1
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Imarisio A, Yahyavi I, Gasparri C, Hassan A, Avenali M, Di Maio A, Buongarzone G, Galandra C, Picascia M, Filosa A, Monti MC, Pacchetti C, Errico F, Rondanelli M, Usiello A, Valente EM. Serum dysregulation of serine and glycine metabolism as predictive biomarker for cognitive decline in frail elderly subjects. Transl Psychiatry 2024; 14:281. [PMID: 38982054 PMCID: PMC11233661 DOI: 10.1038/s41398-024-02991-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/21/2024] [Accepted: 06/26/2024] [Indexed: 07/11/2024] Open
Abstract
Frailty is a common age-related clinical syndrome characterized by a decline in the function of multiple organ systems, increased vulnerability to stressors, and a huge socio-economic burden. Despite recent research efforts, the physiopathological mechanisms underlying frailty remain elusive and biomarkers able to predate its occurrence in the early stages are still lacking. Beyond its physical component, cognitive decline represents a critical domain of frailty associated with higher risk of adverse health outcomes. We measured by High-Performance Liquid Chromatography (HPLC) a pool of serum amino acids including L-glutamate, L-aspartate, glycine, and D-serine, as well as their precursors L-glutamine, L-asparagine, and L-serine in a cohort of elderly subjects encompassing the entire continuum from fitness to frailty. These amino acids are known to orchestrate excitatory and inhibitory neurotransmission, and in turn, to play a key role as intermediates of energy homeostasis and in liver, kidney, muscle, and immune system metabolism. To comprehensively assess frailty, we employed both the Edmonton Frail Scale (EFS), as a practical tool to capture the multidimensionality of frailty, and the frailty phenotype, as a measure of physical function. We found that D-serine and D-/Total serine ratio were independent predictors of EFS but not of physical frailty. Furthermore, higher levels of glycine, glycine/L-serine and D-/Total serine were associated with worse cognition and depressive symptoms in the frail group. These findings suggest that changes in peripheral glycine and serine enantiomers homeostasis may represent a novel biochemical correlate of frailty.
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Affiliation(s)
- Alberto Imarisio
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Neurogenetics Research Centre, IRCCS Mondino Foundation, Pavia, Italy
| | - Isar Yahyavi
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy
- CEINGE Biotecnologie Avanzate Franco Salvatore, Naples, Italy
| | - Clara Gasparri
- Endocrinology and Nutrition Unit, Azienda di Servizi alla Persona "Istituto Santa Margherita", University of Pavia, Pavia, Italy
| | - Amber Hassan
- CEINGE Biotecnologie Avanzate Franco Salvatore, Naples, Italy
| | - Micol Avenali
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Parkinson's Disease and Movement Disorders Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Anna Di Maio
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy
- CEINGE Biotecnologie Avanzate Franco Salvatore, Naples, Italy
| | - Gabriele Buongarzone
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Parkinson's Disease and Movement Disorders Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Caterina Galandra
- Neurogenetics Research Centre, IRCCS Mondino Foundation, Pavia, Italy
| | - Marta Picascia
- Parkinson's Disease and Movement Disorders Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Asia Filosa
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Maria Cristina Monti
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Claudio Pacchetti
- Parkinson's Disease and Movement Disorders Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Francesco Errico
- CEINGE Biotecnologie Avanzate Franco Salvatore, Naples, Italy
- Department of Agricultural Sciences, University of Naples "Federico II", Portici, Italy
| | - Mariangela Rondanelli
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Alessandro Usiello
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy.
- CEINGE Biotecnologie Avanzate Franco Salvatore, Naples, Italy.
| | - Enza Maria Valente
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Neurogenetics Research Centre, IRCCS Mondino Foundation, Pavia, Italy
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2
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Arias-Moliz MT, Ordinola-Zapata R, Staley C, Pérez-Carrasco V, García-Salcedo JA, Uroz-Torres D, Soriano M. Exploring the root canal microbiome in previously treated teeth: A comparative study of diversity and metabolic pathways across two geographical locations. Int Endod J 2024; 57:885-894. [PMID: 37209012 DOI: 10.1111/iej.13934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 05/21/2023]
Abstract
AIM To analyse and compare the root canal microbiome present in root-filled teeth of two different geographical populations, and to study their functional potential using a next-generation sequencing approach. METHODOLOGY Sequencing data obtained from surgical specimens from previously treated teeth with periapical bone loss from Spain and USA were included in the study. Taxa were classified using SILVA v.138 database. Differences in genera abundances among the 10 most abundant genera were evaluated using a Kruskal-Wallis test. Alpha diversity indices were calculated in mothur. The Shannon and Chao1 indices were used. Analyses of similarity (ANOSIM) to determine differences in community composition were done in mothur, with Bonferroni correction for multiple comparisons. p-Values < .05 were considered statistically significant. Identification of enriched bacteria function prediction in the study groups (KEGG pathways) was carried out by linear discriminant analysis effect size (LEfSe) via Python 3.7.6. RESULTS A greater alpha-diversity (Shannon and Chao1 indices) was observed from samples obtained in Spain (p = .002). Geography showed no significant effects on community composition via an ANOSIM using Bray-Curtis dissimilarities (R = 0.03, p = .21). Bacterial functional analysis prediction obtained by PICRUSt showed that 5.7% KEGG pathways differed between the Spain and US samples. CONCLUSIONS The taxonomic assessment alone does not fully capture the microbiome's differences from two different geographical locations. Carbohydrate and amino acid metabolism were enriched in samples from Spain, while samples from USA had a higher representation of pathways related to nitrogen, propanoate metabolism, and secretion systems.
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Affiliation(s)
- M T Arias-Moliz
- Department of Microbiology, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - R Ordinola-Zapata
- Division of Endodontics, Department of Restorative Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - C Staley
- Division of Basic & Translational Research, Department of Surgery, University of Minnesota, Minneapolis, Minnesota, USA
| | - V Pérez-Carrasco
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain
- Microbiology Unit, University Hospital Virgen de las Nieves, Granada, Spain
| | - J A García-Salcedo
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain
- Microbiology Unit, University Hospital Virgen de las Nieves, Granada, Spain
| | | | - M Soriano
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain
- Center for Research in Mediterranean Intensive Agrosystems and Agri-Food Biotechnology (CIAIMBITAL), University of Almeria, Almería, Spain
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3
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Mishra N, Gutheil WG. Stereoselective Amine-omics Using Heavy Atom Isotope Labeled l- and d-Marfey's Reagents. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1217-1226. [PMID: 38683793 PMCID: PMC11160435 DOI: 10.1021/jasms.4c00036] [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: 01/30/2024] [Revised: 03/20/2024] [Accepted: 04/05/2024] [Indexed: 05/02/2024]
Abstract
Biological amines and amino acids play essential roles in many biochemical processes. The chemical complexity of biological samples is challenging, and the selective identification and quantification of amines and amino acid stereoisomers would be very useful for amine-focused "amino-omics" studies. Many amines and amino acids are chiral, and their stereoisomers cannot be resolved on achiral media without chiral derivatization. In prior studies, we demonstrated the use of Marfey's reagent─a chiral derivatization reagent for amines and phenolic OH groups─for the LC-MS/MS resolution and quantification of amines and amino acid stereoisomers. In this study, a heavy atom isotope labeled Marfey's reagent approach for the stereoselective detection and quantification of amines and amino acids was developed. Heavy (13C2) l-Marfey's (Hl-Mar) and heavy (2H3) d-Marfey's (Hd-Mar) were synthesized from 13C2-l-Ala and 2H3-d-Ala, respectively. Both light and heavy Marfey's reagents were used to derivatize standard amine mixtures, which were analyzed by LC-QToF-HRMS. Aligned peak lists were comparatively analyzed by light vs heavy Mar mass differences to identify mono-, di-, and tri-Marfey's adducts and then by the retention time difference between l- and d-Mar derivatives to identify stereoisomers. This approach was then applied to identify achiral and chiral amine and amino acid components in a methicillin-resistant Staphylococcus aureus (MRSA) extract. This approach shows high analytical selectivity and reproducibility.
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Affiliation(s)
- Nitish
R. Mishra
- Division of Pharmacology
and Pharmaceutical Sciences, School of Pharmacy, University of Missouri—Kansas City, Kansas City, Missouri 64108, United States
| | - William G. Gutheil
- Division of Pharmacology
and Pharmaceutical Sciences, School of Pharmacy, University of Missouri—Kansas City, Kansas City, Missouri 64108, United States
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4
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Zha Z, Wang R, Wang Q, Chen F, Ye Z, Li Y. A fast and efficient liquid chromatography-tandem mass spectrometry method for measuring l- and d-amino acids in the urine of patients with immunoglobulin A nephropathy. Biomed Chromatogr 2024; 38:e5866. [PMID: 38618866 DOI: 10.1002/bmc.5866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 04/16/2024]
Abstract
Immunoglobulin nephropathy (IgAN) stands as the most prevalent primary glomerular nephropathy globally, typically diagnosed through an invasive renal biopsy. Emerging research suggests the significant involvement of chiral amino acids in kidney disease progression. This study introduces a nonderivative LC-tandem mass spectrometry approach, offering efficient separation outcomes within 15 min for identifying chiral amino acids in human urine samples. Subsequently, using this method, the analysis of l- and d-amino acids in the urine of both patients with IgAN and healthy individuals was conducted. Fourteen d-amino acids and 20 l-amino acids were identified in the urine samples obtained from 17 patients with IgAN and 21 healthy individuals. The results indicated notable variances in the concentrations of both l- and d-amino acids between the IgAN and healthy control groups. In contrast to the healthy group, the IgAN group exhibited higher mean urine concentrations of most l-amino acids and lower concentrations of d-amino acids. Furthermore, correlations between amino acids and clinical markers were investigated. These results propose a novel method for monitoring trace amino acids in urine samples and introduce a new concept for potential markers of IgAN.
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Affiliation(s)
- Zhijian Zha
- Third Clinical School, Shanxi University of Traditional Chinese Medicine, Taiyuan City, Shanxi Province, China
| | - Ruihua Wang
- Third Clinical School, Shanxi University of Traditional Chinese Medicine, Taiyuan City, Shanxi Province, China
| | - Qian Wang
- Shanxi Provincial Key Laboratory of Kidney Disease, Taiyuan, China
| | - Fahui Chen
- Third Clinical School, Shanxi University of Traditional Chinese Medicine, Taiyuan City, Shanxi Province, China
| | - Ziyang Ye
- Third Clinical School, Shanxi University of Traditional Chinese Medicine, Taiyuan City, Shanxi Province, China
| | - Yafeng Li
- Third Clinical School, Shanxi University of Traditional Chinese Medicine, Taiyuan City, Shanxi Province, China
- Chronic Kidney Disease Medical and Pharmaceutical Basic Research Innovation Center of the Ministry of Education of the People's Republic of China, Taiyuan, China
- Department of Nephrology, Shanxi Provincial People's Hospital (Fifth Hospital), Shanxi Medical University, Taiyuan, China
- Core Laboratory, Shanxi Provincial People's Hospital (Fifth Hospital), Shanxi Medical University, Taiyuan, China
- Academy of Microbial Ecology, Shanxi Medical University, Taiyuan, China
- Hejin Municipal People's Hospital, Hejin, China
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5
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Miyamoto T. Multifunctional enzymes related to amino acid metabolism in bacteria. Biosci Biotechnol Biochem 2024; 88:585-593. [PMID: 38439669 DOI: 10.1093/bbb/zbae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/29/2024] [Indexed: 03/06/2024]
Abstract
In bacteria, d-amino acids are primarily synthesized from l-amino acids by amino acid racemases, but some bacteria use d-amino acid aminotransferases to synthesize d-amino acids. d-Amino acids are peptidoglycan components in the cell wall involved in several physiological processes, such as bacterial growth, biofilm dispersal, and peptidoglycan metabolism. Therefore, their metabolism and physiological roles have attracted increasing attention. Recently, we identified novel bacterial d-amino acid metabolic pathways, which involve amino acid racemases, with broad substrate specificity, as well as multifunctional enzymes with d-amino acid-metabolizing activity. Here, I review these multifunctional enzymes and their related d- and l-amino acid metabolic pathways in Escherichia coli and the hyperthermophile Thermotoga maritima.
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Affiliation(s)
- Tetsuya Miyamoto
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
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6
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Zhang P, Liu Z. Structural insights into the transporting and catalyzing mechanism of DltB in LTA D-alanylation. Nat Commun 2024; 15:3404. [PMID: 38649359 PMCID: PMC11035591 DOI: 10.1038/s41467-024-47783-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 04/12/2024] [Indexed: 04/25/2024] Open
Abstract
DltB, a model member of the Membrane-Bound O-AcylTransferase (MBOAT) superfamily, plays a crucial role in D-alanylation of the lipoteichoic acid (LTA), a significant component of the cell wall of gram-positive bacteria. This process stabilizes the cell wall structure, influences bacterial virulence, and modulates the host immune response. Despite its significance, the role of DltB is not well understood. Through biochemical analysis and cryo-EM imaging, we discover that Streptococcus thermophilus DltB forms a homo-tetramer on the cell membrane. We further visualize DltB in an apo form, in complex with DltC, and in complex with its inhibitor amsacrine (m-AMSA). Each tetramer features a central hole. The C-tunnel of each protomer faces the intratetramer interface and provides access to the periphery membrane. Each protomer binds a DltC without changing the tetrameric organization. A phosphatidylglycerol (PG) molecule in the substrate-binding site may serve as an LTA carrier. The inhibitor m-AMSA bound to the L-tunnel of each protomer blocks the active site. The tetrameric organization of DltB provides a scaffold for catalyzing D-alanyl transfer and regulating the channel opening and closing. Our findings unveil DltB's dual function in the D-alanylation pathway, and provide insight for targeting DltB as a anti-virulence antibiotic.
