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Arteaga JE, Cerros K, Rivera-Becerril E, Lara AR, Le Borgne S, Sigala JC. Furfural biotransformation in Acinetobacter baylyi ADP1 and Acinetobacter schindleri ACE. Biotechnol Lett 2021; 43:1043-1050. [PMID: 33590377 DOI: 10.1007/s10529-021-03094-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 02/03/2021] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To determine furfural biotransformation capabilities of Acinetobacter baylyi ADP1 and Acinetobacter schindleri ACE. RESULTS Acinetobacter baylyi ADP1 and A. schindleri ACE could not use furfural as sole carbon source but when acetate was used as substrate, ADP1 and ACE biotransformed 1 g furfural/l in 5 and 9 h, respectively. In both cases, the product of this biotransformation was difurfuryl-ether as shown by FT-IR and 1H and 13C NMR spectroscopy. The presence of furfural decreased the specific growth rate in acetate by 27% in ADP1 and 53% in ACE. For both strains, the MIC of furfural was 1.25 g/l. Nonetheless, ADP1 biotransformed 2 g furfural/l at a rate of 1 g/l/h in the stationary phase of growth. A transcriptional analysis of possible dehydrogenases involved in this biotransformation, identified that the areB and frmA genes were highly overexpressed after the exposure of ADP1 to furfural. The products of these genes are a benzyl-alcohol dehydrogenase and an alcohol dehydrogenase. CONCLUSIONS Acinetobacter baylyi ADP1 is a candidate for the biological detoxification of furfural, a fermentation inhibitor present in lignocellulosic hydrolysates, with the possible direct involvement of the AreB and FrmA enzymes in the process.
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Affiliation(s)
- José Eduardo Arteaga
- Posgrado en Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, 05348, Mexico City, Mexico
| | - Karina Cerros
- Posgrado en Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, 05348, Mexico City, Mexico
| | - Ernesto Rivera-Becerril
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, 05348, Mexico City, Mexico
| | - Alvaro R Lara
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa. Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Alcaldía Cuajimalpa, 05348, Mexico City, Mexico
| | - Sylvie Le Borgne
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa. Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Alcaldía Cuajimalpa, 05348, Mexico City, Mexico
| | - Juan-Carlos Sigala
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa. Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Alcaldía Cuajimalpa, 05348, Mexico City, Mexico.
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Stuani L, Lechaplais C, Salminen AV, Ségurens B, Durot M, Castelli V, Pinet A, Labadie K, Cruveiller S, Weissenbach J, de Berardinis V, Salanoubat M, Perret A. Novel metabolic features in Acinetobacter baylyi ADP1 revealed by a multiomics approach. Metabolomics 2014; 10:1223-1238. [PMID: 25374488 PMCID: PMC4213383 DOI: 10.1007/s11306-014-0662-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 04/07/2014] [Indexed: 11/26/2022]
Abstract
Expansive knowledge of bacterial metabolism has been gained from genome sequencing output, but the high proportion of genes lacking a proper functional annotation in a given genome still impedes the accurate prediction of the metabolism of a cell. To access to a more global view of the functioning of the soil bacterium Acinetobacter baylyi ADP1, we adopted a multi 'omics' approach. Application of RNA-seq transcriptomics and LC/MS-based metabolomics, along with the systematic phenotyping of the complete collection of single-gene deletion mutants of A. baylyi ADP1 made possible to interrogate on the metabolic perturbations encountered by the bacterium upon a biotic change. Shifting the sole carbon source from succinate to quinate elicited in the cell not only a specific transcriptional response, necessary to catabolize the new carbon source, but also a major reorganization of the transcription pattern. Here, the expression of more than 12 % of the total number of genes was affected, most of them being of unknown function. These perturbations were ultimately reflected in the metabolome, in which the concentration of about 50 % of the LC/MS-detected metabolites was impacted. And the differential regulation of many genes of unknown function is probably related to the synthesis of the numerous unidentified compounds that were present exclusively in quinate-grown cells. Together, these data suggest that A. baylyi ADP1 metabolism involves unsuspected enzymatic reactions that await discovery.
