Ancient balancing selection maintains incompatible versions of the galactose pathway in yeast

Metabolic pathways differ across species but are expected to be similar within a species. We discovered two functional, incompatible versions of the galactose pathway in Saccharomyces cerevisiae. We identified a three-locus genetic interaction for growth in galactose, and used precisely engineered alleles to show that it arises from variation in the galactose utilization genes GAL2, GAL1/10/7, and phosphoglucomutase (PGM1), and that the reference allele of PGM1 is incompatible with the alternative alleles of the other genes. Multiloci balancing selection has maintained the two incompatible versions of the pathway for millions of years. Strains with alternative alleles are found primarily in galactose-rich dairy environments, and they grow faster in galactose but slower in glucose, revealing a trade-off on which balancing selection may have acted.

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Ancient balancing selection maintains incompatible versions of a conserved metabolic pathway in yeast

10.1101/829325 ◽

2019 ◽

Cited By ~ 1

Author(s):

James Boocock ◽

Meru J Sadhu ◽

Joshua S Bloom ◽

Leonid Kruglyak

Keyword(s):

Saccharomyces Cerevisiae ◽

Metabolic Pathway ◽

Genetic Interaction ◽

Balancing Selection ◽

Sensu Stricto ◽

The Other ◽

Reference Allele ◽

Metabolic Genes ◽

Species Cluster ◽

Metabolic Strategies

AbstractDifferences in nutrient availability have led to the evolution of diverse metabolic strategies across species, but within species these strategies are expected to be similar. Here, we discovered that the galactose metabolic pathway in the yeast Saccharomyces cerevisiae exists in two functionally distinct, incompatible states maintained by ancient balancing selection. We identified a genetic interaction for growth in galactose among the metabolic genes GAL2, GAL1/10/7, and PGM1. We engineered strains with all allelic combinations at these loci and showed that the reference allele of PGM1 is incompatible with the alternative alleles of the other genes. We observed a strong signature of ancient balancing selection at all three loci and found that the alternative alleles diverged from the reference alleles before the birth of the Saccharomyces sensu stricto species cluster 10-20 million years ago. Strains with the alternative alleles are found primarily in galactose-rich dairy environments, and they grow faster in galactose, but slower in glucose, revealing a tradeoff on which balancing selection may have acted.

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Population dynamics of Saccharomyces cerevisiae PE-2 and CAT-1 in CO-culture for the production of ethanol

Acta Scientiarum Technology ◽

10.4025/actascitechnol.v42i1.43427 ◽

2020 ◽

Vol 42 ◽

pp. e43427

Author(s):

Mayara Vieira Santos ◽

Adriana Régia Marques Souza ◽

Maria Carolina Santos Silva ◽

Gabriel Luis Castiglioni

Keyword(s):

Saccharomyces Cerevisiae ◽

Population Dynamics ◽

Acetic Acid ◽

Ethanol Production ◽

Metabolic Pathways ◽

The Other ◽

Yeast Strains ◽

Pure Cultures ◽

Fermentation Monitoring ◽

Biotechnological Processes

In the Brazilian industries, the inoculum used throughout the harvest of ethanol production consists of a combination of two or more yeast strains. The combination of yeasts may influence in the metabolic pathways of microorganisms and increase the yields and production rates of some compounds. In biotechnological processes with co-culture, one microorganism can prevail over the other. Therefore, the knowledge about how the population dynamics occurs during fermentation allows modifications in the process in order to obtain higher yields and to achieve greater fermentative efficiency. The aim of this study was to investigate the fermentation with synthetic sugar cane broth in co-culture of Saccharomyces cerevisiae strains CAT-1 and PE-2 followed by molecular fermentation monitoring. The concentration of biomass, ethanol, glycerol, acetic acid and residual sucrose were monitored to verify the influence of different combinations during the fermentation. The mixture of CAT-1 and PE-2 presented the highest ethanol production, with higher performance of fermentative parameters than pure cultures

