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Xiao F, Zhang Y, Zhang L, Li S, Chen W, Shi G, Li Y. Advancing Bacillus licheniformis as a Superior Expression Platform through Promoter Engineering. Microorganisms 2024; 12:1693. [PMID: 39203534 PMCID: PMC11356801 DOI: 10.3390/microorganisms12081693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 08/14/2024] [Accepted: 08/15/2024] [Indexed: 09/03/2024] Open
Abstract
Bacillus licheniformis is recognised as an exceptional expression platform in biomanufacturing due to its ability to produce high-value products. Consequently, metabolic engineering of B. licheniformis is increasingly pursued to enhance its utility as a biomanufacturing vehicle. Effective B. licheniformis cell factories require promoters that enable regulated expression of target genes. This review discusses recent advancements in the characterisation, synthesis, and engineering of B. licheniformis promoters. We highlight the application of constitutive promoters, quorum sensing promoters, and inducible promoters in protein and chemical synthesis. Additionally, we summarise efforts to expand the promoter toolbox through hybrid promoter engineering, transcription factor-based inducible promoter engineering, and ribosome binding site (RBS) engineering.
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Affiliation(s)
- Fengxu Xiao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (F.X.); (Y.Z.); (L.Z.); (S.L.); (G.S.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China;
| | - Yupeng Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (F.X.); (Y.Z.); (L.Z.); (S.L.); (G.S.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China;
| | - Lihuan Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (F.X.); (Y.Z.); (L.Z.); (S.L.); (G.S.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Siyu Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (F.X.); (Y.Z.); (L.Z.); (S.L.); (G.S.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China;
| | - Guiyang Shi
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (F.X.); (Y.Z.); (L.Z.); (S.L.); (G.S.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Youran Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (F.X.); (Y.Z.); (L.Z.); (S.L.); (G.S.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
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Choe D, Olson CA, Szubin R, Yang H, Sung J, Feist AM, Palsson BO. Advancing the scale of synthetic biology via cross-species transfer of cellular functions enabled by iModulon engraftment. Nat Commun 2024; 15:2356. [PMID: 38490991 PMCID: PMC10943186 DOI: 10.1038/s41467-024-46486-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 02/29/2024] [Indexed: 03/18/2024] Open
Abstract
Machine learning applied to large compendia of transcriptomic data has enabled the decomposition of bacterial transcriptomes to identify independently modulated sets of genes, such iModulons represent specific cellular functions. The identification of iModulons enables accurate identification of genes necessary and sufficient for cross-species transfer of cellular functions. We demonstrate cross-species transfer of: 1) the biotransformation of vanillate to protocatechuate, 2) a malonate catabolic pathway, 3) a catabolic pathway for 2,3-butanediol, and 4) an antimicrobial resistance to ampicillin found in multiple Pseudomonas species to Escherichia coli. iModulon-based engineering is a transformative strategy as it includes all genes comprising the transferred cellular function, including genes without functional annotation. Adaptive laboratory evolution was deployed to optimize the cellular function transferred, revealing mutations in the host. Combining big data analytics and laboratory evolution thus enhances the level of understanding of systems biology, and synthetic biology for strain design and development.
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Affiliation(s)
- Donghui Choe
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Connor A Olson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Richard Szubin
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Hannah Yang
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jaemin Sung
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Adam M Feist
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Copenhagen, Denmark
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Copenhagen, Denmark.
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Li W, Huang X, Liu H, Lian H, Xu B, Zhang W, Sun X, Wang W, Jia S, Zhong C. Improvement in bacterial cellulose production by co-culturing Bacillus cereus and Komagataeibacter xylinus. Carbohydr Polym 2023; 313:120892. [PMID: 37182977 DOI: 10.1016/j.carbpol.2023.120892] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 05/16/2023]
Abstract
Bacterial cellulose (BC) is a bio-produced nanostructure material widely used in biomedical, food, and paper-manufacturing industries. However, low production efficiency and high-cost have limited its industrial applications. This study aimed to examine the level of improvement in BC production by co-culturing Bacillus cereus and Komagataeibacter xylinus. The BC yield in corn stover enzymatic hydrolysate was found to be obviously enhanced from 1.2 to 4.4 g/L after the aforementioned co-culturing. The evidence indicated that acetoin (AC) and 2,3-butanediol (2,3-BD) produced by B. cereus were the key factors dominating BC increment. The mechanism underlying BC increment was that AC and 2,3-BD increased the specific activity of AC dehydrogenase and the contents of adenosine triphosphate (ATP) and acetyl coenzyme A (acetyl-CoA), thus promoting the growth and energy level of K. xylinus. Meanwhile, the immobilization of BC could also facilitate oxygen acquisition in B. cereus under static conditions. This study was novel in reporting that the co-culture could effectively enhance BC production from the lignocellulosic enzymatic hydrolysate.
