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Boltyanskaya Y, Zhilina T, Grouzdev D, Detkova E, Pimenov N, Kevbrin V. Halanaerobium polyolivorans sp. nov.-A Novel Halophilic Alkalitolerant Bacterium Capable of Polyol Degradation: Physiological Properties and Genomic Insights. Microorganisms 2023; 11:2325. [PMID: 37764169 PMCID: PMC10536098 DOI: 10.3390/microorganisms11092325] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/16/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
A search for the microorganisms responsible for the anaerobic degradation of osmoprotectants in soda lakes resulted in the isolation of a novel halophilic and alkalitolerant strain, designated Z-7514T. The cells were Gram-stain-negative and non-endospore-forming rods. Optimal growth occurs at 1.6-2.1 M Na+, pH 8.0-8.5, and 31-35 °C. The strain utilized mainly sugars, low molecular polyols, and ethanolamine as well. The G+C content of the genomic DNA of strain Z-7514T was 33.3 mol%. Phylogenetic and phylogenomic analyses revealed that strain Z-7514T belongs to the genus Halanaerobium. On the basis of phenotypic properties and the dDDH and ANI values with close validly published species, it was proposed to evolve strain Z-7514T within the genus Halanaerobium into novel species, for which the name Halanaerobium polyolivorans sp. nov. was proposed. The type strain was Z-7514T (=KCTC 25405T = VKM B-3577T). For species of the genus Halanaerobium, the utilization of ethylene glycol, propylene glycol, and ethanolamine were shown for the first time. The anaerobic degradation of glycols and ethanolamine by strain Z-7514T may represent a novel metabiotic pathway within the alkaliphilic microbial community. Based on a detailed genomic analysis, the main pathways of catabolism of most of the used substrates have been identified.
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Affiliation(s)
- Yulia Boltyanskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia; (Y.B.); (T.Z.); (E.D.); (N.P.)
| | - Tatjana Zhilina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia; (Y.B.); (T.Z.); (E.D.); (N.P.)
| | | | - Ekaterina Detkova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia; (Y.B.); (T.Z.); (E.D.); (N.P.)
| | - Nikolay Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia; (Y.B.); (T.Z.); (E.D.); (N.P.)
| | - Vadim Kevbrin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia; (Y.B.); (T.Z.); (E.D.); (N.P.)
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2
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Ermolaeva SA, Parfenov VA, Karalkin PA, Khesuani YD, Domnin PA. Experimentally Created Magnetic Force in Microbiological Space and On-Earth Studies: Perspectives and Restrictions. Cells 2023; 12:cells12020338. [PMID: 36672273 PMCID: PMC9856290 DOI: 10.3390/cells12020338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/07/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Magnetic force and gravity are two fundamental forces affecting all living organisms, including bacteria. On Earth, experimentally created magnetic force can be used to counterbalance gravity and place living organisms in conditions of magnetic levitation. Under conditions of microgravity, magnetic force becomes the only force that moves bacteria, providing an acceleration towards areas of the lowest magnetic field and locking cells in this area. In this review, we consider basic principles and experimental systems used to create a magnetic force strong enough to balance gravity. Further, we describe how magnetic levitation is applied in on-Earth microbiological studies. Next, we consider bacterial behavior under combined conditions of microgravity and magnetic force onboard a spacecraft. At last, we discuss restrictions on applications of magnetic force in microbiological studies and the impact of these restrictions on biotechnological applications under space and on-Earth conditions.
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Affiliation(s)
- Svetlana A. Ermolaeva
- Gamaleya National Research Centre for Epidemiology and Microbiology, 123098 Moscow, Russia
- Correspondence: ; Tel.: +7-499-193-4375
| | - Vladislav A. Parfenov
- Institute of Metallurgy and Material Science, Russian Academy of Sciences, 119334 Moscow, Russia
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 115409 Moscow, Russia
| | - Pavel A. Karalkin
- Institute of Cluster Oncology, Sechenov First Moscow State Medical University, 127473 Moscow, Russia
| | | | - Pavel A. Domnin
- Gamaleya National Research Centre for Epidemiology and Microbiology, 123098 Moscow, Russia
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3
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Knox HL, Booker SJ. Structural characterization of cobalamin-dependent radical S-adenosylmethionine methylases. Methods Enzymol 2022; 669:3-27. [PMID: 35644177 DOI: 10.1016/bs.mie.2021.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cobalamin-dependent radical S-adenosylmethionine (SAM) methylases catalyze key steps in the biosynthesis of numerous biomolecules, including protein cofactors, antibiotics, herbicides, and other natural products, but have remained a relatively understudied subclass of radical SAM enzymes due to their inherent insolubility upon overproduction in Escherichia coli. These enzymes contain two cofactors: a [4Fe-4S] cluster that is ligated by three cysteine residues, and a cobalamin cofactor typically bound by residues in the N-terminal portion of the enzyme. Recent advances in the expression and purification of these enzymes in their active states and with both cofactors present has allowed for more detailed biochemical studies as well as structure determination by X-ray crystallography. Herein, we use KsTsrM and TokK to highlight methods for the structural characterization of cobalamin-dependent radical SAM (RS) enzymes and describe recent advances in in the overproduction and purification of these enzymes.
