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Zhang J, Liu Y, Hu J, Leng G, Liu X, Cui Z, Wang W, Ma Y, Sha S. Cellulase Promotes Mycobacterial Biofilm Dispersal in Response to a Decrease in the Bacterial Metabolite Gamma-Aminobutyric Acid. Int J Mol Sci 2024; 25:1051. [PMID: 38256125 PMCID: PMC10816823 DOI: 10.3390/ijms25021051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/08/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024] Open
Abstract
Biofilm dispersal contributes to bacterial spread and disease transmission. However, its exact mechanism, especially that in the pathogen Mycobacterium tuberculosis, is unclear. In this study, the cellulase activity of the M. tuberculosis Rv0062 protein was characterized, and its effect on mycobacterial biofilm dispersal was analyzed by observation of the structure and components of Rv0062-treated biofilm in vitro. Meanwhile, the metabolite factors that induced cellulase-related biofilm dispersal were also explored with metabolome analysis and further validations. The results showed that Rv0062 protein had a cellulase activity with a similar optimum pH (6.0) and lower optimum temperature (30 °C) compared to the cellulases from other bacteria. It promoted mycobacterial biofilm dispersal by hydrolyzing cellulose, the main component of extracellular polymeric substrates of mycobacterial biofilm. A metabolome analysis revealed that 107 metabolites were significantly altered at different stages of M. smegmatis biofilm development. Among them, a decrease in gamma-aminobutyric acid (GABA) promoted cellulase-related biofilm dispersal, and this effect was realized with the down-regulation of the bacterial signal molecule c-di-GMP. All these findings suggested that cellulase promotes mycobacterial biofilm dispersal and that this process is closely associated with biofilm metabolite alterations.
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Affiliation(s)
- Jiaqi Zhang
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China; (J.Z.); (Y.L.); (J.H.); (G.L.); (X.L.); (Z.C.); (W.W.)
| | - Yingying Liu
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China; (J.Z.); (Y.L.); (J.H.); (G.L.); (X.L.); (Z.C.); (W.W.)
| | - Junxing Hu
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China; (J.Z.); (Y.L.); (J.H.); (G.L.); (X.L.); (Z.C.); (W.W.)
| | - Guangxian Leng
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China; (J.Z.); (Y.L.); (J.H.); (G.L.); (X.L.); (Z.C.); (W.W.)
| | - Xining Liu
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China; (J.Z.); (Y.L.); (J.H.); (G.L.); (X.L.); (Z.C.); (W.W.)
| | - Zailin Cui
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China; (J.Z.); (Y.L.); (J.H.); (G.L.); (X.L.); (Z.C.); (W.W.)
| | - Wenzhen Wang
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China; (J.Z.); (Y.L.); (J.H.); (G.L.); (X.L.); (Z.C.); (W.W.)
| | - Yufang Ma
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China; (J.Z.); (Y.L.); (J.H.); (G.L.); (X.L.); (Z.C.); (W.W.)
- Department of Microbiology, Dalian Medical University, Dalian 116044, China
| | - Shanshan Sha
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China; (J.Z.); (Y.L.); (J.H.); (G.L.); (X.L.); (Z.C.); (W.W.)
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Baquero F, Rodríguez-Beltrán J, Coque TM, del Campo R. Boosting Fitness Costs Associated with Antibiotic Resistance in the Gut: On the Way to Biorestoration of Susceptible Populations. Biomolecules 2024; 14:76. [PMID: 38254676 PMCID: PMC10812938 DOI: 10.3390/biom14010076] [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: 11/25/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
The acquisition and expression of antibiotic resistance implies changes in bacterial cell physiology, imposing fitness costs. Many human opportunistic pathogenic bacteria, such as those causing urinary tract or bloodstream infections, colonize the gut. In this opinionated review, we will examine the various types of stress that these bacteria might suffer during their intestinal stay. These stresses, and their compensatory responses, probably have a fitness cost, which might be additive to the cost of expressing antibiotic resistance. Such an effect could result in a disadvantage relative to antibiotic susceptible populations that might replace the resistant ones. The opinion proposed in this paper is that the effect of these combinations of fitness costs should be tested in antibiotic resistant bacteria with susceptible ones as controls. This testing might provide opportunities to increase the bacterial gut stress boosting physiological biomolecules or using dietary interventions. This approach to reduce the burden of antibiotic-resistant populations certainly must be answered empirically. In the end, the battle against antibiotic resistance should be won by antibiotic-susceptible organisms. Let us help them prevail.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), 28034 Madrid, Spain
- Network Center for Biomedical Research in Epidemiology and Public Health (CIBER-ESP), 28029 Madrid, Spain
| | - Jerónimo Rodríguez-Beltrán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), 28034 Madrid, Spain
- Network Center for Biomedical Research in Infectious Diseases (CIBER-INFEC), 28034 Madrid, Spain
| | - Teresa M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), 28034 Madrid, Spain
- Network Center for Biomedical Research in Infectious Diseases (CIBER-INFEC), 28034 Madrid, Spain
| | - Rosa del Campo
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), 28034 Madrid, Spain
- Network Center for Biomedical Research in Infectious Diseases (CIBER-INFEC), 28034 Madrid, Spain
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Zheng Y, Bonfili L, Wei T, Eleuteri AM. Understanding the Gut-Brain Axis and Its Therapeutic Implications for Neurodegenerative Disorders. Nutrients 2023; 15:4631. [PMID: 37960284 PMCID: PMC10648099 DOI: 10.3390/nu15214631] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/25/2023] [Accepted: 10/28/2023] [Indexed: 11/15/2023] Open
Abstract
The gut-brain axis (GBA) is a complex bidirectional communication network connecting the gut and brain. It involves neural, immune, and endocrine communication pathways between the gastrointestinal (GI) tract and the central nervous system (CNS). Perturbations of the GBA have been reported in many neurodegenerative disorders (NDDs), such as Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS), among others, suggesting a possible role in disease pathogenesis. The gut microbiota is a pivotal component of the GBA, and alterations in its composition, known as gut dysbiosis, have been associated with GBA dysfunction and neurodegeneration. The gut microbiota might influence the homeostasis of the CNS by modulating the immune system and, more directly, regulating the production of molecules and metabolites that influence the nervous and endocrine systems, making it a potential therapeutic target. Preclinical trials manipulating microbial composition through dietary intervention, probiotic and prebiotic supplementation, and fecal microbial transplantation (FMT) have provided promising outcomes. However, its clear mechanism is not well understood, and the results are not always consistent. Here, we provide an overview of the major components and communication pathways of the GBA, as well as therapeutic approaches targeting the GBA to ameliorate NDDs.
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Affiliation(s)
- Yadong Zheng
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, MC, Italy; (Y.Z.); (L.B.)
- School of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Laura Bonfili
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, MC, Italy; (Y.Z.); (L.B.)
| | - Tao Wei
- School of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Anna Maria Eleuteri
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, MC, Italy; (Y.Z.); (L.B.)
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Doranga S, Conway T. OmpC-Dependent Bile Tolerance Contributes to E. coli Colonization of the Mammalian Intestine. Microbiol Spectr 2023; 11:e0524122. [PMID: 37014216 PMCID: PMC10269588 DOI: 10.1128/spectrum.05241-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/09/2023] [Indexed: 04/05/2023] Open
Abstract
Escherichia coli persistently colonizes the mammalian intestine by mechanisms that are not fully understood. Previously, we found when streptomycin-treated mice were fed E. coli MG1655, the intestine selected for envZ missense mutants that outcompeted the wild type. The better-colonizing envZ mutants had a higher level of OmpC and reduced OmpF. This suggested the EnvZ/OmpR two-component system and outer membrane proteins play a role in colonization. In this study, we show that wild-type E. coli MG1655 outcompetes an envZ-ompR knockout mutant. Moreover, ompA and ompC knockout mutants are outcompeted by the wild type, while an ompF knockout mutant colonizes better than the wild type. Outer membrane protein gels show the ompF mutant overproduces OmpC. An ompC mutant is more sensitive to bile salts than the wild type and ompF mutant. The ompC mutant initiates colonization slowly because it is sensitive to physiological concentrations of bile salts in the intestine. Overexpression of ompC under the control of a constitutive promoter confers a colonization advantage only when ompF is deleted. These results indicate that fine-tuning of OmpC and OmpF levels is needed to maximize competitive fitness in the intestine. RNA sequencing reveals the EnvZ/OmpR two-component system is active in the intestine: ompC is upregulated and ompF is downregulated. While other factors could also contribute to the advantage provided by OmpC, we provide evidence that OmpC is important for E. coli to colonize the intestine because its smaller pore size excludes bile salts or other unknown toxic substances, while OmpF is deleterious because its larger pore size allows bile salts or other unknown toxic substances to enter the periplasm. IMPORTANCE Every mammalian intestine is colonized with Escherichia coli. Although E. coli is one of the most studied model organisms, how it colonizes the intestine is not fully understood. Here, we investigated the role of the EnvZ/OmpR two-component system and outer membrane proteins in colonization of the mouse intestine by E. coli. We report that an ompC mutant is a poor colonizer, while an ompF mutant, which overproduces OmpC, outcompetes the wild type. OmpF has a larger pore size that allows toxic bile salts or other toxic compounds into the cell and is deleterious for colonization of the intestine. OmpC has a smaller pore size and excludes bile salts. Our findings provide insights into why E. coli fine-tunes the levels of OmpC and OmpF during colonization via the EnvZ/OmpR two-component system.
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Affiliation(s)
- Sudhir Doranga
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Tyrrell Conway
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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5
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Kumar GD, Oguadinma IC, Mishra A, Suh JH, Singh M. Influence of antibiotic-resistance and exudate on peroxyacetic acid tolerance in O157 and non-O157 Shiga toxin producing E. coli. Int J Food Microbiol 2023; 391-393:110144. [PMID: 36842254 DOI: 10.1016/j.ijfoodmicro.2023.110144] [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: 10/02/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/21/2023]
Abstract
Shiga toxin producing Escherichia coli (STEC) continues to cause foodborne outbreaks associated with beef and beef products despite consistent use of antimicrobial interventions. In this study, the influence of antibiotic resistance (ABR) in E. coli O157:H7 H1730, O157:H7 43,895, O121:H19 and O26:H11 on tolerance to peroxyacetic acid (PAA) was evaluated. Further, bactericidal concentrations of PAA in the presence of nutrient rich media (Tryptic Soy Broth, TSB and beef exudates) and nutrient deficient media (Sterile Deionized Water, SDW and Phosphate Buffered Saline, PBS) were evaluated for all bacterial strains. Antibiotic resistance to ampicillin (amp C), or ampicillin and streptomycin (amp P strep C) was generated in each bacterial strain through incremental exposure to the antibiotics or by plasmid transformation (n = 12 total strains). The mean bactericidal concentrations of PAA were higher (p ≤ 0.05) in nutrient rich media (205.55 ± 31.11 in beef exudate and 195.83 ± 25.00 ppm in TSB) than in nutrient deficient media (57.91 ± 11.97 ppm in SDW and 56.66 ± 9.56 ppm in PBS). Strain O157: H7 ampP strepC was the most tolerant to PAA (p ≤ 0.05). At 200 ppm in nutrient rich media and 60 ppm in nutrient deficient media, all bacterial strains declined in population to below the limit of detection. Analysis of the beef exudates indicated the presence of diverse amino acids that have been associated with acid tolerance. The results from this study indicate that beef exudates could contribute to acid tolerance and suggest that some STEC bacterial strains with certain ABR profiles might be more tolerant to PAA.
