Remodeling of the Streptococcus agalactiae transcriptome in response to growth temperature
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ABSTRACT:
ORGANISM(S): Streptococcus agalactiae
PROVIDER: GSE11666 | GEO | 2008/09/01
SECONDARY ACCESSION(S): PRJNA106181
REPOSITORIES: GEO
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Project description:To understand the extent to which GBS modify gene expression in response to temperatures encountered in the various hosts, we conducted a whole genome transcriptome analysis of organisms grown at 30°C and 40°C. We identified extensive transcriptome remodeling at various stages of growth, especially in the stationary phase (significant transcript changes occurred for 25% of the genes). A large proportion of genes involved in metabolism was up-regulated at 30°C in stationary phase, which reflects a slowing of bacterial metabolism in the early stages of its shift to growth at lower temperature followed by an acceleration in the later stages. Conversely, genes up-regulated at 40°C relative to 30°C include those encoding virulence factors such as hemolysins and extracellular secreted proteins with LPXTG motifs. Over-expression of hemolysins was linked to larger zones of hemolysis and enhanced hemolytic activity at 40°C. A key theme identified by our study was that genes involved in purine metabolism and iron acquisition were significantly up-regulated at 40°C. Three cultures of GBS grown in rich Todd-Hewitt Yeast extract medium at 30°C and three cultures grown at 40°C served as a source of RNA samples collected at mid-logarithmic phase, late-logarithmic phase, and stationary growth phase. RNA was isolated using a modified Trizol method, and targets for hybridization with custom Affymetrix chip were generated as we have described previously. Genes with 30°C/40°C ratio greater than 2 and less than 0.5 (P value less than 0.05), were considered differentially expressed.
2008-09-01 | E-GEOD-11666 | biostudies-arrayexpress
Project description:In this study we report that B. melitensis at the late logarithmic phase of growth are more invasive for HeLa cells than at mid logarithmic or stationary growth phases. Microarray analysis of B. melitensis gene expression identified 414 up- and 40 down-regulated genes in late-log growth phase compared to the stationary growth phase. The vast majority of the up-regulated genes in late-log cultures were those associated with DNA replication, transcription and translation, intermediate metabolism, energy production and conversion, membrane transport and cell envelope, biogenesis and outer membrane, while the down-regulated genes were distributed among several functional categories. This first Brucella global gene expression study provides novel information on growth phase-specific gene regulation important not only for understanding Brucella physiology but also the initial molecular interactions between Brucella and its host. Keywords: Comparison bacterial growth phase normalized to genomic DNA
2009-05-14 | GSE11192 | GEO
Project description:Gene expression profiles of bakerâs yeast during initial dough-fermentation were investigated using liquid fermentation media to obtain insights at the molecular level into rapid adaptation mechanisms of bakerâs yeast. Results showed that onset of fermentation caused drastic changes in gene expression profiles within 15 min. Genes involved in the tricarboxylic acid (TCA) cycle were down-regulated and genes involved in glycolysis were up-regulated, indicating a metabolic shift from respiration to fermentation. Genes involved in ethanol production (PDC genes and ADH1), in glycerol synthesis (GPD1 and HOR2), and in low-affinity hexose transporters (HXT1 and HXT3) were up-regulated at the beginning of model dough-fermentation. Among genes up-regulated at 15 min, several genes classified as transcription were down-regulated within 30 min. These down-regulated genes are involved in messenger RNA splicing and ribosomal protein biogenesis, in zinc finger transcription factor proteins, and in transcriptional regulator (SRB8, MIG1). In contrast, genes involved in amino acid metabolism and in vitamin metabolism, such as arginine biosynthesis, riboflavin biosynthesis, and thiamin biosynthesis, were subsequently up-regulated after 30 min. Interestingly, the genes involved in the unfolded protein response (UPR) pathway were also subsequently up-regulated. Our study presents the first overall description of the transcriptional response of bakerâs yeast during dough-fermentation, and will thus help clarify genomic responses to various stresses during commercial fermentation processes. Experiment Overall Design: Saccharomyces cerevisiae T128 was used as a model of typical commercial bakerâs yeast used in Japan. After 18 h cultivation, cells in stationary phase were collected by centrifugation (2,700 ï g for 5 min). Some of the cell pellets were suspended in 900 ml of sterilized water. Cells for no-fermentation control were harvested after the fed-butch cultivation and stored until RNA extraction. Cell pellets (11,700 OD units) were suspended in 390 ml of lequid fermentation (LF) medium in a 500-ml flask and then fermented for 300 min. To investigate gene expression profiles during initial stages of dough-fermentation, cell samples for DNA microarray analysis were obtained from each culture medium at 15 min, 30 min, and 60 min. Cells in stationary phase were then collected by centrifugation (2,700ï g for 5 min), and stored until RNA extraction.
