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Zumsteg J, Hirschler A, Carapito C, Maurer L, Villette C, Heintz D, Dahl C, El Nayal A, Sangal V, Mahmoud H, Van Dorsselaer A, Ismail W. Mechanistic insights into sulfur source-driven physiological responses and metabolic reorganization in the fuel-biodesulfurizing Rhodococcus qingshengii IGTS8. Appl Environ Microbiol 2023; 89:e0082623. [PMID: 37655899 PMCID: PMC10537767 DOI: 10.1128/aem.00826-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 06/30/2023] [Indexed: 09/02/2023] Open
Abstract
Comparative proteomics and untargeted metabolomics were combined to study the physiological and metabolic adaptations of Rhodococcus qingshengii IGTS8 under biodesulfurization conditions. After growth in a chemically defined medium with either dibenzothiophene (DBT) or MgSO4 as the sulfur source, many differentially produced proteins and metabolites associated with several metabolic and physiological processes were detected including the metabolism of carbohydrates, amino acids, lipids, nucleotides, vitamins, protein synthesis, transcriptional regulation, cell envelope biogenesis, and cell division. Increased production of the redox cofactor mycofactocin and associated proteins was one of the most striking adaptations under biodesulfurization conditions. While most central metabolic enzymes were less abundant in the presence of DBT, a key enzyme of the glyoxylate shunt, isocitrate lyase, was up to 26-fold more abundant. Several C1 metabolism and oligotrophy-related enzymes were significantly more abundant in the biodesulfurizing culture. R. qingshengii IGTS8 exhibited oligotrophic growth in liquid and solid media under carbon starvation. Moreover, the oligotrophic growth was faster on the solid medium in the presence of DBT compared to MgSO4 cultures. In the DBT culture, the cell envelope and phospholipids were remodeled, with lower levels of phosphatidylethanolamine and unsaturated and short-chain fatty acids being the most prominent changes. Biodesulfurization increased the biosynthesis of osmoprotectants (ectoine and mannosylglycerate) as well as glutamate and induced the stringent response. Our findings reveal highly diverse and overlapping stress responses that could protect the biodesulfurizing culture not only from the associated sulfate limitation but also from chemical, oxidative, and osmotic stress, allowing efficient resource management. IMPORTANCE Despite decades of research, a commercially viable bioprocess for fuel desulfurization has not been developed yet. This is mainly due to lack of knowledge of the physiology and metabolism of fuel-biodesulfurizing bacteria. Being a stressful condition, biodesulfurization could provoke several stress responses that are not understood. This is particularly important because a thorough understanding of the microbial stress response is essential for the development of environmentally friendly and industrially efficient microbial biocatalysts. Our comparative systems biology studies provide a mechanistic understanding of the biology of biodesulfurization, which is crucial for informed developments through the rational design of recombinant biodesulfurizers and optimization of the bioprocess conditions. Our findings enhance the understanding of the physiology, metabolism, and stress response not only in biodesulfurizing bacteria but also in rhodococci, a precious group of biotechnologically important bacteria.
