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Zhang Y, Chen R, Zhang D, Qi S, Liu Y. Metabolite interactions between host and microbiota during health and disease: Which feeds the other? Biomed Pharmacother 2023; 160:114295. [PMID: 36709600 DOI: 10.1016/j.biopha.2023.114295] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/20/2023] [Accepted: 01/20/2023] [Indexed: 01/30/2023] Open
Abstract
Metabolites produced by the host and microbiota play a crucial role in how human bodies develop and remain healthy. Most of these metabolites are produced by microbiota and hosts in the digestive tract. Metabolites in the gut have important roles in energy metabolism, cellular communication, and host immunity, among other physiological activities. Although numerous host metabolites, such as free fatty acids, amino acids, and vitamins, are found in the intestine, metabolites generated by gut microbiota are equally vital for intestinal homeostasis. Furthermore, microbiota in the gut is the sole source of some metabolites, including short-chain fatty acids (SCFAs). Metabolites produced by microbiota, such as neurotransmitters and hormones, may modulate and significantly affect host metabolism. The gut microbiota is becoming recognized as a second endocrine system. A variety of chronic inflammatory disorders have been linked to aberrant host-microbiota interplays, but the precise mechanisms underpinning these disturbances and how they might lead to diseases remain to be fully elucidated. Microbiome-modulated metabolites are promising targets for new drug discovery due to their endocrine function in various complex disorders. In humans, metabolotherapy for the prevention or treatment of various disorders will be possible if we better understand the metabolic preferences of bacteria and the host in specific tissues and organs. Better disease treatments may be possible with the help of novel complementary therapies that target host or bacterial metabolism. The metabolites, their physiological consequences, and functional mechanisms of the host-microbiota interplays will be highlighted, summarized, and discussed in this overview.
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Affiliation(s)
- Yan Zhang
- Department of Anethesiology, China-Japan Union Hospital of Jilin University, Changchun 130033, People's Republic of China.
| | - Rui Chen
- Department of Pediatrics, China-Japan Union Hospital of Jilin University, Changchun 130033, People's Republic of China.
| | - DuoDuo Zhang
- Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China.
| | - Shuang Qi
- Department of Anethesiology, China-Japan Union Hospital of Jilin University, Changchun 130033, People's Republic of China.
| | - Yan Liu
- Department of Hand and Foot Surgery, China-Japan Union Hospital of Jilin University, Changchun 130033, People's Republic of China.
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Huynh TN, Stewart V. Purine catabolism by enterobacteria. Adv Microb Physiol 2023; 82:205-266. [PMID: 36948655 DOI: 10.1016/bs.ampbs.2023.01.001] [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] [Indexed: 02/13/2023]
Abstract
Purines are abundant among organic nitrogen sources and have high nitrogen content. Accordingly, microorganisms have evolved different pathways to catabolize purines and their metabolic products such as allantoin. Enterobacteria from the genera Escherichia, Klebsiella and Salmonella have three such pathways. First, the HPX pathway, found in the genus Klebsiella and very close relatives, catabolizes purines during aerobic growth, extracting all four nitrogen atoms in the process. This pathway includes several known or predicted enzymes not previously observed in other purine catabolic pathways. Second, the ALL pathway, found in strains from all three species, catabolizes allantoin during anaerobic growth in a branched pathway that also includes glyoxylate assimilation. This allantoin fermentation pathway originally was characterized in a gram-positive bacterium, and therefore is widespread. Third, the XDH pathway, found in strains from Escherichia and Klebsiella spp., at present is ill-defined but likely includes enzymes to catabolize purines during anaerobic growth. Critically, this pathway may include an enzyme system for anaerobic urate catabolism, a phenomenon not previously described. Documenting such a pathway would overturn the long-held assumption that urate catabolism requires oxygen. Overall, this broad capability for purine catabolism during either aerobic or anaerobic growth suggests that purines and their metabolites contribute to enterobacterial fitness in a variety of environments.
