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Tabares M, Kashefi K, Reguera G. Adaptive responses of Trichlorobacter lovleyi to nitrite detoxification reveal overlooked contributions of Geobacterales to nitrate ammonification. THE ISME JOURNAL 2025; 19:wraf054. [PMID: 40101204 PMCID: PMC11972089 DOI: 10.1093/ismejo/wraf054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Revised: 01/20/2025] [Accepted: 03/17/2025] [Indexed: 03/20/2025]
Abstract
Poorly understood microorganisms "short-circuit" the nitrogen cycle via the dissimilatory nitrate reduction to ammonium to retain the element in agricultural lands and stimulate crop productivity. The prevalence of Geobacterales closely related to Trichlorobacter lovleyi in nitrate ammonification hotspots motivated us to investigate adaptive responses contributing to ammonification rates in the laboratory type strain T. lovleyi SZ. Here, we describe the identification of tightly regulated pathways for efficient nitrate foraging and respiration with acetate, an important intermediate of organic matter degradation that Geobacterales efficiently assimilate and oxidize. Challenging the established dogma that high carbon/nitrate ratios stimulate the reduction of nitrate to ammonium, T. lovleyi doubled rapidly across a wide range of ratios provided nitrate concentrations were low enough to prevent the accumulation of the toxic nitrite intermediate. Yet, excess electrons during hydrogenotrophic growth alleviated nitrite toxicity and stimulated the reduction of nitrate to ammonium even under conditions of severe acetate limitation. These findings underscore the importance of nitrite toxicity in the ammonification of nitrate by Geobacterales and provide much needed mechanistic understanding of microbial adaptations contributing to soil nitrogen conservation. This information is critical to enhance the predictive value of genomic-based traits in environmental surveys and to guide strategies for sustainable management of nitrogen fertilization as well as mitigation of green-house emissions and agrochemical leaching from agricultural lands.
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Affiliation(s)
- Marcela Tabares
- Department of Microbiology, Genetics & Immunology, Michigan State University, East Lansing, MI 48824, United States
| | - Kazem Kashefi
- Department of Microbiology, Genetics & Immunology, Michigan State University, East Lansing, MI 48824, United States
| | - Gemma Reguera
- Department of Microbiology, Genetics & Immunology, Michigan State University, East Lansing, MI 48824, United States
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Sánchez-Osuna M, Cortés P, Lee M, Smith AT, Barbé J, Erill I. Non-canonical LexA proteins regulate the SOS response in the Bacteroidetes. Nucleic Acids Res 2021; 49:11050-11066. [PMID: 34614190 PMCID: PMC8565304 DOI: 10.1093/nar/gkab773] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/18/2021] [Accepted: 10/04/2021] [Indexed: 02/07/2023] Open
Abstract
Lesions to DNA compromise chromosome integrity, posing a direct threat to cell survival. The bacterial SOS response is a widespread transcriptional regulatory mechanism to address DNA damage. This response is coordinated by the LexA transcriptional repressor, which controls genes involved in DNA repair, mutagenesis and cell-cycle control. To date, the SOS response has been characterized in most major bacterial groups, with the notable exception of the Bacteroidetes. No LexA homologs had been identified in this large, diverse and ecologically important phylum, suggesting that it lacked an inducible mechanism to address DNA damage. Here, we report the identification of a novel family of transcriptional repressors in the Bacteroidetes that orchestrate a canonical response to DNA damage in this phylum. These proteins belong to the S24 peptidase family, but are structurally different from LexA. Their N-terminal domain is most closely related to CI-type bacteriophage repressors, suggesting that they may have originated from phage lytic phase repressors. Given their role as SOS regulators, however, we propose to designate them as non-canonical LexA proteins. The identification of a new class of repressors orchestrating the SOS response illuminates long-standing questions regarding the origin and plasticity of this transcriptional network.
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Affiliation(s)
- Miquel Sánchez-Osuna
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08192 Bellaterra, Spain
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08192 Bellaterra, Spain
| | - Mark Lee
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Aaron T Smith
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Jordi Barbé
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08192 Bellaterra, Spain
| | - Ivan Erill
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08192 Bellaterra, Spain.,Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA
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Timinskas K, Venclovas Č. New insights into the structures and interactions of bacterial Y-family DNA polymerases. Nucleic Acids Res 2019; 47:4393-4405. [PMID: 30916324 PMCID: PMC6511836 DOI: 10.1093/nar/gkz198] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/09/2019] [Accepted: 03/19/2019] [Indexed: 11/15/2022] Open
Abstract
Bacterial Y-family DNA polymerases are usually classified into DinB (Pol IV), UmuC (the catalytic subunit of Pol V) and ImuB, a catalytically dead essential component of the ImuA-ImuB-DnaE2 mutasome. However, the true diversity of Y-family polymerases is unknown. Furthermore, for most of them the structures are unavailable and interactions are poorly characterized. To gain a better understanding of bacterial Y-family DNA polymerases, we performed a detailed computational study. It revealed substantial diversity, far exceeding traditional classification. We found that a large number of subfamilies feature a C-terminal extension next to the common Y-family region. Unexpectedly, in most C-terminal extensions we identified a region homologous to the N-terminal oligomerization motif of RecA. This finding implies a universal mode of interaction between Y-family members and RecA (or ImuA), in the case of Pol V strongly supported by experimental data. In gram-positive bacteria, we identified a putative Pol V counterpart composed of a Y-family polymerase, a YolD homolog and RecA. We also found ImuA-ImuB-DnaE2 variants lacking ImuA, but retaining active or inactive Y-family polymerase, a standalone ImuB C-terminal domain and/or DnaE2. In summary, our analyses revealed that, despite considerable diversity, bacterial Y-family polymerases share previously unanticipated similarities in their structural domains/motifs and interactions.
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Affiliation(s)
- Kęstutis Timinskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Česlovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
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Abstract
The family Geobacteraceae, with its only valid genus Geobacter, comprises deltaproteobacteria ubiquitous in soil, sediments, and subsurface environments where metal reduction is an active process. Research for almost three decades has provided novel insights into environmental processes and biogeochemical reactions not previously known to be carried out by microorganisms. At the heart of the environmental roles played by Geobacter bacteria is their ability to integrate redox pathways and regulatory checkpoints that maximize growth efficiency with electron donors derived from the decomposition of organic matter while respiring metal oxides, particularly the often abundant oxides of ferric iron. This metabolic specialization is complemented by versatile metabolic reactions, respiratory chains, and sensory networks that allow specific members to adaptively respond to environmental cues to integrate organic and inorganic contaminants in their oxidative and reductive metabolism, respectively. Thus, Geobacteraceae are important members of the microbial communities that degrade hydrocarbon contaminants under iron-reducing conditions and that contribute, directly or indirectly, to the reduction of radionuclides, toxic metals, and oxidized species of nitrogen. Their ability to produce conductive pili as nanowires for discharging respiratory electrons to solid-phase electron acceptors and radionuclides, or for wiring cells in current-harvesting biofilms highlights the unique physiological traits that make these organisms attractive biological platforms for bioremediation, bioenergy, and bioelectronics application. Here we review some of the most notable physiological features described in Geobacter species since the first model representatives were recovered in pure culture. We provide a historical account of the environmental research that has set the foundation for numerous physiological studies and the laboratory tools that had provided novel insights into the role of Geobacter in the functioning of microbial communities from pristine and contaminated environments. We pay particular attention to latest research, both basic and applied, that has served to expand the field into new directions and to advance interdisciplinary knowledge. The electrifying physiology of Geobacter, it seems, is alive and well 30 years on.
