1
|
Meriläinen E, Efimova E, Santala V, Santala S. Carbon-wise utilization of lignin-related compounds by synergistically employing anaerobic and aerobic bacteria. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:78. [PMID: 38851749 PMCID: PMC11161944 DOI: 10.1186/s13068-024-02526-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 05/30/2024] [Indexed: 06/10/2024]
Abstract
BACKGROUND Lignin is a highly abundant but strongly underutilized natural resource that could serve as a sustainable feedstock for producing chemicals by microbial cell factories. Because of the heterogeneous nature of the lignin feedstocks, the biological upgrading of lignin relying on the metabolic routes of aerobic bacteria is currently considered as the most promising approach. However, the limited substrate range and the inefficient catabolism of the production hosts hinder the upgrading of lignin-related aromatics. Particularly, the aerobic O-demethylation of the methoxyl groups in aromatic substrates is energy-limited, inhibits growth, and results in carbon loss in the form of CO2. RESULTS In this study, we present a novel approach for carbon-wise utilization of lignin-related aromatics by the integration of anaerobic and aerobic metabolisms. In practice, we employed an acetogenic bacterium Acetobacterium woodii for anaerobic O-demethylation of aromatic compounds, which distinctively differs from the aerobic O-demethylation; in the process, the carbon from the methoxyl groups is fixed together with CO2 to form acetate, while the aromatic ring remains unchanged. These accessible end-metabolites were then utilized by an aerobic bacterium Acinetobacter baylyi ADP1. By utilizing this cocultivation approach, we demonstrated an upgrading of guaiacol, an abundant but inaccessible substrate to most microbes, into a plastic precursor muconate, with a nearly equimolar yields (0.9 mol/mol in a small-scale cultivation and 1.0 mol/mol in a one-pot bioreactor cultivation). The process required only a minor genetic engineering, namely a single gene knock-out. Noticeably, by employing a metabolic integration of the two bacteria, it was possible to produce biomass and muconate by utilizing only CO2 and guaiacol as carbon sources. CONCLUSIONS By the novel approach, we were able to overcome the issues related to aerobic O-demethylation of methoxylated aromatic substrates and demonstrated carbon-wise conversion of lignin-related aromatics to products with yields unattainable by aerobic processes. This study highlights the power of synergistic integration of distinctive metabolic features of bacteria, thus unlocking new opportunities for harnessing microbial cocultures in upgrading challenging feedstocks.
Collapse
Affiliation(s)
- Ella Meriläinen
- Faculty of Engineering and Natural Sciences, Tampere University, Hervanta Campus, Korkeakoulunkatu 8, 33720, Tampere, Finland
| | - Elena Efimova
- Faculty of Engineering and Natural Sciences, Tampere University, Hervanta Campus, Korkeakoulunkatu 8, 33720, Tampere, Finland
| | - Ville Santala
- Faculty of Engineering and Natural Sciences, Tampere University, Hervanta Campus, Korkeakoulunkatu 8, 33720, Tampere, Finland
| | - Suvi Santala
- Faculty of Engineering and Natural Sciences, Tampere University, Hervanta Campus, Korkeakoulunkatu 8, 33720, Tampere, Finland.
| |
Collapse
|
2
|
Ren X, Palmer LD. Acinetobacter Metabolism in Infection and Antimicrobial Resistance. Infect Immun 2023:e0043322. [PMID: 37191522 DOI: 10.1128/iai.00433-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Acinetobacter infections have high rates of mortality due to an increasing incidence of infections by multidrug-resistant (MDR) and extensively-drug-resistant (XDR) strains. Therefore, new therapeutic strategies for the treatment of Acinetobacter infections are urgently needed. Acinetobacter spp. are Gram-negative coccobacilli that are obligate aerobes and can utilize a wide variety of carbon sources. Acinetobacter baumannii is the main cause of Acinetobacter infections, and recent work has identified multiple strategies A. baumannii uses to acquire nutrients and replicate in the face of host nutrient restriction. Some host nutrient sources also serve antimicrobial and immunomodulatory functions. Hence, understanding Acinetobacter metabolism during infection may provide new insights into novel infection control measures. In this review, we focus on the role of metabolism during infection and in resistance to antibiotics and other antimicrobial agents and discuss the possibility that metabolism may be exploited to identify novel targets to treat Acinetobacter infections.
Collapse
Affiliation(s)
- Xiaomei Ren
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
| | - Lauren D Palmer
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
| |
Collapse
|
3
|
Dhamale T, Saha BK, Papade SE, Singh S, Phale PS. A unique global metabolic trait of Pseudomonas bharatica CSV86 T: metabolism of aromatics over simple carbon sources and co-metabolism with organic acids. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35925665 DOI: 10.1099/mic.0.001206] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Hierarchical utilization of substrate by microbes (utilization of simple carbon sources prior to complex ones) poses a major limitation to the efficient remediation of aromatic pollutants. Aromatic compounds, being complex and reduced in nature, appear to be a deferred choice as the carbon source in the presence of a plethora of simple organic compounds in the environment. The soil bacterium Pseudomonas bharatica CSV86T displays a unique carbon source utilization hierarchy. It preferentially utilizes aromatics over glucose and co-metabolizes them with succinate or pyruvate (Basu et al., 2006, Applied and Environmental Microbiology, 72 : 22226-2230). In the present study, the substrate utilization hierarchy for strain CSV86T was tested for additional simple carbon sources such as glycerol, acetate, and tri-carboxylic acid (TCA) cycle intermediates like α-ketoglutarate and fumarate. When grown on a mixture of aromatics (benzoate or naphthalene) plus glycerol, the strain displayed a diauxic growth profile with significantly high activity of aromatic utilization enzymes (catechol 1,2- or 2,3-dioxygenase, respectively) in the first-log phase. This suggests utilization of aromatics in the first-log phase followed by glycerol in the second-log phase. On a mixture of an aromatic plus organic acid (acetate, α-ketoglutarate or fumarate), the strain displayed a monoauxic growth profile, indicating co-metabolism. Interestingly, the presence of glycerol, acetate, α-ketoglutarate or fumarate does not repress metabolism/utilization of the aromatic. Thus, the substrate utilization hierarchy of strain CSV86T is aromatics=organic acids>glucose/glycerol, which is unique as compared to other Pseudomonas species, where degradation of aromatics is repressed by glycerol, glucose, acetate or organic acids, including TCA cycle intermediates. This novel substrate utilization hierarchy appears to be a global metabolic phenomenon in strain CSV86T, thus implying it to be an ideal host for metabolic engineering as well as for its potential application in bioremediation.
Collapse
Affiliation(s)
- Tushar Dhamale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
| | - Braja Kishor Saha
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
| | - Sandesh E Papade
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
| | - Srushti Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India.,Present address: Presently affiliated to TCR Therapeutics, Inc., 100 Binney Street, Cambridge, MA 02142, USA
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
| |
Collapse
|
4
|
Breisch J, Huber LS, Kraiczy P, Hubloher J, Averhoff B. The ß-ketoadipate pathway of Acinetobacter baumannii is involved in complement resistance and affects resistance against aromatic antibiotics. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:170-178. [PMID: 35023294 DOI: 10.1111/1758-2229.13042] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
Acinetobacter baumannii can thrive on a broad range of substrates such as sugars, alcohols, lipids, amino acids and aromatic compounds. The latter three are abundant in the human host and are potential candidates as carbon sources for the metabolic adaptation of A. baumannii to the human host. In this study we determined the biodegradative activities of A. baumannii AYE with monocyclic aromatic compounds. Deletion of genes encoding the key enzymes of the ß-ketoadipate pathway, the protocatechuate-3,4-dioxygenase (ΔpcaHG) and the catechol-1,2-dioxygenase (ΔcatA), led to a complete loss of growth on benzoate and p-hydroxybenzoate, suggesting that these substrates are metabolized via the two distinct branches (pca and cat) of this pathway. Furthermore, we investigated the potential role of these gene products in host adaptation by analyzing the capability of the mutants to resist complement-mediated killing. These studies revealed that the mutants exhibit a decreased complement resistance, but a dramatic increase in survival in normal human serum in the presence of p-hydroxybenzoate or protocatechuate. These results indicate that the ß-ketoadipate pathway plays a role in adaptation of A. baumannii to the human host. Moreover, the single and double mutants exhibited increased antibiotic resistances indicating a link between the two dioxygenases and antibiotic resistance.
Collapse
Affiliation(s)
- Jennifer Breisch
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Lisa Sophie Huber
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Peter Kraiczy
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Josephine Hubloher
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Beate Averhoff
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
| |
Collapse
|
5
|
Characterization of highly ferulate-tolerant Acinetobacter baylyi ADP1 isolates by a rapid reverse-engineering method. Appl Environ Microbiol 2021; 88:e0178021. [PMID: 34788063 DOI: 10.1128/aem.01780-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Adaptive laboratory evolution (ALE) is a powerful approach for improving phenotypes of microbial hosts. Evolved strains typically contain numerous mutations that can be revealed by whole-genome sequencing. However, determining the contribution of specific mutations to new phenotypes is typically challenging and laborious. This task is complicated by factors such as the mutation type, the genomic context, and the interplay between different mutations. Here, a novel approach was developed to identify the significance of mutations in strains evolved from Acinetobacter baylyi ADP1. This method, termed Rapid Advantageous Mutation ScrEening and Selection (RAMSES), was used to analyze mutants that emerged from stepwise adaptation to, and consumption of, high levels of ferulate, a common lignin-derived aromatic compound. After whole-genome sequence analysis, RAMSES allowed rapid determination of effective mutations and seamless introduction of the beneficial mutations into the chromosomes of new strains with different genetic backgrounds. This simple approach to reverse-engineering exploits the natural competence and high recombination efficiency of ADP1. Mutated DNA, added directly to growing cells, replaces homologous chromosomal regions to generate transformants that will become enriched if there is selective benefit. Thus, advantageous mutations can be rapidly identified. Here, the growth advantage of transformants under selective pressure revealed key mutations in genes related to aromatic transport, including hcaE, hcaK, and vanK, and a gene, ACIAD0482, which is associated with lipopolysaccharide synthesis. This study provides insights into enhanced utilization of industrially relevant aromatic substrates and demonstrates the use of A. baylyi ADP1 as a convenient platform for strain development and evolution studies. Importance Microbial conversion of lignin-enriched streams is a promising approach for lignin valorization. However, the lignin-derived aromatic compounds are toxic to cells at relevant concentrations. Although adaptive laboratory evolution (ALE) is a powerful approach to develop more tolerant strains, it is typically laborious to identify the mechanisms underlying phenotypic improvement. We employed Acinetobacter baylyi ADP1, an aromatic compound degrading strain that may be useful for biotechnology. The natural competence and high recombination efficiency of this strain can be exploited for critical applications such as the breakdown of lignin and plastics, abundant polymers composed of aromatic subunits. The natural transformability of this bacterium enabled us to develop a novel approach for rapid screening of advantageous mutations from ALE-derived aromatic-tolerant ADP1-derived strains. We clarified the mechanisms and genetic targets for improved tolerance towards common lignin-derived aromatic compounds. This study facilitates metabolic engineering for lignin valorization.
