1
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Porras-Dominguez J, Lothier J, Limami AM, Tcherkez G. d-amino acids metabolism reflects the evolutionary origin of higher plants and their adaptation to the environment. PLANT, CELL & ENVIRONMENT 2024; 47:1503-1512. [PMID: 38251436 DOI: 10.1111/pce.14826] [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: 06/22/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024]
Abstract
d-amino acids are the d stereoisomers of the common l-amino acids found in proteins. Over the past two decades, the occurrence of d-amino acids in plants has been reported and circumstantial evidence for a role in various processes, including interaction with soil microorganisms or interference with cellular signalling, has been provided. However, examples are not numerous and d-amino acids can also be detrimental, some of them inhibiting growth and development. Thus, the persistence of d-amino acid metabolism in plants is rather surprising, and the evolutionary origins of d-amino acid metabolism are currently unclear. Systemic analysis of sequences associated with d-amino acid metabolism enzymes shows that they are not simply inherited from cyanobacterial metabolism. In fact, the history of plant d-amino acid metabolism enzymes likely involves multiple steps, cellular compartments, gene transfers and losses. Regardless of evolutionary steps, enzymes of d-amino acid metabolism, such as d-amino acid transferases or racemases, have been retained by higher plants and have not simply been eliminated, so it is likely that they fulfil important metabolic roles such as serine, folate or plastid peptidoglycan metabolism. We suggest that d-amino acid metabolism may have been critical to support metabolic functions required during the evolution of land plants.
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Affiliation(s)
- Jaime Porras-Dominguez
- Institut de Recherche en Horticulture et Semences, INRAe, Université d'Angers, Beaucouzé, France
| | - Jérémy Lothier
- Institut de Recherche en Horticulture et Semences, INRAe, Université d'Angers, Beaucouzé, France
| | - Anis M Limami
- Institut de Recherche en Horticulture et Semences, INRAe, Université d'Angers, Beaucouzé, France
| | - Guillaume Tcherkez
- Institut de Recherche en Horticulture et Semences, INRAe, Université d'Angers, Beaucouzé, France
- Research School of Biology, Australian National University, Canberra, Australia
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2
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Yang J, Ran Y, Liu S, Ren C, Lou Y, Ju P, Li G, Li X, Zhang D. Synergistic D-Amino Acids Based Antimicrobial Cocktails Formulated via High-Throughput Screening and Machine Learning. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307173. [PMID: 38126652 PMCID: PMC10916672 DOI: 10.1002/advs.202307173] [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: 09/28/2023] [Revised: 11/29/2023] [Indexed: 12/23/2023]
Abstract
Antimicrobial resistance (AMR) from pathogenic bacterial biofilms has become a global health issue while developing novel antimicrobials is inefficient and costly. Combining existing multiple drugs with enhanced efficacy and/or reduced toxicity may be a promising approach to treat AMR. D-amino acids mixtures coupled with antibiotics can provide new therapies for drug-resistance infection with reduced toxicity by lower drug dosage requirements. However, iterative trial-and-error experiments are not tenable to prioritize credible drug formulations, owing to the extremely large number of possible combinations. Herein, a new avenue is provide to accelerate the exploration of desirable antimicrobial formulations via high-throughput screening and machine learning optimization. Such an intelligent method can navigate the large search space and rapidly identify the D-amino acid mixtures with the highest anti-biofilm efficiency and also the synergisms between D-amino acid mixtures and antibiotics. The optimized drug cocktails exhibit high antimicrobial efficacy while remaining non-toxic, which is demonstrated not only from in vitro assessments but also the first in vivo study using a lung infection mouse model.
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Affiliation(s)
- Jingzhi Yang
- Beijing Advanced Innovation Center for Materials Genome EngineeringInstitute for Advanced Materials and TechnologyUniversity of Science and Technology BeijingBeijing100083China
- National Materials Corrosion and Protection Data CenterUniversity of Science and Technology BeijingBeijing100083China
| | - Yami Ran
- Beijing Advanced Innovation Center for Materials Genome EngineeringInstitute for Advanced Materials and TechnologyUniversity of Science and Technology BeijingBeijing100083China
- National Materials Corrosion and Protection Data CenterUniversity of Science and Technology BeijingBeijing100083China
- BRI Southeast Asia Network for Corrosion and ProtectionShunde Graduate School of University of Science and Technology BeijingFoshan528000China
| | - Shaopeng Liu
- Beijing Advanced Innovation Center for Materials Genome EngineeringInstitute for Advanced Materials and TechnologyUniversity of Science and Technology BeijingBeijing100083China
- National Materials Corrosion and Protection Data CenterUniversity of Science and Technology BeijingBeijing100083China
| | - Chenhao Ren
- Beijing Advanced Innovation Center for Materials Genome EngineeringInstitute for Advanced Materials and TechnologyUniversity of Science and Technology BeijingBeijing100083China
- National Materials Corrosion and Protection Data CenterUniversity of Science and Technology BeijingBeijing100083China
| | - Yuntian Lou
- Beijing Advanced Innovation Center for Materials Genome EngineeringInstitute for Advanced Materials and TechnologyUniversity of Science and Technology BeijingBeijing100083China
- National Materials Corrosion and Protection Data CenterUniversity of Science and Technology BeijingBeijing100083China
- BRI Southeast Asia Network for Corrosion and ProtectionShunde Graduate School of University of Science and Technology BeijingFoshan528000China
| | - Pengfei Ju
- Shanghai Aerospace Equipment ManufacturerShanghai200245China
| | - Guoliang Li
- College of Materials Science and EngineeringBeijing University of Chemical TechnologyBeijing100029China
| | - Xiaogang Li
- Beijing Advanced Innovation Center for Materials Genome EngineeringInstitute for Advanced Materials and TechnologyUniversity of Science and Technology BeijingBeijing100083China
- National Materials Corrosion and Protection Data CenterUniversity of Science and Technology BeijingBeijing100083China
- BRI Southeast Asia Network for Corrosion and ProtectionShunde Graduate School of University of Science and Technology BeijingFoshan528000China
| | - Dawei Zhang
- Beijing Advanced Innovation Center for Materials Genome EngineeringInstitute for Advanced Materials and TechnologyUniversity of Science and Technology BeijingBeijing100083China
- National Materials Corrosion and Protection Data CenterUniversity of Science and Technology BeijingBeijing100083China
- BRI Southeast Asia Network for Corrosion and ProtectionShunde Graduate School of University of Science and Technology BeijingFoshan528000China
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3
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Han SW, Jang Y, Kook J, Jang J, Shin JS. Reprogramming biocatalytic futile cycles through computational engineering of stereochemical promiscuity to create an amine racemase. Nat Commun 2024; 15:49. [PMID: 38169460 PMCID: PMC10761954 DOI: 10.1038/s41467-023-44218-7] [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: 05/22/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
Repurposing the intrinsic properties of natural enzymes can offer a viable solution to current synthetic challenges through the development of novel biocatalytic processes. Although amino acid racemases are ubiquitous in living organisms, an amine racemase (AR) has not yet been discovered despite its synthetic potential for producing chiral amines. Here, we report the creation of an AR based on the serendipitous discovery that amine transaminases (ATAs) can perform stereoinversion of 2-aminobutane. Kinetic modeling revealed that the unexpected off-pathway activity results from stereochemically promiscuous futile cycles due to incomplete stereoselectivity for 2-aminobutane. This finding motivated us to engineer an S-selective ATA through in silico alanine scanning and empirical combinatorial mutations, creating an AR with broad substrate specificity. The resulting AR, carrying double point mutations, enables the racemization of both enantiomers of diverse chiral amines in the presence of a cognate ketone. This strategy may be generally applicable to a wide range of transaminases, paving the way for the development of new-to-nature racemases.
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Affiliation(s)
- Sang-Woo Han
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
- Department of Biotechnology, Konkuk University, Chungju, South Korea
| | - Youngho Jang
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
| | - Jihyun Kook
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
| | - Jeesu Jang
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
| | - Jong-Shik Shin
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea.
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4
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Mazzotta S, Rositano V, Senaldi L, Bernardi A, Allegrini P, Appendino G. Scalemic natural products. Nat Prod Rep 2023; 40:1647-1671. [PMID: 37439042 DOI: 10.1039/d3np00014a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Covering: up to the end of 2022The area of scalemic natural products is often enigmatic from a mechanistic standpoint, since low optical purity is observed in compounds having multiple contiguous stereogenic centers resulting from mechanistically distinct biogenetic steps. A scalemic state is rarely the result of a sloppy enzymatic activity, rather resulting from the expression of antipodal enzymes/directing proteins or from the erosion of optical purity by enzymatic or spontaneous reactions. Evidence for these processes is critically reviewed, identifying the mechanisms most often associated to the enzymatic generation of scalemic natural products and also discussing analytical exploitations of natural products' scalemicity.
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Affiliation(s)
- Sarah Mazzotta
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Vincenzo Rositano
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
- Indena SpA, Via Don Minzoni 6, 20049 Settala, MI, Italy
| | - Luca Senaldi
- Indena SpA, Via Don Minzoni 6, 20049 Settala, MI, Italy
| | - Anna Bernardi
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | | | - Giovanni Appendino
- Dipartimento di Scienze del Farmaco, Largo Donegani 2, 28100 Novara, Italy.
