1
|
Dadi P, Pauling CW, Shrivastava A, Shah DD. Synthesis of versatile neuromodulatory molecules by a gut microbial glutamate decarboxylase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.02.583032. [PMID: 38915512 PMCID: PMC11195143 DOI: 10.1101/2024.03.02.583032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Dysbiosis of the microbiome correlates with many neurological disorders, yet very little is known about the chemistry that controls the production of neuromodulatory molecules by gut microbes. Here, we found that an enzyme glutamate decarboxylase (BfGAD) of a gut microbe Bacteroides fragilis forms multiple neuromodulatory molecules such as γ-aminobutyric acid (GABA), hypotaurine, taurine, homotaurine, and β-alanine. We evolved BfGAD and doubled its taurine productivity. Additionally, we increased its specificity towards the substrate L-glutamate. Here, we provide a chemical strategy via which the BfGAD activity could be fine-tuned. In future, this strategy could be used to modulate the production of neuromodulatory molecules by gut microbes.
Collapse
Affiliation(s)
- Pavani Dadi
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85281
- School of Life Sciences, Arizona State University, Tempe, AZ 85281
| | - Clint W. Pauling
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85281
- School of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ 85306
| | - Abhishek Shrivastava
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85281
- School of Life Sciences, Arizona State University, Tempe, AZ 85281
| | - Dhara D. Shah
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85281
- School of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ 85306
| |
Collapse
|
2
|
Jiang L, Song C, Ai C, Wen C, Song S. Modulation effect of sulfated polysaccharide from Sargassum fusiforme on gut microbiota and their metabolites in vitro fermentation. Front Nutr 2024; 11:1400063. [PMID: 38751743 PMCID: PMC11094809 DOI: 10.3389/fnut.2024.1400063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 04/10/2024] [Indexed: 05/18/2024] Open
Abstract
The present study demonstrated the digestion behavior and fermentation characteristics of a sulfated polysaccharide from Sargassum fusiforme (SFSP) in the simulated digestion tract environment. The results showed that the molecular weight of two components in SFSP could not be changed by simulated digestion, and no free monosaccharide was produced. This indicates that most of SFSP can reach the colon as prototypes. During the fermentation with human intestinal flora in vitro, the higher-molecular-weight component of SFSP was utilized, the total sugar content decreased by 16%, the reducing sugar content increased, and the galactose content in monosaccharide composition decreased relatively. This indicates that SFSP can be selectively utilized by human intestinal flora. At the same time, SFSP also changed the structure of intestinal flora. Compared with the blank group, SFSP significantly increased the abundance of Bacteroidetes and decreased the abundance of Firmicutes. At the genus level, the abundances of Bacteroides and Megamonas increased, while the abundances of Shigella, Klebsiella, and Collinsella decreased. Moreover, the concentrations of total short-chain fatty acids (SCFAs), acetic, propionic and n-butyric acids significantly increased compared to the blank group. SFSP could down-regulate the contents of trimethylamine, piperidone and secondary bile acid in fermentation broth. The contents of nicotinic acid, pantothenic acid and other organic acids were increased. Therefore, SFSP shows significant potential to regulate gut microbiota and promote human health.
Collapse
Affiliation(s)
| | | | | | | | - Shuang Song
- SKL of Marine Food Processing and Safety Control, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, National and Local Joint Engineering Laboratory for Marine Bioactive Polysaccharide Development and Application, Liaoning Key Laboratory of Food Nutrition and Health, School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
| |
Collapse
|
3
|
Paloyan A, Sargsyan A, Karapetyan MD, Hambardzumyan A, Kocharov S, Panosyan H, Dyukova K, Kinosyan M, Krueger A, Piergentili C, Stanley WA, Djoko KY, Baslé A, Marles‐Wright J, Antranikian G. Structural and biochemical characterisation of the N-carbamoyl-β-alanine amidohydrolase from Rhizobium radiobacter MDC 8606. FEBS J 2023; 290:5566-5580. [PMID: 37634202 PMCID: PMC10952681 DOI: 10.1111/febs.16943] [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: 05/05/2023] [Revised: 07/21/2023] [Accepted: 08/25/2023] [Indexed: 08/29/2023]
Abstract
N-carbamoyl-β-alanine amidohydrolase (CβAA) constitutes one of the most important groups of industrially relevant enzymes used in the production of optically pure amino acids and derivatives. In this study, a CβAA-encoding gene from Rhizobium radiobacter strain MDC 8606 was cloned and overexpressed in Escherichia coli. The purified recombinant enzyme (RrCβAA) showed a specific activity of 14 U·mg-1 using N-carbamoyl-β-alanine as a substrate with an optimum activity at 55 °C and pH 8.0. In this work, we report also the first prokaryotic CβAA structure at a resolution of 2.0 Å. A discontinuous catalytic domain and a dimerisation domain attached through a flexible hinge region at the domain interface have been revealed. We identify key ligand binding residues, including a conserved glutamic acid (Glu131), histidine (H385) and arginine (Arg291). Our results allowed us to explain the preference of the enzyme for linear carbamoyl substrates, as large and branched carbamoyl substrates cannot fit in the active site of the enzyme. This work envisages the use of RrCβAA from R. radiobacter MDC 8606 for the industrial production of L-α-, L-β- and L-γ-amino acids. The structural analysis provides new insights on enzyme-substrate interaction, which shed light on engineering of CβAAs for high catalytic activity and broad substrate specificity.
