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Ortiz-Medina JF, Poole MR, Grunden AM, Call DF. Nitrogen Fixation and Ammonium Assimilation Pathway Expression of Geobacter sulfurreducens Changes in Response to the Anode Potential in Microbial Electrochemical Cells. Appl Environ Microbiol 2023; 89:e0207322. [PMID: 36975810 PMCID: PMC10132095 DOI: 10.1128/aem.02073-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/07/2023] [Indexed: 03/29/2023] Open
Abstract
Nitrogen gas (N2) fixation in the anode-respiring bacterium Geobacter sulfurreducens occurs through complex, multistep processes. Optimizing ammonium (NH4+) production from this bacterium in microbial electrochemical technologies (METs) requires an understanding of how those processes are regulated in response to electrical driving forces. In this study, we quantified gene expression levels (via RNA sequencing) of G. sulfurreducens growing on anodes fixed at two different potentials (-0.15 V and +0.15 V versus standard hydrogen electrode). The anode potential had a significant impact on the expression levels of N2 fixation genes. At -0.15 V, the expression of nitrogenase genes, such as nifH, nifD, and nifK, significantly increased relative to that at +0.15 V, as well as genes associated with NH4+ uptake and transformation, such as glutamine and glutamate synthetases. Metabolite analysis confirmed that both of these organic compounds were present in significantly higher intracellular concentrations at -0.15 V. N2 fixation rates (estimated using the acetylene reduction assay and normalized to total protein) were significantly larger at -0.15 V. Genes expressing flavin-based electron bifurcation complexes, such as electron-transferring flavoproteins (EtfAB) and the NADH-dependent ferredoxin:NADP reductase (NfnAB), were also significantly upregulated at -0.15 V, suggesting that these mechanisms may be involved in N2 fixation at that potential. Our results show that in energy-constrained situations (i.e., low anode potential), the cells increase per-cell respiration and N2 fixation rates. We hypothesize that at -0.15 V, they increase N2 fixation activity to help maintain redox homeostasis, and they leverage electron bifurcation as a strategy to optimize energy generation and use. IMPORTANCE Biological nitrogen fixation coupled with ammonium recovery provides a sustainable alternative to the carbon-, water-, and energy-intensive Haber-Bosch process. Aerobic biological nitrogen fixation technologies are hindered by oxygen gas inhibition of the nitrogenase enzyme. Electrically driving biological nitrogen fixation in anaerobic microbial electrochemical technologies overcomes this challenge. Using Geobacter sulfurreducens as a model exoelectrogenic diazotroph, we show that the anode potential in microbial electrochemical technologies has a significant impact on nitrogen gas fixation rates, ammonium assimilation pathways, and expression of genes associated with nitrogen gas fixation. These findings have important implications for understanding regulatory pathways of nitrogen gas fixation and will help identify target genes and operational strategies to enhance ammonium production in microbial electrochemical technologies.
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Affiliation(s)
- Juan F. Ortiz-Medina
- Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Mark R. Poole
- Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Amy M. Grunden
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Douglas F. Call
- Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, North Carolina, USA
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2
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Gao X, Qian Q, Zhu Y, Chen Z, Xu J, Xu W, Jiang Q, Wang J, Zhang X. Transcriptomic and phenotype analysis revealed the role of rpoS in stress resistance and virulence of pathogenic Enterobacter cloacae from Macrobrachium rosenbergii. Front Microbiol 2022; 13:1030955. [PMID: 36439857 PMCID: PMC9684176 DOI: 10.3389/fmicb.2022.1030955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/31/2022] [Indexed: 12/03/2023] Open
Abstract
