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Illava G, Gillilan R, Ando N. Development of in-line anoxic small-angle X-ray scattering and structural characterization of an oxygen-sensing transcriptional regulator. J Biol Chem 2023; 299:105039. [PMID: 37442238 PMCID: PMC10425943 DOI: 10.1016/j.jbc.2023.105039] [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: 05/21/2023] [Revised: 07/01/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
Oxygen-sensitive metalloenzymes are responsible for many of the most fundamental biochemical processes in nature, from the reduction of dinitrogen in nitrogenase to the biosynthesis of photosynthetic pigments. However, biophysical characterization of such proteins under anoxic conditions can be challenging, especially at noncryogenic temperatures. In this study, we introduce the first in-line anoxic small-angle X-ray scattering (anSAXS) system at a major national synchrotron source, featuring both batch-mode and chromatography-mode capabilities. To demonstrate chromatography-coupled anSAXS, we investigated the oligomeric interconversions of the fumarate and nitrate reduction (FNR) transcription factor, which is responsible for the transcriptional response to changing oxygen conditions in the facultative anaerobe Escherichia coli. Previous work has shown that FNR contains a labile [4Fe-4S] cluster that is degraded when oxygen is present and that this change in cluster composition leads to the dissociation of the DNA-binding dimeric form. Using anSAXS, we provide the first direct structural evidence for the oxygen-induced dissociation of the E. coli FNR dimer and its correlation with cluster composition. We further demonstrate how complex FNR-DNA interactions can be studied by investigating the promoter region of the anaerobic ribonucleotide reductase genes, nrdDG, which contains tandem FNR-binding sites. By coupling size-exclusion chromatography-anSAXS with full-spectrum UV-Vis analysis, we show that the [4Fe-4S] cluster-containing dimeric form of FNR can bind to both sites in the nrdDG promoter region. The development of in-line anSAXS greatly expands the toolbox available for the study of complex metalloproteins and provides a foundation for future expansions.
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Affiliation(s)
- Gabrielle Illava
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA; Center for High Energy X-ray Sciences (CHEXS), Ithaca, New York, USA
| | - Richard Gillilan
- Center for High Energy X-ray Sciences (CHEXS), Ithaca, New York, USA.
| | - Nozomi Ando
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA.
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2
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Yee WX, Barnes G, Lavender H, Tang CM. Meningococcal factor H-binding protein: implications for disease susceptibility, virulence, and vaccines. Trends Microbiol 2023; 31:805-815. [PMID: 36941192 PMCID: PMC10914675 DOI: 10.1016/j.tim.2023.02.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/23/2023]
Abstract
Neisseria meningitidis is a human-adapted pathogen that causes meningitis and sepsis worldwide. N. meningitidis factor H-binding protein (fHbp) provides a mechanism for immune evasion by binding human complement factor H (CFH) to protect it from complement-mediated killing. Here, we discuss features of fHbp which enable it to engage human CFH (hCFH), and the regulation of fHbp expression. Studies of host susceptibility and bacterial genome-wide association studies (GWAS) highlight the importance of the interaction between fHbp and CFH and other complement factors, such as CFHR3, on the development of invasive meningococcal disease (IMD). Understanding the basis of fHbp:CFH interactions has also informed the design of next-generation vaccines as fHbp is a protective antigen. Structure-informed refinement of fHbp vaccines will help to combat the threat posed by the meningococcus, and accelerate the elimination of IMD.
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Affiliation(s)
- Wearn-Xin Yee
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Grace Barnes
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Hayley Lavender
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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3
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Illava G, Gillilan R, Ando N. Development of in-line anoxic small-angle X-ray scattering and structural characterization of an oxygen-sensing transcriptional regulator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.18.541370. [PMID: 37292723 PMCID: PMC10245656 DOI: 10.1101/2023.05.18.541370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Oxygen-sensitive metalloenzymes are responsible for many of the most fundamental biochemical processes in nature, from the reduction of di-nitrogen in nitrogenase to the biosynthesis of photosynthetic pigments. However, biophysical characterization of such proteins under anoxic conditions can be challenging, especially at non-cryogenic temperatures. In this study, we introduce the first in-line anoxic small-angle X-ray scattering (anSAXS) system at a major national synchrotron source, featuring both batch-mode and chromatography-mode capabilities. To demonstrate chromatography-coupled anSAXS, we investigated the oligomeric interconversions of the Fumarate and Nitrate Reduction (FNR) transcription factor, which is responsible for the transcriptional response to changing oxygen conditions in the facultative anaerobe Escherichia coli . Previous work has shown that FNR contains a labile [4Fe-4S] cluster that is degraded when oxygen is present, and that this change in cluster composition leads to the dissociation of the DNA-binding dimeric form. Using anSAXS, we provide the first direct structural evidence for the oxygen-induced dissociation of the E. coli FNR dimer and its correlation with cluster composition. We further demonstrate how complex FNR-DNA interactions can be studied by investigating the promoter region of the anaerobic ribonucleotide reductase genes, nrdDG , which contains tandem FNR binding sites. By coupling SEC-anSAXS with full spectrum UV-Vis analysis, we show that the [4Fe-4S] clustercontaining dimeric form of FNR can bind to both sites in the nrdDG promoter region. The development of in-line anSAXS greatly expands the toolbox available for the study of complex metalloproteins and provides a foundation for future expansions.
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4
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Krol E, Werel L, Essen LO, Becker A. Structural and functional diversity of bacterial cyclic nucleotide perception by CRP proteins. MICROLIFE 2023; 4:uqad024. [PMID: 37223727 PMCID: PMC10187061 DOI: 10.1093/femsml/uqad024] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/07/2023] [Accepted: 04/28/2023] [Indexed: 05/25/2023]
Abstract
Cyclic AMP (cAMP) is a ubiquitous second messenger synthesized by most living organisms. In bacteria, it plays highly diverse roles in metabolism, host colonization, motility, and many other processes important for optimal fitness. The main route of cAMP perception is through transcription factors from the diverse and versatile CRP-FNR protein superfamily. Since the discovery of the very first CRP protein CAP in Escherichia coli more than four decades ago, its homologs have been characterized in both closely related and distant bacterial species. The cAMP-mediated gene activation for carbon catabolism by a CRP protein in the absence of glucose seems to be restricted to E. coli and its close relatives. In other phyla, the regulatory targets are more diverse. In addition to cAMP, cGMP has recently been identified as a ligand of certain CRP proteins. In a CRP dimer, each of the two cyclic nucleotide molecules makes contacts with both protein subunits and effectuates a conformational change that favors DNA binding. Here, we summarize the current knowledge on structural and physiological aspects of E. coli CAP compared with other cAMP- and cGMP-activated transcription factors, and point to emerging trends in metabolic regulation related to lysine modification and membrane association of CRP proteins.
