Gene expression and survival changes in <i>Saccharomyces cerevisiae</i> during suspension culture

Johanson, Kelly; Allen, Patricia; González-Villalobos, Romer A.; Baker, Chasity B.; D’Elia, Riccardo V.; Hammond, Timothy G.

doi:10.1002/bit.20810

Cited by 15 publications

(14 citation statements)

References 35 publications

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“…Of these, 513 were up-regulated and 384 were down-regulated); Previous microarray analyses of yeast growing in LSMMG also showed expression changes, although the total number of genes involved was much less than we observed [1,2]. In a related study, Johanson et al [2] identified 140 differentially expressed genes in which a significant number of genes are involved in catalytic activity. Few are the same as genes identified in our experiment.…”

Section: Resultscontrasting

confidence: 43%

“…Cellular responses to the environment are mediated by phenotypic changes ultimately driven by alterations in gene expression, some of which resemble environmental stress responses [1,2]. Microorganisms such as yeast serve as powerful eukaryotic models for experimentally investigating the effects of microgravity.…”

Section: Introductionmentioning

confidence: 99%

“…Our initial examination of gene expression in yeast cells exposed to LSMMG conditions provided some of the first lines of evidence that microgravity influences certain aspects of phenotypic and behavioral traits in yeast [1] and showed that growth in HARVs might be regulated transcriptionally by activation through two promoter elements, one with direct ties to a well-studied signal transduction pathway. Johanson et al [2] expanded the initial gene expression study in S. cerevisiae and identified significant genes with changes in gene expression in response to low-shear conditions [1,2]. …”

Section: Introductionmentioning

confidence: 99%

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Yeast genomic expression patterns in response to low-shear modeled microgravity

et al. 2007

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The low-shear microgravity environment, modeled by rotating suspension culture bioreactors called high aspect ratio vessels (HARVs), allows investigation in ground-based studies of the effects of microgravity on eukaryotic cells and provides insights into the impact of space flight on cellular physiology. We have previously demonstrated that low-shear modeled microgravity (LSMMG) causes significant phenotypic changes of a select group of Saccharomyces cerevisiae genes associated with the establishment of cell polarity, bipolar budding, and cell separation. However, the mechanisms cells utilize to sense and respond to microgravity and the fundamental gene expression changes that occur are largely unknown. In this study, we examined the global transcriptional response of yeast cells grown under LSMMG conditions using DNA microarray analysis in order to determine if exposure to LSMMG results in changes in gene expression.Results: LSMMG differentially changed the expression of a significant number of genes (1372) when yeast cells were cultured for either five generations or twenty-five generations in HARVs, as compared to cells grown under identical conditions in normal gravity. We identified genes in cell wall integrity signaling pathways containing MAP kinase cascades that may provide clues to novel physiological responses of eukaryotic cells to the external stress of a low-shear modeled microgravity environment. A comparison of the microgravity response to other environmental stress response (ESR) genes showed that 26% of the genes that respond significantly to LSMMG are involved in a general environmental stress response, while 74% of the genes may represent a unique transcriptional response to microgravity. In addition, we found changes in genes involved in budding, cell polarity establishment, and cell separation that validate our hypothesis that phenotypic changes observed in cells grown in microgravity are reflected in genome-wide changes.This study documents a considerable response to yeast cell growth in low-shear modeled microgravity that is evident, at least in part, by changes in gene expression. Notably, we identified genes that are involved in cell signaling pathways that allow cells to detect environmental changes, to respond within the cell, and to change accordingly, as well as genes of unknown function that may have a unique transcriptional response to microgravity. We also uncovered significant changes in the expression of many genes involved in cell polarization and bud formation that correlate well with the phenotypic effects observed in yeast cells when grown under similar conditions. These results are noteworthy as they have implications for human space flight.

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Section: Resultscontrasting

confidence: 43%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Yeast genomic expression patterns in response to low-shear modeled microgravity

et al. 2007

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“…One such bioreactor named as high-aspect-ratio vessel (HARV, Synthecon) [3] was used in this study. The HARV employed for cell suspension culture and tissue growth permits cell growth in suspension and minimizes the fluid shear levels encountered by cells [1], [4]. When the cell culture vessel rotates, microbial cells do not settle down but revolve around a horizontal axis and continuously fall through the fluid at 1×g terminal velocity condition, which lead to 1∼2×10 −2 gravity environment [5].…”

Section: Introductionmentioning

confidence: 99%

Transcriptional Profiling of Protein Expression Related Genes of Pichia pastoris under Simulated Microgravity