Enterobacter cloacae is widely distributed in the aquatic environment, and has been determined as a novel pathogen of various aquatic animals recently. Our previous studies have indicated E. cloacae caused repeated infections in Macrobrachium rosenbergii, suggesting a high survival ability of the bacteria, and rpoS gene has been known to regulate stress response and virulence of many bacteria. In this study, the E. cloacae-rpoS RNAi strain was constructed by RNAi technology, and the regulation role of rpoS in stress resistance and virulence of E. cloacae was explored by transcriptomic and phenotype analysis. The transcriptome analysis showed a total of 488 differentially expressed genes (DEGs) were identified between rpoS-RNAi and wild-type strains, including 30 up-regulated genes and 458 down-regulated genes, and these down-regulated DEGs were mainly related to environmental response, biofilm formation, bacterial type II secretory system, flagellin, fimbrillin, and chemotactic protein which associated with bacterial survival and virulence. The phenotype changes also showed the E. cloacae-rpoS RNAi strain exhibited significantly decreasing abilities of survival in environmental stresses (starvation, salinity, low pH, and oxidative stress), biofilm production, movement, adhesion to cells, pathogenicity, and colonization to M. rosenbergii. These results reveal that rpoS plays an important regulatory role in environmental stress adaptation and virulence of E. cloacae.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xiaojun Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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3
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Tian L, Yan X, Wang D, Du Q, Wan Y, Zhou L, Li T, Liao C, Li N, Wang X. Two key Geobacter species of wastewater-enriched electroactive biofilm respond differently to electric field. WATER RESEARCH 2022; 213:118185. [PMID: 35183018 DOI: 10.1016/j.watres.2022.118185] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
Electroactive biofilms have attracted increasing attention due to their unique ability to exchange electrons with electrodes. Geobacter spp. are widely found to be dominant in biofilms in acetate-rich environments when an appropriate voltage is applied, but it is still largely unknown how these bacteria are selectively enriched. Herein, two key Geobacter spp. that have been demonstrated predominant in wastewater-enriched electroactive biofilm after long-term operation, G. sulfurreducens and G. anodireducens, responded to electric field (EF) differently, leading to a higher abundance of EF-sensitive G. anodireducens in the strong EF region after cocultivation with G. sulfurreducens. Transcriptome analysis indicated that two-component systems containing sensor histidine kinases and response regulators were the key for EF sensing in G. anodireducens rather than in G. sulfurreducens, which are closely connected to chemotaxis, c-di-GMP, fatty acid metabolism, pilus, oxidative phosphorylation and transcription, resulting in an increase in extracellular polymeric substance secretion and rapid cell proliferation. Our data reveal the mechanism by which EF select specific Geobacter spp. over time, providing new insights into Geobacter biofilm formation regulated by electricity.
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Affiliation(s)
- Lili Tian
- MOE Key Laboratory of Pollution Processes and Environmental Criteria / Tianjin Key Laboratory of Environmental Remediation and Pollution Control / College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Xuejun Yan
- MOE Key Laboratory of Pollution Processes and Environmental Criteria / Tianjin Key Laboratory of Environmental Remediation and Pollution Control / College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Dongbin Wang
- School of Public Health, Guangdong Medical University, Xincheng Road, Dongguan 523000, China
| | - Qing Du
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Tianjin 300384, China
| | - Yuxuan Wan
- MOE Key Laboratory of Pollution Processes and Environmental Criteria / Tianjin Key Laboratory of Environmental Remediation and Pollution Control / College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Lean Zhou
- School of Hydraulic Engineering, Changsha University of Science and Technology, Changsha 410114, China
| | - Tian Li
- MOE Key Laboratory of Pollution Processes and Environmental Criteria / Tianjin Key Laboratory of Environmental Remediation and Pollution Control / College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Chengmei Liao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria / Tianjin Key Laboratory of Environmental Remediation and Pollution Control / College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Nan Li
- School of Environmental Science and Engineering, Tianjin University, No. 35 Yaguan Road, Jinnan District, Tianjin 300350, China
| | - Xin Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria / Tianjin Key Laboratory of Environmental Remediation and Pollution Control / College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China.
