eukaryotic and prokaryotic microbes, has been a topic of debate. One reason for the continued debate is the lack of obvious benefit from cell death in the context of a single cell. However, unicellularity is relative, as most of these microbes dwell in communities of varying complexities, often with complicated spatial organization. In these spatially organized microbial communities, such as yeast and bacterial colonies and biofilms growing on solid surfaces, cells differentiate into specialized types, and the whole community often behaves like a simple multicellular organism. As these communities develop and age, cell death appears to offer benefits to the community as a whole. This review explores the potential roles of cell death in spatially organized communities of yeasts and draws analogies to similar communities of bacteria. The natural dying processes in microbial cell communities are only partially understood and may result from suicidal death genes, (self-)sabotage (without death effectors), or from non-autonomous mechanisms driven by interactions with other differentiated cells. We focus on processes occurring during the stratification of yeast colonies, the formation of the extracellular matrix in biofilms, and discuss potential roles of cell death in shaping the organization, differentiation, and overall physiology of these microbial structures.

• MeSH
• biofilmy růst a vývoj   MeSH
• buněčná diferenciace * MeSH
• buněčná smrt MeSH
• kvasinky * cytologie   MeSH
• Saccharomyces cerevisiae * cytologie   MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

Gcn4p belongs to conserved AP-1 transcription factors involved in many cellular processes, including cell proliferation, stress response, and nutrient availability in yeast and mammals. AP-1 activities are regulated at different levels, such as translational activation or protein degradation, which increases the variability of regulation under different conditions. Gcn4p activity in unstructured yeast liquid cultures increases upon amino acid deficiency and is rapidly eliminated upon amino acid excess. Gcn2p kinase is the major described regulator of Gcn4p that enables GCN4 mRNA translation via the uORFs mechanism. Here, we show that Gcn4p is specifically active in U cells in the upper regions and inactive in L cells in the lower regions of differentiated colonies. Using in situ microscopy in combination with analysis of mutants and strains with GFP at different positions in the translational regulatory region of Gcn4p, we show that cell-specific Gcn4p activity is independent of Gcn2p or other translational or transcriptional regulation. Genetically, biochemically, and microscopically, we identified cell-specific proteasomal degradation as a key mechanism that diversifies Gcn4p function between U and L cells. The identified regulation leading to active Gcn4p in U cells with amino acids and efficient degradation in starved L cells differs from known regulations of Gcn4p in yeast but shows similarities to the activity of AP-1 ATF4 in mammals during insulin signaling. These findings may open new avenues for understanding the parallel activities of Gcn4p/ATF4 and reveal a novel biological role for cell type-specific regulation of proteasome-dependent degradation.IMPORTANCEIn nature, microbes usually live in spatially structured communities and differentiate into precisely localized, functionally specialized cells. The coordinated interplay of cells and their response to environmental changes, such as starvation, followed by metabolic adaptation, is critical for the survival of the entire community. Transcription factor Gcn4p is responsible for yeast adaptation under amino acid starvation in liquid cultures, and its activity is regulated mainly at the level of translation involving Gcn2p kinase. Whether Gcn4p functions in structured communities was unknown. We show that translational regulation of Gcn4p plays no role in the development of colony subpopulations; the main regulation occurs at the level of stabilization of the Gcn4p molecule in the cells of one subpopulation and its proteasomal degradation in the other. This regulation ensures specific spatiotemporal activity of Gcn4p in the colony. Our work highlights differences in regulatory networks in unorganized populations and organized structures of yeast, which in many respects resemble multicellular organisms.

