scholarly journals O-glycosyltransferases from Homo sapiens contributes to the biosynthesis of Glycyrrhetic Acid 3-O-mono-β-D-glucuronide and Glycyrrhizin in Saccharomyces cerevisiae

2021 ◽  
Vol 6 (3) ◽  
pp. 173-179
Author(s):  
Ke Xu ◽  
Yu-jia Zhao ◽  
Nadeem Ahmad ◽  
Jing-nan Wang ◽  
Bo Lv ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Homo Sapiens ◽  
Glycyrrhetic Acid

scholarly journals Evolutionary and Functional Analysis of the Invariant SWIM Domain in the Conserved Shu2/SWS1 Protein Family from Saccharomyces cerevisiae to Homo sapiens

Genetics ◽  
2015 ◽  
Vol 199 (4) ◽  
pp. 1023-1033 ◽  
Author(s):  
Stephen K. Godin ◽  
Camille Meslin ◽  
Faiz Kabbinavar ◽  
Dominique S. Bratton-Palmer ◽  
Christina Hornack ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Functional Analysis ◽  
Homo Sapiens ◽  
Protein Family

A robust correlation estimator and nonlinear recurrent model to infer genetic interactions in Saccharomyces cerevisiae and pathways of pulmonary disease in Homo sapiens

Biosystems ◽  
2009 ◽  
Vol 98 (3) ◽  
pp. 160-175 ◽  
Author(s):  
Cheng-Long Chuang ◽  
Chung-Ming Chen ◽  
Wai-Si Wong ◽  
Kun-Nan Tsai ◽  
Err-Cheng Chan ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Pulmonary Disease ◽  
Homo Sapiens ◽  
Genetic Interactions

scholarly journals On the design of linked datasets mapping networks of collaboration in the genomic sequencing of Saccharomyces cerevisiae, Homo sapiens, and Sus scrofa

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 1200
Author(s):  
Mark Wong ◽  
Rhodri Leng
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Sus Scrofa ◽  
Scientific Literature ◽  
Homo Sapiens ◽  
Genomic Sequencing ◽  
Scientific Publications ◽  
Institutional Collaboration ◽  
European Nucleotide Archive ◽  
The Future ◽  
Over Time

This paper describes a unique two-step methodology used to construct six linked bibliometric datasets covering the sequencing of Saccharomyces cerevisiae, Homo sapiens, and Sus scrofa genomes. First, we retrieved all sequence submission data from the European Nucleotide Archive (ENA), including accession numbers associated with each species. Second, we used these accession numbers to construct queries to retrieve peer-reviewed scientific publications that first linked to these sequence lengths in the scientific literature. For each species, this resulted in two associated datasets: 1) A .csv file documenting the PMID of each article describing new sequences, all paper authors, all institutional affiliations of each author, countries of institution, year of first submission to the ENA, and the year of article publication, and 2) A .csv file documenting all institutions submitting to the ENA, number of nucleotides sequenced, number of submissions per institution in a given year, and years of submission to the database. In several upcoming publications, we utilise these datasets to understand how institutional collaboration shaped sequencing efforts, and to systematically identify important institutions and changes in network structures over time. This paper, therefore, should aid researchers who would like to use these data for future analyses by making the methodology that underpins it transparent. Further, by detailing our methodology, researchers may be able to utilise our approach to construct similar datasets in the future.

scholarly journals On the design of linked datasets mapping networks of collaboration in the genomic sequencing of Saccharomyces cerevisiae, Homo sapiens, and Sus scrofa

F1000Research ◽  
2020 ◽  
Vol 8 ◽  
pp. 1200
Author(s):  
Mark Wong ◽  
Rhodri Leng
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Sus Scrofa ◽  
Scientific Literature ◽  
Homo Sapiens ◽  
Genomic Sequencing ◽  
Scientific Publications ◽  
Institutional Collaboration ◽  
European Nucleotide Archive ◽  
The Future ◽  
Over Time

This paper describes a unique two-step methodology used to construct six linked bibliometric datasets covering the sequencing of Saccharomyces cerevisiae, Homo sapiens, and Sus scrofa genomes. First, we retrieved all sequence submission data from the European Nucleotide Archive (ENA), including accession numbers associated with each species. Second, we used these accession numbers to construct queries to retrieve peer-reviewed scientific publications that first linked to these sequence lengths in the scientific literature. For each species, this resulted in two associated datasets: 1) A .csv file documenting the PMID of each article describing new sequences, all paper authors, all institutional affiliations of each author, countries of institution, year of first submission to the ENA, and the year of article publication, and 2) A .csv file documenting all institutions submitting to the ENA, number of nucleotides sequenced, number of submissions per institution in a given year, and years of submission to the database. In several upcoming publications, we utilise these datasets to understand how institutional collaboration shaped sequencing efforts, and to systematically identify important institutions and changes in network structures over time. This paper, therefore, should aid researchers who would like to use these data for future analyses by making the methodology that underpins it transparent. Further, by detailing our methodology, researchers may be able to utilise our approach to construct similar datasets in the future.

