Staff information

PNNL Publications

2012

• Edwards M, A Hall, L Shi, JK Fredrickson, JM Zachara, JN Butt, D Richardson, and TA Clarke. 2012. "The Crystal Structure of the Extracellular 11-heme Cytochrome UndA Reveals a Conserved 10-heme Motif and Defined Binding Site for Soluble Iron Chelates." Structure 20(7):1275-1284.  doi:10.1016/j.str.2012.04.016
• Liu J, Z Wang, SM Belchik, M Edwards, C Liu, DW Kennedy, ED Merkley, MS Lipton, JN Butt, D Richardson, JM Zachara, JK Fredrickson, KM Rosso, and L Shi. 2012. "Identification and Characterization of MtoA: a Decaheme c-Type Cytochrome of the Neutrophilic Fe(II)-oxidizing Bacterium Sideroxydans lithotrophicus ES-1." Frontiers in Microbiological Chemistry 3:Article No. 37.  doi:10.3389/fmicb.2012.00037
• Marritt S, TG Lowe, J Bye, DG McMillan, L Shi, JK Fredrickson, JM Zachara, DJ Richardson, MR Cheesman, LJ Jeuken, and JN Butt. 2012. "A Functional Description of CymA, an Electron Transfer Hub Supporting Anaerobic Respiratory Flexibility in Shewanella." Biochemical Journal 444(3):465-474.  doi:10.1042/BJ20120197
• Plymale AE, VL Bailey, JK Fredrickson, SM Heald, EC Buck, L Shi, Z Wang, CT Resch, DA Moore, and H Bolton, Jr. 2012. "Biotic and Abiotic Reduction and Solubilization of Pu(IV)O2·xH2O(am) as Affected by Anthraquinone-2,6-disulfonate (AQDS) and Ethylenediaminetetraacetate (EDTA)." Environmental Science & Technology 46(4):2132-2140.  doi:10.1021/es2030752
• Richardson DJ, JN Butt, JK Fredrickson, JM Zachara, L Shi, MJ Edwards, GF White, N Baiden, AJ Gates, S Marritt, and TA Clarke. 2012. "The 'porin-cytochrome' model for microbe-to-mineral electron transfer." Molecular Microbiology 85(2):201-212.  doi:10.1111/j.1365-2958.2012.08088.x
• Richardson DJ, M Edwards, GF White, N Baiden, RS Hartshorne, JK Fredrickson, L Shi, JM Zachara, AJ Gates, JN Butt, and T Clarke. 2012. "Exploring the biochemistry at the extracellular redox frontier of bacterial mineral Fe(III) respiration." Biochemical Society: Transactions 40(3):493-500. 
• Shi L, KM Rosso, TA Clarke, DJ Richardson, JM Zachara, and JK Fredrickson. 2012. "Molecular Underpinnings of Fe(III) Oxide Reduction by Shewanella oneidensis MR-1." Frontiers in Microbiological Chemistry 3:Article No. 50.  doi:10.3389/fmicb.2012.00050
• Tomanicek SJ, A Johs, MS Sawhney, L Shi, and L Liang. 2012. "Crystallization and preliminary X-ray crystallographic studies of the outer membrane cytochrome OmcA from Shewanella oneidensis MR-1." Acta Crystallographica. Section F 68(1):53-55.  doi:10.1107/S1744309111046082
• Yang H, H Ghandi, L Shi, HW Kreuzer, N Ostrom, and EL Hegg. 2012. "Using Gas Chromatography/Isotope Ratio Mass Spectrometry to Determine the Fractionation Factor for H2 Production by Hydrogenases." Rapid Communications in Mass Spectrometry 26(1):61-68.  doi:10.1002/rcm.5298

