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Akarsu H, Bordes P, Mansour M, Bigot DJ, Genevaux P, Falquet L. TASmania: A bacterial Toxin-Antitoxin Systems database. PLoS Comput Biol 2019; 15:e1006946. [PMID: 31022176 PMCID: PMC6504116 DOI: 10.1371/journal.pcbi.1006946] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 05/07/2019] [Accepted: 03/11/2019] [Indexed: 11/30/2022] Open
Abstract
Bacterial Toxin-Antitoxin systems (TAS) are involved in key biological functions including plasmid maintenance, defense against phages, persistence and virulence. They are found in nearly all phyla and classified into 6 different types based on the mode of inactivation of the toxin, with the type II TAS being the best characterized so far. We have herein developed a new in silico discovery pipeline named TASmania, which mines the >41K assemblies of the EnsemblBacteria database for known and uncharacterized protein components of type I to IV TAS loci. Our pipeline annotates the proteins based on a list of curated HMMs, which leads to >2.106 loci candidates, including orphan toxins and antitoxins, and organises the candidates in pseudo-operon structures in order to identify new TAS candidates based on a guilt-by-association strategy. In addition, we classify the two-component TAS with an unsupervised method on top of the pseudo-operon (pop) gene structures, leading to 1567 “popTA” models offering a more robust classification of the TAs families. These results give valuable clues in understanding the toxin/antitoxin modular structures and the TAS phylum specificities. Preliminary in vivo work confirmed six putative new hits in Mycobacterium tuberculosis as promising candidates. The TASmania database is available on the following server https://shiny.bioinformatics.unibe.ch/apps/tasmania/. TASmania offers an extensive annotation of TA loci in a very large database of bacterial genomes, which represents a resource of crucial importance for the microbiology community. TASmania supports i) the discovery of new TA families; ii) the design of a robust experimental strategy by taking into account potential interferences in trans; iii) the comparative analysis between TA loci content, phylogeny and/or phenotypes (pathogenicity, persistence, stress resistance, associated host types) by providing a vast repertoire of annotated assemblies. Our database contains TA annotations of a given strain not only mapped to its core genome but also to its plasmids, whenever applicable.
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Affiliation(s)
- Hatice Akarsu
- Department of Biology, University of Fribourg & Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Patricia Bordes
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Moise Mansour
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Donna-Joe Bigot
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Pierre Genevaux
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Laurent Falquet
- Department of Biology, University of Fribourg & Swiss Institute of Bioinformatics, Fribourg, Switzerland
- * E-mail:
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Roy M, Kundu A, Bhunia A, Das Gupta S, De S, Das AK. Structural characterization of VapB46 antitoxin from
Mycobacterium tuberculosis
: insights into VapB46–
DNA
binding. FEBS J 2019; 286:1174-1190. [DOI: 10.1111/febs.14737] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 10/24/2018] [Accepted: 12/17/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Madhurima Roy
- Department of Biotechnology Indian Institute of Technology Kharagpur India
| | - Anirban Kundu
- Department of Biotechnology Indian Institute of Technology Kharagpur India
| | | | | | - Soumya De
- School of Bioscience Indian Institute of Technology Kharagpur India
| | - Amit Kumar Das
- Department of Biotechnology Indian Institute of Technology Kharagpur India
- School of Bioscience Indian Institute of Technology Kharagpur India
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Gao B, Chi L, Tu P, Gao N, Lu K. The Carbamate Aldicarb Altered the Gut Microbiome, Metabolome, and Lipidome of C57BL/6J Mice. Chem Res Toxicol 2019; 32:67-79. [PMID: 30406643 DOI: 10.1021/acs.chemrestox.8b00179] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The gut microbiome is highly involved in numerous aspects of host physiology, from energy harvest to stress response, and can confer many benefits to the host. The gut microbiome development could be affected by genetic and environmental factors, including pesticides. The carbamate insecticide aldicarb has been extensively used in agriculture, which raises serious public health concerns. However, the impact of aldicarb on the gut microbiome, host metabolome, and lipidome has not been well studied yet. Herein, we use multiomics approaches, including16S rRNA sequencing, shotgun metagenomics sequencing, metabolomics, and lipidomics, to elucidate aldicarb-induced toxicity in the gut microbiome and the host metabolic homeostasis. We demonstrated that aldicarb perturbed the gut microbiome development trajectory, enhanced gut bacterial pathogenicity, altered complex lipid profile, and induced oxidative stress, protein degradation, and DNA damage. The brain metabolism was also disturbed by the aldicarb exposure. These findings may provide a novel understanding of the toxicity of carbamate insecticides.
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Affiliation(s)
- Bei Gao
- Department of Environmental Sciences and Engineering , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States.,NIH West Coast Metabolomics Center , University of California , Davis , California 95616 , United States
| | - Liang Chi
- Department of Environmental Sciences and Engineering , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Pengcheng Tu
- Department of Environmental Sciences and Engineering , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Nan Gao
- National Engineering Research Center for Biotechnology, School of Biotechnology and Pharmaceutical Engineering , Nanjing Tech University , Nanjing 211816 , China
| | - Kun Lu
- Department of Environmental Sciences and Engineering , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
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Bobinger T, Burkardt P, B Huttner H, Manaenko A. Programmed Cell Death after Intracerebral Hemorrhage. Curr Neuropharmacol 2018; 16:1267-1281. [PMID: 28571544 PMCID: PMC6251052 DOI: 10.2174/1570159x15666170602112851] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/26/2017] [Accepted: 06/01/2017] [Indexed: 01/01/2023] Open
Abstract
Background: Intracerebral hemorrhage (ICH) accounts for up to 15% of all strokes and is characterized by high rates of mortality and morbidity. The post-ICH brain injury can be distinguished in 1) primary, which are caused by disrup-tion and mechanical deformation of brain tissue due to hematoma growth and 2) secondary, which are induced by microglia activation, mitochondrial dysfunction, neurotransmitter and inflammatory mediator release. Although these events typically lead to necrosis, the occurrence of programmed cell death has also been reported after ICH. Methods: We reviewed recent publications describing advance in pre- and clinic ICH research. Results: At present, treatment of ICH patients is based on oral anticoagulant reversal, management of blood pressure and other medical complications. Several pre-clinical studies showed promising results and demonstrated that anti-oxidative and anti-inflammatory treatments reduced neuronal cell death, however, to date, all of these attempts have failed in randomized controlled clinical trials. Yet, the time frame of administration may be crucial in translation from animal to clinical studies. Furthermore, the latest pre-clinical research points toward the existence of other, apoptosis-unrelated forms kinds of pro-grammed cell death. Conclusion: Our review summarizes current knowledge of pathways leading to programmed cell death after ICH in addition to data from clinical trials. Some of the pre-clinical results have not yet demonstrated clinical confirmation, however they sig-nificantly contribute to our understanding of post-ICH pathology and can contribute to development of new therapeutic ap-proaches, decreasing mortality and improving ICH patients’ quality of life.
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Affiliation(s)
- Tobias Bobinger
- Department of Neurology, University of Erlangen-Nuremberg, Schwabachanlage 6, Erlangen 91054, Germany
| | - Petra Burkardt
- Department of Neurology, University of Erlangen-Nuremberg, Schwabachanlage 6, Erlangen 91054, Germany
| | - Hagen B Huttner
- Department of Neurology, University of Erlangen-Nuremberg, Schwabachanlage 6, Erlangen 91054, Germany
| | - Anatol Manaenko
- Department of Neurology, University of Erlangen-Nuremberg, Schwabachanlage 6, Erlangen 91054, Germany
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van der Aart LT, Spijksma GK, Harms A, Vollmer W, Hankemeier T, van Wezel GP. High-Resolution Analysis of the Peptidoglycan Composition in Streptomyces coelicolor. J Bacteriol 2018; 200:e00290-18. [PMID: 30061355 PMCID: PMC6153666 DOI: 10.1128/jb.00290-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/27/2018] [Indexed: 11/20/2022] Open
Abstract
The bacterial cell wall maintains cell shape and protects against bursting by turgor. A major constituent of the cell wall is peptidoglycan (PG), which is continuously modified to enable cell growth and differentiation through the concerted activity of biosynthetic and hydrolytic enzymes. Streptomycetes are Gram-positive bacteria with a complex multicellular life style alternating between mycelial growth and the formation of reproductive spores. This involves cell wall remodeling at apical sites of the hyphae during cell elongation and autolytic degradation of the vegetative mycelium during the onset of development and antibiotic production. Here, we show that there are distinct differences in the cross-linking and maturation of the PGs between exponentially growing vegetative hyphae and the aerial hyphae that undergo sporulation. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis identified over 80 different muropeptides, revealing that major PG hydrolysis takes place over the course of mycelial growth. Half of the dimers lacked one of the disaccharide units in transition-phase cells, most likely due to autolytic activity. The deacetylation of MurNAc to MurN was particularly pronounced in spores and strongly reduced in sporulation mutants with a deletion of bldD or whiG, suggesting that MurN is developmentally regulated. Altogether, our work highlights the dynamic and growth phase-dependent changes in the composition of the PG in StreptomycesIMPORTANCE Streptomycetes are bacteria with a complex lifestyle and are model organisms for bacterial multicellularity. From a single spore, a large multigenomic multicellular mycelium is formed, which differentiates to form spores. Programmed cell death is an important event during the onset of morphological differentiation. In this work, we provide new insights into the changes in the peptidoglycan composition and over time, highlighting changes over the course of development and between growing mycelia and spores. This revealed dynamic changes in the peptidoglycan when the mycelia aged, with extensive peptidoglycan hydrolysis and, in particular, an increase in the proportion of 3-3 cross-links. Additionally, we identified a muropeptide that accumulates predominantly in the spores and may provide clues toward spore development.
