scholarly journals Candida albicansdispersed cells signify a developmental state distinct from biofilm and planktonic phases

2018 ◽  
Author(s):  
Priya Uppuluri ◽  
Maikel Acosta Zaldivar ◽  
Matthew Z Anderson ◽  
Matthew J. Dunn ◽  
Judith Berman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Carbon Sources ◽  
Developmental State ◽  
Yeast Cells ◽  
Direct Access ◽  
Biofilm Model ◽  
Definition Of ◽  
Biofilm Development ◽  
External Signals ◽  
Dispersed Cells

AbstractCandida albicanssurface-attached biofilms are sites of amplification of an infection through continuous discharge of cells capable of initiating new infectious foci. Yeast cells released from biofilms on intravenous catheters have direct access to the bloodstream. We previously reported that dispersed cells are largely lateral yeast cells that originate from the hyphal layers of the biofilm. Compared to their planktonic counterparts, these biofilm-dispersed yeast cells displayed enhanced virulence-associated gene expression and drug resistance. Little is known about the molecular properties of dispersed cells. We found that the inducer of dispersal,PES1, genetically interacts with the repressor of filamentation,NRG1, in a manner that supports a genetic definition of dispersed cells as yeast. We combined a flow biofilm model with RNA sequencing technology, to identify transcriptomic characteristics of freshly dispersed yeast cells versus biofilms or age-matched planktonic yeast cells growing in glucose-rich medium. Dispersed cells largely inherited a biofilm-like mRNA profile but with one stark difference: dispersed cells were transcriptionally reprogrammed to metabolize alternative carbon sources, while their sessile parents expressed glycolytic genes, despite exposure to the same nutritional signals. Our studies hence define dispersal cell production as an intrinsic step of biofilm development which generates propagules capable of colonizing distant host sites. This developmental step anticipates the need for virulence-associated gene expression before experiencing the associated external signals.

scholarly journals Candida albicansDispersed Cells Are Developmentally Distinct from Biofilm and Planktonic Cells

mBio ◽  
2018 ◽  
Vol 9 (4) ◽  
Author(s):  
Priya Uppuluri ◽  
Maikel Acosta Zaldívar ◽  
Matthew Z. Anderson ◽  
Matthew J. Dunn ◽  
Judith Berman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Candida Albicans ◽  
Carbon Sources ◽  
Yeast Cells ◽  
Direct Access ◽  
Molecular Characteristics ◽  
Content Type ◽  
Biofilm Dispersal ◽  
Biofilm Development ◽  
Dispersed Cells

ABSTRACTCandida albicanssurface-attached biofilms such as those formed on intravenous catheters with direct access to the bloodstream often serve as a nidus for continuous release of cells capable of initiating new infectious foci. We previously reported that cells dispersed from a biofilm are yeast cells that originate from the top-most hyphal layers of the biofilm. Compared to their planktonic counterparts, these biofilm dispersal yeast cells displayed enhanced virulence-associated characteristics and drug resistance. However, little is known about their molecular properties. To address that issue, in this study we aimed to define the molecular characteristics of these biofilm dispersal cells. We found that the inducer of dispersal,PES1, genetically interacts with the repressor of filamentation,NRG1, in a manner consistent with the definition of dispersed cells as yeast cells. Further, using a flow biofilm model, we performed comprehensive comparative RNA sequencing on freshly dispersed cells in order to identify unique transcriptomic characteristics. Gene expression analysis demonstrated that dispersed cells largely inherit a biofilm-like mRNA profile. Strikingly, however, dispersed cells seemed transcriptionally reprogrammed to acquire nutrients such as zinc and amino acids and to metabolize alternative carbon sources, while their biofilm-associated parent cells did not induce the same high-affinity transporters or express gluconeogenetic genes, despite exposure to the same nutritional signals. Collectively, the findings from this study characterize cell dispersal as an intrinsic step of biofilm development which generates propagules more adept at colonizing distant host sites. This developmental step anticipates the need for virulence-associated gene expression before the cells experience the associated external signals.IMPORTANCECandida albicanssurface-attached biofilms serve as a reservoir of cells to perpetuate and expand an infection; cells released from biofilms on catheters have direct access to the bloodstream. Biofilm dispersal yeast cells exhibit enhanced adhesion, invasion, and biofilm formation compared to their planktonic counterparts. Here, we show using transcriptome sequencing (RNA-seq) that dispersed yeast cells are developmentally distinct from the cells in their parent biofilms as well as from planktonic yeast cells. Dispersal cells possess an anticipatory expression pattern that primes them to infect new sites in the host, to survive in nutrient-starved niches, and to invade new sites. These studies identified dispersal cells as a unique proliferative cell type of the biofilm and showed that they could serve as targets for antibiofilm drug development in the future.

