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Fan C, Xie Z, Zheng D, Zhang R, Li Y, Shi J, Cheng M, Wang Y, Zhou Y, Zhan Y, Yan Y. Overview of indigo biosynthesis by Flavin-containing Monooxygenases: History, industrialization challenges, and strategies. Biotechnol Adv 2024; 73:108374. [PMID: 38729229 DOI: 10.1016/j.biotechadv.2024.108374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/24/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
Indigo is a natural dye extensively used in the global textile industry. However, the conventional synthesis of indigo using toxic compounds like aniline, formaldehyde, and hydrogen cyanide has led to environmental pollution and health risks for workers. This method also faces growing economic, sustainability, and environmental challenges. To address these issues, the concept of bio-indigo or indigo biosynthesis has been proposed as an alternative to aniline-based indigo synthesis. Among various enzymes, Flavin-containing Monooxygenases (FMOs) have shown promise in achieving a high yield of bio-indigo. However, the industrialization of indigo biosynthesis still encounters several challenges. This review focuses on the historical development of indigo biosynthesis mediated by FMOs. It highlights several factors that have hindered industrialization, including the use of unsuitable chassis (Escherichia coli), the toxicity of indole, the high cost of the substrate L-tryptophan, the water-insolubility of the product indigo, the requirement of reducing reagents such as sodium dithionite, and the relatively low yield and high cost compared to chemical synthesis. Additionally, this paper summarizes various strategies to enhance the yield of indigo synthesized by FMOs, including redundant sequence deletion, semi-rational design, cheap precursor research, NADPH regeneration, large-scale fermentation, and enhancement of water solubility of indigo.
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Affiliation(s)
- Changxin Fan
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China; Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - Ziqi Xie
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China; Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - Da Zheng
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China; Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - Ruihan Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China; Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - Yijin Li
- Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - Jiacheng Shi
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China; Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - Mingyuan Cheng
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China; Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - Yifei Wang
- Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - Yu Zhou
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China.
| | - Yi Zhan
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China.
| | - Yunjun Yan
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China.
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2
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Zhang J, Ma Q, Wang C, Lu S, Fan S. Biodegradation characteristics and genomic analysis of a newly isolated indole-degrading strain Pseudomonas aeruginosa Jade-X. Int Microbiol 2024; 27:449-457. [PMID: 37490176 DOI: 10.1007/s10123-023-00408-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/07/2023] [Accepted: 07/18/2023] [Indexed: 07/26/2023]
Abstract
Indole is a typical heterocyclic compound derived from tryptophan widespread in nature. Pseudomonas aeruginosa is one of the most common opportunistic pathogens everywhere in the world. Indole and P. aeruginosa will encounter inevitably; however, the indole transformation process by P. aeruginosa remains unclear. Herein, an indole-degrading strain of P. aeruginosa Jade-X was isolated from activated sludge. Strain Jade-X could degrade 1 mmol/L indole within 48 h with the inoculum size of 1% (v/v). It showed high efficiency in indole degradation under the conditions of 30-42 °C, pH 5.0-9.0, and NaCl concentration less than 2.5%. The complete genome of strain Jade-X was sequenced which was 6508614 bp in length with one chromosome. Bioinformatic analyses showed that strain Jade-X did not contain the indole oxygenase gene. Three cytochrome P450 genes were identified and up-regulated in the indole degradation process by RT-qPCR analysis, while cytochrome P450 inhibitors did not affect the indole degradation process. It suggested that indole oxidation was catalyzed by an unraveled enzyme. An ant gene cluster was identified, among which the anthranilate 1,2-dioxygenase and catechol 1,2-dioxygenase genes were upregulated. An indole-anthranilate-catechol pathway was proposed in indole degradation by strain P. aeruginosa Jade-X. This study enriched our understanding of the indole biodegradation process in P. aeruginosa.
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Affiliation(s)
- Jiaxin Zhang
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Qiao Ma
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China.
| | - Caihong Wang
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Shuxian Lu
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Shengqiang Fan
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China.
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Funkhouser-Jones LJ, Xu R, Wilke G, Fu Y, Schriefer LA, Makimaa H, Rodgers R, Kennedy EA, VanDussen KL, Stappenbeck TS, Baldridge MT, Sibley LD. Microbiota-produced indole metabolites disrupt mitochondrial function and inhibit Cryptosporidium parvum growth. Cell Rep 2023; 42:112680. [PMID: 37384526 PMCID: PMC10530208 DOI: 10.1016/j.celrep.2023.112680] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 05/08/2023] [Accepted: 06/07/2023] [Indexed: 07/01/2023] Open
Abstract
Cryptosporidiosis is a leading cause of life-threatening diarrhea in young children in resource-poor settings. To explore microbial influences on susceptibility, we screened 85 microbiota-associated metabolites for their effects on Cryptosporidium parvum growth in vitro. We identify eight inhibitory metabolites in three main classes: secondary bile salts/acids, a vitamin B6 precursor, and indoles. Growth restriction of C. parvum by indoles does not depend on the host aryl hydrocarbon receptor (AhR) pathway. Instead, treatment impairs host mitochondrial function and reduces total cellular ATP, as well as directly reducing the membrane potential in the parasite mitosome, a degenerate mitochondria. Oral administration of indoles, or reconstitution of the gut microbiota with indole-producing bacteria, delays life cycle progression of the parasite in vitro and reduces the severity of C. parvum infection in mice. Collectively, these findings indicate that microbiota metabolites impair mitochondrial function and contribute to colonization resistance to Cryptosporidium infection.
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Affiliation(s)
- Lisa J Funkhouser-Jones
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rui Xu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Georgia Wilke
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Yong Fu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lawrence A Schriefer
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Heyde Makimaa
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel Rodgers
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Elizabeth A Kennedy
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kelli L VanDussen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Megan T Baldridge
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - L David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
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4
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Funkhouser-Jones LJ, Xu R, Wilke G, Fu Y, Shriefer LA, Makimaa H, Rodgers R, Kennedy EA, VanDussen KL, Stappenbeck TS, Baldridge MT, Sibley LD. Microbiota produced indole metabolites disrupt host cell mitochondrial energy production and inhibit Cryptosporidium parvum growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542157. [PMID: 37292732 PMCID: PMC10245909 DOI: 10.1101/2023.05.25.542157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cryptosporidiosis is a leading cause of life-threatening diarrhea in young children in resource-poor settings. Susceptibility rapidly declines with age, associated with changes in the microbiota. To explore microbial influences on susceptibility, we screened 85 microbiota- associated metabolites enriched in the adult gut for their effects on C. parvum growth in vitro. We identified eight inhibitory metabolites in three main classes: secondary bile salts/acids, a vitamin B 6 precursor, and indoles. Growth restriction of C. parvum by indoles did not depend on the host aryl hydrocarbon receptor (AhR) pathway. Instead, treatment impaired host mitochondrial function and reduced total cellular ATP, as well as directly reduced the membrane potential in the parasite mitosome, a degenerate mitochondria. Oral administration of indoles, or reconstitution of the gut microbiota with indole producing bacteria, delayed life cycle progression of the parasite in vitro and reduced severity of C. parvum infection in mice. Collectively, these findings indicate that microbiota metabolites contribute to colonization resistance to Cryptosporidium infection.
