1
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Jenney FE, Wang H, George SJ, Xiong J, Guo Y, Gee LB, Marizcurrena JJ, Castro-Sowinski S, Staskiewicz A, Yoda Y, Hu MY, Tamasaku K, Nagasawa N, Li L, Matsuura H, Doukov T, Cramer SP. Temperature-dependent iron motion in extremophile rubredoxins - no need for 'corresponding states'. Sci Rep 2024; 14:12197. [PMID: 38806591 PMCID: PMC11133467 DOI: 10.1038/s41598-024-62261-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 05/15/2024] [Indexed: 05/30/2024] Open
Abstract
Extremophile organisms are known that can metabolize at temperatures down to - 25 °C (psychrophiles) and up to 122 °C (hyperthermophiles). Understanding viability under extreme conditions is relevant for human health, biotechnological applications, and our search for life elsewhere in the universe. Information about the stability and dynamics of proteins under environmental extremes is an important factor in this regard. Here we compare the dynamics of small Fe-S proteins - rubredoxins - from psychrophilic and hyperthermophilic microorganisms, using three different nuclear techniques as well as molecular dynamics calculations to quantify motion at the Fe site. The theory of 'corresponding states' posits that homologous proteins from different extremophiles have comparable flexibilities at the optimum growth temperatures of their respective organisms. Although 'corresponding states' would predict greater flexibility for rubredoxins that operate at low temperatures, we find that from 4 to 300 K, the dynamics of the Fe sites in these homologous proteins are essentially equivalent.
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Affiliation(s)
- Francis E Jenney
- Georgia Campus, Philadelphia College of Osteopathic Medicine, Suwanee, GA, 30024, USA
| | | | | | - Jin Xiong
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Leland B Gee
- LCLS, SLAC National Laboratory, Stanford, CA, 94025, USA
| | | | | | - Anna Staskiewicz
- Georgia Campus, Philadelphia College of Osteopathic Medicine, Suwanee, GA, 30024, USA
| | - Yoshitaka Yoda
- Precision Spectroscopy Division, SPring-8/JASRI, Sayo, Hyogo, 679-5198, Japan
| | - Michael Y Hu
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL, 60439, USA
| | | | - Nobumoto Nagasawa
- Precision Spectroscopy Division, SPring-8/JASRI, Sayo, Hyogo, 679-5198, Japan
| | - Lei Li
- Synchrotron Radiation Research Center, Hyogo, 679-5165, Japan
| | | | - Tzanko Doukov
- SSRL, SLAC National Laboratory, Stanford, CA, 94025, USA
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2
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Groves JT, Feng L, Austin RN. Structure and Function of Alkane Monooxygenase (AlkB). Acc Chem Res 2023; 56:3665-3675. [PMID: 38032826 DOI: 10.1021/acs.accounts.3c00590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Every year, perhaps as much as 800 million tons of hydrocarbons enters the environment; alkanes make up a large percentage of it. Most are transformed by organisms that utilize these molecules as sources of energy and carbon. Both aerobic and anaerobic alkane transformation chemistries exist, capitalizing on the presence of alkanes in both oxic and anoxic environments. Over the past 40 years, tremendous progress has been made in understanding the structure and mechanism of enzymes that catalyze the transformation of methane. By contrast, progress involving enzymes that transform liquid alkanes has been slower with the first structures of AlkB, the predominant aerobic alkane hydroxylase in the environment, appearing in 2023. Because of the fundamental importance of C-H bond activation chemistries, interest in understanding how biology activates and transforms alkanes is high.In this Account, we focus on steps we have taken to understand the mechanism and structure of alkane monooxygenase (AlkB), the metalloenzyme that dominates the transformation of liquid alkanes in the environment (not to be confused with another AlkB that is an α-ketogluturate-dependent enzyme involved in DNA repair). First, we briefly describe what is known about the prevalence of AlkB in the environment and its role in the carbon cycle. Then we review the key findings from our recent high-resolution cryoEM structure of AlkB and highlight important similarities and differences in the structures of members of class III diiron enzymes. Functional studies, which we summarize, from a number of single residue variants enable us to say a great deal about how the structure of AlkB facilitates its function. Next, we overview work from our laboratories using mechanistically diagnostic radical clock substrates to characterize the mechanism of AlkB and contextualize the results we have obtained on AlkB with results we have obtained on other alkane-oxidizing enzymes and explain these results in light of the enzyme's structure. Finally, we integrate recent work in our laboratories with information from prior studies of AlkB, and relevant model systems, to create a holistic picture of the enzyme. We end by pointing to critical questions that still need to be answered, questions about the electronic structure of the active site of the enzyme throughout the reaction cycle and about whether and to what extent the enzyme plays functional roles in biology beyond simply initiating the degradation of alkanes.
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Affiliation(s)
- John T Groves
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Liang Feng
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, United States
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3
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Vázquez Rosas Landa M, De Anda V, Rohwer RR, Angelova A, Waldram G, Gutierrez T, Baker BJ. Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean. mSystems 2023; 8:e0061923. [PMID: 37702502 PMCID: PMC10654063 DOI: 10.1128/msystems.00619-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 07/19/2023] [Indexed: 09/14/2023] Open
Abstract
IMPORTANCE Petroleum pollution in the ocean has increased because of rapid population growth and modernization, requiring urgent remediation. Our understanding of the metabolic response of native microbial communities to oil spills is not well understood. Here, we explored the baseline hydrocarbon-degrading communities of a subarctic Atlantic region to uncover the metabolic potential of the bacteria that inhabit the surface and subsurface water. We conducted enrichments with a 13C-labeled hydrocarbon to capture the fraction of the community actively using the hydrocarbon. We then combined this approach with metagenomics to identify the metabolic potential of this hydrocarbon-degrading community. This revealed previously undescribed uncultured bacteria with unique metabolic mechanisms involved in aerobic hydrocarbon degradation, indicating that temperature may be pivotal in structuring hydrocarbon-degrading baseline communities. Our findings highlight gaps in our understanding of the metabolic complexity of hydrocarbon degradation by native marine microbial communities.
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Affiliation(s)
- Mirna Vázquez Rosas Landa
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, Texas, USA
- Instituto de Ciencias del Mar y Limnologia Universidad Nacional Autónoma de Mexico, Unidad Académica de Ecologia y Biodiversidad Acuática, Mexico City, Mexico
| | - Valerie De Anda
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, Texas, USA
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Robin R. Rohwer
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Angelina Angelova
- School of Engineering and Physical Sciences, Institute of Mechanical, Process and Energy Engineering (IMPEE), Heriot-Watt University, Edinburgh, United Kingdom
| | - Georgia Waldram
- School of Engineering and Physical Sciences, Institute of Mechanical, Process and Energy Engineering (IMPEE), Heriot-Watt University, Edinburgh, United Kingdom
| | - Tony Gutierrez
- School of Engineering and Physical Sciences, Institute of Mechanical, Process and Energy Engineering (IMPEE), Heriot-Watt University, Edinburgh, United Kingdom
| | - Brett J. Baker
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, Texas, USA
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
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4
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Schultes FPJ, Haarmann M, Tischler D, Mügge C. Primary alcohols as substrates or products in whole-cell biocatalysis: Toxicity for Escherichia coli expression strains. MOLECULAR CATALYSIS 2023. [DOI: 10.1016/j.mcat.2023.112979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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5
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Sah D, Rai JPN, Ghosh A, Chakraborty M. A review on biosurfactant producing bacteria for remediation of petroleum contaminated soils. 3 Biotech 2022; 12:218. [PMID: 35965658 PMCID: PMC9365905 DOI: 10.1007/s13205-022-03277-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/21/2022] [Indexed: 11/01/2022] Open
Abstract
The discharge of potentially toxic petroleum hydrocarbons into the environment has been a matter of concern, as these organic pollutants accumulate in many ecosystems due to their hydrophobicity and low bioavailability. Petroleum hydrocarbons are neurotoxic and carcinogenic organic pollutants, extremely harmful to human and environmental health. Traditional treatment methods for removing hydrocarbons from polluted areas, including various mechanical and chemical strategies, are ineffective and costly. However, many indigenous microorganisms in soil and water can utilise hydrocarbon compounds as sources of carbon and energy and hence, can be employed to degrade hydrocarbon contaminants. Therefore, bioremediation using bacteria that degrade petroleum hydrocarbons is commonly viewed as an environmentally acceptable and effective method. The efficacy of bioremediation can be boosted further by using potential biosurfactant-producing microorganisms, as biosurfactants reduce surface tension, promote emulsification and micelle formation, making hydrocarbons bio-available for microbial breakdown. Further, introducing nanoparticles can improve the solubility of hydrophobic hydrocarbons as well as microbial synthesis of biosurfactants, hence establishing a favourable environment for microbial breakdown of these chemicals. The review provides insights into the role of microbes in the bioremediation of soils contaminated with petroleum hydrocarbons and emphasises the significance of biosurfactants and potential biosurfactant-producing bacteria. The review partly focusses on how nanotechnology is being employed in different critical bioremediation processes.
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Affiliation(s)
- Diksha Sah
- Department of Environmental Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - J. P. N. Rai
- Department of Environmental Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Ankita Ghosh
- Department of Environmental Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Moumita Chakraborty
- Department of Environmental Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
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6
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Li Y, Zheng B, Yang Y, Chen K, Chen X, Huang X, Wang X. Soil microbial ecological effect of shale gas oil-based drilling cuttings pyrolysis residue used as soil covering material. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129231. [PMID: 35739751 DOI: 10.1016/j.jhazmat.2022.129231] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/13/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
The residue derived from oil-based drilling cutting pyrolysis could be used as paving materials. Some petroleum hydrocarbons remain in the residue after pyrolysis and cause severe environmental pollution. In this study, the soil column leaching experiments were carried out under different leaching amounts, and the vertical migration characteristics of petroleum hydrocarbons in soil and the dynamic response mechanism of microorganisms to petroleum hydrocarbons were analyzed. The result showed that the soil pH value and water content with different leaching amounts did not differ significantly, but the vertical migration ability of each petroleum hydrocarbon component was different. In petroleum hydrocarbon contaminated soil, the relative abundance of Proteobacteria maintained a high level (23.6%-60.7%). At the genus level, the relative abundance of Massilia decreased with the leaching amount increased. According to PICRUSt, Monooxygenase [EC: 1.14.13.-] played a significant role in petroleum hydrocarbon degradation. While Long-chain-fatty-acid-CoA ligase [EC: 6.2.1.3] had the highest relative abundance. By studying the influence of shale gas oil-based drilling cuttings pyrolysis residue on soil physical and chemical properties and soil microorganisms, this work provides scientific ecological assessment for the resource application of pyrolysis residue.
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Affiliation(s)
- Yuting Li
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Baiping Zheng
- Chongqing Environment & Sanitation Group, Chongqing 401121, China
| | - Yinghuan Yang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Kejin Chen
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Xiangle Chen
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Xin Huang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Xiang Wang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; College of Environment and Ecology, Chongqing University, Chongqing 400044, China.