scholarly journals Genome-wide analysis of Homo sapiens, Arabidopsis thaliana, and Saccharomyces cerevisiae reveals novel attributes of tail-anchored membrane proteins

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Glauber Costa Brito ◽  
Wiebke Schormann ◽  
Satinder K. Gidda ◽  
Robert T. Mullen ◽  
David W. Andrews
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Arabidopsis Thaliana ◽  
Membrane Proteins ◽  
Transmembrane Domain ◽  
Homo Sapiens ◽  
Amino Acid Sequences ◽  
Bimolecular Fluorescence Complementation ◽  
Bioinformatics Analyses ◽  
Novel Proteins ◽  
Species Specific

Abstract Background Tail-anchored membrane proteins (TAMPs) differ from other integral membrane proteins, because they contain a single transmembrane domain at the extreme carboxyl-terminus and are therefore obliged to target to membranes post-translationally. Although 3–5% of all transmembrane proteins are predicted to be TAMPs only a small number are well characterized. Results To identify novel putative TAMPs across different species, we used TAMPfinder software to identify 859, 657 and 119 putative TAMPs in human (Homo sapiens), plant (Arabidopsis thaliana), and yeast (Saccharomyces cerevisiae), respectively. Bioinformatics analyses of these putative TAMP sequences suggest that the list is highly enriched for authentic TAMPs. To experimentally validate the software predictions several human and plant proteins identified by TAMPfinder that were previously uncharacterized were expressed in cells and visualized at subcellular membranes by fluorescence microscopy and further analyzed by carbonate extraction or by bimolecular fluorescence complementation. With the exception of the pro-apoptotic protein harakiri, which is, peripherally bound to the membrane this subset of novel proteins behave like genuine TAMPs. Comprehensive bioinformatics analysis of the generated TAMP datasets revealed previously unappreciated common and species-specific features such as the unusual size distribution of and the propensity of TAMP proteins to be part of larger complexes. Additionally, novel features of the amino acid sequences that anchor TAMPs to membranes were also revealed. Conclusions The findings in this study more than double the number of predicted annotated TAMPs and provide new insights into the common and species-specific features of TAMPs. Furthermore, the list of TAMPs and annotations provide a resource for further investigation.

scholarly journals Myb-Related Schizosaccharomyces pombecdc5p Is Structurally and Functionally Conserved in Eukaryotes

1998 ◽  
Vol 18 (7) ◽  
pp. 4097-4108 ◽  
Author(s):  
Ryoma Ohi ◽  
Anna Feoktistova ◽  
Stacey McCann ◽  
Virginia Valentine ◽  
A. Thomas Look ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Drosophila Melanogaster ◽  
Transcriptional Activation ◽  
Homo Sapiens ◽  
Family Members ◽  
Temperature Sensitive ◽  
Related Protein ◽  
Hydrophobic Residues ◽  
Functional Conservation

ABSTRACT Schizosaccharomyces pombe cdc5p is a Myb-related protein that is essential for G2/M progression. To explore the structural and functional conservation of Cdc5 throughout evolution, we isolated Cdc5-related genes and cDNAs fromSaccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and Homo sapiens. Supporting the notion that these Cdc5 gene family members are functionally homologous to S. pombe cdc5 +, human and fly Cdc5 cDNAs are capable of complementing the temperature-sensitive lethality of the S. pombe cdc5-120 mutant. Furthermore, S. cerevisiae CEF1(S. cerevisiae homolog of cdc5 +), like S. pombe cdc5 +, is essential during G2/M. The location of the cdc5-120 mutation, as well as mutational analyses of Cef1p, indicate that the Myb repeats of cdc5p and Cef1p are important for their function in vivo. However, we found that unlike in c-Myb, single residue substitutions of glycines for hydrophobic residues within the Myb repeats of Cef1p, which are essential for maintaining structure of the Myb domain, did not impair Cef1p function in vivo. Rather, multiple W-to-G substitutions were required to inactivate Cef1p, and many of the substitution mutants were found to confer temperature sensitivity. Although it is possible that Cef1p acts as a transcriptional activator, we have demonstrated that Cef1p is not involved in transcriptional activation of a class of G2/M-regulated genes typified by SWI5. Collectively, these results suggest that Cdc5 family members participate in a novel pathway to regulate G2/M progression.

