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Wright Z, Seymour M, Paszczak K, Truttmann T, Senn K, Stilp S, Jansen N, Gosz M, Goeden L, Anantharaman V, Aravind L, Waters LS. The small protein MntS evolved from a signal peptide and acquired a novel function regulating manganese homeostasis in Escherichia coli. Mol Microbiol 2024; 121:152-166. [PMID: 38104967 PMCID: PMC10842292 DOI: 10.1111/mmi.15206] [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: 09/15/2023] [Revised: 11/17/2023] [Accepted: 11/24/2023] [Indexed: 12/19/2023]
Abstract
Small proteins (<50 amino acids) are emerging as ubiquitous and important regulators in organisms ranging from bacteria to humans, where they commonly bind to and regulate larger proteins during stress responses. However, fundamental aspects of small proteins, such as their molecular mechanism of action, downregulation after they are no longer needed, and their evolutionary provenance, are poorly understood. Here, we show that the MntS small protein involved in manganese (Mn) homeostasis binds and inhibits the MntP Mn transporter. Mn is crucial for bacterial survival in stressful environments but is toxic in excess. Thus, Mn transport is tightly controlled at multiple levels to maintain optimal Mn levels. The small protein MntS adds a new level of regulation for Mn transporters, beyond the known transcriptional and post-transcriptional control. We also found that MntS binds to itself in the presence of Mn, providing a possible mechanism of downregulating MntS activity to terminate its inhibition of MntP Mn export. MntS is homologous to the signal peptide of SitA, the periplasmic metal-binding subunit of a Mn importer. Remarkably, the homologous signal peptide regions can substitute for MntS, demonstrating a functional relationship between MntS and these signal peptides. Conserved gene neighborhoods support that MntS evolved from the signal peptide of an ancestral SitA protein, acquiring a life of its own with a distinct function in Mn homeostasis.
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Affiliation(s)
- Zachary Wright
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Mackenzie Seymour
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Kalista Paszczak
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Taylor Truttmann
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Katherine Senn
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Samuel Stilp
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Nickolas Jansen
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Magdalyn Gosz
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Lindsay Goeden
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - L. Aravind
- National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Lauren S. Waters
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
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2
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Hernandez-Morfa M, Olivero NB, Zappia VE, Piñas GE, Reinoso-Vizcaino NM, Cian MB, Nuñez-Fernandez M, Cortes PR, Echenique J. The oxidative stress response of Streptococcus pneumoniae: its contribution to both extracellular and intracellular survival. Front Microbiol 2023; 14:1269843. [PMID: 37789846 PMCID: PMC10543277 DOI: 10.3389/fmicb.2023.1269843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 08/28/2023] [Indexed: 10/05/2023] Open
Abstract
Streptococcus pneumoniae is a gram-positive, aerotolerant bacterium that naturally colonizes the human nasopharynx, but also causes invasive infections and is a major cause of morbidity and mortality worldwide. This pathogen produces high levels of H2O2 to eliminate other microorganisms that belong to the microbiota of the respiratory tract. However, it also induces an oxidative stress response to survive under this stressful condition. Furthermore, this self-defense mechanism is advantageous in tolerating oxidative stress imposed by the host's immune response. This review provides a comprehensive overview of the strategies employed by the pneumococcus to survive oxidative stress. These strategies encompass the utilization of H2O2 scavengers and thioredoxins, the adaptive response to antimicrobial host oxidants, the regulation of manganese and iron homeostasis, and the intricate regulatory networks that control the stress response. Here, we have also summarized less explored aspects such as the involvement of reparation systems and polyamine metabolism. A particular emphasis is put on the role of the oxidative stress response during the transient intracellular life of Streptococcus pneumoniae, including coinfection with influenza A and the induction of antibiotic persistence in host cells.
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Affiliation(s)
- Mirelys Hernandez-Morfa
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI-CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Nadia B. Olivero
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI-CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Victoria E. Zappia
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI-CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - German E. Piñas
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI-CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Nicolas M. Reinoso-Vizcaino
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI-CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Melina B. Cian
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI-CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Mariana Nuñez-Fernandez
- Centro de Química Aplicada, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Paulo R. Cortes
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI-CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Jose Echenique
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI-CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
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Pavić D, Grbin D, Blagajac A, Ćurko J, Fiket Ž, Bielen A. Impact of nutrients and trace elements on freshwater microbial communities in Croatia: identifying bacterial bioindicator taxa. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-28179-4. [PMID: 37328727 DOI: 10.1007/s11356-023-28179-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/05/2023] [Indexed: 06/18/2023]
Abstract
Since aquatic microbial communities promptly respond to environmental changes, it is now evident that they can complement traditional taxa such as fish, macroinvertebrates and algae as bioindicators of water quality. The aim of this study was to correlate the physico-chemical parameters of water with the microbial community structure and the occurrence of putative bioindicator taxa. Thirty-five water samples were collected throughout Croatia and their physico-chemical parameters, including the concentration of trace elements using the high-resolution inductively coupled plasma mass spectrometry (HR-ICP-MS), and the composition of the microbial communities by high-throughput sequencing of the 16S rRNA marker gene, were analysed in parallel. Partial least squares regression (PLS-R) modelling revealed that a number of microbial taxa were positively correlated with some of the water parameters. For example, some taxa from the phylum Proteobacteria were positively correlated with the ion content of the water (e.g. Erythrobacter, Rhodobacteraceae, Alteromonadaceae), while some Firmicutes taxa, such as the well-known faecal indicators Enterococcus and Clostridium, were correlated with nutrient content (ammonium and total phosphorus). Among the trace elements, uranium was positively correlated with a highest number of microbial taxa. The results obtained will aid in development of protocols for eDNA-based biological assessment of water quality.
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Affiliation(s)
- Dora Pavić
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Dorotea Grbin
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Amalija Blagajac
- Department of Food Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Josip Ćurko
- Department of Food Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Željka Fiket
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ana Bielen
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia.
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Wright Z, Seymour M, Paszczak K, Truttmann T, Senn K, Stilp S, Jansen N, Gosz M, Goeden L, Anantharaman V, Aravind L, Waters LS. The small protein MntS evolved from a signal peptide and acquired a novel function regulating manganese homeostasis in Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543501. [PMID: 37398132 PMCID: PMC10312517 DOI: 10.1101/2023.06.02.543501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Small proteins (< 50 amino acids) are emerging as ubiquitous and important regulators in organisms ranging from bacteria to humans, where they commonly bind to and regulate larger proteins during stress responses. However, fundamental aspects of small proteins, such as their molecular mechanism of action, downregulation after they are no longer needed, and their evolutionary provenance are poorly understood. Here we show that the MntS small protein involved in manganese (Mn) homeostasis binds and inhibits the MntP Mn transporter. Mn is crucial for bacterial survival in stressful environments, but is toxic in excess. Thus, Mn transport is tightly controlled at multiple levels to maintain optimal Mn levels. The small protein MntS adds a new level of regulation for Mn transporters, beyond the known transcriptional and post-transcriptional control. We also found that MntS binds to itself in the presence of Mn, providing a possible mechanism of downregulating MntS activity to terminate its inhibition of MntP Mn export. MntS is homologous to the signal peptide of SitA, the periplasmic metal-binding subunit of a Mn importer. Remarkably, the homologous signal peptide regions can substitute for MntS, demonstrating a functional relationship between MntS and these signal peptides. Conserved gene-neighborhoods support that MntS evolved from an ancestral SitA, acquiring a life of its own with a distinct function in Mn homeostasis. Significance This study demonstrates that the MntS small protein binds and inhibits the MntP Mn exporter, adding another layer to the complex regulation of Mn homeostasis. MntS also interacts with itself in cells with Mn, which could prevent it from regulating MntP. We propose that MntS and other small proteins might sense environmental signals and shut off their own regulation via binding to ligands (e.g., metals) or other proteins. We also provide evidence that MntS evolved from the signal peptide region of the Mn importer, SitA. Homologous SitA signal peptides can recapitulate MntS activities, showing that they have a second function beyond protein secretion. Overall, we establish that small proteins can emerge and develop novel functionalities from gene remnants.
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Phakatkar AH, Gonçalves JM, Zhou J, Ritter TG, Tamadoni Saray M, Sorokina LV, Amiri A, Angnes L, Shokuhfar T, Shahbazian-Yassar R. Enhanced Bacterial Growth by Polyelemental Glycerolate Particles. ACS APPLIED BIO MATERIALS 2023; 6:1515-1524. [PMID: 36933270 DOI: 10.1021/acsabm.2c01052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
While polyelemental alloys are shown to be promising for healthcare applications, their effectiveness in promoting bacterial growth remains unexplored. In the present work, we evaluated the interaction of polyelemental glycerolate particles (PGPs) with Escherichia coli (E. coli) bacteria. PGPs were synthesized using the solvothermal route, and nanoscale random distribution of metal cations in the glycerol matrix of PGPs was confirmed. We observed 7-fold growth of E. coli bacteria upon 4 h of interaction with quinary glycerolate (NiZnMnMgSr-Gly) particles in comparison to control E. coli bacteria. Nanoscale microscopic studies on bacteria interactions with PGPs showed the release of metal cations in the bacterium cytoplasm from PGPs. The electron microscopy imaging and chemical mapping indicated bacterial biofilm formation on PGPs without causing significant cell membrane damage. The data showed that the presence of glycerol in PGPs is effective in controlling the release of metal cations, thus preventing bacterial toxicity. The presence of multiple metal cations is expected to provide synergistic effects of nutrients needed for bacterial growth. The present work provides key microscopic insights of mechanisms by which PGPs enhance biofilm growth. This study opens the door for future applications of PGPs in areas where bacterial growth is essential including healthcare, clean energy, and the food industry.
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Affiliation(s)
- Abhijit H Phakatkar
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Josué M Gonçalves
- Department of Mechanical & Industrial Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States.,Department of Fundamental Chemistry, University of Sao Paulo, Sao Paulo, SP 05508-060, Brazil
| | - Jianshu Zhou
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Timothy G Ritter
- Department of Civil, Materials, and Environmental Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Mahmoud Tamadoni Saray
- Department of Mechanical & Industrial Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Lioudmila V Sorokina
- Department of Civil, Materials, and Environmental Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Azadeh Amiri
- Department of Mechanical & Industrial Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Lucio Angnes
- Department of Fundamental Chemistry, University of Sao Paulo, Sao Paulo, SP 05508-060, Brazil
| | - Tolou Shokuhfar
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Reza Shahbazian-Yassar
- Department of Mechanical & Industrial Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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6
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Metal-Responsive Transcription Factors Co-Regulate Anti-Sigma Factor (Rsd) and Ribosome Dimerization Factor Expression. Int J Mol Sci 2023; 24:ijms24054717. [PMID: 36902154 PMCID: PMC10003395 DOI: 10.3390/ijms24054717] [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: 12/27/2022] [Revised: 02/15/2023] [Accepted: 02/20/2023] [Indexed: 03/05/2023] Open
Abstract
Bacteria exposed to stress survive by regulating the expression of several genes at the transcriptional and translational levels. For instance, in Escherichia coli, when growth is arrested in response to stress, such as nutrient starvation, the anti-sigma factor Rsd is expressed to inactivate the global regulator RpoD and activate the sigma factor RpoS. However, ribosome modulation factor (RMF) expressed in response to growth arrest binds to 70S ribosomes to form inactive 100S ribosomes and inhibit translational activity. Moreover, stress due to fluctuations in the concentration of metal ions essential for various intracellular pathways is regulated by a homeostatic mechanism involving metal-responsive transcription factors (TFs). Therefore, in this study, we examined the binding of a few metal-responsive TFs to the promoter regions of rsd and rmf through promoter-specific TF screening and studied the effects of these TFs on the expression of rsd and rmf in each TF gene-deficient E. coli strain through quantitative PCR, Western blot imaging, and 100S ribosome formation analysis. Our results suggest that several metal-responsive TFs (CueR, Fur, KdpE, MntR, NhaR, PhoP, ZntR, and ZraR) and metal ions (Cu2+, Fe2+, K+, Mn2+, Na+, Mg2+, and Zn2+) influence rsd and rmf gene expression while regulating transcriptional and translational activities.