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7
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M. tuberculosis AlkX Encoded by rv3249c Regulates a Conserved Alkane Hydroxylase System That Is Important for Replication in Macrophages and Biofilm Formation. Microbiol Spectr 2022; 10:e0196922. [PMID: 35938806 PMCID: PMC9430723 DOI: 10.1128/spectrum.01969-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis is a highly specialized human pathogen. The success of M. tuberculosis is due to its ability to replicate within host macrophages, resist host immune responses, and ultimately enter a persistent state during a latent tuberculosis infection. Understanding how M. tuberculosis adapts to and replicates in the intracellular environment of the host is crucial for the development of novel, targeted therapeutics. We report the characterization of an M. tuberculosis mutant lacking Rv3249c, a TetR transcriptional regulator. We show that Rv3249c directly represses the adjacent alkB-rubA-rubB operon encoding an alkane hydroxylase/rubredoxin system. For consistency with related systems, we have named the rv3249c gene alkX. The alkX mutant survived better than wild-type M. tuberculosis inside macrophages. This could be phenocopied by overexpression of the alkB-rubA-rubB locus. We hypothesized that the improved intracellular survival phenotype is a result of increased fitness of the mutant; however, we found that the alkX mutant had a defect when grown on some host-associated carbon sources in vitro. We also found that the alkX mutant had a defect in biofilm formation, also linked to the overexpression of the alkB-rubAB genes. Combined, these results define the primary role of AlkX as a transcriptional repressor of the alkB-rubAB operon and suggest the operon contributes to intracellular survival of the pathogen. IMPORTANCE Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), is the leading cause of death worldwide due to a single infectious agent. It is important to understand how M. tuberculosis adapts to and replicates in the intracellular environment of the host. In this study, we characterized the TetR transcriptional regulator Rv3249c and show that it regulates a highly conserved alkane hydroxylase/rubredoxin system. Our data demonstrate that the AlkBRubAB system contributes to the success of the bacterium in host macrophages.
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8
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Williams SC, Austin RN. An Overview of the Electron-Transfer Proteins That Activate Alkane Monooxygenase (AlkB). Front Microbiol 2022; 13:845551. [PMID: 35295299 PMCID: PMC8918992 DOI: 10.3389/fmicb.2022.845551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Alkane-oxidizing enzymes play an important role in the global carbon cycle. Alkane monooxygenase (AlkB) oxidizes most of the medium-chain length alkanes in the environment. The first AlkB identified was from P. putida GPo1 (initially known as P. oleovorans) in the early 1970s, and it continues to be the family member about which the most is known. This AlkB is found as part of the OCT operon, in which all of the key proteins required for growth on alkanes are present. The AlkB catalytic cycle requires that the diiron active site be reduced. In P. putida GPo1, electrons originate from NADH and arrive at AlkB via the intermediacy of a flavin reductase and an iron–sulfur protein (a rubredoxin). In this Mini Review, we will review what is known about the canonical arrangement of electron-transfer proteins that activate AlkB and, more importantly, point to several other arrangements that are possible. These other arrangements include the presence of a simpler rubredoxin than what is found in the canonical arrangement, as well as two other classes of AlkBs with fused electron-transfer partners. In one class, a rubredoxin is fused to the hydroxylase and in another less well-explored class, a ferredoxin reductase and a ferredoxin are fused to the hydroxylase. We review what is known about the biochemistry of these electron-transfer proteins, speculate on the biological significance of this diversity, and point to key questions for future research.
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Affiliation(s)
| | - Rachel Narehood Austin
- Department of Chemistry, Barnard College, Columbia University, New York City, NY, United States
- *Correspondence: Rachel Narehood Austin,
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9
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Williams SC, Forsberg AP, Lee J, Vizcarra CL, Lopatkin AJ, Austin RN. Investigation of the prevalence and catalytic activity of rubredoxin-fused alkane monooxygenases (AlkBs). J Inorg Biochem 2021; 219:111409. [PMID: 33752122 DOI: 10.1016/j.jinorgbio.2021.111409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/28/2021] [Accepted: 02/21/2021] [Indexed: 10/21/2022]
Abstract
Interest in understanding the environmental distribution of the alkane monooxygenase (AlkB) enzyme led to the identification of over 100 distinct alkane monooxygenase (AlkB) enzymes containing a covalently bound, or fused, rubredoxin. The rubredoxin-fused AlkB from Dietzia cinnamea was cloned as a full-length protein and as a truncated protein with the rubredoxin domain deleted. A point mutation (V91W) was introduced into the full-length protein, with the goal of assessing how steric bulk in the putative substrate channel might affect selectivity. Based on activity studies with alkane and alkene substrates, the rubredoxin-fused AlkB oxidizes a similar range of alkane substrates relative to its rubredoxin domain-deletion counterpart. Oxidation of terminal alkenes generated both an epoxide and a terminal aldehyde. The products of V91W-mutant-catalyzed oxidation of alkenes had a higher aldehyde-to-epoxide ratio than the products formed in the presence of the wild type protein. These results are consistent with this mutation causing a structural change impacting substrate positioning.
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Affiliation(s)
- Shoshana C Williams
- Department of Chemistry, Barnard College, 3009 Broadway, New York, NY 10027, USA
| | - Allison P Forsberg
- Department of Chemistry, Barnard College, 3009 Broadway, New York, NY 10027, USA
| | - Juliet Lee
- Department of Chemistry, Barnard College, 3009 Broadway, New York, NY 10027, USA
| | - Christina L Vizcarra
- Department of Chemistry, Barnard College, 3009 Broadway, New York, NY 10027, USA
| | - Allison J Lopatkin
- Department of Biology, Barnard College, 3009 Broadway, New York, NY 10027, USA; Data Science Institute Columbia University, New York, NY 10027 USA
| | - Rachel N Austin
- Department of Chemistry, Barnard College, 3009 Broadway, New York, NY 10027, USA.
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10
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Schubeis T, Schwarzer TS, Le Marchand T, Stanek J, Movellan KT, Castiglione K, Pintacuda G, Andreas LB. Resonance assignment of the outer membrane protein AlkL in lipid bilayers by proton-detected solid-state NMR. BIOMOLECULAR NMR ASSIGNMENTS 2020; 14:295-300. [PMID: 32607893 DOI: 10.1007/s12104-020-09964-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/19/2020] [Indexed: 06/11/2023]
Abstract
Most commonly small outer membrane proteins, possessing between 8 and 12 β-strands, are not involved in transport but fulfill diverse functions such as cell adhesion or binding of ligands. An intriguing exception are the 8-stranded β-barrel proteins of the OmpW family, which are implicated in the transport of small molecules. A representative example is AlkL from Pseudomonas putida GPoI, which functions as a passive importer of hydrophobic molecules. This role is of high interest with respect to both fundamental biological understanding and industrial applications in biocatalysis, since this protein is frequently utilized in biotransformation of alkanes. While the transport function of AlkL is generally accepted, a controversy in the transport mechanism still exists. In order to address this, we are pursuing a structural study of recombinantly produced AlkL reconstituted in lipid bilayers using solid-state NMR spectroscopy. In this manuscript we present 1H, 13C and 15N chemical shift assignments obtained via a suite of 3D experiments employing high magnetic fields (1 GHz and 800 MHz) and the latest magic-angle spinning (MAS) approaches at fast (60-111) kHz rates. We additionally analyze the secondary structure prediction in comparison with those of published structures of homologous proteins.
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Affiliation(s)
- Tobias Schubeis
- Centre de RMN à Très Hauts Champs de Lyon (FRE 2034 - CNRS, UCB Lyon 1, ENS Lyon), Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Tom S Schwarzer
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstraße 15, 85748, Garching, Germany
| | - Tanguy Le Marchand
- Centre de RMN à Très Hauts Champs de Lyon (FRE 2034 - CNRS, UCB Lyon 1, ENS Lyon), Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Jan Stanek
- Centre de RMN à Très Hauts Champs de Lyon (FRE 2034 - CNRS, UCB Lyon 1, ENS Lyon), Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Kumar Tekwani Movellan
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Kathrin Castiglione
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstraße 15, 85748, Garching, Germany
- Institute of Bioprocess Engineering, FAU Erlangen-Nürnberg, Paul-Gordan Str. 3, 91052, Erlangen, Germany
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs de Lyon (FRE 2034 - CNRS, UCB Lyon 1, ENS Lyon), Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France.
| | - Loren B Andreas
- Centre de RMN à Très Hauts Champs de Lyon (FRE 2034 - CNRS, UCB Lyon 1, ENS Lyon), Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France.
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany.
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11
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n-Alkane Distribution—A Paleovegetation Change Indicator during the Period from Late Glacial to Late Holocene on Russian Plain (Bryansk Region). GEOSCIENCES 2020. [DOI: 10.3390/geosciences10030086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Loess-paleosol series are well preserved in the south part of the Russian Plain. However, these sequences have a low number of studies on their organic matter, such as researches of isotope composition, n-alkane and other biomarkers. Thus, the purpose of the study was to reconstruct vegetation conditions from the Late Glacial to Late Holocene. We used the leaf wax-derived n-alkanes to detect vegetation evolution of the Bryansk Region. The stable carbon isotope composition of organic matter and pedogenic carbonates was carried out for the same aim. Three paleosols (of Lasko, Bølling-Allerød warmings and Holocene second humus horizons) and modern soils of different relief positions were investigated. n-Alkane distribution, as well as isotope composition indicates changes from grassy to woody vegetation during this period. The use of biomarkers such as n-alkanes helps to more clearly interpret isotopic data.
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12
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Hackbusch S, Noirungsee N, Viamonte J, Sun X, Bubenheim P, Kostka JE, Müller R, Liese A. Influence of pressure and dispersant on oil biodegradation by a newly isolated Rhodococcus strain from deep-sea sediments of the gulf of Mexico. MARINE POLLUTION BULLETIN 2020; 150:110683. [PMID: 31753565 DOI: 10.1016/j.marpolbul.2019.110683] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 09/14/2019] [Accepted: 10/21/2019] [Indexed: 06/10/2023]
Abstract
A new Rhodococcus strain, capable of degrading crude oil, was isolated from the Gulf of Mexico deep-sea sediment and was investigated for its biodegradation characteristics under atmospheric as well as under deep-sea pressure (1500 m = 15 MPa). Additionally, the effect of dispersant (Corexit EC9500A) addition was studied. Rhodococcus sp. PC20 was shown to degrade 60.5 ± 10.7% of the saturated and aromatic fraction of crude oil at atmospheric pressure and 74.2 ± 9.1% at deep-sea level pressure within 96 h. Degradation rates, especially for monoaromatic hydrocarbons, were significantly higher at elevated pressure compared to atmospheric pressure. This study found a growth inhibiting effect at a dispersant to oil ratio of 1:100 and higher. This effect of the dispersant was enhanced when elevated pressure was applied.