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Affiliation(s)
- Hayley L Knox
- The Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Squire J Booker
- The Department of Chemistry, The Pennsylvania State University, University Park, PA, United States; The Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States; The Howard Hughes Medical Institute, The Pennsylvania State University, University Park, PA, United States.
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4
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Toraya T, Tobimatsu T, Mori K, Yamanishi M, Shibata N. Coenzyme B 12-dependent eliminases: Diol and glycerol dehydratases and ethanolamine ammonia-lyase. Methods Enzymol 2022; 668:181-242. [PMID: 35589194 DOI: 10.1016/bs.mie.2021.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Adenosylcobalamin (AdoCbl) or coenzyme B12-dependent enzymes catalyze intramolecular group-transfer reactions and ribonucleotide reduction in a wide variety of organisms from bacteria to animals. They use a super-reactive primary-carbon radical formed by the homolysis of the coenzyme's Co-C bond for catalysis and thus belong to the larger class of "radical enzymes." For understanding the general mechanisms of radical enzymes, it is of great importance to establish the general mechanism of AdoCbl-dependent catalysis using enzymes that catalyze the simplest reactions-such as diol dehydratase, glycerol dehydratase and ethanolamine ammonia-lyase. These enzymes are often called "eliminases." We have studied AdoCbl and eliminases for more than a half century. Progress has always been driven by the development of new experimental methodologies. In this chapter, we describe our investigations on these enzymes, including their metabolic roles, gene cloning, preparation, characterization, activity assays, and mechanistic studies, that have been conducted using a wide range of biochemical and structural methodologies we have developed.
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Affiliation(s)
- Tetsuo Toraya
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan.
| | - Takamasa Tobimatsu
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Koichi Mori
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Mamoru Yamanishi
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Naoki Shibata
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo, Japan
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Chowdhury NP, Moon J, Müller V. Adh4, an alcohol dehydrogenase controls alcohol formation within bacterial microcompartments in the acetogenic bacterium Acetobacterium woodii. Environ Microbiol 2020; 23:499-511. [PMID: 33283462 DOI: 10.1111/1462-2920.15340] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/18/2020] [Accepted: 11/30/2020] [Indexed: 01/23/2023]
Abstract
Acetobacterium woodii utilizes the Wood-Ljungdahl pathway for reductive synthesis of acetate from carbon dioxide. However, A. woodii can also perform non-acetogenic growth on 1,2-propanediol (1,2-PD) where instead of acetate, equal amounts of propionate and propanol are produced as metabolic end products. Metabolism of 1,2-PD occurs via encapsulated metabolic enzymes within large proteinaceous bodies called bacterial microcompartments. While the genome of A. woodii harbours 11 genes encoding putative alcohol dehydrogenases, the BMC-encapsulated propanol-generating alcohol dehydrogenase remains unidentified. Here, we show that Adh4 of A. woodii is the alcohol dehydrogenase required for propanol/ethanol formation within these microcompartments. It catalyses the NADH-dependent reduction of propionaldehyde or acetaldehyde to propanol or ethanol and primarily functions to recycle NADH within the BMC. Removal of adh4 gene from the A. woodii genome resulted in slow growth on 1,2-PD and the mutant displayed reduced propanol and enhanced propionate formation as a metabolic end product. In sum, the data suggest that Adh4 is responsible for propanol formation within the BMC and is involved in redox balancing in the acetogen, A. woodii.
