scholarly journals Improving Industrially Relevant Phenotypic Traits by Engineering Chromosome Copy Number in Saccharomyces pastorianus

2020 ◽  
Vol 11 ◽  
Author(s):  
Arthur R. Gorter de Vries ◽  
Ewout Knibbe ◽  
Roderick van Roosmalen ◽  
Marcel van den Broek ◽  
Pilar de la Torre Cortés ◽  
...  
Keyword(s):  
Copy Number ◽  
Phenotypic Traits ◽  
Chromosome Copy Number ◽  
Saccharomyces Pastorianus

scholarly journals Chromosomal Copy Number Variation in Saccharomyces pastorianus Is Evidence for Extensive Genome Dynamics in Industrial Lager Brewing Strains

2015 ◽  
Vol 81 (18) ◽  
pp. 6253-6267 ◽  
Author(s):  
M. van den Broek ◽  
I. Bolat ◽  
J. F. Nijkamp ◽  
E. Ramos ◽  
M. A. H. Luttik ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Phenotypic Traits ◽  
Genome Sequences ◽  
Content Type ◽  
Chromosome Copy Number ◽  
Group I ◽  
Saccharomyces Pastorianus ◽  
Karyotypic Variability ◽  
Number Variation

ABSTRACTLager brewing strains ofSaccharomyces pastorianusare natural interspecific hybrids originating from the spontaneous hybridization ofSaccharomyces cerevisiaeandSaccharomyces eubayanus. Over the past 500 years,S. pastorianushas been domesticated to become one of the most important industrial microorganisms. Production of lager-type beers requires a set of essential phenotypes, including the ability to ferment maltose and maltotriose at low temperature, the production of flavors and aromas, and the ability to flocculate. Understanding of the molecular basis of complex brewing-related phenotypic traits is a prerequisite for rational strain improvement. While genome sequences have been reported, the variability and dynamics ofS. pastorianusgenomes have not been investigated in detail. Here, using deep sequencing and chromosome copy number analysis, we showed thatS. pastorianusstrain CBS1483 exhibited extensive aneuploidy. This was confirmed by quantitative PCR and by flow cytometry. As a direct consequence of this aneuploidy, a massive number of sequence variants was identified, leading to at least 1,800 additional protein variants inS. pastorianusCBS1483. Analysis of eight additionalS. pastorianusstrains revealed that the previously defined group I strains showed comparable karyotypes, while group II strains showed large interstrain karyotypic variability. Comparison of three strains with nearly identical genome sequences revealed substantial chromosome copy number variation, which may contribute to strain-specific phenotypic traits. The observed variability of lager yeast genomes demonstrates that systematic linking of genotype to phenotype requires a three-dimensional genome analysis encompassing physical chromosomal structures, the copy number of individual chromosomes or chromosomal regions, and the allelic variation of copies of individual genes.

scholarly journals Sex differences in circadian food anticipatory activity are not altered by individual manipulations of sex hormones or sex chromosome copy number in mice

PLoS ONE ◽  
2018 ◽  
Vol 13 (1) ◽  
pp. e0191373 ◽  
Author(s):  
Antonio Aguayo ◽  
Camille S. Martin ◽  
Timothy F. Huddy ◽  
Maya Ogawa-Okada ◽  
Jamie L. Adkins ◽  
...  
Keyword(s):  
Sex Differences ◽  
Sex Hormones ◽  
Copy Number ◽  
Sex Chromosome ◽  
Chromosome Copy Number ◽  
Food Anticipatory Activity ◽  
Anticipatory Activity

scholarly journals Extensive protein dosage compensation in aneuploid human cancers

2021 ◽  
Author(s):  
Klaske Marijke Schukken ◽  
Jason Meyer Sheltzer
Keyword(s):  
Protein Expression ◽  
Dosage Compensation ◽  
Copy Number ◽  
Human Cancer ◽  
Tumor Development ◽  
Driver Genes ◽  
Human Cancer Cell Lines ◽  
Chromosome Copy Number ◽  
Human Cancers ◽  
Copy Number Changes

