ChIP-seq for transcriptional regulator CodY of Lactococcus lactis
Ontology highlight
ABSTRACT:
ORGANISM(S): Lactococcus lactis
PROVIDER: GSE139902 | GEO | 2022/01/28
REPOSITORIES: GEO
Similar Datasets
Project description:CodY of Lactococcus lactis MG1363 is a transcriptional regulator that represses the expression of several genes encoding proteins of the proteolytic system. DNA microarray analysis, comparing the expression profiles of L. lactis MG1363 and an isogenic strain in which codY was mutated, was used to determine the CodY regulon. In peptide-rich medium and exponentially growing cells, where CodY exerts strong repressing activity, the expression of over 30 genes was significantly increased upon removal of codY. The differentially expressed genes included those predominantly involved in amino acid transport and metabolism. In addition, several genes belonging to other functional categories were derepressed, stressing the pleiotropic role of CodY. Scrutinizing the transcriptome data with bioinformatics tools revealed the presence of a novel overrepresented motif in the upstream regions of several of the genes derepressed in L. lactis MG1363codY. Evidence is presented that this 15-bps cis-sequence, AATTTTCWGAAAATT, serves as a high-affinity binding site for CodY, as shown by electrophoretic mobility shift assays and DNaseI footprinting analyses. The presence of this CodY-box is sufficient to evoke CodY-mediated regulation in vivo. A copy of this motif is also present in the upstream region of codY itself. It is shown that CodY regulates its own synthesis and requires the CodY-box and branched-chain amino acids to interact with its promoter. Keywords: genetic modification
2005-07-22 | GSE2823 | GEO
Project description:ChIP-seq for transcriptional regulator CodY of Lactococcus lactis
| PRJNA587502 | ENA
Project description:Our transcriptome data shows that ythA, which is a PspC family transcriptional regulator, obviously affects amino acid metabolism, pyrimidine biosynthesis and nisin immunity.
2018-03-14 | GSE101424 | GEO
Project description:pBL1 is a Lactococcus lactis theta-replicating 10.9-kbp plasmid that encodes the synthetic machinery of the bacteriocin Lcn972. In this work, the transcriptomes of exponentially growing L. lactis with and without pBL1 were compared. A discrete response was observed with a total of ten genes showing significantly changed expression. Up-regulation of the lactococcal oligopeptide uptake system (opp) was observed, likely linked to a higher nitrogen demand required for Lcn972 biosynthesis. Striking, celB coding for the membrane porter IIC of the cellobiose-PTS and the upstream gene llmg0186 were down-regulated. Growth profiles for L. lactis strains MG1363, MG1363/pBL1 and MG1363ΔcelB grown in CDM-cellobiose confirmed slower growth of pBL1 and ΔcelB while no differences were scored on glucose. The presence of pBL1 shifted the fermentation products towards a mixed acid profile and promoted substantial changes in intracellular pool sizes for glycolytic intermediates in cellobiose-growing cells as determined by HPLC and NMR. Overall, these data support the genetic evidence of a constriction in cellobiose uptake. Notably, several cell wall precursors accumulated, while other UDP-activated sugars pools were lower, which could reflect rerouting of precursors towards the production of structural or storage polysaccharides. Moreover, slow cellobiose-growing cells and those lacking celB were more tolerant to Lcn972 than cellobiose adapted cells. Thus, down-regulation of celB could help to build-up a response against the antimicrobial activity of Lcn972 enhancing self-immunity of the producer cells. The transcriptomes of Lactococcus lactis MG1614 with and without the bacteriocinogenic plasmid pBL1, grown under laboratory conditions, were compared using three biological replicates.