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Affiliation(s)
- Nilanjan Pal Chowdhury
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Frankfurt, Germany
| | - Jimyung Moon
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Frankfurt, Germany
| | - Volker Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Frankfurt, Germany
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6
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Modulation of Enterohaemorrhagic Escherichia coli Survival and Virulence in the Human Gastrointestinal Tract. Microorganisms 2018; 6:microorganisms6040115. [PMID: 30463258 PMCID: PMC6313751 DOI: 10.3390/microorganisms6040115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/16/2018] [Accepted: 11/18/2018] [Indexed: 01/05/2023] Open
Abstract
Enterohaemorrhagic Escherichia coli (EHEC) is a major foodborne pathogen responsible for human diseases ranging from diarrhoea to life-threatening complications. Survival of the pathogen and modulation of virulence gene expression along the human gastrointestinal tract (GIT) are key features in bacterial pathogenesis, but remain poorly described, due to a paucity of relevant model systems. This review will provide an overview of the in vitro and in vivo studies investigating the effect of abiotic (e.g., gastric acid, bile, low oxygen concentration or fluid shear) and biotic (e.g., gut microbiota, short chain fatty acids or host hormones) parameters of the human gut on EHEC survival and/or virulence (especially in relation with motility, adhesion and toxin production). Despite their relevance, these studies display important limitations considering the complexity of the human digestive environment. These include the evaluation of only one single digestive parameter at a time, lack of dynamic flux and compartmentalization, and the absence of a complex human gut microbiota. In a last part of the review, we will discuss how dynamic multi-compartmental in vitro models of the human gut represent a novel platform for elucidating spatial and temporal modulation of EHEC survival and virulence along the GIT, and provide new insights into EHEC pathogenesis.
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A Cobalamin Activity-Based Probe Enables Microbial Cell Growth and Finds New Cobalamin-Protein Interactions across Domains. Appl Environ Microbiol 2018; 84:AEM.00955-18. [PMID: 30006406 DOI: 10.1128/aem.00955-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/25/2018] [Indexed: 01/07/2023] Open
Abstract
Understanding the factors that regulate microbe function and microbial community assembly, function, and fitness is a grand challenge. A critical factor and an important enzyme cofactor and regulator of gene expression is cobalamin (vitamin B12). Our knowledge of the roles of vitamin B12 is limited, because technologies that enable in situ characterization of microbial metabolism and gene regulation with minimal impact on cell physiology are needed. To meet this need, we show that a synthetic probe mimic of B12 supports the growth of B12-auxotrophic bacteria and archaea. We demonstrate that a B12 activity-based probe (B12-ABP) is actively transported into Escherichia coli cells and converted to adenosyl-B12-ABP akin to native B12 Identification of the proteins that bind the B12-ABP in vivo in E. coli, a Rhodobacteraceae sp. and Haloferax volcanii, demonstrate the specificity for known and novel B12 protein targets. The B12-ABP also regulates the B12 dependent RNA riboswitch btuB and the transcription factor EutR. Our results demonstrate a new approach to gain knowledge about the role of B12 in microbe functions. Our approach provides a powerful nondisruptive tool to analyze B12 interactions in living cells and can be used to discover the role of B12 in diverse microbial systems.IMPORTANCE We demonstrate that a cobalamin chemical probe can be used to investigate in vivo roles of vitamin B12 in microbial growth and regulation by supporting the growth of B12 auxotrophic bacteria and archaea, enabling biological activity with three different cell macromolecules (RNA, DNA, and proteins), and facilitating functional proteomics to characterize B12-protein interactions. The B12-ABP is both transcriptionally and translationally able to regulate gene expression analogous to natural vitamin B12 The application of the B12-ABP at biologically relevant concentrations facilitates a unique way to measure B12 microbial dynamics and identify new B12 protein targets in bacteria and archaea. We demonstrate that the B12-ABP can be used to identify in vivo protein interactions across diverse microbes, from E. coli to microbes isolated from naturally occurring phototrophic biofilms to the salt-tolerant archaea Haloferax volcanii.