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Affiliation(s)
- Elizaveta Krol
- Department of Biology, Philipps-Universität Marburg, Karl-von-Frisch-Straße 8, 35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
| | - Laura Werel
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Lars Oliver Essen
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Anke Becker
- Corresponding author. Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35043 Marburg. E-mail:
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5
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Huang LH, Li XJ, Wang YT, Jia SR, Xin B, Zhong C. Enhancing bacterial cellulose production with hypoxia-inducible factors. Appl Microbiol Biotechnol 2022; 106:7099-7112. [PMID: 36184690 DOI: 10.1007/s00253-022-12192-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/18/2022] [Indexed: 12/01/2022]
Abstract
Komagataeibacter xylinus is an aerobic strain that produces bacterial cellulose (BC). Oxygen levels play a critical role in regulating BC synthesis in K. xylinus, and an increase in oxygen tension generally means a decrease in BC production. Fumarate nitrate reduction protein (FNR) and aerobic respiration control protein A (ArcA) are hypoxia-inducible factors, which can signal whether oxygen is present in the environment. In this study, FNR and ArcA were used to enhance the efficiency of oxygen signaling in K. xylinus, and globally regulate the transcription of the genome to cope with hypoxic conditions, with the goal of improving growth and BC production. FNR and ArcA were individually overexpressed in K. xylinus, and the engineered strains were cultivated under different oxygen tensions to explore how their overexpression affects cellular metabolism and regulation. Although FNR overexpression did not improve BC production, ArcA overexpression increased BC production by 24.0% and 37.5% as compared to the control under oxygen tensions of 15% and 40%, respectively. Transcriptome analysis showed that FNR and ArcA overexpression changed the way K. xylinus coped with oxygen tension changes, and that both FNR and ArcA overexpression enhanced the BC synthesis pathway. The results of this study provide a new perspective on the effect of oxygen signaling on growth and BC production in K. xylinus and suggest a promising strategy for enhancing BC production through metabolic engineering. KEY POINTS: • K. xylinus BC production increased after overexpression of ArcA • The young's modulus is enhanced by the ArcA overexpression • ArcA and FNR overexpression changed how cells coped with changes in oxygen tension.
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Affiliation(s)
- Long-Hui Huang
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China.,Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin, People's Republic of China
| | - Xue-Jing Li
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China.,Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin, People's Republic of China
| | - Yi-Tong Wang
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China.,Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin, People's Republic of China
| | - Shi-Ru Jia
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China.,Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin, People's Republic of China
| | - Bo Xin
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China. .,Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin, People's Republic of China.
| | - Cheng Zhong
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China. .,Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin, People's Republic of China.
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6
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Microaerobic conditions enhance laccase production from Rheinheimera sp. in an economical medium. Arch Microbiol 2022; 204:562. [PMID: 35980477 DOI: 10.1007/s00203-022-03170-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 05/19/2022] [Accepted: 08/04/2022] [Indexed: 12/06/2022]
Abstract
Statistical optimization of aeration conditions viz. aerobic, microaerobic and anaerobic, was performed using response surface methodology (RSM) utilizing soybean meal as medium to enhance the production of laccase from Rheinheimera sp. Maximum laccase yield (18.48 × 105 U/L) was obtained under microaerobic (static) conditions sustained for 12 h in tandem with 26 h aerobically (150 rpm) grown culture, which was 17.03-fold higher than laccase production in the starting M162 medium under aerobic conditions (150 rpm). The reduction in incubation time from 72 to 38 h and utilization of cost-effective soybean meal as medium, which is easily available from local market, have provided a promising, eco-friendly method of laccase enzyme production. Enhanced expression of laccase gene under microaerobic conditions corresponded to the increased expression of fnr (fumarate nitrate reductase) gene, the oxygen sensing global regulator. The putative FNR-binding site upstream of laccase transcription initiation site was predicted to play an imperative role in Rheinheimera sp. adaptation from aerobic to microaerobic conditions and for enhanced laccase production.
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7
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Velours C, Zhou J, Zecchin P, He N, Salameh M, Golinelli-Cohen MP, Golinelli-Pimpaneau B. Determination of the Absolute Molar Mass of [Fe-S]-Containing Proteins Using Size Exclusion Chromatography-Multi-Angle Light Scattering (SEC-MALS). Biomolecules 2022; 12:biom12020270. [PMID: 35204772 PMCID: PMC8961635 DOI: 10.3390/biom12020270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/25/2022] [Accepted: 02/03/2022] [Indexed: 12/12/2022] Open
Abstract
Size Exclusion Chromatography coupled with Multi-Angle Light Scattering (SEC-MALS) is a technique that determines the absolute molar mass (molecular weight) of macromolecules in solution, such as proteins or polymers, by detecting their light scattering intensity. Because SEC-MALS does not rely on the assumption of the globular state of the analyte and the calibration of standards, the molar mass can be obtained for proteins of any shape, as well as for intrinsically disordered proteins and aggregates. Yet, corrections need to be made for samples that absorb light at the wavelength of the MALS laser, such as iron–sulfur [Fe-S] cluster-containing proteins. We analyze several examples of [2Fe-2S] and [4Fe-4S] cluster-containing proteins, for which various corrections were applied to determine the absolute molar mass of both the apo- and holo-forms. Importantly, the determination of the absolute molar mass of the [2Fe-2S]-containing holo-NEET proteins allowed us to ascertain a change in the oligomerization state upon cluster binding and, thus, to highlight one essential function of the cluster.
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Affiliation(s)
- Christophe Velours
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 33076 Bordeaux, France
- Institute for Integrative Biology of the Cell (I2BC), CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
- Correspondence: (C.V.); (B.G.-P.)
| | - Jingjing Zhou
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, 11 Place Marcelin Berthelot, 75231 Paris, France; (J.Z.); (P.Z.); (N.H.)
| | - Paolo Zecchin
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, 11 Place Marcelin Berthelot, 75231 Paris, France; (J.Z.); (P.Z.); (N.H.)
| | - Nisha He
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, 11 Place Marcelin Berthelot, 75231 Paris, France; (J.Z.); (P.Z.); (N.H.)
| | - Myriam Salameh
- Institut de Chimie des Substances Naturelles, Université Paris-Saclay, CNRS, UPR2301, 91198 Gif-sur-Yvette, France; (M.S.); (M.-P.G.-C.)
| | - Marie-Pierre Golinelli-Cohen
- Institut de Chimie des Substances Naturelles, Université Paris-Saclay, CNRS, UPR2301, 91198 Gif-sur-Yvette, France; (M.S.); (M.-P.G.-C.)
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, 11 Place Marcelin Berthelot, 75231 Paris, France; (J.Z.); (P.Z.); (N.H.)
- Correspondence: (C.V.); (B.G.-P.)
