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Hellequin E, Collin S, Seder-Colomina M, Véquaud P, Anquetil C, Kish A, Huguet A. Membrane lipid adaptation of soil Bacteroidetes isolates to temperature and pH. Front Microbiol 2023; 14:1032032. [PMID: 36950164 PMCID: PMC10025309 DOI: 10.3389/fmicb.2023.1032032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/15/2023] [Indexed: 03/08/2023] Open
Abstract
3-hydroxy fatty acids (3-OH FAs) are characteristic components of the Gram-negative bacterial membrane, recently proposed as promising temperature and pH (paleo) proxies in soil. Nevertheless, to date, the relationships between the 3-OH FA distribution and temperature/pH are only based on empirical studies, with no ground truthing work at the microbial level. This work investigated the influence of growth temperature and pH on the lipid composition of three strains of soil Gram-negative bacteria belonging to the Bacteroidetes phylum. Even though non-hydroxy FAs were more abundant than 3-OH FAs in the investigated strains, our results suggest that 3-OH FAs are involved in the membrane adaptation of these bacteria to temperature. The strains shared a common adaptation mechanism to temperature, with a significant increase in the ratio of anteiso vs. iso or normal 3-OH FAs at lower temperature. In contrast with temperature, no common adaptation mechanism to pH was observed, as the variations in the FA lipid profiles differed from one strain to another. We suggest that models reconstructing environmental changes in soils should include the whole suite of 3-OH FAs present in the membrane of Gram-negative bacteria, as all of them could be influenced by temperature or pH at the microbial level.
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Affiliation(s)
- Eve Hellequin
- Sorbonne Université, CNRS, EPHE, PSL, UMR METIS, Paris, France
- *Correspondence: Eve Hellequin,
| | - Sylvie Collin
- Sorbonne Université, CNRS, EPHE, PSL, UMR METIS, Paris, France
| | | | - Pierre Véquaud
- Sorbonne Université, CNRS, EPHE, PSL, UMR METIS, Paris, France
| | | | - Adrienne Kish
- Muséum National d'Histoire naturelle, CNRS, Unité Molécules de Communication et Adaptation des Microorganismes UMR7245 MCAM, Paris, France
| | - Arnaud Huguet
- Sorbonne Université, CNRS, EPHE, PSL, UMR METIS, Paris, France
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Xie L, Yoshida N, Ishii S, Meng L. Isolation and Polyphasic Characterization of Desulfuromonas versatilis sp. Nov., an Electrogenic Bacteria Capable of Versatile Metabolism Isolated from a Graphene Oxide-Reducing Enrichment Culture. Microorganisms 2021; 9:1953. [PMID: 34576847 PMCID: PMC8465243 DOI: 10.3390/microorganisms9091953] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 01/11/2023] Open
Abstract
In this study, a novel electrogenic bacterium denoted as strain NIT-T3 of the genus Desulfuromonas was isolated from a graphene-oxide-reducing enrichment culture that was originally obtained from a mixture of seawater and coastal sand. Strain NIT-T3 utilized hydrogen and various organic acids as electron donors and exhibited respiration using electrodes, ferric iron, nitrate, and elemental sulfur. The strain contained C16:1ω7c, C16:0, and C15:0 as major fatty acids and MK-8, 9, and 7 as the major respiratory quinones. Strain NIT-T3 contained four 16S rRNA genes and showed 95.7% similarity to Desulfuromonasmichiganensis BB1T, the closest relative. The genome was 4.7 Mbp in size and encoded 76 putative c-type cytochromes, which included 6 unique c-type cytochromes (<40% identity) compared to those in the database. Based on the physiological and genetic uniqueness, and wide metabolic capability, strain NIT-T3 is proposed as a type strain of 'Desulfuromonas versatilis' sp. nov.