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Affiliation(s)
- Lizah T van der Aart
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Gerwin K Spijksma
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Amy Harms
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Thomas Hankemeier
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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Zhao Y, Onda K, Sugiyama K, Yuan B, Tanaka S, Takagi N, Hirano T. Antitumor effects of arsenic disulfide on the viability, migratory ability, apoptosis and autophagy of breast cancer cells. Oncol Rep 2018; 41:27-42. [PMID: 30320388 PMCID: PMC6278372 DOI: 10.3892/or.2018.6780] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 09/04/2018] [Indexed: 12/13/2022] Open
Abstract
In the present study, the antitumor effects of arsenic disulfide (As2S2) on the proliferative, survival and migratory ability of human breast cancer MCF-7 and MDA-MB-231 cells were investigated, and its potential underlying molecular mechanisms with an emphasis on cell cycle arrest, apoptosis induction, autophagy induction and reactive oxygen species (ROS) generation were determined. The results indicated that As2S2 significantly inhibited the viability, survival and migration of breast cancer cells in a dose-dependent manner. In addition, it was identified that As2S2 induced cell cycle arrest primarily at G2/M phase in the two breast cancer cell lines by regulating the expression of associated proteins, including cyclin B1 and cell division cycle protein 2. In addition to cell cycle arrest, As2S2 also triggered the induction of apoptosis in cells by activating the expression of pro-apoptotic proteins, including caspase-7 and −8, as well as increasing the B-cell lymphoma 2 (Bcl-2)-associated X protein/Bcl-2 ratio, while decreasing the protein expression of anti-apoptotic B-cell lymphoma extra-large. In addition, As2S2 stimulated the accumulation of microtubule-associated protein 1A/1B-light chain 3 (LC3)-II and increased the LC3-II/LC3-I ratio, indicating the occurrence of autophagy. As2S2 treatment also inhibited the protein expression of matrix metalloproteinase-9 (MMP-9), but increased the intracellular accumulation of ROS in the two breast cancer cell lines, which may assist in alleviating metastasis and attenuating the progression of breast cancer. Taken together, the results of the present study suggest that As2S2 inhibits the progression of human breast cancer cells through the regulation of cell cycle arrest, intrinsic and extrinsic apoptosis, autophagy, MMP-9 signaling and ROS generation.
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Affiliation(s)
- Yuxue Zhao
- Department of Clinical Pharmacology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192‑0392, Japan
| | - Kenji Onda
- Department of Clinical Pharmacology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192‑0392, Japan
| | - Kentaro Sugiyama
- Department of Clinical Pharmacology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192‑0392, Japan
| | - Bo Yuan
- Department of Applied Biochemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192‑0392, Japan
| | - Sachiko Tanaka
- Department of Clinical Pharmacology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192‑0392, Japan
| | - Norio Takagi
- Department of Applied Biochemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192‑0392, Japan
| | - Toshihiko Hirano
- Department of Clinical Pharmacology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192‑0392, Japan
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Tu P, Bian X, Chi L, Gao B, Ru H, Knobloch TJ, Weghorst CM, Lu K. Characterization of the Functional Changes in Mouse Gut Microbiome Associated with Increased Akkermansia muciniphila Population Modulated by Dietary Black Raspberries. ACS OMEGA 2018; 3:10927-10937. [PMID: 30288460 PMCID: PMC6166222 DOI: 10.1021/acsomega.8b00064] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/13/2018] [Indexed: 06/08/2023]
Abstract
Gut microbiome plays an essential role in host health through host-gut microbiota metabolic interactions. Desirable modulation of beneficial gut bacteria, such as Akkermansia muciniphila, can confer health benefits by altering microbiome-related metabolic profiles. The purpose of this study is to examine the effects of a black raspberry-rich diet to reshape the gut microbiome by selectively boosting A. muciniphila population in C57BL/6J mice. Remarkable changes of the mouse gut microbiome were revealed at both compositional and functional levels with an expected increase of A. muciniphila in concert with a profound impact on multiple gut microbiome-related functions, including vitamin biosynthesis, aromatic amino acid metabolism, carbohydrate metabolism, and oxidative stress. These functional alterations in the gut microbiome by an easily accessed freeze-dried black raspberry-supplemented diet may provide novel insights on the improvement of human health via gut microbiome modulation.
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Affiliation(s)
- Pengcheng Tu
- Department
of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27519, United States
| | - Xiaoming Bian
- Department
of Environmental Health Science, University
of Georgia, Athens, Georgia 30602, United States
| | - Liang Chi
- Department
of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27519, United States
| | - Bei Gao
- Department
of Environmental Health Science, University
of Georgia, Athens, Georgia 30602, United States
| | - Hongyu Ru
- Department
of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27519, United States
| | - Thomas J. Knobloch
- Division of Environmental
Health Sciences, College of Public Health and Comprehensive
Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Christopher M. Weghorst
- Division of Environmental
Health Sciences, College of Public Health and Comprehensive
Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Kun Lu
- Department
of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27519, United States
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The SCO1731 methyltransferase modulates actinorhodin production and morphological differentiation of Streptomyces coelicolor A3(2). Sci Rep 2018; 8:13686. [PMID: 30209340 PMCID: PMC6135851 DOI: 10.1038/s41598-018-32027-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/18/2018] [Indexed: 02/07/2023] Open
Abstract
Streptomyces coelicolor is a Gram-positive microorganism often used as a model of physiological and morphological differentiation in streptomycetes, prolific producers of secondary metabolites with important biological activities. In the present study, we analysed Streptomyces coelicolor growth and differentiation in the presence of the hypo-methylating agent 5′-aza-2′-deoxycytidine (5-aza-dC) in order to investigate whether cytosine methylation has a role in differentiation. We found that cytosine demethylation caused a delay in spore germination, aerial mycelium development, sporulation, as well as a massive impairment of actinorhodin production. Thus, we searched for putative DNA methyltransferase genes in the genome and constructed a mutant of the SCO1731 gene. The analysis of the SCO1731::Tn5062 mutant strain demonstrated that inactivation of SCO1731 leads to a strong decrease of cytosine methylation and almost to the same phenotype obtained after 5-aza-dC treatment. Altogether, our data demonstrate that cytosine methylation influences morphological differentiation and actinorhodin production in S. coelicolor and expand our knowledge on this model bacterial system.
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Misfolded Protein Linked Strategies Toward Biomarker Development for Neurodegenerative Diseases. Mol Neurobiol 2018; 56:2559-2578. [DOI: 10.1007/s12035-018-1232-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 07/10/2018] [Indexed: 12/14/2022]
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Bacterial RecA Protein Promotes Adenoviral Recombination during In Vitro Infection. mSphere 2018; 3:3/3/e00105-18. [PMID: 29925671 PMCID: PMC6010623 DOI: 10.1128/msphere.00105-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 06/03/2018] [Indexed: 12/30/2022] Open
Abstract
Adenoviruses are common human mucosal pathogens of the gastrointestinal, respiratory, and genitourinary tracts and ocular surface. Here, we report finding Chi-like sequences in adenovirus recombination hot spots. Adenovirus coinfection in the presence of bacterial RecA protein facilitated homologous recombination between viruses. Genetic recombination led to evolution of an important external feature on the adenoviral capsid, namely, the penton base protein hypervariable loop 2, which contains the arginine-glycine-aspartic acid motif critical to viral internalization. We speculate that free Rec proteins present in gastrointestinal secretions upon bacterial cell death facilitate the evolution of human adenoviruses through homologous recombination, an example of viral commensalism and the complexity of virus-host interactions, including regional microbiota. Adenovirus infections in humans are common and sometimes lethal. Adenovirus-derived vectors are also commonly chosen for gene therapy in human clinical trials. We have shown in previous work that homologous recombination between adenoviral genomes of human adenovirus species D (HAdV-D), the largest and fastest growing HAdV species, is responsible for the rapid evolution of this species. Because adenovirus infection initiates in mucosal epithelia, particularly at the gastrointestinal, respiratory, genitourinary, and ocular surfaces, we sought to determine a possible role for mucosal microbiota in adenovirus genome diversity. By analysis of known recombination hot spots across 38 human adenovirus genomes in species D (HAdV-D), we identified nucleotide sequence motifs similar to bacterial Chi sequences, which facilitate homologous recombination in the presence of bacterial Rec enzymes. These motifs, referred to here as ChiAD, were identified immediately 5′ to the sequence encoding penton base hypervariable loop 2, which expresses the arginine-glycine-aspartate moiety critical to adenoviral cellular entry. Coinfection with two HAdV-Ds in the presence of an Escherichia coli lysate increased recombination; this was blocked in a RecA mutant strain, E. coli DH5α, or upon RecA depletion. Recombination increased in the presence of E. coli lysate despite a general reduction in viral replication. RecA colocalized with viral DNA in HAdV-D-infected cell nuclei and was shown to bind specifically to ChiAD sequences. These results indicate that adenoviruses may repurpose bacterial recombination machinery, a sharing of evolutionary mechanisms across a diverse microbiota, and unique example of viral commensalism. IMPORTANCE Adenoviruses are common human mucosal pathogens of the gastrointestinal, respiratory, and genitourinary tracts and ocular surface. Here, we report finding Chi-like sequences in adenovirus recombination hot spots. Adenovirus coinfection in the presence of bacterial RecA protein facilitated homologous recombination between viruses. Genetic recombination led to evolution of an important external feature on the adenoviral capsid, namely, the penton base protein hypervariable loop 2, which contains the arginine-glycine-aspartic acid motif critical to viral internalization. We speculate that free Rec proteins present in gastrointestinal secretions upon bacterial cell death facilitate the evolution of human adenoviruses through homologous recombination, an example of viral commensalism and the complexity of virus-host interactions, including regional microbiota.
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de Paula AB, Taparelli JR, Alonso RCB, Innocentini-Mei LH, Puppin-Rontani RM. Synthesis and application of triclosan methacrylate monomer in resin composites. Clin Oral Investig 2018; 23:965-974. [DOI: 10.1007/s00784-018-2521-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 06/07/2018] [Indexed: 11/28/2022]
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Quorum Sensing Extracellular Death Peptides Enhance the Endoribonucleolytic Activities of Mycobacterium tuberculosis MazF Toxins. mBio 2018; 9:mBio.00685-18. [PMID: 29717013 PMCID: PMC5930309 DOI: 10.1128/mbio.00685-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
mazEF is a toxin-antitoxin module located on chromosomes of most bacteria. MazF toxins are endoribonucleases antagonized by MazE antitoxins. Previously, we characterized several quorum sensing peptides called "extracellular death factors" (EDFs). When secreted from bacterial cultures, EDFs induce interspecies cell death. EDFs also enhance the endoribonucleolytic activity of Escherichia coli MazF. Mycobacterium tuberculosis carries several mazEF modules. Among them, the endoribonucleolytic activities of MazF proteins mt-1, mt-3, and mt-6 were identified. MazF-mt6 and MazF-mt-3 cleave M. tuberculosis rRNAs. Here we report the in vitro effects of EDFs on the endoribonucleolytic activities of M. tuberculosis MazFs. Escherichia coli EDF (EcEDF) and the three Pseudomonas aeruginosa EDFs (PaEDFs) individually enhance the endoribonucleolytic activities of MazF-mt6 and MazF-mt3 and overcome the inhibitory effect of MazE-mt3 or MazE-mt6 on the endoribonucleolytic activities of the respective toxins. We propose that these EDFs can serve as a basis for a novel class of antibiotics against M. tuberculosis. Mycobacterium tuberculosis is one of the leading causes of death from infectious disease. M. tuberculosis is highly drug resistant, and drug delivery to the infected site is very difficult. In previous studies, we showed that extracellular death factors (EDFs) can work as quorum sensing molecules which participate in interspecies bacterial cell death. In this study, we demonstrated the role of different EDFs in the endoribonucleolytic activities of M. tuberculosis MazFs. Escherichia coli EDF (EcEDF) and the three Pseudomonas aeruginosa EDFs (PaEDFs) individually enhance the endoribonucleolytic activities of MazF-mt6 and MazF-mt3. The current report provides a basis for the use of the EDF peptides EcEDF and PaEDF as novel antibiotics against M. tuberculosis.
