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Saghaï A, Hallin S. Diversity and ecology of NrfA-dependent ammonifying microorganisms. Trends Microbiol 2024; 32:602-613. [PMID: 38462391 DOI: 10.1016/j.tim.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 03/12/2024]
Abstract
Nitrate ammonifiers are a taxonomically diverse group of microorganisms that reduce nitrate to ammonium, which is released, and thereby contribute to the retention of nitrogen in ecosystems. Despite their importance for understanding the fate of nitrate, they remain a largely overlooked group in the nitrogen cycle. Here, we present the latest advances on free-living microorganisms using NrfA to reduce nitrite during ammonification. We describe their diversity and ecology in terrestrial and aquatic environments, as well as the environmental factors influencing the competition for nitrate with denitrifiers that reduce nitrate to gaseous nitrogen species, including the greenhouse gas nitrous oxide (N2O). We further review the capacity of ammonifiers for other redox reactions, showing that they likely play multiple roles in the cycling of elements.
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Affiliation(s)
- Aurélien Saghaï
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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2
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Reji L, Darnajoux R, Zhang X. A genomic view of environmental and life history controls on microbial nitrogen acquisition strategies. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13220. [PMID: 38057292 PMCID: PMC10866080 DOI: 10.1111/1758-2229.13220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/15/2023] [Indexed: 12/08/2023]
Abstract
Microorganisms have evolved diverse strategies to acquire the vital element nitrogen (N) from the environment. Ecological and physiological controls on the distribution of these strategies among microbes remain unclear. In this study, we examine the distribution of 10 major N acquisition strategies in taxonomically and metabolically diverse microbial genomes, including those from the Genomic Catalogue of Earth's Microbiomes dataset. We utilize a marker gene-based approach to assess relationships between N acquisition strategy prevalence and microbial life history strategies. Our results underscore energetic costs of assimilation as a broad control on strategy distribution. The most prevalent strategies are the uptake of ammonium and simple amino acids, which have relatively low energetic costs, while energy-intensive biological nitrogen fixation is the least common. Deviations from the energy-based framework include the higher-than-expected prevalence of the assimilatory pathway for chitin, a large organic polymer. Energy availability is also important, with aerobic chemoorganotrophs and oxygenic phototrophs notably possessing ~2-fold higher numbers of total strategies compared to anaerobic microbes. Environmental controls are evidenced by the enrichment of inorganic N assimilation strategies among free-living taxa compared to host-associated taxa. Physiological constraints such as pathway incompatibility add complexity to N acquisition strategy distributions. Finally, we discuss the necessity for microbially-relevant spatiotemporal environmental metadata for improving mechanistic and prediction-oriented analyses of genomic data.
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Affiliation(s)
- Linta Reji
- Department of GeosciencesPrinceton UniversityPrincetonNew JerseyUSA
- High Meadows Environmental InstitutePrinceton UniversityPrincetonNew JerseyUSA
| | - Romain Darnajoux
- Department of GeosciencesPrinceton UniversityPrincetonNew JerseyUSA
| | - Xinning Zhang
- Department of GeosciencesPrinceton UniversityPrincetonNew JerseyUSA
- High Meadows Environmental InstitutePrinceton UniversityPrincetonNew JerseyUSA
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3
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Fiévet A, Merrouch M, Brasseur G, Eve D, Biondi EG, Valette O, Pauleta SR, Dolla A, Dermoun Z, Burlat B, Aubert C. OrpR is a σ 54 -dependent activator using an iron-sulfur cluster for redox sensing in Desulfovibrio vulgaris Hildenborough. Mol Microbiol 2021; 116:231-244. [PMID: 33595838 PMCID: PMC8359166 DOI: 10.1111/mmi.14705] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/15/2021] [Accepted: 02/15/2021] [Indexed: 01/15/2023]
Abstract
Enhancer binding proteins (EBPs) are key players of σ54 -regulation that control transcription in response to environmental signals. In the anaerobic microorganism Desulfovibrio vulgaris Hildenborough (DvH), orp operons have been previously shown to be coregulated by σ54 -RNA polymerase, the integration host factor IHF and a cognate EBP, OrpR. In this study, ChIP-seq experiments indicated that the OrpR regulon consists of only the two divergent orp operons. In vivo data revealed that (i) OrpR is absolutely required for orp operons transcription, (ii) under anaerobic conditions, OrpR binds on the two dedicated DNA binding sites and leads to high expression levels of the orp operons, (iii) increasing the redox potential of the medium leads to a drastic down-regulation of the orp operons expression. Moreover, combining functional and biophysical studies on the anaerobically purified OrpR leads us to propose that OrpR senses redox potential variations via a redox-sensitive [4Fe-4S]2+ cluster in the sensory PAS domain. Overall, the study herein presents the first characterization of a new Fe-S redox regulator belonging to the σ54 -dependent transcriptional regulator family probably advantageously selected by cells adapted to the anaerobic lifestyle to monitor redox stress conditions.