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4
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One step forward, two steps back: Transcriptional advancements and fermentation phenomena in Actinobacillus succinogenes 130Z. PLoS One 2021; 16:e0245407. [PMID: 33939701 PMCID: PMC8092802 DOI: 10.1371/journal.pone.0245407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/13/2021] [Indexed: 11/19/2022] Open
Abstract
Within the field of bioproduction, non-model organisms offer promise as bio-platform candidates. Non-model organisms can possess natural abilities to consume complex feedstocks, produce industrially useful chemicals, and withstand extreme environments that can be ideal for product extraction. However, non-model organisms also come with unique challenges due to lack of characterization. As a consequence, developing synthetic biology tools, predicting growth behavior, and building computational models can be difficult. There have been many advancements that have improved work with non-model organisms to address broad limitations, however each organism can come with unique surprises. Here we share our work in the non-model bacterium Actinobacillus succinognes 130Z, which includes both advancements in synthetic biology toolkit development and pitfalls in unpredictable fermentation behaviors. To develop a synthetic biology “tool kit” for A. succinogenes, information gleaned from a growth study and antibiotic screening was used to characterize 22 promoters which demonstrated a 260-fold range of fluorescence protein expression. The strongest of the promoters was incorporated into an inducible system for tunable gene control in A. succinogenes using the promoter for the lac operon as a template. This system flaunted a 481-fold range of expression and no significant basal expression. These findings were accompanied by unexpected changes in fermentation products characterized by a loss of succinic acid and increase in lactic acid after approximately 10 months in the lab. During evaluation of the fermentation shifts, new tests of the synthetic biology tools in a succinic acid producing strain revealed a significant loss in their functionality. Contamination and mutation were ruled out as causes and further testing is needed to elucidate the driving factors. The significance of this work is to share a successful tool development strategy that could be employed in other non-model species, report on an unfortunate phenomenon that needs addressed for further development of A. succinogenes, and provide a cautionary tale for those undertaking non-model research. In sharing our findings, we seek to provide tools and necessary information for further development of A. succinogenes as a platform for bioproduction of succinic acid and to illustrate the importance of diligent and long-term observation when working with non-model bacteria.
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Feng L, Bi W, Chen S, Zhu J, Liu X. Regulatory function of sigma factors RpoS/RpoN in adaptation and spoilage potential of Shewanella baltica. Food Microbiol 2021; 97:103755. [PMID: 33653528 DOI: 10.1016/j.fm.2021.103755] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 01/10/2021] [Accepted: 01/29/2021] [Indexed: 02/06/2023]
Abstract
Shewanella baltica is a typical specific spoilage organism causing the deterioration of seafood, but the exact regulation of its adaptive and competitive dominance in diverse environments remains undefined. In this study, the regulatory function of two sigma factors, RpoS and RpoN, in environmental adaptation and spoilage potential were evaluated in S. baltica SB02. Two in-frame deletion mutants, ΔrpoS and ΔrpoN, were constructed to explore the roles in their motility, biofilm formation, stress response and spoilage potential, as well as antibiotics by comparing the phenotypes and transcription with those of wild type (WT) strain. Compared with WT strain, the ΔrpoN showed the slower growth and weaker motility due to loss of flagella, while swimming of the ΔrpoS was increased. Deletion of rpoN significantly decreased biofilm biomass, and production of exopolysaccharide and pellicle, resulting in a thinner biofilm structure, while ΔrpoS formed the looser aggregation in biofilm. Resistance of S. baltica to NaCl, heat, ethanol and three oxidizing disinfectants apparently declined in the two mutants compared to WT strain. The ΔrpoN mutant decreased sensory score, accumulation of trimethylamine, putrescine and TVB-N and protease activity, while a weaker effect was observed in ΔrpoS. The two mutants had significantly higher susceptibility to antibiotics than WT strain, especially ΔrpoN. Deficiency of rpoN and rpoS significantly repressed the activities of two diketopiperazines related to quorum sensing (QS). Furthermore, transcriptome analyses revealed that RpoN was involved in the regulation of the expression of 143 genes, mostly including flagellar assembly, nitrogen and amino acid metabolism, ABC transporters. Transcript changes of seven differentially expressed coding sequences were in agreement with the phenotypes observed in the two mutants. Our findings reveal that RpoN, as a central regulator, controls the fitness and bacterial spoilage in S. baltica, while RpoS is a key regulatory factor of stress response. Characterization of these two sigma regulons in Shewanella has expanded current understanding of a possible co-regulatory mechanism with QS for adaptation and spoilage potential.