Collapse
|
6
|
Arvay E, Biggs BW, Guerrero L, Jiang V, Tyo K. Engineering Acinetobacter baylyi ADP1 for mevalonate production from lignin-derived aromatic compounds. Metab Eng Commun 2021; 13:e00173. [PMID: 34430203 PMCID: PMC8367835 DOI: 10.1016/j.mec.2021.e00173] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 05/04/2021] [Accepted: 05/05/2021] [Indexed: 01/16/2023] Open
Abstract
Utilization of lignin, an abundant renewable resource, is limited by its heterogenous composition and complex structure. Biological valorization of lignin provides advantages over traditional chemical processing as it occurs at ambient temperature and pressure and does not use harsh chemicals. Furthermore, the ability to biologically funnel heterogenous substrates to products eliminates the need for costly downstream processing and separation of feedstocks. However, lack of relevant metabolic networks and low tolerance to degradation products of lignin limits the application of traditional engineered model organisms. To circumvent this obstacle, we employed Acinetobacter baylyi ADP1, which natively catabolizes lignin-derived aromatic substrates through the β-ketoadipate pathway, to produce mevalonate from lignin-derived compounds. We enabled expression of the mevalonate pathway in ADP1 and validated activity in the presence of multiple lignin-derived aromatic substrates. Furthermore, by knocking out wax ester synthesis and utilizing fed-batch cultivation, we improved mevalonate titers 7.5-fold to 1014 mg/L (6.8 mM). This work establishes a foundation and provides groundwork for future efforts to engineer improved production of mevalonate and derivatives from lignin-derived aromatics using ADP1. Acinetobacter baylyi ADP1 expresses the mevalonate pathway functionally Mevalonate is produced in the presence of multiple lignin-derived compounds Mevalonate is produced from solely lignin-derived aromatic carbon A wax ester knockout strain grown in fed-batch improves mevalonate titer 7.5-fold Lignin-derived compound fed-batch produces more mevalonate than glucose-fed
Collapse
Affiliation(s)
- Erika Arvay
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.,Biotechnology Training Program, Northwestern University, Evanston, IL, USA
| | - Bradley W Biggs
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.,Biotechnology Training Program, Northwestern University, Evanston, IL, USA
| | - Laura Guerrero
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Virginia Jiang
- Department of Chemical Engineering, Columbia University, New York, NY, USA
| | - Keith Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| |
Collapse
|
7
|
Ackermann YS, Li WJ, Op de Hipt L, Niehoff PJ, Casey W, Polen T, Köbbing S, Ballerstedt H, Wynands B, O'Connor K, Blank LM, Wierckx N. Engineering adipic acid metabolism in Pseudomonas putida. Metab Eng 2021; 67:29-40. [PMID: 33965615 DOI: 10.1016/j.ymben.2021.05.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/12/2021] [Accepted: 05/01/2021] [Indexed: 12/20/2022]
Abstract
Bio-upcycling of plastics is an upcoming alternative approach for the valorization of diverse polymer waste streams that are too contaminated for traditional recycling technologies. Adipic acid and other medium-chain-length dicarboxylates are key components of many plastics including polyamides, polyesters, and polyurethanes. This study endows Pseudomonas putida KT2440 with efficient metabolism of these dicarboxylates. The dcaAKIJP genes from Acinetobacter baylyi, encoding initial uptake and activation steps for dicarboxylates, were heterologously expressed. Genomic integration of these dca genes proved to be a key factor in efficient and reliable expression. In spite of this, adaptive laboratory evolution was needed to connect these initial steps to the native metabolism of P. putida, thereby enabling growth on adipate as sole carbon source. Genome sequencing of evolved strains revealed a central role of a paa gene cluster, which encodes parts of the phenylacetate metabolic degradation pathway with parallels to adipate metabolism. Fast growth required the additional disruption of the regulator-encoding psrA, which upregulates redundant β-oxidation genes. This knowledge enabled the rational reverse engineering of a strain that can not only use adipate, but also other medium-chain-length dicarboxylates like suberate and sebacate. The reverse engineered strain grows on adipate with a rate of 0.35 ± 0.01 h-1, reaching a final biomass yield of 0.27 ± 0.00 gCDW gadipate-1. In a nitrogen-limited medium this strain produced polyhydroxyalkanoates from adipate up to 25% of its CDW. This proves its applicability for the upcycling of mixtures of polymers made from fossile resources into biodegradable counterparts.
Collapse
Affiliation(s)
- Yannic S Ackermann
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Wing-Jin Li
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Leonie Op de Hipt
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Paul-Joachim Niehoff
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - William Casey
- Bioplastech Ltd., NovaUCD, Belfield Innovation Park, University College Dublin, Dublin, Ireland
| | - Tino Polen
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Sebastian Köbbing
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Hendrik Ballerstedt
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Benedikt Wynands
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Kevin O'Connor
- UCD Earth Institute and School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland; BiOrbic Bioeconomy SFI Research Centre, University College Dublin, Dublin, Ireland
| | - Lars M Blank
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Nick Wierckx
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany.
| |
Collapse
|
8
|
Pardo I, Jha RK, Bermel RE, Bratti F, Gaddis M, McIntyre E, Michener W, Neidle EL, Dale T, Beckham GT, Johnson CW. Gene amplification, laboratory evolution, and biosensor screening reveal MucK as a terephthalic acid transporter in Acinetobacter baylyi ADP1. Metab Eng 2020; 62:260-274. [DOI: 10.1016/j.ymben.2020.09.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 09/11/2020] [Accepted: 09/19/2020] [Indexed: 12/19/2022]
|
9
|
Suárez GA, Dugan KR, Renda BA, Leonard SP, Gangavarapu LS, Barrick JE. Rapid and assured genetic engineering methods applied to Acinetobacter baylyi ADP1 genome streamlining. Nucleic Acids Res 2020; 48:4585-4600. [PMID: 32232367 PMCID: PMC7192602 DOI: 10.1093/nar/gkaa204] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 03/15/2020] [Accepted: 03/18/2020] [Indexed: 01/10/2023] Open
Abstract
One goal of synthetic biology is to improve the efficiency and predictability of living cells by removing extraneous genes from their genomes. We demonstrate improved methods for engineering the genome of the metabolically versatile and naturally transformable bacterium Acinetobacter baylyi ADP1 and apply them to a genome streamlining project. In Golden Transformation, linear DNA fragments constructed by Golden Gate Assembly are directly added to cells to create targeted deletions, edits, or additions to the chromosome. We tested the dispensability of 55 regions of the ADP1 chromosome using Golden Transformation. The 18 successful multiple-gene deletions ranged in size from 21 to 183 kb and collectively accounted for 23.4% of its genome. The success of each multiple-gene deletion attempt could only be partially predicted on the basis of an existing collection of viable ADP1 single-gene deletion strains and a new transposon insertion sequencing (Tn-Seq) dataset that we generated. We further show that ADP1’s native CRISPR/Cas locus is active and can be retargeted using Golden Transformation. We reprogrammed it to create a CRISPR-Lock, which validates that a gene has been successfully removed from the chromosome and prevents it from being reacquired. These methods can be used together to implement combinatorial routes to further genome streamlining and for more rapid and assured metabolic engineering of this versatile chassis organism.
Collapse
Affiliation(s)
- Gabriel A Suárez
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Kyle R Dugan
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Brian A Renda
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Sean P Leonard
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Lakshmi Suryateja Gangavarapu
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jeffrey E Barrick
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| |
Collapse
|
10
|
Ho MT, Li MSM, McDowell T, MacDonald J, Yuan ZC. Characterization and genomic analysis of a diesel-degrading bacterium, Acinetobacter calcoaceticus CA16, isolated from Canadian soil. BMC Biotechnol 2020; 20:39. [PMID: 32711499 PMCID: PMC7477861 DOI: 10.1186/s12896-020-00632-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 07/16/2020] [Indexed: 12/18/2022] Open
Abstract
Background With the high demand for diesel across the world, environmental decontamination from its improper usage, storage and accidental spills becomes necessary. One highly environmentally friendly and cost-effective decontamination method is to utilize diesel-degrading microbes as a means for bioremediation. Here, we present a newly isolated and identified strain of Acinetobacter calcoaceticus (‘CA16’) as a candidate for the bioremediation of diesel-contaminated areas. Results Acinetobacter calcoaceticus CA16 was able to survive and grow in minimal medium with diesel as the only source of carbon. We determined through metabolomics that A. calcoaceticus CA16 appears to be efficient at diesel degradation. Specifically, CA16 is able to degrade 82 to 92% of aliphatic alkane hydrocarbons (CnHn + 2; where n = 12–18) in 28 days. Several diesel-degrading genes (such as alkM and xcpR) that are present in other microbes were also found to be activated in CA16. Conclusions The results presented here suggest that Acinetobacter strain CA16 has good potential in the bioremediation of diesel-polluted environments.
Collapse
Affiliation(s)
- Margaret T Ho
- Department of Microbiology and Immunology, The University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 5B7, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Michelle S M Li
- Department of Microbiology and Immunology, The University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 5B7, Canada
| | - Tim McDowell
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, N5V 4T3, Canada
| | - Jacqueline MacDonald
- Department of Microbiology and Immunology, The University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 5B7, Canada
| | - Ze-Chun Yuan
- Department of Microbiology and Immunology, The University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 5B7, Canada. .,London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, N5V 4T3, Canada.
| |
Collapse
|
11
|
Phale PS, Malhotra H, Shah BA. Degradation strategies and associated regulatory mechanisms/features for aromatic compound metabolism in bacteria. ADVANCES IN APPLIED MICROBIOLOGY 2020; 112:1-65. [PMID: 32762865 DOI: 10.1016/bs.aambs.2020.02.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
As a result of anthropogenic activity, large number of recalcitrant aromatic compounds have been released into the environment. Consequently, microbial communities have adapted and evolved to utilize these compounds as sole carbon source, under both aerobic and anaerobic conditions. The constitutive expression of enzymes necessary for metabolism imposes a heavy energy load on the microbe which is overcome by arrangement of degradative genes as operons which are induced by specific inducers. The segmentation of pathways into upper, middle and/or lower operons has allowed microbes to funnel multiple compounds into common key aromatic intermediates which are further metabolized through central carbon pathway. Various proteins belonging to diverse families have evolved to regulate the transcription of individual operons participating in aromatic catabolism. These proteins, complemented with global regulatory mechanisms, carry out the regulation of aromatic compound metabolic pathways in a concerted manner. Additionally, characteristics like chemotaxis, preferential utilization, pathway compartmentalization and biosurfactant production confer an advantage to the microbe, thus making bioremediation of the aromatic pollutants more efficient and effective.