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Affiliation(s)
- Li Xie
- Department of Civil Engineering, Nagoya Institute of Technology (Nitech), Nagoya 466-8555, Aichi, Japan; (L.X.); (L.M.)
| | - Naoko Yoshida
- Department of Civil Engineering, Nagoya Institute of Technology (Nitech), Nagoya 466-8555, Aichi, Japan; (L.X.); (L.M.)
| | - Shun’ichi Ishii
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka 237-0061, Kanagawa, Japan;
| | - Lingyu Meng
- Department of Civil Engineering, Nagoya Institute of Technology (Nitech), Nagoya 466-8555, Aichi, Japan; (L.X.); (L.M.)
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Wei W, Plymale A, Zhu Z, Ma X, Liu F, Yu XY. In Vivo Molecular Insights into Syntrophic Geobacter Aggregates. Anal Chem 2020; 92:10402-10411. [PMID: 32614167 DOI: 10.1021/acs.analchem.0c00653] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Direct interspecies electron transfer (DIET) has been considered as a novel and highly efficient strategy in both natural anaerobic environments and artificial microbial fuel cells. A syntrophic model consisting of Geobacter metallireducens and Geobacter sulfurreducens was studied in this work. We conducted in vivo molecular mapping of the outer surface of the syntrophic community as the interface of nutrients and energy exchange. System for Analysis at the Liquid Vacuum Interface combined with time-of-flight secondary ion mass spectrometry was employed to capture the molecular distribution of syntrophic Geobacter communities in the living and hydrated state. Principal component analysis with selected peaks revealed that syntrophic Geobacter aggregates were well differentiated from other control samples, including syntrophic planktonic cells, pure cultured planktonic cells, and single population biofilms. Our in vivo imaging indicated that a unique molecular surface was formed. Specifically, aromatic amino acids, phosphatidylethanolamine components, and large water clusters were identified as key components that favored the DIET of syntrophic Geobacter aggregates. Moreover, the molecular changes in depths of the Geobacter aggregates were captured using dynamic depth profiling. Our findings shed new light on the interface components supporting electron transfer in syntrophic communities based on in vivo molecular imaging.
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Affiliation(s)
- Wenchao Wei
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, P. R. China.,Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Andrew Plymale
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Zihua Zhu
- Environmental and Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Xiang Ma
- Department of Chemistry, Grand View University, Des Moines, Iowa 50316, United States
| | - Fanghua Liu
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, P. R. China
| | - Xiao-Ying Yu
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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Ueno A, Shimizu S, Hashimoto M, Adachi T, Matsushita T, Okuyama H, Yoshida K. Effects of Aerobic Growth on the Fatty Acid and Hydrocarbon Compositions of Geobacter bemidjiensis Bem T. J Oleo Sci 2017; 66:93-101. [PMID: 27928141 DOI: 10.5650/jos.ess16122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Geobacter spp., regarded as strict anaerobes, have been reported to grow under aerobic conditions. To elucidate the role of fatty acids in aerobiosis of Geobacter spp., we studied the effect of aerobiosis on fatty acid composition and turnover in G. bemidjiensis BemT. G. bemidjiensis BemT was grown under the following different culture conditions: anaerobic culture for 4 days (type 1) and type 1 culture followed by 2-day anaerobic (type 2) or aerobic culture (anaerobic-to-aerobic shift; type 3). The mean cell weight of the type 3 culture was approximately 2.5-fold greater than that of type 1 and 2 cultures. The fatty acid methyl ester and hydrocarbon fraction contained hexadecanoic (16:0), 9-cis-hexadecenoic [16:1(9c)], tetradecanoic (14:0), tetradecenoic [14:1(7c)] acids, hentriacontanonaene, and hopanoids, but not long-chain polyunsaturated fatty acids. The type 3 culture contained higher levels of 14:0 and 14:1(7c) and lower levels of 16:0 and 16:1(9c) compared with type 1 and 2 cultures. The weight ratio of extracted lipid per dry cell was lower in the type 3 culture than in the type 1 and 2 cultures. We concluded that anaerobically-grown G. bemidjiensis BemT followed by aerobiosis were enhanced in growth, fatty acid turnover, and de novo fatty acid synthesis.
