1
|
Savijoki K, Deptula P, Roberts RJ, Hammarén M, Yli-Kauhaluoma J, Varmanen P, Parikka M. Revised whole genome and DNA methylome of Mycobacterium marinum type strain ATCC 927 T. Microbiol Resour Announc 2024; 13:e0101623. [PMID: 38415640 PMCID: PMC11008211 DOI: 10.1128/mra.01016-23] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
Mycobacterium marinum, a slow-growing Actinobacterium, typically induces tuberculosis-like disease in fish. Here, we report a new reference sequence for M. marinum ATCC 927T, along with its DNA methylome. This aims to maximize the research potential of this type strain and facilitates investigations into the pathomechanisms of human tuberculosis.
Collapse
Affiliation(s)
- Kirsi Savijoki
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
- Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Paulina Deptula
- Department of Food Science (FOOD), University of Copenhagen, Frederiksberg, Denmark
| | | | - Milka Hammarén
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jari Yli-Kauhaluoma
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Pekka Varmanen
- Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Mataleena Parikka
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| |
Collapse
|
2
|
Perković I, Poljak T, Savijoki K, Varmanen P, Maravić-Vlahoviček G, Beus M, Kučević A, Džajić I, Rajić Z. Synthesis and Biological Evaluation of New Quinoline and Anthranilic Acid Derivatives as Potential Quorum Sensing Inhibitors. Molecules 2023; 28:5866. [PMID: 37570836 PMCID: PMC10420644 DOI: 10.3390/molecules28155866] [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: 07/05/2023] [Revised: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Inhibiting quorum sensing (QS), a central communication system, is a promising strategy to combat bacterial pathogens without antibiotics. Here, we designed novel hybrid compounds targeting the PQS (Pseudomonas quinolone signal)-dependent quorum sensing (QS) of Pseudomonas aeruginosa that is one of the multidrug-resistant and highly virulent pathogens with urgent need of new antibacterial strategies. We synthesized 12 compounds using standard procedures to combine halogen-substituted anthranilic acids with 4-(2-aminoethyl/4-aminobuthyl)amino-7-chloroquinoline, linked via 1,3,4-oxadiazole. Their antibiofilm activities were first pre-screened using Gram-negative Chromobacterium violaceum-based reporter, which identified compounds 15-19 and 23 with the highest anti-QS and minimal bactericidal effects in a single experiment. These five compounds were then evaluated against P. aeruginosa PAO1 to assess their ability to prevent biofilm formation, eradicate pre-formed biofilms, and inhibit virulence using pyocyanin as a representative marker. Compound 15 displayed the most potent antibiofilm effect, reducing biofilm formation by nearly 50% and pre-formed biofilm masses by 25%. On the other hand, compound 23 exhibited the most significant antivirulence effect, reducing pyocyanin synthesis by over 70%. Thus, our study highlights the potential of 1,3,4-oxadiazoles 15 and 23 as promising scaffolds to combat P. aeruginosa. Additionally, interactive QS systems should be considered to achieve maximal anti-QS activity against this clinically relevant species.
Collapse
Affiliation(s)
- Ivana Perković
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia; (G.M.-V.); (M.B.); (A.K.); (Z.R.)
| | | | - Kirsi Savijoki
- Department of Food and Nutrition, Faculty of Agriculture and Forestry, University of Helsinki, 00014 Helsinki, Finland;
| | - Pekka Varmanen
- Department of Food and Nutrition, Faculty of Agriculture and Forestry, University of Helsinki, 00014 Helsinki, Finland;
| | - Gordana Maravić-Vlahoviček
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia; (G.M.-V.); (M.B.); (A.K.); (Z.R.)
| | - Maja Beus
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia; (G.M.-V.); (M.B.); (A.K.); (Z.R.)
| | - Anja Kučević
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia; (G.M.-V.); (M.B.); (A.K.); (Z.R.)
| | - Ivan Džajić
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Zrinka Rajić
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia; (G.M.-V.); (M.B.); (A.K.); (Z.R.)
| |
Collapse
|
3
|
Hautala K, Pursiainen J, Näreaho A, Nyman T, Varmanen P, Sukura A, Nielsen MK, Savijoki K. Label-free quantitative proteomics and immunoblotting identifies immunoreactive and other excretory-secretory (E/S) proteins of Anoplocephala perfoliata. Front Immunol 2022; 13:1045468. [DOI: 10.3389/fimmu.2022.1045468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/24/2022] [Indexed: 11/17/2022] Open
Abstract
Anoplocephala perfoliata is a common tapeworm in horses causing colic and even mortalities. Current diagnostic tests to detect A. perfoliata infections have their limitations and an improved method is needed. Immunoreactive excretory/secretory proteins (E/S proteome) of this parasite can provide promising candidates for diagnostic tests. We compared E/S proteins produced by small (length < 20 mm, width < 5 mm) and large (length 20 to 40 mm, width 5 to 10 mm) A. perfoliata worms in vitro by label-free quantitative proteomics using a database composed of related Hymenolepis diminuta, Echinococcus multilocularis/granulosus and Taenia aseatica proteins for protein identifications. Altogether, 509 E/S proteins were identified after incubating the worms in vitro for three and eight hours. The greatest E/S proteome changes suggested both worm size- and time-dependent changes in cytoskeleton remodeling, apoptosis, and production of antigens/immunogens. The E/S proteins collected at the three-hour time point represented the natural conditions better than those collected at the eight-hour time point, and thereby contained the most relevant diagnostic targets. Immunoblotting using antibodies from horses tested positive/negative for A. perfoliata indicated strongest antigenicity/immunogenicity with 13-, 30- and 100-kDa proteins, involving a thioredoxin, heat-shock chaperone 90 (Hsp90), dynein light chain component (DYNLL), tubulin-specific chaperone A (TBCA) and signaling pathway modulators (14-3-3 and Sj-Ts4). This is among the first studies identifying new diagnostic targets and A. perfoliata antigens eliciting a IgG-response in horses.
Collapse
|
4
|
Beus M, Persoons L, Daelemans D, Schols D, Savijoki K, Varmanen P, Yli-Kauhaluoma J, Pavić K, Zorc B. Anthranilamides with quinoline and β-carboline scaffolds: design, synthesis, and biological activity. Mol Divers 2022; 26:2595-2612. [PMID: 34997441 PMCID: PMC8741576 DOI: 10.1007/s11030-021-10347-8] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 11/02/2021] [Indexed: 11/27/2022]
Abstract
In the present study, we report the design and synthesis of novel amide-type hybrid molecules based on anthranilic acid and quinoline or β-carboline heterocyclic scaffolds. Three types of biological screenings were performed: (i) in vitro antiproliferative screening against a panel of solid tumor and leukemia cell lines, (ii) antiviral screening against several RNA viruses, and (iii) anti-quorum sensing screening using gram-negative Chromobacterium violaceum as the reporter strain. Antiproliferative screening revealed a high activity of several compounds. Anthranilamides 12 and 13 with chloroquine core and halogenated anthranilic acid were the most active agents toward diverse cancer cell lines such as glioblastoma, pancreatic adenocarcinoma, colorectal carcinoma, lung carcinoma, acute lymphoblastic, acute myeloid, chronic myeloid leukemia, and non-Hodgkin lymphoma, but also against noncancerous cell lines. Boc-protected analogs 2 and 3 showed moderate activities against the tested cancer cells without toxic effects against noncancerous cells. A nonhalogenated quinoline derivative 10 with N-benzylanthranilic acid residue was equally active as 12 and 13 and selective toward tumor cells. Chloroquine and quinoline anthranilamides 10-13 exerted pronounced antiviral effect against human coronaviruses 229E and OC43, whereas 12 and 13 against coronavirus OC43 (EC50 values in low micromolar range; selectivity indices from 4.6 to > 10.4). Anthranilamides 14 and 16 with PQ core inhibited HIV-1 with EC50 values of 9.3 and 14.1 µM, respectively. Compound 13 displayed significant anti-quorum/biofilm effect against the quorum sensing reporter strain (IC50 of 3.7 μM) with no apparent bactericidal effect.
Collapse
Affiliation(s)
- Maja Beus
- Department of Medicinal Chemistry, Faculty of Pharmacy and Biochemistry, University of Zagreb, 10 000, Zagreb, Croatia
| | - Leentje Persoons
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, 3000, Leuven, Belgium
| | - Dirk Daelemans
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, 3000, Leuven, Belgium
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, 3000, Leuven, Belgium
| | - Kirsi Savijoki
- Drug Research Program, Division of Pharmaceutical Biosciences, University of Helsinki, 00014, Helsinki, Finland.,Department of Food and Nutrition, University of Helsinki, 00014, Helsinki, Finland
| | - Pekka Varmanen
- Department of Food and Nutrition, University of Helsinki, 00014, Helsinki, Finland
| | - Jari Yli-Kauhaluoma
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, University of Helsinki, 00014, Helsinki, Finland
| | - Kristina Pavić
- Department of Medicinal Chemistry, Faculty of Pharmacy and Biochemistry, University of Zagreb, 10 000, Zagreb, Croatia
| | - Branka Zorc
- Department of Medicinal Chemistry, Faculty of Pharmacy and Biochemistry, University of Zagreb, 10 000, Zagreb, Croatia.
| |
Collapse
|
5
|
Chamlagain B, Peltonen L, Edelmann M, Ramos-Diaz JM, Kemppinen A, Jouppila K, Varmanen P, Piironen V. Bioaccessibility of vitamin B12 synthesized by Propionibacterium freudenreichii and from products made with fermented wheat bran extract. Curr Res Food Sci 2021; 4:499-502. [PMID: 34382008 PMCID: PMC8340120 DOI: 10.1016/j.crfs.2021.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/23/2021] [Accepted: 07/23/2021] [Indexed: 12/29/2022] Open
Abstract
The bioaccessibility of vitamin B12 (B12) in plant-based products fortified using wheat bran extract fermented with B12-producing food-grade Propionibacterium freudenreichii was studied by applying a standard static in vitro model. At first, a culture of P. freudenreichii, fresh or heat-treated, was subjected to in vitro assays. Then, food ingredients or products were evaluated for their in vitro bioaccessibility: spray-dried wheat bran extract powder, pasta made with an extruder using fermented bran extract and breads made with spray-dried powder or with added cyanocobalamin. B12 bioaccessibility from the fresh P. freudenreichii culture was only ca. 53%, which, when heated, increased to 73%. The bioaccessibility of B12 from the food products varied from 75% (spray-dried powder) to 95% (breads). B12 from the fortified bread was as bioaccessible as from the bread made with added cyanocobalamin (99%). The in vitro results suggest that B12 synthesized by P. freudenreichii, when fortified in the studied cereal-based products, is largely bioaccessible and could be available for absorption. Plant-based products fortified using fermentation with P. freudenreichii could thus be considered excellent sources of bioaccessible B12.
