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Pavlov AA, McLain H, Glavin DP, Elsila JE, Dworkin J, House CH, Zhang Z. Radiolytic Effects on Biological and Abiotic Amino Acids in Shallow Subsurface Ices on Europa and Enceladus. ASTROBIOLOGY 2024; 24:698-709. [PMID: 39023275 DOI: 10.1089/ast.2023.0120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Europa and Enceladus are key targets to search for evidence of life in our solar system. However, the surface and shallow subsurface of both airless icy moons are constantly bombarded by ionizing radiation that could degrade chemical biosignatures. Therefore, sampling of icy surfaces in future life detection missions to Europa and Enceladus requires a clear understanding of the necessary ice depth where unaltered organic biomolecules might be present. We conducted radiolysis experiments by exposing individual amino acids in ices and amino acids from dead microorganisms in ices to gamma radiation to simulate conditions on these icy worlds. In the pure amino acid samples, glycine did not show a detectable decrease in abundance, whereas the abundance of isovaline decreased by 40% after 4 MGy of exposure. Amino acids in dead Escherichia coli (E. coli) organic matter exhibited a gradual decline in abundances with the increase of exposure dosage, although at much slower rates than individual amino acids. The majority of amino acids in dead A. woodii samples demonstrated a step function decline as opposed to a gradual decline. After the initial drop in abundance with 1 MGy of exposure, those amino acids did not display further decreases in abundance after exposure up to 4 MGy. New radiolysis constants for isolated amino acids and amino acids in dead E. coli material for Europa/Enceladus-like conditions have been derived. Slow rates of amino acid destruction in biological samples under Europa and Enceladus-like surface conditions bolster the case for future life detection measurements by Europa and Enceladus lander missions. Based on our measurements, the "safe" sampling depth on Europa is ∼20 cm at high latitudes of the trailing hemisphere in the area of little impact gardening. Subsurface sampling is not required for the detection of amino acids on Enceladus-these molecules will survive radiolysis at any location on the Enceladus surface. If the stability of amino acids observed in A. woodii organic materials is confirmed in other microorganisms, then the survival of amino acids from a potential biosphere in Europa ice would be significantly increased.
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Affiliation(s)
| | - Hannah McLain
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Department of Chemistry, Catholic University of America, Washington, District of Columbia, USA
- Center for Research and Exploration in Space Science and Technology, NASA/GSFC Greenbelt, Maryland, USA
| | | | - Jamie E Elsila
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
| | - Jason Dworkin
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
| | - Christopher H House
- Department of Geosciences and Earth and Environment Systems Institute, The Pennsylvania State University, Pennsylvania, USA
| | - Zhidan Zhang
- Department of Geosciences and Earth and Environment Systems Institute, The Pennsylvania State University, Pennsylvania, USA
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Casto-Boggess LD, Golozar M, Butterworth AL, Mathies RA. Optimization of Fluorescence Labeling of Trace Analytes: Application to Amino Acid Biosignature Detection with Pacific Blue. Anal Chem 2021; 94:1240-1247. [PMID: 34965088 DOI: 10.1021/acs.analchem.1c04465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescence labeling of biomolecules and fluorescence detection platforms provide a powerful approach to high-sensitivity bioanalysis. Reactive probes can be chosen to target specific functional groups to enable selective analysis of a chosen class of analytes. Particularly, when targeting trace levels of analytes, it is important to optimize the reaction chemistry to maximize the labeling efficiency and minimize the background. Here, we develop methods to optimize the labeling and detection of Pacific Blue (PB)-tagged amino acids. A model is developed to quantitate labeling kinetics and completeness in the circumstance where analyte labeling and reactive probe hydrolysis are in competition. The rates of PB hydrolysis and amino acid labeling are determined as a function of pH. Labeling kinetics and completeness as a function of PB concentration are found to depend on the ratio of the hydrolysis time to the initial labeling time, which depends on the initial PB concentration. Finally, the optimized labeling and detection conditions are used to perform capillary electrophoresis analysis demonstrating 100 pM sensitivities and high-efficiency separations of an 11 amino acid test set. This work provides a quantitative optimization model that is applicable to a variety of reactive probes and targets. Our approach is particularly useful for the analysis of trace amine and amino acid biosignatures in extraterrestrial samples. For illustration, our optimized conditions (reaction at 4 °C in a pH 8.5 buffer) are used to detect trace amino acid analytes at the 100 pM level in an Antarctic ice core sample.