Aneuploidy is a hallmark of human cancers, but the effects of aneuploidy on protein expression remain poorly understood. To uncover how chromosome copy number changes influence the cancer proteome, we have conducted an analysis of hundreds of human cancer cell lines with matched copy number, RNA expression, and protein expression data. We found that a majority of proteins exhibit dosage compensation and fail to change by the degree expected based on chromosome copy number alone. We uncovered a variety of gene groups that were recurrently buffered upon both chromosome gain and loss, including protein complex subunits and cell cycle genes. Several genetic and biophysical factors were predictive of protein buffering, highlighting complex post-translational regulatory mechanisms that maintain appropriate gene product dosage. Finally, we established that chromosomal aneuploidy has an unexpectedly moderate effect on the expression of oncogenes and tumor suppressors, demonstrating that these key cancer drivers can be subject to dosage compensation as well. In total, our comprehensive analysis of aneuploidy and dosage compensation across cancers will help identify the key driver genes encoded on altered chromosomes and will shed light on the overall consequences of aneuploidy during tumor development.

scholarly journals X chromosome copy number variants: incidental ECS findings and the importance of clarifying reproductive risks

2022 ◽  
Vol 226 (1) ◽  
pp. S571
Author(s):  
Julia Wilkinson ◽  
Allie Carrasquedo ◽  
Sarah Grams ◽  
Melissa Strassberg ◽  
Sarah Poll ◽  
...  
Keyword(s):  
X Chromosome ◽  
Copy Number ◽  
Copy Number Variants ◽  
Chromosome Copy Number

Heat stress in the presence of low RNA polymerase activity increases chromosome copy number in Escherichia coli

1988 ◽  
Vol 212 (2) ◽  
pp. 203-206 ◽  
Author(s):  
Elena C. Guzman ◽  
Alfonso Jimenez-Sanchez ◽  
Elisha Orr ◽  
Robert H. Pritchard
Keyword(s):  
Escherichia Coli ◽  
Heat Stress ◽  
Rna Polymerase ◽  
Copy Number ◽  
Polymerase Activity ◽  
Chromosome Copy Number ◽  
Rna Polymerase Activity

Polyploidy in halophilic archaea: regulation, evolutionary advantages, and gene conversion

2019 ◽  
Vol 47 (3) ◽  
pp. 933-944 ◽  
Author(s):  
Katharina Ludt ◽  
Jörg Soppa
Keyword(s):  
Gene Conversion ◽  
Copy Number ◽  
Replication Origin ◽  
Origin Recognition Complex ◽  
Gene Dosage ◽  
Halophilic Archaea ◽  
Chromosome Copy Number ◽  
Efficient Gene ◽  
Replication Control ◽  
The Many

AbstractAll analyzed haloarachea are polyploid. In addition, haloarchaea contain more than one type of chromosome, and thus the gene dosage can be regulated independently on different replicons. Haloarchaea and several additional archaea have more than one replication origin on their major chromosome, in stark contrast with bacteria, which have a single replication origin. Two of these replication origins of Haloferax volcanii have been studied in detail and turned out to have very different properties. The chromosome copy number appears to be regulated in response to growth phases and environmental factors. Archaea typically contain about two Origin Recognition Complex (ORC) proteins, which are homologous to eukaryotic ORC proteins. However, haloarchaea are the only archaeal group that contains a multitude of ORC proteins. All 16 ORC protein paralogs from H. volcanii are involved in chromosome copy number regulation. Polyploidy has many evolutionary advantages for haloarchaea, e.g. a high resistance to desiccation, survival over geological times, and the relaxation of cell cycle-specific replication control. A further advantage is the ability to grow in the absence of external phosphate while using the many genome copies as internal phosphate storage polymers. Very efficient gene conversion operates in haloarchaea and results in the unification of genome copies. Taken together, haloarchaea are excellent models to study many aspects of genome biology in prokaryotes, exhibiting properties that have not been found in bacteria.

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