101
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Natural variation in CDC28 underlies morphological phenotypes in an environmental yeast isolate. Genetics 2011; 188:723-30. [PMID: 21527779 DOI: 10.1534/genetics.111.128819] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Morphological differences among individuals in a species represent one of the most striking aspects of biology, and a primary aim of modern genetics is to uncover the molecular basis of morphological variation. In a survey of meiosis phenotypes among environmental isolates of Saccharomyces cerevisiae, we observed an unusual arrangement of meiotic spores within the spore sac in a strain from Ivory Coast, West Africa. We mined population genomic data to identify CDC28 as the major genetic determinant of meiotic and budding cell shape behaviors in this strain. Molecular genetic methods confirmed the role of the Ivory Coast variant of CDC28 in the arrangement of spores after meiosis, in the shape of budding cells in rich medium and in the morphology of filamentous growth during nitrogen limitation. Our results shed new light on the role of CDC28 in yeast cell division, and our work suggests that with the growing availability of genomic data sets in many systems, a priori prediction of functional variants will become an increasingly powerful strategy in molecular genetics.
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102
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A tradeoff drives the evolution of reduced metal resistance in natural populations of yeast. PLoS Genet 2011; 7:e1002034. [PMID: 21483812 PMCID: PMC3069115 DOI: 10.1371/journal.pgen.1002034] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Accepted: 02/09/2011] [Indexed: 01/05/2023] Open
Abstract
Various types of genetic modification and selective forces have been implicated
in the process of adaptation to novel or adverse environments. However, the
underlying molecular mechanisms are not well understood in most natural
populations. Here we report that a set of yeast strains collected from Evolution
Canyon (EC), Israel, exhibit an extremely high tolerance to the heavy metal
cadmium. We found that cadmium resistance is primarily caused by an enhanced
function of a metal efflux pump, PCA1. Molecular analyses
demonstrate that this enhancement can be largely attributed to mutations in the
promoter sequence, while mutations in the coding region have a minor effect.
Reconstruction experiments show that three single nucleotide substitutions in
the PCA1 promoter quantitatively increase its activity and thus
enhance the cells' cadmium resistance. Comparison among different yeast
species shows that the critical nucleotides found in EC strains are conserved
and functionally important for cadmium resistance in other species, suggesting
that they represent an ancestral type. However, these nucleotides had diverged
in most Saccharomyces cerevisiae populations, which gave cells
growth advantages under conditions where cadmium is low or absent. Our results
provide a rare example of a selective sweep in yeast populations driven by a
tradeoff in metal resistance. Understanding the genetic and molecular bases of adaptive mutations allows us to
gain insight into how new biological functions evolve. In natural populations,
examples in which adaptive mutations are characterized at the molecular level
are still rare. We studied wild yeast strains isolated from Evolution Canyon
(EC), Israel, that exhibit an extremely high tolerance to the heavy metal
cadmium. We found that high cadmium resistance was mainly caused by DNA sequence
changes in the promoter of a metal transport gene, PCA1.These
mutations increase PCA1 gene expression, thus leading to a more
efficient cadmium pump-out. Comparison among different yeast species shows that
the critical nucleotides found in EC strains are conserved and functionally
important for cadmium resistance in other species, suggesting that they
represent an ancestral type. When the PCA1 sequence and the
cadmium resistance in different S. cerevisiae populations
collected globally were compared, we found that most populations carried weak
PCA1 alleles and had a low cadmium tolerance. Since cells
carrying the strong PCA1 allele grow slowly under low-cadmium
conditions, it is likely that the tradeoff between cadmium resistance and growth
rate drives the evolution of reduced cadmium tolerance in most S.
cerevisiae populations.
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103
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Evolutionary engineered Saccharomyces cerevisiae wine yeast strains with increased in vivo flux through the pentose phosphate pathway. Metab Eng 2011; 13:263-71. [PMID: 21300171 DOI: 10.1016/j.ymben.2011.01.008] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 12/22/2010] [Accepted: 01/26/2011] [Indexed: 12/21/2022]
Abstract
Amplification of the flux toward the pentose phosphate (PP) pathway might be of interest for various S. cerevisiae based industrial applications. We report an evolutionary engineering strategy based on a long-term batch culture on gluconate, a substrate that is poorly assimilated by S. cerevisiae cells and is metabolized by the PP pathway. After adaptation for various periods of time, we selected strains that had evolved a greater consumption capacity for gluconate. (13)C metabolic flux analysis on glucose revealed a redirection of carbon flux from glycolysis towards the PP pathway and a greater synthesis of lipids. The relative flux into the PP pathway was 17% for the evolved strain (ECA5) versus 11% for the parental strain (EC1118). During wine fermentation, the evolved strains displayed major metabolic changes, such as lower levels of acetate production, higher fermentation rates and enhanced production of aroma compounds. These represent a combination of novel traits, which are of great interest in the context of modern winemaking.
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104
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Govender P, Kroppenstedt S, Bauer FF. Novel wine-mediated FLO11 flocculation phenotype of commercial Saccharomyces cerevisiae wine yeast strains with modified FLO gene expression. FEMS Microbiol Lett 2011; 317:117-26. [PMID: 21251052 DOI: 10.1111/j.1574-6968.2011.02219.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Depending on the genetic background of Saccharomyces strains, a wide range of phenotypic adhesion identities can be directly attributed to the FLO11-encoded glycoprotein, which includes asexual flocculation, invasive growth and pseudohyphal formation, flor formation and adhesion to biotic and abiotic surfaces. In a previous study, we reported that HSP30-mediated stationary-phase expression of the native chromosomal FLO11 ORF in two nonflocculent commercial Saccharomyces cerevisiae wine yeast strains, BM45 or VIN13 did not generate a flocculent phenotype under either standard laboratory media or synthetic MS300 must fermentation conditions. In the present study, the BM45- and VIN13-derived HSP30p-FLO11 wine yeast transformants were observed to be exclusively and strongly flocculent under authentic red wine-making conditions, thus suggesting that this specific fermentation environment specifically contributes to the development of a flocculent phenotype, which is insensitive to either glucose or mannose. Furthermore, irrespective of the strain involved this phenotype displayed both Ca(2+)-dependent and Ca(2+)-independent flocculation characteristics. A distinct advantage of this unique FLO11-based phenotype was highlighted in its ability to dramatically promote faster lees settling rates. Moreover, wines produced by BM45-F11H and VIN13-F11H transformants were significantly less turbid than those produced by their wild-type parental strains.
