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

2019 ◽  
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.

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

Science ◽  
2021 ◽  
Vol 371 (6527) ◽  
pp. 415-419
Author(s):  
James Boocock ◽  
Meru J. Sadhu ◽  
Arun Durvasula ◽  
Joshua S. Bloom ◽  
Leonid Kruglyak
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Metabolic Pathways ◽  
Genetic Interaction ◽  
Balancing Selection ◽  
The Other ◽  
Reference Allele ◽  
Trade Off ◽  
Galactose Utilization

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.

scholarly journals RECOMBINATION BETWEEN GENES LOCATED ON NONHOMOLOGOUS CHROMOSOMES IN SACCHAROMYCES CEREVISIAE

Genetics ◽  
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.

scholarly journals Flux, toxicity and protein expression costs shape genetic interaction in a metabolic pathway

2018 ◽  
Author(s):  
Harry Kemble ◽  
Catherine Eisenhauer ◽  
Alejandro Couce ◽  
Audrey Chapron ◽  
Mélanie Magnan ◽  
...  
Keyword(s):  
Protein Expression ◽  
Molecular Interactions ◽  
Metabolic Pathway ◽  
Genetic Background ◽  
Genetic Interaction ◽  
Mechanistic Model ◽  
Metabolic Genes ◽  
Simultaneous Impact ◽  
Molecular Phenotypes ◽  
The Impact

AbstractOur ability to predict the impact of mutations on traits relevant for disease and evolution remains severely limited by the dependence of their effects on the genetic background and environment. Even when molecular interactions between genes are known, it is unclear how these translate to organism-level interactions between alleles. We therefore characterized the interplay of genetic and environmental dependencies in determining fitness by quantifying ~4,000 fitness interactions between expression variants of two metabolic genes, in different environments. We detect a remarkable variety of environment-dependent interactions, and demonstrate they can be quantitatively explained by a mechanistic model accounting for catabolic flux, metabolite toxicity and expression costs. Complex fitness interactions between mutations can therefore be predicted simply from their simultaneous impact on a few connected molecular phenotypes.

scholarly journals Ability for Anaerobic Growth Is Not Sufficient for Development of the Petite Phenotype in Saccharomyces kluyveri

2001 ◽  
Vol 183 (8) ◽  
pp. 2485-2489 ◽  
Author(s):  
Kasper Mo/ller ◽  
Lisbeth Olsson ◽  
Jure Piškur
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Positive Characteristic ◽  
Kluyveromyces Lactis ◽  
Sensu Stricto ◽  
Point Of View ◽  
The Other ◽  
Anaerobic Growth ◽  
Anaerobic Conditions ◽  
Saccharomyces Kluyveri ◽  
Petite Mutants

ABSTRACT Saccharomyces cerevisiae is a petite-phenotype-positive (“petite-positive”) yeast, which can successfully grow in the absence of oxygen. On the other hand, Kluyveromyces lactisas well as many other yeasts are petite negative and cannot grow anaerobically. In this paper, we show that Saccharomyces kluyveri can grow under anaerobic conditions, but while it can generate respiration-deficient mutants, it cannot generate true petite mutants. From a phylogenetic point of view, S. kluyveri is apparently more closely related to S. cerevisiae than toK. lactis. These observations suggest that the progenitor of the modern Saccharomyces and Kluyveromycesyeasts, as well as other related genera, was a petite-negative and aerobic yeast. Upon separation of the K. lactis andS. kluyveri-S. cerevisiae lineages, the latter developed the ability to grow anaerobically. However, while the S. kluyveri lineage has remained petite negative, the lineage leading to the modern Saccharomyces sensu stricto and sensu lato yeasts has developed the petite-positive characteristic.

Suitability of forms of preparing seeds of Dalbergia miscolobium Benth for exposure to the tetrazolium test / Adequação das formas de preparação de sementes de Dalbergia miscolobium Benth para exposição ao teste de tetrazolium

2017 ◽  
Vol 1 (1) ◽  
Author(s):  
Juliana Martins de Mesquita Matos ◽  
Rosana De Carvalho Cristo Martins ◽  
Valéria Regina Bellotto ◽  
Lilian Gomes da Silva Rocha ◽  
Eloiza Aparecida Barbosa ◽  
...  
Keyword(s):  
Endangered Species ◽  
Filter Paper ◽  
Federal District ◽  
Complete Removal ◽  
Sensu Stricto ◽  
The Other ◽  
Distrito Federal ◽  
Viable Seeds ◽  
Range Test ◽  
Tetrazolium Test