• Klíčová slova
• Saccharomyces cerevisiae, cell-specific regulation, differentiated colonies, proteasomal degradation, spatially structured populations, transcription factor, yeast,
• MeSH
• protein-serin-threoninkinasy metabolismus   genetika   MeSH
• proteolýza MeSH
• proteosyntéza MeSH
• regulace genové exprese u hub * MeSH
• Saccharomyces cerevisiae - proteiny * genetika   metabolismus   MeSH
• Saccharomyces cerevisiae * genetika   metabolismus   MeSH
• stabilita proteinů MeSH
• transkripční faktory bZIP * metabolismus   genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• GCN2 protein, S cerevisiae MeSH Prohlížeč
• GCN4 protein, S cerevisiae MeSH Prohlížeč
• protein-serin-threoninkinasy MeSH
• Saccharomyces cerevisiae - proteiny * MeSH
• transkripční faktory bZIP * MeSH

Cells must change their properties in order to adapt to a constantly changing environment. Most of the cellular sensing and regulatory mechanisms described so far are based on proteins that serve as sensors, signal transducers, and effectors of signalling pathways, resulting in altered cell physiology. In recent years, however, remarkable examples of the critical role of non-coding RNAs in some of these regulatory pathways have been described in various organisms. In this review, we focus on all classes of non-coding RNAs that play regulatory roles during stress response, starvation, and ageing in different yeast species as well as in structured yeast populations. Such regulation can occur, for example, by modulating the amount and functional state of tRNAs, rRNAs, or snRNAs that are directly involved in the processes of translation and splicing. In addition, long non-coding RNAs and microRNA-like molecules are bona fide regulators of the expression of their target genes. Non-coding RNAs thus represent an additional level of cellular regulation that is gradually being uncovered.

• Klíčová slova
• RNA modifications, epitranscriptome, lncRNA, tRNA, yeast,
• MeSH
• mikro RNA * genetika   MeSH
• RNA dlouhá nekódující * genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• mikro RNA * MeSH
• RNA dlouhá nekódující * MeSH

Yeast populations can undergo diversification during their growth and ageing, leading to the formation of different cell-types. Differentiation into two major subpopulations, differing in cell size and density and exhibiting distinct physiological and metabolic properties, was described in planktonic liquid cultures and in populations of colonies growing on semisolid surfaces. Here, we compare stress resistance, metabolism and expression of marker genes in seven differentiated cell subpopulations emerging during cultivation in liquid fermentative or respiratory media and during colony development on the same type of solid media. The results show that the more-dense cell subpopulations are more stress resistant than the less-dense subpopulations under all cultivation conditions tested. On the other hand, respiratory capacity, enzymatic activities and marker gene expression differed more between subpopulations. These characteristics are more influenced by the lifestyle of the population (colony vs. planktonic cultivation) and the medium composition. Only in the population growing in liquid respiratory medium, two subpopulations do not form as in the other conditions tested, but all cells exhibit a range of characteristics of the more-dense subpopulations. This suggests that signals for cell differentiation may be triggered by prior metabolic reprogramming or by an unknown signal from the structured environment in the colony.

• MeSH
• buněčná diferenciace MeSH
• fermentace MeSH
• Saccharomyces cerevisiae * metabolismus   MeSH
• sušené kvasnice * MeSH
• Publikační typ
• časopisecké články MeSH

Single-celled yeasts form spatially structured populations - colonies and biofilms, either alone (single-species biofilms) or in cooperation with other microorganisms (mixed-species biofilms). Within populations, yeast cells develop in a coordinated manner, interact with each other and differentiate into specialized cell subpopulations that can better adapt to changing conditions (e.g. by reprogramming metabolism during nutrient deficiency) or protect the overall population from external influences (e.g. via extracellular matrix). Various omics tools together with specialized techniques for separating differentiated cells and in situ microscopy have revealed important processes and cell interactions in these structures, which are summarized here. Nevertheless, current knowledge is still only a small part of the mosaic of complexity and diversity of the multicellular structures that yeasts form in different environments. Future challenges include the use of integrated multi-omics approaches and a greater emphasis on the analysis of differentiated cell subpopulations with specific functions.

• Klíčová slova
• Biofilms, Cell differentiation, Colonies, Multicellular yeast structures, Regulation, Spatial community structure,
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

During development of yeast colonies, various cell subpopulations form, which differ in their properties and specifically localize within the structure. Three branches of mitochondrial retrograde (RTG) signaling play a role in colony development and differentiation, each of them activating the production of specific markers in different cell types. Here, aiming to identify proteins and processes controlled by the RTG pathway, we analyzed proteomes of individual cell subpopulations from colonies of strains, mutated in genes of the RTG pathway. Resulting data, along with microscopic analyses revealed that the RTG pathway predominantly regulates processes in U cells, long-lived cells with unique properties, which are localized in upper colony regions. Rtg proteins therein activate processes leading to amino acid biosynthesis, including transport of metabolic intermediates between compartments, but also repress expression of mitochondrial ribosome components, thus possibly contributing to reduced mitochondrial translation in U cells. The results reveal the RTG pathway's role in activating metabolic processes, important in U cell adaptation to altered nutritional conditions. They also point to the important role of Rtg regulators in repressing mitochondrial activity in U cells.