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Affiliation(s)
- Patrick Govender
- Department of Biochemistry, University of KwaZulu-Natal, Durban, South Africa
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105
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Cell signals, cell contacts, and the organization of yeast communities. EUKARYOTIC CELL 2011; 10:466-73. [PMID: 21296916 DOI: 10.1128/ec.00313-10] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Even relatively simple species have evolved mechanisms to organize individual organisms into communities, such that the fitness of the group is greater than the fitness of isolated individuals. Within the fungal kingdom, the ability of many yeast species to organize into communities is crucial for their growth and survival, and this property has important impacts both on the economy and on human health. Over the last few years, studies of Saccharomyces cerevisiae have revealed several fundamental properties of yeast communities. First, strain-to-strain variation in the structures of these groups is attributable in part to variability in the expression and functions of adhesin proteins. Second, the extracellular matrix surrounding these communities can protect them from environmental stress and may also be important in cell signaling. Finally, diffusible signals between cells contribute to community organization so that different regions of a community express different genes and adopt different cell fates. These findings provide an arena in which to view fundamental mechanisms by which contacts and signals between individual organisms allow them to assemble into functional communities.
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106
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Sicard D, Legras JL. Bread, beer and wine: yeast domestication in the Saccharomyces sensu stricto complex. C R Biol 2011; 334:229-36. [PMID: 21377618 DOI: 10.1016/j.crvi.2010.12.016] [Citation(s) in RCA: 175] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Yeasts of the Saccharomyces sensu stricto species complex are able to convert sugar into ethanol and CO(2) via fermentation. They have been used for thousands years by mankind for fermenting food and beverages. In the Neolithic times, fermentations were probably initiated by naturally occurring yeasts, and it is unknown when humans started to consciously add selected yeast to make beer, wine or bread. Interestingly, such human activities gave rise to the creation of new species in the Saccharomyces sensu stricto complex by interspecies hybridization or polyploidization. Within the S. cerevisiae species, they have led to the differentiation of genetically distinct groups according to the food process origin. Although the evolutionary history of wine yeast populations has been well described, the histories of other domesticated yeasts need further investigation.
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Affiliation(s)
- Delphine Sicard
- Université Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, Gif-sur-Yvette, France.
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107
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White MG, Piccirillo S, Dusevich V, Law DJ, Kapros T, Honigberg SM. Flo11p adhesin required for meiotic differentiation in Saccharomyces cerevisiae minicolonies grown on plastic surfaces. FEMS Yeast Res 2011; 11:223-32. [PMID: 21205160 DOI: 10.1111/j.1567-1364.2010.00712.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Saccharomyces cerevisiae grown on plastic surfaces formed organized structures, termed minicolonies, that consisted of a core of round (yeast-like) cells surrounded by chains of filamentous cells (pseudohyphae). Minicolonies had a much higher affinity for plastic than unstructured yeast communities growing on the same surface. Pseudohyphae at the surface of these colonies developed further into chains of asci. These structures suggest that pseudohyphal differentiation and sporulation are sequential processes in minicolonies. Consistent with this idea, minicolonies grown under conditions that stimulated pseudohyphal differentiation contained higher frequencies of asci. Furthermore, a flo11Δ mutant, which fails to form pseudohyphae, yielded normal sporulation in cultures, but was defective for minicolony sporulation. When minicolonies were dispersed in water and cells were then allowed to settle on the plastic surface, these cells sporulated very efficiently. Taken together, our results suggest that sporulation in minicolonies is stimulated by pseudohyphal differentiation because these pseudohyphae are dispersed from the core of the colony.
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Affiliation(s)
- Melissa G White
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, USA
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108
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Gemayel R, Vinces MD, Legendre M, Verstrepen KJ. Variable tandem repeats accelerate evolution of coding and regulatory sequences. Annu Rev Genet 2011; 44:445-77. [PMID: 20809801 DOI: 10.1146/annurev-genet-072610-155046] [Citation(s) in RCA: 390] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genotype-to-phenotype mapping commonly focuses on two major classes of mutations: single nucleotide polymorphisms (SNPs) and copy number variation (CNV). Here, we discuss an underestimated third class of genotypic variation: changes in microsatellite and minisatellite repeats. Such tandem repeats (TRs) are ubiquitous, unstable genomic elements that have historically been designated as nonfunctional "junk DNA" and are therefore mostly ignored in comparative genomics. However, as many as 10% to 20% of eukaryotic genes and promoters contain an unstable repeat tract. Mutations in these repeats often have fascinating phenotypic consequences. For example, changes in unstable repeats located in or near human genes can lead to neurodegenerative diseases such as Huntington disease. Apart from their role in disease, variable repeats also confer useful phenotypic variability, including cell surface variability, plasticity in skeletal morphology, and tuning of the circadian rhythm. As such, TRs combine characteristics of genetic and epigenetic changes that may facilitate organismal evolvability.
