Genomes to Life Contractor-Grantee Workshop III
February 6-9, 2005, Washington, D.C.
Genomics:GTL Program Projects
Shewanella Federation
40
Comparative Analysis of Gene Expression Profiles of Shewanella oneidensis MR-1 Following Exposure to Ionizing Radiation and Ultraviolet Radiation
Xiaoyun Qiu1*(qiuxiaoy@msu.edu), George Sundin1, Michael J. Daly2, Alexander Vasilenko2, Marina V. Omelchenko3, Jizhong Zhou4, Liyou Wu4, Mary S. Lipton5, and James M. Tiedje1
1Michigan State University, East Lansing, MI; 2Uniformed Services University of the Health Sciences, Bethesda, MD; 3National Institutes of Health, Bethesda, MD; 4Oak Ridge National Laboratory, Oak Ridge, TN; and 5Pacific Northwest National Laboratory, Richland, WA
Shewanella oneidensis MR-1, a Gamma proteobacterium, is notable in the terminal electron acceptors it uses including some toxic metal ions and radionuclides. Thus it has potential for bioremediation. However, MR-1 is highly sensitive to both ionizing radiation (IR) and ultraviolet radiation (UVR). We delineated the genomic response of Shewanella oneidensis MR-1 to gamma ray, UVC (254 nm), UVB (290-320 nm), UVA (320-400 nm) and natural solar radiation. A total of 5.9-, 4.2-, 3.9-, 8.1-, and 28.0% of the MR-1 genome showed differential expression (P<0.05 and fold >2), respectively, at a dose that yielded about 20% survival rate. The gene expression profile of MR-1 in response to ionizing radiation is more similar to that of UVC, which is characterized by the induction of SOS response and prophage synthesis, plus a strong induction of antioxidant enzymes. Genomic response to UVB is a combination of the UVC and UVA patterns, which represents a shift from shorter wavelength of UVR-induced direct DNA damage and activation of prophages to longer wavelength of UVR-induced global photo-oxidative damage. We observed the traditional UVA-induced stress responses in MR-1 such as induction of antioxidant enzymes and proteins, sequestration of the transition metals and activation of the degradative pathways, however, the induction of heavy metal and multidrug efflux pumps is a previously unknown phenotype for this stress. Consistent with natural solar UV radiation composition (about 95% UVA and 5% UVB), genomic response to solar radiation is more similar to that of UVA but with more genes induced for detoxification. In addition, the number of differentially expressed genes from most functional categories was much greater than for UVB or UVA or their sum. This unique gene expression profile indicates that natural solar radiation impacts biological processes in a much more complex way than previously thought.
Comparative genome analysis indicates that S. oneidensis MR-1 encodes a complex set of DNA repair and detoxification genes. For example, about 2.8% of the MR-1 genome is dedicated to DNA repair, replication and recombination, which is very similar to that of Escherichia coli K12 (2.7%) and the extremely radiation resistant Deinococcus radiodurans R1 (3.1%). However, only about 5.8- and 13.9% of those genes were induced in MR-1 by UVC and gamma ray, respectively, which is much lower than in E. coli K12 (15.7% were induced by UVC) and in D. radiodurans (22.0% were induced by gamma ray). This result indicates that alteration in gene content and gene regulation, which may be the consequence of lack of recent natural selection, contribute to the high radiation sensitivity of MR-1.
Although we observed a strong induction of the SOS response in MR-1 following exposure to IR or short wavelength UVR (UVC and UVB), DNA damage caused during irradiation itself might not be the primary cause of cell death since there is relatively little DNA damage in MR-1 following 40 Gy or 3.3 J m-2 of UVC. MR-1 is a respiratory generalist and is very rich in cytochromes, which together with other respiratory chain components such as flavins and quinones are an important source of oxidative stress. A recent study by Daly et al. showed that in contrast to D. radiodurans, MR-1 accumulates exceptionally high Fe and low Mn levels. Accumulation of Mn in bacteria has been proposed to serve as non-enzymatic antioxidants during recovery after radiation exposure. Collectively, the results support that irradiated S. oneidensis is responding to oxidative stress elicited by metabolism-induced free radicals produced during recovery. For Fe-rich, Mn-poor cells such as S. oneidensis, death at low doses of IR might be caused by a combination of oxidative stress and the induction of lytic prophages, as proposed following recovery from UV radiation.
* Presenting author
