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Margaret Romine

Microbiology
Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-18
Richland, WA 99352

Biography

Dr. Romine is a Scientist in the Microbiology Group of the Biological Sciences Division at the Pacific Northwest National Laboratory. Dr. Romine's research interests are on the application and integration of experimental and computational approaches to identify and characterize bacteria in pure and mixed cultures, either contrived in the laboratory or extracted directly from the environment. She currently is Co-PI on multi-institution DOE GTL: Genomes to Life grant focused on characterizing microbial interactions between autotrophic and heterotrophic microbes from Yellowstone National Park and meromictic lakes in Washington State. Her primary roles on this project involve maintaining/updating the genome annotation, developing targeted gene knock-out mutants to probe and validate gene functions, utilizing comparative genomics to predict new gene functions and map them to cellular subsystems, and to integrate this information with results from various experimental data types (e.g., microarrays and global proteomics) to develop systems level descriptions of MR-1 metabolism. She also is leading an effort within this project that is focused on interrogating methods of gene transfer in these communities and identifying the pool of functions that are mobilized.

Research Interests

  • Application and integration of experimental and computational approaches to identify and characterize bacteria in pure and mixed cultures
  • She currently is Co-PI on multi-institution DOE GTL: Genomes to Life grant focused on characterizing microbial interactions between autotrophic and heterotrophic microbes from Yellowstone National Park.

Education and Credentials

  • Ph.D., Microbiology, University of Texas, Austin
  • B.S., Microbiology, University of Illinois, Champagne-Urbana
  • Postdoctoral Research Fellow, Environmental Microbiology Group, Pacific Northwest National Laboratory, Richland, WA
  • Postdoctoral Research Fellow, Hematology Department, M.D. Anderson Cancer Institute, Houston, TX

Affiliations and Professional Service

  • American Society of Microbiology

Awards and Recognitions

  • 1997 R&D 100 Award for RubberCycle Technology
  • 1996 Discover Magazine Environmental Technology Finalist for RubberCycle technology
  • 1982 Outstanding Undergraduate Research Thesis Award

PNNL Publications

2014

  • Sadler NC, MR Melnicki, MH Serres, ED Merkley, WB Chrisler, EA Hill, MF Romine, S Kim, EM Zink, S Datta, RD Smith, AS Beliaev, A Konopka, and AT Wright. 2014. "Live Cell Chemical Profiling of Temporal Redox Dynamics in a Photoautotrophic Cyanobacterium." ACS Chemical Biology 9(1):291-300.  doi:10.1021/cb400769v

2013

  • Bonissone S, N Gupta, MF Romine, RA Bradshaw, and PA Pevzner. 2013. "N-terminal protein processing: A comparative proteogenomic analysis." Molecular & Cellular Proteomics. MCP 12(1):14-28.  doi:10.1074/mcp.M112.019075
  • Kozubal M, MF Romine, R Jennings, Z Jay, SG Tringe, DB Rusch, J Beam, LA McCue, and WP Inskeep. 2013. "Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park." The ISME Journal 7(3):622-634.  doi:10.1038/ismej.2012.132
  • Taylor RC, BJM Webb-Robertson, LM Markillie, MH Serres, BE Linggi, JT Aldrich, EA Hill, MF Romine, MS Lipton, and HS Wiley. 2013. "Changes in Translational Efficiency is a Dominant Regulatory Mechanism in the Environmental Response of Bacteria." Integrative Biology 5(11):1393-1406.  doi:10.1039/C3IB40120K

2012

  • Mitchell AC, L Peterson, CL Reardon, SB Reed, DE Culley, MF Romine, and GG Geesey. 2012. "Role of Outer Membrane C-Type Cytochromes MtrC and OmcA in Shewanella Oneidensis MR-1 Cell Production, Accumulation, and Detachment During Respiration on Hematite." Geobiology 10(4):355-370.  doi:10.1111/j.1472-4669.2012.00321.x