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Affiliation(s)
- Govindaraj Dev Kumar
- Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, GA, USA.
| | | | - Abhinav Mishra
- Department of Food Science & Technology, University of Georgia, Athens, GA, USA
| | - Joon Hyuk Suh
- Department of Food Science & Technology, University of Georgia, Athens, GA, USA
| | - Manpreet Singh
- Department of Food Science & Technology, University of Georgia, Athens, GA, USA
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Hou J, Meng S, Zhang B, Ruan R, Zhang Y, Wang Z, Song M, Bai Z. Effect of RNA interference with glutamate decarboxylase on acid resistance of Trichinella spiralis. Acta Trop 2023; 241:106869. [PMID: 36849092 DOI: 10.1016/j.actatropica.2023.106869] [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: 11/25/2022] [Revised: 01/24/2023] [Accepted: 02/18/2023] [Indexed: 02/27/2023]
Abstract
Trichinella spiralis is a zoonotic parasite that infects most mammals, even humans. Glutamate decarboxylase (GAD) is an important enzyme in glutamate-dependent acid resistance system 2 (AR2), but the GAD of T. spiralis in AR2 is unclear. We aimed to investigate the role of T. spiralis glutamate decarboxylase (TsGAD) in AR2. We silenced the TsGAD gene to evaluate the AR of T. spiralis muscle larvae (ML) in vivo and in vitro via siRNA. The results showed that recombinant TsGAD was recognized by anti-rTsGAD polyclonal antibody (57 kDa), and qPCR indicated that TsGAD transcription peaked at pH 2.5 for 1 h compared to that with pH 6.6 phosphate-buffered saline. Indirect immunofluorescence assays revealed that TsGAD was expressed in the epidermis of ML. After TsGAD silencing in vitro, TsGAD transcription and the survival rate of ML decreased by 15.2% and 17%, respectively, compared with those of the PBS group. Both TsGAD enzymatic activity and the acid adjustment of siRNA1-silenced ML were weakened. In vivo, each mouse was orally infected with 300 siRNA1-silenced ML. On days 7 and 42 post-infection, the reduction rates of adult worms and ML were 31.5% and 49.05%, respectively. Additionally, the reproductive capacity index and larvae per gram of ML were 62.51±7.32 and 1250.22±146.48, respectively, lower than those of the PBS group. Haematoxylin-eosin staining revealed many inflammatory cells infiltrating the nurse cells in the diaphragm of mice infected with siRNA1-silenced ML. The survival rate of the F1 generation ML was 27% higher than that of the F0 generation ML, but there was no difference from the PBS group. These results first indicated that GAD plays a crucial role in AR2 of T. spiralis. TsGAD gene silencing reduced the worm burden in mice, providing data for the comprehensive study of the AR system of T. spiralis and a new idea for the prevention of trichinosis.
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Affiliation(s)
- Jiaming Hou
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, China
| | - Shi Meng
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, China
| | - Bohan Zhang
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, China
| | - Rulin Ruan
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, China
| | - Yan Zhang
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, China
| | - Ze Wang
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, China
| | - Mingxin Song
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, China.
| | - Zhikun Bai
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, China.
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The Effect of γ-Aminobutyric Acid Addition on In Vitro Ruminal Fermentation Characteristics and Methane Production of Diets Differing in Forage-to-Concentrate Ratio. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9020105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Gamma-aminobutyric acid (GABA), known as the most abundant inhibitory neurotransmitter in the mammalian brain, can permeate ruminal epithelia by passive diffusion and enrich in the rumen environment. To explore whether the addition of GABA can regulate rumen fermentation characteristics as well as methane production, a 2 × 6 factorial in vitro rumen batch culture was conducted to determine the supplemental effect of GABA at inclusion levels of 0 (Control), 10, 20, 30, 40 and 50 mg in culture fluids on rumen fermentation of two total mixed rations (HF—a high-fiber ration consisted of 70% corn silage and 30% concentrate; and LF—a low-fiber ration consisted of 30% corn silage and 70% concentrate). After 72 h in vitro incubation of two rations with mixed rumen microoganisms obtained from five rumen-cannulated lactating Holstein dairy cows, increasing GABA addition linearly increased cumulative gas production in the LF group, though in vitro dry matter digestibility was not affected in either the LF or HF group. Kinetic gas production analysis noted that increasing GABA addition mostly decreased the gas production rate (i.e., RmaxG), as well as the ration digestion rate (RmaxS) to reach maximum fermentation. The GABA addition did not affect pH or microbial growth (i.e., MCP). However, total volatile fatty acid production in both LF and HF groups all linearly increased with the increase in GABA addition. Along with the increase in GABA addition in both LF and HF groups, the ratio of non-glucogenic to glucogenic volatile fatty acids both increased, while the molar proportions of propionate and valerate were significantly decreased, and the acetate and butyrate proportions were increased after 72 h in vitro rumen fermentation. The time-course change of fermentation end-products generally showed that carbon dioxide declined from approximately 89% to 74%, and methane increased from approximately 11% to 26%. After 72 h in vitro fermentation, molar methane proportion was greater in the LF than in the HF group, and increasing GABA addition quadratically increased methane production in the LF group while a slight increase occurred in the HF group.
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Sheng C, Chu X, He Y, Ding Q, Jia S, Shi Q, Sun R, Song L, Du W, Liang Y, Chen N, Yang Y, Wang X. Alterations in Peripheral Metabolites as Key Actors in Alzheimer's Disease. Curr Alzheimer Res 2023; 20:379-393. [PMID: 37622711 DOI: 10.2174/1567205020666230825091147] [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: 02/28/2023] [Revised: 06/24/2023] [Accepted: 07/20/2023] [Indexed: 08/26/2023]
Abstract
Growing evidence supports that Alzheimer's disease (AD) could be regarded as a metabolic disease, accompanying central and peripheral metabolic disturbance. Nowadays, exploring novel and potentially alternative hallmarks for AD is needed. Peripheral metabolites based on blood and gut may provide new biochemical insights about disease mechanisms. These metabolites can influence brain energy homeostasis, maintain gut mucosal integrity, and regulate the host immune system, which may further play a key role in modulating the cognitive function and behavior of AD. Recently, metabolomics has been used to identify key AD-related metabolic changes and define metabolic changes during AD disease trajectory. This review aims to summarize the key blood- and microbial-derived metabolites that are altered in AD and identify the potential metabolic biomarkers of AD, which will provide future targets for precision therapeutic modulation.
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Affiliation(s)
- Can Sheng
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China
| | - Xu Chu
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China
| | - Yan He
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China
| | - Qingqing Ding
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China
| | - Shulei Jia
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qiguang Shi
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China
| | - Ran Sun
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China
| | - Li Song
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China
| | - Wenying Du
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, 100053, China
| | - Yuan Liang
- Department of Clinical Medicine, Jining Medical University, Jining, 272067, China
| | - Nian Chen
- Department of Clinical Medicine, Jining Medical University, Jining, 272067, China
| | - Yan Yang
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China
| | - Xiaoni Wang
- Department of Neurology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310020, China
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Liu S, Wen B, Du G, Wang Y, Ma X, Yu H, Zhang J, Fan S, Zhou H, Xin F. Coordinated regulation of Bacteroides thetaiotaomicron glutamate decarboxylase activity by multiple elements under different pH. Food Chem 2022; 403:134436. [DOI: 10.1016/j.foodchem.2022.134436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/14/2022] [Accepted: 09/25/2022] [Indexed: 11/28/2022]
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Kumar Palepu MS, Dandekar MP. Remodeling of microbiota gut-brain axis using psychobiotics in depression. Eur J Pharmacol 2022; 931:175171. [PMID: 35926568 DOI: 10.1016/j.ejphar.2022.175171] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/14/2022] [Accepted: 07/21/2022] [Indexed: 12/11/2022]
Abstract
Depression is a multifaceted psychiatric disorder mainly orchestrated by dysfunction of neuroendocrine, neurochemical, immune, and metabolic systems. The interconnection of gut microbiota perturbation with the central nervous system disorders has been well documented in recent times. Indeed, alteration of commensal intestinal microflora is noted in several psychiatric disorders such as anxiety and depression, which are presumed to be routed through the enteric nervous system, autonomic nervous system, endocrine, and immune system. This review summarises the new mechanisms underlying the crosstalk between gut microbiota and brain involved in the management of depression. Depression-induced changes in the commensal intestinal microbiota are majorly linked with the disruption of gut integrity, hyperinflammation, and modulation of short-chain fatty acids, neurotransmitters, kynurenine metabolites, endocannabinoids, brain-derived neurotropic factors, hypothalamic-pituitary-adrenal axis, and gut peptides. The restoration of gut microbiota with prebiotics, probiotics, postbiotics, synbiotics, and fermented foods (psychobiotics) has gained a considerable attention for the management of depression. Recent evidence also propose the role of gut microbiota in the process of treatment-resistant depression. Thus, remodeling of the microbiota-gut-brain axis using psychobiotics appears to be a promising therapeutic approach for the reversal of psychiatric disorders, and it is imperative to decipher the underlying mechanisms for gut-brain crosstalk.
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Affiliation(s)
- Mani Surya Kumar Palepu
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, India
| | - Manoj P Dandekar
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, India.
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Rohles C, Pauli S, Gießelmann G, Kohlstedt M, Becker J, Wittmann C. Systems metabolic engineering of Corynebacterium glutamicum eliminates all by-products for selective and high-yield production of the platform chemical 5-aminovalerate. Metab Eng 2022; 73:168-181. [PMID: 35917915 DOI: 10.1016/j.ymben.2022.07.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/01/2022] [Accepted: 07/13/2022] [Indexed: 11/29/2022]
Abstract
5-aminovalerate (AVA) is a platform chemical of substantial commercial value to derive nylon-5 and five-carbon derivatives like δ-valerolactam, 1,5-pentanediol, glutarate, and 5-hydroxyvalerate. De-novo bio-production synthesis of AVA using metabolically engineered cell factories is regarded as exemplary route to provide this chemical in a sustainable way. So far, this route is limited by low titers, rates and yields and suffers from high levels of by-products. To overcome these limitations, we developed a novel family of AVA producing C. glutamicum cell factories. Stepwise optimization included (i) improved AVA biosynthesis by expression balancing of the heterologous davAB genes from P. putida, (ii) reduced formation of the by-product glutarate by disruption of the catabolic y-aminobutyrate pathway (iii), increased AVA export, and (iv) reduced AVA re-import via native and heterologous transporters to account for the accumulation of intracellular AVA up to 300 mM. Strain C. glutamicum AVA-5A, obtained after several optimization rounds, produced 48.3 g L-1 AVA in a fed-batch process and achieved a high yield of 0.21 g g-1. Surprisingly in later stages, the mutant suddenly accumulated glutarate to an extent equivalent to 30% of the amount of AVA formed, tenfold more than in the early process, displaying a severe drawback toward industrial production. Further exploration led to the discovery that ArgD, naturally aminating N-acetyl-l-ornithine during l-arginine biosynthesis, exhibits deaminating side activity on AVA toward glutarate formation. This promiscuity became relevant because of the high intracellular AVA level and the fact that ArgD became unoccupied with the gradually stronger switch-off of anabolism during production. Glutarate formation was favorably abolished in the advanced strains AVA-6A, AVA-6B, and AVA-7, all lacking argD. In a fed-batch process, C. glutamicum AVA-7 produced 46.5 g L-1 AVA at a yield of 0.34 g g-1 and a maximum productivity of 1.52 g L-1 h-1, outperforming all previously reported efforts and stetting a milestone toward industrial manufacturing of AVA. Notably, the novel cell factories are fully genome-based, offering high genetic stability and requiring no selection markers.
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Affiliation(s)
- Christina Rohles
- Institute of Systems Biotechnology, Saarland University, Germany
| | - Sarah Pauli
- Institute of Systems Biotechnology, Saarland University, Germany
| | | | | | - Judith Becker
- Institute of Systems Biotechnology, Saarland University, Germany
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12
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Li Z, Nees M, Bettenbrock K, Rinas U. Is energy excess the initial trigger of carbon overflow metabolism? Transcriptional network response of carbon-limited Escherichia coli to transient carbon excess. Microb Cell Fact 2022; 21:67. [PMID: 35449049 PMCID: PMC9027384 DOI: 10.1186/s12934-022-01787-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/26/2022] [Indexed: 12/20/2022] Open
Abstract
Background Escherichia coli adapted to carbon-limiting conditions is generally geared for energy-efficient carbon utilization. This includes also the efficient utilization of glucose, which serves as a source for cellular building blocks as well as energy. Thus, catabolic and anabolic functions are balanced under these conditions to minimize wasteful carbon utilization. Exposure to glucose excess interferes with the fine-tuned coupling of anabolism and catabolism leading to the so-called carbon overflow metabolism noticeable through acetate formation and eventually growth inhibition. Results Cellular adaptations towards sudden but timely limited carbon excess conditions were analyzed by exposing slow-growing cells in steady state glucose-limited continuous culture to a single glucose pulse. Concentrations of metabolites as well as time-dependent transcriptome alterations were analyzed and a transcriptional network analysis performed to determine the most relevant transcription and sigma factor combinations which govern these adaptations. Down-regulation of genes related to carbon catabolism is observed mainly at the level of substrate uptake and downstream of pyruvate and not in between in the glycolytic pathway. It is mainly accomplished through the reduced activity of CRP-cAMP and through an increased influence of phosphorylated ArcA. The initiated transcriptomic change is directed towards down-regulation of genes, which contribute to active movement, carbon uptake and catabolic carbon processing, in particular to down-regulation of genes which contribute to efficient energy generation. Long-term changes persisting after glucose depletion and consumption of acetete encompassed reduced expression of genes related to active cell movement and enhanced expression of genes related to acid resistance, in particular acid resistance system 2 (GABA shunt) which can be also considered as an inefficient bypass of the TCA cycle. Conclusions Our analysis revealed that the major part of the trancriptomic response towards the glucose pulse is not directed towards enhanced cell proliferation but towards protection against excessive intracellular accumulation of potentially harmful concentration of metabolites including among others energy rich compounds such as ATP. Thus, resources are mainly utilized to cope with “overfeeding” and not for growth including long-lasting changes which may compromise the cells future ability to perform optimally under carbon-limiting conditions (reduced motility and ineffective substrate utilization). Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01787-4.