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Affiliation(s)
- Lucille Stuani
- Direction des Sciences du Vivant, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Evry, France
- CNRS-UMR8030, Evry, France
- Université d’Evry Val d’Essonne, Evry, France
| | - Christophe Lechaplais
- Direction des Sciences du Vivant, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Evry, France
- CNRS-UMR8030, Evry, France
- Université d’Evry Val d’Essonne, Evry, France
| | - Aaro V. Salminen
- Direction des Sciences du Vivant, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Evry, France
- CNRS-UMR8030, Evry, France
- Université d’Evry Val d’Essonne, Evry, France
- Department of Chemistry and Bioengineering, Tampere University of Technology, Korkeakoulunkatu 10, 33720 Tampere, Finland
| | - Béatrice Ségurens
- Direction des Sciences du Vivant, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Evry, France
- CNRS-UMR8030, Evry, France
- Université d’Evry Val d’Essonne, Evry, France
| | - Maxime Durot
- Direction des Sciences du Vivant, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Evry, France
- CNRS-UMR8030, Evry, France
- Université d’Evry Val d’Essonne, Evry, France
| | - Vanina Castelli
- Direction des Sciences du Vivant, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Evry, France
- CNRS-UMR8030, Evry, France
- Université d’Evry Val d’Essonne, Evry, France
| | - Agnès Pinet
- Direction des Sciences du Vivant, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Evry, France
- CNRS-UMR8030, Evry, France
- Université d’Evry Val d’Essonne, Evry, France
| | - Karine Labadie
- Direction des Sciences du Vivant, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Evry, France
- CNRS-UMR8030, Evry, France
- Université d’Evry Val d’Essonne, Evry, France
| | - Stéphane Cruveiller
- Direction des Sciences du Vivant, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Evry, France
- CNRS-UMR8030, Evry, France
- Université d’Evry Val d’Essonne, Evry, France
| | - Jean Weissenbach
- Direction des Sciences du Vivant, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Evry, France
- CNRS-UMR8030, Evry, France
- Université d’Evry Val d’Essonne, Evry, France
| | - Véronique de Berardinis
- Direction des Sciences du Vivant, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Evry, France
- CNRS-UMR8030, Evry, France
- Université d’Evry Val d’Essonne, Evry, France
| | - Marcel Salanoubat
- Direction des Sciences du Vivant, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Evry, France
- CNRS-UMR8030, Evry, France
- Université d’Evry Val d’Essonne, Evry, France
| | - Alain Perret
- Direction des Sciences du Vivant, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Evry, France
- CNRS-UMR8030, Evry, France
- Université d’Evry Val d’Essonne, Evry, France
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Essential biological processes of an emerging pathogen: DNA replication, transcription, and cell division in Acinetobacter spp. Microbiol Mol Biol Rev 2010; 74:273-97. [PMID: 20508250 DOI: 10.1128/mmbr.00048-09] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Within the last 15 years, members of the bacterial genus Acinetobacter have risen from relative obscurity to be among the most important sources of hospital-acquired infections. The driving force for this has been the remarkable ability of these organisms to acquire antibiotic resistance determinants, with some strains now showing resistance to every antibiotic in clinical use. There is an urgent need for new antibacterial compounds to combat the threat imposed by Acinetobacter spp. and other intractable bacterial pathogens. The essential processes of chromosomal DNA replication, transcription, and cell division are attractive targets for the rational design of antimicrobial drugs. The goal of this review is to examine the wealth of genome sequence and gene knockout data now available for Acinetobacter spp., highlighting those aspects of essential systems that are most suitable as drug targets. Acinetobacter spp. show several key differences from other pathogenic gammaproteobacteria, particularly in global stress response pathways. The involvement of these pathways in short- and long-term antibiotic survival suggests that Acinetobacter spp. cope with antibiotic-induced stress differently from other microorganisms.
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Fischer R, Bleichrodt FS, Gerischer UC. Aromatic degradative pathways in Acinetobacter baylyi underlie carbon catabolite repression. MICROBIOLOGY-SGM 2008; 154:3095-3103. [PMID: 18832315 DOI: 10.1099/mic.0.2008/016907-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Carbon catabolite repression is an important mechanism allowing efficient carbon source utilization. In the soil bacterium Acinetobacter baylyi, this mechanism has been shown to apply to the aromatic degradative pathways for the substrates protocatechuate, p-hydroxybenzoate and vanillate. In this investigation, transcriptional fusions with the gene for luciferase in the gene clusters for the degradation of benzyl esters, anthranilate, benzoate, hydroxycinnamates and dicarboxylates (are, ant, ben, hca and dca genes) were constructed and established in the chromosome of A. baylyi. The respective strains revealed the presence of strong carbon catabolite repression at the transcriptional level. In all cases, succinate and acetate in combination had the strongest repressing effect, and pyruvate (or lactate in case of the ben and hca genes) allowed the highest expression when these carbon sources were supplied together with the respective inducer. The pattern of repression for the different cosubstrates was similar for all operons investigated and was also observed in the absence of the respective inducing compounds, indicating a mechanism that is independent of the respective specific regulators. Repression by acetate and succinate varied between 88 % for the hca genes and 99 % for the pca genes.