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Affiliation(s)
- Laura D Casto-Boggess
- Space Sciences Laboratory, University of California Berkeley, Berkeley, California 94720-7450, United States
| | - Matin Golozar
- Chemistry Department and Space Sciences Laboratory, University of California Berkeley, Berkeley, California 94720, United States
| | - Anna L Butterworth
- Space Sciences Laboratory, University of California Berkeley, Berkeley, California 94720-7450, United States
| | - Richard A Mathies
- Chemistry Department and Space Sciences Laboratory, University of California Berkeley, Berkeley, California 94720, United States
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Burgay F, Barbaro E, Cappelletti D, Turetta C, Gallet JC, Isaksson E, Stenni B, Dreossi G, Scoto F, Barbante C, Spolaor A. First discrete iron(II) records from Dome C (Antarctica) and the Holtedahlfonna glacier (Svalbard). CHEMOSPHERE 2021; 267:129335. [PMID: 33352366 DOI: 10.1016/j.chemosphere.2020.129335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/10/2020] [Accepted: 12/13/2020] [Indexed: 06/12/2023]
Abstract
Fe(II) is more soluble and bioavailable than Fe(III) species, therefore the investigation of their relative abundance and redox processes is relevant to better assess the supply of bioavailable iron to the ocean and its impact on marine productivity. In this context, we present a discrete chemiluminescence-based method for the determination of Fe(II) in firn matrices. The method was applied on discrete samples from a snow pit collected at Dome C (DC, Antarctica) and on a shallow firn core from the Holtedahlfonna glacier (HDF, Svalbard), providing the first Fe(II) record from both Antarctica and Svalbard. The method showed low detection limits (0.006 ng g-1 for DC and 0.003 ng g-1 for the HDF) and a precision ranging from 3% to 20% RSD. Fe(II) concentrations ranged between the LoD and 0.077 ng g-1 and between the LoD and 0.300 ng g-1 for the Antarctic and Arctic samples, respectively. The Fe(II) contribution with respect to the total dissolved Fe was comparable in both sites accounting, on average, for 5% and 3%, respectively. We found that Fe(II) correctly identified the Pinatubo/Cerro Hudson eruption in the DC record, demonstrating its reliability as volcanic tracer, while, on the HDF core, we provided the first preliminary insight on the processes that might influence Fe speciation in firn matrices (i.e. organic ligands and pH influences).
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Affiliation(s)
- François Burgay
- Ca' Foscari University of Venice, Department of Environmental Sciences, Informatics and Statistics, Via Torino, 155, Venice, Italy; Institute of Polar Sciences, National Research Council, Campus Scientifico, Via Torino, 155, Venice, Italy.
| | - Elena Barbaro
- Institute of Polar Sciences, National Research Council, Campus Scientifico, Via Torino, 155, Venice, Italy; Ca' Foscari University of Venice, Department of Environmental Sciences, Informatics and Statistics, Via Torino, 155, Venice, Italy
| | - David Cappelletti
- Università degli Studi di Perugia, Dipartimento di Chimica, Biologia e Biotecnologie, Via Elce di Sotto 8, Perugia, Italy
| | - Clara Turetta
- Institute of Polar Sciences, National Research Council, Campus Scientifico, Via Torino, 155, Venice, Italy
| | | | | | - Barbara Stenni
- Ca' Foscari University of Venice, Department of Environmental Sciences, Informatics and Statistics, Via Torino, 155, Venice, Italy; Institute of Polar Sciences, National Research Council, Campus Scientifico, Via Torino, 155, Venice, Italy
| | - Giuliano Dreossi
- Institute of Polar Sciences, National Research Council, Campus Scientifico, Via Torino, 155, Venice, Italy
| | - Federico Scoto
- Institute of Atmospheric Sciences and Climate, National Research Council, Lecce, Italy
| | - Carlo Barbante
- Ca' Foscari University of Venice, Department of Environmental Sciences, Informatics and Statistics, Via Torino, 155, Venice, Italy; Institute of Polar Sciences, National Research Council, Campus Scientifico, Via Torino, 155, Venice, Italy
| | - Andrea Spolaor
- Institute of Polar Sciences, National Research Council, Campus Scientifico, Via Torino, 155, Venice, Italy; Ca' Foscari University of Venice, Department of Environmental Sciences, Informatics and Statistics, Via Torino, 155, Venice, Italy