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Affiliation(s)
- Zhaopeng Li
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Brunswick, Germany.,Technical Chemistry - Life Science, Leibniz University of Hannover, Callinstr. 5, 30167, Hannover, Germany
| | - Markus Nees
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106, Magdeburg, Germany
| | - Katja Bettenbrock
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106, Magdeburg, Germany
| | - Ursula Rinas
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Brunswick, Germany. .,Technical Chemistry - Life Science, Leibniz University of Hannover, Callinstr. 5, 30167, Hannover, Germany.
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13
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Division of labor and collective functionality in Escherichia coli under acid stress. Commun Biol 2022; 5:327. [PMID: 35393532 PMCID: PMC8989999 DOI: 10.1038/s42003-022-03281-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 03/03/2022] [Indexed: 11/09/2022] Open
Abstract
The acid stress response is an important factor influencing the transmission of intestinal microbes such as the enterobacterium Escherichia coli. E. coli activates three inducible acid resistance systems - the glutamate decarboxylase, arginine decarboxylase, and lysine decarboxylase systems to counteract acid stress. Each system relies on the activity of a proton-consuming reaction catalyzed by a specific amino acid decarboxylase and a corresponding antiporter. Activation of these three systems is tightly regulated by a sophisticated interplay of membrane-integrated and soluble regulators. Using a fluorescent triple reporter strain, we quantitatively illuminated the cellular individuality during activation of each of the three acid resistance (AR) systems under consecutively increasing acid stress. Our studies highlight the advantages of E. coli in possessing three AR systems that enable division of labor in the population, which ensures survival over a wide range of low pH values.
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14
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Schwan WR, Luedtke J, Engelbrecht K, Mollinger J, Wheaton A, Foster JW, Wolchak R. Regulation of Escherichia coli fim gene transcription by GadE and other acid tolerance gene products. MICROBIOLOGY (READING, ENGLAND) 2022; 168:001149. [PMID: 35316170 PMCID: PMC9558354 DOI: 10.1099/mic.0.001149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 01/26/2022] [Indexed: 11/18/2022]
Abstract
Uropathogenic Escherichia coli (UPEC) cause millions of urinary tract infections each year in the United States. Type 1 pili are important for adherence of UPEC to uroepithelial cells in the human and murine urinary tracts where osmolality and pH vary. Previous work has shown that an acidic pH adversely affects the expression of type 1 pili. To determine if acid tolerance gene products may be regulating E. coli fim gene expression, a bank of K-12 strain acid tolerance gene mutants were screened using fimA-lux, fimB-lux, and fimE-lux fusions on single copy number plasmids. We have determined that a mutation in gadE increased transcription of all three fim genes, suggesting that GadE may be acting as a repressor in a low pH environment. Complementation of the gadE mutation restored fim gene transcription to wild-type levels. Moreover, mutations in gadX, gadW, crp, and cya also affected transcription of the three fim genes. To verify the role GadE plays in type 1 pilus expression, the NU149 gadE UPEC strain was tested. The gadE mutant had higher fimE gene transcript levels, a higher frequency of Phase-OFF positioning of fimS, and hemagglutination titres that were lower in strain NU149 gadE cultured in low pH medium as compared to the wild-type bacteria. The data demonstrate that UPEC fim genes are regulated directly or indirectly by the GadE protein and this could have some future bearing on the ability to prevent urinary tract infections by acidifying the urine and shutting off fim gene expression.
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Affiliation(s)
| | | | | | | | | | - John W. Foster
- University South Alabama College of Medicine, Mobile, AL, USA
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15
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Wan X, Saltepe B, Yu L, Wang B. Programming living sensors for environment, health and biomanufacturing. Microb Biotechnol 2021; 14:2334-2342. [PMID: 33960658 PMCID: PMC8601174 DOI: 10.1111/1751-7915.13820] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/05/2021] [Accepted: 04/11/2021] [Indexed: 01/10/2023] Open
Abstract
Synthetic biology offers new tools and capabilities of engineering cells with desired functions for example as new biosensing platforms leveraging engineered microbes. In the last two decades, bacterial cells have been programmed to sense and respond to various input cues for versatile purposes including environmental monitoring, disease diagnosis and adaptive biomanufacturing. Despite demonstrated proof-of-concept success in the laboratory, the real-world applications of microbial sensors have been restricted due to certain technical and societal limitations. Yet, most limitations can be addressed by new technological developments in synthetic biology such as circuit design, biocontainment and machine learning. Here, we summarize the latest advances in synthetic biology and discuss how they could accelerate the development, enhance the performance and address the present limitations of microbial sensors to facilitate their use in the field. We view that programmable living sensors are promising sensing platforms to achieve sustainable, affordable and easy-to-use on-site detection in diverse settings.
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Affiliation(s)
- Xinyi Wan
- Centre for Synthetic and Systems BiologySchool of Biological SciencesUniversity of EdinburghEdinburghEH9 3FFUK
- Hangzhou Innovation CenterZhejiang UniversityHangzhou311200China
| | - Behide Saltepe
- Centre for Synthetic and Systems BiologySchool of Biological SciencesUniversity of EdinburghEdinburghEH9 3FFUK
| | - Luyang Yu
- The Provincial International Science and Technology Cooperation Base for Engineering BiologyInternational CampusZhejiang UniversityHaining314400China
- College of Life SciencesZhejiang UniversityHangzhou310058China
| | - Baojun Wang
- Centre for Synthetic and Systems BiologySchool of Biological SciencesUniversity of EdinburghEdinburghEH9 3FFUK
- Hangzhou Innovation CenterZhejiang UniversityHangzhou311200China
- The Provincial International Science and Technology Cooperation Base for Engineering BiologyInternational CampusZhejiang UniversityHaining314400China
- College of Life SciencesZhejiang UniversityHangzhou310058China
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16
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Wu X, Kitahara G, Suenaga T, Naramoto K, Sekiguchi S, Goto Y, Osawa T. Association of intrauterine presence of Lactobacillus spp. with inflammation and pathogenic bacteria in the uterus in postpartum dairy cows. J Reprod Dev 2021; 67:340-344. [PMID: 34602527 PMCID: PMC8668369 DOI: 10.1262/jrd.2021-023] [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] [Indexed: 11/20/2022] Open
Abstract
The aim of this study was to clarify the influence of Lactobacillus spp. on the degree of endometrial inflammation in the postpartum period and the
relationship between Lactobacillus spp. and pathogenic bacteria in the endometrium of postpartum dairy cows. Endometrial samples were collected from 41
Holstein-Friesian cows at 4 and 8 weeks postpartum using cytobrushes for polymorphonuclear neutrophil (PMN) count and bacterial culture to isolate Lactobacillus
spp., Escherichiacoli, and Trueperella pyogenes. The 4-week samples were divided into four groups (E+L+), (E+L−),
(E−L+), (E−L−) according to whether endometritis was diagnosed (E+) and Lactobacillus spp. was isolated (L+). The diagnostic criterion for cytological
endometritis was > 18% PMN. The average PMN% in the E+L+ group was lower than that in the E+L-group (P < 0.05) at 8 weeks postpartum. There were no significant correlations between the
number of colonies of Lactobacillus spp. and E. coli or between that of Lactobacillus spp. and T. pyogenes.
Lactobacillus spp. could reduce PMN% in dairy cows with endometritis during the puerperal period. In conclusion, the intrauterine presence of
Lactobacillus spp. may have a positive effect on uterine involution in postpartum dairy cows.
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Affiliation(s)
- Xinyue Wu
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Go Kitahara
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki 889-1692, Japan.,Laboratory of Theriogenology, Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Tetsuya Suenaga
- Laboratory of Theriogenology, Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Kanami Naramoto
- Laboratory of Theriogenology, Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Satoshi Sekiguchi
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki 889-1692, Japan.,Laboratory of Animal Infectious Disease and Prevention, Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Yoshitaka Goto
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki 889-1692, Japan.,Laboratory of Veterinary Microbiology, Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Takeshi Osawa
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki 889-1692, Japan.,Laboratory of Theriogenology, Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
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17
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Doifode T, Giridharan VV, Generoso JS, Bhatti G, Collodel A, Schulz PE, Forlenza OV, Barichello T. The impact of the microbiota-gut-brain axis on Alzheimer's disease pathophysiology. Pharmacol Res 2021; 164:105314. [PMID: 33246175 DOI: 10.1016/j.phrs.2020.105314] [Citation(s) in RCA: 140] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/18/2020] [Accepted: 11/20/2020] [Indexed: 12/17/2022]
Abstract
The gut microbiota is a complex ecosystem that comprises of more than 100 trillion symbiotic microbial cells. The microbiota, the gut, and the brain form an association, 'the microbiota-gut-brain axis,' and synchronize the gut with the central nervous system and modify the behavior and brain immune homeostasis. The bidirectional communication between gut and brain occurs via the immune system, the vagus nerve, the enteric nervous system, and microbial metabolites, including short-chain fatty acids (SCFAs), proteins, and tryptophan metabolites. Recent studies have implicated the gut microbiota in many neurodegenerative diseases, including Alzheimer's disease (AD). In this review, we present an overview of gut microbiota, including Firmicutes, Bacteroidetes, SCFA, tryptophan, bacterial composition, besides age-related changes in gut microbiota composition, the microbiota-gut-brain axis pathways, the role of gut metabolites in amyloid-beta clearance, and gut microbiota modulation from experimental and clinical AD models. Understanding the role of the microbiota may provide new targets for treatment to delay the onset, progression, or reverse AD, and may help in reducing the prevalence of AD.
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Affiliation(s)
- Tejaswini Doifode
- Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Vijayasree V Giridharan
- Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Jaqueline S Generoso
- Experimental Physiopathology Laboratory, Graduate Program in Health Sciences, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, Brazil
| | - Gursimrat Bhatti
- Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Allan Collodel
- Experimental Physiopathology Laboratory, Graduate Program in Health Sciences, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, Brazil
| | - Paul E Schulz
- Neurocognitive Disorders Center, Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Orestes V Forlenza
- Laboratory of Neuroscience (LIM-27), Department and Institute of Psychiatry, Hospital das Clínicas HCFMUSP, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Tatiana Barichello
- Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA; Experimental Physiopathology Laboratory, Graduate Program in Health Sciences, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, Brazil.
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18
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Mapping the Transcriptional and Fitness Landscapes of a Pathogenic E. coli Strain: The Effects of Organic Acid Stress under Aerobic and Anaerobic Conditions. Genes (Basel) 2020; 12:genes12010053. [PMID: 33396416 PMCID: PMC7824302 DOI: 10.3390/genes12010053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/22/2020] [Accepted: 12/29/2020] [Indexed: 12/31/2022] Open
Abstract
Several methods are available to probe cellular responses to external stresses at the whole genome level. RNAseq can be used to measure changes in expression of all genes following exposure to stress, but gives no information about the contribution of these genes to an organism’s ability to survive the stress. The relative contribution of each non-essential gene in the genome to the fitness of the organism under stress can be obtained using methods that use sequencing to estimate the frequencies of members of a dense transposon library grown under different conditions, for example by transposon-directed insertion sequencing (TraDIS). These two methods thus probe different aspects of the underlying biology of the organism. We were interested to determine the extent to which the data from these two methods converge on related genes and pathways. To do this, we looked at a combination of biologically meaningful stresses. The human gut contains different organic short-chain fatty acids (SCFAs) produced by fermentation of carbon compounds, and Escherichia coli is exposed to these in its passage through the gut. Their effect is likely to depend on both the ambient pH and the level of oxygen present. We, therefore, generated RNAseq and TraDIS data on a uropathogenic E. coli strain grown at either pH 7 or pH 5.5 in the presence or absence of three SCFAs (acetic, propionic and butyric), either aerobically or anaerobically. Our analysis identifies both known and novel pathways as being likely to be important under these conditions. There is no simple correlation between gene expression and fitness, but we found a significant overlap in KEGG pathways that are predicted to be enriched following analysis of the data from the two methods, and the majority of these showed a fitness signature that would be predicted from the gene expression data, assuming expression to be adaptive. Genes which are not in the E. coli core genome were found to be particularly likely to show a positive correlation between level of expression and contribution to fitness.
