The stability of mRNA was investigated for the first time at the genomic scale during carbon starvation adaptation of Lactococcus lactis IL1403. In exponential phase, mRNA half-lives were correlated positively to open reading frame length. A polypurine sequence, AGGAG, was identified as a putative 5-stabilizer and inverted repeated sequences as a 3-destabilizer. These original findings suggested that multiple pathways of mRNA degradation should coexist: internal cleavage, endonuclease cleavage initiated at the 5-end, and exonuclease attack at the 3-end. During carbon starvation adaptation, mRNA stability globally increased, but specific mechanisms allowing a wide range of stabilization factors between genes and differential kinetic evolution were involved. A formal method allowing the quantification of the relative influences of transcription and degradation on the mRNA pool control was developed and applied in L. lactis. Gene expression was mostly controlled by altered transcription prior to carbon source exhaustion, while the influence of mRNA stability increased during the starvation phase. This study highlighted that stability modulation in response to adverse growth conditions can govern gene regulation to the same extent as transcription in bacteria.

Adaptation of Lactococcus lactis towards progressive carbon starvation is mediated by three different types of transcriptomic responses: (i) global responses, i.e., general decreases of functions linked to bacterial growth and lack of induction of the general stress response; (ii) specific responses functionally related to glucose exhaustion, i.e., underexpression of central metabolism genes, induction of alternative sugar transport and metabolism, and induction of the arginine deiminase pathway; and (iii) other responses never described previously during carbon starvation.Fundamental knowledge concerning the adaptation of Lactococcus lactis to adverse environments and more particularly to carbon starvation is still very fragmented. Studies have generally been focused on glycolysis and bacterial survival (15,19,23,24,26), providing only parceled results. In order to provide a more exhaustive picture of the adaptation, carbon starvation in L. lactis was investigated with whole-transcriptome analyses. Transcriptomic data were integrated in a more global physiological study based on metabolic flux determination, amino acid consumption, and measurement of certain enzyme activities. Modifications in the transcriptional profile were analyzed during progressive adaptation, allowing carbon starvation stimulons, a prerequisite of regulation network analysis, to be identified.Overview and dynamic analysis. The growth of L. lactis IL-1403 and its adaptation towards glucose starvation were investigated with a pH-regulated fermentor and in the chemically defined medium CDM (22), commonly used for L. lactis cultivation (Fig. 1). After an exponential phase associated with nutrient excess (0 to 5 h) and a short deceleration phase due to decreasing glucose concentration, a nongrowth stationary phase characterized by glucose exhaustion succeeded after 6 h of fermentation. The first 1.5 h of stationary phase corresponded to simple carbon starvation, since glucose was totally consumed but other nutrients, and particularly amino acids, were still available. Arginine was significantly consumed by nongrowing cells and was also exhausted from the medium after 1.5 h of starvation. The metabolism remained homolactic all along the fermentation since no fermentation products other than lactate accumulated significantly.Whole-genome transcripts were measured on nylon membranes after hybridization of cDNA labeled by retro-transcription with [P 33 ]dCTP in the different phases of the culture: exponential phase, deceleration phase, onset of carbon starvation (1.25 h), and after 3.5 h of starvation when arginine was no longer available. Three independent measurements were studied, and abundance ratios were calculated with the exponential phase as the reference in order to characterize expression pattern evolution. Only 30% of the genome was involved in the response to carbon starvation, as 704 genes showed at least one significant expression variation during the fermentation (Student's t test with a P value below 0.05). Globally, two times mo...

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.