scholarly journals RTM1: a member of a new family of telomeric repeated genes in yeast.

Genetics ◽  
1995 ◽  
Vol 140 (3) ◽  
pp. 945-956
Author(s):  
F Ness ◽  
M Aigle
Keyword(s):  
Ethanol Production ◽  
Laboratory Strain ◽  
Genomic Rearrangement ◽  
Yeast Gene ◽  
New Family ◽  
Nonessential Gene ◽  
Industrial Strains ◽  
Multiple Copies ◽  
New Yeast ◽  
Industrial Yeasts

Abstract We have isolated a new yeast gene called RTM1 whose overexpression confers resistance to the toxicity of molasses. The RTM1 gene encodes a hydrophobic 34-kD protein that contains seven potential transmembrane-spanning segments. Analysis of a series of industrial strains shows that the sequence is present in multiple copies and in variable locations in the genome. RTM loci are always physically associated with SUC telomeric loci. The SUC-RTM sequences are located between X and Y' subtelomeric sequences at chromosome ends. Surprisingly RTM sequences are not detected in the laboratory strain X2180. The lack of this sequence is associated with the absence of any SUC telomeric gene previously described. This observation raises the question of the origin of this nonessential gene. The particular subtelomeric position might explain the SUC-RTM sequence amplification observed in the genome of yeasts used in industrial biomass or ethanol production with molasses as substrate. This SUC-RTM sequence dispersion seems to be a good example of genomic rearrangement playing a role in evolution and environmental adaptation in these industrial yeasts.

scholarly journals Scaffolding proteins guide the evolution of algal light harvesting antennas

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Harry W. Rathbone ◽  
Katharine A. Michie ◽  
Michael J. Landsberg ◽  
Beverley R. Green ◽  
Paul M. G. Curmi
Keyword(s):  
Hydrophobic Surface ◽  
Scaffolding Protein ◽  
Secondary Endosymbiosis ◽  
Scaffolding Proteins ◽  
Α Subunit ◽  
Binding Partner ◽  
Photosynthetic Organisms ◽  
New Family ◽  
Red Algal ◽  
Multiple Copies

AbstractPhotosynthetic organisms have developed diverse antennas composed of chromophorylated proteins to increase photon capture. Cryptophyte algae acquired their photosynthetic organelles (plastids) from a red alga by secondary endosymbiosis. Cryptophytes lost the primary red algal antenna, the red algal phycobilisome, replacing it with a unique antenna composed of αβ protomers, where the β subunit originates from the red algal phycobilisome. The origin of the cryptophyte antenna, particularly the unique α subunit, is unknown. Here we show that the cryptophyte antenna evolved from a complex between a red algal scaffolding protein and phycoerythrin β. Published cryo-EM maps for two red algal phycobilisomes contain clusters of unmodelled density homologous to the cryptophyte-αβ protomer. We modelled these densities, identifying a new family of scaffolding proteins related to red algal phycobilisome linker proteins that possess multiple copies of a cryptophyte-α-like domain. These domains bind to, and stabilise, a conserved hydrophobic surface on phycoerythrin β, which is the same binding site for its primary partner in the red algal phycobilisome, phycoerythrin α. We propose that after endosymbiosis these scaffolding proteins outcompeted the primary binding partner of phycoerythrin β, resulting in the demise of the red algal phycobilisome and emergence of the cryptophyte antenna.

ACR1, a yeast ATF/CREB repressor

1992 ◽  
Vol 12 (12) ◽  
pp. 5394-5405
Author(s):  
A C Vincent ◽  
K Struhl
Keyword(s):  
Dna Binding ◽  
Cyclic Amp ◽  
Dna Sequences ◽  
Transcriptional Repressors ◽  
Yeast Gene ◽  
Yeast Saccharomyces Cerevisiae ◽  
Viral Oncogenes ◽  
Activation Of Transcription ◽  
Bzip Domain ◽  
New Yeast