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Affiliation(s)
- Wenchao Li
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, 300457 Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science & Technology, 300457 Tianjin, PR China
| | - Xinxin Huang
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, 300457 Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science & Technology, 300457 Tianjin, PR China
| | - Huan Liu
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, 300457 Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science & Technology, 300457 Tianjin, PR China
| | - Hao Lian
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, 300457 Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science & Technology, 300457 Tianjin, PR China
| | - Bin Xu
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, 300457 Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science & Technology, 300457 Tianjin, PR China
| | - Wenjin Zhang
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, 300457 Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science & Technology, 300457 Tianjin, PR China
| | - Xuewen Sun
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, 300457 Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science & Technology, 300457 Tianjin, PR China
| | - Wei Wang
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, 300457 Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science & Technology, 300457 Tianjin, PR China
| | - Shiru Jia
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, 300457 Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science & Technology, 300457 Tianjin, PR China
| | - Cheng Zhong
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, 300457 Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science & Technology, 300457 Tianjin, PR China.
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Yang J, Liang R, Mao Y, Dong P, Zhu L, Luo X, Zhang Y, Yang X. Potential inhibitory effect of carbon dioxide on the spoilage behaviors of Pseudomonas fragi in high-oxygen packaged beef during refrigerated storage. Food Microbiol 2023; 112:104229. [PMID: 36906301 DOI: 10.1016/j.fm.2023.104229] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/15/2023] [Accepted: 01/21/2023] [Indexed: 01/24/2023]
Abstract
Pseudomonas fragi is a dominant meat spoilage organism under high-oxygen modified atmosphere packaging (HiOx-MAP). This work investigated the effects of CO2 on P. fragi growth and the related spoilage phenomena of HiOx-MAP beef. Minced beef incubated with P. fragi T1, a strain owning the strongest spoilage potential among isolates, was stored under CO2-enriched HiOx-MAP (TMAP; 50% O2/40% CO2/10% N2) or non-CO2 HiOx-MAP (CMAP; 50% O2/50% N2) at 4 °C for 14 days. Compared to CMAP, TMAP maintained sufficient O2 levels to endow beef with higher a* values and meat color stability due to lower P. fragi counts from day 1 (P < 0.05). TMAP samples also showed lower (P < 0.05) lipase activity and protease activity within 14-days and 6-days than CMAP samples respectively. TMAP delayed the significantly increased pH and total volatile basic nitrogen contents occurred in CMAP beef during storage. Despite TMAP markedly promoted the lipid oxidation associated with higher concentrations of hexanal and 2,3-octanedione than CMAP (P < 0.05), TMAP beef retained an acceptable organoleptic odor due to a CO2-inhibition on the microbial-induced 2,3-butanedione and ethyl 2-butenoate formation. This study provided a comprehensive insight into the antibacterial mechanism of CO2 on P. fragi in HiOx-MAP beef.
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Affiliation(s)
- Jun Yang
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, PR China; National R&D Center for Beef Processing Technology, Tai'an, Shandong, 271018, PR China
| | - Rongrong Liang
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, PR China; National R&D Center for Beef Processing Technology, Tai'an, Shandong, 271018, PR China
| | - Yanwei Mao
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, PR China; National R&D Center for Beef Processing Technology, Tai'an, Shandong, 271018, PR China
| | - Pengcheng Dong
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, PR China; National R&D Center for Beef Processing Technology, Tai'an, Shandong, 271018, PR China
| | - Lixian Zhu
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, PR China; National R&D Center for Beef Processing Technology, Tai'an, Shandong, 271018, PR China
| | - Xin Luo
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, PR China; National R&D Center for Beef Processing Technology, Tai'an, Shandong, 271018, PR China
| | - Yimin Zhang
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, PR China; National R&D Center for Beef Processing Technology, Tai'an, Shandong, 271018, PR China.
| | - Xiaoyin Yang
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, PR China; National R&D Center for Beef Processing Technology, Tai'an, Shandong, 271018, PR China.
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Moreno R, Yuste L, Rojo F. The acetoin assimilation pathway of Pseudomonas putida KT2440 is regulated by overlapping global regulatory elements that respond to nutritional cues. Environ Microbiol 2023; 25:515-531. [PMID: 36482024 PMCID: PMC10107126 DOI: 10.1111/1462-2920.16304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
Many microorganisms produce and excrete acetoin (3-hydroxy-2-butanone) when growing in environments that contain glucose or other fermentable carbon sources. This excreted compound can then be assimilated by other bacterial species such as pseudomonads. This work shows that acetoin is not a preferred carbon source of Pseudomonas putida, and that the induction of genes required for its assimilation is down-modulated by different, independent, global regulatory systems when succinate, glucose or components of the LB medium are also present. The expression of the acetoin degradation genes was found to rely on the RpoN alternative sigma factor and to be modulated by the Crc/Hfq, Cyo and PTSNtr regulatory elements, with the impact of the latter three varying according to the carbon source present in addition to acetoin. Pyruvate, a poor carbon source for P. putida, did not repress acetoin assimilation. Indeed, the presence of acetoin significantly improved growth on pyruvate, revealing these compounds to have a synergistic effect. This would provide a clear competitive advantage to P. putida when growing in environments in which all the preferred carbon sources have been depleted and pyruvate and acetoin remain as leftovers from the fermentation of sugars by other microorganisms.
