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Castillo H, Li X, Schilkey F, Smith GB. Transcriptome analysis reveals a stress response of Shewanella oneidensis deprived of background levels of ionizing radiation. PLoS One 2018; 13:e0196472. [PMID: 29768440 PMCID: PMC5955497 DOI: 10.1371/journal.pone.0196472] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/13/2018] [Indexed: 11/21/2022] Open
Abstract
Natural ionizing background radiation has exerted a constant pressure on organisms since the first forms of life appeared on Earth, so that cells have developed molecular mechanisms to avoid or repair damages caused directly by radiation or indirectly by radiation-induced reactive oxygen species (ROS). In the present study, we investigated the transcriptional effect of depriving Shewanella oneidensis cultures of background levels of radiation by growing the cells in a mine 655 m underground, thus reducing the dose rate from 72.1 to 0.9 nGy h-1 from control to treatment, respectively. RNASeq transcriptome analysis showed the differential expression of 4.6 and 7.6% of the S. oneidensis genome during early- and late-exponential phases of growth, respectively. The greatest change observed in the treatment was the downregulation of ribosomal proteins (21% of all annotated ribosomal protein genes during early- and 14% during late-exponential) and tRNA genes (14% of all annotated tRNA genes in early-exponential), indicating a marked decrease in protein translation. Other significant changes were the upregulation of membrane transporters, implying an increase in the traffic of substrates across the cell membrane, as well as the up and downregulation of genes related to respiration, which could be interpreted as a response to insufficient oxidants in the cells. In other reports, there is evidence in multiple species that some ROS not just lead to oxidative stress, but act as signaling molecules to control cellular metabolism at the transcriptional level. Consistent with these reports, several genes involved in the metabolism of carbon and biosynthesis of amino acids were also regulated, lending support to the idea of a wide metabolic response. Our results indicate that S. oneidensis is sensitive to the withdrawal of background levels of ionizing radiation and suggest that a transcriptional response is required to maintain homeostasis and retain normal growth.
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Affiliation(s)
- Hugo Castillo
- Department of Biology, New Mexico State University, Las Cruces, NM, United States of America
| | - Xiaoping Li
- Department of Botany and Plant Pathology, Oregon State University, Hermiston, OR, United States of America
| | - Faye Schilkey
- National Center for Genome Resources, Santa Fe, NM, United States of America
| | - Geoffrey B Smith
- Department of Biology, New Mexico State University, Las Cruces, NM, United States of America
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Castillo H, Schoderbek D, Dulal S, Escobar G, Wood J, Nelson R, Smith G. Stress induction in the bacteria Shewanella oneidensis and Deinococcus radiodurans in response to below-background ionizing radiation. Int J Radiat Biol 2015; 91:749-56. [PMID: 26073528 DOI: 10.3109/09553002.2015.1062571] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE The 'Linear no-threshold' (LNT) model predicts that any amount of radiation increases the risk of organisms to accumulate negative effects. Several studies at below background radiation levels (4.5-11.4 nGy h(-1)) show decreased growth rates and an increased susceptibility to oxidative stress. The purpose of our study is to obtain molecular evidence of a stress response in Shewanella oneidensis and Deinococcus radiodurans grown at a gamma dose rate of 0.16 nGy h(-1), about 400 times less than normal background radiation. MATERIALS AND METHODS Bacteria cultures were grown at a dose rate of 0.16 or 71.3 nGy h(-1) gamma irradiation. Total RNA was extracted from samples at early-exponential and stationary phases for the rt-PCR relative quantification (radiation-deprived treatment/background radiation control) of the stress-related genes katB (catalase), recA (recombinase), oxyR (oxidative stress transcriptional regulator), lexA (SOS regulon transcriptional repressor), dnaK (heat shock protein 70) and SOA0154 (putative heavy metal efflux pump). RESULTS Deprivation of normal levels of radiation caused a reduction in growth of both bacterial species, accompanied by the upregulation of katB, recA, SOA0154 genes in S. oneidensis and the upregulation of dnaK in D. radiodurans. When cells were returned to background radiation levels, growth rates recovered and the stress response dissipated. CONCLUSIONS Our results indicate that below-background levels of radiation inhibited growth and elicited a stress response in two species of bacteria, contrary to the LNT model prediction.
