scholarly journals Revisiting the Taxonomic Synonyms and Populations of Saccharomyces cerevisiae—Phylogeny, Phenotypes, Ecology and Domestication

2020 ◽  
Vol 8 (6) ◽  
pp. 903 ◽  
Author(s):  
Ana Pontes ◽  
Mathias Hutzler ◽  
Patrícia H. Brito ◽  
José Paulo Sampaio
Keyword(s):  
Saccharomyces Cerevisiae ◽  
New World ◽  
Current Model ◽  
Distinct Species ◽  
Saccharomyces Boulardii ◽  
Natural Environments ◽  
Wild Populations ◽  
Saccharomyces Diastaticus ◽  
Reference Strains ◽  
Type Strains

Saccharomyces cerevisiae—the most emblematic and industrially relevant yeast—has a long list of taxonomical synonyms. Formerly considered as distinct species, some of the synonyms represent variants with important industrial implications, like Saccharomyces boulardii or Saccharomyces diastaticus, but with an unclear status, especially among the fermentation industry, the biotechnology community and biologists not informed on taxonomic matters. Here, we use genomics to investigate a group of 45 reference strains (type strains) of former Saccharomyces species that are currently regarded as conspecific with S. cerevisiae. We show that these variants are distributed across the phylogenetic spectrum of domesticated lineages of S. cerevisiae, with emphasis on the most relevant technological groups, but absent in wild lineages. We analyzed the phylogeny of a representative and well-balanced dataset of S. cerevisiae genomes that deepened our current ecological and biogeographic assessment of wild populations and allowed the distinction, among wild populations, of those associated with low- or high-sugar natural environments. Some wild lineages from China were merged with wild lineages from other regions in Asia and in the New World, thus giving more resolution to the current model of expansion from Asia to the rest of the world. We reassessed several key domestication markers among the different domesticated populations. In some cases, we could trace their origin to wild reservoirs, while in other cases gene inactivation associated with domestication was also found in wild populations, thus suggesting that natural adaptation to sugar-rich environments predated domestication.

scholarly journals Phylogeny and differentiation of species of the genus Gluconacetobacter and related taxa based on multilocus sequence analyses of housekeeping genes and reclassification of Acetobacter xylinus subsp. sucrofermentans as Gluconacetobacter sucrofermentans (Toyosaki et al. 1996) sp. nov., comb. nov.

2010 ◽  
Vol 60 (10) ◽  
pp. 2277-2283 ◽  
Author(s):  
Ilse Cleenwerck ◽  
Paul De Vos ◽  
Luc De Vuyst
Keyword(s):  
Phylogenetic Trees ◽  
Housekeeping Genes ◽  
Distinct Species ◽  
Species Differentiation ◽  
Sequence Analyses ◽  
Phylogenetic Groups ◽  
The Family ◽  
Single Genus ◽  
Reference Strains ◽  
Type Strains

Three housekeeping genes (dnaK, groEL and rpoB) of strains belonging to the genus Gluconacetobacter (37 strains) or related taxa (38 strains) were sequenced. Reference strains of the 15 species of the genus Gluconacetobacter were included. Phylogenetic trees generated using these gene sequences confirmed the existence of two phylogenetic groups within the genus Gluconacetobacter. These groups clustered separately in trees constructed using concatenated sequences of the three genes, indicating that the genus Gluconacetobacter should not remain a single genus and should be split, as suggested previously. Multilocus sequence analysis (MLSA) of the three housekeeping genes also proved useful for species differentiation in the family Acetobacteraceae. It also suggested that Gluconacetobacter xylinus LMG 18788, better known as the type and only strain of Acetobacter xylinus subsp. sucrofermentans, represents a distinct species in the genus Gluconacetobacter, and is not a true G. xylinus strain. In previous studies, this strain showed less than 70 % DNA relatedness to the type strains of G. xylinus and Gluconacetobacter nataicola, the phylogenetically nearest relatives, and could be distinguished from them phenotypically. Additionally, AFLP and (GTG)5-PCR DNA fingerprinting data supported its reclassification within a distinct species. The name Gluconacetobacter sucrofermentans (Toyosaki et al. 1996) sp. nov., comb. nov. is proposed.