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Affiliation(s)
- Pingfeng Zhang
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China.
| | - Zheng Liu
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China.
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7
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Imarisio A, Yahyavi I, Avenali M, Di Maio A, Buongarzone G, Galandra C, Picascia M, Filosa A, Gasparri C, Monti MC, Rondanelli M, Pacchetti C, Errico F, Valente EM, Usiello A. Blood D-serine levels correlate with aging and dopaminergic treatment in Parkinson's disease. Neurobiol Dis 2024; 192:106413. [PMID: 38253208 DOI: 10.1016/j.nbd.2024.106413] [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: 12/28/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 01/24/2024] Open
Abstract
We recently described increased D- and L-serine concentrations in the striatum of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-treated monkeys, the post-mortem caudate-putamen of human Parkinson's disease (PD) brains and the cerebrospinal fluid (CSF) of de novo living PD patients. However, data regarding blood D- and L-serine levels in PD are scarce. Here, we investigated whether the serum profile of D- and L-serine, as well as the other glutamate N-methyl-D-aspartate ionotropic receptor (NMDAR)-related amino acids, (i) differs between PD patients and healthy controls (HC) and (ii) correlates with clinical-demographic features and levodopa equivalent daily dose (LEDD) in PD. Eighty-three consecutive PD patients and forty-one HC were enrolled. PD cohort underwent an extensive clinical characterization. Serum levels of D- and L-serine, L-glutamate, L-glutamine, L-aspartate, L-asparagine and glycine were determined using High Performance Liquid Chromatography. In age- and sex-adjusted analyses, no differences emerged in the serum levels of D-serine, L-serine and other NMDAR-related amino acids between PD and HC. However, we found that D-serine and D-/Total serine ratio positively correlated with age in PD but not in HC, and also with PD age at onset. Moreover, we found that higher LEDD correlated with lower levels of D-serine and the other excitatory amino acids. Following these results, the addition of LEDD as covariate in the analyses disclosed a selective significant increase of D-serine in PD compared to HC (Δ ≈ 38%). Overall, these findings suggest that serum D-serine and D-/Total serine may represent a valuable biochemical signature of PD.
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Affiliation(s)
- Alberto Imarisio
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy; Neurogenetics Research Centre, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Isar Yahyavi
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy; CEINGE Biotecnologie Avanzate Franco Salvatore, Naples, Italy
| | - Micol Avenali
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy; Parkinson's Disease and Movement Disorders Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Anna Di Maio
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy; CEINGE Biotecnologie Avanzate Franco Salvatore, Naples, Italy
| | - Gabriele Buongarzone
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy; Parkinson's Disease and Movement Disorders Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Caterina Galandra
- Neurogenetics Research Centre, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Marta Picascia
- Parkinson's Disease and Movement Disorders Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Asia Filosa
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy
| | - Clara Gasparri
- Endocrinology and Nutrition Unit, Azienda di Servizi alla Persona "Istituto Santa Margherita", University of Pavia, 27100 Pavia, Italy
| | - Maria Cristina Monti
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy
| | - Mariangela Rondanelli
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy
| | - Claudio Pacchetti
- Parkinson's Disease and Movement Disorders Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Francesco Errico
- CEINGE Biotecnologie Avanzate Franco Salvatore, Naples, Italy; Department of Agricultural Sciences, University of Naples "Federico II", 80055 Portici, Italy
| | - Enza Maria Valente
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy; Neurogenetics Research Centre, IRCCS Mondino Foundation, 27100 Pavia, Italy.
| | - Alessandro Usiello
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy; CEINGE Biotecnologie Avanzate Franco Salvatore, Naples, Italy
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8
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Koatale P, Welling MM, Ndlovu H, Kgatle M, Mdanda S, Mdlophane A, Okem A, Takyi-Williams J, Sathekge MM, Ebenhan T. Insights into Peptidoglycan-Targeting Radiotracers for Imaging Bacterial Infections: Updates, Challenges, and Future Perspectives. ACS Infect Dis 2024; 10:270-286. [PMID: 38290525 PMCID: PMC10862554 DOI: 10.1021/acsinfecdis.3c00443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 02/01/2024]
Abstract
The unique structural architecture of the peptidoglycan allows for the stratification of bacteria as either Gram-negative or Gram-positive, which makes bacterial cells distinguishable from mammalian cells. This classification has received attention as a potential target for diagnostic and therapeutic purposes. Bacteria's ability to metabolically integrate peptidoglycan precursors during cell wall biosynthesis and recycling offers an opportunity to target and image pathogens in their biological state. This Review explores the peptidoglycan biosynthesis for bacteria-specific targeting for infection imaging. Current and potential radiolabeled peptidoglycan precursors for bacterial infection imaging, their development status, and their performance in vitro and/or in vivo are highlighted. We conclude by providing our thoughts on how to shape this area of research for future clinical translation.
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Affiliation(s)
- Palesa
C. Koatale
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Mick M. Welling
- Interventional
Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Honest Ndlovu
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Mankgopo Kgatle
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Sipho Mdanda
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Amanda Mdlophane
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Ambrose Okem
- Department
of Anaesthesia, School of Clinical Medicine, University of Witwatersrand, 2050 Johannesburg, South Africa
| | - John Takyi-Williams
- Pharmacokinetic
and Mass Spectrometry Core, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Mike M. Sathekge
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Thomas Ebenhan
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
- DSI/NWU Pre-clinical
Drug Development Platform, North West University, 2520 Potchefstroom, South Africa
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9
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Li XY, Zeng ZX, Cheng ZX, Wang YL, Yuan LJ, Zhai ZY, Gong W. Common pathogenic bacteria-induced reprogramming of the host proteinogenic amino acids metabolism. Amino Acids 2023; 55:1487-1499. [PMID: 37814028 PMCID: PMC10689525 DOI: 10.1007/s00726-023-03334-w] [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: 04/02/2023] [Accepted: 09/12/2023] [Indexed: 10/11/2023]
Abstract
Apart from cancer, metabolic reprogramming is also prevalent in other diseases, such as bacterial infections. Bacterial infections can affect a variety of cells, tissues, organs, and bodies, leading to a series of clinical diseases. Common Pathogenic bacteria include Helicobacter pylori, Salmonella enterica, Mycobacterium tuberculosis, Staphylococcus aureus, and so on. Amino acids are important and essential nutrients in bacterial physiology and support not only their proliferation but also their evasion of host immune defenses. Many pathogenic bacteria or opportunistic pathogens infect the host and lead to significant changes in metabolites, especially the proteinogenic amino acids, to inhibit the host's immune mechanism to achieve its immune evasion and pathogenicity. Here, we review the regulation of host metabolism, while host cells are infected by some common pathogenic bacteria, and discuss how amino acids of metabolic reprogramming affect bacterial infections, revealing the potential adjunctive application of amino acids alongside antibiotics.
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Affiliation(s)
- Xiao-Yue Li
- The First School of Clinical Medicine, Southern Medical University, Guangdong, 510515, China
| | - Zi-Xin Zeng
- The First School of Clinical Medicine, Southern Medical University, Guangdong, 510515, China
| | - Zhi-Xing Cheng
- The First School of Clinical Medicine, Southern Medical University, Guangdong, 510515, China
| | - Yi-Lin Wang
- The First School of Clinical Medicine, Southern Medical University, Guangdong, 510515, China
| | - Liang-Jun Yuan
- The First School of Clinical Medicine, Southern Medical University, Guangdong, 510515, China
| | - Zhi-Yong Zhai
- Shenzhen Hospital, Southern Medical University, Shenzhen Clinical Medical College, Southern Medical University, Guangdong, 518101, China.
| | - Wei Gong
- Shenzhen Hospital, Southern Medical University, Shenzhen Clinical Medical College, Southern Medical University, Guangdong, 518101, China.
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10
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Inoue K, Fujihara A. Differentiation of free d-amino acids and amino acid isomers in solution using tandem mass spectrometry of hydrogen-bonded clusters. J Pharm Biomed Anal 2023; 234:115567. [PMID: 37441889 DOI: 10.1016/j.jpba.2023.115567] [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: 05/01/2023] [Revised: 06/21/2023] [Accepted: 07/09/2023] [Indexed: 07/15/2023]
Abstract
Free d-amino acids and amino acid isomers were differentiated using tandem mass spectrometry without chromatographic separation. Ultraviolet photodissociation and water adsorption of leucine (Leu) and isoleucine (Ile) enantiomers hydrogen-bonded with tryptophan (Trp) were investigated at 8 K in the gas phase. The enantiomer-selective Cα-Cβ bond cleavage of Trp was observed in the product ion spectra obtained by 285 nm photoexcitation, where the abundance of NH2CHCOOH-eliminated ion of heterochiral H+(d-Trp)(l-Leu) was higher than that of homochiral H+(l-Trp)(l-Leu). When comparing water adsorption on the surfaces of the heterochiral and homochiral clusters in a cold ion trap, the number of water molecules adsorbed on the heterochiral cluster was greater than that adsorbed on the homochiral cluster. These results indicate that the stronger intermolecular interactions within the homochiral H+(l-Trp)(l-Leu) compared to the heterochiral cluster inhibit enantiomer-selective photodissociation. Leu and Ile were differentiated by the isomer-selective Cα-Cβ bond cleavage of Trp in the clusters. Calibration curves for the differentiation of isomeric amino acids and their enantiomers were developed using monitoring isomer- and enantiomer-selective photodissociation, indicating that the molar fractions in solution could be determined from a single product ion spectrum.
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Affiliation(s)
- Kanako Inoue
- Department of Chemistry, Graduate School of Science, Osaka Metropolitan University, Osaka 599-8531, Japan
| | - Akimasa Fujihara
- Department of Chemistry, Graduate School of Science, Osaka Metropolitan University, Osaka 599-8531, Japan.
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11
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Du Q, Wang X, Chen J, Wang Y, Liu W, Wang L, Liu H, Jiang L, Nie Z. Machine learning encodes urine and serum metabolic patterns for autoimmune disease discrimination, classification and metabolic dysregulation analysis. Analyst 2023; 148:4318-4330. [PMID: 37547947 DOI: 10.1039/d3an01051a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
There is a wide variety of autoimmune diseases (ADs) with complex pathogenesis and their accurate diagnosis is difficult to achieve because of their vague symptoms. Metabolomics has been proven to be an efficient tool in the analysis of metabolic disorders to provide clues about the mechanism and diagnosis of diseases. Previous studies of the metabolomics analysis of ADs were not competent in their discrimination. Herein, a liquid chromatography tandem mass spectrometry (LC-MS) strategy combined with machine learning is proposed for the discrimination and classification of ADs. Urine and serum samples were collected from 267 subjects consisting of 127 healthy controls (HC) and 140 AD patients, including those with rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), sicca syndrome (SS), ankylosing spondylitis (AS), systemic scleroderma (SSc) and connective tissue disease (CTD). Machine learning algorithms were encoded for the discrimination and classification of ADs with metabolomic patterns obtained by LC-MS, and satisfactory results were achieved. Notably, urine samples exhibited higher accuracy for disease differentiation and triage than serum samples. Apart from that, differential metabolites were selected and metabolite panels were evaluated to demonstrate their representativeness. Metabolic dysregulations were also investigated to gain more knowledge about the pathogenesis of ADs. This research provides a promising method for the application of metabolomics combined with machine learning in precision medicine.
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Affiliation(s)
- Qiuyao Du
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junyu Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiran Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenlan Liu
- Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Liping Wang
- Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Huihui Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lixia Jiang
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province 341000, China.
| | - Zongxiu Nie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
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12
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Du S, Wey M, Armstrong DW. d-Amino acids in biological systems. Chirality 2023; 35:508-534. [PMID: 37074214 DOI: 10.1002/chir.23562] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 04/20/2023]
Abstract
Investigations on the occurrence and biochemical roles of free D-amino acids and D-amino acid-containing peptides and proteins in living systems have increased in frequency and significance. Their occurrence and roles may vary substantially with progression from microbiotic to evermore advanced macrobiotic systems. We now understand many of the biosynthetic and regulatory pathways, which are outlined herein. Important uses for D-amino acids in plants, invertebrates, and vertebrates are reviewed. Given its importance, a separate section on the occurrence and role of D-amino acids in human disease is presented.
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Affiliation(s)
- Siqi Du
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas, USA
| | - Michael Wey
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas, USA
| | - Daniel W Armstrong
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas, USA
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13
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Shilova SA, Matyuta IO, Khrenova MG, Nikolaeva AY, Klyachko NL, Minyaev ME, Khomutov AR, Boyko KM, Popov VO, Bezsudnova EY. In search for structural targets for engineering d-amino acid transaminase: modulation of pH optimum and substrate specificity. Biochem J 2023; 480:1267-1284. [PMID: 37548495 DOI: 10.1042/bcj20230233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/21/2023] [Accepted: 08/07/2023] [Indexed: 08/08/2023]
Abstract
The development of biocatalysts requires reorganization of the enzyme's active site to facilitate the productive binding of the target substrate and improve turnover number at desired conditions. Pyridoxal-5'-phosphate (PLP) - dependent transaminases are highly efficient biocatalysts for asymmetric amination of ketones and keto acids. However, transaminases, being stereoselective enzymes, have a narrow substrate specificity due to the ordered structure of the active site and work only in neutral-alkaline media. Here, we investigated the d-amino acid transaminase from Aminobacterium colombiense, with the active site organized differently from that of the canonical d-amino acid transaminase from Bacillus sp. YM-1. Using a combination of site-directed mutagenesis, kinetic analysis, molecular modeling, and structural analysis we determined the active site residues responsible for substrate binding, substrate differentiation, thermostability of a functional dimer, and affecting the pH optimum. We demonstrated that the high specificity toward d-glutamate/α-ketoglutarate is due to the interactions of a γ-carboxylate group with K237 residue, while binding of other substrates stems from the effectiveness of their accommodation in the active site optimized for d-glutamate/α-ketoglutarate binding. Furthermore, we showed that the K237A substitution shifts the catalytic activity optimum to acidic pH. Our findings are useful for achieving target substrate specificity and demonstrate the potential for developing and optimizing transaminases for various applications.