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7
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Huynh U, Zastrow ML. Metallobiology of Lactobacillaceae in the gut microbiome. J Inorg Biochem 2023; 238:112023. [PMID: 36270041 PMCID: PMC9888405 DOI: 10.1016/j.jinorgbio.2022.112023] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/26/2022] [Accepted: 10/03/2022] [Indexed: 11/21/2022]
Abstract
Lactobacillaceae are a diverse family of lactic acid bacteria found in the gut microbiota of humans and many animals. These bacteria exhibit beneficial effects on intestinal health, including modulating the immune system and providing protection against pathogens, and many species are frequently used as probiotics. Gut bacteria acquire essential metal ions, like iron, zinc, and manganese, through the host diet and changes to the levels of these metals are often linked to alterations in microbial community composition, susceptibility to infection, and gastrointestinal diseases. Lactobacillaceae are frequently among the organisms increased or decreased in abundance due to changes in metal availability, yet many of the molecular mechanisms underlying these changes have yet to be defined. Metal requirements and metallotransporters have been studied in some species of Lactobacillaceae, but few of the mechanisms used by these bacteria to respond to metal limitation or excess have been investigated. This review provides a current overview of these mechanisms and covers how iron, zinc, and manganese impact Lactobacillaceae in the gut microbiota with an emphasis on their biochemical roles, requirements, and homeostatic mechanisms in several species.
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Affiliation(s)
- Uyen Huynh
- Department of Chemistry, University of Houston, Houston, TX, USA
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8
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Iron Acquisition Mechanisms and Their Role in the Virulence of Acinetobacter baumannii. Infect Immun 2022; 90:e0022322. [PMID: 36066263 PMCID: PMC9584212 DOI: 10.1128/iai.00223-22] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Iron is an essential element for survival of most organisms. One mechanism of host defense is to tightly chelate iron to several proteins to limit its extracellular availability. This has forced pathogens such as Acinetobacter baumannii to adapt mechanisms for the acquisition and utilization of iron even in iron-limiting conditions. A. baumannii uses a variety of iron acquisition strategies to meet its iron requirements. It can lyse erythrocytes to harvest the heme molecules, use iron-chelating siderophores, and use outer membrane vesicles to acquire iron. Iron acquisition pathways, in general, have been seen to affect many other virulence factors such as cell adherence, cell motility, and biofilm formation. The knowledge gained from research on iron acquisition led to the synthesis of the antibiotic cefiderocol, which uses iron uptake pathways for entry into the cell with some success as a novel cephalosporin. Understanding the mechanisms of iron acquisition of A. baumannii allows for insight into clinical infections and offer potential targets for novel antibiotics or potentiators of current drugs.
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Valenti R, Jabłońska J, Tawfik DS. Characterization of ancestral Fe/Mn superoxide dismutases indicates their cambialistic origin. Protein Sci 2022; 31:e4423. [PMID: 36173172 PMCID: PMC9490801 DOI: 10.1002/pro.4423] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/29/2022] [Accepted: 08/09/2022] [Indexed: 11/10/2022]
Abstract
Superoxide dismutases (SODs) are critical metalloenzymes mitigating the damages of the modern oxygenated world. However, the emergence of one family of SODs, the Fe/Mn SOD, has been recurrently proposed to predate the great oxygenation event (GOE). This ancient family lacks metal binding selectivity, but displays strong catalytic selectivity. Therefore, some homologues would only be active when bound to Fe or Mn, although others, dubbed cambialistic, would function when loaded with either ion. This posed the longstanding question about the identity of the cognate metal ion of the first SODs to emerge. In this work, we utilize ancestral sequence reconstruction techniques to infer the earliest SODs. We show that the “ancestors” are active in vivo and in vitro. Further, we test their metal specificity and demonstrate that they are cambialistic in nature. Our findings shed light on how the predicted Last Common Universal Ancestor was capable of dealing with decomposition of the superoxide anion, and the early relationship between life, oxygen, and metal ion availability.
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Affiliation(s)
- Rosario Valenti
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot Israel
| | - Jagoda Jabłońska
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot Israel
| | - Dan S. Tawfik
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot Israel
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10
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Xie S, Xu B, Tang R, Chen S, Lei C, Nie Z. Kinetics Accelerated CRISPR-Cas12a Enabling Live-Cell Monitoring of Mn 2+ Homeostasis. Anal Chem 2022; 94:10159-10167. [PMID: 35786883 DOI: 10.1021/acs.analchem.2c01461] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The CRISPR/Cas12a system has been repurposed as a versatile nuclei acid bio-imaging tool, but its utility in sensing non-nucleic acid analytes in living cells has been less exploited. Herein, we demonstrated the ability of Mn2+ to accelerate cleavage kinetics of Cas12a and deployed for live-cell Mn2+ sensing by leveraging the accelerated trans-cleavage for signal reporting. In this work, we found that Mn2+ could significantly boost both the cis-cleavage and trans-cleavage activities of Cas12a. On the basis of this phenomenon, we harnessed CRISPR-Cas12a as a direct sensing system for Mn2+, which achieved robust Mn2+ detection in the concentration range of 0.5-700 μM within 15 min in complex biological samples. Furthermore, we also demonstrated the versatility of this system to sense Mn2+ in the cytoplasm of living cells. With the usage of a conditional guide RNA, this Cas12a-based sensing method was applied to study the cytotoxicity of Mn2+ in living nerve cells, offering a valuable tool to reveal the cellular response of nerve cells to Mn2+ disorder and homeostasis.
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Affiliation(s)
- Shiyi Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Benfeng Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Rui Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Siyu Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
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11
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Djahanschiri B, Di Venanzio G, Distel JS, Breisch J, Dieckmann MA, Goesmann A, Averhoff B, Göttig S, Wilharm G, Feldman MF, Ebersberger I. Evolutionarily stable gene clusters shed light on the common grounds of pathogenicity in the Acinetobacter calcoaceticus-baumannii complex. PLoS Genet 2022; 18:e1010020. [PMID: 35653398 PMCID: PMC9162365 DOI: 10.1371/journal.pgen.1010020] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/04/2022] [Indexed: 11/19/2022] Open
Abstract
Nosocomial pathogens of the Acinetobacter calcoaceticus-baumannii (ACB) complex are a cautionary example for the world-wide spread of multi- and pan-drug resistant bacteria. Aiding the urgent demand for novel therapeutic targets, comparative genomics studies between pathogens and their apathogenic relatives shed light on the genetic basis of human-pathogen interaction. Yet, existing studies are limited in taxonomic scope, sensing of the phylogenetic signal, and resolution by largely analyzing genes independent of their organization in functional gene clusters. Here, we explored more than 3,000 Acinetobacter genomes in a phylogenomic framework integrating orthology-based phylogenetic profiling and microsynteny conservation analyses. We delineate gene clusters in the type strain A. baumannii ATCC 19606 whose evolutionary conservation indicates a functional integration of the subsumed genes. These evolutionarily stable gene clusters (ESGCs) reveal metabolic pathways, transcriptional regulators residing next to their targets but also tie together sub-clusters with distinct functions to form higher-order functional modules. We shortlisted 150 ESGCs that either co-emerged with the pathogenic ACB clade or are preferentially found therein. They provide a high-resolution picture of genetic and functional changes that coincide with the manifestation of the pathogenic phenotype in the ACB clade. Key innovations are the remodeling of the regulatory-effector cascade connecting LuxR/LuxI quorum sensing via an intermediate messenger to biofilm formation, the extension of micronutrient scavenging systems, and the increase of metabolic flexibility by exploiting carbon sources that are provided by the human host. We could show experimentally that only members of the ACB clade use kynurenine as a sole carbon and energy source, a substance produced by humans to fine-tune the antimicrobial innate immune response. In summary, this study provides a rich and unbiased set of novel testable hypotheses on how pathogenic Acinetobacter interact with and ultimately infect their human host. It is a comprehensive resource for future research into novel therapeutic strategies. The spread of multi- and pan-drug resistant bacterial pathogens is a worldwide threat to human health. Understanding the genetics of host colonization and infection can substantially help in devising novel ways of treatment. Acinetobacter baumannii, a nosocomial pathogen ranked top by the World Health Organization in the list of bacteria for which novel therapeutic approaches are needed, is a prime example. Here, we have carved out the genetic make-up that distinguishes A. baumannii and its pathogenic next relatives from other and mostly apathogenic Acinetobacter species. We found a rich spectrum of pathways and regulatory modules that reveal how the pathogens have modified biofilm formation, iron scavenging, and their carbohydrate metabolism to adapt to their human host. Among these, the capability to metabolize kynurenine is particularly intriguing. Humans produce this substance to contain bacterial invaders and to fine-tune the innate immune response. But A. baumannii and closely related pathogens found a way to feed on kynurenine. This suggests that the pathogens might be able to dysregulate the human immune response. In summary, our study substantially deepens the understanding of how a highly critical pathogen interacts with its host, which substantially eases the identification of novel targets for innovative therapeutic strategies.
