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Open Access Research article

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

Clémentine Dressaire12, Emma Redon13, Helene Milhem45, Philippe Besse45, Pascal Loubière12 and Muriel Cocaign-Bousquet12*

Author Affiliations

1 Université de Toulouse; INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France

2 UMR5504, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, CNRS, INRA, 31400 Toulouse, France

3 Laboratoire de Biologie et Biotechnologies marines, IBFA, UMR100 IFREMER, Physiologie et Ecophysiologie des Mollusques Marins, Université de Caen Basse-Normandie, Esplanade de la Paix, F14032 Caen Cedex, France

4 Université de Toulouse ; INSA ; F-31077 Toulouse, France

5 CNRS ; IMT (Institut de Mathématiques de Toulouse) ; F-31077 Toulouse, France

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BMC Genomics 2008, 9:343  doi:10.1186/1471-2164-9-343

Published: 21 July 2008

Abstract

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 at different growth rates ranging from 0.09 to 0.47 h-1. Growth rate was conditioned by isoleucine supply. Although carbon 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 transposon related genes were down regulated as growth rate increased. 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 27%).

Two regulators potentially involved in the growth rate regulations, llrE and yabB, have been identified. 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, thus indicating the relationship between genes expression and their location on chromosome. 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.

Conclusion

This work of integrative biology was performed at the global level using transcriptomic analysis obtained in various growth conditions. It raised the importance of growth rate regulations in bacteria but also participated to the elucidation of the involved mechanism. Though the mechanism controlling growth rate is not yet fully understood in L. lactis, one expected regulatory mechanism has been ruled out, two potential regulators have been pointed out and the involvement of gene location on the chromosome has also been found to be involved in the expression regulation of these growth related genes.