Collapse
Affiliation(s)
- Ani Paloyan
- Scientific and Production Center “Armbiotechnology” of NAS RAYerevanArmenia
| | - Armen Sargsyan
- Scientific and Production Center “Armbiotechnology” of NAS RAYerevanArmenia
| | | | | | - Sergei Kocharov
- The Scientific Technological Centre of Organic and Pharmaceutical Chemistry SNPO of NAS RAYerevanArmenia
| | - Henry Panosyan
- The Scientific Technological Centre of Organic and Pharmaceutical Chemistry SNPO of NAS RAYerevanArmenia
| | - Karine Dyukova
- Scientific and Production Center “Armbiotechnology” of NAS RAYerevanArmenia
| | - Marina Kinosyan
- Scientific and Production Center “Armbiotechnology” of NAS RAYerevanArmenia
| | - Anna Krueger
- Authority for the Environment, Climate, Energy and Agriculture in HamburgHamburgGermany
| | - Cecilia Piergentili
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Will A. Stanley
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle upon TyneUK
| | | | - Arnaud Baslé
- Newcastle University Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Jon Marles‐Wright
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle upon TyneUK
- Newcastle University Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | | |
Collapse
|
4
|
Zhao K, Tang H, Zhang B, Zou S, Liu Z, Zheng Y. Microbial production of vitamin B5: current status and prospects. Crit Rev Biotechnol 2023; 43:1172-1192. [PMID: 36210178 DOI: 10.1080/07388551.2022.2104690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 07/01/2022] [Indexed: 11/03/2022]
Abstract
Vitamin B5, also called D-pantothenic acid (D-PA), is a necessary micronutrient that plays an essential role in maintaining the physiological function of an organism. It is widely used in: food, medicine, feed, cosmetics, and other fields. Currently, the production of D-PA in industry heavily relies on chemical processes and enzymatic catalysis. With an increasing demand on the market, replacing chemical-based production of D-PA with microbial fermentation utilizing renewable resources is necessary. In this review, the physiological role and applications of D-PA were firstly introduced, after which the biosynthesis pathways and enzymes will be summarized. Subsequently, a series of cell factory development strategies for excessive D-PA production are analyzed and discussed. Finally, the prospect of microbial production of D-PA production has been prospected.
Collapse
Affiliation(s)
- Kuo Zhao
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Heng Tang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Bo Zhang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Shuping Zou
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Zhiqiang Liu
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Yuguo Zheng
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| |
Collapse
|
5
|
Ballesteros-Gutiérrez M, Albareda M, Barbas C, López-Gonzálvez Á, Dunn MF, Palacios JM. A host-specific diaminobutyrate aminotransferase contributes to symbiotic performance, homoserine metabolism, and competitiveness in the Rhizobium leguminosarum/ Pisum sativum system. Front Microbiol 2023; 14:1182563. [PMID: 37260681 PMCID: PMC10228743 DOI: 10.3389/fmicb.2023.1182563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/25/2023] [Indexed: 06/02/2023] Open
Abstract
Rhizobium leguminosarum bv. viciae (Rlv) UPM791 effectively nodulates pea and lentil, but bacteroids contain a number of proteins differentially expressed depending on the host. One of these host-dependent proteins (C189) is similar to a diaminobutyrate-2-oxoglutarate aminotransferase (DABA-AT). DABA-AT activity was demonstrated with cell extracts and with purified protein, so C189 was renamed as Dat. The dat gene was strongly induced in the central, active area of pea nodules, but not in lentil. Mutants defective in dat were impaired in symbiotic performance with pea plants, exhibiting reduced shoot dry weight, smaller nodules, and a lower competitiveness for nodulation. In contrast, there were no significant differences between mutant and wild-type in symbiosis with lentil plants. A comparative metabolomic approach using cell-free extracts from bacteroids induced in pea and lentil showed significant differences among the strains in pea bacteroids whereas no significant differences were found in lentil. Targeted metabolomic analysis revealed that the dat mutation abolished the presence of 2,4-diaminobutyrate (DABA) in pea nodules, indicating that DABA-AT reaction is oriented toward the production of DABA from L-aspartate semialdehyde. This analysis also showed the presence of L-homoserine, a likely source of aspartate semialdehyde, in pea bacteroids but not in those induced in lentil. The dat mutant showed impaired growth when cells were grown with L-homoserine as nitrogen source. Inclusion of DABA or L-homoserine as N source suppressed pantothenate auxotropy in Rlv UPM791, suggesting DABA as source of the pantothenate precursor β-alanine. These data indicate that Rlv UPM791 Dat enzyme is part of an adaptation mechanism of this bacterium to a homoserine-rich environment such as pea nodule and rhizosphere.