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Affiliation(s)
- Bardya Djahanschiri
- Applied Bioinformatics Group, Inst. of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Gisela Di Venanzio
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Jesus S. Distel
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Jennifer Breisch
- Inst. of Molecular Biosciences, Department of Molecular Microbiology and Bioenergetics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Gießen, Gießen, Germany
| | - Beate Averhoff
- Inst. of Molecular Biosciences, Department of Molecular Microbiology and Bioenergetics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Stephan Göttig
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University, Frankfurt, Germany
| | | | - Mario F. Feldman
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Inst. of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (S-BIKF), Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
- * E-mail:
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12
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Huynh U, Qiao M, King J, Trinh B, Valdez J, Haq M, Zastrow ML. Differential Effects of Transition Metals on Growth and Metal Uptake for Two Distinct Lactobacillus Species. Microbiol Spectr 2022; 10:e0100621. [PMID: 35080431 PMCID: PMC8791193 DOI: 10.1128/spectrum.01006-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022] Open
Abstract
Lactobacillus is a genus of Gram-positive bacteria and comprises a major part of the lactic acid bacteria group that converts sugars to lactic acid. Lactobacillus species found in the gut microbiota are considered beneficial to human health and commonly used in probiotic formulations, but their molecular functions remain poorly defined. Microbes require metal ions for growth and function and must acquire them from the surrounding environment. Therefore, lactobacilli need to compete with other gut microbes for these nutrients, although their metal requirements are not well-understood. Indeed, the abundance of lactobacilli in the microbiota is frequently affected by dietary intake of essential metals like zinc, manganese, and iron, but few studies have investigated the role of metals, especially zinc, in the physiology and metabolism of Lactobacillus species. Here, we investigated metal uptake by quantifying total cellular metal contents and compared how transition metals affect the growth of two distinct Lactobacillus species, Lactobacillus plantarum ATCC 14917 and Lactobacillus acidophilus ATCC 4356. When grown in rich or metal-limited medium, both species took up more manganese, zinc, and iron compared with other transition metals measured. Distinct zinc-, manganese- and iron-dependent patterns were observed in the growth kinetics for these species and while certain levels of each metal promoted the growth kinetics of both Lactobacillus species, the effects depend significantly on the culture medium and growth conditions. IMPORTANCE The gastrointestinal tract contains trillions of microorganisms, which are central to human health. Lactobacilli are considered beneficial microbiota members and are often used in probiotics, but their molecular functions, and especially those which are metal-dependent, remain poorly defined. Abundance of lactobacilli in the microbiota is frequently affected by dietary intake of essential metals like manganese, zinc, and iron, but results are complex, sometimes contradictory, and poorly predictable. There is a significant need to understand how host diet and metabolism will affect the microbiota, given that changes in microbiota composition are linked with disease and infection. The significance of our research is in gaining insight to how metals distinctly affect individual Lactobacillus species, which could lead to novel therapeutics and improved medical treatment. Growth kinetics and quantification of metal contents highlights how distinct species can respond differently to varied metal availability and provide a foundation for future molecular and mechanistic studies.
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Affiliation(s)
- Uyen Huynh
- Department of Chemistry, University of Houston, Houston, Texas, United States
| | - Muxin Qiao
- Department of Chemistry, University of Houston, Houston, Texas, United States
| | - John King
- Department of Chemistry, University of Houston, Houston, Texas, United States
| | - Brittany Trinh
- Department of Chemistry, University of Houston, Houston, Texas, United States
| | - Juventino Valdez
- Department of Chemistry, University of Houston, Houston, Texas, United States
| | - Marium Haq
- Department of Chemistry, University of Houston, Houston, Texas, United States
| | - Melissa L. Zastrow
- Department of Chemistry, University of Houston, Houston, Texas, United States
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13
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Abstract
Iron acquisition is essential for almost all living organisms. In certain environments, ferrous iron is the most prevalent form of this element. Feo is the most widespread system for ferrous iron uptake in bacteria and is critical for virulence in some species. The canonical architecture of Feo consists of a large transmembrane nucleoside triphosphatase (NTPase) protein, FeoB, and two accessory cytoplasmic proteins, FeoA and FeoC. The role of the latter components and the mechanism by which Feo orchestrates iron transport are unclear. In this study, we conducted a comparative analysis of Feo protein sequences to gain insight into the evolutionary history of this transporter. We identified instances of how horizontal gene transfer contributed to the evolution of Feo. Also, we found that FeoC, while absent in most lineages, is largely present in the Gammaproteobacteria group, although its sequence is poorly conserved. We propose that FeoC, which may couple FeoB NTPase activity with pore opening, was an ancestral element that has been dispensed with through mutations in FeoA and FeoB in some lineages. We provide experimental evidence supporting this hypothesis by isolating and characterizing FeoC-independent mutants of the Vibrio cholerae Feo system. Also, we confirmed that the closely related species Shewanella oneidensis does not require FeoC; thus, Vibrio FeoC sequences may resemble transitional forms on an evolutionary pathway toward FeoC-independent transporters. Finally, by combining data from our bioinformatic analyses with this experimental evidence, we propose an evolutionary model for the Feo system in bacteria. IMPORTANCE Feo, a ferrous iron transport system composed of three proteins (FeoA, -B, and -C), is the most prevalent bacterial iron transporter. It plays an important role in iron acquisition in low-oxygen environments and some host-pathogen interactions. The large transmembrane protein FeoB provides the channel for the transport of iron into the bacterial cell, but the functions of the two small, required accessory proteins FeoA and FeoC are not well understood. Analysis of the evolution of this transporter shows that FeoC is poorly conserved and has been lost from many bacterial lineages. Experimental evidence indicates that FeoC may have different functions in different species that retain this protein, and the loss of FeoC is promoted by mutations in FeoA or by the fusion of FeoA and FeoB.
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14
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Gingerich AD, Mousa JJ. Diverse Mechanisms of Protective Anti-Pneumococcal Antibodies. Front Cell Infect Microbiol 2022; 12:824788. [PMID: 35155281 PMCID: PMC8834882 DOI: 10.3389/fcimb.2022.824788] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/11/2022] [Indexed: 02/05/2023] Open
Abstract
The gram-positive bacterium Streptococcus pneumoniae is a leading cause of pneumonia, otitis media, septicemia, and meningitis in children and adults. Current prevention and treatment efforts are primarily pneumococcal conjugate vaccines that target the bacterial capsule polysaccharide, as well as antibiotics for pathogen clearance. While these methods have been enormously effective at disease prevention and treatment, there has been an emergence of non-vaccine serotypes, termed serotype replacement, and increasing antibiotic resistance among these serotypes. To combat S. pneumoniae, the immune system must deploy an arsenal of antimicrobial functions. However, S. pneumoniae has evolved a repertoire of evasion techniques and is able to modulate the host immune system. Antibodies are a key component of pneumococcal immunity, targeting both the capsule polysaccharide and protein antigens on the surface of the bacterium. These antibodies have been shown to play a variety of roles including increasing opsonophagocytic activity, enzymatic and toxin neutralization, reducing bacterial adherence, and altering bacterial gene expression. In this review, we describe targets of anti-pneumococcal antibodies and describe antibody functions and effectiveness against S. pneumoniae.
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Affiliation(s)
- Aaron D. Gingerich
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Jarrod J. Mousa
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- Department of Biochemistry and Molecular Biology, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, United States
- *Correspondence: Jarrod J. Mousa,
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15
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Shi C, Maktabdar M. Lactic Acid Bacteria as Biopreservation Against Spoilage Molds in Dairy Products - A Review. Front Microbiol 2022; 12:819684. [PMID: 35154045 PMCID: PMC8826399 DOI: 10.3389/fmicb.2021.819684] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 12/21/2021] [Indexed: 12/22/2022] Open
Abstract
Mold spoilage of dairy products such as yogurt is a concern in dairy industry. Not only does it lead to substantial food waste, economic losses, and even brand image damage, but it may also cause public health concern due to the potential production of mycotoxin. Good hygiene practices are necessary to prevent contamination, but contamination may nevertheless occur at the production site and, not least, at the site of the consumer. In recent years, there has been a growing interest from consumers for "clean label" food products, which are natural, less-processed, and free of added, chemical preservatives, and a wish for shelf lives of considerable length in order to minimize food waste. This has sparked an interest in using lactic acid bacteria (LAB) or their metabolites as biopreservatives as a way to limit the growth of spoilage organisms in dairy products. A range of compounds produced by LAB with potential antifungal activity have been described as contributing factors to the inhibitory effect of LAB. More recently, growth inhibition effects caused by specific competitive exclusion have been elucidated. It has also become clear that the sensitivity toward both individual antifungal compounds and competition mechanisms differ among molds. In this review, the main spoilage molds encountered in dairy products are introduced, and an overview of the antifungal activity of LAB against different spoilage molds is presented including the main antifungal compounds derived from LAB cultures and the sensitivity of the spoilage molds observed toward these compounds. The recent findings of the role of competitive exclusion with emphasis on manganese depletion and the possible implications of this for biopreservation are described. Finally, some of the knowledge gaps, future challenges, and trends in the application of LAB biopreservation in dairy products are discussed.
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Affiliation(s)
- Ce Shi
- Section of Food Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
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16
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Hemkemeyer M, Schwalb SA, Heinze S, Joergensen RG, Wichern F. Functions of elements in soil microorganisms. Microbiol Res 2021; 252:126832. [PMID: 34508963 DOI: 10.1016/j.micres.2021.126832] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022]
Abstract
The soil microbial community fulfils various functions, such as nutrient cycling and carbon (C) sequestration, therefore contributing to maintenance of soil fertility and mitigation of global warming. In this context, a major focus of research has been on C, nitrogen (N) and phosphorus (P) cycling. However, from aquatic and other environments, it is well known that other elements beyond C, N, and P are essential for microbial functioning. Nonetheless, for soil microorganisms this knowledge has not yet been synthesised. To gain a better mechanistic understanding of microbial processes in soil systems, we aimed at summarising the current knowledge on the function of a range of essential or beneficial elements, which may affect the efficiency of microbial processes in soil. This knowledge is discussed in the context of microbial driven nutrient and C cycling. Our findings may support future investigations and data evaluation, where other elements than C, N, and P affect microbial processes.
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Affiliation(s)
- Michael Hemkemeyer
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany.
| | - Sanja A Schwalb
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany
| | - Stefanie Heinze
- Department of Soil Science & Soil Ecology, Ruhr-University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Rainer Georg Joergensen
- Department of Soil Biology and Plant Nutrition, University of Kassel, Nordbahnhofstr. 1a, 37213 Witzenhausen, Germany
| | - Florian Wichern
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany
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17
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Rummel PS, Beule L, Hemkemeyer M, Schwalb SA, Wichern F. Black Soldier Fly Diet Impacts Soil Greenhouse Gas Emissions From Frass Applied as Fertilizer. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.709993] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Increased global production of animal-based protein results in high greenhouse gas (GHG) emissions and other adverse consequences for human and planetary health. Recently, commercial insect rearing has been claimed a more sustainable source of animal protein. However, this system also leaves residues called frass, which—depending on the insect diet—is rich in carbon (C) and nitrogen (N), and could thus be used as fertilizer in agriculture. The impact of this kind of fertilizer on soil GHG emissions is yet unknown. Therefore, we investigated the effect of black soldier fly (Hermetia illucens L.) frass derived from a carbohydrate (Carb-) or a protein (Prot-) based diet applied at two different application rates to an arable soil on C and N fluxes and microbial properties in a 40-day incubation experiment. CO2, N2O, NO, N2, CH4, water extractable organic C (WEOC), and inorganic N were continuously measured quantitatively. At the end of the incubation, microbial biomass (MB), stoichiometry, community composition, and abundance of functional genes were assessed. Along with a strong increase in WEOC and CO2, Carb-frass caused strong initial N2O emissions associated with high N and C availability. In contrast, Prot-frass showed lower CO2 emissions and N2O release, although soil nitrate levels were higher. At the end of incubation, MB was significantly increased, which was more pronounced following Carb-frass as compared to Prot-frass application, and at higher amendment rates. Fungal abundance increased most from both frass types with an even stronger response at higher application rates, whereas bacterial abundance rose following Carb-frass as compared to Prot-application. Abundance of functional genes related to ammonia-oxidizing bacteria and archaea were enhanced by high frass application but did not clearly differ between frass types. C use efficiency of microorganisms, as revealed by the metabolic quotient, was most strongly reduced in the high Prot-frass application rate. Overall, insect diet influenced available C and N in frass and thus affected mineralization dynamics, GHG emissions, and microbial growth. Overall, emissions were very high undermining the potential environmental benefit of insect based protein production and calling for more detailed analyses before frass is widely applied in agriculture.