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Affiliation(s)
- Lisa J. Funkhouser-Jones
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Rui Xu
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Georgia Wilke
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Yong Fu
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Lawrence A. Shriefer
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Heyde Makimaa
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Rachel Rodgers
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Elizabeth A. Kennedy
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Kelli L. VanDussen
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Thaddeus S. Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Megan T. Baldridge
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - L. David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
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Ahmad S, Mohammed M, Mekala LP, Anusha R, Sasikala C, Ramana CV. Stable isotope-assisted metabolite profiling reveals new insights into L-tryptophan chemotrophic metabolism of Rubrivivax benzoatilyticus. World J Microbiol Biotechnol 2023; 39:98. [PMID: 36781830 DOI: 10.1007/s11274-023-03537-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 01/31/2023] [Indexed: 02/15/2023]
Abstract
Anoxygenic photosynthetic bacteria (APB) are metabolically versatile, capable of surviving with an extended range of carbon and nitrogen sources. This group of phototrophic bacteria have remarkable metabolic plasticity in utilizing an array of organic compounds as carbon source/electron donors and nitrogen sources with sophisticated growth modes. Rubrivivax benzoatilyticus JA2 is one such photosynthetic bacterium utilizes L-tryptophan as nitrogen source under phototrophic growth mode and produces an array of indolic compounds of biotechnological significance. However, chemotrophic L-tryptophan metabolism is largely unexplored and studying L-tryptophan metabolism under chemotrophic mode would provide new insights into metabolic potential of strain JA2. In the present study, we employed stable-isotopes assisted metabolite profiling to unravel the L-tryptophan catabolism in Rubrivivax benzoatilyticus strain JA2 under chemotrophic (dark aerobic) conditions. Utilization of L-tryptophan as a nitrogen source for growth and simultaneous production of indole derivatives was observed in strain JA2. Liquid chromatography mass spectrometry (LC-MS) analysis of exo-metabolite profiling of carbon labeled L-tryptophan (13C11) fed cultures of strain JA2 revealed at least seventy labeled metabolites. Of these, only fourteen metabolites were confirmed using standards, while sixteen were putative and forty metabolites remained unidentified. L-tryptophan chemotrophic catabolism revealed multiple catabolic pathways and distinct differential catabolism of L-tryptophan under chemotropic state as compared to photo-catabolism of L-tryptophan in strain JA2.
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Affiliation(s)
- Shabbir Ahmad
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Mujahid Mohammed
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India.,Department of Botany, Bharathidasan Government College for Women, Muthialpet, Puducherry U.T., 605003, India
| | - Lakshmi Prasuna Mekala
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India.,Department of Plant Science, Avvaiyar Government College for Women, Karaikal, Puducherry- U.T., 609 602, India
| | - Rai Anusha
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | | | - Chintalapati Venkata Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India.
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6
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Kim H, Moon S, Ham S, Lee K, Römling U, Lee C. Cytoplasmic molecular chaperones in Pseudomonas species. J Microbiol 2022; 60:1049-1060. [PMID: 36318358 DOI: 10.1007/s12275-022-2425-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/20/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Pseudomonas is widespread in various environmental and host niches. To promote rejuvenation, cellular protein homeostasis must be finely tuned in response to diverse stresses, such as extremely high and low temperatures, oxidative stress, and desiccation, which can result in protein homeostasis imbalance. Molecular chaperones function as key components that aid protein folding and prevent protein denaturation. Pseudomonas, an ecologically important bacterial genus, includes human and plant pathogens as well as growth-promoting symbionts and species useful for bioremediation. In this review, we focus on protein quality control systems, particularly molecular chaperones, in ecologically diverse species of Pseudomonas, including the opportunistic human pathogen Pseudomonas aeruginosa, the plant pathogen Pseudomonas syringae, the soil species Pseudomonas putida, and the psychrophilic Pseudomonas antarctica.
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Affiliation(s)
- Hyunhee Kim
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea
| | - Seongjoon Moon
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea
| | - Soojeong Ham
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea
| | - Kihyun Lee
- CJ Bioscience, Seoul, 04527, Republic of Korea
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Changhan Lee
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea.
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7
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Indole decreases the virulence of the bivalve model pathogens Vibrio tasmaniensis LGP32 and Vibrio crassostreae J2-9. Sci Rep 2022; 12:5749. [PMID: 35388110 PMCID: PMC8986839 DOI: 10.1038/s41598-022-09799-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/17/2022] [Indexed: 12/13/2022] Open
Abstract
Indole signaling plays an important role in bacterial pathogenesis. In this study, the impact of indole on biofilm formation, swimming and swarming motility were explored in Vibrio tasmaniensis LGP32 and Vibrio crassostreae J2-9, two model pathogens of bivalves. The results showed that indole decreased swimming and swarming motility in both strains, and decreased biofilm formation in V. crassostreae J2-9. Furthermore, indole affected a large number of genes at RNA level, including genes related to metabolism, ABC transporters, flagellar assembly, chemotaxis, and response regulators. Finally, the bacterial virulence towards mussel larvae was decreased by pretreatment with indole in both V. tasmaniensis LGP32 and V. crassostreae J2-9. After 5 days, the survival rate of mussel larvae increased 2.4-fold and 2.8-fold in mussel larvae challenged with V. tasmaniensis LGP32 pretreated with 200 µM and 500 µM indole, respectively. The survival rate of mussel larvae increased 1.5-fold and 1.9-fold in mussel larvae challenged with V. crassostreae J2-9 pretreated with 200 µM and 500 µM indole, respectively. These data indicate that indole has a significant impact on the virulence of V. tasmaniensis LGP32 and V. crassostreae J2-9, and indole signaling could be a promising target for antivirulence therapy.
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8
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Kerbs A, Burgardt A, Veldmann KH, Schäffer T, Lee JH, Wendisch VF. Fermentative production of halogenated tryptophan derivatives with Corynebacterium glutamicum overexpressing tryptophanase or decarboxylase genes. Chembiochem 2022; 23:e202200007. [PMID: 35224830 PMCID: PMC9315010 DOI: 10.1002/cbic.202200007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/25/2022] [Indexed: 11/24/2022]
Abstract
The aromatic amino acid l‐tryptophan serves as a precursor for many valuable compounds such as neuromodulators, indoleamines and indole alkaloids. In this work, tryptophan biosynthesis was extended by halogenation followed by decarboxylation to the respective tryptamines or cleavage to the respective indoles. Either the tryptophanase genes tnaAs from E. coli and Proteus vulgaris or the aromatic amino acid decarboxylase genes AADCs from Bacillus atrophaeus, Clostridium sporogenes, and Ruminococcus gnavus were expressed in Corynebacterium glutamicum strains producing (halogenated) tryptophan. Regarding indoles, final titers of 16 mg L−1 7‐Cl‐indole and 23 mg L−1 7‐Br‐indole were attained. Tryptamine production led to a much higher titer of 2.26 g L−1 upon expression of AADC from B. atrophaeus. AADC enzymes were shown to be active with halogenated tryptophan in vitro and in vivo and supported production of 0.36 g L−1 7‐Br‐tryptamine with a volumetric productivity of 8.3 mg L−1 h−1 in a fed‐batch fermentation.
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Affiliation(s)
- Anastasia Kerbs
- Bielefeld University: Universitat Bielefeld, Genetics of Prokaryotes, GERMANY
| | - Arthur Burgardt
- Bielefeld University: Universitat Bielefeld, Genetics of Prokaryotes, GERMANY
| | - Kareen H Veldmann
- Bielefeld University: Universitat Bielefeld, Genetisc of Prokaryotes, GERMANY
| | - Thomas Schäffer
- Bielefeld University: Universitat Bielefeld, Fermentation Technology, GERMANY
| | - Jin-Ho Lee
- Kyungsung University, Food Science and Biotechnology, KOREA, REPUBLIC OF
| | - Volker F Wendisch
- Bielefeld University: Universitat Bielefeld, Genetics of Prokaryotes, Universitätsstr. 25, 33615, Bielefeld, GERMANY
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Dai C, Ma F, Ma Q, Yang J, Li Y, Yang B, Qu Y. Investigation of indole biodegradation by Cupriavidus sp. strain IDO with emphases on downstream biotransformation and indigo production. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:8369-8381. [PMID: 34490563 DOI: 10.1007/s11356-021-14444-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 05/12/2021] [Indexed: 06/13/2023]
Abstract
Indole, as a typical N-heterocyclic aromatic pollutant, poses risks to living things; however, indole-biotransformation mechanisms remain under-discussed, especially those related to its downstream biotransformation. Here, we systematically investigated the characteristics of indole degradation by strain Cupriavidus sp. IDO. We found that Cupriavidus sp. IDO could utilize 25 to 150 mg/L indole within 40 h and identified three intermediates (2-oxindole, indigo, and isatin). Additionally, integrated genomics and proteomics analysis of the indole biotransformation mechanism in strain IDO revealed 317 proteins showing significant changes (262 upregulated and 55 downregulated) in the presence of indole. Among these, three clusters containing indole oxidoreductase, CoA-thioester ligase, and gentisate 1,2-oxidoreductase were identified as potentially responsible for upstream and downstream indole metabolism. Moreover, HPLC-MS and -omics analysis offered insight into the indole-degradation pathway in strain IDO. Furthermore, the indole oxidoreductase IndAB, which initiates indole degradation, was heterologously expressed in Escherichia coli BL21(DE3). Optimization by the response surface methodology resulted in a maximal production of 135.0 mg/L indigo by the recombination strains in tryptophan medium. This work enriches our understanding of the indole-biodegradation process and provides new insights into multiple indole-degradation pathways in natural environments.