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Wang Y, Pan Y, Zhu T, Wang A, Lu Y, Lv L, Zhang K, Li Z. Enhanced performance and microbial community analysis of bioelectrochemical system integrated with bio-contact oxidation reactor for treatment of wastewater containing azo dye. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 634:616-627. [PMID: 29635204 DOI: 10.1016/j.scitotenv.2018.03.346] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 03/27/2018] [Accepted: 03/28/2018] [Indexed: 06/08/2023]
Abstract
Feasibility and superiority of the bioelectrochemical system integrated with biocontact oxidation (BES-BCO) for degradation and/or mineralization of azo dyes have been confirmed. In this study, the effects of hydraulic retention time (HRT), applied voltage, and dissolved oxygen (DO) concentration at the bioanode on the performance of BES-BCO and traditional BES were investigated. Using the response surface methodology, the optimum values of HRT, applied voltage, and DO concentration at the bioanode of BES-BCO were investigated to obtain the maximum decolouration and COD removal efficiency and minimum specific energy consumption (SEC). The microbial community structure in BES-BCO was studied for analyzing the change following the introduction of oxygen. The optimised solution was an applied voltage of 0.59V, HRT of 12h, and DO concentration of 0.96mg/L at the bioanode. Under such conditions, the DE, COD removal efficiency, and SEC values were 94.62±0.63%, 89.12±0. 32%, and 687.57±3.86J/g, respectively. In addition, after changing from BES to BES-BCO, the bacterial community structure of the bioanode underwent significant changes. Several aerobic aniline-degrading bacteria and anode-respiration bacteria (ARB) were found to dominate the community of the anode biofilm. The results showed that the removal of azo dye degradation by-products was closely correlated with the o-bioanode and the BCO bacterial community structure.
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Affiliation(s)
- Youzhao Wang
- School of Mechanical Engineering and Automation, Northeastern University, Shenyang 110004, China
| | - Yuan Pan
- School of Mechanical Engineering and Automation, Northeastern University, Shenyang 110004, China.
| | - Tong Zhu
- School of Mechanical Engineering and Automation, Northeastern University, Shenyang 110004, China.
| | - Aijie Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yalun Lu
- School of Mechanical Engineering and Automation, Northeastern University, Shenyang 110004, China
| | - Liting Lv
- School of Mechanical Engineering and Automation, Northeastern University, Shenyang 110004, China
| | - Kuo Zhang
- School of Mechanical Engineering and Automation, Northeastern University, Shenyang 110004, China
| | - Zijun Li
- School of Mechanical Engineering and Automation, Northeastern University, Shenyang 110004, China
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Erill I, Campoy S, Kılıç S, Barbé J. The Verrucomicrobia LexA-Binding Motif: Insights into the Evolutionary Dynamics of the SOS Response. Front Mol Biosci 2016; 3:33. [PMID: 27489856 PMCID: PMC4951493 DOI: 10.3389/fmolb.2016.00033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 07/04/2016] [Indexed: 12/20/2022] Open
Abstract
The SOS response is the primary bacterial mechanism to address DNA damage, coordinating multiple cellular processes that include DNA repair, cell division, and translesion synthesis. In contrast to other regulatory systems, the composition of the SOS genetic network and the binding motif of its transcriptional repressor, LexA, have been shown to vary greatly across bacterial clades, making it an ideal system to study the co-evolution of transcription factors and their regulons. Leveraging comparative genomics approaches and prior knowledge on the core SOS regulon, here we define the binding motif of the Verrucomicrobia, a recently described phylum of emerging interest due to its association with eukaryotic hosts. Site directed mutagenesis of the Verrucomicrobium spinosum recA promoter confirms that LexA binds a 14 bp palindromic motif with consensus sequence TGTTC-N4-GAACA. Computational analyses suggest that recognition of this novel motif is determined primarily by changes in base-contacting residues of the third alpha helix of the LexA helix-turn-helix DNA binding motif. In conjunction with comparative genomics analysis of the LexA regulon in the Verrucomicrobia phylum, electrophoretic shift assays reveal that LexA binds to operators in the promoter region of DNA repair genes and a mutagenesis cassette in this organism, and identify previously unreported components of the SOS response. The identification of tandem LexA-binding sites generating instances of other LexA-binding motifs in the lexA gene promoter of Verrucomicrobia species leads us to postulate a novel mechanism for LexA-binding motif evolution. This model, based on gene duplication, successfully addresses outstanding questions in the intricate co-evolution of the LexA protein, its binding motif and the regulatory network it controls.
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Affiliation(s)
- Ivan Erill
- Erill Lab, Department of Biological Sciences, University of Maryland Baltimore County Baltimore, MD, USA
| | - Susana Campoy
- Unitat de Microbiologia, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona Barcelona, Spain
| | - Sefa Kılıç
- Erill Lab, Department of Biological Sciences, University of Maryland Baltimore County Baltimore, MD, USA
| | - Jordi Barbé
- Unitat de Microbiologia, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona Barcelona, Spain
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An SOS Regulon under Control of a Noncanonical LexA-Binding Motif in the Betaproteobacteria. J Bacteriol 2015; 197:2622-30. [PMID: 25986903 DOI: 10.1128/jb.00035-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 05/09/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The SOS response is a transcriptional regulatory network governed by the LexA repressor that activates in response to DNA damage. In the Betaproteobacteria, LexA is known to target a palindromic sequence with the consensus sequence CTGT-N8-ACAG. We report the characterization of a LexA regulon in the iron-oxidizing betaproteobacterium Sideroxydans lithotrophicus. In silico and in vitro analyses show that LexA targets six genes by recognizing a binding motif with the consensus sequence GAACGaaCGTTC, which is strongly reminiscent of the Bacillus subtilis LexA-binding motif. We confirm that the closely related Gallionella capsiferriformans shares the same LexA-binding motif, and in silico analyses indicate that this motif is also conserved in the Nitrosomonadales and the Methylophilales. Phylogenetic analysis of LexA and the alpha subunit of DNA polymerase III (DnaE) reveal that the organisms harboring this noncanonical LexA form a compact taxonomic cluster within the Betaproteobacteria. However, their lexA gene is unrelated to the standard Betaproteobacteria lexA, and there is evidence of its spread through lateral gene transfer. In contrast to other reported cases of noncanonical LexA-binding motifs, the regulon of S. lithotrophicus is comparable in size and function to that of many other Betaproteobacteria, suggesting that a convergent SOS regulon has reevolved under the control of a new LexA protein. Analysis of the DNA-binding domain of S. lithotrophicus LexA reveals little sequence similarity with that of other LexA proteins targeting similar binding motifs, suggesting that network structure may limit site evolution or that structural constrains make the B. subtilis-type motif an optimal interface for multiple LexA sequences. IMPORTANCE Understanding the evolution of transcriptional systems enables us to address important questions in microbiology, such as the emergence and transfer potential of different regulatory systems to regulate virulence or mediate responses to stress. The results reported here constitute the first characterization of a noncanonical LexA protein regulating a standard SOS regulon. This is significant because it illustrates how a complex transcriptional program can be put under the control of a novel transcriptional regulator. Our results also reveal a substantial degree of plasticity in the LexA recognition domain, raising intriguing questions about the space of protein-DNA interfaces and the specific evolutionary constrains faced by these elements.
