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Krishnamurthy S, Gunasegaran B, Paul-Heng M, Mohamedali A, P Klare W, Pang CNI, Gluch L, Shin JS, Chan C, Baker MS, Ahn SB, Heng B. Recombinant Protein Spectral Library (rPSL) DIA-MS method improves identification and quantification of low-abundance cancer-associated and kynurenine pathway proteins. Commun Chem 2025; 8:141. [PMID: 40348885 PMCID: PMC12065878 DOI: 10.1038/s42004-025-01531-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Accepted: 04/22/2025] [Indexed: 05/14/2025] Open
Abstract
Data-independent acquisition mass spectrometry (DIA-MS) is a powerful tool for quantitative proteomics, but a well-constructed reference spectral library is crucial to optimize DIA analysis, particularly for low-abundance proteins. In this study, we evaluate the efficacy of a recombinant protein spectral library (rPSL), generated from tryptic digestion of 42 human recombinant proteins, in enhancing the detection and quantification of lower-abundance cancer-associated proteins. Additionally, we generated a combined sample-specific biological-rPSL by integrating the rPSL with a spectral library derived from pooled biological samples. We compared the performance of these libraries for DIA data extraction with standard methods, including sample-specific biological spectral library and library-free DIA methods. Our specific focus was on quantifying cancer-associated proteins, including key enzymes involved in kynurenine pathway, across patient-derived tissues and cell lines. Both rPSL and biological-rPSL-DIA approaches provided significantly improved coverage of lower-abundance proteins, enhancing sensitivity and more consistent protein quantification across matched tumour and adjacent noncancerous tissues from breast and colorectal cancer patients and in cancer cell lines. Overall, our study demonstrates that rPSL and biological-rPSL coupled with DIA-MS workflows, can address the limitations of both biological library-based and library-free DIA methods, offering a robust approach for quantifying low-abundance cancer-associated proteins in complex biological samples.
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Affiliation(s)
- Shivani Krishnamurthy
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Bavani Gunasegaran
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Moumita Paul-Heng
- Transplantation Immunobiology Research Group, Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Abidali Mohamedali
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
- Faculty of Science and Engineering, School of Natural Sciences, Macquarie University, Sydney, Australia
| | - William P Klare
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - C N Ignatius Pang
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Laurence Gluch
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
- The Strathfield Breast and Thyroid Centre, Strathfield, Sydney, Australia
| | - Joo-Shik Shin
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, Sydney, Australia
- Central Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Charles Chan
- Department of Anatomical Pathology, NSW Health Pathology, Concord Hospital, Sydney, NSW, Australia
- Concord Institute of Academic Surgery, Concord Clinical School, Faculty of Medicine and Health, Concord Hospital, The University of Sydney, Sydney, Australia
| | - Mark S Baker
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Seong Beom Ahn
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia.
| | - Benjamin Heng
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia.
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Liao R, Zhang W, Xu R, Li K, Wei W, Sheng R. Endophytic microbial communities and functional shifts in Hemarthria compressa grass in response to Silicon and Selenium amendment. BMC PLANT BIOLOGY 2025; 25:169. [PMID: 39924486 PMCID: PMC11808958 DOI: 10.1186/s12870-025-06178-6] [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: 11/18/2024] [Accepted: 01/30/2025] [Indexed: 02/11/2025]
Abstract
BACKGROUND Hemarthria compressa, a widely cultivated forage grass, is critical for supporting livestock production and maintaining the ecological balance in grassland ecosystems. Enhancing its stress resistance and productivity is crucial for sustainable grassland utilization and development. Silicon (Si) and Selenium (Se) are recognized as beneficial nutrients that promote plant growth and stress tolerance, and modulate of plant-microorganism interactions. However, the intricate linkages between the endophytes shifts and host grass growth induced by Si/Se amendments are poorly understood. In this study, a pot experiment was conducted to examine the effects of foliar-applied Si/Se on the growth and nutritional quality of H. compressa grass, as well as the composition, diversity and potential functions of endophytic bacteria in leaves. RESULTS Both Si and Se treatments significantly improved grass biomass by approximately 17%. Nutritional quality was also improved, with Si application increased plant Si and neutral detergent fiber contents by 25.6% and 5.8%, while Se significantly enhanced the grass Se content from 0.055 mg kg-1 to 0.636 mg kg-1. Furthermore, Si/Se amendments altered the structure of the leaf endophytic bacterial community, resulting in an increased alpha diversity and a more modularized co-occurrence network. Moreover, both Si and Se treatments enriched plant growth-promoting bacterial genera such as Brevundimonas and Truepera. Metabolic function analysis revealed that Si application promoted chlorophyllide biosynthesis by 152%, several carbon metabolism pathways by 35-152%, and redox-related pathways by 57-93%, while the starch biosynthesis pathway was downregulated by 79% of the endophytic bacterial community. In contrast, Se application mainly enhanced starch degradation, CMP-legionamine biosynthesis by 71% and TCA cycle-related pathways by 23-58%, while reducing L-threonine metabolism by 98%. These specific functional changes in the endophytic bacteria induced by Si/Se amendments were closely linked with the observed growth promotion and stress resistance of the host H. compressa grass. CONCLUSIONS Si and Se amendments not only enhanced the growth and nutritional quality of H. compressa grass, but also altered the community structure and functional traits of endophytic bacteria in grass. The enrichment of beneficial endophytes and the modification of community metabolic functions within the endophytic community may play important synergistic effects on improving grass growth.
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Affiliation(s)
- Rujia Liao
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
- College of Resource and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenzhao Zhang
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Risheng Xu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Ke Li
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Wenxue Wei
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Rong Sheng
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China.
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Campbell J, Wang Y. Observing extradiol dioxygenases in action through a crystalline lens. Methods Enzymol 2024; 704:3-25. [PMID: 39300653 DOI: 10.1016/bs.mie.2024.05.020] [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: 09/22/2024]
Abstract
Extradiol dioxygenases are a class of non-heme iron-dependent enzymes found in eukaryotes and prokaryotes that play a vital role in the aerobic catabolism of aromatic compounds. They are generally divided into three evolutionarily independent superfamilies with different protein folds. Our recent studies have shed light on the catalytic mechanisms and structure-function relationships of two specific extradiol dioxygenases: 3-hydroxyanthranilate-3,4-dioxygenase, a Type III enzyme essential in mammals for producing a precursor for nicotinamide adenine dinucleotide, and L-3,4-dihydroxyphenylalanine dioxygenase, an uncommon form of Type I enzymes involved in natural product biosynthesis. This work details the expression and isolation methods for these extradiol dioxygenases and introduces approaches to achieve homogeneity and high occupancy of the enzyme metal centers. Techniques such as ultraviolet-visible and electron paramagnetic resonance spectroscopies, as well as oxygen electrode measurements, are discussed for probing the interaction of the non-heme iron center with ligands and characterizing enzymatic activities. Moreover, protein crystallization has been demonstrated as a powerful tool to study these enzymes. We highlight in crystallo reactions and single-crystal spectroscopic methods to further elucidate enzymatic functions and protein dynamics.
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Affiliation(s)
- Jackson Campbell
- Department of Chemistry, University of Georgia, Athens, GA, United States
| | - Yifan Wang
- Department of Chemistry, University of Georgia, Athens, GA, United States.
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Ringenbach S, Yoza R, Jones PA, Du M, Klugh KL, Peterson LW, Colabroy KL. Discovery and characterization of l-DOPA 2,3-dioxygenase from Streptomyces hygroscopicus jingganensis. Arch Biochem Biophys 2024; 755:109967. [PMID: 38556098 DOI: 10.1016/j.abb.2024.109967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/19/2024] [Accepted: 03/21/2024] [Indexed: 04/02/2024]
Abstract
The largest natural reservoir of untapped carbon can be found in the cell-wall strengthening, plant woody-tissue polymer, lignin - a polymer of catechols or 1,2-dihydroxybenzene monomers. The catecholic carbon of lignin could be valorized into feedstocks and natural products by way of catabolic and biosynthetic transformations, including the oxygen-dependent cleavage reaction of extradiol dioxygenase (EDX) enzymes. The EDX l-DOPA 2,3-dioxygenase was first discovered as part of a biosynthetic gene cluster to the natural product antibiotic, lincomycin, and also contributes to the biosyntheses of anthramycin, sibiromycin, tomaymycin, porothramycin and hormaomycin. Using these l-DOPA 2,3-dioxygenases as a starting point, we searched sequence space in order to identify new sources of dioxygenase driven natural product diversity. A "vicinal-oxygen-chelate (VOC) family protein" from Streptomyces hygroscopicus jingganensis was identified using bioinformatic methods and biochemically investigated for dioxygenase activity against a suite of natural and synthetic catechols. Steady-state oxygen consumption assays were used to screen and identify substrates, and a steady-state kinetic model of oxygen consumption was developed to evaluate activity of the S. hygroscopicus jingganensis VOC-family-protein with respect to activity of l-DOPA 2,3-dioxygenases from Streptomyces lincolnensis and Streptomyces sclerotialus. Lastly, these data were integrated with steady-state kinetic methods to observe the formation of the EDX cleavage product with UV-visible spectroscopy. The genomic context and enzymatic activity of the S. hygroscopicus jingganensis VOC family protein are consistent with a l-DOPA 2,3-dioxygenase contained within a cryptic biosynthetic pathway.
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Affiliation(s)
- Sara Ringenbach
- Department of Chemistry, Muhlenberg College, 2400 Chew St, Allentown, PA, 18104, USA
| | - Riri Yoza
- Department of Chemistry, Muhlenberg College, 2400 Chew St, Allentown, PA, 18104, USA
| | - Paige A Jones
- Department of Chemistry, Muhlenberg College, 2400 Chew St, Allentown, PA, 18104, USA
| | - Muxue Du
- Department of Chemistry, Muhlenberg College, 2400 Chew St, Allentown, PA, 18104, USA
| | - Kameron L Klugh
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, TN, 38112, USA
| | - Larryn W Peterson
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, TN, 38112, USA
| | - Keri L Colabroy
- Department of Chemistry, Muhlenberg College, 2400 Chew St, Allentown, PA, 18104, USA.
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Tian Z, Zhao M, Sui X, Li X, Qin L, Chen ZJ, Zhao S, Zhao H. Associations between vaginal microbiota and endometrial polypoid lesions in women of reproductive age: a cross-sectional study. Reprod Biomed Online 2024; 48:103602. [PMID: 38101145 DOI: 10.1016/j.rbmo.2023.103602] [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: 07/02/2023] [Revised: 09/04/2023] [Accepted: 10/03/2023] [Indexed: 12/17/2023]
Abstract
RESEARCH QUESTION What are the different characteristics of vaginal microbial composition between patients with endometrial polypoid lesions and controls? DESIGN This cohort study compared the pre-operative microbial compositions of vaginal samples in a cohort of 703 women with endometrial polypoid lesions [293 and 410 women diagnosed and not diagnosed with polyps pathologically (polyps group and not-polyps group, respectively] and 703 women in the control group. Bacterial abundance, diversity, differential taxa and microbial network structure were assessed using 16S rRNA gene sequencing. Predictive algorithms were used to determine the functional pathways of vaginal microbiota within the cohort. RESULTS The control group exhibited higher relative abundance of Lactobacillus crispatus in comparison with the polypoid lesions group (P = 0.0427). Beta diversity of vaginal microbiota differed significantly between the groups (P < 0.05). Comparing the polyps group with the not-polyps group, Leptotrichia spp. and Cutibacterium spp. were more abundant in the polyps group, and Fannyhessea spp., Acinetobacter spp. and Achromobacter spp. were more abundant in the not-polyps group. The control group exhibited higher abundance of Bifidobacterium spp., Achromobacter spp. and Escherichia/Shigella spp. (false discovery rate < 0.05). Furthermore, the polyps group and not-polyps group displayed more complex co-occurrence networks compared with the control group. CONCLUSIONS The results of this study provide compelling evidence supporting associations between vaginal microbiota and endometrial polypoid lesions, highlighting the potential relationship between a well-balanced vaginal microbial ecosystem and a healthy intrauterine environment.
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Affiliation(s)
- Zhaomei Tian
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China; National Research Centre for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Maoning Zhao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China; National Research Centre for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Xinlei Sui
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China; National Research Centre for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Xiao Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China; National Research Centre for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Lang Qin
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China; National Research Centre for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Zi-Jiang Chen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China; Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China; National Research Centre for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China; Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan, Shandong, China; Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China; Centre for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shigang Zhao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China; Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China; National Research Centre for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China; Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan, Shandong, China; Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
| | - Han Zhao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China; Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China; National Research Centre for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China; Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan, Shandong, China; Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China.