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18
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Soldatova AV, Fu W, Romano CA, Tao L, Casey WH, Britt RD, Tebo BM, Spiro TG. Metallo-inhibition of Mnx, a bacterial manganese multicopper oxidase complex. J Inorg Biochem 2021; 224:111547. [PMID: 34403930 DOI: 10.1016/j.jinorgbio.2021.111547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/28/2021] [Accepted: 07/13/2021] [Indexed: 11/29/2022]
Abstract
The manganese oxidase complex, Mnx, from Bacillus sp. PL-12 contains a multicopper oxidase (MCO) and oxidizes dissolved Mn(II) to form insoluble manganese oxide (MnO2) mineral. Previous kinetic and spectroscopic analyses have shown that the enzyme's mechanism proceeds through an activation step that facilitates formation of a series of binuclear Mn complexes in the oxidation states II, III, and IV on the path to MnO2 formation. We now demonstrate that the enzyme is inhibited by first-row transition metals in the order of the Irving-Williams series. Zn(II) strongly (Ki ~ 1.5 μM) inhibits both activation and turnover steps, as well as the rate of Mn(II) binding. The combined Zn(II) and Mn(II) concentration dependence establishes that the inhibition is non-competitive. This result is supported by electron paramagnetic resonance (EPR) spectroscopy, which reveals unaltered Mnx-bound Mn(II) EPR signals, both mono- and binuclear, in the presence of Zn(II). We infer that inhibitory metals bind at a site separate from the substrate sites and block the conformation change required to activate the enzyme, a case of allosteric inhibition. The likely biological role of this inhibitory site is discussed in the context of Bacillus spore physiology. While Cu(II) inhibits Mnx strongly, in accord with the Irving-Williams series, it increases Mnx activation at low concentrations, suggesting that weakly bound Cu, in addition to the four canonical MCO-Cu, may support enzyme activity, perhaps as an electron transfer agent.
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Affiliation(s)
- Alexandra V Soldatova
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States
| | - Wen Fu
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Christine A Romano
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Lizhi Tao
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - William H Casey
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States; Earth and Planetary Sciences Department, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - R David Britt
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Bradley M Tebo
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Thomas G Spiro
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States.
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19
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Bosma EF, Rau MH, van Gijtenbeek LA, Siedler S. Regulation and distinct physiological roles of manganese in bacteria. FEMS Microbiol Rev 2021; 45:6284802. [PMID: 34037759 PMCID: PMC8632737 DOI: 10.1093/femsre/fuab028] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/21/2021] [Indexed: 02/06/2023] Open
Abstract
Manganese (Mn2+) is an essential trace element within organisms spanning the entire tree of life. In this review, we provide an overview of Mn2+ transport and the regulation of its homeostasis in bacteria, with a focus on its functions beyond being a cofactor for enzymes. Crucial differences in Mn2+ homeostasis exist between bacterial species that can be characterized to have an iron- or manganese-centric metabolism. Highly iron-centric species require minimal Mn2+ and mostly use it as a mechanism to cope with oxidative stress. As a consequence, tight regulation of Mn2+ uptake is required, while organisms that use both Fe2+ and Mn2+ need other layers of regulation for maintaining homeostasis. We will focus in detail on manganese-centric bacterial species, in particular lactobacilli, that require little to no Fe2+ and use Mn2+ for a wider variety of functions. These organisms can accumulate extraordinarily high amounts of Mn2+ intracellularly, enabling the nonenzymatic use of Mn2+ for decomposition of reactive oxygen species while simultaneously functioning as a mechanism of competitive exclusion. We further discuss how Mn2+ accumulation can provide both beneficial and pathogenic bacteria with advantages in thriving in their niches.
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Affiliation(s)
- Elleke F Bosma
- Chr. Hansen A/S, Discovery, R&D, 2970 Hoersholm, Denmark
| | - Martin H Rau
- Chr. Hansen A/S, Discovery, R&D, 2970 Hoersholm, Denmark
| | | | - Solvej Siedler
- Corresponding author: Boege Allé 10-12, 2970 Hoersholm, Denmark. Tel: +45 52 18 08 25; E-mail:
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20
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Yang Y, Yue Y, Song N, Li C, Yuan Z, Wang Y, Ma Y, Li H, Zhang F, Wang W, Jia H, Li P, Li X, Wang Q, Ding Z, Dong H, Gu L, Li B. The YdiU Domain Modulates Bacterial Stress Signaling through Mn 2+-Dependent UMPylation. Cell Rep 2021; 32:108161. [PMID: 32966796 DOI: 10.1016/j.celrep.2020.108161] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 07/17/2020] [Accepted: 08/26/2020] [Indexed: 12/28/2022] Open
Abstract
Sensing stressful conditions and adjusting the cellular metabolism to adapt to the environment are essential activities for bacteria to survive in variable situations. Here, we describe a stress-related protein, YdiU, and characterize YdiU as an enzyme that catalyzes the covalent attachment of uridine-5'-monophosphate to a protein tyrosine/histidine residue, an unusual modification defined as UMPylation. Mn2+ serves as an essential co-factor for YdiU-mediated UMPylation. UTP and Mn2+ binding converts YdiU to an aggregate-prone state facilitating the recruitment of chaperones. The UMPylation of chaperones prevents them from binding co-factors or clients, thereby impairing their function. Consistent with the recent finding that YdiU acts as an AMPylator, we further demonstrate that the self-AMPylation of YdiU padlocks its chaperone-UMPylation activity. A detailed mechanism is proposed based on the crystal structures of Apo-YdiU and YdiU-AMPNPP-Mn2+ and on molecular dynamics simulation models of YdiU-UTP-Mn2+ and YdiU-UTP-peptide. In vivo data demonstrate that YdiU effectively protects Salmonella from stress-induced ATP depletion through UMPylation.
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Affiliation(s)
- Yinlong Yang
- Key Laboratory of Rare and Uncommon Diseases, Department of Microbiology, Institute of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250062, China; School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan, Shandong 250062, China
| | - Yingying Yue
- Key Laboratory of Rare and Uncommon Diseases, Department of Microbiology, Institute of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250062, China
| | - Nannan Song
- Key Laboratory of Rare and Uncommon Diseases, Department of Microbiology, Institute of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250062, China
| | - Cuiling Li
- Key Laboratory of Rare and Uncommon Diseases, Department of Microbiology, Institute of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250062, China
| | - Zenglin Yuan
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Yan Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong 266003, China
| | - Yue Ma
- Key Laboratory of Rare and Uncommon Diseases, Department of Microbiology, Institute of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250062, China; School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan, Shandong 250062, China
| | - Hui Li
- Key Laboratory of Rare and Uncommon Diseases, Department of Microbiology, Institute of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250062, China; School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan, Shandong 250062, China
| | - Fengyu Zhang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Weiwei Wang
- Key Laboratory of Rare and Uncommon Diseases, Department of Microbiology, Institute of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250062, China
| | - Haihong Jia
- Key Laboratory of Rare and Uncommon Diseases, Department of Microbiology, Institute of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250062, China
| | - Peng Li
- Key Laboratory of Rare and Uncommon Diseases, Department of Microbiology, Institute of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250062, China
| | - Xiaobing Li
- Key Laboratory of Rare and Uncommon Diseases, Department of Microbiology, Institute of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250062, China
| | - Qi Wang
- Key Laboratory of Rare and Uncommon Diseases, Department of Microbiology, Institute of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250062, China; School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan, Shandong 250062, China
| | - Zhe Ding
- Advanced Medical Research Institute, Translational Medicine Core Facility, Shandong University, Jinan, Shandong 250012, China
| | - Hongjie Dong
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Bingqing Li
- Key Laboratory of Rare and Uncommon Diseases, Department of Microbiology, Institute of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250062, China.
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21
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Scott NR, Mann B, Tuomanen EI, Orihuela CJ. Multi-Valent Protein Hybrid Pneumococcal Vaccines: A Strategy for the Next Generation of Vaccines. Vaccines (Basel) 2021; 9:209. [PMID: 33801372 PMCID: PMC8002124 DOI: 10.3390/vaccines9030209] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/23/2021] [Accepted: 02/25/2021] [Indexed: 12/15/2022] Open
Abstract
Streptococcus pneumoniae (Spn) is a bacterial pathogen known to colonize the upper respiratory tract and cause serious opportunistic diseases such as pneumonia, bacteremia, sepsis and meningitis. As a consequence, millions of attributable deaths occur annually, especially among infants, the elderly and immunocompromised individuals. Although current vaccines, composed of purified pneumococcal polysaccharide in free form or conjugated to a protein carrier, are widely used and have been demonstrated to be effective in target groups, Spn has continued to colonize and cause life-threatening disease in susceptible populations. This lack of broad protection highlights the necessity of improving upon the current "gold standard" pneumococcal vaccines to increase protection both by decreasing colonization and reducing the incidence of sterile-site infections. Over the past century, most of the pneumococcal proteins that play an essential role in colonization and pathogenesis have been identified and characterized. Some of these proteins have the potential to serve as antigens in a multi-valent protein vaccine that confers capsule independent protection. This review seeks to summarize the benefits and limitations of the currently employed vaccine strategies, describes how leading candidate proteins contribute to pneumococcal disease development, and discusses the potential of these proteins as protective antigens-including as a hybrid construct.
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Affiliation(s)
- Ninecia R. Scott
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Beth Mann
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (B.M.); (E.I.T.)
| | - Elaine I. Tuomanen
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (B.M.); (E.I.T.)
| | - Carlos J. Orihuela
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
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22
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Kundra P, Rachmühl C, Lacroix C, Geirnaert A. Role of Dietary Micronutrients on Gut Microbial Dysbiosis and Modulation in Inflammatory Bowel Disease. Mol Nutr Food Res 2021. [DOI: 10.1002/mnfr.201901271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Palni Kundra
- Laboratory of Food Biotechnology Institute of Food Nutrition and Health Schmelzbergstrasse 7 Zürich 8092 Switzerland
| | - Carole Rachmühl
- Laboratory of Food Biotechnology Institute of Food Nutrition and Health Schmelzbergstrasse 7 Zürich 8092 Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology Institute of Food Nutrition and Health Schmelzbergstrasse 7 Zürich 8092 Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology Institute of Food Nutrition and Health Schmelzbergstrasse 7 Zürich 8092 Switzerland
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Manganese homeostasis at the host-pathogen interface and in the host immune system. Semin Cell Dev Biol 2021; 115:45-53. [PMID: 33419608 DOI: 10.1016/j.semcdb.2020.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 02/07/2023]
Abstract
Manganese serves as an indispensable catalytic center and the structural core of various enzymes that participate in a plethora of biological processes, including oxidative phosphorylation, glycosylation, and signal transduction. In pathogenic microorganisms, manganese is required for survival by maintaining basic biochemical activity and virulence; in contrast, the host utilizes a process known as nutritional immunity to sequester manganese from invading pathogens. Recent epidemiological and animal studies have shown that manganese increases the immune response in a wide range of vertebrates, including humans, rodents, birds, and fish. On the other hand, excess manganese can cause neurotoxicity and other detrimental effects. Here, we review recent data illustrating the essential role of manganese homeostasis at the host-pathogen interface and in the host immune system. We also discuss the accumulating body of evidence that manganese modulates various signaling pathways in immune processes. Finally, we discuss the key molecular players involved in manganese's immune regulatory function, as well as the clinical implications with respect to cancer immunotherapy.
