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Liwinski T, Lang UE, Brühl AB, Schneider E. Exploring the Therapeutic Potential of Gamma-Aminobutyric Acid in Stress and Depressive Disorders through the Gut-Brain Axis. Biomedicines 2023; 11:3128. [PMID: 38137351 PMCID: PMC10741010 DOI: 10.3390/biomedicines11123128] [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: 09/27/2023] [Revised: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Research conducted on individuals with depression reveals that major depressive disorders (MDDs) coincide with diminished levels of the inhibitory neurotransmitter γ-aminobutyric acid (GABA) in the brain, as well as modifications in the subunit composition of the primary receptors (GABAA receptors) responsible for mediating GABAergic inhibition. Furthermore, there is substantial evidence supporting the significant role of GABA in regulating stress within the brain, which is a pivotal vulnerability factor in mood disorders. GABA is readily available and approved as a food supplement in many countries. Although there is substantial evidence indicating that orally ingested GABA may affect GABA receptors in peripheral tissues, there is comparatively less evidence supporting its direct action within the brain. Emerging evidence highlights that oral GABA intake may exert beneficial effects on the brain and psyche through the gut-brain axis. While GABA enjoys wide consumer acceptance in Eastern Asian markets, with many consumers reporting favorable effects on stress regulation, mood, and sleep, rigorous independent research is still largely lacking. Basic research, coupled with initial clinical findings, makes GABA an intriguing neuro-nutritional compound deserving of clinical studies in individuals with depression and other psychological problems.
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Affiliation(s)
| | | | | | - Else Schneider
- University Psychiatric Clinics Basel, Clinic for Adults, University of Basel, CH-4002 Basel, Switzerland; (T.L.); (U.E.L.); (A.B.B.)
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2
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Nie Q, Sun Y, Li M, Zuo S, Chen C, Lin Q, Nie S. Targeted modification of gut microbiota and related metabolites via dietary fiber. Carbohydr Polym 2023; 316:120986. [PMID: 37321707 DOI: 10.1016/j.carbpol.2023.120986] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 06/17/2023]
Abstract
Intake of dietary fiber has been proven to have several beneficial effects in maintaining host homeostasis and health. Here, we investigated the effects of different fibers on gut microbiota and related metabolites in rats. Healthy rats were supplemented with guar gum, carrageenan, glucomannan, β-glucan, arabinoxylan, apple pectin, xylan, arabinogalactan, and xanthan gum, and these dietary fibers exhibited commonality and specificity on gut microbiota and related metabolites. The abundance of Phascolarctobacterium, Prevotella, Treponema, Butyricimonas, Bacteroides, and Lactobacillus was selectively increased by different dietary fibers, whereas the abundance of Clostridium perfringens and Bacteroides fragilis were decreased by all of these fibers. Indole-3-lactic acid was significantly increased by β-glucan treatment, indicating the relationship between indole-3-lactic acid and Lactobacillus. Furthermore, Some species from Bacteroides were validated to produce indole-3-lactic acid, indole-3-acetic acid, and kynurenine (such as B. fragilis, B. ovatus, B. thetaiotaomicron, and B. xylanisolvens). These results provide important information on dietary guidelines based on the modification of gut microecology.
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Affiliation(s)
- Qixing Nie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology, Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang 330047, China
| | - Yonggan Sun
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology, Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang 330047, China
| | - Mingzhi Li
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology, Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang 330047, China
| | - Sheng Zuo
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology, Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang 330047, China
| | - Chunhua Chen
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology, Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang 330047, China
| | - Qiongni Lin
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology, Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang 330047, China
| | - Shaoping Nie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology, Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang 330047, China.
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Shimokawa H, Sakanaka M, Fujisawa Y, Ohta H, Sugiyama Y, Kurihara S. N-Carbamoylputrescine Amidohydrolase of Bacteroides thetaiotaomicron, a Dominant Species of the Human Gut Microbiota. Biomedicines 2023; 11:biomedicines11041123. [PMID: 37189741 DOI: 10.3390/biomedicines11041123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/15/2023] [Accepted: 03/22/2023] [Indexed: 05/17/2023] Open
Abstract
Polyamines are bioactive amines that play a variety of roles, such as promoting cell proliferation and protein synthesis, and the intestinal lumen contains up to several mM polyamines derived from the gut microbiota. In the present study, we conducted genetic and biochemical analyses of the polyamine biosynthetic enzyme N-carbamoylputrescine amidohydrolase (NCPAH) that converts N-carbamoylputrescine to putrescine, a precursor of spermidine in Bacteroides thetaiotaomicron, which is one of the most dominant species in the human gut microbiota. First, ncpah gene deletion and complemented strains were generated, and the intracellular polyamines of these strains cultured in a polyamine-free minimal medium were analyzed using high-performance liquid chromatography. The results showed that spermidine detected in the parental and complemented strains was depleted in the gene deletion strain. Next, purified NCPAH-(His)6 was analyzed for enzymatic activity and found to be capable of converting N-carbamoylputrescine to putrescine, with a Michaelis constant (Km) and turnover number (kcat) of 730 µM and 0.8 s-1, respectively. Furthermore, the NCPAH activity was strongly (>80%) inhibited by agmatine and spermidine, and moderately (≈50%) inhibited by putrescine. This feedback inhibition regulates the reaction catalyzed by NCPAH and may play a role in intracellular polyamine homeostasis in B. thetaiotaomicron.
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Affiliation(s)
- Hiromi Shimokawa
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi 921-8836, Ishikawa, Japan
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa 649-6493, Wakayama, Japan
| | - Mikiyasu Sakanaka
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi 921-8836, Ishikawa, Japan
| | - Yuki Fujisawa
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi 921-8836, Ishikawa, Japan
| | - Hirokazu Ohta
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi 921-8836, Ishikawa, Japan
| | - Yuta Sugiyama
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi 921-8836, Ishikawa, Japan
| | - Shin Kurihara
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi 921-8836, Ishikawa, Japan
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa 649-6493, Wakayama, Japan
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4
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Krysenko S, Wohlleben W. Polyamine and Ethanolamine Metabolism in Bacteria as an Important Component of Nitrogen Assimilation for Survival and Pathogenicity. Med Sci (Basel) 2022; 10:40. [PMID: 35997332 PMCID: PMC9397018 DOI: 10.3390/medsci10030040] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
Nitrogen is an essential element required for bacterial growth. It serves as a building block for the biosynthesis of macromolecules and provides precursors for secondary metabolites. Bacteria have developed the ability to use various nitrogen sources and possess two enzyme systems for nitrogen assimilation involving glutamine synthetase/glutamate synthase and glutamate dehydrogenase. Microorganisms living in habitats with changeable availability of nutrients have developed strategies to survive under nitrogen limitation. One adaptation is the ability to acquire nitrogen from alternative sources including the polyamines putrescine, cadaverine, spermidine and spermine, as well as the monoamine ethanolamine. Bacterial polyamine and monoamine metabolism is not only important under low nitrogen availability, but it is also required to survive under high concentrations of these compounds. Such conditions can occur in diverse habitats such as soil, plant tissues and human cells. Strategies of pathogenic and non-pathogenic bacteria to survive in the presence of poly- and monoamines offer the possibility to combat pathogens by using their capability to metabolize polyamines as an antibiotic drug target. This work aims to summarize the knowledge on poly- and monoamine metabolism in bacteria and its role in nitrogen metabolism.
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Affiliation(s)
- Sergii Krysenko
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Department of Microbiology and Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany;
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, 72076 Tübingen, Germany
| | - Wolfgang Wohlleben
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Department of Microbiology and Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany;
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, 72076 Tübingen, Germany
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5
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Thongbhubate K, Irie K, Sakai Y, Itoh A, Suzuki H. Improvement of putrescine production through the arginine decarboxylase pathway in Escherichia coli K-12. AMB Express 2021; 11:168. [PMID: 34910273 PMCID: PMC8674398 DOI: 10.1186/s13568-021-01330-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 12/04/2021] [Indexed: 12/03/2022] Open
Abstract
In the bio-based polymer industry, putrescine is in the spotlight for use as a material. We constructed strains of Escherichia coli to assess its putrescine production capabilities through the arginine decarboxylase pathway in batch fermentation. N-Acetylglutamate (ArgA) synthase is subjected to feedback inhibition by arginine. Therefore, the 19th amino acid residue, Tyr, of argA was substituted with Cys to desensitize the feedback inhibition of arginine, resulting in improved putrescine production. The inefficient initiation codon GTG of argA was substituted with the effective ATG codon, but its replacement did not affect putrescine production. The essential genes for the putrescine production pathway, speA and speB, were cloned into the same plasmid with argAATG Y19C to form an operon. These genes were introduced under different promoters; lacIp, lacIqp, lacIq1p, and T5p. Among these, the T5 promoter demonstrated the best putrescine production. In addition, disruption of the puuA gene encoding enzyme of the first step of putrescine degradation pathway increased the putrescine production. Of note, putrescine production was not affected by the disruption of patA, which encodes putrescine aminotransferase, the initial enzyme of another putrescine utilization pathway. We also report that the strain KT160, which has a genomic mutation of YifEQ100TAG, had the greatest putrescine production. At 48 h of batch fermentation, strain KT160 grown in terrific broth with 0.01 mM IPTG produced 19.8 mM of putrescine.