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Shapira S, Shapira A, Kazanov D, Hevroni G, Kraus S, Arber N. Selective eradication of cancer cells by delivery of adenovirus-based toxins. Oncotarget 2018; 8:38581-38591. [PMID: 28445136 PMCID: PMC5503555 DOI: 10.18632/oncotarget.16934] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 03/13/2017] [Indexed: 01/17/2023] Open
Abstract
Background and objective KRAS mutation is an early event in colorectal cancer carcinogenesis. We previously reported that a recombinant adenovirus, carrying a pro-apoptotic gene (PUMA) under the regulation of Ets/AP1 (RAS-responsive elements) suppressed the growth of cancer cells harboring hyperactive KRAS. We propose to exploit the hyperactive RAS pathway, rather than to inhibit it as was previously tried and failed repeatedly. We aim to improve efficacy by substituting PUMA with a more potent toxin, the bacterial MazF-MazE toxin-antitoxin system, under a very tight regulation. Results A massive cell death, in a dose-dependent manner, reaching 73% at MOI 10 was seen in KRAS cells as compared to 22% in WT cells. Increase expression of MazE (the anti-toxin) protected normal cells from any possible internal or external leakage of the system and confirmed the selectivity, specificity and safety of the targeting system. Considerable tumor shrinkage (61%) was demonstrated in vivo following MazEF-encoding adenovirus treatment without any side effects. Design Efficient vectors for cancer-directed gene delivery were constructed; “pAdEasy-Py4-SV40mP-mCherry-MazF”“pAdEasy-Py4-SV40mP-mCherry-MazF-IRES-TetR-CMVmp-MazE-IRES-EGFP“,“pAdEasy-ΔPy4-SV40mP-mCherry-MazF-IRES-TetR-CMVmp-MazE-IRES-EGFP “and “pAdEasy-mCherry”. Virus particles were produced and their potency was tested. Cell death was measured qualitatively by using the fluorescent microscopy and colony formation assay, and was quantified by MTT. FACS analysis using annexin V and RedDot2 dyes was performed for measuring apoptotic and dead cells, respectively. In vivo tumor formation was measured in a xenograft model. Conclusions A proof of concept for a novel cancer safe and effective gene therapy exploiting an aberrant hyperactive pathway is achievable.
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Affiliation(s)
- Shiran Shapira
- Laboratory of Molecular Biology, The Integrated Cancer Prevention Center, Tel Aviv Sourasky Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Assaf Shapira
- Department of Molecular Microbiology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel-Aviv, Israel
| | - Diana Kazanov
- Laboratory of Molecular Biology, The Integrated Cancer Prevention Center, Tel Aviv Sourasky Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Gil Hevroni
- Laboratory of Molecular Biology, The Integrated Cancer Prevention Center, Tel Aviv Sourasky Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Sarah Kraus
- Laboratory of Molecular Biology, The Integrated Cancer Prevention Center, Tel Aviv Sourasky Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Nadir Arber
- Laboratory of Molecular Biology, The Integrated Cancer Prevention Center, Tel Aviv Sourasky Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
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65
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Abstract
Dying cells subjected to apoptotic programs are engulfed by neighboring cells or by professional phagocytes, without inflammation or immunological reactions in the tissue where apoptosis takes place. Apoptotic cells release danger-associated project signals to their neighbours, through different molecular patterns, stimulate antigen production and immune responses. Microenvironmental effects with several functional consequences indicate that cell death is a complex process and may take place in several ways. This idea is expressed by the title of the Special Issue and by the title of the guest editorial "Mille modis morimur" meaning that not only multicellular organisms, but also single cells may die in a thousand ways. This idea is demonstrated by the papers serving as examples for cell death. Apoptosis was induced by clary sage oil in Candida cells. Heavy metal (Gd) induced cell motility and apoptosis was found in mammalian cells. RNA oxidation enhanced the reversion frequency of apoptosis in yeast mutants. The frequency of apoptotic micronucleus formation increased in a concentration-dependent manner by methotrexate. The antioxidant coenzyme Q10 protected renal proximal tubule cells against nicotine-induced apoptosis. The synergy of 2-deoxy-D-glucose combined with berberine induced lysosome/autophagy. The mitochondrial apoptotic pathway could be regulated by glucocorticoid receptor in collaboration with Bcl-2 family proteins in developing T cells. Cylindrospermopsin induced biochemical changes led to apoptosis in plants. Mechanisms of stress seriously impacted the risk of apoptosis. Transcriptional control of apoptotic cell clearance was achieved by macrophage nuclear receptors. Finally, the clinical aspects of apoptosis-induced lymphopenia were reviewed in sepsis and other severe injuries. These examples not only support the view of many ways of cell death, but predict further potential ways to induce or reduce the risk of cell death.
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66
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Lee Y, Lee HR, Kim K, Choi SQ. Static and Dynamic Permeability Assay for Hydrophilic Small Molecules Using a Planar Droplet Interface Bilayer. Anal Chem 2018; 90:1660-1667. [PMID: 29308648 DOI: 10.1021/acs.analchem.7b03004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Because numerous drugs are administered through an oral route and primarily absorbed at the intestine, the prediction of drug permeability across an intestinal epithelial cell membrane has been a crucial issue in drug discovery. Thus, various in vitro permeability assays have been developed such as the Caco-2 assay, the parallel artificial membrane permeability assay (PAMPA), the phospholipid vesicle-based permeation assays (PVPA) and Permeapad. However, because of the time-consuming and quite expensive process for culturing cells in the Caco-2 assay and the unknown microscopic membrane structures of the other assays, a simpler yet more accurate and versatile technique is still required. Accordingly, we developed a new platform to measure the permeability of small molecules across a planar freestanding lipid bilayer with a well-defined area and structure. The lipid bilayer was constructed within a conventional UV spectrometer cell, and the transport of drug molecules across the bilayer was recorded by UV absorbance over time. We then computed the permeability from the time-dependent diffusion equation. We tested this assay for five exemplary hydrophilic drugs and compared their values with previously reported ones. We found that our assay has a much higher permeability compared to the other techniques, and this higher permeability is related to the thickness of the lipid bilayer. Also we were able to measure the dynamic permeability upon the addition of a membrane-disrupting surfactant demonstrating that our assay has the capability to detect real-time changes in permeability across the lipid bilayer.
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Affiliation(s)
- Yohan Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141, Korea
| | - Hyun-Ro Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141, Korea
| | - KyuHan Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141, Korea
| | - Siyoung Q Choi
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141, Korea
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67
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Libby E, Driscoll WW, Ratcliff WC. Programmed cell death can increase the efficacy of microbial bet -hedging. Sci Rep 2018; 8:1120. [PMID: 29348455 PMCID: PMC5773525 DOI: 10.1038/s41598-017-18687-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/13/2017] [Indexed: 11/09/2022] Open
Abstract
Programmed cell death (PCD) occurs in both unicellular and multicellular organisms. While PCD plays a key role in the development and maintenance of multicellular organisms, explaining why single-celled organisms would evolve to actively commit suicide has been far more challenging. Here, we explore the potential for PCD to act as an accessory to microbial bet-hedging strategies that utilize stochastic phenotype switching. We consider organisms that face unpredictable and recurring disasters, in which fitness depends on effective phenotypic diversification. We show that when reproductive opportunities are limited by carrying capacity, PCD drives population turnover, providing increased opportunities for phenotypic diversification through stochastic phenotype switching. The main cost of PCD, providing resources for growth to a PCD(−) competitor, is ameliorated by genetic assortment in spatially structured populations. Using agent -based simulations, we explore how basic demographic factors, namely bottlenecks and local dispersal, can generate sufficient spatial structure to favor the evolution of high PCD rates.
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Affiliation(s)
- Eric Libby
- Santa Fe Institute, Santa Fe, NM, 87501, USA
| | - William W Driscoll
- Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, MN, 55108, USA
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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68
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Abstract
Apoptosis is a form of active cell death engaged by developmental cues as well as many different cellular stresses in which the dying cell essentially 'packages' itself for removal. The process of apoptotic cell death, as defined at the molecular level, is unique to the Metazoa (animals). Yet active cell death exists in non-animal organisms, and in some cases molecules involved in such death show some sequence similarities to those involved in apoptosis, leading to extensive speculation regarding the evolution of apoptosis. Here, we examine such speculation from the perspective of the functional properties of molecules of the mitochondrial apoptotic cell death pathway. We suggest scenarios for the evolution of one pathway of apoptosis, the mitochondrial pathway, and consider how they might be tested. We conclude with a 'Just So Story' of how the mitochondrial pathway of apoptosis might have evolved during eukaryotic evolution.
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Affiliation(s)
- Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Patrick Fitzgerald
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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69
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Jaén-Luchoro D, Aliaga-Lozano F, Gomila RM, Gomila M, Salvà-Serra F, Lalucat J, Bennasar-Figueras A. First insights into a type II toxin-antitoxin system from the clinical isolate Mycobacterium sp. MHSD3, similar to epsilon/zeta systems. PLoS One 2017; 12:e0189459. [PMID: 29236773 PMCID: PMC5728571 DOI: 10.1371/journal.pone.0189459] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 11/28/2017] [Indexed: 01/21/2023] Open
Abstract
A putative type II toxin-antitoxin (TA) system was found in the clinical isolate Mycobacterium sp. MHSD3, a strain closely related to Mycobacterium chelonae. Further analyses of the protein sequences of the two genes revealed the presence of domains related to a TA system. BLAST analyses indicated the presence of closely related proteins in the genomes of other recently published M. chelonae strains. The functionality of both elements of the TA system was demonstrated when expressed in Escherichia coli cells, and the predicted structure of the toxin is very similar to those of well-known zeta-toxins, leading to the definition of a type II TA system similar to epsilon/zeta TA systems in strains that are closely related to M. chelonae.