Collapse
Affiliation(s)
- Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India.
| | - Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Bhavik A Shah
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| |
Collapse
|
12
|
Jiang B, Xing Y, Li G, Zhang N, Lian L, Sun G, Zhang D. iTRAQ-Based Comparative Proteomic Analysis of Acinetobacter baylyi ADP1 Under DNA Damage in Relation to Different Carbon Sources. Front Microbiol 2020; 10:2906. [PMID: 31993023 PMCID: PMC6971185 DOI: 10.3389/fmicb.2019.02906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 12/02/2019] [Indexed: 12/27/2022] Open
Abstract
DNA damage response allows microorganisms to repair or bypass DNA damage and maintain the genome integrity. It has attracted increasing attention but the underlying influential factors affecting DNA damage response are still unclear. In this work, isobaric tags for relative and absolute quantification (iTRAQ)-based proteomic analysis was used to investigate the influence of carbon sources on the translational response of Acinetobacter baylyi ADP1 to DNA damage. After cultivating in a nutrient-rich medium (LB) and defined media supplemented with four different carbon sources (acetate, citrate, pyruvate, and succinate), a total of 2807 proteins were identified. Among them, 84 proteins involved in stress response were significantly altered, indicating the strong influence of carbon source on the response of A. baylyi ADP1 to DNA damage and other stresses. As the first study on the comparative global proteomic changes in A. baylyi ADP1 under DNA damage across nutritional environments, our findings revealed that DNA damage response in A. baylyi ADP1 at the translational level is significantly altered by carbon source, providing an insight into the complex protein interactions across carbon sources and offering theoretical clues for further study to elucidate their general regulatory mechanism to adapt to different nutrient environments.
Collapse
Affiliation(s)
- Bo Jiang
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, China.,Beijing Key Laboratory of Resource-Oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, China
| | - Yi Xing
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, China.,Beijing Key Laboratory of Resource-Oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, China
| | - Guanghe Li
- School of Environment, Tsinghua University, Beijing, China.,State Key Joint Laboratory of Environmental Simulation and Pollution Control, Tsinghua University, Beijing, China
| | - Nana Zhang
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, China.,Beijing Key Laboratory of Resource-Oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, China
| | - Luning Lian
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, China.,Beijing Key Laboratory of Resource-Oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, China
| | - Guangdong Sun
- School of Environment, Tsinghua University, Beijing, China.,State Key Joint Laboratory of Environmental Simulation and Pollution Control, Tsinghua University, Beijing, China
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing, China.,State Key Joint Laboratory of Environmental Simulation and Pollution Control, Tsinghua University, Beijing, China
| |
Collapse
|
13
|
Becker J, Wittmann C. A field of dreams: Lignin valorization into chemicals, materials, fuels, and health-care products. Biotechnol Adv 2019; 37:107360. [DOI: 10.1016/j.biotechadv.2019.02.016] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 02/07/2023]
|
14
|
Lee S, Kang M, Bae JH, Sohn JH, Sung BH. Bacterial Valorization of Lignin: Strains, Enzymes, Conversion Pathways, Biosensors, and Perspectives. Front Bioeng Biotechnol 2019; 7:209. [PMID: 31552235 PMCID: PMC6733911 DOI: 10.3389/fbioe.2019.00209] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/19/2019] [Indexed: 12/17/2022] Open
Abstract
Lignin, an aromatic polymer found in plants, has been studied for years in many biological fields. Initially, when biofuel was produced from lignocellulosic biomass, lignin was regarded as waste generated by the biorefinery and had to be removed, because of its inhibitory effects on fermentative bacteria. Although it has since proven to be a natural resource for bio-products with considerable potential, its utilization is confined by its complex structure. Hence, the microbial degradation of lignin has attracted researchers' interest to overcome this problem. From this perspective, the studies have primarily focused on fungal systems, such as extracellular peroxidase and laccase from white- and brown-rot fungi. However, recent reports have suggested that bacteria play an increasing role in breaking down lignin. This paper, therefore, reviews the role of bacteria in lignin and lignin-related research. Several reports on bacterial species in soil that can degrade lignin and their enzymes are included. In addition, a cellulolytic anaerobic bacterium capable of solubilizing lignin and carbohydrate simultaneously has recently been identified, even though the enzyme involved has not been discovered yet. The assimilation of lignin-derived small molecules and their conversion to renewable chemicals by bacteria, such as muconic acid and polyhydroxyalkanoates, including genetic modification to enhance their capability was discussed. This review also covers the indirect use of bacteria for lignin degradation, which is concerned with whole-cell biosensors designed to detect the aromatic chemicals released from lignin transformation.
Collapse
Affiliation(s)
- Siseon Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Minsik Kang
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biosystems and Bioengineering, Korea University of Science and Technology, Daejeon, South Korea
| | - Jung-Hoon Bae
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jung-Hoon Sohn
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biosystems and Bioengineering, Korea University of Science and Technology, Daejeon, South Korea
| | - Bong Hyun Sung
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biosystems and Bioengineering, Korea University of Science and Technology, Daejeon, South Korea
| |
Collapse
|
15
|
Salmela M, Lehtinen T, Efimova E, Santala S, Santala V. Alkane and wax ester production from lignin‐related aromatic compounds. Biotechnol Bioeng 2019; 116:1934-1945. [DOI: 10.1002/bit.27005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/29/2019] [Accepted: 04/18/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Milla Salmela
- Faculty of Engineering and Natural Sciences, Hervanta CampusTampere UniversityTampere Finland
| | - Tapio Lehtinen
- Faculty of Engineering and Natural Sciences, Hervanta CampusTampere UniversityTampere Finland
| | - Elena Efimova
- Faculty of Engineering and Natural Sciences, Hervanta CampusTampere UniversityTampere Finland
| | - Suvi Santala
- Faculty of Engineering and Natural Sciences, Hervanta CampusTampere UniversityTampere Finland
| | - Ville Santala
- Faculty of Engineering and Natural Sciences, Hervanta CampusTampere UniversityTampere Finland
| |
Collapse
|
16
|
Brink DP, Ravi K, Lidén G, Gorwa-Grauslund MF. Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database. Appl Microbiol Biotechnol 2019; 103:3979-4002. [PMID: 30963208 PMCID: PMC6486533 DOI: 10.1007/s00253-019-09692-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/06/2019] [Accepted: 02/09/2019] [Indexed: 12/18/2022]
Abstract
Lignin is a heterogeneous aromatic biopolymer and a major constituent of lignocellulosic biomass, such as wood and agricultural residues. Despite the high amount of aromatic carbon present, the severe recalcitrance of the lignin macromolecule makes it difficult to convert into value-added products. In nature, lignin and lignin-derived aromatic compounds are catabolized by a consortia of microbes specialized at breaking down the natural lignin and its constituents. In an attempt to bridge the gap between the fundamental knowledge on microbial lignin catabolism, and the recently emerging field of applied biotechnology for lignin biovalorization, we have developed the eLignin Microbial Database ( www.elignindatabase.com ), an openly available database that indexes data from the lignin bibliome, such as microorganisms, aromatic substrates, and metabolic pathways. In the present contribution, we introduce the eLignin database, use its dataset to map the reported ecological and biochemical diversity of the lignin microbial niches, and discuss the findings.
Collapse
Affiliation(s)
- Daniel P Brink
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden.
| | - Krithika Ravi
- Department of Chemical Engineering, Lund University, Lund, Sweden
| | - Gunnar Lidén
- Department of Chemical Engineering, Lund University, Lund, Sweden
| | - Marie F Gorwa-Grauslund
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden
| |
Collapse
|
17
|
Ravi K, Abdelaziz OY, Nöbel M, García-Hidalgo J, Gorwa-Grauslund MF, Hulteberg CP, Lidén G. Bacterial conversion of depolymerized Kraft lignin. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:56. [PMID: 30923564 PMCID: PMC6420747 DOI: 10.1186/s13068-019-1397-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/08/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Lignin is a potential feedstock for microbial conversion into various chemicals. However, the microbial degradation rate of native or technical lignin is low, and chemical depolymerization is needed to obtain reasonable conversion rates. In the current study, nine bacterial strains belonging to the Pseudomonas and Rhodococcus genera were evaluated for their ability to grow on alkaline-treated softwood lignin as a sole carbon source. RESULTS Pseudomonas fluorescens DSM 50090 and Rhodococcus opacus DSM1069 showed the best growth of the tested species on plates with lignin. Further evaluation of P. fluorescens and R. opacus was made in liquid cultivations with depolymerized softwood Kraft lignin (DL) at a concentration of 1 g/L. Size-exclusion chromatography (SEC) showed that R. opacus consumed most of the available lower-molecular weight compounds (approximately 0.1-0.4 kDa) in the DL, but the weight distribution of larger fractions was almost unaffected. Importantly, the consumed compounds included guaiacol-one of the main monomers in the DL. SEC analysis of P. fluorescens culture broth, in contrast, did not show a large conversion of low-molecular weight compounds, and guaiacol remained unconsumed. However, a significant shift in molecular weight distribution towards lower average weights was seen after cultivation with P. fluorescens. CONCLUSIONS Rhodococcus opacus and P. fluorescens were identified as two potential microbial candidates for the conversion/consumption of base-catalyzed depolymerized lignin, acting on low- and high-molecular weight lignin fragments, respectively. These findings will be of relevance for designing bioconversion of softwood Kraft lignin.
Collapse
Affiliation(s)
- Krithika Ravi
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Omar Y. Abdelaziz
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Matthias Nöbel
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
- Present Address: Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072 Australia
| | - Javier García-Hidalgo
- Department of Chemistry, Applied Microbiology, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Marie F. Gorwa-Grauslund
- Department of Chemistry, Applied Microbiology, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | | | - Gunnar Lidén
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| |
Collapse
|
18
|
Synthetic metabolic pathway for the production of 1-alkenes from lignin-derived molecules. Microb Cell Fact 2019; 18:48. [PMID: 30857542 PMCID: PMC6410514 DOI: 10.1186/s12934-019-1097-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/28/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Integration of synthetic metabolic pathways to catabolically diverse chassis provides new opportunities for sustainable production. One attractive scenario is the use of abundant waste material to produce a readily collectable product, which can reduce the production costs. Towards that end, we established a cellular platform for the production of semivolatile medium-chain α-olefins from lignin-derived molecules: we constructed 1-undecene synthesis pathway in Acinetobacter baylyi ADP1 using ferulate, a lignin-derived model compound, as the sole carbon source for both cell growth and product synthesis. RESULTS In order to overcome the toxicity of ferulate, we first applied adaptive laboratory evolution to A. baylyi ADP1, resulting in a highly ferulate-tolerant strain. The adapted strain exhibited robust growth in 100 mM ferulate while the growth of the wild type strain was completely inhibited. Next, we expressed two heterologous enzymes in the wild type strain to confer 1-undecene production from glucose: a fatty acid decarboxylase UndA from Pseudomonas putida, and a thioesterase 'TesA from Escherichia coli. Finally, we constructed the 1-undecene synthesis pathway in the ferulate-tolerant strain. The engineered cells were able to produce biomass and 1-undecene solely from ferulate, and excreted the product directly to the culture headspace. CONCLUSIONS In this study, we employed a bacterium Acinetobacter baylyi ADP1 to integrate a natural aromatics degrading pathway to a synthetic production route, allowing the upgradation of lignin derived molecules to value-added products. We developed a highly ferulate-tolerant strain and established the biosynthesis of an industrially relevant chemical, 1-undecene, solely from the lignin-derived model compound. This study reports the production of alkenes from lignin derived molecules for the first time and demonstrates the potential of lignin as a sustainable resource in the bio-based synthesis of valuable products.