2008-06-12 | E-GEOD-3043 | biostudies-arrayexpress
Project description:In the present investigation, we conducted a bacterial transcriptome dynamics analysis during GBS incubation with human blood. We observed large modification in the expression of numerous genes, but GBS transcriptome was different with the blood of one donor. More genes were up-regulated and less down-regulated in respect to the other donors. The serotype III GBS reference strain NEM316 was cultivated in Todd Hewitt broth supplemented with 0.2% yeast extract (THY) in 5% CO2 at 37°C until OD reached 0.7. Culture was harvested by centrifugation 8 minutes at 4000 x g at 37°C, then suspended in phosphate-buffered saline (PBS). Fresh heparinized human blood was obtained from one healthy volunteer in accordance with a protocol approved by the Institutional Review Board of the Methodist Hospital Research Institute. The blood was maintained at 37°C no more than one hour prior to use. Bacterial suspension was then incubated with theblood at 37°C and 40°C under slight rotation to avoid sedimentation of blood and bacterial cells. Samples were removed for microarrays analysis immediately after adding bacteria, and after 30 and 90 minutes of incubation. Thus, we obtained results for five time points: immediately after mixing the bacterium with the blood (time 0), after 30 minutes of contact with blood (time 1) at 37°C and 40°C, and after after 90 minutes of contact with blood (time 1) at 37°C and 40°C.
2009-06-01 | E-GEOD-12201 | biostudies-arrayexpress
Project description:In the present investigation, we conducted a bacterial transcriptome dynamics analysis during GBS incubation with human blood. We observed a large modification in the expression of genes involved in transcriptional regulation and in the metabolism of carbohydrates, purins/pyrimidins and inorganic ions, and an up-regulation of genes involved in attachment and plasminogen contact. We also observed differences in the expression of GBS genes in blood at 40° relative to 37°C.
2008-11-01 | GSE11705 | GEO
Project description:In the present investigation, we conducted a bacterial transcriptome dynamics analysis during GBS incubation with human blood. We observed a large modification in the expression of genes involved in transcriptional regulation and in the metabolism of carbohydrates, purins/pyrimidins and inorganic ions, and an up-regulation of genes involved in attachment and plasminogen contact. We also observed differences in the expression of GBS genes in blood at 40° relative to 37°C. The serotype III GBS reference strain NEM316 was cultivated in Todd Hewitt broth supplemented with 0.2% yeast extract (THY) in 5% CO2 at 37°C until OD reached 0.7. Culture was harvested by centrifugation 8 minutes at 4000 x g at 37°C, then suspended in phosphate-buffered saline (PBS). Fresh heparinized human blood was obtained from seven healthy voluntary donors (four males and three females) in accordance with a protocol approved by the Institutional Review Board of the Methodist Hospital Research Institute. The blood was maintained at 37°C no more than one hour prior to use. Bacterial suspension was then incubated with the blood of each donor at 37°C and 40°C under slight rotation to avoid sedimentation of blood and bacterial cells (the volume of blood was equivalent to the volume of bacterial culture prior to centrifugation). Samples were removed for microarrays analysis immediately after adding bacteria, and after 30 and 90 minutes of incubation. Thus, for each of the seven blood donors, we obtained results for five time points: immediately after mixing the bacterium with the blood (time 0), after 30 minutes of contact with blood (time 1) at 37°C and 40°C, and after 90 minutes of contact with blood (time 2) at 37°C and 40°C.