A Mutation in a Saccharomyces cerevisiae Gene (RAD3) Required for Nucleotide Excision Repair and Transcription Increases the Efficiency of Mismatch Correction

Genetics ◽  
1996 ◽  
Vol 144 (2) ◽  
pp. 459-466 ◽  
Author(s):  
Yingying Yang ◽  
Anthony L Johnson ◽  
Leland H Johnston ◽  
Wolfram Siede ◽  
Errol C Friedberg ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mismatch Repair ◽  
Excision Repair ◽  
Spontaneous Mutation ◽  
Surprising Result ◽  
Spontaneous Mutation Rate ◽  
Mismatch Correction ◽  
Nucleotide Excision ◽  
Repair Genes ◽  
Type Strains

Abstract RAD3 functions in DNA repair and transcription in Saccharomyces cerevisiae and particular rad3 alleles confer a mutator phenotype, possibly as a consequence of defective mismatch correction. We assessed the potential involvement of the Rad3 protein in mismatch correction by comparing heteroduplex repair in isogenic rad3-1 and wild-type strains. The rad3-1 allele increased the spontaneous mutation rate but did not prevent heteroduplex repair or bias its directionality. Instead, the efficiency of mismatch correction was enhanced in the rad3-1 strain. This surprising result prompted us to examine expression of yeast mismatch repair genes. We determined that MSH2, but not MLH1, is transcriptionally regulated during the cell-cycle like PMSl, and that rad3-1 does not increase the transcript levels for these genes in log phase cells. These observations suggest that the rad3-1 mutation gives rise to an enhanced efficiency of mismatch correction via a process that does not involve transcriptional regulation of mismatch repair. Interestingly, mismatch repair also was more efficient when error-editing by yeast DNA polymerase δ was eliminated. We discuss our results in relation to possible mechanisms that may link the rad3-1 mutation to mismatch correction efficiency.

scholarly journals Influences of Histone Stoichiometry on the Target Site Preference of Retrotransposons Ty1 and Ty2 in Saccharomyces cerevisiae

Genetics ◽  
1996 ◽  
Vol 142 (3) ◽  
pp. 761-776 ◽  
Author(s):  
Lori A Rinckel ◽  
David J Garfinkel
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Promoter Region ◽  
Target Site ◽  
Site Preference ◽  
Wild Type ◽  
Histone Proteins ◽  
Protein Levels ◽  
In The Wild ◽  
Type Strains ◽  
Orientation Bias

Abstract In Saccharomyces cerevisiae, the target site specificity of the retrotransposon Ty1 appears to involve the Ty integration complex recognizing chromatin structures. To determine whether changes in chromatin structure affect Ty1 and Ty2 target site preference, we analyzed Ty transposition at the CAN1 locus in mutants containing altered levels of histone proteins. A Δhta1-htb1 mutant with decreased levels of H2A and H2B histone proteins showed a pattern of Ty1 and Ty2 insertions at CAN1 that was significantly different from that of both the wild-type and a Δhta2-htb2 mutant, which does not have altered histone protein levels. Altered levels of H2A and H2B proteins disrupted a dramatic orientation bias in the CAN1 promoter region. In the wild-type strains, few Ty1 and Ty2 insertions in the promoter region were oriented opposite to the direction of CAN1 transcription. In the Δhta1-htb1 background, however, numerous Ty1 and Ty2 insertions were in the opposite orientation clustered within the TATA region. This altered insertion pattern does not appear to be due to a bias caused by selecting canavanine resistant isolates in the different HTA1-HTB1 backgrounds. Our results suggest that reduced levels of histone proteins alter Ty target site preference and disrupt an asymmetric Ty insertion pattern.

scholarly journals Controle biológico de antracnose em pós-colheita de banana “Maçã” com Saccharomyces spp.

2017 ◽  
Vol 43 (1) ◽  
pp. 49-51 ◽  
Author(s):  
Anderson Luis Heling ◽  
Odair José Kuhn ◽  
José Renato Stangarlin ◽  
Nicanor Pilarski Henkemeier ◽  
Sidiane Coltro-Roncato ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Saccharomyces Boulardii ◽  
Colletotrichum Musae

RESUMO Este trabalho objetivou analisar o controle biológico do Colletotrichum musae em bananas por meio de Saccharomyces cerevisiae e Saccharomyces boulardii. Células de S. cerevisiae foram obtidas a partir do fermento de panificação Fleischmann®. Células de S. boulardii foram obtidas a partir do medicamento Floratil®. Utilizou-se um cacho de banana colhido de área orgânica, os frutos passaram por um processo de assepsia, em seguida foram tratados com células de S. cerevisiae, S. boulardii e ambas as leveduras na concentração de 2 g L-1, após 24 horas inoculou-se o C. musae em três pontos por fruto. Para avaliar-se o efeito da concentração de células no tratamento o processo foi repetido, tratando-se os frutos com concentrações de 0; 0,5; 1; 2; 4 e 8 g L-1 de S. cerevisiae e S. boulardii, avaliou-se a área lesionada, a cada 48 horas, por 14 dias. Também avaliou-se o halo de inibição e a produção de compostos voláteis, ambos in vitro, para analisar se há ocorrência de antagonismo. Observou-se que o tratamento com as leveduras reduz o progresso da doença, e que S. cerevisiae e S. boulardii apresentam maior eficiência na concentração de 5,5 e 6,3 g L-1, respectivamente, apresentando redução de 48% e 35% do progresso da doença, respectivamente. Observou-se a formação de halo de inibição e produção de compostos voláteis, indicando que estas leveduras atuam por meio de antagonismo. Deste modo, estas leveduras são potencias agentes de controle biológico do C. musae.