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Hare JM, Ferrell JC, Witkowski TA, Grice AN. Prophage induction and differential RecA and UmuDAb transcriptome regulation in the DNA damage responses of Acinetobacter baumannii and Acinetobacter baylyi. PLoS One 2014; 9:e93861. [PMID: 24709747 PMCID: PMC3978071 DOI: 10.1371/journal.pone.0093861] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 03/08/2014] [Indexed: 11/21/2022] Open
Abstract
The SOS response to DNA damage that induces up to 10% of the prokaryotic genome requires RecA action to relieve LexA transcriptional repression. In Acinetobacter species, which lack LexA, the error-prone polymerase accessory UmuDAb is instead required for ddrR induction after DNA damage, suggesting it might be a LexA analog. RNA-Seq experiments defined the DNA damage transcriptome (mitomycin C-induced) of wild type, recA and umuDAb mutant strains of both A. baylyi ADP1 and A. baumannii ATCC 17978. Of the typical SOS response genes, few were differentially regulated in these species; many were repressed or absent. A striking 38.4% of all ADP1 genes, and 11.4% of all 17978 genes, were repressed under these conditions. In A. baylyi ADP1, 66 genes (2.0% of the genome), including a CRISPR/Cas system, were DNA damage-induced, and belonged to four regulons defined by differential use of recA and umuDAb. In A. baumannii ATCC 17978, however, induction of 99% of the 152 mitomycin C-induced genes depended on recA, and only 28 of these genes required umuDAb for their induction. 90% of the induced A. baumannii genes were clustered in three prophage regions, and bacteriophage particles were observed after mitomycin C treatment. These prophages encoded esvI, esvK1, and esvK2, ethanol-stimulated virulence genes previously identified in a Caenorhabditis elegans model, as well as error-prone polymerase alleles. The induction of all 17978 error-prone polymerase alleles, whether prophage-encoded or not, was recA dependent, but only these DNA polymerase V-related genes were de-repressed in the umuDAb mutant in the absence of DNA damage. These results suggest that both species possess a robust and complex DNA damage response involving both recA-dependent and recA-independent regulons, and further demonstrates that although umuDAb has a specialized role in repressing error-prone polymerases, additional regulators likely participate in these species' transcriptional response to DNA damage.
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Affiliation(s)
- Janelle M. Hare
- Department of Biology and Chemistry, Morehead State University, Morehead, Kentucky, United States of America
- * E-mail:
| | - Joshua C. Ferrell
- Department of Biology and Chemistry, Morehead State University, Morehead, Kentucky, United States of America
| | - Travis A. Witkowski
- Department of Biology and Chemistry, Morehead State University, Morehead, Kentucky, United States of America
| | - Alison N. Grice
- Department of Biology and Chemistry, Morehead State University, Morehead, Kentucky, United States of America
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Fonseca LS, da Silva JB, Milanez JS, Monteiro-Vitorello CB, Momo L, de Morais ZM, Vasconcellos SA, Marques MV, Ho PL, da Costa RMA. Leptospira interrogans serovar copenhageni harbors two lexA genes involved in SOS response. PLoS One 2013; 8:e76419. [PMID: 24098496 PMCID: PMC3789691 DOI: 10.1371/journal.pone.0076419] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 08/28/2013] [Indexed: 11/24/2022] Open
Abstract
Bacteria activate a regulatory network in response to the challenges imposed by DNA damage to genetic material, known as the SOS response. This system is regulated by the RecA recombinase and by the transcriptional repressor lexA. Leptospira interrogans is a pathogen capable of surviving in the environment for weeks, being exposed to a great variety of stress agents and yet retaining its ability to infect the host. This study aims to investigate the behavior of L. interrogans serovar Copenhageni after the stress induced by DNA damage. We show that L. interrogans serovar Copenhageni genome contains two genes encoding putative LexA proteins (lexA1 and lexA2) one of them being potentially acquired by lateral gene transfer. Both genes are induced after DNA damage, but the steady state levels of both LexA proteins drop, probably due to auto-proteolytic activity triggered in this condition. In addition, seven other genes were up-regulated following UV-C irradiation, recA, recN, dinP, and four genes encoding hypothetical proteins. This set of genes is potentially regulated by LexA1, as it showed binding to their promoter regions. All these regions contain degenerated sequences in relation to the previously described SOS box, TTTGN 5CAAA. On the other hand, LexA2 was able to bind to the palindrome TTGTAN10TACAA, found in its own promoter region, but not in the others. Therefore, the L. interrogans serovar Copenhageni SOS regulon may be even more complex, as a result of LexA1 and LexA2 binding to divergent motifs. New possibilities for DNA damage response in Leptospira are expected, with potential influence in other biological responses such as virulence.
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Affiliation(s)
- Luciane S Fonseca
- Centro de Biotecnologia, Instituto Butantan, São Paulo, Brazil ; Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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10
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Cambray G, Sanchez-Alberola N, Campoy S, Guerin É, Da Re S, González-Zorn B, Ploy MC, Barbé J, Mazel D, Erill I. Prevalence of SOS-mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons. Mob DNA 2011; 2:6. [PMID: 21529368 PMCID: PMC3108266 DOI: 10.1186/1759-8753-2-6] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 04/30/2011] [Indexed: 11/26/2022] Open
Abstract
Background Integrons are found in hundreds of environmental bacterial species, but are mainly known as the agents responsible for the capture and spread of antibiotic-resistance determinants between Gram-negative pathogens. The SOS response is a regulatory network under control of the repressor protein LexA targeted at addressing DNA damage, thus promoting genetic variation in times of stress. We recently reported a direct link between the SOS response and the expression of integron integrases in Vibrio cholerae and a plasmid-borne class 1 mobile integron. SOS regulation enhances cassette swapping and capture in stressful conditions, while freezing the integron in steady environments. We conducted a systematic study of available integron integrase promoter sequences to analyze the extent of this relationship across the Bacteria domain. Results Our results showed that LexA controls the expression of a large fraction of integron integrases by binding to Escherichia coli-like LexA binding sites. In addition, the results provide experimental validation of LexA control of the integrase gene for another Vibrio chromosomal integron and for a multiresistance plasmid harboring two integrons. There was a significant correlation between lack of LexA control and predicted inactivation of integrase genes, even though experimental evidence also indicates that LexA regulation may be lost to enhance expression of integron cassettes. Conclusions Ancestral-state reconstruction on an integron integrase phylogeny led us to conclude that the ancestral integron was already regulated by LexA. The data also indicated that SOS regulation has been actively preserved in mobile integrons and large chromosomal integrons, suggesting that unregulated integrase activity is selected against. Nonetheless, additional adaptations have probably arisen to cope with unregulated integrase activity. Identifying them may be fundamental in deciphering the uneven distribution of integrons in the Bacteria domain.