Collapse
Affiliation(s)
- Marta Ballesteros-Gutiérrez
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Consejo Superior de Investigaciones Científicas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Spain
| | - Marta Albareda
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Consejo Superior de Investigaciones Científicas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Coral Barbas
- Facultad de Farmacia, Center for Metabolomics and Bioanalysis (CEMBIO), Universidad San Pablo-CEU, Boadilla del Monte, Spain
| | - Ángeles López-Gonzálvez
- Facultad de Farmacia, Center for Metabolomics and Bioanalysis (CEMBIO), Universidad San Pablo-CEU, Boadilla del Monte, Spain
| | - Michael F. Dunn
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas-Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - José M. Palacios
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Consejo Superior de Investigaciones Científicas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| |
Collapse
|
6
|
Guo J, Sun X, Yuan Y, Chen Q, Ou Z, Deng Z, Ma T, Liu T. Metabolic Engineering of Saccharomyces cerevisiae for Vitamin B5 Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:7408-7417. [PMID: 37154424 DOI: 10.1021/acs.jafc.3c01082] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Vitamin B5, also called d-pantothenic acid, is an essential vitamin in the human body and is widely used in pharmaceuticals, nutritional supplements, food, and cosmetics. However, few studies have investigated the microbial production of d-pantothenic acid, especially in Saccharomyces cerevisiae. By employing a systematic optimization strategy, we screened seven key genes in d-pantothenic acid biosynthesis from diverse species, including bacteria, yeast, fungi, algae, plants, animals, etc., and constructed an efficient heterologous d-pantothenic acid pathway in S. cerevisiae. By adjusting the copy number of the pathway modules, knocking out the endogenous bypass gene, balancing NADPH utilization, and regulating the GAL inducible system, a high-yield d-pantothenic acid-producing strain, DPA171, which can regulate gene expression using glucose, was constructed. By optimizing fed-batch fermentation, DPA171 produced 4.1 g/L d-pantothenic acid, which is the highest titer in S. cerevisiae to date. This study provides guidance for the development of vitamin B5 microbial cell factories.
Collapse
Affiliation(s)
- Jiaxuan Guo
- Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xixi Sun
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yujie Yuan
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Qitong Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zutian Ou
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zixin Deng
- Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- State Key Laboratory of Microbial Metabolism, Department of Bioengineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Tian Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Tiangang Liu
- Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- State Key Laboratory of Microbial Metabolism, Department of Bioengineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
- Hesheng Tech, Co., Ltd., Wuhan 430073, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
| |
Collapse
|
7
|
van Gelderen TA, Ladisa C, Salazar-Moscoso M, Folgado C, Habibi HR, Ribas L. Metabolomic and transcriptomic profiles after immune stimulation in the zebrafish testes. Genomics 2023; 115:110581. [PMID: 36796654 DOI: 10.1016/j.ygeno.2023.110581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/09/2023] [Accepted: 02/11/2023] [Indexed: 02/16/2023]
Abstract
Fish farms are prone to disease outbreaks and stress due to high-density rearing conditions in tanks and sea cages, adversely affecting growth, reproduction, and metabolism. To understand the molecular mechanisms affected in the gonads of breeder fish after an immune challenge, we investigated the metabolome and the transcriptome profiles in zebrafish testes after inducing an immune response. After 48 h of the immune challenge, ultra-high-performance liquid chromatography (LC-MS) and transcriptomic analysis by RNA-seq (Illumina) resulted in 20 different released metabolites and 80 differentially expressed genes. Among these, glutamine and succinic acid were the most abundant metabolites released and 27,5% of the genes belong to either the immune or reproduction systems. Pathway analysis based on metabolomic and transcriptomic crosstalk identified cad and iars genes that act simultaneously with succinate metabolite. This study deciphers interactions between reproduction and immune systems and provides a basis to improve protocols in generating more resistant broodstock.