scholarly journals Effect of overexpression of SNF1 on the transcriptional and metabolic landscape of baker’s yeast under freezing stress

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Lu Meng ◽  
Xu Yang ◽  
Xue Lin ◽  
Huan-Yuan Jiang ◽  
Xiao-Ping Hu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Kinase ◽  
Cellular Response ◽  
Carbon Sources ◽  
Cell Activity ◽  
Baker’S Yeast ◽  
Yeast Cells ◽  
Freezing Stress ◽  
Baker's Yeast ◽  
Cell Tolerance

Abstract Background Freezing stress is the key factor that affecting the cell activity and fermentation performance of baker’s yeast in frozen dough production. Generally, cells protect themselves from injury and maintain metabolism by regulating gene expression and modulating metabolic patterns in stresses. The Snf1 protein kinase is an important regulator of yeast in response to stresses. In this study, we aim to study the role of the catalytic subunit of Snf1 protein kinase in the cell tolerance and dough leavening ability of baker’s yeast during freezing. Furthermore, the effects of SNF1 overexpression on the global gene expression and metabolite profile of baker’s yeast before and after freezing were analysed using RNA-sequencing and untargeted UPLC − QTOF-MS/MS, respectively. Results The results suggest that overexpression of SNF1 was effective in enhancing the cell tolerance and fermentation capacity of baker’s yeast in freezing, which may be related to the upregulated proteasome, altered metabolism of carbon sources and protectant molecules, and changed cell membrane components. SNF1 overexpression altered the level of leucin, proline, serine, isoleucine, arginine, homocitrulline, glycerol, palmitic acid, lysophosphatidylcholine (LysoPC), and lysophosphatidylethanolamine (LysoPE) before freezing, conferring cells resistance in freezing. After freezing, relative high level of proline, lysine, and glycerol maintained by SNF1 overexpression with increased content of LysoPC and LysoPE. Conclusions This study will increase the knowledge of the cellular response of baker’s yeast cells to freezing and provide new opportunities for the breeding of low-temperature resistant strains.

scholarly journals Characterization of Nutrient-Induced Dispersion in Pseudomonas aeruginosa PAO1 Biofilm

2004 ◽  
Vol 186 (21) ◽  
pp. 7312-7326 ◽  
Author(s):  
K. Sauer ◽  
M. C. Cullen ◽  
A. H. Rickard ◽  
L. A. H. Zeef ◽  
D. G. Davies ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pseudomonas Aeruginosa ◽  
Ribosomal Proteins ◽  
Carbon Sources ◽  
Gene Families ◽  
Carbon Substrate ◽  
Sudden Increase ◽  
Proteomic Data ◽  
Genes Encoding ◽  
Dispersed Cells