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6
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Rodríguez-Herrero V, Peris A, Camacho M, Bautista V, Esclapez J, Bonete MJ. Novel Glutamate-Putrescine Ligase Activity in Haloferax mediterranei: A New Function for glnA-2 Gene. Biomolecules 2021; 11:biom11081156. [PMID: 34439822 PMCID: PMC8394153 DOI: 10.3390/biom11081156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/25/2021] [Accepted: 07/31/2021] [Indexed: 02/06/2023] Open
Abstract
The genome of the halophilic archaea Haloferax mediterranei contains three ORFs that show homology with glutamine synthetase (GS) (glnA-1, glnA-2, and glnA-3). Previous studies have focused on the role of GlnA-1, suggesting that proteins GlnA-2 and GlnA-3 could play a different role to that of GS. Glutamine synthetase (EC 6.3.1.2) belongs to the class of ligases, including 20 subclasses of other different enzymes, such as aspartate–ammonia ligase (EC 6.3.1.1), glutamate–ethylamine ligase (EC 6.3.1.6), and glutamate–putrescine ligase (EC 6.3.1.11). The reaction catalyzed by glutamate–putrescine ligase is comparable to the reaction catalyzed by glutamine synthetase (GS). Both enzymes can bind a glutamate molecule to an amino group: ammonium (GS) or putrescine (glutamate–putrescine ligase). In addition, they present the characteristic catalytic domain of GS, showing significant similarities in their structure. Although these proteins are annotated as GS, the bioinformatics and experimental results obtained in this work indicate that the GlnA-2 protein (HFX_1688) is a glutamate–putrescine ligase, involved in polyamine catabolism. The most significant results are those related to glutamate–putrescine ligase’s activity and the analysis of the transcriptional and translational expression of the glnA-2 gene in the presence of different nitrogen sources. This work confirms a new metabolic pathway in the Archaea domain which extends the knowledge regarding the utilization of alternative nitrogen sources in this domain.
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Affiliation(s)
- Verónica Rodríguez-Herrero
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Division, Faculty of Science, University of Alicante, 03080 Alicante, Spain; (V.R.-H.); (M.C.); (V.B.)
| | - Arnau Peris
- Institute for Integrative Systems Biology, I2SysBio, Campus Burjassot, University of Valencia-CSIC, 46908 Valencia, Spain;
| | - Mónica Camacho
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Division, Faculty of Science, University of Alicante, 03080 Alicante, Spain; (V.R.-H.); (M.C.); (V.B.)
| | - Vanesa Bautista
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Division, Faculty of Science, University of Alicante, 03080 Alicante, Spain; (V.R.-H.); (M.C.); (V.B.)
| | - Julia Esclapez
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Division, Faculty of Science, University of Alicante, 03080 Alicante, Spain; (V.R.-H.); (M.C.); (V.B.)
- Correspondence: (J.E.); (M.-J.B.); Tel.: +34-965-903-880 (J.E. & M.-J.B.)
| | - María-José Bonete
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Division, Faculty of Science, University of Alicante, 03080 Alicante, Spain; (V.R.-H.); (M.C.); (V.B.)
- Correspondence: (J.E.); (M.-J.B.); Tel.: +34-965-903-880 (J.E. & M.-J.B.)
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7
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Levine M, Lohinai ZM. Resolving the Contradictory Functions of Lysine Decarboxylase and Butyrate in Periodontal and Intestinal Diseases. J Clin Med 2021; 10:jcm10112360. [PMID: 34072136 PMCID: PMC8198195 DOI: 10.3390/jcm10112360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 05/14/2021] [Indexed: 11/16/2022] Open
Abstract
Periodontal disease is a common, bacterially mediated health problem worldwide. Mastication (chewing) repeatedly traumatizes the gingiva and periodontium, causing traces of inflammatory exudate, gingival crevicular fluid (GCF), to appear in crevices between the teeth and gingiva. Inadequate tooth cleaning causes a dentally adherent microbial biofilm composed of commensal salivary bacteria to appear around these crevices where many bacteria grow better on GCF than in saliva. We reported that lysine decarboxylase (Ldc) from Eikenella corrodens depletes the GCF of lysine by converting it to cadaverine and carbon dioxide. Lysine is an amino acid essential for the integrity and continuous renewal of dentally attached epithelium acting as a barrier to microbial products. Unless removed regularly by oral hygiene, bacterial products invade the lysine-deprived dental attachment where they stimulate inflammation that enhances GCF exudation. Cadaverine increases and supports the development of a butyrate-producing microbiome that utilizes the increased GCF substrates to slowly destroy the periodontium (dysbiosis). A long-standing paradox is that acid-induced Ldc and butyrate production support a commensal (probiotic) microbiome in the intestine. Here, we describe how the different physiologies of the respective tissues explain how the different Ldc and butyrate functions impact the progression and control of these two chronic diseases.
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Affiliation(s)
- Martin Levine
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Correspondence:
| | - Zsolt M. Lohinai
- Department of Conservative Dentistry, Semmelweis University, H-1088 Budapest, Hungary;
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8
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Otaru N, Ye K, Mujezinovic D, Berchtold L, Constancias F, Cornejo FA, Krzystek A, de Wouters T, Braegger C, Lacroix C, Pugin B. GABA Production by Human Intestinal Bacteroides spp.: Prevalence, Regulation, and Role in Acid Stress Tolerance. Front Microbiol 2021; 12:656895. [PMID: 33936013 PMCID: PMC8082179 DOI: 10.3389/fmicb.2021.656895] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/24/2021] [Indexed: 12/11/2022] Open
Abstract
The high neuroactive potential of metabolites produced by gut microbes has gained traction over the last few years, with metagenomic-based studies suggesting an important role of microbiota-derived γ-aminobutyric acid (GABA) in modulating mental health. Emerging evidence has revealed the presence of the glutamate decarboxylase (GAD)-encoding gene, a key enzyme to produce GABA, in the prominent human intestinal genus Bacteroides. Here, we investigated GABA production by Bacteroides in culture and metabolic assays combined with comparative genomics and phylogenetics. A total of 961 Bacteroides genomes were analyzed in silico and 17 metabolically and genetically diverse human intestinal isolates representing 11 species were screened in vitro. Using the model organism Bacteroides thetaiotaomicron DSM 2079, we determined GABA production kinetics, its impact on milieu pH, and we assessed its role in mitigating acid-induced cellular damage. We showed that the GAD-system consists of at least four highly conserved genes encoding a GAD, a glutaminase, a glutamate/GABA antiporter, and a potassium channel. We demonstrated a high prevalence of the GAD-system among Bacteroides with 90% of all Bacteroides genomes (96% in human gut isolates only) harboring all genes of the GAD-system and 16 intestinal Bacteroides strains producing GABA in vitro (ranging from 0.09 to 60.84 mM). We identified glutamate and glutamine as precursors of GABA production, showed that the production is regulated by pH, and that the GAD-system acts as a protective mechanism against acid stress in Bacteroides, mitigating cell death and preserving metabolic activity. Our data also indicate that the GAD-system might represent the only amino acid-dependent acid tolerance system in Bacteroides. Altogether, our results suggest an important contribution of Bacteroides in the regulation of the GABAergic system in the human gut.
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Affiliation(s)
- Nize Otaru
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland.,Nutrition Research Unit, University Children's Hospital Zürich, Zürich, Switzerland
| | - Kun Ye
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Denisa Mujezinovic
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Laura Berchtold
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland.,PharmaBiome AG, Zürich, Switzerland
| | - Florentin Constancias
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Fabián A Cornejo
- Max Planck Unit for the Science of Pathogens, Berlin, Germany.,Laboratory of Molecular Microbiology, Faculty of Chemistry and Biology, University of Santiago, Santiago, Chile
| | - Adam Krzystek
- Laboratory of Human Nutrition, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | | | - Christian Braegger
- Nutrition Research Unit, University Children's Hospital Zürich, Zürich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Benoit Pugin
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
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Yamamoto T, Liu Y, Sumiyoshi T, Hasegawa Y, Iwaki H. A novel piperidine degradation mechanism in a newly isolated piperidine degrader Pseudomonas sp. strain KU43P. J GEN APPL MICROBIOL 2020; 66:265-272. [PMID: 32641635 DOI: 10.2323/jgam.2019.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The degradation pathways in microorganisms for piperidine, a secondary amine with various applications, are not yet fully understood, especially in non-Mycobacterium species. In this study, we have identified a piperidine-degrading isolate (KU43P) from a soil sample collected in a cultivation field in Osaka, Japan, and characterized its mechanisms of piperidine degradation, thereby furthering current understanding of the process. The genome of isolate KU43P consists of a 5,869,691-bp circular chromosome with 62.67% GC content and with 5,294 predicted protein-coding genes, 77 tRNA genes, and 22 rRNA genes. 16S rRNA gene sequence analysis and average nucleotide identity analysis suggest that the isolate is a novel species of the Pseudomonas putida group in the genus Pseudomonas. The genomic region encoding the piperidine degradation pathway, designated as the pip gene cluster, was identified using transposon mutagenesis and reverse transcription polymerase chain reaction. Deletion analyses of pipA, which encodes a glutamine synthetase (GS)-like protein, and pipBa, which encodes a cytochrome P450 monooxygenase, indicate that pipA and pipBa are involved in piperidine metabolism and suggest that pipA is involved in the first step of the piperidine metabolic pathway. Escherichia coli whole cells overexpressing PipA converted piperidine and glutamate to γ-glutamylpiperidide, and crude cell extract enzyme assays of PipA showed that this reaction requires ATP and Mg2+. These results clearly show that pipA encodes γ-glutamylpiperidide synthetase and that piperidine is first glutamylated and then hydroxylated in the piperidine degradation pathway of Pseudomonas sp. strain KU43P. This study has filled a void in the general knowledge of the microbial degradation of amine compounds.