• Klíčová slova
• Saccharomyces cerevisiae, colony development and differentiation, mitochondrial retrograde signaling, proteomic analysis, yeast colonies,
• MeSH
• aminokyseliny metabolismus   MeSH
• analýza jednotlivých buněk MeSH
• biosyntetické dráhy genetika   MeSH
• chromatografie kapalinová MeSH
• intracelulární signální peptidy a proteiny genetika   metabolismus   MeSH
• mitochondrie genetika   metabolismus   MeSH
• proteom genetika   metabolismus   MeSH
• proteomika MeSH
• regulace genové exprese u hub genetika   MeSH
• represorové proteiny genetika   metabolismus   MeSH
• Saccharomyces cerevisiae - proteiny genetika   metabolismus   MeSH
• Saccharomyces cerevisiae genetika   metabolismus   MeSH
• signální transdukce genetika   MeSH
• tandemová hmotnostní spektrometrie MeSH
• transkripční faktory BHLH-Zip genetika   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• aminokyseliny MeSH
• intracelulární signální peptidy a proteiny MeSH
• MKS1 protein, S cerevisiae MeSH Prohlížeč
• proteom MeSH
• represorové proteiny MeSH
• RTG1 protein, S cerevisiae MeSH Prohlížeč
• RTG2 protein, S cerevisiae MeSH Prohlížeč
• RTG3 protein, S cerevisiae MeSH Prohlížeč
• Saccharomyces cerevisiae - proteiny MeSH
• transkripční faktory BHLH-Zip MeSH

Yeast form complex highly organized colonies in which cells undergo spatiotemporal phenotypic differentiation in response to local gradients of nutrients, metabolites, and specific signaling molecules. Colony fitness depends on cell interactions, cooperation, and the division of labor between differentiated cell subpopulations. Here, we describe the regulation and dynamics of the expansion of papillae that arise during colony aging, which consist of cells that overcome colony regulatory rules and disrupt the synchronized colony structure. We show that papillae specifically expand within the U cell subpopulation in differentiated colonies. Papillae emerge more frequently in some strains than in others. Genomic analyses further revealed that the Whi2p-Psr1p/Psr2p complex (WPPC) plays a key role in papillae expansion. We show that cells lacking a functional WPPC have a sizable interaction-specific fitness advantage attributable to production of and resistance to a diffusible compound that inhibits growth of other cells. Competitive superiority and high relative fitness of whi2 and psr1psr2 strains are particularly pronounced in dense spatially structured colonies and are independent of TORC1 and Msn2p/Msn4p regulators previously associated with the WPPC function. The WPPC function, described here, might be a regulatory mechanism that balances cell competition and cooperation in dense yeast populations and, thus, contributes to cell synchronization, pattern formation, and the expansion of cells with a competitive fitness advantage.

• Klíčová slova
• chimeric populations, competitive advantage, interaction-specific fitness inequality, interference competition, yeast multicellularity,
• MeSH
• membránové proteiny genetika   metabolismus   MeSH
• proliferace buněk fyziologie   MeSH
• proteinfosfatasy genetika   metabolismus   MeSH
• regulace genové exprese u hub fyziologie   MeSH
• Saccharomyces cerevisiae - proteiny genetika   metabolismus   MeSH
• Saccharomyces cerevisiae genetika   metabolismus   MeSH
• signální transdukce fyziologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• membránové proteiny MeSH
• proteinfosfatasy MeSH
• PSR1 protein, S cerevisiae MeSH Prohlížeč
• PSR2 protein, S cerevisiae MeSH Prohlížeč
• Saccharomyces cerevisiae - proteiny MeSH
• Whi2 protein, S cerevisiae MeSH Prohlížeč