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Affiliation(s)
- Julie Zumsteg
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Aurélie Hirschler
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS, Université de Strasbourg, IPHC UMR 7178, Infrastructure Nationale de Protéomique ProFI FR2048, Strasbourg, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS, Université de Strasbourg, IPHC UMR 7178, Infrastructure Nationale de Protéomique ProFI FR2048, Strasbourg, France
| | - Loïc Maurer
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
- Département mécanique, ICube Laboratoire des sciences de l’ingénieur, de l’informatique et de l’imagerie, UNISTRA/CNRS/ENGEES/INSA, Strasbourg, France
| | - Claire Villette
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Dimitri Heintz
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Ashraf El Nayal
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Huda Mahmoud
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait City, Kuwait
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS, Université de Strasbourg, IPHC UMR 7178, Infrastructure Nationale de Protéomique ProFI FR2048, Strasbourg, France
| | - Wael Ismail
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
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Zhang Z, Huang C, Du B, Xie C, Jiang L, Tang S, Xu X. Draft genome sequence of a new carotenoid-producing strain Brevibacterium sp. XU54, isolated from radioactive soil in Xinjiang, China. 3 Biotech 2022; 12:298. [PMID: 36276479 PMCID: PMC9522940 DOI: 10.1007/s13205-022-03366-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 09/17/2022] [Indexed: 11/01/2022] Open
Abstract
Some species of the genus Brevibacterium are orange bacteria involved in cheese ripening, synthesis of odoriferous compounds, and carotenoids with aromatic end groups. Here, we report the genome sequence of Brevibacterium sp. XU54, isolated from radioactive soil in Xinjiang, China. The genome of XU54 consists of 4,899,099 base pairs with a GC content of 62.2%. The genome sequence was annotated with 4453 genes, encoding 4260 proteins, 13 rRNAs, and 49 tRNAs. 16S rRNA BLAST and comparative genomic analysis both indicated that XU54 may be a new species of Brevibacterium. In addition, compared to the type strains, some enzymes related to sulfur metabolism showed a low similarity of 66.85, 79.53 and 14.61%, respectively. The carotenoids biosynthesis gene cluster was identified and analyzed according to the genomic data, which revealed relatively low identity (5-85%) with existing strains. The optimum conditions for its growth and carotenoid production were then discussed. The whole-genome sequence of Brevibacterium sp. XU54 will be beneficial for utilizing these newly identified genes in carotenoid biosynthesis and regulation of sulfur metabolism pathway to promote the production of novel carotenoids and other structurally diverse compounds through combinatorial biosynthesis, which facilitates cheese ripening and coloration. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03366-1.
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Affiliation(s)
- Zhidong Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816 Jiangsu China
| | - Chunyan Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046 Jiangsu China
| | - Bangmian Du
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046 Jiangsu China
| | - Chengjia Xie
- School of Chemical Engineering, Yangzhou Polytechnic Institute, Yangzhou, 225127 Jiangsu China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 Jiangsu China
| | - Susu Tang
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816 Jiangsu China
| | - Xian Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046 Jiangsu China
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Kunota TTR, Rahman MA, Truebody BE, Mackenzie JS, Saini V, Lamprecht DA, Adamson JH, Sevalkar RR, Lancaster JR, Berney M, Glasgow JN, Steyn AJC. Mycobacterium tuberculosis H 2S Functions as a Sink to Modulate Central Metabolism, Bioenergetics, and Drug Susceptibility. Antioxidants (Basel) 2021; 10:1285. [PMID: 34439535 PMCID: PMC8389258 DOI: 10.3390/antiox10081285] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/04/2021] [Accepted: 08/07/2021] [Indexed: 02/03/2023] Open
Abstract
H2S is a potent gasotransmitter in eukaryotes and bacteria. Host-derived H2S has been shown to profoundly alter M. tuberculosis (Mtb) energy metabolism and growth. However, compelling evidence for endogenous production of H2S and its role in Mtb physiology is lacking. We show that multidrug-resistant and drug-susceptible clinical Mtb strains produce H2S, whereas H2S production in non-pathogenic M. smegmatis is barely detectable. We identified Rv3684 (Cds1) as an H2S-producing enzyme in Mtb and show that cds1 disruption reduces, but does not eliminate, H2S production, suggesting the involvement of multiple genes in H2S production. We identified endogenous H2S to be an effector molecule that maintains bioenergetic homeostasis by stimulating respiration primarily via cytochrome bd. Importantly, H2S plays a key role in central metabolism by modulating the balance between oxidative phosphorylation and glycolysis, and it functions as a sink to recycle sulfur atoms back to cysteine to maintain sulfur homeostasis. Lastly, Mtb-generated H2S regulates redox homeostasis and susceptibility to anti-TB drugs clofazimine and rifampicin. These findings reveal previously unknown facets of Mtb physiology and have implications for routine laboratory culturing, understanding drug susceptibility, and improved diagnostics.