scholarly journals Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species

2021 ◽  
Vol 12 ◽  
Author(s):  
Ola Alessa ◽  
Yoshitoshi Ogura ◽  
Yoshiko Fujitani ◽  
Hideto Takami ◽  
Tetsuya Hayashi ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Phylogenetic Relationship ◽  
Distinct Species ◽  
Genotypic Differences ◽  
Clade C ◽  
Single Genus ◽  
Almost All ◽  
Type Strains ◽  
Dependent Pathway ◽  
Insight Into

The pink-pigmented facultative methylotrophs (PPFMs), a major bacterial group found in the plant phyllosphere, comprise two genera: Methylobacterium and Methylorubrum. They have been separated into three major clades: A, B (Methylorubrum), and C. Within these genera, however, some species lack either pigmentation or methylotrophy, which raises the question of what actually defines the PPFMs. The present study employed a comprehensive comparative genomics approach to reveal the phylogenetic relationship among the PPFMs and to explain the genotypic differences that confer their different phenotypes. We newly sequenced the genomes of 29 relevant-type strains to complete a dataset for almost all validly published species in the genera. Through comparative analysis, we revealed that methylotrophy, nitrate utilization, and anoxygenic photosynthesis are hallmarks differentiating the PPFMs from the other Methylobacteriaceae. The Methylobacterium species in clade A, including the type species Methylobacterium organophilum, were phylogenetically classified into six subclades, each possessing relatively high genomic homology and shared phenotypic characteristics. One of these subclades is phylogenetically close to Methylorubrum species; this finding led us to reunite the two genera into a single genus Methylobacterium. Clade C, meanwhile, is composed of phylogenetically distinct species that share relatively higher percent G+C content and larger genome sizes, including larger numbers of secondary metabolite clusters. Most species of clade C and some of clade A have the glutathione-dependent pathway for formaldehyde oxidation in addition to the H4MPT pathway. Some species cannot utilize methanol due to their lack of MxaF-type methanol dehydrogenase (MDH), but most harbor an XoxF-type MDH that enables growth on methanol in the presence of lanthanum. The genomes of PPFMs encode between two and seven (average 3.7) genes for pyrroloquinoline quinone-dependent alcohol dehydrogenases, and their phylogeny is distinctly correlated with their genomic phylogeny. All PPFMs were capable of synthesizing auxin and did not induce any immune response in rice cells. Other phenotypes including sugar utilization, antibiotic resistance, and antifungal activity correlated with their phylogenetic relationship. This study provides the first inclusive genotypic insight into the phylogeny and phenotypes of PPFMs.

scholarly journals Bradyrhizobium tropiciagri sp. nov. and Bradyrhizobium embrapense sp. nov., nitrogen-fixing symbionts of tropical forage legumes

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4424-4433 ◽  
Author(s):  
Jakeline Renata Marçon Delamuta ◽  
Renan Augusto Ribeiro ◽  
Ernesto Ormeño-Orrillo ◽  
Marcia Maria Parma ◽  
Itamar Soares Melo ◽  
...  
Keyword(s):  
Environmental Sustainability ◽  
Type Strain ◽  
Housekeeping Genes ◽  
Distinct Species ◽  
Nucleotide Identity ◽  
Pcr Analysis ◽  
Rrna Gene ◽  
Tropical Pastures ◽  
Pasture Legumes ◽  
Type Strains