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Affiliation(s)
| | | | | | - Danaé Eve
- Aix Marseille Univ, CNRS, LCB, Marseille, France
| | | | | | - Sofia R Pauleta
- Microbial Stress Lab, UCIBIO, REQUIMTE, Dept. Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Alain Dolla
- Aix Marseille Univ, Toulon Univ, CNRS, IRD, MIO, Marseille, France
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4
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Kalam S, Basu A, Ahmad I, Sayyed RZ, El-Enshasy HA, Dailin DJ, Suriani NL. Recent Understanding of Soil Acidobacteria and Their Ecological Significance: A Critical Review. Front Microbiol 2020; 11:580024. [PMID: 33193209 PMCID: PMC7661733 DOI: 10.3389/fmicb.2020.580024] [Citation(s) in RCA: 206] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 10/08/2020] [Indexed: 11/13/2022] Open
Abstract
Acidobacteria represents an underrepresented soil bacterial phylum whose members are pervasive and copiously distributed across nearly all ecosystems. Acidobacterial sequences are abundant in soils and represent a significant fraction of soil microbial community. Being recalcitrant and difficult-to-cultivate under laboratory conditions, holistic, polyphasic approaches are required to study these refractive bacteria extensively. Acidobacteria possesses an inventory of genes involved in diverse metabolic pathways, as evidenced by their pan-genomic profiles. Because of their preponderance and ubiquity in the soil, speculations have been made regarding their dynamic roles in vital ecological processes viz., regulation of biogeochemical cycles, decomposition of biopolymers, exopolysaccharide secretion, and plant growth promotion. These bacteria are expected to have genes that might help in survival and competitive colonization in the rhizosphere, leading to the establishment of beneficial relationships with plants. Exploration of these genetic attributes and more in-depth insights into the belowground mechanics and dynamics would lead to a better understanding of the functions and ecological significance of this enigmatic phylum in the soil-plant environment. This review is an effort to provide a recent update into the diversity of genes in Acidobacteria useful for characterization, understanding ecological roles, and future biotechnological perspectives.
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Affiliation(s)
- Sadaf Kalam
- Department of Biochemistry, St. Ann's College for Women, Hyderabad, India
| | - Anirban Basu
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Iqbal Ahmad
- Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, India
| | - R Z Sayyed
- Department of Microbiology, PSGVP Mandal's, Arts, Science and Commerce College, Shahada, India
| | - Hesham Ali El-Enshasy
- Institute of Bioproduct Development, Universiti Teknologi Malaysia (UTM), Skudai, Malaysia.,School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia (UTM), Skudai, Malaysia.,City of Scientific Research and Technological Applications, New Borg El-Arab, Egypt
| | - Daniel Joe Dailin
- Institute of Bioproduct Development, Universiti Teknologi Malaysia (UTM), Skudai, Malaysia.,School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia (UTM), Skudai, Malaysia
| | - Ni Luh Suriani
- Biology Department, Faculty of Mathematics and Natural Science, Udayana University, Bali, Indonesia
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5
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Li K, Wu G, Liao Y, Zeng Q, Wang H, Liu F. RpoN1 and RpoN2 play different regulatory roles in virulence traits, flagellar biosynthesis, and basal metabolism in Xanthomonas campestris. MOLECULAR PLANT PATHOLOGY 2020; 21:907-922. [PMID: 32281725 PMCID: PMC7280030 DOI: 10.1111/mpp.12938] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/18/2020] [Accepted: 03/18/2020] [Indexed: 05/08/2023]
Abstract
Homologous regulatory factors are widely present in bacteria, but whether homologous regulators synergistically or differentially regulate different biological functions remains mostly unknown. Here, we report that the homologous regulators RpoN1 and RpoN2 of the plant pathogen Xanthomonas campestris pv. campestris (Xcc) play different regulatory roles with respect to virulence traits, flagellar biosynthesis, and basal metabolism. RpoN2 directly regulated Xcc fliC and fliQ to modulate flagellar synthesis in X. campestris, thus affecting the swimming motility of X. campestris. Mutation of rpoN2 resulted in reduced production of biofilms and extracellular polysaccharides in Xcc. These defects may together cause reduced virulence of the rpoN2 mutant against the host plant. Moreover, we demonstrated that RpoN1 could regulate branched-chain fatty acid production and modulate the synthesis of diffusible signal factor family quorum sensing signals. Although RpoN1 and RpoN2 are homologues, the regulatory roles and biological functions of these proteins were not interchangeable. Overall, our report provides new insights into the two different molecular roles that form the basis for the transcriptional specialization of RpoN homologues.