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Spolaor A, Varin C, Pedeli X, Christille JM, Kirchgeorg T, Giardi F, Cappelletti D, Turetta C, Cairns WRL, Gambaro A, Bernagozzi A, Gallet JC, Björkman MP, Barbaro E. Source, timing and dynamics of ionic species mobility in the Svalbard annual snowpack. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 751:141640. [PMID: 32892077 DOI: 10.1016/j.scitotenv.2020.141640] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/29/2020] [Accepted: 08/09/2020] [Indexed: 06/11/2023]
Abstract
Nearly all ice core archives from the Arctic and middle latitudes (such as the Alps), apart from some very high elevation sites in Greenland and the North Pacific, are strongly influenced by melting processes. The increases in the average Arctic temperature has enhanced surface snow melting even of higher elevation ice caps, especially on the Svalbard Archipelago. The increase of the frequency and altitude of winter "rain on snow" events as well as the increase of the length of the melting season have had a direct impact on the chemical composition of the seasonal and permanent snow layers due to different migration processes of water-soluble species, such as inorganic ions. This re-allocation along the snowpack of ionic species could significantly modify the original chemical signal present in the annual snow. This paper aims to give a picture of the evolution of the seasonal snow strata with a daily time resolution to better understand: a) the processes that can influence deposition b) the distribution of ions in annual snow c) the impact of the presence of liquid water on chemical re-distribution within the annual snow pack. Specifically, the chemical composition of the first 100 cm of seasonal snow on the Austre Brøggerbreen Glacier (Spitsbergen, Svalbard Islands, Norway) was monitored daily from the 27th of March to the 31st of May 2015. The experimental period covered almost the entire Arctic spring until the melting season. This unique dataset gives us a daily picture of the snow pack composition, and helps us to understand the behaviour of cations (K+, Ca2+, Na+, Mg2+) and anions (Br-, I-, SO42-, NO3-, Cl-, MSA) in the Svalbard snow pack. We demonstrate that biologically related depositions occur only at the end of the snow season and that rain and melting events have different impacts on the snowpack chemistry.
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Affiliation(s)
- Andrea Spolaor
- Institute of Polar Sciences, ISP-CNR, Via Torino 155, 30172 Venice-Mestre, Italy; Ca' Foscari University of Venice, Department of Environmental Sciences, Informatics and Statistics, Via Torino 155, 30172 Venice-Mestre, Italy.
| | - Cristiano Varin
- Ca' Foscari University of Venice, Department of Environmental Sciences, Informatics and Statistics, Via Torino 155, 30172 Venice-Mestre, Italy
| | - Xanthi Pedeli
- Athens University of Economics and Business, Department of Statistics, 76 Patision Street, 10434 Athens, Greece
| | - Jean Marc Christille
- Astronomical Observatory of the Autonomous Region of the Aosta Valley (OAVdA), Loc. Lignan 39, 11020 Nus, AO, Italy; Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, I-06123 Perugia, Italy
| | - Torben Kirchgeorg
- Ca' Foscari University of Venice, Department of Environmental Sciences, Informatics and Statistics, Via Torino 155, 30172 Venice-Mestre, Italy
| | - Fabio Giardi
- Department of Physics and Astronomy, University of Florence, Via Giovanni Sansone, 1, I-50019 Sesto Fiorentino, Florence, Italy
| | - David Cappelletti
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, I-06123 Perugia, Italy
| | - Clara Turetta
- Institute of Polar Sciences, ISP-CNR, Via Torino 155, 30172 Venice-Mestre, Italy; Ca' Foscari University of Venice, Department of Environmental Sciences, Informatics and Statistics, Via Torino 155, 30172 Venice-Mestre, Italy
| | - Warren R L Cairns
- Institute of Polar Sciences, ISP-CNR, Via Torino 155, 30172 Venice-Mestre, Italy; Ca' Foscari University of Venice, Department of Environmental Sciences, Informatics and Statistics, Via Torino 155, 30172 Venice-Mestre, Italy
| | - Andrea Gambaro
- Institute of Polar Sciences, ISP-CNR, Via Torino 155, 30172 Venice-Mestre, Italy; Ca' Foscari University of Venice, Department of Environmental Sciences, Informatics and Statistics, Via Torino 155, 30172 Venice-Mestre, Italy
| | - Andrea Bernagozzi
- Astronomical Observatory of the Autonomous Region of the Aosta Valley (OAVdA), Loc. Lignan 39, 11020 Nus, AO, Italy
| | | | - Mats P Björkman
- University of Gothenburg, Department of Earth Sciences, Box 460, 40530 Göteborg, Sweden
| | - Elena Barbaro
- Institute of Polar Sciences, ISP-CNR, Via Torino 155, 30172 Venice-Mestre, Italy; Ca' Foscari University of Venice, Department of Environmental Sciences, Informatics and Statistics, Via Torino 155, 30172 Venice-Mestre, Italy
