Academic journal article Genetics

The Genetic Architecture of Biofilm Formation in a Clinical Isolate of Saccharomyces Cerevisiae

Academic journal article Genetics

The Genetic Architecture of Biofilm Formation in a Clinical Isolate of Saccharomyces Cerevisiae

Article excerpt

ABSTRACT 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.

BIOFILMS are complex, surface-adherent communities of microbes. They are ubiquitous in nature and in the human environment (Donlan and Costerton 2002; López et al. 2010). Not only can they be life threatening when they form in the human body (Hall-Stoodley et al. 2004), but biofilms also create problems when they form on human-made structures, ranging from merely annoying (shower curtains) to hazardous (nuclear power plants) (Flemming 2002). Because of the frequency with which we interact with biofilms, characterizing the cellular mechanisms that regulate them and understanding the genetic basis of their variation are of great interest.

The ability to form biofilms is a multifactorial trait, resulting from the interactions of several lower-level properties, including cell-cell and cell-substrate adhesion; production of extracellular matrix; and spatial heterogeneity in cell morphology, growth, and division. Recent studies have demonstrated that the budding yeast Saccharomyces forms microbial communities that have these biofilm characteristics (Kuthan et al. 2003; Váchová et al. 2011). These characteristics are present in mats that form on softagar (Reynolds and Fink 2001) and in complex colony biofilms (sometimes referred to as "fluffy colonies") that are distinguished from nonbiofilm colonies (also described as simple or smooth colonies) by intricate, organized, and strain-specific architecture (Supporting Information, Figure S1) (Palková and Váchová 2006; Granek and Magwene 2010; Honigberg 2011). These complex colony biofilms are also formed by the more prevalent fungal pathogens Candida albicans (Hall et al. 2010) and Cryptococcus neoformans (Goldman et al. 1998), where they are associated with pathogenicity.

There is substantial variation among natural isolates of Saccharomyces cerevisiae in the propensity to form biofilms, the architectures produced, and the effect of environmental signals on biofilm phenotypes (i.e., genotype-by-environment interactions) (Palková 2004; Granek and Magwene 2010). …

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