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8
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Ma X, Ma L, Huo YX. Reconstructing the transcription regulatory network to optimize resource allocation for robust biosynthesis. Trends Biotechnol 2021; 40:735-751. [PMID: 34895933 DOI: 10.1016/j.tibtech.2021.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 11/07/2021] [Accepted: 11/08/2021] [Indexed: 11/16/2022]
Abstract
An ideal microbial cell factory (MCF) should deliver maximal resources to production, which conflicts with the microbe's native growth-oriented resource allocation strategy and can therefore lead to early termination of the high-yield period. Reallocating resources from growth to production has become a critical factor in constructing robust MCFs. Instead of strengthening specific biosynthetic pathways, emerging endeavors are focused on rearranging the gene regulatory network to fundamentally reprogram the resource allocation pattern. Combining this idea with transcriptional regulation within the hierarchical regulatory network, this review discusses recent engineering strategies targeting the transcription machinery, module networks, regulatory edges, and bottom network layer. This global view will help to construct a production-oriented phenotype that fully harnesses the potential of MCFs.
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Affiliation(s)
- Xiaoyan Ma
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, People's Republic of China
| | - Lianjie Ma
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, People's Republic of China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, People's Republic of China; Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, People's Republic of China.
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9
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10
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Sun D, Zhou X, Liu C, Zhu J, Ru Y, Liu W, Liu J. Fnr Negatively Regulates Prodigiosin Synthesis in Serratia sp. ATCC 39006 During Aerobic Fermentation. Front Microbiol 2021; 12:734854. [PMID: 34603264 PMCID: PMC8485047 DOI: 10.3389/fmicb.2021.734854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/20/2021] [Indexed: 12/18/2022] Open
Abstract
The well-known Crp/Fnr family regulator Fnr has long been recognized as an oxygen sensor to regulate multiple biological processes, including the switch between aerobic/anaerobic metabolism, nitrogen fixation, bioluminescence, infection, and virulence. In most cases, Fnr was found to be active under anaerobic conditions. However, its role in aerobic antibiotic metabolism has not yet been revealed. In this research, we report that in the model organism, Serratia sp. ATCC 39006, Fnr (Ser39006_013370) negatively regulates prodigiosin production by binding to the spacer between the −10 and −35 region in the promoter of prodigiosin biosynthetic gene cluster under aerobic conditions. Fnr was also shown to modulate the anti-bacterial activity and motility by regulating pathway-specific regulatory genes, indicating that Fnr acts as a global regulator in Serratia sp. ATCC 39006. For the first time, we describe that Fnr regulates antibiotic synthesis in the presence of oxygen, which expands the known physiological functions of Fnr and benefits the further investigation of this important transcriptional regulator.
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Affiliation(s)
- Di Sun
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Xuge Zhou
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Cong Liu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jingrong Zhu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yunrui Ru
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Weijie Liu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jiawen Liu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
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11
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Song X, Cronan JE. A conserved and seemingly redundant Escherichia coli biotin biosynthesis gene expressed only during anaerobic growth. Mol Microbiol 2021; 116:1315-1327. [PMID: 34597430 PMCID: PMC8599648 DOI: 10.1111/mmi.14826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 11/30/2022]
Abstract
Biotin is an essential metabolic cofactor and de novo biotin biosynthetic pathways are widespread in microorganisms and plants. Biotin synthetic genes are generally found clustered into bio operons to facilitate tight regulation since biotin synthesis is a metabolically expensive process. Dethiobiotin synthetase (DTBS) catalyzes the penultimate step of biotin biosynthesis, the formation of 7,8-diaminononanoate (DAPA). In Escherichia coli, DTBS is encoded by the bio operon gene bioD. Several studies have reported transcriptional activation of ynfK a gene of unknown function, under anaerobic conditions. Alignments of YnfK with BioD have led to suggestions that YnfK has DTBS activity. We report that YnfK is a functional DTBS, although an enzyme of poor activity that is poorly expressed. Supplementation of growth medium with DAPA or substitution of BioD active site residues for the corresponding YnfK residues greatly improved the DTBS activity of YnfK. We confirmed that FNR activates transcriptional level of ynfK during anaerobic growth and identified the FNR binding site of ynfK. The ynfK gene is well conserved in γ-proteobacteria.
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Affiliation(s)
- Xuejiao Song
- Department of Biochemistry, University of Illinois, Urbana, Illinois, USA
| | - John E Cronan
- Department of Biochemistry, University of Illinois, Urbana, Illinois, USA.,Department of Microbiology, University of Illinois, Urbana, Illinois, USA
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12
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Gonzaga de França Lopes L, Gouveia Júnior FS, Karine Medeiros Holanda A, Maria Moreira de Carvalho I, Longhinotti E, Paulo TF, Abreu DS, Bernhardt PV, Gilles-Gonzalez MA, Cirino Nogueira Diógenes I, Henrique Silva Sousa E. Bioinorganic systems responsive to the diatomic gases O2, NO, and CO: From biological sensors to therapy. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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13
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Price EE, Román-Rodríguez F, Boyd JM. Bacterial approaches to sensing and responding to respiration and respiration metabolites. Mol Microbiol 2021; 116:1009-1021. [PMID: 34387370 DOI: 10.1111/mmi.14795] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 08/03/2021] [Accepted: 08/09/2021] [Indexed: 11/29/2022]
Abstract
Bacterial respiration of diverse substrates is a primary contributor to the diversity of life. Respiration also drives alterations in the geosphere and tethers ecological nodes together. It provides organisms with a means to dissipate reductants and generate potential energy in the form of an electrochemical gradient. Mechanisms have evolved to sense flux through respiratory pathways and sense the altered concentrations of respiration substrates or byproducts. These genetic regulatory systems promote efficient utilization of respiration substrates, as well as fine tune metabolism to promote cellular fitness and negate the accumulation of toxic byproducts. Many bacteria can respire one or more chemicals, and these regulatory systems promote the prioritization of high energy metabolites. Herein we focus on regulatory paradigms and discuss systems that sense the concentrations of respiration substrates and flux through respiratory pathways. This is a broad field of study, and therefore we focus on key fundamental and recent developments and highlight specific systems that capture the diversity of sensing mechanisms.