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Affiliation(s)
- Chunxiao Dai
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Fang Ma
- State Key Lab of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin, 150090, China.
| | - Qiao Ma
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Jing Yang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yan Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Bingyu Yang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China.
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10
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Stankov V, Stankov MN, Cvetnić M, Sigurnjak Bureš M, Ukić Š, Kučić Grgić D, Lončarić Božić A, Kušić H, Bolanča T. Environmental aspects of UV-C-based processes for the treatment of oxytetracycline in water. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 277:116797. [PMID: 33647807 DOI: 10.1016/j.envpol.2021.116797] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
This study is focused on oxytetracycline (OTC) degradation by direct photolysis (UV-C) and photobased advanced oxidation processes (AOPs) (UV-C/H2O2 and UV-C/S2O82-). OTC degradation pathways were revealed by LC-MS/MS and GC-MS/MS analyses. The evolution/degradation profiles of 12 detected byproducts were correlated with changes in biodegradability and toxicity toward Vibrio fischeri recorded during the treatment. Both photobased AOPs yielded higher OTC degradation and mineralization rates than direct photolysis. The OTC degradation pathway was found to be rather specific regarding the main reactive species (HO• or SO4•-)/mechanism, yielding different patterns in toxicity changes, while biodegradability profiles were less affected. Biodegradability was correlated with the observed degradation and mineralization kinetics. The recorded toxicity changes indicate that byproducts formed by initial OTC degradation are more toxic than the parent pollutant. The prolonged treatment resulted in the formation of byproducts that contributed to a decrease in toxicity and an increase in biodegradability, as particularly emphasized in the case of UV-C/S2O82-.
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Affiliation(s)
- Vladimir Stankov
- Sample Control D.o.o., Franje Puškarića 18, 10250, Lučko, Croatia; University of Zagreb, Faculty of Chemical Engineering and Technology, Marulićev Trg 19, 10000, Zagreb, Croatia
| | - Mirjana Novak Stankov
- University of Zagreb, Faculty of Chemical Engineering and Technology, Marulićev Trg 19, 10000, Zagreb, Croatia
| | - Matija Cvetnić
- University of Zagreb, Faculty of Chemical Engineering and Technology, Marulićev Trg 19, 10000, Zagreb, Croatia
| | - Marija Sigurnjak Bureš
- University of Zagreb, Faculty of Chemical Engineering and Technology, Marulićev Trg 19, 10000, Zagreb, Croatia
| | - Šime Ukić
- University of Zagreb, Faculty of Chemical Engineering and Technology, Marulićev Trg 19, 10000, Zagreb, Croatia
| | - Dajana Kučić Grgić
- University of Zagreb, Faculty of Chemical Engineering and Technology, Marulićev Trg 19, 10000, Zagreb, Croatia
| | - Ana Lončarić Božić
- University of Zagreb, Faculty of Chemical Engineering and Technology, Marulićev Trg 19, 10000, Zagreb, Croatia
| | - Hrvoje Kušić
- University of Zagreb, Faculty of Chemical Engineering and Technology, Marulićev Trg 19, 10000, Zagreb, Croatia.
| | - Tomislav Bolanča
- University of Zagreb, Faculty of Chemical Engineering and Technology, Marulićev Trg 19, 10000, Zagreb, Croatia; University North, Trg Dr. Žarka Dolinara 1, Koprivnica, 48000, Croatia
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11
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Physiological Response of Corynebacterium glutamicum to Indole. Microorganisms 2020; 8:microorganisms8121945. [PMID: 33302489 PMCID: PMC7764795 DOI: 10.3390/microorganisms8121945] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/04/2020] [Accepted: 12/05/2020] [Indexed: 12/20/2022] Open
Abstract
The aromatic heterocyclic compound indole is widely spread in nature. Due to its floral odor indole finds application in dairy, flavor, and fragrance products. Indole is an inter- and intracellular signaling molecule influencing cell division, sporulation, or virulence in some bacteria that synthesize it from tryptophan by tryptophanase. Corynebacterium glutamicum that is used for the industrial production of amino acids including tryptophan lacks tryptophanase. To test if indole is metabolized by C. glutamicum or has a regulatory role, the physiological response to indole by this bacterium was studied. As shown by RNAseq analysis, indole, which inhibited growth at low concentrations, increased expression of genes involved in the metabolism of iron, copper, and aromatic compounds. In part, this may be due to iron reduction as indole was shown to reduce Fe3+ to Fe2+ in the culture medium. Mutants with improved tolerance to indole were selected by adaptive laboratory evolution. Among the mutations identified by genome sequencing, mutations in three transcriptional regulator genes were demonstrated to be causal for increased indole tolerance. These code for the regulator of iron homeostasis DtxR, the regulator of oxidative stress response RosR, and the hitherto uncharacterized Cg3388. Gel mobility shift analysis revealed that Cg3388 binds to the intergenic region between its own gene and the iolT2-rhcM2D2 operon encoding inositol uptake system IolT2, maleylacetate reductase, and catechol 1,2-dioxygenase. Increased RNA levels of rhcM2 in a cg3388 deletion strain indicated that Cg3388 acts as repressor. Indole, hydroquinone, and 1,2,4-trihydroxybenzene may function as inducers of the iolT2-rhcM2D2 operon in vivo as they interfered with DNA binding of Cg3388 at physiological concentrations in vitro. Cg3388 was named IhtR.
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12
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The Role of the Kynurenine Signaling Pathway in Different Chronic Pain Conditions and Potential Use of Therapeutic Agents. Int J Mol Sci 2020; 21:ijms21176045. [PMID: 32842609 PMCID: PMC7503462 DOI: 10.3390/ijms21176045] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/11/2020] [Accepted: 08/19/2020] [Indexed: 12/11/2022] Open
Abstract
Tryptophan (TRP) is an essential, aromatic amino acid catabolized by indoleamine 2,3-dioxygenase (IDO) and tryptophan 2,3-dioxygenase (TDO) enzymes into kynurenine. The IDO enzyme is expressed in peripheral tissues and the central nervous system. Another enzyme of interest in the kynurenine signaling pathway is kynurenine 3-monooxygenase (KMO). The purpose of this review is to discuss the role of TRP and the kynurenine signaling pathway in different chronic pain patients. The IDO-1, IDO-2, and KMO enzymes and the kynurenine metabolite have been shown to be involved in the pathogenesis of neuropathic pain and other painful conditions (migraine, cluster headache, etc.) as well as depressive behavior. We highlighted the analgesic potential of novel agents targeting the enzymes of the kynurenine signaling pathway to explore their efficacy in both future basic science and transitional studies. Upcoming studies conducted on animal models will need to take into consideration the differences in TRP metabolism between human and non-human species. Since chronic painful conditions and depression have common pathophysiological patterns, and the kynurenine signaling pathway is involved in both of them, future clinical studies should aim to have outcomes targeting not only pain, but also functionality, mood changes, and quality of life.