Members of the mammalian ATF/CREB family of transcription factors, which are associated with regulation by cyclic AMP and viral oncogenes, bind common DNA sequences (consensus TGACGTCA) via a bZIP domain. In the yeast Saccharomyces cerevisiae, ATF/CREB-like sequences confer either repression or activation of transcription, depending on the promoter context. By isolating mutations that alleviate the repression mediated by ATF/CREB sites, we define a new yeast gene, ACR1, which encodes an ATF/CREB transcriptional repressor. ACR1 contains a bZIP domain that is necessary for homodimer formation and specific DNA binding to an ATF/CREB site. Within the bZIP domain, ACR1 most strongly resembles the mammalian cyclic AMP-responsive transcriptional regulators CREB and CREM; it is less similar to GCN4 and YAP1, two previously described yeast bZIP transcriptional activators that recognize the related AP-1 sequence (consensus TGACTCA). Interestingly, deletion of the ACR1 gene causes increased transcription through ATF/CREB sites that does not depend on GCN4 or YAP1. Moreover, extracts from acr1 deletion strains contain one or more ATF/CREB-like DNA-binding activities. These genetic and biochemical observations suggest that S. cerevisiae contains a family of ATF/CREB proteins that function as transcriptional repressors or activators.

scholarly journals Comparison of Two Alternative Dominant Selectable Markers for Wine Yeast Transformation

2004 ◽  
Vol 70 (12) ◽  
pp. 7018-7023 ◽  
Author(s):  
Eduardo Cebollero ◽  
Ramon Gonzalez
Keyword(s):  
Laboratory Strain ◽  
Wine Yeast ◽  
Selection Marker ◽  
Selectable Markers ◽  
Yeast Strains ◽  
Strain Transformation ◽  
Wine Yeast Strain ◽  
Industrial Strains ◽  
Resistance Markers ◽  
Selection For

ABSTRACT Genetic improvement of industrial yeast strains is restricted by the availability of selectable transformation markers. Antibiotic resistance markers have to be avoided for public health reasons, while auxotrophy markers are generally not useful for wine yeast strain transformation because most industrial Saccharomyces cerevisiae strains are prototrophic. For this work, we performed a comparative study of the usefulness of two alternative dominant selectable markers in both episomic and centromeric plasmids. Even though the selection for sulfite resistance conferred by FZF1-4 resulted in a larger number of transformants for a laboratory strain, the p-fluoro-dl-phenylalanine resistance conferred by ARO4-OFP resulted in a more suitable selection marker for all industrial strains tested. Both episomic and centromeric constructions carrying this marker resulted in transformation frequencies close to or above 103 transformants per μg of DNA for the three wine yeast strains tested.

scholarly journals HybridMine: A Pipeline for Allele Inheritance and Gene Copy Number Prediction in Hybrid Genomes and Its Application to Industrial Yeasts

2020 ◽  
Vol 8 (10) ◽  
pp. 1554
Author(s):  
Soukaina Timouma ◽  
Jean-Marc Schwartz ◽  
Daniela Delneri
Keyword(s):  
Programming Languages ◽  
Functional Annotation ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Saccharomyces Pastorianus ◽  
Industrial Strains ◽  
New Yeast ◽  
High Level ◽  
User Friendly ◽  
Genome Scale

Genome-scale computational approaches are opening opportunities to model and predict favorable combination of traits for strain development. However, mining the genome of complex hybrids is not currently an easy task, due to the high level of redundancy and presence of homologous. For example, Saccharomyces pastorianus is an allopolyploid sterile yeast hybrid used in brewing to produce lager-style beers. The development of new yeast strains with valuable industrial traits such as improved maltose utilization or balanced flavor profiles are now a major ambition and challenge in craft brewing and distilling industries. Moreover, no genome annotation for most of these industrial strains have been published. Here, we developed HybridMine, a new user-friendly, open-source tool for functional annotation of hybrid aneuploid genomes of any species by predicting parental alleles including paralogs. Our benchmark studies showed that HybridMine produced biologically accurate results for hybrid genomes compared to other well-established software. As proof of principle, we carried out a comprehensive structural and functional annotation of complex yeast hybrids to enable system biology prediction studies. HybridMine is developed in Python, Perl, and Bash programming languages and is available in GitHub.