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Affiliation(s)
- Erin E Price
- Department of Biochemistry & Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Franklin Román-Rodríguez
- Department of Biochemistry & Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Jeffrey M Boyd
- Department of Biochemistry & Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
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14
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Fassler R, Zuily L, Lahrach N, Ilbert M, Reichmann D. The Central Role of Redox-Regulated Switch Proteins in Bacteria. Front Mol Biosci 2021; 8:706039. [PMID: 34277710 PMCID: PMC8282892 DOI: 10.3389/fmolb.2021.706039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/18/2021] [Indexed: 01/11/2023] Open
Abstract
Bacteria possess the ability to adapt to changing environments. To enable this, cells use reversible post-translational modifications on key proteins to modulate their behavior, metabolism, defense mechanisms and adaptation of bacteria to stress. In this review, we focus on bacterial protein switches that are activated during exposure to oxidative stress. Such protein switches are triggered by either exogenous reactive oxygen species (ROS) or endogenous ROS generated as by-products of the aerobic lifestyle. Both thiol switches and metal centers have been shown to be the primary targets of ROS. Cells take advantage of such reactivity to use these reactive sites as redox sensors to detect and combat oxidative stress conditions. This in turn may induce expression of genes involved in antioxidant strategies and thus protect the proteome against stress conditions. We further describe the well-characterized mechanism of selected proteins that are regulated by redox switches. We highlight the diversity of mechanisms and functions (as well as common features) across different switches, while also presenting integrative methodologies used in discovering new members of this family. Finally, we point to future challenges in this field, both in uncovering new types of switches, as well as defining novel additional functions.
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Affiliation(s)
- Rosi Fassler
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lisa Zuily
- Aix-Marseille University, CNRS, BIP, UMR 7281, IMM, Marseille, France
| | - Nora Lahrach
- Aix-Marseille University, CNRS, BIP, UMR 7281, IMM, Marseille, France
| | - Marianne Ilbert
- Aix-Marseille University, CNRS, BIP, UMR 7281, IMM, Marseille, France
| | - Dana Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem, Israel
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15
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Maio N, Zhang DL, Ghosh MC, Jain A, SantaMaria AM, Rouault TA. Mechanisms of cellular iron sensing, regulation of erythropoiesis and mitochondrial iron utilization. Semin Hematol 2021; 58:161-174. [PMID: 34389108 DOI: 10.1053/j.seminhematol.2021.06.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/08/2021] [Accepted: 06/10/2021] [Indexed: 12/11/2022]
Abstract
To maintain an adequate iron supply for hemoglobin synthesis and essential metabolic functions while counteracting iron toxicity, humans and other vertebrates have evolved effective mechanisms to conserve and finely regulate iron concentration, storage, and distribution to tissues. At the systemic level, the iron-regulatory hormone hepcidin is secreted by the liver in response to serum iron levels and inflammation. Hepcidin regulates the expression of the sole known mammalian iron exporter, ferroportin, to control dietary absorption, storage and tissue distribution of iron. At the cellular level, iron regulatory proteins 1 and 2 (IRP1 and IRP2) register cytosolic iron concentrations and post-transcriptionally regulate the expression of iron metabolism genes to optimize iron availability for essential cellular processes, including heme biosynthesis and iron-sulfur cluster biogenesis. Genetic malfunctions affecting the iron sensing mechanisms or the main pathways that utilize iron in the cell cause a broad range of human diseases, some of which are characterized by mitochondrial iron accumulation. This review will discuss the mechanisms of systemic and cellular iron sensing with a focus on the main iron utilization pathways in the cell, and on human conditions that arise from compromised function of the regulatory axes that control iron homeostasis.
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Affiliation(s)
- Nunziata Maio
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - De-Liang Zhang
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Manik C Ghosh
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Anshika Jain
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Anna M SantaMaria
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Tracey A Rouault
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD.
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16
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Mühlenhoff U, Braymer JJ, Christ S, Rietzschel N, Uzarska MA, Weiler BD, Lill R. Glutaredoxins and iron-sulfur protein biogenesis at the interface of redox biology and iron metabolism. Biol Chem 2021; 401:1407-1428. [PMID: 33031050 DOI: 10.1515/hsz-2020-0237] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/21/2020] [Indexed: 11/15/2022]
Abstract
The physiological roles of the intracellular iron and redox regulatory systems are intimately linked. Iron is an essential trace element for most organisms, yet elevated cellular iron levels are a potent generator and amplifier of reactive oxygen species and redox stress. Proteins binding iron or iron-sulfur (Fe/S) clusters, are particularly sensitive to oxidative damage and require protection from the cellular oxidative stress protection systems. In addition, key components of these systems, most prominently glutathione and monothiol glutaredoxins are involved in the biogenesis of cellular Fe/S proteins. In this review, we address the biochemical role of glutathione and glutaredoxins in cellular Fe/S protein assembly in eukaryotic cells. We also summarize the recent developments in the role of cytosolic glutaredoxins in iron metabolism, in particular the regulation of fungal iron homeostasis. Finally, we discuss recent insights into the interplay of the cellular thiol redox balance and oxygen with that of Fe/S protein biogenesis in eukaryotes.
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Affiliation(s)
- Ulrich Mühlenhoff
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, D-35032Marburg, Germany.,SYNMIKRO Center for Synthetic Microbiology, Philipps-Universität Marburg, Hans-Meerwein-Str., D-35043Marburg, Germany
| | - Joseph J Braymer
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, D-35032Marburg, Germany.,SYNMIKRO Center for Synthetic Microbiology, Philipps-Universität Marburg, Hans-Meerwein-Str., D-35043Marburg, Germany
| | - Stefan Christ
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, D-35032Marburg, Germany
| | - Nicole Rietzschel
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, D-35032Marburg, Germany
| | - Marta A Uzarska
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, D-35032Marburg, Germany.,Intercollegiate Faculty of Biotechnology, University of Gdansk, Abrahama 58, 80-307Gdansk, Poland
| | - Benjamin D Weiler
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, D-35032Marburg, Germany
| | - Roland Lill
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, D-35032Marburg, Germany.,SYNMIKRO Center for Synthetic Microbiology, Philipps-Universität Marburg, Hans-Meerwein-Str., D-35043Marburg, Germany
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17
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Muskhelishvili G, Sobetzko P, Mehandziska S, Travers A. Composition of Transcription Machinery and Its Crosstalk with Nucleoid-Associated Proteins and Global Transcription Factors. Biomolecules 2021; 11:biom11070924. [PMID: 34206477 PMCID: PMC8301835 DOI: 10.3390/biom11070924] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 11/24/2022] Open
Abstract
The coordination of bacterial genomic transcription involves an intricate network of interdependent genes encoding nucleoid-associated proteins (NAPs), DNA topoisomerases, RNA polymerase subunits and modulators of transcription machinery. The central element of this homeostatic regulatory system, integrating the information on cellular physiological state and producing a corresponding transcriptional response, is the multi-subunit RNA polymerase (RNAP) holoenzyme. In this review article, we argue that recent observations revealing DNA topoisomerases and metabolic enzymes associated with RNAP supramolecular complex support the notion of structural coupling between transcription machinery, DNA topology and cellular metabolism as a fundamental device coordinating the spatiotemporal genomic transcription. We analyse the impacts of various combinations of RNAP holoenzymes and global transcriptional regulators such as abundant NAPs, on genomic transcription from this viewpoint, monitoring the spatiotemporal patterns of couplons—overlapping subsets of the regulons of NAPs and RNAP sigma factors. We show that the temporal expression of regulons is by and large, correlated with that of cognate regulatory genes, whereas both the spatial organization and temporal expression of couplons is distinctly impacted by the regulons of NAPs and sigma factors. We propose that the coordination of the growth phase-dependent concentration gradients of global regulators with chromosome configurational dynamics determines the spatiotemporal patterns of genomic expression.