Collapse
Affiliation(s)
- Bhawani Chamlagain
- Department of Food and Nutrition, University of Helsinki, P.O. Box 66, FI, 00014, University of Helsinki, Finland
| | - Liisa Peltonen
- Department of Food and Nutrition, University of Helsinki, P.O. Box 66, FI, 00014, University of Helsinki, Finland
| | - Minnamari Edelmann
- Department of Food and Nutrition, University of Helsinki, P.O. Box 66, FI, 00014, University of Helsinki, Finland
| | - Jose Martin Ramos-Diaz
- Department of Food and Nutrition, University of Helsinki, P.O. Box 66, FI, 00014, University of Helsinki, Finland
| | - Asmo Kemppinen
- Department of Food and Nutrition, University of Helsinki, P.O. Box 66, FI, 00014, University of Helsinki, Finland
| | - Kirsi Jouppila
- Department of Food and Nutrition, University of Helsinki, P.O. Box 66, FI, 00014, University of Helsinki, Finland
| | - Pekka Varmanen
- Department of Food and Nutrition, University of Helsinki, P.O. Box 66, FI, 00014, University of Helsinki, Finland
| | - Vieno Piironen
- Department of Food and Nutrition, University of Helsinki, P.O. Box 66, FI, 00014, University of Helsinki, Finland
| |
Collapse
|
6
|
Xie C, Coda R, Chamlagain B, Edelmann M, Varmanen P, Piironen V, Katina K. Fermentation of cereal, pseudo-cereal and legume materials with Propionibacterium freudenreichii and Levilactobacillus brevis for vitamin B12 fortification. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110431] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
7
|
Ojala T, Lindford A, Savijoki K, Lagus H, Tommila J, Medlar A, Kuusela P, Varmanen P, Holm L, Vuola J, Kankuri E, Kankainen M. Metatranscriptomic assessment of burn wound infection clearance. Clin Microbiol Infect 2020; 27:144-146. [PMID: 32712245 DOI: 10.1016/j.cmi.2020.07.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/22/2020] [Accepted: 07/16/2020] [Indexed: 11/16/2022]
Affiliation(s)
- Teija Ojala
- Department of Pharmacology, University of Helsinki, Helsinki, Finland
| | - Andrew Lindford
- Department of Plastic Surgery, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Kirsi Savijoki
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | - Heli Lagus
- Department of Plastic Surgery, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Jenni Tommila
- Department of Pharmacology, University of Helsinki, Helsinki, Finland
| | - Alan Medlar
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Pentti Kuusela
- Department of Bacteriology and Immunology, Haartman Institute, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Pekka Varmanen
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | - Liisa Holm
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jyrki Vuola
- Department of Plastic Surgery, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Esko Kankuri
- Department of Pharmacology, University of Helsinki, Helsinki, Finland
| | - Matti Kankainen
- Medical and Clinical Genetics, University of Helsinki, Helsinki University Hospital, Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
8
|
Savijoki K, Miettinen I, Nyman TA, Kortesoja M, Hanski L, Varmanen P, Fallarero A. Growth Mode and Physiological State of Cells Prior to Biofilm Formation Affect Immune Evasion and Persistence of Staphylococcus aureus. Microorganisms 2020; 8:E106. [PMID: 31940921 PMCID: PMC7023439 DOI: 10.3390/microorganisms8010106] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 01/01/2023] Open
Abstract
The present study investigated Staphylococcus aureus ATCC25923 surfaceomes (cell surface proteins) during prolonged growth by subjecting planktonic and biofilm cultures (initiated from exponential or stationary cells) to label-free quantitative surfaceomics and phenotypic confirmations. The abundance of adhesion, autolytic, hemolytic, and lipolytic proteins decreased over time in both growth modes, while an opposite trend was detected for many tricarboxylic acid (TCA) cycle, reactive oxygen species (ROS) scavenging, Fe-S repair, and peptidolytic moonlighters. In planktonic cells, these changes were accompanied by decreasing and increasing adherence to hydrophobic surface and fibronectin, respectively. Specific RNA/DNA binding (cold-shock protein CspD and ribosomal proteins) and the immune evasion (SpA, ClfA, and IsaB) proteins were notably more abundant on fully mature biofilms initiated with stationary-phase cells (SDBF) compared to biofilms derived from exponential cells (EDBF) or equivalent planktonic cells. The fully matured SDBF cells demonstrated higher viability in THP-1 monocyte/macrophage cells compared to the EDBF cells. Peptidoglycan strengthening, specific urea-cycle, and detoxification enzymes were more abundant on planktonic than biofilm cells, indicating the activation of growth-mode specific pathways during prolonged cultivation. Thus, we show that S. aureus shapes its surfaceome in a growth mode-dependent manner to reach high levofloxacin tolerance (>200-times the minimum biofilm inhibitory concentration). This study also demonstrates that the phenotypic state of the cells prior to biofilm formation affects the immune-evasion and persistence-related traits of S. aureus.
Collapse
Affiliation(s)
- Kirsi Savijoki
- Pharmaceutical Design and Discovery (PharmDD) Group, Pharmaceutical Biology, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5, 00014 Helsinki, Finland; (I.M.); (M.K.); (L.H.); (A.F.)
| | - Ilkka Miettinen
- Pharmaceutical Design and Discovery (PharmDD) Group, Pharmaceutical Biology, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5, 00014 Helsinki, Finland; (I.M.); (M.K.); (L.H.); (A.F.)
| | - Tuula A. Nyman
- Department of Immunology, Institute of Clinical Medicine, University of Oslo and Rikshospitalet Oslo, 0372 Oslo, Norway; or
| | - Maarit Kortesoja
- Pharmaceutical Design and Discovery (PharmDD) Group, Pharmaceutical Biology, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5, 00014 Helsinki, Finland; (I.M.); (M.K.); (L.H.); (A.F.)
| | - Leena Hanski
- Pharmaceutical Design and Discovery (PharmDD) Group, Pharmaceutical Biology, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5, 00014 Helsinki, Finland; (I.M.); (M.K.); (L.H.); (A.F.)
| | - Pekka Varmanen
- Department of Food and Nutrition, University of Helsinki, 00014 Helsinki, Finland;
| | - Adyary Fallarero
- Pharmaceutical Design and Discovery (PharmDD) Group, Pharmaceutical Biology, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5, 00014 Helsinki, Finland; (I.M.); (M.K.); (L.H.); (A.F.)
| |
Collapse
|
9
|
Deptula P, Loivamaa I, Smolander OP, Laine P, Roberts RJ, Piironen V, Paulin L, Savijoki K, Auvinen P, Varmanen P. Red-Brown Pigmentation of Acidipropionibacterium jensenii Is Tied to Haemolytic Activity and cyl-Like Gene Cluster. Microorganisms 2019; 7:microorganisms7110512. [PMID: 31671651 PMCID: PMC6920887 DOI: 10.3390/microorganisms7110512] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/21/2019] [Accepted: 10/29/2019] [Indexed: 01/28/2023] Open
Abstract
The novel Acidipropionibacterium genus encompasses species of industrial importance but also those associated with food spoilage. In particular, Acidipropionibacterium acidipropionici, Acidipropionibacterium thoenii, and Acidipropionibacterium jensenii play an important role in food fermentation, as biopreservatives, or as potential probiotics. Notably, A. jensenii and A. thoenii can cause brown spot defects in Swiss-type cheeses, which have been tied to the rhamnolipid pigment granadaene. In the pathogenic bacterium Streptococcus agalactiae, production of granadaene depends on the presence of a cyl gene cluster, an important virulence factor linked with haemolytic activity. Here, we show that the production of granadaene in pigmented Acidipropionibacterium, including A. jensenii, A. thoenii, and Acidipropionibacterium virtanenii, is tied to haemolytic activity and the presence of a cyl-like gene cluster. Furthermore, we propose a PCR-based test, which allows pinpointing acidipropionibacteria with the cyl-like gene cluster. Finally, we present the first two whole genome sequence analyses of the A. jensenii strains as well as testing phenotypic characteristics important for industrial applications. In conclusion, the present study sheds light on potential risks associated with the presence of pigmented Acidipropionibacterium strains in food fermentation. In addition, the results presented here provide ground for development of a quick and simple diagnostic test instrumental in avoiding potential negative effects of Acidipropionibacterium strains with haemolytic activity on food quality.
Collapse
Affiliation(s)
- Paulina Deptula
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland.
- Department of Food Sciences, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark.
| | - Iida Loivamaa
- Department of Food and Nutrition, University of Helsinki, 00014 Helsinki, Finland.
| | | | - Pia Laine
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland.
| | | | - Vieno Piironen
- Department of Food and Nutrition, University of Helsinki, 00014 Helsinki, Finland.
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland.
| | - Kirsi Savijoki
- Division of Pharmaceutical Biosciences, University of Helsinki, 00014 Helsinki, Finland.
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland.
| | - Pekka Varmanen
- Department of Food and Nutrition, University of Helsinki, 00014 Helsinki, Finland.
| |
Collapse
|
10
|
Xie C, Coda R, Chamlagain B, Varmanen P, Piironen V, Katina K. Co-fermentation of Propionibacterium freudenreichii and Lactobacillus brevis in Wheat Bran for in situ Production of Vitamin B12. Front Microbiol 2019; 10:1541. [PMID: 31333632 PMCID: PMC6624789 DOI: 10.3389/fmicb.2019.01541] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 06/20/2019] [Indexed: 02/05/2023] Open
Abstract
The present study investigated the effect of co-fermentation on vitamin B12 content and microbiological composition of wheat bran. Propionibacterium freudenreichii DSM 20271 was used as the producer of vitamin while Lactobacillus brevis ATCC 14869 was selected to ensure the microbial safety of the bran dough. Fermentation trials were conducted in bioreactors to monitor and adjust the pH of the ferments. Vitamin B12 level reached 357 ± 8 ng/g dry weight (dw) after 1 day of pH-controlled fermentation with P. freudenreichii monoculture and remained stable thereafter. In co-fermentation with L. brevis, slightly less vitamin B12 (255 ± 31 ng/g dw) was produced in 1 day and an effective inhibition of the growth of total Enterobacteriaceae and Bacillus cereus was obtained. On day 3, vitamin B12 content in pH-controlled co-fermentation increased to 332 ± 44 ng/g dw. On the other hand, without a pH control, co-fermentation resulted in a stronger inhibition of Enterobacteriaceae and B. cereus but a lower level of vitamin B12 (183 ± 5 ng/g dw on day 3). These results demonstrated that wheat bran fermented by P. freudenreichii and L. brevis can be a promising way to produce vitamin B12 fortified plant-origin food ingredients, which could reduce cereal waste streams and contribute to a more resilient food chain.
Collapse
Affiliation(s)
- Chong Xie
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | - Rossana Coda
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | - Bhawani Chamlagain
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | - Pekka Varmanen
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | - Vieno Piironen
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | - Kati Katina
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| |
Collapse
|
11
|
Savijoki K, Nyman TA, Kainulainen V, Miettinen I, Siljamäki P, Fallarero A, Sandholm J, Satokari R, Varmanen P. Growth Mode and Carbon Source Impact the Surfaceome Dynamics of Lactobacillus rhamnosus GG. Front Microbiol 2019; 10:1272. [PMID: 31231350 PMCID: PMC6560171 DOI: 10.3389/fmicb.2019.01272] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/22/2019] [Indexed: 12/17/2022] Open
Abstract
Bacterial biofilms have clear implications in disease and in food applications involving probiotics. Here, we show that switching the carbohydrate source from glucose to fructose increased the biofilm formation and the total surface-antigenicity of a well-known probiotic, Lactobacillus rhamnosus GG. Surfaceomes (all cell surface-associated proteins) of GG cells grown with glucose and fructose in planktonic and biofilm cultures were identified and compared, which indicated carbohydrate source-dependent variations, especially during biofilm growth. The most distinctive differences under these conditions were detected with several surface adhesins (e.g., MBF, SpaC pilus protein and penicillin-binding proteins), enzymes (glycoside hydrolases, PrsA, PrtP, PrtR, and HtrA) and moonlighting proteins (glycolytic, transcription/translation and stress-associated proteins, r-proteins, tRNA synthetases, Clp family proteins, PepC, PepN, and PepA). The abundance of several known adhesins and candidate moonlighters, including enzymes acting on casein-derived peptides (ClpP, PepC, and PepN), increased in the biofilm cells grown on fructose, from which the surface-associated aminopeptidase activity mediated by PepC and PepN was further confirmed by an enzymatic assay. The mucus binding factor (MBF) was found most abundant in fructose grown biofilm cells whereas SpaC adhesin was identified specifically from planktonic cells growing on fructose. An additional indirect ELISA indicated both growth mode- and carbohydrate-dependent differences in abundance of SpaC, whereas the overall adherence of GG assessed with porcine mucus indicated that the carbon source and the growth mode affected mucus adhesion. The adherence of GG cells to mucus was almost completely inhibited by anti-SpaC antibodies regardless of growth mode and/or carbohydrate source, indicating the key role of the SpaCBA pilus in adherence under the tested conditions. Altogether, our results suggest that carbon source and growth mode coordinate mechanisms shaping the proteinaceous composition of GG cell surface, which potentially contributes to resistance, nutrient acquisition and cell-cell interactions under different conditions. In conclusion, the present study shows that different growth regimes and conditions can have a profound impact on the adherent and antigenic features of GG, thereby providing new information on how to gain additional benefits from this probiotic.