Collapse
|
19
|
Ravi K, Abdelaziz OY, Nöbel M, García-Hidalgo J, Gorwa-Grauslund MF, Hulteberg CP, Lidén G. Bacterial conversion of depolymerized Kraft lignin. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:240. [PMID: 30202435 PMCID: PMC6123935 DOI: 10.1186/s13068-018-1240-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/27/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Lignin is a potential feedstock for microbial conversion into various chemicals. However, the degradation rate of native or technical lignin is low, and depolymerization is needed to obtain reasonable conversion rates. In the current study, base-catalyzed depolymerization-using NaOH (5 wt%)-of softwood Kraft lignin was conducted in a continuous-flow reactor system at temperatures in the range 190-240 °C and residence times of 1 or 2 min. The ability of growth of nine bacterial strains belonging to the genera Pseudomonas and Rhodococcus was tested using the alkaline-treated lignin as a sole carbon source. RESULTS Pseudomonas fluorescens and Rhodococcus opacus showed the best growth of the tested species on plates with lignin. Further evaluation of P. fluorescens and R. opacus was made in liquid cultivations with depolymerized lignin (DL) at a concentration of 1 g/L. Size exclusion chromatography (SEC) showed that R. opacus consumed most of the available lower molecular weight compounds (approximately 0.1-0.4 kDa) in the DL, but the weight distribution of larger fractions was almost unaffected. Importantly, the consumed compounds included guaiacol-one of the main monomers in the DL. SEC analysis of P. fluorescens culture broth, in contrast, did not show a large conversion of low molecular weight compounds, and guaiacol remained unconsumed. However, a significant shift in molecular weight distribution towards lower average weights was seen. CONCLUSIONS Rhodococcus opacus and P. fluorescens were identified as two potential microbial candidates for the conversion/consumption of base-catalyzed depolymerized lignin, acting on low and high molecular weight lignin fragments, respectively. These findings will be of relevance for designing bioconversion of softwood Kraft lignin.
Collapse
Affiliation(s)
- Krithika Ravi
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Omar Y. Abdelaziz
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Matthias Nöbel
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
- Present Address: Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072 Australia
| | - Javier García-Hidalgo
- Department of Chemistry, Applied Microbiology, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Marie F. Gorwa-Grauslund
- Department of Chemistry, Applied Microbiology, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | | | - Gunnar Lidén
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| |
Collapse
|
20
|
Herrou J, Czyż DM, Fiebig A, Willett JW, Kim Y, Wu R, Babnigg G, Crosson S. Molecular control of gene expression by Brucella BaaR, an IclR-type transcriptional repressor. J Biol Chem 2018; 293:7437-7456. [PMID: 29567835 PMCID: PMC5949995 DOI: 10.1074/jbc.ra118.002045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/19/2018] [Indexed: 01/06/2023] Open
Abstract
The general stress response sigma factor σE1 directly and indirectly regulates the transcription of dozens of genes that influence stress survival and host infection in the zoonotic pathogen Brucella abortus Characterizing the functions of σE1-regulated genes therefore would contribute to our understanding of B. abortus physiology and infection biology. σE1 indirectly activates transcription of the IclR family regulator Bab2_0215, but the function of this regulator remains undefined. Here, we present a structural and functional characterization of Bab2_0215, which we have named B rucella adipic acid-activated regulator (BaaR). We found that BaaR adopts a classic IclR-family fold and directly represses the transcription of two operons with predicted roles in carboxylic acid oxidation. BaaR binds two sites on chromosome II between baaR and a divergently transcribed hydratase/dehydrogenase (acaD2), and it represses transcription of both genes. We identified three carboxylic acids (adipic acid, tetradecanedioic acid, and ϵ-aminocaproic acid) and a lactone (ϵ-caprolactone) that enhance transcription from the baaR and acaD2 promoters. However, neither the activating acids nor caprolactone enhanced transcription by binding directly to BaaR. Induction of baaR transcription by adipic acid required the gene bab2_0213, which encodes a major facilitator superfamily transporter, suggesting that Bab2_0213 transports adipic acid across the inner membrane. We conclude that a suite of structurally related organic molecules activate transcription of genes repressed by BaaR. Our study provides molecular-level understanding of a gene expression program in B. abortus that is downstream of σE1.
Collapse
Affiliation(s)
- Julien Herrou
- Departments of Biochemistry and Molecular Biology, Chicago, Illinois 60637; Howard Taylor Ricketts Laboratory, University of Chicago, Argonne, Illinois 60439
| | - Daniel M Czyż
- Departments of Biochemistry and Molecular Biology, Chicago, Illinois 60637; Howard Taylor Ricketts Laboratory, University of Chicago, Argonne, Illinois 60439
| | - Aretha Fiebig
- Howard Taylor Ricketts Laboratory, University of Chicago, Argonne, Illinois 60439
| | - Jonathan W Willett
- Departments of Biochemistry and Molecular Biology, Chicago, Illinois 60637; Howard Taylor Ricketts Laboratory, University of Chicago, Argonne, Illinois 60439
| | | | - Ruiying Wu
- Argonne National Laboratory, Argonne, Illinois 60439
| | | | - Sean Crosson
- Departments of Biochemistry and Molecular Biology, Chicago, Illinois 60637; Howard Taylor Ricketts Laboratory, University of Chicago, Argonne, Illinois 60439; Microbiology, University of Chicago, Chicago, Illinois 60637.
| |
Collapse
|
21
|
Yaguchi A, Robinson A, Mihealsick E, Blenner M. Metabolism of aromatics by Trichosporon oleaginosus while remaining oleaginous. Microb Cell Fact 2017; 16:206. [PMID: 29149902 PMCID: PMC5693591 DOI: 10.1186/s12934-017-0820-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/11/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The oleaginous yeast, Trichosporon oleaginosus, has been extensively studied for its ability to metabolize non-conventional feedstocks. These include phenol-containing waste streams, such as distillery wastewater, or streams consisting of non-conventional sugars, such as hydrolyzed biomass and various bagasse. An initial BLAST search suggests this yeast has putative aromatic metabolizing genes. Given the desirability to valorize underutilized feedstocks such as lignin, we investigated the ability of T. oleaginosus to tolerate and metabolize lignin-derived aromatic compounds. RESULTS Trichosporon oleaginosus can tolerate and metabolize model lignin monoaromatics and associated intermediates within funneling pathways. Growth rates and biomass yield were similar to glucose when grown in 4-hydroxybenzoic acid (pHBA) and resorcinol, but had an increased lag phase when grown in phenol. Oleaginous behavior was observed using resorcinol as a sole carbon source. Fed-batch feeding resulted in lipid accumulation of 69.5% on a dry weight basis. CONCLUSIONS Though the exact pathway of aromatic metabolism remains to be determined for T. oleaginosus, the results presented in this work motivate use of this organism for lignin valorization and phenolic wastewater bioremediation. Trichosporon oleaginosus is the first yeast shown to be oleaginous while growing on aromatic substrates, and shows great promise as a model industrial microbe for biochemical and biofuel production from depolymerized lignin.
Collapse
Affiliation(s)
- Allison Yaguchi
- Department of Chemical and Biomolecular Engineering, Clemson University, 206 S. Palmetto Blvd., Clemson, SC 29634 USA
| | - Alana Robinson
- Department of Chemical and Biomolecular Engineering, Clemson University, 206 S. Palmetto Blvd., Clemson, SC 29634 USA
| | - Erin Mihealsick
- Department of Chemical and Biomolecular Engineering, Clemson University, 206 S. Palmetto Blvd., Clemson, SC 29634 USA
| | - Mark Blenner
- Department of Chemical and Biomolecular Engineering, Clemson University, 206 S. Palmetto Blvd., Clemson, SC 29634 USA
| |
Collapse
|
22
|
Sigala JC, Suárez BP, Lara AR, Borgne SL, Bustos P, Santamaría RI, González V, Martinez A. Genomic and physiological characterization of a laboratory-isolated Acinetobacter schindleri ACE strain that quickly and efficiently catabolizes acetate. MICROBIOLOGY-SGM 2017; 163:1052-1064. [PMID: 28671531 DOI: 10.1099/mic.0.000488] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
An Acinetobacter strain, designated ACE, was isolated in the laboratory. Phylogenetic tests and average nucleotide identity value comparisons suggested that ACE belongs to the species Acinetobacterschindleri. We report for the first time the complete genome sequence of an A. schindleri strain, which consists of a single circular chromosome of 3 001 209 bp with an overall DNA G+C content of 42.9 mol% and six plasmids that account for 266 844 bp of extrachromosomal material. The presence or absence of genes related to carbon catabolism and antibiotic resistance were in agreement with the phenotypic characterization of ACE. This strain grew faster and with a higher biomass yield on acetate than the reference strain Acinetobacter baylyi ADP1. However, ACE did not use aromatic compounds and was unable to grow on common carbon sources, such as glucose, xylose, glycerol or citrate. The gluconeogenic and the catechol pathways are complete in ACE, but compounds that are converted to protocatechuate did not sustain growth since some genes of this pathway are missing. Likewise, this strain could not grow on glucose because it lacks the genes of the Entner-Doudoroff pathway. Minimal inhibitory concentration data showed that ACE was susceptible to most of the antimicrobial agents recommended for the clinical treatment of Acinetobacter spp. Some genes related to a possible human-microbe interaction were found in the ACE genome. ACE is likely to have a low pathogenic risk, as is the case with other A. schindleri strains. These results provide a valuable reference for broadening the knowledge of the biology of Acinetobacter.
Collapse
Affiliation(s)
- Juan-Carlos Sigala
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Delegación Cuajimalpa, Ciudad de México 05348, México
| | - Brisa Paola Suárez
- Posgrado en Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Ciudad de México, México
| | - Alvaro R Lara
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Delegación Cuajimalpa, Ciudad de México 05348, México
| | - Sylvie Le Borgne
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Delegación Cuajimalpa, Ciudad de México 05348, México
| | - Patricia Bustos
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apdo. Postal 565-A, Cuernavaca, Morelos 62210, México
| | - Rosa Isela Santamaría
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apdo. Postal 565-A, Cuernavaca, Morelos 62210, México
| | - Víctor González
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apdo. Postal 565-A, Cuernavaca, Morelos 62210, México
| | - Alfredo Martinez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Morelos 62250, México
| |
Collapse
|
23
|
Kannisto M, Efimova E, Karp M, Santala V. Growth and wax ester production of an Acinetobacter baylyi ADP1 mutant deficient in exopolysaccharide capsule synthesis. ACTA ACUST UNITED AC 2017; 44:99-105. [DOI: 10.1007/s10295-016-1872-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 11/10/2016] [Indexed: 10/20/2022]
Abstract
Abstract
Acinetobacter baylyi ADP1 naturally produces wax esters that could be used as a raw material in industrial applications. We attempted to improve wax ester yield of A. baylyi ADP1 by removing rmlA, a gene involved in exopolysaccharide production. Growth rate, biomass formation and wax ester yield on 4-hydroxybenzoate were not affected, but the rmlA− strain grew slower on acetate, while reaching similar biomass and wax ester yield. The rmlA− cells had malformed shape and large size and grew poorly on glucose without expression of the gene for pyruvate kinase (pykF) from Escherichia coli. The pykF-expressing rmlA− strain had similar growth rate, lowered biomass formation and improved wax ester production on glucose as compared to the wild-type strain expressing pykF. Cultivation of the pykF-expressing rmlA− strain on an elevated glucose concentration in a medium supplemented with amino acids resulted in doubled molar wax ester yield and acetate production.