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Affiliation(s)
- Tafara T. R. Kunota
- Africa Health Research Institute, University of KwaZulu Natal, Durban 4001, South Africa; (T.T.R.K.); (M.A.R.); (B.E.T.); (J.S.M.); (D.A.L.); (J.H.A.)
| | - Md. Aejazur Rahman
- Africa Health Research Institute, University of KwaZulu Natal, Durban 4001, South Africa; (T.T.R.K.); (M.A.R.); (B.E.T.); (J.S.M.); (D.A.L.); (J.H.A.)
| | - Barry E. Truebody
- Africa Health Research Institute, University of KwaZulu Natal, Durban 4001, South Africa; (T.T.R.K.); (M.A.R.); (B.E.T.); (J.S.M.); (D.A.L.); (J.H.A.)
| | - Jared S. Mackenzie
- Africa Health Research Institute, University of KwaZulu Natal, Durban 4001, South Africa; (T.T.R.K.); (M.A.R.); (B.E.T.); (J.S.M.); (D.A.L.); (J.H.A.)
| | - Vikram Saini
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India;
| | - Dirk A. Lamprecht
- Africa Health Research Institute, University of KwaZulu Natal, Durban 4001, South Africa; (T.T.R.K.); (M.A.R.); (B.E.T.); (J.S.M.); (D.A.L.); (J.H.A.)
| | - John H. Adamson
- Africa Health Research Institute, University of KwaZulu Natal, Durban 4001, South Africa; (T.T.R.K.); (M.A.R.); (B.E.T.); (J.S.M.); (D.A.L.); (J.H.A.)
| | - Ritesh R. Sevalkar
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (R.R.S.); (J.N.G.)
| | - Jack R. Lancaster
- Department of Pharmacology and Chemical Biology, Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA;
| | - Michael Berney
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY 10462, USA;
| | - Joel N. Glasgow
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (R.R.S.); (J.N.G.)
| | - Adrie J. C. Steyn
- Africa Health Research Institute, University of KwaZulu Natal, Durban 4001, South Africa; (T.T.R.K.); (M.A.R.); (B.E.T.); (J.S.M.); (D.A.L.); (J.H.A.)
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (R.R.S.); (J.N.G.)
- Centers for AIDS Research and Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Zhu L, Zeng C, Yang S, Hou Z, Wang Y, Hu X, Senoo K, Wei W. Diversity and specificity of the bacterial community in Chinese horse milk cheese. Microbiologyopen 2020; 9:e1066. [PMID: 32741094 PMCID: PMC7424250 DOI: 10.1002/mbo3.1066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/24/2020] [Accepted: 05/12/2020] [Indexed: 11/15/2022] Open
Abstract
The nutrition and flavor of cheese are generated by the microbial community. Thus, horse milk cheese with unique nutrition and flavor, an increasingly popular local cheese of the Xinjiang Uygur Autonomous Region of China, is considered to have diverse and specific bacterial community. To verify this hypothesis, horse, cow, and goat milk cheese samples produced under the same environmental conditions and manufacturing process were collected, and the 16S rRNA gene was targeted to determine the bacterial population size and community composition by real‐time quantitative PCR and high‐throughput sequencing. The bacterial community of horse milk cheese had a significantly larger bacterial population size, greater species richness, and a more diverse composition than those of cow and goat milk cheeses. Unlike the absolute dominance of Lactococcus and Streptococcus in cow and goat milk cheeses, Lactobacillus and Streptococcus dominated the bacterial community as the starter lactic acid bacteria in horse milk cheese. Additionally, horse milk cheese also contains a higher abundance of unclassified secondary bacteria and specific secondary bacteria (e.g., Psychrobacter, Sulfurisoma, Halomonas, and Brevibacterium) than cow and goat milk cheeses. These abundant, diverse, and specific starter lactic acid bacteria and secondary bacteria may generate unique nutrition and flavor of horse milk cheese.