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Affiliation(s)
- Daniel Jaén-Luchoro
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
- * E-mail:
| | - Francisco Aliaga-Lozano
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Laboratorio de Biología Molecular, Clínica Rotger, Palma de Mallorca, Spain
| | - Rosa Maria Gomila
- Serveis Cientifico-Tècnics, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Margarita Gomila
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Francisco Salvà-Serra
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
| | - Jorge Lalucat
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Institut Mediterrani d’Estudis Avançats (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Antoni Bennasar-Figueras
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Area de Enfermedades Infecciosas, Instituto Universitario de Investigaciones en Ciencias de la Salud (IUNICS-UIB), Universitat de les Illes Balears, Palma de Mallorca, Spain
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70
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Yassin AF, Langenberg S, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Mukherjee S, Reddy TBK, Daum C, Shapiro N, Ivanova N, Woyke T, Kyrpides NC. Draft genome sequence of Actinotignum schaalii DSM 15541T: Genetic insights into the lifestyle, cell fitness and virulence. PLoS One 2017; 12:e0188914. [PMID: 29216246 PMCID: PMC5720513 DOI: 10.1371/journal.pone.0188914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/15/2017] [Indexed: 11/19/2022] Open
Abstract
The permanent draft genome sequence of Actinotignum schaalii DSM 15541T is presented. The annotated genome includes 2,130,987 bp, with 1777 protein-coding and 58 rRNA-coding genes. Genome sequence analysis revealed absence of genes encoding for: components of the PTS systems, enzymes of the TCA cycle, glyoxylate shunt and gluconeogensis. Genomic data revealed that A. schaalii is able to oxidize carbohydrates via glycolysis, the nonoxidative pentose phosphate and the Entner-Doudoroff pathways. Besides, the genome harbors genes encoding for enzymes involved in the conversion of pyruvate to lactate, acetate and ethanol, which are found to be the end products of carbohydrate fermentation. The genome contained the gene encoding Type I fatty acid synthase required for de novo FAS biosynthesis. The plsY and plsX genes encoding the acyltransferases necessary for phosphatidic acid biosynthesis were absent from the genome. The genome harbors genes encoding enzymes responsible for isoprene biosynthesis via the mevalonate (MVA) pathway. Genes encoding enzymes that confer resistance to reactive oxygen species (ROS) were identified. In addition, A. schaalii harbors genes that protect the genome against viral infections. These include restriction-modification (RM) systems, type II toxin-antitoxin (TA), CRISPR-Cas and abortive infection system. A. schaalii genome also encodes several virulence factors that contribute to adhesion and internalization of this pathogen such as the tad genes encoding proteins required for pili assembly, the nanI gene encoding exo-alpha-sialidase, genes encoding heat shock proteins and genes encoding type VII secretion system. These features are consistent with anaerobic and pathogenic lifestyles. Finally, resistance to ciprofloxacin occurs by mutation in chromosomal genes that encode the subunits of DNA-gyrase (GyrA) and topisomerase IV (ParC) enzymes, while resistant to metronidazole was due to the frxA gene, which encodes NADPH-flavin oxidoreductase.
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Affiliation(s)
- Atteyet F. Yassin
- Institut für medizinische Mikrobiologie und Immunologie der Universität Bonn, Bonn, Germany
- * E-mail:
| | - Stefan Langenberg
- Klinik und Poliklinik für Hals-Nasen-Ohrenheilkunde/Chirurgie, Bonn, Germany
| | - Marcel Huntemann
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Alicia Clum
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Manoj Pillay
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Krishnaveni Palaniappan
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Neha Varghese
- Klinik und Poliklinik für Hals-Nasen-Ohrenheilkunde/Chirurgie, Bonn, Germany
| | - Natalia Mikhailova
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Supratim Mukherjee
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - T. B. K. Reddy
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Chris Daum
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Nicole Shapiro
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Nikos C. Kyrpides
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
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71
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Ghosh P, Levine H. Morphodynamics of a growing microbial colony driven by cell death. Phys Rev E 2017; 96:052404. [PMID: 29347664 DOI: 10.1103/physreve.96.052404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Indexed: 06/07/2023]
Abstract
Bacterial cells can often self-organize into multicellular structures with complex spatiotemporal morphology. In this work, we study the spatiotemporal dynamics of a growing microbial colony in the presence of cell death. We present an individual-based model of nonmotile bacterial cells which grow and proliferate by consuming diffusing nutrients on a semisolid two-dimensional surface. The colony spreads by growth forces and sliding motility of cells and undergoes cell death followed by subsequent disintegration of the dead cells in the medium. We model cell death by considering two possible situations: In one of the cases, cell death occurs in response to the limitation of local nutrients, while the other case corresponds to an active death process, known as apoptotic or programmed cell death. We demonstrate how the colony morphology is influenced by the presence of cell death. Our results show that cell death facilitates transitions from roughly circular to highly branched structures at the periphery of an expanding colony. Interestingly, our results also reveal that for the colonies which are growing in higher initial nutrient concentrations, cell death occurs much earlier compared to the colonies which are growing in lower initial nutrient concentrations. This work provides new insights into the branched patterning of growing bacterial colonies as a consequence of complex interplay among the biochemical and mechanical effects.
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Affiliation(s)
- Pushpita Ghosh
- Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Texas 77005, USA
- Department of Bioengineering, Rice University, Texas 77005, USA
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72
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Gonçalves AP, Heller J, Daskalov A, Videira A, Glass NL. Regulated Forms of Cell Death in Fungi. Front Microbiol 2017; 8:1837. [PMID: 28983298 PMCID: PMC5613156 DOI: 10.3389/fmicb.2017.01837] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 09/07/2017] [Indexed: 12/15/2022] Open
Abstract
Cell death occurs in all domains of life. While some cells die in an uncontrolled way due to exposure to external cues, other cells die in a regulated manner as part of a genetically encoded developmental program. Like other eukaryotic species, fungi undergo programmed cell death (PCD) in response to various triggers. For example, exposure to external stress conditions can activate PCD pathways in fungi. Calcium redistribution between the extracellular space, the cytoplasm and intracellular storage organelles appears to be pivotal for this kind of cell death. PCD is also part of the fungal life cycle, in which it occurs during sexual and asexual reproduction, aging, and as part of development associated with infection in phytopathogenic fungi. Additionally, a fungal non-self-recognition mechanism termed heterokaryon incompatibility (HI) also involves PCD. Some of the molecular players mediating PCD during HI show remarkable similarities to major constituents involved in innate immunity in metazoans and plants. In this review we discuss recent research on fungal PCD mechanisms in comparison to more characterized mechanisms in metazoans. We highlight the role of PCD in fungi in response to exogenic compounds, fungal development and non-self-recognition processes and discuss identified intracellular signaling pathways and molecules that regulate fungal PCD.
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Affiliation(s)
- A Pedro Gonçalves
- Plant and Microbial Biology Department, University of California, BerkeleyBerkeley, CA, United States
| | - Jens Heller
- Plant and Microbial Biology Department, University of California, BerkeleyBerkeley, CA, United States
| | - Asen Daskalov
- Plant and Microbial Biology Department, University of California, BerkeleyBerkeley, CA, United States
| | - Arnaldo Videira
- Instituto de Ciências Biomédicas de Abel Salazar, Universidade do PortoPorto, Portugal.,I3S - Instituto de Investigação e Inovação em SaúdePorto, Portugal
| | - N Louise Glass
- Plant and Microbial Biology Department, University of California, BerkeleyBerkeley, CA, United States
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73
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Temmel H, Müller C, Sauert M, Vesper O, Reiss A, Popow J, Martinez J, Moll I. The RNA ligase RtcB reverses MazF-induced ribosome heterogeneity in Escherichia coli. Nucleic Acids Res 2017; 45:4708-4721. [PMID: 27789694 PMCID: PMC5416887 DOI: 10.1093/nar/gkw1018] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 10/18/2016] [Indexed: 12/22/2022] Open
Abstract
When Escherichia coli encounters stress, the endoribonuclease MazF initiates a post-transcriptional response that results in the reprogramming of protein synthesis. By removing the 3΄-terminus of the 16S rRNA, MazF generates specialized ribosomes that selectively translate mRNAs likewise processed by MazF. Given the energy required for de novo ribosome biosynthesis, we considered the existence of a repair mechanism operating upon stress relief to recycle the modified ribosomes. Here, we show that the stress-ribosomes and the 3΄-terminal 16S rRNA fragment are stable during adverse conditions. Moreover, employing in vitro and in vivo approaches we demonstrate that the RNA ligase RtcB catalyzes the re-ligation of the truncated 16S rRNA present in specialized ribosomes Thereby their ability to translate canonical mRNAs is fully restored. Together, our findings not only provide a physiological function for the RNA ligase RtcB in bacteria but highlight the reversibility of ribosome heterogeneity, a crucial but hitherto undescribed concept for translational regulation.
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Affiliation(s)
- Hannes Temmel
- Max F. Perutz Laboratories, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9/4, A-1030 Vienna, Austria
| | - Christian Müller
- Max F. Perutz Laboratories, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9/4, A-1030 Vienna, Austria
| | - Martina Sauert
- Max F. Perutz Laboratories, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9/4, A-1030 Vienna, Austria
| | - Oliver Vesper
- Max F. Perutz Laboratories, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9/4, A-1030 Vienna, Austria
| | - Ariela Reiss
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), A-1030 Vienna, Austria and Max F. Perutz Laboratories, Department of Medical Biochemistry, Medical University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9/4, A-1030 Vienna, Austria
| | - Johannes Popow
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), A-1030 Vienna, Austria and Max F. Perutz Laboratories, Department of Medical Biochemistry, Medical University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9/4, A-1030 Vienna, Austria
| | - Javier Martinez
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), A-1030 Vienna, Austria and Max F. Perutz Laboratories, Department of Medical Biochemistry, Medical University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9/4, A-1030 Vienna, Austria
| | - Isabella Moll
- Max F. Perutz Laboratories, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9/4, A-1030 Vienna, Austria
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74
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Singh R, Miriyala SS, Giri L, Mitra K, Kareenhalli VV. Identification of unstructured model for subtilin production through Bacillus subtilis using hybrid genetic algorithm. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.06.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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75
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Han W, Xu Y, Feng X, Liang YX, Huang L, Shen Y, She Q. NQO-Induced DNA-Less Cell Formation Is Associated with Chromatin Protein Degradation and Dependent on A 0A 1-ATPase in Sulfolobus. Front Microbiol 2017; 8:1480. [PMID: 28855893 PMCID: PMC5557786 DOI: 10.3389/fmicb.2017.01480] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/24/2017] [Indexed: 12/29/2022] Open
Abstract
To investigate DNA damage response in the model crenarchaeon Sulfolobus islandicus, four different DNA damage agents were tested for their effects on cell death of this archaeon, including UV irradiation, methyl methanesulfonate, cisplatin, and 4-nitroquinoline 1-oxide (NQO). Cell death featured with DNA-less cell formation was revealed in DNA damage treatment with each agent. Cellular responses upon NQO treatment were characterized in details, and following sequential events were revealed, including: a modest accumulation of G1/S phase cells, membrane depolarization, proteolytic degradation of chromatin proteins, and chromosomal DNA degradation. Further insights into the process were gained from studying drugs that affect the archaeal ATP synthase, including a proton gradient uncoupler and an ATP synthase inhibitor. Whereas the proton uncoupler-mediated excess proton influx yielded cell death as observed for the NQO treatment, inhibition of ATP synthase attenuated NQO-induced membrane depolarization and DNA-less cell formation. In conclusion, the NQO-induced cell death in S. islandicus is characterized by proteolytic degradation of chromatin protein, and chromosomal DNA degradation, which probably represents a common feature for the cell death induced by different DNA damage agents.
