Control of bacterial phenotype and chromosomal gene expression by single plasmids of Lactococcus lactis IL594

Plasmid-free Lactococcus lactis IL1403 is one of the best-characterized representatives of lactic acid bacteria (LAB), intensively used in broad microbiology worldwide. Its parent strain, L. lactis IL594, contains seven plasmids (pIL1-pIL7) with resolved DNA sequences and an indicated role for overall plasmid load in enhancing host adaptive potential. To determine how individual plasmids manipulate the expression of phenotypes and chromosomal genes, we conducted global comparative phenotypic analyses combined with transcriptomic studies in plasmid-free L. lactis IL1403, multi-plasmid L. lactis IL594 and its single-plasmid derivatives. The presence of pIL2, pIL4 and pIL5 led to the most pronounced phenotypic differences in the metabolism of several carbon sources, including some β-glycosides and organic acids. The pIL5 plasmid also contributed to increased tolerance to some antimicrobial compounds and heavy metal ions, especially those in the toxic cation group. Comparative transcriptomics showed significant variation in the expression levels of up to 189 chromosomal genes due to the presence of single plasmids, and 435 unique chromosomal genes that are resultant of the activity of all plasmids, which may suggest that the observed phenotypic changes are not only the result of direct action of their own genes, but also originate from indirect actions through cross-talk between plasmids and the chromosome. The data obtained here indicate that plasmid maintenance leads to the development of important mechanisms of global gene regulation that provide changes in the central metabolic pathways and adaptive properties of L. lactis, and suggest the possibility of a similar phenomenon among other groups of bacteria. The comparison of transcriptomes of the Lactococcus lactis IL1403 strain containing no plasmids to strains, IL1618, IL1421, IL2661, IL1619, IL1420, IL1530 containing single plasmids, or IL1392 strain containing a subset of four plasmids pIL1, pIL2, pIL3, pIL5, or IL594 strain containing seven plasmids (pIL1 to pIL7). Bacteria cells were grown in the medium with cellobiose as carbon source to mid-exponential growth phase (OD600 0.6-0.7). For every sample, two biological replicates were performed; for each of them two technical replicates with dye swapping were done.