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8
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Cobalamin-dependent dehydratases and a deaminase: Radical catalysis and reactivating chaperones. Arch Biochem Biophys 2014; 544:40-57. [DOI: 10.1016/j.abb.2013.11.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 11/04/2013] [Accepted: 11/08/2013] [Indexed: 01/12/2023]
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9
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Fowler CC, Sugiman-Marangos S, Junop MS, Brown ED, Li Y. Exploring intermolecular interactions of a substrate binding protein using a riboswitch-based sensor. ACTA ACUST UNITED AC 2013; 20:1502-12. [PMID: 24290881 DOI: 10.1016/j.chembiol.2013.10.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 10/06/2013] [Accepted: 10/12/2013] [Indexed: 12/31/2022]
Abstract
The study of biological transporters can be hampered by a dearth of methodology for tracking their activity within cells. Here, we present a means of monitoring the function of transport machinery within bacteria, exploiting a genetically encoded riboswitch-based sensor to detect the accumulation of the substrate in the cytoplasm. This method was used to investigate the model ABC transporter BtuC2D2F, which permits vitamin B12 uptake in Escherichia coli. We exploited the wealth of structural data available for this transporter to probe the functional and mechanistic importance of key residues of the substrate binding protein BtuF that are predicted to support its interaction with its substrate or with the BtuC channel-forming subunits. Our results reveal molecular interaction requirements for substrate binding proteins and demonstrate the utility of riboswitch-based sensors in the study of biological transport.
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Affiliation(s)
- Casey C Fowler
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Seiji Sugiman-Marangos
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Murray S Junop
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada; Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada; Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada; Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada.
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10
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Bologna FP, Campos-Bermudez VA, Saavedra DD, Andreo CS, Drincovich MF. Characterization of Escherichia coli EutD: a phosphotransacetylase of the ethanolamine operon. J Microbiol 2010; 48:629-36. [PMID: 21046341 DOI: 10.1007/s12275-010-0091-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Accepted: 05/11/2010] [Indexed: 10/18/2022]
Abstract
The Escherichia coli genes pta and eutD encode proteins containing the phosphate-acetyltransferase domain. EutD is composed only by this domain and belongs to the ethanolamine operon. This enzyme has not been characterized yet, and its relationship to the multimodular E. coli phosphotransacetylase (Pta) remains unclear. In the present work, a detailed characterization of EutD from E. coli (EcEutD) was performed. The enzyme is a more efficient phosphotransacetylase than E. coli Pta (EcPta) in catalyzing its reaction in either direction and assembles as a dimer, being differentially modulated by EcPta effectors. When comparing EutD and Pta, both from E. coli, certain divergent regions of the primary structure responsible for their unique properties can be found. The growth on acetate of the E. coli pta acs double-mutant strain, was complemented by either introducing EcEutD or by inducing the eut operon with ethanolamine. In this case, the expression of a phosphotransacetylase different from Pta was confirmed by activity assays. Overall, the results indicate that EcEutD and Pta, although able to catalyse the same reaction, display differential efficiency and regulation, and also differ in the induction of their expression. However, under certain growth conditions, they can fulfil equal roles in E. coli metabolism.
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Affiliation(s)
- Federico P Bologna
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Suipacha, 531 Rosario, Argentina
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Akita K, Hieda N, Baba N, Kawaguchi S, Sakamoto H, Nakanishi Y, Yamanishi M, Mori K, Toraya T. Purification and some properties of wild-type and N-terminal-truncated ethanolamine ammonia-lyase of Escherichia coli. J Biochem 2009; 147:83-93. [PMID: 19762342 DOI: 10.1093/jb/mvp145] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The methods of homologous high-level expression and simple large-scale purification for coenzyme B(12)-dependent ethanolamine ammonia-lyase of Escherichia coli were developed. The eutB and eutC genes in the eut operon encoded the large and small subunits of the enzyme, respectively. The enzyme existed as the heterododecamer alpha(6)beta(6). Upon active-site titration with adeninylpentylcobalamin, a strong competitive inhibitor for coenzyme B(12), the binding of 1 mol of the inhibitor per mol of the alphabeta unit caused complete inhibition of enzyme, in consistent with its subunit structure. EPR spectra indicated the formation of substrate-derived radicals during catalysis and the binding of cobalamin in the base-on mode, i.e. with 5,6-dimethylbenzimidazole coordinating to the cobalt atom. The purified wild-type enzyme underwent aggregation and inactivation at high concentrations. Limited proteolysis with trypsin indicated that the N-terminal region is not essential for catalysis. His-tagged truncated enzymes were similar to the wild-type enzyme in catalytic properties, but more resistant to p-chloromercuribenzoate than the wild-type enzyme. A truncated enzyme was highly soluble even in the absence of detergent and resistant to aggregation and oxidative inactivation at high concentrations, indicating that a short N-terminal sequence is sufficient to change the solubility and stability of the enzyme.