2011

  • Romine MF. 2011. "Genome-wide protein localization prediction strategies for gram negative bacteria." BMC Genomics 12((Suppl 1)):Adricle No. S1.  doi:10.1186/1471-2164-12-S1-S1
  • Cao B, L Shi, RN Brown, Y Xiong, JK Fredrickson, MF Romine, MJ Marshall, MS Lipton, and H Beyenal. 2011. "Extracellular Polymeric Substances from Shewanella sp. HRCR-1 Biofilms: Characterization by Infrared Spectroscopy and Proteomics." Environmental Microbiology 13(4):1018-1031.  doi:10.1111/j.1462-2920.2010.02407.x
  • Cruz-Garza C, AE Murray, JLM Rodrigues, JA Gralnick, LA McCue, MF Romine, FE Loffler, and JM Tiedje. 2011. "Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1." BMC Microbiology 11:Article No. 64.  doi:10.1186/1471-2180-11-64
  • Galeazzi L, P Bocci, A Amici, L Brunetti, S Ruggieri, MF Romine, SB Reed, A Osterman, DA Rodionov, L Sorci, and N Raffaelli. 2011. "IDENTIFICATION OF NICOTINAMIDE MONONUCLEOTIDE DEAMIDASE OF THE BACTERIAL PYRIDINE NUCLEOTIDE CYCLE REVEALS A NOVEL BROADLY CONSERVED AMIDOHYDROLASE FAMILY." Journal of Biological Chemistry 286(46):40365-40375.  doi:10.1074/jbc.M111.275818
  • Leyn S, X Li, Q Zheng, P Novichkov, SB Reed, MF Romine, JK Fredrickson, C Yang, AL Osterman, and DA Rodionov. 2011. "Control of Proteobacterial Central Carbon Metabolism by the HexR Transcriptional Regulator. A Case Study in Shewanella oneidensis." Journal of Biological Chemistry 286(41):35782-35794.  doi:10.1074/jbc.M111.267963
  • Rodionov DA, P Novichkov, ED Stavrovskaya, IA Rodionova, X Li, MD Kazanov, DA Ravcheev, AV Gerasimova, AE Kazakov, GY Kovaleva, EA Permina, ON Laikova, R Overbeek, MF Romine, JK Fredrickson, AP Arkin, I Dubchak, AL Osterman, and MS Gelfand. 2011. "Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus." BMC Genomics 12(Suppl 1):Article No. S3. 
  • Shirodkar S, SB Reed, MF Romine, and D Saffarini. 2011. "The octaheme SirA catalyses dissimilatory sulfite reduction in Shewanella oneidensis MR-1." Environmental Microbiology 13(1):108-115.  doi:10.1111/j.1462-2920.2010.02313.x