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Affiliation(s)
- Wenyuan Han
- Archaea Centre, Department of Biology, University of CopenhagenCopenhagen, Denmark
| | - Yanqun Xu
- Archaea Centre, Department of Biology, University of CopenhagenCopenhagen, Denmark.,State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Xu Feng
- Archaea Centre, Department of Biology, University of CopenhagenCopenhagen, Denmark.,State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Yun X Liang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing, China
| | - Yulong Shen
- State Key Laboratory of Microbial Technology, Shandong UniversityJinan, China
| | - Qunxin She
- Archaea Centre, Department of Biology, University of CopenhagenCopenhagen, Denmark.,State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural UniversityWuhan, China
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76
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Li T, Weng Y, Ma X, Tian B, Dai S, Jin Y, Liu M, Li J, Yu J, Hua Y. Deinococcus radiodurans Toxin-Antitoxin MazEF-dr Mediates Cell Death in Response to DNA Damage Stress. Front Microbiol 2017; 8:1427. [PMID: 28798741 PMCID: PMC5526972 DOI: 10.3389/fmicb.2017.01427] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/14/2017] [Indexed: 01/30/2023] Open
Abstract
Here we identified a functional MazEF-dr system in the exceptionally stress-resistant bacterium D. radiodurans. We showed that overexpression of the toxin MazF-dr inhibited the growth of Escherichia coli. The toxic effect of MazF-dr was due to its sequence-specific endoribonuclease activity on RNAs containing a consensus 5′ACA3′, and it could be neutralized by MazE-dr. The MazF-dr showed a special cleavage preference for the nucleotide present before the ACA sequence with the order by U>A>G>C. MazEF-dr mediated the death of D. radiodurans cells under sub-lethal dose of stresses. The characteristics of programmed cell death (PCD) including membrane blebbing, loss of membrane integrity and cytoplasm condensation occurred in a fraction of the wild-type population at sub-lethal concentration of the DNA damaging agent mitomycin C (MMC); however, a MazEF-dr mutation relieved the cell death, suggesting that MazEF-dr mediated cell death through its endoribonuclease activity in response to DNA damage stress. The MazEF-dr-mediated cell death of a fraction of the population might serve as a survival strategy for the remaining population of D. radiodurans under DNA damage stress.
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Affiliation(s)
- Tao Li
- Key Laboratory of Nuclear Agricultural Science of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang UniversityHangzhou, China
| | - Yulan Weng
- Key Laboratory of Nuclear Agricultural Science of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang UniversityHangzhou, China
| | - Xiaoqiong Ma
- Central Laboratory, The First Affiliated Hospital of Zhejiang Chinese Medical UniversityHangzhou, China
| | - Bing Tian
- Key Laboratory of Nuclear Agricultural Science of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang UniversityHangzhou, China
| | - Shang Dai
- Key Laboratory of Nuclear Agricultural Science of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang UniversityHangzhou, China
| | - Ye Jin
- Key Laboratory of Nuclear Agricultural Science of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang UniversityHangzhou, China
| | - Mengjia Liu
- Key Laboratory of Nuclear Agricultural Science of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang UniversityHangzhou, China
| | - Jiulong Li
- Key Laboratory of Nuclear Agricultural Science of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang UniversityHangzhou, China
| | - Jiangliu Yu
- Key Laboratory of Nuclear Agricultural Science of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang UniversityHangzhou, China
| | - Yuejin Hua
- Key Laboratory of Nuclear Agricultural Science of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang UniversityHangzhou, China
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77
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Xia J, Feng B, Shao Q, Yuan Y, Wang XS, Chen N, Wu S. Virtual Screening against Phosphoglycerate Kinase 1 in Quest of Novel Apoptosis Inhibitors. Molecules 2017. [PMID: 28635653 PMCID: PMC5720137 DOI: 10.3390/molecules22061029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Inhibition of apoptosis is a potential therapy to treat human diseases such as neurodegenerative disorders (e.g., Parkinson’s disease), stroke, and sepsis. Due to the lack of druggable targets, it remains a major challenge to discover apoptosis inhibitors. The recent repositioning of a marketed drug (i.e., terazosin) as an anti-apoptotic agent uncovered a novel target (i.e., human phosphoglycerate kinase 1 (hPgk1)). In this study, we developed a virtual screening (VS) pipeline based on the X-ray structure of Pgk1/terazosin complex and applied it to a screening campaign for potential anti-apoptotic agents. The hierarchical filters in the pipeline (i.e., similarity search, a pharmacophore model, a shape-based model, and molecular docking) rendered 13 potential hits from Specs chemical library. By using PC12 cells (exposed to rotenone) as a cell model for bioassay, we first identified that AK-918/42829299, AN-465/41520984, and AT-051/43421517 were able to protect PC12 cells from rotenone-induced cell death. Molecular docking suggested these hit compounds were likely to bind to hPgk1 in a similar mode to terazosin. In summary, we not only present a versatile VS pipeline for potential apoptosis inhibitors discovery, but also provide three novel-scaffold hit compounds that are worthy of further development and biological study.
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Affiliation(s)
- Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Bo Feng
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Qianhang Shao
- Department of Pharmacology, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Yuhe Yuan
- Department of Pharmacology, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Xiang Simon Wang
- Molecular Modeling and Drug Discovery Core Laboratory for District of Columbia Center for AIDS Research (DC CFAR), Department of Pharmaceutical Sciences, College of Pharmacy, Howard University, Washington, DC 20059, USA.
| | - Naihong Chen
- Department of Pharmacology, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Song Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
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78
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Zhang Z, Chai W, Xiong R, Zhou L, Huang Y. Printing-induced cell injury evaluation during laser printing of 3T3 mouse fibroblasts. Biofabrication 2017. [DOI: 10.1088/1758-5090/aa6ed9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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79
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Zhang Z, Chai W, Xiong R, Zhou L, Huang Y. Printing-induced cell injury evaluation during laser printing of 3T3 mouse fibroblasts. Biofabrication 2017. [DOI: 10.1088/1758-5090/aa6ed9/.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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80
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Zhang Z, Chai W, Xiong R, Zhou L, Huang Y. Printing-induced cell injury evaluation during laser printing of 3T3 mouse fibroblasts. Biofabrication 2017. [PMID: 28631624 DOI: 10.1088/1758-5090/aa6ed9/] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Three-dimensional bioprinting has emerged as a promising solution for the freeform fabrication of living cellular constructs, which can be used for tissue/organ transplantation and tissue models. During bioprinting, some living cells are unavoidably injured and may become necrotic or apoptotic cells. This study aims to investigate the printing-induced cell injury and evaluates injury types of post-printing cells using the annexin V/7-aminoactinomycin D and FAM-DEVD-FMK/propidium iodide assays during laser printing of NIH 3T3 mouse fibroblasts. As observed, the percentage of post-printing early apoptotic mouse fibroblasts increases with the incubation time, indicating that post-printing apoptotic mouse fibroblasts have different initiation lag times of apoptosis due to different levels of mechanical stress exerted during laser printing. Post-printing necrotic mouse fibroblasts can be detected immediately after printing, while post-printing early apoptotic mouse fibroblasts need time to develop into a late apoptotic stage. The minimum time needed for post-printing early apoptotic mouse fibroblasts to complete their apoptosis pathway and transition into late apoptotic mouse fibroblasts is from 4 h to 5 h post-printing. The resulting knowledge of the evolution of different apoptotic post-printing mouse fibroblasts will help better design future experiments to quantitatively determine, model, and mitigate the post-printing cell injury based on molecular signal pathway modeling.
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Affiliation(s)
- Zhengyi Zhang
- School of Naval Architecture and Ocean Engineering, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China. Dept. of Mechanical and Aerospace Engineering, Univ. of Florida, Gainesville, FL 32611, United States of America
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81
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Wagner A, Whitaker RJ, Krause DJ, Heilers JH, van Wolferen M, van der Does C, Albers SV. Mechanisms of gene flow in archaea. Nat Rev Microbiol 2017; 15:492-501. [DOI: 10.1038/nrmicro.2017.41] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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82
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Yang QE, Walsh TR. Toxin-antitoxin systems and their role in disseminating and maintaining antimicrobial resistance. FEMS Microbiol Rev 2017; 41:343-353. [PMID: 28449040 PMCID: PMC5812544 DOI: 10.1093/femsre/fux006] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Indexed: 12/20/2022] Open
Abstract
Toxin-antitoxin systems (TAs) are ubiquitous among bacteria and play a crucial role in the dissemination and evolution of antibiotic resistance, such as maintaining multi-resistant plasmids and inducing persistence formation. Generally, activities of the toxins are neutralised by their conjugate antitoxins. In contrast, antitoxins are more liable to degrade under specific conditions such as stress, and free active toxins interfere with essential cellular processes including replication, translation and cell-wall synthesis. TAs have also been shown to be responsible for plasmid maintenance, stress management, bacterial persistence and biofilm formation. We discuss here the recent findings of these multifaceted TAs (type I-VI) and in particular examine the role of TAs in augmenting the dissemination and maintenance of multi-drug resistance in bacteria.
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Affiliation(s)
- Qiu E. Yang
- Division of Infection and Immunity, Heath Park Hospital, Cardiff University, Cardiff CF14 4XN, UK
| | - Timothy R. Walsh
- Division of Infection and Immunity, Heath Park Hospital, Cardiff University, Cardiff CF14 4XN, UK
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83
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Autophagy regulatory molecule, TMEM74, interacts with BIK and inhibits BIK-induced apoptosis. Cell Signal 2017; 36:34-41. [PMID: 28412412 DOI: 10.1016/j.cellsig.2017.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/20/2017] [Accepted: 04/08/2017] [Indexed: 12/19/2022]
Abstract
TMEM74 (Transmembrane protein 74), a lysosome transmembrane protein, induces cell autophagy. Knockdown of TMEM74 abolished EBSS-induced autophagy. BIK, belonging to BOP (BH3-only protein) protein family, has been reported to induce cell apoptosis. Autophagy and apoptosis, as different pathways regulated by extra- or intra-cellular signals precisely, both play a crucial role in processes of intra-cellular substrates degradation, energy metabolism and cell survival. However, the relationship between autophagy and apoptosis still remains elusive. To elucidate the putative new relationship and further identify the function of TMEM74, we performed the study mainly using co-immunoprecipitation, immunoblotting, fluorescent location and basic cell biologic experimental techniques. In the present study, for the first time, it is demonstrated that autophagy-related protein TMEM74 co-localizes with apoptosis-related protein BIK in subcellular organelles. The data indicated that TMEM74 associates with BIK via TM domains of TMEM74 and BH3 domain of BIK. Further investigations revealed that TMEM74 inhibits BIK-induced apoptosis by interacting with BIK, as evidenced by the results that autophagosome formation inhibitor could not block the inhibition effect completely. On the contrary, knockdown of TMEM74 and the TM domain-deficient mutant led to deprivation of the function. Overall, the results revealed the autophagy modulator TMEM74 interrelates with apoptosis inducer BIK and inhibits its function, which provides a novel crosstalk point between autophagy and apoptosis to enlarge our understanding of the programmed cell death.