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Affiliation(s)
- Sofia A Shilova
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Ilya O Matyuta
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Maria G Khrenova
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Alena Y Nikolaeva
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Natalia L Klyachko
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail E Minyaev
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alex R Khomutov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Konstantin M Boyko
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Vladimir O Popov
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina Yu Bezsudnova
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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14
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Umeda S, Sujino T, Miyamoto K, Yoshimatsu Y, Harada Y, Nishiyama K, Aoto Y, Adachi K, Hayashi N, Amafuji K, Moritoki N, Shibata S, Sasaki N, Mita M, Tanemoto S, Ono K, Mikami Y, Sasabe J, Takabayashi K, Hosoe N, Suzuki T, Sato T, Atarashi K, Teratani T, Ogata H, Nakamoto N, Shiomi D, Ashida H, Kanai T. D-amino Acids Ameliorate Experimental Colitis and Cholangitis by Inhibiting Growth of Proteobacteria: Potential Therapeutic Role in Inflammatory Bowel Disease. Cell Mol Gastroenterol Hepatol 2023; 16:1011-1031. [PMID: 37567385 PMCID: PMC10632532 DOI: 10.1016/j.jcmgh.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/03/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023]
Abstract
BACKGROUND & AIMS D-amino acids, the chiral counterparts of protein L-amino acids, were primarily produced and utilized by microbes, including those in the human gut. However, little was known about how orally administered or microbe-derived D-amino acids affected the gut microbial community or gut disease progression. METHODS The ratio of D- to L-amino acids was analyzed in feces and blood from patients with ulcerative colitis (UC) and healthy controls. Also, composition of microbe was analyzed from patients with UC. Mice were treated with D-amino acid in dextran sulfate sodium colitis model and liver cholangitis model. RESULTS The ratio of D- to L-amino acids was lower in the feces of patients with UC than that of healthy controls. Supplementation of D-amino acids ameliorated UC-related experimental colitis and liver cholangitis by inhibiting growth of Proteobacteria. Addition of D-alanine, a major building block for bacterial cell wall formation, to culture medium inhibited expression of the ftsZ gene required for cell fission in the Proteobacteria Escherichia coli and Klebsiella pneumoniae, thereby inhibiting growth. Overexpression of ftsZ restored growth of E. coli even when D-alanine was present. We found that D-alanine not only inhibited invasion of pathological K. pneumoniae into the host via pore formation in intestinal epithelial cells but also inhibited growth of E. coli and generation of antibiotic-resistant strains. CONCLUSIONS D-amino acids might have potential for use in novel therapeutic approaches targeting Proteobacteria-associated dysbiosis and antibiotic-resistant bacterial diseases by means of their effects on the intestinal microbiota community.
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Affiliation(s)
- Satoko Umeda
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Tomohisa Sujino
- Center for Diagnostic and Therapeutic Endoscopy, Keio University School of Medicine, Tokyo, Japan.
| | - Kentaro Miyamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan; Miyarisan Pharmaceutical Co, Ltd., Tokyo, Japan
| | - Yusuke Yoshimatsu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yosuke Harada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Keita Nishiyama
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan; JSR-Keio University Medical and Chemical Innovation Center (JKiC), Keio University School of Medicine, Tokyo, Japan
| | - Yoshimasa Aoto
- JSR-Keio University Medical and Chemical Innovation Center (JKiC), JSR Corp, Tokyo, Japan
| | - Keika Adachi
- JSR-Keio University Medical and Chemical Innovation Center (JKiC), JSR Corp, Tokyo, Japan
| | - Naoki Hayashi
- JSR-Keio University Medical and Chemical Innovation Center (JKiC), JSR Corp, Tokyo, Japan
| | - Kimiko Amafuji
- JSR-Keio University Medical and Chemical Innovation Center (JKiC), JSR Corp, Tokyo, Japan
| | - Nobuko Moritoki
- Electron Microscope Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Shinsuke Shibata
- Electron Microscope Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Nobuo Sasaki
- Institute of Molecular and Cellular Regulation, Gunma University, Maebashi City, Japan
| | | | - Shun Tanemoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Keiko Ono
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yohei Mikami
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Jumpei Sasabe
- Department of Pharmacology, School of Medicine, Keio University, Tokyo, Japan
| | - Kaoru Takabayashi
- Center for Diagnostic and Therapeutic Endoscopy, Keio University School of Medicine, Tokyo, Japan
| | - Naoki Hosoe
- Center for Diagnostic and Therapeutic Endoscopy, Keio University School of Medicine, Tokyo, Japan
| | - Toshihiko Suzuki
- Department of Bacterial Infection and Host Response, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Toshiro Sato
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Koji Atarashi
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Toshiaki Teratani
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Haruhiko Ogata
- Center for Diagnostic and Therapeutic Endoscopy, Keio University School of Medicine, Tokyo, Japan
| | - Nobuhiro Nakamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Daisuke Shiomi
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Hiroshi Ashida
- Department of Bacterial Infection and Host Response, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan; Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan; AMED-CREST, Tokyo, Japan.
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15
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Bearne SL. Design and evaluation of substrate-product analog inhibitors for racemases and epimerases utilizing a 1,1-proton transfer mechanism. Methods Enzymol 2023; 690:397-444. [PMID: 37858537 DOI: 10.1016/bs.mie.2023.06.014] [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: 10/21/2023]
Abstract
Racemases and epimerases catalyze the inversion of stereochemistry at asymmetric carbon atoms to generate stereoisomers that often play important roles in normal and pathological physiology. Consequently, there is interest in developing inhibitors of these enzymes for drug discovery. A strategy for the rational design of substrate-product analog (SPA) inhibitors of racemases and epimerases utilizing a direct 1,1-proton transfer mechanism is elaborated. This strategy assumes that two groups on the asymmetric carbon atom remain fixed at active-site binding determinants, while the hydrogen and third, motile group move during catalysis, with the latter potentially traveling between an R- and S-pocket at the active site. SPAs incorporate structural features of the substrate and product, often with geminal disubstitution on the asymmetric carbon atom to simultaneously present the motile group to both the R- and S-pockets. For racemases operating on substrates bearing three polar groups (glutamate, aspartate, and serine racemases) or with compact, hydrophobic binding pockets (proline racemase), substituent motion is limited and the design strategy furnishes inhibitors with poor or modest binding affinities. The approach is most successful when substrates have a large, motile hydrophobic group that binds at a plastic and/or capacious hydrophobic site. Potent inhibitors were developed for mandelate racemase, isoleucine epimerase, and α-methylacyl-CoA racemase using the SPA inhibitor design strategy, exhibiting binding affinities ranging from substrate-like to exceeding that of the substrate by 100-fold. This rational approach for designing inhibitors of racemases and epimerases having the appropriate active-site architectures is a useful strategy for furnishing compounds for drug development.
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Affiliation(s)
- Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada; Department of Chemistry, Dalhousie University, Halifax, NS, Canada.
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16
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Katsube S, Sakai K, Ando T, Tobe R, Yoneyama H. l-Alanine Exporter AlaE Functions as One of the d-Alanine Exporters in Escherichia coli. Int J Mol Sci 2023; 24:10242. [PMID: 37373388 DOI: 10.3390/ijms241210242] [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: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
d-amino acids have recently been found to be present in the extracellular milieu at millimolar levels and are therefore assumed to play a physiological function. However, the pathway (or potential pathways) by which these d-amino acids are secreted remains unknown. Recently, Escherichia coli has been found to possess one or more energy-dependent d-alanine export systems. To gain insight into these systems, we developed a novel screening system in which cells expressing a putative d-alanine exporter could support the growth of d-alanine auxotrophs in the presence of l-alanyl-l-alanine. In the initial screening, five d-alanine exporter candidates, AlaE, YmcD, YciC, YraM, and YidH, were identified. Transport assays of radiolabeled d-alanine in cells expressing these candidates indicated that YciC and AlaE resulted in lower intracellular levels of d-alanine. Further detailed transport assays of AlaE in intact cells showed that it exports d-alanine in an expression-dependent manner. In addition, the growth constraints on cells in the presence of 90 mM d-alanine were mitigated by the overexpression of AlaE, implying that AlaE could export free d-alanine in addition to l-alanine under conditions in which intracellular d/l-alanine levels are raised. This study also shows, for the first time, that YciC could function as a d-alanine exporter in intact cells.
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Affiliation(s)
- Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Keiichiro Sakai
- Laboratory of Animal Microbiology, Department of Animal Science, Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki Aza Aoba, Aoba-ku, Sendai 980-0845, Japan
| | - Tasuke Ando
- Laboratory of Animal Microbiology, Department of Animal Science, Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki Aza Aoba, Aoba-ku, Sendai 980-0845, Japan
| | - Ryuta Tobe
- Laboratory of Animal Microbiology, Department of Animal Science, Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki Aza Aoba, Aoba-ku, Sendai 980-0845, Japan
| | - Hiroshi Yoneyama
- Laboratory of Animal Microbiology, Department of Animal Science, Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki Aza Aoba, Aoba-ku, Sendai 980-0845, Japan
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17
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Annila A. Chiral conformity emerges from the least-time free energy consumption. Interface Focus 2023; 13:20220074. [PMID: 37065265 PMCID: PMC10102724 DOI: 10.1098/rsfs.2022.0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/17/2023] [Indexed: 04/18/2023] Open
Abstract
The prevalence of chirally pure biological polymers is often assumed to stem from some slight preference for one chiral form at the origin of life. Likewise, the predominance of matter over antimatter is presumed to follow from some subtle bias for matter at the dawn of the universe. However, rather than being imposed from the start, handedness standards in societies emerged to make things work. Since work is the universal measure of transferred energy, it is reasoned that standards at all scales and scopes emerge to consume free energy. Free energy minimization, equal to entropy maximization, turns out to be the second law of thermodynamics when derived from statistical physics of open systems. This many-body theory is based on the atomistic axiom that everything comprises the same fundamental elements known as quanta of action; hence, everything follows the same law. According to the thermodynamic principle, the flows of energy naturally select standard structures over less-fit functional forms to consume free energy in the least time. Thermodynamics making no distinction between animate and inanimate renders the question of life's handedness meaningless and deems the search for an intrinsic difference between matter and antimatter pointless.
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Affiliation(s)
- Arto Annila
- Department of Physics, University of Helsinki, Helsinki, Finland
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18
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Gao L, Xu P, Ren J. A sensitive and economical method for simultaneous determination of D/L- amino acids profile in foods by HPLC-UV: Application in fermented and unfermented foods discrimination. Food Chem 2023; 410:135382. [PMID: 36628920 DOI: 10.1016/j.foodchem.2022.135382] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/29/2022] [Accepted: 12/31/2022] [Indexed: 01/07/2023]
Abstract
This work described a sensitive and economical HPLC-UV method with FDAA derivatization to simultaneously detect 36 D/l-amino acids, which provides higher sensitivity and lower cost than other HPLC-based methods. It was validated for linearity range (8-1000 µmol/L), limits of detection (2.68-62.44 pmol/L), limits of quantification (2.93 to 208.13 pmol/L), intraday precision (0.30 % - 5.31 %), interday precision (1.96 % - 8.04 %) and accuracy (86.53 % - 121.46 %). This method was then applied in the determination of D/L- amino acids abundance in fermented and unfermented food materials and showed the characteristics of each type of foods. The method also demonstrated good performance in another application case for the discrimination of different types of food materials based on D/L- amino acids profile. It emphasizes the ability of the method to study the characteristics, distribution and abundance of d-amino acids in foods and their potential application in food quality control.
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Affiliation(s)
- Li Gao
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Piao Xu
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Jiaoyan Ren
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, China.
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19
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Kouakou YI, Lee RJ. Interkingdom Detection of Bacterial Quorum-Sensing Molecules by Mammalian Taste Receptors. Microorganisms 2023; 11:1295. [PMID: 37317269 DOI: 10.3390/microorganisms11051295] [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: 04/25/2023] [Revised: 05/11/2023] [Accepted: 05/13/2023] [Indexed: 06/16/2023] Open
Abstract
Bitter and sweet taste G protein-coupled receptors (known as T2Rs and T1Rs, respectively) were originally identified in type II taste cells on the tongue, where they signal perception of bitter and sweet tastes, respectively. Over the past ~15 years, taste receptors have been identified in cells all over the body, demonstrating a more general chemosensory role beyond taste. Bitter and sweet taste receptors regulate gut epithelial function, pancreatic β cell secretion, thyroid hormone secretion, adipocyte function, and many other processes. Emerging data from a variety of tissues suggest that taste receptors are also used by mammalian cells to "eavesdrop" on bacterial communications. These receptors are activated by several quorum-sensing molecules, including acyl-homoserine lactones and quinolones from Gram-negative bacteria such as Pseudomonas aeruginosa, competence stimulating peptides from Streptococcus mutans, and D-amino acids from Staphylococcus aureus. Taste receptors are an arm of immune surveillance similar to Toll-like receptors and other pattern recognition receptors. Because they are activated by quorum-sensing molecules, taste receptors report information about microbial population density based on the chemical composition of the extracellular environment. This review summarizes current knowledge of bacterial activation of taste receptors and identifies important questions remaining in this field.