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Affiliation(s)
- Steffen Hackbusch
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Nuttapol Noirungsee
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Juan Viamonte
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Xiaoxu Sun
- Georgia Institute of Technology School of Biology and Earth & Atmospheric Sciences, Atlanta, GA, USA.
| | - Paul Bubenheim
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Joel E Kostka
- Georgia Institute of Technology School of Biology and Earth & Atmospheric Sciences, Atlanta, GA, USA.
| | - Rudolf Müller
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Andreas Liese
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
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13
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Gibu N, Kasai D, Ikawa T, Akiyama E, Fukuda M. Characterization and Transcriptional Regulation of n-Alkane Hydroxylase Gene Cluster of Rhodococcus jostii RHA1. Microorganisms 2019; 7:microorganisms7110479. [PMID: 31652785 PMCID: PMC6921075 DOI: 10.3390/microorganisms7110479] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/17/2019] [Accepted: 10/21/2019] [Indexed: 11/16/2022] Open
Abstract
Gram-positive actinomycete Rhodococcus jostii RHA1 is able to grow on C10 to C19 n-alkanes as a sole source of carbon and energy. To clarify, the n-alkane utilization pathway-a cluster of 5 genes (alkBrubA1A2BalkU) which appeared to be involved in n-alkane degradation-was identified and the transcriptional regulation of these genes was characterized. Reverse transcription-PCR analyses revealed that these genes constituted an operon and were transcribed in the presence of n-alkane. Inactivation of alkB led to the absence of the ability to utilize n-undecane. The alkB mutation resulted in reduction of growth rates on C10 and C12 n-alkanes; however, growths on C13 to C19 n-alkanes were not affected by this mutation. These results suggested that alkB was essential for the utilization of C10 to C12 n-alkanes. Inactivation of alkU showed the constitutive expression of alkB. Purified AlkU is able to bind to the putative promoter region of alkB, suggesting that AlkU played a role in repression of the transcription of alk operon. The results of this study indicated that alkB was involved in the medium-chain n-alkanes degradation of strain RHA1 and the transcription of alk operon was negatively regulated by alkU-encoded regulator. This report is important to understand the n-alkane degradation pathway of R. jostii, including the transcriptional regulation of alk gene cluster.
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Affiliation(s)
- Namiko Gibu
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Japan
| | - Daisuke Kasai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Japan.
| | - Takumi Ikawa
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Japan
| | - Emiko Akiyama
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Japan
| | - Masao Fukuda
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Japan
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14
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He Q, Bennett GN, San KY, Wu H. Biosynthesis of Medium-Chain ω-Hydroxy Fatty Acids by AlkBGT of Pseudomonas putida GPo1 With Native FadL in Engineered Escherichia coli. Front Bioeng Biotechnol 2019; 7:273. [PMID: 31681749 PMCID: PMC6812396 DOI: 10.3389/fbioe.2019.00273] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/01/2019] [Indexed: 12/19/2022] Open
Abstract
Hydroxy fatty acids (HFAs) are valuable compounds that are widely used in medical, cosmetic and food fields. Production of ω-HFAs via bioconversion by engineered Escherichia coli has received a lot of attention because this process is environmentally friendly. In this study, a whole-cell bio-catalysis strategy was established to synthesize medium-chain ω-HFAs based on the AlkBGT hydroxylation system from Pseudomonas putida GPo1. The effects of blocking the β-oxidation of fatty acids (FAs) and enhancing the transportation of FAs on ω-HFAs bio-production were also investigated. When fadE and fadD were deleted, the consumption of decanoic acid decreased, and the yield of ω-hydroxydecanoic acid was enhanced remarkably. Additionally, the co-expression of the FA transporter protein, FadL, played an important role in increasing the conversion rate of ω-hydroxydecanoic acid. As a result, the concentration and yield of ω-hydroxydecanoic acid in NH03(pBGT-fadL) increased to 309 mg/L and 0.86 mol/mol, respectively. This whole-cell bio-catalysis system was further applied to the biosynthesis of ω-hydroxyoctanoic acid and ω-hydroxydodecanoic acid using octanoic acid and dodecanoic acid as substrates, respectively. The concentrations of ω-hydroxyoctanoic acid and ω-hydroxydodecanoic acid reached 275.48 and 249.03 mg/L, with yields of 0.63 and 0.56 mol/mol, respectively. This study demonstrated that the overexpression of AlkBGT coupled with native FadL is an efficient strategy to synthesize medium-chain ω-HFAs from medium-chain FAs in fadE and fadD mutant E. coli strains.
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Affiliation(s)
- Qiaofei He
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - George N. Bennett
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, United States
| | - Ka-Yiu San
- Department of Bioengineering, Rice University, Houston, TX, United States
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, United States
| | - Hui Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai, China
- Key Laboratory of Bio-based Material Engineering of China National Light Industry Council, Shanghai, China
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15
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Kaliakin DS, Fedorov DG, Alexeev Y, Varganov SA. Locating Minimum Energy Crossings of Different Spin States Using the Fragment Molecular Orbital Method. J Chem Theory Comput 2019; 15:6074-6084. [DOI: 10.1021/acs.jctc.9b00641] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Danil S. Kaliakin
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557-0216, United States
| | - Dmitri G. Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba 305-8568, Japan
| | - Yuri Alexeev
- Computational Science Division and Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Sergey A. Varganov
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557-0216, United States
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16
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Severino R, Froufe HJC, Barroso C, Albuquerque L, Lobo-da-Cunha A, da Costa MS, Egas C. High-quality draft genome sequence of Gaiella occulta isolated from a 150 meter deep mineral water borehole and comparison with the genome sequences of other deep-branching lineages of the phylum Actinobacteria. Microbiologyopen 2019; 8:e00840. [PMID: 30977302 PMCID: PMC6741124 DOI: 10.1002/mbo3.840] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 01/25/2023] Open
Abstract
Gaiella occulta strain F2‐233T (=CECT 7815 = LMG 26412), isolated from a 150 meter deep mineral water aquifer, was deemed a candidate for high‐quality draft genome sequencing because of the rare environment from which it was isolated. The draft genome sequence (QQZY00000000) of strain F2‐233T is composed of approximately 3 Mb, predicted 3,119 protein‐coding genes of which 2,545 were assigned putative functions. Genome analysis was done by comparison with the other deep‐branching Actinobacteria neighbors Rubrobacter radiotolerans, Solirubrobacter soli and Thermoleophilum album. The genes for the tricarboxylic acid cycle, gluconeogenesis and pentose phosphate pathway, were identified in G. occulta, R. radiotolerans, S. soli and T. album genomes. Genes of the Embden–Meyerhof–Parnas pathway and nitrate reduction were identified in G. occulta, R. radiotolerans and S. soli, but not in the T. album genome. Alkane degradation is precluded by genome analysis in G. occulta. Genes involved in myo‐inositol metabolism were found in both S. soli and G. occulta genomes. A Calvin–Benson–Bassham (CBB) cycle with a type I RuBisCO was identified in G. occulta genome, as well. However, experimental growth under several conditions was negative and CO2 fixation could not be proven in G. occulta.
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Affiliation(s)
- Rita Severino
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Hugo J C Froufe
- Next Generation Sequencing Unit, Biocant, Cantanhede, Portugal
| | - Cristina Barroso
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Next Generation Sequencing Unit, Biocant, Cantanhede, Portugal
| | - Luciana Albuquerque
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Alexandre Lobo-da-Cunha
- CIMAR/CIIMAR-Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal.,Laboratório de Biologia Celular, Instituto de Ciências Biomédicas Abel Salazar, ICBAS, Universidade do Porto, Porto, Portugal
| | - Milton S da Costa
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Conceição Egas
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Next Generation Sequencing Unit, Biocant, Cantanhede, Portugal
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17
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Gregson BH, Metodieva G, Metodiev MV, Golyshin PN, McKew BA. Differential Protein Expression During Growth on Medium Versus Long-Chain Alkanes in the Obligate Marine Hydrocarbon-Degrading Bacterium Thalassolituus oleivorans MIL-1. Front Microbiol 2018; 9:3130. [PMID: 30619200 PMCID: PMC6304351 DOI: 10.3389/fmicb.2018.03130] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/04/2018] [Indexed: 02/02/2023] Open
Abstract
The marine obligate hydrocarbonoclastic bacterium Thalassolituus oleivorans MIL-1 metabolizes a broad range of aliphatic hydrocarbons almost exclusively as carbon and energy sources. We used LC-MS/MS shotgun proteomics to identify proteins involved in aerobic alkane degradation during growth on medium- (n-C14) or long-chain (n-C28) alkanes. During growth on n-C14, T. oleivorans expresses an alkane monooxygenase system involved in terminal oxidation including two alkane 1-monooxygenases, a ferredoxin, a ferredoxin reductase and an aldehyde dehydrogenase. In contrast, during growth on long-chain alkanes (n-C28), T. oleivorans may switch to a subterminal alkane oxidation pathway evidenced by significant upregulation of Baeyer-Villiger monooxygenase and an esterase, proteins catalyzing ketone and ester metabolism, respectively. The metabolite (primary alcohol) generated from terminal oxidation of an alkane was detected during growth on n-C14 but not on n-C28 also suggesting alternative metabolic pathways. Expression of both active and passive transport systems involved in uptake of long-chain alkanes was higher when compared to the non-hydrocarbon control, including a TonB-dependent receptor, a FadL homolog and a specialized porin. Also, an inner membrane transport protein involved in the export of an outer membrane protein was expressed. This study has demonstrated the substrate range of T. oleivorans is larger than previously reported with growth from n-C10 up to n-C32. It has also greatly enhanced our understanding of the fundamental physiology of T. oleivorans, a key bacterium that plays a significant role in natural attenuation of marine oil pollution, by identifying key enzymes expressed during the catabolism of n-alkanes.
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Affiliation(s)
- Benjamin H Gregson
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Gergana Metodieva
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Metodi V Metodiev
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, Bangor, United Kingdom.,School of Natural Sciences, College of Environmental Sciences and Engineering, Bangor University, Bangor, United Kingdom
| | - Boyd A McKew
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
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18
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Defois C, Ratel J, Garrait G, Denis S, Le Goff O, Talvas J, Mosoni P, Engel E, Peyret P. Food Chemicals Disrupt Human Gut Microbiota Activity And Impact Intestinal Homeostasis As Revealed By In Vitro Systems. Sci Rep 2018; 8:11006. [PMID: 30030472 PMCID: PMC6054606 DOI: 10.1038/s41598-018-29376-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 07/04/2018] [Indexed: 12/22/2022] Open
Abstract
Growing evidence indicates that the human gut microbiota interacts with xenobiotics, including persistent organic pollutants and foodborne chemicals. The toxicological relevance of the gut microbiota-pollutant interplay is of great concern since chemicals may disrupt gut microbiota functions, with a potential impairment of host homeostasis. Herein we report within batch fermentation systems the impact of food contaminants (polycyclic aromatic hydrocarbons, polychlorobiphenyls, brominated flame retardants, dioxins, pesticides and heterocyclic amines) on the human gut microbiota by metatranscriptome and volatolome i.e. “volatile organic compounds” analyses. Inflammatory host cell response caused by microbial metabolites following the pollutants-gut microbiota interaction, was evaluated on intestinal epithelial TC7 cells. Changes in the volatolome pattern analyzed via solid-phase microextraction coupled to gas chromatography-mass spectrometry mainly resulted in an imbalance in sulfur, phenolic and ester compounds. An increase in microbial gene expression related to lipid metabolism processes as well as the plasma membrane, periplasmic space, protein kinase activity and receptor activity was observed following dioxin, brominated flame retardant and heterocyclic amine exposure. Conversely, all food contaminants tested induced a decreased in microbial transcript levels related to ribosome, translation and nucleic acid binding. Finally, we demonstrated that gut microbiota metabolites resulting from pollutant disturbances may promote the establishment of a pro-inflammatory state in the gut, as stated with the release of cytokine IL-8 by intestinal epithelial cells.
