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Yang X, Zhang Y, Zhao G. Artificial carbon assimilation: From unnatural reactions and pathways to synthetic autotrophic systems. Biotechnol Adv 2024; 70:108294. [PMID: 38013126 DOI: 10.1016/j.biotechadv.2023.108294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/26/2023] [Accepted: 11/18/2023] [Indexed: 11/29/2023]
Abstract
Synthetic biology is being increasingly used to establish novel carbon assimilation pathways and artificial autotrophic strains that can be used in low-carbon biomanufacturing. Currently, artificial pathway design has made significant progress from advocacy to practice within a relatively short span of just over ten years. However, there is still huge scope for exploration of pathway diversity, operational efficiency, and host suitability. The accelerated research process will bring greater opportunities and challenges. In this paper, we provide a comprehensive summary and interpretation of representative one-carbon assimilation pathway designs and artificial autotrophic strain construction work. In addition, we propose some feasible design solutions based on existing research results and patterns to promote the development and application of artificial autotrophy.
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Affiliation(s)
- Xue Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China; Haihe Laboratory of Synthetic Biology, Tianjin 300308, China
| | - Yanfei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.
| | - Guoping Zhao
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China; CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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2
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Complete Genome Sequences of the Soil Oxalotrophic Bacterium Cupriavidus oxalaticus Strain Ox1 and Its Derived mCherry-Tagged Strain. Microbiol Resour Announc 2022; 11:e0018122. [PMID: 35924938 PMCID: PMC9476978 DOI: 10.1128/mra.00181-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report the complete genome sequences of the soil oxalotrophic bacterium Cupriavidus oxalaticus Ox1 and a derived mCherry-tagged strain. The genome size is approximately 6.69 Mb, with a GC content of 66.9%. The genome sequence of C. oxalaticus Ox1 contains a complete operon for the degradation and assimilation of oxalate.
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Liu M, Devlin JC, Hu J, Volkova A, Battaglia TW, Ho M, Asplin JR, Byrd A, Loke P, Li H, Ruggles KV, Tsirigos A, Blaser MJ, Nazzal L. Microbial genetic and transcriptional contributions to oxalate degradation by the gut microbiota in health and disease. eLife 2021; 10:e63642. [PMID: 33769280 PMCID: PMC8062136 DOI: 10.7554/elife.63642] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/23/2021] [Indexed: 12/14/2022] Open
Abstract
Over-accumulation of oxalate in humans may lead to nephrolithiasis and nephrocalcinosis. Humans lack endogenous oxalate degradation pathways (ODP), but intestinal microbes can degrade oxalate using multiple ODPs and protect against its absorption. The exact oxalate-degrading taxa in the human microbiota and their ODP have not been described. We leverage multi-omics data (>3000 samples from >1000 subjects) to show that the human microbiota primarily uses the type II ODP, rather than type I. Furthermore, among the diverse ODP-encoding microbes, an oxalate autotroph, Oxalobacter formigenes, dominates this function transcriptionally. Patients with inflammatory bowel disease (IBD) frequently suffer from disrupted oxalate homeostasis and calcium oxalate nephrolithiasis. We show that the enteric oxalate level is elevated in IBD patients, with highest levels in Crohn's disease (CD) patients with both ileal and colonic involvement consistent with known nephrolithiasis risk. We show that the microbiota ODP expression is reduced in IBD patients, which may contribute to the disrupted oxalate homeostasis. The specific changes in ODP expression by several important taxa suggest that they play distinct roles in IBD-induced nephrolithiasis risk. Lastly, we colonize mice that are maintained in the gnotobiotic facility with O. formigenes, using either a laboratory isolate or an isolate we cultured from human stools, and observed a significant reduction in host fecal and urine oxalate levels, supporting our in silico prediction of the importance of the microbiome, particularly O. formigenes in host oxalate homeostasis.
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Affiliation(s)
- Menghan Liu
- NYU Langone HealthNew YorkUnited States
- Vilcek Institute of Graduate Biomedical SciencesNew YorkUnited States
| | - Joseph C Devlin
- NYU Langone HealthNew YorkUnited States
- Vilcek Institute of Graduate Biomedical SciencesNew YorkUnited States
| | - Jiyuan Hu
- NYU Langone HealthNew YorkUnited States
| | - Angelina Volkova
- NYU Langone HealthNew YorkUnited States
- Vilcek Institute of Graduate Biomedical SciencesNew YorkUnited States
| | | | - Melody Ho
- NYU Langone HealthNew YorkUnited States
| | - John R Asplin
- Litholink Corporation, Laboratory Corporation of America HoldingsChicagoUnited States
| | - Allyson Byrd
- Department of Cancer Immunology, Genentech IncSouth San FranciscoUnited States
| | - P'ng Loke
- NYU Langone HealthNew YorkUnited States
| | - Huilin Li
- NYU Langone HealthNew YorkUnited States
| | | | | | - Martin J Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers UniversityNew YorkUnited States
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Microbial Community Analysis Provides Insights into the Effects of Tetrahydrofuran on 1,4-Dioxane Biodegradation. Appl Environ Microbiol 2019; 85:AEM.00244-19. [PMID: 30926731 DOI: 10.1128/aem.00244-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/20/2019] [Indexed: 11/20/2022] Open
Abstract
Tetrahydrofuran (THF) is known to induce the biodegradation of 1,4-dioxane (dioxane), an emerging contaminant, but the mechanisms by which THF affects dioxane biodegradation in microbial communities are not well understood. To fill this knowledge gap, changes in the microbial community structure in microcosm experiments with synthetic medium and landfill leachate were examined over time using 16S rRNA gene amplicon sequencing and functional gene quantitative PCR assays. The overarching hypothesis being tested was that THF promoted dioxane biodegradation by increasing the abundance of dioxane-degrading bacteria in the consortium. The data revealed that in experiments with synthetic medium, the addition of THF significantly increased the abundance of Pseudonocardia, a genus with several representatives that can grow on both dioxane and THF, and of Rhodococ cus ruber, a species that can use THF as the primary growth substrate while cometabolizing dioxane. However, in similar experiments with landfill leachate, only R. ruber was significantly enriched. When the THF concentration was higher than the dioxane concentration, THF competitively inhibited dioxane degradation since dioxane degradation was negligible, while the dioxane-degrading bacteria and the corresponding THF/dioxane monooxygenase gene copies increased by a few orders of magnitude.IMPORTANCE Widespread in groundwater and carcinogenic to humans, 1,4-dioxane (dioxane) is attracting significant attention in recent years. Advanced oxidation processes can effectively remove dioxane but require high energy consumption and operation costs. Biological removal of dioxane is of particular interest due to the ability of some bacteria to mineralize dioxane at a low energy cost. Although dioxane is generally considered recalcitrant to biodegradation, more than 20 types of bacteria can degrade dioxane as the sole electron donor substrate or the secondary electron donor substrate. In the latter case, tetrahydrofuran (THF) is commonly studied as the primary electron donor substrate. Previous work has shown that THF promotes dioxane degradation at a low THF concentration but inhibits dioxane degradation at a high THF concentration. Our work expanded on the previous work by mechanically examining the effects of THF on dioxane degradation in a microbial community context.
