Static, aerobic, and respiratory transcriptomes of Lactococcus lactis
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ABSTRACT:
ORGANISM(S): Lactococcus lactis subsp. lactis
PROVIDER: GSE8182 | GEO | 2008/05/27
SECONDARY ACCESSION(S): PRJNA101083
REPOSITORIES: GEO
Similar Datasets
Project description:Compare the physiological state between static, aerobic, and respiratory growth of Lactococcus lactis subsp. lactis CHCC2862 using whole genome transcriptomes. NOTE: the biological replicate array GSM243206 is dye-swapped relative to GSM202337 (unlike the two other biological replicate arrays GSM243203 and GSM24205). Keywords: Physiological response to aerobic and respiratory growth relative to static. Static stationary cultures of CHCC2862 (Chr. Hansen Culture Collection, Hørsholm, Denmark) were inoculated into fresh pre-heated medium at the relevant conditions. OD600 was followed over time. At OD 1.0 samples were harvested for RNA isolation.
2008-05-27 | E-GEOD-8182 | biostudies-arrayexpress
Project description:Static, aerobic, and respiratory transcriptomes of Lactococcus lactis
| PRJNA101083 | ENA
Project description:The transcriptome of Actinobacillus pleuropneumoniae 4h static biofilms was compared to the transcriptome of 6h static biofilm 4 samples were analyzed which included 3 biological replicate, 1 technical replicate and 1 dye swap
2013-05-20 | E-GEOD-43822 | biostudies-arrayexpress
Project description:Comparison of L. lactis NZ9000 ΔlmrR versus L. lactis NZ9000 wild type Keywords: Transcription profiling
2007-10-04 | GSE9168 | GEO
Project description:Amino acid assimilation and metabolism are crucial for bacterial growth and survival and this is particularly obvious for lactic acid bacteria (LAB) that are generally auxotroph for various amino acids. However, amino acid assimilation is poorly characterized and a complete description of the response during amino acid starvation is still lacking in LAB. In this context, the global response of the LAB model Lactococcus lactis was characterized during isoleucine starvation in batch culture. The stress was imposed by isoleucine natural consumption in an initially rich chemically defined medium. Dynamic analyses were performed both using transcriptomic and proteomic approaches. The response was found to occur gradually and could be divided into three major parts that were firstly deduced from transcriptomic analysis and generally corroborated by proteomic results: (i) a global repression of biogenic processes (transcription, translation, and carbon metabolism and transport), (ii) a specific response related to the limiting nutrient (numerous pathways belonging to carbon or nitrogen metabolism and leading to isoleucine supply were activated) and (iii) an additional response connected to oxidative stress (induction of aerobic metabolism, electron transport, thioredoxin metabolism and pyruvate dehydrogenase). The involvement of various regulatory mechanisms such as growth rate regulation, stringent response, CodY, GlnR, and CcpA regulations, was discussed on the basis of transcriptomic data comparisons. Above the full description of L. lactis isoleucine starvation response, this work additionally provided a complex but realistic outlook of the regulation network involved in isoleucine starvation. Such integrated and comparative approach will allow, by its implementation to other regulations and environmental conditions, the whole regulatory network of L. lactis or any other microorganism to be deciphered. Batch cultivation of Lactococcus lactis IL1403 were carried out on a chemically defined medium and under controlled conditions (30 °C, pH 6.6, nitrogen atmosphere). Cell samples were harvested at steady state. Total RNA was extracted from these samples and radiolabelled cDNA were prepared and hybridized on nylon arrays. 1948 amplicons specific of Lactococcus lactis IL1403 genes were spotted twice on the array. Samples corresponding to various growth rates were analyzed simultaneously and 3 independent repetitions were performed.
2011-09-21 | E-GEOD-12962 | biostudies-arrayexpress
Project description:Amino acid assimilation and metabolism are crucial for bacterial growth and survival and this is particularly obvious for lactic acid bacteria (LAB) that are generally auxotroph for various amino acids. However, amino acid assimilation is poorly characterized and a complete description of the response during amino acid starvation is still lacking in LAB. In this context, the global response of the LAB model Lactococcus lactis was characterized during isoleucine starvation in batch culture. The stress was imposed by isoleucine natural consumption in an initially rich chemically defined medium. Dynamic analyses were performed both using transcriptomic and proteomic approaches. The response was found to occur gradually and could be divided into three major parts that were firstly deduced from transcriptomic analysis and generally corroborated by proteomic results: (i) a global repression of biogenic processes (transcription, translation, and carbon metabolism and transport), (ii) a specific response related to the limiting nutrient (numerous pathways belonging to carbon or nitrogen metabolism and leading to isoleucine supply were activated) and (iii) an additional response connected to oxidative stress (induction of aerobic metabolism, electron transport, thioredoxin metabolism and pyruvate dehydrogenase). The involvement of various regulatory mechanisms such as growth rate regulation, stringent response, CodY, GlnR, and CcpA regulations, was discussed on the basis of transcriptomic data comparisons. Above the full description of L. lactis isoleucine starvation response, this work additionally provided a complex but realistic outlook of the regulation network involved in isoleucine starvation. Such integrated and comparative approach will allow, by its implementation to other regulations and environmental conditions, the whole regulatory network of L. lactis or any other microorganism to be deciphered.
