1
|
Morales LT, González-García LN, Orozco MC, Restrepo S, Vives MJ. The genomic study of an environmental isolate of Scedosporium apiospermum shows its metabolic potential to degrade hydrocarbons. Stand Genomic Sci 2017; 12:71. [PMID: 29225727 PMCID: PMC5716253 DOI: 10.1186/s40793-017-0287-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/23/2017] [Indexed: 01/04/2023] Open
Abstract
Crude oil contamination of soils and waters is a worldwide problem, which has been actively addressed in recent years. Sequencing genomes of microorganisms involved in the degradation of hydrocarbons have allowed the identification of several promoters, genes, and degradation pathways of these contaminants. This knowledge allows a better understanding of the functional dynamics of microbial degradation. Here, we report a first draft of the 44.2 Mbp genome assembly of an environmental strain of the fungus Scedosporium apiospermum. The assembly consisted of 178 high-quality DNA scaffolds with 1.93% of sequence repeats identified. A total of 11,195 protein-coding genes were predicted including a diverse group of gene families involved in hydrocarbon degradation pathways like dioxygenases and cytochrome P450. The metabolic pathways identified in the genome can potentially degrade hydrocarbons like chloroalkane/alkene, chorocyclohexane, and chlorobenzene, benzoate, aminobenzoate, fluorobenzoate, toluene, caprolactam, geraniol, naphthalene, styrene, atrazine, dioxin, xylene, ethylbenzene, and polycyclic aromatic hydrocarbons. The comparison analysis between this strain and the previous sequenced clinical strain showed important differences in terms of annotated genes involved in the hydrocarbon degradation process.
Collapse
Affiliation(s)
- Laura T Morales
- Centro de Investigaciones Microbiológicas, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Laura N González-García
- Laboratorio de Micología y Fitopatología Uniandes, Universidad de los Andes, Bogotá, Colombia
| | - María C Orozco
- Centro de Investigaciones Microbiológicas, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Silvia Restrepo
- Laboratorio de Micología y Fitopatología Uniandes, Universidad de los Andes, Bogotá, Colombia
| | - Martha J Vives
- Centro de Investigaciones Microbiológicas, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.,Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| |
Collapse
|
2
|
Adachi T, Izumi A, Rea D, Park SY, Tame JRH, Roper DI. Expression, purification and crystallization of 2-oxo-hept-4-ene-1,7-dioate hydratase (HpcG) from Escherichia coli C. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:1010-2. [PMID: 17012798 PMCID: PMC2225172 DOI: 10.1107/s1744309106035901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Accepted: 09/05/2006] [Indexed: 12/02/2022]
Abstract
The gene encoding 2-oxo-hept-3-ene-1,7-dioic acid (OHED) hydratase (HpcG) was cloned into the high-expression plasmid pET26b and overexpressed in Escherichia coli BL21(DE3). The enzyme was purified in three steps to greater than 95% purity prior to crystallization. Crystals were obtained by the hanging-drop vapour-diffusion method at 277 K in a number of screening conditions. Crystals measuring up to 1.5 mm in their longest dimension were grown from solutions containing polyethylene glycol 20 000. The crystals belonged to space group P4(1)2(1)2 or P4(3)2(1)2, with unit-cell parameters a = 136, b = 136, c = 192 A. A complete data set was collected to 2.1 A from a single cryocooled crystal at 100 K using synchrotron radiation.
Collapse
Affiliation(s)
- Tomoko Adachi
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, England
| | - Atsushi Izumi
- Division of Protein Design, Yokohama City University, Suehiro 1-7-29, Yokohama, Kanagawa 230-0045, Japan
| | - Dean Rea
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, England
| | - Sam-Yong Park
- Division of Protein Design, Yokohama City University, Suehiro 1-7-29, Yokohama, Kanagawa 230-0045, Japan
| | - Jeremy R. H. Tame
- Division of Protein Design, Yokohama City University, Suehiro 1-7-29, Yokohama, Kanagawa 230-0045, Japan
| | - David I. Roper
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, England
| |
Collapse
|
3
|
Brik A, Dawson PE, Keinan E. The product of the natural reaction catalyzed by 4-oxalocrotonate tautomerase becomes an affinity label of its mutant. Bioorg Med Chem 2002; 10:3891-7. [PMID: 12413840 DOI: 10.1016/s0968-0896(02)00385-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerization of 4-oxalocrotonate, 1, to 2-oxo-3E-hexenedioate, 3, using a general acid/base mechanism that involves a conserved N-terminal proline residue. The P1A and P1G mutants have been shown to catalyze this isomerization but at reduced rates. Analysis of these mutants by mass spectrometry demonstrated that P1A is susceptible to a 1,4-addition of the N-terminal primary amine across the double bond of enone 3 to form a covalent adduct. Although slower than the isomerization reaction, the addition is fast, with 50% of the active sites being alkylated within 12 min. By contrast, the wt4-OT shows no detectable modification over 24 h. These results support the hypothesis that avoidance of nucleophilic reactions, such as the irreversible Michael addition to the product, could be a contributing factor in the evolutionary conservation of N-terminal proline residues in 4OT.