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Suzuki K, Shinohara Y, Kurniawan YN. Role of Plasmids in Beer Spoilage Lactic Acid Bacteria: A Review. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2020. [DOI: 10.1080/03610470.2020.1843899] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Koji Suzuki
- Asahi Quality and Innovations, Ltd., Moriya, Japan
| | - Yuji Shinohara
- Department of Safety Technology Development, Analytical Science Laboratories, Asahi Quality and Innovations, Ltd., Moriya, Japan
| | - Yohanes Novi Kurniawan
- Department of Safety Technology Development, Analytical Science Laboratories, Asahi Quality and Innovations, Ltd., Moriya, Japan
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25
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Wünsch D, Strijkstra A, Wöhlbrand L, Freese HM, Scheve S, Hinrichs C, Trautwein K, Maczka M, Petersen J, Schulz S, Overmann J, Rabus R. Global Response of Phaeobacter inhibens DSM 17395 to Deletion of Its 262-kb Chromid Encoding Antibiotic Synthesis. Microb Physiol 2020; 30:9-24. [PMID: 32958725 DOI: 10.1159/000508591] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/11/2020] [Indexed: 11/19/2022]
Abstract
The marine alphaproteobacterium Phaeobacter inhibens DSM 17395, a member of the Roseobacter group, was recently shown to markedly enhance growth upon deletion of its 262-kb chromid encoding biosynthesis of tropodithietic acid (TDA). To scrutinize the metabolic/regulatory adaptations that underlie enhanced growth of the Δ262 mutant, its transcriptome and proteome compared to the wild type were investigated in process-controlled bioreactors with Casamino Acids as growth substrate. Genome resequencing revealed only few additional genetic changes (a heterogenic insertion, prophage activation, and several point mutations) between wild type and Δ262 mutant, albeit with no conceivable effect on the studied growth physiology. The abundances of the vast majority of transcripts and proteins involved in the catabolic network for complete substrate oxidation to CO2 were found to be unchanged, suggesting that the enhanced amino acid utilization of the Δ262 mutant did not require elevated synthesis of most enzymes of the catabolic network. Similarly, constituents of genetic information processing and cellular processes remained mostly unchanged. In contrast, 426 genes displayed differential expression, of which 410 were localized on the 3.2-Mb chromosome, 5 on the 65-kb chromid, and 11 on the 78-kb chromid. Notably, the branched-chain amino transferase IlvE acting on rapidly utilized Val, Ile, and Leu was upregulated. Moreover, the transportome was reconfigured, as evidenced from increased abundances of transcripts and proteins of several uptake systems for amino acids and inorganic nutrients (e.g., phosphate). Some components of the respiratory chain were also upregulated, which correlates with the higher respiration rates of the Δ262 mutant. Furthermore, chromosomally encoded transcripts and proteins that are peripherally related to TDA biosynthesis (e.g., the serine acyl transferase CysE) were strongly downregulated in the Δ262 mutant. Taken together, these observations reflect adaptations to enhanced growth as well as the functional interconnectivity of the replicons of P. inhibens DSM 17395.
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Affiliation(s)
- Daniel Wünsch
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Annemieke Strijkstra
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Heike M Freese
- Department Microbial Ecology and Diversity, Leibniz Institute German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine Scheve
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Christina Hinrichs
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Kathleen Trautwein
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Michael Maczka
- Institute of Organic Chemistry, Technische Universität Carolo-Wilhelmina zu Braunschweig, Braunschweig, Germany
| | - Jörn Petersen
- Department Microbial Ecology and Diversity, Leibniz Institute German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Stefan Schulz
- Institute of Organic Chemistry, Technische Universität Carolo-Wilhelmina zu Braunschweig, Braunschweig, Germany
| | - Jörg Overmann
- Department Microbial Ecology and Diversity, Leibniz Institute German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany,
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Costa OYA, Oguejiofor C, Zühlke D, Barreto CC, Wünsche C, Riedel K, Kuramae EE. Impact of Different Trace Elements on the Growth and Proteome of Two Strains of Granulicella, Class "Acidobacteriia". Front Microbiol 2020; 11:1227. [PMID: 32625179 PMCID: PMC7315648 DOI: 10.3389/fmicb.2020.01227] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/14/2020] [Indexed: 12/24/2022] Open
Abstract
Acidobacteria represents one of the most dominant bacterial groups across diverse ecosystems. However, insight into their ecology and physiology has been hampered by difficulties in cultivating members of this phylum. Previous cultivation efforts have suggested an important role of trace elements for the proliferation of Acidobacteria, however, the impact of these metals on their growth and metabolism is not known. In order to gain insight into this relationship, we evaluated the effect of trace element solution SL10 on the growth of two strains (5B5 and WH15) of Acidobacteria belonging to the genus Granulicella and studied the proteomic responses to manganese (Mn). Granulicella species had highest growth with the addition of Mn, as well as higher tolerance to this metal compared to seven other metal salts. Variations in tolerance to metal salt concentrations suggests that Granulicella sp. strains possess different mechanisms to deal with metal ion homeostasis and stress. Furthermore, Granulicella sp. 5B5 might be more adapted to survive in an environment with higher concentration of several metal ions when compared to Granulicella sp. WH15. The proteomic profiles of both strains indicated that Mn was more important in enhancing enzymatic activity than to protein expression regulation. In the genomic analyses, we did not find the most common transcriptional regulation of Mn homeostasis, but we found candidate transporters that could be potentially involved in Mn homeostasis for Granulicella species. The presence of such transporters might be involved in tolerance to higher Mn concentrations, improving the adaptability of bacteria to metal enriched environments, such as the decaying wood-rich Mn environment from which these two Granulicella strains were isolated.
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Affiliation(s)
- Ohana Y A Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Chidinma Oguejiofor
- Department of Soil Science and Meteorology, Michael Okpara University of Agriculture, Umudike, Nigeria
| | - Daniela Zühlke
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Cristine C Barreto
- Genomic Sciences and Biotechnology Program, Catholic University of Brasilia, Distrito Federal, Brazil
| | - Christine Wünsche
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, Netherlands
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The Cation Diffusion Facilitator Family Protein EmfA Confers Resistance to Manganese Toxicity in Brucella abortus 2308 and Is an Essential Virulence Determinant in Mice. J Bacteriol 2019; 202:JB.00357-19. [PMID: 31591273 DOI: 10.1128/jb.00357-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 10/01/2019] [Indexed: 11/20/2022] Open
Abstract
The gene designated bab_rs23470 in the Brucella abortus 2308 genome encodes an ortholog of the cation diffusion facilitator family protein EmfA which has been linked to resistance to Mn toxicity in Rhizobium etli A B. abortus emfA null mutant derived from strain 2308 displays increased sensitivity to elevated levels of Mn in the growth medium compared to that of the parent strain but wild-type resistance to Fe, Mg, Zn, Cu, Co, and Ni. Inductively coupled plasma mass spectroscopy also indicates that the B. abortus emfA mutant retains significantly higher levels of cellular Mn after exposure to this metal than the parent strain, which is consistent with the proposed role of EmfA as a Mn exporter. Phenotypic analysis of mutants indicates that EmfA plays a much more important role in maintaining Mn homeostasis and preventing the toxicity of this metal in Brucella than does the Mn-responsive transcriptional regulator Mur. EmfA is also an essential virulence determinant for B. abortus 2308 in C57BL/6 and C57BL/6Nramp1+/+ mice, which suggests that avoiding Mn toxicity plays a critical role in Brucella pathogenesis.IMPORTANCE Mn nutrition is essential for the basic physiology and virulence of Brucella strains. The results of the study presented here demonstrate that the cation diffusion facilitator (CDF)-type metal exporter EmfA plays critical roles in maintaining Mn homeostasis and preventing Mn toxicity in Brucella and is an essential virulence determinant for these bacteria. EmfA and other cellular components involved in Mn homeostasis represent attractive targets for the development of improved vaccines and chemotherapeutic strategies for preventing and treating brucellosis in humans and animals.
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RNA-Independent DNA Cleavage Activities of Cas9 and Cas12a. Cell Rep 2019; 21:3728-3739. [PMID: 29281823 PMCID: PMC5760271 DOI: 10.1016/j.celrep.2017.11.100] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 10/13/2017] [Accepted: 11/29/2017] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems provide bacteria and archaea with sequence-specific protection against invading mobile genetic elements. In the presence of divalent metal ions, Cas9 and Cas12a (formerly Cpf1) proteins target and cleave DNA that is complementary to a cognate guide RNA. The recognition of a protospacer adjacent motif (PAM) sequence in the target DNA by Cas9 and Cas12a is essential for cleavage. This RNA-guided DNA targeting is widely used for gene-editing methods. Here, we show that Francisella tularensis novicida (Fno) Cas12a, FnoCas9, and Streptococcus pyogenes Cas9 (SpyCas9) cleave DNA without a guide RNA in the presence of Mn2+ ions. Substrate requirements for the RNA-independent activity vary. FnoCas9 preferentially nicks double-stranded plasmid, SpyCas9 degrades single-stranded plasmid, and FnoCas12a cleaves both substrates. These observations suggest that the identities and levels of intracellular metals, along with the Cas9/Cas12a ortholog employed, could have significant impacts in genome editing applications.
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29
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The role of metal ions in the virulence and viability of bacterial pathogens. Biochem Soc Trans 2019; 47:77-87. [PMID: 30626704 DOI: 10.1042/bst20180275] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/08/2018] [Accepted: 11/29/2018] [Indexed: 01/18/2023]
Abstract
Metal ions fulfil a plethora of essential roles within bacterial pathogens. In addition to acting as necessary cofactors for cellular proteins, making them indispensable for both protein structure and function, they also fulfil roles in signalling and regulation of virulence. Consequently, the maintenance of cellular metal ion homeostasis is crucial for bacterial viability and pathogenicity. It is therefore unsurprising that components of the immune response target and exploit both the essentiality of metal ions and their potential toxicity toward invading bacteria. This review provides a brief overview of the transition metal ions iron, manganese, copper and zinc during infection. These essential metal ions are discussed in the context of host modulation of bioavailability, bacterial acquisition and efflux, metal-regulated virulence factor expression and the molecular mechanisms that contribute to loss of viability and/or virulence during host-imposed metal stress.