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Arumugam B, Palanisamy UD, Chua KH, Kuppusamy UR. Protective effect of myricetin derivatives from Syzygium malaccense against hydrogen peroxide-induced stress in ARPE-19 cells. Mol Vis 2019; 25:47-59. [PMID: 30820141 PMCID: PMC6379087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 02/05/2019] [Indexed: 12/03/2022] Open
Abstract
PURPOSE Oxidative stress is implicated in the etiology of diabetes and its debilitating complications, such as diabetic retinopathy (DR). Various flavonoids have been reported to be useful in reducing DR progression. Myricetin derivatives (F2) isolated from leaf extract of Syzygium malaccense have the potential to serve as functional food as reported previously. The present study was performed with the aim of determining the antioxidant potential and protective effect of myricetin derivatives (F2) isolated from leaf extract of S. malaccense against glucose oxidase (GO)-induced hydrogen peroxide (H2O2) production that causes oxidative stress in ARPE-19 (RPE) cells. METHODS Antioxidant properties were assessed through various radical (DPPH, ABTS, and nitric oxide) scavenging assays and determination of total phenolic content and ferric reducing antioxidant power level. ARPE-19 cells were preincubated with samples before the addition of GO (to generate H2O2). Cell viability, change in intracellular reactive oxygen species (ROS), H2O2 levels in cell culture supernatant, and gene expression were assessed. RESULTS F2 showed higher antioxidant levels than the extract when assessed for radical scavenging activities and ferric reducing antioxidant power. F2 protected the ARPE-19 cells against GO-H2O2-induced oxidative stress by reducing the production of H2O2 and intracellular reactive oxygen species. This was achieved by the activation of nuclear factor erythroid 2-related factor 2 (Nrf2/NFE2L2) and superoxide dismutase (SOD2), as well as downregulation of nitric oxide producer (NOS2) at the transcriptional level. CONCLUSIONS The results showed that myricetin derivatives from S. malaccense have the capacity to exert considerable exogenous antioxidant activities and stimulate endogenous antioxidant activities. Therefore, these derivatives have excellent potential to be developed as therapeutic agents for managing DR.
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Affiliation(s)
- Bavani Arumugam
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Uma Devi Palanisamy
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Umah Rani Kuppusamy
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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Palmieri F, Estoppey A, House GL, Lohberger A, Bindschedler S, Chain PSG, Junier P. Oxalic acid, a molecule at the crossroads of bacterial-fungal interactions. ADVANCES IN APPLIED MICROBIOLOGY 2018; 106:49-77. [PMID: 30798804 DOI: 10.1016/bs.aambs.2018.10.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Oxalic acid is the most ubiquitous and common low molecular weight organic acid produced by living organisms. Oxalic acid is produced by fungi, bacteria, plants, and animals. The aim of this review is to give an overview of current knowledge about the microbial cycling of oxalic acid through ecosystems. Here we review the production and degradation of oxalic acid, as well as its implications in the metabolism for fungi, bacteria, plants, and animals. Indeed, fungi are well known producers of oxalic acid, while bacteria are considered oxalic acid consumers. However, this framework may need to be modified, because the ability of fungi to degrade oxalic acid and the ability of bacteria to produce it, have been poorly investigated. Finally, we will highlight the role of fungi and bacteria in oxalic acid cycling in soil, plant and animal ecosystems.
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Affiliation(s)
- Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Aislinn Estoppey
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Geoffrey L House
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Andrea Lohberger
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
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7
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Doronina NV, Kaparullina EN, Chemodurova AA, Trotsenko YA. Paracoccus simplex sp. nov., a New Methylamine-Utilizing Facultative Methylotroph. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718050077] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Maronpot RR, Koyanagi M, Davis J, Recio L, Marbury D, Boyle M, Hayashi SM. Safety assessment and single-dose toxicokinetics of the flavouring agent myricitrin in Sprague–Dawley rats. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2015; 32:1799-809. [DOI: 10.1080/19440049.2015.1084653] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Danilova OV, Kulichevskaya IS, Rozova ON, Detkova EN, Bodelier PLE, Trotsenko YA, Dedysh SN. Methylomonas paludis sp. nov., the first acid-tolerant member of the genus
Methylomonas
, from an acidic wetland. Int J Syst Evol Microbiol 2013; 63:2282-2289. [DOI: 10.1099/ijs.0.045658-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic methanotrophic bacterium was isolated from an acidic (pH 3.9) Sphagnum peat bog in north-eastern Russia and designated strain MG30T. Cells of this strain were Gram-negative, pale pink-pigmented, non-motile, thick rods that were covered by large polysaccharide capsules and contained an intracytoplasmic membrane system typical of type I methanotrophs. They possessed a particulate methane monooxygenase enzyme (pMMO) and utilized only methane and methanol. Carbon was assimilated via the ribulose-monophosphate pathway; nitrogen was fixed via an oxygen-sensitive nitrogenase. Strain MG30T was able to grow at a pH range of 3.8–7.3 (optimum pH 5.8–6.4) and at temperatures between 8 and 30 °C (optimum 20–25 °C). The major cellular fatty acids were C16 : 1ω5t, C16 : 1ω8c, C16 : 1ω7c and C14 : 0; the DNA G+C content was 48.5 mol%. The isolate belongs to the family
Methylococcaceae
of the class
Gammaproteobacteria
and displayed 94.7–96.9 % 16S rRNA gene sequence similarity to members of the genus
Methylomonas
. However, strain MG30T differed from all taxonomically characterized members of this genus by the absence of motility, the ability to grow in acidic conditions and low DNA G+C content. Therefore, we propose to classify this strain as representing a novel, acid-tolerant species of the genus
Methylomonas
, Methylomonas paludis sp. nov. Strain MG30T ( = DSM 24973T = VKM B-2745T) is the type strain.