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Affiliation(s)
- Renata Moreno
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Cantoblanco, Madrid, Spain
| | - Luis Yuste
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Cantoblanco, Madrid, Spain
| | - Fernando Rojo
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Cantoblanco, Madrid, Spain
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Magalhães AP, França A, Pereira MO, Cerca N. Unveiling Co-Infection in Cystic Fibrosis Airways: Transcriptomic Analysis of Pseudomonas aeruginosa and Staphylococcus aureus Dual-Species Biofilms. Front Genet 2022; 13:883199. [PMID: 35873457 PMCID: PMC9298864 DOI: 10.3389/fgene.2022.883199] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/26/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Andreia Patrícia Magalhães
- LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal.,LABBELS-Associate Laboratory, Braga, Portugal
| | - Angela França
- LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal.,LABBELS-Associate Laboratory, Braga, Portugal
| | - Maria Olívia Pereira
- LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal.,LABBELS-Associate Laboratory, Braga, Portugal
| | - Nuno Cerca
- LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal.,LABBELS-Associate Laboratory, Braga, Portugal
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Zarrella TM, Khare A. Systematic identification of molecular mediators of interspecies sensing in a community of two frequently coinfecting bacterial pathogens. PLoS Biol 2022; 20:e3001679. [PMID: 35727825 PMCID: PMC9249247 DOI: 10.1371/journal.pbio.3001679] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 07/01/2022] [Accepted: 05/17/2022] [Indexed: 11/18/2022] Open
Abstract
Bacteria typically exist in dynamic, multispecies communities where polymicrobial interactions influence fitness. Elucidating the molecular mechanisms underlying these interactions is critical for understanding and modulating bacterial behavior in natural environments. While bacterial responses to foreign species are frequently characterized at the molecular and phenotypic level, the exogenous molecules that elicit these responses are understudied. Here, we outline a systematic strategy based on transcriptomics combined with genetic and biochemical screens of promoter-reporters to identify the molecules from one species that are sensed by another. We utilized this method to study interactions between the pathogens Pseudomonas aeruginosa and Staphylococcus aureus that are frequently found in coinfections. We discovered that P. aeruginosa senses diverse staphylococcal exoproducts including the metallophore staphylopine (StP), intermediate metabolites citrate and acetoin, and multiple molecules that modulate its iron starvation response. We observed that StP inhibits biofilm formation and that P. aeruginosa can utilize citrate and acetoin for growth, revealing that these interactions have both antagonistic and beneficial effects. Due to the unbiased nature of our approach, we also identified on a genome scale the genes in S. aureus that affect production of each sensed exoproduct, providing possible targets to modify multispecies community dynamics. Further, a combination of these identified S. aureus products recapitulated a majority of the transcriptional response of P. aeruginosa to S. aureus supernatant, validating our screening strategy. Cystic fibrosis (CF) clinical isolates of both S. aureus and P. aeruginosa also showed varying degrees of induction or responses, respectively, which suggests that these interactions are widespread among pathogenic strains. Our screening approach thus identified multiple S. aureus secreted molecules that are sensed by P. aeruginosa and affect its physiology, demonstrating the efficacy of this approach, and yielding new insight into the molecular basis of interactions between these two species.
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Affiliation(s)
- Tiffany M. Zarrella
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Postdoctoral Research Associate Training Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Anupama Khare
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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Adolf LA, Heilbronner S. Nutritional Interactions between Bacterial Species Colonising the Human Nasal Cavity: Current Knowledge and Future Prospects. Metabolites 2022; 12:489. [PMID: 35736422 PMCID: PMC9229137 DOI: 10.3390/metabo12060489] [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: 04/14/2022] [Revised: 05/16/2022] [Accepted: 05/25/2022] [Indexed: 12/10/2022] Open
Abstract
The human nasal microbiome can be a reservoir for several pathogens, including Staphylococcus aureus. However, certain harmless nasal commensals can interfere with pathogen colonisation, an ability that could be exploited to prevent infection. Although attractive as a prophylactic strategy, manipulation of nasal microbiomes to prevent pathogen colonisation requires a better understanding of the molecular mechanisms of interaction that occur between nasal commensals as well as between commensals and pathogens. Our knowledge concerning the mechanisms of pathogen exclusion and how stable community structures are established is patchy and incomplete. Nutrients are scarce in nasal cavities, which makes competitive or mutualistic traits in nutrient acquisition very likely. In this review, we focus on nutritional interactions that have been shown to or might occur between nasal microbiome members. We summarise concepts of nutrient release from complex host molecules and host cells as well as of intracommunity exchange of energy-rich fermentation products and siderophores. Finally, we discuss the potential of genome-based metabolic models to predict complex nutritional interactions between members of the nasal microbiome.