Collapse
Affiliation(s)
- Kirsi Savijoki
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland.,Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
| | - Tuula A Nyman
- Department of Immunology, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Veera Kainulainen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ilkka Miettinen
- Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
| | - Pia Siljamäki
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | - Adyary Fallarero
- Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
| | - Jouko Sandholm
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland
| | - Reetta Satokari
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Pekka Varmanen
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| |
Collapse
|
12
|
Deptula P, Smolander OP, Laine P, Roberts RJ, Edelmann M, Peltola P, Piironen V, Paulin L, Storgårds E, Savijoki K, Laitila A, Auvinen P, Varmanen P. Acidipropionibacterium virtanenii sp. nov., isolated from malted barley. Int J Syst Evol Microbiol 2018; 68:3175-3183. [PMID: 30156530 DOI: 10.1099/ijsem.0.002965] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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] [Indexed: 12/11/2022] Open
Abstract
A Gram-stain-positive, catalase-positive and pleomorphic rod organism was isolated from malted barley in Finland, classified initially by partial 16S rRNA gene sequencing and originally deposited in the VTT Culture Collection as a strain of Propionibacterium acidipropionici (currently Acidipropionibacterium acidipropionici). The subsequent comparison of the whole 16S rRNA gene with other representatives of the genus Acidipropionibacterium revealed that the strain belongs to a novel species, most closely related to Acidipropionibacterium microaerophilum and Acidipropionibacterium acidipropionici, with similarity values of 98.46 and 98.31 %, respectively. The whole genome sequencing using PacBio RS II platform allowed further comparison of the genome with all of the other DNA sequences available for the type strains of the Acidipropionibacterium species. Those comparisons revealed the highest similarity of strain JS278T to A. acidipropionici, which was confirmed by the average nucleotide identity analysis. The genome of strain JS278T is intermediate in size compared to the A. acidipropionici and Acidipropionibacterium jensenii at 3 432 872 bp, the G+C content is 68.4 mol%. The strain fermented a wide range of carbon sources, and produced propionic acid as the major fermentation product. Besides its poor ability to grow at 37 °C and positive catalase reaction, the observed phenotype was almost indistinguishable from those of A. acidipropionici and A. jensenii. Based on our findings, we conclude that the organism represents a novel member of the genus Acidipropionibacterium, for which we propose the name Acidipropionibacteriumvirtanenii sp. nov. The type strain is JS278T (=VTT E-113202T=DSM 106790T).
Collapse
Affiliation(s)
- Paulina Deptula
- 1Department of Food and Nutrition, University of Helsinki, 00014 Helsinki, Finland
| | | | - Pia Laine
- 2Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | | | - Minnamari Edelmann
- 1Department of Food and Nutrition, University of Helsinki, 00014 Helsinki, Finland
| | | | - Vieno Piironen
- 1Department of Food and Nutrition, University of Helsinki, 00014 Helsinki, Finland
| | - Lars Paulin
- 2Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Erna Storgårds
- 5VTT Technical Research Centre of Finland, 02044 VTT, Finland
| | - Kirsi Savijoki
- 1Department of Food and Nutrition, University of Helsinki, 00014 Helsinki, Finland
| | - Arja Laitila
- 5VTT Technical Research Centre of Finland, 02044 VTT, Finland
| | | | - Pekka Varmanen
- 1Department of Food and Nutrition, University of Helsinki, 00014 Helsinki, Finland
| |
Collapse
|
13
|
Xie C, Coda R, Chamlagain B, Edelmann M, Deptula P, Varmanen P, Piironen V, Katina K. In situ fortification of vitamin B12 in wheat flour and wheat bran by fermentation with Propionibacterium freudenreichii. J Cereal Sci 2018. [DOI: 10.1016/j.jcs.2018.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
14
|
Frohnmeyer E, Deptula P, Nyman TA, Laine PKS, Vihinen H, Paulin L, Auvinen P, Jokitalo E, Piironen V, Varmanen P, Savijoki K. Secretome profiling of Propionibacterium freudenreichii reveals highly variable responses even among the closely related strains. Microb Biotechnol 2018; 11:510-526. [PMID: 29488359 PMCID: PMC5902329 DOI: 10.1111/1751-7915.13254] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 01/19/2018] [Indexed: 12/20/2022] Open
Abstract
This study compared the secretomes (proteins exported out of the cell) of Propionibacterium freudenreichii of different origin to identify plausible adaptation factors. Phylosecretomics indicated strain‐specific variation in secretion of adhesins/invasins (SlpA, InlA), cell‐wall hydrolysing (NlpC60 peptidase, transglycosylase), protective (RpfB) and moonlighting (DnaK, GroEL, GaPDH, IDH, ENO, ClpB) enzymes and/or proteins. Detailed secretome comparison suggested that one of the cereal strains (JS14) released a tip fimbrillin (FimB) in to the extracellular milieu, which was in line with the electron microscopy and genomic analyses, indicating the lack of surface‐associated fimbrial‐like structures, predicting a mutated type‐2 fimbrial gene cluster (fimB‐fimA‐srtC2) and production of anchorless FimB. Instead, the cereal strain produced high amounts of SlpB that tentatively mediated adherent growth on hydrophilic surface and adherence to hydrophobic material. One of the dairy strains (JS22), producing non‐covalently bound surface‐proteins (LspA, ClpB, AraI) and releasing SlpA and InlA into the culture medium, was found to form clumps under physiological conditions. The JS22 strain lacked SlpB and displayed a non‐clumping and biofilm‐forming phenotype only under conditions of increased ionic strength (300 mM NaCl). However, this strain cultured under the same conditions was not adherent to hydrophobic support, which supports the contributory role of SlpB in mediating hydrophobic interactions. Thus, this study reports significant secretome variation in P. freudenreichii and suggests that strain‐specific differences in protein export, modification and protein–protein interactions have been the driving forces behind the adaptation of this bacterial species.
Collapse
Affiliation(s)
- Esther Frohnmeyer
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
| | - Paulina Deptula
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
| | - Tuula A Nyman
- Department of Immunology, Institute of Clinical Medicine, University of Oslo, 0424 Oslo, Norway
| | - Pia K S Laine
- DNA Sequencing and Genomics Lab, Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Helena Vihinen
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Lars Paulin
- DNA Sequencing and Genomics Lab, Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Petri Auvinen
- DNA Sequencing and Genomics Lab, Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Vieno Piironen
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
| | - Pekka Varmanen
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
| | - Kirsi Savijoki
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
| |
Collapse
|
15
|
Chamlagain B, Sugito TA, Deptula P, Edelmann M, Kariluoto S, Varmanen P, Piironen V. In situ production of active vitamin B12 in cereal matrices using Propionibacterium freudenreichii. Food Sci Nutr 2017; 6:67-76. [PMID: 29387363 PMCID: PMC5778212 DOI: 10.1002/fsn3.528] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/22/2017] [Accepted: 08/23/2017] [Indexed: 12/19/2022] Open
Abstract
The in situ production of active vitamin B12 was investigated in aqueous cereal‐based matrices with three strains of food‐grade Propionibacterium freudenreichii. Matrices prepared from malted barley flour (33% w/v; BM), barley flour (6%; BF), and wheat aleurone (15%; AM) were fermented. The effect of cobalt and the lower ligand 5,6‐dimethylbenzimidazole (DMBI) or its natural precursors (riboflavin and nicotinamide) on active B12 production was evaluated. Active B12 production was confirmed by UHPLC–UV–MS analysis. A B12 content of 12–37 μg·kg−1 was produced in BM; this content increased 10‐fold with cobalt and reached 940–1,480 μg·kg−1 with both cobalt and DMBI. With riboflavin and nicotinamide, B12 production in cobalt‐supplemented BM increased to 712 μg·kg−1. Approximately, 10 μg·kg−1 was achieved in BF and AM and was increased to 80 μg·kg−1 in BF and 260 μg·kg−1 in AM with cobalt and DMBI. The UHPLC and microbiological assay (MBA) results agreed when both cobalt and DMBI or riboflavin and nicotinamide were supplemented. However, MBA gave ca. 20%–40% higher results in BM and AM supplemented with cobalt, indicating the presence of human inactive analogues, such as pseudovitamin B12. This study demonstrates that cereal products can be naturally fortified with active B12 to a nutritionally relevant level by fermenting with P. freudenreichii.
Collapse
Affiliation(s)
- Bhawani Chamlagain
- Department of Food and Environmental Sciences University of Helsinki Helsinki Finland
| | - Tessa A Sugito
- Department of Food and Environmental Sciences University of Helsinki Helsinki Finland
| | - Paulina Deptula
- Department of Food and Environmental Sciences University of Helsinki Helsinki Finland
| | - Minnamari Edelmann
- Department of Food and Environmental Sciences University of Helsinki Helsinki Finland
| | - Susanna Kariluoto
- Department of Food and Environmental Sciences University of Helsinki Helsinki Finland
| | - Pekka Varmanen
- Department of Food and Environmental Sciences University of Helsinki Helsinki Finland
| | - Vieno Piironen
- Department of Food and Environmental Sciences University of Helsinki Helsinki Finland
| |
Collapse
|
16
|
Deptula P, Laine PK, Roberts RJ, Smolander OP, Vihinen H, Piironen V, Paulin L, Jokitalo E, Savijoki K, Auvinen P, Varmanen P. De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii. BMC Genomics 2017; 18:790. [PMID: 29037147 PMCID: PMC5644110 DOI: 10.1186/s12864-017-4165-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 06/07/2017] [Accepted: 10/05/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Propionibacterium freudenreichii is an industrially important bacterium granted the Generally Recognized as Safe (the GRAS) status, due to its long safe use in food bioprocesses. Despite the recognized role in the food industry and in the production of vitamin B12, as well as its documented health-promoting potential, P. freudenreichii remained poorly characterised at the genomic level. At present, only three complete genome sequences are available for the species. RESULTS We used the PacBio RS II sequencing platform to generate complete genomes of 20 P. freudenreichii strains and compared them in detail. Comparative analyses revealed both sequence conservation and genome organisational diversity among the strains. Assembly from long reads resulted in the discovery of additional circular elements: two putative conjugative plasmids and three active, lysogenic bacteriophages. It also permitted characterisation of the CRISPR-Cas systems. The use of the PacBio sequencing platform allowed identification of DNA modifications, which in turn allowed characterisation of the restriction-modification systems together with their recognition motifs. The observed genomic differences suggested strain variation in surface piliation and specific mucus binding, which were validated by experimental studies. The phenotypic characterisation displayed large diversity between the strains in ability to utilise a range of carbohydrates, to grow at unfavourable conditions and to form a biofilm. CONCLUSION The complete genome sequencing allowed detailed characterisation of the industrially important species, P. freudenreichii by facilitating the discovery of previously unknown features. The results presented here lay a solid foundation for future genetic and functional genomic investigations of this actinobacterial species.