2010

  • Brown RN, MF Romine, AA Schepmoes, RD Smith, and MS Lipton. 2010. "Mapping the Subcellular Proteome of Shewanella oneidensis MR-1 using Sarkosyl-based fractionation and LC-MS/MS protein identification." Journal of Proteome Research 9(9):4454-4463.  doi:10.1021/pr100215h
  • Gao H, S Barua, Y Liang, L Wu, Y Dong, SB Reed, J Chen, DE Culley, DW Kennedy, Y Yang, Z He, KH Nealson, JK Fredrickson, JM Tiedje, MF Romine, and J Zhou. 2010. "Impacts of Shewanella oneidensis c-type cytochromes on aerobic and anaerobic respiration." Microbial Biotechnology 3(4):455-466.  doi:10.1111/j.1751-7915.2010.00181.x
  • Harris HW, MY El-Naggar, O Bretschger, MJ Ward, MF Romine, A Obraztsova, and KH Nealson. 2010. "Electrokinesis is a microbial behavior that requires extracellular electron transport." Proceedings of the National Academy of Sciences of the United States of America 107(1):326-331.  doi:10.1073/pnas.0907468107
  • Karpinets TV, A Obraztsova, Y Wang, DD Schmoyer, G Kora, BH Park, MH Serres, MF Romine, ML Land, TB Kothe, JK Fredrickson, KH Nealson, and E Uberbacher. 2010. "Conserved synteny at the protein family level reveals genes underlying Shewanella species cold tolerance and predicts their novel phenotypes." Functional & Integrative Genomics 10(1):97-110. 
  • Pinchuk GE, EA Hill, OV Geydebrekht, J De Ingeniis, X Zhang, A Osterman, JH Scott, SB Reed, MF Romine, A Konopka, AS Beliaev, JK Fredrickson, and JL Reed. 2010. "Constraint-Based Model of Shewanella oneidensis MR-1 Metabolism: a Tool for Data Analysis and Hypothesis Generation." PLoS Computational Biology 6(6):Art. No. e1000822.  doi:10.1371/journal.pcbi.1000822
  • Rodionov DA, C Yang, X Li, IA Rodionova, Y Wang, A Obraztsova, OP Zagnitko, R Overbeek, MF Romine, SB Reed, JK Fredrickson, KH Nealson, and AL Osterman. 2010. "Genomic encyclopedia of sugar utilization pathways in the Shewanella genus ." BMC Genomics 11(494):, doi:10.1186/1471-2164-11-494
  • Zhang H, RN Brown, W Qian, ME Monroe, SO Purvine, RJ Moore, MA Gritsenko, L Shi, MF Romine, JK Fredrickson, L Pasa-Tolic, RD Smith, and MS Lipton. 2010. "Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with 18O labeling." Journal of Proteome Research 9(5):2160-2169. 

2009

  • Pinchuk GE, DA Rodionov, C Yang, X Li, AL Osterman, E Dervyn, OV Geydebrekht, SB Reed, MF Romine, FR Collart, J Scott, JK Fredrickson, and AS Beliaev. 2009. "Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals previously uncharacterized machinery for lactate utilization." Proceedings of the National Academy of Sciences of the United States of America 106(8):2874-2879. 
  • Gao H, Z Yang, S Barua, SB Reed, MF Romine, KH Nealson, JK Fredrickson, JM Tiedje, and J Zhou. 2009. "Reduction of Nitrate in Shewanella oneidensis depends on atypical NAP and NRF systems with NapB as a preferred electron transport protein from CymA to NapA." The ISME Journal 3(8):966-976.  doi:10.1038/ismej.2009.40
  • Konstantinidis K, MH Serres, MF Romine, JLM Rodrigues, JM Auchutung, LA McCue, MS Lipton, A Obraztsova, CS Giometti, KH Nealson, JK Fredrickson, and JM Tiedje. 2009. "Comparative systems biology across an evolutionary gradient within the Shewanella genus ." Proceedings of the National Academy of Sciences of the United States of America 106(37):15909-15914.  doi:10.1073/pnas.0902000106
  • Syed M, TV Karpinets, M Leuze, G Kora, MF Romine, and E Uberbacher. 2009. "Shewregdb: Database and visualization environment for experimental and predicted regulatory information in Shewanella oneidensis mr-1." Bioinformation 4(4):169-172. 