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Affiliation(s)
- Lifang Feng
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province, 310018, China
| | - Weiwei Bi
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province, 310018, China
| | - Shuai Chen
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province, 310018, China
| | - Junli Zhu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province, 310018, China.
| | - Xiaoxiang Liu
- Faculty of Basic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang Province, 310053, China
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6
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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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7
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Yu YY, Fang Z, Gao L, Song H, Yang L, Mao B, Shi W, Yong YC. Engineering of bacterial electrochemical activity with global regulator manipulation. Electrochem commun 2018. [DOI: 10.1016/j.elecom.2017.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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8
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Dostálová H, Holátko J, Busche T, Rucká L, Rapoport A, Halada P, Nešvera J, Kalinowski J, Pátek M. Assignment of sigma factors of RNA polymerase to promoters in Corynebacterium glutamicum. AMB Express 2017. [PMID: 28651382 PMCID: PMC5483222 DOI: 10.1186/s13568-017-0436-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Corynebacterium glutamicum is an important industrial producer of various amino acids and other metabolites. The C. glutamicum genome encodes seven sigma subunits (factors) of RNA polymerase: the primary sigma factor SigA (σA), the primary-like σB and five alternative sigma factors (σC, σD, σE, σH and σM). We have developed in vitro and in vivo methods to assign particular sigma factors to individual promoters of different classes. In vitro transcription assays and measurements of promoter activity using the overexpression of a single sigma factor gene and the transcriptional fusion of the promoter to the gfpuv reporter gene enabled us to reliably define the sigma factor dependency of promoters. To document the strengths of these methods, we tested examples of respective promoters for each C. glutamicum sigma factor. Promoters of the rshA (anti-sigma for σH) and trxB1 (thioredoxin) genes were found to be σH-dependent, whereas the promoter of the sigB gene (sigma factor σB) was σE- and σH-dependent. It was confirmed that the promoter of the cg2556 gene (iron-regulated membrane protein) is σC-dependent as suggested recently by other authors. The promoter of cmt1 (trehalose corynemycolyl transferase) was found to be clearly σD-dependent. No σM-dependent promoter was identified. The typical housekeeping promoter P2sigA (sigma factor σA) was proven to be σA-dependent but also recognized by σB. Similarly, the promoter of fba (fructose-1,6-bisphosphate aldolase) was confirmed to be σB-dependent but also functional with σA. The study provided demonstrations of the broad applicability of the developed methods and produced original data on the analyzed promoters.
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9
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Bentham RB, Bryson K, Szabadkai G. MCbiclust: a novel algorithm to discover large-scale functionally related gene sets from massive transcriptomics data collections. Nucleic Acids Res 2017; 45:8712-8730. [PMID: 28911113 PMCID: PMC5587796 DOI: 10.1093/nar/gkx590] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 07/01/2017] [Indexed: 12/16/2022] Open
Abstract
The potential to understand fundamental biological processes from gene expression data has grown in parallel with the recent explosion of the size of data collections. However, to exploit this potential, novel analytical methods are required, capable of discovering large co-regulated gene networks. We found current methods limited in the size of correlated gene sets they could discover within biologically heterogeneous data collections, hampering the identification of multi-gene controlled fundamental cellular processes such as energy metabolism, organelle biogenesis and stress responses. Here we describe a novel biclustering algorithm called Massively Correlated Biclustering (MCbiclust) that selects samples and genes from large datasets with maximal correlated gene expression, allowing regulation of complex networks to be examined. The method has been evaluated using synthetic data and applied to large bacterial and cancer cell datasets. We show that the large biclusters discovered, so far elusive to identification by existing techniques, are biologically relevant and thus MCbiclust has great potential in the analysis of transcriptomics data to identify large-scale unknown effects hidden within the data. The identified massive biclusters can be used to develop improved transcriptomics based diagnosis tools for diseases caused by altered gene expression, or used for further network analysis to understand genotype-phenotype correlations.