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19
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Galle LM, Cutsail Iii GE, Nischwitz V, DeBeer S, Span I. Spectroscopic characterization of the Co-substituted C-terminal domain of rubredoxin-2. Biol Chem 2018; 399:787-798. [PMID: 29894292 DOI: 10.1515/hsz-2018-0142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/25/2018] [Indexed: 11/15/2022]
Abstract
Pseudomonas putida rubredoxin-2 (Rxn2) is an essential member of the alkane hydroxylation pathway and transfers electrons from a reductase to the membrane-bound hydroxylase. The regioselective hydroxylation of linear alkanes is a challenging chemical transformation of great interest for the chemical industry. Herein, we report the preparation and spectroscopic characterization of cobalt-substituted P. putida Rxn2 and a truncated version of the protein consisting of the C-terminal domain of the protein. Our spectroscopic data on the Co-substituted C-terminal domain supports a high-spin Co(II) with a distorted tetrahedral coordination environment. Investigation of the two-domain protein Rxn2 provides insights into the metal-binding properties of the N-terminal domain, the role of which is not well understood so far. Circular dichroism, electron paramagnetic resonance and X-ray absorption spectroscopies support an alternative Co-binding site within the N-terminal domain, which appears to not be relevant in nature. We have shown that chemical reconstitution in the presence of Co leads to incorporation of Co(II) into the active site of the C-terminal domain, but not the N-terminal domain of Rxn2 indicating distinct roles for the two rubredoxin domains.
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Affiliation(s)
- Lisa M Galle
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - George E Cutsail Iii
- Max Planck Institute for Chemical Energy Conversion, D-45470 Mülheim an der Ruhr, Germany
| | - Volker Nischwitz
- Central Institute for Engineering, Electronics and Analytics (ZEA-3), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, D-45470 Mülheim an der Ruhr, Germany
| | - Ingrid Span
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
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20
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Guerra AB, Oliveira JS, Silva-Portela RCB, Araújo W, Carlos AC, Vasconcelos ATR, Freitas AT, Domingos YS, de Farias MF, Fernandes GJT, Agnez-Lima LF. Metagenome enrichment approach used for selection of oil-degrading bacteria consortia for drill cutting residue bioremediation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 235:869-880. [PMID: 29353803 DOI: 10.1016/j.envpol.2018.01.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/28/2017] [Accepted: 01/05/2018] [Indexed: 06/07/2023]
Abstract
Drill cuttings leave behind thousands of tons of residues without adequate treatment, generating a large environmental liability. Therefore knowledge about the microbial community of drilling residue may be useful for developing bioremediation strategies. In this work, samples of drilling residue were enriched in different culture media in the presence of petroleum, aiming to select potentially oil-degrading bacteria and biosurfactant producers. Total DNA was extracted directly from the drill cutting samples and from two enriched consortia and sequenced using the Ion Torrent platform. Taxonomic analysis revealed the predominance of Proteobacteria in the metagenome from the drill cuttings, while Firmicutes was enriched in consortia samples. Functional analysis using the Biosurfactants and Biodegradation Database (BioSurfDB) revealed a similar pattern among the three samples regarding hydrocarbon degradation and biosurfactants production pathways. However, some statistical differences were observed between samples. Namely, the pathways related to the degradation of fatty acids, chloroalkanes, and chloroalkanes were enriched in consortia samples. The degradation colorimetric assay using dichlorophenolindophenol as an indicator was positive for several hydrocarbon substrates. The consortia were also able to produce biosurfactants, with biosynthesis of iturin, lichnysin, and surfactin among the more abundant pathways. A microcosms assay followed by gas chromatography analysis showed the efficacy of the consortia in degrading alkanes, as we observed a reduction of around 66% and 30% for each consortium in total alkanes. These data suggest the potential use of these consortia in the bioremediation of drilling residue based on autochthonous bioaugmentation.
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Affiliation(s)
- Alaine B Guerra
- Department of Cellular Biology and Genetics, UFRN, Natal, Rio Grande do Norte, 59078900, Brazil
| | - Jorge S Oliveira
- Department of Cellular Biology and Genetics, UFRN, Natal, Rio Grande do Norte, 59078900, Brazil; Instituto de Engenharia de Sistemas e Computadores/Instituto Superior Técnico (INESC-ID/IST), Universidade de Lisboa, Portugal
| | - Rita C B Silva-Portela
- Department of Cellular Biology and Genetics, UFRN, Natal, Rio Grande do Norte, 59078900, Brazil
| | - Wydemberg Araújo
- Department of Cellular Biology and Genetics, UFRN, Natal, Rio Grande do Norte, 59078900, Brazil
| | - Aline C Carlos
- Department of Cellular Biology and Genetics, UFRN, Natal, Rio Grande do Norte, 59078900, Brazil
| | - Ana Tereza R Vasconcelos
- Instituto de Engenharia de Sistemas e Computadores/Instituto Superior Técnico (INESC-ID/IST), Universidade de Lisboa, Portugal
| | | | | | | | - Glauber José Turolla Fernandes
- Centro de Tecnologias do Gás e Energias Renováveis - CTGAS-ER, Natal, RN, Brazil; Universidade Potiguar, Av. Engenheiro Roberto Freire 2184, Natal, RN, 59082902, Brazil
| | - Lucymara F Agnez-Lima
- Department of Cellular Biology and Genetics, UFRN, Natal, Rio Grande do Norte, 59078900, Brazil.
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21
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Mao Z, Liou SH, Khadka N, Jenney FE, Goodin DB, Seefeldt LC, Adams MWW, Cramer SP, Larsen DS. Cluster-Dependent Charge-Transfer Dynamics in Iron-Sulfur Proteins. Biochemistry 2018; 57:978-990. [PMID: 29303562 DOI: 10.1021/acs.biochem.7b01159] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Photoinduced charge-transfer dynamics and the influence of cluster size on the dynamics were investigated using five iron-sulfur clusters: the 1Fe-4S cluster in Pyrococcus furiosus rubredoxin, the 2Fe-2S cluster in Pseudomonas putida putidaredoxin, the 4Fe-4S cluster in nitrogenase iron protein, and the 8Fe-7S P-cluster and the 7Fe-9S-1Mo FeMo cofactor in nitrogenase MoFe protein. Laser excitation promotes the iron-sulfur clusters to excited electronic states that relax to lower states. The electronic relaxation lifetimes of the 1Fe-4S, 8Fe-7S, and 7Fe-9S-1Mo clusters are on the picosecond time scale, although the dynamics of the MoFe protein is a mixture of the dynamics of the latter two clusters. The lifetimes of the 2Fe-2S and 4Fe-4S clusters, however, extend to several nanoseconds. A competition between reorganization energies and the density of electronic states (thus electronic coupling between states) mediates the charge-transfer lifetimes, with the 2Fe-2S cluster of Pdx and the 4Fe-4S cluster of Fe protein lying at the optimum leading to them having significantly longer lifetimes. Their long lifetimes make them the optimal candidates for long-range electron transfer and as external photosensitizers for other photoactivated chemical reactions like solar hydrogen production. Potential electron-transfer and hole-transfer pathways that possibly facilitate these charge transfers are proposed.
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Affiliation(s)
- Ziliang Mao
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
| | - Shu-Hao Liou
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
| | - Nimesh Khadka
- Department of Chemistry and Biochemistry, Utah State University , 0300 Old Main Hill, Logan, Utah 84322, United States
| | - Francis E Jenney
- Georgia Campus, Philadelphia College of Osteopathic Medicine , Suwanee, Georgia 30024, United States
| | - David B Goodin
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University , 0300 Old Main Hill, Logan, Utah 84322, United States
| | - Michael W W Adams
- Department of Biochemistry, The University of Georgia , Athens, Georgia 30602, United States
| | - Stephen P Cramer
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
| | - Delmar S Larsen
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
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22
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Pathak M, Sarma HK, Bhattacharyya KG, Subudhi S, Bisht V, Lal B, Devi A. Characterization of a Novel Polymeric Bioflocculant Produced from Bacterial Utilization of n-Hexadecane and Its Application in Removal of Heavy Metals. Front Microbiol 2017; 8:170. [PMID: 28223975 PMCID: PMC5293801 DOI: 10.3389/fmicb.2017.00170] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 01/24/2017] [Indexed: 11/13/2022] Open
Abstract
A novel polymeric bioflocculant was produced by a bacterium utilizing degradation of n-hexadecane as the energy source. The bioflocculant was produced with a bioflocculating activity of 87.8%. The hydrocarbon degradation was confirmed by gas chromatography-mass spectrometry analysis and was further supported with contact angle measurements for the changes in hydrophobic nature of the culture medium. A specific aerobic degradation pathway followed by the bacterium during the bioflocculant production and hydrocarbon utilization process has been proposed. FT-IR, SEM-EDX, LC/MS, and 1H NMR measurements indicated the presence of carbohydrates and proteins as the major components of the bioflocculant. The bioflocculant was characterized for its carbohydrate monomer constituents and its practical applicability was established for removing the heavy metals (Ni2+, Zn2+, Cd2+, Cu2+, and Pb2+) from aqueous solutions at concentrations of 1–50 mg L-1. The highest activity of the bioflocculant was observed with Ni2+ with 79.29 ± 0.12% bioflocculation efficiency.