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Affiliation(s)
- Taisei Yamamoto
- Department of Life Science & Biotechnology, Kansai University
| | - Yaxuan Liu
- Department of Life Science & Biotechnology, Kansai University
| | | | - Yoshie Hasegawa
- Department of Life Science & Biotechnology, Kansai University
| | - Hiroaki Iwaki
- Department of Life Science & Biotechnology, Kansai University
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10
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Dougherty MW, Kudin O, Mühlbauer M, Neu J, Gharaibeh RZ, Jobin C. Gut microbiota maturation during early human life induces enterocyte proliferation via microbial metabolites. BMC Microbiol 2020; 20:205. [PMID: 32652929 PMCID: PMC7353703 DOI: 10.1186/s12866-020-01892-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 07/02/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The intestinal tract undergoes a period of cellular maturation during early life, primarily characterized by the organization of epithelial cells into specialized crypt and villus structures. These processes are in part mediated by the acquisition of microbes. Infants delivered at term typically harbor a stable, low diversity microbiota characterized by an overrepresentation of various Bacilli spp., while pre-term infants are colonized by an assortment of bacteria during the first several weeks after delivery. However, the functional effects of these changes on intestinal epithelium homeostasis and maturation remain unclear. To study these effects, human neonate feces were obtained from term and pre-term infants. Fecal 16S rDNA sequencing and global untargeted LC-MS were performed to characterize microbial composition and metabolites from each population. Murine enteral organoids (enteroids) were cultured with 0.22 μm filtered stool supernatant pooled from term or pre-term infants. RESULTS Term and pre-term microbial communities differed significantly from each other by principle components analysis (PCoA, PERMANOVA p < 0.001), with the pre-term microbiome characterized by increased OTU diversity (Wilcox test p < 0.01). Term communities were less diverse and dominated by Bacilli (81.54%). Pre-term stools had an increased abundance of vitamins, amino acid derivatives and unconjugated bile acids. Pathway analysis revealed a significant increase in multiple metabolic pathways in pre-term samples mapped to E. coli using the KEGG database related to the fermentation of various amino acids and vitamin biosynthesis. Enteroids cultured with supernatant from pre-term stools proliferated at a higher rate than those cultured with supernatant from term stools (cell viability: 207% vs. 147.7%, p < 0.01), grew larger (area: 81,189μm2 vs. 41,777μm2, p < 0.001), and bud at a higher rate (6.5 vs. 4, p < 0.01). Additionally, genes involved in stem cell proliferation were upregulated in pre-term stool treated enteroid cultures (Lgr5, Ephb2, Ascl2 Sox9) but not term stool treated enteroids. CONCLUSIONS Our findings indicate that microbial metabolites from the more diverse gut microbiome associated with pre-term infants facilitate stem cell proliferation. Therefore, perturbations of the pre-term microbiota may impair intestinal homeostasis.
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Affiliation(s)
- Michael W Dougherty
- Department of Medicine, Division of Gastroenterology, University of Florida, CGRC, 2033 Mowry Rd, Florida, 32610, USA
| | - Oleksandr Kudin
- Department of Pediatrics, University of Florida, Gainesville, Florida, USA
| | - Marcus Mühlbauer
- Department of Medicine, Division of Gastroenterology, University of Florida, CGRC, 2033 Mowry Rd, Florida, 32610, USA
| | - Josef Neu
- Department of Pediatrics, University of Florida, Gainesville, Florida, USA
| | - Raad Z Gharaibeh
- Department of Medicine, Division of Gastroenterology, University of Florida, CGRC, 2033 Mowry Rd, Florida, 32610, USA
| | - Christian Jobin
- Department of Medicine, Division of Gastroenterology, University of Florida, CGRC, 2033 Mowry Rd, Florida, 32610, USA.
- Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA.
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11
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Identification of Host Adaptation Genes in Extraintestinal Pathogenic Escherichia coli during Infection in Different Hosts. Infect Immun 2019; 87:IAI.00666-19. [PMID: 31501251 DOI: 10.1128/iai.00666-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 08/30/2019] [Indexed: 01/11/2023] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) is an important human and animal pathogen. Despite the apparent similarities in their known virulence attributes, some ExPEC strains can cross the host species barrier and present a zoonotic potential, whereas other strains exhibit host specificity, suggesting the existence of unknown mechanisms that remain to be identified. We applied a transposon-directed insertion site sequencing (TraDIS) strategy to investigate the ExPEC XM strain, which is capable of crossing the host species barrier, and to screen for virulence-essential genes in both mammalian (mouse) and avian (duck) models of E. coli-related septicemia. We identified 151 genes essential for systemic infection in both mammalian and avian models, 97 required only in the mammalian model, and 280 required only in the avian model. Ten genes/gene clusters were selected for further validation, and their contributions to ExPEC virulence in both mammalian and avian models or mammalian- or avian-only models were confirmed by animal tests. This represents the first comprehensive genome-wide analysis of virulence-essential genes required for systemic infections in two different host species and provides a further comprehensive understanding of ExPEC-related virulence, host specificity, and adaptation.
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12
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Strecker A, Schubert C, Zedler S, Steinmetz P, Unden G. DcuA of aerobically grownEscherichia coliserves as a nitrogen shuttle (L‐aspartate/fumarate) for nitrogen uptake. Mol Microbiol 2018; 109:801-811. [DOI: 10.1111/mmi.14074] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/27/2018] [Accepted: 07/02/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Alexander Strecker
- Microbiology and Wine Research, Institute of Molecular Physiology (IMP) Johannes Gutenberg‐University Mainz Mainz 55099Germany
| | - Christopher Schubert
- Microbiology and Wine Research, Institute of Molecular Physiology (IMP) Johannes Gutenberg‐University Mainz Mainz 55099Germany
| | - Sandra Zedler
- Microbiology and Wine Research, Institute of Molecular Physiology (IMP) Johannes Gutenberg‐University Mainz Mainz 55099Germany
| | - Philipp Steinmetz
- Microbiology and Wine Research, Institute of Molecular Physiology (IMP) Johannes Gutenberg‐University Mainz Mainz 55099Germany
| | - Gottfried Unden
- Microbiology and Wine Research, Institute of Molecular Physiology (IMP) Johannes Gutenberg‐University Mainz Mainz 55099Germany
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13
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Slabu I, Galman JL, Lloyd RC, Turner NJ. Discovery, Engineering, and Synthetic Application of Transaminase Biocatalysts. ACS Catal 2017. [DOI: 10.1021/acscatal.7b02686] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Iustina Slabu
- School
of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, M1 7DN Manchester, United Kingdom
| | - James L. Galman
- School
of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, M1 7DN Manchester, United Kingdom
| | - Richard C. Lloyd
- Dr.
Reddy’s Laboratories, Chirotech Technology Centre, CB4 0PE Cambridge, United Kingdom
| | - Nicholas J. Turner
- School
of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, M1 7DN Manchester, United Kingdom
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Moitinho-Silva L, Díez-Vives C, Batani G, Esteves AIS, Jahn MT, Thomas T. Integrated metabolism in sponge-microbe symbiosis revealed by genome-centered metatranscriptomics. THE ISME JOURNAL 2017; 11:1651-1666. [PMID: 28338677 PMCID: PMC5520145 DOI: 10.1038/ismej.2017.25] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 01/10/2017] [Accepted: 01/19/2017] [Indexed: 12/21/2022]
Abstract
Despite an increased understanding of functions in sponge microbiomes, the interactions among the symbionts and between symbionts and host are not well characterized. Here we reconstructed the metabolic interactions within the sponge Cymbastela concentrica microbiome in the context of functional features of symbiotic diatoms and the host. Three genome bins (CcPhy, CcNi and CcThau) were recovered from metagenomic data of C. concentrica, belonging to the proteobacterial family Phyllobacteriaceae, the Nitrospira genus and the thaumarchaeal order Nitrosopumilales. Gene expression was estimated by mapping C. concentrica metatranscriptomic reads. Our analyses indicated that CcPhy is heterotrophic, while CcNi and CcThau are chemolithoautotrophs. CcPhy expressed many transporters for the acquisition of dissolved organic compounds, likely available through the sponge's filtration activity and symbiotic carbon fixation. Coupled nitrification by CcThau and CcNi was reconstructed, supported by the observed close proximity of the cells in fluorescence in situ hybridization. CcPhy facultative anaerobic respiration and assimilation by diatoms may consume the resulting nitrate. Transcriptional analysis of diatom and sponge functions indicated that these organisms are likely sources of organic compounds, for example, creatine/creatinine and dissolved organic carbon, for other members of the symbiosis. Our results suggest that organic nitrogen compounds, for example, creatine, creatinine, urea and cyanate, fuel the nitrogen cycle within the sponge. This study provides an unprecedented view of the metabolic interactions within sponge-microbe symbiosis, bridging the gap between cell- and community-level knowledge.