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RECOMBINATION BETWEEN GENES LOCATED ON NONHOMOLOGOUS CHROMOSOMES IN SACCHAROMYCES CEREVISIAE

Genetics ◽

10.1093/genetics/101.3-4.369 ◽

1982 ◽

Vol 101 (3-4) ◽

pp. 369-404

Author(s):

Margaret Dubay Mikus ◽

Thomas D Petes

Keyword(s):

Saccharomyces Cerevisiae ◽

Genetic Interaction ◽

Common Type ◽

Genetic Interactions ◽

The Other ◽

Physical Analysis ◽

Ura3 Gene ◽

Leu2 Gene ◽

Transfer Of Information ◽

Repeated Genes

ABSTRACT We constructed strains of Saccharomyces cerevisiae that contained two different mutant alleles of either the leu2 gene or the ura3 gene. These repeated genes were located on nonhomologous chromosomes; the two ura3- alleles were located on chromosomes V and XII and the two leu2- alleles were located on chromosomes III and XII. Genetic interactions between the two mutant copies of a gene were detected by the generation of either Leu+ or Ura+ revertants. Both spontaneous and ultraviolet irradiation-induced revertants were examined. By genetic and physical analysis, we have shown that Leu+ or Ura+ revertants can arise by a variety of different genetic interactions. The most common type of genetic interaction is the nonreciprocal transfer of information from one repeat to the other. We also detected reciprocal recombination between repeated genes, resulting in reciprocally translocated chromosomes.

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Black Hole Algorithm for Sustainable Design of Counterfort Retaining Walls

Sustainability ◽

10.3390/su12072767 ◽

2020 ◽

Vol 12 (7) ◽

pp. 2767 ◽

Cited By ~ 13

Author(s):

Víctor Yepes ◽

José V. Martí ◽

José García

Keyword(s):

Black Hole ◽

Sustainable Design ◽

Retaining Walls ◽

The Other ◽

Trade Off ◽

Construction Company ◽

Geometric Variables ◽

The Stability ◽

The Cost ◽

Black Hole Algorithm

The optimization of the cost and CO 2 emissions in earth-retaining walls is of relevance, since these structures are often used in civil engineering. The optimization of costs is essential for the competitiveness of the construction company, and the optimization of emissions is relevant in the environmental impact of construction. To address the optimization, black hole metaheuristics were used, along with a discretization mechanism based on min–max normalization. The stability of the algorithm was evaluated with respect to the solutions obtained; the steel and concrete values obtained in both optimizations were analyzed. Additionally, the geometric variables of the structure were compared. Finally, the results obtained were compared with another algorithm that solved the problem. The results show that there is a trade-off between the use of steel and concrete. The solutions that minimize CO 2 emissions prefer the use of concrete instead of those that optimize the cost. On the other hand, when comparing the geometric variables, it is seen that most remain similar in both optimizations except for the distance between buttresses. When comparing with another algorithm, the results show a good performance in optimization using the black hole algorithm.

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Recombination of Ty elements in yeast can be induced by a double-strand break.

Genetics ◽

10.1093/genetics/140.1.67 ◽

1995 ◽

Vol 140 (1) ◽

pp. 67-77 ◽

Cited By ~ 1

Author(s):

A Parket ◽

O Inbar ◽

M Kupiec

Keyword(s):