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19
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Cozannet M, Borrel G, Roussel E, Moalic Y, Allioux M, Sanvoisin A, Toffin L, Alain K. New Insights into the Ecology and Physiology of Methanomassiliicoccales from Terrestrial and Aquatic Environments. Microorganisms 2020; 9:E30. [PMID: 33374130 PMCID: PMC7824343 DOI: 10.3390/microorganisms9010030] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/19/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
Members of the archaeal order Methanomassiliicoccales are methanogens mainly associated with animal digestive tracts. However, environmental members remain poorly characterized as no representatives not associated with a host have been cultivated so far. In this study, metabarcoding screening combined with quantitative PCR analyses on a collection of diverse non-host-associated environmental samples revealed that Methanomassiliicoccales were very scarce in most terrestrial and aquatic ecosystems. Relative abundance of Methanomassiliicoccales and substrates/products of methanogenesis were monitored during incubation of environmental slurries. A sediment slurry enriched in Methanomassiliicoccales was obtained from a freshwater sample. It allowed the reconstruction of a high-quality metagenome-assembled genome (MAG) corresponding to a new candidate species, for which we propose the name of Candidatus 'Methanomassiliicoccus armoricus MXMAG1'. Comparison of the annotated genome of MXMAG1 with the published genomes and MAGs from Methanomassiliicoccales belonging to the 2 known clades ('free-living'/non-host-associated environmental clade and 'host-associated'/digestive clade) allowed us to explore the putative physiological traits of Candidatus 'M. armoricus MXMAG1'. As expected, Ca. 'Methanomassiliicoccus armoricus MXMAG1' had the genetic potential to produce methane by reduction of methyl compounds and dihydrogen oxidation. This MAG encodes for several putative physiological and stress response adaptations, including biosynthesis of trehalose (osmotic and temperature regulations), agmatine production (pH regulation), and arsenic detoxication, by reduction and excretion of arsenite, a mechanism that was only present in the 'free-living' clade. An analysis of co-occurrence networks carried out on environmental samples and slurries also showed that Methanomassiliicoccales detected in terrestrial and aquatic ecosystems were strongly associated with acetate and dihydrogen producing bacteria commonly found in digestive habitats and which have been reported to form syntrophic relationships with methanogens.
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Affiliation(s)
- Marc Cozannet
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
| | - Guillaume Borrel
- Unit Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institute Pasteur, 75015 Paris, France;
| | - Erwan Roussel
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
| | - Yann Moalic
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
| | - Maxime Allioux
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
| | - Amandine Sanvoisin
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
| | - Laurent Toffin
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
| | - Karine Alain
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
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20
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Suganya K, Koo BS. Gut-Brain Axis: Role of Gut Microbiota on Neurological Disorders and How Probiotics/Prebiotics Beneficially Modulate Microbial and Immune Pathways to Improve Brain Functions. Int J Mol Sci 2020; 21:E7551. [PMID: 33066156 PMCID: PMC7589356 DOI: 10.3390/ijms21207551] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/06/2020] [Accepted: 10/09/2020] [Indexed: 02/07/2023] Open
Abstract
The gut microbiome acts as an integral part of the gastrointestinal tract (GIT) that has the largest and vulnerable surface with desirable features to observe foods, nutrients, and environmental factors, as well as to differentiate commensals, invading pathogens, and others. It is well-known that the gut has a strong connection with the central nervous system (CNS) in the context of health and disease. A healthy gut with diverse microbes is vital for normal brain functions and emotional behaviors. In addition, the CNS controls most aspects of the GI physiology. The molecular interaction between the gut/microbiome and CNS is complex and bidirectional, ensuring the maintenance of gut homeostasis and proper digestion. Besides this, several mechanisms have been proposed, including endocrine, neuronal, toll-like receptor, and metabolites-dependent pathways. Changes in the bidirectional relationship between the GIT and CNS are linked with the pathogenesis of gastrointestinal and neurological disorders; therefore, the microbiota/gut-and-brain axis is an emerging and widely accepted concept. In this review, we summarize the recent findings supporting the role of the gut microbiota and immune system on the maintenance of brain functions and the development of neurological disorders. In addition, we highlight the recent advances in improving of neurological diseases by probiotics/prebiotics/synbiotics and fecal microbiota transplantation via the concept of the gut-brain axis.
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Affiliation(s)
- Kanmani Suganya
- Department of Oriental Medicine, Dongguk University, Gyeongju 38066, Korea;
- Department of Oriental Neuropsychiatry, Graduate School of Oriental Medicine, Dongguk University, Ilsan Hospital, 814 Siksa-dong, Goyang-si, Gyeonggi-do 10326, Korea
| | - Byung-Soo Koo
- Department of Oriental Medicine, Dongguk University, Gyeongju 38066, Korea;
- Department of Oriental Neuropsychiatry, Graduate School of Oriental Medicine, Dongguk University, Ilsan Hospital, 814 Siksa-dong, Goyang-si, Gyeonggi-do 10326, Korea
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21
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Bistoletti M, Bosi A, Banfi D, Giaroni C, Baj A. The microbiota-gut-brain axis: Focus on the fundamental communication pathways. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 176:43-110. [PMID: 33814115 DOI: 10.1016/bs.pmbts.2020.08.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Michela Bistoletti
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Annalisa Bosi
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Davide Banfi
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Cristina Giaroni
- Department of Medicine and Surgery, University of Insubria, Varese, Italy.
| | - Andreina Baj
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
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22
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Abstract
The ability to detect disease early and deliver precision therapy would be transformative for the treatment of human illnesses. To achieve these goals, biosensors that can pinpoint when and where diseases emerge are needed. Rapid advances in synthetic biology are enabling us to exploit the information-processing abilities of living cells to diagnose disease and then treat it in a controlled fashion. For example, living sensors could be designed to precisely sense disease biomarkers, such as by-products of inflammation, and to respond by delivering targeted therapeutics in situ. Here, we provide an overview of ongoing efforts in microbial biosensor design, highlight translational opportunities, and discuss challenges for enabling sense-and-respond precision medicines.
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Affiliation(s)
- Maria Eugenia Inda
- MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Research Laboratory of Electronics, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Timothy K. Lu
- MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Research Laboratory of Electronics, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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23
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Brameyer S, Hoyer E, Bibinger S, Burdack K, Lassak J, Jung K. Molecular design of a signaling system influences noise in protein abundance under acid stress in different γ-Proteobacteria. J Bacteriol 2020; 202:JB.00121-20. [PMID: 32482722 PMCID: PMC8404709 DOI: 10.1128/jb.00121-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/22/2020] [Indexed: 12/16/2022] Open
Abstract
Bacteria have evolved different signaling systems to sense and adapt to acid stress. One of these systems, the CadABC-system, responds to a combination of low pH and lysine availability. In Escherichia coli, the two signals are sensed by the pH sensor and transcription activator CadC and the co-sensor LysP, a lysine-specific transporter. Activated CadC promotes the transcription of the cadBA operon, which codes for the lysine decarboxylase CadA and the lysine/cadaverine antiporter CadB. The copy number of CadC is controlled translationally. Using a bioinformatics approach, we identified the presence of CadC with ribosomal stalling motifs together with LysP in species of the Enterobacteriaceae family. In contrast, we identified CadC without stalling motifs in species of the Vibrionaceae family, but the LysP co-sensor was not identified. Therefore, we compared the output of the Cad system in single cells of the distantly related organisms E. coli and V. campbellii using fluorescently-tagged CadB as the reporter. We observed a heterogeneous output in E. coli, and all the V. campbellii cells produced CadB. The copy number of the pH sensor CadC in E. coli was extremely low (≤4 molecules per cell), but it was 10-fold higher in V. campbellii An increase in the CadC copy number in E. coli correlated with a decrease in heterogeneous behavior. This study demonstrated how small changes in the design of a signaling system allow a homogeneous output and, thus, adaptation of Vibrio species that rely on the CadABC-system as the only acid resistance system.Importance Acid resistance is an important property of bacteria, such as Escherichia coli, to survive acidic environments like the human gastrointestinal tract. E. coli possess both passive and inducible acid resistance systems to counteract acidic environments. Thus, E. coli evolved sophisticated signaling systems to sense and appropriately respond to environmental acidic stress by regulating the activity of its three inducible acid resistance systems. One of these systems is the Cad system that is only induced under moderate acidic stress in a lysine-rich environment by the pH-responsive transcriptional regulator CadC. The significance of our research is in identifying the molecular design of the Cad systems in different Proteobacteria and their target expression noise at single cell level during acid stress conditions.
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Affiliation(s)
- Sophie Brameyer
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Elisabeth Hoyer
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Sebastian Bibinger
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Korinna Burdack
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Jürgen Lassak
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Kirsten Jung
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
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Schwan WR, Flohr NL, Multerer AR, Starkey JC. GadE regulates fliC gene transcription and motility in Escherichia coli. World J Clin Infect Dis 2020; 10:14-23. [PMID: 32728533 PMCID: PMC7388676 DOI: 10.5495/wjcid.v10.i1.14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/25/2020] [Accepted: 05/05/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Escherichia coli (E. coli) express flagella to ascend human urinary tracts. To survive in the acidic pH of human urine, E. coli uses the glutamate decarboxylase acid response system, which is regulated by the GadE protein.
AIM To determine if growth in an acidic pH environment affected fliC transcription and whether GadE regulated that transcription.
METHODS A fliC-lacZ reporter fusion was created on a single copy number plasmid to assess the effects of acidic pH on fliC transcription. Further, a ΔgadE mutant strain of a uropathogenic E. coli was created and tested for motility compared to the wild-type strain.
RESULTS Escherichia coli cells carrying the fliC-lacZ fusion displayed significantly less fliC transcription when grown in an acidic pH medium compared to when grown in a neutral pH medium. Transcription of fliC fell further when the E. coli was grown in an acidic pH/high osmolarity environment. Since GadE is a critical regulator of one acid response system, fliC transcription was tested in a gadE mutant strain grown under acidic conditions. Expression of fliC was derepressed in the E. coli gadE mutant strain grown under acidic conditions compared to that in wild-type bacteria under the same conditions. Furthermore, a gadE mutation in a uropathogenic E. coli background exhibited significantly greater motility than the wild-type strain following growth in an acidic medium.
CONCLUSION Together, our results suggest that GadE may down-regulate fliC transcription and motility in E. coli grown under acidic conditions.
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Affiliation(s)
- William R Schwan
- Department of Microbiology, University of Wisconsin-La Crosse, La Crosse, WI 54601, United States
| | - Nicole L Flohr
- Department of Microbiology, University of Wisconsin-La Crosse, La Crosse, WI 54601, United States
| | - Abigail R Multerer
- Department of Microbiology, University of Wisconsin-La Crosse, La Crosse, WI 54601, United States
| | - Jordan C Starkey
- Department of Microbiology, University of Wisconsin-La Crosse, La Crosse, WI 54601, United States
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Silva Júnior CD, Martins CCS, Dias FTF, Sitanaka NY, Ferracioli LB, Moraes JE, Pizzolante CC, Budiño FEL, Pereira R, Tizioto P, Paula VRC, Coutinho LL, Ruiz US. The use of an alternative feed additive, containing benzoic acid, thymol, eugenol, and piperine, improved growth performance, nutrient and energy digestibility, and gut health in weaned piglets. J Anim Sci 2020; 98:skaa119. [PMID: 32280983 PMCID: PMC7229883 DOI: 10.1093/jas/skaa119] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/09/2020] [Indexed: 02/01/2023] Open
Abstract
This research evaluated a feed additive (benzoic acid, eugenol, thymol, and piperine), associated or not with colistin, in weaned piglets feeding. The parameters evaluated were growth performance, apparent total tract digestibility (ATTD) of nutrients, diarrhea incidence, intestinal morphology, relative weights of digestive organs, microbial diversity, and the percentages of operational taxonomic units of microorganisms in the cecum content of pigs. One-hundred and eight crossbred piglets (5.3 ± 0.5 kg) were used in a three-phase feeding program (21 to 35, 36 to 50, 51 to 65 d of age) and fed a control diet with no inclusion of growth promoter feed additive, a diet with 40 ppm of colistin, a diet with 0.3% of alternative additive, and a diet with 0.3% of alternative additive and 40 ppm of colistin. The diets were based on corn, soybean meal, dairy products, and spray-dried blood plasma and formulated to provide 3.40, 3.38, and 3.20 Mcal of ME/kg and 14.5, 13.3, and 10.9 g/kg of digestible lysine, in phases 1, 2, and 3, respectively. The piglets were housed three per pen, with nine replicates per diet, in a complete randomized block design based on initial BW. The data were submitted to ANOVA and means were separated by Tukey test (5%), using SAS. Pigs fed diets with the alternative feed additive had greater (P < 0.05) ADG (114.3 vs. 91.8 g) and ADFI (190.1 vs. 163.3 g) in phase 1 than pigs fed diets without the product. The alternative additive improved (P < 0.05) ATTD of crude protein (CP) in phase 1 (71.0% vs. 68.6%), gross energy in phases 1 (77.4% vs. 75.2%) and 3 (79.0% vs. 77.1%), and dry matter in phase 3 (79.1% vs. 77.1%). The antibiotic inclusion in the diets increased (P < 0.05) ATTD of CP in phase 1 (71.5% vs. 68.2%). The alternative feed additive tended (P = 0.06) to increase (46%) normal feces frequency, decreased (P < 0.05) goblet cells count (104.3 vs. 118.1) in the jejunum, and decreased (P < 0.05) small intestine (4.60% vs. 4.93%) and colon (1.41% vs. 1.65%) relative weights, compared with pigs not fed with the alternative additive. There was a tendency (P = 0.09) for a lower concentration of Escherichia-Shigella (1.46% vs. 3.5%) and lower (P < 0.05) percentage of Campylobacter (0.52% vs. 10.21%) in the cecum content of piglets fed diets containing essential oils and benzoic acid compared with pigs fed diets without the alternative feed additive. The alternative feed additive was effective in improving growth performance, diets digestibility, and gut health in piglets soon after weaning.