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Affiliation(s)
- Yobouet Ines Kouakou
- Department of Otorhinolaryngology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert J Lee
- Department of Otorhinolaryngology and Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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20
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Gonda Y, Matsuda A, Adachi K, Ishii C, Suzuki M, Osaki A, Mita M, Nishizaki N, Ohtomo Y, Shimizu T, Yasui M, Hamase K, Sasabe J. Mammals sustain amino acid homochirality against chiral conversion by symbiotic microbes. Proc Natl Acad Sci U S A 2023; 120:e2300817120. [PMID: 37014864 PMCID: PMC10104486 DOI: 10.1073/pnas.2300817120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/07/2023] [Indexed: 04/05/2023] Open
Abstract
Mammals exhibit systemic homochirality of amino acids in L-configurations. While ribosomal protein synthesis requires rigorous chiral selection for L-amino acids, both endogenous and microbial enzymes convert diverse L-amino acids to D-configurations in mammals. However, it is not clear how mammals manage such diverse D-enantiomers. Here, we show that mammals sustain systemic stereo dominance of L-amino acids through both enzymatic degradation and excretion of D-amino acids. Multidimensional high performance liquidchromatography analyses revealed that in blood, humans and mice maintain D-amino acids at less than several percent of the corresponding L-enantiomers, while D-amino acids comprise ten to fifty percent of the L-enantiomers in urine and feces. Germ-free experiments showed that vast majority of D-amino acids, except for D-serine, detected in mice are of microbial origin. Experiments involving mice that lack enzymatic activity to catabolize D-amino acids showed that catabolism is central to the elimination of diverse microbial D-amino acids, whereas excretion into urine is of minor importance under physiological conditions. Such active regulation of amino acid homochirality depends on maternal catabolism during the prenatal period, which switches developmentally to juvenile catabolism along with the growth of symbiotic microbes after birth. Thus, microbial symbiosis largely disturbs homochirality of amino acids in mice, whereas active host catabolism of microbial D-amino acids maintains systemic predominance of L-amino acids. Our findings provide fundamental insight into how the chiral balance of amino acids is governed in mammals and further expand the understanding of interdomain molecular homeostasis in host-microbial symbiosis.
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Affiliation(s)
- Yusuke Gonda
- Department of Pharmacology, Keio University School of Medicine, 160-8582Tokyo, Japan
- Department of Pediatrics, Juntendo University Urayasu Hospital, 279-0021Chiba, Japan
| | - Akina Matsuda
- Department of Pharmacology, Keio University School of Medicine, 160-8582Tokyo, Japan
- Department of Pediatrics, Juntendo UniversityFaculty of Medicine, 113-8431Tokyo, Japan
| | - Kenichiro Adachi
- Department of Pharmacology, Keio University School of Medicine, 160-8582Tokyo, Japan
| | - Chiharu Ishii
- Department of Drug Discovery and Evolution, Graduate School of Pharmaceutical Sciences, Kyushu University, 812-8582Fukuoka, Japan
| | - Masataka Suzuki
- Department of Pharmacology, Keio University School of Medicine, 160-8582Tokyo, Japan
| | - Akina Osaki
- Department of Pharmacology, Keio University School of Medicine, 160-8582Tokyo, Japan
| | | | - Naoto Nishizaki
- Department of Pediatrics, Juntendo University Urayasu Hospital, 279-0021Chiba, Japan
| | - Yoshiyuki Ohtomo
- Department of Pediatrics, Juntendo University Nerima Hospital, 177-8521Tokyo, Japan
| | - Toshiaki Shimizu
- Department of Pediatrics, Juntendo UniversityFaculty of Medicine, 113-8431Tokyo, Japan
| | - Masato Yasui
- Department of Pharmacology, Keio University School of Medicine, 160-8582Tokyo, Japan
| | - Kenji Hamase
- Department of Drug Discovery and Evolution, Graduate School of Pharmaceutical Sciences, Kyushu University, 812-8582Fukuoka, Japan
| | - Jumpei Sasabe
- Department of Pharmacology, Keio University School of Medicine, 160-8582Tokyo, Japan
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21
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Metagenomic Type IV Aminotransferases Active toward (R)-Methylbenzylamine. Catalysts 2023. [DOI: 10.3390/catal13030587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023] Open
Abstract
Aminotransferases (ATs) are pyridoxal 5′-phosphate-dependent enzymes that catalyze the reversible transfer of an amino group from an amino donor to a keto substrate. ATs are promising biocatalysts that are replacing traditional chemical routes for the production of chiral amines. In this study, an in silico-screening of a metagenomic library isolated from the Curonian Lagoon identified 11 full-length fold type IV aminotransferases that were successfully expressed and used for substrate profiling. Three of them (AT-872, AT-1132, and AT-4421) were active toward (R)-methylbenzylamine. Purified proteins showed activity with L- and D-amino acids and various aromatic compounds such as (R)-1-aminotetraline. AT-872 and AT-1132 exhibited thermostability and retained about 55% and 80% of their activities, respectively, even after 24 h of incubation at 50 °C. Active site modeling revealed that AT-872 and AT-4421 have an unusual active site environment similar to the AT of Haliscomenobacter hydrossis, while AT-1132 appeared to be structurally related to the AT from thermophilic archaea Geoglobus acetivorans. Thus, we have identified and characterized PLP fold type IV ATs that were active toward both amino acids and a variety of (R)-amines.
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22
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Caldwell M, Hughes M, Wei F, Ngo C, Pascua R, Pugazhendhi AS, Coathup MJ. Promising applications of D-amino acids in periprosthetic joint infection. Bone Res 2023; 11:14. [PMID: 36894568 PMCID: PMC9998894 DOI: 10.1038/s41413-023-00254-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/02/2023] [Accepted: 02/10/2023] [Indexed: 03/11/2023] Open
Abstract
Due to the rise in our aging population, a disproportionate demand for total joint arthroplasty (TJA) in the elderly is forecast. Periprosthetic joint infection (PJI) represents one of the most challenging complications that can occur following TJA, and as the number of primary and revision TJAs continues to rise, an increasing PJI burden is projected. Despite advances in operating room sterility, antiseptic protocols, and surgical techniques, approaches to prevent and treat PJI remain difficult, primarily due to the formation of microbial biofilms. This difficulty motivates researchers to continue searching for an effective antimicrobial strategy. The dextrorotatory-isoforms of amino acids (D-AAs) are essential components of peptidoglycan within the bacterial cell wall, providing strength and structural integrity in a diverse range of species. Among many tasks, D-AAs regulate cell morphology, spore germination, and bacterial survival, evasion, subversion, and adhesion in the host immune system. When administered exogenously, accumulating data have demonstrated that D-AAs play a pivotal role against bacterial adhesion to abiotic surfaces and subsequent biofilm formation; furthermore, D-AAs have substantial efficacy in promoting biofilm disassembly. This presents D-AAs as promising and novel targets for future therapeutic approaches. Despite their emerging antibacterial efficacy, their role in disrupting PJI biofilm formation, the disassembly of established TJA biofilm, and the host bone tissue response remains largely unexplored. This review aims to examine the role of D-AAs in the context of TJAs. Data to date suggest that D-AA bioengineering may serve as a promising future strategy in the prevention and treatment of PJI.
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Affiliation(s)
- Matthew Caldwell
- Biionix Cluster & College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Orlando, FL, 32827, USA
| | - Megan Hughes
- School of Biosciences, Cardiff University, CF10 3AT, Wales, UK
| | - Fei Wei
- Biionix Cluster & College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Orlando, FL, 32827, USA
| | - Christopher Ngo
- Biionix Cluster & College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Orlando, FL, 32827, USA
| | - Raven Pascua
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Orlando, FL, 32827, USA
| | - Abinaya Sindu Pugazhendhi
- Biionix Cluster & College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Orlando, FL, 32827, USA
| | - Melanie J Coathup
- Biionix Cluster & College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Orlando, FL, 32827, USA.
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23
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Shilova SA, Khrenova MG, Matyuta IO, Nikolaeva AY, Rakitina TV, Klyachko NL, Minyaev ME, Boyko KM, Popov VO, Bezsudnova EY. To the Understanding of Catalysis by D-Amino Acid Transaminases: A Case Study of the Enzyme from Aminobacterium colombiense. Molecules 2023; 28:molecules28052109. [PMID: 36903355 PMCID: PMC10003956 DOI: 10.3390/molecules28052109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
Pyridoxal-5'-phosphate (PLP)-dependent transaminases are highly efficient biocatalysts for stereoselective amination. D-amino acid transaminases can catalyze stereoselective transamination producing optically pure D-amino acids. The knowledge of substrate binding mode and substrate differentiation mechanism in D-amino acid transaminases comes down to the analysis of the transaminase from Bacillus subtilis. However, at least two groups of D-amino acid transaminases differing in the active site organization are known today. Here, we present a detailed study of D-amino acid transaminase from the gram-negative bacterium Aminobacterium colombiense with a substrate binding mode different from that for the transaminase from B. subtilis. We study the enzyme using kinetic analysis, molecular modeling, and structural analysis of holoenzyme and its complex with D-glutamate. We compare the multipoint binding of D-glutamate with the binding of other substrates, D-aspartate and D-ornithine. QM/MM MD simulation reveals that the substrate can act as a base and its proton can be transferred from the amino group to the α-carboxylate group. This process occurs simultaneously with the nucleophilic attack of the PLP carbon atom by the nitrogen atom of the substrate forming gem-diamine at the transimination step. This explains the absence of the catalytic activity toward (R)-amines that lack an α-carboxylate group. The obtained results clarify another substrate binding mode in D-amino acid transaminases and underpinned the substrate activation mechanism.
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Affiliation(s)
- Sofia A. Shilova
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Maria G. Khrenova
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ilya O. Matyuta
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Alena Y. Nikolaeva
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Tatiana V. Rakitina
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
| | - Natalia L. Klyachko
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Mikhail E. Minyaev
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Vladimir O. Popov
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ekaterina Yu. Bezsudnova
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
- Correspondence:
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24
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Bakunova AK, Kostyukov AA, Kuzmin VA, Popov VO, Bezsudnova EY. Mechanistic aspects of the transamination reactions catalyzed by D-amino acid transaminase from Haliscomenobacter hydrossis. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140886. [PMID: 36496204 DOI: 10.1016/j.bbapap.2022.140886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/17/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022]
Abstract
Pyridoxal-5'-phosphate-(PLP-) dependent D-amino acid transaminases (DAATs) catalyze stereoselective reversible transfer of the amino group between D-amino acids and keto acids. In vivo DAATs are commonly known to synthesize D-glutamate for cell wall peptidoglycans. Today DAATs meet increasing attention for application in the synthesis of D-amino acids, whereas little is known about the mechanism of substrate recognition and catalytic steps of the D-amino acids conversion by DAATs. In this work, the pre-steady-state kinetics of the half-reactions of DAAT from Haliscomenobacter hydrossis with D-glutamate, D-alanine, D-leucine, and D-phenylalanine was examined at two wavelengths, 416 and 330 nm, using a stopped-flow technique. Monophasic kinetics was observed with specific substrates D-glutamate and D-alanine, whereas half-reactions with D-leucine and D-phenylalanine exhibited biphasic kinetics. All half-reactions proceeded until the complete conversion of PLP due to the release of the pyridoxamine-5'-phosphate form of cofactor from the holoenzyme . Comparison of kinetic parameters of half-reactions and the overall transamination reactions for D-leucine, D-phenylalanine revealed the increase in the rates of deamination of these substrates in the overall reaction with α-ketoglutarate. In the overall transamination reaction, the catalytic turnover rates for D-leucine and D-phenylalanine increased by 260 and 60 times, correspondingly, comparing with the slowest step rate constants in the half-reactions. We suggested the activating effect by a specific substrate α-ketoglutarate in the overall transamination reaction. The study of half-reactions helped to quantify the specificity of DAAT from H. hydrossis for D-amino acids with different properties. The results obtained are the first detailed analysis of half-reactions catalyzed by DAAT.
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Affiliation(s)
- Alina K Bakunova
- A.N.Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russian Federation
| | - Alexey A Kostyukov
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin st., 4, 119334 Moscow, Russian Federation
| | - Vladimir A Kuzmin
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin st., 4, 119334 Moscow, Russian Federation
| | - Vladimir O Popov
- A.N.Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russian Federation
| | - Ekaterina Yu Bezsudnova
- A.N.Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russian Federation.
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25
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Yoshikawa S, Taniguchi K, Sawamura H, Ikeda Y, Tsuji A, Matsuda S. Advantageous tactics with certain probiotics for the treatment of graft-versus-host-disease after hematopoietic stem cell transplantation. World J Hematol 2023; 10:15-24. [DOI: 10.5315/wjh.v10.i2.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/03/2022] [Accepted: 11/23/2022] [Indexed: 01/17/2023] Open
Abstract
Hematopoietic stem cell transplantation (HSCT) becomes a standard form of cellular therapy for patients with malignant diseases. HSCT is the first-choice of immunotherapy, although HSCT can be associated with many complications such as graft-versus-host disease (GVHD) which is a major cause of morbidity and mortality after allogeneic HSCT. It has been shown that certain gut microbiota could exert protective and/or regenerative immunomodulatory effects by the production of short-chain fatty acids (SCFAs) such as butyrate in the experimental models of GVHD after allogeneic HSCT. Loss of gut commensal bacteria which can produce SCFAs may worsen dysbiosis, increasing the risk of GVHD. Expression of G-protein coupled receptors such as GPR41 seems to be upre-gulated in the presence of commensal bacteria, which might be associated with the biology of regulatory T cells (Tregs). Treg cells are a suppressive subset of CD4 positive T lymphocytes implicated in the prevention of GVHD after allogeneic HSCT. Here, we discuss the current findings of the relationship between the modification of gut microbiota and the GVHD-related immunity, which suggested that tactics with certain probiotics for the beneficial symbiosis in gut-immune axis might lead to the elevation of safety in the allogeneic HSCT.