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Xu Y, Xiao H, Wu D, Long C. Abiotic and Biological Degradation of Atmospheric Proteinaceous Matter Can Contribute Significantly to Dissolved Amino Acids in Wet Deposition. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:6551-6561. [PMID: 32391688 DOI: 10.1021/acs.est.0c00421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Atmospheric proteinaceous matter is characterized by ubiquity and potential bioavailability. However, little is known about the origins, secondary production processes, and biogeochemical role of proteinaceous matter in wet deposition. Precipitation samples were collected in suburban Guiyang (southwestern China) over a 1 year period to investigate their chemical components, mainly including dissolved combined amino acids (DCAAs), dissolved free AAs (DFAAs), and nonleachable particulate AAs (PAAs). Glycine was most abundant in the DFAAs, while the dominant species in DCAAs and PAAs was glutamic acid (including deaminated glutamine). The total DCAA, DFAA, and PAA concentrations peaked on average in spring (min. in summer). On average, the contribution of DCAA-nitrogen (median of 3.44%) to dissolved organic nitrogen was 5-fold higher than that of DFAA-nitrogen (median of 0.60%). Correlation analyses of AAs with ozone, nitrogen dioxide, and the quantitative degradation index suggest that DC(/F)AAs are linked with both abiotic and biological degradation of proteinaceous matter. Moreover, the high FAA scavenging ratios indicate the presence of postdepositional degradation of atmospheric proteinaceous matter. Further, the positive matrix factorization results suggest that the degradation of atmospheric proteinaceous matter markedly contributes to DCAAs and DFAAs in precipitation. Overall, the results suggest that the secondary processes involved in the degradation of atmospheric proteinaceous matter significantly promote direct bioavailability of AA-nitrogen.
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Affiliation(s)
- Yu Xu
- Key Laboratory of Poyang Lake Environment and Resource Utilization of Ministry of Education, School of Resource, Environmental and Chemical Engineering, Nanchang University, Nanchang 330031, China
| | - Huayun Xiao
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daishe Wu
- Key Laboratory of Poyang Lake Environment and Resource Utilization of Ministry of Education, School of Resource, Environmental and Chemical Engineering, Nanchang University, Nanchang 330031, China
| | - Chaojun Long
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, No. 99, Linchengxi Road, Guiyang 550081, China
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Zangrando R, Zanella V, Karroca O, Barbaro E, Kehrwald NM, Battistel D, Morabito E, Gambaro A, Barbante C. Dissolved organic matter in the deep TALDICE ice core: A nano-UPLC-nano-ESI-HRMS method. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 700:134432. [PMID: 31693954 DOI: 10.1016/j.scitotenv.2019.134432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/11/2019] [Accepted: 09/11/2019] [Indexed: 06/10/2023]
Abstract
Trace organic compounds in deep ice cores supply important paleoclimatic information. Untargeted analyses of dissolved organic matter provide an overview of molecular species in ice samples however, sample volumes usually required for these analyses are generally not available from deep ice cores. Here, we developed an analytical method using a nano-UPLC-nano-ESI-HRMS to detect major molecular species in ice cores. Samples (4 µL) from the TALos Dome Ice CorE (TALDICE), allowed investigating molecular species across a range of depths including during glacial and interglacial periods. We detected 317 chemical species that were tentatively assigned to fatty acids, hydroxy fatty acids and their degradation products (oxo-fatty acids and dicarboxylic acids), as well as oxidation byproducts of isoprene and monoterpenes. These compounds indicate that the main sources of the organic fraction are microbes as well as primary and secondary aerosols. Interglacial samples encompass a wide range of species including compounds from the oxidation of isoprene and monoterpenes as well as unsaturated fatty acids, while the glacial samples contained less diverse species. This difference may be due to decreased temperatures during the glacial period inhibiting terrestrial vegetation growth and increasing the sea ice extent, thereby weakening the emission sources.