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Affiliation(s)
- Keita Akita
- Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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12
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Sheppard DE, Penrod JT, Bobik T, Kofoid E, Roth JR. Evidence that a B12-adenosyl transferase is encoded within the ethanolamine operon of Salmonella enterica. J Bacteriol 2004; 186:7635-44. [PMID: 15516577 PMCID: PMC524904 DOI: 10.1128/jb.186.22.7635-7644.2004] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Adenosylcobalamin (Ado-B12) is both the cofactor and inducer of ethanolamine ammonia lyase (EA-lyase), a catabolic enzyme for ethanolamine. De novo synthesis of Ado-B12 by Salmonella enterica occurs only under anaerobic conditions. Therefore, aerobic growth on ethanolamine requires import of Ado-B12 or a precursor (CN-B12 or OH-B12) that can be adenosylated internally. Several known enzymes adenosylate corrinoids. The CobA enzyme transfers adenosine from ATP to a biosynthetic intermediate in de novo B12 synthesis and to imported CN-B12, OH-B12, or Cbi (a B12 precursor). The PduO adenosyl transferase is encoded in an operon (pdu) for cobalamin-dependent propanediol degradation and is induced by propanediol. Evidence is presented here that a third transferase (EutT) is encoded within the operon for ethanolamine utilization (eut). Surprisingly, these three transferases share no apparent sequence similarity. CobA produces sufficient Ado-B12 to initiate eut operon induction and to serve as a cofactor for EA-lyase when B12 levels are high. Once the eut operon is induced, the EutT transferase supplies more Ado-B12 during the period of high demand. Another protein encoded in the operon (EutA) protects EA-lyase from inhibition by CN-B12 but does so without adenosylation of this corrinoid.
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Affiliation(s)
- David E Sheppard
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
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Toraya T. Radical catalysis in coenzyme B12-dependent isomerization (eliminating) reactions. Chem Rev 2003; 103:2095-127. [PMID: 12797825 DOI: 10.1021/cr020428b] [Citation(s) in RCA: 312] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tetsuo Toraya
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-naka, Okayama 700-8530, Japan.
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14
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Sherburn RE, Large PJ. Amine borate catabolism by bacteria isolated from contaminated metal-working fluids. J Appl Microbiol 1999; 87:668-75. [PMID: 10594706 DOI: 10.1046/j.1365-2672.1999.00906.x] [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]
Abstract
Four bacterial strains (tentatively identified as strains of Aeromonas, Pseudomonas, Flavobacterium and Bacillus) isolated from contaminated metal-working fluids were assayed for the capacity to utilize the borate derivatives of monoethanolamine (MEA), diethanolamine (DEA) and triethanolamine (TEA). Two of these strains, isolates AV1 (Flavobacterium) and CL1 (Bacillus) were capable of growth on each of the borate esters with cell yields of 0.6 gl - 1 for AV1 cultured on DEA- and TEA-borate, 0.3-0.4 gl - 1 for CL1 cultured on DEA- and TEA-borate and approximately 1.4 gl - 1 for AV1 and CL1 cultured on MEA-borate. In the case of strain CL1, growth yields on TEA- or DEA-borate as substrates were doubled by the addition of potassium ions. Lower ethanolamines, glycolaldehyde, acetaldehyde and ammonia were identified as breakdown products. The enzymes produced during growth upon the alkanolamine borates were shown to possess similar properties to those seen for cells cultured upon alkanolamine hydrochlorides.
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15
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Kofoid E, Rappleye C, Stojiljkovic I, Roth J. The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins. J Bacteriol 1999; 181:5317-29. [PMID: 10464203 PMCID: PMC94038 DOI: 10.1128/jb.181.17.5317-5329.1999] [Citation(s) in RCA: 215] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The eut operon of Salmonella typhimurium encodes proteins involved in the cobalamin-dependent degradation of ethanolamine. Previous genetic analysis revealed six eut genes that are needed for aerobic use of ethanolamine; one (eutR), encodes a positive regulator which mediates induction of the operon by vitamin B12 plus ethanolamine. The DNA sequence of the eut operon included 17 genes, suggesting a more complex pathway than that revealed genetically. We have correlated an open reading frame in the sequence with each of the previously identified genes. Nonpolar insertion and deletion mutations made with the Tn10-derived transposable element T-POP showed that at least 10 of the 11 previously undetected eut genes have no Eut phenotype under the conditions tested. Of the dispensable eut genes, five encode apparent homologues of proteins that serve (in other organisms) as shell proteins of the carboxysome. This bacterial organelle, found in photosynthetic and sulfur-oxidizing bacteria, may contribute to CO2 fixation by concentrating CO2 and excluding oxygen. The presence of these homologues in the eut operon of Salmonella suggests that CO2 fixation may be a feature of ethanolamine catabolism in Salmonella.
