151
|
Magainin 2 Induces Bacterial Cell Death Showing Apoptotic Properties. Curr Microbiol 2014; 69:794-801. [DOI: 10.1007/s00284-014-0657-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 05/24/2014] [Indexed: 10/25/2022]
|
152
|
Santosh Kumar B, Raghavendra Guru Prasad A, Madhu G, Raveendra Reddy P, Ravindranath L. Synthesis and in silico studies of pyrrolidine sulfonamide based dipeptides as β-gluscosidase inhibitors. ANNALES PHARMACEUTIQUES FRANÇAISES 2014; 72:256-66. [DOI: 10.1016/j.pharma.2014.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Revised: 02/11/2014] [Accepted: 02/17/2014] [Indexed: 01/14/2023]
|
153
|
Cohen A, Sendersky E, Carmeli S, Schwarz R. Collapsing aged culture of the cyanobacterium Synechococcus elongatus produces compound(s) toxic to photosynthetic organisms. PLoS One 2014; 9:e100747. [PMID: 24959874 PMCID: PMC4069110 DOI: 10.1371/journal.pone.0100747] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 05/30/2014] [Indexed: 12/22/2022] Open
Abstract
Phytoplankton mortality allows effective nutrient cycling, and thus plays a pivotal role in driving biogeochemical cycles. A growing body of literature demonstrates the involvement of regulated death programs in the abrupt collapse of phytoplankton populations, and particularly implicates processes that exhibit characteristics of metazoan programmed cell death. Here, we report that the cell-free, extracellular fluid (conditioned medium) of a collapsing aged culture of the cyanobacterium Synechococcus elongatus is toxic to exponentially growing cells of this cyanobacterium, as well as to a large variety of photosynthetic organisms, but not to eubacteria. The toxic effect, which is light-dependent, involves oxidative stress, as suggested by damage alleviation by antioxidants, and the very high sensitivity of a catalase-mutant to the conditioned medium. At relatively high cell densities, S. elongatus cells survived the deleterious effect of conditioned medium in a process that required de novo protein synthesis. Application of conditioned medium from a collapsing culture caused severe pigment bleaching not only in S. elongatus cells, but also resulted in bleaching of pigments in a cell free extract. The latter observation indicates that the elicited damage is a direct effect that does not require an intact cell, and therefore, is mechanistically different from the metazoan-like programmed cell death described for phytoplankton. We suggest that S. elongatus in aged cultures are triggered to produce a toxic compound, and thus, this process may be envisaged as a novel regulated death program.
Collapse
Affiliation(s)
- Assaf Cohen
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Eleonora Sendersky
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | | | - Rakefet Schwarz
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| |
Collapse
|
154
|
Abstract
Discoveries in cytogenetics, molecular biology, and genomics have revealed that genome change is an active cell-mediated physiological process. This is distinctly at variance with the pre-DNA assumption that genetic changes arise accidentally and sporadically. The discovery that DNA changes arise as the result of regulated cell biochemistry means that the genome is best modelled as a read-write (RW) data storage system rather than a read-only memory (ROM). The evidence behind this change in thinking and a consideration of some of its implications are the subjects of this article. Specific points include the following: cells protect themselves from accidental genome change with proofreading and DNA damage repair systems; localized point mutations result from the action of specialized trans-lesion mutator DNA polymerases; cells can join broken chromosomes and generate genome rearrangements by non-homologous end-joining (NHEJ) processes in specialized subnuclear repair centres; cells have a broad variety of natural genetic engineering (NGE) functions for transporting, diversifying and reorganizing DNA sequences in ways that generate many classes of genomic novelties; natural genetic engineering functions are regulated and subject to activation by a range of challenging life history events; cells can target the action of natural genetic engineering functions to particular genome locations by a range of well-established molecular interactions, including protein binding with regulatory factors and linkage to transcription; and genome changes in cancer can usefully be considered as consequences of the loss of homeostatic control over natural genetic engineering functions.
Collapse
Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, GCISW123B, 979 E. 57th Street, Chicago, IL 60637, USA
| |
Collapse
|
155
|
Li K, Wu D, Chen X, Zhang T, Zhang L, Yi Y, Miao Z, Jin N, Bi X, Wang H, Xu J, Wang D. Current and emerging biomarkers of cell death in human disease. BIOMED RESEARCH INTERNATIONAL 2014; 2014:690103. [PMID: 24949464 PMCID: PMC4052120 DOI: 10.1155/2014/690103] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 04/17/2014] [Indexed: 01/18/2023]
Abstract
Cell death is a critical biological process, serving many important functions within multicellular organisms. Aberrations in cell death can contribute to the pathology of human diseases. Significant progress made in the research area enormously speeds up our understanding of the biochemical and molecular mechanisms of cell death. According to the distinct morphological and biochemical characteristics, cell death can be triggered by extrinsic or intrinsic apoptosis, regulated necrosis, autophagic cell death, and mitotic catastrophe. Nevertheless, the realization that all of these efforts seek to pursue an effective treatment and cure for the disease has spurred a significant interest in the development of promising biomarkers of cell death to early diagnose disease and accurately predict disease progression and outcome. In this review, we summarize recent knowledge about cell death, survey current and emerging biomarkers of cell death, and discuss the relationship with human diseases.
Collapse
Affiliation(s)
- Kongning Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Deng Wu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xi Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Ting Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Lu Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Ying Yi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Zhengqiang Miao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Nana Jin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xiaoman Bi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Hongwei Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Jianzhen Xu
- College of Bioengineering, Henan University of Technology, Zhengzhou 450001, China
| | - Dong Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| |
Collapse
|
156
|
Yang M, Gao CH, Hu J, Dong C, He ZG. Characterization of the interaction between a SirR family transcriptional factor ofMycobacterium tuberculosis, encoded by Rv2788, and a pair of toxin-antitoxin proteins RelJ/K, encoded by Rv3357 and Rv3358. FEBS J 2014; 281:2726-37. [DOI: 10.1111/febs.12815] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 03/30/2014] [Accepted: 04/09/2014] [Indexed: 01/17/2023]
Affiliation(s)
- Min Yang
- National Key Laboratory of Agricultural Microbiology; Proteomics Research Center; College of Life Science and Technology; Huazhong Agricultural University; Wuhan China
| | - Chun-Hui Gao
- National Key Laboratory of Agricultural Microbiology; Proteomics Research Center; College of Life Science and Technology; Huazhong Agricultural University; Wuhan China
| | - Jialing Hu
- National Key Laboratory of Agricultural Microbiology; Proteomics Research Center; College of Life Science and Technology; Huazhong Agricultural University; Wuhan China
| | - Chao Dong
- National Key Laboratory of Agricultural Microbiology; Proteomics Research Center; College of Life Science and Technology; Huazhong Agricultural University; Wuhan China
| | - Zheng-Guo He
- National Key Laboratory of Agricultural Microbiology; Proteomics Research Center; College of Life Science and Technology; Huazhong Agricultural University; Wuhan China
| |
Collapse
|
157
|
Rakleova G, Pouneva I, Dobrev N, Tchorbadjieva M. Differentially Secreted Proteins of Antarctic and Mesophilic Strains ofSynechocystis SalinaandChlorella Vulgarisafter UV-B and Temperature Stress Treatment. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2013.0002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
158
|
Zhou H, Weir MD, Antonucci JM, Schumacher GE, Zhou XD, Xu HHK. Evaluation of three-dimensional biofilms on antibacterial bonding agents containing novel quaternary ammonium methacrylates. Int J Oral Sci 2014; 6:77-86. [PMID: 24722581 PMCID: PMC4071290 DOI: 10.1038/ijos.2014.18] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2014] [Indexed: 02/05/2023] Open
Abstract
Antibacterial adhesives are promising to inhibit biofilms and secondary caries. The objectives of this study were to synthesize and incorporate quaternary ammonium methacrylates into adhesives, and investigate the alkyl chain length effects on three-dimensional biofilms adherent on adhesives for the first time. Six quaternary ammonium methacrylates with chain lengths of 3, 6, 9, 12, 16 and 18 were synthesized and incorporated into Scotchbond Multi-Purpose. Streptococcus mutans bacteria were cultured on resin to form biofilms. Confocal laser scanning microscopy was used to measure biofilm thickness, live/dead volumes and live-bacteria percentage vs. distance from resin surface. Biofilm thickness was the greatest for Scotchbond control; it decreased with increasing chain length, reaching a minimum at chain length 16. Live-biofilm volume had a similar trend. Dead-biofilm volume increased with increasing chain length. The adhesive with chain length 9 had 37% live bacteria near resin surface, but close to 100% live bacteria in the biofilm top section. For chain length 16, there were nearly 0% live bacteria throughout the three-dimensional biofilm. In conclusion, strong antibacterial activity was achieved by adding quaternary ammonium into adhesive, with biofilm thickness and live-biofilm volume decreasing as chain length was increased from 3 to 16. Antibacterial adhesives typically only inhibited bacteria close to its surface; however, adhesive with chain length 16 had mostly dead bacteria in the entire three-dimensional biofilm. Antibacterial adhesive with chain length 16 is promising to inhibit biofilms at the margins and combat secondary caries.