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84
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McGivney E, Han L, Avellan A, VanBriesen J, Gregory KB. Disruption of Autolysis in Bacillus subtilis using TiO 2 Nanoparticles. Sci Rep 2017; 7:44308. [PMID: 28303908 PMCID: PMC5355886 DOI: 10.1038/srep44308] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 02/07/2017] [Indexed: 02/07/2023] Open
Abstract
In contrast to many nanotoxicity studies where nanoparticles (NPs) are observed to be toxic or reduce viable cells in a population of bacteria, we observed that increasing concentration of TiO2 NPs increased the cell survival of Bacillus subtilis in autolysis-inducing buffer by 0.5 to 5 orders of magnitude over an 8 hour exposure. Molecular investigations revealed that TiO2 NPs prevent or delay cell autolysis, an important survival and growth-regulating process in bacterial populations. Overall, the results suggest two potential mechanisms for the disruption of autolysis by TiO2 NPs in a concentration dependent manner: (i) directly, through TiO2 NP deposition on the cell wall, delaying the collapse of the protonmotive-force and preventing the onset of autolysis; and (ii) indirectly, through adsorption of autolysins on TiO2 NP, limiting the activity of released autolysins and preventing further lytic activity. Enhanced darkfield microscopy coupled to hyperspectral analysis was used to map TiO2 deposition on B. subtilis cell walls and released enzymes, supporting both mechanisms of autolysis interference. The disruption of autolysis in B. subtilis cultures by TiO2 NPs suggests the mechanisms and kinetics of cell death may be influenced by nano-scale metal oxide materials, which are abundant in natural systems.
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Affiliation(s)
- Eric McGivney
- Department of Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
- Center for the Environmental Implications of Nanotechnology (CEINT), Duke University, Durham, North Carolina, USA
| | - Linchen Han
- Department of Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Astrid Avellan
- Department of Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
- Center for the Environmental Implications of Nanotechnology (CEINT), Duke University, Durham, North Carolina, USA
| | - Jeanne VanBriesen
- Department of Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
- Center for the Environmental Implications of Nanotechnology (CEINT), Duke University, Durham, North Carolina, USA
| | - Kelvin B. Gregory
- Department of Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
- Center for the Environmental Implications of Nanotechnology (CEINT), Duke University, Durham, North Carolina, USA
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85
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Srikumar A, Krishna PS, Sivaramakrishna D, Kopfmann S, Hess WR, Swamy MJ, Lin-Chao S, Prakash JSS. The Ssl2245-Sll1130 Toxin-Antitoxin System Mediates Heat-induced Programmed Cell Death in Synechocystis sp. PCC6803. J Biol Chem 2017; 292:4222-4234. [PMID: 28104802 DOI: 10.1074/jbc.m116.748178] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 01/17/2017] [Indexed: 12/13/2022] Open
Abstract
Two putative heat-responsive genes, ssl2245 and sll1130, constitute an operon that also has characteristics of a toxin-antitoxin system, thus joining several enigmatic features. Closely related orthologs of Ssl2245 and Sll1130 exist in widely different bacteria, which thrive under environments with large fluctuations in temperature and salinity, among which some are thermo-epilithic biofilm-forming cyanobacteria. Transcriptome analyses revealed that the clustered regularly interspaced short palindromic repeats (CRISPR) genes as well as several hypothetical genes were commonly up-regulated in Δssl2245 and Δsll1130 mutants. Genes coding for heat shock proteins and pilins were also induced in Δsll1130 We observed that the majority of cells in a Δsll1130 mutant strain remained unicellular and viable after prolonged incubation at high temperature (50 °C). In contrast, the wild type formed large cell clumps of dead and live cells, indicating the attempt to form biofilms under harsh conditions. Furthermore, we observed that Sll1130 is a heat-stable ribonuclease whose activity was inhibited by Ssl2245 at optimal temperatures but not at high temperatures. In addition, we demonstrated that Ssl2245 is physically associated with Sll1130 by electrostatic interactions, thereby inhibiting its activity at optimal growth temperature. This association is lost upon exposure to heat, leaving Sll1130 to exhibit its ribonuclease activity. Thus, the activation of Sll1130 leads to the degradation of cellular RNA and thereby heat-induced programmed cell death that in turn supports the formation of a more resistant biofilm for the surviving cells. We suggest to designate Ssl2245 and Sll1130 as MazE and MazF, respectively.
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Affiliation(s)
- Afshan Srikumar
- From the Department of Biotechnology and Bioinformatics, School of Life Sciences and
| | - Pilla Sankara Krishna
- From the Department of Biotechnology and Bioinformatics, School of Life Sciences and
| | | | - Stefan Kopfmann
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany, and
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany, and
| | - Musti J Swamy
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Sue Lin-Chao
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Jogadhenu S S Prakash
- From the Department of Biotechnology and Bioinformatics, School of Life Sciences and
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86
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Valadbeigi H, Sadeghifard N, Salehi MB. Assessment of biofilm formation in Pseudomonas aeruginosa by antisense mazE-PNA. Microb Pathog 2017; 104:28-31. [PMID: 28062294 DOI: 10.1016/j.micpath.2017.01.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Revised: 12/28/2016] [Accepted: 01/02/2017] [Indexed: 01/22/2023]
Abstract
The hallmark patogenicity in Pseudomonas aeruginosa (P. aeruginosa) is biofilm formation that is not easy to eradicate, because it has variety mechanisms for antibiotic resistance. In addition, toxin-antitoxin (TA) system may play role in biofilm formation. The current study aimed to evaluate the role of TA loci in biofilm formation. Therefore, 18 P. aeruginosa clinical isolates were collected and evaluated for specific biofilm and TA genes. The analysis by RT-qPCR demonstrated that expression of mazE antitoxin in biofilm formation was increase. On the other hand, mazE antitoxin TA system was used as target for antisense PNA. mazE-PNA was able to influence in biofilm formation and was inhibit at 5,10 and 15 μM concentrations biofilm formation in P. aeruginosa. Therefore, it could be highlighted target for anti-biofilm target to eradicate P. aeruginosa biofilm producer.
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Affiliation(s)
- Hassan Valadbeigi
- Department of Microbiology, Science and Research Branch, Islamic Azad University, Fars, Iran; Department of Microbiology, Shiraz Branch, Islamic Azad University, Shiraz, Iran.
| | - Nourkhoda Sadeghifard
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran.
| | - Majid Baseri Salehi
- Department of Microbiology, Kazeroun Branch, Islamic Azad University, Kazeroun, Iran.
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87
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Jaiswal S, Paul P, Padhi C, Ray S, Ryan D, Dash S, Suar M. The Hha-TomB Toxin-Antitoxin System Shows Conditional Toxicity and Promotes Persister Cell Formation by Inhibiting Apoptosis-Like Death in S. Typhimurium. Sci Rep 2016; 6:38204. [PMID: 27910884 PMCID: PMC5133643 DOI: 10.1038/srep38204] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 06/03/2016] [Indexed: 11/09/2022] Open
Abstract
Toxin-antitoxin (TA) modules are two component “addictive” genetic elements found on either plasmid or bacterial chromosome, sometimes on both. TA systems perform a wide range of functions like biofilm formation, persistence, programmed cell death, phage abortive infection etc. Salmonella has been reported to contain several such TA systems. However, the hemolysin expression modulating protein (Hha) and its adjacent uncharacterized hypothetical protein TomB (previously known as YbaJ), have not been listed as a TA module in Salmonella. In this study we established that Hha and TomB form a bonafide TA system where Hha serves as a toxin while TomB functions as an antitoxin. Interestingly, the toxicity of Hha was conditional causing cell death under acid stress. The antitoxin attenuated the toxicity of Hha by forming a TA complex through stable interactions. The Hha-TomB TA system was found to increase persistence and inhibit programmed cell death under antibiotic stress where a phenotypically diverse population expressing differential level of TA components was observed. Therefore we propose that Hha and TomB prevent cells from committing suicide thereby promoting persister cell formation.
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Affiliation(s)
- Sangeeta Jaiswal
- School of Biotechnology, KIIT University, Bhubaneswar-751024, Odisha, India
| | - Prajita Paul
- School of Biotechnology, KIIT University, Bhubaneswar-751024, Odisha, India
| | | | - Shilpa Ray
- School of Biotechnology, KIIT University, Bhubaneswar-751024, Odisha, India
| | - Daniel Ryan
- School of Biotechnology, KIIT University, Bhubaneswar-751024, Odisha, India
| | - Shantoshini Dash
- School of Biotechnology, KIIT University, Bhubaneswar-751024, Odisha, India
| | - Mrutyunjay Suar
- School of Biotechnology, KIIT University, Bhubaneswar-751024, Odisha, India
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88
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The Role of Deoxycytidine Kinase (dCK) in Radiation-Induced Cell Death. Int J Mol Sci 2016; 17:ijms17111939. [PMID: 27879648 PMCID: PMC5133934 DOI: 10.3390/ijms17111939] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/12/2016] [Accepted: 11/14/2016] [Indexed: 12/26/2022] Open
Abstract
Deoxycytidine kinase (dCK) is a key enzyme in deoxyribonucleoside salvage and the anti-tumor activity for many nucleoside analogs. dCK is activated in response to ionizing radiation (IR)-induced DNA damage and it is phosphorylated on Serine 74 by the Ataxia-Telangiectasia Mutated (ATM) kinase in order to activate the cell cycle G2/M checkpoint. However, whether dCK plays a role in radiation-induced cell death is less clear. In this study, we genetically modified dCK expression by knocking down or expressing a WT (wild-type), S74A (abrogates phosphorylation) and S74E (mimics phosphorylation) of dCK. We found that dCK could decrease IR-induced total cell death and apoptosis. Moreover, dCK increased IR-induced autophagy and dCK-S74 is required for it. Western blotting showed that the ratio of phospho-Akt/Akt, phospho-mTOR/mTOR, phospho-P70S6K/P70S6K significantly decreased in dCK-WT and dCK-S74E cells than that in dCK-S74A cells following IR treatment. Reciprocal experiment by co-immunoprecipitation showed that mTOR can interact with wild-type dCK. IR increased polyploidy and decreased G2/M arrest in dCK knock-down cells as compared with control cells. Taken together, phosphorylated and activated dCK can inhibit IR-induced cell death including apoptosis and mitotic catastrophe, and promote IR-induced autophagy through PI3K/Akt/mTOR pathway.