Multicellular structures formed by yeasts and other microbes are valuable models for investigating the processes of cell-cell interaction and pattern formation, as well as cell signaling and differentiation. These processes are essential for the organization and development of diverse microbial communities that are important in everyday life. Two major types of multicellular structures are formed by yeast Saccharomyces cerevisiae on semisolid agar. These are colonies formed by laboratory or domesticated strains and structured colony biofilms formed by wild strains. These structures differ in spatiotemporal organization and cellular differentiation. Using state-of-the-art microscopy and mutant analysis, we investigated the distribution of cells within colonies and colony biofilms and the involvement of specific processes therein. We show that prominent differences between colony and biofilm structure are determined during early stages of development and are associated with the different distribution of growing cells. Two distinct cell distribution patterns were identified-the zebra-type and the leopard-type, which are genetically determined. The role of Flo11p in cell adhesion and extracellular matrix production is essential for leopard-type distribution, because FLO11 deletion triggers the switch to zebra-type cell distribution. However, both types of cell organization are independent of cell budding polarity and cell separation as determined using respective mutants.

• Klíčová slova
• Flo11p adhesin, cell adhesion, cell organization, colonies and biofilms, laboratory and wild Saccharomyces cerevisiae strains, structure development, yeast multicellular structures,
• MeSH
• biofilmy * MeSH
• buněčné dělení MeSH
• membránové glykoproteiny genetika   metabolismus   MeSH
• mikrobiální interakce MeSH
• mutace MeSH
• Saccharomyces cerevisiae - proteiny genetika   metabolismus   MeSH
• Saccharomyces cerevisiae cytologie   metabolismus   fyziologie   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• FLO11 protein, S cerevisiae MeSH Prohlížeč
• membránové glykoproteiny MeSH
• Saccharomyces cerevisiae - proteiny MeSH

Yeasts create multicellular structures of varying complexity, such as more complex colonies and biofilms and less complex flocs, each of which develops via different mechanisms. Colony biofilms originate from one or more cells that, through growth and division, develop a complicated three-dimensional structure consisting of aerial parts, agar-embedded invasive parts and a central cavity, filled with extracellular matrix. In contrast, flocs arise relatively quickly by aggregation of planktonic cells growing in liquid cultures after they reach the appropriate growth phase and/or exhaust nutrients such as glucose. Creation of both types of structures is dependent on the presence of flocculins: Flo11p in the former case and Flo1p in the latter. We recently showed that formation of both types of structures by wild Saccharomyces cerevisiae strain BR-F is regulated via transcription regulators Tup1p and Cyc8p, but in a divergent manner. Biofilm formation is regulated by Cyc8p and Tup1p antagonistically: Cyc8p functions as a repressor of FLO11 gene expression and biofilm formation, whereas Tup1p counteracts the Cyc8p repressor function and positively regulates biofilm formation and Flo11p expression. In addition, Tup1p stabilizes Flo11p probably by repressing a gene coding for a cell wall or extracellular protease that is involved in Flo11p degradation. In contrast, formation of BR-F flocs is co-repressed by the Cyc8p-Tup1p complex. These findings point to different mechanisms involved in yeast multicellularity.

• Klíčová slova
• Adhesion and invasion, Colony biofilm, Cyc8p and Tup1p, Flocculation, Yeast multicellular structures,
• MeSH
• biofilmy MeSH
• buněčná stěna genetika   metabolismus   MeSH
• druhová specificita MeSH
• jaderné proteiny genetika   metabolismus   MeSH
• regulace genové exprese u hub * MeSH
• represorové proteiny genetika   metabolismus   MeSH
• Saccharomyces cerevisiae - proteiny genetika   metabolismus   MeSH
• Saccharomyces cerevisiae klasifikace   genetika   fyziologie   MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• CYC8 protein, S cerevisiae MeSH Prohlížeč
• jaderné proteiny MeSH
• represorové proteiny MeSH
• Saccharomyces cerevisiae - proteiny MeSH
• TUP1 protein, S cerevisiae MeSH Prohlížeč