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Affiliation(s)
- Akio Ueno
- Horonobe Research Institute for the Subsurface Environment (H-RISE), NOASTEC
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6
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Geobacter anodireducens sp. nov., an exoelectrogenic microbe in bioelectrochemical systems. Int J Syst Evol Microbiol 2014; 64:3485-3491. [DOI: 10.1099/ijs.0.061598-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A previously isolated exoelectrogenic bacterium, strain SD-1T, was further characterized and identified as a representative of a novel species of the genus
Geobacter
. Strain SD-1T was Gram-negative, aerotolerant, anaerobic, non-spore-forming, non-fermentative and non-motile. Cells were short, curved rods (0.8–1.3 µm long and 0.3 µm in diameter). Growth of strain SD-1T was observed at 15–42 °C and pH 6.0–8.5, with optimal growth at 30–35 °C and pH 7. Analysis of 16S rRNA gene sequences indicated that the isolate was a member of the genus
Geobacter
, with the closest known relative being
Geobacter sulfurreducens
PCAT (98 % similarity). Similar to other members of the genus
Geobacter
, strain SD-1T used soluble or insoluble Fe(III) as the sole electron acceptor coupled with the oxidation of acetate. However, SD-1T could not reduce fumarate as an electron acceptor with acetate oxidization, which is an important physiological trait for
G. sulfurreducens
. Moreover, SD-1T could grow in media containing as much as 3 % NaCl, while
G. sulfurreducens
PCAT can tolerate just half this concentration, and this difference in salt tolerance was even more obvious when cultivated in bioelectrochemical systems. DNA–DNA hybridization analysis of strain SD-1T and its closest relative,
G. sulfurreducens
ATCC 51573T, showed a relatedness of 61.6 %. The DNA G+C content of strain SD-1T was 58.9 mol%. Thus, on the basis of these characteristics, strain SD-1T was not assigned to
G. sulfurreducens
, and was instead classified in the genus
Geobacter
as a representative of a novel species. The name Geobacter anodireducens sp. nov. is proposed, with the type strain SD-1T ( = CGMCC 1.12536T = KCTC 4672T).
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7
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Zhou S, Yang G, Lu Q, Wu M. Geobacter soli sp. nov., a dissimilatory Fe(III)-reducing bacterium isolated from forest soil. Int J Syst Evol Microbiol 2014; 64:3786-3791. [PMID: 25139417 DOI: 10.1099/ijs.0.066662-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Fe(III)-reducing bacterium, designated GSS01(T), was isolated from a forest soil sample using a liquid medium containing acetate and ferrihydrite as electron donor and electron acceptor, respectively. Cells of strain GSS01(T) were strictly anaerobic, Gram-stain-negative, motile, non-spore-forming and slightly curved rod-shaped. Growth occurred at 16-40 °C and optimally at 30 °C. The DNA G+C content was 60.9 mol%. The major respiratory quinone was MK-8. The major fatty acids were C(16:0), C(18:0) and C(16:1)ω7c/C(16:1)ω6c. Strain GSS01(T) was able to grow with ferrihydrite, Fe(III) citrate, Mn(IV), sulfur, nitrate or anthraquinone-2,6-disulfonate, but not with fumarate, as sole electron acceptor when acetate was the sole electron donor. The isolate was able to utilize acetate, ethanol, glucose, lactate, butyrate, pyruvate, benzoate, benzaldehyde, m-cresol and phenol but not toluene, p-cresol, propionate, malate or succinate as sole electron donor when ferrihydrite was the sole electron acceptor. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain GSS01(T) was most closely related to Geobacter sulfurreducens PCA(T) (98.3% sequence similarity) and exhibited low similarities (94.9-91.8%) to the type strains of other species of the genus Geobacter. The DNA-DNA relatedness between strain GSS01(T) and G. sulfurreducens PCA(T) was 41.4 ± 1.1%. On the basis of phylogenetic analysis, phenotypic characterization and physiological tests, strain GSS01(T) is believed to represent a novel species of the genus Geobacter, and the name Geobacter soli sp. nov. is proposed. The type strain is GSS01(T) ( =KCTC 4545(T) =MCCC 1K00269(T)).