Collapse
Affiliation(s)
- Paulina Deptula
- Department of Food and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Pia K. Laine
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | | | | | - Helena Vihinen
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Vieno Piironen
- Department of Food and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Eija Jokitalo
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Kirsi Savijoki
- Department of Food and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Pekka Varmanen
- Department of Food and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| |
Collapse
|
17
|
Deptula P, Chamlagain B, Edelmann M, Sangsuwan P, Nyman TA, Savijoki K, Piironen V, Varmanen P. Food-Like Growth Conditions Support Production of Active Vitamin B12 by Propionibacterium freudenreichii 2067 without DMBI, the Lower Ligand Base, or Cobalt Supplementation. Front Microbiol 2017; 8:368. [PMID: 28337185 PMCID: PMC5340759 DOI: 10.3389/fmicb.2017.00368] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 02/22/2017] [Indexed: 01/01/2023] Open
Abstract
Propionibacterium freudenreichii is a traditional dairy bacterium and a producer of short chain fatty acids (propionic and acetic acids) as well as vitamin B12. In food applications, it is a promising organism for in situ fortification with B12 vitamin since it is generally recognized as safe (GRAS) and it is able to synthesize biologically active form of the vitamin. In the present study, vitamin B12 and pseudovitamin biosynthesis by P. freudenreichii was monitored by UHPLC as a function of growth in food-like conditions using a medium mimicking cheese environment, without cobalt or 5,6-dimethylbenzimidazole (DMBI) supplementation. Parallel growth experiments were performed in industrial-type medium known to support the biosynthesis of vitamin B12. The production of other key metabolites in the two media were determined by HPLC, while the global protein production was compared by gel-based proteomics to assess the effect of growth conditions on the physiological status of the strain and on the synthesis of different forms of vitamin. The results revealed distinct protein and metabolite production, which reflected the growth conditions and the potential of P. freudenreichii for synthesizing nutritionally relevant amounts of active vitamin B12 regardless of the metabolic state of the cells.
Collapse
Affiliation(s)
- Paulina Deptula
- Department of Food and Environmental Sciences, University of Helsinki Helsinki, Finland
| | - Bhawani Chamlagain
- Department of Food and Environmental Sciences, University of Helsinki Helsinki, Finland
| | - Minnamari Edelmann
- Department of Food and Environmental Sciences, University of Helsinki Helsinki, Finland
| | - Panchanit Sangsuwan
- Department of Food and Environmental Sciences, University of Helsinki Helsinki, Finland
| | - Tuula A Nyman
- Proteomics Unit, Institute of Biotechnology, University of Helsinki Helsinki, Finland
| | - Kirsi Savijoki
- Department of Food and Environmental Sciences, University of Helsinki Helsinki, Finland
| | - Vieno Piironen
- Department of Food and Environmental Sciences, University of Helsinki Helsinki, Finland
| | - Pekka Varmanen
- Department of Food and Environmental Sciences, University of Helsinki Helsinki, Finland
| |
Collapse
|
18
|
Breüner A, Frees D, Varmanen P, Boguta AM, Hammer K, Martinussen J, Kilstrup M. Ribosomal dimerization factor YfiA is the major protein synthesized after abrupt glucose depletion in Lactococcus lactis. Microbiology (Reading) 2016; 162:1829-1839. [PMID: 27557864 DOI: 10.1099/mic.0.000362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We analysed the response of the model bacterium Lactococcus lactis to abrupt depletion of glucose after several generations of exponential growth. Glucose depletion resulted in a drastic drop in the energy charge accompanied by an extremely low GTP level and an almost total arrest of protein synthesis. Strikingly, the cell prioritized the continued synthesis of a few proteins, of which the ribosomal dimerization factor YfiA was the most highly expressed. Transcriptome analysis showed no immediate decrease in total mRNA levels despite the lowered nucleotide pools and only marginally increased levels of the yfiA transcript. Severe up-regulation of genes in the FruR, CcpA, ArgR and AhrC regulons were consistent with a downshift in carbon and energy source. Based upon the results, we suggest that transcription proceeded long enough to record the transcriptome changes from activation of the FruR, CcpA, ArgR and AhrC regulons, while protein synthesis stopped due to an extremely low GTP concentration emerging a few minutes after glucose depletion. The yfiA deletion mutant exhibited a longer lag phase upon replenishment of glucose and a faster death rate after prolonged starvation supporting that YfiA-mediated ribosomal dimerization is important for keeping long-term starved cells viable and competent for growth initiation.
Collapse
Affiliation(s)
- Anne Breüner
- Metabolic Signaling and Regulation Group, DTU Bioengineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Dorte Frees
- Metabolic Signaling and Regulation Group, DTU Bioengineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Pekka Varmanen
- Metabolic Signaling and Regulation Group, DTU Bioengineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Anna Monika Boguta
- Metabolic Signaling and Regulation Group, DTU Bioengineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Karin Hammer
- Metabolic Signaling and Regulation Group, DTU Bioengineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jan Martinussen
- Metabolic Signaling and Regulation Group, DTU Bioengineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Mogens Kilstrup
- Metabolic Signaling and Regulation Group, DTU Bioengineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| |
Collapse
|
19
|
Savijoki K, Skogman M, Fallarero A, Nyman TA, Sukura A, Vuorela P, Varmanen P. Penicillin G increases the synthesis of a suicidal marker (CidC) and virulence (HlgBC) proteins in Staphylococcus aureus biofilm cells. Int J Med Microbiol 2016; 306:69-74. [PMID: 26725755 DOI: 10.1016/j.ijmm.2015.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 10/30/2015] [Accepted: 11/29/2015] [Indexed: 10/22/2022] Open
Abstract
The present study reports the effect of Penicillin G (PenG) on the proteome dynamics of the Staphylococcus aureus strain Newman during biofilm mode of growth. The viability of the 18-h-old biofilm cells challenged with PenG at the concentration of 1mgmL(-1) was first assessed by plate counting, resazurin and LIVE/DEAD fluorescence staining, which indicated that the viability was reduced by ∼35% and ∼90% at 2h and 24h, respectively, after the addition of PenG. Subsequent two-dimensional difference gel electrophoresis (2D DIGE) assay of the treated and non-treated biofilm cells at the indicated time points revealed 45 proteins showing time- and treatment-specific change (1.5-fold, p<0.01). The 2D DIGE results suggested that the PenG-induced decrease in viability was accompanied by an increased synthesis of pyruvate oxidase (CidC), a suicidal marker known to potentiate acetate-dependent cell death in S. aureus. Increased abundance was also found for the TCA cycle associated malate-quinone oxidoreductase (Mqo), the ClpC ATPase, the HlgBC toxin and phage-associated proteins, which suggests that surviving cells have induced these activities as a last effort to overcome lethal doses of PenG. Proteomic results also revealed that the surviving cells were likely to strengthen their peptidoglycan due to the increased abundance of cell-wall biogenesis associated proteins, FemA and Pbp2; a phenomenon associated with dormancy in S. aureus.
Collapse
Affiliation(s)
- Kirsi Savijoki
- Department of Food and Environmental Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Finland; Institute of Biotechnology, University of Helsinki, Finland; Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Finland.
| | - Malena Skogman
- Pharmaceutical Biology, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Finland
| | - Adyary Fallarero
- Pharmaceutical Biology, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Finland
| | - Tuula A Nyman
- Institute of Biotechnology, University of Helsinki, Finland
| | - Antti Sukura
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Finland
| | - Pia Vuorela
- Pharmaceutical Biology, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Finland
| | - Pekka Varmanen
- Department of Food and Environmental Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Finland
| |
Collapse
|
20
|
Deptula P, Kylli P, Chamlagain B, Holm L, Kostiainen R, Piironen V, Savijoki K, Varmanen P. BluB/CobT2 fusion enzyme activity reveals mechanisms responsible for production of active form of vitamin B₁₂ by Propionibacterium freudenreichii. Microb Cell Fact 2015; 14:186. [PMID: 26597297 PMCID: PMC4657239 DOI: 10.1186/s12934-015-0363-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 10/18/2015] [Indexed: 01/02/2023] Open
Abstract
Background Propionibacterium freudenreichii is a food grade bacterium that has gained attention as a producer of appreciable amounts of cobalamin, a cobamide with activity of vitamin B12. Production of active form of vitamin is a prerequisite for attempts to naturally fortify foods with B12 by microbial fermentation. Active vitamin B12 is distinguished from the pseudovitamin by the presence of 5,6-dimethylbenzimidazole (DMBI) as the lower ligand. Genomic data indicate that P. freudenreichii possesses a fusion gene, bluB/cobT2, coding for a predicted phosphoribosyltransferase/nitroreductase, which is presumably involved in production of vitamin B12. Understanding the mechanisms affecting the synthesis of different vitamin forms is useful for rational strain selection and essential for engineering of strains with improved B12 production properties. Results Here, we investigated the activity of heterologously expressed and purified fusion enzyme BluB/CobT2. Our results show that BluB/CoBT2 is responsible for the biosynthesis of the DMBI base and its activation into α-ribazole phosphate, preparing it for attachment as the lower ligand of cobalamin. The fusion enzyme was found to be efficient in metabolite channeling and the enzymes’ inability to react with adenine, a lower ligand present in the pseudovitamin, revealed a mechanism favoring the production of the active form of the vitamin. P. freudenreichii did not produce cobalamin under strictly anaerobic conditions, confirming the requirement of oxygen for DMBI synthesis. In vivo experiments also revealed a clear preference for incorporating DMBI over adenine into cobamide under both microaerobic and anaerobic conditions. Conclusions The herein described BluB/CobT2 is responsible for the production and activation of DMBI. Fusing those two activities results in high pressure towards production of the true vitamin B12 by efficiently activating DMBI formed within the same enzymatic complex. This indicates that BluB/CobT2 is the crucial enzyme in the B12 biosynthetic pathway of P. freudenreichii. The GRAS organism status and the preference for synthesizing active vitamin form make P. freudenreichii a unique candidate for the in situ production of vitamin B12 within food products. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0363-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Paulina Deptula
- Department of Food and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland.
| | - Petri Kylli
- Division of Pharmaceutical Chemistry and Technology, University of Helsinki, 00014, Helsinki, Finland.
| | - Bhawani Chamlagain
- Department of Food and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland.
| | - Liisa Holm
- Institute of Biotechnology, University of Helsinki, 00014, Helsinki, Finland.
| | - Risto Kostiainen
- Division of Pharmaceutical Chemistry and Technology, University of Helsinki, 00014, Helsinki, Finland.
| | - Vieno Piironen
- Department of Food and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland.
| | - Kirsi Savijoki
- Department of Food and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland.
| | - Pekka Varmanen
- Department of Food and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland.
| |
Collapse
|
21
|
Koskinen P, Deptula P, Smolander OP, Tamene F, Kammonen J, Savijoki K, Paulin L, Piironen V, Auvinen P, Varmanen P. Complete genome sequence of Propionibacterium freudenreichii DSM 20271(T). Stand Genomic Sci 2015; 10:83. [PMID: 26500719 PMCID: PMC4619572 DOI: 10.1186/s40793-015-0082-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 10/15/2015] [Indexed: 11/10/2022] Open
Abstract
Propionibacterium freudenreichii subsp. freudenreichii DSM 20271T is the type strain of species Propionibacterium freudenreichii that has a long history of safe use in the production dairy products and B12 vitamin. P. freudenreichii is the type species of the genus Propionibacterium which contains Gram-positive, non-motile and non-sporeforming bacteria with a high G + C content. We describe the genome of P. freudenreichii subsp. freudenreichii DSM 20271T consisting of a 2,649,166 bp chromosome containing 2320 protein-coding genes and 50 RNA-only encoding genes.