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Dyachenko EI, Bel’skaya LV. The Role of Amino Acids in Non-Enzymatic Antioxidant Mechanisms in Cancer: A Review. Metabolites 2023; 14:28. [PMID: 38248831 PMCID: PMC10818545 DOI: 10.3390/metabo14010028] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
Currently, the antioxidant properties of amino acids and their role in the physicochemical processes accompanying oxidative stress in cancer remain unclear. Cancer cells are known to extensively uptake amino acids, which are used as an energy source, antioxidant precursors that reduce oxidative stress in cancer, and as regulators of inhibiting or inducing tumor cell-associated gene expression. This review examines nine amino acids (Cys, His, Phe, Met, Trp, Tyr, Pro, Arg, Lys), which play a key role in the non-enzymatic oxidative process in various cancers. Conventionally, these amino acids can be divided into two groups, in one of which the activity increases (Cys, Phe, Met, Pro, Arg, Lys) in cancer, and in the other, it decreases (His, Trp, Tyr). The review examines changes in the metabolism of nine amino acids in eleven types of oncology. We have identified the main nonspecific mechanisms of changes in the metabolic activity of amino acids, and described direct and indirect effects on the redox homeostasis of cells. In the future, this will help to understand better the nature of life of a cancer cell and identify therapeutic targets more effectively.
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Affiliation(s)
| | - Lyudmila V. Bel’skaya
- Biochemistry Research Laboratory, Omsk State Pedagogical University, Omsk 644099, Russia;
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Hu Z, Feng L, Jiang Q, Wang W, Tan B, Tang X, Yin Y. Intestinal tryptophan metabolism in disease prevention and swine production. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2023; 15:364-374. [PMID: 38058568 PMCID: PMC10695851 DOI: 10.1016/j.aninu.2023.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 07/05/2023] [Accepted: 08/11/2023] [Indexed: 12/08/2023]
Abstract
Tryptophan (Trp) is an essential amino acid that cannot be synthesized by animals. It has been characterized into two different isomers, levorotation-Trp (L-Trp) and dextrorotation-Trp (D-Trp), based on their distinct molecule orientation. Intestinal epithelial cells and gut microbiota are involved in metabolizing L-Trp in the gut via the activation of the kynurenine, serotonin, and indole pathways. However, knowledge regarding D-Trp metabolism in the gut remains unclear. In this review, we briefly update the current understanding of intestinal L/D-Trp metabolism and the function of their metabolites in modulating the gut physiology and diseases. Finally, we summarize the effects of Trp nutrition on swine production at different stages, including growth performance in weaned piglets and growing pigs, as well as the reproduction performance in sows.
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Affiliation(s)
- Zhenguo Hu
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Science, Changsha, Hunan 410125, China
| | - Luya Feng
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Qian Jiang
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Wenliang Wang
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Bi'e Tan
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Xiongzhuo Tang
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Yulong Yin
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Science, Changsha, Hunan 410125, China
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Xu L, Li W, Ling L, Zhang Z, Cui Z, Ge J, Wang Y, Meng Q, Wang Y, Liu K, Zhou J, Zeng F, Wang J, Wu J. A Sedentary Lifestyle Changes the Composition and Predicted Functions of the Gut Bacterial and Fungal Microbiota of Subjects from the Same Company. Curr Microbiol 2023; 80:368. [PMID: 37831112 PMCID: PMC10575810 DOI: 10.1007/s00284-023-03480-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 09/11/2023] [Indexed: 10/14/2023]
Abstract
A sedentary lifestyle affects the diversity and composition of the gut microbiota, but previous studies have mainly focused on bacteria instead of fungi. Here, we compared both the fecal bacterial and fungal microbiota compositions and functions in sedentary persons and controls. Subjects from the China Railway Corporation, including 99 inspectors and 88 officials, were enrolled in our study. Fecal microbiota communities were analyzed using 16S rRNA gene sequencing for bacteria and ITS sequencing for fungi. We found that the diversity of the gut microbiota of the sedentary group was significantly lower than that of the control group (P < 0.05). The sedentary group had a higher abundance of Firmicutes, a lower abundance of Actinobacteria and Proteobacteria and a higher abundance of Ascomycota, and a lower abundance of Basidiomycota. Furthermore, functional prediction analysis of the fungal microbiota revealed more L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde, more phospholipid remodeling (phosphatidylethanolamine, yeast), and more L-tyrosine degradation I, as well as less pentose phosphate pathway (non-oxidative branch), less adenosine nucleotide biosynthesis and less L-valine biosynthesis in the sedentary group (P < 0.05). Thus, a sedentary lifestyle changes the composition and function of the gut microbiota. It may change the pentose phosphate pathway (non-oxidative branch), nucleic acid and amino acid biosynthesis and phospholipid metabolism in fungi.
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Affiliation(s)
- Longwei Xu
- Department of Gastroenterology, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
- Department of Gastroenterology, School of Clinical Medicine, Peking University Ninth, Beijing, 100038, China
| | - Wenkun Li
- Department of Gastroenterology, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
- Department of Gastroenterology, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Lu Ling
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Ziran Zhang
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Zilu Cui
- Department of Gastroenterology, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Jiang Ge
- Department of Gastroenterology, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
| | - Yun Wang
- Department of Gastroenterology, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
- Department of Gastroenterology, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Qianlong Meng
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Yadan Wang
- Department of Gastroenterology, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
| | - Kuiliang Liu
- Department of Gastroenterology, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
- Department of Gastroenterology, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Jun Zhou
- Department of Clinical Research Center, Dazhou Central Hospital, Sichuan, China
| | - Fanxin Zeng
- Department of Clinical Research Center, Dazhou Central Hospital, Sichuan, China.
| | - Jing Wang
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China.
| | - Jing Wu
- Department of Gastroenterology, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China.
- Department of Gastroenterology, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China.
- Department of Gastroenterology, School of Clinical Medicine, Peking University Ninth, Beijing, 100038, China.
- , No. 95, Yongan Road, Xicheng District, Beijing, 100050, China.
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Girithar HN, Staats Pires A, Ahn SB, Guillemin GJ, Gluch L, Heng B. Involvement of the kynurenine pathway in breast cancer: updates on clinical research and trials. Br J Cancer 2023; 129:185-203. [PMID: 37041200 PMCID: PMC10338682 DOI: 10.1038/s41416-023-02245-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 03/04/2023] [Accepted: 03/17/2023] [Indexed: 04/13/2023] Open
Abstract
Breast cancer (BrCa) is the leading cause of cancer incidence and mortality in women worldwide. While BrCa treatment has been shown to be highly successful if detected at an early stage, there are few effective strategies to treat metastatic tumours. Hence, metastasis remains the main cause in most of BrCa deaths, highlighting the need for new approaches in this group of patients. Immunotherapy has been gaining attention as a new treatment for BrCa metastasis and the kynurenine pathway (KP) has been suggested as one of the potential targets. The KP is the major biochemical pathway in tryptophan (TRP) metabolism, catabolising TRP to nicotinamide adenine dinucleotide (NAD+). The KP has been reported to be elevated under inflammatory conditions such as cancers and that its activity suppresses immune surveillance. Dysregulation of the KP has previously been reported implicated in BrCa. This review aims to discuss and provide an update on the current mechanisms involved in KP-mediated immune suppression and cancer growth. Furthermore, we also provide a summary on 58 studies about the involvement of the KP and BrCa and five clinical trials targeting KP enzymes and their outcome.
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Affiliation(s)
- Hemaasri-Neya Girithar
- Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ananda Staats Pires
- Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Seong Beom Ahn
- Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Gilles J Guillemin
- Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Laurence Gluch
- The Strathfield Breast Centre, Strathfield, NSW, Australia
| | - Benjamin Heng
- Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia.
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Gong Y, Chen A, Zhang G, Shen Q, Zou L, Li J, Miao YB, Liu W. Cracking Brain Diseases from Gut Microbes-Mediated Metabolites for Precise Treatment. Int J Biol Sci 2023; 19:2974-2998. [PMID: 37416776 PMCID: PMC10321288 DOI: 10.7150/ijbs.85259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/24/2023] [Indexed: 07/08/2023] Open
Abstract
The gut-brain axis has been a subject of significant interest in recent years. Understanding the link between the gut and brain axis is crucial for the treatment of disorders. Here, the intricate components and unique relationship between gut microbiota-derived metabolites and the brain are explained in detail. Additionally, the association between gut microbiota-derived metabolites and the integrity of the blood-brain barrier and brain health is emphasized. Meanwhile, gut microbiota-derived metabolites with their recent applications, challenges and opportunities their pathways on different disease treatment are focus discussed. The prospective strategy of gut microbiota-derived metabolites potential applies to the brain disease treatments, such as Parkinson's disease and Alzheimer's disease, is proposed. This review provides a broad perspective on gut microbiota-derived metabolites characteristics facilitate understand the connection between gut and brain and pave the way for the development of a new medication delivery system for gut microbiota-derived metabolites.
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Affiliation(s)
- Ying Gong
- Department of Haematology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine of University of Electronic Science and Technology of China, No. 32, West Section 2, First Ring Road, Qingyang District, Chengdu 610000, China
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610041, China
| | - Anmei Chen
- Department of Haematology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine of University of Electronic Science and Technology of China, No. 32, West Section 2, First Ring Road, Qingyang District, Chengdu 610000, China
| | - Guohui Zhang
- Key Laboratory of reproductive medicine, Sichuan Provincial maternity and Child Health Care Hospital, Chengdu 610000, China
| | - Qing Shen
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610041, China
| | - Liang Zou
- School of Food and Biological Engineering, Chengdu University, Chengdu 610106, Sichuan, China
| | - Jiahong Li
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610041, China
| | - Yang-Bao Miao
- Department of Haematology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine of University of Electronic Science and Technology of China, No. 32, West Section 2, First Ring Road, Qingyang District, Chengdu 610000, China
| | - Weixin Liu
- Key Laboratory of reproductive medicine, Sichuan Provincial maternity and Child Health Care Hospital, Chengdu 610000, China
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11
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Qi Z, Sun N, Liu C. Glyoxylate cycle maintains the metabolic homeostasis of Pseudomonas aeruginosa in viable but nonculturable state induced by chlorine stress. Microbiol Res 2023; 270:127341. [PMID: 36870195 DOI: 10.1016/j.micres.2023.127341] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/18/2023] [Accepted: 02/18/2023] [Indexed: 02/23/2023]
Abstract
Bacteria enter a viable but non-culturable (VBNC) state with low metabolic activity to cope with environmental stress (e.g., chlorine disinfection). Elucidating the mechanism and key pathway of VBNC bacteria maintaining low metabolic competence is of great significance to realize their effective control and reduce their environmental and health risks. This study discovered that the glyoxylate cycle is a key metabolic pathway for VBNC bacteria, but not for culturable bacteria. And blocking the glyoxylate cycle pathway inhibited the reactivation and led to the death of VBNC bacteria. The main mechanisms involved the breakdown of material and energy metabolism and the antioxidant system. Gas chromatography-tandem mass spectrometry analysis showed that blocking the glyoxylate cycle led to a disruption of carbohydrate metabolism and fatty acid catabolism in VBNC bacteria. As a result, the energy metabolism system of VBNC bacteria collapsed and the abundance of energy metabolites (ATP, NAD+ and NADP+) decreased significantly. Moreover, the decrease in the level of quorum sensing signaling molecules (quinolinone and N-Butanoyl-D-homoserine lactone) inhibited the synthesis of extracellular polymeric substances (EPSs) and biofilm formation. And the downregulation of glycerophospholipid metabolic competence increased the permeability of cell membranes, leading to the entry of large amounts of hypochlorous acid (HClO) into the bacteria. In addition, the down-regulation of nucleotide metabolism, glutathione metabolism, and the reduction of antioxidant enzyme content resulted in the inability to scavenge reactive oxygen species (ROS) generated by chlorine stress. The large production of ROS and the reduction of antioxidants together led to the breakdown of the antioxidant system of VBNC bacteria. In short, the glyoxylate cycle is the key metabolism pathway of VBNC bacteria for stress resistance and maintaining cellular metabolic balance, and targeting the glyoxylate cycle represents an attractive strategy for developing new and efficient disinfection methods for the control of VBNC bacteria.
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Affiliation(s)
- Zheng Qi
- School of Environmental Science and Engineering, Shandong Key Laboratory of Environmental Processes and Health, China-America CRC for Environment & Health of Shandong Province, Shandong University, 72 Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Na Sun
- Jining Ecology and Environment Bureau, 30 Pipashan Street, Rencheng, Jining, Shandong, PR China
| | - Chunguang Liu
- School of Environmental Science and Engineering, Shandong Key Laboratory of Environmental Processes and Health, China-America CRC for Environment & Health of Shandong Province, Shandong University, 72 Jimo Binhai Road, Qingdao, Shandong 266237, PR China; Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangdong, PR China.