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5
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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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6
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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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7
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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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8
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Liao S, Han J, Jiang C, Zhou B, Jiang Z, Tang J, Ding W, Che Z, Lin H. HS-SPME-GC × GC/MS combined with multivariate statistics analysis to investigate the flavor formation mechanism of tank-fermented broad bean paste. Food Chem X 2022; 17:100556. [PMID: 36845488 PMCID: PMC9943836 DOI: 10.1016/j.fochx.2022.100556] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/15/2022] [Accepted: 12/26/2022] [Indexed: 12/29/2022] Open
Abstract
With the advancement of industrialization, tank fermentation technology is promising for Pixian broad bean paste. This study identified and analyzed the general physicochemical factors and volatile metabolites of fermented broad beans in a thermostatic fermenter. Headspace solid-phase microextraction (HS-SPME)-two-dimensional gas chromatography-mass spectrometry (GC × GC-MS) was applied to detect the volatile compounds in fermented broad beans, while metabolomics was used to explore their physicochemical characteristics and analyze the possible metabolic mechanism. A total of 184 different metabolites were detected, including 36 alcohols, 29 aldehydes, 26 esters, 21 ketones, 14 acids, 14 aromatic compounds, ten heterocycles, nine phenols, nine organonitrogen compounds, seven hydrocarbons, two ethers, and seven other types, which were annotated to various branch metabolic pathways of carbohydrate and amino acid metabolism. This study provides references for subsequent functional microorganism mining to improve the quality of the tank-fermented broad beans and upgrade the Pixian broad bean paste industry.
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Affiliation(s)
- Shiqi Liao
- School of Food and Bio-engineering, Xihua University, Chengdu 610039, China
| | - Jinlin Han
- School of Food and Bio-engineering, Xihua University, Chengdu 610039, China
| | - Chunyan Jiang
- School of Food and Bio-engineering, Xihua University, Chengdu 610039, China
| | - Binbin Zhou
- School of Food and Bio-engineering, Xihua University, Chengdu 610039, China
| | - Zhenju Jiang
- School of Food and Bio-engineering, Xihua University, Chengdu 610039, China
| | - Jie Tang
- School of Food and Bio-engineering, Xihua University, Chengdu 610039, China
| | - Wenwu Ding
- School of Food and Bio-engineering, Xihua University, Chengdu 610039, China,Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chengdu 610039, China
| | - Zhenming Che
- School of Food and Bio-engineering, Xihua University, Chengdu 610039, China,Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chengdu 610039, China
| | - Hongbin Lin
- School of Food and Bio-engineering, Xihua University, Chengdu 610039, China,Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chengdu 610039, China,Corresponding author at: Xihua University, Chengdu 610039, China.
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9
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Bitchagno GTM, Nchiozem-Ngnitedem VA, Melchert D, Fobofou SA. Demystifying racemic natural products in the homochiral world. Nat Rev Chem 2022; 6:806-822. [PMID: 37118098 PMCID: PMC9562063 DOI: 10.1038/s41570-022-00431-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2022] [Indexed: 12/03/2022]
Abstract
Natural products possess structural complexity, diversity and chirality with attractive functions and biological activities that have significantly impacted drug discovery initiatives. Chiral natural products are abundant in nature but rarely occur as racemates. The occurrence of natural products as racemates is very intriguing from a biosynthetic point of view; as enzymes are chiral molecules, enzymatic reactions generating natural products should be stereospecific and lead to single-enantiomer products. Despite several reports in the literature describing racemic mixtures of stereoisomers isolated from natural sources, there has not been a comprehensive review of these intriguing racemic natural products. The discovery of many more natural racemates and their potential enzymatic sources in recent years allows us to describe the distribution and chemical diversity of this ‘class of natural products’ to enrich discussions on biosynthesis. In this Review, we describe the chemical classes, occurrence and distribution of pairs of enantiomers in nature and provide insights about recent advances in analytical methods used for their characterization. Special emphasis is on the biosynthesis, including plausible enzymatic and non-enzymatic formation of natural racemates, and their pharmacological significance. ![]()
Racemic natural products display a wealth of bioactivities and chemical diversity. Their derivation from intriguing racemization processes, through enzymatic or non-enzymatic pathways, are discussed here, as well as their pharmacological properties and the analytical techniques developed for their identification, resolution and characterization.
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10
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Hao X, Yan W, Yang J, Bai Y, Qian H, Lou Y, Ju P, Zhang D. Matrine@chitosan-D-proline nanocapsules as antifouling agents with antibacterial properties and biofilm dispersibility in the marine environment. Front Microbiol 2022; 13:950039. [PMID: 35935227 PMCID: PMC9355532 DOI: 10.3389/fmicb.2022.950039] [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: 05/22/2022] [Accepted: 06/28/2022] [Indexed: 11/20/2022] Open
Abstract
Antifoulants are the most vital substances in antifouling coatings to prevent marine organisms from colonizing the undersea substrate surfaces. In addition to antibacterial performance, inhibition of biofilm formation is an important criterion for antifouling coatings. In this study, we synthesized pH-responsive matrine@chitosan-D-proline (Mat@CS-Pro) nanocapsules of about 280 nm with antibacterial properties and biofilm dispersibility. The prepared Mat@CS-Pro nanocapsules exhibited high-level antibacterial properties, reaching about 93, 88, and 96% for E. coli, S. aureus, and P. aeruginosa, respectively. Such nanocapsules can cause irreversible damage to bacteria and cause them to lose their intact cell structures. Moreover, Mat@CS-Pro nanocapsules also possessed outstanding dispersal biofilm performances, in which the biofilm thickness of E. coli, S. aureus, and P. aeruginosa was decreased by 33, 74, and 42%, respectively, after 3 days of incubation. Besides, the Mat@CS-Pro nanocapsules had remarkable pH-responsive properties. As the environmental pH became acidic, the nanocapsules swelled to about 475 nm and the released concentration could reach 28.5 ppm after immersion for 10 h but maintained a low releasing rate in pH 8 conditions.
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Affiliation(s)
- Xiangping Hao
- National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, China
- Belt and Road Initiative (BRI) Southeast Asia Network for Corrosion and Protection, Ministry of Education (MOE), Shunde Graduate School of University of Science and Technology Beijing, Foshan, China
| | - Weilu Yan
- National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, China
| | - Jingzhi Yang
- National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, China
| | - Yun Bai
- National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, China
| | - Hongchang Qian
- National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, China
- Belt and Road Initiative (BRI) Southeast Asia Network for Corrosion and Protection, Ministry of Education (MOE), Shunde Graduate School of University of Science and Technology Beijing, Foshan, China
| | - Yuntian Lou
- National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, China
- Belt and Road Initiative (BRI) Southeast Asia Network for Corrosion and Protection, Ministry of Education (MOE), Shunde Graduate School of University of Science and Technology Beijing, Foshan, China
| | - Pengfei Ju
- Shanghai Aerospace Equipment Manufacturer, Shanghai, China
- *Correspondence: Pengfei Ju
| | - Dawei Zhang
- National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, China
- Belt and Road Initiative (BRI) Southeast Asia Network for Corrosion and Protection, Ministry of Education (MOE), Shunde Graduate School of University of Science and Technology Beijing, Foshan, China
- Beijing Advanced Innovationation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing, China
- Dawei Zhang
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11
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OYAIDE M, ISHII C, FUJII A, AKITA T, MITA M, NAGANO M, HAMASE K. Enantioselective Determination of Hydroxy Amino Acids in Japanese Traditional Amber Rice Vinegars. CHROMATOGRAPHY 2022. [DOI: 10.15583/jpchrom.2022.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Mai OYAIDE
- Graduate School of Pharmaceutical Sciences, Kyushu University
| | - Chiharu ISHII
- Graduate School of Pharmaceutical Sciences, Kyushu University
| | | | - Takeyuki AKITA
- Graduate School of Pharmaceutical Sciences, Kyushu University
| | | | | | - Kenji HAMASE
- Graduate School of Pharmaceutical Sciences, Kyushu University
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12
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Chernykh AV, Chernykh AV, Radchenko DS, Chheda PR, Rusanov EB, Grygorenko OO, Spies MA, Volochnyuk DM, Komarov IV. A stereochemical journey around spirocyclic glutamic acid analogs. Org Biomol Chem 2022; 20:3183-3200. [PMID: 35348173 PMCID: PMC10170626 DOI: 10.1039/d2ob00146b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A practical divergent synthetic approach is reported for the library of regio- and stereoisomers of glutamic acid analogs built on the spiro[3.3]heptane scaffold. Formation of the spirocyclic scaffold was achieved starting from a common precursor - an O-silylated 2-(hydroxymethyl)cyclobutanone derivative. Its olefination required using the titanium-based Tebbe protocol since the standard Wittig reaction did not work with this particular substrate. The construction of the second cyclobutane ring of the spirocyclic system was achieved through either subsequent dichloroketene addition or Meinwald oxirane rearrangement as the key synthetic steps, depending on the substitution patterns in the target compounds (1,6- or 1,5-, respectively). Further modified Strecker reaction of the resulting racemic spirocyclic ketones with the Ellman's sulfinamide as a chiral auxiliary had low to moderate diastereoselectivity; nevertheless, all stereoisomers were isolated in pure form via chromatographic separation, and their absolute configuration was confirmed by X-ray crystallography. Members of the library were tested for the inhibitory activity against H. pylori glutamate racemase.