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Affiliation(s)
- E Kofoid
- Department of Biology, University of Utah, Salt Lake City, Utah 84112, USA
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16
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Abstract
This review examines deoxyadenosylcobalamin (Ado-B12) biosynthesis, transport, use, and uneven distribution among living forms. We describe how genetic analysis of enteric bacteria has contributed to these issues. Two pathways for corrin ring formation have been found-an aerobic pathway (in P. denitrificans) and an anaerobic pathway (in P. shermanii and S. typhimurium)-that differ in the point of cobalt insertion. Analysis of B12 transport in E. coli reveals two systems: one (with two proteins) for the outer membrane, and one (with three proteins) for the inner membrane. To account for the uneven distribution of B12 in living forms, we suggest that the B12 synthetic pathway may have evolved to allow anaerobic fermentation of small molecules in the absence of an external electron acceptor. Later, evolution of the pathway produced siroheme, (allowing use of inorganic electron acceptors), chlorophyll (O2 production), and heme (aerobic respiration). As oxygen became a larger part of the atmosphere, many organisms lost fermentative functions and retained dependence on newer, B12 functions that did not involve fermentation. Paradoxically, Salmonella spp. synthesize B12 only anaerobically but can use B12 (for degradation of ethanolamine and propanediol) only with oxygen. Genetic analysis of the operons for these degradative functions indicate that anaerobic degradation is important. Recent results suggest that B12 can be synthesized and used during anaerobic respiration using tetrathionate (but not nitrate or fumarate) as an electron acceptor. The branch of enteric taxa from which Salmonella spp. and E. coli evolved appears to have lost the ability to synthesize B12 and the ability to use it in propanediol and glycerol degradation. Salmonella spp., but not E. coli, have acquired by horizontal transfer the ability to synthesize B12 and degrade propanediol. The acquired ability to degrade propanediol provides the selective force that maintains B12 synthesis in this group.
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Affiliation(s)
- J R Roth
- Department of Biology, University of Utah, Salt Lake City 84112, USA
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Sheppard DE, Roth JR. A rationale for autoinduction of a transcriptional activator: ethanolamine ammonia-lyase (EutBC) and the operon activator (EutR) compete for adenosyl-cobalamin in Salmonella typhimurium. J Bacteriol 1994; 176:1287-96. [PMID: 8113167 PMCID: PMC205191 DOI: 10.1128/jb.176.5.1287-1296.1994] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The ethanolamine utilization (eut) operon of Salmonella typhimurium is controlled by a positive regulatory protein (EutR) which stimulates eut operon expression in response to the simultaneous presence of two effectors, ethanolamine and adenosyl-cobalamin (Ado-B12). Ado-B12 is a cofactor for ethanolamine ammonia-lyase (lyase), the first enzyme in the ethanolamine-degradative pathway. The dependence of this pathway on the use of Ado-B12 as an effector in eut operon induction may be explained by its role in the degradation of ethanolamine and the fact that this cofactor is not always made by S. typhimurium. The eutR gene lies within the eut operon, and its autoinduction is required for maximum operon expression. Evidence is presented that the placement of the eutR regulatory gene within the operon provides a means of balancing the competition between lyase and the regulatory protein for a very small pool of Ado-B12. Since both lyase and the regulatory protein are induced, they can compete more equally for a small pool of Ado-B12. This permits both continued eut operon induction and lyase activity. Two general observations support this model. First, mutations that inactivate lyase allow the operon to be fully induced by a lower level of exogenous cobalamin (CN-B12) than required by a wild-type operon. This increase in sensitivity is measured as a reduction in the apparent Km for operon induction by exogenous CN-B12. Second, the maximum level of operon induction by excess CN-B12 is dictated by the level of EutR regulatory protein, regardless of the level of lyase.
