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Abstract
The biosynthesis of wax esters and triglycerides in bacteria is accomplished through the action of the wax ester synthase/acyl-coenzyme A:diacylglycerol acyltransferase (WS/DGAT or wax ester synthase). A hallmark of these enzymes is the broad substrate profile that accepts alcohols, diglycerides, and fatty acyl-CoAs of various carbon chain lengths and degrees of branching. These enzymes have a broad biotechnological potential due to their role in producing high-value lipids or simple fuels similar to biodiesel through biosynthetic routes. Recently, a crystal structure was solved for the wax ester synthase from Marinobacter aquaeolei VT8 (Maqu_0168), providing a much clearer picture of the architecture of this enzyme and enabling a more precise analysis of the important structural features of the protein. In this work, we used the structure to canvas amino acids lining the proposed substrate-binding pockets and tested the effects of exchanging specific residues on the substrate profiles. We also developed an approach to better probe the residues that alter fatty acyl-CoA selectivity, which has proven more difficult to investigate. Our findings provide an improved blueprint for future efforts to understand how these enzymes position substrates for catalysis and to tailor or improve these enzymes in future biosynthetic schemes.
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Affiliation(s)
- Natalia Calixto Mancipe
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Kalene M Mulliner
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Mary H Plunkett
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Brett M Barney
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, Minnesota 55108, United States.,BioTechnology Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
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Plunkett MH, Knutson CM, Barney BM. Key factors affecting ammonium production by an Azotobacter vinelandii strain deregulated for biological nitrogen fixation. Microb Cell Fact 2020; 19:107. [PMID: 32429912 PMCID: PMC7238568 DOI: 10.1186/s12934-020-01362-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 05/04/2020] [Indexed: 11/10/2022] Open
Abstract
Background The obligate aerobe Azotobacter vinelandii is a model organism for the study of biological nitrogen fixation (BNF). This bacterium regulates the process of BNF through the two component NifL and NifA system, where NifA acts as an activator, while NifL acts as an anti-activator based on various metabolic signals within the cell. Disruption of the nifL component in the nifLA operon in a precise manner results in a deregulated phenotype that produces levels of ammonium that far surpass the requirements within the cell, and results in the release of up to 30 mM of ammonium into the growth medium. While many studies have probed the factors affecting growth of A. vinelandii, the features important to maximizing this high-ammonium-releasing phenotype have not been fully investigated. Results In this work, we report the effect of temperature, medium composition, and oxygen requirements on sustaining and maximizing elevated levels of ammonium production from a nitrogenase deregulated strain. We further investigated several pathways, including ammonium uptake through the transporter AmtB, which could limit yields through energy loss or futile recycling steps. Following optimization, we compared sugar consumption and ammonium production, to attain correlations and energy requirements to drive this process in vivo. Ammonium yields indicate that between 5 and 8% of cellular protein is fully active nitrogenase MoFe protein (NifDK) under these conditions. Conclusions These findings provide important process optimization parameters, and illustrate that further improvements to this phenotype can be accomplished by eliminating futile cycles.
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Affiliation(s)
- Mary H Plunkett
- Biotechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA
| | - Carolann M Knutson
- Biotechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA
| | - Brett M Barney
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, 1390 Eckles Avenue, St. Paul, MN, 55108-6130, USA. .,Biotechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA.
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Knutson CM, Plunkett MH, Liming RA, Barney BM. Efforts toward optimization of aerobic biohydrogen reveal details of secondary regulation of biological nitrogen fixation by nitrogenous compounds in Azotobacter vinelandii. Appl Microbiol Biotechnol 2018; 102:10315-10325. [PMID: 30250977 DOI: 10.1007/s00253-018-9363-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 08/16/2018] [Accepted: 08/26/2018] [Indexed: 11/28/2022]
Abstract
Biological nitrogen fixation (BNF) through the enzyme nitrogenase is performed by a unique class of organisms known as diazotrophs. One interesting facet of BNF is that it produces molecular hydrogen (H2) as a requisite by-product. In the absence of N2 substrate, or under conditions that limit access of N2 to the enzyme through modifications of amino acids near the active site, nitrogenase activity can be redirected toward a role as a dedicated hydrogenase. In free-living diazotrophs, nitrogenases are tightly regulated to minimize BNF to meet only the growth requirements of the cell, and are often accompanied by uptake hydrogenases that oxidize the H2 by-product to recover the electrons from this product. The wild-type strain of Azotobacter vinelandii performs all of the tasks described above to minimize losses of H2 while also growing as an obligate aerobe. Individual alterations to A. vinelandii have been demonstrated that disrupt key aspects of the N2 reduction cycle, thereby diverting resources and energy toward the production of H2. In this work, we have combined three approaches to override the primary regulation of BNF and redirect metabolism to drive biological H2 production by nitrogenase in A. vinelandii. The resulting H2-producing strain was further utilized as a surrogate to study secondary, post-transcriptional regulation of BNF by several key nitrogen-containing metabolites. The improvement in yields of H2 that were achieved through various combinations of these three approaches was compared and is presented along with the insights into inhibition of BNF by several nitrogen compounds that are common in various waste streams. The findings indicate that both ammonium and nitrite hinder BNF through this secondary inhibition, but urea and nitrate do not. These results provide essential details to inform future biosynthetic approaches to yield nitrogen products that do not inadvertently inhibit BNF.