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Affiliation(s)
- Anton V Chernykh
- Enamine Ltd, Chervonotkatska Street 78, Kyiv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine.
| | | | - Dmytro S Radchenko
- Enamine Ltd, Chervonotkatska Street 78, Kyiv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine.
| | - Pratik Rajesh Chheda
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutics and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City 52246, Iowa, USA
| | - Eduard B Rusanov
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanska Street 5, Kyiv 02660, Ukraine
| | - Oleksandr O Grygorenko
- Enamine Ltd, Chervonotkatska Street 78, Kyiv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine.
| | - M Ashley Spies
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutics and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City 52246, Iowa, USA.,Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City 52246, Iowa, USA
| | - Dmitriy M Volochnyuk
- Enamine Ltd, Chervonotkatska Street 78, Kyiv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine. .,Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanska Street 5, Kyiv 02660, Ukraine
| | - Igor V Komarov
- Enamine Ltd, Chervonotkatska Street 78, Kyiv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine.
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13
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Abdulbagi M, Wang L, Siddig O, Di B, Li B. D-Amino Acids and D-Amino Acid-Containing Peptides: Potential Disease Biomarkers and Therapeutic Targets? Biomolecules 2021; 11:1716. [PMID: 34827714 PMCID: PMC8615943 DOI: 10.3390/biom11111716] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 12/17/2022] Open
Abstract
In nature, amino acids are found in two forms, L and D enantiomers, except for glycine which does not have a chiral center. The change of one form to the other will lead to a change in the primary structure of proteins and hence may affect the function and biological activity of proteins. Indeed, several D-amino acid-containing peptides (DAACPs) were isolated from patients with cataracts, Alzheimer's and other diseases. Additionally, significant levels of free D-amino acids were found in several diseases, reflecting the disease conditions. Studying the molecular mechanisms of the DAACPs formation and the alteration in D-amino acids metabolism will certainly assist in understanding these diseases and finding new biomarkers and drug targets. In this review, the presence of DAACPs and free D-amino acids and their links with disease development and progress are summarized. Similarly, we highlight some recent advances in analytical techniques that led to improvement in the discovery and analysis of DAACPs and D-amino acids.
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Affiliation(s)
- Mohamed Abdulbagi
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (M.A.); (L.W.); (O.S.)
| | - Liya Wang
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (M.A.); (L.W.); (O.S.)
| | - Orwa Siddig
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (M.A.); (L.W.); (O.S.)
| | - Bin Di
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (M.A.); (L.W.); (O.S.)
- Center Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing 210009, China
- MOE Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing 210009, China
| | - Bo Li
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (M.A.); (L.W.); (O.S.)
- Center Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing 210009, China
- MOE Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing 210009, China
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14
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d-Amino Acids and pLG72 in Alzheimer's Disease and Schizophrenia. Int J Mol Sci 2021; 22:ijms222010917. [PMID: 34681579 PMCID: PMC8535920 DOI: 10.3390/ijms222010917] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/01/2021] [Accepted: 10/06/2021] [Indexed: 01/02/2023] Open
Abstract
Numerous studies over the last several years have shown that d-amino acids, especially d-serine, have been related to brain and neurological disorders. Acknowledged neurological functions of d-amino acids include neurotransmission and learning and memory functions through modulating N-methyl-d-aspartate type glutamate receptors (NMDARs). Aberrant d-amino acids level and polymorphisms of genes related to d-amino acids metabolism are associated with neurodegenerative brain conditions. This review summarizes the roles of d-amino acids and pLG72, also known as d-amino acid oxidase activator, on two neurodegenerative disorders, schizophrenia and Alzheimer’s disease (AD). The scope includes the changes in d-amino acids levels, gene polymorphisms of G72 genomics, and the role of pLG72 on NMDARs and mitochondria in schizophrenia and AD. The clinical diagnostic value of d-amino acids and pLG72 and the therapeutic importance are also reviewed.
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15
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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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16
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Wang W, Wu H, Xiao Q, Zhou H, Li M, Xu Q, Wang Q, Yu F, He J. Crystal structure details of Vibrio fischeri DarR and mutant DarR-M202I from LTTR family reveals their activation mechanism. Int J Biol Macromol 2021; 183:2354-2363. [PMID: 34081954 DOI: 10.1016/j.ijbiomac.2021.05.186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/05/2021] [Accepted: 05/26/2021] [Indexed: 02/02/2023]
Abstract
DarR, a novel member of the LTTR family derived from Vibrio fischeri, activates transcription in response to d-Asp and regulates the overexpression of the racD genes encoding a putative aspartate racemase, RacD. Here, the crystal structure of full-length DarR and its mutant DarR-M202I were obtained by X-ray crystallography. According to the electron density map analysis of full-length DarR, the effector binding site of DarR is occupied by 2-Morpholinoethanesulfonic acid monohydrate (MES), which could interact with amino acids in the effector binding site and stabilize the effector binding site. Furthermore, we elaborated the structure of DarR-M202I, where methionine is replaced by isoleucine resulting in overexpression of the downstream operon. By comparing DarR-MES and DarR-M202I, we found similar behavior of DarR-MES in terms of the stability of the RD active pocket and the deflection angle of the DBD. The Isothermal titration calorimetry and Gel-filtration chromatography experiments showed that only when the target DNA sequence of a particular quasi-palindromic sequence exceeds 19 bp, DarR can effectively bind to racD promoter. This study will help enhance our understanding of the mechanism in the transcriptional regulation of LTTR family transcription factors.
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Affiliation(s)
- Weiwei Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hai Wu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingjie Xiao
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Huan Zhou
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China; Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Minjun Li
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China; Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Qin Xu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China; Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Qisheng Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China; Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China.
| | - Feng Yu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China; Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China.
| | - Jianhua He
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China; The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China.
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17
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Zhang L, Zeng F, McKay CP, Navarro-González R, Sun HJ. Optimizing Chiral Selectivity in Practical Life-Detection Instruments. ASTROBIOLOGY 2021; 21:505-510. [PMID: 33885325 DOI: 10.1089/ast.2020.2381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Preferential uptake of either levorotatory (L) or dextrorotatory (D) enantiomer of a chiral molecule is a potential planetary life-detection method. On Earth, bacteria, as a rule, metabolize D-sugars and L-amino acids. Here, we use growth experiments to identify exceptions to the rule and their potential impact on the method's reliability. Our experiments involve six strains of Bacillus and collective uptake of the sugars glucose and arabinose, and the amino acids alanine, glutamic acid, leucine, cysteine, and serine-all of which are highly soluble. We find that selective uptake is not evident unless (1) each sugar is tested individually and (2) multiple amino acids are tested together in a mixture. Combining sugars should be avoided because, as we show in Bacillus bacteria, the same organisms may catabolize one sugar, glucose, in D-form and another sugar, arabinose, in L-form. Single amino acids should be avoided because bacteria can access certain proteinogenically incompatible enantiomers using specific racemases. Specifically, bacteria contain an alanine acid racemase and can catabolize D-alanine if no other D-amino acids are present. The proposed improvements would reliably separate nonselective chemical reactions from biological reactions and, if life is indicated, inform whether the selective patterns for amino acids and sugars are the same as on Earth.
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Affiliation(s)
- Ling Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Desert Plant Roots Ecology and Vegetation Restoration Laboratory, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, Xinjiang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fanjiang Zeng
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Desert Plant Roots Ecology and Vegetation Restoration Laboratory, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, Xinjiang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Christopher P McKay
- Space Science Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Rafael Navarro-González
- Laboratorio de Química de Plasmas y Estudios Planetarios, Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Henry J Sun
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Las Vegas, Nevada, USA
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18
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TK1211 Encodes an Amino Acid Racemase towards Leucine and Methionine in the Hyperthermophilic Archaeon Thermococcus kodakarensis. J Bacteriol 2021; 203:JB.00617-20. [PMID: 33468590 DOI: 10.1128/jb.00617-20] [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: 11/05/2020] [Accepted: 01/07/2021] [Indexed: 12/22/2022] Open
Abstract
Members of Thermococcales harbor a number of genes encoding putative aminotransferase class III enzymes. Here, we characterized the TK1211 protein from the hyperthermophilic archaeon Thermococcus kodakarensis The TK1211 gene was expressed in T. kodakarensis under the control of the strong, constitutive promoter of the cell surface glycoprotein gene TK0895 (P csg ). The purified protein did not display aminotransferase activity but exhibited racemase activity. An examination of most amino acids indicated that the enzyme was a racemase with relatively high activity toward Leu and Met. Kinetic analysis indicated that Leu was the most preferred substrate. A TK1211 gene disruption strain (ΔTK1211) was constructed and grown on minimal medium supplemented with l- or d-Leu or l- or d-Met. The wild-type T. kodakarensis is not able to synthesize Leu and displays Leu auxotrophy, providing a direct means to examine the Leu racemase activity of the TK1211 protein in vivo When we replaced l-Leu with d-Leu in the medium, the host strain with an intact TK1211 gene displayed an extended lag phase but displayed cell yield similar to that observed in medium with l-Leu. In contrast, the ΔTK1211 strain displayed growth in medium with l-Leu but could not grow with d-Leu. The results indicate that TK1211 encodes a Leu racemase that is active in T. kodakarensis cells and that no other protein exhibits this activity, at least to an extent that can support growth. Growth experiments with l- or d-Met also confirmed the Met racemase activity of the TK1211 protein in T. kodakarensis IMPORTANCE Phylogenetic analysis of aminotransferase class III proteins from all domains of life reveals numerous groups of protein sequences. One of these groups includes a large number of sequences from Thermococcales species and can be divided into four subgroups. Representatives of three of these subgroups have been characterized in detail. This study reveals that a representative from the remaining uncharacterized subgroup is an amino acid racemase with preference toward Leu and Met. Taken together with results of previous studies on enzymes from Pyrococcus horikoshii and Thermococcus kodakarensis, members of the four subgroups now can be presumed to function as a broad-substrate-specificity amino acid racemase (subgroup 1), alanine/serine racemase (subgroup 2), ornithine ω-aminotransferase (subgroup 3), or Leu/Met racemase (subgroup 4).