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Affiliation(s)
- Hugo Castillo
- a Department of Biology , New Mexico State University , Las Cruces , NM , USA
| | - Donald Schoderbek
- b Department of Agriculture , Food, and Nutritional Science, University of Alberta , Edmonton , Alberta, Canada
| | - Santosh Dulal
- c School of Medicine, University of North Carolina , Chapel Hill NC
| | - Gabriela Escobar
- a Department of Biology , New Mexico State University , Las Cruces , NM , USA
| | - Jeffrey Wood
- d Department of Energy-Carlsbad Field Office , Carlsbad , NM , USA
| | - Roger Nelson
- d Department of Energy-Carlsbad Field Office , Carlsbad , NM , USA
| | - Geoffrey Smith
- a Department of Biology , New Mexico State University , Las Cruces , NM , USA
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Wang Y, Lin W, Li J, Pan Y. Changes of cell growth and magnetosome biomineralization in Magnetospirillum magneticum AMB-1 after ultraviolet-B irradiation. Front Microbiol 2013; 4:397. [PMID: 24391631 PMCID: PMC3867805 DOI: 10.3389/fmicb.2013.00397] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 12/04/2013] [Indexed: 11/28/2022] Open
Abstract
Effects of ultraviolet radiation on microorganisms are of great interest in field of microbiology and planetary sciences. In the present study, we used Magnetospirillum magneticum AMB-1 as a model organism to examine the influence of ultraviolet-B (UV-B) radiation on cell growth and magnetite biomineralization of magnetotactic bacteria (MTB). Live AMB-1 cells were exposed to UV-B radiation for 60, 300 and 900 s, which correspond to radiation doses of 120 J/m2, 600 J/m2, and 1800 J/m2, respectively. After irradiation, the amounts of cyclobutane pyrimidine dimers (CPD) and reactive oxygen species (ROS) of the cells were increased, and cell growth was stunted up to ~170 h, depending on the UV-B radiation doses. The UV-B irradiated cells also produced on average more magnetite crystals with larger grain sizes and longer chains, which results in changes of their magnetic properties.
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Affiliation(s)
- Yinzhao Wang
- Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of the Earth's Deep Interior, Institute of Geology and Geophysics, Chinese Academy of Sciences Beijing, China ; France-China Bio-Mineralization and Nano-Structures Laboratory, Chinese Academy of Sciences Beijing, China
| | - Wei Lin
- Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of the Earth's Deep Interior, Institute of Geology and Geophysics, Chinese Academy of Sciences Beijing, China ; France-China Bio-Mineralization and Nano-Structures Laboratory, Chinese Academy of Sciences Beijing, China
| | - Jinhua Li
- Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of the Earth's Deep Interior, Institute of Geology and Geophysics, Chinese Academy of Sciences Beijing, China ; France-China Bio-Mineralization and Nano-Structures Laboratory, Chinese Academy of Sciences Beijing, China
| | - Yongxin Pan
- Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of the Earth's Deep Interior, Institute of Geology and Geophysics, Chinese Academy of Sciences Beijing, China ; France-China Bio-Mineralization and Nano-Structures Laboratory, Chinese Academy of Sciences Beijing, China
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Soule T, Gao Q, Stout V, Garcia-Pichel F. The Global Response ofNostoc punctiformeATCC 29133 to UVA Stress, Assessed in a Temporal DNA Microarray Study. Photochem Photobiol 2012; 89:415-23. [DOI: 10.1111/php.12014] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 10/27/2012] [Indexed: 12/18/2022]
Affiliation(s)
| | - Qunjie Gao
- School of Life Sciences; Arizona State University; Tempe; AZ
| | - Valerie Stout
- School of Life Sciences; Arizona State University; Tempe; AZ
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Wu B, Zhuang WQ, Sahu M, Biswas P, Tang YJ. Cu-doped TiO(2) nanoparticles enhance survival of Shewanella oneidensis MR-1 under ultraviolet light (UV) exposure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2011; 409:4635-4639. [PMID: 21855961 DOI: 10.1016/j.scitotenv.2011.07.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 07/02/2011] [Accepted: 07/17/2011] [Indexed: 05/31/2023]
Abstract
It has been shown that photocatalytic TiO(2) nanoparticles (NPs) can be used as an efficient anti-microbial agent under UV light due to generation of reactive oxygen species (ROS), while Shewanella oneidensis MR-1 is a metal-reducing bacterium highly susceptible to UV radiation. Interestingly, we found that the presence of Cu-doped TiO(2) NPs in the cultural medium dramatically increased the survival rates (based on colony-forming unit) of strain MR-1 by over 10,000-fold (incubation without shaking) and ~200 fold (incubation with shaking) after a 2-h exposure to UV light. Gene expression results (via qPCR measurement) indicated that the DNA repair gene recA in MR-1 was significantly induced by UV exposure (indicating cellular damage under UV stress), but the influence of NPs on recA expression was not statistically evident. Plausible explanations to NP attenuation of UV stresses are: 1. TiO(2) based NPs are capable of scattering and absorbing UV light and thus create a shading effect to protect MR-1 from UV radiation; 2. more importantly, Cu-doped TiO(2) NPs can co-agglomerate with MR-1 to form large flocs that improves cells' survival against the environmental stresses. This study improves our understanding of NP ecological impacts under natural solar radiation and provides useful insights to application of photocatalytic-NPs for bacterial disinfection.