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Affiliation(s)
- Mihirjyoti Pathak
- Environmental Chemistry Laboratory, Resource Management and Environment Section, Life Science Division, Institute of Advanced Study in Science and Technology Guwahati, India
| | - Hridip K Sarma
- Department of Biotechnology, Gauhati University Guwahati, India
| | | | - Sanjukta Subudhi
- Environmental and Industrial Biotechnology Division, The Energy and Resources Institute New Delhi, India
| | - Varsha Bisht
- Environmental and Industrial Biotechnology Division, The Energy and Resources Institute New Delhi, India
| | - Banwari Lal
- Environmental and Industrial Biotechnology Division, The Energy and Resources Institute New Delhi, India
| | - Arundhuti Devi
- Environmental Chemistry Laboratory, Resource Management and Environment Section, Life Science Division, Institute of Advanced Study in Science and Technology Guwahati, India
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23
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dePolo GE, Kaliakin DS, Varganov SA. Spin-Forbidden Transitions between Electronic States in the Active Site of Rubredoxin. J Phys Chem A 2016; 120:8691-8698. [DOI: 10.1021/acs.jpca.6b07717] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gwen E. dePolo
- Department of Chemistry, University of Nevada, Reno, 1664 North
Virginia Street, Reno, Nevada 89557-0216, United States
| | - Danil S. Kaliakin
- Department of Chemistry, University of Nevada, Reno, 1664 North
Virginia Street, Reno, Nevada 89557-0216, United States
| | - Sergey A. Varganov
- Department of Chemistry, University of Nevada, Reno, 1664 North
Virginia Street, Reno, Nevada 89557-0216, United States
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24
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Jung J, Jang IA, Ahn S, Shin B, Kim J, Park C, Jee SC, Sung JS, Park W. Molecular Mechanisms of Enhanced Bacterial Growth on Hexadecane with Red Clay. MICROBIAL ECOLOGY 2015; 70:912-921. [PMID: 25956940 DOI: 10.1007/s00248-015-0624-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
Red clay was previously used to enhance bioremediation of diesel-contaminated soil. It was speculated that the enhanced degradation of diesel was due to increased bacterial growth. In this study, we selected Acinetobacter oleivorans DR1, a soil-borne degrader of diesel and alkanes, as a model bacterium and performed transcriptional analysis using RNA sequencing to investigate the cellular response during hexadecane utilization and the mechanism by which red clay promotes hexadecane degradation. We confirmed that red clay promotes the growth of A. oleivorans DR1 on hexadecane, a major component of diesel, as a sole carbon source. Addition of red clay to hexadecane-utilizing DR1 cells highly upregulated β-oxidation, while genes related to alkane oxidation were highly expressed with and without red clay. Red clay also upregulated genes related to oxidative stress defense, such as superoxide dismutase, catalase, and glutaredoxin genes, suggesting that red clay supports the response of DR1 cells to oxidative stress generated during hexadecane utilization. Increased membrane fluidity in the presence of red clay was confirmed by fatty acid methyl ester analysis at different growth phases, suggesting that enhanced growth on hexadecane could be due to increased uptake of hexadecane coupled with upregulation of downstream metabolism and oxidative stress defense. The monitoring of the bacterial community in soil with red clay for a year revealed that red clay stabilized the community structure.
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Affiliation(s)
- Jaejoon Jung
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 136-713, Republic of Korea
| | - In-Ae Jang
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 136-713, Republic of Korea
| | - Sungeun Ahn
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 136-713, Republic of Korea
| | - Bora Shin
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 136-713, Republic of Korea
| | - Jisun Kim
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 136-713, Republic of Korea
| | - Chulwoo Park
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 136-713, Republic of Korea
| | - Seung Cheol Jee
- Department of Life Science, Dongguk University, Seoul, 100-715, Republic of Korea
| | - Jung-Suk Sung
- Department of Life Science, Dongguk University, Seoul, 100-715, Republic of Korea
| | - Woojun Park
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 136-713, Republic of Korea.
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Islam SMA, Sajed T, Kearney CM, Baker EJ. PredSTP: a highly accurate SVM based model to predict sequential cystine stabilized peptides. BMC Bioinformatics 2015; 16:210. [PMID: 26142484 PMCID: PMC4491269 DOI: 10.1186/s12859-015-0633-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 06/01/2015] [Indexed: 02/07/2023] Open
Abstract
Background Numerous organisms have evolved a wide range of toxic peptides for self-defense and predation. Their effective interstitial and macro-environmental use requires energetic and structural stability. One successful group of these peptides includes a tri-disulfide domain arrangement that offers toxicity and high stability. Sequential tri-disulfide connectivity variants create highly compact disulfide folds capable of withstanding a variety of environmental stresses. Their combination of toxicity and stability make these peptides remarkably valuable for their potential as bio-insecticides, antimicrobial peptides and peptide drug candidates. However, the wide sequence variation, sources and modalities of group members impose serious limitations on our ability to rapidly identify potential members. As a result, there is a need for automated high-throughput member classification approaches that leverage their demonstrated tertiary and functional homology. Results We developed an SVM-based model to predict sequential tri-disulfide peptide (STP) toxins from peptide sequences. One optimized model, called PredSTP, predicted STPs from training set with sensitivity, specificity, precision, accuracy and a Matthews correlation coefficient of 94.86 %, 94.11 %, 84.31 %, 94.30 % and 0.86, respectively, using 200 fold cross validation. The same model outperforms existing prediction approaches in three independent out of sample testsets derived from PDB. Conclusion PredSTP can accurately identify a wide range of cystine stabilized peptide toxins directly from sequences in a species-agnostic fashion. The ability to rapidly filter sequences for potential bioactive peptides can greatly compress the time between peptide identification and testing structural and functional properties for possible antimicrobial and insecticidal candidates. A web interface is freely available to predict STP toxins from http://crick.ecs.baylor.edu/. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0633-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Tanvir Sajed
- Department of Computer Science, University of Alberta, Edmonton, AB, Canada.
| | - Christopher Michel Kearney
- Institute of Biomedical Studies, Baylor University, Waco, TX, USA. .,Department of Biology, Baylor University, Waco, TX, USA.
| | - Erich J Baker
- Institute of Biomedical Studies, Baylor University, Waco, TX, USA. .,Department of Computer Science, Baylor University, One Bear Place #97356, Waco, TX, USA.
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Grant C, Deszcz D, Wei YC, Martínez-Torres RJ, Morris P, Folliard T, Sreenivasan R, Ward J, Dalby P, Woodley JM, Baganz F. Identification and use of an alkane transporter plug-in for applications in biocatalysis and whole-cell biosensing of alkanes. Sci Rep 2014; 4:5844. [PMID: 25068650 PMCID: PMC5376172 DOI: 10.1038/srep05844] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 07/03/2014] [Indexed: 01/31/2023] Open
Abstract
Effective application of whole-cell devices in synthetic biology and biocatalysis will always require consideration of the uptake of molecules of interest into the cell. Here we demonstrate that the AlkL protein from Pseudomonas putida GPo1 is an alkane import protein capable of industrially relevant rates of uptake of C7-C16 n-alkanes. Without alkL expression, native E.coli n-alkane uptake was the rate-limiting step in both the whole-cell bioconversion of C7-C16 n-alkanes and in the activation of a whole-cell alkane biosensor by C10 and C11 alkanes. By coexpression of alkL as a transporter plug-in, specific yields improved by up to 100-fold for bioxidation of >C12 alkanes to fatty alcohols and acids. The alkL protein was shown to be toxic to the host when overexpressed but when expressed from a vector capable of controlled induction, yields of alkane oxidation were improved a further 10-fold (8 g/L and 1.7 g/g of total oxidized products). Further testing of activity on n-octane with the controlled expression vector revealed the highest reported rates of 120 μmol/min/g and 1 g/L/h total oxidized products. This is the first time AlkL has been shown to directly facilitate enhanced uptake of C10-C16 alkanes and represents the highest reported gain in product yields resulting from its use.
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Affiliation(s)
- Chris Grant
- Dept. of Biochemical Engineering, Advanced Centre for Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, U.K
| | - Dawid Deszcz
- Dept. of Biochemical Engineering, Advanced Centre for Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, U.K
| | - Yu-Chia Wei
- Dept. of Biochemical Engineering, Advanced Centre for Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, U.K
| | | | - Phattaraporn Morris
- Dept. of Biochemical Engineering, Advanced Centre for Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, U.K
| | - Thomas Folliard
- Dept. of Biochemical Engineering, Advanced Centre for Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, U.K
| | - Rakesh Sreenivasan
- Dept. of Biochemical Engineering, Advanced Centre for Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, U.K
| | - John Ward
- Dept. of Biochemical Engineering, Advanced Centre for Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, U.K
- Dept. of Structural and Molecular Biology, ISMB, University College London, Gower Street, London WC1E 6BT, U.K
| | - Paul Dalby
- Dept. of Biochemical Engineering, Advanced Centre for Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, U.K
| | - John M. Woodley
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, DK 2800 Lyngby, Denmark
| | - Frank Baganz
- Dept. of Biochemical Engineering, Advanced Centre for Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, U.K
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Cluff MA, Hartsock A, MacRae JD, Carter K, Mouser PJ. Temporal changes in microbial ecology and geochemistry in produced water from hydraulically fractured Marcellus shale gas wells. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:6508-17. [PMID: 24803059 DOI: 10.1021/es501173p] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Microorganisms play several important roles in unconventional gas recovery, from biodegradation of hydrocarbons to souring of wells and corrosion of equipment. During and after the hydraulic fracturing process, microorganisms are subjected to harsh physicochemical conditions within the kilometer-deep hydrocarbon-bearing shale, including high pressures, elevated temperatures, exposure to chemical additives and biocides, and brine-level salinities. A portion of the injected fluid returns to the surface and may be reused in other fracturing operations, a process that can enrich for certain taxa. This study tracked microbial community dynamics using pyrotag sequencing of 16S rRNA genes in water samples from three hydraulically fractured Marcellus shale wells in Pennsylvania, USA over a 328-day period. There was a reduction in microbial richness and diversity after fracturing, with the lowest diversity at 49 days. Thirty-one taxa dominated injected, flowback, and produced water communities, which took on distinct signatures as injected carbon and electron acceptors were attenuated within the shale. The majority (>90%) of the community in flowback and produced fluids was related to halotolerant bacteria associated with fermentation, hydrocarbon oxidation, and sulfur-cycling metabolisms, including heterotrophic genera Halolactibacillus, Vibrio, Marinobacter, Halanaerobium, and Halomonas, and autotrophs belonging to Arcobacter. Sequences related to halotolerant methanogenic genera Methanohalophilus and Methanolobus were detected at low abundance (<2%) in produced waters several months after hydraulic fracturing. Five taxa were strong indicators of later produced fluids. These results provide insight into the temporal trajectory of subsurface microbial communities after "fracking" and have important implications for the enrichment of microbes potentially detrimental to well infrastructure and natural gas fouling during this process.
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Affiliation(s)
- Maryam A Cluff
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University , Columbus, Ohio 43210, United States
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28
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Nie Y, Chi CQ, Fang H, Liang JL, Lu SL, Lai GL, Tang YQ, Wu XL. Diverse alkane hydroxylase genes in microorganisms and environments. Sci Rep 2014; 4:4968. [PMID: 24829093 PMCID: PMC4021335 DOI: 10.1038/srep04968] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 04/07/2014] [Indexed: 11/08/2022] Open
Abstract
AlkB and CYP153 are important alkane hydroxylases responsible for aerobic alkane degradation in bioremediation of oil-polluted environments and microbial enhanced oil recovery. Since their distribution in nature is not clear, we made the investigation among thus-far sequenced 3,979 microbial genomes and 137 metagenomes from terrestrial, freshwater, and marine environments. Hundreds of diverse alkB and CYP153 genes including many novel ones were found in bacterial genomes, whereas none were found in archaeal genomes. Moreover, these genes were detected with different distributional patterns in the terrestrial, freshwater, and marine metagenomes. Hints for horizontal gene transfer, gene duplication, and gene fusion were found, which together are likely responsible for diversifying the alkB and CYP153 genes adapt to the ubiquitous distribution of different alkanes in nature. In addition, different distributions of these genes between bacterial genomes and metagenomes suggested the potentially important roles of unknown or less common alkane degraders in nature.