2011-09-14 | E-GEOD-30625 | 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:CodY is a nutritional regulator mainly involved in amino acid metabolism. It has been extensively studied in Bacillis subtilis and Lactococcus lactis. We investigated the role of CodY in gene regulation and virulence of the human pathogen Streptococcus pneumoniae. We constructed a codY-mutant and examined the effect on gene and protein expression by microarray and 2D DIGE analysis. The pneumococcal CodY-regulon was found to consist predominantly of genes involved in amino acid metabolism, but also several other cellular processes, such as carbon metabolism and iron uptake. By means of electrophoretic mobility shift assays and DNA footprinting, we showed that most targets identified are under direct control of CodY. By mutating DNA predicted to represent the CodY-box based on the L. lactis consensus, we demonstrated that this sequence is indeed required for in vitro DNA-binding to target promoters. Similar to L. lactis, DNA-binding of CodY was enhanced in the presence of the branched chain amino acids isoleucine, leucine, and valine, and not by GTP. We observed in experimental mouse models that CodY is transcribed in the murine nasopharynx and lungs, and is specifically required for colonization. This finding was underscored by the diminished ability of the codY-mutant to adhere to nasopharyngeal cells in vitro. In conclusion, pneumococcal CodY predominantly regulates genes involved in amino acid metabolism and contributes to the early stages of infection, i.e. colonization of the nasopharynx. Keywords: codY
2007-11-20 | GSE7350 | GEO
Project description:pBL1 is a Lactococcus lactis theta-replicating 10.9-kbp plasmid that encodes the synthetic machinery of the bacteriocin Lcn972. In this work, the transcriptomes of exponentially growing L. lactis with and without pBL1 were compared. A discrete response was observed with a total of ten genes showing significantly changed expression. Up-regulation of the lactococcal oligopeptide uptake system (opp) was observed, likely linked to a higher nitrogen demand required for Lcn972 biosynthesis. Striking, celB coding for the membrane porter IIC of the cellobiose-PTS and the upstream gene llmg0186 were down-regulated. Growth profiles for L. lactis strains MG1363, MG1363/pBL1 and MG1363ΔcelB grown in CDM-cellobiose confirmed slower growth of pBL1 and ΔcelB while no differences were scored on glucose. The presence of pBL1 shifted the fermentation products towards a mixed acid profile and promoted substantial changes in intracellular pool sizes for glycolytic intermediates in cellobiose-growing cells as determined by HPLC and NMR. Overall, these data support the genetic evidence of a constriction in cellobiose uptake. Notably, several cell wall precursors accumulated, while other UDP-activated sugars pools were lower, which could reflect rerouting of precursors towards the production of structural or storage polysaccharides. Moreover, slow cellobiose-growing cells and those lacking celB were more tolerant to Lcn972 than cellobiose adapted cells. Thus, down-regulation of celB could help to build-up a response against the antimicrobial activity of Lcn972 enhancing self-immunity of the producer cells.
2011-09-15 | GSE30625 | 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.
2011-09-22 | GSE12962 | GEO
Project description:CodY is a nutritional regulator mainly involved in amino acid metabolism. It has been extensively studied in Bacillis subtilis and Lactococcus lactis. We investigated the role of CodY in gene regulation and virulence of the human pathogen Streptococcus pneumoniae. We constructed a codY-mutant and examined the effect on gene and protein expression by microarray and 2D DIGE analysis. The pneumococcal CodY-regulon was found to consist predominantly of genes involved in amino acid metabolism, but also several other cellular processes, such as carbon metabolism and iron uptake. By means of electrophoretic mobility shift assays and DNA footprinting, we showed that most targets identified are under direct control of CodY. By mutating DNA predicted to represent the CodY-box based on the L. lactis consensus, we demonstrated that this sequence is indeed required for in vitro DNA-binding to target promoters. Similar to L. lactis, DNA-binding of CodY was enhanced in the presence of the branched chain amino acids isoleucine, leucine, and valine, and not by GTP. We observed in experimental mouse models that CodY is transcribed in the murine nasopharynx and lungs, and is specifically required for colonization. This finding was underscored by the diminished ability of the codY-mutant to adhere to nasopharyngeal cells in vitro. In conclusion, pneumococcal CodY predominantly regulates genes involved in amino acid metabolism and contributes to the early stages of infection, i.e. colonization of the nasopharynx. Keywords: codY CodY of Streptococcus pneumoniae: link between nutritional gene regulation and virulence
2010-05-25 | E-GEOD-7350 | 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. 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