ABSTRACT The processes associated with early events in biofilm formation have become a major research focus over the past several years. Events associated with dispersion of cells from late stage biofilms have, however, received little attention. We demonstrate here that dispersal of Pseudomonas aeruginosa PAO1 from biofilms is inducible by a sudden increase in carbon substrate availability. Most efficient at inducing dispersal were sudden increases in availability of succinate > glutamate > glucose that led to ∼80% reductions in surface-associated biofilm biomass. Nutrient-induced biofilm dispersion was associated with increased expression of flagella (fliC) and correspondingly decreased expression of pilus (pilA) genes in dispersed cells. Changes in gene expression associated with dispersion of P. aeruginosa biofilms were studied by using DNA microarray technology. Results corroborated proteomic data that showed gene expression to be markedly different between biofilms and newly dispersed cells. Gene families that were upregulated in dispersed cells included those for flagellar and ribosomal proteins, kinases, and phage PF1. Within the biofilm, genes encoding a number of denitrification pathways and pilus biosynthesis were also upregulated. Interestingly, nutrient-induced dispersion was associated with an increase in the number of Ser/Thr-phosphorylated proteins within the newly dispersed cells, and inhibition of dephosphorylation reduced the extent of nutrient-induced dispersion. This study is the first to demonstrate that dispersal of P. aeruginosa from biofilms can be induced by the addition of simple carbon sources. This study is also the first to demonstrate that dispersal of P. aeruginosa correlates with a specific dispersal phenotype.

scholarly journals The carbon source-dependent pattern of antimicrobial activity and gene expression in Pseudomonas donghuensis P482

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Marta Matuszewska ◽  
Tomasz Maciąg ◽  
Magdalena Rajewska ◽  
Aldona Wierzbicka ◽  
Sylwia Jafra
Keyword(s):  
Gene Expression ◽  
Antimicrobial Activity ◽  
Carbon Source ◽  
Reference Genes ◽  
Plant Pathogens ◽  
Plant Protection ◽  
Carbon Sources ◽  
Unknown Compound ◽  
Fungal Plant Pathogens ◽  
The Impact

AbstractPseudomonas donghuensis P482 is a tomato rhizosphere isolate with the ability to inhibit growth of bacterial and fungal plant pathogens. Herein, we analysed the impact of the carbon source on the antibacterial activity of P482 and expression of the selected genes of three genomic regions in the P482 genome. These regions are involved in the synthesis of pyoverdine, 7-hydroxytropolone (7-HT) and an unknown compound (“cluster 17”) and are responsible for the antimicrobial activity of P482. We showed that the P482 mutants, defective in these regions, show variations and contrasting patterns of growth inhibition of the target pathogen under given nutritional conditions (with glucose or glycerol as a carbon source). We also selected and validated the reference genes for gene expression studies in P. donghuensis P482. Amongst ten candidate genes, we found gyrB, rpoD and mrdA the most stably expressed. Using selected reference genes in RT-qPCR, we assessed the expression of the genes of interest under minimal medium conditions with glucose or glycerol as carbon sources. Glycerol was shown to negatively affect the expression of genes necessary for 7-HT synthesis. The significance of this finding in the light of the role of nutrient (carbon) availability in biological plant protection is discussed.

scholarly journals In Vitro Anti-Biofilm and Antibacterial Properties of Streptococcus downii sp. nov.

2021 ◽  
Vol 9 (2) ◽  
pp. 450
Author(s):  
Maigualida Cuenca ◽  
María Carmen Sánchez ◽  
Pedro Diz ◽  
Lucía Martínez-Lamas ◽  
Maximiliano Álvarez ◽  
...  
Keyword(s):  
Antibacterial Activity ◽  
Quantitative Polymerase Chain Reaction ◽  
Bacterial Load ◽  
Antibacterial Properties ◽  
Antibacterial Activities ◽  
Oral Bacteria ◽  
Periodontal Pathogens ◽  
Biofilm Model ◽  
Biofilm Development

