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Proteome-wide adaptation of Lactococcus cremoris after a carbon upshift

ABSTRACT: Bacteria must adapt their proteome composition to optimize their growth and fitness after an environmental shift. For the lactic acid bacterium Lactococcus cremoris, the shift from galactose to glucose as the main carbon source is associated with large growth rate and physiological changes. This study used protein turnover to investigate the strategies underlying proteome-wide adaptation after a shift from galactose to glucose as the main carbon source for two closely related Lactococcus cremoris strains.

INSTRUMENT(S): Q Exactive HF-X

ORGANISM(S): Lactococcus Lactis Subsp. Cremoris Mg1363

SUBMITTER: Sjef Boeren

LAB HEAD: Sjef Boeren

PROVIDER: PXD041822 | Pride | 2025-02-17

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	BvO355_M_gal_t0A.raw	Raw
	BvO356_M_glc_t15.raw	Raw
	BvO357_M_glc_t30.raw	Raw
	BvO358_M_glc_t45.raw	Raw
	BvO359_M_glc_t60.raw	Raw

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Publications

Carbon upshift in Lactococcus cremoris elicits immediate initiation of proteome-wide adaptation, coinciding with growth acceleration and pyruvate dissipation switching.

van Olst Berdien B Boeren Sjef S Vervoort Jacques J Kleerebezem Michiel M

mBio 20250220 3

Fitness optimization in a dynamic environment requires bacteria to adapt their proteome in a tightly regulated manner by altering protein production and/or degradation. Here, we investigate proteome adaptation in Lactococcus cremoris following a sudden nutrient upshift (e.g., nutrients that allow faster growth) and focus especially on the fate of redundant proteins after the shift. Protein turnover analysis demonstrated that L. cremoris cultures shifted from galactose to glucose, i ...[more]

PMID: 39976430

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Proteome and sugar catabolization capacity of Lactococcus cremoris grown on various sugars

Project description:The lactic acid bacterium Lactococcus cremoris is suggested to repress genes involved in sugar metabolism in a hierarchical way, correlating with the growth rate. For cultures grown on glucose, lactose, galactose and maltose, we unraveled the sugar catabolizing hierarchy by combining the proteome composition and the capacity to catabolize a set of 12 sugars.

2024-01-26 | PXD037169 | Pride

Proteome-wide adaptation of Lactococcus cremoris under temperature changes or translation inhibition

Project description:Growth conditions influence growth rate and the corresponding global proteome composition. It is commonly observed that a higher ribosomal content due to growth rate optimization may impact the level of metabolic proteins. In the case of Lactococcus cremoris, acidification and flavor formation are important traits of their use in cheesemaking. This study correlates the expression level of metabolic (e.g., flavor-relevant) enzymes in relation to the level of ribosomes during growth in defined medium or milk.

2025-02-17 | PXD042113 | Pride

Manganese availability alters the expression of its corresponding transporters and redox-dependent proteins but not superoxide dismutase in Lactococcus cremoris.

Project description:Growth of L. cremoris NCDO712 was not altered when manganese is omitted from its defined medium. This study was conducted in order to compare protein requirements of Lactococcus cremoris NCDO712 to grow in the presence or absence of manganese in defined medium (1% lactose). The majority of protein adaptation involves upregulation of Mn transporters and to a lesser extent various NADH-dependent proteins. Such adaptation is highly relevant for starter culture in dairy fermentation where manganese is limited and NADH homeostasis determines the formation of volatiles during long-term incubation e.g. cheese ripening.

2022-05-16 | PXD030123 | Pride

Proteome-wide adaptation of Lactococcus cremoris during growth in milk and during cheese production and ripening

Project description:The enzymatic repertoire of starter cultures is important for cheese characteristics but is challenging to characterize due to the high protein and fat concentration, and the semi-solid state of the cheese matrix. This study aimed to generate a protocol to characterize the proteome of bacteria harvested from milk and cheese, to assess the proteome differences between Lactococcus cremoris grown in milk and laboratory medium, and to investigate the proteome adaptation during cheese production and ripening.