Collapse
Affiliation(s)
- Ashraf Brik
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | | |
Collapse
|
4
|
Díaz E, Ferrández A, Prieto MA, García JL. Biodegradation of aromatic compounds by Escherichia coli. Microbiol Mol Biol Rev 2001; 65:523-69, table of contents. [PMID: 11729263 PMCID: PMC99040 DOI: 10.1128/mmbr.65.4.523-569.2001] [Citation(s) in RCA: 252] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although Escherichia coli has long been recognized as the best-understood living organism, little was known about its abilities to use aromatic compounds as sole carbon and energy sources. This review gives an extensive overview of the current knowledge of the catabolism of aromatic compounds by E. coli. After giving a general overview of the aromatic compounds that E. coli strains encounter and mineralize in the different habitats that they colonize, we provide an up-to-date status report on the genes and proteins involved in the catabolism of such compounds, namely, several aromatic acids (phenylacetic acid, 3- and 4-hydroxyphenylacetic acid, phenylpropionic acid, 3-hydroxyphenylpropionic acid, and 3-hydroxycinnamic acid) and amines (phenylethylamine, tyramine, and dopamine). Other enzymatic activities acting on aromatic compounds in E. coli are also reviewed and evaluated. The review also reflects the present impact of genomic research and how the analysis of the whole E. coli genome reveals novel aromatic catabolic functions. Moreover, evolutionary considerations derived from sequence comparisons between the aromatic catabolic clusters of E. coli and homologous clusters from an increasing number of bacteria are also discussed. The recent progress in the understanding of the fundamentals that govern the degradation of aromatic compounds in E. coli makes this bacterium a very useful model system to decipher biochemical, genetic, evolutionary, and ecological aspects of the catabolism of such compounds. In the last part of the review, we discuss strategies and concepts to metabolically engineer E. coli to suit specific needs for biodegradation and biotransformation of aromatics and we provide several examples based on selected studies. Finally, conclusions derived from this review may serve as a lead for future research and applications.
Collapse
Affiliation(s)
- E Díaz
- Department of Molecular Microbiology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain.
| | | | | | | |
Collapse
|
5
|
Subramanya HS, Roper DI, Dauter Z, Dodson EJ, Davies GJ, Wilson KS, Wigley DB. Enzymatic ketonization of 2-hydroxymuconate: specificity and mechanism investigated by the crystal structures of two isomerases. Biochemistry 1996; 35:792-802. [PMID: 8547259 DOI: 10.1021/bi951732k] [Citation(s) in RCA: 105] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
5-Carboxymethyl-2-hydroxymuconate isomerase (CHMI) and 4-oxalocrotonate tautomerase (4-OT) are enzymes that catalyze the isomerization of unsaturated ketones. They share a common enzyme mechanism, although they show a preference for different substrates. There is no apparent sequence homology between the enzymes. To investigate the molecular mechanism and the basis for their substrate specificity, we have determined the crystal structures of the two enzymes at high resolution. 4-OT is hexameric, with the subunits arranged with 32 symmetry. CHMI is trimeric and has extensive contacts between subunits, which include secondary structural elements. The central core of the CHMI monomer has a fold similar to a 4-OT dimer, but the secondary structural elements that form the subunit contacts around the 3-fold axis are different in the two enzymes. The region of greatest similarity between the two enzymes is a large pocket that is proposed to be the active site. The enzymes appear to operate via a "one-base" mechanism, and the possible role of residues in this pocket is discussed in view of this idea. Finally, the molecular basis for substrate specificity in the two enzymes is discussed.
