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van Olst B, Nugroho A, Boeren S, Vervoort J, Bachmann H, Kleerebezem M. Bacterial proteome adaptation during fermentation in dairy environments. Food Microbiol 2024; 121:104514. [PMID: 38637076 DOI: 10.1016/j.fm.2024.104514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 04/20/2024]
Abstract
The enzymatic repertoire of starter cultures belonging to the Lactococcus genus determines various important characteristics of fermented dairy products but might change in response to the substantial environmental changes in the manufacturing process. Assessing bacterial proteome adaptation in dairy and other food environments is challenging due to the high matrix-protein concentration and is even further complicated in particularly cheese by the high fat concentrations, the semi-solid state of that matrix, and the non-growing state of the bacteria. Here, we present bacterial harvesting and processing procedures that enable reproducible, high-resolution proteome determination in lactococcal cultures harvested from laboratory media, milk, and miniature Gouda cheese. Comparative proteome analysis of Lactococcus cremoris NCDO712 grown in laboratory medium and milk revealed proteome adaptations that predominantly reflect the differential (micro-)nutrient availability in these two environments. Additionally, the drastic environmental changes during cheese manufacturing only elicited subtle changes in the L. cremoris NCDO712 proteome, including modified expression levels of enzymes involved in flavour formation. The technical advances we describe offer novel opportunities to evaluate bacterial proteomes in relation to their performance in complex, protein- and/or fat-rich food matrices and highlight the potential of steering starter culture performance by preculture condition adjustments.
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Affiliation(s)
- Berdien van Olst
- Host-Microbe Interactomics, Wageningen University & Research, Wageningen, the Netherlands; Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands; TI Food and Nutrition, Wageningen, the Netherlands
| | - Avis Nugroho
- Host-Microbe Interactomics, Wageningen University & Research, Wageningen, the Netherlands; Microbiology Department, NIZO Food Research, Ede, the Netherlands; TI Food and Nutrition, Wageningen, the Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands; TI Food and Nutrition, Wageningen, the Netherlands
| | - Jacques Vervoort
- Host-Microbe Interactomics, Wageningen University & Research, Wageningen, the Netherlands; Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands; TI Food and Nutrition, Wageningen, the Netherlands
| | - Herwig Bachmann
- Microbiology Department, NIZO Food Research, Ede, the Netherlands; Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; TI Food and Nutrition, Wageningen, the Netherlands
| | - Michiel Kleerebezem
- Host-Microbe Interactomics, Wageningen University & Research, Wageningen, the Netherlands; TI Food and Nutrition, Wageningen, the Netherlands.
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Douwenga S, van Olst B, Boeren S, Luo Y, Lai X, Teusink B, Vervoort J, Kleerebezem M, Bachmann H. The hierarchy of sugar catabolization in Lactococcus cremoris. Microbiol Spectr 2023; 11:e0224823. [PMID: 37888986 PMCID: PMC10715065 DOI: 10.1128/spectrum.02248-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE The availability of nutrients to microorganisms varies considerably between different environments, and changes can occur rapidly. As a general rule, a fast growth rate-typically growth on glucose-is associated with the repression of other carbohydrate utilization genes, but it is not clear to what extent catabolite repression is exerted by other sugars. We investigated the hierarchy of sugar utilization after substrate transitions in Lactococcus cremoris. For this, we determined the proteome and carbohydrate utilization capacity after growth on different sugars. The results show that the preparedness of cells for the utilization of "slower" sugars is not strictly determined by the growth rate. The data point to individual proteins relevant for various sugar transitions and suggest that the evolutionary history of the organism might be responsible for deviations from a strictly growth rate-related sugar catabolization hierarchy.