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12
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Newton A, McCann L, Huo L, Liu A. Kynurenine Pathway Regulation at Its Critical Junctions with Fluctuation of Tryptophan. Metabolites 2023; 13:metabo13040500. [PMID: 37110158 PMCID: PMC10143591 DOI: 10.3390/metabo13040500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/14/2023] [Accepted: 03/28/2023] [Indexed: 04/29/2023] Open
Abstract
The kynurenine pathway (KP) is the primary route for the catabolism of the essential amino acid tryptophan. The central KP metabolites are neurologically active molecules or biosynthetic precursors to critical molecules, such as NAD+. Within this pathway are three enzymes of interest, HAO, ACMSD, and AMSDH, whose substrates and/or products can spontaneously cyclize to form side products such as quinolinic acid (QA or QUIN) and picolinic acid. Due to their unstable nature for spontaneous autocyclization, it might be expected that the levels of these side products would be dependent on tryptophan intake; however, this is not the case in healthy individuals. On top of that, the regulatory mechanisms of the KP remain unknown, even after a deeper understanding of the structure and mechanism of the enzymes that handle these unstable KP metabolic intermediates. Thus, the question arises, how do these enzymes compete with the autocyclization of their substrates, especially amidst increased tryptophan levels? Here, we propose the formation of a transient enzyme complex as a regulatory mechanism for metabolite distribution between enzymatic and non-enzymatic routes during periods of increased metabolic intake. Amid high levels of tryptophan, HAO, ACMSD, and AMSDH may bind together, forming a tunnel to shuttle the metabolites through each enzyme, consequently regulating the autocyclization of their products. Though further research is required to establish the formation of transient complexation as a solution to the regulatory mysteries of the KP, our docking model studies support this new hypothesis.
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Affiliation(s)
- Ashley Newton
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Luree McCann
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Lu Huo
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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13
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Su X, Gao Y, Yang R. Gut Microbiota-Derived Tryptophan Metabolites Maintain Gut and Systemic Homeostasis. Cells 2022; 11:2296. [PMID: 35892593 PMCID: PMC9330295 DOI: 10.3390/cells11152296] [Citation(s) in RCA: 159] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/15/2022] [Accepted: 07/23/2022] [Indexed: 12/16/2022] Open
Abstract
Tryptophan is an essential amino acid from dietary proteins. It can be metabolized into different metabolites in both the gut microbiota and tissue cells. Tryptophan metabolites such as indole-3-lactate (ILA), indole-3-acrylate (IAC), indole-3-propionate (IPA), indole-3-aldehyde (IAID), indoleacetic acid (IAA), indole-3-acetaldehyde and Kyn can be produced by intestinal microorganisms through direct Trp transformation and also, partly, the kynurenine (Kyn) pathway. These metabolites play a critical role in maintaining the homeostasis of the gut and systematic immunity and also potentially affect the occurrence and development of diseases such as inflammatory bowel diseases, tumors, obesity and metabolic syndrome, diseases in the nervous system, infectious diseases, vascular inflammation and cardiovascular diseases and hepatic fibrosis. They can not only promote the differentiation and function of anti-inflammatory macrophages, Treg cells, CD4+CD8αα+ regulatory cells, IL-10+ and/or IL-35+B regulatory cells but also IL-22-producing innate lymphoid cells 3 (ILC3), which are involved in maintaining the gut mucosal homeostasis. These findings have important consequences in the immunotherapy against tumor and other immune-associated diseases. We will summarize here the recent advances in understanding the generation and regulation of tryptophan metabolites in the gut microbiota, the role of gut microbiota-derived tryptophan metabolites in different immune cells, the occurrence and development of diseases and immunotherapy against immune-associated diseases.
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Affiliation(s)
- Xiaomin Su
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center, Nankai University, Tianjin 300071, China; (X.S.); (Y.G.)
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
- Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin 300071, China
| | - Yunhuan Gao
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center, Nankai University, Tianjin 300071, China; (X.S.); (Y.G.)
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
- Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin 300071, China
| | - Rongcun Yang
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center, Nankai University, Tianjin 300071, China; (X.S.); (Y.G.)
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
- Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin 300071, China
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14
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TrpNet: Understanding Tryptophan Metabolism across Gut Microbiome. Metabolites 2021; 12:metabo12010010. [PMID: 35050132 PMCID: PMC8777792 DOI: 10.3390/metabo12010010] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 12/12/2022] Open
Abstract
Crosstalk between the gut microbiome and the host plays an important role in animal development and health. Small compounds are key mediators in this host–gut microbiome dialogue. For instance, tryptophan metabolites, generated by biotransformation of tryptophan through complex host–microbiome co-metabolism can trigger immune, metabolic, and neuronal effects at local and distant sites. However, the origin of tryptophan metabolites and the underlying tryptophan metabolic pathway(s) are not well characterized in the current literature. A large number of the microbial contributors of tryptophan metabolism remain unknown, and there is a growing interest in predicting tryptophan metabolites for a given microbiome. Here, we introduce TrpNet, a comprehensive database and analytics platform dedicated to tryptophan metabolism within the context of host (human and mouse) and gut microbiome interactions. TrpNet contains data on tryptophan metabolism involving 130 reactions, 108 metabolites and 91 enzymes across 1246 human gut bacterial species and 88 mouse gut bacterial species. Users can browse, search, and highlight the tryptophan metabolic pathway, as well as predict tryptophan metabolites on the basis of a given taxonomy profile using a Bayesian logistic regression model. We validated our approach using two gut microbiome metabolomics studies and demonstrated that TrpNet was able to better predict alterations in in indole derivatives compared to other established methods.
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15
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Recent advances in clinical trials targeting the kynurenine pathway. Pharmacol Ther 2021; 236:108055. [PMID: 34929198 DOI: 10.1016/j.pharmthera.2021.108055] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/15/2021] [Accepted: 12/13/2021] [Indexed: 12/14/2022]
Abstract
The kynurenine pathway (KP) is the major catabolic pathway for the essential amino acid tryptophan leading to the production of nicotinamide adenine dinucleotide. In inflammatory conditions, the activation of the KP leads to the production of several bioactive metabolites including kynurenine, 3-hydroxykynurenine, 3-hydroxyanthranilic acid, kynurenic acid and quinolinic acid. These metabolites can have redox and immune suppressive activity, be neurotoxic or neuroprotective. While the activity of the pathway is tightly regulated under normal physiological condition, it can be upregulated by immunological activation and inflammation. The dysregulation of the KP has been implicated in wide range of neurological diseases and psychiatric disorders. In this review, we discuss the mechanisms involved in KP-mediated neurotoxicity and immune suppression, and its role in diseases of our expertise including cancer, chronic pain and multiple sclerosis. We also provide updates on the clinical trials evaluating the efficacy of KP inhibitors and/or analogues in each respective disease.
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16
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Involvement of Kynurenine Pathway in Hepatocellular Carcinoma. Cancers (Basel) 2021; 13:cancers13205180. [PMID: 34680327 PMCID: PMC8533819 DOI: 10.3390/cancers13205180] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/08/2021] [Accepted: 10/13/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary The kynurenine pathway (KP) is a biochemical pathway that synthesizes the vital coenzyme, nicotinamide adenine dinucleotide (NAD+). In cancer, the KP is significantly activated, leading to tryptophan depletion and the production of downstream metabolites, which skews the immune response towards tumour tolerance. More specifically, advanced stage cancers that readily metastasize evidence the most dysregulation in KP enzymes, providing a clear link between the KP and cancer morbidity. Consequently, this provides the rationale for an attractive new drug discovery opportunity for adjuvant therapeutics targeting KP-mediated immune tolerance, which would greatly complement current pharmacological interventions. In this review, we summarize recent developments in the roles of the KP and clinical trials examining KP inhibition in liver cancer. Abstract As the second and third leading cancer-related death in men and the world, respectively, primary liver cancer remains a major concern to human health. Despite advances in diagnostic technology, patients with primary liver cancer are often diagnosed at an advanced stage. Treatment options for patients with advanced hepatocarcinoma (HCC) are limited to systemic treatment with multikinase inhibitors and immunotherapy. Furthermore, the 5-year survival rate for these late-stage HCC patients is approximately 12% worldwide. There is an unmet need to identify novel treatment options and/or sensitive blood-based biomarker(s) to detect this cancer at an early stage. Given that the liver harbours the largest proportion of immune cells in the human body, understanding the tumour–immune microenvironment has gained increasing attention as a potential target to treat cancer. The kynurenine pathway (KP) has been proposed to be one of the key mechanisms used by the tumour cells to escape immune surveillance for proliferation and metastasis. In an inflammatory environment such as cancer, the KP is elevated, suppressing local immune cell populations and enhancing tumour growth. In this review, we collectively describe the roles of the KP in cancer and provide information on the latest research into the KP in primary liver cancer.
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17
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Cavalli G, Tengesdal IW, Gresnigt M, Nemkov T, Arts RJW, Domínguez-Andrés J, Molteni R, Stefanoni D, Cantoni E, Cassina L, Giugliano S, Schraa K, Mills TS, Pietras EM, Eisenmensser EZ, Dagna L, Boletta A, D'Alessandro A, Joosten LAB, Netea MG, Dinarello CA. The anti-inflammatory cytokine interleukin-37 is an inhibitor of trained immunity. Cell Rep 2021; 35:108955. [PMID: 33826894 DOI: 10.1016/j.celrep.2021.108955] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/08/2020] [Accepted: 03/17/2021] [Indexed: 02/07/2023] Open
Abstract
Trained immunity (TI) is a de facto innate immune memory program induced in monocytes/macrophages by exposure to pathogens or vaccines, which evolved as protection against infections. TI is characterized by immunometabolic changes and histone post-translational modifications, which enhance production of pro-inflammatory cytokines. As aberrant activation of TI is implicated in inflammatory diseases, tight regulation is critical; however, the mechanisms responsible for this modulation remain elusive. Interleukin-37 (IL-37) is an anti-inflammatory cytokine that curbs inflammation and modulates metabolic pathways. In this study, we show that administration of recombinant IL-37 abrogates the protective effects of TI in vivo, as revealed by reduced host pro-inflammatory responses and survival to disseminated candidiasis. Mechanistically, IL-37 reverses the immunometabolic changes and histone post-translational modifications characteristic of TI in monocytes, thus suppressing cytokine production in response to infection. IL-37 thereby emerges as an inhibitor of TI and as a potential therapeutic target in immune-mediated pathologies.
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Affiliation(s)
- Giulio Cavalli
- Department of Medicine, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA; Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | - Isak W Tengesdal
- Department of Medicine, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - Mark Gresnigt
- Department of Medicine, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA; Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Rob J W Arts
- Department of Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Raffaella Molteni
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | | | - Laura Cassina
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Giugliano
- Laboratory of Mucosal Immunology and Microbiota, Humanitas Clinical and Research Center - IRCCS, via Manzoni 56, 20089 Rozzano (MI), Italy
| | - Kiki Schraa
- Department of Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Taylor S Mills
- Division of Hematology, Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - Eric M Pietras
- Division of Hematology, Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - Elan Z Eisenmensser
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Lorenzo Dagna
- Vita-Salute San Raffaele University, Milan, Italy; Unit of Immunology, Rheumatology, Allergy and Rare Diseases, IRCCS San Raffaele Hospital, Milan, Italy
| | - Alessandra Boletta
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Leo A B Joosten
- Department of Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Mihai G Netea
- Department of Medicine, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Charles A Dinarello
- Department of Medicine, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA.
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18
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Abstract
Bacterial cells utilize toxin-antitoxin systems to inhibit self-reproduction, while maintaining viability, when faced with environmental challenges. The activation of the toxin is often coupled to the induction of cellular response pathways, such as the stringent response, in response to multiple stress conditions. Under these conditions, the cell enters a quiescent state referred to as dormancy or persistence. How toxin activation triggers persistence and induces a systemic stress response in the alphaproteobacteria remains unclear. Here, we report that in Caulobacter, a hipA2-encoded bacterial toxin contributes to bacterial persistence by manipulating intracellular amino acid balance. HipA2 is a serine/threonine kinase that deactivates tryptophanyl-tRNA synthetase by phosphorylation, leading to stalled protein synthesis and the accumulation of free tryptophan. An increased level of tryptophan allosterically activates the adenylyltransferase activity of GlnE that, in turn, deactivates glutamine synthetase GlnA by adenylylation. The inactivation of GlnA promotes the deprivation of glutamine in the cell, which triggers a stringent response. By screening 69 stress conditions, we find that HipBA2 responds to multiple stress signals through the proteolysis of HipB2 antitoxin by the Lon protease and the release of active HipA2 kinase, revealing a molecular mechanism that allows disparate stress conditions to be sensed and funneled into a single response pathway.IMPORTANCE To overcome various environmental challenges, bacterial cells can enter a physiologically quiescent state, known as dormancy or persistence, which balances growth and viability. In this study, we report a new mechanism by which a toxin-antitoxin system responds to harsh environmental conditions or nutrient deprivation by orchestrating a dormant state while preserving viability. The hipA2-encoded kinase functions as a toxin in Caulobacter, inducing bacterial persistence by disturbing the intracellular tryptophan-glutamine balance. A nitrogen regulatory circuit can be regulated by the intracellular level of tryptophan, which mimics the allosteric role of glutamine in this feedback loop. The HipBA2 module senses different types of stress conditions by increasing the intracellular level of tryptophan, which in turn breaks the tryptophan-glutamine balance and induces glutamine deprivation. Our results reveal a molecular mechanism that allows disparate environmental challenges to converge on a common pathway that results in a dormant state.