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Affiliation(s)
- Lin Zhu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Chunlin Zeng
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Sai Yang
- School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, China
| | - Zhaozhi Hou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Yuan Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Xinyu Hu
- School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, China
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Wei Wei
- School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, China
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Pham NP, Landaud S, Lieben P, Bonnarme P, Monnet C. Transcription Profiling Reveals Cooperative Metabolic Interactions in a Microbial Cheese-Ripening Community Composed of Debaryomyces hansenii, Brevibacterium aurantiacum, and Hafnia alvei. Front Microbiol 2019; 10:1901. [PMID: 31474970 PMCID: PMC6706770 DOI: 10.3389/fmicb.2019.01901] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/02/2019] [Indexed: 11/13/2022] Open
Abstract
Ripening cultures containing fungi and bacteria are widely used in smear-ripened cheese production processes, but little is known about the biotic interactions of typical ripening microorganisms at the surface of cheese. We developed a lab-scale mini-cheese model to investigate the biotic interactions of a synthetic community that was composed of Debaryomyces hansenii, Brevibacterium aurantiacum, and Hafnia alvei, three species that are commonly used for smear-ripened cheese production. Transcriptomic analyses of cheese samples produced with different combinations of these three species revealed potential mechanisms of biotic interactions concerning iron acquisition, proteolysis, lipolysis, sulfur metabolism, and D-galactonate catabolism. A strong mutualistic interaction was observed between H. alvei and B. aurantiacum. We propose an explanation of this positive interaction in which B. aurantiacum would benefit from siderophore production by H. alvei, and the latter would be stimulated by the energy compounds liberated from caseins and triglycerides through the action of the proteases and lipases secreted by B. aurantiacum. In the future, it would be interesting to take the iron acquisition systems of cheese-associated strains into account for the purpose of improving the selection of the ripening culture components and their association in mixed cultures.
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Affiliation(s)
- Nguyen-Phuong Pham
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - Sophie Landaud
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - Pascale Lieben
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - Pascal Bonnarme
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - Christophe Monnet
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, Thiverval-Grignon, France
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Anderson MT, Mitchell LA, Sintsova A, Rice KA, Mobley HLT. Sulfur Assimilation Alters Flagellar Function and Modulates the Gene Expression Landscape of Serratia marcescens. mSystems 2019; 4:e00285-19. [PMID: 31387930 PMCID: PMC6687942 DOI: 10.1128/msystems.00285-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/24/2019] [Indexed: 11/29/2022] Open
Abstract
Sulfur is an essential nutrient that contributes to cellular redox homeostasis, transcriptional regulation, and translation initiation when incorporated into different biomolecules. Transport and reduction of extracellular sulfate followed by cysteine biosynthesis is a major pathway of bacterial sulfur assimilation. For the opportunistic pathogen Serratia marcescens, function of the cysteine biosynthesis pathway is required for extracellular phospholipase activity and flagellum-mediated surface motility, but little else is known about the influence of sulfur assimilation on the physiology of this organism. In this work, it was determined that an S. marcescens cysteine auxotroph fails to differentiate into hyperflagellated and elongated swarmer cells and that cysteine, but not other organic sulfur molecules, restores swarming motility to these bacteria. The S. marcescens cysteine auxotroph further exhibits reduced transcription of phospholipase, hemolysin, and flagellin genes, each of which is subject to transcriptional control by the flagellar regulatory system. Based on these data and the central role of cysteine in sulfur assimilation, it was reasoned that environmental sulfur availability may contribute to the regulation of these functions in S. marcescens Indeed, bacteria that are starved for sulfate exhibit substantially reduced transcription of the genes for hemolysin, phospholipase, and the FlhD flagellar master regulator. A global transcriptomic analysis further defined a large set of S. marcescens genes that are responsive to extracellular sulfate availability, including genes that encode membrane transport, nutrient utilization, and metabolism functions. Finally, sulfate availability was demonstrated to alter S. marcescens cytolytic activity, suggesting that sulfate assimilation may impact the virulence of this organism.IMPORTANCE Serratia marcescens is a versatile bacterial species that inhabits diverse environmental niches and is capable of pathogenic interactions with host organisms ranging from insects to humans. This report demonstrates for the first time the extensive impacts that environmental sulfate availability and cysteine biosynthesis have on the transcriptome of S. marcescens The finding that greater than 1,000 S. marcescens genes are differentially expressed depending on sulfate availability suggests that sulfur abundance is a crucial factor that controls the physiology of this organism. Furthermore, the high relative expression levels for the putative virulence factors flagella, phospholipase, and hemolysin in the presence of sulfate suggests that a sulfur-rich host environment could contribute to the transcription of these genes during infection.