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Role of Toxin-Antitoxin-Regulated Persister Population and Indole in Bacterial Heat Tolerance. Appl Environ Microbiol 2020; 86:AEM.00935-20. [PMID: 32503909 DOI: 10.1128/aem.00935-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 05/28/2020] [Indexed: 01/30/2023] Open
Abstract
YafQ is an endoribonuclease toxin that degrades target gene transcripts such as that of tnaA, a gene encoding tryptophanase to synthesize indole from tryptophan. DinJ is the cognate antitoxin of YafQ, and the YafQ-DinJ system was reported to regulate persister formation by controlling indole production in Escherichia coli In this study, we investigated the role of YafQ-DinJ, indole production, and persister population in bacterial heat tolerance. yafQ (ΔyafQ), dinJ (ΔdinJ), and tnaA (ΔtnaA) single-gene knockout mutants showed approximately 10-fold higher heat tolerance than wild-type (WT) E. coli BW25113. Persister fractions of all mutants were slightly larger than that of the WT. Interestingly, these persister cells showed an approximately 100-fold higher heat tolerance than normal cells, but there was no difference among the persister cells of all mutants and the WT in terms of heat tolerance. Indole and its derivatives promoted a drastic reduction of bacterial heat tolerance by just 10 min of pretreatment, which is not sufficient to affect persister formation before heat treatment. Surprisingly, indole and its derivatives also reduced the heat tolerance of persister cells. Among the tested derivatives, 5-iodoindole exhibited the strongest effect on both normal and persister cells.IMPORTANCE Our study demonstrated that a small persister population exhibits significantly higher heat tolerance than normal cells and that this small fraction contributes to the heat tolerance of the total bacterial population. This study also demonstrated that indole, known to inhibit persister formation, and its derivatives are very promising candidates to reduce the heat tolerance of not only normal bacterial cells but also persister cells.
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Puccetti M, Xiroudaki S, Ricci M, Giovagnoli S. Postbiotic-Enabled Targeting of the Host-Microbiota-Pathogen Interface: Hints of Antibiotic Decline? Pharmaceutics 2020; 12:E624. [PMID: 32635461 PMCID: PMC7408102 DOI: 10.3390/pharmaceutics12070624] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/24/2020] [Accepted: 07/01/2020] [Indexed: 02/06/2023] Open
Abstract
Mismanagement of bacterial infection therapies has undermined the reliability and efficacy of antibiotic treatments, producing a profound crisis of the antibiotic drug market. It is by now clear that tackling deadly infections demands novel strategies not only based on the mere toxicity of anti-infective compounds. Host-directed therapies have been the first example as novel treatments with alternate success. Nevertheless, recent advances in the human microbiome research have provided evidence that compounds produced by the microbial metabolism, namely postbiotics, can have significant impact on human health. Such compounds target the host-microbe-pathogen interface rescuing biotic and immune unbalances as well as inflammation, thus providing novel therapeutic opportunities. This work discusses critically, through literature review and personal contributions, these novel nonantibiotic treatment strategies for infectious disease management and resistance prevention, which could represent a paradigm change rocking the foundation of current antibiotic therapy tenets.
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Affiliation(s)
| | | | | | - Stefano Giovagnoli
- Department of Pharmaceutical Sciences, via del Liceo 1, University of Perugia, 06123 Perugia, Italy; (M.P.); (S.X.); (M.R.)
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15
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Local and Universal Action: The Paradoxes of Indole Signalling in Bacteria. Trends Microbiol 2020; 28:566-577. [PMID: 32544443 DOI: 10.1016/j.tim.2020.02.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/05/2020] [Accepted: 02/25/2020] [Indexed: 02/06/2023]
Abstract
Indole is a signalling molecule produced by many bacterial species and involved in intraspecies, interspecies, and interkingdom signalling. Despite the increasing volume of research published in this area, many aspects of indole signalling remain enigmatic. There is disagreement over the mechanism of indole import and export and no clearly defined target through which its effects are exerted. Progress is hindered further by the confused and sometimes contradictory body of indole research literature. We explore the reasons behind this lack of consistency and speculate whether the discovery of a new, pulse mode of indole signalling, together with a move away from the idea of a conventional protein target, might help to overcome these problems and enable the field to move forward.
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Kruk J, Kotarska K, Aboul-Enein BH. Physical exercise and catecholamines response: benefits and health risk: possible mechanisms. Free Radic Res 2020; 54:105-125. [PMID: 32020819 DOI: 10.1080/10715762.2020.1726343] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Beneficial effect of regular moderate physical exercise (PE) and negative effect of severe exercise and/or overtraining as an activator of the sympathetic nervous system (SNS) have been shown in numerous aspects of human health, including reduced risk of cardiovascular disease, neurological disease, depression, and some types of cancer. Moderate-to-vigorous PE stimulates the SNS activation, releasing catecholamines (CATs) adrenaline, noradrenaline, dopamine that play an important regulatory and modulatory actions by affecting metabolic processes and the immune system. Summary of the dispersed literature in this area and explanation of the biological mechanisms operating between PE-CATs and the immune system would lead to a better understanding of the beneficial and negative effects of PE on health. This overview aimed to: demonstrate representative literature findings on the exercise released CATs levels, major functions performed by these hormones, their interactions with the immune system and their effects on carbohydrate and lipid metabolism. Also, mechanisms of cytotoxic free radicals and reactive oxygen species (ROS) generation during CATs oxidation, and molecular mechanisms of CATs response to exercise are discussed to demonstrate positive and negative on human health effects. Owing to the large body of the subject literature, we present a representative cross-section of the published studies in this area. The results show a significant role of CATs in carbohydrate and lipid metabolism, immunity and as generators of ROS, depending on PE intensity and duration. Further investigation of the PE-CATs relationship should validate CATs levels to optimize safe intensity and duration of exercise and individualize their prescription, considering CATs to be applied as markers for a dose of exercise. Also, a better understanding of the biological mechanisms is also needed.
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Affiliation(s)
- Joanna Kruk
- Faculty of Physical Culture and Health, University of Szczecin, Szczecin, Poland
| | - Katarzyna Kotarska
- Faculty of Physical Culture and Health, University of Szczecin, Szczecin, Poland
| | - Basil H Aboul-Enein
- Faculty of Public Health & Policy, London School of Hygiene & Tropical Medicine, London, UK
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17
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Yaikhan T, Chuerboon M, Tippayatham N, Atimuttikul N, Nuidate T, Yingkajorn M, Tun AW, Buncherd H, Tansila N. Indole and Derivatives Modulate Biofilm Formation and Antibiotic Tolerance of Klebsiella pneumoniae. Indian J Microbiol 2019; 59:460-467. [PMID: 31762509 PMCID: PMC6842365 DOI: 10.1007/s12088-019-00830-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 09/30/2019] [Indexed: 12/16/2022] Open
Abstract
Intercellular communication is a crucial process for the multicellular community in both prokaryotes and eukaryotes. Indole has been recognized as a new member of the signal molecules which enables the regulated control of various bacterial phenotypes. To elucidate the inter-species relationship among enteric microorganisms via indole signaling, Klebsiella pneumoniae (KP) culture was treated with indole solution and examined for the pathogenicity by using various phenotypic tests. Both synthetic and naturally-produced indole preparations had no deteriorating effect on growth and autoaggregative capacity of KP. The results showed that biofilm formation of carbapenem-susceptible K. pneumoniae (KP-S) was clearly induced by indole exposure (≈ 2-10 folds), whereas no significant difference was observed in the resistant counterpart. In addition, the tolerance to β-lactam antibiotics of KP was altered upon exposure to indole and/or derivatives assessed by Kirby-Bauer disk diffusion test. Taken together, our finding indicates the functional role of indole in changing or modulating pathogenic behaviors of other bacteria.