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Affiliation(s)
- Rita Gemayel
- Laboratory for Systems Biology, VIB, B-3001 Heverlee, Belgium
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109
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Nakagawa Y, Toda Y, Yamamura H, Hayakawa M, Iimura Y. FLO11 is essential for pellicle formation by wild pellicle-forming yeasts isolated from contaminated wines. J Biosci Bioeng 2011; 111:7-9. [DOI: 10.1016/j.jbiosc.2010.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 07/23/2010] [Accepted: 09/09/2010] [Indexed: 10/19/2022]
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110
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Diversity, variability and fast adaptive evolution of the wine yeast (Saccharomyces cerevisiae) genome—a review. ANN MICROBIOL 2010. [DOI: 10.1007/s13213-010-0086-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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111
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Van Mulders SE, Ghequire M, Daenen L, Verbelen PJ, Verstrepen KJ, Delvaux FR. Flocculation gene variability in industrial brewer’s yeast strains. Appl Microbiol Biotechnol 2010; 88:1321-31. [DOI: 10.1007/s00253-010-2843-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 08/11/2010] [Accepted: 08/12/2010] [Indexed: 11/28/2022]
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112
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St'ovíček V, Váchová L, Kuthan M, Palková Z. General factors important for the formation of structured biofilm-like yeast colonies. Fungal Genet Biol 2010; 47:1012-22. [PMID: 20728557 DOI: 10.1016/j.fgb.2010.08.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 08/06/2010] [Accepted: 08/11/2010] [Indexed: 12/30/2022]
Abstract
The lifestyle of wild and laboratory yeast strains significantly differs. In contrast to the smooth colonies of laboratory strains, wild Saccharomyces cerevisiae strains form biofilm-like, strikingly structured colonies possessing distinctive traits enabling them to better survive in hostile environments in the wild. Here, comparing three sets of strains forming differently structured colonies (fluffy, semi-fluffy and smooth), each derived from ancestors with distinct genetic backgrounds isolated from natural settings (BR-88, BR-99 and BR-103), we specified the factors essential for the formation of structured colonies, i.e. for the lifestyle most likely to be preferred in the wild. The ability to form an abundant extracellular matrix (ECM) is one of the features typical for structured colonies. ECM influences colony architecture and many other physiological properties, such as the capability to retain water in a 2-fold surplus to wet cell biomass. ECM composition, however, differs among distinct strains, depending on their particular genetic background. We further show that the expression of certain genes (AQY1, FLO11) is also strictly related to the particular colony morphology, being highest in the most structured colonies. Flo11p adhesin, important for cell-cell and cell-surface adhesion, is essential for the formation of fluffy colonies and thus significantly contributes to the phenotype variability of wild yeast strains. On the other hand, surprisingly, neither the cell shape nor budding pattern nor the ability to form pseudohyphae directly influences the formation of three-dimensional fluffy colony architecture.
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Affiliation(s)
- Vratislav St'ovíček
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, Prague 2, Czech Republic
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113
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Karunanithi S, Vadaie N, Chavel CA, Birkaya B, Joshi J, Grell L, Cullen PJ. Shedding of the mucin-like flocculin Flo11p reveals a new aspect of fungal adhesion regulation. Curr Biol 2010; 20:1389-95. [PMID: 20619652 DOI: 10.1016/j.cub.2010.06.033] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 06/08/2010] [Accepted: 06/09/2010] [Indexed: 01/01/2023]
Abstract
Cell adhesion is a key feature in the regulation of many biological processes. In the budding yeast Saccharomyces cerevisiae, Flo11p is the major adhesion molecule that controls filamentous growth [1-3] and the expansion of interconnected cells in mats or biofilms [4]. We show here that Flo11p is shed from cells. Flo11p shedding attenuated adherence and contributed to the overall balance in adherence properties that was optimal for filamentous growth and mat formation. Shed Flo11p comprised an essential component of a fluid layer surrounding yeast mats that may be functionally analogous to the mucus secretions of higher eukaryotes. Genome-wide secretion profiling of Flo11p identified new regulatory proteins, including the furin protease Kex2p, which was required for cleavage and maturation of the Flo11p protein. Secreted mucin-like proteins may play unexpected roles in the adherence properties and virulence of microbial pathogens.
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Affiliation(s)
- Sheelarani Karunanithi
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14260-1300, USA
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114
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Ethanol-independent biofilm formation by a flor wine yeast strain of Saccharomyces cerevisiae. Appl Environ Microbiol 2010; 76:4089-91. [PMID: 20435772 DOI: 10.1128/aem.00111-10] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Flor strains of Saccharomyces cerevisiae form a biofilm on the surface of wine at the end of fermentation, when sugar is depleted and growth on ethanol becomes dependent on oxygen. Here, we report greater biofilm formation on glycerol and ethyl acetate and inconsistent formation on succinic, lactic, and acetic acids.
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115
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Thierry A, Dujon B, Richard GF. Megasatellites: a new class of large tandem repeats discovered in the pathogenic yeast Candida glabrata. Cell Mol Life Sci 2010; 67:671-6. [PMID: 19946728 PMCID: PMC11115930 DOI: 10.1007/s00018-009-0216-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Revised: 11/09/2009] [Accepted: 11/10/2009] [Indexed: 11/29/2022]
Abstract
Megasatellites are DNA tandem arrays made of large motifs; they were discovered in the yeast Candida glabrata. They are widespread in this species (40 copies) but are not found in any other hemiascomycete so far, raising the intriguing question of their origin. They are found mainly in genes encoding cell wall products, suggesting that megasatellites were selected for a function linked to cell-cell adhesion or to pathogenicity. Their putative role in promoting genome rearrangements by interfering with DNA replication will also be discussed.
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Affiliation(s)
- Agnès Thierry
- Unité de Génétique Moléculaire des Levures, Institut Pasteur, CNRS URA2171, Université Pierre et Marie Curie UFR 927, 25 rue du Dr Roux, 75015 Paris, France
| | - Bernard Dujon
- Unité de Génétique Moléculaire des Levures, Institut Pasteur, CNRS URA2171, Université Pierre et Marie Curie UFR 927, 25 rue du Dr Roux, 75015 Paris, France
| | - Guy-Franck Richard
- Unité de Génétique Moléculaire des Levures, Institut Pasteur, CNRS URA2171, Université Pierre et Marie Curie UFR 927, 25 rue du Dr Roux, 75015 Paris, France
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116
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FLO gene-dependent phenotypes in industrial wine yeast strains. Appl Microbiol Biotechnol 2009; 86:931-45. [DOI: 10.1007/s00253-009-2381-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Revised: 11/23/2009] [Accepted: 11/23/2009] [Indexed: 10/20/2022]
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117
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Verstrepen KJ, Fink GR. Genetic and epigenetic mechanisms underlying cell-surface variability in protozoa and fungi. Annu Rev Genet 2009; 43:1-24. [PMID: 19640229 DOI: 10.1146/annurev-genet-102108-134156] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Eukaryotic microorganisms have evolved ingenious mechanisms to generate variability at their cell surface, permitting differential adherence, rapid adaptation to changing environments, and evasion of immune surveillance. Fungi such as Saccharomyces cerevisiae and the pathogen Candida albicans carry a family of mucin and adhesin genes that allow adhesion to various surfaces and tissues. Trypanosoma cruzi, T. brucei, and Plasmodium falciparum likewise contain large arsenals of different cell surface adhesion genes. In both yeasts and protozoa, silencing and differential expression of the gene family results in surface variability. Here, we discuss unexpected similarities in the structure and genomic location of the cell surface genes, the role of repeated DNA sequences, and the genetic and epigenetic mechanisms-all of which contribute to the remarkable cell surface variability in these highly divergent microbes.