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Affiliation(s)
- Lucas Moitinho-Silva
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Cristina Díez-Vives
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Giampiero Batani
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Ana IS Esteves
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Martin T Jahn
- Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Torsten Thomas
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia
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15
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Krysenko S, Okoniewski N, Kulik A, Matthews A, Grimpo J, Wohlleben W, Bera A. Gamma-Glutamylpolyamine Synthetase GlnA3 Is Involved in the First Step of Polyamine Degradation Pathway in Streptomyces coelicolor M145. Front Microbiol 2017; 8:726. [PMID: 28487688 PMCID: PMC5403932 DOI: 10.3389/fmicb.2017.00726] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/07/2017] [Indexed: 12/26/2022] Open
Abstract
Streptomyces coelicolor M145 was shown to be able to grow in the presence of high concentrations of polyamines, such as putrescine, cadaverine, spermidine, or spermine, as a sole nitrogen source. However, hardly anything is known about polyamine utilization and its regulation in streptomycetes. In this study, we demonstrated that only one of the three proteins annotated as glutamine synthetase-like protein, GlnA3 (SCO6962), was involved in the catabolism of polyamines. Transcriptional analysis revealed that the expression of glnA3 was strongly induced by exogenous polyamines and repressed in the presence of ammonium. The ΔglnA3 mutant was shown to be unable to grow on defined Evans agar supplemented with putrescine, cadaverine, spermidine, and spermine as sole nitrogen source. HPLC analysis demonstrated that the ΔglnA3 mutant accumulated polyamines intracellularly, but was unable to degrade them. In a rich complex medium supplemented with a mixture of the four different polyamines, the ΔglnA3 mutant grew poorly showing abnormal mycelium morphology and decreased life span in comparison to the parental strain. These observations indicated that the accumulation of polyamines was toxic for the cell. An in silico analysis of the GlnA3 protein model suggested that it might act as a gamma-glutamylpolyamine synthetase catalyzing the first step of polyamine degradation. GlnA3-catalyzed glutamylation of putrescine was confirmed in an enzymatic in vitro assay and the GlnA3 reaction product, gamma-glutamylputrescine, was detected by HPLC/ESI-MS. In this work, the first step of polyamine utilization in S. coelicolor has been elucidated and the putative polyamine utilization pathway has been deduced based on the sequence similarity and transcriptional analysis of homologous genes expressed in the presence of polyamines.
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Affiliation(s)
- Sergii Krysenko
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Department of Microbiology and Biotechnology, University of TübingenTübingen, Germany
| | - Nicole Okoniewski
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Department of Microbiology and Biotechnology, University of TübingenTübingen, Germany
| | - Andreas Kulik
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Department of Microbiology and Biotechnology, University of TübingenTübingen, Germany
| | - Arne Matthews
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Department of Microbiology and Biotechnology, University of TübingenTübingen, Germany
| | - Jan Grimpo
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Department of Microbiology and Biotechnology, University of TübingenTübingen, Germany
| | - Wolfgang Wohlleben
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Department of Microbiology and Biotechnology, University of TübingenTübingen, Germany
| | - Agnieszka Bera
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Department of Microbiology and Biotechnology, University of TübingenTübingen, Germany
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16
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17
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Abstract
This review considers the pathways for the degradation of amino acids and a few related compounds (agmatine, putrescine, ornithine, and aminobutyrate), along with their functions and regulation. Nitrogen limitation and an acidic environment are two physiological cues that regulate expression of several amino acid catabolic genes. The review considers Escherichia coli, Salmonella enterica serovar Typhimurium, and Klebsiella species. The latter is included because the pathways in Klebsiella species have often been thoroughly characterized and also because of interesting differences in pathway regulation. These organisms can essentially degrade all the protein amino acids, except for the three branched-chain amino acids. E. coli, Salmonella enterica serovar Typhimurium, and Klebsiella aerogenes can assimilate nitrogen from D- and L-alanine, arginine, asparagine, aspartate, glutamate, glutamine, glycine, proline, and D- and L-serine. There are species differences in the utilization of agmatine, citrulline, cysteine, histidine, the aromatic amino acids, and polyamines (putrescine and spermidine). Regardless of the pathway of glutamate synthesis, nitrogen source catabolism must generate ammonia for glutamine synthesis. Loss of glutamate synthase (glutamineoxoglutarate amidotransferase, or GOGAT) prevents utilization of many organic nitrogen sources. Mutations that create or increase a requirement for ammonia also prevent utilization of most organic nitrogen sources.
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18
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Hampel A, Huber C, Geffers R, Spona-Friedl M, Eisenreich W, Bange FC. Mycobacterium tuberculosis Is a Natural Ornithine Aminotransferase (rocD) Mutant and Depends on Rv2323c for Growth on Arginine. PLoS One 2015; 10:e0136914. [PMID: 26368558 PMCID: PMC4569260 DOI: 10.1371/journal.pone.0136914] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 08/10/2015] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) possesses a genetic repertoire for metabolic pathways, which are specific and fit to its intracellular life style. Under in vitro conditions, Mtb is known to use arginine as a nitrogen source, but the metabolic pathways for arginine utilization have not been identified. Here we show that, in the presence of arginine, Mtb upregulates a gene cluster which includes an ornithine aminotransferase (rocD) and Rv2323c, a gene of unknown function. Isotopologue analysis by using 13C- or 15N-arginine revealed that in Mtb arginine is not only used as nitrogen source but also as carbon source for the formation of amino acids, in particular of proline. Surprisingly, rocD, which is widespread in other bacteria and is part of the classical arginase pathway turned out to be naturally deleted in Mtb, but not in non-tuberculous mycobacteria. Mtb lacking Rv2323c showed a growth defect on arginine, did not produce proline from arginine, and incorporated less nitrogen derived from arginine in its core nitrogen metabolism. We conclude that the highly induced pathway for arginine utilization in Mtb differs from that of other bacteria including non-tuberculous mycobacteria, probably reflecting a specific metabolic feature of intracellular Mtb.
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Affiliation(s)
- Annegret Hampel
- Department of Medical Microbiology and Hospital Epidemiology, Medical School Hannover, 30625 Hanover, Germany
| | - Claudia Huber
- Lehrstuhl für Biochemie, Technische Universität München, Garching, Germany
| | - Robert Geffers
- Research Group Genome Analytics, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany
| | | | | | - Franz-Christoph Bange
- Department of Medical Microbiology and Hospital Epidemiology, Medical School Hannover, 30625 Hanover, Germany
- * E-mail:
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19
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Walker MC, van der Donk WA. The many roles of glutamate in metabolism. J Ind Microbiol Biotechnol 2015; 43:419-30. [PMID: 26323613 DOI: 10.1007/s10295-015-1665-y] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 07/25/2015] [Indexed: 12/20/2022]
Abstract
The amino acid glutamate is a major metabolic hub in many organisms and as such is involved in diverse processes in addition to its role in protein synthesis. Nitrogen assimilation, nucleotide, amino acid, and cofactor biosynthesis, as well as secondary natural product formation all utilize glutamate in some manner. Glutamate also plays a role in the catabolism of certain amines. Understanding glutamate's role in these various processes can aid in genome mining for novel metabolic pathways or the engineering of pathways for bioremediation or chemical production of valuable compounds.
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Affiliation(s)
- Mark C Walker
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA.
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20
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Steffen-Munsberg F, Vickers C, Kohls H, Land H, Mallin H, Nobili A, Skalden L, van den Bergh T, Joosten HJ, Berglund P, Höhne M, Bornscheuer UT. Bioinformatic analysis of a PLP-dependent enzyme superfamily suitable for biocatalytic applications. Biotechnol Adv 2015; 33:566-604. [PMID: 25575689 DOI: 10.1016/j.biotechadv.2014.12.012] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 12/16/2014] [Accepted: 12/17/2014] [Indexed: 01/25/2023]
Abstract
In this review we analyse structure/sequence-function relationships for the superfamily of PLP-dependent enzymes with special emphasis on class III transaminases. Amine transaminases are highly important for applications in biocatalysis in the synthesis of chiral amines. In addition, other enzyme activities such as racemases or decarboxylases are also discussed. The substrate scope and the ability to accept chemically different types of substrates are shown to be reflected in conserved patterns of amino acids around the active site. These findings are condensed in a sequence-function matrix, which facilitates annotation and identification of biocatalytically relevant enzymes and protein engineering thereof.