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19
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Wang Y, Liu KF, Yang Y, Davis I, Liu A. Observing 3-hydroxyanthranilate-3,4-dioxygenase in action through a crystalline lens. Proc Natl Acad Sci U S A 2020; 117:19720-19730. [PMID: 32732435 PMCID: PMC7443976 DOI: 10.1073/pnas.2005327117] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The synthesis of quinolinic acid from tryptophan is a critical step in the de novo biosynthesis of nicotinamide adenine dinucleotide (NAD+) in mammals. Herein, the nonheme iron-based 3-hydroxyanthranilate-3,4-dioxygenase responsible for quinolinic acid production was studied by performing time-resolved in crystallo reactions monitored by UV-vis microspectroscopy, electron paramagnetic resonance (EPR) spectroscopy, and X-ray crystallography. Seven catalytic intermediates were kinetically and structurally resolved in the crystalline state, and each accompanies protein conformational changes at the active site. Among them, a monooxygenated, seven-membered lactone intermediate as a monodentate ligand of the iron center at 1.59-Å resolution was captured, which presumably corresponds to a substrate-based radical species observed by EPR using a slurry of small-sized single crystals. Other structural snapshots determined at around 2.0-Å resolution include monodentate and subsequently bidentate coordinated substrate, superoxo, alkylperoxo, and two metal-bound enol tautomers of the unstable dioxygenase product. These results reveal a detailed stepwise O-atom transfer dioxygenase mechanism along with potential isomerization activity that fine-tunes product profiling and affects the production of quinolinic acid at a junction of the metabolic pathway.
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Affiliation(s)
- Yifan Wang
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Yu Yang
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Ian Davis
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Aimin Liu
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249;
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20
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Brown J, Robusto B, Morel L. Intestinal Dysbiosis and Tryptophan Metabolism in Autoimmunity. Front Immunol 2020; 11:1741. [PMID: 32849620 PMCID: PMC7417361 DOI: 10.3389/fimmu.2020.01741] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 06/30/2020] [Indexed: 12/12/2022] Open
Abstract
The development of autoimmunity involves complex interactions between genetics and environmental triggers. The gut microbiota is an important environmental constituent that can heavily influence both local and systemic immune reactivity through distinct mechanisms. It is therefore a relevant environmental trigger or amplifier to consider in autoimmunity. This review will examine recent evidence for an association between intestinal dysbiosis and autoimmune diseases, and the mechanisms by which the gut microbiota may contribute to autoimmune activation. We will specifically focus on recent studies connecting tryptophan metabolism to autoimmune disease pathogenesis and discuss evidence for a microbial origin. This will be discussed in the context of our current understanding of how tryptophan metabolites regulate immune responses, and how it may, or may not, be applicable to autoimmunity.
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Affiliation(s)
- Josephine Brown
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Brian Robusto
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Laurence Morel
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, United States
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21
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Geng J, Weitz AC, Dornevil K, Hendrich MP, Liu A. Kinetic and Spectroscopic Characterization of the Catalytic Ternary Complex of Tryptophan 2,3-Dioxygenase. Biochemistry 2020; 59:2813-2822. [PMID: 32659080 DOI: 10.1021/acs.biochem.0c00179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The first step of the kynurenine pathway for l-tryptophan (l-Trp) degradation is catalyzed by heme-dependent dioxygenases, tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase. In this work, we employed stopped-flow optical absorption spectroscopy to study the kinetic behavior of the Michaelis complex of Cupriavidus metallidurans TDO (cmTDO) to improve our understanding of oxygen activation and initial oxidation of l-Trp. On the basis of the stopped-flow results, rapid freeze-quench (RFQ) experiments were performed to capture and characterize this intermediate by Mössbauer spectroscopy. By incorporating the chlorite dismutase-chlorite system to produce high concentrations of solubilized O2, we were able to capture the Michaelis complex of cmTDO in a nearly quantitative yield. The RFQ-Mössbauer results confirmed the identity of the Michaelis complex as an O2-bound ferrous species. They revealed remarkable similarities between the electronic properties of the Michaelis complex and those of the O2 adduct of myoglobin. We also found that the decay of this reactive intermediate is the rate-limiting step of the catalytic reaction. An inverse α-secondary substrate kinetic isotope effect was observed with a kH/kD of 0.87 ± 0.03 when (indole-d5)-l-Trp was employed as the substrate. This work provides an important piece of spectroscopic evidence of the chemical identity of the Michaelis complex of bacterial TDO.
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Affiliation(s)
- Jiafeng Geng
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Andrew C Weitz
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Kednerlin Dornevil
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States.,Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Michael P Hendrich
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Aimin Liu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States.,Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
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Granja-Travez RS, Persinoti GF, Squina FM, Bugg TDH. Functional genomic analysis of bacterial lignin degraders: diversity in mechanisms of lignin oxidation and metabolism. Appl Microbiol Biotechnol 2020; 104:3305-3320. [PMID: 32088760 DOI: 10.1007/s00253-019-10318-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/06/2019] [Accepted: 12/13/2019] [Indexed: 02/07/2023]
Abstract
Although several bacterial lignin-oxidising enzymes have been discovered in recent years, it is not yet clear whether different lignin-degrading bacteria use similar mechanisms for lignin oxidation and degradation of lignin fragments. Genome sequences of 13 bacterial lignin-oxidising bacteria, including new genome sequences for Microbacterium phyllosphaerae and Agrobacterium sp., were analysed for the presence of lignin-oxidising enzymes and aromatic degradation gene clusters that could be used to metabolise the products of lignin degradation. Ten bacterial genomes contain DyP-type peroxidases, and ten bacterial strains contain putative multi-copper oxidases (MCOs), both known to have activity for lignin oxidation. Only one strain lacks both MCOs and DyP-type peroxidase genes. Eleven bacterial genomes contain aromatic degradation gene clusters, of which ten contain the central β-ketoadipate pathway, with variable numbers and types of degradation clusters for other aromatic substrates. Hence, there appear to be diverse metabolic strategies used for lignin oxidation in bacteria, while the β-ketoadipate pathway appears to be the most common route for aromatic metabolism in lignin-degrading bacteria.
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Affiliation(s)
- Rommel Santiago Granja-Travez
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.,Facultad de Ciencias de la Ingeniería e Industrias, Universidad UTE, Quito, Ecuador
| | | | - Fabio M Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil
| | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
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He P, Jiang WD, Liu XA, Feng L, Wu P, Liu Y, Jiang J, Tan BP, Yang QH, Kuang SY, Tang L, Zhou XQ. Dietary biotin deficiency decreased growth performance and impaired the immune function of the head kidney, spleen and skin in on-growing grass carp (Ctenopharyngodon idella). FISH & SHELLFISH IMMUNOLOGY 2020; 97:216-234. [PMID: 31857225 DOI: 10.1016/j.fsi.2019.12.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 12/06/2019] [Accepted: 12/13/2019] [Indexed: 06/10/2023]
Abstract
The aim of this study was to investigate the effects of dietary biotin deficiency on the growth performance and immune function of the head kidney, spleen and skin in on-growing grass carp (Ctenopharyngodon idella). A total of 540 on-growing grass carp (117.11 ± 0.48 g) were fed six diets containing increasing levels of biotin (0.012, 0.110, 0.214, 0.311, 0.427 and 0.518 mg/kg diet) for 70 days. Subsequently, a challenge experiment was performed by infecting them with Aeromonas hydrophila for six days. Our results showed that compared with the appropriate biotin level, (1) biotin deficiency (0.012 mg/kg diet) reduced the activities of lysozyme (LZ) and acid phosphatase (ACP), decreased the contents of complement 3 (C3), C4 and immunoglobulin M (IgM), as well as reduced the mRNA levels of antimicrobial peptides in the head kidney, spleen and skin of on-growing grass carp; (2) biotin deficiency reduced the mRNA levels of anti-microbial substances: liver-expressed antimicrobial peptide (LEAP) -2A, LEAP-2B, hepcidin, β-defensin-1 and mucin 2 in the head kidney, spleen and skin of on-growing grass carp; (3) biotin deficiency increased the mRNA levels of pro-inflammatory cytokines interleukin 1β (IL-1β), IL-6, IL-8, IL-12p40, IL-15, IL-17D, tumour necrosis factor α (TNF-α) and interferon γ2 (IFN-γ2) partially in association with nuclear factor-kappa B (NF-κB) signalling and reduced anti-inflammatory IL-4/13A, IL-10, IL-11 and transforming growth factor β1 (TGF-β1) mRNA levels partially in association with target of rapamycin (TOR) signalling in the head kidney, spleen and skin of on-growing grass carp. Interestingly, biotin deficiency had no effect on the expression of IL-12p35, IL-4/13B, TGF-β2, 4E-BP1 (skin only) or IKKα in the head kidney, spleen and skin of on-growing grass carp. In conclusion, the results indicated that biotin deficiency impaired the immune function of the head kidney, spleen and skin in fish. Finally, based on the percent weight gain (PWG), the ability to prevent skin haemorrhages and lesions, the LZ activity in the head kidney and the C4 content in the spleen, the optimal dietary biotin levels for on-growing grass carp (117-534 g) were estimated as 0.210, 0.230, 0.245 and 0.238 mg/kg diet, respectively.
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Affiliation(s)
- Peng He
- Animal Nutrition Institute, Sichuan Agricultural University, Sichuan, Chengdu, 611130, China
| | - Wei-Dan Jiang
- Animal Nutrition Institute, Sichuan Agricultural University, Sichuan, Chengdu, 611130, China; Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Sichuan, Chengdu, 611130, China; Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Sichuan Agricultural University, Sichuan, Chengdu, 611130, China
| | - Xiang-An Liu
- Animal Nutrition Institute, Sichuan Academy of Animal Science, Chengdu, 610066, China
| | - Lin Feng
- Animal Nutrition Institute, Sichuan Agricultural University, Sichuan, Chengdu, 611130, China; Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Sichuan, Chengdu, 611130, China; Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Sichuan Agricultural University, Sichuan, Chengdu, 611130, China
| | - Pei Wu
- Animal Nutrition Institute, Sichuan Agricultural University, Sichuan, Chengdu, 611130, China; Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Sichuan, Chengdu, 611130, China; Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Sichuan Agricultural University, Sichuan, Chengdu, 611130, China
| | - Yang Liu
- Animal Nutrition Institute, Sichuan Agricultural University, Sichuan, Chengdu, 611130, China; Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Sichuan, Chengdu, 611130, China; Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Sichuan Agricultural University, Sichuan, Chengdu, 611130, China
| | - Jun Jiang
- Animal Nutrition Institute, Sichuan Agricultural University, Sichuan, Chengdu, 611130, China
| | - Bei-Ping Tan
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Qi-Hui Yang
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Sheng-Yao Kuang
- Animal Nutrition Institute, Sichuan Academy of Animal Science, Chengdu, 610066, China
| | - Ling Tang
- Animal Nutrition Institute, Sichuan Academy of Animal Science, Chengdu, 610066, China
| | - Xiao-Qiu Zhou
- Animal Nutrition Institute, Sichuan Agricultural University, Sichuan, Chengdu, 611130, China; Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Sichuan, Chengdu, 611130, China; Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Sichuan Agricultural University, Sichuan, Chengdu, 611130, China.