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Affiliation(s)
- Mark T Anderson
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Lindsay A Mitchell
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Anna Sintsova
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Katherine A Rice
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Harry L T Mobley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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Machover D, Rossi L, Hamelin J, Desterke C, Goldschmidt E, Chadefaux-Vekemans B, Bonnarme P, Briozzo P, Kopečný D, Pierigè F, Magnani M, Mollicone R, Haghighi-Rad F, Gaston-Mathé Y, Dairou J, Boucheix C, Saffroy R. Effects in Cancer Cells of the Recombinant l-Methionine Gamma-Lyase fromBrevibacterium aurantiacum.Encapsulation in Human Erythrocytes for Sustained l-Methionine Elimination. J Pharmacol Exp Ther 2019; 369:489-502. [DOI: 10.1124/jpet.119.256537] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 04/01/2019] [Indexed: 01/20/2023] Open
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Pracharova P, Lieben P, Pollet B, Beckerich JM, Bonnarme P, Landaud S, Swennen D. Geotrichum candidum gene expression and metabolite accumulation inside the cells reflect the strain oxidative stress sensitivity and ability to produce flavour compounds. FEMS Yeast Res 2019; 19:5116167. [PMID: 30295727 PMCID: PMC6211236 DOI: 10.1093/femsyr/foy111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 10/04/2018] [Indexed: 12/02/2022] Open
Abstract
Geotrichum candidum is a fungus-like yeast widely used as a starter culture for cheese ripening for its proteolytic and lipolytic activities and its contribution to the cheese flavours. The sequenced strain G. candidum CLIB 918 was isolated from cheese Pont-L’Evêque. This strain's ability to produce volatile compounds was compared to the ability of a known strong sulphur compound producer G. candidum strain (Gc203). The aminotransferase-coding genes BAT2 and ARO8 were identified to be involved in methionine catabolism. The production of volatile compounds indicated that the sequenced strain was a moderate producer compared to the strong producer strain. The major volatile compounds were produced from sulphur amino acid, branched-chain amino acid and fatty acid metabolisms. Metabolite content of the cells showed that the ability of the strain to produce volatile compounds was inversely proportional to its ability to store amino acids inside the cells. Reduced glutathione, hypotaurine and taurine intracellular concentrations and volatile fatty aldehyde production indicated the role of oxidative stress sensitivity in flavour production. The increase in expression of several genes in a Reblochon-type cheese at the end of ripening confirmed that oxygen and iron were key factors regulating cheese flavour production.
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Affiliation(s)
- P Pracharova
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - P Lieben
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - B Pollet
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - J M Beckerich
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - P Bonnarme
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - S Landaud
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - D Swennen
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850 Thiverval-Grignon, France
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Afshari R, Pillidge CJ, Dias DA, Osborn AM, Gill H. Cheesomics: the future pathway to understanding cheese flavour and quality. Crit Rev Food Sci Nutr 2018; 60:33-47. [DOI: 10.1080/10408398.2018.1512471] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Roya Afshari
- School of Science, RMIT University, Bundoora, Victoria, Australia
| | | | - Daniel A. Dias
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
| | - A. Mark Osborn
- School of Science, RMIT University, Bundoora, Victoria, Australia
| | - Harsharn Gill
- School of Science, RMIT University, Bundoora, Victoria, Australia
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Proteome Remodeling in Response to Sulfur Limitation in " Candidatus Pelagibacter ubique". mSystems 2016; 1:mSystems00068-16. [PMID: 27822545 PMCID: PMC5069961 DOI: 10.1128/msystems.00068-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 06/16/2016] [Indexed: 11/20/2022] Open
Abstract