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118
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Zhao X, Bai F. Yeast flocculation: New story in fuel ethanol production. Biotechnol Adv 2009; 27:849-856. [DOI: 10.1016/j.biotechadv.2009.06.006] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Revised: 06/09/2009] [Accepted: 06/20/2009] [Indexed: 11/26/2022]
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119
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Zara G, Zara S, Pinna C, Marceddu S, Budroni M. FLO11 gene length and transcriptional level affect biofilm-forming ability of wild flor strains of Saccharomyces cerevisiae. MICROBIOLOGY-SGM 2009; 155:3838-3846. [PMID: 19729408 DOI: 10.1099/mic.0.028738-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In Saccharomyces cerevisiae, FLO11 encodes an adhesin that is associated with different phenotypes, such as adherence to solid surfaces, hydrophobicity, mat and air-liquid biofilm formation. In the present study, we analysed FLO11 allelic polymorphisms and FLO11-associated phenotypes of 20 flor strains. We identified 13 alleles of different lengths, varying from 3.0 to 6.1 kb, thus demonstrating that FLO11 is highly polymorphic. Two alleles of 3.1 and 5.0 kb were cloned into strain BY4742 to compare the FLO11-associated phenotypes in the same genetic background. We show that there is a significant correlation between biofilm-forming ability and FLO11 length both in different and in the same genetic backgrounds. Moreover, we propose a multiple regression model that allows prediction of air-liquid biofilm-forming ability on the basis of transcription levels and lengths of FLO11 alleles in a population of S. cerevisiae flor strains. Considering that transcriptional differences are only partially explained by the differences in the promoter sequences, our results are consistent with the hypothesis that FLO11 transcription levels are strongly influenced by genetic background and affect biofilm-forming ability.
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Affiliation(s)
- Giacomo Zara
- Dipartimento di Scienze Ambientali Agrarie e Biotecnologie Agro-alimentari (DISAABA), University of Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Severino Zara
- Dipartimento di Scienze Ambientali Agrarie e Biotecnologie Agro-alimentari (DISAABA), University of Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Claudia Pinna
- Dipartimento di Scienze Ambientali Agrarie e Biotecnologie Agro-alimentari (DISAABA), University of Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Salvatore Marceddu
- Istituto di Scienze delle Produzioni Alimentari (ISPA CNR Sassari), Via dei Mille 48, 07100 Sassari, Italy
| | - Marilena Budroni
- Dipartimento di Scienze Ambientali Agrarie e Biotecnologie Agro-alimentari (DISAABA), University of Sassari, Viale Italia 39, 07100 Sassari, Italy
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120
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Koza A, Hallett PD, Moon CD, Spiers AJ. Characterization of a novel air-liquid interface biofilm of Pseudomonas fluorescens SBW25. MICROBIOLOGY-SGM 2009; 155:1397-1406. [PMID: 19383709 DOI: 10.1099/mic.0.025064-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Pseudomonads are able to form a variety of biofilms that colonize the air-liquid (A-L) interface of static liquid microcosms, and differ in matrix composition, strength, resilience and degrees of attachment to the microcosm walls. From Pseudomonas fluorescens SBW25, mutants have evolved during prolonged adaptation-evolution experiments which produce robust biofilms of the physically cohesive class at the A-L interface, and which have been well characterized. In this study we describe a novel A-L interface biofilm produced by SBW25 that is categorized as a viscous mass (VM)-class biofilm. Several metals were found to induce this biofilm in static King's B microcosms, including copper, iron, lead and manganese, and we have used iron to allow further examination of this structure. Iron was demonstrated to induce SBW25 to express cellulose, which provided the matrix of the biofilm, a weak structure that was readily destroyed by physical disturbance. This was confirmed in situ by a low (0.023-0.047 g) maximum deformation mass and relatively poor attachment as measured by crystal violet staining. Biofilm strength increased with increasing iron concentration, in contrast to attachment levels, which decreased with increasing iron. Furthermore, iron added to mature biofilms significantly increased strength, suggesting that iron also promotes interactions between cellulose fibres that increase matrix interconnectivity. Whilst weak attachment is important in maintaining the biofilm at the A-L interface, surface-interaction effects involving cellulose, which reduced surface tension by approximately 3.8 mN m(-1), may also contribute towards this localization. The fragility and viscoelastic nature of the biofilm were confirmed by controlled-stress amplitude sweep tests to characterize critical rheological parameters, which included a shear modulus of 0.75 Pa, a zero shear viscosity of 0.24 Pa s(-1) and a flow point of 0.028 Pa. Growth and morphological data thus far support a non-specific metal-associated physiological, rather than mutational, origin for production of the SBW25 VM biofilm, which is an example of the versatility of bacteria to inhabit optimal niches within their environment.