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24
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Nguyen DJM, Theodoropoulos G, Li YY, Wu C, Sha W, Feun LG, Lampidis TJ, Savaraj N, Wangpaichitr M. Targeting the Kynurenine Pathway for the Treatment of Cisplatin-Resistant Lung Cancer. Mol Cancer Res 2020; 18:105-117. [PMID: 31628200 PMCID: PMC7262740 DOI: 10.1158/1541-7786.mcr-19-0239] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 07/09/2019] [Accepted: 10/15/2019] [Indexed: 01/02/2023]
Abstract
Cisplatin resistance is a major barrier in the effective treatment of lung cancer. Cisplatin-resistant (CR) lung cancer cells do not primarily use glucose but rather consume amino acids such as glutamine and tryptophan (Trp) for survival. CR cells activate the kynurenine (KYN) pathway (KP) to cope with excessive reactive oxygen species (ROS) and maintain homeostasis for growth and proliferation. Consequently, indoleamine 2,3-dioxygenase-1 (IDO1) becomes an essential enzyme for CR cells' survival because it initiates and regulates the first step in the KP. Increased IDO1 activities and ROS levels are found in CR cells versus cisplatin-sensitive lung cancer. Importantly, significantly greater KYN/Trp ratio (P = 0.005) is detected in serum of patients who fail cisplatin when compared with naïve treatment. Knocking down IDO1 using shRNA or IDO1 inhibitors heightens ROS levels and results in a significant growth inhibitory effect only on CR cells and not on cisplatin-sensitive cells. Exposing CR cells to antioxidant (TIRON) results in suppression of IDO1 activity and confers resistance to IDO1 inhibition, indicating an interrelationship between ROS and IDO1. Because KYN plays a critical role in reprogramming naïve T cells to the immune-suppressive regulatory T-cell (T-reg) phenotype, we observed higher expression of TGFβ, FoxP3, and CD4+CD25+ in mice bearing CR tumors compared with tumors from cisplatin-sensitive counterparts. IMPLICATIONS: Findings suggest that the enzyme-inhibitory activity and antitumor efficacy of IDO1 inhibitors rely in part on ROS levels, arguing that IDO1 expression alone may be insufficient to determine the clinical benefits for this class of experimental cancer drugs. Importantly, IDO1 inhibitors may be more suitable to treat patients with lung cancer who failed cisplatin therapy than naïve treatment patients.
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Affiliation(s)
- Dan J M Nguyen
- Department of Veterans Affairs, Miami VA Healthcare System, Research Service, Miami, Florida
| | - George Theodoropoulos
- Department of Veterans Affairs, Miami VA Healthcare System, Research Service, Miami, Florida
| | - Ying-Ying Li
- Department of Veterans Affairs, Miami VA Healthcare System, Research Service, Miami, Florida
| | - Chunjing Wu
- Department of Veterans Affairs, Miami VA Healthcare System, Research Service, Miami, Florida
| | - Wei Sha
- Department of Veterans Affairs, Miami VA Healthcare System, Research Service, Miami, Florida
| | - Lynn G Feun
- Department of Medicine, Hematology/Oncology, Miller School of Medicine, University of Miami, Miami, Florida
| | - Theodore J Lampidis
- Department of Cell Biology, Miller School of Medicine, University of Miami, Miami, Florida
| | - Niramol Savaraj
- Department of Veterans Affairs, Miami VA Healthcare System, Research Service, Miami, Florida.
- Department of Medicine, Hematology/Oncology, Miller School of Medicine, University of Miami, Miami, Florida
| | - Medhi Wangpaichitr
- Department of Veterans Affairs, Miami VA Healthcare System, Research Service, Miami, Florida.
- Department of Surgery, Cardiothoracic Surgery, Miller School of Medicine, University of Miami, Miami, Florida
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25
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Li P, Oyang X, Xie X, Guo Y, Li Z, Xi J, Zhu D, Ma X, Liu B, Li J, Xiao Z. Perfluorooctanoic acid and perfluorooctane sulfonate co-exposure induced changes of metabolites and defense pathways in lettuce leaves. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 256:113512. [PMID: 31706779 DOI: 10.1016/j.envpol.2019.113512] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/04/2019] [Accepted: 10/28/2019] [Indexed: 06/10/2023]
Abstract
Growing evidence shows plants are at risks of exposure to various per- and polyfluoroalkyl substances (PFASs), however the phytotoxicity induced by these compounds remains largely unknown on the molecular scale. Here, lettuce exposed to both perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) at different concentrations (500, 1000, 2000 and 5000 ng/L) in hydroponic media was investigated via metabolomics. Under the co-exposure conditions, the growth and biomass were not affected by PFOA and PFOS, but metabolic profiles of mineral elements and organic compounds in lettuce leaves were significantly altered. The contents of Na, Mg, Cu, Fe, Ca and Mo were decreased 1.8%-47.8%, but Zn was increased 7.4%-24.2%. The metabolisms of amino acids and peptides, fatty acids and lipids were down-regulated in a dose-dependent manner, while purine and purine nucleosides were up-regulated, exhibiting the stress response to PFOA and PFOS co-exposure. The reduced amounts of phytol (14.8%-77.0%) and abscisic acid (60.7%-73.8%) indicated the alterations in photosynthesis and signal transduction. The metabolism of (poly)phenol, involved in shikimate-phenylpropanoid pathway and flavonoid branch pathway, was strengthened, to cope with the stress of PFASs. As the final metabolites of (poly)phenol biosynthesis, the abundance of various antioxidants was changed. This study offers comprehensive insight of plant response to PFAS co-exposure and enhances the understanding in detoxifying mechanisms.
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Affiliation(s)
- Pengyang Li
- Department of Municipal and Environmental Engineering, Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, Beijing Jiaotong University, Beijing, 100044, China; Laboratory of Quality and Safety Risk Assessments for Agro-products on Environmental Factors (Beijing), Ministry of Agriculture and Rural Affairs, 100029, China
| | - Xihui Oyang
- Laboratory of Quality and Safety Risk Assessments for Agro-products on Environmental Factors (Beijing), Ministry of Agriculture and Rural Affairs, 100029, China; Beijing Municipal Station of Agro-Environmental Monitoring, 100029, China
| | - Xiaocan Xie
- Department of Vegetable Science, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yang Guo
- Beijing Municipal Station of Agro-Environmental Monitoring, 100029, China
| | - Zhifang Li
- Department of Vegetable Science, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Jialin Xi
- Beijing Municipal Station of Agro-Environmental Monitoring, 100029, China
| | - Dongxue Zhu
- Laboratory of Quality and Safety Risk Assessments for Agro-products on Environmental Factors (Beijing), Ministry of Agriculture and Rural Affairs, 100029, China
| | - Xiao Ma
- Laboratory of Quality and Safety Risk Assessments for Agro-products on Environmental Factors (Beijing), Ministry of Agriculture and Rural Affairs, 100029, China
| | - Bin Liu
- Laboratory of Quality and Safety Risk Assessments for Agro-products on Environmental Factors (Beijing), Ministry of Agriculture and Rural Affairs, 100029, China
| | - Jiuyi Li
- Department of Municipal and Environmental Engineering, Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, Beijing Jiaotong University, Beijing, 100044, China.
| | - Zhiyong Xiao
- Laboratory of Quality and Safety Risk Assessments for Agro-products on Environmental Factors (Beijing), Ministry of Agriculture and Rural Affairs, 100029, China; Beijing Municipal Station of Agro-Environmental Monitoring, 100029, China.
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26
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Kaur H, Bose C, Mande SS. Tryptophan Metabolism by Gut Microbiome and Gut-Brain-Axis: An in silico Analysis. Front Neurosci 2019; 13:1365. [PMID: 31920519 PMCID: PMC6930238 DOI: 10.3389/fnins.2019.01365] [Citation(s) in RCA: 183] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 12/03/2019] [Indexed: 12/14/2022] Open
Abstract
The link between gut microbiome and brain is being slowly acknowledged due to the speculated role of resident gut microbial community in altering the functions of gut-brain axis (GBA). Recently, a number of microbial metabolites (referred to as neuro-active metabolites) produced through tryptophan metabolism have been suggested to influence the GBA. In view of this, the current study focuses on microbial tryptophan metabolism pathways which produce neuro-active metabolites. An in silico analysis was performed on bacterial genomes as well as publicly available gut microbiome data. The results provide a comprehensive catalog of the analyzed pathways across bacteria. The analysis indicates an enrichment of tryptophan metabolism pathways in five gut-associated phyla, namely, Actinobacteria, Firmicutes, Bacteroidetes, Proteobacteria, and Fusobacteria. Further, five genera, namely, Clostridium, Burkholderia, Streptomyces, Pseudomonas, and Bacillus have been predicted to be enriched in terms of number of the analyzed tryptophan metabolism pathways, suggesting a higher potential of these bacterial groups to metabolize tryptophan in gut. Analysis of available microbiome data corresponding to gut samples from patients of neurological diseases and healthy individuals suggests probable association of different sets of tryptophan metabolizing bacterial pathways with the etiology of different diseases. The insights obtained from the present study are expected to provide directions toward designing of microbiome based diagnostic and therapeutic approaches for neurological diseases/disorders.
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Affiliation(s)
| | | | - Sharmila S. Mande
- Life Sciences R&D, TCS Research, Tata Consultancy Services, Pune, India
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27
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Yang Y, Liu F, Liu A. Adapting to oxygen: 3-Hydroxyanthrinilate 3,4-dioxygenase employs loop dynamics to accommodate two substrates with disparate polarities. J Biol Chem 2018; 293:10415-10424. [PMID: 29784877 DOI: 10.1074/jbc.ra118.002698] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/18/2018] [Indexed: 11/06/2022] Open
Abstract
3-Hydroxyanthranilate 3,4-dioxygenase (HAO) is an iron-dependent protein that activates O2 and inserts both oxygen atoms into 3-hydroxyanthranilate (3-HAA). An intriguing question is how HAO can rapidly bind O2, even though local O2 concentrations and diffusion rates are relatively low. Here, a close inspection of the HAO structures revealed that substrate- and inhibitor-bound structures exhibit a closed conformation with three hydrophobic loop regions moving toward the catalytic iron center, whereas the ligand-free structure is open. We hypothesized that these loop movements enhance O2 binding to the binary complex of HAO and 3-HAA. We found that the carboxyl end of 3-HAA triggers changes in two loop regions and that the third loop movement appears to be driven by an H-bond interaction between Asn27 and Ile142 Mutational analyses revealed that N27A, I142A, and I142P variants cannot form a closed conformation, and steady-state kinetic assays indicated that these variants have a substantially higher Km for O2 than WT HAO. This observation suggested enhanced hydrophobicity at the iron center resulting from the concerted loop movements after the binding of the primary substrate, which is hydrophilic. Given that O2 is nonpolar, the increased hydrophobicity at the iron center of the binary complex appears to be essential for rapid O2 binding and activation, explaining the reason for the 3-HAA-induced loop movements. Because substrate binding-induced open-to-closed conformational changes are common, the results reported here may help further our understanding of how oxygen is enriched in nonheme iron-dependent dioxygenases.
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Affiliation(s)
- Yu Yang
- From the Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249 and
| | - Fange Liu
- the Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Aimin Liu
- From the Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249 and
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28
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Davis I, Yang Y, Wherritt D, Liu A. Reassignment of the human aldehyde dehydrogenase ALDH8A1 (ALDH12) to the kynurenine pathway in tryptophan catabolism. J Biol Chem 2018; 293:9594-9603. [PMID: 29703752 DOI: 10.1074/jbc.ra118.003320] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 04/25/2018] [Indexed: 12/17/2022] Open
Abstract
The kynurenine pathway is the primary route for l-tryptophan degradation in mammals. Intermediates and side products of this pathway are involved in immune response and neurodegenerative diseases. This makes the study of enzymes, especially those from mammalian sources, of the kynurenine pathway worthwhile. Recent studies on a bacterial version of an enzyme of this pathway, 2-aminomuconate semialdehyde (2-AMS) dehydrogenase (AMSDH), have provided a detailed understanding of the catalytic mechanism and identified residues conserved for muconate semialdehyde recognition and activation. Findings from the bacterial enzyme have prompted the reconsideration of the function of a previously identified human aldehyde dehydrogenase, ALDH8A1 (or ALDH12), which was annotated as a retinal dehydrogenase based on its ability to preferentially oxidize 9-cis-retinal over trans-retinal. Here, we provide compelling bioinformatics and experimental evidence that human ALDH8A1 should be reassigned to the missing 2-AMS dehydrogenase of the kynurenine metabolic pathway. For the first time, the product of the semialdehyde oxidation by AMSDH is also revealed by NMR and high-resolution MS. We found that ALDH8A1 catalyzes the NAD+-dependent oxidation of 2-AMS with a catalytic efficiency equivalent to that of AMSDH from the bacterium Pseudomonas fluorescens Substitution of active-site residues required for substrate recognition, binding, and isomerization in the bacterial enzyme resulted in human ALDH8A1 variants with 160-fold increased Km or no detectable activity. In conclusion, this molecular study establishes an additional enzymatic step in an important human pathway for tryptophan catabolism.