Collapse
Affiliation(s)
- T A van Gelderen
- Institut de Ciències del Mar - Consejo Superior de Investigaciones Científicas (ICM-CSIC), Department of Renewable Marine Resources, 08003 Barcelona, Spain
| | - C Ladisa
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - M Salazar-Moscoso
- Institut de Ciències del Mar - Consejo Superior de Investigaciones Científicas (ICM-CSIC), Department of Renewable Marine Resources, 08003 Barcelona, Spain
| | - C Folgado
- Institut de Ciències del Mar - Consejo Superior de Investigaciones Científicas (ICM-CSIC), Department of Renewable Marine Resources, 08003 Barcelona, Spain
| | - H R Habibi
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - L Ribas
- Institut de Ciències del Mar - Consejo Superior de Investigaciones Científicas (ICM-CSIC), Department of Renewable Marine Resources, 08003 Barcelona, Spain.
| |
Collapse
|
8
|
Perchat N, Dubois C, Mor-Gautier R, Duquesne S, Lechaplais C, Roche D, Fouteau S, Darii E, Perret A. Characterization of a novel β-alanine biosynthetic pathway consisting of promiscuous metabolic enzymes. J Biol Chem 2022; 298:102067. [PMID: 35623386 PMCID: PMC9213253 DOI: 10.1016/j.jbc.2022.102067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/19/2022] [Accepted: 05/22/2022] [Indexed: 10/28/2022] Open
Abstract
Bacteria adapt to utilize the nutrients available in their environment through a sophisticated metabolic system composed of highly specialized enzymes. Although these enzymes can metabolize molecules other than those for which they evolved, their efficiency toward promiscuous substrates is considered too low to be of physiological relevance. Herein, we investigated the possibility that these promiscuous enzymes are actually efficient enough at metabolizing secondary substrates to modify the phenotype of the cell. For example, in the bacterium Acinetobacter baylyi ADP1 (ADP1), panD (coding for l-aspartate decarboxylase) encodes the only protein known to catalyze the synthesis of β-alanine, an obligate intermediate in CoA synthesis. However, we show that the ADP1 ΔpanD mutant could also form this molecule through an unknown metabolic pathway arising from promiscuous enzymes and grow as efficiently as the wildtype strain. Using metabolomic analyses, we identified 1,3-diaminopropane and 3-aminopropanal as intermediates in this novel pathway. We also conducted activity screening and enzyme kinetics to elucidate candidate enzymes involved in this pathway, including 2,4-diaminobutyrate aminotransferase (Dat) and 2,4-diaminobutyrate decarboxylase (Ddc) and validated this pathway in vivo by analyzing the phenotype of mutant bacterial strains. Finally, we experimentally demonstrate that this novel metabolic route is not restricted to ADP1. We propose that the occurrence of conserved genes in hundreds of genomes across many phyla suggests that this previously undescribed pathway is widespread in prokaryotes.
Collapse
Affiliation(s)
- Nadia Perchat
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Christelle Dubois
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Rémi Mor-Gautier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Sophie Duquesne
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Christophe Lechaplais
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - David Roche
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Stéphanie Fouteau
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Ekaterina Darii
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Alain Perret
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.