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Affiliation(s)
- Anna Koza
- SIMBIOS Centre, Level 5 Kydd Building, University of Abertay Dundee, Bell Street, Dundee DD1 1HG, UK
| | - Paul D Hallett
- Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Christina D Moon
- AgResearch Limited, Grasslands Research Centre, Private Bag 11008, Palmerston North, New Zealand
| | - Andrew J Spiers
- SIMBIOS Centre, Level 5 Kydd Building, University of Abertay Dundee, Bell Street, Dundee DD1 1HG, UK
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121
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Conserved WCPL and CX4C domains mediate several mating adhesin interactions in Saccharomyces cerevisiae. Genetics 2009; 182:173-89. [PMID: 19299340 DOI: 10.1534/genetics.108.100073] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Several adhesins are induced by pheromones during mating in Saccharomyces cerevisiae, including Aga1p, Aga2p, Sag1p (Agalpha1p), and Fig2p. These four proteins all participate in or influence a well-studied agglutinin interaction mediated by Aga1p-Aga2p complexes and Sag1p; however, they also play redundant and essential roles in mating via an unknown mechanism. Aga1p and Fig2p both contain repeated, conserved WCPL and CX(4)C domains. This study was directed toward understanding the mechanism underlying the collective requirement of agglutinins and Fig2p for mating. Apart from the well-known agglutinin interaction between Aga2p and Sag1p, three more pairs of interactions in cells of opposite mating type were revealed by this study, including bilateral heterotypic interactions between Aga1p and Fig2p and a homotypic interaction between Fig2p and Fig2p. These four pairs of adhesin interactions are collectively required for maximum mating efficiency and normal zygote morphogenesis. GPI-less, epitope-tagged forms of Aga1p and Fig2p can be co-immunoprecipitated from the culture medium of mating cells in a manner dependent on the WCPL and CX(4)C domains in the R1 repeat of Aga1p. Using site-directed mutagenesis, the conserved residues in Aga1p that interact with Fig2p were identified. Aga1p is involved in two distinct adhesive functions that are independent of each other, which raises the possibility for combinatorial interactions of this protein with its different adhesion receptors, Sag1 and Fig2p, a property of many higher eukaryotic adhesins.
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122
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Charpentier C, Colin A, Alais A, Legras JL. French Jura flor yeasts: genotype and technological diversity. Antonie van Leeuwenhoek 2009; 95:263-73. [DOI: 10.1007/s10482-009-9309-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Accepted: 01/27/2009] [Indexed: 10/21/2022]
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123
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Gibbons JG, Rokas A. Comparative and functional characterization of intragenic tandem repeats in 10 Aspergillus genomes. Mol Biol Evol 2008; 26:591-602. [PMID: 19056904 DOI: 10.1093/molbev/msn277] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Intragenic tandem repeats (ITRs) are consecutive repeats of three or more nucleotides found in coding regions. ITRs are the underlying cause of several human genetic diseases and have been associated with phenotypic variation, including pathogenesis, in several clades of the tree of life. We have examined the evolution and functional role of ITRs in 10 genomes spanning the fungal genus Aspergillus, a clade of relevance to medicine, agriculture, and industry. We identified several hundred ITRs in each of the species examined. ITR content varied extensively between species, with an average 79% of ITRs unique to a given species. For the fraction of conserved ITR regions, sequence comparisons within species and between close relatives revealed that they were highly variable. ITR-containing proteins were evolutionarily less conserved, compositionally distinct, and overrepresented for domains associated with cell-surface localization and function relative to the rest of the proteome. Furthermore, ITRs were preferentially found in proteins involved in transcription, cellular communication, and cell-type differentiation but were underrepresented in proteins involved in metabolism and energy. Importantly, although ITRs were evolutionarily labile, their functional associations appeared. To be remarkably conserved across eukaryotes. Fungal ITRs likely participate in a variety of developmental processes and cell-surface-associated functions, suggesting that their contribution to fungal lifestyle and evolution may be more general than previously assumed.
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Affiliation(s)
- John G Gibbons
- Department of Biological Sciences, Vanderbilt University, Nashville, USA
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124
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Fidalgo M, Barrales RR, Jimenez J. Coding repeat instability in theFLO11gene ofSaccharomycesyeasts. Yeast 2008; 25:879-89. [DOI: 10.1002/yea.1642] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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125
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Richard GF, Kerrest A, Dujon B. Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiol Mol Biol Rev 2008; 72:686-727. [PMID: 19052325 PMCID: PMC2593564 DOI: 10.1128/mmbr.00011-08] [Citation(s) in RCA: 335] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Repeated elements can be widely abundant in eukaryotic genomes, composing more than 50% of the human genome, for example. It is possible to classify repeated sequences into two large families, "tandem repeats" and "dispersed repeats." Each of these two families can be itself divided into subfamilies. Dispersed repeats contain transposons, tRNA genes, and gene paralogues, whereas tandem repeats contain gene tandems, ribosomal DNA repeat arrays, and satellite DNA, itself subdivided into satellites, minisatellites, and microsatellites. Remarkably, the molecular mechanisms that create and propagate dispersed and tandem repeats are specific to each class and usually do not overlap. In the present review, we have chosen in the first section to describe the nature and distribution of dispersed and tandem repeats in eukaryotic genomes in the light of complete (or nearly complete) available genome sequences. In the second part, we focus on the molecular mechanisms responsible for the fast evolution of two specific classes of tandem repeats: minisatellites and microsatellites. Given that a growing number of human neurological disorders involve the expansion of a particular class of microsatellites, called trinucleotide repeats, a large part of the recent experimental work on microsatellites has focused on these particular repeats, and thus we also review the current knowledge in this area. Finally, we propose a unified definition for mini- and microsatellites that takes into account their biological properties and try to point out new directions that should be explored in a near future on our road to understanding the genetics of repeated sequences.
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Affiliation(s)
- Guy-Franck Richard
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, CNRS, URA2171, Université Pierre et Marie Curie, UFR927, 25 rue du Dr. Roux, F-75015, Paris, France.