A new yeast gene, HTR1, required for growth at high temperature, is needed for recovery from mating pheromone-induced G1 arrest

1994 ◽  
Vol 245 (1) ◽  
pp. 107-116 ◽  
Author(s):  
Yoshiko Kikuchi ◽  
Yoshio Oka ◽  
Mariko Kobayashi ◽  
Yukifumi Uesono ◽  
Akio Toh-e ◽  
...  
Keyword(s):  
High Temperature ◽  
G1 Arrest ◽  
Yeast Gene ◽  
Mating Pheromone ◽  
New Yeast

scholarly journals Evolution of the Xenopus piggyBac Transposon Family TxpB: Domesticated and Untamed Strategies of Transposon Subfamilies

2007 ◽  
Vol 24 (12) ◽  
pp. 2648-2656 ◽  
Author(s):  
Akira Hikosaka ◽  
Toshihiro Kobayashi ◽  
Yumiko Saito ◽  
Akira Kawahara
Keyword(s):  
Phylogenetic Analyses ◽  
Single Species ◽  
Single Copy ◽  
Open Reading Frames ◽  
Terminal Inverted Repeat ◽  
Repeat Sequences ◽  
New Family ◽  
Molecular Phylogenetic ◽  
Multiple Copies ◽  
Reading Frames

Abstract A new family, termed TxpB, of DNA transposons belonging to the piggyBac superfamily was found in 3 Xenopus species (Xenopus tropicalis, Xenopus laevis, and Xenopus borealis). Two TxpB subfamilies of Kobuta and Uribo1 were found in all the 3 species, and another subfamily termed Uribo2 was found in X. tropicalis. Molecular phylogenetic analyses of their open reading frames (ORFs) revealed that TxpB transposons have been maintained for over 100 Myr. Both the Uribo1 and the Uribo2 ORFs were present as multiple copies in each genome, and some of them were framed by terminal inverted repeat sequences. In contrast, all the Kobuta ORFs were present as a single copy in each genome and exhibited high evolutionary conservation, suggesting domestication of Kobuta genes by the host. Genomic insertion polymorphisms of the Uribo1 and Uribo2 transposons (nonautonomous type) were observed in a single species of X. tropicalis, indicating recent transposition events. Transfection experiments in cell culture revealed that an expression vector construct for the intact Uribo2 ORF caused precise excision of a nonautonomous Uribo2 element from the target vector construct but that for the Kobuta ORF did not. The present results support our viewpoint that some Uribo2 members are naturally active autonomous transposons, whereas Kobuta members may be domesticated by hosts.

Inability of Petite Mutants of Industrial Yeasts to Utilize Various Sugars, and a Comparison with the Ability of the Parent Strains to Ferment the Same Sugars Microaerophilically

1983 ◽  
Vol 38 (5-6) ◽  
pp. 405-407 ◽  
Author(s):  
J. F. T. Spencer ◽  
D. M. Spencer ◽  
R. Miller
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Methyl Glucoside ◽  
Yeast Strains ◽  
Petite Mutants ◽  
Industrial Strains ◽  
Industrial Yeasts ◽  
Microaerophilic Conditions

A number of industrial strains of Saccharomyces cerevisiae were converted to the petite form and tested for the ability to utilize galactose, maltose, sucrose, α-methyl glucoside and raffinose. The parent strains all metabolized these sugars aerobically. Twelve of the petite forms did not utilize galactose, six failed to utilize maltose, 17 did not utilize x-methyl glucoside, and 18 did not utilize raffinose. The petites of two distiller’s yeast strains did not utilize sucrose. The respiratory-competent parent strains nearly all fermented galactose, maltose, sucrose and raffinose, though 19 strains did not ferment α-methyl glucoside microaerophilically. Three strains did not ferment galactose, two fermented it only after several days adaptation, one did not ferment raffinose, and two did not ferment sucrose under microaerophilic conditions. Six respiratory-competent strains which did not utilize galactose when in the petite form fermented higher (10%) concentrations of glucose and maltose under microaerophilic conditions, but only three of these fermented galactose. The implications of these findings for the use of such strains in industry are discussed briefly.