Saccharomyces Cerevisiae ◽

Cell Cycle ◽

Strand Break ◽

Double Strand Break ◽

The Other ◽

Direct Repeats ◽

Yeast Saccharomyces Cerevisiae ◽

Low Frequencies ◽

Ty Elements ◽

Main Family

Abstract The Ty retrotransposons are the main family of dispersed repeated sequences in the yeast Saccharomyces cerevisiae. These elements are flanked by a pair of long terminal direct repeats (LTRs). Previous experiments have shown that Ty elements recombine at low frequencies, despite the fact that they are present in 30 copies per genome. This frequency is not highly increased by treatments that cause DNA damage, such as UV irradiation. In this study, we show that it is possible to increase the recombination level of a genetically marked Ty by creating a double-strand break in it. This break is repaired by two competing mechanisms: one of them leaves a single LTR in place of the Ty, and the other is a gene conversion event in which the marked Ty is replaced by an ectopically located one. In a strain in which the marked Ty has only one LTR, the double-strand break is repaired by conversion. We have also measured the efficiency of repair and monitored the progression of the cells through the cell-cycle. We found that in the presence of a double-strand break in the marked Ty, a proportion of the cells is unable to resume growth.

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Suppressor Analysis of the Saccharomyces cerevisiae Gene REC104 Reveals a Genetic Interaction With REC102

Genetics ◽

10.1093/genetics/151.4.1261 ◽

1999 ◽

Vol 151 (4) ◽

pp. 1261-1272 ◽

Cited By ~ 1

Author(s):

Laura Salem ◽

Natalie Walter ◽

Robert Malone

Keyword(s):

Saccharomyces Cerevisiae ◽

Meiotic Recombination ◽

Null Allele ◽

Genetic Interaction ◽

In Vitro Mutagenesis ◽

Conditional Mutations ◽

Suppressor Analysis

Abstract REC104 is a gene required for the initiation of meiotic recombination in Saccharomyces cerevisiae. To better understand the role of REC104 in meiosis, we used an in vitro mutagenesis technique to create a set of temperature-conditional mutations in REC104 and used one ts allele (rec104-8) in a screen for highcopy suppressors. An increased dosage of the early exchange gene REC102 was found to suppress the conditional recombinational reduction in rec104-8 as well as in several other conditional rec104 alleles. However, no suppression was observed for a null allele of REC104, indicating that the suppression by REC102 is not “bypass” suppression. Overexpression of the early meiotic genes REC114, RAD50, HOP1, and RED1 fails to suppress any of the rec104 conditional alleles, indicating that the suppression might be specific to REC102.

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Nucleotide Variation at theCHALCONE ISOMERASELocus inArabidopsis thaliana

Genetics ◽

10.1093/genetics/155.2.863 ◽

2000 ◽

Vol 155 (2) ◽

pp. 863-872 ◽

Cited By ~ 14

Author(s):

Helmi Kuittinen ◽

Montserrat Aguadé

Keyword(s):

Nucleotide Diversity ◽

Direct Relationship ◽

Selective Sweep ◽

Balancing Selection ◽

Neutral Theory ◽

Low Frequency ◽

The Other ◽

Nucleotide Variation ◽

Rapid Population Growth ◽

History Of

AbstractAn ~1.9-kb region encompassing the CHI gene, which encodes chalcone isomerase, was sequenced in 24 worldwide ecotypes of Arabidopsis thaliana (L.) Heynh. and in 1 ecotype of A. lyrata ssp. petraea. There was no evidence for dimorphism at the CHI region. A minimum of three recombination events was inferred in the history of the sampled ecotypes of the highly selfing A. thaliana. The estimated nucleotide diversity (θTOTAL = 0.004, θSIL = 0.005) was on the lower part of the range of the corresponding estimates for other gene regions. The skewness of the frequency spectrum toward an excess of low-frequency polymorphisms, together with the bell-shaped distribution of pairwise nucleotide differences at CHI, suggests that A. thaliana has recently experienced a rapid population growth. Although this pattern could also be explained by a recent selective sweep at the studied region, results from the other studied loci and from an AFLP survey seem to support the expansion hypothesis. Comparison of silent polymorphism and divergence at the CHI region and at the Adh1 and ChiA revealed in some cases a significant deviation of the direct relationship predicted by the neutral theory, which would be compatible with balancing selection acting at the latter regions.

