Three-Dimensional Encapsulation ofSaccharomyces cerevisiaein Silicate Matrices Creates Distinct Metabolic States as Revealed by Gene Chip Analysis

Abstract

In order to design hybrid cellular/synthetic devices such as sensors and vaccines, it is important to understand how the metabolic state of living cells changes upon physical confinement within three-dimensional (3D) matrices. We analyze the gene expression patterns of stationary phase Saccharomyces cerevisiae (S. cerevisiae) cells encapsulated within three distinct nanostructured silica matrices and relate those patterns to known naturally occurring metabolic states. Silica encapsulation methods employed were lipid-templated mesophase silica thin films formed by cell-directed assembly (CDA), lipid-templated mesophase silica particles formed by spray drying (SD), and glycerol-doped silica gel monoliths prepared from an aqueous silicate (AqS+g) precursor solution. It was found that the cells for all three-encapsulated methods enter quiescent states characteristic of response to stress, albeit to different degrees and with differences in detail. By the measure of enrichment of stress-related gene ontology categories, we find that the AqS+g encapsulation is more amenable to the cells than CDA and SD encapsulation. We hypothesize that this differential response in the AqS+g encapsulation is related to four properties of the encapsulating gel: (1) oxygen permeability, (2) relative softness of the material, (3) development of a protective sheath around individual cells (visible in TEM micrographs vide infra), and (4) the presence of glycerol in the gel, which has been previously noted to serve as a protectant for encapsulated cells and can serve as the sole carbon source for S. cerevisiae under aerobic conditions. This work represents a combination of experiment and analysis aimed at the design and development of 3D encapsulation procedures to induce, and perhaps control, well-defined physiological behaviors.

Genomic Insights Into Sugar Adaptation in an Extremophile Yeast Zygosaccharomyces rouxii

“…Most of the genes involved in "ribosome" in the Z. rouxii response to 60% w/v sugar concentration were downregulated. This response seems to be consistent with other yeasts under different stresses, for example, Zygosaccharomyces parabilii under lactic acid stress (Ortizmerino et al, 2018), Pichia pastoris under methanol stress, and S. cerevisiae response to silicon encapsulation stress (Fazal et al, 2017). For example, ribosomal protein encoding genes, RPS13 and RPL4B, were downregulated after 4 h ( Table 2) of extreme high sugar stress in Z. rouxii.…”

“…It is reported that cell synthesis ribosome requires energy, reducing gene expression associated with ribosome biogenesis and minimizing energy consumption (Fazal et al, 2017). Decreasing "ribosome" seems to be a general stress response in yeast (Fazal et al, 2017).…”

Entrapment of uropathogenic E. coli cells into ultra-thin sol-gel matrices on gold thin films: A low cost alternative for impedimetric bacteria sensing

“…Compared to imprinting into polymers where cross-linkers are needed (Schirhagl et al, 2010), the formation of thin imprinted organosilicate films with good diffusional penetration, important for sensing driven applications, is generally easier to achieve. Since the pioneering studies of Carturan et al (2004) who encapsulated S. cerevisiae yeast cells into silica gel films and studied its catalytic activity, imprinting of whole cells into inorganic sol-gel matrices rather than polymers (Haupt, 2003) has become a widely proposed approach (Avnir et al, 2005;Eleftheriou et al, 2013;Fazal et al, 2017). These matrices have gained more interest lately for the creation of sensing devices (Borovicka et al, 2013;Chen et al, 2016).…”

From Compartmentalization of Bacteria within Inorganic Macrocellular Beads to the Assembly of Microbial Consortia

“…The benefit of the growth in confined space—compared to traditional bacterial growth in liquid or soft‐agar media—cannot be fully exploited, for example, through the control of quorum sensing in confinement . Here, we use a sol–gel process to confine bacteria while maintaining viability, proliferation and metabolic activity . In contrast to a recently reported approach in which a single matrix was used to integrate cascades, we show a modular assembly concept associating beads functionalized with different types of bacteria working in synergy and thereby creating versatile user‐defined artificial microbial consortia .…”