scholarly journals Robustness and Ethanol Production of Industrial Strains of Saccharomyces cerevisiae Using Different Sugarcane Bagasse Hydrolysates

2019 ◽  
Vol 7 (1) ◽  
pp. 23 ◽  
Author(s):  
Vanessa S. Teixeira ◽  
Suéllen P. H. Azambuja ◽  
Priscila H. Carvalho ◽  
Fátima A. A. Costa ◽  
Patricia R. Kitaka ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Ethanol Production ◽  
Sugarcane Bagasse ◽  
Ethanol Yield ◽  
Raw Materials ◽  
Fermentation Inhibitors ◽  
Severe Condition ◽  
Inhibitor Tolerance ◽  
Industrial Strains ◽  
Materials Used

Sugarcane bagasse is one of the main lignocellulosic raw materials used for the production of second-generation ethanol. Technological studies on fermentation processes have focused on the search for and development of more robust microorganisms that are able to produce bioethanol efficiently and are resistant to the main fermentation inhibitors. The purpose of this study was to evaluate the robustness and ethanol production of industrial strains of Saccharomyces cerevisiae using acid, alkaline, and enzymatic sugarcane bagasse hydrolysates. Hydrolysis was carried out to release fermentable sugars from sugarcane bagasse. Fermentations were performed in shake flasks containing sugarcane hydrolysates supplemented with 150 g L−1 glucose to evaluate the kinetic parameters of the reaction. Inhibitor tolerance was evaluated by incubating cells with different concentrations of inhibitors in 96-well plates. The biomass yield on substrate, ethanol yield on substrate, and ethanol productivity of the six strains were higher in 0.5% acid, 0.5% alkaline, and enzymatic hydrolysates (i.e., under milder conditions). The SA-1 (Santa Adélia-1) strain had a better performance in comparison with the other strains for its ability to produce ethanol in a very severe condition (7% acid hydrolysis) and for its robustness in growing at several inhibitor concentrations.

scholarly journals A Food-Grade Cloning System for Industrial Strains of Lactococcus lactis

2000 ◽  
Vol 66 (4) ◽  
pp. 1253-1258 ◽  
Author(s):  
Kim I. Sørensen ◽  
Rasmus Larsen ◽  
Annette Kibenich ◽  
Mette P. Junge ◽  
Eric Johansen
Keyword(s):  
Lactococcus Lactis ◽  
Selectable Marker ◽  
Laboratory Strain ◽  
Cloning Vector ◽  
Selective Marker ◽  
Food Grade ◽  
Ideal System ◽  
Amber Suppressor ◽  
Industrial Strains ◽  
Slight Growth

ABSTRACT We have previously reported the construction of a food-grade cloning vector for Lactococcus using the ochre suppressor,supB, as the selective marker. This vector, pFG1, causes only a slight growth inhibition in the laboratory strain MG1363 but is unstable in the industrial strains tested. As supBsuppresses both amber and ochre stop codons, which are present in 82% of all known lactococcal genes, this undesirable finding may result from the accumulation of elongated mistranslated polypeptides. Here, we report the development of a new food-grade cloning vector, pFG200, which is suitable for overexpressing a variety of genes in industrial strains of Lactococcus lactis. The vector uses an amber suppressor, supD, as selectable marker and consists entirely of Lactococcus DNA, with the exception of a small polylinker region. Using suppressible pyrimidine auxotrophs, selection and maintenance are efficient in any pyrimidine-free medium including milk. Importantly, the presence of this vector in a variety of industrial strains has no significant effect on the growth rate or the rate of acidification in milk, making this an ideal system for food-grade modification of industrially relevant L. lactisstrains. The usefulness of this system is demonstrated by overexpressing the pepN gene in a number of industrial backgrounds.

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