| |
Collapse
|
9
|
An NMR-Based Metabolomics Assessment of the Effect of Combinations of Natural Feed Items on Juvenile Red Drum, Sciaenops ocellatus. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10040547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This study evaluated the effects of seven diets composed of natural feed components (chopped fish, shrimp, and squid) alone or in combination on the liver metabolite profile of juvenile red drum (Sciaenops ocellatus) cultured in a 24-tank recirculating aquaculture system over the course of 12 weeks using Nuclear Magnetic Resonance (NMR)-based metabolomics. Experimental diets included fish (F), shrimp (SH), squid (SQ), fish and shrimp (FSH), fish and squid (FSQ), shrimp and squid (SHSQ), fish, shrimp, and squid (FSHSQ). A commercial fishmeal-based pelleted diet was used as a control. Fish were fed isocalorically. Red drum liver samples were collected at five different time points: T0, before the start of the trial (n = 12), and subsequently every 3 weeks over the course of 12 weeks (T3, T6, T9, T12), with n = 9 fish/diet/time point. Polar liver extracts were analyzed by NMR-based metabolomics. Multivariate statistical analyses (PCA, PLS-DA) revealed that red drum fed the F diet had a distinct liver metabolite profile from fish fed the other diets, with those fed SH, SQ and the combination diets displaying greater similarities in their metabolome. Results show that 19 metabolites changed significantly among the different dietary treatments, including amino acids and amino acid derivatives, quaternary amines and methylamines, carbohydrates and phospholipids. Specifically, γ-butyrobetaine, N-formimino-L-glutamate (FIGLU), sarcosine and beta-alanine were among the most discriminating metabolites. Significant correlations were found between metabolites and six growth performance parameters (final body weight, total length, condition factor, liver weight, hepatosomatic index, and eviscerated weight). Metabolites identified in this study constitute potential candidates for supplementation in fish feeds for aquaculture and optimization of existing formulations. Additionally, we identified a quaternary amine, γ-butyrobetaine as a potential biomarker of shrimp consumption in red drum. These results warrant further investigation and biomarker validation and have the potential for broader applicability outside of the aquaculture field in future investigations in wild red drum populations and potentially other carnivorous marine fishes.
Collapse
|
10
|
Wang P, Zhou HY, Li B, Ding WQ, Liu ZQ, Zheng YG. Multiplex modification of Escherichia coli for enhanced β-alanine biosynthesis through metabolic engineering. BIORESOURCE TECHNOLOGY 2021; 342:126050. [PMID: 34597803 DOI: 10.1016/j.biortech.2021.126050] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
β-Alanine is the only naturally occurring β-amino acid, widely used in the fine chemical and pharmaceutical fields. In this study, metabolic design strategies were attempted in Escherichia coli W3110 for enhancing β-alanine biosynthesis. Specifically, heterologous L-aspartate-α-decarboxylase was used, the aspartate kinase I and III involved in competitive pathways were down-regulated, the β-alanine uptake system was disrupted, the phosphoenolpyruvate carboxylase was overexpressed, and the isocitrate lyase repressor repressing glyoxylate cycle shunt was delete, the glucose uptake system was modified, and the regeneration of amino donor was up-regulated. On this basis, a plasmid harboring the heterologous panD and aspB was constructed. The resultant strain ALA17/pTrc99a-panDBS-aspBCG could yield 4.20 g/L β-alanine in shake flask and 43.94 g/L β-alanine (a yield of 0.20 g/g glucose) in 5-L bioreactor via fed-batch cultivation. These modification strategies were proved effective and the constructed β-alanine producer was a promising microbial cell factory for industrial production of β-alanine.
Collapse
Affiliation(s)
- Pei Wang
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Hai-Yan Zhou
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Bo Li
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Wen-Qing Ding
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Zhi-Qiang Liu
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China.
| | - Yu-Guo Zheng
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| |
Collapse
|
11
|
Zou SP, Zhao K, Wang ZJ, Zhang B, Liu ZQ, Zheng YG. Overproduction of D-pantothenic acid via fermentation conditions optimization and isoleucine feeding from recombinant Escherichia coli W3110. 3 Biotech 2021; 11:295. [PMID: 34136332 DOI: 10.1007/s13205-021-02773-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 04/03/2021] [Indexed: 12/27/2022] Open
Abstract
D-pantothenic acid (D-PA), as a crucial vitamin, is widely used in food, animal feed, cosmetics, and pharmaceutical industries. In our previous work, recombinant Escherichia coli W3110 for production of D-PA was constructed through metabolic pathway modification. In this study, to enhance D-PA production, statistical optimization techniques including Plackett-Burman (PB) design and Box-Behnken design (BBD) first were adopted to optimize the culture condition. The results showed that the glucose, β-alanine and (NH4)2SO4 have the most significant effects on D-PA biosynthesis. The response surface model based on BBD predicted that the optimal concentration is glucose 56.0 g/L, β-alanine 2.25 g/L and (NH4)2SO4 11.8 g/L, the D-PA titer increases from 3.2 g/L to 6.73 g/L shake flask fermentation. For the fed-batch fermentation in 5 L fermenter, the isoleucine feeding strategy greatly increased the titer and productivity of D-PA. As a result, titer (31.6 g/L) and productivity (13.2 g/L·d) of D-PA were achieved, they increased by 4.66 times and 2.65 times, respectively, compared with batch culture. At the same time, the accumulation of acetate reduced from 29.79 g/L to 8.55 g/L in the fed-batch fermentation. These results demonstrated that the optimization of medium composition and the cell growth rate are important to increase the concentration of D-PA for microbial fermentation. This work laid the foundation for further research on the application of D-PA microbial synthesis. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02773-0.