2011

• Belchik SM, DW Kennedy, A Dohnalkova, Y Wang, PC Sevinc, HJ Wu, Y Lin, HP Lu, JK Fredrickson, and L Shi. 2011. "Extracellular Reduction of Hexavalent Chromium by Cytochromes MtrC and OmcA of Shewanella oneidensis MR-1." Applied and Environmental Microbiology 77(12):4035-4041.  doi:10.1128/AEM.02463-10
• Xiong Y, B Chen, L Shi, JK Fredrickson, DJ Bigelow, and TC Squier. 2011. "Targeted Protein Degradation of Outer Membrane Decaheme Cytochrome MtrC Metal Reductase in Shewanella oneidensis MR-1 Measured Using Biarsenical Probe CrAsH-EDT2." Biochemistry 50(45):9738-9751.  doi:10.1021/bi200602f
• Cao B, B Ahmed, DW Kennedy, Z Wang, L Shi, MJ Marshall, JK Fredrickson, NG Isern, PD Majors, and H Beyenal. 2011. "Contribution of Extracellular Polymeric Substances from Shewanella sp. HRCR-1 Biofilms to U(VI) Immobilization." Environmental Science & Technology 45(13):5483-5490.  doi:10.1021/es200095j
• 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
• Clarke TA, M Edwards, AJ Gates, A Hall, G White, J Bradley, CL Reardon, L Shi, AS Beliaev, MJ Marshall, Z Wang, N Watmough, JK Fredrickson, JM Zachara, JN Butt, and DJ Richardson. 2011. "Structure of a Bacterial Cell Surface Decaheme Electron Conduit." Proceedings of the National Academy of Sciences of the United States of America 108(23):9384-9389.  doi:10.1073/pnas.1017200108
• Qian Y, L Shi, and M Tien. 2011. "SO2907, A Putative TonB-dependent Receptor, Is Involved in Dissimilatory Iron Reduction by Shewanella oneidensis Strain MR-1." Journal of Biological Chemistry 286(39):33973-33980.  doi:10.1074/jbc.M111.262113
• Shi L, SM Belchik, AE Plymale, SM Heald, A Dohnalkova, K Sybirna, H Bottin, TC Squier, JM Zachara, and JK Fredrickson. 2011. "Purification and Characterization of [NiFe]-Hydrogenase of Shewanella oneidensis MR-1." Applied and Environmental Microbiology 77(16):5584-5590. 
• Shi L, SM Belchik, Z Wang, DW Kennedy, A Dohnalkova, MJ Marshall, JM Zachara, and JK Fredrickson. 2011. "Identification and Characterization of UndA-HRCR-6, an Outer Membrane Endecaheme c-Type Cytochrome of Shewanella sp. Strain HRCR-6 ." Applied and Environmental Microbiology 77(15):5521-5523.  doi:10.1128/AEM.00614-11
• Zhang H, F Yang, W Qian, RN Brown, Y Wang, ED Merkley, JH Park, ME Monroe, SO Purvine, RJ Moore, L Shi, JK Fredrickson, L Pasa-Tolic, RD Smith, and MS Lipton. 2011. "Identification of c-Type Heme-Containing Peptides Using Non-Activated IMAC Resin Enrichment and Higher-Energy Collisional Dissociation." Analytical Chemistry 83(19):7260-7268.  doi:10.1021/ac2000829

2010

• Johs A, L Shi, T Droubay, JF Ankner, and L Liang. 2010. "Characterization of the Decaheme c-Type Cytochrome OmcA in Solution and on Hematite Surfaces by Small Angle X-Ray Scattering and Neutron Reflectometry." Biophysical Journal 98(12):3035-3043. 
• Reardon CL, A Dohnalkova, P Nachimuthu, DW Kennedy, D Saffarini, BW Arey, L Shi, Z Wang, DA Moore, JS Mclean, DM Moyles, MJ Marshall, JM Zachara, JK Fredrickson, and AS Beliaev. 2010. "Role of Outer-Membrane Cytochromes MtrC and OmcA in the Biomineralization of Ferrihydrite by Shewanella oneidensis MR-1." Geobiology 8(1):56-68.  doi:10.1111/j.1472-4669.2009.00226.x
• 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