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Affiliation(s)
- Kaihuai Li
- College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
| | - Guichun Wu
- Institute of Plant ProtectionJiangsu Academy of Agricultural SciencesNanjingChina
| | - Yuling Liao
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural OrganismsCollege of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Quan Zeng
- Department of Plant Pathology and EcologyThe Connecticut Agricultural Experiment StationNew HavenCTUSA
| | - Haihong Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural OrganismsCollege of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Fengquan Liu
- College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Institute of Plant ProtectionJiangsu Academy of Agricultural SciencesNanjingChina
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6
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Xu YN, Chen Y. Advances in heavy metal removal by sulfate-reducing bacteria. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2020; 81:1797-1827. [PMID: 32666937 DOI: 10.2166/wst.2020.227] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Industrial development has led to generation of large volumes of wastewater containing heavy metals, which need to be removed before the wastewater is released into the environment. Chemical and electrochemical methods are traditionally applied to treat this type of wastewater. These conventional methods have several shortcomings, such as secondary pollution and cost. Bioprocesses are gradually gaining popularity because of their high selectivities, low costs, and reduced environmental pollution. Removal of heavy metals by sulfate-reducing bacteria (SRB) is an economical and effective alternative to conventional methods. The limitations of and advances in SRB activity have not been comprehensively reviewed. In this paper, recent advances from laboratory studies in heavy metal removal by SRB were reported. Firstly, the mechanism of heavy metal removal by SRB is introduced. Then, the factors affecting microbial activity and metal removal efficiency are elucidated and discussed in detail. In addition, recent advances in selection of an electron donor, enhancement of SRB activity, and improvement of SRB tolerance to heavy metals are reviewed. Furthermore, key points for future studies of the SRB process are proposed.
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Affiliation(s)
- Ya-Nan Xu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China E-mail:
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China E-mail: ; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
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7
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Gao SH, Ho JY, Fan L, Nouwens A, Hoelzle RD, Schulz B, Guo J, Zhou J, Yuan Z, Bond PL. A comparative proteomic analysis of Desulfovibrio vulgaris Hildenborough in response to the antimicrobial agent free nitrous acid. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 672:625-633. [PMID: 30974354 DOI: 10.1016/j.scitotenv.2019.03.442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/12/2019] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
Sulfate reducing bacteria (SRB) can contribute to facilitating serious concrete corrosion through the production of hydrogen sulfide in sewers. Recently, free nitrous acid (FNA) was discovered as a promising antimicrobial agent to inhibit SRB activities thereby limiting hydrogen sulfide production in sewers. However, knowledge of the bacterial response to increasing levels of the antimicrobial agent is unknown. Here we report the proteomic response of Desulfovibrio vulgaris Hildenborough and reveal that the antimicrobial effect of FNA is multi-targeted and dependent on the FNA levels. This was achieved using a sequential window acquisition of all theoretical mass spectrometry analysis to determine protein abundance variations in D. vulgaris during exposure to different FNA concentrations. When exposed to 1.0 μg N/L FNA, nitrite reduction (nitrite reductase) related proteins and nitrosative stress related proteins, including the hybrid cluster protein, showed distinct increased abundances. When exposed to 4.0 and 8.0 μg N/L FNA, increased abundance was detected for proteins putatively involved in nitrite reduction. Abundance of proteins involved in the sulfate reduction pathway (from adenylylphophosulfate to sulfite) and lactate oxidation pathway (from pyruvate to acetate) were initially inhibited in response to FNA at 8 h incubation, and then recovered at 12 h incubation. Lowered ribosomal protein abundance in D. vulgaris was detected, however, total cellular protein levels were mostly constant in the presence or absence of FNA. In addition, this study indicates that proteins coded by genes DVU2543, DVU0772, and DVU3212 potentially participate in resisting oxidative stress with FNA exposure. These findings share new insights for understanding the dynamic responses of D. vulgaris to FNA and could be useful to guide and improve the practical applications of FNA-based technologies for control of sewer corrosion.