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Affiliation(s)
- Georgi Muskhelishvili
- School of Natural Sciences, Agricultural University of Georgia, David Aghmashenebeli Alley 24, Tbilisi 0159, Georgia
- Correspondence:
| | - Patrick Sobetzko
- Department of Chromosome Biology, Philipps-Universität Marburg, LOEWE-Zentrum für Synthetische Mikrobiologie, Hans-Meerwein-Straße, 35043 Marburg, Germany;
| | - Sanja Mehandziska
- School of Engineering and Science, Campus Ring 1, Jacobs University Bremen, 28759 Bremen, Germany;
| | - Andrew Travers
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK;
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
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18
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FNR-Type Regulator GoxR of the Obligatorily Aerobic Acetic Acid Bacterium Gluconobacter oxydans Affects Expression of Genes Involved in Respiration and Redox Metabolism. Appl Environ Microbiol 2021; 87:AEM.00195-21. [PMID: 33741613 DOI: 10.1128/aem.00195-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/09/2021] [Indexed: 12/13/2022] Open
Abstract
Gene expression in the obligately aerobic acetic acid bacterium Gluconobacter oxydans responds to oxygen limitation, but the regulators involved are unknown. In this study, we analyzed a transcriptional regulator named GoxR (GOX0974), which is the only member of the fumarate-nitrate reduction regulator (FNR) family in this species. Evidence that GoxR contains an iron-sulfur cluster was obtained, suggesting that GoxR functions as an oxygen sensor similar to FNR. The direct target genes of GoxR were determined by combining several approaches, including a transcriptome comparison of a ΔgoxR mutant with the wild-type strain and detection of in vivo GoxR binding sites by chromatin affinity purification and sequencing (ChAP-Seq). Prominent targets were the cioAB genes encoding a cytochrome bd oxidase with low O2 affinity, which were repressed by GoxR, and the pnt operon, which was activated by GoxR. The pnt operon encodes a transhydrogenase (pntA1A2B), an NADH-dependent oxidoreductase (GOX0313), and another oxidoreductase (GOX0314). Evidence was obtained for GoxR being active despite a high dissolved oxygen concentration in the medium. We suggest a model in which the very high respiration rates of G. oxydans due to periplasmic oxidations cause an oxygen-limited cytoplasm and insufficient reoxidation of NAD(P)H in the respiratory chain, leading to inhibited cytoplasmic carbohydrate degradation. GoxR-triggered induction of the pnt operon enhances fast interconversion of NADPH and NADH by the transhydrogenase and NADH reoxidation by the GOX0313 oxidoreductase via reduction of acetaldehyde formed by pyruvate decarboxylase to ethanol. In fact, small amounts of ethanol were formed by G. oxydans under oxygen-restricted conditions in a GoxR-dependent manner.IMPORTANCE Gluconobacter oxydans serves as a cell factory for oxidative biotransformations based on membrane-bound dehydrogenases and as a model organism for elucidating the metabolism of acetic acid bacteria. Surprisingly, to our knowledge none of the more than 100 transcriptional regulators encoded in the genome of G. oxydans has been studied experimentally until now. In this work, we analyzed the function of a regulator named GoxR, which belongs to the FNR family. Members of this family serve as oxygen sensors by means of an oxygen-sensitive [4Fe-4S] cluster and typically regulate genes important for growth under anoxic conditions by anaerobic respiration or fermentation. Because G. oxydans has an obligatory aerobic respiratory mode of energy metabolism, it was tempting to elucidate the target genes regulated by GoxR. Our results show that GoxR affects the expression of genes that support the interconversion of NADPH and NADH and the NADH reoxidation by reduction of acetaldehyde to ethanol.
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19
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Huang Y, Lu Z, Jiang T, Zeng Y, Zeng Y, Chen B. Oxygen availability affects the synthesis of quorum sensing signal in the facultative anaerobe Novosphingobium pentaromativorans US6-1. Appl Microbiol Biotechnol 2021; 105:1191-1201. [PMID: 33439275 DOI: 10.1007/s00253-021-11089-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/13/2020] [Accepted: 01/03/2021] [Indexed: 01/01/2023]
Abstract
Bacterial populations rely on quorum sensing (QS) to coordinate their behaviors and are often challenged by the fluctuation in oxygen concentrations in their habitats. Oxygen is a crucial factor that affects bacterial metabolism in multiple ways. However, little is known about whether and how oxygen availability affects QS activities. To fill this gap, we used the facultative anaerobe Novosphingobium pentaromativorans US6-1 as a model system, and observed that the QS signal acyl homoserine-lactones (AHLs) were produced only in anoxic environments, such as biofilm, or liquid medium that initially contained less than 2 mg/L dissolved oxygen, but not in highly oxic environments. Comparative transcriptome analysis revealed that oxygen availability significantly affected the physiological activities in US6-1, including fatty acid metabolism, oxidative phosphorylation, citrate cycle, QS activities, and flagellar assembly. The absence of AHLs in the oxic culture was not due to degradation, but to the very low expression of the AHL synthase gene novI. High concentration of NADH during the middle log phase under static cultivation may be a trigger for AHL synthesis. This is the first report that production of AHLs is coupled with anoxic metabolism in a facultative anaerobe, which extends our knowledge on factors affecting bacterial QS occurrence. KEY POINTS: • AHL production is anoxic cultivation related. • Oxygen availability affects AHL synthesis by influencing novI expression. • Oxygen availability changes many metabolism activities including NADH production.
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Affiliation(s)
- Yili Huang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Bulding NongB, Hangzhou, 310058, China.
| | - Zejia Lu
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Bulding NongB, Hangzhou, 310058, China
| | - Tingting Jiang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Bulding NongB, Hangzhou, 310058, China
| | - Yonghui Zeng
- Department of Environmental Science, Aarhus University, 4000, Roskilde, Denmark
| | - Yanhua Zeng
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Bulding NongB, Hangzhou, 310058, China
| | - Baoliang Chen
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Bulding NongB, Hangzhou, 310058, China
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20
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Bajunaid W, Haidar-Ahmad N, Kottarampatel AH, Ourida Manigat F, Silué N, F. Tchagang C, Tomaro K, Campbell-Valois FX. The T3SS of Shigella: Expression, Structure, Function, and Role in Vacuole Escape. Microorganisms 2020; 8:microorganisms8121933. [PMID: 33291504 PMCID: PMC7762205 DOI: 10.3390/microorganisms8121933] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 12/18/2022] Open
Abstract
Shigella spp. are one of the leading causes of infectious diarrheal diseases. They are Escherichia coli pathovars that are characterized by the harboring of a large plasmid that encodes most virulence genes, including a type III secretion system (T3SS). The archetypal element of the T3SS is the injectisome, a syringe-like nanomachine composed of approximately 20 proteins, spanning both bacterial membranes and the cell wall, and topped with a needle. Upon contact of the tip of the needle with the plasma membrane, the injectisome secretes its protein substrates into host cells. Some of these substrates act as translocators or effectors whose functions are key to the invasion of the cytosol and the cell-to-cell spread characterizing the lifestyle of Shigella spp. Here, we review the structure, assembly, function, and methods to measure the activity of the injectisome with a focus on Shigella, but complemented with data from other T3SS if required. We also present the regulatory cascade that controls the expression of T3SS genes in Shigella. Finally, we describe the function of translocators and effectors during cell-to-cell spread, particularly during escape from the vacuole, a key element of Shigella’s pathogenesis that has yet to reveal all of its secrets.