2008

  • Marshall MJ, AE Plymale, DW Kennedy, L Shi, Z Wang, SB Reed, A Dohnalkova, CJ Simonson, C Liu, D Saffarini, MF Romine, JM Zachara, AS Beliaev, and JK Fredrickson. 2008. "Hydrogenase- and Outer Membrane c-Type Cytochrome-Facilitated Reduction of Technetium(VII) by Shewanella oneidensis MR-1." Environmental Microbiology 10(1):125-136.  doi:10.1111/j.1462-2920.2007.01438.x
  • Pinchuk GE, CG Ammons, DE Culley, SM Li, JS McLean, MF Romine, KH Nealson, JK Fredrickson, and AS Beliaev. 2008. "Utilization of DNA as a Sole Source of Phosphorus, Carbon, and Energy by Shewanella spp.: Ecological and Physiological Implications for Dissimilatory Metal Reduction." Applied and Environmental Microbiology 74(4):1198-1208.  doi:10.1128/AEM.02026-07
  • Fredrickson JK, MF Romine, AS Beliaev, JM Auchutung, ME Driscoll, TS Gardner, KH Nealson, AL Osterman, GE Pinchuk, JL Reed, D Rodionov, JLM Rodrigues, D Saffarini, MH Serres, AM Spormann, IB Zhulin, and JM Tiedje. 2008. "Towards Environmental Systems Biology of Shewanella." Nature Reviews. Microbiology 6(8):592-603.  doi:10.1038/nrmicro1947
  • Gupta N, J Benhamida, V Bhargava, D Goodman, E Kain , I Kerman, N Nguyen , N Ollikainen, J Rodriguez, J Wang, MS Lipton, MF Romine, V Bafna, RD Smith, and PA Pevzner. 2008. "Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes." Genome Research 18(7):1133-1142. 
  • Mclean JS, GE Pinchuk, OV Geydebrekht, CL Bilskis, BA Zakrajsek, EA Hill, D Saffarini, MF Romine, YA Gorby, JK Fredrickson, and AS Beliaev. 2008. "Oxygen-dependent autoaggregation in Shewanella oneidensis MR-1." Environmental Microbiology 10(7):1861-1876.  doi:10.1111/j.1462-2920.2008.01608.x
  • Mclean JS, PD Majors, CL Reardon, CL Bilskis, SB Reed, MF Romine, and JK Fredrickson. 2008. "Investigations of Structure and Metabolism within Shewanella oneidensis MR-1 Biofilms ." Journal of Microbiological Methods 74(1):47-56. 
  • Romine MF, T Carlson, AD Norbeck, LA McCue, and MS Lipton. 2008. "Identification of Mobile Elements and Pseudogenes in the Shewanella oneidensis MR-1 Genome." Applied and Environmental Microbiology 74(10):3257-3265. 

2007

  • Bretschger O, A Obraztsova, CA Sturm, IS Chang, YA Gorby, SB Reed, DE Culley, CL Reardon, S Barua, MF Romine, J Zhou, AS Beliaev, R Bouhenni, D Saffarini, F Mansfeld, BH Kim, JK Fredrickson, and KH Nealson. 2007. "Current Production and Metal Oxide Reduction by Shewanella Oneidensis MR-1 Wild Type and Mutants." Applied and Environmental Microbiology 73(21):7003-7012.  doi:10.1128/AEM.01087-07
  • Driscoll ME, MF Romine, FS Juhn, MH Serres, LA McCue, AS Beliaev, JK Fredrickson, and TS Gardner. 2007. "Identification of diverse carbon utilization pathways in Shewanella oneidensis MR-1 via expression profiling." Genome Informatics 18:287-298. 
  • Gupta N, S Tanner, N Jaitly, JN Adkins, MS Lipton, R Edwards, MF Romine, A Osterman, V Bafna, RD Smith, and PA Pevzner. 2007. "Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation." Genome Research 17(9):1362-1377.  doi:0.1101/gr.6427907
  • Li J, MF Romine, and M Ward. 2007. "Identification and analysis of a highly conserved chemotaxis gene cluster in Shewanella species. ." FEMS Microbiology Letters 273(2):180-186.  doi:10.1111/j.1574-6968.2007.00810.x

