Gene regulation in Lactococcus lactis: the gap between predicted and characterized regulators (original) (raw)
Related papers
Molecular Microbiology, 2004
CodY is a pleiotropic transcriptional regulator conserved in low-G + C Gram-positive bacteria. Two distinct signals have been shown independently to influence the activity of this regulator: the level of intracellular GTP in Bacillus subtilis and the level of intracellular branched-chain amino acids (BCAA) isoleucine, leucine and valine in Lactococcus lactis. Measurement of BCAA and GTP levels in several environmental conditions showed that L. lactis CodY responded to the intracellular BCAA concentrations but not to physiological fluctuations in intracellular GTP. In addition, we demonstrated that CodY from L. lactis did not respond to intracellular GTP even when complementing CodY activity in B. subtilis . However, L. lactis CodY activity could still be modulated in B. subtilis by adding a rich nitrogen source to the growth media. This finding suggests that only BCAA are sensed by L. lactis CodY, whereas both GTP and BCAA signals may be integrated by B. subtilis CodY. The difference in the function of CodY from B. subtilis and L. lactis seems to reflect the difference in the physiology of these two bacteria.
The Transcriptional and Gene Regulatory Network of Lactococcus lactis MG1363 during Growth in Milk
PLoS ONE, 2013
In the present study we examine the changes in the expression of genes of Lactococcus lactis subspecies cremoris MG1363 during growth in milk. To reveal which specific classes of genes (pathways, operons, regulons, COGs) are important, we performed a transcriptome time series experiment. Global analysis of gene expression over time showed that L. lactis adapted quickly to the environmental changes. Using upstream sequences of genes with correlated gene expression profiles, we uncovered a substantial number of putative DNA binding motifs that may be relevant for L. lactis fermentative growth in milk. All available novel and literature-derived data were integrated into network reconstruction building blocks, which were used to reconstruct and visualize the L. lactis gene regulatory network. This network enables easy mining in the chrono-transcriptomics data. A freely available website at http://milkts.molgenrug.nl gives full access to all transcriptome data, to the reconstructed network and to the individual network building blocks.
2000
The genetic elements specifying six putative two-component regulatory systems (2CSs) were identified on the chromosome of Lactococcus lactis MG1363. These 2CSs appear to represent distinct loci, each containing a histidine kinase and response-regulator-encoding gene pair. Transcriptional analysis of the six 2CSs was performed either by generating transcriptional fusions to a reporter gene or by primer extension. Two of the systems
Use of lac regulatory elements for gene expression in Lactobacillus casei
The lactose operon, lacTEGF, of Lactobacillus casei ssp. casei ATCC393 [pLZ15 -] is encoding an antiterminator protein (LacT), the elements (LacE and LacF) of the lactose-specific phosphotransferase system (PTS) and a phospho-β-galactosidase (LacG). The lac operon is repressed by glucose and fructose and is induced by lactose, through the PTS/CcpA signal transduction system and an antiterminator mechanism, respectively. Furthermore, the antiterminator activity of LacT is also negatively modulated possibly by a PTS-mediated phosphorylation event. These strong regulatory mechanisms have been used in this work for the design of expression systems. Hence, Bacillus licheniformis α-amylase has been efficiently expressed from pIAβ5lacamy on lactose grown cells. Furthermore, a food-grade mutant, expressing Lactococcus lactis acetohydroxy acid synthase genes (ilvBN), was obtained with an integrative system, developed using lacG and lacF as homologous sequences for recombination. As a result, ilvBN genes were integrated in tandem between lacG and lacF in the chromosome and were co-ordinately expressed with the genes of the lactose operon.
Cloning, nucleotide sequence, and regulatory analysis of the Lactococcus lactis dnaJ gene
Journal of Bacteriology, 1993
The dncJ gene ofLactococcus lactis was isolated from a genomic library ofL. lactis NIZO R5 and cloned into pUC19. Nucleotide sequencing revealed an open reading frame of 1,137 bp in length, encoding a protein of 379 amino acids. The deduced amino acid sequence showed homology to the DnaJ proteins of Escherichia coli, Mycobacterium tuberculosis, Bacillus subtilis, and Clostridium acetobutylicum. The level of the dnaJ monocistronic mRNA increased approximately threefold after heat shock. The transcription initiation site of the dnaJ
University of Groningen Comparative and functional genomics of lactococci
2017
Whole-genome nucleotide sequencing has revolutionized the genetic, biochemical and molecular biology research on bacteria and indeed, many higher organisms. The genome sequences of the strains of two subspecies of Lactococcus lactis, L. lactis subsp. lactis and L. lactis subsp. cremoris, have been determined. These genomic sequences have permitted two important new approaches to be applied in the research of L. lactis. The analysis of the regulation of expression of all genes under specific circumstances at a given point in time is now possible by DNA microarray technology. The elucidation of the full protein complement of the organism as a function of intrinsic or external factors has been made possible by high-throughput protein identification and analysis techniques combined with the gene-derived know-how of the total protein encoding capacity of the genome. These techniques from the genomics arena, transcriptomics and proteomics, have been recently implemented in the study of va...