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Affiliation(s)
- Thanachaporn Yaikhan
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, 90110 Thailand
| | - Manatsanan Chuerboon
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, 90110 Thailand
| | - Natchapol Tippayatham
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, 90110 Thailand
| | - Nateekarn Atimuttikul
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, 90110 Thailand
| | - Taiyeebah Nuidate
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Songkhla, 90110 Thailand
| | - Mingkwan Yingkajorn
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, 90110 Thailand
| | - Aung Win Tun
- Faculty of Graduate Studies, Mahidol University, Salaya, Nakhon Pathom 73170 Thailand
| | - Hansuk Buncherd
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, 90110 Thailand
| | - Natta Tansila
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, 90110 Thailand
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18
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Sun F, Yuan Q, Wang Y, Cheng L, Li X, Feng W, Xia P. Sub-minimum inhibitory concentration ceftazidime inhibits Escherichia coli biofilm formation by influencing the levels of the ibpA gene and extracellular indole. J Chemother 2019; 32:7-14. [PMID: 31631801 DOI: 10.1080/1120009x.2019.1678913] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Escherichia coli is a common pathogen of bacterial biofilm infections. Sub-minimum inhibitory concentration ceftazidime (sub-MIC CAZ) could inhibit the biofilm formation of E. coli. Deletion of the ibpAB genes could increase the extracellular indole concentration of E. coli and then inhibit biofilm formation. Therefore, we speculated that sub-MIC CAZ might inhibit biofilm formation via ibpAB. In this study, the results showed that sub-MIC CAZ could significantly inhibit biofilm formation, swimming motility and the expression of the ibpA gene, while it could increase the expression of tnaA gene and extracellular indole concentration. Knockout of the ibpA gene resulted in a decrease in biofilm formation and swimming motility and an increase in the indole concentration. When treated with sub-MIC CAZ, the tnaA gene expression, indole concentration, biofilm formation and swimming motility of MG1655 ΔibpA were similar to those of the control group. The results indicated that sub-MIC CAZ might inhibit the biofilm formation of E. coli by increasing the extracellular indole concentration and downregulating the ibpA gene.
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Affiliation(s)
- Fengjun Sun
- Department of Pharmacy, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Qian Yuan
- Department of Pharmacy, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yu Wang
- Department of Pharmacy, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Lin Cheng
- Department of Pharmacy, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xiaoyu Li
- Department of Pharmacy, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Wei Feng
- Department of Pharmacy, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Peiyuan Xia
- Department of Pharmacy, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
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19
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Sun H, Zheng M, Song J, Huang S, Pan Y, Gong R, Lin Z. Multiple-species hormetic phenomena induced by indole: A case study on the toxicity of indole to bacteria, algae and human cells. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 657:46-55. [PMID: 30530218 DOI: 10.1016/j.scitotenv.2018.12.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 11/30/2018] [Accepted: 12/02/2018] [Indexed: 06/09/2023]
Abstract
Hormesis is a dose-response relationship phenomenon characterized by low-dose stimulation and high-dose inhibition. Although hormetic phenomena have been reported in broadly ranging biological areas, there is still no unified mechanism of hormesis. Investigating multiple-species hormesis of one compound and then exploring the possible mechanism may be an effective approach to clarify the reason for the occurrence of hormetic phenomena in a broad range of organisms. In this study, indole was selected as the test chemical due to the broad biological and hormetic effects of indole compounds. The results show that indole induces multiple-species hormetic phenomena in bacteria (Aliivibrio fischeri (A. fischeri), Escherichia coli and Bacillus subtilis), algae (Microcystis aeruginosa and Selenastrum capricornutum), and human cells (human skin fibroblasts and human cervical cancer cells). Through in-depth investigation of the time-dependent hormetic effects of indole, indole derivatives and indole's structural analogs on the bioluminescence of A. fischeri, indole ring has been identified as the potential key structure that causes indole to act on quorum sensing of A. fischeri to induce hormetic effects on the bioluminescence at lag, logarithmic, and stationary phases. Therefore, the occurrence of multiple-species hormetic phenomena is speculated to be derived from the action of indole on the cell-to-cell communication of organism cells. This paper can not only further confirm the generalizability of hormesis but also provide a reasonable explanation for hormesis, which will benefit the development of hormesis and the risk assessment of environmental pollutants.
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Affiliation(s)
- Haoyu Sun
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Min Zheng
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Jinyuan Song
- China Solid Waste and Chemical Management Technology Center, Ministry of Environmental Protection, Beijing 100029, China
| | - Shengyou Huang
- Shanghai International Studies University Bilingual School, Shanghai 200092, China
| | - Yongzheng Pan
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Ruochong Gong
- Shanghai Foreign Language Primary School Affiliated to Shanghai International Studies University, Shanghai 200092, China
| | - Zhifen Lin
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China; Shanghai Key Lab of Chemical Assessment and Sustainability, Shanghai, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, China.
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20
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Indole Inhibits ToxR Regulon Expression in Vibrio cholerae. Infect Immun 2019; 87:IAI.00776-18. [PMID: 30617203 DOI: 10.1128/iai.00776-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 12/21/2018] [Indexed: 12/20/2022] Open
Abstract
Indole is a degradation product of tryptophan that functions as a signaling molecule in many bacteria. This includes Vibrio cholerae, where indole was shown to regulate biofilm and type VI secretion in nontoxigenic environmental isolates. Indole is also produced by toxigenic V. cholerae strains in the human intestine, but its significance in the host is unknown. We investigated the effects of indole on toxigenic V. cholerae O1 El Tor during growth under virulence inducing conditions. The indole transcriptome was defined by RNA sequencing and showed widespread changes in the expression of genes involved in metabolism, biofilm production, and virulence factor production. In contrast, genes involved in type VI secretion were not affected by indole. We subsequently found that indole repressed genes involved in V. cholerae pathogenesis, including the ToxR virulence regulon. Consistent with this, indole inhibited cholera toxin and toxin-coregulated pilus production in a dose-dependent manner. The effects of indole on virulence factor production and biofilm were linked to ToxR and the ToxR-dependent regulator LeuO. The expression of leuO was increased by exogenous indole and linked to repression of the ToxR virulence regulon. This process was dependent on the ToxR periplasmic domain, suggesting that indole was a ToxR agonist. This conclusion was further supported by results showing that the ToxR periplasmic domain contributed to indole-mediated increased biofilm production. Collectively, our results suggest that indole may be a niche-specific cue that can function as a ToxR agonist to modulate virulence gene expression and biofilm production in V. cholerae.
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21
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Gutiérrez‐Huante M, Martínez‐Duncker M, Sauceda E, Sánchez J. The antibiotics potentiator bicarbonate causes upregulation of tryptophanase and iron acquisition proteins inEscherichia coli. Lett Appl Microbiol 2018; 68:87-95. [DOI: 10.1111/lam.13092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/23/2018] [Accepted: 10/23/2018] [Indexed: 11/28/2022]
Affiliation(s)
- M. Gutiérrez‐Huante
- Posgrado en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas Universidad Autónoma del Estado de Morelos Cuernavaca Morelos México
| | - M.E. Martínez‐Duncker
- Facultad de Medicina Universidad Autónoma del Estado de Morelos Cuernavaca Morelos México
| | - E. Sauceda
- Posgrado en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas Universidad Autónoma del Estado de Morelos Cuernavaca Morelos México
| | - J. Sánchez
- Facultad de Medicina Universidad Autónoma del Estado de Morelos Cuernavaca Morelos México
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22
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Ma Q, Zhang X, Qu Y. Biodegradation and Biotransformation of Indole: Advances and Perspectives. Front Microbiol 2018; 9:2625. [PMID: 30443243 PMCID: PMC6221969 DOI: 10.3389/fmicb.2018.02625] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 10/15/2018] [Indexed: 11/17/2022] Open
Abstract
Indole is long regarded as a typical N-heterocyclic aromatic pollutant in industrial and agricultural wastewater, and recently it has been identified as a versatile signaling molecule with wide environmental distributions. An exponentially growing number of researches have been reported on indole due to its significant roles in bacterial physiology, pathogenesis, animal behavior and human diseases. From the viewpoint of both environmental bioremediation and biological studies, the researches on metabolism and fates of indole are important to realize environmental treatment and illuminate its biological function. Indole can be produced from tryptophan by tryptophanase in many bacterial species. Meanwhile, various bacterial strains have obtained the ability to transform and degrade indole. The characteristics and pathways for indole degradation have been investigated for a century, and the functional genes for indole aerobic degradation have also been uncovered recently. Interestingly, many oxygenases have proven to be able to oxidize indole to indigo, and this historic and motivating case for biological applications has attracted intensive attention for decades. Herein, the bacteria, enzymes and pathways for indole production, biodegradation and biotransformation are systematically summarized, and the future researches on indole-microbe interactions are also prospected.