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Affiliation(s)
- Olga V. Danilova
- S.N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Irina S. Kulichevskaya
- S.N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Olga N. Rozova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region, 142292, Russia
| | - Ekaterina N. Detkova
- S.N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Paul L. E. Bodelier
- Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, PO Box 50 6700AB, The Netherlands
| | - Yuri A. Trotsenko
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region, 142292, Russia
| | - Svetlana N. Dedysh
- S.N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
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Abstract
In this study, we investigated the metabolism of ethylene glycol in the Pseudomonas putida strains KT2440 and JM37 by employing growth and bioconversion experiments, directed mutagenesis, and proteome analysis. We found that strain JM37 grew rapidly with ethylene glycol as a sole source of carbon and energy, while strain KT2440 did not grow within 2 days of incubation under the same conditions. However, bioconversion experiments revealed metabolism of ethylene glycol by both strains, with the temporal accumulation of glycolic acid and glyoxylic acid for strain KT2440. This accumulation was further increased by targeted mutagenesis. The key enzymes and specific differences between the two strains were identified by comparative proteomics. In P. putida JM37, tartronate semialdehyde synthase (Gcl), malate synthase (GlcB), and isocitrate lyase (AceA) were found to be induced in the presence of ethylene glycol or glyoxylic acid. Under the same conditions, strain KT2440 showed induction of AceA only. Despite this difference, the two strains were found to use similar periplasmic dehydrogenases for the initial oxidation step of ethylene glycol, namely, the two redundant pyrroloquinoline quinone (PQQ)-dependent enzymes PedE and PedH. From these results we constructed a new pathway for the metabolism of ethylene glycol in P. putida. Furthermore, we conclude that Pseudomonas putida might serve as a useful platform from which to establish a whole-cell biocatalyst for the production of glyoxylic acid from ethylene glycol.
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Oxalyl-coenzyme A reduction to glyoxylate is the preferred route of oxalate assimilation in Methylobacterium extorquens AM1. J Bacteriol 2012; 194:3144-55. [PMID: 22493020 DOI: 10.1128/jb.00288-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Oxalate catabolism is conducted by phylogenetically diverse organisms, including Methylobacterium extorquens AM1. Here, we investigate the central metabolism of this alphaproteobacterium during growth on oxalate by using proteomics, mutant characterization, and (13)C-labeling experiments. Our results confirm that energy conservation proceeds as previously described for M. extorquens AM1 and other characterized oxalotrophic bacteria via oxalyl-coenzyme A (oxalyl-CoA) decarboxylase and formyl-CoA transferase and subsequent oxidation to carbon dioxide via formate dehydrogenase. However, in contrast to other oxalate-degrading organisms, the assimilation of this carbon compound in M. extorquens AM1 occurs via the operation of a variant of the serine cycle as follows: oxalyl-CoA reduction to glyoxylate and conversion to glycine and its condensation with methylene-tetrahydrofolate derived from formate, resulting in the formation of C3 units. The recently discovered ethylmalonyl-CoA pathway operates during growth on oxalate but is nevertheless dispensable, indicating that oxalyl-CoA reductase is sufficient to provide the glyoxylate required for biosynthesis. Analysis of an oxalyl-CoA synthetase- and oxalyl-CoA-reductase-deficient double mutant revealed an alternative, although less efficient, strategy for oxalate assimilation via one-carbon intermediates. The alternative process consists of formate assimilation via the tetrahydrofolate pathway to fuel the serine cycle, and the ethylmalonyl-CoA pathway is used for glyoxylate regeneration. Our results support the notion that M. extorquens AM1 has a plastic central metabolism featuring multiple assimilation routes for C1 and C2 substrates, which may contribute to the rapid adaptation of this organism to new substrates and the eventual coconsumption of substrates under environmental conditions.
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Bravo D, Braissant O, Solokhina A, Clerc M, Daniels AU, Verrecchia E, Junier P. Use of an isothermal microcalorimetry assay to characterize microbial oxalotrophic activity. FEMS Microbiol Ecol 2011; 78:266-74. [PMID: 21696406 DOI: 10.1111/j.1574-6941.2011.01158.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Isothermal microcalorimetry (IMC) has been used in the past to monitor metabolic activities in living systems. A few studies have used it on ecological research. In this study, IMC was used to monitor oxalotrophic activity, a widespread bacterial metabolism found in the environment, and particularly in soils. Six model strains were inoculated in solid angle media with K-oxalate as the sole carbon source. Cupriavidus oxalaticus, Cupriavidus necator, and Streptomyces violaceoruber presented the highest activity (91, 40, and 55 μW, respectively) and a maximum growth rate (μmax h(-1) ) of 0.264, 0.185, and 0.199, respectively, among the strains tested. These three strains were selected to test the incidence of different oxalate sources (Ca, Cu, and Fe-oxalate salts) in the metabolic activity. The highest activity was obtained in Ca-oxalate for C. oxalaticus. Similar experiments were carried out with a model soil to test whether this approach can be used to measure oxalotrophic activity in field samples. Although measuring oxalotrophic activity in a soil was challenging, there was a clear effect of the amendment with oxalate on the metabolic activity measured in soil. The correlation between heat flow and growth suggests that IMC analysis is a powerful method to monitor bacterial oxalotrophic activity.
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Affiliation(s)
- Daniel Bravo
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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13
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Colonic metabolites of berry polyphenols: the missing link to biological activity? Br J Nutr 2010; 104 Suppl 3:S48-66. [DOI: 10.1017/s0007114510003946] [Citation(s) in RCA: 332] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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14
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McNerney T, O'connor ML. Regulation of enzymes associated with C-1 metabolism in three facultative methylotrophs. Appl Environ Microbiol 2010; 40:370-5. [PMID: 16345615 PMCID: PMC291583 DOI: 10.1128/aem.40.2.370-375.1980] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The levels of the oxidation enzyme methanol dehydrogenase and the serine pathway enzymes, hydroxypyruvate reductase, glycerate kinase, serine transhydroxymethylase, serine-glyoxylate aminotransferase, phosphoenolpyruvate carboxylase, and malyl-coenzyme A lyase, were studied in cells of the facultative methylotrophs Pseudomonas AM1, Pseudomonas 3A2 and Hyphomicrobium X grown on different substrates. Induction and dilution curves for these enzymes suggest they may be regulated coordinately in Hyphomicrobium X, but not in Pseudomonas AM1 or 3A2. Glyoxylate stimulated the serine transhydroxymethylase activity in methanol-grown cells of all three organisms. A secondary alcohol dehydrogenase activity was detected at low levels in Pseudomonas AM1 and Hyphomicrobium X, but not in Pseudomonas 3A2.