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Affiliation(s)
- Yong Nie
- College of Engineering, Peking University, Beijing 100871, P. R. China
- Institute of Engineering (Baotou), College of Engineering, Peking University, Baotou 014030, China
| | - Chang-Qiao Chi
- College of Engineering, Peking University, Beijing 100871, P. R. China
| | - Hui Fang
- College of Engineering, Peking University, Beijing 100871, P. R. China
| | - Jie-Liang Liang
- College of Engineering, Peking University, Beijing 100871, P. R. China
| | - She-Lian Lu
- College of Engineering, Peking University, Beijing 100871, P. R. China
| | - Guo-Li Lai
- College of Engineering, Peking University, Beijing 100871, P. R. China
- Institute of Engineering (Baotou), College of Engineering, Peking University, Baotou 014030, China
| | - Yue-Qin Tang
- College of Engineering, Peking University, Beijing 100871, P. R. China
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, China
| | - Xiao-Lei Wu
- College of Engineering, Peking University, Beijing 100871, P. R. China
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 559] [Impact Index Per Article: 55.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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30
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Fritsch J, Siebert E, Priebe J, Zebger I, Lendzian F, Teutloff C, Friedrich B, Lenz O. Rubredoxin-related maturation factor guarantees metal cofactor integrity during aerobic biosynthesis of membrane-bound [NiFe] hydrogenase. J Biol Chem 2014; 289:7982-93. [PMID: 24448806 DOI: 10.1074/jbc.m113.544668] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The membrane-bound [NiFe] hydrogenase (MBH) supports growth of Ralstonia eutropha H16 with H2 as the sole energy source. The enzyme undergoes a complex biosynthesis process that proceeds during cell growth even at ambient O2 levels and involves 14 specific maturation proteins. One of these is a rubredoxin-like protein, which is essential for biosynthesis of active MBH at high oxygen concentrations but dispensable under microaerobic growth conditions. To obtain insights into the function of HoxR, we investigated the MBH protein purified from the cytoplasmic membrane of hoxR mutant cells. Compared with wild-type MBH, the mutant enzyme displayed severely decreased hydrogenase activity. Electron paramagnetic resonance and infrared spectroscopic analyses revealed features resembling those of O2-sensitive [NiFe] hydrogenases and/or oxidatively damaged protein. The catalytic center resided partially in an inactive Niu-A-like state, and the electron transfer chain consisting of three different Fe-S clusters showed marked alterations compared with wild-type enzyme. Purification of HoxR protein from its original host, R. eutropha, revealed only low protein amounts. Therefore, recombinant HoxR protein was isolated from Escherichia coli. Unlike common rubredoxins, the HoxR protein was colorless, rather unstable, and essentially metal-free. Conversion of the atypical iron-binding motif into a canonical one through genetic engineering led to a stable reddish rubredoxin. Remarkably, the modified HoxR protein did not support MBH-dependent growth at high O2. Analysis of MBH-associated protein complexes points toward a specific interaction of HoxR with the Fe-S cluster-bearing small subunit. This supports the previously made notion that HoxR avoids oxidative damage of the metal centers of the MBH, in particular the unprecedented Cys6[4Fe-3S] cluster.
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Affiliation(s)
- Johannes Fritsch
- From the Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Chausseestrasse 117, 10115 Berlin
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31
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Singh K, Chandra S. Treatment of petroleum hydrocarbon polluted environment through bioremediation: a review. Pak J Biol Sci 2014; 17:1-8. [PMID: 24783772 DOI: 10.3923/pjbs.2014.1.8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Bioremediation play key role in the treatment of petroleum hydrocarbon contaminated environment. Exposure of petroleum hydrocarbon into the environment occurs either due to human activities or accidentally and cause environmental pollution. Petroleum hydrocarbon cause many toxic compounds which are potent immunotoxicants and carcinogenic to human being. Remedial methods for the treatment of petroleum contaminated environment include various physiochemical and biological methods. Due to the negative consequences caused by the physiochemical methods, the bioremediation technology is widely adapted and considered as one of the best technology for the treatment of petroleum contaminated environment. Bioremediation utilizes the natural ability of microorganism to degrade the hazardous compound into simpler and non hazardous form. This paper provides a review on the role of bioremediation in the treatment of petroleum contaminated environment, discuss various hazardous effects of petroleum hydrocarbon, various factors influencing biodegradation, role of various enzymes in biodegradation and genetic engineering in bioremediation.
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32
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Gil M, Graña M, Schopfer FJ, Wagner T, Denicola A, Freeman BA, Alzari PM, Batthyány C, Durán R. Inhibition of Mycobacterium tuberculosis PknG by non-catalytic rubredoxin domain specific modification: reaction of an electrophilic nitro-fatty acid with the Fe-S center. Free Radic Biol Med 2013; 65:150-161. [PMID: 23792274 PMCID: PMC4061738 DOI: 10.1016/j.freeradbiomed.2013.06.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 06/10/2013] [Accepted: 06/11/2013] [Indexed: 10/26/2022]
Abstract
PknG from Mycobacterium tuberculosis is a Ser/Thr protein kinase that regulates key metabolic processes within the bacterial cell as well as signaling pathways from the infected host cell. This multidomain protein has a conserved canonical kinase domain with N- and C-terminal flanking regions of unclear functional roles. The N-terminus harbors a rubredoxin-like domain (Rbx), a bacterial protein module characterized by an iron ion coordinated by four cysteine residues. Disruption of the Rbx-metal binding site by simultaneous mutations of all the key cysteine residues significantly impairs PknG activity. This encouraged us to evaluate the effect of a nitro-fatty acid (9- and 10-nitro-octadeca-9-cis-enoic acid; OA-NO2) on PknG activity. Fatty acid nitroalkenes are electrophilic species produced during inflammation and metabolism that react with nucleophilic residues of target proteins (i.e., Cys and His), modulating protein function and subcellular distribution in a reversible manner. Here, we show that OA-NO2 inhibits kinase activity by covalently adducting PknG remote from the catalytic domain. Mass spectrometry-based analysis established that cysteines located at Rbx are the specific targets of the nitroalkene. Cys-nitroalkylation is a Michael addition reaction typically reverted by thiols. However, the reversible OA-NO2-mediated nitroalkylation of the kinase results in an irreversible inhibition of PknG. Cys adduction by OA-NO2 induced iron release from the Rbx domain, revealing a new strategy for the specific inhibition of PknG. These results affirm the relevance of the Rbx domain as a target for PknG inhibition and support that electrophilic lipid reactions of Rbx-Cys may represent a new drug strategy for specific PknG inhibition.
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Affiliation(s)
- Magdalena Gil
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo, Uruguay; Unidad de Bioquímica y Proteómica Analíticas, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Uruguay
| | - Martín Graña
- Unidad de Bioinformática, Institut Pasteur de Montevideo, Uruguay
| | - Francisco J Schopfer
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Tristan Wagner
- Unité de Microbiologie Structurale & CNRS URA 2185, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Ana Denicola
- Laboratorio de Fisicoquímica Biológica, Facultad de Ciencias, Universidad de la República, Uruguay
| | - Bruce A Freeman
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Pedro M Alzari
- Unité de Microbiologie Structurale & CNRS URA 2185, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Carlos Batthyány
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Uruguay.
| | - Rosario Durán
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo, Uruguay; Unidad de Bioquímica y Proteómica Analíticas, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Uruguay.
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Procópio L, de Cassia Pereira e Silva M, van Elsas JD, Seldin L. Transcriptional profiling of genes involved in n-hexadecane compounds assimilation in the hydrocarbon degrading Dietzia cinnamea P4 strain. Braz J Microbiol 2013; 44:633-41. [PMID: 24294263 PMCID: PMC3833169 DOI: 10.1590/s1517-83822013000200044] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Accepted: 07/23/2012] [Indexed: 11/24/2022] Open
Abstract
The petroleum-derived degrading Dietzia cinnamea strain P4 recently had its genome sequenced and annotated. This allowed employing the data on genes that are involved in the degradation of n-alkanes. To examine the physiological behavior of strain P4 in the presence of n-alkanes, the strain was grown under varying conditions of pH and temperature. D. cinnamea P4 was able to grow at pH 7.0–9.0 and at temperatures ranging from 35 ºC to 45 ºC. Experiments of gene expression by real-time quantitative RT-PCR throughout the complete growth cycle clearly indicated the induction of the regulatory gene alkU (TetR family) during early growth. During the logarithmic phase, a large increase in transcriptional levels of a lipid transporter gene was noted. Also, the expression of a gene that encodes the protein fused rubredoxin-alkane monooxygenase was enhanced. Both genes are probably under the influence of the AlkU regulator.
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Affiliation(s)
- Luciano Procópio
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde, Ilha do Fundão, Rio de Janeiro, RJ, Brazil. ; Department of Microbial Ecology, University of Groningen, Kerklaan, Haren, The Netherlands
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part I. {Fe(SγCys)4} proteins. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2013.02.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Teimoori A, Ahmadian S, Madadkar-Sobhani A. Biochemical characterization of two recombinant ferredoxin reductases from Alcanivorax borkumensis SK2. Biotechnol Appl Biochem 2013; 59:457-64. [PMID: 23586955 DOI: 10.1002/bab.1047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2012] [Accepted: 09/22/2012] [Indexed: 11/10/2022]
Abstract
Alcanivorax borkumensis strain SK2 is a cosmopolitan oil-degrading oligotrophic marine γ-proteobacterium that exclusively uses petroleum hydrocarbons as sources of carbon and energy. Its ubiquity and unusual physiology suggest its global importance in the removal of hydrocarbons from polluted marine systems. The genome of A. borkumensis SK2 was recently sequenced. Two ferredoxin-nicotinamide adenine dinucleotide phosphate (NADPH) reductase genes (ABO_0145 and ABO_0203) have been annotated for this bacterium. In the present study, the expression, purification, and kinetic properties of these two genes were explored by constructing the prokaryotic expression vectors (pET21a) for the first time. Isopropyl β-D-thiogalactoside (0.5 mM) was used for induction of exponentially growing cells (30 °C, overnight). Most of the proteins were expressed in inclusion body. Partial purification of recombinant enzymes was performed by ion-exchange chromatography on a DEAE-sepharose column using only one linear gradient of sodium chloride ranging between 0 and 500 mM. The recombinant enzymes displayed reductase activity, which was optimal at pH 6.0 and 45 °C. Ferredoxin-NADPH reductases exhibited several outstanding properties that made them excellent model proteins to address broad biological questions. This study serves as the basis for further investigations of the biotechnological potential of these enzymes.