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Mandal SK, Adhikari R, Sharma A, Chandravanshi M, Gogoi P, Kanaujia SP. Designating ligand specificities to metal uptake ABC transporters in Thermus thermophilus HB8. Metallomics 2019; 11:597-612. [DOI: 10.1039/c8mt00374b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Acquisition of different metal ions by metal uptake ABC transporters of Thermus thermophilus HB8 for accomplishing its various cellular functions.
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Affiliation(s)
- Suraj Kumar Mandal
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Rahi Adhikari
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Anjaney Sharma
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Monika Chandravanshi
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Prerana Gogoi
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Shankar Prasad Kanaujia
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
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31
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Sengupta S, Mondal A, Dutta D, Parrack P. HflX protein protects Escherichia coli from manganese stress. J Biosci 2018. [DOI: 10.1007/s12038-018-9807-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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32
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MntC-Dependent Manganese Transport Is Essential for Staphylococcus aureus Oxidative Stress Resistance and Virulence. mSphere 2018; 3:3/4/e00336-18. [PMID: 30021878 PMCID: PMC6052334 DOI: 10.1128/msphere.00336-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Work outlined in this report demonstrated that MntC-dependent manganese transport is required for S. aureus virulence. These study results support the model that MntC-specific antibodies elicited by a vaccine have the potential to disrupt S. aureus manganese transport and thus abrogate to its virulence. Staphylococcus aureus is a human pathogen that has developed several approaches to evade the immune system, including a strategy to resist oxidative killing by phagocytes. This resistance is mediated by production of superoxide dismutase (SOD) enzymes which use manganese as a cofactor. S. aureus encodes two manganese ion transporters, MntABC and MntH, and a possible Nramp family manganese transporter, exemplified by S. aureus N315 SA1432. Their relative contributions to manganese transport have not been well defined in clinically relevant isolates. For this purpose, insertional inactivation mutations were introduced into mntC, mntH, and SA1432 individually and in combination. mntC was necessary for full resistance to methyl viologen, a compound that generates intracellular free radicals. In contrast, strains with an intact mntH gene had a minimal increase in resistance that was revealed only in mntC strains, and no change was observed upon mutation of SA1432 in strains lacking both mntC and mntH. Similarly, MntC alone was required for high cellular SOD activity. In addition, mntC strains were attenuated in a murine sepsis model. To further link these observations to manganese transport, an S. aureus MntC protein lacking manganese binding activity was designed, expressed, and purified. While circular dichroism experiments demonstrated that the secondary and tertiary structures of this protein were unaltered, a defect in manganese binding was confirmed by isothermal titration calorimetry. Unlike complementation with wild-type mntC, introduction of the manganese-binding defective allele into the chromosome of an mntC strain did not restore resistance to oxidative stress or virulence. Collectively, these results underscore the importance of MntC-dependent manganese transport in S. aureus oxidative stress resistance and virulence. IMPORTANCE Work outlined in this report demonstrated that MntC-dependent manganese transport is required for S. aureus virulence. These study results support the model that MntC-specific antibodies elicited by a vaccine have the potential to disrupt S. aureus manganese transport and thus abrogate to its virulence.
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Fernandes SO, Surya Prakash L, Balan Binish M, Padinchati Krishnan K, John Kurian P. Changes in morphology and metabolism enable Mn-oxidizing bacteria from mid-oceanic ridge environment to counter metal-induced stress. J Basic Microbiol 2018. [DOI: 10.1002/jobm.201700580] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | - Palayil John Kurian
- National Centre for Antarctic and Ocean Research; Headland Sada; Vasco-da-Gama Goa India
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Chen Y, Shen Y, Wang W, Wei D. Mn 2+ modulates the expression of cellulase genes in Trichoderma reesei Rut-C30 via calcium signaling. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:54. [PMID: 29507606 PMCID: PMC5831609 DOI: 10.1186/s13068-018-1055-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 02/18/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND The filamentous fungus Trichoderma reesei Rut-C30 is one of the most vital fungi for the production of cellulases, which can be used for biofuel production from lignocellulose. Nevertheless, the mechanism of transmission of external stimuli and signals in modulating cellulase production in T. reesei Rut-C30 remains unclear. Calcium is a known second messenger regulating cellulase gene expression in T. reesei. RESULTS In this study, we found that a biologically relevant extracellular Mn2+ concentration markedly stimulates cellulase production, total protein secretion, and the intracellular Mn2+ concentration of Rut-C30, a cellulase hyper-producing strain of T. reesei. Furthermore, we identified two Mn2+ transport proteins, designated as TPHO84-1 and TPHO84-2, indicating that they are upstream in the signaling pathway that leads to cellulase upregulation. We also found that Mn2+ induced a significant increase in cytosolic Ca2+ concentration, and that this increased cytosolic Ca2+ might be a key step in the Mn2+-mediated regulation of cellulase gene transcription and production. The utilization of LaCl3 to block plasma membrane Ca2+ channels, and deletion of crz1 (calcineurin-responsive zinc finger transcription factor 1) to interrupt calcium signaling, showed that Mn2+ exerts the induction of cellulase genes via calcium channels and calcium signaling. To substantiate this, we identified a Ca2+/Mn2+ P-type ATPase, TPMR1, which could play a pivotal role in Ca2+/Mn2+ homeostasis and Mn2+ induction of cellulase genes in T. reesei Rut-C30. CONCLUSIONS Taken together, our results revealed for the first time that Mn2+ stimulates cellulase production, and demonstrates that Mn2+ upregulates cellulase genes via calcium channels and calcium signaling. Our research also provides a direction to facilitate enhanced cellulase production by T. reesei.
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Affiliation(s)
- Yumeng Chen
- State Key Lab of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, East China University of Science and Technology, 130 Meilong Road, P.O.B. 311, Shanghai, 200237 China
| | - Yaling Shen
- State Key Lab of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, East China University of Science and Technology, 130 Meilong Road, P.O.B. 311, Shanghai, 200237 China
| | - Wei Wang
- State Key Lab of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, East China University of Science and Technology, 130 Meilong Road, P.O.B. 311, Shanghai, 200237 China
| | - Dongzhi Wei
- State Key Lab of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, East China University of Science and Technology, 130 Meilong Road, P.O.B. 311, Shanghai, 200237 China
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35
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Maladaptive DNA repair is the ultimate contributor to the death of trimethoprim-treated cells under aerobic and anaerobic conditions. Proc Natl Acad Sci U S A 2017; 114:11512-11517. [PMID: 29073080 PMCID: PMC5664507 DOI: 10.1073/pnas.1706236114] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Antibiotic resistance leads to substantial mortality and morbidity and significant economic cost because it seriously undermines our ability to treat bacterial infections. Therefore, a better understanding of the effect of antibiotics on bacteria is needed to increase the effectiveness of treatments and slow the emergence of resistance. The bactericidal effects of antibiotics are triggered by target-specific interactions, but there is growing evidence that an important part of their cytotoxicity results from metabolic disturbances induced by treatment. In this article, we report that the perturbation of DNA replication by a wide-spectrum antibiotic, trimethoprim, affects bacterial metabolism, which provokes the production of genotoxic agents and DNA damage, whose processing ultimately contributes to cell death under both aerobic and anaerobic conditions. The bactericidal effects of antibiotics are undoubtedly triggered by target-specific interactions, but there is growing evidence that an important aspect of cytotoxicity results from treatment-induced metabolic perturbations. In this study, we characterized molecular mechanisms whereby trimethoprim treatment results in cell death, using Escherichia coli as the model organism. E. coli cells grown in rich medium that contained all amino acids and low amounts of thymidine were treated with trimethoprim under aerobic and anaerobic conditions. Under these growth conditions, accelerated thymine depletion is the primary trigger of the processes leading to cell death. Thymine depletion-induced DNA replication stress leads to the production of reactive oxygen species under aerobic conditions and of the DNA-damaging byproducts of nitrate respiration under anaerobic conditions. Lowering the DNA replication initiation rate by introducing the dnaA(Sx) allele or by overexpressing Hda protein reduces the number of active replication forks, which reduces the consumption of thymidine and increases resistance to trimethoprim under both aerobic and anaerobic conditions. Analysis of the involvement of DNA repair enzymes in trimethoprim-induced cytotoxicity clearly indicates that different amounts and/or different types of DNA lesions are produced in the presence or absence of oxygen. Maladaptive processing of the DNA damage by DNA repair enzymes, in particular by MutM and MutY DNA glycosylases, ultimately contributes to cell death.
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36
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Chi L, Gao B, Bian X, Tu P, Ru H, Lu K. Manganese-induced sex-specific gut microbiome perturbations in C57BL/6 mice. Toxicol Appl Pharmacol 2017; 331:142-153. [PMID: 28610994 PMCID: PMC5653225 DOI: 10.1016/j.taap.2017.06.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 06/07/2017] [Accepted: 06/10/2017] [Indexed: 12/26/2022]
Abstract
Overexposure to manganese (Mn) leads to toxic effects, such as promoting the development of Parkinson's-like neurological disorders. The gut microbiome is deeply involved in immune development, host metabolism, and xenobiotics biotransformation, and significantly influences central nervous system (CNS) via the gut-brain axis, i.e. the biochemical signaling between the gastrointestinal tract and the CNS. However, it remains unclear whether Mn can affect the gut microbiome and its metabolic functions, particularly those linked to neurotoxicity. In addition, sex-specific effects of Mn have been reported, with no mechanism being identified yet. Recently, we have shown that the gut microbiome is largely different between males and females, raising the possibility that differential gut microbiome responses may contribute to sex-selective toxicity of Mn. Here, we applied high-throughput sequencing and gas chromatography-mass spectrometry (GC-MS) metabolomics to explore how Mn2+ exposure affects the gut microbiome and its metabolism in C57BL/6 mice. Mn2+ exposure perturbed the gut bacterial compositions, functional genes and fecal metabolomes in a highly sex-specific manner. In particular, bacterial genes and/or key metabolites of neurotransmitter synthesis and pro-inflammatory mediators are significantly altered by Mn2+ exposure, which can potentially affect chemical signaling of gut-brain interactions. Likewise, functional genes involved in iron homeostasis, flagellar motility, quorum sensing, and Mn transportation/oxidation are also widely changed by Mn2+ exposure. Taken together, this study has demonstrated that Mn2+ exposure perturbs the gut microbiome and its metabolic functions, which highlights the potential role of the gut microbiome in Mn2+ toxicity, particularly its sex-specific toxic effects.
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Affiliation(s)
- Liang Chi
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, 27599, United States
| | - Bei Gao
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, United States
| | - Xiaoming Bian
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, United States
| | - Pengcheng Tu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, 27599, United States
| | - Hongyu Ru
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC 27607, United States
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, 27599, United States.