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Affiliation(s)
- D E Sheppard
- School of Life and Health Sciences, University of Delaware, Newark 19716
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Faust LP, Babior BM. Overexpression, purification, and some properties of the AdoCbl-dependent ethanolamine ammonia-lyase from Salmonella typhimurium. Arch Biochem Biophys 1992; 294:50-4. [PMID: 1550360 DOI: 10.1016/0003-9861(92)90135-j] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Recombinant ethanolamine ammonia-lyase from S. typhimurium has been overexpressed and purified in large quantities by a simple procedure. The molecular weight of the native enzyme is about 480 kDa, and it contains two active sites/molecule as shown by kinetic studies and by titration with CNCbl. Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis confirms earlier cloning studies indicating that it is composed of two kinds of subunits, one of MW 31 kDa and the other of MW 50 kDa. These subunits, inactive by themselves, combine to produce an active enzyme whose composition is most likely alpha 6 beta 6. The Km for AdoCbl is 0.5 microM, and the turnover number is 55 s-1 per active site at 22 degrees C.
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Affiliation(s)
- L P Faust
- Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, California 92037
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Faust LR, Connor JA, Roof DM, Hoch JA, Babior BM. Cloning, sequencing, and expression of the genes encoding the adenosylcobalamin-dependent ethanolamine ammonia-lyase of Salmonella typhimurium. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)38368-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Roof DM, Roth JR. Functions required for vitamin B12-dependent ethanolamine utilization in Salmonella typhimurium. J Bacteriol 1989; 171:3316-23. [PMID: 2656649 PMCID: PMC210052 DOI: 10.1128/jb.171.6.3316-3323.1989] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
When B12 is available, Salmonella typhimurium can degrade ethanolamine to provide a source of carbon and nitrogen. B12 is essential since it is a cofactor for ethanolamine ammonia-lyase, the first enzyme in ethanolamine breakdown. S. typhimurium makes B12 only under anaerobic conditions; in the presence of oxygen, exogenous B12 must be provided to permit ethanolamine utilization. Genes required for ethanolamine utilization are encoded in the eut operon. For complementation testing, an F' plasmid containing the eut genes was constructed by transposition of the eut operon (flanked by two Tn10 elements) to an existing F plasmid. Complementation tests defined six genes in the eut operon. Three of these genes encode enzymes known to be involved in degradation of ethanolamine: ethanolamine ammonia-lyase (eutB and eutC) and acetaldehyde dehydrogenase (eutE). One gene (eutR) seems to encode a positive regulatory protein required for induction of transcription of eut. The function of one of the remaining two genes (eutA) was shown to be required for ethanolamine utilization only when cyano-B12 or hydroxy-B12 were the precursors of the adenosyl-B12 cofactor of ethanolamine ammonia-lyase; eutA mutants could use ethanolamine as the nitrogen source only when adenosyl-B12 was provided. No function has been assigned to the eutD gene, which is required for use of ethanolamine as a carbon source. Ethanolamine uptake assays of eut mutants suggest that no ethanolamine permease is encoded in the eut operon.
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Affiliation(s)
- D M Roof
- Department of Biology, University of Utah, Salt Lake City 84112
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21
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Abstract
Ethanolamine can serve as the sole source of carbon and nitrogen for Salmonella typhimurium if vitamin B12 is present to serve as a cofactor. The pathway for ethanolamine utilization has been investigated in order to understand its regulation and determine whether the pathway is important to the selective forces that have maintained the ability to synthesize B12 in S. typhimurium. We isolated mutants that are defective in ethanolamine utilization (eut mutants). These mutants defined a cluster of genes located between purC and cysA at 50 min on the Salmonella chromosome. A genetic map of the eut region was constructed. Included in the map are mutations which affect ethanolamine ammonia lyase, the first degradative enzyme, and mutations which affect the second enzyme in the pathway, acetaldehyde dehydrogenase. Transcriptional regulation of the eut genes was studied by using eut-lac operon fusions created by insertion of Mu d lac. Transcription is induced by the simultaneous presence of ethanolamine and B12 in the growth medium. The eut genes constitute a single unit of transcription. One class of mutations located at the promoter-distal end of the eut operon prevent induction of transcription.