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Affiliation(s)
- Rita Fischer
- Institute for Microbiology and Biotechnology, University of Ulm, D-89069 Ulm, Germany
| | - Fenja S Bleichrodt
- Institute for Microbiology and Biotechnology, University of Ulm, D-89069 Ulm, Germany
| | - Ulrike C Gerischer
- Institute for Microbiology and Biotechnology, University of Ulm, D-89069 Ulm, Germany
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Jones RM, Williams PA. Mutational analysis of the critical bases involved in activation of the AreR-regulated sigma54-dependent promoter in Acinetobacter sp. strain ADP1. Appl Environ Microbiol 2003; 69:5627-35. [PMID: 12957953 PMCID: PMC194964 DOI: 10.1128/aem.69.9.5627-5635.2003] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The areR gene in Acinetobacter sp. strain ADP1 regulates the expression of the areCBA genes, which determine growth on benzyl alkanoates. AreR is a member of the NtrC/XylR family of regulatory proteins as determined by sequence homology. Seventy-nine bases upstream of the start of transcription is a region carrying two overlapping inverted repeat (IR) sequences that we predict to be the AreR binding site, also known as the upstream activator site (UAS). IR1 is a near-perfect (16 of 17 bp) repeat separated by 1 bp, and IR2 consists of 9- and 7-bp perfect repeats with a 3-bp gap, with the central bases of the two arms of the repeat separated by 44 and 22 bp. We report here a method for site-directed mutagenesis of chromosomal genes in ADP1 in which linear fragments generated by overlap extension PCR are used to transform ADP1 via its natural transformation system and recombinants are selected by a marker exchange-eviction strategy with a newly created sacB-Km cassette. This method was used to generate 38 strains with designed mutations in the putative UAS upstream of areCBA. The effects of the mutations on areCBA expression were measured by enzyme assays of benzyl alcohol dehydrogenase (AreB) and by reporter gene assays of lacZ inserted into areA. Substitutions or deletions in IR1 had more deleterious effects upon expression when they were in its central region, which overlaps the left arm of IR2, than when they were in its outer regions. By contrast, substitutions in the right arm of IR2 resulted in mutants with relatively high expression levels compared to that of the wild type. Effects of deletions in the right arm of IR2 were very dependent upon the length of the deletion, with 3- or 5-bp deletions reducing expression by >90% whereas an 11-bp deletion in the same area reduced the expression levels by only 50%, suggesting that alterations in the distance and the orientation of the UAS relative to the -24, -12 sigma(54) promoter are critical.
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Affiliation(s)
- Rheinallt M Jones
- School of Biological Sciences, University of Wales Bangor, Bangor, Gwynedd LL57 2UW, Wales, United Kingdom
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Clark TJ, Momany C, Neidle EL. The benPK operon, proposed to play a role in transport, is part of a regulon for benzoate catabolism in Acinetobacter sp. strain ADP1. MICROBIOLOGY (READING, ENGLAND) 2002; 148:1213-1223. [PMID: 11932465 DOI: 10.1099/00221287-148-4-1213] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
BenM and CatM are distinct, but similar, LysR-type transcriptional regulators of the soil bacterium Acinetobacter sp. strain ADP1. Together, the two regulators control the expression of at least 14 genes involved in the degradation of aromatic compounds via the catechol branch of the beta-ketoadipate pathway. In these studies, BenM and CatM were each purified to homogeneity to test the possibility that they regulate the expression of two additional genes, benP and benK, that are adjacent to benM on the chromosome. Each regulator bound to a DNA fragment containing the benP promoter region. Additional transcriptional studies suggested that benP and benK are co-transcribed as an operon, and a site of transcription initiation was identified. Alignment of this initiation site with those of several CatM- and BenM-regulated genes revealed common regulatory motifs. Mutants lacking both CatM and BenM failed to activate benP transcription. The ability of each protein to regulate gene expression was inferred from strains lacking either CatM or BenM that were still capable of increasing benP expression in response to cis,cis-muconate. This compound has previously been shown to induce all enzymes of the catechol branch of the beta-ketoadipate pathway through a complex transcriptional circuit involving CatM and BenM. Thus, the regulated expression of the benPK operon in concert with other genes of the regulon is consistent with the model that BenP, a putative outer-membrane porin, and BenK, an inner-membrane permease, transport aromatic compounds in strain ADP1.
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Affiliation(s)
- Todd J Clark
- Department of Microbiology, University of Georgia, Athens, GA 30602-2605, USA1
| | - Cory Momany
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602, USA2
| | - Ellen L Neidle
- Department of Microbiology, University of Georgia, Athens, GA 30602-2605, USA1
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