The aim of this study was to evaluate the potential anti-biofilm and antibacterial activities of Streptococcus downii sp. nov. To test anti-biofilm properties, Streptococcus mutans, Actinomyces naeslundii, Veillonella parvula, Fusobacterium nucleatum, Porphyromonas gingivalis, and Aggregatibacter actinomycetemcomitans were grown in a biofilm model in the presence or not of S. downii sp. nov. for up to 120 h. For the potential antibacterial activity, 24 h-biofilms were exposed to S. downii sp. nov for 24 and 48 h. Biofilms structures and bacterial viability were studied by microscopy, and the effect in bacterial load by quantitative polymerase chain reaction. A generalized linear model was constructed, and results were considered as statistically significant at p < 0.05. The presence of S. downii sp. nov. during biofilm development did not affect the structure of the community, but an anti-biofilm effect against S. mutans was observed (p < 0.001, after 96 and 120 h). For antibacterial activity, after 24 h of exposure to S. downii sp. nov., counts of S. mutans (p = 0.019) and A. actinomycetemcomitans (p = 0.020) were significantly reduced in well-structured biofilms. Although moderate, anti-biofilm and antibacterial activities of S. downii sp. nov. against oral bacteria, including some periodontal pathogens, were demonstrated in an in vitro biofilm model.

scholarly journals Screening and Genetic Network Analysis of Genes Involved in Freezing and Thawing Resistance in DaMDHAR—Expressing Saccharomyces cerevisiae Using Gene Expression Profiling

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 219
Author(s):  
Il-Sup Kim ◽  
Woong Choi ◽  
Jonghyeon Son ◽  
Jun Hyuck Lee ◽  
Hyoungseok Lee ◽  
...  
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Transcription Factors ◽  
Stress Tolerance ◽  
Genetic Network ◽  
Yeast Cells ◽  
Enzymatic Antioxidants ◽  
Freezing And Thawing ◽  
Metal Ion Homeostasis ◽  
Transgenic Yeast

The cryoprotection of cell activity is a key determinant in frozen-dough technology. Although several factors that contribute to freezing tolerance have been reported, the mechanism underlying the manner in which yeast cells respond to freezing and thawing (FT) stress is not well established. Therefore, the present study demonstrated the relationship between DaMDHAR encoding monodehydroascorbate reductase from Antarctic hairgrass Deschampsia antarctica and stress tolerance to repeated FT cycles (FT2) in transgenic yeast Saccharomyces cerevisiae. DaMDHAR-expressing yeast (DM) cells identified by immunoblotting analysis showed high tolerance to FT stress conditions, thereby causing lower damage for yeast cells than wild-type (WT) cells with empty vector alone. To detect FT2 tolerance-associated genes, 3′-quant RNA sequencing was employed using mRNA isolated from DM and WT cells exposed to FT (FT2) conditions. Approximately 332 genes showed ≥2-fold changes in DM cells and were classified into various groups according to their gene expression. The expressions of the changed genes were further confirmed using western blot analysis and biochemical assay. The upregulated expression of 197 genes was associated with pentose phosphate pathway, NADP metabolic process, metal ion homeostasis, sulfate assimilation, β-alanine metabolism, glycerol synthesis, and integral component of mitochondrial and plasma membrane (PM) in DM cells under FT2 stress, whereas the expression of the remaining 135 genes was partially related to protein processing, selenocompound metabolism, cell cycle arrest, oxidative phosphorylation, and α-glucoside transport under the same condition. With regard to transcription factors in DM cells, MSN4 and CIN5 were activated, but MSN2 and MGA1 were not. Regarding antioxidant systems and protein kinases in DM cells under FT stress, CTT1, GTO, GEX1, and YOL024W were upregulated, whereas AIF1, COX2, and TRX3 were not. Gene activation represented by transcription factors and enzymatic antioxidants appears to be associated with FT2-stress tolerance in transgenic yeast cells. RCK1, MET14, and SIP18, but not YPK2, have been known to be involved in the protein kinase-mediated signalling pathway and glycogen synthesis. Moreover, SPI18 and HSP12 encoding hydrophilin in the PM were detected. Therefore, it was concluded that the genetic network via the change of gene expression levels of multiple genes contributing to the stabilization and functionality of the mitochondria and PM, not of a single gene, might be the crucial determinant for FT tolerance in DaMDAHR-expressing transgenic yeast. These findings provide a foundation for elucidating the DaMDHAR-dependent molecular mechanism of the complex functional resistance in the cellular response to FT stress.