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Affiliation(s)
- Shu-Hong Gao
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Jun Yuan Ho
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Lu Fan
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Amanda Nouwens
- School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Robert D Hoelzle
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Benjamin Schulz
- School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Philip L Bond
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia.
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8
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Simultaneous Biological and Chemical Removal of Sulfate and Fe(II)EDTA-NO in Anaerobic Conditions and Regulation of Sulfate Reduction Products. MINERALS 2019. [DOI: 10.3390/min9060330] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In the simultaneous flue gas desulfurization and denitrification by biological combined with chelating absorption technology, SO2 and NO are converted into sulfate and Fe(II)EDTA-NO which need to be reduced in biological reactor. Increasing the removal loads of sulfate and Fe(II)EDTA-NO and converting sulfate to elemental sulfur will benefit the application of this process. A moving-bed biofilm reactor was adopted for sulfate and Fe(II)EDTA-NO biological reduction. The removal efficiencies of the sulfate and Fe(II)EDTA-NO were 96% and 92% with the influent loads of 2.88 kg SO42−·m−3·d−1 and 0.48 kg NO·m−3·d−1. The sulfide produced by sulfate reduction could be reduced by increasing the concentrations of Fe(II)EDTA-NO and Fe(III)EDTA. The main reduction products of sulfate and Fe(II)EDTA-NO were elemental sulfur and N2. It was found that the dominant strain of sulfate reducing bacteria in the system was Desulfomicrobium. Pseudomonas, Sulfurovum and Arcobacter were involved in the reduction of Fe(II)EDTA-NO.
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9
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Rajeev L, Luning EG, Zane GM, Juba TR, Kazakov AE, Novichkov PS, Wall JD, Mukhopadhyay A. LurR is a regulator of the central lactate oxidation pathway in sulfate-reducing Desulfovibrio species. PLoS One 2019; 14:e0214960. [PMID: 30964892 PMCID: PMC6456213 DOI: 10.1371/journal.pone.0214960] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/22/2019] [Indexed: 11/18/2022] Open
Abstract
The central carbon/lactate utilization pathway in the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough, is encoded by the highly conserved operon DVU3025-3033. Our earlier in vitro genome-wide study had suggested a network of four two-component system regulators that target this large operon; however, how these four regulators control this operon was not known. Here, we probe the regulation of the lactate utilization operon with mutant strains and DNA-protein binding assays. We show that the LurR response regulator is required for optimal growth and complete lactate utilization, and that it activates the DVU3025-3033 lactate oxidation operon as well as DVU2451, a lactate permease gene, in the presence of lactate. We show by electrophoretic mobility shift assays that LurR binds to three sites in the upstream region of DVU3025, the first gene of the operon. NrfR, a response regulator that is activated under nitrite stress, and LurR share similar binding site motifs and bind the same sites upstream of DVU3025. The DVU3025 promoter also has a binding site motif (Pho box) that is bound by PhoB, a two-component response regulator activated under phosphate limitation. The lactate utilization operon, the regulator LurR, and LurR binding sites are conserved across the order Desulfovibrionales whereas possible modulation of the lactate utilization genes by additional regulators such as NrfR and PhoB appears to be limited to D. vulgaris.