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Affiliation(s)
- Qiao Ma
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, China
| | - Xuwang Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Food and Environment, Dalian University of Technology, Panjin, China
| | - Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
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23
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Liu J, Summers D. Indole at low concentration helps exponentially growing Escherichia coli survive at high temperature. PLoS One 2017; 12:e0188853. [PMID: 29216232 PMCID: PMC5720752 DOI: 10.1371/journal.pone.0188853] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/14/2017] [Indexed: 12/25/2022] Open
Abstract
A culture of stationary phase Escherichia coli cells has been reported to produce copious indole when exposed to high temperature (50°C), and this response has been proposed to aid survival. We reinvestigated this phenomenon and found that indole production under these conditions is probably not a direct response to heat stress. Rather, E. coli produces indole when growth is prevented, irrespective of whether this is due to heat stress, antibiotic treatment or the removal of nutrients. Moreover, 300μM indole produced at 50°C does not improve the viability of heat stressed cells. Interestingly, a much lower concentration of indole (20 μM) improves the survival of an indole-negative strain (ΔtnaA) when heat stressed during exponential growth. In addition we have shown that the distribution of tryptophanase, the enzyme responsible for indole synthesis, is highly heterogeneous among cells in a population, except during the transition between exponential and stationary phases. The observation that, despite the presence of the tryptophanase, very little indole is produced during early exponential phase suggests that there is post-translational regulation of the enzyme.
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Affiliation(s)
- Junyan Liu
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - David Summers
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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24
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Qu Y, Ma Q, Liu Z, Wang W, Tang H, Zhou J, Xu P. Unveiling the biotransformation mechanism of indole in a Cupriavidus sp. strain. Mol Microbiol 2017; 106:905-918. [PMID: 28963777 DOI: 10.1111/mmi.13852] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2017] [Indexed: 01/13/2023]
Abstract
Indole, an important signaling molecule as well as a typical N-heterocyclic aromatic pollutant, is widespread in nature. However, the biotransformation mechanisms of indole are still poorly studied. Here, we sought to unlock the genetic determinants of indole biotransformation in strain Cupriavidus sp. SHE based on genomics, proteomics and functional studies. A total of 177 proteins were notably altered (118 up- and 59 downregulated) in cells grown in indole mineral salt medium when compared with that in sodium citrate medium. RT-qPCR and gene knockout assays demonstrated that an indole oxygenase gene cluster was responsible for the indole upstream metabolism. A functional indole oxygenase, termed IndA, was identified in the cluster, and its catalytic efficiency was higher than those of previously reported indole oxidation enzymes. Furthermore, the indole downstream metabolism was found to proceed via the atypical CoA-thioester pathway rather than conventional gentisate and salicylate pathways. This unusual pathway was catalyzed by a conserved 2-aminobenzoyl-CoA gene cluster, among which the 2-aminobenzoyl-CoA ligase initiated anthranilate transformation. This study unveils the genetic determinants of indole biotransformation and will provide new insights into our understanding of indole biodegradation in natural environments and its functional studies.
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Affiliation(s)
- Yuanyuan Qu
- State Key Laboratory of Fine Chemicals, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Qiao Ma
- State Key Laboratory of Fine Chemicals, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Ziyan Liu
- State Key Laboratory of Fine Chemicals, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Weiwei Wang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Jiti Zhou
- State Key Laboratory of Fine Chemicals, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
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Indole Biodegradation in Acinetobacter sp. Strain O153: Genetic and Biochemical Characterization. Appl Environ Microbiol 2017; 83:AEM.01453-17. [PMID: 28778892 DOI: 10.1128/aem.01453-17] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 07/26/2017] [Indexed: 01/30/2023] Open
Abstract
Indole is a molecule of considerable biochemical significance, acting as both an interspecies signal molecule and a building block of biological elements. Bacterial indole degradation has been demonstrated for a number of cases; however, very little is known about genes and proteins involved in this process. This study reports the cloning and initial functional characterization of genes (iif and ant cluster) responsible for indole biodegradation in Acinetobacter sp. strain O153. The catabolic cascade was reconstituted in vitro with recombinant proteins, and each protein was assigned an enzymatic function. Degradation starts with oxidation, mediated by the IifC and IifD flavin-dependent two-component oxygenase system. Formation of indigo is prevented by IifB, and the final product, anthranilic acid, is formed by IifA, an enzyme which is both structurally and functionally comparable to cofactor-independent oxygenases. Moreover, the iif cluster was identified in the genomes of a wide range of bacteria, suggesting the potential of widespread Iif-mediated indole degradation. This work provides novel insights into the genetic background of microbial indole biodegradation.IMPORTANCE The key finding of this research is identification of the genes responsible for microbial biodegradation of indole, a toxic N-heterocyclic compound. A large amount of indole is present in urban wastewater and sewage sludge, creating a demand for an efficient and eco-friendly means to eliminate this pollutant. A common strategy of oxidizing indole to indigo has the major drawback of producing insoluble material. Genes and proteins of Acinetobacter sp. strain O153 (DSM 103907) reported here pave the way for effective and indigo-free indole removal. In addition, this work suggests possible novel means of indole-mediated bacterial interactions and provides the basis for future research on indole metabolism.
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Kim J, Shin B, Park C, Park W. Indole-Induced Activities of β-Lactamase and Efflux Pump Confer Ampicillin Resistance in Pseudomonas putida KT2440. Front Microbiol 2017; 8:433. [PMID: 28352264 PMCID: PMC5348495 DOI: 10.3389/fmicb.2017.00433] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/01/2017] [Indexed: 11/13/2022] Open
Abstract
Indole, which is widespread in microbial communities, has received attention because of its effects on bacterial physiology. Pseudomonas putida and Pseudomonas aeruginosa can acquire ampicillin (Amp) resistance during growth on indole-Amp agar. Transcriptome, mutant, and inhibitor studies have suggested that Amp resistance induced by indole can be attributed to increased gene expression of ttgAB encoding two genes of RND-type multidrug efflux operons and an ampC encoding β-lactamase. Expression, enzyme activities, and mutational analyses indicated that AmpC β-lactamase is important for acquiring Amp resistance of P. putida in the presence of indole. Here, we show, for the first time, that volatile indole increased Amp-resistant cells. Consistent with results of the volatile indole assay, a low concentration of indole in liquid culture promoted growth initially, but led to mutagenesis after indole was depleted, which could not be observed at high indole concentrations. Interestingly, ttgAB and ampC gene expression levels correlate with the concentration of indole, which might explain the low number of Amp-mutated cells in high indole concentrations. The expression levels of genes involved in mutagenesis, namely rpoS, recA, and mutS, were also modulated by indole. Our data indicates that indole reduces Amp-induced heterogeneity by promoting expression of TtgABC or MexAB-OprM efflux pumps and the indole-induced β-lactamase in P. putida and P. aeruginosa.