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Upstream – News in Genomics

Comparative and Functional Genomics ◽

10.1002/cfg.172 ◽

2002 ◽

Vol 3 (3) ◽

pp. 221-225

Keyword(s):

Saccharomyces Cerevisiae ◽

Ovarian Cancer ◽

Oryza Sativa ◽

Schizosaccharomyces Pombe ◽

Fission Yeast ◽

Proteomic Analysis ◽

Large Scale ◽

Protein Complexes ◽

The Other ◽

Blood Samples

In recent months a bumper crop of genomes has been completed, including the fission yeast (Schizosaccharomyces pombe) and rice (Oryza sativa). Two large-scale studies ofSaccharomyces cerevisiaeprotein complexes provided a picture of the eukaryotic proteome as a network of complexes. Amongst the other stories of interest was a demonstration that proteomic analysis of blood samples can be used to detect ovarian cancer, perhaps even as early as stage I.

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Genome-wide mapping of unexplored essential regions in the Saccharomyces cerevisiae genome: evidence for hidden synthetic lethal combinations in a genetic interaction network

Nucleic Acids Research ◽

10.1093/nar/gku576 ◽

2014 ◽

Vol 42 (15) ◽

pp. 9838-9853 ◽

Cited By ~ 6

Author(s):

Saeed Kaboli ◽

Takuya Yamakawa ◽

Keisuke Sunada ◽

Tao Takagaki ◽

Yu Sasano ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Genetic Interaction ◽

Interaction Network ◽

Essential Genes ◽

Genetic Interactions ◽

Lethal Gene ◽

Synthetic Lethal ◽

Genome Wide ◽

A Genome ◽

Wide Scale

Abstract Despite systematic approaches to mapping networks of genetic interactions in Saccharomyces cerevisiae, exploration of genetic interactions on a genome-wide scale has been limited. The S. cerevisiae haploid genome has 110 regions that are longer than 10 kb but harbor only non-essential genes. Here, we attempted to delete these regions by PCR-mediated chromosomal deletion technology (PCD), which enables chromosomal segments to be deleted by a one-step transformation. Thirty-three of the 110 regions could be deleted, but the remaining 77 regions could not. To determine whether the 77 undeletable regions are essential, we successfully converted 67 of them to mini-chromosomes marked with URA3 using PCR-mediated chromosome splitting technology and conducted a mitotic loss assay of the mini-chromosomes. Fifty-six of the 67 regions were found to be essential for cell growth, and 49 of these carried co-lethal gene pair(s) that were not previously been detected by synthetic genetic array analysis. This result implies that regions harboring only non-essential genes contain unidentified synthetic lethal combinations at an unexpectedly high frequency, revealing a novel landscape of genetic interactions in the S. cerevisiae genome. Furthermore, this study indicates that segmental deletion might be exploited for not only revealing genome function but also breeding stress-tolerant strains.

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Identifying opportunities for value chain development in the Kenyan coffee sector

Outlook on Agriculture ◽

10.1177/0030727018766956 ◽

2018 ◽

Vol 47 (2) ◽

pp. 150-159 ◽

Cited By ~ 1

Author(s):

Emerta Aragie

Keyword(s):

Value Chain ◽

Export Performance ◽

Export Subsidy ◽

The Other ◽

Cash Crop ◽

Trade Off ◽

Cash Crops ◽

Standard Value ◽

Coffee Sector ◽

Productivity Gains

By developing a model that describes the Kenyan coffee value chain, this study evaluates opportunities emanating from four scenarios representing productivity gains in the various value chain stages of the coffee sector and additional three scenarios reflecting shifts in market situations. Results show that productivity-enhancing policies have stronger effects on coffee output and export performance if they target the milling stage of the value chain. Export subsidy and favourable external marketing conditions also have stronger effects, distributed comparably across the various value chain stages. We, however, found that these gains in the coffee sector come at the expense of other cash crops such as cotton, tea, sugar and tobacco. The approach followed in this study is relevant as this trade-off between coffee and the other cash crop sectors may not be visibly shown using standard value chain approaches.

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