The alphaproteobacterium "Candidatus Pelagibacter ubique" strain HTCC1062 and most other members of the SAR11 clade lack genes for assimilatory sulfate reduction, making them dependent on organosulfur compounds that occur naturally in seawater. To investigate how these cells adapt to sulfur limitation, batch cultures were grown in defined medium containing either limiting or nonlimiting amounts of dimethylsulfoniopropionate (DMSP) as the sole sulfur source. Protein and mRNA expression were measured before, during, and after the transition from exponential growth to stationary phase. Two distinct responses were observed, one as DMSP became exhausted and another as the cells acclimated to a sulfur-limited environment. The first response was characterized by increased transcription and translation of all "Ca. Pelagibacter ubique" genes downstream from the previously confirmed S-adenosyl methionine (SAM) riboswitches bhmT, mmuM, and metY. The proteins encoded by these genes were up to 33 times more abundant as DMSP became limiting. Their predicted function is to shunt all available sulfur to methionine. The secondary response, observed during sulfur-limited stationary phase, was a 6- to 10-fold increase in the transcription of the heme c shuttle-encoding gene ccmC and two small genes of unknown function (SAR11_1163 and SAR11_1164). This bacterium's strategy for coping with sulfur stress appears to be intracellular redistribution to support methionine biosynthesis rather than increasing organosulfur import. Many of the genes and SAM riboswitches involved in this response are located in a hypervariable genome region (HVR). One of these HVR genes, ordL, is located downstream from a conserved motif that evidence suggests is a novel riboswitch. IMPORTANCE "Ca. Pelagibacter ubique" is a key driver of marine biogeochemistry cycles and a model for understanding how minimal genomes evolved in free-living anucleate organisms. This study explores the unusual sulfur acquisition strategy that has evolved in these cells, which lack assimilatory sulfate reduction and instead rely on reduced sulfur compounds found in oxic marine environments to meet their cellular quotas. Our findings demonstrate that the sulfur acquisition systems are constitutively expressed but the enzymatic steps leading to the essential sulfur-containing amino acid methionine are regulated by a unique array of riboswitches and genes, many of which are encoded in a rapidly evolving genome region. These findings support mounting evidence that streamlined cells have evolved regulatory mechanisms that minimize transcriptional switching and, unexpectedly, localize essential sulfur acquisition genes in a genome region normally associated with adaption to environmental variation.
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Deng YF, Di Liao X, Wang Y, Liang JB, Tufarelli V. Prebiotics MitigateIn VitroSulfur-Containing Odour Generation in Caecal Content of Pigs. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2015.3762] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Zhang L, Jiang W, Nan J, Almqvist J, Huang Y. The Escherichia coli CysZ is a pH dependent sulfate transporter that can be inhibited by sulfite. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:1809-16. [DOI: 10.1016/j.bbamem.2014.03.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 03/08/2014] [Accepted: 03/10/2014] [Indexed: 12/27/2022]
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Recent advances in recombinant protein expression by Corynebacterium, Brevibacterium, and Streptomyces: from transcription and translation regulation to secretion pathway selection. Appl Microbiol Biotechnol 2013; 97:9597-608. [PMID: 24068337 DOI: 10.1007/s00253-013-5250-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Revised: 09/03/2013] [Accepted: 09/05/2013] [Indexed: 12/14/2022]
Abstract
Gram-positive bacteria are widely used to produce recombinant proteins, amino acids, organic acids, higher alcohols, and polymers. Many proteins have been expressed in Gram-positive hosts such as Corynebacterium, Brevibacterium, and Streptomyces. The favorable and advantageous characteristics (e.g., high secretion capacity and efficient production of metabolic products) of these species have increased the biotechnological applications of bacteria. However, owing to multiplicity from genes encoding the proteins and expression hosts, the expression of recombinant proteins is limited in Gram-positive bacteria. Because there is a very recent review about protein expression in Bacillus subtilis, here we summarize recent strategies for efficient expression of recombinant proteins in the other three typical Gram-positive bacteria (Corynebacterium, Brevibacterium, and Streptomyces) and discuss future prospects. We hope that this review will contribute to the development of recombinant protein expression in Corynebacterium, Brevibacterium, and Streptomyces.