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Affiliation(s)
- Waad Bajunaid
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Nathaline Haidar-Ahmad
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Anwer Hasil Kottarampatel
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - France Ourida Manigat
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Navoun Silué
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Caetanie F. Tchagang
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Kyle Tomaro
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - François-Xavier Campbell-Valois
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (W.B.); (N.H.-A.); (A.H.K.); (F.O.M.); (N.S.); (C.F.T.); (K.T.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Correspondence:
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21
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RirA of Dinoroseobacter shibae senses iron via a [3Fe-4S]1+ cluster co-ordinated by three cysteine residues. Biochem J 2020; 477:191-212. [PMID: 31860023 DOI: 10.1042/bcj20180734] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 12/15/2022]
Abstract
In the marine bacterium, Dinoroseobacter shibae the transcription factor rhizobial iron regulator A (RirA) is involved in the adaptation to iron-limited growth conditions. In vitro iron and sulfide content determinations in combination with UV/Vis and electron paramagnetic resonance (EPR) spectroscopic analyses using anaerobically purified, recombinant RirA protein suggested a [3Fe-4S]1+ cluster as a cofactor. In vivo Mössbauer spectroscopy also corroborated the presence of a [3Fe-4S]1+ cluster in RirA. Moreover, the cluster was found to be redox stable. Three out of four highly conserved cysteine residues of RirA (Cys 91, Cys 99, Cys 105) were found essential for the [3Fe-4S]1+ cluster coordination. The dimeric structure of the RirA protein was independent of the presence of the [3Fe-4S]1+ cluster. Electro mobility shift assays demonstrated the essential role of an intact [3Fe-4S]1+ cluster for promoter binding by RirA. The DNA binding site was identified by DNase I footprinting. Mutagenesis studies in combination with DNA binding assays confirmed the promoter binding site as 3'-TTAAN10AATT-5'. This work describes a novel mechanism for the direct sensing of cellular iron levels in bacteria by an iron-responsive transcriptional regulator using the integrity of a redox-inactive [3Fe-4S]1+ cluster, and further contributes to the general understanding of iron regulation in marine bacteria.
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22
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Wan T, Li S, Beltran DG, Schacht A, Zhang L, Becker DF, Zhang L. Structural basis of non-canonical transcriptional regulation by the σA-bound iron-sulfur protein WhiB1 in M. tuberculosis. Nucleic Acids Res 2020; 48:501-516. [PMID: 31807774 PMCID: PMC6954389 DOI: 10.1093/nar/gkz1133] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 11/15/2019] [Accepted: 11/21/2019] [Indexed: 11/27/2022] Open
Abstract
WhiB1 is a monomeric iron–sulfur cluster-containing transcription factor in the WhiB-like family that is widely distributed in actinobacteria including the notoriously persistent pathogen Mycobacterium tuberculosis (M. tuberculosis). WhiB1 plays multiple roles in regulating cell growth and responding to nitric oxide stress in M. tuberculosis, but its underlying mechanism is unclear. Here we report a 1.85 Å-resolution crystal structure of the [4Fe–4S] cluster-bound (holo-) WhiB1 in complex with the C-terminal domain of the σ70-family primary sigma factor σA of M. tuberculosis containing the conserved region 4 (σA4). Region 4 of the σ70-family primary sigma factors is commonly used by transcription factors for gene activation, and holo-WhiB1 has been proposed to activate gene expression via binding to σA4. The complex structure, however, unexpectedly reveals that the interaction between WhiB1 and σA4 is dominated by hydrophobic residues in the [4Fe–4S] cluster binding pocket, distinct from previously characterized canonical σ704-bound transcription activators. Furthermore, we show that holo-WhiB1 represses transcription by interaction with σA4in vitro and that WhiB1 must interact with σA4 to perform its essential role in supporting cell growth in vivo. Together, these results demonstrate that holo-WhiB1 regulates gene expression by a non-canonical mechanism relative to well-characterized σA4-dependent transcription activators.
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Affiliation(s)
| | | | | | | | | | | | - LiMei Zhang
- Department of Biochemistry.,Redox Biology Center.,Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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23
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Lacasse MJ, Sebastiampillai S, Côté JP, Hodkinson N, Brown ED, Zamble DB. A whole-cell, high-throughput hydrogenase assay to identify factors that modulate [NiFe]-hydrogenase activity. J Biol Chem 2019; 294:15373-15385. [PMID: 31455635 DOI: 10.1074/jbc.ra119.008101] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 08/08/2019] [Indexed: 12/25/2022] Open
Abstract
[NiFe]-hydrogenases have attracted attention as potential therapeutic targets or components of a hydrogen-based economy. [NiFe]-hydrogenase production is a complicated process that requires many associated accessory proteins that supply the requisite cofactors and substrates. Current methods for measuring hydrogenase activity have low throughput and often require specialized conditions and reagents. In this work, we developed a whole-cell high-throughput hydrogenase assay based on the colorimetric reduction of benzyl viologen to explore the biological networks of these enzymes in Escherichia coli We utilized this assay to screen the Keio collection, a set of nonlethal single-gene knockouts in E. coli BW25113. The results of this screen highlighted the assay's specificity and revealed known components of the intricate network of systems that underwrite [NiFe]-hydrogenase activity, including nickel homeostasis and formate dehydrogenase activities as well as molybdopterin and selenocysteine biosynthetic pathways. The screen also helped identify several new genetic components that modulate hydrogenase activity. We examined one E. coli strain with undetectable hydrogenase activity in more detail (ΔeutK), finding that nickel delivery to the enzyme active site was completely abrogated, and tracked this effect to an ancillary and unannotated lack of the fumarate and nitrate reduction (FNR) anaerobic regulatory protein. Collectively, these results demonstrate that the whole-cell assay developed here can be used to uncover new information about bacterial [NiFe]-hydrogenase production and to probe the cellular components of microbial nickel homeostasis.