2011-09-22 | GSE12962 | GEO
Project description:Triplicate chemostat cultivations were carried out with L. lactis subsp. lactis IL1403 at specific growth rates 0.1 and 0.5 h-1 on a chemically defined medium, where both, glucose and lysin (Lys) were jointly limiting the growth. After reaching the steady physiological state, medium was switched to heavy Lys (13C615N2-Lys) containing medium and incorporation of heavy amino acid into biomass was observed over the time course. Samples were collected before the medium switch (0 h) and 0.5; 1.5; 5; and 10 h after the medium switch. Cells were lysed in SDS lysis buffer and digested with trypsin according to Filter Aided Sample Preparation protocol (FASP). LC-MS/MS analysis were performed on Agilent 1200 series nanoflow system connected to a LTQ Orbitrap mass-spectrometer equipped with a nanoelectrospray ion source. Raw data files were analyzed with the MaxQuant software package (version 1.2.7.4). Generated peak lists were searched using the Andromeda search engine (built into MaxQuant) against L. lactis database (downloaded 28.06.2012 from http://www.genome.jp/kegg/genes.html). MaxQuant searches were performed with full tryptic specificity, a maximum of two missed cleavages and a mass tolerance of 0.5 Da for fragment ions. Carbamidomethylation of cysteine was set as a fixed modification and methionine oxidation and protein N-terminal acetylation were set as variable modification. The required false discovery rate (FDR) was set to 1% both for peptide and protein levels and the minimum required peptide length was set to six amino acids. In addition, "Match between runs" option with a time window of 1.5 min was allowed.
2014-01-28 | PXD000494 | Pride
Project description:For the first time in Lactococcus lactis, amino acid starvation response was characterized. The natural imposition of isoleucine starvation, by its consumption during growth, associated to transcript profiling, allowed defining exhaustively this stress stimulon. It consisted of a general induction of nitrogen metabolism (amino acid biosynthesis and transport, proteolytic system and proteases), a strong repression of genes encoding major physiological activities (translation, transcription, carbon metabolism, purine and pyrimidine biosynthesis and fatty acid metabolism) and the induction of unexpected cross responses to acid, osmotic and oxidative stresses. Keywords: stress response, time course Isoleucine starvation was imposed by the consumption of this amino acid during the growth of Lactococcus lactis IL1403 on ILV0.1 medium (CDM with ten-fold reduced concentrations of isoleucine, leucine and valine) and under controlled conditions (30 °C, pH 6.6, nitrogen atmosphere). Cell samples were harvested in exponential phase and after 30 min, 1.7 h and 3.5 h of isoleucine starvation. Total RNA was extracted from these samples and radiolabelled cDNA were prepared and hybridized on nylon arrays. 2053 amplicons specific of Lactococcus lactis IL1403 genes were spotted twice on the array. The 4 time-points were analyzed simultaneously and 3 independent repetitions were performed.
2010-06-25 | E-GEOD-4872 | biostudies-arrayexpress
Project description:Lactococcus lactis NZ9000 and its parent MG1363 are the most commonly used lactic acid bacteria for expression and physiological studies. We noted unexpected but significant differences in the growth behaviors of both strains. We sequenced the entire genomes of the original NZ9000 and MG1363 strains using an ultradeep sequencing strategy. The analysis of the L. lactis NZ9000 genome yielded 79 differences, mostly point mutations, with the annotated genome sequence of L. lactis MG1363. Resequencing of the MG1363 strain revealed that 73 out of the 79 differences were due to errors in the published sequence. Comparative transcriptomic studies revealed several differences in the regulation of genes involved in sugar fermentation, which can be explained by two specific mutations in a region of the ptcC promoter with a key role in the regulation of cellobiose and glucose uptake.
2010-11-11 | GSE21759 | GEO