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Affiliation(s)
- Guillaume Cambray
- Institut Pasteur, Unité Plasticité du Génome Bactérien, CNRS URA 2171, 75015 Paris, France
| | - Neus Sanchez-Alberola
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.,Department of Biological Sciences, University of Maryland Baltimore County, Baltimore 21228, USA
| | - Susana Campoy
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Émilie Guerin
- Université de Limoges, Faculté de Médecine, EA3175, INSERM, Equipe Avenir, Limoges 87000, France
| | - Sandra Da Re
- Université de Limoges, Faculté de Médecine, EA3175, INSERM, Equipe Avenir, Limoges 87000, France
| | - Bruno González-Zorn
- Departamento de Sanidad Animal, Facultad de Veterinaria, and VISAVET, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Marie-Cécile Ploy
- Université de Limoges, Faculté de Médecine, EA3175, INSERM, Equipe Avenir, Limoges 87000, France
| | - Jordi Barbé
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore 21228, USA
| | - Didier Mazel
- Institut Pasteur, Unité Plasticité du Génome Bactérien, CNRS URA 2171, 75015 Paris, France
| | - Ivan Erill
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore 21228, USA
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11
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Lovley DR, Ueki T, Zhang T, Malvankar NS, Shrestha PM, Flanagan KA, Aklujkar M, Butler JE, Giloteaux L, Rotaru AE, Holmes DE, Franks AE, Orellana R, Risso C, Nevin KP. Geobacter: the microbe electric's physiology, ecology, and practical applications. Adv Microb Physiol 2011; 59:1-100. [PMID: 22114840 DOI: 10.1016/b978-0-12-387661-4.00004-5] [Citation(s) in RCA: 412] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Geobacter species specialize in making electrical contacts with extracellular electron acceptors and other organisms. This permits Geobacter species to fill important niches in a diversity of anaerobic environments. Geobacter species appear to be the primary agents for coupling the oxidation of organic compounds to the reduction of insoluble Fe(III) and Mn(IV) oxides in many soils and sediments, a process of global biogeochemical significance. Some Geobacter species can anaerobically oxidize aromatic hydrocarbons and play an important role in aromatic hydrocarbon removal from contaminated aquifers. The ability of Geobacter species to reductively precipitate uranium and related contaminants has led to the development of bioremediation strategies for contaminated environments. Geobacter species produce higher current densities than any other known organism in microbial fuel cells and are common colonizers of electrodes harvesting electricity from organic wastes and aquatic sediments. Direct interspecies electron exchange between Geobacter species and syntrophic partners appears to be an important process in anaerobic wastewater digesters. Functional and comparative genomic studies have begun to reveal important aspects of Geobacter physiology and regulation, but much remains unexplored. Quantifying key gene transcripts and proteins of subsurface Geobacter communities has proven to be a powerful approach to diagnose the in situ physiological status of Geobacter species during groundwater bioremediation. The growth and activity of Geobacter species in the subsurface and their biogeochemical impact under different environmental conditions can be predicted with a systems biology approach in which genome-scale metabolic models are coupled with appropriate physical/chemical models. The proficiency of Geobacter species in transferring electrons to insoluble minerals, electrodes, and possibly other microorganisms can be attributed to their unique "microbial nanowires," pili that conduct electrons along their length with metallic-like conductivity. Surprisingly, the abundant c-type cytochromes of Geobacter species do not contribute to this long-range electron transport, but cytochromes are important for making the terminal electrical connections with Fe(III) oxides and electrodes and also function as capacitors, storing charge to permit continued respiration when extracellular electron acceptors are temporarily unavailable. The high conductivity of Geobacter pili and biofilms and the ability of biofilms to function as supercapacitors are novel properties that might contribute to the field of bioelectronics. The study of Geobacter species has revealed a remarkable number of microbial physiological properties that had not previously been described in any microorganism. Further investigation of these environmentally relevant and physiologically unique organisms is warranted.
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Affiliation(s)
- Derek R Lovley
- Department of Microbiology and Environmental Biotechnology Center, University of Massachusetts, Amherst, Massachusetts, USA
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12
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Qu Y, Brown P, Barbe JF, Puljic M, Merino E, Adkins RM, Lovley DR, Krushkal J. GSEL Version 2, an Online Genome-Wide Query System of Operon Organization and Regulatory Sequence Elements of Geobacter sulfurreducens. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2009; 13:439-49. [DOI: 10.1089/omi.2009.0081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Yanhua Qu
- Department of Preventive Medicine, The University of Tennessee Health Science Center, Memphis, Tennessee
| | - Peter Brown
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts
| | - Jose F. Barbe
- Department of Preventive Medicine, The University of Tennessee Health Science Center, Memphis, Tennessee
| | - Marko Puljic
- Department of Preventive Medicine, The University of Tennessee Health Science Center, Memphis, Tennessee
- Department of Mathematical Sciences, University of Memphis, Memphis, Tennessee
| | - Enrique Merino
- Department of Pediatrics, The University of Tennessee Health Science Center, Memphis, Tennessee
| | - Ronald M. Adkins
- Department of Molecular Microbiology, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Morelos, México
| | - Derek R. Lovley
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts
| | - Julia Krushkal
- Department of Preventive Medicine, The University of Tennessee Health Science Center, Memphis, Tennessee
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13
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Yang MK, Hsu CH, Sung VL. Analyses of binding sequences of the two LexA proteins of Xanthomonas axonopodis pathovar citri. Mol Genet Genomics 2008; 280:49-58. [PMID: 18437426 DOI: 10.1007/s00438-008-0344-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Accepted: 04/07/2008] [Indexed: 10/22/2022]
Abstract
Xanthomonas axonopodis pv. citri (X. axonopodis pv. citri) possesses two lexA genes, designated lexA1 and lexA2. Electrophoretic mobility shift data show that LexA1 binds to both lexA1 and lexA2 promoters, but LexA2 does not bind to the lexA1 promoter, suggesting that LexA1 and LexA2 play different roles in regulating the expression of SOS genes. In this study, we have determined that LexA2 binds to a 14-bp dyad-spacer-dyad palindromic sequence, 5'-TGTACAAATGTACA-3', located at nucleotides -41 to -28 relative to the translation start site of lexA2 of X. axonopodis pv. citri. The two spacer nucleotides in this sequence can be changed from AA to TT without affecting LexA2 binding; all other base deletions or substitutions abolish LexA2 binding. The LexA1 binding sequence in the promoter region of lexA2 is TTAGTACTAAAGTTATAA and is located at -133 to -116, and that in the lexA1 gene is AGTAGTAATACTACT located at nucleotides -19 to -5 relative to the translation start site of lexA1. Any base change in the latter sequence abolishes LexA1 binding.