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Affiliation(s)
- Lea A. Adolf
- Interfaculty Institute for Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, UKT Tübingen, 72076 Tübingen, Germany;
| | - Simon Heilbronner
- Interfaculty Institute for Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, UKT Tübingen, 72076 Tübingen, Germany;
- German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, 72076 Tübingen, Germany
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Phylogenetic Analysis with Prediction of Cofactor or Ligand Binding for Pseudomonas aeruginosa PAS and Cache Domains. Microbiol Spectr 2021; 9:e0102621. [PMID: 34937179 PMCID: PMC8694187 DOI: 10.1128/spectrum.01026-21] [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] [Indexed: 11/20/2022] Open
Abstract
PAS domains are omnipresent building blocks of multidomain proteins in all domains of life. Bacteria possess a variety of PAS domains in intracellular proteins and the related Cache domains in periplasmic or extracellular proteins. PAS and Cache domains are predominant in sensory systems, often carry cofactors or bind ligands, and serve as dimerization domains in protein association. To aid our understanding of the wide distribution of these domains, we analyzed the proteome of the opportunistic human pathogen Pseudomonas aeruginosa PAO1 in silico. The ability of this bacterium to survive under different environmental conditions, to switch between planktonic and sessile/biofilm lifestyle, or to evade stresses, notably involves c-di-GMP regulatory proteins or depends on sensory pathways involving multidomain proteins that possess PAS or Cache domains. Maximum likelihood phylogeny was used to group PAS and Cache domains on the basis of amino acid sequence. Conservation of cofactor- or ligand-coordinating amino acids aided by structure-based comparison was used to inform function. The resulting classification presented here includes PAS domains that are candidate binders of carboxylic acids, amino acids, fatty acids, flavin adenine dinucleotide (FAD), 4-hydroxycinnamic acid, and heme. These predictions are put in context to previously described phenotypic data, often generated from deletion mutants. The analysis predicts novel functions for sensory proteins and sheds light on functional diversification in a large set of proteins with similar architecture. IMPORTANCE To adjust to a variety of life conditions, bacteria typically use multidomain proteins, where the modular structure allows functional differentiation. Proteins responding to environmental cues and regulating physiological responses are found in chemotaxis pathways that respond to a wide range of stimuli to affect movement. Environmental cues also regulate intracellular levels of cyclic-di-GMP, a universal bacterial secondary messenger that is a key determinant of bacterial lifestyle and virulence. We study Pseudomonas aeruginosa, an organism known to colonize a broad range of environments that can switch lifestyle between the sessile biofilm and the planktonic swimming form. We have investigated the PAS and Cache domains, of which we identified 101 in 70 Pseudomonas aeruginosa PAO1 proteins, and have grouped these by phylogeny with domains of known structure. The resulting data set integrates sequence analysis and structure prediction to infer ligand or cofactor binding. With this data set, functional predictions for PAS and Cache domain-containing proteins are made.
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Liu Y, Wang X, Ma L, Lü M, Zhang W, Lü C, Gao C, Xu P, Ma C. Dehydrogenation Mechanism of Three Stereoisomers of Butane-2,3-Diol in Pseudomonas putida KT2440. Front Bioeng Biotechnol 2021; 9:728767. [PMID: 34513815 PMCID: PMC8427195 DOI: 10.3389/fbioe.2021.728767] [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: 06/22/2021] [Accepted: 08/09/2021] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas putida KT2440 is a promising chassis of industrial biotechnology due to its metabolic versatility. Butane-2,3-diol (2,3-BDO) is a precursor of numerous value-added chemicals. It is also a microbial metabolite which widely exists in various habiting environments of P. putida KT2440. It was reported that P. putida KT2440 is able to use 2,3-BDO as a sole carbon source for growth. There are three stereoisomeric forms of 2,3-BDO: (2R,3R)-2,3-BDO, meso-2,3-BDO and (2S,3S)-2,3-BDO. However, whether P. putida KT2440 can utilize three stereoisomeric forms of 2,3-BDO has not been elucidated. Here, we revealed the genomic and enzymic basis of P. putida KT2440 for dehydrogenation of different stereoisomers of 2,3-BDO into acetoin, which will be channeled to central mechanism via acetoin dehydrogenase enzyme system. (2R,3R)-2,3-BDO dehydrogenase (PP0552) was detailedly characterized and identified to participate in (2R,3R)-2,3-BDO and meso-2,3-BDO dehydrogenation. Two quinoprotein alcohol dehydrogenases, PedE (PP2674) and PedH (PP2679), were confirmed to be responsible for (2S,3S)-2,3-BDO dehydrogenation. The function redundancy and inverse regulation of PedH and PedE by lanthanide availability provides a mechanism for the adaption of P. putida KT2440 to variable environmental conditions. Elucidation of the mechanism of 2,3-BDO catabolism in P. putida KT2440 would provide new insights for bioproduction of 2,3-BDO-derived chemicals based on this robust chassis.
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Affiliation(s)
- Yidong Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiuqing Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Liting Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Min Lü
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Wen Zhang
- Center for Gene and Immunotherapy, The Second Hospital of Shandong University, Jinan, China
| | - Chuanjuan Lü
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Chao Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Cuiqing Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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C4 Bacterial Volatiles Improve Plant Health. Pathogens 2021; 10:pathogens10060682. [PMID: 34072921 PMCID: PMC8227687 DOI: 10.3390/pathogens10060682] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/10/2021] [Accepted: 05/24/2021] [Indexed: 02/04/2023] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) associated with plant roots can trigger plant growth promotion and induced systemic resistance. Several bacterial determinants including cell-wall components and secreted compounds have been identified to date. Here, we review a group of low-molecular-weight volatile compounds released by PGPR, which improve plant health, mostly by protecting plants against pathogen attack under greenhouse and field conditions. We particularly focus on C4 bacterial volatile compounds (BVCs), such as 2,3-butanediol and acetoin, which have been shown to activate the plant immune response and to promote plant growth at the molecular level as well as in large-scale field applications. We also disc/ uss the potential applications, metabolic engineering, and large-scale fermentation of C4 BVCs. The C4 bacterial volatiles act as airborne signals and therefore represent a new type of biocontrol agent. Further advances in the encapsulation procedure, together with the development of standards and guidelines, will promote the application of C4 volatiles in the field.