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Affiliation(s)
- T McNerney
- Department of Microbiology and Immunology, University of Washington, Seattle, Washington 98195
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15
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Abstract
Strain DM1, a facultative methylotrophic bacterium utilizing methanol, formate, mono-, di-, and trimethylamine, as well as dichloromethane as C1 substrates was isolated as an airborne contaminant. The organism is a strictly aerobic, gram-negative, oxidase-positive short rod, motile by a single lateral flagellum. Enzyme assays in crude extracts suggested that it assimilates C1 compounds by the serine/isocitrate lyase-negative pathway. Experiments with extended cultures demonstrated that dichloromethane is a growth-inhibitory substrate. The maximum specific growth rate of 0.11 h was reached between 2 and 5 mM dichloromethane. The release of Cl from dichloromethane paralleled growth in extended and continuous cultures. Molar growth yields on methanol and on dichloromethane were 18.6 and 15.7 g/mol, respectively. Since attempts to demonstrate dehalogenation of dichloromethane by crude extracts failed, a dehalogenation assay with resting cells was developed. Maximum dehalogenating activity of cell suspensions was at pH 9.0. The reaction was partially and reversibly inhibited by anaerobiosis. During a shift of a chemostat culture from methanol to dichloromethane as the carbon source, the dehalogenating activity of resting cells was increased at least 500-fold.
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Affiliation(s)
- W Brunner
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, CH-8092 Zurich, Switzerland
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16
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Alternative route for glyoxylate consumption during growth on two-carbon compounds by Methylobacterium extorquens AM1. J Bacteriol 2010; 192:1813-23. [PMID: 20118267 DOI: 10.1128/jb.01166-09] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methylobacterium extorquens AM1 is a facultative methylotroph capable of growth on both single-carbon and multicarbon compounds. Mutants defective in a pathway involved in converting acetyl-coenzyme A (CoA) to glyoxylate (the ethylmalonyl-CoA pathway) are unable to grow on both C(1) and C(2) compounds, showing that both modes of growth have this pathway in common. However, growth on C(2) compounds via the ethylmalonyl-CoA pathway should require glyoxylate consumption via malate synthase, but a mutant lacking malyl-CoA/beta-methylmalyl-CoA lyase activity (MclA1) that is assumed to be responsible for malate synthase activity still grows on C(2) compounds. Since glyoxylate is toxic to this bacterium, it seemed likely that a system is in place to keep it from accumulating. In this study, we have addressed this question and have shown by microarray analysis, mutant analysis, metabolite measurements, and (13)C-labeling experiments that M. extorquens AM1 contains an additional malyl-CoA/beta-methylmalyl-CoA lyase (MclA2) that appears to take part in glyoxylate metabolism during growth on C(2) compounds. In addition, an alternative pathway appears to be responsible for consuming part of the glyoxylate, converting it to glycine, methylene-H(4)F, and serine. Mutants lacking either pathway have a partial defect for growth on ethylamine, while mutants lacking both pathways are unable to grow appreciably on ethylamine. Our results suggest that the malate synthase reaction is a bottleneck for growth on C(2) compounds by this bacterium, which is partially alleviated by this alternative route for glyoxylate consumption. This strategy of multiple enzymes/pathways for the consumption of a toxic intermediate reflects the metabolic versatility of this facultative methylotroph and is a model for other metabolic networks involving high flux through toxic intermediates.
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Vecherskaya M, Dijkema C, Saad HR, Stams AJM. Microaerobic and anaerobic metabolism of a Methylocystis parvus strain isolated from a denitrifying bioreactor. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:442-449. [PMID: 23765898 DOI: 10.1111/j.1758-2229.2009.00069.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
An obligate methanotrophic bacterium, strain MTS, was isolated from a methane-fed microaerobic denitrifying bioreactor. 16S rRNA and DNA-DNA hybridization analysis revealed that this organism was most closely related to Methylocystis parvus, a Type II methanotroph, belonging to the α-subclass of the Proteobacteria. The metabolism of the bacterium under microaerobic and anaerobic conditions was studied by (13) C-NMR. (13) C-labelled poly-β-hydroxybutyrate (PHB) formation occurred in cell suspensions incubated with (13) C-labelled methane at low (5-10%) oxygen concentration. Under these conditions low levels of succinate, acetate and 2,3-butanediol were formed and excreted into the culture medium. Intracellular PHB degradation was observed in intact cells under anaerobic conditions in the absence of an exogenous carbon source during a long-term incubation of 90 days. Multiple (13) C-labelled β-hydroxybutyrate, butyrate, acetate, acetone, isopropanol, 2,3-butanediol and succinate were identified as products in in vivo(13) C-NMR spectra and in the spectra of culture medium during the dynamic PHB degradation. The isolated obligate methanotroph clearly shows a fermentative metabolism of PHB under anaerobic conditions. The excreted products may serve as substrates for denitrifying bacteria.
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Affiliation(s)
- Margarita Vecherskaya
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, the Netherlands. Laboratory of Biophysics, Wageningen University, Dreijenplein 3, 6703 HA, Wageningen, the Netherlands. Department of Biological Systems, Universidad Autónoma Metropolitana, 06960 Mexico City, Mexico
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18
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McCarty PL. Thermodynamic electron equivalents model for bacterial yield prediction: modifications and comparative evaluations. Biotechnol Bioeng 2007; 97:377-88. [PMID: 17089390 DOI: 10.1002/bit.21250] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Modifications are made to an earlier thermodynamic model (TEEM1) for prediction of maximum microbial yields from aerobic and anaerobic as well as heterotrophic and autotrophic growth. The revised model (TEEM2) corrects for lower yields found with aerobic oxidations of organic compounds where an oxygenase is involved and with growth on single-carbon (C1) compounds. TEEM1 and TEEM2 are based on energy release and consumption as determined from the reduction potential or Gibbs free energy of (1/2)-reaction reduction equations together with losses of energy during energy transfer. Energy transfer efficiency is a key parameter needed to make predictions with TEEM2, and was determined through evaluations with extensive data sets on aerobic heterotrophic yield available in the literature. For compounds following normal catabolic pathways, the best-fit value for energy transfer efficiency was 0.37, which permitted accurate predictions of growth with a precision of 15%-20% as determined by standard deviation. Using the same energy transfer efficiency, a similar precision, but somewhat less accuracy was found for organic compounds where oxidation involves an oxygenase (estimates 8% too high) and for C1 compounds (estimates 17% too high). In spite of the somewhat lower accuracy, the TEEM2 modifications resulted in improved predictions over TEEM1 and the comparison models.
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Affiliation(s)
- Perry L McCarty
- Silas H. Palmer Professor Emeritus, Department of Civil and Environmental Engineering, Stanford University, Stanford, California 94305-4020, USA.