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19
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Renick PJ, Mulgaonkar A, Co CM, Wu CY, Zhou N, Velazquez A, Pennington J, Sherwood A, Dong H, Castellino L, Öz OK, Tang L, Sun X. Imaging of Actively Proliferating Bacterial Infections by Targeting the Bacterial Metabolic Footprint with d-[5- 11C]-Glutamine. ACS Infect Dis 2021; 7:347-361. [PMID: 33476123 DOI: 10.1021/acsinfecdis.0c00617] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Since most d-amino acids (DAAs) are utilized by bacterial cells but not by mammalian eukaryotic hosts, recently DAA-based molecular imaging strategies have been extensively explored for noninvasively differentiating bacterial infections from the host's inflammatory responses. Given glutamine's pivotal role in bacterial survival, cell growth, biofilm formation, and even virulence, here we report a new positron emission tomography (PET) imaging approach using d-5-[11C]glutamine (d-[5-11C]-Gln) for potential clinical assessment of bacterial infection through a comparative study with its l-isomer counterpart, l-[5-11C]-Gln. In both control and infected mice, l-[5-11C]-Gln had substantially higher uptake levels than d-[5-11C]-Gln in most organs except the kidneys, showing the expected higher use of l-[5-11C]-Gln by mammalian tissues and more efficient renal excretion of d-[5-11C]-Gln. Importantly, our work demonstrates that PET imaging with d-[5-11C]-Gln is capable of detecting infections induced by both Escherichia coli (E. coli) and methicillin-resistant Staphylococcus aureus (MRSA) in a dual-infection murine myositis model with significantly higher infection-to-background contrast than with l-[5-11C]-Gln (in E. coli, 1.64; in MRSA, 2.62, p = 0.0004). This can be attributed to the fact that d-[5-11C]-Gln is utilized by bacteria while being more efficiently cleared from the host tissues. We confirmed the bacterial infection imaging specificity of d-[5-11C]-Gln by comparing its uptake in active bacterial infections versus sterile inflammation and with 2-deoxy-2-[18F]fluoroglucose ([18F]FDG). These results together demonstrate the translational potential of PET imaging with d-[5-11C]-Gln for the noninvasive detection of bacterial infectious diseases in humans.
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20
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Identification of an l-serine/l-threonine dehydratase with glutamate racemase activity in mammals. Biochem J 2020; 477:4221-4241. [DOI: 10.1042/bcj20200721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/12/2020] [Accepted: 10/20/2020] [Indexed: 02/02/2023]
Abstract
Recent investigations have shown that multiple d-amino acids are present in mammals and these compounds have distinctive physiological functions. Free d-glutamate is present in various mammalian tissues and cells and in particular, it is presumably correlated with cardiac function, and much interest is growing in its unique metabolic pathways. Recently, we first identified d-glutamate cyclase as its degradative enzyme in mammals, whereas its biosynthetic pathway in mammals is unclear. Glutamate racemase is a most probable candidate, which catalyzes interconversion between d-glutamate and l-glutamate. Here, we identified the cDNA encoding l-serine dehydratase-like (SDHL) as the first mammalian clone with glutamate racemase activity. This rat SDHL had been deposited in mammalian databases as a protein of unknown function and its amino acid sequence shares ∼60% identity with that of l-serine dehydratase. Rat SDHL was expressed in Escherichia coli, and the enzymatic properties of the recombinant were characterized. The results indicated that rat SDHL is a multifunctional enzyme with glutamate racemase activity in addition to l-serine/l-threonine dehydratase activity. This clone is hence abbreviated as STDHgr. Further experiments using cultured mammalian cells confirmed that d-glutamate was synthesized and l-serine and l-threonine were decomposed. It was also found that SDHL (STDHgr) contributes to the homeostasis of several other amino acids.
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21
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Wang R, Zhang Z, Sun J, Jiao N. Differences in bioavailability of canonical and non-canonical D-amino acids for marine microbes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 733:139216. [PMID: 32454292 DOI: 10.1016/j.scitotenv.2020.139216] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/22/2020] [Accepted: 05/03/2020] [Indexed: 06/11/2023]
Abstract
Dissolved organic matter (DOM) accounts for >95% of total marine organic matter, and >95% of marine DOM is refractory to biodegradation. The recalcitrancy of DOM determines its residence time and thus is of great concern regarding to carbon sequestration in the ocean. However, the recalcitrancy of DOM not only varies among different compounds but also within different conformations of a same molecule such as L-amino acids (L-AAs) and D-amino acids (D-AAs). While the former is labile, the latter is refractory and used as a proxy for estimation of bacterial refractory DOM in the ocean. However, some D-AAs are also reported to be bioavailable. To clarify the controversy, we examined the bioavailability of two types of D-AAs: canonical D-AAs, which mainly present as bacterial cell wall components, and non-canonical D-AAs (NCDAAs), which are secreted by various bacteria as signaling molecules in bacterial physiology. Bioassay experiments were conducted with nine marine bacterial strains and a natural microbial community. D-AAs were poorly utilized by the strains as sole carbon or nitrogen sources compared with L-AAs, in addition, NCDAAs were barely used compared with canonical D-AAs. In comparison, the microbial community consumed all three canonical D-AAs (D-alanine, D-aspartic acid and D-glutamic acid) as efficiently as their corresponding L-AAs when supplied separately; however, L-AAs were preferentially used over D-AAs when both forms were provided simultaneously. Remarkably, two NCDAAs, D-methionine and D-leucine, were poorly utilized regardless of the presence of the L-enantiomers. It was found for the first time that NCDAAs are relatively more refractory than canonical D-AAs to microbial utilization. This novel recognition of difference in recalcitrancy between NCDAAs and canonical D-AAs lays the foundation for a better understanding of carbon cycling and more accurate estimation of carbon storage in the ocean.
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Affiliation(s)
- Rui Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China; Institute of Marine Microbes and Ecospheres, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, People's Republic of China
| | - Zilian Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China; Institute of Marine Microbes and Ecospheres, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, People's Republic of China.
| | - Jia Sun
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China; Institute of Marine Microbes and Ecospheres, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, People's Republic of China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China; Institute of Marine Microbes and Ecospheres, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, People's Republic of China.
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22
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Bearne SL. Through the Looking Glass: Chiral Recognition of Substrates and Products at the Active Sites of Racemases and Epimerases. Chemistry 2020; 26:10367-10390. [DOI: 10.1002/chem.201905826] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/09/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Stephen L. Bearne
- Department of Biochemistry & Molecular BiologyDepartment of ChemistryDalhousie University Halifax, Nova Scotia B3H 4R2 Canada
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23
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Parker MFL, Flavell RR, Luu JM, Rosenberg OS, Ohliger MA, Wilson DM. Small Molecule Sensors Targeting the Bacterial Cell Wall. ACS Infect Dis 2020; 6:1587-1598. [PMID: 32433879 DOI: 10.1021/acsinfecdis.9b00515] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This review highlights recent efforts to detect bacteria using engineered small molecules that are processed and incorporated similarly to their natural counterparts. There are both scientific and clinical justifications for these endeavors. The use of detectable, cell-wall targeted chemical probes has elucidated microbial behavior, with several fluorescent labeling methods in widespread laboratory use. Furthermore, many existing efforts including ours, focus on developing new imaging tools to study infection in clinical practice. The bacterial cell wall, a remarkably rich and complex structure, is an outstanding target for bacteria-specific detection. Several cell wall components are found in bacteria but not mammals, especially peptidoglycan, lipopolysaccharide, and teichoic acids. As this review highlights, the development of laboratory tools for fluorescence microscopy has vastly outstripped related positron emission tomography (PET) or single photon emission computed tomography (SPECT) radiotracer development. However, there is great synergy between these chemical strategies, which both employ mimicry of endogenous substrates to incorporate detectable structures. As the field of bacteria-specific imaging grows, it will be important to understand the mechanisms involved in microbial incorporation of radionuclides. Additionally, we will highlight the clinical challenges motivating this imaging effort.