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Affiliation(s)
- Ian Davis
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249
| | - Yu Yang
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249
| | - Daniel Wherritt
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249
| | - Aimin Liu
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249
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Ceppa F, Mancini A, Tuohy K. Current evidence linking diet to gut microbiota and brain development and function. Int J Food Sci Nutr 2018; 70:1-19. [DOI: 10.1080/09637486.2018.1462309] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Florencia Ceppa
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all‘Adige, Trento, Italy
| | - Andrea Mancini
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all‘Adige, Trento, Italy
| | - Kieran Tuohy
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all‘Adige, Trento, Italy
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30
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Xie H, Hou Y, Cheng J, Openkova MS, Xia B, Wang W, Li A, Yang K, Li J, Xu H, Yang C, Ma L, Li Z, Fan X, Li K, Lou G. Metabolic profiling and novel plasma biomarkers for predicting survival in epithelial ovarian cancer. Oncotarget 2018; 8:32134-32146. [PMID: 28389631 PMCID: PMC5458273 DOI: 10.18632/oncotarget.16739] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/22/2017] [Indexed: 11/25/2022] Open
Abstract
Epithelial ovarian cancer (EOC) is one of the most lethal gynecological malignancies around the world, and patients with ovarian cancer always have an extremely poor chance of survival. Therefore, it is meaningful to develop a highly efficient model that can predict the overall survival for EOC. In order to investigate whether metabolites could be used to predict the survival of EOC, we performed a metabolic analysis of 98 plasma samples with follow-up information, based on the ultra-performance liquid chromatography mass spectrometry (UPLC/MS) systems in both positive (ESI+) and negative (ESI-) modes. Four metabolites: Kynurenine, Acetylcarnitine, PC (42:11), and LPE(22:0/0:0) were selected as potential predictive biomarkers. The AUC value of metabolite-based risk score, together with pathological stages in predicting three-year survival rate was 0.80. The discrimination performance of these four biomarkers between short-term mortality and long-term survival was excellent, with an AUC value of 0.82. In conclusion, our plasma metabolomics study presented the dysregulated metabolism related to the survival of EOC, and plasma metabolites could be utilized to predict the overall survival and discriminate the short-term mortality and long-term survival for EOC patients. These results could provide supplementary information for further study about EOC survival mechanism and guiding the appropriate clinical treatment.
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Affiliation(s)
- Hongyu Xie
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin 150086, China
| | - Yan Hou
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin 150086, China
| | - Jinlong Cheng
- Department of Gynecology Oncology, the Tumor Hospital, Harbin Medical University, Harbin 150086, China
| | | | - Bairong Xia
- Department of Gynecology Oncology, the Tumor Hospital, Harbin Medical University, Harbin 150086, China
| | - Wenjie Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin 150086, China
| | - Ang Li
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin 150086, China
| | - Kai Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin 150086, China
| | - Junnan Li
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin 150086, China
| | - Huan Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin 150086, China
| | - Chunyan Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin 150086, China
| | - Libing Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin 150086, China
| | - Zhenzi Li
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin 150086, China
| | - Xin Fan
- School of Basic Medical Sciences, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Kang Li
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin 150086, China
| | - Ge Lou
- Department of Gynecology Oncology, the Tumor Hospital, Harbin Medical University, Harbin 150086, China
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31
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The Small RNA ncS35 Regulates Growth in Burkholderia cenocepacia J2315. mSphere 2018; 3:mSphere00579-17. [PMID: 29359187 PMCID: PMC5760752 DOI: 10.1128/msphere.00579-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 12/13/2017] [Indexed: 12/16/2022] Open
Abstract
Small RNAs play an important role in the survival of bacteria in diverse environments. We explored the physiological role of ncS35, a small RNA expressed in B. cenocepacia J2315, an opportunistic pathogen in cystic fibrosis patients. In cystic fibrosis patients, infections can lead to “cepacia syndrome,” a rapidly progressing and often fatal pneumonia. Infections with Burkholderia spp. are difficult to threat with antibiotics because of their high intrinsic resistance and ability to form biofilms. We show that ncS35 attenuates the growth and reduces the metabolic rate of B. cenocepacia and influences biofilm structure. This demonstrates that as-yet-uncharacterized small RNAs with regulatory function can influence physiological traits of B. cenocepacia that are relevant for infection. Burkholderia cenocepacia J2315 is a member of the B. cepacia complex. It has a large genome with three replicons and one plasmid; 7,261 genes code for annotated proteins, while 113 code for functional RNAs. Small regulatory RNAs of B. cenocepacia have not yet been functionally characterized. We investigated a small regulatory RNA, designated ncS35, that was discovered by differential RNA sequencing. Its expression under various conditions was quantified, and a deletion mutant, ΔncS35, was constructed. Compared to planktonic growth in a rich medium, the expression of ncS35 was elevated when B. cenocepacia J2315 was grown in biofilms and in minimal medium. Cells of the deletion mutant showed increased aggregation, higher metabolic activity, a higher growth rate, and an increased susceptibility to tobramycin. A transcriptomic analysis revealed upregulation of the phenylacetic acid and tryptophan degradation pathways in ΔncS35. Computational target prediction indicated that ncS35 likely interacts with the first gene of the tryptophan degradation pathway. Overall, we demonstrated that small RNA ncS35 is a noncoding RNA with an attenuating effect on the metabolic rate and growth. It is possible that slower growth protects B. cenocepacia J2315 against stressors acting on fast-dividing cells and enhances survival under unfavorable conditions. IMPORTANCE Small RNAs play an important role in the survival of bacteria in diverse environments. We explored the physiological role of ncS35, a small RNA expressed in B. cenocepacia J2315, an opportunistic pathogen in cystic fibrosis patients. In cystic fibrosis patients, infections can lead to “cepacia syndrome,” a rapidly progressing and often fatal pneumonia. Infections with Burkholderia spp. are difficult to threat with antibiotics because of their high intrinsic resistance and ability to form biofilms. We show that ncS35 attenuates the growth and reduces the metabolic rate of B. cenocepacia and influences biofilm structure. This demonstrates that as-yet-uncharacterized small RNAs with regulatory function can influence physiological traits of B. cenocepacia that are relevant for infection.
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Crnovčić I, Rückert C, Semsary S, Lang M, Kalinowski J, Keller U. Genetic interrelations in the actinomycin biosynthetic gene clusters of Streptomyces antibioticus IMRU 3720 and Streptomyces chrysomallus ATCC11523, producers of actinomycin X and actinomycin C. Adv Appl Bioinform Chem 2017; 10:29-46. [PMID: 28435299 PMCID: PMC5391158 DOI: 10.2147/aabc.s117707] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Sequencing the actinomycin (acm) biosynthetic gene cluster of Streptomyces antibioticus IMRU 3720, which produces actinomycin X (Acm X), revealed 20 genes organized into a highly similar framework as in the bi-armed acm C biosynthetic gene cluster of Streptomyces chrysomallus but without an attached additional extra arm of orthologues as in the latter. Curiously, the extra arm of the S. chrysomallus gene cluster turned out to perfectly match the single arm of the S. antibioticus gene cluster in the same order of orthologues including the the presence of two pseudogenes, scacmM and scacmN, encoding a cytochrome P450 and its ferredoxin, respectively. Orthologues of the latter genes were both missing in the principal arm of the S. chrysomallus acm C gene cluster. All orthologues of the extra arm showed a G +C-contents different from that of their counterparts in the principal arm. Moreover, the similarities of translation products from the extra arm were all higher to the corresponding translation products of orthologue genes from the S. antibioticus acm X gene cluster than to those encoded by the principal arm of their own gene cluster. This suggests that the duplicated structure of the S. chrysomallus acm C biosynthetic gene cluster evolved from previous fusion between two one-armed acm gene clusters each from a different genetic background. However, while scacmM and scacmN in the extra arm of the S. chrysomallus acm C gene cluster are mutated and therefore are non-functional, their orthologues saacmM and saacmN in the S. antibioticus acm C gene cluster show no defects seemingly encoding active enzymes with functions specific for Acm X biosynthesis. Both acm biosynthetic gene clusters lack a kynurenine-3-monooxygenase gene necessary for biosynthesis of 3-hydroxy-4-methylanthranilic acid, the building block of the Acm chromophore, which suggests participation of a genome-encoded relevant monooxygenase during Acm biosynthesis in both S. chrysomallus and S. antibioticus.
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Affiliation(s)
- Ivana Crnovčić
- Institut für Chemie, Technische Universität Berlin, Berlin-Charlottenburg
| | - Christian Rückert
- Technology Platform Genomics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Siamak Semsary
- Institut für Chemie, Technische Universität Berlin, Berlin-Charlottenburg
| | - Manuel Lang
- Institut für Chemie, Technische Universität Berlin, Berlin-Charlottenburg
| | - Jörn Kalinowski
- Technology Platform Genomics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Ullrich Keller
- Institut für Chemie, Technische Universität Berlin, Berlin-Charlottenburg
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Understanding the role of the kynurenine pathway in human breast cancer immunobiology. Oncotarget 2016; 7:6506-20. [PMID: 26646699 PMCID: PMC4872729 DOI: 10.18632/oncotarget.6467] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 11/25/2015] [Indexed: 02/06/2023] Open
Abstract
Breast cancer (BrCa) is the leading cause of cancer related death in women. While current diagnostic modalities provide opportunities for early medical intervention, significant proportions of breast tumours escape treatment and metastasize. Gaining increasing recognition as a factor in tumour metastasis is the local immuno-surveillance environment. Following identification of the role played by the enzyme indoleamine dioxygenase 1 (IDO1) in mediating maternal foetal tolerance, the kynurenine pathway (KP) of tryptophan metabolism has emerged as a key metabolic pathway contributing to immune escape. In inflammatory conditions activation of the KP leads to the production of several immune-modulating metabolites including kynurenine, kynurenic acid, 3-hydroxykynurenine, anthranilic acid, 3-hydroxyanthranilic acid, picolinic acid and quinolinic acid. KP over-activation was first described in BrCa patients in the early 1960s. More evidence has since emerged to suggest that the IDO1 is elevated in advanced BrCa patients and is associated with poor prognosis. Further, IDO1 positive breast tumours have a positive correlation with the density of immune suppressive Foxp3+ T regulatory cells and lymph node metastasis. The analysis of clinical microarray data in invasive BrCa compared to normal tissue showed, using two microarray databank (cBioportal and TCGA), that 86.3% and 91.4% BrCa patients have altered KP enzyme expression respectively. Collectively, these data highlight the key roles played by KP activation in BrCa, particularly in basal BrCa subtypes where expression of most KP enzymes was altered. Accordingly, the use of KP enzyme inhibitors in addition to standard chemotherapy regimens may present a viable therapeutic approach.
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ElRamlawy KG, Fujimura T, Baba K, Kim JW, Kawamoto C, Isobe T, Abe T, Hodge-Hanson K, Downs DM, Refaat IH, Beshr Al-Azhary D, Aki T, Asaoku Y, Hayashi T, Katsutani T, Tsuboi S, Ono K, Kawamoto S. Der f 34, a Novel Major House Dust Mite Allergen Belonging to a Highly Conserved Rid/YjgF/YER057c/UK114 Family of Imine Deaminases. J Biol Chem 2016; 291:21607-21615. [PMID: 27539850 DOI: 10.1074/jbc.m116.728006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 08/18/2016] [Indexed: 12/17/2022] Open
Abstract
The high prevalence of house dust mite (HDM) allergy is a growing health problem worldwide, and the characterization of clinically important HDM allergens is a prerequisite for the development of diagnostic and therapeutic strategies. Here, we report a novel HDM allergen that belongs structurally to the highly conserved Rid/YjgF/YER057c/UK114 family (Rid family) with imine deaminase activity. Isolated HDM cDNA, named der f 34, encodes 128 amino acids homologous to Rid-like proteins. This new protein belongs to the Rid family and has seven conserved residues involved in enamine/imine deaminase activity. Indeed, we demonstrated that purified Der f 34 had imine deaminase activity that preferentially acted on leucine and methionine. Native Der f 34 showed a high IgE binding frequency as revealed by two-dimensional immunoblotting (62.5%) or ELISA (68%), which was comparable with those of a major HDM allergen Der f 2 (77.5 and 79%, respectively). We also found that Der f 34 showed cross-reactivity with another prominent indoor allergen source, Aspergillus fumigatus This is the first report showing that the Rid family imine deaminase represents an additional important pan-allergen that is conserved across organisms.