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19
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Oxalotrophic Paracoccus alcaliphilus isolated from Amorphophallus sp. rhizoplane. World J Microbiol Biotechnol 2007. [DOI: 10.1007/s11274-007-9397-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Dedysh SN, Smirnova KV, Khmelenina VN, Suzina NE, Liesack W, Trotsenko YA. Methylotrophic autotrophy in Beijerinckia mobilis. J Bacteriol 2005; 187:3884-8. [PMID: 15901717 PMCID: PMC1112052 DOI: 10.1128/jb.187.11.3884-3888.2005] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Representatives of the genus Beijerinckia are known as heterotrophic, dinitrogen-fixing bacteria which utilize a wide range of multicarbon compounds. Here we show that at least one of the currently known species of this genus, i.e., Beijerinckia mobilis, is also capable of methylotrophic metabolism coupled with the ribulose bisphosphate (RuBP) pathway of C1 assimilation. A complete suite of dehydrogenases commonly involved in the sequential oxidation of methanol via formaldehyde and formate to CO2 was detected in cell extracts of B. mobilis grown on CH3OH. Carbon dioxide produced by oxidation of methanol was further assimilated via the RuBP pathway as evidenced by reasonably high activities of phosphoribulokinase and ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO). Detection and partial sequence analysis of genes encoding the large subunits of methanol dehydrogenase (mxaF) and form I RubisCO (cbbL) provided genotypic evidence for methylotrophic autotrophy in B. mobilis.
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Affiliation(s)
- Svetlana N Dedysh
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia.
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21
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Tamer AU, Aragno M, Sahin N. Isolation and characterization of a new type of aerobic, oxalic acid utilizing bacteria, and proposal of Oxalicibacterium flavum gen. nov., sp. nov. Syst Appl Microbiol 2002; 25:513-9. [PMID: 12583711 DOI: 10.1078/07232020260517643] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A mesophilic, aerobic oxalic acid utilizing yellow-pigmented bacterium has been isolated from litter of oxalate producing plants in the region of Izmir (Turkey). It is motile by means of 1-3 polar flagella. Optimal growth occurred between 25-30 degrees C at pH 6.9. The G+C content of DNA is 62-64 mol % (Tm). Based on its morphological and biochemical features the organism belongs to the genus Pseudomonas, but differs from all the previously described species. The taxonomic relationships among strains described as or previously tentatively assigned to the genus Pseudomonas were investigated using numerical classification, DNA base composition and DNA-DNA hybridization. 16S rDNA sequences were determined for the strain TA17. On the basis of 16S rDNA sequence comparisons, physiological and biochemical characteristics, it is proposed to classify TA17T in a new genus and species for which the name Oxalicibacterium flavum gen. nov., sp. nov. is proposed. The type strain is TA17T (= NEU98T, = LMG 21571T).
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Affiliation(s)
- Abdurrahman U Tamer
- Celal Bayar Universitesi, Fen Edebiyat Fakültesi, Biyoloji Bölümü, Manisa, Turkey
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22
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Sahin N, Işik K, Tamer AU, Goodfellow M. Taxonomic position of "Pseudomonas oxalaticus" strain ox14T (DSM 1105T) (Khambata and Bhat, 1953) and its description in the genus Ralstonia as Ralstonia oxalatica comb. nov. Syst Appl Microbiol 2000; 23:206-9. [PMID: 10930072 DOI: 10.1016/s0723-2020(00)80006-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
"Pseudomonas oxalaticus" strain Ox1T (= DSM 1105T), which was described as an oxalate-decomposing bacterium, was reinvestigated to clarify its taxonomic position. 16S ribosomal DNA sequence comparisons demonstrated that this species is phylogenetically related to the species of the genus Ralstonia. and represents a new species. The result of the DNA-DNA hybridization value was supported in this placement. Strain Ox1T is closely related to Ralstonia eutropha with a less than 60% DNA-DNA hybridization value. The new name Ralstonia oxalatica comb. nov. is proposed to strain Ox1T, on the basis of these results and previously published data for the G+C content of the genomic DNA and the phenotypic characters.
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Affiliation(s)
- N Sahin
- Celal Bayar Universitesi, Fen Edebiyat Fakültesi, Biyoloji Bölümü, Turkey.
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23
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Kuhner CH, Hartman PA, Allison MJ. Generation of a proton motive force by the anaerobic oxalate-degrading bacterium Oxalobacter formigenes. Appl Environ Microbiol 1996; 62:2494-500. [PMID: 8779588 PMCID: PMC168031 DOI: 10.1128/aem.62.7.2494-2500.1996] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The generation of transmembrane ion gradients by Oxalobacter formigenes cells metabolizing oxalate was studied. The magnitudes of both the transmembrane electrical potential (delta psi) and the pH gradient (internal alkaline) decreased with increasing external pH; quantitatively, the delta psi was the most important component of the proton motive force. As the extracellular pH of metabolizing cells was increased, intracellular pH increased and remained alkaline relative to the external pH, indicating that O. formigenes possesses a limited capacity to regulate internal pH. The generation of a delta psi by concentrated suspensions of O. formigenes cells was inhibited by the K+ ionophore valinomycin and the protonophore carbonyl cyanide-m-chlorophenylhydrazone, but not by the Na+ ionophore monensin. The H+ ATPase inhibitor N,N'-dicyclohexyl-carbodiimide inhibited oxalate catabolism but did not dissipate the delta psi. The results support the concept that energy from oxalate metabolism by O. formigenes is conserved not as a sodium ion gradient but rather, at least partially, as a transmembrane hydrogen ion gradient produced during the electrogenic exchange of substrate (oxalate) and product (formate) and from internal proton consumption during oxalate decarboxylation.
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Affiliation(s)
- C H Kuhner
- Department of Microbiology, Immunology, and Preventive Medicine, Iowa State University, Ames 50011, USA
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24
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Smith LM, Meijer WG, Dijkhuizen L, Goodwin PM. A protein having similarity with methylmalonyl-CoA mutase is required for the assimilation of methanol and ethanol by Methylobacterium extorquens AM1. MICROBIOLOGY (READING, ENGLAND) 1996; 142 ( Pt 3):675-684. [PMID: 8868443 DOI: 10.1099/13500872-142-3-675] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A 4.0 kb region of Methylobacterium extorquens AM1 DNA which complements three mutants unable to convert acetyl-CoA to glyoxylate (and therefore defective in the assimilation of methanol and ethanol) has been isolated and sequenced. It contains two ORFs and the 3'-end of a third one. The mutations in all three mutants mapped within the first ORF, which was designated meaA; it encodes a protein having similarity with methylmalonyl-CoA mutase. However, methylmalonyl-CoA mutase was measured in extracts of one of the mutants and the specific activity was found to be similar to that in extracts of wild-type cells. Furthermore, although the predicted meaA gene product has the proposed cobalamin-binding site, it does not contain a highly conserved sequence (RIARNT) which is present in all known methylmalonyl-CoA mutases; meaA may therefore encode a novel vitamin-B12-dependent enzyme. The predicted polypeptide encoded by the second ORF did not have similarity with any known proteins. The partial ORF encoded a protein with similarity with the 3-oxoacyl-[acyl-carrier-protein] reductases; it was not essential for growth on methanol or ethanol.