• Chowdhury SM, L Shi, H Yoon, C Ansong, LM Rommereim, AD Norbeck, KJ Auberry, RJ Moore, JN Adkins, F Heffron, and RD Smith. 2009. "A method for investigating protein-protein interactions related to Salmonella typhimurium pathogenesis ." Journal of Proteome Research 8(3):1504-1514 . 
• Hartshorne RS, CL Reardon, DE Ross, J Nuester, TA Clarke, AJ Gates, PC Mills, JK Fredrickson, JM Zachara, L Shi, AS Beliaev, MJ Marshall, M Tien, SL Brantley, JN Butt, and D Richardson. 2009. "Characterization of an electron conduit between bacteria and the extracellular environment." Proceedings of the National Academy of Sciences of the United States of America 106(52):22169-22174.  doi:10.1073/pnas.0900086106
• Lower BH, R Yongsunthon, L Shi, L Wildling, HJ Gruber, NS Wigginton, CL Reardon, GE Pinchuk, T Droubay, JF Boily, and S Lower. 2009. "Antibody recognition force microscopy shows that outer membrane cytochromes OmcA and MtrC are expressed on the exterior surface of Shewanella oneidensis MR-1." Applied and Environmental Microbiology 75(9):2931-2935. 
• Meitl LA, CM Eggleston, PJ Colberg, N Khare, CL Reardon, and L Shi. 2009. "Electrochemical interaction of Shewanella oneidensis MR-1 and its outer membrane cytochromes OmcA and MtrC with hematite electrodes." Geochimica et Cosmochimica Acta 73(18):5292-5307.  doi:10.1016/j.gca.2009.06.021
• Shi L, C Ansong, HS Smallwood, LM Rommereim, JE McDermott, HM Brewer, AD Norbeck, RC Taylor, JK Gustin, F Heffron, RD Smith, and JN Adkins. 2009. "Proteome of Salmonella enterica serotype Tyhimurium Grown in Low Mg2+/pH Medium." Journal of Proteomics and Bioinformatics 2(9):388-397.  doi:10.4172/jpb.1000099
• Shi L, C Ansong, HS Smallwood, LM Rommereim, JE McDermott, HM Brewer, AD Norbeck, RC Taylor, JK Gustin, F Heffron, RD Smith, and JN Adkins. 2009. "Proteome of Salmonella Enterica SerotypeTyphimurium Grown in a Low Mg2+/pH Medium." Journal of Proteomics and Bioinformatics 2(9):388-397.  doi:10.4172/jpb.1000099
• Shi L, D Richardson, Z Wang, SN Kerisit, KM Rosso, JM Zachara, and JK Fredrickson. 2009. "The Roles of Outer Membrane Cytochromes of Shewanella and Geobacter in Extracellular Electron Transfer." Environmental Microbiology Reports 1(4):220-227.  doi:10.1111/j.1758-2229.2009.00035.x
• Shi L, SM Chowdhury, HS Smallwood, H Yoon, HM Mottaz-Brewer, AD Norbeck, JE McDermott, TRW Clauss, F Heffron, RD Smith, and JN Adkins. 2009. "Proteomic Investigation of the Time Course Responses of RAW 264.7 Macrophages to Infection with Salmonella enterica." Infection and Immunity 77(8):3227-3233.  doi:10.1128/IAI.00063-09
• Taylor RC, M Singhal, JB Weller, S Khoshnevis, L Shi, and JE McDermott. 2009. "A Network Inference Workflow Applied to Virulence-Related Processes in Salmonella typhimurium ." In Annals of the New York Academy of Sciences, vol. 1158, pp. 143-158.  PubMed, New York, NY. 