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Affiliation(s)
- Lara Rajeev
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Eric G. Luning
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Thomas R. Juba
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Alexey E. Kazakov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Pavel S. Novichkov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail:
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10
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The Porphyromonas gingivalis Hybrid Cluster Protein Hcp Is Required for Growth with Nitrite and Survival with Host Cells. Infect Immun 2019; 87:IAI.00572-18. [PMID: 30670550 DOI: 10.1128/iai.00572-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 01/11/2019] [Indexed: 12/13/2022] Open
Abstract
Although the periodontal pathogen Porphyromonas gingivalis must withstand high levels of nitrosative stress while in the oral cavity, the mechanisms of nitrosative stress defense are not well understood in this organism. Previously we showed that the transcriptional regulator HcpR plays a significant role in defense, and here we further defined its regulon. Our study shows that hcp (PG0893), a putative nitric oxide (NO) reductase, is the only gene significantly upregulated in response to nitrite (NO2) and that this regulation is dependent on HcpR. An isogenic mutant deficient in hcp is not able to grow with 200 μM nitrite, demonstrating that the sensitivity of the HcpR mutant is mediated through Hcp. We further define the molecular mechanisms of HcpR interaction with the hcp promoter through mutational analysis of the inverted repeat present within the promoter. Although other putative nitrosative stress protection mechanisms present on the nrfAH operon are also found in the P. gingivalis genome, we show that their gene products play no role in growth of the bacterium with nitrite. As growth of the hcp-deficient strain was also significantly diminished in the presence of a nitric oxide-producing compound, S-nitrosoglutathione (GSNO), Hcp appears to be the primary means by which P. gingivalis responds to NO2 --based stress. Finally, we show that Hcp is required for survival with host cells but that loss of Hcp has no effect on association and entry of P. gingivalis into human oral keratinocytes.
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11
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Rajeev L, Garber ME, Zane GM, Price MN, Dubchak I, Wall JD, Novichkov PS, Mukhopadhyay A, Kazakov AE. A new family of transcriptional regulators of tungstoenzymes and molybdate/tungstate transport. Environ Microbiol 2019; 21:784-799. [PMID: 30536693 DOI: 10.1111/1462-2920.14500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/03/2018] [Accepted: 12/07/2018] [Indexed: 11/30/2022]
Abstract
Bacterial genes for molybdenum-containing and tungsten-containing enzymes are often differentially regulated depending on the metal availability in the environment. Here, we describe a new family of transcription factors with an unusual DNA-binding domain related to excisionases of bacteriophages. These transcription factors are associated with genes for various molybdate and tungstate-specific transporting systems as well as molybdo/tungsto-enzymes in a wide range of bacterial genomes. We used a combination of computational and experimental techniques to study a member of the TF family, named TaoR (for tungsten-containing aldehyde oxidoreductase regulator). In Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, TaoR activates expression of aldehyde oxidoreductase aor and represses tungsten-specific ABC-type transporter tupABC genes under tungsten-replete conditions. TaoR binding sites at aor promoter were identified by electrophoretic mobility shift assay and DNase I footprinting. We also reconstructed TaoR regulons in 45 Deltaproteobacteria by comparative genomics approach and predicted target genes for TaoR family members in other Proteobacteria and Firmicutes.
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Affiliation(s)
- L Rajeev
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - M E Garber
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Comparative Biochemistry, University of California, Berkeley, CA, 94720, USA
| | - G M Zane
- Biochemistry and Molecular Microbiology & Immunology Department, University of Missouri, Columbia, MO, 65211, USA
| | - M N Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - I Dubchak
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - J D Wall
- Biochemistry and Molecular Microbiology & Immunology Department, University of Missouri, Columbia, MO, 65211, USA
| | - P S Novichkov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Energy, Knowledge Base, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - A Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Comparative Biochemistry, University of California, Berkeley, CA, 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - A E Kazakov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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12
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Gnandt D, Na S, Koslowski T. Simulating biological charge transfer: Continuum dielectric theory or molecular dynamics? Biophys Chem 2018; 241:1-7. [PMID: 30036762 DOI: 10.1016/j.bpc.2018.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/01/2018] [Indexed: 10/28/2022]
Abstract
We study the thermodynamic parameters of Marcus's theory of charge transfer, the driving forces and the reorganization energies, using two widely applied approaches to bioenergetic problems that seem to be radically different: continuum dielectric theory via a numerical solution of Poisson's equation, and the thermodynamic integration approach based upon classical Newtonian molecular dynamics, as perfomed by Na et al., PCCP 19, 18,938 (2017). With application to a nitrite reductase NrfHA protein heterodimer, we obtain an excellent agreement between the respective driving forces with an r.m.s. deviation of 1.7 kcal/mol, and a lower limit to the reorganization energies. The computational methods turn out to be mutually supportive: molecular dynamics can be used to determine the parameters of a dielectric theory computation, which on the other hand can be used to properly rescale the reorganization energies and partition them into aqueous and protein contributions. In addition, we use the electrostatic approach to study the influence of Ca2+ ions on the free energy landscape of charge transfer.