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12
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Purification and Characterization of (2R,3R)-2,3-Butanediol Dehydrogenase of the Human Pathogen Neisseria gonorrhoeae FA1090 Produced in Escherichia coli. Mol Biotechnol 2021; 63:491-501. [PMID: 33763825 DOI: 10.1007/s12033-021-00308-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 02/12/2021] [Indexed: 12/22/2022]
Abstract
2,3-Butanediol dehydrogenase (BDH), also known as acetoin/diacetyl reductase, is a pivotal enzyme for the formation of 2,3-butanediol (2,3-BD), a chiral compound with potential roles in the virulence of certain pathogens. Here, a NAD(H)-dependent (2R,3R)-BDH from Neisseria gonorrhoeae FA1090 (NgBDH), the causative agent of gonorrhoea, was functionally characterized. Sequence analysis indicated that it belongs to zinc-containing medium-chain dehydrogenase/reductase family. The recombinant NgBDH migrated as a single band with a size of around 45 kDa on SDS-PAGE and could be confirmed by Western blotting and mass spectrometry. For the oxidation of either (2R,3R)-2,3-BD or meso-2,3-BD, the enzyme exhibited a broad pH optimum between pH 9.5 to 11.5. For the reduction of (3R/3S)-acetoin, the pH optimum was around 6.5. The enzyme could catalyze the stereospecific oxidation of (2R,3R)-2,3-BD (Km = 0.16 mM, kcat/Km = 673 s-1 · mM-1) and meso-BD (Km = 0.72 mM, kcat/Km = 165 s-1 · mM-1). Moreover, it could also reduce (3R/3S)-acetoin with a Km of 0.14 mM and a kcat/Km of 885 s-1 · mM-1. The results presented here contribute to understand the 2,3-BD metabolism in N. gonorrhoeae and pave the way for studying the influence of 2,3-BD metabolism on the virulence of this pathogen in the future.
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13
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Wang D, Oh BR, Lee S, Kim DH, Joe MH. Process optimization for mass production of 2,3-butanediol by Bacillus subtilis CS13. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:15. [PMID: 33419471 PMCID: PMC7791975 DOI: 10.1186/s13068-020-01859-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 12/13/2020] [Indexed: 05/07/2023]
Abstract
BACKGROUND Bacillus subtilis CS13 was previously isolated for 2,3-butanediol (2,3-BD) and poly-γ-glutamic acid (γ-PGA) co-production. When culturing this strain without L-glutamic acid in the medium, 2,3-BD is the main metabolic product. 2,3-BD is an important substance and fuel with applications in the chemical, food, and pharmaceutical industries. However, the yield and productivity for the B. subtilis strain should be improved for more efficient production of 2,3-BD. RESULTS The medium composition, which contained 281.1 g/L sucrose, 21.9 g/L ammonium citrate, and 3.6 g/L MgSO4·7H2O, was optimized by response surface methodology for 2,3-BD production using B. subtilis CS13. The maximum amount of 2,3-BD (125.5 ± 3.1 g/L) was obtained from the optimized medium after 96 h. The highest concentration and productivity of 2,3-BD were achieved simultaneously at an agitation speed of 500 rpm and aeration rate of 2 L/min in the batch cultures. A total of 132.4 ± 4.4 g/L 2,3-BD was obtained with a productivity of 2.45 ± 0.08 g/L/h and yield of 0.45 g2,3-BD/gsucrose by fed-batch fermentation. The meso-2,3-BD/2,3-BD ratio of the 2,3-BD produced by B. subtilis CS13 was 92.1%. Furthermore, 89.6 ± 2.8 g/L 2,3-BD with a productivity of 2.13 ± 0.07 g/L/h and yield of 0.42 g2,3-BD/gsugar was achieved using molasses as a carbon source. CONCLUSIONS The production of 2,3-BD by B. subtilis CS13 showed a higher concentration, productivity, and yield compared to the reported generally recognized as safe 2,3-BD producers. These results suggest that B. subtilis CS13 is a promising strain for industrial-scale production of 2,3-BD.
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Affiliation(s)
- Dexin Wang
- Radiation Utilization and Facilities Management Division, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup, 56212, Republic of Korea
- Department of Bioactive Material Sciences, Institute for Molecular Biology and Genetics, Center for Fungal Pathogenesis, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Baek-Rock Oh
- Microbial Biotechnology Research Center, Jeonbuk Branch Institute, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Republic of Korea
| | - Sungbeom Lee
- Radiation Research Division, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup, 56212, Republic of Korea
- Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Dae-Hyuk Kim
- Department of Bioactive Material Sciences, Institute for Molecular Biology and Genetics, Center for Fungal Pathogenesis, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Min-Ho Joe
- Radiation Utilization and Facilities Management Division, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup, 56212, Republic of Korea.