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Gori K, Ryssel M, Arneborg N, Jespersen L. Isolation and identification of the microbiota of Danish farmhouse and industrially produced surface-ripened cheeses. MICROBIAL ECOLOGY 2013; 65:602-615. [PMID: 23224222 PMCID: PMC3621994 DOI: 10.1007/s00248-012-0138-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 10/22/2012] [Indexed: 06/01/2023]
Abstract
For studying the microbiota of four Danish surface-ripened cheeses produced at three farmhouses and one industrial dairy, both a culture-dependent and culture-independent approach were used. After dereplication of the initial set of 433 isolates by (GTG)5-PCR fingerprinting, 217 bacterial and 25 yeast isolates were identified by sequencing of the 16S rRNA gene or the D1/D2 domain of the 26S rRNA gene, respectively. At the end of ripening, the cheese core microbiota of the farmhouse cheeses consisted of the mesophilic lactic acid bacteria (LAB) starter cultures Lactococcus lactis subsp. lactis and Leuconostoc mesenteorides as well as non-starter LAB including different Lactobacillus spp. The cheese from the industrial dairy was almost exclusively dominated by Lb. paracasei. The surface bacterial microbiota of all four cheeses were dominated by Corynebacterium spp. and/or Brachybacterium spp. Brevibacterium spp. was found to be subdominant compared to other bacteria on the farmhouse cheeses, and no Brevibacterium spp. was found on the cheese from the industrial dairy, even though B. linens was used as surface-ripening culture. Moreover, Gram-negative bacteria identified as Alcalignes faecalis and Proteus vulgaris were found on one of the farmhouse cheeses. The surface yeast microbiota consisted primarily of one dominating species for each cheese. For the farmhouse cheeses, the dominant yeast species were Yarrowia lipolytica, Geotrichum spp. and Debaryomyces hansenii, respectively, and for the cheese from the industrial dairy, D. hansenii was the dominant yeast species. Additionally, denaturing gradient gel electrophoresis (DGGE) analysis revealed that Streptococcus thermophilus was present in the farmhouse raw milk cheese analysed in this study. Furthermore, DGGE bands corresponding to Vagococcus carniphilus, Psychrobacter spp. and Lb. curvatus on the cheese surfaces indicated that these bacterial species may play a role in cheese ripening.
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Affiliation(s)
- Klaus Gori
- Department of Food Science, Food Microbiology, Faculty of Life Sciences, University of Copenhagen, Frederiksberg C, Denmark.
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Steele J, Broadbent J, Kok J. Perspectives on the contribution of lactic acid bacteria to cheese flavor development. Curr Opin Biotechnol 2012; 24:135-41. [PMID: 23279928 DOI: 10.1016/j.copbio.2012.12.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 12/06/2012] [Accepted: 12/06/2012] [Indexed: 11/16/2022]
Abstract
It has been known since the 1960s that lactic acid bacteria are essential for the development of cheese flavor. In the ensuing 50 years significant research has been directed at understanding the microbiology, genetics and biochemistry of this process. This review briefly covers the current status of cheese flavor development and then provides our vision for approaches which will enhance our understanding of this process. The long-term goal of this area of research is to enable technology (i.e. cultures and enzymes) that results in consistent rapid development of cheese variety-specific characteristic flavors.
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Affiliation(s)
- James Steele
- University of Wisconsin-Madison, Department of Food Science, 1605 Linden Drive, Madison, WI 53706, USA
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New insights into sulfur metabolism in yeasts as revealed by studies of Yarrowia lipolytica. Appl Environ Microbiol 2012; 79:1200-11. [PMID: 23220962 DOI: 10.1128/aem.03259-12] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yarrowia lipolytica, located at the frontier of hemiascomycetous yeasts and fungi, is an excellent candidate for studies of metabolism evolution. This yeast, widely recognized for its technological applications, in particular produces volatile sulfur compounds (VSCs) that fully contribute to the flavor of smear cheese. We report here a relevant global vision of sulfur metabolism in Y. lipolytica based on a comparison between high- and low-sulfur source supplies (sulfate, methionine, or cystine) by combined approaches (transcriptomics, metabolite profiling, and VSC analysis). The strongest repression of the sulfate assimilation pathway was observed in the case of high methionine supply, together with a large accumulation of sulfur intermediates. A high sulfate supply seems to provoke considerable cellular stress via sulfite production, resulting in a decrease of the availability of the glutathione pathway's sulfur intermediates. The most limited effect was observed for the cystine supply, suggesting that the intracellular cysteine level is more controlled than that of methionine and sulfate. Using a combination of metabolomic profiling and genetic experiments, we revealed taurine and hypotaurine metabolism in yeast for the first time. On the basis of a phylogenetic study, we then demonstrated that this pathway was lost by some of the hemiascomycetous yeasts during evolution.