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Affiliation(s)
- Cláudio D Silva Júnior
- Faculty of Agricultural and Technological Sciences, São Paulo State University, Dracena, SP, Brazil
| | | | | | | | | | - José E Moraes
- Institute of Animal Science and Pastures, Nova Odessa, SP, Brazil
| | | | - Fábio E L Budiño
- Institute of Animal Science and Pastures, Nova Odessa, SP, Brazil
| | - Rafaela Pereira
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Polyana Tizioto
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
- NGS Soluções Genômicas, Piracicaba, SP, Brazil
| | - Vinicius R C Paula
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Luiz L Coutinho
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Urbano S Ruiz
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
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Ueno H, Tsutsuura S, Inoue A, Murata M. Bactericidal Effects of Coffee and Chlorogenic Acid on Escherichia coli and Salmonella spp. under Low pH or Gastric Acid Conditions. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2020. [DOI: 10.3136/fstr.26.247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Hiroko Ueno
- Department of Nutrition and Food Science, Ochanomizu University
| | - Satomi Tsutsuura
- Department of Nutrition and Food Science, Ochanomizu University
- Institute for Research Promotion, Niigata University
| | - Aoi Inoue
- Department of Nutrition and Food Science, Ochanomizu University
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A Brief Review on the Non-protein Amino Acid, Gamma-amino Butyric Acid (GABA): Its Production and Role in Microbes. Curr Microbiol 2019; 77:534-544. [PMID: 31844936 DOI: 10.1007/s00284-019-01839-w] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/03/2019] [Indexed: 12/26/2022]
Abstract
Gamma-Aminobutyric acid (GABA) is a non-protein amino acid widely distributed in nature. It is produced through irreversible α-decarboxylation of glutamate by enzyme glutamate decarboxylase (GAD). GABA and GAD have been found in plants, animals, and microorganisms. GABA is distributed throughout the human body and it is involved in the regulation of cardiovascular conditions such as blood pressure and heart rate, and plays a role in the reduction of anxiety and pain. Although researchers had produced GABA by chemical method earlier it became less acceptable as it pollutes the environment. Researchers now use a more promising microbial method for the production of GABA. In the drug and food industry, demand for GABA is immense. So, large scale conversion of GABA by microbes has got much attention. So this review focuses on the isolation source, production, and functions of GABA in the microbial system. We also summarize the mechanism of action of GABA and its shunt pathway.
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Ribeiro da Cunha B, Fonseca LP, Calado CRC. A phenotypic screening bioassay for Escherichia coli stress and antibiotic responses based on Fourier-transform infrared (FTIR) spectroscopy and multivariate analysis. J Appl Microbiol 2019; 127:1776-1789. [PMID: 31464358 DOI: 10.1111/jam.14429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 08/21/2019] [Accepted: 08/21/2019] [Indexed: 12/22/2022]
Abstract
AIMS To develop and optimize a Fourier-transform infrared spectroscopy (FTIRS) phenotypic screening bioassay for stress responses, regarding the effect of nutrient content, bacterial growth phase and stress agent exposure time. METHODS AND RESULTS A high-throughput FTIRS bioassay was developed to distinguish the stress responses of Escherichia coli to sodium hydroxide, hydrochloric acid, sodium chloride, sodium hypochlorite and ethanol. Principal component analysis and hierarchical clustering were used to quantify the effect of each parameter on bioassay performance, namely its reproducibility and metabolic resolution. Bioassay performance varied greatly, ranging from poor to very good. Spectra were partitioned into biologically relevant regions to evaluate their contributions to bioassay performance, but further improvements were not observed. Bioassay optimization was validated against empirical parameters, which confirmed a closer representation of known mechanisms on the antibiotic-induced stress responses. CONCLUSIONS The optimized bioassay used standard nutrient content, cells in the late-stationary growth phase and a one-shift exposure duration. Only the optimized bioassay adequately and reproducibly distinguished the E. coli stress and antibiotic responses. The absence of performance improvements using partitioned spectra indicated that stress responses are imprinted on the whole-spectra metabolic signature. SIGNIFICANCE AND IMPACT OF THE STUDY Highly optimized FTIRS bioassay parameters are vital in capturing whole-spectra metabolic signatures that can be used for satisfactory and reproducible phenotypic screening of stress and antibiotic responses.
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Affiliation(s)
- B Ribeiro da Cunha
- iBB - Institute of Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, Lisboa, Portugal.,ISEL - Instituto Superior de Engenharia de Lisboa (ISEL), Instituto Politécnico de Lisboa (IPL), Lisboa, Portugal
| | - L P Fonseca
- iBB - Institute of Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, Lisboa, Portugal
| | - C R C Calado
- ISEL - Instituto Superior de Engenharia de Lisboa (ISEL), Instituto Politécnico de Lisboa (IPL), Lisboa, Portugal
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29
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Cryan JF, O'Riordan KJ, Cowan CSM, Sandhu KV, Bastiaanssen TFS, Boehme M, Codagnone MG, Cussotto S, Fulling C, Golubeva AV, Guzzetta KE, Jaggar M, Long-Smith CM, Lyte JM, Martin JA, Molinero-Perez A, Moloney G, Morelli E, Morillas E, O'Connor R, Cruz-Pereira JS, Peterson VL, Rea K, Ritz NL, Sherwin E, Spichak S, Teichman EM, van de Wouw M, Ventura-Silva AP, Wallace-Fitzsimons SE, Hyland N, Clarke G, Dinan TG. The Microbiota-Gut-Brain Axis. Physiol Rev 2019; 99:1877-2013. [DOI: 10.1152/physrev.00018.2018] [Citation(s) in RCA: 1243] [Impact Index Per Article: 248.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The importance of the gut-brain axis in maintaining homeostasis has long been appreciated. However, the past 15 yr have seen the emergence of the microbiota (the trillions of microorganisms within and on our bodies) as one of the key regulators of gut-brain function and has led to the appreciation of the importance of a distinct microbiota-gut-brain axis. This axis is gaining ever more traction in fields investigating the biological and physiological basis of psychiatric, neurodevelopmental, age-related, and neurodegenerative disorders. The microbiota and the brain communicate with each other via various routes including the immune system, tryptophan metabolism, the vagus nerve and the enteric nervous system, involving microbial metabolites such as short-chain fatty acids, branched chain amino acids, and peptidoglycans. Many factors can influence microbiota composition in early life, including infection, mode of birth delivery, use of antibiotic medications, the nature of nutritional provision, environmental stressors, and host genetics. At the other extreme of life, microbial diversity diminishes with aging. Stress, in particular, can significantly impact the microbiota-gut-brain axis at all stages of life. Much recent work has implicated the gut microbiota in many conditions including autism, anxiety, obesity, schizophrenia, Parkinson’s disease, and Alzheimer’s disease. Animal models have been paramount in linking the regulation of fundamental neural processes, such as neurogenesis and myelination, to microbiome activation of microglia. Moreover, translational human studies are ongoing and will greatly enhance the field. Future studies will focus on understanding the mechanisms underlying the microbiota-gut-brain axis and attempt to elucidate microbial-based intervention and therapeutic strategies for neuropsychiatric disorders.
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Affiliation(s)
- John F. Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Kenneth J. O'Riordan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Caitlin S. M. Cowan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Kiran V. Sandhu
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Thomaz F. S. Bastiaanssen
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Marcus Boehme
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Martin G. Codagnone
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Sofia Cussotto
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Christine Fulling
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Anna V. Golubeva
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Katherine E. Guzzetta
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Minal Jaggar
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Caitriona M. Long-Smith
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Joshua M. Lyte
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Jason A. Martin
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Alicia Molinero-Perez
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Gerard Moloney
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Emanuela Morelli
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Enrique Morillas
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Rory O'Connor
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Joana S. Cruz-Pereira
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Veronica L. Peterson
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Kieran Rea
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Nathaniel L. Ritz
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Eoin Sherwin
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Simon Spichak
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Emily M. Teichman
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Marcel van de Wouw
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Ana Paula Ventura-Silva
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Shauna E. Wallace-Fitzsimons
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Niall Hyland
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Gerard Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Timothy G. Dinan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
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Key J, Kohli A, Bárcena C, López-Otín C, Heidler J, Wittig I, Auburger G. Global Proteome of LonP1+/- Mouse Embryonal Fibroblasts Reveals Impact on Respiratory Chain, but No Interdependence between Eral1 and Mitoribosomes. Int J Mol Sci 2019; 20:E4523. [PMID: 31547314 PMCID: PMC6770551 DOI: 10.3390/ijms20184523] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/02/2019] [Accepted: 09/09/2019] [Indexed: 12/11/2022] Open
Abstract
Research on healthy aging shows that lifespan reductions are often caused by mitochondrial dysfunction. Thus, it is very interesting that the deletion of mitochondrial matrix peptidase LonP1 was observed to abolish embryogenesis, while deletion of the mitochondrial matrix peptidase Caseinolytic Mitochondrial Matrix Peptidase Proteolytic Subunit (ClpP) prolonged survival. To unveil the targets of each enzyme, we documented the global proteome of LonP1+/- mouse embryonal fibroblasts (MEF), for comparison with ClpP-/- depletion. Proteomic profiles of LonP1+/- MEF generated by label-free mass spectrometry were further processed with the STRING (Search tool for the retrieval of interacting genes) webserver Heidelberg for protein interactions. ClpP was previously reported to degrade Eral1 as a chaperone involved in mitoribosome assembly, so ClpP deficiency triggers the accumulation of mitoribosomal subunits and inefficient translation. LonP1+/- MEF also showed Eral1 accumulation, but no systematic effect on mitoribosomal subunits. In contrast to ClpP-/- profiles, several components of the respiratory complex-I membrane arm, of the glutathione pathway and of lysosomes were accumulated, whereas the upregulation of numerous innate immune defense components was similar. Overall, LonP1, as opposed to ClpP, appears to have no effect on translational machinery, instead it shows enhanced respiratory dysfunction; this agrees with reports on the human CODAS syndrome (syndrome with cerebral, ocular, dental, auricular, and skeletal anomalies) caused by LonP1 mutations.
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Affiliation(s)
- Jana Key
- Experimental Neurology, Goethe University Medical School, 60590 Frankfurt am Main, Germany.
| | - Aneesha Kohli
- Experimental Neurology, Goethe University Medical School, 60590 Frankfurt am Main, Germany.
| | - Clea Bárcena
- Departamento de Bioquimica y Biologia Molecular, Facultad de Medicina, Instituto Universitario de Oncologia (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain.
| | - Carlos López-Otín
- Departamento de Bioquimica y Biologia Molecular, Facultad de Medicina, Instituto Universitario de Oncologia (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain.
| | - Juliana Heidler
- Functional Proteomics Group, Goethe-University Hospital, 60590 Frankfurt am Main, Germany.
| | - Ilka Wittig
- Functional Proteomics Group, Goethe-University Hospital, 60590 Frankfurt am Main, Germany.
| | - Georg Auburger
- Experimental Neurology, Goethe University Medical School, 60590 Frankfurt am Main, Germany.