Collapse
Affiliation(s)
- Han Zhou
- 1] Department of Endodontics, Prosthodontics and Operative Dentistry, University of Maryland Dental School, Baltimore, USA [2] State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Michael D Weir
- Department of Endodontics, Prosthodontics and Operative Dentistry, University of Maryland Dental School, Baltimore, USA
| | - Joseph M Antonucci
- Biomaterials Group, Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, USA
| | - Gary E Schumacher
- Dr. Anthony Volpe Research Center, American Dental Association Foundation, Gaithersburg, USA
| | - Xue-Dong Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Hockin H K Xu
- 1] Department of Endodontics, Prosthodontics and Operative Dentistry, University of Maryland Dental School, Baltimore, USA [2] Center for Stem Cell Biology & Regenerative Medicine, University of Maryland School of Medicine, Baltimore, USA [3] Department of Mechanical Engineering, University of Maryland, Baltimore County, USA
| |
Collapse
|
159
|
Lehmann JS, Matthias MA, Vinetz JM, Fouts DE. Leptospiral pathogenomics. Pathogens 2014; 3:280-308. [PMID: 25437801 PMCID: PMC4243447 DOI: 10.3390/pathogens3020280] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Revised: 03/22/2014] [Accepted: 03/28/2014] [Indexed: 11/30/2022] Open
Abstract
Leptospirosis, caused by pathogenic spirochetes belonging to the genus Leptospira, is a zoonosis with important impacts on human and animal health worldwide. Research on the mechanisms of Leptospira pathogenesis has been hindered due to slow growth of infectious strains, poor transformability, and a paucity of genetic tools. As a result of second generation sequencing technologies, there has been an acceleration of leptospiral genome sequencing efforts in the past decade, which has enabled a concomitant increase in functional genomics analyses of Leptospira pathogenesis. A pathogenomics approach, by coupling of pan-genomic analysis of multiple isolates with sequencing of experimentally attenuated highly pathogenic Leptospira, has resulted in the functional inference of virulence factors. The global Leptospira Genome Project supported by the U.S. National Institute of Allergy and Infectious Diseases to which key scientific contributions have been made from the international leptospirosis research community has provided a new roadmap for comprehensive studies of Leptospira and leptospirosis well into the future. This review describes functional genomics approaches to apply the data generated by the Leptospira Genome Project towards deepening our knowledge of virulence factors of Leptospira using the emerging discipline of pathogenomics.
Collapse
Affiliation(s)
- Jason S Lehmann
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, CA 92093-0741, USA.
| | - Michael A Matthias
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, CA 92093-0741, USA.
| | - Joseph M Vinetz
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, CA 92093-0741, USA.
| | | |
Collapse
|
160
|
Nigam A, Gupta D, Sharma A. Treatment of infectious disease: beyond antibiotics. Microbiol Res 2014; 169:643-51. [PMID: 24661689 DOI: 10.1016/j.micres.2014.02.009] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 12/09/2013] [Accepted: 02/23/2014] [Indexed: 11/29/2022]
Abstract
Several antibiotics have been discovered following the discovery of penicillin. These antibiotics had been helpful in treatment of infectious diseases considered dread for centuries. The advent of multiple drug resistance in microbes has posed new challenge to researchers. The scientists are now evaluating alternatives for combating infectious diseases. This review focuses on major alternatives to antibiotics on which preliminary work had been carried out. These promising anti-microbial include: phages, bacteriocins, killing factors, antibacterial activities of non-antibiotic drugs and quorum quenching.
Collapse
Affiliation(s)
- Anshul Nigam
- IPLS Building, School of Life Science, Pondicherry University, Puducherry 605014, India.
| | - Divya Gupta
- Department of Biotechnology, Mangalayatan University, Beswan, Aligarh, Uttar Pradesh 202145, India
| | - Ashwani Sharma
- Computer-Chemie-Centrum, Universität Erlangen-Nürnberg, Nägelsbachstr. 25, 91052 Erlangen, Germany
| |
Collapse
|
161
|
Wen Y, Behiels E, Devreese B. Toxin-Antitoxin systems: their role in persistence, biofilm formation, and pathogenicity. Pathog Dis 2014; 70:240-9. [DOI: 10.1111/2049-632x.12145] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 01/15/2014] [Accepted: 01/15/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- Yurong Wen
- Unit for Biological Mass Spectrometry and Proteomics; Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE); Ghent University; Ghent Belgium
| | - Ester Behiels
- Unit for Biological Mass Spectrometry and Proteomics; Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE); Ghent University; Ghent Belgium
| | - Bart Devreese
- Unit for Biological Mass Spectrometry and Proteomics; Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE); Ghent University; Ghent Belgium
| |
Collapse
|
162
|
Bertram R, Schuster CF. Post-transcriptional regulation of gene expression in bacterial pathogens by toxin-antitoxin systems. Front Cell Infect Microbiol 2014; 4:6. [PMID: 24524029 PMCID: PMC3905216 DOI: 10.3389/fcimb.2014.00006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 01/13/2014] [Indexed: 01/27/2023] Open
Abstract
Toxin-antitoxin (TA) systems are small genetic elements ubiquitous in prokaryotic genomes that encode toxic proteins targeting various vital cellular functions. Typically, toxin activity is controlled by adjacently encoded protein or RNA antitoxins and unleashed as a consequence of genetic fluctuations or stressful conditions. Whereas some TA systems interfere with replication or cell wall synthesis, most of them influence transcriptional and post-transcriptional gene regulation. Antitoxin proteins often act as DNA binding transcriptional regulators and many TA toxins exhibit endoribonuclease activity to selectively degrade different RNA species and thus alter gene expression patterns. Some TA RNases cleave tRNA, tmRNAs or rRNAs, whereas most commonly mRNAs either in association with the ribosome or as free transcripts, are targeted. Examples are provided on how TA toxins differentially shape gene expression in bacterial pathogens by creating specialized ribosomes or by altering the transcriptome and how this may be tied in the control of pathogenicity factors.
Collapse
Affiliation(s)
- Ralph Bertram
- Department of Microbial Genetics, Faculty of Science, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen Tübingen, Germany
| | - Christopher F Schuster
- Department of Microbial Genetics, Faculty of Science, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen Tübingen, Germany
| |
Collapse
|
163
|
Cheng HY, Soo VWC, Islam S, McAnulty MJ, Benedik MJ, Wood TK. Toxin GhoT of the GhoT/GhoS toxin/antitoxin system damages the cell membrane to reduce adenosine triphosphate and to reduce growth under stress. Environ Microbiol 2014; 16:1741-54. [PMID: 24373067 DOI: 10.1111/1462-2920.12373] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/04/2013] [Accepted: 12/14/2013] [Indexed: 11/27/2022]
Abstract
Toxin/antitoxin (TA) systems perhaps enable cells to reduce their metabolism to weather environmental challenges although there is little evidence to support this hypothesis. Escherichia coli GhoT/GhoS is a TA system in which toxin GhoT expression is reduced by cleavage of its messenger RNA (mRNA) by antitoxin GhoS, and TA system MqsR/MqsA controls GhoT/GhoS through differential mRNA decay. However, the physiological role of GhoT has not been determined. We show here through transmission electron microscopy, confocal microscopy and fluorescent stains that GhoT reduces metabolism by damaging the membrane and that toxin MqsR (a 5'-GCU-specific endoribonuclease) causes membrane damage in a GhoT-dependent manner. This membrane damage results in reduced cellular levels of ATP and the disruption of proton motive force (PMF). Normally, GhoT is localized to the pole and does not cause cell lysis under physiological conditions. Introduction of an F38R substitution results in loss of GhoT toxicity, ghost cell production and membrane damage while retaining the pole localization. Also, deletion of ghoST or ghoT results in significantly greater initial growth in the presence of antimicrobials. Collectively, these results demonstrate that GhoT reduces metabolism by reducing ATP and PMF and that this reduction in metabolism is important for growth with various antimicrobials.
