10.5061/DRYAD.MN71G
Granek, Joshua A.
Duke University
Murray, Debra
Duke University
Kayıkçı, Ömür
Duke University
Magwene, Paul M.
Duke University
Data from: The genetic architecture of biofilm formation in a clinical
isolate of Saccharomyces cerevisiae
Dryad
dataset
2013
colony morphology
Bulk Segregant Analysis
cAMP-PKA
Biofilm
Natural Variation
2013-03-05T16:38:50Z
2013-03-05T16:38:50Z
en
https://doi.org/10.1534/genetics.112.142067
4637411 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Biofilms are microbial communities that form on surfaces. They are the
primary form of microbial growth in nature and can have detrimental
impacts on human health. Some strains of the budding yeast Saccharomyces
cerevisiae form colony biofilms, and there is substantial variation in
colony architecture between biofilm-forming strains. To identify the
genetic basis of biofilm variation, we developed a novel version of
quantitative trait locus mapping, which leverages cryptic variation in a
clinical isolate of S. cerevisiae. We mapped 13 loci linked to
heterogeneity in biofilm architecture and identified the gene most closely
associated with each locus. Of these candidate genes, six are members of
the cyclic AMP-protein kinase A pathway, an evolutionarily conserved cell
signaling network. Principal among these is CYR1, which encodes the enzyme
that catalyzes production of cAMP. Through a combination of gene
expression measurements, cell signaling assays, and gene overexpression,
we determined the functional effects of allelic variation at CYR1. We
found that increased pathway activity resulting from protein coding and
expression variation of CYR1 enhances the formation of colony biofilms.
Four other candidate genes encode kinases and transcription factors that
are targets of this pathway. The protein products of several of these
genes together regulate expression of the sixth candidate, FLO11, which
encodes a cell adhesion protein. Our results indicate that epistatic
interactions between alleles with both positive and negative effects on
cyclic AMP-protein kinase A signaling underlie much of the architectural
variation we observe in colony biofilms. They are also among the first to
demonstrate genetic variation acting at multiple levels of an integrated
signaling and regulatory network. Based on these results, we propose a
mechanistic model that relates genetic variation to gene network function
and phenotypic outcomes.
Bulk Genotype TableThis file contains the allele counts (number of
occurrences of an allele in a sequencing read) for each heterozygous site
found in YJM311 from the YJM311 (parental), simple, intermediate, and
complex se- quencing runs, and the G-statistic values at each of these
sites for the pairwise comparisons between the simple, intermediate, and
complex pools. Note that heterozygous sites where neither allele matched
the reference sequence are very rare, so were excluded from these results.
Each row in the file contains data on a single heterozygous site
identified in YJM311. The coordinates are based on Saccharomyces Genome
Database (SGD) release r62, (release date: February 18,
2009).bsa_geno_table.csvIndividual Segregant Phenotype and Genotype
TableThis file compiles phenotype and genotype data collected on
individual segregants from the Bulk Segregant Analysis. Each row in the
file contains data on a single segregant.seg_strain_table.csv