Collapse
Affiliation(s)
- Patrik Koskinen
- Institute of Biotechnology, University of Helsinki, PO Box 56 (Viikinkaari 9), 00014 Helsinki, Finland
| | - Paulina Deptula
- Department of Food and Environmental Sciences, University of Helsinki, PO Box 66 (Agnes Sjöbergin katu 2), 00014 Helsinki, Finland
| | - Olli-Pekka Smolander
- Institute of Biotechnology, University of Helsinki, PO Box 56 (Viikinkaari 9), 00014 Helsinki, Finland
| | - Fitsum Tamene
- Institute of Biotechnology, University of Helsinki, PO Box 56 (Viikinkaari 9), 00014 Helsinki, Finland
| | - Juhana Kammonen
- Institute of Biotechnology, University of Helsinki, PO Box 56 (Viikinkaari 9), 00014 Helsinki, Finland
| | - Kirsi Savijoki
- Department of Food and Environmental Sciences, University of Helsinki, PO Box 66 (Agnes Sjöbergin katu 2), 00014 Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, PO Box 56 (Viikinkaari 9), 00014 Helsinki, Finland
| | - Vieno Piironen
- Department of Food and Environmental Sciences, University of Helsinki, PO Box 66 (Agnes Sjöbergin katu 2), 00014 Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, PO Box 56 (Viikinkaari 9), 00014 Helsinki, Finland
| | - Pekka Varmanen
- Department of Food and Environmental Sciences, University of Helsinki, PO Box 66 (Agnes Sjöbergin katu 2), 00014 Helsinki, Finland
| |
Collapse
|
22
|
Espino E, Koskenniemi K, Mato-Rodriguez L, Nyman TA, Reunanen J, Koponen J, Öhman T, Siljamäki P, Alatossava T, Varmanen P, Savijoki K. Uncovering Surface-Exposed Antigens of Lactobacillus rhamnosus by Cell Shaving Proteomics and Two-Dimensional Immunoblotting. J Proteome Res 2014; 14:1010-24. [DOI: 10.1021/pr501041a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Eva Espino
- Department
of Food and Environmental Sciences, ‡Department of Veterinary Biosciences, and §Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | | | - Lourdes Mato-Rodriguez
- Department
of Food and Environmental Sciences, ‡Department of Veterinary Biosciences, and §Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | | | | | | | | | - Pia Siljamäki
- Department
of Food and Environmental Sciences, ‡Department of Veterinary Biosciences, and §Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Tapani Alatossava
- Department
of Food and Environmental Sciences, ‡Department of Veterinary Biosciences, and §Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Pekka Varmanen
- Department
of Food and Environmental Sciences, ‡Department of Veterinary Biosciences, and §Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Kirsi Savijoki
- Department
of Food and Environmental Sciences, ‡Department of Veterinary Biosciences, and §Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| |
Collapse
|
23
|
Salomäki T, Karonen T, Siljamäki P, Savijoki K, Nyman TA, Varmanen P, Iivanainen A. A Streptococcus uberis transposon mutant screen reveals a negative role for LiaR homologue in biofilm formation. J Appl Microbiol 2014; 118:1-10. [PMID: 25308550 DOI: 10.1111/jam.12664] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/03/2014] [Accepted: 10/07/2014] [Indexed: 11/30/2022]
Abstract
AIMS The environmental pathogen Streptococcus uberis causes intramammary infections in dairy cows. Because biofilm growth might contribute to Strep. uberis mastitis, we conducted a biological screen to identify genes potentially involved in the regulation of biofilm growth. METHODS AND RESULTS By screening a transposon mutant library of Strep. uberis, we determined that the disruption of 13 genes (including hasA, coaC, clpP, miaA, nox and uidA) led to increased biofilm formation. One of the genes (SUB1382) encoded a homologue of the LiaR response regulator (RR) of the Bacillus subtilis two-component signalling system (TCS). Electrophoretic mobility shift assays revealed that DNA binding by LiaR was greatly enhanced by phosphorylation. Two-dimensional differential in-gel electrophoresis analyses of the liaR mutant and the parental Strep. uberis strain revealed five differentially produced proteins with at least a 1·5-fold change in relative abundance (P < 0·05). CONCLUSIONS The DNA-binding protein LiaR is a potential regulator of biofilm formation by Strep. uberis. SIGNIFICANCE AND IMPACT OF THE STUDY Several molecular primary and downstream targets involved in biofilm formation by Strep. uberis were identified. This provides a solid foundation for further studies on the regulation of biofilm formation in this important pathogen.
Collapse
Affiliation(s)
- T Salomäki
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | | | | | | | | | | | | |
Collapse
|
24
|
Savijoki K, Iivanainen A, Siljamäki P, Laine PK, Paulin L, Karonen T, Pyörälä S, Kankainen M, Nyman TA, Salomäki T, Koskinen P, Holm L, Simojoki H, Taponen S, Sukura A, Kalkkinen N, Auvinen P, Varmanen P. Genomics and Proteomics Provide New Insight into the Commensal and Pathogenic Lifestyles of Bovine- and Human-Associated Staphylococcus epidermidis Strains. J Proteome Res 2014; 13:3748-3762. [DOI: 10.1021/pr500322d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
25
|
Siljamäki P, Varmanen P, Kankainen M, Pyörälä S, Karonen T, Iivanainen A, Auvinen P, Paulin L, Laine PK, Taponen S, Simojoki H, Sukura A, Nyman TA, Savijoki K. Comparative proteome profiling of bovine and human Staphylococcus epidermidis strains for screening specifically expressed virulence and adaptation proteins. Proteomics 2014; 14:1890-4. [PMID: 24909406 DOI: 10.1002/pmic.201300275] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 03/19/2014] [Accepted: 06/02/2014] [Indexed: 01/19/2023]
Abstract
The present study reports a comparative proteome cataloging of a bovine mastitis and a human-associated Staphylococcus epidermidis strain with a specific focus on surfome (cell-wall bound and extracellular) proteins. Protein identification by 1DE coupled with LC-MS/MS analyses resulted in 1400 and 1287 proteins from the bovine (PM221) and human (ATCC12228) strains, respectively, covering over 50% of all predicted and more than 30% of all predicted surfome proteins in both strains. Comparison of the identification results suggests elevated levels of proteins involved in adherence, biofilm formation, signal transduction, house-keeping functions, and immune evasion in PM221, whereas ATCC12228 was more effective in expressing host defense evasion proteases, skin adaptation lipases, hemagglutination, and heavy-metal resistance proteins. Phenotypic analyses showed that only PM221 displays protein- and DNA-mediated adherent growth, and that PM221 was more efficient in cleaving tributyrin, a natural compound of milk fat under low CO2 conditions. These findings are in line with the identification data and suggest that distinct expression of lipases and adhesive surfome proteins could lead to the observed phenotypes. This study is the first extensive survey of S. epidermidis proteomes to date, providing several protein candidates to be examined for their roles in adaptation and virulence in vivo. All MS data have been deposited in the ProteomeXchange with identifier PXD000404 (http://proteomecentral.proteomexchange.org/dataset/PXD000404).
Collapse
Affiliation(s)
- Pia Siljamäki
- Institute of Biotechnology, Proteomics Unit, University of Helsinki, Helsinki, Finland; Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Siljamäki P, Varmanen P, Kankainen M, Sukura A, Savijoki K, Nyman TA. Comparative exoprotein profiling of different Staphylococcus epidermidis strains reveals potential link between nonclassical protein export and virulence. J Proteome Res 2014; 13:3249-61. [PMID: 24840314 DOI: 10.1021/pr500075j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Staphylococcus epidermidis (SE) includes commensal and pathogenic strains capable of infecting humans and animals. This study reports global exoproteome profiling of bovine mastitis strain PM221 and two human strains, commensal-type ATCC12228 and sepsis-associated RP62A. We identified 451, 395, and 518 proteins from culture supernatants of PM221, ATCC12228, and RP62A, respectively. Comparison of the identified exoproteomes revealed several strain-specific differences related to secreted antigens and adhesins, higher virulence capability for RP62A, and similarities between the PM221 and RP62A exoproteomes. The majority of the identified proteins (∼80%) were predicted to be cytoplasmic, including proteins known to be associated in membrane vesicles (MVs) in Staphylococcus aureus and immunogenic/adhesive moonlighting proteins. Enrichment of MV fractions from culture supernatants and analysis of their protein composition indicated that this nonclassical protein secretion pathway was being exploited under the conditions used and that there are strain-specific differences in nonclassical protein export. In addition, several predicted cell-surface proteins were identified in the culture media. In summary, the present study is the first in-depth exoproteome analysis of SE highlighting strain-specific factors able to contribute to virulence and adaptation.
Collapse
Affiliation(s)
- Pia Siljamäki
- Department of Food and Environmental Sciences, ‡Institute of Biotechnology, and §Department of Veterinary Biosciences, University of Helsinki , FI-00014 Helsinki, Finland
| | | | | | | | | | | |
Collapse
|
27
|
Wasik AA, Koskelainen S, Hyvönen ME, Musante L, Lehtonen E, Koskenniemi K, Tienari J, Vaheri A, Kerjaschki D, Szalay C, Révész C, Varmanen P, Nyman TA, Hamar P, Holthöfer H, Lehtonen S. Ezrin Is Down-Regulated in Diabetic Kidney Glomeruli and Regulates Actin Reorganization and Glucose Uptake via GLUT1 in Cultured Podocytes. The American Journal of Pathology 2014; 184:1727-39. [DOI: 10.1016/j.ajpath.2014.03.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 02/28/2014] [Accepted: 03/05/2014] [Indexed: 01/27/2023]
|
28
|
Koponen J, Laakso K, Koskenniemi K, Kankainen M, Savijoki K, Nyman TA, de Vos WM, Tynkkynen S, Kalkkinen N, Varmanen P. Effect of acid stress on protein expression and phosphorylation in Lactobacillus rhamnosus GG. J Proteomics 2012; 75:1357-74. [DOI: 10.1016/j.jprot.2011.11.009] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Revised: 10/19/2011] [Accepted: 11/07/2011] [Indexed: 10/15/2022]
|
29
|
Frees D, Andersen JH, Hemmingsen L, Koskenniemi K, Bæk KT, Muhammed MK, Gudeta DD, Nyman TA, Sukura A, Varmanen P, Savijoki K. New Insights into Staphylococcus aureus Stress Tolerance and Virulence Regulation from an Analysis of the Role of the ClpP Protease in the Strains Newman, COL, and SA564. J Proteome Res 2011; 11:95-108. [DOI: 10.1021/pr200956s] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dorte Frees
- Department of Veterinary Disease Biology, Faculty of Life Sciences, University of Copenhagen, Stigbøjlen 4 DK-1870, Frederiksberg C, Denmark
| | - Julie Hove Andersen
- Department of Veterinary Disease Biology, Faculty of Life Sciences, University of Copenhagen, Stigbøjlen 4 DK-1870, Frederiksberg C, Denmark
| | - Lene Hemmingsen
- Department of Veterinary Disease Biology, Faculty of Life Sciences, University of Copenhagen, Stigbøjlen 4 DK-1870, Frederiksberg C, Denmark
- Department of Veterinary Biosciences, University of Helsinki, Finland
| | | | - Kristoffer T. Bæk
- Department of Veterinary Disease Biology, Faculty of Life Sciences, University of Copenhagen, Stigbøjlen 4 DK-1870, Frederiksberg C, Denmark
| | - Musemma Kedir Muhammed
- Department of Veterinary Disease Biology, Faculty of Life Sciences, University of Copenhagen, Stigbøjlen 4 DK-1870, Frederiksberg C, Denmark
| | - Dereje Dadi Gudeta
- Department of Veterinary Disease Biology, Faculty of Life Sciences, University of Copenhagen, Stigbøjlen 4 DK-1870, Frederiksberg C, Denmark
| | - Tuula A. Nyman
- Institute of Biotechnology, University of Helsinki, Finland
| | - Antti Sukura
- Department of Veterinary Biosciences, University of Helsinki, Finland
| | - Pekka Varmanen
- Department of Food and Environmental Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Finland
| | - Kirsi Savijoki
- Institute of Biotechnology, University of Helsinki, Finland
| |
Collapse
|
30
|
Laakso K, Koskenniemi K, Koponen J, Kankainen M, Surakka A, Salusjärvi T, Auvinen P, Savijoki K, Nyman TA, Kalkkinen N, Tynkkynen S, Varmanen P. Growth phase-associated changes in the proteome and transcriptome of Lactobacillus rhamnosus GG in industrial-type whey medium. Microb Biotechnol 2011; 4:746-66. [PMID: 21883975 PMCID: PMC3815411 DOI: 10.1111/j.1751-7915.2011.00275.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The growth phase during which probiotic bacteria are harvested and consumed can strongly influence their performance as health‐promoting agents. In this study, global transcriptomic and proteomic changes were studied in the widely used probiotic Lactobacillus rhamnosus GG during growth in industrial‐type whey medium under strictly defined bioreactor conditions. The expression of 636 genes (P ≤ 0.01) and 116 proteins (P < 0.05) changed significantly over time. Of the significantly differentially produced proteins, 61 were associated with alterations at the transcript level. The most remarkable growth phase‐dependent changes occurred during the transition from the exponential to the stationary growth phase and were associated with the shift from glucose fermentation to galactose utilization and the transition from homolactic to mixed acid fermentation. Furthermore, several genes encoding proteins proposed to promote the survival and persistence of L. rhamnosus GG in the host and proteins that directly contribute to human health showed temporal changes in expression. Our results suggest that L. rhamnosus GG has a highly flexible and adaptable metabolism and that the growth stage during which bacterial cells are harvested and consumed should be taken into consideration to gain the maximal benefit from probiotic bacteria.