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Affiliation(s)
- Jisun Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul Korea
| | - Bora Shin
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul Korea
| | - Chulwoo Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul Korea
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Brinkman CL, Schmidt-Malan SM, Karau MJ, Greenwood-Quaintance K, Hassett DJ, Mandrekar JN, Patel R. Exposure of Bacterial Biofilms to Electrical Current Leads to Cell Death Mediated in Part by Reactive Oxygen Species. PLoS One 2016; 11:e0168595. [PMID: 27992529 PMCID: PMC5167413 DOI: 10.1371/journal.pone.0168595] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 12/02/2016] [Indexed: 01/01/2023] Open
Abstract
Bacterial biofilms may form on indwelling medical devices such as prosthetic joints, heart valves and catheters, causing challenging-to-treat infections. We have previously described the ‘electricidal effect’, in which bacterial biofilms are decreased following exposure to direct electrical current. Herein, we sought to determine if the decreased bacterial quantities are due to detachment of biofilms or cell death and to investigate the role that reactive oxygen species (ROS) play in the observed effect. Using confocal and electron microscopy and flow cytometry, we found that direct current (DC) leads to cell death and changes in the architecture of biofilms formed by Gram-positive and Gram-negative bacteria. Reactive oxygen species (ROS) appear to play a role in DC-associated cell death, as there was an increase in ROS-production by Staphylococcus aureus and Staphylococcus epidermidis biofilms following exposure to DC. An increase in the production of ROS response enzymes catalase and superoxide dismutase (SOD) was observed for S. aureus, S. epidermidis and Pseudomonas aeruginosa biofilms following exposure to DC. Additionally, biofilms were protected from cell death when supplemented with antioxidants and oxidant scavengers, including catalase, mannitol and Tempol. Knocking out SOD (sodAB) in P. aeruginosa led to an enhanced DC effect. Microarray analysis of P. aeruginosa PAO1 showed transcriptional changes in genes related to the stress response and cell death. In conclusion, the electricidal effect results in death of bacteria in biofilms, mediated, at least in part, by production of ROS.
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Affiliation(s)
- Cassandra L. Brinkman
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Suzannah M. Schmidt-Malan
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Melissa J. Karau
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Kerryl Greenwood-Quaintance
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Daniel J. Hassett
- Department of Molecular Genetics, Biochemistry & Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, United States of America
| | - Jayawant N. Mandrekar
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research Mayo Clinic, Rochester, MN, United States of America
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN, United States of America
- * E-mail:
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28
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Lai Y, Xu Z, Yan A. A novel regulatory circuit to control indole biosynthesis protectsEscherichia colifrom nitrosative damages during the anaerobic respiration of nitrate. Environ Microbiol 2016; 19:598-610. [DOI: 10.1111/1462-2920.13527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/08/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Yong Lai
- School of Biological Sciences; The University of Hong Kong; Hong Kong SAR
| | - Zeling Xu
- School of Biological Sciences; The University of Hong Kong; Hong Kong SAR
| | - Aixin Yan
- School of Biological Sciences; The University of Hong Kong; Hong Kong SAR
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Ahn S, Jung J, Jang IA, Madsen EL, Park W. Role of Glyoxylate Shunt in Oxidative Stress Response. J Biol Chem 2016; 291:11928-38. [PMID: 27036942 DOI: 10.1074/jbc.m115.708149] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Indexed: 12/16/2022] Open
Abstract
The glyoxylate shunt (GS) is a two-step metabolic pathway (isocitrate lyase, aceA; and malate synthase, glcB) that serves as an alternative to the tricarboxylic acid cycle. The GS bypasses the carbon dioxide-producing steps of the tricarboxylic acid cycle and is essential for acetate and fatty acid metabolism in bacteria. GS can be up-regulated under conditions of oxidative stress, antibiotic stress, and host infection, which implies that it plays important but poorly explored roles in stress defense and pathogenesis. In many bacterial species, including Pseudomonas aeruginosa, aceA and glcB are not in an operon, unlike in Escherichia coli In P. aeruginosa, we explored relationships between GS genes and growth, transcription profiles, and biofilm formation. Contrary to our expectations, deletion of aceA in P. aeruginosa improved cell growth under conditions of oxidative and antibiotic stress. Transcriptome data suggested that aceA mutants underwent a metabolic shift toward aerobic denitrification; this was supported by additional evidence, including up-regulation of denitrification-related genes, decreased oxygen consumption without lowering ATP yield, increased production of denitrification intermediates (NO and N2O), and increased cyanide resistance. The aceA mutants also produced a thicker exopolysaccharide layer; that is, a phenotype consistent with aerobic denitrification. A bioinformatic survey across known bacterial genomes showed that only microorganisms capable of aerobic metabolism possess the glyoxylate shunt. This trend is consistent with the hypothesis that the GS plays a previously unrecognized role in allowing bacteria to tolerate oxidative stress.
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Affiliation(s)
- Sungeun Ahn
- From the Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea and
| | - Jaejoon Jung
- From the Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea and
| | - In-Ae Jang
- From the Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea and
| | - Eugene L Madsen
- the Department of Microbiology, Cornell University, Ithaca, New York 14853
| | - Woojun Park
- From the Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea and
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Isolation of Indole Utilizing Bacteria Arthrobacter sp. and Alcaligenes sp. From Livestock Waste. Indian J Microbiol 2016; 56:158-166. [PMID: 27570307 DOI: 10.1007/s12088-016-0570-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/04/2016] [Indexed: 01/10/2023] Open
Abstract
Indole is an interspecies and interkingdom signaling molecule widespread in different environmental compartment. Although multifaceted roles of indole in different biological systems have been established, little information is available on the microbial utilization of indole in the context of combating odor emissions from different types of waste. The present study was aimed at identifying novel bacteria capable of utilizing indole as the sole carbon and energy source. From the selective enrichment of swine waste and cattle feces, we identified Gram-positive and Gram-negative bacteria belonging to the genera Arthrobacter and Alcaligenes. Bacteria belonging to the genus Alcaligenes showed higher rates of indole utilization than Arthrobacter. Indole at 1.0 mM for growth was completely utilized by Alcaligenes sp. in 16 h. Both strains produced two intermediates, anthranilic acid and isatin, during aerobic indole metabolism. These isolates were also able to grow on several indole derivatives. Interestingly, an adaptive response in terms of a decrease in cell size was observed in both strains in the presence of indole. The present study will help to explain the degradation of indole by different bacteria and also the pathways through which it is catabolized. Furthermore, these novel bacterial isolates could be potentially useful for the in situ attenuation of odorant indole and its derivatives emitted from different types of livestock waste.
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31
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O'Farrell K, Harkin A. Stress-related regulation of the kynurenine pathway: Relevance to neuropsychiatric and degenerative disorders. Neuropharmacology 2015; 112:307-323. [PMID: 26690895 DOI: 10.1016/j.neuropharm.2015.12.004] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/02/2015] [Accepted: 12/08/2015] [Indexed: 02/08/2023]
Abstract
The kynurenine pathway (KP), which is activated in times of stress and infection has been implicated in the pathophysiology of neurodegenerative and psychiatric disorders. Activation of this tryptophan metabolising pathway results in the production of neuroactive metabolites which have the potential to interfere with normal neuronal functioning which may contribute to altered neuronal transmission and the emergence of symptoms of these brain disorders. This review investigates the involvement of the KP in a range of neurological disorders, examining recent in vitro, in vivo and clinical discoveries highlights evidence to indicate that the KP is a potential therapeutic target in both neurodegenerative and stress-related neuropsychiatric disorders. Furthermore, this review identifies gaps in our knowledge with regard to this field which are yet to be examined to lead to a more comprehensive understanding of the role of KP activation in brain health and disease. This article is part of the Special Issue entitled 'The Kynurenine Pathway in Health and Disease'.
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Affiliation(s)
- Katherine O'Farrell
- Neuropsychopharmacology Research Group, School of Pharmacy and Pharmaceutical Sciences & Trinity College Institute of Neuroscience, Trinity College Dublin, Ireland
| | - Andrew Harkin
- Neuropsychopharmacology Research Group, School of Pharmacy and Pharmaceutical Sciences & Trinity College Institute of Neuroscience, Trinity College Dublin, Ireland; Neuroimmunology Research Group, Department of Physiology, School of Medicine & Trinity College Institute of Neuroscience, Trinity College Dublin, Ireland.