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Affiliation(s)
- Mei-Kwei Yang
- Department of Life Science, Fu Jen University, 510 Chun-Chen Road, Taipei 242, Taiwan, ROC.
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14
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Mahadevan R, Yan B, Postier B, Nevin KP, Woodard TL, O'Neil R, Coppi MV, Methé BA, Krushkal J. Characterizing Regulation of Metabolism inGeobacter sulfurreducensthrough Genome-Wide Expression Data and Sequence Analysis. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2008; 12:33-59. [DOI: 10.1089/omi.2007.0043] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Radhakrishnan Mahadevan
- Department of Chemical Engineering & Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts
| | - Bin Yan
- Department of Preventive Medicine, University of Tennessee Health Science Center, 66 Memphis, Tennessee
| | - Brad Postier
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts
| | - Kelly P. Nevin
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts
| | - Trevor L. Woodard
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts
| | - Regina O'Neil
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts
| | - Maddalena V. Coppi
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts
| | | | - Julia Krushkal
- Department of Preventive Medicine, University of Tennessee Health Science Center, 66 Memphis, Tennessee
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15
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Abstract
The SOS regulon is a paradigm of bacterial responses to DNA damage. A wide variety of bacterial species possess homologs of lexA and recA, the central players in the regulation of the SOS circuit. Nevertheless, the genes actually regulated by the SOS have been determined only experimentally in a few bacterial species. In this work, we describe 37 genes regulated in a LexA-dependent manner in the alphaproteobacterium Caulobacter crescentus. In agreement with previous results, we have found that the direct repeat GTTCN7GTTC is the SOS operator of C. crescentus, which was confirmed by site-directed mutagenesis studies of the imuA promoter. Several potential promoter regions containing the SOS operator were identified in the genome, and the expression of the corresponding genes was analyzed for both the wild type and the lexA strain, demonstrating that the vast majority of these genes are indeed SOS regulated. Interestingly, many of these genes encode proteins with unknown functions, revealing the potential of this approach for the discovery of novel genes involved in cellular responses to DNA damage in prokaryotes, and illustrating the diversity of SOS-regulated genes among different bacterial species.
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16
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Erill I, Campoy S, Barbé J. Aeons of distress: an evolutionary perspective on the bacterial SOS response. FEMS Microbiol Rev 2007; 31:637-56. [PMID: 17883408 DOI: 10.1111/j.1574-6976.2007.00082.x] [Citation(s) in RCA: 252] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The SOS response of bacteria is a global regulatory network targeted at addressing DNA damage. Governed by the products of the lexA and recA genes, it co-ordinates a comprehensive response against DNA lesions and its description in Escherichia coli has stood for years as a textbook paradigm of stress-response systems in bacteria. In this paper we review the current state of research on the SOS response outside E. coli. By retracing research on the identification of multiple diverging LexA-binding motifs across the Bacteria Domain, we show how this work has led to the description of a minimum regulon core, but also of a heterogeneous collection of SOS regulatory networks that challenges many tenets of the E. coli model. We also review recent attempts at reconstructing the evolutionary history of the SOS network that have cast new light on the SOS response. Exploiting the newly gained knowledge on LexA-binding motifs and the tight association of LexA with a recently described mutagenesis cassette, these works put forward likely evolutionary scenarios for the SOS response, and we discuss their relevance on the ultimate nature of this stress-response system and the evolutionary pressures driving its evolution.
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Affiliation(s)
- Ivan Erill
- Biomedical Applications Group, Centro Nacional de Microelectrónica, Barcelona, Spain
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17
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Abstract
In contrast to the vast majority of the members of the domain Bacteria, several Pseudomonas and Xanthomonas species have two lexA genes, whose products have been shown to recognize different LexA binding motifs, making them an interesting target for studying the interplay between cohabiting LexA regulons in a single species. Here we report an analysis of the genetic composition of the two LexA regulons of Pseudomonas putida KT2440 performed with a genomic microarray. The data obtained indicate that one of the two LexA proteins (LexA1) seems to be in control of the conventional Escherichia coli-like SOS response, while the other LexA protein (LexA2) regulates only its own transcriptional unit, which includes the imuA, imuB, and dnaE2 genes, and a gene (PP_3901) from a resident P. putida prophage. Furthermore, PP_3901 is also regulated by LexA1 and is required for DNA damage-mediated induction of several P. putida resident prophage genes. In silico searches suggested that this marked asymmetry in regulon contents also occurs in other Pseudomonas species with two lexA genes, and the implications of this asymmetry in the evolution of the SOS network are discussed.
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18
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Yan B, Lovley DR, Krushkal J. Genome-wide similarity search for transcription factors and their binding sites in a metal-reducing prokaryote Geobacter sulfurreducens. Biosystems 2006; 90:421-41. [PMID: 17184904 DOI: 10.1016/j.biosystems.2006.10.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2006] [Revised: 09/21/2006] [Accepted: 10/20/2006] [Indexed: 12/26/2022]
Abstract
The knowledge obtained from understanding individual elements involved in gene regulation is important for reconstructing gene regulatory networks, a key for understanding cellular behavior. To study gene regulatory interactions in a model microorganism, Geobacter sulfurreducens, which participates in metal reduction and energy harvesting, we investigated the presence of 59 known Escherichia coli transcription factors and predicted transcription regulatory sites in its genome. The supplementary material, available at http://www.geobacter.org/research/genomescan/, provides the results of similarity comparisons that identified regulatory proteins of G. sulfurreducens and the genome locations of the predicted regulatory sites, including the list of putative regulatory elements in the upstream regions of every predicted operon and singleton open reading frame. Regulatory sequence elements, predicted using genome similarity searches to matrices of established transcription regulatory elements from E. coli, provide an initial insight into regulation of genes and operons in G. sulfurreducens. The predicted regulatory elements were predominantly located in the upstream regions of operons and singleton open reading frames. The validity of the predictions was examined using a permutation approach. Sequence similarity searches indicate that E. coli transcription factors ArgR, CytR, DeoR, FlhCD (both FlhC and FlhD subunits), FruR, GalR, GlpR, H-NS, LacI, MetJ, PurR, TrpR, and Tus are likely missing from G. sulfurreducens. Phylogenetic analysis suggests that one HU subunit is present in G. sulfurreducens as compared to two subunits in E. coli, while each of the two E. coli IHF subunits, HimA and HimD, have two homologs in G. sulfurreducens. The closest homolog of E. coli RpoE in G. sulfurreducens may be more similar to FecI than to RpoE. These findings represent the first step in the understanding of the regulatory relationships in G. sulfurreducens on the genome scale.