Collapse
Affiliation(s)
- H S Subramanya
- Laboratory of Molecular Biophysics, University of Oxford, U.K
| | | | | | | | | | | | | |
Collapse
|
6
|
Prieto MA, Díaz E, García JL. Molecular characterization of the 4-hydroxyphenylacetate catabolic pathway of Escherichia coli W: engineering a mobile aromatic degradative cluster. J Bacteriol 1996; 178:111-20. [PMID: 8550403 PMCID: PMC177627 DOI: 10.1128/jb.178.1.111-120.1996] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We have determined and analyzed the nucleic acid sequence of a 14,855-bp region that contains the complete gene cluster encoding the 4-hydroxyphenylacetic acid (4-HPA) degradative pathway of Escherichia coli W (ATCC 11105). This catabolic pathway is composed by 11 genes, i.e., 8 enzyme-encoding genes distributed in two putative operons, hpaBC (4-HPA hydroxylase operon) and hpaGEDFHI (meta-cleavage operon); 2 regulatory genes, hpaR and hpaA; and the gene, hpaX, that encodes a protein related to the superfamily of transmembrane facilitators and appears to be cotranscribed with hpaA. Although comparisons with other aromatic catabolic pathways revealed interesting similarities, some of the genes did not present any similarity to their corresponding counterparts in other pathways, suggesting different evolutionary origins. The cluster is flanked by two genes homologous to the estA (carbon starvation protein) and tsr (serine chemoreceptor) genes of E. coli K-12. A detailed genetic analysis of this region has provided a singular example of how E. coli becomes adapted to novel nutritional sources by the recruitment of a catabolic cassette. Furthermore, the presence of the pac gene in the proximity of the 4-HPA cluster suggests that the penicillin G acylase was a recent acquisition to improve the ability of E. coli W to metabolize a wider range of substrates, enhancing its catabolic versatility. Five repetitive extragenic palindromic sequences that might be involved in transcriptional regulation were found within the cluster. The complete 4-HPA cluster was cloned in plasmid and transposon cloning vectors that were used to engineer E. coli K-12 strains able to grow on 4-HPA. We report here also the in vitro design of new biodegradative capabilities through the construction of a transposable cassette containing the wide substrate range 4-HPA hydroxylase, in order to expand the ortho-cleavage pathway of Pseudomonas putida KT2442 and allow the new recombinant strain to use phenol as the only carbon source.
Collapse
Affiliation(s)
- M A Prieto
- Department of Molecular Microbiology, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | | |
Collapse
|
7
|
Roper DI, Stringfellow JM, Cooper RA. Sequence of the hpcC and hpcG genes of the meta-fission homoprotocatechuic acid pathway of Escherichia coli C: nearly 40% amino-acid identity with the analogous enzymes of the catechol pathway. Gene 1995; 156:47-51. [PMID: 7737515 DOI: 10.1016/0378-1119(95)00082-h] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The meta-fission pathway for homoprotocatechuic acid (HPC) catabolism is chemically analogous to the oxidative meta-fission pathway for catechol degradation and so provides an opportunity to investigate how the enzymes of chemically similar, but specific, pathways might have arisen. Two more genes of the HPC pathway from Escherichia coli C, hpcC, encoding 5-carboxymethyl-2-hydroxymuconic acid semialdehyde (CHMS) dehydrogenase, and hpcG, encoding 2-oxohept-3-ene-1,7-dioic acid (OHED) hydratase, have now been sequenced to aid this analysis. The CHMS dehydrogenase showed 40% amino acid (aa) sequence identity with the corresponding enzyme of the catechol pathway, and the OHED hydratase showed 36% aa sequence identity with the catechol pathway hydratase. The CHMS dehydrogenase is a member of the aldehyde dehydrogenase superfamily that includes enzymes from animal, plant and microbial sources. Since it appears that the dioxygenase, isomerase and decarboxylase enzymes of the two pathways are not closely related, it is proposed that the two sets of enzymes have arisen separately, but with the muconic acid semialdehyde dehydrogenases and the hydratases being recruited, respectively, from the same ancestral sources.
Collapse
Affiliation(s)
- D I Roper
- Department of Biochemistry, University of Leicester, UK
| | | | | |
Collapse
|
8
|
Roper DI, Subramanya HS, Shingler V, Wigley DB. Preliminary crystallographic analysis of 4-oxalocrotonate tautomerase reveals the oligomeric structure of the enzyme. J Mol Biol 1994; 243:799-801. [PMID: 7966298 DOI: 10.1016/0022-2836(94)90050-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Crystals of recombinant 4-oxalocrotonate tautomerase from Pseudomonas sp. strain CF600 have been obtained in a form suitable for X-ray analysis. The enzyme is a highly efficient catalyst and is unusual in that it consists of subunits of only 62 amino acids. It crystallises in the triclinic space group, P1, with unit cell dimensions a = 39.6 A, b = 51.5 A, c = 51.6 A, alpha = 60.0 degrees, beta = 81.4 degrees, gamma = 69.6 degrees. The crystals diffract to beyond 1.9 A resolution and are stable to irradiation with X-rays. Preliminary crystallographic data are not consistent with the previously suggested pentameric structure, but indicate that the complex is in fact a hexamer with 32 symmetry.