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Affiliation(s)
- Kareem Gamal ElRamlawy
- From the Hiroshima Research Center for Healthy Aging (HiHA), Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan.,the Department of Zoology, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Takashi Fujimura
- From the Hiroshima Research Center for Healthy Aging (HiHA), Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan,
| | - Koji Baba
- From the Hiroshima Research Center for Healthy Aging (HiHA), Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Ji Won Kim
- From the Hiroshima Research Center for Healthy Aging (HiHA), Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Chika Kawamoto
- From the Hiroshima Research Center for Healthy Aging (HiHA), Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Toshihide Isobe
- From the Hiroshima Research Center for Healthy Aging (HiHA), Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Takuya Abe
- From the Hiroshima Research Center for Healthy Aging (HiHA), Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Kelsey Hodge-Hanson
- the Department of Microbiology, University of Georgia, Athens, Georgia 30602
| | - Diana M Downs
- the Department of Microbiology, University of Georgia, Athens, Georgia 30602
| | - Inas Hussein Refaat
- the Department of Zoology, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Diaa Beshr Al-Azhary
- the Department of Zoology, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Tsunehiro Aki
- From the Hiroshima Research Center for Healthy Aging (HiHA), Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Yoshiko Asaoku
- the Takanobashi Central Hospital, Hiroshima, Hiroshima 730-0042
| | | | | | | | - Kazuhisa Ono
- From the Hiroshima Research Center for Healthy Aging (HiHA), Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan.,the Department of Food Sciences and Biotechnology, Faculty of Life Sciences, Hiroshima Institute of Technology, Hiroshima, Hiroshima 731-5193, Japan
| | - Seiji Kawamoto
- From the Hiroshima Research Center for Healthy Aging (HiHA), Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan,
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Lakshman TR, Chatterjee S, Chakraborty B, Paine TK. Substrate-dependent aromatic ring fission of catechol and 2-aminophenol with O2 catalyzed by a nonheme iron complex of a tripodal N4 ligand. Dalton Trans 2016; 45:8835-44. [PMID: 27148606 DOI: 10.1039/c5dt04541j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The catalytic reactivity of an iron(ii) complex [(TPA)Fe(II)(CH3CN)2](2+) (1) (TPA = tris(2-pyridylmethyl)amine) towards oxygenative aromatic C-C bond cleavage of catechol and 2-aminophenol is presented. Complex 1 exhibits catalytic and regioselective C-C bond cleavage of 3,5-di-tert-butylcatechol (H2DBC) to form intradiol products, whereas it catalyzes extradiol-type C-C bond cleavage of 2-amino-4,6-di-tert-butylphenol (H2AP). The catalytic reactions are found to be pH-dependent and the complex exhibits maximum turnovers at pH 5 in acetonitrile-phthalate buffer. An iron(iii)-catecholate complex [(TPA)Fe(III)(DBC)](+) (2) is formed in the ring cleavage of catechol. In the extradiol-type cleavage of H2AP, an iron(iii)-2-iminobenzosemiquinonate complex [(TPA)Fe(III)(ISQ)](2+) (3) (ISQ = 4,6-di-tert-butyl-2-iminobenzosemiquinonate radical anion) is observed in the reaction pathway. This work shows the importance of the nature of 'redox non-innocent' substrates in governing the mode of ring fission reactivity.
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Affiliation(s)
- Triloke Ranjan Lakshman
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A&2B Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India.
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Functional Characterization of a Novel Member of the Amidohydrolase 2 Protein Family, 2-Hydroxy-1-Naphthoic Acid Nonoxidative Decarboxylase from Burkholderia sp. Strain BC1. J Bacteriol 2016; 198:1755-1763. [PMID: 27068590 DOI: 10.1128/jb.00250-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 04/01/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The gene encoding a nonoxidative decarboxylase capable of catalyzing the transformation of 2-hydroxy-1-naphthoic acid (2H1NA) to 2-naphthol was identified, recombinantly expressed, and purified to homogeneity. The putative gene sequence of the decarboxylase (hndA) encodes a 316-amino-acid protein (HndA) with a predicted molecular mass of 34 kDa. HndA exhibited high identity with uncharacterized amidohydrolase 2 proteins of various Burkholderia species, whereas it showed a modest 27% identity with γ-resorcylate decarboxylase, a well-characterized nonoxidative decarboxylase belonging to the amidohydrolase superfamily. Biochemically characterized HndA demonstrated strict substrate specificity toward 2H1NA, whereas inhibition studies with HndA indicated the presence of zinc as the transition metal center, as confirmed by atomic absorption spectroscopy. A three-dimensional structural model of HndA, followed by docking analysis, identified the conserved metal-coordinating and substrate-binding residues, while their importance in catalysis was validated by site-directed mutagenesis. IMPORTANCE Microbial nonoxidative decarboxylases play a crucial role in the metabolism of a large array of carboxy aromatic chemicals released into the environment from a variety of natural and anthropogenic sources. Among these, hydroxynaphthoic acids are usually encountered as pathway intermediates in the bacterial degradation of polycyclic aromatic hydrocarbons. The present study reveals biochemical and molecular characterization of a 2-hydroxy-1-naphthoic acid nonoxidative decarboxylase involved in an alternative metabolic pathway which can be classified as a member of the small repertoire of nonoxidative decarboxylases belonging to the amidohydrolase 2 family of proteins. The strict substrate specificity and sequence uniqueness make it a novel member of the metallo-dependent hydrolase superfamily.
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Li L, Feng L, Jiang WD, Jiang J, Wu P, Kuang SY, Tang L, Tang WN, Zhang YA, Zhou XQ, Liu Y. Dietary pantothenic acid deficiency and excess depress the growth, intestinal mucosal immune and physical functions by regulating NF-κB, TOR, Nrf2 and MLCK signaling pathways in grass carp (Ctenopharyngodon idella). FISH & SHELLFISH IMMUNOLOGY 2015; 45:399-413. [PMID: 25957886 DOI: 10.1016/j.fsi.2015.04.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/23/2015] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
This study investigated the effects of dietary pantothenic acid (PA) on the growth, intestinal mucosal immune and physical barrier, and relative mRNA levels of signaling molecules in the intestine of grass carp (Ctenopharyngodon idella). A total of 540 grass carp (253.44 ± 0.69 g) were fed six diets with graded levels of PA (PA1, PA15, PA30, PA45, PA60 and PA75 diets) for 8 weeks. The results indicated that compared with PA deficiency (PA1 diet) and excess (PA75 diet) groups, optimal PA supplementation increased (P < 0.05): (1) percent weight gain (PWG), feed intake and feed efficiency; (2) lysozyme activity, complement 3 content, liver-expressed antimicrobial peptide 2 and hepcidin, interleukin 10, transforming growth factor β1 and inhibitor of κBα mRNA levels in some intestinal segments; (3) activities and mRNA levels of copper/zinc superoxide dismutase, manganese superoxide dismutase, catalase, glutathione peroxidase, glutathione S-transferases and glutathione reductase, and NF-E2-related factor 2 (Nrf2) mRNA level in the whole intestine; (4) Claudin b, Claudin 3, Claudin c, Occludin and ZO-1 mRNA levels in some intestinal segments of grass carp. Conversely, optimal PA supplementation decreased (P < 0.05): (1) tumor necrosis factor α, interleukin 1β, interferon γ2, interleukin 8, nuclear factor κB P65 (NF-κB P65), IκB kinase α, IκB kinase β, IκB kinase γ and target of rapamycin (TOR) mRNA expression levels in some intestinal segments; (2) reactive oxygen species, malondialdehyde and protein carbonyl contents, and Kelch-like ECH-associating protein 1a, Kelch-like ECH-associating protein 1b in the intestine; (3) Claudin 12, Claudin 15a and myosin light-chain kinase (MLCK) mRNA levels in some intestinal segments of grass carp. In conclusion, optimum PA promoted growth, intestinal mucosal immune and physical function, as well as regulated mRNA levels of signaling molecules NF-κB P65, TOR, Nrf2 and MLCK in grass carp intestine. Based on the quadratic regression analysis of PWG and intestinal lysozyme activity, the optimal PA levels in grass carp (253.44-745.25 g) were estimated to be 37.73 mg/kg and 41.38 mg/kg diet, respectively.
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Affiliation(s)
- Li Li
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Lin Feng
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Fish Nutrition and Safety Production University Key Laboratory of Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Wei-Dan Jiang
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Fish Nutrition and Safety Production University Key Laboratory of Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Jun Jiang
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Fish Nutrition and Safety Production University Key Laboratory of Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Pei Wu
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Fish Nutrition and Safety Production University Key Laboratory of Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Sheng-Yao Kuang
- Animal Nutrition Institute, Sichuan Academy of Animal Science, Chengdu 610066, Sichuan, China
| | - Ling Tang
- Animal Nutrition Institute, Sichuan Academy of Animal Science, Chengdu 610066, Sichuan, China
| | - Wu-Neng Tang
- Animal Nutrition Institute, Sichuan Academy of Animal Science, Chengdu 610066, Sichuan, China
| | - Yong-An Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiao-Qiu Zhou
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Fish Nutrition and Safety Production University Key Laboratory of Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
| | - Yang Liu
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Fish Nutrition and Safety Production University Key Laboratory of Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
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Davis I, Liu A. What is the tryptophan kynurenine pathway and why is it important to neurotherapeutics? Expert Rev Neurother 2015; 15:719-21. [PMID: 26004930 DOI: 10.1586/14737175.2015.1049999] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The kynurenine pathway has received increasing attention as its connection to inflammation, the immune system and neurological conditions has become more apparent. It is the primary route for tryptophan catabolism in the liver and the starting point for the synthesis of nicotinamide adenine dinucleotide in mammals. Dysregulation or overactivation of this pathway can lead to immune system activation and accumulation of potentially neurotoxic compounds. These aspects make the kynurenine pathway a promising target for therapeutic development to treat inflammation and disease with neurological aspects, especially in cancer patients undergoing chemotherapy.
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Affiliation(s)
- Ian Davis
- Department of Chemistry, Atlanta, GA 30303, USA
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Niehaus TD, Gerdes S, Hodge-Hanson K, Zhukov A, Cooper AJL, ElBadawi-Sidhu M, Fiehn O, Downs DM, Hanson AD. Genomic and experimental evidence for multiple metabolic functions in the RidA/YjgF/YER057c/UK114 (Rid) protein family. BMC Genomics 2015; 16:382. [PMID: 25975565 PMCID: PMC4433059 DOI: 10.1186/s12864-015-1584-3] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 04/27/2015] [Indexed: 12/03/2022] Open
Abstract
Background It is now recognized that enzymatic or chemical side-reactions can convert normal metabolites to useless or toxic ones and that a suite of enzymes exists to mitigate such metabolite damage. Examples are the reactive imine/enamine intermediates produced by threonine dehydratase, which damage the pyridoxal 5'-phosphate cofactor of various enzymes causing inactivation. This damage is pre-empted by RidA proteins, which hydrolyze the imines before they do harm. RidA proteins belong to the YjgF/YER057c/UK114 family (here renamed the Rid family). Most other members of this diverse and ubiquitous family lack defined functions. Results Phylogenetic analysis divided the Rid family into a widely distributed, apparently archetypal RidA subfamily and seven other subfamilies (Rid1 to Rid7) that are largely confined to bacteria and often co-occur in the same organism with RidA and each other. The Rid1 to Rid3 subfamilies, but not the Rid4 to Rid7 subfamilies, have a conserved arginine residue that, in RidA proteins, is essential for imine-hydrolyzing activity. Analysis of the chromosomal context of bacterial RidA genes revealed clustering with genes for threonine dehydratase and other pyridoxal 5'-phosphate-dependent enzymes, which fits with the known RidA imine hydrolase activity. Clustering was also evident between Rid family genes and genes specifying FAD-dependent amine oxidases or enzymes of carbamoyl phosphate metabolism. Biochemical assays showed that Salmonella enterica RidA and Rid2, but not Rid7, can hydrolyze imines generated by amino acid oxidase. Genetic tests indicated that carbamoyl phosphate overproduction is toxic to S. enterica cells lacking RidA, and metabolomic profiling of Rid knockout strains showed ten-fold accumulation of the carbamoyl phosphate-related metabolite dihydroorotate. Conclusions Like the archetypal RidA subfamily, the Rid2, and probably the Rid1 and Rid3 subfamilies, have imine-hydrolyzing activity and can pre-empt damage from imines formed by amine oxidases as well as by pyridoxal 5'-phosphate enzymes. The RidA subfamily has an additional damage pre-emption role in carbamoyl phosphate metabolism that has yet to be biochemically defined. Finally, the Rid4 to Rid7 subfamilies appear not to hydrolyze imines and thus remain mysterious. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1584-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas D Niehaus
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA.
| | - Svetlana Gerdes
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA.
| | | | - Aleksey Zhukov
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA.
| | - Arthur J L Cooper
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY, 10595, USA.
| | - Mona ElBadawi-Sidhu
- Metabolomics Core, UC Davis Genome Center, University of California Davis, Davis, CA, 95616, USA.
| | - Oliver Fiehn
- Metabolomics Core, UC Davis Genome Center, University of California Davis, Davis, CA, 95616, USA.
| | - Diana M Downs
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA.