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126
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Espinazo-Romeu M, Cantoral JM, Matallana E, Aranda A. Btn2p is involved in ethanol tolerance and biofilm formation in flor yeast. FEMS Yeast Res 2008; 8:1127-36. [DOI: 10.1111/j.1567-1364.2008.00397.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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127
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Kovács MÃ, StupareviÄ I, MrÅ¡a V, Maráz A. Characterization of Ccw7p cell wall proteins and the encoding genes ofSaccharomyces cerevisiaewine yeast strains: relevance for flor formation. FEMS Yeast Res 2008; 8:1115-26. [DOI: 10.1111/j.1567-1364.2008.00413.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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128
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Kucheryava N, Bowen JK, Sutherland PW, Conolly JJ, Mesarich CH, Rikkerink EH, Kemen E, Plummer KM, Hahn M, Templeton MD. Two novel Venturia inaequalis genes induced upon morphogenetic differentiation during infection and in vitro growth on cellophane. Fungal Genet Biol 2008; 45:1329-39. [DOI: 10.1016/j.fgb.2008.07.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Revised: 07/09/2008] [Accepted: 07/15/2008] [Indexed: 11/29/2022]
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129
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Thierry A, Bouchier C, Dujon B, Richard GF. Megasatellites: a peculiar class of giant minisatellites in genes involved in cell adhesion and pathogenicity in Candida glabrata. Nucleic Acids Res 2008; 36:5970-82. [PMID: 18812401 PMCID: PMC2566889 DOI: 10.1093/nar/gkn594] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Minisatellites are DNA tandem repeats that are found in all sequenced genomes. In the yeast Saccharomyces cerevisiae, they are frequently encountered in genes encoding cell wall proteins. Minisatellites present in the completely sequenced genome of the pathogenic yeast Candida glabrata were similarly analyzed, and two new types of minisatellites were discovered: minisatellites that are composed of two different intermingled repeats (called compound minisatellites), and minisatellites containing unusually long repeated motifs (126–429 bp). These long repeat minisatellites may reach unusual length for such elements (up to 10 kb). Due to these peculiar properties, they have been named ‘megasatellites’. They are found essentially in genes involved in cell–cell adhesion, and could therefore be involved in the ability of this opportunistic pathogen to colonize the human host. In addition to megasatellites, found in large paralogous gene families, there are 93 minisatellites with simple shorter motifs, comparable to those found in S. cerevisiae. Most of the time, these minisatellites are not conserved between C. glabrata and S. cerevisiae, although their host genes are well conserved, raising the question of an active mechanism creating minisatellites de novo in hemiascomycetes.
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Affiliation(s)
- Agnès Thierry
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, CNRS, URA2171, F-75015 Paris, France
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130
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A catalog of neutral and deleterious polymorphism in yeast. PLoS Genet 2008; 4:e1000183. [PMID: 18769710 PMCID: PMC2515631 DOI: 10.1371/journal.pgen.1000183] [Citation(s) in RCA: 173] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Accepted: 07/30/2008] [Indexed: 11/30/2022] Open
Abstract
The abundance and identity of functional variation segregating in natural populations is paramount to dissecting the molecular basis of quantitative traits as well as human genetic diseases. Genome sequencing of multiple organisms of the same species provides an efficient means of cataloging rearrangements, insertion, or deletion polymorphisms (InDels) and single-nucleotide polymorphisms (SNPs). While inbreeding depression and heterosis imply that a substantial amount of polymorphism is deleterious, distinguishing deleterious from neutral polymorphism remains a significant challenge. To identify deleterious and neutral DNA sequence variation within Saccharomyces cerevisiae, we sequenced the genome of a vineyard and oak tree strain and compared them to a reference genome. Among these three strains, 6% of the genome is variable, mostly attributable to variation in genome content that results from large InDels. Out of the 88,000 polymorphisms identified, 93% are SNPs and a small but significant fraction can be attributed to recent interspecific introgression and ectopic gene conversion. In comparison to the reference genome, there is substantial evidence for functional variation in gene content and structure that results from large InDels, frame-shifts, and polymorphic start and stop codons. Comparison of polymorphism to divergence reveals scant evidence for positive selection but an abundance of evidence for deleterious SNPs. We estimate that 12% of coding and 7% of noncoding SNPs are deleterious. Based on divergence among 11 yeast species, we identified 1,666 nonsynonymous SNPs that disrupt conserved amino acids and 1,863 noncoding SNPs that disrupt conserved noncoding motifs. The deleterious coding SNPs include those known to affect quantitative traits, and a subset of the deleterious noncoding SNPs occurs in the promoters of genes that show allele-specific expression, implying that some cis-regulatory SNPs are deleterious. Our results show that the genome sequences of both closely and distantly related species provide a means of identifying deleterious polymorphisms that disrupt functionally conserved coding and noncoding sequences. DNA sequence variation makes an important contribution to most traits that vary in natural populations. However, mapping mutations that underlie a trait of interest is a significant challenge. Genome sequencing of multiple organisms provides a complete list of DNA sequence differences responsible for any trait that differs among the organisms. Yet, distinguishing those DNA sequence variants that contribute to a trait from all other variants is not easy. Here, we sequence the genomes of two strains of yeast and, through comparisons with a reference genome, we catalog multiple types of DNA sequence variation among the three strains. Using a variety of comparative genomics methods, we show that a substantial fraction of DNA sequence variations has deleterious effects on fitness. Finally, we show that a subset of deleterious mutations is associated with changes in gene expression levels. Our results imply that comparative genomics methods will be a valuable approach to identifying DNA sequence changes underlying numerous traits of interest.
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131
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Identification of novel activation mechanisms for FLO11 regulation in Saccharomyces cerevisiae. Genetics 2008; 178:145-56. [PMID: 18202364 DOI: 10.1534/genetics.107.081315] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Adhesins play a central role in the cellular response of eukaryotic microorganisms to their host environment. In pathogens such as Candida spp. and other fungi, adhesins are responsible for adherence to mammalian tissues, and in Saccharomyces spp. yeasts also confer adherence to solid surfaces and to other yeast cells. The analysis of FLO11, the main adhesin identified in Saccharomyces cerevisiae, has revealed complex mechanisms, involving both genetic and epigenetic regulation, governing the expression of this critical gene. We designed a genomewide screen to identify new regulators of this pivotal adhesin in budding yeasts. We took advantage of a specific FLO11 allele that confers very high levels of FLO11 expression to wild "flor" strains of S. cerevisiae. We screened for mutants that abrogated the increased FLO11 expression of this allele using the loss of the characteristic fluffy-colony phenotype and a reporter plasmid containing GFP controlled by the same FLO11 promoter. Using this approach, we isolated several genes whose function was essential to maintain the expression of FLO11. In addition to previously characterized activators, we identified a number of novel FLO11 activators, which reveal the pH response pathway and chromatin-remodeling complexes as central elements involved in FLO11 activation.