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Affiliation(s)
- Michael J Lacasse
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | | | - Jean-Philippe Côté
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.,Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Nicholas Hodkinson
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.,Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Deborah B Zamble
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada .,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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24
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Osorio H, Mettert E, Kiley P, Dopson M, Jedlicki E, Holmes DS. Identification and Unusual Properties of the Master Regulator FNR in the Extreme Acidophile Acidithiobacillus ferrooxidans. Front Microbiol 2019; 10:1642. [PMID: 31379789 PMCID: PMC6659574 DOI: 10.3389/fmicb.2019.01642] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/02/2019] [Indexed: 12/28/2022] Open
Abstract
The ability to conserve energy in the presence or absence of oxygen provides a metabolic versatility that confers an advantage in natural ecosystems. The switch between alternative electron transport systems is controlled by the fumarate nitrate reduction transcription factor (FNR) that senses oxygen via an oxygen-sensitive [4Fe-4S]2+ iron-sulfur cluster. Under O2 limiting conditions, FNR plays a key role in allowing bacteria to transition from aerobic to anaerobic lifestyles. This is thought to occur via transcriptional activation of genes involved in anaerobic respiratory pathways and by repression of genes involved in aerobic energy production. The Proteobacterium Acidithiobacillus ferrooxidans is a model species for extremely acidophilic microorganisms that are capable of aerobic and anaerobic growth on elemental sulfur coupled to oxygen and ferric iron reduction, respectively. In this study, an FNR-like protein (FNRAF) was discovered in At. ferrooxidans that exhibits a primary amino acid sequence and major motifs and domains characteristic of the FNR family of proteins, including an effector binding domain with at least three of the four cysteines known to coordinate an [4Fe-4S]2+ center, a dimerization domain, and a DNA binding domain. Western blotting with antibodies against Escherichia coli FNR (FNREC) recognized FNRAF. FNRAF was able to drive expression from the FNR-responsive E. coli promoter PnarG, suggesting that it is functionally active as an FNR-like protein. Upon air exposure, FNRAF demonstrated an unusual lack of sensitivity to oxygen compared to the archetypal FNREC. Comparison of the primary amino acid sequence of FNRAF with that of other natural and mutated FNRs, including FNREC, coupled with an analysis of the predicted tertiary structure of FNRAF using the crystal structure of the related FNR from Aliivibrio fisheri as a template revealed a number of amino acid changes that could potentially stabilize FNRAF in the presence of oxygen. These include a truncated N terminus and amino acid changes both around the putative Fe-S cluster coordinating cysteines and also in the dimer interface. Increased O2 stability could allow At. ferrooxidans to survive in environments with fluctuating O2 concentrations, providing an evolutionary advantage in natural, and engineered environments where oxygen gradients shape the bacterial community.
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Affiliation(s)
- Héctor Osorio
- Center for Bioinformatics and Genome Biology, Fundación Ciencia y Vida, Santiago, Chile
| | - Erin Mettert
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Patricia Kiley
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Eugenia Jedlicki
- Center for Bioinformatics and Genome Biology, Fundación Ciencia y Vida, Santiago, Chile
| | - David S Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia y Vida, Santiago, Chile.,Universidad San Sebastian, Santiago, Chile.,Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
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Fischer M, Falke D, Rönitz J, Haase A, Damelang T, Pawlik T, Sawers RG. Hypoxia-induced synthesis of respiratory nitrate reductase 2 of Streptomyces coelicolor A3(2) depends on the histidine kinase OsdK in mycelium but not in spores. MICROBIOLOGY-SGM 2019; 165:905-916. [PMID: 31259680 DOI: 10.1099/mic.0.000829] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The three nitrate reductases (Nar) of the saprophytic aerobic actinobacterium Streptomyces coelicolor A3(2) contribute to survival when oxygen becomes limiting. In the current study, we focused on synthesis of the Nar2 enzyme, which is the main Nar enzyme present and active in exponentially growing mycelium. Synthesis of Nar2 can, however, also be induced in spores after extended periods of anoxic incubation. The osdRK genes (oxygen stress and development) were recently identified to encode a two-component system important for expression of the nar2 operon in mycelium. OsdK is a predicted histidine kinase and we show here that an osdK mutant completely lacks Nar2 enzyme activity in mycelium. Recovery of Nar2 enzyme activity was achieved by re-introduction of the osdRK genes into the mutant on an integrative plasmid. In anoxically incubated spores, however, the osdK mutant retained the ability to synthesize NarG2, the catalytic subunit of Nar2. We could also demonstrate that synthesis of NarG2 in spores occurred only under hypoxic conditions; anoxia, as well as O2 concentrations significantly higher than 1 % in the gas-phase, failed to result in induction of NarG2 synthesis. Together, these findings indicate that, although Nar2 synthesis in both mycelium and spores is induced by oxygen limitation, different mechanisms control these processes and only Nar2 synthesis in mycelium is under the control of the OsdKR two-component system.
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Affiliation(s)
- Marco Fischer
- Institute of Biology/ Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Dörte Falke
- Institute of Biology/ Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Jakob Rönitz
- Institute of Biology/ Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Alexander Haase
- Institute of Biology/ Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Timon Damelang
- Institute of Biology/ Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Tony Pawlik
- Institute of Biology/ Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - R Gary Sawers
- Institute of Biology/ Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
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26
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Sevilla E, Bes MT, González A, Peleato ML, Fillat MF. Redox-Based Transcriptional Regulation in Prokaryotes: Revisiting Model Mechanisms. Antioxid Redox Signal 2019; 30:1651-1696. [PMID: 30073850 DOI: 10.1089/ars.2017.7442] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
SIGNIFICANCE The successful adaptation of microorganisms to ever-changing environments depends, to a great extent, on their ability to maintain redox homeostasis. To effectively maintain the redox balance, cells have developed a variety of strategies mainly coordinated by a battery of transcriptional regulators through diverse mechanisms. Recent Advances: This comprehensive review focuses on the main mechanisms used by major redox-responsive regulators in prokaryotes and their relationship with the different redox signals received by the cell. An overview of the corresponding regulons is also provided. CRITICAL ISSUES Some regulators are difficult to classify since they may contain several sensing domains and respond to more than one signal. We propose a classification of redox-sensing regulators into three major groups. The first group contains one-component or direct regulators, whose sensing and regulatory domains are in the same protein. The second group comprises the classical two-component systems involving a sensor kinase that transduces the redox signal to its DNA-binding partner. The third group encompasses a heterogeneous group of flavin-based photosensors whose mechanisms are not always fully understood and are often involved in more complex regulatory networks. FUTURE DIRECTIONS Redox-responsive transcriptional regulation is an intricate process as identical signals may be sensed and transduced by different transcription factors, which often interplay with other DNA-binding proteins with or without regulatory activity. Although there is much information about some key regulators, many others remain to be fully characterized due to the instability of their clusters under oxygen. Understanding the mechanisms and the regulatory networks operated by these regulators is essential for the development of future applications in biotechnology and medicine.