Collapse
Affiliation(s)
- Matti Kannisto
- grid.6986.1 0000000093279856 Department of Chemistry and Bioengineering Tampere University of Technology Korkeakoulunkatu 8 Tampere Finland
| | - Elena Efimova
- grid.6986.1 0000000093279856 Department of Chemistry and Bioengineering Tampere University of Technology Korkeakoulunkatu 8 Tampere Finland
| | - Matti Karp
- grid.6986.1 0000000093279856 Department of Chemistry and Bioengineering Tampere University of Technology Korkeakoulunkatu 8 Tampere Finland
| | - Ville Santala
- grid.6986.1 0000000093279856 Department of Chemistry and Bioengineering Tampere University of Technology Korkeakoulunkatu 8 Tampere Finland
| |
Collapse
|
24
|
Biological valorization of low molecular weight lignin. Biotechnol Adv 2016; 34:1318-1346. [DOI: 10.1016/j.biotechadv.2016.10.001] [Citation(s) in RCA: 228] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 09/06/2016] [Accepted: 10/04/2016] [Indexed: 12/14/2022]
|
25
|
Kim Y, Joachimiak G, Bigelow L, Babnigg G, Joachimiak A. How Aromatic Compounds Block DNA Binding of HcaR Catabolite Regulator. J Biol Chem 2016; 291:13243-56. [PMID: 27129205 DOI: 10.1074/jbc.m115.712067] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Indexed: 11/06/2022] Open
Abstract
Bacterial catabolism of aromatic compounds from various sources including phenylpropanoids and flavonoids that are abundant in soil plays an important role in the recycling of carbon in the ecosystem. We have determined the crystal structures of apo-HcaR from Acinetobacter sp. ADP1, a MarR/SlyA transcription factor, in complexes with hydroxycinnamates and a specific DNA operator. The protein regulates the expression of the hca catabolic operon in Acinetobacter and related bacterial strains, allowing utilization of hydroxycinnamates as sole sources of carbon. HcaR binds multiple ligands, and as a result the transcription of genes encoding several catabolic enzymes is increased. The 1.9-2.4 Å resolution structures presented here explain how HcaR recognizes four ligands (ferulate, 3,4-dihydroxybenzoate, p-coumarate, and vanillin) using the same binding site. The ligand promiscuity appears to be an adaptation to match a broad specificity of hydroxycinnamate catabolic enzymes while responding to toxic thioester intermediates. Structures of apo-HcaR and in complex with a specific DNA hca operator when combined with binding studies of hydroxycinnamates show how aromatic ligands render HcaR unproductive in recognizing a specific DNA target. The current study contributes to a better understanding of the hca catabolic operon regulation mechanism by the transcription factor HcaR.
Collapse
Affiliation(s)
- Youngchang Kim
- From the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439
| | | | | | - Gyorgy Babnigg
- From the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439
| | - Andrzej Joachimiak
- From the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439
| |
Collapse
|
26
|
Patterns of Endemism and Habitat Selection in Coalbed Microbial Communities. Appl Environ Microbiol 2015; 81:7924-37. [PMID: 26341214 DOI: 10.1128/aem.01737-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 09/02/2015] [Indexed: 11/20/2022] Open
Abstract
Microbially produced methane, a versatile, cleaner-burning alternative energy resource to fossil fuels, is sourced from a variety of natural and engineered ecosystems, including marine sediments, anaerobic digesters, shales, and coalbeds. There is a prevailing interest in developing environmental biotechnologies to enhance methane production. Here, we use small-subunit rRNA gene sequencing and metagenomics to better describe the interplay between coalbed methane (CBM) well conditions and microbial communities in the Alberta Basin. Our results show that CBM microbial community structures display patterns of endemism and habitat selection across the Alberta Basin, consistent with observations from other geographical locations. While some phylum-level taxonomic patterns were observed, relative abundances of specific taxonomic groups were localized to discrete wells, likely shaped by local environmental conditions, such as coal rank and depth-dependent physicochemical conditions. To better resolve functional potential within the CBM milieu, a metagenome from a deep volatile-bituminous coal sample was generated. This sample was dominated by Rhodobacteraceae genotypes, resolving a near-complete population genome bin related to Celeribacter sp. that encoded metabolic pathways for the degradation of a wide range of aromatic compounds and the production of methanogenic substrates via acidogenic fermentation. Genomic comparisons between the Celeribacter sp. population genome and related organisms isolated from different environments reflected habitat-specific selection pressures that included nitrogen availability and the ability to utilize diverse carbon substrates. Taken together, our observations reveal that both endemism and metabolic specialization should be considered in the development of biostimulation strategies for nonproductive wells or for those with declining productivity.
Collapse
|
27
|
Onur G, Yilmaz F, Icgen B. Diesel Oil Degradation Potential of a Bacterium Inhabiting Petroleum Hydrocarbon Contaminated Surface Waters and Characterization of Its Emulsification Ability. J SURFACTANTS DETERG 2015. [DOI: 10.1007/s11743-015-1697-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
28
|
How KY, Hong KW, Sam CK, Koh CL, Yin WF, Chan KG. Unravelling the genome of long chain N-acylhomoserine lactone-producing Acinetobacter sp. strain GG2 and identification of its quorum sensing synthase gene. Front Microbiol 2015; 6:240. [PMID: 25926817 PMCID: PMC4396500 DOI: 10.3389/fmicb.2015.00240] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 03/11/2015] [Indexed: 12/22/2022] Open
Abstract
Myriad proteobacteria use N-acyl homoserine lactone (AHL) molecules as quorum sensing (QS) signals to regulate different physiological functions, including virulence, antibiotic production, and biofilm formation. Many of these proteobacteria possess LuxI/LuxR system as the QS mechanism. Recently, we reported the 3.89 Mb genome of Acinetobacter sp. strain GG2. In this work, the genome of this long chain AHL-producing bacterium was unravelled which led to the molecular characterization of luxI homologue, designated as aciI. This 552 bp gene was cloned and overexpressed in Escherichia coli BL21(DE3). The purified protein was ∼20.5 kDa and is highly similar to several autoinducer proteins of LuxI family among Acinetobacter species. To verify the AHL synthesis activity of this protein, high-resolution liquid chromatography–mass spectrometry analysis revealed the production of 3-oxo-dodecanoyl-homoserine lactone and 3-hydroxy-dodecanoyl-homoserine lactone from induced E. coli harboring the recombinant AciI. Our data show for the first time, the cloning and characterization of the luxI homologue from Acinetobacter sp. strain GG2, and confirmation of its AHLs production. These data are of great significance as the annotated genome of strain GG2 has provided a valuable insight in the study of autoinducer molecules and its roles in QS mechanism of the bacterium.
Collapse
Affiliation(s)
- Kah Yan How
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Kar-Wai Hong
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Choon-Kook Sam
- Natural Sciences and Science Education Academic Group, National Institute of Education, Nanyang Technological University Singapore, Singapore
| | - Chong-Lek Koh
- Natural Sciences and Science Education Academic Group, National Institute of Education, Nanyang Technological University Singapore, Singapore
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| |
Collapse
|
29
|
Jiang B, Song Y, Zhang D, Huang WE, Zhang X, Li G. The influence of carbon sources on the expression of the recA gene and genotoxicity detection by an Acinetobacter bioreporter. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2015; 17:835-843. [PMID: 25764502 DOI: 10.1039/c4em00692e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Bacterial whole-cell bioreporters are practical and reliable analytical tools to assess the toxicity and bioavailability of environmental contaminants, yet evidence has shown that their performance could be affected by different carbon sources. This paper evaluated the influence of carbon sources on the recA gene (ACIAD1385) in a DNA damage-inducible recA::luxCDABE Acinetobacter bioreporter and optimized the induction conditions for its practical application in environmental monitoring. Different carbon sources, including LB, potassium acetate (MMA), sodium citrate (MMC), sodium pyruvate (MMP), and sodium succinate (MMS), significantly influenced (p < 0.05) the bioluminescence intensity of the genotoxicity bioreporter. A reverse transcription quantitative PCR (RT-qPCR) showed the different expression levels of the DNA damage-inducible gene recA (p < 0.05), suggesting that carbon sources influenced the DNA damage response in the Acinetobacter bioreporter at the transcriptional level. Additionally, proteomic analysis identified 122 proteins that were differentially expressed after exposure to mitomycin C in defined media and LB, and 5 of them were related to the DNA damage response, indicating the effects of carbon sources on the DNA damage response in Acinetobacter at the translational level. The repression effect caused by the rich medium, LB, was possibly related to the mechanism of carbon catabolite repression. Our results suggest that the practical application of Acinetobacter bioreporters to the genotoxicity assessment of polycyclic aromatic hydrocarbon (PAH)-contaminated soils could be significantly improved by using a standard medium of defined composition, as this could increase their sensitivity.
Collapse
Affiliation(s)
- Bo Jiang
- School of Environment, Tsinghua University, Beijing, 100084, PR China.
| | | | | | | | | | | |
Collapse
|
30
|
Jung J, Park W. Acinetobacter species as model microorganisms in environmental microbiology: current state and perspectives. Appl Microbiol Biotechnol 2015; 99:2533-48. [PMID: 25693672 DOI: 10.1007/s00253-015-6439-y] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 01/23/2015] [Accepted: 01/26/2015] [Indexed: 01/11/2023]
Abstract
Acinetobacter occupies an important position in nature because of its ubiquitous presence in diverse environments such as soils, fresh water, oceans, sediments, and contaminated sites. Versatile metabolic characteristics allow species of this genus to catabolize a wide range of natural compounds, implying active participation in the nutrient cycle in the ecosystem. On the other hand, multi-drug-resistant Acinetobacter baumannii causing nosocomial infections with high mortality has been raising serious concerns in medicine. Due to the ecological and clinical importance of the genus, Acinetobacter was proposed as a model microorganism for environmental microbiological studies, pathogenicity tests, and industrial production of chemicals. For these reasons, Acinetobacter has attracted significant attention in scientific and biotechnological fields, but only limited research areas such as natural transformation and aromatic compound degradation have been intensively investigated, while important physiological characteristics including quorum sensing, motility, and stress response have been neglected. The aim of this review is to summarize the recent achievements in Acinetobacter research with a special focus on strain DR1 and to compare the similarities and differences between species or other genera. Research areas that require more attention in future research are also suggested.