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132
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Adaptive evolution of a lactose-consuming Saccharomyces cerevisiae recombinant. Appl Environ Microbiol 2008; 74:1748-56. [PMID: 18245248 DOI: 10.1128/aem.00186-08] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The construction of Saccharomyces cerevisiae strains that ferment lactose has biotechnological interest, particularly for cheese whey fermentation. A flocculent lactose-consuming S. cerevisiae recombinant expressing the LAC12 (lactose permease) and LAC4 (beta-galactosidase) genes of Kluyveromyces lactis was constructed previously but showed poor efficiency in lactose fermentation. This strain was therefore subjected to an evolutionary engineering process (serial transfer and dilution in lactose medium), which yielded an evolved recombinant strain that consumed lactose twofold faster, producing 30% more ethanol than the original recombinant. We identified two molecular events that targeted the LAC construct in the evolved strain: a 1,593-bp deletion in the intergenic region (promoter) between LAC4 and LAC12 and a decrease of the plasmid copy number by about 10-fold compared to that in the original recombinant. The results suggest that the intact promoter was unable to mediate the induction of the transcription of LAC4 and LAC12 by lactose in the original recombinant and that the deletion established the transcriptional induction of both genes in the evolved strain. We propose that the tuning of the expression of the heterologous LAC genes in the evolved recombinant was accomplished by the interplay between the decreased copy number of both genes and the different levels of transcriptional induction for LAC4 and LAC12 resulting from the changed promoter structure. Nevertheless, our results do not exclude other possible mutations that may have contributed to the improved lactose fermentation phenotype. This study illustrates the usefulness of simple evolutionary engineering approaches in strain improvement. The evolved strain efficiently fermented threefold-concentrated cheese whey, providing an attractive alternative for the fermentation of lactose-based media.
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133
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Sears KE, Goswami A, Flynn JJ, Niswander LA. The correlated evolution of Runx2 tandem repeats, transcriptional activity, and facial length in carnivora. Evol Dev 2008; 9:555-65. [PMID: 17976052 DOI: 10.1111/j.1525-142x.2007.00196.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
To assess the ability of protein-coding mutations to contribute to subtle, inter-specific morphologic evolution, here, we test the hypothesis that mutations within the protein-coding region of runt-related transcription factor 2 (Runx2) have played a role in facial evolution in 30 species from a naturally evolving group, the mammalian order Carnivora. Consistent with this hypothesis, we find significant correlations between changes in Runx2 glutamine-alanine tandem-repeat ratio, and both Runx2 transcriptional activity and carnivoran facial length. Furthermore, we identify a potential evolutionary mechanism for the correlation between Runx2 tandem repeat ratio and facial length. Specifically, our results are consistent with the Runx2 tandem repeat system providing a flexible genetic mechanism to rapidly change the timing of ossification. These heterochronic changes, in turn, potentially act on existing allometric variation in carnivoran facial length to generate the disparity in adult facial lengths observed among carnivoran species. Our results suggest that despite potentially great pleiotropic effects, changes to the protein-coding regions of genes such as Runx2 do occur and have the potential to affect subtle morphologic evolution across a diverse array of species in naturally evolving lineages.
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Affiliation(s)
- K E Sears
- Pediatrics Department, Howard Hughes Medical Institute, University of Colorado at Denver and Health Sciences Center, 12800 East, 19th Avenue, Aurora, CO 80045, USA.
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134
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Legendre M, Pochet N, Pak T, Verstrepen KJ. Sequence-based estimation of minisatellite and microsatellite repeat variability. Genome Res 2007; 17:1787-96. [PMID: 17978285 DOI: 10.1101/gr.6554007] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Variable tandem repeats are frequently used for genetic mapping, genotyping, and forensics studies. Moreover, variation in some repeats underlies rapidly evolving traits or certain diseases. However, mutation rates vary greatly from repeat to repeat, and as a consequence, not all tandem repeats are suitable genetic markers or interesting unstable genetic modules. We developed a model, "SERV," that predicts the variability of a broad range of tandem repeats in a wide range of organisms. The nonlinear model uses three basic characteristics of the repeat (number of repeated units, unit length, and purity) to produce a numeric "VARscore" that correlates with repeat variability. SERV was experimentally validated using a large set of different artificial repeats located in the Saccharomyces cerevisiae URA3 gene. Further in silico analysis shows that SERV outperforms existing models and accurately predicts repeat variability in bacteria and eukaryotes, including plants and humans. Using SERV, we demonstrate significant enrichment of variable repeats within human genes involved in transcriptional regulation, chromatin remodeling, morphogenesis, and neurogenesis. Moreover, SERV allows identification of known and candidate genes involved in repeat-based diseases. In addition, we demonstrate the use of SERV for the selection and comparison of suitable variable repeats for genotyping and forensic purposes. Our analysis indicates that tandem repeats used for genotyping should have a VARscore between 1 and 3. SERV is publicly available from http://hulsweb1.cgr.harvard.edu/SERV/.
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Affiliation(s)
- Matthieu Legendre
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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135
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Dranginis AM, Rauceo JM, Coronado JE, Lipke PN. A biochemical guide to yeast adhesins: glycoproteins for social and antisocial occasions. Microbiol Mol Biol Rev 2007; 71:282-94. [PMID: 17554046 PMCID: PMC1899881 DOI: 10.1128/mmbr.00037-06] [Citation(s) in RCA: 219] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fungi are nonmotile eukaryotes that rely on their adhesins for selective interaction with the environment and with other fungal cells. Glycosylphosphatidylinositol (GPI)-cross-linked adhesins have essential roles in mating, colony morphology, host-pathogen interactions, and biofilm formation. We review the structure and binding properties of cell wall-bound adhesins of ascomycetous yeasts and relate them to their effects on cellular interactions, with particular emphasis on the agglutinins and flocculins of Saccharomyces and the Als proteins of Candida. These glycoproteins share common structural motifs tailored to surface activity and biological function. After being secreted to the outer face of the plasma membrane, they are covalently anchored in the wall through modified GPI anchors, with their binding domains elevated beyond the wall surface on highly glycosylated extended stalks. N-terminal globular domains bind peptide or sugar ligands, with between millimolar and nanomolar affinities. These affinities and the high density of adhesins and ligands at the cell surface determine microscopic and macroscopic characteristics of cell-cell associations. Central domains often include Thr-rich tandemly repeated sequences that are highly glycosylated. These domains potentiate cell-to-cell binding, but the molecular mechanism of such an association is not yet clear. These repeats also mediate recombination between repeats and between genes. The high levels of recombination and epigenetic regulation are sources of variation which enable the population to continually exploit new niches and resources.