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Affiliation(s)
- Robert B Bentham
- Department of Cell and Developmental Biology, Consortium for Mitochondrial Research, University College London, London WC1E 6BT, UK.,The Francis Crick Institute, London NW1 1AT, UK
| | - Kevin Bryson
- Department of Computer Sciences, University College London, London WC1E 6BT, UK
| | - Gyorgy Szabadkai
- Department of Cell and Developmental Biology, Consortium for Mitochondrial Research, University College London, London WC1E 6BT, UK.,The Francis Crick Institute, London NW1 1AT, UK.,Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
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10
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Novel DNA Binding and Regulatory Activities for σ 54 (RpoN) in Salmonella enterica Serovar Typhimurium 14028s. J Bacteriol 2017; 199:JB.00816-16. [PMID: 28373272 DOI: 10.1128/jb.00816-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 03/27/2017] [Indexed: 01/13/2023] Open
Abstract
The variable sigma (σ) subunit of the bacterial RNA polymerase (RNAP) holoenzyme, which is responsible for promoter specificity and open complex formation, plays a strategic role in the response to environmental changes. Salmonella enterica serovar Typhimurium utilizes the housekeeping σ70 and five alternative sigma factors, including σ54 The σ54-RNAP differs from other σ-RNAP holoenzymes in that it forms a stable closed complex with the promoter and requires ATP hydrolysis by an activated cognate bacterial enhancer binding protein (bEBP) to transition to an open complex and initiate transcription. In S. Typhimurium, σ54-dependent promoters normally respond to one of 13 different bEBPs, each of which is activated under a specific growth condition. Here, we utilized a constitutively active, promiscuous bEBP to perform a genome-wide identification of σ54-RNAP DNA binding sites and the transcriptome of the σ54 regulon of S. Typhimurium. The position and context of many of the identified σ54 RNAP DNA binding sites suggest regulatory roles for σ54-RNAP that connect the σ54 regulon to regulons of other σ factors to provide a dynamic response to rapidly changing environmental conditions.IMPORTANCE The alternative sigma factor σ54 (RpoN) is required for expression of genes involved in processes with significance in agriculture, bioenergy production, bioremediation, and host-microbe interactions. The characterization of the σ54 regulon of the versatile pathogen S. Typhimurium has expanded our understanding of the scope of the σ54 regulon and how it links to other σ regulons within the complex regulatory network for gene expression in bacteria.
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Binder SC, Eckweiler D, Schulz S, Bielecka A, Nicolai T, Franke R, Häussler S, Meyer-Hermann M. Functional modules of sigma factor regulons guarantee adaptability and evolvability. Sci Rep 2016; 6:22212. [PMID: 26915971 PMCID: PMC4768184 DOI: 10.1038/srep22212] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 02/10/2016] [Indexed: 01/30/2023] Open
Abstract
The focus of modern molecular biology turns from assigning functions to individual genes towards understanding the expression and regulation of complex sets of molecules. Here, we provide evidence that alternative sigma factor regulons in the pathogen Pseudomonas aeruginosa largely represent insulated functional modules which provide a critical level of biological organization involved in general adaptation and survival processes. Analysis of the operational state of the sigma factor network revealed that transcription factors functionally couple the sigma factor regulons and significantly modulate the transcription levels in the face of challenging environments. The threshold quality of newly evolved transcription factors was reached faster and more robustly in in silico testing when the structural organization of sigma factor networks was taken into account. These results indicate that the modular structures of alternative sigma factor regulons provide P. aeruginosa with a robust framework to function adequately in its environment and at the same time facilitate evolutionary change. Our data support the view that widespread modularity guarantees robustness of biological networks and is a key driver of evolvability.