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Affiliation(s)
- TuAnh Ngoc Huynh
- Department of Food Science, University of Wisconsin, Madison, WI, United States
| | - Valley Stewart
- Department of Microbiology & Molecular Genetics, University of California, Davis, CA, United States.
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田 婷, 陈 邬, 梁 美, 玛依娜·卡哈尔, 李 瑞, 孙 玉. [Screening, domestication and identification of intestinal uric acid degrading bacteria in low uric acid population]. SHENG WU YI XUE GONG CHENG XUE ZA ZHI = JOURNAL OF BIOMEDICAL ENGINEERING = SHENGWU YIXUE GONGCHENGXUE ZAZHI 2022; 39:792-797. [PMID: 36008344 PMCID: PMC10957345 DOI: 10.7507/1001-5515.202111028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 05/10/2022] [Indexed: 06/15/2023]
Abstract
As the largest ecosystem of human body, intestinal microorganisms participate in the synthesis and metabolism of uric acid. Developing and utilizing intestinal bacteria to degrade uric acid might provide new ideas for the treatment of hyperuricemia. The fecal samples of people with low uric acid were inoculated into uric acid selective medium with the concentration of 1.5 mmol/L for preliminary screening, and the initially screened strains that may have degradation ability were domesticated by concentration gradient method, and the strains with high uric acid degradation rate were identified by 16S rRNA sequencing method. A strain of high-efficiency uric acid degrading bacteria was screened and domesticated from the feces of people with low uric acid. The degradation rate of uric acid could reach 50.2%. It was identified as Escherichia coli. The isolation and domestication of high efficient uric acid degrading strains can not only provide scientific basis for the study of the mechanism of intestinal microbial degradation of uric acid, but also reserve biological strains for the treatment of hyperuricemia and gout in the future.
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Affiliation(s)
- 婷婷 田
- 新疆医科大学 基础医学院(乌鲁木齐 830000)Basic Medical College, Xinjiang Medical University, Urumqi 830000, P. R. China
| | - 邬锦 陈
- 新疆医科大学 基础医学院(乌鲁木齐 830000)Basic Medical College, Xinjiang Medical University, Urumqi 830000, P. R. China
| | - 美婷 梁
- 新疆医科大学 基础医学院(乌鲁木齐 830000)Basic Medical College, Xinjiang Medical University, Urumqi 830000, P. R. China
| | - 玛依娜·卡哈尔
- 新疆医科大学 基础医学院(乌鲁木齐 830000)Basic Medical College, Xinjiang Medical University, Urumqi 830000, P. R. China
| | - 瑞 李
- 新疆医科大学 基础医学院(乌鲁木齐 830000)Basic Medical College, Xinjiang Medical University, Urumqi 830000, P. R. China
| | - 玉萍 孙
- 新疆医科大学 基础医学院(乌鲁木齐 830000)Basic Medical College, Xinjiang Medical University, Urumqi 830000, P. R. China
- 新疆医科大学 基础医学院 形态中心(乌鲁木齐 830000)Morphological Center, Basic Medical College, Xinjiang Medical University, Urumqi 830000, P. R. China
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Urso A, Prince A. Anti-Inflammatory Metabolites in the Pathogenesis of Bacterial Infection. Front Cell Infect Microbiol 2022; 12:925746. [PMID: 35782110 PMCID: PMC9240774 DOI: 10.3389/fcimb.2022.925746] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/23/2022] [Indexed: 01/13/2023] Open
Abstract
Host and pathogen metabolism have a major impact on the outcome of infection. The microenvironment consisting of immune and stromal cells drives bacterial proliferation and adaptation, while also shaping the activity of the immune system. The abundant metabolites itaconate and adenosine are classified as anti-inflammatory, as they help to contain the local damage associated with inflammation, oxidants and proteases. A growing literature details the many roles of these immunometabolites in the pathogenesis of infection and their diverse functions in specific tissues. Some bacteria, notably P. aeruginosa, actively metabolize these compounds, others, such as S. aureus respond by altering their own metabolic programs selecting for optimal fitness. For most of the model systems studied to date, these immunometabolites promote a milieu of tolerance, limiting local immune clearance mechanisms, along with promoting bacterial adaptation. The generation of metabolites such as adenosine and itaconate can be host protective. In the setting of acute inflammation, these compounds also represent potential therapeutic targets to prevent infection.