Collapse
Affiliation(s)
- Hsin-Yao Cheng
- Department of Chemical Engineering, Pennsylvania State University, State College, PA, 16802, USA
| | | | | | | | | | | |
Collapse
|
164
|
Barth T, Bruges G, Meiwes A, Mogk S, Mudogo CN, Duszenko M. Staurosporine-Induced Cell Death in <em>Trypanosoma brucei</em> and the Role of Endonuclease G during Apoptosis. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/ojapo.2014.32003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
165
|
Abstract
Although the concept of programmed cell death (PCD) in bacteria has been met with scepticism, a growing body of evidence suggests that it can no longer be ignored. Several recent studies indicate that the phenotypic manifestations of apoptosis, which are processes that are associated with ordered cellular disassembly in eukaryotes, are conserved in bacteria. In this Opinion article, I propose a model for the coordinated control of potential bacterial PCD effectors and argue that the processes involved are functionally analogous to eukaryotic PCD systems.
Collapse
Affiliation(s)
- Kenneth W Bayles
- Center for Staphylococcal Research, Department of Pathology & Microbiology, The University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
| |
Collapse
|
166
|
Shih CJ, Chen PY, Liaw CC, Lai YM, Yang YL. Bringing microbial interactions to light using imaging mass spectrometry. Nat Prod Rep 2014; 31:739-55. [DOI: 10.1039/c3np70091g] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
167
|
Chen L, Xu Q, Tu J, Ge Y, Liu J, Liang FT. Increasing RpoS expression causes cell death in Borrelia burgdorferi. PLoS One 2013; 8:e83276. [PMID: 24358270 PMCID: PMC3865164 DOI: 10.1371/journal.pone.0083276] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 11/11/2013] [Indexed: 01/25/2023] Open
Abstract
RpoS, one of the two alternative σ factors in Borrelia burgdorferi, is tightly controlled by multiple regulators and, in turn, determines expression of many critical virulence factors. Here we show that increasing RpoS expression causes cell death. The immediate effect of increasing RpoS expression was to promote bacterial division and as a consequence result in a rapid increase in cell number before causing bacterial death. No DNA fragmentation or degradation was observed during this induced cell death. Cryo-electron microscopy showed induced cells first formed blebs, which were eventually released from dying cells. Apparently blebbing initiated cell disintegration leading to cell death. These findings led us to hypothesize that increasing RpoS expression triggers intracellular programs and/or pathways that cause spirochete death. The potential biological significance of induced cell death may help B. burgdorferi regulate its population to maintain its life cycle in nature.
Collapse
Affiliation(s)
- Linxu Chen
- Department of Pathobiological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Qilong Xu
- Department of Pathobiological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Jiagang Tu
- Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, Taxes, United States of America
| | - Yihe Ge
- Department of Pathobiological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Jun Liu
- Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, Taxes, United States of America
| | - Fang Ting Liang
- Department of Pathobiological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- * E-mail:
| |
Collapse
|
168
|
Biel FM, Allen FA, Häse CC. Autolysis in Vibrio tubiashii and Vibrio coralliilyticus. Can J Microbiol 2013; 60:57-63. [PMID: 24498982 DOI: 10.1139/cjm-2013-0654] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Vibrio tubiashii has been linked to disease outbreaks in molluscan species, including oysters, geoducks, and clams, and shellfish hatcheries in the Pacific Northwest have been plagued by intermittent vibriosis outbreaks since 2006. Like V. tubiashii, Vibrio coralliilyticus has recently been described as an oyster pathogen in addition to its role in coral disease. Here, we describe an autolysis phenotype in V. tubiashii and its close relative V. coralliilyticus and characterize the effects of environmental conditions on this phenotype. We also explored whether the survivors of autolysis were resistant to the phenotype and if material from the autolysed culture would either regrow or have a population of viable cells. Ultimately, this work contributes to the larger understanding of bacterial population dynamics as it relates to aquaculture pathogens.
Collapse
Affiliation(s)
- Frances M Biel
- a Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, 125 Veterinary Research Laboratory, Corvallis, OR 97331, USA
| | | | | |
Collapse
|
169
|
Toxin-antitoxin genes of the Gram-positive pathogen Streptococcus pneumoniae: so few and yet so many. Microbiol Mol Biol Rev 2013. [PMID: 23204366 DOI: 10.1128/mmbr.00030-12] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Pneumococcal infections cause up to 2 million deaths annually and raise a large economic burden and thus constitute an important threat to mankind. Because of the increase in the antibiotic resistance of Streptococcus pneumoniae clinical isolates, there is an urgent need to find new antimicrobial approaches to triumph over pneumococcal infections. Toxin-antitoxin (TA) systems (TAS), which are present in most living bacteria but not in eukaryotes, have been proposed as an effective strategy to combat bacterial infections. Type II TAS comprise a stable toxin and a labile antitoxin that form an innocuous TA complex under normal conditions. Under stress conditions, TA synthesis will be triggered, resulting in the degradation of the labile antitoxin and the release of the toxin protein, which would poison the host cells. The three functional chromosomal TAS from S. pneumoniae that have been studied as well as their molecular characteristics are discussed in detail in this review. Furthermore, a meticulous bioinformatics search has been performed for 48 pneumococcal genomes that are found in public databases, and more putative TAS, homologous to well-characterized ones, have been revealed. Strikingly, several unusual putative TAS, in terms of components and genetic organizations previously not envisaged, have been discovered and are further discussed. Previously, we reported a novel finding in which a unique pneumococcal DNA signature, the BOX element, affected the regulation of the pneumococcal yefM-yoeB TAS. This BOX element has also been found in some of the other pneumococcal TAS. In this review, we also discuss possible relationships between some of the pneumococcal TAS with pathogenicity, competence, biofilm formation, persistence, and an interesting phenomenon called bistability.
Collapse
|
170
|
Lin SJ, Austriaco N. Aging and cell death in the other yeasts, Schizosaccharomyces pombe and Candida albicans. FEMS Yeast Res 2013; 14:119-35. [PMID: 24205865 DOI: 10.1111/1567-1364.12113] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 09/18/2013] [Accepted: 10/10/2013] [Indexed: 12/22/2022] Open
Abstract
How do cells age and die? For the past 20 years, the budding yeast, Saccharomyces cerevisiae, has been used as a model organism to uncover the genes that regulate lifespan and cell death. More recently, investigators have begun to interrogate the other yeasts, the fission yeast, Schizosaccharomyces pombe, and the human fungal pathogen, Candida albicans, to determine if similar longevity and cell death pathways exist in these organisms. After summarizing the longevity and cell death phenotypes in S. cerevisiae, this mini-review surveys the progress made in the study of both aging and programed cell death (PCD) in the yeast models, with a focus on the biology of S. pombe and C. albicans. Particular emphasis is placed on the similarities and differences between the two types of aging, replicative aging, and chronological aging, and between the three types of cell death, intrinsic apoptosis, autophagic cell death, and regulated necrosis, found in these yeasts. The development of the additional microbial models for aging and PCD in the other yeasts may help further elucidate the mechanisms of longevity and cell death regulation in eukaryotes.
Collapse
Affiliation(s)
- Su-Ju Lin
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA, USA
| | | |
Collapse
|
171
|
Kang SJ, Kim DH, Lee BJ. NMR study on small proteins from Helicobacter pylori for antibiotic target discovery: a review. Molecules 2013; 18:13410-24. [PMID: 24177697 PMCID: PMC6269979 DOI: 10.3390/molecules181113410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 10/24/2013] [Accepted: 10/27/2013] [Indexed: 01/15/2023] Open
Abstract
Due to the widespread and increasing appearance of antibiotic resistance, a new strategy is needed for developing novel antibiotics. Especially, there are no specific antibiotics for Helicobacter pylori (H. pylori). H. pylori are bacteria that live in the stomach and are related to many serious gastric problems such as peptic ulcers, chronic gastritis, mucosa-associated lymphoid tissue lymphoma, and gastric cancer. Because of its importance as a human pathogen, it's worth studying the structure and function of the proteins from H. pylori. After the sequencing of the H. pylori strain 26695 in 1997, more than 1,600 genes were identified from H. pylori. Until now, the structures of 334 proteins from H. pylori have been determined. Among them, 309 structures were determined by X-ray crystallography and 25 structures by Nuclear Magnetic Resonance (NMR), respectively. Overall, the structures of large proteins were determined by X-ray crystallography and those of small proteins by NMR. In our lab, we have studied the structural and functional characteristics of small proteins from H. pylori. In this review, 25 NMR structures of H. pylori proteins will be introduced and their structure-function relationships will be discussed.