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Affiliation(s)
- Shungui Zhou
- Guangdong Institute of Eco-environmental and Soil Sciences, Guangzhou 510650, PR China
| | - Guiqin Yang
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, PR China
- Guangdong Institute of Eco-environmental and Soil Sciences, Guangzhou 510650, PR China
| | - Qin Lu
- Guangdong Institute of Eco-environmental and Soil Sciences, Guangzhou 510650, PR China
| | - Min Wu
- Guangdong Institute of Eco-environmental and Soil Sciences, Guangzhou 510650, PR China
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8
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Poerschmann J, Schultze-Nobre L. Structural characterization of organic intermediates arising from xylenol degradation by laboratory-scale constructed wetlands. CHEMOSPHERE 2014; 109:120-127. [PMID: 24393564 DOI: 10.1016/j.chemosphere.2013.12.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 12/09/2013] [Accepted: 12/11/2013] [Indexed: 06/03/2023]
Abstract
A mixture of xylenols (2,6-, 3,4-, 3,5-) was subjected to laboratory-scale constructed wetland treatment using helophytes. Conversion efficiencies under aerobic conditions ranged from 89% to 94%; the corresponding numbers under anaerobic conditions were lower. The studies were focused on the identification of stable organic intermediates. Identification was performed by a combination of GC/MS analysis and pre-chromatographic derivatization of the lyophilizates. In addition to common intermediates including citraconate, succinate and dimethyl benzenediols, an array of α- and β-ketoadipic acid carboxylates could be identified. The ketoadipic acid carboxylates have not been known to be formed in bioremediation of phenols including xylenols so far. Mechanisms for the formation of ketoadipic acid carboxylates are proposed. Chemotaxonomic considerations using diagnostic fatty acids provided mounting evidence that organic matter originating from plants prevailed over bacterial organic matter. Biomarkers indicated a virtual absence of fungi and algae.
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Affiliation(s)
- J Poerschmann
- UFZ - Helmholtz Center for Environmental Research, Department of Environmental Engineering, Permoserstr. 15, D-04318 Leipzig, Germany.
| | - L Schultze-Nobre
- UFZ - Helmholtz Center for Environmental Research, Department of Environmental Biotechnology, Germany
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9
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Feist AM, Nagarajan H, Rotaru AE, Tremblay PL, Zhang T, Nevin KP, Lovley DR, Zengler K. Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens. PLoS Comput Biol 2014; 10:e1003575. [PMID: 24762737 PMCID: PMC3998878 DOI: 10.1371/journal.pcbi.1003575] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 03/05/2014] [Indexed: 11/18/2022] Open
Abstract
Geobacter species are of great interest for environmental and biotechnology applications as they can carry out direct electron transfer to insoluble metals or other microorganisms and have the ability to assimilate inorganic carbon. Here, we report on the capability and key enabling metabolic machinery of Geobacter metallireducens GS-15 to carry out CO2 fixation and direct electron transfer to iron. An updated metabolic reconstruction was generated, growth screens on targeted conditions of interest were performed, and constraint-based analysis was utilized to characterize and evaluate critical pathways and reactions in G. metallireducens. The novel capability of G. metallireducens to grow autotrophically with formate and Fe(III) was predicted and subsequently validated in vivo. Additionally, the energetic cost of transferring electrons to an external electron acceptor was determined through analysis of growth experiments carried out using three different electron acceptors (Fe(III), nitrate, and fumarate) by systematically isolating and examining different parts of the electron transport chain. The updated reconstruction will serve as a knowledgebase for understanding and engineering Geobacter and similar species.