2006

  • Marshall MJ, AS Beliaev, A Dohnalkova, DW Kennedy, L Shi, Z Wang, MI Boyanov, B Lai, KM Kemner, JS Mclean, SB Reed, DE Culley, VL Bailey, CJ Simonson, D Saffarini, MF Romine, JM Zachara, and JK Fredrickson. 2006. "c-Type Cytochrome-Dependent Formation of U(IV) Nanoparticles by Shewanella oneidensis ." PloS Biology 4(8):1324-1333. 
  • Gorby YA, S Yanina, JS Mclean, KM Rosso, DM Moyles, A Dohnalkova, TJ Beveridge, IS Chang, BH Kim, KS Kim, DE Culley, SB Reed, MF Romine, D Saffarini, EA Hill, L Shi, DA Elias, DW Kennedy, GE Pinchuk, K Watanabe, S Ishii, B Logan, KH Nealson, and JK Fredrickson. 2006. "Electrically Conductive Bacterial Nanowires Produced by Shewanella Oneidensis Strain MR-1 and Other Microorganisms ." Proceedings of the National Academy of Sciences of the United States of America 103(30):11358-11363. 
  • Lipton MS, MF Romine, ME Monroe, DA Elias, L Pasa-Tolic, GA Anderson, DJ Anderson, JK Fredrickson, KK Hixson, CD Masselon, HM Mottaz, N Tolic, and RD Smith. 2006. "AMT Tag Approach to Proteomic Characterization of Deinococcus Radiodurans and Shewanella Oneidensis ." In Microbial Proteomics, Methods of Biochemical Analysis, vol. 49, ed. I. Humphery-Smith and M. Hecker, pp. 113-134.  John Wiley & Sons, Inc., Hoboken, NJ. 
  • Yang C, DA Rodionov, X Li, ON Laikova, MS Gelfand, OP Zagnitko, MF Romine, A Obraztova, KH Nealson, and A Osterman. 2006. "Comparative Genomics and Experimental Characterization of N-Acetylglucosamine Utilization Pathway of Shewanella oneidensis." Journal of Biological Chemistry 281(40):29872-29885.  doi:10.1074/jbc.M605052200

2005

  • Beliaev AS, DM Klingeman, J Klappenbach, L Wu, MF Romine, JM Tiedje, KH Nealson, JK Fredrickson, and J Zhou. 2005. "Global Transcriptome Analysis of Shewanella oneidensis MR-1 Exposed to Different Terminal Electron Acceptors." Journal of Bacteriology 187(20):7138-7145.  doi:10.1128/JB.187.20.7138-7145.2005
  • Elias DA, ME Monroe, MJ Marshall, MF Romine, AS Beliaev, JK Fredrickson, GA Anderson, RD Smith, and MS Lipton. 2005. "Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS based proteomics based proteomics." Proteomics 5(12):3120-3130.  doi:10.1002/pmic.200401140
  • Fredrickson JK, and MF Romine. 2005. "Genome-Assisted Analysis of Dissimilatory Metal-Reducing Bacteria." Current Opinion in Biotechnology 16(3):269-274. 
  • Gonzalez-Gil G, JE Amonette, MF Romine, YA Gorby, and GG Geesey. 2005. "Bioreduction of Natural Specular Hematite under Flow Conditions." Geochimica et Cosmochimica Acta 69(5):1145-1155. 
  • Kolker E, AF Picone, MY Galperin, MF Romine, R Higdon, KS Makarova, N Kolker, GA Anderson, X Qiu, KJ Auberry, G Babnigg, AS Beliaev, P Edlefsen, DA Elias, YA Gorby, T Holzman, J Klappenbach, K Konstantinidis, ML Land, MS Lipton, LA McCue, ME Monroe, L Pasa-Tolic, GE Pinchuk, SO Purvine, M Serres, S Tsapin, BA Zakrajsek, W Zhu, J Zhou, F Larimer, C Lawrence, M Riley, FR Collart, JR Yates, III, RD Smith, CS Giometti, K Nealson, JK Fredrickson, and JM Tiedje. 2005. "Global Profiling of Shewanella oneidensis MR-1: Expression of Hypothetical Genes and Improved functional annotations." Proceedings of the National Academy of Sciences of the United States of America 102(6):2099-2104. 
  • Yang F, B Bogdanov, EF Strittmatter, AN Vilkov, MA Gritsenko, L Shi, DA Elias, S Ni, MF Romine, L Pasa-Tolic, MS Lipton, and RD Smith. 2005. "Characterization of purified c-type heme-containing peptides and identification of c-type heme-attachment sites in Shewanella oneidenis cytochromes using mass spectrometry." Journal of Proteome Research 4(3):846-854.  doi:10.1021/pr0497475