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Affiliation(s)
- Bin Yan
- Department of Preventive Medicine, University of Tennessee Health Science Center, 66 N. Pauline St., Ste. 633, Memphis, TN 38163, USA
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19
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Holmes DE, Chaudhuri SK, Nevin KP, Mehta T, Methé BA, Liu A, Ward JE, Woodard TL, Webster J, Lovley DR. Microarray and genetic analysis of electron transfer to electrodes in Geobacter sulfurreducens. Environ Microbiol 2006; 8:1805-15. [PMID: 16958761 DOI: 10.1111/j.1462-2920.2006.01065.x] [Citation(s) in RCA: 217] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Whole-genome analysis of gene expression in Geobacter sulfurreducens revealed 474 genes with transcript levels that were significantly different during growth with an electrode as the sole electron acceptor versus growth on Fe(III) citrate. The greatest response was a more than 19-fold increase in transcript levels for omcS, which encodes an outer-membrane cytochrome previously shown to be required for Fe(III) oxide reduction. Quantitative reverse transcription polymerase chain reaction and Northern analyses confirmed the higher levels of omcS transcripts, which increased as power production increased. Deletion of omcS inhibited current production that was restored when omcS was expressed in trans. Transcript expression and genetic analysis suggested that OmcE, another outer-membrane cytochrome, is also involved in electron transfer to electrodes. Surprisingly, genes for other proteins known to be important in Fe(III) reduction such as the outer-membrane c-type cytochrome, OmcB, and the electrically conductive pilin "nanowires" did not have higher transcript levels on electrodes, and deletion of the relevant genes did not inhibit power production. Changes in the transcriptome suggested that cells growing on electrodes were subjected to less oxidative stress than cells growing on Fe(III) citrate and that a number of genes annotated as encoding metal efflux proteins or proteins of unknown function may be important for growth on electrodes. These results demonstrate for the first time that it is possible to evaluate gene expression, and hence the metabolic state, of microorganisms growing on electrodes on a genome-wide basis and suggest that OmcS, and to a lesser extent OmcE, are important in electron transfer to electrodes. This has important implications for the design of electrode materials and the genetic engineering of microorganisms to improve the function of microbial fuel cells.
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Affiliation(s)
- Dawn E Holmes
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA.
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20
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Hare JM, Perkins SN, Gregg-Jolly LA. A constitutively expressed, truncated umuDC operon regulates the recA-dependent DNA damage induction of a gene in Acinetobacter baylyi strain ADP1. Appl Environ Microbiol 2006; 72:4036-43. [PMID: 16751513 PMCID: PMC1489636 DOI: 10.1128/aem.02774-05] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2005] [Accepted: 02/28/2006] [Indexed: 11/20/2022] Open
Abstract
In response to environmentally caused DNA damage, SOS genes are up-regulated due to RecA-mediated relief of LexA repression. In Escherichia coli, the SOS umuDC operon is required for DNA damage checkpoint functions and for replicating damaged DNA in the error-prone process called SOS mutagenesis. In the model soil bacterium Acinetobacter baylyi strain ADP1, however, the content, regulation, and function of the umuDC operon are unusual. The umuC gene is incomplete, and a remnant of an ISEhe3-like transposase has replaced the middle 57% of the umuC coding region. The umuD open reading frame is intact, but it is 1.5 times the size of other umuD genes and has an extra 5' region that lacks homology to known umuD genes. Analysis of a umuD::lacZ fusion showed that umuD was expressed at very high levels in both the absence and presence of mitomycin C and that this expression was not affected in a recA-deficient background. The umuD mutation did not affect the growth rate or survival after UV-induced DNA damage. However, the UmuD-like protein found in ADP1 (UmuDAb) was required for induction of an adjacent DNA damage-inducible gene, ddrR. The umuD mutation specifically reduced the DNA damage induction of the RecA-dependent DNA damage-inducible ddrR locus by 83% (from 12.9-fold to 2.3-fold induction), but it did not affect the 33.9-fold induction of benA, an unrelated benzoate degradation gene. These data suggest that the response of the ADP1 umuDC operon to DNA damage is unusual and that UmuDAb specifically regulates the expression of at least one DNA damage-inducible gene.
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Affiliation(s)
- Janelle M Hare
- Department of Biological & Environmental Sciences, 327-G Lappin Hall, Morehead State University, Morehead, KY 40351, USA.
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21
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Fredrickson JK, Romine MF. Genome-assisted analysis of dissimilatory metal-reducing bacteria. Curr Opin Biotechnol 2005; 16:269-74. [PMID: 15961027 DOI: 10.1016/j.copbio.2005.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Revised: 03/20/2005] [Accepted: 04/04/2005] [Indexed: 10/25/2022]
Abstract
The availability of whole genome sequences for Shewanella oneidensis and Geobacter sulfurreducens has provided numerous new biological insights into the function of these model dissimilatory metal-reducing bacteria. Many of these findings, including the identification of a high number of c-type cytochromes in both organisms, have resulted from comparative genomic analyses, and several have been experimentally confirmed. These genome sequences have also aided the identification of genes important for the reduction of metal ions and other electron acceptors utilized during anaerobic growth, by facilitating the identification of genes disrupted by random insertions. Technologies for assaying global expression patterns for genes and proteins have also been employed, but their application has been limited mainly to the analysis of the role of global regulatory genes and to identifying genes expressed or repressed in response to specific electron acceptors. It is anticipated that details of the mechanisms of metal ion respiration, and metabolism in general, will eventually be revealed by comprehensive, systems-level analyses enabled by functional genomics data.
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Affiliation(s)
- James K Fredrickson
- Pacific Northwest National Laboratory, PO Box 999, Richland, Washington 99352, USA.