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Affiliation(s)
- Sayuri Yoshikawa
- Food Science and Nutrition, Nara Women's University, Nara 630-8506, Japan
| | - Kurumi Taniguchi
- Food Science and Nutrition, Nara Women's University, Nara 630-8506, Japan
| | - Haruka Sawamura
- Food Science and Nutrition, Nara Women's University, Nara 630-8506, Japan
| | - Yuka Ikeda
- Food Science and Nutrition, Nara Women's University, Nara 630-8506, Japan
| | - Ai Tsuji
- Food Science and Nutrition, Nara Women's University, Nara 630-8506, Japan
| | - Satoru Matsuda
- Food Science and Nutrition, Nara Women's University, Nara 630-8506, Japan
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26
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Zhu H, Xu C, Chen Y, Liang Y. His-Ala-Phe-Lys peptide from Burkholderia arboris possesses antifungal activity. Front Microbiol 2022; 13:1071530. [PMID: 36560956 PMCID: PMC9763614 DOI: 10.3389/fmicb.2022.1071530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
Burkholderia arboris, which belongs to the Burkholderia cepacia complex, has been shown to possess antifungal activity against several plant fungal pathogens; however, the antifungal compounds are yet to be identified. Here, we identified the antifungal compounds produced by B. arboris using genetic and metabolomic approaches. We generated a Tn5 transposon mutation library of 3,000 B. arboris mutants and isolated three mutants with reduced antifungal activity against the plant fungal pathogen Fusarium oxysporum. Among the mutants, the M464 mutant exhibited the weakest antifungal activity. In the M464 genome, the transposon was inserted into the cobA gene, encoding uroporphyrin-III methyltransferase. Deletion of the cobA gene also resulted in reduced antifungal activity, indicating that the cobA gene contributed to the antifungal activity of B. arboris. Furthermore, a comparison of the differential metabolites between wild type B. arboris and the ∆cobA mutant showed a significantly decreased level of tetrapeptide His-Ala-Phe-Lys (Hafk) in the ∆cobA mutant. Therefore, a Hafk peptide with D-amino acid residues was synthesized and its antifungal activity was evaluated. Notably, the Hafk peptide displayed significant antifungal activity against F. oxysporum and Botrytis cinerea, two plant pathogens that cause destructive fungal diseases. Overall, a novel antifungal compound (Hafk) that can be used for the biocontrol of fungal diseases in plants was identified in B. arboris.
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Affiliation(s)
- Huajie Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Cuihong Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yicun Chen
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China,*Correspondence: Yan Liang, ; Yicun Chen,
| | - Yan Liang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, China,*Correspondence: Yan Liang, ; Yicun Chen,
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27
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Asymmetric Synthesis of Enantiomerically Pure Aliphatic and Aromatic D-Amino Acids Catalyzed by Transaminase from Haliscomenobacter hydrossis. Catalysts 2022. [DOI: 10.3390/catal12121551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
D-amino acids are valuable building blocks for the synthesis of biologically active compounds and pharmaceuticals. The asymmetric synthesis of chiral amino acids from prochiral ketones using stereoselective enzymes is a well-known but far from exhausted approach for large-scale production. Herein, we investigated a pyridoxal-5′-phosphate-dependent D-amino acid transaminase from Haliscomenobacter hydrossis as a potential biocatalyst for the enzymatic asymmetric synthesis of optically pure aliphatic and aromatic D-amino acids. We studied the catalytic efficiency and stereoselectivity of transaminase from H. hydrossis in the amination of aliphatic and aromatic α-keto acids, using D-glutamate as a source of the amino group. We constructed a one-pot three-enzyme system, which included transaminase and two auxiliary enzymes, hydroxyglutarate dehydrogenase, and glucose dehydrogenase, to produce D-amino acids with a product yield of 95–99% and an enantiomeric excess of more than 99%. We estimated the stability of the transaminase and the cofactor leakage under reaction conditions. It was found that a high concentration of α-keto acids as well as a low reaction temperature (30 °C) can reduce the cofactor leakage under reaction conditions. The obtained results demonstrated the efficiency of transaminase from H. hydrossis in the asymmetric synthesis of enantiomerically pure D-amino acids.
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28
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Miyamoto T, Saitoh Y, Katane M, Sekine M, Homma H. YgeA is involved in L- and D-homoserine metabolism in Escherichia coli. FEMS Microbiol Lett 2022; 369:6754731. [PMID: 36214408 DOI: 10.1093/femsle/fnac096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 08/06/2022] [Accepted: 10/07/2022] [Indexed: 12/13/2022] Open
Abstract
Noncanonical D-amino acids are involved in peptidoglycan and biofilm metabolism in bacteria. Previously, we identified amino acid racemases with broad substrate specificity, including YgeA from Escherichia coli, which strongly prefers homoserine as a substrate. In this study, we investigated the functions of this enzyme in vivo. When wild-type and ygeA-deficient E. coli strains were cultured in minimal medium containing D-homoserine, the D-homoserine level was significantly higher in the ygeA-deficient strain than in the wild-type strain, in which it was almost undetectable. Additionally, D-homoserine was detected in YgeA-expressed E. coli cells cultured in minimal medium containing L-homoserine. The growth of the ygeA-deficient strain was significantly impaired in minimal medium with or without supplemental D-homoserine, while L-methionine, L-threonine or L-isoleucine, which are produced via L-homoserine, restored the growth impairment. Furthermore, the wild-type strain formed biofilms significantly more efficiently than the ygeA-deficient strain. Addition of L- or D-homoserine significantly suppressed biofilm formation in the wild-type strain, whereas this addition had no significant effect in the ygeA-deficient strain. Together, these data suggest that YgeA acts as an amino acid racemase and plays a role in L- and D-homoserine metabolism in E. coli.
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Affiliation(s)
- Tetsuya Miyamoto
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo 108-8641, Japan
| | - Yasuaki Saitoh
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo 108-8641, Japan
| | - Masumi Katane
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo 108-8641, Japan
| | - Masae Sekine
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo 108-8641, Japan
| | - Hiroshi Homma
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo 108-8641, Japan
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29
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Promising Application of D-Amino Acids toward Clinical Therapy. Int J Mol Sci 2022; 23:ijms231810794. [PMID: 36142706 PMCID: PMC9503604 DOI: 10.3390/ijms231810794] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/25/2022] Open
Abstract
The versatile roles of D-amino acids (D-AAs) in foods, diseases, and organisms, etc., have been widely reported. They have been regarded, not only as biomarkers of diseases but also as regulators of the physiological function of organisms. Over the past few decades, increasing data has revealed that D-AAs have great potential in treating disease. D-AAs also showed overwhelming success in disengaging biofilm, which might provide promise to inhibit microbial infection. Moreover, it can effectively restrain the growth of cancer cells. Herein, we reviewed recent reports on the potential of D-AAs as therapeutic agents for treating neurological disease or tissue/organ injury, ameliorating reproduction function, preventing biofilm infection, and inhibiting cancer cell growth. Additionally, we also reviewed the potential application of D-AAs in drug modification, such as improving biostability and efficiency, which has a better effect on therapy or diagnosis.
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30
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Peluso P, Chankvetadze B. Recognition in the Domain of Molecular Chirality: From Noncovalent Interactions to Separation of Enantiomers. Chem Rev 2022; 122:13235-13400. [PMID: 35917234 DOI: 10.1021/acs.chemrev.1c00846] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules underlies enantioselective recognition as a fundamental phenomenon regulating life and human activities. Thus, noncovalent interactions represent the narrative thread of a fascinating story which goes across several disciplines of medical, chemical, physical, biological, and other natural sciences. This review has been conceived with the awareness that a modern attitude toward molecular chirality and its consequences needs to be founded on multidisciplinary approaches to disclose the molecular basis of essential enantioselective phenomena in the domain of chemical, physical, and life sciences. With the primary aim of discussing this topic in an integrated way, a comprehensive pool of rational and systematic multidisciplinary information is provided, which concerns the fundamentals of chirality, a description of noncovalent interactions, and their implications in enantioselective processes occurring in different contexts. A specific focus is devoted to enantioselection in chromatography and electromigration techniques because of their unique feature as "multistep" processes. A second motivation for writing this review is to make a clear statement about the state of the art, the tools we have at our disposal, and what is still missing to fully understand the mechanisms underlying enantioselective recognition.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB, CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, I-07100 Sassari, Italy
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Avenue 3, 0179 Tbilisi, Georgia
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31
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Vahdati SN, Behboudi H, Navasatli SA, Tavakoli S, Safavi M. New insights into the inhibitory roles and mechanisms of D-amino acids in bacterial biofilms in medicine, industry, and agriculture. Microbiol Res 2022; 263:127107. [PMID: 35843196 DOI: 10.1016/j.micres.2022.127107] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 11/26/2022]
Abstract
Biofilms are complex aggregates of microbes that are tightly protected by an extracellular matrix (ECM) and may attach to a surface or adhere together. A higher persistence of bacteria on biofilms makes them resistant not only to harsh conditions but also to various antibiotics which led to the emergence of problems in different applications. Recently, it has been discovered that many bacteria produce and release various D-amino acids (D-AAs) to inhibit biofilm formation, which made a great deal of interest in research into the control of bacterial biofilms in diverse fields, such as human health, industrial settings, and medical devices. D-AAs have various mechanisms to inhibit bacterial biofilms such as: (i) interfering with protein synthesis (ii) Inhibition of extracellular polymeric materials (EPS) productions (protein, eDNA, and polysaccharide) (iii) Inhibition of quorum sensing (autoinducers), and (iv) interfere with peptidoglycan synthesis, these various modes of action, enables these small molecules to inhibit both Gram-negative and Gram-positive bacterial biofilms. Since most biofilms are multi-species, D-AAs in combination with other antimicrobial agents are good choices to combat a variety of bacterial biofilms without displaying toxicity on human cells. This review article addressed the role of D-AAs in controlling several bacterial biofilms and described the possible or definite mechanisms involved in this process.
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Affiliation(s)
- Saeed Niazi Vahdati
- Institute of Biochemistry and Biophysics, Department of Biochemistry, University of Tehran, Tehran, Iran
| | - Hossein Behboudi
- Department of Biology, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran.
| | - Sepideh Aliniaye Navasatli
- Institute of Biochemistry and Biophysics, Department of Biochemistry, University of Tehran, Tehran, Iran
| | - Sara Tavakoli
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Maliheh Safavi
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, Iran
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32
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Determination of sequence and absolute configuration of peptide amino acids by HPLC-MS/CD-based detection of liberated N-terminus phenylthiohydantoin amino acids. Sci Rep 2022; 12:10285. [PMID: 35717509 PMCID: PMC9206679 DOI: 10.1038/s41598-022-14205-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 06/02/2022] [Indexed: 11/25/2022] Open
Abstract
We report a method for the simultaneous determination of the sequence and absolute configuration of peptide amino acids using a combination of Edman degradation and HPLC–MS/CD. Phenylthiohydantoin (PTH) derivatives of 20 pairs of standard d- and l-amino acids were synthesized by the Edman reaction. The CD spectra of the derivatives revealed that each pair of the PTH derivatives exhibited the absorption with opposite signs at around 270 nm. These standard PTH derivatives showed well-resolved resolution without interference from byproducts in the ion chromatogram and clear positive/negative CD absorptions when subjected on a reversed phase HPLC–MS system coupled with a CD-2095 HPLC detector. This method was applied for the detection of a synthetic pentapeptide and a natural depsipeptide (halicylindramide C). The sequence and configuration of the pentapeptide and up to eight residues of halicylindramide C were successfully analyzed by this method. The amino acid configuration of the pentapeptide was also determined successfully by subjecting its acid hydrolysates to the Edman reaction followed by HPLC–MS/CD.
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33
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Dai W, Liu J, Qiu Y, Teng Z, Li S, Yuan H, Huang J, Xiang H, Tang H, Wang B, Chen J, Wu H. Gut Microbial Dysbiosis and Cognitive Impairment in Bipolar Disorder: Current Evidence. Front Pharmacol 2022; 13:893567. [PMID: 35677440 PMCID: PMC9168430 DOI: 10.3389/fphar.2022.893567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/20/2022] [Indexed: 12/11/2022] Open
Abstract
Recent studies have reported that the gut microbiota influences mood and cognitive function through the gut-brain axis, which is involved in the pathophysiology of neurocognitive and mental disorders, including Parkinson’s disease, Alzheimer’s disease, and schizophrenia. These disorders have similar pathophysiology to that of cognitive dysfunction in bipolar disorder (BD), including neuroinflammation and dysregulation of various neurotransmitters (i.e., serotonin and dopamine). There is also emerging evidence of alterations in the gut microbial composition of patients with BD, suggesting that gut microbial dysbiosis contributes to disease progression and cognitive impairment in BD. Therefore, microbiota-centered treatment might be an effective adjuvant therapy for BD-related cognitive impairment. Given that studies focusing on connections between the gut microbiota and BD-related cognitive impairment are lagging behind those on other neurocognitive disorders, this review sought to explore the potential mechanisms of how gut microbial dysbiosis affects cognitive function in BD and identify potential microbiota-centered treatment.