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Affiliation(s)
| | - Alice Prince
- *Correspondence: Alice Prince, ; Andreacarola Urso,
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Uncultured Microbial Phyla Suggest Mechanisms for Multi-Thousand-Year Subsistence in Baltic Sea Sediments. mBio 2019; 10:mBio.02376-18. [PMID: 30992358 PMCID: PMC6469976 DOI: 10.1128/mbio.02376-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Much of life on Earth exists in a very slow-growing state, with microbes from deeply buried marine sediments representing an extreme example. These environments are like natural laboratories that have run multi-thousand-year experiments that are impossible to perform in a laboratory. We borrowed some techniques that are commonly used in laboratory experiments and applied them to these natural samples to make hypotheses about how these microbes subsist for so long at low activity. We found that some methods for stabilizing proteins and nucleic acids might be used by many members of the community. We also found evidence for niche differentiation strategies, and possibly cross-feeding, suggesting that even though they are barely growing, complex ecological interactions continue to occur over ultralong timescales. Energy-starved microbes in deep marine sediments subsist at near-zero growth for thousands of years, yet the mechanisms for their subsistence are unknown because no model strains have been cultivated from most of these groups. We investigated Baltic Sea sediments with single-cell genomics, metabolomics, metatranscriptomics, and enzyme assays to identify possible subsistence mechanisms employed by uncultured Atribacteria, Aminicenantes, Actinobacteria group OPB41, Aerophobetes, Chloroflexi, Deltaproteobacteria, Desulfatiglans, Bathyarchaeota, and Euryarchaeota marine group II lineages. Some functions appeared to be shared by multiple lineages, such as trehalose production and NAD+-consuming deacetylation, both of which have been shown to increase cellular life spans in other organisms by stabilizing proteins and nucleic acids, respectively. Other possible subsistence mechanisms differed between lineages, possibly providing them different physiological niches. Enzyme assays and transcripts suggested that Atribacteria and Actinobacteria group OPB41 catabolized sugars, whereas Aminicenantes and Atribacteria catabolized peptides. Metabolite and transcript data suggested that Atribacteria utilized allantoin, possibly as an energetic substrate or chemical protectant, and also possessed energy-efficient sodium pumps. Atribacteria single-cell amplified genomes (SAGs) recruited transcripts for full pathways for the production of all 20 canonical amino acids, and the gene for amino acid exporter YddG was one of their most highly transcribed genes, suggesting that they may benefit from metabolic interdependence with other cells. Subsistence of uncultured phyla in deep subsurface sediments may occur through shared strategies of using chemical protectants for biomolecular stabilization, but also by differentiating into physiological niches and metabolic interdependencies.