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Affiliation(s)
- Afsaneh Teimoori
- Department of Biochemistry, Institute of Biochemistry and Biophysics-IBB, University of Tehran, Tehran, Iran
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36
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Cytochrome P450 initiates degradation of cis-dichloroethene by Polaromonas sp. strain JS666. Appl Environ Microbiol 2013; 79:2263-72. [PMID: 23354711 DOI: 10.1128/aem.03445-12] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polaromonas sp. strain JS666 grows on cis-1,2-dichoroethene (cDCE) as the sole carbon and energy source under aerobic conditions, but the degradation mechanism and the enzymes involved are unknown. In this study, we established the complete pathway for cDCE degradation through heterologous gene expression, inhibition studies, enzyme assays, and analysis of intermediates. Several lines of evidence indicate that a cytochrome P450 monooxygenase catalyzes the initial step of cDCE degradation. Both the transient accumulation of dichloroacetaldehyde in cDCE-degrading cultures and dichloroacetaldehyde dehydrogenase activities in cell extracts of JS666 support a pathway for degradation of cDCE through dichloroacetaldehyde. The mechanism minimizes the formation of cDCE epoxide. The molecular phylogeny of the cytochrome P450 gene and the organization of neighboring genes suggest that the cDCE degradation pathway recently evolved in a progenitor capable of degrading 1,2-dichloroethane either by the recruitment of the cytochrome P450 monooxygenase gene from an alkane catabolic pathway or by selection for variants of the P450 in a preexisting 1,2-dichloroethane catabolic pathway. The results presented here add yet another role to the broad array of productive reactions catalyzed by cytochrome P450 enzymes.
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Chakraborty J, Ghosal D, Dutta A, Dutta TK. An insight into the origin and functional evolution of bacterial aromatic ring-hydroxylating oxygenases. J Biomol Struct Dyn 2012; 30:419-36. [PMID: 22694139 DOI: 10.1080/07391102.2012.682208] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Bacterial aromatic ring-hydroxylating oxygenases (RHOs) are multicomponent enzyme systems which have potential utility in bioremediation of aromatic compounds in the environment. To cope with the enormous diversity of aromatic compounds in the environment, this enzyme family has evolved remarkably exhibiting broad substrate specificity. RHOs are multicomponent enzymes comprising of a homo- or hetero-multimeric terminal oxygenase and one or more electron transport (ET) protein(s). The present study attempts in depicting the evolutionary scenarios that might have occurred during the evolution of RHOs, by analyzing a set of available sequences including those obtained from complete genomes. A modified classification scheme identifying four new RHO types has been suggested on the basis of their evolutionary and functional behaviours, in relation to structural configuration of substrates and preferred oxygenation site(s). The present scheme emphasizes on the fact that the phylogenetic affiliation of RHOs is distributed among four distinct 'Similarity classes', independent of the constituent ET components. Similar combination of RHO components that was previously considered to be equivalent and classified together [Kweon et al., BMC Biochemistry 9, 11 (2008)] were found here in distinct similarity classes indicating the role of substrate-binding terminal oxygenase in guiding the evolution of RHOs irrespective of the nature of constituent ET components. Finally, a model for evolution of the multicomponent RHO enzyme system has been proposed, beginning from genesis of the terminal oxygenase components followed by recruitment of constituent ET components, finally evolving into various 'extant' RHO types.
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Singh SN, Kumari B, Mishra S. Microbial Degradation of Alkanes. ENVIRONMENTAL SCIENCE AND ENGINEERING 2012. [DOI: 10.1007/978-3-642-23789-8_17] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Nie Y, Liang J, Fang H, Tang YQ, Wu XL. Two novel alkane hydroxylase-rubredoxin fusion genes isolated from a Dietzia bacterium and the functions of fused rubredoxin domains in long-chain n-alkane degradation. Appl Environ Microbiol 2011; 77:7279-88. [PMID: 21873474 PMCID: PMC3194844 DOI: 10.1128/aem.00203-11] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 08/19/2011] [Indexed: 11/20/2022] Open
Abstract
Two alkane hydroxylase-rubredoxin fusion gene homologs (alkW1 and alkW2) were cloned from a Dietzia strain, designated DQ12-45-1b, which can grow on crude oil and n-alkanes ranging in length from 6 to 40 carbon atoms as sole carbon sources. Both AlkW1 and AlkW2 have an integral-membrane alkane monooxygenase (AlkB) conserved domain and a rubredoxin (Rd) conserved domain which are fused together. Phylogenetic analysis showed that these two AlkB-fused Rd domains formed a novel third cluster with all the Rds from the alkane hydroxylase-rubredoxin fusion gene clusters in Gram-positive bacteria and that this third cluster was distant from the known AlkG1- and AlkG2-type Rds. Expression of the alkW1 gene in DQ12-45-1b was induced when cells were grown on C(8) to C(32) n-alkanes as sole carbon sources, but expression of the alkW2 gene was not detected. Functional heterologous expression in an alkB deletion mutant of Pseudomonas fluorescens KOB2Δ1 suggested the alkW1 could restore the growth of KOB2Δ1 on C(14) and C(16) n-alkanes and induce faster growth on C(18) to C(32) n-alkanes than alkW1ΔRd, the Rd domain deletion mutant gene of alkW1, which also caused faster growth than KOB2Δ1 itself. In addition, the artificial fusion of AlkB from the Gram-negative P. fluorescens CHA0 and the Rds from both Gram-negative P. fluorescens CHA0 and Gram-positive Dietzia sp. DQ12-45-1b significantly increased the degradation of C(32) alkane compared to that seen with AlkB itself. In conclusion, the alkW1 gene cloned from Dietzia species encoded an alkane hydroxylase which increased growth on and degradation of n-alkanes up to C(32) in length, with its fused rubredoxin domain being necessary to maintain the functions. In addition, the fusion of alkane hydroxylase and rubredoxin genes from both Gram-positive and -negative bacteria can increase the degradation of long-chain n-alkanes (such as C(32)) in the Gram-negative bacterium.
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Affiliation(s)
- Yong Nie
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Jieliang Liang
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Hui Fang
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Yue-Qin Tang
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Xiao-Lei Wu
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
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Teimoori A, Ahmadian S, Madadkar-Sobhani A, Bambai B. Rubredoxin reductase from Alcanivorax borkumensis: expression and characterization. Biotechnol Prog 2011; 27:1383-9. [PMID: 21714118 DOI: 10.1002/btpr.653] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2010] [Revised: 04/21/2011] [Indexed: 11/11/2022]
Abstract
Oil pollution is an environmental problem of increasing importance. Alcanivorax borkumensis, with a high potential for biotechnological applications, is a key marine hydrocarbonoclastic bacterium and plays a critical role in the bioremediation of oil-polluted marine systems. In oil degrading bacteria, the first step of alkane degradation is catalyzed by a monooxygenase. The reducing electrons are tunneled from NAD(P)H via rubredoxin, one of the most primitive metalloproteins, to the hydroxylase. Rubredoxin reductase is a flavoprotein catalyzing the reduction of rubredoxin. There are two rubredoxin genes, alkG and rubA, in A. borkumensis genome. In this work, the genes encoding rubredoxin reductase (ABO_0162, rubB) and AlkG(ABO_2708, alkG) were cloned and functionally overexpressed in E. coli. Our results demonstrate that RubB could reduce AlkG, therefore compensating for the absence of AlkT, also a rubredoxin reductase, missing in A. borkumensis SK2 genome. These results will increase our knowledge concerning biological alkane degradation and will lead us to design more efficient biotransformation and bioremediation systems.
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Affiliation(s)
- Afsaneh Teimoori
- Dept. of Biochemistry, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
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41
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Gamiz-Hernandez AP, Kieseritzky G, Ishikita H, Knapp EW. Rubredoxin Function: Redox Behavior from Electrostatics. J Chem Theory Comput 2011; 7:742-52. [DOI: 10.1021/ct100476h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ana Patricia Gamiz-Hernandez
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Fabeckstrasse 36a, D-14195, Berlin, Germany
| | - Gernot Kieseritzky
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Fabeckstrasse 36a, D-14195, Berlin, Germany
| | - Hiroshi Ishikita
- Career-Path Promotion Unit for Young Life Scientists, Kyoto University, 202 Building E, Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - E. W. Knapp
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Fabeckstrasse 36a, D-14195, Berlin, Germany
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42
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Bihari Z, Szvetnik A, Szabó Z, Blastyák A, Zombori Z, Balázs M, Kiss I. Functional analysis of long-chain n-alkane degradation by Dietzia spp. FEMS Microbiol Lett 2011; 316:100-7. [DOI: 10.1111/j.1574-6968.2010.02198.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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43
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Acyl-homoserine lactone binding to and stability of the orphan Pseudomonas aeruginosa quorum-sensing signal receptor QscR. J Bacteriol 2010; 193:421-8. [PMID: 21097632 DOI: 10.1128/jb.01041-10] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Pseudomonas aeruginosa transcription factor QscR responds to a variety of fatty acyl-homoserine lactones (HSLs), including N-3-oxododecanoyl-HSL (3OC12-HSL), which is produced and detected by the P. aeruginosa quorum-sensing circuit LasI and LasR. As is true for LasR and many other acyl-HSL-dependent transcription factors, production of soluble QscR in sufficient amounts for purification requires growth of recombinant bacteria in the presence of an appropriate acyl-HSL. QscR is thought to bind 3OC12-HSL relatively weakly compared to LasR, and unlike LasR, binding of purified QscR to target DNA was shown to strongly depend on exogenously added 3OC12-HSL. We show that purified QscR is dimeric at sufficiently high concentrations and monomeric at lower concentrations. Furthermore, QscR bound 3OC12-HSL more tightly than previously believed. Purified QscR retained 3OC12-HSL, and at sufficiently high concentrations, it bound target DNA in the absence of added 3OC12-HSL. We also obtained soluble QscR from recombinant Escherichia coli grown in the presence of N-3-oxohexanoyl-HSL (3OC6-HSL) instead of 3OC12-HSL, and because 3OC6-HSL bound much more loosely to QscR than other acyl-HSLs tested, we were able to exchange 3OC6-HSL with other acyl-HSLs in vitro and then estimate binding affinities of QscR for different acyl-HSLs and for target DNA. Our data support a model whereby QscR polypeptides fold properly in the absence of an acyl-HSL, but soluble, acyl-HSL-free QscR does not accumulate because it is subject to rapid aggregation or proteolysis.
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44
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Das N, Chandran P. Microbial degradation of petroleum hydrocarbon contaminants: an overview. BIOTECHNOLOGY RESEARCH INTERNATIONAL 2010; 2011:941810. [PMID: 21350672 PMCID: PMC3042690 DOI: 10.4061/2011/941810] [Citation(s) in RCA: 443] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Revised: 06/28/2010] [Accepted: 07/07/2010] [Indexed: 11/20/2022]
Abstract
One of the major environmental problems today is hydrocarbon contamination resulting from the activities related to the petrochemical industry. Accidental releases of petroleum products are of particular concern in the environment. Hydrocarbon components have been known to belong to the family of carcinogens and neurotoxic organic pollutants. Currently accepted disposal methods of incineration or burial insecure landfills can become prohibitively expensive when amounts of contaminants are large. Mechanical and chemical methods generally used to remove hydrocarbons from contaminated sites have limited effectiveness and can be expensive. Bioremediation is the promising technology for the treatment of these contaminated sites since it is cost-effective and will lead to complete mineralization. Bioremediation functions basically on biodegradation, which may refer to complete mineralization of organic contaminants into carbon dioxide, water, inorganic compounds, and cell protein or transformation of complex organic contaminants to other simpler organic compounds by biological agents like microorganisms. Many indigenous microorganisms in water and soil are capable of degrading hydrocarbon contaminants. This paper presents an updated overview of petroleum hydrocarbon degradation by microorganisms under different ecosystems.