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Affiliation(s)
- Wenyu Dai
- National Clinical Research Center for Mental Disorders, Department of Psychiatry, China National Technology Institute on Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Jieyu Liu
- Department of Ultrasound Diagnostic, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Yan Qiu
- National Clinical Research Center for Mental Disorders, Department of Psychiatry, China National Technology Institute on Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Ziwei Teng
- National Clinical Research Center for Mental Disorders, Department of Psychiatry, China National Technology Institute on Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Sujuan Li
- National Clinical Research Center for Mental Disorders, Department of Psychiatry, China National Technology Institute on Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Hui Yuan
- Department of Ultrasound Diagnostic, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Jing Huang
- National Clinical Research Center for Mental Disorders, Department of Psychiatry, China National Technology Institute on Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Hui Xiang
- National Clinical Research Center for Mental Disorders, Department of Psychiatry, China National Technology Institute on Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Hui Tang
- National Clinical Research Center for Mental Disorders, Department of Psychiatry, China National Technology Institute on Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Bolun Wang
- Department of Radiology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Jindong Chen
- National Clinical Research Center for Mental Disorders, Department of Psychiatry, China National Technology Institute on Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Haishan Wu
- National Clinical Research Center for Mental Disorders, Department of Psychiatry, China National Technology Institute on Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, China
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Iwata Y, Nakade Y, Kitajima S, Nakagawa SY, Oshima M, Sakai N, Ogura H, Sato K, Toyama T, Yamamura Y, Miyagawa T, Yamazaki H, Hara A, Shimizu M, Furuichi K, Mita M, Hamase K, Tanaka T, Nishida M, Muramatsu W, Yamamoto H, Shichino S, Ueha S, Matsushima K, Wada T. Protective Effect of D-Alanine Against Acute Kidney Injury. Am J Physiol Renal Physiol 2022; 322:F667-F679. [PMID: 35435002 DOI: 10.1152/ajprenal.00198.2021] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Recent studies revealed the connection between amino acid chirality and diseases. We previously reported that the gut microbiota produced various D-amino acids in a murine acute kidney injury (AKI) model. Here, we further explore the pathophysiological role of D-Alanine (Ala) in AKI. METHODS We analyzed the transcripts of the N-methyl-D-aspartate (NMDA) receptor, a receptor for D-Ala, in tubular epithelial cells (TECs). Then, the therapeutic effect of D-Ala was assessed in vivo and in vitro. Lastly, the plasma level of D-Ala was evaluated in AKI patients. RESULTS The Grin genes encoding NMDA receptor subtypes were expressed in TECs. Hypoxia condition changes the gene expressions of Grin1, Grin2A and Grin2B. D-Ala protected TECs from hypoxia-related cell injury and induced proliferation after hypoxia. These protective effects are associated with the chirality of D-Ala. D-Ala inhibits ROS production and improves mitochondrial membrane potential, through NMDA receptor signaling. The ratio of D-Ala/L-Ala was increased in feces, plasma, and urine after the induction of I/R. Moreover, enterobacteriaceae, such as Escherichia coli, Klebsiella oxytoca produced D-Ala. The oral administration of D-Ala ameliorated kidney injury after I/R induction in mice. The deficiency of NMDA subunit NR1 on tubular cell worsened kidney damage in AKI. In addition, the plasma level of D-Ala was increased and reflected the level of renal function in AKI patients. CONCLUSIONS D-Ala has protective effects on I/R-induced kidney injury. Moreover, the plasma level of D-Ala reflects the eGFR in AKI patients. D-Ala could be a promising therapeutic target and potential biomarker for AKI.
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Affiliation(s)
- Yasunori Iwata
- Division of Infection Control, Kanazawa University Hospital, Kanazawa, Japan.,Department of Nephrology and Laboratory Medicine, Kanazawa University, Kanazawa, Japan
| | - Yusuke Nakade
- Department of Nephrology and Laboratory Medicine, Kanazawa University, Kanazawa, Japan
| | - Shinji Kitajima
- Division of Blood Purification, Kanazawa University Hospital, Kanazawa, Japan.,Department of Nephrology and Laboratory Medicine, Kanazawa University, Kanazawa, Japan
| | | | - Megumi Oshima
- Department of Nephrology and Laboratory Medicine, Kanazawa University, Kanazawa, Japan
| | - Norihiko Sakai
- Division of Blood Purification, Kanazawa University Hospital, Kanazawa, Japan.,Department of Nephrology and Laboratory Medicine, Kanazawa University, Kanazawa, Japan
| | - Hisayuki Ogura
- Department of Nephrology and Laboratory Medicine, Kanazawa University, Kanazawa, Japan
| | - Koichi Sato
- Department of Nephrology and Laboratory Medicine, Kanazawa University, Kanazawa, Japan
| | - Tadashi Toyama
- Department of Nephrology and Laboratory Medicine, Kanazawa University, Kanazawa, Japan
| | - Yuta Yamamura
- Department of Nephrology and Laboratory Medicine, Kanazawa University, Kanazawa, Japan
| | - Taro Miyagawa
- Department of Nephrology and Laboratory Medicine, Kanazawa University, Kanazawa, Japan
| | - Hiroka Yamazaki
- Department of Nephrology and Laboratory Medicine, Kanazawa University, Kanazawa, Japan
| | - Akinori Hara
- Department of Nephrology and Laboratory Medicine, Kanazawa University, Kanazawa, Japan
| | - Miho Shimizu
- Department of Nephrology and Laboratory Medicine, Kanazawa University, Kanazawa, Japan
| | - Kengo Furuichi
- Division of Nephrology, Kanazawa Medical University School of Medicine, Ishikawa, Kanazawa, Japan
| | | | - Kenji Hamase
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Tomohiro Tanaka
- National Institute for Physiological Sciences and Exploratory Research Center on Life and Living Systems and Center for Novel Science Initiatives, National Institutes of Natural Sciences, Aichi, Japan
| | - Motohiro Nishida
- National Institute for Physiological Sciences and Exploratory Research Center on Life and Living Systems and Center for Novel Science Initiatives, National Institutes of Natural Sciences, Aichi, Japan
| | - Wataru Muramatsu
- Molecular Catalyst Research Center, Chubu University, Aichi, Japan
| | - Hisashi Yamamoto
- Molecular Catalyst Research Center, Chubu University, Aichi, Japan
| | - Shigeyuki Shichino
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Chiba, Tokyo University of Science, Tokyo, Japan
| | - Satoshi Ueha
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Chiba, Tokyo University of Science, Tokyo, Japan
| | - Kouji Matsushima
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Chiba, Tokyo University of Science, Tokyo, Japan
| | - Takashi Wada
- Department of Nephrology and Laboratory Medicine, Kanazawa University, Kanazawa, Japan
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35
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Miyamoto T, Moriya T, Katane M, Saitoh Y, Sekine M, Sakai‐Kato K, Oshima T, Homma H. Identification of a novel
d
‐amino acid aminotransferase involved in
d
‐glutamate biosynthetic pathways in the hyperthermophile
Thermotoga maritima. FEBS J 2022; 289:5933-5946. [DOI: 10.1111/febs.16452] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/22/2022] [Accepted: 04/01/2022] [Indexed: 02/02/2023]
Affiliation(s)
- Tetsuya Miyamoto
- Graduate School of Pharmaceutical Sciences Kitasato University Tokyo Japan
| | - Toshiyuki Moriya
- Institute of Environmental Microbiology Kyowa Kako Co. Tokyo Japan
| | - Masumi Katane
- Graduate School of Pharmaceutical Sciences Kitasato University Tokyo Japan
| | - Yasuaki Saitoh
- Graduate School of Pharmaceutical Sciences Kitasato University Tokyo Japan
| | - Masae Sekine
- Graduate School of Pharmaceutical Sciences Kitasato University Tokyo Japan
| | - Kumiko Sakai‐Kato
- Graduate School of Pharmaceutical Sciences Kitasato University Tokyo Japan
| | - Tairo Oshima
- Institute of Environmental Microbiology Kyowa Kako Co. Tokyo Japan
| | - Hiroshi Homma
- Graduate School of Pharmaceutical Sciences Kitasato University Tokyo Japan
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Nagase N, Ikeda Y, Tsuji A, Kitagishi Y, Matsuda S. Efficacy of probiotics on the modulation of gut microbiota in the treatment of diabetic nephropathy. World J Diabetes 2022; 13:150-160. [PMID: 35432750 PMCID: PMC8984564 DOI: 10.4239/wjd.v13.i3.150] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/21/2021] [Accepted: 02/13/2022] [Indexed: 02/06/2023] Open
Abstract
Diabetic nephropathy (DN) is a major cause of end-stage renal disease, and therapeutic options for preventing its progression are insufficient. The number of patients with DN has been increasing in Asian countries because of westernization of dietary lifestyle, which may be associated with the following changes in gut microbiota. Alterations in the gut microbiota composition can lead to an imbalanced gastrointestinal environment that promotes abnormal production of metabolites and/or inflammatory status. Functional microenvironments of the gut could be changed in the different stages of DN. In particular, altered levels of short chain fatty acids, D-amino acids, and reactive oxygen species biosynthesis in the gut have been shown to be relevant to the pathogenesis of the DN. So far, evidence suggests that the gut microbiota may play a key role in determining networks in the development of DN. Interventions directing the gut microbiota deserve further investigation as a new protective therapy in DN. In this review, we discuss the potential roles of the gut microbiota and future perspectives in the protection and/or treatment of kidneys.
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Affiliation(s)
- Nozomi Nagase
- Department of Food Science and Nutrition, Nara Women's University, Nara 630-8506, Japan
| | - Yuka Ikeda
- Department of Food Science and Nutrition, Nara Women's University, Nara 630-8506, Japan
| | - Ai Tsuji
- Department of Food Science and Nutrition, Nara Women's University, Nara 630-8506, Japan
| | - Yasuko Kitagishi
- Department of Food Science and Nutrition, Nara Women's University, Nara 630-8506, Japan
| | - Satoru Matsuda
- Department of Food Science and Nutrition, Nara Women's University, Nara 630-8506, Japan
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37
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Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing. Appl Environ Microbiol 2022; 88:e0243021. [PMID: 35285712 DOI: 10.1128/aem.02430-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas putida KT2440 has long been studied for its diverse and robust metabolisms, yet many genes and proteins imparting these growth capacities remain uncharacterized. Using pooled mutant fitness assays, we identified genes and proteins involved in the assimilation of 52 different nitrogen containing compounds. To assay amino acid biosynthesis, 19 amino acid drop-out conditions were also tested. From these 71 conditions, significant fitness phenotypes were elicited in 672 different genes including 100 transcriptional regulators and 112 transport-related proteins. We divide these conditions into 6 classes, and propose assimilatory pathways for the compounds based on this wealth of genetic data. To complement these data, we characterize the substrate range of three promiscuous aminotransferases relevant to metabolic engineering efforts in vitro. Furthermore, we examine the specificity of five transcriptional regulators, explaining some fitness data results and exploring their potential to be developed into useful synthetic biology tools. In addition, we use manifold learning to create an interactive visualization tool for interpreting our BarSeq data, which will improve the accessibility and utility of this work to other researchers. IMPORTANCE Understanding the genetic basis of P. putida's diverse metabolism is imperative for us to reach its full potential as a host for metabolic engineering. Many target molecules of the bioeconomy and their precursors contain nitrogen. This study provides functional evidence linking hundreds of genes to their roles in the metabolism of nitrogenous compounds, and provides an interactive tool for visualizing these data. We further characterize several aminotransferases, lactamases, and regulators, which are of particular interest for metabolic engineering.
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38
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Chiral resolution of plasma amino acids reveals enantiomer-selective associations with organ functions. Amino Acids 2022; 54:421-432. [PMID: 35226151 DOI: 10.1007/s00726-022-03140-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/10/2022] [Indexed: 02/07/2023]
Abstract
Plasma amino acids reflect the dynamics of amino acids in organs and their levels have clinical significance. Amino acids as clinical indicators have been evaluated as a mixture of D- and L-amino acids because D-enantiomers are believed to be physiologically nonexistent. However, it has become clear that some D-amino acids are synthesized by endogenous enzymes and symbiotic bacteria. Here, using a two-dimensional HPLC system, we measured enantiomers of all proteinogenic amino acids in plasma and urine and analyzed for correlation with other biochemical parameters in humans who underwent health checkups at our institutional hospital. Four D-amino acids (D-asparagine, D-alanine, D-serine, and D-proline) were detected in the plasma, amounting to less than 1% of the quantities of L-amino acids, but in the urine at several tens of percent, showing that D-amino acids have much higher fractional excretion than their L-counterparts. Detected plasma D-amino acids and D-/L-amino acid ratios were well correlated with renal parameters, such as blood urea nitrogen, creatinine, and cystatin C. On the other hand, a set of plasma L-amino acids were associated with body mass index and correlated with metabolic parameters such as liver enzymes, lipids, blood glucose, and uric acid. Thus, chiral resolution of plasma amino acids revealed totally different associations of the enantiomers with organ functions, and warrants further investigation for clinical and laboratory usefulness.