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14
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Mobilization of Iron Stored in Bacterioferritin Is Required for Metabolic Homeostasis in Pseudomonas aeruginosa. Pathogens 2020; 9:pathogens9120980. [PMID: 33255203 PMCID: PMC7760384 DOI: 10.3390/pathogens9120980] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/22/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
Iron homeostasis offers a significant bacterial vulnerability because pathogens obtain essential iron from their mammalian hosts, but host-defenses maintain vanishingly low levels of free iron. Although pathogens have evolved mechanisms to procure host-iron, these depend on well-regulated iron homeostasis. To disrupt iron homeostasis, our work has targeted iron mobilization from the iron storage protein bacterioferritin (BfrB) by blocking a required interaction with its cognate ferredoxin partner (Bfd). The blockade of the BfrB–Bfd complex by deletion of the bfd gene (Δbfd) causes iron to irreversibly accumulate in BfrB. In this study we used mass spectrometry and NMR spectroscopy to compare the proteomic response and the levels of key intracellular metabolites between wild type (wt) and isogenic ΔbfdP. aeruginosa strains. We find that the irreversible accumulation of unusable iron in BfrB leads to acute intracellular iron limitation, even if the culture media is iron-sufficient. Importantly, the iron limitation and concomitant iron metabolism dysregulation trigger a cascade of events that lead to broader metabolic homeostasis disruption, which includes sulfur limitation, phenazine-mediated oxidative stress, suboptimal amino acid synthesis and altered carbon metabolism.
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15
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Poh WH, Lin J, Colley B, Müller N, Goh BC, Schleheck D, El Sahili A, Marquardt A, Liang Y, Kjelleberg S, Lescar J, Rice SA, Klebensberger J. The SiaABC threonine phosphorylation pathway controls biofilm formation in response to carbon availability in Pseudomonas aeruginosa. PLoS One 2020; 15:e0241019. [PMID: 33156827 PMCID: PMC7647112 DOI: 10.1371/journal.pone.0241019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/06/2020] [Indexed: 12/17/2022] Open
Abstract
The critical role of bacterial biofilms in chronic human infections calls for novel anti-biofilm strategies targeting the regulation of biofilm development. However, the regulation of biofilm development is very complex and can include multiple, highly interconnected signal transduction/response pathways, which are incompletely understood. We demonstrated previously that in the opportunistic, human pathogen P. aeruginosa, the PP2C-like protein phosphatase SiaA and the di-guanylate cyclase SiaD control the formation of macroscopic cellular aggregates, a type of suspended biofilms, in response to surfactant stress. In this study, we demonstrate that the SiaABC proteins represent a signal response pathway that functions through a partner switch mechanism to control biofilm formation. We also demonstrate that SiaABCD functionality is dependent on carbon substrate availability for a variety of substrates, and that upon carbon starvation, SiaB mutants show impaired dispersal, in particular with the primary fermentation product ethanol. This suggests that carbon availability is at least one of the key environmental cues integrated by the SiaABCD system. Further, our biochemical, physiological and crystallographic data reveals that the phosphatase SiaA and its kinase counterpart SiaB balance the phosphorylation status of their target protein SiaC at threonine 68 (T68). Crystallographic analysis of the SiaA-PP2C domain shows that SiaA is present as a dimer. Dynamic modelling of SiaA with SiaC suggested that SiaA interacts strongly with phosphorylated SiaC and dissociates rapidly upon dephosphorylation of SiaC. Further, we show that the known phosphatase inhibitor fumonisin inhibits SiaA mediated phosphatase activity in vitro. In conclusion, the present work improves our understanding of how P. aeuruginosa integrates specific environmental conditions, such as carbon availability and surfactant stress, to regulate cellular aggregation and biofilm formation. With the biochemical and structural characterization of SiaA, initial data on the catalytic inhibition of SiaA, and the interaction between SiaA and SiaC, our study identifies promising targets for the development of biofilm-interference drugs to combat infections of this aggressive opportunistic pathogen.
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Affiliation(s)
- Wee-Han Poh
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Jianqing Lin
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Brendan Colley
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Nicolai Müller
- Konstanz Research School Chemical Biology, Departments of Chemistry and Biology, University of Konstanz, Konstanz, Germany
| | - Boon Chong Goh
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - David Schleheck
- Konstanz Research School Chemical Biology, Departments of Chemistry and Biology, University of Konstanz, Konstanz, Germany
| | - Abbas El Sahili
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
- The School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Andreas Marquardt
- Konstanz Research School Chemical Biology, Departments of Chemistry and Biology, University of Konstanz, Konstanz, Germany
| | - Yang Liang
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- The School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
- The School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Julien Lescar
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
- The School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Scott A. Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- The School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- The ithree Institute, The University of Technology Sydney, Sydney, Australia
| | - Janosch Klebensberger
- University of Stuttgart, Institute of Biochemistry and Technical Biochemistry, Stuttgart, Germany
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16
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Camus L, Briaud P, Bastien S, Elsen S, Doléans-Jordheim A, Vandenesch F, Moreau K. Trophic cooperation promotes bacterial survival of Staphylococcus aureus and Pseudomonas aeruginosa. ISME JOURNAL 2020; 14:3093-3105. [PMID: 32814867 DOI: 10.1038/s41396-020-00741-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/30/2020] [Accepted: 08/06/2020] [Indexed: 01/07/2023]
Abstract
In the context of infection, Pseudomonas aeruginosa and Staphylococcus aureus are frequently co-isolated, particularly in cystic fibrosis (CF) patients. Within lungs, the two pathogens exhibit a range of competitive and coexisting interactions. In the present study, we explored the impact of S. aureus on the physiology of P. aeruginosa in the context of coexistence. Transcriptomic analyses showed that S. aureus significantly and specifically affects the expression of numerous genes involved in P. aeruginosa carbon and amino acid metabolism. In particular, 65% of the strains presented considerable overexpression of the genes involved in the acetoin catabolic (aco) pathway. We demonstrated that acetoin is (i) produced by clinical S. aureus strains, (ii) detected in sputa from CF patients and (iii) involved in P. aeruginosa's aco system induction. Furthermore, acetoin is catabolized by P. aeruginosa, a metabolic process that improves the survival of both pathogens by providing a new carbon source for P. aeruginosa and avoiding the toxic accumulation of acetoin on S. aureus. Due to its beneficial effects on both bacteria, acetoin catabolism could testify to the establishment of trophic cooperation between S. aureus and P. aeruginosa in the CF lung environment, thus promoting their persistence.