Collapse
Affiliation(s)
- Jaejoon Jung
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 136-713, Republic of Korea
| | | |
Collapse
|
31
|
Kannisto MS, Mangayil RK, Shrivastava-Bhattacharya A, Pletschke BI, Karp MT, Santala VP. Metabolic engineering of Acinetobacter baylyi ADP1 for removal of Clostridium butyricum growth inhibitors produced from lignocellulosic hydrolysates. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:198. [PMID: 26628912 PMCID: PMC4666034 DOI: 10.1186/s13068-015-0389-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 11/16/2015] [Indexed: 05/05/2023]
Abstract
BACKGROUND Pretreatment of lignocellulosic biomass can produce inhibitory compounds that are harmful for microorganisms used in the production of biofuels and other chemicals from lignocellulosic sugars. Selective inhibitor removal can be achieved with biodetoxification where microorganisms catabolize the inhibitors without consuming the sugars. We engineered the strictly aerobic Acinetobacter baylyi ADP1 for detoxification of lignocellulosic hydrolysates by removing the gene for glucose dehydrogenase, gcd, which catalyzes the first step in its glucose catabolism. RESULTS The engineered A. baylyi ADP1 strain was shown to be incapable of consuming the main sugar components of lignocellulosic hydrolysates, i.e., glucose, xylose, and arabinose, but rapidly utilized acetate and formate. Formate was consumed during growth on acetate and by stationary phase cells, and this was enhanced in the presence of a common aromatic inhibitor of lignocellulosic hydrolysates, 4-hydroxybenzoate. The engineered strain tolerated glucose well up to 70 g/l, and the consumption of glucose, xylose, or arabinose was not observed in prolonged cultivations. The engineered strain was applied in removal of oxygen, a gaseous inhibitor of anaerobic fermentations. Co-cultivation with the A. baylyi ADP1 gcd knockout strain under initially aerobic conditions allowed the strictly anaerobic Clostridium butyricum to grow and produce hydrogen (H2) from sugars of the enzymatic rice straw hydrolysate. CONCLUSIONS We demonstrated that the model organism of bacterial genetics and metabolism, A. baylyi ADP1, could be engineered to be an efficient biodetoxification strain of lignocellulosic hydrolysates. Only one gene knockout was required to completely eliminate sugar consumption and the strain could be used in production of anaerobic conditions for the strictly anaerobic hydrogen producer, C. butyricum. Because of these encouraging results, we believe that A. baylyi ADP1 is a promising candidate for the detoxification of lignocellulosic hydrolysates for bioprocesses.
Collapse
Affiliation(s)
- Matti S. Kannisto
- />Department of Chemistry and Bioengineering, Tampere University of Technology, Korkeakoulunkatu 8, Tampere, Finland
| | - Rahul K. Mangayil
- />Department of Chemistry and Bioengineering, Tampere University of Technology, Korkeakoulunkatu 8, Tampere, Finland
| | | | - Brett I. Pletschke
- />Department of Biochemistry and Microbiology, Enzyme Synergy Programme, Rhodes University, Grahamstown, 6140 South Africa
| | - Matti T. Karp
- />Department of Chemistry and Bioengineering, Tampere University of Technology, Korkeakoulunkatu 8, Tampere, Finland
| | - Ville P. Santala
- />Department of Chemistry and Bioengineering, Tampere University of Technology, Korkeakoulunkatu 8, Tampere, Finland
| |
Collapse
|
32
|
Lahme S, Trautwein K, Strijkstra A, Dörries M, Wöhlbrand L, Rabus R. Benzoate mediates the simultaneous repression of anaerobic 4-methylbenzoate and succinate utilization in Magnetospirillum sp. strain pMbN1. BMC Microbiol 2014; 14:269. [PMID: 25344702 PMCID: PMC4268860 DOI: 10.1186/s12866-014-0269-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 10/15/2014] [Indexed: 11/13/2022] Open
Abstract
Background At high concentrations of organic substrates, microbial utilization of preferred substrates (i.e., supporting fast growth) often results in diauxic growth with hierarchical substrate depletion. Unlike the carbon catabolite repression-mediated discriminative utilization of carbohydrates, the substrate preferences of non-carbohydrate-utilizing bacteria for environmentally relevant compound classes (e.g., aliphatic or aromatic acids) are rarely investigated. The denitrifying alphaproteobacterium Magnetospirillum sp. strain pMbN1 anaerobically degrades a wide variety of aliphatic and aromatic compounds and is unique for anaerobic degradation of 4-methylbenzoate. The latter proceeds via a distinct reaction sequence analogous to the central anaerobic benzoyl-CoA pathway to intermediates of central metabolism. Considering the presence of these two different anaerobic “aromatic ring degrading” pathways, substrate preferences of Magnetospirillum sp. strain pMbN1 were investigated. Anaerobic growth and substrate consumption were monitored in binary and ternary mixtures of 4-methylbenzoate, benzoate and succinate, in conjuction with time-resolved abundance profiling of selected transcripts and/or proteins related to substrate uptake and catabolism. Results Diauxic growth with benzoate preference was observed for binary and ternary substrate mixtures containing 4-methylbenzoate and succinate (despite adaptation of Magnetospirillum sp. strain pMbN1 to one of the latter two substrates). On the contrary, 4-methylbenzoate and succinate were utilized simultaneously from a binary mixture, as well as after benzoate depletion from the ternary mixture. Apparently, simultaneous repression of 4-methylbenzoate and succinate utilization from the ternary substrate mixture resulted from (i) inhibition of 4-methylbenzoate uptake, and (ii) combined inhibition of succinate uptake (via the two transporters DctPQM and DctA) and succinate conversion to acetyl-CoA (via pyruvate dehydrogenase). The benzoate-mediated repression of C4-dicarboxylate utilization in Magnetospirillum sp. strain pMbN1 differs from that recently described for “Aromatoleum aromaticum” EbN1 (involving only DctPQM). Conclusions The preferential or simultaneous utilization of benzoate and other aromatic acids from mixtures with aliphatic acids may represent a more common nutritional behavior among (anaerobic) degradation specialist than previously thought. Preference of Magnetospirillum sp. strain pMbN1 for benzoate from mixtures with 4-methylbenzoate, and thus temporal separation of the benzoyl-CoA (first) and 4-methylbenzoyl-CoA (second) pathway, may reflect a catabolic tuning towards metabolic efficiency and the markedly broader range of aromatic substrates feeding into the central anaerobic benzoyl-CoA pathway. Electronic supplementary material The online version of this article (doi:10.1186/s12866-014-0269-4) contains supplementary material, which is available to authorized users.
Collapse
|
33
|
Metabolic engineering of Acinetobacter baylyi ADP1 for improved growth on gluconate and glucose. Appl Environ Microbiol 2014; 80:7021-7. [PMID: 25192990 DOI: 10.1128/aem.01837-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A high growth rate in bacterial cultures is usually achieved by optimizing growth conditions, but metabolism of the bacterium limits the maximal growth rate attainable on the carbon source used. This limitation can be circumvented by engineering the metabolism of the bacterium. Acinetobacter baylyi has become a model organism for studies of bacterial metabolism and metabolic engineering due to its wide substrate spectrum and easy-to-engineer genome. It produces naturally storage lipids, such as wax esters, and has a unique gluconate catabolism as it lacks a gene for pyruvate kinase. We engineered the central metabolism of A. baylyi ADP1 more favorable for gluconate catabolism by expressing the pyruvate kinase gene (pykF) of Escherichia coli. This modification increased growth rate when cultivated on gluconate or glucose as a sole carbon source in a batch cultivation. The engineered cells reached stationary phase on these carbon sources approximately twice as fast as control cells carrying an empty plasmid and produced similar amount of biomass. Furthermore, when grown on either gluconate or glucose, pykF expression did not lead to significant accumulation of overflow metabolites and consumption of the substrate remained unaltered. Increased growth rate on glucose was not accompanied with decreased wax ester production, and the pykF-expressing cells accumulated significantly more of these storage lipids with respect to cultivation time.
Collapse
|
34
|
Acinetobacter phage genome is similar to Sphinx 2.36, the circular DNA copurified with TSE infected particles. Sci Rep 2014; 3:2240. [PMID: 23867905 PMCID: PMC3715749 DOI: 10.1038/srep02240] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 07/04/2013] [Indexed: 01/14/2023] Open
Abstract
While analyzing plasmids of Acinetobacter sp. DS002 we have detected a circular DNA molecule pTS236, which upon further investigation is identified as the genome of a phage. The phage genome has shown sequence similarity to the recently discovered Sphinx 2.36 DNA sequence co-purified with the Transmissible Spongiform Encephalopathy (TSE) particles isolated from infected brain samples collected from diverse geographical regions. As in Sphinx 2.36, the phage genome also codes for three proteins. One of them codes for RepA and is shown to be involved in replication of pTS236 through rolling circle (RC) mode. The other two translationally coupled ORFs, orf106 and orf96, code for coat proteins of the phage. Although an orf96 homologue was not previously reported in Sphinx 2.36, a closer examination of DNA sequence of Sphinx 2.36 revealed its presence downstream of orf106 homologue. TEM images and infection assays revealed existence of phage AbDs1 in Acinetobacter sp. DS002.
Collapse
|
35
|
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.
Collapse
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
| |
Collapse
|
36
|
Purification and characterization of an NAD+-dependent XylB-like aryl alcohol dehydrogenase identified in Acinetobacter baylyi ADP1. Appl Environ Microbiol 2012; 78:8743-52. [PMID: 23042182 DOI: 10.1128/aem.02224-12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gene xylB(ADP1) from Acinetobacter baylyi ADP1 (gene annotation number ACIAD1578), coding for a putative aryl alcohol dehydrogenase, was heterologously expressed in Escherichia coli BL21(DE3). The respective aryl alcohol dehydrogenase was purified by fast protein liquid chromatography to apparent electrophoretic homogeneity. The predicted molecular weight of 39,500 per subunit was confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. According to the native M(w) as determined by gel filtration, the enzyme forms dimers and therefore seems to be XylB related. The enzyme showed the highest activity at 40°C. For both the reduction and the oxidation reactions, the pH for optimum activity was 6.5. The enzyme was NADH dependent and able to reduce medium- to long-chain n-alkylaldehydes, methyl-branched aldehydes, and aromatic aldehydes, with benzaldehyde yielding the highest activity. The oxidation reaction with the corresponding alcohols showed only 2.2% of the reduction activity, with coniferyl alcohol yielding the highest activity. Maximum activities for the reduction and the oxidation reaction were 104.5 and 2.3 U mg(-1) of protein, respectively. The enzyme activity was affected by low concentrations of Ag(+) and Hg(2+) and high concentrations of Cu(2+), Zn(2+), and Fe(2+). The gene xylB(ADP1) seems to be expressed constitutively and an involvement in coniferyl alcohol degradation is suggested. However, the enzyme is most probably not involved in the degradation of benzyl alcohol, anisalcohol, salicyl alcohol, vanillyl alcohol, cinnamyl alcohol, or aliphatic and isoprenoid alcohols.