Collapse
Affiliation(s)
- Su-Jin Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Korea.
| | | | | |
Collapse
|
172
|
Demidenok OI, Goncharenko AV. Bacterial toxin-antitoxin systems and perspectives for their application in medicine. APPL BIOCHEM MICRO+ 2013. [DOI: 10.1134/s0003683813060070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
173
|
Santiago-Rodriguez TM, Toranzos GA, Bayman P, Massey SE, Cano RJ. Sociomicrobiome of wood decay in a tropical rain forest: unraveling complexity. SPRINGERPLUS 2013; 2:435. [PMID: 24052931 PMCID: PMC3776085 DOI: 10.1186/2193-1801-2-435] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 08/15/2013] [Indexed: 11/25/2022]
Abstract
Given that microbial interactions in nature are very complex, we propose that quorum-sensing, as well as quorum-quenching, phenazine and secondary metabolite production, resistance and toxin-antitoxin systems within a microbial community should all comprise the battery of processes involving the study of what we would define as the “sociomicrobiome”. In the present study the genes/molecules, subsystems and taxonomic breakup of the mentioned processes were identified in decaying tropical wood from the El Yunque rainforest in Puerto Rico, and soil using a shotgun metagenomic approach. The rapid decomposition of wood and litter in tropical regions suggests that processes in these settings are governed by unexplored microbes with the potential of being further studied and exploited for various purposes. Both ecosystems were characterized by the presence of specific genes/molecules, subsystems and microbes associated with the mentioned processes, although the average abundances for specific processes differed. Of the sociomicrobiomes studied, that from El Yunque was found to be the most complex. The approach considered in the present study could also be applied to study the sociomicrobiome of other ecosystems.
Collapse
|
174
|
Mruk I, Kobayashi I. To be or not to be: regulation of restriction-modification systems and other toxin-antitoxin systems. Nucleic Acids Res 2013; 42:70-86. [PMID: 23945938 PMCID: PMC3874152 DOI: 10.1093/nar/gkt711] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
One of the simplest classes of genes involved in programmed death is that containing the toxin–antitoxin (TA) systems of prokaryotes. These systems are composed of an intracellular toxin and an antitoxin that neutralizes its effect. These systems, now classified into five types, were initially discovered because some of them allow the stable maintenance of mobile genetic elements in a microbial population through postsegregational killing or the death of cells that have lost these systems. Here, we demonstrate parallels between some TA systems and restriction–modification systems (RM systems). RM systems are composed of a restriction enzyme (toxin) and a modification enzyme (antitoxin) and limit the genetic flux between lineages with different epigenetic identities, as defined by sequence-specific DNA methylation. The similarities between these systems include their postsegregational killing and their effects on global gene expression. Both require the finely regulated expression of a toxin and antitoxin. The antitoxin (modification enzyme) or linked protein may act as a transcriptional regulator. A regulatory antisense RNA recently identified in an RM system can be compared with those RNAs in TA systems. This review is intended to generalize the concept of TA systems in studies of stress responses, programmed death, genetic conflict and epigenetics.
Collapse
Affiliation(s)
- Iwona Mruk
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, Gdansk, 80-308, Poland, Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan and Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | | |
Collapse
|
175
|
Häcker G. Is there, and should there be, apoptosis in bacteria? Microbes Infect 2013; 15:640-4. [DOI: 10.1016/j.micinf.2013.05.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/22/2013] [Accepted: 05/22/2013] [Indexed: 11/30/2022]
|
176
|
Regulation of toxin–antitoxin systems by proteolysis. Plasmid 2013; 70:33-41. [DOI: 10.1016/j.plasmid.2013.01.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/24/2013] [Accepted: 01/25/2013] [Indexed: 11/19/2022]
|
177
|
Ramisetty BCM, Natarajan B, Santhosh RS. mazEF-mediated programmed cell death in bacteria: "what is this?". Crit Rev Microbiol 2013; 41:89-100. [PMID: 23799870 DOI: 10.3109/1040841x.2013.804030] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Toxin-antitoxin (TA) systems consist of a bicistronic operon, encoding a toxin and an antitoxin. They are widely distributed in the prokaryotic kingdom, often in multiple numbers. TAs are implicated in contradicting phenomena of persistence and programmed cell death (PCD) in bacteria. mazEF TA system, one of the widely distributed type II toxin-antitoxin systems, is particularly implicated in PCD of Escherichia coli. Nutrient starvation, antibiotic stress, heat shock, DNA damage and other kinds of stresses are shown to elicit mazEF-mediated-PCD. ppGpp and extracellular death factor play a central role in regulating mazEF-mediated PCD. The activation of mazEF system is achieved through inhibition of transcription or translation of mazEF loci. Upon activation, MazF cleaves RNA in a ribosome-independent fashion and subsequent processes result in cell death. It is hypothesized that PCD aids in perseverance of the population during stress; the surviving minority of the cells can scavenge the nutrients released by the dead cells, a kind of "nutritional-altruism." Issues regarding the strains, reproducibility of experimental results and ecological plausibility necessitate speculation. We review the molecular mechanisms of the activation of mazEF TA system, the consequences leading to cell death and the pros and cons of the altruism hypothesis from an ecological perspective.
Collapse
|
178
|
Ikeda M, Shinozaki Y, Uchida K, Ohshika Y, Furukohri A, Maki H, Akiyama MT. Quick replication fork stop by overproduction of Escherichia coli DinB produces non-proliferative cells with an aberrant chromosome. Genes Genet Syst 2013; 87:221-31. [PMID: 23229309 DOI: 10.1266/ggs.87.221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Escherichia coli dinB encodes the translesion DNA polymerase DinB, which can inhibit progression of replication forks in a dose-dependent manner, independent of exogenous DNA damage. We reported previously that overproduction of DinB from a multicopy dinB plasmid immediately abolished ongoing replication fork progression, and the cells rapidly and drastically lost colony-forming ability, although the mechanisms underlying this lethality by severe replication fork stress remained unclear. Here, we show that the reduced colony-forming ability in the dinB-overexpressing cells is independent of the specific toxin genes that trigger programmed bacterial cell death when replication is blocked by depletion of the dNTP pool. After DinB abolished replication fork progression and colony-forming ability, most of the cells were still viable, as judged by fluorescent dye staining, but contained irregularly shaped nucleoids in which chromosomal DNA was preferentially lost in the replication terminus region relative to the replication origin region. Flow cytometric analysis of the cells revealed chromosomal damage and the eventual appearance of cell populations with less than single-chromosome DNA content, reminiscent of sub-G1 cells with lethal DNA content produced during eukaryotic apoptosis. This reduced DNA content was not observed after replication fork progression was quickly stopped in temperature-sensitive dnaB helicase mutant cells at a non-permissive temperature. Thus, the quick replication stop provoked by excess DinB uniquely generates temporarily viable but non-reproductive cells possessing a fatally depleted chromosomal content, which may represent one of the possible fates of an E. coli cell whose replication is overwhelmingly compromised.