Gene insulation. Part II: natural strategies in vertebrates

2010 ◽  
Vol 88 (6) ◽  
pp. 885-898 ◽  
Author(s):  
Michèle Amouyal
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Protein Interactions ◽  
Dna Looping ◽  
Chromatin Domain ◽  
Trna Genes ◽  
Binding Factor ◽  
Genomic Environment ◽  
Nuclear Structures ◽  
Definition Of

The way a gene is insulated from its genomic environment in vertebrates is not basically different from what is observed in yeast and Drosophila (preceding article in this issue). If the formation of a looped chromatin domain, whether generated by attachment to the nuclear matrix or not, has become a classic way to confine an enhancer to a specific genomic domain and to coordinate, sequentially or simultaneously, gene expression in a given program, its role has been extended to new networks of genes or regulators within the same gene. A wider definition of the bases of the chromatin loops (nonchromosomal nuclear structures or genomic interacting elements) is also available. However, whereas insulation in Drosophila is due to a variety of proteins, in vertebrates insulators are still practically limited to CTCF (the CCCTC-binding factor), which appears in all cases to be the linchpin of an architecture that structures the assembly of DNA–protein interactions for gene regulation. As in yeast and Drosophila, the economy of means is the rule and the same unexpected diversion of known transcription elements (active or poised RNA polymerases, TFIIIC elements out of tRNA genes, permanent histone replacement) is observed, with variants peculiar to CTCF. Thus, besides structuring DNA looping, CTCF is a barrier to DNA methylation or interferes with all sorts of transcription processes, such as that generating heterochromatin.

Identification of ferrichrome- and ferrioxamine B-mediated iron uptake by Aspergillus fumigatus

2016 ◽  
Vol 473 (9) ◽  
pp. 1203-1213 ◽  
Author(s):  
Yong-Sung Park ◽  
Ju-Yeon Kim ◽  
Cheol-Won Yun
Keyword(s):  
Gene Expression ◽  
Plasma Membrane ◽  
Aspergillus Fumigatus ◽  
Virulence Factors ◽  
Membrane Transporters ◽  
Yeast Cells ◽  
Double Deletion ◽  
Ferrioxamine B ◽  
Uptake Activity ◽  
Opportunistic Fungal Pathogen

Aspergillus fumigatus is an opportunistic fungal pathogen for immunocompromised patients, and genes involved in siderophore metabolism have been identified as virulence factors. Recently, we identified the membrane transporters sit1 and sit2, which are putative virulence factors of A. fumigatus; sit1 and sit2 are homologous to yeast Sit1, and sit1 and sit2 gene expression was up-regulated after iron depletion. When expressed heterologously in Saccharomyces cerevisiae, sit1 and sit2 were localized to the plasma membrane; sit1 efficiently complemented ferrichrome (FC) and ferrioxamine B (FOB) uptake in yeast cells, whereas sit2 complemented only FC uptake. Deletion of sit1 resulted in a decrease in FOB and FC uptake, and deletion of sit2 resulted in a decrease in FC uptake in A. fumigatus. It is of interest that a sit1 and sit2 double-deletion mutant resulted in a synergistic decrease in FC uptake activity. Both sit1 and sit2 were localized to the plasma membrane in A. fumigatus. The expression levels of the sit1 and sit2 genes were dependent on hapX under low-but not high-iron conditions. Furthermore, mirB, and sidA gene expression was up-regulated and sreA expression down-regulated when sit1 and sit2 were deleted. Although sit1 and sit2 failed to affect mouse survival rate, these genes affected conidial killing activity. Taken together, our results suggest that sit1 and sit2 are siderophore transporters and putative virulence factors localized to the plasma membrane.

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