Collapse
Affiliation(s)
- Shu-Ping Zou
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
| | - Kuo Zhao
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
| | - Zhi-Jian Wang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
| | - Bo Zhang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
| | - Zhi-Qiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
| | - Yu-Guo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
| |
Collapse
|
12
|
Hu Y, Cronan JE. α-proteobacteria synthesize biotin precursor pimeloyl-ACP using BioZ 3-ketoacyl-ACP synthase and lysine catabolism. Nat Commun 2020; 11:5598. [PMID: 33154364 PMCID: PMC7645780 DOI: 10.1038/s41467-020-19251-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/28/2020] [Indexed: 11/09/2022] Open
Abstract
Pimelic acid, a seven carbon α,ω-dicarboxylic acid (heptanedioic acid), is known to provide seven of the ten biotin carbon atoms including all those of the valeryl side chain. Distinct pimelate synthesis pathways were recently elucidated in Escherichia coli and Bacillus subtilis where fatty acid synthesis plus dedicated biotin enzymes produce the pimelate moiety. In contrast, the α-proteobacteria which include important plant and mammalian pathogens plus plant symbionts, lack all of the known pimelate synthesis genes and instead encode bioZ genes. Here we report a pathway in which BioZ proteins catalyze a 3-ketoacyl-acyl carrier protein (ACP) synthase III-like reaction to produce pimeloyl-ACP with five of the seven pimelate carbon atoms being derived from glutaryl-CoA, an intermediate in lysine degradation. Agrobacterium tumefaciens strains either deleted for bioZ or which encode a BioZ active site mutant are biotin auxotrophs, as are strains defective in CaiB which catalyzes glutaryl-CoA synthesis from glutarate and succinyl-CoA.
Collapse
Affiliation(s)
- Yuanyuan Hu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - John E Cronan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| |
Collapse
|
13
|
López-Sámano M, Beltrán LFLA, Sánchez-Thomas R, Dávalos A, Villaseñor T, García-García JD, García-de Los Santos A. A novel way to synthesize pantothenate in bacteria involves β-alanine synthase present in uracil degradation pathway. Microbiologyopen 2020; 9:e1006. [PMID: 32112625 PMCID: PMC7142369 DOI: 10.1002/mbo3.1006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/05/2020] [Accepted: 01/15/2020] [Indexed: 11/07/2022] Open
Abstract
Pantothenate is an indispensable vitamin precursor of the synthesis of coenzyme A (CoA), a key metabolite required in over 100 metabolic reactions. β-Alanine (β-ala) is an indispensable component of pantothenate. Due to the metabolic relevance of this pathway, we assumed that orthologous genes for ß-alanine synthesis would be present in the genomes of bacteria, archaea, and eukaryotes. However, comparative genomic studies revealed that orthologous gene replacement and loss of synteny occur at high frequency in panD genes. We have previously reported the atypical plasmid-encoded location of the pantothenate pathway genes panC and panB (two copies) in R. etli CFN42. This study also revealed the unexpected absence of a panD gene encoding the aspartate decarboxylase enzyme (ADC), required for the synthesis of β-ala. The aim of this study was to identify the source of β-alanine in Rhizobium etli CFN42. In this study, we present a bioinformatic analysis and an experimental validation demonstrating that the source of β-ala in this R. etli comes from β-alanine synthase, the last enzyme of the uracil degradation pathway.
Collapse
Affiliation(s)
- Mariana López-Sámano
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autonoma de México, Cuernavaca, Morelos, México
| | | | - Rosina Sánchez-Thomas
- Departamento de Bioquímica, Instituto Nacional de Cardiología "Ignacio Chávez", Tlalpan, México
| | - Araceli Dávalos
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autonoma de México, Cuernavaca, Morelos, México
| | - Tomás Villaseñor
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, UNAM, Cuernavaca, México
| | | | - Alejandro García-de Los Santos
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autonoma de México, Cuernavaca, Morelos, México
| |
Collapse
|