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Affiliation(s)
- Bing Wu
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
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Abstract
The shewanellae are ubiquitous in aquatic and sedimentary systems that are chemically stratified on a permanent or seasonal basis. In addition to their ability to utilize a diverse array of terminal electron acceptors, the microorganisms have evolved both common and unique responding mechanisms to cope with various stresses. This paper focuses on the response and adaptive mechanism of the shewanellae, largely based on transcriptional data.
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Enhancement of UV light sensitivity of a Vibrio parahaemolyticus O3:K6 pandemic strain due to natural lysogenization by a telomeric phage. Appl Environ Microbiol 2009; 75:1697-702. [PMID: 19151181 DOI: 10.1128/aem.01995-08] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Vibrio parahaemolyticus O3:K6 pandemic clonal strain was first observed in southern Chile in 2004 and has since caused approximately 8,000 seafood-related diarrhea cases in this region. The massive proliferation of the original clonal population offers a unique opportunity to study the evolution of a bacterial pathogen in its natural environment by detection and characterization of emerging bacterial variants. Here, we describe a group of pandemic variants characterized by the presence of a 42-kb extrachromosomal DNA that can be recovered by alkaline extraction. Upon treatment with mitomycin C, these variants lyse with production of a myovirus containing DNA of equal size to the plasmid but which cannot be recovered by alkaline extraction. Plasmid and phage DNAs show similar restriction patterns corresponding to enzyme sites in a circular permutation. Sequenced regions showed 81 to 99% nucleotide similarity to bacteriophage VHML of Vibrio harveyi. Altogether these observations indicate that the 42-kb plasmid corresponds to a prophage, consisting of a linear DNA with terminal hairpins of a telomeric temperate phage with a linear genome. Bacteria containing the prophage were 7 to 15 times more sensitive to UV radiation, likely due to phage induction by UV irradiation as plasmid curing restored the original sensitivity. The enhanced UV sensitivity could have a significant role in reducing the survival and propagation capability of the V. parahaemolyticus pandemic strain in the ocean.
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Bertin PN, Médigue C, Normand P. Advances in environmental genomics: towards an integrated view of micro-organisms and ecosystems. MICROBIOLOGY-SGM 2008; 154:347-359. [PMID: 18227239 DOI: 10.1099/mic.0.2007/011791-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Microbial genome sequencing has, for the first time, made accessible all the components needed for both the elaboration and the functioning of a cell. Associated with other global methods such as protein and mRNA profiling, genomics has considerably extended our knowledge of physiological processes and their diversity not only in human, animal and plant pathogens but also in environmental isolates. At a higher level of complexity, the so-called meta approaches have recently shown great promise in investigating microbial communities, including uncultured micro-organisms. Combined with classical methods of physico-chemistry and microbiology, these endeavours should provide us with an integrated view of how micro-organisms adapt to particular ecological niches and participate in the dynamics of ecosystems.
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Affiliation(s)
- Philippe N Bertin
- Génétique Moléculaire, Génomique et Microbiologie, Université Louis Pasteur, UMR7156 CNRS, Strasbourg, France
| | | | - Philippe Normand
- Ecologie Microbienne, Université Claude Bernard - Lyon 1, UMR5557 CNRS, Villeurbanne, France
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