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Affiliation(s)
- Loraine M Smith
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
- School of Cell and Molecular Biology, NESCOT, Reigate Road, Epsom KT17 3DS, UK
| | - Wim G Meijer
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
| | - Lubbert Dijkhuizen
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
| | - Pat M Goodwin
- School of Cell and Molecular Biology, NESCOT, Reigate Road, Epsom KT17 3DS, UK
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25
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Pol A, Op den Camp HJ, Mees SG, Kersten MA, van der Drift C. Isolation of a dimethylsulfide-utilizing Hyphomicrobium species and its application in biofiltration of polluted air. Biodegradation 1994; 5:105-12. [PMID: 7765115 DOI: 10.1007/bf00700635] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The methylotrophic bacterium Hyphomicrobium VS was enriched and isolated, using activated sewage sludge as inoculum in mineral medium containing dimethylsulfide (DMS) at a low concentration to prevent toxicity. DMS concentrations above 1 mM proved to be growth inhibiting. Hyphomicrobium VS could use DMS, dimethylsulfoxide (DMSO), methanol, formaldehyde, formate, and methylated amines as carbon and energy source. Carbon was assimilated via the serine pathway. DMS-grown cells respired sulfide, thiosulfate, methanethiol, dimethyldisulfide and dimethyltrisulfide. To test Hyphomicrobium VS for application in biofiltration of air polluted with volatile sulfur compounds two laboratory scale trickling biofilters with polyurethane and lava stone as carrier material were started up by inoculation with this bacterium. Both methanol- and DMS-grown cells could be used. Only a short adaptation period was needed. Short term experiments showed that high concentrations of DMS (1-2 mumol l-1) were removed very efficiently by the biofilters at space velocities up to 100 h-1.
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Affiliation(s)
- A Pol
- Department of Microbiology & Evolutionary Biology, Faculty of Science, University of Nijmegen, The Netherlands
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26
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Topp E, Hanson RS, Ringelberg DB, White DC, Wheatcroft R. Isolation and characterization of an N-methylcarbamate insecticide-degrading methylotrophic bacterium. Appl Environ Microbiol 1993; 59:3339-49. [PMID: 7504430 PMCID: PMC182457 DOI: 10.1128/aem.59.10.3339-3349.1993] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A gram-negative bacterium which hydrolyzed aryl N-methylcarbamate insecticides was isolated from an agricultural soil which quickly degraded these pesticides. This organism, designated strain ER2, grew on carbofuran as a sole source of carbon and nitrogen with a doubling time of 3 h in a mineral salts medium. The aromatic nucleus of the molecule was not metabolized, and carbofuran 7-phenol accumulated as the end product of metabolism. The insecticides carbaryl, bendiocarb, and propoxur were similarly hydrolyzed, with each yielding the corresponding phenol. Strain ER2 contained two plasmids (120 and 130 kb). A probe cloned from the pDL11 plasmid of Achromobacter sp. strain WM111, which encodes the carbofuran hydrolase (mcd) gene (P. H. Tomasek and J. S. Karns, J. Bacteriol. 171:4038-4044, 1989), hybridized to the 120-kb plasmid. Restriction fragment profiles of pDL11 and strain ER2 plasmid DNAs suggested that the 120-kb plasmid of strain ER2 is very similar to pDL11. On the basis of the results of biochemical tests, 16S rRNA sequence analysis, and membrane lipid analyses, strain ER2 was found to be a phylogenetically unique type II methylotroph. The constitutive carbofuran hydrolase activity in glucose-grown cells increased sevenfold when strain ER2 was grown in the presence of 100 mg of carbofuran per liter as the sole source of carbon and nitrogen or as the sole nitrogen source in the presence of glucose. Growth on carbofuran resulted in the induction of enzymes required for methylamine-dependent respiration and the serine pathway of formaldehyde assimilation. These results indicate that the carbofuran hydrolase mcd gene is conserved on a plasmid found in organisms from different geographic areas and that the specific activity of carbofuran degradation may increase in response to carbofuran treatment.
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Affiliation(s)
- E Topp
- Centre for Land and Biological Resources Research, Agriculture Canada, Central Experimental Farm, Ottawa, Ontario
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27
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Arps PJ, Fulton GF, Minnich EC, Lidstrom ME. Genetics of serine pathway enzymes in Methylobacterium extorquens AM1: phosphoenolpyruvate carboxylase and malyl coenzyme A lyase. J Bacteriol 1993; 175:3776-83. [PMID: 8509332 PMCID: PMC204794 DOI: 10.1128/jb.175.12.3776-3783.1993] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Methylobacterium extorquens AM1 is a facultative methylotrophic bacterium that uses the serine pathway for formaldehyde incorporation as its assimilation pathway during growth on one-carbon compounds. A DNA region from M. extorquens AM1 previously shown to contain genes for the serine pathway enzymes malyl coenzyme A (CoA) lyase and hydroxypyruvate reductase has been characterized in more detail. Insertion mutagenesis revealed an additional region required for growth on one-carbon compounds, and all of the insertion mutants in this region lacked activity for another serine pathway enzyme, the acetyl-CoA-independent phosphoenolpyruvate (PEP) carboxylase. Expression analysis with Escherichia coli of DNA fragments that included the malyl-CoA lyase and PEP carboxylase regions identified five polypeptides, all transcribed in the same direction. Three of these polypeptides were expressed from the region necessary for the acetyl-CoA-independent PEP carboxylase, one was expressed from the region containing the malyl-CoA lyase gene, and the fifth was expressed from a region immediately downstream from the gene encoding hydroxypyruvate reductase. All six genes are transcribed in the same direction, but the transposon insertion data suggest that they are not all cotranscribed.