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39
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Muranaka Y, Mizutani A, Kobayashi M, Nakamoto K, Matsue M, Nishi K, Yamazaki K, Nishii R, Shikano N, Okamoto S, Kawai K. Comparison of L- and D-Amino Acids for Bacterial Imaging in Lung Infection Mouse Model. Int J Mol Sci 2022; 23:ijms23052467. [PMID: 35269610 PMCID: PMC8910731 DOI: 10.3390/ijms23052467] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 12/12/2022] Open
Abstract
The effectiveness of L- and D-amino acids for detecting the early stage of infection in bacterial imaging was compared. We evaluated the accumulation of 3H-L-methionine (Met), 3H-D-Met, 3H-L-alanine (Ala), and 3H-D-Ala in E. coli EC-14 and HaCaT cells. Biological distribution was assessed in control and lung-infection-model mice with EC-14 using 3H-L- and D-Met, and 18F-FDG. A maximum accumulation of 3H-L- and D-Met, and 3H-L- and D-Ala occurred in the growth phase of EC-14 in vitro. The accumulation of 3H-L-Met and L-Ala was greater than that of 3H-D-Met and D-Ala in both EC-14 and HaCaT cells. For all radiotracers, the accumulation was greater in EC-14 than in HaCaT cells at early time points. The accumulation was identified at 5 min after injection in EC-14, whereas the accumulation gradually increased in HaCaT cells over time. There was little difference in biodistribution between 3H-L-and D-Met except in the brain. 3H-L- and D-Met were sensitive for detecting areas of infection after the spread of bacteria throughout the body, whereas 18F-FDG mainly detected primary infection areas. Therefore, 11C-L- and D-Met, radioisotopes that differ only in terms of 3H labeling, could be superior to 18F-FDG for detecting bacterial infection in lung-infection-model mice.
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Affiliation(s)
- Yuka Muranaka
- Division of Health Sciences, Graduate School of Medical Sciences, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa 920-1192, Ishikawa, Japan; (Y.M.); (K.N.)
| | - Asuka Mizutani
- Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa 920-1192, Ishikawa, Japan; (A.M.); (M.K.); (S.O.)
| | - Masato Kobayashi
- Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa 920-1192, Ishikawa, Japan; (A.M.); (M.K.); (S.O.)
| | - Koya Nakamoto
- Division of Health Sciences, Graduate School of Medical Sciences, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa 920-1192, Ishikawa, Japan; (Y.M.); (K.N.)
| | - Miki Matsue
- Ishikawa Prefectural Institute of Public Health and Environmental Science, 1-11, Taiyogaoka, Kanazawa 920-1154, Ishikawa, Japan;
| | - Kodai Nishi
- Department of Radioisotope Medicine, Atomic Bomb Disease Institute, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Nagasaki, Japan;
| | - Kana Yamazaki
- Department of Molecular Imaging and Theranostics, Institute for Quantum Medical Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba 263-8555, Chiba, Japan; (K.Y.); (R.N.)
| | - Ryuichi Nishii
- Department of Molecular Imaging and Theranostics, Institute for Quantum Medical Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba 263-8555, Chiba, Japan; (K.Y.); (R.N.)
| | - Naoto Shikano
- Department of Radiological Sciences, Ibaraki Prefectural University of Health Sciences, 4669-2 Ami, Inashiki 300-0394, Ibaraki, Japan;
| | - Shigefumi Okamoto
- Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa 920-1192, Ishikawa, Japan; (A.M.); (M.K.); (S.O.)
- Advanced Health Care Science Research Unit, Innovative Integrated Bio-Research Core Institute for Frontier Science Initiative, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa 920-0942, Ishikawa, Japan
| | - Keiichi Kawai
- Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa 920-1192, Ishikawa, Japan; (A.M.); (M.K.); (S.O.)
- Biomedical Imaging Research Center, University of Fukui, 23-3 Matsuokashimoaizuki, Eiheiji 910-1193, Fukui, Japan
- Correspondence: ; Tel.: +81-76-265-2527; Fax: +81-76-234-4366
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40
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D-Amino Acids as a Biomarker in Schizophrenia. Diseases 2022; 10:diseases10010009. [PMID: 35225861 PMCID: PMC8883943 DOI: 10.3390/diseases10010009] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 02/04/2023] Open
Abstract
D-amino acids may play key roles for specific physiological functions in different organs including the brain. Importantly, D-amino acids have been detected in several neurological disorders such as schizophrenia, amyotrophic lateral sclerosis, and age-related disorders, reflecting the disease conditions. Relationships between D-amino acids and neurophysiology may involve the significant contribution of D-Serine or D-Aspartate to the synaptic function, including neurotransmission and synaptic plasticity. Gut-microbiota could play important roles in the brain-function, since bacteria in the gut provide a significant contribution to the host pool of D-amino acids. In addition, the alteration of the composition of the gut microbiota might lead to schizophrenia. Furthermore, D-amino acids are known as a physiologically active substance, constituting useful biomarkers of several brain disorders including schizophrenia. In this review, we wish to provide an outline of the roles of D-amino acids in brain health and neuropsychiatric disorders with a focus on schizophrenia, which may shed light on some of the superior diagnoses and/or treatments of schizophrenia.
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41
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Fonseca JR, Lucio M, Harir M, Schmitt-Kopplin P. Mining for Active Molecules in Probiotic Supernatant by Combining Non-Targeted Metabolomics and Immunoregulation Testing. Metabolites 2022; 12:metabo12010035. [PMID: 35050158 PMCID: PMC8778235 DOI: 10.3390/metabo12010035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/23/2021] [Accepted: 12/25/2021] [Indexed: 11/16/2022] Open
Abstract
Chronic respiratory diseases such as asthma are highly prevalent in industrialized countries. As cases are expected to rise, there is a growing demand for alternative therapies. Our recent research on the potential benefits of probiotics suggests that they could prevent and reduce the symptoms of many diseases by modulating the host immune system with secreted metabolites. This article presents the first steps of the research that led us to identify the immunoregulatory bioactivity of the amino acid d-Trp reported in our previous study. Here we analyzed the cell culture metabolic footprinting of 25 commercially available probiotic strains to associate metabolic pathway activity information with their respective immune modulatory activity observed in vitro. Crude probiotic supernatant samples were processed in three different ways prior to untargeted analysis in positive and negative ionization mode by direct infusion ESI-FT-ICR-MS: protein precipitation and solid phase extraction (SPE) using HLB and CN-E sorbent cartridges. The data obtained were submitted to multivariate statistical analyses to distinguish supernatant samples into the bioactive and non-bioactive group. Pathway analysis using discriminant molecular features showed an overrepresentation of the tryptophan metabolic pathway for the bioactive supernatant class, suggesting that molecules taking part in that pathway may be involved in the immunomodulatory activity observed in vitro. This work showcases the potential of metabolomics to drive product development and novel bioactive compound discovery out of complex biological samples in a top-down manner.
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Affiliation(s)
- Juliano Roldan Fonseca
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, 85764 Neuherberg, Germany; (J.R.F.); (M.H.); (P.S.-K.)
| | - Marianna Lucio
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, 85764 Neuherberg, Germany; (J.R.F.); (M.H.); (P.S.-K.)
- Correspondence: ; Tel.: +49-89-3187-3775
| | - Mourad Harir
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, 85764 Neuherberg, Germany; (J.R.F.); (M.H.); (P.S.-K.)
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, 85764 Neuherberg, Germany; (J.R.F.); (M.H.); (P.S.-K.)
- Analytical Food Chemistry, Technical University of Munich, 85354 Freising, Germany
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42
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Miyamoto T, Saitoh Y, Katane M, Sekine M, Sakai-Kato K, Homma H. Acetylornithine aminotransferase TM1785 performs multiple functions in the hyperthermophile Thermotoga maritima. FEBS Lett 2021; 595:2931-2941. [PMID: 34747014 DOI: 10.1002/1873-3468.14222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/29/2021] [Accepted: 10/31/2021] [Indexed: 02/02/2023]
Abstract
The hyperthermophilic bacterium Thermotoga maritima peptidoglycan contains unusual d-lysine alongside typical d-alanine and d-glutamate. We previously identified lysine racemase and threonine dehydratase, but knowledge of d-amino acid metabolism remains limited. Herein, we identified and characterized T. maritima acetylornithine aminotransferase TM1785. The enzyme was most active towards acetyl-l-ornithine, but also utilized l-glutamate, l-ornithine and acetyl-l-lysine as amino donors, and 2-oxoglutarate was the preferred amino acceptor. TM1785 also displayed racemase activity towards four amino acids and lyase activity towards l-cysteine, but no dehydratase activity towards l-serine, l-threonine or corresponding d-amino acids. Catalytic efficiency (kcat /Km ) was highest for aminotransferase activity and lowest for racemase activity. TM1785 is a novel acetylornithine aminotransferase associated with l-arginine biosynthesis that possesses two additional distinct activities.
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Affiliation(s)
- Tetsuya Miyamoto
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Yasuaki Saitoh
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Masumi Katane
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Masae Sekine
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Kumiko Sakai-Kato
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Hiroshi Homma
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
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43
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Portillo AE, Readel E, Armstrong DW. Production of both l- and d- N-acyl-homoserine lactones by Burkholderia cepacia and Vibrio fischeri. Microbiologyopen 2021; 10:e1242. [PMID: 34964286 PMCID: PMC8591449 DOI: 10.1002/mbo3.1242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/23/2021] [Indexed: 11/10/2022] Open
Abstract
Quorum sensing (QS) is a complex process in which molecules, such as l-N-acyl-homoserine lactones (l-AHLs), are produced as essential signaling molecules allowing bacteria to detect and respond to cell population density by gene regulation. Few studies have considered the natural production and role of the opposite enantiomers, d-AHLs. In this work, production of d,l-AHLs by Burkholderia cepacia and Vibrio fischeri was monitored over time, with significant amounts of d-AHLs detected. Bioluminescence of V. fischeri was observed with maximum bioluminescence correlating with the maximum concentrations of both l- and d- octanoyl-homoserine lactones (l- and d-OHL). l-Methionine, a precursor to l-AHLs, was examined via supplementation studies conducted by growing three parallel cultures of B. cepacia in M9 minimal media with added l-, d-, or d,l-methionine and observing their effect on the production of d,l-AHL by B. cepacia. The results show that addition of any methionine (l-, d-, or d,l-) does not affect the overall ratio of l- to d-AHLs, that is d-AHL production was not selectively enhanced by d-methionine addition. However, the overall AHL (l- and d-) concentration does increase with the addition of any methionine supplement. These findings indicate the possibility of a distinct biosynthetic pathway for d-AHL production, possibly exposing a new dimension within bacterial communication.
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Affiliation(s)
- Abiud E. Portillo
- Department of Chemistry and BiochemistryThe University of Texas at ArlingtonArlingtonTexasUSA
| | - Elizabeth Readel
- Department of Chemistry and BiochemistryThe University of Texas at ArlingtonArlingtonTexasUSA
| | - Daniel W. Armstrong
- Department of Chemistry and BiochemistryThe University of Texas at ArlingtonArlingtonTexasUSA
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Liu H, Chen Y, Ye J, Xu H, Zhu Z, Xu T. Effects of different amino acids and their configurations on methane yield and biotransformation of intermediate metabolites during anaerobic digestion. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 296:113152. [PMID: 34217942 DOI: 10.1016/j.jenvman.2021.113152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 06/17/2021] [Accepted: 06/22/2021] [Indexed: 06/13/2023]
Abstract
Anaerobic digestion (AD) comprises a series of biochemical reactions, with methane as one of the target products. Amino acids (AAs) are important molecular and primary intermediate products when protein is the main component of organic waste/wastewater. The L (levorotatory, left-handed)-configuration is natural for AAs, while D (dextrorotatory, right-handed) -AAs also widely exist in the natural environment and can be generated by racemization. However, the effects and underlying mechanisms of natural AAs and their enantiomers on the methane yield and the underlying mechanisms remain unclear. In this study, the effects of certain widespread L-AAs and their enantiomers on two-stage AD and the mechanisms therein were investigated. The AAs enantiomers showed variable or even opposite effects on different processes. The methane yield from a model monosaccharide (glucose) decreased by 57% with D-leucine addition. The butyrate generation and the methane yield from propionate were sensitive to the AA configuration and were inhibited by D-leucine by 80% and 61.8%, respectively, with D-leucine addition, while the volatile fatty acids concentration was slightly increased with the addition of L-leucine. The related mechanisms were further investigated in terms of key enzymes and microbial communities. The addition of D-Leucine decreased acetic acid production from homoacetogens by 30.2% due to the inhibition of key enzymes involved in hydrogen generation and consumption. The transform of butyryl CoA to butyryl phosphate was the rate-limiting step, with the related enzyme (phosphotransbutylase) was inhibited by D-leucine. Furthermore, the bacteria related to butyric acid generation and organic matter degradation were inhibited by D-leucine, while the methanogenic archaea remained stable irrespective of leucine addition. The effect of D-AAs on microorganisms is related to the type of sludge. In this study, the methanogenetic seed sludge was granular and did not dissociate after treatment; however, the D-AAs could trigger biofilm disassembly and reduce the stability of the sludge floc. The study provides a novel method for regulating AD by adding specific AAs with L or D configuration.
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Affiliation(s)
- Hui Liu
- Shanghai Academy of Environmental Sciences, 200233, Shanghai, China.