BMC Genomics, 2008
A key problem in the sequence-based reconstruction of regulatory networks in bacteria is the lack of specificity in operator predictions. The problem is especially prominent in the identification of transcription factor (TF) specific binding sites. More in particular, homologous TFs are abundant and, as they are structurally very similar, it proves difficult to distinguish the related operators by automated means. This also holds for the LacI-family, a family of TFs that is wellstudied and has many members that fulfill crucial roles in the control of carbohydrate catabolism in bacteria including catabolite repression. To overcome the specificity problem, a comprehensive footprinting approach was formulated to identify TF-specific operator motifs and was applied to the LacI-family of TFs in the model gram positive organism, Lactobacillus plantarum WCFS1. The main premise behind the approach is that only orthologous sequences that share orthologous genomic context will share equivalent regulatory sites.
Comparative and functional genomics of lactococci
FEMS Microbiology Reviews, 2005
Whole-genome nucleotide sequencing has revolutionized the genetic, biochemical and molecular biology research on bacteria and indeed, many higher organisms. The genome sequences of the strains of two subspecies of Lactococcus lactis, L. lactis subsp. lactis and L. lactis subsp. cremoris, have been determined. These genomic sequences have permitted two important new approaches to be applied in the research of L. lactis. The analysis of the regulation of expression of all genes under specific circumstances at a given point in time is now possible by DNA microarray technology. The elucidation of the full protein complement of the organism as a function of intrinsic or external factors has been made possible by high-throughput protein identification and analysis techniques combined with the gene-derived know-how of the total protein encoding capacity of the genome. These techniques from the genomics arena, transcriptomics and proteomics, have been recently implemented in the study of various aspects of growth and functioning of L. lactis. In this paper we discuss a number of similarities and differences between the two lactococcal genome sequences and review the current status of genomics research in L. lactis. We also propose future directions with respect to both answering fundamental questions more quickly and more completely, as well as opening new avenues for biotechnological applications.
Regulatory Phenotyping Reveals Important Diversity within the Species Lactococcus lactis
Applied and Environmental Microbiology, 2009
The diversity in regulatory phenotypes among a collection of 84 Lactococcus lactis strains isolated from dairy and nondairy origin was explored. The specific activities of five enzymes were assessed in cell extracts of all strains grown in two different media, a nutritionally rich broth and a relatively poor chemically defined medium. The five investigated enzymes, branched chain aminotransferase (BcaT), aminopeptidase N (PepN), X-prolyl dipeptidyl peptidase (PepX), alpha-hydroxyisocaproic acid dehydrogenase (HicDH), and esterase, are involved in nitrogen and fatty acid metabolism and catalyze key steps in the production of important dairy flavor compounds. The investigated cultures comprise 75 L. lactis subsp. lactis isolates (including 7 L. lactis subsp. lactis biovar diacetylactis isolates) and 9 L. lactis subsp. cremoris isolates. All L. lactis subsp. cremoris and 22 L. lactis subsp. lactis (including 6 L. lactis subsp. lactis biovar diacetylactis) cultures originated from a dairy environment. All other cultures originated from (fermented) plant materials and were isolated at different geographic locations. Correlation analysis of specific enzyme activities revealed significantly different regulatory phenotypes for dairy and nondairy isolates. The enzyme activities in the two investigated media were in general poorly correlated and revealed a high degree of regulatory diversity within this collection of closely related strains. To the best of our knowledge, these results represent the most extensive diversity analysis of regulatory phenotypes within a single bacterial species to date. The presented findings underline the importance of the availability of screening procedures for, e.g., industrially relevant enzyme activities in models closely mimicking application conditions. Moreover, they corroborate the notion that regulatory changes are important drivers of evolution.