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Affiliation(s)
- David Gnandt
- Institut für Physikalische Chemie, Universität Freiburg, Albertstraße 23a, 79104 Freiburg im Breisgau, Germany
| | - Sehee Na
- Institut für Physikalische Chemie, Universität Freiburg, Albertstraße 23a, 79104 Freiburg im Breisgau, Germany
| | - Thorsten Koslowski
- Institut für Physikalische Chemie, Universität Freiburg, Albertstraße 23a, 79104 Freiburg im Breisgau, Germany.
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13
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Eichorst SA, Trojan D, Roux S, Herbold C, Rattei T, Woebken D. Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments. Environ Microbiol 2018; 20:1041-1063. [PMID: 29327410 PMCID: PMC5900883 DOI: 10.1111/1462-2920.14043] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 12/16/2017] [Accepted: 01/08/2018] [Indexed: 12/11/2022]
Abstract
Members of the phylum Acidobacteria are abundant and ubiquitous across soils. We performed a large-scale comparative genome analysis spanning subdivisions 1, 3, 4, 6, 8 and 23 (n = 24) with the goal to identify features to help explain their prevalence in soils and understand their ecophysiology. Our analysis revealed that bacteriophage integration events along with transposable and mobile elements influenced the structure and plasticity of these genomes. Low- and high-affinity respiratory oxygen reductases were detected in multiple genomes, suggesting the capacity for growing across different oxygen gradients. Among many genomes, the capacity to use a diverse collection of carbohydrates, as well as inorganic and organic nitrogen sources (such as via extracellular peptidases), was detected - both advantageous traits in environments with fluctuating nutrient environments. We also identified multiple soil acidobacteria with the potential to scavenge atmospheric concentrations of H2 , now encompassing mesophilic soil strains within the subdivision 1 and 3, in addition to a previously identified thermophilic strain in subdivision 4. This large-scale acidobacteria genome analysis reveal traits that provide genomic, physiological and metabolic versatility, presumably allowing flexibility and versatility in the challenging and fluctuating soil environment.
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Affiliation(s)
- Stephanie A. Eichorst
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network “Chemistry Meets Biology”, University of ViennaViennaAustria
| | - Daniela Trojan
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network “Chemistry Meets Biology”, University of ViennaViennaAustria
| | - Simon Roux
- Department of EnergyJoint Genome InstituteWalnut CreekCAUSA
| | - Craig Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network “Chemistry Meets Biology”, University of ViennaViennaAustria
| | - Thomas Rattei
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem ScienceResearch Network “Chemistry Meets Biology”, University of ViennaViennaAustria
| | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network “Chemistry Meets Biology”, University of ViennaViennaAustria
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14
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Microbially Mediated Coupling of Fe and N Cycles by Nitrate-Reducing Fe(II)-Oxidizing Bacteria in Littoral Freshwater Sediments. Appl Environ Microbiol 2018; 84:AEM.02013-17. [PMID: 29101195 DOI: 10.1128/aem.02013-17] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 10/31/2017] [Indexed: 11/20/2022] Open
Abstract
Nitrate-reducing iron(II)-oxidizing bacteria have been known for approximately 20 years. There has been much debate as to what extent the reduction of nitrate and the oxidation of ferrous iron are coupled via enzymatic pathways or via abiotic processes induced by nitrite formed by heterotrophic denitrification. The aim of the present study was to assess the coupling of nitrate reduction and iron(II) oxidation by monitoring changes in substrate concentrations, as well as in the activity of nitrate-reducing bacteria in natural littoral freshwater sediment, in response to stimulation with nitrate and iron(II). In substrate-amended microcosms, we found that the biotic oxidation of ferrous iron depended on the simultaneous microbial reduction of nitrate. Additionally, the abiotic oxidation of ferrous iron by nitrite in sterilized sediment was not fast enough to explain the iron oxidation rates observed in microbially active sediment. Furthermore, the expression levels of genes coding for enzymes crucial for nitrate reduction were in some setups stimulated by the presence of ferrous iron. These results indicate that there is a direct influence of ferrous iron on bacterial denitrification and support the hypothesis that microbial nitrate reduction is stimulated by biotic iron(II) oxidation.IMPORTANCE The coupling of nitrate reduction and Fe(II) oxidation affects the environment at a local scale, e.g., by changing nutrient or heavy metal mobility in soils due to the formation of Fe(III) minerals, as well as at a global scale, e.g., by the formation of the primary greenhouse gas nitrous oxide. Although the coupling of nitrate reduction and Fe(II) oxidation was reported 20 years ago and has been studied intensively since then, the underlying mechanisms still remain unknown. One of the main knowledge gaps is the extent of enzymatic Fe(II) oxidation coupled to nitrate reduction, which has frequently been questioned in the literature. In the present study, we provide evidence for microbially mediated nitrate-reducing Fe(II) oxidation in freshwater sediments. This evidence is based on the rates of nitrate reduction and Fe(II) oxidation determined in microcosm incubations and on the effect of iron on the expression of genes required for denitrification.