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Affiliation(s)
- Laura Camus
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Paul Briaud
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Sylvère Bastien
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Sylvie Elsen
- Université Grenoble Alpes, CNRS ERL5261, CEA-IRIG-BCI, INSERM UMR1036, 38000, Grenoble, France
| | - Anne Doléans-Jordheim
- Institut des agents infectieux, Hospices Civils de Lyon, Lyon, France.,Bactéries Pathogènes Opportunistes et Environnement, UMR CNRS 5557 Ecologie Microbienne, Université Lyon 1 and VetAgro Sup, Villeurbanne, France
| | - François Vandenesch
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France.,Institut des agents infectieux, Hospices Civils de Lyon, Lyon, France.,Centre National de Référence des Staphylocoques, Hospices Civils de Lyon, Lyon, France
| | - Karen Moreau
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France.
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17
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Thöming JG, Tomasch J, Preusse M, Koska M, Grahl N, Pohl S, Willger SD, Kaever V, Müsken M, Häussler S. Parallel evolutionary paths to produce more than one Pseudomonas aeruginosa biofilm phenotype. NPJ Biofilms Microbiomes 2020; 6:2. [PMID: 31934344 PMCID: PMC6954232 DOI: 10.1038/s41522-019-0113-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/16/2019] [Indexed: 01/28/2023] Open
Abstract
Studying parallel evolution of similar traits in independent within-species lineages provides an opportunity to address evolutionary predictability of molecular changes underlying adaptation. In this study, we monitored biofilm forming capabilities, motility, and virulence phenotypes of a plethora of phylogenetically diverse clinical isolates of the opportunistic pathogen Pseudomonas aeruginosa. We also recorded biofilm-specific and planktonic transcriptional responses. We found that P. aeruginosa isolates could be stratified based on the production of distinct organismal traits. Three major biofilm phenotypes, which shared motility and virulence phenotypes, were produced repeatedly in several isolates, indicating that the phenotypes evolved via parallel or convergent evolution. Of note, while we found a restricted general response to the biofilm environment, the individual groups of biofilm phenotypes reproduced biofilm transcriptional profiles that included the expression of well-known biofilm features, such as surface adhesive structures and extracellular matrix components. Our results provide insights into distinct ways to make a biofilm and indicate that genetic adaptations can modulate multiple pathways for biofilm development that are followed by several independent clinical isolates. Uncovering core regulatory pathways that drive biofilm-associated growth and tolerance towards environmental stressors promises to give clues to host and environmental interactions and could provide useful targets for new clinical interventions.
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Affiliation(s)
- Janne G. Thöming
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Clinical Microbiology, Copenhagen University Hospital – Rigshospitalet, Copenhagen, Denmark
| | - Jürgen Tomasch
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Matthias Preusse
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Michal Koska
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Nora Grahl
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sarah Pohl
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sven D. Willger
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Volkhard Kaever
- Research Core Unit Metabolomics and Institute of Pharmacology, Hannover Medical School, Hannover, Germany
| | - Mathias Müsken
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Clinical Microbiology, Copenhagen University Hospital – Rigshospitalet, Copenhagen, Denmark
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
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18
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Zhang M, Kang Z, Guo X, Guo S, Xiao D, Liu Y, Ma C, Gao C, Xu P. Regulation of Glutarate Catabolism by GntR Family Regulator CsiR and LysR Family Regulator GcdR in Pseudomonas putida KT2440. mBio 2019; 10:e01570-19. [PMID: 31363033 PMCID: PMC6667623 DOI: 10.1128/mbio.01570-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 07/02/2019] [Indexed: 01/16/2023] Open
Abstract
Glutarate, a metabolic intermediate in the catabolism of several amino acids and aromatic compounds, can be catabolized through both the glutarate hydroxylation pathway and the glutaryl-coenzyme A (glutaryl-CoA) dehydrogenation pathway in Pseudomonas putida KT2440. The elucidation of the regulatory mechanism could greatly aid in the design of biotechnological alternatives for glutarate production. In this study, it was found that a GntR family protein, CsiR, and a LysR family protein, GcdR, regulate the catabolism of glutarate by repressing the transcription of csiD and lhgO, two key genes in the glutarate hydroxylation pathway, and by activating the transcription of gcdH and gcoT, two key genes in the glutaryl-CoA dehydrogenation pathway, respectively. Our data suggest that CsiR and GcdR are independent and that there is no cross-regulation between the two pathways. l-2-Hydroxyglutarate (l-2-HG), a metabolic intermediate in the glutarate catabolism with various physiological functions, has never been elucidated in terms of its metabolic regulation. Here, we reveal that two molecules, glutarate and l-2-HG, act as effectors of CsiR and that P. putida KT2440 uses CsiR to sense glutarate and l-2-HG and to utilize them effectively. This report broadens our understanding of the bacterial regulatory mechanisms of glutarate and l-2-HG catabolism and may help to identify regulators of l-2-HG catabolism in other species.IMPORTANCE Glutarate is an attractive dicarboxylate with various applications. Clarification of the regulatory mechanism of glutarate catabolism could help to block the glutarate catabolic pathways, thereby improving glutarate production through biotechnological routes. Glutarate is a toxic metabolite in humans, and its accumulation leads to a hereditary metabolic disorder, glutaric aciduria type I. The elucidation of the functions of CsiR and GcdR as regulators that respond to glutarate could help in the design of glutarate biosensors for the rapid detection of glutarate in patients with glutaric aciduria type I. In addition, CsiR was identified as a regulator that also regulates l-2-HG metabolism. The identification of CsiR as a regulator that responds to l-2-HG could help in the discovery and investigation of other regulatory proteins involved in l-2-HG catabolism.