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Affiliation(s)
- D M Roof
- Department of Biology, University of Utah 84112
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Wolf JB, Brey RN. Isolation and genetic characterizations of Bacillus megaterium cobalamin biosynthesis-deficient mutants. J Bacteriol 1986; 166:51-8. [PMID: 3082859 PMCID: PMC214555 DOI: 10.1128/jb.166.1.51-58.1986] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Ethanolamine is deaminated by the action of ethanolamine ammonia-lyase (EC 4.3.1.7), an adenosylcobalamin-dependent enzyme. Consequently, to grow on ethanolamine as a sole nitrogen source, Bacillus megaterium requires vitamin B12. Identification of B. megaterium mutants deficient for growth on ethanolamine as the sole nitrogen source yielded a total of 34 vitamin B12 auxotrophs. The vitamin B12 auxotrophs were divided into two major phenotypic groups: Cob mutants, which could use cobinamide or vitamin B12 to grow on ethanolamine, and Cbl mutants, which could be supplemented only by vitamin B12. The Cob mutants were resolved into six classes and the Cbl mutants were resolved into three, based on the spectrum of cobalt-labeled corrinoid compounds which they accumulated. Although some radiolabeled cobalamin was detected in the wild type, little or none was evident in the auxotrophs. The results indicate that Cob mutants contain lesions in biosynthetic steps before the synthesis of combinamide, while Cbl mutants are defective in the conversion of cobinamide to cobalamin. Analysis of phage-mediated transduction experiments revealed tight genetic linkage within the Cob class and within the Cbl class. Similar transduction analysis indicated the Cob and Cbl classes are weakly linked. In addition, cross-feeding experiments in which extracts prepared from mutants were examined for their effect on growth of various other mutants allowed a partial ordering of mutations within the cobalamin biosynthetic pathway.
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Shukla SD, Turner JM. Microbial metabolism of amino alcohols. Biosynthetic utilization of ethanolamine for lipid synthesis by bacteria. Biochem J 1980; 186:13-9. [PMID: 7370003 PMCID: PMC1161499 DOI: 10.1042/bj1860013] [Citation(s) in RCA: 7] [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
1. Ten bacteria utilizing [2-14C]ethanol-2-amine as the sole or major source of nitrogen for growth on glycerol + salts medium incorporated radioactivity into a variety of bacterial substances. A high proportion was commonly found in lipid fractions, particularly in the case of Erwinia carotovora. 2. Detailed studies of [14C]ethanolamine incorporation into lipids by five bacteria, including E. carotovora, showed that all detectable lipids were labelled. Even where phosphatidylethanolamine was the major lipid labelled, radioactivity was predominantly in the fatty acid rather than the base moiety. The labelled fatty acids were identified in each case. 3. The addition of acetate to growth media decreased the incorporation of radioactivity from ethanolamine into both fatty acid and phosphatidyl-base fragments of lipids from all the bacteria except Mycobacterium smegmatis. Experiments with [3H]ethanolamine and [14C]acetate confirmed that unlabelled acetate decreased the incorporation of both radioactive isotopes into lipids, except in the case of M. smegmatis. 4. Enzyme studies suggested one of two metabolic routes between ethanolamine and acetyl-CoA for each of four bacteria. A role for ethanolamine O-phosphate was not obligatory for the incorporation of [14C]ethanolamine into phospholipids, but correlated with CoA-independent aldehyde dehydrogenase activity.
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Blackwell CM, Turner JM. Microbial metabolism of amino alcohols. Formation of coenzyme B12-dependent ethanolamine ammonia-lyase and its concerted induction in Escherichia coli. Biochem J 1978; 176:751-7. [PMID: 371614 PMCID: PMC1186297 DOI: 10.1042/bj1760751] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
1. Kinetic studies of ethanolamine ammonia-lyase formation by Escherichia coli suggested that coenzyme B12 (5'-deoxyadenosylcobalamin), with ethanolamine, is a co-inducer. 2. Enzymic and immunological tests failed to show the formation of complementary enzyme components induced separately by ethanolamine and cobalamin respectively. 3. Although specific for ethanolamine as the substrate, enzyme formation was induced by certain analogues, e.g. 2-aminopropan-1-ol. 4. Experiments with cyano[57Co]-cobalamin suggested that neither coenzyme B12 nor some more tightly bound coenzymically inactive cobamide was necessary for enzyme stability in vitro. 5. Mutants of E. coli were obtained which formed ethanolamine ammonia-lyase apoenzyme constitutively, showing that neither ethanolamine nor cobalamin was required for assembly or post-transcriptional stability of the enzyme in vivo. Constitutive enzyme formation was subject to catabolite repression, particularly by glucose. 6. It appears likely that ethanolamine and coenzyme B12, acting in concert, induce ethanolamine ammonia-lyase formation. The term 'concerted' induction is proposed for this phenomenon.
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