scholarly journals De Novo Production of Glycyrrhetic Acid 3-O-mono-β-D-glucuronide in Saccharomyces cerevisiae

2021 ◽  
Vol 9 ◽  
Author(s):  
Ying Huang ◽  
Dan Jiang ◽  
Guangxi Ren ◽  
Yan Yin ◽  
Yifan Sun ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Biosynthetic Pathway ◽  
De Novo ◽  
Glycyrrhetic Acid ◽  
Cytochrome P450 Enzymes ◽  
Short Supply ◽  
Food Industries ◽  
Alternative Approach ◽  
Engineered Yeast ◽  
Shake Flasks

Glycyrrhetic acid 3-O-mono-β-D-glucuronide (GAMG) is a rare compound in licorice and its short supply limits the wide applications in the pharmaceutical, cosmetic, and food industries. In this study, de novo biosynthesis of GAMG was achieved in engineered Saccharomyces cerevisiae strains based on the CRISPR/Cas9 genome editing technology. The introduction of GAMG biosynthetic pathway resulted in the construction of a GAMG-producing yeast strain for the first time. Through optimizing the biosynthetic pathway, improving the folding and catalysis microenvironment for cytochrome P450 enzymes (CYPs), enhancing the supply of UDP-glucuronic acid (UDP-GlcA), preventing product degradation, and optimizing the fermentation conditions, the production of GAMG was increased from 0.02 μg/L to 92.00 μg/L in shake flasks (4,200-fold), and the conversion rate of glycyrrhetic acid (GA) to GAMG was higher than 56%. The engineered yeast strains provide an alternative approach for the production of glycosylated triterpenoids.

scholarly journals Four subunits that are shared by the three classes of RNA polymerase are functionally interchangeable between Homo sapiens and Saccharomyces cerevisiae.

1995 ◽  
Vol 15 (9) ◽  
pp. 4702-4710 ◽  
Author(s):  
G V Shpakovski ◽  
J Acker ◽  
M Wintzerith ◽  
J F Lacroix ◽  
P Thuriaux ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Homo Sapiens ◽  
Binding Domain ◽  
Zinc Binding ◽  
Carboxy Terminal ◽  
Zinc Binding Domain ◽  
Yeast Mutants ◽  
Rna Polymerase Subunits

Four cDNAs encoding human polypeptides hRPB7.0, hRPB7.6, hRPB17, and hRPB14.4 (referred to as Hs10 alpha, Hs10 beta, Hs8, and Hs6, respectively), homologous to the ABC10 alpha, ABC10 beta, ABC14.5, and ABC23 RNA polymerase subunits (referred to as Sc10 alpha, Sc10 beta, Sc8, and Sc6, respectively) of Saccharomyces cerevisiae, were cloned and characterized for their ability to complement defective yeast mutants. Hs10 alpha and the corresponding Sp10 alpha of Schizosaccharomyces pombe can complement an S. cerevisiae mutant (rpc10-delta::HIS3) defective in Sc10 alpha. The peptide sequences are highly conserved in their carboxy-terminal halves, with an invariant motif CX2CX12RCX2CGXR corresponding to a canonical zinc-binding domain. Hs10 beta, Sc10 beta, and the N subunit of archaeal RNA polymerase are homologous. An invariant CX2CGXnCCR motif presumably forms an atypical zinc-binding domain. Hs10 beta, but not the archaeal subunit, complemented an S. cerevisiae mutant (rpb10-delta 1::HIS3) lacking Sc10 beta. Hs8 complemented a yeast mutant (rpb8-delta 1::LYS2) defective in the corresponding Sc8 subunit, although with a strong thermosensitive phenotype. Interspecific complementation also occurred with Hs6 and with the corresponding Dm6 cDNA of Drosophila melanogaster. Hs6 cDNA and the Sp6 cDNA of S. pombe are dosage-dependent suppressors of rpo21-4, a mutation generating a slowly growing yeast defective in the largest subunit of RNA polymerase II. Finally, a doubly chimeric S. cerevisiae strain bearing the Sp6 cDNA and the human Hs10 beta cDNA was also viable. No interspecific complementation was observed for the human hRPB25 (Hs5) homolog of the yeast ABC27 (Sc5) subunit.

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