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Xu Z, Wang C, Dong X, Hu T, Wang L, Zhao W, Zhu S, Li G, Hu Y, Gao Q, Wan J, Liu Z, Sun J. Chronic alcohol exposure induced gut microbiota dysbiosis and its correlations with neuropsychic behaviors and brain BDNF/Gabra1 changes in mice. Biofactors 2019; 45:187-199. [PMID: 30417952 DOI: 10.1002/biof.1469] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/26/2018] [Indexed: 12/14/2022]
Abstract
Alcohol addiction can cause brain dysfunction and many other diseases. Recently, increasing evidences have suggested that gut microbiota plays a vital role in regulating alcohol addiction. However, the exact mechanism has not yet been elucidated. Here, our study focused on the intestinal bacteria alternations and their correlations with alcohol-induced neuropsychic behaviors. When consuming alcohol over 3-week period, animals gradually displayed anxiety/depression-like behaviors. Moreover, 16S rRNA sequencing showed significant intestinal microflora dysbiosis and distinct community composition. Actinobacteria and Cyanobacteria were both increased at the phylum level. At the genus level, Adlercreutzia spp., Allobaculum spp., and Turicibacter spp. were increased whereas Helicobacter spp. was decreased. We also found that the distances in inner zone measured by open field test and 4% (v/v) alcohol preference percentages were significantly correlated with Adlercreutzia spp. The possible mechanisms were explored and we found the expression of brain-derived neurotrophic factor (BDNF) and α1 subunit of γ-aminobutyric acid A receptor (Gabra1) were both decreased in prefrontal cortex (PFC). Especially, further correlation analyses demonstrated that decreased Adlercreutzia spp. was positively correlated with alcohol preference and negatively correlated with anxiety-like behavior and BDNF/Gabra1 changes in PFC. Similar relationships were observed between Allobaculum spp. and alcohol preference and BDNF changes. Helicobacter spp. and Turicibacter spp. were also correlated with PFC BDNF and hippocampus Gabra1 level. Taken together, our study showed that gut microbiota dysbiosis during chronic alcohol exposure was closely correlated with alcohol-induced neuropsychic behaviors and BDNF/Gabra1 expression, which provides a new perspective for understanding underlying mechanisms in alcohol addiction. © 2018 BioFactors, 45(2):187-199, 2019.
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Affiliation(s)
- Zheng Xu
- Department of Anatomy, Shandong University School of Basic medicine, Jinan, Shandong, China
| | - Can Wang
- School of Medicine, Lanzhou University, Lanzhou, Gansu, China
| | - Xiaoguang Dong
- Department of Orthopedic, Osteological Hospital of Yishengjian, Qingdao, Shandong, China
| | - Tao Hu
- Department of Orthopedic, Osteological Hospital of Yishengjian, Qingdao, Shandong, China
| | - Lingling Wang
- Department of Hematology, School of Nursing Shandong University, Jinan, Shandong, China
| | - Wenbo Zhao
- Department of Anatomy, Shandong University School of Basic medicine, Jinan, Shandong, China
| | - Shaowei Zhu
- Department of Anatomy, Shandong University School of Basic medicine, Jinan, Shandong, China
| | - Guibao Li
- Department of Anatomy, Shandong University School of Basic medicine, Jinan, Shandong, China
| | - Yanlai Hu
- Department of Anatomy, Shandong University School of Basic medicine, Jinan, Shandong, China
| | - Qing Gao
- Department of Anatomy, Shandong University School of Basic medicine, Jinan, Shandong, China
| | - Jiale Wan
- Department of Anatomy, Shandong University School of Basic medicine, Jinan, Shandong, China
| | - Zengxun Liu
- Department of Anatomy, Shandong University School of Basic medicine, Jinan, Shandong, China
| | - Jinhao Sun
- Department of Anatomy, Shandong University School of Basic medicine, Jinan, Shandong, China
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Król JE. Regulatory loop between the CsrA system and NhaR, a high salt/high pH regulator. PLoS One 2018; 13:e0209554. [PMID: 30589862 PMCID: PMC6307784 DOI: 10.1371/journal.pone.0209554] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 12/07/2018] [Indexed: 11/24/2022] Open
Abstract
In E. coli, under high pH/high salt conditions, a major Na+/H+ antiporter (NhaA) is activated to maintain an internal pH level. Its expression is induced by a specific regulator NhaR, which is also responsible for osmC and pgaA regulation. Here I report that the NhaR regulator affects the carbon storage regulatory Csr system. I found that the expression of all major components of the Csr system-CsrA regulator, CsrB and CsrC small RNAs, and the CsrB and CsrC stability were indirectly affected by nhaR mutation under stress conditions. Using a combination of experimental and in silico analyses, I concluded that the mechanism of regulation included direct and indirect activation of a two-component system (TCS) response regulator-UvrY. NhaR regulation involved interactions with the regulators H-NS and SdiA and was affected by a naturally occurring spontaneous IS5 insertion in the promoter region. A regulatory circuit was proposed and discussed.
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Affiliation(s)
- Jarosław E. Król
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
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Khaleque HN, Shafique R, Kaksonen AH, Boxall NJ, Watkin EL. Quantitative proteomics using SWATH-MS identifies mechanisms of chloride tolerance in the halophilic acidophile Acidihalobacter prosperus DSM 14174. Res Microbiol 2018; 169:638-648. [DOI: 10.1016/j.resmic.2018.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 02/08/2023]
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Lombardi VC, De Meirleir KL, Subramanian K, Nourani SM, Dagda RK, Delaney SL, Palotás A. Nutritional modulation of the intestinal microbiota; future opportunities for the prevention and treatment of neuroimmune and neuroinflammatory disease. J Nutr Biochem 2018; 61:1-16. [PMID: 29886183 PMCID: PMC6195483 DOI: 10.1016/j.jnutbio.2018.04.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 04/11/2018] [Accepted: 04/13/2018] [Indexed: 01/09/2023]
Abstract
The gut-brain axis refers to the bidirectional communication between the enteric nervous system and the central nervous system. Mounting evidence supports the premise that the intestinal microbiota plays a pivotal role in its function and has led to the more common and perhaps more accurate term gut-microbiota-brain axis. Numerous studies have identified associations between an altered microbiome and neuroimmune and neuroinflammatory diseases. In most cases, it is unknown if these associations are cause or effect; notwithstanding, maintaining or restoring homeostasis of the microbiota may represent future opportunities when treating or preventing these diseases. In recent years, several studies have identified the diet as a primary contributing factor in shaping the composition of the gut microbiota and, in turn, the mucosal and systemic immune systems. In this review, we will discuss the potential opportunities and challenges with respect to modifying and shaping the microbiota through diet and nutrition in order to treat or prevent neuroimmune and neuroinflammatory disease.
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Affiliation(s)
- Vincent C Lombardi
- Nevada Center for Biomedical Research, University of Nevada, Reno, 1664 N. Virginia St. MS 0552, Reno, NV, 89557, USA; University of Nevada, Reno, School of Medicine, Department of Pathology, 1664 N. Virginia St. MS 0357, Reno, NV, 89557, USA.
| | - Kenny L De Meirleir
- Nevada Center for Biomedical Research, University of Nevada, Reno, 1664 N. Virginia St. MS 0552, Reno, NV, 89557, USA.
| | - Krishnamurthy Subramanian
- Nevada Center for Biomedical Research, University of Nevada, Reno, 1664 N. Virginia St. MS 0552, Reno, NV, 89557, USA.
| | - Sam M Nourani
- University of Nevada, Reno, School of Medicine, Department of Internal Medicine, 1664 N. Virginia St. MS 0357, Reno, NV, 89557, USA; Advanced Therapeutic, General Gastroenterology & Hepatology Digestive Health Associates, Reno, NV, USA.
| | - Ruben K Dagda
- University of Nevada, Reno, School of Medicine, Department of Pharmacology, 1664 N. Virginia St. MS 0318, Reno, NV, 89557, USA.
| | | | - András Palotás
- Kazan Federal University, Institute of Fundamental Medicine and Biology, (Volga Region) 18 Kremlyovskaya St., Kazan, 420008, Republic of Tatarstan, Russian Federation; Asklepios-Med (private medical practice and research center), Kossuth Lajos sgt. 23, Szeged, H-6722, Hungary.
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Stress Resistance Development and Genome-Wide Transcriptional Response of Escherichia coli O157:H7 Adapted to Sublethal Thymol, Carvacrol, and trans-Cinnamaldehyde. Appl Environ Microbiol 2018; 84:AEM.01616-18. [PMID: 30217837 DOI: 10.1128/aem.01616-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/02/2018] [Indexed: 01/05/2023] Open
Abstract
Thymol, carvacrol, and trans-cinnamaldehyde are essential oil (EO) compounds with broad-spectrum antimicrobial activities against foodborne pathogens, including Escherichia coli O157:H7. However, little is known regarding direct resistance and cross-resistance development in E. coli O157:H7 after adaptation to sublethal levels of these compounds, and information is scarce on microbial adaptive responses at a molecular level. The present study demonstrated that E. coli O157:H7 was able to grow in the presence of sublethal thymol (1/2T), carvacrol (1/2C), or trans-cinnamaldehyde (1/2TC), displaying an extended lag phase duration and a lower maximum growth rate. EO-adapted cells developed direct resistance against lethal EO treatments and cross-resistance against heat (58°C) and oxidative (50 mM H2O2) stresses. However, no induction of acid resistance (simulated gastric fluid, pH 1.5) was observed. RNA sequencing revealed a large number (310 to 338) of differentially expressed (adjusted P value [Padj ], <0.05; fold change, ≥5) genes in 1/2T and 1/2C cells, while 1/2TC cells only showed 27 genes with altered expression. In accordance with resistance phenotypes, the genes related to membrane, heat, and oxidative stress responses and genes related to iron uptake and metabolism were upregulated. Conversely, virulence genes associated with motility, biofilm formation, and efflux pumps were repressed. This study demonstrated the development of direct resistance and cross-resistance and characterized whole-genome transcriptional responses in E. coli O157:H7 adapted to sublethal thymol, carvacrol, or trans-cinnamaldehyde. The data suggested that caution should be exercised when using EO compounds as food antimicrobials, due to the potential stress resistance development in E. coli O157:H7.IMPORTANCE The present study was designed to understand transcriptomic changes and the potential development of direct and cross-resistance in essential oil (EO)-adapted Escherichia coli O157:H7. The results demonstrated altered growth behaviors of E. coli O157:H7 during adaptation in sublethal thymol, carvacrol, and trans-cinnamaldehyde. Generally, EO-adapted bacteria showed enhanced resistance against subsequent lethal EO, heat, and oxidative stresses, with no induction of acid resistance in simulated gastric fluid. A transcriptomic analysis revealed the upregulation of related stress resistance genes and a downregulation of various virulence genes in EO-adapted cells. This study provides new insights into microbial EO adaptation behaviors and highlights the risk of resistance development in adapted bacteria.
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Xu D, Zhang L. Metabolic engineering of Escherichia coli for agmatine production. Eng Life Sci 2018; 19:13-20. [PMID: 32624951 DOI: 10.1002/elsc.201800104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/07/2018] [Accepted: 09/25/2018] [Indexed: 01/03/2023] Open
Abstract
Agmatine is a kind of important biogenic amine. The chemical synthesis route is not a desirable choice for industrial production of agmatine. To date, there are no reports on the fermentative production of agmatine by microorganism. In this study, the base Escherichia coli strain AUX4 (JM109 ∆speC ∆speF ∆speB ∆argR) capable of excreting agmatine into the culture medium was first constructed by sequential deletions of the speC and speF genes encoding the ornithine decarboxylase isoenzymes, the speB gene encoding agmatine ureohydrolase and the regulation gene argR responsible for the negative control of the arg regulon. The speA gene encoding arginine decarboxylase harboured by the pKK223-3 plasmid was overexpressed in AUX4, resulting in the engineered strain AUX5. The batch and fed-batch fermentations of the AUX5 strain were conducted in a 3-L bioreactor, and the results showed that the AUX5 strain was able to produce 1.13 g agmatine L-1 with the yield of 0.11 g agmatine g-1 glucose in the batch fermentation and the fed-batch fermentation of AUX5 allowed the production of 15.32 g agmatine L-1 with the productivity of 0.48 g agmatine L-1 h-1, demonstrating the potential of E. coli as an industrial producer of agmatine.
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Affiliation(s)
- Daqing Xu
- College of Life Sciences Hebei Agricultural University Baoding P. R. China
| | - Lirong Zhang
- College of Plant Protection Hebei Agricultural University Baoding P. R. China
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Zhao H, Zhou F, Xing Q, Cao Z, Liu J, Zhu G. The soluble transhydrogenase UdhA affecting the glutamate-dependent acid resistance system of Escherichia coli under acetate stress. Biol Open 2018; 7:7/9/bio031856. [PMID: 30201831 PMCID: PMC6176936 DOI: 10.1242/bio.031856] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The soluble transhydrogenase (UdhA) is one of two transhydrogenases that play a role in maintaining the balance between NAD(H) pools and NADP(H) pools in Escherichia coli. Although UdhA has been extensively used in metabolic engineering and biocatalysis for cofactor regeneration, its role in acid resistance has not been reported. Here we used DNA microarray to explore the impact of UdhA on transcript levels. We demonstrated that during growth on acetate, the expression of genes involved in the respiratory chain and Gad acid resistance system was inhibited in the udhA-knockout strain. The deletion of udhA significantly repressed the expression of six genes (gadA, gadB, gadC, gadE, hdeA and hdeB) which are involved in Gad acid resistance and resulted in low survival of the bacterium at a low pH of 4.9. Moreover, UdhA was essential for NADH production which is important for the adaptive growth of E. coli on acetate, while NADH concentration in the udhA-knockout strain was quite low and supplemental NADH significantly increased the expression of acid resistance genes and survival of the udhA-knockout strain. These results demonstrated that UdhA is an important source of NADH of E. coli growth on acetate and affects Gad acid resistance system under acetate stress. Summary: UdhA function stated in this study helps us to understand the physiological roles of UdhA affecting NADH production and Gad acid resistance system in E.coli in acetate environment.