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Affiliation(s)
- Matthew F. L. Parker
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California 94158, United States
| | - Robert R. Flavell
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California 94158, United States
| | - Justin M. Luu
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California 94158, United States
| | - Oren S. Rosenberg
- Department of Medicine, University of California, San Francisco, San Francisco, California 94158, United States
| | - Michael A. Ohliger
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California 94158, United States
- Department of Radiology, Zuckerberg San Francisco General Hospital, San Francisco, California 94110, United States
| | - David M. Wilson
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California 94158, United States
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Glavin DP, Burton AS, Elsila JE, Aponte JC, Dworkin JP. The Search for Chiral Asymmetry as a Potential Biosignature in our Solar System. Chem Rev 2019; 120:4660-4689. [DOI: 10.1021/acs.chemrev.9b00474] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Daniel P. Glavin
- NASA Goddard Space Flight Center, Greenbelt, Maryland 20771, United States
| | - Aaron S. Burton
- NASA Johnson Space Center, Houston, Texas 77058, United States
| | - Jamie E. Elsila
- NASA Goddard Space Flight Center, Greenbelt, Maryland 20771, United States
| | - José C. Aponte
- NASA Goddard Space Flight Center, Greenbelt, Maryland 20771, United States
- Catholic University of America, Washington, D.C. 20064, United States
| | - Jason P. Dworkin
- NASA Goddard Space Flight Center, Greenbelt, Maryland 20771, United States
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25
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Hill PW, Broughton R, Bougoure J, Havelange W, Newsham KK, Grant H, Murphy DV, Clode P, Ramayah S, Marsden KA, Quilliam RS, Roberts P, Brown C, Read DJ, Deluca TH, Bardgett RD, Hopkins DW, Jones DL. Angiosperm symbioses with non-mycorrhizal fungal partners enhance N acquisition from ancient organic matter in a warming maritime Antarctic. Ecol Lett 2019; 22:2111-2119. [PMID: 31621153 PMCID: PMC6899649 DOI: 10.1111/ele.13399] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/26/2019] [Accepted: 09/10/2019] [Indexed: 01/01/2023]
Abstract
In contrast to the situation in plants inhabiting most of the world’s ecosystems, mycorrhizal fungi are usually absent from roots of the only two native vascular plant species of maritime Antarctica, Deschampsia antarctica and Colobanthus quitensis. Instead, a range of ascomycete fungi, termed dark septate endophytes (DSEs), frequently colonise the roots of these plant species. We demonstrate that colonisation of Antarctic vascular plants by DSEs facilitates not only the acquisition of organic nitrogen as early protein breakdown products, but also as non‐proteinaceous d‐amino acids and their short peptides, accumulated in slowly‐decomposing organic matter, such as moss peat. Our findings suggest that, in a warming maritime Antarctic, this symbiosis has a key role in accelerating the replacement of formerly dominant moss communities by vascular plants, and in increasing the rate at which ancient carbon stores laid down as moss peat over centuries or millennia are returned to the atmosphere as CO2.
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Affiliation(s)
- Paul W Hill
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Richard Broughton
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 OET, UK.,Institute of Aquaculture, University of Stirling, Stirling, UK
| | - Jeremy Bougoure
- Faculty of Science, SoilsWest, UWA School of Agriculture and Environment, University of Western Australia, Crawley, WA, 6009, Australia.,Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Crawley, WA, 6009, Australia
| | | | - Kevin K Newsham
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - Helen Grant
- Life Sciences Mass Spectrometry Facility, Lancaster Environment Centre, Lancaster, LA1 4AP, UK
| | - Daniel V Murphy
- Faculty of Science, SoilsWest, UWA School of Agriculture and Environment, University of Western Australia, Crawley, WA, 6009, Australia
| | - Peta Clode
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Crawley, WA, 6009, Australia.,UWA School of Biological Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | - Soshila Ramayah
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Karina A Marsden
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| | - Richard S Quilliam
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK.,Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Paula Roberts
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Caley Brown
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - David J Read
- Animal and Plant Sciences, University of Sheffield, Western bank, Sheffield, S10 2TN, UK
| | - Thomas H Deluca
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK.,WA Franke College of Forestry and Conservation, University of Montana, Missoula, MT, 59812, USA
| | - Richard D Bardgett
- School of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PL, UK
| | - David W Hopkins
- SRUC - Scotland's Rural College, West Mains Road, Edinburgh, EH9 3JG, UK
| | - Davey L Jones
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK.,Faculty of Science, SoilsWest, UWA School of Agriculture and Environment, University of Western Australia, Crawley, WA, 6009, Australia
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26
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Abstract
Natural and nonnatural amino acids represent important building blocks for the development of peptidomimetic scaffolds, especially for targeting proteolytic enzymes and for addressing protein–protein interactions. Among all the different amino acids derivatives, proline is particularly relevant in chemical biology and medicinal chemistry due to its secondary structure’s inducing and stabilizing properties. Also, the pyrrolidine ring is a conformationally constrained template that can direct appendages into specific clefts of the enzyme binding site. Thus, many papers have appeared in the literature focusing on the use of proline and its derivatives as scaffolds for medicinal chemistry applications. In this review paper, an insight into the different biological outcomes of d-proline and l-proline in enzyme inhibitors is presented, especially when associated with matrix metalloprotease and metallo-β-lactamase enzymes.
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27
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Ushimaru R, Liu HW. Biosynthetic Origin of the Atypical Stereochemistry in the Thioheptose Core of Albomycin Nucleoside Antibiotics. J Am Chem Soc 2019; 141:2211-2214. [PMID: 30673214 DOI: 10.1021/jacs.8b12565] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Albomycins are peptidyl thionucleoside natural products that display antimicrobial activity against clinically important pathogens. Their structures are characterized by a thioheptose with atypical stereochemistry including a d-xylofuranose ring modified with a d-amino acid moiety. Herein it is demonstrated that AbmH is a pyridoxal 5'-phosphate (PLP)-dependent transaldolase that catalyzes a threo-selective aldol-type reaction to generate the thioheptose core with a d-ribofuranose ring and an l-amino acid moiety. The conversion of l-to d-amino acid configuration is catalyzed by the PLP-dependent epimerase AbmD. The d- ribo to d- xylo conversion of the thiofuranose ring appears according to gene deletion experiments to be mediated by AbmJ, which is annotated as a radical S-adenosyl-l-methionine (SAM) enzyme. These studies establish several key steps in the assembly of the thioheptose core during the biosynthesis of albomycins.
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Affiliation(s)
- Richiro Ushimaru
- Department of Chemistry, and Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Hung-Wen Liu
- Department of Chemistry, and Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy , University of Texas at Austin , Austin , Texas 78712 , United States
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28
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Raboni S, Marchetti M, Faggiano S, Campanini B, Bruno S, Marchesani F, Margiotta M, Mozzarelli A. The Energy Landscape of Human Serine Racemase. Front Mol Biosci 2019; 5:112. [PMID: 30687716 PMCID: PMC6333871 DOI: 10.3389/fmolb.2018.00112] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/26/2018] [Indexed: 12/17/2022] Open
Abstract
Human serine racemase is a pyridoxal 5′-phosphate (PLP)-dependent dimeric enzyme that catalyzes the reversible racemization of L-serine and D-serine and their dehydration to pyruvate and ammonia. As D-serine is the co-agonist of the N-methyl-D-aspartate receptors for glutamate, the most abundant excitatory neurotransmitter in the brain, the structure, dynamics, function, regulation and cellular localization of serine racemase have been investigated in detail. Serine racemase belongs to the fold-type II of the PLP-dependent enzyme family and structural models from several orthologs are available. The comparison of structures of serine racemase co-crystallized with or without ligands indicates the presence of at least one open and one closed conformation, suggesting that conformational flexibility plays a relevant role in enzyme regulation. ATP, Mg2+, Ca2+, anions, NADH and protein interactors, as well as the post-translational modifications nitrosylation and phosphorylation, finely tune the racemase and dehydratase activities and their relative reaction rates. Further information on serine racemase structure and dynamics resulted from the search for inhibitors with potential therapeutic applications. The cumulative knowledge on human serine racemase allowed obtaining insights into its conformational landscape and into the mechanisms of cross-talk between the effector binding sites and the active site.
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Affiliation(s)
- Samanta Raboni
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | - Serena Faggiano
- Department of Food and Drug, University of Parma, Parma, Italy.,Institute of Biophysics, National Research Council, Pisa, Italy
| | | | - Stefano Bruno
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | | | - Andrea Mozzarelli
- Department of Food and Drug, University of Parma, Parma, Italy.,Institute of Biophysics, National Research Council, Pisa, Italy.,National Institute of Biostructures and Biosystems, Rome, Italy
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29
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Jones RM, Popham DL, Schmidt AL, Neidle EL, Stabb EV. Vibrio fischeri DarR Directs Responses to d-Aspartate and Represents a Group of Similar LysR-Type Transcriptional Regulators. J Bacteriol 2018; 200:e00773-17. [PMID: 29437849 PMCID: PMC6040199 DOI: 10.1128/jb.00773-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 01/24/2018] [Indexed: 01/11/2023] Open
Abstract
Mounting evidence suggests that d-amino acids play previously underappreciated roles in diverse organisms. In bacteria, even d-amino acids that are absent from canonical peptidoglycan (PG) may act as growth substrates, as signals, or in other functions. Given these proposed roles and the ubiquity of d-amino acids, the paucity of known d-amino-acid-responsive transcriptional control mechanisms in bacteria suggests that such regulation awaits discovery. We found that DarR, a LysR-type transcriptional regulator (LTTR), activates transcription in response to d-Asp. The d-Glu auxotrophy of a Vibrio fischerimurI::Tn mutant was suppressed, with the wild-type PG structure maintained, by a point mutation in darR This darR mutation resulted in the overexpression of an adjacent operon encoding a putative aspartate racemase, RacD, which compensated for the loss of the glutamate racemase encoded by murI Using transcriptional reporters, we found that wild-type DarR activated racD transcription in response to exogenous d-Asp but not upon the addition of l-Asp, l-Glu, or d-Glu. A DNA sequence typical of LTTR-binding sites was identified between darR and the divergently oriented racD operon, and scrambling this sequence eliminated activation of the reporter in response to d-Asp. In several proteobacteria, genes encoding LTTRs similar to DarR are linked to genes with predicted roles in d- and/or l-Asp metabolism. To test the functional similarities in another bacterium, darR and racD mutants were also generated in Acinetobacter baylyi In V. fischeri and A. baylyi, growth on d-Asp required the presence of both darR and racD Our results suggest that multiple bacteria have the ability to sense and respond to d-Asp.IMPORTANCE d-Amino acids are prevalent in the environment and are generated by organisms from all domains of life. Although some biological roles for d-amino acids are understood, in other cases, their functions remain uncertain. Given the ubiquity of d-amino acids, it seems likely that bacteria will initiate transcriptional responses to them. Elucidating d-amino acid-responsive regulators along with the genes they control will help uncover bacterial uses of d-amino acids. Here, we report the discovery of DarR, a novel LTTR in V. fischeri that mediates a transcriptional response to environmental d-Asp and underpins the catabolism of d-Asp. DarR represents the founding member of a group of bacterial homologs that we hypothesize control aspects of aspartate metabolism in response to d-Asp and/or to d-Asp-containing peptides.