Collapse
Affiliation(s)
- Mio Ikeda
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama,Ikoma, Nara 630-0192, Japan
| | | | | | | | | | | | | |
Collapse
|
179
|
Zheng W, Rasmussen U, Zheng S, Bao X, Chen B, Gao Y, Guan X, Larsson J, Bergman B. Multiple Modes of Cell Death Discovered in a Prokaryotic (Cyanobacterial) Endosymbiont. PLoS One 2013; 8:e66147. [PMID: 23822984 PMCID: PMC3688857 DOI: 10.1371/journal.pone.0066147] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 05/02/2013] [Indexed: 02/01/2023] Open
Abstract
Programmed cell death (PCD) is a genetically-based cell death mechanism with vital roles in eukaryotes. Although there is limited consensus on similar death mode programs in prokaryotes, emerging evidence suggest that PCD events are operative. Here we present cell death events in a cyanobacterium living endophytically in the fern Azolla microphylla, suggestive of PCD. This symbiosis is characterized by some unique traits such as a synchronized development, a vertical transfer of the cyanobacterium between plant generations, and a highly eroding cyanobacterial genome. A combination of methods was used to identify cell death modes in the cyanobacterium. Light- and electron microscopy analyses showed that the proportion of cells undergoing cell death peaked at 53.6% (average 20%) of the total cell population, depending on the cell type and host developmental stage. Biochemical markers used for early and late programmed cell death events related to apoptosis (Annexin V-EGFP and TUNEL staining assays), together with visualization of cytoskeleton alterations (FITC-phalloidin staining), showed that all cyanobacterial cell categories were affected by cell death. Transmission electron microscopy revealed four modes of cell death: apoptotic-like, autophagic-like, necrotic-like and autolytic-like. Abiotic stresses further enhanced cell death in a dose and time dependent manner. The data also suggest that dynamic changes in the peptidoglycan cell wall layer and in the cytoskeleton distribution patterns may act as markers for the various cell death modes. The presence of a metacaspase homolog (domain p20) further suggests that the death modes are genetically programmed. It is therefore concluded that multiple, likely genetically programmed, cell death modes exist in cyanobacteria, a finding that may be connected with the evolution of cell death in the plant kingdom.
Collapse
Affiliation(s)
- Weiwen Zheng
- Key Laboratory of Bio-Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Biotech Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Ulla Rasmussen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Siping Zheng
- Biotech Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Xiaodong Bao
- Department of Plant Pathology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Bin Chen
- Biotech Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Yuan Gao
- Key Laboratory of Bio-Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiong Guan
- Key Laboratory of Bio-Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - John Larsson
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Birgitta Bergman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- * E-mail:
| |
Collapse
|
180
|
Abstract
Escherichia coli mazEF is a toxin-antitoxin stress-induced module mediating cell death. It requires the quorum-sensing signal (QS) “extracellular death factor” (EDF), the penta-peptide NNWNN (EcEDF), enhancing the endoribonucleolytic activity of E. coli toxin MazF. Here we discovered that E. coli mazEF-mediated cell death could be triggered by QS peptides from the supernatants (SN) of the Gram-positive bacterium Bacillus subtilis and the Gram-negative bacterium Pseudomonas aeruginosa. In the SN of B. subtilis, we found one EDF, the hexapeptide RGQQNE, called BsEDF. In the SN of P. aeruginosa, we found three EDFs: the nonapeptide INEQTVVTK, called PaEDF-1, and two hexadecapeptides, VEVSDDGSGGNTSLSQ, called PaEDF-2, and APKLSDGAAAGYVTKA, called PaEDF-3. When added to a diluted E. coli cultures, each of these peptides acted as an interspecies EDF that triggered mazEF-mediated death. Furthermore, though their sequences are very different, each of these EDFs amplified the endoribonucleolytic activity of E. coli MazF, probably by interacting with different sites on E. coli MazF. Finally, we suggest that EDFs may become the basis for a new class of antibiotics that trigger death from outside the bacterial cells. Bacteria communicate with one another via quorum-sensing signal (QS) molecules. QS provides a mechanism for bacteria to monitor each other’s presence and to modulate gene expression in response to population density. Previously, we added E. coli EDF (EcEDF), the peptide NNWNN, to this list of QS molecules. Here we extended the group of QS peptides to several additional different peptides. The new EDFs are produced by two other bacteria, Bacillus subtilis and Pseudomonas aeruginosa. Thus, in this study we established a “new family of EDFs.” This family provides the first example of quorum-sensing molecules participating in interspecies bacterial cell death. Furthermore, each of these peptides provides the basis of a new class of antibiotics triggering death by acting from outside the cell.
Collapse
|
181
|
Tanouchi Y, Lee AJ, Meredith H, You L. Programmed cell death in bacteria and implications for antibiotic therapy. Trends Microbiol 2013; 21:265-70. [PMID: 23684151 DOI: 10.1016/j.tim.2013.04.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/09/2013] [Accepted: 04/11/2013] [Indexed: 10/26/2022]
Abstract
It is now well appreciated that programmed cell death (PCD) plays critical roles in the life cycle of diverse bacterial species. It is an apparently paradoxical behavior as it does not benefit the cells undergoing PCD. However, growing evidence suggests that PCD can be 'altruistic': the dead cells may directly or indirectly benefit survivors through generation of public goods. This property provides a potential explanation on how PCD can evolve as an extreme form of cooperation, although many questions remain to be addressed. From another perspective, as PCD plays a critical role in bacterial pathogenesis, it has been proposed as a potential target for new antibacterial therapy. To this end, understanding the population and evolutionary dynamics resulting from PCD and public goods production may be a key to the success of designing effective antibiotic treatment.
Collapse
Affiliation(s)
- Yu Tanouchi
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | | | | | | |
Collapse
|
182
|
Frey W, Gusbeth C, Schwartz T. Inactivation of Pseudomonas putida by pulsed electric field treatment: a study on the correlation of treatment parameters and inactivation efficiency in the short-pulse range. J Membr Biol 2013; 246:769-81. [PMID: 23660812 DOI: 10.1007/s00232-013-9547-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/17/2013] [Indexed: 01/19/2023]
Abstract
An important issue for an economic application of the pulsed electric field treatment for bacterial decontamination of wastewater is the specific treatment energy needed for effective reduction of bacterial populations. The present experimental study performed in a field amplitude range of 40 > E > 200 kV/cm and for a suspension conductivity of 0.01 = κ(e) > 0.2 S/m focusses on the application of short pulses, 25 ns > T > 10 μs, of rectangular, bipolar and exponential shape and was made on Pseudomonas putida, which is a typical and widespread wastewater microorganism. The comparison of inactivation results with calculations of the temporal and azimuthal membrane charging dynamics using the model of Pauly and Schwan revealed that for efficient inactivation, membrane segments at the cell equator have to be charged quickly and to a sufficiently high value, on the order of 0.5 V. After fulfilling this basic condition by an appropriate choice of pulse field strength and duration, the log rate of inactivation for a given suspension conductivity of 0.2 S/m was found to be independent of the duration of individual pulses for constant treatment energy expenditure. Moreover, experimental results suggest that even pulse shape plays a minor role in inactivation efficiency. The variation of the suspension conductivity resulted in comparable inactivation performance of identical pulse parameters if the product of pulse duration and number of pulses was the same, i.e., required treatment energy can be linearly downscaled for lower conductivities, provided that pulse amplitude and duration are selected for entire membrane surface permeabilization.
Collapse
Affiliation(s)
- Wolfgang Frey
- Institute for Pulsed Power and Microwave Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen, 76344, Germany,
| | | | | |
Collapse
|
183
|
Taylor-Brown E, Hurd H. The first suicides: a legacy inherited by parasitic protozoans from prokaryote ancestors. Parasit Vectors 2013; 6:108. [PMID: 23597031 PMCID: PMC3640913 DOI: 10.1186/1756-3305-6-108] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 04/05/2013] [Indexed: 12/23/2022] Open
Abstract
It is more than 25 years since the first report that a protozoan parasite could die by a process resulting in a morphological phenotype akin to apoptosis. Since then these phenotypes have been observed in many unicellular parasites, including trypanosomatids and apicomplexans, and experimental evidence concerning the molecular pathways that are involved is growing. These observations support the view that this form of programmed cell death is an ancient one that predates the evolution of multicellularity. Here we review various hypotheses that attempt to explain the origin of apoptosis, and look for support for these hypotheses amongst the parasitic protists as, with the exception of yeast, most of the work on death mechanisms in unicellular organisms has focussed on them. We examine the role that addiction modules may have played in the original eukaryote cell and the part played by mitochondria in the execution of present day cells, looking for examples from Leishmania spp. Trypanosoma spp. and Plasmodium spp. In addition, the expanding knowledge of proteases, nucleases and other molecules acting in protist execution pathways has enabled comparisons to be made with extant Archaea and bacteria and with biochemical pathways that evolved in metazoans. These comparisons lend support to the original sin hypothesis but also suggest that present-day death pathways may have had multifaceted beginnings.
