RNA-Seq of Clostridium ljungdahlii with CO as the sources of carbon and energy in exponetial phase against stationary phase
ABSTRACT: More than 5 g/L ethanol was detected at 84 h in the late-exponential phase with 0.1 MPa at pH 6.0 in the batch fermentation of C. ljungdahlii grown autotrophically. Interestingly, ethanol started to be reassimilated in the stationary phase. In order to understand the metabolic flux of ethanol, comparative transcriptome between exponential and stationary phases were performed.
Project description:Clostridium ljungdahlii not only utilizes CO, but also H2 as energy source during autotrophic growth. In theory, CO is a more energetically and thermodynamically favourable energy source than H2 in the gas fermentation of C. ljungdahlii. However, how C. ljungdahlii conserves energy for growth and ethanol/acetate formation grown on CO or CO2/H2 is not in great detail. In this study, C. ljungdahlii was fermented on CO and CO2/ H2 at pH 6.0 with 0.1 MPa gas pressure. C. ljungdahlii produced 27 g/L acetate, 9 g/L ethanol, 8 g/L 2,3-butanediol and traces of lactate in the presence of CO as energy source, while it produced 25.8 0.1 g/L acetate, 1.8 0.1 g/L ethanol, 0.7 0.01g/L 2,3-butanediol and trances of lactate in the same fermentation condition using H2 as energy source. Therefore, comparative transcriptomes between cells grown on CO and cells grown on H2/CO2 were performed to investigate gene expression profiles based on three biological replicates.
Project description:P. tricornutum (Bacillariophyta, Pennatae, NEPCC640) was obtained from the Algal Center of the Institute of Oceanology of the Chinese Academy of Sciences. The cells were cultured in a modified f/2 medium (Guillard, 1975) at 20 +/- 1C, and illuminated with 120 umol photon m-2 s-1 under a 12:12 light: dark cycle. Flasks were shaken by the researchers twice a day at the fixed times. Experiments were conducted in triplicate in 3L sterilized and acid-washed Erlenmeyer flask containing 2L medium. The equipment used in this study is similar to the ones used in previous ocean acidification research (Fu et al., 2007; Hutchins et al., 2007; Wu et al., 2010). Prior to inoculation, the mediums were treated by different CO2 concentrations. The low CO2 medium was bubbled with ambient air of about 400 ppmv (low CO2, LC) and the high CO2 medium was bubbled with pre-mixed air-CO2 mixtures (1000 ppmv; high CO2, HC) from a plant growth CO2 chamber (HP400G-D, Ruihua Instrument & Equipment Ltd, Wuhan, China) with a variation of less than 5%. Semi-continuous cultures were used to maintain the pH stability during P. tricornutum growth in the present study, All the cultures were diluted to 1x104 cells mL-1 with fresh medium and pre-acclimated to the desired CO2 level every 24 h to maintain an exponential growth phase and minimize pH fluctuations of the cells. Cultures were harvested after 8 months of semi-continuous incubation. Significant differences between the carbonate systems in different cultures.
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. Early stationary phase gene expression was detected in total bacterial RNA of V. parahaemolyticus. Two phases (exponential phase and early stationary phase) were used in 8 biological replicates. Gene expression in exponential phase was used for normalization.
Project description:Transcriptional profiling of Salmonella Typhimurium strains SL1344 in exponential and stationary phase cultures Overall design: The transcriptome of wild-type Salmonella Typhimurium SL1344 was determined in cultures grown in LB (Lennox broth) to exponential phase (OD 0.2) and stationary phase (OD 2.0)
Project description:We reported that analysis of PQQ metabolism in Gluconobacter oxydasns strain at gene expression level. Acoording to present study that pqqB gene can strengthen the transport of PQQ. Wild type strain and pqqB-overexpression strain were compared to find other candidate key genes which can encoded proteins are involved in PQQ transport. Results provide important information of the response of pqqB-overexpression, such as genes encoded membrane proteins and other indirectly functional genes. The mRNA of wild type (WT) and pqqB-overexpression mutant (TB) strains, collected at exponential growth phase, were generated by deep sequencingusing Illumina Miseq.
