An expanded regulatory network temporally controls Candida albicans biofilm formation

Abstract

Summary C andida albicans biofilms are composed of highly adherent and densely arranged cells with properties distinct from those of free‐floating (planktonic) cells. These biofilms are a significant medical problem because they commonly form on implanted medical devices, are drug resistant and are difficult to remove. C . albicans biofilms are not static structures; rather they are dynamic and develop over time. Here we characterize gene expression in biofilms during their development, and by comparing them to multiple planktonic reference states, we identify patterns of gene expression relevant to biofilm formation. In particular, we document time‐dependent changes in genes involved in adhesion and metabolism, both of which are at the core of biofilm development. Additionally, we identify three new regulators of biofilm formation, Flo8, Gal4, and Rfx2, which play distinct roles during biofilm development over time. Flo8 is required for biofilm formation at all time points, and Gal4 and Rfx2 are needed for proper biofilm formation at intermediate time points.

Plasticity of Candida albicans Biofilms

“…Of the latter genes, 405 (23%) were found to be regulated similarly by both methods (see the supplemental material in reference 200), which is a surprisingly low level of correspondence. The study by Nobile et al (200) was followed by an additional one by the same group, using the same model and the same microarray platform but not including an RNA-Seq analysis (245). In the supplemental material of the expanded study (245), comparison of the transcription profiles of planktonic (log-phase) cells and biofilms identified 238 genes that were upregulated or downregulated Ն2-fold and were also identified as similarly regulated in the study of Nobile et al (200).…”

“…The study by Nobile et al (200) was followed by an additional one by the same group, using the same model and the same microarray platform but not including an RNA-Seq analysis (245). In the supplemental material of the expanded study (245), comparison of the transcription profiles of planktonic (log-phase) cells and biofilms identified 238 genes that were upregulated or downregulated Ն2-fold and were also identified as similarly regulated in the study of Nobile et al (200). However, 845 additional genes were found to be differentially regulated Ն2-fold that were not assessed in the Nobile et al a The compositions of the media are given in Table 1. or downregulation versus upregulation) Ն2-fold in the two studies.…”

“…Profiling can be performed by assessing genome-wide transcription by using microarrays (195,200,(244)(245)(246)(247)(248), NanoString nCounter technology (249,250), and RNA sequencing (RNA-Seq) (197,200) or by using quantitative reverse transcription-PCR (RT-PCR) or Northern blot analysis of a smaller, select group of genes (251). Such comparisons are often made between biofilm preparations and planktonic cultures.…”

“…The formation of C. albicans biofilms in in vitro models must be regulated by an underlying developmental program involving cellular differentiation, the divergence of cellular phenotypes, complex cell-cell interactions, and signaling that changes with time. Time-dependent changes during biofilm formation have been demonstrated for gene expression (244)(245)(246)(247)292), cellular phenotype (168,179,183,184), architecture (183,184), and the deposition of ECM (293)(294)(295)(296). Hence, by definition, there is an ordered sequence of dependent events, and in some cases parallel pathways, with a time table, in complex developmental programs (297).…”

Assessment and Optimizations of Candida albicans In Vitro Biofilm Assays

“…For example, in vitro assays have been used to screen large mutant libraries to identify the genes required for biofilm formation. The findings from these assays were then verified using in vivo models (13)(14)(15)(16)(17)(18)(19)(20)(21). Likewise, in vitro assays have been used as the initial step to identify compounds that inhibit and/or disrupt biofilm formation before the compounds are tested for toxicity in cell culture and in in vivo models (22)(23)(24)(25).…”