Collapse
|
184
|
Palmer SR, Miller JH, Abranches J, Zeng L, Lefebure T, Richards VP, Lemos JA, Stanhope MJ, Burne RA. Phenotypic heterogeneity of genomically-diverse isolates of Streptococcus mutans. PLoS One 2013; 8:e61358. [PMID: 23613838 PMCID: PMC3628994 DOI: 10.1371/journal.pone.0061358] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 03/07/2013] [Indexed: 11/18/2022] Open
Abstract
High coverage, whole genome shotgun (WGS) sequencing of 57 geographically- and genetically-diverse isolates of Streptococcus mutans from individuals of known dental caries status was recently completed. Of the 57 sequenced strains, fifteen isolates, were selected based primarily on differences in gene content and phenotypic characteristics known to affect virulence and compared with the reference strain UA159. A high degree of variability in these properties was observed between strains, with a broad spectrum of sensitivities to low pH, oxidative stress (air and paraquat) and exposure to competence stimulating peptide (CSP). Significant differences in autolytic behavior and in biofilm development in glucose or sucrose were also observed. Natural genetic competence varied among isolates, and this was correlated to the presence or absence of competence genes, comCDE and comX, and to bacteriocins. In general strains that lacked the ability to become competent possessed fewer genes for bacteriocins and immunity proteins or contained polymorphic variants of these genes. WGS sequence analysis of the pan-genome revealed, for the first time, components of a Type VII secretion system in several S. mutans strains, as well as two putative ORFs that encode possible collagen binding proteins located upstream of the cnm gene, which is associated with host cell invasiveness. The virulence of these particular strains was assessed in a wax-worm model. This is the first study to combine a comprehensive analysis of key virulence-related phenotypes with extensive genomic analysis of a pathogen that evolved closely with humans. Our analysis highlights the phenotypic diversity of S. mutans isolates and indicates that the species has evolved a variety of adaptive strategies to persist in the human oral cavity and, when conditions are favorable, to initiate disease.
Collapse
Affiliation(s)
- Sara R. Palmer
- Department of Oral Biology, University of Florida, Gainesville, Florida, United States of America
| | - James H. Miller
- Center for Oral Biology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Jacqueline Abranches
- Center for Oral Biology, University of Rochester Medical Center, Rochester, New York, United States of America
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Lin Zeng
- Department of Oral Biology, University of Florida, Gainesville, Florida, United States of America
| | - Tristan Lefebure
- Université de Lyon, CNRS, Ecologie des Hydrosystèmes Naturels et Anthropisés; Université Lyon, Villeurbanne, France
- Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Vincent P. Richards
- Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - José A. Lemos
- Center for Oral Biology, University of Rochester Medical Center, Rochester, New York, United States of America
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Michael J. Stanhope
- Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Robert A. Burne
- Department of Oral Biology, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
| |
Collapse
|
185
|
Abstract
Autophagy is a process in which a eukaryotic (but not prokaryotic) cell destroys its own components through the lysosomal machinery. This tightly regulated process is essential for normal cell growth, development, and homeostasis, serving to maintain a balance between synthesis and degradation, resulting in the recycling of cellular products. Here we try to expand the concept of autophagy and define it as a general mechanism of regulation encompassing various levels of the biosphere. Interestingly, one of the consequences of such an approach is that we must presume an existence of the autophagic processes in the prokaryotic domain.
Collapse
Affiliation(s)
- Petro Starokadomskyy
- Department of Internal Medicine; University of Texas Southwestern Medical Center; Dallas, TX USA
| | | |
Collapse
|
186
|
Yagüe P, López-García MT, Rioseras B, Sánchez J, Manteca A. Pre-sporulation stages of Streptomyces differentiation: state-of-the-art and future perspectives. FEMS Microbiol Lett 2013; 342:79-88. [PMID: 23496097 DOI: 10.1111/1574-6968.12128] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 03/12/2013] [Indexed: 11/30/2022] Open
Abstract
Streptomycetes comprise very important industrial bacteria, producing two-thirds of all clinically relevant secondary metabolites. They are mycelial microorganisms with complex developmental cycles that include programmed cell death (PCD) and sporulation. Industrial fermentations are usually performed in liquid cultures (large bioreactors), conditions in which Streptomyces strains generally do not sporulate, and it was traditionally assumed that there was no differentiation. In this work, we review the current knowledge on Streptomyces pre-sporulation stages of Streptomyces differentiation.
Collapse
Affiliation(s)
- Paula Yagüe
- Área de Microbiología, Departamento de Biología Funcional, and IUBA, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
| | | | | | | | | |
Collapse
|
187
|
Characterization of the phd-doc and ccd toxin-antitoxin cassettes from Vibrio superintegrons. J Bacteriol 2013; 195:2270-83. [PMID: 23475970 DOI: 10.1128/jb.01389-12] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Toxin-antitoxin (TA) systems have been reported in the genomes of most bacterial species, and their role when located on the chromosome is still debated. TA systems are particularly abundant in the massive cassette arrays associated with chromosomal superintegrons (SI). Here, we describe the characterization of two superintegron cassettes encoding putative TA systems. The first is the phd-doc(SI) system identified in Vibrio cholerae N16961. We determined its distribution in 36 V. cholerae strains and among five V. metschnikovii strains. We show that this cassette, which is in position 72 of the V. cholerae N16961 cassette array, is functional, carries its own promoter, and is expressed from this location. Interestingly, the phd-doc(SI) system is unable to control its own expression, most likely due to the absence of any DNA-binding domain on the antitoxin. In addition, this SI system is able to cross talk with the canonical P1 phage system. The second cassette that we characterized is the ccd(Vfi) cassette found in the V. fischeri superintegron. We demonstrate that CcdB(Vfi) targets DNA-gyrase, as the canonical CcB(F) toxin, and that ccd(Vfi) regulates its expression in a fashion similar to the ccd(F) operon of the conjugative plasmid F. We also establish that this cassette is functional and expressed in its chromosomal context in V. fischeri CIP 103206T. We tested its functional interactions with the ccdAB(F) system and found that CcdA(Vfi) is specific for its associated CcdB(Vfi) and cannot prevent CcdB(F) toxicity. Based on these results, we discuss the possible biological functions of these TA systems in superintegrons.
Collapse
|
188
|
Zhao J, Wang Q, Li M, Heijstra BD, Wang S, Liang Q, Qi Q. Escherichia coli toxin gene hipA affects biofilm formation and DNA release. Microbiology (Reading) 2013; 159:633-640. [DOI: 10.1099/mic.0.063784-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Junqiao Zhao
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
| | - Qian Wang
- National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
| | - Mingji Li
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
| | - Björn D. Heijstra
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Shengjun Wang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
| | - Quanfeng Liang
- National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
| | - Qingsheng Qi
- National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
| |
Collapse
|
189
|
Park SJ, Son WS, Lee BJ. Structural overview of toxin-antitoxin systems in infectious bacteria: a target for developing antimicrobial agents. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1155-67. [PMID: 23459128 DOI: 10.1016/j.bbapap.2013.02.027] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 02/18/2013] [Accepted: 02/20/2013] [Indexed: 11/17/2022]
Abstract
The bacterial toxin-antitoxin (TA) system is a module that may play a role in cell survival under stress conditions. Generally, toxin molecules act as negative regulators in cell survival and antitoxin molecules as positive regulators. Thus, the expression levels and interactions between toxins and antitoxins should be systematically harmonized so that bacteria can escape such harmful conditions. Since TA systems are able to control the fate of bacteria, they are considered potent targets for the development of new antimicrobial agents. TA systems are widely prevalent with a variety of systems existing in bacteria: there are three types of bacterial TA systems depending on the property of the antitoxin which binds either the protein toxin or mRNA coding the toxin protein. Moreover, the multiplicity of TA genes has been observed even in species of bacteria. Therefore, knowledge on TA systems such as the individual characteristics of TA systems, integrative working mechanisms of various TA systems in bacteria, interactions between toxin molecules and cellular targets, and so on is currently limited due to their complexity. In this regard, it would be helpful to know the structural characteristics of TA modules for understanding TA systems in bacteria. Until now, 85 out of the total structures deposited in PDB have been bacterial TA system proteins including TA complexes or isolated toxins/antitoxins. Here, we summarized the structural information of TA systems and analyzed the structural characteristics of known TA modules from several bacteria, especially focusing on the TA modules of several infectious bacteria.