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China.
| | - Jianfeng Ye
- Shanghai Academy of Environmental Sciences, 200233, Shanghai, China.
| | - Huiting Xu
- Shanghai Academy of Environmental Sciences, 200233, Shanghai, China
| | - Zhihao Zhu
- Shanghai Academy of Environmental Sciences, 200233, Shanghai, China
| | - Tianchen Xu
- Shanghai Academy of Environmental Sciences, 200233, Shanghai, China
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Metabolomics Comparison of Drug-Resistant and Drug-Susceptible Pseudomonas aeruginosa Strain (Intra- and Extracellular Analysis). Int J Mol Sci 2021; 22:ijms221910820. [PMID: 34639158 PMCID: PMC8509183 DOI: 10.3390/ijms221910820] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/30/2021] [Accepted: 10/02/2021] [Indexed: 12/23/2022] Open
Abstract
Pseudomonas aeruginosa is a common human pathogen belonging to the ESKAPE group. The multidrug resistance of bacteria is a considerable problem in treating patients and may lead to increased morbidity and mortality rate. The natural resistance in these organisms is caused by the production of specific enzymes and biofilm formation, while acquired resistance is multifactorial. Precise recognition of potential antibiotic resistance on different molecular levels is essential. Metabolomics tools may aid in the observation of the flux of low molecular weight compounds in biochemical pathways yielding additional information about drug-resistant bacteria. In this study, the metabolisms of two P. aeruginosa strains were compared-antibiotic susceptible vs. resistant. Analysis was performed on both intra- and extracellular metabolites. The 1H NMR method was used together with multivariate and univariate data analysis, additionally analysis of the metabolic pathways with the FELLA package was performed. The results revealed the differences in P. aeruginosa metabolism of drug-resistant and drug-susceptible strains and provided direct molecular information about P. aeruginosa response for different types of antibiotics. The most significant differences were found in the turnover of amino acids. This study can be a valuable source of information to complement research on drug resistance in P. aeruginosa.
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Bakunova AK, Nikolaeva AY, Rakitina TV, Isaikina TY, Khrenova MG, Boyko KM, Popov VO, Bezsudnova EY. The Uncommon Active Site of D-Amino Acid Transaminase from Haliscomenobacter hydrossis: Biochemical and Structural Insights into the New Enzyme. Molecules 2021; 26:molecules26165053. [PMID: 34443642 PMCID: PMC8401098 DOI: 10.3390/molecules26165053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 02/02/2023] Open
Abstract
Among industrially important pyridoxal-5’-phosphate (PLP)-dependent transaminases of fold type IV D-amino acid transaminases are the least studied. However, the development of cascade enzymatic processes, including the synthesis of D-amino acids, renewed interest in their study. Here, we describe the identification, biochemical and structural characterization of a new D-amino acid transaminase from Haliscomenobacter hydrossis (Halhy). The new enzyme is strictly specific towards D-amino acids and their keto analogs; it demonstrates one of the highest rates of transamination between D-glutamate and pyruvate. We obtained the crystal structure of the Halhy in the holo form with the protonated Schiff base formed by the K143 and the PLP. Structural analysis revealed a novel set of the active site residues that differ from the key residues forming the active sites of the previously studied D-amino acids transaminases. The active site of Halhy includes three arginine residues, one of which is unique among studied transaminases. We identified critical residues for the Halhy catalytic activity and suggested functions of the arginine residues based on the comparative structural analysis, mutagenesis, and molecular modeling simulations. We suggested a strong positive charge in the O-pocket and the unshaped P-pocket as a structural code for the D-amino acid specificity among transaminases of PLP fold type IV. Characteristics of Halhy complement our knowledge of the structural basis of substrate specificity of D-amino acid transaminases and the sequence-structure-function relationships in these enzymes.
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Affiliation(s)
- Alina K. Bakunova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia; (A.K.B.); (A.Y.N.); (T.V.R.); (T.Y.I.); (M.G.K.); (K.M.B.); (V.O.P.)
| | - Alena Yu. Nikolaeva
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia; (A.K.B.); (A.Y.N.); (T.V.R.); (T.Y.I.); (M.G.K.); (K.M.B.); (V.O.P.)
| | - Tatiana V. Rakitina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia; (A.K.B.); (A.Y.N.); (T.V.R.); (T.Y.I.); (M.G.K.); (K.M.B.); (V.O.P.)
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia
| | - Tatiana Y. Isaikina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia; (A.K.B.); (A.Y.N.); (T.V.R.); (T.Y.I.); (M.G.K.); (K.M.B.); (V.O.P.)
| | - Maria G. Khrenova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia; (A.K.B.); (A.Y.N.); (T.V.R.); (T.Y.I.); (M.G.K.); (K.M.B.); (V.O.P.)
- Chemistry Department, Lomonosov Moscow State University, Leninskiye Gory 1/3, 119991 Moscow, Russia
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia; (A.K.B.); (A.Y.N.); (T.V.R.); (T.Y.I.); (M.G.K.); (K.M.B.); (V.O.P.)
| | - Vladimir O. Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia; (A.K.B.); (A.Y.N.); (T.V.R.); (T.Y.I.); (M.G.K.); (K.M.B.); (V.O.P.)
| | - Ekaterina Yu. Bezsudnova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia; (A.K.B.); (A.Y.N.); (T.V.R.); (T.Y.I.); (M.G.K.); (K.M.B.); (V.O.P.)
- Correspondence: author E-mail:
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Bezsudnova EY, Nikolaeva AY, Bakunova AK, Rakitina TV, Suplatov DA, Popov VO, Boyko KM. Probing the role of the residues in the active site of the transaminase from Thermobaculum terrenum. PLoS One 2021; 16:e0255098. [PMID: 34324538 PMCID: PMC8320979 DOI: 10.1371/journal.pone.0255098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/11/2021] [Indexed: 11/28/2022] Open
Abstract
Creating biocatalysts for (R)-selective amination effectively is highly desirable in organic synthesis. Despite noticeable progress in the engineering of (R)-amine activity in pyridoxal-5’-phosphate-dependent transaminases of fold type IV, the specialization of the activity is still an intuitive task, as there is poor understanding of sequence-structure-function relationships. In this study, we analyzed this relationship in transaminase from Thermobaculum terrenum, distinguished by expanded substrate specificity and activity in reactions with L-amino acids and (R)-(+)-1-phenylethylamine using α-ketoglutarate and pyruvate as amino acceptors. We performed site-directed mutagenesis to create a panel of the enzyme variants, which differ in the active site residues from the parent enzyme to a putative transaminase specific to (R)-primary amines. The variants were examined in the overall transamination reactions and half-reaction with (R)-(+)-1-phenylethylamine. A structural analysis of the most prominent variants revealed a spatial reorganization in the active sites, which caused changes in activity. Although the specialization to (R)-amine transaminase was not implemented, we succeeded in understanding the role of the particular active site residues in expanding substrate specificity of the enzyme. We showed that the specificity for (R)-(+)-1-phenylethylamine in transaminase from T. terrenum arises without sacrificing the specificity for L-amino acids and α-ketoglutarate and in consensus with it.
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Affiliation(s)
- Ekaterina Yu Bezsudnova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Alena Yu Nikolaeva
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Alina K Bakunova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Tatiana V Rakitina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation.,Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Dmitry A Suplatov
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Moscow, Russian Federation
| | - Vladimir O Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Konstantin M Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
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Sugahara H, Nagayama K, Ikeda S, Hirota T, Nakamura Y. D- and l-amino acid concentrations in culture broth of Lactobacillus are highly dependent on the phylogenetic group of Lactobacillus. Biochem Biophys Rep 2021; 27:101073. [PMID: 34286112 PMCID: PMC8278531 DOI: 10.1016/j.bbrep.2021.101073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/12/2021] [Accepted: 07/02/2021] [Indexed: 01/24/2023] Open
Abstract
d-amino acids produced by Lactobacillus are thought to contribute to the taste quality and health functions; however, no studies have comprehensively evaluated the concentrations of the D- and L-forms of amino acids separately in individual Lactobacillus strains. To gain insight into amino acid concentrations in Lactobacillus, we evaluated amino acid concentrations in culture broth of Lactobacillus separately for the D- and L-forms. Lactobacillus strains were cultured in culture broth, and the amino acid concentrations in supernatant were assessed. The amino acid concentrations obtained by liquid chromatography-tandem mass spectrometry (LC-MS/MS) were subjected to cluster analysis based on Bray-Curtis distance with Ward's minimum variance method. In the analysis of amino acid concentrations under culture with different monosaccharides, the distances among strains cultured with the same monosaccharide were significantly greater than those among cultures of the same strain under different monosaccharides (p < 0.01). The cluster analysis of amino acid concentrations under culture with the same monosaccharide suggested that strains belonging to the same phylogenetic group of Lactobacillus exhibited similar concentrations of amino acids. Data analyses of 70 strains belonging to 17 Lactobacillus taxa indicated that the concentrations of amino acids were highly dependent on the phylogenetic group of Lactobacillus and that the group differences in amino acid concentration were strongly driven by differences in l-serine and d-alanine concentrations. Our results indicate that it is important to evaluate D- and l-amino acids separately when evaluating variations in amino acid concentrations. Because d-alanine has the potential to affect taste quality, the results of this study may provide insight into the taste quality of fermented food produced by Lactobacillus.
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Affiliation(s)
- Hirosuke Sugahara
- Core Technology Laboratories, Asahi Quality & Innovations, Ltd., 1-21, Midori 1-Chome, Moriya-Shi, Ibaraki, 302-0106, Japan
| | - Keitaro Nagayama
- Core Technology Laboratories, Asahi Quality & Innovations, Ltd., 1-21, Midori 1-Chome, Moriya-Shi, Ibaraki, 302-0106, Japan
| | - Shiori Ikeda
- Core Technology Laboratories, Asahi Quality & Innovations, Ltd., 1-21, Midori 1-Chome, Moriya-Shi, Ibaraki, 302-0106, Japan
| | - Tatsuhiko Hirota
- Core Technology Laboratories, Asahi Quality & Innovations, Ltd., 1-21, Midori 1-Chome, Moriya-Shi, Ibaraki, 302-0106, Japan
| | - Yasunori Nakamura
- Core Technology Laboratories, Asahi Quality & Innovations, Ltd., 1-21, Midori 1-Chome, Moriya-Shi, Ibaraki, 302-0106, Japan
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Kawakami R, Kinoshita C, Kawase T, Sato M, Hayashi J, Sakuraba H, Ohshima T. Characterization of a novel moderate-substrate specificity amino acid racemase from the hyperthermophilic archaeon Thermococcus litoralis. Biosci Biotechnol Biochem 2021; 85:1650-1657. [PMID: 33942867 DOI: 10.1093/bbb/zbab078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 04/27/2021] [Indexed: 02/02/2023]
Abstract
The amino acid sequence of the OCC_10945 gene product from the hyperthermophilic archaeon Thermococcus litoralis DSM5473, originally annotated as γ-aminobutyrate aminotransferase, is highly similar to that of the uncharacterized pyridoxal 5'-phosphate (PLP)-dependent amino acid racemase from Pyrococcus horikoshii. The OCC_10945 enzyme was successfully overexpressed in Escherichia coli by coexpression with a chaperone protein. The purified enzyme demonstrated PLP-dependent amino acid racemase activity primarily toward Met and Leu. Although PLP contributed to enzyme stability, it only loosely bound to this enzyme. Enzyme activity was strongly inhibited by several metal ions, including Co2+ and Zn2+, and nonsubstrate amino acids such as l-Arg and l-Lys. These results suggest that the underlying PLP-binding and substrate recognition mechanisms in this enzyme are significantly different from those of the other archaeal and bacterial amino acid racemases. This is the first description of a novel PLP-dependent amino acid racemase with moderate substrate specificity in hyperthermophilic archaea.
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Affiliation(s)
- Ryushi Kawakami
- Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Japan
| | - Chinatsu Kinoshita
- Department of Bioscience and Bioindustry, Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Tomoki Kawase
- Department of Bioscience and Bioindustry, Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Mikio Sato
- Department of Bioscience and Bioindustry, Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Junji Hayashi
- Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Japan
| | - Haruhiko Sakuraba
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Kita-gun, Japan
| | - Toshihisa Ohshima
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, Osaka, Japan
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50
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Identification and biochemical characterization of threonine dehydratase from the hyperthermophile Thermotoga maritima. Amino Acids 2021; 53:903-915. [PMID: 33938999 DOI: 10.1007/s00726-021-02993-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/21/2021] [Indexed: 01/14/2023]
Abstract
The peptidoglycan of the hyperthermophile Thermotoga maritima contains an unusual component, D-lysine (D-Lys), in addition to the typical D-alanine (D-Ala) and D-glutamate (D-Glu). In a previous study, we identified a Lys racemase that is presumably associated with D-Lys biosynthesis. However, our understanding of D-amino acid metabolism in T. maritima and other bacteria remains limited, although D-amino acids in the peptidoglycan are crucial for preserving bacterial cell structure and resistance to environmental threats. Herein, we characterized enzymatic and structural properties of TM0356 that shares a high amino acid sequence identity with serine (Ser) racemase. The results revealed that TM0356 forms a tetramer with each subunit containing a pyridoxal 5'-phosphate as a cofactor. The enzyme did not exhibit racemase activity toward various amino acids including Ser, and dehydratase activity was highest toward L-threonine (L-Thr). It also acted on L-Ser and L-allo-Thr, but not on the corresponding D-amino acids. The catalytic mechanism did not follow typical Michaelis-Menten kinetics; it displayed a sigmoidal dependence on substrate concentration, with highest catalytic efficiency (kcat/K0.5) toward L-Thr. Interestingly, dehydratase activity was insensitive to allosteric regulators L-valine and L-isoleucine (L-Ile) at low concentrations, while these L-amino acids are inhibitors at high concentrations. Thus, TM0356 is a biosynthetic Thr dehydratase responsible for the conversion of L-Thr to α-ketobutyrate and ammonia, which is presumably involved in the first step of the biosynthesis of L-Ile.
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