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Affiliation(s)
- Fabian Steffen-Munsberg
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany; KTH Royal Institute of Technology, School of Biotechnology, Division of Industrial Biotechnology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Clare Vickers
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Hannes Kohls
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany; Protein Biochemistry, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Henrik Land
- KTH Royal Institute of Technology, School of Biotechnology, Division of Industrial Biotechnology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Hendrik Mallin
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Alberto Nobili
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Lilly Skalden
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Tom van den Bergh
- Bio-Prodict, Nieuwe Marktstraat 54E, 6511 AA Nijmegen, The Netherlands
| | - Henk-Jan Joosten
- Bio-Prodict, Nieuwe Marktstraat 54E, 6511 AA Nijmegen, The Netherlands
| | - Per Berglund
- KTH Royal Institute of Technology, School of Biotechnology, Division of Industrial Biotechnology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Matthias Höhne
- Protein Biochemistry, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany.
| | - Uwe T Bornscheuer
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany.
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21
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Kim YS, Shin HC, Lee JH. Two mechanisms for putrescine-dependent transcriptional expression of the putrescine aminotransferase gene, ygjG, in Escherichia coli. Arch Microbiol 2014; 196:611-8. [PMID: 24906570 DOI: 10.1007/s00203-014-0991-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 04/27/2014] [Accepted: 05/06/2014] [Indexed: 01/26/2023]
Abstract
In this study, on evaluating the physiological function and mechanism of putrescine, we found that putrescine supplementation (1 mM) increases transcription of the putrescine aminotransferase gene, ygjG. Putrescine-dependent expression was confirmed by measuring β-galactosidase activity and with reverse transcription-polymerase chain reaction. To understand the role of putrescine in ygjG expression, we genetically characterized and found that a knockout mutation in an alternative sigma factor, rpoS, abolished putrescine-dependent ygjG-lacZ expression. In the rpoS mutant, RpoS overexpression complemented the mutant phenotype. However, RpoS overexpression induced ygjG-lacZ expression with putrescine supplementation but not without supplementation. We also found that the loss of putrescine-dependent ygjG-lacZ expression induced by rpoS was completely restored under nitrogen-starvation conditions. The putrescine-dependent expression of ygjG-lacZ under this condition was clearly dependent on another alternative sigma factor, rpoN, and its cognate activator ntrC. These results show that rpoS is required for putrescine-dependent ygjG-lacZ expression, but the effect of putrescine on this expression is not caused by simple modulation of RpoS synthesis. Putrescine-dependent expression of ygjG-lacZ was controlled by at least two sigma factors: rpoS under excess nitrogen conditions and rpoN under nitrogen-starvation conditions. These results suggest that putrescine plays an important role in the nitrogen regulation system.
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Affiliation(s)
- Young-Sik Kim
- Department of Biological Science, Sungkyunkwan University, Suwon, 440-746, Korea,
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22
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Foster A, Barnes N, Speight R, Keane MA. Genomic organisation, activity and distribution analysis of the microbial putrescine oxidase degradation pathway. Syst Appl Microbiol 2013; 36:457-66. [DOI: 10.1016/j.syapm.2013.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 06/25/2013] [Accepted: 06/28/2013] [Indexed: 12/29/2022]
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GC–MS-based metabolomics study of the responses to arachidonic acid in Blakeslea trispora. Fungal Genet Biol 2013; 57:33-41. [DOI: 10.1016/j.fgb.2013.06.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 05/19/2013] [Accepted: 06/04/2013] [Indexed: 11/15/2022]
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24
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Foster A, Barnes N, Speight R, Morris PC, Keane MA. Role of amine oxidase expression to maintain putrescine homeostasis in Rhodococcus opacus. Enzyme Microb Technol 2013; 52:286-95. [DOI: 10.1016/j.enzmictec.2013.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 12/12/2012] [Accepted: 01/07/2013] [Indexed: 10/27/2022]
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Investigation of proteomic responses of Streptomyces lydicus to pitching ratios for improving streptolydigin production. BIOTECHNOL BIOPROC E 2012. [DOI: 10.1007/s12257-012-0173-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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26
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Abstract
Putrescine as the sole carbon source requires a novel catabolic pathway with glutamylated intermediates. Nitrogen limitation does not induce genes of this glutamylated putrescine (GP) pathway but instead induces genes for a putrescine catabolic pathway that starts with a transaminase-dependent deamination. We determined pathway utilization with putrescine as the sole nitrogen source by examining mutants with defects in both pathways. Blocks in both the GP and transaminase pathways were required to prevent growth with putrescine as the sole nitrogen source. Genetic and biochemical analyses showed redundant enzymes for γ-aminobutyraldehyde dehydrogenase (PatD/YdcW and PuuC), γ-aminobutyrate transaminase (GabT and PuuE), and succinic semialdehyde dehydrogenase (GabD and PuuC). PuuC is a nonspecific aldehyde dehydrogenase that oxidizes all the aldehydes in putrescine catabolism. A puuP mutant failed to use putrescine as the nitrogen source, which implies one major transporter for putrescine as the sole nitrogen source. Analysis of regulation of the GP pathway shows induction by putrescine and not by a product of putrescine catabolism and shows that putrescine accumulates in puuA, puuB, and puuC mutants but not in any other mutant. We conclude that two independent sets of enzymes can completely degrade putrescine to succinate and that their relative importance depends on the environment.
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Effects of Sodium Octanoate, Acylated Ghrelin, and Desacylated Ghrelin on the Growth of Genetically Engineered Escherichia Coli. J Med Biochem 2011. [DOI: 10.2478/v10011-011-0020-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Effects of Sodium Octanoate, Acylated Ghrelin, and Desacylated Ghrelin on the Growth of Genetically EngineeredEscherichia ColiAcylated ghrelin is a 28-amino acid peptide hormone bearing a fatty acid group based on octanoic acid (caprylic acid) at the serine which is located at position 3 and at the N-terminus. If this fatty acid is cleaved from acylated ghrelin, the remaining peptide is referred to as desacylated ghrelin. Free fatty acids (FFAs) can kill or inhibit the growth of bacteria. The purpose of this study was to test this ability using acylated ghrelin, desacylated ghrelin, and sodium octanoate (caprylic acid) as carbon sources for the genetically engineeredEscherichia colistrains MK79 and MK57. For this experimental work, minimal medium was modified by replacing glucose with equal concentrations of acylated ghrelin, desacylated ghrelin, or sodium octanoate. Bacterial optical density, viability, alpha-amylase production, plasmid stability and pH of the growth medium were measured during these experiments. The media that allowed most growth, based on viable cell counts and the OD600of MK79, was minimal medium, followed by the medium containing desacylated ghrelin or acylated ghrelin, and finally the medium containing sodium octanoate. The same order was observed for MK57. Neither of the strains lost plasmids during the entire course of each experiment. There was also little change in the pH of any of the media used for both strains. These results suggest that sodium octanoate, acylated ghrelin, and desacylated ghrelin, when compared with minimal medium, inhibitEscherichia coligrowth. Proliferation was lowest when sodium octanoate was used as the carbon source, followed by acylated ghrelin and desacylated ghrelin. Therefore, the acylated ghrelin found previously in human saliva might help to inhibit pathogenic microorganisms, and acylated ghrelin levels below a critical concentration in saliva could result in an increased risk of oral infection.
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28
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Regulatory role for l-arginine in the utilization of amino acids by pig small-intestinal bacteria. Amino Acids 2011; 43:233-44. [DOI: 10.1007/s00726-011-1067-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 08/25/2011] [Indexed: 12/16/2022]
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29
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Schneider J, Wendisch VF. Biotechnological production of polyamines by bacteria: recent achievements and future perspectives. Appl Microbiol Biotechnol 2011; 91:17-30. [PMID: 21552989 DOI: 10.1007/s00253-011-3252-0] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 03/14/2011] [Accepted: 03/14/2011] [Indexed: 11/26/2022]
Abstract
In Bacteria, the pathways of polyamine biosynthesis start with the amino acids L-lysine, L-ornithine, L-arginine, or L-aspartic acid. Some of these polyamines are of special interest due to their use in the production of engineering plastics (e.g., polyamides) or as curing agents in polymer applications. At present, the polyamines for industrial use are mainly synthesized on chemical routes. However, since a commercial market for polyamines as well as an industry for the fermentative production of amino acid exist, and since bacterial strains overproducing the polyamine precursors L-lysine, L-ornithine, and L-arginine are known, it was envisioned to engineer these amino acid-producing strains for polyamine production. Only recently, researchers have investigated the potential of amino acid-producing strains of Corynebacterium glutamicum and Escherichia coli for polyamine production. This mini-review illustrates the current knowledge of polyamine metabolism in Bacteria, including anabolism, catabolism, uptake, and excretion. The recent advances in engineering the industrial model bacteria C. glutamicum and E. coli for efficient production of the most promising polyamines, putrescine (1,4-diaminobutane), and cadaverine (1,5-diaminopentane), are discussed in more detail.