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Affiliation(s)
- Sieze Douwenga
- TI Food and Nutrition, Wageningen, the Netherlands
- Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Berdien van Olst
- TI Food and Nutrition, Wageningen, the Netherlands
- Host-Microbe Interactomics, Wageningen University & Research, Wageningen, the Netherlands
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Sjef Boeren
- TI Food and Nutrition, Wageningen, the Netherlands
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Yanzhang Luo
- MAGNEtic resonance research FacilitY (MAGNEFY), Wageningen University & Research, Wageningen, the Netherlands
| | - Xin Lai
- Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Bas Teusink
- TI Food and Nutrition, Wageningen, the Netherlands
- Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Jacques Vervoort
- TI Food and Nutrition, Wageningen, the Netherlands
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Michiel Kleerebezem
- TI Food and Nutrition, Wageningen, the Netherlands
- Host-Microbe Interactomics, Wageningen University & Research, Wageningen, the Netherlands
| | - Herwig Bachmann
- TI Food and Nutrition, Wageningen, the Netherlands
- Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Microbiology Department, NIZO Food Research, Ede, the Netherlands
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Chen Y, van Pelt‐KleinJan E, van Olst B, Douwenga S, Boeren S, Bachmann H, Molenaar D, Nielsen J, Teusink B. Proteome constraints reveal targets for improving microbial fitness in nutrient-rich environments. Mol Syst Biol 2021; 17:e10093. [PMID: 33821549 PMCID: PMC8022198 DOI: 10.15252/msb.202010093] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 11/28/2022] Open
Abstract
Cells adapt to different conditions via gene expression that tunes metabolism for maximal fitness. Constraints on cellular proteome may limit such expression strategies and introduce trade-offs. Resource allocation under proteome constraints has explained regulatory strategies in bacteria. It is unclear, however, to what extent these constraints can predict evolutionary changes, especially for microorganisms that evolved under nutrient-rich conditions, i.e., multiple available nitrogen sources, such as Lactococcus lactis. Here, we present a proteome-constrained genome-scale metabolic model of L. lactis (pcLactis) to interpret growth on multiple nutrients. Through integration of proteomics and flux data, in glucose-limited chemostats, the model predicted glucose and arginine uptake as dominant constraints at low growth rates. Indeed, glucose and arginine catabolism were found upregulated in evolved mutants. At high growth rates, pcLactis correctly predicted the observed shutdown of arginine catabolism because limited proteome availability favored lactate for ATP production. Thus, our model-based analysis is able to identify and explain the proteome constraints that limit growth rate in nutrient-rich environments and thus form targets of fitness improvement.
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Affiliation(s)
- Yu Chen
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
- Novo Nordisk Foundation Center for BiosustainabilityChalmers University of TechnologyGothenburgSweden
| | - Eunice van Pelt‐KleinJan
- TiFNWageningenthe Netherlands
- Systems Biology LabAmsterdam Institute of Molecular and Life Sciences (AIMMS)Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Berdien van Olst
- TiFNWageningenthe Netherlands
- Host‐Microbe InteractomicsWageningen University & ResearchWageningenThe Netherlands
- Laboratory of BiochemistryWageningen University & ResearchWageningenThe Netherlands
| | - Sieze Douwenga
- TiFNWageningenthe Netherlands
- Systems Biology LabAmsterdam Institute of Molecular and Life Sciences (AIMMS)Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Sjef Boeren
- TiFNWageningenthe Netherlands
- Laboratory of BiochemistryWageningen University & ResearchWageningenThe Netherlands
| | - Herwig Bachmann
- TiFNWageningenthe Netherlands
- Systems Biology LabAmsterdam Institute of Molecular and Life Sciences (AIMMS)Vrije Universiteit AmsterdamAmsterdamThe Netherlands
- NIZO Food ResearchEdeThe Netherlands
| | - Douwe Molenaar
- TiFNWageningenthe Netherlands
- Systems Biology LabAmsterdam Institute of Molecular and Life Sciences (AIMMS)Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Jens Nielsen
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
- Novo Nordisk Foundation Center for BiosustainabilityChalmers University of TechnologyGothenburgSweden
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkLyngbyDenmark
- BioInnovation InstituteCopenhagen NDenmark
| | - Bas Teusink
- TiFNWageningenthe Netherlands
- Systems Biology LabAmsterdam Institute of Molecular and Life Sciences (AIMMS)Vrije Universiteit AmsterdamAmsterdamThe Netherlands
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