Wang

et al. 2011

PLoS ONE

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The physiological responses and transcription profiling of Pichia pastoris GS115 to simulated microgravity (SMG) were substantially changed compared with normal gravity (NG) control. We previously reported that the recombinant P. pastoris grew faster under SMG than NG during methanol induction phase and the efficiencies of recombinant enzyme production and secretion were enhanced under SMG, which was considered as the consequence of changed transcriptional levels of some key genes. In this work, transcriptiome profiling of P. pastoris cultured under SMG and NG conditions at exponential and stationary phases were determined using next-generation sequencing (NGS) technologies. Four categories of 141 genes function as methanol utilization, protein chaperone, RNA polymerase and protein transportation or secretion classified according to Gene Ontology (GO) were chosen to be analyzed on the basis of NGS results. And 80 significantly changed genes were weighted and estimated by Cluster 3.0. It was found that most genes of methanol metabolism (85% of 20 genes) and protein transportation or secretion (82.2% of 45 genes) were significantly up-regulated under SMG. Furthermore the quantity and fold change of up-regulated genes in exponential phase of each category were higher than those of stationary phase. The results indicate that the up-regulated genes of methanol metabolism and protein transportation or secretion mainly contribute to enhanced production and secretion of the recombinant protein under SMG.

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“…In addition to anchorage-dependent cells, the gene expression of the budding yeast, Saccharomyces cerevisiae, is affected by shear stress. [23] It is therefore desirable to take shear damage into account when designing and fabricating microchannel or bioreactor. [7] This Communication addresses a method of forming bottleshaped, hollow polymeric microstructures inside a microfluidic channel for potential shear-protecting cell reservoirs.…”

mentioning

confidence: 99%

Fabrication of Hollow Polymeric Microstructures for Shear‐Protecting Cell‐Containers

et al. 2008

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Microfluidic systems have played a major role in the development of high-throughput cell screening, biological analysis, cell-based biosensors, and tissue engineering because they offer miniaturized systems with reduced use of reagents, short reaction times, increased speed of analysis, potential for parallel operation, and precise control/monitoring of cellular behavior. [1][2][3][4][5] In cell-based microfluidic devices, it is important to capture living cells in predefined locations of the microfluidic channel.[6] In addition, continuous nutrition, oxygen supply, and waste removal through the culture medium must be ensured for long-term cell culture. [7,8] Previous studies have demonstrated immobilization of anchorage-dependent cells within particular regions of a microfluidic channel by utilizing laminar flow, [9,10] prepatterned ligands, [11] addressable microfluidic networks, [12] cell-encapsulating hydrogels, [13][14][15][16] or engraved microwells. [17][18][19] Despite the success of these approaches, there are still potential limitations that restrict the widespread use of these techniques. For example, the patterned regions are restricted to the flow of a laminar stream in laminar flow patterning, while the cell encapsulation inside hydrogels is usually irreversible and compromises cell viability owing to exposure to a toxic photoinitiator and radiation. Cell docking into microwells by exploiting stationary conditions (sedimentation) or a receding meniscus is also an attractive strategy for shear protection because of its simplicity and low-expertise requirements. However, the cells can be flooded in a subsequent analysis and damaged by a laminarly flowing stream, resulting in shear-induced alteration in cell behavior.A critical factor for proper functioning of cell-based microdevices is the minimization of shear stress from a medium flow. [6,8] In microchannels, the medium flows over the adhered or suspending cells while markedly influencing cell growth, cellular function, and viability regardless of the cell type. [20][21][22] This is because hydrodynamic forces acting on the cell surface induce cell deformation and decrease in cell-substrate interactions (for anchorage-dependent cells), thus affecting cellular viability, function, and gene expression. In addition to anchorage-dependent cells, the gene expression of the budding yeast, Saccharomyces cerevisiae, is affected by shear stress.[23]It is therefore desirable to take shear damage into account when designing and fabricating microchannel or bioreactor. [7] This Communication addresses a method of forming bottleshaped, hollow polymeric microstructures inside a microfluidic channel for potential shear-protecting cell reservoirs. In particular, the geometry of the cell container was tailored such that the width of the neck is narrower than that of the bottom, capable of offering diffusive mass transport and stable, noninvasive microenvironment against shear stress. Using these hollow structures as cell-docking containers, yeast cells were captured ...

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Gene expression and survival changes in Saccharomyces cerevisiae during suspension culture

Cited by 15 publications

References 35 publications

Yeast genomic expression patterns in response to low-shear modeled microgravity

Yeast genomic expression patterns in response to low-shear modeled microgravity

Transcriptional Profiling of Protein Expression Related Genes of Pichia pastoris under Simulated Microgravity

Fabrication of Hollow Polymeric Microstructures for Shear‐Protecting Cell‐Containers

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