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Affiliation(s)
- P J Arps
- Keck Laboratories, California Institute of Technology, Pasadena 91125
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28
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Ivanovsky RN, Krasilnikova EN, Fal YI. A pathway of the autotrophic CO2 fixation in Chloroflexus aurantiacus. Arch Microbiol 1993. [DOI: 10.1007/bf00248481] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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29
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GÃrio FM, Marcos JC, Amaral-Collaço M. Transition metal requirement to express high level NAD+-dependent formate dehydrogenase from a serine-type methylotrophic bacterium. FEMS Microbiol Lett 1992. [DOI: 10.1111/j.1574-6968.1992.tb05456.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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30
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Baev MV, Kuznetsov EV, Skladnev DA, Govorukhina NI, Sterkin VE, Tsygankov YD. Growth and enzymological characteristics of a pink-pigmented facultative methylotroph Methylobacterium sp. MB1. Folia Microbiol (Praha) 1992; 37:93-101. [PMID: 1505877 DOI: 10.1007/bf02836611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Growth characteristics of batch and continuous cultures of the pink facultative methylotroph Methylobacterium sp. MB1 were determined. The response of a chemostat culture to a pulse increase of methanol concentration was studied. Malate, succinate and oxaloacetate additions to the methanol-supplemented medium decreased batch culture growth inhibition by methanol. The carotenoid content in cells grown in a chemostat decreased with increasing growth rate. The key enzyme activities of C1-metabolism were measured in a chemostat culture at different dilution rates.
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Affiliation(s)
- M V Baev
- Institute of Genetics and Selection of Industrial Microorganisms, Moscow, Russian Federation
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31
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[55] Assay of assimilatory enzymes in crude extracts of serine pathway methylotrophs. Methods Enzymol 1990. [DOI: 10.1016/0076-6879(90)88057-h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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32
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Raj HD. Oligotrophic methylotrophs: Ancylobacter (basonym "Microcyclus" Orskov) Raj gen. nov. Crit Rev Microbiol 1989; 17:89-106. [PMID: 2692603 DOI: 10.3109/10408418909105743] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Abstract
Four new methane-oxidizing bacteria have been isolated from marine samples taken at the Hyperion sewage outfall, near Los Angeles, CA. These bacteria require NaCl for growth. All exhibit characteristics typical of Type I methanotrophs, except they contain enzyme activities of both the ribulose monophosphate pathway and the serine cycle. All four strains are characterized by rapid growth in liquid culture and on agar plates, and all have temperature optima above 35 degrees C. One strain, chosen for further study, has been shown to maintain broadhost range cloning vectors and is currently being used for genetic studies.
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Affiliation(s)
- M E Lidstrom
- Keck Laboratories, California Institute of Technology, Pasadena 91125
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Sieburth JN, Johnson PW, Eberhardt MA, Sieracki ME, Lidstrom M, Laux D. The first methane-oxidizing bacterium from the upper mixing layer of the deep ocean:Methylomonas pelagica sp. nov. Curr Microbiol 1987. [DOI: 10.1007/bf01568138] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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35
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Dijken J, Harder W, Beardsmore A, Quayle J. Dihydroxyacetone: An intermediate in the assimilation of methanol by yeasts? FEMS Microbiol Lett 1987. [DOI: 10.1111/j.1574-6968.1987.tb02009.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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36
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Cavanaugh CM, Levering PR, Maki JS, Mitchell R, Lidstrom ME. Symbiosis of methylotrophic bacteria and deep-sea mussels. Nature 1987. [DOI: 10.1038/325346a0] [Citation(s) in RCA: 155] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Mapping of some genes involved in C-1 metabolism in the facultative methylotroph Methylobacterium sp strain AM1 (Pseudomonas AM1). Arch Microbiol 1985. [DOI: 10.1007/bf00411043] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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38
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Brooke A, Attwood M. Regulation of enzyme synthesis in Hyphomicrobium X: Growth on mixtures of methylamine and ethanol in continuous cultures. FEMS Microbiol Lett 1985. [DOI: 10.1111/j.1574-6968.1985.tb00871.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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39
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Fulton GL, Nunn DN, Lidstrom ME. Molecular cloning of a malyl coenzyme A lyase gene from Pseudomonas sp. strain AM1, a facultative methylotroph. J Bacteriol 1984; 160:718-23. [PMID: 6094488 PMCID: PMC214796 DOI: 10.1128/jb.160.2.718-723.1984] [Citation(s) in RCA: 87] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
A genomic library containing HindIII partial digests of Pseudomonas sp. strain AM1 DNA was constructed in the broad-host-range cosmid pVK100. PCT57, a Pseudomonas sp. strain AM1 methanol mutant deficient in malyl coenzyme A lyase activity, was complemented to a methanol-positive phenotype by mobilization of the pVK100 library into PCT57 recipients with the ColE1/RK2 mobilizing plasmid pRK2013. Six different complemented isolates all contained a recombinant plasmid carrying the same 19.6-kilobase-pair Pseudomonas sp. strain AM1 DNA insert. Subcloning and complementation analysis demonstrated that the gene deficient in PCT57 (mcl-1) was located in a 1.6-kilobase-pair region within a 7.4-kilobase-pair EcoRI-HindIII fragment.
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40
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Konopka A, Szentes M. Autotrophic Growth of Gas Vacuolate Strains of
Microcyclus aquaticus
on Methanol and Hydrogen. Appl Environ Microbiol 1984; 47:870-2. [PMID: 16346525 PMCID: PMC239779 DOI: 10.1128/aem.47.4.870-872.1984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Seven strains of
Microcyclus aquaticus
were found to be capable of growth on methanol and hydrogen as energy sources. Carbon was incorporated as CO
2
via the Calvin cycle, as shown by the presence of ribulosebisphosphate carboxylase activity in methanol-grown cells and by the absence of key enzymes of the ribulose monophosphate and serine pathways. In addition, incoporation of [
14
C]methanol into cells was diminished when cultures were incubated in gas atmospheres enriched with carbon dioxide.
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Affiliation(s)
- A Konopka
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47906
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41
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Behrendt U, Bang WG, Wagner F. The Production ofL-serine with a methylotrophic microorganism using theL-serine pathway and coupling with anL-tryptophan-producing process. Biotechnol Bioeng 1984; 26:308-14. [DOI: 10.1002/bit.260260403] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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42
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Van der Drift C, De Windt FE. Glyoxylate conversion by Hyphomicrobium species grown on allantoin as nitrogen source. Antonie Van Leeuwenhoek 1983; 49:167-72. [PMID: 6614900 DOI: 10.1007/bf00393675] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Glyoxylate, formed as a result of allantoin degradation, is converted by Hyphomicrobium species to glycerate via tartronate semialdehyde. Glyoxylate carboligase and tartronate semialdehyde reductase, the two enzymes involved, are present only in cells grown on allantoin as nitrogen source.