2025-03-12 | PXD046375 | Pride

Investigating proteome constraints of Lactococcus lactis grown in a nutrient-rich environment

Project description:Proteomics comparison of wild type Lactococcus lactis MG1363 with a mutant strain that has a point mutation in the global carbon catabolite repression regulator (CcpA) grown under glucose-limited chemostat conditions at D = 0.5 /h.

2021-03-01 | PXD021956 | Pride

Comparative proteomics investigating the physiological roles of menaquinones (vitamin K2) in Lactococcus cremoris

Project description:This study examined phenotypes of Lactococcus cremoris strains MG1363 and mutants with different vitamin K2 chain length profile, to understand the physiological roles of short-chain and long-chain menaquinones (vitamin K2) in L. cremoris.

2022-05-20 | PXD030833 | Pride

AKT but not MYC promotes reactive oxygen species-mediated cell death in oxidative culture

Project description:In addition to driving tumorigenesis, oncogenes can create metabolic vulnerabilities in cancer cells. Here, we tested how the oncogenes AKT and MYC affect the ability to shift between respiration and glycolysis. Using immortalized mammary epithelial cellsMCF10A, we discovered constitutively active AKT but not MYC induced cell death in galactose culture, where cells must rely on oxidative phosphorylation for energy generation. However, the negative effects of AKT were short-lived, and AKT-expressing cells recommenced growth after ~15 days in galactose culture. To identify the mechanisms regulating AKT-mediated cell death, we first used metabolomics and found that AKT cells dying in galactose culture exhibited upregulated glutathione metabolism. Next, using shotgun proteomics, we discovered AKT cells dying in galactose upregulated proteins related to nonsense-mediated mRNA decay (NMD), a known response to oxidative stress. We therefore measured levels of reactive oxygen species (ROS) and discovered galactose culture induced ROS only in cells expressing AKT. Additionally, we found thatdiscovered the ROS scavenger catalase rescued AKT-expressing cells from galactose culture-induced cell death. We then demonstrated that breast cancer cell lines with constitutively active AKT signaling also exhibited cell death in galactose culture and rescue by catalase. Together, our results demonstrate that AKT but not MYC induces a metabolic vulnerability in cancer cells, namely the that restricted flexibility to use oxidative phosphorylation.

2020-03-19 | PXD015122 | Pride

Lactococcus cremoris

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| PRJNA739240 | ENA

Transcription profiling of Saccharomyces Histone H3 K4,36,79R mutant 0 hr

Project description:Total RNA from two replicate cultures of wild-type and mutant strains was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by H3 K4,36,79R mutant. Cells were grown in galactose media to give the 0 hour timepoint. Experiment Overall Design: Histone H3 K4,36,79R time course. Cells were grown in galactose media and then shifted to glucose media, which repressed the expression of wild-type histone H3, leaving the histone H3 K4,36,79R mutant as the sole source of histone H3 protein in the cell. Total RNA was isolated from replicate cultures of wild-type and mutant histone H3 at various time points after the shift to glucose media (0, 6, and 9 hours). Expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by H3 K4,36,79R mutant.

2008-06-14 | E-GEOD-6326 | biostudies-arrayexpress

Transcription profiling of S. cerevisiae H3 K4,36,79R mutant vs wild type in glucose media

Project description:Total RNA from two replicate cultures of wild-type and mutant strains was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by H3 K4,36,79R mutant. Cells were grown in galactose media and then shifted to glucose media for 9 hours to give the 9 hour time point. Experiment Overall Design: Histone H3 K4,36,79R time course. Cells were grown in galactose media and then shifted to glucose media, which repressed the expression of wild-type histone H3, leaving the histone H3 K4,36,79R mutant as the sole source of histone H3 protein in the cell. Total RNA was isolated from replicate cultures of wild-type and mutant histone H3 at various time points after the shift to glucose media (0, 6, and 9 hours). Expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by H3 K4,36,79R mutant.

2008-06-14 | E-GEOD-6328 | biostudies-arrayexpress