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Affiliation(s)
- Manman Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Department of Radiobiology, Institute of Radiation Medicine of Chinese Academy of Medical Science & Peking Union Medical College, Tianjin, People's Republic of China
| | - Zhaoqi Kang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Xiaoting Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Shiting Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Dan Xiao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Yidong Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Cuiqing Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Chao Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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19
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Tuttobene MR, Fernández-García L, Blasco L, Cribb P, Ambroa A, Müller GL, Fernández-Cuenca F, Bleriot I, Rodríguez RE, Barbosa BGV, Lopez-Rojas R, Trastoy R, López M, Bou G, Tomás M, Mussi MA. Quorum and Light Signals Modulate Acetoin/Butanediol Catabolism in Acinetobacter spp. Front Microbiol 2019; 10:1376. [PMID: 31281296 PMCID: PMC6595428 DOI: 10.3389/fmicb.2019.01376] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/03/2019] [Indexed: 12/25/2022] Open
Abstract
Acinetobacter spp. are found in all environments on Earth due to their extraordinary capacity to survive in the presence of physical and chemical stressors. In this study, we analyzed global gene expression in airborne Acinetobacter sp. strain 5-2Ac02 isolated from hospital environment in response to quorum network modulators and found that they induced the expression of genes of the acetoin/butanediol catabolism, volatile compounds shown to mediate interkingdom interactions. Interestingly, the acoN gene, annotated as a putative transcriptional regulator, was truncated in the downstream regulatory region of the induced acetoin/butanediol cluster in Acinetobacter sp. strain 5-2Ac02, and its functioning as a negative regulator of this cluster integrating quorum signals was confirmed in Acinetobacter baumannii ATCC 17978. Moreover, we show that the acetoin catabolism is also induced by light and provide insights into the light transduction mechanism by showing that the photoreceptor BlsA interacts with and antagonizes the functioning of AcoN in A. baumannii, integrating also a temperature signal. The data support a model in which BlsA interacts with and likely sequesters AcoN at this condition, relieving acetoin catabolic genes from repression, and leading to better growth under blue light. This photoregulation depends on temperature, occurring at 23°C but not at 30°C. BlsA is thus a dual regulator, modulating different transcriptional regulators in the dark but also under blue light, representing thus a novel concept. The overall data show that quorum modulators as well as light regulate the acetoin catabolic cluster, providing a better understanding of environmental as well as clinical bacteria.
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Affiliation(s)
- Marisel Romina Tuttobene
- Centro de Estudios Fotosintéticos y Bioquímicos de Rosario (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Laura Fernández-García
- Microbiology Department-Biomedical Research Institute A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Lucía Blasco
- Microbiology Department-Biomedical Research Institute A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Pamela Cribb
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Rosario, Argentina
| | - Anton Ambroa
- Microbiology Department-Biomedical Research Institute A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Gabriela Leticia Müller
- Centro de Estudios Fotosintéticos y Bioquímicos de Rosario (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Felipe Fernández-Cuenca
- Clinical Unit for Infectious Diseases, Microbiology and Preventive Medicine, Hospital Universitario Virgen Macarena, Seville, Spain.,Department of Microbiology and Medicine, University of Seville, Seville, Spain.,Biomedicine Institute of Seville (IBIS), Seville, Spain
| | - Inés Bleriot
- Centro de Estudios Fotosintéticos y Bioquímicos de Rosario (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | | | - Beatriz G V Barbosa
- Microbial Resistance Laboratory, Biological Sciences Institute, University of Pernambuco (UPE), Recife, Brazil
| | - Rafael Lopez-Rojas
- Clinical Unit for Infectious Diseases, Microbiology and Preventive Medicine, Hospital Universitario Virgen Macarena, Seville, Spain.,Department of Microbiology and Medicine, University of Seville, Seville, Spain.,Biomedicine Institute of Seville (IBIS), Seville, Spain
| | - Rocío Trastoy
- Microbiology Department-Biomedical Research Institute A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - María López
- Microbiology Department-Biomedical Research Institute A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Germán Bou
- Centro de Estudios Fotosintéticos y Bioquímicos de Rosario (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - María Tomás
- Microbiology Department-Biomedical Research Institute A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - María A Mussi
- Centro de Estudios Fotosintéticos y Bioquímicos de Rosario (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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