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Affiliation(s)
- Hanjun Zhao
- The Research Center of Life Omics and Health, College of Life Sciences, Anhui Normal University, No.1 Beijing East Road, Wuhu 241000, Anhui, China
| | - Feng Zhou
- The Research Center of Life Omics and Health, College of Life Sciences, Anhui Normal University, No.1 Beijing East Road, Wuhu 241000, Anhui, China
| | - Quan Xing
- The Research Center of Life Omics and Health, College of Life Sciences, Anhui Normal University, No.1 Beijing East Road, Wuhu 241000, Anhui, China
| | - Zhengyu Cao
- The Research Center of Life Omics and Health, College of Life Sciences, Anhui Normal University, No.1 Beijing East Road, Wuhu 241000, Anhui, China
| | - Jie Liu
- The Research Center of Life Omics and Health, College of Life Sciences, Anhui Normal University, No.1 Beijing East Road, Wuhu 241000, Anhui, China
| | - Guoping Zhu
- The Research Center of Life Omics and Health, College of Life Sciences, Anhui Normal University, No.1 Beijing East Road, Wuhu 241000, Anhui, China
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Short-Chain Fatty Acids Alter Metabolic and Virulence Attributes of Borrelia burgdorferi. Infect Immun 2018; 86:IAI.00217-18. [PMID: 29891543 DOI: 10.1128/iai.00217-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 06/06/2018] [Indexed: 12/22/2022] Open
Abstract
Borrelia burgdorferi responds to a variety of host-derived factors and appropriately alters its gene expression for adaptation under different host-specific conditions. We previously showed that various levels of acetate, a short-chain fatty acid (SCFA), altered the protein profile of B. burgdorferi In this study, we determined the effects of other physiologically relevant SCFAs in the regulation of metabolic/virulence-associated proteins using mutant borrelial strains. No apparent increase in the synthesis of outer surface protein C (OspC) was noted when a carbon storage regulator A (csrA of B. burgdorferi, or csrABb ) mutant (mt) was propagated within dialysis membrane chambers implanted within rat peritoneal cavity, while the parental wild type (wt; B31-A3 strain) and csrABb cis-complemented strain (ct) had increased OspC with a reciprocal reduction in OspA levels. Growth rates of wt, mt, ct, 7D (csrABb mutant lacking 7 amino acids at the C terminus), and 8S (csrABb with site-specific changes altering its RNA-binding properties) borrelial strains were similar in the presence of acetate. Increased levels of propionate and butyrate reduced the growth rates of all strains tested, with mt and 8S exhibiting profound growth deficits at higher concentrations of propionate. Transcriptional levels of rpoS and ospC were elevated on supplementation of SCFAs compared to those of untreated spirochetes. Immunoblot analysis revealed elevated levels of RpoS, OspC, and DbpA with increased levels of SCFAs. Physiological levels of SCFAs prevalent in select human and rodent fluids were synergistic with mammalian host temperature and pH to increase the levels of aforementioned proteins, which could impact the colonization of B. burgdorferi during the mammalian phase of infection.
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Braun HS, Sponder G, Aschenbach JR, Kerner K, Bauerfeind R, Deiner C. The GadX regulon affects virulence gene expression and adhesion of porcine enteropathogenic Escherichia coli in vitro. Vet Anim Sci 2017; 3:10-17. [PMID: 32734036 PMCID: PMC7386710 DOI: 10.1016/j.vas.2017.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 02/19/2017] [Accepted: 04/26/2017] [Indexed: 12/31/2022] Open
Abstract
The ability of enteropathogenic Escherichia coli (EPEC) to express virulence factor genes and develop attaching and effacing (AE) lesions is inhibited in acidic environmental conditions. This inhibition is due to the activation of transcription factor GadX, which upregulates expression of glutamic acid decarboxylase (Gad). Gad, in turn, produces γ-aminobutyric acid (GABA), which was recently shown to have a beneficial effect on the jejunal epithelium in vitro due to increased mucin-1 levels. In the present study, we sought to test whether forced GadX activation/overexpression abolishes virulence associated features of EPEC and provokes increased GABA production. EPEC strains were isolated from diarrheic pigs and submitted to activation of GadX by acidification as well as gadX overexpression via an inducible expression vector plasmid. GABA concentrations in the growth medium, ability for adhesion to porcine intestinal epithelial cells (IPEC-J2) and virulence gene expression were determined. Growth in acidified media led to increased GABA levels, upregulated gadA/B expression and downregulated mRNA synthesis of the bacterial adhesin intimin. EPEC strains transformed with the gadX gene produced 2.1–3.4-fold higher GABA levels than empty-vector controls and completely lost their ability to adhere to IPEC-J2 cells and to induce actin accumulation. We conclude that intensified gadX activation can abolish the ability of EPEC to adhere to the intestinal epithelium by reducing the expression of major virulence genes.
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Affiliation(s)
- Hannah-Sophie Braun
- Institute of Veterinary Physiology, Freie Universität Berlin, Oertzenweg 19b, 14163 Berlin, Germany
- Corresponding author.
| | - Gerhard Sponder
- Institute of Veterinary Physiology, Freie Universität Berlin, Oertzenweg 19b, 14163 Berlin, Germany
| | - Jörg R. Aschenbach
- Institute of Veterinary Physiology, Freie Universität Berlin, Oertzenweg 19b, 14163 Berlin, Germany
| | - Katharina Kerner
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University, Frankfurter Strasse 85-89, 35392 Gießen, Germany
| | - Rolf Bauerfeind
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University, Frankfurter Strasse 85-89, 35392 Gießen, Germany
| | - Carolin Deiner
- Institute of Veterinary Physiology, Freie Universität Berlin, Oertzenweg 19b, 14163 Berlin, Germany
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Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12. J Bacteriol 2017; 199:JB.00755-16. [PMID: 28115545 DOI: 10.1128/jb.00755-16] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/12/2017] [Indexed: 01/31/2023] Open
Abstract
The alternative sigma factor RpoS is a central regulator of many stress responses in Escherichia coli The level of functional RpoS differs depending on the stress. The effect of these differing concentrations of RpoS on global transcriptional responses remains unclear. We investigated the effect of RpoS concentration on the transcriptome during stationary phase in rich media. We found that 23% of genes in the E. coli genome are regulated by RpoS, and we identified many RpoS-transcribed genes and promoters. We observed three distinct classes of response to RpoS by genes in the regulon: genes whose expression changes linearly with increasing RpoS level, genes whose expression changes dramatically with the production of only a little RpoS ("sensitive" genes), and genes whose expression changes very little with the production of a little RpoS ("insensitive"). We show that sequences outside the core promoter region determine whether an RpoS-regulated gene is sensitive or insensitive. Moreover, we show that sensitive and insensitive genes are enriched for specific functional classes and that the sensitivity of a gene to RpoS corresponds to the timing of induction as cells enter stationary phase. Thus, promoter sensitivity to RpoS is a mechanism to coordinate specific cellular processes with growth phase and may also contribute to the diversity of stress responses directed by RpoS.IMPORTANCE The sigma factor RpoS is a global regulator that controls the response to many stresses in Escherichia coli Different stresses result in different levels of RpoS production, but the consequences of this variation are unknown. We describe how changing the level of RpoS does not influence all RpoS-regulated genes equally. The cause of this variation is likely the action of transcription factors that bind the promoters of the genes. We show that the sensitivity of a gene to RpoS levels explains the timing of expression as cells enter stationary phase and that genes with different RpoS sensitivities are enriched for specific functional groups. Thus, promoter sensitivity to RpoS is a mechanism that coordinates specific cellular processes in response to stresses.
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Shewaramani S, Finn TJ, Leahy SC, Kassen R, Rainey PB, Moon CD. Anaerobically Grown Escherichia coli Has an Enhanced Mutation Rate and Distinct Mutational Spectra. PLoS Genet 2017; 13:e1006570. [PMID: 28103245 PMCID: PMC5289635 DOI: 10.1371/journal.pgen.1006570] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 02/02/2017] [Accepted: 01/04/2017] [Indexed: 12/21/2022] Open
Abstract
Oxidative stress is a major cause of mutation but little is known about how growth in the absence of oxygen impacts the rate and spectrum of mutations. We employed long-term mutation accumulation experiments to directly measure the rates and spectra of spontaneous mutation events in Escherichia coli populations propagated under aerobic and anaerobic conditions. To detect mutations, whole genome sequencing was coupled with methods of analysis sufficient to identify a broad range of mutational classes, including structural variants (SVs) generated by movement of repetitive elements. The anaerobically grown populations displayed a mutation rate nearly twice that of the aerobic populations, showed distinct asymmetric mutational strand biases, and greater insertion element activity. Consistent with mutation rate and spectra observations, genes for transposition and recombination repair associated with SVs were up-regulated during anaerobic growth. Together, these results define differences in mutational spectra affecting the evolution of facultative anaerobes.
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Affiliation(s)
- Sonal Shewaramani
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Thomas J. Finn
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Sinead C. Leahy
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Rees Kassen
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Paul B. Rainey
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI ParisTech), CNRS UMR 8231, PSL Research University, Paris, France
| | - Christina D. Moon
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
- * E-mail:
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Aquino P, Honda B, Jaini S, Lyubetskaya A, Hosur K, Chiu JG, Ekladious I, Hu D, Jin L, Sayeg MK, Stettner AI, Wang J, Wong BG, Wong WS, Alexander SL, Ba C, Bensussen SI, Bernstein DB, Braff D, Cha S, Cheng DI, Cho JH, Chou K, Chuang J, Gastler DE, Grasso DJ, Greifenberger JS, Guo C, Hawes AK, Israni DV, Jain SR, Kim J, Lei J, Li H, Li D, Li Q, Mancuso CP, Mao N, Masud SF, Meisel CL, Mi J, Nykyforchyn CS, Park M, Peterson HM, Ramirez AK, Reynolds DS, Rim NG, Saffie JC, Su H, Su WR, Su Y, Sun M, Thommes MM, Tu T, Varongchayakul N, Wagner TE, Weinberg BH, Yang R, Yaroslavsky A, Yoon C, Zhao Y, Zollinger AJ, Stringer AM, Foster JW, Wade J, Raman S, Broude N, Wong WW, Galagan JE. Coordinated regulation of acid resistance in Escherichia coli. BMC SYSTEMS BIOLOGY 2017; 11:1. [PMID: 28061857 PMCID: PMC5217608 DOI: 10.1186/s12918-016-0376-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 12/07/2016] [Indexed: 12/29/2022]
Abstract
Background Enteric Escherichia coli survives the highly acidic environment of the stomach through multiple acid resistance (AR) mechanisms. The most effective system, AR2, decarboxylates externally-derived glutamate to remove cytoplasmic protons and excrete GABA. The first described system, AR1, does not require an external amino acid. Its mechanism has not been determined. The regulation of the multiple AR systems and their coordination with broader cellular metabolism has not been fully explored. Results We utilized a combination of ChIP-Seq and gene expression analysis to experimentally map the regulatory interactions of four TFs: nac, ntrC, ompR, and csiR. Our data identified all previously in vivo confirmed direct interactions and revealed several others previously inferred from gene expression data. Our data demonstrate that nac and csiR directly modulate AR, and leads to a regulatory network model in which all four TFs participate in coordinating acid resistance, glutamate metabolism, and nitrogen metabolism. This model predicts a novel mechanism for AR1 by which the decarboxylation enzymes of AR2 are used with internally derived glutamate. This hypothesis makes several testable predictions that we confirmed experimentally. Conclusions Our data suggest that the regulatory network underlying AR is complex and deeply interconnected with the regulation of GABA and glutamate metabolism, nitrogen metabolism. These connections underlie and experimentally validated model of AR1 in which the decarboxylation enzymes of AR2 are used with internally derived glutamate. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0376-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patricia Aquino
- Department of Biomedical Engineering, Boston University, Boston, USA.,BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Brent Honda
- Department of Biomedical Engineering, Boston University, Boston, USA
| | - Suma Jaini
- Department of Biomedical Engineering, Boston University, Boston, USA
| | | | - Krutika Hosur
- Department of Biomedical Engineering, Boston University, Boston, USA.,BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Joanna G Chiu
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Iriny Ekladious
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Dongjian Hu
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Lin Jin
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Marianna K Sayeg
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Arion I Stettner
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Julia Wang
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Brandon G Wong
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Winnie S Wong
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | | | - Cong Ba
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Seth I Bensussen
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - David B Bernstein
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Dana Braff
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Susie Cha
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Daniel I Cheng
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Jang Hwan Cho
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Kenny Chou
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - James Chuang
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Daniel E Gastler
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Daniel J Grasso
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | | | - Chen Guo
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Anna K Hawes
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Divya V Israni
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Saloni R Jain
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Jessica Kim
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Junyu Lei
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Hao Li
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - David Li
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Qian Li
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | | | - Ning Mao
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Salwa F Masud
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Cari L Meisel
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Jing Mi
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | | | - Minhee Park
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Hannah M Peterson
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Alfred K Ramirez
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Daniel S Reynolds
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Nae Gyune Rim
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Jared C Saffie
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Hang Su
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Wendell R Su
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Yaqing Su
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Meng Sun
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Meghan M Thommes
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Tao Tu
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | | | - Tyler E Wagner
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | | | - Rouhui Yang
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | | | - Christine Yoon
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | - Yanyu Zhao
- BE605 Course, Biomedical Engineering, Boston University, Boston, USA
| | | | - Anne M Stringer
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - John W Foster
- Department of Microbiology and Immunology, University of South Alabama College of Medicine, Mobile, AL, 36688, USA
| | - Joseph Wade
- Wadsworth Center, New York State Department of Health, Albany, NY, USA.,Department of Biomedical Sciences, University at Albany, Albany, NY, USA
| | - Sahadaven Raman
- Department of Microbiology and Immunology, University of South Alabama College of Medicine, Mobile, AL, 36688, USA
| | - Natasha Broude
- Department of Biomedical Engineering, Boston University, Boston, USA
| | - Wilson W Wong
- Department of Biomedical Engineering, Boston University, Boston, USA
| | - James E Galagan
- Department of Biomedical Engineering, Boston University, Boston, USA. .,Bioinformatics program, Boston University, Boston, USA. .,National Emerging Infectious Diseases Laboratory, Boston University, Boston, USA.