Collapse
|
37
|
Knockaert D, Raes K, Wille C, Struijs K, Van Camp J. Metabolism of ferulic acid during growth of Lactobacillus plantarum and Lactobacillus collinoides. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2012; 92:2291-2296. [PMID: 22351494 DOI: 10.1002/jsfa.5623] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 11/24/2011] [Accepted: 01/14/2012] [Indexed: 05/31/2023]
Abstract
BACKGROUND Food-isolated lactic acid bacteria can transform ferulic acid (FA) into several products. Since quantification of these metabolites during the different bacterial growth phases is lacking, the aim of this study was to identify and quantify conversion products of FA and to follow the kinetics of FA metabolism during growth of Lactobacillus plantarum and Lactobacillus collinoides. RESULTS Lactobacillus plantarum and Lactobacillus collinoides were incubated in MRS broth, to which different amounts of FA were added (final concentrations of 0, 0.5, 1.5 and 3 mmol L⁻¹), at 30 °C until the late stationary phase. Lactobacillus plantarum metabolised FA into 4-vinylguaiacol (4-VG) and hydroferulic acid (HFA). Conversion to 4-VG started simultaneously with the degradation of FA, while formation of HFA started in the mid-exponential phase. Lactobacillus collinoides only formed 4-VG, mainly in the stationary phase. No significant effect of the different amounts of FA was seen on the growth and fermentation characteristics of both bacteria. CONCLUSION The results demonstrate that both bacteria are able to convert FA. However, start of conversion differs between the two strains. The different amounts of FA had no influence on the growth and fermentation characteristics of both bacteria.
Collapse
Affiliation(s)
- Dries Knockaert
- Department of Food Safety and Food Quality, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | | | | | | | | |
Collapse
|
38
|
Zhang D, Zhao Y, He Y, Wang Y, Zhao Y, Zheng Y, Wei X, Zhang L, Li Y, Jin T, Wu L, Wang H, Davison PA, Xu J, Huang WE. Characterization and modeling of transcriptional cross-regulation in Acinetobacter baylyi ADP1. ACS Synth Biol 2012; 1:274-83. [PMID: 23651250 DOI: 10.1021/sb3000244] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Synthetic biology involves reprogramming and engineering of regulatory genes in innovative ways for the implementation of novel tasks. Transcriptional gene regulation systems induced by small molecules in prokaryotes provide a rich source for logic gates. Cross-regulation, whereby a promoter is activated by different molecules or different promoters are activated by one molecule, can be used to design an OR-gate and achieve cross-talk between gene networks in cells. Acinetobacter baylyi ADP1 is naturally transformable, readily editing its chromosomal DNA, which makes it a convenient chassis for synthetic biology. The catabolic genes for salicylate, benzoate, and catechol metabolism are located within a supraoperonic cluster (-sal-are-ben-cat-) in the chromosome of A. baylyi ADP1, which are separately regulated by LysR-type transcriptional regulators (LTTRs). ADP1-based biosensors were constructed in which salA, benA, and catB were fused with a reporter gene cassette luxCDABE under the separate control of SalR, BenM, and CatM regulators. Salicylate, benzoate, catechol, and associated metabolites were found to mediate cross-regulation among sal, ben, and cat operons. A new mathematical model was developed by considering regulator-inducer binding and promoter activation as two separate steps. This model fits the experimental data well and is shown to predict cross-regulation performance.
Collapse
Affiliation(s)
- Dayi Zhang
- Kroto Research
Institute, University of Sheffield, Broad
Lane, Sheffield S3 7HQ,
U.K
| | - Yun Zhao
- BGI-Shenzhen, Shenzhen 518083, P.R. China
- Shenzhen Key Laboratory of Environmental Microbial Genomics and Application,
Shenzhen 518083, P.R. China
| | - Yi He
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
| | - Yun Wang
- Kroto Research
Institute, University of Sheffield, Broad
Lane, Sheffield S3 7HQ,
U.K
| | - Yiyu Zhao
- Kroto Research
Institute, University of Sheffield, Broad
Lane, Sheffield S3 7HQ,
U.K
- BGI-Shenzhen, Shenzhen 518083, P.R. China
| | - Yi Zheng
- BGI-Shenzhen, Shenzhen 518083, P.R. China
| | - Xia Wei
- BGI-Shenzhen, Shenzhen 518083, P.R. China
| | | | - Yuzhen Li
- BGI-Shenzhen, Shenzhen 518083, P.R. China
| | - Tao Jin
- BGI-Shenzhen, Shenzhen 518083, P.R. China
| | - Lin Wu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
| | - Hui Wang
- Centre for Ecology and Hydrology, Wallingford, Banson Road, Wallingford
OX10 8BB, U.K
| | - Paul A. Davison
- Kroto Research
Institute, University of Sheffield, Broad
Lane, Sheffield S3 7HQ,
U.K
| | - Junguang Xu
- BGI-Shenzhen, Shenzhen 518083, P.R. China
- Shenzhen Key Laboratory of Environmental Microbial Genomics and Application,
Shenzhen 518083, P.R. China
| | - Wei E. Huang
- Kroto Research
Institute, University of Sheffield, Broad
Lane, Sheffield S3 7HQ,
U.K
| |
Collapse
|
39
|
Zhang C, Anderson AJ. Utilization of pyrene and benzoate in Mycobacterium isolate KMS is regulated differentially by catabolic repression. J Basic Microbiol 2012; 53:81-92. [PMID: 22733411 DOI: 10.1002/jobm.201100480] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2011] [Accepted: 01/07/2012] [Indexed: 12/21/2022]
Abstract
The soil isolate, Mycobacterium sp. strain KMS, utilizes an array of carbon compounds including the aromatics benzoate and pyrene as sole carbon sources. Growth on pyrene induced both chromosomal and plasmid nidA genes encoding pyrene ring-hydroxylating dioxygenase α-subunits for pyrene oxidation. Diauxic growth occurred when KMS was cultured with pyrene plus either acetate, succinate, fructose, or benzoate and nidA expression only was detected in the second slower log-phase period. Potential cAMP-CRP binding sites exist within the promoter region of both nidA genes indicating that cAMP-CRP may be involved in catabolite repression of pyrene utilization. When cultured with benzoate plus either acetate, succinate, or fructose, there was no diauxic growth. Also there was no diauxic growth on fructose plus succinate or acetate. Expression of a benA gene, encoding a benzoate dioxygenase α-subunit involved in the initiation of benzoate oxidation, was detected in log-phase cells from the benzoate-mixed substrate cultures at the same level as when the cells were cultured on benzoate alone. These findings suggested that catabolite repression of pyrene but not benzoate occurred in isolate KMS. These differences may help the microbe exploit the varied carbon sources available in the soil and rhizosphere environments.
Collapse
Affiliation(s)
- Chun Zhang
- Department of Biology, Utah State University, Logan, Utah 84322-5305, USA
| | | |
Collapse
|
40
|
Characterization of novel diesel-degrading strains Acinetobacter haemolyticus MJ01 and Acinetobacter johnsonii MJ4 isolated from oil-contaminated soil. World J Microbiol Biotechnol 2012; 28:2057-67. [DOI: 10.1007/s11274-012-1008-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 01/24/2012] [Indexed: 10/14/2022]
|
41
|
Benzoate mediates repression of C(4)-dicarboxylate utilization in "Aromatoleum aromaticum" EbN1. J Bacteriol 2011; 194:518-28. [PMID: 22081395 DOI: 10.1128/jb.05072-11] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Diauxic growth was observed in anaerobic C(4)-dicarboxylate-adapted cells of "Aromatoleum aromaticum" EbN1 due to preferred benzoate utilization from a substrate mixture of a C(4)-dicarboxylate (succinate, fumarate, or malate) and benzoate. Differential protein profiles (two-dimensional difference gel electrophoresis [2D DIGE]) revealed dynamic changes in abundance for proteins involved in anaerobic benzoate catabolism and C(4)-dicarboxylate uptake. In the first active growth phase, benzoate utilization was paralleled by maximal abundance of proteins involved in anaerobic benzoate degradation (e.g., benzoyl-coenzyme A [CoA] reductase) and minimal abundance of DctP (EbA4158), the periplasmic binding protein of a predicted C(4)-dicarboxylate tripartite ATP-independent periplasmic (TRAP) transporter (DctPQM). The opposite was observed during subsequent succinate utilization in the second active growth phase. The increased dctP (respectively, dctPQM) transcript and DctP protein abundance following benzoate depletion suggests that repression of C(4)-dicarboxylate uptake seems to be a main determinant for the observed diauxie.
Collapse
|
42
|
Kang YS, Jung J, Jeon CO, Park W. Acinetobacter oleivorans sp. nov. is capable of adhering to and growing on diesel-oil. J Microbiol 2011; 49:29-34. [PMID: 21369976 DOI: 10.1007/s12275-011-0315-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 09/29/2010] [Indexed: 12/18/2022]
Abstract
A diesel-oil and n-hexadecane-degrading novel bacterial strain, designated DR1(T), was isolated from a rice paddy in Deok-So, South Korea. The strain DR1(T) cells were Gram-negative, aerobic coccobacilli, and grew at 20-37°C with the optimal temperature of 30°C, and an optimal pH of 6-8. Interestingly, strain DR1(T) was highly motile (swimming and swarming motility) using its fimbriae, and generated N-acyl homoserine lactones as quorum-sensing signals. The predominant respiratory quinone as identified as ubiquinone-9 (Q-9) and DNA G+C content was 41.4 mol%. Comparative 16S rRNA gene sequence-based phylogenetic analysis placed the strain in a clade with the species A. calcoaceticus, A. haemolyticus, A. baumannii, A. baylyi, and A. beijerinckii, with which it evidenced sequence similarities of 98.2%, 97.4%, 97.2%, 97.1%, and 97.0%, respectively. DNA-DNA hybridization values between strain DR1(T) and other Acinetobacter spp. were all less than 20%. The physiological and taxonomic characteristics with the DNA-DNA hybridization data supported the identification of strain DR1(T) in the genus Acinetobacter as a novel species, for which the name Acinetobacter oleivorans sp. nov. is proposed. The type strain is DR1(T) (=KCTC 23045(T) =JCM 16667(T)).
Collapse
Affiliation(s)
- Yoon-Suk Kang
- Division of Environmental Science and Ecological Engineering, Korea University, Seoul, 136-713, Republic of Korea
| | | | | | | |
Collapse
|
43
|
Kang YS, Park W. Contribution of quorum-sensing system to hexadecane degradation and biofilm formation in Acinetobacter sp. strain DR1. J Appl Microbiol 2010; 109:1650-9. [PMID: 20629796 DOI: 10.1111/j.1365-2672.2010.04793.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS To investigate roles of quorum-sensing (QS) system in Acinetobacter sp. strain DR1 and rifampicin-resistant variant (hereinafter DR1R). METHODS AND RESULTS The DR1 strain generated three putative acyl homoserine lactones (AHLs), while the DR1R produced only one signal and QS signal production was abrogated in the aqsI (LuxI homolog) mutant. The hexadecane-degradation and biofilm-formation capabilities of DR1, DR1R, and aqsI mutants were compared, along with their proteomic data. Proteomics analysis revealed that the AHL lactonase responsible for degrading QS signal was highly upregulated in both DR1R and aqsI mutant, also showed that several proteins, including ppGpp synthase, histidine kinase sensors, might be under the control of QS signalling. Interestingly, biofilm-formation and hexadecane-biodegradation abilities were reduced more profoundly in the aqsI mutant. These altered phenotypes of the aqsI mutant were restored via the addition of free wild-type cell supernatant and exogenous C(12) -AHL. CONCLUSIONS The QS system in strain DR1 contributes to hexadecane degradation and biofilm formation. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first report to demonstrate that a specific QS signal appears to be a critical factor for hexadecane degradation and biofilm formation in Acinetobacter sp. strain DR1.