Dalbergia miscolobium or Jacarandá do Cerrado is a species of legume in the Fabaceae family. It occurs in the sensu stricto Cerrado and in the dystrophic cerradão. It shows potential for landscaping and for recovering damaged areas. It is an endangered species and therefore is protected by the law that prevents cut in areas of the Federal District (Decree No. 14.783/93). The purpose of this study was to determine the best procedure to prepare seeds of Dalbergia miscolobium to assess viability in the tetrazolium test. We carried out the following treatments: i) hydration on filter paper at 25 ° C, ii) hydration on filter paper at 25 ° C followed by a cut in the tegument and iii) hydration on filter paper at 25 ° C followed bya complete removal of the tegument. The results were analyzed using analysis of variance and the Tukey range test. The analyzes showed that the best procedure to prepare seeds of Dalbergia miscolobium is the treatment in which there is a hydration followed by the complete removal of the integument. Where 78% of the seeds showed uniform staining, indicating that the seeds analyzed are of good quality. The other treatments, hydration and hydration followed by cutting, showed respectively 35% and 41% of viable seeds. RESUMO A Dalbergia miscolobium ou Jacarandá do Cerrado é uma espécie de leguminosa da família Fabaceae. Ocorre no sentido stricto Cerrado e no cerradão distrófico. Possui potencial para paisagismo e para recuperar áreas degradadas. É uma espécie ameaçada de extinção e, portanto, está protegida pela lei que previne o corte em áreas do Distrito Federal (Decreto 14.783 / 93). O objetivo deste estudo foi determinar o melhor procedimento de prepararação das sementes de Dalbergia miscolobium para serem submetidas à análise de viabilidade pelo teste de tetrazólio. Foram realizados os seguintes tratamentos: i) hidratação em papel de filtro a 25 ° C, ii) hidratação em papel de filtro a 25 ° C seguida de um corte no tegumento e iii) hidratação em papel de filtro a 25 ° C seguido de remoção completa do tegumento. Os resultados foram analisados utilizando-se a análise de variância e o teste de médias de Tukey. As análises mostraram que o melhor procedimento para preparar sementes de Dalbergia miscolobium é o tratamento em que há uma hidratação seguida pela remoção completa do tegumento, onde 78% das sementes apresentaram coloração uniforme, indicando que as sementes analisadas são de boa qualidade. Os demais tratamentos, hidratação e hidratação seguida de corte, mostraram respectivamente 35% e 41% de sementes viáveis.

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

Genetics ◽  
1995 ◽  
Vol 140 (1) ◽  
pp. 67-77 ◽  
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.

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

Genetics ◽  
1999 ◽  
Vol 151 (4) ◽  
pp. 1261-1272 ◽  
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.

scholarly journals Nucleotide Variation at theCHALCONE ISOMERASELocus inArabidopsis thaliana

Genetics ◽  
2000 ◽  
Vol 155 (2) ◽  
pp. 863-872 ◽  
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.

scholarly journals Eurasian and North American phylogeny of Turolian hipparionine horses (Perissodactyla, Mammalia) in China

1992 ◽  
Vol 6 ◽  
pp. 305-305
Author(s):  
Mahito Watabe
Keyword(s):  
North America ◽  
North American ◽  
Northern China ◽  
Sensu Stricto ◽  
The Other ◽  
Dental Morphology ◽  
Facial Morphology ◽  
Open Land ◽  
Specialized Form ◽  
Eastern Half

The late Miocene Chinese hipparions are morphologically diversified showing similarity to both western Old World's and North American forms. Two Chinese taxa that are phylogenetically related to western Old World's forms are Hipparion fossatum (= H. forstende) from Baode (Shanxi) and H. hippidiodus from Qingyang (Gansu) and Baode. The former is related to H. mediterraneum and the latter to H. urmiense - platygenys from the Turolian localities in the western Old World. H. fossatum and H. hippidiodus are associated with the “dorcadoides” (open-land) and “mixed” faunas in northern China. Hipparion fossatum that is characterized by POF located close to the orbit co-occurs with large and morphologically specialized form, H. dermatorhinum in Baode (Loc.30). H. hippidiodus with reduced POF is discovered with smaller H. coelophyes in Loc. 43, 44 (Baode) and Loc. 115 (Gansu).The hipparions associated with the “gaudryi” (forest) fauna are characterized by well defined and small POF located far from the orbit. Those forms are: H. platyodus from Loc. 70; H. ptychodus from Loc. 73; H. tylodus from Hsi-Liang in Yushe - Wuxiang basins; and H. sefvei from Loc. 12 at Xin-an in Henan province. H. coelophyes from Baode (Loc.43 & 44) and Qingyang (Loc. 115) also show similar facial morphology to the these forms, although it has small size and shallow POF. Those forms are similar in facial and dental morphology to Hipparion sensu stricto and some species of Cormohipparion in North America.The assemblages of Chinese hipparions are composed of two groups whose members are phylogenetically similar to the forms from both western part of Eurasia and North America. The “gaudryi” fauna is considered younger than the other two on the basis of faunal analyses. The similarity in hipparionine taxonomy between northern China and North America in the latest Miocene is an evidences for possible faunal interchange(s) occurred during that period, as suggested by taxonomic analyses on carnivores and proboscideans in eastern half of Eurasia and North America.

scholarly journals Upstream – News in Genomics

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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