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Affiliation(s)
- Carolann M Knutson
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, 1390 Eckles Avenue, St. Paul, MN, 55108-6130, USA.,Biotechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA
| | - Mary H Plunkett
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, 1390 Eckles Avenue, St. Paul, MN, 55108-6130, USA.,Biotechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA
| | - Rachel A Liming
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, 1390 Eckles Avenue, St. Paul, MN, 55108-6130, USA
| | - Brett M Barney
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, 1390 Eckles Avenue, St. Paul, MN, 55108-6130, USA. .,Biotechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA.
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Arriola MB, Velmurugan N, Zhang Y, Plunkett MH, Hondzo H, Barney BM. Genome sequences of Chlorella sorokiniana UTEX 1602 and Micractinium conductrix SAG 241.80: implications to maltose excretion by a green alga. Plant J 2018; 93:566-586. [PMID: 29178410 DOI: 10.1111/tpj.13789] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 11/14/2017] [Indexed: 06/07/2023]
Abstract
Green algae represent a key segment of the global species capable of photoautotrophic-driven biological carbon fixation. Algae partition fixed-carbon into chemical compounds required for biomass, while diverting excess carbon into internal storage compounds such as starch and lipids or, in certain cases, into targeted extracellular compounds. Two green algae were selected to probe for critical components associated with sugar production and release in a model alga. Chlorella sorokiniana UTEX 1602 - which does not release significant quantities of sugars to the extracellular space - was selected as a control to compare with the maltose-releasing Micractinium conductrix SAG 241.80 - which was originally isolated from an endosymbiotic association with the ciliate Paramecium bursaria. Both strains were subjected to three sequencing approaches to assemble their genomes and annotate their genes. This analysis was further complemented with transcriptional studies during maltose release by M. conductrix SAG 241.80 versus conditions where sugar release is minimal. The annotation revealed that both strains contain homologs for the key components of a putative pathway leading to cytosolic maltose accumulation, while transcriptional studies found few changes in mRNA levels for the genes associated with these established intracellular sugar pathways. A further analysis of potential sugar transporters found multiple homologs for SWEETs and tonoplast sugar transporters. The analysis of transcriptional differences revealed a lesser and more measured global response for M. conductrix SAG 241.80 versus C. sorokiniana UTEX 1602 during conditions resulting in sugar release, providing a catalog of genes that might play a role in extracellular sugar transport.
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Affiliation(s)
- Matthew B Arriola
- Biotechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA
| | - Natarajan Velmurugan
- Biotechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, MN, 55108, USA
| | - Ying Zhang
- Minnesota Supercomputing Institute, University of Minnesota, St. Paul, MN, 55108, USA
| | - Mary H Plunkett
- Biotechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, MN, 55108, USA
| | - Hanna Hondzo
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, MN, 55108, USA
| | - Brett M Barney
- Biotechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, MN, 55108, USA
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Ledbetter RN, Garcia Costas AM, Lubner CE, Mulder DW, Tokmina-Lukaszewska M, Artz JH, Patterson A, Magnuson TS, Jay ZJ, Duan HD, Miller J, Plunkett MH, Hoben JP, Barney BM, Carlson RP, Miller AF, Bothner B, King PW, Peters JW, Seefeldt LC. The Electron Bifurcating FixABCX Protein Complex from Azotobacter vinelandii: Generation of Low-Potential Reducing Equivalents for Nitrogenase Catalysis. Biochemistry 2017; 56:4177-4190. [PMID: 28704608 DOI: 10.1021/acs.biochem.7b00389] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The biological reduction of dinitrogen (N2) to ammonia (NH3) by nitrogenase is an energetically demanding reaction that requires low-potential electrons and ATP; however, pathways used to deliver the electrons from central metabolism to the reductants of nitrogenase, ferredoxin or flavodoxin, remain unknown for many diazotrophic microbes. The FixABCX protein complex has been proposed to reduce flavodoxin or ferredoxin using NADH as the electron donor in a process known as electron bifurcation. Herein, the FixABCX complex from Azotobacter vinelandii was purified and demonstrated to catalyze an electron bifurcation reaction: oxidation of NADH (Em = -320 mV) coupled to reduction of flavodoxin semiquinone (Em = -460 mV) and reduction of coenzyme Q (Em = 10 mV). Knocking out fix genes rendered Δrnf A. vinelandii cells unable to fix dinitrogen, confirming that the FixABCX system provides another route for delivery of electrons to nitrogenase. Characterization of the purified FixABCX complex revealed the presence of flavin and iron-sulfur cofactors confirmed by native mass spectrometry, electron paramagnetic resonance spectroscopy, and transient absorption spectroscopy. Transient absorption spectroscopy further established the presence of a short-lived flavin semiquinone radical, suggesting that a thermodynamically unstable flavin semiquinone may participate as an intermediate in the transfer of an electron to flavodoxin. A structural model of FixABCX, generated using chemical cross-linking in conjunction with homology modeling, revealed plausible electron transfer pathways to both high- and low-potential acceptors. Overall, this study informs a mechanism for electron bifurcation, offering insight into a unique method for delivery of low-potential electrons required for energy-intensive biochemical conversions.