Collapse
Affiliation(s)
- Kati Laakso
- Research and Development, Valio Ltd, Helsinki, Finland
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Savijoki K, Lietzén N, Kankainen M, Alatossava T, Koskenniemi K, Varmanen P, Nyman TA. Comparative Proteome Cataloging of Lactobacillus rhamnosus Strains GG and Lc705. J Proteome Res 2011; 10:3460-73. [DOI: 10.1021/pr2000896] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Kirsi Savijoki
- Institute of Biotechnology, University of Helsinki, Finland
- Department of Food and Environmental Sciences, University of Helsinki, Finland
| | - Niina Lietzén
- Institute of Biotechnology, University of Helsinki, Finland
| | | | - Tapani Alatossava
- Department of Food and Environmental Sciences, University of Helsinki, Finland
| | | | - Pekka Varmanen
- Department of Food and Environmental Sciences, University of Helsinki, Finland
| | - Tuula A. Nyman
- Institute of Biotechnology, University of Helsinki, Finland
| |
Collapse
|
32
|
Koskenniemi K, Laakso K, Koponen J, Kankainen M, Greco D, Auvinen P, Savijoki K, Nyman TA, Surakka A, Salusjärvi T, de Vos WM, Tynkkynen S, Kalkkinen N, Varmanen P. Proteomics and transcriptomics characterization of bile stress response in probiotic Lactobacillus rhamnosus GG. Mol Cell Proteomics 2010; 10:M110.002741. [PMID: 21078892 DOI: 10.1074/mcp.m110.002741] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lactobacillus rhamnosus GG (GG) is a widely used and intensively studied probiotic bacterium. Although the health benefits of strain GG are well documented, the systematic exploration of mechanisms by which this strain exerts probiotic effects in the host has only recently been initiated. The ability to survive the harsh conditions of the gastrointestinal tract, including gastric juice containing bile salts, is one of the vital characteristics that enables a probiotic bacterium to transiently colonize the host. Here we used gene expression profiling at the transcriptome and proteome levels to investigate the cellular response of strain GG toward bile under defined bioreactor conditions. The analyses revealed that in response to growth of strain GG in the presence of 0.2% ox gall the transcript levels of 316 genes changed significantly (p < 0.01, t test), and 42 proteins, including both intracellular and surface-exposed proteins (i.e. surfome), were differentially abundant (p < 0.01, t test in total proteome analysis; p < 0.05, t test in surfome analysis). Protein abundance changes correlated with transcriptome level changes for 14 of these proteins. The identified proteins suggest diverse and specific changes in general stress responses as well as in cell envelope-related functions, including in pathways affecting fatty acid composition, cell surface charge, and thickness of the exopolysaccharide layer. These changes are likely to strengthen the cell envelope against bile-induced stress and signal the GG cells of gut entrance. Notably, the surfome analyses demonstrated significant reduction in the abundance of a protein catalyzing the synthesis of exopolysaccharides, whereas a protein dedicated for active removal of bile compounds from the cells was up-regulated. These findings suggest a role for these proteins in facilitating the well founded interaction of strain GG with the host mucus in the presence of sublethal doses of bile. The significance of these findings in terms of the functionality of a probiotic bacterium is discussed.
Collapse
Affiliation(s)
- Kerttu Koskenniemi
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Varhimo E, Varmanen P, Fallarero A, Skogman M, Pyörälä S, Iivanainen A, Sukura A, Vuorela P, Savijoki K. Alpha- and β-casein components of host milk induce biofilm formation in the mastitis bacterium Streptococcus uberis. Vet Microbiol 2010; 149:381-9. [PMID: 21130586 DOI: 10.1016/j.vetmic.2010.11.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 10/15/2010] [Accepted: 11/08/2010] [Indexed: 12/01/2022]
Abstract
Streptococcus uberis is an environmental udder pathogen that infects cattle and can cause persistent intramammary infection (IMI), despite the fact that isolates are mainly susceptible to antibiotics. As biofilm growth can cause persistent infection, the ability of ten S. uberis isolates from clinical and subclinical IMIs to form biofilms on the polystyrene surface of a conventional 96-microplates model was examined. Biofilm formation was judged by different staining methods (crystal violet and resazurin) and by atomic force and fluorescence microscopy. These analyses revealed that two out of ten S. uberis strains tested were able to form biofilms. Upon treatment with Proteinase K, biofilms of S. uberis were completely disintegrated, which indicates that biofilm formation is protein-mediated in these strains. Addition of trace amounts of milk, the natural growth medium of S. uberis, significantly increased biofilm formation by most of the strains initially classified as non-biofilm producers. Alpha-casein and β-casein were the primary inducers of biofilm growth, and casein degradation by serine protease activity was required to achieve maximal biofilm production. These results suggest that the extracellular proteolytic activity of S. uberis contributes to an increased biofilm formation. Such a mode of growth induced by host proteins might help to explain the persistence of IMIs caused by this pathogen.
Collapse
Affiliation(s)
- Emilia Varhimo
- Department of Veterinary Biosciences, P.O. Box 66, University of Helsinki, FI-00014, Helsinki, Finland
| | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Koskenniemi K, Koponen J, Kankainen M, Savijoki K, Tynkkynen S, de Vos WM, Kalkkinen N, Varmanen P. Proteome Analysis of Lactobacillus rhamnosus GG Using 2-D DIGE and Mass Spectrometry Shows Differential Protein Production in Laboratory and Industrial-Type Growth Media. J Proteome Res 2009; 8:4993-5007. [DOI: 10.1021/pr9003823] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Kerttu Koskenniemi
- Department of Basic Veterinary Sciences, University of Helsinki, Finland, Institute of Biotechnology, University of Helsinki, Finland, Valio Ltd., Helsinki, Finland, and Department of Food Technology, University of Helsinki, Finland
| | - Johanna Koponen
- Department of Basic Veterinary Sciences, University of Helsinki, Finland, Institute of Biotechnology, University of Helsinki, Finland, Valio Ltd., Helsinki, Finland, and Department of Food Technology, University of Helsinki, Finland
| | - Matti Kankainen
- Department of Basic Veterinary Sciences, University of Helsinki, Finland, Institute of Biotechnology, University of Helsinki, Finland, Valio Ltd., Helsinki, Finland, and Department of Food Technology, University of Helsinki, Finland
| | - Kirsi Savijoki
- Department of Basic Veterinary Sciences, University of Helsinki, Finland, Institute of Biotechnology, University of Helsinki, Finland, Valio Ltd., Helsinki, Finland, and Department of Food Technology, University of Helsinki, Finland
| | - Soile Tynkkynen
- Department of Basic Veterinary Sciences, University of Helsinki, Finland, Institute of Biotechnology, University of Helsinki, Finland, Valio Ltd., Helsinki, Finland, and Department of Food Technology, University of Helsinki, Finland
| | - Willem M. de Vos
- Department of Basic Veterinary Sciences, University of Helsinki, Finland, Institute of Biotechnology, University of Helsinki, Finland, Valio Ltd., Helsinki, Finland, and Department of Food Technology, University of Helsinki, Finland
| | - Nisse Kalkkinen
- Department of Basic Veterinary Sciences, University of Helsinki, Finland, Institute of Biotechnology, University of Helsinki, Finland, Valio Ltd., Helsinki, Finland, and Department of Food Technology, University of Helsinki, Finland
| | - Pekka Varmanen
- Department of Basic Veterinary Sciences, University of Helsinki, Finland, Institute of Biotechnology, University of Helsinki, Finland, Valio Ltd., Helsinki, Finland, and Department of Food Technology, University of Helsinki, Finland
| |
Collapse
|
35
|
Poutanen M, Varhimo E, Kalkkinen N, Sukura A, Varmanen P, Savijoki K. Two-dimensional difference gel electrophoresis analysis of Streptococcus uberis in response to mutagenesis-inducing ciprofloxacin challenge. J Proteome Res 2009; 8:246-55. [PMID: 19032024 DOI: 10.1021/pr800384j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In Streptococcus uberis, the fluoroquinolone antibiotic ciprofloxacin induces a mutagenic response that is distinct from the SOS paradigm. Two-dimensional differential gel electrophoresis was employed to investigate the effect of ciprofloxacin exposure on the proteome of S. uberis. Twenty-four protein spots exhibiting differential expression (p < 0.05) were identified as enzymes with potential role in oxidative stress, NADH generation and nucleotide biosynthesis. We suggest that these metabolic changes provide S. uberis means to stimulate mutagenesis and adaptation.
Collapse
Affiliation(s)
- Marjo Poutanen
- Institute of Biotechnology, and Department of Basic Veterinary Sciences, University of Helsinki, Finland
| | | | | | | | | | | |
Collapse
|
36
|
Varhimo E, Savijoki K, Jefremoff H, Jalava J, Sukura A, Varmanen P. Ciprofloxacin induces mutagenesis to antibiotic resistance independent of UmuC inStreptococcus uberis. Environ Microbiol 2008; 10:2179-83. [DOI: 10.1111/j.1462-2920.2008.01634.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
37
|
Suokko A, Poutanen M, Savijoki K, Kalkkinen N, Varmanen P. ClpL is essential for induction of thermotolerance and is potentially part of the HrcA regulon in Lactobacillus gasseri. Proteomics 2008; 8:1029-41. [PMID: 18240137 DOI: 10.1002/pmic.200700925] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Stress-inducible proteins are likely to contribute to the survival and activity of probiotic bacteria during industrial processes and in the gastrointestinal tract. The recently published genome sequence of probiotic Lactobacillus gasseri ATCC 33323 suggests the presence of ClpC, ClpE, ClpL, and ClpX from the Clp ATPase family of stress proteins. The heat-shock response of L. gasseri was studied using 2-D DIGE. A total of 20 protein spots showing significant (p<0.05) increase in abundance after 30 min heat-shock were identified, including DnaK, GroEL, ClpC, ClpE, and ClpL. To study the physiological role of ClpL, one of the most highly induced proteins during heat-shock, its corresponding gene was inactivated. The DeltaclpL mutant strain had growth characteristics that were indistinguishable from wild-type under several stress conditions. However, in the absence of functional ClpL, L. gasseri exhibited drastically reduced survival at a lethal temperature and was unable to induce thermotolerance. Genome sequences indicate that the expression of clp genes in several Lactobacillus species is regulated by HrcA, instead of CtsR, the conserved clp gene regulator of low G+C Gram-positive bacteria. Electrophoretic mobility shift assays using L. gasseri HrcA protein and clpL upstream fragments revealed, for the first time, a direct interaction between HrcA and the promoter of a clp gene from a Lactobacillus.