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Affiliation(s)
- Sebastian C Binder
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Denitsa Eckweiler
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, 30265 Hannover, Germany.,Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Sebastian Schulz
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, 30265 Hannover, Germany.,Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Agata Bielecka
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, 30265 Hannover, Germany.,Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Tanja Nicolai
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Raimo Franke
- Department of Chemical Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, 30265 Hannover, Germany.,Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Michael Meyer-Hermann
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany.,Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, 38124 Braunschweig, Germany
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12
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Scarless Genome Editing and Stable Inducible Expression Vectors for Geobacter sulfurreducens. Appl Environ Microbiol 2015; 81:7178-86. [PMID: 26253675 PMCID: PMC4579418 DOI: 10.1128/aem.01967-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 07/29/2015] [Indexed: 11/20/2022] Open
Abstract
Metal reduction by members of the Geobacteraceae is encoded by multiple gene clusters, and the study of extracellular electron transfer often requires biofilm development on surfaces. Genetic tools that utilize polar antibiotic cassette insertions limit mutant construction and complementation. In addition, unstable plasmids create metabolic burdens that slow growth, and the presence of antibiotics such as kanamycin can interfere with the rate and extent of Geobacter biofilm growth. We report here genetic system improvements for the model anaerobic metal-reducing bacterium Geobacter sulfurreducens. A motile strain of G. sulfurreducens was constructed by precise removal of a transposon interrupting the fgrM flagellar regulator gene using SacB/sucrose counterselection, and Fe(III) citrate reduction was eliminated by deletion of the gene encoding the inner membrane cytochrome imcH. We also show that RK2-based plasmids were maintained in G. sulfurreducens for over 15 generations in the absence of antibiotic selection in contrast to unstable pBBR1 plasmids. Therefore, we engineered a series of new RK2 vectors containing native constitutive Geobacter promoters, and modified one of these promoters for VanR-dependent induction by the small aromatic carboxylic acid vanillate. Inducible plasmids fully complemented ΔimcH mutants for Fe(III) reduction, Mn(IV) oxide reduction, and growth on poised electrodes. A real-time, high-throughput Fe(III) citrate reduction assay is described that can screen numerous G. sulfurreducens strain constructs simultaneously and shows the sensitivity of imcH expression by the vanillate system. These tools will enable more sophisticated genetic studies in G. sulfurreducens without polar insertion effects or need for multiple antibiotics.
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13
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Schulz S, Eckweiler D, Bielecka A, Nicolai T, Franke R, Dötsch A, Hornischer K, Bruchmann S, Düvel J, Häussler S. Elucidation of sigma factor-associated networks in Pseudomonas aeruginosa reveals a modular architecture with limited and function-specific crosstalk. PLoS Pathog 2015; 11:e1004744. [PMID: 25780925 PMCID: PMC4362757 DOI: 10.1371/journal.ppat.1004744] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 02/11/2015] [Indexed: 12/31/2022] Open
Abstract
Sigma factors are essential global regulators of transcription initiation in bacteria which confer promoter recognition specificity to the RNA polymerase core enzyme. They provide effective mechanisms for simultaneously regulating expression of large numbers of genes in response to challenging conditions, and their presence has been linked to bacterial virulence and pathogenicity. In this study, we constructed nine his-tagged sigma factor expressing and/or deletion mutant strains in the opportunistic pathogen Pseudomonas aeruginosa. To uncover the direct and indirect sigma factor regulons, we performed mRNA profiling, as well as chromatin immunoprecipitation coupled to high-throughput sequencing. We furthermore elucidated the de novo binding motif of each sigma factor, and validated the RNA- and ChIP-seq results by global motif searches in the proximity of transcriptional start sites (TSS). Our integrated approach revealed a highly modular network architecture which is composed of insulated functional sigma factor modules. Analysis of the interconnectivity of the various sigma factor networks uncovered a limited, but highly function-specific, crosstalk which orchestrates complex cellular processes. Our data indicate that the modular structure of sigma factor networks enables P. aeruginosa to function adequately in its environment and at the same time is exploited to build up higher-level functions by specific interconnections that are dominated by a participation of RpoN. Pseudomonas aeruginosa is well known for its high adaptability to a large range of environmental conditions, including those encountered within the human host. Transcription initiation represents a major regulatory target which drives versatility, and enables bacterial adaptation to challenging conditions and expression of virulence and pathogenicity. In bacteria, this process is largely orchestrated by sigma factors. Here, we performed an integrative approach, and by the combined use of three global profiling technologies uncovered the networks of 10 alternative sigma factors in the opportunistic pathogen P. aeruginosa. We demonstrate that these networks largely represent self-contained functional modules which exhibit a limited but highly specific crosstalk to build up higher-level functions. Our results do not only give extensive information on sigma factor binding sites throughout the P. aeruginosa genome, but also advance the understanding of sigma factor network architecture which provides bacteria with a framework to function adequately in their environment.
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Affiliation(s)
- Sebastian Schulz
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Denitsa Eckweiler
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Agata Bielecka
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Tanja Nicolai
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Raimo Franke
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Andreas Dötsch
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Klaus Hornischer
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sebastian Bruchmann
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Juliane Düvel
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- * E-mail:
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