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22
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Yang MK, Su SR, Sung VL. Identification and characterization of a second lexA gene of Xanthomonas axonopodis Pathovar citri. Appl Environ Microbiol 2005; 71:3589-98. [PMID: 16000766 PMCID: PMC1169025 DOI: 10.1128/aem.71.7.3589-3598.2005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We previously identified and characterized a lexA gene from Xanthomonas axonopodis pv. citri. For this study, we cloned and expressed a lexA homologue from X. axonopodis pv. citri. This gene was designated lexA2, and the previously identified lexA gene was renamed lexA1. The coding region of lexA2 is 606 bp long and shares 59% nucleotide sequence identity with lexA1. Analyses of the deduced amino acid sequence revealed that LexA2 has structures that are characteristic of LexA proteins, including a helix-turn-helix DNA binding domain and conserved amino acid residues required for the autocleavage of LexA. The lexA2 mutant, which was constructed by gene replacement, was 4 orders of magnitude more resistant to the DNA-damaging agent mitomycin C at 0.1 microg/ml and 1 order of magnitude more resistant to another DNA-damaging agent, methylmethane sulfonate at 30 microg/ml, than the wild type. A lexA1 lexA2 double mutant had the same degree of susceptibility to mitomycin C as the lexA1 or lexA2 single mutant but was 1 order of magnitude more resistant to methylmethane sulfonate at 30 microg/ml than the lexA1 or lexA2 single mutant. These results suggest that LexA1 and LexA2 play different roles in regulating the production of methyltransferases that are required for repairing DNA damage caused by methylmethane sulfonate. A mitomycin C treatment also caused LexA2 to undergo autocleavage, as seen with LexA1. The results of electrophoresis mobility shift assays revealed that LexA2 does not bind the lexA1 promoter. It binds to both the lexA2 and recA promoters. However, neither LexA2 nor LexA1 appears to regulate recA expression, as lexA1, lexA2, and lexA1 lexA2 mutants did not become constitutive for recA transcription and RecA production. These results suggest that recA expression in X. axonopodis pv. citri is regulated by mechanisms that have yet to be identified.
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Affiliation(s)
- Mei-Kwei Yang
- Department of Life Science, Fu Jen University, 510 Chun-Chen Road, Taipei 242, Taiwan, Republic of China.
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23
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Cuñé J, Cullen P, Mazon G, Campoy S, Adler B, Barbe J. The Leptospira interrogans lexA gene is not autoregulated. J Bacteriol 2005; 187:5841-5. [PMID: 16077133 PMCID: PMC1196068 DOI: 10.1128/jb.187.16.5841-5845.2005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Footprinting and mutagenesis experiments demonstrated that Leptospira interrogans LexA binds the palindrome TTTGN(5)CAAA found in the recA promoter but not in the lexA promoter. In silico analysis revealed that none of the other canonical SOS genes is under direct control of LexA, making the leptospiral lexA gene the first described which is not autoregulated.
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Affiliation(s)
- Jordi Cuñé
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
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24
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Campoy S, Salvador N, Cortés P, Erill I, Barbé J. Expression of canonical SOS genes is not under LexA repression in Bdellovibrio bacteriovorus. J Bacteriol 2005; 187:5367-75. [PMID: 16030231 PMCID: PMC1196036 DOI: 10.1128/jb.187.15.5367-5375.2005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The here-reported identification of the LexA-binding sequence of Bdellovibrio bacteriovorus, a bacterial predator belonging to the delta-Proteobacteria, has made possible a detailed study of its LexA regulatory network. Surprisingly, only the lexA gene and a multiple gene cassette including dinP and dnaE homologues are regulated by the LexA protein in this bacterium. In vivo expression analyses have confirmed that this gene cassette indeed forms a polycistronic unit that, like the lexA gene, is DNA damage inducible in B. bacteriovorus. Conversely, genes such as recA, uvrA, ruvCAB, and ssb, which constitute the canonical core of the Proteobacteria SOS system, are not repressed by the LexA protein in this organism, hinting at a persistent selective pressure to maintain both the lexA gene and its regulation on the reported multiple gene cassette. In turn, in vitro experiments show that the B. bacteriovorus LexA-binding sequence is not recognized by other delta-Proteobacteria LexA proteins but binds to the cyanobacterial LexA repressor. This places B. bacteriovorus LexA at the base of the delta-Proteobacteria LexA family, revealing a high degree of conservation in the LexA regulatory sequence prior to the diversification and specialization seen in deeper groups of the Proteobacteria phylum.
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Affiliation(s)
- Susana Campoy
- Centre de Recerca en Sanitat Animal (CReSA), 08193 Bellaterra, Spain
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25
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Min B, Cheng S, Logan BE. Electricity generation using membrane and salt bridge microbial fuel cells. WATER RESEARCH 2005; 39:1675-86. [PMID: 15899266 DOI: 10.1016/j.watres.2005.02.002] [Citation(s) in RCA: 201] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2004] [Revised: 02/02/2005] [Indexed: 05/02/2023]
Abstract
Microbial fuel cells (MFCs) can be used to directly generate electricity from the oxidation of dissolved organic matter, but optimization of MFCs will require that we know more about the factors that can increase power output such as the type of proton exchange system which can affect the system internal resistance. Power output in a MFC containing a proton exchange membrane was compared using a pure culture (Geobacter metallireducens) or a mixed culture (wastewater inoculum). Power output with either inoculum was essentially the same, with 40+/-1mW/m2 for G. metallireducens and 38+/-1mW/m2 for the wastewater inoculum. We also examined power output in a MFC with a salt bridge instead of a membrane system. Power output by the salt bridge MFC (inoculated with G. metallireducens) was 2.2mW/m2. The low power output was directly attributed to the higher internal resistance of the salt bridge system (19920+/-50 Ohms) compared to that of the membrane system (1286+/-1Ohms) based on measurements using impedance spectroscopy. In both systems, it was observed that oxygen diffusion from the cathode chamber into the anode chamber was a factor in power generation. Nitrogen gas sparging, L-cysteine (a chemical oxygen scavenger), or suspended cells (biological oxygen scavenger) were used to limit the effects of gas diffusion into the anode chamber. Nitrogen gas sparging, for example, increased overall Coulombic efficiency (47% or 55%) compared to that obtained without gas sparging (19%). These results show that increasing power densities in MFCs will require reducing the internal resistance of the system, and that methods are needed to control the dissolved oxygen flux into the anode chamber in order to increase overall Coulombic efficiency.
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Affiliation(s)
- Booki Min
- Department of Civil and Environmental Engineering, The Pennsylvania State University, 212 Sackett Bld., University Park, PA, USA
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26
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Logan BE, Murano C, Scott K, Gray ND, Head IM. Electricity generation from cysteine in a microbial fuel cell. WATER RESEARCH 2005; 39:942-952. [PMID: 15743641 DOI: 10.1016/j.watres.2004.11.019] [Citation(s) in RCA: 190] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2004] [Revised: 10/18/2004] [Accepted: 11/22/2004] [Indexed: 05/24/2023]
Abstract
In a microbial fuel cell (MFC), power can be generated from the oxidation of organic matter by bacteria at the anode, with reduction of oxygen at the cathode. Proton exchange membranes used in MFCs are permeable to oxygen, resulting in the diffusion of oxygen into the anode chamber. This could either lower power generation by obligate anaerobes or result in the loss in electron donor from aerobic respiration by facultative or other aerobic bacteria. In order to maintain anaerobic conditions in conventional anaerobic laboratory cultures, chemical oxygen scavengers such as cysteine are commonly used. It is shown here that cysteine can serve as a substrate for electricity generation by bacteria in a MFC. A two-chamber MFC containing a proton exchange membrane was inoculated with an anaerobic marine sediment. Over a period of a few weeks, electricity generation gradually increased to a maximum power density of 19 mW/m(2) (700 or 1000 Omega resistor; 385 mg/L of cysteine). Power output increased to 39 mW/m(2) when cysteine concentrations were increased up to 770 mg/L (493 Omega resistor). The use of a more active cathode with Pt- or Pt-Ru, increased the maximum power from 19 to 33 mW/m(2) demonstrating that cathode efficiency limited power generation. Power was always immediately generated upon addition of fresh medium, but initial power levels consistently increased by ca. 30% during the first 24 h. Electron recovery as electricity was 14% based on complete cysteine oxidation, with an additional 14% (28% total) potentially lost to oxygen diffusion through the proton exchange membrane. 16S rRNA-based analysis of the biofilm on the anode of the MFC indicated that the predominant organisms were Shewanella spp. closely related to Shewanella affinis (37% of 16S rRNA gene sequences recovered in clone libraries).