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Affiliation(s)
- Richard M Jones
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - David L Popham
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Alicia L Schmidt
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Ellen L Neidle
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Eric V Stabb
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
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30
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Kawakami R, Ohshida T, Sakuraba H, Ohshima T. A Novel PLP-Dependent Alanine/Serine Racemase From the Hyperthermophilic Archaeon Pyrococcus horikoshii OT-3. Front Microbiol 2018; 9:1481. [PMID: 30038603 PMCID: PMC6047364 DOI: 10.3389/fmicb.2018.01481] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 06/13/2018] [Indexed: 01/05/2023] Open
Abstract
We recently identified and characterized a novel broad substrate specificity amino acid racemase (BAR) from the hyperthermophilic archaeon Pyrococcus horikoshii OT-3. Three genes, PH0782, PH1423, and PH1501, encoding homologs exhibiting about 45% sequence identity with BAR were present in the P. horikoshii genome. In this study, we detected pyridoxal 5′-phosphate (PLP)-dependent amino acid racemase activity in the protein encoded by PH0782. The enzyme showed activity toward Ala, Ser, Thr, and Val, but the catalytic efficiency with Thr or Val was much lower than with Ala or Ser. The enzyme was therefore designated Ala/Ser racemase (ASR). Like BAR, ASR was highly stable at high temperatures and over a wide range of pHs, though its hexameric structure differed from the dimeric structure of BAR. No activity was detected in K291A or D234A ASR mutants. This suggests that, as in Ile 2-epimerase (ILEP) from Lactobacillus buchneri JCM1115, these residues are involved in Schiff base formation and substrate interaction, respectively. Unlike BAR, enhanced ASR activity was not detected in P. horikoshii cells cultivated in the presence of D-Ala or D-Ser. This is the first description of a PLP-dependent fold type I ASR in 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
| | - Tatsuya Ohshida
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Kagawa, Japan
| | - Haruhiko Sakuraba
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Kagawa, Japan
| | - Toshihisa Ohshima
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, Osaka, Japan
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31
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SEREEKITTIKUL N, KOGA R, AKITA T, FURUSHO A, REISCHL R, MITA M, FUJII A, HASHIGUCHI K, NAGANO M, LINDNER W, HAMASE K. Multi-Dimensional HPLC Analysis of Serine Containing Chiral Dipeptides in Japanese Traditional Amber Rice Vinegar. CHROMATOGRAPHY 2018. [DOI: 10.15583/jpchrom.2018.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Nutchaya SEREEKITTIKUL
- Graduate School of Pharmaceutical Sciences, Kyushu University
- Faculty of Pharmacy, Mahidol University
| | - Reiko KOGA
- Graduate School of Pharmaceutical Sciences, Kyushu University
- Faculty of Pharmaceutical Sciences, Fukuoka University
| | - Takeyuki AKITA
- Graduate School of Pharmaceutical Sciences, Kyushu University
| | - Aogu FURUSHO
- Graduate School of Pharmaceutical Sciences, Kyushu University
| | | | | | | | | | | | | | - Kenji HAMASE
- Graduate School of Pharmaceutical Sciences, Kyushu University
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32
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Orrego AH, López-Gallego F, Espaillat A, Cava F, Guisan JM, Rocha-Martin J. One-step Synthesis of α-Keto Acids from Racemic Amino Acids by A Versatile Immobilized Multienzyme Cell-free System. ChemCatChem 2018. [DOI: 10.1002/cctc.201800359] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Alejandro H. Orrego
- Department of Biocatalysis; Institute of Catalysis and Petrochemistry (ICP) CSIC; Campus UAM. Cantoblanco. 28049 Madrid Spain
| | - Fernando López-Gallego
- Departamento de Química Orgánica; Instituto de Síntesis Química y Catálisis Homogénea (ISQCH); CSIC-Universidad de Zaragoza; 50009 Zaragoza Spain
- ARAID Foundation; Zaragoza Spain
| | - Akbar Espaillat
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden; Umea Centre for Microbial Research; Umea University; Umea Sweden
| | - Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden; Umea Centre for Microbial Research; Umea University; Umea Sweden
| | - José M. Guisan
- Department of Biocatalysis; Institute of Catalysis and Petrochemistry (ICP) CSIC; Campus UAM. Cantoblanco. 28049 Madrid Spain
| | - Javier Rocha-Martin
- Department of Biocatalysis; Institute of Catalysis and Petrochemistry (ICP) CSIC; Campus UAM. Cantoblanco. 28049 Madrid Spain
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33
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Expression of Pyridoxal 5'-Phosphate-Independent Racemases Can Reduce 2-Aminoacrylate Stress in Salmonella enterica. J Bacteriol 2018; 200:JB.00751-17. [PMID: 29440254 DOI: 10.1128/jb.00751-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 02/09/2018] [Indexed: 11/20/2022] Open
Abstract
The RidA protein (PF01042) from Salmonella enterica is a deaminase that quenches 2-aminoacrylate (2AA) and other reactive metabolites. In the absence of RidA, 2AA accumulates, damages cellular enzymes, and compromises the metabolic network. In vitro, RidA homologs from all domains of life deaminate 2AA, and RidA proteins from plants, bacteria, yeast, and humans complement the mutant phenotype of a ridA mutant strain of S. enterica In the present study, a methanogenic archaeon, Methanococcus maripaludis S2, was used to probe alternative mechanisms to restore metabolic balance. M. maripaludis MMP0739, which is annotated as an aspartate/glutamate racemase, complemented a ridA mutant strain and reduced the intracellular 2AA burden. The aspartate/glutamate racemase YgeA from Escherichia coli or S. enterica, when provided in trans, similarly restored wild-type growth to a ridA mutant. These results uncovered a new mechanism to ameliorate metabolic stress, and they suggest that direct quenching by RidA is not the only strategy to quench 2AA.IMPORTANCE 2-Aminoacrylate is an endogenously generated reactive metabolite that can damage cellular enzymes if not directly quenched by the conserved deaminase RidA. This study used an archaeon to identify a RidA-independent mechanism to prevent metabolic stress caused by 2AA. The data suggest that a gene product annotated as an aspartate/glutamate racemase (MMP0739) produces a metabolite that can quench 2AA, expanding our understanding of strategies available to quench reactive metabolites.
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34
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Variations of l- and d-amino acid levels in the brain of wild-type and mutant mice lacking d-amino acid oxidase activity. Anal Bioanal Chem 2018. [DOI: 10.1007/s00216-018-0979-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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35
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Triple serine loop region regulates the aspartate racemase activity of the serine/aspartate racemase family. Amino Acids 2017; 49:1743-1754. [PMID: 28744579 DOI: 10.1007/s00726-017-2472-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/20/2017] [Indexed: 02/02/2023]
Abstract
Recently, we cloned and characterized eleven serine and aspartate racemases (SerR and AspR, respectively) from animals. These SerRs and AspRs are not separated by their racemase functions and form a serine/aspartate racemase family cluster based on phylogenetic analysis. Moreover, we have proposed that the AspR-specific triple serine loop region at amino acid positions 150-152 may be responsible for the large AspR activity. In the present study, to test this hypothesis, we prepared and characterized fourteen mutants in this region of animal SerRs and AspRs. The large AspR activity in Acropora and Crassostrea AspR was reduced to <0.04% of wild-type after substitution of the triple serine loop region. Conversely, introducing the triple serine loop region into Acropora, Crassostrea, and Penaeus SerR drastically increased the AspR activity. Those mutants showed similar or higher substrate affinity for aspartate than serine and showed 11-683-fold higher k cat and 28-351-fold higher k cat/K m values for aspartate than serine racemization. Furthermore, we introduced serine residues in all combinations at position 150-152 in mouse SerR. These mutants revealed that a change in the enzyme function from SerR to AspR can be caused by introduction of Ser151 and Ser152, and addition of the third serine residue at position 150 further enhances the enzyme specificity for aspartate due to a decrease in the serine racemase and serine dehydratase activity. Here, we provide convincing evidence that the AspR gene has evolved from the SerR gene by acquisition of the triple serine loop region.
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36
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Abstract
More than half a century ago researchers thought that D-amino acids had a minor function compared to L-enantiomers in biological processes. Many evidences have shown that D-amino acids are present in high concentration in microorganisms, plants, mammals and humans and fulfil specific biological functions. In the brain of mammals, D-serine (D-Ser) acts as a co-agonist of the N-methyl-D-aspartate (NMDA)-type glutamate receptors, responsible for learning, memory and behaviour. D-Ser metabolism is relevant for disorders associated with an altered function of the NMDA receptor, such as schizophrenia, ischemia, epilepsy and neurodegenerative disorders. On the other hand, D-aspartate (D-Asp) is one of the major regulators of adult neurogenesis and plays an important role in the development of endocrine function. D-Asp is present in the neuroendocrine and endocrine tissues and testes, and regulates the synthesis and secretion of hormones and spermatogenesis. Also food proteins contain D-amino acids that are naturally originated or processing-induced under conditions such as high temperatures, acid and alkali treatments and fermentation processes. The presence of D-amino acids in dairy products denotes thermal and alkaline treatments and microbial contamination. Two enzymes are involved in the metabolism of D-amino acids: amino acid racemase in the synthesis and D-amino acid oxidase in the degradation.