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Affiliation(s)
- Anne M Dranginis
- Department of Biological Science, St John's University, Queens, New York, USA
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136
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Shieh JC, Cheng YC, Su MC, Moore M, Choo Y, Klug A. Tailor-made zinc-finger transcription factors activate FLO11 gene expression with phenotypic consequences in the yeast Saccharomyces cerevisiae. PLoS One 2007; 2:e746. [PMID: 17710146 PMCID: PMC1939876 DOI: 10.1371/journal.pone.0000746] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2007] [Accepted: 07/17/2007] [Indexed: 11/19/2022] Open
Abstract
Cys2His2 zinc fingers are eukaryotic DNA-binding motifs, capable of distinguishing different DNA sequences, and are suitable for engineering artificial transcription factors. In this work, we used the budding yeast Saccharomyces cerevisiae to study the ability of tailor-made zinc finger proteins to activate the expression of the FLO11 gene, with phenotypic consequences. Two three-finger peptides were identified, recognizing sites from the 5' UTR of the FLO11 gene with nanomolar DNA-binding affinity. The three-finger domains and their combined six-finger motif, recognizing an 18-bp site, were fused to the activation domain of VP16 or VP64. These transcription factor constructs retained their DNA-binding ability, with the six-finger ones being the highest in affinity. However, when expressed in haploid yeast cells, only one three-finger recombinant transcription factor was able to activate the expression of FLO11 efficiently. Unlike in the wild-type, cells with such transcriptional activation displayed invasive growth and biofilm formation, without any requirement for glucose depletion. The VP16 and VP64 domains appeared to act equally well in the activation of FLO11 expression, with comparable effects in phenotypic alteration. We conclude that the functional activity of tailor-made transcription factors in cells is not easily predicted by the in vitro DNA-binding activity.
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Affiliation(s)
- Jia-Ching Shieh
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan.
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137
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Dai S, Chen T, Chong K, Xue Y, Liu S, Wang T. Proteomics identification of differentially expressed proteins associated with pollen germination and tube growth reveals characteristics of germinated Oryza sativa pollen. Mol Cell Proteomics 2006; 6:207-30. [PMID: 17132620 DOI: 10.1074/mcp.m600146-mcp200] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mature pollen from most plant species is metabolically quiescent; however, after pollination, it germinates quickly and gives rise to a pollen tube to transport sperms into the embryo sac. Because methods for collecting a large amount of in vitro germinated pollen grains for transcriptomics and proteomics studies from model plants of Arabidopsis and rice are not available, molecular information about the germination developmental process is lacking. Here we describe a method for obtaining a large quantity of in vitro germinating rice pollen for proteomics study. Two-dimensional electrophoresis of approximately 2300 protein spots revealed 186 that were differentially expressed in mature and germinated pollen. Most showed a changed level of expression, and only 66 appeared to be specific to developmental stages. Furthermore 160 differentially expressed protein spots were identified on mass spectrometry to match 120 diverse protein species. These proteins involve different cellular and metabolic processes with obvious functional skew toward wall metabolism, protein synthesis and degradation, cytoskeleton dynamics, and carbohydrate/energy metabolism. Wall metabolism-related proteins are prominently featured in the differentially expressed proteins and the pollen proteome as compared with rice sporophytic proteomes. Our study also revealed multiple isoforms and differential expression patterns between isoforms of a protein. These results provide novel insights into pollen function specialization.
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Affiliation(s)
- Shaojun Dai
- Research Center for Molecular and Developmental Biology, Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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138
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Barash D, Sikorski J, Perry EB, Nevo E, Nudler E. Adaptive Mutations In RNA-Based Regulatory Mechanisms: Computational and Experimental Investigations. Isr J Ecol Evol 2006. [DOI: 10.1560/ijee_52_3-4_263] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recent discoveries of RNA-based regulatory mechanisms have prompted substantial interest in how they formed and the extent to which varying environmental conditions have influenced their evolution. One class of RNA-based regulatory mechanism that has been found in bacteria is the riboswitch, regulating the biosynthesis of certain vitamins by an RNA genetic control element that senses small molecules and responds with a structural change that affects transcription termination or translation initiation without the participation of proteins. By taking the thiamin pyrophosphate (TPP)-riboswitch inBacillus subtilisas a model system, we wish to examine whether beneficial mutations may exist at the level of RNA that will cause an improvement in organism fitness. By computationally analyzing the difference in primary and secondary structure of theB. subtilisTPP-riboswitch collected from the xeric "African" south-facing slope (SFS) vs. the mesic, "European", north-facing slope (NFS) in "Evolution Canyon" III at Nahal Shaharut, southern Israel, we wish to experimentally study the environmental effect on transcription termination in these RNA-based regulatory mechanisms that are believed to be of ancient origin in the evolutionary time scale. Computational results, so far, indicate that specific mutations affect the riboswitch conformation by causing a global rearrangement. We would like to check whether such mutations could be adaptive mutations that may have a beneficial fitness effect, taking the TPP-riboswitch as a model system at the micro-scale. Empirical results so far indicate that in the promoter region of the TPP-riboswitch, all mutations increase nucleotide GC content in the xeric SFS, whereas in the mesic NFS they increase AT content. Preliminary examination of termination efficiency of strains found exclusively on one slope or the other, reveal increased termination efficiency in the presence of TPP and at more moderate temperatures, but only a suggestion of greater termination efficiency from strains found on both slopes. We expect that further results will shed light on the mutational differences of TPP-riboswitch sequences found on opposite slopes of "Evolution Canyon" III at Nahal Shaharut, potentially leading to interesting discoveries that relate to the topic of adaptive, nonrandom mutations.
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Affiliation(s)
- Danny Barash
- Institute of Evolution, University of Haifa
- Department of Computer Science, Ben-Gurion University of the Negev
| | - Johannes Sikorski
- Institute of Evolution, University of Haifa
- Deutsche Sammlung von Mikroorganismen und Zellkulturen GMbH (DSMZ)
| | | | | | - Evgeny Nudler
- Department of Biochemistry, New York University Medical School,
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