2008-10-31 | E-GEOD-11705 | biostudies-arrayexpress
Project description:Cotton (Gossypium hirsutum L.) is one of the most important cash crops worldwide. In semi-arid/arid regions, drought stress causes growth limitation and decrease of yield. Of all the organs of a plant, fine root is the central part consisting of the root system to contribute to plant water and nutrient taken up. However, the research on the molecular mechanism underlying fine root response to soil drought has not been well understood in cotton. To better characterize the proteomic changes of cotton fine roots under drought stress, 70±5% and 40±5% soil relative water content were designed as control (CK) and drought stress (DS) groups, respectively. Tandem mass tags (TMT) technology was used to determine the proteome profiles in fine roots. The proteomic differences between CK and DS were pairwise compared at 0, 30, and 45 days after drought stress (DAD). A total of 11,628 proteins were identified, of which 10,344 proteins contained quantitative information. According to the morphological, physiological, and biochemical characteristics, 30 and 45 DAD were selected as critical stages for further analysis. Results showed that 118 differentially expressed proteins (DEPs) were up-regulated and 105 down-regulated in DS 30 versus CK 30; 662 DEPs were up-regulated, and 611 were down-regulated in DS 45 versus CK 45. The DEP functions were determined for their classified pathways, mainly associated with carbohydrate metabolism, energy metabolism, fatty acid metabolism, amino acid metabolism, and secondary metabolite biosynthesis. DEPs related to phytohormone and stress/defense response were also identified. To verify the accuracy of the TMT results, 20 DEPs were randomly selected for parallel reaction monitoring (PRM) verification. And results showed that the quantitative results of TMT are consistent with those of PRM, which proved that the TMT results of this study are reliable. In this article we describe changes in the protein profiles occurring in response to drought stress in cotton fine roots. Proteomic analyses of plant responses to stressors could lead to the introduction of cotton cultivars with high resistance to drought stress. Such plants would be valuable for high yielding under drought as well as other unfavorable environmental conditions.
2020-06-24 | PXD017736 | Pride
Project description:In this study we report that B. melitensis at the late logarithmic phase of growth are more invasive for HeLa cells than at mid logarithmic or stationary growth phases. Microarray analysis of B. melitensis gene expression identified 414 up- and 40 down-regulated genes in late-log growth phase compared to the stationary growth phase. The vast majority of the up-regulated genes in late-log cultures were those associated with DNA replication, transcription and translation, intermediate metabolism, energy production and conversion, membrane transport and cell envelope, biogenesis and outer membrane, while the down-regulated genes were distributed among several functional categories. This first Brucella global gene expression study provides novel information on growth phase-specific gene regulation important not only for understanding Brucella physiology but also the initial molecular interactions between Brucella and its host. Keywords: Comparison bacterial growth phase normalized to genomic DNA There are two kind of samples consisting of RNA isolated from Brucella melitensis grown logarithmically or at stationary phase. There are four biological replicates of each sample. Every Brucella melitensis open reading frame was printed in triplicate on each microarray, thereby providing three technical replicates for each biological replicates. Each replicate was normalized against labeled Brucella melitensis genomic DNA.
2010-05-19 | E-GEOD-11192 | biostudies-arrayexpress
Project description:Naturally bacteria are commonly forced to remain in stationary phase. There is no increase in cell mass, however, cell division keep on. Vibrio (V.) parahaemolyticus is an aquatic bacterium capable of causing foodborne gastroenteritis outbreaks all over the world. So far, little is known about whole genomic expression of V. parahaemolyticus in the early stationary phase compared with the phase of exponential growth. Since under starvation cell sizes decrease and endogenous metabolism reduces, genes are considered to be highly repressed in the stationary phase. However, our data shows in total 172 induced genes, while 61 genes were repressed in the early stationary phase compared with exponential phase. In fatty acid and phospholipid metabolism functional category only induced genes were found, whereas in three other metabolic functional groups appeared no significant up-regulated genes (adjusted P-value<0.05). Genes in two metabolic functional categories remained stable in the early stationary phase. DAVID analyses were carried out exploring the gene regulation. In total, ten functional categories showed a total up-regulation in early stationary phase, while only three metabolic functional categories showed a down-regulation and four categories showed stably in early stationary phase.
2015-01-31 | GSE65448 | GEO
Project description:To identify genes differentially expressed during the molt, we collected RNA 30-40 minutes after feeding cessation at the start of the fourth larval stage (L4) lethargus. Additional time points for RNA collection were in the mid-L4 stage, approximately four hours prior to lethargus, and in the young adult stage, four hours after lethargus. These samples were interrogated with the Affymetrix C. elegans Genome Array. A total of 1,804 gene transcripts were up regulated, and 1,088 gene transcripts were down regulated, during the L4 lethargus period compared to the L4 and Adult stages (false discovery rate (FDR) < 0.05).
2014-04-18 | GSE46289 | GEO