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Affiliation(s)
- Jens Schneider
- Genetics of Prokaryotes, Department of Biology & CeBiTec, Bielefeld University, Bielefeld, Germany
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Blachier F, Mariotti F, Huneau JF, Tomé D. Effects of amino acid-derived luminal metabolites on the colonic epithelium and physiopathological consequences. Amino Acids 2006; 33:547-62. [PMID: 17146590 DOI: 10.1007/s00726-006-0477-9] [Citation(s) in RCA: 301] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Accepted: 11/09/2006] [Indexed: 02/07/2023]
Abstract
Depending on the amount of alimentary proteins, between 6 and 18 g nitrogenous material per day enter the large intestine lumen through the ileocaecal junction. This material is used as substrates by the flora resulting eventually in the presence of a complex mixture of metabolites including ammonia, hydrogen sulfide, short and branched-chain fatty acids, amines; phenolic, indolic and N-nitroso compounds. The beneficial versus deleterious effects of these compounds on the colonic epithelium depend on parameters such as their luminal concentrations, the duration of the colonic stasis, the detoxication capacity of epithelial cells in response to increase of metabolite concentrations, the cellular metabolic utilization of these metabolites as well as their effects on colonocyte intermediary and oxidative metabolism. Furthermore, the effects of metabolites on electrolyte movements through the colonic epithelium must as well be taken into consideration for such an evaluation. The situation is further complicated by the fact that other non-nitrogenous compounds are believed to interfere with these various phenomenons. Finally, the pathological consequences of the presence of excessive concentrations of these compounds are related to the short- and, most important, long-term effects of these compounds on the rapid colonic epithelium renewing and homeostasis.
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Affiliation(s)
- F Blachier
- Unité Mixte de Recherche de Physiologie de la Nutrition et du Comportement Alimentaire, Institut National de la Recherche Agronomique - Institut National Agronomique Paris-Grignon, Paris, France.
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Meyer A, Eskandari S, Grallath S, Rentsch D. AtGAT1, a high affinity transporter for gamma-aminobutyric acid in Arabidopsis thaliana. J Biol Chem 2006; 281:7197-204. [PMID: 16407306 PMCID: PMC3009663 DOI: 10.1074/jbc.m510766200] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Functional characterization of Arabidopsis thaliana GAT1 in heterologous expression systems, i.e. Saccharomyces cerevisiae and Xenopus laevis oocytes, revealed that AtGAT1 (At1g08230) codes for an H(+)-driven, high affinity gamma-aminobutyric acid (GABA) transporter. In addition to GABA, other omega-aminofatty acids and butylamine are recognized. In contrast to the most closely related proteins of the proline transporter family, proline and glycine betaine are not transported by AtGAT1. AtGAT1 does not share sequence similarity with any of the non-plant GABA transporters described so far, and analyses of substrate selectivity and kinetic properties showed that AtGAT1-mediated transport is similar but distinct from that of mammalian, bacterial, and S. cerevisiae GABA transporters. Consistent with a role in GABA uptake into cells, transient expression of AtGAT1/green fluorescent protein fusion proteins in tobacco protoplasts revealed localization at the plasma membrane. In planta, AtGAT1 expression was highest in flowers and under conditions of elevated GABA concentrations such as wounding or senescence.
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Affiliation(s)
- Andreas Meyer
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Sepehr Eskandari
- Biological Sciences Department, California State Polytechnic University, Pomona, California 91768-4032
| | - Silke Grallath
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Doris Rentsch
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
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Llewellyn NM, Spencer JB. Biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics. Nat Prod Rep 2006; 23:864-74. [PMID: 17119636 DOI: 10.1039/b604709m] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The 2-deoxystreptamine-containing aminoglycosides are an important class of clinically valuable antibiotics. A deep understanding of the biosynthesis of these natural products is required to enable efforts to rationally manipulate and engineer the biological production of novel aminoglycosides. This review discusses the development of our biosynthetic knowledge over the past half-century, with emphasis on the relatively recent contributions of molecular biology to the elucidation of these biosynthetic pathways.
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Affiliation(s)
- Nicholas M Llewellyn
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UKCB2 1EW.
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Samsonova NN, Smirnov SV, Novikova AE, Ptitsyn LR. Identification ofEscherichia coliK12 YdcW protein as a γ-aminobutyraldehyde dehydrogenase. FEBS Lett 2005; 579:4107-12. [PMID: 16023116 DOI: 10.1016/j.febslet.2005.06.038] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2005] [Revised: 06/17/2005] [Accepted: 06/17/2005] [Indexed: 10/25/2022]
Abstract
Gamma-aminobutyraldehyde dehydrogenase (ABALDH) from wild-type E. coli K12 was purified to apparent homogeneity and identified as YdcW by MS-analysis. YdcW exists as a tetramer of 202+/-29 kDa in the native state, a molecular mass of one subunit was determined as 51+/-3 kDa. Km parameters of YdcW for gamma-aminobutyraldehyde, NAD+ and NADP+ were 41+/-7, 54+/-10 and 484+/-72 microM, respectively. YdcW is the unique ABALDH in E. coli K12. A coupling action of E. coli YgjG putrescine transaminase and YdcW dehydrogenase in vitro resulted in conversion of putrescine into gamma-aminobutyric acid.
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Affiliation(s)
- Natalya N Samsonova
- Ajinomoto-Genetika Research Institute, 1st Dorozhny pr. 1, Moscow 117545, Russia.
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Michel-Reydellet N, Calhoun K, Swartz J. Amino acid stabilization for cell-free protein synthesis by modification of the Escherichia coli genome. Metab Eng 2005; 6:197-203. [PMID: 15256209 DOI: 10.1016/j.ymben.2004.01.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2003] [Accepted: 01/16/2004] [Indexed: 11/24/2022]
Abstract
Cell-free biology provides a unique opportunity to assess and to manipulate microbial systems by inverse metabolic engineering. We have applied this approach to amino acid metabolism, one of the systems in cell-free biology that limits protein synthesis reactions. Four amino acids (arginine, tryptophan, serine and cysteine) are depleted during a 3-h batch cell-free protein synthesis reaction under various conditions. By modifying the genome of the Escherichia coli strain used to make the cell extract, we see significant stabilization of arginine, tryptophan and serine. Cysteine, however, continues to be degraded. Cell-free protein synthesis with the modified cell extract produces increased yields of the cysteine-free protein Outer Membrane Protein T (OmpT).
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Kurihara S, Oda S, Kato K, Kim HG, Koyanagi T, Kumagai H, Suzuki H. A novel putrescine utilization pathway involves gamma-glutamylated intermediates of Escherichia coli K-12. J Biol Chem 2004; 280:4602-8. [PMID: 15590624 DOI: 10.1074/jbc.m411114200] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A novel bacterial putrescine utilization pathway was discovered. Seven genes, the functions of whose products were not known, are involved in this novel pathway. Five of them encode enzymes that catabolize putrescine; one encodes a putrescine importer, and the other encodes a transcriptional regulator. This novel pathway involves six sequential steps as follows: 1) import of putrescine; 2) ATP-dependent gamma-glutamylation of putrescine; 3) oxidization of gamma-glutamylputrescine; 4) dehydrogenation of gamma-glutamyl-gamma-aminobutyraldehyde; 5) hydrolysis of the gamma-glutamyl linkage of gamma-glutamyl-gamma-aminobutyrate; and 6) transamination of gamma-aminobutyrate to form the final product of this pathway, succinate semialdehyde, which is the precursor of succinate.
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Affiliation(s)
- Shin Kurihara
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
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Samsonova NN, Smirnov SV, Altman IB, Ptitsyn LR. Molecular cloning and characterization of Escherichia coli K12 ygjG gene. BMC Microbiol 2003; 3:2. [PMID: 12617754 PMCID: PMC150594 DOI: 10.1186/1471-2180-3-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2002] [Accepted: 01/31/2003] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND Putrescine is the intermediate product of arginine decarboxylase pathway in Escherichia coli which can be used as an alternative nitrogen source. Transaminase and dehydrogenase enzymes seem to be implicated in the degradative pathway of putrescine, in which this compound is converted into gamma-aminobutyrate. But genes coding for these enzymes have not been identified so far. RESULTS The 1.8-kbp DNA fragment containing E. coli K12 ygjG gene with aer-ygjG intergenic region was examined. It was found that the fragment contains sigma54-depended open reading frame (ORF) of 1,380 nucleotides encoding a 459-amino acid polypeptide of approximately 49.6 kDa. The cytidine (C) residue localized 10 bp downstream of the sigma54 promoter sequence was identified as the first mRNA base. The UUG translation initiation codon is situated 36 nucleotides downstream of the mRNA start. The YgjG was expressed as a his6-tag fused protein and purified to homogeneity. The protein catalyzed putrescine:2-oxoglutaric acid (2-OG) aminotransferase reaction (PATase, EC 2.6.1.29). The Km values for putrescine and 2-OG were found to be 9.2 mM and 19.0 mM, respectively. The recombinant enzyme also was able to transaminate cadaverine and, in lower extent, spermidine, and gave maximum activity at pH 9.0. CONCLUSION Expression of E. coli K12 ygjG coding region revealed sigma54-depended ORF which encodes a 459-amino acid protein with putrescine:2-OG aminotransferase activity. The enzyme also was able to transaminate cadaverine and, in lower extent, spermidine.