2008

• Lower BH, RD Lins, ZW Oestreicher, TP Straatsma, MF Hochella Jr., L Shi, and S Lower. 2008. "In Vitro Evolution of a Peptide with a Hematite Binding Motif That May Constitute a Natural Metal-Oxide Binding Archetype ." Environmental Science & Technology 42(10):3821-3827.  doi:10.1021/es702688c
• 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
• Brewer HM, AD Norbeck, JN Adkins, NP Manes, C Ansong, L Shi, Y Rikihisa, T Kikuchi, S Wong, RD Estep, F Heffron, L Pasa-Tolic, and RD Smith. 2008. "Optimization of proteomic sample preparation procedures for comprehensive protein characterization of pathogenic systems." Journal of Biomolecular Techniques:JBT 19(5):285-295. 
• Clarke TA, T Holley, RS Hartshorne, JK Fredrickson, JM Zachara, L Shi, and D Richardson. 2008. "The role of multihaem cytochromes in the respiration of nitrite in Escherichia coli and Fe(III) in Shewanella oneidensis." Biochemical Society: Transactions 36(Pt. 5):1005-1010.  doi:10.1042/BST0361005
• Eggleston CM, J Voros, L Shi, BH Lower, T Droubay, and PJ Colberg. 2008. "Binding and Direct Electrochemistry of OmcA, an Outer-Membrane Cytochrome from an Iron Reducing Bacterium, with Oxide Electrodes: A Candidate Biofuel Cell System." Inorganica Chimica Acta 361(3):769-777.  doi:10.1016/j.ica.2007.07.015
• Rodland KD, JN Adkins, C Ansong, SM Chowdhury, NP Manes, L Shi, H Yoon, RD Smith, and F Heffron. 2008. "Use of high-throughput mass spectrometry to elucidate host pathogen interactions in Salmonella." Future Microbiology 3(6):625-634. 
• Shi L, S Deng, MJ Marshall, Z Wang, DW Kennedy, A Dohnalkova, HM Mottaz, EA Hill, YA Gorby, AS Beliaev, DJ Richardson, JM Zachara, and JK Fredrickson. 2008. " Direct Involvement of Type II Secretion System in Extracellular Translocation of Shewanella Oneidensis Outer Membrane Cytochromes MtrC and OmcA." Journal of Bacteriology 190(15):5512-5516.  doi:10.1128/JB.00514-08
• Wang Z, C Liu, X Wang, MJ Marshall, JM Zachara, KM Rosso, M Dupuis, JK Fredrickson, SM Heald, and L Shi. 2008. "Kinetics of Reduction of Fe(III) Complexes by Outer Membrane Cytochromes MtrC and OmcA of Shewanella oneidensis MR-1." Applied and Environmental Microbiology 74(21):6746-6755.  doi:10.1128/AEM.01454-08
• Zhang H, X Tang, GR Munske, NL Zakharova, L Yang, C Zheng, MA Wolff, N Tolic, GA Anderson, L Shi, MJ Marshall, JK Fredrickson, and JE Bruce. 2008. "In Vivo Identification of the Outer Membrane Protein OmcA-MtrC Interaction Network in Shewanella oneidensis MR-1 Cells Using Novel Hydrophobic Chemical Cross-Linkers." Journal of Proteome Research 7(4):1712-1720.  doi:10.1021/pr7007658

2007

• Lower BH, L Shi, R Yongsunthon, T Droubay, DE Mccready, and S Lower. 2007. "Specific Bonds between an Iron Oxide Surface and Outer Membrane Cytochromes MtrC and OmcA from Shewanella oneidensis MR-1." Journal of Bacteriology 189(13):4944-4952.  doi:10.1128/JB.01518-06
• Hartshorne RS, BN Jepson, TA Clarke, SJ Field, JK Fredrickson, JM Zachara, L Shi, JN Butt, and D Richardson. 2007. "Characterization of Shewanella oneidensis MtrC: a cell-surface decaheme cytochrome involved in respiratory electron transport to extracellular electron acceptors." Journal of Biological Inorganic Chemistry 12(7):1083-1094.  doi:10.1007/s00775-007-0278-y
• Shi L, TC Squier, JM Zachara, and JK Fredrickson. 2007. "Respiration of metal (hydr)oxides by Shewanella and Geobacter: a key role for multihaem c-type cytochromes." Molecular Microbiology 65(1):12-20.  doi:10.1111/j.1365-2958.2007.05783.x
• Wigginton NS, KM Rosso, BH Lower, L Shi, and MF Hochella. 2007. "Electron tunneling properties of outer-membrane decaheme cytochromes from Shewanella oneidensis." Geochimica et Cosmochimica Acta 71(3):543-555. 