Collapse
Affiliation(s)
- Sung Jean Park
- College of Pharmacy, Gachon University, Yeonsu-gu, Incheon, Republic of Korea
| | | | | |
Collapse
|
190
|
Dorsey-Oresto A, Lu T, Mosel M, Wang X, Salz T, Drlica K, Zhao X. YihE kinase is a central regulator of programmed cell death in bacteria. Cell Rep 2013; 3:528-37. [PMID: 23416055 DOI: 10.1016/j.celrep.2013.01.026] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 01/15/2013] [Accepted: 01/22/2013] [Indexed: 02/01/2023] Open
Abstract
Stress-mediated programmed cell death (PCD) in bacteria has recently attracted attention, largely because it raises novel possibilities for controlling pathogens. How PCD in bacteria is regulated to avoid population extinction due to transient, moderate stress remains a central question. Here, we report that the YihE protein kinase is a key regulator that protects Escherichia coli from antimicrobial and environmental stressors by antagonizing the MazEF toxin-antitoxin module. YihE was linked to a reactive oxygen species (ROS) cascade, and a deficiency of yihE stimulated stress-induced PCD even after stress dissipated. YihE was partially regulated by the Cpx envelope stress-response system, which, along with MazF toxin and superoxide, has both protective and destructive roles that help bacteria make a live-or-die decision in response to stress. YihE probably acts early in the stress response to limit self-sustaining ROS production and PCD. Inhibition of YihE may provide a way of enhancing antimicrobial lethality and attenuating virulence.
Collapse
Affiliation(s)
- Angella Dorsey-Oresto
- Public Health Research Institute Center, New Jersey Medical School, UMDNJ, Newark, NJ 07103, USA
| | | | | | | | | | | | | |
Collapse
|
191
|
Schuster CF, Bertram R. Toxin-antitoxin systems are ubiquitous and versatile modulators of prokaryotic cell fate. FEMS Microbiol Lett 2013; 340:73-85. [DOI: 10.1111/1574-6968.12074] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 12/24/2012] [Accepted: 01/03/2013] [Indexed: 10/27/2022] Open
Affiliation(s)
- Christopher F. Schuster
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin; Lehrbereich Mikrobielle Genetik; Eberhard Karls Universität Tübingen; Waldhäuser Str. 70/8; Tübingen; Germany
| | - Ralph Bertram
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin; Lehrbereich Mikrobielle Genetik; Eberhard Karls Universität Tübingen; Waldhäuser Str. 70/8; Tübingen; Germany
| |
Collapse
|
192
|
Han KD, Ahn DH, Lee SA, Min YH, Kwon AR, Ahn HC, Lee BJ. Identification of chromosomal HP0892-HP0893 toxin-antitoxin proteins in Helicobacter pylori and structural elucidation of their protein-protein interaction. J Biol Chem 2013; 288:6004-13. [PMID: 23297406 PMCID: PMC3581365 DOI: 10.1074/jbc.m111.322784] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial chromosomal toxin-antitoxin (TA) systems have been proposed not only to play an important role in the stress response, but also to be associated with antibiotic resistance. Here, we identified the chromosomal HP0892-HP0893 TA proteins in the gastric pathogen, Helicobacter pylori, and structurally characterized their protein-protein interaction. Previously, HP0892 protein was suggested to be a putative TA toxin based on its structural similarity to other RelE family TA toxins. In this study, we demonstrated that HP0892 binds to HP0893 strongly with a stoichiometry of 1:1, and HP0892-HP0893 interaction occurs mainly between the N-terminal secondary structure elements of HP0892 and the C-terminal region of HP0893. HP0892 cleaved mRNA in vitro, preferentially at the 5' end of A or G, and the RNase activity of HP0892 was inhibited by HP0893. In addition, heterologous expression of HP0892 in Escherichia coli cells led to cell growth arrest, and the cell toxicity of HP0892 was neutralized by co-expression with HP0893. From these results and a structural comparison with other TA toxins, it is concluded that HP0892 is a toxin with intrinsic RNase activity and HP0893 is an antitoxin against HP0892 from a TA system of H. pylori. It has been known that hp0893 gene and another TA antitoxin gene, hp0895, of H. pylori, are both genomic open reading frames that correspond to genes that are potentially expressed in response to interactions with the human gastric mucosa. Therefore, it is highly probable that TA systems of H. pylori are involved in virulence of H. pylori.
Collapse
Affiliation(s)
- Kyung-Doo Han
- Advanced Analysis Center, Korea Institute of Science and Technology, Seoungbuk-gu, Seoul 136-791, Korea
| | | | | | | | | | | | | |
Collapse
|
193
|
Brinkman CL, Bumgarner R, Kittichotirat W, Dunman PM, Kuechenmeister LJ, Weaver KE. Characterization of the effects of an rpoC mutation that confers resistance to the Fst peptide toxin-antitoxin system toxin. J Bacteriol 2013; 195:156-66. [PMID: 23104812 PMCID: PMC3536179 DOI: 10.1128/jb.01597-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 10/22/2012] [Indexed: 01/24/2023] Open
Abstract
Overexpression of the Fst toxin in Enterococcus faecalis strain OG1X leads to defects in chromosome segregation, cell division and, eventually, membrane integrity. The M7 mutant derivative of OG1X is resistant to most of these effects but shows a slight growth defect in the absence of Fst. Full-genome sequencing revealed two differences between M7 and its OG1X parent. First, OG1X contains a frameshift mutation that inactivates the etaR response regulator gene, while M7 is a wild-type revertant for etaR. Second, the M7 mutant contains a missense mutation in the rpoC gene, which encodes the β' subunit of RNA polymerase. Mutagenesis experiments revealed that the rpoC mutation was primarily responsible for the resistance phenotype. Microarray analysis revealed that a number of transporters were induced in OG1X when Fst was overexpressed. These transporters were not induced in M7 in response to Fst, and further experiments indicated that this had a direct protective effect on the mutant cells. Therefore, exposure of cells to Fst appears to have a cascading effect, first causing membrane stress and then potentiation of these effects by overexpression of certain transporters.
Collapse
Affiliation(s)
- Cassandra L. Brinkman
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, South Dakota, USA
| | - Roger Bumgarner
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | | | - Paul M. Dunman
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Lisa J. Kuechenmeister
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Keith E. Weaver
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, South Dakota, USA
| |
Collapse
|
194
|
Aoki W, Ueda T, Tatsukami Y, Kitahara N, Morisaka H, Kuroda K, Ueda M. Time-course proteomic profile of Candida albicans during adaptation to a fetal serum. Pathog Dis 2012; 67:67-75. [PMID: 23620121 DOI: 10.1111/2049-632x.12003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 08/31/2012] [Accepted: 08/31/2012] [Indexed: 01/09/2023] Open
Abstract
Candida albicans is a commensal organism; however, it causes fatal diseases if the host immunity is compromised. The mortality rate is very high due to the lack of effective treatment, leading to ceaseless demand for novel pharmaceuticals. In this study, time-course proteomics of C. albicans during adaptation to fetal bovine serum (FBS) was described. Time-course proteomics is a promising way to understand the exact process of going adaptation in dynamically changing environments. Candida albicans was cultivated in yeast nitrogen base (YNB) ± FBS media, and we identified 1418 proteins in the endpoint samples incubated for 0 or 60 min by a LC-MS/MS system with a long monolithic silica capillary column. Next, we carried out time-course proteomics of the YNB + FBS samples to identify top-priority proteins for adaption to FBS. We identified 16 proteins as nascent/newly synthesized proteins, and they were recognized as candidates of important virulent factors. Gene ontology analysis revealed that transport-related proteins were enriched in the 16 proteins, indicating that C. albicans probably put priority in time on the acquisition of essential elements. Time-course proteomics of C. albicans revealed the order of priority to adapt to FBS. Depicting time-course dynamics will lead to profound understandings of virulence of C. albicans.