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32
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Ma Q, Qu Y, Zhang X, Liu Z, Li H, Zhang Z, Wang J, Shen W, Zhou J. Systematic investigation and microbial community profile of indole degradation processes in two aerobic activated sludge systems. Sci Rep 2015; 5:17674. [PMID: 26657581 PMCID: PMC4675989 DOI: 10.1038/srep17674] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 11/03/2015] [Indexed: 01/26/2023] Open
Abstract
Indole is widely spread in various environmental matrices. Indole degradation by bacteria has been reported previously, whereas its degradation processes driven by aerobic microbial community were as-yet unexplored. Herein, eight sequencing batch bioreactors fed with municipal and coking activated sludges were constructed for aerobic treatment of indole. The whole operation processes contained three stages, i.e. stage I, glucose and indole as carbon sources; stage II, indole as carbon source; and stage III, indole as carbon and nitrogen source. Indole could be completely removed in both systems. Illumina sequencing revealed that alpha diversity was reduced after indole treatment and microbial communities were significantly distinct among the three stages. At genus level, Azorcus and Thauera were dominant species in stage I in both systems, while Alcaligenes, Comamonas and Pseudomonas were the core genera in stage II and III in municipal sludge system, Alcaligenes and Burkholderia in coking sludge system. In addition, four strains belonged to genera Comamonas, Burkholderia and Xenophilus were isolated using indole as sole carbon source. Burkholderia sp. IDO3 could remove 100 mg/L indole completely within 14 h, the highest degradation rate to date. These findings provide novel information and enrich our understanding of indole aerobic degradation processes.
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Affiliation(s)
- Qiao Ma
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Xuwang Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Ziyan Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Huijie Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Zhaojing Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Jingwei Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Wenli Shen
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Jiti Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
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Shin B, Park W. Synergistic Effect of Oleanolic Acid on Aminoglycoside Antibiotics against Acinetobacter baumannii. PLoS One 2015; 10:e0137751. [PMID: 26360766 PMCID: PMC4567131 DOI: 10.1371/journal.pone.0137751] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 08/20/2015] [Indexed: 01/08/2023] Open
Abstract
Difficulties involved in treating drug-resistant pathogens have created a need for new therapies. In this study, we investigated the possibility of using oleanolic acid (OA), a natural pentacyclic triterpenoid, as a natural adjuvant for antibiotics against Acinetobacter baumannii. High concentrations of OA can kill cells, partly because it generates reactive oxygen species. Measurement of the fractional inhibitory concentration (FIC) for OA and time-kill experiments demonstrated that it only synergizes with aminoglycoside antibiotics (e.g., gentamicin, kanamycin). Other classes of antibiotics (e.g., ampicillin, rifampicin, norfloxacin, chloramphenicol, and tetracycline) have no interactions with OA. Microarray and quantitative reverse transcription-PCR analysis indicated that genes involved in ATP synthesis and cell membrane permeability, the gene encoding glycosyltransferase, peptidoglycan-related genes, phage-related genes, and DNA repair genes were upregulated under OA. OA highly induces the expression of adk, which encodes an adenylate kinase, and des6, which encodes a linoleoyl-CoA desaturase, and deletion of these genes increased FICs; these observations indicate that adk and des6 are involved in the synergism of OA with aminoglycosides. Data obtained using 8-anilino-1-naphthalenesulfonic acid, fluorescence-conjugated gentamicin, and membrane fatty acid analysis indicates that adk and des6 are involved in changes in membrane permeability. Proton-motive force and ATP synthesis tests show that those genes are also involved in energy metabolism. Taken together, our data show that OA boosts aminoglycoside uptake by changing membrane permeability and energy metabolism in A. baumannii.
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Affiliation(s)
- Bora Shin
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
- * E-mail:
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Indole: a signaling molecule or a mere metabolic byproduct that alters bacterial physiology at a high concentration? J Microbiol 2015; 53:421-8. [PMID: 26115989 DOI: 10.1007/s12275-015-5273-3] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 06/17/2015] [Accepted: 06/18/2015] [Indexed: 10/23/2022]
Abstract
Indole is an organic compound that is widespread in microbial communities inhabiting diverse habitats, like the soil environment and human intestines. Measurement of indole production is a traditional method for the identification of microbial species. Escherichia coli can produce millimolar concentrations of indole in the stationary growth phase under nutrient-rich conditions. Indole has received considerable attention because of its remarkable effects on various biological functions of the microbial communities, for example, biofilm formation, motility, virulence, plasmid stability, and antibiotic resistance. Indole may function as an intercellular signaling molecule, like a quorum-sensing signal. Nevertheless, a receptor system for indole and the function of this compound in coordinated behavior of a microbial population (which are requirements for a true signaling molecule) have not yet been confirmed. Recent findings suggest that a long-known quorum-sensing regulator, E. coli's SdiA, cannot recognize indole and that this compound may simply cause membrane disruption and energy reduction, which can lead to various changes in bacterial physiology including unstable folding of a quorum-sensing regulator. Indole appears to be responsible for acquisition of antibiotic resistance via the formation of persister cells and activation of an exporter. This review highlights and summarizes the current knowledge about indole as a multitrophic molecule among bacteria, together with recently identified new avenues of research.
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Arora PK, Bae H. Biodegradation of 4-chloroindole by Exiguobacterium sp. PMA. JOURNAL OF HAZARDOUS MATERIALS 2015; 284:261-268. [PMID: 25463241 DOI: 10.1016/j.jhazmat.2014.11.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 11/05/2014] [Accepted: 11/14/2014] [Indexed: 06/04/2023]
Abstract
Exiguobacterium sp. PMA utilized 4-chloroindole as its sole source of carbon and energy. The effect of initial concentrations of substrate on the 4-chloroindole degradation was studied and observed that strain PMA was capable of degrading 4-chloroindole up to concentration of 0.5mM. The degradation pathway of 4-chloroindole was studied for Exiguobacterium sp. PMA based on metabolites identified by gas chromatography-mass spectrometry. 4-Chloroindole was initially dehalogenated to indole that was further degraded via isatin, anthranilic acid, and salicylic acid. The potential of strain PMA to degrade 4-chloroindole in soil was monitored using soil microcosms, and it was observed that the cells of strain PMA efficiently degraded 4-chloroindole in the soil. The results of microcosm studies show that strain PMA may be used for bioremediation of 4-chloroindole-contaminated sites. This is the first report of the bacterial degradation of 4-chloroindole.
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Affiliation(s)
- Pankaj Kumar Arora
- School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Republic of Korea.
| | - Hanhong Bae
- School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Republic of Korea.
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Survival of a novel endophytic fungus Phomopsis liquidambari B3 in the indole-contaminated soil detected by real-time PCR and its effects on the indigenous microbial community. Microbiol Res 2014; 169:881-7. [DOI: 10.1016/j.micres.2014.05.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 04/21/2014] [Accepted: 05/28/2014] [Indexed: 11/22/2022]
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Kim J, Park W. Indole inhibits bacterial quorum sensing signal transmission by interfering with quorum sensing regulator folding. MICROBIOLOGY-SGM 2013; 159:2616-2625. [PMID: 24025605 DOI: 10.1099/mic.0.070615-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Quorum sensing (QS)-dependent biofilm formation and motility were controlled by AqsR in Acinetobacter oleivorans DR1. QS-controlled phenotypes appeared to be inhibited by indole and the aqsR mutant had the same phenotypes. We demonstrated that the turnover rate of AqsR became more rapid without the N-acylhomoserine lactone (AHL) signal, and that indole could increase the expression of many protease and chaperone proteins. The addition of exogenous indole decreased the expression of two AqsR-targeted genes: AOLE_03905 (putative surface adhesion protein) and AOLE_11355 (L-asparaginase). The overexpression of AqsR in Escherichia coli was impossible with the indole treatment. Surprisingly, our [(35)S]methionine pulse-labelling data demonstrated that the stability and folding of AqsR protein decreased in the presence of indole without changing aqsR mRNA expression in E. coli. Interestingly, indole resulted in a loss of TraR-dependent traG expression in an Agrobacterium tumefaciens indicator strain. However, when indole was added after incubation with exogenous AHL, indole could not inhibit the TraR-dependent expression of the traG promoter. This indicated that AHL-bound TraR could be protective against indole, but TraR without AHL could not be active in the presence of indole. Here, we provided evidence for the first time showing that the indole effect on QS-controlled bacterial phenotypes is due to inhibited QS regulator folding and not a reduced QS signal.
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Affiliation(s)
- Jisun Kim
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul 136-713, Republic of Korea
| | - Woojun Park
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul 136-713, Republic of Korea
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