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA.
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Xu JD, Xing WM, Yuan TJ, Chen J, Lu H. Metabolic changes in the urine of andrographolide sodium bisulfite-treated rats. Hum Exp Toxicol 2015; 35:162-9. [DOI: 10.1177/0960327115579429] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In recent years, andrographolide sodium bisulfite (ASB) has been reported to cause acute renal failure frequently in clinical practice. We hypothesized that changes in metabolic profile could have occurred after administration of ASB. To investigate the metabolic changes caused by ASB-induced nephrotoxicity, metabonomics method was utilized to depict the urine metabolic characteristics and find the specific urine biomarkers associated with ASB-induced nephrotoxicity. Sprague-Dawley rats were randomly assigned into three experimental groups. They received a single daily injection of vehicle (0.9% sodium chloride solution) or ASB at a dose of 100 or 600 mg kg−1 day−1 for 7 days. Twelve-hour urine was collected after the last administration. The routine urinalysis was measured by a urine automatic analyzer while urinary metabolites were evaluated using gas chromatography/mass spectrometry. The acquired data were processed by multivariate principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), and orthogonal PLS-DA. After 7-day administration of ASB, the positive urine samples in protein, occult blood, and ketones were increased, presenting dose dependence. The PCA and PLS-DA models were capable of distinguishing the difference between ASB-treated group and control. Biomarkers such as 1,5-anhydroglucitol, d-erythro-sphingosine, and 2-ketoadipate were identified as the most influential factors in ASB-induced nephrotoxicity.
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Affiliation(s)
- JD Xu
- School of Pharmacology, Zhejiang Chinese Medical University, Hangzhou, China
| | - WM Xing
- School of Pharmacology, Zhejiang Chinese Medical University, Hangzhou, China
| | - TJ Yuan
- School of Pharmacology, Zhejiang Chinese Medical University, Hangzhou, China
| | - J Chen
- School of Pharmacology, Zhejiang Chinese Medical University, Hangzhou, China
| | - H Lu
- School of Pharmacology, Zhejiang Chinese Medical University, Hangzhou, China
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Chatterjee S, Paine TK. Oxygenative Aromatic Ring Cleavage of 2-Aminophenol with Dioxygen Catalyzed by a Nonheme Iron Complex: Catalytic Functional Model of 2-Aminophenol Dioxygenases. Inorg Chem 2015; 54:1720-7. [DOI: 10.1021/ic502658p] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Sayanti Chatterjee
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Tapan Kanti Paine
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
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Niehaus TD, Nguyen TND, Gidda SK, ElBadawi-Sidhu M, Lambrecht JA, McCarty DR, Downs DM, Cooper AJL, Fiehn O, Mullen RT, Hanson AD. Arabidopsis and maize RidA proteins preempt reactive enamine/imine damage to branched-chain amino acid biosynthesis in plastids. THE PLANT CELL 2014; 26:3010-22. [PMID: 25070638 PMCID: PMC4145128 DOI: 10.1105/tpc.114.126854] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 07/02/2014] [Accepted: 07/08/2014] [Indexed: 05/19/2023]
Abstract
RidA (for Reactive Intermediate Deaminase A) proteins are ubiquitous, yet their function in eukaryotes is unclear. It is known that deleting Salmonella enterica ridA causes Ser sensitivity and that S. enterica RidA and its homologs from other organisms hydrolyze the enamine/imine intermediates that Thr dehydratase forms from Ser or Thr. In S. enterica, the Ser-derived enamine/imine inactivates a branched-chain aminotransferase; RidA prevents this damage. Arabidopsis thaliana and maize (Zea mays) have a RidA homolog that is predicted to be plastidial. Expression of either homolog complemented the Ser sensitivity of the S. enterica ridA mutant. The purified proteins hydrolyzed the enamines/imines formed by Thr dehydratase from Ser or Thr and protected the Arabidopsis plastidial branched-chain aminotransferase BCAT3 from inactivation by the Ser-derived enamine/imine. In vitro chloroplast import assays and in vivo localization of green fluorescent protein fusions showed that Arabidopsis RidA and Thr dehydratase are chloroplast targeted. Disrupting Arabidopsis RidA reduced root growth and raised the root and shoot levels of the branched-chain amino acid biosynthesis intermediate 2-oxobutanoate; Ser treatment exacerbated these effects in roots. Supplying Ile reversed the root growth defect. These results indicate that plastidial RidA proteins can preempt damage to BCAT3 and Ile biosynthesis by hydrolyzing the Ser-derived enamine/imine product of Thr dehydratase.
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Affiliation(s)
- Thomas D Niehaus
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Thuy N D Nguyen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Satinder K Gidda
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Mona ElBadawi-Sidhu
- Metabolics Core, UC Davis Genome Center, University of California, Davis, California 95616
| | | | - Donald R McCarty
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Diana M Downs
- Department of Microbiology, University of Georgia, Athens, Georgia 30602
| | - Arthur J L Cooper
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595
| | - Oliver Fiehn
- Metabolics Core, UC Davis Genome Center, University of California, Davis, California 95616
| | - Robert T Mullen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
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Chakraborty B, Bhunya S, Paul A, Paine TK. Reactivity of Biomimetic Iron(II)-2-aminophenolate Complexes toward Dioxygen: Mechanistic Investigations on the Oxidative C–C Bond Cleavage of Substituted 2-Aminophenols. Inorg Chem 2014; 53:4899-912. [DOI: 10.1021/ic403043e] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Biswarup Chakraborty
- Department of Inorganic Chemistry, ‡Raman Center for Atomic, Molecular and Optical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Sourav Bhunya
- Department of Inorganic Chemistry, ‡Raman Center for Atomic, Molecular and Optical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Ankan Paul
- Department of Inorganic Chemistry, ‡Raman Center for Atomic, Molecular and Optical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Tapan Kanti Paine
- Department of Inorganic Chemistry, ‡Raman Center for Atomic, Molecular and Optical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
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Banerjee S, Halder P, Paine TK. Probing the Reactivity of Redox-Active 2-Aminophenolates on Iron Complexes of a Carbanionic N3C Donor Ligand. Z Anorg Allg Chem 2014. [DOI: 10.1002/zaac.201300630] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Geng J, Liu A. Heme-dependent dioxygenases in tryptophan oxidation. Arch Biochem Biophys 2013; 544:18-26. [PMID: 24295960 DOI: 10.1016/j.abb.2013.11.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 11/19/2013] [Accepted: 11/20/2013] [Indexed: 12/29/2022]
Abstract
L-Tryptophan is an essential amino acid for mammals. It is utilized not only for protein synthesis but also for the biosynthesis of serotonin and melatonin by the serotonin pathway as well as nicotinamide adenine dinucleotide by the kynurenine pathway. Although the kynurenine pathway is responsible for the catabolism of over 90% of l-tryptophan in the mammalian intracellular and extracellular pools, the scientific field was dominated in the last century by studies of the serotonin pathway, due to the physiological significance of the latter's catabolic intermediates and products. However, in the past decade, the focus gradually reversed as the link between the kynurenine pathway and various neurodegenerative disorders and immune diseases is increasingly highlighted. Notably, the first step of this pathway, which is catalyzed by heme-dependent dioxygenases, has been proven to be a potential target for immune regulation and cancer treatment. A thorough understanding of the intriguing chemistry of the heme-dependent dioxygenases may yield insight for the drug discovery of these prevalent illnesses. In this review, we survey enzymatic and mechanistic studies, initially started by Kotake and Masayama over 70 years ago, at the molecular level on the heme-dependent tryptophan dioxygenation reactions.
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Affiliation(s)
- Jiafeng Geng
- Department of Chemistry, Georgia State University, 50 Decatur Street SE, Atlanta, GA 30303, United States
| | - Aimin Liu
- Department of Chemistry, Georgia State University, 50 Decatur Street SE, Atlanta, GA 30303, United States.
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Abstract
Burkholderia cenocepacia and Burkholderia multivorans are opportunistic drug-resistant pathogens that account for the majority of Burkholderia cepacia complex infections in cystic fibrosis patients and also infect other immunocompromised individuals. While they share similar genetic compositions, B. cenocepacia and B. multivorans exhibit important differences in pathogenesis. We have developed reconciled genome-scale metabolic network reconstructions of B. cenocepacia J2315 and B. multivorans ATCC 17616 in parallel (designated iPY1537 and iJB1411, respectively) to compare metabolic abilities and contextualize genetic differences between species. The reconstructions capture the metabolic functions of the two species and give insight into similarities and differences in their virulence and growth capabilities. The two reconstructions have 1,437 reactions in common, and iPY1537 and iJB1411 have 67 and 36 metabolic reactions unique to each, respectively. After curating the extensive reservoir of metabolic genes in Burkholderia, we identified 6 genes essential to growth that are unique to iPY1513 and 13 genes uniquely essential to iJB1411. The reconstructions were refined and validated by comparing in silico growth predictions to in vitro growth capabilities of B. cenocepacia J2315, B. cenocepacia K56-2, and B. multivorans ATCC 17616 on 104 carbon sources. Overall, we identified functional pathways that indicate B. cenocepacia can produce a wider array of virulence factors compared to B. multivorans, which supports the clinical observation that B. cenocepacia is more virulent than B. multivorans. The reconciled reconstructions provide a framework for generating and testing hypotheses on the metabolic and virulence capabilities of these two related emerging pathogens.
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Lambrecht JA, Schmitz GE, Downs DM. RidA proteins prevent metabolic damage inflicted by PLP-dependent dehydratases in all domains of life. mBio 2013; 4:e00033-13. [PMID: 23386433 PMCID: PMC3565831 DOI: 10.1128/mbio.00033-13] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 01/15/2013] [Indexed: 11/30/2022] Open
Abstract
Pyridoxal 5'-phosphate (PLP) is a coenzyme synthesized by all forms of life. Relevant to the work reported here is the mechanism of the PLP-dependent threonine/serine dehydratases, which generate reactive enamine/imine intermediates that are converted to keto acids by members of the RidA family of enzymes. The RidA protein of Salmonella enterica serovar Typhimurium LT2 is the founding member of this broadly conserved family of proteins (formerly known as YjgF/YER057c/UK114). RidA proteins were recently shown to be enamine deaminases. Here we demonstrate the damaging potential of enamines in the absence of RidA proteins. Notably, S. enterica strains lacking RidA have decreased activity of the PLP-dependent transaminase B enzyme IlvE, an enzyme involved in branched-chain amino acid biosynthesis. We reconstituted the threonine/serine dehydratase (IlvA)-dependent inhibition of IlvE in vitro, show that the in vitro system reflects the mechanism of RidA function in vivo, and show that IlvE inhibition is prevented by RidA proteins from all domains of life. We conclude that 2-aminoacrylate (2AA) inhibition represents a new type of metabolic damage, and this finding provides an important physiological context for the role of the ubiquitous RidA family of enamine deaminases in preventing damage by 2AA. IMPORTANCE External stresses that disrupt metabolic components can perturb cellular functions and affect growth. A similar consequence is expected if endogenously generated metabolites are reactive and persist in the cellular environment. Here we show that the metabolic intermediate 2-aminoacrylate (2AA) causes significant cellular damage if allowed to accumulate aberrantly. Furthermore, we show that the widely conserved protein RidA prevents this accumulation by facilitating conversion of 2AA to a stable metabolite. This work demonstrates that the reactive metabolite 2AA, previously considered innocuous in the cell due to a short half-life in aqueous solution, can survive in the cellular environment long enough to cause damage. This work provides insights into the roles and persistence of reactive metabolites in vivo and shows that the RidA family of proteins is able to prevent damage caused by a reactive intermediate that is created as a consequence of PLP-dependent chemistry.
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Chakraborty B, Paine TK. Aromatic ring cleavage of 2-amino-4-tert-butylphenol by a nonheme iron(II) complex: functional model of 2-aminophenol dioxygenases. Angew Chem Int Ed Engl 2012. [PMID: 23197337 DOI: 10.1002/anie.201206922] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Biswarup Chakraborty
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
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49
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Chakraborty B, Paine TK. Aromatic Ring Cleavage of 2-Amino-4-tert-butylphenol by a Nonheme Iron(II) Complex: Functional Model of 2-Aminophenol Dioxygenases. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206922] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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50
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Adams S, Braidy N, Bessesde A, Brew BJ, Grant R, Teo C, Guillemin GJ. The Kynurenine Pathway in Brain Tumor Pathogenesis. Cancer Res 2012; 72:5649-57. [DOI: 10.1158/0008-5472.can-12-0549] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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