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Affiliation(s)
- Nilanjana Das
- Environmental Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu 632014, India
| | - Preethy Chandran
- Environmental Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu 632014, India
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45
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Abstract
Pollution of soil and water environments by crude oil has been, and is still today, an important problem. Crude oil is a complex mixture of thousands of compounds. Among them, alkanes constitute the major fraction. Alkanes are saturated hydrocarbons of different sizes and structures. Although they are chemically very inert, most of them can be efficiently degraded by several microorganisms. This review summarizes current knowledge on how microorganisms degrade alkanes, focusing on the biochemical pathways used and on how the expression of pathway genes is regulated and integrated within cell physiology.
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Affiliation(s)
- Fernando Rojo
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Campus de la Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.
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Kang YS, Park W. Protection against diesel oil toxicity by sodium chloride-induced exopolysaccharides in Acinetobacter sp. strain DR1. J Biosci Bioeng 2009; 109:118-23. [PMID: 20129094 DOI: 10.1016/j.jbiosc.2009.08.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Revised: 07/21/2009] [Accepted: 08/02/2009] [Indexed: 11/16/2022]
Abstract
Acinetobacter sp. strain DR1 is capable of growth on diesel oil. Interestingly, the degradation of diesel oil by the strain DR1 is enhanced in the presence of sodium chloride (NaCl). However, the growth rate of strain DR1 is not affected by the presence of NaCl. Northern blot analysis has also demonstrated that the effect of NaCl on the degradation of diesel oil is not attributable to increased levels of alkane hydroxylase (AlkM-type) gene expression. Rather, we have noted an increase in the exopolysaccharide (EPS) yields of strain DR1 under high NaCl conditions (9-fold). The lag-time of diesel oil biodegradation was significantly shorter in the strain DR1 with exogenous EPS than in the controls, although EPS alone does not support the growth of strain DR1. The recovery of strain DR1 when exposed to diesel oil was accelerated when exogenous EPS was added to the medium. The overproduction of EPS was also noted in the presence of diesel oil and n-hexadecane. The data indicated that EPS overproduction might play a protective role against diesel oil toxicity. Along with the results of the soil microcosm tests, the data presented herein demonstrated that NaCl-induced EPS is associated with a reduction in diesel oil toxicity, and thus increases diesel oil biodegradation in Acinetobacter sp. strain DR1.
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Affiliation(s)
- Yoon-Suk Kang
- Division of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
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47
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Stamper DM, Montgomery MT. Biological treatment and toxicity of low concentrations of oily wastewater (bilgewater). Can J Microbiol 2008; 54:687-93. [DOI: 10.1139/w08-053] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The biodegradability and toxicity of low concentrations of oily wastewater (bilgewater) were tested under simulated sanitary wastewater treatment conditions. This was done to establish the feasibility of a combined shipboard oily and nonoily wastewater treatment system. The biodegradability of oily wastewater was determined by proxy;14C-labeled dodecane, toluene, and phenanthrene (representing alkane, aromatic, and polyaromatic compounds, respectively) were mineralized in petroleum fuels and lubricants. We found that low concentrations of oily wastewater components were mineralized, even in the presence of more abundant substrates (such as synthetic graywater, containing vegetable oil, detergent, gelatin, and starch). The toxic effects of diesel fuel and several other components of oily wastewater (such as surfactants and a synthetic lubricant) on a naïve wastewater assemblage was also tested. In concentrations much higher than would be expected under normal shipboard conditions, we found no evidence of toxic effects of the bilgewater compounds tested. Thus, a combined shipboard bilgewater and sanitary wastewater system might be feasible.
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Affiliation(s)
- David M. Stamper
- NAVSEA Carderock Division, Biological Sciences Group, Code 617, 9500 MacArthur Blvd, West Bethesda, MD 20817, USA
- Naval Research Laboratory, Marine Biochemistry Section, Code 6114, 4555 Overlook Avenue, Washington, DC 20375, USA
| | - Michael T. Montgomery
- NAVSEA Carderock Division, Biological Sciences Group, Code 617, 9500 MacArthur Blvd, West Bethesda, MD 20817, USA
- Naval Research Laboratory, Marine Biochemistry Section, Code 6114, 4555 Overlook Avenue, Washington, DC 20375, USA
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48
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Hagelueken G, Wiehlmann L, Adams TM, Kolmar H, Heinz DW, Tüummler B, Schubert WD. Crystal structure of the electron transfer complex rubredoxin rubredoxin reductase of Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2007; 104:12276-81. [PMID: 17636129 PMCID: PMC1941462 DOI: 10.1073/pnas.0702919104] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Crude oil spills represent a major ecological threat because of the chemical inertness of the constituent n-alkanes. The Gram-negative bacterium Pseudomonas aeruginosa is one of the few bacterial species able to metabolize such compounds. Three chromosomal genes, rubB, rubA1, and rubA2 coding for an NAD(P)H:rubredoxin reductase (RdxR) and two rubredoxins (Rdxs) are indispensable for this ability. They constitute an electron transport (ET) pathway that shuttles reducing equivalents from carbon metabolism to the membrane-bound alkane hydroxylases AlkB1 and AlkB2. The RdxR-Rdx system also is crucial as part of the oxidative stress response in archaea or anaerobic bacteria. The redox couple has been analyzed in detail as a model system for ET processes. We have solved the structure of RdxR of P. aeruginosa both alone and in complex with Rdx, without the need for cross-linking, and both structures were refined at 2.40- and 2.45-A resolution, respectively. RdxR consists of two cofactor-binding domains and a C-terminal domain essential for the specific recognition of Rdx. Only a small number of direct interactions govern mutual recognition of RdxR and Rdx, corroborating the transient nature of the complex. The shortest distance between the redox centers is observed to be 6.2 A.
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Affiliation(s)
| | - Lutz Wiehlmann
- Klinische Forschergruppe OE 6711, Medizinische Hochschule Hannover, Carl Neuberg Strasse 1, D-30625 Hannover, Germany; and
| | - Thorsten M. Adams
- Klinische Forschergruppe OE 6711, Medizinische Hochschule Hannover, Carl Neuberg Strasse 1, D-30625 Hannover, Germany; and
| | - Harald Kolmar
- Clemens Schoepf Institute for Organic Chemistry and Biochemistry, Darmstadt University of Technology, Petersenstrasse 22, D-64287 Darmstadt, Germany
| | - Dirk W. Heinz
- Division of Structural Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Burkhard Tüummler
- Klinische Forschergruppe OE 6711, Medizinische Hochschule Hannover, Carl Neuberg Strasse 1, D-30625 Hannover, Germany; and
| | - Wolf-Dieter Schubert
- Molecular Host–Pathogen Interactions
- To whom correspondence should be addressed. E-mail:
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49
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Tan ML, Bizzarri AR, Xiao Y, Cannistraro S, Ichiye T, Manzoni C, Cerullo G, Adams MWW, Jenney FE, Cramer SP. Observation of terahertz vibrations in Pyrococcus furiosus rubredoxin via impulsive coherent vibrational spectroscopy and nuclear resonance vibrational spectroscopy – interpretation by molecular mechanics. J Inorg Biochem 2007; 101:375-84. [PMID: 17204331 DOI: 10.1016/j.jinorgbio.2006.09.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2006] [Revised: 09/28/2006] [Accepted: 09/29/2006] [Indexed: 10/24/2022]
Abstract
We have used impulsive coherent vibrational spectroscopy (ICVS) to study the Fe(S-Cys)(4) site in oxidized rubredoxin (Rd) from Pyrococcus furiosus (Pf). In this experiment, a 15 fs visible laser pulse is used to coherently pump the sample to an excited electronic state, and a second <10 fs pulse is used to probe the change in transmission as a function of the time delay. PfRd was observed to relax to the ground state by a single exponential decay with time constants of approximately 255-275 fs. Superimposed on this relaxation are oscillations caused by coherent excitation of vibrational modes in both excited and ground electronic states. Fourier transformation reveals the frequencies of these modes. The strongest ICV mode with 570 nm excitation is the symmetric Fe-S stretching mode near 310 cm(-1), compared to 313 cm(-1) in the low temperature resonance Raman. If the rubredoxin is pumped at 520 nm, a set of strong bands occurs between 20 and 110 cm(-1). Finally, there is a mode at approximately 500 cm(-1) which is similar to features near 508 cm(-1) in blue Cu proteins that have been attributed to excited state vibrations. Normal mode analysis using 488 protein atoms and 558 waters gave calculated spectra that are in good agreement with previous nuclear resonance vibrational spectra (NRVS) results. The lowest frequency normal modes are identified as collective motions of the entire protein or large segments of polypeptide. Motion in these modes may affect the polar environment of the redox site and thus tune the electron transfer functions in rubredoxins.
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Affiliation(s)
- Ming-Liang Tan
- Department of Applied Science, University of California, Davis, CA 95616, USA
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50
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Kane SR, Chakicherla AY, Chain PSG, Schmidt R, Shin MW, Legler TC, Scow KM, Larimer FW, Lucas SM, Richardson PM, Hristova KR. Whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1. J Bacteriol 2007; 189:1931-45. [PMID: 17158667 PMCID: PMC1855728 DOI: 10.1128/jb.01259-06] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Accepted: 11/29/2006] [Indexed: 11/20/2022] Open
Abstract
Methylibium petroleiphilum PM1 is a methylotroph distinguished by its ability to completely metabolize the fuel oxygenate methyl tert-butyl ether (MTBE). Strain PM1 also degrades aromatic (benzene, toluene, and xylene) and straight-chain (C(5) to C(12)) hydrocarbons present in petroleum products. Whole-genome analysis of PM1 revealed an approximately 4-Mb circular chromosome and an approximately 600-kb megaplasmid, containing 3,831 and 646 genes, respectively. Aromatic hydrocarbon and alkane degradation, metal resistance, and methylotrophy are encoded on the chromosome. The megaplasmid contains an unusual t-RNA island, numerous insertion sequences, and large repeated elements, including a 40-kb region also present on the chromosome and a 29-kb tandem repeat encoding phosphonate transport and cobalamin biosynthesis. The megaplasmid also codes for alkane degradation and was shown to play an essential role in MTBE degradation through plasmid-curing experiments. Discrepancies between the insertion sequence element distribution patterns, the distributions of best BLASTP hits among major phylogenetic groups, and the G+C contents of the chromosome (69.2%) and plasmid (66%), together with comparative genome hybridization experiments, suggest that the plasmid was recently acquired and apparently carries the genetic information responsible for PM1's ability to degrade MTBE. Comparative genomic hybridization analysis with two PM1-like MTBE-degrading environmental isolates (approximately 99% identical 16S rRNA gene sequences) showed that the plasmid was highly conserved (ca. 99% identical), whereas the chromosomes were too diverse to conduct resequencing analysis. PM1's genome sequence provides a foundation for investigating MTBE biodegradation and exploring the genetic regulation of multiple biodegradation pathways in M. petroleiphilum and other MTBE-degrading beta-proteobacteria.
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Affiliation(s)
- Staci R Kane
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
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