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. 
• Smallwood HS, L Shi, and TC Squier. 2006. "Increases in Calmodulin Abundance and Stabilization of Activated iNOS Mediate Bacterial Killing in RAW 264.7 Macrophages." Biochemistry 45(32):9717-9726.  doi:10.1021/bi060485p
• 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. 
• Shi L, B Chen, Z Wang, DA Elias, MU Mayer, YA Gorby, S Ni, BH Lower, DW Kennedy, DS Wunschel, HM Mottaz, MJ Marshall, EA Hill, AS Beliaev, JM Zachara, JK Fredrickson, and TC Squier. 2006. "Isolation of a High-Affinity Functional Protein Complex between OmcA and MtrC: Two Outer Membrane Decaheme c-type Cytochromes of Shewanella oneidensis MR-1 ." Journal of Bacteriology 188(13):4705-4714.  doi:10.1128/JB.01966-05
• Shi L, JN Adkins, JR Coleman, AA Schepmoes, A Dohnalkova, HM Mottaz, AD Norbeck, SO Purvine, NP Manes, HS Smallwood, HH Wang, J Forbes, P Gros, S Uzzau, KD Rodland, F Heffron, RD Smith, and TC Squier. 2006. "Proteomic Analysis of Salmonella enterica Serovar Typhimurium Isolated from RAW 264.7 Macrophages: identification of a novel protein that contributes to the replication of serovar Typhimurium inside macrophages." Journal of Biological Chemistry 281:29131-29140.  doi:10.1074/jbc.M604640200
• Xiong Y, L Shi, B Chen, MU Mayer, BH Lower, londer, S Bose, MF Hochella, JM Zachara, JK Fredrickson, and TC Squier. 2006. "High-Affinity Binding and Direct Electron Transfer to Solid Metals by the Shewanella oneidensis MR-1 Outer Membrane c-type Cytochrome OmcA." Journal of the American Chemical Society 128(43):13978-13979.  doi:10.1021/ja063526d

2005

• Zhang W, and L Shi. 2005. "Distribution and evolution of multiple-step phosphorelay in prokaryotes: lateral domain recruitment involved in the formation of hybrid-type histidine kinases ." Microbiology 151:2159-2173. 
• Li R, MB Potters, L Shi, and PJ Kennelly. 2005. "The Protein Phosphatases of Synechocystis sp. Strain PCC 6803: Open Reading Frames sll1033 and sll1387 Encode Enzymes That Exhibit both Protein-Serine and Protein-Tyrosine Phosphatase Activity In Vitro." Journal of Bacteriology 187(17):5877-5884.  doi:10.1128/JB.187.17.5877-5884.2005
• Markillie LM, CT Lin, JN Adkins, DL Auberry, EA Hill, BS Hooker, PA Moore, RJ Moore, L Shi, HS Wiley, and V Kery. 2005. "Simple Protein Complex Purification and Identification Method Suitable for High- throughput Mapping of Protein Interaction Networks." Journal of Proteome Research 4(2):268-274.  doi:10.1021/pr049847a
• Mayer MU, L Shi, and TC Squier. 2005. "One-step, non-denaturing isolation of an RNA polymerase enzyme complex using an improved multi-use affinity probe resin." Molecular Biosystems 1(1):53-56.  doi:10.1039/b500950b
• Shi L, CT Lin, LM Markillie, TC Squier, and BS Hooker. 2005. "Over-expression of Multi-heme C-type Cytochromes." BioTechniques 38(2):297-299. 
• 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

• Shi L. 2004. "MANGANESE-DEPENDENT PROTEIN O-PHOSPHATASES IN PROKARYOTES AND THEIR BIOLOGICAL FUNCTIONS." Frontiers in Bioscience 9:1382-1397. 
• Zhang W, and L Shi. 2004. "Evolution of the PPM-family protein phosphatases in Streptomyces: duplication of catalytic domain and lateral recruitment of additional sensory domains." Microbiology 150(12):4189-4197. 
• Shi L, and W Zhang. 2004. "Comparative analysis of eukaryotic-type protein phosphatases in two Streptomyces genomes." Microbiology 150:2247-2256. 
• Warren MA, LM Kucharski, A Veenstra, L Shi, PF Grulich, and ME Maguire. 2004. "The CorA Mg2+ Transporter Is a Homotetramer." Journal of Bacteriology 186(14):4605-4612.