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Affiliation(s)
- Rhesa N Ledbetter
- Department of Chemistry and Biochemistry, Utah State University , Logan, Utah 84322, United States
| | - Amaya M Garcia Costas
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Carolyn E Lubner
- National Renewable Energy Laboratory , Golden, Colorado 80401, United States
| | - David W Mulder
- National Renewable Energy Laboratory , Golden, Colorado 80401, United States
| | - Monika Tokmina-Lukaszewska
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Jacob H Artz
- Institute of Biological Chemistry, Washington State University , Pullman, Washington 99163, United States
| | - Angela Patterson
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Timothy S Magnuson
- Department of Biological Sciences, Idaho State University , Pocatello, Idaho 83201, United States
| | - Zackary J Jay
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering and Thermal Biology Institute, Montana State University , Bozeman, Montana 59717, United States
| | - H Diessel Duan
- Department of Chemistry, University of Kentucky , Lexington, Kentucky 40506, United States
| | - Jacquelyn Miller
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Mary H Plunkett
- Department of Bioproducts and Biosystems Engineering and Biotechnology Institute, University of Minnesota , St. Paul, Minnesota 55108, United States
| | - John P Hoben
- Department of Chemistry, University of Kentucky , Lexington, Kentucky 40506, United States
| | - Brett M Barney
- Department of Bioproducts and Biosystems Engineering and Biotechnology Institute, University of Minnesota , St. Paul, Minnesota 55108, United States
| | - Ross P Carlson
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering and Thermal Biology Institute, Montana State University , Bozeman, Montana 59717, United States
| | - Anne-Frances Miller
- Department of Chemistry, University of Kentucky , Lexington, Kentucky 40506, United States
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Paul W King
- National Renewable Energy Laboratory , Golden, Colorado 80401, United States
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States.,Institute of Biological Chemistry, Washington State University , Pullman, Washington 99163, United States
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University , Logan, Utah 84322, United States
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Barney BM, Eberhart LJ, Ohlert JM, Knutson CM, Plunkett MH. Gene Deletions Resulting in Increased Nitrogen Release by Azotobacter vinelandii: Application of a Novel Nitrogen Biosensor. Appl Environ Microbiol 2015; 81:4316-28. [PMID: 25888177 PMCID: PMC4475869 DOI: 10.1128/aem.00554-15] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/13/2015] [Indexed: 11/20/2022] Open
Abstract
Azotobacter vinelandii is a widely studied model diazotrophic (nitrogen-fixing) bacterium and also an obligate aerobe, differentiating it from many other diazotrophs that require environments low in oxygen for the function of the nitrogenase. As a free-living bacterium, A. vinelandii has evolved enzymes and transporters to minimize the loss of fixed nitrogen to the surrounding environment. In this study, we pursued efforts to target specific enzymes and further developed screens to identify individual colonies of A. vinelandii producing elevated levels of extracellular nitrogen. Targeted deletions were done to convert urea into a terminal product by disrupting the urease genes that influence the ability of A. vinelandii to recycle the urea nitrogen within the cell. Construction of a nitrogen biosensor strain was done to rapidly screen several thousand colonies disrupted by transposon insertional mutagenesis to identify strains with increased extracellular nitrogen production. Several disruptions were identified in the ammonium transporter gene amtB that resulted in the production of sufficient levels of extracellular nitrogen to support the growth of the biosensor strain. Further studies substituting the biosensor strain with the green alga Chlorella sorokiniana confirmed that levels of nitrogen produced were sufficient to support the growth of this organism when the medium was supplemented with sufficient sucrose to support the growth of the A. vinelandii in coculture. The nature and quantities of nitrogen released by urease and amtB disruptions were further compared to strains reported in previous efforts that altered the nifLA regulatory system to produce elevated levels of ammonium. These results reveal alternative approaches that can be used in various combinations to yield new strains that might have further application in biofertilizer schemes.
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Affiliation(s)
- Brett M Barney
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, Minnesota, USA Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Lauren J Eberhart
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, Minnesota, USA Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Janet M Ohlert
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, Minnesota, USA
| | - Carolann M Knutson
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, Minnesota, USA
| | - Mary H Plunkett
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, Minnesota, USA
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