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37
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Ouedraogo D, Ball J, Iyer A, Reis RAG, Vodovoz M, Gadda G. Amine oxidation by d-arginine dehydrogenase in Pseudomonas aeruginosa. Arch Biochem Biophys 2017. [PMID: 28625766 DOI: 10.1016/j.abb.2017.06.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
d-Arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) is a flavin-dependent oxidoreductase, which is part of a novel two-enzyme racemization system that functions to convert d-arginine to l-arginine. PaDADH contains a noncovalently linked FAD that shows the highest activity with d-arginine. The enzyme exhibits broad substrate specificity towards d-amino acids, particularly with cationic and hydrophobic d-amino acids. Biochemical studies have established the structure and the mechanistic properties of the enzyme. The enzyme is a true dehydrogenase because it displays no reactivity towards molecular oxygen. As established through solvent and multiple kinetic isotope studies, PaDADH catalyzes an asynchronous CH and NH bond cleavage via a hydride transfer mechanism. Steady-state kinetic studies with d-arginine and d-histidine are consistent with the enzyme following a ping-pong bi-bi mechanism. As shown by a combination of crystallography, kinetic and computational data, the shape and flexibility of loop L1 in the active site of PaDADH are important for substrate capture and broad substrate specificity.
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Affiliation(s)
- Daniel Ouedraogo
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States
| | - Jacob Ball
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States
| | - Archana Iyer
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States
| | - Renata A G Reis
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States
| | - Maria Vodovoz
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States; Department of Biology, Georgia State University, Atlanta, GA 30302, United States; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302, United States; Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30302, United States.
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38
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Awad R, Gans P, Reiser JB. Structural insights into the substrate recognition and reaction specificity of the PLP-dependent fold-type I isoleucine 2-epimerase from Lactobacillus buchneri. Biochimie 2017; 137:165-173. [DOI: 10.1016/j.biochi.2017.03.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 02/02/2017] [Accepted: 03/21/2017] [Indexed: 02/02/2023]
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39
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The identification of ᴅ-tryptophan as a bioactive substance for postembryonic ovarian development in the planarian Dugesia ryukyuensis. Sci Rep 2017; 7:45175. [PMID: 28338057 PMCID: PMC5364533 DOI: 10.1038/srep45175] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 02/20/2017] [Indexed: 12/24/2022] Open
Abstract
Many metazoans start germ cell development during embryogenesis, while some metazoans possessing pluripotent stem cells undergo postembryonic germ cell development. The latter reproduce asexually but develop germ cells from pluripotent stem cells or dormant primordial germ cells when they reproduce sexually. Sexual induction of the planarian Dugesia ryukyuensis is an important model for postembryonic germ cell development. In this experimental system, hermaphroditic reproductive organs are differentiated in presumptive gonadal regions by the administration of a crude extract from sexual planarians to asexual ones. However, the substances involved in the first event during postembryonic germ cell development, i.e., ovarian development, remain unknown. Here, we aimed to identify a bioactive compound associated with postembryonic ovarian development. Bioassay-guided fractionation identified ʟ-tryptophan (Trp) on the basis of electrospray ionization–mass spectrometry, circular dichroism, and nuclear magnetic resonance spectroscopy. Originally masked by a large amount of ʟ-Trp, ᴅ-Trp was detected by reverse-phase high-performance liquid chromatography. The ovary-inducing activity of ᴅ-Trp was 500 times more potent than that of ʟ-Trp. This is the first report describing a role for an intrinsic ᴅ-amino acid in postembryonic germ cell development. Our findings provide a novel insight into the mechanisms of germ cell development regulated by low-molecular weight bioactive compounds.
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40
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Naranjo-Ortíz MA, Brock M, Brunke S, Hube B, Marcet-Houben M, Gabaldón T. Widespread Inter- and Intra-Domain Horizontal Gene Transfer of d-Amino Acid Metabolism Enzymes in Eukaryotes. Front Microbiol 2016; 7:2001. [PMID: 28066338 PMCID: PMC5169069 DOI: 10.3389/fmicb.2016.02001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/29/2016] [Indexed: 01/22/2023] Open
Abstract
Analysis of the growing number of available fully-sequenced genomes has shown that Horizontal Gene Transfer (HGT) in eukaryotes is more common than previously thought. It has been proposed that genes with certain functions may be more prone to HGT than others, but we still have a very poor understanding of the selective forces driving eukaryotic HGT. Recent work uncovered that d-amino acid racemases have been commonly transferred from bacteria to fungi, but their role in the receiving organisms is currently unknown. Here, we set out to assess whether d-amino acid racemases are commonly transferred to and between eukaryotic groups. For this we performed a global survey that used a novel automated phylogeny-based HGT-detection algorithm (Abaccus). Our results revealed that at least 7.0% of the total eukaryotic racemase repertoire is the result of inter- or intra-domain HGT. These transfers are significantly enriched in plant-associated fungi. For these, we hypothesize a possible role for the acquired racemases allowing to exploit minoritary nitrogen sources in plant biomass, a nitrogen-poor environment. Finally, we performed experiments on a transferred aspartate-glutamate racemase in the fungal human pathogen Candida glabrata, which however revealed no obvious biological role.
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Affiliation(s)
- Miguel A Naranjo-Ortíz
- Centre for Genomic Regulation, The Barcelona Institute of Science and TechnologyBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain
| | - Matthias Brock
- Fungal Genetics and Biology Group, School of Life Sciences, University of Nottingham Nottingham, UK
| | - Sascha Brunke
- Department of Microbial Pathogenicity Mechanisms, Hans Knoell Institute Jena Jena, Germany
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Hans Knoell Institute JenaJena, Germany; Friedrich Schiller UniversityJena, Germany; Center for Sepsis Control and Care, University HospitalJena, Germany
| | - Marina Marcet-Houben
- Centre for Genomic Regulation, The Barcelona Institute of Science and TechnologyBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation, The Barcelona Institute of Science and TechnologyBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA)Barcelona, Spain
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41
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Efficient Production of Enantiopure d-Lysine from l-Lysine by a Two-Enzyme Cascade System. Catalysts 2016. [DOI: 10.3390/catal6110168] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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42
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Hernández SB, Cava F. Environmental roles of microbial amino acid racemases. Environ Microbiol 2015; 18:1673-85. [DOI: 10.1111/1462-2920.13072] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 09/15/2015] [Accepted: 09/27/2015] [Indexed: 02/02/2023]
Affiliation(s)
- Sara B. Hernández
- Laboratory for Molecular Infection Medicine Sweden; Department of Molecular Biology; Umeå Centre for Microbial Research; Umeå University; 90187 Umeå Sweden
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden; Department of Molecular Biology; Umeå Centre for Microbial Research; Umeå University; 90187 Umeå Sweden
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43
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Kubota T, Shimamura S, Kobayashi T, Nunoura T, Deguchi S. Distribution of eukaryotic serine racemases in the bacterial domain and characterization of a representative protein in Roseobacter litoralis Och 149. MICROBIOLOGY-SGM 2015; 162:53-61. [PMID: 26475231 DOI: 10.1099/mic.0.000200] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Two distinct bacterial and eukaryotic serine racemases (SRs) have been identified based on phylogenetic and biochemical characteristics. Although some reports have suggested that marine heterotrophic bacteria have the potential to produce d-serine, the gene encoding bacterial SRs is not found in those bacterial genomes. In this study, using in-depth genomic analysis, we found that eukaryotic SR homologues were distributed widely in various bacterial genomes. Additionally, we selected a eukaryotic SR homologue from a marine heterotrophic bacterium, Roseobacter litoralis Och 149 (RiSR), and constructed an RiSR gene expression system in Escherichia coli for studying the properties of the enzyme. Among the tested amino acids, the recombinant RiSR exhibited both racemization and dehydration activities only towards serine, similar to many eukaryotic SRs. Mg2+ and MgATP enhanced both activities of RiSR, whereas EDTA abolished these enzymatic activities. The enzymatic properties and domain structure of RiSR were similar to those of eukaryotic SRs, particularly mammalian SRs. However, RiSR showed lower catalytic efficiency for L-serine dehydration (kcat/Km=0.094 min(-1) mM(-1)) than those of eukaryotic SRs reported to date (kcat/Km=0.6-21 min(-1) mM(-1)). In contrast, the catalytic efficiency for L-serine racemization of RiSR (kcat/Km=3.14 min(-1) mM(-1)) was 34-fold higher than that of l-serine dehydration. These data suggested that RiSR primarily catalysed serine racemization rather than dehydration.