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44
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Mazzoli R, Pessione E. The Neuro-endocrinological Role of Microbial Glutamate and GABA Signaling. Front Microbiol 2016; 7:1934. [PMID: 27965654 PMCID: PMC5127831 DOI: 10.3389/fmicb.2016.01934] [Citation(s) in RCA: 204] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 11/17/2016] [Indexed: 12/11/2022] Open
Abstract
Gut microbiota provides the host with multiple functions (e.g., by contributing to food digestion, vitamin supplementation, and defense against pathogenic strains) and interacts with the host organism through both direct contact (e.g., through surface antigens) and soluble molecules, which are produced by the microbial metabolism. The existence of the so-called gut–brain axis of bi-directional communication between the gastrointestinal tract and the central nervous system (CNS) also supports a communication pathway between the gut microbiota and neural circuits of the host, including the CNS. An increasing body of evidence has shown that gut microbiota is able to modulate gut and brain functions, including the mood, cognitive functions, and behavior of humans. Nonetheless, given the extreme complexity of this communication network, its comprehension is still at its early stage. The present contribution will attempt to provide a state-of-the art description of the mechanisms by which gut microbiota can affect the gut–brain axis and the multiple cellular and molecular communication circuits (i.e., neural, immune, and humoral). In this context, special attention will be paid to the microbial strains that produce bioactive compounds and display ascertained or potential probiotic activity. Several neuroactive molecules (e.g., catecholamines, histamine, serotonin, and trace amines) will be considered, with special focus on Glu and GABA circuits, receptors, and signaling. From the basic science viewpoint, “microbial endocrinology” deals with those theories in which neurochemicals, produced by both multicellular organisms and prokaryotes (e.g., serotonin, GABA, glutamate), are considered as a common shared language that enables interkingdom communication. With regards to its application, research in this area opens the way toward the possibility of the future use of neuroactive molecule-producing probiotics as therapeutic agents for the treatment of neurogastroenteric and/or psychiatric disorders.
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Affiliation(s)
- Roberto Mazzoli
- Laboratory of Biochemistry, Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino Torino, Italy
| | - Enrica Pessione
- Laboratory of Biochemistry, Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino Torino, Italy
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45
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Duport C, Jobin M, Schmitt P. Adaptation in Bacillus cereus: From Stress to Disease. Front Microbiol 2016; 7:1550. [PMID: 27757102 PMCID: PMC5047918 DOI: 10.3389/fmicb.2016.01550] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/15/2016] [Indexed: 12/23/2022] Open
Abstract
Bacillus cereus is a food-borne pathogen that causes diarrheal disease in humans. After ingestion, B. cereus experiences in the human gastro-intestinal tract abiotic physical variables encountered in food, such as acidic pH in the stomach and changing oxygen conditions in the human intestine. B. cereus responds to environmental changing conditions (stress) by reversibly adjusting its physiology to maximize resource utilization while maintaining structural and genetic integrity by repairing and minimizing damage to cellular infrastructure. As reviewed in this article, B. cereus adapts to acidic pH and changing oxygen conditions through diverse regulatory mechanisms and then exploits its metabolic flexibility to grow and produce enterotoxins. We then focus on the intricate link between metabolism, redox homeostasis, and enterotoxins, which are recognized as important contributors of food-borne disease.
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Affiliation(s)
- Catherine Duport
- Sécurité et Qualité des Produits d'Origine Végétale, UMR0408, Avignon Université, Institut National de la Recherche Agronomique Avignon, France
| | - Michel Jobin
- Sécurité et Qualité des Produits d'Origine Végétale, UMR0408, Avignon Université, Institut National de la Recherche Agronomique Avignon, France
| | - Philippe Schmitt
- Sécurité et Qualité des Produits d'Origine Végétale, UMR0408, Avignon Université, Institut National de la Recherche Agronomique Avignon, France
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46
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Utturkar SM, Cude WN, Robeson MS, Yang ZK, Klingeman DM, Land ML, Allman SL, Lu TYS, Brown SD, Schadt CW, Podar M, Doktycz MJ, Pelletier DA. Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis. Appl Environ Microbiol 2016; 82:5698-708. [PMID: 27422831 PMCID: PMC5007785 DOI: 10.1128/aem.01285-16] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 07/07/2016] [Indexed: 12/11/2022] Open
Abstract
UNLABELLED Bacterial endophytes that colonize Populus trees contribute to nutrient acquisition, prime immunity responses, and directly or indirectly increase both above- and below-ground biomasses. Endophytes are embedded within plant material, so physical separation and isolation are difficult tasks. Application of culture-independent methods, such as metagenome or bacterial transcriptome sequencing, has been limited due to the predominance of DNA from the plant biomass. Here, we describe a modified differential and density gradient centrifugation-based protocol for the separation of endophytic bacteria from Populus roots. This protocol achieved substantial reduction in contaminating plant DNA, allowed enrichment of endophytic bacteria away from the plant material, and enabled single-cell genomics analysis. Four single-cell genomes were selected for whole-genome amplification based on their rarity in the microbiome (potentially uncultured taxa) as well as their inferred abilities to form associations with plants. Bioinformatics analyses, including assembly, contamination removal, and completeness estimation, were performed to obtain single-amplified genomes (SAGs) of organisms from the phyla Armatimonadetes, Verrucomicrobia, and Planctomycetes, which were unrepresented in our previous cultivation efforts. Comparative genomic analysis revealed unique characteristics of each SAG that could facilitate future cultivation efforts for these bacteria. IMPORTANCE Plant roots harbor a diverse collection of microbes that live within host tissues. To gain a comprehensive understanding of microbial adaptations to this endophytic lifestyle from strains that cannot be cultivated, it is necessary to separate bacterial cells from the predominance of plant tissue. This study provides a valuable approach for the separation and isolation of endophytic bacteria from plant root tissue. Isolated live bacteria provide material for microbiome sequencing, single-cell genomics, and analyses of genomes of uncultured bacteria to provide genomics information that will facilitate future cultivation attempts.
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Affiliation(s)
- Sagar M Utturkar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
| | - W Nathan Cude
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Michael S Robeson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Zamin K Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Dawn M Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Miriam L Land
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Steve L Allman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Tse-Yuan S Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Steven D Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Dale A Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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47
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Cowley LA, Dallman TJ, Fitzgerald S, Irvine N, Rooney PJ, McAteer SP, Day M, Perry NT, Bono JL, Jenkins C, Gally DL. Short-term evolution of Shiga toxin-producing Escherichia coli O157:H7 between two food-borne outbreaks. Microb Genom 2016; 2:e000084. [PMID: 28348875 PMCID: PMC5320650 DOI: 10.1099/mgen.0.000084] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/08/2016] [Indexed: 01/21/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) O157:H7 is a public health threat and outbreaks occur worldwide. Here, we investigate genomic differences between related STEC O157:H7 that caused two outbreaks, eight weeks apart, at the same restaurant. Short-read genome sequencing divided the outbreak strains into two sub-clusters separated by only three single-nucleotide polymorphisms in the core genome while traditional typing identified them as separate phage types, PT8 and PT54. Isolates did not cluster with local strains but with those associated with foreign travel to the Middle East/North Africa. Combined long-read sequencing approaches and optical mapping revealed that the two outbreak strains had undergone significant microevolution in the accessory genome with prophage gain, loss and recombination. In addition, the PT54 sub-type had acquired a 240 kbp multi-drug resistance (MDR) IncHI2 plasmid responsible for the phage type switch. A PT54 isolate had a general fitness advantage over a PT8 isolate in rich medium, including an increased capacity to use specific amino acids and dipeptides as a nitrogen source. The second outbreak was considerably larger and there were multiple secondary cases indicative of effective human-to-human transmission. We speculate that MDR plasmid acquisition and prophage changes have adapted the PT54 strain for human infection and transmission. Our study shows the added insights provided by combining whole-genome sequencing approaches for outbreak investigations.
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Affiliation(s)
- Lauren A Cowley
- 1Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, NW9 5EQ London, UK
| | - Timothy J Dallman
- 1Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, NW9 5EQ London, UK
| | - Stephen Fitzgerald
- 2Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, EH25 9RG Roslin, UK
| | - Neil Irvine
- 3Public Health Agency, 12-22 Linenhall St, BT2 8BS Belfast, Northern Ireland
| | - Paul J Rooney
- 4Microbiology Laboratory, Royal Victoria Hospital, BT12 6BA Belfast, Northern Ireland
| | - Sean P McAteer
- 2Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, EH25 9RG Roslin, UK
| | - Martin Day
- 1Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, NW9 5EQ London, UK
| | - Neil T Perry
- 1Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, NW9 5EQ London, UK
| | - James L Bono
- 5U.S. Meat Animal Research Center, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, Nebraska 68933-0166, USA
| | - Claire Jenkins
- 1Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, NW9 5EQ London, UK
| | - David L Gally
- 2Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, EH25 9RG Roslin, UK
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48
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Kiarie E, Walsh MC, Nyachoti CM. Performance, digestive function, and mucosal responses to selected feed additives for pigs. J Anim Sci 2016. [DOI: 10.2527/jas.2015-9835] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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49
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Abeyrathne PD, Chami M, Stahlberg H. Biochemical and biophysical approaches to study the structure and function of the chloride channel (ClC) family of proteins. Biochimie 2016; 128-129:154-62. [PMID: 27554851 DOI: 10.1016/j.biochi.2016.08.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 08/19/2016] [Indexed: 11/30/2022]
Abstract
The chloride channel (ClC) protein family comprises both chloride (Cl(-)) channels and chloride/proton (Cl(-)/H(+)) antiporters. In prokaryotes and eukaryotes, these proteins mediate the movement of Cl(-) ions across the membrane. In eukaryotes, ClC proteins play a role in the stabilization of membrane potential, epithelial ion transport, hippocampal neuroprotection, cardiac pacemaker activity and vesicular acidification. Moreover, mutations in the genes encoding ClC proteins can cause genetic disease in humans. In prokaryotes, the Cl(-)/H(+) antiporters, such as ClC-ec1 found in Escherichia coli promote proton expulsion in the extreme acid-resistance response common to enteric bacteria. To date, structural and functional studies of the prokaryotic protein have revealed unique structural features, including complicated transmembrane topology with 18 α-helices in each subunit and an anion-coordinating region in each subunit. Several different approaches such as X-ray crystallography, NMR, biochemical studies, and molecular dynamics simulations have been applied to the study of ClC proteins. Continued study of the unique structure and function of this diverse family of proteins has the potential to lead to the development of novel therapeutic targets for neuronal, renal, bone, and food-borne diseases.
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Affiliation(s)
- Priyanka D Abeyrathne
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, WRO-1508 Mattenstrasse 26, CH-4058, Basel, Switzerland.
| | - Mohamed Chami
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, WRO-1508 Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, WRO-1508 Mattenstrasse 26, CH-4058, Basel, Switzerland
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50
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Mycothiol peroxidase MPx protects Corynebacterium glutamicum against acid stress by scavenging ROS. Biotechnol Lett 2016; 38:1221-8. [DOI: 10.1007/s10529-016-2099-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 03/31/2016] [Indexed: 10/22/2022]
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