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Affiliation(s)
- Roberta Zangrando
- Institute of Polar Sciences CNR, Via Torino 155, 30172 Mestre (VE), Italy.
| | - Veronica Zanella
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via Torino 155, 30170 Mestre, VE, Italy
| | - Ornela Karroca
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via Torino 155, 30170 Mestre, VE, Italy
| | - Elena Barbaro
- Institute of Polar Sciences CNR, Via Torino 155, 30172 Mestre (VE), Italy
| | - Natalie M Kehrwald
- U.S. Geological Survey, Geosciences and Environmental Change Science Center, Denver Federal Center, MS 980, Denver, CO 80225, USA
| | - Dario Battistel
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via Torino 155, 30170 Mestre, VE, Italy
| | - Elisa Morabito
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via Torino 155, 30170 Mestre, VE, Italy
| | - Andrea Gambaro
- Institute of Polar Sciences CNR, Via Torino 155, 30172 Mestre (VE), Italy; Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via Torino 155, 30170 Mestre, VE, Italy
| | - Carlo Barbante
- Institute of Polar Sciences CNR, Via Torino 155, 30172 Mestre (VE), Italy; Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via Torino 155, 30170 Mestre, VE, Italy
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Vecchiato M, Barbaro E, Spolaor A, Burgay F, Barbante C, Piazza R, Gambaro A. Fragrances and PAHs in snow and seawater of Ny-Ålesund (Svalbard): Local and long-range contamination. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 242:1740-1747. [PMID: 30061079 DOI: 10.1016/j.envpol.2018.07.095] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 07/17/2018] [Accepted: 07/21/2018] [Indexed: 06/08/2023]
Abstract
Polar regions are fragile ecosystems threatened by both long-range pollution and local human contamination. In this context, the environmental distribution of the Personal Care Products (PCPs) represent a major knowledge gap. Following preliminary Antarctic studies, Fragrance Materials (FMs) were analyzed in the seawater and snow collected in the area of Ny-Ålesund, Svalbard, to investigate local and long-range contamination. Polycyclic Aromatic Hydrocarbons (PAHs), including Retene, were determined in parallel to help the identification of the governing processes. Concentrations of FMs up to 72 ng L-1 were detected in the surface snow near the settlement and at increasing distances, in relation to the prevailing winds. PAHs follow a similar scheme, with levels of Retene up to 1.8 μg L-1, likely deriving from the occurrence of this compound in the coal dust due to the previous mining activities in the area. The snow seasonal deposition of FMs and PAHs was estimated in a snowpit dug at the top of the Austre Brøggerbreen glacier, indicating the long-range atmospheric transport (LRAT) of these compounds.
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Affiliation(s)
- Marco Vecchiato
- Department of Environmental Sciences, Informatics and Statistics (DAIS), Ca' Foscari University of Venice, Via Torino 155, 30172 Venezia-Mestre, Venice, Italy.