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Affiliation(s)
- Adam M. Feist
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (AMF); (KZ)
| | - Harish Nagarajan
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Amelia-Elena Rotaru
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Pier-Luc Tremblay
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Tian Zhang
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Kelly P. Nevin
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Derek R. Lovley
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Karsten Zengler
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (AMF); (KZ)
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Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site. Proc Natl Acad Sci U S A 2014; 111:3389-94. [PMID: 24550478 DOI: 10.1073/pnas.1321621111] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Proline utilization A (PutA) proteins are bifunctional peripheral membrane flavoenzymes that catalyze the oxidation of L-proline to L-glutamate by the sequential activities of proline dehydrogenase and aldehyde dehydrogenase domains. Located at the inner membrane of Gram-negative bacteria, PutAs play a major role in energy metabolism by coupling the oxidation of proline imported from the environment to the reduction of membrane-associated quinones. Here, we report seven crystal structures of the 1,004-residue PutA from Geobacter sulfurreducens, along with determination of the protein oligomeric state by small-angle X-ray scattering and kinetic characterization of substrate channeling and quinone reduction. The structures reveal an elaborate and dynamic tunnel system featuring a 75-Å-long tunnel that links the two active sites and six smaller tunnels that connect the main tunnel to the bulk medium. The locations of these tunnels and their responses to ligand binding and flavin reduction suggest hypotheses about how proline, water, and quinones enter the tunnel system and where L-glutamate exits. Kinetic measurements show that glutamate production from proline occurs without a lag phase, consistent with substrate channeling and implying that the observed tunnel is functionally relevant. Furthermore, the structure of reduced PutA complexed with menadione bisulfite reveals the elusive quinone-binding site. The benzoquinone binds within 4.0 Å of the flavin si face, consistent with direct electron transfer. The location of the quinone site implies that the concave surface of the PutA dimer approaches the membrane. Altogether, these results provide insight into how PutAs couple proline oxidation to quinone reduction.
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ten Brink F, Schoepp-Cothenet B, van Lis R, Nitschke W, Baymann F. Multiple Rieske/cytb complexes in a single organism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1392-406. [PMID: 23507620 DOI: 10.1016/j.bbabio.2013.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 03/01/2013] [Accepted: 03/06/2013] [Indexed: 11/28/2022]
Abstract
Most organisms contain a single Rieske/cytb complex. This enzyme can be integrated in any respiratory or photosynthetic electron transfer chain that is quinone-based and sufficiently energy rich to allow for the turnover of three enzymes - a quinol reductase, a Rieske/cytb complex and a terminal oxidase. Despite this universal usability of the enzyme a variety of phylogenetically distant organisms have multiple copies thereof and no reason for this redundancy is obvious. In this review we present an overview of the distribution of multiple copies among species and describe their properties from the scarce experimental results, analysis of their amino acid sequences and genomic context. We discuss the predicted redox properties of the Rieske cluster in relation to the nature of the pool quinone. It appears that acidophilic iron-oxidizing bacteria specialized one of their two copies for reverse electron transfer, archaeal Thermoprotei adapted their three copies to the interaction with different oxidases and several, phylogenetically unrelated species imported a second complex with a putative heme ci that may confer some yet to be determined properties to the complex. These hypothesis and all the more the so far completely unexplained cases call for further studies and we put forward a number of suggestions for future research that we hope to be stimulating for the field. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
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Affiliation(s)
- F ten Brink
- BIP/UMR7281, FR3479, CNRS/AMU, 13 chemin Joseph Aiguier, 13009 Marseille, France
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Viulu S, Nakamura K, Okada Y, Saitou S, Takamizawa K. Geobacter
luticola sp. nov., an Fe(III)-reducing bacterium isolated from lotus field mud. Int J Syst Evol Microbiol 2013; 63:442-448. [DOI: 10.1099/ijs.0.039321-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel species of Fe(III)-reducing bacterium, designated strain OSK6T, belonging to the genus
Geobacter
, was isolated from lotus field mud in Japan. Strain OSK6T was isolated using a solid medium containing acetate, Fe(III)-nitrilotriacetate (NTA) and gellan gum. The isolate is a strictly anaerobic, Gram-negative, motile, straight rod-shaped bacterium, 0.6–1.9 µm long and 0.2–0.4 µm wide. The growth of the isolate occurred at 20–40 °C with optima of 30–37 °C and pH 6.5–7.5 in the presence of up to 0.5 g NaCl l−1. The G+C content of the genomic DNA was determined by HPLC to be 59.7 mol%. The major respiratory quinone was MK-8. The major fatty acids were 16 : 1ω7c and 16 : 0. Strain OSK6T was able to grow with Fe(III)-NTA, ferric citrate, amorphous iron (III) hydroxide and nitrate, but not with fumarate, malate or sulfate as electron acceptors. Among examined substrates grown with Fe(III)-NTA, the isolate grew on acetate, lactate, pyruvate and succinate. Analysis of the near full-length 16S rRNA gene sequence revealed that strain OSK6T is closely related to
Geobacter daltonii
and
Geobacter toluenoxydans
with 95.6 % similarity to the type strains of these species. On the basis of phylogenetic analysis and physiological tests, strain OSK6T is described as a representative of a novel species,
Geobacter
luticola sp. nov.; the type strain is OSK6T ( = DSM 24905T = JCM 17780T).