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Affiliation(s)
- Bruce E Logan
- Department of Civil and Environmental Engineering, The Pennsylvania State University, 212 Sackett Bldg, University Park, PA 16802, USA.
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27
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Nahrstedt H, Schröder C, Meinhardt F. Evidence for two recA genes mediating DNA repair in Bacillus megaterium. Microbiology (Reading) 2005; 151:775-787. [PMID: 15758224 DOI: 10.1099/mic.0.27626-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Isolation and subsequent knockout of arecA-homologous gene inBacillus megateriumDSM 319 resulted in a mutant displaying increased sensitivity to mitomycin C. However, this mutant did not exhibit UV hypersensitivity, a finding which eventually led to identification of a second functionalrecAgene. Evidence forrecAduplicates was also obtained for two otherB. megateriumstrains. In agreement with potential DinR boxes located within their promoter regions, expression of both genes (recA1andrecA2) was found to be damage-inducible. Transcription from therecA2promoter was significantly higher than that ofrecA1. Since arecA2knockout could not be achieved, functional complementation studies were performed inEscherichia coli. Heterologous expression in a RecA null mutant resulted in increased survival after UV irradiation and mitomycin C treatment, proving bothrecAgene products to be functional in DNA repair. Thus, there is evidence for an SOS-like pathway inB. megateriumthat differs from that ofBacillus subtilis.
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Affiliation(s)
- Hannes Nahrstedt
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstraße 3, 48149 Münster, Germany
| | - Christine Schröder
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstraße 3, 48149 Münster, Germany
| | - Friedhelm Meinhardt
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstraße 3, 48149 Münster, Germany
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28
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Holmes DE, Nevin KP, Lovley DR. In situ expression of nifD in Geobacteraceae in subsurface sediments. Appl Environ Microbiol 2005; 70:7251-9. [PMID: 15574924 PMCID: PMC535187 DOI: 10.1128/aem.70.12.7251-7259.2004] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In order to determine whether the metabolic state of Geobacteraceae involved in bioremediation of subsurface sediments might be inferred from levels of mRNA for key genes, in situ expression of nifD, a highly conserved gene involved in nitrogen fixation, was investigated. When Geobacter sulfurreducens was grown without a source of fixed nitrogen in chemostats with acetate provided as the limiting electron donor and Fe(III) as the electron acceptor, levels of nifD transcripts were 4 to 5 orders of magnitude higher than in chemostat cultures provided with ammonium. In contrast, the number of transcripts of recA and the 16S rRNA gene were slightly lower in the absence of ammonium. The addition of acetate to organic- and nitrogen-poor subsurface sediments stimulated the growth of Geobacteraceae and Fe(III) reduction, as well as the expression of nifD in Geobacteraceae. Levels of nifD transcripts in Geobacteraceae decreased more than 100-fold within 2 days after the addition of 100 microM ammonium, while levels of recA and total bacterial 16S rRNA in Geobacteraceae remained relatively constant. Ammonium amendments had no effect on rates of Fe(III) reduction in acetate-amended sediments or toluene degradation in petroleum-contaminated sediments, suggesting that other factors, such as the rate that Geobacteraceae could access Fe(III) oxides, limited Fe(III) reduction. These results demonstrate that it is possible to monitor one aspect of the in situ metabolic state of Geobacteraceae species in subsurface sediments via analysis of mRNA levels, which is the first step toward a more global analysis of in situ gene expression related to nutrient status and stress response during bioremediation by Geobacteraceae.
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Affiliation(s)
- Dawn E Holmes
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA.
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Abella M, Erill I, Jara M, Mazón G, Campoy S, Barbé J. Widespread distribution of a lexA-regulated DNA damage-inducible multiple gene cassette in the Proteobacteria phylum. Mol Microbiol 2004; 54:212-22. [PMID: 15458417 DOI: 10.1111/j.1365-2958.2004.04260.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The SOS response comprises a set of cellular functions aimed at preserving bacterial cell viability in front of DNA injuries. The SOS network, negatively regulated by the LexA protein, is found in many bacterial species that have not suffered major reductions in their gene contents, but presents distinctly divergent LexA-binding sites across the Bacteria domain. In this article, we report the identification and characterization of an imported multiple gene cassette in the Gamma Proteobacterium Pseudomonas putida that encodes a LexA protein, an inhibitor of cell division (SulA), an error-prone polymerase (DinP) and the alpha subunit of DNA polymerase III (DnaE). We also demonstrate that these genes constitute a DNA damage-inducible operon that is regulated by its own encoded LexA protein, and we establish that the latter is a direct derivative of the Gram-positive LexA protein. In addition, in silico analyses reveal that this multiple gene cassette is also present in many Proteobacteria families, and that both its gene content and LexA-binding sequence have evolved over time, ultimately giving rise to the lexA lineage of extant Gamma Proteobacteria.
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Affiliation(s)
- Marc Abella
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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Mazón G, Lucena JM, Campoy S, Fernández de Henestrosa AR, Candau P, Barbé J. LexA-binding sequences in Gram-positive and cyanobacteria are closely related. Mol Genet Genomics 2003; 271:40-9. [PMID: 14652736 DOI: 10.1007/s00438-003-0952-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2003] [Accepted: 10/29/2003] [Indexed: 10/26/2022]
Abstract
The lexA gene of the cyanobacterium Anabaena sp. strain PCC7120 has been cloned by PCR amplification with primers designed after TBLASTN analysis of its genome sequence using the Escherichia coli LexA sequence as a probe. After over-expression in E. coli and subsequent purification, footprinting experiments demonstrated that the Anabaena LexA protein binds to the sequence TAGTACTAATGTTCTA, which is found upstream of its own coding gene. Directed mutagenesis and sequence comparison of promoters of other Anabaena genes, as well as those of several cyanobacteria, allowed us to define the motif RGTACNNNDGTWCB as the LexA box in this bacterial phylum. Substitution of a single nucleotide in this motif present in the Anabena lexA promoter is sufficient to enable it to bind the Bacillus subtilis LexA protein. These data indicate that Cyanobacteria and Gram-positive bacteria are phylogenetically closely related.
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Affiliation(s)
- G Mazón
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
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