Biological nitrogen fixation is a key process for agricultural production and environmental sustainability, but there are comparatively few studies of symbionts of tropical pasture legumes, as well as few described species of the genus Bradyrhizobium, although it is the predominant rhizobial genus in the tropics. A detailed polyphasic study was conducted with two strains of the genus Bradyrhizobium used in commercial inoculants for tropical pastures in Brazil, CNPSo 1112T, isolated from perennial soybean (Neonotonia wightii), and CNPSo 2833T, from desmodium (Desmodium heterocarpon). Based on 16S-rRNA gene phylogeny, both strains were grouped in the Bradyrhizobium elkanii superclade, but were not clearly clustered with any known species. Multilocus sequence analysis of three (glnII, gyrB and recA) and five (plus atpD and dnaK) housekeeping genes confirmed that the strains are positioned in two distinct clades. Comparison with intergenic transcribed spacer sequences of type strains of described species of the genus Bradyrhizobium showed similarity lower than 93.1 %, and differences were confirmed by BOX-PCR analysis. Nucleotide identity of three housekeeping genes with type strains of described species ranged from 88.1 to 96.2 %. Average nucleotide identity of genome sequences showed values below the threshold for distinct species of the genus Bradyrhizobium ( < 90.6 %), and the value between the two strains was also below this threshold (91.2 %). Analysis of nifH and nodC gene sequences positioned the two strains in a clade distinct from other species of the genus Bradyrhizobium. Morphophysiological, genotypic and genomic data supported the description of two novel species in the genus Bradyrhizobium, Bradyrhizobium tropiciagri sp. nov. (type strain CNPSo 1112T = SMS 303T = BR 1009T = SEMIA 6148T = LMG 28867T) and Bradyrhizobium embrapense sp. nov. (type strain CNPSo 2833T = CIAT 2372T = BR 2212T = SEMIA 6208T = U674T = LMG 2987).

scholarly journals The effect of probiotic nutrition of Saccharomyces boulardii and Saccharomyces cerevisiae on yield, antioxidant activity and expression of interleukin-6 gene in Holstein calves

2020 ◽  
Vol 45 (4) ◽  
pp. 328-337
Author(s):  
S. Sabooni ◽  
M. Chamani ◽  
A. A. Sadeghi ◽  
M. Amin-Afshar ◽  
N. E. J. Kashan
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Antioxidant Activity ◽  
Interleukin 6 ◽  
Experimental Treatment ◽  
Saccharomyces Boulardii ◽  
Randomized Design ◽  
Significant Difference ◽  
Performance Traits ◽  
Holstein Calves

An experiment was performed to investigate the probiotic effect of Saccharomyces boulardii and Saccharomyces cerevisiae on yield, antioxidant activity, and expression of interleukin-6 gene in Holstein calves. Sixteen calves were divided into 4 dietary treatments with 4 calves/treatment. Experimental treatment diets include 1) control (without probiotic use), 2) milk soluble probiotics based on S. boulardii (1 g/kg), 3) milk soluble probiotics based on S. cerevisiae (1 g/kg) and 4) A mixture of yeast probiotics S. boulardii and S. cerevisiae as a solution in dairy milk (1 g/kg each). The completely randomized design was used in this experiment. The results showed that feeding S. boulardii and S. cerevisiae did not have a significant effect on performance traits compared with control. There was no significant difference between the different treatments for the number of antioxidant enzymes compared to the controls. Superoxide dismutase (SOD) in the treatments used probiotics were higher than the control. The expression of interleukin-6 gene expression was increased significantly (P<0.05) for treatments 3 and 4 on Days 10, 30 and 60 compared to the control. In conclusion, addition of probiotics did not alter performance traits of antioxidant activity, but the S. cerevisaetreatment did increase interleukin-6 gene expression which suggests an effect on the immune system. 

scholarly journals Stenotrophomonas africana Drancourt et al. 1997 is a later synonym of Stenotrophomonas maltophilia (Hugh 1981) Palleroni and Bradbury 1993

2004 ◽  
Vol 54 (4) ◽  
pp. 1235-1237 ◽  
Author(s):  
Tom Coenye ◽  
Elke Vanlaere ◽  
Enevold Falsen ◽  
Peter Vandamme
Keyword(s):  
Dna Hybridization ◽  
Stenotrophomonas Maltophilia ◽  
Biochemical Characterization ◽  
Cell Protein ◽  
Protein Patterns ◽  
Whole Cell ◽  
Sds Page ◽  
Binding Level ◽  
Reference Strains ◽  
Type Strains

Type and reference strains of Stenotrophomonas maltophilia and Stenotrophomonas africana were compared with each other and with the type strains of other Stenotrophomonas species, using SDS-PAGE of whole-cell proteins, DNA–DNA hybridization and extensive biochemical characterization. S. maltophilia LMG 958T and S. africana LMG 22072T had very similar whole-cell-protein patterns and were also biochemically very similar. A DNA–DNA binding level of 70 % between both type strains confirmed that S. africana and S. maltophilia represent the same taxon. It is concluded that S. africana is a later synonym of S. maltophilia.

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