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Affiliation(s)
- Samson Viulu
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido 501-1193, Gifu, Japan
| | - Kohei Nakamura
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido 501-1193, Gifu, Japan
| | - Yurina Okada
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido 501-1193, Gifu, Japan
| | - Sakiko Saitou
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido 501-1193, Gifu, Japan
| | - Kazuhiro Takamizawa
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido 501-1193, Gifu, Japan
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido 501-1193, Gifu, Japan
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Viulu S, Nakamura K, Kojima A, Yoshiyasu Y, Saitou S, Takamizawa K. Geobacter sulfurreducens subsp. ethanolicus, subsp. nov., an ethanol-utilizing dissimilatory Fe(III)-reducing bacterium from a lotus field. J GEN APPL MICROBIOL 2013; 59:325-34. [DOI: 10.2323/jgam.59.325] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Poerschmann J, Koschorreck M, Górecki T. Organic matter in sediments of an acidic mining lake as assessed by lipid analysis. Part I: fatty acids. THE SCIENCE OF THE TOTAL ENVIRONMENT 2012; 414:614-623. [PMID: 22119026 DOI: 10.1016/j.scitotenv.2011.10.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 09/28/2011] [Accepted: 10/03/2011] [Indexed: 05/31/2023]
Abstract
Fatty acid (FA) patterns of sediments collected from the bottom of an acidic mine pit lake (AML) at different depths (surface sediment: 0 to 1cm; deep sediment: 4 to 5 cm) were studied to characterize microbial communities and the sources of sedimentary organic matter (SOM). Studies were performed on the molecular level utilizing source-specific, diagnostic FA biomarkers. The biomarker-based approach has been used widely in marine sediment studies, but has not been applied for sediments from AMLs so far. Combined FA concentrations in the surface sediment were higher compared to those in the deep sediment (497 vs. 127 μg g(-1)d.w., respectively). This was related to deposition of autochthonous biomass and higher terrestrial plants onto the surface sediment, as well as--to lesser extent--with higher bacterial activity on the sediment-water interface. The FA distribution in both sediments was characterized by a strong even-over-odd preference and was bimodal in nature: there was a cluster at nC(14)-nC(18) characteristic of chiefly autochthonous (algal and bacterial) SOM production, and another cluster at nC(22-28) related to input from higher plants. The FA distribution in the surface sediment pointed to higher terrestrial input compared to autochthonous contribution to SOM (67%:33%) as an estimate. Fingerprinting of viable bacteria was accomplished through signature FA markers including branched C(15) and C(17) surrogates, cyclopropanoic acids, 3-hydroxy (OH) acids and monounsaturated surrogates with unusual double bond localization. The abundance of Gram-negative bacteria was higher in the surface sediment as evidenced by total diagnostic 3-OH-fatty acids (37 μg g(-1) versus 25 μg g(-1)). Potential source taxa in both sediment layers included acidophilic iron- and sulfur-oxidizing bacteria including Acidithiobacillus ferrooxidans. High abundances of terminally branched C(15) and C(17) surrogates in both sediments pointed to sulfate- and iron-reducing bacteria. Signature FAs characteristic of methanotrophs were virtually lacking in both sediments.
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Affiliation(s)
- Juergen Poerschmann
- UFZ-Helmholtz Center for Environmental Research, Department of Environmental Engineering, Permoserstr 15, 04318 Leipzig, Germany.