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Affiliation(s)
- Natalya N Samsonova
- Ajinomoto-Genetika Research Institute, 1Dorozhny pr. 1, Moscow, 113545, Russia
| | - Sergey V Smirnov
- Ajinomoto-Genetika Research Institute, 1Dorozhny pr. 1, Moscow, 113545, Russia
| | - Irina B Altman
- Ajinomoto-Genetika Research Institute, 1Dorozhny pr. 1, Moscow, 113545, Russia
| | - Leonid R Ptitsyn
- Ajinomoto-Genetika Research Institute, 1Dorozhny pr. 1, Moscow, 113545, Russia
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Schneider BL, Ruback S, Kiupakis AK, Kasbarian H, Pybus C, Reitzer L. The Escherichia coli gabDTPC operon: specific gamma-aminobutyrate catabolism and nonspecific induction. J Bacteriol 2002; 184:6976-86. [PMID: 12446648 PMCID: PMC135471 DOI: 10.1128/jb.184.24.6976-6986.2002] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nitrogen limitation induces the nitrogen-regulated (Ntr) response, which includes proteins that assimilate ammonia and scavenge nitrogen. Nitrogen limitation also induces catabolic pathways that degrade four metabolically related compounds: putrescine, arginine, ornithine, and gamma-aminobutyrate (GABA). We analyzed the structure, function, and regulation of the gab operon, whose products degrade GABA, a proposed intermediate in putrescine catabolism. We showed that the gabDTPC gene cluster constitutes an operon based partially on coregulation of GabT and GabD activities and the polarity of an insertion in gabT on gabC. A DeltagabDT mutant grew normally on all of the nitrogen sources tested except GABA. The unexpected growth with putrescine resulted from specific induction of gab-independent enzymes. Nac was required for gab transcription in vivo and in vitro. Ntr induction did not require GABA, but various nitrogen sources did not induce enzyme activity equally. A gabC (formerly ygaE) mutant grew faster with GABA and had elevated levels of gab operon products, which suggests that GabC is a repressor. GabC is proposed to reduce nitrogen source-specific modulation of expression. Unlike a wild-type strain, a gabC mutant utilized GABA as a carbon source and such growth required sigma(S). Previous studies showing sigma(S)-dependent gab expression in stationary phase involved gabC mutants, which suggests that such expression does not occur in wild-type strains. The seemingly narrow catabolic function of the gab operon is contrasted with the nonspecific (nitrogen source-independent) induction. We propose that the gab operon and the Ntr response itself contribute to putrescine and polyamine homeostasis.
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Affiliation(s)
- Barbara L Schneider
- Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson 75083-0688, USA
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Lu CD, Itoh Y, Nakada Y, Jiang Y. Functional analysis and regulation of the divergent spuABCDEFGH-spuI operons for polyamine uptake and utilization in Pseudomonas aeruginosa PAO1. J Bacteriol 2002; 184:3765-73. [PMID: 12081945 PMCID: PMC135167 DOI: 10.1128/jb.184.14.3765-3773.2002] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A multiple-gene locus for polyamine uptake and utilization was discovered in Pseudomonas aeruginosa PAO1. This locus contained nine genes designated spuABCDEFGHI (spu for spermidine and putrescine utilization). The physiological functions of the spu genes in utilization of two polyamines (putrescine and spermidine) were analyzed by using Tn5 transposon-mediated spu knockout mutants. Growth and uptake experiments support that the spuDEFGH genes specify components of a major ABC-type transport system for spermidine uptake, and enzymatic measurements indicated that spuC encodes putrescine aminotransferase with pyruvate as the amino group receptor. Although spuA and spuB mutants showed an apparent defect in spermidine utilization, the biochemical functions of the gene products have yet to be elucidated. Assays of lacZ fusions demonstrated the presence of agmatine-, putrescine-, and spermidine-inducible promoters for the spuABCDEFGH operon and the divergently transcribed spuI gene of unknown function. Since the observed induction effect of agmatine was abolished in an aguA mutant where conversion of agmatine into putrescine was blocked, putrescine or spermidine, but not agmatine, serves as the inducer molecule of the spuA-spuI divergent promoters. S1 nuclease mappings confirmed further the induction effects of the polyamines on transcription of the divergent promoters and localized the transcription initiation sites. Gel retardation assays with extracts from the cells grown on putrescine or spermidine demonstrated the presence of a polyamine-responsive regulatory protein interacting with the divergent promoter region. Finally, the absence of the putrescine-inducible spuA expression and putrescine aminotransferase (spuC) formation in the cbrB mutant indicated that the spu operons are regulated by the global CbrAB two-component system perhaps via the putative polyamine-responsive transcriptional activator.
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Affiliation(s)
- Chung-Dar Lu
- Department of Biology, Georgia State University, Atlanta 30303, USA
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Abstract
This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.
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Affiliation(s)
- M K Berlyn
- Department of Biology and School of Forestry and Environmental Studies, Yale University, New Haven, Connecticut 06520-8104, USA.
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40
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Schneider BL, Kiupakis AK, Reitzer LJ. Arginine catabolism and the arginine succinyltransferase pathway in Escherichia coli. J Bacteriol 1998; 180:4278-86. [PMID: 9696779 PMCID: PMC107427 DOI: 10.1128/jb.180.16.4278-4286.1998] [Citation(s) in RCA: 116] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/1997] [Accepted: 06/03/1998] [Indexed: 11/20/2022] Open
Abstract
Arginine catabolism produces ammonia without transferring nitrogen to another compound, yet the only known pathway of arginine catabolism in Escherichia coli (through arginine decarboxylase) does not produce ammonia. Our aims were to find the ammonia-producing pathway of arginine catabolism in E. coli and to examine its function. We showed that the only previously described pathway of arginine catabolism, which does not produce ammonia, accounted for only 3% of the arginine consumed. A search for another arginine catabolic pathway led to discovery of the ammonia-producing arginine succinyltransferase (AST) pathway in E. coli. Nitrogen limitation induced this pathway in both E. coli and Klebsiella aerogenes, but the mechanisms of activation clearly differed in these two organisms. We identified the E. coli gene for succinylornithine aminotransferase, the third enzyme of the AST pathway, which appears to be the first of an astCADBE operon. Its disruption prevented arginine catabolism, impaired ornithine utilization, and affected the synthesis of all the enzymes of the AST pathway. Disruption of astB eliminated succinylarginine dihydrolase activity and prevented arginine utilization but did not impair ornithine catabolism. Overproduction of AST enzymes resulted in faster growth with arginine and aspartate. We conclude that the AST pathway is necessary for aerobic arginine catabolism in E. coli and that at least one enzyme of this pathway contributes to ornithine catabolism.
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Affiliation(s)
- B L Schneider
- Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, Texas 75083-0688, USA
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41
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Abstract
The sequence (2,700 bp) between the aldH and pspF genes of Escherichia coli was determined. The pspF gene encodes a sigma54 transcriptional activator of the phage shock protein (psp) operon (pspA to pspE). Downstream of the pspF transcribed region are two open reading frames (ORFs), ordL and goaG, convergently oriented with respect to pspF. These two ORFs, together with the adjacent aldH gene, may constitute a novel operon (aldH-ordL-goaG). The goaG-pspF intergenic region contains a complex extragenic mosaic element, RIB. The structure of this RIB element, which belongs to the BIME-1 family, is Y(REP1) > 16 < Z1(REP2), where Y and Z1 are palindromic units and the central 16 bases contain an L motif with an ihf consensus sequence. DNA fragments containing the L motif of the psp RIB element effectively bind integration host factor (IHF), while the Y palindromic unit (REP1) of the same RIB element binds DNA gyrase weakly. Computer prediction of the pspF mRNA secondary structure suggested that the transcribed stem-loop structures formed by the 3'-flanking region of the pspF transcript containing the RIB element can stabilize and protect pspF mRNA. Analysis of pspF steady-state mRNA levels showed that transcripts with an intact RIB element are much more abundant than those truncated at the 3' end by deletion of either the entire RIB element or a single Z1 sequence (REP2). Thus, the pspF 3'-flanking region containing the RIB element has an important role in the stabilization of the pspF transcript.
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Affiliation(s)
- G Jovanovic
- Laboratory of Genetics, Rockefeller University, New York 10021, USA
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Calvo JM, Matthews RG. The leucine-responsive regulatory protein, a global regulator of metabolism in Escherichia coli. Microbiol Rev 1994; 58:466-90. [PMID: 7968922 PMCID: PMC372976 DOI: 10.1128/mr.58.3.466-490.1994] [Citation(s) in RCA: 251] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The leucine-responsive regulatory protein (Lrp) regulates the expression of more than 40 genes and proteins in Escherichia coli. Among the operons that are positively regulated by Lrp are operons involved in amino acid biosynthesis (ilvIH, serA)), in the biosynthesis of pili (pap, fan, fim), and in the assimilation of ammonia (glnA, gltBD). Negatively regulated operons include operons involved in amino acid catabolism (sdaA, tdh) and peptide transport (opp) and the operon coding for Lrp itself (lrp). Detailed studies of a few members of the regulon have shown that Lrp can act directly to activate or repress transcription of target operons. A substantial fraction of operons regulated by Lrp are also regulated by leucine, and the effect of leucine on expression of these operons requires a functional Lrp protein. The patterns of regulation are surprising and interesting: in some cases activation or repression mediated by Lrp is antagonized by leucine, in other cases Lrp-mediated activation or repression is potentiated by leucine, and in still other cases leucine has no effect on Lrp-mediated regulation. Current research is just beginning to elucidate the detailed mechanisms by which Lrp can mediate such a broad spectrum of regulatory effects. Our view of the role of Lrp in metabolism may change as more members of the regulon are identified and their regulation characterized, but at this point Lrp seems to be important in regulating nitrogen metabolism and one-carbon metabolism, permitting adaptations to feast and to famine.