Collapse
Affiliation(s)
- D I Roper
- Department of Chemistry, University of York, Heslington, U.K
| | | | | | | |
Collapse
|
9
|
Roper DI, Cooper RA. Purification, nucleotide sequence and some properties of a bifunctional isomerase/decarboxylase from the homoprotocatechuate degradative pathway of Escherichia coli C. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 217:575-80. [PMID: 8223600 DOI: 10.1111/j.1432-1033.1993.tb18279.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A 1.8-kbp region of DNA that appeared from deletion subcloning to code for 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase and 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase was investigated further. By nucleotide sequencing, a single open reading frame was found encoding a polypeptide of M(r)44514. One of the deletion subclones expressed the decarboxylase and isomerase activities at elevated levels and was used to facilitate purification of the enzyme(s). Both activities copurified, indicating that they were distinct activities of the same protein. Some kinetic properties of the purified isomerase/decarboxylase protein were investigated and it was shown that there is a 49,000-fold preference for 2-hydroxyhepta-2,4-diene-1,7-dioate over the structurally related compound 5-carboxymethyl-2-hydroxymuconate, the substrate of a second isomerase in the same catabolic pathway. Comparison of the amino acid sequences of the two isomerases showed only a low level of similarity, suggesting that these two enzymes are not evolutionarily related. However, comparison of the N-terminal half of the isomerase/decarboxylase sequence (residues 1-202) with the second half (residues 203-406) showed significant similarity, suggesting that a duplication may have occurred to produce the bifunctional gene.
Collapse
Affiliation(s)
- D I Roper
- Department of Biochemistry, University of Leicester, England
| | | |
Collapse
|
10
|
Roper DI, Fawcett T, Cooper RA. The Escherichia coli C homoprotocatechuate degradative operon: hpc gene order, direction of transcription and control of expression. MOLECULAR & GENERAL GENETICS : MGG 1993; 237:241-50. [PMID: 8384293 DOI: 10.1007/bf00282806] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Homoprotocatechuate (HPC; 3,4-dihydroxyphenylacetate) is catabolized to Krebs cycle intermediates via extradiol (meta-) cleavage and the necessary enzymes are chromosomally encoded in a variety of bacteria. Based on an analysis of the cloned pathway genes, the Escherichia coli C hpc gene cluster was thought to be arranged in two gene blocks transcribed from a central, divergent, operator/promoter region, which was negatively regulated by the Hpc repressor. By a variety of techniques including expression of cloned hpc genes in pUC18/19 vectors, unidirectional deletion subcloning, hybridization studies and nucleotide sequencing it has now been shown that the hpc pathway structural genes are transcribed in one direction. These experiments have also indicated that a decarboxylase and an isomerase of the pathway are encoded by a single gene (hpcE) and have established the exact structural gene order as hpcRphpcECBDGH. The position of the putative regulatory gene, hpcR, is upstream of the first structural gene (hpcE) for the Hpc pathway enzymes. The deduced open reading frame for the Hpc repressor specifies a protein of 148 amino acids with a subunit molecular weight of 17 kDa. The region between hpcR and the first gene for the pathway enzymes has a sequence similar to that for catabolite activator protein (CAP) binding. This region is immediately upstream of a promoter for the pathway structural genes, which has been identified by transcript mapping.
Collapse
Affiliation(s)
- D I Roper
- Department of Biochemistry, University of Leicester, UK
| | | | | |
Collapse
|
11
|
Chen L, Kenyon G, Curtin F, Harayama S, Bembenek M, Hajipour G, Whitman C. 4-Oxalocrotonate tautomerase, an enzyme composed of 62 amino acid residues per monomer. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)37101-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
12
|
Roper DI, Cooper RA. Subcloning and nucleotide sequence of the 3,4-dihydroxyphenylacetate (homoprotocatechuate) 2,3-dioxygenase gene from Escherichia coli C. FEBS Lett 1990; 275:53-7. [PMID: 2261999 DOI: 10.1016/0014-5793(90)81437-s] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A cloned gene encoding the Escherichia coli C homoprotocatechuate (HPC) dioxygenase, an aromatic ring cleavage enzyme, was used to produce large amounts of the protein. Preparations of E. coli C HPC dioxygenase, whether expressed from the cloned gene or produced by the bacterium, lost activity very rapidly. The pure protein showed one type of subunit of Mr 33,000. The first 21 N-terminal amino acids were sequenced and the data used to confirm that the open reading frame of 831 bp, identified from the nucleotide sequence, encoded HPC dioxygenase. Comparison of the derived amino acid sequence with those of other extradiol and intradiol dioxygenases showed no obvious similarity to any of them.
Collapse
Affiliation(s)
- D I Roper
- Department of Biochemistry, University of Leicester, UK
| | | |
Collapse
|