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Ramelot TA, Smola MJ, Lee HW, Ciccosanti C, Hamilton K, Acton TB, Xiao R, Everett JK, Prestegard JH, Montelione GT, Kennedy MA. Solution structure of 4'-phosphopantetheine - GmACP3 from Geobacter metallireducens: a specialized acyl carrier protein with atypical structural features and a putative role in lipopolysaccharide biosynthesis. Biochemistry 2011; 50:1442-53. [PMID: 21235239 PMCID: PMC3063093 DOI: 10.1021/bi101932s] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
GmACP3 from Geobacter metallireducens is a specialized acyl carrier protein (ACP) whose gene, gmet_2339, is located near genes encoding many proteins involved in lipopolysaccharide (LPS) biosynthesis, indicating a likely function for GmACP3 in LPS production. By overexpression in Escherichia coli, about 50% holo-GmACP3 and 50% apo-GmACP3 were obtained. Apo-GmACP3 exhibited slow precipitation and non-monomeric behavior by (15)N NMR relaxation measurements. Addition of 4'-phosphopantetheine (4'-PP) via enzymatic conversion by E. coli holo-ACP synthase resulted in stable >95% holo-GmACP3 that was characterized as monomeric by (15)N relaxation measurements and had no indication of conformational exchange. We have determined a high-resolution solution structure of holo-GmACP3 by standard NMR methods, including refinement with two sets of NH residual dipolar couplings, allowing for a detailed structural analysis of the interactions between 4'-PP and GmACP3. Whereas the overall four helix bundle topology is similar to previously solved ACP structures, this structure has unique characteristics, including an ordered 4'-PP conformation that places the thiol at the entrance to a central hydrophobic cavity near a conserved hydrogen-bonded Trp-His pair. These residues are part of a conserved WDSLxH/N motif found in GmACP3 and its orthologs. The helix locations and the large hydrophobic cavity are more similar to medium- and long-chain acyl-ACPs than to other apo- and holo-ACP structures. Taken together, structural characterization along with bioinformatic analysis of nearby genes suggests that GmACP3 is involved in lipid A acylation, possibly by atypical long-chain hydroxy fatty acids, and potentially is involved in synthesis of secondary metabolites.
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Affiliation(s)
- Theresa A. Ramelot
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States and the Northeast Structural Genomics Consortium
| | - Matthew J. Smola
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States and the Northeast Structural Genomics Consortium
| | - Hsiau-Wei Lee
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States and the Northeast Structural Genomics Consortium
| | - Colleen Ciccosanti
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States and the Northeast Structural Genomics Consortium
| | - Keith Hamilton
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States and the Northeast Structural Genomics Consortium
| | - Thomas B. Acton
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States and the Northeast Structural Genomics Consortium
| | - Rong Xiao
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States and the Northeast Structural Genomics Consortium
| | - John K. Everett
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States and the Northeast Structural Genomics Consortium
| | - James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States and the Northeast Structural Genomics Consortium
| | - Gaetano T. Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States and the Northeast Structural Genomics Consortium
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey, 08854, United States
| | - Michael A. Kennedy
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States and the Northeast Structural Genomics Consortium
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Nowicka B, Kruk J. Occurrence, biosynthesis and function of isoprenoid quinones. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1587-605. [PMID: 20599680 DOI: 10.1016/j.bbabio.2010.06.007] [Citation(s) in RCA: 303] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 06/09/2010] [Accepted: 06/14/2010] [Indexed: 12/23/2022]
Abstract
Isoprenoid quinones are one of the most important groups of compounds occurring in membranes of living organisms. These compounds are composed of a hydrophilic head group and an apolar isoprenoid side chain, giving the molecules a lipid-soluble character. Isoprenoid quinones function mainly as electron and proton carriers in photosynthetic and respiratory electron transport chains and these compounds show also additional functions, such as antioxidant function. Most of naturally occurring isoprenoid quinones belong to naphthoquinones or evolutionary younger benzoquinones. Among benzoquinones, the most widespread and important are ubiquinones and plastoquinones. Menaquinones, belonging to naphthoquinones, function in respiratory and photosynthetic electron transport chains of bacteria. Phylloquinone K(1), a phytyl naphthoquinone, functions in the photosynthetic electron transport in photosystem I. Ubiquinones participate in respiratory chains of eukaryotic mitochondria and some bacteria. Plastoquinones are components of photosynthetic electron transport chains of cyanobacteria and plant chloroplasts. Biosynthetic pathway of isoprenoid quinones has been described, as well as their additional, recently recognized, diverse functions in bacterial, plant and animal metabolism.
