The Presence of Plasmids in Lactococcus lactis IL594 Determines Changes in the Host Phenotype and Expression of Chromosomal Genes

Abstract

The L. lactis IL594 strain contains seven plasmids (pIL1 to pIL7) and is the parental strain of the plasmid-free L. lactis IL1403, one of the most studied lactic acid bacteria (LAB) strain. The genetic sequences of pIL1 to pIL7 plasmids have been recently described, however the knowledge of global changes in host phenotype and transcriptome remains poor. In the present study, global phenotypic analyses were combined with transcriptomic studies to evaluate a potential influence of plasmidic genes on overall gene expression in industrially important L. lactis strains. High-throughput screening of phenotypes differences revealed pronounced phenotypic differences in favor of IL594 during the metabolism of some C-sources, including lactose and β-glucosides. A plasmids-bearing strain presented increased resistance to unfavorable growth conditions, including the presence of heavy metal ions and antimicrobial compounds. Global comparative transcriptomic study of L. lactis strains revealed variation in the expression of over 370 of chromosomal genes caused by plasmids presence. The general trend presented upregulated energy metabolism and biosynthetic genes, differentially expressed regulators, prophages and cell resistance proteins. Our findings suggest that plasmids maintenance leads to significant perturbation in global gene regulation that provides change in central metabolic pathways and adaptive properties of the IL594 cells.

Control of Bacterial Phenotype and Chromosomal Gene Expression by Single Plasmids of Lactococcus lactis IL594

“…Among them, the transcription of cadA, cbiO, pacL, and yuhE, encoding components of mono-and divalent cation efflux systems (Cs + , Co 2+ , Zn 2+ ), were most strongly activated. Interestingly, the phenotypic effect of enhanced tolerance to cesium, cadmium, and cobalt ions was observed in IL1619 and IL594, supporting our previous speculation of the important role of plasmid pIL5 in enhancing the cellular tolerance of L. lactis [11]. Here, we also confirmed the previously described phenomenon of plasmid-induced repression of all three components of the mtsABC operon encoding the manganese ABC transport system in L. lactis IL594 [10].…”

“…Increased tolerance to antimicrobial compounds and metal ions represents an important mechanism of LAB environmental adaptation. Here, we showed that the presence of plasmids in L. lactis led to subtle differences in the tolerance of theirs hosts to several chemical compounds, with most changes observed in strain IL1619 with pIL5, confirming our previous suspicion of its importance in enhancing cell resistance in the multiplasmid L. lactis IL594 [ 11 ]. These findings imply that pIL5 may play a role in increasing cell defense by the action of its own resistance genes and/or by regulating the expression of the chromosomal ones.…”

“…In a previous study, we indicated the role of the overall plasmid load in strain IL594 in enhancing the metabolism of more complex carbon compounds, such as certain β-glycosides [ 11 ]. Here, we specified that plasmids residing in strains IL2661 and/or IL1392 are mainly involved in this process, as their presence led to the enhancement of their hosts of the use of lactose and its derivatives as well as β-glucosides, such as esculin and gentiobiose.…”

“…Differentially expressed genes were grouped based on putative functions of the encoded proteins into COG categories using the WebMGA RPS-blast tool (Weizong-Lab) ( , accessed on 15 January 2023). Due to the different results between biological repeats, both in this work and in our previous studies [ 11 ], in the current paper, we did not present or include differently regulated genes from the COG X category (Mobilome: prophages, transposons) in the comparisons. The complete transcriptome analysis data were deposited in the Gene Expression Omnibus ( , accessed on 12 April 2023) under accession no: GSE229414.…”

“…Differentially expressed genes are involved in carbohydrate and global energy metabolism, the transport and metabolism of amino acids, nucleotides, and inorganic ions, and defense mechanisms. The presence of the gene pool from pIL1–pIL7 plasmids, through the slightly increased tolerance to a range of antimicrobial compounds, improves the overall fitness and metabolic capacity of the host [ 11 ]. While the plasmid control of chromosomally encoded genes is not unusual, only a few reports on detailed plasmid–chromosome crosstalk analyses can be found, and data on this phenomenon in lactic fermentation bacteria in particular are lacking.…”