Project description:Ms1 RNA is ~300 nt sRNA that is highly expressed in stationary phase of growth and binds to the RNA polymerase (RNAP) core. We assume that by binding to RNAP, Ms1 could regulate transcription. Our aim was to reveal the most prominent changes in the transcriptome upon entry into stationary phase that might be dependent on Ms1. We performed RNA-seq data to characterize exponential (Ms_WT_exp) and stationary phase (Ms_WT_stat) transcriptome in M. smegmatis in wild type cells. In addition, we compared the transcriptome of the Ms1 knockout cells (Ms_KO_stat) with wild type cells in stationary phase and in exponential phase (Ms_KO_exp).
Project description:The cold shock proteins belong to a family of RNA binding proteins presenting a highly conserved domain, called cold shock domain (CSD). They are involved in various cellular processes, including adaptation to low temperature, nutritional stress, cell growth and stationary phase. Here we investigate the role of CspC in C. crescentus stationary phase and the molecular mechanisms underlying gene regulation by this protein. A global transcriptional profiling experiment comparing cspC and the wild type strain both at exponential and stationary phases was carried out. The results showed that the absence of cspC affected the transcription of 20 genes at exponential phase and 65 genes at stationary phase. Genes encoding enzymes of the glyoxylate cycle were severely downregulated in the mutant at stationary phase. The stationary phase-induced RNA binding protein CspC has an important role in gene expression at this phase. It is required for the expression of the essential gene sciP, the ECF sigma factor sigU, as well as of the genes for the glyoxylate cycle enzymes and for oxidative stress response. Two and three replicates were performed to determine the stationary phase stimulon and CspC regulon, respectively. Each replicate was conducted with an independent biological sample.
Project description:Comparison of Bacillus subtilis wild type and cshA mutant at exponential versus stationary phase. Detailed description (other than provided below) of growth conditions, RNA preparation, cDNA synthesis and hybridization conditions can be found in the submitted paper. Bacillus subtilis 168 wild type and its cshA derivative strain were grown in CSE-Glu medium and cells were harvested at mid exponential (OD600 ~0.8) and early stationary phase (OD600 ~2.2-2.4). For both time points, 4 biological replicates were used and 2 were mixed after cDNA labeling, resulting 2 slides for both exponential and stationary phase. Dye swaps are included in both experiments.
Project description:Growth phase dependent transcriptional and translational changes of Hb. salinarum were examined. In the genome-wide transcriptome analysis, gene expression in exponential versus stationary growth phase was monitored on DNA microarrays. In the global study of translational regulation, the relative amounts of free versus polysome-bound mRNA (separated by gradient centrifugation) were quantified in exponential as well as stationary growth phase using DNA microarrays.
Project description:The objective was to determine the role of Krüppel-like factor 5 (KLF5) in radiation-induced intestinal injury. Mice with intestinal-specific knockdown of KLF5 (Cre+ mice) were generated and their response to radiation was compared with controls (Cre- mice). Mice were given 15 Gy total body irradiation (TBI). The mice intestines were harvested at 6h post TBI and screened for differentially expressed genes by microarray analysis. We identified 11,004 and 2,466 differentially expressed genes in non-irradiated and irradiated mice at 6h post TBI, respectively. KLF5 knockdown down-regulated genes related to DNA damage repair pathways such as nucleotide excision repair, mismatch repair, non-homologous end joining and the Fanconi anemia pathway, which may suggest a novel function of KLF5. A four chip study using total RNA recovered from four pooled intestine tissues of four experimental groups. The four experimental groups respectively were the 6h-cre+ group, 6h-cre- group, con-cre+ group and con-cre- group. Equal mass amounts of total RNA were pooled from each small intestine to yield a sample representing RNA from 3 separate mice in each group. One pooled sample in every group were tested with one chip. Each chip measures the expression level of 44,170 genes from C57BL/6 mouse (background) with three 60-mer probe pairs per gene.