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Affiliation(s)
- Beatrycze Nowicka
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
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Sukovich DJ, Seffernick JL, Richman JE, Gralnick JA, Wackett LP. Widespread head-to-head hydrocarbon biosynthesis in bacteria and role of OleA. Appl Environ Microbiol 2010; 76:3850-62. [PMID: 20418421 PMCID: PMC2893475 DOI: 10.1128/aem.00436-10] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Accepted: 04/13/2010] [Indexed: 11/20/2022] Open
Abstract
Previous studies identified the oleABCD genes involved in head-to-head olefinic hydrocarbon biosynthesis. The present study more fully defined the OleABCD protein families within the thiolase, alpha/beta-hydrolase, AMP-dependent ligase/synthase, and short-chain dehydrogenase superfamilies, respectively. Only 0.1 to 1% of each superfamily represents likely Ole proteins. Sequence analysis based on structural alignments and gene context was used to identify highly likely ole genes. Selected microorganisms from the phyla Verucomicrobia, Planctomyces, Chloroflexi, Proteobacteria, and Actinobacteria were tested experimentally and shown to produce long-chain olefinic hydrocarbons. However, different species from the same genera sometimes lack the ole genes and fail to produce olefinic hydrocarbons. Overall, only 1.9% of 3,558 genomes analyzed showed clear evidence for containing ole genes. The type of olefins produced by different bacteria differed greatly with respect to the number of carbon-carbon double bonds. The greatest number of organisms surveyed biosynthesized a single long-chain olefin, 3,6,9,12,15,19,22,25,28-hentriacontanonaene, that contains nine double bonds. Xanthomonas campestris produced the greatest number of distinct olefin products, 15 compounds ranging in length from C(28) to C(31) and containing one to three double bonds. The type of long-chain product formed was shown to be dependent on the oleA gene in experiments with Shewanella oneidensis MR-1 ole gene deletion mutants containing native or heterologous oleA genes expressed in trans. A strain deleted in oleABCD and containing oleA in trans produced only ketones. Based on these observations, it was proposed that OleA catalyzes a nondecarboxylative thiolytic condensation of fatty acyl chains to generate a beta-ketoacyl intermediate that can decarboxylate spontaneously to generate ketones.
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Affiliation(s)
- David J. Sukovich
- Graduate Program in Microbiology, Immunology, and Cancer Biology, BioTechnology Institute, Department of Biochemistry, Molecular Biology and Biophysics, Department of Microbiology, University of Minnesota, St. Paul, Minnesota 55108
| | - Jennifer L. Seffernick
- Graduate Program in Microbiology, Immunology, and Cancer Biology, BioTechnology Institute, Department of Biochemistry, Molecular Biology and Biophysics, Department of Microbiology, University of Minnesota, St. Paul, Minnesota 55108
| | - Jack E. Richman
- Graduate Program in Microbiology, Immunology, and Cancer Biology, BioTechnology Institute, Department of Biochemistry, Molecular Biology and Biophysics, Department of Microbiology, University of Minnesota, St. Paul, Minnesota 55108
| | - Jeffrey A. Gralnick
- Graduate Program in Microbiology, Immunology, and Cancer Biology, BioTechnology Institute, Department of Biochemistry, Molecular Biology and Biophysics, Department of Microbiology, University of Minnesota, St. Paul, Minnesota 55108
| | - Lawrence P. Wackett
- Graduate Program in Microbiology, Immunology, and Cancer Biology, BioTechnology Institute, Department of Biochemistry, Molecular Biology and Biophysics, Department of Microbiology, University of Minnesota, St. Paul, Minnesota 55108
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