2004

  • Fredrickson JK, JM Zachara, DL Balkwill, DW Kennedy, SMW Li, HM Kostandarithes, MJ Daly, MF Romine, and FJ Brockman. 2004. "Geomicrobiology of High Level Nuclear Waste-Contaminated Vadose Sediments at the Hanford Site, Washington State." Applied and Environmental Microbiology 70(7):4230-4241. 
  • Micic M, D Hu, YD Suh, GJ Newton, MF Romine, and HP Lu. 2004. "Correlated Atomic Force Microscopy and Flourescence Lifetime Imaging of Live Bacterial Cells." Colloids and Surfaces. B, Biointerfaces 34:205-212. 
  • Romine MF, DA Elias, ME Monroe, KJ Auberry, R Fang, JK Fredrickson, GA Anderson, RD Smith, and MS Lipton. 2004. "Validation of Shewanella oneidensis MR-1 Small Proteins by AMT Tag-based Proteome Analysis." OMICS. A Journal of Integrative Biology 8(3):239-254. 

2003

  • Balkwill DL, JK Fredrickson, and MF Romine. 2003. "Sphingomonas and Related Genera." In The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community, 3rd ed. Release 3.14, ed. M. Dworkin.  Springer-Verlag, New York, NY. 

2002

  • Lipton MS, L Pasa-Tolic, GA Anderson, DJ Anderson, DL Auberry, JR Battista, MJ Daly, JK Fredrickson, KK Hixson, HM Kostandarithes, CD Masselon, LM Markillie, RJ Moore, MF Romine, Y Shen, EF Strittmatter, N Tolic, HR Udseth, A Venkateswaran, KK Wong, R Zhao, and RD Smith. 2002. "Global Analysis of Deinococcus Radiodurans Proteome by Csing Accurate Mass Tags." Proceedings of the National Academy of Sciences of the United States of America 99(17):11049-11054. 

2000

  • D'Souza M, MF Romine, and N Maltsev. 2000. "SENTRA, a Database of Signal Transduction Proteins." Nucleic Acids Research 28:335-336. 
  • Magnuson JK, MF Romine, DR Burris, and MT Kingsley. 2000. "Trichloroethene Reductive Dehalogenase from Dehalococcoides ethenogenes: Sequence of tceA and Substrate Range Characterization." Applied and Environmental Microbiology 66:5141-5147. 

1999

  • Romine MF, LC Stillwell, KK Wong, SJ Thurston, EC Sisk, CW Sensen, T Gaasterland, JK Fredrickson, and JD Saffer. 1999. "Complete sequence of a 184 kb catabolic plasmid from Sphingomonas aromaticivorans strain F199." Journal of Bacteriology 181(5):1585-1602. 
  • Fredrickson JK, DL Balkwill, MF Romine, and T Shi. 1999. "Ecology, physiology, and phylogeny of deep subsurface Sphingomonas sp." Journal of Industrial Microbiology and Biotechnology 23(4-5):273-283. 
  • Fredrickson JK, DL Balkwill, MF Romine, and T Shi. 1999. "Ecology, physiology, and phylogeny of deep subsurface Sphingomonas sp." Journal of Industrial Microbiology and Biotechnology 23:273-283. 
  • Mormile MR, MF Romine, MT Garcia, A Ventosa, TJ Bailey, and BM Peyton. 1999. "Halomonas campisalis sp. nov., a denitrifying, moderately haloalkaliphilic bacterium." Systematic and Applied Microbiology 22:551-558. 
  • Romine MF, JK Fredrickson, and SMW Li. 1999. "Induction of Aromatic Catabolic Activity in Sphingomonas Aromaticivorans Strain F199." Journal of Industrial Microbiology and Biotechnology 23:303-313. 

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