Collapse
Affiliation(s)
- Aki Suokko
- Department of Basic Veterinary Sciences, University of Helsinki, Finland
| | | | | | | | | |
Collapse
|
38
|
Frees D, Savijoki K, Varmanen P, Ingmer H. Clp ATPases and ClpP proteolytic complexes regulate vital biological processes in low GC, Gram-positive bacteria. Mol Microbiol 2007; 63:1285-95. [PMID: 17302811 DOI: 10.1111/j.1365-2958.2007.05598.x] [Citation(s) in RCA: 212] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Clp proteolytic complexes consisting of a proteolytic core flanked by Clp ATPases are widely conserved in bacteria, and their biological roles have received considerable interest. In particular, mutants in the clp genes in the low-GC-content Gram-positive phyla Bacillales and Lactobacillales display a diverse range of phenotypic changes including general stress sensitivity, aberrant cell morphology, failure to initiate developmental programs, and for pathogens, severely attenuated virulence. Extensive research dedicated to unravelling the molecular mechanisms underlying these complex phenotypes has led to fascinating new insights that will be covered by this review. First, Clp ATPases and ClpP-containing proteolytic complexes play indispensable roles in cellular protein quality control systems by refolding or degrading damaged proteins in both stressed and non-stressed cells. Secondly, ClpP proteases and the chaperone activity of Clp ATPases are important for controlling stability and activity of central transcriptional regulators, thereby exerting tremendous impact on cell physiology. Targets include major stress regulators like Spx (oxidative stress), the antisigma factor RsiW (alkaline stress) and HdiR (DNA damage) in addition to regulators of developmental programs like ComK (competence development), sigmaH and Sda (sporulation). Thus, Clp proteins are central in co-ordinating developmental decisions and stress response in low GC Gram-positive bacteria.
Collapse
Affiliation(s)
- Dorte Frees
- Department of Veterinary Pathobiology, Faculty of Life Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
| | | | | | | |
Collapse
|
39
|
Varhimo E, Savijoki K, Jalava J, Kuipers OP, Varmanen P. Identification of a novel streptococcal gene cassette mediating SOS mutagenesis in Streptococcus uberis. J Bacteriol 2007; 189:5210-22. [PMID: 17513475 PMCID: PMC1951879 DOI: 10.1128/jb.00473-07] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Accepted: 05/08/2007] [Indexed: 11/20/2022] Open
Abstract
Streptococci have been considered to lack the classical SOS response, defined by increased mutation after UV exposure and regulation by LexA. Here we report the identification of a potential self-regulated SOS mutagenesis gene cassette in the Streptococcaceae family. Exposure to UV light was found to increase mutations to antibiotic resistance in Streptococcus uberis cultures. The mutational spectra revealed mainly G:C-->A:T transitions, and Northern analyses demonstrated increased expression of a Y-family DNA polymerase resembling UmuC under DNA-damaging conditions. In the absence of the Y-family polymerase, S. uberis cells were sensitive to UV light and to mitomycin C. Furthermore, the UV-induced mutagenesis was almost completely abolished in cells deficient in the Y-family polymerase. The gene encoding the Y-family polymerase was localized in a four-gene operon including two hypothetical genes and a gene encoding a HdiR homolog. Electrophoretic mobility shift assays demonstrated that S. uberis HdiR binds specifically to an inverted repeat sequence in the promoter region of the four-gene operon. Database searches revealed conservation of the gene cassette in several Streptococcus species, including at least one genome each of Streptococcus pyogenes, Streptococcus agalactiae, Streptococcus mitis, Streptococcus sanguinis, and Streptococcus thermophilus strains. In addition, the umuC operon was localized in several mobile DNA elements of Streptococcus and Lactococcus species. We conclude that the hdiR-umuC-ORF3-ORF4 operon represents a novel gene cassette capable of mediating SOS mutagenesis among members of the Streptococcaceae.
Collapse
MESH Headings
- Amino Acid Sequence
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Sequence
- Blotting, Northern
- Ciprofloxacin/pharmacology
- DNA Damage
- Drug Resistance, Bacterial/genetics
- Electrophoretic Mobility Shift Assay
- Gene Expression Regulation, Bacterial/drug effects
- Gene Expression Regulation, Bacterial/radiation effects
- Genes, Bacterial
- Mitomycin/pharmacology
- Models, Genetic
- Molecular Sequence Data
- Mutagenesis
- Mutation
- Operon
- Rifampin/pharmacology
- SOS Response, Genetics/drug effects
- SOS Response, Genetics/genetics
- SOS Response, Genetics/radiation effects
- Sequence Homology, Nucleic Acid
- Streptococcus/drug effects
- Streptococcus/genetics
- Streptococcus/radiation effects
- Ultraviolet Rays
Collapse
Affiliation(s)
- Emilia Varhimo
- University of Helsinki, Department of Basic Veterinary Sciences, P.O. Box 66, FIN-00014, Finland
| | | | | | | | | |
Collapse
|
40
|
Abstract
AIMS To evaluate strains of lactobacilli for their ability to persist and secrete heterologous protein in the oral cavity. METHODS AND RESULTS Four different strains of common oral lactobacilli, Lactobacillus brevis, Lactobacillus johnsonii, Lactobacillus murinus and Lactobacillus plantarum, were transformed with the plasmid pKTH2121, which contains a secretion cassette for beta-lactamase. Lactobacilli isolated from the mouth of host mice were also transformed with pKTH2121 for later feeding. Lactococcus lactis, transformed with pKTH2121, was also fed to mice as a negative control. All transformed isolates were fed to C57Black mice in varying schedules. The number of transformed bacteria persisting in the mouth was reported as a percentage of total oral bacteria recovered by swabbing. CONCLUSIONS The transformed L. lactis, L. brevis, L. johnsonii, L. murinus, and the endogenous murine lactobacillus strain failed to persist in the mouth. Transformed L. plantarum, however, persisted in the mouth and comprised up to 25% of the total lactobacilli at 18 h and 10% at 24 h after feeding. L. plantarum recovered after feeding retained its ability to secrete beta-lactamase into culture medium efficiently. Beta-lactamase activity could be detected in oral secretions at 8 h after feedings. After repeated feedings, however, the L. plantarum containing pKTH2121 gradually lost its ability to persist after feedings. This experiment demonstrates that L. plantarum can transiently colonize the oral mucosa in large numbers, while continuously secreting foreign proteins, raising the possibility of using lactobacilli as a vector for delivery of oral mucosal peptides.
Collapse
Affiliation(s)
- Y Oh
- Department of Thoracic/Head & Neck Medical Oncology, UT M.D. Anderson Cancer Center, Houston, TX 77030, USA.
| | | | | | | | | | | | | |
Collapse
|
41
|
Savijoki K, Ingmer H, Varmanen P. Proteolytic systems of lactic acid bacteria. Appl Microbiol Biotechnol 2006; 71:394-406. [PMID: 16628446 DOI: 10.1007/s00253-006-0427-1] [Citation(s) in RCA: 377] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Revised: 03/13/2006] [Accepted: 03/13/2006] [Indexed: 11/28/2022]
Abstract
Lactic acid bacteria (LAB) have a very long history of use in the manufacturing processes of fermented foods and a great deal of effort was made to investigate and manipulate the role of LAB in these processes. Today, the diverse group of LAB includes species that are among the best-studied microorganisms and proteolysis is one of the particular physiological traits of LAB of which detailed knowledge was obtained. The proteolytic system involved in casein utilization provides cells with essential amino acids during growth in milk and is also of industrial importance due to its contribution to the development of the organoleptic properties of fermented milk products. For the most extensively studied LAB, Lactococcus lactis, a model for casein proteolysis, transport, peptidolysis, and regulation thereof is now established. In addition to nutrient processing, cellular proteolysis plays a critical role in polypeptide quality control and in many regulatory circuits by keeping basal levels of regulatory proteins low and removing them when they are no longer needed. As part of the industrial processes, LAB are challenged by various stress conditions that are likely to affect metabolic activities, including proteolysis. While environmental stress responses of LAB have received increasing interest in recent years, our current knowledge on stress-related proteolysis in LAB is almost exclusively based on studies on L. lactis. This review provides the current status in the research of proteolytic systems of LAB with industrial relevance.
Collapse
Affiliation(s)
- Kirsi Savijoki
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, University of Helsinki, P.O. Box 66, Helsinki, 00014, Finland.
| | | | | |
Collapse
|
42
|
Savijoki K, Suokko A, Palva A, Varmanen P. New convenient defined media for [35S]methionine labelling and proteomic analyses of probiotic lactobacilli. Lett Appl Microbiol 2006; 42:202-9. [PMID: 16478505 DOI: 10.1111/j.1472-765x.2005.01853.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To develop experimental conditions for efficient protein radiolabelling and two-dimensional (2D) polyacrylamide gel electrophoresis for investigation of stress proteomes of probiotic Lactobacillus spp. METHODS AND RESULTS Three chemically defined media (CDM) optimized from a commercial medium supported rapid growth of the probiotic Lactobacillus rhamnosus E97800, Lactobacillus brevis ATCC 8287 and Lactobacillus reuteri E97849, and a broad range of other lactic acid bacteria. These CDM allowed efficient protein radiolabelling, requiring as little as 200 mul of logarithmic culture and pulse-chase labelling of 20 min to detect c. 300 distinct protein spots in a mini-scale 2D-gel. Proteins including DnaK, GroEL and ClpATPases were identified from the 2D-gels by immunoblotting. CONCLUSIONS Radiolabelling coupled with 2D gel electrophoresis provides a sensitive means to monitor changes in protein synthesis rates in probistic lactobacilli. SIGNIFICANCE AND IMPACT OF THE STUDY Efficient tools for proteomic analyses of probiotic Lactobacillus were developed and applied for stress-response studies.
Collapse
Affiliation(s)
- K Savijoki
- Division of Microbiology and Epidemiology, Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | | | | | | |
Collapse
|
43
|
Savijoki K, Suokko A, Palva A, Valmu L, Kalkkinen N, Varmanen P. Effect of heat-shock and bile salts on protein synthesis of Bifidobacterium longum revealed by [35S]methionine labelling and two-dimensional gel electrophoresis. FEMS Microbiol Lett 2005; 248:207-15. [PMID: 15990254 DOI: 10.1016/j.femsle.2005.05.032] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2005] [Revised: 05/18/2005] [Accepted: 05/20/2005] [Indexed: 10/25/2022] Open
Abstract
Experimental conditions for efficient protein radiolabelling and two-dimensional gel electrophoresis were developed for Bifidobacterium longum. Using these tools, protein synthesis in cells before and after heat-shock and bile salts treatment was investigated. Following heat-stress, 13 proteins were upregulated, of which HtrA, DnaK and GroEL were also moderately induced by bile salts, indicating close relationship between the heat and bile salts responses in bifidobacteria. Our work indicated that, as a consequence of prolonged heat-stress, HtrA undergoes sequential modification and proteolysis, and that this mechanism could be employed by bifidobacteria to respond to heat-stress.