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Hu J, Zhao L, Yang M. A GntR family transcription factor positively regulates mycobacterial isoniazid resistance by controlling the expression of a putative permease. BMC Microbiol 2015; 15:214. [PMID: 26474554 PMCID: PMC4609117 DOI: 10.1186/s12866-015-0556-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 10/08/2015] [Indexed: 01/13/2023] Open
Abstract
Background Bacteria use transcriptional regulation to respond to environmental stresses. Specifically, exposure to antibacterial drugs is deemed to be an atypical stress, and altering transcriptional regulation in response to such stress can increase bacterial drug resistance. However, only a few transcription factors that regulate drug resistance have been reported. Results In the present study, a GntR family transcription factor, encoded by the MSMEG_0535 (Ms0535) gene, was shown to be an isoniazid (INH) resistance regulator in Mycobacterium smegmatis. When the Ms0535 gene was overexpressed, cells showed a significant increase in INH resistance. First, the interaction between Ms0535 and its own promoter was determined, and a conserved 26-bp palindromic DNA binding motif was identified using electrophoretic mobility shift and DNaseI footprinting assays. Second, quantitative reverse transcription-PCR assays showed that Ms0535 acted as a transcriptional activator, and positively regulated its own expression, as well as that of a permease encoded by the MSMEG_0534 (Ms0534) gene. Similar to the case for the Ms0535 gene, a recombinant Ms0534-overexpressing strain also exhibited increased INH resistance compared with the wild-type strain. Furthermore, we showed that Ms0535 and Ms0534 deletion strains were more sensitive to INH than the wild-type strain. Interestingly, overexpressing Ms0534 in the Ms0535 deletion strain enhanced its INH resistance. In contrast, the Ms0534 deletion strain was still sensitive to INH even when Ms0535 was overexpressed. These findings suggest that Ms0534 is an effector protein that affects INH resistance in M. smegmatis. Conclusions In summary, the GntR transcriptional regulator Ms0535 positively regulates INH resistance by transcriptionally regulating the expression of the Ms0534 permease in M. smegmatis. These results improve our understanding of the role of transcriptional regulation in INH drug resistance in mycobacteria. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0556-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jialing Hu
- National Key Laboratory of Agricultural Microbiology, Center for Proteomics Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Lei Zhao
- National Key Laboratory of Agricultural Microbiology, Center for Proteomics Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Min Yang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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Martínez-Gómez AI, Soriano-Maldonado P, Andújar-Sánchez M, Clemente-Jiménez JM, Rodríguez-Vico F, Neira JL, Las Heras-Vázquez FJ, Martínez-Rodríguez S. Biochemical and mutational studies of allantoinase from Bacillus licheniformis CECT 20T. Biochimie 2013; 99:178-88. [PMID: 24333989 DOI: 10.1016/j.biochi.2013.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 12/03/2013] [Indexed: 10/25/2022]
Abstract
Allantoinases (allantoin amidohydrolase, E.C. 3.5.2.5) catalyze the hydrolysis of the amide bond of allantoin to form allantoic acid, in those organisms where allantoin is not the final product of uric acid degradation. Despite their importance in the purine catabolic pathway, sequences of microbial allantoinases with proven activity are scarce, and only the enzyme from Escherichia coli (AllEco) has been studied in detail in the genomic era. In this work, we report the cloning, purification and characterization of the recombinant allantoinase from Bacillus licheniformis CECT 20T (AllBali). The enzyme was a homotetramer with an apparent Tm of 62 ± 1 °C. Optimal parameters for the enzyme activity were pH 7.5 and 50 °C, showing apparent Km and kcat values of 17.7 ± 2.7 mM and 24.4 ± 1.5 s(-1), respectively. Co(2+) proved to be the most effective cofactor, inverting the enantioselectivity of AllBali when compared to that previously reported for other allantoinases. The common ability of different cyclic amidohydrolases to hydrolyze distinct substrates to the natural one also proved true for AllBali. The enzyme was able to hydrolyze hydantoin, dihydrouracil and 5-ethyl-hydantoin, although at relative rates 3-4 orders of magnitude lower than with allantoin. Mutagenesis experiments suggest that S292 is likely implicated in the binding of the allantoin ring through the carbonyl group of the polypeptide main chain, which is the common mechanism observed in other members of the amidohydrolase family. In addition, our results suggest an allosteric effect of H2O2 toward allantoinase.