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89
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Oron-Gottesman A, Sauert M, Moll I, Engelberg-Kulka H. A Stress-Induced Bias in the Reading of the Genetic Code in Escherichia coli. mBio 2016; 7:e01855-16. [PMID: 27935840 PMCID: PMC5111409 DOI: 10.1128/mbio.01855-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 10/20/2016] [Indexed: 01/30/2023] Open
Abstract
Escherichia coli mazEF is an extensively studied stress-induced toxin-antitoxin (TA) system. The toxin MazF is an endoribonuclease that cleaves RNAs at ACA sites. Thereby, under stress, the induced MazF generates a stress-induced translation machinery (STM), composed of MazF-processed mRNAs and selective ribosomes that specifically translate the processed mRNAs. Here, we further characterized the STM system, finding that MazF cleaves only ACA sites located in the open reading frames of processed mRNAs, while out-of-frame ACAs are resistant. This in-frame ACA cleavage of MazF seems to depend on MazF binding to an extracellular-death-factor (EDF)-like element in ribosomal protein bS1 (bacterial S1), apparently causing MazF to be part of STM ribosomes. Furthermore, due to the in-frame MazF cleavage of ACAs under stress, a bias occurs in the reading of the genetic code causing the amino acid threonine to be encoded only by its synonym codon ACC, ACU, or ACG, instead of by ACA. IMPORTANCE The genetic code is a universal characteristic of all living organisms. It defines the set of rules by which nucleotide triplets specify which amino acid will be incorporated into a protein. Our results represent the first existing report on a stress-induced bias in the reading of the genetic code. We found that in E. coli, under stress, the amino acid threonine is encoded only by its synonym codon ACC, ACU, or ACG, instead of by ACA. This is because under stress, MazF generates a stress-induced translation machinery (STM) in which MazF cleaves in-frame ACA sites of the processed mRNAs.
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Affiliation(s)
- Adi Oron-Gottesman
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Martina Sauert
- Department of Microbiology, Max F. Perutz Laboratories, Center for Molecular Biology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Isabella Moll
- Department of Microbiology, Max F. Perutz Laboratories, Center for Molecular Biology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Hanna Engelberg-Kulka
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
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90
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Bloom-Ackermann Z, Steinberg N, Rosenberg G, Oppenheimer-Shaanan Y, Pollack D, Ely S, Storzi N, Levy A, Kolodkin-Gal I. Toxin-Antitoxin systems eliminate defective cells and preserve symmetry in Bacillus subtilis biofilms. Environ Microbiol 2016; 18:5032-5047. [PMID: 27450630 DOI: 10.1111/1462-2920.13471] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/07/2016] [Accepted: 07/20/2016] [Indexed: 01/02/2023]
Abstract
Toxin-antitoxin modules are gene pairs encoding a toxin and its antitoxin, and are found on the chromosomes of many bacteria, including pathogens. Here, we characterize the specific contribution of the TxpA and YqcG toxins in elimination of defective cells from developing Bacillus subtilis biofilms. On nutrient limitation, defective cells accumulated in the biofilm breaking its symmetry. Deletion of the toxins resulted in accumulation of morphologically abnormal cells, and interfered with the proper development of the multicellular community. Dual physiological responses are of significance for TxpA and YqcG activation: nitrogen deprivation enhances the transcription of both TxpA and YqcG toxins, and simultaneously sensitizes the biofilm cells to their activity. Furthermore, we demonstrate that while both toxins when overexpressed affect the morphology of the developing biofilm, the toxin TxpA can act to lyse and dissolve pre-established B. subtilis biofilms.
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Affiliation(s)
- Zohar Bloom-Ackermann
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Nitai Steinberg
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Gili Rosenberg
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | | | - Dan Pollack
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Shir Ely
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Nimrod Storzi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Asaf Levy
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
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91
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Identification and characterization of chromosomal relBE toxin-antitoxin locus in Streptomyces cattleya DSM46488. Sci Rep 2016; 6:32047. [PMID: 27534445 PMCID: PMC4989188 DOI: 10.1038/srep32047] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/01/2016] [Indexed: 01/25/2023] Open
Abstract
The relBE family of Type II toxin-antitoxin (TA) systems have been widely reported in bacteria but none in Streptomyces. With the conserved domain searches for TA pairs in the sequenced Streptomyces genomes, we identified two putative relBE loci, relBE1sca and relBE2sca, on the chromosome of Streptomyces cattleya DSM 46488. Overexpression of the S. cattleya toxin RelE2sca caused severe growth inhibition of E. coli and S. lividans, but RelE1sca had no toxic effect. The toxicity of RelE2sca could be abolished by the co-expression of its cognate RelB2sca antitoxin. Moreover, the RelBE2sca complex, or the antitoxin RelB2sca alone, specifically interacted with the relBE2sca operon and repressed its transcription. The relBE2sca operon transcription was induced under osmotic stress, along with the ClpP proteinase genes. The subsequent in vivo analysis showed that the antitoxin was degraded by ClpP. Interestingly, the E. coli antitoxin RelBeco was able to alleviate the toxicity of S. cattleya RelE2sca while the mutant RelB2sca(N61V&M68L) but not the wild type could alleviate the toxicity of E. coli RelEeco as well. The experimental demonstration of the relBEsca locus might be helpful to investigate the key roles of type II TA systems in Streptomyces physiology and environmental stress responses.
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92
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Zhou H, Liu H, Weir MD, Reynolds MA, Zhang K, Xu HHK. Three-dimensional biofilm properties on dental bonding agent with varying quaternary ammonium charge densities. J Dent 2016; 53:73-81. [PMID: 27472954 DOI: 10.1016/j.jdent.2016.07.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/19/2016] [Accepted: 07/26/2016] [Indexed: 10/21/2022] Open
Abstract
OBJECTIVES Tooth-restoration interfaces are the weak link with secondary caries causing restoration failure. The objectives of this study were to develop an antimicrobial bonding agent with dimethylaminododecyl methacrylate (DMAHDM), and investigate the effects of quaternary amine charge density on three-dimensional (3D) biofilms on dental resin for the first time. METHODS DMAHDM was synthesized and incorporated into Scotchbond Multi-Purpose bonding agent at mass fractions of 0% (control), 2.5%, 5%, 7.5% and 10%. Streptococcus mutans bacteria were inoculated on the polymerized resin and cultured for two days to form biofilms. Confocal laser scanning microscopy was used to measure biofilm thickness, live and dead biofilm volumes, and live bacteria percentage in 3D biofilm vs. distance from resin surface. RESULTS Charge density of the resin had a significant effect on the antibacterial efficacy (p<0.05). Biofilms on control resin had the greatest thicknesses. Biofilm thickness and live biofilm volume decreased with increasing surface charge density (p<0.05). There were significant variations in bacterial viability along the 3D biofilm thickness (p<0.05). At 2.5% and 5% DMAHDM, the bacterial inhibition was the greatest on or near the resin surface, and the killing effect decreased away from the resin surface. At 10% DMAHDM, the entire 3D biofilm was dead and the percentage of live bacteria was nearly 0% throughout the biofilm thickness. CONCLUSIONS Adding new antibacterial monomer DMAHDM into dental bonding agent yielded a strong antimicrobial activity, substantially decreasing the 3D biofilm thickness, live biofilm volume, and percentage of live bacteria on cross-sections through the biofilm thickness. SIGNIFICANCE Novel DMAHDM-containing bonding agent with capability of inhibiting 3D biofilms is promising for a wide range of dental restorative and preventive applications to inhibit biofilms at the tooth-restoration margins and prevent secondary caries.
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Affiliation(s)
- Han Zhou
- Department of Endodontics, Periodontics and Prosthodontics, University of Maryland School of Dentistry, Baltimore, MD 21201, USA; State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, China
| | - Huaibing Liu
- Restorative Business Unit, Dentsply Sirona, Milford, DE 19963, USA
| | - Michael D Weir
- Department of Endodontics, Periodontics and Prosthodontics, University of Maryland School of Dentistry, Baltimore, MD 21201, USA
| | - Mark A Reynolds
- Department of Endodontics, Periodontics and Prosthodontics, University of Maryland School of Dentistry, Baltimore, MD 21201, USA
| | - Ke Zhang
- Department of Endodontics, Periodontics and Prosthodontics, University of Maryland School of Dentistry, Baltimore, MD 21201, USA; Department of Orthodontics, School of Stomatology, Capital Medical University, Beijing, China.
| | - Hockin H K Xu
- Department of Endodontics, Periodontics and Prosthodontics, University of Maryland School of Dentistry, Baltimore, MD 21201, USA; Center for Stem Cell Biology & Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Department of Mechanical Engineering, University of Maryland, Baltimore County, MD 21250, USA.
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93
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Toxin-Antitoxin Modules Are Pliable Switches Activated by Multiple Protease Pathways. Toxins (Basel) 2016; 8:toxins8070214. [PMID: 27409636 PMCID: PMC4963847 DOI: 10.3390/toxins8070214] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 06/24/2016] [Accepted: 06/27/2016] [Indexed: 02/06/2023] Open
Abstract
Toxin-antitoxin (TA) modules are bacterial regulatory switches that facilitate conflicting outcomes for cells by promoting a pro-survival phenotypic adaptation and/or by directly mediating cell death, all through the toxin activity upon degradation of antitoxin. Intensive study has revealed specific details of TA module functions, but significant gaps remain about the molecular details of activation via antitoxin degradation used by different bacteria and in different environments. This review summarizes the current state of knowledge about the interaction of antitoxins with cellular proteases Lon and ClpP to mediate TA module activation. An understanding of these processes can answer long-standing questions regarding stochastic versus specific activation of TA modules and provide insight into the potential for manipulation of TA modules to alter bacterial growth.
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94
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Asplund-Samuelsson J, Sundh J, Dupont CL, Allen AE, McCrow JP, Celepli NA, Bergman B, Ininbergs K, Ekman M. Diversity and Expression of Bacterial Metacaspases in an Aquatic Ecosystem. Front Microbiol 2016; 7:1043. [PMID: 27458440 PMCID: PMC4933709 DOI: 10.3389/fmicb.2016.01043] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/22/2016] [Indexed: 11/13/2022] Open
Abstract
Metacaspases are distant homologs of metazoan caspase proteases, implicated in stress response, and programmed cell death (PCD) in bacteria and phytoplankton. While the few previous studies on metacaspases have relied on cultured organisms and sequenced genomes, no studies have focused on metacaspases in a natural setting. We here present data from the first microbial community-wide metacaspase survey; performed by querying metagenomic and metatranscriptomic datasets from the brackish Baltic Sea, a water body characterized by pronounced environmental gradients and periods of massive cyanobacterial blooms. Metacaspase genes were restricted to ~4% of the bacteria, taxonomically affiliated mainly to Bacteroidetes, Alpha- and Betaproteobacteria and Cyanobacteria. The gene abundance was significantly higher in larger or particle-associated bacteria (>0.8 μm), and filamentous Cyanobacteria dominated metacaspase gene expression throughout the bloom season. Distinct seasonal expression patterns were detected for the three metacaspase genes in Nodularia spumigena, one of the main bloom-formers. Clustering of normalized gene expression in combination with analyses of genomic and assembly data suggest functional diversification of these genes, and possible roles of the metacaspase genes related to stress responses, i.e., sulfur metabolism in connection to oxidative stress, and nutrient stress induced cellular differentiation. Co-expression of genes encoding metacaspases and nodularin toxin synthesis enzymes was also observed in Nodularia spumigena. The study shows that metacaspases represent an adaptation of potentially high importance for several key organisms in the Baltic Sea, most prominently Cyanobacteria, and open up for further exploration of their physiological roles in microbes and assessment of their ecological impact in aquatic habitats.