| | - Elena Barbaro
- Institute for the Dynamics of Environmental Processes (IDPA-CNR), Via Torino 155, 30172, Venezia-Mestre, Venice, Italy
| | - Andrea Spolaor
- Institute for the Dynamics of Environmental Processes (IDPA-CNR), Via Torino 155, 30172, Venezia-Mestre, Venice, Italy
| | - Francois Burgay
- Department of Environmental Sciences, Informatics and Statistics (DAIS), Ca' Foscari University of Venice, Via Torino 155, 30172 Venezia-Mestre, Venice, Italy
| | - Carlo Barbante
- Department of Environmental Sciences, Informatics and Statistics (DAIS), Ca' Foscari University of Venice, Via Torino 155, 30172 Venezia-Mestre, Venice, Italy; Institute for the Dynamics of Environmental Processes (IDPA-CNR), Via Torino 155, 30172, Venezia-Mestre, Venice, Italy
| | - Rossano Piazza
- Department of Environmental Sciences, Informatics and Statistics (DAIS), Ca' Foscari University of Venice, Via Torino 155, 30172 Venezia-Mestre, Venice, Italy; Institute for the Dynamics of Environmental Processes (IDPA-CNR), Via Torino 155, 30172, Venezia-Mestre, Venice, Italy
| | - Andrea Gambaro
- Department of Environmental Sciences, Informatics and Statistics (DAIS), Ca' Foscari University of Venice, Via Torino 155, 30172 Venezia-Mestre, Venice, Italy; Institute for the Dynamics of Environmental Processes (IDPA-CNR), Via Torino 155, 30172, Venezia-Mestre, Venice, Italy
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Naganuma T, Iinuma Y, Nishiwaki H, Murase R, Masaki K, Nakai R. Enhanced Bacterial Growth and Gene Expression of D-Amino Acid Dehydrogenase With D-Glutamate as the Sole Carbon Source. Front Microbiol 2018; 9:2097. [PMID: 30233558 PMCID: PMC6131576 DOI: 10.3389/fmicb.2018.02097] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 08/16/2018] [Indexed: 02/02/2023] Open
Abstract
In a search for life-supporting, not life-assisting, D-amino acid metabolism, an environmental strain that grows better with D-glutamate as the sole carbon source was isolated from an ordinary river. The strain, designated as A25, exhibited a faster growth rate and greater cell yield with D-glutamate than with L-glutamate. Conversely, the D/L ratio of total cellular glutamate was as low as 4/96, which suggests that D-glutamate is more likely catabolized than anabolized. Strain A25 was phylogenetically most closely related to the gamma-proteobacterial species Raoultella ornithinolytica, with a 16S rRNA gene sequence similarity of 100%. A standard strain, R. ornithinolytica JCM 6096T, also showed similarly enhanced growth with D-glutamate, which was proven for the first time. Gene expression of the enzymes involved in D-amino acid metabolism was assayed by reverse-transcription quantitative PCR (RT-qPCR) using specifically designed primers. The targets were the genes encoding D-amino acid dehydrogenase (DAD; EC 1.4.99.1), glutamate racemase (EC 5.1.1.3), D-glutamate oxidase (EC 1.4.3.7 or EC 1.4.3.15), and UDP-N-acetyl-α-D-muramoyl-L-alanyl-D-glutamate ligase (EC 6.3.2.9). As a result, the growth of strains A25 and R. ornithinolytica JCM 6096T on D-glutamate was conspicuously associated with the enhanced expression of the DAD gene (dadA) in the exponential phase compared with the other enzyme genes. Pseudomonas aeruginosa is also known to grow on D-glutamate as the sole carbon source but to a lesser degree than with L-glutamate. A standard strain of P. aeruginosa, JCM 5962T, was tested for gene expression of the relevant enzymes by RT-qPCR and also showed enhanced dadA expression, but in the stationary phase. Reduction of ferricyanide with D-glutamate was detected in cell extracts of the tested strains, implying probable involvement of DAD in the D-glutamate catabolizing activity. DAD-mediated catalysis may have advantages in the one-step production of α-keto acids and non-production of H2O2 over other enzymes such as racemase and D-amino acid oxidase. The physiological and biochemical importance of DAD in D-amino acid metabolism is discussed.
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Affiliation(s)
- Takeshi Naganuma
- Graduate School of Biosphere Science, Hiroshima University, Higashihiroshima, Japan.,School of Biological Science, Hiroshima University, Higashihiroshima, Japan.,Astrobiology Center, National Institutes of Natural Sciences, Tokyo, Japan
| | - Yoshiakira Iinuma
- Graduate School of Biosphere Science, Hiroshima University, Higashihiroshima, Japan
| | - Hitomi Nishiwaki
- Graduate School of Biosphere Science, Hiroshima University, Higashihiroshima, Japan
| | - Ryota Murase
- School of Biological Science, Hiroshima University, Higashihiroshima, Japan
| | - Kazuo Masaki
- National Research Institute of Brewing, Higashihiroshima, Japan
| | - Ryosuke Nakai
- Microbial and Genetic Resources Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.,Applied Molecular Microbiology Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Japan
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