Collapse
Affiliation(s)
- Wataru Aoki
- Japan Society for the Promotion of Science, Sakyo-ku, Kyoto, Japan
| | | | | | | | | | | | | |
Collapse
|
195
|
Asplund-Samuelsson J, Bergman B, Larsson J. Prokaryotic caspase homologs: phylogenetic patterns and functional characteristics reveal considerable diversity. PLoS One 2012. [PMID: 23185476 PMCID: PMC3501461 DOI: 10.1371/journal.pone.0049888] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Caspases accomplish initiation and execution of apoptosis, a programmed cell death process specific to metazoans. The existence of prokaryotic caspase homologs, termed metacaspases, has been known for slightly more than a decade. Despite their potential connection to the evolution of programmed cell death in eukaryotes, the phylogenetic distribution and functions of these prokaryotic metacaspase sequences are largely uncharted, while a few experiments imply involvement in programmed cell death. Aiming at providing a more detailed picture of prokaryotic caspase homologs, we applied a computational approach based on Hidden Markov Model search profiles to identify and functionally characterize putative metacaspases in bacterial and archaeal genomes. Out of the total of 1463 analyzed genomes, merely 267 (18%) were identified to contain putative metacaspases, but their taxonomic distribution included most prokaryotic phyla and a few archaea (Euryarchaeota). Metacaspases were particularly abundant in Alphaproteobacteria, Deltaproteobacteria and Cyanobacteria, which harbor many morphologically and developmentally complex organisms, and a distinct correlation was found between abundance and phenotypic complexity in Cyanobacteria. Notably, Bacillus subtilis and Escherichia coli, known to undergo genetically regulated autolysis, lacked metacaspases. Pfam domain architecture analysis combined with operon identification revealed rich and varied configurations among the metacaspase sequences. These imply roles in programmed cell death, but also e.g. in signaling, various enzymatic activities and protein modification. Together our data show a wide and scattered distribution of caspase homologs in prokaryotes with structurally and functionally diverse sub-groups, and with a potentially intriguing evolutionary role. These features will help delineate future characterizations of death pathways in prokaryotes.
Collapse
|
196
|
Applerot G, Lellouche J, Lipovsky A, Nitzan Y, Lubart R, Gedanken A, Banin E. Understanding the antibacterial mechanism of CuO nanoparticles: revealing the route of induced oxidative stress. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2012; 8:3326-3337. [PMID: 22888058 DOI: 10.1002/smll.201200772] [Citation(s) in RCA: 296] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 06/15/2012] [Indexed: 06/01/2023]
Abstract
To date, there is still a lack of definite knowledge regarding the interaction of CuO nanoparticles with bacteria and the possible permeation of the nanoparticles into bacterial cells. This study was aimed at shedding light on the size-dependent (from the microscale down to the small nanoscale) antibacterial activity of CuO. The potent antibacterial activity of CuO nanoparticles was found to be due to ROS-generation by the nanoparticles attached to the bacterial cells, which in turn provoked an enhancement of the intracellular oxidative stress. This paradigm was confirmed by several assays such as lipid peroxidation and reporter strains of oxidative stress. Furthermore, electron microscopy indicated that the small nanoparticles of CuO penetrated the cells. Collectively, the results reported herein may reconcile conflicting concepts in the literature concerning the antibacterial mechanism of CuO nanoparticles, as well as highlight the potential for developing sustainable CuO nanoparticles-based devices for inhibiting bacterial infections.
Collapse
Affiliation(s)
- Guy Applerot
- Department of Chemistry and Kanbar Laboratory for Nanomaterials, Bar-Ilan University Center for Advanced Materials & Nanotechnology, Bar-Ilan University, Ramat-Gan 52900, Israel
| | | | | | | | | | | | | |
Collapse
|
197
|
Abstract
What are the origins of programmed cell death (PCD)? In this issue of Developmental Cell, Eastwood et al. (2012) uncover an ancient developmental program of nuclear destruction in yeast, implying that some PCD mechanisms could have emerged from nonlethal processes before the divergence of fungi and metazoan.
Collapse
Affiliation(s)
- Lior Aram
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | | |
Collapse
|
198
|
Rankin DJ, Turner LA, Heinemann JA, Brown SP. The coevolution of toxin and antitoxin genes drives the dynamics of bacterial addiction complexes and intragenomic conflict. Proc Biol Sci 2012; 279:3706-15. [PMID: 22787022 PMCID: PMC3415908 DOI: 10.1098/rspb.2012.0942] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 06/20/2012] [Indexed: 12/12/2022] Open
Abstract
Bacterial genomes commonly contain 'addiction' gene complexes that code for both a toxin and a corresponding antitoxin. As long as both genes are expressed, cells carrying the complex can remain healthy. However, loss of the complex (including segregational loss in daughter cells) can entail death of the cell. We develop a theoretical model to explore a number of evolutionary puzzles posed by toxin-antitoxin (TA) population biology. We first extend earlier results demonstrating that TA complexes can spread on plasmids, as an adaptation to plasmid competition in spatially structured environments, and highlight the role of kin selection. We then considered the emergence of TA complexes on plasmids from previously unlinked toxin and antitoxin genes. We find that one of these traits must offer at least initially a direct advantage in some but not all environments encountered by the evolving plasmid population. Finally, our study predicts non-transitive 'rock-paper-scissors' dynamics to be a feature of intragenomic conflict mediated by TA complexes. Intragenomic conflict could be sufficient to select deleterious genes on chromosomes and helps to explain the previously perplexing observation that many TA genes are found on bacterial chromosomes.
Collapse
Affiliation(s)
- Daniel J. Rankin
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Building Y27, Winterthurerstrasse 190, 8057 Zürich, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge Bâtiment Génopode, 1015 Lausanne, Switzerland
| | - Leighton A. Turner
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Jack A. Heinemann
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Sam P. Brown
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
- Centre for Immunity, Infection and Evolution, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
| |
Collapse
|
199
|
Cloning, expression, purification, and biochemical characterisation of the FIC motif containing protein of Mycobacterium tuberculosis. Protein Expr Purif 2012; 86:58-67. [PMID: 22982230 DOI: 10.1016/j.pep.2012.08.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Revised: 08/28/2012] [Accepted: 08/29/2012] [Indexed: 01/01/2023]
Abstract
The role of FIC (Filamentation induced by cAMP)(2) domain containing proteins in the regulation of many vital pathways, mostly through the transfer of NMPs from NTPs to specific target proteins (NMPylation), in microorganisms, higher eukaryotes, and plants is emerging. The identity and function of FIC domain containing protein of the human pathogen, Mycobacterium tuberculosis, remains unknown. In this regard, M. tuberculosis fic gene (Mtfic) was cloned, overexpressed, and purified to homogeneity for its biochemical characterisation. It has the characteristic FIC motif, HPFREGNGRSTR (HPFxxGNGRxxR), spanning 144th to 155th residue. Neither the His-tagged nor the GST-tagged MtFic protein, overexpressed in Escherichia coli, nor expression of Mtfic in Mycobacterium smegmatis, yielded the protein in the soluble fraction. However, the maltose binding protein (MBP) tagged MtFic (MBP-MtFic) could be obtained partly in the soluble fraction. The cloned, overexpressed, and purified recombinant MBP-MtFic showed conversion of ATP, GTP, CTP, and UTP into AMP, GMP, CMP, and UMP, respectively. Sequence alignment with several FIC motif containing proteins, complemented with homology modeling on the FIC motif containing protein, VbhT of Bartonella schoenbuchensis as the template, showed conservation and interaction of residues constituting the FIC domain. Site-specific mutagenesis of the His144, or Glu148, or Asn150 of the FIC motif, or of Arg87 residue that constitutes the FIC domain, or complete deletion of the FIC motif, abolished the NTP to NMP conversion activity. The design of NMP formation assay using the recombinant, soluble MtFic would enable identification of its target substrate for NMPylation.
Collapse
|
200
|
Moll I, Engelberg-Kulka H. Selective translation during stress in Escherichia coli. Trends Biochem Sci 2012; 37:493-8. [PMID: 22939840 DOI: 10.1016/j.tibs.2012.07.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/25/2012] [Accepted: 07/27/2012] [Indexed: 12/18/2022]
Abstract
The bacterial stress response, a strategy to cope with environmental changes, is generally known to operate on the transcriptional level. Here, we discuss a novel paradigm for stress adaptation at the post-transcriptional level, based on the recent discovery of a stress-induced modified form of the translation machinery in Escherichia coli that is generated by MazF, the toxin component of the toxin-antitoxin (TA) module mazEF. Under stress, the induced endoribonuclease MazF removes the 3'-terminal 43 nucleotides of the 16S rRNA of ribosomes and, concomitantly, the 5'-untranslated regions (UTRs) of specific transcripts. This elegant mechanism enables selective translation due to the complementary effect of MazF on ribosomes and mRNAs, and also represents the first example of functional ribosome heterogeneity based on rRNA alteration.
Collapse
Affiliation(s)
- Isabella Moll
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, 1030 Vienna, Austria.
| | | |
Collapse
|