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Affiliation(s)
- Ana Isabel Martínez-Gómez
- Dpto. Química y Física, Universidad de Almería, Campus de Excelencia Internacional Agroalimentario, ceiA3, 04120 Almería, Spain; Centro de Investigación en Biotecnología Agroalimentaria, BITAL, Almería, Spain
| | - Pablo Soriano-Maldonado
- Dpto. Química y Física, Universidad de Almería, Campus de Excelencia Internacional Agroalimentario, ceiA3, 04120 Almería, Spain; Centro de Investigación en Biotecnología Agroalimentaria, BITAL, Almería, Spain
| | - Montserrat Andújar-Sánchez
- Dpto. Química y Física, Universidad de Almería, Campus de Excelencia Internacional Agroalimentario, ceiA3, 04120 Almería, Spain; Centro de Investigación en Biotecnología Agroalimentaria, BITAL, Almería, Spain
| | - Josefa María Clemente-Jiménez
- Dpto. Química y Física, Universidad de Almería, Campus de Excelencia Internacional Agroalimentario, ceiA3, 04120 Almería, Spain; Centro de Investigación en Biotecnología Agroalimentaria, BITAL, Almería, Spain
| | - Felipe Rodríguez-Vico
- Dpto. Química y Física, Universidad de Almería, Campus de Excelencia Internacional Agroalimentario, ceiA3, 04120 Almería, Spain; Centro de Investigación en Biotecnología Agroalimentaria, BITAL, Almería, Spain
| | - José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Complex Systems Physics Institute, 50009 Zaragoza, Spain
| | - Francisco Javier Las Heras-Vázquez
- Dpto. Química y Física, Universidad de Almería, Campus de Excelencia Internacional Agroalimentario, ceiA3, 04120 Almería, Spain; Centro de Investigación en Biotecnología Agroalimentaria, BITAL, Almería, Spain
| | - Sergio Martínez-Rodríguez
- Dpto. Química y Física, Universidad de Almería, Campus de Excelencia Internacional Agroalimentario, ceiA3, 04120 Almería, Spain; Centro de Investigación en Biotecnología Agroalimentaria, BITAL, Almería, Spain; Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Dpto. Química Física, Universidad de Granada, 18071 Granada, Spain.
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Delineation of the caffeine C-8 oxidation pathway in Pseudomonas sp. strain CBB1 via characterization of a new trimethyluric acid monooxygenase and genes involved in trimethyluric acid metabolism. J Bacteriol 2012; 194:3872-82. [PMID: 22609920 DOI: 10.1128/jb.00597-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The molecular basis of the ability of bacteria to live on caffeine via the C-8 oxidation pathway is unknown. The first step of this pathway, caffeine to trimethyluric acid (TMU), has been attributed to poorly characterized caffeine oxidases and a novel quinone-dependent caffeine dehydrogenase. Here, we report the detailed characterization of the second enzyme, a novel NADH-dependent trimethyluric acid monooxygenase (TmuM), a flavoprotein that catalyzes the conversion of TMU to 1,3,7-trimethyl-5-hydroxyisourate (TM-HIU). This product spontaneously decomposes to racemic 3,6,8-trimethylallantoin (TMA). TmuM prefers trimethyluric acids and, to a lesser extent, dimethyluric acids as substrates, but it exhibits no activity on uric acid. Homology models of TmuM against uric acid oxidase HpxO (which catalyzes uric acid to 5-hydroxyisourate) reveal a much bigger and hydrophobic cavity to accommodate the larger substrates. Genes involved in the caffeine C-8 oxidation pathway are located in a 25.2-kb genomic DNA fragment of CBB1, including cdhABC (coding for caffeine dehydrogenase) and tmuM (coding for TmuM). Comparison of this gene cluster to the uric acid-metabolizing gene cluster and pathway of Klebsiella pneumoniae revealed two major open reading frames coding for the conversion of TM-HIU to S-(+)-trimethylallantoin [S-(+)-TMA]. The first one, designated tmuH, codes for a putative TM-HIU hydrolase, which catalyzes the conversion of TM-HIU to 3,6,8-trimethyl-2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (TM-OHCU). The second one, designated tmuD, codes for a putative TM-OHCU decarboxylase which catalyzes the conversion of TM-OHCU to S-(+)-TMA. Based on a combination of enzymology and gene-analysis, a new degradative pathway for caffeine has been proposed via TMU, TM-HIU, TM-OHCU to S-(+)-TMA.
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