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15
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Cadby IT, Faulkner M, Cheneby J, Long J, van Helden J, Dolla A, Cole JA. Coordinated response of the Desulfovibrio desulfuricans 27774 transcriptome to nitrate, nitrite and nitric oxide. Sci Rep 2017; 7:16228. [PMID: 29176637 PMCID: PMC5701242 DOI: 10.1038/s41598-017-16403-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/08/2017] [Indexed: 01/06/2023] Open
Abstract
The sulfate reducing bacterium Desulfovibrio desulfuricans inhabits both the human gut and external environments. It can reduce nitrate and nitrite as alternative electron acceptors to sulfate to support growth. Like other sulphate reducing bacteria, it can also protect itself against nitrosative stress caused by NO generated when nitrite accumulates. By combining in vitro experiments with bioinformatic and RNA-seq data, metabolic responses to nitrate or NO and how nitrate and nitrite reduction are coordinated with the response to nitrosative stress were revealed. Although nitrate and nitrite reduction are tightly regulated in response to substrate availability, the global responses to nitrate or NO were largely regulated independently. Multiple NADH dehydrogenases, transcription factors of unknown function and genes for iron uptake were differentially expressed in response to electron acceptor availability or nitrosative stress. Amongst many fascinating problems for future research, the data revealed a YtfE orthologue, Ddes_1165, that is implicated in the repair of nitrosative damage. The combined data suggest that three transcription factors coordinate this regulation in which NrfS-NrfR coordinates nitrate and nitrite reduction to minimize toxicity due to nitrite accumulation, HcpR1 serves a global role in regulating the response to nitrate, and HcpR2 regulates the response to nitrosative stress.
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Affiliation(s)
- Ian T Cadby
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Matthew Faulkner
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
- The Institute of Integrative Biology, Bioscience building, University of Liverpool, Liverpool, Merseyside, L69 7ZB, UK
| | - Jeanne Cheneby
- Aix Marseille Univ, INSERM, TAGC, UMR_S 1090, 163, Avenue de Luminy, 13288, Marseille, France
| | - Justine Long
- Aix Marseille Univ, INSERM, TAGC, UMR_S 1090, 163, Avenue de Luminy, 13288, Marseille, France
| | - Jacques van Helden
- Aix Marseille Univ, INSERM, TAGC, UMR_S 1090, 163, Avenue de Luminy, 13288, Marseille, France
| | - Alain Dolla
- Aix Marseille Univ, CNRS, LCB, Marseille, France
| | - Jeffrey A Cole
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
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16
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Sousa JR, Silveira CM, Fontes P, Roma-Rodrigues C, Fernandes AR, Van Driessche G, Devreese B, Moura I, Moura JJ, Almeida MG. Understanding the response of Desulfovibrio desulfuricans ATCC 27774 to the electron acceptors nitrate and sulfate - biosynthetic costs modulate substrate selection. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1455-1469. [DOI: 10.1016/j.bbapap.2017.07.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/12/2017] [Accepted: 07/21/2017] [Indexed: 11/27/2022]
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