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Guerrero-Mendiola C, García-Trejo JJ, Encalada R, Saavedra E, Ramírez-Silva L. The contribution of two isozymes to the pyruvate kinase activity of Vibrio cholerae: One K+-dependent constitutively active and another K+-independent with essential allosteric activation. PLoS One 2017; 12:e0178673. [PMID: 28686591 PMCID: PMC5501398 DOI: 10.1371/journal.pone.0178673] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/17/2017] [Indexed: 11/18/2022] Open
Abstract
In a previous phylogenetic study of the family of pyruvate kinase EC (2.7.1.40), a cluster with Glu117 and another with Lys117 were found (numbered according to the rabbit muscle enzyme). The sequences with Glu117 have been found to be K+-dependent, whereas those with Lys117 were K+-independent. Interestingly, only γ-proteobacteria exhibit sequences in both branches of the tree. In this context, it was explored whether these phylogenetically distinct pyruvate kinases were both expressed and contribute to the pyruvate kinase activity in Vibrio cholerae. The main findings of this work showed that the isozyme with Glu117 is an active K+-dependent enzyme. At the same substrate concentration, its Vmax in the absence of fructose 1,6 bisphosphate was 80% of that with its effector. This result is in accordance with the non-essential activation described by allosteric ligands for most pyruvate kinases. In contrast, the pyruvate kinase with Lys117 was a K+-independent enzyme displaying an allosteric activation by ribose 5-phosphate. At the same substrate concentration, its activity without the effector was 0.5% of the one obtained in the presence of ribose 5-phosphate, indicating that this sugar monophosphate is a strong activator of this enzyme. This absolute allosteric dependence is a novel feature of pyruvate kinase activity. Interestingly, in the K+-independent enzyme, Mn2+ may "mimic" the allosteric effect of Rib 5-P. Despite their different allosteric behavior, both isozymes display a rapid equilibrium random order kinetic mechanism. The intracellular concentrations of fructose 1,6-bisphosphate and ribose 5-phosphate in Vibrio cholerae have been experimentally verified to be sufficient to induce maximal activation of both enzymes. In addition, Western blot analysis indicated that both enzymes were co-expressed. Therefore, it is concluded that VcIPK and VcIIPK contribute to the activity of pyruvate kinase in this γ-proteobacterium.
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Affiliation(s)
- Carlos Guerrero-Mendiola
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - José J. García-Trejo
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Rusely Encalada
- Departamento de Bioquímica, Instituto Nacional de Cardiología, Ignacio Chávez, Ciudad de México, México
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología, Ignacio Chávez, Ciudad de México, México
| | - Leticia Ramírez-Silva
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
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Ranawat P, Rawat S. Radiation resistance in thermophiles: mechanisms and applications. World J Microbiol Biotechnol 2017; 33:112. [DOI: 10.1007/s11274-017-2279-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 04/26/2017] [Indexed: 12/28/2022]
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Chen Z, Wang X, Yang F, Hu Q, Tong H, Dong X. Molecular Insights into Hydrogen Peroxide-sensing Mechanism of the Metalloregulator MntR in Controlling Bacterial Resistance to Oxidative Stresses. J Biol Chem 2017; 292:5519-5531. [PMID: 28223356 DOI: 10.1074/jbc.m116.764126] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 01/28/2017] [Indexed: 11/06/2022] Open
Abstract
Manganese contributes to anti-oxidative stress particularly in catalase-devoid bacteria, and DtxR family metalloregulators, through sensing cellular Mn2+ content, regulate its homeostasis. Here, we show that metalloregulator MntR (So-MntR) functions dually as Mn2+ and H2O2 sensors in mediating H2O2 resistance by an oral streptococcus. H2O2 disrupted So-MntR binding to Mn2+ transporter mntABC promoter and induced disulfide-linked dimerization of the protein. Mass spectrometry identified Cys-11/Cys-156 and Cys-11/Cys-11 disulfide-linked peptides in H2O2-treated So-MntR. Site mutagenesis of Cys-11 and Cys-156 and particularly Cys-11 abolished H2O2-induced disulfide-linked dimers and weakened H2O2 damage on So-MntR binding, indicating that H2O2 inactivates So-MntR via disulfide-linked dimerization. So-MntR C123S mutant was extremely sensitive to H2O2 oxidization in dimerization/oligomerization, probably because the mutagenesis caused a conformational change that facilitates Cys-11/Cys-156 disulfide linkage. Intermolecular Cys-11/Cys-11 disulfide was detected in C123S/C156S double mutant. Redox Western blot detected So-MntR oligomers in air-exposed cells but remarkably decreased upon H2O2 pulsing, suggesting a proteolysis of the disulfide-linked So-MntR oligomers. Remarkably, elevated C11S and C156S but much lower C123S proteins were detected in H2O2-pulsed cells, confirming Cys-11 and Cys-156 contributed to H2O2-induced oligomerization and degradation. Accordingly, in the C11S and C156S mutants, expression of mntABC and cellular Mn2+ decreased, but H2O2 susceptibility increased. In the C123S mutant, increased mntABC expression, cellular Mn2+ content, and manganese-mediated H2O2 survival were determined. Given the wide distribution of Cys-11 in streptococcal DtxR-like metalloregulators, the disclosed redox regulatory function and mechanism of So-MntR can be employed by the DtxR family proteins in bacterial resistance to oxidative stress.
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Affiliation(s)
- Zhaoyuan Chen
- From the State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, China.,School of Life Sciences, University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing 100049, China, and
| | - Xinhui Wang
- From the State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, China.,School of Life Sciences, University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing 100049, China, and
| | - Fan Yang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qingqing Hu
- From the State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, China.,School of Life Sciences, University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing 100049, China, and
| | - Huichun Tong
- From the State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, China, .,School of Life Sciences, University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing 100049, China, and
| | - Xiuzhu Dong
- From the State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, China, .,School of Life Sciences, University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing 100049, China, and
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Abstract
The importance of manganese in the physiology of marine microbes, the biogeochemistry of the ocean and the health of microbial communities of past and present is emerging. Manganese is distributed widely throughout the global ocean, taking the form of an essential antioxidant (Mn2+), a potent oxidant (Mn3+) and strong adsorbent (Mn oxides) sequestering disproportionately high levels of trace metals and nutrients in comparison to the surrounding seawater. Manganese is, in fact, linked to nearly all other elemental cycles and intricately involved in the health, metabolism and function of the ocean's microbiome. Here, we briefly review the diversity of microbes and pathways responsible for the transformation of Mn within the three Mn pools and their distribution within the marine environment. Despite decades of interrogation, we still have much to learn about the players, mechanisms and consequences of the Mn cycle, and new and exciting discoveries are being made at a rapid rate. What is clear is the dynamic and ever-inspiring complexity of reactions involving Mn, and the acknowledgement that microorganisms are the catalytic engine driving the Mn cycle.
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Affiliation(s)
- Colleen M Hansel
- Woods Hole Oceanographic Institution, Woods Hole, MA, United States.
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Stacy A, Abraham N, Jorth P, Whiteley M. Microbial Community Composition Impacts Pathogen Iron Availability during Polymicrobial Infection. PLoS Pathog 2016; 12:e1006084. [PMID: 27973608 PMCID: PMC5156373 DOI: 10.1371/journal.ppat.1006084] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 11/21/2016] [Indexed: 01/07/2023] Open
Abstract
Iron is an essential nutrient for bacterial pathogenesis, but in the host, iron is tightly sequestered, limiting its availability for bacterial growth. Although this is an important arm of host immunity, most studies examine how bacteria respond to iron restriction in laboratory rather than host settings, where the microbiome can potentially alter pathogen strategies for acquiring iron. One of the most important transcriptional regulators controlling bacterial iron homeostasis is Fur. Here we used a combination of RNA-seq and chromatin immunoprecipitation (ChIP)-seq to characterize the iron-restricted and Fur regulons of the biofilm-forming opportunistic pathogen Aggregatibacter actinomycetemcomitans. We discovered that iron restriction and Fur regulate 4% and 3.5% of the genome, respectively. While most genes in these regulons were related to iron uptake and metabolism, we found that Fur also directly regulates the biofilm-dispersing enzyme Dispersin B, allowing A. actinomycetemcomitans to escape from iron-scarce environments. We then leveraged these datasets to assess the availability of iron to A. actinomycetemcomitans in its primary infection sites, abscesses and the oral cavity. We found that A. actinomycetemcomitans is not restricted for iron in a murine abscess mono-infection, but becomes restricted for iron upon co-infection with the oral commensal Streptococcus gordonii. Furthermore, in the transition from health to disease in human gum infection, A. actinomycetemcomitans also becomes restricted for iron. These results suggest that host iron availability is heterogeneous and dependent on the infecting bacterial community. One of the most well-studied phenomena in microbiology is nutritional immunity, or how the host withholds nutrients such as iron to combat infection. As part of this, researchers have characterized how many pathogens respond to iron restriction. However, these studies are often conducted in laboratory media rather than the host. As a result, they overlook how the host environment, such as its microbiome, might alter pathogen behavior regarding iron during infection. To address this gap, we used an opportunistic pathogen that causes abscess and oral cavity infections. We defined how it responds to iron restriction in vitro and then used this data to assess its iron status in vivo. Our results show that in mono-culture abscesses the pathogen is not starved for iron but in co-culture abscesses and multispecies gum disease it is starved for iron. Therefore, host environments are not uniformly restricted for iron, and the microbiome can modulate iron availability to pathogens.
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Affiliation(s)
- Apollo Stacy
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, John Ring LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, TX United States of America
| | - Nader Abraham
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, John Ring LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, TX United States of America
| | - Peter Jorth
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, John Ring LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, TX United States of America
| | - Marvin Whiteley
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, John Ring LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, TX United States of America
- * E-mail:
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Abstract
The review highlights the intrinsic problems in the acquisition of ferric iron (FeIII) by pathogenic microorganisms, and bacteria in particular, during their infection of animals. Acquisition of iron from host sources, such as ferritin, transferrin, and heme compounds, is discussed. Acquisition can be by direct contact, via a surface receptor protein of the bacterium, with one of the iron-containing compounds, but more frequently iron is acquired by the production of a siderophore. Over 500 different siderophores are now known; they work by having a superior binding power to that of the host iron-containing materials. They literally strip the iron out of these molecules. They are low-molecular-weight (< 1,000 Da) compounds that are produced in response to iron deprivation, which is a primary host defense mechanism against infections. The iron–siderophore complex is small enough to be taken up into the bacterial cells, usually via an active transport process; the iron is removed from the siderophore, normally by a reductive process, and is then incorporated into the various apoproteins of the bacterial cell or is stored within the bacteria in the form of bacterioferritin. To combat the effectiveness of the siderophores, animals may synthesize specific proteins to bind and nullify their action. The role of one such protein, siderocalin (= lipocalin 2), is discussed. However, these countermeasures have, in turn, been thwarted by at least one bacterium, Salmonella, glycosylating its siderophore (enterobactin/enterochelin) so that binding of the modified siderophore (now termed salmochelin) with lipocalin can no longer occur.