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43
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Herbert R, Westwater S. Nitrogen assimilation in a methanol-utilising strain ofRhodopseudomonas acidophila. FEMS Microbiol Lett 1981. [DOI: 10.1111/j.1574-6968.1981.tb07638.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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44
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Ratomahenina R, Galzy P. Mutation modifying the serine pathway in methylotrophic bacteria. Folia Microbiol (Praha) 1981; 26:179-83. [PMID: 6792008 DOI: 10.1007/bf02927420] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Methylotrophic bacteria, Gram-positive, with the serine pathway, were shown to have their growth inhibited by 0.5% glycine. The effects of this amino acid on individual enzyme activities were studied in wild and mutant strains of Micrococcus varians and Bacillus licheniformis. The enzymes studied were glycerate dehydrogenase (EC 1.1.1.29), isocitrate lyase (EC 4.1.3.1), serine hydroxymethyltransferase (EC 2.1.2.1) and glycine--oxaloacetate aminotransferase (EC 2.6.1.35). The last-named enzyme was found to be inhibited, the kinetic constants having been determined for two strain types.
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45
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Levering PR, van Dijken JP, Veenhius M, Harder W. Arthrobacter P1, a fast growing versatile methylotroph with amine oxidase as a key enzyme in the metabolism of methylated amines. Arch Microbiol 1981; 129:72-80. [PMID: 7224781 DOI: 10.1007/bf00417184] [Citation(s) in RCA: 74] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A facultative methylotrophic bacterium was isolated from enrichment cultures containing methylamine as the sole carbon source. It was tentatively identified as an Arthrobacter species. Extracts of cells grown on methylamine or ethylamine contained high levels of amine oxidase (E.C. 1.4.3) activity. Glucose- or choline-grown cells lacked this enzyme. Oxidation of primary amines by the enzyme resulted in the formation of H2O2; as a consequence high levels of catalase were present in methylamine- and ethylamine-grown cells. The significance of catalase in vivo was demonstrated by addition of 20 mM aminotriazole (a catalase inhibitor) to exponentially growing cells. This completely blocked growth on methylamine whereas growth on glucose was hardly affected. Cytochemical studies showed that methylamine-dependent H2O2 production mainly occurred on invaginations of the cytoplasmic membrane. Assimilation of formaldehyde which is generated during methylamine oxidation was by the FBP variant of the RuMP cycle of formaldehyde fixation. The absence of NAD-dependent formaldehyde and formate dehydrogenases indicated the operation of a non-linear oxidation sequence for formaldehyde via hexulose phosphate synthase. Enzyme profiles of the organism grown on various substrates suggested that the synthesis of amine oxidase, catalase and the enzymes of the RuMP cycle is not under coordinate control.
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Herbert RA, Macfarlane GT. Asparagine and glutamine metabolism in Rhodopseudomonas acidophila. Arch Microbiol 1980; 128:233-8. [PMID: 7212928 DOI: 10.1007/bf00406164] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Rhodopseudomonas acidophila strain 7050 achieved balance growth when provided with either asparagine or glutamine as nitrogen source. Under these growth conditions R. acidophila synthesized a mixed amidase which exhibited similar activity (223--422 nmol/min . mg protein) against either nitrogen source. Determination of the free intracellular amino acid pools show that deamidation of asparagine and glutamine resulted in elevated levels of both aspartate and glutamate. Cell-free extracts of R. acidophila showed significant aminotransferase activity, particularly glutamine-oxaloacetate aminotransferase (89.7--209.3 nmol/min . mg protein), glycine oxaloacetate aminotransferase (135--227 nmol/min . mg protein), alanine glyoxylate aminotransferase (66.3--163.2 nmol/min . mg protein) and serine-glyoxylate aminotransferase (57.1--68.4 nmol/min . mg protein). Short term labelling experiments using 14C-glyoxylate show that glycine plays an important role in amino nitrogen transfer in R. acidophila and that the enzymes for the metabolism of glyoxylate via glycine, serine and hydroxypyruvate were present in cell-free extracts. These data confirm that R. acidophila can satisfy all its' nitrogen requirements by transamination.
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Dawson KA, Allison MJ, Hartman PA. Isolation and some characteristics of anaerobic oxalate-degrading bacteria from the rumen. Appl Environ Microbiol 1980; 40:833-9. [PMID: 7425628 PMCID: PMC291667 DOI: 10.1128/aem.40.4.833-839.1980] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Obligately anaerobic oxalate-degrading bacteria were isolated from an enriched population of rumen bacteria in an oxalate-containing medium that had been depleted of other readily metabolized substrates. These organisms, which are the first reported anaerobic oxalate degraders isolated from the rumen, were gram negative, nonmotile rods. They grew in a medium containing sodium oxalate, yeast extract, cysteine, and minerals. The only substrate that supported growth was oxalate. Growth was directly related to the concentration of oxalate in the medium (1 to 111 mM), and cell yields were approximately 1.1 g (dry weight)/mol of oxalate degraded. Oxalate was stoichiometrically degraded to CO2 and formate. These anaerobes occupy a unique ecological niche and are distinct from any previously described oxalate-degrading bacteria.
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Lynch MJ, Wopat AE, O'connor ML. Characterization of Two New Facultative Methanotrophs. Appl Environ Microbiol 1980; 40:400-7. [PMID: 16345617 PMCID: PMC291588 DOI: 10.1128/aem.40.2.400-407.1980] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two new facultative methane-oxidizing bacteria have been isolated from lake water enrichments. The organisms have been characterized in terms of colony types, growth characteristics, the guanine plus cytosine content of their deoxyribonucleic acid, thin sections, oxidation rates, and carbon assimilation pathways. Methane-grown cells of both organisms contained intracytoplasmic membranes similar to those described as type II in other methanotrophic bacteria. Neither organism had such membranes when grown heterotrophically. Both organisms assimilated methane by way of the isocitrate lyase-negative serine pathway for formaldehyde incorporation. The enzymes of this pathway were high in specific activity in cells grown on methane and were at low levels in cells grown either on heterotrophic substrates or on heterotrophic substrates plus methane. It is proposed that both organisms be classified in the genus
Methylobacterium
as two new species,
Methylobacterium ethanolicum
and
Methylobacterium hypolimneticum.
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Affiliation(s)
- M J Lynch
- Department of Microbiology and Immunology, SC-42, University of Washington, Seattle, Washington 98195
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Braun W, Kaltwasser H. Untersuchungen zum Glyoxyls�urestoffwechsel vonBacillus fastidiosus Stamm 83. Arch Microbiol 1979. [DOI: 10.1007/bf00689976] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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