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Affiliation(s)
- J M Calvo
- Section of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853
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Abstract
The information currently available on the breakdown of spermidine and putrescine by microorganisms is reviewed. Two major metabolic routes have been described, one for the free bases via delta 1-pyrroline (4-aminobutyraldehyde), the other via N-acetyl derivatives. In both pathways oxidases or aminotransferases are the key enzymes in removing the nitrogen atoms. The two routes converge at 4-aminobutyrate, which is then metabolized via succinate. The degradation of putrescine in Escherichia coli has been well characterized at both genetic and biochemical levels, but for other bacteria much less information is available. The C3 moiety of spermidine is broken down via beta-alanine, but the metabolism of this compound and its precursors is poorly understood. In yeasts, a catabolic route for spermidine and putrescine via N-acetyl derivatives has been described in Candida boidinii, and the evidence for its occurrence in other species is reviewed. Except for the terminal step of this pathway, the same group of enzymes can metabolize both the C3 and C4 moieties of spermidine. It is likely that other routes of polyamine catabolism also exist in both bacteria and yeasts.
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Affiliation(s)
- P J Large
- Department of Applied Biology, University of Hull, UK
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Moreno-Vivián C, Soler G, Castillo F. Arginine catabolism in the phototrophic bacterium Rhodobacter capsulatus E1F1. Purification and properties of arginase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 204:531-7. [PMID: 1541268 DOI: 10.1111/j.1432-1033.1992.tb16664.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The phototrophic bacterium Rhodobacter capsulatus E1F1 grew with L-arginine or L-homoarginine as nitrogen source under light/anaerobiosis. However, when L-arginine was used as the only source of both carbon and nitrogen, the bacterium exhibited weak growth levels and the excess of nitrogen was excreted to the medium as ammonia. By contrast, L-ornithine was used under phototrophic conditions as either nitrogen or carbon source. Other compounds of the arginine catabolic pathways, such as putrescine or proline, also supported phototrophic growth of this bacterium. Under heterotrophic/dark conditions, R. capsulatus always showed a low growth rate with those nitrogen compounds. Cells growing on media containing L-arginine, L-homoarginine or L-ornithine induced an Mn(2+)-dependent arginase activity regardless of the presence of ammonium ions and other readily utilizable nitrogen sources. Arginase activity was strongly inhibited by Zn2+, Cu2+, borate, L-cysteine, L-ornithine and gamma-guanidinobutyrate. Mercurials also inactivated arginase, the activity being partially restored by the presence of thiols. Arginase was purified to electrophoretic homogeneity and found to consist of four identical subunits of 31 kDa. The molecular parameters and kinetic constants of arginase from R. capsulatus E1F1 resembled those previously described for the Saccharomyces cerevisiae enzyme rather than those of bacterial arginases.
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Affiliation(s)
- C Moreno-Vivián
- Departamento de Bioquímica, Facultad de Ciencias, Universidad de Córdoba, Spain
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Quintilla FX, Baldoma L, Badia J, Aguilar J. Aldehyde dehydrogenase induction by glutamate in Escherichia coli. Role of 2-oxoglutarate. EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 202:1321-5. [PMID: 1684935 DOI: 10.1111/j.1432-1033.1991.tb16506.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In Escherichia coli, an aldehyde dehydrogenase that catalyzes the oxidation of L-lactaldehyde to L-lactate is induced not only by L-fucose, L-rhamnose or D-arabinose, but also by growth in the presence of glutamate or amino acids yielding glutamate, with the exception of proline. Induction by these amino acids requires glutamate accumulation. 4-Aminobutyric acid also induces this aldehyde dehydrogenase through its transamination to glutamate. Growth on 2-oxoglutarate, the tricarboxylic acid cycle intermediate with which glutamate is in equilibrium, also induces this aldehyde dehydrogenase. Conditions in which the conversion of 2-oxoglutarate into glutamate is highly restricted displayed unchanged rates of induction by 2-oxoglutarate, indicating that glutamate induces the aldehyde dehydrogenase through 2-oxoglutarate formation. Evidence is presented showing that L-fucose- and 2-oxoglutarate-inducing systems share the same regulatory protein. Induction by growth on either of these two compounds is repressed both by glucose and by glycerol. Addition of cAMP to these cultures partially recovers the glucose-repressed aldehyde dehydrogenase activity, while this nucleotide has no effect on the glycerol-mediated repression. These results indicate that ald is under carbon regulation mediated by at least two different mechanisms.
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Affiliation(s)
- F X Quintilla
- Department of Biochemistry, Faculty of Pharmacy, University of Barcelona, Spain
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Metzer E, Halpern YS. In vivo cloning and characterization of the gabCTDP gene cluster of Escherichia coli K-12. J Bacteriol 1990; 172:3250-6. [PMID: 2188954 PMCID: PMC209132 DOI: 10.1128/jb.172.6.3250-3256.1990] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The gabCTDP gene cluster, which specifies and regulates synthesis of the gamma-aminobutyrate (GABA) transport carrier, of glutamate-succinic semialdehyde transaminase, and of succinic semialdehyde dehydrogenase, responsible for the uptake and metabolism of gamma-aminobutyric acid in Escherichia coli K-12, was cloned in vivo, using the mini-Mu replicon bacteriophage Mu dI5086 as the vector. A subclone containing a 7.8-kilobase (kb) EcoRI-HindIII fragment complemented all of our Gab- mutants. By restriction mapping, this DNA fragment was located at kb 2800.5 to 2808.5 on the physical map of the E. coli K-12 chromosome. A subclone containing a 1.8-kb EcoRI-SalI fragment complemented the gab-repressed strain CS101A (wild-type gabC) but did not complement any gab structural gene mutants. The gab genes are divergently transcribed from promoters located in the vicinity of the unique BamHI site. Transcription in both directions is under dual control of catabolite repression and nitrogen regulation. Using a procaryotic DNA-directed translation system, we observed three insert-coded polypeptide bands of 53 to 55, 45 to 48, and 40 to 43 kilodaltons (kDa). In vivo studies with subcloned fragments of the gab DNA identified the 53- to 55- and 45- to 48-kDa bands as products of the BamHI-SalI fragment and the 40- to 43-kDa band as the product of the EcoRI-SalI fragment. An additional 26- to 28-kDa band was identified as the product of the BamHI-HindIII fragment. Furthermore, the BamHI-SalI fragment was shown to specify synthesis of the two GABA enzymes, whereas synthesis of the GABA carrier was specified by the BamHI-HindIII fragment. No catalytic function in addition to its regulatory role could be attributed to the EcoRI-SalI gene product.
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Affiliation(s)
- E Metzer
- Department of Molecular Biology, Hebrew University-Hadassah Medical School, Jerusalem, Israel
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Prieto-Santos MI, Martín-Checa J, Balaña-Fouce R, Garrido-Pertierra A. A pathway for putrescine catabolism in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA 1986; 880:242-4. [PMID: 3510672 DOI: 10.1016/0304-4165(86)90085-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Escherichia coli mutants able to grow in putrescine have been isolated from gamma-aminobutyrate mutants. These mutants show putrescine-alpha-ketoglutarate transaminase and gamma-aminobutyraldehyde dehydrogenase activities. Both enzymes have been characterized, the first of them showing an apparent Km for putrescine of 22.5 microM and the second an apparent Km of 37 microM for NAD and 18 microM for delta-1-pyrroline; the optimum pH values were 7.2 and 5.4, respectively, for the two enzymes.
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Shaibe E, Metzer E, Halpern YS. Control of utilization of L-arginine, L-ornithine, agmatine, and putrescine as nitrogen sources in Escherichia coli K-12. J Bacteriol 1985; 163:938-42. [PMID: 3897202 PMCID: PMC219223 DOI: 10.1128/jb.163.3.938-942.1985] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The regulation of the synthesis of the enzymes involved in the utilization of L-arginine, L-ornithine, agmatine, and putrescine as a sole nitrogen source in Escherichia coli K-12 was examined. The synthesis of agmatine ureohydrolase, putrescine aminotransferase, and pyrroline dehydrogenase is dually controlled by catabolite repression and nitrogen availability. Catabolite repression of agmatine ureohydrolase, but not that of putrescine aminotransferase or pyrroline dehydrogenase, is relieved by the addition of cAMP. Agmatine ureohydrolase synthesis in addition is subject to induction by L-arginine and agmatine. Arginine decarboxylase and ornithine decarboxylase synthesis is not sensitive to catabolite repression or to stimulation by nitrogen limitation or subject to substrate induction.
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