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Pepi M, Borra M, Tamburrino S, Saggiomo M, Viola A, Biffali E, Balestra C, Sprovieri M, Casotti R. A Bacillus sp. isolated from sediments of the Sarno River mouth, Gulf of Naples (Italy) produces a biofilm biosorbing Pb(II). THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 562:588-595. [PMID: 27110973 DOI: 10.1016/j.scitotenv.2016.04.097] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 04/13/2016] [Accepted: 04/13/2016] [Indexed: 06/05/2023]
Abstract
A Pb-resistant bacterial strain (named hereinafter Pb15) has been isolated from highly polluted marine sediments at the Sarno River mouth, Italy, using an enrichment culture to which Pb(II) 0.48mmoll(-1) were added. 16S rRNA gene sequencing (Sanger) allowed assignment of the isolate to the genus Bacillus, with Bacillus pumilus as the closest species. The isolate is resistant to Pb(II) with a minimum inhibitory concentration (MIC) of 4.8mmoll(-1) and is also resistant to Cd(II) and Mn(II) with MIC of 2.22mmoll(-1) and 18.20mmoll(-1), respectively. Inductively coupled plasma atomic emission spectrometry (ICP-AES) showed that Pb inoculated in the growth medium is absorbed by the bacterial cells at removal efficiencies of 31.02% and 28.21% in the presence of 0.48mmoll(-1) or 1.20mmoll(-1) Pb(II), respectively. Strain Pb15 forms a brown and compact biofilm when grown in presence of Pb(II). Scanning Electron Microscopy (SEM) coupled with Energy Dispersive X-ray Spectroscopy (SEM-EDS) confirm that the biofilm contains Pb, suggesting an active biosorption of this metal by the bacterial cells, sequestering 14% of inoculated Pb as evidenced by microscopic analyses. Altogether, these observations support evidence that strain Pb15 has potentials for being used in bioremediation of its native polluted sediments, with engineering solutions to be found in order to eliminate the adsorbed Pb before replacement of sediments in situ.
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Affiliation(s)
- Milva Pepi
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Marco Borra
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Stella Tamburrino
- Consiglio Nazionale delle Ricerche, Istituto per l'Ambiente Marino Costiero UOS Capo Granitola, Palermo, Italy
| | - Maria Saggiomo
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Alfio Viola
- Università di Catania, Corso Italia 57, I-95129 Catania, Italy
| | - Elio Biffali
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Cecilia Balestra
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Mario Sprovieri
- Consiglio Nazionale delle Ricerche, Istituto per l'Ambiente Marino Costiero UOS Capo Granitola, Palermo, Italy
| | - Raffaella Casotti
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.
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Mhatre E, Troszok A, Gallegos-Monterrosa R, Lindstädt S, Hölscher T, Kuipers OP, Kovács ÁT. The impact of manganese on biofilm development of Bacillus subtilis. MICROBIOLOGY-SGM 2016; 162:1468-1478. [PMID: 27267987 DOI: 10.1099/mic.0.000320] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacterial biofilms are dynamic and structurally complex communities, involving cell-to-cell interactions. In recent years, various environmental signals that induce the complex biofilm development of the Gram-positive bacterium Bacillus subtilis have been identified. These signalling molecules are often media components or molecules produced by the cells themselves, as well as those of other interacting species. The responses can also be due to depletion of certain molecules in the vicinity of the cells. Extracellular manganese (Mn2+) is essential for proper biofilm development of B. subtilis. Mn2+ is also a component of practically all laboratory biofilm-promoting media used for B. subtilis. Comparison of complex colony biofilms in the presence or absence of supplemented Mn2+ using microarray analyses revealed that genes involved in biofilm formation are indeed downregulated in the absence of Mn2+. In addition, Mn2+ also affects the transcription of several other genes involved in distinct differentiation pathways of various cellular processes. The effects of Mn2+ on other biofilm-related traits like motility, antimicrobial production, stress and sporulation were followed using fluorescent reporter strains. The global transcriptome and morphology studies highlight the importance of Mn2+ during biofilm development and provide an overview on the expressional changes in colony biofilms in B. subtilis.
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Affiliation(s)
- Eisha Mhatre
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Agnieszka Troszok
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Ramses Gallegos-Monterrosa
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Stefanie Lindstädt
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Theresa Hölscher
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Oscar P Kuipers
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Ákos T Kovács
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
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Zhang L, Butler CA, Khan HSG, Dashper SG, Seers CA, Veith PD, Zhang JG, Reynolds EC. Characterisation of the Porphyromonas gingivalis Manganese Transport Regulator Orthologue. PLoS One 2016; 11:e0151407. [PMID: 27007570 PMCID: PMC4805248 DOI: 10.1371/journal.pone.0151407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/26/2016] [Indexed: 11/19/2022] Open
Abstract
PgMntR is a predicted member of the DtxR family of transcriptional repressors responsive to manganese in the anaerobic periodontal pathogen Porphyromonas gingivalis. Our bioinformatic analyses predicted that PgMntR had divalent metal binding site(s) with elements of both manganous and ferrous ion specificity and that PgMntR has unusual twin C-terminal FeoA domains. We produced recombinant PgMntR and four variants to probe the specificity of metal binding and its impact on protein structure and DNA binding. PgMntR dimerised in the absence of a divalent transition metal cation. PgMntR bound three Mn(II) per monomer with an overall dissociation constant Kd 2.0 x 10(-11) M at pH 7.5. PgMntR also bound two Fe(II) with distinct binding affinities, Kd1 2.5 x 10(-10) M and Kd2 ≤ 6.0 x 10(-8) M at pH 6.8. Two of the metal binding sites may form a binuclear centre with two bound Mn2+ being bridged by Cys108 but this centre provided only one site for Fe2+. Binding of Fe2+ or Mn2+ did not have a marked effect on the PgMntR secondary structure. Apo-PgMntR had a distinct affinity for the promoter region of the gene encoding the only known P. gingivalis manganese transporter, FB2. Mn2+ increased the DNA binding affinity of PgMntR whilst Fe2+ destabilised the protein-DNA complex in vitro. PgMntR did not bind the promoter DNA of the gene encoding the characterised iron transporter FB1. The C-terminal FeoA domain was shown to be essential for PgMntR structure/function, as its removal caused the introduction of an intramolecular disulfide bond and abolished the binding of Mn2+ and DNA. These data indicate that PgMntR is a novel member of the DtxR family that may function as a transcriptional repressor switch to specifically regulate manganese transport and homeostasis in an iron-dependent manner.
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Affiliation(s)
- Lianyi Zhang
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Catherine A. Butler
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Hasnah S. G. Khan
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Stuart G. Dashper
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Christine A. Seers
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Paul D. Veith
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jian-Guo Zhang
- Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Eric C. Reynolds
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, Victoria, Australia
- * E-mail:
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Kafil HS, Mobarez AM, Moghadam MF, Hashemi ZS, Yousefi M. Gentamicin induces efaA expression and biofilm formation in Enterococcus faecalis. Microb Pathog 2016; 92:30-35. [DOI: 10.1016/j.micpath.2015.12.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 12/18/2015] [Accepted: 12/22/2015] [Indexed: 11/16/2022]
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Mandal B, Singha S, Dey SK, Mazumdar S, Mondal TK, Karmakar P, Kumar S, Das S. Synthesis, crystal structure from PXRD of a MnII(purp)2complex, interaction with DNA at different temperatures and pH and lack of stimulated ROS formation by the complex. RSC Adv 2016. [DOI: 10.1039/c6ra09387f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
MnII(purpurin)2crystal structure done from PXRD is the second report on hydroxy-9,10-anthraquinone with a 3d-transition metal. DNA binding of complex is better and ROS generation less than purpurin. Complex maintains biological activity of purpurin.
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Affiliation(s)
- Bitapi Mandal
- Department of Chemistry (Inorganic Section)
- Jadavpur University
- Kolkata-700032
- India
| | - Soumen Singha
- Department of Physics
- Jadavpur University
- Kolkata-700032
- India
| | | | - Swagata Mazumdar
- Department of Life Science and Biotechnology
- Jadavpur University
- Kolkata-700032
- India
| | - Tapan Kumar Mondal
- Department of Chemistry (Inorganic Section)
- Jadavpur University
- Kolkata-700032
- India
| | - Parimal Karmakar
- Department of Life Science and Biotechnology
- Jadavpur University
- Kolkata-700032
- India
| | - Sanjay Kumar
- Department of Physics
- Jadavpur University
- Kolkata-700032
- India
| | - Saurabh Das
- Department of Chemistry (Inorganic Section)
- Jadavpur University
- Kolkata-700032
- India
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A. Alhasawi A, D. Appanna V. Manganese orchestrates a metabolic shift leading to the increased bioconversion of glycerol into α-ketoglutarate. AIMS BIOENGINEERING 2016. [DOI: 10.3934/bioeng.2017.1.12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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49
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Sugrue E, Hartley CJ, Scott C, Jackson CJ. The Evolution of New Catalytic Mechanisms for Xenobiotic Hydrolysis in Bacterial Metalloenzymes. Aust J Chem 2016. [DOI: 10.1071/ch16426] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
An increasing number of bacterial metalloenzymes have been shown to catalyse the breakdown of xenobiotics in the environment, while others exhibit a variety of promiscuous xenobiotic-degrading activities. Several different evolutionary processes have allowed these enzymes to gain or enhance xenobiotic-degrading activity. In this review, we have surveyed the range of xenobiotic-degrading metalloenzymes, and discuss the molecular and catalytic basis for the development of new activities. We also highlight how our increased understanding of the natural evolution of xenobiotic-degrading metalloenzymes can be been applied to laboratory enzyme design.
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50
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Kaluskar ZM, Garrison-Schilling KL, McCarter KS, Lambert B, Simar SR, Pettis GS. Manganese is an additional cation that enhances colonial phase variation of Vibrio vulnificus. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:789-794. [PMID: 26147440 DOI: 10.1111/1758-2229.12318] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 06/26/2015] [Indexed: 06/04/2023]
Abstract
Vibrio vulnificus, an inhabitant of marine and estuarine environments around the world, is the leading cause of reported seafood-related deaths in the United States. Disease is caused by opaque colony-forming strains that produce capsular polysaccharide, loss of which results in an unencapsulated translucent phenotype with diminished virulence potential. Rugose is a third phenotypic variant of V. vulnificus, and produces a separate exopolysaccharide that results in a dry, wrinkled appearance and the ability to form profuse biofilms. Phase variation among these three phenotypes is influenced by several environmental factors, including the presence of calcium in the medium (Garrison-Schilling et al.). In this study, we have identified a second cation, manganese, which substantially increases the propensity of opaque V. vulnificus strains to switch to translucent or rugose phenotypes. In comparative studies, manganese and calcium promoted switching to the same phenotype for some strains but to different phenotypes for others, results of which indicate that the two cations do not always promote the same changes in underlying gene expression. The data here provide further evidence that exposure of V. vulnificus to select cations results in phenotypic changes that impact both virulence capacity and ecology of the organism.
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Affiliation(s)
- Zelam M Kaluskar
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
| | | | - Kevin S McCarter
- Department of Experimental Statistics, Louisiana State University, 171 Martin D. Woodin Hall, Baton Rouge, LA, 70803, USA
| | - Bliss Lambert
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
| | - Shelby R Simar
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
| | - Gregg S Pettis
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
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