Transcriptomics

Dataset Information

5

Response of Lactococcus lactis to different growth rates


ABSTRACT: The development of transcriptomic tools has allowed exhaustive description of stress responses. These responses always superimpose a general response associated to growth rate decrease and a specific one corresponding to the stress. The exclusive growth rate response can be achieved through chemostat cultivation, enabling all parameters to remain constant except the growth rate. We analysed metabolic and transcriptomic responses of Lactococcus lactis in continuous cultures at different growth rates ranging from 0.09 to 0.47 h-1. Growth rate was conditioned by isoleucine supply. Although the metabolism was constant and homolactic, a widespread transcriptomic response involving 30 % of the genome was observed. The expression of genes encoding physiological functions associated with biogenesis increased with growth rate (transcription, translation, fatty acid and phospholipids metabolism). Many phages, prophages and transposons related genes were down regulated by growth rate suggesting genome plasticity to be involved in the adaptation to slow growth. The growth rate response was compared to carbon and amino-acid starvation transcriptomic responses, revealing constant and significant involvement of growth rate regulations in these two stressful conditions (overlap 26%). Although stringent response mechanism is considered as the one governing growth deceleration in bacteria, the rigorous comparison of the two transcriptomic responses clearly indicated the mechanisms are distinct. Moreover it was established that genes positively regulated by growth rate are preferentially located in the vicinity of replication origin while those negatively regulated are mainly encountered at the opposite. This result demonstrates the often neglected relationship between genes expression and their location on chromosome. Keywords: growth rate impact, continuous cultures Continuous 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.

ORGANISM(S): Lactococcus lactis  

SUBMITTER: Redon Emma   Muriel Cocaign-Bousquet  Dressaire Clémentine  Loubière Pascal  Cocaign-Bousquet Muriel 

PROVIDER: E-GEOD-10256 | ArrayExpress | 2010-06-25

SECONDARY ACCESSION(S): GSE10256PRJNA108447

REPOSITORIES: GEO, ArrayExpress

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Publications

Growth rate regulated genes and their wide involvement in the Lactococcus lactis stress responses.

Dressaire Clémentine C   Redon Emma E   Milhem Helene H   Besse Philippe P   Loubière Pascal P   Cocaign-Bousquet Muriel M  

BMC genomics 20080721


BACKGROUND: The development of transcriptomic tools has allowed exhaustive description of stress responses. These responses always superimpose a general response associated to growth rate decrease and a specific one corresponding to the stress. The exclusive growth rate response can be achieved through chemostat cultivation, enabling all parameters to remain constant except the growth rate. RESULTS: We analysed metabolic and transcriptomic responses of Lactococcus lactis in continuous cultures a  ...[more]

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