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Affiliation(s)
- Emma Sevilla
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - María Teresa Bes
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - Andrés González
- 2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain.,4 Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
| | - María Luisa Peleato
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - María F Fillat
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
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Muras V, Toulouse C, Fritz G, Steuber J. Respiratory Membrane Protein Complexes Convert Chemical Energy. Subcell Biochem 2019; 92:301-335. [PMID: 31214991 DOI: 10.1007/978-3-030-18768-2_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The invention of a biological membrane which is used as energy storage system to drive the metabolism of a primordial, unicellular organism represents a key event in the evolution of life. The innovative, underlying principle of this key event is respiration. In respiration, a lipid bilayer with insulating properties is chosen as the site for catalysis of an exergonic redox reaction converting substrates offered from the environment, using the liberated Gibbs free energy (ΔG) for the build-up of an electrochemical H+ (proton motive force, PMF) or Na+ gradient (sodium motive force, SMF) across the lipid bilayer. Very frequently , several redox reactions are performed in a consecutive manner, with the first reaction delivering a product which is used as substrate for the second redox reaction, resulting in a respiratory chain. From today's perspective, the (mostly) unicellular bacteria and archaea seem to be much simpler and less evolved when compared to multicellular eukaryotes. However, they are overwhelmingly complex with regard to the various respiratory chains which permit survival in very different habitats of our planet, utilizing a plethora of substances to drive metabolism. This includes nitrogen, sulfur and carbon compounds which are oxidized or reduced by specialized, respiratory enzymes of bacteria and archaea which lie at the heart of the geochemical N, S and C-cycles. This chapter gives an overview of general principles of microbial respiration considering thermodynamic aspects, chemical reactions and kinetic restraints. The respiratory chains of Escherichia coli and Vibrio cholerae are discussed as models for PMF- versus SMF-generating processes, respectively. We introduce main redox cofactors of microbial respiratory enzymes, and the concept of intra-and interelectron transfer. Since oxygen is an electron acceptor used by many respiratory chains, the formation and removal of toxic oxygen radicals is described. Promising directions of future research are respiratory enzymes as novel bacterial targets, and biotechnological applications relying on respiratory complexes.
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Affiliation(s)
- Valentin Muras
- Institute of Microbiology, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Charlotte Toulouse
- Institute of Microbiology, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Günter Fritz
- Institute of Microbiology, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Julia Steuber
- Institute of Microbiology, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany.
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TosR-Mediated Regulation of Adhesins and Biofilm Formation in Uropathogenic Escherichia coli. mSphere 2018; 3:3/3/e00222-18. [PMID: 29769381 PMCID: PMC5956150 DOI: 10.1128/msphere.00222-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 04/23/2018] [Indexed: 02/07/2023] Open
Abstract
Uropathogenic Escherichia coli strains utilize a variety of adherence factors that assist in colonization of the host urinary tract. TosA (type one secretion A) is a nonfimbrial adhesin that is predominately expressed during murine urinary tract infection (UTI), binds to kidney epithelial cells, and promotes survival during invasive infections. The tosRCBDAEF operon encodes the secretory machinery necessary for TosA localization to the E. coli cell surface, as well as the transcriptional regulator TosR. TosR binds upstream of the tos operon and in a concentration-dependent manner either induces or represses tosA expression. TosR is a member of the PapB family of fimbrial regulators that can participate in cross talk between fimbrial operons. TosR also binds upstream of the pap operon and suppresses PapA production. However, the scope of TosR-mediated cross talk is understudied and may be underestimated. To quantify the global effects of TosR-mediated regulation on the E. coli CFT073 genome, we induced expression of tosR, collected mRNA, and performed high-throughput RNA sequencing (RNA-Seq). These findings show that production of TosR affected the expression of genes involved with adhesins, including P, F1C, and Auf fimbriae, nitrate-nitrite transport, microcin secretion, and biofilm formation.IMPORTANCE Uropathogenic E. coli strains cause the majority of UTIs, which are the second most common bacterial infection in humans. During a UTI, bacteria adhere to cells within the urinary tract, using a number of different fimbrial and nonfimbrial adhesins. Biofilms can also develop on the surfaces of catheters, resulting in complications such as blockage. In this work, we further characterized the regulator TosR, which links both adhesin production and biofilm formation and likely plays a crucial function during UTI and disseminated infection.
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Phenazines Regulate Nap-Dependent Denitrification in Pseudomonas aeruginosa Biofilms. J Bacteriol 2018; 200:JB.00031-18. [PMID: 29463605 DOI: 10.1128/jb.00031-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 02/14/2018] [Indexed: 12/29/2022] Open
Abstract
Microbes in biofilms face the challenge of substrate limitation. In particular, oxygen often becomes limited for cells in Pseudomonas aeruginosa biofilms growing in the laboratory or during host colonization. Previously we found that phenazines, antibiotics produced by P. aeruginosa, balance the intracellular redox state of cells in biofilms. Here, we show that genes involved in denitrification are induced in phenazine-null (Δphz) mutant biofilms grown under an aerobic atmosphere, even in the absence of nitrate. This finding suggests that resident cells employ a bet-hedging strategy to anticipate the potential availability of nitrate and counterbalance their highly reduced redox state. Consistent with our previous characterization of aerobically grown colonies supplemented with nitrate, we found that the pathway that is induced in Δphz mutant colonies combines the nitrate reductase activity of the periplasmic enzyme Nap with the downstream reduction of nitrite to nitrogen gas catalyzed by the enzymes Nir, Nor, and Nos. This regulatory relationship differs from the denitrification pathway that functions under anaerobic growth, with nitrate as the terminal electron acceptor, which depends on the membrane-associated nitrate reductase Nar. We identified the sequences in the promoter regions of the nap and nir operons that are required for the effects of phenazines on expression. We also show that specific phenazines have differential effects on nap gene expression. Finally, we provide evidence that individual steps of the denitrification pathway are catalyzed at different depths within aerobically grown biofilms, suggesting metabolic cross-feeding between community subpopulations.IMPORTANCE An understanding of the unique physiology of cells in biofilms is critical to our ability to treat fungal and bacterial infections. Colony biofilms of the opportunistic pathogen Pseudomonas aeruginosa grown under an aerobic atmosphere but without nitrate express a denitrification pathway that differs from that used for anaerobic growth. We report that the components of this pathway are induced by electron acceptor limitation and that they are differentially expressed over the biofilm depth. These observations suggest that (i) P. aeruginosa exhibits "bet hedging," in that it expends energy and resources to prepare for nitrate availability when other electron acceptors are absent, and (ii) cells in distinct biofilm microniches may be able to exchange substrates to catalyze full denitrification.
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