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Affiliation(s)
- Takaaki Kubota
- Research and Development Center for Marine Biosciences, Marine Functional Biology Group, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Shigeru Shimamura
- Research and Development Center for Marine Biosciences, Marine Functional Biology Group, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Tohru Kobayashi
- Research and Development Center for Marine Biosciences, Marine Functional Biology Group, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Takuro Nunoura
- Research and Development Center for Marine Biosciences, Marine Functional Biology Group, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Shigeru Deguchi
- Research and Development Center for Marine Biosciences, Marine Functional Biology Group, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
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44
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Toogood HS, Cheallaigh AN, Tait S, Mansell DJ, Jervis A, Lygidakis A, Humphreys L, Takano E, Gardiner JM, Scrutton NS. Enzymatic Menthol Production: One-Pot Approach Using Engineered Escherichia coli. ACS Synth Biol 2015; 4:1112-23. [PMID: 26017480 DOI: 10.1021/acssynbio.5b00092] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Menthol isomers are high-value monoterpenoid commodity chemicals, produced naturally by mint plants, Mentha spp. Alternative clean biosynthetic routes to these compounds are commercially attractive. Optimization strategies for biocatalytic terpenoid production are mainly focused on metabolic engineering of the biosynthesis pathway within an expression host. We circumvent this bottleneck by combining pathway assembly techniques with classical biocatalysis methods to engineer and optimize cell-free one-pot biotransformation systems and apply this strategy to the mint biosynthesis pathway. Our approach allows optimization of each pathway enzyme and avoidance of monoterpenoid toxicity issues to the host cell. We have developed a one-pot (bio)synthesis of (1R,2S,5R)-(-)-menthol and (1S,2S,5R)-(+)-neomenthol from pulegone, using recombinant Escherichia coli extracts containing the biosynthetic genes for an "ene"-reductase (NtDBR from Nicotiana tabacum) and two menthone dehydrogenases (MMR and MNMR from Mentha piperita). Our modular engineering strategy allowed each step to be optimized to improve the final production level. Moderate to highly pure menthol (79.1%) and neomenthol (89.9%) were obtained when E. coli strains coexpressed NtDBR with only MMR or MNMR, respectively. This one-pot biocatalytic method allows easier optimization of each enzymatic step and easier modular combination of reactions to ultimately generate libraries of pure compounds for use in high-throughput screening. It will be, therefore, a valuable addition to the arsenal of biocatalysis strategies, especially when applied for (semi)-toxic chemical compounds.
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Affiliation(s)
| | | | | | | | | | | | - Luke Humphreys
- Medicines
Research Centre, GlaxoSmithKline, Gunnel’s Wood Road, Stevenage, Herts SG1 2NY, U.K
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45
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Kawakami R, Ohmori T, Sakuraba H, Ohshima T. Identification of a novel amino acid racemase from a hyperthermophilic archaeon Pyrococcus horikoshii OT-3 induced by D-amino acids. Amino Acids 2015; 47:1579-87. [PMID: 25963389 DOI: 10.1007/s00726-015-2001-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Accepted: 04/30/2015] [Indexed: 10/23/2022]
Abstract
To date, there have been few reports analyzing the amino acid requirement for growth of hyperthermophilic archaea. We here found that the hyperthermophilic archaeon Pyrococcus horikoshii OT-3 requires Thr, Leu, Val, Phe, Tyr, Trp, His and Arg in the medium for growth, and shows slow growth in medium lacking Met or Ile. This largely corresponds to the presence, or absence, of genes related to amino acid biosynthesis in its genome, though there are exceptions. The amino acid requirements were dramatically lost by addition of D-isomers of Met, Leu, Val, allo-Ile, Phe, Tyr, Trp and Arg. Tracer analysis using (14)C-labeled D-Trp showed that D-Trp in the medium was used as a protein component in the cells, suggesting the presence of D-amino acid metabolic enzymes. Pyridoxal 5'-phosphate (PLP)-dependent racemase activity toward Met, Leu and Phe was detected in crude extract of P. horikoshii and was enhanced in cells grown in the medium supplemented with D-amino acids, especially D-allo-Ile. The gene encoding the racemase was narrowed down to one open reading frame on the basis of enzyme purification from P. horikoshii cells, and the recombinant enzyme exhibited PLP-dependent racemase activity toward several amino acids, including Met, Leu and Phe, but not Pro, Asp or Glu. This is the first report showing the presence in a hyperthermophilic archaeon of a PLP-dependent amino acid racemase with broad substrate specificity that is likely responsible for utilization of D-amino acids for growth.
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Affiliation(s)
- Ryushi Kawakami
- Division of Environmental Symbiosis Studies, Graduate School of Integrated Arts and Sciences, Tokushima University, 1-1, Minamijosanjima-cho, Tokushima, Tokushima, 770-8502, Japan,
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46
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Gannavaram S, Sirin S, Sherman W, Gadda G. Mechanistic and Computational Studies of the Reductive Half-Reaction of Tyrosine to Phenylalanine Active Site Variants of d-Arginine Dehydrogenase. Biochemistry 2014; 53:6574-83. [PMID: 25243743 DOI: 10.1021/bi500917q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Sarah Sirin
- Schrödinger, LLC, 120 West 45st Street, New York, New York 10036, United States
| | - Woody Sherman
- Schrödinger, LLC, 120 West 45st Street, New York, New York 10036, United States
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47
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Alvarez L, Espaillat A, Hermoso JA, de Pedro MA, Cava F. Peptidoglycan remodeling by the coordinated action of multispecific enzymes. Microb Drug Resist 2014; 20:190-8. [PMID: 24799190 DOI: 10.1089/mdr.2014.0047] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The peptidoglycan (PG) cell wall constitutes the main defense barrier of bacteria against environmental insults and acts as communication interface. The biochemistry of this macromolecule has been well characterized throughout the years but recent discoveries have unveiled its chemical plasticity under environmental stresses. Non-canonical D-amino acids (NCDAA) are produced and released to the extracellular media by diverse bacteria. Such molecules govern cell wall adaptation to challenging environments through their incorporation into the polymer, a widespread capability among bacteria that reveals the inherent catalytic plasticity of the enzymes involved in the cell wall metabolism. Here, we analyze the recent structural and biochemical characterization of Bsr, a new family of broad spectrum racemases able to generate a wide range of NCDAA. We also discuss the necessity of a coordinated action of PG multispecific enzymes to generate adequate levels of modification in the murein sacculus. Finally, we also highlight how this catalytic plasticity of NCDAA-incorporating enzymes has allowed the development of new revolutionary methodologies for the study of PG modes of growth and in vivo dynamics.
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Affiliation(s)
- Laura Alvarez
- 1 Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University , Umeå, Sweden
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48
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D-Alanine in the islets of Langerhans of rat pancreas. Biochem Biophys Res Commun 2014; 447:328-33. [PMID: 24721429 DOI: 10.1016/j.bbrc.2014.03.153] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 03/31/2014] [Indexed: 11/24/2022]
Abstract
Relatively high levels of D-alanine (D-Ala), an endogenous D-amino acid, have been found in the endocrine systems of several animals, especially in the anterior pituitary; however, its functional importance remains largely unknown. We observed D-Ala in islets of Langerhans isolated from rat pancreas in significantly higher levels than in the anterior/intermediate pituitary; specifically, 180±60 fmol D-Ala per islet (300±100 nmol/gislet), and 10±2.5 nmol/g of wet tissue in pituitary. Additionally, 12±5% of the free Ala in the islets was in the d form, almost an order of magnitude higher than the percentage of D-Ala found in the pituitary. Surprisingly, glucose stimulation of the islets resulted in D-Ala release of 0.6±0.5 fmol per islet. As D-Ala is stored in islets and released in response to changes in extracellular glucose, D-Ala may have a hormonal role.
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49
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Racemization in reverse: evidence that D-amino acid toxicity on Earth is controlled by bacteria with racemases. PLoS One 2014; 9:e92101. [PMID: 24647559 PMCID: PMC3960212 DOI: 10.1371/journal.pone.0092101] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 02/17/2014] [Indexed: 11/19/2022] Open
Abstract
D-amino acids are toxic for life on Earth. Yet, they form constantly due to geochemical racemization and bacterial growth (the cell walls of which contain D-amino acids), raising the fundamental question of how they ultimately are recycled. This study provides evidence that bacteria use D-amino acids as a source of nitrogen by running enzymatic racemization in reverse. Consequently, when soils are inundated with racemic amino acids, resident bacteria consume D- as well as L-enantiomers, either simultaneously or sequentially depending on the level of their racemase activity. Bacteria thus protect life on Earth by keeping environments D-amino acid free.
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50
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Chiral amino acid analysis of Japanese traditional Kurozu and the developmental changes during earthenware jar fermentation processes. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 966:187-92. [PMID: 24582151 DOI: 10.1016/j.jchromb.2014.01.034] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 01/22/2014] [Accepted: 01/23/2014] [Indexed: 02/08/2023]
Abstract
Enantioselective amino acid metabolome analysis of the Japanese traditional black vinegars (amber rice vinegar, Kurozu) was performed using two-dimensional high-performance liquid chromatography combining a microbore-monolithic ODS column and narrowbore-enantioselective columns. d-Amino acids, the enantiomers of widely observed l-amino acids, are currently paid attention as novel physiologically active substances, and the foodstuffs and beverages containing high amounts of d-amino acids are the subjects of interest. In the present study, the amino acid enantiomers were determined by two-dimensional HPLC techniques after pre-column fluorescence derivatization with 4-fluoro-7-nitro-2,1,3-benzoxadiazole. In the first dimension, the amino acid enantiomers are separated as their d plus l mixtures by the reversed-phase mode, then the d-amino acids and their l-counterparts are separately determined in the second dimension by the enantioselective columns. As a result, large amounts of d-Ala (800-4000nmol/mL), d-Asp (200-400nmol/mL) and d-Glu (150-500nmol/mL) were observed in some of the traditionally produced Kurozu vinegars. Relatively large or small amounts of d-Ser (50-100nmol/mL), d-Leu (10-50nmol/mL) and d-allo-Ile (less than 20nmol/mL) were also present in these samples. Developmental changes in the d-amino acid amounts during the fermentation and aging processes have also been investigated.
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