Collapse
Affiliation(s)
- Y-S Kang
- Division of Environmental Science and Ecological Engineering, Korea University, Seoul, Korea
| | | |
Collapse
|
44
|
Rojo F. Carbon catabolite repression in Pseudomonas : optimizing metabolic versatility and interactions with the environment. FEMS Microbiol Rev 2010; 34:658-84. [PMID: 20412307 DOI: 10.1111/j.1574-6976.2010.00218.x] [Citation(s) in RCA: 332] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Metabolically versatile free-living bacteria have global regulation systems that allow cells to selectively assimilate a preferred compound among a mixture of several potential carbon sources. This process is known as carbon catabolite repression (CCR). CCR optimizes metabolism, improving the ability of bacteria to compete in their natural habitats. This review summarizes the regulatory mechanisms responsible for CCR in the bacteria of the genus Pseudomonas, which can live in many different habitats. Although the information available is still limited, the molecular mechanisms responsible for CCR in Pseudomonas are clearly different from those of Enterobacteriaceae or Firmicutes. An understanding of the molecular mechanisms underlying CCR is important to know how metabolism is regulated and how bacteria degrade compounds in the environment. This is particularly relevant for compounds that are degraded slowly and accumulate, creating environmental problems. CCR has a major impact on the genes involved in the transport and metabolism of nonpreferred carbon sources, but also affects the expression of virulence factors in several bacterial species, genes that are frequently directed to allow the bacterium to gain access to new sources of nutrients. Finally, CCR has implications in the optimization of biotechnological processes such as biotransformations or bioremediation strategies.
Collapse
Affiliation(s)
- Fernando Rojo
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Madrid, Spain.
| |
Collapse
|
45
|
Kang YS, Park W. Trade-off between antibiotic resistance and biological fitness in Acinetobacter sp. strain DR1. Environ Microbiol 2010; 12:1304-18. [PMID: 20192959 DOI: 10.1111/j.1462-2920.2010.02175.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rifampicin, a bactericidal antibiotic drug, is routinely used to make an environmental recipient selective in laboratory-conjugation experiments. We noticed, inadvertently, that the rifampicin-resistant Acinetobacter sp. strain DR1, a recently discovered hexadecane-degrading environmental isolate, exhibited a substantial loss of quorum sensing signalling. The domesticated ampicillin-resistant strain, DR1, evidenced more dramatic phenotypic changes than were observed in the rifampicin-resistant cells: a complete loss of quorum sensing, a loss in swimming and swarming motilities, poor fimbrial expression, increased rigidity in membrane fatty acid composition and reduced hexadecane degradation capability. Interestingly, the motility of strain DR1 grown adjacent to a streptomycin-producing Streptomyces griceus was permanently abrogated, where this change was heritable and other phenotypic changes could not be detected. In this study, we have reported for the first time that the in situ acquisition of antibiotic resistance may reduce biological fitness, including losses in the production of quorum sensing signals, motility and substrate utilization, and each antibiotic is associated with different degrees of phenotypic and genetic alterations. Our data also suggested that the domestication of environmental isolates should be approached with caution, as there are phenotypic variations in antibiotic-resistant cells that might not be noticeable unless all possible phenotypic assays are conducted.
Collapse
Affiliation(s)
- Yoon-Suk Kang
- Division of Environmental Science and Ecological Engineering, Korea University, Seoul, Korea
| | | |
Collapse
|
46
|
Li D, Yan Y, Ping S, Chen M, Zhang W, Li L, Lin W, Geng L, Liu W, Lu W, Lin M. Genome-wide investigation and functional characterization of the beta-ketoadipate pathway in the nitrogen-fixing and root-associated bacterium Pseudomonas stutzeri A1501. BMC Microbiol 2010; 10:36. [PMID: 20137101 PMCID: PMC2907835 DOI: 10.1186/1471-2180-10-36] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 02/08/2010] [Indexed: 11/20/2022] Open
Abstract
Background Soil microorganisms are mainly responsible for the complete mineralization of aromatic compounds that usually originate from plant products or environmental pollutants. In many cases, structurally diverse aromatic compounds can be converted to a small number of structurally simpler intermediates, which are metabolized to tricarboxylic acid intermediates via the β-ketoadipate pathway. This strategy provides great metabolic flexibility and contributes to increased adaptation of bacteria to their environment. However, little is known about the evolution and regulation of the β-ketoadipate pathway in root-associated diazotrophs. Results In this report, we performed a genome-wide analysis of the benzoate and 4-hydroxybenzoate catabolic pathways of Pseudomonas stutzeri A1501, with a focus on the functional characterization of the β-ketoadipate pathway. The P. stutzeri A1501 genome contains sets of catabolic genes involved in the peripheral pathways for catabolism of benzoate (ben) and 4-hydroxybenzoate (pob), and in the catechol (cat) and protocatechuate (pca) branches of the β-ketoadipate pathway. A particular feature of the catabolic gene organization in A1501 is the absence of the catR and pcaK genes encoding a LysR family regulator and 4-hydroxybenzoate permease, respectively. Furthermore, the BenR protein functions as a transcriptional activator of the ben operon, while transcription from the catBC promoter can be activated in response to benzoate. Benzoate degradation is subject to carbon catabolite repression induced by glucose and acetate in A1501. The HPLC analysis of intracellular metabolites indicated that low concentrations of 4-hydroxybenzoate significantly enhance the ability of A1501 to degrade benzoate. Conclusions The expression of genes encoding proteins involved in the β-ketoadipate pathway is tightly modulated by both pathway-specific and catabolite repression controls in A1501. This strain provides an ideal model system for further study of the evolution and regulation of aromatic catabolic pathways.
Collapse
Affiliation(s)
- Danhua Li
- College of Biological Sciences, China Agricultural University, Beijing 100094, China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Bleichrodt FS, Fischer R, Gerischer UC. The beta-ketoadipate pathway of Acinetobacter baylyi undergoes carbon catabolite repression, cross-regulation and vertical regulation, and is affected by Crc. MICROBIOLOGY-SGM 2010; 156:1313-1322. [PMID: 20110298 DOI: 10.1099/mic.0.037424-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The degradation of many structurally diverse aromatic compounds in Acinetobacter baylyi is accomplished by the beta-ketoadipate pathway. In addition to specific induction of expression by certain aromatic compounds, this pathway is regulated by complex mechanisms at multiple levels, which are the topic of this study. Multiple operons feeding into the beta-ketoadipate pathway are controlled by carbon catabolite repression (CCR) caused by succinate plus acetate. The pathways under study enable the catabolism of benzoate (ben), catechol (catA), cis,cis-muconate (catB,C,I,J,F,D), vanillate (van), hydroxycinnamates (hca), dicarboxylates (dca), salicylate (sal), anthranilate (ant) and benzyl esters (are). For analysis of CCR at the transcriptional level a luciferase reporter gene cassette was introduced into the operons. The Crc (catabolite repression control) protein is involved in repression of all operons (except for catA), as demonstrated by the analysis of respective crc strains. In addition, cross-regulation was demonstrated for the vanA,B, hca and dca operons. The presence of protocatechuate caused transcriptional repression of the vanA,B- and hca-encoded funnelling pathways (vertical regulation). Thus the results presented extend the understanding both of CCR and of the effects of Crc for all aromatic degradative pathways of A. baylyi and increase the number of operons known to be controlled by two additional mechanisms, cross-regulation and vertical regulation.
Collapse
Affiliation(s)
- Fenja S Bleichrodt
- Institute of Microbiology and Biotechnology, University of Ulm, 89069 Ulm, Germany
| | - Rita Fischer
- Institute of Microbiology and Biotechnology, University of Ulm, 89069 Ulm, Germany
| | - Ulrike C Gerischer
- Institute of Microbiology and Biotechnology, University of Ulm, 89069 Ulm, Germany
| |
Collapse
|
48
|
de Berardinis V, Durot M, Weissenbach J, Salanoubat M. Acinetobacter baylyi ADP1 as a model for metabolic system biology. Curr Opin Microbiol 2009; 12:568-76. [PMID: 19709925 DOI: 10.1016/j.mib.2009.07.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Accepted: 07/15/2009] [Indexed: 01/20/2023]
Abstract
Information produced by the annotation of an 'average bacterial genome' can be separated into three parts. One-third represents what we know, another third what we think we know, and the last third what we know we do not know. Knowledge of metabolism is also described by this three thirds rule. Understanding how a cell operates will require a better knowledge of the two ignored thirds of its parts. Moreover, metabolism needs to be further investigated using organisms whose life styles are different from those of model organisms. In this short review, we present Acinetobacter baylyi ADP1 as an environmental model especially suitable for large-scale genetic manipulation. Resources have been constructed in the past few years that can form the basis for diverse metabolic studies: the genome sequence, a single gene mutant collection, and a genome-scale metabolic model.
Collapse
|
49
|
de las Rivas B, Rodríguez H, Curiel JA, Landete JM, Muñoz R. Molecular screening of wine lactic acid bacteria degrading hydroxycinnamic acids. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2009; 57:490-494. [PMID: 19099460 DOI: 10.1021/jf803016p] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The potential to produce volatile phenols from hydroxycinnamic acids was investigated for lactic acid bacteria (LAB) isolated from Spanish grape must and wine. A PCR assay was developed for the detection of LAB that potentially produce volatile phenols. Synthetic degenerate oligonucleotides for the specific detection of the pdc gene encoding a phenolic acid decarboxylase were designed. The pdc PCR assay amplifies a 321 bp DNA fragment from phenolic acid decarboxylase. The pdc PCR method was applied to 85 strains belonging to the 6 main wine LAB species. Lactobacillus plantarum, Lactobacillus brevis, and Pediococcus pentosaceus strains produce a positive response in the pdc PCR assay, whereas Oenococcus oeni, Lactobacillus hilgardii, and Leuconostoc mesenteroides strains did not produce the expected PCR product. The production of vinyl and ethyl derivatives from hydroxycinnamic acids in culture media was determined by high-performance liquid chromatography. A relationship was found between pdc PCR amplification and volatile phenol production, so that the LAB strains that gave a positive pdc PCR response produce volatile phenols, whereas strains that did not produce a PCR amplicon did not produce volatile phenols. The proposed method could be useful for a preliminary identification of LAB strains able to produce volatile phenols in wine.
Collapse
Affiliation(s)
- Blanca de las Rivas
- Departamento de Microbiología, Instituto de Fermentaciones Industriales, Madrid, Spain
| | | | | | | | | |
Collapse
|