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Affiliation(s)
- Johannes Asplund-Samuelsson
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
| | - John Sundh
- Science for Life Laboratory, Department of Biology and Environmental Science, Linnaeus UniversitySolna, Sweden
| | - Chris L. Dupont
- Microbial and Environmental Genomics, J. Craig Venter InstituteSan Diego, CA, USA
| | - Andrew E. Allen
- Microbial and Environmental Genomics, J. Craig Venter InstituteSan Diego, CA, USA
| | - John P. McCrow
- Microbial and Environmental Genomics, J. Craig Venter InstituteSan Diego, CA, USA
| | - Narin A. Celepli
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
| | - Birgitta Bergman
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
| | - Karolina Ininbergs
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
| | - Martin Ekman
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
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95
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Durand P, Sym S, Michod R. Programmed Cell Death and Complexity in Microbial Systems. Curr Biol 2016; 26:R587-R593. [DOI: 10.1016/j.cub.2016.05.057] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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96
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Nagy G, Pinczes G, Pinter G, Pocsi I, Prokisch J, Banfalvi G. In Situ Electron Microscopy of Lactomicroselenium Particles in Probiotic Bacteria. Int J Mol Sci 2016; 17:E1047. [PMID: 27376279 PMCID: PMC4964423 DOI: 10.3390/ijms17071047] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/22/2016] [Accepted: 06/27/2016] [Indexed: 11/16/2022] Open
Abstract
Electron microscopy was used to test whether or not (a) in statu nascendi synthesized, and in situ measured, nanoparticle size does not differ significantly from the size of nanoparticles after their purification; and (b) the generation of selenium is detrimental to the bacterial strains that produce them. Elemental nano-sized selenium produced by probiotic latic acid bacteria was used as a lactomicroselenium (lactomicroSel) inhibitor of cell growth in the presence of lactomicroSel, and was followed by time-lapse microscopy. The size of lactomicroSel produced by probiotic bacteria was measured in situ and after isolation and purification. For these measurements the TESLA BS 540 transmission electron microscope was converted from analog (aTEM) to digital processing (dTEM), and further to remote-access internet electron microscopy (iTEM). Lactobacillus acidophilus produced fewer, but larger, lactomicroSel nanoparticles (200-350 nm) than Lactobacillus casei (L. casei), which generated many, smaller lactomicroSel particles (85-200 nm) and grains as a cloudy, less electrodense material. Streptococcus thermophilus cells generated selenoparticles (60-280 nm) in a suicidic manner. The size determined in situ in lactic acid bacteria was significantly lower than those measured by scanning electron microscopy after the isolation of lactomicroSel particles obtained from lactobacilli (100-500 nm), but higher relative to those isolated from Streptococcus thermopilus (50-100 nm). These differences indicate that smaller lactomicroSel particles could be more toxic to the producing bacteria themselves and discrepancies in size could have implications with respect to the applications of selenium nanoparticles as prebiotics.
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Affiliation(s)
- Gabor Nagy
- Department of Biotechnology and Microbiology, University of Debrecen, Debrecen 4010, Hungary.
| | - Gyula Pinczes
- Department of Biotechnology and Microbiology, University of Debrecen, Debrecen 4010, Hungary.
| | - Gabor Pinter
- Department of Biotechnology and Microbiology, University of Debrecen, Debrecen 4010, Hungary.
| | - Istvan Pocsi
- Department of Biotechnology and Microbiology, University of Debrecen, Debrecen 4010, Hungary.
| | - Jozsef Prokisch
- Department of Animal Breeding, University of Debrecen, Debrecen 4010, Hungary.
| | - Gaspar Banfalvi
- Department of Biotechnology and Microbiology, University of Debrecen, Debrecen 4010, Hungary.
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97
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Evolution of the SpoIISABC Toxin-Antitoxin-Antitoxin System in Bacilli. Toxins (Basel) 2016; 8:toxins8060180. [PMID: 27294956 PMCID: PMC4926146 DOI: 10.3390/toxins8060180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 06/01/2016] [Accepted: 06/02/2016] [Indexed: 11/23/2022] Open
Abstract
Programmed cell death in bacteria is generally associated with two-component toxin-antitoxin systems. The SpoIISABC system, originally identified in Bacillus subtilis, consists of three components: a SpoIISA toxin and the SpoIISB and SpoIISC antitoxins. SpoIISA is a membrane-bound protein, while SpoIISB and SpoIISC are small cytosolic antitoxins, which are able to bind SpoIISA and neutralize its toxicity. In the presented bioinformatics analysis, a taxonomic distribution of the genes of the SpoIISABC system is investigated; their conserved regions and residues are identified; and their phylogenetic relationships are inferred. The SpoIISABC system is part of the core genome in members of the Bacillus genus of the Firmicutes phylum. Its presence in some non-bacillus species is likely the result of horizontal gene transfer. The SpoIISB and SpoIISC antitoxins originated by gene duplications, which occurred independently in the B. subtilis and B. cereus lineages. In the B. cereus lineage, the SpoIIS module is present in two different architectures.
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98
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Desperate times call for desperate measures: benefits and costs of toxin-antitoxin systems. Curr Genet 2016; 63:69-74. [PMID: 27276988 DOI: 10.1007/s00294-016-0622-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 06/03/2016] [Accepted: 06/04/2016] [Indexed: 10/21/2022]
Abstract
Toxin-antitoxin (TA) loci were first described as killing systems for plasmid maintenance. The surprisingly abundant presence of TA loci in bacterial chromosomes has stimulated an extensive research in the recent decade aimed to understand the biological importance of these potentially deadly systems. Accumulating evidence suggests that the evolutionary success of genomic TA systems could be explained by their ability to increase bacterial fitness under stress conditions. While TA systems remain quiescent under favorable growth conditions, the toxins can be activated in response to stress resulting in growth suppression and development of stress-tolerant dormant state. Yet, several studies suggest that the TA-mediated stress protection is costly and traded off against decreased fitness under normal growth conditions. Here, we give an overview of the fitness benefits of the chromosomal TA systems, and discuss the costs of TA-mediated stress protection.
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99
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Ramisetty BCM, Raj S, Ghosh D. Escherichia coli MazEF toxin-antitoxin system does not mediate programmed cell death. J Basic Microbiol 2016; 56:1398-1402. [PMID: 27259116 DOI: 10.1002/jobm.201600247] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/20/2016] [Indexed: 11/06/2022]
Abstract
Toxin-antitoxins systems (TAS) are prokaryotic operons containing two small overlapping genes which encode two components referred to as toxin and antitoxin. Involvement of TAS in bacterial programmed cell death (PCD) is highly controversial. MazEF, a typical type II TAS, is particularly implicated in mediating PCD in Escherichia coli. Hence, we compared the metabolic fitness and stress tolerance of E. coli strains (MC4100 and its mazEF-derivative) which were extensively used by proponents of mazEF-mediated PCD. We found that both the strains are deficient in relA gene and that the ΔmazEF strain has lower fitness and stress tolerance compared to wild type MC4100. We could not reproduce mazEF mediated PCD which emphasizes the need for skeptic approach to the PCD hypothesis.
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Affiliation(s)
| | - Swati Raj
- School of Chemical and Biotechnology, SASTRA University, Thirumalaisamudram, Thanjavur, India
| | - Dimpy Ghosh
- School of Chemical and Biotechnology, SASTRA University, Thirumalaisamudram, Thanjavur, India
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100
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Cao Y, Cheng F, Yao W, Bao B, Zhang K, Zhang L, Ding A. Toxicity of Pekinenin C from Euphorbia Pekinensis Radix on Rat Small Intestinal Crypt Epithelial Cell and Its Apoptotic Mechanism. Int J Mol Sci 2016; 17:E850. [PMID: 27271594 PMCID: PMC4926384 DOI: 10.3390/ijms17060850] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 05/16/2016] [Accepted: 05/17/2016] [Indexed: 01/10/2023] Open
Abstract
Pekinenin C is a casbane diterpenoid separated from the root of the traditional Chinese medicine, Euphorbia pekinensis Rupr., which is used as drug for the treatment of edema, ascites, and hydrothorax. Whereas pekinenin C exhibits severe cytotoxicity, the exact toxicity mechanism is unclear. In this study, the effects of pekinenin C on cell inhibition, cell cycle, and cell apoptosis were examined to explain its toxic mechanism. The proliferation of IEC-6 cells was accessed via MTT colorimetric assay after incubated with different concentrations of pekinenin C. Pekinenin C-treated IEC-6 cells labeled with RNase/PI and Annexin V/PI were analyzed by flow cytometric analyses for evaluation of cell cycle distribution and cell apoptosis, respectively. The apoptosis mechanism of pekinenin C on IEC-6 was investigated through assaying the activities of caspase-3, 8, 9 by enzyme-linked immunosorbent assay (ELISA), protein expression of Bax, Bcl-2, apoptosis-inducing factor (AIF), Apaf-1, Fas-associated death domain (FADD) and type 1-associated death domain (TRADD) by Western-blot, mRNA expression of Fas receptor (FasR), Fas ligand (FasL), tumor necrosis factor receptor (TNFR1) and NF-κB by RT-PCR. The results showed that pekinenin C has exhibited obvious IEC-6 cells toxicity and the IC50 value was 2.1 μg·mL(-1). Typical apoptosis characteristics were observed under a transmission electron microscopy, and it was found that pekinenin C could cause G0/G1 phase arrest in IEC-6 cells in a dose-dependent manner and induce apoptosis of IEC-6 cells. Additionally, pekinenin C could increase the expressions of Bax, AIF, Apaf-1, FasR, FasL, TNFR1 and NF-κB, suppress the expression of Bcl-2, FADD and TRADD, then activate caspase-3, 8, 9 cascades, and at last result in apoptosis. These results demonstrated that pekinenin C effectively promoted cell apoptosis, and induced IEC-6 cells apoptosis through both the mitochondrial and death receptor pathways.
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Affiliation(s)
- Yudan Cao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Fangfang Cheng
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Weifeng Yao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Beihua Bao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Kaicheng Zhang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Li Zhang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Anwei Ding
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
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