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Roux A, Xu Y, Heilier JF, Olivier MF, Ezan E, Tabet JC, Junot C. Annotation of the human adult urinary metabolome and metabolite identification using ultra high performance liquid chromatography coupled to a linear quadrupole ion trap-Orbitrap mass spectrometer. Anal Chem 2012; 84:6429-37. [PMID: 22770225 DOI: 10.1021/ac300829f] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Metabolic profiles of biofluids obtained by atmospheric pressure ionization mass spectrometry-based technologies contain hundreds to thousands of features, most of them remaining unknown or at least not characterized in analytical systems. We report here on the annotation of the human adult urinary metabolome and metabolite identification from electrospray ionization mass spectrometry (ESI-MS)-based metabolomics data sets. Features of biological interest were first of all annotated using the ESI-MS database of the laboratory. They were also grouped, thanks to software tools, and annotated using public databases. Metabolite identification was achieved using two complementary approaches: (i) formal identification by matching chromatographic retention times, mass spectra, and also product ion spectra (if required) of metabolites to be characterized in biological data sets to those of reference compounds and (ii) putative identification from biological data thanks to MS/MS experiments for metabolites not available in our chemical library. By these means, 384 metabolites corresponding to 1484 annotated features (659 in negative ion mode and 825 in positive ion mode) were characterized in human urine samples. Of these metabolites, 192 and 66 were formally and putatively identified, respectively, and 54 are reported in human urine for the first time. These lists of features could be used by other laboratories to annotate their ESI-MS metabolomics data sets.
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Affiliation(s)
- Aurelie Roux
- CEA-Centre d'Etude de Saclay, Gif-sur-Yvette, France
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Wang T, Leyh TS. Three-stage assembly of the cysteine synthase complex from Escherichia coli. J Biol Chem 2011; 287:4360-7. [PMID: 22179612 DOI: 10.1074/jbc.m111.288423] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Control of sulfur metabolism in plants and bacteria is linked, in significant measure, to the behavior of the cysteine synthase complex (CSC). The complex is comprised of the two enzymes that catalyze the final steps in cysteine biosynthesis: serine O-acetyltransferase (SAT, EC 2.3.1.30), which produces O-acetyl-L-serine, and O-acetyl-L-serine sulfhydrylase (OASS, EC 2.5.1.47), which converts it to cysteine. SAT (a dimer of homotrimers) binds a maximum of two molecules of OASS (a dimer) in an interaction believed to involve docking of the C terminus from a protomer in an SAT trimer into an OASS active site. This interaction inactivates OASS catalysis and prevents further binding to the trimer; thus, the system exhibits a contact-induced inactivation of half of each biomolecule. To better understand the dynamics and energetics that underlie formation of the CSC, the interactions of OASS and SAT from Escherichia coli were studied at equilibrium and in the pre-steady state. Using an experimental strategy that initiates dissociation of the CSC at different points in the CSC-forming reaction, three stable forms of the complex were identified. Comparison of the binding behaviors of SAT and its C-terminal peptide supports a mechanism in which SAT interacts with OASS in a non-allosteric interaction involving its C terminus. This early docking event appears to fasten the proteins in close proximity and thus prepares the system to engage in a series of subsequent, energetically favorable isomerizations that inactivate OASS and produce the fully isomerized CSC.
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Affiliation(s)
- Ting Wang
- Department of Microbiology and Immunology, The Albert Einstein College of Medicine, Bronx, New York 10461, USA
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Hébert A, Forquin-Gomez MP, Roux A, Aubert J, Junot C, Loux V, Heilier JF, Bonnarme P, Beckerich JM, Landaud S. Exploration of sulfur metabolism in the yeast Kluyveromyces lactis. Appl Microbiol Biotechnol 2011; 91:1409-23. [DOI: 10.1007/s00253-011-3481-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 06/29/2011] [Accepted: 07/13/2011] [Indexed: 10/17/2022]
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