Collapse
Affiliation(s)
- Kirsi Savijoki
- University of Helsinki, Faculty of Veterinary Medicine, Department of Basic Veterinary Sciences, Division of Microbiology and Epidemiology, P.O. Box 66, FIN-00014 University of Helsinki, Finland.
| | | | | | | | | | | |
Collapse
|
44
|
Abstract
Two genes encoding ClpL ATPase proteins were identified in a probiotic Lactobacillus rhamnosus strain, E-97800. Sequence analyses revealed that the genes, designated clpL1 and clpL2, share 80% identity. The clpL2 gene showed the highest degree of identity (98.5%) to a clpL gene from Lactobacillus plantarum WCFSI, while it was not detected in three other L. rhamnosus strains studied. According to Northern analyses, the expression of clpL1 and the clpL2 were induced during heat shock by > 20- and 3-fold, respectively. The functional promoter regions were determined by primer extension analyses, and the clpL1 promoter was found to be overlapped by an inverted repeat structure identical to the conserved CIRCE element, indicating that clpL1 belongs to the HrcA regulon in L. rhamnosus. No consensus binding sites for HrcA or CtsR could be identified in the clpL2 promoter region. Interestingly, the clpL2 gene was found to be surrounded by truncated transposase genes and flanked by inverted repeat structures nearly identical to the terminal repeats of the ISLpl1 from L. plantarum HN38. Furthermore, clpL2 was shown to be mobilized during prolonged cultivation at elevated temperature. The presence of a gene almost identical to clpL2 in L. plantarum and its absence in other L. rhamnosus strains suggest that the L. rhamnosus E-97800 has acquired the clpL2 gene via horizontal transfer. No change in the stress tolerance of the ClpL2-deficient derivative of E-97800 compared to the parental strain was observed.
Collapse
Affiliation(s)
- Aki Suokko
- Division of Microbiology and Epidemiology, Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, University of Helsinki, University of Helsinki, Helsinki, Finland
| | | | | | | | | |
Collapse
|
45
|
Savijoki K, Ingmer H, Frees D, Vogensen FK, Palva A, Varmanen P. Heat and DNA damage induction of the LexA-like regulator HdiR from Lactococcus lactis is mediated by RecA and ClpP. Mol Microbiol 2003; 50:609-21. [PMID: 14617183 DOI: 10.1046/j.1365-2958.2003.03713.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The SOS response is a paradigm for bacterial cells response to DNA damage. Yet some bacteria lack a homologue of the SOS regulator, LexA, including the Gram-positive, Lactococcus lactis. In this organism we have identified a negative transcriptional regulator, HdiR that induces target gene expression both upon DNA damage and heat shock. Gel mobility shift assays revealed that the binding site for HdiR is located within an inverted repeat structure. HdiR is able to carry out a self-cleavage reaction in vitro at high pHs, while in vivo it undergoes RecA-dependent self-cleavage in the presence of a DNA-damaging agent. Intriguingly, the N-terminal cleavage product of HdiR retains DNA binding activity, and only when degraded by the Clp protease, is gene expression induced. Thus, the activity of HdiR in response to DNA damage is controlled by sequential proteolysis, involving self-cleavage and Clp-dependent degradation of HdiR. During heat-stress, limited self-cleavage occurs; however, recA and clpP are still required for full induction of target gene expression. Thus, our data show that common elements are involved in both the DNA damage and the heat-mediated induction of the HdiR regulon.
Collapse
Affiliation(s)
- Kirsi Savijoki
- University of Helsinki, Faculty of Veterinary Medicine, Department of Basic Veterinary Sciences, Division of Microbiology and Epidemiology, PO Box 57, 00014 Helsinki University, Helsinki, Finland
| | | | | | | | | | | |
Collapse
|
46
|
Abstract
The heat shock response in bacterial cells is characterized by rapid induction of heat shock protein expression, followed by an adaptation period during which heat shock protein synthesis decreases to a new steady-state level. In this study we found that after a shift to a high temperature the Clp ATPase (ClpE) in Lactococcus lactis is required for such a decrease in expression of a gene negatively regulated by the heat shock regulator (CtsR). Northern blot analysis showed that while a shift to a high temperature in wild-type cells resulted in a temporal increase followed by a decrease in expression of clpP encoding the proteolytic component of the Clp protease complex, this decrease was delayed in the absence of ClpE. Site-directed mutagenesis of the zinc-binding motif conserved in ClpE ATPases interfered with the ability to repress CtsR-dependent expression. Quantification of ClpE by Western blot analysis revealed that at a high temperature ClpE is subjected to ClpP-dependent processing and that disruption of the zinc finger domain renders ClpE more susceptible. Interestingly, this domain resembles the N-terminal region of McsA, which was recently reported to interact with the CtsR homologue in Bacillus subtilis. Thus, our data point to a regulatory role of ClpE in turning off clpP gene expression following temporal heat shock induction, and we propose that this effect is mediated through CtsR.
Collapse
Affiliation(s)
- Pekka Varmanen
- Department of Dairy and Food Science, The Royal Veterinary and Agricultural University, DK-1958 Frederiksberg C, Denmark.
| | | | | | | | | |
Collapse
|
47
|
Frees D, Varmanen P, Ingmer H. Inactivation of a gene that is highly conserved in Gram-positive bacteria stimulates degradation of non-native proteins and concomitantly increases stress tolerance in Lactococcus lactis. Mol Microbiol 2001; 41:93-103. [PMID: 11454203 DOI: 10.1046/j.1365-2958.2001.02503.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Exposure of cells to elevated temperatures triggers the synthesis of chaperones and proteases including components of the conserved Clp protease complex. We demonstrated previously that the proteolytic subunit, ClpP, plays a major role in stress tolerance and in the degradation of non-native proteins in the Gram-positive bacterium Lactococcus lactis. Here, we used transposon mutagenesis to generate mutants in which the temperature- and puromycin-sensitive phenotype of a lactococcal clpP null mutant was partly alleviated. In all mutants obtained, the transposon was inserted in the L. lactis trmA gene. When analysing a clpP, trmA double mutant, we found that the expression normally induced from the clpP and dnaK promoters in the clpP mutant was reduced to wild-type level upon introduction of the trmA disruption. Additionally, the degradation of puromycyl-containing polypeptides was increased, suggesting that inactivation of trmA compensates for the absence of ClpP by stimulating an as yet unidentified protease that degrades misfolded proteins. When trmA was disrupted in wild-type cells, both stress tolerance and proteolysis of puromycyl peptides was enhanced above wild-type level. Based on our results, we propose that TrmA, which is well conserved in several Gram-positive bacteria, affects the degradation of non-native proteins and thereby controls stress tolerance.
Collapse
Affiliation(s)
- D Frees
- Department of Veterinary Microbiology, Stigbøjlen 4, Denmark
| | | | | |
Collapse
|
48
|
Varmanen P, Ingmer H, Vogensen FK. ctsR of Lactococcus lactis encodes a negative regulator of clp gene expression. Microbiology (Reading) 2000; 146 ( Pt 6):1447-1455. [PMID: 10846223 DOI: 10.1099/00221287-146-6-1447] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Bacteria undergo a complex programme of differential gene expression in response to stress. In Bacillus subtilis, it was recently shown that CtsR, a negative transcriptional regulator, mediates stress-induced expression of components of the Clp protease complex. In this study, a gene was identified in the Gram-positive bacterium Lactococcus lactis that encodes a 17 kDa product with 38% identity to the CtsR protein of B. subtilis. By Northern analyses it was found that in a L. lactis strain carrying a large internal deletion of ctsR, including the region encoding a putative helix-turn-helix motif, the amounts of clpC, clpP, clpB and clpE mRNAs were increased 3-8-fold compared to those present in wild-type L. lactis MG1363. In another ctsR mutant strain in which only one-third of CtsR was deleted, leaving the putative DNA-binding domain and the C-terminal 29 amino acids intact, only minor derepression of clp gene expression was observed and, furthermore, all the clp genes were still induced by heat. These results indicate that the amino acids of CtsR involved in temperature sensing are located either close to the DNA-binding domain or in the C-terminal part of the protein. Thus, in L. lactis in addition to B. subtilis, CtsR is a key regulator of heat-shock-induced gene expression, suggesting that the presence of CtsR-homologous DNA-binding sites observed in many Gram-positive bacteria reflects functional heat-shock regulatory systems.
Collapse
Affiliation(s)
- Pekka Varmanen
- The Royal Veterinary and Agricultural University, Department of Dairy and Food Science, DK-1958 Frederiksberg C, Denmark1
| | - Hanne Ingmer
- The Royal Veterinary and Agricultural University, Department of Veterinary Microbiology, DK-1870 Frederiksberg C, Denmark2
| | - Finn K Vogensen
- The Royal Veterinary and Agricultural University, Department of Dairy and Food Science, DK-1958 Frederiksberg C, Denmark1
| |
Collapse
|
49
|
Varmanen P, Savijoki K, Avall S, Palva A, Tynkkynen S. X-prolyl dipeptidyl aminopeptidase gene (pepX) is part of the glnRA operon in Lactobacillus rhamnosus. J Bacteriol 2000; 182:146-54. [PMID: 10613874 PMCID: PMC94251 DOI: 10.1128/jb.182.1.146-154.2000] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A peptidase gene expressing X-prolyl dipeptidyl aminopeptidase (PepX) activity was cloned from Lactobacillus rhamnosus 1/6 by using the chromogenic substrate L-glycyl-L-prolyl-beta-naphthylamide for screening of a genomic library in Escherichia coli. The nucleotide sequence of a 3.5-kb HindIII fragment expressing the peptidase activity revealed one complete open reading frame (ORF) of 2,391 nucleotides. The 797-amino-acid protein encoded by this ORF was shown to be 40, 39, and 36% identical with PepXs from Lactobacillus helveticus, Lactobacillus delbrueckii, and Lactococcus lactis, respectively. By Northern analysis with a pepX-specific probe, transcripts of 4.5 and 7.0 kb were detected, indicating that pepX is part of a polycistronic operon in L. rhamnosus. Cloning and sequencing of the upstream region of pepX revealed the presence of two ORFs of 360 and 1,338 bp that were shown to be able to encode proteins with high homology to GlnR and GlnA proteins, respectively. By multiple primer extension analyses, the only functional promoter in the pepX region was located 25 nucleotides upstream of glnR. Northern analysis with glnA- and pepX-specific probes indicated that transcription from glnR promoter results in a 2.0-kb dicistronic glnR-glnA transcript and also in a longer read-through polycistronic transcript of 7.0 kb that was detected with both probes in samples from cells in exponential growth phase. The glnA gene was disrupted by a single-crossover recombinant event using a nonreplicative plasmid carrying an internal part of glnA. In the disruption mutant, glnRA-specific transcription was derepressed 10-fold compared to the wild type, but the 7.0-kb transcript was no longer detectable with either the glnA- or pepX-specific probe, demonstrating that pepX is indeed part of glnRA operon in L. rhamnosus. Reverse transcription-PCR analysis further supported this operon structure. An extended stem-loop structure was identified immediately upstream of pepX in the glnA-pepX intergenic region, a sequence that showed homology to a 23S-5S intergenic spacer and to several other L. rhamnosus-related entries in data banks.
Collapse
Affiliation(s)
- P Varmanen
- R&D, Valio Ltd., FIN-00039 Valio, Helsinki, Finland.
| | | | | | | | | |
Collapse
|
50
|
Abstract
A gene (htrA) coding for a stress-inducible HtrA-like protein from Lactobacillus helveticus CNRZ32 was cloned, sequenced, and characterized. The deduced amino acid sequence of the gene exhibited 30% identity with the HtrA protein from Escherichia coli; the putative catalytic triad and a PDZ domain that characterize the HtrA family of known bacterial serine proteases were also found in the sequence. Expression of the L. helveticus htrA gene in a variety of stress conditions was analyzed at the transcriptional level. The strongest induction, resulting in over an eightfold increase in the htrA transcription level, was found in growing CNRZ32 cells exposed to 4% (wt/vol) NaCl. Enhanced htrA mRNA expression was also seen in CNRZ32 cells after exposure to puromycin, ethanol, or heat. The reporter gene gusA was integrated in the Lactobacillus chromosome downstream of the htrA promoter by a double-crossover event which also interrupted the wild-type gene. The expression of gusA in the stress conditions tested was similar to that of htrA itself. In addition, the presence of an intact htrA gene facilitated growth under heat stress but not under salt stress.
Collapse
Affiliation(s)
- A Smeds
- Agricultural Research Centre of Finland, Food Research Institute, Jokioinen 31600, Finland
| | | | | |
Collapse
|